Multiple sequence alignment - TraesCS3A01G506800

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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 TraesCS3A01G506800 chr3A 100.000 3341 0 0 1 3341 728107968 728104628 0.000000e+00 6170.0
1 TraesCS3A01G506800 chr3A 92.593 2376 104 24 1 2351 728257647 728255319 0.000000e+00 3347.0
2 TraesCS3A01G506800 chr3A 83.689 938 134 19 2413 3341 728255310 728254383 0.000000e+00 867.0
3 TraesCS3A01G506800 chr3D 95.942 1577 49 3 782 2354 598097763 598096198 0.000000e+00 2543.0
4 TraesCS3A01G506800 chr3D 92.696 753 47 4 2591 3341 598085502 598084756 0.000000e+00 1079.0
5 TraesCS3A01G506800 chr3D 89.767 772 44 16 1 756 598098584 598097832 0.000000e+00 955.0
6 TraesCS3A01G506800 chr3D 78.862 1107 193 27 1224 2321 551574846 551575920 0.000000e+00 710.0
7 TraesCS3A01G506800 chr3D 81.776 214 28 5 404 613 598098391 598098185 5.730000e-38 169.0
8 TraesCS3A01G506800 chr7D 93.044 1222 53 5 849 2070 555404745 555403556 0.000000e+00 1757.0
9 TraesCS3A01G506800 chr7D 81.685 546 97 3 2561 3105 160871896 160871353 5.080000e-123 451.0
10 TraesCS3A01G506800 chr7D 94.464 289 16 0 2066 2354 555394735 555394447 2.360000e-121 446.0
11 TraesCS3A01G506800 chr7D 92.742 124 9 0 723 846 555422959 555422836 2.650000e-41 180.0
12 TraesCS3A01G506800 chr7D 89.510 143 12 3 2413 2553 555394441 555394300 9.530000e-41 178.0
13 TraesCS3A01G506800 chr5B 84.911 1405 181 19 972 2350 636901996 636900597 0.000000e+00 1391.0
14 TraesCS3A01G506800 chr5D 83.569 1412 191 23 971 2355 506163364 506161967 0.000000e+00 1284.0
15 TraesCS3A01G506800 chr3B 93.571 840 54 0 1237 2076 805042042 805041203 0.000000e+00 1253.0
16 TraesCS3A01G506800 chr3B 79.801 1307 224 24 1049 2332 782677385 782678674 0.000000e+00 915.0
17 TraesCS3A01G506800 chr3B 78.718 1217 203 36 1049 2237 732110636 732111824 0.000000e+00 761.0
18 TraesCS3A01G506800 chr3B 77.573 1195 225 34 1033 2204 734145339 734144165 0.000000e+00 682.0
19 TraesCS3A01G506800 chr3B 91.373 510 26 5 1845 2354 805038243 805037752 0.000000e+00 682.0
20 TraesCS3A01G506800 chr3B 90.719 431 21 8 1924 2354 805022598 805022187 1.050000e-154 556.0
21 TraesCS3A01G506800 chr3B 92.625 339 22 2 902 1238 805042423 805042086 5.010000e-133 484.0
22 TraesCS3A01G506800 chr3B 86.685 368 19 17 576 936 805037703 805037359 6.760000e-102 381.0
23 TraesCS3A01G506800 chr3B 88.182 330 20 11 576 898 805022138 805021821 3.150000e-100 375.0
24 TraesCS3A01G506800 chr3B 77.536 138 29 2 448 583 39674457 39674594 7.680000e-12 82.4
25 TraesCS3A01G506800 chr3B 96.970 33 0 1 2413 2444 805037746 805037714 2.000000e-03 54.7
26 TraesCS3A01G506800 chr4D 81.017 590 110 2 2561 3149 425695118 425694530 5.050000e-128 468.0
27 TraesCS3A01G506800 chr7A 81.607 560 96 6 2561 3114 142950448 142951006 1.090000e-124 457.0
28 TraesCS3A01G506800 chr6D 81.655 556 94 6 2562 3114 407203912 407203362 3.930000e-124 455.0
29 TraesCS3A01G506800 chr6D 80.241 582 108 4 2561 3139 429134260 429133683 6.620000e-117 431.0
30 TraesCS3A01G506800 chr2D 82.037 540 92 5 2561 3098 572048246 572048782 3.930000e-124 455.0
31 TraesCS3A01G506800 chr2B 80.961 562 102 5 2564 3122 27913280 27912721 1.100000e-119 440.0
32 TraesCS3A01G506800 chr7B 77.536 138 29 2 448 583 733599909 733599772 7.680000e-12 82.4


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 TraesCS3A01G506800 chr3A 728104628 728107968 3340 True 6170.000000 6170 100.000000 1 3341 1 chr3A.!!$R1 3340
1 TraesCS3A01G506800 chr3A 728254383 728257647 3264 True 2107.000000 3347 88.141000 1 3341 2 chr3A.!!$R2 3340
2 TraesCS3A01G506800 chr3D 598096198 598098584 2386 True 1222.333333 2543 89.161667 1 2354 3 chr3D.!!$R2 2353
3 TraesCS3A01G506800 chr3D 598084756 598085502 746 True 1079.000000 1079 92.696000 2591 3341 1 chr3D.!!$R1 750
4 TraesCS3A01G506800 chr3D 551574846 551575920 1074 False 710.000000 710 78.862000 1224 2321 1 chr3D.!!$F1 1097
5 TraesCS3A01G506800 chr7D 555403556 555404745 1189 True 1757.000000 1757 93.044000 849 2070 1 chr7D.!!$R2 1221
6 TraesCS3A01G506800 chr7D 160871353 160871896 543 True 451.000000 451 81.685000 2561 3105 1 chr7D.!!$R1 544
7 TraesCS3A01G506800 chr5B 636900597 636901996 1399 True 1391.000000 1391 84.911000 972 2350 1 chr5B.!!$R1 1378
8 TraesCS3A01G506800 chr5D 506161967 506163364 1397 True 1284.000000 1284 83.569000 971 2355 1 chr5D.!!$R1 1384
9 TraesCS3A01G506800 chr3B 782677385 782678674 1289 False 915.000000 915 79.801000 1049 2332 1 chr3B.!!$F3 1283
10 TraesCS3A01G506800 chr3B 732110636 732111824 1188 False 761.000000 761 78.718000 1049 2237 1 chr3B.!!$F2 1188
11 TraesCS3A01G506800 chr3B 734144165 734145339 1174 True 682.000000 682 77.573000 1033 2204 1 chr3B.!!$R1 1171
