Multiple sequence alignment - TraesCS6D01G033600

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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 TraesCS6D01G033600 chr6D 100.000 2480 0 0 1 2480 14143628 14141149 0.000000e+00 4580
1 TraesCS6D01G033600 chr6D 88.268 537 47 8 1 535 465735874 465736396 1.620000e-176 628
2 TraesCS6D01G033600 chr6A 95.862 1015 39 1 1466 2480 15445234 15444223 0.000000e+00 1639
3 TraesCS6D01G033600 chr6A 92.389 854 29 9 714 1538 15446083 15445237 0.000000e+00 1184
4 TraesCS6D01G033600 chr5D 95.298 553 25 1 2 553 135090639 135091191 0.000000e+00 876
5 TraesCS6D01G033600 chr5D 86.047 430 44 8 1 427 140431156 140430740 4.870000e-122 448
6 TraesCS6D01G033600 chr5D 97.980 198 3 1 349 545 135085797 135085994 2.360000e-90 342
7 TraesCS6D01G033600 chr1A 93.011 558 36 3 1 556 30393898 30393342 0.000000e+00 811
8 TraesCS6D01G033600 chr1A 94.898 196 9 1 350 544 30398670 30398475 3.100000e-79 305
9 TraesCS6D01G033600 chr7A 92.973 555 37 2 1 553 595205914 595205360 0.000000e+00 808
10 TraesCS6D01G033600 chr7A 90.317 568 35 7 1 553 694429196 694428634 0.000000e+00 726
11 TraesCS6D01G033600 chr7A 95.385 195 8 1 350 543 595210800 595210606 2.400000e-80 309
12 TraesCS6D01G033600 chr2D 87.293 543 50 18 1 535 574432368 574431837 9.810000e-169 603
13 TraesCS6D01G033600 chr4B 84.037 545 68 17 1 535 4932452 4932987 7.910000e-140 507
14 TraesCS6D01G033600 chr6B 83.794 543 68 16 4 535 149473675 149473142 4.760000e-137 497
15 TraesCS6D01G033600 chr1B 95.263 190 7 2 350 537 30838420 30838231 1.440000e-77 300


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 TraesCS6D01G033600 chr6D 14141149 14143628 2479 True 4580.0 4580 100.0000 1 2480 1 chr6D.!!$R1 2479
1 TraesCS6D01G033600 chr6D 465735874 465736396 522 False 628.0 628 88.2680 1 535 1 chr6D.!!$F1 534
2 TraesCS6D01G033600 chr6A 15444223 15446083 1860 True 1411.5 1639 94.1255 714 2480 2 chr6A.!!$R1 1766
3 TraesCS6D01G033600 chr5D 135090639 135091191 552 False 876.0 876 95.2980 2 553 1 chr5D.!!$F2 551
4 TraesCS6D01G033600 chr1A 30393342 30393898 556 True 811.0 811 93.0110 1 556 1 chr1A.!!$R1 555
5 TraesCS6D01G033600 chr7A 595205360 595205914 554 True 808.0 808 92.9730 1 553 1 chr7A.!!$R1 552
6 TraesCS6D01G033600 chr7A 694428634 694429196 562 True 726.0 726 90.3170 1 553 1 chr7A.!!$R3 552
7 TraesCS6D01G033600 chr2D 574431837 574432368 531 True 603.0 603 87.2930 1 535 1 chr2D.!!$R1 534
8 TraesCS6D01G033600 chr4B 4932452 4932987 535 False 507.0 507 84.0370 1 535 1 chr4B.!!$F1 534
9 TraesCS6D01G033600 chr6B 149473142 149473675 533 True 497.0 497 83.7940 4 535 1 chr6B.!!$R1 531

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
615 639 0.033781 TTTGTACCGTTCCCTGTCCG 59.966 55.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1556 1684 0.31777 AAATCTGTTGGTTGCACGCG 60.318 50.0 3.53 3.53 0.0 6.01 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
87 89 0.173481 CTTGAAGTCGAGGATGCCGA 59.827 55.000 0.00 0.00 0.00 5.54
165 167 4.681978 GTGGAACGGCAGCGAGGT 62.682 66.667 0.00 0.00 0.00 3.85
329 344 4.124126 GTGGGAGGGGGAGGGGAT 62.124 72.222 0.00 0.00 0.00 3.85
513 534 7.439356 ACAACAAACTCATCAGGATATACATCG 59.561 37.037 0.00 0.00 31.33 3.84
553 577 3.799366 ACATGACGTGGTAGTTCAACAA 58.201 40.909 0.00 0.00 0.00 2.83
554 578 4.385825 ACATGACGTGGTAGTTCAACAAT 58.614 39.130 0.00 0.00 0.00 2.71
555 579 5.543714 ACATGACGTGGTAGTTCAACAATA 58.456 37.500 0.00 0.00 0.00 1.90
556 580 5.637810 ACATGACGTGGTAGTTCAACAATAG 59.362 40.000 0.00 0.00 0.00 1.73
557 581 3.991773 TGACGTGGTAGTTCAACAATAGC 59.008 43.478 0.00 0.00 0.00 2.97
558 582 2.991190 ACGTGGTAGTTCAACAATAGCG 59.009 45.455 0.00 0.00 0.00 4.26
559 583 2.347452 CGTGGTAGTTCAACAATAGCGG 59.653 50.000 0.00 0.00 0.00 5.52
560 584 2.095372 GTGGTAGTTCAACAATAGCGGC 59.905 50.000 0.00 0.00 0.00 6.53
561 585 1.669265 GGTAGTTCAACAATAGCGGCC 59.331 52.381 0.00 0.00 0.00 6.13
562 586 2.352388 GTAGTTCAACAATAGCGGCCA 58.648 47.619 2.24 0.00 0.00 5.36
