Multiple sequence alignment - TraesCS3B01G096500

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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 TraesCS3B01G096500 chr3B 100.000 2610 0 0 1 2610 64507601 64510210 0.000000e+00 4820
1 TraesCS3B01G096500 chr3B 86.431 877 60 34 906 1766 64416685 64415852 0.000000e+00 905
2 TraesCS3B01G096500 chr3B 94.646 523 24 2 2091 2610 64596332 64596853 0.000000e+00 808
3 TraesCS3B01G096500 chr3B 95.643 482 13 1 2137 2610 64414791 64414310 0.000000e+00 767
4 TraesCS3B01G096500 chr3B 85.547 256 25 7 1797 2047 64596081 64596329 9.270000e-65 257
5 TraesCS3B01G096500 chr3B 93.750 112 4 3 1658 1769 64595975 64596083 5.780000e-37 165
6 TraesCS3B01G096500 chr3A 86.370 2135 166 66 1 2085 52557359 52555300 0.000000e+00 2215
7 TraesCS3B01G096500 chr3A 95.455 132 3 1 2442 2573 52555276 52555148 9.470000e-50 207
8 TraesCS3B01G096500 chr3D 85.473 1067 82 46 572 1616 40787466 40786451 0.000000e+00 1044
9 TraesCS3B01G096500 chr3D 90.120 415 25 3 36 447 40787985 40787584 2.300000e-145 525
10 TraesCS3B01G096500 chr3D 79.032 310 23 19 1668 1946 40786325 40786027 9.600000e-40 174
11 TraesCS3B01G096500 chr4A 83.122 237 31 7 2327 2560 605136318 605136088 9.470000e-50 207
12 TraesCS3B01G096500 chr5B 82.353 238 31 10 2327 2560 710209635 710209405 2.050000e-46 196
13 TraesCS3B01G096500 chr5D 81.933 238 32 10 2327 2560 556619108 556618878 9.530000e-45 191


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 TraesCS3B01G096500 chr3B 64507601 64510210 2609 False 4820 4820 100.000000 1 2610 1 chr3B.!!$F1 2609
1 TraesCS3B01G096500 chr3B 64414310 64416685 2375 True 836 905 91.037000 906 2610 2 chr3B.!!$R1 1704
2 TraesCS3B01G096500 chr3B 64595975 64596853 878 False 410 808 91.314333 1658 2610 3 chr3B.!!$F2 952
3 TraesCS3B01G096500 chr3A 52555148 52557359 2211 True 1211 2215 90.912500 1 2573 2 chr3A.!!$R1 2572
4 TraesCS3B01G096500 chr3D 40786027 40787985 1958 True 581 1044 84.875000 36 1946 3 chr3D.!!$R1 1910

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
26 27 0.179032 ATGAACCTCCACACACGCAA 60.179 50.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2020 2931 0.096454 CGATCGATCGCCAGCGTATA 59.904 55.0 32.34 0.0 43.84 1.47 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
22 23 1.981256 ACCAATGAACCTCCACACAC 58.019 50.000 0.00 0.00 0.00 3.82
24 25 0.238289 CAATGAACCTCCACACACGC 59.762 55.000 0.00 0.00 0.00 5.34
26 27 0.179032 ATGAACCTCCACACACGCAA 60.179 50.000 0.00 0.00 0.00 4.85
151 152 1.621317 TGACCGATGACTAAGCAACCA 59.379 47.619 0.00 0.00 0.00 3.67
152 153 2.236146 TGACCGATGACTAAGCAACCAT 59.764 45.455 0.00 0.00 0.00 3.55
153 154 2.609459 GACCGATGACTAAGCAACCATG 59.391 50.000 0.00 0.00 0.00 3.66
154 155 2.027192 ACCGATGACTAAGCAACCATGT 60.027 45.455 0.00 0.00 0.00 3.21
155 156 3.009723 CCGATGACTAAGCAACCATGTT 58.990 45.455 0.00 0.00 0.00 2.71
156 157 3.181507 CCGATGACTAAGCAACCATGTTG 60.182 47.826 2.65 2.65 0.00 3.33
157 158 3.436704 CGATGACTAAGCAACCATGTTGT 59.563 43.478 8.58 0.00 0.00 3.32