12 TraesCS3A01G506800 chr3B 805037359 805042423 5064 True 570.940000 1253 92.244800 576 2444 5 chr3B.!!$R3 1868
13 TraesCS3A01G506800 chr3B 805021821 805022598 777 True 465.500000 556 89.450500 576 2354 2 chr3B.!!$R2 1778
14 TraesCS3A01G506800 chr4D 425694530 425695118 588 True 468.000000 468 81.017000 2561 3149 1 chr4D.!!$R1 588
15 TraesCS3A01G506800 chr7A 142950448 142951006 558 False 457.000000 457 81.607000 2561 3114 1 chr7A.!!$F1 553
16 TraesCS3A01G506800 chr6D 407203362 407203912 550 True 455.000000 455 81.655000 2562 3114 1 chr6D.!!$R1 552
17 TraesCS3A01G506800 chr6D 429133683 429134260 577 True 431.000000 431 80.241000 2561 3139 1 chr6D.!!$R2 578
18 TraesCS3A01G506800 chr2D 572048246 572048782 536 False 455.000000 455 82.037000 2561 3098 1 chr2D.!!$F1 537
19 TraesCS3A01G506800 chr2B 27912721 27913280 559 True 440.000000 440 80.961000 2564 3122 1 chr2B.!!$R1 558

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
824 854 0.250252 TGCAAGCGAGAACATCCACA 60.25 50.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2369 5754 0.119155 AAGGTGGAGATGGAGGTGGA 59.881 55.0 0.0 0.0 0.0 4.02 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
62 64 5.727791 GCAGTGTTGTTGTCTTTGAGTACTG 60.728 44.000 0.00 0.00 35.99 2.74
97 99 6.930164 TCAGACAATGTAGCTTAAAAACCGTA 59.070 34.615 0.00 0.00 0.00 4.02
98 100 7.441760 TCAGACAATGTAGCTTAAAAACCGTAA 59.558 33.333 0.00 0.00 0.00 3.18
99 101 8.071368 CAGACAATGTAGCTTAAAAACCGTAAA 58.929 33.333 0.00 0.00 0.00 2.01
100 102 8.071967 AGACAATGTAGCTTAAAAACCGTAAAC 58.928 33.333 0.00 0.00 0.00 2.01
101 103 7.140705 ACAATGTAGCTTAAAAACCGTAAACC 58.859 34.615 0.00 0.00 0.00 3.27
102 104 5.341407 TGTAGCTTAAAAACCGTAAACCG 57.659 39.130 0.00 0.00 0.00 4.44
103 105 4.813697 TGTAGCTTAAAAACCGTAAACCGT 59.186 37.500 0.00 0.00 33.66 4.83
145 147 5.894393 AGAGAGTACCATTTAGCTAGCTCAA 59.106 40.000 23.26 17.85 0.00 3.02
352 374 6.976934 ACAAAGGAAATTACTCACCAATGT 57.023 33.333 0.00 0.00 0.00 2.71
585 615 5.450965 CCAATGCCATCTTCGCTAGATTTTT 60.451 40.000 0.00 0.00 41.78 1.94
589 619 5.294306 TGCCATCTTCGCTAGATTTTTAGTG 59.706 40.000 0.00 0.00 41.78 2.74
590 620 5.523916 GCCATCTTCGCTAGATTTTTAGTGA 59.476 40.000 0.00 0.00 41.78 3.41
591 621 6.037172 GCCATCTTCGCTAGATTTTTAGTGAA 59.963 38.462 0.00 8.29 43.91 3.18
592 622 7.402640 CCATCTTCGCTAGATTTTTAGTGAAC 58.597 38.462 0.00 0.00 42.27 3.18
593 623 7.278868 CCATCTTCGCTAGATTTTTAGTGAACT 59.721 37.037 0.00 0.00 42.27 3.01
594 624 7.582435 TCTTCGCTAGATTTTTAGTGAACTG 57.418 36.000 0.00 0.00 42.27 3.16
595 625 7.152645 TCTTCGCTAGATTTTTAGTGAACTGT 58.847 34.615 0.00 0.00 42.27 3.55
596 626 6.706055 TCGCTAGATTTTTAGTGAACTGTG 57.294 37.500 0.00 0.00 37.27 3.66
597 627 6.452242 TCGCTAGATTTTTAGTGAACTGTGA 58.548 36.000 0.00 0.00 37.27 3.58
598 628 6.926826 TCGCTAGATTTTTAGTGAACTGTGAA 59.073 34.615 0.00 0.00 37.27 3.18
599 629 7.439955 TCGCTAGATTTTTAGTGAACTGTGAAA 59.560 33.333 0.00 0.00 37.27 2.69
608 638 9.959749 TTTTAGTGAACTGTGAAAAACATATCC 57.040 29.630 0.00 0.00 38.39 2.59
611 641 7.227156 AGTGAACTGTGAAAAACATATCCTCT 58.773 34.615 0.00 0.00 38.39 3.69
612 642 8.375506 AGTGAACTGTGAAAAACATATCCTCTA 58.624 33.333 0.00 0.00 38.39 2.43
613 643 8.999431 GTGAACTGTGAAAAACATATCCTCTAA 58.001 33.333 0.00 0.00 38.39 2.10
614 644 9.219603 TGAACTGTGAAAAACATATCCTCTAAG 57.780 33.333 0.00 0.00 38.39 2.18
615 645 9.436957 GAACTGTGAAAAACATATCCTCTAAGA 57.563 33.333 0.00 0.00 38.39 2.10
616 646 9.965902 AACTGTGAAAAACATATCCTCTAAGAT 57.034 29.630 0.00 0.00 38.39 2.40
617 647 9.606631 ACTGTGAAAAACATATCCTCTAAGATC 57.393 33.333 0.00 0.00 38.39 2.75
618 648 9.829507 CTGTGAAAAACATATCCTCTAAGATCT 57.170 33.333 0.00 0.00 38.39 2.75
624 654 9.621239 AAAACATATCCTCTAAGATCTATCCCA 57.379 33.333 0.00 0.00 0.00 4.37
627 657 7.838696 ACATATCCTCTAAGATCTATCCCACAG 59.161 40.741 0.00 0.00 0.00 3.66
628 658 5.932027 TCCTCTAAGATCTATCCCACAGA 57.068 43.478 0.00 0.00 0.00 3.41
629 659 6.476409 TCCTCTAAGATCTATCCCACAGAT 57.524 41.667 0.00 0.00 39.15 2.90
630 660 6.868826 TCCTCTAAGATCTATCCCACAGATT 58.131 40.000 0.00 0.00 36.33 2.40
631 661 6.951198 TCCTCTAAGATCTATCCCACAGATTC 59.049 42.308 0.00 0.00 36.33 2.52
632 662 6.723515 CCTCTAAGATCTATCCCACAGATTCA 59.276 42.308 0.00 0.00 36.33 2.57
636 666 4.592351 AGATCTATCCCACAGATTCACCAG 59.408 45.833 0.00 0.00 36.33 4.00
637 667 3.724478 TCTATCCCACAGATTCACCAGT 58.276 45.455 0.00 0.00 36.33 4.00
638 668 2.795231 ATCCCACAGATTCACCAGTG 57.205 50.000 0.00 0.00 0.00 3.66
639 669 1.434188 TCCCACAGATTCACCAGTGT 58.566 50.000 0.00 0.00 0.00 3.55
640 670 1.347707 TCCCACAGATTCACCAGTGTC 59.652 52.381 0.00 0.00 0.00 3.67
641 671 1.611673 CCCACAGATTCACCAGTGTCC 60.612 57.143 0.00 0.00 0.00 4.02
642 672 1.072173 CCACAGATTCACCAGTGTCCA 59.928 52.381 0.00 0.00 0.00 4.02
