Multiple sequence alignment - TraesCS2D01G475100

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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 TraesCS2D01G475100 chr2D 100.000 3696 0 0 1 3696 577610685 577606990 0.000000e+00 6826.0
1 TraesCS2D01G475100 chr2D 90.066 1520 141 8 1202 2716 522689271 522690785 0.000000e+00 1962.0
2 TraesCS2D01G475100 chr2D 89.958 1434 139 3 1285 2716 522749232 522750662 0.000000e+00 1845.0
3 TraesCS2D01G475100 chr2D 81.781 1213 205 12 1323 2527 522752626 522753830 0.000000e+00 1002.0
4 TraesCS2D01G475100 chr2D 92.500 40 1 2 1074 1113 462477815 462477778 5.160000e-04 56.5
5 TraesCS2D01G475100 chr2D 97.059 34 0 1 1079 1112 462477810 462477842 5.160000e-04 56.5
6 TraesCS2D01G475100 chr2B 94.625 1935 74 9 1119 3030 694943882 694945809 0.000000e+00 2970.0
7 TraesCS2D01G475100 chr2B 89.894 1514 141 5 1202 2712 615735934 615737438 0.000000e+00 1938.0
8 TraesCS2D01G475100 chr2B 90.586 1434 128 7 1286 2716 615788433 615789862 0.000000e+00 1893.0
9 TraesCS2D01G475100 chr2B 87.078 681 72 11 3027 3696 694946864 694947539 0.000000e+00 756.0
10 TraesCS2D01G475100 chr2B 91.205 307 17 4 767 1072 694943496 694943793 3.440000e-110 409.0
11 TraesCS2D01G475100 chr2A 95.509 1670 58 4 1119 2771 715806598 715808267 0.000000e+00 2652.0
12 TraesCS2D01G475100 chr2A 89.398 1462 150 5 1251 2711 667959412 667960869 0.000000e+00 1836.0
13 TraesCS2D01G475100 chr2A 92.887 942 51 9 2759 3691 715808288 715809222 0.000000e+00 1354.0
14 TraesCS2D01G475100 chr2A 80.014 1386 255 17 1323 2697 667964302 667965676 0.000000e+00 1005.0
15 TraesCS2D01G475100 chr2A 79.000 1400 267 24 1317 2698 667942226 667943616 0.000000e+00 931.0
16 TraesCS2D01G475100 chr2A 86.614 762 66 22 24 780 715804930 715805660 0.000000e+00 809.0
17 TraesCS2D01G475100 chr2A 89.680 281 18 5 792 1072 715806239 715806508 7.600000e-92 348.0
18 TraesCS2D01G475100 chr5D 91.113 1339 86 12 1317 2643 551892007 551890690 0.000000e+00 1783.0
19 TraesCS2D01G475100 chr5D 94.286 70 4 0 963 1032 551918430 551918361 1.400000e-19 108.0
20 TraesCS2D01G475100 chr5B 86.853 251 33 0 1710 1960 700201352 700201102 7.810000e-72 281.0
21 TraesCS2D01G475100 chr1D 97.143 35 0 1 1079 1113 338920269 338920302 1.430000e-04 58.4
22 TraesCS2D01G475100 chr7B 97.059 34 0 1 1079 1112 730173759 730173791 5.160000e-04 56.5
23 TraesCS2D01G475100 chr4D 97.059 34 0 1 1079 1112 113171929 113171897 5.160000e-04 56.5
24 TraesCS2D01G475100 chr4D 97.059 34 0 1 1079 1112 299314388 299314356 5.160000e-04 56.5
