Multiple sequence alignment - TraesCS3A01G442600

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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 TraesCS3A01G442600 chr3A 100.000 3947 0 0 1 3947 684523294 684519348 0.000000e+00 7289.0
1 TraesCS3A01G442600 chr3A 87.832 452 44 7 2926 3372 684467347 684466902 1.630000e-143 520.0
2 TraesCS3A01G442600 chr3A 89.412 85 9 0 3856 3940 684583490 684583406 1.500000e-19 108.0
3 TraesCS3A01G442600 chr3A 89.286 84 9 0 3857 3940 684582064 684581981 5.390000e-19 106.0
4 TraesCS3A01G442600 chr3D 92.805 1501 81 16 678 2154 547513275 547511778 0.000000e+00 2148.0
5 TraesCS3A01G442600 chr3D 88.740 1270 88 26 2148 3371 547522508 547521248 0.000000e+00 1502.0
6 TraesCS3A01G442600 chr3D 91.168 1019 69 7 2373 3372 547511588 547510572 0.000000e+00 1363.0
7 TraesCS3A01G442600 chr3D 92.153 943 44 15 892 1807 547523809 547522870 0.000000e+00 1304.0
8 TraesCS3A01G442600 chr3D 92.788 416 28 2 3532 3947 547510028 547509615 5.640000e-168 601.0
9 TraesCS3A01G442600 chr3D 96.575 292 10 0 1850 2141 547522870 547522579 5.930000e-133 484.0
10 TraesCS3A01G442600 chr3D 84.889 450 41 8 2926 3372 547502934 547502509 2.820000e-116 429.0
11 TraesCS3A01G442600 chr3D 96.753 154 5 0 3374 3527 547510466 547510313 1.410000e-64 257.0
12 TraesCS3A01G442600 chr3D 90.278 144 10 3 2148 2287 547511747 547511604 6.740000e-43 185.0
13 TraesCS3A01G442600 chr3D 90.426 94 9 0 3528 3621 547520688 547520595 1.490000e-24 124.0
14 TraesCS3A01G442600 chr3D 88.095 84 10 0 3857 3940 547621620 547621537 2.510000e-17 100.0
15 TraesCS3A01G442600 chr5B 84.441 572 73 7 1 564 77703964 77703401 2.070000e-152 549.0
16 TraesCS3A01G442600 chr5B 96.000 50 2 0 517 566 176565438 176565487 9.090000e-12 82.4
17 TraesCS3A01G442600 chr5D 85.502 538 61 8 27 555 74724049 74724578 2.680000e-151 545.0
18 TraesCS3A01G442600 chr5D 87.460 311 37 2 27 336 74733332 74733641 1.350000e-94 357.0
19 TraesCS3A01G442600 chr5D 87.681 138 10 4 418 555 74733699 74733829 1.900000e-33 154.0
20 TraesCS3A01G442600 chr5D 89.706 68 5 1 497 564 164567472 164567537 7.030000e-13 86.1
21 TraesCS3A01G442600 chr7A 81.086 571 84 11 1 554 272336988 272337551 6.060000e-118 435.0
22 TraesCS3A01G442600 chr6A 75.616 406 92 7 8 409 570731868 570731466 1.120000e-45 195.0
23 TraesCS3A01G442600 chr1D 85.185 162 24 0 83 244 22108539 22108378 2.440000e-37 167.0
24 TraesCS3A01G442600 chr7B 90.164 122 5 4 433 554 231321200 231321314 6.830000e-33 152.0
25 TraesCS3A01G442600 chr7D 75.000 380 65 17 202 564 613444433 613444067 8.840000e-32 148.0


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 TraesCS3A01G442600 chr3A 684519348 684523294 3946 True 7289.0 7289 100.0000 1 3947 1 chr3A.!!$R2 3946
1 TraesCS3A01G442600 chr3D 547509615 547513275 3660 True 910.8 2148 92.7584 678 3947 5 chr3D.!!$R3 3269
2 TraesCS3A01G442600 chr3D 547520595 547523809 3214 True 853.5 1502 91.9735 892 3621 4 chr3D.!!$R4 2729
3 TraesCS3A01G442600 chr5B 77703401 77703964 563 True 549.0 549 84.4410 1 564 1 chr5B.!!$R1 563
4 TraesCS3A01G442600 chr5D 74724049 74724578 529 False 545.0 545 85.5020 27 555 1 chr5D.!!$F1 528
5 TraesCS3A01G442600 chr7A 272336988 272337551 563 False 435.0 435 81.0860 1 554 1 chr7A.!!$F1 553

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
199 201 0.037605 CGTTTACCTCTCCGCCAACT 60.038 55.0 0.00 0.00 0.00 3.16 F
1180 1207 0.173708 CGACTACTGGAACTGGAGCC 59.826 60.0 0.00 0.00 42.44 4.70 F
1382 1409 0.248289 AATTCACTTGGCATGCAGGC 59.752 50.0 21.36 16.47 44.50 4.85 F
1397 1435 0.314935 CAGGCGGCAGTTCAAACATT 59.685 50.0 13.08 0.00 0.00 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1482 1520 0.528017 GATATCTCGGCGAGCATCCA 59.472 55.000 31.01 14.82 0.00 3.41 R
2625 2757 1.085796 TAAGCCATCCCCTCCCCAA 59.914 57.895 0.00 0.00 0.00 4.12 R
2782 2914 1.590525 CAATGACCGCCATGCATGC 60.591 57.895 21.69 11.82 35.24 4.06 R
3068 3230 2.093921 TCTGACCACGAGACAAACACAA 60.094 45.455 0.00 0.00 0.00 3.33 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
52 53 1.886585 CCCACAGTCTCTCGGTCTG 59.113 63.158 0.00 0.00 35.60 3.51
66 67 2.922503 TCTGGTGCCGAGGCTGAA 60.923 61.111 15.75 0.00 42.51 3.02
73 74 0.464036 TGCCGAGGCTGAATATCGTT 59.536 50.000 15.75 0.00 42.51 3.85
81 82 1.537202 GCTGAATATCGTTCCATGGCC 59.463 52.381 6.96 0.00 0.00 5.36
85 86 2.727123 ATATCGTTCCATGGCCAACA 57.273 45.000 10.96 0.00 0.00 3.33
88 89 0.327924 TCGTTCCATGGCCAACATCT 59.672 50.000 10.96 0.00 37.84 2.90
94 95 2.101783 CCATGGCCAACATCTTTGCTA 58.898 47.619 10.96 0.00 37.84 3.49
99 100 2.819608 GGCCAACATCTTTGCTAAGTGA 59.180 45.455 7.77 0.00 32.98 3.41
