Multiple sequence alignment - TraesCS4A01G118600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


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 TraesCS4A01G118600 chr4A 100.000 3683 0 0 1 3683 146396995 146400677 0.000000e+00 6802.0
1 TraesCS4A01G118600 chr4A 90.819 1819 150 14 1 1808 506012119 506013931 0.000000e+00 2418.0
2 TraesCS4A01G118600 chr4A 100.000 1091 0 0 4076 5166 146401070 146402160 0.000000e+00 2015.0
3 TraesCS4A01G118600 chr4A 85.299 653 51 8 4279 4918 337462608 337463228 2.620000e-177 632.0
4 TraesCS4A01G118600 chr4A 82.915 597 87 11 2667 3262 357803329 357803911 1.650000e-144 523.0
5 TraesCS4A01G118600 chr4A 81.720 558 88 11 2706 3262 360500142 360500686 2.190000e-123 453.0
6 TraesCS4A01G118600 chr4A 87.500 96 12 0 4076 4171 337458117 337458212 1.520000e-20 111.0
7 TraesCS4A01G118600 chr4A 100.000 54 0 0 4166 4219 337462392 337462445 3.290000e-17 100.0
8 TraesCS4A01G118600 chr4A 76.667 180 34 7 2664 2839 20578831 20578656 5.510000e-15 93.5
9 TraesCS4A01G118600 chr5A 93.231 1817 105 14 1 1808 55745910 55744103 0.000000e+00 2658.0
10 TraesCS4A01G118600 chr5A 90.869 1818 152 10 1 1808 642030292 642032105 0.000000e+00 2425.0
11 TraesCS4A01G118600 chr5A 100.000 36 0 0 2933 2968 689253265 689253230 3.340000e-07 67.6
12 TraesCS4A01G118600 chr3A 93.069 1818 111 11 1 1808 631428786 631430598 0.000000e+00 2645.0
13 TraesCS4A01G118600 chr3A 90.097 1858 155 19 6 1846 98705124 98703279 0.000000e+00 2385.0
14 TraesCS4A01G118600 chr3A 96.947 262 8 0 1844 2105 522717898 522717637 1.710000e-119 440.0
15 TraesCS4A01G118600 chr3A 96.241 266 9 1 1845 2109 741483196 741483461 7.940000e-118 435.0
16 TraesCS4A01G118600 chr3A 96.241 266 9 1 1845 2109 741557116 741557381 7.940000e-118 435.0
17 TraesCS4A01G118600 chr6A 92.189 1818 124 14 1 1808 65326369 65324560 0.000000e+00 2555.0
18 TraesCS4A01G118600 chr6A 92.024 1818 127 14 1 1808 65319643 65317834 0.000000e+00 2538.0
19 TraesCS4A01G118600 chr6A 95.501 889 14 7 4279 5166 279746730 279747593 0.000000e+00 1397.0
20 TraesCS4A01G118600 chr6A 95.579 769 29 3 4279 5047 586056168 586056931 0.000000e+00 1227.0
21 TraesCS4A01G118600 chr6A 96.699 727 12 2 2966 3683 279745616 279746339 0.000000e+00 1199.0
22 TraesCS4A01G118600 chr6A 88.616 571 57 7 2103 2670 207983905 207984470 0.000000e+00 688.0
23 TraesCS4A01G118600 chr6A 80.194 515 86 15 2677 3187 390194847 390195349 6.320000e-99 372.0
24 TraesCS4A01G118600 chr6A 97.156 211 5 1 4076 4285 279746431 279746641 6.360000e-94 355.0
25 TraesCS4A01G118600 chr6A 94.798 173 8 1 4114 4285 586055907 586056079 8.530000e-68 268.0
26 TraesCS4A01G118600 chr6A 100.000 36 0 0 2933 2968 153110026 153109991 3.340000e-07 67.6
27 TraesCS4A01G118600 chr6A 100.000 36 0 0 2933 2968 550731898 550731863 3.340000e-07 67.6
28 TraesCS4A01G118600 chr1A 91.515 1815 141 9 1 1808 62879054 62877246 0.000000e+00 2486.0
29 TraesCS4A01G118600 chr1A 87.094 1356 142 14 509 1846 354137038 354135698 0.000000e+00 1504.0
30 TraesCS4A01G118600 chr1A 90.819 806 65 5 4365 5164 255202659 255203461 0.000000e+00 1070.0
31 TraesCS4A01G118600 chr1A 89.924 526 43 5 4645 5164 423296283 423295762 0.000000e+00 669.0
32 TraesCS4A01G118600 chr1A 89.827 521 43 5 4645 5159 423107280 423106764 0.000000e+00 660.0
33 TraesCS4A01G118600 chr1A 89.827 521 43 6 4645 5159 423170699 423170183 0.000000e+00 660.0
34 TraesCS4A01G118600 chr1A 89.922 516 42 5 4645 5154 423234394 423233883 0.000000e+00 656.0
35 TraesCS4A01G118600 chr1A 97.043 372 9 2 4796 5166 435569713 435569343 4.390000e-175 625.0
36 TraesCS4A01G118600 chr1A 96.212 264 10 0 1844 2107 447114351 447114614 2.860000e-117 433.0
37 TraesCS4A01G118600 chr1A 79.545 176 30 5 2667 2839 179448366 179448538 2.530000e-23 121.0
38 TraesCS4A01G118600 chr1A 77.586 174 35 3 2667 2839 272644928 272645098 9.150000e-18 102.0
39 TraesCS4A01G118600 chr1A 97.297 37 1 0 2667 2703 244185099 244185063 4.320000e-06 63.9
40 TraesCS4A01G118600 chr4D 90.363 1816 153 16 3 1808 274039062 274040865 0.000000e+00 2364.0
41 TraesCS4A01G118600 chr4D 91.635 801 57 5 4365 5159 349449328 349448532 0.000000e+00 1099.0
42 TraesCS4A01G118600 chr4D 88.772 570 56 7 2103 2670 296313202 296312639 0.000000e+00 691.0
43 TraesCS4A01G118600 chr4D 88.204 568 55 8 2109 2670 139474808 139474247 0.000000e+00 667.0
44 TraesCS4A01G118600 chr4D 100.000 36 0 0 2933 2968 386833031 386832996 3.340000e-07 67.6
45 TraesCS4A01G118600 chr7A 87.121 1879 195 24 1 1846 383138147 383136283 0.000000e+00 2085.0
