Multiple sequence alignment - TraesCS7D01G369400

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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 TraesCS7D01G369400 chr7D 100.000 3195 0 0 1 3195 478326569 478329763 0.000000e+00 5901.0
1 TraesCS7D01G369400 chr7D 87.165 2088 154 69 351 2419 478573206 478571214 0.000000e+00 2266.0
2 TraesCS7D01G369400 chr7D 82.396 551 92 5 1636 2184 478333869 478334416 2.880000e-130 475.0
3 TraesCS7D01G369400 chr7D 80.446 404 65 10 1736 2132 478576435 478576831 2.410000e-76 296.0
4 TraesCS7D01G369400 chr7D 77.163 416 63 24 1115 1520 478370386 478370779 2.500000e-51 213.0
5 TraesCS7D01G369400 chr7D 87.363 182 15 3 2425 2599 478569922 478569742 5.400000e-48 202.0
6 TraesCS7D01G369400 chr7D 86.188 181 23 1 2090 2270 478532693 478532515 9.040000e-46 195.0
7 TraesCS7D01G369400 chr7D 86.179 123 12 2 187 309 478573328 478573211 9.300000e-26 128.0
8 TraesCS7D01G369400 chr7B 93.233 1936 103 13 1284 3194 503472836 503474768 0.000000e+00 2824.0
9 TraesCS7D01G369400 chr7B 87.404 1040 72 26 225 1253 503471782 503472773 0.000000e+00 1140.0
10 TraesCS7D01G369400 chr7B 91.317 714 45 12 1284 1990 504244361 504243658 0.000000e+00 959.0
11 TraesCS7D01G369400 chr7B 92.562 363 19 4 1986 2348 504237787 504237433 6.110000e-142 514.0
12 TraesCS7D01G369400 chr7B 84.969 479 36 22 400 865 504245210 504244755 1.350000e-123 453.0
13 TraesCS7D01G369400 chr7B 93.385 257 17 0 997 1253 504244681 504244425 6.470000e-102 381.0
14 TraesCS7D01G369400 chr7B 77.307 401 63 24 1131 1520 503506435 503506818 8.980000e-51 211.0
15 TraesCS7D01G369400 chr7B 88.652 141 12 2 2374 2513 375543304 375543441 5.480000e-38 169.0
16 TraesCS7D01G369400 chr7B 92.241 116 6 3 60 173 503471671 503471785 9.170000e-36 161.0
17 TraesCS7D01G369400 chr7B 90.741 108 7 1 202 309 504246247 504246143 1.190000e-29 141.0
18 TraesCS7D01G369400 chr7A 88.936 2142 117 45 246 2362 517415522 517413476 0.000000e+00 2532.0
19 TraesCS7D01G369400 chr7A 85.281 2439 212 95 193 2599 516998971 516996648 0.000000e+00 2379.0
20 TraesCS7D01G369400 chr7A 82.310 554 92 4 1635 2185 516989670 516989120 2.880000e-130 475.0
21 TraesCS7D01G369400 chr7A 80.000 510 76 22 1639 2132 670946630 670946131 1.410000e-93 353.0
22 TraesCS7D01G369400 chr7A 87.500 248 20 4 2351 2597 517413259 517413022 3.140000e-70 276.0
23 TraesCS7D01G369400 chr7A 83.732 209 26 6 2935 3140 516993607 516993404 1.170000e-44 191.0
24 TraesCS7D01G369400 chr7A 82.297 209 29 6 2935 3138 516995156 516994951 1.180000e-39 174.0
25 TraesCS7D01G369400 chr7A 78.571 238 35 9 2913 3140 517412717 517412486 3.320000e-30 143.0
26 TraesCS7D01G369400 chr6B 88.725 204 16 4 2311 2513 591329477 591329674 3.180000e-60 243.0
27 TraesCS7D01G369400 chr6B 84.925 199 28 2 1323 1520 173391986 173392183 1.940000e-47 200.0
28 TraesCS7D01G369400 chr6B 85.294 102 15 0 1123 1224 173391805 173391906 4.360000e-19 106.0
29 TraesCS7D01G369400 chr6B 88.235 51 4 2 2719 2768 152183717 152183668 3.440000e-05 60.2
30 TraesCS7D01G369400 chr4B 88.235 204 17 4 2311 2513 283206984 283207181 1.480000e-58 237.0