563 587 1.904287 AGTTCAACAATAGCGGCCAA 58.096 45.000 2.24 0.00 0.00 4.52
564 588 2.235016 AGTTCAACAATAGCGGCCAAA 58.765 42.857 2.24 0.00 0.00 3.28
565 589 2.030274 AGTTCAACAATAGCGGCCAAAC 60.030 45.455 2.24 0.00 0.00 2.93
566 590 0.885196 TCAACAATAGCGGCCAAACC 59.115 50.000 2.24 0.00 0.00 3.27
567 591 0.600557 CAACAATAGCGGCCAAACCA 59.399 50.000 2.24 0.00 39.03 3.67
568 592 1.204467 CAACAATAGCGGCCAAACCAT 59.796 47.619 2.24 0.00 39.03 3.55
569 593 1.555967 ACAATAGCGGCCAAACCATT 58.444 45.000 2.24 0.00 39.03 3.16
570 594 1.204467 ACAATAGCGGCCAAACCATTG 59.796 47.619 2.24 5.32 39.03 2.82
571 595 1.204467 CAATAGCGGCCAAACCATTGT 59.796 47.619 2.24 0.00 39.03 2.71
572 596 0.817013 ATAGCGGCCAAACCATTGTG 59.183 50.000 2.24 0.00 39.03 3.33
573 597 0.538516 TAGCGGCCAAACCATTGTGT 60.539 50.000 2.24 0.00 39.03 3.72
574 598 1.068921 GCGGCCAAACCATTGTGTT 59.931 52.632 2.24 0.00 39.03 3.32
575 599 0.531753 GCGGCCAAACCATTGTGTTT 60.532 50.000 2.24 0.00 38.95 2.83
576 600 1.946745 CGGCCAAACCATTGTGTTTT 58.053 45.000 2.24 0.00 36.33 2.43
577 601 1.596727 CGGCCAAACCATTGTGTTTTG 59.403 47.619 2.24 0.00 36.33 2.44
578 602 1.946081 GGCCAAACCATTGTGTTTTGG 59.054 47.619 12.85 12.85 36.33 3.28
579 603 2.420687 GGCCAAACCATTGTGTTTTGGA 60.421 45.455 19.18 0.00 36.33 3.53
580 604 2.611751 GCCAAACCATTGTGTTTTGGAC 59.388 45.455 19.18 9.33 36.33 4.02
581 605 3.681313 GCCAAACCATTGTGTTTTGGACT 60.681 43.478 19.18 0.00 36.33 3.85
582 606 4.119136 CCAAACCATTGTGTTTTGGACTC 58.881 43.478 12.06 0.00 36.33 3.36
583 607 4.382470 CCAAACCATTGTGTTTTGGACTCA 60.382 41.667 12.06 0.00 36.33 3.41
584 608 5.358922 CAAACCATTGTGTTTTGGACTCAT 58.641 37.500 0.00 0.00 36.33 2.90
585 609 4.853924 ACCATTGTGTTTTGGACTCATC 57.146 40.909 0.00 0.00 36.79 2.92
586 610 3.253188 ACCATTGTGTTTTGGACTCATCG 59.747 43.478 0.00 0.00 36.79 3.84
587 611 3.253188 CCATTGTGTTTTGGACTCATCGT 59.747 43.478 0.00 0.00 34.81 3.73
588 612 4.261572 CCATTGTGTTTTGGACTCATCGTT 60.262 41.667 0.00 0.00 34.81 3.85
589 613 5.049060 CCATTGTGTTTTGGACTCATCGTTA 60.049 40.000 0.00 0.00 34.81 3.18
590 614 5.666969 TTGTGTTTTGGACTCATCGTTAG 57.333 39.130 0.00 0.00 32.31 2.34
591 615 4.951254 TGTGTTTTGGACTCATCGTTAGA 58.049 39.130 0.00 0.00 0.00 2.10
592 616 5.547465 TGTGTTTTGGACTCATCGTTAGAT 58.453 37.500 0.00 0.00 37.65 1.98
593 617 5.995282 TGTGTTTTGGACTCATCGTTAGATT 59.005 36.000 0.00 0.00 34.23 2.40
594 618 6.485313 TGTGTTTTGGACTCATCGTTAGATTT 59.515 34.615 0.00 0.00 34.23 2.17
595 619 6.797033 GTGTTTTGGACTCATCGTTAGATTTG 59.203 38.462 0.00 0.00 34.23 2.32
596 620 6.485313 TGTTTTGGACTCATCGTTAGATTTGT 59.515 34.615 0.00 0.00 34.23 2.83
597 621 7.012894 TGTTTTGGACTCATCGTTAGATTTGTT 59.987 33.333 0.00 0.00 34.23 2.83
598 622 7.504924 TTTGGACTCATCGTTAGATTTGTTT 57.495 32.000 0.00 0.00 34.23 2.83
599 623 6.480524 TGGACTCATCGTTAGATTTGTTTG 57.519 37.500 0.00 0.00 34.23 2.93
600 624 5.995282 TGGACTCATCGTTAGATTTGTTTGT 59.005 36.000 0.00 0.00 34.23 2.83
601 625 7.156000 TGGACTCATCGTTAGATTTGTTTGTA 58.844 34.615 0.00 0.00 34.23 2.41
602 626 7.117236 TGGACTCATCGTTAGATTTGTTTGTAC 59.883 37.037 0.00 0.00 34.23 2.90
603 627 7.360575 ACTCATCGTTAGATTTGTTTGTACC 57.639 36.000 0.00 0.00 34.23 3.34
604 628 6.090358 ACTCATCGTTAGATTTGTTTGTACCG 59.910 38.462 0.00 0.00 34.23 4.02
605 629 5.927689 TCATCGTTAGATTTGTTTGTACCGT 59.072 36.000 0.00 0.00 34.23 4.83
606 630 6.424509 TCATCGTTAGATTTGTTTGTACCGTT 59.575 34.615 0.00 0.00 34.23 4.44
607 631 6.214205 TCGTTAGATTTGTTTGTACCGTTC 57.786 37.500 0.00 0.00 0.00 3.95
608 632 5.177327 TCGTTAGATTTGTTTGTACCGTTCC 59.823 40.000 0.00 0.00 0.00 3.62
609 633 5.615325 CGTTAGATTTGTTTGTACCGTTCCC 60.615 44.000 0.00 0.00 0.00 3.97
610 634 4.094830 AGATTTGTTTGTACCGTTCCCT 57.905 40.909 0.00 0.00 0.00 4.20
611 635 3.818773 AGATTTGTTTGTACCGTTCCCTG 59.181 43.478 0.00 0.00 0.00 4.45
612 636 2.713863 TTGTTTGTACCGTTCCCTGT 57.286 45.000 0.00 0.00 0.00 4.00
613 637 2.243602 TGTTTGTACCGTTCCCTGTC 57.756 50.000 0.00 0.00 0.00 3.51
