Multiple sequence alignment - TraesCS7B01G393800

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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 TraesCS7B01G393800 chr7B 100.000 5675 0 0 1 5675 660363521 660357847 0.000000e+00 10480.0
1 TraesCS7B01G393800 chr7B 95.502 578 25 1 1 577 672259475 672260052 0.000000e+00 922.0
2 TraesCS7B01G393800 chr7B 89.464 541 38 13 894 1425 699156350 699155820 0.000000e+00 665.0
3 TraesCS7B01G393800 chr7B 93.093 333 21 2 247 577 672286332 672286664 2.380000e-133 486.0
4 TraesCS7B01G393800 chr7B 93.114 334 20 3 247 577 672351568 672351901 2.380000e-133 486.0
5 TraesCS7B01G393800 chr7B 89.623 106 9 2 2928 3033 84214179 84214282 3.570000e-27 134.0
6 TraesCS7B01G393800 chr7B 92.000 75 6 0 497 571 694938274 694938348 7.780000e-19 106.0
7 TraesCS7B01G393800 chr7A 94.363 2111 94 14 845 2939 679927607 679925506 0.000000e+00 3216.0
8 TraesCS7B01G393800 chr7A 93.929 1186 47 10 3020 4195 679925508 679924338 0.000000e+00 1768.0
9 TraesCS7B01G393800 chr7A 92.593 1188 67 12 4174 5353 679924323 679923149 0.000000e+00 1687.0
10 TraesCS7B01G393800 chr7D 92.664 2140 93 40 828 2939 588068315 588066212 0.000000e+00 3024.0
11 TraesCS7B01G393800 chr7D 94.947 1128 40 6 3077 4195 588065994 588064875 0.000000e+00 1751.0
12 TraesCS7B01G393800 chr7D 90.394 1041 56 22 4664 5675 588064308 588063283 0.000000e+00 1328.0
13 TraesCS7B01G393800 chr7D 93.838 568 27 3 4153 4712 588064873 588064306 0.000000e+00 848.0
14 TraesCS7B01G393800 chr7D 96.429 56 2 0 3020 3075 588066214 588066159 6.050000e-15 93.5
15 TraesCS7B01G393800 chr2B 90.115 607 38 14 894 1491 369808859 369808266 0.000000e+00 769.0
16 TraesCS7B01G393800 chr2B 91.057 123 10 1 127 248 38263372 38263494 1.260000e-36 165.0
17 TraesCS7B01G393800 chr2B 90.566 106 8 1 183 288 38263488 38263591 7.670000e-29 139.0
18 TraesCS7B01G393800 chr1B 88.640 581 17 13 1 580 52568304 52568836 0.000000e+00 662.0
19 TraesCS7B01G393800 chr1B 87.737 579 21 4 1 577 52569067 52569597 1.040000e-176 630.0
20 TraesCS7B01G393800 chr1B 86.905 84 9 2 1219 1301 622482506 622482424 6.050000e-15 93.5
21 TraesCS7B01G393800 chr6B 94.681 94 5 0 2929 3022 13827517 13827610 4.580000e-31 147.0
22 TraesCS7B01G393800 chr6B 90.909 77 7 0 1016 1092 203919922 203919998 2.800000e-18 104.0
23 TraesCS7B01G393800 chr4B 96.591 88 3 0 2938 3025 4233601 4233514 4.580000e-31 147.0
24 TraesCS7B01G393800 chr1A 95.604 91 4 0 1 91 157836237 157836147 4.580000e-31 147.0
25 TraesCS7B01G393800 chr1A 85.000 100 14 1 472 571 17162692 17162790 3.620000e-17 100.0
26 TraesCS7B01G393800 chr1A 86.905 84 9 2 1219 1301 547318178 547318096 6.050000e-15 93.5
27 TraesCS7B01G393800 chr5B 95.556 90 4 0 2933 3022 62940318 62940407 1.650000e-30 145.0
28 TraesCS7B01G393800 chr5B 93.056 72 4 1 495 566 519740016 519739946 2.800000e-18 104.0
29 TraesCS7B01G393800 chr5D 94.624 93 4 1 2933 3025 40912866 40912957 5.930000e-30 143.0
30 TraesCS7B01G393800 chr5D 91.753 97 8 0 2934 3030 322375745 322375841 9.920000e-28 135.0
31 TraesCS7B01G393800 chr5A 95.556 90 3 1 2934 3022 450750797 450750708 5.930000e-30 143.0
32 TraesCS7B01G393800 chrUn 90.196 102 9 1 2930 3031 111025293 111025393 1.280000e-26 132.0
33 TraesCS7B01G393800 chr1D 93.333 90 5 1 2938 3026 64145523 64145434 1.280000e-26 132.0
34 TraesCS7B01G393800 chr1D 86.905 84 9 2 1219 1301 452493434 452493352 6.050000e-15 93.5
35 TraesCS7B01G393800 chr1D 90.909 66 5 1 155 219 427905105 427905170 2.820000e-13 87.9
36 TraesCS7B01G393800 chr1D 100.000 30 0 0 292 321 291091003 291090974 7.940000e-04 56.5
37 TraesCS7B01G393800 chr1D 92.308 39 2 1 160 197 116480405 116480443 3.000000e-03 54.7
38 TraesCS7B01G393800 chr4A 90.698 86 6 2 496 580 648466991 648466907 4.650000e-21 113.0
39 TraesCS7B01G393800 chr4A 96.296 54 2 0 20 73 546015035 546015088 7.830000e-14 89.8
40 TraesCS7B01G393800 chr3B 86.408 103 13 1 469 571 488534981 488535082 1.670000e-20 111.0
41 TraesCS7B01G393800 chr6D 91.139 79 7 0 1016 1094 114228937 114229015 2.160000e-19 108.0
42 TraesCS7B01G393800 chr6A 91.139 79 7 0 1016 1094 142780236 142780314 2.160000e-19 108.0
43 TraesCS7B01G393800 chr4D 95.000 40 1 1 160 198 226259297 226259336 1.710000e-05 62.1
44 TraesCS7B01G393800 chr2D 92.308 39 2 1 160 197 189671700 189671738 3.000000e-03 54.7
45 TraesCS7B01G393800 chr2D 96.970 33 0 1 166 197 592575840 592575808 3.000000e-03 54.7


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 TraesCS7B01G393800 chr7B 660357847 660363521 5674 True 10480.000000 10480 100.000000 1 5675 1 chr7B.!!$R1 5674
1 TraesCS7B01G393800 chr7B 672259475 672260052 577 False 922.000000 922 95.502000 1 577 1 chr7B.!!$F2 576
2 TraesCS7B01G393800 chr7B 699155820 699156350 530 True 665.000000 665 89.464000 894 1425 1 chr7B.!!$R2 531
3 TraesCS7B01G393800 chr7A 679923149 679927607 4458 True 2223.666667 3216 93.628333 845 5353 3 chr7A.!!$R1 4508
4 TraesCS7B01G393800 chr7D 588063283 588068315 5032 True 1408.900000 3024 93.654400 828 5675 5 chr7D.!!$R1 4847
