Multiple sequence alignment - TraesCS5A01G191700

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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 TraesCS5A01G191700 chr5A 100.000 2621 0 0 1 2621 395840669 395838049 0.000000e+00 4841.0
1 TraesCS5A01G191700 chr5A 87.849 609 32 19 1015 1614 395848084 395847509 0.000000e+00 676.0
2 TraesCS5A01G191700 chr5A 83.784 222 17 9 1661 1876 395847519 395847311 2.660000e-45 193.0
3 TraesCS5A01G191700 chr5A 86.928 153 18 2 2387 2537 395846663 395846511 1.250000e-38 171.0
4 TraesCS5A01G191700 chr5D 85.914 1647 107 53 711 2291 302014700 302016287 0.000000e+00 1640.0
5 TraesCS5A01G191700 chr5D 87.849 609 47 14 1015 1614 302003913 302004503 0.000000e+00 689.0
6 TraesCS5A01G191700 chr5D 97.414 232 5 1 2391 2621 302016333 302016564 6.800000e-106 394.0
7 TraesCS5A01G191700 chr5D 88.028 142 15 1 2387 2528 302011689 302011828 1.610000e-37 167.0
8 TraesCS5A01G191700 chr5D 83.784 148 14 6 483 628 302014194 302014333 5.890000e-27 132.0
9 TraesCS5A01G191700 chr5B 84.642 1465 79 50 711 2082 345047564 345048975 0.000000e+00 1325.0
10 TraesCS5A01G191700 chr5B 87.908 612 38 16 1015 1614 344951042 344951629 0.000000e+00 688.0
11 TraesCS5A01G191700 chr5B 90.814 479 38 4 2147 2621 345049109 345049585 1.020000e-178 636.0
12 TraesCS5A01G191700 chr5B 82.517 143 23 2 2387 2528 344952492 344952633 9.850000e-25 124.0
13 TraesCS5A01G191700 chr5B 84.444 90 10 4 599 684 345047210 345047299 4.650000e-13 86.1
14 TraesCS5A01G191700 chr5B 93.103 58 3 1 1839 1895 344951764 344951821 1.670000e-12 84.2
15 TraesCS5A01G191700 chr6A 96.061 457 12 3 1 452 119755427 119754972 0.000000e+00 739.0
16 TraesCS5A01G191700 chr6A 96.061 457 12 3 1 452 617993445 617993900 0.000000e+00 739.0
17 TraesCS5A01G191700 chr3B 96.061 457 12 3 1 452 831934 832389 0.000000e+00 739.0
18 TraesCS5A01G191700 chr3B 96.061 457 12 3 1 452 642002110 642001655 0.000000e+00 739.0
19 TraesCS5A01G191700 chr3B 95.842 457 13 4 1 452 832923 833378 0.000000e+00 734.0
20 TraesCS5A01G191700 chr3B 95.833 456 14 3 1 452 832429 832883 0.000000e+00 732.0
21 TraesCS5A01G191700 chr3B 95.842 457 12 4 1 452 833418 833872 0.000000e+00 732.0
22 TraesCS5A01G191700 chr7A 95.833 456 14 3 1 452 46063709 46064163 0.000000e+00 732.0
23 TraesCS5A01G191700 chr2A 95.455 462 15 4 1 458 83004790 83005249 0.000000e+00 732.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G191700 chr5A 395838049 395840669 2620 True 4841.000000 4841 100.000000 1 2621 1 chr5A.!!$R1 2620
1 TraesCS5A01G191700 chr5A 395846511 395848084 1573 True 346.666667 676 86.187000 1015 2537 3 chr5A.!!$R2 1522
2 TraesCS5A01G191700 chr5D 302003913 302004503 590 False 689.000000 689 87.849000 1015 1614 1 chr5D.!!$F1 599
3 TraesCS5A01G191700 chr5D 302011689 302016564 4875 False 583.250000 1640 88.785000 483 2621 4 chr5D.!!$F2 2138
4 TraesCS5A01G191700 chr5B 345047210 345049585 2375 False 682.366667 1325 86.633333 599 2621 3 chr5B.!!$F2 2022
