Multiple sequence alignment - TraesCS6D01G018900

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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 TraesCS6D01G018900 chr6D 100.000 8829 0 0 1 8829 7677753 7686581 0.000000e+00 16305.0
1 TraesCS6D01G018900 chr6D 88.177 1201 136 6 1009 2205 7961850 7963048 0.000000e+00 1426.0
2 TraesCS6D01G018900 chr6D 93.153 701 23 12 5301 5977 7655233 7655932 0.000000e+00 1005.0
3 TraesCS6D01G018900 chr6D 80.921 1216 153 30 3089 4263 7904270 7905447 0.000000e+00 887.0
4 TraesCS6D01G018900 chr6D 95.766 496 20 1 2391 2885 7654173 7654668 0.000000e+00 798.0
5 TraesCS6D01G018900 chr6D 77.984 1131 199 39 1106 2201 8249836 8250951 0.000000e+00 664.0
6 TraesCS6D01G018900 chr6D 87.366 467 32 13 2886 3330 24254545 24255006 2.200000e-140 510.0
7 TraesCS6D01G018900 chr6D 87.097 465 36 11 2886 3330 7654703 7655163 1.020000e-138 505.0
8 TraesCS6D01G018900 chr6D 87.273 440 52 4 5430 5866 7905226 7905664 4.760000e-137 499.0
9 TraesCS6D01G018900 chr6D 89.412 340 28 7 2541 2876 24253310 24253645 1.060000e-113 422.0
10 TraesCS6D01G018900 chr6D 84.348 345 44 6 5094 5430 7681416 7681758 6.610000e-86 329.0
11 TraesCS6D01G018900 chr6D 84.348 345 44 6 3664 4006 7682846 7683182 6.610000e-86 329.0
12 TraesCS6D01G018900 chr6D 80.556 396 37 12 4737 5104 7681003 7681386 1.460000e-67 268.0
13 TraesCS6D01G018900 chr6D 80.556 396 37 12 3251 3634 7682489 7682856 1.460000e-67 268.0
14 TraesCS6D01G018900 chr6D 81.818 297 25 14 4832 5101 24255076 24255370 1.150000e-53 222.0
15 TraesCS6D01G018900 chr6D 86.935 199 22 3 1013 1207 7874142 7874340 4.150000e-53 220.0
16 TraesCS6D01G018900 chr6D 94.928 138 7 0 8076 8213 7685685 7685822 5.370000e-52 217.0
17 TraesCS6D01G018900 chr6D 89.759 166 15 2 3983 4146 24260313 24260478 2.500000e-50 211.0
18 TraesCS6D01G018900 chr6D 83.333 228 27 4 5430 5656 7681803 7682020 5.410000e-47 200.0
19 TraesCS6D01G018900 chr6D 79.286 280 51 7 4266 4542 7655627 7655902 1.170000e-43 189.0
20 TraesCS6D01G018900 chr6D 89.928 139 8 1 4737 4869 7655084 7655222 3.280000e-39 174.0
21 TraesCS6D01G018900 chr6D 82.266 203 31 4 3113 3313 8251339 8251538 4.240000e-38 171.0
22 TraesCS6D01G018900 chr6D 76.974 304 55 9 3035 3328 8658273 8657975 9.170000e-35 159.0
23 TraesCS6D01G018900 chr6D 87.302 126 8 4 1009 1134 7695032 7695149 4.300000e-28 137.0
24 TraesCS6D01G018900 chr6D 80.503 159 25 5 4102 4254 8144952 8144794 5.600000e-22 117.0
25 TraesCS6D01G018900 chr6D 79.114 158 22 8 4108 4255 8989467 8989623 2.030000e-16 99.0
26 TraesCS6D01G018900 chr6D 98.182 55 1 0 7362 7416 112516106 112516052 7.300000e-16 97.1
27 TraesCS6D01G018900 chr6D 85.714 84 9 3 915 998 24251778 24251858 1.580000e-12 86.1
28 TraesCS6D01G018900 chr6D 90.566 53 5 0 3 55 216146288 216146340 4.420000e-08 71.3
29 TraesCS6D01G018900 chr6D 90.385 52 4 1 7367 7418 111181586 111181536 5.720000e-07 67.6
30 TraesCS6D01G018900 chr6D 97.222 36 1 0 893 928 7885588 7885623 2.660000e-05 62.1
31 TraesCS6D01G018900 chr6D 97.222 36 1 0 893 928 7961717 7961752 2.660000e-05 62.1
32 TraesCS6D01G018900 chr6B 92.885 3317 158 27 1004 4262 14303253 14306549 0.000000e+00 4747.0
33 TraesCS6D01G018900 chr6B 84.277 1889 151 54 2479 4268 54420671 54418830 0.000000e+00 1709.0
34 TraesCS6D01G018900 chr6B 85.140 1716 184 42 521 2202 14323016 14324694 0.000000e+00 1690.0
35 TraesCS6D01G018900 chr6B 86.595 1201 142 12 1013 2205 14399892 14398703 0.000000e+00 1308.0
36 TraesCS6D01G018900 chr6B 86.016 1230 147 13 997 2205 13934134 13932909 0.000000e+00 1295.0
37 TraesCS6D01G018900 chr6B 85.599 1236 155 14 989 2205 14311065 14312296 0.000000e+00 1275.0
38 TraesCS6D01G018900 chr6B 85.620 1217 146 23 1010 2205 14455067 14453859 0.000000e+00 1251.0
39 TraesCS6D01G018900 chr6B 85.098 1228 161 13 997 2205 39311025 39312249 0.000000e+00 1234.0
40 TraesCS6D01G018900 chr6B 82.271 1444 194 28 1328 2723 14318227 14319656 0.000000e+00 1192.0
41 TraesCS6D01G018900 chr6B 87.959 789 75 13 3487 4268 39328622 39329397 0.000000e+00 913.0
42 TraesCS6D01G018900 chr6B 77.545 1100 210 29 1119 2194 14333505 14334591 5.820000e-176 628.0
43 TraesCS6D01G018900 chr6B 86.832 524 15 25 4264 4742 39329559 39330073 3.630000e-148 536.0
44 TraesCS6D01G018900 chr6B 90.258 349 26 7 2541 2885 39327866 39328210 4.860000e-122 449.0
45 TraesCS6D01G018900 chr6B 87.597 387 22 13 2886 3251 39328245 39328626 8.190000e-115 425.0
