Multiple sequence alignment - TraesCS4D01G204700

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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 TraesCS4D01G204700 chr4D 100.000 3580 0 0 1 3580 352129492 352133071 0.000000e+00 6612
1 TraesCS4D01G204700 chr4A 90.282 2943 139 56 306 3184 113318965 113316106 0.000000e+00 3714
2 TraesCS4D01G204700 chr4A 92.143 420 16 4 3177 3580 113312732 113312314 8.620000e-161 577
3 TraesCS4D01G204700 chr4A 89.123 285 13 8 1 270 113319650 113319369 4.430000e-89 339
4 TraesCS4D01G204700 chr4B 84.575 2282 154 92 708 2874 435436012 435433814 0.000000e+00 2082
5 TraesCS4D01G204700 chr4B 82.872 578 37 38 1 543 435436724 435436174 2.520000e-126 462


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 TraesCS4D01G204700 chr4D 352129492 352133071 3579 False 6612.000000 6612 100.0000 1 3580 1 chr4D.!!$F1 3579
1 TraesCS4D01G204700 chr4A 113312314 113319650 7336 True 1543.333333 3714 90.5160 1 3580 3 chr4A.!!$R1 3579
2 TraesCS4D01G204700 chr4B 435433814 435436724 2910 True 1272.000000 2082 83.7235 1 2874 2 chr4B.!!$R1 2873

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
675 1139 0.094216 CATTGCAGAGCGACGTTGAG 59.906 55.0 7.08 0.0 0.00 3.02 F
1211 1724 0.038744 CAAACCTGTCTGGGCTCCAT 59.961 55.0 0.33 0.0 41.11 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2235 2829 0.036164 TCACCTGGATTTGGTCGTGG 59.964 55.0 0.00 0.00 35.28 4.94 R
2693 3301 0.454600 TAGGCTTCTACTTCGGCGTG 59.545 55.0 6.85 3.77 0.00 5.34 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
89 93 5.638596 TCTCGTTTTCTAGCACTACATGA 57.361 39.130 0.00 0.00 0.00 3.07
90 94 5.399858 TCTCGTTTTCTAGCACTACATGAC 58.600 41.667 0.00 0.00 0.00 3.06
92 96 5.720202 TCGTTTTCTAGCACTACATGACAT 58.280 37.500 0.00 0.00 0.00 3.06
137 150 6.804295 GCTCGGTAACAGTAGATGATAGAATG 59.196 42.308 0.00 0.00 0.00 2.67
205 221 1.687563 TGAGCCAATCATCATGCCAG 58.312 50.000 0.00 0.00 31.12 4.85
206 222 1.064240 TGAGCCAATCATCATGCCAGT 60.064 47.619 0.00 0.00 31.12 4.00
207 223 2.173143 TGAGCCAATCATCATGCCAGTA 59.827 45.455 0.00 0.00 31.12 2.74
248 264 6.628856 GCGTGTAATAAGTCAATGCATGTTAG 59.371 38.462 0.00 0.00 0.00 2.34
259 278 6.017934 GTCAATGCATGTTAGTAGTATGTGGG 60.018 42.308 0.00 0.00 0.00 4.61
261 280 5.429681 TGCATGTTAGTAGTATGTGGGTT 57.570 39.130 0.00 0.00 0.00 4.11
262 281 5.182487 TGCATGTTAGTAGTATGTGGGTTG 58.818 41.667 0.00 0.00 0.00 3.77
263 282 5.046231 TGCATGTTAGTAGTATGTGGGTTGA 60.046 40.000 0.00 0.00 0.00 3.18
264 283 5.878116 GCATGTTAGTAGTATGTGGGTTGAA 59.122 40.000 0.00 0.00 0.00 2.69
265 284 6.183360 GCATGTTAGTAGTATGTGGGTTGAAC 60.183 42.308 0.00 0.00 0.00 3.18
266 285 5.472148 TGTTAGTAGTATGTGGGTTGAACG 58.528 41.667 0.00 0.00 0.00 3.95