25 TraesCS2D01G475100 chr4A 97.059 34 0 1 1079 1112 601204593 601204625 5.160000e-04 56.5
26 TraesCS2D01G475100 chr3D 97.059 34 0 1 1079 1112 542391332 542391300 5.160000e-04 56.5
27 TraesCS2D01G475100 chr1A 97.059 34 0 1 1079 1112 551875731 551875699 5.160000e-04 56.5


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 TraesCS2D01G475100 chr2D 577606990 577610685 3695 True 6826.000000 6826 100.000000 1 3696 1 chr2D.!!$R2 3695
1 TraesCS2D01G475100 chr2D 522689271 522690785 1514 False 1962.000000 1962 90.066000 1202 2716 1 chr2D.!!$F2 1514
2 TraesCS2D01G475100 chr2D 522749232 522753830 4598 False 1423.500000 1845 85.869500 1285 2716 2 chr2D.!!$F3 1431
3 TraesCS2D01G475100 chr2B 615735934 615737438 1504 False 1938.000000 1938 89.894000 1202 2712 1 chr2B.!!$F1 1510
4 TraesCS2D01G475100 chr2B 615788433 615789862 1429 False 1893.000000 1893 90.586000 1286 2716 1 chr2B.!!$F2 1430
5 TraesCS2D01G475100 chr2B 694943496 694947539 4043 False 1378.333333 2970 90.969333 767 3696 3 chr2B.!!$F3 2929
6 TraesCS2D01G475100 chr2A 667959412 667965676 6264 False 1420.500000 1836 84.706000 1251 2711 2 chr2A.!!$F2 1460
7 TraesCS2D01G475100 chr2A 715804930 715809222 4292 False 1290.750000 2652 91.172500 24 3691 4 chr2A.!!$F3 3667
8 TraesCS2D01G475100 chr2A 667942226 667943616 1390 False 931.000000 931 79.000000 1317 2698 1 chr2A.!!$F1 1381
9 TraesCS2D01G475100 chr5D 551890690 551892007 1317 True 1783.000000 1783 91.113000 1317 2643 1 chr5D.!!$R1 1326

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
834 1406 0.032952 GTGGAGGTGTACTGCGACAA 59.967 55.0 0.0 0.0 41.01 3.18 F
1157 1773 0.036388 TGTCACCCGAGATTTGCTCC 60.036 55.0 0.0 0.0 40.70 4.70 F
1162 1778 0.391130 CCCGAGATTTGCTCCGAACA 60.391 55.0 0.0 0.0 40.70 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1786 2434 0.037697 CACGCAGTAGCTGGTGGTTA 60.038 55.0 0.0 0.0 41.61 2.85 R
2456 3127 0.679505 TAGTTGCAGACAAGCTCCGT 59.320 50.0 0.0 0.0 36.16 4.69 R
3122 6562 1.699730 TCGGGAAGTCTGAACTGTCA 58.300 50.0 0.0 0.0 35.36 3.58 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
111 113 9.586435 AAGGTGCAAAGTTCTAATAATAATTGC 57.414 29.630 0.00 0.00 41.56 3.56
289 293 8.154203 CCTTTTTATGTTATTTGGGAAACTGGT 58.846 33.333 0.00 0.00 0.00 4.00
290 294 8.894768 TTTTTATGTTATTTGGGAAACTGGTG 57.105 30.769 0.00 0.00 0.00 4.17
291 295 6.597832 TTATGTTATTTGGGAAACTGGTGG 57.402 37.500 0.00 0.00 0.00 4.61
293 297 4.148838 TGTTATTTGGGAAACTGGTGGAG 58.851 43.478 0.00 0.00 0.00 3.86
310 314 4.885325 GGTGGAGAAACTAACTGAAAACCA 59.115 41.667 0.00 0.00 0.00 3.67
