Multiple sequence alignment - TraesCS2D01G356500

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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 TraesCS2D01G356500 chr2D 100.000 8371 0 0 1 8371 458919190 458910820 0.000000e+00 15459.0
1 TraesCS2D01G356500 chr2D 95.954 173 7 0 522 694 458918551 458918379 1.780000e-71 281.0
2 TraesCS2D01G356500 chr2D 95.954 173 7 0 640 812 458918669 458918497 1.780000e-71 281.0
3 TraesCS2D01G356500 chr2D 90.196 51 5 0 8246 8296 542905823 542905873 5.420000e-07 67.6
4 TraesCS2D01G356500 chr2A 95.918 7104 205 33 697 7756 602135432 602128370 0.000000e+00 11433.0
5 TraesCS2D01G356500 chr2A 91.680 637 31 8 1 635 602135931 602135315 0.000000e+00 863.0
6 TraesCS2D01G356500 chr2A 80.684 497 57 24 7863 8335 602128369 602127888 4.810000e-92 350.0
7 TraesCS2D01G356500 chr2A 94.118 119 5 2 637 753 602135433 602135315 6.680000e-41 180.0
8 TraesCS2D01G356500 chr2A 92.373 118 7 1 579 694 602135432 602135315 5.200000e-37 167.0
9 TraesCS2D01G356500 chr2B 95.045 7164 231 58 637 7745 539811761 539804667 0.000000e+00 11149.0
10 TraesCS2D01G356500 chr2B 95.290 637 15 3 7747 8371 539803852 539803219 0.000000e+00 996.0
11 TraesCS2D01G356500 chr2B 89.625 694 37 20 1 694 539812243 539811585 0.000000e+00 850.0
12 TraesCS2D01G356500 chr2B 90.909 176 15 1 579 753 539811760 539811585 1.400000e-57 235.0
13 TraesCS2D01G356500 chr2B 94.017 117 6 1 697 812 539811760 539811644 8.640000e-40 176.0
14 TraesCS2D01G356500 chr2B 90.541 74 7 0 7864 7937 539803817 539803744 1.920000e-16 99.0
15 TraesCS2D01G356500 chr2B 90.566 53 5 0 8067 8119 539803482 539803430 4.190000e-08 71.3


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 TraesCS2D01G356500 chr2D 458910820 458919190 8370 True 5340.333333 15459 97.302667 1 8371 3 chr2D.!!$R1 8370
1 TraesCS2D01G356500 chr2A 602127888 602135931 8043 True 2598.600000 11433 90.954600 1 8335 5 chr2A.!!$R1 8334
2 TraesCS2D01G356500 chr2B 539803219 539812243 9024 True 1939.471429 11149 92.284714 1 8371 7 chr2B.!!$R1 8370

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
682 684 0.100325 TGCGGTGCAAGTCAAGTTTG 59.900 50.000 0.00 0.00 34.76 2.93 F
683 685 0.100503 GCGGTGCAAGTCAAGTTTGT 59.899 50.000 0.00 0.00 0.00 2.83 F
1032 1095 0.676151 GCTCAAGGAACAGAGGCCAG 60.676 60.000 5.01 0.00 34.16 4.85 F
1348 1411 3.813443 AGCCAGCAGATATTCAACGAAT 58.187 40.909 0.00 0.00 36.20 3.34 F
3210 3309 1.394917 GCTGTTGATGCTACTTCCGTG 59.605 52.381 0.00 0.00 0.00 4.94 F
3989 4089 0.039346 TTTGTGTGTGATGGCATGCG 60.039 50.000 12.44 0.00 0.00 4.73 F
3990 4090 1.171549 TTGTGTGTGATGGCATGCGT 61.172 50.000 12.44 2.22 0.00 5.24 F
5345 5455 0.107831 TGAGCGTTTGTGGTTAGCCT 59.892 50.000 0.00 0.00 35.27 4.58 F
7111 7236 0.604073 TCGGGTACGTGCATCTTTCA 59.396 50.000 5.86 0.00 41.85 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2376 2456 1.133823 TCAAGTTTGAGAGGCCTGCAA 60.134 47.619 12.00 12.28 32.50 4.08 R
2542 2622 5.127845 TGCTTTACAAACAATTGGTTCAGGA 59.872 36.000 5.55 0.00 39.29 3.86 R
2756 2852 6.868339 CAGTGATGCCGTTACAATATCTCATA 59.132 38.462 0.00 0.00 0.00 2.15 R
3235 3334 0.107410 TTGTCAGCACCCTTCAACGT 60.107 50.000 0.00 0.00 0.00 3.99 R
4934 5043 1.002468 CGGATCCACGATTCAAATGCC 60.002 52.381 13.41 0.00 35.47 4.40 R
4935 5044 1.002468 CCGGATCCACGATTCAAATGC 60.002 52.381 13.41 0.00 35.47 3.56 R
5440 5555 1.541588 CAAAAGGCCTACAGAACAGCC 59.458 52.381 5.16 0.00 46.13 4.85 R
7162 7287 0.107456 AGGCCTGCGACAAGGATATG 59.893 55.000 3.11 0.00 40.02 1.78 R
8200 9164 0.886490 AGGCTCCACAAGTTTGCTCG 60.886 55.000 0.00 0.00 0.00 5.03 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
199 200 2.028130 TCTGATCCTCTCTTCTTCGGC 58.972 52.381 0.00 0.00 0.00 5.54
203 204 3.823873 TGATCCTCTCTTCTTCGGCTATC 59.176 47.826 0.00 0.00 0.00 2.08
237 238 0.599728 TGGGCATTTTTGCAGTTCGC 60.600 50.000 0.00 0.00 42.89 4.70
282 283 3.047877 CTTGGTGCGGACGGAACC 61.048 66.667 3.10 3.10 0.00 3.62
317 318 4.789012 CATATTTGCAGGGTTCTGTGTT 57.211 40.909 0.00 0.00 42.78 3.32
318 319 4.737054 CATATTTGCAGGGTTCTGTGTTC 58.263 43.478 0.00 0.00 42.78 3.18
319 320 2.435372 TTTGCAGGGTTCTGTGTTCT 57.565 45.000 0.00 0.00 42.78 3.01
320 321 1.679139 TTGCAGGGTTCTGTGTTCTG 58.321 50.000 0.00 0.00 42.78 3.02
321 322 0.546122 TGCAGGGTTCTGTGTTCTGT 59.454 50.000 0.00 0.00 42.78 3.41
322 323 1.064758 TGCAGGGTTCTGTGTTCTGTT 60.065 47.619 0.00 0.00 42.78 3.16
323 324 1.604278 GCAGGGTTCTGTGTTCTGTTC 59.396 52.381 0.00 0.00 42.78 3.18