5 TraesCS7B01G393800 chr2B 369808266 369808859 593 True 769.000000 769 90.115000 894 1491 1 chr2B.!!$R1 597
6 TraesCS7B01G393800 chr1B 52568304 52569597 1293 False 646.000000 662 88.188500 1 580 2 chr1B.!!$F1 579

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
809 812 0.036306 CTCCCCTACGCACACCTTTT 59.964 55.000 0.00 0.0 0.00 2.27 F
1510 1627 0.109873 CTTGCTCCTCGCTTTGCTTG 60.110 55.000 0.00 0.0 40.11 4.01 F
2022 2143 0.108615 AGCCGATCGTCTGGTGAAAG 60.109 55.000 15.09 0.0 0.00 2.62 F
3519 3815 1.068753 CATTGCGGCCAACCAACAA 59.931 52.632 2.24 0.0 36.42 2.83 F
4075 4371 1.081840 GCTCAGCTTGCGGTTGTTC 60.082 57.895 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2022 2143 0.250727 TTGCCAGAAGCCTGTGGTAC 60.251 55.000 0.0 0.0 42.71 3.34 R
3419 3715 1.002888 TGCTGGCTCTTCTTTCTCCTG 59.997 52.381 0.0 0.0 0.00 3.86 R
3677 3973 1.741401 TTCCACGATGGCAAGAGCG 60.741 57.895 0.0 0.0 43.41 5.03 R
4333 4679 1.589716 GCGATTTGCTGCCTCCTTGT 61.590 55.000 0.0 0.0 41.73 3.16 R
5633 6058 0.103823 TCCCCCTCCCCAAGTAACAA 60.104 55.000 0.0 0.0 0.00 2.83 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
86 87 1.153939 GATGCGAGATCGGGATCGG 60.154 63.158 4.18 1.61 42.48 4.18
465 468 2.766345 TTTACGATTAGTGGCGGGTT 57.234 45.000 0.00 0.00 0.00 4.11
467 470 3.883830 TTACGATTAGTGGCGGGTTAA 57.116 42.857 0.00 0.00 0.00 2.01
487 490 0.397254 CGTGAGGTGGGAGGAGGTAT 60.397 60.000 0.00 0.00 0.00 2.73
488 491 1.880941 GTGAGGTGGGAGGAGGTATT 58.119 55.000 0.00 0.00 0.00 1.89
525 528 0.178955 TAACCGAGTGAGGTGGGACA 60.179 55.000 0.00 0.00 45.21 4.02
535 538 6.294508 CGAGTGAGGTGGGACAAAAATAAAAT 60.295 38.462 0.00 0.00 44.16 1.82
567 570 5.450688 GCGACCTATCAACTGAGACATTAGT 60.451 44.000 0.00 0.00 0.00 2.24
582 585 9.916360 TGAGACATTAGTAGTTTAGATCTACCA 57.084 33.333 0.67 0.00 38.66 3.25
585 588 9.828852 GACATTAGTAGTTTAGATCTACCATCG 57.171 37.037 0.67 0.00 38.66 3.84
586 589 8.794553 ACATTAGTAGTTTAGATCTACCATCGG 58.205 37.037 0.67 0.00 38.66 4.18
587 590 9.011095 CATTAGTAGTTTAGATCTACCATCGGA 57.989 37.037 0.67 0.00 38.66 4.55
588 591 8.618702 TTAGTAGTTTAGATCTACCATCGGAG 57.381 38.462 0.67 0.00 38.66 4.63
589 592 4.857509 AGTTTAGATCTACCATCGGAGC 57.142 45.455 0.67 0.00 0.00 4.70
590 593 3.253677 AGTTTAGATCTACCATCGGAGCG 59.746 47.826 0.67 0.00 0.00 5.03
591 594 2.853235 TAGATCTACCATCGGAGCGA 57.147 50.000 0.00 0.00 41.13 4.93
593 596 3.351794 AGATCTACCATCGGAGCGATA 57.648 47.619 0.00 0.00 45.19 2.92
594 597 3.892284 AGATCTACCATCGGAGCGATAT 58.108 45.455 0.00 0.00 45.19 1.63
595 598 3.880490 AGATCTACCATCGGAGCGATATC 59.120 47.826 0.00 0.00 45.19 1.63
596 599 3.351794 TCTACCATCGGAGCGATATCT 57.648 47.619 0.34 0.00 45.19 1.98
597 600 4.482952 TCTACCATCGGAGCGATATCTA 57.517 45.455 0.34 0.00 45.19 1.98
598 601 4.190001 TCTACCATCGGAGCGATATCTAC 58.810 47.826 0.34 0.00 45.19 2.59
599 602 2.791655 ACCATCGGAGCGATATCTACA 58.208 47.619 0.34 0.00 45.19 2.74
600 603 3.154710 ACCATCGGAGCGATATCTACAA 58.845 45.455 0.34 0.00 45.19 2.41
601 604 3.572682 ACCATCGGAGCGATATCTACAAA 59.427 43.478 0.34 0.00 45.19 2.83
602 605 4.220821 ACCATCGGAGCGATATCTACAAAT 59.779 41.667 0.34 0.00 45.19 2.32
603 606 5.417894 ACCATCGGAGCGATATCTACAAATA 59.582 40.000 0.34 0.00 45.19 1.40
604 607 5.744345 CCATCGGAGCGATATCTACAAATAC 59.256 44.000 0.34 0.00 45.19 1.89
605 608 5.952526 TCGGAGCGATATCTACAAATACA 57.047 39.130 0.34 0.00 0.00 2.29
606 609 5.696822 TCGGAGCGATATCTACAAATACAC 58.303 41.667 0.34 0.00 0.00 2.90
607 610 5.239963 TCGGAGCGATATCTACAAATACACA 59.760 40.000 0.34 0.00 0.00 3.72
608 611 6.072119 TCGGAGCGATATCTACAAATACACAT 60.072 38.462 0.34 0.00 0.00 3.21
609 612 6.586463 CGGAGCGATATCTACAAATACACATT 59.414 38.462 0.34 0.00 0.00 2.71
610 613 7.116376 CGGAGCGATATCTACAAATACACATTT 59.884 37.037 0.34 0.00 34.60 2.32
611 614 8.774586 GGAGCGATATCTACAAATACACATTTT 58.225 33.333 0.34 0.00 31.82 1.82
639 642 9.793259 TTTTATCTTCTGACAGAGTAATTTGGT 57.207 29.630 5.10 0.00 0.00 3.67
640 643 8.777865 TTATCTTCTGACAGAGTAATTTGGTG 57.222 34.615 5.10 0.00 0.00 4.17
641 644 6.419484 TCTTCTGACAGAGTAATTTGGTGA 57.581 37.500 5.10 0.00 0.00 4.02
642 645 7.009179 TCTTCTGACAGAGTAATTTGGTGAT 57.991 36.000 5.10 0.00 0.00 3.06
643 646 6.875726 TCTTCTGACAGAGTAATTTGGTGATG 59.124 38.462 5.10 0.00 0.00 3.07
644 647 4.937620 TCTGACAGAGTAATTTGGTGATGC 59.062 41.667 0.00 0.00 0.00 3.91
645 648 4.009675 TGACAGAGTAATTTGGTGATGCC 58.990 43.478 0.00 0.00 37.90 4.40
653 656 4.002506 TGGTGATGCCACGCGACT 62.003 61.111 15.93 0.00 43.61 4.18
654 657 3.490759 GGTGATGCCACGCGACTG 61.491 66.667 15.93 0.00 44.09 3.51
655 658 2.738521 GTGATGCCACGCGACTGT 60.739 61.111 15.93 0.00 33.10 3.55
656 659 2.030412 TGATGCCACGCGACTGTT 59.970 55.556 15.93 0.00 0.00 3.16
657 660 2.316867 TGATGCCACGCGACTGTTG 61.317 57.895 15.93 0.00 0.00 3.33
658 661 3.027170 GATGCCACGCGACTGTTGG 62.027 63.158 15.93 11.32 0.00 3.77
659 662 3.825160 ATGCCACGCGACTGTTGGT 62.825 57.895 15.93 0.00 0.00 3.67
660 663 3.712881 GCCACGCGACTGTTGGTC 61.713 66.667 15.93 2.13 41.28 4.02
661 664 2.279851 CCACGCGACTGTTGGTCA 60.280 61.111 15.93 0.00 44.70 4.02
662 665 1.667830 CCACGCGACTGTTGGTCAT 60.668 57.895 15.93 0.00 44.70 3.06