31 TraesCS7D01G369400 chr6D 84.848 198 30 0 1323 1520 90922940 90923137 1.940000e-47 200.0
32 TraesCS7D01G369400 chr6D 84.314 102 16 0 1123 1224 90922746 90922847 2.030000e-17 100.0
33 TraesCS7D01G369400 chr6A 84.848 198 30 0 1323 1520 109135962 109136159 1.940000e-47 200.0
34 TraesCS7D01G369400 chr6A 81.053 95 14 4 2588 2681 464426609 464426518 4.420000e-09 73.1
35 TraesCS7D01G369400 chr3A 83.417 199 31 2 1323 1520 113922265 113922068 1.960000e-42 183.0
36 TraesCS7D01G369400 chr5B 87.943 141 13 2 2374 2513 381102307 381102444 2.550000e-36 163.0
37 TraesCS7D01G369400 chr1A 91.228 57 3 1 3140 3194 478210251 478210307 3.420000e-10 76.8
38 TraesCS7D01G369400 chr1A 89.474 57 4 1 3140 3194 478211792 478211848 1.590000e-08 71.3
39 TraesCS7D01G369400 chr1B 89.130 46 4 1 2719 2764 123434426 123434382 4.450000e-04 56.5


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 TraesCS7D01G369400 chr7D 478326569 478329763 3194 False 5901.000000 5901 100.000000 1 3195 1 chr7D.!!$F1 3194
1 TraesCS7D01G369400 chr7D 478569742 478573328 3586 True 865.333333 2266 86.902333 187 2599 3 chr7D.!!$R2 2412
2 TraesCS7D01G369400 chr7D 478333869 478334416 547 False 475.000000 475 82.396000 1636 2184 1 chr7D.!!$F2 548
3 TraesCS7D01G369400 chr7B 503471671 503474768 3097 False 1375.000000 2824 90.959333 60 3194 3 chr7B.!!$F3 3134
4 TraesCS7D01G369400 chr7B 504243658 504246247 2589 True 483.500000 959 90.103000 202 1990 4 chr7B.!!$R2 1788
5 TraesCS7D01G369400 chr7A 517412486 517415522 3036 True 983.666667 2532 85.002333 246 3140 3 chr7A.!!$R3 2894
6 TraesCS7D01G369400 chr7A 516989120 516998971 9851 True 804.750000 2379 83.405000 193 3140 4 chr7A.!!$R2 2947

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
795 1748 0.036765 TCCGGCCATGAACTGTGTAC 60.037 55.0 2.24 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2577 5149 0.031721 GTCAACTATAGGCGGGTCGG 59.968 60.0 4.43 0.0 0.0 4.79 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 4.708177 AGCCAAATACTACCAGCTACATG 58.292 43.478 0.00 0.00 0.00 3.21
27 28 4.164221 AGCCAAATACTACCAGCTACATGT 59.836 41.667 2.69 2.69 0.00 3.21
28 29 5.365605 AGCCAAATACTACCAGCTACATGTA 59.634 40.000 5.25 5.25 0.00 2.29
29 30 6.043243 AGCCAAATACTACCAGCTACATGTAT 59.957 38.462 5.91 0.00 0.00 2.29
30 31 7.234782 AGCCAAATACTACCAGCTACATGTATA 59.765 37.037 5.91 0.00 0.00 1.47
31 32 7.331193 GCCAAATACTACCAGCTACATGTATAC 59.669 40.741 5.91 1.94 0.00 1.47
32 33 8.364894 CCAAATACTACCAGCTACATGTATACA 58.635 37.037 8.27 8.27 0.00 2.29
33 34 9.411801 CAAATACTACCAGCTACATGTATACAG 57.588 37.037 11.91 6.29 0.00 2.74
34 35 7.704578 ATACTACCAGCTACATGTATACAGG 57.295 40.000 15.66 15.66 0.00 4.00
35 36 4.833380 ACTACCAGCTACATGTATACAGGG 59.167 45.833 20.64 13.00 30.95 4.45
36 37 3.654273 ACCAGCTACATGTATACAGGGT 58.346 45.455 20.64 17.52 30.95 4.34
37 38 4.811498 ACCAGCTACATGTATACAGGGTA 58.189 43.478 20.64 17.68 30.95 3.69
38 39 4.833380 ACCAGCTACATGTATACAGGGTAG 59.167 45.833 27.33 27.33 39.07 3.18
40 41 4.189639 GCTACATGTATACAGGGTAGCC 57.810 50.000 35.06 25.70 46.55 3.93