101 102 4.418392 GCCAACATCTTTGCTAAGTGATG 58.582 43.478 7.77 7.93 41.24 3.07
134 135 4.658071 CAACTTCTCTACGAGCTCTCTTC 58.342 47.826 12.85 0.00 0.00 2.87
157 159 0.180642 TGTTGACAAGGCCACCGTTA 59.819 50.000 5.01 0.00 0.00 3.18
166 168 1.065053 AGGCCACCGTTATGTATTGCA 60.065 47.619 5.01 0.00 0.00 4.08
199 201 0.037605 CGTTTACCTCTCCGCCAACT 60.038 55.000 0.00 0.00 0.00 3.16
200 202 1.607251 CGTTTACCTCTCCGCCAACTT 60.607 52.381 0.00 0.00 0.00 2.66
201 203 2.501261 GTTTACCTCTCCGCCAACTTT 58.499 47.619 0.00 0.00 0.00 2.66
214 216 2.508867 CCAACTTTGTTCATCATCGCG 58.491 47.619 0.00 0.00 0.00 5.87
215 217 2.159430 CCAACTTTGTTCATCATCGCGA 59.841 45.455 13.09 13.09 0.00 5.87
235 237 4.083537 GCGACACCAAACATATTGAGTTGA 60.084 41.667 0.00 0.00 0.00 3.18
241 243 9.466497 ACACCAAACATATTGAGTTGAATATCT 57.534 29.630 0.00 0.00 0.00 1.98
254 256 5.291128 AGTTGAATATCTACTTTGTTCGCGG 59.709 40.000 6.13 0.00 28.33 6.46
277 279 3.421567 GTGGCTCTTGGTCACCTTT 57.578 52.632 0.00 0.00 44.10 3.11
336 345 1.303236 CATGACGAAGGGGTTGCCA 60.303 57.895 0.00 0.00 0.00 4.92
399 408 4.891566 GACGCTTCGACTGTGGAT 57.108 55.556 0.00 0.00 0.00 3.41
453 471 5.194432 ACACATGTACTCTAATCTCCGTCT 58.806 41.667 0.00 0.00 0.00 4.18
496 514 3.960755 TGGACGTGATGATCTTCCTGTAT 59.039 43.478 0.00 0.00 0.00 2.29
497 515 4.202151 TGGACGTGATGATCTTCCTGTATG 60.202 45.833 0.00 0.00 0.00 2.39
498 516 4.202161 GGACGTGATGATCTTCCTGTATGT 60.202 45.833 0.00 0.00 0.00 2.29
499 517 5.009710 GGACGTGATGATCTTCCTGTATGTA 59.990 44.000 0.00 0.00 0.00 2.29
500 518 5.833082 ACGTGATGATCTTCCTGTATGTAC 58.167 41.667 6.17 0.00 0.00 2.90
501 519 5.359860 ACGTGATGATCTTCCTGTATGTACA 59.640 40.000 0.00 0.00 34.56 2.90
502 520 6.040955 ACGTGATGATCTTCCTGTATGTACAT 59.959 38.462 13.93 13.93 35.36 2.29
503 521 6.584184 CGTGATGATCTTCCTGTATGTACATC 59.416 42.308 12.68 5.06 35.36 3.06
555 573 7.772757 TGAATACATGTGTGTTGCATCCTATTA 59.227 33.333 9.11 0.00 39.77 0.98
557 575 8.696043 ATACATGTGTGTTGCATCCTATTATT 57.304 30.769 9.11 0.00 39.77 1.40
559 577 7.259882 ACATGTGTGTTGCATCCTATTATTTG 58.740 34.615 0.00 0.00 34.01 2.32
564 582 8.840321 GTGTGTTGCATCCTATTATTTGTCTAT 58.160 33.333 0.00 0.00 0.00 1.98
595 613 8.593492 TGCTCACATACATAAATACACTCATC 57.407 34.615 0.00 0.00 0.00 2.92
596 614 8.424133 TGCTCACATACATAAATACACTCATCT 58.576 33.333 0.00 0.00 0.00 2.90
597 615 9.265901 GCTCACATACATAAATACACTCATCTT 57.734 33.333 0.00 0.00 0.00 2.40
608 626 6.775939 ATACACTCATCTTATGAATGCACG 57.224 37.500 0.00 0.00 39.95 5.34
609 627 3.310774 ACACTCATCTTATGAATGCACGC 59.689 43.478 0.00 0.00 39.95 5.34
610 628 3.310501 CACTCATCTTATGAATGCACGCA 59.689 43.478 0.00 0.00 39.11 5.24
611 629 4.024302 CACTCATCTTATGAATGCACGCAT 60.024 41.667 0.00 0.00 39.11 4.73
613 631 5.759763 ACTCATCTTATGAATGCACGCATTA 59.240 36.000 16.80 6.77 45.50 1.90
614 632 5.989249 TCATCTTATGAATGCACGCATTAC 58.011 37.500 16.80 11.07 45.50 1.89
615 633 5.526846 TCATCTTATGAATGCACGCATTACA 59.473 36.000 16.80 15.55 45.50 2.41
616 634 5.155509 TCTTATGAATGCACGCATTACAC 57.844 39.130 16.80 6.16 45.50 2.90
617 635 2.456942 ATGAATGCACGCATTACACG 57.543 45.000 16.80 0.00 45.50 4.49
618 636 1.152510 TGAATGCACGCATTACACGT 58.847 45.000 16.80 0.00 45.50 4.49
619 637 1.127766 TGAATGCACGCATTACACGTC 59.872 47.619 16.80 4.89 45.50 4.34
620 638 0.446222 AATGCACGCATTACACGTCC 59.554 50.000 15.38 0.00 43.92 4.79
621 639 1.692148 ATGCACGCATTACACGTCCG 61.692 55.000 0.00 0.00 42.96 4.79
622 640 2.089936 GCACGCATTACACGTCCGA 61.090 57.895 0.00 0.00 42.96 4.55
623 641 1.418342 GCACGCATTACACGTCCGAT 61.418 55.000 0.00 0.00 42.96 4.18
624 642 0.570734 CACGCATTACACGTCCGATC 59.429 55.000 0.00 0.00 42.96 3.69
625 643 0.454600 ACGCATTACACGTCCGATCT 59.545 50.000 0.00 0.00 40.28 2.75
626 644 1.135199 ACGCATTACACGTCCGATCTT 60.135 47.619 0.00 0.00 40.28 2.40
627 645 1.924524 CGCATTACACGTCCGATCTTT 59.075 47.619 0.00 0.00 0.00 2.52
628 646 3.110358 CGCATTACACGTCCGATCTTTA 58.890 45.455 0.00 0.00 0.00 1.85
629 647 3.734231 CGCATTACACGTCCGATCTTTAT 59.266 43.478 0.00 0.00 0.00 1.40
630 648 4.913345 CGCATTACACGTCCGATCTTTATA 59.087 41.667 0.00 0.00 0.00 0.98
631 649 5.400188 CGCATTACACGTCCGATCTTTATAA 59.600 40.000 0.00 0.00 0.00 0.98
632 650 6.398621 CGCATTACACGTCCGATCTTTATAAG 60.399 42.308 0.00 0.00 0.00 1.73
633 651 6.615839 GCATTACACGTCCGATCTTTATAAGC 60.616 42.308 0.00 0.00 0.00 3.09
634 652 4.380841 ACACGTCCGATCTTTATAAGCA 57.619 40.909 0.00 0.00 0.00 3.91
635 653 4.110482 ACACGTCCGATCTTTATAAGCAC 58.890 43.478 0.00 0.00 0.00 4.40
636 654 4.109766 CACGTCCGATCTTTATAAGCACA 58.890 43.478 0.00 0.00 0.00 4.57
