Multiple sequence alignment - TraesCS6A01G121000

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BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6A01G121000 chr6A 100.000 6301 0 0 1 6301 93267457 93273757 0.000000e+00 11636.0
1 TraesCS6A01G121000 chr6A 93.362 2591 142 20 1259 3829 544166263 544168843 0.000000e+00 3805.0
2 TraesCS6A01G121000 chr6A 93.048 1237 70 10 4072 5302 93205287 93206513 0.000000e+00 1794.0
3 TraesCS6A01G121000 chr6A 95.503 934 26 5 5305 6226 515665148 515664219 0.000000e+00 1478.0
4 TraesCS6A01G121000 chr6A 90.600 500 28 6 3347 3831 616374803 616374308 0.000000e+00 645.0
5 TraesCS6A01G121000 chr6A 82.792 616 68 13 5653 6233 608220240 608219628 3.370000e-142 516.0
6 TraesCS6A01G121000 chr6A 90.785 293 25 1 3543 3833 579136269 579135977 2.130000e-104 390.0
7 TraesCS6A01G121000 chr6A 85.294 170 22 3 5410 5578 608220427 608220260 8.400000e-39 172.0
8 TraesCS6A01G121000 chr6A 86.076 158 16 4 1147 1302 581809548 581809701 1.410000e-36 165.0
9 TraesCS6A01G121000 chr6A 96.907 97 3 0 3830 3926 93169635 93169731 5.050000e-36 163.0
10 TraesCS6A01G121000 chr6A 94.286 70 4 0 5308 5377 93283828 93283759 2.400000e-19 108.0
11 TraesCS6A01G121000 chr6A 93.151 73 5 0 5305 5377 515660061 515660133 2.400000e-19 108.0
12 TraesCS6A01G121000 chr6A 93.056 72 5 0 6229 6300 215817377 215817448 8.640000e-19 106.0
13 TraesCS6A01G121000 chr7A 95.145 2554 95 8 1301 3831 725471757 725469210 0.000000e+00 4002.0
14 TraesCS6A01G121000 chr7A 91.961 2749 139 18 1142 3831 709853622 709856347 0.000000e+00 3777.0
15 TraesCS6A01G121000 chr7A 94.717 1855 87 4 1651 3497 725697896 725699747 0.000000e+00 2872.0
16 TraesCS6A01G121000 chr7A 90.079 252 11 3 5996 6233 26441422 26441673 1.320000e-81 315.0
17 TraesCS6A01G121000 chr7A 95.714 70 3 0 6231 6300 468951199 468951268 5.160000e-21 113.0
18 TraesCS6A01G121000 chr7A 93.421 76 4 1 6226 6300 290923733 290923808 1.860000e-20 111.0
19 TraesCS6A01G121000 chr2A 93.122 2646 127 14 1206 3831 35937818 35940428 0.000000e+00 3827.0
20 TraesCS6A01G121000 chr2A 93.513 2528 113 18 1145 3655 620730360 620727867 0.000000e+00 3712.0
21 TraesCS6A01G121000 chr2A 93.062 2551 123 17 1145 3653 293050889 293048351 0.000000e+00 3681.0
22 TraesCS6A01G121000 chr2A 79.520 625 125 2 4681 5302 743265932 743265308 5.800000e-120 442.0
23 TraesCS6A01G121000 chr2A 76.149 805 140 38 3830 4610 743266803 743266027 5.960000e-100 375.0
24 TraesCS6A01G121000 chr2A 95.833 72 3 0 6230 6301 70142352 70142281 3.990000e-22 117.0
25 TraesCS6A01G121000 chr2A 95.714 70 3 0 6232 6301 82359617 82359548 5.160000e-21 113.0
26 TraesCS6A01G121000 chr4A 92.667 2591 139 15 1261 3831 684300561 684298002 0.000000e+00 3685.0
27 TraesCS6A01G121000 chr4A 93.082 1778 105 9 2062 3831 539141523 539143290 0.000000e+00 2586.0
28 TraesCS6A01G121000 chr4A 88.929 822 67 10 5433 6233 719705898 719706716 0.000000e+00 992.0
29 TraesCS6A01G121000 chr4A 90.909 418 36 2 4 419 727415200 727414783 1.530000e-155 560.0
30 TraesCS6A01G121000 chr4A 92.734 289 21 0 3543 3831 322651598 322651310 9.770000e-113 418.0
31 TraesCS6A01G121000 chr4A 88.673 309 30 4 418 725 727414728 727414424 7.710000e-99 372.0
32 TraesCS6A01G121000 chr4A 98.571 70 1 0 6231 6300 520088051 520087982 2.390000e-24 124.0
33 TraesCS6A01G121000 chr5A 94.610 2282 83 13 1265 3516 556781819 556779548 0.000000e+00 3496.0
34 TraesCS6A01G121000 chr5A 93.708 1033 57 2 1141 2171 401269187 401270213 0.000000e+00 1541.0
35 TraesCS6A01G121000 chr5A 76.270 1437 295 35 3897 5302 82300170 82301591 0.000000e+00 723.0
36 TraesCS6A01G121000 chr5A 91.260 389 33 1 9 397 406838875 406838488 4.330000e-146 529.0
37 TraesCS6A01G121000 chr5A 95.502 289 13 0 3543 3831 566137536 566137248 4.450000e-126 462.0
38 TraesCS6A01G121000 chr5A 93.836 292 16 2 3543 3834 556779292 556779003 7.500000e-119 438.0
39 TraesCS6A01G121000 chr5A 88.141 312 33 3 418 725 685999049 685998738 9.980000e-98 368.0
40 TraesCS6A01G121000 chr5A 97.143 70 2 0 6232 6301 49120855 49120924 1.110000e-22 119.0
41 TraesCS6A01G121000 chr1A 92.651 2327 116 23 1138 3451 477755169 477752885 0.000000e+00 3299.0
42 TraesCS6A01G121000 chr1A 93.728 1977 87 15 1871 3831 420528996 420530951 0.000000e+00 2929.0
43 TraesCS6A01G121000 chr1A 92.929 1287 70 14 2561 3831 520127399 520128680 0.000000e+00 1853.0
44 TraesCS6A01G121000 chr1A 85.564 949 85 9 5305 6233 467225264 467224348 0.000000e+00 946.0
45 TraesCS6A01G121000 chr1A 90.162 681 45 10 3168 3831 509010352 509011027 0.000000e+00 867.0
46 TraesCS6A01G121000 chr1A 90.016 611 50 6 3231 3831 131254904 131255513 0.000000e+00 780.0
47 TraesCS6A01G121000 chr1A 82.714 619 69 13 5650 6233 461766992 461767607 3.370000e-142 516.0
48 TraesCS6A01G121000 chr1A 93.056 288 16 2 3543 3830 499975925 499975642 9.770000e-113 418.0
49 TraesCS6A01G121000 chr1A 92.308 286 22 0 3546 3831 514133269 514132984 2.110000e-109 407.0
50 TraesCS6A01G121000 chr1A 91.696 289 22 1 3543 3831 103310742 103310456 3.540000e-107 399.0
51 TraesCS6A01G121000 chr1A 71.721 732 150 36 3897 4609 590767772 590767079 1.090000e-32 152.0
52 TraesCS6A01G121000 chr1A 90.909 77 5 2 6224 6300 4719549 4719475 1.120000e-17 102.0
53 TraesCS6A01G121000 chr1A 92.857 70 5 0 6231 6300 242782624 242782693 1.120000e-17 102.0
54 TraesCS6A01G121000 chr1A 92.754 69 5 0 6232 6300 224803490 224803558 4.020000e-17 100.0
55 TraesCS6A01G121000 chr1D 88.117 2592 236 38 1279 3833 411731472 411728916 0.000000e+00 3014.0
56 TraesCS6A01G121000 chr1D 86.757 589 67 7 3257 3837 66765737 66765152 0.000000e+00 645.0
57 TraesCS6A01G121000 chr1D 95.455 66 3 0 6235 6300 323497875 323497810 8.640000e-19 106.0
58 TraesCS6A01G121000 chr1D 92.857 70 4 1 6231 6300 128521024 128520956 4.020000e-17 100.0
59 TraesCS6A01G121000 chr1D 92.857 70 3 2 6232 6300 212501823 212501891 4.020000e-17 100.0
60 TraesCS6A01G121000 chr1D 92.754 69 5 0 6232 6300 385629786 385629718 4.020000e-17 100.0
61 TraesCS6A01G121000 chr6D 90.565 1982 157 16 1862 3831 108453777 108455740 0.000000e+00 2597.0
62 TraesCS6A01G121000 chr6D 92.711 1372 63 16 3830 5193 77623802 77625144 0.000000e+00 1945.0
63 TraesCS6A01G121000 chr6D 86.913 1490 158 21 3830 5302 56928657 56927188 0.000000e+00 1637.0
64 TraesCS6A01G121000 chr6D 89.951 408 39 1 14 419 445652075 445651668 5.600000e-145 525.0
65 TraesCS6A01G121000 chr6D 89.512 410 41 1 12 419 16178732 16178323 9.360000e-143 518.0
66 TraesCS6A01G121000 chr6D 88.673 309 33 2 418 725 16178268 16177961 5.960000e-100 375.0
67 TraesCS6A01G121000 chr6D 88.333 240 16 5 918 1145 77623566 77623805 1.730000e-70 278.0
68 TraesCS6A01G121000 chr6D 84.615 208 24 6 942 1145 56928857 56928654 3.850000e-47 200.0
69 TraesCS6A01G121000 chr6D 92.982 114 8 0 5189 5302 77625830 77625943 3.910000e-37 167.0
70 TraesCS6A01G121000 chr6D 92.857 70 3 2 6231 6300 161140614 161140547 4.020000e-17 100.0
71 TraesCS6A01G121000 chr6D 92.857 70 2 3 6232 6300 78021166 78021233 1.450000e-16 99.0
72 TraesCS6A01G121000 chr6D 96.610 59 1 1 6230 6288 47098885 47098828 5.200000e-16 97.1