41 42 3.576982 GCTACATGTATACAGGGTAGCCA 59.423 47.826 35.06 15.45 46.55 4.75
42 43 4.039973 GCTACATGTATACAGGGTAGCCAA 59.960 45.833 35.06 15.20 46.55 4.52
43 44 5.454187 GCTACATGTATACAGGGTAGCCAAA 60.454 44.000 35.06 14.71 46.55 3.28
44 45 5.646692 ACATGTATACAGGGTAGCCAAAT 57.353 39.130 20.64 5.88 30.95 2.32
45 46 6.757173 ACATGTATACAGGGTAGCCAAATA 57.243 37.500 20.64 4.89 30.95 1.40
46 47 6.531021 ACATGTATACAGGGTAGCCAAATAC 58.469 40.000 20.64 16.19 30.95 1.89
47 48 6.329197 ACATGTATACAGGGTAGCCAAATACT 59.671 38.462 20.64 5.47 30.95 2.12
48 49 7.511371 ACATGTATACAGGGTAGCCAAATACTA 59.489 37.037 20.64 8.64 30.95 1.82
49 50 7.294017 TGTATACAGGGTAGCCAAATACTAC 57.706 40.000 14.62 7.46 39.44 2.73
50 51 3.814005 ACAGGGTAGCCAAATACTACG 57.186 47.619 14.62 0.00 40.78 3.51
51 52 3.102204 ACAGGGTAGCCAAATACTACGT 58.898 45.455 14.62 0.00 40.78 3.57
52 53 4.280819 ACAGGGTAGCCAAATACTACGTA 58.719 43.478 14.62 0.00 40.78 3.57
53 54 4.098501 ACAGGGTAGCCAAATACTACGTAC 59.901 45.833 14.62 0.00 40.78 3.67
54 55 4.340381 CAGGGTAGCCAAATACTACGTACT 59.660 45.833 14.62 0.00 40.78 2.73
55 56 5.532406 CAGGGTAGCCAAATACTACGTACTA 59.468 44.000 14.62 0.00 40.78 1.82
56 57 5.532779 AGGGTAGCCAAATACTACGTACTAC 59.467 44.000 14.62 0.00 40.78 2.73
57 58 5.299279 GGGTAGCCAAATACTACGTACTACA 59.701 44.000 5.96 0.00 40.78 2.74
58 59 6.015940 GGGTAGCCAAATACTACGTACTACAT 60.016 42.308 5.96 0.00 40.78 2.29
63 64 7.500227 AGCCAAATACTACGTACTACATGTAGA 59.500 37.037 34.16 17.73 45.95 2.59
108 110 6.471233 TGTCCTATCTCCAGACTAATTGTG 57.529 41.667 0.00 0.00 0.00 3.33
169 171 4.033358 CGTCCTTACGTACAACTCTACGAT 59.967 45.833 5.79 0.00 44.21 3.73
170 172 5.497273 GTCCTTACGTACAACTCTACGATC 58.503 45.833 5.79 0.00 41.75 3.69
171 173 5.063944 GTCCTTACGTACAACTCTACGATCA 59.936 44.000 5.79 0.00 41.75 2.92
172 174 5.292834 TCCTTACGTACAACTCTACGATCAG 59.707 44.000 5.79 0.00 41.75 2.90
173 175 5.064452 CCTTACGTACAACTCTACGATCAGT 59.936 44.000 5.79 0.00 41.75 3.41
174 176 6.402983 CCTTACGTACAACTCTACGATCAGTT 60.403 42.308 5.79 0.00 41.75 3.16
175 177 5.368256 ACGTACAACTCTACGATCAGTTT 57.632 39.130 5.79 0.00 41.75 2.66
176 178 5.766222 ACGTACAACTCTACGATCAGTTTT 58.234 37.500 5.79 0.00 41.75 2.43
177 179 6.211515 ACGTACAACTCTACGATCAGTTTTT 58.788 36.000 5.79 0.00 41.75 1.94
178 180 6.361748 ACGTACAACTCTACGATCAGTTTTTC 59.638 38.462 5.79 0.00 41.75 2.29
179 181 6.581542 CGTACAACTCTACGATCAGTTTTTCT 59.418 38.462 0.00 0.00 41.75 2.52
180 182 7.114529 CGTACAACTCTACGATCAGTTTTTCTT 59.885 37.037 0.00 0.00 41.75 2.52
181 183 9.403110 GTACAACTCTACGATCAGTTTTTCTTA 57.597 33.333 0.00 0.00 30.06 2.10
182 184 8.522178 ACAACTCTACGATCAGTTTTTCTTAG 57.478 34.615 0.00 0.00 30.06 2.18
183 185 7.116519 ACAACTCTACGATCAGTTTTTCTTAGC 59.883 37.037 0.00 0.00 30.06 3.09
184 186 6.926313 ACTCTACGATCAGTTTTTCTTAGCT 58.074 36.000 0.00 0.00 0.00 3.32
185 187 8.053026 ACTCTACGATCAGTTTTTCTTAGCTA 57.947 34.615 0.00 0.00 0.00 3.32
191 193 7.117956 ACGATCAGTTTTTCTTAGCTAAACTCC 59.882 37.037 7.74 1.33 39.40 3.85
216 220 4.210746 CGATCAGTTGATGCTGGATTAGTG 59.789 45.833 0.00 0.00 37.12 2.74
