Multiple sequence alignment - TraesCS2A01G213400

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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 TraesCS2A01G213400 chr2A 100.000 4191 0 0 1 4191 198742445 198746635 0.000000e+00 7740.0
1 TraesCS2A01G213400 chr2D 92.902 2522 79 34 1730 4191 186314234 186316715 0.000000e+00 3574.0
2 TraesCS2A01G213400 chr2D 93.391 696 26 11 1050 1726 186313387 186314081 0.000000e+00 1013.0
3 TraesCS2A01G213400 chr2D 96.134 569 17 4 1 566 186312201 186312767 0.000000e+00 924.0
4 TraesCS2A01G213400 chr2D 97.030 202 6 0 810 1011 186312883 186313084 1.440000e-89 340.0
5 TraesCS2A01G213400 chr2D 94.309 123 4 3 728 847 186312767 186312889 7.160000e-43 185.0
6 TraesCS2A01G213400 chr2D 92.647 68 2 1 3217 3284 186315769 186315833 1.240000e-15 95.3
7 TraesCS2A01G213400 chr2B 88.474 1553 73 34 1730 3222 239507844 239509350 0.000000e+00 1779.0
8 TraesCS2A01G213400 chr2B 88.070 570 16 22 728 1245 239506769 239507338 2.750000e-176 628.0
9 TraesCS2A01G213400 chr2B 86.475 451 34 16 1296 1726 239507333 239507776 1.760000e-128 470.0
10 TraesCS2A01G213400 chr2B 85.174 344 22 11 124 443 239506405 239506743 4.040000e-85 326.0
11 TraesCS2A01G213400 chr7B 86.538 104 12 2 604 707 439553847 439553948 3.420000e-21 113.0
12 TraesCS2A01G213400 chr7B 88.764 89 7 3 628 713 25880373 25880285 5.730000e-19 106.0
13 TraesCS2A01G213400 chr4A 93.421 76 5 0 631 706 616411770 616411845 3.420000e-21 113.0
14 TraesCS2A01G213400 chr5D 89.535 86 9 0 631 716 288133392 288133477 4.430000e-20 110.0
15 TraesCS2A01G213400 chr5D 91.026 78 7 0 631 708 377315088 377315165 5.730000e-19 106.0
16 TraesCS2A01G213400 chr3B 93.243 74 5 0 631 704 385088945 385088872 4.430000e-20 110.0
17 TraesCS2A01G213400 chr1A 93.243 74 5 0 636 709 9839334 9839261 4.430000e-20 110.0
18 TraesCS2A01G213400 chr5B 89.535 86 7 2 631 716 463194661 463194578 1.590000e-19 108.0
19 TraesCS2A01G213400 chr3A 92.105 76 6 0 631 706 663477940 663478015 1.590000e-19 108.0


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 TraesCS2A01G213400 chr2A 198742445 198746635 4190 False 7740.000000 7740 100.000000 1 4191 1 chr2A.!!$F1 4190
1 TraesCS2A01G213400 chr2D 186312201 186316715 4514 False 1021.883333 3574 94.402167 1 4191 6 chr2D.!!$F1 4190
2 TraesCS2A01G213400 chr2B 239506405 239509350 2945 False 800.750000 1779 87.048250 124 3222 4 chr2B.!!$F1 3098

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
646 672 0.106669 GGCCCTTCCCACCTATTGAC 60.107 60.0 0.0 0.0 0.0 3.18 F
647 673 0.106669 GCCCTTCCCACCTATTGACC 60.107 60.0 0.0 0.0 0.0 4.02 F
2568 3144 0.038892 CAGCAGCTTTCGCCAAATGT 60.039 50.0 0.0 0.0 36.6 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2214 2759 0.179026 CCATGGCAGTGAGATGGGAG 60.179 60.0 0.0 0.0 34.14 4.30 R
2617 3194 0.451783 CCGCCAAGTAAACATCAGGC 59.548 55.0 0.0 0.0 38.73 4.85 R
3939 4567 0.246910 GTCGGAACCACTTCTCCCTC 59.753 60.0 0.0 0.0 0.00 4.30 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
34 35 2.112297 GGGCGTCAACTGGGAACA 59.888 61.111 0.00 0.00 39.59 3.18
37 38 1.507141 GGCGTCAACTGGGAACACAG 61.507 60.000 2.28 2.28 44.03 3.66
44 45 4.308458 TGGGAACACAGTCGCCCG 62.308 66.667 0.00 0.00 43.70 6.13
70 71 1.720694 CCAAGCAAACACCGGTTCGT 61.721 55.000 2.97 0.00 35.82 3.85
73 74 2.900167 GCAAACACCGGTTCGTCCC 61.900 63.158 2.97 0.00 35.82 4.46
74 75 1.524165 CAAACACCGGTTCGTCCCA 60.524 57.895 2.97 0.00 35.82 4.37
75 76 1.227734 AAACACCGGTTCGTCCCAG 60.228 57.895 2.97 0.00 35.82 4.45
203 206 0.322975 CAGTGCAGTTGGCTAGGAGT 59.677 55.000 0.00 0.00 45.15 3.85
245 255 5.392380 CGCAAGAAAATGTCAGGCTATTTCT 60.392 40.000 0.00 0.00 40.90 2.52
381 403 2.962827 GACTGTCGAGACGTCCGCA 61.963 63.158 13.01 15.09 32.66 5.69
468 494 0.464036 TGGATCGATTTGCTACGGCT 59.536 50.000 0.00 0.00 39.59 5.52
566 592 1.819208 GCATGCATGGTGCTCCGTA 60.819 57.895 27.34 0.00 45.31 4.02
567 593 1.375853 GCATGCATGGTGCTCCGTAA 61.376 55.000 27.34 0.00 45.31 3.18
568 594 1.093972 CATGCATGGTGCTCCGTAAA 58.906 50.000 19.40 0.00 45.31 2.01
569 595 1.472082 CATGCATGGTGCTCCGTAAAA 59.528 47.619 19.40 0.00 45.31 1.52
570 596 0.878416 TGCATGGTGCTCCGTAAAAC 59.122 50.000 0.00 0.00 45.31 2.43
571 597 0.170339 GCATGGTGCTCCGTAAAACC 59.830 55.000 0.00 0.00 40.96 3.27
572 598 1.821216 CATGGTGCTCCGTAAAACCT 58.179 50.000 0.00 0.00 36.30 3.50
573 599 2.159382 CATGGTGCTCCGTAAAACCTT 58.841 47.619 0.00 0.00 36.30 3.50