5 TraesCS5A01G191700 chr5B 344951042 344952633 1591 False 298.733333 688 87.842667 1015 2528 3 chr5B.!!$F1 1513
6 TraesCS5A01G191700 chr3B 831934 833872 1938 False 734.250000 739 95.894500 1 452 4 chr3B.!!$F1 451

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
588 3056 0.028902 ACTTCGTTGACCGCTTTTGC 59.971 50.0 0.0 0.0 43.23 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2123 5564 0.10741 ACAAACTCGTGTTGCTCCCA 60.107 50.0 3.24 0.0 36.39 4.37 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
244 246 6.249035 TGGAAAGTATCGGTTGATTTGAAC 57.751 37.500 0.00 0.00 35.99 3.18
397 403 2.649531 AAACCGGATGAAAGTGGTGA 57.350 45.000 9.46 0.00 34.26 4.02
436 442 0.969894 AGCGAGACTACCAACTGCTT 59.030 50.000 0.00 0.00 0.00 3.91
443 449 5.393135 CGAGACTACCAACTGCTTCATTAGA 60.393 44.000 0.00 0.00 0.00 2.10
525 2992 2.350388 CGGCATATATCAAACCGGCAAC 60.350 50.000 0.00 0.00 40.18 4.17
529 2997 4.319766 GCATATATCAAACCGGCAACAGAG 60.320 45.833 0.00 0.00 0.00 3.35
582 3050 0.382636 CGAACAACTTCGTTGACCGC 60.383 55.000 13.11 0.05 45.28 5.68
583 3051 0.935196 GAACAACTTCGTTGACCGCT 59.065 50.000 13.11 0.00 45.28 5.52
584 3052 1.329599 GAACAACTTCGTTGACCGCTT 59.670 47.619 13.11 0.00 45.28 4.68
588 3056 0.028902 ACTTCGTTGACCGCTTTTGC 59.971 50.000 0.00 0.00 43.23 3.68
601 3069 1.070309 GCTTTTGCGTGACTGACTGAG 60.070 52.381 0.00 0.00 34.86 3.35
603 3071 3.381045 CTTTTGCGTGACTGACTGAGTA 58.619 45.455 0.00 0.00 33.83 2.59
606 3074 2.946564 TGCGTGACTGACTGAGTAATG 58.053 47.619 0.00 0.00 33.83 1.90
628 3096 1.875963 GAAGGTTCCGTACGTCCGA 59.124 57.895 15.21 1.15 0.00 4.55
629 3097 0.179179 GAAGGTTCCGTACGTCCGAG 60.179 60.000 15.21 0.00 0.00 4.63
630 3098 0.890996 AAGGTTCCGTACGTCCGAGT 60.891 55.000 15.21 2.74 0.00 4.18
631 3099 0.036388 AGGTTCCGTACGTCCGAGTA 60.036 55.000 15.21 0.00 0.00 2.59
632 3100 0.375106 GGTTCCGTACGTCCGAGTAG 59.625 60.000 15.21 0.00 0.00 2.57
633 3101 0.247854 GTTCCGTACGTCCGAGTAGC 60.248 60.000 15.21 0.00 0.00 3.58
634 3102 1.369091 TTCCGTACGTCCGAGTAGCC 61.369 60.000 15.21 0.00 0.00 3.93
635 3103 2.108514 CCGTACGTCCGAGTAGCCA 61.109 63.158 15.21 0.00 0.00 4.75
636 3104 1.351012 CGTACGTCCGAGTAGCCAG 59.649 63.158 7.22 0.00 0.00 4.85
637 3105 1.063811 GTACGTCCGAGTAGCCAGC 59.936 63.158 0.00 0.00 0.00 4.85
638 3106 2.117156 TACGTCCGAGTAGCCAGCC 61.117 63.158 0.00 0.00 0.00 4.85
639 3107 2.547640 TACGTCCGAGTAGCCAGCCT 62.548 60.000 0.00 0.00 0.00 4.58
640 3108 2.496817 GTCCGAGTAGCCAGCCTG 59.503 66.667 0.00 0.00 0.00 4.85
641 3109 2.037367 TCCGAGTAGCCAGCCTGT 59.963 61.111 0.00 0.00 0.00 4.00
642 3110 2.185350 CCGAGTAGCCAGCCTGTG 59.815 66.667 0.00 0.00 0.00 3.66
643 3111 2.650116 CCGAGTAGCCAGCCTGTGT 61.650 63.158 0.00 0.00 0.00 3.72
684 3173 2.294791 TGGTTTGCCAATTCCAAGTACG 59.705 45.455 0.37 0.00 42.83 3.67
685 3174 2.295070 GGTTTGCCAATTCCAAGTACGT 59.705 45.455 0.00 0.00 34.09 3.57
