Multiple sequence alignment - TraesCS3A01G214300

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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 TraesCS3A01G214300 chr3A 100.000 4625 0 0 1 4625 389130640 389126016 0.000000e+00 8541.0
1 TraesCS3A01G214300 chr3A 98.571 70 1 0 606 675 389129992 389129923 1.750000e-24 124.0
2 TraesCS3A01G214300 chr3A 98.571 70 1 0 649 718 389130035 389129966 1.750000e-24 124.0
3 TraesCS3A01G214300 chr3A 79.532 171 30 5 1016 1184 515913607 515913774 2.920000e-22 117.0
4 TraesCS3A01G214300 chr3B 94.621 3328 136 21 633 3954 388106811 388103521 0.000000e+00 5114.0
5 TraesCS3A01G214300 chr3B 95.380 671 19 9 3963 4625 388103333 388102667 0.000000e+00 1057.0
6 TraesCS3A01G214300 chr3B 92.484 612 44 2 1 612 388114160 388113551 0.000000e+00 874.0
7 TraesCS3A01G214300 chr3D 95.008 2524 76 19 2140 4625 294347911 294345400 0.000000e+00 3917.0
8 TraesCS3A01G214300 chr3D 94.467 1211 43 10 634 1827 294350778 294349575 0.000000e+00 1844.0
9 TraesCS3A01G214300 chr3D 89.901 604 58 3 10 612 347902448 347901847 0.000000e+00 774.0
10 TraesCS3A01G214300 chr3D 87.956 274 18 6 1824 2097 294348173 294347915 4.490000e-80 309.0
11 TraesCS3A01G214300 chr3D 80.588 170 30 3 1016 1184 396211794 396211961 1.350000e-25 128.0
12 TraesCS3A01G214300 chr3D 94.286 70 4 0 606 675 294350764 294350695 1.760000e-19 108.0
13 TraesCS3A01G214300 chr2D 89.274 606 59 6 10 612 296351336 296350734 0.000000e+00 754.0
14 TraesCS3A01G214300 chr5D 89.430 596 57 6 18 612 391190046 391190636 0.000000e+00 747.0
15 TraesCS3A01G214300 chr4A 88.557 603 65 4 12 612 570417216 570417816 0.000000e+00 728.0
16 TraesCS3A01G214300 chr5B 88.557 603 62 5 10 608 206940097 206940696 0.000000e+00 725.0
17 TraesCS3A01G214300 chr5B 88.889 72 6 2 3659 3729 98372767 98372697 2.290000e-13 87.9
18 TraesCS3A01G214300 chr5A 88.758 596 62 5 18 612 584568359 584567768 0.000000e+00 725.0
19 TraesCS3A01G214300 chr6A 88.591 596 65 3 18 612 183101130 183100537 0.000000e+00 721.0
20 TraesCS3A01G214300 chr2B 87.948 614 70 4 1 612 253698677 253698066 0.000000e+00 721.0
21 TraesCS3A01G214300 chr1A 81.347 193 32 4 994 1184 536667028 536666838 2.230000e-33 154.0
22 TraesCS3A01G214300 chr1D 80.829 193 33 4 994 1184 441296943 441297133 1.040000e-31 148.0
23 TraesCS3A01G214300 chr1B 80.829 193 33 4 994 1184 599332784 599332974 1.040000e-31 148.0
24 TraesCS3A01G214300 chr6B 93.220 59 4 0 3659 3717 92070771 92070829 2.290000e-13 87.9
25 TraesCS3A01G214300 chr6B 88.889 72 6 2 3659 3729 267780172 267780242 2.290000e-13 87.9


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 TraesCS3A01G214300 chr3A 389126016 389130640 4624 True 2929.666667 8541 99.047333 1 4625 3 chr3A.!!$R1 4624
1 TraesCS3A01G214300 chr3B 388102667 388106811 4144 True 3085.500000 5114 95.000500 633 4625 2 chr3B.!!$R2 3992
2 TraesCS3A01G214300 chr3B 388113551 388114160 609 True 874.000000 874 92.484000 1 612 1 chr3B.!!$R1 611
