Multiple sequence alignment - TraesCS2D01G492800

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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 TraesCS2D01G492800 chr2D 100.000 2981 0 0 1 2981 590365234 590368214 0.000000e+00 5505.0
1 TraesCS2D01G492800 chr2D 81.553 412 43 13 6 386 590343861 590344270 2.890000e-80 309.0
2 TraesCS2D01G492800 chr2D 94.845 97 5 0 385 481 590344522 590344618 5.150000e-33 152.0
3 TraesCS2D01G492800 chr2B 94.376 1458 57 10 1535 2981 715599913 715601356 0.000000e+00 2215.0
4 TraesCS2D01G492800 chr2B 85.505 1090 85 39 385 1461 715598821 715599850 0.000000e+00 1070.0
5 TraesCS2D01G492800 chr2A 95.108 1022 44 6 1961 2981 724747170 724748186 0.000000e+00 1605.0
6 TraesCS2D01G492800 chr2A 87.007 1039 74 31 385 1416 724745231 724746215 0.000000e+00 1114.0
7 TraesCS2D01G492800 chr2A 95.659 622 25 2 1535 2155 724746310 724746930 0.000000e+00 998.0
8 TraesCS2D01G492800 chr2A 98.974 195 2 0 1961 2155 724746954 724747148 1.700000e-92 350.0
9 TraesCS2D01G492800 chr2A 82.955 264 21 6 144 386 724744801 724745061 1.800000e-52 217.0
10 TraesCS2D01G492800 chr2A 87.805 123 11 2 1 119 724744230 724744352 1.110000e-29 141.0
11 TraesCS2D01G492800 chr3B 82.453 587 81 14 2412 2981 188701915 188702496 7.420000e-136 494.0
12 TraesCS2D01G492800 chr3B 97.917 48 1 0 1935 1982 188614945 188614992 1.900000e-12 84.2
13 TraesCS2D01G492800 chr3A 83.878 459 51 11 2540 2981 145620253 145620705 1.650000e-112 416.0


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 TraesCS2D01G492800 chr2D 590365234 590368214 2980 False 5505.0 5505 100.000000 1 2981 1 chr2D.!!$F1 2980
1 TraesCS2D01G492800 chr2D 590343861 590344618 757 False 230.5 309 88.199000 6 481 2 chr2D.!!$F2 475
2 TraesCS2D01G492800 chr2B 715598821 715601356 2535 False 1642.5 2215 89.940500 385 2981 2 chr2B.!!$F1 2596
3 TraesCS2D01G492800 chr2A 724744230 724748186 3956 False 737.5 1605 91.251333 1 2981 6 chr2A.!!$F1 2980
4 TraesCS2D01G492800 chr3B 188701915 188702496 581 False 494.0 494 82.453000 2412 2981 1 chr3B.!!$F2 569

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
797 1520 0.311477 TGGTTTTACTTTTCGGCGCC 59.689 50.0 19.07 19.07 0.0 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2403 3597 0.476338 TGTGGCCCTTGACTGCTTTA 59.524 50.0 0.0 0.0 0.0 1.85 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
68 69 3.747099 AGCTTGTGCATCGTTGAATAC 57.253 42.857 0.00 0.00 42.74 1.89
106 115 2.358957 CTTGGTTGCTCCGATCATTGA 58.641 47.619 0.00 0.00 39.52 2.57
107 116 2.488204 TGGTTGCTCCGATCATTGAA 57.512 45.000 0.00 0.00 39.52 2.69
113 122 3.461061 TGCTCCGATCATTGAAGATGTC 58.539 45.455 0.00 0.00 0.00 3.06
126 135 2.661176 AGATGTCTAGGTTTGGGGGA 57.339 50.000 0.00 0.00 0.00 4.81
127 136 2.929301 AGATGTCTAGGTTTGGGGGAA 58.071 47.619 0.00 0.00 0.00 3.97
128 137 3.265489 AGATGTCTAGGTTTGGGGGAAA 58.735 45.455 0.00 0.00 0.00 3.13
131 140 5.494706 AGATGTCTAGGTTTGGGGGAAATTA 59.505 40.000 0.00 0.00 0.00 1.40
166 599 3.975992 GCGTGAGGCAAATAGTGTG 57.024 52.632 0.00 0.00 42.87 3.82