217 221 3.877559 TCAGTTGATGCTGGATTAGTGG 58.122 45.455 0.00 0.00 37.12 4.00
218 222 3.264193 TCAGTTGATGCTGGATTAGTGGT 59.736 43.478 0.00 0.00 37.12 4.16
262 266 2.191513 CGATTCATGGGCCAGCCTG 61.192 63.158 13.78 5.71 36.10 4.85
303 307 6.626623 GCTTCAAACTGTGAGATGGCAATAAT 60.627 38.462 0.00 0.00 37.61 1.28
311 315 9.881649 ACTGTGAGATGGCAATAATATATACAG 57.118 33.333 0.00 0.00 36.35 2.74
312 316 9.881649 CTGTGAGATGGCAATAATATATACAGT 57.118 33.333 0.00 0.00 0.00 3.55
433 1332 1.960763 CTAGCAACAGCACGCACCA 60.961 57.895 0.00 0.00 0.00 4.17
481 1384 1.741770 AGCAACATTCGGTCCTCGC 60.742 57.895 0.00 0.00 39.05 5.03
515 1419 1.402720 CGAAATTTCCACCAATGCGCT 60.403 47.619 9.73 0.00 0.00 5.92
528 1432 2.202676 GCGCTGACTCGGAGGAAG 60.203 66.667 10.23 7.34 0.00 3.46
529 1433 2.701780 GCGCTGACTCGGAGGAAGA 61.702 63.158 10.23 0.00 0.00 2.87
530 1434 1.431440 CGCTGACTCGGAGGAAGAG 59.569 63.158 10.23 4.45 41.27 2.85
531 1435 1.813192 GCTGACTCGGAGGAAGAGG 59.187 63.158 10.23 0.00 39.90 3.69
532 1436 0.681564 GCTGACTCGGAGGAAGAGGA 60.682 60.000 10.23 0.00 39.90 3.71
533 1437 1.840737 CTGACTCGGAGGAAGAGGAA 58.159 55.000 10.23 0.00 39.90 3.36
570 1480 0.394762 ACAGCCTATACCCGTGACGA 60.395 55.000 6.54 0.00 0.00 4.20
741 1692 2.031616 CCATGCCGGAGCGATCAT 59.968 61.111 5.05 0.00 44.31 2.45
764 1715 1.200948 GTCAACCAAATCCAGCTGCTC 59.799 52.381 8.66 0.00 0.00 4.26
790 1743 0.742281 CAGAGTCCGGCCATGAACTG 60.742 60.000 2.24 8.22 0.00 3.16
795 1748 0.036765 TCCGGCCATGAACTGTGTAC 60.037 55.000 2.24 0.00 0.00 2.90
934 1913 1.302033 GCCACCCTATGCATCTCGG 60.302 63.158 0.19 3.53 0.00 4.63
955 1943 0.248784 TCATCGAGCTCGCATCACAG 60.249 55.000 30.97 14.12 39.60 3.66
967 1955 3.067320 TCGCATCACAGGAGTTATCTCTG 59.933 47.826 0.97 0.00 40.29 3.35
1057 2046 3.898627 CTCGCCGTCGTGCTCTGTT 62.899 63.158 4.57 0.00 36.96 3.16
1254 2243 2.557056 CACCGTTCCTCTCTACTGTTGA 59.443 50.000 0.00 0.00 0.00 3.18
1258 2247 4.322049 CCGTTCCTCTCTACTGTTGATTGT 60.322 45.833 0.00 0.00 0.00 2.71
1259 2248 4.623167 CGTTCCTCTCTACTGTTGATTGTG 59.377 45.833 0.00 0.00 0.00 3.33
1262 2251 6.174720 TCCTCTCTACTGTTGATTGTGTTT 57.825 37.500 0.00 0.00 0.00 2.83
1263 2252 5.991606 TCCTCTCTACTGTTGATTGTGTTTG 59.008 40.000 0.00 0.00 0.00 2.93
1266 2279 7.246674 TCTCTACTGTTGATTGTGTTTGTTC 57.753 36.000 0.00 0.00 0.00 3.18
1272 2285 6.039717 ACTGTTGATTGTGTTTGTTCTGCTAT 59.960 34.615 0.00 0.00 0.00 2.97
1273 2286 6.207928 TGTTGATTGTGTTTGTTCTGCTATG 58.792 36.000 0.00 0.00 0.00 2.23
1277 2290 6.484977 TGATTGTGTTTGTTCTGCTATGTGTA 59.515 34.615 0.00 0.00 0.00 2.90
1278 2291 6.875948 TTGTGTTTGTTCTGCTATGTGTAT 57.124 33.333 0.00 0.00 0.00 2.29
1279 2292 6.480524 TGTGTTTGTTCTGCTATGTGTATC 57.519 37.500 0.00 0.00 0.00 2.24
1281 2294 6.484977 TGTGTTTGTTCTGCTATGTGTATCAA 59.515 34.615 0.00 0.00 0.00 2.57
1282 2295 7.012799 TGTGTTTGTTCTGCTATGTGTATCAAA 59.987 33.333 0.00 0.00 0.00 2.69
1286 2313 7.075674 TGTTCTGCTATGTGTATCAAATGTG 57.924 36.000 0.00 0.00 0.00 3.21
1291 2318 5.295045 TGCTATGTGTATCAAATGTGCTGAG 59.705 40.000 0.00 0.00 0.00 3.35
1298 2325 6.801862 GTGTATCAAATGTGCTGAGGTTTAAC 59.198 38.462 0.00 0.00 0.00 2.01