267 286 3.604875 AGTAGTATGTGGGTTGAACGG 57.395 47.619 0.00 0.00 0.00 4.44
268 287 2.004733 GTAGTATGTGGGTTGAACGGC 58.995 52.381 0.00 0.00 0.00 5.68
269 288 0.322187 AGTATGTGGGTTGAACGGCC 60.322 55.000 0.00 0.00 0.00 6.13
270 289 0.606944 GTATGTGGGTTGAACGGCCA 60.607 55.000 2.24 0.00 0.00 5.36
367 764 1.987807 ATGGCCTTCTCCATCCCGTG 61.988 60.000 3.32 0.00 43.00 4.94
376 773 2.660206 CATCCCGTGTTCCCGTGA 59.340 61.111 0.00 0.00 0.00 4.35
431 830 4.854399 TCTCACGTGTTTATTTTGGCAAG 58.146 39.130 16.51 0.35 0.00 4.01
438 837 5.615106 CGTGTTTATTTTGGCAAGCTACGTA 60.615 40.000 0.00 0.00 0.00 3.57
452 851 5.275067 AGCTACGTACTACTACTACTGCT 57.725 43.478 0.00 0.00 0.00 4.24
454 853 4.318689 GCTACGTACTACTACTACTGCTGC 60.319 50.000 0.00 0.00 0.00 5.25
506 925 1.168714 CGAAGAGGGGAAGGCAAAAG 58.831 55.000 0.00 0.00 0.00 2.27
523 944 4.489810 CAAAAGCAACCCACGCATTTATA 58.510 39.130 0.00 0.00 29.87 0.98
541 966 5.909621 TTATATATAGGTGCACCTCGGAC 57.090 43.478 41.00 11.32 44.77 4.79
552 977 4.097589 GTGCACCTCGGACTACTACTTAAT 59.902 45.833 5.22 0.00 32.16 1.40
569 994 6.290294 ACTTAATTAGCGGAGTAGTTGGAA 57.710 37.500 0.00 0.00 0.00 3.53
576 1001 2.673368 GCGGAGTAGTTGGAATGAACTG 59.327 50.000 0.00 0.00 36.80 3.16
577 1002 2.673368 CGGAGTAGTTGGAATGAACTGC 59.327 50.000 0.00 0.00 38.46 4.40
607 1050 2.099098 CGGCTTCTCTCCTCTTCTCTTC 59.901 54.545 0.00 0.00 0.00 2.87
610 1053 3.381590 GCTTCTCTCCTCTTCTCTTCTCC 59.618 52.174 0.00 0.00 0.00 3.71
616 1080 4.785914 TCTCCTCTTCTCTTCTCCTCTACA 59.214 45.833 0.00 0.00 0.00 2.74
647 1111 3.336138 ACGGTTTCATCCTTCTTCCTC 57.664 47.619 0.00 0.00 0.00 3.71
662 1126 0.986527 TCCTCTCCTTCTGCATTGCA 59.013 50.000 11.50 11.50 36.92 4.08
671 1135 2.357396 TGCATTGCAGAGCGACGT 60.357 55.556 7.38 0.00 33.32 4.34
675 1139 0.094216 CATTGCAGAGCGACGTTGAG 59.906 55.000 7.08 0.00 0.00 3.02
693 1157 5.163854 CGTTGAGGAGCAGGTTGTTTATTAG 60.164 44.000 0.00 0.00 0.00 1.73
776 1251 2.159707 CGTGCGGTTTGAATCTTGTAGG 60.160 50.000 0.00 0.00 0.00 3.18
777 1252 2.161609 GTGCGGTTTGAATCTTGTAGGG 59.838 50.000 0.00 0.00 0.00 3.53
827 1323 5.634896 CAACCAGTTGTTCATATTGCTCTC 58.365 41.667 2.27 0.00 34.00 3.20
841 1351 0.733223 GCTCTCGAAGTTCGTGTCCC 60.733 60.000 23.67 10.82 41.35 4.46
867 1377 6.552445 AGCTGTAGATCACCAGAATAAAGT 57.448 37.500 13.96 0.00 0.00 2.66
879 1392 6.816640 CACCAGAATAAAGTTGGAATCTCGTA 59.183 38.462 0.00 0.00 35.89 3.43
934 1447 1.691976 TCACCGGAACTGAATGTGTCT 59.308 47.619 9.46 0.00 0.00 3.41
938 1451 1.126846 CGGAACTGAATGTGTCTTCGC 59.873 52.381 0.00 0.00 0.00 4.70
964 1477 2.424956 GTTCCAGGTGATGAAATCCTGC 59.575 50.000 5.07 0.00 44.73 4.85
974 1487 2.320339 GAAATCCTGCGAGCTGCTGC 62.320 60.000 7.01 11.90 46.63 5.25