73 TraesCS6A01G121000 chr6D 95.161 62 2 1 6230 6290 130149336 130149397 5.200000e-16 97.1
74 TraesCS6A01G121000 chr6D 96.429 56 2 0 6233 6288 27464201 27464146 6.730000e-15 93.5
75 TraesCS6A01G121000 chr6D 90.000 70 7 0 6231 6300 322535039 322535108 2.420000e-14 91.6
76 TraesCS6A01G121000 chr6D 90.000 70 7 0 6231 6300 374816106 374816037 2.420000e-14 91.6
77 TraesCS6A01G121000 chr6D 90.000 70 5 2 6232 6299 271614278 271614347 8.700000e-14 89.8
78 TraesCS6A01G121000 chr3D 87.450 2255 191 45 1145 3348 500888568 500886355 0.000000e+00 2512.0
79 TraesCS6A01G121000 chr3D 91.827 416 34 0 4 419 577412070 577412485 1.180000e-161 580.0
80 TraesCS6A01G121000 chr3D 90.686 408 38 0 12 419 143236857 143236450 1.540000e-150 544.0
81 TraesCS6A01G121000 chr3D 89.713 418 41 2 4 419 606302270 606302687 3.340000e-147 532.0
82 TraesCS6A01G121000 chr3D 90.645 310 25 4 418 725 549377145 549376838 5.880000e-110 409.0
83 TraesCS6A01G121000 chr3D 88.997 309 32 2 418 725 589431442 589431749 1.280000e-101 381.0
84 TraesCS6A01G121000 chr3D 88.065 310 32 5 418 725 143236395 143236089 4.640000e-96 363.0
85 TraesCS6A01G121000 chr3D 85.321 327 34 9 5820 6136 477870769 477871091 6.090000e-85 326.0
86 TraesCS6A01G121000 chr3D 93.056 72 5 0 6228 6299 467496956 467496885 8.640000e-19 106.0
87 TraesCS6A01G121000 chr5D 88.808 2064 152 35 1265 3302 528691538 528689528 0.000000e+00 2459.0
88 TraesCS6A01G121000 chr5D 88.756 418 44 3 4 419 37119436 37119852 5.640000e-140 508.0
89 TraesCS6A01G121000 chr5D 77.118 791 136 31 3830 4609 88465218 88465974 3.510000e-112 416.0
90 TraesCS6A01G121000 chr5D 77.191 719 143 15 3897 4604 88469979 88470687 3.540000e-107 399.0
91 TraesCS6A01G121000 chr5D 94.030 67 4 0 6231 6297 72529356 72529422 1.120000e-17 102.0
92 TraesCS6A01G121000 chr6B 93.962 1474 82 3 3830 5302 150222031 150223498 0.000000e+00 2222.0
93 TraesCS6A01G121000 chr6B 92.268 194 15 0 952 1145 150221841 150222034 6.220000e-70 276.0
94 TraesCS6A01G121000 chr6B 100.000 70 0 0 6232 6301 705848956 705849025 5.130000e-26 130.0
95 TraesCS6A01G121000 chr6B 95.522 67 3 0 6231 6297 525163171 525163237 2.400000e-19 108.0
96 TraesCS6A01G121000 chrUn 94.012 1386 62 6 2462 3831 150818568 150817188 0.000000e+00 2080.0
97 TraesCS6A01G121000 chrUn 87.482 1382 115 25 2458 3831 364367128 364365797 0.000000e+00 1541.0
98 TraesCS6A01G121000 chrUn 87.342 553 58 7 3286 3831 20485582 20486129 1.930000e-174 623.0
99 TraesCS6A01G121000 chrUn 84.598 448 52 6 3397 3831 1922711 1922268 4.510000e-116 429.0
100 TraesCS6A01G121000 chrUn 84.689 418 47 5 3427 3831 418864179 418863766 9.840000e-108 401.0
101 TraesCS6A01G121000 chrUn 84.874 357 37 6 3486 3829 93261841 93262193 1.680000e-90 344.0
102 TraesCS6A01G121000 chrUn 84.874 357 37 6 3486 3829 252510874 252510522 1.680000e-90 344.0
103 TraesCS6A01G121000 chrUn 97.872 47 1 0 6231 6277 65831038 65830992 1.460000e-11 82.4
104 TraesCS6A01G121000 chrUn 95.918 49 2 0 6230 6278 310357867 310357819 5.240000e-11 80.5
105 TraesCS6A01G121000 chrUn 89.062 64 6 1 6228 6290 1599085 1599148 1.880000e-10 78.7
106 TraesCS6A01G121000 chrUn 94.231 52 1 2 6228 6277 17480292 17480241 1.880000e-10 78.7
107 TraesCS6A01G121000 chrUn 100.000 41 0 0 6231 6271 36352391 36352431 6.770000e-10 76.8
108 TraesCS6A01G121000 chrUn 95.833 48 1 1 6231 6277 195377475 195377522 6.770000e-10 76.8
109 TraesCS6A01G121000 chrUn 100.000 41 0 0 6231 6271 214882614 214882574 6.770000e-10 76.8
110 TraesCS6A01G121000 chrUn 94.000 50 2 1 6231 6279 94204822 94204773 2.440000e-09 75.0
111 TraesCS6A01G121000 chrUn 92.593 54 1 3 6230 6281 480090591 480090643 2.440000e-09 75.0
112 TraesCS6A01G121000 chrUn 93.878 49 2 1 6230 6277 39720903 39720855 8.760000e-09 73.1
113 TraesCS6A01G121000 chrUn 93.750 48 3 0 6231 6278 83568272 83568225 8.760000e-09 73.1
114 TraesCS6A01G121000 chrUn 90.741 54 3 2 6231 6283 42521953 42521901 3.150000e-08 71.3
115 TraesCS6A01G121000 chrUn 90.741 54 4 1 6226 6278 47774093 47774040 3.150000e-08 71.3
116 TraesCS6A01G121000 chrUn 90.909 55 2 3 6231 6284 324823334 324823386 3.150000e-08 71.3
117 TraesCS6A01G121000 chrUn 90.909 55 2 3 6231 6284 353611400 353611452 3.150000e-08 71.3
118 TraesCS6A01G121000 chrUn 84.058 69 8 3 6231 6296 32325355 32325423 5.270000e-06 63.9
119 TraesCS6A01G121000 chr4D 89.546 1521 133 16 2318 3831 386124468 386122967 0.000000e+00 1905.0
120 TraesCS6A01G121000 chr4D 86.225 951 79 17 5304 6233 388825657 388826576 0.000000e+00 983.0
121 TraesCS6A01G121000 chr4D 87.011 793 62 15 5462 6233 388840087 388840859 0.000000e+00 856.0
122 TraesCS6A01G121000 chr4D 86.447 546 62 7 3293 3831 175189493 175188953 7.040000e-164 588.0
123 TraesCS6A01G121000 chr4D 88.969 417 44 2 3 419 272431914 272431500 1.210000e-141 514.0
124 TraesCS6A01G121000 chr4D 89.000 100 11 0 5307 5406 388845395 388845296 2.390000e-24 124.0
125 TraesCS6A01G121000 chr4D 94.203 69 4 0 6232 6300 442758109 442758041 8.640000e-19 106.0
126 TraesCS6A01G121000 chr4D 95.161 62 2 1 6230 6290 14403827 14403888 5.200000e-16 97.1
127 TraesCS6A01G121000 chr4D 94.643 56 1 2 6231 6284 2850682 2850737 1.130000e-12 86.1
128 TraesCS6A01G121000 chr4D 94.444 54 2 1 6231 6284 96610228 96610280 1.460000e-11 82.4
129 TraesCS6A01G121000 chr4D 96.078 51 1 1 6227 6277 366274412 366274363 1.460000e-11 82.4
130 TraesCS6A01G121000 chr4D 94.340 53 2 1 6228 6279 373876745 373876797 5.240000e-11 80.5
131 TraesCS6A01G121000 chr4D 87.143 70 4 5 6231 6296 505004562 505004494 2.440000e-09 75.0
132 TraesCS6A01G121000 chr5B 91.277 940 60 12 5307 6227 648266200 648267136 0.000000e+00 1262.0
133 TraesCS6A01G121000 chr5B 89.571 489 44 5 5303 5787 511014804 511014319 1.160000e-171 614.0
134 TraesCS6A01G121000 chr5B 87.734 481 50 6 5311 5787 511013848 511013373 2.570000e-153 553.0
135 TraesCS6A01G121000 chr5B 77.423 784 140 26 3830 4603 94048526 94049282 3.490000e-117 433.0
136 TraesCS6A01G121000 chr5B 77.577 718 142 17 3897 4604 94087445 94088153 3.510000e-112 416.0
137 TraesCS6A01G121000 chr5B 89.153 295 28 4 416 709 140116442 140116151 1.290000e-96 364.0
138 TraesCS6A01G121000 chr4B 88.211 950 88 10 5305 6233 175852413 175851467 0.000000e+00 1112.0
139 TraesCS6A01G121000 chr4B 94.286 70 4 0 6232 6301 51002994 51003063 2.400000e-19 108.0
140 TraesCS6A01G121000 chr4B 92.958 71 3 2 6231 6300 364184687 364184756 1.120000e-17 102.0
141 TraesCS6A01G121000 chr2D 77.583 1423 281 29 3908 5302 610377954 610376542 0.000000e+00 826.0
142 TraesCS6A01G121000 chr2D 77.162 1515 270 53 3830 5302 610404455 610402975 0.000000e+00 811.0
143 TraesCS6A01G121000 chr2D 94.366 71 4 0 6230 6300 24863985 24863915 6.680000e-20 110.0
144 TraesCS6A01G121000 chr7B 82.857 805 96 19 5367 6133 640505720 640504920 0.000000e+00 684.0
145 TraesCS6A01G121000 chr7B 93.258 89 5 1 6015 6102 677077578 677077666 5.130000e-26 130.0
146 TraesCS6A01G121000 chr7B 94.366 71 4 0 6230 6300 741241127 741241057 6.680000e-20 110.0
147 TraesCS6A01G121000 chr2B 88.225 569 54 9 5458 6016 565948581 565949146 0.000000e+00 667.0
