Multiple sequence alignment - TraesCS7B01G290700

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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 TraesCS7B01G290700 chr7B 100.000 3424 0 0 1 3424 526885443 526882020 0.000000e+00 6324
1 TraesCS7B01G290700 chr7B 94.615 260 6 1 3165 3424 526876676 526876425 2.480000e-106 396
2 TraesCS7B01G290700 chr7A 92.458 2864 104 47 1 2806 564348153 564345344 0.000000e+00 3989
3 TraesCS7B01G290700 chr7A 88.795 589 52 11 2837 3423 564345342 564344766 0.000000e+00 710
4 TraesCS7B01G290700 chr7D 93.779 2395 64 35 329 2683 498529494 498527145 0.000000e+00 3518
5 TraesCS7B01G290700 chr7D 90.456 461 33 9 2965 3424 498501676 498501226 6.320000e-167 597
6 TraesCS7B01G290700 chr7D 82.121 330 25 14 1 323 498529836 498529534 5.670000e-63 252
7 TraesCS7B01G290700 chr7D 88.550 131 10 1 2670 2795 498526471 498526341 1.650000e-33 154
8 TraesCS7B01G290700 chr6A 83.556 225 33 3 1264 1486 183766952 183766730 1.250000e-49 207
9 TraesCS7B01G290700 chr6A 87.647 170 19 2 1907 2075 183766397 183766229 2.700000e-46 196
10 TraesCS7B01G290700 chr6D 88.235 170 18 2 1907 2075 140038278 140038446 5.790000e-48 202
11 TraesCS7B01G290700 chr6B 87.647 170 19 2 1907 2075 239913788 239913956 2.700000e-46 196


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 TraesCS7B01G290700 chr7B 526882020 526885443 3423 True 6324.0 6324 100.0000 1 3424 1 chr7B.!!$R2 3423
1 TraesCS7B01G290700 chr7A 564344766 564348153 3387 True 2349.5 3989 90.6265 1 3423 2 chr7A.!!$R1 3422
2 TraesCS7B01G290700 chr7D 498526341 498529836 3495 True 1308.0 3518 88.1500 1 2795 3 chr7D.!!$R2 2794
3 TraesCS7B01G290700 chr6A 183766229 183766952 723 True 201.5 207 85.6015 1264 2075 2 chr6A.!!$R1 811

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
815 895 0.327924 TTTCACTCATGGGCACGGAT 59.672 50.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2640 2820 0.664224 TCCGCCGTTTCTTTGGTTTC 59.336 50.0 0.0 0.0 0.0 2.78 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
191 209 2.747467 GCAGCTGGTGATGTCATACCAT 60.747 50.000 17.12 0.77 45.28 3.55
192 210 3.494924 GCAGCTGGTGATGTCATACCATA 60.495 47.826 17.12 0.00 45.28 2.74
193 211 4.060900 CAGCTGGTGATGTCATACCATAC 58.939 47.826 5.57 9.03 45.28 2.39
194 212 3.071602 AGCTGGTGATGTCATACCATACC 59.928 47.826 12.00 0.00 45.28 2.73
195 213 3.181455 GCTGGTGATGTCATACCATACCA 60.181 47.826 12.00 0.00 45.28 3.25
241 262 2.749776 TCCGTTCATACACACACACAG 58.250 47.619 0.00 0.00 0.00 3.66
242 263 2.362717 TCCGTTCATACACACACACAGA 59.637 45.455 0.00 0.00 0.00 3.41
243 264 2.475111 CCGTTCATACACACACACAGAC 59.525 50.000 0.00 0.00 0.00 3.51
244 265 3.120041 CGTTCATACACACACACAGACA 58.880 45.455 0.00 0.00 0.00 3.41
367 428 5.295045 TCACACGAACCTTTTCTCTTTTACC 59.705 40.000 0.00 0.00 0.00 2.85
405 466 2.370445 CGTGCCTCATCCCTCCCTT 61.370 63.158 0.00 0.00 0.00 3.95
527 595 1.035139 TAATTAGTCTCCCCGTCCGC 58.965 55.000 0.00 0.00 0.00 5.54
641 717 2.123640 GGACGGAGGAGAGGAGGG 60.124 72.222 0.00 0.00 0.00 4.30
773 849 5.121454 CGGATAAGGTATCGTACAGACTACC 59.879 48.000 0.00 6.11 36.03 3.18
815 895 0.327924 TTTCACTCATGGGCACGGAT 59.672 50.000 0.00 0.00 0.00 4.18