158 159 4.083324 CGATGACTAAGCAACCATGTTGTT 60.083 41.667 8.58 0.00 0.00 2.83
159 160 5.562696 CGATGACTAAGCAACCATGTTGTTT 60.563 40.000 12.50 12.50 0.00 2.83
160 161 5.590530 TGACTAAGCAACCATGTTGTTTT 57.409 34.783 13.00 8.53 0.00 2.43
161 162 5.347342 TGACTAAGCAACCATGTTGTTTTG 58.653 37.500 13.00 13.12 0.00 2.44
162 163 5.126222 TGACTAAGCAACCATGTTGTTTTGA 59.874 36.000 18.69 3.18 0.00 2.69
205 206 6.671614 TGGATCGCTTAATTTCGTTATGTT 57.328 33.333 0.00 0.00 0.00 2.71
247 248 2.754658 CCACCGGTACCTCGAGCT 60.755 66.667 6.87 0.00 0.00 4.09
338 342 3.309954 GCGAGAGAAGTCTTTGTGTTTGT 59.690 43.478 0.00 0.00 30.97 2.83
379 383 3.019564 GCCATTTCTTGATGGTACTGCT 58.980 45.455 5.85 0.00 46.74 4.24
382 386 4.096984 CCATTTCTTGATGGTACTGCTTCC 59.903 45.833 0.00 0.00 41.37 3.46
384 388 3.616956 TCTTGATGGTACTGCTTCCTG 57.383 47.619 0.00 0.00 0.00 3.86
385 389 2.012673 CTTGATGGTACTGCTTCCTGC 58.987 52.381 0.00 0.00 43.25 4.85
422 426 1.477295 GTAGCTAGTTTCCGGCTCTGT 59.523 52.381 0.00 0.00 37.50 3.41
439 443 2.019984 CTGTTTTGCTCTATCCTGGCC 58.980 52.381 0.00 0.00 0.00 5.36
440 444 1.354031 TGTTTTGCTCTATCCTGGCCA 59.646 47.619 4.71 4.71 0.00 5.36
447 451 2.837947 CTCTATCCTGGCCATATGGGA 58.162 52.381 23.30 13.47 40.01 4.37
452 456 2.431997 TCCTGGCCATATGGGAATTCT 58.568 47.619 23.30 0.00 40.01 2.40
466 470 3.065371 GGGAATTCTGAATTTGCGACGAT 59.935 43.478 16.14 0.00 0.00 3.73
473 477 4.033243 TCTGAATTTGCGACGATCTGAATG 59.967 41.667 0.00 0.00 0.00 2.67
486 490 3.817709 TCTGAATGTCCGTGCATATCA 57.182 42.857 0.00 0.00 0.00 2.15
492 496 5.179929 TGAATGTCCGTGCATATCATTCATC 59.820 40.000 22.78 9.49 44.77 2.92
493 497 4.341366 TGTCCGTGCATATCATTCATCT 57.659 40.909 0.00 0.00 0.00 2.90
497 501 6.138761 GTCCGTGCATATCATTCATCTTTTC 58.861 40.000 0.00 0.00 0.00 2.29
501 505 6.017687 CGTGCATATCATTCATCTTTTCCTGA 60.018 38.462 0.00 0.00 0.00 3.86
511 515 2.683968 TCTTTTCCTGATGGTCGTTCG 58.316 47.619 0.00 0.00 34.23 3.95
512 516 1.732259 CTTTTCCTGATGGTCGTTCGG 59.268 52.381 0.00 0.00 34.23 4.30
513 517 0.682852 TTTCCTGATGGTCGTTCGGT 59.317 50.000 0.00 0.00 34.23 4.69
516 520 1.071071 TCCTGATGGTCGTTCGGTTTT 59.929 47.619 0.00 0.00 34.23 2.43
521 525 1.526686 GGTCGTTCGGTTTTGGGGT 60.527 57.895 0.00 0.00 0.00 4.95
529 533 1.807226 GGTTTTGGGGTAGCGATGC 59.193 57.895 0.00 0.00 0.00 3.91
542 546 3.023946 AGCGATGCACTCTCATCATAC 57.976 47.619 0.00 0.00 42.15 2.39
543 547 2.363359 AGCGATGCACTCTCATCATACA 59.637 45.455 0.00 0.00 42.15 2.29
544 548 3.006644 AGCGATGCACTCTCATCATACAT 59.993 43.478 0.00 0.00 42.15 2.29
545 549 4.219288 AGCGATGCACTCTCATCATACATA 59.781 41.667 0.00 0.00 42.15 2.29
558 562 5.991606 TCATCATACATAGTTAGTTGCCAGC 59.008 40.000 0.00 0.00 0.00 4.85
559 563 5.351948 TCATACATAGTTAGTTGCCAGCA 57.648 39.130 0.00 0.00 0.00 4.41
560 564 5.359756 TCATACATAGTTAGTTGCCAGCAG 58.640 41.667 0.00 0.00 0.00 4.24
561 565 3.703001 ACATAGTTAGTTGCCAGCAGT 57.297 42.857 0.00 0.00 0.00 4.40
563 567 1.808411 TAGTTAGTTGCCAGCAGTGC 58.192 50.000 7.13 7.13 0.00 4.40