148 TraesCS6A01G121000 chr2B 89.084 513 38 5 5738 6233 651945185 651945696 6.940000e-174 621.0
149 TraesCS6A01G121000 chr2B 78.793 613 118 12 4684 5289 41473328 41472721 9.840000e-108 401.0
150 TraesCS6A01G121000 chr2B 81.633 392 67 5 4915 5302 745765444 745765054 2.830000e-83 320.0
151 TraesCS6A01G121000 chr2B 84.328 134 8 7 6086 6207 705684597 705684729 1.110000e-22 119.0
152 TraesCS6A01G121000 chr2B 86.275 102 11 3 5305 5405 382581443 382581344 2.400000e-19 108.0
153 TraesCS6A01G121000 chr2B 94.286 70 4 0 6231 6300 492186128 492186059 2.400000e-19 108.0
154 TraesCS6A01G121000 chr3A 89.501 381 32 7 3461 3834 19311090 19310711 5.720000e-130 475.0
155 TraesCS6A01G121000 chr3A 89.577 307 28 4 421 725 702907389 702907085 2.760000e-103 387.0
156 TraesCS6A01G121000 chr1B 89.320 309 31 2 418 725 550980101 550979794 2.760000e-103 387.0
157 TraesCS6A01G121000 chr1B 94.286 70 3 1 6231 6300 22986166 22986098 8.640000e-19 106.0
158 TraesCS6A01G121000 chr3B 96.053 76 2 1 6227 6301 808664850 808664925 8.580000e-24 122.0
159 TraesCS6A01G121000 chr3B 94.286 70 4 0 6231 6300 502640509 502640440 2.400000e-19 108.0
160 TraesCS6A01G121000 chr7D 94.286 70 4 0 6231 6300 485848097 485848166 2.400000e-19 108.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G121000 chr6A 93267457 93273757 6300 False 11636.000000 11636 100.0000 1 6301 1 chr6A.!!$F3 6300
1 TraesCS6A01G121000 chr6A 544166263 544168843 2580 False 3805.000000 3805 93.3620 1259 3829 1 chr6A.!!$F6 2570
2 TraesCS6A01G121000 chr6A 93205287 93206513 1226 False 1794.000000 1794 93.0480 4072 5302 1 chr6A.!!$F2 1230
3 TraesCS6A01G121000 chr6A 515664219 515665148 929 True 1478.000000 1478 95.5030 5305 6226 1 chr6A.!!$R2 921
4 TraesCS6A01G121000 chr6A 608219628 608220427 799 True 344.000000 516 84.0430 5410 6233 2 chr6A.!!$R5 823
5 TraesCS6A01G121000 chr7A 725469210 725471757 2547 True 4002.000000 4002 95.1450 1301 3831 1 chr7A.!!$R1 2530
6 TraesCS6A01G121000 chr7A 709853622 709856347 2725 False 3777.000000 3777 91.9610 1142 3831 1 chr7A.!!$F4 2689
7 TraesCS6A01G121000 chr7A 725697896 725699747 1851 False 2872.000000 2872 94.7170 1651 3497 1 chr7A.!!$F5 1846
8 TraesCS6A01G121000 chr2A 35937818 35940428 2610 False 3827.000000 3827 93.1220 1206 3831 1 chr2A.!!$F1 2625
9 TraesCS6A01G121000 chr2A 620727867 620730360 2493 True 3712.000000 3712 93.5130 1145 3655 1 chr2A.!!$R4 2510
10 TraesCS6A01G121000 chr2A 293048351 293050889 2538 True 3681.000000 3681 93.0620 1145 3653 1 chr2A.!!$R3 2508
11 TraesCS6A01G121000 chr2A 743265308 743266803 1495 True 408.500000 442 77.8345 3830 5302 2 chr2A.!!$R5 1472
12 TraesCS6A01G121000 chr4A 684298002 684300561 2559 True 3685.000000 3685 92.6670 1261 3831 1 chr4A.!!$R3 2570
13 TraesCS6A01G121000 chr4A 539141523 539143290 1767 False 2586.000000 2586 93.0820 2062 3831 1 chr4A.!!$F1 1769
14 TraesCS6A01G121000 chr4A 719705898 719706716 818 False 992.000000 992 88.9290 5433 6233 1 chr4A.!!$F2 800
15 TraesCS6A01G121000 chr4A 727414424 727415200 776 True 466.000000 560 89.7910 4 725 2 chr4A.!!$R4 721
16 TraesCS6A01G121000 chr5A 556779003 556781819 2816 True 1967.000000 3496 94.2230 1265 3834 2 chr5A.!!$R4 2569
17 TraesCS6A01G121000 chr5A 401269187 401270213 1026 False 1541.000000 1541 93.7080 1141 2171 1 chr5A.!!$F3 1030
18 TraesCS6A01G121000 chr5A 82300170 82301591 1421 False 723.000000 723 76.2700 3897 5302 1 chr5A.!!$F2 1405
19 TraesCS6A01G121000 chr1A 477752885 477755169 2284 True 3299.000000 3299 92.6510 1138 3451 1 chr1A.!!$R4 2313
20 TraesCS6A01G121000 chr1A 420528996 420530951 1955 False 2929.000000 2929 93.7280 1871 3831 1 chr1A.!!$F4 1960
21 TraesCS6A01G121000 chr1A 520127399 520128680 1281 False 1853.000000 1853 92.9290 2561 3831 1 chr1A.!!$F7 1270
22 TraesCS6A01G121000 chr1A 467224348 467225264 916 True 946.000000 946 85.5640 5305 6233 1 chr1A.!!$R3 928
23 TraesCS6A01G121000 chr1A 509010352 509011027 675 False 867.000000 867 90.1620 3168 3831 1 chr1A.!!$F6 663
24 TraesCS6A01G121000 chr1A 131254904 131255513 609 False 780.000000 780 90.0160 3231 3831 1 chr1A.!!$F1 600
25 TraesCS6A01G121000 chr1A 461766992 461767607 615 False 516.000000 516 82.7140 5650 6233 1 chr1A.!!$F5 583
26 TraesCS6A01G121000 chr1D 411728916 411731472 2556 True 3014.000000 3014 88.1170 1279 3833 1 chr1D.!!$R5 2554
27 TraesCS6A01G121000 chr1D 66765152 66765737 585 True 645.000000 645 86.7570 3257 3837 1 chr1D.!!$R1 580
28 TraesCS6A01G121000 chr6D 108453777 108455740 1963 False 2597.000000 2597 90.5650 1862 3831 1 chr6D.!!$F2 1969
29 TraesCS6A01G121000 chr6D 56927188 56928857 1669 True 918.500000 1637 85.7640 942 5302 2 chr6D.!!$R7 4360
30 TraesCS6A01G121000 chr6D 77623566 77625943 2377 False 796.666667 1945 91.3420 918 5302 3 chr6D.!!$F6 4384
31 TraesCS6A01G121000 chr6D 16177961 16178732 771 True 446.500000 518 89.0925 12 725 2 chr6D.!!$R6 713
32 TraesCS6A01G121000 chr3D 500886355 500888568 2213 True 2512.000000 2512 87.4500 1145 3348 1 chr3D.!!$R2 2203
33 TraesCS6A01G121000 chr3D 143236089 143236857 768 True 453.500000 544 89.3755 12 725 2 chr3D.!!$R4 713
34 TraesCS6A01G121000 chr5D 528689528 528691538 2010 True 2459.000000 2459 88.8080 1265 3302 1 chr5D.!!$R1 2037
35 TraesCS6A01G121000 chr5D 88465218 88465974 756 False 416.000000 416 77.1180 3830 4609 1 chr5D.!!$F3 779
36 TraesCS6A01G121000 chr5D 88469979 88470687 708 False 399.000000 399 77.1910 3897 4604 1 chr5D.!!$F4 707
37 TraesCS6A01G121000 chr6B 150221841 150223498 1657 False 1249.000000 2222 93.1150 952 5302 2 chr6B.!!$F3 4350
38 TraesCS6A01G121000 chrUn 150817188 150818568 1380 True 2080.000000 2080 94.0120 2462 3831 1 chrUn.!!$R9 1369
39 TraesCS6A01G121000 chrUn 364365797 364367128 1331 True 1541.000000 1541 87.4820 2458 3831 1 chrUn.!!$R13 1373
40 TraesCS6A01G121000 chrUn 20485582 20486129 547 False 623.000000 623 87.3420 3286 3831 1 chrUn.!!$F2 545
41 TraesCS6A01G121000 chr4D 386122967 386124468 1501 True 1905.000000 1905 89.5460 2318 3831 1 chr4D.!!$R4 1513
42 TraesCS6A01G121000 chr4D 388825657 388826576 919 False 983.000000 983 86.2250 5304 6233 1 chr4D.!!$F5 929
43 TraesCS6A01G121000 chr4D 388840087 388840859 772 False 856.000000 856 87.0110 5462 6233 1 chr4D.!!$F6 771
44 TraesCS6A01G121000 chr4D 175188953 175189493 540 True 588.000000 588 86.4470 3293 3831 1 chr4D.!!$R1 538
45 TraesCS6A01G121000 chr5B 648266200 648267136 936 False 1262.000000 1262 91.2770 5307 6227 1 chr5B.!!$F3 920
46 TraesCS6A01G121000 chr5B 511013373 511014804 1431 True 583.500000 614 88.6525 5303 5787 2 chr5B.!!$R2 484
47 TraesCS6A01G121000 chr5B 94048526 94049282 756 False 433.000000 433 77.4230 3830 4603 1 chr5B.!!$F1 773
48 TraesCS6A01G121000 chr5B 94087445 94088153 708 False 416.000000 416 77.5770 3897 4604 1 chr5B.!!$F2 707
49 TraesCS6A01G121000 chr4B 175851467 175852413 946 True 1112.000000 1112 88.2110 5305 6233 1 chr4B.!!$R1 928
50 TraesCS6A01G121000 chr2D 610376542 610377954 1412 True 826.000000 826 77.5830 3908 5302 1 chr2D.!!$R2 1394
51 TraesCS6A01G121000 chr2D 610402975 610404455 1480 True 811.000000 811 77.1620 3830 5302 1 chr2D.!!$R3 1472