686 3175 3.502979 GGTTTGCCAATTCCAAGTACGTA 59.497 43.478 0.00 0.00 34.09 3.57
687 3176 4.469552 GTTTGCCAATTCCAAGTACGTAC 58.530 43.478 18.10 18.10 0.00 3.67
689 3178 3.741249 TGCCAATTCCAAGTACGTACAA 58.259 40.909 26.55 12.93 0.00 2.41
691 3180 3.425758 GCCAATTCCAAGTACGTACAAGC 60.426 47.826 26.55 11.52 0.00 4.01
692 3181 3.749088 CCAATTCCAAGTACGTACAAGCA 59.251 43.478 26.55 6.48 0.00 3.91
693 3182 4.142902 CCAATTCCAAGTACGTACAAGCAG 60.143 45.833 26.55 10.93 0.00 4.24
696 3185 2.230508 TCCAAGTACGTACAAGCAGGAG 59.769 50.000 26.55 7.21 0.00 3.69
697 3186 1.993370 CAAGTACGTACAAGCAGGAGC 59.007 52.381 26.55 0.00 42.56 4.70
723 3480 2.994186 AATGAAATGGAAGGCATGCC 57.006 45.000 30.12 30.12 0.00 4.40
748 3505 3.053849 GCCTCTCCGTCTGACCGTC 62.054 68.421 1.55 0.00 0.00 4.79
831 3588 0.251608 AATCCCCCTTTTCCACCGTG 60.252 55.000 0.00 0.00 0.00 4.94
860 3617 0.883153 TATTCCCGCGCGCTCTATAA 59.117 50.000 30.48 15.74 0.00 0.98
870 3627 2.852413 CGCGCTCTATAAATACCATCGG 59.148 50.000 5.56 0.00 0.00 4.18
871 3628 2.603560 GCGCTCTATAAATACCATCGGC 59.396 50.000 0.00 0.00 0.00 5.54
872 3629 3.187700 CGCTCTATAAATACCATCGGCC 58.812 50.000 0.00 0.00 0.00 6.13
873 3630 3.187700 GCTCTATAAATACCATCGGCCG 58.812 50.000 22.12 22.12 0.00 6.13
879 3636 2.050836 AATACCATCGGCCGCCATCA 62.051 55.000 23.51 2.08 0.00 3.07
893 3650 1.642037 CCATCAGCGCCACTCACAAG 61.642 60.000 2.29 0.00 0.00 3.16
894 3651 0.952497 CATCAGCGCCACTCACAAGT 60.952 55.000 2.29 0.00 35.60 3.16
895 3652 0.671781 ATCAGCGCCACTCACAAGTC 60.672 55.000 2.29 0.00 31.71 3.01
896 3653 1.595109 CAGCGCCACTCACAAGTCA 60.595 57.895 2.29 0.00 31.71 3.41
899 3656 1.436195 GCGCCACTCACAAGTCACAA 61.436 55.000 0.00 0.00 31.71 3.33
900 3657 0.304705 CGCCACTCACAAGTCACAAC 59.695 55.000 0.00 0.00 31.71 3.32
901 3658 1.378531 GCCACTCACAAGTCACAACA 58.621 50.000 0.00 0.00 31.71 3.33
902 3659 1.331756 GCCACTCACAAGTCACAACAG 59.668 52.381 0.00 0.00 31.71 3.16
903 3660 1.942657 CCACTCACAAGTCACAACAGG 59.057 52.381 0.00 0.00 31.71 4.00
904 3661 1.331756 CACTCACAAGTCACAACAGGC 59.668 52.381 0.00 0.00 31.71 4.85
905 3662 1.065491 ACTCACAAGTCACAACAGGCA 60.065 47.619 0.00 0.00 0.00 4.75
906 3663 2.016318 CTCACAAGTCACAACAGGCAA 58.984 47.619 0.00 0.00 0.00 4.52
907 3664 1.742831 TCACAAGTCACAACAGGCAAC 59.257 47.619 0.00 0.00 0.00 4.17
908 3665 1.472082 CACAAGTCACAACAGGCAACA 59.528 47.619 0.00 0.00 41.41 3.33
918 3675 0.381801 ACAGGCAACAACAAAGCTCG 59.618 50.000 0.00 0.00 41.41 5.03
923 3680 2.787129 GGCAACAACAAAGCTCGTTTAC 59.213 45.455 0.00 0.00 0.00 2.01
966 3723 2.441901 AGCCCGAGGAGAGAGCAG 60.442 66.667 0.00 0.00 0.00 4.24
972 3729 4.127040 AGGAGAGAGCAGCGCACG 62.127 66.667 11.47 0.01 0.00 5.34
1236 4029 1.080705 GTCCTCGTCCTTCCACACG 60.081 63.158 0.00 0.00 37.36 4.49
1638 4453 3.785189 ATACCGTCGCATCGCACCC 62.785 63.158 0.00 0.00 0.00 4.61
1662 4478 2.550208 GGTTGTTGGTCTGATCGTTCCT 60.550 50.000 0.00 0.00 0.00 3.36