570 597 2.882761 AGTTGCCAGCAGTGCATATATG 59.117 45.455 19.20 8.45 38.76 1.78
578 605 6.110707 CCAGCAGTGCATATATGTCATCATA 58.889 40.000 19.20 0.00 40.26 2.15
583 610 6.035327 CAGTGCATATATGTCATCATACACCG 59.965 42.308 14.14 0.73 39.03 4.94
614 644 3.071874 TGGTTGCAATAGGGAGAACAG 57.928 47.619 0.59 0.00 0.00 3.16
631 661 5.644644 AGAACAGAAGTTGCTGAAAAACAG 58.355 37.500 0.00 0.00 42.78 3.16
646 676 4.853924 AAAACAGTGGTAGATTTGCCAG 57.146 40.909 0.00 0.00 39.96 4.85
648 678 4.307032 AACAGTGGTAGATTTGCCAGAT 57.693 40.909 0.00 0.00 39.96 2.90
651 681 4.471386 ACAGTGGTAGATTTGCCAGATAGT 59.529 41.667 0.00 0.00 39.96 2.12
652 682 5.053145 CAGTGGTAGATTTGCCAGATAGTC 58.947 45.833 0.00 0.00 39.96 2.59
654 684 5.367937 AGTGGTAGATTTGCCAGATAGTCAT 59.632 40.000 0.00 0.00 39.96 3.06
655 685 6.554982 AGTGGTAGATTTGCCAGATAGTCATA 59.445 38.462 0.00 0.00 39.96 2.15
656 686 7.071196 AGTGGTAGATTTGCCAGATAGTCATAA 59.929 37.037 0.00 0.00 39.96 1.90
657 687 7.880195 GTGGTAGATTTGCCAGATAGTCATAAT 59.120 37.037 0.00 0.00 39.96 1.28
673 711 6.198639 AGTCATAATACAGAGGTCAGAAGGT 58.801 40.000 0.00 0.00 0.00 3.50
700 738 7.341805 ACATCTCTTTTACTTATCCTGTGCAT 58.658 34.615 0.00 0.00 0.00 3.96
755 793 4.708177 GGCAAGATAAGTATGAAGCCTGA 58.292 43.478 0.00 0.00 37.89 3.86
759 797 3.906846 AGATAAGTATGAAGCCTGAGGGG 59.093 47.826 0.00 0.00 38.36 4.79
782 820 6.183361 GGGGGAAGAAATATCTTTTGGAATGG 60.183 42.308 0.00 0.00 45.91 3.16
783 821 6.384015 GGGGAAGAAATATCTTTTGGAATGGT 59.616 38.462 0.00 0.00 45.91 3.55
784 822 7.563556 GGGGAAGAAATATCTTTTGGAATGGTA 59.436 37.037 0.00 0.00 45.91 3.25
785 823 8.414003 GGGAAGAAATATCTTTTGGAATGGTAC 58.586 37.037 0.00 0.00 45.91 3.34
786 824 8.966868 GGAAGAAATATCTTTTGGAATGGTACA 58.033 33.333 0.00 0.00 45.91 2.90
882 928 1.040646 TCCAGACAGGACACACTCAC 58.959 55.000 0.00 0.00 43.07 3.51
932 979 4.355437 CCTGATCGTCAAGCTAACTACAG 58.645 47.826 0.00 0.00 0.00 2.74
936 988 3.985008 TCGTCAAGCTAACTACAGCAAA 58.015 40.909 0.00 0.00 44.35 3.68
937 989 3.987868 TCGTCAAGCTAACTACAGCAAAG 59.012 43.478 0.00 0.00 44.35 2.77
938 990 3.423645 CGTCAAGCTAACTACAGCAAAGC 60.424 47.826 0.00 0.00 44.35 3.51
939 991 3.498397 GTCAAGCTAACTACAGCAAAGCA 59.502 43.478 0.00 0.00 44.35 3.91
940 992 4.024048 GTCAAGCTAACTACAGCAAAGCAA 60.024 41.667 0.00 0.00 44.35 3.91
941 993 4.214119 TCAAGCTAACTACAGCAAAGCAAG 59.786 41.667 0.00 0.00 44.35 4.01
942 994 2.485814 AGCTAACTACAGCAAAGCAAGC 59.514 45.455 0.00 0.00 44.35 4.01
943 995 2.726066 GCTAACTACAGCAAAGCAAGCG 60.726 50.000 0.00 0.00 41.40 4.68
1036 1089 4.680237 CCTTGTCGGCCGTGCTGA 62.680 66.667 27.15 1.01 42.08 4.26
1193 1253 5.471456 TCTCGTACGTTTTCTCTACCTCTTT 59.529 40.000 16.05 0.00 0.00 2.52
1194 1254 5.455392 TCGTACGTTTTCTCTACCTCTTTG 58.545 41.667 16.05 0.00 0.00 2.77
1218 1288 1.288350 CTGATTGAGCTTGAGCCGAG 58.712 55.000 0.00 0.00 43.38 4.63
1222 1292 4.443266 GAGCTTGAGCCGAGCCGT 62.443 66.667 9.94 0.00 41.50 5.68
1224 1294 3.793144 GCTTGAGCCGAGCCGTTG 61.793 66.667 3.67 0.00 35.00 4.10
1256 1328 1.134521 TCTGGTGGTTGCCATATCGTC 60.135 52.381 0.00 0.00 37.96 4.20