972 1061 3.642778 GAGGCGCTGCTGGTCGTTA 62.643 63.158 7.64 0.00 0.00 3.18
988 1077 1.337821 GTTACCGTGCGAGTCTTGAG 58.662 55.000 0.00 0.00 0.00 3.02
989 1078 1.068748 GTTACCGTGCGAGTCTTGAGA 60.069 52.381 0.00 0.00 0.00 3.27
1110 1199 1.947146 CCTGTTGTTCGCGTCGTCA 60.947 57.895 5.77 0.00 0.00 4.35
1278 1367 3.083349 CGGGAGGAGTGGATGGCA 61.083 66.667 0.00 0.00 0.00 4.92
1317 1406 3.959975 GGCAACAAGTTCGCCGCA 61.960 61.111 9.49 0.00 35.79 5.69
1492 1581 2.555664 ACATTGTCCAGGTCCATCTCT 58.444 47.619 0.00 0.00 0.00 3.10
1493 1582 2.503356 ACATTGTCCAGGTCCATCTCTC 59.497 50.000 0.00 0.00 0.00 3.20
1495 1588 2.151502 TGTCCAGGTCCATCTCTCTC 57.848 55.000 0.00 0.00 0.00 3.20
1498 1591 1.648568 TCCAGGTCCATCTCTCTCCTT 59.351 52.381 0.00 0.00 0.00 3.36
1499 1592 2.038659 CCAGGTCCATCTCTCTCCTTC 58.961 57.143 0.00 0.00 0.00 3.46
1503 1598 1.953686 GTCCATCTCTCTCCTTCCTCG 59.046 57.143 0.00 0.00 0.00 4.63
1504 1599 1.847088 TCCATCTCTCTCCTTCCTCGA 59.153 52.381 0.00 0.00 0.00 4.04
1511 1606 2.104963 TCTCTCCTTCCTCGATCGATCA 59.895 50.000 24.40 5.07 0.00 2.92
1518 1613 2.375146 TCCTCGATCGATCAGTTTCCA 58.625 47.619 24.40 0.00 0.00 3.53
1521 1616 3.367607 CTCGATCGATCAGTTTCCACTC 58.632 50.000 24.40 0.00 0.00 3.51
1522 1617 2.752903 TCGATCGATCAGTTTCCACTCA 59.247 45.455 24.40 0.00 0.00 3.41
1524 1619 4.578928 TCGATCGATCAGTTTCCACTCATA 59.421 41.667 24.40 0.00 0.00 2.15
1525 1620 4.677378 CGATCGATCAGTTTCCACTCATAC 59.323 45.833 24.40 0.00 0.00 2.39
1526 1621 5.592054 GATCGATCAGTTTCCACTCATACA 58.408 41.667 20.52 0.00 0.00 2.29
1527 1622 5.598416 TCGATCAGTTTCCACTCATACAT 57.402 39.130 0.00 0.00 0.00 2.29
1528 1623 6.709018 TCGATCAGTTTCCACTCATACATA 57.291 37.500 0.00 0.00 0.00 2.29
1529 1624 6.504398 TCGATCAGTTTCCACTCATACATAC 58.496 40.000 0.00 0.00 0.00 2.39
1530 1625 6.096282 TCGATCAGTTTCCACTCATACATACA 59.904 38.462 0.00 0.00 0.00 2.29
1531 1626 6.925718 CGATCAGTTTCCACTCATACATACAT 59.074 38.462 0.00 0.00 0.00 2.29
1532 1627 7.095899 CGATCAGTTTCCACTCATACATACATG 60.096 40.741 0.00 0.00 0.00 3.21
1533 1628 6.946340 TCAGTTTCCACTCATACATACATGT 58.054 36.000 2.69 2.69 44.48 3.21
1534 1629 8.073467 TCAGTTTCCACTCATACATACATGTA 57.927 34.615 8.27 8.27 46.21 2.29
1535 1630 7.979537 TCAGTTTCCACTCATACATACATGTAC 59.020 37.037 7.96 0.00 45.11 2.90
1536 1631 7.763985 CAGTTTCCACTCATACATACATGTACA 59.236 37.037 7.96 0.00 45.11 2.90
1537 1632 7.764443 AGTTTCCACTCATACATACATGTACAC 59.236 37.037 7.96 0.00 45.11 2.90
1538 1633 6.156748 TCCACTCATACATACATGTACACC 57.843 41.667 7.96 0.00 45.11 4.16
1559 1654 3.578688 CACACACTGACTGATGATTCGA 58.421 45.455 0.00 0.00 0.00 3.71
1560 1655 3.989817 CACACACTGACTGATGATTCGAA 59.010 43.478 0.00 0.00 0.00 3.71
1561 1656 3.990469 ACACACTGACTGATGATTCGAAC 59.010 43.478 0.00 0.00 0.00 3.95
1563 1658 4.687948 CACACTGACTGATGATTCGAACTT 59.312 41.667 0.00 0.00 0.00 2.66
1564 1659 5.863935 CACACTGACTGATGATTCGAACTTA 59.136 40.000 0.00 0.00 0.00 2.24
1567 1662 7.604164 ACACTGACTGATGATTCGAACTTAATT 59.396 33.333 0.00 0.00 0.00 1.40
1568 1663 9.087424 CACTGACTGATGATTCGAACTTAATTA 57.913 33.333 0.00 0.00 0.00 1.40
1569 1664 9.307121 ACTGACTGATGATTCGAACTTAATTAG 57.693 33.333 0.00 1.09 0.00 1.73
1570 1665 8.131455 TGACTGATGATTCGAACTTAATTAGC 57.869 34.615 0.00 0.00 0.00 3.09