1665 4481 0.530744 TTGGTCTGATCGTTCCTCCG 59.469 55.000 0.00 0.00 0.00 4.63
1666 4482 1.227002 GGTCTGATCGTTCCTCCGC 60.227 63.158 0.00 0.00 0.00 5.54
1706 4537 3.996363 TGATCGTTGAATGTTCAGACCAG 59.004 43.478 0.00 0.00 38.61 4.00
1707 4538 2.143122 TCGTTGAATGTTCAGACCAGC 58.857 47.619 0.00 0.00 38.61 4.85
1708 4539 2.146342 CGTTGAATGTTCAGACCAGCT 58.854 47.619 0.00 0.00 38.61 4.24
1709 4540 2.096069 CGTTGAATGTTCAGACCAGCTG 60.096 50.000 6.78 6.78 46.31 4.24
1710 4541 1.527034 TGAATGTTCAGACCAGCTGC 58.473 50.000 8.66 0.00 44.52 5.25
1711 4542 0.445436 GAATGTTCAGACCAGCTGCG 59.555 55.000 8.66 4.27 44.52 5.18
1712 4543 0.035317 AATGTTCAGACCAGCTGCGA 59.965 50.000 8.66 0.00 44.52 5.10
1713 4544 0.390866 ATGTTCAGACCAGCTGCGAG 60.391 55.000 8.66 0.00 44.52 5.03
1895 4807 0.031585 GGCTTTCGGTTGTGGGTTTC 59.968 55.000 0.00 0.00 0.00 2.78
1896 4808 0.031585 GCTTTCGGTTGTGGGTTTCC 59.968 55.000 0.00 0.00 0.00 3.13
1897 4809 1.687563 CTTTCGGTTGTGGGTTTCCT 58.312 50.000 0.00 0.00 0.00 3.36
1898 4810 2.028876 CTTTCGGTTGTGGGTTTCCTT 58.971 47.619 0.00 0.00 0.00 3.36
1899 4811 1.394618 TTCGGTTGTGGGTTTCCTTG 58.605 50.000 0.00 0.00 0.00 3.61
2015 4968 8.810652 TTATTTGTTCCATGTAACTTGAAAGC 57.189 30.769 2.65 0.00 0.00 3.51
2024 4977 4.304110 TGTAACTTGAAAGCCTACAGTCG 58.696 43.478 2.89 0.00 0.00 4.18
2088 5529 3.476295 AATGCAGACAACATAAGTGCG 57.524 42.857 0.00 0.00 36.92 5.34
2092 5533 4.000325 TGCAGACAACATAAGTGCGTTAT 59.000 39.130 0.00 0.00 36.92 1.89
2096 5537 6.464834 GCAGACAACATAAGTGCGTTATAAAC 59.535 38.462 0.00 0.00 29.54 2.01
2126 5567 9.408648 AGATGAAAATACTAGTACCAAATTGGG 57.591 33.333 17.27 0.00 43.37 4.12
2129 5570 7.338449 TGAAAATACTAGTACCAAATTGGGAGC 59.662 37.037 17.27 5.85 43.37 4.70
2131 5572 4.650972 ACTAGTACCAAATTGGGAGCAA 57.349 40.909 17.27 0.00 43.37 3.91
2136 5577 0.958091 CCAAATTGGGAGCAACACGA 59.042 50.000 3.60 0.00 32.67 4.35
2137 5578 1.068333 CCAAATTGGGAGCAACACGAG 60.068 52.381 3.60 0.00 32.67 4.18
2138 5579 1.608590 CAAATTGGGAGCAACACGAGT 59.391 47.619 0.00 0.00 0.00 4.18
2139 5580 1.981256 AATTGGGAGCAACACGAGTT 58.019 45.000 0.00 0.00 38.88 3.01
2140 5581 1.981256 ATTGGGAGCAACACGAGTTT 58.019 45.000 0.00 0.00 35.28 2.66
2141 5582 1.021202 TTGGGAGCAACACGAGTTTG 58.979 50.000 0.00 0.00 35.28 2.93
2142 5583 0.107410 TGGGAGCAACACGAGTTTGT 60.107 50.000 0.00 0.00 35.28 2.83
2143 5584 1.021968 GGGAGCAACACGAGTTTGTT 58.978 50.000 0.00 0.00 40.46 2.83
2144 5585 1.002792 GGGAGCAACACGAGTTTGTTC 60.003 52.381 0.00 0.14 37.62 3.18
2145 5586 1.668751 GGAGCAACACGAGTTTGTTCA 59.331 47.619 0.00 0.00 37.62 3.18
2152 5593 4.336532 ACACGAGTTTGTTCAACTTGAC 57.663 40.909 8.65 0.00 46.53 3.18
2160 5601 6.267817 AGTTTGTTCAACTTGACATGTGATG 58.732 36.000 1.15 0.00 43.89 3.07
2293 6327 5.560966 AATTACTGCCAGATAAAACCACG 57.439 39.130 0.00 0.00 0.00 4.94
2297 6331 3.074412 CTGCCAGATAAAACCACGACTT 58.926 45.455 0.00 0.00 0.00 3.01
2305 6339 7.962918 CCAGATAAAACCACGACTTAAAGAATG 59.037 37.037 0.00 0.00 0.00 2.67