167 600 1.438651 GCGTGAGGCAAATAGTGTGA 58.561 50.000 0.00 0.00 42.87 3.58
182 615 1.741770 GTGACCCCACAAGCTAGCG 60.742 63.158 9.55 0.00 42.72 4.26
207 640 1.449778 GCTAGGGTTTGTCCTCCGC 60.450 63.158 0.00 0.00 38.30 5.54
230 680 1.212616 CACCTCAATCGATCCTTCGC 58.787 55.000 0.00 0.00 45.10 4.70
247 701 4.375272 CTTCGCTAGATTGTGGATGATGT 58.625 43.478 0.00 0.00 0.00 3.06
254 708 7.148171 CGCTAGATTGTGGATGATGTATCTCTA 60.148 40.741 0.00 0.00 36.03 2.43
279 733 6.569179 TTGAGTTGGAATAAAACTAGCCAC 57.431 37.500 0.00 0.00 37.98 5.01
333 788 7.517417 CGACTATGCTAGGTTTATCTTTGCTTG 60.517 40.741 0.00 0.00 0.00 4.01
344 799 0.318107 CTTTGCTTGAAGCCACACCG 60.318 55.000 15.43 0.00 41.51 4.94
382 840 4.609947 CAATTTTGCTAACTGTGCTCACA 58.390 39.130 2.48 2.48 39.32 3.58
386 844 0.371645 GCTAACTGTGCTCACATCGC 59.628 55.000 2.90 1.17 41.01 4.58
468 1181 4.722700 AGCACCATGTCGCCACCC 62.723 66.667 0.25 0.00 0.00 4.61
556 1269 1.130186 GTCGACAGAGTCCCGTAAGAC 59.870 57.143 11.55 0.00 43.02 3.01
691 1408 1.674359 AACGAGTGTTTCCACATGCA 58.326 45.000 0.00 0.00 44.39 3.96
715 1432 4.924305 AACACTCCAGACAGTAACGTAA 57.076 40.909 0.00 0.00 0.00 3.18
717 1434 3.633525 ACACTCCAGACAGTAACGTAACA 59.366 43.478 0.00 0.00 0.00 2.41
718 1435 4.227538 CACTCCAGACAGTAACGTAACAG 58.772 47.826 0.00 0.00 0.00 3.16
719 1436 4.023450 CACTCCAGACAGTAACGTAACAGA 60.023 45.833 0.00 0.00 0.00 3.41
720 1437 4.581824 ACTCCAGACAGTAACGTAACAGAA 59.418 41.667 0.00 0.00 0.00 3.02
721 1438 5.068198 ACTCCAGACAGTAACGTAACAGAAA 59.932 40.000 0.00 0.00 0.00 2.52
722 1439 6.092955 TCCAGACAGTAACGTAACAGAAAT 57.907 37.500 0.00 0.00 0.00 2.17
723 1440 5.924254 TCCAGACAGTAACGTAACAGAAATG 59.076 40.000 0.00 0.00 0.00 2.32
724 1441 5.389516 CCAGACAGTAACGTAACAGAAATGC 60.390 44.000 0.00 0.00 0.00 3.56
725 1442 5.176774 CAGACAGTAACGTAACAGAAATGCA 59.823 40.000 0.00 0.00 0.00 3.96
730 1447 7.095774 ACAGTAACGTAACAGAAATGCAAGTAG 60.096 37.037 0.00 0.00 0.00 2.57
731 1448 4.663636 ACGTAACAGAAATGCAAGTAGC 57.336 40.909 0.00 0.00 45.96 3.58
747 1464 5.220931 GCAAGTAGCTCATTTGGTGATAAGG 60.221 44.000 0.00 0.00 41.15 2.69
776 1499 1.480954 CTGTGTACGGCAAGGATAGGT 59.519 52.381 0.00 0.00 0.00 3.08
790 1513 7.214381 GCAAGGATAGGTTTGGTTTTACTTTT 58.786 34.615 0.00 0.00 0.00 2.27
791 1514 7.384115 GCAAGGATAGGTTTGGTTTTACTTTTC 59.616 37.037 0.00 0.00 0.00 2.29
793 1516 6.208007 AGGATAGGTTTGGTTTTACTTTTCGG 59.792 38.462 0.00 0.00 0.00 4.30
794 1517 4.049546 AGGTTTGGTTTTACTTTTCGGC 57.950 40.909 0.00 0.00 0.00 5.54
795 1518 2.790448 GGTTTGGTTTTACTTTTCGGCG 59.210 45.455 0.00 0.00 0.00 6.46
796 1519 2.122563 TTGGTTTTACTTTTCGGCGC 57.877 45.000 0.00 0.00 0.00 6.53
797 1520 0.311477 TGGTTTTACTTTTCGGCGCC 59.689 50.000 19.07 19.07 0.00 6.53
798 1521 0.726787 GGTTTTACTTTTCGGCGCCG 60.727 55.000 42.13 42.13 41.35 6.46
799 1522 0.726787 GTTTTACTTTTCGGCGCCGG 60.727 55.000 44.95 31.84 40.25 6.13
800 1523 1.165284 TTTTACTTTTCGGCGCCGGT 61.165 50.000 44.95 35.28 40.25 5.28
801 1524 1.567746 TTTACTTTTCGGCGCCGGTC 61.568 55.000 44.95 10.53 40.25 4.79