1059 1572 4.456253 AGCGACGACTACGGTGCG 62.456 66.667 0.00 0.00 44.18 5.34
1064 1577 0.661187 GACGACTACGGTGCGTTTCA 60.661 55.000 6.90 0.00 44.46 2.69
1065 1578 0.936297 ACGACTACGGTGCGTTTCAC 60.936 55.000 0.00 0.00 44.90 3.18
1066 1579 1.771044 GACTACGGTGCGTTTCACG 59.229 57.895 0.00 0.00 46.56 4.35
1067 1580 0.936297 GACTACGGTGCGTTTCACGT 60.936 55.000 0.00 0.00 46.56 4.49
1068 1581 0.528249 ACTACGGTGCGTTTCACGTT 60.528 50.000 0.00 0.00 46.56 3.99
1070 1583 0.248990 TACGGTGCGTTTCACGTTCT 60.249 50.000 0.00 0.00 46.56 3.01
1090 1603 3.114616 CTGCCACGCGGTTCTCTG 61.115 66.667 12.47 0.00 33.28 3.35
1091 1604 3.865929 CTGCCACGCGGTTCTCTGT 62.866 63.158 12.47 0.00 33.28 3.41
1095 1608 0.172578 CCACGCGGTTCTCTGTGATA 59.827 55.000 12.47 0.00 34.29 2.15
1112 1625 9.414295 CTCTGTGATAATCTCTCTGAAATCATC 57.586 37.037 0.00 0.00 35.24 2.92
1121 1634 8.721019 ATCTCTCTGAAATCATCTTCTGTTTC 57.279 34.615 0.00 0.00 0.00 2.78
1147 1660 3.084039 TGCAGTGAAATGTGAATCCTCC 58.916 45.455 0.00 0.00 0.00 4.30
1149 1662 3.128242 GCAGTGAAATGTGAATCCTCCAG 59.872 47.826 0.00 0.00 0.00 3.86
1198 1711 4.457466 ACGGAATGTAAGTTGTCAAACCT 58.543 39.130 0.00 0.00 36.94 3.50
1199 1712 4.274950 ACGGAATGTAAGTTGTCAAACCTG 59.725 41.667 0.00 0.00 36.94 4.00
1201 1714 5.560183 CGGAATGTAAGTTGTCAAACCTGTC 60.560 44.000 0.00 0.00 36.94 3.51
1202 1715 5.531287 GGAATGTAAGTTGTCAAACCTGTCT 59.469 40.000 0.00 0.00 36.94 3.41
1204 1717 4.196193 TGTAAGTTGTCAAACCTGTCTGG 58.804 43.478 0.00 0.00 36.94 3.86
1205 1718 2.348411 AGTTGTCAAACCTGTCTGGG 57.652 50.000 0.33 0.00 41.11 4.45
1207 1720 0.550914 TTGTCAAACCTGTCTGGGCT 59.449 50.000 0.33 0.00 41.11 5.19
1208 1721 0.108585 TGTCAAACCTGTCTGGGCTC 59.891 55.000 0.33 0.00 41.11 4.70
1209 1722 0.606673 GTCAAACCTGTCTGGGCTCC 60.607 60.000 0.33 0.00 41.11 4.70
1210 1723 1.059584 TCAAACCTGTCTGGGCTCCA 61.060 55.000 0.33 0.00 41.11 3.86
1211 1724 0.038744 CAAACCTGTCTGGGCTCCAT 59.961 55.000 0.33 0.00 41.11 3.41
1212 1725 1.281867 CAAACCTGTCTGGGCTCCATA 59.718 52.381 0.33 0.00 41.11 2.74
1214 1727 1.898863 ACCTGTCTGGGCTCCATATT 58.101 50.000 0.33 0.00 41.11 1.28
1218 1731 4.160329 CCTGTCTGGGCTCCATATTACTA 58.840 47.826 0.00 0.00 30.82 1.82
1220 1733 3.901844 TGTCTGGGCTCCATATTACTACC 59.098 47.826 0.00 0.00 30.82 3.18
1221 1734 3.901844 GTCTGGGCTCCATATTACTACCA 59.098 47.826 0.00 0.00 30.82 3.25
1222 1735 3.901844 TCTGGGCTCCATATTACTACCAC 59.098 47.826 0.00 0.00 30.82 4.16
1223 1736 3.646162 CTGGGCTCCATATTACTACCACA 59.354 47.826 0.00 0.00 30.82 4.17
1224 1737 3.646162 TGGGCTCCATATTACTACCACAG 59.354 47.826 0.00 0.00 0.00 3.66
1225 1738 3.008049 GGGCTCCATATTACTACCACAGG 59.992 52.174 0.00 0.00 0.00 4.00