2306 6340 8.717821 CAGATAAAACCACGACTTAAAGAATGA 58.282 33.333 0.00 0.00 0.00 2.57
2308 6342 9.704098 GATAAAACCACGACTTAAAGAATGATC 57.296 33.333 0.00 0.00 0.00 2.92
2313 6347 5.220662 CCACGACTTAAAGAATGATCGCATT 60.221 40.000 0.00 0.00 47.00 3.56
2331 6365 4.470462 GCATTATGATTGATCTCAACCGC 58.530 43.478 0.00 0.00 38.86 5.68
2528 6642 3.965379 TGTGAATCTAAACCCGCAGTA 57.035 42.857 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
226 228 6.877611 AACTTGTTCAAATCAACCGATACT 57.122 33.333 0.00 0.00 0.00 2.12
410 416 1.629043 TGGTAGTCTCGCTTTCAGGT 58.371 50.000 0.00 0.00 0.00 4.00
415 421 1.344763 AGCAGTTGGTAGTCTCGCTTT 59.655 47.619 0.00 0.00 0.00 3.51
470 476 9.227777 ACGCTTCCTGTTTTTCTATTACTTTAT 57.772 29.630 0.00 0.00 0.00 1.40
471 477 8.611654 ACGCTTCCTGTTTTTCTATTACTTTA 57.388 30.769 0.00 0.00 0.00 1.85
472 478 7.308408 GGACGCTTCCTGTTTTTCTATTACTTT 60.308 37.037 1.07 0.00 39.13 2.66
473 479 6.148976 GGACGCTTCCTGTTTTTCTATTACTT 59.851 38.462 1.07 0.00 39.13 2.24
474 480 5.642491 GGACGCTTCCTGTTTTTCTATTACT 59.358 40.000 1.07 0.00 39.13 2.24
475 481 5.445540 CGGACGCTTCCTGTTTTTCTATTAC 60.446 44.000 7.75 0.00 40.23 1.89
479 485 2.036217 TCGGACGCTTCCTGTTTTTCTA 59.964 45.455 7.75 0.00 40.23 2.10
480 486 1.202604 TCGGACGCTTCCTGTTTTTCT 60.203 47.619 7.75 0.00 40.23 2.52
481 487 1.070108 GTCGGACGCTTCCTGTTTTTC 60.070 52.381 7.75 0.00 40.23 2.29
484 490 0.600255 CTGTCGGACGCTTCCTGTTT 60.600 55.000 7.75 0.00 40.23 2.83
485 491 1.006102 CTGTCGGACGCTTCCTGTT 60.006 57.895 7.75 0.00 40.23 3.16
486 492 2.651361 CTGTCGGACGCTTCCTGT 59.349 61.111 7.75 0.00 40.23 4.00
487 493 2.811317 GCTGTCGGACGCTTCCTG 60.811 66.667 7.75 1.42 40.23 3.86
488 494 4.421479 CGCTGTCGGACGCTTCCT 62.421 66.667 17.92 0.00 40.23 3.36
505 2972 2.621055 TGTTGCCGGTTTGATATATGCC 59.379 45.455 1.90 0.00 0.00 4.40
525 2992 1.674764 ATCAGCTCACGCCTCCTCTG 61.675 60.000 0.00 0.00 36.60 3.35
529 2997 2.279120 CGATCAGCTCACGCCTCC 60.279 66.667 0.00 0.00 36.60 4.30
540 3008 1.067582 GGCCGAGGTTACCGATCAG 59.932 63.158 0.00 0.00 0.00 2.90
541 3009 3.213264 GGCCGAGGTTACCGATCA 58.787 61.111 0.00 0.00 0.00 2.92
582 3050 2.205074 ACTCAGTCAGTCACGCAAAAG 58.795 47.619 0.00 0.00 0.00 2.27
583 3051 2.309528 ACTCAGTCAGTCACGCAAAA 57.690 45.000 0.00 0.00 0.00 2.44
584 3052 3.446310 TTACTCAGTCAGTCACGCAAA 57.554 42.857 0.00 0.00 36.43 3.68
588 3056 3.604198 CGTTCATTACTCAGTCAGTCACG 59.396 47.826 0.00 0.00 36.43 4.35
590 3058 5.447624 TTCGTTCATTACTCAGTCAGTCA 57.552 39.130 0.00 0.00 36.43 3.41
591 3059 4.859798 CCTTCGTTCATTACTCAGTCAGTC 59.140 45.833 0.00 0.00 36.43 3.51
592 3060 4.281182 ACCTTCGTTCATTACTCAGTCAGT 59.719 41.667 0.00 0.00 39.41 3.41
593 3061 4.810790 ACCTTCGTTCATTACTCAGTCAG 58.189 43.478 0.00 0.00 0.00 3.51
594 3062 4.866508 ACCTTCGTTCATTACTCAGTCA 57.133 40.909 0.00 0.00 0.00 3.41
595 3063 5.765072 GAACCTTCGTTCATTACTCAGTC 57.235 43.478 0.00 0.00 46.49 3.51