3 TraesCS3A01G214300 chr3D 294345400 294350778 5378 True 1544.500000 3917 92.929250 606 4625 4 chr3D.!!$R2 4019
4 TraesCS3A01G214300 chr3D 347901847 347902448 601 True 774.000000 774 89.901000 10 612 1 chr3D.!!$R1 602
5 TraesCS3A01G214300 chr2D 296350734 296351336 602 True 754.000000 754 89.274000 10 612 1 chr2D.!!$R1 602
6 TraesCS3A01G214300 chr5D 391190046 391190636 590 False 747.000000 747 89.430000 18 612 1 chr5D.!!$F1 594
7 TraesCS3A01G214300 chr4A 570417216 570417816 600 False 728.000000 728 88.557000 12 612 1 chr4A.!!$F1 600
8 TraesCS3A01G214300 chr5B 206940097 206940696 599 False 725.000000 725 88.557000 10 608 1 chr5B.!!$F1 598
9 TraesCS3A01G214300 chr5A 584567768 584568359 591 True 725.000000 725 88.758000 18 612 1 chr5A.!!$R1 594
10 TraesCS3A01G214300 chr6A 183100537 183101130 593 True 721.000000 721 88.591000 18 612 1 chr6A.!!$R1 594
11 TraesCS3A01G214300 chr2B 253698066 253698677 611 True 721.000000 721 87.948000 1 612 1 chr2B.!!$R1 611

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
953 963 1.221414 GCGCAACCAGATCTGATACC 58.779 55.0 24.62 8.55 0.00 2.73 F
1195 1205 0.108041 CGCGAGGTAAAGCCCCTAAA 60.108 55.0 0.00 0.00 38.26 1.85 F
1648 1672 0.463833 GGGGGAAGACCATTGCTACG 60.464 60.0 0.00 0.00 42.91 3.51 F
1805 1836 0.677288 TAGCTAGGTGTGCGTGTTGT 59.323 50.0 4.27 0.00 35.28 3.32 F
2704 4144 0.678048 GGATGGACACTTGACCTGGC 60.678 60.0 0.00 0.00 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1805 1836 0.178932 AGGAGTAGGTGACACTGCCA 60.179 55.0 5.39 0.00 35.15 4.92 R
3075 4524 0.534203 GAAGCCCGGTTCTCAACACA 60.534 55.0 0.00 0.00 0.00 3.72 R
3147 4598 1.086067 CAGCCATGACCACTACTGCG 61.086 60.0 0.00 0.00 0.00 5.18 R
3477 4928 1.165907 TCCAAAGCTGCTTGACACCG 61.166 55.0 16.73 0.94 0.00 4.94 R
4458 6124 0.816825 CGATGAGGCAAGGACCCATG 60.817 60.0 0.00 0.00 0.00 3.66 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
69 72 7.015389 AGAGAGTAAATAGTGGGTACAATAGGC 59.985 40.741 0.00 0.00 29.85 3.93
236 244 4.575885 TCTCCCCAACAATAAGAGTTTCG 58.424 43.478 0.00 0.00 0.00 3.46
461 470 3.119673 GGATGATCGACATAGCATCGTCT 60.120 47.826 0.00 0.00 42.00 4.18
467 476 1.337071 GACATAGCATCGTCTTCGGGA 59.663 52.381 0.00 0.00 37.69 5.14
520 529 4.201841 GGTAACGTTTGCAACTACAACAGT 60.202 41.667 5.91 0.00 40.05 3.55
528 537 2.484264 GCAACTACAACAGTCACATCCC 59.516 50.000 0.00 0.00 36.04 3.85
529 538 3.807209 GCAACTACAACAGTCACATCCCT 60.807 47.826 0.00 0.00 36.04 4.20
545 555 6.159575 TCACATCCCTACAAATTCCAATAGGA 59.840 38.462 0.00 0.00 43.93 2.94
574 584 6.071784 AGCAGTTGATTTATCAGTCATTTGCA 60.072 34.615 9.63 0.00 38.19 4.08
614 624 6.012658 GTGTGAGCTTATTCAAACCAATGA 57.987 37.500 0.00 0.00 30.52 2.57
615 625 6.446318 GTGTGAGCTTATTCAAACCAATGAA 58.554 36.000 0.00 0.00 43.03 2.57
616 626 6.363357 GTGTGAGCTTATTCAAACCAATGAAC 59.637 38.462 0.00 0.00 41.78 3.18
617 627 6.265196 TGTGAGCTTATTCAAACCAATGAACT 59.735 34.615 0.00 0.00 41.78 3.01
618 628 6.583806 GTGAGCTTATTCAAACCAATGAACTG 59.416 38.462 0.00 0.00 41.78 3.16