46 TraesCS4A01G118600 chr7A 88.070 570 62 5 2103 2670 57284837 57285402 0.000000e+00 671.0
47 TraesCS4A01G118600 chr7A 96.667 270 9 0 1845 2114 506291583 506291314 2.840000e-122 449.0
48 TraesCS4A01G118600 chr7A 95.896 268 11 0 1841 2108 599647079 599647346 7.940000e-118 435.0
49 TraesCS4A01G118600 chr7A 95.849 265 11 0 1844 2108 308119121 308118857 3.700000e-116 429.0
50 TraesCS4A01G118600 chr7A 100.000 37 0 0 2933 2969 565750402 565750366 9.280000e-08 69.4
51 TraesCS4A01G118600 chr2A 92.984 955 44 10 2667 3620 265593727 265592795 0.000000e+00 1371.0
52 TraesCS4A01G118600 chr2A 88.368 576 56 9 2103 2673 414645769 414645200 0.000000e+00 682.0
53 TraesCS4A01G118600 chr2A 88.103 580 56 12 2103 2675 414720292 414719719 0.000000e+00 676.0
54 TraesCS4A01G118600 chr2A 88.434 562 59 5 2103 2662 722771056 722770499 0.000000e+00 673.0
55 TraesCS4A01G118600 chr2A 96.591 264 9 0 1842 2105 625961473 625961210 6.140000e-119 438.0
56 TraesCS4A01G118600 chr2A 95.539 269 11 1 1844 2112 52099640 52099373 3.700000e-116 429.0
57 TraesCS4A01G118600 chr2A 96.698 212 4 3 4076 4285 265586951 265586741 2.960000e-92 350.0
58 TraesCS4A01G118600 chr2A 100.000 73 0 0 3611 3683 265587115 265587043 9.020000e-28 135.0
59 TraesCS4A01G118600 chr6B 95.337 772 32 3 4279 5050 199018806 199018039 0.000000e+00 1223.0
60 TraesCS4A01G118600 chr6B 88.652 890 75 9 4289 5164 383823524 383822647 0.000000e+00 1061.0
61 TraesCS4A01G118600 chr6B 95.238 210 10 0 4076 4285 199019104 199018895 2.980000e-87 333.0
62 TraesCS4A01G118600 chr6B 85.897 78 10 1 2658 2735 576574701 576574625 1.190000e-11 82.4
63 TraesCS4A01G118600 chr1B 95.189 769 33 3 4279 5047 229489825 229490589 0.000000e+00 1212.0
64 TraesCS4A01G118600 chr1B 88.956 498 33 5 4679 5164 512138268 512137781 3.440000e-166 595.0
65 TraesCS4A01G118600 chr1B 82.776 598 90 11 2667 3262 197781986 197782572 5.930000e-144 521.0
66 TraesCS4A01G118600 chr1B 88.378 413 38 2 4279 4681 512150254 512149842 6.010000e-134 488.0
67 TraesCS4A01G118600 chr1B 82.949 434 57 11 3263 3683 512151046 512150617 4.880000e-100 375.0
68 TraesCS4A01G118600 chr1B 87.833 263 31 1 3001 3262 334539132 334538870 1.810000e-79 307.0
69 TraesCS4A01G118600 chr1B 85.185 270 36 4 2665 2932 334539511 334539244 1.830000e-69 274.0
70 TraesCS4A01G118600 chr1B 94.220 173 9 1 4114 4285 229489564 229489736 3.970000e-66 263.0
71 TraesCS4A01G118600 chr1B 92.361 144 11 0 4076 4219 512150533 512150390 6.780000e-49 206.0
72 TraesCS4A01G118600 chr1B 84.112 214 29 4 4279 4492 526998161 526998369 8.770000e-48 202.0
73 TraesCS4A01G118600 chr1B 87.500 72 9 0 2666 2737 288557232 288557161 3.310000e-12 84.2
74 TraesCS4A01G118600 chr1B 100.000 38 0 0 2933 2970 144729925 144729962 2.580000e-08 71.3
75 TraesCS4A01G118600 chr1B 90.385 52 5 0 2666 2717 399302337 399302286 9.280000e-08 69.4
76 TraesCS4A01G118600 chr1B 90.196 51 5 0 2667 2717 267807260 267807210 3.340000e-07 67.6
77 TraesCS4A01G118600 chr1B 83.099 71 12 0 2667 2737 375902708 375902638 1.200000e-06 65.8
78 TraesCS4A01G118600 chr7B 94.408 769 40 3 4279 5047 264474653 264475418 0.000000e+00 1179.0
79 TraesCS4A01G118600 chr7B 84.359 601 68 13 2666 3262 383665171 383665749 2.700000e-157 566.0
80 TraesCS4A01G118600 chr7B 83.721 602 72 16 2668 3262 499460815 499461397 3.520000e-151 545.0
81 TraesCS4A01G118600 chr7B 95.714 210 8 1 4076 4285 264474356 264474564 2.300000e-88 337.0
82 TraesCS4A01G118600 chr3B 90.135 892 74 8 4281 5164 309749986 309750871 0.000000e+00 1147.0
83 TraesCS4A01G118600 chr3B 87.179 273 31 4 2667 2937 829043705 829043975 1.810000e-79 307.0
84 TraesCS4A01G118600 chr3B 92.417 211 15 1 4076 4285 283125021 283125231 3.020000e-77 300.0
85 TraesCS4A01G118600 chr3B 80.370 433 44 21 3269 3683 309749229 309749638 1.820000e-74 291.0
86 TraesCS4A01G118600 chr3B 78.832 274 47 11 2666 2933 322204385 322204653 1.910000e-39 174.0
87 TraesCS4A01G118600 chr2D 88.632 563 59 5 2103 2664 290165676 290166234 0.000000e+00 680.0
88 TraesCS4A01G118600 chr5D 88.112 572 59 8 2103 2670 130362026 130361460 0.000000e+00 671.0
89 TraesCS4A01G118600 chr5D 87.243 243 26 4 1571 1810 263526029 263526269 6.590000e-69 272.0
90 TraesCS4A01G118600 chr1D 84.959 605 75 13 2665 3262 228334154 228334749 2.660000e-167 599.0
91 TraesCS4A01G118600 chr1D 85.383 561 71 10 2705 3262 228329870 228330422 5.800000e-159 571.0
92 TraesCS4A01G118600 chr4B 84.000 600 73 13 2667 3262 472485498 472484918 5.840000e-154 555.0