311 315 5.358725 GGTGGAGAAACTAACTGAAAACCAA 59.641 40.000 0.00 0.00 0.00 3.67
312 316 6.127563 GGTGGAGAAACTAACTGAAAACCAAA 60.128 38.462 0.00 0.00 0.00 3.28
313 317 7.317390 GTGGAGAAACTAACTGAAAACCAAAA 58.683 34.615 0.00 0.00 0.00 2.44
314 318 7.979537 GTGGAGAAACTAACTGAAAACCAAAAT 59.020 33.333 0.00 0.00 0.00 1.82
315 319 9.191479 TGGAGAAACTAACTGAAAACCAAAATA 57.809 29.630 0.00 0.00 0.00 1.40
321 325 8.642908 ACTAACTGAAAACCAAAATAAACTGC 57.357 30.769 0.00 0.00 0.00 4.40
322 326 8.474831 ACTAACTGAAAACCAAAATAAACTGCT 58.525 29.630 0.00 0.00 0.00 4.24
323 327 7.538303 AACTGAAAACCAAAATAAACTGCTG 57.462 32.000 0.00 0.00 0.00 4.41
324 328 6.048509 ACTGAAAACCAAAATAAACTGCTGG 58.951 36.000 0.00 0.00 0.00 4.85
355 359 1.878953 ATATTTCCCGCTTGCTACCG 58.121 50.000 0.00 0.00 0.00 4.02
360 364 2.396157 CCCGCTTGCTACCGTTTCC 61.396 63.158 0.00 0.00 0.00 3.13
399 403 0.037326 TTAGAGGGCGCTTGTGTGAG 60.037 55.000 7.64 0.00 0.00 3.51
431 435 4.331356 ACGCACACAACGTCCTAC 57.669 55.556 0.00 0.00 40.28 3.18
461 465 3.372440 CCCACTTTTAAGGGCATCTCT 57.628 47.619 0.00 0.00 38.44 3.10
473 477 2.092323 GGCATCTCTAACCAAACCCAC 58.908 52.381 0.00 0.00 0.00 4.61
474 478 1.737793 GCATCTCTAACCAAACCCACG 59.262 52.381 0.00 0.00 0.00 4.94
486 490 3.004002 CCAAACCCACGAAGTTTAACTCC 59.996 47.826 0.00 0.00 41.61 3.85
514 518 1.007238 CCTCCTCACTCTAACTCCCCA 59.993 57.143 0.00 0.00 0.00 4.96
569 573 2.028020 CGAACCCTCAAACTTAGCTCCT 60.028 50.000 0.00 0.00 0.00 3.69
586 590 3.491267 GCTCCTCAAACGAATTAGATCCG 59.509 47.826 0.00 0.00 0.00 4.18
603 607 2.370349 TCCGACATGGAAGTCTCTCTC 58.630 52.381 0.00 0.00 46.38 3.20
604 608 1.407258 CCGACATGGAAGTCTCTCTCC 59.593 57.143 0.00 0.00 42.00 3.71
616 620 4.619679 AGTCTCTCTCCCTATTCTTGCTT 58.380 43.478 0.00 0.00 0.00 3.91
617 621 4.649218 AGTCTCTCTCCCTATTCTTGCTTC 59.351 45.833 0.00 0.00 0.00 3.86
618 622 3.964031 TCTCTCTCCCTATTCTTGCTTCC 59.036 47.826 0.00 0.00 0.00 3.46
619 623 3.966665 CTCTCTCCCTATTCTTGCTTCCT 59.033 47.826 0.00 0.00 0.00 3.36
620 624 4.366267 TCTCTCCCTATTCTTGCTTCCTT 58.634 43.478 0.00 0.00 0.00 3.36
621 625 4.407296 TCTCTCCCTATTCTTGCTTCCTTC 59.593 45.833 0.00 0.00 0.00 3.46
623 627 4.785376 TCTCCCTATTCTTGCTTCCTTCTT 59.215 41.667 0.00 0.00 0.00 2.52
625 629 5.501156 TCCCTATTCTTGCTTCCTTCTTTC 58.499 41.667 0.00 0.00 0.00 2.62
626 630 5.251700 TCCCTATTCTTGCTTCCTTCTTTCT 59.748 40.000 0.00 0.00 0.00 2.52
628 632 5.588246 CCTATTCTTGCTTCCTTCTTTCTCC 59.412 44.000 0.00 0.00 0.00 3.71
629 633 4.713792 TTCTTGCTTCCTTCTTTCTCCT 57.286 40.909 0.00 0.00 0.00 3.69