52 TraesCS6A01G121000 chr7B 640504920 640505720 800 True 684.000000 684 82.8570 5367 6133 1 chr7B.!!$R1 766
53 TraesCS6A01G121000 chr2B 565948581 565949146 565 False 667.000000 667 88.2250 5458 6016 1 chr2B.!!$F1 558
54 TraesCS6A01G121000 chr2B 651945185 651945696 511 False 621.000000 621 89.0840 5738 6233 1 chr2B.!!$F2 495
55 TraesCS6A01G121000 chr2B 41472721 41473328 607 True 401.000000 401 78.7930 4684 5289 1 chr2B.!!$R1 605

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
845 905 0.092351 CATCGTCGCGCGTAAAAGTT 59.908 50.000 30.98 5.16 42.13 2.66 F
846 906 0.092351 ATCGTCGCGCGTAAAAGTTG 59.908 50.000 30.98 11.32 42.13 3.16 F
851 911 0.164217 CGCGCGTAAAAGTTGGCTTA 59.836 50.000 24.19 0.00 33.95 3.09 F
1608 1865 0.388520 CATCACGTGAAGCTCCGACA 60.389 55.000 24.13 0.00 0.00 4.35 F
1979 2348 1.463444 GACATACTTCTTTTGCGCCGT 59.537 47.619 4.18 0.00 0.00 5.68 F
3628 4315 1.594310 GGGAGAAGAAGAGCGCAGT 59.406 57.895 11.47 0.00 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2310 2685 0.108615 ATGACGACAAGAGAAGCCCG 60.109 55.000 0.00 0.0 0.00 6.13 R
2648 3072 1.786937 ACCCAAGTGGCACAAATGAA 58.213 45.000 21.41 0.0 44.16 2.57 R
2894 3318 1.102978 GAGCGGGCAATTACACCAAT 58.897 50.000 0.00 0.0 0.00 3.16 R
3341 3779 0.322906 CCTCCTCAAAGCTCCCCAAC 60.323 60.000 0.00 0.0 0.00 3.77 R
3899 4597 2.121538 AGCCTCAGCGATACGAGCA 61.122 57.895 0.00 0.0 46.67 4.26 R
5676 7167 0.387929 AGGTCTTCTGACGCGAACAA 59.612 50.000 15.93 0.0 43.79 2.83 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 1.268539 GCGCCTATAAAATTGCAGCGT 60.269 47.619 11.90 0.00 43.68 5.07
70 71 3.813166 GCCTATAAAATTGCAGCGTCCTA 59.187 43.478 0.00 0.00 0.00 2.94
134 137 2.430244 GACACGTCATCACCGCGT 60.430 61.111 4.92 0.00 39.59 6.01
262 265 2.342648 GAACCTTCGACACCGCCT 59.657 61.111 0.00 0.00 35.37 5.52
330 333 1.144093 TCCCGTTGGGACATGAACTTT 59.856 47.619 0.00 0.00 46.17 2.66
331 334 2.423660 TCCCGTTGGGACATGAACTTTT 60.424 45.455 0.00 0.00 46.17 2.27
401 404 1.337071 GCTTATCACCGACGAGGATCA 59.663 52.381 8.56 0.00 45.00 2.92
445 504 2.715749 TCCCGCAAGACATCATCAAT 57.284 45.000 0.00 0.00 43.02 2.57
453 512 4.669318 CAAGACATCATCAATGAGCAACC 58.331 43.478 0.00 0.00 40.64 3.77
469 528 1.521450 AACCGTTCTTCGCCGAGAGA 61.521 55.000 0.00 0.00 38.35 3.10
493 552 0.253868 TGGAGAGGGAGGAGAGGAGA 60.254 60.000 0.00 0.00 0.00 3.71
524 583 1.437986 GCCTATCGCGAGGACAAGT 59.562 57.895 16.66 0.00 39.15 3.16
579 638 1.751924 GCTAGGAGATGTGTCGTCCTT 59.248 52.381 0.00 0.00 41.21 3.36
607 667 3.096541 CGACGAGCGTTCCTTAACA 57.903 52.632 0.00 0.00 35.16 2.41
612 672 2.494870 ACGAGCGTTCCTTAACACCTAT 59.505 45.455 0.00 0.00 35.16 2.57
627 687 0.738975 CCTATGCTCAGACGTCGGAA 59.261 55.000 18.91 6.21 0.00 4.30
630 690 0.888619 ATGCTCAGACGTCGGAAGAA 59.111 50.000 18.91 8.71 45.01 2.52
640 700 1.067846 CGTCGGAAGAAGACATCACCA 60.068 52.381 0.00 0.00 45.01 4.17
649 709 0.617413 AGACATCACCAAGGCAGAGG 59.383 55.000 0.00 0.00 0.00 3.69
678 738 5.521735 GTCGGAGAATGACGAGTAGTAGTAA 59.478 44.000 0.00 0.00 39.69 2.24
725 785 5.174035 CGTAGGAGAATGCTTTGAACTATCG 59.826 44.000 0.00 0.00 38.32 2.92
726 786 4.446371 AGGAGAATGCTTTGAACTATCGG 58.554 43.478 0.00 0.00 22.99 4.18
727 787 4.162320 AGGAGAATGCTTTGAACTATCGGA 59.838 41.667 0.00 0.00 22.99 4.55
728 788 4.509600 GGAGAATGCTTTGAACTATCGGAG 59.490 45.833 0.00 0.00 0.00 4.63
729 789 5.091261 AGAATGCTTTGAACTATCGGAGT 57.909 39.130 0.00 0.00 41.56 3.85
730 790 5.112686 AGAATGCTTTGAACTATCGGAGTC 58.887 41.667 0.00 0.00 37.44 3.36
731 791 3.953712 TGCTTTGAACTATCGGAGTCA 57.046 42.857 0.00 0.00 37.44 3.41
732 792 4.265904 TGCTTTGAACTATCGGAGTCAA 57.734 40.909 0.00 0.00 37.44 3.18
733 793 4.637276 TGCTTTGAACTATCGGAGTCAAA 58.363 39.130 0.00 0.00 37.44 2.69
734 794 5.245531 TGCTTTGAACTATCGGAGTCAAAT 58.754 37.500 8.46 0.00 37.44 2.32
735 795 5.122239 TGCTTTGAACTATCGGAGTCAAATG 59.878 40.000 8.46 5.88 37.44 2.32
736 796 5.122396 GCTTTGAACTATCGGAGTCAAATGT 59.878 40.000 8.46 0.00 37.44 2.71
737 797 6.480524 TTTGAACTATCGGAGTCAAATGTG 57.519 37.500 0.00 0.00 37.44 3.21
738 798 5.147330 TGAACTATCGGAGTCAAATGTGT 57.853 39.130 0.00 0.00 37.44 3.72
739 799 6.275494 TGAACTATCGGAGTCAAATGTGTA 57.725 37.500 0.00 0.00 37.44 2.90
740 800 6.873997 TGAACTATCGGAGTCAAATGTGTAT 58.126 36.000 0.00 0.00 37.44 2.29
741 801 6.978659 TGAACTATCGGAGTCAAATGTGTATC 59.021 38.462 0.00 0.00 37.44 2.24
742 802 5.520632 ACTATCGGAGTCAAATGTGTATCG 58.479 41.667 0.00 0.00 29.95 2.92
743 803 4.649088 ATCGGAGTCAAATGTGTATCGA 57.351 40.909 0.00 0.00 0.00 3.59
744 804 4.443913 TCGGAGTCAAATGTGTATCGAA 57.556 40.909 0.00 0.00 0.00 3.71
745 805 5.006153 TCGGAGTCAAATGTGTATCGAAT 57.994 39.130 0.00 0.00 0.00 3.34
746 806 5.416083 TCGGAGTCAAATGTGTATCGAATT 58.584 37.500 0.00 0.00 0.00 2.17
747 807 6.566141 TCGGAGTCAAATGTGTATCGAATTA 58.434 36.000 0.00 0.00 0.00 1.40
748 808 7.207383 TCGGAGTCAAATGTGTATCGAATTAT 58.793 34.615 0.00 0.00 0.00 1.28
749 809 8.354426 TCGGAGTCAAATGTGTATCGAATTATA 58.646 33.333 0.00 0.00 0.00 0.98
750 810 8.639428 CGGAGTCAAATGTGTATCGAATTATAG 58.361 37.037 0.00 0.00 0.00 1.31
751 811 9.477484 GGAGTCAAATGTGTATCGAATTATAGT 57.523 33.333 0.00 0.00 0.00 2.12
776 836 3.101019 AAAAACATAACGCGCCTGC 57.899 47.368 5.73 0.00 37.91 4.85
777 837 0.596082 AAAAACATAACGCGCCTGCT 59.404 45.000 5.73 0.00 39.65 4.24
778 838 1.444836 AAAACATAACGCGCCTGCTA 58.555 45.000 5.73 0.00 39.65 3.49
779 839 1.444836 AAACATAACGCGCCTGCTAA 58.555 45.000 5.73 0.00 39.65 3.09
780 840 1.444836 AACATAACGCGCCTGCTAAA 58.555 45.000 5.73 0.00 39.65 1.85
781 841 1.444836 ACATAACGCGCCTGCTAAAA 58.555 45.000 5.73 0.00 39.65 1.52
782 842 1.129811 ACATAACGCGCCTGCTAAAAC 59.870 47.619 5.73 0.00 39.65 2.43
783 843 0.372334 ATAACGCGCCTGCTAAAACG 59.628 50.000 5.73 0.00 39.65 3.60
784 844 1.628447 TAACGCGCCTGCTAAAACGG 61.628 55.000 5.73 0.00 39.65 4.44
785 845 4.811761 CGCGCCTGCTAAAACGGC 62.812 66.667 0.00 0.00 39.65 5.68
786 846 3.431725 GCGCCTGCTAAAACGGCT 61.432 61.111 0.00 0.00 41.61 5.52
787 847 2.785258 CGCCTGCTAAAACGGCTC 59.215 61.111 0.00 0.00 41.61 4.70
788 848 2.785258 GCCTGCTAAAACGGCTCG 59.215 61.111 0.00 0.00 40.62 5.03
789 849 2.750888 GCCTGCTAAAACGGCTCGG 61.751 63.158 0.00 0.00 40.62 4.63
790 850 2.106683 CCTGCTAAAACGGCTCGGG 61.107 63.158 0.00 0.00 0.00 5.14
791 851 2.744709 TGCTAAAACGGCTCGGGC 60.745 61.111 0.00 0.00 37.82 6.13
800 860 2.513897 GGCTCGGGCGTGCTTTAT 60.514 61.111 0.00 0.00 39.81 1.40
801 861 2.112815 GGCTCGGGCGTGCTTTATT 61.113 57.895 0.00 0.00 39.81 1.40
802 862 1.654023 GGCTCGGGCGTGCTTTATTT 61.654 55.000 0.00 0.00 39.81 1.40
803 863 0.170339 GCTCGGGCGTGCTTTATTTT 59.830 50.000 0.00 0.00 0.00 1.82
804 864 1.399089 GCTCGGGCGTGCTTTATTTTA 59.601 47.619 0.00 0.00 0.00 1.52
805 865 2.790123 GCTCGGGCGTGCTTTATTTTAC 60.790 50.000 0.00 0.00 0.00 2.01
806 866 1.394227 TCGGGCGTGCTTTATTTTACG 59.606 47.619 0.00 0.00 39.37 3.18
807 867 1.530236 CGGGCGTGCTTTATTTTACGG 60.530 52.381 0.00 0.00 37.06 4.02
809 869 1.176838 GCGTGCTTTATTTTACGGCG 58.823 50.000 4.80 4.80 37.06 6.46
810 870 1.805286 CGTGCTTTATTTTACGGCGG 58.195 50.000 13.24 0.00 33.27 6.13