644 674 3.055167 CCACAGATTCACCAGTGTCCATA 60.055 47.826 0.00 0.00 0.00 2.74
647 677 4.186926 CAGATTCACCAGTGTCCATACAG 58.813 47.826 0.00 0.00 35.91 2.74
649 679 4.532126 AGATTCACCAGTGTCCATACAGAA 59.468 41.667 0.00 0.00 35.91 3.02
651 681 4.698201 TCACCAGTGTCCATACAGAAAA 57.302 40.909 0.00 0.00 35.91 2.29
652 682 4.385825 TCACCAGTGTCCATACAGAAAAC 58.614 43.478 0.00 0.00 35.91 2.43
653 683 3.502211 CACCAGTGTCCATACAGAAAACC 59.498 47.826 0.00 0.00 35.91 3.27
655 685 4.202567 ACCAGTGTCCATACAGAAAACCAT 60.203 41.667 0.00 0.00 35.91 3.55
658 688 5.010282 AGTGTCCATACAGAAAACCATTCC 58.990 41.667 0.00 0.00 35.91 3.01
659 689 4.157840 GTGTCCATACAGAAAACCATTCCC 59.842 45.833 0.00 0.00 35.91 3.97
660 690 4.202620 TGTCCATACAGAAAACCATTCCCA 60.203 41.667 0.00 0.00 0.00 4.37
661 691 4.770010 GTCCATACAGAAAACCATTCCCAA 59.230 41.667 0.00 0.00 0.00 4.12
664 694 1.970640 ACAGAAAACCATTCCCAAGCC 59.029 47.619 0.00 0.00 0.00 4.35
666 696 2.568509 CAGAAAACCATTCCCAAGCCAT 59.431 45.455 0.00 0.00 0.00 4.40
668 698 2.629017 AAACCATTCCCAAGCCATCT 57.371 45.000 0.00 0.00 0.00 2.90
673 703 3.073650 ACCATTCCCAAGCCATCTATCTC 59.926 47.826 0.00 0.00 0.00 2.75
674 704 3.073503 CCATTCCCAAGCCATCTATCTCA 59.926 47.826 0.00 0.00 0.00 3.27
677 707 3.387962 TCCCAAGCCATCTATCTCACTT 58.612 45.455 0.00 0.00 0.00 3.16
678 708 3.389329 TCCCAAGCCATCTATCTCACTTC 59.611 47.826 0.00 0.00 0.00 3.01
679 709 3.135348 CCCAAGCCATCTATCTCACTTCA 59.865 47.826 0.00 0.00 0.00 3.02
681 711 5.012458 CCCAAGCCATCTATCTCACTTCATA 59.988 44.000 0.00 0.00 0.00 2.15
682 712 6.296317 CCCAAGCCATCTATCTCACTTCATAT 60.296 42.308 0.00 0.00 0.00 1.78
683 713 7.166851 CCAAGCCATCTATCTCACTTCATATT 58.833 38.462 0.00 0.00 0.00 1.28
686 716 9.941325 AAGCCATCTATCTCACTTCATATTTAG 57.059 33.333 0.00 0.00 0.00 1.85
687 717 9.319060 AGCCATCTATCTCACTTCATATTTAGA 57.681 33.333 0.00 0.00 0.00 2.10
688 718 9.585099 GCCATCTATCTCACTTCATATTTAGAG 57.415 37.037 0.00 0.00 0.00 2.43
695 725 9.875708 ATCTCACTTCATATTTAGAGGTCTACT 57.124 33.333 0.00 0.00 0.00 2.57
747 777 5.756833 ACGGTTTACACAAGTCTTTTCTAGG 59.243 40.000 0.00 0.00 0.00 3.02
756 786 8.190784 ACACAAGTCTTTTCTAGGAACAATTTG 58.809 33.333 0.00 0.00 0.00 2.32
757 787 8.405531 CACAAGTCTTTTCTAGGAACAATTTGA 58.594 33.333 2.79 0.00 0.00 2.69
758 788 8.966868 ACAAGTCTTTTCTAGGAACAATTTGAA 58.033 29.630 2.79 0.00 0.00 2.69
762 792 9.965824 GTCTTTTCTAGGAACAATTTGAATTGA 57.034 29.630 20.04 0.35 46.72 2.57
765 795 9.541143 TTTTCTAGGAACAATTTGAATTGAACC 57.459 29.630 20.04 19.23 46.72 3.62
767 797 8.421249 TCTAGGAACAATTTGAATTGAACCAT 57.579 30.769 20.04 13.71 46.72 3.55
768 798 8.306038 TCTAGGAACAATTTGAATTGAACCATG 58.694 33.333 20.04 16.21 46.72 3.66
770 800 7.682628 AGGAACAATTTGAATTGAACCATGAT 58.317 30.769 20.04 6.80 46.72 2.45
772 802 9.434420 GGAACAATTTGAATTGAACCATGATAA 57.566 29.630 20.04 0.00 46.72 1.75
779 809 8.455903 TTGAATTGAACCATGATAATCTCTCC 57.544 34.615 0.00 0.00 0.00 3.71
780 810 6.707608 TGAATTGAACCATGATAATCTCTCCG 59.292 38.462 0.00 0.00 0.00 4.63
782 812 6.724893 TTGAACCATGATAATCTCTCCGTA 57.275 37.500 0.00 0.00 0.00 4.02
783 813 6.918067 TGAACCATGATAATCTCTCCGTAT 57.082 37.500 0.00 0.00 0.00 3.06
785 815 8.417273 TGAACCATGATAATCTCTCCGTATAA 57.583 34.615 0.00 0.00 0.00 0.98
786 816 8.523658 TGAACCATGATAATCTCTCCGTATAAG 58.476 37.037 0.00 0.00 0.00 1.73
788 818 6.381420 ACCATGATAATCTCTCCGTATAAGGG 59.619 42.308 4.77 0.00 0.00 3.95
789 819 6.381420 CCATGATAATCTCTCCGTATAAGGGT 59.619 42.308 4.77 0.00 0.00 4.34
793 823 7.946219 TGATAATCTCTCCGTATAAGGGTACAA 59.054 37.037 4.77 0.00 0.00 2.41
794 824 8.716674 ATAATCTCTCCGTATAAGGGTACAAA 57.283 34.615 4.77 0.00 0.00 2.83
795 825 6.651975 ATCTCTCCGTATAAGGGTACAAAG 57.348 41.667 4.77 0.00 0.00 2.77
796 826 4.340381 TCTCTCCGTATAAGGGTACAAAGC 59.660 45.833 4.77 0.00 0.00 3.51
797 827 3.385755 TCTCCGTATAAGGGTACAAAGCC 59.614 47.826 4.77 0.00 44.09 4.35
803 833 4.783667 GGGTACAAAGCCGACACA 57.216 55.556 0.00 0.00 32.57 3.72
804 834 3.009612 GGGTACAAAGCCGACACAA 57.990 52.632 0.00 0.00 32.57 3.33
807 837 1.401018 GGTACAAAGCCGACACAATGC 60.401 52.381 0.00 0.00 0.00 3.56
808 838 1.265635 GTACAAAGCCGACACAATGCA 59.734 47.619 0.00 0.00 0.00 3.96
809 839 0.743688 ACAAAGCCGACACAATGCAA 59.256 45.000 0.00 0.00 0.00 4.08
810 840 1.269206 ACAAAGCCGACACAATGCAAG 60.269 47.619 0.00 0.00 0.00 4.01
811 841 0.318955 AAAGCCGACACAATGCAAGC 60.319 50.000 0.00 0.00 0.00 4.01
812 842 2.462255 AAGCCGACACAATGCAAGCG 62.462 55.000 0.00 0.00 0.00 4.68
815 845 1.291184 CCGACACAATGCAAGCGAGA 61.291 55.000 0.00 0.00 0.00 4.04
816 846 0.512518 CGACACAATGCAAGCGAGAA 59.487 50.000 0.00 0.00 0.00 2.87
818 848 1.264020 GACACAATGCAAGCGAGAACA 59.736 47.619 0.00 0.00 0.00 3.18
819 849 1.881973 ACACAATGCAAGCGAGAACAT 59.118 42.857 0.00 0.00 0.00 2.71