324 325 1.867233 CAGGGTTCTGTGTTCTGTTCG 59.133 52.381 0.00 0.00 36.30 3.95
325 326 1.202651 AGGGTTCTGTGTTCTGTTCGG 60.203 52.381 0.00 0.00 0.00 4.30
326 327 0.586802 GGTTCTGTGTTCTGTTCGGC 59.413 55.000 0.00 0.00 0.00 5.54
327 328 1.295792 GTTCTGTGTTCTGTTCGGCA 58.704 50.000 0.00 0.00 0.00 5.69
523 525 4.125912 GCGTCTGCATACAATCTTCATC 57.874 45.455 2.93 0.00 42.15 2.92
524 526 3.806521 GCGTCTGCATACAATCTTCATCT 59.193 43.478 2.93 0.00 42.15 2.90
525 527 4.272018 GCGTCTGCATACAATCTTCATCTT 59.728 41.667 2.93 0.00 42.15 2.40
526 528 5.557893 GCGTCTGCATACAATCTTCATCTTC 60.558 44.000 2.93 0.00 42.15 2.87
561 563 0.105964 TACTGCGGTGCAAGTCAAGT 59.894 50.000 8.92 0.00 38.41 3.16
565 567 2.226330 TGCGGTGCAAGTCAAGTTTAT 58.774 42.857 0.00 0.00 34.76 1.40
566 568 2.621055 TGCGGTGCAAGTCAAGTTTATT 59.379 40.909 0.00 0.00 34.76 1.40
567 569 2.979813 GCGGTGCAAGTCAAGTTTATTG 59.020 45.455 0.00 0.00 0.00 1.90
568 570 3.304391 GCGGTGCAAGTCAAGTTTATTGA 60.304 43.478 0.00 0.00 0.00 2.57
569 571 4.615912 GCGGTGCAAGTCAAGTTTATTGAT 60.616 41.667 0.00 0.00 0.00 2.57
570 572 5.460646 CGGTGCAAGTCAAGTTTATTGATT 58.539 37.500 0.00 0.00 0.00 2.57
571 573 6.607689 CGGTGCAAGTCAAGTTTATTGATTA 58.392 36.000 0.00 0.00 0.00 1.75
572 574 7.250569 CGGTGCAAGTCAAGTTTATTGATTAT 58.749 34.615 0.00 0.00 0.00 1.28
573 575 8.394877 CGGTGCAAGTCAAGTTTATTGATTATA 58.605 33.333 0.00 0.00 0.00 0.98
599 601 9.771534 ATTAGCAATCTTCTGATAGTAACTTCC 57.228 33.333 0.00 0.00 31.70 3.46
600 602 7.430760 AGCAATCTTCTGATAGTAACTTCCT 57.569 36.000 0.00 0.00 31.70 3.36
601 603 7.856415 AGCAATCTTCTGATAGTAACTTCCTT 58.144 34.615 0.00 0.00 31.70 3.36
602 604 8.982723 AGCAATCTTCTGATAGTAACTTCCTTA 58.017 33.333 0.00 0.00 31.70 2.69
603 605 9.036671 GCAATCTTCTGATAGTAACTTCCTTAC 57.963 37.037 0.00 0.00 32.22 2.34
606 608 7.773149 TCTTCTGATAGTAACTTCCTTACTGC 58.227 38.462 3.48 0.00 44.20 4.40
607 609 7.396339 TCTTCTGATAGTAACTTCCTTACTGCA 59.604 37.037 3.48 0.00 44.20 4.41
608 610 7.101652 TCTGATAGTAACTTCCTTACTGCAG 57.898 40.000 13.48 13.48 44.20 4.41
609 611 6.663953 TCTGATAGTAACTTCCTTACTGCAGT 59.336 38.462 25.12 25.12 44.20 4.40
610 612 6.631016 TGATAGTAACTTCCTTACTGCAGTG 58.369 40.000 29.57 13.43 44.20 3.66
611 613 3.665190 AGTAACTTCCTTACTGCAGTGC 58.335 45.455 29.57 8.58 43.06 4.40
612 614 2.638480 AACTTCCTTACTGCAGTGCA 57.362 45.000 29.57 18.58 36.92 4.57
613 615 2.638480 ACTTCCTTACTGCAGTGCAA 57.362 45.000 29.57 15.42 38.41 4.08
614 616 2.222027 ACTTCCTTACTGCAGTGCAAC 58.778 47.619 29.57 0.00 38.41 4.17
615 617 6.483369 GTAACTTCCTTACTGCAGTGCAACT 61.483 44.000 29.57 9.65 39.00 3.16
616 618 8.202900 GTAACTTCCTTACTGCAGTGCAACTC 62.203 46.154 29.57 6.30 37.45 3.01
670 672 3.007635 AGTAATTTCCTTACTGCGGTGC 58.992 45.455 8.92 0.00 46.61 5.01
671 673 1.904287 AATTTCCTTACTGCGGTGCA 58.096 45.000 8.92 0.00 36.92 4.57
672 674 1.904287 ATTTCCTTACTGCGGTGCAA 58.096 45.000 8.92 0.00 38.41 4.08
673 675 1.234821 TTTCCTTACTGCGGTGCAAG 58.765 50.000 8.92 4.73 38.41 4.01
674 676 0.107831 TTCCTTACTGCGGTGCAAGT 59.892 50.000 8.92 0.00 38.41 3.16
675 677 0.320421 TCCTTACTGCGGTGCAAGTC 60.320 55.000 8.92 0.00 38.41 3.01
676 678 0.602638 CCTTACTGCGGTGCAAGTCA 60.603 55.000 8.92 0.00 38.41 3.41
677 679 1.225855 CTTACTGCGGTGCAAGTCAA 58.774 50.000 8.92 0.00 38.41 3.18
678 680 1.195448 CTTACTGCGGTGCAAGTCAAG 59.805 52.381 8.92 0.00 38.41 3.02
679 681 0.105964 TACTGCGGTGCAAGTCAAGT 59.894 50.000 8.92 0.00 38.41 3.16
680 682 0.748005 ACTGCGGTGCAAGTCAAGTT 60.748 50.000 0.00 0.00 38.41 2.66
681 683 0.381801 CTGCGGTGCAAGTCAAGTTT 59.618 50.000 0.00 0.00 38.41 2.66
682 684 0.100325 TGCGGTGCAAGTCAAGTTTG 59.900 50.000 0.00 0.00 34.76 2.93
683 685 0.100503 GCGGTGCAAGTCAAGTTTGT 59.899 50.000 0.00 0.00 0.00 2.83
684 686 1.469079 GCGGTGCAAGTCAAGTTTGTT 60.469 47.619 0.00 0.00 0.00 2.83
685 687 2.184448 CGGTGCAAGTCAAGTTTGTTG 58.816 47.619 0.00 0.00 0.00 3.33
686 688 2.159448 CGGTGCAAGTCAAGTTTGTTGA 60.159 45.455 0.00 0.00 0.00 3.18
687 689 3.489059 CGGTGCAAGTCAAGTTTGTTGAT 60.489 43.478 0.00 0.00 0.00 2.57
688 690 4.432712 GGTGCAAGTCAAGTTTGTTGATT 58.567 39.130 0.00 0.00 0.00 2.57
689 691 5.587289 GGTGCAAGTCAAGTTTGTTGATTA 58.413 37.500 0.00 0.00 0.00 1.75
690 692 6.215845 GGTGCAAGTCAAGTTTGTTGATTAT 58.784 36.000 0.00 0.00 0.00 1.28
691 693 7.367285 GGTGCAAGTCAAGTTTGTTGATTATA 58.633 34.615 0.00 0.00 0.00 0.98
692 694 8.028938 GGTGCAAGTCAAGTTTGTTGATTATAT 58.971 33.333 0.00 0.00 0.00 0.86
693 695 9.410556 GTGCAAGTCAAGTTTGTTGATTATATT 57.589 29.630 0.00 0.00 0.00 1.28