1226 1739 3.901844 GGCTCCATATTACTACCACAGGA 59.098 47.826 0.00 0.00 0.00 3.86
1227 1740 4.021016 GGCTCCATATTACTACCACAGGAG 60.021 50.000 0.00 0.00 43.22 3.69
1228 1741 4.589374 GCTCCATATTACTACCACAGGAGT 59.411 45.833 0.00 0.00 42.53 3.85
1229 1742 5.279056 GCTCCATATTACTACCACAGGAGTC 60.279 48.000 0.00 0.00 42.53 3.36
1230 1743 6.027025 TCCATATTACTACCACAGGAGTCT 57.973 41.667 0.00 0.00 0.00 3.24
1231 1744 6.069331 TCCATATTACTACCACAGGAGTCTC 58.931 44.000 0.00 0.00 0.00 3.36
1232 1745 5.244178 CCATATTACTACCACAGGAGTCTCC 59.756 48.000 11.31 11.31 36.58 3.71
1233 1746 3.820195 TTACTACCACAGGAGTCTCCA 57.180 47.619 21.26 0.00 39.61 3.86
1234 1747 2.930109 ACTACCACAGGAGTCTCCAT 57.070 50.000 21.26 5.75 39.61 3.41
1235 1748 2.461695 ACTACCACAGGAGTCTCCATG 58.538 52.381 21.26 17.05 39.61 3.66
1239 1752 2.187958 CCACAGGAGTCTCCATGGTTA 58.812 52.381 24.77 0.00 39.15 2.85
1258 1775 2.434884 CCGCGTGAAGTGGCTGAT 60.435 61.111 4.92 0.00 44.46 2.90
1262 1779 1.639298 GCGTGAAGTGGCTGATGGAC 61.639 60.000 0.00 0.00 0.00 4.02
1284 1801 3.254024 TTCCTTCCCCGTGAGCAGC 62.254 63.158 0.00 0.00 0.00 5.25
1287 1804 3.965539 CTTCCCCGTGAGCAGCAGG 62.966 68.421 0.00 0.00 0.00 4.85
1450 1970 5.424121 TCTCTTTGCTTACTTGTTTCTGC 57.576 39.130 0.00 0.00 0.00 4.26
1451 1971 5.126067 TCTCTTTGCTTACTTGTTTCTGCT 58.874 37.500 0.00 0.00 0.00 4.24
1452 1972 5.237344 TCTCTTTGCTTACTTGTTTCTGCTC 59.763 40.000 0.00 0.00 0.00 4.26
1453 1973 5.126067 TCTTTGCTTACTTGTTTCTGCTCT 58.874 37.500 0.00 0.00 0.00 4.09
1454 1974 4.818534 TTGCTTACTTGTTTCTGCTCTG 57.181 40.909 0.00 0.00 0.00 3.35
1465 1985 3.986442 TTCTGCTCTGATCTGATCTCG 57.014 47.619 17.82 9.56 0.00 4.04
1639 2179 3.564644 TCTCTTCTAATCCCGTGATCGAC 59.435 47.826 0.00 0.00 39.71 4.20
1683 2223 3.202829 AGGTGATGTGGTGTTTACGTT 57.797 42.857 0.00 0.00 0.00 3.99
1690 2230 2.186891 GTGGTGTTTACGTTTGTTGGC 58.813 47.619 0.00 0.00 0.00 4.52
1691 2231 1.816835 TGGTGTTTACGTTTGTTGGCA 59.183 42.857 0.00 0.00 0.00 4.92
1885 2431 1.063327 TGACGTTGCGTTTGCCTTG 59.937 52.632 0.00 0.00 41.37 3.61
1890 2436 2.494530 TTGCGTTTGCCTTGTCCCC 61.495 57.895 0.00 0.00 41.78 4.81
1935 2481 1.664965 GGCCGTGTGTCTGTCAGAC 60.665 63.158 23.67 23.67 45.26 3.51
1952 2504 6.901037 CTGTCAGACAGTACACTTGAAGTGAA 60.901 42.308 30.03 2.94 43.54 3.18
1984 2536 0.445436 GATCAGCTGCACGGAACAAG 59.555 55.000 9.47 0.00 0.00 3.16
2259 2853 2.046285 CCAAATCCAGGTGACCGCC 61.046 63.158 0.00 0.00 0.00 6.13
2340 2940 2.347490 GGTGTCTCACCGGTGCAT 59.653 61.111 30.25 0.00 44.95 3.96
2341 2941 1.302511 GGTGTCTCACCGGTGCATT 60.303 57.895 30.25 0.00 44.95 3.56
2593 3196 3.864583 GCTCTGTAGCTCAACTGATGAAG 59.135 47.826 0.00 0.00 45.85 3.02
