Multiple sequence alignment - TraesCS3A01G261500

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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 TraesCS3A01G261500 chr3A 100.000 3305 0 0 1 3305 484634244 484630940 0.000000e+00 6104
1 TraesCS3A01G261500 chr3B 96.006 2629 72 11 682 3305 473690998 473688398 0.000000e+00 4242
2 TraesCS3A01G261500 chr3B 92.043 465 27 7 1 461 473691689 473691231 0.000000e+00 645
3 TraesCS3A01G261500 chr3B 85.263 190 5 9 459 628 473691196 473691010 1.220000e-39 174
4 TraesCS3A01G261500 chr3D 95.405 914 36 4 2394 3305 363592906 363591997 0.000000e+00 1450
5 TraesCS3A01G261500 chr3D 95.335 343 14 2 719 1059 363593275 363592933 8.070000e-151 544
6 TraesCS3A01G261500 chr3D 86.595 373 33 8 1 368 363593820 363593460 2.390000e-106 396


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 TraesCS3A01G261500 chr3A 484630940 484634244 3304 True 6104.000000 6104 100.000 1 3305 1 chr3A.!!$R1 3304
1 TraesCS3A01G261500 chr3B 473688398 473691689 3291 True 1687.000000 4242 91.104 1 3305 3 chr3B.!!$R1 3304
2 TraesCS3A01G261500 chr3D 363591997 363593820 1823 True 796.666667 1450 92.445 1 3305 3 chr3D.!!$R1 3304

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
657 726 0.041312 GTGCGTCGCAAGTTCACATT 60.041 50.0 23.58 0.00 41.47 2.71 F
658 727 0.041400 TGCGTCGCAAGTTCACATTG 60.041 50.0 19.38 0.00 34.76 2.82 F
673 742 0.095245 CATTGATGCGTGTCACGGTC 59.905 55.0 25.70 11.36 42.82 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1526 1601 1.471684 AGACGACGACTTGTGGTATCC 59.528 52.381 0.0 0.0 39.88 2.59 R
1548 1623 1.497991 TTTCTCTGAAGGCGTGTTCG 58.502 50.000 0.0 0.0 40.37 3.95 R
2424 2499 1.606668 TGGTGTTTCATCAACTTCGCC 59.393 47.619 0.0 0.0 36.21 5.54 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
105 109 1.585006 CTACGAGGAACAGCACCGT 59.415 57.895 0.00 0.00 37.27 4.83
129 133 1.093159 GGCTTCATGGCTTCTCAGTG 58.907 55.000 0.00 0.00 38.32 3.66
131 135 2.430465 GCTTCATGGCTTCTCAGTGAA 58.570 47.619 0.00 0.00 0.00 3.18
143 147 6.279513 CTTCTCAGTGAAGGATTACTCTGT 57.720 41.667 4.53 0.00 46.25 3.41
144 148 5.906113 TCTCAGTGAAGGATTACTCTGTC 57.094 43.478 0.00 0.00 0.00 3.51
145 149 5.575157 TCTCAGTGAAGGATTACTCTGTCT 58.425 41.667 0.00 0.00 0.00 3.41
146 150 5.417266 TCTCAGTGAAGGATTACTCTGTCTG 59.583 44.000 0.00 0.00 0.00 3.51
147 151 4.464244 TCAGTGAAGGATTACTCTGTCTGG 59.536 45.833 0.00 0.00 0.00 3.86
202 210 4.627467 ACTATTTGTAGCAAGAGAACAGCG 59.373 41.667 0.00 0.00 0.00 5.18
236 244 1.202568 CGCCATGCTCTATCTGGAACA 60.203 52.381 0.00 0.00 31.38 3.18
252 260 2.350484 GGAACAGTGCCGCTAAAACTTC 60.350 50.000 0.00 0.00 0.00 3.01
253 261 0.865769 ACAGTGCCGCTAAAACTTCG 59.134 50.000 0.00 0.00 0.00 3.79