46 TraesCS6D01G018900 chr6B 88.328 317 25 9 688 998 39310677 39310987 3.890000e-98 370.0
47 TraesCS6D01G018900 chr6B 91.710 193 15 1 273 465 39310678 39310487 5.250000e-67 267.0
48 TraesCS6D01G018900 chr6B 80.303 396 38 12 4737 5104 14305539 14305922 6.800000e-66 263.0
49 TraesCS6D01G018900 chr6B 75.706 531 81 26 2241 2746 79037655 79038162 1.150000e-53 222.0
50 TraesCS6D01G018900 chr6B 79.402 301 50 8 3035 3328 15749126 15748831 1.500000e-47 202.0
51 TraesCS6D01G018900 chr6B 77.303 304 47 16 3648 3948 52565764 52565480 9.170000e-35 159.0
52 TraesCS6D01G018900 chr6B 73.704 521 76 35 3748 4255 15712410 15711938 7.140000e-31 147.0
53 TraesCS6D01G018900 chr6B 78.981 157 23 8 4108 4255 16322862 16323017 2.030000e-16 99.0
54 TraesCS6D01G018900 chr6B 95.082 61 3 0 4195 4255 16426439 16426499 7.300000e-16 97.1
55 TraesCS6D01G018900 chr6B 91.111 45 4 0 893 937 14402571 14402527 2.660000e-05 62.1
56 TraesCS6D01G018900 chr4A 88.373 1875 169 31 999 2853 667425287 667427132 0.000000e+00 2209.0
57 TraesCS6D01G018900 chr4A 85.039 1945 215 34 989 2885 667379992 667381908 0.000000e+00 1910.0
58 TraesCS6D01G018900 chr4A 80.114 1398 193 52 2895 4268 667427226 667428562 0.000000e+00 963.0
59 TraesCS6D01G018900 chr4A 82.215 984 83 48 2895 3820 667381951 667382900 0.000000e+00 763.0
60 TraesCS6D01G018900 chr4A 87.113 582 40 16 5430 5977 667383099 667383679 2.090000e-175 627.0
61 TraesCS6D01G018900 chr4A 83.759 431 48 13 3858 4268 667382906 667383334 1.070000e-103 388.0
62 TraesCS6D01G018900 chr4A 81.849 292 28 7 6321 6591 667384432 667384719 1.150000e-53 222.0
63 TraesCS6D01G018900 chr4A 78.947 285 47 8 4266 4542 667428601 667428880 1.960000e-41 182.0
64 TraesCS6D01G018900 chr4A 82.609 184 18 8 5987 6165 667384009 667384183 5.520000e-32 150.0
65 TraesCS6D01G018900 chr4A 89.091 55 6 0 1 55 339445756 339445702 1.590000e-07 69.4
66 TraesCS6D01G018900 chr6A 86.132 1882 212 21 1008 2856 7977695 7979560 0.000000e+00 1984.0
67 TraesCS6D01G018900 chr6A 83.878 1929 230 35 1008 2885 12420349 12422247 0.000000e+00 1764.0
68 TraesCS6D01G018900 chr6A 87.253 1216 142 10 995 2205 8170441 8171648 0.000000e+00 1375.0
69 TraesCS6D01G018900 chr6A 86.991 761 70 15 3515 4262 7980478 7981222 0.000000e+00 830.0
70 TraesCS6D01G018900 chr6A 77.865 1152 206 34 1096 2212 8624464 8623327 0.000000e+00 669.0
71 TraesCS6D01G018900 chr6A 77.104 297 48 15 3648 3943 8802907 8802630 4.270000e-33 154.0
72 TraesCS6D01G018900 chr6A 76.569 239 40 12 4737 4968 7980018 7980247 5.600000e-22 117.0
73 TraesCS6D01G018900 chr6A 98.246 57 1 0 7362 7418 91891218 91891162 5.640000e-17 100.0
74 TraesCS6D01G018900 chr6A 92.647 68 5 0 7351 7418 145532359 145532426 2.030000e-16 99.0
75 TraesCS6D01G018900 chr6A 90.741 54 5 0 7365 7418 117285534 117285481 1.230000e-08 73.1
76 TraesCS6D01G018900 chr6A 89.091 55 6 0 1 55 270246501 270246447 1.590000e-07 69.4
77 TraesCS6D01G018900 chr6A 97.222 36 1 0 893 928 8170323 8170358 2.660000e-05 62.1
78 TraesCS6D01G018900 chr4D 93.963 1143 44 15 7705 8829 493748787 493747652 0.000000e+00 1705.0
79 TraesCS6D01G018900 chr4D 97.049 576 10 5 8261 8829 503116421 503115846 0.000000e+00 963.0
80 TraesCS6D01G018900 chr4D 96.095 589 16 5 8248 8829 508665722 508666310 0.000000e+00 953.0
81 TraesCS6D01G018900 chr4D 81.301 615 59 29 7709 8283 365415929 365416527 1.750000e-121 448.0
82 TraesCS6D01G018900 chr4D 96.479 142 5 0 7933 8074 493748409 493748268 1.480000e-57 235.0
83 TraesCS6D01G018900 chr4D 94.444 144 3 1 8075 8213 493748558 493748415 5.370000e-52 217.0
84 TraesCS6D01G018900 chr4D 91.753 97 8 0 8116 8212 365416228 365416324 1.550000e-27 135.0
85 TraesCS6D01G018900 chr4D 96.491 57 2 0 7362 7418 31262053 31261997 2.620000e-15 95.3
86 TraesCS6D01G018900 chr4D 96.491 57 2 0 7362 7418 36977172 36977116 2.620000e-15 95.3
87 TraesCS6D01G018900 chr4D 96.491 57 2 0 7362 7418 77528328 77528272 2.620000e-15 95.3
88 TraesCS6D01G018900 chr4D 96.491 57 2 0 7362 7418 207226123 207226179 2.620000e-15 95.3
89 TraesCS6D01G018900 chr4D 96.491 57 2 0 7362 7418 234956346 234956402 2.620000e-15 95.3
90 TraesCS6D01G018900 chr4D 96.491 57 2 0 7362 7418 289704151 289704095 2.620000e-15 95.3
91 TraesCS6D01G018900 chr4D 96.491 57 2 0 7362 7418 291161111 291161167 2.620000e-15 95.3
92 TraesCS6D01G018900 chr4D 96.491 57 2 0 7362 7418 316080957 316081013 2.620000e-15 95.3
93 TraesCS6D01G018900 chr4D 96.491 57 2 0 7362 7418 316081835 316081891 2.620000e-15 95.3