630 634 4.713792 TCTTGCTTCCTTCTTTCTCCTT 57.286 40.909 0.00 0.00 0.00 3.36
639 643 5.158889 TCCTTCTTTCTCCTTCTTCCTTCT 58.841 41.667 0.00 0.00 0.00 2.85
669 673 4.491676 CAAGCAACCAAGGATGATTTCTG 58.508 43.478 0.01 0.00 0.00 3.02
672 676 3.434309 CAACCAAGGATGATTTCTGGGT 58.566 45.455 0.00 0.00 0.00 4.51
691 695 4.588951 TGGGTGGTAGATAATGTGAGCTAG 59.411 45.833 0.00 0.00 0.00 3.42
739 743 2.574006 AGCAATTTGACAGAGGCTCA 57.426 45.000 18.26 0.00 0.00 4.26
748 752 2.094494 TGACAGAGGCTCATCGAGTTTC 60.094 50.000 18.26 0.00 31.39 2.78
757 762 6.115446 AGGCTCATCGAGTTTCATTTCATTA 58.885 36.000 0.00 0.00 31.39 1.90
834 1406 0.032952 GTGGAGGTGTACTGCGACAA 59.967 55.000 0.00 0.00 41.01 3.18
871 1443 6.072452 ACGTTTTCCTTCCTCTTGAATTGATC 60.072 38.462 0.00 0.00 31.06 2.92
906 1478 4.505191 GTGACGCAACAACTAACTACTTCA 59.495 41.667 0.00 0.00 0.00 3.02
910 1483 7.601130 TGACGCAACAACTAACTACTTCATAAT 59.399 33.333 0.00 0.00 0.00 1.28
950 1523 5.700832 TCAACTCGTCTACTTGCATGATTTT 59.299 36.000 6.60 0.00 0.00 1.82
951 1524 6.204688 TCAACTCGTCTACTTGCATGATTTTT 59.795 34.615 6.60 0.00 0.00 1.94
952 1525 5.931532 ACTCGTCTACTTGCATGATTTTTG 58.068 37.500 6.60 0.00 0.00 2.44
965 1538 8.929827 TGCATGATTTTTGTGTATAAATCTGG 57.070 30.769 0.00 0.00 40.02 3.86
1030 1603 2.359900 GCATTTCGTGGAAGATGGACT 58.640 47.619 0.00 0.00 0.00 3.85
1053 1626 6.757010 ACTTGGTAAGTGTATTAATCTGCGAG 59.243 38.462 0.00 0.00 41.01 5.03
1057 1630 6.198591 GGTAAGTGTATTAATCTGCGAGTCAC 59.801 42.308 0.00 0.00 0.00 3.67
1072 1645 1.028905 GTCACCTCCGATCCTGAGAG 58.971 60.000 8.18 0.27 31.26 3.20
1074 1647 1.496857 TCACCTCCGATCCTGAGAGAT 59.503 52.381 8.18 0.00 31.26 2.75
1075 1648 2.711547 TCACCTCCGATCCTGAGAGATA 59.288 50.000 8.18 0.00 31.26 1.98
1076 1649 2.817258 CACCTCCGATCCTGAGAGATAC 59.183 54.545 8.18 0.00 31.26 2.24
1077 1650 2.080693 CCTCCGATCCTGAGAGATACG 58.919 57.143 8.18 0.00 31.26 3.06
1083 1661 7.335055 CTCCGATCCTGAGAGATACGTAGTAC 61.335 50.000 0.08 0.00 37.71 2.73
1084 1662 9.396964 CTCCGATCCTGAGAGATACGTAGTACT 62.397 48.148 0.00 0.00 37.71 2.73
1108 1686 9.362151 ACTAAAATTGAGTCACTTATTTTGGGA 57.638 29.630 20.15 6.25 34.64 4.37
1109 1687 9.626045 CTAAAATTGAGTCACTTATTTTGGGAC 57.374 33.333 18.17 0.00 33.59 4.46
1110 1688 5.880054 ATTGAGTCACTTATTTTGGGACG 57.120 39.130 0.00 0.00 33.84 4.79
1111 1689 3.670625 TGAGTCACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 33.84 4.79
1112 1690 3.007635 GAGTCACTTATTTTGGGACGGG 58.992 50.000 0.00 0.00 33.84 5.28
1114 1692 3.151554 GTCACTTATTTTGGGACGGGTT 58.848 45.455 0.00 0.00 0.00 4.11