2594 3197 4.381398 GCTCTGTAGCTCAACTGATGAAGA 60.381 45.833 0.00 0.00 45.85 2.87
2595 3198 5.718146 CTCTGTAGCTCAACTGATGAAGAA 58.282 41.667 0.00 0.00 37.67 2.52
2618 3222 8.407064 AGAAGATTACGTTGGTTAGAGTCTATG 58.593 37.037 0.00 0.00 0.00 2.23
2676 3284 3.001330 CCGCGTCCTTCTATGACAAATTC 59.999 47.826 4.92 0.00 32.91 2.17
2699 3307 2.354072 GCTAGCTAGCTCACGCCG 60.354 66.667 33.71 5.19 45.62 6.46
2700 3308 2.835705 GCTAGCTAGCTCACGCCGA 61.836 63.158 33.71 0.00 45.62 5.54
2701 3309 1.728069 CTAGCTAGCTCACGCCGAA 59.272 57.895 23.26 0.00 36.60 4.30
2892 3501 3.315749 GGCAGTCTAGTAACGCTATCTGT 59.684 47.826 0.00 0.00 35.72 3.41
2929 3538 9.665264 CCGCTTAGTTCCTCAAAAATAAATATC 57.335 33.333 0.00 0.00 0.00 1.63
3081 3690 4.362932 TTGTTTGCTTGAAATGTCGTGA 57.637 36.364 0.00 0.00 0.00 4.35
3105 3714 9.311916 TGAAAATCTTGATTGTAGGTTGTTTTG 57.688 29.630 0.00 0.00 0.00 2.44
3110 3719 4.355437 TGATTGTAGGTTGTTTTGTTGCG 58.645 39.130 0.00 0.00 0.00 4.85
3112 3721 1.117234 GTAGGTTGTTTTGTTGCGCG 58.883 50.000 0.00 0.00 0.00 6.86
3138 3747 3.103911 GTTGCGTCGTCCGTCTGG 61.104 66.667 0.00 0.00 39.32 3.86
3148 3757 1.401148 CGTCCGTCTGGTGTCTACTTG 60.401 57.143 0.00 0.00 36.30 3.16
3173 3782 0.955428 TTGCTCGCGCCTGAATCTTT 60.955 50.000 0.00 0.00 34.43 2.52
3175 3784 0.522076 GCTCGCGCCTGAATCTTTTG 60.522 55.000 0.00 0.00 0.00 2.44
3245 7237 3.890128 TGCTAATTCGCGTCTAGATGAG 58.110 45.455 16.39 12.70 0.00 2.90
3248 7240 2.697431 ATTCGCGTCTAGATGAGAGC 57.303 50.000 16.39 6.59 33.72 4.09
3337 7343 5.926214 TTTTATGTTCATCCGTCGTGAAA 57.074 34.783 0.34 0.00 37.34 2.69
3386 7392 7.810766 AGTGAGTGTTTTTATGTTTTGTGTG 57.189 32.000 0.00 0.00 0.00 3.82
3404 7410 4.038162 TGTGTGTTAGGTTATTTTGTGGGC 59.962 41.667 0.00 0.00 0.00 5.36
3416 7422 3.451141 TTTGTGGGCTGTAGCTTTTTG 57.549 42.857 3.63 0.00 41.70 2.44
3489 7497 6.959904 ACTGTGTATCTAGAGGAGAGTGTAA 58.040 40.000 0.00 0.00 37.70 2.41
3520 7528 7.447374 TTTTCCTTTCGAATTTGCTAGATGA 57.553 32.000 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 93 4.722855 GCGCGGCTTTGGCAATGT 62.723 61.111 8.83 0.00 40.87 2.71
90 94 4.721111 TGCGCGGCTTTGGCAATG 62.721 61.111 8.83 4.50 40.87 2.82
205 221 5.579718 ACACGCAGATGTCATTAGTACTAC 58.420 41.667 0.91 0.00 0.00 2.73
206 222 5.830000 ACACGCAGATGTCATTAGTACTA 57.170 39.130 0.00 0.00 0.00 1.82
207 223 4.720649 ACACGCAGATGTCATTAGTACT 57.279 40.909 0.00 0.00 0.00 2.73
248 264 2.004733 GCCGTTCAACCCACATACTAC 58.995 52.381 0.00 0.00 0.00 2.73
259 278 1.209127 CCGTTCATGGCCGTTCAAC 59.791 57.895 0.00 0.04 0.00 3.18
367 764 0.034896 TCAAAGGAGCTCACGGGAAC 59.965 55.000 17.19 0.00 0.00 3.62
376 773 2.174360 GCCAAGGAAATCAAAGGAGCT 58.826 47.619 0.00 0.00 0.00 4.09