93 TraesCS4A01G118600 chr4B 85.377 212 24 4 4279 4490 251833318 251833522 4.050000e-51 213.0
94 TraesCS4A01G118600 chr4B 77.841 176 33 5 2667 2839 373348004 373348176 2.540000e-18 104.0
95 TraesCS4A01G118600 chr4B 91.429 70 6 0 2665 2734 404627426 404627357 4.260000e-16 97.1
96 TraesCS4A01G118600 chr4B 87.324 71 9 0 2667 2737 401273568 401273638 1.190000e-11 82.4
97 TraesCS4A01G118600 chr4B 100.000 36 0 0 2933 2968 60366747 60366712 3.340000e-07 67.6
98 TraesCS4A01G118600 chr4B 87.931 58 6 1 3352 3408 126081495 126081438 3.340000e-07 67.6
99 TraesCS4A01G118600 chr4B 82.609 69 12 0 2667 2735 233241726 233241658 1.550000e-05 62.1
100 TraesCS4A01G118600 chr5B 83.721 602 74 14 2665 3262 221836398 221836979 9.780000e-152 547.0
101 TraesCS4A01G118600 chr5B 81.488 605 68 24 2662 3262 216510547 216509983 1.700000e-124 457.0
102 TraesCS4A01G118600 chr5B 76.812 276 53 11 2664 2933 236283109 236283379 1.500000e-30 145.0
103 TraesCS4A01G118600 chr5B 100.000 36 0 0 2933 2968 234875961 234875996 3.340000e-07 67.6
104 TraesCS4A01G118600 chr6D 82.759 609 86 15 2659 3261 219727072 219726477 4.580000e-145 525.0
105 TraesCS4A01G118600 chr6D 100.000 36 0 0 2933 2968 408219860 408219825 3.340000e-07 67.6
106 TraesCS4A01G118600 chrUn 86.306 314 34 3 4279 4583 308997529 308997216 2.980000e-87 333.0
107 TraesCS4A01G118600 chrUn 86.306 314 34 3 4279 4583 377638312 377638625 2.980000e-87 333.0
108 TraesCS4A01G118600 chrUn 94.393 107 4 2 4860 4965 300809831 300809936 4.140000e-36 163.0
109 TraesCS4A01G118600 chr7D 88.571 245 27 1 2688 2932 626246163 626246406 3.910000e-76 296.0
110 TraesCS4A01G118600 chr2B 96.748 123 3 1 4164 4285 613240403 613240525 2.440000e-48 204.0
111 TraesCS4A01G118600 chr2B 77.899 276 49 10 2667 2935 746314221 746313951 1.490000e-35 161.0
112 TraesCS4A01G118600 chr2B 94.872 39 2 0 3370 3408 297456720 297456682 1.550000e-05 62.1


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 TraesCS4A01G118600 chr4A 146396995 146402160 5165 False 4408.500000 6802 100.0000 1 5166 2 chr4A.!!$F5 5165
1 TraesCS4A01G118600 chr4A 506012119 506013931 1812 False 2418.000000 2418 90.8190 1 1808 1 chr4A.!!$F4 1807
2 TraesCS4A01G118600 chr4A 357803329 357803911 582 False 523.000000 523 82.9150 2667 3262 1 chr4A.!!$F2 595
3 TraesCS4A01G118600 chr4A 360500142 360500686 544 False 453.000000 453 81.7200 2706 3262 1 chr4A.!!$F3 556
4 TraesCS4A01G118600 chr4A 337462392 337463228 836 False 366.000000 632 92.6495 4166 4918 2 chr4A.!!$F6 752
5 TraesCS4A01G118600 chr5A 55744103 55745910 1807 True 2658.000000 2658 93.2310 1 1808 1 chr5A.!!$R1 1807
6 TraesCS4A01G118600 chr5A 642030292 642032105 1813 False 2425.000000 2425 90.8690 1 1808 1 chr5A.!!$F1 1807
7 TraesCS4A01G118600 chr3A 631428786 631430598 1812 False 2645.000000 2645 93.0690 1 1808 1 chr3A.!!$F1 1807
8 TraesCS4A01G118600 chr3A 98703279 98705124 1845 True 2385.000000 2385 90.0970 6 1846 1 chr3A.!!$R1 1840
9 TraesCS4A01G118600 chr6A 65324560 65326369 1809 True 2555.000000 2555 92.1890 1 1808 1 chr6A.!!$R2 1807
10 TraesCS4A01G118600 chr6A 65317834 65319643 1809 True 2538.000000 2538 92.0240 1 1808 1 chr6A.!!$R1 1807
11 TraesCS4A01G118600 chr6A 279745616 279747593 1977 False 983.666667 1397 96.4520 2966 5166 3 chr6A.!!$F3 2200
12 TraesCS4A01G118600 chr6A 586055907 586056931 1024 False 747.500000 1227 95.1885 4114 5047 2 chr6A.!!$F4 933
13 TraesCS4A01G118600 chr6A 207983905 207984470 565 False 688.000000 688 88.6160 2103 2670 1 chr6A.!!$F1 567
14 TraesCS4A01G118600 chr6A 390194847 390195349 502 False 372.000000 372 80.1940 2677 3187 1 chr6A.!!$F2 510
15 TraesCS4A01G118600 chr1A 62877246 62879054 1808 True 2486.000000 2486 91.5150 1 1808 1 chr1A.!!$R1 1807
16 TraesCS4A01G118600 chr1A 354135698 354137038 1340 True 1504.000000 1504 87.0940 509 1846 1 chr1A.!!$R3 1337
17 TraesCS4A01G118600 chr1A 255202659 255203461 802 False 1070.000000 1070 90.8190 4365 5164 1 chr1A.!!$F2 799
18 TraesCS4A01G118600 chr1A 423295762 423296283 521 True 669.000000 669 89.9240 4645 5164 1 chr1A.!!$R7 519
19 TraesCS4A01G118600 chr1A 423106764 423107280 516 True 660.000000 660 89.8270 4645 5159 1 chr1A.!!$R4 514
20 TraesCS4A01G118600 chr1A 423170183 423170699 516 True 660.000000 660 89.8270 4645 5159 1 chr1A.!!$R5 514
21 TraesCS4A01G118600 chr1A 423233883 423234394 511 True 656.000000 656 89.9220 4645 5154 1 chr1A.!!$R6 509
22 TraesCS4A01G118600 chr4D 274039062 274040865 1803 False 2364.000000 2364 90.3630 3 1808 1 chr4D.!!$F1 1805