1125 1741 1.249407 GGACGGGTTGCCAAATTACA 58.751 50.000 0.00 0.00 0.00 2.41
1157 1773 0.036388 TGTCACCCGAGATTTGCTCC 60.036 55.000 0.00 0.00 40.70 4.70
1162 1778 0.391130 CCCGAGATTTGCTCCGAACA 60.391 55.000 0.00 0.00 40.70 3.18
1165 1781 2.002586 CGAGATTTGCTCCGAACATGT 58.997 47.619 0.00 0.00 40.70 3.21
1170 1795 2.472695 TTGCTCCGAACATGTAAGCT 57.527 45.000 17.81 0.00 34.11 3.74
1172 1797 2.346803 TGCTCCGAACATGTAAGCTTC 58.653 47.619 0.00 4.67 34.11 3.86
1214 1848 1.856265 CTGCGTTGGCCTCTGGTTTC 61.856 60.000 3.32 0.00 38.85 2.78
1224 1858 1.202806 CCTCTGGTTTCTTCACTGCCA 60.203 52.381 0.00 0.00 0.00 4.92
1249 1886 2.159212 ACATATAACGTGCCGTAGTGCA 60.159 45.455 0.00 0.00 39.99 4.57
1292 1938 1.595382 AGTCAGCACCACAGAACGC 60.595 57.895 0.00 0.00 0.00 4.84
1514 2162 1.292541 GTCCAGTTCCACGACCTCC 59.707 63.158 0.00 0.00 0.00 4.30
1641 2289 4.838486 CGCGGCTCTCCTCGACAC 62.838 72.222 0.00 0.00 42.87 3.67
1654 2302 3.444805 GACACGCTCTCCGGCTCT 61.445 66.667 0.00 0.00 42.52 4.09
1786 2434 2.704572 CTTCTTGGAAGAATGGACGCT 58.295 47.619 2.33 0.00 43.52 5.07
1794 2442 0.981183 AGAATGGACGCTAACCACCA 59.019 50.000 0.00 0.00 40.36 4.17
2320 2991 4.028490 GTGATCACCGGGTGGGCA 62.028 66.667 26.07 20.23 40.62 5.36
2398 3069 1.187087 GGAACTCGACCATGGAGAGT 58.813 55.000 28.94 28.94 46.01 3.24
2779 4208 6.049955 TCAGCCAGTGTATTTAAAGCTAGT 57.950 37.500 0.00 0.00 0.00 2.57
2877 5189 5.181245 AGTTTGCAATGGACTATGTACACAC 59.819 40.000 0.00 0.00 0.00 3.82
3062 6502 2.821969 CACTCCCCAAACCTTCTTCATG 59.178 50.000 0.00 0.00 0.00 3.07
3075 6515 1.078497 TTCATGTCTTCGGGCGCAT 60.078 52.632 10.83 0.00 0.00 4.73
3131 6571 6.048732 TGCCTTATATGTCTTGACAGTTCA 57.951 37.500 9.39 0.00 0.00 3.18
3141 6581 1.699730 TGACAGTTCAGACTTCCCGA 58.300 50.000 0.00 0.00 32.54 5.14
3148 6588 2.033194 CAGACTTCCCGAAACCCGC 61.033 63.158 0.00 0.00 36.84 6.13
3188 6628 4.215109 AGATGGGGGTTGTTTGTATATGC 58.785 43.478 0.00 0.00 0.00 3.14
3201 6641 2.235155 TGTATATGCCCGTTGTGTCAGT 59.765 45.455 0.00 0.00 0.00 3.41
3215 6655 2.092968 GTGTCAGTTCTGGCCCATCATA 60.093 50.000 0.00 0.00 0.00 2.15
3296 7727 4.594920 TGGCTGAACAATTTAAAATGGGGA 59.405 37.500 8.10 0.00 0.00 4.81
3315 7746 2.166254 GGAACAAATCGTTGCCATCCAT 59.834 45.455 0.00 0.00 39.89 3.41
3336 7767 5.356426 CATTGACAAGTCCACCGACATATA 58.644 41.667 0.00 0.00 41.87 0.86
3432 8628 4.905429 AGTTGGAATTTAACATTTGCCCC 58.095 39.130 8.60 0.00 0.00 5.80
3610 9240 3.808189 TGATCTCCCCTTTCTCTTCCTT 58.192 45.455 0.00 0.00 0.00 3.36