821 851 1.470098 ACAATGCAAGCGAGAACATCC 59.530 47.619 0.00 0.00 0.00 3.51
822 852 1.469703 CAATGCAAGCGAGAACATCCA 59.530 47.619 0.00 0.00 0.00 3.41
823 853 1.089920 ATGCAAGCGAGAACATCCAC 58.910 50.000 0.00 0.00 0.00 4.02
824 854 0.250252 TGCAAGCGAGAACATCCACA 60.250 50.000 0.00 0.00 0.00 4.17
825 855 1.089920 GCAAGCGAGAACATCCACAT 58.910 50.000 0.00 0.00 0.00 3.21
826 856 1.063174 GCAAGCGAGAACATCCACATC 59.937 52.381 0.00 0.00 0.00 3.06
827 857 1.667724 CAAGCGAGAACATCCACATCC 59.332 52.381 0.00 0.00 0.00 3.51
828 858 1.198713 AGCGAGAACATCCACATCCT 58.801 50.000 0.00 0.00 0.00 3.24
829 859 1.556911 AGCGAGAACATCCACATCCTT 59.443 47.619 0.00 0.00 0.00 3.36
830 860 2.026822 AGCGAGAACATCCACATCCTTT 60.027 45.455 0.00 0.00 0.00 3.11
831 861 2.352960 GCGAGAACATCCACATCCTTTC 59.647 50.000 0.00 0.00 0.00 2.62
832 862 2.939103 CGAGAACATCCACATCCTTTCC 59.061 50.000 0.00 0.00 0.00 3.13
834 864 4.530875 GAGAACATCCACATCCTTTCCAT 58.469 43.478 0.00 0.00 0.00 3.41
835 865 4.530875 AGAACATCCACATCCTTTCCATC 58.469 43.478 0.00 0.00 0.00 3.51
837 867 3.624777 ACATCCACATCCTTTCCATCAC 58.375 45.455 0.00 0.00 0.00 3.06
838 868 3.267812 ACATCCACATCCTTTCCATCACT 59.732 43.478 0.00 0.00 0.00 3.41
839 869 4.474651 ACATCCACATCCTTTCCATCACTA 59.525 41.667 0.00 0.00 0.00 2.74
840 870 5.133322 ACATCCACATCCTTTCCATCACTAT 59.867 40.000 0.00 0.00 0.00 2.12
841 871 5.296151 TCCACATCCTTTCCATCACTATC 57.704 43.478 0.00 0.00 0.00 2.08
842 872 4.103153 TCCACATCCTTTCCATCACTATCC 59.897 45.833 0.00 0.00 0.00 2.59
843 873 4.141413 CCACATCCTTTCCATCACTATCCA 60.141 45.833 0.00 0.00 0.00 3.41
845 875 6.066690 CACATCCTTTCCATCACTATCCAAT 58.933 40.000 0.00 0.00 0.00 3.16
846 876 6.548622 CACATCCTTTCCATCACTATCCAATT 59.451 38.462 0.00 0.00 0.00 2.32
847 877 6.774656 ACATCCTTTCCATCACTATCCAATTC 59.225 38.462 0.00 0.00 0.00 2.17
884 914 7.954666 TCATTTTAAGAAGATAAACCCCTGG 57.045 36.000 0.00 0.00 0.00 4.45
915 992 5.939457 GCACGTCTATGCATGTAGACTATA 58.061 41.667 21.62 0.00 45.34 1.31
1008 1091 1.876497 GCAGGAGAAAAATGGGCGCA 61.876 55.000 10.83 5.70 0.00 6.09
1067 1156 1.073706 AGGTGGAGGTGGTGGAGTT 60.074 57.895 0.00 0.00 0.00 3.01
1132 1221 3.707640 CTCTCCCCGCTCGACCTCT 62.708 68.421 0.00 0.00 0.00 3.69
1138 1227 3.184683 CGCTCGACCTCTTGCTGC 61.185 66.667 0.00 0.00 0.00 5.25
1186 1275 0.750911 CTTCTACCCGTACCGCTCCT 60.751 60.000 0.00 0.00 0.00 3.69
1187 1276 0.323725 TTCTACCCGTACCGCTCCTT 60.324 55.000 0.00 0.00 0.00 3.36
1401 1541 4.504916 CCCGAGCTGAGGACGCTG 62.505 72.222 6.40 0.00 37.96 5.18
1562 1702 1.371183 CGTGGTCTGCCTTCTCCAA 59.629 57.895 0.00 0.00 35.27 3.53
1663 1818 1.585006 GACGCCTTCTCGGTCTTCA 59.415 57.895 0.00 0.00 34.25 3.02
1669 1827 2.245438 CTTCTCGGTCTTCAGCCCCC 62.245 65.000 0.00 0.00 0.00 5.40
1869 5239 4.814294 GACGCTACCACCCGCCTG 62.814 72.222 0.00 0.00 0.00 4.85
1908 5278 2.438254 CGCAGCATAAGGCCACCA 60.438 61.111 5.01 0.00 46.50 4.17
1993 5363 2.590645 CCTCCTCGGAGTCGGAGA 59.409 66.667 24.95 12.47 44.54 3.71
2145 5524 2.581354 GAGCTGCGGGTGATCAGT 59.419 61.111 0.00 0.00 33.09 3.41
2251 5630 2.654863 TCGTCTATCTGATGGACAGCA 58.345 47.619 26.80 12.22 45.38 4.41
2367 5752 4.394712 CGGCTCCACCACCTCCAC 62.395 72.222 0.00 0.00 39.03 4.02
2368 5753 4.035102 GGCTCCACCACCTCCACC 62.035 72.222 0.00 0.00 38.86 4.61
2369 5754 2.930562 GCTCCACCACCTCCACCT 60.931 66.667 0.00 0.00 0.00 4.00
2370 5755 2.960688 GCTCCACCACCTCCACCTC 61.961 68.421 0.00 0.00 0.00 3.85
2371 5756 2.203938 TCCACCACCTCCACCTCC 60.204 66.667 0.00 0.00 0.00 4.30
2372 5757 2.529136 CCACCACCTCCACCTCCA 60.529 66.667 0.00 0.00 0.00 3.86
2373 5758 2.750350 CACCACCTCCACCTCCAC 59.250 66.667 0.00 0.00 0.00 4.02
2374 5759 2.529389 ACCACCTCCACCTCCACC 60.529 66.667 0.00 0.00 0.00 4.61
2375 5760 2.203998 CCACCTCCACCTCCACCT 60.204 66.667 0.00 0.00 0.00 4.00
2376 5761 2.294078 CCACCTCCACCTCCACCTC 61.294 68.421 0.00 0.00 0.00 3.85
2377 5762 2.122954 ACCTCCACCTCCACCTCC 59.877 66.667 0.00 0.00 0.00 4.30
2378 5763 2.122729 CCTCCACCTCCACCTCCA 59.877 66.667 0.00 0.00 0.00 3.86
2379 5764 1.307343 CCTCCACCTCCACCTCCAT 60.307 63.158 0.00 0.00 0.00 3.41
2380 5765 1.341156 CCTCCACCTCCACCTCCATC 61.341 65.000 0.00 0.00 0.00 3.51
2381 5766 0.326048 CTCCACCTCCACCTCCATCT 60.326 60.000 0.00 0.00 0.00 2.90
2382 5767 0.325671 TCCACCTCCACCTCCATCTC 60.326 60.000 0.00 0.00 0.00 2.75
2383 5768 1.341156 CCACCTCCACCTCCATCTCC 61.341 65.000 0.00 0.00 0.00 3.71
2384 5769 0.618680 CACCTCCACCTCCATCTCCA 60.619 60.000 0.00 0.00 0.00 3.86
2385 5770 0.618968 ACCTCCACCTCCATCTCCAC 60.619 60.000 0.00 0.00 0.00 4.02
2386 5771 1.341156 CCTCCACCTCCATCTCCACC 61.341 65.000 0.00 0.00 0.00 4.61
2387 5772 0.326048 CTCCACCTCCATCTCCACCT 60.326 60.000 0.00 0.00 0.00 4.00
2388 5773 0.119155 TCCACCTCCATCTCCACCTT 59.881 55.000 0.00 0.00 0.00 3.50