304 313 3.645660 TGGAGCACGGGCATTCCA 61.646 61.111 16.16 16.16 40.81 3.53
318 328 1.479323 CATTCCAATGAGTGCTTGGGG 59.521 52.381 2.16 0.00 42.83 4.96
334 344 4.704833 GGCTCCGGCACTGCTTCA 62.705 66.667 0.00 0.00 40.87 3.02
376 386 3.097137 CTGCTGCTGCTGCTTAGCG 62.097 63.158 27.67 10.25 44.01 4.26
478 529 5.659463 CCTTGTTGAACAGATTTTCCAACA 58.341 37.500 0.00 0.00 30.99 3.33
526 577 3.955471 TGTTTCTGGAATAAGGAGGCTG 58.045 45.455 0.00 0.00 0.00 4.85
527 578 2.685388 GTTTCTGGAATAAGGAGGCTGC 59.315 50.000 0.00 0.00 0.00 5.25
528 579 1.885049 TCTGGAATAAGGAGGCTGCT 58.115 50.000 1.28 1.28 0.00 4.24
529 580 1.487976 TCTGGAATAAGGAGGCTGCTG 59.512 52.381 10.05 0.00 0.00 4.41
532 583 0.839946 GAATAAGGAGGCTGCTGGGA 59.160 55.000 10.05 0.00 0.00 4.37
533 584 0.548510 AATAAGGAGGCTGCTGGGAC 59.451 55.000 10.05 0.00 0.00 4.46
534 585 1.690219 ATAAGGAGGCTGCTGGGACG 61.690 60.000 10.05 0.00 0.00 4.79
535 586 2.798445 TAAGGAGGCTGCTGGGACGA 62.798 60.000 10.05 0.00 0.00 4.20
600 669 0.250295 CCGGGTCACAAAAGCTCTCA 60.250 55.000 0.00 0.00 0.00 3.27
617 686 3.479505 CTCACACTTGAGTAGGAGACG 57.520 52.381 5.70 0.00 43.95 4.18
628 697 2.814913 TAGGAGACGGCGAGTGCAGA 62.815 60.000 16.62 0.00 45.35 4.26
629 698 2.258591 GAGACGGCGAGTGCAGAA 59.741 61.111 16.62 0.00 45.35 3.02
630 699 1.372997 GAGACGGCGAGTGCAGAAA 60.373 57.895 16.62 0.00 45.35 2.52
636 705 2.856032 CGAGTGCAGAAACGCTGG 59.144 61.111 0.00 0.00 45.03 4.85
637 706 2.671177 CGAGTGCAGAAACGCTGGG 61.671 63.158 0.00 0.00 45.03 4.45
638 707 2.281761 AGTGCAGAAACGCTGGGG 60.282 61.111 0.00 0.00 45.03 4.96
639 708 2.594592 GTGCAGAAACGCTGGGGT 60.595 61.111 0.00 0.00 45.03 4.95
640 709 2.594303 TGCAGAAACGCTGGGGTG 60.594 61.111 0.00 0.00 45.03 4.61
641 710 4.043200 GCAGAAACGCTGGGGTGC 62.043 66.667 0.00 0.00 45.03 5.01
650 719 4.988598 CTGGGGTGCGTCGCAAGT 62.989 66.667 23.58 0.00 41.47 3.16
651 720 4.555709 TGGGGTGCGTCGCAAGTT 62.556 61.111 23.58 0.00 41.47 2.66
652 721 3.723348 GGGGTGCGTCGCAAGTTC 61.723 66.667 23.58 9.38 41.47 3.01
653 722 2.970324 GGGTGCGTCGCAAGTTCA 60.970 61.111 23.58 0.00 41.47 3.18
654 723 2.248431 GGTGCGTCGCAAGTTCAC 59.752 61.111 23.58 8.17 41.47 3.18
655 724 2.530497 GGTGCGTCGCAAGTTCACA 61.530 57.895 23.58 0.00 41.47 3.58
656 725 1.569493 GTGCGTCGCAAGTTCACAT 59.431 52.632 23.58 0.00 41.47 3.21
657 726 0.041312 GTGCGTCGCAAGTTCACATT 60.041 50.000 23.58 0.00 41.47 2.71
658 727 0.041400 TGCGTCGCAAGTTCACATTG 60.041 50.000 19.38 0.00 34.76 2.82
659 728 0.234625 GCGTCGCAAGTTCACATTGA 59.765 50.000 13.44 0.00 39.48 2.57
660 729 1.135972 GCGTCGCAAGTTCACATTGAT 60.136 47.619 13.44 0.00 39.48 2.57
661 730 2.498905 CGTCGCAAGTTCACATTGATG 58.501 47.619 0.00 0.00 39.48 3.07
662 731 2.245096 GTCGCAAGTTCACATTGATGC 58.755 47.619 0.00 0.00 39.48 3.91
