Multiple sequence alignment - TraesCS4B01G315000

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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 TraesCS4B01G315000 chr4B 100.000 2375 0 0 1 2375 604442525 604444899 0.000000e+00 4386
1 TraesCS4B01G315000 chr4B 89.427 558 56 3 152 707 604324356 604324912 0.000000e+00 701
2 TraesCS4B01G315000 chr4A 88.049 820 57 11 832 1612 684840622 684841439 0.000000e+00 933
3 TraesCS4B01G315000 chr4A 81.524 617 100 11 1628 2237 733536123 733536732 1.640000e-136 496
4 TraesCS4B01G315000 chr4A 81.188 606 100 10 1639 2237 598588979 598589577 2.140000e-130 475
5 TraesCS4B01G315000 chr4A 91.919 99 7 1 2276 2374 684841540 684841637 1.140000e-28 137
6 TraesCS4B01G315000 chr5D 86.217 711 88 7 1 707 230709946 230710650 0.000000e+00 761
7 TraesCS4B01G315000 chr5D 81.260 619 102 11 1628 2237 486226158 486225545 2.740000e-134 488
8 TraesCS4B01G315000 chr4D 86.218 624 58 8 879 1477 478225756 478226376 0.000000e+00 651
9 TraesCS4B01G315000 chr4D 81.981 616 95 12 1630 2237 108832867 108833474 2.110000e-140 508
10 TraesCS4B01G315000 chr7D 81.716 711 108 15 7 708 423715099 423715796 7.360000e-160 573
11 TraesCS4B01G315000 chr7D 80.000 635 111 12 1617 2244 52260184 52260809 2.780000e-124 455
12 TraesCS4B01G315000 chr5B 81.523 709 118 11 9 709 354327471 354326768 2.650000e-159 571
13 TraesCS4B01G315000 chr5B 82.180 477 75 7 1628 2097 710358105 710358578 3.680000e-108 401
14 TraesCS4B01G315000 chr3D 81.503 692 114 12 3 685 113215540 113214854 7.420000e-155 556
15 TraesCS4B01G315000 chr5A 80.587 716 112 23 10 708 531669044 531668339 5.810000e-146 527
16 TraesCS4B01G315000 chr1D 83.507 576 83 10 1 569 346707548 346706978 5.810000e-146 527
17 TraesCS4B01G315000 chr1D 80.729 576 100 9 1628 2196 363798470 363799041 2.800000e-119 438
18 TraesCS4B01G315000 chr1D 79.669 605 99 20 1652 2243 232144086 232143493 4.720000e-112 414
19 TraesCS4B01G315000 chr1D 82.180 477 74 8 1628 2097 254638413 254637941 1.320000e-107 399
20 TraesCS4B01G315000 chr1D 80.420 286 49 5 1955 2237 36549674 36549955 6.650000e-51 211
21 TraesCS4B01G315000 chr1B 82.272 581 87 14 7 577 466947162 466946588 2.740000e-134 488
22 TraesCS4B01G315000 chr1B 80.589 577 98 12 1628 2196 487014512 487015082 1.300000e-117 433
23 TraesCS4B01G315000 chr2B 82.301 565 90 9 11 569 409305119 409305679 4.590000e-132 481
24 TraesCS4B01G315000 chr2D 81.138 615 101 11 1617 2223 8380591 8379984 1.650000e-131 479
25 TraesCS4B01G315000 chr2D 80.587 613 102 12 1628 2232 542198339 542197736 7.740000e-125 457
26 TraesCS4B01G315000 chr6B 79.934 608 110 9 1637 2237 33971020 33970418 1.010000e-118 436
27 TraesCS4B01G315000 chr1A 79.459 628 114 13 1616 2233 447639473 447640095 4.690000e-117 431
28 TraesCS4B01G315000 chr6D 79.741 617 96 21 1630 2235 189414300 189414898 1.020000e-113 420
29 TraesCS4B01G315000 chr7B 82.128 470 74 7 1773 2235 108270564 108270098 6.150000e-106 394
30 TraesCS4B01G315000 chr7B 79.412 340 60 9 1902 2237 747849009 747848676 5.110000e-57 231


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 TraesCS4B01G315000 chr4B 604442525 604444899 2374 False 4386 4386 100.000 1 2375 1 chr4B.!!$F2 2374
1 TraesCS4B01G315000 chr4B 604324356 604324912 556 False 701 701 89.427 152 707 1 chr4B.!!$F1 555
2 TraesCS4B01G315000 chr4A 684840622 684841637 1015 False 535 933 89.984 832 2374 2 chr4A.!!$F3 1542
3 TraesCS4B01G315000 chr4A 733536123 733536732 609 False 496 496 81.524 1628 2237 1 chr4A.!!$F2 609
4 TraesCS4B01G315000 chr4A 598588979 598589577 598 False 475 475 81.188 1639 2237 1 chr4A.!!$F1 598
5 TraesCS4B01G315000 chr5D 230709946 230710650 704 False 761 761 86.217 1 707 1 chr5D.!!$F1 706
6 TraesCS4B01G315000 chr5D 486225545 486226158 613 True 488 488 81.260 1628 2237 1 chr5D.!!$R1 609
7 TraesCS4B01G315000 chr4D 478225756 478226376 620 False 651 651 86.218 879 1477 1 chr4D.!!$F2 598
8 TraesCS4B01G315000 chr4D 108832867 108833474 607 False 508 508 81.981 1630 2237 1 chr4D.!!$F1 607
9 TraesCS4B01G315000 chr7D 423715099 423715796 697 False 573 573 81.716 7 708 1 chr7D.!!$F2 701
10 TraesCS4B01G315000 chr7D 52260184 52260809 625 False 455 455 80.000 1617 2244 1 chr7D.!!$F1 627
11 TraesCS4B01G315000 chr5B 354326768 354327471 703 True 571 571 81.523 9 709 1 chr5B.!!$R1 700
12 TraesCS4B01G315000 chr3D 113214854 113215540 686 True 556 556 81.503 3 685 1 chr3D.!!$R1 682
13 TraesCS4B01G315000 chr5A 531668339 531669044 705 True 527 527 80.587 10 708 1 chr5A.!!$R1 698
14 TraesCS4B01G315000 chr1D 346706978 346707548 570 True 527 527 83.507 1 569 1 chr1D.!!$R3 568