637 655 4.745125 CACGTCCGATCTTTATAAGCACAT 59.255 41.667 0.00 0.00 0.00 3.21
638 656 4.982916 ACGTCCGATCTTTATAAGCACATC 59.017 41.667 0.00 0.00 0.00 3.06
639 657 5.221263 ACGTCCGATCTTTATAAGCACATCT 60.221 40.000 0.00 0.00 0.00 2.90
640 658 5.343593 CGTCCGATCTTTATAAGCACATCTC 59.656 44.000 0.00 0.00 0.00 2.75
641 659 6.216569 GTCCGATCTTTATAAGCACATCTCA 58.783 40.000 0.00 0.00 0.00 3.27
642 660 6.364706 GTCCGATCTTTATAAGCACATCTCAG 59.635 42.308 0.00 0.00 0.00 3.35
643 661 6.265422 TCCGATCTTTATAAGCACATCTCAGA 59.735 38.462 0.00 0.00 0.00 3.27
644 662 7.039434 TCCGATCTTTATAAGCACATCTCAGAT 60.039 37.037 0.00 0.00 0.00 2.90
645 663 8.246871 CCGATCTTTATAAGCACATCTCAGATA 58.753 37.037 0.00 0.00 0.00 1.98
646 664 9.071221 CGATCTTTATAAGCACATCTCAGATAC 57.929 37.037 0.00 0.00 0.00 2.24
653 671 5.431420 AGCACATCTCAGATACTAAGTCG 57.569 43.478 0.00 0.00 0.00 4.18
654 672 4.277174 AGCACATCTCAGATACTAAGTCGG 59.723 45.833 0.00 0.00 0.00 4.79
655 673 4.541779 CACATCTCAGATACTAAGTCGGC 58.458 47.826 0.00 0.00 0.00 5.54
656 674 4.036852 CACATCTCAGATACTAAGTCGGCA 59.963 45.833 0.00 0.00 0.00 5.69
657 675 4.036971 ACATCTCAGATACTAAGTCGGCAC 59.963 45.833 0.00 0.00 0.00 5.01
658 676 3.617284 TCTCAGATACTAAGTCGGCACA 58.383 45.455 0.00 0.00 0.00 4.57
659 677 4.014406 TCTCAGATACTAAGTCGGCACAA 58.986 43.478 0.00 0.00 0.00 3.33
660 678 4.106029 TCAGATACTAAGTCGGCACAAC 57.894 45.455 0.00 0.00 0.00 3.32
661 679 3.508402 TCAGATACTAAGTCGGCACAACA 59.492 43.478 0.00 0.00 0.00 3.33
662 680 4.159693 TCAGATACTAAGTCGGCACAACAT 59.840 41.667 0.00 0.00 0.00 2.71
663 681 4.504461 CAGATACTAAGTCGGCACAACATC 59.496 45.833 0.00 0.00 0.00 3.06
664 682 4.402793 AGATACTAAGTCGGCACAACATCT 59.597 41.667 0.00 0.00 0.00 2.90
665 683 3.402628 ACTAAGTCGGCACAACATCTT 57.597 42.857 0.00 0.00 0.00 2.40
666 684 4.530710 ACTAAGTCGGCACAACATCTTA 57.469 40.909 0.00 0.00 0.00 2.10
667 685 4.890088 ACTAAGTCGGCACAACATCTTAA 58.110 39.130 0.00 0.00 0.00 1.85
668 686 4.929808 ACTAAGTCGGCACAACATCTTAAG 59.070 41.667 0.00 0.00 0.00 1.85
669 687 3.678056 AGTCGGCACAACATCTTAAGA 57.322 42.857 7.82 7.82 0.00 2.10
670 688 4.207891 AGTCGGCACAACATCTTAAGAT 57.792 40.909 12.37 12.37 34.56 2.40
671 689 4.579869 AGTCGGCACAACATCTTAAGATT 58.420 39.130 15.49 0.10 31.21 2.40
672 690 4.393062 AGTCGGCACAACATCTTAAGATTG 59.607 41.667 15.49 14.93 31.21 2.67
673 691 4.391830 GTCGGCACAACATCTTAAGATTGA 59.608 41.667 20.54 6.23 31.21 2.57
674 692 4.631377 TCGGCACAACATCTTAAGATTGAG 59.369 41.667 20.54 15.28 31.21 3.02
675 693 4.631377 CGGCACAACATCTTAAGATTGAGA 59.369 41.667 20.54 0.00 31.21 3.27
676 694 5.122239 CGGCACAACATCTTAAGATTGAGAA 59.878 40.000 20.54 0.00 31.21 2.87
690 708 9.838339 TTAAGATTGAGAAATGTCTATCCCTTC 57.162 33.333 0.00 0.00 32.80 3.46
693 711 5.620738 TGAGAAATGTCTATCCCTTCCTG 57.379 43.478 0.00 0.00 32.80 3.86
699 717 3.366396 TGTCTATCCCTTCCTGACAGTC 58.634 50.000 0.93 0.00 33.45 3.51
702 720 2.630889 ATCCCTTCCTGACAGTCTCA 57.369 50.000 1.31 0.00 0.00 3.27
706 724 2.354503 CCCTTCCTGACAGTCTCATGTG 60.355 54.545 1.31 0.00 32.25 3.21
710 728 1.620323 CCTGACAGTCTCATGTGTCCA 59.380 52.381 10.65 0.95 42.11 4.02
725 743 4.013050 TGTGTCCACATTCACAACTTCAA 58.987 39.130 0.00 0.00 40.81 2.69
728 746 3.983344 GTCCACATTCACAACTTCAATGC 59.017 43.478 0.00 0.00 31.74 3.56
731 749 4.370049 CACATTCACAACTTCAATGCCAA 58.630 39.130 0.00 0.00 31.74 4.52
732 750 4.446385 CACATTCACAACTTCAATGCCAAG 59.554 41.667 0.00 0.00 31.74 3.61
733 751 2.798976 TCACAACTTCAATGCCAAGC 57.201 45.000 0.00 0.00 0.00 4.01
769 787 9.220767 GAGATCTACTACAATTTTGTTTCCACT 57.779 33.333 0.00 0.00 42.35 4.00
823 841 2.946650 CTGGACCCCCAACCCCAT 60.947 66.667 0.00 0.00 42.98 4.00
839 861 1.706866 CCCATCCCTGCTTGGATCATA 59.293 52.381 4.79 0.00 43.39 2.15
882 905 7.797038 AAGAAACAAACAAATACTACTCGGT 57.203 32.000 0.00 0.00 0.00 4.69
922 945 5.394883 GGAATAGACGGTGGATAGTGACAAA 60.395 44.000 0.00 0.00 0.00 2.83
1004 1031 2.044806 GCATACGGCTCAGGGATGGT 62.045 60.000 0.00 0.00 40.25 3.55
1068 1095 1.678101 CCTAGGTACGAACTTACCGGG 59.322 57.143 6.32 0.00 45.60 5.73
1111 1138 0.895530 TGAATCGACTGACCTGGACC 59.104 55.000 0.00 0.00 0.00 4.46
1163 1190 4.424566 GTCCGGCGGCTACAACGA 62.425 66.667 23.83 0.00 0.00 3.85
1164 1191 4.424566 TCCGGCGGCTACAACGAC 62.425 66.667 23.83 0.00 35.62 4.34
1180 1207 0.173708 CGACTACTGGAACTGGAGCC 59.826 60.000 0.00 0.00 42.44 4.70
1209 1236 1.528542 CGGATACTCGAGCTCCCCA 60.529 63.158 22.43 0.62 0.00 4.96
1332 1359 2.551287 CGTCCCAAACATCACCAAGGTA 60.551 50.000 0.00 0.00 0.00 3.08
1335 1362 1.199097 CCAAACATCACCAAGGTACGC 59.801 52.381 0.00 0.00 0.00 4.42