3680 9826 0.667792 GGCGGATATCTTCTCACGGC 60.668 60.000 2.05 5.22 39.55 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 5.125097 TGCAAACATGCCTTCAATTGTTTTT 59.875 32.000 5.13 0.00 39.55 1.94
15 16 4.639310 TGCAAACATGCCTTCAATTGTTTT 59.361 33.333 5.13 0.00 39.55 2.43
16 17 4.197750 TGCAAACATGCCTTCAATTGTTT 58.802 34.783 5.13 0.00 41.58 2.83
17 18 3.806380 TGCAAACATGCCTTCAATTGTT 58.194 36.364 5.13 0.00 33.93 2.83
18 19 3.472283 TGCAAACATGCCTTCAATTGT 57.528 38.095 5.13 0.00 0.00 2.71
19 20 6.671614 ATAATGCAAACATGCCTTCAATTG 57.328 33.333 0.00 0.00 36.36 2.32
20 21 8.789825 TTAATAATGCAAACATGCCTTCAATT 57.210 26.923 0.00 0.00 36.36 2.32
21 22 8.789825 TTTAATAATGCAAACATGCCTTCAAT 57.210 26.923 0.00 0.00 36.36 2.57
22 23 8.613060 TTTTAATAATGCAAACATGCCTTCAA 57.387 26.923 0.00 0.00 36.36 2.69
27 28 9.676195 AAAACTTTTTAATAATGCAAACATGCC 57.324 25.926 0.00 0.00 36.36 4.40
85 87 9.586435 GCAATTATTATTAGAACTTTGCACCTT 57.414 29.630 0.00 0.00 38.40 3.50
87 89 8.925161 TGCAATTATTATTAGAACTTTGCACC 57.075 30.769 3.14 0.00 42.11 5.01
261 264 9.554395 CAGTTTCCCAAATAACATAAAAAGGTT 57.446 29.630 0.00 0.00 0.00 3.50
279 282 2.658807 AGTTTCTCCACCAGTTTCCC 57.341 50.000 0.00 0.00 0.00 3.97
286 290 4.885325 GGTTTTCAGTTAGTTTCTCCACCA 59.115 41.667 0.00 0.00 0.00 4.17
289 293 7.469537 TTTTGGTTTTCAGTTAGTTTCTCCA 57.530 32.000 0.00 0.00 0.00 3.86
381 385 1.185618 ACTCACACAAGCGCCCTCTA 61.186 55.000 2.29 0.00 0.00 2.43
431 435 3.947834 CCTTAAAAGTGGGTGCTCCTATG 59.052 47.826 4.53 0.00 36.20 2.23
461 465 5.192176 AGTTAAACTTCGTGGGTTTGGTTA 58.808 37.500 11.20 0.00 37.45 2.85
473 477 3.999001 GGTGTTAGGGGAGTTAAACTTCG 59.001 47.826 0.00 0.00 0.00 3.79
474 478 5.238624 AGGTGTTAGGGGAGTTAAACTTC 57.761 43.478 0.00 0.00 0.00 3.01
486 490 2.239681 AGAGTGAGGAGGTGTTAGGG 57.760 55.000 0.00 0.00 0.00 3.53
535 539 3.704566 TGAGGGTTCGATTAGCTACACAT 59.295 43.478 0.00 0.00 0.00 3.21
544 548 5.416271 AGCTAAGTTTGAGGGTTCGATTA 57.584 39.130 0.00 0.00 0.00 1.75
547 551 2.028385 GGAGCTAAGTTTGAGGGTTCGA 60.028 50.000 0.00 0.00 0.00 3.71
569 573 4.808895 CCATGTCGGATCTAATTCGTTTGA 59.191 41.667 0.00 0.00 36.56 2.69
586 590 2.745968 AGGGAGAGAGACTTCCATGTC 58.254 52.381 0.00 0.00 46.56 3.06
603 607 5.504853 AGAAAGAAGGAAGCAAGAATAGGG 58.495 41.667 0.00 0.00 0.00 3.53
604 608 5.588246 GGAGAAAGAAGGAAGCAAGAATAGG 59.412 44.000 0.00 0.00 0.00 2.57
616 620 5.158889 AGAAGGAAGAAGGAGAAAGAAGGA 58.841 41.667 0.00 0.00 0.00 3.36
617 621 5.497464 AGAAGGAAGAAGGAGAAAGAAGG 57.503 43.478 0.00 0.00 0.00 3.46
618 622 8.154203 ACTTTAGAAGGAAGAAGGAGAAAGAAG 58.846 37.037 0.00 0.00 0.00 2.85
619 623 8.035448 ACTTTAGAAGGAAGAAGGAGAAAGAA 57.965 34.615 0.00 0.00 0.00 2.52