811 871 1.541475 GTGCTTTATTTTACGGCGGC 58.459 50.000 13.24 0.00 0.00 6.53
812 872 0.452585 TGCTTTATTTTACGGCGGCC 59.547 50.000 13.24 9.54 0.00 6.13
830 890 4.233635 GCTTGAGCCAGCGCATCG 62.234 66.667 11.47 0.00 37.52 3.84
831 891 2.816958 CTTGAGCCAGCGCATCGT 60.817 61.111 11.47 0.00 37.52 3.73
832 892 2.806856 CTTGAGCCAGCGCATCGTC 61.807 63.158 11.47 0.96 37.52 4.20
842 902 2.392591 GCATCGTCGCGCGTAAAA 59.607 55.556 30.98 14.25 42.13 1.52
843 903 1.644364 GCATCGTCGCGCGTAAAAG 60.644 57.895 30.98 18.51 42.13 2.27
844 904 1.700029 CATCGTCGCGCGTAAAAGT 59.300 52.632 30.98 9.45 42.13 2.66
845 905 0.092351 CATCGTCGCGCGTAAAAGTT 59.908 50.000 30.98 5.16 42.13 2.66
846 906 0.092351 ATCGTCGCGCGTAAAAGTTG 59.908 50.000 30.98 11.32 42.13 3.16
847 907 1.506277 CGTCGCGCGTAAAAGTTGG 60.506 57.895 30.98 5.60 35.54 3.77
848 908 1.790896 GTCGCGCGTAAAAGTTGGC 60.791 57.895 30.98 0.00 0.00 4.52
849 909 1.957186 TCGCGCGTAAAAGTTGGCT 60.957 52.632 30.98 0.00 0.00 4.75
850 910 1.082366 CGCGCGTAAAAGTTGGCTT 60.082 52.632 24.19 0.00 36.30 4.35
851 911 0.164217 CGCGCGTAAAAGTTGGCTTA 59.836 50.000 24.19 0.00 33.95 3.09
852 912 1.201987 CGCGCGTAAAAGTTGGCTTAT 60.202 47.619 24.19 0.00 33.95 1.73
853 913 2.437626 GCGCGTAAAAGTTGGCTTATC 58.562 47.619 8.43 0.00 33.95 1.75
854 914 2.095372 GCGCGTAAAAGTTGGCTTATCT 59.905 45.455 8.43 0.00 33.95 1.98
855 915 3.425758 GCGCGTAAAAGTTGGCTTATCTT 60.426 43.478 8.43 0.00 33.95 2.40
856 916 4.201744 GCGCGTAAAAGTTGGCTTATCTTA 60.202 41.667 8.43 0.00 33.95 2.10
857 917 5.253335 CGCGTAAAAGTTGGCTTATCTTAC 58.747 41.667 0.00 0.00 33.95 2.34
858 918 5.253335 GCGTAAAAGTTGGCTTATCTTACG 58.747 41.667 13.73 13.73 33.95 3.18
859 919 5.253335 CGTAAAAGTTGGCTTATCTTACGC 58.747 41.667 8.73 0.00 33.95 4.42
860 920 5.063060 CGTAAAAGTTGGCTTATCTTACGCT 59.937 40.000 8.73 0.00 33.95 5.07
861 921 4.946784 AAAGTTGGCTTATCTTACGCTG 57.053 40.909 0.00 0.00 33.95 5.18
862 922 3.611766 AGTTGGCTTATCTTACGCTGT 57.388 42.857 0.00 0.00 0.00 4.40
863 923 4.730949 AGTTGGCTTATCTTACGCTGTA 57.269 40.909 0.00 0.00 0.00 2.74
864 924 5.277857 AGTTGGCTTATCTTACGCTGTAT 57.722 39.130 0.00 0.00 0.00 2.29
865 925 5.671493 AGTTGGCTTATCTTACGCTGTATT 58.329 37.500 0.00 0.00 0.00 1.89
866 926 5.753921 AGTTGGCTTATCTTACGCTGTATTC 59.246 40.000 0.00 0.00 0.00 1.75
867 927 5.531122 TGGCTTATCTTACGCTGTATTCT 57.469 39.130 0.00 0.00 0.00 2.40
868 928 5.914033 TGGCTTATCTTACGCTGTATTCTT 58.086 37.500 0.00 0.00 0.00 2.52
869 929 6.346096 TGGCTTATCTTACGCTGTATTCTTT 58.654 36.000 0.00 0.00 0.00 2.52
870 930 6.821665 TGGCTTATCTTACGCTGTATTCTTTT 59.178 34.615 0.00 0.00 0.00 2.27
871 931 7.335924 TGGCTTATCTTACGCTGTATTCTTTTT 59.664 33.333 0.00 0.00 0.00 1.94
901 961 2.555782 GCATTGCGCGTCTGTTGA 59.444 55.556 8.43 0.00 0.00 3.18
902 962 1.082169 GCATTGCGCGTCTGTTGAA 60.082 52.632 8.43 0.00 0.00 2.69
903 963 1.061799 GCATTGCGCGTCTGTTGAAG 61.062 55.000 8.43 0.00 0.00 3.02
904 964 0.512518 CATTGCGCGTCTGTTGAAGA 59.487 50.000 8.43 0.00 0.00 2.87
905 965 1.129251 CATTGCGCGTCTGTTGAAGAT 59.871 47.619 8.43 0.00 37.23 2.40
906 966 0.512518 TTGCGCGTCTGTTGAAGATG 59.487 50.000 8.43 0.00 43.79 2.90
912 972 1.388093 CGTCTGTTGAAGATGCTCACG 59.612 52.381 0.00 0.00 37.23 4.35
913 973 2.677199 GTCTGTTGAAGATGCTCACGA 58.323 47.619 0.00 0.00 37.23 4.35
914 974 3.257393 GTCTGTTGAAGATGCTCACGAT 58.743 45.455 0.00 0.00 37.23 3.73
915 975 4.424626 GTCTGTTGAAGATGCTCACGATA 58.575 43.478 0.00 0.00 37.23 2.92
916 976 4.502282 GTCTGTTGAAGATGCTCACGATAG 59.498 45.833 0.00 0.00 37.23 2.08
929 989 2.399611 GATAGGCAACGTGCGTGC 59.600 61.111 13.07 8.49 46.21 5.34
933 993 2.423290 TAGGCAACGTGCGTGCTACA 62.423 55.000 10.31 0.00 46.21 2.74
962 1037 4.481195 AGCGCTGAGGCTTTTCAA 57.519 50.000 10.39 0.00 41.39 2.69
984 1059 1.614903 GCAATGCCAATGCTAGCCATA 59.385 47.619 13.29 0.00 40.64 2.74
985 1060 2.608752 GCAATGCCAATGCTAGCCATAC 60.609 50.000 13.29 0.00 40.64 2.39
988 1063 1.064832 TGCCAATGCTAGCCATACACA 60.065 47.619 13.29 0.60 38.71 3.72
1028 1103 2.668212 CGGCGTTTTCCTGCTCCA 60.668 61.111 0.00 0.00 0.00 3.86
1045 1120 1.607801 CCATCTCGTCCTGCTCACCA 61.608 60.000 0.00 0.00 0.00 4.17
1115 1191 2.034066 CACACCGAGCCCACCATT 59.966 61.111 0.00 0.00 0.00 3.16
1143 1219 4.039092 CTGGGCCACCTCCACCTG 62.039 72.222 0.00 0.00 37.76 4.00
1346 1524 9.537192 CATATGGCATCTTTCAACACAAAATAT 57.463 29.630 1.65 0.00 0.00 1.28
1397 1617 6.321717 TCACACAAACAAGTTGATGAAGTTC 58.678 36.000 10.54 0.00 39.87 3.01
1398 1618 6.072230 TCACACAAACAAGTTGATGAAGTTCA 60.072 34.615 10.54 8.27 39.87 3.18
1399 1619 6.753279 CACACAAACAAGTTGATGAAGTTCAT 59.247 34.615 18.31 18.31 40.34 2.57
1400 1620 6.753279 ACACAAACAAGTTGATGAAGTTCATG 59.247 34.615 22.93 11.29 37.20 3.07
1401 1621 5.750067 ACAAACAAGTTGATGAAGTTCATGC 59.250 36.000 22.93 14.04 37.20 4.06
1402 1622 4.510038 ACAAGTTGATGAAGTTCATGCC 57.490 40.909 22.93 10.04 37.20 4.40
1403 1623 3.256631 ACAAGTTGATGAAGTTCATGCCC 59.743 43.478 22.93 9.34 37.20 5.36
1404 1624 3.159213 AGTTGATGAAGTTCATGCCCA 57.841 42.857 22.93 11.82 37.20 5.36
1405 1625 2.821969 AGTTGATGAAGTTCATGCCCAC 59.178 45.455 22.93 11.04 37.20 4.61
1406 1626 2.557924 GTTGATGAAGTTCATGCCCACA 59.442 45.455 22.93 11.11 37.20 4.17
1407 1627 2.874014 TGATGAAGTTCATGCCCACAA 58.126 42.857 22.93 0.00 37.20 3.33
1408 1628 2.821378 TGATGAAGTTCATGCCCACAAG 59.179 45.455 22.93 0.00 37.20 3.16
1409 1629 2.363306 TGAAGTTCATGCCCACAAGT 57.637 45.000 0.08 0.00 0.00 3.16
1410 1630 2.665165 TGAAGTTCATGCCCACAAGTT 58.335 42.857 0.08 0.00 0.00 2.66
1411 1631 3.030291 TGAAGTTCATGCCCACAAGTTT 58.970 40.909 0.08 0.00 0.00 2.66
1412 1632 4.211125 TGAAGTTCATGCCCACAAGTTTA 58.789 39.130 0.08 0.00 0.00 2.01
1413 1633 4.646945 TGAAGTTCATGCCCACAAGTTTAA 59.353 37.500 0.08 0.00 0.00 1.52
1414 1634 5.127845 TGAAGTTCATGCCCACAAGTTTAAA 59.872 36.000 0.08 0.00 0.00 1.52
1415 1635 5.606348 AGTTCATGCCCACAAGTTTAAAA 57.394 34.783 0.00 0.00 0.00 1.52
1416 1636 6.173427 AGTTCATGCCCACAAGTTTAAAAT 57.827 33.333 0.00 0.00 0.00 1.82
1422 1642 4.040217 TGCCCACAAGTTTAAAATCATGCT 59.960 37.500 0.00 0.00 0.00 3.79
1524 1781 1.020333 CGTCTTCGTCCTCGTCCTCT 61.020 60.000 0.00 0.00 38.33 3.69
1558 1815 1.771565 TTCTTCCGCCTCCGAAGATA 58.228 50.000 1.40 0.00 33.74 1.98
1608 1865 0.388520 CATCACGTGAAGCTCCGACA 60.389 55.000 24.13 0.00 0.00 4.35
1676 1933 3.431486 GGAGGCTCATCGAAAGACATTCT 60.431 47.826 17.69 0.00 46.97 2.40
1967 2336 4.406456 TGTTGGGCAAGATTGACATACTT 58.594 39.130 0.02 0.00 38.18 2.24
1979 2348 1.463444 GACATACTTCTTTTGCGCCGT 59.537 47.619 4.18 0.00 0.00 5.68
2185 2556 3.813166 CACCTCGTTGGCTTCTTTTCTTA 59.187 43.478 0.00 0.00 40.22 2.10
2242 2616 5.130145 TCATCATCTCCTTTCCTCTTCTTCC 59.870 44.000 0.00 0.00 0.00 3.46
2310 2685 1.892209 ATGAAACCGAGTTGGGTGTC 58.108 50.000 0.24 0.00 43.49 3.67
2366 2765 4.095211 TCCTCCTCCTCATCATCATCATC 58.905 47.826 0.00 0.00 0.00 2.92
2377 2776 9.511272 CCTCATCATCATCATCCAACTTAATTA 57.489 33.333 0.00 0.00 0.00 1.40
2394 2793 6.148150 ACTTAATTATTCGCTTCCGTTTGTCA 59.852 34.615 0.00 0.00 35.54 3.58
2451 2850 7.351952 TCTTCCATTTCTCATCATCCTTCAAT 58.648 34.615 0.00 0.00 0.00 2.57