94 TraesCS6D01G018900 chr4D 100.000 43 0 0 8195 8237 365416324 365416366 7.350000e-11 80.5
95 TraesCS6D01G018900 chr7D 93.942 1139 45 14 7709 8829 316381645 316382777 0.000000e+00 1700.0
96 TraesCS6D01G018900 chr7D 96.284 592 13 4 8245 8829 10555853 10555264 0.000000e+00 963.0
97 TraesCS6D01G018900 chr7D 78.040 1102 211 24 1122 2204 161390721 161391810 0.000000e+00 665.0
98 TraesCS6D01G018900 chr7D 91.694 301 17 7 7709 8004 608434141 608434438 2.290000e-110 411.0
99 TraesCS6D01G018900 chr7D 96.479 142 5 0 7933 8074 316382020 316382161 1.480000e-57 235.0
100 TraesCS6D01G018900 chr7D 93.750 144 4 1 8075 8213 316381871 316382014 2.500000e-50 211.0
101 TraesCS6D01G018900 chr7D 88.079 151 16 1 5252 5402 486201475 486201327 2.530000e-40 178.0
102 TraesCS6D01G018900 chr7D 87.805 82 10 0 7337 7418 93229940 93230021 7.300000e-16 97.1
103 TraesCS6D01G018900 chr7D 96.226 53 2 0 3 55 335997267 335997215 4.390000e-13 87.9
104 TraesCS6D01G018900 chr7D 90.385 52 5 0 3 54 300189767 300189716 1.590000e-07 69.4
105 TraesCS6D01G018900 chr5D 93.761 1138 43 14 7714 8829 77001605 77002736 0.000000e+00 1683.0
106 TraesCS6D01G018900 chr5D 96.147 597 14 3 8242 8829 168500891 168501487 0.000000e+00 966.0
107 TraesCS6D01G018900 chr5D 95.238 273 9 3 7702 7971 121083759 121083488 6.330000e-116 429.0
108 TraesCS6D01G018900 chr5D 94.444 144 3 1 8075 8213 77001826 77001969 5.370000e-52 217.0
109 TraesCS6D01G018900 chr5D 89.873 158 14 1 5244 5401 446154226 446154071 1.500000e-47 202.0
110 TraesCS6D01G018900 chr5D 90.361 83 8 0 7336 7418 166750095 166750013 9.370000e-20 110.0
111 TraesCS6D01G018900 chr5D 95.082 61 3 0 7362 7422 463514560 463514620 7.300000e-16 97.1
112 TraesCS6D01G018900 chr5D 96.491 57 2 0 7362 7418 179013867 179013923 2.620000e-15 95.3
113 TraesCS6D01G018900 chr5D 92.157 51 3 1 7367 7417 342492583 342492632 4.420000e-08 71.3
114 TraesCS6D01G018900 chr7B 86.832 1086 83 23 4924 5977 640002867 640003924 0.000000e+00 1158.0
115 TraesCS6D01G018900 chr7B 78.636 1100 203 24 1123 2204 123655645 123656730 0.000000e+00 701.0
116 TraesCS6D01G018900 chr7B 80.915 634 107 12 63 690 300671857 300672482 1.030000e-133 488.0
117 TraesCS6D01G018900 chr7B 80.349 631 103 13 63 691 672910700 672911311 8.080000e-125 459.0
118 TraesCS6D01G018900 chr7B 79.283 642 105 19 63 696 500773731 500773110 2.950000e-114 424.0
119 TraesCS6D01G018900 chr7B 82.816 419 53 11 3037 3455 639999858 640000257 3.030000e-94 357.0
120 TraesCS6D01G018900 chr7B 83.784 222 30 4 4051 4268 640003375 640003594 1.160000e-48 206.0
121 TraesCS6D01G018900 chr7B 91.304 92 6 2 2882 2973 639999526 639999615 3.350000e-24 124.0
122 TraesCS6D01G018900 chr7B 87.156 109 7 2 4737 4839 640000070 640000177 5.600000e-22 117.0
123 TraesCS6D01G018900 chr1D 96.939 588 11 2 8248 8829 196484161 196483575 0.000000e+00 979.0
124 TraesCS6D01G018900 chr1D 97.391 575 9 1 8261 8829 460859192 460859766 0.000000e+00 974.0
125 TraesCS6D01G018900 chr1D 90.154 325 22 8 7712 8030 196484582 196484262 1.770000e-111 414.0
126 TraesCS6D01G018900 chr1D 92.000 75 4 1 7362 7434 395990533 395990459 4.360000e-18 104.0
127 TraesCS6D01G018900 chr1D 95.082 61 3 0 7362 7422 348604157 348604217 7.300000e-16 97.1
128 TraesCS6D01G018900 chr1D 96.491 57 2 0 7362 7418 329001486 329001542 2.620000e-15 95.3
129 TraesCS6D01G018900 chr1D 90.566 53 5 0 3 55 159535020 159535072 4.420000e-08 71.3
130 TraesCS6D01G018900 chr1D 91.489 47 4 0 7372 7418 262175019 262175065 2.060000e-06 65.8
131 TraesCS6D01G018900 chr2D 96.599 588 14 5 8248 8829 405625397 405624810 0.000000e+00 970.0
132 TraesCS6D01G018900 chr2D 95.987 598 15 6 8241 8829 421784445 421785042 0.000000e+00 963.0
133 TraesCS6D01G018900 chr2D 95.307 277 10 2 7709 7982 416392354 416392630 3.780000e-118 436.0
134 TraesCS6D01G018900 chr2D 96.721 61 2 0 7362 7422 649592283 649592223 1.570000e-17 102.0
135 TraesCS6D01G018900 chr2D 89.873 79 2 2 7362 7434 116214131 116214053 7.300000e-16 97.1
136 TraesCS6D01G018900 chr2D 88.158 76 4 4 8075 8147 416392580 416392653 1.580000e-12 86.1
137 TraesCS6D01G018900 chrUn 96.429 588 14 2 8248 8829 80049526 80050112 0.000000e+00 963.0
138 TraesCS6D01G018900 chrUn 100.000 425 0 0 3277 3701 476555064 476554640 0.000000e+00 785.0
139 TraesCS6D01G018900 chrUn 81.905 315 27 10 4818 5104 476555019 476554707 1.150000e-58 239.0
140 TraesCS6D01G018900 chrUn 75.379 528 87 26 2241 2746 27945108 27944602 1.930000e-51 215.0