694 696 9.409312 TGCAAGTCAAGTTTGTTGATTATATTG 57.591 29.630 0.00 0.00 0.00 1.90
695 697 8.863049 GCAAGTCAAGTTTGTTGATTATATTGG 58.137 33.333 0.00 0.00 0.00 3.16
696 698 8.863049 CAAGTCAAGTTTGTTGATTATATTGGC 58.137 33.333 0.00 0.00 0.00 4.52
697 699 8.121305 AGTCAAGTTTGTTGATTATATTGGCA 57.879 30.769 0.00 0.00 0.00 4.92
698 700 8.584157 AGTCAAGTTTGTTGATTATATTGGCAA 58.416 29.630 0.68 0.68 0.00 4.52
699 701 9.369904 GTCAAGTTTGTTGATTATATTGGCAAT 57.630 29.630 18.01 18.01 0.00 3.56
700 702 9.585099 TCAAGTTTGTTGATTATATTGGCAATC 57.415 29.630 17.41 3.18 0.00 2.67
701 703 9.590451 CAAGTTTGTTGATTATATTGGCAATCT 57.410 29.630 17.41 9.80 33.26 2.40
703 705 9.807649 AGTTTGTTGATTATATTGGCAATCTTC 57.192 29.630 17.41 9.83 33.26 2.87
704 706 9.807649 GTTTGTTGATTATATTGGCAATCTTCT 57.192 29.630 17.41 0.34 33.26 2.85
705 707 9.806203 TTTGTTGATTATATTGGCAATCTTCTG 57.194 29.630 17.41 0.00 33.26 3.02
706 708 8.750515 TGTTGATTATATTGGCAATCTTCTGA 57.249 30.769 17.41 0.00 33.26 3.27
707 709 9.358406 TGTTGATTATATTGGCAATCTTCTGAT 57.642 29.630 17.41 6.08 33.26 2.90
716 718 7.849804 TTGGCAATCTTCTGATAGTAACTTC 57.150 36.000 0.00 0.00 31.70 3.01
717 719 6.349300 TGGCAATCTTCTGATAGTAACTTCC 58.651 40.000 0.00 0.00 31.70 3.46
718 720 6.156949 TGGCAATCTTCTGATAGTAACTTCCT 59.843 38.462 0.00 0.00 31.70 3.36
719 721 7.051000 GGCAATCTTCTGATAGTAACTTCCTT 58.949 38.462 0.00 0.00 31.70 3.36
720 722 8.204836 GGCAATCTTCTGATAGTAACTTCCTTA 58.795 37.037 0.00 0.00 31.70 2.69
721 723 9.036671 GCAATCTTCTGATAGTAACTTCCTTAC 57.963 37.037 0.00 0.00 32.22 2.34
724 726 7.773149 TCTTCTGATAGTAACTTCCTTACTGC 58.227 38.462 3.48 0.00 44.20 4.40
725 727 7.396339 TCTTCTGATAGTAACTTCCTTACTGCA 59.604 37.037 3.48 0.00 44.20 4.41
726 728 7.101652 TCTGATAGTAACTTCCTTACTGCAG 57.898 40.000 13.48 13.48 44.20 4.41
727 729 6.663953 TCTGATAGTAACTTCCTTACTGCAGT 59.336 38.462 25.12 25.12 44.20 4.40
728 730 6.631016 TGATAGTAACTTCCTTACTGCAGTG 58.369 40.000 29.57 13.43 44.20 3.66
729 731 3.665190 AGTAACTTCCTTACTGCAGTGC 58.335 45.455 29.57 8.58 43.06 4.40
730 732 2.638480 AACTTCCTTACTGCAGTGCA 57.362 45.000 29.57 18.58 36.92 4.57
731 733 2.638480 ACTTCCTTACTGCAGTGCAA 57.362 45.000 29.57 15.42 38.41 4.08
732 734 2.222027 ACTTCCTTACTGCAGTGCAAC 58.778 47.619 29.57 0.00 38.41 4.17
733 735 6.483369 GTAACTTCCTTACTGCAGTGCAACT 61.483 44.000 29.57 9.65 39.00 3.16
734 736 8.202900 GTAACTTCCTTACTGCAGTGCAACTC 62.203 46.154 29.57 6.30 37.45 3.01
752 754 9.956720 GTGCAACTCAAGCTTATTGATTATATT 57.043 29.630 17.16 0.00 0.00 1.28
753 755 9.955208 TGCAACTCAAGCTTATTGATTATATTG 57.045 29.630 17.16 6.22 0.00 1.90
801 862 1.603802 TGCAGTGCAAGTCAAGCTTAC 59.396 47.619 17.26 0.00 34.76 2.34
897 959 4.467084 GGAATCGAGCCGTGGCCA 62.467 66.667 0.00 0.00 43.17 5.36
932 994 2.896685 CCTCTGAGTCTATCCATGGTCC 59.103 54.545 12.58 0.00 0.00 4.46
948 1010 0.723790 GTCCGTGACACTGTACGTCG 60.724 60.000 3.68 0.00 38.56 5.12
978 1041 2.107204 ACTTGAGGCAGTGATCAGGTTT 59.893 45.455 0.00 0.00 32.42 3.27
1032 1095 0.676151 GCTCAAGGAACAGAGGCCAG 60.676 60.000 5.01 0.00 34.16 4.85
1240 1303 5.374921 CTCATATCTTCAGAGTTTGGCCAT 58.625 41.667 6.09 0.00 0.00 4.40
1348 1411 3.813443 AGCCAGCAGATATTCAACGAAT 58.187 40.909 0.00 0.00 36.20 3.34
2050 2130 4.220724 TGGGACGAGTTAGCCTTATATGT 58.779 43.478 0.00 0.00 0.00 2.29
2060 2140 9.555727 GAGTTAGCCTTATATGTCAACCAATTA 57.444 33.333 0.00 0.00 0.00 1.40
2376 2456 7.926674 TGATGTATGATGTGTGTCTTCATTT 57.073 32.000 0.00 0.00 40.11 2.32
2756 2852 6.681368 GCTTGAGAAAACTGGAAACACTGAAT 60.681 38.462 0.00 0.00 35.60 2.57
2780 2876 5.276461 TGAGATATTGTAACGGCATCACT 57.724 39.130 0.00 0.00 0.00 3.41
3081 3180 6.496571 CCGTGTTTAAGTTGTTGGTTTGATA 58.503 36.000 0.00 0.00 0.00 2.15
3092 3191 8.822805 AGTTGTTGGTTTGATATCTTAGGTCTA 58.177 33.333 3.98 0.00 0.00 2.59
3181 3280 9.628500 ATCAGGTTTTACATCCTTTCCTTATAC 57.372 33.333 0.00 0.00 30.91 1.47
3210 3309 1.394917 GCTGTTGATGCTACTTCCGTG 59.605 52.381 0.00 0.00 0.00 4.94
3211 3310 2.930887 GCTGTTGATGCTACTTCCGTGA 60.931 50.000 0.00 0.00 0.00 4.35
3235 3334 4.207165 AGTTTCTTTGGCTTAGTCTTGCA 58.793 39.130 0.00 0.00 0.00 4.08
3243 3342 2.096218 GGCTTAGTCTTGCACGTTGAAG 60.096 50.000 0.00 0.00 0.00 3.02
3579 3678 7.445707 AGAGATGTTTTTACCTCTTCTGTTTCC 59.554 37.037 0.00 0.00 32.55 3.13
3946 4045 2.039613 TGCTGTCCATATGGTGAACACA 59.960 45.455 21.28 15.83 36.34 3.72
3989 4089 0.039346 TTTGTGTGTGATGGCATGCG 60.039 50.000 12.44 0.00 0.00 4.73
3990 4090 1.171549 TTGTGTGTGATGGCATGCGT 61.172 50.000 12.44 2.22 0.00 5.24