663 732 1.253116 CGCAAGTTCACATTGATGCG 58.747 50.000 7.90 7.90 43.67 4.73
664 733 1.400113 CGCAAGTTCACATTGATGCGT 60.400 47.619 12.32 0.00 43.95 5.24
665 734 1.980844 GCAAGTTCACATTGATGCGTG 59.019 47.619 0.00 0.00 34.34 5.34
666 735 2.605338 GCAAGTTCACATTGATGCGTGT 60.605 45.455 0.00 0.00 34.66 4.49
667 736 3.228749 CAAGTTCACATTGATGCGTGTC 58.771 45.455 0.00 0.00 34.66 3.67
668 737 2.493035 AGTTCACATTGATGCGTGTCA 58.507 42.857 0.00 0.00 34.66 3.58
669 738 2.224079 AGTTCACATTGATGCGTGTCAC 59.776 45.455 0.00 0.00 34.66 3.67
670 739 0.789601 TCACATTGATGCGTGTCACG 59.210 50.000 21.02 21.02 45.88 4.35
671 740 0.179217 CACATTGATGCGTGTCACGG 60.179 55.000 25.70 10.33 42.82 4.94
672 741 0.602638 ACATTGATGCGTGTCACGGT 60.603 50.000 25.70 10.96 42.82 4.83
673 742 0.095245 CATTGATGCGTGTCACGGTC 59.905 55.000 25.70 11.36 42.82 4.79
674 743 0.320334 ATTGATGCGTGTCACGGTCA 60.320 50.000 25.70 16.52 42.82 4.02
675 744 0.943835 TTGATGCGTGTCACGGTCAG 60.944 55.000 25.70 0.00 42.82 3.51
676 745 1.080772 GATGCGTGTCACGGTCAGA 60.081 57.895 25.70 0.00 42.82 3.27
677 746 0.666274 GATGCGTGTCACGGTCAGAA 60.666 55.000 25.70 0.00 42.82 3.02
678 747 0.944311 ATGCGTGTCACGGTCAGAAC 60.944 55.000 25.70 8.54 42.82 3.01
679 748 2.308039 GCGTGTCACGGTCAGAACC 61.308 63.158 25.70 3.68 42.82 3.62
680 749 1.663702 CGTGTCACGGTCAGAACCC 60.664 63.158 17.75 0.00 43.21 4.11
691 760 2.755103 GGTCAGAACCCCATTGATGTTC 59.245 50.000 9.10 9.10 39.93 3.18
697 766 3.077484 ACCCCATTGATGTTCACAGAG 57.923 47.619 0.00 0.00 0.00 3.35
698 767 1.747355 CCCCATTGATGTTCACAGAGC 59.253 52.381 0.00 0.00 0.00 4.09
814 884 2.574018 GGAAACCCTTGCCCTGCAC 61.574 63.158 0.00 0.00 38.71 4.57
851 922 3.495806 CCCTCAATTGCTCATCCTCCTAC 60.496 52.174 0.00 0.00 0.00 3.18
1089 1160 2.448542 ATCCACCGGATCCTGGGG 60.449 66.667 18.18 18.18 38.09 4.96
1107 1178 4.344865 GGAGGGAAAGGTGCGCCA 62.345 66.667 20.59 0.00 37.19 5.69
1122 1193 2.053627 GCGCCATTCTTGTTCTGTTTG 58.946 47.619 0.00 0.00 0.00 2.93
1125 1196 4.791411 GCGCCATTCTTGTTCTGTTTGTAA 60.791 41.667 0.00 0.00 0.00 2.41
1134 1205 7.422399 TCTTGTTCTGTTTGTAAGCAATTACC 58.578 34.615 0.00 0.00 34.18 2.85
1135 1206 6.079424 TGTTCTGTTTGTAAGCAATTACCC 57.921 37.500 0.00 0.00 34.18 3.69
1136 1207 5.830991 TGTTCTGTTTGTAAGCAATTACCCT 59.169 36.000 0.00 0.00 34.18 4.34
1137 1208 6.999272 TGTTCTGTTTGTAAGCAATTACCCTA 59.001 34.615 0.00 0.00 34.18 3.53
1138 1209 7.040961 TGTTCTGTTTGTAAGCAATTACCCTAC 60.041 37.037 0.00 0.00 34.18 3.18
1139 1210 6.535540 TCTGTTTGTAAGCAATTACCCTACA 58.464 36.000 0.00 0.00 34.18 2.74
1140 1211 6.428771 TCTGTTTGTAAGCAATTACCCTACAC 59.571 38.462 0.00 0.00 34.18 2.90
1141 1212 6.300703 TGTTTGTAAGCAATTACCCTACACT 58.699 36.000 0.00 0.00 34.18 3.55
1142 1213 7.451732 TGTTTGTAAGCAATTACCCTACACTA 58.548 34.615 0.00 0.00 34.18 2.74