15 TraesCS4B01G315000 chr1D 363798470 363799041 571 False 438 438 80.729 1628 2196 1 chr1D.!!$F2 568
16 TraesCS4B01G315000 chr1D 232143493 232144086 593 True 414 414 79.669 1652 2243 1 chr1D.!!$R1 591
17 TraesCS4B01G315000 chr1B 466946588 466947162 574 True 488 488 82.272 7 577 1 chr1B.!!$R1 570
18 TraesCS4B01G315000 chr1B 487014512 487015082 570 False 433 433 80.589 1628 2196 1 chr1B.!!$F1 568
19 TraesCS4B01G315000 chr2B 409305119 409305679 560 False 481 481 82.301 11 569 1 chr2B.!!$F1 558
20 TraesCS4B01G315000 chr2D 8379984 8380591 607 True 479 479 81.138 1617 2223 1 chr2D.!!$R1 606
21 TraesCS4B01G315000 chr2D 542197736 542198339 603 True 457 457 80.587 1628 2232 1 chr2D.!!$R2 604
22 TraesCS4B01G315000 chr6B 33970418 33971020 602 True 436 436 79.934 1637 2237 1 chr6B.!!$R1 600
23 TraesCS4B01G315000 chr1A 447639473 447640095 622 False 431 431 79.459 1616 2233 1 chr1A.!!$F1 617
24 TraesCS4B01G315000 chr6D 189414300 189414898 598 False 420 420 79.741 1630 2235 1 chr6D.!!$F1 605

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
968 989 0.110688 CGTCATTCAGTTGCGTGGTG 60.111 55.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2102 2188 0.33812 TTTTTAGAGGGCCATGGGGG 59.662 55.0 15.13 0.0 40.85 5.4 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
40 41 2.636893 AGGAGCGGAGATTTCTATGCAT 59.363 45.455 3.79 3.79 0.00 3.96
46 47 4.322349 GCGGAGATTTCTATGCATACCTCT 60.322 45.833 1.16 2.64 0.00 3.69
68 71 0.536687 CCTCATGAGGCCGCAATGAT 60.537 55.000 28.45 0.00 42.44 2.45
141 145 4.953579 ACAGTTTCCTCTTTGGTGCTAAAA 59.046 37.500 0.00 0.00 37.07 1.52
225 229 2.951745 CGATCACGAGCTCGGCAC 60.952 66.667 36.93 23.26 44.95 5.01
304 308 3.581332 AGACCACCTTTCGTCAGGATAAA 59.419 43.478 9.31 0.00 37.39 1.40
333 337 4.191804 TCCTGTCCCCTTTCAAAATTGA 57.808 40.909 0.00 0.00 34.92 2.57
367 371 1.339631 CCTTCCCGCCTGTGTGATAAA 60.340 52.381 0.00 0.00 0.00 1.40
368 372 2.643551 CTTCCCGCCTGTGTGATAAAT 58.356 47.619 0.00 0.00 0.00 1.40
554 566 2.231380 AAGATGGCCCGAACCTGGT 61.231 57.895 0.00 0.00 0.00 4.00
585 598 8.210946 TCTCTTGTTCTTTCCTTCTCAACAATA 58.789 33.333 0.00 0.00 36.60 1.90
671 684 1.070786 GAACACGCCCCAGAGTTCA 59.929 57.895 0.00 0.00 40.05 3.18
675 688 0.535102 CACGCCCCAGAGTTCAAACT 60.535 55.000 0.00 0.00 43.16 2.66
696 715 1.917336 TACTGGGTTTGCGGATCCCC 61.917 60.000 6.06 9.36 40.41 4.81
708 727 0.179468 GGATCCCCGATTCCGACAAA 59.821 55.000 0.00 0.00 38.22 2.83
709 728 1.407712 GGATCCCCGATTCCGACAAAA 60.408 52.381 0.00 0.00 38.22 2.44
710 729 2.361789 GATCCCCGATTCCGACAAAAA 58.638 47.619 0.00 0.00 38.22 1.94
711 730 2.500392 TCCCCGATTCCGACAAAAAT 57.500 45.000 0.00 0.00 38.22 1.82
712 731 3.630892 TCCCCGATTCCGACAAAAATA 57.369 42.857 0.00 0.00 38.22 1.40
713 732 4.159244 TCCCCGATTCCGACAAAAATAT 57.841 40.909 0.00 0.00 38.22 1.28
714 733 3.880490 TCCCCGATTCCGACAAAAATATG 59.120 43.478 0.00 0.00 38.22 1.78
715 734 3.630312 CCCCGATTCCGACAAAAATATGT 59.370 43.478 0.00 0.00 38.22 2.29
716 735 4.817464 CCCCGATTCCGACAAAAATATGTA 59.183 41.667 0.00 0.00 38.22 2.29
717 736 5.277634 CCCCGATTCCGACAAAAATATGTAC 60.278 44.000 0.00 0.00 38.22 2.90
718 737 5.526111 CCCGATTCCGACAAAAATATGTACT 59.474 40.000 0.00 0.00 38.22 2.73
719 738 6.037830 CCCGATTCCGACAAAAATATGTACTT 59.962 38.462 0.00 0.00 38.22 2.24
720 739 7.123830 CCGATTCCGACAAAAATATGTACTTC 58.876 38.462 0.00 0.00 38.22 3.01
721 740 7.011109 CCGATTCCGACAAAAATATGTACTTCT 59.989 37.037 0.00 0.00 38.22 2.85
722 741 8.388103 CGATTCCGACAAAAATATGTACTTCTT 58.612 33.333 0.00 0.00 38.22 2.52
723 742 9.704098 GATTCCGACAAAAATATGTACTTCTTC 57.296 33.333 0.00 0.00 32.57 2.87
724 743 8.610248 TTCCGACAAAAATATGTACTTCTTCA 57.390 30.769 0.00 0.00 32.57 3.02
725 744 8.786826 TCCGACAAAAATATGTACTTCTTCAT 57.213 30.769 0.00 0.00 32.57 2.57
726 745 8.879759 TCCGACAAAAATATGTACTTCTTCATC 58.120 33.333 0.00 0.00 32.57 2.92
727 746 8.122952 CCGACAAAAATATGTACTTCTTCATCC 58.877 37.037 0.00 0.00 32.57 3.51
728 747 8.122952 CGACAAAAATATGTACTTCTTCATCCC 58.877 37.037 0.00 0.00 32.57 3.85
729 748 7.985476 ACAAAAATATGTACTTCTTCATCCCG 58.015 34.615 0.00 0.00 0.00 5.14
730 749 7.827236 ACAAAAATATGTACTTCTTCATCCCGA 59.173 33.333 0.00 0.00 0.00 5.14
731 750 8.338259 CAAAAATATGTACTTCTTCATCCCGAG 58.662 37.037 0.00 0.00 0.00 4.63
732 751 6.732896 AATATGTACTTCTTCATCCCGAGT 57.267 37.500 0.00 0.00 0.00 4.18
733 752 6.732896 ATATGTACTTCTTCATCCCGAGTT 57.267 37.500 0.00 0.00 0.00 3.01
734 753 7.834881 ATATGTACTTCTTCATCCCGAGTTA 57.165 36.000 0.00 0.00 0.00 2.24
735 754 5.320549 TGTACTTCTTCATCCCGAGTTAC 57.679 43.478 0.00 0.00 0.00 2.50