1359 1386 3.115556 GTGCCAACGAGCAACCAA 58.884 55.556 0.00 0.00 46.19 3.67
1380 1407 2.230508 ACTCAATTCACTTGGCATGCAG 59.769 45.455 21.36 11.91 35.43 4.41
1382 1409 0.248289 AATTCACTTGGCATGCAGGC 59.752 50.000 21.36 16.47 44.50 4.85
1396 1434 1.959085 CAGGCGGCAGTTCAAACAT 59.041 52.632 13.08 0.00 0.00 2.71
1397 1435 0.314935 CAGGCGGCAGTTCAAACATT 59.685 50.000 13.08 0.00 0.00 2.71
1503 1541 0.528017 GATGCTCGCCGAGATATCCA 59.472 55.000 20.05 6.03 0.00 3.41
1516 1554 3.829601 GAGATATCCATCCTTGAGTCGGT 59.170 47.826 0.00 0.00 0.00 4.69
1537 1575 1.227943 CGGAGGTACATGGCCATGG 60.228 63.158 41.25 26.58 42.91 3.66
1621 1659 0.790814 CCGCTGAAGAAAACGAGGAC 59.209 55.000 0.00 0.00 0.00 3.85
1624 1662 1.542547 GCTGAAGAAAACGAGGACCCA 60.543 52.381 0.00 0.00 0.00 4.51
1625 1663 2.876079 GCTGAAGAAAACGAGGACCCAT 60.876 50.000 0.00 0.00 0.00 4.00
1626 1664 3.412386 CTGAAGAAAACGAGGACCCATT 58.588 45.455 0.00 0.00 0.00 3.16
1631 1672 5.174037 AGAAAACGAGGACCCATTCATTA 57.826 39.130 0.00 0.00 0.00 1.90
1632 1673 5.755849 AGAAAACGAGGACCCATTCATTAT 58.244 37.500 0.00 0.00 0.00 1.28
1635 1676 2.069273 CGAGGACCCATTCATTATCGC 58.931 52.381 0.00 0.00 0.00 4.58
1818 1867 1.832912 GCCATGGTCCTCCGATCTT 59.167 57.895 14.67 0.00 36.30 2.40
2103 2152 5.161943 ACAGGTAGTAATTGTGTCCTTCC 57.838 43.478 0.00 0.00 0.00 3.46
2104 2153 4.844655 ACAGGTAGTAATTGTGTCCTTCCT 59.155 41.667 0.00 0.00 0.00 3.36
2118 2167 5.355910 GTGTCCTTCCTCAAAACTTGTGTTA 59.644 40.000 0.00 0.00 34.96 2.41
2125 2174 6.491394 TCCTCAAAACTTGTGTTATCAAACG 58.509 36.000 0.00 0.00 38.53 3.60
2267 2380 2.647683 TCCAGCCATTACAACACACA 57.352 45.000 0.00 0.00 0.00 3.72
2268 2381 2.226330 TCCAGCCATTACAACACACAC 58.774 47.619 0.00 0.00 0.00 3.82
2269 2382 1.952990 CCAGCCATTACAACACACACA 59.047 47.619 0.00 0.00 0.00 3.72
2270 2383 2.360483 CCAGCCATTACAACACACACAA 59.640 45.455 0.00 0.00 0.00 3.33
2271 2384 3.005684 CCAGCCATTACAACACACACAAT 59.994 43.478 0.00 0.00 0.00 2.71
2272 2385 4.501229 CCAGCCATTACAACACACACAATT 60.501 41.667 0.00 0.00 0.00 2.32
2273 2386 5.049167 CAGCCATTACAACACACACAATTT 58.951 37.500 0.00 0.00 0.00 1.82
2274 2387 6.212235 CAGCCATTACAACACACACAATTTA 58.788 36.000 0.00 0.00 0.00 1.40
2275 2388 6.699204 CAGCCATTACAACACACACAATTTAA 59.301 34.615 0.00 0.00 0.00 1.52
2278 2391 8.555361 GCCATTACAACACACACAATTTAATTT 58.445 29.630 0.00 0.00 0.00 1.82
2329 2454 7.981789 TGTCACATTCAAGTAGATATTCTGGTC 59.018 37.037 0.00 0.00 0.00 4.02
2341 2466 6.672593 AGATATTCTGGTCCTTAATTTGGCA 58.327 36.000 0.00 0.00 0.00 4.92
2350 2475 5.051153 GTCCTTAATTTGGCAAAACCGAAA 58.949 37.500 17.70 6.26 45.40 3.46
2357 2482 7.736447 AATTTGGCAAAACCGAAATCATTTA 57.264 28.000 17.70 0.00 45.40 1.40
2525 2656 1.464997 GTTGCCTTTCCTCAGCTTACG 59.535 52.381 0.00 0.00 0.00 3.18
2533 2664 5.875359 CCTTTCCTCAGCTTACGAAATAAGT 59.125 40.000 0.00 0.00 42.19 2.24
2535 2666 5.654603 TCCTCAGCTTACGAAATAAGTCA 57.345 39.130 0.00 0.00 42.19 3.41
2544 2675 6.202379 GCTTACGAAATAAGTCATCCCCTAAC 59.798 42.308 0.00 0.00 42.19 2.34
2555 2686 5.251700 AGTCATCCCCTAACTTTGTTGAGAT 59.748 40.000 0.00 0.00 0.00 2.75
2558 2689 7.010160 TCATCCCCTAACTTTGTTGAGATTTT 58.990 34.615 0.00 0.00 0.00 1.82
2598 2730 4.586306 ACTAGTTTAGGAACCCCAATGG 57.414 45.455 0.00 0.00 36.39 3.16
2601 2733 4.692523 AGTTTAGGAACCCCAATGGATT 57.307 40.909 0.00 0.00 36.39 3.01
2657 2789 4.944317 GGATGGCTTACTTTCTAAGCTGTT 59.056 41.667 10.97 0.00 46.58 3.16
2671 2803 3.229697 AGCTGTTAAAAGAACTGGCCT 57.770 42.857 3.32 0.00 0.00 5.19
2672 2804 3.566351 AGCTGTTAAAAGAACTGGCCTT 58.434 40.909 3.32 0.00 0.00 4.35
2790 2922 3.918591 GTCAAGTCAAAAGAGCATGCATG 59.081 43.478 22.70 22.70 0.00 4.06
2803 2935 2.202650 GCATGGCGGTCATTGTGC 60.203 61.111 0.00 0.00 32.92 4.57
2819 2951 2.083774 TGTGCTGCTGGTTATAGTTGC 58.916 47.619 0.00 0.00 0.00 4.17
2877 3009 5.837437 AGACAGGAAATACATAAGAGCGAG 58.163 41.667 0.00 0.00 0.00 5.03
2934 3066 3.617284 TGATGTCGCAGGAAGTACTCTA 58.383 45.455 0.00 0.00 0.00 2.43
2991 3150 9.586435 CATCTTAGTTAGTTACACATGATCACA 57.414 33.333 0.00 0.00 0.00 3.58
3045 3207 5.128499 TGTTCTGGCAAAAATGGAAAGAGAA 59.872 36.000 0.00 0.00 0.00 2.87
3050 3212 7.872483 TCTGGCAAAAATGGAAAGAGAATAAAC 59.128 33.333 0.00 0.00 0.00 2.01
3068 3230 7.510343 AGAATAAACATTATTTAGCAGCCCCAT 59.490 33.333 0.00 0.00 0.00 4.00
3089 3251 1.478916 TGTGTTTGTCTCGTGGTCAGA 59.521 47.619 0.00 0.00 0.00 3.27
3092 3254 3.673809 GTGTTTGTCTCGTGGTCAGATAC 59.326 47.826 0.00 0.00 0.00 2.24
3107 3269 6.183360 TGGTCAGATACTAAGCAATAACCTCC 60.183 42.308 0.00 0.00 0.00 4.30
3295 3457 1.622811 CAGCTTTCTCACCACCTCTCT 59.377 52.381 0.00 0.00 0.00 3.10