431 830 4.318689 GCAGCAGTAGTAGTAGTACGTAGC 60.319 50.000 16.13 16.13 33.97 3.58
438 837 4.466370 TGGAATTGCAGCAGTAGTAGTAGT 59.534 41.667 0.00 0.00 0.00 2.73
452 851 2.639347 TCACTCTTCTCCTGGAATTGCA 59.361 45.455 0.00 0.00 33.01 4.08
454 853 5.334414 CGTTTTCACTCTTCTCCTGGAATTG 60.334 44.000 0.00 0.00 33.01 2.32
506 925 5.646360 ACCTATATATAAATGCGTGGGTTGC 59.354 40.000 0.00 0.00 0.00 4.17
552 977 4.222145 AGTTCATTCCAACTACTCCGCTAA 59.778 41.667 0.00 0.00 34.70 3.09
576 1001 3.859409 GAGAGAAGCCGCTCTGCTAGC 62.859 61.905 8.10 8.10 44.92 3.42
577 1002 0.030638 GAGAGAAGCCGCTCTGCTAG 59.969 60.000 10.37 0.00 44.92 3.42
607 1050 3.243234 CGTAAGGCTCATGTGTAGAGGAG 60.243 52.174 0.00 0.00 33.72 3.69
662 1126 2.206515 CTGCTCCTCAACGTCGCTCT 62.207 60.000 0.00 0.00 0.00 4.09
671 1135 5.705441 CACTAATAAACAACCTGCTCCTCAA 59.295 40.000 0.00 0.00 0.00 3.02
675 1139 5.959618 AACACTAATAAACAACCTGCTCC 57.040 39.130 0.00 0.00 0.00 4.70
693 1157 5.516339 CACCACAACAAGATGAAGAAAACAC 59.484 40.000 0.00 0.00 0.00 3.32
804 1290 5.633830 AGAGCAATATGAACAACTGGTTG 57.366 39.130 11.35 11.35 45.58 3.77
812 1308 4.562789 CGAACTTCGAGAGCAATATGAACA 59.437 41.667 5.15 0.00 43.74 3.18
825 1321 1.443872 CGGGGACACGAACTTCGAG 60.444 63.158 17.97 12.26 43.74 4.04
827 1323 1.443872 CTCGGGGACACGAACTTCG 60.444 63.158 9.68 9.68 46.93 3.79
841 1351 1.393603 TCTGGTGATCTACAGCTCGG 58.606 55.000 11.03 0.00 45.86 4.63
934 1447 1.301401 CACCTGGAACGGAAGCGAA 60.301 57.895 0.00 0.00 36.31 4.70
938 1451 2.472695 TTCATCACCTGGAACGGAAG 57.527 50.000 0.00 0.00 36.31 3.46
964 1477 2.960659 CGATCTGGCAGCAGCTCG 60.961 66.667 10.34 11.35 41.70 5.03
1059 1572 0.534203 TGGCAGGGAGAACGTGAAAC 60.534 55.000 0.00 0.00 37.13 2.78
1064 1577 4.681978 GCGTGGCAGGGAGAACGT 62.682 66.667 9.49 0.00 38.28 3.99
1083 1596 9.248291 GATTTCAGAGAGATTATCACAGAGAAC 57.752 37.037 0.00 0.00 0.00 3.01
1090 1603 9.985730 AGAAGATGATTTCAGAGAGATTATCAC 57.014 33.333 0.00 0.00 33.31 3.06
1091 1604 9.984190 CAGAAGATGATTTCAGAGAGATTATCA 57.016 33.333 0.00 0.00 34.31 2.15
1095 1608 9.165035 GAAACAGAAGATGATTTCAGAGAGATT 57.835 33.333 0.00 0.00 33.14 2.40
1112 1625 4.572985 TCACTGCAATTGGAAACAGAAG 57.427 40.909 15.15 8.75 44.54 2.85
1121 1634 4.628333 GGATTCACATTTCACTGCAATTGG 59.372 41.667 7.72 0.00 0.00 3.16
1198 1711 3.901844 GGTAGTAATATGGAGCCCAGACA 59.098 47.826 0.41 0.00 36.75 3.41
1199 1712 3.901844 TGGTAGTAATATGGAGCCCAGAC 59.098 47.826 0.41 0.00 36.75 3.51
1201 1714 3.646162 TGTGGTAGTAATATGGAGCCCAG 59.354 47.826 0.41 0.00 36.75 4.45
1202 1715 3.646162 CTGTGGTAGTAATATGGAGCCCA 59.354 47.826 0.00 0.00 38.19 5.36
1204 1717 3.901844 TCCTGTGGTAGTAATATGGAGCC 59.098 47.826 0.00 0.00 0.00 4.70
1205 1718 4.589374 ACTCCTGTGGTAGTAATATGGAGC 59.411 45.833 0.00 0.00 42.38 4.70