1595 2626 5.840940 ACTACACGTTCTGCACTTATTTC 57.159 39.130 0.00 0.00 0.00 2.17
1602 2634 4.143030 CGTTCTGCACTTATTTCACTGGAG 60.143 45.833 0.00 0.00 0.00 3.86
2206 3247 5.747342 AGACCCAACTAAAAAGTACACACA 58.253 37.500 0.00 0.00 0.00 3.72
2385 3663 6.474819 TGTTGGTCGTAAAAGTGTATCATG 57.525 37.500 0.00 0.00 0.00 3.07
2640 5214 7.848223 GCATGAGTGTGCATACCATATATTA 57.152 36.000 10.29 0.00 44.43 0.98
2680 5254 5.784578 AAGCCCCTACAAAAGTTTACAAG 57.215 39.130 0.00 0.00 0.00 3.16
2697 5271 1.267806 CAAGCACTCCACATTGACCAC 59.732 52.381 0.00 0.00 0.00 4.16
2698 5272 0.250901 AGCACTCCACATTGACCACC 60.251 55.000 0.00 0.00 0.00 4.61
2711 5285 1.422402 TGACCACCCTCCACCTAAAAC 59.578 52.381 0.00 0.00 0.00 2.43
2725 5299 5.280521 CCACCTAAAACCACATTCTACTCCT 60.281 44.000 0.00 0.00 0.00 3.69
2728 5302 5.875359 CCTAAAACCACATTCTACTCCTCAC 59.125 44.000 0.00 0.00 0.00 3.51
2741 5315 1.682684 CCTCACTACTCGCCCACCT 60.683 63.158 0.00 0.00 0.00 4.00
2748 5322 0.622136 TACTCGCCCACCTCTCTACA 59.378 55.000 0.00 0.00 0.00 2.74
2752 5326 0.739561 CGCCCACCTCTCTACACTAC 59.260 60.000 0.00 0.00 0.00 2.73
2753 5327 1.682394 CGCCCACCTCTCTACACTACT 60.682 57.143 0.00 0.00 0.00 2.57
2759 5333 4.385865 CCACCTCTCTACACTACTGAGGAT 60.386 50.000 13.42 0.00 45.07 3.24
2800 5383 9.276590 CTTTGATAGCATAAATGTCTATGACCA 57.723 33.333 9.93 3.06 31.94 4.02
2885 5815 1.680651 CTGAGTGGAGGAGGCTCGT 60.681 63.158 9.87 9.87 32.32 4.18
3162 8626 0.586319 AGAACAATGTCCGTGCGTTG 59.414 50.000 6.80 6.80 40.24 4.10
3166 8630 0.998226 CAATGTCCGTGCGTTGCAAG 60.998 55.000 0.00 0.00 41.47 4.01
3184 10903 9.256477 CGTTGCAAGGATATAAATGTTCTAGTA 57.744 33.333 13.85 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 5.365605 ACATGTAGCTGGTAGTATTTGGCTA 59.634 40.000 0.00 0.00 0.00 3.93
4 5 4.164221 ACATGTAGCTGGTAGTATTTGGCT 59.836 41.667 0.00 0.00 0.00 4.75
5 6 4.451900 ACATGTAGCTGGTAGTATTTGGC 58.548 43.478 0.00 0.00 0.00 4.52
6 7 8.364894 TGTATACATGTAGCTGGTAGTATTTGG 58.635 37.037 11.91 0.00 0.00 3.28
7 8 9.411801 CTGTATACATGTAGCTGGTAGTATTTG 57.588 37.037 11.91 0.00 0.00 2.32
8 9 8.585881 CCTGTATACATGTAGCTGGTAGTATTT 58.414 37.037 11.91 0.00 0.00 1.40
9 10 7.178628 CCCTGTATACATGTAGCTGGTAGTATT 59.821 40.741 22.61 4.66 0.00 1.89
10 11 6.663953 CCCTGTATACATGTAGCTGGTAGTAT 59.336 42.308 22.61 2.83 0.00 2.12
11 12 6.008331 CCCTGTATACATGTAGCTGGTAGTA 58.992 44.000 22.61 5.40 0.00 1.82
12 13 4.833380 CCCTGTATACATGTAGCTGGTAGT 59.167 45.833 22.61 6.16 0.00 2.73
13 14 4.833380 ACCCTGTATACATGTAGCTGGTAG 59.167 45.833 22.61 15.76 0.00 3.18
14 15 4.811498 ACCCTGTATACATGTAGCTGGTA 58.189 43.478 22.61 7.05 0.00 3.25
15 16 3.654273 ACCCTGTATACATGTAGCTGGT 58.346 45.455 22.61 18.24 0.00 4.00
16 17 4.322049 GCTACCCTGTATACATGTAGCTGG 60.322 50.000 33.89 21.00 44.67 4.85
17 18 4.322049 GGCTACCCTGTATACATGTAGCTG 60.322 50.000 36.16 20.38 45.87 4.24
18 19 3.833070 GGCTACCCTGTATACATGTAGCT 59.167 47.826 36.16 14.40 45.87 3.32
19 20 3.576982 TGGCTACCCTGTATACATGTAGC 59.423 47.826 33.71 33.71 45.87 3.58
20 21 5.801531 TTGGCTACCCTGTATACATGTAG 57.198 43.478 24.72 24.72 35.73 2.74