619 629 6.489700 TGAGCTTATTCAAACCAATGAACTGA 59.510 34.615 0.00 0.00 41.78 3.41
620 630 6.681777 AGCTTATTCAAACCAATGAACTGAC 58.318 36.000 0.00 0.00 41.78 3.51
621 631 6.265196 AGCTTATTCAAACCAATGAACTGACA 59.735 34.615 0.00 0.00 41.78 3.58
622 632 6.922957 GCTTATTCAAACCAATGAACTGACAA 59.077 34.615 0.00 0.00 41.78 3.18
623 633 7.599998 GCTTATTCAAACCAATGAACTGACAAT 59.400 33.333 0.00 0.00 41.78 2.71
628 638 9.906660 TTCAAACCAATGAACTGACAATAATAC 57.093 29.630 0.00 0.00 34.50 1.89
629 639 8.519526 TCAAACCAATGAACTGACAATAATACC 58.480 33.333 0.00 0.00 0.00 2.73
630 640 7.404671 AACCAATGAACTGACAATAATACCC 57.595 36.000 0.00 0.00 0.00 3.69
631 641 6.731467 ACCAATGAACTGACAATAATACCCT 58.269 36.000 0.00 0.00 0.00 4.34
632 642 6.828785 ACCAATGAACTGACAATAATACCCTC 59.171 38.462 0.00 0.00 0.00 4.30
633 643 6.828273 CCAATGAACTGACAATAATACCCTCA 59.172 38.462 0.00 0.00 0.00 3.86
634 644 7.339212 CCAATGAACTGACAATAATACCCTCAA 59.661 37.037 0.00 0.00 0.00 3.02
635 645 7.865706 ATGAACTGACAATAATACCCTCAAC 57.134 36.000 0.00 0.00 0.00 3.18
636 646 7.016153 TGAACTGACAATAATACCCTCAACT 57.984 36.000 0.00 0.00 0.00 3.16
637 647 8.141298 TGAACTGACAATAATACCCTCAACTA 57.859 34.615 0.00 0.00 0.00 2.24
680 690 8.141298 TGAACTGACAATAATACCCTCAACTA 57.859 34.615 0.00 0.00 0.00 2.24
684 694 7.120923 TGACAATAATACCCTCAACTACTCC 57.879 40.000 0.00 0.00 0.00 3.85
687 697 5.810080 ATAATACCCTCAACTACTCCTGC 57.190 43.478 0.00 0.00 0.00 4.85
770 780 3.132029 TTGAGCACCCACACCCCTG 62.132 63.158 0.00 0.00 0.00 4.45
953 963 1.221414 GCGCAACCAGATCTGATACC 58.779 55.000 24.62 8.55 0.00 2.73
964 974 6.042552 ACCAGATCTGATACCTTCGATTTGAT 59.957 38.462 24.62 0.00 29.35 2.57
1193 1203 1.380246 TCGCGAGGTAAAGCCCCTA 60.380 57.895 3.71 0.00 38.26 3.53
1194 1204 0.971959 TCGCGAGGTAAAGCCCCTAA 60.972 55.000 3.71 0.00 38.26 2.69
1195 1205 0.108041 CGCGAGGTAAAGCCCCTAAA 60.108 55.000 0.00 0.00 38.26 1.85
1196 1206 1.474498 CGCGAGGTAAAGCCCCTAAAT 60.474 52.381 0.00 0.00 38.26 1.40
1197 1207 2.224113 CGCGAGGTAAAGCCCCTAAATA 60.224 50.000 0.00 0.00 38.26 1.40
1232 1242 0.796312 CAACCGTCTGTACATGTGGC 59.204 55.000 9.11 1.72 0.00 5.01
1251 1261 1.749258 GTGGTTCCAATCGGGGCTC 60.749 63.158 0.00 0.00 37.22 4.70
1298 1308 2.642254 CTCGTAGCAACGGGGGTGA 61.642 63.158 0.00 0.00 46.18 4.02
1299 1309 2.433664 CGTAGCAACGGGGGTGAC 60.434 66.667 0.00 0.00 45.50 3.67
1362 1372 1.500474 ATTACTGCCTGCCTAGCTGA 58.500 50.000 0.00 0.00 33.78 4.26
1365 1375 1.197430 ACTGCCTGCCTAGCTGAACT 61.197 55.000 0.00 0.00 33.78 3.01
1513 1524 2.669569 CGCCACTTGTGACTGGGG 60.670 66.667 1.89 0.00 34.49 4.96
1572 1591 9.256477 CACTATTTATGAACTTTAGCATACGGA 57.744 33.333 0.00 0.00 0.00 4.69
1602 1621 4.040217 GGAGATCTCTTGTATGTGCCATCT 59.960 45.833 21.81 0.00 0.00 2.90
1648 1672 0.463833 GGGGGAAGACCATTGCTACG 60.464 60.000 0.00 0.00 42.91 3.51
1668 1692 2.084546 GTCAGCAATTTCCGGTTAGCT 58.915 47.619 0.00 2.38 0.00 3.32
1681 1712 2.298610 GGTTAGCTGGGGTTTATGCTC 58.701 52.381 0.00 0.00 37.02 4.26