614 638 1.202675 TGTTTGTACCGTTCCCTGTCC 60.203 52.381 0.00 0.00 0.00 4.02
615 639 0.033781 TTTGTACCGTTCCCTGTCCG 59.966 55.000 0.00 0.00 0.00 4.79
616 640 1.818959 TTGTACCGTTCCCTGTCCGG 61.819 60.000 0.00 0.00 46.93 5.14
617 641 3.384532 TACCGTTCCCTGTCCGGC 61.385 66.667 0.00 0.00 45.49 6.13
619 643 4.760047 CCGTTCCCTGTCCGGCAG 62.760 72.222 16.22 16.22 44.63 4.85
620 644 4.003788 CGTTCCCTGTCCGGCAGT 62.004 66.667 19.93 0.00 43.55 4.40
621 645 2.047179 GTTCCCTGTCCGGCAGTC 60.047 66.667 19.93 7.89 43.55 3.51
622 646 3.319198 TTCCCTGTCCGGCAGTCC 61.319 66.667 19.93 0.00 43.55 3.85
648 672 3.395669 GGTACGGCAAGCGTCATC 58.604 61.111 0.00 0.00 0.00 2.92
649 673 2.514013 GGTACGGCAAGCGTCATCG 61.514 63.158 0.00 0.00 40.37 3.84
650 674 1.515519 GTACGGCAAGCGTCATCGA 60.516 57.895 0.00 0.00 39.71 3.59
651 675 0.870307 GTACGGCAAGCGTCATCGAT 60.870 55.000 0.00 0.00 39.71 3.59
652 676 0.179121 TACGGCAAGCGTCATCGATT 60.179 50.000 0.00 0.00 46.59 3.34
653 677 0.179121 ACGGCAAGCGTCATCGATTA 60.179 50.000 0.00 0.00 43.83 1.75
654 678 0.504384 CGGCAAGCGTCATCGATTAG 59.496 55.000 0.00 0.00 43.83 1.73
655 679 0.861837 GGCAAGCGTCATCGATTAGG 59.138 55.000 0.00 0.00 43.83 2.69
656 680 0.233332 GCAAGCGTCATCGATTAGGC 59.767 55.000 14.75 14.75 43.83 3.93
657 681 0.504384 CAAGCGTCATCGATTAGGCG 59.496 55.000 16.13 11.23 43.83 5.52
658 682 0.102481 AAGCGTCATCGATTAGGCGT 59.898 50.000 16.13 11.67 43.83 5.68
659 683 0.595053 AGCGTCATCGATTAGGCGTG 60.595 55.000 16.13 0.00 39.71 5.34
660 684 1.846648 CGTCATCGATTAGGCGTGC 59.153 57.895 0.00 0.00 39.71 5.34
661 685 1.846648 GTCATCGATTAGGCGTGCG 59.153 57.895 0.00 0.00 0.00 5.34
662 686 0.594028 GTCATCGATTAGGCGTGCGA 60.594 55.000 0.00 0.00 37.17 5.10
663 687 0.313987 TCATCGATTAGGCGTGCGAT 59.686 50.000 0.00 7.50 43.45 4.58
664 688 1.139989 CATCGATTAGGCGTGCGATT 58.860 50.000 0.00 0.00 41.04 3.34
665 689 1.125021 CATCGATTAGGCGTGCGATTC 59.875 52.381 0.00 0.00 41.04 2.52
666 690 0.596600 TCGATTAGGCGTGCGATTCC 60.597 55.000 0.00 0.00 0.00 3.01
667 691 0.874175 CGATTAGGCGTGCGATTCCA 60.874 55.000 0.00 0.00 0.00 3.53
668 692 1.295792 GATTAGGCGTGCGATTCCAA 58.704 50.000 0.00 0.00 0.00 3.53
669 693 1.668751 GATTAGGCGTGCGATTCCAAA 59.331 47.619 0.00 0.00 0.00 3.28
670 694 1.083489 TTAGGCGTGCGATTCCAAAG 58.917 50.000 0.00 0.00 0.00 2.77
671 695 1.366111 TAGGCGTGCGATTCCAAAGC 61.366 55.000 0.00 0.00 0.00 3.51
672 696 2.202479 GCGTGCGATTCCAAAGCC 60.202 61.111 0.00 0.00 0.00 4.35
673 697 2.690778 GCGTGCGATTCCAAAGCCT 61.691 57.895 0.00 0.00 0.00 4.58
674 698 1.366111 GCGTGCGATTCCAAAGCCTA 61.366 55.000 0.00 0.00 0.00 3.93
675 699 0.373716 CGTGCGATTCCAAAGCCTAC 59.626 55.000 0.00 0.00 0.00 3.18
676 700 0.733150 GTGCGATTCCAAAGCCTACC 59.267 55.000 0.00 0.00 0.00 3.18
677 701 0.618458 TGCGATTCCAAAGCCTACCT 59.382 50.000 0.00 0.00 0.00 3.08
678 702 1.300481 GCGATTCCAAAGCCTACCTC 58.700 55.000 0.00 0.00 0.00 3.85
679 703 1.571919 CGATTCCAAAGCCTACCTCG 58.428 55.000 0.00 0.00 0.00 4.63
680 704 1.136305 CGATTCCAAAGCCTACCTCGA 59.864 52.381 0.00 0.00 0.00 4.04
681 705 2.224066 CGATTCCAAAGCCTACCTCGAT 60.224 50.000 0.00 0.00 0.00 3.59
682 706 3.005472 CGATTCCAAAGCCTACCTCGATA 59.995 47.826 0.00 0.00 0.00 2.92
683 707 4.322049 CGATTCCAAAGCCTACCTCGATAT 60.322 45.833 0.00 0.00 0.00 1.63
684 708 4.336889 TTCCAAAGCCTACCTCGATATG 57.663 45.455 0.00 0.00 0.00 1.78
685 709 3.305720 TCCAAAGCCTACCTCGATATGT 58.694 45.455 0.00 0.00 0.00 2.29
686 710 3.709653 TCCAAAGCCTACCTCGATATGTT 59.290 43.478 0.00 0.00 0.00 2.71
687 711 4.058817 CCAAAGCCTACCTCGATATGTTC 58.941 47.826 0.00 0.00 0.00 3.18
688 712 4.442893 CCAAAGCCTACCTCGATATGTTCA 60.443 45.833 0.00 0.00 0.00 3.18
689 713 4.323553 AAGCCTACCTCGATATGTTCAC 57.676 45.455 0.00 0.00 0.00 3.18
690 714 3.296854 AGCCTACCTCGATATGTTCACA 58.703 45.455 0.00 0.00 0.00 3.58
691 715 3.704566 AGCCTACCTCGATATGTTCACAA 59.295 43.478 0.00 0.00 0.00 3.33
692 716 3.802685 GCCTACCTCGATATGTTCACAAC 59.197 47.826 0.00 0.00 0.00 3.32