663 666 1.626654 CCACGCGACTGTTGGTCATC 61.627 60.000 15.93 0.00 44.70 2.92
664 667 1.733041 ACGCGACTGTTGGTCATCG 60.733 57.895 15.93 0.00 44.70 3.84
665 668 2.444624 CGCGACTGTTGGTCATCGG 61.445 63.158 0.00 0.00 44.70 4.18
666 669 2.740714 GCGACTGTTGGTCATCGGC 61.741 63.158 0.00 0.00 44.70 5.54
667 670 1.079819 CGACTGTTGGTCATCGGCT 60.080 57.895 0.00 0.00 44.70 5.52
668 671 0.670546 CGACTGTTGGTCATCGGCTT 60.671 55.000 0.00 0.00 44.70 4.35
669 672 1.079503 GACTGTTGGTCATCGGCTTC 58.920 55.000 0.00 0.00 43.94 3.86
670 673 0.687354 ACTGTTGGTCATCGGCTTCT 59.313 50.000 0.00 0.00 0.00 2.85
671 674 1.338200 ACTGTTGGTCATCGGCTTCTC 60.338 52.381 0.00 0.00 0.00 2.87
672 675 0.036388 TGTTGGTCATCGGCTTCTCC 60.036 55.000 0.00 0.00 0.00 3.71
681 684 4.951963 GGCTTCTCCGGCGGATCG 62.952 72.222 31.23 19.28 0.00 3.69
742 745 4.530857 GACACCTCCGGCCCGATG 62.531 72.222 3.71 0.00 0.00 3.84
744 747 4.530857 CACCTCCGGCCCGATGTC 62.531 72.222 3.71 0.00 0.00 3.06
745 748 4.779733 ACCTCCGGCCCGATGTCT 62.780 66.667 3.71 0.00 0.00 3.41
746 749 3.917760 CCTCCGGCCCGATGTCTC 61.918 72.222 3.71 0.00 0.00 3.36
747 750 3.917760 CTCCGGCCCGATGTCTCC 61.918 72.222 3.71 0.00 0.00 3.71
750 753 4.570663 CGGCCCGATGTCTCCGTC 62.571 72.222 0.00 0.00 37.33 4.79
751 754 4.222847 GGCCCGATGTCTCCGTCC 62.223 72.222 0.00 0.00 0.00 4.79
752 755 4.222847 GCCCGATGTCTCCGTCCC 62.223 72.222 0.00 0.00 0.00 4.46
753 756 2.442272 CCCGATGTCTCCGTCCCT 60.442 66.667 0.00 0.00 0.00 4.20
754 757 2.491022 CCCGATGTCTCCGTCCCTC 61.491 68.421 0.00 0.00 0.00 4.30
755 758 1.454111 CCGATGTCTCCGTCCCTCT 60.454 63.158 0.00 0.00 0.00 3.69
756 759 1.448922 CCGATGTCTCCGTCCCTCTC 61.449 65.000 0.00 0.00 0.00 3.20
757 760 1.448922 CGATGTCTCCGTCCCTCTCC 61.449 65.000 0.00 0.00 0.00 3.71
758 761 1.448922 GATGTCTCCGTCCCTCTCCG 61.449 65.000 0.00 0.00 0.00 4.63
759 762 3.519930 GTCTCCGTCCCTCTCCGC 61.520 72.222 0.00 0.00 0.00 5.54
781 784 2.437002 GGTGTGGGCGCCGAATTA 60.437 61.111 22.54 3.53 35.34 1.40
782 785 1.822186 GGTGTGGGCGCCGAATTAT 60.822 57.895 22.54 0.00 35.34 1.28
783 786 1.647084 GTGTGGGCGCCGAATTATC 59.353 57.895 22.54 4.49 0.00 1.75
784 787 1.525077 TGTGGGCGCCGAATTATCC 60.525 57.895 22.54 3.66 0.00 2.59
785 788 2.280524 TGGGCGCCGAATTATCCG 60.281 61.111 22.54 0.00 0.00 4.18
786 789 2.029964 GGGCGCCGAATTATCCGA 59.970 61.111 22.54 0.00 0.00 4.55
787 790 2.315386 GGGCGCCGAATTATCCGAC 61.315 63.158 22.54 0.00 0.00 4.79
788 791 1.300697 GGCGCCGAATTATCCGACT 60.301 57.895 12.58 0.00 0.00 4.18
789 792 1.282930 GGCGCCGAATTATCCGACTC 61.283 60.000 12.58 0.00 0.00 3.36
790 793 1.282930 GCGCCGAATTATCCGACTCC 61.283 60.000 0.00 0.00 0.00 3.85
791 794 0.314302 CGCCGAATTATCCGACTCCT 59.686 55.000 0.00 0.00 0.00 3.69
792 795 1.666311 CGCCGAATTATCCGACTCCTC 60.666 57.143 0.00 0.00 0.00 3.71
793 796 1.336980 GCCGAATTATCCGACTCCTCC 60.337 57.143 0.00 0.00 0.00 4.30
794 797 1.272769 CCGAATTATCCGACTCCTCCC 59.727 57.143 0.00 0.00 0.00 4.30
795 798 1.272769 CGAATTATCCGACTCCTCCCC 59.727 57.143 0.00 0.00 0.00 4.81
796 799 2.610873 GAATTATCCGACTCCTCCCCT 58.389 52.381 0.00 0.00 0.00 4.79
797 800 3.775910 GAATTATCCGACTCCTCCCCTA 58.224 50.000 0.00 0.00 0.00 3.53
798 801 2.671896 TTATCCGACTCCTCCCCTAC 57.328 55.000 0.00 0.00 0.00 3.18
799 802 0.399454 TATCCGACTCCTCCCCTACG 59.601 60.000 0.00 0.00 0.00 3.51
800 803 2.980105 ATCCGACTCCTCCCCTACGC 62.980 65.000 0.00 0.00 0.00 4.42
801 804 2.439701 CGACTCCTCCCCTACGCA 60.440 66.667 0.00 0.00 0.00 5.24
802 805 2.772691 CGACTCCTCCCCTACGCAC 61.773 68.421 0.00 0.00 0.00 5.34
803 806 1.681327 GACTCCTCCCCTACGCACA 60.681 63.158 0.00 0.00 0.00 4.57
804 807 1.946475 GACTCCTCCCCTACGCACAC 61.946 65.000 0.00 0.00 0.00 3.82
805 808 2.682494 TCCTCCCCTACGCACACC 60.682 66.667 0.00 0.00 0.00 4.16
806 809 2.683933 CCTCCCCTACGCACACCT 60.684 66.667 0.00 0.00 0.00 4.00
807 810 2.291043 CCTCCCCTACGCACACCTT 61.291 63.158 0.00 0.00 0.00 3.50
808 811 1.677552 CTCCCCTACGCACACCTTT 59.322 57.895 0.00 0.00 0.00 3.11
809 812 0.036306 CTCCCCTACGCACACCTTTT 59.964 55.000 0.00 0.00 0.00 2.27
810 813 0.475044 TCCCCTACGCACACCTTTTT 59.525 50.000 0.00 0.00 0.00 1.94
887 890 1.571955 CCCCCTTGCTAAAATTGGCT 58.428 50.000 3.17 0.00 35.49 4.75
1105 1123 4.880426 TCAGCCCCTCCGATCCCC 62.880 72.222 0.00 0.00 0.00 4.81
1131 1238 0.239347 GGTTGCCGCATGCTCATATC 59.761 55.000 17.13 7.21 42.00 1.63
1157 1264 2.037641 CGTCTGATTATCCTGCATCCCA 59.962 50.000 0.00 0.00 0.00 4.37
1186 1294 6.614657 TCCTGTATCTGTCTGATTATCCTGA 58.385 40.000 0.00 0.00 36.65 3.86
1189 1297 7.818446 CCTGTATCTGTCTGATTATCCTGAATG 59.182 40.741 0.00 0.00 36.65 2.67
1190 1298 8.482852 TGTATCTGTCTGATTATCCTGAATGA 57.517 34.615 0.00 0.00 36.65 2.57
1195 1303 7.454066 TCTGTCTGATTATCCTGAATGATAGCT 59.546 37.037 0.00 0.00 0.00 3.32
1220 1333 4.504596 TGCTAATGCGCCCCAGGG 62.505 66.667 4.18 0.00 43.34 4.45
1367 1481 0.605589 CCATGCGGCCTTGGTAAAAA 59.394 50.000 0.00 0.00 32.94 1.94
1495 1609 3.891049 AGAATTGGATAGTGGGTCTTGC 58.109 45.455 0.00 0.00 0.00 4.01
1510 1627 0.109873 CTTGCTCCTCGCTTTGCTTG 60.110 55.000 0.00 0.00 40.11 4.01