3991 4091 1.171549 TGTGTGTGATGGCATGCGTT 61.172 50.000 12.44 0.30 0.00 4.84
4011 4111 5.505654 GCGTTATGGGATACATGTTTCCTTG 60.506 44.000 27.74 15.46 40.82 3.61
4085 4185 2.711009 TCTCTGTTTCCTTCACCCACAT 59.289 45.455 0.00 0.00 0.00 3.21
4308 4408 8.308931 ACGAGGTGAGTATTAATCACTGTTTAA 58.691 33.333 20.07 0.00 45.18 1.52
4601 4710 1.411493 GAAAGTACCGAGAAGGCGCG 61.411 60.000 0.00 0.00 46.52 6.86
4642 4751 6.902224 AGAAAACCCAAACGAAAATGAAAG 57.098 33.333 0.00 0.00 0.00 2.62
4791 4900 3.083122 AGATGAAAGCAGAGGCATGTT 57.917 42.857 0.00 0.00 44.61 2.71
4792 4901 3.428532 AGATGAAAGCAGAGGCATGTTT 58.571 40.909 0.00 0.00 44.61 2.83
4959 5068 2.812358 TGAATCGTGGATCCGGTATG 57.188 50.000 7.39 0.00 0.00 2.39
4973 5083 4.328536 TCCGGTATGCTAAACAACACAAT 58.671 39.130 0.00 0.00 0.00 2.71
4983 5093 2.151502 ACAACACAATGTGGGGACAA 57.848 45.000 18.37 0.00 46.06 3.18
5113 5223 7.094634 TGAGTTCCTTCAGCATGTCTTAATTTC 60.095 37.037 0.00 0.00 37.40 2.17
5213 5323 8.425577 AATAGAACAATCATCGAGTTAACCAG 57.574 34.615 0.88 0.00 0.00 4.00
5245 5355 5.183140 AGTTTACTGTTGTGGAATGGCATAC 59.817 40.000 0.00 0.00 0.00 2.39
5266 5376 9.783256 GCATACGATTTTTATTTACCAGACTTT 57.217 29.630 0.00 0.00 0.00 2.66
5310 5420 0.247185 ATGGGGCATTCTTGTTTGCG 59.753 50.000 0.00 0.00 39.78 4.85
5343 5453 2.989422 ATTGAGCGTTTGTGGTTAGC 57.011 45.000 0.00 0.00 0.00 3.09
5345 5455 0.107831 TGAGCGTTTGTGGTTAGCCT 59.892 50.000 0.00 0.00 35.27 4.58
5347 5457 2.000447 GAGCGTTTGTGGTTAGCCTAG 59.000 52.381 0.00 0.00 35.27 3.02
5466 5581 2.229792 TCTGTAGGCCTTTTGCAGTTG 58.770 47.619 12.58 0.00 43.89 3.16
5556 5671 3.060339 CGCTTTGCCAAATTCTGTTTCAC 60.060 43.478 0.00 0.00 0.00 3.18
5575 5690 2.408704 CACGAACTGTTGATTCTCCGTC 59.591 50.000 0.00 0.00 0.00 4.79
5626 5741 9.895138 TTTTAGTAGTCCAGTTGAAAAGTTAGT 57.105 29.630 0.00 0.00 0.00 2.24
5631 5746 7.085052 AGTCCAGTTGAAAAGTTAGTTTGTC 57.915 36.000 0.00 0.00 0.00 3.18
5721 5836 6.604735 GTGATCACCATAACACTGGAATAC 57.395 41.667 15.31 0.00 39.73 1.89
5727 5842 7.625469 TCACCATAACACTGGAATACATGTAA 58.375 34.615 10.14 0.00 39.73 2.41
5924 6042 3.297134 ACCACTGGTTCACACAATTCT 57.703 42.857 0.00 0.00 27.29 2.40
5964 6082 1.706866 TCATGATAGAGGGGCCAATGG 59.293 52.381 4.39 0.00 0.00 3.16
6079 6197 3.631227 TGCACACATTTCATTGACAGTGA 59.369 39.130 15.30 0.00 0.00 3.41
6359 6477 3.126514 GCATGAATTCACTGAGGTCACTG 59.873 47.826 11.07 2.14 0.00 3.66
6421 6539 6.682611 GCAGCTCTTACAAGTATGTCTCTCAT 60.683 42.308 0.00 0.00 41.05 2.90
6444 6562 1.340405 GCCCAGGTCTTGTGATGATGT 60.340 52.381 0.00 0.00 0.00 3.06
6462 6583 7.286087 TGATGATGTATAGCTCAGCCAAATTTT 59.714 33.333 0.00 0.00 0.00 1.82
6613 6735 1.005924 ACTTCCATAACCTTGCCCCTG 59.994 52.381 0.00 0.00 0.00 4.45
6640 6762 5.999205 TCCGTATTTCCACTGTTTACCTA 57.001 39.130 0.00 0.00 0.00 3.08
6667 6791 9.302345 TCTAGATGCTAAATTTCTGTCGTTTAG 57.698 33.333 0.00 0.00 38.07 1.85
6713 6838 3.251972 GCAAGATAGCCCTTTATGACAGC 59.748 47.826 0.00 0.00 0.00 4.40
6741 6866 3.367498 GCCCGGTGTTGCAATAATTTGTA 60.367 43.478 0.59 0.00 35.17 2.41
6761 6886 3.485463 AGTCTTTCGGATGTGTTTGGA 57.515 42.857 0.00 0.00 0.00 3.53
6772 6897 5.106357 CGGATGTGTTTGGACATAACATCAA 60.106 40.000 14.10 0.00 37.99 2.57
6834 6959 2.540101 CGGATTAACGCACCTTGATCTC 59.460 50.000 0.00 0.00 0.00 2.75
6902 7027 7.901029 TGTAAGGGTGCATGATTAAATCAAAA 58.099 30.769 0.00 0.00 43.50 2.44
7001 7126 2.588034 GGGCTAATCACCGACGCC 60.588 66.667 0.00 0.00 39.98 5.68
7111 7236 0.604073 TCGGGTACGTGCATCTTTCA 59.396 50.000 5.86 0.00 41.85 2.69
7114 7239 2.356135 GGGTACGTGCATCTTTCACAT 58.644 47.619 5.86 0.00 34.27 3.21
7126 7251 7.436080 GTGCATCTTTCACATTTCTTTCTTTCA 59.564 33.333 0.00 0.00 34.73 2.69
7128 7253 8.645487 GCATCTTTCACATTTCTTTCTTTCATC 58.355 33.333 0.00 0.00 0.00 2.92
7134 7259 5.477984 CACATTTCTTTCTTTCATCTCCCCA 59.522 40.000 0.00 0.00 0.00 4.96
7135 7260 5.713861 ACATTTCTTTCTTTCATCTCCCCAG 59.286 40.000 0.00 0.00 0.00 4.45
7144 7269 1.195115 CATCTCCCCAGAACTTCCGA 58.805 55.000 0.00 0.00 30.24 4.55
7152 7277 3.324846 CCCCAGAACTTCCGATATGATCA 59.675 47.826 0.00 0.00 0.00 2.92
7162 7287 7.148641 ACTTCCGATATGATCATCACAGTTAC 58.851 38.462 12.53 0.00 0.00 2.50
7462 7588 6.561614 ACATACATAGTCTTGTGAGTTACGG 58.438 40.000 0.00 0.00 0.00 4.02
7469 7595 1.831736 CTTGTGAGTTACGGGAGGGAT 59.168 52.381 0.00 0.00 0.00 3.85
7470 7596 1.946984 TGTGAGTTACGGGAGGGATT 58.053 50.000 0.00 0.00 0.00 3.01
7471 7597 1.553248 TGTGAGTTACGGGAGGGATTG 59.447 52.381 0.00 0.00 0.00 2.67
7634 7763 3.305398 TGGTGTTTGCGAAGTTTTGTT 57.695 38.095 0.00 0.00 0.00 2.83