21 22 6.757173 ATTTGGCTACCCTGTATACATGTA 57.243 37.500 8.27 8.27 0.00 2.29
22 23 5.646692 ATTTGGCTACCCTGTATACATGT 57.353 39.130 5.91 2.69 0.00 3.21
23 24 6.769512 AGTATTTGGCTACCCTGTATACATG 58.230 40.000 5.91 3.42 0.00 3.21
24 25 7.309621 CGTAGTATTTGGCTACCCTGTATACAT 60.310 40.741 5.91 0.00 36.40 2.29
25 26 6.016024 CGTAGTATTTGGCTACCCTGTATACA 60.016 42.308 5.25 5.25 36.40 2.29
26 27 6.015940 ACGTAGTATTTGGCTACCCTGTATAC 60.016 42.308 0.00 0.00 41.94 1.47
27 28 6.070656 ACGTAGTATTTGGCTACCCTGTATA 58.929 40.000 0.00 0.00 41.94 1.47
28 29 4.897670 ACGTAGTATTTGGCTACCCTGTAT 59.102 41.667 0.00 0.00 41.94 2.29
29 30 4.280819 ACGTAGTATTTGGCTACCCTGTA 58.719 43.478 0.00 0.00 41.94 2.74
30 31 3.102204 ACGTAGTATTTGGCTACCCTGT 58.898 45.455 0.00 0.00 41.94 4.00
31 32 3.814005 ACGTAGTATTTGGCTACCCTG 57.186 47.619 0.00 0.00 41.94 4.45
45 46 9.388506 AGTATTTGTCTACATGTAGTACGTAGT 57.611 33.333 27.83 16.44 36.84 2.73
48 49 9.166173 TGTAGTATTTGTCTACATGTAGTACGT 57.834 33.333 27.83 15.72 41.52 3.57
74 75 6.956435 TCTGGAGATAGGACAATACTATGCAT 59.044 38.462 3.79 3.79 31.58 3.96
75 76 6.209589 GTCTGGAGATAGGACAATACTATGCA 59.790 42.308 0.00 0.00 31.58 3.96
76 77 6.435904 AGTCTGGAGATAGGACAATACTATGC 59.564 42.308 0.00 0.00 31.58 3.14
77 78 9.521841 TTAGTCTGGAGATAGGACAATACTATG 57.478 37.037 0.00 0.00 31.58 2.23
80 81 8.865090 CAATTAGTCTGGAGATAGGACAATACT 58.135 37.037 0.00 0.00 32.98 2.12
81 82 8.643324 ACAATTAGTCTGGAGATAGGACAATAC 58.357 37.037 0.00 0.00 32.98 1.89
108 110 1.645034 CATGTGGATGTCGAGGTCAC 58.355 55.000 0.00 0.00 0.00 3.67
148 150 5.178061 TGATCGTAGAGTTGTACGTAAGGA 58.822 41.667 0.00 0.00 44.94 3.36
169 171 6.202188 CGTGGAGTTTAGCTAAGAAAAACTGA 59.798 38.462 14.69 1.14 42.06 3.41
170 172 6.202188 TCGTGGAGTTTAGCTAAGAAAAACTG 59.798 38.462 14.69 3.00 42.06 3.16
171 173 6.285990 TCGTGGAGTTTAGCTAAGAAAAACT 58.714 36.000 10.60 10.60 44.05 2.66
172 174 6.535274 TCGTGGAGTTTAGCTAAGAAAAAC 57.465 37.500 6.24 3.63 34.13 2.43
173 175 6.932400 TGATCGTGGAGTTTAGCTAAGAAAAA 59.068 34.615 6.24 0.00 0.00 1.94
174 176 6.460781 TGATCGTGGAGTTTAGCTAAGAAAA 58.539 36.000 6.24 0.00 0.00 2.29
175 177 6.032956 TGATCGTGGAGTTTAGCTAAGAAA 57.967 37.500 6.24 0.00 0.00 2.52
176 178 5.185249 ACTGATCGTGGAGTTTAGCTAAGAA 59.815 40.000 6.24 0.00 0.00 2.52
177 179 4.705507 ACTGATCGTGGAGTTTAGCTAAGA 59.294 41.667 6.24 0.00 0.00 2.10
178 180 5.000012 ACTGATCGTGGAGTTTAGCTAAG 58.000 43.478 6.24 0.00 0.00 2.18
179 181 5.047590 TCAACTGATCGTGGAGTTTAGCTAA 60.048 40.000 0.86 0.86 29.73 3.09
180 182 4.461431 TCAACTGATCGTGGAGTTTAGCTA 59.539 41.667 0.00 0.00 29.73 3.32
181 183 3.258372 TCAACTGATCGTGGAGTTTAGCT 59.742 43.478 0.00 0.00 29.73 3.32
182 184 3.585862 TCAACTGATCGTGGAGTTTAGC 58.414 45.455 0.00 0.00 29.73 3.09
183 185 4.033358 GCATCAACTGATCGTGGAGTTTAG 59.967 45.833 0.00 0.00 29.73 1.85
184 186 3.932710 GCATCAACTGATCGTGGAGTTTA 59.067 43.478 0.00 0.00 29.73 2.01
185 187 2.744202 GCATCAACTGATCGTGGAGTTT 59.256 45.455 0.00 0.00 29.73 2.66
191 193 2.014335 TCCAGCATCAACTGATCGTG 57.986 50.000 0.00 0.00 40.25 4.35
216 220 1.005450 TGGGCCAATCTGAAAGGTACC 59.995 52.381 2.13 2.73 0.00 3.34