23 TraesCS4A01G118600 chr4D 349448532 349449328 796 True 1099.000000 1099 91.6350 4365 5159 1 chr4D.!!$R3 794
24 TraesCS4A01G118600 chr4D 296312639 296313202 563 True 691.000000 691 88.7720 2103 2670 1 chr4D.!!$R2 567
25 TraesCS4A01G118600 chr4D 139474247 139474808 561 True 667.000000 667 88.2040 2109 2670 1 chr4D.!!$R1 561
26 TraesCS4A01G118600 chr7A 383136283 383138147 1864 True 2085.000000 2085 87.1210 1 1846 1 chr7A.!!$R2 1845
27 TraesCS4A01G118600 chr7A 57284837 57285402 565 False 671.000000 671 88.0700 2103 2670 1 chr7A.!!$F1 567
28 TraesCS4A01G118600 chr2A 265592795 265593727 932 True 1371.000000 1371 92.9840 2667 3620 1 chr2A.!!$R2 953
29 TraesCS4A01G118600 chr2A 414645200 414645769 569 True 682.000000 682 88.3680 2103 2673 1 chr2A.!!$R3 570
30 TraesCS4A01G118600 chr2A 414719719 414720292 573 True 676.000000 676 88.1030 2103 2675 1 chr2A.!!$R4 572
31 TraesCS4A01G118600 chr2A 722770499 722771056 557 True 673.000000 673 88.4340 2103 2662 1 chr2A.!!$R6 559
32 TraesCS4A01G118600 chr6B 383822647 383823524 877 True 1061.000000 1061 88.6520 4289 5164 1 chr6B.!!$R1 875
33 TraesCS4A01G118600 chr6B 199018039 199019104 1065 True 778.000000 1223 95.2875 4076 5050 2 chr6B.!!$R3 974
34 TraesCS4A01G118600 chr1B 229489564 229490589 1025 False 737.500000 1212 94.7045 4114 5047 2 chr1B.!!$F4 933
35 TraesCS4A01G118600 chr1B 197781986 197782572 586 False 521.000000 521 82.7760 2667 3262 1 chr1B.!!$F2 595
36 TraesCS4A01G118600 chr1B 512149842 512151046 1204 True 356.333333 488 87.8960 3263 4681 3 chr1B.!!$R7 1418
37 TraesCS4A01G118600 chr1B 334538870 334539511 641 True 290.500000 307 86.5090 2665 3262 2 chr1B.!!$R6 597
38 TraesCS4A01G118600 chr7B 264474356 264475418 1062 False 758.000000 1179 95.0610 4076 5047 2 chr7B.!!$F3 971
39 TraesCS4A01G118600 chr7B 383665171 383665749 578 False 566.000000 566 84.3590 2666 3262 1 chr7B.!!$F1 596
40 TraesCS4A01G118600 chr7B 499460815 499461397 582 False 545.000000 545 83.7210 2668 3262 1 chr7B.!!$F2 594
41 TraesCS4A01G118600 chr3B 309749229 309750871 1642 False 719.000000 1147 85.2525 3269 5164 2 chr3B.!!$F4 1895
42 TraesCS4A01G118600 chr2D 290165676 290166234 558 False 680.000000 680 88.6320 2103 2664 1 chr2D.!!$F1 561
43 TraesCS4A01G118600 chr5D 130361460 130362026 566 True 671.000000 671 88.1120 2103 2670 1 chr5D.!!$R1 567
44 TraesCS4A01G118600 chr1D 228329870 228334749 4879 False 585.000000 599 85.1710 2665 3262 2 chr1D.!!$F1 597
45 TraesCS4A01G118600 chr4B 472484918 472485498 580 True 555.000000 555 84.0000 2667 3262 1 chr4B.!!$R5 595
46 TraesCS4A01G118600 chr5B 221836398 221836979 581 False 547.000000 547 83.7210 2665 3262 1 chr5B.!!$F1 597
47 TraesCS4A01G118600 chr5B 216509983 216510547 564 True 457.000000 457 81.4880 2662 3262 1 chr5B.!!$R1 600
48 TraesCS4A01G118600 chr6D 219726477 219727072 595 True 525.000000 525 82.7590 2659 3261 1 chr6D.!!$R1 602

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
550 559 1.001641 GTGCCCTGACTCCTTGCAT 60.002 57.895 0.0 0.0 34.04 3.96 F
2374 2428 0.322322 TAACGCTCCATGTTCCGGTT 59.678 50.000 0.0 0.0 0.00 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2379 2433 0.458543 CGAGATCAAGGTGTGTCGGG 60.459 60.0 0.0 0.00 0.00 5.14 R
4384 6291 0.398318 ACAGGAGCTCCAGGACAAAC 59.602 55.0 33.9 4.03 38.89 2.93 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
26 27 6.923670 AGTACTTCATCCCTTCATACTCCTA 58.076 40.000 0.00 0.00 0.00 2.94
156 158 4.211794 CACCCTTGAAATGCACAAATTCAC 59.788 41.667 0.00 0.00 33.13 3.18
550 559 1.001641 GTGCCCTGACTCCTTGCAT 60.002 57.895 0.00 0.00 34.04 3.96
628 637 2.290071 GGACCTTTCCGTTCCAATCAGA 60.290 50.000 0.00 0.00 29.98 3.27
854 863 8.915871 TTTCATTTCTTCTTTCTTCTGTTGTG 57.084 30.769 0.00 0.00 0.00 3.33
1017 1027 7.608761 GTGTTCTTTATGGGTGTGTCCTATTTA 59.391 37.037 0.00 0.00 38.39 1.40
1022 1032 5.725551 ATGGGTGTGTCCTATTTATCCAA 57.274 39.130 0.00 0.00 33.45 3.53
1076 1086 5.418840 TCATTTCCATAAGGCTTCAACTTCC 59.581 40.000 1.30 0.00 33.74 3.46
1089 1099 1.990160 AACTTCCGGGACACAAGCCA 61.990 55.000 0.00 0.00 0.00 4.75
1108 1118 3.152341 CCAAGACTTTGGCAGAGTCAAT 58.848 45.455 32.00 20.94 46.84 2.57
1120 1130 9.612066 TTTGGCAGAGTCAATTTAAATTCTTTT 57.388 25.926 10.53 0.00 0.00 2.27
1164 1174 8.675705 CATCTATTGATGGTTTGGTACATACA 57.324 34.615 9.04 0.00 44.63 2.29
1404 1427 9.973450 ATACACACAATGCAAACAATAGTTTTA 57.027 25.926 0.00 0.00 45.32 1.52
1405 1428 8.885494 ACACACAATGCAAACAATAGTTTTAT 57.115 26.923 0.00 0.00 45.32 1.40