7644 7773 1.866601 GAAGTTTTGTTGCATGGTGCC 59.133 47.619 0.00 0.00 44.23 5.01
7659 7788 1.082117 GTGCCACGATCCTGGTTACG 61.082 60.000 11.75 1.14 33.30 3.18
7670 7799 1.135083 CCTGGTTACGATTCTCAGCGT 60.135 52.381 0.00 0.00 43.86 5.07
7709 7839 3.678529 CGTGTGATATGGTGGTGTGATGA 60.679 47.826 0.00 0.00 0.00 2.92
7710 7840 3.873361 GTGTGATATGGTGGTGTGATGAG 59.127 47.826 0.00 0.00 0.00 2.90
7760 8703 0.466922 AACAGCAGCAGCCAACTCTT 60.467 50.000 0.00 0.00 43.56 2.85
7763 8706 0.179009 AGCAGCAGCCAACTCTTTCA 60.179 50.000 0.00 0.00 43.56 2.69
7781 8724 5.184864 TCTTTCAAAGTGGCAAACTCTCAAA 59.815 36.000 0.00 0.00 38.56 2.69
8006 8954 5.277601 TCAGTTCAACTAAACTAATGCGC 57.722 39.130 0.00 0.00 37.38 6.09
8148 9112 7.275920 ACTAGAAGCACCTACAATTTAGATGG 58.724 38.462 0.00 0.00 0.00 3.51
8200 9164 5.779922 TGTAAGTCTCAACCTGTGTATCAC 58.220 41.667 0.00 0.00 34.56 3.06
8237 9201 5.585047 GGAGCCTCGTGTTGTAATTAAATCT 59.415 40.000 0.00 0.00 0.00 2.40
8347 9323 1.818674 GCCCGAAATTTCTCCACACAT 59.181 47.619 15.92 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
312 313 3.669536 TGATTATGCCGAACAGAACACA 58.330 40.909 0.00 0.00 30.95 3.72
313 314 4.260784 GGATGATTATGCCGAACAGAACAC 60.261 45.833 0.00 0.00 30.95 3.32
314 315 3.876914 GGATGATTATGCCGAACAGAACA 59.123 43.478 0.00 0.00 30.95 3.18
324 325 0.962356 CCCCTGCGGATGATTATGCC 60.962 60.000 0.00 0.00 0.00 4.40
325 326 1.589716 GCCCCTGCGGATGATTATGC 61.590 60.000 0.00 0.00 0.00 3.14
326 327 0.037303 AGCCCCTGCGGATGATTATG 59.963 55.000 0.00 0.00 44.33 1.90
327 328 2.468015 AGCCCCTGCGGATGATTAT 58.532 52.632 0.00 0.00 44.33 1.28
344 345 1.230635 CCCACGAACAGAGCAACCAG 61.231 60.000 0.00 0.00 0.00 4.00
573 575 9.771534 GGAAGTTACTATCAGAAGATTGCTAAT 57.228 33.333 0.00 0.00 35.67 1.73
574 576 8.982723 AGGAAGTTACTATCAGAAGATTGCTAA 58.017 33.333 0.00 0.00 35.67 3.09
575 577 8.540507 AGGAAGTTACTATCAGAAGATTGCTA 57.459 34.615 0.00 0.00 35.67 3.49
576 578 7.430760 AGGAAGTTACTATCAGAAGATTGCT 57.569 36.000 0.00 0.00 35.67 3.91
577 579 9.036671 GTAAGGAAGTTACTATCAGAAGATTGC 57.963 37.037 0.00 0.00 38.44 3.56
591 593 3.399330 TGCACTGCAGTAAGGAAGTTAC 58.601 45.455 21.20 0.00 41.39 2.50
592 594 3.762407 TGCACTGCAGTAAGGAAGTTA 57.238 42.857 21.20 0.00 33.32 2.24
593 595 2.618709 GTTGCACTGCAGTAAGGAAGTT 59.381 45.455 21.20 0.00 40.61 2.66
594 596 2.158755 AGTTGCACTGCAGTAAGGAAGT 60.159 45.455 21.20 15.34 40.61 3.01
595 597 2.481952 GAGTTGCACTGCAGTAAGGAAG 59.518 50.000 21.20 7.18 40.61 3.46
596 598 2.158827 TGAGTTGCACTGCAGTAAGGAA 60.159 45.455 21.20 13.09 40.61 3.36
597 599 1.416030 TGAGTTGCACTGCAGTAAGGA 59.584 47.619 21.20 6.68 40.61 3.36
598 600 1.882912 TGAGTTGCACTGCAGTAAGG 58.117 50.000 21.20 8.83 40.61 2.69
599 601 2.350197 GCTTGAGTTGCACTGCAGTAAG 60.350 50.000 21.20 17.86 40.61 2.34
600 602 1.603802 GCTTGAGTTGCACTGCAGTAA 59.396 47.619 21.20 8.69 40.61 2.24
601 603 1.202687 AGCTTGAGTTGCACTGCAGTA 60.203 47.619 21.20 1.09 40.61 2.74
602 604 0.465097 AGCTTGAGTTGCACTGCAGT 60.465 50.000 15.25 15.25 40.61 4.40
603 605 0.666913 AAGCTTGAGTTGCACTGCAG 59.333 50.000 13.48 13.48 40.61 4.41
604 606 1.965935 TAAGCTTGAGTTGCACTGCA 58.034 45.000 9.86 0.00 36.47 4.41
605 607 3.058016 TCAATAAGCTTGAGTTGCACTGC 60.058 43.478 9.86 0.00 0.00 4.40
606 608 4.754372 TCAATAAGCTTGAGTTGCACTG 57.246 40.909 9.86 0.00 0.00 3.66
607 609 5.972107 AATCAATAAGCTTGAGTTGCACT 57.028 34.783 9.86 0.00 0.00 4.40
608 610 9.956720 AATATAATCAATAAGCTTGAGTTGCAC 57.043 29.630 9.86 0.00 0.00 4.57
609 611 9.955208 CAATATAATCAATAAGCTTGAGTTGCA 57.045 29.630 9.86 3.21 0.00 4.08
654 656 1.234821 CTTGCACCGCAGTAAGGAAA 58.765 50.000 0.00 0.00 40.61 3.13
655 657 0.107831 ACTTGCACCGCAGTAAGGAA 59.892 50.000 7.75 0.00 40.61 3.36
656 658 0.320421 GACTTGCACCGCAGTAAGGA 60.320 55.000 7.75 0.00 40.61 3.36
657 659 0.602638 TGACTTGCACCGCAGTAAGG 60.603 55.000 7.75 0.00 40.61 2.69
658 660 1.195448 CTTGACTTGCACCGCAGTAAG 59.805 52.381 0.00 2.54 40.61 2.34
659 661 1.225855 CTTGACTTGCACCGCAGTAA 58.774 50.000 0.00 0.00 40.61 2.24
660 662 0.105964 ACTTGACTTGCACCGCAGTA 59.894 50.000 0.00 0.00 40.61 2.74
661 663 0.748005 AACTTGACTTGCACCGCAGT 60.748 50.000 0.00 0.00 40.61 4.40
662 664 0.381801 AAACTTGACTTGCACCGCAG 59.618 50.000 0.00 0.00 40.61 5.18
663 665 0.100325 CAAACTTGACTTGCACCGCA 59.900 50.000 0.00 0.00 36.47 5.69
664 666 0.100503 ACAAACTTGACTTGCACCGC 59.899 50.000 0.00 0.00 0.00 5.68
665 667 2.159448 TCAACAAACTTGACTTGCACCG 60.159 45.455 0.00 0.00 0.00 4.94