2389 5774 0.254178 CCACCTCCATCTCCACCTTG 59.746 60.000 0.00 0.00 0.00 3.61
2390 5775 0.987294 CACCTCCATCTCCACCTTGT 59.013 55.000 0.00 0.00 0.00 3.16
2391 5776 1.065854 CACCTCCATCTCCACCTTGTC 60.066 57.143 0.00 0.00 0.00 3.18
2392 5777 0.543749 CCTCCATCTCCACCTTGTCC 59.456 60.000 0.00 0.00 0.00 4.02
2393 5778 1.279496 CTCCATCTCCACCTTGTCCA 58.721 55.000 0.00 0.00 0.00 4.02
2394 5779 0.984230 TCCATCTCCACCTTGTCCAC 59.016 55.000 0.00 0.00 0.00 4.02
2395 5780 0.692476 CCATCTCCACCTTGTCCACA 59.308 55.000 0.00 0.00 0.00 4.17
2396 5781 1.611673 CCATCTCCACCTTGTCCACAC 60.612 57.143 0.00 0.00 0.00 3.82
2397 5782 0.693049 ATCTCCACCTTGTCCACACC 59.307 55.000 0.00 0.00 0.00 4.16
2398 5783 1.073199 CTCCACCTTGTCCACACCC 59.927 63.158 0.00 0.00 0.00 4.61
2399 5784 1.694525 TCCACCTTGTCCACACCCA 60.695 57.895 0.00 0.00 0.00 4.51
2400 5785 1.528309 CCACCTTGTCCACACCCAC 60.528 63.158 0.00 0.00 0.00 4.61
2401 5786 1.528309 CACCTTGTCCACACCCACC 60.528 63.158 0.00 0.00 0.00 4.61
2402 5787 2.281484 CCTTGTCCACACCCACCG 60.281 66.667 0.00 0.00 0.00 4.94
2403 5788 2.508928 CTTGTCCACACCCACCGT 59.491 61.111 0.00 0.00 0.00 4.83
2404 5789 1.597027 CTTGTCCACACCCACCGTC 60.597 63.158 0.00 0.00 0.00 4.79
2405 5790 2.040009 CTTGTCCACACCCACCGTCT 62.040 60.000 0.00 0.00 0.00 4.18
2406 5791 2.035237 TTGTCCACACCCACCGTCTC 62.035 60.000 0.00 0.00 0.00 3.36
2407 5792 2.920912 TCCACACCCACCGTCTCC 60.921 66.667 0.00 0.00 0.00 3.71
2408 5793 3.238497 CCACACCCACCGTCTCCA 61.238 66.667 0.00 0.00 0.00 3.86
2409 5794 2.813726 CCACACCCACCGTCTCCAA 61.814 63.158 0.00 0.00 0.00 3.53
2410 5795 1.147376 CACACCCACCGTCTCCAAA 59.853 57.895 0.00 0.00 0.00 3.28
2411 5796 0.884704 CACACCCACCGTCTCCAAAG 60.885 60.000 0.00 0.00 0.00 2.77
2445 5831 1.304134 GGGCCTTTCACCCGTCAAT 60.304 57.895 0.84 0.00 37.67 2.57
2474 5860 2.515398 CTCCACTGCCACCACCAA 59.485 61.111 0.00 0.00 0.00 3.67
2475 5861 1.601759 CTCCACTGCCACCACCAAG 60.602 63.158 0.00 0.00 0.00 3.61
2510 5896 2.668550 GTTGGGGAGCCACGTCAC 60.669 66.667 0.00 0.00 0.00 3.67
2512 5898 2.879233 TTGGGGAGCCACGTCACTC 61.879 63.158 5.90 5.90 0.00 3.51
2514 5900 2.574399 GGGAGCCACGTCACTCTC 59.426 66.667 12.71 6.42 33.29 3.20
2518 5904 0.733729 GAGCCACGTCACTCTCGTAT 59.266 55.000 7.03 0.00 39.55 3.06
2520 5906 1.135373 AGCCACGTCACTCTCGTATTG 60.135 52.381 0.00 0.00 39.55 1.90
2523 5909 1.649171 CACGTCACTCTCGTATTGTGC 59.351 52.381 0.00 0.00 39.55 4.57
2530 5916 4.159693 TCACTCTCGTATTGTGCCAGTATT 59.840 41.667 0.00 0.00 0.00 1.89
2559 5945 5.389859 TGGCGTGAGAAATTTTCAATCAT 57.610 34.783 11.53 0.00 0.00 2.45
2589 5975 5.975693 AAATTACAACCATGTTCGTGGAT 57.024 34.783 16.70 3.21 42.02 3.41
2614 6000 3.673809 CCTAACAACGACTACAAGCAGTC 59.326 47.826 0.00 0.00 41.33 3.51
2719 6110 1.598130 CGTGCTAAGGCCCCATAGC 60.598 63.158 20.42 20.42 41.79 2.97
2785 6177 8.939201 AGTAGATCGGAAGCATCAAATATATG 57.061 34.615 0.00 0.00 0.00 1.78
2790 6182 7.984422 TCGGAAGCATCAAATATATGAACAT 57.016 32.000 0.00 0.00 32.06 2.71
2791 6183 7.809665 TCGGAAGCATCAAATATATGAACATG 58.190 34.615 0.00 0.00 32.06 3.21
2898 6290 2.159819 CTCCACACACCCTCTGACGG 62.160 65.000 0.00 0.00 0.00 4.79
3004 6440 6.136071 CCAATGAAGACACTGAACGTAAAAG 58.864 40.000 0.00 0.00 0.00 2.27
3142 6583 5.456921 AGGCTTGGGATCTTTTCTTATGA 57.543 39.130 0.00 0.00 0.00 2.15
3150 6591 6.058833 GGGATCTTTTCTTATGAAGGAGGAC 58.941 44.000 0.00 0.00 33.28 3.85
3156 6597 8.974238 TCTTTTCTTATGAAGGAGGACGTATTA 58.026 33.333 0.00 0.00 33.28 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 18 1.002257 TGCGCATCACCCACTGATT 60.002 52.632 5.66 0.00 37.53 2.57
62 64 0.460987 CATTGTCTGACGGAGGGAGC 60.461 60.000 2.98 0.00 0.00 4.70
97 99 4.240096 CGTCCTACAATGTAAGACGGTTT 58.760 43.478 27.52 0.00 44.86 3.27
98 100 3.841643 CGTCCTACAATGTAAGACGGTT 58.158 45.455 27.52 0.00 44.86 4.44
99 101 3.498927 CGTCCTACAATGTAAGACGGT 57.501 47.619 27.52 0.00 44.86 4.83
102 104 4.639310 TCTCTCCGTCCTACAATGTAAGAC 59.361 45.833 11.14 11.14 0.00 3.01
103 105 4.851843 TCTCTCCGTCCTACAATGTAAGA 58.148 43.478 0.00 0.00 0.00 2.10
310 332 7.716123 TCCTTTGTTTTAAAGTGGATCTAACGA 59.284 33.333 0.00 0.00 0.00 3.85
343 365 2.768253 AGCGAAGATGACATTGGTGA 57.232 45.000 0.00 0.00 0.00 4.02
352 374 9.594478 TCATTACTTAAAATGTAGCGAAGATGA 57.406 29.630 0.00 0.00 37.94 2.92
415 444 3.211045 GCTCGGTTAGCCCATCAAATAA 58.789 45.455 0.00 0.00 46.25 1.40
515 544 4.037089 GTGGATCTAACGGTTGTGGTTTTT 59.963 41.667 3.07 0.00 0.00 1.94
585 615 8.375506 AGAGGATATGTTTTTCACAGTTCACTA 58.624 33.333 0.00 0.00 39.40 2.74
589 619 9.436957 TCTTAGAGGATATGTTTTTCACAGTTC 57.563 33.333 0.00 0.00 39.40 3.01
590 620 9.965902 ATCTTAGAGGATATGTTTTTCACAGTT 57.034 29.630 0.00 0.00 39.40 3.16
591 621 9.606631 GATCTTAGAGGATATGTTTTTCACAGT 57.393 33.333 0.00 0.00 39.40 3.55