1440 1469 0.383949 TTTTGTGGCTGTCGGAAAGC 59.616 50.000 11.86 11.86 40.06 3.51
1441 1470 0.749818 TTTGTGGCTGTCGGAAAGCA 60.750 50.000 21.13 5.47 42.69 3.91
1443 1472 0.955428 TGTGGCTGTCGGAAAGCATC 60.955 55.000 21.13 13.24 42.69 3.91
1444 1473 0.955428 GTGGCTGTCGGAAAGCATCA 60.955 55.000 21.13 8.58 42.69 3.07
1447 1476 1.401539 GGCTGTCGGAAAGCATCAAAC 60.402 52.381 21.13 0.00 42.69 2.93
1448 1477 1.266718 GCTGTCGGAAAGCATCAAACA 59.733 47.619 15.28 0.00 40.52 2.83
1539 1569 4.514781 AAATCTTTAAGGTCGCCAAACC 57.485 40.909 0.00 0.00 39.80 3.27
1557 1587 6.462347 GCCAAACCCTTCAAGTCTTTTTCATA 60.462 38.462 0.00 0.00 0.00 2.15
1563 1593 6.886459 CCCTTCAAGTCTTTTTCATATCTCCA 59.114 38.462 0.00 0.00 0.00 3.86
1575 1605 8.821686 TTTTCATATCTCCAATGGCTTCTTTA 57.178 30.769 0.00 0.00 0.00 1.85
1597 1627 2.613026 TCGTGCTTGTCCTTCTCAAA 57.387 45.000 0.00 0.00 0.00 2.69
1609 1639 5.305128 TGTCCTTCTCAAATTCTTTTGCCAT 59.695 36.000 0.00 0.00 41.66 4.40
1658 1690 6.094464 TCTCGTGACGTCCTTTAATATTCTGA 59.906 38.462 14.12 0.00 0.00 3.27
1679 1711 3.281727 AGTTGCAGTCCAAACTTCTGA 57.718 42.857 0.00 0.00 34.68 3.27
1710 1742 1.548081 CTTGGCATGAACCATGGTCA 58.452 50.000 20.07 17.69 41.64 4.02
1721 1753 4.780554 TGAACCATGGTCATACTGTCCTTA 59.219 41.667 20.07 0.00 0.00 2.69
1746 1778 1.954382 CCTGACGAATCTCCGGTATCA 59.046 52.381 0.00 0.00 0.00 2.15
1846 1895 9.178758 AGGTCCATCTTAAATTTCTTGATGTAC 57.821 33.333 18.32 14.99 34.44 2.90
1847 1896 9.178758 GGTCCATCTTAAATTTCTTGATGTACT 57.821 33.333 18.32 0.00 34.44 2.73
1849 1898 9.396022 TCCATCTTAAATTTCTTGATGTACTCC 57.604 33.333 18.32 0.00 34.44 3.85
1850 1899 8.624776 CCATCTTAAATTTCTTGATGTACTCCC 58.375 37.037 18.32 0.00 34.44 4.30
1851 1900 9.401058 CATCTTAAATTTCTTGATGTACTCCCT 57.599 33.333 14.59 0.00 32.39 4.20
1852 1901 9.620259 ATCTTAAATTTCTTGATGTACTCCCTC 57.380 33.333 0.00 0.00 0.00 4.30
1853 1902 8.047310 TCTTAAATTTCTTGATGTACTCCCTCC 58.953 37.037 0.00 0.00 0.00 4.30
1854 1903 3.887621 TTTCTTGATGTACTCCCTCCG 57.112 47.619 0.00 0.00 0.00 4.63
1855 1904 2.526888 TCTTGATGTACTCCCTCCGT 57.473 50.000 0.00 0.00 0.00 4.69
1856 1905 2.816411 TCTTGATGTACTCCCTCCGTT 58.184 47.619 0.00 0.00 0.00 4.44
1857 1906 3.170717 TCTTGATGTACTCCCTCCGTTT 58.829 45.455 0.00 0.00 0.00 3.60
1858 1907 3.581332 TCTTGATGTACTCCCTCCGTTTT 59.419 43.478 0.00 0.00 0.00 2.43
1859 1908 4.041198 TCTTGATGTACTCCCTCCGTTTTT 59.959 41.667 0.00 0.00 0.00 1.94
1860 1909 5.246656 TCTTGATGTACTCCCTCCGTTTTTA 59.753 40.000 0.00 0.00 0.00 1.52
1862 1911 6.057321 TGATGTACTCCCTCCGTTTTTATT 57.943 37.500 0.00 0.00 0.00 1.40
1863 1912 6.478129 TGATGTACTCCCTCCGTTTTTATTT 58.522 36.000 0.00 0.00 0.00 1.40
1864 1913 7.622713 TGATGTACTCCCTCCGTTTTTATTTA 58.377 34.615 0.00 0.00 0.00 1.40
1865 1914 7.767198 TGATGTACTCCCTCCGTTTTTATTTAG 59.233 37.037 0.00 0.00 0.00 1.85
1866 1915 7.008021 TGTACTCCCTCCGTTTTTATTTAGT 57.992 36.000 0.00 0.00 0.00 2.24
1870 1919 4.392754 TCCCTCCGTTTTTATTTAGTTCGC 59.607 41.667 0.00 0.00 0.00 4.70
1871 1920 4.154556 CCCTCCGTTTTTATTTAGTTCGCA 59.845 41.667 0.00 0.00 0.00 5.10
1872 1921 5.163693 CCCTCCGTTTTTATTTAGTTCGCAT 60.164 40.000 0.00 0.00 0.00 4.73
1887 1936 6.811253 AGTTCGCATATTAGTTTTGGTCAA 57.189 33.333 0.00 0.00 0.00 3.18
1888 1937 7.209471 AGTTCGCATATTAGTTTTGGTCAAA 57.791 32.000 0.00 0.00 0.00 2.69
1890 1939 6.811253 TCGCATATTAGTTTTGGTCAAAGT 57.189 33.333 0.00 0.00 32.41 2.66
1891 1940 6.837992 TCGCATATTAGTTTTGGTCAAAGTC 58.162 36.000 0.00 0.00 30.16 3.01
1893 1942 7.041030 TCGCATATTAGTTTTGGTCAAAGTCAA 60.041 33.333 0.00 0.00 30.16 3.18
1894 1943 7.271223 CGCATATTAGTTTTGGTCAAAGTCAAG 59.729 37.037 0.00 0.00 30.16 3.02
1895 1944 7.062255 GCATATTAGTTTTGGTCAAAGTCAAGC 59.938 37.037 0.00 0.00 30.16 4.01
1896 1945 6.715347 ATTAGTTTTGGTCAAAGTCAAGCT 57.285 33.333 0.00 0.00 30.16 3.74
1897 1946 6.524101 TTAGTTTTGGTCAAAGTCAAGCTT 57.476 33.333 0.00 0.00 39.52 3.74
1899 1948 6.524101 AGTTTTGGTCAAAGTCAAGCTTTA 57.476 33.333 0.00 0.00 44.95 1.85
1900 1949 6.330278 AGTTTTGGTCAAAGTCAAGCTTTAC 58.670 36.000 2.40 2.40 44.95 2.01
1901 1950 5.906113 TTTGGTCAAAGTCAAGCTTTACA 57.094 34.783 13.07 0.00 44.95 2.41
1902 1951 5.906113 TTGGTCAAAGTCAAGCTTTACAA 57.094 34.783 13.07 0.00 44.95 2.41
1903 1952 5.906113 TGGTCAAAGTCAAGCTTTACAAA 57.094 34.783 13.07 0.00 44.95 2.83
1905 1954 5.417580 TGGTCAAAGTCAAGCTTTACAAACT 59.582 36.000 13.07 2.11 44.95 2.66
1906 1955 6.071616 TGGTCAAAGTCAAGCTTTACAAACTT 60.072 34.615 13.07 7.60 44.95 2.66
1911 1960 8.634475 AAAGTCAAGCTTTACAAACTTTGATC 57.366 30.769 13.07 0.00 44.90 2.92