1207 1720 6.027025 AGACTCCTGTGGTAGTAATATGGA 57.973 41.667 0.00 0.00 0.00 3.41
1208 1721 5.244178 GGAGACTCCTGTGGTAGTAATATGG 59.756 48.000 14.72 0.00 32.53 2.74
1209 1722 5.833667 TGGAGACTCCTGTGGTAGTAATATG 59.166 44.000 22.14 0.00 37.46 1.78
1210 1723 6.027025 TGGAGACTCCTGTGGTAGTAATAT 57.973 41.667 22.14 0.00 37.46 1.28
1211 1724 5.461516 TGGAGACTCCTGTGGTAGTAATA 57.538 43.478 22.14 0.00 37.46 0.98
1212 1725 4.332683 TGGAGACTCCTGTGGTAGTAAT 57.667 45.455 22.14 0.00 37.46 1.89
1214 1727 3.627492 CCATGGAGACTCCTGTGGTAGTA 60.627 52.174 26.17 6.59 37.85 1.82
1218 1731 0.178891 ACCATGGAGACTCCTGTGGT 60.179 55.000 30.70 30.70 45.09 4.16
1220 1733 2.093447 GGTAACCATGGAGACTCCTGTG 60.093 54.545 21.47 18.73 37.46 3.66
1221 1734 2.188817 GGTAACCATGGAGACTCCTGT 58.811 52.381 21.47 13.40 37.46 4.00
1222 1735 2.990066 GGTAACCATGGAGACTCCTG 57.010 55.000 21.47 16.24 37.46 3.86
1239 1752 4.988598 CAGCCACTTCACGCGGGT 62.989 66.667 8.89 0.00 0.00 5.28
1262 1779 0.955919 GCTCACGGGGAAGGAACAAG 60.956 60.000 0.00 0.00 0.00 3.16
1284 1801 3.592814 TAGTCGGCGGCGATCCTG 61.593 66.667 36.75 4.98 0.00 3.86
1393 1913 7.977853 ACTGTATGTACACGAAGTAAATAAGGG 59.022 37.037 0.00 0.00 41.61 3.95
1450 1970 1.610038 AGCAGCGAGATCAGATCAGAG 59.390 52.381 13.14 4.56 0.00 3.35
1451 1971 1.608109 GAGCAGCGAGATCAGATCAGA 59.392 52.381 13.14 0.00 31.47 3.27
1452 1972 1.663730 CGAGCAGCGAGATCAGATCAG 60.664 57.143 13.14 7.28 44.57 2.90
1453 1973 0.310232 CGAGCAGCGAGATCAGATCA 59.690 55.000 13.14 0.00 44.57 2.92
1454 1974 1.003262 GCGAGCAGCGAGATCAGATC 61.003 60.000 1.64 1.64 44.57 2.75
1568 2088 2.029288 CAGTACGGTGGCAGCAGTG 61.029 63.158 17.80 7.44 0.00 3.66
1577 2097 3.851976 AGAGTAAAGAGCAGTACGGTG 57.148 47.619 0.00 0.00 0.00 4.94
1606 2126 6.519043 CGGGATTAGAAGAGAAGATGGCAATA 60.519 42.308 0.00 0.00 0.00 1.90
1620 2140 2.604855 CGGTCGATCACGGGATTAGAAG 60.605 54.545 0.00 0.00 40.21 2.85
1639 2179 4.868171 TCGGTTTTTGTATCTTGAGATCGG 59.132 41.667 0.00 0.00 36.05 4.18
1646 2186 5.682943 TCACCTTCGGTTTTTGTATCTTG 57.317 39.130 0.00 0.00 31.02 3.02
1683 2223 4.999950 ACAGAAAAACAAACATGCCAACAA 59.000 33.333 0.00 0.00 0.00 2.83
1690 2230 5.176223 GGATGCTGACAGAAAAACAAACATG 59.824 40.000 6.65 0.00 0.00 3.21
1691 2231 5.069516 AGGATGCTGACAGAAAAACAAACAT 59.930 36.000 6.65 0.00 0.00 2.71
1749 2289 2.765250 CTTCCGTCACAGACCACCGG 62.765 65.000 0.00 0.00 39.98 5.28
1752 2292 0.946221 CTGCTTCCGTCACAGACCAC 60.946 60.000 0.00 0.00 33.10 4.16
1831 2371 4.069304 TGTAGTATTTCTTGGCTTTGCGT 58.931 39.130 0.00 0.00 0.00 5.24
1935 2481 5.986135 AGCTAGTTTCACTTCAAGTGTACTG 59.014 40.000 25.39 19.10 46.03 2.74
1962 2514 0.445436 GTTCCGTGCAGCTGATCAAG 59.555 55.000 20.43 9.08 0.00 3.02