606 3074 1.331241 GACGTACGGAACCTTCGTTC 58.669 55.000 21.06 0.00 46.52 3.95
628 3096 0.911525 ATCCACACAGGCTGGCTACT 60.912 55.000 20.34 0.00 37.29 2.57
629 3097 0.462759 GATCCACACAGGCTGGCTAC 60.463 60.000 20.34 0.00 37.29 3.58
630 3098 1.626356 GGATCCACACAGGCTGGCTA 61.626 60.000 20.34 0.00 37.29 3.93
631 3099 2.673523 GATCCACACAGGCTGGCT 59.326 61.111 20.34 0.00 37.29 4.75
632 3100 2.439156 GGATCCACACAGGCTGGC 60.439 66.667 20.34 0.00 37.29 4.85
633 3101 1.077930 CTGGATCCACACAGGCTGG 60.078 63.158 20.34 10.34 37.29 4.85
634 3102 1.748122 GCTGGATCCACACAGGCTG 60.748 63.158 11.44 14.16 37.29 4.85
635 3103 1.908340 GAGCTGGATCCACACAGGCT 61.908 60.000 21.79 21.79 37.29 4.58
636 3104 1.451028 GAGCTGGATCCACACAGGC 60.451 63.158 11.44 12.76 37.29 4.85
637 3105 0.177604 GAGAGCTGGATCCACACAGG 59.822 60.000 11.44 1.33 35.30 4.00
638 3106 0.179116 CGAGAGCTGGATCCACACAG 60.179 60.000 11.44 1.77 37.76 3.66
639 3107 0.900182 ACGAGAGCTGGATCCACACA 60.900 55.000 11.44 0.00 0.00 3.72
640 3108 0.179124 GACGAGAGCTGGATCCACAC 60.179 60.000 11.44 6.09 0.00 3.82
641 3109 0.323816 AGACGAGAGCTGGATCCACA 60.324 55.000 11.44 0.00 0.00 4.17
642 3110 0.383949 GAGACGAGAGCTGGATCCAC 59.616 60.000 11.44 8.29 0.00 4.02
643 3111 1.098129 CGAGACGAGAGCTGGATCCA 61.098 60.000 15.27 15.27 0.00 3.41
684 3173 2.010145 TCGAATGCTCCTGCTTGTAC 57.990 50.000 0.00 0.00 40.48 2.90
685 3174 2.760634 TTCGAATGCTCCTGCTTGTA 57.239 45.000 0.00 0.00 40.48 2.41
686 3175 1.896220 TTTCGAATGCTCCTGCTTGT 58.104 45.000 0.00 0.00 40.48 3.16
687 3176 2.421073 TCATTTCGAATGCTCCTGCTTG 59.579 45.455 0.00 0.00 40.48 4.01
689 3178 2.408271 TCATTTCGAATGCTCCTGCT 57.592 45.000 0.00 0.00 40.48 4.24
691 3180 4.096833 TCCATTTCATTTCGAATGCTCCTG 59.903 41.667 0.00 0.00 32.32 3.86
692 3181 4.272489 TCCATTTCATTTCGAATGCTCCT 58.728 39.130 0.00 0.00 32.32 3.69
693 3182 4.637483 TCCATTTCATTTCGAATGCTCC 57.363 40.909 0.00 0.00 32.32 4.70
696 3185 3.553105 GCCTTCCATTTCATTTCGAATGC 59.447 43.478 0.00 0.00 32.32 3.56
697 3186 4.746729 TGCCTTCCATTTCATTTCGAATG 58.253 39.130 0.00 0.00 32.32 2.67
748 3505 3.417275 ATCTCGGCCGCGAACAGAG 62.417 63.158 23.35 11.85 0.00 3.35
816 3573 1.176619 GGTTCACGGTGGAAAAGGGG 61.177 60.000 8.50 0.00 0.00 4.79
843 3600 0.032952 ATTTATAGAGCGCGCGGGAA 59.967 50.000 33.06 15.66 0.00 3.97
860 3617 1.302511 GATGGCGGCCGATGGTATT 60.303 57.895 33.48 4.95 0.00 1.89
873 3630 3.503363 GTGAGTGGCGCTGATGGC 61.503 66.667 4.71 0.00 37.64 4.40
879 3636 1.595382 GTGACTTGTGAGTGGCGCT 60.595 57.895 7.64 0.00 35.88 5.92
889 3646 1.832883 TGTTGCCTGTTGTGACTTGT 58.167 45.000 0.00 0.00 0.00 3.16
893 3650 2.645730 TTGTTGTTGCCTGTTGTGAC 57.354 45.000 0.00 0.00 0.00 3.67
894 3651 2.673610 GCTTTGTTGTTGCCTGTTGTGA 60.674 45.455 0.00 0.00 0.00 3.58
895 3652 1.660104 GCTTTGTTGTTGCCTGTTGTG 59.340 47.619 0.00 0.00 0.00 3.33
896 3653 1.550072 AGCTTTGTTGTTGCCTGTTGT 59.450 42.857 0.00 0.00 0.00 3.32
