Multiple sequence alignment - TraesCS3A01G374200

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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 TraesCS3A01G374200 chr3A 100.000 2366 0 0 1 2366 623823793 623821428 0.000000e+00 4370
1 TraesCS3A01G374200 chr3B 91.892 962 32 21 648 1589 641988428 641987493 0.000000e+00 1303
2 TraesCS3A01G374200 chr3B 87.359 799 49 20 1589 2366 641987464 641986697 0.000000e+00 869
3 TraesCS3A01G374200 chr3B 93.952 248 12 3 1 248 641989093 641988849 2.870000e-99 372
4 TraesCS3A01G374200 chr3B 86.425 221 13 5 246 461 641988800 641988592 2.370000e-55 226
5 TraesCS3A01G374200 chr3D 92.279 803 32 12 798 1589 481070472 481069689 0.000000e+00 1112
6 TraesCS3A01G374200 chr3D 89.664 803 37 13 1586 2366 481069662 481068884 0.000000e+00 981
7 TraesCS3A01G374200 chr3D 93.333 225 14 1 468 692 481075407 481075184 4.870000e-87 331


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 TraesCS3A01G374200 chr3A 623821428 623823793 2365 True 4370.0 4370 100.0000 1 2366 1 chr3A.!!$R1 2365
1 TraesCS3A01G374200 chr3B 641986697 641989093 2396 True 692.5 1303 89.9070 1 2366 4 chr3B.!!$R1 2365
2 TraesCS3A01G374200 chr3D 481068884 481070472 1588 True 1046.5 1112 90.9715 798 2366 2 chr3D.!!$R2 1568

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
625 718 0.249322 GCATACTACCGCCACGACAT 60.249 55.0 0.0 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2193 2358 2.011947 GACAGAACTGCATGCATAGCA 58.988 47.619 22.97 18.52 44.86 3.49 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
136 137 6.037281 TGCAAAACATGTTGTCGTAGTCTAAA 59.963 34.615 12.82 0.00 0.00 1.85
138 139 7.589954 GCAAAACATGTTGTCGTAGTCTAAATT 59.410 33.333 12.82 0.00 0.00 1.82
286 339 7.598118 TGATTTGCCATTTTGTGTTGTATACAG 59.402 33.333 5.56 0.00 37.45 2.74
287 340 6.641169 TTGCCATTTTGTGTTGTATACAGA 57.359 33.333 5.56 0.00 37.45 3.41
288 341 6.641169 TGCCATTTTGTGTTGTATACAGAA 57.359 33.333 5.56 0.00 38.16 3.02
289 342 7.225784 TGCCATTTTGTGTTGTATACAGAAT 57.774 32.000 5.56 0.00 39.47 2.40
290 343 7.089538 TGCCATTTTGTGTTGTATACAGAATG 58.910 34.615 5.56 11.96 44.10 2.67
294 347 9.128107 CATTTTGTGTTGTATACAGAATGGTTC 57.872 33.333 5.56 0.00 42.36 3.62
295 348 7.809546 TTTGTGTTGTATACAGAATGGTTCA 57.190 32.000 5.56 0.00 43.62 3.18
313 366 7.859325 TGGTTCAAGTATTATCTTTGTAGCC 57.141 36.000 0.00 0.00 0.00 3.93
390 443 1.173043 TTTGTGCTAAATCCCCAGCG 58.827 50.000 0.00 0.00 40.79 5.18
403 456 1.437573 CCAGCGTAATCCAGCGAGA 59.562 57.895 0.00 0.00 38.61 4.04
439 492 4.908601 ATGTGGATCAACAGTGGTTAGA 57.091 40.909 9.25 0.00 34.87 2.10