693 717 4.679639 GCCTACCTCGATATGTTCACAACA 60.680 45.833 0.00 0.00 46.94 3.33
694 718 4.804139 CCTACCTCGATATGTTCACAACAC 59.196 45.833 0.00 0.00 45.50 3.32
695 719 3.596214 ACCTCGATATGTTCACAACACC 58.404 45.455 0.00 0.00 45.50 4.16
696 720 3.007506 ACCTCGATATGTTCACAACACCA 59.992 43.478 0.00 0.00 45.50 4.17
697 721 4.000325 CCTCGATATGTTCACAACACCAA 59.000 43.478 0.00 0.00 45.50 3.67
698 722 4.454161 CCTCGATATGTTCACAACACCAAA 59.546 41.667 0.00 0.00 45.50 3.28
699 723 5.390885 CCTCGATATGTTCACAACACCAAAG 60.391 44.000 0.00 0.00 45.50 2.77
700 724 5.060506 TCGATATGTTCACAACACCAAAGT 58.939 37.500 0.00 0.00 45.50 2.66
701 725 5.178623 TCGATATGTTCACAACACCAAAGTC 59.821 40.000 0.00 0.00 45.50 3.01
702 726 5.049749 CGATATGTTCACAACACCAAAGTCA 60.050 40.000 0.00 0.00 45.50 3.41
703 727 3.840890 TGTTCACAACACCAAAGTCAC 57.159 42.857 0.00 0.00 36.25 3.67
704 728 2.160615 TGTTCACAACACCAAAGTCACG 59.839 45.455 0.00 0.00 36.25 4.35
705 729 0.730265 TCACAACACCAAAGTCACGC 59.270 50.000 0.00 0.00 0.00 5.34
706 730 0.588730 CACAACACCAAAGTCACGCG 60.589 55.000 3.53 3.53 0.00 6.01
707 731 1.022451 ACAACACCAAAGTCACGCGT 61.022 50.000 5.58 5.58 0.00 6.01
708 732 0.931702 CAACACCAAAGTCACGCGTA 59.068 50.000 13.44 0.00 0.00 4.42
709 733 0.932399 AACACCAAAGTCACGCGTAC 59.068 50.000 13.44 11.10 0.00 3.67
710 734 0.179105 ACACCAAAGTCACGCGTACA 60.179 50.000 13.44 0.00 0.00 2.90
711 735 1.144969 CACCAAAGTCACGCGTACAT 58.855 50.000 13.44 0.75 0.00 2.29
712 736 1.126113 CACCAAAGTCACGCGTACATC 59.874 52.381 13.44 2.48 0.00 3.06
721 745 1.137194 CGCGTACATCACCGGTGTA 59.863 57.895 32.74 20.21 0.00 2.90
734 758 0.177836 CGGTGTATGGCCAGTGATCA 59.822 55.000 13.05 2.71 0.00 2.92
761 785 0.179084 TGCCTCGATCGGTGGAATTC 60.179 55.000 24.91 12.03 0.00 2.17
767 791 2.028476 TCGATCGGTGGAATTCAACAGT 60.028 45.455 16.41 2.17 30.96 3.55
773 797 0.250124 TGGAATTCAACAGTCCGCGT 60.250 50.000 4.92 0.00 33.87 6.01
774 798 0.165944 GGAATTCAACAGTCCGCGTG 59.834 55.000 4.92 0.00 0.00 5.34
775 799 1.144969 GAATTCAACAGTCCGCGTGA 58.855 50.000 4.92 0.00 0.00 4.35
776 800 0.865769 AATTCAACAGTCCGCGTGAC 59.134 50.000 16.80 16.80 44.82 3.67
783 807 3.167945 GTCCGCGTGACGTAACCG 61.168 66.667 6.91 0.80 41.42 4.44
811 846 1.157870 AACGACACTGGGAGCAAACG 61.158 55.000 0.00 0.00 0.00 3.60
893 928 2.475466 GCCTCCGACCGTCGATGTA 61.475 63.158 22.40 4.08 43.74 2.29
902 937 4.615961 CCGACCGTCGATGTAAAATATCTC 59.384 45.833 22.40 0.00 43.74 2.75
904 939 5.564504 CGACCGTCGATGTAAAATATCTCTC 59.435 44.000 16.03 0.00 43.74 3.20
1019 1067 1.729267 ATGCCTCCCACCACCAAGTT 61.729 55.000 0.00 0.00 0.00 2.66
1020 1068 1.603739 GCCTCCCACCACCAAGTTC 60.604 63.158 0.00 0.00 0.00 3.01
1021 1069 1.074951 CCTCCCACCACCAAGTTCC 59.925 63.158 0.00 0.00 0.00 3.62
1022 1070 1.427072 CCTCCCACCACCAAGTTCCT 61.427 60.000 0.00 0.00 0.00 3.36
1023 1071 0.036875 CTCCCACCACCAAGTTCCTC 59.963 60.000 0.00 0.00 0.00 3.71
1024 1072 1.074951 CCCACCACCAAGTTCCTCC 59.925 63.158 0.00 0.00 0.00 4.30
1032 1080 1.199615 CCAAGTTCCTCCTCCTCCTC 58.800 60.000 0.00 0.00 0.00 3.71
1040 1088 2.015726 TCCTCCTCCTCCTCCTCCC 61.016 68.421 0.00 0.00 0.00 4.30
1150 1201 3.007516 CGTTCAAACGCGGTGTCA 58.992 55.556 12.47 0.00 46.06 3.58
1153 1204 0.587985 GTTCAAACGCGGTGTCACAC 60.588 55.000 12.47 0.00 0.00 3.82
1242 1293 4.643387 AGCAACCGGACTGGCCAC 62.643 66.667 9.46 0.00 43.94 5.01
1348 1399 7.936301 GCCAGATAAGTCCATCTCTATTTTCTT 59.064 37.037 0.00 0.00 32.83 2.52
1389 1440 0.734889 ATCTCGCCTGCAATTTTCCG 59.265 50.000 0.00 0.00 0.00 4.30
1462 1513 4.828072 AACTTGAGATACCTGAACCTCC 57.172 45.455 0.00 0.00 0.00 4.30
1464 1515 2.940514 TGAGATACCTGAACCTCCCA 57.059 50.000 0.00 0.00 0.00 4.37
1476 1604 1.933021 ACCTCCCATGTACAAGTCGA 58.067 50.000 0.00 0.00 0.00 4.20
1528 1656 4.285863 ACCTCTCTAAGCTGCAGTATCTT 58.714 43.478 16.64 12.53 0.00 2.40
1556 1684 3.368248 TCCTACACCACCTACACCATAC 58.632 50.000 0.00 0.00 0.00 2.39
1557 1685 2.100252 CCTACACCACCTACACCATACG 59.900 54.545 0.00 0.00 0.00 3.06