1682 1713 2.092375 GGTTAGCTGGGGTTTATGCTCT 60.092 50.000 0.00 0.00 37.02 4.09
1683 1714 3.206964 GTTAGCTGGGGTTTATGCTCTC 58.793 50.000 0.00 0.00 37.02 3.20
1684 1715 1.589414 AGCTGGGGTTTATGCTCTCT 58.411 50.000 0.00 0.00 0.00 3.10
1707 1738 2.684001 TTTGTGACTGTGAGACGGTT 57.316 45.000 0.00 0.00 37.93 4.44
1714 1745 3.572682 TGACTGTGAGACGGTTCTTATGT 59.427 43.478 0.00 0.00 37.93 2.29
1725 1756 3.689649 CGGTTCTTATGTTTTGCTAGGCT 59.310 43.478 0.00 0.00 0.00 4.58
1786 1817 2.307098 AGCTACCAGGACAGAGCAATTT 59.693 45.455 0.00 0.00 37.40 1.82
1805 1836 0.677288 TAGCTAGGTGTGCGTGTTGT 59.323 50.000 4.27 0.00 35.28 3.32
1807 1838 1.841663 GCTAGGTGTGCGTGTTGTGG 61.842 60.000 0.00 0.00 0.00 4.17
1815 1846 2.468670 GCGTGTTGTGGCAGTGTCA 61.469 57.895 0.00 0.00 0.00 3.58
1819 1850 0.833949 TGTTGTGGCAGTGTCACCTA 59.166 50.000 24.45 10.33 37.35 3.08
1847 3283 3.791320 ACTGGATGACCCTCTTGTAGAA 58.209 45.455 0.00 0.00 35.38 2.10
1927 3363 8.853077 TGAAATGATAACTGTCACTTCAATCT 57.147 30.769 0.00 0.00 40.22 2.40
1940 3376 8.043113 TGTCACTTCAATCTAACAAGATATGCT 58.957 33.333 0.00 0.00 0.00 3.79
2000 3436 2.198827 CAAGTCATGCAAGGTACCCA 57.801 50.000 8.74 0.00 0.00 4.51
2001 3437 1.812571 CAAGTCATGCAAGGTACCCAC 59.187 52.381 8.74 0.00 0.00 4.61
2002 3438 1.362224 AGTCATGCAAGGTACCCACT 58.638 50.000 8.74 0.00 0.00 4.00
2029 3465 4.080863 GTGAGGGAAATATGTCTGTCCTGT 60.081 45.833 0.00 0.00 0.00 4.00
2030 3466 4.536090 TGAGGGAAATATGTCTGTCCTGTT 59.464 41.667 0.00 0.00 0.00 3.16
2089 3525 8.416329 GGAAACATTTTATGTCATCCTTATGCT 58.584 33.333 13.28 0.00 44.07 3.79
2109 3545 1.241165 TGATCACCTGTGCAGCTTTG 58.759 50.000 0.00 0.00 0.00 2.77
2297 3734 4.942852 AGCACATATAGCTCTCTGTGAAC 58.057 43.478 18.17 4.99 41.11 3.18
2358 3795 4.808558 TCAACTGTTGCCTGCAAATATTC 58.191 39.130 15.52 0.00 37.70 1.75
2397 3834 4.517285 TGATCTGAGTTATTGGCAGGAAC 58.483 43.478 5.67 5.67 0.00 3.62
2414 3851 5.525378 GCAGGAACAGTGTAGGATATTTCTG 59.475 44.000 0.00 0.00 0.00 3.02
2543 3980 1.210478 AGTGCAACCTCAGTCAAGTGT 59.790 47.619 0.00 0.00 37.80 3.55
2549 3986 1.204941 ACCTCAGTCAAGTGTATCCGC 59.795 52.381 0.00 0.00 0.00 5.54
2568 4008 3.057596 CCGCATTCTGGTTATGTGTTGTT 60.058 43.478 0.00 0.00 32.88 2.83
2569 4009 4.545610 CGCATTCTGGTTATGTGTTGTTT 58.454 39.130 0.00 0.00 0.00 2.83
2570 4010 4.382457 CGCATTCTGGTTATGTGTTGTTTG 59.618 41.667 0.00 0.00 0.00 2.93
2571 4011 5.288804 GCATTCTGGTTATGTGTTGTTTGT 58.711 37.500 0.00 0.00 0.00 2.83
2574 4014 4.677584 TCTGGTTATGTGTTGTTTGTTGC 58.322 39.130 0.00 0.00 0.00 4.17
2592 4032 7.426929 TTGTTGCTGTTGTTGTTTACATTTT 57.573 28.000 0.00 0.00 36.44 1.82
2635 4075 9.725019 GTTATATAATCCAGATTCATGTGGTCA 57.275 33.333 3.04 0.00 41.62 4.02
2644 4084 4.946157 AGATTCATGTGGTCATTCTTGGAC 59.054 41.667 0.00 0.00 31.15 4.02
2704 4144 0.678048 GGATGGACACTTGACCTGGC 60.678 60.000 0.00 0.00 0.00 4.85
2907 4356 4.038642 TGTTTTCCAACTTGCATTCCCTAC 59.961 41.667 0.00 0.00 33.58 3.18
3075 4524 6.872547 GGAGAGGACTAAACGTGTATTTTTCT 59.127 38.462 0.00 0.00 0.00 2.52