1571 1666 7.763985 TGACTGATGATTCGAACTTAATTAGCA 59.236 33.333 0.00 0.00 0.00 3.49
1572 1667 8.492673 ACTGATGATTCGAACTTAATTAGCAA 57.507 30.769 0.00 0.00 0.00 3.91
1573 1668 8.607459 ACTGATGATTCGAACTTAATTAGCAAG 58.393 33.333 0.00 0.00 0.00 4.01
1574 1669 7.409697 TGATGATTCGAACTTAATTAGCAAGC 58.590 34.615 0.00 0.00 0.00 4.01
1575 1670 6.119144 TGATTCGAACTTAATTAGCAAGCC 57.881 37.500 0.00 0.00 0.00 4.35
1576 1671 5.645929 TGATTCGAACTTAATTAGCAAGCCA 59.354 36.000 0.00 0.00 0.00 4.75
1577 1672 5.950758 TTCGAACTTAATTAGCAAGCCAA 57.049 34.783 0.00 0.00 0.00 4.52
1578 1673 5.545658 TCGAACTTAATTAGCAAGCCAAG 57.454 39.130 0.00 0.00 0.00 3.61
1579 1674 4.098416 CGAACTTAATTAGCAAGCCAAGC 58.902 43.478 0.00 0.00 0.00 4.01
1580 1675 4.142600 CGAACTTAATTAGCAAGCCAAGCT 60.143 41.667 0.71 0.71 45.77 3.74
1604 1703 8.748412 GCTATATCTTACACTGGAGATGAATCT 58.252 37.037 7.21 0.00 40.50 2.40
1613 1712 6.766944 ACACTGGAGATGAATCTGATTTGATC 59.233 38.462 4.11 9.21 37.25 2.92
1720 1821 2.715763 ACAAGAAGGACCCCTACTCA 57.284 50.000 0.00 0.00 31.13 3.41
1861 1962 4.096003 CGGGTGAAGGTGGCCGAT 62.096 66.667 0.00 0.00 0.00 4.18
1963 2112 2.024176 TCAAGGAGAAGCCCTACACA 57.976 50.000 0.00 0.00 34.95 3.72
2092 2241 2.564975 GTCCGTCCGTCGACACAT 59.435 61.111 17.16 0.00 42.86 3.21
2125 2280 3.574396 TCTCCGTTCTTGTCACTCTGAAT 59.426 43.478 0.00 0.00 0.00 2.57
2165 2327 1.851053 CTCTGCTTGTGATGATCGACG 59.149 52.381 0.00 0.00 0.00 5.12
2391 2553 0.549950 CTTCAGGATGGGGTGCATCT 59.450 55.000 0.00 0.00 36.16 2.90
2427 2592 1.453155 ACCGGTGCATTCTTGATCAC 58.547 50.000 6.12 0.00 0.00 3.06
2587 2767 6.397272 TCTGAATGGTTTAATTTCACATGGC 58.603 36.000 0.00 0.00 0.00 4.40
2608 2788 3.861840 CGATCAAGACCCAACAGTGTAT 58.138 45.455 0.00 0.00 0.00 2.29
2652 2832 6.790232 ATTTCTCACTGGAAACCAAAGAAA 57.210 33.333 16.97 16.97 39.08 2.52
2712 3586 9.069082 GTCGAATATATATGTGTAGAGGGCTAT 57.931 37.037 0.00 0.00 0.00 2.97
2724 3598 4.042271 AGAGGGCTATAGCTAGACTTCC 57.958 50.000 23.53 14.18 39.39 3.46
2737 3611 5.071519 AGCTAGACTTCCAATATGCAGATGT 59.928 40.000 0.00 0.00 0.00 3.06
2759 3633 5.948758 TGTATGCATATTTGAGTGAAACCCA 59.051 36.000 10.16 0.00 37.80 4.51
2761 3635 5.327616 TGCATATTTGAGTGAAACCCATG 57.672 39.130 0.00 0.00 37.80 3.66
2763 3637 5.105797 TGCATATTTGAGTGAAACCCATGAC 60.106 40.000 0.00 0.00 37.80 3.06
2784 3658 5.551583 TGACCATGGGCCTAATATATGAAGT 59.448 40.000 17.19 0.00 0.00 3.01
2806 3680 7.964604 AGTCAAAAATAAACTAGACGAAGCT 57.035 32.000 0.00 0.00 0.00 3.74
2807 3681 8.019769 AGTCAAAAATAAACTAGACGAAGCTC 57.980 34.615 0.00 0.00 0.00 4.09
2808 3682 6.948777 GTCAAAAATAAACTAGACGAAGCTCG 59.051 38.462 0.00 4.36 46.93 5.03
2821 3695 4.431035 GCTCGTATAGCCGCCAAA 57.569 55.556 0.00 0.00 46.25 3.28
2822 3696 2.685364 GCTCGTATAGCCGCCAAAA 58.315 52.632 0.00 0.00 46.25 2.44
2823 3697 1.011333 GCTCGTATAGCCGCCAAAAA 58.989 50.000 0.00 0.00 46.25 1.94
2862 3736 3.068307 ACTCGGCTATACACAAGATCACC 59.932 47.826 0.00 0.00 0.00 4.02
2863 3737 3.028130 TCGGCTATACACAAGATCACCA 58.972 45.455 0.00 0.00 0.00 4.17
2891 3765 1.141657 GATCTCCATGCTTGTGGGCTA 59.858 52.381 0.00 0.00 39.80 3.93
2896 3770 1.038681 CATGCTTGTGGGCTATGGCA 61.039 55.000 2.58 0.00 40.87 4.92