802 1525 2.712325 TTACTTTTCGGCGCCGGTCA 62.712 55.000 44.95 28.12 40.25 4.02
803 1526 3.788766 CTTTTCGGCGCCGGTCAG 61.789 66.667 44.95 32.22 40.25 3.51
804 1527 4.612412 TTTTCGGCGCCGGTCAGT 62.612 61.111 44.95 0.00 40.25 3.41
895 1619 2.204244 TTTCTCCCCCACCCCTCC 60.204 66.667 0.00 0.00 0.00 4.30
935 1661 2.231380 GGGGTCCTCTCCTTTGCCA 61.231 63.158 0.00 0.00 0.00 4.92
963 1689 1.259840 CCCAACATCCCAAGCCAAGG 61.260 60.000 0.00 0.00 0.00 3.61
987 1713 2.123982 CATTGCCCCTGCCTCCTC 60.124 66.667 0.00 0.00 36.33 3.71
993 1719 1.614824 CCCCTGCCTCCTCTTCAGT 60.615 63.158 0.00 0.00 0.00 3.41
998 1725 0.906756 TGCCTCCTCTTCAGTCCTGG 60.907 60.000 0.00 0.00 0.00 4.45
1008 1735 3.453717 TCTTCAGTCCTGGAATGGATGAG 59.546 47.826 22.52 15.03 38.52 2.90
1066 1793 0.875059 CGTTTGCCAAGGAGAAGGAC 59.125 55.000 0.00 0.00 0.00 3.85
1091 1818 2.280552 ACCCCGACGCTGCTTCTTA 61.281 57.895 4.58 0.00 0.00 2.10
1092 1819 1.144057 CCCCGACGCTGCTTCTTAT 59.856 57.895 4.58 0.00 0.00 1.73
1100 1827 1.503294 GCTGCTTCTTATACCTCGCC 58.497 55.000 0.00 0.00 0.00 5.54
1101 1828 1.874320 GCTGCTTCTTATACCTCGCCC 60.874 57.143 0.00 0.00 0.00 6.13
1102 1829 1.689273 CTGCTTCTTATACCTCGCCCT 59.311 52.381 0.00 0.00 0.00 5.19
1103 1830 1.687123 TGCTTCTTATACCTCGCCCTC 59.313 52.381 0.00 0.00 0.00 4.30
1104 1831 1.336056 GCTTCTTATACCTCGCCCTCG 60.336 57.143 0.00 0.00 0.00 4.63
1105 1832 1.269998 CTTCTTATACCTCGCCCTCGG 59.730 57.143 0.00 0.00 36.13 4.63
1144 1871 1.136690 GTTGTCGTCGTGCTCATTGA 58.863 50.000 0.00 0.00 0.00 2.57
1146 1873 0.031449 TGTCGTCGTGCTCATTGACA 59.969 50.000 0.00 0.00 34.27 3.58
1147 1874 0.435008 GTCGTCGTGCTCATTGACAC 59.565 55.000 8.45 8.45 32.91 3.67
1166 1893 0.255890 CCGAATCTGGGTGATGGGTT 59.744 55.000 0.00 0.00 35.21 4.11
1168 1895 1.767759 GAATCTGGGTGATGGGTTGG 58.232 55.000 0.00 0.00 35.21 3.77
1174 1901 0.323999 GGGTGATGGGTTGGGTTACC 60.324 60.000 0.00 0.00 37.47 2.85
1175 1902 0.702316 GGTGATGGGTTGGGTTACCT 59.298 55.000 0.00 0.00 38.30 3.08
1185 1912 2.611520 GGGTTACCTCCCATCCGAA 58.388 57.895 0.00 0.00 46.30 4.30
1329 2061 4.083003 TGCACCTTGATAACGTGGAATTTC 60.083 41.667 0.00 0.00 0.00 2.17
1373 2107 6.255453 CCTGTATGAAACACCAAAACTTTGTG 59.745 38.462 1.76 3.27 33.67 3.33
1382 2116 3.119280 ACCAAAACTTTGTGACCCTTTCG 60.119 43.478 1.76 0.00 36.45 3.46
1399 2133 3.745332 TTCGAACAACATGCATGCTAG 57.255 42.857 26.53 17.77 0.00 3.42
1419 2155 4.618920 AGTAACAGGTCTTCAAATCGGT 57.381 40.909 0.00 0.00 0.00 4.69
1523 2275 9.592196 TTACTAAAATATACTCTATGGGACGGT 57.408 33.333 0.00 0.00 0.00 4.83
1524 2276 7.893658 ACTAAAATATACTCTATGGGACGGTG 58.106 38.462 0.00 0.00 0.00 4.94
1525 2277 5.740290 AAATATACTCTATGGGACGGTGG 57.260 43.478 0.00 0.00 0.00 4.61
1526 2278 2.011122 ATACTCTATGGGACGGTGGG 57.989 55.000 0.00 0.00 0.00 4.61
1527 2279 0.928505 TACTCTATGGGACGGTGGGA 59.071 55.000 0.00 0.00 0.00 4.37
1528 2280 0.397254 ACTCTATGGGACGGTGGGAG 60.397 60.000 0.00 0.00 0.00 4.30
1529 2281 0.397254 CTCTATGGGACGGTGGGAGT 60.397 60.000 0.00 0.00 0.00 3.85