141 TraesCS6D01G018900 chrUn 78.431 204 31 7 4339 4531 27943658 27943457 4.330000e-23 121.0
142 TraesCS6D01G018900 chrUn 98.214 56 1 0 7363 7418 50668550 50668495 2.030000e-16 99.0
143 TraesCS6D01G018900 chr7A 78.455 1100 208 21 1123 2204 162577916 162579004 0.000000e+00 691.0
144 TraesCS6D01G018900 chr3D 95.327 321 11 3 7709 8026 47789883 47790202 2.840000e-139 507.0
145 TraesCS6D01G018900 chr3D 80.351 285 35 16 7976 8250 47790230 47790503 6.990000e-46 196.0
146 TraesCS6D01G018900 chr3D 93.684 95 5 1 8075 8169 47790109 47790202 3.320000e-29 141.0
147 TraesCS6D01G018900 chr3D 84.058 69 6 5 3 67 288722649 288722582 2.660000e-05 62.1
148 TraesCS6D01G018900 chr5B 78.807 637 125 7 63 696 440264038 440264667 3.810000e-113 420.0
149 TraesCS6D01G018900 chr5B 94.118 68 3 1 7351 7418 346974610 346974544 1.570000e-17 102.0
150 TraesCS6D01G018900 chr5B 90.411 73 7 0 7362 7434 498639609 498639537 7.300000e-16 97.1
151 TraesCS6D01G018900 chr1B 80.899 534 94 7 161 691 15779251 15778723 1.770000e-111 414.0
152 TraesCS6D01G018900 chr1B 77.899 276 47 11 3648 3922 630652000 630652262 9.170000e-35 159.0
153 TraesCS6D01G018900 chr3B 78.445 566 114 8 117 680 501419111 501418552 6.520000e-96 363.0
154 TraesCS6D01G018900 chr3B 78.462 520 85 16 175 690 55045675 55046171 1.850000e-81 315.0
155 TraesCS6D01G018900 chr3B 78.596 285 54 7 415 696 73677507 73677227 1.960000e-41 182.0
156 TraesCS6D01G018900 chr2A 80.049 406 74 6 293 696 561263368 561262968 2.410000e-75 294.0
157 TraesCS6D01G018900 chr2A 85.938 64 4 5 2 62 345566710 345566649 7.400000e-06 63.9
158 TraesCS6D01G018900 chr5A 91.667 72 6 0 7362 7433 116217865 116217794 5.640000e-17 100.0
159 TraesCS6D01G018900 chr5A 92.647 68 5 0 7351 7418 176666750 176666683 2.030000e-16 99.0
160 TraesCS6D01G018900 chr5A 89.091 55 6 0 1 55 217644198 217644252 1.590000e-07 69.4
161 TraesCS6D01G018900 chr1A 98.182 55 1 0 7362 7416 550504633 550504687 7.300000e-16 97.1
162 TraesCS6D01G018900 chr1A 92.982 57 4 0 7362 7418 244686684 244686740 5.680000e-12 84.2
163 TraesCS6D01G018900 chr4B 91.304 69 6 0 7350 7418 83187468 83187536 2.620000e-15 95.3


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 TraesCS6D01G018900 chr6D 7677753 7686581 8828 False 16305.000000 16305 100.000000 1 8829 1 chr6D.!!$F1 8828
1 TraesCS6D01G018900 chr6D 7961717 7963048 1331 False 744.050000 1426 92.699500 893 2205 2 chr6D.!!$F11 1312
2 TraesCS6D01G018900 chr6D 7904270 7905664 1394 False 693.000000 887 84.097000 3089 5866 2 chr6D.!!$F10 2777
3 TraesCS6D01G018900 chr6D 7654173 7655932 1759 False 534.200000 1005 89.046000 2391 5977 5 chr6D.!!$F8 3586
4 TraesCS6D01G018900 chr6D 8249836 8251538 1702 False 417.500000 664 80.125000 1106 3313 2 chr6D.!!$F12 2207
5 TraesCS6D01G018900 chr6D 24251778 24255370 3592 False 310.025000 510 86.077500 915 5101 4 chr6D.!!$F13 4186
6 TraesCS6D01G018900 chr6D 7681003 7685822 4819 False 268.500000 329 84.678167 3251 8213 6 chr6D.!!$F9 4962
7 TraesCS6D01G018900 chr6B 14303253 14306549 3296 False 2505.000000 4747 86.594000 1004 5104 2 chr6B.!!$F6 4100
8 TraesCS6D01G018900 chr6B 54418830 54420671 1841 True 1709.000000 1709 84.277000 2479 4268 1 chr6B.!!$R7 1789
9 TraesCS6D01G018900 chr6B 14318227 14324694 6467 False 1441.000000 1690 83.705500 521 2723 2 chr6B.!!$F7 2202
10 TraesCS6D01G018900 chr6B 13932909 13934134 1225 True 1295.000000 1295 86.016000 997 2205 1 chr6B.!!$R1 1208
11 TraesCS6D01G018900 chr6B 14311065 14312296 1231 False 1275.000000 1275 85.599000 989 2205 1 chr6B.!!$F1 1216
12 TraesCS6D01G018900 chr6B 14453859 14455067 1208 True 1251.000000 1251 85.620000 1010 2205 1 chr6B.!!$R2 1195
13 TraesCS6D01G018900 chr6B 39310677 39312249 1572 False 802.000000 1234 86.713000 688 2205 2 chr6B.!!$F8 1517
14 TraesCS6D01G018900 chr6B 14398703 14402571 3868 True 685.050000 1308 88.853000 893 2205 2 chr6B.!!$R8 1312
15 TraesCS6D01G018900 chr6B 14333505 14334591 1086 False 628.000000 628 77.545000 1119 2194 1 chr6B.!!$F2 1075
16 TraesCS6D01G018900 chr6B 39327866 39330073 2207 False 580.750000 913 88.161500 2541 4742 4 chr6B.!!$F9 2201
17 TraesCS6D01G018900 chr6B 79037655 79038162 507 False 222.000000 222 75.706000 2241 2746 1 chr6B.!!$F5 505
18 TraesCS6D01G018900 chr4A 667425287 667428880 3593 False 1118.000000 2209 82.478000 999 4542 3 chr4A.!!$F2 3543
19 TraesCS6D01G018900 chr4A 667379992 667384719 4727 False 676.666667 1910 83.764000 989 6591 6 chr4A.!!$F1 5602