736 755 5.014858 TGTACTTCTTCATCCCGAGTTACT 58.985 41.667 0.00 0.00 0.00 2.24
737 756 5.479375 TGTACTTCTTCATCCCGAGTTACTT 59.521 40.000 0.00 0.00 0.00 2.24
738 757 4.822026 ACTTCTTCATCCCGAGTTACTTG 58.178 43.478 0.00 0.00 0.00 3.16
739 758 4.283722 ACTTCTTCATCCCGAGTTACTTGT 59.716 41.667 0.00 0.00 0.00 3.16
740 759 4.451629 TCTTCATCCCGAGTTACTTGTC 57.548 45.455 0.00 0.00 0.00 3.18
741 760 2.933495 TCATCCCGAGTTACTTGTCG 57.067 50.000 0.00 0.00 35.91 4.35
742 761 1.135199 TCATCCCGAGTTACTTGTCGC 60.135 52.381 0.00 0.00 34.78 5.19
743 762 0.892755 ATCCCGAGTTACTTGTCGCA 59.107 50.000 0.00 0.00 34.78 5.10
744 763 0.242825 TCCCGAGTTACTTGTCGCAG 59.757 55.000 0.00 0.00 34.78 5.18
745 764 0.242825 CCCGAGTTACTTGTCGCAGA 59.757 55.000 0.00 0.00 34.78 4.26
746 765 1.336517 CCCGAGTTACTTGTCGCAGAA 60.337 52.381 0.00 0.00 39.69 3.02
747 766 2.400399 CCGAGTTACTTGTCGCAGAAA 58.600 47.619 0.00 0.00 39.69 2.52
748 767 2.993899 CCGAGTTACTTGTCGCAGAAAT 59.006 45.455 0.00 0.00 39.69 2.17
749 768 3.432252 CCGAGTTACTTGTCGCAGAAATT 59.568 43.478 0.00 0.00 39.69 1.82
750 769 4.434330 CCGAGTTACTTGTCGCAGAAATTC 60.434 45.833 0.00 0.00 39.69 2.17
751 770 4.149922 CGAGTTACTTGTCGCAGAAATTCA 59.850 41.667 0.00 0.00 39.69 2.57
752 771 5.344207 AGTTACTTGTCGCAGAAATTCAC 57.656 39.130 0.00 0.00 39.69 3.18
753 772 4.814234 AGTTACTTGTCGCAGAAATTCACA 59.186 37.500 0.00 0.00 39.69 3.58
754 773 5.470098 AGTTACTTGTCGCAGAAATTCACAT 59.530 36.000 0.00 0.00 39.69 3.21
755 774 4.410492 ACTTGTCGCAGAAATTCACATC 57.590 40.909 0.00 0.00 39.69 3.06
756 775 3.189287 ACTTGTCGCAGAAATTCACATCC 59.811 43.478 0.00 0.00 39.69 3.51
757 776 2.777094 TGTCGCAGAAATTCACATCCA 58.223 42.857 0.00 0.00 39.69 3.41
758 777 3.346315 TGTCGCAGAAATTCACATCCAT 58.654 40.909 0.00 0.00 39.69 3.41
759 778 3.758023 TGTCGCAGAAATTCACATCCATT 59.242 39.130 0.00 0.00 39.69 3.16
760 779 4.218200 TGTCGCAGAAATTCACATCCATTT 59.782 37.500 0.00 0.00 39.69 2.32
761 780 5.414144 TGTCGCAGAAATTCACATCCATTTA 59.586 36.000 0.00 0.00 39.69 1.40
762 781 6.095300 TGTCGCAGAAATTCACATCCATTTAT 59.905 34.615 0.00 0.00 39.69 1.40
763 782 6.634436 GTCGCAGAAATTCACATCCATTTATC 59.366 38.462 0.00 0.00 39.69 1.75
764 783 5.916883 CGCAGAAATTCACATCCATTTATCC 59.083 40.000 0.00 0.00 0.00 2.59
765 784 6.459985 CGCAGAAATTCACATCCATTTATCCA 60.460 38.462 0.00 0.00 0.00 3.41
766 785 7.439381 GCAGAAATTCACATCCATTTATCCAT 58.561 34.615 0.00 0.00 0.00 3.41
767 786 7.929785 GCAGAAATTCACATCCATTTATCCATT 59.070 33.333 0.00 0.00 0.00 3.16
768 787 9.826574 CAGAAATTCACATCCATTTATCCATTT 57.173 29.630 0.00 0.00 0.00 2.32
771 790 9.826574 AAATTCACATCCATTTATCCATTTCTG 57.173 29.630 0.00 0.00 0.00 3.02
772 791 6.964807 TCACATCCATTTATCCATTTCTGG 57.035 37.500 0.00 0.00 44.64 3.86
773 792 5.834742 TCACATCCATTTATCCATTTCTGGG 59.165 40.000 0.00 0.00 43.34 4.45
774 793 5.834742 CACATCCATTTATCCATTTCTGGGA 59.165 40.000 0.00 0.00 43.34 4.37
775 794 6.495872 CACATCCATTTATCCATTTCTGGGAT 59.504 38.462 0.00 0.00 46.62 3.85
776 795 6.495872 ACATCCATTTATCCATTTCTGGGATG 59.504 38.462 13.60 13.60 44.70 3.51
777 796 6.278438 TCCATTTATCCATTTCTGGGATGA 57.722 37.500 4.25 0.00 44.70 2.92
778 797 6.309357 TCCATTTATCCATTTCTGGGATGAG 58.691 40.000 4.25 0.00 44.70 2.90
779 798 6.073314 CCATTTATCCATTTCTGGGATGAGT 58.927 40.000 4.25 0.00 44.70 3.41
780 799 7.073598 TCCATTTATCCATTTCTGGGATGAGTA 59.926 37.037 4.25 0.00 44.70 2.59
781 800 7.725397 CCATTTATCCATTTCTGGGATGAGTAA 59.275 37.037 4.25 0.00 44.70 2.24
782 801 9.305555 CATTTATCCATTTCTGGGATGAGTAAT 57.694 33.333 4.25 0.00 44.70 1.89
783 802 9.887862 ATTTATCCATTTCTGGGATGAGTAATT 57.112 29.630 4.25 0.00 44.70 1.40
787 806 7.461749 TCCATTTCTGGGATGAGTAATTATCC 58.538 38.462 5.45 5.45 43.34 2.59
788 807 7.073598 TCCATTTCTGGGATGAGTAATTATCCA 59.926 37.037 14.98 2.12 43.74 3.41
789 808 7.725397 CCATTTCTGGGATGAGTAATTATCCAA 59.275 37.037 14.98 3.74 43.74 3.53
790 809 9.305555 CATTTCTGGGATGAGTAATTATCCAAT 57.694 33.333 14.98 4.37 43.74 3.16
791 810 9.887862 ATTTCTGGGATGAGTAATTATCCAATT 57.112 29.630 14.98 0.00 43.74 2.32
792 811 9.713684 TTTCTGGGATGAGTAATTATCCAATTT 57.286 29.630 14.98 0.00 43.74 1.82
793 812 9.713684 TTCTGGGATGAGTAATTATCCAATTTT 57.286 29.630 14.98 0.00 43.74 1.82
794 813 9.135189 TCTGGGATGAGTAATTATCCAATTTTG 57.865 33.333 14.98 0.00 43.74 2.44
795 814 8.837099 TGGGATGAGTAATTATCCAATTTTGT 57.163 30.769 14.98 0.00 43.74 2.83
796 815 8.694540 TGGGATGAGTAATTATCCAATTTTGTG 58.305 33.333 14.98 0.00 43.74 3.33
797 816 8.912988 GGGATGAGTAATTATCCAATTTTGTGA 58.087 33.333 14.98 0.00 43.74 3.58
798 817 9.736023 GGATGAGTAATTATCCAATTTTGTGAC 57.264 33.333 8.95 0.00 41.97 3.67