574 600 1.600023 TGGTGCTCCGTAAAACCTTG 58.400 50.000 0.00 0.00 36.30 3.61
575 601 1.134037 TGGTGCTCCGTAAAACCTTGT 60.134 47.619 0.00 0.00 36.30 3.16
576 602 2.104451 TGGTGCTCCGTAAAACCTTGTA 59.896 45.455 0.00 0.00 36.30 2.41
577 603 3.140623 GGTGCTCCGTAAAACCTTGTAA 58.859 45.455 0.00 0.00 0.00 2.41
578 604 3.058708 GGTGCTCCGTAAAACCTTGTAAC 60.059 47.826 0.00 0.00 0.00 2.50
579 605 3.811497 GTGCTCCGTAAAACCTTGTAACT 59.189 43.478 0.00 0.00 0.00 2.24
580 606 4.060205 TGCTCCGTAAAACCTTGTAACTC 58.940 43.478 0.00 0.00 0.00 3.01
581 607 3.122445 GCTCCGTAAAACCTTGTAACTCG 59.878 47.826 0.00 0.00 0.00 4.18
582 608 4.301628 CTCCGTAAAACCTTGTAACTCGT 58.698 43.478 0.00 0.00 0.00 4.18
583 609 5.446143 TCCGTAAAACCTTGTAACTCGTA 57.554 39.130 0.00 0.00 0.00 3.43
584 610 5.837437 TCCGTAAAACCTTGTAACTCGTAA 58.163 37.500 0.00 0.00 0.00 3.18
585 611 5.689961 TCCGTAAAACCTTGTAACTCGTAAC 59.310 40.000 0.00 0.00 0.00 2.50
586 612 5.691754 CCGTAAAACCTTGTAACTCGTAACT 59.308 40.000 0.00 0.00 0.00 2.24
587 613 6.129088 CCGTAAAACCTTGTAACTCGTAACTC 60.129 42.308 0.00 0.00 0.00 3.01
588 614 6.417635 CGTAAAACCTTGTAACTCGTAACTCA 59.582 38.462 0.00 0.00 0.00 3.41
589 615 7.115378 CGTAAAACCTTGTAACTCGTAACTCAT 59.885 37.037 0.00 0.00 0.00 2.90
590 616 7.797038 AAAACCTTGTAACTCGTAACTCATT 57.203 32.000 0.00 0.00 0.00 2.57
591 617 7.797038 AAACCTTGTAACTCGTAACTCATTT 57.203 32.000 0.00 0.00 0.00 2.32
592 618 8.891671 AAACCTTGTAACTCGTAACTCATTTA 57.108 30.769 0.00 0.00 0.00 1.40
593 619 9.498176 AAACCTTGTAACTCGTAACTCATTTAT 57.502 29.630 0.00 0.00 0.00 1.40
595 621 9.578439 ACCTTGTAACTCGTAACTCATTTATAC 57.422 33.333 0.00 0.00 0.00 1.47
596 622 8.740369 CCTTGTAACTCGTAACTCATTTATACG 58.260 37.037 0.00 0.00 42.70 3.06
597 623 9.282247 CTTGTAACTCGTAACTCATTTATACGT 57.718 33.333 0.00 0.00 42.15 3.57
598 624 8.605354 TGTAACTCGTAACTCATTTATACGTG 57.395 34.615 0.00 5.10 42.15 4.49
599 625 8.236586 TGTAACTCGTAACTCATTTATACGTGT 58.763 33.333 0.00 0.00 45.77 4.49
600 626 9.702726 GTAACTCGTAACTCATTTATACGTGTA 57.297 33.333 0.00 0.00 44.18 2.90
602 628 8.606727 ACTCGTAACTCATTTATACGTGTAAC 57.393 34.615 4.05 0.00 43.57 2.50
603 629 8.236586 ACTCGTAACTCATTTATACGTGTAACA 58.763 33.333 4.05 0.00 43.57 2.41
604 630 9.229784 CTCGTAACTCATTTATACGTGTAACAT 57.770 33.333 4.05 0.07 42.15 2.71
605 631 9.571810 TCGTAACTCATTTATACGTGTAACATT 57.428 29.630 4.05 0.00 42.15 2.71
617 643 5.580705 CGTGTAACATTACTCGTAACTCG 57.419 43.478 14.83 0.00 42.39 4.18
618 644 5.315982 CGTGTAACATTACTCGTAACTCGA 58.684 41.667 14.83 0.00 42.39 4.04
619 645 5.961843 CGTGTAACATTACTCGTAACTCGAT 59.038 40.000 14.83 0.00 42.41 3.59
620 646 6.467047 CGTGTAACATTACTCGTAACTCGATT 59.533 38.462 14.83 0.00 42.41 3.34
621 647 7.007725 CGTGTAACATTACTCGTAACTCGATTT 59.992 37.037 14.83 0.00 42.41 2.17
622 648 8.100306 GTGTAACATTACTCGTAACTCGATTTG 58.900 37.037 0.00 0.00 42.06 2.32
628 654 2.789208 TCGTAACTCGATTTGCTACGG 58.211 47.619 8.75 0.00 44.01 4.02
629 655 1.254570 CGTAACTCGATTTGCTACGGC 59.745 52.381 0.00 0.00 42.86 5.68
630 656 1.591619 GTAACTCGATTTGCTACGGCC 59.408 52.381 0.00 0.00 37.74 6.13
631 657 0.743345 AACTCGATTTGCTACGGCCC 60.743 55.000 0.00 0.00 37.74 5.80
632 658 1.144057 CTCGATTTGCTACGGCCCT 59.856 57.895 0.00 0.00 37.74 5.19
633 659 0.462047 CTCGATTTGCTACGGCCCTT 60.462 55.000 0.00 0.00 37.74 3.95
634 660 0.461339 TCGATTTGCTACGGCCCTTC 60.461 55.000 0.00 0.00 37.74 3.46
635 661 1.436983 CGATTTGCTACGGCCCTTCC 61.437 60.000 0.00 0.00 37.74 3.46
636 662 1.076995 ATTTGCTACGGCCCTTCCC 60.077 57.895 0.00 0.00 37.74 3.97
637 663 1.858739 ATTTGCTACGGCCCTTCCCA 61.859 55.000 0.00 0.00 37.74 4.37
638 664 2.757980 TTTGCTACGGCCCTTCCCAC 62.758 60.000 0.00 0.00 37.74 4.61
639 665 4.484872 GCTACGGCCCTTCCCACC 62.485 72.222 0.00 0.00 0.00 4.61
640 666 2.687566 CTACGGCCCTTCCCACCT 60.688 66.667 0.00 0.00 0.00 4.00
641 667 1.382146 CTACGGCCCTTCCCACCTA 60.382 63.158 0.00 0.00 0.00 3.08
642 668 0.763223 CTACGGCCCTTCCCACCTAT 60.763 60.000 0.00 0.00 0.00 2.57
643 669 0.326808 TACGGCCCTTCCCACCTATT 60.327 55.000 0.00 0.00 0.00 1.73
644 670 1.152963 CGGCCCTTCCCACCTATTG 60.153 63.158 0.00 0.00 0.00 1.90
645 671 1.632018 CGGCCCTTCCCACCTATTGA 61.632 60.000 0.00 0.00 0.00 2.57
646 672 0.106669 GGCCCTTCCCACCTATTGAC 60.107 60.000 0.00 0.00 0.00 3.18
647 673 0.106669 GCCCTTCCCACCTATTGACC 60.107 60.000 0.00 0.00 0.00 4.02
648 674 1.295020 CCCTTCCCACCTATTGACCA 58.705 55.000 0.00 0.00 0.00 4.02
649 675 1.638589 CCCTTCCCACCTATTGACCAA 59.361 52.381 0.00 0.00 0.00 3.67