3329 3491 4.156008 GTCAGTTTTTATGTAGGTGCCTGG 59.844 45.833 0.12 0.00 0.00 4.45
3335 3497 5.483685 TTTATGTAGGTGCCTGGCTATAG 57.516 43.478 21.03 0.00 0.00 1.31
3415 3681 7.753580 TCGACATTGGCTATATATGAAGTTACG 59.246 37.037 0.00 0.00 0.00 3.18
3582 4148 1.228552 AGGCGCCACAACCAAAGAT 60.229 52.632 31.54 0.00 0.00 2.40
3642 4208 6.876257 CGGTTTTCCCAAATAATCCAATTTCA 59.124 34.615 0.00 0.00 36.42 2.69
3647 4213 8.434589 TTCCCAAATAATCCAATTTCACTTCT 57.565 30.769 0.00 0.00 0.00 2.85
3706 4272 5.695363 GCGACTTGTTTTCTACCTAGTTCTT 59.305 40.000 0.00 0.00 0.00 2.52
3708 4274 6.700520 CGACTTGTTTTCTACCTAGTTCTTGT 59.299 38.462 0.00 0.00 0.00 3.16
3710 4276 6.700520 ACTTGTTTTCTACCTAGTTCTTGTCG 59.299 38.462 0.00 0.00 0.00 4.35
3723 4289 5.476614 AGTTCTTGTCGTATTTCCTGGTAC 58.523 41.667 0.00 0.00 0.00 3.34
3730 4296 1.125633 TATTTCCTGGTACCGCCTCC 58.874 55.000 7.57 0.00 38.35 4.30
3754 4320 5.789643 TCTATGGGCCAGATTTTATTTGC 57.210 39.130 13.78 0.00 0.00 3.68
3755 4321 3.843893 ATGGGCCAGATTTTATTTGCC 57.156 42.857 13.78 0.00 38.16 4.52
3781 4347 3.881688 CTCTCCCTATTGCCAACTCAATG 59.118 47.826 0.00 0.00 37.27 2.82
3813 4379 8.154649 ACAATTTTATAGACCGTGATCCATTC 57.845 34.615 0.00 0.00 0.00 2.67
3847 4413 3.459232 ACAATCGTCACATCCATCGAT 57.541 42.857 0.00 0.00 43.30 3.59
3852 4418 1.269051 CGTCACATCCATCGATCGGAA 60.269 52.381 16.41 0.00 35.77 4.30
3863 4429 1.289109 CGATCGGAACCACGCACTTT 61.289 55.000 7.38 0.00 0.00 2.66
3865 4431 0.034896 ATCGGAACCACGCACTTTCT 59.965 50.000 0.00 0.00 0.00 2.52
3892 4458 4.575973 GCCCTCGGCCATGCAGAT 62.576 66.667 2.24 0.00 44.06 2.90
3897 4463 1.769098 CTCGGCCATGCAGATGTTCG 61.769 60.000 2.24 0.00 31.76 3.95
3898 4464 2.827051 CGGCCATGCAGATGTTCGG 61.827 63.158 2.24 0.00 0.00 4.30
3933 4499 3.210012 AAGCACGCCCCATGGAACT 62.210 57.895 15.22 0.00 0.00 3.01
3940 4506 2.362889 CCCATGGAACTGGTGGCC 60.363 66.667 15.22 0.00 34.23 5.36
3944 4510 0.967380 CATGGAACTGGTGGCCCTTC 60.967 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
52 53 0.946221 CGATATTCAGCCTCGGCACC 60.946 60.000 11.02 0.00 44.88 5.01
66 67 2.727123 TGTTGGCCATGGAACGATAT 57.273 45.000 18.40 0.00 0.00 1.63
73 74 0.896923 GCAAAGATGTTGGCCATGGA 59.103 50.000 18.40 0.00 32.56 3.41
81 82 5.093457 CAGCATCACTTAGCAAAGATGTTG 58.907 41.667 0.00 0.00 41.13 3.33
85 86 2.686915 GCCAGCATCACTTAGCAAAGAT 59.313 45.455 0.00 0.00 36.50 2.40
88 89 2.205022 AGCCAGCATCACTTAGCAAA 57.795 45.000 0.00 0.00 0.00 3.68
94 95 2.042831 GCCGAAGCCAGCATCACTT 61.043 57.895 0.00 0.00 0.00 3.16
99 100 1.589716 GAAGTTGCCGAAGCCAGCAT 61.590 55.000 0.00 0.00 38.69 3.79
101 102 1.916697 GAGAAGTTGCCGAAGCCAGC 61.917 60.000 0.00 0.00 38.69 4.85
134 135 0.890996 GGTGGCCTTGTCAACAGGAG 60.891 60.000 3.32 0.00 0.00 3.69
157 159 3.120199 GCAGAGACGTTGTTGCAATACAT 60.120 43.478 0.59 0.00 36.59 2.29
183 185 1.418637 ACAAAGTTGGCGGAGAGGTAA 59.581 47.619 0.00 0.00 0.00 2.85
199 201 1.463056 GGTGTCGCGATGATGAACAAA 59.537 47.619 14.06 0.00 0.00 2.83
200 202 1.075542 GGTGTCGCGATGATGAACAA 58.924 50.000 14.06 0.00 0.00 2.83
201 203 0.037790 TGGTGTCGCGATGATGAACA 60.038 50.000 14.06 0.08 0.00 3.18
214 216 9.722056 GATATTCAACTCAATATGTTTGGTGTC 57.278 33.333 0.00 0.00 30.44 3.67
215 217 9.466497 AGATATTCAACTCAATATGTTTGGTGT 57.534 29.630 0.00 0.00 30.44 4.16
235 237 2.870411 GCCCGCGAACAAAGTAGATATT 59.130 45.455 8.23 0.00 0.00 1.28
241 243 1.669760 CCTGCCCGCGAACAAAGTA 60.670 57.895 8.23 0.00 0.00 2.24
254 256 2.360475 GACCAAGAGCCACCTGCC 60.360 66.667 0.00 0.00 42.71 4.85
274 276 2.213499 AGGCACGTGAAGAAGTCAAAG 58.787 47.619 22.23 0.00 38.23 2.77
277 279 1.000506 GGTAGGCACGTGAAGAAGTCA 59.999 52.381 22.23 0.00 0.00 3.41
280 282 1.546476 AGAGGTAGGCACGTGAAGAAG 59.454 52.381 22.23 0.00 0.00 2.85
336 345 2.884894 ACTCCTCGAAAACTGACGTT 57.115 45.000 0.00 0.00 34.03 3.99
395 404 1.003839 GTCGCTCAACACCCATCCA 60.004 57.895 0.00 0.00 0.00 3.41
398 407 1.134401 CATAGGTCGCTCAACACCCAT 60.134 52.381 0.00 0.00 32.45 4.00
399 408 0.249120 CATAGGTCGCTCAACACCCA 59.751 55.000 0.00 0.00 32.45 4.51
453 471 6.553852 GTCCAGGACTAAACCCTAATGAGATA 59.446 42.308 12.94 0.00 31.64 1.98
496 514 6.318900 CCAGTGCCGATATATAGAGATGTACA 59.681 42.308 0.00 0.00 0.00 2.90
497 515 6.542735 TCCAGTGCCGATATATAGAGATGTAC 59.457 42.308 0.00 0.00 0.00 2.90
498 516 6.659824 TCCAGTGCCGATATATAGAGATGTA 58.340 40.000 0.00 0.00 0.00 2.29
499 517 5.510430 TCCAGTGCCGATATATAGAGATGT 58.490 41.667 0.00 0.00 0.00 3.06
500 518 6.445475 CATCCAGTGCCGATATATAGAGATG 58.555 44.000 0.00 0.00 0.00 2.90
501 519 6.647334 CATCCAGTGCCGATATATAGAGAT 57.353 41.667 0.00 0.00 0.00 2.75