1453 1525 0.315886 CCAAAAACGTAACCCTGCCC 59.684 55.000 0.00 0.00 0.00 5.36
1519 1595 6.995686 TCACTATAAATGGAAACTGTGTGTGT 59.004 34.615 0.00 0.00 0.00 3.72
1520 1596 7.041440 TCACTATAAATGGAAACTGTGTGTGTG 60.041 37.037 0.00 0.00 0.00 3.82
1521 1597 3.799281 AAATGGAAACTGTGTGTGTGG 57.201 42.857 0.00 0.00 0.00 4.17
1522 1598 2.727123 ATGGAAACTGTGTGTGTGGA 57.273 45.000 0.00 0.00 0.00 4.02
1523 1599 2.727123 TGGAAACTGTGTGTGTGGAT 57.273 45.000 0.00 0.00 0.00 3.41
1524 1600 2.296792 TGGAAACTGTGTGTGTGGATG 58.703 47.619 0.00 0.00 0.00 3.51
1525 1601 1.608590 GGAAACTGTGTGTGTGGATGG 59.391 52.381 0.00 0.00 0.00 3.51
1526 1602 2.571212 GAAACTGTGTGTGTGGATGGA 58.429 47.619 0.00 0.00 0.00 3.41
1567 1643 2.652496 GAGGCGTGCGACGATCTC 60.652 66.667 11.94 12.25 46.05 2.75
1602 1678 2.750237 GGCGCCCTACCAAACCAG 60.750 66.667 18.11 0.00 0.00 4.00
1609 1685 2.816337 GCCCTACCAAACCAGCAAGTAA 60.816 50.000 0.00 0.00 0.00 2.24
1613 1689 5.310451 CCTACCAAACCAGCAAGTAACTAA 58.690 41.667 0.00 0.00 0.00 2.24
1616 1692 4.820173 ACCAAACCAGCAAGTAACTAACTC 59.180 41.667 0.00 0.00 37.50 3.01
1617 1693 4.819630 CCAAACCAGCAAGTAACTAACTCA 59.180 41.667 0.00 0.00 37.50 3.41
1618 1694 5.298276 CCAAACCAGCAAGTAACTAACTCAA 59.702 40.000 0.00 0.00 37.50 3.02
1619 1695 6.430451 CAAACCAGCAAGTAACTAACTCAAG 58.570 40.000 0.00 0.00 37.50 3.02
1620 1696 4.065789 ACCAGCAAGTAACTAACTCAAGC 58.934 43.478 0.00 0.00 37.50 4.01
1621 1697 4.065088 CCAGCAAGTAACTAACTCAAGCA 58.935 43.478 0.00 0.00 37.50 3.91
1622 1698 4.153117 CCAGCAAGTAACTAACTCAAGCAG 59.847 45.833 0.00 0.00 37.50 4.24
1623 1699 3.748568 AGCAAGTAACTAACTCAAGCAGC 59.251 43.478 0.00 0.00 37.50 5.25
1624 1700 3.748568 GCAAGTAACTAACTCAAGCAGCT 59.251 43.478 0.00 0.00 37.50 4.24
1626 1702 5.163943 GCAAGTAACTAACTCAAGCAGCTAC 60.164 44.000 0.00 0.00 37.50 3.58
1627 1703 5.986501 AGTAACTAACTCAAGCAGCTACT 57.013 39.130 0.00 0.00 30.33 2.57
1629 1705 6.854778 AGTAACTAACTCAAGCAGCTACTAC 58.145 40.000 0.00 0.00 30.33 2.73
1630 1706 4.358494 ACTAACTCAAGCAGCTACTACG 57.642 45.455 0.00 0.00 0.00 3.51
1632 1708 3.936372 AACTCAAGCAGCTACTACGAA 57.064 42.857 0.00 0.00 0.00 3.85
1633 1709 3.219052 ACTCAAGCAGCTACTACGAAC 57.781 47.619 0.00 0.00 0.00 3.95
1635 1711 4.008330 ACTCAAGCAGCTACTACGAACTA 58.992 43.478 0.00 0.00 0.00 2.24
1637 1713 4.008330 TCAAGCAGCTACTACGAACTACT 58.992 43.478 0.00 0.00 0.00 2.57
1638 1714 5.181009 TCAAGCAGCTACTACGAACTACTA 58.819 41.667 0.00 0.00 0.00 1.82
1639 1715 5.821470 TCAAGCAGCTACTACGAACTACTAT 59.179 40.000 0.00 0.00 0.00 2.12
1640 1716 6.318144 TCAAGCAGCTACTACGAACTACTATT 59.682 38.462 0.00 0.00 0.00 1.73
1644 1720 7.041916 AGCAGCTACTACGAACTACTATTAGTG 60.042 40.741 6.60 0.04 38.65 2.74
1645 1721 7.254727 GCAGCTACTACGAACTACTATTAGTGT 60.255 40.741 6.60 0.62 38.65 3.55
1646 1722 9.254133 CAGCTACTACGAACTACTATTAGTGTA 57.746 37.037 6.60 0.00 38.65 2.90
1647 1723 9.823647 AGCTACTACGAACTACTATTAGTGTAA 57.176 33.333 6.60 0.00 38.65 2.41
1791 2051 8.767478 TTCGTTCGTCTTAAATTCTTAATCCT 57.233 30.769 0.00 0.00 0.00 3.24