20 TraesCS6D01G018900 chr6A 12420349 12422247 1898 False 1764.000000 1764 83.878000 1008 2885 1 chr6A.!!$F1 1877
21 TraesCS6D01G018900 chr6A 7977695 7981222 3527 False 977.000000 1984 83.230667 1008 4968 3 chr6A.!!$F3 3960
22 TraesCS6D01G018900 chr6A 8170323 8171648 1325 False 718.550000 1375 92.237500 893 2205 2 chr6A.!!$F4 1312
23 TraesCS6D01G018900 chr6A 8623327 8624464 1137 True 669.000000 669 77.865000 1096 2212 1 chr6A.!!$R1 1116
24 TraesCS6D01G018900 chr4D 503115846 503116421 575 True 963.000000 963 97.049000 8261 8829 1 chr4D.!!$R5 568
25 TraesCS6D01G018900 chr4D 508665722 508666310 588 False 953.000000 953 96.095000 8248 8829 1 chr4D.!!$F4 581
26 TraesCS6D01G018900 chr4D 493747652 493748787 1135 True 719.000000 1705 94.962000 7705 8829 3 chr4D.!!$R6 1124
27 TraesCS6D01G018900 chr4D 365415929 365416527 598 False 221.166667 448 91.018000 7709 8283 3 chr4D.!!$F6 574
28 TraesCS6D01G018900 chr7D 10555264 10555853 589 True 963.000000 963 96.284000 8245 8829 1 chr7D.!!$R1 584
29 TraesCS6D01G018900 chr7D 316381645 316382777 1132 False 715.333333 1700 94.723667 7709 8829 3 chr7D.!!$F4 1120
30 TraesCS6D01G018900 chr7D 161390721 161391810 1089 False 665.000000 665 78.040000 1122 2204 1 chr7D.!!$F2 1082
31 TraesCS6D01G018900 chr5D 168500891 168501487 596 False 966.000000 966 96.147000 8242 8829 1 chr5D.!!$F1 587
32 TraesCS6D01G018900 chr5D 77001605 77002736 1131 False 950.000000 1683 94.102500 7714 8829 2 chr5D.!!$F5 1115
33 TraesCS6D01G018900 chr7B 123655645 123656730 1085 False 701.000000 701 78.636000 1123 2204 1 chr7B.!!$F1 1081
34 TraesCS6D01G018900 chr7B 300671857 300672482 625 False 488.000000 488 80.915000 63 690 1 chr7B.!!$F2 627
35 TraesCS6D01G018900 chr7B 672910700 672911311 611 False 459.000000 459 80.349000 63 691 1 chr7B.!!$F3 628
36 TraesCS6D01G018900 chr7B 500773110 500773731 621 True 424.000000 424 79.283000 63 696 1 chr7B.!!$R1 633
37 TraesCS6D01G018900 chr7B 639999526 640003924 4398 False 392.400000 1158 86.378400 2882 5977 5 chr7B.!!$F4 3095
38 TraesCS6D01G018900 chr1D 460859192 460859766 574 False 974.000000 974 97.391000 8261 8829 1 chr1D.!!$F5 568
39 TraesCS6D01G018900 chr1D 196483575 196484582 1007 True 696.500000 979 93.546500 7712 8829 2 chr1D.!!$R2 1117
40 TraesCS6D01G018900 chr2D 405624810 405625397 587 True 970.000000 970 96.599000 8248 8829 1 chr2D.!!$R2 581
41 TraesCS6D01G018900 chr2D 421784445 421785042 597 False 963.000000 963 95.987000 8241 8829 1 chr2D.!!$F1 588
42 TraesCS6D01G018900 chrUn 80049526 80050112 586 False 963.000000 963 96.429000 8248 8829 1 chrUn.!!$F1 581
43 TraesCS6D01G018900 chr7A 162577916 162579004 1088 False 691.000000 691 78.455000 1123 2204 1 chr7A.!!$F1 1081
44 TraesCS6D01G018900 chr3D 47789883 47790503 620 False 281.333333 507 89.787333 7709 8250 3 chr3D.!!$F1 541
45 TraesCS6D01G018900 chr5B 440264038 440264667 629 False 420.000000 420 78.807000 63 696 1 chr5B.!!$F1 633
46 TraesCS6D01G018900 chr1B 15778723 15779251 528 True 414.000000 414 80.899000 161 691 1 chr1B.!!$R1 530
47 TraesCS6D01G018900 chr3B 501418552 501419111 559 True 363.000000 363 78.445000 117 680 1 chr3B.!!$R2 563

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
21 22 0.035439 GGGATCCGCTCCTTTTGTGA 60.035 55.0 5.45 0.00 44.28 3.58 F
42 43 0.100146 AGATCGGCCGTACGAAGTTC 59.900 55.0 27.15 11.34 46.92 3.01 F
216 218 0.107017 CCTGCTCCAAATCCCGATGT 60.107 55.0 0.00 0.00 0.00 3.06 F
953 5258 0.180406 AAGACCAGCACACCTTTCGT 59.820 50.0 0.00 0.00 0.00 3.85 F
954 5259 0.249911 AGACCAGCACACCTTTCGTC 60.250 55.0 0.00 0.00 0.00 4.20 F
1384 8326 0.318762 GGCGTGGAGAGAACTCTGTT 59.681 55.0 9.16 0.00 40.61 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1546 8491 1.103803 GTCAGAGCCGAGGACATGTA 58.896 55.000 0.00 0.00 0.00 2.29 R
2165 9124 0.744414 GAATCTAGCCGGCACTTGCA 60.744 55.000 31.54 6.06 44.36 4.08 R
2800 10018 4.097892 ACGAATTTTGGGGCTTCATATCAC 59.902 41.667 0.00 0.00 0.00 3.06 R
3053 11386 5.878406 ATGCTACTAGCCAACTACTGAAT 57.122 39.130 5.58 0.00 41.51 2.57 R
3143 11482 6.620678 ACCATACAAGCATCAATTTGTGTAC 58.379 36.000 0.00 0.00 37.98 2.90 R
8237 20419 1.475280 TCGATCACGAGACCCGAAATT 59.525 47.619 6.69 0.00 43.81 1.82 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
18 19 3.813596 CGGGATCCGCTCCTTTTG 58.186 61.111 5.45 0.00 44.28 2.44
19 20 1.078426 CGGGATCCGCTCCTTTTGT 60.078 57.895 5.45 0.00 44.28 2.83
20 21 1.369091 CGGGATCCGCTCCTTTTGTG 61.369 60.000 5.45 0.00 44.28 3.33