1150 1221 5.409826 GCAATTACCCTACACTATCTGCATC 59.590 44.000 0.00 0.00 0.00 3.91
1161 1232 6.051717 ACACTATCTGCATCACCATAGTTTC 58.948 40.000 0.00 0.00 31.04 2.78
1162 1233 6.126940 ACACTATCTGCATCACCATAGTTTCT 60.127 38.462 0.00 0.00 31.04 2.52
1163 1234 6.423302 CACTATCTGCATCACCATAGTTTCTC 59.577 42.308 0.00 0.00 31.04 2.87
1165 1236 3.118261 TCTGCATCACCATAGTTTCTCCC 60.118 47.826 0.00 0.00 0.00 4.30
1167 1238 2.092429 GCATCACCATAGTTTCTCCCCA 60.092 50.000 0.00 0.00 0.00 4.96
1169 1240 4.202441 CATCACCATAGTTTCTCCCCAAG 58.798 47.826 0.00 0.00 0.00 3.61
1170 1241 2.026262 TCACCATAGTTTCTCCCCAAGC 60.026 50.000 0.00 0.00 0.00 4.01
1171 1242 1.285078 ACCATAGTTTCTCCCCAAGCC 59.715 52.381 0.00 0.00 0.00 4.35
1172 1243 1.668419 CATAGTTTCTCCCCAAGCCG 58.332 55.000 0.00 0.00 0.00 5.52
1173 1244 1.209504 CATAGTTTCTCCCCAAGCCGA 59.790 52.381 0.00 0.00 0.00 5.54
1174 1245 0.611714 TAGTTTCTCCCCAAGCCGAC 59.388 55.000 0.00 0.00 0.00 4.79
1204 1279 1.178534 ACACCGATGTTGGGCTTTGG 61.179 55.000 0.00 0.00 34.46 3.28
1242 1317 1.876156 CTGCTGTGGAAGAACAGGAAC 59.124 52.381 6.48 0.00 46.22 3.62
1344 1419 1.227350 CCAGATCGCCATCTTCGCA 60.227 57.895 0.00 0.00 37.25 5.10
1365 1440 0.171679 TGCTTGCCATCTTCATTGCG 59.828 50.000 0.00 0.00 0.00 4.85
1402 1477 1.372087 CTTCGACAGGCATGGCTTCC 61.372 60.000 20.85 12.92 29.20 3.46
1414 1489 1.604604 TGGCTTCCTTTCTTTCCACG 58.395 50.000 0.00 0.00 0.00 4.94
1433 1508 2.166829 CGGAGAGGAGATATCCCAGTG 58.833 57.143 1.81 0.00 35.74 3.66
1441 1516 8.798975 AGAGGAGATATCCCAGTGTTTATTTA 57.201 34.615 1.81 0.00 0.00 1.40
1548 1623 0.877071 TACCACAAGTCGTCGTCTCC 59.123 55.000 0.00 0.00 0.00 3.71
1573 1648 0.393537 CGCCTTCAGAGAAATGGCCT 60.394 55.000 3.32 0.00 40.40 5.19
1725 1800 4.422073 TGTGACAAGTCTTGTTCCAGAT 57.578 40.909 19.09 0.00 45.52 2.90
1729 1804 3.654414 ACAAGTCTTGTTCCAGATCGAC 58.346 45.455 12.62 0.00 42.22 4.20
1788 1863 7.341030 TGAATCAACCAGATTAGACATGACAT 58.659 34.615 0.00 0.00 46.76 3.06
1790 1865 4.877823 TCAACCAGATTAGACATGACATGC 59.122 41.667 15.49 8.35 0.00 4.06
1799 1874 3.693807 AGACATGACATGCCACTCAAAT 58.306 40.909 15.49 0.00 0.00 2.32
1818 1893 8.612619 ACTCAAATCAACGTTTAGCCAATATAG 58.387 33.333 0.00 0.00 0.00 1.31
1844 1919 6.083630 TCACAACGTTATTTTGCTATTGCTC 58.916 36.000 0.00 0.00 40.48 4.26
1845 1920 6.072728 TCACAACGTTATTTTGCTATTGCTCT 60.073 34.615 0.00 0.00 40.48 4.09
1846 1921 6.582295 CACAACGTTATTTTGCTATTGCTCTT 59.418 34.615 0.00 0.00 40.48 2.85
1992 2067 9.408069 AGTAGAACAGAAATAGTAACGTTCAAG 57.592 33.333 2.82 0.00 36.16 3.02
2012 2087 7.038154 TCAAGAAAACCAAATACAGAAGGTG 57.962 36.000 0.00 0.00 33.93 4.00
2295 2370 0.390472 GAGGCCCTGTCAAGACGAAG 60.390 60.000 0.00 0.00 0.00 3.79