2897 3771 0.324552 ATGCTTGTGGGCTATGGCAA 60.325 50.000 2.58 0.00 40.87 4.52
2912 3786 2.415426 CAAAACCCACCGTGGTGC 59.585 61.111 16.55 0.00 44.16 5.01
2917 3791 2.202878 CCCACCGTGGTGCGATAG 60.203 66.667 16.55 0.00 44.16 2.08
2943 3818 4.858850 AGATACATTTGATGGCCTTGACA 58.141 39.130 3.32 0.00 33.60 3.58
2952 3827 1.305201 TGGCCTTGACAGTTTTCGTC 58.695 50.000 3.32 0.00 0.00 4.20
2956 3831 2.223180 GCCTTGACAGTTTTCGTCGTTT 60.223 45.455 0.00 0.00 36.11 3.60
2993 3868 1.789523 TACTACATGGGGAGGAGTGC 58.210 55.000 0.00 0.00 0.00 4.40
3000 3875 2.424733 GGGGAGGAGTGCCGTAGTC 61.425 68.421 0.00 0.00 39.96 2.59
3008 3883 4.155733 TGCCGTAGTCATGCCCCG 62.156 66.667 0.00 0.00 0.00 5.73
3010 3885 2.417516 CCGTAGTCATGCCCCGAG 59.582 66.667 0.00 0.00 0.00 4.63
3042 3917 5.291128 GTGTTGATCGATGAACCTCGTTAAT 59.709 40.000 22.42 0.00 39.62 1.40
3050 3925 9.760077 ATCGATGAACCTCGTTAATAAATACTT 57.240 29.630 0.00 0.00 39.62 2.24
3051 3926 9.027129 TCGATGAACCTCGTTAATAAATACTTG 57.973 33.333 0.00 0.00 39.62 3.16
3073 3948 3.449018 GTCTCTGGGTCTAAATCTCTGCA 59.551 47.826 0.00 0.00 0.00 4.41
3100 3975 7.946207 TGATGCAACTGGTAAATTCTAACAAA 58.054 30.769 0.00 0.00 0.00 2.83
3137 4012 2.674357 GTTGCAAATTGGATCATGGTGC 59.326 45.455 0.00 0.00 0.00 5.01
3148 4023 4.409901 TGGATCATGGTGCGGATGATATAT 59.590 41.667 5.22 0.00 40.03 0.86
3151 4026 4.932146 TCATGGTGCGGATGATATATACG 58.068 43.478 0.00 0.00 0.00 3.06
3159 4034 6.972901 GTGCGGATGATATATACGAAGATGAA 59.027 38.462 0.00 0.00 0.00 2.57
3160 4035 7.649705 GTGCGGATGATATATACGAAGATGAAT 59.350 37.037 0.00 0.00 0.00 2.57
3161 4036 7.862873 TGCGGATGATATATACGAAGATGAATC 59.137 37.037 0.00 0.00 0.00 2.52
3162 4037 7.862873 GCGGATGATATATACGAAGATGAATCA 59.137 37.037 0.00 0.00 0.00 2.57
3163 4038 9.905171 CGGATGATATATACGAAGATGAATCAT 57.095 33.333 0.00 0.00 35.97 2.45
3194 4069 5.627499 ACACAACATGGTGATGTATGTTC 57.373 39.130 19.90 0.00 43.53 3.18
3199 4074 8.461222 CACAACATGGTGATGTATGTTCTAAAT 58.539 33.333 19.90 0.00 43.53 1.40
3200 4075 9.023962 ACAACATGGTGATGTATGTTCTAAATT 57.976 29.630 19.90 0.00 43.53 1.82
3234 4110 1.377366 TAGGAGCGAGTGGAGCGAAG 61.377 60.000 0.00 0.00 40.04 3.79
3241 4117 2.435059 GTGGAGCGAAGTGGAGGC 60.435 66.667 0.00 0.00 0.00 4.70
3242 4118 3.706373 TGGAGCGAAGTGGAGGCC 61.706 66.667 0.00 0.00 0.00 5.19
3263 4139 0.872388 AAACGATTGAAGTCGCCCAC 59.128 50.000 0.00 0.00 45.12 4.61
3267 4143 0.169009 GATTGAAGTCGCCCACTTGC 59.831 55.000 0.42 0.00 46.10 4.01
3268 4144 1.244019 ATTGAAGTCGCCCACTTGCC 61.244 55.000 0.42 0.00 46.10 4.52
3271 4147 4.643387 AGTCGCCCACTTGCCCAC 62.643 66.667 0.00 0.00 26.56 4.61
3272 4148 4.643387 GTCGCCCACTTGCCCACT 62.643 66.667 0.00 0.00 0.00 4.00
3273 4149 3.884774 TCGCCCACTTGCCCACTT 61.885 61.111 0.00 0.00 0.00 3.16
3274 4150 3.673484 CGCCCACTTGCCCACTTG 61.673 66.667 0.00 0.00 0.00 3.16
3275 4151 3.305516 GCCCACTTGCCCACTTGG 61.306 66.667 0.00 0.00 37.09 3.61
3284 4160 3.368822 CCCACTTGGCCATGTGTG 58.631 61.111 36.25 27.90 35.46 3.82
3285 4161 1.228521 CCCACTTGGCCATGTGTGA 60.229 57.895 36.25 11.26 35.46 3.58
3286 4162 1.526575 CCCACTTGGCCATGTGTGAC 61.527 60.000 36.25 0.00 35.46 3.67
3287 4163 0.822944 CCACTTGGCCATGTGTGACA 60.823 55.000 36.25 9.84 35.46 3.58