1912 1961 7.333528 AGTCAAGCTTTACAAACTTTGATCA 57.666 32.000 13.07 0.00 0.00 2.92
1913 1962 7.771183 AGTCAAGCTTTACAAACTTTGATCAA 58.229 30.769 13.07 3.38 0.00 2.57
2051 2100 9.545105 TTCTATAAACTTGGTCAAACTTTACGA 57.455 29.630 0.00 0.00 0.00 3.43
2053 2102 9.807386 CTATAAACTTGGTCAAACTTTACGAAG 57.193 33.333 0.00 0.00 37.43 3.79
2079 2128 9.974750 GTTTGACTTCAGTTAACTCTAATATGC 57.025 33.333 4.77 0.00 0.00 3.14
2080 2129 9.719355 TTTGACTTCAGTTAACTCTAATATGCA 57.281 29.630 4.77 0.00 0.00 3.96
2081 2130 8.932945 TGACTTCAGTTAACTCTAATATGCAG 57.067 34.615 4.77 0.00 0.00 4.41
2082 2131 8.749354 TGACTTCAGTTAACTCTAATATGCAGA 58.251 33.333 4.77 0.00 0.00 4.26
2083 2132 9.243637 GACTTCAGTTAACTCTAATATGCAGAG 57.756 37.037 4.77 11.37 44.28 3.35
2101 2150 8.593945 ATGCAGAGTAAATAAAAATGAAGGGA 57.406 30.769 0.00 0.00 0.00 4.20
2151 2200 5.411669 ACCAGCTAAGGTTAAAACTTCATCG 59.588 40.000 0.00 0.00 39.34 3.84
2152 2201 5.324697 CAGCTAAGGTTAAAACTTCATCGC 58.675 41.667 0.00 0.00 0.00 4.58
2193 2243 4.202609 CCATTAGCCCTCTACCATCCAATT 60.203 45.833 0.00 0.00 0.00 2.32
2211 2261 9.320352 CATCCAATTCTTTTGATGAAATGCATA 57.680 29.630 0.00 0.00 37.23 3.14
2234 2285 6.817765 ATTTATCTCAACACGGTGACAATT 57.182 33.333 16.29 0.00 0.00 2.32
2235 2286 7.915293 ATTTATCTCAACACGGTGACAATTA 57.085 32.000 16.29 0.00 0.00 1.40
2236 2287 6.961359 TTATCTCAACACGGTGACAATTAG 57.039 37.500 16.29 3.64 0.00 1.73
2237 2288 3.064207 TCTCAACACGGTGACAATTAGC 58.936 45.455 16.29 0.00 0.00 3.09
2238 2289 2.805671 CTCAACACGGTGACAATTAGCA 59.194 45.455 16.29 0.00 0.00 3.49
2239 2290 3.407698 TCAACACGGTGACAATTAGCAT 58.592 40.909 16.29 0.00 0.00 3.79
2240 2291 4.570930 TCAACACGGTGACAATTAGCATA 58.429 39.130 16.29 0.00 0.00 3.14
2244 2295 3.312421 CACGGTGACAATTAGCATAAGGG 59.688 47.826 0.74 0.00 0.00 3.95
2290 2342 2.762327 TGTCTATGCTCATGTCTCTGCA 59.238 45.455 0.00 0.00 39.83 4.41
2374 2428 0.322322 TAACGCTCCATGTTCCGGTT 59.678 50.000 0.00 0.00 0.00 4.44
2480 2534 7.992754 ACAAATCTGAAAATTCTACAGAGCT 57.007 32.000 12.33 0.00 42.55 4.09
2591 2645 7.123098 TGGTCTTAGTTGTCCGATATCTTGTAA 59.877 37.037 0.34 0.00 0.00 2.41
2600 2654 9.443323 TTGTCCGATATCTTGTAATTCTTGAAA 57.557 29.630 0.34 0.00 0.00 2.69
2643 2699 2.685897 CGTGTGGTCAAAAAGGGAAAGA 59.314 45.455 0.00 0.00 0.00 2.52
2654 2710 8.857098 GTCAAAAAGGGAAAGAGGTATAGTTTT 58.143 33.333 0.00 0.00 0.00 2.43
2710 4331 1.484444 AACTCGCTTCCAGGAGGCTT 61.484 55.000 20.72 6.37 32.35 4.35
2717 4338 3.009115 CCAGGAGGCTTCCCCGAA 61.009 66.667 11.97 0.00 45.24 4.30
2739 4360 1.782028 AAAGCTTCGTTGGCCGTCAC 61.782 55.000 0.00 0.00 37.94 3.67
2789 4412 3.181520 CGGATCTTCACAGCGGTTAAAAG 60.182 47.826 0.00 0.00 0.00 2.27
2858 4484 2.906897 CGGCACACTGGTTGGCTT 60.907 61.111 3.48 0.00 0.00 4.35
2859 4485 1.599518 CGGCACACTGGTTGGCTTA 60.600 57.895 3.48 0.00 0.00 3.09
2889 4516 1.503818 TTTCGAGTGCAGGGCGTTTC 61.504 55.000 0.00 0.00 0.00 2.78
2935 4564 2.104331 CAATCCCCCGTCTCGTCG 59.896 66.667 0.00 0.00 0.00 5.12
2941 4570 4.337060 CCCGTCTCGTCGTGCACA 62.337 66.667 18.64 0.81 0.00 4.57
2944 4573 1.729484 CGTCTCGTCGTGCACACAT 60.729 57.895 18.64 0.00 0.00 3.21
2945 4574 1.775344 GTCTCGTCGTGCACACATG 59.225 57.895 18.64 8.14 0.00 3.21
2957 4586 1.629013 CACACATGCATCGTCTACGT 58.371 50.000 0.00 0.00 40.80 3.57
2958 4587 2.792749 CACACATGCATCGTCTACGTA 58.207 47.619 0.00 0.00 40.80 3.57
2959 4588 2.783832 CACACATGCATCGTCTACGTAG 59.216 50.000 16.73 16.73 40.80 3.51
2960 4589 1.781429 CACATGCATCGTCTACGTAGC 59.219 52.381 18.00 11.68 40.80 3.58
2961 4590 1.404035 ACATGCATCGTCTACGTAGCA 59.596 47.619 18.00 20.22 46.71 3.49
2962 4591 2.047040 CATGCATCGTCTACGTAGCAG 58.953 52.381 18.00 13.32 46.24 4.24
2963 4592 1.092348 TGCATCGTCTACGTAGCAGT 58.908 50.000 18.00 1.05 41.87 4.40
2964 4593 1.471287 TGCATCGTCTACGTAGCAGTT 59.529 47.619 18.00 6.34 41.87 3.16
2965 4594 2.094906 TGCATCGTCTACGTAGCAGTTT 60.095 45.455 18.00 4.18 41.87 2.66
2966 4595 2.530700 GCATCGTCTACGTAGCAGTTTC 59.469 50.000 18.00 2.28 40.80 2.78
2967 4596 2.515641 TCGTCTACGTAGCAGTTTCG 57.484 50.000 18.00 13.56 40.80 3.46
4253 6058 5.692115 TGGTTCCAGTCTATGAGCAATTA 57.308 39.130 0.00 0.00 0.00 1.40
4384 6291 2.027192 TCCTTGTCAAGAAAGGGATCGG 60.027 50.000 14.42 0.00 43.78 4.18
4588 6502 6.070656 TCATTGAAGTTGTCTTTCCCAATCT 58.929 36.000 0.00 0.00 33.64 2.40
4632 6546 7.138736 ACTTGATTGCTTGTGTATTTGTGTAC 58.861 34.615 0.00 0.00 0.00 2.90
4702 6616 0.108138 ACATCGCTCTACAGGGTTGC 60.108 55.000 0.00 0.00 36.28 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 8.529476 GTTTTATCTCGATATGTGGTATACCCT 58.471 37.037 19.42 6.70 34.29 4.34