2345 2420 8.439971 AGCTGTCAGGACATAATAATAATTCCA 58.560 33.333 2.09 0.00 41.01 3.53
2424 2499 2.893637 CACGAACCAAGTCCCAGATAG 58.106 52.381 0.00 0.00 0.00 2.08
2732 2808 6.687604 AGTACTAATGGAATGTGTTTTTGCC 58.312 36.000 0.00 0.00 0.00 4.52
2825 2901 1.238439 CAAAGCTTCGCCCAAGAGAA 58.762 50.000 0.00 0.00 33.29 2.87
3011 3087 8.514330 ACCTTCAAAACAAATAGTGAAGTACA 57.486 30.769 10.42 0.00 43.51 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 109 1.679977 GAAGCCATGAAGCCCTGCA 60.680 57.895 0.00 0.00 0.00 4.41
129 133 3.515901 ACCACCAGACAGAGTAATCCTTC 59.484 47.826 0.00 0.00 0.00 3.46
131 135 3.191888 ACCACCAGACAGAGTAATCCT 57.808 47.619 0.00 0.00 0.00 3.24
137 141 1.133792 CCCAAAACCACCAGACAGAGT 60.134 52.381 0.00 0.00 0.00 3.24
139 143 1.142870 CTCCCAAAACCACCAGACAGA 59.857 52.381 0.00 0.00 0.00 3.41
140 144 1.609208 CTCCCAAAACCACCAGACAG 58.391 55.000 0.00 0.00 0.00 3.51
143 147 0.467290 GTGCTCCCAAAACCACCAGA 60.467 55.000 0.00 0.00 0.00 3.86
144 148 0.754957 TGTGCTCCCAAAACCACCAG 60.755 55.000 0.00 0.00 0.00 4.00
145 149 0.324738 TTGTGCTCCCAAAACCACCA 60.325 50.000 0.00 0.00 0.00 4.17
146 150 0.389025 CTTGTGCTCCCAAAACCACC 59.611 55.000 0.00 0.00 0.00 4.61
147 151 1.338020 CTCTTGTGCTCCCAAAACCAC 59.662 52.381 0.00 0.00 0.00 4.16
236 244 2.443887 TACGAAGTTTTAGCGGCACT 57.556 45.000 1.45 0.00 37.78 4.40
252 260 2.160117 CGTGCAATGCAAAAGCTTTACG 60.160 45.455 10.44 11.95 41.47 3.18
253 261 2.155539 CCGTGCAATGCAAAAGCTTTAC 59.844 45.455 10.44 8.62 41.47 2.01
318 328 3.123620 CTGAAGCAGTGCCGGAGC 61.124 66.667 12.58 2.48 40.48 4.70
371 381 1.899814 ACCTTGGACATGTCTCGCTAA 59.100 47.619 24.50 11.44 0.00 3.09
376 386 2.227388 CAGCAAACCTTGGACATGTCTC 59.773 50.000 24.50 15.19 0.00 3.36
434 444 2.422597 CACTTTTATCGGTGTGCTCCA 58.577 47.619 0.00 0.00 0.00 3.86
455 465 5.659463 TGTTGGAAAATCTGTTCAACAAGG 58.341 37.500 0.00 0.00 31.57 3.61
478 529 1.472026 GCCATTTCGCCATTGCTCAAT 60.472 47.619 0.00 0.00 34.43 2.57
532 583 2.214181 ATTTCTGACGGCGCTCTCGT 62.214 55.000 6.90 8.96 44.03 4.18
533 584 1.517257 ATTTCTGACGGCGCTCTCG 60.517 57.895 6.90 4.93 39.07 4.04
534 585 2.002127 CATTTCTGACGGCGCTCTC 58.998 57.895 6.90 2.22 0.00 3.20
535 586 2.103042 GCATTTCTGACGGCGCTCT 61.103 57.895 6.90 0.00 0.00 4.09
540 609 0.459585 TACTCCGCATTTCTGACGGC 60.460 55.000 0.00 0.00 39.99 5.68
545 614 4.201628 CGTCTTTCTTACTCCGCATTTCTG 60.202 45.833 0.00 0.00 0.00 3.02
600 669 0.889306 GCCGTCTCCTACTCAAGTGT 59.111 55.000 0.00 0.00 0.00 3.55
633 702 4.988598 ACTTGCGACGCACCCCAG 62.989 66.667 24.42 19.36 38.71 4.45
634 703 4.555709 AACTTGCGACGCACCCCA 62.556 61.111 24.42 6.93 38.71 4.96
635 704 3.723348 GAACTTGCGACGCACCCC 61.723 66.667 24.42 8.44 38.71 4.95
636 705 2.970324 TGAACTTGCGACGCACCC 60.970 61.111 24.42 12.06 38.71 4.61