3296 4172 1.013596 CATGTGTGACAACGTGTGGT 58.986 50.000 0.00 0.00 33.26 4.16
3312 4188 2.520968 GTTGAAGGGGTGCCAGGT 59.479 61.111 0.00 0.00 0.00 4.00
3316 4192 3.110031 AAGGGGTGCCAGGTGGTT 61.110 61.111 0.00 0.00 37.57 3.67
3328 4204 5.128663 GTGCCAGGTGGTTATAAATGGAAAT 59.871 40.000 0.00 0.00 37.57 2.17
3345 4221 5.609423 TGGAAATCAAAGGAAACACAATGG 58.391 37.500 0.00 0.00 0.00 3.16
3362 4238 2.084610 TGGATCAAAGAGCACACGAG 57.915 50.000 0.00 0.00 0.00 4.18
3387 4263 3.437049 GCCTAGCCCAAAATATCGATCAC 59.563 47.826 0.00 0.00 0.00 3.06
3403 4279 5.915857 TCGATCACGAATTTCTGAAACAAG 58.084 37.500 4.73 2.41 45.74 3.16
3405 4281 5.334105 CGATCACGAATTTCTGAAACAAGGT 60.334 40.000 4.73 0.00 42.66 3.50
3408 4284 4.970003 CACGAATTTCTGAAACAAGGTGAC 59.030 41.667 4.73 0.00 0.00 3.67
3412 4288 1.865865 TCTGAAACAAGGTGACGAGC 58.134 50.000 0.00 0.00 0.00 5.03
3423 4299 1.071605 GTGACGAGCATGGAGAACAC 58.928 55.000 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
191 209 4.673298 CGCCGGTGTGTGCTGGTA 62.673 66.667 6.91 0.00 37.24 3.25
220 238 3.127589 CTGTGTGTGTGTATGAACGGAA 58.872 45.455 0.00 0.00 0.00 4.30
241 262 3.050619 CGTTTCTGTGGTAGAGTGTGTC 58.949 50.000 0.00 0.00 36.61 3.67
242 263 2.802057 GCGTTTCTGTGGTAGAGTGTGT 60.802 50.000 0.00 0.00 36.61 3.72
243 264 1.792949 GCGTTTCTGTGGTAGAGTGTG 59.207 52.381 0.00 0.00 36.61 3.82
244 265 1.687123 AGCGTTTCTGTGGTAGAGTGT 59.313 47.619 0.00 0.00 36.61 3.55
367 428 2.409715 CGCACCTGCAATATCTGTATCG 59.590 50.000 0.00 0.00 42.21 2.92
641 717 1.218230 GCACGATCGAATGCCTCCTC 61.218 60.000 24.34 0.00 35.73 3.71
705 781 2.290093 GAGAATAGCTGATGCCTGTTGC 59.710 50.000 0.00 0.00 40.80 4.17
706 782 2.543012 CGAGAATAGCTGATGCCTGTTG 59.457 50.000 0.00 0.00 40.80 3.33
707 783 2.484417 CCGAGAATAGCTGATGCCTGTT 60.484 50.000 0.00 0.00 40.80 3.16
708 784 1.069823 CCGAGAATAGCTGATGCCTGT 59.930 52.381 0.00 0.00 40.80 4.00
709 785 1.069823 ACCGAGAATAGCTGATGCCTG 59.930 52.381 0.00 0.00 40.80 4.85
710 786 1.069823 CACCGAGAATAGCTGATGCCT 59.930 52.381 0.00 0.00 40.80 4.75
711 787 1.202580 ACACCGAGAATAGCTGATGCC 60.203 52.381 0.00 0.00 40.80 4.40
773 849 3.905678 CTCCCTACGGCCTGCTCG 61.906 72.222 0.00 0.00 0.00 5.03
815 895 0.892755 ACACGATCCGAGGCAAAGTA 59.107 50.000 0.00 0.00 0.00 2.24
851 937 1.876497 TTGCCGTACCTACCGTGGAC 61.876 60.000 0.00 0.00 0.00 4.02
971 1060 0.520404 GTCTCAAGACTCGCACGGTA 59.480 55.000 2.86 0.00 41.65 4.02
972 1061 1.286260 GTCTCAAGACTCGCACGGT 59.714 57.895 2.86 0.00 41.65 4.83
988 1077 0.681243 GAAAGCATGGGTGAGGGGTC 60.681 60.000 0.00 0.00 0.00 4.46
989 1078 1.142688 AGAAAGCATGGGTGAGGGGT 61.143 55.000 0.00 0.00 0.00 4.95
1278 1367 0.787084 TGAAGAGGTGGGAGAGGTCT 59.213 55.000 0.00 0.00 0.00 3.85
1492 1581 2.158740 ACTGATCGATCGAGGAAGGAGA 60.159 50.000 23.84 0.00 0.00 3.71
1493 1582 2.226330 ACTGATCGATCGAGGAAGGAG 58.774 52.381 23.84 13.50 0.00 3.69
1495 1588 3.376540 GAAACTGATCGATCGAGGAAGG 58.623 50.000 23.84 13.08 0.00 3.46
1498 1591 2.099263 GTGGAAACTGATCGATCGAGGA 59.901 50.000 23.84 11.04 0.00 3.71
1499 1592 2.099921 AGTGGAAACTGATCGATCGAGG 59.900 50.000 23.84 17.03 0.00 4.63
1503 1598 5.592054 TGTATGAGTGGAAACTGATCGATC 58.408 41.667 18.72 18.72 0.00 3.69