1558 1686 0.248289 ACACCACCTACACCATACGC 59.752 55.000 0.00 0.00 0.00 4.42
1675 1803 4.793731 CCTCGTATCGTGAATATGATTCCG 59.206 45.833 0.00 1.48 35.72 4.30
1697 1825 5.409826 CCGTCTTTGCAAGTTCTCTATCTTT 59.590 40.000 0.00 0.00 0.00 2.52
1709 1837 3.764434 TCTCTATCTTTCTGGTTGCTCGT 59.236 43.478 0.00 0.00 0.00 4.18
1717 1845 5.529430 TCTTTCTGGTTGCTCGTTTCATAAA 59.471 36.000 0.00 0.00 0.00 1.40
1740 1868 2.281761 CCAACAGCTCCCACGCTT 60.282 61.111 0.00 0.00 38.41 4.68
1742 1870 1.597854 CAACAGCTCCCACGCTTGA 60.598 57.895 0.00 0.00 38.41 3.02
1748 1876 1.371183 CTCCCACGCTTGAACCTCA 59.629 57.895 0.00 0.00 0.00 3.86
1847 1975 4.608948 AGTCTCAAGTACCTCAACCTTG 57.391 45.455 0.00 0.00 37.51 3.61
1999 2127 6.029346 AGAAACCTATGCAATTTGGAAGTG 57.971 37.500 0.00 0.00 0.00 3.16
2012 2140 5.923733 TTTGGAAGTGCTAAACCTTGAAA 57.076 34.783 0.00 0.00 0.00 2.69
2096 2224 4.636206 GCCCACTAAGAGAACTGTATTTGG 59.364 45.833 0.00 0.00 0.00 3.28
2122 2250 3.652057 AACAATATCACTGGGACCCTG 57.348 47.619 15.59 15.59 0.00 4.45
2138 2266 3.949885 CTGCCAGCTGGGATTGCCA 62.950 63.158 33.46 19.98 40.01 4.92
2143 2271 1.279846 CCAGCTGGGATTGCCAAATTT 59.720 47.619 26.14 0.00 40.01 1.82
2157 2285 3.663025 CCAAATTTACCAGTTTGGCCAG 58.337 45.455 5.11 0.00 45.37 4.85
2162 2290 0.320374 TACCAGTTTGGCCAGTCTCG 59.680 55.000 5.11 3.91 42.67 4.04
2178 2306 2.288458 GTCTCGTCCTCTCTGATAACCG 59.712 54.545 0.00 0.00 0.00 4.44
2190 2318 4.274978 TCTGATAACCGTATGACTGGACA 58.725 43.478 0.00 0.00 0.00 4.02
2191 2319 4.893524 TCTGATAACCGTATGACTGGACAT 59.106 41.667 0.00 0.00 0.00 3.06
2213 2341 0.464554 GCCCACTGAGATTGGTAGGC 60.465 60.000 0.00 0.00 33.70 3.93
2293 2421 6.015504 CGAAGAACATTTCTATGGTTTCACG 58.984 40.000 0.00 0.00 39.61 4.35
2382 2510 2.941720 CCCTGAAACTAGAGCAAGCATC 59.058 50.000 0.00 0.00 0.00 3.91
2408 2536 3.201930 TGCATCTTGCCAAATAGGTCCTA 59.798 43.478 0.00 0.00 44.23 2.94
2467 2595 8.183536 GCTGATTACATTGATATGTCAAACACA 58.816 33.333 9.08 4.06 46.67 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 0.596577 CTCACTCTCGACGGGACAAA 59.403 55.000 0.00 0.00 0.00 2.83
268 270 1.450848 GCTGCTGCTGATGCCACTA 60.451 57.895 10.92 0.00 38.71 2.74
269 271 2.750637 GCTGCTGCTGATGCCACT 60.751 61.111 10.92 0.00 38.71 4.00
329 344 3.008923 TGTTGGTAATCAGAGCCATGTCA 59.991 43.478 0.00 0.00 31.71 3.58
465 484 6.914665 TGTAACCAGTAGGCCTAGTCTATAA 58.085 40.000 17.74 0.00 39.06 0.98
513 534 5.748630 TCATGTCACGTTATGTAATCTCTGC 59.251 40.000 0.00 0.00 0.00 4.26
553 577 0.817013 CACAATGGTTTGGCCGCTAT 59.183 50.000 0.00 0.00 41.21 2.97
554 578 0.538516 ACACAATGGTTTGGCCGCTA 60.539 50.000 0.00 0.00 41.21 4.26
555 579 1.398958 AACACAATGGTTTGGCCGCT 61.399 50.000 0.00 0.00 41.21 5.52
556 580 0.531753 AAACACAATGGTTTGGCCGC 60.532 50.000 0.00 0.00 39.40 6.53
557 581 1.946745 AAAACACAATGGTTTGGCCG 58.053 45.000 0.00 0.00 35.67 6.13
562 586 5.600696 GATGAGTCCAAAACACAATGGTTT 58.399 37.500 0.00 0.00 37.86 3.27
563 587 4.261572 CGATGAGTCCAAAACACAATGGTT 60.262 41.667 0.00 0.00 37.94 3.67
564 588 3.253188 CGATGAGTCCAAAACACAATGGT 59.747 43.478 0.00 0.00 37.94 3.55
565 589 3.253188 ACGATGAGTCCAAAACACAATGG 59.747 43.478 0.00 0.00 38.09 3.16
566 590 4.488126 ACGATGAGTCCAAAACACAATG 57.512 40.909 0.00 0.00 31.98 2.82
567 591 5.995282 TCTAACGATGAGTCCAAAACACAAT 59.005 36.000 0.00 0.00 31.98 2.71
568 592 5.361427 TCTAACGATGAGTCCAAAACACAA 58.639 37.500 0.00 0.00 31.98 3.33
569 593 4.951254 TCTAACGATGAGTCCAAAACACA 58.049 39.130 0.00 0.00 32.80 3.72
570 594 6.481954 AATCTAACGATGAGTCCAAAACAC 57.518 37.500 0.00 0.00 0.00 3.32
571 595 6.485313 ACAAATCTAACGATGAGTCCAAAACA 59.515 34.615 0.00 0.00 0.00 2.83
572 596 6.899114 ACAAATCTAACGATGAGTCCAAAAC 58.101 36.000 0.00 0.00 0.00 2.43
573 597 7.504924 AACAAATCTAACGATGAGTCCAAAA 57.495 32.000 0.00 0.00 0.00 2.44
574 598 7.012894 ACAAACAAATCTAACGATGAGTCCAAA 59.987 33.333 0.00 0.00 0.00 3.28
575 599 6.485313 ACAAACAAATCTAACGATGAGTCCAA 59.515 34.615 0.00 0.00 0.00 3.53
576 600 5.995282 ACAAACAAATCTAACGATGAGTCCA 59.005 36.000 0.00 0.00 0.00 4.02