810 829 8.231692 TCCAATTTTGTGACAAGTAATTCAGA 57.768 30.769 5.29 3.89 0.00 3.27
811 830 8.352201 TCCAATTTTGTGACAAGTAATTCAGAG 58.648 33.333 5.29 0.00 0.00 3.35
812 831 7.596248 CCAATTTTGTGACAAGTAATTCAGAGG 59.404 37.037 5.29 1.78 0.00 3.69
813 832 5.689383 TTTGTGACAAGTAATTCAGAGGC 57.311 39.130 0.00 0.00 0.00 4.70
814 833 4.350368 TGTGACAAGTAATTCAGAGGCA 57.650 40.909 0.00 0.00 0.00 4.75
815 834 4.713553 TGTGACAAGTAATTCAGAGGCAA 58.286 39.130 0.00 0.00 0.00 4.52
816 835 4.756642 TGTGACAAGTAATTCAGAGGCAAG 59.243 41.667 0.00 0.00 0.00 4.01
817 836 4.997395 GTGACAAGTAATTCAGAGGCAAGA 59.003 41.667 0.00 0.00 0.00 3.02
818 837 5.645497 GTGACAAGTAATTCAGAGGCAAGAT 59.355 40.000 0.00 0.00 0.00 2.40
819 838 5.645067 TGACAAGTAATTCAGAGGCAAGATG 59.355 40.000 0.00 0.00 0.00 2.90
820 839 5.564550 ACAAGTAATTCAGAGGCAAGATGT 58.435 37.500 0.00 0.00 0.00 3.06
821 840 5.413833 ACAAGTAATTCAGAGGCAAGATGTG 59.586 40.000 0.00 0.00 0.00 3.21
822 841 4.521146 AGTAATTCAGAGGCAAGATGTGG 58.479 43.478 0.00 0.00 0.00 4.17
823 842 3.446442 AATTCAGAGGCAAGATGTGGT 57.554 42.857 0.00 0.00 0.00 4.16
824 843 4.574674 AATTCAGAGGCAAGATGTGGTA 57.425 40.909 0.00 0.00 0.00 3.25
825 844 4.574674 ATTCAGAGGCAAGATGTGGTAA 57.425 40.909 0.00 0.00 0.00 2.85
826 845 3.616956 TCAGAGGCAAGATGTGGTAAG 57.383 47.619 0.00 0.00 0.00 2.34
827 846 3.173151 TCAGAGGCAAGATGTGGTAAGA 58.827 45.455 0.00 0.00 0.00 2.10
828 847 3.196469 TCAGAGGCAAGATGTGGTAAGAG 59.804 47.826 0.00 0.00 0.00 2.85
829 848 2.093235 AGAGGCAAGATGTGGTAAGAGC 60.093 50.000 0.00 0.00 0.00 4.09
830 849 1.630369 AGGCAAGATGTGGTAAGAGCA 59.370 47.619 0.00 0.00 0.00 4.26
831 850 2.240667 AGGCAAGATGTGGTAAGAGCAT 59.759 45.455 0.00 0.00 0.00 3.79
832 851 3.019564 GGCAAGATGTGGTAAGAGCATT 58.980 45.455 0.00 0.00 0.00 3.56
833 852 3.445096 GGCAAGATGTGGTAAGAGCATTT 59.555 43.478 0.00 0.00 0.00 2.32
834 853 4.082026 GGCAAGATGTGGTAAGAGCATTTT 60.082 41.667 0.00 0.00 0.00 1.82
835 854 5.473039 GCAAGATGTGGTAAGAGCATTTTT 58.527 37.500 0.00 0.00 0.00 1.94
863 882 3.766676 ACAGTGTGTCGTAGCATCTAG 57.233 47.619 0.00 0.00 0.00 2.43
877 896 0.947660 ATCTAGCCATGCGCATGTCG 60.948 55.000 39.70 29.31 41.38 4.35
881 900 0.321034 AGCCATGCGCATGTCGATAT 60.321 50.000 39.70 20.72 41.38 1.63
915 934 3.244112 ACCTATAAATGCTAGTGGCGACC 60.244 47.826 0.00 0.00 45.43 4.79
968 989 0.110688 CGTCATTCAGTTGCGTGGTG 60.111 55.000 0.00 0.00 0.00 4.17
1010 1041 0.743688 GTGACCAACATGCCAACACA 59.256 50.000 0.00 0.00 0.00 3.72
1068 1099 2.654877 CGGTGCAAGTCCGGTACT 59.345 61.111 0.00 0.30 43.68 2.73
1072 1103 1.839747 TGCAAGTCCGGTACTGGGT 60.840 57.895 20.89 5.79 38.88 4.51
1282 1313 2.927580 TTCCTCGACGTCCTGTGGC 61.928 63.158 10.58 0.00 0.00 5.01
1333 1376 4.176752 GCCGGCGGGGAAGAGATT 62.177 66.667 29.48 0.00 38.47 2.40
1457 1500 2.222727 AGTGGGCAGCAGCTTCTCT 61.223 57.895 0.00 0.00 41.70 3.10
1470 1513 1.784525 CTTCTCTCACGGTTCACACC 58.215 55.000 0.00 0.00 40.16 4.16
1509 1552 8.087750 TCTGGCACAAGGAAATTAATAAACTTG 58.912 33.333 17.46 17.46 38.70 3.16
1536 1599 0.381801 CACACCAAGCTCTGCGTTTT 59.618 50.000 0.00 0.00 0.00 2.43
1650 1721 7.537306 ACCAAAAACGTTCGATCTATTCATTTG 59.463 33.333 0.00 4.07 0.00 2.32
1669 1741 6.432472 TCATTTGCAATCATGGTAGTACAACA 59.568 34.615 10.47 0.00 0.00 3.33
1674 1746 6.039829 TGCAATCATGGTAGTACAACAAACAA 59.960 34.615 2.06 0.00 0.00 2.83
1721 1793 6.294453 CCAGATTCATAGATGAGCTAACGACT 60.294 42.308 0.00 0.00 38.19 4.18
1722 1794 6.581919 CAGATTCATAGATGAGCTAACGACTG 59.418 42.308 0.00 0.00 38.19 3.51
1748 1820 2.771089 AGCATTGAAGCGAGACAAAGA 58.229 42.857 0.00 0.00 40.15 2.52
1756 1828 2.733593 GAGACAAAGACGCGCCGT 60.734 61.111 5.73 2.55 45.10 5.68
1797 1872 0.955905 GAGCCGGGCAAAACTTGTTA 59.044 50.000 23.09 0.00 0.00 2.41
1798 1873 0.671796 AGCCGGGCAAAACTTGTTAC 59.328 50.000 23.09 0.00 0.00 2.50
1815 1890 5.471556 TGTTACAATAGACAGTCGGGAAA 57.528 39.130 0.00 0.00 0.00 3.13
1844 1921 1.843851 CTAAGCCCCATAGGACCAACA 59.156 52.381 0.00 0.00 38.24 3.33
1849 1926 0.392461 CCCATAGGACCAACACACCG 60.392 60.000 0.00 0.00 33.47 4.94
1850 1927 0.323629 CCATAGGACCAACACACCGT 59.676 55.000 0.00 0.00 0.00 4.83
1873 1950 2.960129 CTACCGCCGCCGATGAAC 60.960 66.667 0.00 0.00 36.29 3.18
1926 2008 4.227538 AGACACGAACATAGACGAACAAG 58.772 43.478 0.00 0.00 0.00 3.16
1929 2011 4.174009 CACGAACATAGACGAACAAGGAT 58.826 43.478 0.00 0.00 0.00 3.24
1947 2029 2.064762 GATCAGATCCGAGCAAATCCG 58.935 52.381 0.00 0.00 0.00 4.18
1966 2048 2.285083 CGCCAAAGATAAATCCACCGA 58.715 47.619 0.00 0.00 0.00 4.69
1984 2067 1.135373 CGAAGATACACCTCACACGCT 60.135 52.381 0.00 0.00 0.00 5.07