521 614 9.487442 AATTTAAAGGGGCTGATTTACATCTAA 57.513 29.630 0.00 0.00 0.00 2.10
532 625 7.572724 GCTGATTTACATCTAAGCACCATCATC 60.573 40.741 0.00 0.00 31.51 2.92
550 643 9.471702 ACCATCATCTCAAATTTCAACTATTCT 57.528 29.630 0.00 0.00 0.00 2.40
606 699 1.206578 GTCAAATGGACACACCGCG 59.793 57.895 0.00 0.00 46.19 6.46
607 700 2.126888 CAAATGGACACACCGCGC 60.127 61.111 0.00 0.00 42.61 6.86
608 701 2.593148 AAATGGACACACCGCGCA 60.593 55.556 8.75 0.00 42.61 6.09
609 702 1.971167 AAATGGACACACCGCGCAT 60.971 52.632 8.75 0.00 42.61 4.73
610 703 0.675208 AAATGGACACACCGCGCATA 60.675 50.000 8.75 0.00 42.61 3.14
611 704 1.366111 AATGGACACACCGCGCATAC 61.366 55.000 8.75 0.00 42.61 2.39
612 705 2.125673 GGACACACCGCGCATACT 60.126 61.111 8.75 0.00 0.00 2.12
613 706 1.140161 GGACACACCGCGCATACTA 59.860 57.895 8.75 0.00 0.00 1.82
614 707 1.143969 GGACACACCGCGCATACTAC 61.144 60.000 8.75 0.00 0.00 2.73
615 708 1.143969 GACACACCGCGCATACTACC 61.144 60.000 8.75 0.00 0.00 3.18
616 709 2.103538 ACACCGCGCATACTACCG 59.896 61.111 8.75 0.00 0.00 4.02
617 710 3.327754 CACCGCGCATACTACCGC 61.328 66.667 8.75 0.00 46.17 5.68
618 711 4.580551 ACCGCGCATACTACCGCC 62.581 66.667 8.75 0.00 46.88 6.13
619 712 4.578898 CCGCGCATACTACCGCCA 62.579 66.667 8.75 0.00 46.88 5.69
620 713 3.327754 CGCGCATACTACCGCCAC 61.328 66.667 8.75 0.00 46.88 5.01
621 714 3.327754 GCGCATACTACCGCCACG 61.328 66.667 0.30 0.00 44.10 4.94
622 715 2.410060 CGCATACTACCGCCACGA 59.590 61.111 0.00 0.00 0.00 4.35
623 716 1.942712 CGCATACTACCGCCACGAC 60.943 63.158 0.00 0.00 0.00 4.34
624 717 1.140161 GCATACTACCGCCACGACA 59.860 57.895 0.00 0.00 0.00 4.35
625 718 0.249322 GCATACTACCGCCACGACAT 60.249 55.000 0.00 0.00 0.00 3.06
626 719 1.487482 CATACTACCGCCACGACATG 58.513 55.000 0.00 0.00 0.00 3.21
627 720 1.066454 CATACTACCGCCACGACATGA 59.934 52.381 0.00 0.00 0.00 3.07
628 721 0.736636 TACTACCGCCACGACATGAG 59.263 55.000 0.00 0.00 0.00 2.90
629 722 1.878522 CTACCGCCACGACATGAGC 60.879 63.158 0.00 0.00 0.00 4.26
630 723 3.365291 TACCGCCACGACATGAGCC 62.365 63.158 0.00 0.00 0.00 4.70
631 724 4.457496 CCGCCACGACATGAGCCT 62.457 66.667 0.00 0.00 0.00 4.58
632 725 3.190849 CGCCACGACATGAGCCTG 61.191 66.667 0.00 0.00 0.00 4.85
633 726 2.265739 GCCACGACATGAGCCTGA 59.734 61.111 0.00 0.00 0.00 3.86
634 727 1.153289 GCCACGACATGAGCCTGAT 60.153 57.895 0.00 0.00 0.00 2.90
635 728 1.156645 GCCACGACATGAGCCTGATC 61.157 60.000 0.00 0.00 0.00 2.92
636 729 0.463204 CCACGACATGAGCCTGATCT 59.537 55.000 0.00 0.00 0.00 2.75
637 730 1.683385 CCACGACATGAGCCTGATCTA 59.317 52.381 0.00 0.00 0.00 1.98
638 731 2.544694 CCACGACATGAGCCTGATCTAC 60.545 54.545 0.00 0.00 0.00 2.59