2481 2880 7.775093 TCATAGCAATGAGGCAAAGTAAATACT 59.225 33.333 0.00 0.00 37.20 2.12
2592 3001 2.099098 AGTTAGCACCAACAACAAGCAC 59.901 45.455 0.00 0.00 0.00 4.40
2603 3012 2.736192 ACAACAAGCACAACAAAGCAAC 59.264 40.909 0.00 0.00 0.00 4.17
2625 3047 7.361713 GCAACTTTAGCACCAACATGTAAGATA 60.362 37.037 0.00 0.00 0.00 1.98
2648 3072 9.717942 GATAAAATGGCACTTACTCTATCATCT 57.282 33.333 0.00 0.00 0.00 2.90
2894 3318 3.069443 TGCATAGTAAGATGTCATCGGCA 59.931 43.478 7.18 7.15 0.00 5.69
2958 3382 2.603473 CACCCTCCTCGTCCACCA 60.603 66.667 0.00 0.00 0.00 4.17
3066 3493 8.058667 TGCATCATCATTGAGACTACAATTTT 57.941 30.769 0.00 0.00 38.25 1.82
3215 3653 1.956170 CAACGAGTGAGCTTGCGGT 60.956 57.895 0.00 0.00 0.00 5.68
3628 4315 1.594310 GGGAGAAGAAGAGCGCAGT 59.406 57.895 11.47 0.00 0.00 4.40
3816 4508 4.191485 CGTCTGTTTAGCGCGCCG 62.191 66.667 30.33 17.82 0.00 6.46
3820 4512 2.048409 TGTTTAGCGCGCCGGTTA 60.048 55.556 30.33 11.09 38.83 2.85
4050 4748 0.668401 GGTACAACTACACCGCGCTT 60.668 55.000 5.56 0.00 0.00 4.68
4077 4775 2.447572 TCCCACAGCACCCACTCA 60.448 61.111 0.00 0.00 0.00 3.41
4266 4983 1.230635 GCTGGTGCTGAACGTGATGT 61.231 55.000 0.00 0.00 36.03 3.06
4343 5060 2.416547 CGTCGAGGAGTCGTTTAAGGTA 59.583 50.000 0.00 0.00 46.85 3.08
4346 5063 4.074970 TCGAGGAGTCGTTTAAGGTAGTT 58.925 43.478 0.00 0.00 46.85 2.24
4477 5206 2.126965 CCTCGTCGACGACCACAC 60.127 66.667 34.97 0.00 44.22 3.82
4578 5316 3.186001 CGAGTACTACACTGACAACGTCT 59.814 47.826 0.00 0.00 37.72 4.18
4642 5386 0.885196 TCCGACATGACATCGTCACA 59.115 50.000 0.00 0.00 45.65 3.58
4646 5390 3.489229 CCGACATGACATCGTCACATACT 60.489 47.826 0.00 0.00 45.65 2.12
4674 5436 1.202320 GCAACGTAACGTCCAACCG 59.798 57.895 0.00 0.00 39.99 4.44
4751 5520 4.521062 ACGATGGCGCTGCTCCTC 62.521 66.667 7.64 4.42 42.48 3.71
4754 5523 4.479993 ATGGCGCTGCTCCTCACC 62.480 66.667 7.64 0.00 0.00 4.02
4827 5596 2.182030 GACGGCTTGTCGAGGAGG 59.818 66.667 0.45 0.00 37.96 4.30
4858 5627 1.923148 CAACCTCCCCTACCTCCAATT 59.077 52.381 0.00 0.00 0.00 2.32
4991 5760 0.250124 TCGTGAACTCGTGGGCAATT 60.250 50.000 0.00 0.00 0.00 2.32
5051 5826 0.909610 TGCCGGAGAGGTTCTTGGAT 60.910 55.000 5.05 0.00 43.70 3.41
5527 6993 2.379907 ACAATCCCCATCTTGTTCCACT 59.620 45.455 0.00 0.00 31.74 4.00
5661 7152 0.664466 CGAGTGATGCGTGTCTGTGT 60.664 55.000 0.00 0.00 0.00 3.72
5797 8240 1.083806 CGAGTATGTGCGTGCATGGT 61.084 55.000 8.27 0.00 0.00 3.55
5917 8387 1.072331 ACTGATGAACCAACGCCTTCT 59.928 47.619 0.00 0.00 0.00 2.85
6128 8620 1.001378 GCAGCTGTTCATGTCCGTTTT 60.001 47.619 16.64 0.00 0.00 2.43
6243 8747 7.142306 ACTTCTCTAAATTACCGAAAAAGGC 57.858 36.000 0.00 0.00 33.69 4.35
6244 8748 6.940867 ACTTCTCTAAATTACCGAAAAAGGCT 59.059 34.615 0.00 0.00 33.69 4.58
6245 8749 7.447545 ACTTCTCTAAATTACCGAAAAAGGCTT 59.552 33.333 0.00 0.00 33.69 4.35
6246 8750 7.754851 TCTCTAAATTACCGAAAAAGGCTTT 57.245 32.000 6.68 6.68 33.69 3.51
6247 8751 7.813645 TCTCTAAATTACCGAAAAAGGCTTTC 58.186 34.615 13.76 0.41 33.69 2.62
6249 8753 2.691984 TTACCGAAAAAGGCTTTCGC 57.308 45.000 13.76 7.41 46.89 4.70
6259 8763 3.509659 GCTTTCGCCCCGCTTTAT 58.490 55.556 0.00 0.00 0.00 1.40
6260 8764 2.697819 GCTTTCGCCCCGCTTTATA 58.302 52.632 0.00 0.00 0.00 0.98
6261 8765 1.018910 GCTTTCGCCCCGCTTTATAA 58.981 50.000 0.00 0.00 0.00 0.98
6262 8766 1.402613 GCTTTCGCCCCGCTTTATAAA 59.597 47.619 0.00 0.00 0.00 1.40
6263 8767 2.034179 GCTTTCGCCCCGCTTTATAAAT 59.966 45.455 0.00 0.00 0.00 1.40
6264 8768 3.251487 GCTTTCGCCCCGCTTTATAAATA 59.749 43.478 0.00 0.00 0.00 1.40
6265 8769 4.261280 GCTTTCGCCCCGCTTTATAAATAA 60.261 41.667 0.00 0.00 0.00 1.40
6266 8770 5.733937 GCTTTCGCCCCGCTTTATAAATAAA 60.734 40.000 0.00 0.00 0.00 1.40
6279 8783 8.185003 CTTTATAAATAAAGCAACCACCAAGC 57.815 34.615 9.01 0.00 41.69 4.01
6280 8784 5.736951 ATAAATAAAGCAACCACCAAGCA 57.263 34.783 0.00 0.00 0.00 3.91
6281 8785 3.385193 AATAAAGCAACCACCAAGCAC 57.615 42.857 0.00 0.00 0.00 4.40
6282 8786 1.769026 TAAAGCAACCACCAAGCACA 58.231 45.000 0.00 0.00 0.00 4.57
6283 8787 0.901124 AAAGCAACCACCAAGCACAA 59.099 45.000 0.00 0.00 0.00 3.33
6284 8788 1.122227 AAGCAACCACCAAGCACAAT 58.878 45.000 0.00 0.00 0.00 2.71
6285 8789 0.390124 AGCAACCACCAAGCACAATG 59.610 50.000 0.00 0.00 0.00 2.82
6286 8790 0.104671 GCAACCACCAAGCACAATGT 59.895 50.000 0.00 0.00 0.00 2.71
6287 8791 1.473080 GCAACCACCAAGCACAATGTT 60.473 47.619 0.00 0.00 0.00 2.71
6288 8792 2.472816 CAACCACCAAGCACAATGTTC 58.527 47.619 0.00 0.00 0.00 3.18
6289 8793 1.774110 ACCACCAAGCACAATGTTCA 58.226 45.000 0.00 0.00 0.00 3.18
6290 8794 1.408702 ACCACCAAGCACAATGTTCAC 59.591 47.619 0.00 0.00 0.00 3.18
6291 8795 1.408340 CCACCAAGCACAATGTTCACA 59.592 47.619 0.00 0.00 0.00 3.58
6292 8796 2.159128 CCACCAAGCACAATGTTCACAA 60.159 45.455 0.00 0.00 0.00 3.33
6293 8797 3.117794 CACCAAGCACAATGTTCACAAG 58.882 45.455 0.00 0.00 0.00 3.16
6294 8798 2.101249 ACCAAGCACAATGTTCACAAGG 59.899 45.455 0.00 0.00 0.00 3.61
6295 8799 2.101249 CCAAGCACAATGTTCACAAGGT 59.899 45.455 0.00 0.00 0.00 3.50
6296 8800 3.317711 CCAAGCACAATGTTCACAAGGTA 59.682 43.478 0.00 0.00 0.00 3.08
6297 8801 4.290155 CAAGCACAATGTTCACAAGGTAC 58.710 43.478 0.00 0.00 0.00 3.34
6298 8802 2.884639 AGCACAATGTTCACAAGGTACC 59.115 45.455 2.73 2.73 0.00 3.34
6299 8803 2.621055 GCACAATGTTCACAAGGTACCA 59.379 45.455 15.94 0.00 0.00 3.25
6300 8804 3.550030 GCACAATGTTCACAAGGTACCAC 60.550 47.826 15.94 2.47 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.820871 CTAGCGTGAGAGCTCCCTTT 59.179 55.000 10.93 0.00 45.67 3.11
9 10 2.468831 CAAATCTAGCGTGAGAGCTCC 58.531 52.381 10.93 2.40 45.67 4.70
41 42 0.584396 CAATTTTATAGGCGCGCCGA 59.416 50.000 41.70 38.31 41.95 5.54
66 67 0.752009 AACGAGAGAGCGGCATAGGA 60.752 55.000 1.45 0.00 35.12 2.94
70 71 2.510238 GCAACGAGAGAGCGGCAT 60.510 61.111 1.45 0.00 35.12 4.40
123 126 1.447663 CATGGTGACGCGGTGATGA 60.448 57.895 12.47 0.00 0.00 2.92
401 404 2.202756 GCCTTCGGTTCTCGCGAT 60.203 61.111 10.36 0.00 39.05 4.58
445 504 1.959226 GGCGAAGAACGGTTGCTCA 60.959 57.895 0.00 0.00 42.83 4.26
453 512 0.798771 CCTTCTCTCGGCGAAGAACG 60.799 60.000 21.88 16.86 40.15 3.95
469 528 1.156322 TCTCCTCCCTCTCCACCCTT 61.156 60.000 0.00 0.00 0.00 3.95
543 602 4.185394 TCCTAGCGCGATGTTGAATTTAA 58.815 39.130 12.10 0.00 0.00 1.52
570 629 0.391597 GTTGGAGTCCAAGGACGACA 59.608 55.000 25.22 12.91 44.82 4.35
579 638 2.649034 GCTCGTCGTTGGAGTCCA 59.351 61.111 8.12 8.12 34.00 4.02
604 664 1.135373 CGACGTCTGAGCATAGGTGTT 60.135 52.381 14.70 0.00 0.00 3.32
607 667 0.393944 TCCGACGTCTGAGCATAGGT 60.394 55.000 14.70 0.00 0.00 3.08
612 672 0.241213 CTTCTTCCGACGTCTGAGCA 59.759 55.000 14.70 0.00 0.00 4.26
627 687 1.980765 TCTGCCTTGGTGATGTCTTCT 59.019 47.619 0.00 0.00 0.00 2.85
630 690 0.617413 CCTCTGCCTTGGTGATGTCT 59.383 55.000 0.00 0.00 0.00 3.41
640 700 2.344203 CCGACTCGACCTCTGCCTT 61.344 63.158 0.00 0.00 0.00 4.35
649 709 0.725686 TCGTCATTCTCCGACTCGAC 59.274 55.000 0.00 0.00 0.00 4.20
693 753 8.178313 TCAAAGCATTCTCCTACGATAGATAA 57.822 34.615 0.00 0.00 41.38 1.75
711 771 3.953712 TGACTCCGATAGTTCAAAGCA 57.046 42.857 0.00 0.00 39.07 3.91
712 772 5.122396 ACATTTGACTCCGATAGTTCAAAGC 59.878 40.000 14.31 0.00 39.07 3.51