1866 2768 7.412063 ACGTAATTTCATTTATAGAAACCCGC 58.588 34.615 0.00 0.00 37.76 6.13
2020 2931 5.017490 CCGTCCATCCTATTCTACCTACAT 58.983 45.833 0.00 0.00 0.00 2.29
2067 2980 1.407979 GATCCTGCCCAGCAAATCAAG 59.592 52.381 6.70 0.00 38.41 3.02
2075 2988 2.066262 CCAGCAAATCAAGCAAGCAAG 58.934 47.619 0.00 0.00 0.00 4.01
2092 3005 0.865769 AAGAGTGCAAAACCTACGCG 59.134 50.000 3.53 3.53 0.00 6.01
2115 3028 1.337071 TCCGATCGATCCAGCAGTAAC 59.663 52.381 18.66 0.00 0.00 2.50
2116 3029 1.603172 CCGATCGATCCAGCAGTAACC 60.603 57.143 18.66 0.00 0.00 2.85
2120 3033 2.695359 TCGATCCAGCAGTAACCAAAC 58.305 47.619 0.00 0.00 0.00 2.93
2121 3034 2.301870 TCGATCCAGCAGTAACCAAACT 59.698 45.455 0.00 0.00 0.00 2.66
2178 3091 2.887568 GACGTGATCCAGCGCCTG 60.888 66.667 2.29 1.18 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 0.028902 GTTTGCGTGTGTGGAGGTTC 59.971 55.000 0.00 0.00 0.00 3.62
22 23 4.783242 AGCATGTTAACTTAGTGTTTGCG 58.217 39.130 7.22 0.00 41.17 4.85
24 25 7.667043 TCCTAGCATGTTAACTTAGTGTTTG 57.333 36.000 7.22 1.02 39.89 2.93
26 27 8.685838 TTTTCCTAGCATGTTAACTTAGTGTT 57.314 30.769 7.22 2.07 42.31 3.32
130 131 2.271800 GGTTGCTTAGTCATCGGTCAG 58.728 52.381 0.00 0.00 0.00 3.51
151 152 8.095792 TCAATAATGGCTCATTCAAAACAACAT 58.904 29.630 4.01 0.00 35.54 2.71
152 153 7.440198 TCAATAATGGCTCATTCAAAACAACA 58.560 30.769 4.01 0.00 35.54 3.33
153 154 7.887996 TCAATAATGGCTCATTCAAAACAAC 57.112 32.000 4.01 0.00 35.54 3.32
185 186 5.737290 GCACAACATAACGAAATTAAGCGAT 59.263 36.000 0.00 0.00 0.00 4.58
189 190 6.607689 TCCTGCACAACATAACGAAATTAAG 58.392 36.000 0.00 0.00 0.00 1.85
192 193 4.082787 CCTCCTGCACAACATAACGAAATT 60.083 41.667 0.00 0.00 0.00 1.82
205 206 2.210013 AAGCTCGTCCTCCTGCACA 61.210 57.895 0.00 0.00 0.00 4.57
247 248 2.163010 CAGGTTCTAACTACGGAGCGAA 59.837 50.000 0.00 0.00 0.00 4.70
282 283 3.964688 TGAGGTAACACTGAGAACAAGGA 59.035 43.478 0.00 0.00 41.41 3.36
382 386 0.523072 ATTGCACAGCTTAACCGCAG 59.477 50.000 0.00 0.00 33.48 5.18
384 388 0.240945 ACATTGCACAGCTTAACCGC 59.759 50.000 0.00 0.00 0.00 5.68
385 389 2.476185 GCTACATTGCACAGCTTAACCG 60.476 50.000 0.00 0.00 32.46 4.44
422 426 4.401022 CATATGGCCAGGATAGAGCAAAA 58.599 43.478 13.05 0.00 0.00 2.44
439 443 5.916883 GTCGCAAATTCAGAATTCCCATATG 59.083 40.000 8.90 4.06 0.00 1.78
440 444 5.277974 CGTCGCAAATTCAGAATTCCCATAT 60.278 40.000 8.90 0.00 0.00 1.78
447 451 4.631377 TCAGATCGTCGCAAATTCAGAATT 59.369 37.500 2.20 2.20 0.00 2.17
452 456 3.684305 ACATTCAGATCGTCGCAAATTCA 59.316 39.130 0.00 0.00 0.00 2.57
466 470 3.817709 TGATATGCACGGACATTCAGA 57.182 42.857 0.00 0.00 0.00 3.27
473 477 5.679734 AAAGATGAATGATATGCACGGAC 57.320 39.130 0.00 0.00 0.00 4.79
486 490 4.848357 ACGACCATCAGGAAAAGATGAAT 58.152 39.130 4.84 0.00 44.34 2.57
492 496 1.732259 CCGAACGACCATCAGGAAAAG 59.268 52.381 0.00 0.00 38.69 2.27
493 497 1.071071 ACCGAACGACCATCAGGAAAA 59.929 47.619 0.00 0.00 38.69 2.29
497 501 1.196808 CAAAACCGAACGACCATCAGG 59.803 52.381 0.00 0.00 42.21 3.86