650 676 2.244769 CCCTTCCCACCTATTGACCAAT 59.755 50.000 0.64 0.64 34.93 3.16
651 677 3.555966 CCTTCCCACCTATTGACCAATC 58.444 50.000 0.00 0.00 32.50 2.67
652 678 3.053693 CCTTCCCACCTATTGACCAATCA 60.054 47.826 0.00 0.00 32.50 2.57
653 679 3.931907 TCCCACCTATTGACCAATCAG 57.068 47.619 0.00 0.00 35.83 2.90
654 680 3.459828 TCCCACCTATTGACCAATCAGA 58.540 45.455 0.00 0.00 35.83 3.27
655 681 4.047166 TCCCACCTATTGACCAATCAGAT 58.953 43.478 0.00 0.00 35.83 2.90
656 682 4.478317 TCCCACCTATTGACCAATCAGATT 59.522 41.667 0.00 0.00 35.83 2.40
657 683 5.669904 TCCCACCTATTGACCAATCAGATTA 59.330 40.000 0.00 0.00 35.83 1.75
658 684 6.159575 TCCCACCTATTGACCAATCAGATTAA 59.840 38.462 0.00 0.00 35.83 1.40
659 685 7.006509 CCCACCTATTGACCAATCAGATTAAT 58.993 38.462 0.00 0.00 35.83 1.40
660 686 7.175641 CCCACCTATTGACCAATCAGATTAATC 59.824 40.741 7.41 7.41 35.83 1.75
661 687 7.175641 CCACCTATTGACCAATCAGATTAATCC 59.824 40.741 11.92 0.00 35.83 3.01
662 688 7.941238 CACCTATTGACCAATCAGATTAATCCT 59.059 37.037 11.92 0.00 35.83 3.24
663 689 8.506083 ACCTATTGACCAATCAGATTAATCCTT 58.494 33.333 11.92 1.25 35.83 3.36
664 690 9.359653 CCTATTGACCAATCAGATTAATCCTTT 57.640 33.333 11.92 1.08 35.83 3.11
667 693 9.880157 ATTGACCAATCAGATTAATCCTTTTTG 57.120 29.630 11.92 10.38 35.83 2.44
668 694 8.421249 TGACCAATCAGATTAATCCTTTTTGT 57.579 30.769 11.92 5.34 0.00 2.83
669 695 9.527157 TGACCAATCAGATTAATCCTTTTTGTA 57.473 29.630 11.92 0.00 0.00 2.41
683 709 9.811995 AATCCTTTTTGTAAAACCTTGTAACTC 57.188 29.630 0.00 0.00 0.00 3.01
684 710 7.474190 TCCTTTTTGTAAAACCTTGTAACTCG 58.526 34.615 0.00 0.00 0.00 4.18
685 711 7.121020 TCCTTTTTGTAAAACCTTGTAACTCGT 59.879 33.333 0.00 0.00 0.00 4.18
686 712 7.756272 CCTTTTTGTAAAACCTTGTAACTCGTT 59.244 33.333 0.00 0.00 0.00 3.85
687 713 9.131416 CTTTTTGTAAAACCTTGTAACTCGTTT 57.869 29.630 0.00 0.00 0.00 3.60
688 714 8.450385 TTTTGTAAAACCTTGTAACTCGTTTG 57.550 30.769 0.00 0.00 0.00 2.93
689 715 6.740411 TGTAAAACCTTGTAACTCGTTTGT 57.260 33.333 0.00 0.00 0.00 2.83
690 716 7.840342 TGTAAAACCTTGTAACTCGTTTGTA 57.160 32.000 0.00 0.00 0.00 2.41
691 717 7.683746 TGTAAAACCTTGTAACTCGTTTGTAC 58.316 34.615 0.00 0.00 0.00 2.90
692 718 6.740411 AAAACCTTGTAACTCGTTTGTACA 57.260 33.333 0.00 0.00 0.00 2.90
693 719 5.978934 AACCTTGTAACTCGTTTGTACAG 57.021 39.130 0.00 0.00 0.00 2.74
694 720 4.374399 ACCTTGTAACTCGTTTGTACAGG 58.626 43.478 0.00 0.00 0.00 4.00
695 721 4.141869 ACCTTGTAACTCGTTTGTACAGGT 60.142 41.667 0.00 0.00 0.00 4.00
696 722 5.068987 ACCTTGTAACTCGTTTGTACAGGTA 59.931 40.000 0.00 0.00 0.00 3.08
697 723 5.632347 CCTTGTAACTCGTTTGTACAGGTAG 59.368 44.000 0.00 0.00 0.00 3.18
698 724 4.549458 TGTAACTCGTTTGTACAGGTAGC 58.451 43.478 0.00 0.00 0.00 3.58
699 725 3.738830 AACTCGTTTGTACAGGTAGCA 57.261 42.857 0.00 0.00 0.00 3.49
700 726 3.955650 ACTCGTTTGTACAGGTAGCAT 57.044 42.857 0.00 0.00 0.00 3.79
701 727 4.267349 ACTCGTTTGTACAGGTAGCATT 57.733 40.909 0.00 0.00 0.00 3.56
702 728 5.395682 ACTCGTTTGTACAGGTAGCATTA 57.604 39.130 0.00 0.00 0.00 1.90
703 729 5.166398 ACTCGTTTGTACAGGTAGCATTAC 58.834 41.667 0.00 0.00 0.00 1.89
704 730 5.047519 ACTCGTTTGTACAGGTAGCATTACT 60.048 40.000 0.00 0.00 0.00 2.24
705 731 5.404946 TCGTTTGTACAGGTAGCATTACTC 58.595 41.667 0.00 0.00 0.00 2.59
706 732 5.047872 TCGTTTGTACAGGTAGCATTACTCA 60.048 40.000 0.00 0.00 0.00 3.41
707 733 5.810587 CGTTTGTACAGGTAGCATTACTCAT 59.189 40.000 0.00 0.00 0.00 2.90
708 734 6.312918 CGTTTGTACAGGTAGCATTACTCATT 59.687 38.462 0.00 0.00 0.00 2.57
709 735 7.464358 GTTTGTACAGGTAGCATTACTCATTG 58.536 38.462 0.00 0.00 0.00 2.82
710 736 6.294361 TGTACAGGTAGCATTACTCATTGT 57.706 37.500 0.00 0.00 0.00 2.71
711 737 7.412853 TGTACAGGTAGCATTACTCATTGTA 57.587 36.000 0.00 0.00 0.00 2.41
712 738 7.842982 TGTACAGGTAGCATTACTCATTGTAA 58.157 34.615 0.00 0.00 44.22 2.41
714 740 8.979574 GTACAGGTAGCATTACTCATTGTAATC 58.020 37.037 0.00 0.00 45.74 1.75
715 741 6.992715 ACAGGTAGCATTACTCATTGTAATCC 59.007 38.462 0.00 0.00 45.74 3.01
716 742 6.992123 CAGGTAGCATTACTCATTGTAATCCA 59.008 38.462 0.00 0.00 45.74 3.41
717 743 7.498900 CAGGTAGCATTACTCATTGTAATCCAA 59.501 37.037 0.00 0.00 45.74 3.53
718 744 8.220559 AGGTAGCATTACTCATTGTAATCCAAT 58.779 33.333 0.00 0.00 45.74 3.16
719 745 8.507249 GGTAGCATTACTCATTGTAATCCAATC 58.493 37.037 0.00 0.00 45.74 2.67
720 746 9.056005 GTAGCATTACTCATTGTAATCCAATCA 57.944 33.333 0.00 0.00 45.74 2.57
721 747 8.162878 AGCATTACTCATTGTAATCCAATCAG 57.837 34.615 0.00 0.00 45.74 2.90