637 706 1.841663 ATGTGAACTTGCGACGCACC 61.842 55.000 24.42 12.42 38.71 5.01
638 707 0.041312 AATGTGAACTTGCGACGCAC 60.041 50.000 24.42 11.81 38.71 5.34
639 708 0.041400 CAATGTGAACTTGCGACGCA 60.041 50.000 20.50 20.50 36.47 5.24
640 709 0.234625 TCAATGTGAACTTGCGACGC 59.765 50.000 14.19 14.19 0.00 5.19
641 710 2.498905 CATCAATGTGAACTTGCGACG 58.501 47.619 0.00 0.00 0.00 5.12
642 711 2.245096 GCATCAATGTGAACTTGCGAC 58.755 47.619 0.00 0.00 0.00 5.19
643 712 2.617250 GCATCAATGTGAACTTGCGA 57.383 45.000 0.00 0.00 0.00 5.10
644 713 1.253116 CGCATCAATGTGAACTTGCG 58.747 50.000 9.49 9.49 43.67 4.85
645 714 1.980844 CACGCATCAATGTGAACTTGC 59.019 47.619 10.35 0.00 40.61 4.01
646 715 3.228749 GACACGCATCAATGTGAACTTG 58.771 45.455 10.35 1.25 40.61 3.16
647 716 2.877786 TGACACGCATCAATGTGAACTT 59.122 40.909 10.35 0.00 40.61 2.66
648 717 2.224079 GTGACACGCATCAATGTGAACT 59.776 45.455 10.35 0.00 40.61 3.01
649 718 2.574322 GTGACACGCATCAATGTGAAC 58.426 47.619 10.35 2.59 40.61 3.18
650 719 1.194322 CGTGACACGCATCAATGTGAA 59.806 47.619 16.06 0.00 40.61 3.18
651 720 0.789601 CGTGACACGCATCAATGTGA 59.210 50.000 16.06 0.00 40.61 3.58
652 721 0.179217 CCGTGACACGCATCAATGTG 60.179 55.000 22.46 1.61 40.91 3.21
653 722 0.602638 ACCGTGACACGCATCAATGT 60.603 50.000 22.46 9.99 40.91 2.71
654 723 0.095245 GACCGTGACACGCATCAATG 59.905 55.000 22.46 9.34 40.91 2.82
655 724 0.320334 TGACCGTGACACGCATCAAT 60.320 50.000 22.46 2.90 40.91 2.57
656 725 0.943835 CTGACCGTGACACGCATCAA 60.944 55.000 24.47 13.98 40.91 2.57
657 726 1.372872 CTGACCGTGACACGCATCA 60.373 57.895 22.46 23.11 40.91 3.07
658 727 0.666274 TTCTGACCGTGACACGCATC 60.666 55.000 22.46 20.12 40.91 3.91
659 728 0.944311 GTTCTGACCGTGACACGCAT 60.944 55.000 22.46 12.37 40.91 4.73
660 729 1.590525 GTTCTGACCGTGACACGCA 60.591 57.895 22.46 14.41 40.91 5.24
661 730 2.308039 GGTTCTGACCGTGACACGC 61.308 63.158 22.46 10.38 40.91 5.34
662 731 3.932289 GGTTCTGACCGTGACACG 58.068 61.111 21.02 21.02 42.11 4.49
670 739 2.514458 ACATCAATGGGGTTCTGACC 57.486 50.000 0.00 0.00 45.75 4.02
671 740 3.191371 GTGAACATCAATGGGGTTCTGAC 59.809 47.826 15.14 6.26 41.07 3.51
672 741 3.181435 TGTGAACATCAATGGGGTTCTGA 60.181 43.478 15.14 3.82 41.07 3.27
673 742 3.156293 TGTGAACATCAATGGGGTTCTG 58.844 45.455 15.14 0.00 41.07 3.02
674 743 3.074390 TCTGTGAACATCAATGGGGTTCT 59.926 43.478 15.14 0.00 41.07 3.01
675 744 3.420893 TCTGTGAACATCAATGGGGTTC 58.579 45.455 9.78 9.78 40.91 3.62
676 745 3.424703 CTCTGTGAACATCAATGGGGTT 58.575 45.455 0.00 0.00 0.00 4.11
677 746 2.881403 GCTCTGTGAACATCAATGGGGT 60.881 50.000 0.00 0.00 0.00 4.95
678 747 1.747355 GCTCTGTGAACATCAATGGGG 59.253 52.381 0.00 0.00 0.00 4.96
679 748 2.439409 TGCTCTGTGAACATCAATGGG 58.561 47.619 0.00 0.00 0.00 4.00