899 3656 0.381801 CGAGCTTTGTTGTTGCCTGT 59.618 50.000 0.00 0.00 0.00 4.00
900 3657 0.381801 ACGAGCTTTGTTGTTGCCTG 59.618 50.000 0.00 0.00 0.00 4.85
901 3658 1.102978 AACGAGCTTTGTTGTTGCCT 58.897 45.000 4.66 0.00 0.00 4.75
902 3659 1.921243 AAACGAGCTTTGTTGTTGCC 58.079 45.000 6.11 0.00 0.00 4.52
903 3660 2.787129 GGTAAACGAGCTTTGTTGTTGC 59.213 45.455 6.11 0.00 0.00 4.17
904 3661 4.022464 TGGTAAACGAGCTTTGTTGTTG 57.978 40.909 6.11 0.00 0.00 3.33
905 3662 4.578928 AGATGGTAAACGAGCTTTGTTGTT 59.421 37.500 6.11 0.00 0.00 2.83
906 3663 4.134563 AGATGGTAAACGAGCTTTGTTGT 58.865 39.130 6.11 1.13 0.00 3.32
907 3664 4.666655 CGAGATGGTAAACGAGCTTTGTTG 60.667 45.833 6.11 0.00 0.00 3.33
908 3665 3.432252 CGAGATGGTAAACGAGCTTTGTT 59.568 43.478 0.00 0.00 0.00 2.83
918 3675 3.482722 TCGACAGACGAGATGGTAAAC 57.517 47.619 0.00 0.00 46.45 2.01
954 3711 2.202730 GTGCGCTGCTCTCTCCTC 60.203 66.667 9.73 0.00 0.00 3.71
972 3729 0.798771 AGCTCGATCGCGTGTTTCTC 60.799 55.000 11.09 0.00 38.98 2.87
1271 4064 4.760047 CTCGGAAGGTGGTGGCGG 62.760 72.222 0.00 0.00 0.00 6.13
1272 4065 2.725203 TTTCTCGGAAGGTGGTGGCG 62.725 60.000 0.00 0.00 0.00 5.69
1273 4066 1.072505 TTTCTCGGAAGGTGGTGGC 59.927 57.895 0.00 0.00 0.00 5.01
1276 4069 1.344763 CTCTGTTTCTCGGAAGGTGGT 59.655 52.381 0.00 0.00 0.00 4.16
1615 4426 0.161658 GCGATGCGACGGTATCATTG 59.838 55.000 0.00 0.00 35.26 2.82
1638 4453 2.426522 ACGATCAGACCAACAACCATG 58.573 47.619 0.00 0.00 0.00 3.66
1662 4478 3.371097 GAGCCAATCACGGAGCGGA 62.371 63.158 0.00 0.00 0.00 5.54
1695 4511 1.005748 CTCGCAGCTGGTCTGAACA 60.006 57.895 17.12 0.00 45.72 3.18
1706 4537 3.797546 GCCTGAGTTGCTCGCAGC 61.798 66.667 0.00 0.00 41.50 5.25
1707 4538 1.670406 AAGCCTGAGTTGCTCGCAG 60.670 57.895 6.33 6.33 42.27 5.18
1708 4539 1.962822 CAAGCCTGAGTTGCTCGCA 60.963 57.895 0.00 0.00 38.34 5.10
1709 4540 1.669115 TCAAGCCTGAGTTGCTCGC 60.669 57.895 0.00 0.00 38.34 5.03
1710 4541 0.320247 AGTCAAGCCTGAGTTGCTCG 60.320 55.000 0.00 0.00 38.34 5.03
1711 4542 1.889545 AAGTCAAGCCTGAGTTGCTC 58.110 50.000 4.55 0.00 42.51 4.26
1895 4807 3.187022 GTGCAAGCCAATAAAAAGCAAGG 59.813 43.478 0.00 0.00 31.78 3.61
1896 4808 4.060205 AGTGCAAGCCAATAAAAAGCAAG 58.940 39.130 0.00 0.00 31.78 4.01
1897 4809 4.057432 GAGTGCAAGCCAATAAAAAGCAA 58.943 39.130 0.00 0.00 31.78 3.91
1898 4810 3.554752 GGAGTGCAAGCCAATAAAAAGCA 60.555 43.478 0.00 0.00 0.00 3.91
1899 4811 2.995939 GGAGTGCAAGCCAATAAAAAGC 59.004 45.455 0.00 0.00 0.00 3.51
1966 4898 5.695851 AGAATGTGCTTACAACAAAGGAG 57.304 39.130 0.00 0.00 0.00 3.69
1999 4949 5.003804 ACTGTAGGCTTTCAAGTTACATGG 58.996 41.667 0.00 1.69 32.18 3.66
2015 4968 9.537848 GTTTACAACAAATAAATCGACTGTAGG 57.462 33.333 0.00 0.00 0.00 3.18
2041 4994 8.152898 TGATTGATGACTAATGTAGAATCCCAG 58.847 37.037 0.00 0.00 0.00 4.45
2102 5543 9.408648 CTCCCAATTTGGTACTAGTATTTTCAT 57.591 33.333 14.26 0.00 35.17 2.57
2103 5544 7.338449 GCTCCCAATTTGGTACTAGTATTTTCA 59.662 37.037 14.26 0.55 35.17 2.69
