Multiple sequence alignment - TraesCS4B01G239400

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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 TraesCS4B01G239400 chr4B 100.000 3204 0 0 1 3204 496523023 496526226 0.000000e+00 5917.0
1 TraesCS4B01G239400 chr4B 77.322 463 89 15 7 461 659662188 659662642 3.170000e-65 259.0
2 TraesCS4B01G239400 chr4B 83.902 205 26 7 330 529 659662660 659662862 4.220000e-44 189.0
3 TraesCS4B01G239400 chr4D 93.333 1530 51 18 819 2321 401524887 401526392 0.000000e+00 2213.0
4 TraesCS4B01G239400 chr4D 88.221 798 34 25 2413 3204 401527553 401528296 0.000000e+00 898.0
5 TraesCS4B01G239400 chr4D 100.000 36 0 0 2321 2356 401526455 401526490 2.060000e-07 67.6
6 TraesCS4B01G239400 chr4A 89.292 1653 84 47 718 2321 59268563 59270171 0.000000e+00 1986.0
7 TraesCS4B01G239400 chr4A 77.893 484 96 9 1552 2028 578383004 578382525 1.120000e-74 291.0
8 TraesCS4B01G239400 chr4A 89.823 226 17 6 2558 2778 59270562 59270786 5.230000e-73 285.0
9 TraesCS4B01G239400 chr4A 93.902 164 9 1 2806 2969 59271891 59272053 2.470000e-61 246.0
10 TraesCS4B01G239400 chr4A 83.681 288 18 8 2921 3204 59270918 59271180 8.880000e-61 244.0
11 TraesCS4B01G239400 chr4A 93.662 142 6 2 2733 2873 59270776 59270915 3.240000e-50 209.0
12 TraesCS4B01G239400 chr4A 82.564 195 10 2 2978 3172 59276027 59276197 1.990000e-32 150.0
13 TraesCS4B01G239400 chr4A 87.179 78 7 3 2316 2391 59270225 59270301 5.690000e-13 86.1
14 TraesCS4B01G239400 chr2B 81.437 501 87 6 6 503 358050602 358050105 3.850000e-109 405.0
15 TraesCS4B01G239400 chr5B 77.778 540 103 14 7 536 703328477 703329009 1.860000e-82 316.0
16 TraesCS4B01G239400 chr5B 76.731 520 111 10 16 529 51035153 51034638 6.770000e-72 281.0
17 TraesCS4B01G239400 chr3A 77.944 535 98 17 7 529 472485948 472485422 1.860000e-82 316.0
18 TraesCS4B01G239400 chr5A 77.528 534 102 14 7 529 19160181 19159655 4.020000e-79 305.0
19 TraesCS4B01G239400 chr1A 77.407 540 104 16 1 529 218226455 218226987 4.020000e-79 305.0
20 TraesCS4B01G239400 chr7B 77.406 478 100 8 1 476 579817064 579817535 8.750000e-71 278.0
21 TraesCS4B01G239400 chr6D 76.481 540 107 14 7 529 450362258 450361722 3.150000e-70 276.0
22 TraesCS4B01G239400 chr3D 87.288 118 9 5 427 539 157474405 157474289 2.590000e-26 130.0


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 TraesCS4B01G239400 chr4B 496523023 496526226 3203 False 5917.000000 5917 100.000000 1 3204 1 chr4B.!!$F1 3203