2013 2097 1.153823 CTAGACGCACCACCGGAAG 60.154 63.158 9.46 0.00 0.00 3.46
2046 2132 5.358725 GCGGGAAGACCTTTATTCCATTTTA 59.641 40.000 6.33 0.00 45.70 1.52
2066 2152 3.706373 GGAGCCGCCCTTGTCTCA 61.706 66.667 0.00 0.00 0.00 3.27
2067 2153 2.347490 GAGCCGCCCTTGTCTCAA 59.653 61.111 0.00 0.00 0.00 3.02
2073 2159 0.811281 CGCCCTTGTCTCAAATTCCC 59.189 55.000 0.00 0.00 0.00 3.97
2097 2183 3.380320 AGCAGGACACAAAACCTAACAAC 59.620 43.478 0.00 0.00 34.87 3.32
2099 2185 2.946990 AGGACACAAAACCTAACAACGG 59.053 45.455 0.00 0.00 34.47 4.44
2101 2187 3.002965 GGACACAAAACCTAACAACGGAG 59.997 47.826 0.00 0.00 0.00 4.63
2102 2188 2.356695 ACACAAAACCTAACAACGGAGC 59.643 45.455 0.00 0.00 0.00 4.70
2103 2189 1.951602 ACAAAACCTAACAACGGAGCC 59.048 47.619 0.00 0.00 0.00 4.70
2104 2190 1.268625 CAAAACCTAACAACGGAGCCC 59.731 52.381 0.00 0.00 0.00 5.19
2105 2191 0.251033 AAACCTAACAACGGAGCCCC 60.251 55.000 0.00 0.00 0.00 5.80
2106 2192 2.133359 AACCTAACAACGGAGCCCCC 62.133 60.000 0.00 0.00 0.00 5.40
2109 2195 0.748005 CTAACAACGGAGCCCCCATG 60.748 60.000 0.00 0.00 34.14 3.66
2237 2327 1.134371 GGTAGAGGCACCCTAGCTTTG 60.134 57.143 0.00 0.00 34.29 2.77
2238 2328 1.134371 GTAGAGGCACCCTAGCTTTGG 60.134 57.143 0.00 0.00 31.76 3.28
2247 2337 2.130272 CCTAGCTTTGGGAAGGAACC 57.870 55.000 0.00 0.00 33.34 3.62
2248 2338 1.636003 CCTAGCTTTGGGAAGGAACCT 59.364 52.381 0.00 0.00 33.34 3.50
2249 2339 2.041755 CCTAGCTTTGGGAAGGAACCTT 59.958 50.000 5.74 5.74 39.23 3.50
2263 2353 7.981102 GAAGGAACCTTCTGTAACTGTAAAT 57.019 36.000 21.88 0.00 46.38 1.40
2264 2354 7.981102 AAGGAACCTTCTGTAACTGTAAATC 57.019 36.000 0.00 0.00 0.00 2.17
2265 2355 7.074653 AGGAACCTTCTGTAACTGTAAATCA 57.925 36.000 0.00 0.00 0.00 2.57
2266 2356 7.690256 AGGAACCTTCTGTAACTGTAAATCAT 58.310 34.615 0.00 0.00 0.00 2.45
2267 2357 8.164070 AGGAACCTTCTGTAACTGTAAATCATT 58.836 33.333 0.00 0.00 0.00 2.57
2268 2358 8.793592 GGAACCTTCTGTAACTGTAAATCATTT 58.206 33.333 0.00 0.00 0.00 2.32
2282 2372 9.196552 CTGTAAATCATTTTTCTTTCTTCCCAC 57.803 33.333 0.00 0.00 0.00 4.61
2285 2375 7.601705 AATCATTTTTCTTTCTTCCCACTCA 57.398 32.000 0.00 0.00 0.00 3.41
2287 2377 5.890985 TCATTTTTCTTTCTTCCCACTCACA 59.109 36.000 0.00 0.00 0.00 3.58
2293 2383 0.764271 TCTTCCCACTCACACATGCA 59.236 50.000 0.00 0.00 0.00 3.96
2300 2390 4.586421 TCCCACTCACACATGCATTTTTAA 59.414 37.500 0.00 0.00 0.00 1.52
2355 2445 8.826710 ACTGTTGAACCAAATATCGTATATGTG 58.173 33.333 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.473647 CCTCGGGATGCAGGCTCA 61.474 66.667 0.00 0.00 0.00 4.26
40 41 3.117657 CCTCATGAGGCGAGAGGTA 57.882 57.895 28.45 0.00 43.11 3.08
68 71 1.153066 TTGGTCTTCACGGCTTGCA 60.153 52.632 0.00 0.00 0.00 4.08
71 74 4.800554 CCTTGGTCTTCACGGCTT 57.199 55.556 0.00 0.00 0.00 4.35
76 79 0.108585 TGTCTGGCCTTGGTCTTCAC 59.891 55.000 3.32 0.00 0.00 3.18
80 83 3.488423 CCTGTCTGGCCTTGGTCT 58.512 61.111 3.32 0.00 0.00 3.85
105 108 2.129555 AAACTGTCCCTCATGCGCCT 62.130 55.000 4.18 0.00 0.00 5.52
141 145 2.357517 CGCGCCTGTCCTTGTCTT 60.358 61.111 0.00 0.00 0.00 3.01
171 175 1.000496 AAGGGAAACTTCTAGGGCCC 59.000 55.000 16.46 16.46 32.85 5.80
264 268 1.301677 CTTCGCCTGCAAAGGTCCTC 61.302 60.000 0.00 0.00 0.00 3.71
304 308 3.655777 TGAAAGGGGACAGGAAGTACATT 59.344 43.478 0.00 0.00 30.17 2.71
333 337 1.683441 GAAGGGATCCCACAACGGT 59.317 57.895 32.69 7.14 38.92 4.83
367 371 2.555664 AGTGGTCTTGGTCCTCATCAT 58.444 47.619 0.00 0.00 0.00 2.45
368 372 2.030027 AGTGGTCTTGGTCCTCATCA 57.970 50.000 0.00 0.00 0.00 3.07
507 518 2.621070 AGACCCTACTCCTGCTTTTGA 58.379 47.619 0.00 0.00 0.00 2.69
539 551 0.406361 TTTAACCAGGTTCGGGCCAT 59.594 50.000 8.57 0.00 0.00 4.40
554 566 9.627123 TTGAGAAGGAAAGAACAAGAGATTTAA 57.373 29.630 0.00 0.00 0.00 1.52
605 618 1.956629 GCTCGCTACACCCAAGGCTA 61.957 60.000 0.00 0.00 0.00 3.93
646 659 1.228124 TGGGGCGTGTTCCAAGAAG 60.228 57.895 0.00 0.00 0.00 2.85
652 665 1.671379 GAACTCTGGGGCGTGTTCC 60.671 63.158 0.00 0.00 34.47 3.62
671 684 2.657143 TCCGCAAACCCAGTAAAGTTT 58.343 42.857 0.00 0.00 36.65 2.66
675 688 1.614850 GGGATCCGCAAACCCAGTAAA 60.615 52.381 5.45 0.00 42.81 2.01
696 715 7.906160 AGAAGTACATATTTTTGTCGGAATCG 58.094 34.615 0.00 0.00 37.82 3.34
708 727 7.125792 ACTCGGGATGAAGAAGTACATATTT 57.874 36.000 0.00 0.00 0.00 1.40
709 728 6.732896 ACTCGGGATGAAGAAGTACATATT 57.267 37.500 0.00 0.00 0.00 1.28
710 729 6.732896 AACTCGGGATGAAGAAGTACATAT 57.267 37.500 0.00 0.00 0.00 1.78
711 730 6.832384 AGTAACTCGGGATGAAGAAGTACATA 59.168 38.462 0.00 0.00 0.00 2.29
712 731 5.657302 AGTAACTCGGGATGAAGAAGTACAT 59.343 40.000 0.00 0.00 0.00 2.29