577 601 6.481954 ACAAACAAATCTAACGATGAGTCC 57.518 37.500 0.00 0.00 0.00 3.85
578 602 7.453838 GGTACAAACAAATCTAACGATGAGTC 58.546 38.462 0.00 0.00 0.00 3.36
579 603 6.090358 CGGTACAAACAAATCTAACGATGAGT 59.910 38.462 0.00 0.00 0.00 3.41
580 604 6.090358 ACGGTACAAACAAATCTAACGATGAG 59.910 38.462 0.00 0.00 0.00 2.90
581 605 5.927689 ACGGTACAAACAAATCTAACGATGA 59.072 36.000 0.00 0.00 0.00 2.92
582 606 6.160664 ACGGTACAAACAAATCTAACGATG 57.839 37.500 0.00 0.00 0.00 3.84
583 607 6.128472 GGAACGGTACAAACAAATCTAACGAT 60.128 38.462 0.00 0.00 0.00 3.73
584 608 5.177327 GGAACGGTACAAACAAATCTAACGA 59.823 40.000 0.00 0.00 0.00 3.85
585 609 5.376537 GGAACGGTACAAACAAATCTAACG 58.623 41.667 0.00 0.00 0.00 3.18
586 610 5.471116 AGGGAACGGTACAAACAAATCTAAC 59.529 40.000 0.00 0.00 0.00 2.34
587 611 5.470777 CAGGGAACGGTACAAACAAATCTAA 59.529 40.000 0.00 0.00 0.00 2.10
588 612 4.998672 CAGGGAACGGTACAAACAAATCTA 59.001 41.667 0.00 0.00 0.00 1.98
589 613 3.818773 CAGGGAACGGTACAAACAAATCT 59.181 43.478 0.00 0.00 0.00 2.40
590 614 3.566742 ACAGGGAACGGTACAAACAAATC 59.433 43.478 0.00 0.00 36.82 2.17
591 615 3.558033 ACAGGGAACGGTACAAACAAAT 58.442 40.909 0.00 0.00 36.82 2.32
592 616 2.944349 GACAGGGAACGGTACAAACAAA 59.056 45.455 0.00 0.00 39.51 2.83
593 617 2.563702 GACAGGGAACGGTACAAACAA 58.436 47.619 0.00 0.00 39.51 2.83
594 618 1.202675 GGACAGGGAACGGTACAAACA 60.203 52.381 0.00 0.00 39.45 2.83
595 619 1.516161 GGACAGGGAACGGTACAAAC 58.484 55.000 0.00 0.00 39.45 2.93
596 620 0.033781 CGGACAGGGAACGGTACAAA 59.966 55.000 0.00 0.00 39.65 2.83
597 621 1.667151 CGGACAGGGAACGGTACAA 59.333 57.895 0.00 0.00 39.65 2.41
598 622 2.277591 CCGGACAGGGAACGGTACA 61.278 63.158 0.00 0.00 39.65 2.90
599 623 2.575461 CCGGACAGGGAACGGTAC 59.425 66.667 0.00 0.00 42.53 3.34
635 659 0.504384 CTAATCGATGACGCTTGCCG 59.496 55.000 0.00 0.00 44.21 5.69
636 660 0.861837 CCTAATCGATGACGCTTGCC 59.138 55.000 0.00 0.00 39.58 4.52
637 661 0.233332 GCCTAATCGATGACGCTTGC 59.767 55.000 0.00 0.00 39.58 4.01
638 662 0.504384 CGCCTAATCGATGACGCTTG 59.496 55.000 0.00 0.00 39.58 4.01
639 663 0.102481 ACGCCTAATCGATGACGCTT 59.898 50.000 0.00 0.00 39.58 4.68
640 664 0.595053 CACGCCTAATCGATGACGCT 60.595 55.000 0.00 0.00 39.58 5.07
641 665 1.846648 CACGCCTAATCGATGACGC 59.153 57.895 0.00 0.00 39.58 5.19
642 666 1.846648 GCACGCCTAATCGATGACG 59.153 57.895 0.00 3.31 41.26 4.35
643 667 0.594028 TCGCACGCCTAATCGATGAC 60.594 55.000 0.00 0.00 0.00 3.06
644 668 0.313987 ATCGCACGCCTAATCGATGA 59.686 50.000 0.00 0.00 39.78 2.92
645 669 1.125021 GAATCGCACGCCTAATCGATG 59.875 52.381 0.00 0.00 40.91 3.84
646 670 1.419374 GAATCGCACGCCTAATCGAT 58.581 50.000 0.00 0.00 42.60 3.59
647 671 0.596600 GGAATCGCACGCCTAATCGA 60.597 55.000 0.00 0.00 35.34 3.59
648 672 0.874175 TGGAATCGCACGCCTAATCG 60.874 55.000 0.00 0.00 0.00 3.34
649 673 1.295792 TTGGAATCGCACGCCTAATC 58.704 50.000 0.00 0.00 0.00 1.75
650 674 1.670811 CTTTGGAATCGCACGCCTAAT 59.329 47.619 0.00 0.00 0.00 1.73
651 675 1.083489 CTTTGGAATCGCACGCCTAA 58.917 50.000 0.00 0.00 0.00 2.69
652 676 1.366111 GCTTTGGAATCGCACGCCTA 61.366 55.000 0.00 0.00 0.00 3.93
653 677 2.690778 GCTTTGGAATCGCACGCCT 61.691 57.895 0.00 0.00 0.00 5.52
654 678 2.202479 GCTTTGGAATCGCACGCC 60.202 61.111 0.00 0.00 0.00 5.68
655 679 1.366111 TAGGCTTTGGAATCGCACGC 61.366 55.000 0.00 0.00 0.00 5.34
656 680 0.373716 GTAGGCTTTGGAATCGCACG 59.626 55.000 0.00 0.00 0.00 5.34
657 681 0.733150 GGTAGGCTTTGGAATCGCAC 59.267 55.000 0.00 0.00 0.00 5.34
658 682 0.618458 AGGTAGGCTTTGGAATCGCA 59.382 50.000 0.00 0.00 0.00 5.10
659 683 1.300481 GAGGTAGGCTTTGGAATCGC 58.700 55.000 0.00 0.00 0.00 4.58
660 684 1.136305 TCGAGGTAGGCTTTGGAATCG 59.864 52.381 0.00 0.00 0.00 3.34
661 685 2.981859 TCGAGGTAGGCTTTGGAATC 57.018 50.000 0.00 0.00 0.00 2.52
662 686 4.348168 ACATATCGAGGTAGGCTTTGGAAT 59.652 41.667 0.00 0.00 0.00 3.01
663 687 3.709653 ACATATCGAGGTAGGCTTTGGAA 59.290 43.478 0.00 0.00 0.00 3.53
664 688 3.305720 ACATATCGAGGTAGGCTTTGGA 58.694 45.455 0.00 0.00 0.00 3.53