1530 2282 0.928505 TCTATGGGACGGTGGGAGTA 59.071 55.000 0.00 0.00 0.00 2.59
1531 2283 1.038280 CTATGGGACGGTGGGAGTAC 58.962 60.000 0.00 0.00 0.00 2.73
1532 2284 0.632835 TATGGGACGGTGGGAGTACT 59.367 55.000 0.00 0.00 0.00 2.73
1533 2285 0.252558 ATGGGACGGTGGGAGTACTT 60.253 55.000 0.00 0.00 0.00 2.24
1534 2286 0.901580 TGGGACGGTGGGAGTACTTC 60.902 60.000 0.00 0.00 0.00 3.01
1535 2287 0.901580 GGGACGGTGGGAGTACTTCA 60.902 60.000 2.92 0.00 0.00 3.02
1536 2288 1.192428 GGACGGTGGGAGTACTTCAT 58.808 55.000 2.92 0.00 0.00 2.57
1537 2289 2.381911 GGACGGTGGGAGTACTTCATA 58.618 52.381 2.92 0.00 0.00 2.15
1538 2290 2.762327 GGACGGTGGGAGTACTTCATAA 59.238 50.000 2.92 0.00 0.00 1.90
1539 2291 3.387050 GGACGGTGGGAGTACTTCATAAT 59.613 47.826 2.92 0.00 0.00 1.28
1540 2292 4.369182 GACGGTGGGAGTACTTCATAATG 58.631 47.826 2.92 0.00 0.00 1.90
1541 2293 3.134081 ACGGTGGGAGTACTTCATAATGG 59.866 47.826 2.92 0.00 0.00 3.16
1544 2296 5.454755 CGGTGGGAGTACTTCATAATGGATT 60.455 44.000 2.92 0.00 0.00 3.01
1548 2300 7.657761 GTGGGAGTACTTCATAATGGATTACTG 59.342 40.741 2.92 0.00 0.00 2.74
1560 2312 8.562892 CATAATGGATTACTGGAGAACACAATC 58.437 37.037 0.00 0.00 0.00 2.67
1580 2332 6.986817 ACAATCTCACGGTTCTTTCCATATAG 59.013 38.462 0.00 0.00 0.00 1.31
1625 2377 8.566260 TCAAATTGCAAATTATTCAAAACAGGG 58.434 29.630 1.71 0.00 0.00 4.45
1626 2378 8.351461 CAAATTGCAAATTATTCAAAACAGGGT 58.649 29.630 1.71 0.00 0.00 4.34
1627 2379 9.566432 AAATTGCAAATTATTCAAAACAGGGTA 57.434 25.926 1.71 0.00 0.00 3.69
1630 2383 5.575218 GCAAATTATTCAAAACAGGGTACGG 59.425 40.000 0.00 0.00 0.00 4.02
1707 2460 4.272489 GGAAGTCCCAATCATTCACATCA 58.728 43.478 0.00 0.00 34.14 3.07
1713 2466 6.718454 AGTCCCAATCATTCACATCAATATCC 59.282 38.462 0.00 0.00 0.00 2.59
1716 2469 7.884877 TCCCAATCATTCACATCAATATCCTAC 59.115 37.037 0.00 0.00 0.00 3.18
1799 2552 2.770802 AGAGCAATACAGCAGGATCAGT 59.229 45.455 0.00 0.00 36.85 3.41
2164 3351 5.875224 TGAATAAAGTGACAGATGGTCCAA 58.125 37.500 0.00 0.00 46.38 3.53
2251 3445 8.758829 ACCATCTATTCACTTCTTATACACACA 58.241 33.333 0.00 0.00 0.00 3.72
2252 3446 9.035607 CCATCTATTCACTTCTTATACACACAC 57.964 37.037 0.00 0.00 0.00 3.82
2253 3447 9.586435 CATCTATTCACTTCTTATACACACACA 57.414 33.333 0.00 0.00 0.00 3.72
2254 3448 8.981724 TCTATTCACTTCTTATACACACACAC 57.018 34.615 0.00 0.00 0.00 3.82
2255 3449 8.581578 TCTATTCACTTCTTATACACACACACA 58.418 33.333 0.00 0.00 0.00 3.72
2258 3452 6.342111 TCACTTCTTATACACACACACAACA 58.658 36.000 0.00 0.00 0.00 3.33
2272 3466 2.240160 ACACAACACCACAAGTTAGGGA 59.760 45.455 0.00 0.00 0.00 4.20
2361 3555 8.467963 AATCAGTATTGCCATGAATGATTACA 57.532 30.769 5.52 0.00 34.94 2.41
2362 3556 7.500720 TCAGTATTGCCATGAATGATTACAG 57.499 36.000 0.00 0.00 0.00 2.74
2364 3558 8.210265 TCAGTATTGCCATGAATGATTACAGTA 58.790 33.333 0.00 0.00 0.00 2.74
2403 3597 0.037419 GGGCCACAACATTCGCAAAT 60.037 50.000 4.39 0.00 0.00 2.32
2408 3602 3.181531 GCCACAACATTCGCAAATAAAGC 60.182 43.478 0.00 0.00 0.00 3.51
2509 3708 6.018669 ACAAGCTCGTCTAGTTTTCTTTTCTG 60.019 38.462 0.00 0.00 0.00 3.02