1523 1640 5.048782 TCGCTTTGCTTGTCTATGTTGATTT 60.049 36.000 0.00 0.00 0.00 2.17
1531 1648 9.625747 TGCTTGTCTATGTTGATTTATAATCCA 57.374 29.630 0.00 0.00 0.00 3.41
1572 1689 5.340439 ACCGTTTATCTTGGTTCTCCTAG 57.660 43.478 0.00 0.00 37.80 3.02
1605 1725 4.274978 TGTCCATTGTGAGATGCATGAAT 58.725 39.130 2.46 0.00 0.00 2.57
1620 1740 5.500234 TGCATGAATAACTAGCAAGGAGTT 58.500 37.500 0.00 0.00 40.27 3.01
1623 1743 7.039784 TGCATGAATAACTAGCAAGGAGTTTTT 60.040 33.333 0.00 0.00 38.16 1.94
1624 1744 7.274250 GCATGAATAACTAGCAAGGAGTTTTTG 59.726 37.037 0.00 0.00 38.16 2.44
1656 1776 2.605338 CGAAAAGGGTGTGCATTGACTG 60.605 50.000 0.00 0.00 0.00 3.51
1662 1782 5.372343 AGGGTGTGCATTGACTGATAATA 57.628 39.130 0.00 0.00 0.00 0.98
1669 1789 7.166970 GTGTGCATTGACTGATAATATTTGCTG 59.833 37.037 0.00 0.00 0.00 4.41
1720 1840 7.285858 GTGATACATAGGTTACTGAGAGAAGGT 59.714 40.741 0.00 0.00 0.00 3.50
1823 1943 4.881850 CGAGCCCATTAGGTTTGTTCTATT 59.118 41.667 0.00 0.00 38.26 1.73
2022 2143 0.108615 AGCCGATCGTCTGGTGAAAG 60.109 55.000 15.09 0.00 0.00 2.62
2119 2243 4.764679 TTGGTTGTCATGACTGTAATGC 57.235 40.909 25.55 8.39 0.00 3.56
2123 2247 2.989909 TGTCATGACTGTAATGCTGGG 58.010 47.619 25.55 0.00 0.00 4.45
2134 2258 2.661574 AATGCTGGGGTGTTGGCACT 62.662 55.000 0.00 0.00 44.65 4.40
2222 2346 2.124277 TGCAGAAGCTACTACTCCGA 57.876 50.000 0.00 0.00 42.74 4.55
2257 2381 6.126507 TGCCAGGTTTGATTATAGGAAGATCA 60.127 38.462 0.00 0.00 0.00 2.92
2558 2682 2.167693 GGATGTCATCCTACGTGTTCCA 59.832 50.000 22.64 0.00 46.19 3.53
2702 2829 3.498777 GCAGGTACAGAAAGTCAGGTTTC 59.501 47.826 0.00 0.00 36.79 2.78
2719 2846 7.497579 GTCAGGTTTCTTCTTCTTCTTCTTCTT 59.502 37.037 0.00 0.00 0.00 2.52
2720 2847 7.713073 TCAGGTTTCTTCTTCTTCTTCTTCTTC 59.287 37.037 0.00 0.00 0.00 2.87
2721 2848 7.714813 CAGGTTTCTTCTTCTTCTTCTTCTTCT 59.285 37.037 0.00 0.00 0.00 2.85
2722 2849 7.931407 AGGTTTCTTCTTCTTCTTCTTCTTCTC 59.069 37.037 0.00 0.00 0.00 2.87
2723 2850 7.172532 GGTTTCTTCTTCTTCTTCTTCTTCTCC 59.827 40.741 0.00 0.00 0.00 3.71
2724 2851 7.610580 TTCTTCTTCTTCTTCTTCTTCTCCT 57.389 36.000 0.00 0.00 0.00 3.69
2725 2852 7.610580 TCTTCTTCTTCTTCTTCTTCTCCTT 57.389 36.000 0.00 0.00 0.00 3.36
2943 3070 7.317722 ACAGAGGGAATATTTATGTACTCCC 57.682 40.000 4.73 4.73 42.52 4.30
2948 3075 7.317722 GGGAATATTTATGTACTCCCTCTGT 57.682 40.000 5.51 0.00 39.61 3.41
2949 3076 8.431910 GGGAATATTTATGTACTCCCTCTGTA 57.568 38.462 5.51 0.00 39.61 2.74
2950 3077 8.877195 GGGAATATTTATGTACTCCCTCTGTAA 58.123 37.037 5.51 0.00 39.61 2.41
2964 3091 8.425703 ACTCCCTCTGTAAAGAAATATAAGAGC 58.574 37.037 0.00 0.00 0.00 4.09
2965 3092 7.434492 TCCCTCTGTAAAGAAATATAAGAGCG 58.566 38.462 0.00 0.00 0.00 5.03
2966 3093 7.069578 TCCCTCTGTAAAGAAATATAAGAGCGT 59.930 37.037 0.00 0.00 0.00 5.07
2967 3094 7.711339 CCCTCTGTAAAGAAATATAAGAGCGTT 59.289 37.037 0.00 0.00 0.00 4.84
2968 3095 9.099454 CCTCTGTAAAGAAATATAAGAGCGTTT 57.901 33.333 0.00 0.00 0.00 3.60
2985 3112 9.570488 AAGAGCGTTTAGATAACTACTTTAGTG 57.430 33.333 0.00 0.00 39.39 2.74
2986 3113 8.954350 AGAGCGTTTAGATAACTACTTTAGTGA 58.046 33.333 0.00 0.00 39.39 3.41
2987 3114 9.733219 GAGCGTTTAGATAACTACTTTAGTGAT 57.267 33.333 0.00 0.00 39.39 3.06
2988 3115 9.733219 AGCGTTTAGATAACTACTTTAGTGATC 57.267 33.333 3.29 3.29 44.00 2.92
3209 3499 2.108952 AGCCACCTTCTTCATTCCTTGT 59.891 45.455 0.00 0.00 0.00 3.16
3274 3570 1.805345 CGAGAGTGGTGAGTACGTTCT 59.195 52.381 0.00 0.00 0.00 3.01
3379 3675 2.234908 GCAGAGTTCACCTAGTGACCAT 59.765 50.000 0.00 0.00 42.60 3.55
3412 3708 1.202770 CCACAGGAAACCGAGAAACCT 60.203 52.381 0.00 0.00 0.00 3.50
3419 3715 3.242969 GGAAACCGAGAAACCTGTTGAAC 60.243 47.826 0.00 0.00 0.00 3.18
3465 3761 1.371183 CACCCGAAGAAGAGCCACA 59.629 57.895 0.00 0.00 0.00 4.17
3516 3812 2.522923 ACCATTGCGGCCAACCAA 60.523 55.556 2.24 2.90 39.03 3.67
3517 3813 2.048316 CCATTGCGGCCAACCAAC 60.048 61.111 2.24 0.00 32.95 3.77
3518 3814 2.733301 CATTGCGGCCAACCAACA 59.267 55.556 2.24 0.00 32.95 3.33
3519 3815 1.068753 CATTGCGGCCAACCAACAA 59.931 52.632 2.24 0.00 36.42 2.83
3565 3861 3.519107 TCCACTATGTTCTGCCTTCATGA 59.481 43.478 0.00 0.00 0.00 3.07
3608 3904 2.770164 ATCTTACACGCTTGCTCCTT 57.230 45.000 0.00 0.00 0.00 3.36
3677 3973 2.111756 CTTGAACAAAGCAACGCACTC 58.888 47.619 0.00 0.00 0.00 3.51
3827 4123 7.736447 ATCTTTAAGGTTGTATCTGCTATGC 57.264 36.000 0.00 0.00 0.00 3.14
3828 4124 6.889198 TCTTTAAGGTTGTATCTGCTATGCT 58.111 36.000 0.00 0.00 0.00 3.79
3849 4145 4.060900 CTGCTAAATACCGCATCATGACT 58.939 43.478 0.00 0.00 35.32 3.41
3979 4275 2.674380 CCAACCAGCTGTCAGCCC 60.674 66.667 21.32 0.00 43.77 5.19
4000 4296 5.240891 CCCAGTGGTATGTATATCTTGCTG 58.759 45.833 8.74 0.00 0.00 4.41
4075 4371 1.081840 GCTCAGCTTGCGGTTGTTC 60.082 57.895 0.00 0.00 0.00 3.18
4082 4378 1.332375 GCTTGCGGTTGTTCAGTTGTA 59.668 47.619 0.00 0.00 0.00 2.41
4111 4407 5.255710 TGAGCTGCAGAATCTAGTTAGTC 57.744 43.478 20.43 0.00 0.00 2.59
4130 4426 3.560068 AGTCACGGGCAATTTTATCGATC 59.440 43.478 0.00 0.00 0.00 3.69
4142 4438 8.869897 GCAATTTTATCGATCCTCGTGATATTA 58.130 33.333 0.00 0.00 41.35 0.98