639 732 1.683917 ACGACATGAGCCTGATCTACC 59.316 52.381 0.00 0.00 0.00 3.18
640 733 1.959985 CGACATGAGCCTGATCTACCT 59.040 52.381 0.00 0.00 0.00 3.08
641 734 2.030363 CGACATGAGCCTGATCTACCTC 60.030 54.545 0.00 0.00 0.00 3.85
642 735 2.961741 GACATGAGCCTGATCTACCTCA 59.038 50.000 0.00 10.62 38.54 3.86
643 736 3.577848 GACATGAGCCTGATCTACCTCAT 59.422 47.826 0.00 13.30 43.68 2.90
645 738 1.690893 TGAGCCTGATCTACCTCATGC 59.309 52.381 0.00 0.00 37.14 4.06
646 739 0.678395 AGCCTGATCTACCTCATGCG 59.322 55.000 0.00 0.00 40.43 4.73
670 763 1.876497 CGGGTGTGCCTCCATTTTGG 61.876 60.000 0.00 0.00 39.43 3.28
706 799 6.787957 ACATAGCCTAAGTATTGTACATCCCT 59.212 38.462 0.00 0.00 0.00 4.20
732 832 1.000731 TGCATTTACAACTGGCTTGGC 59.999 47.619 0.00 0.00 33.66 4.52
743 843 1.152881 GGCTTGGCTATGGACCTGG 60.153 63.158 0.00 0.00 0.00 4.45
900 1002 2.857748 CACGTATATGCAAAGCGAGACA 59.142 45.455 9.61 0.00 0.00 3.41
981 1083 1.530323 GCCCTAAGAACAAGGCGAAA 58.470 50.000 0.00 0.00 35.30 3.46
1011 1113 1.003355 CACACCAATGGCGACTCCT 60.003 57.895 0.00 0.00 35.26 3.69
1297 1402 2.125106 CTTCCGCTGCTACCCCAC 60.125 66.667 0.00 0.00 0.00 4.61
1311 1416 3.406200 CCACCTCCTCCCCTGCAG 61.406 72.222 6.78 6.78 0.00 4.41
1312 1417 4.106925 CACCTCCTCCCCTGCAGC 62.107 72.222 8.66 0.00 0.00 5.25
1313 1418 4.664267 ACCTCCTCCCCTGCAGCA 62.664 66.667 8.66 0.00 0.00 4.41
1314 1419 3.795041 CCTCCTCCCCTGCAGCAG 61.795 72.222 16.23 16.23 0.00 4.24
1315 1420 4.486503 CTCCTCCCCTGCAGCAGC 62.487 72.222 17.81 0.00 42.57 5.25
1462 1574 5.734720 CATTCCTTGCCTCTGTTTACTCTA 58.265 41.667 0.00 0.00 0.00 2.43
1483 1595 7.125792 TCTATGATCCTGGACCTAAAGAAAC 57.874 40.000 0.00 0.00 0.00 2.78
1528 1641 4.137543 AGTTGGAAGGTCAATTCTGTGTC 58.862 43.478 0.00 0.00 0.00 3.67
1558 1671 5.726308 TGGAGATCATTCTGGAGAAGGTTTA 59.274 40.000 0.00 0.00 37.16 2.01
1568 1681 7.038154 TCTGGAGAAGGTTTAAATTGTTGTG 57.962 36.000 0.00 0.00 0.00 3.33
1572 1685 8.141268 TGGAGAAGGTTTAAATTGTTGTGATTC 58.859 33.333 0.00 0.00 0.00 2.52
1580 1693 9.956797 GTTTAAATTGTTGTGATTCATGTATGC 57.043 29.630 0.00 0.00 0.00 3.14
1619 1762 3.181501 CCATTCCGCATCGTATTTGTTGT 60.182 43.478 0.00 0.00 0.00 3.32
1627 1770 4.549599 GCATCGTATTTGTTGTGTTTCTCG 59.450 41.667 0.00 0.00 0.00 4.04
1633 1776 1.378531 TGTTGTGTTTCTCGCTGCTT 58.621 45.000 0.00 0.00 0.00 3.91
1634 1777 1.330521 TGTTGTGTTTCTCGCTGCTTC 59.669 47.619 0.00 0.00 0.00 3.86
1641 1784 4.390297 GTGTTTCTCGCTGCTTCTCTAAAT 59.610 41.667 0.00 0.00 0.00 1.40
1664 1807 9.773328 AAATAGATACAATGTTTCATTGTCGTG 57.227 29.630 24.72 4.59 41.81 4.35
1677 1820 3.737032 TTGTCGTGGTTCATGTACTCA 57.263 42.857 2.29 0.00 0.00 3.41