2527 3726 2.303022 TCTGTTCACCTCCATGAAGGAC 59.697 50.000 4.34 0.00 43.07 3.85
2538 3737 5.500234 CTCCATGAAGGACCATCTGTTAAA 58.500 41.667 0.00 0.00 43.07 1.52
2638 3842 4.834496 TGAAGGAGATCAAATTTGCCACTT 59.166 37.500 13.54 13.88 0.00 3.16
2743 3949 3.366396 GACTCTCCATAGTTCCCAGACA 58.634 50.000 0.00 0.00 0.00 3.41
2745 3951 3.772025 ACTCTCCATAGTTCCCAGACAAG 59.228 47.826 0.00 0.00 0.00 3.16
2833 4039 5.335504 GCACTCTCTTGCTAAAGAATGCTTT 60.336 40.000 3.62 3.62 41.89 3.51
2947 4162 7.703621 GCTTGTAAATACATTCTAGTCGTGGTA 59.296 37.037 0.00 0.00 35.89 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 3.244805 GCAACCAAGGTAGGGAAAGTAGT 60.245 47.826 0.00 0.00 0.00 2.73
73 74 3.009143 AGCAACCAAGGTAGGGAAAGTAG 59.991 47.826 0.00 0.00 0.00 2.57
87 96 2.488204 TCAATGATCGGAGCAACCAA 57.512 45.000 0.00 0.00 38.90 3.67
106 115 2.929301 TCCCCCAAACCTAGACATCTT 58.071 47.619 0.00 0.00 0.00 2.40
107 116 2.661176 TCCCCCAAACCTAGACATCT 57.339 50.000 0.00 0.00 0.00 2.90
166 599 1.153549 CTCGCTAGCTTGTGGGGTC 60.154 63.158 13.93 0.00 0.00 4.46
167 600 2.982130 CTCGCTAGCTTGTGGGGT 59.018 61.111 13.93 0.00 0.00 4.95
182 615 1.383523 GACAAACCCTAGCCATGCTC 58.616 55.000 0.00 0.00 40.44 4.26
207 640 0.179100 AGGATCGATTGAGGTGCGTG 60.179 55.000 0.00 0.00 0.00 5.34
254 708 7.574967 CGTGGCTAGTTTTATTCCAACTCAAAT 60.575 37.037 0.00 0.00 35.95 2.32
305 759 6.144724 GCAAAGATAAACCTAGCATAGTCGAG 59.855 42.308 0.00 0.00 36.82 4.04
307 761 5.986135 AGCAAAGATAAACCTAGCATAGTCG 59.014 40.000 0.00 0.00 36.82 4.18
312 766 6.405176 GCTTCAAGCAAAGATAAACCTAGCAT 60.405 38.462 3.89 0.00 41.89 3.79
333 788 1.873698 TGTTTACTCGGTGTGGCTTC 58.126 50.000 0.00 0.00 0.00 3.86
382 840 5.559035 GCGAGATTAGCTTTGTTTATGCGAT 60.559 40.000 0.00 0.00 32.44 4.58
386 844 4.966366 GCTGCGAGATTAGCTTTGTTTATG 59.034 41.667 0.00 0.00 36.99 1.90
436 1149 2.074576 GGTGCTTTCGGTTAGGAGTTC 58.925 52.381 0.00 0.00 0.00 3.01
468 1181 7.662897 GGATTAGCCGGGATAAGATAGATTAG 58.337 42.308 10.83 0.00 0.00 1.73
556 1269 3.752222 GGCTCATCAGGATAAGCATCTTG 59.248 47.826 6.74 0.00 39.12 3.02
691 1408 3.118884 ACGTTACTGTCTGGAGTGTTTGT 60.119 43.478 0.00 0.00 0.00 2.83
715 1432 5.336213 CCAAATGAGCTACTTGCATTTCTGT 60.336 40.000 7.22 0.00 45.94 3.41
717 1434 4.768968 ACCAAATGAGCTACTTGCATTTCT 59.231 37.500 7.22 0.00 45.94 2.52
718 1435 4.860907 CACCAAATGAGCTACTTGCATTTC 59.139 41.667 7.22 0.00 45.94 2.17
719 1436 4.523943 TCACCAAATGAGCTACTTGCATTT 59.476 37.500 4.87 4.87 45.94 2.32
720 1437 4.081406 TCACCAAATGAGCTACTTGCATT 58.919 39.130 0.00 0.00 45.94 3.56
721 1438 3.689347 TCACCAAATGAGCTACTTGCAT 58.311 40.909 0.00 0.00 45.94 3.96
722 1439 3.138884 TCACCAAATGAGCTACTTGCA 57.861 42.857 0.00 0.00 45.94 4.08
723 1440 5.220931 CCTTATCACCAAATGAGCTACTTGC 60.221 44.000 0.00 0.00 41.91 4.01
724 1441 5.220931 GCCTTATCACCAAATGAGCTACTTG 60.221 44.000 0.00 0.00 41.91 3.16
725 1442 4.884164 GCCTTATCACCAAATGAGCTACTT 59.116 41.667 0.00 0.00 41.91 2.24
730 1447 1.334869 CGGCCTTATCACCAAATGAGC 59.665 52.381 0.00 0.00 41.91 4.26