3087 4536 5.907391 CGTGTATTTTTCTGTGTTGAGAACC 59.093 40.000 0.00 0.00 31.53 3.62
3147 4598 1.376037 CGTTCAAGGCCTGGTCTCC 60.376 63.158 5.69 0.00 0.00 3.71
3207 4658 1.281925 CCACATGGGCTAGTTCCCCT 61.282 60.000 0.00 0.00 45.97 4.79
3214 4665 0.694783 GGCTAGTTCCCCTTAGGCCT 60.695 60.000 11.78 11.78 35.73 5.19
3227 4678 3.564352 CCTTAGGCCTGGTTCTCCATTTT 60.564 47.826 17.99 0.00 43.43 1.82
3246 4697 7.755822 TCCATTTTGTATATTTACGTGTTTGCC 59.244 33.333 0.00 0.00 0.00 4.52
3259 4710 3.328505 GTGTTTGCCATCTTCAAATGGG 58.671 45.455 5.15 0.00 45.40 4.00
3304 4755 5.299028 TGAGCCGTAATTTGATTATGCACAT 59.701 36.000 0.00 0.00 31.82 3.21
3420 4871 8.885693 AGTCTGATCAGTGGCTTGTATATATA 57.114 34.615 21.92 0.00 0.00 0.86
3421 4872 9.486123 AGTCTGATCAGTGGCTTGTATATATAT 57.514 33.333 21.92 0.00 0.00 0.86
3477 4928 1.541588 GCATTGTGGAAGGAGGTTGAC 59.458 52.381 0.00 0.00 0.00 3.18
3690 5141 4.378459 GCTTGTCGAAATTACCTGTCTTGG 60.378 45.833 0.00 0.00 0.00 3.61
3718 5169 8.716909 TCACAATTTTGTTTCTGAAAAGTTTCC 58.283 29.630 4.09 0.00 39.91 3.13
3786 5237 4.799949 TCAATAATTTGCTCGCTCAATTGC 59.200 37.500 0.00 0.00 32.61 3.56
3822 5274 4.196971 GTGGTCTGTAACTTGTTCCACTT 58.803 43.478 11.60 0.00 40.14 3.16
3892 5344 7.147312 CCATTTCTTGTTGCAGATGAAAGTAA 58.853 34.615 11.83 4.05 31.50 2.24
3951 5584 4.504461 GTCATCCATAGCGTCTTGTAGTTG 59.496 45.833 0.00 0.00 0.00 3.16
3957 5590 6.071784 TCCATAGCGTCTTGTAGTTGAAGTAA 60.072 38.462 0.00 0.00 0.00 2.24
3960 5593 4.389077 AGCGTCTTGTAGTTGAAGTAATGC 59.611 41.667 0.00 0.00 0.00 3.56
3973 5606 1.812571 AGTAATGCAGGTTGAAAGCCG 59.187 47.619 0.00 0.00 0.00 5.52
4051 5684 2.656560 AGACTAGCTGTGCTAAACGG 57.343 50.000 0.00 0.00 40.82 4.44
4084 5717 7.553881 TTAGATTGCCTAATGACTTGCTAAC 57.446 36.000 0.00 0.00 32.67 2.34
4333 5983 1.675641 GATGGAAAGCACCGCCAGT 60.676 57.895 0.00 0.00 34.74 4.00
4453 6119 1.960763 TCGCGTATCATGGCATGGC 60.961 57.895 26.15 19.60 0.00 4.40
4454 6120 2.253051 CGCGTATCATGGCATGGCA 61.253 57.895 25.52 25.52 0.00 4.92
4455 6121 1.579964 CGCGTATCATGGCATGGCAT 61.580 55.000 27.75 27.75 0.00 4.40
4456 6122 0.109458 GCGTATCATGGCATGGCATG 60.109 55.000 41.70 41.70 0.00 4.06
4457 6123 0.524414 CGTATCATGGCATGGCATGG 59.476 55.000 43.81 31.06 0.00 3.66
4599 6267 6.423604 ACAACAAAAGAAACTCAAACCACTTG 59.576 34.615 0.00 0.00 36.25 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 72 5.580691 TGGTCGATGAATTTAGTAAGCACAG 59.419 40.000 0.00 0.00 0.00 3.66
236 244 7.094592 CCTCTCCCTTCAGTCAAAAAGAAATAC 60.095 40.741 0.00 0.00 0.00 1.89
311 319 8.617290 AGAAACAAAGTTCGGTGAATAGTATT 57.383 30.769 0.00 0.00 32.50 1.89
393 401 4.744237 ACAGGGGCTATTATTGATTGCAT 58.256 39.130 0.00 0.00 38.10 3.96
487 496 5.950758 TGCAAACGTTACCATCTTAACAT 57.049 34.783 0.00 0.00 32.32 2.71
520 529 6.159575 TCCTATTGGAATTTGTAGGGATGTGA 59.840 38.462 0.00 0.00 39.87 3.58
528 537 9.950496 ACTGCTATATCCTATTGGAATTTGTAG 57.050 33.333 0.00 3.92 46.80 2.74
574 584 7.398024 AGCTCACACCTACTGAAATATCTTTT 58.602 34.615 0.00 0.00 0.00 2.27