713 732 5.014858 AGTAACTCGGGATGAAGAAGTACA 58.985 41.667 0.00 0.00 0.00 2.90
714 733 5.579564 AGTAACTCGGGATGAAGAAGTAC 57.420 43.478 0.00 0.00 0.00 2.73
715 734 5.479375 ACAAGTAACTCGGGATGAAGAAGTA 59.521 40.000 0.00 0.00 0.00 2.24
716 735 4.283722 ACAAGTAACTCGGGATGAAGAAGT 59.716 41.667 0.00 0.00 0.00 3.01
717 736 4.822026 ACAAGTAACTCGGGATGAAGAAG 58.178 43.478 0.00 0.00 0.00 2.85
718 737 4.617530 CGACAAGTAACTCGGGATGAAGAA 60.618 45.833 0.00 0.00 0.00 2.52
719 738 3.119602 CGACAAGTAACTCGGGATGAAGA 60.120 47.826 0.00 0.00 0.00 2.87
720 739 3.179830 CGACAAGTAACTCGGGATGAAG 58.820 50.000 0.00 0.00 0.00 3.02
721 740 2.673043 GCGACAAGTAACTCGGGATGAA 60.673 50.000 0.00 0.00 0.00 2.57
722 741 1.135199 GCGACAAGTAACTCGGGATGA 60.135 52.381 0.00 0.00 0.00 2.92
723 742 1.278238 GCGACAAGTAACTCGGGATG 58.722 55.000 0.00 0.00 0.00 3.51
724 743 0.892755 TGCGACAAGTAACTCGGGAT 59.107 50.000 0.00 0.00 0.00 3.85
725 744 0.242825 CTGCGACAAGTAACTCGGGA 59.757 55.000 0.00 0.00 0.00 5.14
726 745 0.242825 TCTGCGACAAGTAACTCGGG 59.757 55.000 0.00 0.00 0.00 5.14
727 746 2.060326 TTCTGCGACAAGTAACTCGG 57.940 50.000 0.00 0.00 0.00 4.63
728 747 4.149922 TGAATTTCTGCGACAAGTAACTCG 59.850 41.667 0.00 0.00 0.00 4.18
729 748 5.050363 TGTGAATTTCTGCGACAAGTAACTC 60.050 40.000 0.00 0.00 0.00 3.01
730 749 4.814234 TGTGAATTTCTGCGACAAGTAACT 59.186 37.500 0.00 0.00 0.00 2.24
731 750 5.090652 TGTGAATTTCTGCGACAAGTAAC 57.909 39.130 0.00 0.00 0.00 2.50
732 751 5.106712 GGATGTGAATTTCTGCGACAAGTAA 60.107 40.000 0.00 0.00 0.00 2.24
733 752 4.391830 GGATGTGAATTTCTGCGACAAGTA 59.608 41.667 0.00 0.00 0.00 2.24
734 753 3.189287 GGATGTGAATTTCTGCGACAAGT 59.811 43.478 0.00 0.00 0.00 3.16
735 754 3.189080 TGGATGTGAATTTCTGCGACAAG 59.811 43.478 0.00 0.00 0.00 3.16
736 755 3.145286 TGGATGTGAATTTCTGCGACAA 58.855 40.909 0.00 0.00 0.00 3.18
737 756 2.777094 TGGATGTGAATTTCTGCGACA 58.223 42.857 0.00 0.00 0.00 4.35
738 757 4.361451 AATGGATGTGAATTTCTGCGAC 57.639 40.909 0.00 0.00 0.00 5.19
739 758 6.238731 GGATAAATGGATGTGAATTTCTGCGA 60.239 38.462 0.00 0.00 0.00 5.10
740 759 5.916883 GGATAAATGGATGTGAATTTCTGCG 59.083 40.000 0.00 0.00 0.00 5.18
741 760 6.808829 TGGATAAATGGATGTGAATTTCTGC 58.191 36.000 0.00 0.00 0.00 4.26
742 761 9.826574 AAATGGATAAATGGATGTGAATTTCTG 57.173 29.630 0.00 0.00 0.00 3.02
745 764 9.826574 CAGAAATGGATAAATGGATGTGAATTT 57.173 29.630 0.00 0.00 0.00 1.82
746 765 8.426489 CCAGAAATGGATAAATGGATGTGAATT 58.574 33.333 0.00 0.00 0.00 2.17
747 766 7.015877 CCCAGAAATGGATAAATGGATGTGAAT 59.984 37.037 0.00 0.00 0.00 2.57
748 767 6.324512 CCCAGAAATGGATAAATGGATGTGAA 59.675 38.462 0.00 0.00 0.00 3.18
749 768 5.834742 CCCAGAAATGGATAAATGGATGTGA 59.165 40.000 0.00 0.00 0.00 3.58
750 769 5.834742 TCCCAGAAATGGATAAATGGATGTG 59.165 40.000 0.00 0.00 0.00 3.21
751 770 6.029492 TCCCAGAAATGGATAAATGGATGT 57.971 37.500 0.00 0.00 0.00 3.06
752 771 6.722590 TCATCCCAGAAATGGATAAATGGATG 59.277 38.462 8.10 8.10 45.08 3.51
753 772 6.866621 TCATCCCAGAAATGGATAAATGGAT 58.133 36.000 0.00 0.00 40.68 3.41
754 773 6.126097 ACTCATCCCAGAAATGGATAAATGGA 60.126 38.462 0.00 0.00 40.68 3.41
755 774 6.073314 ACTCATCCCAGAAATGGATAAATGG 58.927 40.000 0.00 0.00 40.68 3.16
756 775 8.696043 TTACTCATCCCAGAAATGGATAAATG 57.304 34.615 0.00 0.00 40.68 2.32
757 776 9.887862 AATTACTCATCCCAGAAATGGATAAAT 57.112 29.630 0.00 0.00 40.68 1.40
761 780 8.112183 GGATAATTACTCATCCCAGAAATGGAT 58.888 37.037 0.00 0.00 43.46 3.41
762 781 7.073598 TGGATAATTACTCATCCCAGAAATGGA 59.926 37.037 3.08 0.00 40.11 3.41
763 782 7.233632 TGGATAATTACTCATCCCAGAAATGG 58.766 38.462 3.08 0.00 40.11 3.16
764 783 8.696043 TTGGATAATTACTCATCCCAGAAATG 57.304 34.615 3.08 0.00 40.11 2.32
765 784 9.887862 AATTGGATAATTACTCATCCCAGAAAT 57.112 29.630 3.08 0.00 40.11 2.17
766 785 9.713684 AAATTGGATAATTACTCATCCCAGAAA 57.286 29.630 3.08 0.00 40.11 2.52
767 786 9.713684 AAAATTGGATAATTACTCATCCCAGAA 57.286 29.630 3.08 0.00 40.11 3.02
768 787 9.135189 CAAAATTGGATAATTACTCATCCCAGA 57.865 33.333 3.08 0.00 40.11 3.86
769 788 8.917088 ACAAAATTGGATAATTACTCATCCCAG 58.083 33.333 3.08 0.00 40.11 4.45
770 789 8.694540 CACAAAATTGGATAATTACTCATCCCA 58.305 33.333 3.08 0.00 40.11 4.37
771 790 8.912988 TCACAAAATTGGATAATTACTCATCCC 58.087 33.333 3.08 0.00 40.11 3.85
772 791 9.736023 GTCACAAAATTGGATAATTACTCATCC 57.264 33.333 0.00 0.00 41.05 3.51
784 803 8.859090 TCTGAATTACTTGTCACAAAATTGGAT 58.141 29.630 5.13 0.00 0.00 3.41
785 804 8.231692 TCTGAATTACTTGTCACAAAATTGGA 57.768 30.769 5.13 2.04 0.00 3.53
786 805 7.596248 CCTCTGAATTACTTGTCACAAAATTGG 59.404 37.037 5.13 0.00 0.00 3.16
787 806 7.115378 GCCTCTGAATTACTTGTCACAAAATTG 59.885 37.037 5.13 0.00 0.00 2.32