665 689 3.753294 ACATATCGAGGTAGGCTTTGG 57.247 47.619 0.00 0.00 0.00 3.28
666 690 4.508124 GTGAACATATCGAGGTAGGCTTTG 59.492 45.833 0.00 0.00 0.00 2.77
667 691 4.161565 TGTGAACATATCGAGGTAGGCTTT 59.838 41.667 0.00 0.00 0.00 3.51
668 692 3.704566 TGTGAACATATCGAGGTAGGCTT 59.295 43.478 0.00 0.00 0.00 4.35
669 693 3.296854 TGTGAACATATCGAGGTAGGCT 58.703 45.455 0.00 0.00 0.00 4.58
670 694 3.728076 TGTGAACATATCGAGGTAGGC 57.272 47.619 0.00 0.00 0.00 3.93
671 695 4.804139 GTGTTGTGAACATATCGAGGTAGG 59.196 45.833 0.00 0.00 44.35 3.18
672 696 4.804139 GGTGTTGTGAACATATCGAGGTAG 59.196 45.833 0.00 0.00 44.35 3.18
673 697 4.221041 TGGTGTTGTGAACATATCGAGGTA 59.779 41.667 0.00 0.00 44.35 3.08
674 698 3.007506 TGGTGTTGTGAACATATCGAGGT 59.992 43.478 0.00 0.00 44.35 3.85
675 699 3.595173 TGGTGTTGTGAACATATCGAGG 58.405 45.455 0.00 0.00 44.35 4.63
676 700 5.179368 ACTTTGGTGTTGTGAACATATCGAG 59.821 40.000 0.00 0.00 44.35 4.04
677 701 5.060506 ACTTTGGTGTTGTGAACATATCGA 58.939 37.500 0.00 0.00 44.35 3.59
678 702 5.049749 TGACTTTGGTGTTGTGAACATATCG 60.050 40.000 0.00 0.00 44.35 2.92
679 703 6.142817 GTGACTTTGGTGTTGTGAACATATC 58.857 40.000 0.00 0.00 44.35 1.63
680 704 5.277779 CGTGACTTTGGTGTTGTGAACATAT 60.278 40.000 0.00 0.00 44.35 1.78
681 705 4.034626 CGTGACTTTGGTGTTGTGAACATA 59.965 41.667 0.00 0.00 44.35 2.29
682 706 3.181501 CGTGACTTTGGTGTTGTGAACAT 60.182 43.478 0.00 0.00 44.35 2.71
683 707 2.160615 CGTGACTTTGGTGTTGTGAACA 59.839 45.455 0.00 0.00 39.52 3.18
684 708 2.780993 CGTGACTTTGGTGTTGTGAAC 58.219 47.619 0.00 0.00 0.00 3.18
685 709 1.131504 GCGTGACTTTGGTGTTGTGAA 59.868 47.619 0.00 0.00 0.00 3.18
686 710 0.730265 GCGTGACTTTGGTGTTGTGA 59.270 50.000 0.00 0.00 0.00 3.58
687 711 0.588730 CGCGTGACTTTGGTGTTGTG 60.589 55.000 0.00 0.00 0.00 3.33
688 712 1.022451 ACGCGTGACTTTGGTGTTGT 61.022 50.000 12.93 0.00 0.00 3.32
689 713 0.931702 TACGCGTGACTTTGGTGTTG 59.068 50.000 24.59 0.00 0.00 3.33
690 714 0.932399 GTACGCGTGACTTTGGTGTT 59.068 50.000 24.59 0.00 0.00 3.32
691 715 0.179105 TGTACGCGTGACTTTGGTGT 60.179 50.000 24.59 0.00 0.00 4.16
692 716 1.126113 GATGTACGCGTGACTTTGGTG 59.874 52.381 24.59 0.00 0.00 4.17
693 717 1.269883 TGATGTACGCGTGACTTTGGT 60.270 47.619 24.59 0.00 0.00 3.67
694 718 1.126113 GTGATGTACGCGTGACTTTGG 59.874 52.381 24.59 0.00 0.00 3.28
695 719 1.126113 GGTGATGTACGCGTGACTTTG 59.874 52.381 24.59 0.00 0.00 2.77
696 720 1.425412 GGTGATGTACGCGTGACTTT 58.575 50.000 24.59 8.07 0.00 2.66
697 721 0.731514 CGGTGATGTACGCGTGACTT 60.732 55.000 24.59 13.61 0.00 3.01
698 722 1.154093 CGGTGATGTACGCGTGACT 60.154 57.895 24.59 5.37 0.00 3.41
699 723 2.156446 CCGGTGATGTACGCGTGAC 61.156 63.158 24.59 16.11 0.00 3.67
700 724 2.179767 CCGGTGATGTACGCGTGA 59.820 61.111 24.59 8.87 0.00 4.35
701 725 2.126228 ACCGGTGATGTACGCGTG 60.126 61.111 24.59 3.61 0.00 5.34
702 726 1.585267 TACACCGGTGATGTACGCGT 61.585 55.000 40.21 19.17 0.00 6.01
703 727 0.248743 ATACACCGGTGATGTACGCG 60.249 55.000 40.21 11.64 35.43 6.01
704 728 1.205657 CATACACCGGTGATGTACGC 58.794 55.000 40.21 0.00 35.43 4.42
705 729 1.847818 CCATACACCGGTGATGTACG 58.152 55.000 40.21 19.98 35.43 3.67
706 730 1.578583 GCCATACACCGGTGATGTAC 58.421 55.000 40.21 24.36 35.43 2.90
707 731 0.466543 GGCCATACACCGGTGATGTA 59.533 55.000 40.21 22.70 36.98 2.29
708 732 1.223487 GGCCATACACCGGTGATGT 59.777 57.895 40.21 21.17 0.00 3.06
709 733 0.815213 CTGGCCATACACCGGTGATG 60.815 60.000 40.21 32.04 0.00 3.07
710 734 1.271840 ACTGGCCATACACCGGTGAT 61.272 55.000 40.21 24.69 45.28 3.06
711 735 1.916273 ACTGGCCATACACCGGTGA 60.916 57.895 40.21 23.58 45.28 4.02
712 736 2.668632 ACTGGCCATACACCGGTG 59.331 61.111 32.83 32.83 45.28 4.94
721 745 0.761187 ACGCTATGATCACTGGCCAT 59.239 50.000 5.51 0.00 0.00 4.40
734 758 1.008424 CGATCGAGGCACACGCTAT 60.008 57.895 10.26 0.00 43.29 2.97
761 785 0.935831 TTACGTCACGCGGACTGTTG 60.936 55.000 20.38 6.06 44.68 3.33
777 801 2.670210 CGTTCGCCCCAACGGTTAC 61.670 63.158 0.00 0.00 44.43 2.50