731 1448 2.614057 GTCGGCCTTATCACCAAATGAG 59.386 50.000 0.00 0.00 41.91 2.90
747 1464 2.874780 CGTACACAGAGCGTCGGC 60.875 66.667 0.00 0.00 40.37 5.54
776 1499 2.461903 GCGCCGAAAAGTAAAACCAAA 58.538 42.857 0.00 0.00 0.00 3.28
794 1517 3.733960 TCGACTGACTGACCGGCG 61.734 66.667 0.00 0.00 0.00 6.46
795 1518 2.126424 GTCGACTGACTGACCGGC 60.126 66.667 8.70 0.00 42.08 6.13
796 1519 2.176055 CGTCGACTGACTGACCGG 59.824 66.667 14.70 0.00 43.21 5.28
797 1520 2.176055 CCGTCGACTGACTGACCG 59.824 66.667 14.70 0.00 43.21 4.79
798 1521 1.235948 ACTCCGTCGACTGACTGACC 61.236 60.000 14.70 0.00 43.21 4.02
799 1522 0.110147 CACTCCGTCGACTGACTGAC 60.110 60.000 14.70 0.00 43.21 3.51
800 1523 1.853114 GCACTCCGTCGACTGACTGA 61.853 60.000 14.70 1.61 43.21 3.41
801 1524 1.442857 GCACTCCGTCGACTGACTG 60.443 63.158 14.70 12.32 43.21 3.51
802 1525 2.627737 GGCACTCCGTCGACTGACT 61.628 63.158 14.70 0.00 43.21 3.41
803 1526 1.303799 TAGGCACTCCGTCGACTGAC 61.304 60.000 14.70 7.16 41.75 3.51
804 1527 0.393944 ATAGGCACTCCGTCGACTGA 60.394 55.000 14.70 11.91 41.75 3.41
817 1540 1.824852 TCTTGCTCGTTCAGATAGGCA 59.175 47.619 0.00 0.00 0.00 4.75
869 1593 3.572642 GGTGGGGGAGAAAGAAAAAGAA 58.427 45.455 0.00 0.00 0.00 2.52
870 1594 2.158370 GGGTGGGGGAGAAAGAAAAAGA 60.158 50.000 0.00 0.00 0.00 2.52
871 1595 2.248248 GGGTGGGGGAGAAAGAAAAAG 58.752 52.381 0.00 0.00 0.00 2.27
872 1596 1.132977 GGGGTGGGGGAGAAAGAAAAA 60.133 52.381 0.00 0.00 0.00 1.94
873 1597 0.485543 GGGGTGGGGGAGAAAGAAAA 59.514 55.000 0.00 0.00 0.00 2.29
874 1598 0.404346 AGGGGTGGGGGAGAAAGAAA 60.404 55.000 0.00 0.00 0.00 2.52
875 1599 0.845102 GAGGGGTGGGGGAGAAAGAA 60.845 60.000 0.00 0.00 0.00 2.52
876 1600 1.229853 GAGGGGTGGGGGAGAAAGA 60.230 63.158 0.00 0.00 0.00 2.52
877 1601 2.309504 GGAGGGGTGGGGGAGAAAG 61.310 68.421 0.00 0.00 0.00 2.62
898 1622 1.456923 CCATATATGCACACGCGACTG 59.543 52.381 15.93 8.42 42.97 3.51
902 1626 0.602638 ACCCCATATATGCACACGCG 60.603 55.000 3.53 3.53 42.97 6.01
903 1627 1.156736 GACCCCATATATGCACACGC 58.843 55.000 7.24 0.00 39.24 5.34
904 1628 1.347707 AGGACCCCATATATGCACACG 59.652 52.381 7.24 0.00 0.00 4.49
907 1631 2.237392 GGAGAGGACCCCATATATGCAC 59.763 54.545 7.24 0.00 0.00 4.57
935 1661 0.259938 GGGATGTTGGGAGCTTGGAT 59.740 55.000 0.00 0.00 0.00 3.41
963 1689 1.115326 GGCAGGGGCAATGGTTATCC 61.115 60.000 0.00 0.00 43.71 2.59
987 1713 3.433314 CCTCATCCATTCCAGGACTGAAG 60.433 52.174 8.41 1.09 41.30 3.02
993 1719 1.213678 CAAGCCTCATCCATTCCAGGA 59.786 52.381 0.00 0.00 43.01 3.86
998 1725 1.820519 TGTTGCAAGCCTCATCCATTC 59.179 47.619 0.00 0.00 0.00 2.67
1008 1735 1.288127 CAGAGCCTTGTTGCAAGCC 59.712 57.895 0.00 0.00 0.00 4.35
1066 1793 2.579201 AGCGTCGGGGTGATCTTG 59.421 61.111 0.00 0.00 0.00 3.02
1127 1854 0.031449 TGTCAATGAGCACGACGACA 59.969 50.000 0.00 0.00 32.17 4.35
1146 1873 0.914417 ACCCATCACCCAGATTCGGT 60.914 55.000 0.00 0.00 33.72 4.69
1147 1874 0.255890 AACCCATCACCCAGATTCGG 59.744 55.000 0.00 0.00 33.72 4.30
1168 1895 1.492764 TCTTCGGATGGGAGGTAACC 58.507 55.000 0.00 0.00 37.17 2.85