1 TraesCS4B01G239400 chr4B 659662188 659662862 674 False 224.000000 259 80.612000 7 529 2 chr4B.!!$F2 522
2 TraesCS4B01G239400 chr4D 401524887 401528296 3409 False 1059.533333 2213 93.851333 819 3204 3 chr4D.!!$F1 2385
3 TraesCS4B01G239400 chr4A 59268563 59276197 7634 False 458.014286 1986 88.586143 718 3204 7 chr4A.!!$F1 2486
4 TraesCS4B01G239400 chr5B 703328477 703329009 532 False 316.000000 316 77.778000 7 536 1 chr5B.!!$F1 529
5 TraesCS4B01G239400 chr5B 51034638 51035153 515 True 281.000000 281 76.731000 16 529 1 chr5B.!!$R1 513
6 TraesCS4B01G239400 chr3A 472485422 472485948 526 True 316.000000 316 77.944000 7 529 1 chr3A.!!$R1 522
7 TraesCS4B01G239400 chr5A 19159655 19160181 526 True 305.000000 305 77.528000 7 529 1 chr5A.!!$R1 522
8 TraesCS4B01G239400 chr1A 218226455 218226987 532 False 305.000000 305 77.407000 1 529 1 chr1A.!!$F1 528
9 TraesCS4B01G239400 chr6D 450361722 450362258 536 True 276.000000 276 76.481000 7 529 1 chr6D.!!$R1 522

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
634 802 0.03779 GGCCCGATGTAGATGCTCTC 60.038 60.0 0.0 0.0 0.0 3.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2528 3955 0.179009 ACCGCACCGTCTATAGCCTA 60.179 55.0 0.0 0.0 0.0 3.93 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
30 31 3.134127 GTTGGCCGCATGACCCTC 61.134 66.667 0.00 0.00 0.00 4.30
31 32 4.776322 TTGGCCGCATGACCCTCG 62.776 66.667 0.00 0.00 0.00 4.63
48 49 2.431683 GTTGCCCTCTGTGCCTGA 59.568 61.111 0.00 0.00 0.00 3.86
70 71 1.206115 GCACCAAAAACGGCAACTCG 61.206 55.000 0.00 0.00 0.00 4.18
94 95 2.193536 GCAAGGACTGCCCGTTTGT 61.194 57.895 0.00 0.00 46.13 2.83
98 99 2.258726 GGACTGCCCGTTTGTGGTC 61.259 63.158 0.00 0.00 0.00 4.02
100 101 2.590575 CTGCCCGTTTGTGGTCGT 60.591 61.111 0.00 0.00 0.00 4.34
102 103 2.589442 GCCCGTTTGTGGTCGTGA 60.589 61.111 0.00 0.00 0.00 4.35
104 105 0.671163 GCCCGTTTGTGGTCGTGATA 60.671 55.000 0.00 0.00 0.00 2.15
116 117 1.787155 GTCGTGATATGGTCGCATGTC 59.213 52.381 0.00 0.00 37.18 3.06
119 120 2.771089 GTGATATGGTCGCATGTCCAT 58.229 47.619 18.02 18.02 44.62 3.41
147 148 4.899239 GGGAGGCGCTGATGGACG 62.899 72.222 7.64 0.00 0.00 4.79
165 166 2.579201 CGATGTCGCTCCCACCTT 59.421 61.111 0.00 0.00 0.00 3.50
166 167 1.811266 CGATGTCGCTCCCACCTTG 60.811 63.158 0.00 0.00 0.00 3.61
177 178 1.456331 CCACCTTGCATGGGGATCC 60.456 63.158 22.07 1.92 33.18 3.36
187 188 2.691252 GGGGATCCCGGACTGGTT 60.691 66.667 24.90 0.00 36.85 3.67
192 193 1.420430 GATCCCGGACTGGTTGGATA 58.580 55.000 0.73 0.00 37.72 2.59
200 201 3.745480 CGGACTGGTTGGATATGCTCATT 60.745 47.826 0.00 0.00 0.00 2.57