1722 1865 8.546083 ACTAATATTTCATCTCAGTCCTCTGT 57.454 34.615 0.00 0.00 41.91 3.41
1751 1914 1.522668 TGGTATGCACTGTTGTGAGC 58.477 50.000 0.00 0.00 46.55 4.26
1778 1941 6.516739 TGATAGAGAAGTCTGAACGAACAT 57.483 37.500 0.00 0.00 33.84 2.71
1779 1942 6.325596 TGATAGAGAAGTCTGAACGAACATG 58.674 40.000 0.00 0.00 33.84 3.21
1780 1943 3.321497 AGAGAAGTCTGAACGAACATGC 58.679 45.455 0.00 0.00 0.00 4.06
1783 1946 2.820059 AGTCTGAACGAACATGCTGA 57.180 45.000 0.00 0.00 0.00 4.26
1907 2070 8.686334 CAGTGGCCTTAACATTATTGTTATCTT 58.314 33.333 3.32 0.00 45.33 2.40
1980 2143 6.974622 GTGGTAGGAATTTTAATGTGCTCATG 59.025 38.462 1.29 0.00 34.19 3.07
1989 2152 9.768662 AATTTTAATGTGCTCATGAAAGAGTTT 57.231 25.926 10.42 3.27 36.23 2.66
2009 2172 7.390718 AGAGTTTACTCCAGCGACATTTTTATT 59.609 33.333 6.28 0.00 43.88 1.40
2042 2205 6.037172 CAGTCCATTATCAAACTTCCCTTACG 59.963 42.308 0.00 0.00 0.00 3.18
2049 2213 6.997239 ATCAAACTTCCCTTACGTATTTCC 57.003 37.500 0.00 0.00 0.00 3.13
2058 2222 5.301551 TCCCTTACGTATTTCCGTAGCATTA 59.698 40.000 0.00 0.00 43.46 1.90
2067 2231 1.975680 TCCGTAGCATTATTCCTCCCC 59.024 52.381 0.00 0.00 0.00 4.81
2098 2262 7.867909 TCCTGATCTGTTATAGCGAACTATTTG 59.132 37.037 0.00 0.00 39.81 2.32
2112 2277 7.383572 AGCGAACTATTTGACTTATCTATGCAG 59.616 37.037 0.00 0.00 0.00 4.41
2126 2291 6.932356 ATCTATGCAGTTATCTTGTGTTGG 57.068 37.500 0.00 0.00 0.00 3.77
2205 2370 1.617357 TGGTGTTTTGCTATGCATGCA 59.383 42.857 25.04 25.04 38.76 3.96
2282 2448 8.527810 ACCGGAAACATCAAAATATTATGTGTT 58.472 29.630 9.46 3.75 34.20 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 101 6.985645 ACAACATGTTTTGCAATTCATGTACT 59.014 30.769 31.25 21.90 46.33 2.73
268 320 9.128107 GAACCATTCTGTATACAACACAAAATG 57.872 33.333 7.06 9.42 33.45 2.32
274 327 7.435068 ACTTGAACCATTCTGTATACAACAC 57.565 36.000 7.06 0.00 33.45 3.32
286 339 9.937175 GCTACAAAGATAATACTTGAACCATTC 57.063 33.333 0.00 0.00 0.00 2.67
287 340 8.903820 GGCTACAAAGATAATACTTGAACCATT 58.096 33.333 0.00 0.00 0.00 3.16
288 341 7.226720 CGGCTACAAAGATAATACTTGAACCAT 59.773 37.037 0.00 0.00 0.00 3.55
289 342 6.537301 CGGCTACAAAGATAATACTTGAACCA 59.463 38.462 0.00 0.00 0.00 3.67
290 343 6.018180 CCGGCTACAAAGATAATACTTGAACC 60.018 42.308 0.00 0.00 0.00 3.62
291 344 6.511282 GCCGGCTACAAAGATAATACTTGAAC 60.511 42.308 22.15 0.00 0.00 3.18
292 345 5.526111 GCCGGCTACAAAGATAATACTTGAA 59.474 40.000 22.15 0.00 0.00 2.69
293 346 5.054477 GCCGGCTACAAAGATAATACTTGA 58.946 41.667 22.15 0.00 0.00 3.02
294 347 4.814234 TGCCGGCTACAAAGATAATACTTG 59.186 41.667 29.70 0.00 0.00 3.16