788 807 7.147976 GCCTCTGAATTACTTGTCACAAAATT 58.852 34.615 0.60 0.60 0.00 1.82
789 808 6.265196 TGCCTCTGAATTACTTGTCACAAAAT 59.735 34.615 0.00 0.00 0.00 1.82
790 809 5.592282 TGCCTCTGAATTACTTGTCACAAAA 59.408 36.000 0.00 0.00 0.00 2.44
791 810 5.129634 TGCCTCTGAATTACTTGTCACAAA 58.870 37.500 0.00 0.00 0.00 2.83
792 811 4.713553 TGCCTCTGAATTACTTGTCACAA 58.286 39.130 0.00 0.00 0.00 3.33
793 812 4.350368 TGCCTCTGAATTACTTGTCACA 57.650 40.909 0.00 0.00 0.00 3.58
794 813 4.997395 TCTTGCCTCTGAATTACTTGTCAC 59.003 41.667 0.00 0.00 0.00 3.67
795 814 5.227569 TCTTGCCTCTGAATTACTTGTCA 57.772 39.130 0.00 0.00 0.00 3.58
796 815 5.645497 ACATCTTGCCTCTGAATTACTTGTC 59.355 40.000 0.00 0.00 0.00 3.18
797 816 5.413833 CACATCTTGCCTCTGAATTACTTGT 59.586 40.000 0.00 0.00 0.00 3.16
798 817 5.163683 CCACATCTTGCCTCTGAATTACTTG 60.164 44.000 0.00 0.00 0.00 3.16
799 818 4.946157 CCACATCTTGCCTCTGAATTACTT 59.054 41.667 0.00 0.00 0.00 2.24
800 819 4.018960 ACCACATCTTGCCTCTGAATTACT 60.019 41.667 0.00 0.00 0.00 2.24
801 820 4.265073 ACCACATCTTGCCTCTGAATTAC 58.735 43.478 0.00 0.00 0.00 1.89
802 821 4.574674 ACCACATCTTGCCTCTGAATTA 57.425 40.909 0.00 0.00 0.00 1.40
803 822 3.446442 ACCACATCTTGCCTCTGAATT 57.554 42.857 0.00 0.00 0.00 2.17
804 823 4.225942 TCTTACCACATCTTGCCTCTGAAT 59.774 41.667 0.00 0.00 0.00 2.57
805 824 3.582647 TCTTACCACATCTTGCCTCTGAA 59.417 43.478 0.00 0.00 0.00 3.02
806 825 3.173151 TCTTACCACATCTTGCCTCTGA 58.827 45.455 0.00 0.00 0.00 3.27
807 826 3.529533 CTCTTACCACATCTTGCCTCTG 58.470 50.000 0.00 0.00 0.00 3.35
808 827 2.093235 GCTCTTACCACATCTTGCCTCT 60.093 50.000 0.00 0.00 0.00 3.69
809 828 2.284190 GCTCTTACCACATCTTGCCTC 58.716 52.381 0.00 0.00 0.00 4.70
810 829 1.630369 TGCTCTTACCACATCTTGCCT 59.370 47.619 0.00 0.00 0.00 4.75
811 830 2.113860 TGCTCTTACCACATCTTGCC 57.886 50.000 0.00 0.00 0.00 4.52
812 831 4.708726 AAATGCTCTTACCACATCTTGC 57.291 40.909 0.00 0.00 0.00 4.01
836 855 3.685272 TGCTACGACACACTGTTCAAAAA 59.315 39.130 0.00 0.00 0.00 1.94
837 856 3.263261 TGCTACGACACACTGTTCAAAA 58.737 40.909 0.00 0.00 0.00 2.44
838 857 2.894902 TGCTACGACACACTGTTCAAA 58.105 42.857 0.00 0.00 0.00 2.69
839 858 2.588027 TGCTACGACACACTGTTCAA 57.412 45.000 0.00 0.00 0.00 2.69
840 859 2.296190 AGATGCTACGACACACTGTTCA 59.704 45.455 0.00 0.00 0.00 3.18
841 860 2.947852 AGATGCTACGACACACTGTTC 58.052 47.619 0.00 0.00 0.00 3.18
842 861 3.673594 GCTAGATGCTACGACACACTGTT 60.674 47.826 0.00 0.00 38.95 3.16
843 862 2.159366 GCTAGATGCTACGACACACTGT 60.159 50.000 0.00 0.00 38.95 3.55
844 863 2.455032 GCTAGATGCTACGACACACTG 58.545 52.381 0.00 0.00 38.95 3.66
845 864 1.405821 GGCTAGATGCTACGACACACT 59.594 52.381 0.00 0.00 42.39 3.55
846 865 1.134367 TGGCTAGATGCTACGACACAC 59.866 52.381 0.00 0.00 42.39 3.82
847 866 1.470051 TGGCTAGATGCTACGACACA 58.530 50.000 0.00 0.00 42.39 3.72
848 867 2.398498 CATGGCTAGATGCTACGACAC 58.602 52.381 0.00 0.00 42.39 3.67
849 868 1.269778 GCATGGCTAGATGCTACGACA 60.270 52.381 8.74 0.00 44.57 4.35
850 869 1.423395 GCATGGCTAGATGCTACGAC 58.577 55.000 8.74 0.00 44.57 4.34
851 870 0.039165 CGCATGGCTAGATGCTACGA 60.039 55.000 12.95 0.00 45.60 3.43
852 871 1.621301 GCGCATGGCTAGATGCTACG 61.621 60.000 0.30 1.94 45.60 3.51
853 872 0.601046 TGCGCATGGCTAGATGCTAC 60.601 55.000 5.66 6.96 45.60 3.58
863 882 0.095935 GATATCGACATGCGCATGGC 59.904 55.000 43.46 42.03 43.37 4.40
866 885 2.001812 GAGGATATCGACATGCGCAT 57.998 50.000 19.28 19.28 40.61 4.73
915 934 3.031964 CTTTGCAAGAGGCTCGCCG 62.032 63.158 9.22 2.64 45.15 6.46
1010 1041 0.985490 GCTCCTCCTCATCCCCTTGT 60.985 60.000 0.00 0.00 0.00 3.16
1035 1066 4.154347 CGCTCCAGGGTCCTCAGC 62.154 72.222 7.21 7.21 0.00 4.26
1261 1292 2.504244 CAGGACGTCGAGGAACGC 60.504 66.667 12.85 0.00 46.40 4.84
1282 1313 1.517832 GTCTCCGTGGTCCATCTGG 59.482 63.158 0.00 0.00 0.00 3.86
1440 1483 1.744741 GAGAGAAGCTGCTGCCCAC 60.745 63.158 12.44 4.22 40.80 4.61
1457 1500 2.110213 GCCAGGTGTGAACCGTGA 59.890 61.111 0.00 0.00 34.28 4.35
1470 1513 0.393402 TGCCAGATGCTAACTGCCAG 60.393 55.000 0.00 0.00 42.00 4.85
1509 1552 1.279271 AGAGCTTGGTGTGGTATGACC 59.721 52.381 0.00 0.00 39.22 4.02
1536 1599 4.331717 GCGAATCTCCAACTAATCCGAAAA 59.668 41.667 0.00 0.00 0.00 2.29
1538 1601 3.118920 TGCGAATCTCCAACTAATCCGAA 60.119 43.478 0.00 0.00 0.00 4.30
1539 1602 2.429250 TGCGAATCTCCAACTAATCCGA 59.571 45.455 0.00 0.00 0.00 4.55
1633 1703 7.325338 CCATGATTGCAAATGAATAGATCGAAC 59.675 37.037 11.85 0.00 0.00 3.95
1650 1721 6.007936 TGTTTGTTGTACTACCATGATTGC 57.992 37.500 4.98 0.00 0.00 3.56
1695 1767 5.536538 TCGTTAGCTCATCTATGAATCTGGT 59.463 40.000 0.00 0.00 36.18 4.00