620 624 7.619512 ACTTTAGAAGGAAGAAGGAGAAAGA 57.380 36.000 0.00 0.00 0.00 2.52
621 625 7.389330 GGAACTTTAGAAGGAAGAAGGAGAAAG 59.611 40.741 0.00 0.00 0.00 2.62
623 627 6.329197 TGGAACTTTAGAAGGAAGAAGGAGAA 59.671 38.462 0.00 0.00 0.00 2.87
625 629 6.115448 TGGAACTTTAGAAGGAAGAAGGAG 57.885 41.667 0.00 0.00 0.00 3.69
626 630 6.509523 TTGGAACTTTAGAAGGAAGAAGGA 57.490 37.500 0.00 0.00 0.00 3.36
628 632 5.765182 TGCTTGGAACTTTAGAAGGAAGAAG 59.235 40.000 0.00 0.00 0.00 2.85
629 633 5.690865 TGCTTGGAACTTTAGAAGGAAGAA 58.309 37.500 0.00 0.00 0.00 2.52
630 634 5.304686 TGCTTGGAACTTTAGAAGGAAGA 57.695 39.130 0.00 0.00 0.00 2.87
639 643 3.904717 TCCTTGGTTGCTTGGAACTTTA 58.095 40.909 5.10 0.00 0.00 1.85
669 673 4.561734 GCTAGCTCACATTATCTACCACCC 60.562 50.000 7.70 0.00 0.00 4.61
672 676 5.712446 CCTAGCTAGCTCACATTATCTACCA 59.288 44.000 23.26 0.00 0.00 3.25
691 695 2.420687 GCCATCTACCATATGCCCTAGC 60.421 54.545 0.00 0.00 40.48 3.42
730 734 2.662006 TGAAACTCGATGAGCCTCTG 57.338 50.000 0.00 0.00 32.04 3.35
757 762 5.980715 CCCGCAGTGTTTTTAAACTGTTAAT 59.019 36.000 6.87 0.00 44.59 1.40
871 1443 0.878523 TGCGTCACTGGTTTCCTTCG 60.879 55.000 0.00 0.00 0.00 3.79
906 1478 3.266772 TGAGGACTTGGCCTGTCAATTAT 59.733 43.478 23.78 9.55 38.73 1.28
910 1483 0.843309 TTGAGGACTTGGCCTGTCAA 59.157 50.000 23.78 12.53 38.73 3.18
950 1523 4.634004 CGCAGTTCCCAGATTTATACACAA 59.366 41.667 0.00 0.00 0.00 3.33
951 1524 4.081365 TCGCAGTTCCCAGATTTATACACA 60.081 41.667 0.00 0.00 0.00 3.72
952 1525 4.270325 GTCGCAGTTCCCAGATTTATACAC 59.730 45.833 0.00 0.00 0.00 2.90
1030 1603 6.636705 ACTCGCAGATTAATACACTTACCAA 58.363 36.000 0.00 0.00 33.89 3.67
1053 1626 1.028905 CTCTCAGGATCGGAGGTGAC 58.971 60.000 11.71 0.00 33.18 3.67
1057 1630 2.080693 CGTATCTCTCAGGATCGGAGG 58.919 57.143 11.71 4.85 33.18 4.30
1083 1661 9.626045 GTCCCAAAATAAGTGACTCAATTTTAG 57.374 33.333 14.43 9.77 31.97 1.85
1084 1662 8.293867 CGTCCCAAAATAAGTGACTCAATTTTA 58.706 33.333 14.43 2.50 31.97 1.52
1091 1669 3.007635 CCCGTCCCAAAATAAGTGACTC 58.992 50.000 0.00 0.00 0.00 3.36
1094 1672 3.150767 CAACCCGTCCCAAAATAAGTGA 58.849 45.455 0.00 0.00 0.00 3.41
1097 1675 1.203758 GGCAACCCGTCCCAAAATAAG 59.796 52.381 0.00 0.00 0.00 1.73
1100 1678 0.760945 TTGGCAACCCGTCCCAAAAT 60.761 50.000 0.00 0.00 35.80 1.82
1106 1684 1.201414 CTGTAATTTGGCAACCCGTCC 59.799 52.381 0.00 0.00 0.00 4.79
1107 1685 1.201414 CCTGTAATTTGGCAACCCGTC 59.799 52.381 0.00 0.00 0.00 4.79
1108 1686 1.202952 TCCTGTAATTTGGCAACCCGT 60.203 47.619 0.00 0.00 0.00 5.28