722 748 7.994911 AGCATTACTCATTGTAATCCAATCAGA 59.005 33.333 0.00 0.00 45.74 3.27
723 749 8.790718 GCATTACTCATTGTAATCCAATCAGAT 58.209 33.333 0.00 0.00 45.74 2.90
822 896 0.732571 GTGTGCGAGAGAGAGAGAGG 59.267 60.000 0.00 0.00 0.00 3.69
824 898 1.101049 GTGCGAGAGAGAGAGAGGGG 61.101 65.000 0.00 0.00 0.00 4.79
962 1036 1.520342 CGCTTCTCTGCTGGCTACC 60.520 63.158 0.00 0.00 0.00 3.18
982 1057 2.515429 CCCTGCTATATATGGCCCCATT 59.485 50.000 17.41 0.00 37.82 3.16
1027 1106 1.138661 CACAAGGCTCCTCATCTCCTC 59.861 57.143 0.00 0.00 0.00 3.71
1029 1108 0.641601 AAGGCTCCTCATCTCCTCCT 59.358 55.000 0.00 0.00 0.00 3.69
1035 1114 3.641046 CTCCTCATCTCCTCCTTCTTCA 58.359 50.000 0.00 0.00 0.00 3.02
1158 1501 2.167219 CCACATCAGGCTACACGCG 61.167 63.158 3.53 3.53 40.44 6.01
1268 1611 0.685131 CATGCCCATCCTTTGCTCCA 60.685 55.000 0.00 0.00 0.00 3.86
1272 1615 2.409870 CCATCCTTTGCTCCACGGC 61.410 63.158 0.00 0.00 0.00 5.68
1319 1662 1.632589 AATTGGCCTTTTTCCTCGCT 58.367 45.000 3.32 0.00 0.00 4.93
1359 1704 0.491823 TCTTTCTCCCCACCTCCAGA 59.508 55.000 0.00 0.00 0.00 3.86
1368 1713 1.237285 CCACCTCCAGAAAGCCAACG 61.237 60.000 0.00 0.00 0.00 4.10
1429 1788 0.733150 GCAAACTCCAGCCGTTATCC 59.267 55.000 0.00 0.00 0.00 2.59
1454 1813 0.446222 TTCATTTCTAAGCGCGTGGC 59.554 50.000 8.43 0.00 44.05 5.01
1479 1839 7.442364 GCTTATCTAACTGGTGCATTCTTATGA 59.558 37.037 0.00 0.00 33.37 2.15
1498 1858 4.572985 TGACAAACCTTGCAGAAATCAG 57.427 40.909 0.00 0.00 0.00 2.90
1531 1891 3.665675 AAGACATGGACGAGGCGGC 62.666 63.158 0.00 0.00 0.00 6.53
1576 1936 4.126437 GAGAAGCTAAGCAGAATCTTCCC 58.874 47.826 0.00 0.00 35.11 3.97
1578 1938 4.018960 AGAAGCTAAGCAGAATCTTCCCAA 60.019 41.667 0.00 0.00 35.11 4.12
1580 1940 2.948315 GCTAAGCAGAATCTTCCCAAGG 59.052 50.000 0.00 0.00 0.00 3.61
1581 1941 3.623453 GCTAAGCAGAATCTTCCCAAGGT 60.623 47.826 0.00 0.00 0.00 3.50
1622 1982 2.682856 ACAATATGTCAACCGGTCATGC 59.317 45.455 8.04 0.46 0.00 4.06
1623 1983 2.945008 CAATATGTCAACCGGTCATGCT 59.055 45.455 8.04 0.00 0.00 3.79
1624 1984 2.022764 TATGTCAACCGGTCATGCTG 57.977 50.000 8.04 1.12 0.00 4.41
1693 2072 8.920665 CGTAAGATCTTGATCCATTTATCTGTC 58.079 37.037 18.47 0.00 43.02 3.51
1728 2112 9.409918 TCATCTAGAGTATGTTAACTGCTAGTT 57.590 33.333 7.22 6.74 41.97 2.24
1751 2284 6.197364 TGTTAGTTCAAATTCGTTTGGTGT 57.803 33.333 1.55 0.00 32.99 4.16
1753 2286 4.974368 AGTTCAAATTCGTTTGGTGTGA 57.026 36.364 1.55 0.00 32.99 3.58
1787 2320 2.040278 AGTTCATACAGCCCTTTCAGCA 59.960 45.455 0.00 0.00 0.00 4.41
1806 2342 4.874966 CAGCAAAAAGGGTGAAATTTGACA 59.125 37.500 10.02 0.00 38.52 3.58
1814 2350 3.868661 GGGTGAAATTTGACAAGCGTTTT 59.131 39.130 10.02 0.00 0.00 2.43
1822 2358 3.077229 TGACAAGCGTTTTGGTCATTG 57.923 42.857 1.78 0.00 35.51 2.82
1838 2374 5.277147 GTCATTGCAGGGCACTGAAGATG 62.277 52.174 23.23 18.73 46.54 2.90
1939 2475 7.389330 TCAAATTAAAGATCTTTCGGTGTAGCA 59.611 33.333 23.70 0.67 34.23 3.49
1951 2490 1.406341 GGTGTAGCAATCTAACCCGCA 60.406 52.381 0.00 0.00 0.00 5.69
1979 2518 4.202441 TGCAGAATCTGGGAAAAGCTATC 58.798 43.478 12.66 0.00 31.21 2.08
1982 2521 5.195940 CAGAATCTGGGAAAAGCTATCCAA 58.804 41.667 17.63 7.87 38.80 3.53
2139 2679 3.873952 GTGAGAACTCTGAACTTTGTGCT 59.126 43.478 3.51 0.00 0.00 4.40
2157 2698 2.383245 CTTGCCGTGGACAGTCACCT 62.383 60.000 2.17 0.00 34.36 4.00
2204 2749 4.302455 GCATCATGCTACCTGTACTACTG 58.698 47.826 1.02 0.00 40.96 2.74
2214 2759 4.268359 ACCTGTACTACTGCACTAGGTAC 58.732 47.826 5.52 6.49 35.45 3.34
2519 3088 2.229792 TGAGGTGCAAAAGGTAAGCAG 58.770 47.619 0.00 0.00 39.21 4.24
2563 3139 2.674033 ATGCAGCAGCTTTCGCCA 60.674 55.556 0.00 0.00 42.74 5.69
2564 3140 2.270257 ATGCAGCAGCTTTCGCCAA 61.270 52.632 0.00 0.00 42.74 4.52
2565 3141 1.808531 ATGCAGCAGCTTTCGCCAAA 61.809 50.000 0.00 0.00 42.74 3.28
2566 3142 1.080298 GCAGCAGCTTTCGCCAAAT 60.080 52.632 0.00 0.00 37.91 2.32
2567 3143 1.349259 GCAGCAGCTTTCGCCAAATG 61.349 55.000 0.00 0.00 37.91 2.32
2568 3144 0.038892 CAGCAGCTTTCGCCAAATGT 60.039 50.000 0.00 0.00 36.60 2.71
2569 3145 0.038892 AGCAGCTTTCGCCAAATGTG 60.039 50.000 0.00 0.00 36.60 3.21
2570 3146 0.318955 GCAGCTTTCGCCAAATGTGT 60.319 50.000 0.00 0.00 36.60 3.72
2571 3147 1.869342 GCAGCTTTCGCCAAATGTGTT 60.869 47.619 0.00 0.00 36.60 3.32
2572 3148 2.472816 CAGCTTTCGCCAAATGTGTTT 58.527 42.857 0.00 0.00 36.60 2.83
2573 3149 2.865551 CAGCTTTCGCCAAATGTGTTTT 59.134 40.909 0.00 0.00 36.60 2.43