1174 1901 4.348863 AAGAATGATCTTCGGATGGGAG 57.651 45.455 0.00 0.00 42.26 4.30
1185 1912 5.362143 TGAAGATGACTCCGAAGAATGATCT 59.638 40.000 0.00 0.00 37.57 2.75
1203 1930 1.226435 GCTCGACGACGCTGAAGAT 60.226 57.895 1.48 0.00 39.58 2.40
1290 2017 1.137404 GCAAAGCATGTACCTGGCG 59.863 57.895 0.00 0.00 0.00 5.69
1329 2061 1.241165 GTAGGGAAACACAAACGGGG 58.759 55.000 0.00 0.00 0.00 5.73
1373 2107 1.606668 TGCATGTTGTTCGAAAGGGTC 59.393 47.619 0.00 0.00 0.00 4.46
1382 2116 5.295431 TGTTACTAGCATGCATGTTGTTC 57.705 39.130 26.79 17.26 0.00 3.18
1399 2133 4.083484 CCAACCGATTTGAAGACCTGTTAC 60.083 45.833 0.00 0.00 37.39 2.50
1419 2155 4.244066 CATGTCATTTTGAATTCGGCCAA 58.756 39.130 2.24 0.00 0.00 4.52
1499 2251 7.039223 CCACCGTCCCATAGAGTATATTTTAGT 60.039 40.741 0.00 0.00 0.00 2.24
1508 2260 0.928505 TCCCACCGTCCCATAGAGTA 59.071 55.000 0.00 0.00 0.00 2.59
1510 2262 0.397254 ACTCCCACCGTCCCATAGAG 60.397 60.000 0.00 0.00 0.00 2.43
1511 2263 0.928505 TACTCCCACCGTCCCATAGA 59.071 55.000 0.00 0.00 0.00 1.98
1514 2266 0.252558 AAGTACTCCCACCGTCCCAT 60.253 55.000 0.00 0.00 0.00 4.00
1515 2267 0.901580 GAAGTACTCCCACCGTCCCA 60.902 60.000 0.00 0.00 0.00 4.37
1516 2268 0.901580 TGAAGTACTCCCACCGTCCC 60.902 60.000 0.00 0.00 0.00 4.46
1517 2269 1.192428 ATGAAGTACTCCCACCGTCC 58.808 55.000 0.00 0.00 0.00 4.79
1518 2270 4.369182 CATTATGAAGTACTCCCACCGTC 58.631 47.826 0.00 0.00 0.00 4.79
1519 2271 3.134081 CCATTATGAAGTACTCCCACCGT 59.866 47.826 0.00 0.00 0.00 4.83
1520 2272 3.386726 TCCATTATGAAGTACTCCCACCG 59.613 47.826 0.00 0.00 0.00 4.94
1521 2273 5.568620 ATCCATTATGAAGTACTCCCACC 57.431 43.478 0.00 0.00 0.00 4.61
1522 2274 7.657761 CAGTAATCCATTATGAAGTACTCCCAC 59.342 40.741 0.00 0.00 0.00 4.61
1523 2275 7.202093 CCAGTAATCCATTATGAAGTACTCCCA 60.202 40.741 0.00 0.00 0.00 4.37
1524 2276 7.016268 TCCAGTAATCCATTATGAAGTACTCCC 59.984 40.741 0.00 0.00 0.00 4.30
1525 2277 7.963532 TCCAGTAATCCATTATGAAGTACTCC 58.036 38.462 0.00 0.00 0.00 3.85
1526 2278 8.861086 TCTCCAGTAATCCATTATGAAGTACTC 58.139 37.037 0.00 0.00 0.00 2.59
1527 2279 8.783660 TCTCCAGTAATCCATTATGAAGTACT 57.216 34.615 0.00 0.00 0.00 2.73
1528 2280 9.262358 GTTCTCCAGTAATCCATTATGAAGTAC 57.738 37.037 0.00 0.00 0.00 2.73
1529 2281 8.988060 TGTTCTCCAGTAATCCATTATGAAGTA 58.012 33.333 0.00 0.00 0.00 2.24
1530 2282 7.770897 GTGTTCTCCAGTAATCCATTATGAAGT 59.229 37.037 0.00 0.00 0.00 3.01
1531 2283 7.770433 TGTGTTCTCCAGTAATCCATTATGAAG 59.230 37.037 0.00 0.00 0.00 3.02
1532 2284 7.629157 TGTGTTCTCCAGTAATCCATTATGAA 58.371 34.615 0.00 0.00 0.00 2.57
1533 2285 7.194112 TGTGTTCTCCAGTAATCCATTATGA 57.806 36.000 0.00 0.00 0.00 2.15
1534 2286 7.864108 TTGTGTTCTCCAGTAATCCATTATG 57.136 36.000 0.00 0.00 0.00 1.90
1535 2287 8.497745 AGATTGTGTTCTCCAGTAATCCATTAT 58.502 33.333 0.00 0.00 32.29 1.28
1536 2288 7.861629 AGATTGTGTTCTCCAGTAATCCATTA 58.138 34.615 0.00 0.00 32.29 1.90
1537 2289 6.725364 AGATTGTGTTCTCCAGTAATCCATT 58.275 36.000 0.00 0.00 32.29 3.16
1538 2290 6.070021 TGAGATTGTGTTCTCCAGTAATCCAT 60.070 38.462 0.00 0.00 41.24 3.41