592 622 9.829507 AGATCTTAGAGGATATGTTTTTCACAG 57.170 33.333 0.00 0.00 39.40 3.66
598 628 9.621239 TGGGATAGATCTTAGAGGATATGTTTT 57.379 33.333 0.00 0.00 0.00 2.43
599 629 9.041354 GTGGGATAGATCTTAGAGGATATGTTT 57.959 37.037 0.00 0.00 0.00 2.83
602 632 8.058235 TCTGTGGGATAGATCTTAGAGGATATG 58.942 40.741 0.00 0.00 0.00 1.78
604 634 7.590359 TCTGTGGGATAGATCTTAGAGGATA 57.410 40.000 0.00 0.00 0.00 2.59
605 635 6.476409 TCTGTGGGATAGATCTTAGAGGAT 57.524 41.667 0.00 0.00 0.00 3.24
606 636 5.932027 TCTGTGGGATAGATCTTAGAGGA 57.068 43.478 0.00 0.00 0.00 3.71
607 637 6.723515 TGAATCTGTGGGATAGATCTTAGAGG 59.276 42.308 0.00 0.00 33.92 3.69
608 638 7.309744 GGTGAATCTGTGGGATAGATCTTAGAG 60.310 44.444 0.00 0.00 33.92 2.43
611 641 6.143206 TGGTGAATCTGTGGGATAGATCTTA 58.857 40.000 0.00 0.00 33.92 2.10
612 642 4.971282 TGGTGAATCTGTGGGATAGATCTT 59.029 41.667 0.00 0.00 33.92 2.40
613 643 4.560739 TGGTGAATCTGTGGGATAGATCT 58.439 43.478 0.00 0.00 33.92 2.75
614 644 4.346418 ACTGGTGAATCTGTGGGATAGATC 59.654 45.833 0.00 0.00 33.92 2.75
615 645 4.102210 CACTGGTGAATCTGTGGGATAGAT 59.898 45.833 0.00 0.00 36.49 1.98
616 646 3.452264 CACTGGTGAATCTGTGGGATAGA 59.548 47.826 0.00 0.00 34.38 1.98
617 647 3.198635 ACACTGGTGAATCTGTGGGATAG 59.801 47.826 7.78 0.00 39.75 2.08
618 648 3.181329 ACACTGGTGAATCTGTGGGATA 58.819 45.455 7.78 0.00 39.75 2.59
619 649 1.988107 ACACTGGTGAATCTGTGGGAT 59.012 47.619 7.78 0.00 39.75 3.85
620 650 1.347707 GACACTGGTGAATCTGTGGGA 59.652 52.381 7.78 0.00 39.75 4.37
621 651 1.611673 GGACACTGGTGAATCTGTGGG 60.612 57.143 7.78 0.00 39.75 4.61
622 652 1.072173 TGGACACTGGTGAATCTGTGG 59.928 52.381 7.78 0.00 39.75 4.17
623 653 2.549064 TGGACACTGGTGAATCTGTG 57.451 50.000 7.78 0.00 40.76 3.66
624 654 3.582647 TGTATGGACACTGGTGAATCTGT 59.417 43.478 7.78 0.00 0.00 3.41
627 657 4.471904 TCTGTATGGACACTGGTGAATC 57.528 45.455 7.78 0.00 0.00 2.52
628 658 4.908601 TTCTGTATGGACACTGGTGAAT 57.091 40.909 7.78 1.62 0.00 2.57
629 659 4.698201 TTTCTGTATGGACACTGGTGAA 57.302 40.909 7.78 0.00 0.00 3.18
630 660 4.385825 GTTTTCTGTATGGACACTGGTGA 58.614 43.478 7.78 0.00 0.00 4.02
631 661 3.502211 GGTTTTCTGTATGGACACTGGTG 59.498 47.826 0.00 0.00 0.00 4.17
632 662 3.137544 TGGTTTTCTGTATGGACACTGGT 59.862 43.478 0.00 0.00 0.00 4.00
636 666 4.157840 GGGAATGGTTTTCTGTATGGACAC 59.842 45.833 0.00 0.00 0.00 3.67
637 667 4.202620 TGGGAATGGTTTTCTGTATGGACA 60.203 41.667 0.00 0.00 0.00 4.02
638 668 4.340617 TGGGAATGGTTTTCTGTATGGAC 58.659 43.478 0.00 0.00 0.00 4.02
639 669 4.666412 TGGGAATGGTTTTCTGTATGGA 57.334 40.909 0.00 0.00 0.00 3.41
640 670 4.381932 GCTTGGGAATGGTTTTCTGTATGG 60.382 45.833 0.00 0.00 0.00 2.74
641 671 4.381932 GGCTTGGGAATGGTTTTCTGTATG 60.382 45.833 0.00 0.00 0.00 2.39
642 672 3.769300 GGCTTGGGAATGGTTTTCTGTAT 59.231 43.478 0.00 0.00 0.00 2.29
644 674 1.970640 GGCTTGGGAATGGTTTTCTGT 59.029 47.619 0.00 0.00 0.00 3.41
647 677 2.833943 AGATGGCTTGGGAATGGTTTTC 59.166 45.455 0.00 0.00 0.00 2.29
649 679 2.629017 AGATGGCTTGGGAATGGTTT 57.371 45.000 0.00 0.00 0.00 3.27
651 681 3.059097 AGATAGATGGCTTGGGAATGGT 58.941 45.455 0.00 0.00 0.00 3.55
652 682 3.073503 TGAGATAGATGGCTTGGGAATGG 59.926 47.826 0.00 0.00 0.00 3.16
653 683 4.070716 GTGAGATAGATGGCTTGGGAATG 58.929 47.826 0.00 0.00 0.00 2.67
655 685 3.387962 AGTGAGATAGATGGCTTGGGAA 58.612 45.455 0.00 0.00 0.00 3.97
658 688 4.412796 TGAAGTGAGATAGATGGCTTGG 57.587 45.455 0.00 0.00 0.00 3.61
659 689 8.618702 AAATATGAAGTGAGATAGATGGCTTG 57.381 34.615 0.00 0.00 0.00 4.01
660 690 9.941325 CTAAATATGAAGTGAGATAGATGGCTT 57.059 33.333 0.00 0.00 0.00 4.35
661 691 9.319060 TCTAAATATGAAGTGAGATAGATGGCT 57.681 33.333 0.00 0.00 0.00 4.75
756 786 6.708054 ACGGAGAGATTATCATGGTTCAATTC 59.292 38.462 0.00 0.00 0.00 2.17
757 787 6.595682 ACGGAGAGATTATCATGGTTCAATT 58.404 36.000 0.00 0.00 0.00 2.32
758 788 6.179906 ACGGAGAGATTATCATGGTTCAAT 57.820 37.500 0.00 0.00 0.00 2.57
761 791 7.976734 CCTTATACGGAGAGATTATCATGGTTC 59.023 40.741 0.00 0.00 0.00 3.62
762 792 7.093289 CCCTTATACGGAGAGATTATCATGGTT 60.093 40.741 0.00 0.00 0.00 3.67
763 793 6.381420 CCCTTATACGGAGAGATTATCATGGT 59.619 42.308 0.00 0.00 0.00 3.55
764 794 6.381420 ACCCTTATACGGAGAGATTATCATGG 59.619 42.308 0.00 0.00 0.00 3.66
765 795 7.411486 ACCCTTATACGGAGAGATTATCATG 57.589 40.000 0.00 0.00 0.00 3.07
767 797 7.464273 TGTACCCTTATACGGAGAGATTATCA 58.536 38.462 0.00 0.00 0.00 2.15
768 798 7.934855 TGTACCCTTATACGGAGAGATTATC 57.065 40.000 0.00 0.00 0.00 1.75
770 800 7.255730 GCTTTGTACCCTTATACGGAGAGATTA 60.256 40.741 0.00 0.00 0.00 1.75
772 802 5.010820 GCTTTGTACCCTTATACGGAGAGAT 59.989 44.000 0.00 0.00 0.00 2.75
773 803 4.340381 GCTTTGTACCCTTATACGGAGAGA 59.660 45.833 0.00 0.00 0.00 3.10
774 804 4.501058 GGCTTTGTACCCTTATACGGAGAG 60.501 50.000 0.00 0.00 0.00 3.20
775 805 3.385755 GGCTTTGTACCCTTATACGGAGA 59.614 47.826 0.00 0.00 0.00 3.71