666 668 3.502191 TCAACAAACTTGACTTGCACC 57.498 42.857 0.00 0.00 0.00 5.01
667 669 8.970691 ATATAATCAACAAACTTGACTTGCAC 57.029 30.769 0.00 0.00 0.00 4.57
668 670 9.409312 CAATATAATCAACAAACTTGACTTGCA 57.591 29.630 0.00 0.00 0.00 4.08
669 671 8.863049 CCAATATAATCAACAAACTTGACTTGC 58.137 33.333 0.00 0.00 0.00 4.01
670 672 8.863049 GCCAATATAATCAACAAACTTGACTTG 58.137 33.333 0.00 0.00 0.00 3.16
671 673 8.584157 TGCCAATATAATCAACAAACTTGACTT 58.416 29.630 0.00 0.00 0.00 3.01
672 674 8.121305 TGCCAATATAATCAACAAACTTGACT 57.879 30.769 0.00 0.00 0.00 3.41
673 675 8.755696 TTGCCAATATAATCAACAAACTTGAC 57.244 30.769 0.00 0.00 0.00 3.18
674 676 9.585099 GATTGCCAATATAATCAACAAACTTGA 57.415 29.630 0.00 0.00 34.31 3.02
675 677 9.590451 AGATTGCCAATATAATCAACAAACTTG 57.410 29.630 0.00 0.00 36.11 3.16
677 679 9.807649 GAAGATTGCCAATATAATCAACAAACT 57.192 29.630 0.00 0.00 36.11 2.66
678 680 9.807649 AGAAGATTGCCAATATAATCAACAAAC 57.192 29.630 0.00 0.00 36.11 2.93
679 681 9.806203 CAGAAGATTGCCAATATAATCAACAAA 57.194 29.630 0.00 0.00 36.11 2.83
680 682 9.187996 TCAGAAGATTGCCAATATAATCAACAA 57.812 29.630 0.00 0.00 36.11 2.83
681 683 8.750515 TCAGAAGATTGCCAATATAATCAACA 57.249 30.769 0.00 0.00 36.11 3.33
690 692 9.547753 GAAGTTACTATCAGAAGATTGCCAATA 57.452 33.333 0.00 0.00 35.67 1.90
691 693 7.500559 GGAAGTTACTATCAGAAGATTGCCAAT 59.499 37.037 0.00 0.00 35.67 3.16
692 694 6.823689 GGAAGTTACTATCAGAAGATTGCCAA 59.176 38.462 0.00 0.00 35.67 4.52
693 695 6.156949 AGGAAGTTACTATCAGAAGATTGCCA 59.843 38.462 0.00 0.00 35.67 4.92
694 696 6.587273 AGGAAGTTACTATCAGAAGATTGCC 58.413 40.000 0.00 0.00 35.67 4.52
695 697 9.036671 GTAAGGAAGTTACTATCAGAAGATTGC 57.963 37.037 0.00 0.00 38.44 3.56
709 711 3.399330 TGCACTGCAGTAAGGAAGTTAC 58.601 45.455 21.20 0.00 41.39 2.50
710 712 3.762407 TGCACTGCAGTAAGGAAGTTA 57.238 42.857 21.20 0.00 33.32 2.24
711 713 2.618709 GTTGCACTGCAGTAAGGAAGTT 59.381 45.455 21.20 0.00 40.61 2.66
712 714 2.158755 AGTTGCACTGCAGTAAGGAAGT 60.159 45.455 21.20 15.34 40.61 3.01
713 715 2.481952 GAGTTGCACTGCAGTAAGGAAG 59.518 50.000 21.20 7.18 40.61 3.46
714 716 2.158827 TGAGTTGCACTGCAGTAAGGAA 60.159 45.455 21.20 13.09 40.61 3.36
715 717 1.416030 TGAGTTGCACTGCAGTAAGGA 59.584 47.619 21.20 6.68 40.61 3.36
716 718 1.882912 TGAGTTGCACTGCAGTAAGG 58.117 50.000 21.20 8.83 40.61 2.69
717 719 2.350197 GCTTGAGTTGCACTGCAGTAAG 60.350 50.000 21.20 17.86 40.61 2.34
718 720 1.603802 GCTTGAGTTGCACTGCAGTAA 59.396 47.619 21.20 8.69 40.61 2.24
719 721 1.202687 AGCTTGAGTTGCACTGCAGTA 60.203 47.619 21.20 1.09 40.61 2.74
720 722 0.465097 AGCTTGAGTTGCACTGCAGT 60.465 50.000 15.25 15.25 40.61 4.40
721 723 0.666913 AAGCTTGAGTTGCACTGCAG 59.333 50.000 13.48 13.48 40.61 4.41
722 724 1.965935 TAAGCTTGAGTTGCACTGCA 58.034 45.000 9.86 0.00 36.47 4.41
723 725 3.058016 TCAATAAGCTTGAGTTGCACTGC 60.058 43.478 9.86 0.00 0.00 4.40
724 726 4.754372 TCAATAAGCTTGAGTTGCACTG 57.246 40.909 9.86 0.00 0.00 3.66
725 727 5.972107 AATCAATAAGCTTGAGTTGCACT 57.028 34.783 9.86 0.00 0.00 4.40
726 728 9.956720 AATATAATCAATAAGCTTGAGTTGCAC 57.043 29.630 9.86 0.00 0.00 4.57
727 729 9.955208 CAATATAATCAATAAGCTTGAGTTGCA 57.045 29.630 9.86 3.21 0.00 4.08
754 756 8.897752 GCAAGGAAATTACTATCAGAAGATTGT 58.102 33.333 0.00 0.00 41.82 2.71
755 757 9.118300 AGCAAGGAAATTACTATCAGAAGATTG 57.882 33.333 0.00 0.00 35.67 2.67
756 758 9.118300 CAGCAAGGAAATTACTATCAGAAGATT 57.882 33.333 0.00 0.00 35.67 2.40
757 759 7.228308 GCAGCAAGGAAATTACTATCAGAAGAT 59.772 37.037 0.00 0.00 38.29 2.40
758 760 6.540189 GCAGCAAGGAAATTACTATCAGAAGA 59.460 38.462 0.00 0.00 0.00 2.87
759 761 6.317140 TGCAGCAAGGAAATTACTATCAGAAG 59.683 38.462 0.00 0.00 0.00 2.85
760 762 6.179756 TGCAGCAAGGAAATTACTATCAGAA 58.820 36.000 0.00 0.00 0.00 3.02
761 763 5.744171 TGCAGCAAGGAAATTACTATCAGA 58.256 37.500 0.00 0.00 0.00 3.27
762 764 5.587844 ACTGCAGCAAGGAAATTACTATCAG 59.412 40.000 15.27 0.00 0.00 2.90
763 765 5.355071 CACTGCAGCAAGGAAATTACTATCA 59.645 40.000 15.27 0.00 0.00 2.15
764 766 5.731686 GCACTGCAGCAAGGAAATTACTATC 60.732 44.000 15.27 0.00 0.00 2.08
765 767 4.096984 GCACTGCAGCAAGGAAATTACTAT 59.903 41.667 15.27 0.00 0.00 2.12
766 768 3.440173 GCACTGCAGCAAGGAAATTACTA 59.560 43.478 15.27 0.00 0.00 1.82
767 769 2.229784 GCACTGCAGCAAGGAAATTACT 59.770 45.455 15.27 0.00 0.00 2.24
768 770 2.030007 TGCACTGCAGCAAGGAAATTAC 60.030 45.455 15.27 0.00 42.46 1.89
769 771 2.237643 TGCACTGCAGCAAGGAAATTA 58.762 42.857 15.27 0.00 42.46 1.40
770 772 1.042229 TGCACTGCAGCAAGGAAATT 58.958 45.000 15.27 0.00 42.46 1.82