4198 4544 9.723601 TTTCAATCCCCAAAATCAGAAATAAAG 57.276 29.630 0.00 0.00 0.00 1.85
4333 4679 2.353889 GACAGCCTATACGAAGACGACA 59.646 50.000 0.00 0.00 42.66 4.35
4335 4681 2.096980 CAGCCTATACGAAGACGACACA 59.903 50.000 0.00 0.00 42.66 3.72
4366 4712 0.108804 AATCGCCAGTGTGACCTACG 60.109 55.000 0.00 0.00 32.92 3.51
4401 4747 1.343142 GTGAACCCATTTGACCCCAAC 59.657 52.381 0.00 0.00 30.88 3.77
4530 4879 1.589727 GCAGCAGCAACAACACCAC 60.590 57.895 0.00 0.00 41.58 4.16
4611 4963 2.020181 GCCGGATTATCCAACCCGTTT 61.020 52.381 5.05 0.00 40.30 3.60
4626 4978 0.721718 CGTTTGGAGATCCGTTCAGC 59.278 55.000 0.00 0.00 39.43 4.26
4687 5039 1.331756 AGATTTAGCCTGAATTGCGCG 59.668 47.619 0.00 0.00 0.00 6.86
4731 5129 2.127271 TTCGGTCAGTCGTATACCCA 57.873 50.000 0.00 0.00 0.00 4.51
4732 5130 1.382522 TCGGTCAGTCGTATACCCAC 58.617 55.000 0.00 0.00 0.00 4.61
4733 5131 0.383231 CGGTCAGTCGTATACCCACC 59.617 60.000 0.00 0.00 0.00 4.61
4734 5132 0.749049 GGTCAGTCGTATACCCACCC 59.251 60.000 0.00 0.00 0.00 4.61
4767 5165 5.584253 TCTGAGGAGCAACTTGTATAGTC 57.416 43.478 0.00 0.00 35.54 2.59
4777 5175 6.073003 AGCAACTTGTATAGTCTGAACTTTGC 60.073 38.462 0.00 0.00 38.59 3.68
4780 5178 5.934625 ACTTGTATAGTCTGAACTTTGCTGG 59.065 40.000 0.00 0.00 36.92 4.85
4850 5248 1.196581 TCGTTTGAATGCCATGACACG 59.803 47.619 0.00 0.00 0.00 4.49
4858 5256 1.802069 TGCCATGACACGATTTCGAA 58.198 45.000 7.01 0.00 43.02 3.71
4861 5259 2.095969 GCCATGACACGATTTCGAACAA 60.096 45.455 7.01 0.00 43.02 2.83
4863 5261 3.059257 CCATGACACGATTTCGAACAACA 60.059 43.478 7.01 0.77 43.02 3.33
4882 5280 2.292569 ACAAGCACATCTCAGCAAACAG 59.707 45.455 0.00 0.00 0.00 3.16
4921 5322 8.408043 TCATCATCACACAACCTAGAAAAATT 57.592 30.769 0.00 0.00 0.00 1.82
4942 5343 6.780706 ATTACCAGTAACTGAAACTGTTCG 57.219 37.500 11.27 0.00 42.30 3.95
4981 5382 2.168521 GGCAGTAGCACAAGAGATGGTA 59.831 50.000 0.00 0.00 44.61 3.25
4985 5392 4.327357 CAGTAGCACAAGAGATGGTAAACG 59.673 45.833 0.00 0.00 32.18 3.60
5185 5595 2.515398 CACTTCACCCAGTGGCCA 59.485 61.111 0.00 0.00 40.60 5.36
5187 5597 2.078665 ACTTCACCCAGTGGCCAGT 61.079 57.895 5.11 6.41 33.87 4.00
5188 5598 1.601759 CTTCACCCAGTGGCCAGTG 60.602 63.158 30.55 30.55 33.87 3.66
5189 5599 3.790416 TTCACCCAGTGGCCAGTGC 62.790 63.158 31.82 9.54 33.87 4.40
5190 5600 4.584518 CACCCAGTGGCCAGTGCA 62.585 66.667 31.82 0.00 40.13 4.57
5191 5601 3.819652 ACCCAGTGGCCAGTGCAA 61.820 61.111 31.82 0.00 40.13 4.08
5192 5602 2.283388 CCCAGTGGCCAGTGCAAT 60.283 61.111 31.82 0.00 40.13 3.56
5194 5604 2.642254 CCAGTGGCCAGTGCAATGG 61.642 63.158 31.82 28.45 43.72 3.16
5195 5605 1.604308 CAGTGGCCAGTGCAATGGA 60.604 57.895 35.90 14.25 43.57 3.41
5196 5606 1.153524 AGTGGCCAGTGCAATGGAA 59.846 52.632 35.90 20.23 43.57 3.53
5197 5607 1.181098 AGTGGCCAGTGCAATGGAAC 61.181 55.000 35.90 29.05 43.57 3.62
5198 5608 1.153524 TGGCCAGTGCAATGGAACT 59.846 52.632 35.90 1.07 43.57 3.01
5199 5609 0.403655 TGGCCAGTGCAATGGAACTA 59.596 50.000 35.90 14.81 43.57 2.24
5200 5610 0.811281 GGCCAGTGCAATGGAACTAC 59.189 55.000 35.90 17.54 43.57 2.73
5271 5681 1.884926 CTCCTCATCCGGAAAGCGC 60.885 63.158 9.01 0.00 31.44 5.92
5325 5735 1.008079 GCAAGTGCAAGACCACAGC 60.008 57.895 0.00 0.00 41.59 4.40
5388 5799 0.314302 ACCGTCACTCCAAGAACTCG 59.686 55.000 0.00 0.00 0.00 4.18
5422 5833 1.076841 TGGGTTTGATGCCAGGATGAA 59.923 47.619 0.00 0.00 39.69 2.57
5434 5845 4.471025 TGCCAGGATGAAAACTAGAGATGA 59.529 41.667 0.00 0.00 39.69 2.92
5461 5872 6.777101 TGCGCGTGATTTATACTTTGTTAAT 58.223 32.000 8.43 0.00 0.00 1.40
5462 5873 6.902948 TGCGCGTGATTTATACTTTGTTAATC 59.097 34.615 8.43 0.00 0.00 1.75
5488 5913 3.071023 TCGATCAATAAGCCCGGAAGAAT 59.929 43.478 0.73 0.00 0.00 2.40
5497 5922 4.890158 AGCCCGGAAGAATTGAATTTTT 57.110 36.364 0.73 0.00 0.00 1.94
5498 5923 5.993748 AGCCCGGAAGAATTGAATTTTTA 57.006 34.783 0.73 0.00 0.00 1.52
5499 5924 5.720202 AGCCCGGAAGAATTGAATTTTTAC 58.280 37.500 0.73 0.00 0.00 2.01
5500 5925 4.561213 GCCCGGAAGAATTGAATTTTTACG 59.439 41.667 16.24 16.24 39.57 3.18
5524 5949 0.704076 ATTGCTAAACAGGGGAGCCA 59.296 50.000 0.00 0.00 35.24 4.75
5570 5995 1.561542 CTATTCTGGGGCTGTCCTTGT 59.438 52.381 0.00 0.00 35.33 3.16
5583 6008 0.521291 TCCTTGTGCTGCAAATACGC 59.479 50.000 2.77 0.00 36.53 4.42
5592 6017 1.867233 CTGCAAATACGCGCCTATTCT 59.133 47.619 5.73 1.54 33.35 2.40
5614 6039 1.540707 GGGCGTTTCGGGAATTGTTTA 59.459 47.619 0.00 0.00 0.00 2.01
5616 6041 3.367600 GGGCGTTTCGGGAATTGTTTATT 60.368 43.478 0.00 0.00 0.00 1.40
5618 6043 5.400703 GGCGTTTCGGGAATTGTTTATTTA 58.599 37.500 0.00 0.00 0.00 1.40
5654 6079 0.624254 GTTACTTGGGGAGGGGGAAG 59.376 60.000 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
422 425 1.065273 CGTACCGAATCCTCCACCG 59.935 63.158 0.00 0.00 0.00 4.94
432 435 3.085443 TCGTAAAAACCACGTACCGAA 57.915 42.857 0.00 0.00 40.27 4.30
452 455 1.275856 TCACGTTAACCCGCCACTAAT 59.724 47.619 0.00 0.00 0.00 1.73
465 468 0.613853 CCTCCTCCCACCTCACGTTA 60.614 60.000 0.00 0.00 0.00 3.18
467 470 1.797018 TACCTCCTCCCACCTCACGT 61.797 60.000 0.00 0.00 0.00 4.49
488 491 9.737844 ACTCGGTTATTTTTGGTACCTATTTTA 57.262 29.630 14.36 0.00 0.00 1.52