201 202 4.503123 CGGACTGGTTGGATATGCTCATTA 60.503 45.833 0.00 0.00 0.00 1.90
206 207 4.660303 TGGTTGGATATGCTCATTACTCCT 59.340 41.667 0.00 0.00 0.00 3.69
209 210 6.211584 GGTTGGATATGCTCATTACTCCTCTA 59.788 42.308 0.00 0.00 0.00 2.43
239 240 4.664677 AGACACCGTCGCAGTGGC 62.665 66.667 6.59 3.37 44.05 5.01
267 269 5.777449 TCCTCTACACCATCTGGAATTCTA 58.223 41.667 5.23 0.00 38.94 2.10
282 284 1.267121 TTCTAGAAGGAGCGCAACCT 58.733 50.000 18.15 18.15 39.69 3.50
284 286 2.453521 TCTAGAAGGAGCGCAACCTTA 58.546 47.619 29.29 18.52 46.14 2.69
286 288 0.977395 AGAAGGAGCGCAACCTTAGT 59.023 50.000 29.29 20.29 46.14 2.24
298 300 4.152759 CGCAACCTTAGTATTTTCAACGGA 59.847 41.667 0.00 0.00 0.00 4.69
314 316 0.251073 CGGAACCCGTCTAACCCATT 59.749 55.000 0.00 0.00 42.73 3.16
328 330 2.361610 CATTTGGAGGTGGCGGCT 60.362 61.111 11.43 0.00 0.00 5.52
388 390 2.526873 AGGGTCCAAGTGGCGACT 60.527 61.111 0.00 0.00 34.44 4.18
397 399 0.690762 AAGTGGCGACTGGTATTGGT 59.309 50.000 0.71 0.00 30.61 3.67
409 411 6.403200 CGACTGGTATTGGTTGATTTGTAAGG 60.403 42.308 0.00 0.00 0.00 2.69
412 414 5.047660 TGGTATTGGTTGATTTGTAAGGCAC 60.048 40.000 0.00 0.00 0.00 5.01
430 442 2.867647 GCACTTTTGATTTGTGGAGGGC 60.868 50.000 0.00 0.00 32.85 5.19
434 446 4.164030 ACTTTTGATTTGTGGAGGGCTTTT 59.836 37.500 0.00 0.00 0.00 2.27
462 622 1.901159 TCCTCCGAAAAACCCGTCATA 59.099 47.619 0.00 0.00 0.00 2.15
467 627 4.325119 TCCGAAAAACCCGTCATATTTGA 58.675 39.130 0.00 0.00 0.00 2.69
546 714 3.655276 AAAGCCCATACGTATAGGTCG 57.345 47.619 19.33 8.29 0.00 4.79
547 715 1.542492 AGCCCATACGTATAGGTCGG 58.458 55.000 19.33 11.06 0.00 4.79
548 716 0.108945 GCCCATACGTATAGGTCGGC 60.109 60.000 19.33 15.03 0.00 5.54
549 717 1.250328 CCCATACGTATAGGTCGGCA 58.750 55.000 11.46 0.00 0.00 5.69
550 718 1.822990 CCCATACGTATAGGTCGGCAT 59.177 52.381 11.46 0.00 0.00 4.40
551 719 2.416836 CCCATACGTATAGGTCGGCATG 60.417 54.545 11.46 0.72 0.00 4.06
552 720 2.490509 CCATACGTATAGGTCGGCATGA 59.509 50.000 7.96 0.00 31.46 3.07
553 721 3.427638 CCATACGTATAGGTCGGCATGAG 60.428 52.174 7.96 0.00 31.46 2.90
554 722 0.959553 ACGTATAGGTCGGCATGAGG 59.040 55.000 0.00 0.00 0.00 3.86
555 723 0.388649 CGTATAGGTCGGCATGAGGC 60.389 60.000 0.00 0.00 43.74 4.70
563 731 2.581354 GGCATGAGGCGTCTGAGT 59.419 61.111 8.06 0.00 46.16 3.41
564 732 1.812922 GGCATGAGGCGTCTGAGTG 60.813 63.158 8.06 0.00 46.16 3.51
565 733 1.216444 GCATGAGGCGTCTGAGTGA 59.784 57.895 8.06 0.00 0.00 3.41
566 734 0.805322 GCATGAGGCGTCTGAGTGAG 60.805 60.000 8.06 0.00 0.00 3.51