569 587 9.212641 GATGAGTGTATTTATGTATGTGAGCAT 57.787 33.333 0.00 0.00 39.03 3.79
570 588 8.424133 AGATGAGTGTATTTATGTATGTGAGCA 58.576 33.333 0.00 0.00 0.00 4.26
571 589 8.824159 AGATGAGTGTATTTATGTATGTGAGC 57.176 34.615 0.00 0.00 0.00 4.26
582 600 8.764287 CGTGCATTCATAAGATGAGTGTATTTA 58.236 33.333 11.97 0.00 45.49 1.40
583 601 7.633621 CGTGCATTCATAAGATGAGTGTATTT 58.366 34.615 11.97 0.00 45.49 1.40
584 602 6.293081 GCGTGCATTCATAAGATGAGTGTATT 60.293 38.462 11.97 0.00 45.49 1.89
585 603 5.178252 GCGTGCATTCATAAGATGAGTGTAT 59.822 40.000 11.97 0.00 45.49 2.29
586 604 4.507756 GCGTGCATTCATAAGATGAGTGTA 59.492 41.667 11.97 6.31 45.49 2.90
587 605 3.310774 GCGTGCATTCATAAGATGAGTGT 59.689 43.478 11.97 0.00 45.49 3.55
588 606 3.310501 TGCGTGCATTCATAAGATGAGTG 59.689 43.478 7.41 7.41 46.19 3.51
589 607 3.534554 TGCGTGCATTCATAAGATGAGT 58.465 40.909 0.00 0.00 40.94 3.41
590 608 4.744136 ATGCGTGCATTCATAAGATGAG 57.256 40.909 0.51 0.00 40.94 2.90
591 609 5.526846 TGTAATGCGTGCATTCATAAGATGA 59.473 36.000 22.21 0.39 44.50 2.92
592 610 5.622448 GTGTAATGCGTGCATTCATAAGATG 59.378 40.000 22.21 0.00 44.50 2.90
593 611 5.558844 CGTGTAATGCGTGCATTCATAAGAT 60.559 40.000 22.21 0.22 44.50 2.40
594 612 4.260172 CGTGTAATGCGTGCATTCATAAGA 60.260 41.667 22.21 2.53 44.50 2.10
595 613 3.961860 CGTGTAATGCGTGCATTCATAAG 59.038 43.478 22.21 9.46 44.50 1.73
596 614 3.372514 ACGTGTAATGCGTGCATTCATAA 59.627 39.130 22.21 3.62 44.50 1.90
597 615 2.933260 ACGTGTAATGCGTGCATTCATA 59.067 40.909 22.21 8.45 44.50 2.15
598 616 1.737236 ACGTGTAATGCGTGCATTCAT 59.263 42.857 22.21 3.13 44.50 2.57
599 617 1.127766 GACGTGTAATGCGTGCATTCA 59.872 47.619 22.21 16.49 44.50 2.57
600 618 1.797964 GACGTGTAATGCGTGCATTC 58.202 50.000 22.21 14.43 44.50 2.67
601 619 3.967734 GACGTGTAATGCGTGCATT 57.032 47.368 22.20 22.20 46.85 3.56
604 622 1.418342 ATCGGACGTGTAATGCGTGC 61.418 55.000 0.00 0.00 44.99 5.34
605 623 0.570734 GATCGGACGTGTAATGCGTG 59.429 55.000 0.00 0.00 43.04 5.34
606 624 0.454600 AGATCGGACGTGTAATGCGT 59.545 50.000 0.00 0.00 45.86 5.24
607 625 1.556564 AAGATCGGACGTGTAATGCG 58.443 50.000 0.00 0.00 0.00 4.73
608 626 6.615839 GCTTATAAAGATCGGACGTGTAATGC 60.616 42.308 0.00 0.00 0.00 3.56
609 627 6.419710 TGCTTATAAAGATCGGACGTGTAATG 59.580 38.462 0.00 0.00 0.00 1.90
610 628 6.420008 GTGCTTATAAAGATCGGACGTGTAAT 59.580 38.462 0.00 0.00 0.00 1.89
611 629 5.745294 GTGCTTATAAAGATCGGACGTGTAA 59.255 40.000 0.00 0.00 0.00 2.41
612 630 5.163632 TGTGCTTATAAAGATCGGACGTGTA 60.164 40.000 0.00 0.00 0.00 2.90
613 631 4.110482 GTGCTTATAAAGATCGGACGTGT 58.890 43.478 0.00 0.00 0.00 4.49
614 632 4.109766 TGTGCTTATAAAGATCGGACGTG 58.890 43.478 0.00 0.00 0.00 4.49
615 633 4.380841 TGTGCTTATAAAGATCGGACGT 57.619 40.909 0.00 0.00 0.00 4.34
616 634 5.223382 AGATGTGCTTATAAAGATCGGACG 58.777 41.667 0.00 0.00 0.00 4.79
617 635 6.216569 TGAGATGTGCTTATAAAGATCGGAC 58.783 40.000 0.00 0.00 0.00 4.79
618 636 6.265422 TCTGAGATGTGCTTATAAAGATCGGA 59.735 38.462 0.00 0.00 0.00 4.55
619 637 6.450545 TCTGAGATGTGCTTATAAAGATCGG 58.549 40.000 0.00 0.00 0.00 4.18
620 638 9.071221 GTATCTGAGATGTGCTTATAAAGATCG 57.929 37.037 4.96 0.00 0.00 3.69
627 645 8.722394 CGACTTAGTATCTGAGATGTGCTTATA 58.278 37.037 4.96 0.00 0.00 0.98
628 646 7.308891 CCGACTTAGTATCTGAGATGTGCTTAT 60.309 40.741 4.96 0.00 0.00 1.73
629 647 6.017026 CCGACTTAGTATCTGAGATGTGCTTA 60.017 42.308 4.96 0.00 0.00 3.09
630 648 5.221145 CCGACTTAGTATCTGAGATGTGCTT 60.221 44.000 4.96 0.00 0.00 3.91
631 649 4.277174 CCGACTTAGTATCTGAGATGTGCT 59.723 45.833 4.96 3.52 0.00 4.40
632 650 4.541779 CCGACTTAGTATCTGAGATGTGC 58.458 47.826 4.96 0.00 0.00 4.57
633 651 4.036852 TGCCGACTTAGTATCTGAGATGTG 59.963 45.833 4.96 0.00 0.00 3.21
634 652 4.036971 GTGCCGACTTAGTATCTGAGATGT 59.963 45.833 4.96 0.00 0.00 3.06
635 653 4.036852 TGTGCCGACTTAGTATCTGAGATG 59.963 45.833 4.96 0.00 0.00 2.90
636 654 4.207955 TGTGCCGACTTAGTATCTGAGAT 58.792 43.478 0.00 0.00 0.00 2.75
637 655 3.617284 TGTGCCGACTTAGTATCTGAGA 58.383 45.455 0.00 0.00 0.00 3.27
638 656 4.106197 GTTGTGCCGACTTAGTATCTGAG 58.894 47.826 0.00 0.00 0.00 3.35
639 657 3.508402 TGTTGTGCCGACTTAGTATCTGA 59.492 43.478 0.00 0.00 0.00 3.27
640 658 3.845178 TGTTGTGCCGACTTAGTATCTG 58.155 45.455 0.00 0.00 0.00 2.90
641 659 4.402793 AGATGTTGTGCCGACTTAGTATCT 59.597 41.667 0.00 0.00 0.00 1.98
642 660 4.683832 AGATGTTGTGCCGACTTAGTATC 58.316 43.478 0.00 0.00 0.00 2.24
643 661 4.737855 AGATGTTGTGCCGACTTAGTAT 57.262 40.909 0.00 0.00 0.00 2.12
644 662 4.530710 AAGATGTTGTGCCGACTTAGTA 57.469 40.909 0.00 0.00 0.00 1.82