156 158 8.329346 AGGATATGAGAAATATGGTCTATGGG 57.671 38.462 0.00 0.00 0.00 4.00
365 372 9.856488 GAGACTTGTGATAATTAGTTGTGTCTA 57.144 33.333 0.00 0.00 31.27 2.59
454 461 1.202722 GGAAACCTCGGGAGTTGTCAA 60.203 52.381 0.00 0.00 0.00 3.18
628 637 2.912956 TGACCCACAGGAAATAGAAGCT 59.087 45.455 0.00 0.00 36.73 3.74
880 889 3.775316 CCCACTACCCTTCTTAGTGTCAT 59.225 47.826 8.34 0.00 43.38 3.06
888 897 2.830293 GGACTACCCACTACCCTTCTT 58.170 52.381 0.00 0.00 34.14 2.52
1017 1027 2.224329 TGTGCATGCAAGCTTTTTGGAT 60.224 40.909 24.58 0.00 34.99 3.41
1022 1032 1.604693 GCTCTGTGCATGCAAGCTTTT 60.605 47.619 27.75 0.00 42.31 2.27
1076 1086 0.535102 AAGTCTTGGCTTGTGTCCCG 60.535 55.000 0.00 0.00 0.00 5.14
1089 1099 6.959639 TTAAATTGACTCTGCCAAAGTCTT 57.040 33.333 0.00 0.00 42.93 3.01
1120 1130 0.690762 GGCAGGGAGTAACCACTTGA 59.309 55.000 0.00 0.00 41.20 3.02
1164 1174 1.073199 GGTGCTGCTACTTGGTGGT 59.927 57.895 0.00 0.00 0.00 4.16
1404 1427 9.247861 AGCCACAAAAATAAAATCTGTCTCTAT 57.752 29.630 0.00 0.00 0.00 1.98
1405 1428 8.514594 CAGCCACAAAAATAAAATCTGTCTCTA 58.485 33.333 0.00 0.00 0.00 2.43
1422 1446 0.749818 TGCTTTCCGACAGCCACAAA 60.750 50.000 4.10 0.00 36.33 2.83
1440 1469 5.283294 TGTGAGCTGTCATTTTGTTTGATG 58.717 37.500 0.00 0.00 34.36 3.07
1441 1470 5.518848 TGTGAGCTGTCATTTTGTTTGAT 57.481 34.783 0.00 0.00 34.36 2.57
1443 1472 5.108141 CGATTGTGAGCTGTCATTTTGTTTG 60.108 40.000 0.00 0.00 34.36 2.93
1444 1473 4.977963 CGATTGTGAGCTGTCATTTTGTTT 59.022 37.500 0.00 0.00 34.36 2.83
1447 1476 4.151258 ACGATTGTGAGCTGTCATTTTG 57.849 40.909 0.00 0.00 34.36 2.44
1448 1477 4.539870 CAACGATTGTGAGCTGTCATTTT 58.460 39.130 0.00 0.00 34.36 1.82
1484 1513 6.402981 AGAAGACCAAACCCCTGTTATATT 57.597 37.500 0.00 0.00 33.30 1.28
1539 1569 7.928307 TGGAGATATGAAAAAGACTTGAAGG 57.072 36.000 0.00 0.00 0.00 3.46
1557 1587 5.163258 ACGATCTAAAGAAGCCATTGGAGAT 60.163 40.000 6.95 3.69 0.00 2.75
1563 1593 3.878778 AGCACGATCTAAAGAAGCCATT 58.121 40.909 0.00 0.00 0.00 3.16
1575 1605 1.895798 TGAGAAGGACAAGCACGATCT 59.104 47.619 0.00 0.00 0.00 2.75
1597 1627 7.558807 TCAACAGAGATGATATGGCAAAAGAAT 59.441 33.333 0.00 0.00 0.00 2.40
1609 1639 3.128764 ACTTCGCGTCAACAGAGATGATA 59.871 43.478 5.77 0.00 0.00 2.15
1658 1690 3.620488 TCAGAAGTTTGGACTGCAACTT 58.380 40.909 0.00 0.00 44.26 2.66
1679 1711 3.499338 TCATGCCAAGGATGTTGAAACT 58.501 40.909 0.00 0.00 0.00 2.66
1710 1742 5.014858 TCGTCAGGAACTTAAGGACAGTAT 58.985 41.667 7.53 0.00 34.60 2.12
1721 1753 1.204941 CCGGAGATTCGTCAGGAACTT 59.795 52.381 0.00 0.00 37.50 2.66
1746 1778 1.203100 AGCTGGAGGATGCAAAACCTT 60.203 47.619 10.88 0.00 34.45 3.50
1846 1895 5.446875 GCGAACTAAATAAAAACGGAGGGAG 60.447 44.000 0.00 0.00 0.00 4.30
1847 1896 4.392754 GCGAACTAAATAAAAACGGAGGGA 59.607 41.667 0.00 0.00 0.00 4.20
1848 1897 4.154556 TGCGAACTAAATAAAAACGGAGGG 59.845 41.667 0.00 0.00 0.00 4.30
1849 1898 5.285798 TGCGAACTAAATAAAAACGGAGG 57.714 39.130 0.00 0.00 0.00 4.30
1852 1901 9.925268 ACTAATATGCGAACTAAATAAAAACGG 57.075 29.630 0.00 0.00 0.00 4.44
1860 1909 8.952278 TGACCAAAACTAATATGCGAACTAAAT 58.048 29.630 0.00 0.00 0.00 1.40
1862 1911 7.908827 TGACCAAAACTAATATGCGAACTAA 57.091 32.000 0.00 0.00 0.00 2.24
1863 1912 7.908827 TTGACCAAAACTAATATGCGAACTA 57.091 32.000 0.00 0.00 0.00 2.24
1864 1913 6.811253 TTGACCAAAACTAATATGCGAACT 57.189 33.333 0.00 0.00 0.00 3.01
1865 1914 7.081976 ACTTTGACCAAAACTAATATGCGAAC 58.918 34.615 0.00 0.00 0.00 3.95
1866 1915 7.041030 TGACTTTGACCAAAACTAATATGCGAA 60.041 33.333 0.00 0.00 0.00 4.70
1870 1919 8.299570 AGCTTGACTTTGACCAAAACTAATATG 58.700 33.333 0.00 0.00 0.00 1.78
1871 1920 8.409358 AGCTTGACTTTGACCAAAACTAATAT 57.591 30.769 0.00 0.00 0.00 1.28
1872 1921 7.817418 AGCTTGACTTTGACCAAAACTAATA 57.183 32.000 0.00 0.00 0.00 0.98
1876 1925 5.405935 AAAGCTTGACTTTGACCAAAACT 57.594 34.783 0.00 0.00 47.00 2.66
1882 1931 6.330278 AAGTTTGTAAAGCTTGACTTTGACC 58.670 36.000 15.19 0.00 45.94 4.02
2027 2076 9.807386 CTTCGTAAAGTTTGACCAAGTTTATAG 57.193 33.333 0.00 2.48 40.73 1.31
2028 2077 9.328845 ACTTCGTAAAGTTTGACCAAGTTTATA 57.671 29.630 0.00 0.00 43.28 0.98
2030 2079 7.614124 ACTTCGTAAAGTTTGACCAAGTTTA 57.386 32.000 0.00 0.00 43.28 2.01
2031 2080 6.505044 ACTTCGTAAAGTTTGACCAAGTTT 57.495 33.333 0.00 0.00 43.28 2.66
2053 2102 9.974750 GCATATTAGAGTTAACTGAAGTCAAAC 57.025 33.333 14.14 0.00 39.63 2.93
2054 2103 9.719355 TGCATATTAGAGTTAACTGAAGTCAAA 57.281 29.630 14.14 0.00 39.63 2.69