21 22 0.035439 GGGATCCGCTCCTTTTGTGA 60.035 55.000 5.45 0.00 44.28 3.58
22 23 1.613255 GGGATCCGCTCCTTTTGTGAA 60.613 52.381 5.45 0.00 44.28 3.18
25 26 2.631160 TCCGCTCCTTTTGTGAAAGA 57.369 45.000 0.70 0.00 44.03 2.52
28 29 2.159653 CCGCTCCTTTTGTGAAAGATCG 60.160 50.000 0.70 1.93 44.03 3.69
29 30 2.159653 CGCTCCTTTTGTGAAAGATCGG 60.160 50.000 0.70 0.00 44.03 4.18
31 32 2.159382 TCCTTTTGTGAAAGATCGGCC 58.841 47.619 0.00 0.00 44.03 6.13
33 34 1.535462 CTTTTGTGAAAGATCGGCCGT 59.465 47.619 27.15 12.96 44.03 5.68
34 35 2.459060 TTTGTGAAAGATCGGCCGTA 57.541 45.000 27.15 12.70 0.00 4.02
36 37 0.457166 TGTGAAAGATCGGCCGTACG 60.457 55.000 27.15 8.69 0.00 3.67
38 39 0.527113 TGAAAGATCGGCCGTACGAA 59.473 50.000 27.15 5.24 46.92 3.85
39 40 1.197910 GAAAGATCGGCCGTACGAAG 58.802 55.000 27.15 7.54 46.92 3.79
40 41 0.529378 AAAGATCGGCCGTACGAAGT 59.471 50.000 27.15 2.70 46.92 3.01
42 43 0.100146 AGATCGGCCGTACGAAGTTC 59.900 55.000 27.15 11.34 46.92 3.01
43 44 0.869028 GATCGGCCGTACGAAGTTCC 60.869 60.000 27.15 8.43 46.92 3.62
45 46 2.090524 CGGCCGTACGAAGTTCCAC 61.091 63.158 19.50 0.00 37.78 4.02
46 47 1.291272 GGCCGTACGAAGTTCCACT 59.709 57.895 18.76 0.00 37.78 4.00
48 49 0.735287 GCCGTACGAAGTTCCACTCC 60.735 60.000 18.76 0.00 37.78 3.85
51 52 1.001048 CGTACGAAGTTCCACTCCACA 60.001 52.381 10.44 0.00 37.78 4.17
52 53 2.352421 CGTACGAAGTTCCACTCCACAT 60.352 50.000 10.44 0.00 37.78 3.21
53 54 2.457366 ACGAAGTTCCACTCCACATC 57.543 50.000 0.00 0.00 37.78 3.06
54 55 1.691976 ACGAAGTTCCACTCCACATCA 59.308 47.619 0.00 0.00 37.78 3.07
55 56 2.289072 ACGAAGTTCCACTCCACATCAG 60.289 50.000 0.00 0.00 37.78 2.90
56 57 2.704572 GAAGTTCCACTCCACATCAGG 58.295 52.381 0.00 0.00 0.00 3.86
57 58 2.030027 AGTTCCACTCCACATCAGGA 57.970 50.000 0.00 0.00 36.00 3.86
95 96 0.317103 CAACCTATCTCTCGGCGTCG 60.317 60.000 1.15 1.15 37.82 5.12
101 102 3.432588 CTCTCGGCGTCGTGGAGT 61.433 66.667 20.38 0.00 37.69 3.85
102 103 3.669036 CTCTCGGCGTCGTGGAGTG 62.669 68.421 20.38 5.82 37.69 3.51
119 120 4.020928 TGGAGTGCGGAGTTTTAGATGTTA 60.021 41.667 0.00 0.00 0.00 2.41
142 143 0.838122 CCCTTCCCTCACCTGTGACT 60.838 60.000 0.00 0.00 35.46 3.41
145 146 1.417890 CTTCCCTCACCTGTGACTGTT 59.582 52.381 0.00 0.00 35.46 3.16
147 148 0.250467 CCCTCACCTGTGACTGTTGG 60.250 60.000 0.00 0.00 35.46 3.77
155 156 0.822944 TGTGACTGTTGGGCATGTGG 60.823 55.000 0.00 0.00 34.28 4.17
167 168 1.597742 GCATGTGGTGTCTGTGAGTT 58.402 50.000 0.00 0.00 0.00 3.01
179 180 0.251253 TGTGAGTTGCATGGCCATCA 60.251 50.000 17.61 14.27 0.00 3.07
211 213 2.054453 GGCACCTGCTCCAAATCCC 61.054 63.158 0.00 0.00 41.70 3.85
216 218 0.107017 CCTGCTCCAAATCCCGATGT 60.107 55.000 0.00 0.00 0.00 3.06
223 225 4.265073 CTCCAAATCCCGATGTTCTCTTT 58.735 43.478 0.00 0.00 0.00 2.52
226 228 2.787473 ATCCCGATGTTCTCTTTGCA 57.213 45.000 0.00 0.00 0.00 4.08
281 283 1.745489 GCTAGACCTGGTTTGGGCG 60.745 63.158 0.00 0.00 40.90 6.13
282 284 1.677552 CTAGACCTGGTTTGGGCGT 59.322 57.895 0.00 0.00 40.90 5.68
287 289 3.353836 CTGGTTTGGGCGTGTCGG 61.354 66.667 0.00 0.00 0.00 4.79
291 293 2.124653 TTTGGGCGTGTCGGTTGT 60.125 55.556 0.00 0.00 0.00 3.32
300 302 1.098712 GTGTCGGTTGTTTGCCTCCA 61.099 55.000 0.00 0.00 0.00 3.86
322 325 1.455032 GGGGACGCCAAATAAGGGG 60.455 63.158 3.14 0.00 46.27 4.79
339 342 1.070134 GGGGCAAACCAAAAGAAGGTC 59.930 52.381 0.00 0.00 42.91 3.85
342 345 1.407618 GCAAACCAAAAGAAGGTCGGT 59.592 47.619 0.00 0.00 38.76 4.69
364 367 1.526917 GGCAAGAGTGGCGCCATAT 60.527 57.895 35.23 24.91 45.52 1.78
365 368 0.250295 GGCAAGAGTGGCGCCATATA 60.250 55.000 35.23 6.15 45.52 0.86
396 399 2.173143 TGTGGCTGCTTGATGGATGATA 59.827 45.455 0.00 0.00 0.00 2.15
398 401 3.439476 GTGGCTGCTTGATGGATGATATC 59.561 47.826 0.00 0.00 0.00 1.63
433 436 2.409064 TCCTCTTGGACTGGGTTGTA 57.591 50.000 0.00 0.00 37.46 2.41
441 444 1.142262 GGACTGGGTTGTAGTTGTGGT 59.858 52.381 0.00 0.00 0.00 4.16
450 453 2.128535 TGTAGTTGTGGTTTGGGAGGA 58.871 47.619 0.00 0.00 0.00 3.71
465 468 1.112113 GAGGAGCCCGATGTCTTGTA 58.888 55.000 0.00 0.00 0.00 2.41
505 508 1.005037 TCACTTGGCGTGGTAGCAG 60.005 57.895 0.00 0.00 43.94 4.24
521 524 2.841044 AGTGTCGGGGTTGGTCGT 60.841 61.111 0.00 0.00 0.00 4.34
533 4803 1.135517 GTTGGTCGTTGTTGTGCACTT 60.136 47.619 19.41 0.00 0.00 3.16
547 4832 2.098614 TGCACTTGAAGAGTTTGGCAA 58.901 42.857 0.00 0.00 36.10 4.52
696 4988 2.675844 GCAAAACTTTTGCCTCGGTTTT 59.324 40.909 23.40 5.08 40.86 2.43
697 4989 3.866327 GCAAAACTTTTGCCTCGGTTTTA 59.134 39.130 23.40 0.00 39.04 1.52