612 622 7.016153 AGTTGAGGGTATTATTGTCAGTTCA 57.984 36.000 0.00 0.00 0.00 3.18
613 623 8.258708 AGTAGTTGAGGGTATTATTGTCAGTTC 58.741 37.037 0.00 0.00 0.00 3.01
614 624 8.147244 AGTAGTTGAGGGTATTATTGTCAGTT 57.853 34.615 0.00 0.00 0.00 3.16
615 625 7.147707 GGAGTAGTTGAGGGTATTATTGTCAGT 60.148 40.741 0.00 0.00 0.00 3.41
616 626 7.070074 AGGAGTAGTTGAGGGTATTATTGTCAG 59.930 40.741 0.00 0.00 0.00 3.51
617 627 6.901300 AGGAGTAGTTGAGGGTATTATTGTCA 59.099 38.462 0.00 0.00 0.00 3.58
618 628 7.210873 CAGGAGTAGTTGAGGGTATTATTGTC 58.789 42.308 0.00 0.00 0.00 3.18
619 629 6.408206 GCAGGAGTAGTTGAGGGTATTATTGT 60.408 42.308 0.00 0.00 0.00 2.71
620 630 5.992217 GCAGGAGTAGTTGAGGGTATTATTG 59.008 44.000 0.00 0.00 0.00 1.90
621 631 5.071923 GGCAGGAGTAGTTGAGGGTATTATT 59.928 44.000 0.00 0.00 0.00 1.40
622 632 4.593634 GGCAGGAGTAGTTGAGGGTATTAT 59.406 45.833 0.00 0.00 0.00 1.28
623 633 3.965347 GGCAGGAGTAGTTGAGGGTATTA 59.035 47.826 0.00 0.00 0.00 0.98
624 634 2.772515 GGCAGGAGTAGTTGAGGGTATT 59.227 50.000 0.00 0.00 0.00 1.89
625 635 2.399580 GGCAGGAGTAGTTGAGGGTAT 58.600 52.381 0.00 0.00 0.00 2.73
626 636 1.621622 GGGCAGGAGTAGTTGAGGGTA 60.622 57.143 0.00 0.00 0.00 3.69
627 637 0.910088 GGGCAGGAGTAGTTGAGGGT 60.910 60.000 0.00 0.00 0.00 4.34
628 638 0.909610 TGGGCAGGAGTAGTTGAGGG 60.910 60.000 0.00 0.00 0.00 4.30
629 639 0.984230 TTGGGCAGGAGTAGTTGAGG 59.016 55.000 0.00 0.00 0.00 3.86
630 640 2.814336 GTTTTGGGCAGGAGTAGTTGAG 59.186 50.000 0.00 0.00 0.00 3.02
631 641 2.488347 GGTTTTGGGCAGGAGTAGTTGA 60.488 50.000 0.00 0.00 0.00 3.18
632 642 1.886542 GGTTTTGGGCAGGAGTAGTTG 59.113 52.381 0.00 0.00 0.00 3.16
633 643 1.497286 TGGTTTTGGGCAGGAGTAGTT 59.503 47.619 0.00 0.00 0.00 2.24
634 644 1.145571 TGGTTTTGGGCAGGAGTAGT 58.854 50.000 0.00 0.00 0.00 2.73
635 645 2.286365 TTGGTTTTGGGCAGGAGTAG 57.714 50.000 0.00 0.00 0.00 2.57
636 646 2.109128 TCATTGGTTTTGGGCAGGAGTA 59.891 45.455 0.00 0.00 0.00 2.59
637 647 1.133199 TCATTGGTTTTGGGCAGGAGT 60.133 47.619 0.00 0.00 0.00 3.85
680 690 0.468029 CACTGGTTTTGGGCAGGAGT 60.468 55.000 0.00 0.00 0.00 3.85
684 694 1.067516 CAGTTCACTGGTTTTGGGCAG 59.932 52.381 0.00 0.00 40.20 4.85
687 697 2.374184 TGTCAGTTCACTGGTTTTGGG 58.626 47.619 7.11 0.00 43.91 4.12
790 800 2.359967 CGAGAGGGAGGGGGTGAAC 61.360 68.421 0.00 0.00 0.00 3.18
792 802 2.299727 GATCGAGAGGGAGGGGGTGA 62.300 65.000 0.00 0.00 0.00 4.02
793 803 1.834822 GATCGAGAGGGAGGGGGTG 60.835 68.421 0.00 0.00 0.00 4.61
794 804 2.014033 GAGATCGAGAGGGAGGGGGT 62.014 65.000 0.00 0.00 0.00 4.95
953 963 2.032178 GCGGAAAGGGATCAAATCGAAG 59.968 50.000 0.00 0.00 0.00 3.79
1193 1203 8.527810 ACGGTTGGACACATAAATCATTTATTT 58.472 29.630 0.00 0.00 40.87 1.40
1194 1204 8.062065 ACGGTTGGACACATAAATCATTTATT 57.938 30.769 0.00 0.00 33.73 1.40
1195 1205 7.556275 AGACGGTTGGACACATAAATCATTTAT 59.444 33.333 0.00 0.00 36.31 1.40
1196 1206 6.882140 AGACGGTTGGACACATAAATCATTTA 59.118 34.615 0.00 0.00 0.00 1.40
1197 1207 5.710099 AGACGGTTGGACACATAAATCATTT 59.290 36.000 0.00 0.00 0.00 2.32