2105 5546 7.179269 TGCTCCCAATTTGGTACTAGTATTTT 58.821 34.615 14.26 0.00 35.17 1.82
2109 5550 5.013287 TGTTGCTCCCAATTTGGTACTAGTA 59.987 40.000 14.26 0.00 35.17 1.82
2111 5552 4.156008 GTGTTGCTCCCAATTTGGTACTAG 59.844 45.833 14.26 7.19 35.17 2.57
2112 5553 4.076394 GTGTTGCTCCCAATTTGGTACTA 58.924 43.478 14.26 0.00 35.17 1.82
2114 5555 2.351350 CGTGTTGCTCCCAATTTGGTAC 60.351 50.000 14.26 4.00 35.17 3.34
2115 5556 1.883275 CGTGTTGCTCCCAATTTGGTA 59.117 47.619 14.26 0.00 35.17 3.25
2116 5557 0.673437 CGTGTTGCTCCCAATTTGGT 59.327 50.000 14.26 0.00 35.17 3.67
2117 5558 0.958091 TCGTGTTGCTCCCAATTTGG 59.042 50.000 8.56 8.56 37.25 3.28
2118 5559 1.608590 ACTCGTGTTGCTCCCAATTTG 59.391 47.619 0.00 0.00 32.75 2.32
2119 5560 1.981256 ACTCGTGTTGCTCCCAATTT 58.019 45.000 0.00 0.00 32.75 1.82
2121 5562 1.608590 CAAACTCGTGTTGCTCCCAAT 59.391 47.619 3.24 0.00 36.39 3.16
2123 5564 0.107410 ACAAACTCGTGTTGCTCCCA 60.107 50.000 3.24 0.00 36.39 4.37
2124 5565 1.002792 GAACAAACTCGTGTTGCTCCC 60.003 52.381 3.24 0.00 41.78 4.30
2125 5566 1.668751 TGAACAAACTCGTGTTGCTCC 59.331 47.619 3.24 0.00 41.78 4.70
2126 5567 3.098636 GTTGAACAAACTCGTGTTGCTC 58.901 45.455 3.24 2.28 41.78 4.26
2137 5578 6.264832 TCATCACATGTCAAGTTGAACAAAC 58.735 36.000 7.25 0.00 39.24 2.93
2138 5579 6.448207 TCATCACATGTCAAGTTGAACAAA 57.552 33.333 7.25 0.00 0.00 2.83
2139 5580 6.638096 ATCATCACATGTCAAGTTGAACAA 57.362 33.333 7.25 0.00 0.00 2.83
2140 5581 6.638096 AATCATCACATGTCAAGTTGAACA 57.362 33.333 7.25 8.68 0.00 3.18
2141 5582 7.140705 TGAAATCATCACATGTCAAGTTGAAC 58.859 34.615 7.25 2.99 31.50 3.18
2142 5583 7.274603 TGAAATCATCACATGTCAAGTTGAA 57.725 32.000 7.25 0.00 31.50 2.69
2143 5584 6.880942 TGAAATCATCACATGTCAAGTTGA 57.119 33.333 0.08 0.08 31.50 3.18
2144 5585 7.435784 TGTTTGAAATCATCACATGTCAAGTTG 59.564 33.333 0.00 0.00 37.92 3.16
2145 5586 7.490840 TGTTTGAAATCATCACATGTCAAGTT 58.509 30.769 0.00 0.00 37.92 2.66
2152 5593 8.528917 AGAAACATGTTTGAAATCATCACATG 57.471 30.769 27.85 22.49 44.83 3.21
2213 5845 4.631813 CCTCCATTCTTTTACAGGAAGTCG 59.368 45.833 0.00 0.00 0.00 4.18
2219 5851 5.126061 CCATTCACCTCCATTCTTTTACAGG 59.874 44.000 0.00 0.00 0.00 4.00
2222 5854 6.095021 GGTACCATTCACCTCCATTCTTTTAC 59.905 42.308 7.15 0.00 32.98 2.01
2223 5855 6.184789 GGTACCATTCACCTCCATTCTTTTA 58.815 40.000 7.15 0.00 32.98 1.52
2260 6294 1.202348 GGCAGTAATTTGTCAGCCACC 59.798 52.381 0.00 0.00 41.63 4.61
2305 6339 6.541086 GGTTGAGATCAATCATAATGCGATC 58.459 40.000 0.91 0.00 36.96 3.69
2306 6340 5.121298 CGGTTGAGATCAATCATAATGCGAT 59.879 40.000 6.64 0.00 36.80 4.58
2308 6342 4.705492 CGGTTGAGATCAATCATAATGCG 58.295 43.478 6.64 0.00 36.80 4.73
2313 6347 4.100035 ACTCTGCGGTTGAGATCAATCATA 59.900 41.667 6.64 0.00 36.80 2.15
2528 6642 3.299340 ACACTGTTTCTATTCGACGCT 57.701 42.857 0.00 0.00 0.00 5.07
2531 6645 9.690434 GATGATTTTACACTGTTTCTATTCGAC 57.310 33.333 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.