771 773 2.736197 TGCACTGCAGCAAGGAAAT 58.264 47.368 15.27 0.00 42.46 2.17
772 774 4.256462 TGCACTGCAGCAAGGAAA 57.744 50.000 15.27 0.00 42.46 3.13
867 929 3.594134 CTCGATTCCCTAGCATCCATTC 58.406 50.000 0.00 0.00 0.00 2.67
897 959 0.034059 CAGAGGTGCGTGTTCTTCCT 59.966 55.000 0.00 0.00 0.00 3.36
932 994 1.521411 GATCGACGTACAGTGTCACG 58.479 55.000 17.83 17.83 43.63 4.35
948 1010 3.386078 TCACTGCCTCAAGTCTATGGATC 59.614 47.826 0.00 0.00 0.00 3.36
978 1041 1.330521 GCGAGTTCTTGCACTGAACAA 59.669 47.619 24.66 0.00 44.30 2.83
1032 1095 1.561542 AGTTGATCCTCATGGACCACC 59.438 52.381 0.00 0.00 46.51 4.61
1176 1239 1.153066 TCTGGCCACGCAAAGTTCA 60.153 52.632 0.00 0.00 0.00 3.18
1207 1270 5.462240 TCTGAAGATATGAGGTCACAGGAT 58.538 41.667 0.00 0.00 0.00 3.24
1210 1273 5.850557 ACTCTGAAGATATGAGGTCACAG 57.149 43.478 0.00 0.00 32.58 3.66
1240 1303 4.623814 CCAAGAAGAGGCATCGCA 57.376 55.556 0.00 0.00 0.00 5.10
1348 1411 0.611200 ATGTAGCTACACCGCACCAA 59.389 50.000 28.28 2.85 39.30 3.67
1566 1632 6.670617 ACAGGGATAAGCTAGACTTGTACTA 58.329 40.000 8.98 0.00 39.58 1.82
1567 1633 5.520751 ACAGGGATAAGCTAGACTTGTACT 58.479 41.667 8.98 3.50 39.58 2.73
1568 1634 5.855740 ACAGGGATAAGCTAGACTTGTAC 57.144 43.478 8.98 4.23 39.58 2.90
2050 2130 8.877864 AATAGTGTGGAAGATTAATTGGTTGA 57.122 30.769 0.00 0.00 0.00 3.18
2060 2140 6.463049 CCTGATACCGAATAGTGTGGAAGATT 60.463 42.308 0.00 0.00 0.00 2.40
2376 2456 1.133823 TCAAGTTTGAGAGGCCTGCAA 60.134 47.619 12.00 12.28 32.50 4.08
2542 2622 5.127845 TGCTTTACAAACAATTGGTTCAGGA 59.872 36.000 5.55 0.00 39.29 3.86
2756 2852 6.868339 CAGTGATGCCGTTACAATATCTCATA 59.132 38.462 0.00 0.00 0.00 2.15
3038 3137 6.181908 ACACGGCTAAATTTATAAACCCTCA 58.818 36.000 0.00 0.00 0.00 3.86
3081 3180 7.235812 GTGGGATAGTTTGGATAGACCTAAGAT 59.764 40.741 0.00 0.00 39.86 2.40
3092 3191 6.410853 CCAGATTTAGGTGGGATAGTTTGGAT 60.411 42.308 0.00 0.00 0.00 3.41
3210 3309 5.687730 GCAAGACTAAGCCAAAGAAACTTTC 59.312 40.000 0.00 0.00 0.00 2.62
3211 3310 5.127031 TGCAAGACTAAGCCAAAGAAACTTT 59.873 36.000 0.00 0.00 0.00 2.66
3235 3334 0.107410 TTGTCAGCACCCTTCAACGT 60.107 50.000 0.00 0.00 0.00 3.99
3243 3342 4.261801 ACTATACACAATTGTCAGCACCC 58.738 43.478 8.48 0.00 37.15 4.61
3579 3678 4.442375 AAACTCCATACACTGACTCTCG 57.558 45.455 0.00 0.00 0.00 4.04
3930 4029 4.908601 AGAGTTGTGTTCACCATATGGA 57.091 40.909 28.77 3.58 38.94 3.41
3989 4089 7.404671 AACAAGGAAACATGTATCCCATAAC 57.595 36.000 0.00 0.00 42.34 1.89
3990 4090 7.671819 TCAAACAAGGAAACATGTATCCCATAA 59.328 33.333 0.00 0.00 42.34 1.90
3991 4091 7.178573 TCAAACAAGGAAACATGTATCCCATA 58.821 34.615 0.00 0.00 42.34 2.74
4011 4111 5.105716 TGAGCTAGACACCTACATCTCAAAC 60.106 44.000 0.00 0.00 0.00 2.93
4107 4207 5.070001 CAGATTCAGGTCACAAAAGGGTAA 58.930 41.667 0.00 0.00 0.00 2.85
4601 4710 7.309012 GGGTTTTCTAGTTGGTTTGTAAGATCC 60.309 40.741 0.00 0.00 0.00 3.36
4642 4751 5.507482 GGGGCTGTTCTTAGTTTCTTGTTTC 60.507 44.000 0.00 0.00 0.00 2.78
4791 4900 4.637534 GCAAGATCCTCTGCATGTTCTTAA 59.362 41.667 7.07 0.00 0.00 1.85
4792 4901 4.194640 GCAAGATCCTCTGCATGTTCTTA 58.805 43.478 7.07 0.00 0.00 2.10
4821 4930 5.058149 AGAAAATGAATAACATGCACGCA 57.942 34.783 0.00 0.00 39.39 5.24
4934 5043 1.002468 CGGATCCACGATTCAAATGCC 60.002 52.381 13.41 0.00 35.47 4.40
4935 5044 1.002468 CCGGATCCACGATTCAAATGC 60.002 52.381 13.41 0.00 35.47 3.56
4959 5068 2.625790 TCCCCACATTGTGTTGTTTAGC 59.374 45.455 15.34 0.00 0.00 3.09
4973 5083 6.430864 ACATCATATACAAATTGTCCCCACA 58.569 36.000 0.22 0.00 0.00 4.17
4983 5093 8.757982 AGGAGCAAAGAACATCATATACAAAT 57.242 30.769 0.00 0.00 0.00 2.32
5128 5238 5.710567 AGTGAGACATGCTACTACAGTTGTA 59.289 40.000 0.00 0.00 0.00 2.41
5129 5239 4.524714 AGTGAGACATGCTACTACAGTTGT 59.475 41.667 0.00 0.00 0.00 3.32
5186 5296 8.038351 TGGTTAACTCGATGATTGTTCTATTCA 58.962 33.333 5.42 0.00 0.00 2.57
5193 5303 4.579869 AGCTGGTTAACTCGATGATTGTT 58.420 39.130 5.42 0.00 0.00 2.83
5194 5304 4.184629 GAGCTGGTTAACTCGATGATTGT 58.815 43.478 5.42 0.00 0.00 2.71
5270 5380 5.106791 CCATCAATGCTATACTGCTAACTGC 60.107 44.000 0.00 0.00 43.25 4.40
5310 5420 4.475944 ACGCTCAATACAAATTTCTGCAC 58.524 39.130 0.00 0.00 0.00 4.57
5343 5453 3.851098 AGACAGAAAGCGCTAAACTAGG 58.149 45.455 12.05 2.48 0.00 3.02
5345 5455 5.892160 TCTAGACAGAAAGCGCTAAACTA 57.108 39.130 12.05 8.25 0.00 2.24
5347 5457 5.840940 TTTCTAGACAGAAAGCGCTAAAC 57.159 39.130 12.05 5.20 44.13 2.01
5409 5524 6.554334 TCAATTAGTGCTTTACAACAGGAC 57.446 37.500 0.00 0.00 32.96 3.85