1232 1242 3.131478 GCCCCGATTGGAACCACG 61.131 66.667 0.00 0.00 37.49 4.94
1251 1261 1.863454 GATCCACTGATACTGCGCAAG 59.137 52.381 13.05 8.20 43.44 4.01
1362 1372 2.698797 CACCCCATACTACGATCCAGTT 59.301 50.000 0.00 0.00 0.00 3.16
1365 1375 1.062734 ACCACCCCATACTACGATCCA 60.063 52.381 0.00 0.00 0.00 3.41
1474 1485 4.034048 CGGTGGCTATACATTGAACACTTC 59.966 45.833 0.00 0.00 0.00 3.01
1513 1524 3.812053 AGAACTATGCAATCGCTCAATCC 59.188 43.478 0.00 0.00 39.64 3.01
1572 1591 6.541641 GCACATACAAGAGATCTCCAAGATTT 59.458 38.462 19.30 2.97 34.53 2.17
1576 1595 4.125703 GGCACATACAAGAGATCTCCAAG 58.874 47.826 19.30 11.54 0.00 3.61
1648 1672 2.084546 AGCTAACCGGAAATTGCTGAC 58.915 47.619 9.46 0.00 0.00 3.51
1660 1684 1.021968 GCATAAACCCCAGCTAACCG 58.978 55.000 0.00 0.00 0.00 4.44
1691 1722 2.510768 AAGAACCGTCTCACAGTCAC 57.489 50.000 0.00 0.00 30.70 3.67
1702 1733 3.439129 GCCTAGCAAAACATAAGAACCGT 59.561 43.478 0.00 0.00 0.00 4.83
1707 1738 3.265737 TCCCAGCCTAGCAAAACATAAGA 59.734 43.478 0.00 0.00 0.00 2.10
1714 1745 2.683742 GCATAGTCCCAGCCTAGCAAAA 60.684 50.000 0.00 0.00 0.00 2.44
1725 1756 5.172687 TGTGAACAATTAGCATAGTCCCA 57.827 39.130 0.00 0.00 0.00 4.37
1786 1817 0.677288 ACAACACGCACACCTAGCTA 59.323 50.000 0.00 0.00 0.00 3.32
1805 1836 0.178932 AGGAGTAGGTGACACTGCCA 60.179 55.000 5.39 0.00 35.15 4.92
1807 1838 2.826725 AGTTAGGAGTAGGTGACACTGC 59.173 50.000 5.39 0.00 34.82 4.40
1868 3304 3.947196 TGCATCTCCATCCACATACAAAC 59.053 43.478 0.00 0.00 0.00 2.93
1994 3430 1.053424 TCCCTCACACAAGTGGGTAC 58.947 55.000 1.95 0.00 45.07 3.34
1995 3431 1.809133 TTCCCTCACACAAGTGGGTA 58.191 50.000 1.95 0.00 45.07 3.69
1996 3432 0.923358 TTTCCCTCACACAAGTGGGT 59.077 50.000 1.95 0.00 45.07 4.51
1997 3433 2.292828 ATTTCCCTCACACAAGTGGG 57.707 50.000 5.08 0.00 46.14 4.61
1998 3434 4.335416 ACATATTTCCCTCACACAAGTGG 58.665 43.478 5.08 0.00 45.91 4.00
2000 3436 5.221925 ACAGACATATTTCCCTCACACAAGT 60.222 40.000 0.00 0.00 0.00 3.16
2001 3437 5.248640 ACAGACATATTTCCCTCACACAAG 58.751 41.667 0.00 0.00 0.00 3.16
2002 3438 5.241403 ACAGACATATTTCCCTCACACAA 57.759 39.130 0.00 0.00 0.00 3.33
2070 3506 8.623903 GTGATCAAGCATAAGGATGACATAAAA 58.376 33.333 0.00 0.00 34.73 1.52
2072 3508 6.712095 GGTGATCAAGCATAAGGATGACATAA 59.288 38.462 0.00 0.00 34.73 1.90
2077 3513 4.164796 ACAGGTGATCAAGCATAAGGATGA 59.835 41.667 0.00 0.00 34.73 2.92
2081 3517 2.357009 GCACAGGTGATCAAGCATAAGG 59.643 50.000 0.00 0.00 0.00 2.69
2089 3525 1.610038 CAAAGCTGCACAGGTGATCAA 59.390 47.619 2.65 0.00 39.39 2.57
2151 3588 4.162888 TGCTACATCTGTGATGTCTCCATT 59.837 41.667 15.30 0.00 33.76 3.16
2297 3734 3.754323 ACATGCAGAAAAATGGCAAATGG 59.246 39.130 0.00 0.00 41.43 3.16
2397 3834 9.363763 CTATACATGCAGAAATATCCTACACTG 57.636 37.037 0.00 0.00 0.00 3.66
2414 3851 3.313526 CAGTCAAACCTGCCTATACATGC 59.686 47.826 0.00 0.00 0.00 4.06
2462 3899 4.881273 ACATACACAAGTCAAGAAGCAACA 59.119 37.500 0.00 0.00 0.00 3.33
2543 3980 4.415881 ACACATAACCAGAATGCGGATA 57.584 40.909 0.00 0.00 31.97 2.59