512 515 6.014584 GGATTTTATTTTTGTCCCACCTCACT 60.015 38.462 0.00 0.00 0.00 3.41
525 528 4.160594 GTCGCGTTCCGGATTTTATTTTT 58.839 39.130 4.15 0.00 37.59 1.94
535 538 1.314534 TTGATAGGTCGCGTTCCGGA 61.315 55.000 5.77 0.00 37.59 5.14
567 570 4.454847 CGCTCCGATGGTAGATCTAAACTA 59.545 45.833 3.40 0.00 0.00 2.24
580 583 3.850122 TTGTAGATATCGCTCCGATGG 57.150 47.619 10.10 0.00 46.43 3.51
581 584 6.251589 GTGTATTTGTAGATATCGCTCCGATG 59.748 42.308 10.10 0.00 46.43 3.84
583 586 5.239963 TGTGTATTTGTAGATATCGCTCCGA 59.760 40.000 0.00 0.00 41.13 4.55
585 588 7.891183 AATGTGTATTTGTAGATATCGCTCC 57.109 36.000 0.00 0.00 0.00 4.70
613 616 9.793259 ACCAAATTACTCTGTCAGAAGATAAAA 57.207 29.630 3.67 0.00 0.00 1.52
614 617 9.219603 CACCAAATTACTCTGTCAGAAGATAAA 57.780 33.333 3.67 0.00 0.00 1.40
615 618 8.593679 TCACCAAATTACTCTGTCAGAAGATAA 58.406 33.333 3.67 4.04 0.00 1.75
616 619 8.134202 TCACCAAATTACTCTGTCAGAAGATA 57.866 34.615 3.67 0.00 0.00 1.98
617 620 7.009179 TCACCAAATTACTCTGTCAGAAGAT 57.991 36.000 3.67 0.00 0.00 2.40
618 621 6.419484 TCACCAAATTACTCTGTCAGAAGA 57.581 37.500 3.67 0.00 0.00 2.87
619 622 6.402983 GCATCACCAAATTACTCTGTCAGAAG 60.403 42.308 3.67 1.28 0.00 2.85
620 623 5.412594 GCATCACCAAATTACTCTGTCAGAA 59.587 40.000 3.67 0.00 0.00 3.02
621 624 4.937620 GCATCACCAAATTACTCTGTCAGA 59.062 41.667 1.78 1.78 0.00 3.27
622 625 4.095483 GGCATCACCAAATTACTCTGTCAG 59.905 45.833 0.00 0.00 38.86 3.51
623 626 4.009675 GGCATCACCAAATTACTCTGTCA 58.990 43.478 0.00 0.00 38.86 3.58
624 627 4.622701 GGCATCACCAAATTACTCTGTC 57.377 45.455 0.00 0.00 38.86 3.51
637 640 3.490759 CAGTCGCGTGGCATCACC 61.491 66.667 5.77 0.00 40.65 4.02
638 641 2.317609 AACAGTCGCGTGGCATCAC 61.318 57.895 5.77 0.00 40.36 3.06
639 642 2.030412 AACAGTCGCGTGGCATCA 59.970 55.556 5.77 0.00 0.00 3.07
640 643 2.476051 CAACAGTCGCGTGGCATC 59.524 61.111 5.77 0.00 0.00 3.91
641 644 3.049674 CCAACAGTCGCGTGGCAT 61.050 61.111 5.77 0.00 0.00 4.40
642 645 4.539083 ACCAACAGTCGCGTGGCA 62.539 61.111 12.19 0.00 0.00 4.92
643 646 3.712881 GACCAACAGTCGCGTGGC 61.713 66.667 12.19 0.00 35.30 5.01
650 653 1.079503 GAAGCCGATGACCAACAGTC 58.920 55.000 0.00 0.00 46.51 3.51
651 654 0.687354 AGAAGCCGATGACCAACAGT 59.313 50.000 0.00 0.00 0.00 3.55
652 655 1.363744 GAGAAGCCGATGACCAACAG 58.636 55.000 0.00 0.00 0.00 3.16
653 656 0.036388 GGAGAAGCCGATGACCAACA 60.036 55.000 0.00 0.00 0.00 3.33
654 657 2.768834 GGAGAAGCCGATGACCAAC 58.231 57.895 0.00 0.00 0.00 3.77
664 667 4.951963 CGATCCGCCGGAGAAGCC 62.952 72.222 13.12 0.00 34.05 4.35
730 733 3.917760 GGAGACATCGGGCCGGAG 61.918 72.222 27.98 20.76 0.00 4.63
734 737 4.222847 GGACGGAGACATCGGGCC 62.223 72.222 0.00 0.00 45.77 5.80
735 738 4.222847 GGGACGGAGACATCGGGC 62.223 72.222 0.00 0.00 33.06 6.13
736 739 2.442272 AGGGACGGAGACATCGGG 60.442 66.667 0.00 0.00 0.00 5.14
737 740 1.448922 GAGAGGGACGGAGACATCGG 61.449 65.000 0.00 0.00 0.00 4.18
738 741 1.448922 GGAGAGGGACGGAGACATCG 61.449 65.000 0.00 0.00 0.00 3.84
739 742 1.448922 CGGAGAGGGACGGAGACATC 61.449 65.000 0.00 0.00 0.00 3.06
740 743 1.454111 CGGAGAGGGACGGAGACAT 60.454 63.158 0.00 0.00 0.00 3.06
741 744 2.045242 CGGAGAGGGACGGAGACA 60.045 66.667 0.00 0.00 0.00 3.41
742 745 3.519930 GCGGAGAGGGACGGAGAC 61.520 72.222 0.00 0.00 0.00 3.36
764 767 1.782028 GATAATTCGGCGCCCACACC 61.782 60.000 23.46 0.01 0.00 4.16
765 768 1.647084 GATAATTCGGCGCCCACAC 59.353 57.895 23.46 2.19 0.00 3.82
766 769 1.525077 GGATAATTCGGCGCCCACA 60.525 57.895 23.46 4.83 0.00 4.17
767 770 2.604174 CGGATAATTCGGCGCCCAC 61.604 63.158 23.46 4.25 0.00 4.61
768 771 2.280524 CGGATAATTCGGCGCCCA 60.281 61.111 23.46 4.67 0.00 5.36
769 772 2.029964 TCGGATAATTCGGCGCCC 59.970 61.111 23.46 4.12 0.00 6.13
770 773 1.282930 GAGTCGGATAATTCGGCGCC 61.283 60.000 19.07 19.07 37.31 6.53
771 774 1.282930 GGAGTCGGATAATTCGGCGC 61.283 60.000 0.00 0.00 37.31 6.53
772 775 0.314302 AGGAGTCGGATAATTCGGCG 59.686 55.000 0.00 0.00 37.31 6.46
773 776 1.336980 GGAGGAGTCGGATAATTCGGC 60.337 57.143 0.00 0.00 0.00 5.54
774 777 1.272769 GGGAGGAGTCGGATAATTCGG 59.727 57.143 0.00 0.00 0.00 4.30
775 778 1.272769 GGGGAGGAGTCGGATAATTCG 59.727 57.143 0.00 0.00 0.00 3.34
776 779 2.610873 AGGGGAGGAGTCGGATAATTC 58.389 52.381 0.00 0.00 0.00 2.17
777 780 2.797285 AGGGGAGGAGTCGGATAATT 57.203 50.000 0.00 0.00 0.00 1.40
778 781 2.554785 CGTAGGGGAGGAGTCGGATAAT 60.555 54.545 0.00 0.00 0.00 1.28
779 782 1.202855 CGTAGGGGAGGAGTCGGATAA 60.203 57.143 0.00 0.00 0.00 1.75
780 783 0.399454 CGTAGGGGAGGAGTCGGATA 59.601 60.000 0.00 0.00 0.00 2.59
781 784 1.150992 CGTAGGGGAGGAGTCGGAT 59.849 63.158 0.00 0.00 0.00 4.18
782 785 2.593978 CGTAGGGGAGGAGTCGGA 59.406 66.667 0.00 0.00 0.00 4.55
783 786 3.217743 GCGTAGGGGAGGAGTCGG 61.218 72.222 0.00 0.00 0.00 4.79
784 787 2.439701 TGCGTAGGGGAGGAGTCG 60.440 66.667 0.00 0.00 0.00 4.18
785 788 1.681327 TGTGCGTAGGGGAGGAGTC 60.681 63.158 0.00 0.00 0.00 3.36
786 789 1.982938 GTGTGCGTAGGGGAGGAGT 60.983 63.158 0.00 0.00 0.00 3.85
787 790 2.722201 GGTGTGCGTAGGGGAGGAG 61.722 68.421 0.00 0.00 0.00 3.69