645 663 3.402628 AAGATGTTGTGCCGACTTAGT 57.597 42.857 0.00 0.00 0.00 2.24
646 664 5.168569 TCTTAAGATGTTGTGCCGACTTAG 58.831 41.667 0.00 0.00 0.00 2.18
647 665 5.142061 TCTTAAGATGTTGTGCCGACTTA 57.858 39.130 0.00 0.00 0.00 2.24
648 666 4.002906 TCTTAAGATGTTGTGCCGACTT 57.997 40.909 0.00 0.00 0.00 3.01
649 667 3.678056 TCTTAAGATGTTGTGCCGACT 57.322 42.857 0.00 0.00 0.00 4.18
650 668 4.391830 TCAATCTTAAGATGTTGTGCCGAC 59.608 41.667 18.61 0.00 34.49 4.79
651 669 4.574892 TCAATCTTAAGATGTTGTGCCGA 58.425 39.130 18.61 3.57 34.49 5.54
652 670 4.631377 TCTCAATCTTAAGATGTTGTGCCG 59.369 41.667 18.61 7.83 34.49 5.69
653 671 6.500684 TTCTCAATCTTAAGATGTTGTGCC 57.499 37.500 18.61 0.00 34.49 5.01
654 672 8.025445 ACATTTCTCAATCTTAAGATGTTGTGC 58.975 33.333 18.61 0.00 34.49 4.57
655 673 9.552114 GACATTTCTCAATCTTAAGATGTTGTG 57.448 33.333 18.61 14.59 34.49 3.33
656 674 9.512588 AGACATTTCTCAATCTTAAGATGTTGT 57.487 29.630 18.61 13.13 34.49 3.32
662 680 9.218525 AGGGATAGACATTTCTCAATCTTAAGA 57.781 33.333 7.82 7.82 32.75 2.10
663 681 9.844257 AAGGGATAGACATTTCTCAATCTTAAG 57.156 33.333 0.00 0.00 32.75 1.85
664 682 9.838339 GAAGGGATAGACATTTCTCAATCTTAA 57.162 33.333 0.00 0.00 32.75 1.85
665 683 8.432805 GGAAGGGATAGACATTTCTCAATCTTA 58.567 37.037 0.00 0.00 32.75 2.10
666 684 7.128573 AGGAAGGGATAGACATTTCTCAATCTT 59.871 37.037 0.00 0.00 32.75 2.40
667 685 6.619023 AGGAAGGGATAGACATTTCTCAATCT 59.381 38.462 0.00 0.00 32.75 2.40
668 686 6.709846 CAGGAAGGGATAGACATTTCTCAATC 59.290 42.308 0.00 0.00 32.75 2.67
669 687 6.388100 TCAGGAAGGGATAGACATTTCTCAAT 59.612 38.462 0.00 0.00 32.75 2.57
670 688 5.726308 TCAGGAAGGGATAGACATTTCTCAA 59.274 40.000 0.00 0.00 32.75 3.02
671 689 5.129485 GTCAGGAAGGGATAGACATTTCTCA 59.871 44.000 0.00 0.00 32.75 3.27
672 690 5.129485 TGTCAGGAAGGGATAGACATTTCTC 59.871 44.000 0.00 0.00 34.59 2.87
673 691 5.032846 TGTCAGGAAGGGATAGACATTTCT 58.967 41.667 0.00 0.00 34.59 2.52
674 692 5.104735 ACTGTCAGGAAGGGATAGACATTTC 60.105 44.000 4.53 0.00 38.40 2.17
675 693 4.785376 ACTGTCAGGAAGGGATAGACATTT 59.215 41.667 4.53 0.00 38.40 2.32
676 694 4.366267 ACTGTCAGGAAGGGATAGACATT 58.634 43.478 4.53 0.00 38.40 2.71
690 708 1.620323 TGGACACATGAGACTGTCAGG 59.380 52.381 10.88 0.00 42.95 3.86
693 711 2.820059 TGTGGACACATGAGACTGTC 57.180 50.000 0.00 2.29 36.21 3.51
706 724 3.983344 GCATTGAAGTTGTGAATGTGGAC 59.017 43.478 0.00 0.00 31.03 4.02
710 728 4.624015 CTTGGCATTGAAGTTGTGAATGT 58.376 39.130 0.00 0.00 31.03 2.71
721 739 0.762082 TGGGTTGGCTTGGCATTGAA 60.762 50.000 0.00 0.00 0.00 2.69
725 743 2.053865 CGATGGGTTGGCTTGGCAT 61.054 57.895 0.00 0.00 0.00 4.40
728 746 0.107017 ATCTCGATGGGTTGGCTTGG 60.107 55.000 0.00 0.00 0.00 3.61
731 749 1.689273 GTAGATCTCGATGGGTTGGCT 59.311 52.381 0.00 0.00 0.00 4.75
732 750 1.689273 AGTAGATCTCGATGGGTTGGC 59.311 52.381 0.00 0.00 0.00 4.52
733 751 3.889538 TGTAGTAGATCTCGATGGGTTGG 59.110 47.826 0.00 0.00 0.00 3.77
769 787 8.882736 CAGCAGATTTACATTGTGATTGTACTA 58.117 33.333 0.00 0.00 29.60 1.82
778 796 5.587443 TCATCCTCAGCAGATTTACATTGTG 59.413 40.000 0.00 0.00 0.00 3.33
823 841 4.437967 TGGATATATGATCCAAGCAGGGA 58.562 43.478 8.36 0.00 44.54 4.20
871 893 1.134491 GCCAGGCAAACCGAGTAGTAT 60.134 52.381 6.55 0.00 42.76 2.12
874 896 0.605319 TTGCCAGGCAAACCGAGTAG 60.605 55.000 25.43 0.00 45.96 2.57
1004 1031 2.219458 CCGAGTAGTCCAAGCTATCGA 58.781 52.381 0.00 0.00 30.80 3.59
1068 1095 2.101249 CTCAGTCCTCTTCATCCTCTGC 59.899 54.545 0.00 0.00 0.00 4.26
1163 1190 0.910088 GGGGCTCCAGTTCCAGTAGT 60.910 60.000 0.00 0.00 0.00 2.73
1164 1191 1.627297 GGGGGCTCCAGTTCCAGTAG 61.627 65.000 4.16 0.00 35.00 2.57
1342 1369 1.299089 GTTGGTTGCTCGTTGGCAC 60.299 57.895 0.00 0.00 42.27 5.01
1356 1383 3.581755 CATGCCAAGTGAATTGAGTTGG 58.418 45.455 22.96 22.96 45.78 3.77
1357 1384 2.991190 GCATGCCAAGTGAATTGAGTTG 59.009 45.455 6.36 5.57 41.83 3.16
1358 1385 2.629137 TGCATGCCAAGTGAATTGAGTT 59.371 40.909 16.68 0.00 41.83 3.01
1359 1386 2.230508 CTGCATGCCAAGTGAATTGAGT 59.769 45.455 16.68 0.00 41.83 3.41
1380 1407 2.324860 GTTAATGTTTGAACTGCCGCC 58.675 47.619 0.00 0.00 0.00 6.13
1382 1409 3.634568 TGGTTAATGTTTGAACTGCCG 57.365 42.857 0.00 0.00 0.00 5.69
1384 1411 6.366061 GGAAGAATGGTTAATGTTTGAACTGC 59.634 38.462 0.00 0.00 0.00 4.40
1385 1412 7.596248 CAGGAAGAATGGTTAATGTTTGAACTG 59.404 37.037 0.00 0.00 0.00 3.16
1387 1414 6.868339 CCAGGAAGAATGGTTAATGTTTGAAC 59.132 38.462 0.00 0.00 32.85 3.18
1388 1415 6.518200 GCCAGGAAGAATGGTTAATGTTTGAA 60.518 38.462 0.00 0.00 40.17 2.69
1390 1417 5.170748 GCCAGGAAGAATGGTTAATGTTTG 58.829 41.667 0.00 0.00 40.17 2.93
1396 1434 4.272489 CATCTGCCAGGAAGAATGGTTAA 58.728 43.478 0.00 0.00 40.17 2.01