2574 3150 3.309410 CAGCTTTCGCCAAATGTGTTTTT 59.691 39.130 0.00 0.00 36.60 1.94
2615 3192 1.273688 GTTTTGTTTGCGCGAAAGGT 58.726 45.000 12.68 0.00 0.00 3.50
2616 3193 1.656594 GTTTTGTTTGCGCGAAAGGTT 59.343 42.857 12.68 0.00 0.00 3.50
2617 3194 1.272781 TTTGTTTGCGCGAAAGGTTG 58.727 45.000 12.68 0.00 0.00 3.77
2633 3210 3.157087 AGGTTGCCTGATGTTTACTTGG 58.843 45.455 0.00 0.00 29.57 3.61
2686 3264 1.136147 GATGCTGGCGCTTGTCAAG 59.864 57.895 7.64 8.31 36.97 3.02
2739 3317 2.107141 CGATCCGTGGCTCCCTTC 59.893 66.667 0.00 0.00 0.00 3.46
2766 3344 1.383523 GCCTGCCAGTCTCATTTACC 58.616 55.000 0.00 0.00 0.00 2.85
2769 3347 2.237143 CCTGCCAGTCTCATTTACCTGA 59.763 50.000 0.00 0.00 0.00 3.86
2834 3422 5.421212 TTGGTGCTGAAAAATGAAAATGC 57.579 34.783 0.00 0.00 0.00 3.56
2885 3473 0.744281 TGCACGATCTATTGCGGAGA 59.256 50.000 0.00 0.00 41.96 3.71
2887 3475 2.224042 TGCACGATCTATTGCGGAGAAT 60.224 45.455 0.00 0.00 41.96 2.40
2899 3487 2.268920 GAGAATCTGGCCCGTGCA 59.731 61.111 0.00 0.00 40.13 4.57
3000 3588 2.182284 CATCGTCGCGGTTACCCA 59.818 61.111 6.13 0.00 0.00 4.51
3165 3758 6.720288 GGTATGCTAGTAGAACTTCTGGGATA 59.280 42.308 0.00 0.00 0.00 2.59
3294 3892 1.404315 GGAGATGCTTTTCTCGACCGT 60.404 52.381 6.02 0.00 42.57 4.83
3332 3930 3.769739 TGCTTAGTTGTGTGGAGATGT 57.230 42.857 0.00 0.00 0.00 3.06
3339 3937 3.807622 AGTTGTGTGGAGATGTTTACACG 59.192 43.478 0.00 0.00 44.69 4.49
3359 3957 6.730175 ACACGAACATTTTACTATGTTGCAA 58.270 32.000 6.71 0.00 45.98 4.08
3360 3958 6.855914 ACACGAACATTTTACTATGTTGCAAG 59.144 34.615 0.00 0.00 45.98 4.01
3379 3988 5.178797 GCAAGAGCCACACTATAGAGAAAA 58.821 41.667 6.78 0.00 33.58 2.29
3381 3990 5.346181 AGAGCCACACTATAGAGAAAACC 57.654 43.478 6.78 0.00 0.00 3.27
3382 3991 4.777896 AGAGCCACACTATAGAGAAAACCA 59.222 41.667 6.78 0.00 0.00 3.67
3417 4026 3.822735 CGAGGGGTAGGTTATATGTCGAA 59.177 47.826 0.00 0.00 0.00 3.71
3421 4030 3.924686 GGGTAGGTTATATGTCGAATGCG 59.075 47.826 0.00 0.00 39.35 4.73
3424 4033 4.316205 AGGTTATATGTCGAATGCGTGA 57.684 40.909 0.00 0.00 38.98 4.35
3503 4112 5.562696 CGAGTAGTACTACCCGAAAAACACA 60.563 44.000 27.19 0.00 39.20 3.72
3509 4118 3.628942 ACTACCCGAAAAACACAAAGGAC 59.371 43.478 0.00 0.00 0.00 3.85
3669 4297 4.354208 TTCTATCCTCTTTCTCCCACCT 57.646 45.455 0.00 0.00 0.00 4.00
3688 4316 4.811557 CACCTTTTCTTCTCGTCTGTTTCT 59.188 41.667 0.00 0.00 0.00 2.52
3790 4418 8.800370 TTTATTGCATTTTATTTCTTTCCCCC 57.200 30.769 0.00 0.00 0.00 5.40
3816 4444 9.173021 CTCTCTTACTCACTCATTCTCTCTTTA 57.827 37.037 0.00 0.00 0.00 1.85
3828 4456 8.746052 TCATTCTCTCTTTAAAGTTTTCACCA 57.254 30.769 14.74 0.00 0.00 4.17
3832 4460 7.425606 TCTCTCTTTAAAGTTTTCACCATTGC 58.574 34.615 14.74 0.00 0.00 3.56
3835 4463 7.920682 TCTCTTTAAAGTTTTCACCATTGCTTC 59.079 33.333 14.74 0.00 0.00 3.86
3903 4531 7.397192 ACTTCAAAGTAATGGTATTGCCTTCAT 59.603 33.333 0.00 0.00 37.52 2.57
3911 4539 3.204158 TGGTATTGCCTTCATACCACCAT 59.796 43.478 7.57 0.00 43.65 3.55
3939 4567 2.644299 TCCATATTAGGACCCCATGCAG 59.356 50.000 0.00 0.00 31.23 4.41
3991 4619 1.209127 CAACGCGGGGACACATTTC 59.791 57.895 12.47 0.00 0.00 2.17
4015 4643 1.639298 GCTCGCGTTCATTTCTGCCT 61.639 55.000 5.77 0.00 0.00 4.75
4031 4659 2.317609 CCTGCGTGGACAGAAACCG 61.318 63.158 0.00 0.00 40.25 4.44
4066 4694 3.846744 GCGACACATTTTGCGTTTGTCTA 60.847 43.478 0.00 0.00 35.46 2.59
4078 4706 4.201676 TGCGTTTGTCTATTTATGTCTGCG 60.202 41.667 0.00 0.00 0.00 5.18
4087 4715 1.966901 TTATGTCTGCGCGGACCCAT 61.967 55.000 38.87 29.84 35.54 4.00
4095 4723 2.044946 GCGGACCCATTTCCTGCT 60.045 61.111 0.00 0.00 34.39 4.24
4151 4779 2.504899 CAGACGCGTCGCATGTCT 60.505 61.111 31.56 18.42 43.43 3.41
4163 4793 4.101448 ATGTCTGCCGGGCTCACC 62.101 66.667 21.46 6.11 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 4.921847 TGTTTGCTTGGCGCGTGC 62.922 61.111 13.78 13.78 43.27 5.34
96 98 4.796231 CCAGCCGTTCGTCCTCCG 62.796 72.222 0.00 0.00 38.13 4.63
98 100 1.668101 ATCTCCAGCCGTTCGTCCTC 61.668 60.000 0.00 0.00 0.00 3.71
99 101 1.682684 ATCTCCAGCCGTTCGTCCT 60.683 57.895 0.00 0.00 0.00 3.85
102 104 2.125512 GCATCTCCAGCCGTTCGT 60.126 61.111 0.00 0.00 0.00 3.85
122 124 1.709147 CGAAGATGCAAAGGGCCTCG 61.709 60.000 6.46 1.74 41.46 4.63
125 127 2.048603 AGCGAAGATGCAAAGGGCC 61.049 57.895 0.00 0.00 43.89 5.80
203 206 1.847818 CGACGGCCAAAATCGAGATA 58.152 50.000 2.24 0.00 38.10 1.98
381 403 2.631545 AGTGAACCTACCGTAGCAAACT 59.368 45.455 0.00 0.00 0.00 2.66
468 494 3.017442 CAAGTGGAGTAGATCGGTGAGA 58.983 50.000 0.00 0.00 0.00 3.27