2549 3986 6.292274 GCAACAAACAACACATAACCAGAATG 60.292 38.462 0.00 0.00 0.00 2.67
2568 4008 7.171508 TCAAAATGTAAACAACAACAGCAACAA 59.828 29.630 0.00 0.00 42.70 2.83
2569 4009 6.646653 TCAAAATGTAAACAACAACAGCAACA 59.353 30.769 0.00 0.00 42.70 3.33
2570 4010 7.054855 TCAAAATGTAAACAACAACAGCAAC 57.945 32.000 0.00 0.00 42.70 4.17
2571 4011 6.312426 CCTCAAAATGTAAACAACAACAGCAA 59.688 34.615 0.00 0.00 42.70 3.91
2574 4014 9.180678 GATACCTCAAAATGTAAACAACAACAG 57.819 33.333 0.00 0.00 42.70 3.16
2635 4075 9.911788 AGTGAAGTTCATAATATGTCCAAGAAT 57.088 29.630 9.18 0.00 0.00 2.40
2704 4144 5.665459 TGGTTCAACAAAACAAGGTTATGG 58.335 37.500 0.00 0.00 29.42 2.74
2800 4240 4.648970 GCTGGTTAAGACATCGTTAAAGC 58.351 43.478 0.00 0.00 0.00 3.51
2907 4356 8.020861 CCACAATGTCAAATAAAAATCTGTGG 57.979 34.615 0.00 0.00 42.80 4.17
3075 4524 0.534203 GAAGCCCGGTTCTCAACACA 60.534 55.000 0.00 0.00 0.00 3.72
3147 4598 1.086067 CAGCCATGACCACTACTGCG 61.086 60.000 0.00 0.00 0.00 5.18
3214 4665 8.670135 CACGTAAATATACAAAATGGAGAACCA 58.330 33.333 0.00 0.00 40.01 3.67
3227 4678 7.334671 TGAAGATGGCAAACACGTAAATATACA 59.665 33.333 0.00 0.00 32.02 2.29
3246 4697 2.299582 TGTTGCACCCCATTTGAAGATG 59.700 45.455 0.00 0.00 0.00 2.90
3259 4710 6.512415 GCTCATGAAAGATATAGTGTTGCACC 60.512 42.308 0.00 0.00 34.49 5.01
3304 4755 2.767960 TCCTTGCACTGATCAGCATAGA 59.232 45.455 22.83 12.68 40.94 1.98
3420 4871 5.827797 TGGTAGACTGAAGAAAACAGCAAAT 59.172 36.000 0.00 0.00 38.74 2.32
3421 4872 5.189928 TGGTAGACTGAAGAAAACAGCAAA 58.810 37.500 0.00 0.00 38.74 3.68
3477 4928 1.165907 TCCAAAGCTGCTTGACACCG 61.166 55.000 16.73 0.94 0.00 4.94
3690 5141 9.877137 AAACTTTTCAGAAACAAAATTGTGAAC 57.123 25.926 1.62 0.00 40.83 3.18
3875 5327 8.081633 CCAATAAGTTTACTTTCATCTGCAACA 58.918 33.333 0.00 0.00 37.40 3.33
3892 5344 9.547279 ACCAAAGAAAAGGATATCCAATAAGTT 57.453 29.630 23.81 5.21 38.89 2.66
3905 5357 3.570912 ACGAGGAACCAAAGAAAAGGA 57.429 42.857 0.00 0.00 0.00 3.36
3951 5584 3.670627 CGGCTTTCAACCTGCATTACTTC 60.671 47.826 0.00 0.00 0.00 3.01
3957 5590 2.964978 GCGGCTTTCAACCTGCAT 59.035 55.556 0.00 0.00 0.00 3.96
3960 5593 1.573829 TTAGCGCGGCTTTCAACCTG 61.574 55.000 8.83 0.00 40.44 4.00
3973 5606 1.359848 ACTGTGCAGTATGTTAGCGC 58.640 50.000 0.00 0.00 40.43 5.92
4051 5684 4.724279 TTAGGCAATCTAATTCTCCCCC 57.276 45.455 0.00 0.00 33.34 5.40
4084 5717 6.176183 ACCTTCTTTCAGGTCATGTTATGAG 58.824 40.000 0.00 0.00 44.63 2.90
4237 5881 1.743252 CTTCGCCAGCAAGGAGGAC 60.743 63.158 0.00 0.00 41.22 3.85
4333 5983 2.548067 GGAGACGCTTCAGAACAAGGAA 60.548 50.000 0.00 0.00 0.00 3.36
4453 6119 3.213264 GCAAGGACCCATGCCATG 58.787 61.111 8.37 0.00 34.96 3.66
4457 6123 1.076485 ATGAGGCAAGGACCCATGC 60.076 57.895 10.68 10.68 39.58 4.06
4458 6124 0.816825 CGATGAGGCAAGGACCCATG 60.817 60.000 0.00 0.00 0.00 3.66
4599 6267 1.079612 GCATGCAACTGAAAGGGCC 60.080 57.895 14.21 0.00 39.30 5.80


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

AutoCloner maintained by Alex Coulton.