1504 1599 5.598416 TGTATGAGTGGAAACTGATCGAT 57.402 39.130 0.00 0.00 0.00 3.59
1511 1606 7.764443 GTGTACATGTATGTATGAGTGGAAACT 59.236 37.037 9.18 0.00 44.25 2.66
1518 1613 6.071051 TGTGTGGTGTACATGTATGTATGAGT 60.071 38.462 9.18 0.00 44.25 3.41
1521 1616 6.035975 CAGTGTGTGGTGTACATGTATGTATG 59.964 42.308 9.18 0.00 44.25 2.39
1522 1617 6.071051 TCAGTGTGTGGTGTACATGTATGTAT 60.071 38.462 9.18 0.00 44.25 2.29
1524 1619 4.039852 TCAGTGTGTGGTGTACATGTATGT 59.960 41.667 9.18 2.75 42.24 2.29
1525 1620 4.388773 GTCAGTGTGTGGTGTACATGTATG 59.611 45.833 9.18 0.00 42.24 2.39
1526 1621 4.283467 AGTCAGTGTGTGGTGTACATGTAT 59.717 41.667 9.18 0.00 42.24 2.29
1527 1622 3.639561 AGTCAGTGTGTGGTGTACATGTA 59.360 43.478 0.08 0.08 42.24 2.29
1528 1623 2.434336 AGTCAGTGTGTGGTGTACATGT 59.566 45.455 2.69 2.69 42.24 3.21
1529 1624 2.802247 CAGTCAGTGTGTGGTGTACATG 59.198 50.000 0.00 0.00 42.24 3.21
1530 1625 2.698274 TCAGTCAGTGTGTGGTGTACAT 59.302 45.455 0.00 0.00 42.24 2.29
1531 1626 2.104170 TCAGTCAGTGTGTGGTGTACA 58.896 47.619 0.00 0.00 36.82 2.90
1532 1627 2.882927 TCAGTCAGTGTGTGGTGTAC 57.117 50.000 0.00 0.00 0.00 2.90
1533 1628 2.962421 TCATCAGTCAGTGTGTGGTGTA 59.038 45.455 7.37 0.00 0.00 2.90
1534 1629 1.762370 TCATCAGTCAGTGTGTGGTGT 59.238 47.619 7.37 0.00 0.00 4.16
1535 1630 2.531522 TCATCAGTCAGTGTGTGGTG 57.468 50.000 2.40 2.40 0.00 4.17
1536 1631 3.668447 GAATCATCAGTCAGTGTGTGGT 58.332 45.455 0.00 0.00 0.00 4.16
1537 1632 2.669924 CGAATCATCAGTCAGTGTGTGG 59.330 50.000 0.00 0.00 0.00 4.17
1538 1633 3.578688 TCGAATCATCAGTCAGTGTGTG 58.421 45.455 0.00 0.00 0.00 3.82
1559 1654 8.697507 ATATAGCTTGGCTTGCTAATTAAGTT 57.302 30.769 13.91 1.95 44.73 2.66
1560 1655 8.160106 AGATATAGCTTGGCTTGCTAATTAAGT 58.840 33.333 13.91 2.51 44.73 2.24
1561 1656 8.558973 AGATATAGCTTGGCTTGCTAATTAAG 57.441 34.615 13.91 0.00 44.73 1.85
1563 1658 9.436957 GTAAGATATAGCTTGGCTTGCTAATTA 57.563 33.333 13.46 5.88 44.73 1.40
1564 1659 7.939039 TGTAAGATATAGCTTGGCTTGCTAATT 59.061 33.333 13.46 9.97 44.73 1.40
1567 1662 6.042093 AGTGTAAGATATAGCTTGGCTTGCTA 59.958 38.462 13.46 12.70 45.49 3.49
1568 1663 5.059833 GTGTAAGATATAGCTTGGCTTGCT 58.940 41.667 13.46 9.44 40.44 3.91
1569 1664 5.049818 CAGTGTAAGATATAGCTTGGCTTGC 60.050 44.000 13.46 0.00 40.44 4.01
1570 1665 5.468072 CCAGTGTAAGATATAGCTTGGCTTG 59.532 44.000 13.46 6.78 40.44 4.01
1571 1666 5.366768 TCCAGTGTAAGATATAGCTTGGCTT 59.633 40.000 13.46 0.00 40.44 4.35
1572 1667 4.901849 TCCAGTGTAAGATATAGCTTGGCT 59.098 41.667 13.46 5.75 43.41 4.75
1573 1668 5.011125 TCTCCAGTGTAAGATATAGCTTGGC 59.989 44.000 13.46 6.81 0.00 4.52
1574 1669 6.656632 TCTCCAGTGTAAGATATAGCTTGG 57.343 41.667 13.46 6.42 0.00 3.61
1575 1670 7.890515 TCATCTCCAGTGTAAGATATAGCTTG 58.109 38.462 13.46 0.00 31.10 4.01
1576 1671 8.484214 TTCATCTCCAGTGTAAGATATAGCTT 57.516 34.615 8.52 8.52 31.10 3.74
1577 1672 8.663209 ATTCATCTCCAGTGTAAGATATAGCT 57.337 34.615 5.26 0.00 31.10 3.32
1578 1673 8.748412 AGATTCATCTCCAGTGTAAGATATAGC 58.252 37.037 5.26 1.35 31.10 2.97
1580 1675 9.813826 TCAGATTCATCTCCAGTGTAAGATATA 57.186 33.333 5.26 0.00 34.22 0.86
1604 1703 3.064408 GCGATGAACTGCAGATCAAATCA 59.936 43.478 27.68 16.88 30.66 2.57
1613 1712 4.214383 CGCCGCGATGAACTGCAG 62.214 66.667 13.48 13.48 0.00 4.41