698 4990 4.509970 GCAAAACTTTTGCCTCGGTTTTAT 59.490 37.500 23.40 0.00 39.04 1.40
699 4991 5.007234 GCAAAACTTTTGCCTCGGTTTTATT 59.993 36.000 23.40 0.00 39.04 1.40
768 5060 8.934023 TGAACTGGATTTTTCTAGTTTGGTAT 57.066 30.769 6.25 0.00 40.66 2.73
891 5196 2.083774 GCAACGAGTGGATGGAAATGA 58.916 47.619 0.00 0.00 0.00 2.57
899 5204 1.004161 TGGATGGAAATGAGCCGTTGA 59.996 47.619 0.00 0.00 0.00 3.18
948 5253 2.302157 GGTAACTAAGACCAGCACACCT 59.698 50.000 0.00 0.00 36.91 4.00
950 5255 3.577805 AACTAAGACCAGCACACCTTT 57.422 42.857 0.00 0.00 0.00 3.11
952 5257 2.069273 CTAAGACCAGCACACCTTTCG 58.931 52.381 0.00 0.00 0.00 3.46
953 5258 0.180406 AAGACCAGCACACCTTTCGT 59.820 50.000 0.00 0.00 0.00 3.85
954 5259 0.249911 AGACCAGCACACCTTTCGTC 60.250 55.000 0.00 0.00 0.00 4.20
955 5260 1.557443 GACCAGCACACCTTTCGTCG 61.557 60.000 0.00 0.00 0.00 5.12
956 5261 2.551270 CAGCACACCTTTCGTCGC 59.449 61.111 0.00 0.00 0.00 5.19
957 5262 2.665185 AGCACACCTTTCGTCGCC 60.665 61.111 0.00 0.00 0.00 5.54
958 5263 3.723348 GCACACCTTTCGTCGCCC 61.723 66.667 0.00 0.00 0.00 6.13
1134 8061 2.438614 TCTCTCTCCACCGCCTCG 60.439 66.667 0.00 0.00 0.00 4.63
1135 8062 4.200283 CTCTCTCCACCGCCTCGC 62.200 72.222 0.00 0.00 0.00 5.03
1384 8326 0.318762 GGCGTGGAGAGAACTCTGTT 59.681 55.000 9.16 0.00 40.61 3.16
1546 8491 4.473520 CTTGGTCCGGCCGCTCAT 62.474 66.667 22.85 0.00 41.21 2.90
2152 9111 1.276421 ACCTTGCTGAAGACTATGCGT 59.724 47.619 0.00 0.00 0.00 5.24
2165 9124 4.956504 GACTATGCGTCTGCTTGCAAAGT 61.957 47.826 0.00 0.00 45.45 2.66
2646 9860 7.558081 TGCATACTAGAACTAAGAGAGTGTGAT 59.442 37.037 0.00 0.00 38.87 3.06
2761 9977 4.638865 TCAATGCAATCCTGAGTCAATCTG 59.361 41.667 0.00 0.00 0.00 2.90
2771 9987 5.013495 TCCTGAGTCAATCTGTCTTTCCATT 59.987 40.000 0.00 0.00 0.00 3.16
2800 10018 6.336842 AGGTTCTCATTTTTGTCATGAAGG 57.663 37.500 0.00 0.00 30.12 3.46
3111 11449 3.865446 ACCCATTTAGCACTACGTAACC 58.135 45.455 0.00 0.00 0.00 2.85
3143 11482 1.064979 AGCCCTTGTATTTGTACCGGG 60.065 52.381 6.32 0.00 34.62 5.73
8186 20350 4.662961 CCTCCGCACGTCACAGCA 62.663 66.667 0.00 0.00 0.00 4.41
8192 20356 2.029518 CACGTCACAGCAGCCAGA 59.970 61.111 0.00 0.00 0.00 3.86
8237 20419 2.351244 CCAGTCCGGTGCTCTGCTA 61.351 63.158 0.00 0.00 0.00 3.49
8350 20548 0.108615 CTCGCTGTCCGGTGATCTTT 60.109 55.000 0.00 0.00 37.59 2.52
8386 20584 0.179111 CCGAGTTCGCTGGCTTCATA 60.179 55.000 0.00 0.00 38.18 2.15
8388 20586 1.291132 GAGTTCGCTGGCTTCATACC 58.709 55.000 0.00 0.00 0.00 2.73
8574 20772 3.573598 CTGATCGTGCCTATGATGAGAC 58.426 50.000 0.00 0.00 36.12 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.140325 TCTTTCACAAAAGGAGCGGAT 57.860 42.857 0.00 0.00 41.88 4.18
6 7 2.631160 TCTTTCACAAAAGGAGCGGA 57.369 45.000 0.00 0.00 41.88 5.54
9 10 2.414691 GCCGATCTTTCACAAAAGGAGC 60.415 50.000 0.00 0.00 41.88 4.70
10 11 2.162408 GGCCGATCTTTCACAAAAGGAG 59.838 50.000 0.00 0.00 41.88 3.69
11 12 2.159382 GGCCGATCTTTCACAAAAGGA 58.841 47.619 0.00 0.00 41.88 3.36
13 14 1.535462 ACGGCCGATCTTTCACAAAAG 59.465 47.619 35.90 0.00 42.77 2.27
14 15 1.600023 ACGGCCGATCTTTCACAAAA 58.400 45.000 35.90 0.00 0.00 2.44
15 16 2.070783 GTACGGCCGATCTTTCACAAA 58.929 47.619 35.90 0.00 0.00 2.83
16 17 1.717194 GTACGGCCGATCTTTCACAA 58.283 50.000 35.90 0.18 0.00 3.33
17 18 0.457166 CGTACGGCCGATCTTTCACA 60.457 55.000 35.90 1.49 0.00 3.58
18 19 0.179156 TCGTACGGCCGATCTTTCAC 60.179 55.000 35.90 15.27 30.63 3.18
19 20 0.527113 TTCGTACGGCCGATCTTTCA 59.473 50.000 35.90 6.10 36.62 2.69
20 21 1.197910 CTTCGTACGGCCGATCTTTC 58.802 55.000 35.90 13.34 36.62 2.62
21 22 0.529378 ACTTCGTACGGCCGATCTTT 59.471 50.000 35.90 12.08 36.62 2.52
22 23 0.529378 AACTTCGTACGGCCGATCTT 59.471 50.000 35.90 12.54 36.62 2.40
25 26 1.140375 GGAACTTCGTACGGCCGAT 59.860 57.895 35.90 18.92 36.62 4.18
28 29 3.866356 GTGGAACTTCGTACGGCC 58.134 61.111 16.52 9.82 0.00 6.13
39 40 2.393271 CTCCTGATGTGGAGTGGAAC 57.607 55.000 2.62 0.00 46.33 3.62
46 47 0.615331 GACAAGGCTCCTGATGTGGA 59.385 55.000 0.00 0.00 34.52 4.02
48 49 1.678123 CCTGACAAGGCTCCTGATGTG 60.678 57.143 0.00 0.00 36.56 3.21
70 71 2.625790 GCCGAGAGATAGGTTGTCTGAT 59.374 50.000 0.00 0.00 0.00 2.90
74 75 0.739561 ACGCCGAGAGATAGGTTGTC 59.260 55.000 0.00 0.00 0.00 3.18
75 76 0.739561 GACGCCGAGAGATAGGTTGT 59.260 55.000 0.00 0.00 0.00 3.32
78 79 1.153208 ACGACGCCGAGAGATAGGT 60.153 57.895 0.00 0.00 39.50 3.08
95 96 2.450609 TCTAAAACTCCGCACTCCAC 57.549 50.000 0.00 0.00 0.00 4.02