2056 2105 8.749354 TCTGCATATTAGAGTTAACTGAAGTCA 58.251 33.333 14.14 0.26 39.63 3.41
2075 2124 9.693739 TCCCTTCATTTTTATTTACTCTGCATA 57.306 29.630 0.00 0.00 0.00 3.14
2076 2125 8.593945 TCCCTTCATTTTTATTTACTCTGCAT 57.406 30.769 0.00 0.00 0.00 3.96
2077 2126 7.669722 ACTCCCTTCATTTTTATTTACTCTGCA 59.330 33.333 0.00 0.00 0.00 4.41
2078 2127 8.056407 ACTCCCTTCATTTTTATTTACTCTGC 57.944 34.615 0.00 0.00 0.00 4.26
2088 2137 9.986157 TCTAGAGTAGTACTCCCTTCATTTTTA 57.014 33.333 23.82 7.37 46.18 1.52
2089 2138 8.896722 TCTAGAGTAGTACTCCCTTCATTTTT 57.103 34.615 23.82 6.64 46.18 1.94
2090 2139 9.138596 GATCTAGAGTAGTACTCCCTTCATTTT 57.861 37.037 23.82 7.30 46.18 1.82
2091 2140 7.726738 GGATCTAGAGTAGTACTCCCTTCATTT 59.273 40.741 23.82 7.94 46.18 2.32
2092 2141 7.074494 AGGATCTAGAGTAGTACTCCCTTCATT 59.926 40.741 23.82 8.60 46.18 2.57
2093 2142 6.564927 AGGATCTAGAGTAGTACTCCCTTCAT 59.435 42.308 23.82 12.34 46.18 2.57
2094 2143 5.912354 AGGATCTAGAGTAGTACTCCCTTCA 59.088 44.000 23.82 7.01 46.18 3.02
2096 2145 5.073965 CCAGGATCTAGAGTAGTACTCCCTT 59.926 48.000 23.82 10.58 46.18 3.95
2097 2146 4.600111 CCAGGATCTAGAGTAGTACTCCCT 59.400 50.000 23.82 19.28 46.18 4.20
2098 2147 4.351704 ACCAGGATCTAGAGTAGTACTCCC 59.648 50.000 23.82 17.59 46.18 4.30
2099 2148 5.072058 TCACCAGGATCTAGAGTAGTACTCC 59.928 48.000 23.82 10.67 46.18 3.85
2101 2150 6.773583 ATCACCAGGATCTAGAGTAGTACT 57.226 41.667 1.37 1.37 0.00 2.73
2151 2200 1.580815 GAGCACCTATCAGCAAGAGC 58.419 55.000 0.00 0.00 42.56 4.09
2152 2201 1.483827 TGGAGCACCTATCAGCAAGAG 59.516 52.381 0.71 0.00 37.04 2.85
2211 2261 6.817765 AATTGTCACCGTGTTGAGATAAAT 57.182 33.333 0.00 0.00 0.00 1.40
2216 2266 3.064207 GCTAATTGTCACCGTGTTGAGA 58.936 45.455 0.00 0.00 0.00 3.27
2221 2271 3.938963 CCTTATGCTAATTGTCACCGTGT 59.061 43.478 0.00 0.00 0.00 4.49
2244 2295 2.496899 ATCCATGATGTTATCGCCCC 57.503 50.000 0.00 0.00 0.00 5.80
2290 2342 5.809001 TCAACTATGGACTGAAAGCTCATT 58.191 37.500 0.00 0.00 37.60 2.57
2374 2428 2.421751 TCAAGGTGTGTCGGGAAAAA 57.578 45.000 0.00 0.00 0.00 1.94
2378 2432 0.895530 GAGATCAAGGTGTGTCGGGA 59.104 55.000 0.00 0.00 0.00 5.14
2379 2433 0.458543 CGAGATCAAGGTGTGTCGGG 60.459 60.000 0.00 0.00 0.00 5.14
2422 2476 3.460825 AGCTACCCTTATGGAACTTGGA 58.539 45.455 0.00 0.00 38.00 3.53
2480 2534 6.354794 TCCGAAGACTAGGAGAATTTGAAA 57.645 37.500 0.00 0.00 31.95 2.69
2591 2645 4.643784 GGCTGATGAGACCATTTCAAGAAT 59.356 41.667 0.00 0.00 32.09 2.40
2600 2654 2.045524 AGATTCGGCTGATGAGACCAT 58.954 47.619 0.00 0.00 35.29 3.55
2739 4360 1.665679 AGACGCGCCAAAATACAGATG 59.334 47.619 5.73 0.00 0.00 2.90
2847 4473 3.036431 GCAACCTAAGCCAACCAGT 57.964 52.632 0.00 0.00 0.00 4.00
2858 4484 2.489971 CACTCGAAAACAGGCAACCTA 58.510 47.619 0.00 0.00 29.64 3.08
2859 4485 1.308998 CACTCGAAAACAGGCAACCT 58.691 50.000 0.00 0.00 37.17 3.50
2941 4570 1.404035 TGCTACGTAGACGATGCATGT 59.596 47.619 26.53 2.18 42.12 3.21
2944 4573 1.092348 ACTGCTACGTAGACGATGCA 58.908 50.000 26.53 14.96 43.54 3.96
2945 4574 2.190325 AACTGCTACGTAGACGATGC 57.810 50.000 26.53 10.90 43.02 3.91
2946 4575 2.776765 CGAAACTGCTACGTAGACGATG 59.223 50.000 26.53 11.89 43.02 3.84
2948 4577 1.464687 GCGAAACTGCTACGTAGACGA 60.465 52.381 26.53 7.89 43.02 4.20
2950 4579 0.905839 CGCGAAACTGCTACGTAGAC 59.094 55.000 26.53 16.83 0.00 2.59
2951 4580 0.179181 CCGCGAAACTGCTACGTAGA 60.179 55.000 26.53 10.25 0.00 2.59
2952 4581 1.138047 CCCGCGAAACTGCTACGTAG 61.138 60.000 18.47 18.47 0.00 3.51
2953 4582 1.153978 CCCGCGAAACTGCTACGTA 60.154 57.895 8.23 0.00 0.00 3.57
2954 4583 2.431942 CCCGCGAAACTGCTACGT 60.432 61.111 8.23 0.00 0.00 3.57
2955 4584 2.126228 TCCCGCGAAACTGCTACG 60.126 61.111 8.23 0.00 0.00 3.51
2956 4585 0.947180 TTGTCCCGCGAAACTGCTAC 60.947 55.000 8.23 0.00 0.00 3.58
2957 4586 0.249953 TTTGTCCCGCGAAACTGCTA 60.250 50.000 8.23 0.00 0.00 3.49
2958 4587 1.525077 TTTGTCCCGCGAAACTGCT 60.525 52.632 8.23 0.00 0.00 4.24
2959 4588 1.370051 GTTTGTCCCGCGAAACTGC 60.370 57.895 8.23 0.00 0.00 4.40
2960 4589 1.281656 GGTTTGTCCCGCGAAACTG 59.718 57.895 8.23 0.00 33.41 3.16
2961 4590 3.740513 GGTTTGTCCCGCGAAACT 58.259 55.556 8.23 0.00 33.41 2.66
4384 6291 0.398318 ACAGGAGCTCCAGGACAAAC 59.602 55.000 33.90 4.03 38.89 2.93
4524 6438 6.331042 AGGAGTTTAGTTACCTACCCAAAAGT 59.669 38.462 0.00 0.00 0.00 2.66
4588 6502 6.682746 TCAAGTTGTTGTAAAGCAAAACTCA 58.317 32.000 2.11 0.00 39.03 3.41
4632 6546 7.226128 TCAGAGCTGTATGAATATGCAGAAAAG 59.774 37.037 9.13 0.00 46.27 2.27


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

AutoCloner maintained by Alex Coulton.