217 221 2.507407 TGGGCCAATCTGAAAGGTAC 57.493 50.000 2.13 0.00 0.00 3.34
218 222 3.631250 GATTGGGCCAATCTGAAAGGTA 58.369 45.455 39.52 10.15 44.60 3.08
244 248 2.191513 CAGGCTGGCCCATGAATCG 61.192 63.158 6.61 0.00 36.58 3.34
308 312 6.662865 AGCAGCACTCATTCTATATACTGT 57.337 37.500 0.00 0.00 0.00 3.55
309 313 7.116090 GTCAAGCAGCACTCATTCTATATACTG 59.884 40.741 0.00 0.00 0.00 2.74
310 314 7.015098 AGTCAAGCAGCACTCATTCTATATACT 59.985 37.037 0.00 0.00 0.00 2.12
311 315 7.151308 AGTCAAGCAGCACTCATTCTATATAC 58.849 38.462 0.00 0.00 0.00 1.47
312 316 7.295322 AGTCAAGCAGCACTCATTCTATATA 57.705 36.000 0.00 0.00 0.00 0.86
313 317 6.172136 AGTCAAGCAGCACTCATTCTATAT 57.828 37.500 0.00 0.00 0.00 0.86
314 318 5.595885 GAGTCAAGCAGCACTCATTCTATA 58.404 41.667 6.51 0.00 39.17 1.31
315 319 4.440880 GAGTCAAGCAGCACTCATTCTAT 58.559 43.478 6.51 0.00 39.17 1.98
349 354 1.718396 TCAATCAGAAGCAGCACTCG 58.282 50.000 0.00 0.00 0.00 4.18
415 1314 1.300971 ATGGTGCGTGCTGTTGCTAG 61.301 55.000 0.00 0.00 40.48 3.42
433 1332 2.290287 TGCCGTACTGCTCCACCAT 61.290 57.895 10.75 0.00 0.00 3.55
515 1419 2.379972 GATTCCTCTTCCTCCGAGTCA 58.620 52.381 0.00 0.00 0.00 3.41
528 1432 2.794028 GGGTCGGTCCGGATTCCTC 61.794 68.421 7.81 1.05 37.00 3.71
529 1433 2.762875 GGGTCGGTCCGGATTCCT 60.763 66.667 7.81 0.00 37.00 3.36
530 1434 2.440817 ATGGGTCGGTCCGGATTCC 61.441 63.158 7.81 3.73 37.00 3.01
531 1435 1.227556 CATGGGTCGGTCCGGATTC 60.228 63.158 7.81 2.02 37.00 2.52
532 1436 2.908015 CATGGGTCGGTCCGGATT 59.092 61.111 7.81 0.00 37.00 3.01
533 1437 3.861797 GCATGGGTCGGTCCGGAT 61.862 66.667 7.81 0.00 37.00 4.18
570 1480 0.179073 AGAGACGTGTTTGCTGTGCT 60.179 50.000 0.00 0.00 0.00 4.40
578 1488 0.249489 AAGAGCGCAGAGACGTGTTT 60.249 50.000 11.47 0.00 34.88 2.83
688 1635 3.243002 ACGACGCTAACTGCTAGTAATCC 60.243 47.826 0.00 0.00 40.11 3.01
694 1641 1.140407 GGCACGACGCTAACTGCTAG 61.140 60.000 7.24 0.00 41.91 3.42
790 1743 5.450385 CACGTACTACGAAATGCTAGTACAC 59.550 44.000 15.49 0.00 46.05 2.90
795 1748 2.462927 CGCACGTACTACGAAATGCTAG 59.537 50.000 15.49 0.53 46.05 3.42
869 1848 3.449227 TGGACGCTGACCGCCTAG 61.449 66.667 0.00 0.00 41.76 3.02
870 1849 3.755628 GTGGACGCTGACCGCCTA 61.756 66.667 0.00 0.00 41.76 3.93
955 1943 3.003897 CGTGACTAGCCAGAGATAACTCC 59.996 52.174 0.00 0.00 43.53 3.85
967 1955 0.457853 TTGATGCGACGTGACTAGCC 60.458 55.000 0.00 0.00 0.00 3.93
1153 2142 3.869272 CTCCGTCTGCAATGCGGC 61.869 66.667 9.59 3.84 44.58 6.53
1158 2147 2.185350 CGCCTCTCCGTCTGCAAT 59.815 61.111 0.00 0.00 0.00 3.56
1254 2243 5.772825 ACACATAGCAGAACAAACACAAT 57.227 34.783 0.00 0.00 0.00 2.71
1258 2247 7.503521 TTTGATACACATAGCAGAACAAACA 57.496 32.000 0.00 0.00 0.00 2.83
1259 2248 8.023128 ACATTTGATACACATAGCAGAACAAAC 58.977 33.333 0.00 0.00 0.00 2.93
1262 2251 6.403527 GCACATTTGATACACATAGCAGAACA 60.404 38.462 0.00 0.00 0.00 3.18
1263 2252 5.967674 GCACATTTGATACACATAGCAGAAC 59.032 40.000 0.00 0.00 0.00 3.01
1266 2279 5.295045 TCAGCACATTTGATACACATAGCAG 59.705 40.000 0.00 0.00 0.00 4.24
1272 2285 4.019792 ACCTCAGCACATTTGATACACA 57.980 40.909 0.00 0.00 0.00 3.72