5440 5555 1.541588 CAAAAGGCCTACAGAACAGCC 59.458 52.381 5.16 0.00 46.13 4.85
5556 5671 2.917971 GAGACGGAGAATCAACAGTTCG 59.082 50.000 0.00 0.00 36.25 3.95
5626 5741 5.710513 AGCAGCAAGAATAATGTGACAAA 57.289 34.783 0.00 0.00 0.00 2.83
5631 5746 7.756272 TCACAAATTAGCAGCAAGAATAATGTG 59.244 33.333 17.14 17.14 34.76 3.21
5721 5836 5.991328 AGCCGACAAGACATAATTACATG 57.009 39.130 0.00 0.00 0.00 3.21
5727 5842 3.055094 ACCAGAAGCCGACAAGACATAAT 60.055 43.478 0.00 0.00 0.00 1.28
5924 6042 9.739276 ATCATGAAACTTTGAGTGGTATTTCTA 57.261 29.630 0.00 0.00 0.00 2.10
5944 6062 1.706866 CCATTGGCCCCTCTATCATGA 59.293 52.381 0.00 0.00 0.00 3.07
5964 6082 7.678690 GCCAAACATACCACTGTACATTATCAC 60.679 40.741 0.00 0.00 0.00 3.06
6079 6197 4.288626 TGTAGCAAGATAAAAGTCAGGGGT 59.711 41.667 0.00 0.00 0.00 4.95
6229 6347 8.276252 ACCGTTGCATAACTATAGTGAAAAAT 57.724 30.769 6.06 0.00 34.60 1.82
6230 6348 7.675962 ACCGTTGCATAACTATAGTGAAAAA 57.324 32.000 6.06 0.00 34.60 1.94
6231 6349 7.604927 AGAACCGTTGCATAACTATAGTGAAAA 59.395 33.333 6.06 0.00 34.60 2.29
6232 6350 7.101054 AGAACCGTTGCATAACTATAGTGAAA 58.899 34.615 6.06 0.00 34.60 2.69
6233 6351 6.636705 AGAACCGTTGCATAACTATAGTGAA 58.363 36.000 6.06 0.00 34.60 3.18
6359 6477 6.728200 TGTGATTTGGCGATTATCAAGATTC 58.272 36.000 0.00 0.00 30.72 2.52
6421 6539 0.249120 CATCACAAGACCTGGGCGTA 59.751 55.000 0.00 0.00 0.00 4.42
6424 6542 1.340405 ACATCATCACAAGACCTGGGC 60.340 52.381 0.00 0.00 0.00 5.36
6444 6562 4.941263 ACGACAAAATTTGGCTGAGCTATA 59.059 37.500 10.12 0.00 36.19 1.31
6462 6583 5.199000 CAATAACTAACGCAACAAACGACA 58.801 37.500 0.00 0.00 0.00 4.35
6503 6625 7.426929 AACTGCTTAAAGATGTAGACACTTG 57.573 36.000 0.00 0.00 0.00 3.16
6613 6735 6.036844 GGTAAACAGTGGAAATACGGAATCTC 59.963 42.308 0.00 0.00 0.00 2.75
6640 6762 8.723942 AAACGACAGAAATTTAGCATCTAGAT 57.276 30.769 0.00 0.00 0.00 1.98
6667 6791 6.183360 GCCCATATTACAGTTCACAAGTTCTC 60.183 42.308 0.00 0.00 0.00 2.87
6741 6866 3.139077 GTCCAAACACATCCGAAAGACT 58.861 45.455 0.00 0.00 0.00 3.24
6761 6886 6.942576 AGACTTTAGCCAACTTGATGTTATGT 59.057 34.615 0.00 0.00 37.07 2.29
6772 6897 7.459234 ACCAAATAAGTAGACTTTAGCCAACT 58.541 34.615 0.00 0.00 37.40 3.16
6834 6959 4.210120 GCATCAGTTATACGAGCTCCAAAG 59.790 45.833 8.47 0.00 0.00 2.77
6902 7027 6.586344 AGGTGTCGTATGATTGAATTGATCT 58.414 36.000 0.00 0.00 0.00 2.75
7001 7126 2.996621 GTCCTTGATGTTCTTCACTCCG 59.003 50.000 0.00 0.00 0.00 4.63
7111 7236 5.644188 TGGGGAGATGAAAGAAAGAAATGT 58.356 37.500 0.00 0.00 0.00 2.71
7114 7239 5.582950 TCTGGGGAGATGAAAGAAAGAAA 57.417 39.130 0.00 0.00 0.00 2.52
7126 7251 2.182516 ATCGGAAGTTCTGGGGAGAT 57.817 50.000 11.82 0.00 0.00 2.75
7128 7253 2.965831 TCATATCGGAAGTTCTGGGGAG 59.034 50.000 11.82 1.10 0.00 4.30
7134 7259 6.041409 ACTGTGATGATCATATCGGAAGTTCT 59.959 38.462 8.54 0.00 0.00 3.01
7135 7260 6.219473 ACTGTGATGATCATATCGGAAGTTC 58.781 40.000 8.54 0.00 0.00 3.01
7152 7277 5.050490 GCGACAAGGATATGTAACTGTGAT 58.950 41.667 0.00 0.00 32.57 3.06
7162 7287 0.107456 AGGCCTGCGACAAGGATATG 59.893 55.000 3.11 0.00 40.02 1.78
7233 7358 2.060383 CGGCCTCAGATGGTGGAGA 61.060 63.158 0.00 0.00 32.87 3.71
7462 7588 4.428294 TCATCAGATCAACAATCCCTCC 57.572 45.455 0.00 0.00 34.67 4.30
7469 7595 7.763071 CAGTTCAGTCTATCATCAGATCAACAA 59.237 37.037 0.00 0.00 35.67 2.83
7470 7596 7.093596 ACAGTTCAGTCTATCATCAGATCAACA 60.094 37.037 0.00 0.00 35.67 3.33
7471 7597 7.264221 ACAGTTCAGTCTATCATCAGATCAAC 58.736 38.462 0.00 0.00 35.67 3.18
7644 7773 3.181490 TGAGAATCGTAACCAGGATCGTG 60.181 47.826 8.47 8.47 38.61 4.35
7659 7788 1.927895 AACGATCCACGCTGAGAATC 58.072 50.000 0.00 0.00 46.94 2.52
7728 7858 3.441922 TGCTGCTGTTTGTGAGTTGTTTA 59.558 39.130 0.00 0.00 0.00 2.01
7760 8703 5.596836 ATTTGAGAGTTTGCCACTTTGAA 57.403 34.783 0.00 0.00 35.01 2.69
7763 8706 9.860898 GAAATATATTTGAGAGTTTGCCACTTT 57.139 29.630 15.39 0.00 35.01 2.66
7866 8809 5.129485 TGTTGGTTGTTTGGTACCATGAAAT 59.871 36.000 17.17 0.00 43.56 2.17
7867 8810 4.466370 TGTTGGTTGTTTGGTACCATGAAA 59.534 37.500 17.17 4.15 43.56 2.69
7940 8888 1.683943 ATGGATTGAAGGGCATGTCG 58.316 50.000 0.00 0.00 0.00 4.35
8006 8954 5.361135 TGAAGTTGATGTGTTGTGCTATG 57.639 39.130 0.00 0.00 0.00 2.23
8200 9164 0.886490 AGGCTCCACAAGTTTGCTCG 60.886 55.000 0.00 0.00 0.00 5.03
8237 9201 5.748152 GTCAAAAGTTATGCAAGCAGTTCAA 59.252 36.000 0.00 0.00 0.00 2.69
8347 9323 4.961511 GTCGGCCACACGCTGTCA 62.962 66.667 2.24 0.00 44.92 3.58


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

AutoCloner maintained by Alex Coulton.