566 592 7.797038 AATGAGTTACGAGTTACAAGGTTTT 57.203 32.000 0.00 0.00 0.00 2.43
567 593 7.797038 AAATGAGTTACGAGTTACAAGGTTT 57.203 32.000 0.00 0.00 0.00 3.27
569 595 9.578439 GTATAAATGAGTTACGAGTTACAAGGT 57.422 33.333 0.00 0.00 0.00 3.50
570 596 8.740369 CGTATAAATGAGTTACGAGTTACAAGG 58.260 37.037 0.00 0.00 40.77 3.61
571 597 9.282247 ACGTATAAATGAGTTACGAGTTACAAG 57.718 33.333 8.51 0.00 40.77 3.16
572 598 9.064804 CACGTATAAATGAGTTACGAGTTACAA 57.935 33.333 8.51 0.00 40.77 2.41
573 599 8.236586 ACACGTATAAATGAGTTACGAGTTACA 58.763 33.333 8.51 0.00 39.11 2.41
574 600 8.606727 ACACGTATAAATGAGTTACGAGTTAC 57.393 34.615 8.51 0.00 39.11 2.50
576 602 9.065871 GTTACACGTATAAATGAGTTACGAGTT 57.934 33.333 8.51 0.00 41.23 3.01
577 603 8.236586 TGTTACACGTATAAATGAGTTACGAGT 58.763 33.333 8.51 8.84 42.68 4.18
578 604 8.605354 TGTTACACGTATAAATGAGTTACGAG 57.395 34.615 8.51 3.62 40.77 4.18
579 605 9.571810 AATGTTACACGTATAAATGAGTTACGA 57.428 29.630 8.51 0.00 40.77 3.43
584 610 9.229784 CGAGTAATGTTACACGTATAAATGAGT 57.770 33.333 12.49 0.00 40.94 3.41
607 633 4.860799 GCCGTAGCAAATCGAGTTACGAG 61.861 52.174 17.90 10.62 45.14 4.18
608 634 3.044855 GCCGTAGCAAATCGAGTTACGA 61.045 50.000 17.90 0.00 45.14 3.43
609 635 1.254570 GCCGTAGCAAATCGAGTTACG 59.745 52.381 11.30 11.30 43.02 3.18
610 636 1.591619 GGCCGTAGCAAATCGAGTTAC 59.408 52.381 0.00 0.00 42.56 2.50
611 637 1.472026 GGGCCGTAGCAAATCGAGTTA 60.472 52.381 0.00 0.00 42.56 2.24
612 638 0.743345 GGGCCGTAGCAAATCGAGTT 60.743 55.000 0.00 0.00 42.56 3.01
613 639 1.153429 GGGCCGTAGCAAATCGAGT 60.153 57.895 0.00 0.00 42.56 4.18
614 640 0.462047 AAGGGCCGTAGCAAATCGAG 60.462 55.000 0.00 0.00 42.56 4.04
615 641 0.461339 GAAGGGCCGTAGCAAATCGA 60.461 55.000 0.00 0.00 42.56 3.59
616 642 1.436983 GGAAGGGCCGTAGCAAATCG 61.437 60.000 0.00 0.00 42.56 3.34
617 643 1.101635 GGGAAGGGCCGTAGCAAATC 61.102 60.000 0.00 0.00 42.56 2.17
618 644 1.076995 GGGAAGGGCCGTAGCAAAT 60.077 57.895 0.00 0.00 42.56 2.32
619 645 2.353573 GGGAAGGGCCGTAGCAAA 59.646 61.111 0.00 0.00 42.56 3.68
620 646 2.931105 TGGGAAGGGCCGTAGCAA 60.931 61.111 0.00 0.00 42.56 3.91
621 647 3.712907 GTGGGAAGGGCCGTAGCA 61.713 66.667 0.00 0.00 42.56 3.49
622 648 4.484872 GGTGGGAAGGGCCGTAGC 62.485 72.222 0.00 0.00 37.63 3.58
623 649 0.763223 ATAGGTGGGAAGGGCCGTAG 60.763 60.000 0.00 0.00 37.63 3.51
624 650 0.326808 AATAGGTGGGAAGGGCCGTA 60.327 55.000 0.00 0.00 37.63 4.02
625 651 1.618447 AATAGGTGGGAAGGGCCGT 60.618 57.895 0.00 0.00 37.63 5.68
626 652 1.152963 CAATAGGTGGGAAGGGCCG 60.153 63.158 0.00 0.00 37.63 6.13
627 653 0.106669 GTCAATAGGTGGGAAGGGCC 60.107 60.000 0.00 0.00 0.00 5.80
628 654 0.106669 GGTCAATAGGTGGGAAGGGC 60.107 60.000 0.00 0.00 0.00 5.19
629 655 1.295020 TGGTCAATAGGTGGGAAGGG 58.705 55.000 0.00 0.00 0.00 3.95
630 656 3.053693 TGATTGGTCAATAGGTGGGAAGG 60.054 47.826 0.00 0.00 0.00 3.46
631 657 4.080356 TCTGATTGGTCAATAGGTGGGAAG 60.080 45.833 0.00 0.00 33.05 3.46
632 658 3.849574 TCTGATTGGTCAATAGGTGGGAA 59.150 43.478 0.00 0.00 33.05 3.97
633 659 3.459828 TCTGATTGGTCAATAGGTGGGA 58.540 45.455 0.00 0.00 33.05 4.37
634 660 3.931907 TCTGATTGGTCAATAGGTGGG 57.068 47.619 0.00 0.00 33.05 4.61
635 661 7.175641 GGATTAATCTGATTGGTCAATAGGTGG 59.824 40.741 14.95 0.00 33.05 4.61
636 662 7.941238 AGGATTAATCTGATTGGTCAATAGGTG 59.059 37.037 14.95 0.00 33.05 4.00
637 663 8.050316 AGGATTAATCTGATTGGTCAATAGGT 57.950 34.615 14.95 0.00 33.05 3.08
638 664 8.930846 AAGGATTAATCTGATTGGTCAATAGG 57.069 34.615 14.95 0.00 33.05 2.57
641 667 9.880157 CAAAAAGGATTAATCTGATTGGTCAAT 57.120 29.630 14.95 4.68 33.05 2.57
642 668 8.869109 ACAAAAAGGATTAATCTGATTGGTCAA 58.131 29.630 14.95 0.00 33.05 3.18
643 669 8.421249 ACAAAAAGGATTAATCTGATTGGTCA 57.579 30.769 14.95 0.00 0.00 4.02
657 683 9.811995 GAGTTACAAGGTTTTACAAAAAGGATT 57.188 29.630 0.00 0.00 0.00 3.01
658 684 8.132995 CGAGTTACAAGGTTTTACAAAAAGGAT 58.867 33.333 0.00 0.00 0.00 3.24
659 685 7.121020 ACGAGTTACAAGGTTTTACAAAAAGGA 59.879 33.333 0.00 0.00 0.00 3.36
660 686 7.252708 ACGAGTTACAAGGTTTTACAAAAAGG 58.747 34.615 0.00 0.00 0.00 3.11
661 687 8.677871 AACGAGTTACAAGGTTTTACAAAAAG 57.322 30.769 0.00 0.00 0.00 2.27
662 688 8.913656 CAAACGAGTTACAAGGTTTTACAAAAA 58.086 29.630 0.00 0.00 30.73 1.94
663 689 8.081025 ACAAACGAGTTACAAGGTTTTACAAAA 58.919 29.630 0.00 0.00 30.73 2.44
664 690 7.592051 ACAAACGAGTTACAAGGTTTTACAAA 58.408 30.769 0.00 0.00 30.73 2.83
665 691 7.143514 ACAAACGAGTTACAAGGTTTTACAA 57.856 32.000 0.00 0.00 30.73 2.41