1397 1435 3.371917 CCATCTGCCAGGAAGAATGGTTA 60.372 47.826 0.00 0.00 40.17 2.85
1482 1520 0.528017 GATATCTCGGCGAGCATCCA 59.472 55.000 31.01 14.82 0.00 3.41
1503 1541 2.579201 CGCCACCGACTCAAGGAT 59.421 61.111 0.00 0.00 36.29 3.24
1516 1554 3.792736 GGCCATGTACCTCCGCCA 61.793 66.667 0.00 0.00 39.50 5.69
1605 1643 2.543777 TGGGTCCTCGTTTTCTTCAG 57.456 50.000 0.00 0.00 0.00 3.02
1621 1659 1.875963 GCCGGCGATAATGAATGGG 59.124 57.895 12.58 0.00 0.00 4.00
1756 1804 3.554692 GCCGGTCGCTTGTCATCG 61.555 66.667 1.90 0.00 0.00 3.84
1782 1831 1.746615 CGTCAACATCAGGGCAGGG 60.747 63.158 0.00 0.00 0.00 4.45
2103 2152 7.696453 AGAACGTTTGATAACACAAGTTTTGAG 59.304 33.333 0.46 0.00 39.15 3.02
2104 2153 7.531716 AGAACGTTTGATAACACAAGTTTTGA 58.468 30.769 0.46 0.00 39.15 2.69
2118 2167 9.706691 TTCTTATGAAACTCTAGAACGTTTGAT 57.293 29.630 13.23 12.61 33.82 2.57
2177 2290 9.918630 ACTGAAATTTTGATGAAATTCTACTGG 57.081 29.630 0.00 0.00 44.98 4.00
2249 2362 1.952990 TGTGTGTGTTGTAATGGCTGG 59.047 47.619 0.00 0.00 0.00 4.85
2324 2449 4.314961 GGTTTTGCCAAATTAAGGACCAG 58.685 43.478 2.37 0.00 37.17 4.00
2329 2454 5.698545 TGATTTCGGTTTTGCCAAATTAAGG 59.301 36.000 0.00 0.00 36.97 2.69
2350 2475 7.285401 AGCCATTATCACCGAACTTTAAATGAT 59.715 33.333 5.36 5.36 0.00 2.45
2357 2482 3.869246 CGTAGCCATTATCACCGAACTTT 59.131 43.478 0.00 0.00 0.00 2.66
2525 2656 7.939784 ACAAAGTTAGGGGATGACTTATTTC 57.060 36.000 0.00 0.00 36.77 2.17
2533 2664 5.779241 ATCTCAACAAAGTTAGGGGATGA 57.221 39.130 0.00 0.00 0.00 2.92
2535 2666 7.508977 TCAAAAATCTCAACAAAGTTAGGGGAT 59.491 33.333 0.00 0.00 0.00 3.85
2572 2703 7.718314 CCATTGGGGTTCCTAAACTAGTTATAC 59.282 40.741 8.92 3.18 35.61 1.47
2573 2704 7.628505 TCCATTGGGGTTCCTAAACTAGTTATA 59.371 37.037 8.92 3.31 38.11 0.98
2587 2718 3.748989 GCCTCTCTAATCCATTGGGGTTC 60.749 52.174 2.09 0.00 38.79 3.62
2598 2730 7.492352 TTTTTAATAAGCCGCCTCTCTAATC 57.508 36.000 0.00 0.00 0.00 1.75
2625 2757 1.085796 TAAGCCATCCCCTCCCCAA 59.914 57.895 0.00 0.00 0.00 4.12
2782 2914 1.590525 CAATGACCGCCATGCATGC 60.591 57.895 21.69 11.82 35.24 4.06
2790 2922 3.058160 AGCAGCACAATGACCGCC 61.058 61.111 0.00 0.00 0.00 6.13
2803 2935 4.970662 ACAATGCAACTATAACCAGCAG 57.029 40.909 0.00 0.00 38.75 4.24
2877 3009 4.210955 GCAGTCTCGATCAATTCCTTCATC 59.789 45.833 0.00 0.00 0.00 2.92
2934 3066 5.589367 ACCATGCATATCATAACTTCCCT 57.411 39.130 0.00 0.00 33.19 4.20
2991 3150 5.030147 TGTTCTGGTTATCCTGGAGTACAT 58.970 41.667 1.52 0.00 34.13 2.29
3025 3184 7.656948 TGTTTATTCTCTTTCCATTTTTGCCAG 59.343 33.333 0.00 0.00 0.00 4.85
3045 3207 7.071071 ACAATGGGGCTGCTAAATAATGTTTAT 59.929 33.333 0.00 0.00 0.00 1.40
3050 3212 4.099881 ACACAATGGGGCTGCTAAATAATG 59.900 41.667 0.00 0.00 0.00 1.90
3068 3230 2.093921 TCTGACCACGAGACAAACACAA 60.094 45.455 0.00 0.00 0.00 3.33
3092 3254 7.169308 CACGTGTTATAGGAGGTTATTGCTTAG 59.831 40.741 7.58 0.00 0.00 2.18
3107 3269 8.034804 TGATCCAATGGATATCACGTGTTATAG 58.965 37.037 15.75 5.71 43.27 1.31
3193 3355 9.051027 CAAAAGTGCAATAGTTTAGATACAACG 57.949 33.333 0.00 0.00 31.72 4.10
3393 3659 8.988934 ACAACGTAACTTCATATATAGCCAATG 58.011 33.333 0.00 0.00 0.00 2.82
3618 4184 7.882791 AGTGAAATTGGATTATTTGGGAAAACC 59.117 33.333 0.00 0.00 40.81 3.27
3685 4251 6.700520 CGACAAGAACTAGGTAGAAAACAAGT 59.299 38.462 0.00 0.00 0.00 3.16
3706 4272 1.135024 GCGGTACCAGGAAATACGACA 60.135 52.381 13.54 0.00 0.00 4.35
3708 4274 0.461135 GGCGGTACCAGGAAATACGA 59.539 55.000 13.54 0.00 38.86 3.43
3710 4276 1.202615 GGAGGCGGTACCAGGAAATAC 60.203 57.143 13.54 0.00 43.14 1.89
3730 4296 6.161381 GCAAATAAAATCTGGCCCATAGATG 58.839 40.000 0.00 0.00 35.20 2.90
3755 4321 0.993509 TTGGCAATAGGGAGAGGGGG 60.994 60.000 0.00 0.00 0.00 5.40
3765 4331 3.355378 TGGGTCATTGAGTTGGCAATAG 58.645 45.455 1.92 0.00 36.39 1.73
3781 4347 6.987992 TCACGGTCTATAAAATTGTATGGGTC 59.012 38.462 0.00 0.00 0.00 4.46
3813 4379 3.631144 ACGATTGTTGTGCATTTCAGTG 58.369 40.909 0.00 0.00 0.00 3.66
3818 4384 3.706802 TGTGACGATTGTTGTGCATTT 57.293 38.095 0.00 0.00 0.00 2.32
3847 4413 0.878523 CAGAAAGTGCGTGGTTCCGA 60.879 55.000 0.00 0.00 0.00 4.55
3863 4429 3.706373 GAGGGCTTCACCGGCAGA 61.706 66.667 0.00 0.00 40.62 4.26
3883 4449 1.012086 CTGTCCGAACATCTGCATGG 58.988 55.000 0.00 0.00 34.13 3.66
3892 4458 0.528901 CGACACCAACTGTCCGAACA 60.529 55.000 0.00 0.00 46.01 3.18
3897 4463 0.531974 TTCAGCGACACCAACTGTCC 60.532 55.000 0.00 0.00 46.01 4.02
3898 4464 0.861837 CTTCAGCGACACCAACTGTC 59.138 55.000 0.00 0.00 45.38 3.51


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

AutoCloner maintained by Alex Coulton.