1720 1821 2.750637 ATCGTCTCCGGCGACAGT 60.751 61.111 23.51 8.95 41.33 3.55
1963 2112 1.288127 GTAGACGTCCACCTTGCGT 59.712 57.895 13.01 0.00 41.81 5.24
2092 2241 3.557903 AACGGAGAGACGGACGGGA 62.558 63.158 0.00 0.00 38.39 5.14
2165 2327 1.086634 GCGGCCTCAGATTCTGACAC 61.087 60.000 12.38 7.35 35.39 3.67
2261 2423 2.414161 CGACACGATGTAGCTGAACTCA 60.414 50.000 0.00 0.00 0.00 3.41
2391 2553 2.551287 CCGGTATGGACAAGTTGTTGGA 60.551 50.000 10.45 0.00 42.00 3.53
2427 2592 2.819019 TGTGTATCAATGTGGTGGCAAG 59.181 45.455 0.00 0.00 0.00 4.01
2587 2767 2.169832 ACACTGTTGGGTCTTGATCG 57.830 50.000 0.00 0.00 0.00 3.69
2640 2820 0.664224 TCCGCCGTTTCTTTGGTTTC 59.336 50.000 0.00 0.00 0.00 2.78
2652 2832 2.556622 AGTTTCAAATGAAATCCGCCGT 59.443 40.909 11.40 0.00 44.69 5.68
2712 3586 6.268617 ACATCTGCATATTGGAAGTCTAGCTA 59.731 38.462 0.00 0.00 0.00 3.32
2737 3611 6.832900 TCATGGGTTTCACTCAAATATGCATA 59.167 34.615 9.27 9.27 28.99 3.14
2742 3616 5.579047 TGGTCATGGGTTTCACTCAAATAT 58.421 37.500 0.00 0.00 28.99 1.28
2759 3633 6.218315 ACTTCATATATTAGGCCCATGGTCAT 59.782 38.462 11.73 0.00 0.00 3.06
2761 3635 6.067217 ACTTCATATATTAGGCCCATGGTC 57.933 41.667 11.73 0.00 0.00 4.02
2763 3637 6.065976 TGACTTCATATATTAGGCCCATGG 57.934 41.667 4.14 4.14 0.00 3.66
2780 3654 8.496751 AGCTTCGTCTAGTTTATTTTTGACTTC 58.503 33.333 0.00 0.00 0.00 3.01
2784 3658 7.045725 CGAGCTTCGTCTAGTTTATTTTTGA 57.954 36.000 0.00 0.00 34.72 2.69
2829 3703 5.640783 GTGTATAGCCGAGTTACCAGTTTTT 59.359 40.000 0.00 0.00 0.00 1.94
2830 3704 5.173664 GTGTATAGCCGAGTTACCAGTTTT 58.826 41.667 0.00 0.00 0.00 2.43
2831 3705 4.221262 TGTGTATAGCCGAGTTACCAGTTT 59.779 41.667 0.00 0.00 0.00 2.66
2832 3706 3.765511 TGTGTATAGCCGAGTTACCAGTT 59.234 43.478 0.00 0.00 0.00 3.16
2833 3707 3.359033 TGTGTATAGCCGAGTTACCAGT 58.641 45.455 0.00 0.00 0.00 4.00
2834 3708 4.097437 TCTTGTGTATAGCCGAGTTACCAG 59.903 45.833 0.00 0.00 0.00 4.00
2835 3709 4.018490 TCTTGTGTATAGCCGAGTTACCA 58.982 43.478 0.00 0.00 0.00 3.25
2843 3717 3.452755 TGGTGATCTTGTGTATAGCCG 57.547 47.619 0.00 0.00 0.00 5.52
2877 3751 1.038681 TGCCATAGCCCACAAGCATG 61.039 55.000 0.00 0.00 38.69 4.06
2882 3756 0.972883 GGTTTTGCCATAGCCCACAA 59.027 50.000 0.00 0.00 38.69 3.33
2891 3765 2.206536 CCACGGTGGGTTTTGCCAT 61.207 57.895 19.63 0.00 39.65 4.40
2912 3786 5.287274 GCCATCAAATGTATCTCGACTATCG 59.713 44.000 0.00 0.00 42.10 2.92
2917 3791 3.733337 AGGCCATCAAATGTATCTCGAC 58.267 45.455 5.01 0.00 0.00 4.20
2943 3818 7.412237 GGCATAGTATAACAAACGACGAAAACT 60.412 37.037 0.00 0.00 0.00 2.66
2952 3827 8.068893 AGTAAATCGGCATAGTATAACAAACG 57.931 34.615 0.00 0.00 0.00 3.60
2956 3831 9.634163 CATGTAGTAAATCGGCATAGTATAACA 57.366 33.333 0.00 0.00 0.00 2.41
2993 3868 2.417516 CTCGGGGCATGACTACGG 59.582 66.667 14.52 4.04 0.00 4.02
3000 3875 1.372683 CCTACATCCTCGGGGCATG 59.627 63.158 0.00 4.15 0.00 4.06
3008 3883 4.038042 TCATCGATCAACACCTACATCCTC 59.962 45.833 0.00 0.00 0.00 3.71
3010 3885 4.322080 TCATCGATCAACACCTACATCC 57.678 45.455 0.00 0.00 0.00 3.51
3042 3917 9.268282 AGATTTAGACCCAGAGACAAGTATTTA 57.732 33.333 0.00 0.00 0.00 1.40
3050 3925 3.449018 GCAGAGATTTAGACCCAGAGACA 59.551 47.826 0.00 0.00 0.00 3.41