666 692 6.740411 ACAAACGAGTTACAAGGTTTTACA 57.260 33.333 0.00 0.00 30.73 2.41
667 693 7.683746 TGTACAAACGAGTTACAAGGTTTTAC 58.316 34.615 0.00 0.00 30.73 2.01
668 694 7.011295 CCTGTACAAACGAGTTACAAGGTTTTA 59.989 37.037 0.00 0.00 30.73 1.52
669 695 6.183360 CCTGTACAAACGAGTTACAAGGTTTT 60.183 38.462 0.00 0.00 30.73 2.43
670 696 5.295045 CCTGTACAAACGAGTTACAAGGTTT 59.705 40.000 0.00 0.00 33.19 3.27
671 697 4.812626 CCTGTACAAACGAGTTACAAGGTT 59.187 41.667 0.00 0.00 0.00 3.50
672 698 4.141869 ACCTGTACAAACGAGTTACAAGGT 60.142 41.667 0.00 0.00 0.00 3.50
673 699 4.374399 ACCTGTACAAACGAGTTACAAGG 58.626 43.478 0.00 0.00 0.00 3.61
674 700 5.118203 GCTACCTGTACAAACGAGTTACAAG 59.882 44.000 0.00 0.00 0.00 3.16
675 701 4.984161 GCTACCTGTACAAACGAGTTACAA 59.016 41.667 0.00 0.00 0.00 2.41
676 702 4.037803 TGCTACCTGTACAAACGAGTTACA 59.962 41.667 0.00 0.00 0.00 2.41
677 703 4.549458 TGCTACCTGTACAAACGAGTTAC 58.451 43.478 0.00 0.00 0.00 2.50
678 704 4.852134 TGCTACCTGTACAAACGAGTTA 57.148 40.909 0.00 0.00 0.00 2.24
679 705 3.738830 TGCTACCTGTACAAACGAGTT 57.261 42.857 0.00 0.00 0.00 3.01
680 706 3.955650 ATGCTACCTGTACAAACGAGT 57.044 42.857 0.00 0.00 0.00 4.18
681 707 5.408356 AGTAATGCTACCTGTACAAACGAG 58.592 41.667 0.00 0.00 0.00 4.18
682 708 5.047872 TGAGTAATGCTACCTGTACAAACGA 60.048 40.000 0.00 0.00 0.00 3.85
683 709 5.165676 TGAGTAATGCTACCTGTACAAACG 58.834 41.667 0.00 0.00 0.00 3.60
684 710 7.119262 ACAATGAGTAATGCTACCTGTACAAAC 59.881 37.037 0.00 0.00 0.00 2.93
685 711 7.165485 ACAATGAGTAATGCTACCTGTACAAA 58.835 34.615 0.00 0.00 0.00 2.83
686 712 6.707290 ACAATGAGTAATGCTACCTGTACAA 58.293 36.000 0.00 0.00 0.00 2.41
687 713 6.294361 ACAATGAGTAATGCTACCTGTACA 57.706 37.500 0.00 0.00 0.00 2.90
822 896 1.687493 CTCTGTCCTCTCCACCCCC 60.687 68.421 0.00 0.00 0.00 5.40
824 898 0.333312 TCTCTCTGTCCTCTCCACCC 59.667 60.000 0.00 0.00 0.00 4.61
876 950 1.210870 GTGACAAGTGAAACGCGGTA 58.789 50.000 12.47 0.00 45.86 4.02
929 1003 1.549170 GAAGCGAGTAGAGGTTTCCCA 59.451 52.381 0.00 0.00 0.00 4.37
962 1036 3.202818 TGAATGGGGCCATATATAGCAGG 59.797 47.826 4.39 0.00 35.31 4.85
982 1057 1.878069 CCTTGCGTGCGATCGATGA 60.878 57.895 21.57 0.00 0.00 2.92
1027 1106 5.688807 AGAGAGAGAGAGAGATGAAGAAGG 58.311 45.833 0.00 0.00 0.00 3.46
1029 1108 5.359756 CGAGAGAGAGAGAGAGATGAAGAA 58.640 45.833 0.00 0.00 0.00 2.52
1035 1114 2.485479 GCACCGAGAGAGAGAGAGAGAT 60.485 54.545 0.00 0.00 0.00 2.75
1158 1501 2.677199 TGTCTTCGAGAATGTGCTGAC 58.323 47.619 0.00 0.00 0.00 3.51
1268 1611 2.438795 AAACACGTTGTGGGCCGT 60.439 55.556 0.00 0.00 37.94 5.68
1368 1713 1.706287 GCGGCCGATTTCAACTCCTC 61.706 60.000 33.48 1.16 0.00 3.71
1429 1788 2.780014 CGCGCTTAGAAATGAAATGCAG 59.220 45.455 5.56 0.00 0.00 4.41
1454 1813 8.768955 GTCATAAGAATGCACCAGTTAGATAAG 58.231 37.037 0.00 0.00 32.76 1.73
1479 1839 2.629617 CCCTGATTTCTGCAAGGTTTGT 59.370 45.455 0.00 0.00 0.00 2.83
1498 1858 2.830370 CTTTCTCCATGCGCCCCC 60.830 66.667 4.18 0.00 0.00 5.40
1531 1891 0.863799 CATGATCCGTGCCATCTTCG 59.136 55.000 0.00 0.00 0.00 3.79
1576 1936 2.334307 CTGGAACCAGCACACCTTG 58.666 57.895 7.95 0.00 37.24 3.61
1622 1982 2.859929 AGGGTCCCTGGATATGCAG 58.140 57.895 16.78 16.78 29.57 4.41
1751 2284 9.624697 GCTGTATGAACTGTTTTTAATTGATCA 57.375 29.630 0.00 0.00 0.00 2.92
1753 2286 8.034804 GGGCTGTATGAACTGTTTTTAATTGAT 58.965 33.333 0.00 0.00 0.00 2.57
1787 2320 4.570369 CGCTTGTCAAATTTCACCCTTTTT 59.430 37.500 0.00 0.00 0.00 1.94
1806 2342 1.269726 CCTGCAATGACCAAAACGCTT 60.270 47.619 0.00 0.00 0.00 4.68
1814 2350 2.845784 AGTGCCCTGCAATGACCA 59.154 55.556 0.00 0.00 41.47 4.02
1822 2358 1.093159 CTTCATCTTCAGTGCCCTGC 58.907 55.000 0.00 0.00 38.66 4.85
1838 2374 9.008965 AGATCTTTCTTTCTTTCCTTAAGCTTC 57.991 33.333 0.00 0.00 33.66 3.86
1901 2437 7.816031 AGATCTTTAATTTGATTTGGCACACAG 59.184 33.333 0.00 0.00 39.29 3.66
1939 2475 1.821216 CAACAGGTGCGGGTTAGATT 58.179 50.000 0.00 0.00 0.00 2.40
1951 2490 1.067295 TCCCAGATTCTGCAACAGGT 58.933 50.000 8.23 0.00 31.51 4.00
1979 2518 6.287589 ACCACTTCTATGTACTCTTCTTGG 57.712 41.667 0.00 0.00 0.00 3.61
1982 2521 6.948886 TCTGAACCACTTCTATGTACTCTTCT 59.051 38.462 0.00 0.00 0.00 2.85
2124 2664 1.334419 CGGCAAGCACAAAGTTCAGAG 60.334 52.381 0.00 0.00 0.00 3.35
2132 2672 1.723608 CTGTCCACGGCAAGCACAAA 61.724 55.000 0.00 0.00 0.00 2.83
2139 2679 2.110213 GGTGACTGTCCACGGCAA 59.890 61.111 5.17 0.00 37.91 4.52
2204 2749 2.362717 GTGAGATGGGAGTACCTAGTGC 59.637 54.545 0.00 0.00 41.11 4.40