1709 1781 2.671351 GCTTGTAGCAGTCGTTAGCTCA 60.671 50.000 0.00 0.00 41.89 4.26
1710 1782 1.921230 GCTTGTAGCAGTCGTTAGCTC 59.079 52.381 0.00 0.00 41.89 4.09
1722 1794 2.002586 TCTCGCTTCAATGCTTGTAGC 58.997 47.619 13.58 13.58 46.58 3.58
1732 1804 0.859232 GCGTCTTTGTCTCGCTTCAA 59.141 50.000 0.00 0.00 45.29 2.69
1742 1814 0.668096 TGATAACGGCGCGTCTTTGT 60.668 50.000 13.14 5.69 39.99 2.83
1748 1820 3.327754 GCGATGATAACGGCGCGT 61.328 61.111 6.90 0.00 43.97 6.01
1756 1828 1.248486 CGAGGGAGGAGCGATGATAA 58.752 55.000 0.00 0.00 0.00 1.75
1797 1872 3.194968 ACGATTTCCCGACTGTCTATTGT 59.805 43.478 6.21 0.00 0.00 2.71
1798 1873 3.782046 ACGATTTCCCGACTGTCTATTG 58.218 45.455 6.21 0.00 0.00 1.90
1815 1890 1.686325 ATGGGGCTTAGCACGACGAT 61.686 55.000 6.53 0.00 29.41 3.73
1857 1934 3.709880 CTGTTCATCGGCGGCGGTA 62.710 63.158 31.73 14.01 0.00 4.02
1873 1950 5.041951 GATCCTTCTGATCTACGCTACTG 57.958 47.826 0.00 0.00 45.46 2.74
1926 2008 2.421619 GGATTTGCTCGGATCTGATCC 58.578 52.381 23.93 23.93 46.22 3.36
1929 2011 0.530650 GCGGATTTGCTCGGATCTGA 60.531 55.000 3.71 3.71 31.67 3.27
1947 2029 3.945285 TCTTCGGTGGATTTATCTTTGGC 59.055 43.478 0.00 0.00 0.00 4.52
1966 2048 1.893137 TGAGCGTGTGAGGTGTATCTT 59.107 47.619 0.00 0.00 0.00 2.40
1984 2067 4.922791 CGTCTAGCATCGCGATGA 57.077 55.556 44.20 27.52 41.20 2.92
2013 2097 2.042230 TCTTCCCGCCTAGTCCCC 60.042 66.667 0.00 0.00 0.00 4.81
2017 2102 2.242882 TAAAGGTCTTCCCGCCTAGT 57.757 50.000 0.00 0.00 38.74 2.57
2058 2144 2.417933 CTGCTCGGGAATTTGAGACAAG 59.582 50.000 7.30 0.00 34.04 3.16
2066 2152 0.400213 TGTGTCCTGCTCGGGAATTT 59.600 50.000 0.00 0.00 37.10 1.82
2067 2153 0.400213 TTGTGTCCTGCTCGGGAATT 59.600 50.000 0.00 0.00 37.10 2.17
2073 2159 2.163818 TAGGTTTTGTGTCCTGCTCG 57.836 50.000 0.00 0.00 35.51 5.03
2102 2188 0.338120 TTTTTAGAGGGCCATGGGGG 59.662 55.000 15.13 0.00 40.85 5.40
2103 2189 1.485124 GTTTTTAGAGGGCCATGGGG 58.515 55.000 15.13 0.00 37.18 4.96
2104 2190 1.102978 CGTTTTTAGAGGGCCATGGG 58.897 55.000 15.13 0.00 0.00 4.00
2105 2191 1.102978 CCGTTTTTAGAGGGCCATGG 58.897 55.000 7.63 7.63 0.00 3.66
2106 2192 2.017049 CTCCGTTTTTAGAGGGCCATG 58.983 52.381 6.18 0.00 0.00 3.66
2109 2195 1.030488 GGCTCCGTTTTTAGAGGGCC 61.030 60.000 0.00 0.00 35.41 5.80
2113 2199 2.025589 GGAGGGCTCCGTTTTTAGAG 57.974 55.000 0.00 0.00 40.36 2.43
2180 2268 2.750637 GGTCCGCCTCGTCTCTGA 60.751 66.667 0.00 0.00 0.00 3.27
2219 2307 1.204146 CCAAAGCTAGGGTGCCTCTA 58.796 55.000 0.00 0.00 34.61 2.43
2225 2314 0.991920 TCCTTCCCAAAGCTAGGGTG 59.008 55.000 20.41 14.94 46.82 4.61
2237 2327 3.072622 ACAGTTACAGAAGGTTCCTTCCC 59.927 47.826 23.02 9.97 42.30 3.97
2238 2328 4.353383 ACAGTTACAGAAGGTTCCTTCC 57.647 45.455 23.02 10.95 42.30 3.46
2254 2344 9.764363 GGGAAGAAAGAAAAATGATTTACAGTT 57.236 29.630 0.00 0.00 38.47 3.16
2255 2345 8.923270 TGGGAAGAAAGAAAAATGATTTACAGT 58.077 29.630 0.00 0.00 0.00 3.55
2256 2346 9.196552 GTGGGAAGAAAGAAAAATGATTTACAG 57.803 33.333 0.00 0.00 0.00 2.74
2257 2347 8.923270 AGTGGGAAGAAAGAAAAATGATTTACA 58.077 29.630 0.00 0.00 0.00 2.41
2258 2348 9.411801 GAGTGGGAAGAAAGAAAAATGATTTAC 57.588 33.333 0.00 0.00 0.00 2.01
2259 2349 9.142014 TGAGTGGGAAGAAAGAAAAATGATTTA 57.858 29.630 0.00 0.00 0.00 1.40
2260 2350 7.928167 GTGAGTGGGAAGAAAGAAAAATGATTT 59.072 33.333 0.00 0.00 0.00 2.17
2261 2351 7.069826 TGTGAGTGGGAAGAAAGAAAAATGATT 59.930 33.333 0.00 0.00 0.00 2.57
2262 2352 6.550854 TGTGAGTGGGAAGAAAGAAAAATGAT 59.449 34.615 0.00 0.00 0.00 2.45
2263 2353 5.890985 TGTGAGTGGGAAGAAAGAAAAATGA 59.109 36.000 0.00 0.00 0.00 2.57
2264 2354 5.979517 GTGTGAGTGGGAAGAAAGAAAAATG 59.020 40.000 0.00 0.00 0.00 2.32
2265 2355 5.656416 TGTGTGAGTGGGAAGAAAGAAAAAT 59.344 36.000 0.00 0.00 0.00 1.82
2266 2356 5.013547 TGTGTGAGTGGGAAGAAAGAAAAA 58.986 37.500 0.00 0.00 0.00 1.94
2267 2357 4.594970 TGTGTGAGTGGGAAGAAAGAAAA 58.405 39.130 0.00 0.00 0.00 2.29
2268 2358 4.229304 TGTGTGAGTGGGAAGAAAGAAA 57.771 40.909 0.00 0.00 0.00 2.52
2269 2359 3.924114 TGTGTGAGTGGGAAGAAAGAA 57.076 42.857 0.00 0.00 0.00 2.52
2270 2360 3.743521 CATGTGTGAGTGGGAAGAAAGA 58.256 45.455 0.00 0.00 0.00 2.52
2271 2361 2.227388 GCATGTGTGAGTGGGAAGAAAG 59.773 50.000 0.00 0.00 0.00 2.62
2272 2362 2.229792 GCATGTGTGAGTGGGAAGAAA 58.770 47.619 0.00 0.00 0.00 2.52
2273 2363 1.142667 TGCATGTGTGAGTGGGAAGAA 59.857 47.619 0.00 0.00 0.00 2.52
2274 2364 0.764271 TGCATGTGTGAGTGGGAAGA 59.236 50.000 0.00 0.00 0.00 2.87
2277 2367 2.291209 AAATGCATGTGTGAGTGGGA 57.709 45.000 0.00 0.00 0.00 4.37


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

AutoCloner maintained by Alex Coulton.