501 505 0.891904 CCCCAAAACCGAACGACCAT 60.892 55.000 0.00 0.00 0.00 3.55
511 515 0.963355 TGCATCGCTACCCCAAAACC 60.963 55.000 0.00 0.00 0.00 3.27
512 516 0.170339 GTGCATCGCTACCCCAAAAC 59.830 55.000 0.00 0.00 0.00 2.43
513 517 0.037590 AGTGCATCGCTACCCCAAAA 59.962 50.000 0.00 0.00 0.00 2.44
516 520 1.676678 GAGAGTGCATCGCTACCCCA 61.677 60.000 0.00 0.00 0.00 4.96
521 525 3.569701 TGTATGATGAGAGTGCATCGCTA 59.430 43.478 0.00 0.00 45.93 4.26
529 533 7.383572 GGCAACTAACTATGTATGATGAGAGTG 59.616 40.741 0.00 0.00 0.00 3.51
542 546 2.096496 GCACTGCTGGCAACTAACTATG 59.904 50.000 0.00 0.00 37.61 2.23
543 547 2.290260 TGCACTGCTGGCAACTAACTAT 60.290 45.455 1.98 0.00 38.54 2.12
544 548 1.071542 TGCACTGCTGGCAACTAACTA 59.928 47.619 1.98 0.00 38.54 2.24
545 549 0.179020 TGCACTGCTGGCAACTAACT 60.179 50.000 1.98 0.00 38.54 2.24
558 562 6.035327 CGGTGTATGATGACATATATGCACTG 59.965 42.308 21.58 20.21 40.45 3.66
559 563 6.101997 CGGTGTATGATGACATATATGCACT 58.898 40.000 21.58 0.00 40.45 4.40
560 564 5.291858 CCGGTGTATGATGACATATATGCAC 59.708 44.000 12.79 17.60 40.45 4.57
561 565 5.046663 ACCGGTGTATGATGACATATATGCA 60.047 40.000 6.12 11.64 40.45 3.96
563 567 7.147897 ACCTACCGGTGTATGATGACATATATG 60.148 40.741 19.93 11.29 43.51 1.78
570 597 3.814005 AACCTACCGGTGTATGATGAC 57.186 47.619 19.93 0.00 44.73 3.06
578 605 1.134228 ACCAAGAAACCTACCGGTGT 58.866 50.000 19.93 4.09 44.73 4.16
583 610 4.157840 CCTATTGCAACCAAGAAACCTACC 59.842 45.833 0.00 0.00 33.80 3.18
631 661 5.023533 TGACTATCTGGCAAATCTACCAC 57.976 43.478 0.00 0.00 0.00 4.16
642 672 6.209589 TGACCTCTGTATTATGACTATCTGGC 59.790 42.308 0.00 0.00 0.00 4.85
643 673 7.667635 TCTGACCTCTGTATTATGACTATCTGG 59.332 40.741 0.00 0.00 0.00 3.86
646 676 8.519526 CCTTCTGACCTCTGTATTATGACTATC 58.480 40.741 0.00 0.00 0.00 2.08
648 678 7.285629 CACCTTCTGACCTCTGTATTATGACTA 59.714 40.741 0.00 0.00 0.00 2.59
651 681 6.096987 GTCACCTTCTGACCTCTGTATTATGA 59.903 42.308 0.00 0.00 43.35 2.15
652 682 6.276847 GTCACCTTCTGACCTCTGTATTATG 58.723 44.000 0.00 0.00 43.35 1.90
654 684 5.916661 GTCACCTTCTGACCTCTGTATTA 57.083 43.478 0.00 0.00 43.35 0.98
655 685 4.810191 GTCACCTTCTGACCTCTGTATT 57.190 45.455 0.00 0.00 43.35 1.89
673 711 6.818644 GCACAGGATAAGTAAAAGAGATGTCA 59.181 38.462 0.00 0.00 0.00 3.58
706 744 9.983024 TCCATCTTTTGTTACAAATATAGGGAA 57.017 29.630 11.50 0.00 0.00 3.97
707 745 9.627123 CTCCATCTTTTGTTACAAATATAGGGA 57.373 33.333 11.50 13.78 0.00 4.20
710 748 8.902806 TGCCTCCATCTTTTGTTACAAATATAG 58.097 33.333 11.50 6.52 0.00 1.31
711 749 8.815565 TGCCTCCATCTTTTGTTACAAATATA 57.184 30.769 11.50 1.05 0.00 0.86
712 750 7.716799 TGCCTCCATCTTTTGTTACAAATAT 57.283 32.000 11.50 5.95 0.00 1.28
713 751 7.450014 TCTTGCCTCCATCTTTTGTTACAAATA 59.550 33.333 11.50 3.83 0.00 1.40
726 764 6.743773 GCTTCATACTTATCTTGCCTCCATCT 60.744 42.308 0.00 0.00 0.00 2.90
727 765 5.411053 GCTTCATACTTATCTTGCCTCCATC 59.589 44.000 0.00 0.00 0.00 3.51
759 797 7.423844 ACCATTCCAAAAGATATTTCTTCCC 57.576 36.000 0.00 0.00 41.42 3.97
775 813 5.221742 GGGACCAAATTTTTGTACCATTCCA 60.222 40.000 12.22 0.00 36.45 3.53