567 735 0.529833 CATGAGGCGTCTGAGTGAGT 59.470 55.000 8.06 0.00 0.00 3.41
568 736 0.814457 ATGAGGCGTCTGAGTGAGTC 59.186 55.000 8.06 0.00 0.00 3.36
569 737 0.537371 TGAGGCGTCTGAGTGAGTCA 60.537 55.000 8.06 0.00 0.00 3.41
580 748 3.141398 TGAGTGAGTCAGGATTTTGTGC 58.859 45.455 0.00 0.00 0.00 4.57
581 749 2.485814 GAGTGAGTCAGGATTTTGTGCC 59.514 50.000 0.00 0.00 0.00 5.01
582 750 1.541588 GTGAGTCAGGATTTTGTGCCC 59.458 52.381 0.00 0.00 0.00 5.36
583 751 1.177401 GAGTCAGGATTTTGTGCCCC 58.823 55.000 0.00 0.00 0.00 5.80
584 752 0.609131 AGTCAGGATTTTGTGCCCCG 60.609 55.000 0.00 0.00 0.00 5.73
585 753 1.304052 TCAGGATTTTGTGCCCCGG 60.304 57.895 0.00 0.00 0.00 5.73
586 754 2.679996 AGGATTTTGTGCCCCGGC 60.680 61.111 0.00 0.00 42.35 6.13
596 764 4.408378 GCCCCGGCAGTTCTTTTA 57.592 55.556 0.00 0.00 41.49 1.52
597 765 2.180674 GCCCCGGCAGTTCTTTTAG 58.819 57.895 0.00 0.00 41.49 1.85
598 766 1.313091 GCCCCGGCAGTTCTTTTAGG 61.313 60.000 0.00 0.00 41.49 2.69
599 767 0.326927 CCCCGGCAGTTCTTTTAGGA 59.673 55.000 0.00 0.00 0.00 2.94
600 768 1.679032 CCCCGGCAGTTCTTTTAGGAG 60.679 57.143 0.00 0.00 0.00 3.69
601 769 1.679032 CCCGGCAGTTCTTTTAGGAGG 60.679 57.143 0.00 0.00 0.00 4.30
602 770 1.679032 CCGGCAGTTCTTTTAGGAGGG 60.679 57.143 0.00 0.00 0.00 4.30
603 771 1.464734 GGCAGTTCTTTTAGGAGGGC 58.535 55.000 0.00 0.00 0.00 5.19
604 772 1.464734 GCAGTTCTTTTAGGAGGGCC 58.535 55.000 0.00 0.00 0.00 5.80
605 773 1.739067 CAGTTCTTTTAGGAGGGCCG 58.261 55.000 0.00 0.00 39.96 6.13
606 774 0.618981 AGTTCTTTTAGGAGGGCCGG 59.381 55.000 0.00 0.00 39.96 6.13
607 775 0.327259 GTTCTTTTAGGAGGGCCGGT 59.673 55.000 1.90 0.00 39.96 5.28
608 776 1.069775 TTCTTTTAGGAGGGCCGGTT 58.930 50.000 1.90 0.00 39.96 4.44
609 777 1.069775 TCTTTTAGGAGGGCCGGTTT 58.930 50.000 1.90 0.00 39.96 3.27
610 778 1.173913 CTTTTAGGAGGGCCGGTTTG 58.826 55.000 1.90 0.00 39.96 2.93
611 779 0.896479 TTTTAGGAGGGCCGGTTTGC 60.896 55.000 1.90 0.00 39.96 3.68
612 780 3.615509 TTAGGAGGGCCGGTTTGCG 62.616 63.158 1.90 0.00 39.96 4.85
628 796 3.991051 CGCCGGCCCGATGTAGAT 61.991 66.667 23.46 0.00 0.00 1.98
629 797 2.357517 GCCGGCCCGATGTAGATG 60.358 66.667 18.11 0.00 0.00 2.90
630 798 2.357517 CCGGCCCGATGTAGATGC 60.358 66.667 3.71 0.00 0.00 3.91
631 799 2.737180 CGGCCCGATGTAGATGCT 59.263 61.111 0.00 0.00 0.00 3.79
632 800 1.373497 CGGCCCGATGTAGATGCTC 60.373 63.158 0.00 0.00 0.00 4.26
633 801 1.810606 CGGCCCGATGTAGATGCTCT 61.811 60.000 0.00 0.00 0.00 4.09
634 802 0.037790 GGCCCGATGTAGATGCTCTC 60.038 60.000 0.00 0.00 0.00 3.20