101 102 3.682858 GCAGTAACATCTAAAACTCCGCA 59.317 43.478 0.00 0.00 0.00 5.69
102 103 3.063588 GGCAGTAACATCTAAAACTCCGC 59.936 47.826 0.00 0.00 0.00 5.54
119 120 2.208349 AGGTGAGGGAAGGGCAGT 59.792 61.111 0.00 0.00 0.00 4.40
142 143 0.822944 CAGACACCACATGCCCAACA 60.823 55.000 0.00 0.00 0.00 3.33
145 146 1.228215 CACAGACACCACATGCCCA 60.228 57.895 0.00 0.00 0.00 5.36
147 148 0.250467 ACTCACAGACACCACATGCC 60.250 55.000 0.00 0.00 0.00 4.40
155 156 0.239347 GCCATGCAACTCACAGACAC 59.761 55.000 0.00 0.00 0.00 3.67
200 202 1.943340 GAGAACATCGGGATTTGGAGC 59.057 52.381 0.00 0.00 0.00 4.70
211 213 3.669023 GCTCCTTTGCAAAGAGAACATCG 60.669 47.826 35.25 18.46 38.28 3.84
216 218 4.311816 CAAAGCTCCTTTGCAAAGAGAA 57.688 40.909 35.25 20.59 43.07 2.87
226 228 0.390492 GCAAGCCACAAAGCTCCTTT 59.610 50.000 0.00 0.00 44.11 3.11
232 234 3.633951 GCAAGCAAGCCACAAAGC 58.366 55.556 0.00 0.00 0.00 3.51
253 255 0.732880 CAGGTCTAGCAACGTCCACG 60.733 60.000 0.00 0.00 46.33 4.94
281 283 1.098712 TGGAGGCAAACAACCGACAC 61.099 55.000 0.00 0.00 0.00 3.67
282 284 0.817634 CTGGAGGCAAACAACCGACA 60.818 55.000 0.00 0.00 0.00 4.35
287 289 1.515521 CCCGTCTGGAGGCAAACAAC 61.516 60.000 0.00 0.00 37.49 3.32
291 293 2.528127 TCCCCGTCTGGAGGCAAA 60.528 61.111 0.00 0.00 37.49 3.68
300 302 0.107848 CTTATTTGGCGTCCCCGTCT 60.108 55.000 0.00 0.00 40.05 4.18
316 318 2.969262 CCTTCTTTTGGTTTGCCCCTTA 59.031 45.455 0.00 0.00 0.00 2.69
322 325 1.407618 ACCGACCTTCTTTTGGTTTGC 59.592 47.619 0.00 0.00 38.03 3.68
324 327 4.340097 CCTTTACCGACCTTCTTTTGGTTT 59.660 41.667 0.00 0.00 38.03 3.27
327 330 2.228103 GCCTTTACCGACCTTCTTTTGG 59.772 50.000 0.00 0.00 0.00 3.28
339 342 1.635663 CGCCACTCTTGCCTTTACCG 61.636 60.000 0.00 0.00 0.00 4.02
342 345 1.674322 GGCGCCACTCTTGCCTTTA 60.674 57.895 24.80 0.00 45.40 1.85
364 367 0.742990 GCAGCCACATACGCCTTGTA 60.743 55.000 0.00 0.00 37.49 2.41
365 368 2.040544 GCAGCCACATACGCCTTGT 61.041 57.895 0.00 0.00 0.00 3.16
374 377 1.064240 TCATCCATCAAGCAGCCACAT 60.064 47.619 0.00 0.00 0.00 3.21
433 436 0.178990 GCTCCTCCCAAACCACAACT 60.179 55.000 0.00 0.00 0.00 3.16
450 453 2.158900 CCTCAATACAAGACATCGGGCT 60.159 50.000 0.00 0.00 0.00 5.19
454 457 5.171476 AGAACACCTCAATACAAGACATCG 58.829 41.667 0.00 0.00 0.00 3.84
465 468 1.271379 CCCCGACAAGAACACCTCAAT 60.271 52.381 0.00 0.00 0.00 2.57
498 501 1.375523 CAACCCCGACACTGCTACC 60.376 63.158 0.00 0.00 0.00 3.18
505 508 2.109593 AACGACCAACCCCGACAC 59.890 61.111 0.00 0.00 0.00 3.67
521 524 4.484236 CAAACTCTTCAAGTGCACAACAA 58.516 39.130 21.04 6.90 38.58 2.83
533 4803 1.795170 GCGGCTTGCCAAACTCTTCA 61.795 55.000 12.45 0.00 37.76 3.02
641 4930 2.816777 AAGAAGGAGAGAATTGCCCC 57.183 50.000 0.00 0.00 0.00 5.80
711 5003 9.814899 TGTTCAACATTTGTTCTTCATAACAAT 57.185 25.926 3.26 0.00 45.91 2.71
757 5049 9.657419 TGATACATGATGCATATACCAAACTAG 57.343 33.333 0.00 0.00 0.00 2.57
833 5125 5.298276 GCGTCAATCAGGACCCAAATATTAA 59.702 40.000 0.00 0.00 34.24 1.40
834 5126 4.819630 GCGTCAATCAGGACCCAAATATTA 59.180 41.667 0.00 0.00 34.24 0.98
835 5127 3.632145 GCGTCAATCAGGACCCAAATATT 59.368 43.478 0.00 0.00 34.24 1.28
836 5128 3.117888 AGCGTCAATCAGGACCCAAATAT 60.118 43.478 0.00 0.00 34.24 1.28
846 5144 0.455633 GCAAAGCAGCGTCAATCAGG 60.456 55.000 0.00 0.00 0.00 3.86
852 5150 2.628696 CCATGGCAAAGCAGCGTCA 61.629 57.895 0.00 0.00 34.64 4.35
891 5196 4.142182 CCATCCAAATAACATTCAACGGCT 60.142 41.667 0.00 0.00 0.00 5.52
899 5204 3.992999 TCCCTGCCATCCAAATAACATT 58.007 40.909 0.00 0.00 0.00 2.71
952 5257 1.079405 TCAAATGGACTCGGGCGAC 60.079 57.895 0.00 0.00 0.00 5.19
953 5258 1.079405 GTCAAATGGACTCGGGCGA 60.079 57.895 0.00 0.00 43.46 5.54
954 5259 3.486263 GTCAAATGGACTCGGGCG 58.514 61.111 0.00 0.00 43.46 6.13
1546 8491 1.103803 GTCAGAGCCGAGGACATGTA 58.896 55.000 0.00 0.00 0.00 2.29
2165 9124 0.744414 GAATCTAGCCGGCACTTGCA 60.744 55.000 31.54 6.06 44.36 4.08
2800 10018 4.097892 ACGAATTTTGGGGCTTCATATCAC 59.902 41.667 0.00 0.00 0.00 3.06
3053 11386 5.878406 ATGCTACTAGCCAACTACTGAAT 57.122 39.130 5.58 0.00 41.51 2.57
3111 11449 7.759433 ACAAATACAAGGGCTTTTGAAATATCG 59.241 33.333 8.81 0.00 34.13 2.92
3143 11482 6.620678 ACCATACAAGCATCAATTTGTGTAC 58.379 36.000 0.00 0.00 37.98 2.90
8237 20419 1.475280 TCGATCACGAGACCCGAAATT 59.525 47.619 6.69 0.00 43.81 1.82
8350 20548 4.592942 ACTCGGTGTAGTTAGTACCATCA 58.407 43.478 0.00 0.00 34.10 3.07
8574 20772 2.017049 CCTCCTCATAAGCCAAAACCG 58.983 52.381 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.