777 815 4.926832 CGGGACCAAATTTTTGTACCATTC 59.073 41.667 15.84 0.00 36.45 2.67
778 816 4.345547 ACGGGACCAAATTTTTGTACCATT 59.654 37.500 15.84 3.13 36.45 3.16
779 817 3.898741 ACGGGACCAAATTTTTGTACCAT 59.101 39.130 15.84 1.61 36.45 3.55
780 818 3.068307 CACGGGACCAAATTTTTGTACCA 59.932 43.478 15.84 0.00 36.45 3.25
782 820 3.553302 CCCACGGGACCAAATTTTTGTAC 60.553 47.826 0.00 0.00 35.35 2.90
783 821 2.628657 CCCACGGGACCAAATTTTTGTA 59.371 45.455 0.00 0.00 35.35 2.41
784 822 1.414550 CCCACGGGACCAAATTTTTGT 59.585 47.619 0.00 0.00 35.35 2.83
785 823 1.689273 TCCCACGGGACCAAATTTTTG 59.311 47.619 0.00 0.00 39.76 2.44
786 824 1.967779 CTCCCACGGGACCAAATTTTT 59.032 47.619 0.00 0.00 39.76 1.94
879 925 2.288825 GCCTGCTTATATACTGCCGTGA 60.289 50.000 0.00 0.00 0.00 4.35
882 928 2.069273 GTGCCTGCTTATATACTGCCG 58.931 52.381 4.93 0.00 0.00 5.69
932 979 2.429739 GGTGCTCGCTTGCTTTGC 60.430 61.111 0.00 0.00 0.00 3.68
936 988 2.203195 TTGTGGTGCTCGCTTGCT 60.203 55.556 0.00 0.00 0.00 3.91
937 989 2.050985 GTTGTGGTGCTCGCTTGC 60.051 61.111 0.00 0.00 0.00 4.01
938 990 1.845809 GAGGTTGTGGTGCTCGCTTG 61.846 60.000 0.00 0.00 0.00 4.01
939 991 1.598130 GAGGTTGTGGTGCTCGCTT 60.598 57.895 0.00 0.00 0.00 4.68
940 992 2.031163 GAGGTTGTGGTGCTCGCT 59.969 61.111 0.00 0.00 0.00 4.93
941 993 2.758770 TACGAGGTTGTGGTGCTCGC 62.759 60.000 0.00 0.00 40.68 5.03
942 994 0.108804 ATACGAGGTTGTGGTGCTCG 60.109 55.000 0.00 0.00 42.41 5.03
943 995 2.000447 GAATACGAGGTTGTGGTGCTC 59.000 52.381 0.00 0.00 0.00 4.26
1020 1073 3.414700 GTCAGCACGGCCGACAAG 61.415 66.667 35.90 19.06 0.00 3.16
1036 1089 4.078516 GCCCCTTACGGCGACAGT 62.079 66.667 16.62 0.00 39.64 3.55
1113 1166 4.147322 GATGCACGAACGGCACCG 62.147 66.667 7.71 7.71 45.23 4.94
1115 1168 4.147322 CCGATGCACGAACGGCAC 62.147 66.667 9.75 6.44 45.23 5.01
1193 1253 2.873245 GCTCAAGCTCAATCAGTGACCA 60.873 50.000 0.00 0.00 38.21 4.02
1194 1254 1.736681 GCTCAAGCTCAATCAGTGACC 59.263 52.381 0.00 0.00 38.21 4.02
1218 1288 2.543012 CAGATGACAGATGATCAACGGC 59.457 50.000 0.00 0.00 0.00 5.68
1222 1292 3.520721 ACCACCAGATGACAGATGATCAA 59.479 43.478 0.00 0.00 0.00 2.57
1224 1294 3.834489 ACCACCAGATGACAGATGATC 57.166 47.619 0.00 0.00 0.00 2.92
1422 1494 1.787012 GTTTTTGGCTCGTCGTAGGA 58.213 50.000 0.00 0.00 0.00 2.94
1453 1525 6.927936 AGTGCTACAGCTAATATGATTGTGAG 59.072 38.462 2.44 0.00 42.66 3.51
1519 1595 0.186630 CCCTGCATCCATTCCATCCA 59.813 55.000 0.00 0.00 0.00 3.41
1520 1596 0.186873 ACCCTGCATCCATTCCATCC 59.813 55.000 0.00 0.00 0.00 3.51
1521 1597 1.325355 CACCCTGCATCCATTCCATC 58.675 55.000 0.00 0.00 0.00 3.51
1522 1598 0.632835 ACACCCTGCATCCATTCCAT 59.367 50.000 0.00 0.00 0.00 3.41
1523 1599 0.409092 AACACCCTGCATCCATTCCA 59.591 50.000 0.00 0.00 0.00 3.53
1524 1600 1.106285 GAACACCCTGCATCCATTCC 58.894 55.000 0.00 0.00 0.00 3.01
1525 1601 1.106285 GGAACACCCTGCATCCATTC 58.894 55.000 0.00 0.00 29.85 2.67
1526 1602 0.324645 GGGAACACCCTGCATCCATT 60.325 55.000 4.26 0.00 40.49 3.16