777 807 2.101249 CGGCTTTGTACCCTTATACGGA 59.899 50.000 0.00 0.00 0.00 4.69
778 808 2.101249 TCGGCTTTGTACCCTTATACGG 59.899 50.000 0.00 0.00 0.00 4.02
779 809 3.118542 GTCGGCTTTGTACCCTTATACG 58.881 50.000 0.00 0.00 0.00 3.06
780 810 3.867493 GTGTCGGCTTTGTACCCTTATAC 59.133 47.826 0.00 0.00 0.00 1.47
782 812 2.303600 TGTGTCGGCTTTGTACCCTTAT 59.696 45.455 0.00 0.00 0.00 1.73
783 813 1.693062 TGTGTCGGCTTTGTACCCTTA 59.307 47.619 0.00 0.00 0.00 2.69
785 815 0.470766 TTGTGTCGGCTTTGTACCCT 59.529 50.000 0.00 0.00 0.00 4.34
786 816 1.199097 CATTGTGTCGGCTTTGTACCC 59.801 52.381 0.00 0.00 0.00 3.69
788 818 1.265635 TGCATTGTGTCGGCTTTGTAC 59.734 47.619 0.00 0.00 0.00 2.90
789 819 1.598882 TGCATTGTGTCGGCTTTGTA 58.401 45.000 0.00 0.00 0.00 2.41
793 823 1.286880 GCTTGCATTGTGTCGGCTT 59.713 52.632 0.00 0.00 0.00 4.35
794 824 2.956987 GCTTGCATTGTGTCGGCT 59.043 55.556 0.00 0.00 0.00 5.52
795 825 2.502510 CGCTTGCATTGTGTCGGC 60.503 61.111 0.00 0.00 0.00 5.54
796 826 1.133253 CTCGCTTGCATTGTGTCGG 59.867 57.895 0.00 0.00 0.00 4.79
797 827 0.512518 TTCTCGCTTGCATTGTGTCG 59.487 50.000 0.00 0.00 0.00 4.35
798 828 1.264020 TGTTCTCGCTTGCATTGTGTC 59.736 47.619 0.00 0.00 0.00 3.67
799 829 1.308047 TGTTCTCGCTTGCATTGTGT 58.692 45.000 0.00 0.00 0.00 3.72
801 831 1.470098 GGATGTTCTCGCTTGCATTGT 59.530 47.619 0.00 0.00 0.00 2.71
803 833 1.470098 GTGGATGTTCTCGCTTGCATT 59.530 47.619 0.00 0.00 0.00 3.56
804 834 1.089920 GTGGATGTTCTCGCTTGCAT 58.910 50.000 0.00 0.00 0.00 3.96
807 837 1.667724 GGATGTGGATGTTCTCGCTTG 59.332 52.381 0.00 0.00 0.00 4.01
808 838 1.556911 AGGATGTGGATGTTCTCGCTT 59.443 47.619 0.00 0.00 0.00 4.68
809 839 1.198713 AGGATGTGGATGTTCTCGCT 58.801 50.000 0.00 0.00 0.00 4.93
810 840 2.029838 AAGGATGTGGATGTTCTCGC 57.970 50.000 0.00 0.00 0.00 5.03
811 841 2.939103 GGAAAGGATGTGGATGTTCTCG 59.061 50.000 0.00 0.00 0.00 4.04
812 842 3.955471 TGGAAAGGATGTGGATGTTCTC 58.045 45.455 0.00 0.00 0.00 2.87
815 845 4.019174 GTGATGGAAAGGATGTGGATGTT 58.981 43.478 0.00 0.00 0.00 2.71
816 846 3.267812 AGTGATGGAAAGGATGTGGATGT 59.732 43.478 0.00 0.00 0.00 3.06
818 848 5.222007 GGATAGTGATGGAAAGGATGTGGAT 60.222 44.000 0.00 0.00 0.00 3.41
819 849 4.103153 GGATAGTGATGGAAAGGATGTGGA 59.897 45.833 0.00 0.00 0.00 4.02
821 851 5.039920 TGGATAGTGATGGAAAGGATGTG 57.960 43.478 0.00 0.00 0.00 3.21
822 852 5.715439 TTGGATAGTGATGGAAAGGATGT 57.285 39.130 0.00 0.00 0.00 3.06
823 853 6.774170 TGAATTGGATAGTGATGGAAAGGATG 59.226 38.462 0.00 0.00 0.00 3.51
824 854 6.914665 TGAATTGGATAGTGATGGAAAGGAT 58.085 36.000 0.00 0.00 0.00 3.24
825 855 6.325993 TGAATTGGATAGTGATGGAAAGGA 57.674 37.500 0.00 0.00 0.00 3.36
826 856 7.408756 TTTGAATTGGATAGTGATGGAAAGG 57.591 36.000 0.00 0.00 0.00 3.11
872 902 0.616891 ACACGGTCCAGGGGTTTATC 59.383 55.000 0.00 0.00 0.00 1.75
915 992 1.212751 GCGCGCTTCTCCCATTTTT 59.787 52.632 26.67 0.00 0.00 1.94
1132 1221 1.601759 GGCCTCTGTTGAGCAGCAA 60.602 57.895 0.00 0.00 44.66 3.91
1138 1227 1.302832 GGGTGTGGCCTCTGTTGAG 60.303 63.158 3.32 0.00 39.92 3.02
1186 1275 1.301401 CGAAGAAGTCACCGGGCAA 60.301 57.895 6.32 0.00 0.00 4.52
1187 1276 2.204461 TCGAAGAAGTCACCGGGCA 61.204 57.895 6.32 0.00 0.00 5.36
1401 1541 2.166584 CTTCGACGCGGGGAACAAAC 62.167 60.000 12.47 0.00 0.00 2.93
1669 1827 2.219674 GCTCGACGGATAATTTCAGCTG 59.780 50.000 7.63 7.63 0.00 4.24
1677 1835 1.281960 CGACGGCTCGACGGATAAT 59.718 57.895 10.40 0.00 43.06 1.28
1678 1836 2.711311 CGACGGCTCGACGGATAA 59.289 61.111 10.40 0.00 43.06 1.75
1908 5278 3.077556 CAGTAGCCAGGCGGGAGT 61.078 66.667 8.22 0.00 40.01 3.85
1993 5363 2.203294 GGCCACGAACACCAGGTT 60.203 61.111 0.00 0.00 44.10 3.50
2351 5736 4.035102 GGTGGAGGTGGTGGAGCC 62.035 72.222 0.00 0.00 37.90 4.70
2354 5739 2.203938 GGAGGTGGAGGTGGTGGA 60.204 66.667 0.00 0.00 0.00 4.02
2355 5740 2.529136 TGGAGGTGGAGGTGGTGG 60.529 66.667 0.00 0.00 0.00 4.61
2356 5741 2.750350 GTGGAGGTGGAGGTGGTG 59.250 66.667 0.00 0.00 0.00 4.17
2359 5744 2.294078 GGAGGTGGAGGTGGAGGTG 61.294 68.421 0.00 0.00 0.00 4.00
2360 5745 2.122954 GGAGGTGGAGGTGGAGGT 59.877 66.667 0.00 0.00 0.00 3.85
2361 5746 1.307343 ATGGAGGTGGAGGTGGAGG 60.307 63.158 0.00 0.00 0.00 4.30
2362 5747 0.326048 AGATGGAGGTGGAGGTGGAG 60.326 60.000 0.00 0.00 0.00 3.86
2363 5748 0.325671 GAGATGGAGGTGGAGGTGGA 60.326 60.000 0.00 0.00 0.00 4.02
2364 5749 1.341156 GGAGATGGAGGTGGAGGTGG 61.341 65.000 0.00 0.00 0.00 4.61
2365 5750 0.618680 TGGAGATGGAGGTGGAGGTG 60.619 60.000 0.00 0.00 0.00 4.00
2366 5751 0.618968 GTGGAGATGGAGGTGGAGGT 60.619 60.000 0.00 0.00 0.00 3.85
2367 5752 1.341156 GGTGGAGATGGAGGTGGAGG 61.341 65.000 0.00 0.00 0.00 4.30
2368 5753 0.326048 AGGTGGAGATGGAGGTGGAG 60.326 60.000 0.00 0.00 0.00 3.86
2369 5754 0.119155 AAGGTGGAGATGGAGGTGGA 59.881 55.000 0.00 0.00 0.00 4.02