778 802 2.357275 CGTTCGCCCCAACGGTTA 60.357 61.111 0.00 0.00 44.43 2.85
783 807 2.280592 AGTGTCGTTCGCCCCAAC 60.281 61.111 0.00 0.00 0.00 3.77
784 808 2.280524 CAGTGTCGTTCGCCCCAA 60.281 61.111 0.00 0.00 0.00 4.12
811 846 3.614616 CGCCTTGAGTCAAGTCTATGTTC 59.385 47.826 27.07 8.23 39.58 3.18
885 920 8.074972 ACGGTAAGAGAGATATTTTACATCGAC 58.925 37.037 0.00 0.00 0.00 4.20
888 923 8.358148 TGGACGGTAAGAGAGATATTTTACATC 58.642 37.037 0.00 0.00 0.00 3.06
890 925 7.341256 ACTGGACGGTAAGAGAGATATTTTACA 59.659 37.037 0.00 0.00 0.00 2.41
893 928 6.793505 ACTGGACGGTAAGAGAGATATTTT 57.206 37.500 0.00 0.00 0.00 1.82
902 937 6.531948 CAGAAGAATTAACTGGACGGTAAGAG 59.468 42.308 0.00 0.00 0.00 2.85
904 939 6.164176 ACAGAAGAATTAACTGGACGGTAAG 58.836 40.000 0.00 0.00 36.17 2.34
1019 1067 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
1020 1068 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
1021 1069 1.541672 GGAGGAGGAGGAGGAGGAG 59.458 68.421 0.00 0.00 0.00 3.69
1022 1070 2.015726 GGGAGGAGGAGGAGGAGGA 61.016 68.421 0.00 0.00 0.00 3.71
1023 1071 2.612251 GGGAGGAGGAGGAGGAGG 59.388 72.222 0.00 0.00 0.00 4.30
1024 1072 2.612251 GGGGAGGAGGAGGAGGAG 59.388 72.222 0.00 0.00 0.00 3.69
1032 1080 4.410400 GTTGCCACGGGGAGGAGG 62.410 72.222 8.67 0.00 35.59 4.30
1150 1201 3.717294 GCCCGAGGGGTCATGTGT 61.717 66.667 10.61 0.00 46.51 3.72
1242 1293 0.734253 CAAGTCGAAGCTGGAGGACG 60.734 60.000 0.00 0.00 34.68 4.79
1348 1399 0.112995 AGGTGCTCCAAATGCTCCAA 59.887 50.000 7.70 0.00 43.95 3.53
1389 1440 6.961359 TGACCGCAATTGCTACATATATAC 57.039 37.500 26.86 7.86 39.32 1.47
1462 1513 3.993736 TGTTGTCATCGACTTGTACATGG 59.006 43.478 12.86 4.52 33.15 3.66
1464 1515 3.673338 CGTGTTGTCATCGACTTGTACAT 59.327 43.478 0.00 0.00 33.15 2.29
1476 1604 1.260561 GACGAAGCAACGTGTTGTCAT 59.739 47.619 13.73 1.44 46.52 3.06
1528 1656 2.112279 AGGTGGTGTAGGAAAGGTCA 57.888 50.000 0.00 0.00 0.00 4.02
1556 1684 0.317770 AAATCTGTTGGTTGCACGCG 60.318 50.000 3.53 3.53 0.00 6.01
1557 1685 1.851658 AAAATCTGTTGGTTGCACGC 58.148 45.000 0.00 0.00 0.00 5.34
1589 1717 5.700402 AGATGGTGTAGCAAAGGTAGATT 57.300 39.130 0.00 0.00 0.00 2.40
1655 1783 5.391449 AGACGGAATCATATTCACGATACG 58.609 41.667 13.62 0.00 0.00 3.06
1697 1825 3.188460 GCTTTATGAAACGAGCAACCAGA 59.812 43.478 0.00 0.00 35.29 3.86
1709 1837 3.640967 AGCTGTTGGTTGGCTTTATGAAA 59.359 39.130 0.00 0.00 31.81 2.69
1717 1845 2.116125 GGGAGCTGTTGGTTGGCT 59.884 61.111 0.00 0.00 39.16 4.75
1748 1876 4.723309 AGATCAAGCCTCTCAAGTTTTGT 58.277 39.130 0.00 0.00 0.00 2.83
1847 1975 6.590234 ATGACCATACAAAAAGGTTTCTCC 57.410 37.500 0.00 0.00 35.36 3.71
2012 2140 1.209747 GTTCCCATACGAGAGGCCTTT 59.790 52.381 6.77 0.00 0.00 3.11
2036 2164 3.594134 GCAAGCTCTCATACAACTCTGT 58.406 45.455 0.00 0.00 39.75 3.41
2076 2204 7.331026 TCCATCCAAATACAGTTCTCTTAGTG 58.669 38.462 0.00 0.00 0.00 2.74
2096 2224 4.580580 GGTCCCAGTGATATTGTTTCCATC 59.419 45.833 0.00 0.00 0.00 3.51
2122 2250 1.619807 ATTTGGCAATCCCAGCTGGC 61.620 55.000 28.39 15.24 46.39 4.85
2138 2266 4.223144 AGACTGGCCAAACTGGTAAATTT 58.777 39.130 7.01 0.00 40.46 1.82
2143 2271 0.320374 CGAGACTGGCCAAACTGGTA 59.680 55.000 7.01 0.00 40.46 3.25
2157 2285 2.288458 CGGTTATCAGAGAGGACGAGAC 59.712 54.545 0.00 0.00 0.00 3.36
2162 2290 4.822896 AGTCATACGGTTATCAGAGAGGAC 59.177 45.833 0.00 0.00 0.00 3.85
2178 2306 1.065491 TGGGCACATGTCCAGTCATAC 60.065 52.381 0.00 0.00 46.36 2.39
2190 2318 0.700564 ACCAATCTCAGTGGGCACAT 59.299 50.000 0.00 0.00 40.75 3.21
2191 2319 1.278985 CTACCAATCTCAGTGGGCACA 59.721 52.381 0.00 0.00 40.75 4.57
2213 2341 4.392138 GTCTAGGGAAATCAAACCGTTGAG 59.608 45.833 0.00 0.00 46.75 3.02
2331 2459 6.799827 AGCAGACCAGGATCTAGTATAATCT 58.200 40.000 0.00 0.00 0.00 2.40
2362 2490 3.871485 AGATGCTTGCTCTAGTTTCAGG 58.129 45.455 0.00 0.00 0.00 3.86
2408 2536 3.230976 ACCGAAGCCAAGAAGGAAAATT 58.769 40.909 0.00 0.00 41.22 1.82


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

AutoCloner maintained by Alex Coulton.