295 348 4.814771 GTGCCGGCTACAAAGATAATACTT 59.185 41.667 29.70 0.00 0.00 2.24
306 359 0.970640 TACTCAAGTGCCGGCTACAA 59.029 50.000 29.70 3.37 0.00 2.41
313 366 1.878953 AACCAACTACTCAAGTGCCG 58.121 50.000 0.00 0.00 38.88 5.69
376 429 2.152016 GGATTACGCTGGGGATTTAGC 58.848 52.381 0.00 0.00 36.60 3.09
377 430 3.403038 CTGGATTACGCTGGGGATTTAG 58.597 50.000 0.00 0.00 0.00 1.85
390 443 7.331934 TGCTAAATTATCATCTCGCTGGATTAC 59.668 37.037 0.00 0.00 0.00 1.89
499 589 6.062095 GCTTAGATGTAAATCAGCCCCTTTA 58.938 40.000 0.00 0.00 32.20 1.85
521 614 5.479375 AGTTGAAATTTGAGATGATGGTGCT 59.521 36.000 0.00 0.00 0.00 4.40
550 643 9.461312 AATACTTAGGCTATGTTTTGAATGACA 57.539 29.630 16.99 0.00 0.00 3.58
588 681 1.206578 CGCGGTGTGTCCATTTGAC 59.793 57.895 0.00 0.00 44.72 3.18
589 682 2.612567 GCGCGGTGTGTCCATTTGA 61.613 57.895 8.83 0.00 35.57 2.69
590 683 2.126888 GCGCGGTGTGTCCATTTG 60.127 61.111 8.83 0.00 35.57 2.32
591 684 0.675208 TATGCGCGGTGTGTCCATTT 60.675 50.000 8.83 0.00 35.57 2.32
592 685 1.078778 TATGCGCGGTGTGTCCATT 60.079 52.632 8.83 0.00 35.57 3.16
593 686 1.813753 GTATGCGCGGTGTGTCCAT 60.814 57.895 8.83 3.03 35.57 3.41
594 687 1.596895 TAGTATGCGCGGTGTGTCCA 61.597 55.000 8.83 0.00 35.57 4.02
595 688 1.140161 TAGTATGCGCGGTGTGTCC 59.860 57.895 8.83 0.00 0.00 4.02
596 689 1.143969 GGTAGTATGCGCGGTGTGTC 61.144 60.000 8.83 0.00 0.00 3.67
597 690 1.153706 GGTAGTATGCGCGGTGTGT 60.154 57.895 8.83 0.00 0.00 3.72
598 691 2.228241 CGGTAGTATGCGCGGTGTG 61.228 63.158 8.83 0.00 0.00 3.82
599 692 2.103538 CGGTAGTATGCGCGGTGT 59.896 61.111 8.83 0.00 0.00 4.16
600 693 3.327754 GCGGTAGTATGCGCGGTG 61.328 66.667 8.83 0.00 0.00 4.94
601 694 4.580551 GGCGGTAGTATGCGCGGT 62.581 66.667 8.83 0.00 0.00 5.68
602 695 4.578898 TGGCGGTAGTATGCGCGG 62.579 66.667 8.83 0.00 0.00 6.46
603 696 3.327754 GTGGCGGTAGTATGCGCG 61.328 66.667 0.00 0.00 0.00 6.86
604 697 3.327754 CGTGGCGGTAGTATGCGC 61.328 66.667 0.00 0.00 0.00 6.09
605 698 1.942712 GTCGTGGCGGTAGTATGCG 60.943 63.158 0.00 0.00 0.00 4.73
606 699 0.249322 ATGTCGTGGCGGTAGTATGC 60.249 55.000 0.00 0.00 0.00 3.14
607 700 1.066454 TCATGTCGTGGCGGTAGTATG 59.934 52.381 0.00 0.00 0.00 2.39
608 701 1.337071 CTCATGTCGTGGCGGTAGTAT 59.663 52.381 0.00 0.00 0.00 2.12
609 702 0.736636 CTCATGTCGTGGCGGTAGTA 59.263 55.000 0.00 0.00 0.00 1.82
610 703 1.511305 CTCATGTCGTGGCGGTAGT 59.489 57.895 0.00 0.00 0.00 2.73
611 704 1.878522 GCTCATGTCGTGGCGGTAG 60.879 63.158 0.00 0.00 0.00 3.18
612 705 2.183300 GCTCATGTCGTGGCGGTA 59.817 61.111 0.00 0.00 0.00 4.02
613 706 4.760047 GGCTCATGTCGTGGCGGT 62.760 66.667 0.00 0.00 0.00 5.68
614 707 4.457496 AGGCTCATGTCGTGGCGG 62.457 66.667 0.00 0.00 38.61 6.13