680 749 3.692593 TGATGCTCTGTGAACATCAATGG 59.307 43.478 10.14 0.00 45.27 3.16
691 760 0.803117 CTGCACCTTGATGCTCTGTG 59.197 55.000 0.00 0.00 46.28 3.66
697 766 1.503542 CGGAACTGCACCTTGATGC 59.496 57.895 0.00 0.00 46.32 3.91
698 767 1.926511 GCCGGAACTGCACCTTGATG 61.927 60.000 5.05 0.00 38.81 3.07
814 884 0.472898 GAGGGAGGGGAATAAACGGG 59.527 60.000 0.00 0.00 0.00 5.28
851 922 1.213926 AGGAAAGGATAGCTTGGCCTG 59.786 52.381 3.32 0.00 31.06 4.85
1045 1116 2.765969 CCTGTGGAATGGCCCTGT 59.234 61.111 0.00 0.00 34.97 4.00
1102 1173 2.053627 CAAACAGAACAAGAATGGCGC 58.946 47.619 0.00 0.00 0.00 6.53
1107 1178 9.463443 GTAATTGCTTACAAACAGAACAAGAAT 57.537 29.630 0.00 0.00 39.77 2.40
1122 1193 6.424207 GCAGATAGTGTAGGGTAATTGCTTAC 59.576 42.308 0.00 0.00 37.16 2.34
1125 1196 4.408921 TGCAGATAGTGTAGGGTAATTGCT 59.591 41.667 0.00 0.00 0.00 3.91
1134 1205 4.613925 ATGGTGATGCAGATAGTGTAGG 57.386 45.455 0.00 0.00 0.00 3.18
1135 1206 6.338214 ACTATGGTGATGCAGATAGTGTAG 57.662 41.667 0.00 0.00 31.77 2.74
1136 1207 6.731292 AACTATGGTGATGCAGATAGTGTA 57.269 37.500 0.00 0.00 33.01 2.90
1137 1208 5.620738 AACTATGGTGATGCAGATAGTGT 57.379 39.130 0.00 0.00 33.01 3.55
1138 1209 6.286758 AGAAACTATGGTGATGCAGATAGTG 58.713 40.000 0.00 0.00 33.01 2.74
1139 1210 6.463614 GGAGAAACTATGGTGATGCAGATAGT 60.464 42.308 0.00 0.00 33.89 2.12
1140 1211 5.931146 GGAGAAACTATGGTGATGCAGATAG 59.069 44.000 0.00 0.00 0.00 2.08
1141 1212 5.221722 GGGAGAAACTATGGTGATGCAGATA 60.222 44.000 0.00 0.00 0.00 1.98
1142 1213 4.445448 GGGAGAAACTATGGTGATGCAGAT 60.445 45.833 0.00 0.00 0.00 2.90
1150 1221 2.369394 GCTTGGGGAGAAACTATGGTG 58.631 52.381 0.00 0.00 0.00 4.17
1161 1232 1.885163 AACTACGTCGGCTTGGGGAG 61.885 60.000 0.00 0.00 0.00 4.30
1162 1233 0.611618 TAACTACGTCGGCTTGGGGA 60.612 55.000 0.00 0.00 0.00 4.81
1163 1234 0.462789 ATAACTACGTCGGCTTGGGG 59.537 55.000 0.00 0.00 0.00 4.96
1165 1236 1.135527 TCCATAACTACGTCGGCTTGG 59.864 52.381 0.00 0.00 0.00 3.61
1167 1238 1.820519 TGTCCATAACTACGTCGGCTT 59.179 47.619 0.00 0.00 0.00 4.35
1169 1240 1.553308 GTGTCCATAACTACGTCGGC 58.447 55.000 0.00 0.00 0.00 5.54
1170 1241 1.532505 CGGTGTCCATAACTACGTCGG 60.533 57.143 0.00 0.00 0.00 4.79
1171 1242 1.398041 TCGGTGTCCATAACTACGTCG 59.602 52.381 0.00 0.00 0.00 5.12
1172 1243 3.181493 ACATCGGTGTCCATAACTACGTC 60.181 47.826 0.00 0.00 31.41 4.34
1173 1244 2.756760 ACATCGGTGTCCATAACTACGT 59.243 45.455 0.00 0.00 31.41 3.57
1174 1245 3.431922 ACATCGGTGTCCATAACTACG 57.568 47.619 0.00 0.00 31.41 3.51
1182 1257 2.033448 GCCCAACATCGGTGTCCA 59.967 61.111 0.00 0.00 37.67 4.02
1184 1259 0.240945 CAAAGCCCAACATCGGTGTC 59.759 55.000 0.00 0.00 37.67 3.67
1191 1266 0.393820 CTGCAACCAAAGCCCAACAT 59.606 50.000 0.00 0.00 0.00 2.71