715 775 5.547465 ACACATTTGACTCCGATAGTTCAA 58.453 37.500 0.00 0.00 39.07 2.69
725 785 9.477484 ACTATAATTCGATACACATTTGACTCC 57.523 33.333 0.00 0.00 0.00 3.85
758 818 0.596082 AGCAGGCGCGTTATGTTTTT 59.404 45.000 8.43 0.00 45.49 1.94
759 819 1.444836 TAGCAGGCGCGTTATGTTTT 58.555 45.000 8.43 0.00 45.49 2.43
760 820 1.444836 TTAGCAGGCGCGTTATGTTT 58.555 45.000 8.43 0.46 45.49 2.83
761 821 1.444836 TTTAGCAGGCGCGTTATGTT 58.555 45.000 8.43 4.94 45.49 2.71
762 822 1.129811 GTTTTAGCAGGCGCGTTATGT 59.870 47.619 8.43 0.00 45.49 2.29
763 823 1.810197 GTTTTAGCAGGCGCGTTATG 58.190 50.000 8.43 5.41 45.49 1.90
764 824 0.372334 CGTTTTAGCAGGCGCGTTAT 59.628 50.000 8.43 0.00 45.49 1.89
765 825 1.628447 CCGTTTTAGCAGGCGCGTTA 61.628 55.000 8.43 0.00 45.49 3.18
766 826 2.554272 CGTTTTAGCAGGCGCGTT 59.446 55.556 8.43 0.00 45.49 4.84
767 827 3.419759 CCGTTTTAGCAGGCGCGT 61.420 61.111 8.43 0.00 45.49 6.01
768 828 4.811761 GCCGTTTTAGCAGGCGCG 62.812 66.667 0.00 0.00 45.49 6.86
772 832 2.106683 CCCGAGCCGTTTTAGCAGG 61.107 63.158 0.00 0.00 0.00 4.85
773 833 2.750888 GCCCGAGCCGTTTTAGCAG 61.751 63.158 0.00 0.00 0.00 4.24
774 834 2.744709 GCCCGAGCCGTTTTAGCA 60.745 61.111 0.00 0.00 0.00 3.49
775 835 3.861263 CGCCCGAGCCGTTTTAGC 61.861 66.667 0.00 0.00 34.57 3.09
776 836 2.433664 ACGCCCGAGCCGTTTTAG 60.434 61.111 0.00 0.00 34.57 1.85
777 837 2.739287 CACGCCCGAGCCGTTTTA 60.739 61.111 0.00 0.00 34.57 1.52
783 843 1.654023 AAATAAAGCACGCCCGAGCC 61.654 55.000 6.48 0.00 34.57 4.70
784 844 0.170339 AAAATAAAGCACGCCCGAGC 59.830 50.000 1.88 1.88 0.00 5.03
785 845 2.536130 CGTAAAATAAAGCACGCCCGAG 60.536 50.000 0.00 0.00 0.00 4.63
786 846 1.394227 CGTAAAATAAAGCACGCCCGA 59.606 47.619 0.00 0.00 0.00 5.14
787 847 1.530236 CCGTAAAATAAAGCACGCCCG 60.530 52.381 0.00 0.00 33.19 6.13
788 848 1.796253 GCCGTAAAATAAAGCACGCCC 60.796 52.381 0.00 0.00 33.19 6.13
789 849 1.541475 GCCGTAAAATAAAGCACGCC 58.459 50.000 0.00 0.00 33.19 5.68
790 850 1.176838 CGCCGTAAAATAAAGCACGC 58.823 50.000 0.00 0.00 33.19 5.34
791 851 1.805286 CCGCCGTAAAATAAAGCACG 58.195 50.000 0.00 0.00 0.00 5.34
792 852 1.541475 GCCGCCGTAAAATAAAGCAC 58.459 50.000 0.00 0.00 0.00 4.40
793 853 0.452585 GGCCGCCGTAAAATAAAGCA 59.547 50.000 0.00 0.00 0.00 3.91
794 854 0.590481 CGGCCGCCGTAAAATAAAGC 60.590 55.000 24.08 0.00 42.73 3.51
795 855 3.519774 CGGCCGCCGTAAAATAAAG 57.480 52.632 24.08 0.00 42.73 1.85
813 873 4.233635 CGATGCGCTGGCTCAAGC 62.234 66.667 9.73 0.00 40.82 4.01
814 874 2.806856 GACGATGCGCTGGCTCAAG 61.807 63.158 9.73 0.00 40.82 3.02
815 875 2.815211 GACGATGCGCTGGCTCAA 60.815 61.111 9.73 0.00 40.82 3.02
830 890 1.790896 GCCAACTTTTACGCGCGAC 60.791 57.895 39.36 8.00 0.00 5.19
831 891 1.500512 AAGCCAACTTTTACGCGCGA 61.501 50.000 39.36 17.83 29.41 5.87
832 892 0.164217 TAAGCCAACTTTTACGCGCG 59.836 50.000 30.96 30.96 37.33 6.86
833 893 2.095372 AGATAAGCCAACTTTTACGCGC 59.905 45.455 5.73 0.00 37.33 6.86
834 894 4.336532 AAGATAAGCCAACTTTTACGCG 57.663 40.909 3.53 3.53 37.33 6.01
835 895 5.253335 CGTAAGATAAGCCAACTTTTACGC 58.747 41.667 7.79 0.00 40.42 4.42
836 896 5.063060 AGCGTAAGATAAGCCAACTTTTACG 59.937 40.000 13.10 13.10 44.86 3.18
837 897 6.128363 ACAGCGTAAGATAAGCCAACTTTTAC 60.128 38.462 0.00 0.00 43.02 2.01
838 898 5.935789 ACAGCGTAAGATAAGCCAACTTTTA 59.064 36.000 0.00 0.00 43.02 1.52
839 899 4.760204 ACAGCGTAAGATAAGCCAACTTTT 59.240 37.500 0.00 0.00 43.02 2.27
840 900 4.324267 ACAGCGTAAGATAAGCCAACTTT 58.676 39.130 0.00 0.00 43.02 2.66
841 901 3.939066 ACAGCGTAAGATAAGCCAACTT 58.061 40.909 0.00 0.00 43.02 2.66
842 902 3.611766 ACAGCGTAAGATAAGCCAACT 57.388 42.857 0.00 0.00 43.02 3.16
843 903 5.753921 AGAATACAGCGTAAGATAAGCCAAC 59.246 40.000 0.00 0.00 43.02 3.77
844 904 5.914033 AGAATACAGCGTAAGATAAGCCAA 58.086 37.500 0.00 0.00 43.02 4.52
845 905 5.531122 AGAATACAGCGTAAGATAAGCCA 57.469 39.130 0.00 0.00 43.02 4.75
846 906 6.846325 AAAGAATACAGCGTAAGATAAGCC 57.154 37.500 0.00 0.00 43.02 4.35
869 929 2.249337 CAATGCGCGATGTGCTAAAAA 58.751 42.857 12.10 0.00 43.27 1.94
870 930 1.893759 CAATGCGCGATGTGCTAAAA 58.106 45.000 12.10 0.00 43.27 1.52
871 931 0.523125 GCAATGCGCGATGTGCTAAA 60.523 50.000 12.10 0.00 43.27 1.85
872 932 1.062365 GCAATGCGCGATGTGCTAA 59.938 52.632 12.10 0.00 43.27 3.09
873 933 2.708865 GCAATGCGCGATGTGCTA 59.291 55.556 12.10 0.00 43.27 3.49
884 944 1.061799 CTTCAACAGACGCGCAATGC 61.062 55.000 5.73 0.00 41.47 3.56
885 945 0.512518 TCTTCAACAGACGCGCAATG 59.487 50.000 5.73 4.94 0.00 2.82
886 946 1.129251 CATCTTCAACAGACGCGCAAT 59.871 47.619 5.73 0.00 32.83 3.56
887 947 0.512518 CATCTTCAACAGACGCGCAA 59.487 50.000 5.73 0.00 32.83 4.85
888 948 1.900585 GCATCTTCAACAGACGCGCA 61.901 55.000 5.73 0.00 29.35 6.09
889 949 1.225854 GCATCTTCAACAGACGCGC 60.226 57.895 5.73 0.00 29.35 6.86
890 950 0.368227 GAGCATCTTCAACAGACGCG 59.632 55.000 3.53 3.53 45.88 6.01
891 951 1.127582 GTGAGCATCTTCAACAGACGC 59.872 52.381 0.00 0.00 41.33 5.19
892 952 1.388093 CGTGAGCATCTTCAACAGACG 59.612 52.381 0.00 0.00 32.83 4.18
893 953 2.677199 TCGTGAGCATCTTCAACAGAC 58.323 47.619 0.00 0.00 32.83 3.51
894 954 3.599730 ATCGTGAGCATCTTCAACAGA 57.400 42.857 0.00 0.00 34.92 3.41
895 955 3.801050 CCTATCGTGAGCATCTTCAACAG 59.199 47.826 0.00 0.00 34.92 3.16
896 956 3.785486 CCTATCGTGAGCATCTTCAACA 58.215 45.455 0.00 0.00 34.92 3.33
897 957 2.541762 GCCTATCGTGAGCATCTTCAAC 59.458 50.000 0.00 0.00 34.92 3.18
898 958 2.168313 TGCCTATCGTGAGCATCTTCAA 59.832 45.455 0.00 0.00 34.92 2.69
899 959 1.756538 TGCCTATCGTGAGCATCTTCA 59.243 47.619 0.00 0.00 34.92 3.02
900 960 2.515926 TGCCTATCGTGAGCATCTTC 57.484 50.000 0.00 0.00 34.92 2.87
901 961 2.555199 GTTGCCTATCGTGAGCATCTT 58.445 47.619 0.00 0.00 36.20 2.40
902 962 1.536922 CGTTGCCTATCGTGAGCATCT 60.537 52.381 0.00 0.00 36.20 2.90
903 963 0.855349 CGTTGCCTATCGTGAGCATC 59.145 55.000 0.00 0.00 36.20 3.91
904 964 0.175760 ACGTTGCCTATCGTGAGCAT 59.824 50.000 0.00 0.00 38.85 3.79
905 965 1.589630 ACGTTGCCTATCGTGAGCA 59.410 52.632 0.00 0.00 38.85 4.26
906 966 4.496670 ACGTTGCCTATCGTGAGC 57.503 55.556 0.00 0.00 38.85 4.26
910 970 2.092291 CACGCACGTTGCCTATCGT 61.092 57.895 0.00 0.00 41.12 3.73
911 971 2.695055 CACGCACGTTGCCTATCG 59.305 61.111 0.00 0.00 41.12 2.92
912 972 0.804544 TAGCACGCACGTTGCCTATC 60.805 55.000 7.08 0.00 41.12 2.08
913 973 1.082117 GTAGCACGCACGTTGCCTAT 61.082 55.000 7.08 0.00 41.12 2.57
914 974 1.735198 GTAGCACGCACGTTGCCTA 60.735 57.895 7.08 0.13 41.12 3.93
915 975 3.041940 GTAGCACGCACGTTGCCT 61.042 61.111 7.08 0.96 41.12 4.75
916 976 2.764251 CTTGTAGCACGCACGTTGCC 62.764 60.000 7.08 0.00 41.12 4.52
1018 1093 0.324738 AGGACGAGATGGAGCAGGAA 60.325 55.000 0.00 0.00 0.00 3.36
1028 1103 0.613292 ACTGGTGAGCAGGACGAGAT 60.613 55.000 16.69 0.00 0.00 2.75
1099 1174 2.034066 CAATGGTGGGCTCGGTGT 59.966 61.111 0.00 0.00 0.00 4.16
1143 1219 1.005340 CGCCTGTTGAAGATGCTCTC 58.995 55.000 0.00 0.00 0.00 3.20
1305 1481 1.100463 ATATGCAATGCACCGGCGAA 61.100 50.000 11.23 0.00 43.04 4.70
1397 1617 5.163834 GCATGATTTTAAACTTGTGGGCATG 60.164 40.000 0.00 0.00 34.23 4.06
1398 1618 4.937015 GCATGATTTTAAACTTGTGGGCAT 59.063 37.500 0.00 0.00 0.00 4.40