2370 5755 0.254178 CAAGGTGGAGATGGAGGTGG 59.746 60.000 0.00 0.00 0.00 4.61
2371 5756 0.987294 ACAAGGTGGAGATGGAGGTG 59.013 55.000 0.00 0.00 0.00 4.00
2372 5757 1.280457 GACAAGGTGGAGATGGAGGT 58.720 55.000 0.00 0.00 0.00 3.85
2373 5758 0.543749 GGACAAGGTGGAGATGGAGG 59.456 60.000 0.00 0.00 0.00 4.30
2374 5759 1.065854 GTGGACAAGGTGGAGATGGAG 60.066 57.143 0.00 0.00 0.00 3.86
2375 5760 0.984230 GTGGACAAGGTGGAGATGGA 59.016 55.000 0.00 0.00 0.00 3.41
2376 5761 0.692476 TGTGGACAAGGTGGAGATGG 59.308 55.000 0.00 0.00 0.00 3.51
2377 5762 1.611673 GGTGTGGACAAGGTGGAGATG 60.612 57.143 0.00 0.00 0.00 2.90
2378 5763 0.693049 GGTGTGGACAAGGTGGAGAT 59.307 55.000 0.00 0.00 0.00 2.75
2379 5764 1.415672 GGGTGTGGACAAGGTGGAGA 61.416 60.000 0.00 0.00 0.00 3.71
2380 5765 1.073199 GGGTGTGGACAAGGTGGAG 59.927 63.158 0.00 0.00 0.00 3.86
2381 5766 1.694525 TGGGTGTGGACAAGGTGGA 60.695 57.895 0.00 0.00 0.00 4.02
2382 5767 1.528309 GTGGGTGTGGACAAGGTGG 60.528 63.158 0.00 0.00 0.00 4.61
2383 5768 1.528309 GGTGGGTGTGGACAAGGTG 60.528 63.158 0.00 0.00 0.00 4.00
2384 5769 2.923837 GGTGGGTGTGGACAAGGT 59.076 61.111 0.00 0.00 0.00 3.50
2385 5770 2.281484 CGGTGGGTGTGGACAAGG 60.281 66.667 0.00 0.00 0.00 3.61
2386 5771 1.597027 GACGGTGGGTGTGGACAAG 60.597 63.158 0.00 0.00 0.00 3.16
2387 5772 2.035237 GAGACGGTGGGTGTGGACAA 62.035 60.000 0.00 0.00 0.00 3.18
2388 5773 2.445085 AGACGGTGGGTGTGGACA 60.445 61.111 0.00 0.00 0.00 4.02
2389 5774 2.342648 GAGACGGTGGGTGTGGAC 59.657 66.667 0.00 0.00 0.00 4.02
2390 5775 2.920912 GGAGACGGTGGGTGTGGA 60.921 66.667 0.00 0.00 0.00 4.02
2391 5776 2.332312 TTTGGAGACGGTGGGTGTGG 62.332 60.000 0.00 0.00 0.00 4.17
2392 5777 0.884704 CTTTGGAGACGGTGGGTGTG 60.885 60.000 0.00 0.00 0.00 3.82
2393 5778 1.052124 TCTTTGGAGACGGTGGGTGT 61.052 55.000 0.00 0.00 0.00 4.16
2394 5779 0.324943 ATCTTTGGAGACGGTGGGTG 59.675 55.000 0.00 0.00 33.99 4.61
2395 5780 0.613777 GATCTTTGGAGACGGTGGGT 59.386 55.000 0.00 0.00 33.99 4.51
2396 5781 0.613260 TGATCTTTGGAGACGGTGGG 59.387 55.000 0.00 0.00 33.99 4.61
2397 5782 1.550524 TCTGATCTTTGGAGACGGTGG 59.449 52.381 0.00 0.00 33.99 4.61
2398 5783 2.232452 ACTCTGATCTTTGGAGACGGTG 59.768 50.000 10.71 0.00 33.99 4.94
2399 5784 2.530701 ACTCTGATCTTTGGAGACGGT 58.469 47.619 10.71 0.00 33.99 4.83
2400 5785 3.487711 CGTACTCTGATCTTTGGAGACGG 60.488 52.174 10.71 0.00 33.99 4.79
2401 5786 3.487711 CCGTACTCTGATCTTTGGAGACG 60.488 52.174 10.71 13.02 33.99 4.18
2402 5787 3.695060 TCCGTACTCTGATCTTTGGAGAC 59.305 47.826 10.71 5.84 33.99 3.36
2403 5788 3.964411 TCCGTACTCTGATCTTTGGAGA 58.036 45.455 10.71 0.00 36.09 3.71
2404 5789 4.927978 ATCCGTACTCTGATCTTTGGAG 57.072 45.455 0.00 0.00 0.00 3.86
2405 5790 4.141937 CCAATCCGTACTCTGATCTTTGGA 60.142 45.833 0.00 0.00 0.00 3.53
2406 5791 4.122776 CCAATCCGTACTCTGATCTTTGG 58.877 47.826 0.00 0.00 0.00 3.28
2407 5792 4.122776 CCCAATCCGTACTCTGATCTTTG 58.877 47.826 0.00 0.00 0.00 2.77
2408 5793 3.432326 GCCCAATCCGTACTCTGATCTTT 60.432 47.826 0.00 0.00 0.00 2.52
2409 5794 2.103263 GCCCAATCCGTACTCTGATCTT 59.897 50.000 0.00 0.00 0.00 2.40
2410 5795 1.689273 GCCCAATCCGTACTCTGATCT 59.311 52.381 0.00 0.00 0.00 2.75
2411 5796 1.270358 GGCCCAATCCGTACTCTGATC 60.270 57.143 0.00 0.00 0.00 2.92
2445 5831 3.153919 GGCAGTGGAGGTGTTTGATAAA 58.846 45.455 0.00 0.00 0.00 1.40
2510 5896 6.422776 AAAAATACTGGCACAATACGAGAG 57.577 37.500 0.00 0.00 38.70 3.20
2535 5921 5.595885 TGATTGAAAATTTCTCACGCCAAA 58.404 33.333 7.29 0.00 0.00 3.28
2589 5975 3.068448 TGCTTGTAGTCGTTGTTAGGTGA 59.932 43.478 0.00 0.00 0.00 4.02
2614 6000 1.132844 CACGTCTCCGACTCACTCG 59.867 63.158 0.00 0.00 42.54 4.18
2691 6081 0.982673 CCTTAGCACGACGACTTTCG 59.017 55.000 0.00 0.00 46.93 3.46
2719 6110 4.994471 TGCTCTGGTGCGCTGGTG 62.994 66.667 9.73 0.00 35.36 4.17
2785 6177 3.177643 CGTTCGTCTTTGTTTGCATGTTC 59.822 43.478 0.00 0.00 0.00 3.18
2790 6182 3.000523 GTCTACGTTCGTCTTTGTTTGCA 59.999 43.478 0.00 0.00 0.00 4.08
2791 6183 3.529085 GTCTACGTTCGTCTTTGTTTGC 58.471 45.455 0.00 0.00 0.00 3.68
2898 6290 1.136305 TCCTAATGGTGTGTCTAGCGC 59.864 52.381 0.00 0.00 34.23 5.92
3004 6440 0.616964 AGGGACCCCGTTCTAGTTCC 60.617 60.000 7.00 0.00 41.95 3.62
3142 6583 9.756571 AATATACTGAGATAATACGTCCTCCTT 57.243 33.333 0.00 0.00 0.00 3.36
3156 6597 8.439971 TGGGAACATTTGCTAATATACTGAGAT 58.560 33.333 0.00 0.00 33.40 2.75
3271 6714 9.875691 CAGTGATAAATAATATGAATCGGAGGA 57.124 33.333 0.00 0.00 0.00 3.71
3310 6759 8.981647 CGCCGGTTTAGTATAATTTAATACAGT 58.018 33.333 1.90 0.00 35.23 3.55
3311 6760 9.195411 TCGCCGGTTTAGTATAATTTAATACAG 57.805 33.333 1.90 0.00 35.23 2.74
3312 6761 8.977505 GTCGCCGGTTTAGTATAATTTAATACA 58.022 33.333 1.90 0.00 35.23 2.29


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

AutoCloner maintained by Alex Coulton.