1602 1678 3.748568 AGCTGCTTGAGTTAGTTACTTGC 59.251 43.478 0.00 0.00 37.17 4.01
1609 1685 4.008330 TCGTAGTAGCTGCTTGAGTTAGT 58.992 43.478 10.41 0.00 0.00 2.24
1613 1689 2.820787 AGTTCGTAGTAGCTGCTTGAGT 59.179 45.455 10.41 0.00 0.00 3.41
1616 1692 4.358494 AGTAGTTCGTAGTAGCTGCTTG 57.642 45.455 10.41 3.39 0.00 4.01
1617 1693 6.696441 AATAGTAGTTCGTAGTAGCTGCTT 57.304 37.500 10.41 0.00 0.00 3.91
1618 1694 6.991531 ACTAATAGTAGTTCGTAGTAGCTGCT 59.008 38.462 9.94 9.94 37.25 4.24
1619 1695 7.070798 CACTAATAGTAGTTCGTAGTAGCTGC 58.929 42.308 0.00 0.00 38.58 5.25
1620 1696 8.140677 ACACTAATAGTAGTTCGTAGTAGCTG 57.859 38.462 0.00 0.00 38.58 4.24
1621 1697 9.823647 TTACACTAATAGTAGTTCGTAGTAGCT 57.176 33.333 0.00 0.00 38.58 3.32
1647 1723 4.997395 TCTGCTGAGAATAAGAGCGTTTTT 59.003 37.500 0.00 0.00 0.00 1.94
1648 1724 4.569943 TCTGCTGAGAATAAGAGCGTTTT 58.430 39.130 0.00 0.00 0.00 2.43
1649 1725 4.180057 CTCTGCTGAGAATAAGAGCGTTT 58.820 43.478 15.04 0.00 42.73 3.60
1650 1726 3.430098 CCTCTGCTGAGAATAAGAGCGTT 60.430 47.826 21.10 0.00 42.73 4.84
1651 1727 2.100584 CCTCTGCTGAGAATAAGAGCGT 59.899 50.000 21.10 0.00 42.73 5.07
1652 1728 2.100584 ACCTCTGCTGAGAATAAGAGCG 59.899 50.000 21.10 4.46 42.73 5.03
1655 1806 3.621558 TCGACCTCTGCTGAGAATAAGA 58.378 45.455 21.10 10.18 42.73 2.10
1721 1885 4.875536 TGTGCAATAATACAGTACAGGCAG 59.124 41.667 0.00 0.00 0.00 4.85
1722 1886 4.837972 TGTGCAATAATACAGTACAGGCA 58.162 39.130 0.00 0.00 0.00 4.75
1723 1887 7.490962 TTATGTGCAATAATACAGTACAGGC 57.509 36.000 0.00 0.00 31.67 4.85
1724 1888 8.061857 CGTTTATGTGCAATAATACAGTACAGG 58.938 37.037 0.00 0.00 31.67 4.00
1725 1889 8.813282 TCGTTTATGTGCAATAATACAGTACAG 58.187 33.333 0.00 0.00 31.67 2.74
1726 1890 8.705048 TCGTTTATGTGCAATAATACAGTACA 57.295 30.769 0.00 0.00 32.65 2.90
1850 2752 2.567985 ACGGGCGGGTTTCTATAAATG 58.432 47.619 0.00 0.00 0.00 2.32
1866 2768 8.953313 ACTATCTCACCTTTAATTTTTAACGGG 58.047 33.333 7.26 3.37 0.00 5.28
1959 2870 0.249073 CGGAAGCGGACTCGATTGAT 60.249 55.000 0.00 0.00 45.48 2.57
2020 2931 0.096454 CGATCGATCGCCAGCGTATA 59.904 55.000 32.34 0.00 43.84 1.47
2043 2956 0.836606 TTTGCTGGGCAGGATCGATA 59.163 50.000 0.00 0.00 40.61 2.92
2047 2960 1.407979 CTTGATTTGCTGGGCAGGATC 59.592 52.381 9.44 9.44 40.61 3.36
2075 2988 1.076332 ATCGCGTAGGTTTTGCACTC 58.924 50.000 5.77 0.00 0.00 3.51
2082 2995 1.849097 GATCGGAATCGCGTAGGTTT 58.151 50.000 5.77 0.00 36.13 3.27
2092 3005 1.000283 ACTGCTGGATCGATCGGAATC 60.000 52.381 18.81 11.59 0.00 2.52
2115 3028 1.324736 GATCGCGTTCTAGCAGTTTGG 59.675 52.381 5.77 0.00 36.85 3.28
2116 3029 1.007011 CGATCGCGTTCTAGCAGTTTG 60.007 52.381 14.72 0.00 36.85 2.93
2120 3033 1.048494 CATCGATCGCGTTCTAGCAG 58.952 55.000 11.09 0.00 38.98 4.24
2121 3034 0.317854 CCATCGATCGCGTTCTAGCA 60.318 55.000 11.09 0.00 38.98 3.49
2122 3035 1.609840 GCCATCGATCGCGTTCTAGC 61.610 60.000 11.09 8.31 38.98 3.42
2145 3058 1.080705 GTCGTCCAGGTCCAAGTCG 60.081 63.158 0.00 0.00 0.00 4.18
2311 3227 1.361668 ATGTCGCCGCAGATGTTGAC 61.362 55.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.