1539 2291 5.248248 TGAGATTGTGTTCTCCAGTAATCCA 59.752 40.000 0.00 0.00 41.24 3.41
1540 2292 5.582665 GTGAGATTGTGTTCTCCAGTAATCC 59.417 44.000 0.00 0.00 41.24 3.01
1541 2293 5.289675 CGTGAGATTGTGTTCTCCAGTAATC 59.710 44.000 0.00 0.00 41.24 1.75
1544 2296 3.056821 CCGTGAGATTGTGTTCTCCAGTA 60.057 47.826 0.00 0.00 41.24 2.74
1548 2300 2.457366 ACCGTGAGATTGTGTTCTCC 57.543 50.000 0.00 0.00 41.24 3.71
1560 2312 6.150396 AGTCTATATGGAAAGAACCGTGAG 57.850 41.667 0.00 0.00 0.00 3.51
1621 2373 3.947910 TTTGTTAGAGACCGTACCCTG 57.052 47.619 0.00 0.00 0.00 4.45
1707 2460 6.650427 TGAAGACATGTAGCGTAGGATATT 57.350 37.500 0.00 0.00 0.00 1.28
1713 2466 4.106197 GGTCTTGAAGACATGTAGCGTAG 58.894 47.826 24.95 0.00 46.79 3.51
1716 2469 3.238108 AGGTCTTGAAGACATGTAGCG 57.762 47.619 24.95 0.00 46.79 4.26
1752 2505 4.193826 TGTCTTCATCCTCTTGCTGTAC 57.806 45.455 0.00 0.00 0.00 2.90
1783 2536 5.121811 GTTCATGACTGATCCTGCTGTATT 58.878 41.667 0.00 0.00 0.00 1.89
1799 2552 2.083774 GATTTGACCGCTGGTTCATGA 58.916 47.619 0.00 0.00 35.25 3.07
2155 3342 6.633500 TTTTCCGATTATGATTGGACCATC 57.367 37.500 5.94 0.00 44.06 3.51
2156 3343 6.607198 AGTTTTTCCGATTATGATTGGACCAT 59.393 34.615 5.94 0.00 44.06 3.55
2164 3351 9.613428 TGTCTATTGAGTTTTTCCGATTATGAT 57.387 29.630 0.00 0.00 0.00 2.45
2236 3430 5.526111 GGTGTTGTGTGTGTGTATAAGAAGT 59.474 40.000 0.00 0.00 0.00 3.01
2251 3445 2.240160 TCCCTAACTTGTGGTGTTGTGT 59.760 45.455 0.00 0.00 0.00 3.72
2252 3446 2.925724 TCCCTAACTTGTGGTGTTGTG 58.074 47.619 0.00 0.00 0.00 3.33
2253 3447 3.655615 TTCCCTAACTTGTGGTGTTGT 57.344 42.857 0.00 0.00 0.00 3.32
2254 3448 3.067601 GGTTTCCCTAACTTGTGGTGTTG 59.932 47.826 0.00 0.00 36.93 3.33
2255 3449 3.293337 GGTTTCCCTAACTTGTGGTGTT 58.707 45.455 0.00 0.00 36.93 3.32
2258 3452 3.895704 ATGGTTTCCCTAACTTGTGGT 57.104 42.857 0.00 0.00 36.93 4.16
2272 3466 9.689501 TTCCTATCGTTCCTTAATAAATGGTTT 57.310 29.630 0.00 0.00 0.00 3.27
2361 3555 6.169094 CCTTGACTCTGATGAACATGTTACT 58.831 40.000 11.95 1.14 0.00 2.24
2362 3556 5.352569 CCCTTGACTCTGATGAACATGTTAC 59.647 44.000 11.95 6.98 0.00 2.50
2364 3558 4.330250 CCCTTGACTCTGATGAACATGTT 58.670 43.478 11.78 11.78 0.00 2.71
2403 3597 0.476338 TGTGGCCCTTGACTGCTTTA 59.524 50.000 0.00 0.00 0.00 1.85
2408 3602 1.915141 ATTCTTGTGGCCCTTGACTG 58.085 50.000 0.00 0.00 0.00 3.51
2496 3695 5.261216 TGGAGGTGAACAGAAAAGAAAACT 58.739 37.500 0.00 0.00 0.00 2.66
2527 3726 6.642540 GCCTTTCTCTTGTTTTTAACAGATGG 59.357 38.462 0.00 0.00 43.27 3.51
2583 3785 9.436957 TTTGGTTTTGAAGTTTAAAACTATGCA 57.563 25.926 25.97 16.89 43.81 3.96
2638 3842 2.593026 GAAAAGGGATGTGGGTGTTGA 58.407 47.619 0.00 0.00 0.00 3.18
2681 3887 2.209690 TTAGGGCTGGCTACCAAAAC 57.790 50.000 0.00 0.00 30.80 2.43
2743 3949 8.793592 GGAATGTACAAAAGACAAGGTATTCTT 58.206 33.333 0.00 0.00 35.79 2.52
2745 3951 8.106247 TGGAATGTACAAAAGACAAGGTATTC 57.894 34.615 0.00 0.00 0.00 1.75
2833 4039 4.067192 CAAGTGATCCAACTGACATGACA 58.933 43.478 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.