635 803 0.676184 GCCCGATGTAGATGCTCTCA 59.324 55.000 0.00 0.00 0.00 3.27
636 804 1.604185 GCCCGATGTAGATGCTCTCAC 60.604 57.143 0.00 0.00 0.00 3.51
637 805 1.959985 CCCGATGTAGATGCTCTCACT 59.040 52.381 0.00 0.00 0.00 3.41
638 806 2.363680 CCCGATGTAGATGCTCTCACTT 59.636 50.000 0.00 0.00 0.00 3.16
639 807 3.551863 CCCGATGTAGATGCTCTCACTTC 60.552 52.174 0.00 0.00 0.00 3.01
640 808 3.067320 CCGATGTAGATGCTCTCACTTCA 59.933 47.826 0.00 0.00 0.00 3.02
641 809 4.041049 CGATGTAGATGCTCTCACTTCAC 58.959 47.826 0.00 0.00 0.00 3.18
642 810 4.202000 CGATGTAGATGCTCTCACTTCACT 60.202 45.833 0.00 0.00 0.00 3.41
643 811 5.659463 GATGTAGATGCTCTCACTTCACTT 58.341 41.667 0.00 0.00 0.00 3.16
644 812 5.065704 TGTAGATGCTCTCACTTCACTTC 57.934 43.478 0.00 0.00 0.00 3.01
645 813 3.229276 AGATGCTCTCACTTCACTTCG 57.771 47.619 0.00 0.00 0.00 3.79
646 814 2.560542 AGATGCTCTCACTTCACTTCGT 59.439 45.455 0.00 0.00 0.00 3.85
647 815 3.759086 AGATGCTCTCACTTCACTTCGTA 59.241 43.478 0.00 0.00 0.00 3.43
648 816 4.400884 AGATGCTCTCACTTCACTTCGTAT 59.599 41.667 0.00 0.00 0.00 3.06
649 817 3.838120 TGCTCTCACTTCACTTCGTATG 58.162 45.455 0.00 0.00 0.00 2.39
650 818 3.255888 TGCTCTCACTTCACTTCGTATGT 59.744 43.478 0.00 0.00 0.00 2.29
651 819 4.457949 TGCTCTCACTTCACTTCGTATGTA 59.542 41.667 0.00 0.00 0.00 2.29
652 820 4.794246 GCTCTCACTTCACTTCGTATGTAC 59.206 45.833 0.00 0.00 0.00 2.90
653 821 5.392165 GCTCTCACTTCACTTCGTATGTACT 60.392 44.000 0.00 0.00 0.00 2.73
654 822 6.570672 TCTCACTTCACTTCGTATGTACTT 57.429 37.500 0.00 0.00 0.00 2.24
655 823 7.625817 GCTCTCACTTCACTTCGTATGTACTTA 60.626 40.741 0.00 0.00 0.00 2.24
656 824 7.524912 TCTCACTTCACTTCGTATGTACTTAC 58.475 38.462 8.51 8.51 0.00 2.34
657 825 7.173735 TCTCACTTCACTTCGTATGTACTTACA 59.826 37.037 16.55 0.00 40.98 2.41
659 827 7.753580 TCACTTCACTTCGTATGTACTTACATG 59.246 37.037 16.55 9.92 45.77 3.21
660 828 6.530534 ACTTCACTTCGTATGTACTTACATGC 59.469 38.462 16.55 9.28 45.77 4.06
661 829 6.203808 TCACTTCGTATGTACTTACATGCT 57.796 37.500 16.55 0.00 45.77 3.79
662 830 6.627243 TCACTTCGTATGTACTTACATGCTT 58.373 36.000 16.55 0.00 45.77 3.91
663 831 7.764331 TCACTTCGTATGTACTTACATGCTTA 58.236 34.615 16.55 0.18 45.77 3.09
664 832 8.410912 TCACTTCGTATGTACTTACATGCTTAT 58.589 33.333 16.55 0.00 45.77 1.73
665 833 9.031360 CACTTCGTATGTACTTACATGCTTATT 57.969 33.333 16.55 0.00 45.77 1.40
666 834 9.245962 ACTTCGTATGTACTTACATGCTTATTC 57.754 33.333 16.55 0.00 45.77 1.75
667 835 7.847166 TCGTATGTACTTACATGCTTATTCG 57.153 36.000 16.55 5.82 45.77 3.34