1109 1687 1.472480 CTCCTGTAATTTGGCAACCCG 59.528 52.381 0.00 0.00 0.00 5.28
1110 1688 2.802719 TCTCCTGTAATTTGGCAACCC 58.197 47.619 0.00 0.00 0.00 4.11
1111 1689 5.170748 CAAATCTCCTGTAATTTGGCAACC 58.829 41.667 0.00 0.00 38.58 3.77
1125 1741 1.630878 GGGTGACACTCCAAATCTCCT 59.369 52.381 5.39 0.00 0.00 3.69
1138 1754 0.036388 GGAGCAAATCTCGGGTGACA 60.036 55.000 0.00 0.00 42.82 3.58
1170 1795 2.047274 CGGAAGCTTCCTGGCGAA 60.047 61.111 36.30 0.00 45.33 4.70
1214 1848 4.745125 CGTTATATGTAGGTGGCAGTGAAG 59.255 45.833 0.00 0.00 0.00 3.02
1249 1886 0.247736 GTGGCCGATGAGACTGAACT 59.752 55.000 0.00 0.00 0.00 3.01
1292 1938 0.179089 CGCTTCTCTGTCCCCATCAG 60.179 60.000 0.00 0.00 0.00 2.90
1311 1957 1.226773 GCCACAGAATCCATTGCGC 60.227 57.895 0.00 0.00 0.00 6.09
1514 2162 2.353607 GACGTAGCCGGAGATGCG 60.354 66.667 5.05 8.28 38.78 4.73
1564 2212 1.649271 GCATGAGGTGGGAGGGGAAT 61.649 60.000 0.00 0.00 0.00 3.01
1786 2434 0.037697 CACGCAGTAGCTGGTGGTTA 60.038 55.000 0.00 0.00 41.61 2.85
1794 2442 1.213013 CCGTTCTCACGCAGTAGCT 59.787 57.895 0.00 0.00 45.72 3.32
2034 2696 0.887836 CTGCTTGCTCTGCTCCAACA 60.888 55.000 0.00 0.00 0.00 3.33
2037 2699 2.359602 GCTGCTTGCTCTGCTCCA 60.360 61.111 0.00 0.00 38.95 3.86
2320 2991 1.075970 TAGGATCTCCAGCTGCGGT 60.076 57.895 8.66 0.00 38.89 5.68
2456 3127 0.679505 TAGTTGCAGACAAGCTCCGT 59.320 50.000 0.00 0.00 36.16 4.69
2944 5326 4.278310 ACCATCCTGTATTTTTGGGTAGC 58.722 43.478 0.00 0.00 0.00 3.58
3062 6502 2.750888 GGACAATGCGCCCGAAGAC 61.751 63.158 4.18 0.00 0.00 3.01
3122 6562 1.699730 TCGGGAAGTCTGAACTGTCA 58.300 50.000 0.00 0.00 35.36 3.58
3131 6571 2.346365 GCGGGTTTCGGGAAGTCT 59.654 61.111 0.00 0.00 39.69 3.24
3141 6581 2.766345 TTACATACGAAGGCGGGTTT 57.234 45.000 0.00 0.00 43.17 3.27
3148 6588 6.038271 CCCCATCTTTCTTTTACATACGAAGG 59.962 42.308 0.00 0.00 0.00 3.46
3188 6628 1.507141 GCCAGAACTGACACAACGGG 61.507 60.000 3.19 0.00 0.00 5.28
3201 6641 5.337956 AATTGGTATATGATGGGCCAGAA 57.662 39.130 13.78 2.22 0.00 3.02
3239 6679 1.529713 GTAGAGAGAGAGGGCGGGG 60.530 68.421 0.00 0.00 0.00 5.73
3242 6682 0.395862 TTGGGTAGAGAGAGAGGGCG 60.396 60.000 0.00 0.00 0.00 6.13
3243 6683 1.967779 GATTGGGTAGAGAGAGAGGGC 59.032 57.143 0.00 0.00 0.00 5.19
3296 7727 3.257873 TCAATGGATGGCAACGATTTGTT 59.742 39.130 2.33 0.00 43.09 2.83
3315 7746 3.973206 ATATGTCGGTGGACTTGTCAA 57.027 42.857 3.08 0.00 43.79 3.18
3336 7767 5.279960 GGGCAAGTGTCAAATTTTATCCCTT 60.280 40.000 0.00 0.00 0.00 3.95
3569 9076 0.108585 AGTGTTGTGGTGGCTCGATT 59.891 50.000 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.