615 708 2.913054 ATCAGGCTCATGTCGTGGCG 62.913 60.000 0.00 0.00 38.61 5.69
616 709 1.153289 ATCAGGCTCATGTCGTGGC 60.153 57.895 0.00 0.00 0.00 5.01
617 710 0.463204 AGATCAGGCTCATGTCGTGG 59.537 55.000 0.00 0.00 0.00 4.94
618 711 2.544694 GGTAGATCAGGCTCATGTCGTG 60.545 54.545 0.00 0.00 0.00 4.35
619 712 1.683917 GGTAGATCAGGCTCATGTCGT 59.316 52.381 0.00 0.00 0.00 4.34
620 713 1.959985 AGGTAGATCAGGCTCATGTCG 59.040 52.381 0.00 0.00 0.00 4.35
621 714 2.961741 TGAGGTAGATCAGGCTCATGTC 59.038 50.000 0.00 0.00 0.00 3.06
622 715 3.037851 TGAGGTAGATCAGGCTCATGT 57.962 47.619 0.00 0.00 0.00 3.21
623 716 3.927854 CATGAGGTAGATCAGGCTCATG 58.072 50.000 0.00 0.00 41.05 3.07
629 722 2.898729 AACGCATGAGGTAGATCAGG 57.101 50.000 0.00 0.00 34.19 3.86
630 723 4.162072 CGATAACGCATGAGGTAGATCAG 58.838 47.826 0.00 0.00 31.44 2.90
631 724 3.057526 CCGATAACGCATGAGGTAGATCA 60.058 47.826 0.00 0.00 38.29 2.92
632 725 3.502920 CCGATAACGCATGAGGTAGATC 58.497 50.000 0.00 0.00 38.29 2.75
633 726 2.231478 CCCGATAACGCATGAGGTAGAT 59.769 50.000 0.00 0.00 38.29 1.98
634 727 1.611977 CCCGATAACGCATGAGGTAGA 59.388 52.381 0.00 0.00 38.29 2.59
635 728 1.340248 ACCCGATAACGCATGAGGTAG 59.660 52.381 0.00 0.00 38.29 3.18
636 729 1.067974 CACCCGATAACGCATGAGGTA 59.932 52.381 0.00 0.00 38.29 3.08
637 730 0.179084 CACCCGATAACGCATGAGGT 60.179 55.000 0.00 0.00 38.29 3.85
638 731 0.179084 ACACCCGATAACGCATGAGG 60.179 55.000 0.00 0.00 38.29 3.86
639 732 0.930310 CACACCCGATAACGCATGAG 59.070 55.000 0.00 0.00 38.29 2.90
640 733 1.087202 GCACACCCGATAACGCATGA 61.087 55.000 0.00 0.00 38.29 3.07
641 734 1.351707 GCACACCCGATAACGCATG 59.648 57.895 0.00 0.00 38.29 4.06
642 735 1.817941 GGCACACCCGATAACGCAT 60.818 57.895 0.00 0.00 38.29 4.73
643 736 2.435234 GGCACACCCGATAACGCA 60.435 61.111 0.00 0.00 38.29 5.24
644 737 2.125269 AGGCACACCCGATAACGC 60.125 61.111 0.00 0.00 39.21 4.84
645 738 1.520787 GGAGGCACACCCGATAACG 60.521 63.158 0.00 0.00 39.21 3.18
646 739 0.180406 ATGGAGGCACACCCGATAAC 59.820 55.000 0.00 0.00 38.71 1.89
713 806 1.273327 AGCCAAGCCAGTTGTAAATGC 59.727 47.619 0.00 0.00 33.87 3.56
714 807 4.440525 CCATAGCCAAGCCAGTTGTAAATG 60.441 45.833 0.00 0.00 33.87 2.32
716 809 3.088532 CCATAGCCAAGCCAGTTGTAAA 58.911 45.455 0.00 0.00 33.87 2.01
717 810 2.307392 TCCATAGCCAAGCCAGTTGTAA 59.693 45.455 0.00 0.00 33.87 2.41
718 811 1.912731 TCCATAGCCAAGCCAGTTGTA 59.087 47.619 0.00 0.00 33.87 2.41
719 812 0.698238 TCCATAGCCAAGCCAGTTGT 59.302 50.000 0.00 0.00 33.87 3.32
721 814 0.034089 GGTCCATAGCCAAGCCAGTT 60.034 55.000 0.00 0.00 0.00 3.16