788 791 2.682494 GGTGTGCGTAGGGGAGGA 60.682 66.667 0.00 0.00 0.00 3.71
789 792 1.838073 AAAGGTGTGCGTAGGGGAGG 61.838 60.000 0.00 0.00 0.00 4.30
790 793 0.036306 AAAAGGTGTGCGTAGGGGAG 59.964 55.000 0.00 0.00 0.00 4.30
791 794 0.475044 AAAAAGGTGTGCGTAGGGGA 59.525 50.000 0.00 0.00 0.00 4.81
792 795 3.030415 AAAAAGGTGTGCGTAGGGG 57.970 52.632 0.00 0.00 0.00 4.79
840 843 2.018086 AGGGAGAGGAGGAGGGGAG 61.018 68.421 0.00 0.00 0.00 4.30
887 890 1.117150 GATGGTACTTAGCCCGGTGA 58.883 55.000 0.00 0.00 0.00 4.02
1131 1238 3.785486 TGCAGGATAATCAGACGAACAG 58.215 45.455 0.00 0.00 0.00 3.16
1157 1264 7.180051 GGATAATCAGACAGATACAGGAGGAAT 59.820 40.741 0.00 0.00 35.39 3.01
1186 1294 7.313646 GCATTAGCAATTGATGAGCTATCATT 58.686 34.615 10.34 2.39 42.78 2.57
1189 1297 5.322310 CGCATTAGCAATTGATGAGCTATC 58.678 41.667 10.34 0.00 40.23 2.08
1190 1298 4.379186 GCGCATTAGCAATTGATGAGCTAT 60.379 41.667 19.97 1.03 42.59 2.97
1192 1300 2.287427 GCGCATTAGCAATTGATGAGCT 60.287 45.455 19.97 9.10 42.59 4.09
1193 1301 2.049228 GCGCATTAGCAATTGATGAGC 58.951 47.619 10.34 13.37 40.30 4.26
1195 1303 1.337703 GGGCGCATTAGCAATTGATGA 59.662 47.619 10.83 0.00 42.27 2.92
1220 1333 6.040878 CCAAATCCTGCAAAGATCAGAAATC 58.959 40.000 0.00 0.00 33.54 2.17
1495 1609 2.370281 TAGACAAGCAAAGCGAGGAG 57.630 50.000 0.00 0.00 0.00 3.69
1539 1656 8.423906 ACCAAGATAAACGGTATAGAGATGAT 57.576 34.615 0.00 0.00 0.00 2.45
1572 1689 5.299279 TCTCACAATGGACAGAAAGGAAAAC 59.701 40.000 0.00 0.00 0.00 2.43
1605 1725 6.378848 ACCAAACAAAAACTCCTTGCTAGTTA 59.621 34.615 0.00 0.00 36.17 2.24
1620 1740 3.868077 CCTTTTCGATGCACCAAACAAAA 59.132 39.130 0.00 0.00 0.00 2.44
1623 1743 1.339610 CCCTTTTCGATGCACCAAACA 59.660 47.619 0.00 0.00 0.00 2.83
1624 1744 1.339929 ACCCTTTTCGATGCACCAAAC 59.660 47.619 0.00 0.00 0.00 2.93
1669 1789 3.115554 CAGTGTTTTAAGTGCAACCTGC 58.884 45.455 0.00 0.00 45.29 4.85
1720 1840 3.334691 GTCATCTTTGAATGACCCGTCA 58.665 45.455 0.00 0.00 46.43 4.35
2022 2143 0.250727 TTGCCAGAAGCCTGTGGTAC 60.251 55.000 0.00 0.00 42.71 3.34
2027 2148 0.771127 TTACCTTGCCAGAAGCCTGT 59.229 50.000 0.00 0.00 42.71 4.00
2134 2258 0.553819 ACTGTGTGCCTGGGGTAAAA 59.446 50.000 0.00 0.00 0.00 1.52
2222 2346 6.670695 AATCAAACCTGGCAAGAAATAAGT 57.329 33.333 0.00 0.00 0.00 2.24
2280 2404 5.070981 ACAGTGAAGAAGATGAACAAGAGGA 59.929 40.000 0.00 0.00 0.00 3.71
2558 2682 7.600231 TCACAAATTGATTATGGGCATACAT 57.400 32.000 0.00 0.00 34.90 2.29
2702 2829 7.670364 AGAAGGAGAAGAAGAAGAAGAAGAAG 58.330 38.462 0.00 0.00 0.00 2.85
2719 2846 9.886132 GTTTACCAACAATATAGAAGAAGGAGA 57.114 33.333 0.00 0.00 32.54 3.71
2720 2847 9.892130 AGTTTACCAACAATATAGAAGAAGGAG 57.108 33.333 0.00 0.00 35.05 3.69
2938 3065 8.425703 GCTCTTATATTTCTTTACAGAGGGAGT 58.574 37.037 0.00 0.00 0.00 3.85
2939 3066 7.596995 CGCTCTTATATTTCTTTACAGAGGGAG 59.403 40.741 4.76 0.00 40.49 4.30
2940 3067 7.069578 ACGCTCTTATATTTCTTTACAGAGGGA 59.930 37.037 14.96 0.00 40.49 4.20
2941 3068 7.210873 ACGCTCTTATATTTCTTTACAGAGGG 58.789 38.462 8.36 8.36 42.53 4.30
2942 3069 8.649973 AACGCTCTTATATTTCTTTACAGAGG 57.350 34.615 0.00 0.00 0.00 3.69
2959 3086 9.570488 CACTAAAGTAGTTATCTAAACGCTCTT 57.430 33.333 0.00 0.00 36.76 2.85
2960 3087 8.954350 TCACTAAAGTAGTTATCTAAACGCTCT 58.046 33.333 0.00 0.00 36.76 4.09
2961 3088 9.733219 ATCACTAAAGTAGTTATCTAAACGCTC 57.267 33.333 0.00 0.00 36.76 5.03
2962 3089 9.733219 GATCACTAAAGTAGTTATCTAAACGCT 57.267 33.333 3.42 0.00 36.79 5.07
2963 3090 9.733219 AGATCACTAAAGTAGTTATCTAAACGC 57.267 33.333 9.38 0.00 43.99 4.84
3006 3133 9.197306 TGACTGCTATATACTCCTTCTGTAAAA 57.803 33.333 0.00 0.00 0.00 1.52
3007 3134 8.762481 TGACTGCTATATACTCCTTCTGTAAA 57.238 34.615 0.00 0.00 0.00 2.01
3008 3135 8.762481 TTGACTGCTATATACTCCTTCTGTAA 57.238 34.615 0.00 0.00 0.00 2.41
3009 3136 8.941995 ATTGACTGCTATATACTCCTTCTGTA 57.058 34.615 0.00 0.00 0.00 2.74
3010 3137 7.847711 ATTGACTGCTATATACTCCTTCTGT 57.152 36.000 0.00 0.00 0.00 3.41
3011 3138 7.973388 GCTATTGACTGCTATATACTCCTTCTG 59.027 40.741 0.00 0.00 0.00 3.02
3012 3139 7.893302 AGCTATTGACTGCTATATACTCCTTCT 59.107 37.037 0.00 0.00 37.81 2.85
3013 3140 8.062065 AGCTATTGACTGCTATATACTCCTTC 57.938 38.462 0.00 0.00 37.81 3.46
3014 3141 7.123547 GGAGCTATTGACTGCTATATACTCCTT 59.876 40.741 0.00 0.00 39.91 3.36
3015 3142 6.605594 GGAGCTATTGACTGCTATATACTCCT 59.394 42.308 0.00 0.00 39.91 3.69
3016 3143 6.183360 GGGAGCTATTGACTGCTATATACTCC 60.183 46.154 0.00 0.00 39.91 3.85
3017 3144 6.378564 TGGGAGCTATTGACTGCTATATACTC 59.621 42.308 0.00 0.00 39.91 2.59
3018 3145 6.256819 TGGGAGCTATTGACTGCTATATACT 58.743 40.000 0.00 0.00 39.91 2.12
3209 3499 9.126151 CTTCTCTGATGTACTCTTCCATAGTTA 57.874 37.037 0.00 0.00 0.00 2.24
3268 3564 8.333186 GTTTACAATTTTACTGACAGAGAACGT 58.667 33.333 10.08 4.88 0.00 3.99
3333 3629 8.184192 GCTAGCAACAGCAAGAATTAATAGAAA 58.816 33.333 10.63 0.00 41.40 2.52
3379 3675 2.259917 TCCTGTGGAGCTTCATCTTCA 58.740 47.619 0.00 0.00 0.00 3.02
3412 3708 4.130118 GCTCTTCTTTCTCCTGTTCAACA 58.870 43.478 0.00 0.00 0.00 3.33
3419 3715 1.002888 TGCTGGCTCTTCTTTCTCCTG 59.997 52.381 0.00 0.00 0.00 3.86