1204 1279 3.579626 GAACGTCCGCAGCTGCAAC 62.580 63.158 36.03 29.56 42.21 4.17
1219 1294 1.876156 CCTGTTCTTCCACAGCAGAAC 59.124 52.381 5.62 5.62 46.26 3.01
1242 1317 1.374758 GAGAACCCCAGCAGACACG 60.375 63.158 0.00 0.00 0.00 4.49
1344 1419 2.737359 CGCAATGAAGATGGCAAGCATT 60.737 45.455 0.00 0.00 0.00 3.56
1379 1454 1.220206 CCATGCCTGTCGAAGAGCT 59.780 57.895 0.00 0.00 36.95 4.09
1402 1477 2.563179 TCTCCTCTCCGTGGAAAGAAAG 59.437 50.000 0.00 0.00 32.61 2.62
1414 1489 3.252554 ACACTGGGATATCTCCTCTCC 57.747 52.381 0.00 0.00 41.74 3.71
1444 1519 8.736244 GCTAAATACTGGGACAATTACTCAAAA 58.264 33.333 0.00 0.00 38.70 2.44
1445 1520 8.107095 AGCTAAATACTGGGACAATTACTCAAA 58.893 33.333 0.00 0.00 38.70 2.69
1446 1521 7.630082 AGCTAAATACTGGGACAATTACTCAA 58.370 34.615 0.00 0.00 38.70 3.02
1447 1522 7.195374 AGCTAAATACTGGGACAATTACTCA 57.805 36.000 0.00 0.00 38.70 3.41
1526 1601 1.471684 AGACGACGACTTGTGGTATCC 59.528 52.381 0.00 0.00 39.88 2.59
1548 1623 1.497991 TTTCTCTGAAGGCGTGTTCG 58.502 50.000 0.00 0.00 40.37 3.95
1573 1648 2.692557 CCAGTTTGTGGTGAATGGTCAA 59.307 45.455 0.00 0.00 42.17 3.18
1684 1759 5.652014 TCACATGGTTTGTCTTTTCTTGACT 59.348 36.000 0.00 0.00 36.00 3.41
1725 1800 9.825109 TGTTTCTGTATTAATCCATAATGTCGA 57.175 29.630 0.00 0.00 35.77 4.20
1788 1863 3.304391 GCTAAACGTTGATTTGAGTGGCA 60.304 43.478 0.00 0.00 0.00 4.92
1790 1865 3.252215 TGGCTAAACGTTGATTTGAGTGG 59.748 43.478 0.00 0.00 0.00 4.00
1799 1874 6.874664 TGTGAACTATATTGGCTAAACGTTGA 59.125 34.615 0.00 0.00 0.00 3.18
1818 1893 6.362283 AGCAATAGCAAAATAACGTTGTGAAC 59.638 34.615 11.99 0.00 45.49 3.18
1844 1919 9.651718 GAATGTCAGTACAAGTTTAAGTTGAAG 57.348 33.333 18.11 5.93 39.58 3.02
1845 1920 9.168451 TGAATGTCAGTACAAGTTTAAGTTGAA 57.832 29.630 18.11 0.00 39.58 2.69
1846 1921 8.725405 TGAATGTCAGTACAAGTTTAAGTTGA 57.275 30.769 18.11 0.93 39.58 3.18
1879 1954 7.237055 GGGATCCTACCACCTTATAACAATAGT 59.763 40.741 12.58 0.00 0.00 2.12
1992 2067 6.040504 AGTTCCACCTTCTGTATTTGGTTTTC 59.959 38.462 0.00 0.00 0.00 2.29
2012 2087 9.018582 TCCTTTCTGTAGTTACTAGTTAGTTCC 57.981 37.037 0.00 0.00 37.73 3.62
2295 2370 9.508567 GCTTCATGGAGTTTATTTTATCTGAAC 57.491 33.333 2.16 0.00 0.00 3.18
2345 2420 5.488919 TGAAATCTACTCCAGGATCTTGGTT 59.511 40.000 22.17 13.47 39.35 3.67
2354 2429 8.340618 TCATTTTTCTTGAAATCTACTCCAGG 57.659 34.615 0.00 0.00 0.00 4.45
2424 2499 1.606668 TGGTGTTTCATCAACTTCGCC 59.393 47.619 0.00 0.00 36.21 5.54
2685 2761 1.134580 AGATGTCAGAAGGCGATGGTG 60.135 52.381 0.00 0.00 0.00 4.17
2778 2854 3.058016 AGTCATGGCAGTGTTTGATTTCG 60.058 43.478 0.00 0.00 0.00 3.46
2825 2901 6.542821 TCCTACACCAGATTCAAGATGTTTT 58.457 36.000 0.00 0.00 0.00 2.43
3011 3087 5.564259 GCACTGAAATTCTTTGTCTGCTCAT 60.564 40.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.