3051 3926 3.449018 TGCAGAGATTTAGACCCAGAGAC 59.551 47.826 0.00 0.00 0.00 3.36
3053 3928 4.478206 TTGCAGAGATTTAGACCCAGAG 57.522 45.455 0.00 0.00 0.00 3.35
3073 3948 8.121305 TGTTAGAATTTACCAGTTGCATCATT 57.879 30.769 0.00 0.00 0.00 2.57
3100 3975 7.902920 ATTTGCAACCTTTCTCATATACCAT 57.097 32.000 0.00 0.00 0.00 3.55
3107 3982 5.246656 TGATCCAATTTGCAACCTTTCTCAT 59.753 36.000 0.00 0.00 0.00 2.90
3137 4012 9.905171 ATGATTCATCTTCGTATATATCATCCG 57.095 33.333 0.00 0.00 28.26 4.18
3151 4026 4.562789 TGTTGTCGTCGATGATTCATCTTC 59.437 41.667 21.23 13.73 38.59 2.87
3159 4034 2.749776 TGTTGTGTTGTCGTCGATGAT 58.250 42.857 11.16 0.00 0.00 2.45
3160 4035 2.211353 TGTTGTGTTGTCGTCGATGA 57.789 45.000 2.39 2.39 0.00 2.92
3161 4036 2.411418 CCATGTTGTGTTGTCGTCGATG 60.411 50.000 0.00 0.00 0.00 3.84
3162 4037 1.798223 CCATGTTGTGTTGTCGTCGAT 59.202 47.619 0.00 0.00 0.00 3.59
3163 4038 1.213491 CCATGTTGTGTTGTCGTCGA 58.787 50.000 0.00 0.00 0.00 4.20
3199 4074 4.870426 CGCTCCTAAGAAGCATGTCTTTAA 59.130 41.667 4.10 0.00 38.75 1.52
3200 4075 4.159693 TCGCTCCTAAGAAGCATGTCTTTA 59.840 41.667 4.10 0.00 38.75 1.85
3208 4083 0.532573 CCACTCGCTCCTAAGAAGCA 59.467 55.000 0.00 0.00 0.00 3.91
3210 4085 1.202359 GCTCCACTCGCTCCTAAGAAG 60.202 57.143 0.00 0.00 0.00 2.85
3234 4110 1.243902 TCAATCGTTTTGGCCTCCAC 58.756 50.000 3.32 0.00 30.78 4.02
3241 4117 1.401018 GGGCGACTTCAATCGTTTTGG 60.401 52.381 0.00 0.00 44.13 3.28
3242 4118 1.265635 TGGGCGACTTCAATCGTTTTG 59.734 47.619 0.00 0.00 44.13 2.44
3267 4143 1.228521 TCACACATGGCCAAGTGGG 60.229 57.895 36.59 34.75 40.46 4.61
3268 4144 0.822944 TGTCACACATGGCCAAGTGG 60.823 55.000 36.59 26.87 39.99 4.00
3271 4147 0.040157 CGTTGTCACACATGGCCAAG 60.040 55.000 10.96 8.43 0.00 3.61
3272 4148 0.749818 ACGTTGTCACACATGGCCAA 60.750 50.000 10.96 0.00 0.00 4.52
3273 4149 1.153066 ACGTTGTCACACATGGCCA 60.153 52.632 8.56 8.56 0.00 5.36
3274 4150 1.282570 CACGTTGTCACACATGGCC 59.717 57.895 0.00 0.00 0.00 5.36
3275 4151 0.316937 CACACGTTGTCACACATGGC 60.317 55.000 0.00 0.00 0.00 4.40
3276 4152 0.307453 CCACACGTTGTCACACATGG 59.693 55.000 0.00 0.00 0.00 3.66
3277 4153 1.013596 ACCACACGTTGTCACACATG 58.986 50.000 0.00 0.00 0.00 3.21
3278 4154 1.400142 CAACCACACGTTGTCACACAT 59.600 47.619 0.00 0.00 45.79 3.21
3279 4155 0.799393 CAACCACACGTTGTCACACA 59.201 50.000 0.00 0.00 45.79 3.72
3280 4156 3.596865 CAACCACACGTTGTCACAC 57.403 52.632 0.00 0.00 45.79 3.82
3287 4163 0.750182 CACCCCTTCAACCACACGTT 60.750 55.000 0.00 0.00 33.90 3.99
3296 4172 2.520458 CACCTGGCACCCCTTCAA 59.480 61.111 0.00 0.00 0.00 2.69
3312 4188 9.936759 GTTTCCTTTGATTTCCATTTATAACCA 57.063 29.630 0.00 0.00 0.00 3.67
3328 4204 6.323482 TCTTTGATCCATTGTGTTTCCTTTGA 59.677 34.615 0.00 0.00 0.00 2.69
3345 4221 2.412065 GCAACTCGTGTGCTCTTTGATC 60.412 50.000 0.00 0.00 0.00 2.92
3362 4238 3.211045 TCGATATTTTGGGCTAGGCAAC 58.789 45.455 19.14 1.85 0.00 4.17
3387 4263 4.025229 TCGTCACCTTGTTTCAGAAATTCG 60.025 41.667 0.00 0.00 0.00 3.34
3390 4266 3.251004 GCTCGTCACCTTGTTTCAGAAAT 59.749 43.478 0.00 0.00 0.00 2.17
3403 4279 0.037326 TGTTCTCCATGCTCGTCACC 60.037 55.000 0.00 0.00 0.00 4.02
3405 4281 3.514777 GTGTTCTCCATGCTCGTCA 57.485 52.632 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.