1273 2286 5.376854 AAACCTCAGCACATTTGATACAC 57.623 39.130 0.00 0.00 0.00 2.90
1277 2290 5.536161 ACAGTTAAACCTCAGCACATTTGAT 59.464 36.000 0.00 0.00 0.00 2.57
1278 2291 4.887071 ACAGTTAAACCTCAGCACATTTGA 59.113 37.500 0.00 0.00 0.00 2.69
1279 2292 4.977963 CACAGTTAAACCTCAGCACATTTG 59.022 41.667 0.00 0.00 0.00 2.32
1281 2294 4.207165 ACACAGTTAAACCTCAGCACATT 58.793 39.130 0.00 0.00 0.00 2.71
1282 2295 3.820557 ACACAGTTAAACCTCAGCACAT 58.179 40.909 0.00 0.00 0.00 3.21
1286 2313 4.632538 ACAAACACAGTTAAACCTCAGC 57.367 40.909 0.00 0.00 0.00 4.26
1291 2318 4.993905 AGCAGAACAAACACAGTTAAACC 58.006 39.130 0.00 0.00 0.00 3.27
1298 2325 5.220472 CCGATACATAGCAGAACAAACACAG 60.220 44.000 0.00 0.00 0.00 3.66
1406 2433 1.810030 GATCACCTCGAACCCACGC 60.810 63.158 0.00 0.00 0.00 5.34
1566 2593 4.511734 GTGCAGAACGTGTAGTTTTGTAC 58.488 43.478 6.91 6.91 46.69 2.90
1828 2868 1.294659 GGAAGAACTGGCACTGCGAG 61.295 60.000 11.21 11.21 40.17 5.03
2362 3640 6.224584 TCATGATACACTTTTACGACCAACA 58.775 36.000 0.00 0.00 0.00 3.33
2385 3663 9.827411 CATTGTTCTGTATTGATGATGATGATC 57.173 33.333 0.00 0.00 0.00 2.92
2449 5013 5.179368 CCACCGTACATTAGGCATTAGATTG 59.821 44.000 0.00 0.00 0.00 2.67
2577 5149 0.031721 GTCAACTATAGGCGGGTCGG 59.968 60.000 4.43 0.00 0.00 4.79
2619 5193 8.655901 TCCTTTAATATATGGTATGCACACTCA 58.344 33.333 0.00 0.00 0.00 3.41
2638 5212 6.040504 GGGCTTTCTTTGTCTTTCTCCTTTAA 59.959 38.462 0.00 0.00 0.00 1.52
2640 5214 4.342378 GGGCTTTCTTTGTCTTTCTCCTTT 59.658 41.667 0.00 0.00 0.00 3.11
2643 5217 2.558795 GGGGCTTTCTTTGTCTTTCTCC 59.441 50.000 0.00 0.00 0.00 3.71
2652 5226 4.937201 ACTTTTGTAGGGGCTTTCTTTG 57.063 40.909 0.00 0.00 0.00 2.77
2660 5234 3.319689 TGCTTGTAAACTTTTGTAGGGGC 59.680 43.478 0.00 0.00 0.00 5.80
2680 5254 1.244019 GGGTGGTCAATGTGGAGTGC 61.244 60.000 0.00 0.00 0.00 4.40
2697 5271 2.899303 ATGTGGTTTTAGGTGGAGGG 57.101 50.000 0.00 0.00 0.00 4.30
2698 5272 4.034285 AGAATGTGGTTTTAGGTGGAGG 57.966 45.455 0.00 0.00 0.00 4.30
2711 5285 4.035792 CGAGTAGTGAGGAGTAGAATGTGG 59.964 50.000 0.00 0.00 0.00 4.17
2725 5299 0.680280 GAGAGGTGGGCGAGTAGTGA 60.680 60.000 0.00 0.00 0.00 3.41
2728 5302 1.310904 GTAGAGAGGTGGGCGAGTAG 58.689 60.000 0.00 0.00 0.00 2.57
2741 5315 4.976442 ACCCTATCCTCAGTAGTGTAGAGA 59.024 45.833 0.00 0.00 0.00 3.10
2748 5322 6.684538 ACAAATAGACCCTATCCTCAGTAGT 58.315 40.000 0.00 0.00 0.00 2.73
2752 5326 5.151454 AGGACAAATAGACCCTATCCTCAG 58.849 45.833 0.00 0.00 28.75 3.35
2753 5327 5.157770 AGGACAAATAGACCCTATCCTCA 57.842 43.478 0.00 0.00 28.75 3.86
2759 5333 6.385759 TGCTATCAAAGGACAAATAGACCCTA 59.614 38.462 0.00 0.00 31.96 3.53
2800 5383 1.069765 CACCTGCCAGTCTGTCGTT 59.930 57.895 0.00 0.00 0.00 3.85
2857 5448 3.561143 TCCTCCACTCAGAGAGCTTATC 58.439 50.000 3.79 0.00 35.82 1.75
2885 5815 2.324330 CCGCGTTGACATGCTCCAA 61.324 57.895 4.92 0.00 32.03 3.53
3075 8536 4.161189 CCATACATTTGGCCCATTAACACA 59.839 41.667 0.00 0.00 0.00 3.72
3141 8605 1.425412 ACGCACGGACATTGTTCTAC 58.575 50.000 0.00 0.00 0.00 2.59
3162 8626 8.813643 ACGTACTAGAACATTTATATCCTTGC 57.186 34.615 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.