1984 2536 3.180387 GCAACTGCTTTGTCAAAATCGTC 59.820 43.478 0.00 0.00 37.54 4.20
2101 2686 1.535462 AGAAAACGGTAGCATGCACAC 59.465 47.619 21.98 16.64 0.00 3.82
2235 2829 0.036164 TCACCTGGATTTGGTCGTGG 59.964 55.000 0.00 0.00 35.28 4.94
2589 3192 6.989659 ACTCTAACCAACGTAATCTTCTTCA 58.010 36.000 0.00 0.00 0.00 3.02
2593 3196 8.189460 ACATAGACTCTAACCAACGTAATCTTC 58.811 37.037 0.00 0.00 0.00 2.87
2594 3197 7.974501 CACATAGACTCTAACCAACGTAATCTT 59.025 37.037 0.00 0.00 0.00 2.40
2595 3198 7.122353 ACACATAGACTCTAACCAACGTAATCT 59.878 37.037 0.00 0.00 0.00 2.40
2618 3222 1.745087 TCCCGTACCGTTCATCTACAC 59.255 52.381 0.00 0.00 0.00 2.90
2693 3301 0.454600 TAGGCTTCTACTTCGGCGTG 59.545 55.000 6.85 3.77 0.00 5.34
2694 3302 0.739561 CTAGGCTTCTACTTCGGCGT 59.260 55.000 6.85 0.00 0.00 5.68
2695 3303 1.022735 TCTAGGCTTCTACTTCGGCG 58.977 55.000 0.00 0.00 0.00 6.46
2696 3304 3.737032 ATTCTAGGCTTCTACTTCGGC 57.263 47.619 0.00 0.00 0.00 5.54
2699 3307 8.471609 AGTGAAGTTATTCTAGGCTTCTACTTC 58.528 37.037 0.00 0.00 38.41 3.01
2700 3308 8.254508 CAGTGAAGTTATTCTAGGCTTCTACTT 58.745 37.037 0.00 0.00 38.41 2.24
2701 3309 7.147811 CCAGTGAAGTTATTCTAGGCTTCTACT 60.148 40.741 0.00 0.00 38.41 2.57
2892 3501 6.070995 TGAGGAACTAAGCGGAAGAGATTAAA 60.071 38.462 0.00 0.00 41.55 1.52
2929 3538 5.119279 CGTCACTCACTAATGGAAGAAGTTG 59.881 44.000 0.00 0.00 0.00 3.16
3033 3642 7.891561 TGGAAAAAGTGAAAAGAGTTCTTGAA 58.108 30.769 0.00 0.00 36.12 2.69
3051 3660 7.824672 ACATTTCAAGCAAACAAATGGAAAAA 58.175 26.923 12.34 0.00 40.41 1.94
3081 3690 9.665719 AACAAAACAACCTACAATCAAGATTTT 57.334 25.926 0.00 0.00 0.00 1.82
3138 3747 0.790814 GCAAGCCGACAAGTAGACAC 59.209 55.000 0.00 0.00 0.00 3.67
3163 3772 1.067635 CGGCCCAACAAAAGATTCAGG 60.068 52.381 0.00 0.00 0.00 3.86
3164 3773 1.613437 ACGGCCCAACAAAAGATTCAG 59.387 47.619 0.00 0.00 0.00 3.02
3173 3782 2.413765 GCGAAAACGGCCCAACAA 59.586 55.556 0.00 0.00 0.00 2.83
3219 7211 4.491676 TCTAGACGCGAATTAGCAAAACT 58.508 39.130 15.93 6.27 36.85 2.66
3288 7294 1.083401 CAACGACAACGAGCACAGC 60.083 57.895 0.00 0.00 42.66 4.40
3289 7295 0.043053 CACAACGACAACGAGCACAG 60.043 55.000 0.00 0.00 42.66 3.66
3321 7327 3.806316 ATTGTTTCACGACGGATGAAC 57.194 42.857 0.00 0.00 35.82 3.18
3329 7335 3.889196 TTGTGCCTATTGTTTCACGAC 57.111 42.857 0.00 0.00 32.48 4.34
3386 7392 5.392703 GCTACAGCCCACAAAATAACCTAAC 60.393 44.000 0.00 0.00 34.31 2.34
3404 7410 2.814336 GACCCTCCACAAAAAGCTACAG 59.186 50.000 0.00 0.00 0.00 2.74
3416 7422 2.568623 AAAGACACATGACCCTCCAC 57.431 50.000 0.00 0.00 0.00 4.02
3550 7558 8.964420 ACATTAAATCAAACAAATCGTACAGG 57.036 30.769 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.