1399 1619 4.040217 AGCATGATTTTAAACTTGTGGGCA 59.960 37.500 0.00 0.00 0.00 5.36
1400 1620 4.568956 AGCATGATTTTAAACTTGTGGGC 58.431 39.130 0.00 0.00 0.00 5.36
1401 1621 5.634859 GTGAGCATGATTTTAAACTTGTGGG 59.365 40.000 0.00 0.00 0.00 4.61
1402 1622 6.215121 TGTGAGCATGATTTTAAACTTGTGG 58.785 36.000 0.00 0.00 0.00 4.17
1403 1623 7.436080 ACTTGTGAGCATGATTTTAAACTTGTG 59.564 33.333 0.00 0.00 0.00 3.33
1404 1624 7.491682 ACTTGTGAGCATGATTTTAAACTTGT 58.508 30.769 0.00 0.00 0.00 3.16
1405 1625 7.935338 ACTTGTGAGCATGATTTTAAACTTG 57.065 32.000 0.00 0.00 0.00 3.16
1406 1626 8.196771 TGAACTTGTGAGCATGATTTTAAACTT 58.803 29.630 0.00 0.00 0.00 2.66
1407 1627 7.715657 TGAACTTGTGAGCATGATTTTAAACT 58.284 30.769 0.00 0.00 0.00 2.66
1408 1628 7.928908 TGAACTTGTGAGCATGATTTTAAAC 57.071 32.000 0.00 0.00 0.00 2.01
1409 1629 7.814107 GGATGAACTTGTGAGCATGATTTTAAA 59.186 33.333 0.00 0.00 0.00 1.52
1410 1630 7.039853 TGGATGAACTTGTGAGCATGATTTTAA 60.040 33.333 0.00 0.00 0.00 1.52
1411 1631 6.433716 TGGATGAACTTGTGAGCATGATTTTA 59.566 34.615 0.00 0.00 0.00 1.52
1412 1632 5.244402 TGGATGAACTTGTGAGCATGATTTT 59.756 36.000 0.00 0.00 0.00 1.82
1413 1633 4.768448 TGGATGAACTTGTGAGCATGATTT 59.232 37.500 0.00 0.00 0.00 2.17
1414 1634 4.338012 TGGATGAACTTGTGAGCATGATT 58.662 39.130 0.00 0.00 0.00 2.57
1415 1635 3.959293 TGGATGAACTTGTGAGCATGAT 58.041 40.909 0.00 0.00 0.00 2.45
1416 1636 3.421919 TGGATGAACTTGTGAGCATGA 57.578 42.857 0.00 0.00 0.00 3.07
1422 1642 3.897239 ACTTGGTTGGATGAACTTGTGA 58.103 40.909 0.00 0.00 34.66 3.58
1558 1815 3.498614 TGAGGAGAGGGAGGAAGATTT 57.501 47.619 0.00 0.00 0.00 2.17
1608 1865 2.549754 CGTTGAAGATCTTGCCAACACT 59.450 45.455 26.84 0.10 38.91 3.55
1716 1973 2.493675 GGGAGGCATGAGTTTTTCTTCC 59.506 50.000 0.00 0.00 0.00 3.46
1721 1978 3.173953 TGATGGGAGGCATGAGTTTTT 57.826 42.857 0.00 0.00 0.00 1.94
1967 2336 1.083489 CCTCAATACGGCGCAAAAGA 58.917 50.000 10.83 0.00 0.00 2.52
1979 2348 6.428083 TCTTGGACACAACTAACCTCAATA 57.572 37.500 0.00 0.00 32.14 1.90
2214 2585 4.039339 AGAGGAAAGGAGATGATGAGCTT 58.961 43.478 0.00 0.00 0.00 3.74
2242 2616 4.265320 GTGCAAGAAAGACAAAACCGAAAG 59.735 41.667 0.00 0.00 0.00 2.62
2310 2685 0.108615 ATGACGACAAGAGAAGCCCG 60.109 55.000 0.00 0.00 0.00 6.13
2366 2765 5.479716 ACGGAAGCGAATAATTAAGTTGG 57.520 39.130 0.00 0.00 0.00 3.77
2377 2776 1.798813 GAGTGACAAACGGAAGCGAAT 59.201 47.619 0.00 0.00 0.00 3.34
2394 2793 6.942976 AGATTTGGATGATTTGCATTTGAGT 58.057 32.000 0.00 0.00 37.34 3.41
2451 2850 5.500234 ACTTTGCCTCATTGCTATGAAGTA 58.500 37.500 11.94 3.06 40.17 2.24
2481 2880 4.179133 AGGGGAAGATCAAGAAAGGAAGA 58.821 43.478 0.00 0.00 0.00 2.87
2592 3001 3.779759 TGGTGCTAAAGTTGCTTTGTTG 58.220 40.909 4.56 0.00 35.21 3.33
2625 3047 8.049117 TGAAGATGATAGAGTAAGTGCCATTTT 58.951 33.333 0.00 0.00 0.00 1.82
2648 3072 1.786937 ACCCAAGTGGCACAAATGAA 58.213 45.000 21.41 0.00 44.16 2.57
2894 3318 1.102978 GAGCGGGCAATTACACCAAT 58.897 50.000 0.00 0.00 0.00 3.16
2958 3382 4.320494 GCATTTTGAAGACCATGAGTTCGT 60.320 41.667 0.00 0.00 0.00 3.85
3025 3450 4.440880 TGATGCATACATGTCAACGATGA 58.559 39.130 0.00 0.00 36.35 2.92
3341 3779 0.322906 CCTCCTCAAAGCTCCCCAAC 60.323 60.000 0.00 0.00 0.00 3.77
3801 4493 2.489539 TAACCGGCGCGCTAAACAGA 62.490 55.000 32.29 7.81 0.00 3.41
3899 4597 2.121538 AGCCTCAGCGATACGAGCA 61.122 57.895 0.00 0.00 46.67 4.26
4301 5018 1.360393 ACTCCTGGAACCTGCCCAAA 61.360 55.000 0.00 0.00 32.53 3.28
4477 5206 3.121030 CCTTGCTCCGCCTTCGTG 61.121 66.667 0.00 0.00 0.00 4.35
4498 5230 2.818841 TGGTCGTGTGTCCACCAG 59.181 61.111 0.00 0.00 38.41 4.00
4578 5316 1.879380 CACCAAGACGATGCCTTTGAA 59.121 47.619 0.00 0.00 0.00 2.69
4642 5386 7.365741 ACGTTACGTTGCAGCTATATAAGTAT 58.634 34.615 3.95 0.00 36.35 2.12
4646 5390 4.977963 GGACGTTACGTTGCAGCTATATAA 59.022 41.667 12.82 0.00 41.37 0.98
4674 5436 4.446371 CTGAACAGTACCTGGATTGGATC 58.554 47.826 0.00 0.32 35.51 3.36
4858 5627 1.303398 AGGCTCTCCTTCACGACGA 60.303 57.895 0.00 0.00 40.66 4.20
5260 6725 0.898326 GCCCTTGACAAATTCCCGGT 60.898 55.000 0.00 0.00 0.00 5.28
5325 6790 2.759795 GGAGGAGGTTTGCAGCCT 59.240 61.111 11.13 11.13 39.42 4.58
5527 6993 2.032528 CTTGGCTGTCCGCTGGAA 59.967 61.111 0.00 0.00 39.13 3.53
5594 7085 2.651361 CTTCTGGTCTGCCGTCGT 59.349 61.111 0.00 0.00 37.67 4.34
5602 7093 1.687612 CCATGGTGCCTTCTGGTCT 59.312 57.895 2.57 0.00 35.27 3.85
5676 7167 0.387929 AGGTCTTCTGACGCGAACAA 59.612 50.000 15.93 0.00 43.79 2.83
5681 8119 1.671328 TGATCTAGGTCTTCTGACGCG 59.329 52.381 3.53 3.53 43.79 6.01
5773 8215 1.351430 GCACGCACATACTCGCTGAA 61.351 55.000 0.00 0.00 0.00 3.02
5797 8240 3.932580 CTACAAGAGCACGCCGGCA 62.933 63.158 28.98 0.59 35.83 5.69
5825 8269 4.283212 TGAACACGGATATCATATCCAGCA 59.717 41.667 21.61 9.76 38.08 4.41
6128 8620 5.047164 AGAGCACATAACAATGCAATCCAAA 60.047 36.000 0.00 0.00 44.59 3.28
6243 8747 3.982576 ATTTATAAAGCGGGGCGAAAG 57.017 42.857 3.94 0.00 0.00 2.62
6244 8748 5.823353 CTTTATTTATAAAGCGGGGCGAAA 58.177 37.500 8.78 0.00 41.69 3.46
6245 8749 5.427036 CTTTATTTATAAAGCGGGGCGAA 57.573 39.130 8.78 0.00 41.69 4.70
6255 8759 7.600752 GTGCTTGGTGGTTGCTTTATTTATAAA 59.399 33.333 0.00 0.00 0.00 1.40
6256 8760 7.093992 GTGCTTGGTGGTTGCTTTATTTATAA 58.906 34.615 0.00 0.00 0.00 0.98
6257 8761 6.209589 TGTGCTTGGTGGTTGCTTTATTTATA 59.790 34.615 0.00 0.00 0.00 0.98
6258 8762 5.011533 TGTGCTTGGTGGTTGCTTTATTTAT 59.988 36.000 0.00 0.00 0.00 1.40
6259 8763 4.342378 TGTGCTTGGTGGTTGCTTTATTTA 59.658 37.500 0.00 0.00 0.00 1.40
6260 8764 3.133721 TGTGCTTGGTGGTTGCTTTATTT 59.866 39.130 0.00 0.00 0.00 1.40
6261 8765 2.697751 TGTGCTTGGTGGTTGCTTTATT 59.302 40.909 0.00 0.00 0.00 1.40
6262 8766 2.315176 TGTGCTTGGTGGTTGCTTTAT 58.685 42.857 0.00 0.00 0.00 1.40
6263 8767 1.769026 TGTGCTTGGTGGTTGCTTTA 58.231 45.000 0.00 0.00 0.00 1.85
6264 8768 0.901124 TTGTGCTTGGTGGTTGCTTT 59.099 45.000 0.00 0.00 0.00 3.51
6265 8769 1.122227 ATTGTGCTTGGTGGTTGCTT 58.878 45.000 0.00 0.00 0.00 3.91
6266 8770 0.390124 CATTGTGCTTGGTGGTTGCT 59.610 50.000 0.00 0.00 0.00 3.91
6267 8771 0.104671 ACATTGTGCTTGGTGGTTGC 59.895 50.000 0.00 0.00 0.00 4.17
6268 8772 2.159128 TGAACATTGTGCTTGGTGGTTG 60.159 45.455 0.00 0.00 0.00 3.77
6269 8773 2.106566 TGAACATTGTGCTTGGTGGTT 58.893 42.857 0.00 0.00 0.00 3.67
6270 8774 1.408702 GTGAACATTGTGCTTGGTGGT 59.591 47.619 0.00 0.00 0.00 4.16
6271 8775 1.408340 TGTGAACATTGTGCTTGGTGG 59.592 47.619 0.00 0.00 0.00 4.61
6272 8776 2.867287 TGTGAACATTGTGCTTGGTG 57.133 45.000 0.00 0.00 0.00 4.17
6273 8777 2.101249 CCTTGTGAACATTGTGCTTGGT 59.899 45.455 0.00 0.00 0.00 3.67
6274 8778 2.101249 ACCTTGTGAACATTGTGCTTGG 59.899 45.455 0.00 0.00 0.00 3.61
6275 8779 3.441496 ACCTTGTGAACATTGTGCTTG 57.559 42.857 0.00 0.00 0.00 4.01
6276 8780 3.317993 GGTACCTTGTGAACATTGTGCTT 59.682 43.478 4.06 0.00 0.00 3.91
6277 8781 2.884639 GGTACCTTGTGAACATTGTGCT 59.115 45.455 4.06 0.00 0.00 4.40
6278 8782 2.621055 TGGTACCTTGTGAACATTGTGC 59.379 45.455 14.36 0.00 0.00 4.57
6279 8783 4.223320 GTGGTACCTTGTGAACATTGTG 57.777 45.455 14.36 0.00 0.00 3.33


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.