2214 2759 0.179026 CCATGGCAGTGAGATGGGAG 60.179 60.000 0.00 0.00 34.14 4.30
2288 2853 3.405831 TCCATGAACTCTGTGCTCAAAG 58.594 45.455 0.00 0.00 0.00 2.77
2519 3088 6.274579 GGTCTAGTATAACCAAGAAGACTGC 58.725 44.000 0.00 0.00 35.53 4.40
2520 3089 6.496571 CGGTCTAGTATAACCAAGAAGACTG 58.503 44.000 0.00 0.00 35.13 3.51
2521 3090 5.067544 GCGGTCTAGTATAACCAAGAAGACT 59.932 44.000 0.00 0.00 35.13 3.24
2573 3149 6.722328 ACAAAAACACATTTCCCCCTAAAAA 58.278 32.000 0.00 0.00 0.00 1.94
2574 3150 6.314899 ACAAAAACACATTTCCCCCTAAAA 57.685 33.333 0.00 0.00 0.00 1.52
2575 3151 5.959583 ACAAAAACACATTTCCCCCTAAA 57.040 34.783 0.00 0.00 0.00 1.85
2576 3152 5.959583 AACAAAAACACATTTCCCCCTAA 57.040 34.783 0.00 0.00 0.00 2.69
2577 3153 5.959583 AAACAAAAACACATTTCCCCCTA 57.040 34.783 0.00 0.00 0.00 3.53
2578 3154 4.853468 AAACAAAAACACATTTCCCCCT 57.147 36.364 0.00 0.00 0.00 4.79
2579 3155 4.702612 ACAAAACAAAAACACATTTCCCCC 59.297 37.500 0.00 0.00 0.00 5.40
2580 3156 5.888691 ACAAAACAAAAACACATTTCCCC 57.111 34.783 0.00 0.00 0.00 4.81
2581 3157 6.088749 GCAAACAAAACAAAAACACATTTCCC 59.911 34.615 0.00 0.00 0.00 3.97
2582 3158 6.183359 CGCAAACAAAACAAAAACACATTTCC 60.183 34.615 0.00 0.00 0.00 3.13
2583 3159 6.663897 GCGCAAACAAAACAAAAACACATTTC 60.664 34.615 0.30 0.00 0.00 2.17
2615 3192 1.539388 CGCCAAGTAAACATCAGGCAA 59.461 47.619 0.00 0.00 42.10 4.52
2616 3193 1.164411 CGCCAAGTAAACATCAGGCA 58.836 50.000 0.00 0.00 42.10 4.75
2617 3194 0.451783 CCGCCAAGTAAACATCAGGC 59.548 55.000 0.00 0.00 38.73 4.85
2633 3210 1.063488 AACGAAACACAGTTGCCGC 59.937 52.632 0.00 0.00 0.00 6.53
2686 3264 2.024176 TGACTATTTTCTCCTGCGCC 57.976 50.000 4.18 0.00 0.00 6.53
2739 3317 0.392193 AGACTGGCAGGCGAAATGAG 60.392 55.000 20.34 0.00 0.00 2.90
2766 3344 7.622880 GCACATCCACAAACATATATCGATCAG 60.623 40.741 0.00 0.00 0.00 2.90
2769 3347 5.412594 GGCACATCCACAAACATATATCGAT 59.587 40.000 2.16 2.16 34.01 3.59
2885 3473 3.329542 ATCGTGCACGGGCCAGATT 62.330 57.895 36.41 10.55 40.13 2.40
2887 3475 4.451150 GATCGTGCACGGGCCAGA 62.451 66.667 36.41 18.59 40.13 3.86
2899 3487 0.535553 GCTCCTCGACCCTAGATCGT 60.536 60.000 13.82 0.00 40.50 3.73
3165 3758 6.830324 ACACATGATTGGACATTATTACAGCT 59.170 34.615 0.00 0.00 0.00 4.24
3294 3892 1.804372 GCAAATGCGTGTTGGGAAACA 60.804 47.619 0.00 0.00 0.00 2.83
3308 3906 5.048504 ACATCTCCACACAACTAAGCAAATG 60.049 40.000 0.00 0.00 0.00 2.32
3332 3930 8.343366 TGCAACATAGTAAAATGTTCGTGTAAA 58.657 29.630 0.00 0.00 44.79 2.01
3339 3937 6.528072 GGCTCTTGCAACATAGTAAAATGTTC 59.472 38.462 0.00 0.00 45.92 3.18
3359 3957 4.777896 TGGTTTTCTCTATAGTGTGGCTCT 59.222 41.667 0.00 0.00 0.00 4.09
3360 3958 5.086104 TGGTTTTCTCTATAGTGTGGCTC 57.914 43.478 0.00 0.00 0.00 4.70
3379 3988 4.226620 ACCCCTCGATAATTTACACTTGGT 59.773 41.667 0.00 0.00 0.00 3.67
3381 3990 5.989777 CCTACCCCTCGATAATTTACACTTG 59.010 44.000 0.00 0.00 0.00 3.16
3382 3991 5.664457 ACCTACCCCTCGATAATTTACACTT 59.336 40.000 0.00 0.00 0.00 3.16
3503 4112 2.358322 TTTTTCTGCCGGAGTCCTTT 57.642 45.000 5.05 0.00 0.00 3.11
3650 4259 5.190726 AGAAAAGGTGGGAGAAAGAGGATAG 59.809 44.000 0.00 0.00 0.00 2.08
3669 4297 5.913514 CGAGTAGAAACAGACGAGAAGAAAA 59.086 40.000 0.00 0.00 0.00 2.29
3688 4316 1.153823 GCGGCAAAGAGAGCGAGTA 60.154 57.895 0.00 0.00 0.00 2.59
3790 4418 7.630242 AAGAGAGAATGAGTGAGTAAGAGAG 57.370 40.000 0.00 0.00 0.00 3.20
3816 4444 6.295292 GGGATAGAAGCAATGGTGAAAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
3828 4456 6.323225 CAGAAAATTGAGGGGATAGAAGCAAT 59.677 38.462 0.00 0.00 0.00 3.56
3832 4460 5.444176 AGCAGAAAATTGAGGGGATAGAAG 58.556 41.667 0.00 0.00 0.00 2.85
3835 4463 5.046288 AGAGCAGAAAATTGAGGGGATAG 57.954 43.478 0.00 0.00 0.00 2.08
3903 4531 6.322969 CCTAATATGGATACGCTATGGTGGTA 59.677 42.308 0.00 0.00 42.51 3.25
3911 4539 4.264487 TGGGGTCCTAATATGGATACGCTA 60.264 45.833 0.00 0.00 38.52 4.26
3939 4567 0.246910 GTCGGAACCACTTCTCCCTC 59.753 60.000 0.00 0.00 0.00 4.30
3991 4619 0.967803 GAAATGAACGCGAGCAAACG 59.032 50.000 15.93 0.00 0.00 3.60
4031 4659 3.573491 GTCGCCGCATTAGGGTGC 61.573 66.667 0.00 0.00 41.65 5.01
4066 4694 0.814010 GGGTCCGCGCAGACATAAAT 60.814 55.000 24.19 0.00 38.59 1.40
4078 4706 2.044946 AGCAGGAAATGGGTCCGC 60.045 61.111 0.00 0.00 43.03 5.54
4087 4715 3.768757 CCAACCCAAATATGAGCAGGAAA 59.231 43.478 0.00 0.00 0.00 3.13
4095 4723 5.197451 GACACATACCCAACCCAAATATGA 58.803 41.667 0.00 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.