723 816 0.465097 CAGGTCCATAGCCAAGCCAG 60.465 60.000 0.00 0.00 0.00 4.85
750 850 9.862149 AAAGATAGGTTCAGTTCTTTTTAAGGA 57.138 29.630 0.00 0.00 35.46 3.36
812 914 6.939622 TGCGTCCATGATATATTCTCAGAAT 58.060 36.000 4.98 4.98 0.00 2.40
813 915 6.345096 TGCGTCCATGATATATTCTCAGAA 57.655 37.500 0.00 0.00 0.00 3.02
815 917 8.883954 ATATTGCGTCCATGATATATTCTCAG 57.116 34.615 0.00 0.00 0.00 3.35
816 918 9.671279 AAATATTGCGTCCATGATATATTCTCA 57.329 29.630 0.00 0.00 0.00 3.27
821 923 8.335356 GCGTAAAATATTGCGTCCATGATATAT 58.665 33.333 0.00 0.00 45.01 0.86
822 924 7.332182 TGCGTAAAATATTGCGTCCATGATATA 59.668 33.333 0.00 0.00 45.01 0.86
844 946 1.607148 GTGGGCTTAAACTTCTTGCGT 59.393 47.619 0.00 0.00 0.00 5.24
900 1002 4.336280 GCTAGAATGGACCCTGTCTTTTT 58.664 43.478 0.00 0.00 32.47 1.94
981 1083 0.464735 TTGGTGTGGTGCGCTACTTT 60.465 50.000 15.15 0.00 0.00 2.66
993 1095 1.003355 AGGAGTCGCCATTGGTGTG 60.003 57.895 15.63 1.11 40.02 3.82
994 1096 1.003355 CAGGAGTCGCCATTGGTGT 60.003 57.895 15.63 0.00 40.02 4.16
1285 1387 2.689034 AGGAGGTGGGGTAGCAGC 60.689 66.667 0.00 0.00 0.00 5.25
1288 1390 2.768769 GGGAGGAGGTGGGGTAGC 60.769 72.222 0.00 0.00 0.00 3.58
1297 1402 3.795041 CTGCTGCAGGGGAGGAGG 61.795 72.222 21.71 0.00 0.00 4.30
1357 1462 1.810030 GCCTTACTCTTCACGGCGG 60.810 63.158 13.24 0.00 0.00 6.13
1396 1501 6.350445 GCAGGGATTGTTCTGTAACATTTCAT 60.350 38.462 0.00 0.00 44.85 2.57
1462 1574 4.384208 CCGTTTCTTTAGGTCCAGGATCAT 60.384 45.833 1.43 0.00 0.00 2.45
1558 1671 9.357652 GTAAGCATACATGAATCACAACAATTT 57.642 29.630 0.00 0.00 32.02 1.82
1604 1747 4.549599 CGAGAAACACAACAAATACGATGC 59.450 41.667 0.00 0.00 0.00 3.91
1619 1762 3.660501 TTAGAGAAGCAGCGAGAAACA 57.339 42.857 0.00 0.00 0.00 2.83
1627 1770 8.600449 ACATTGTATCTATTTAGAGAAGCAGC 57.400 34.615 0.00 0.00 35.50 5.25
1641 1784 6.876789 ACCACGACAATGAAACATTGTATCTA 59.123 34.615 23.68 0.00 41.76 1.98
1661 1804 2.876091 ACGATGAGTACATGAACCACG 58.124 47.619 0.00 0.00 36.82 4.94
1662 1805 6.736123 ACTATACGATGAGTACATGAACCAC 58.264 40.000 0.00 0.00 38.29 4.16
1664 1807 7.649973 AGAACTATACGATGAGTACATGAACC 58.350 38.462 0.00 0.00 38.29 3.62
1709 1852 2.110188 ACTACCCAACAGAGGACTGAGA 59.890 50.000 0.00 0.00 46.03 3.27
1711 1854 2.696526 ACTACCCAACAGAGGACTGA 57.303 50.000 0.00 0.00 46.03 3.41
1713 1856 3.246021 ACCATACTACCCAACAGAGGACT 60.246 47.826 0.00 0.00 0.00 3.85
1714 1857 3.105283 ACCATACTACCCAACAGAGGAC 58.895 50.000 0.00 0.00 0.00 3.85
1717 1860 4.100963 TGCATACCATACTACCCAACAGAG 59.899 45.833 0.00 0.00 0.00 3.35
1718 1861 4.034410 TGCATACCATACTACCCAACAGA 58.966 43.478 0.00 0.00 0.00 3.41
1719 1862 4.127171 GTGCATACCATACTACCCAACAG 58.873 47.826 0.00 0.00 0.00 3.16