3451 3747 4.508124 GTGGTATATTGTGGCTCTTCTTCG 59.492 45.833 0.00 0.00 0.00 3.79
3465 3761 8.859090 CATCTTCTTCTGAGAGAGTGGTATATT 58.141 37.037 0.00 0.00 32.44 1.28
3516 3812 6.014499 CGGAGTTACTAATAGATCCCCATTGT 60.014 42.308 0.00 0.00 0.00 2.71
3517 3813 6.210784 TCGGAGTTACTAATAGATCCCCATTG 59.789 42.308 0.00 0.00 0.00 2.82
3518 3814 6.320518 TCGGAGTTACTAATAGATCCCCATT 58.679 40.000 0.00 0.00 0.00 3.16
3519 3815 5.900437 TCGGAGTTACTAATAGATCCCCAT 58.100 41.667 0.00 0.00 0.00 4.00
3565 3861 4.584325 TCAAAGAAGCAGGCACTAATTTGT 59.416 37.500 12.72 0.00 36.02 2.83
3677 3973 1.741401 TTCCACGATGGCAAGAGCG 60.741 57.895 0.00 0.00 43.41 5.03
3849 4145 4.338012 TCACTCCCTACATTACTCACGAA 58.662 43.478 0.00 0.00 0.00 3.85
3979 4275 8.526978 AGATACAGCAAGATATACATACCACTG 58.473 37.037 0.00 0.00 0.00 3.66
4075 4371 3.624410 TGCAGCTCAGCATATTACAACTG 59.376 43.478 0.00 0.00 40.11 3.16
4082 4378 4.088056 AGATTCTGCAGCTCAGCATATT 57.912 40.909 9.47 0.00 44.68 1.28
4111 4407 2.878406 AGGATCGATAAAATTGCCCGTG 59.122 45.455 0.00 0.00 0.00 4.94
4130 4426 9.476202 TGAATGTAACAGAATAATATCACGAGG 57.524 33.333 0.00 0.00 0.00 4.63
4170 4466 6.992664 TTTCTGATTTTGGGGATTGAAAGA 57.007 33.333 0.00 0.00 0.00 2.52
4198 4544 4.098807 TGGTACCTTTTCAAAAGCACTTCC 59.901 41.667 14.36 3.32 0.00 3.46
4311 4657 1.945394 TCGTCTTCGTATAGGCTGTCC 59.055 52.381 0.00 0.00 38.33 4.02
4333 4679 1.589716 GCGATTTGCTGCCTCCTTGT 61.590 55.000 0.00 0.00 41.73 3.16
4335 4681 3.595819 GCGATTTGCTGCCTCCTT 58.404 55.556 0.00 0.00 41.73 3.36
4611 4963 2.184322 GCGCTGAACGGATCTCCA 59.816 61.111 0.00 0.00 43.93 3.86
4731 5129 4.294347 CTCCTCAGAATTAGAAGAGGGGT 58.706 47.826 7.41 0.00 46.02 4.95
4732 5130 4.953940 CTCCTCAGAATTAGAAGAGGGG 57.046 50.000 7.41 0.07 46.02 4.79
4733 5131 3.708631 TGCTCCTCAGAATTAGAAGAGGG 59.291 47.826 7.41 0.64 46.02 4.30
4767 5165 5.277828 GGTTTACAGTACCAGCAAAGTTCAG 60.278 44.000 0.00 0.00 35.67 3.02
4777 5175 8.458843 CAATTTCCATAAGGTTTACAGTACCAG 58.541 37.037 0.00 0.00 38.16 4.00
4780 5178 8.789762 ACACAATTTCCATAAGGTTTACAGTAC 58.210 33.333 0.00 0.00 35.89 2.73
4850 5248 4.787598 AGATGTGCTTGTTGTTCGAAATC 58.212 39.130 0.00 0.00 0.00 2.17
4858 5256 1.971481 TGCTGAGATGTGCTTGTTGT 58.029 45.000 0.00 0.00 0.00 3.32
4861 5259 2.292569 CTGTTTGCTGAGATGTGCTTGT 59.707 45.455 0.00 0.00 0.00 3.16
4863 5261 2.854963 TCTGTTTGCTGAGATGTGCTT 58.145 42.857 0.00 0.00 0.00 3.91
4882 5280 7.130917 GTGTGATGATGATAAACAAGCTCATC 58.869 38.462 5.11 5.11 40.27 2.92
4889 5287 8.100164 TCTAGGTTGTGTGATGATGATAAACAA 58.900 33.333 0.00 0.00 0.00 2.83
4921 5322 5.518848 TCGAACAGTTTCAGTTACTGGTA 57.481 39.130 12.79 0.00 43.31 3.25
4942 5343 2.627699 TGCCTGACTTTTTGGGTGAATC 59.372 45.455 0.00 0.00 0.00 2.52
4981 5382 5.386958 TTGAGATCAGTAGTACTGCGTTT 57.613 39.130 23.14 10.88 45.54 3.60
4985 5392 9.138062 CATCAATATTGAGATCAGTAGTACTGC 57.862 37.037 23.14 11.77 42.19 4.40
5091 5498 8.979574 GGTTTCTGCTAATGTACATATGTAGAC 58.020 37.037 15.93 8.70 0.00 2.59
5106 5513 7.924358 TTACCTATCTATGGGTTTCTGCTAA 57.076 36.000 3.11 0.00 42.15 3.09
5153 5563 3.895041 GTGAAGTGGGGGATCAAGAAAAA 59.105 43.478 0.00 0.00 0.00 1.94
5154 5564 3.496331 GTGAAGTGGGGGATCAAGAAAA 58.504 45.455 0.00 0.00 0.00 2.29
5182 5592 1.826385 AGTAGTTCCATTGCACTGGC 58.174 50.000 17.94 5.47 41.68 4.85
5200 5610 3.864160 GCTGAAGAGGACTGAACTGGAAG 60.864 52.174 0.00 0.00 42.29 3.46
5271 5681 3.753272 CCTGGATTAATCGTTATGCAGGG 59.247 47.826 20.26 8.58 45.24 4.45
5319 5729 9.548472 CATTTATCAATGGATCACAGGCTGTGG 62.548 44.444 38.88 24.56 41.07 4.17
5325 5735 7.549839 ACAAACATTTATCAATGGATCACAGG 58.450 34.615 4.70 0.00 43.82 4.00
5363 5774 3.107642 TCTTGGAGTGACGGTTTTCTC 57.892 47.619 0.00 0.00 0.00 2.87
5364 5775 3.118371 AGTTCTTGGAGTGACGGTTTTCT 60.118 43.478 0.00 0.00 0.00 2.52
5388 5799 2.206576 AACCCAGATGCTTTGACTCC 57.793 50.000 0.00 0.00 0.00 3.85
5422 5833 3.062639 CACGCGCATTTCATCTCTAGTTT 59.937 43.478 5.73 0.00 0.00 2.66
5434 5845 5.636837 ACAAAGTATAAATCACGCGCATTT 58.363 33.333 17.75 17.75 0.00 2.32
5497 5922 4.019501 TCCCCTGTTTAGCAATTTACCGTA 60.020 41.667 0.00 0.00 0.00 4.02
5498 5923 3.086282 CCCCTGTTTAGCAATTTACCGT 58.914 45.455 0.00 0.00 0.00 4.83
5499 5924 3.349022 TCCCCTGTTTAGCAATTTACCG 58.651 45.455 0.00 0.00 0.00 4.02
5500 5925 3.130516 GCTCCCCTGTTTAGCAATTTACC 59.869 47.826 0.00 0.00 36.26 2.85
5524 5949 2.366533 CTCTGCAATCCAAGCTCATGT 58.633 47.619 0.00 0.00 0.00 3.21
5555 5980 2.674380 GCACAAGGACAGCCCCAG 60.674 66.667 0.00 0.00 34.66 4.45
5570 5995 0.813610 ATAGGCGCGTATTTGCAGCA 60.814 50.000 16.50 0.00 36.55 4.41
5592 6017 1.974343 CAATTCCCGAAACGCCCCA 60.974 57.895 0.00 0.00 0.00 4.96
5632 6057 1.007607 CCCCCTCCCCAAGTAACAAT 58.992 55.000 0.00 0.00 0.00 2.71
5633 6058 0.103823 TCCCCCTCCCCAAGTAACAA 60.104 55.000 0.00 0.00 0.00 2.83
5634 6059 0.103823 TTCCCCCTCCCCAAGTAACA 60.104 55.000 0.00 0.00 0.00 2.41
5644 6069 1.620818 CCCATTTCCTTCCCCCTCC 59.379 63.158 0.00 0.00 0.00 4.30
5654 6079 0.186143 GTCCCAGATCCCCCATTTCC 59.814 60.000 0.00 0.00 0.00 3.13


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

AutoCloner maintained by Alex Coulton.