1720 1863 3.778075 AGTGCATACCATACTACCCAACA 59.222 43.478 0.00 0.00 0.00 3.33
1721 1864 4.127171 CAGTGCATACCATACTACCCAAC 58.873 47.826 0.00 0.00 0.00 3.77
1722 1865 3.778075 ACAGTGCATACCATACTACCCAA 59.222 43.478 0.00 0.00 0.00 4.12
1751 1914 7.329471 TGTTCGTTCAGACTTCTCTATCAAATG 59.671 37.037 0.00 0.00 0.00 2.32
1778 1941 4.336153 CCAACAGTGCATAATACATCAGCA 59.664 41.667 0.00 0.00 0.00 4.41
1779 1942 4.261322 CCCAACAGTGCATAATACATCAGC 60.261 45.833 0.00 0.00 0.00 4.26
1780 1943 4.276678 CCCCAACAGTGCATAATACATCAG 59.723 45.833 0.00 0.00 0.00 2.90
1783 1946 4.249638 ACCCCAACAGTGCATAATACAT 57.750 40.909 0.00 0.00 0.00 2.29
1941 2104 6.590656 TTCCTACCACCATCATTTAGGATT 57.409 37.500 0.00 0.00 38.47 3.01
1980 2143 3.650139 TGTCGCTGGAGTAAACTCTTTC 58.350 45.455 9.84 0.00 42.48 2.62
1989 2152 4.569162 CCGAATAAAAATGTCGCTGGAGTA 59.431 41.667 0.00 0.00 33.46 2.59
2009 2172 4.561500 TTGATAATGGACTGTTTCCCGA 57.438 40.909 0.00 0.00 45.17 5.14
2042 2205 5.642491 GGGAGGAATAATGCTACGGAAATAC 59.358 44.000 0.00 0.00 0.00 1.89
2049 2213 3.485463 TTGGGGAGGAATAATGCTACG 57.515 47.619 0.00 0.00 0.00 3.51
2058 2222 3.796119 AGATCAGGAATTTGGGGAGGAAT 59.204 43.478 0.00 0.00 0.00 3.01
2067 2231 7.225538 AGTTCGCTATAACAGATCAGGAATTTG 59.774 37.037 0.00 0.00 0.00 2.32
2098 2262 8.879342 ACACAAGATAACTGCATAGATAAGTC 57.121 34.615 0.00 0.00 0.00 3.01
2112 2277 6.985188 TTCAGCTATCCAACACAAGATAAC 57.015 37.500 0.00 0.00 0.00 1.89
2126 2291 8.624776 ACTAGCAATTAATTGGTTTCAGCTATC 58.375 33.333 31.34 10.93 45.24 2.08
2187 2352 2.950433 ACTGCATGCATAGCAAAACAC 58.050 42.857 22.97 0.00 43.62 3.32
2188 2353 3.256383 AGAACTGCATGCATAGCAAAACA 59.744 39.130 22.97 0.00 43.62 2.83
2189 2354 3.611113 CAGAACTGCATGCATAGCAAAAC 59.389 43.478 22.97 14.31 43.62 2.43
2193 2358 2.011947 GACAGAACTGCATGCATAGCA 58.988 47.619 22.97 18.52 44.86 3.49
2205 2370 6.234177 CCAAGGTTCAGATTTAGACAGAACT 58.766 40.000 0.00 0.00 38.78 3.01
2282 2448 4.688879 GTGGAACTGTTGATCGTGACATAA 59.311 41.667 0.00 0.00 0.00 1.90
2290 2462 2.426522 ACATGGTGGAACTGTTGATCG 58.573 47.619 0.00 0.00 36.74 3.69
2291 2463 4.853924 AAACATGGTGGAACTGTTGATC 57.146 40.909 0.00 0.00 36.74 2.92
2292 2464 5.278957 GCTAAAACATGGTGGAACTGTTGAT 60.279 40.000 0.00 0.00 36.74 2.57
2293 2465 4.037446 GCTAAAACATGGTGGAACTGTTGA 59.963 41.667 0.00 0.00 36.74 3.18
2294 2466 4.037923 AGCTAAAACATGGTGGAACTGTTG 59.962 41.667 0.00 0.00 36.74 3.33
2295 2467 4.215109 AGCTAAAACATGGTGGAACTGTT 58.785 39.130 0.00 0.00 36.74 3.16


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

AutoCloner maintained by Alex Coulton.