668 836 6.361481 TCGTATGTACTTACATGCTTATTCGC 59.639 38.462 16.55 0.00 45.77 4.70
669 837 6.143278 CGTATGTACTTACATGCTTATTCGCA 59.857 38.462 16.55 0.00 45.77 5.10
670 838 6.918892 ATGTACTTACATGCTTATTCGCAA 57.081 33.333 0.94 0.00 44.66 4.85
671 839 6.729391 TGTACTTACATGCTTATTCGCAAA 57.271 33.333 0.00 0.00 44.06 3.68
672 840 7.135089 TGTACTTACATGCTTATTCGCAAAA 57.865 32.000 0.00 0.00 44.06 2.44
673 841 7.585867 TGTACTTACATGCTTATTCGCAAAAA 58.414 30.769 0.00 0.00 44.06 1.94
709 877 9.158233 ACATACAGTACGTGCTTATATTTTTGT 57.842 29.630 2.37 0.00 0.00 2.83
710 878 9.982291 CATACAGTACGTGCTTATATTTTTGTT 57.018 29.630 2.37 0.00 0.00 2.83
713 881 9.389570 ACAGTACGTGCTTATATTTTTGTTTTC 57.610 29.630 2.37 0.00 0.00 2.29
714 882 9.388346 CAGTACGTGCTTATATTTTTGTTTTCA 57.612 29.630 2.37 0.00 0.00 2.69
715 883 9.607285 AGTACGTGCTTATATTTTTGTTTTCAG 57.393 29.630 0.00 0.00 0.00 3.02
716 884 9.601971 GTACGTGCTTATATTTTTGTTTTCAGA 57.398 29.630 0.00 0.00 0.00 3.27
717 885 8.728088 ACGTGCTTATATTTTTGTTTTCAGAG 57.272 30.769 0.00 0.00 0.00 3.35
718 886 8.564574 ACGTGCTTATATTTTTGTTTTCAGAGA 58.435 29.630 0.00 0.00 0.00 3.10
719 887 9.393249 CGTGCTTATATTTTTGTTTTCAGAGAA 57.607 29.630 0.00 0.00 0.00 2.87
728 896 8.939201 TTTTTGTTTTCAGAGAAATGTATGCA 57.061 26.923 0.00 0.00 0.00 3.96
731 899 4.970662 TTTCAGAGAAATGTATGCAGCC 57.029 40.909 0.00 0.00 0.00 4.85
732 900 2.923121 TCAGAGAAATGTATGCAGCCC 58.077 47.619 0.00 0.00 0.00 5.19
737 905 2.176364 AGAAATGTATGCAGCCCCATCT 59.824 45.455 0.00 0.00 0.00 2.90
738 906 3.395607 AGAAATGTATGCAGCCCCATCTA 59.604 43.478 0.00 0.00 0.00 1.98
739 907 3.430042 AATGTATGCAGCCCCATCTAG 57.570 47.619 0.00 0.00 0.00 2.43
741 909 2.970987 TGTATGCAGCCCCATCTAGTA 58.029 47.619 0.00 0.00 0.00 1.82
745 913 2.477245 TGCAGCCCCATCTAGTAGAAA 58.523 47.619 3.45 0.00 0.00 2.52
755 923 7.256368 GCCCCATCTAGTAGAAAGCTAACTAAT 60.256 40.741 3.45 0.00 0.00 1.73
756 924 8.091449 CCCCATCTAGTAGAAAGCTAACTAATG 58.909 40.741 3.45 9.74 0.00 1.90
761 929 8.361139 TCTAGTAGAAAGCTAACTAATGATGGC 58.639 37.037 0.00 0.00 0.00 4.40
762 930 6.889198 AGTAGAAAGCTAACTAATGATGGCA 58.111 36.000 0.00 0.00 0.00 4.92
763 931 6.763610 AGTAGAAAGCTAACTAATGATGGCAC 59.236 38.462 0.00 0.00 0.00 5.01
788 956 8.034804 ACATTTGACACTAAAAATATCCAAGCC 58.965 33.333 0.00 0.00 0.00 4.35
795 963 4.888326 AAAAATATCCAAGCCAAGCACA 57.112 36.364 0.00 0.00 0.00 4.57
796 964 4.888326 AAAATATCCAAGCCAAGCACAA 57.112 36.364 0.00 0.00 0.00 3.33
797 965 4.460948 AAATATCCAAGCCAAGCACAAG 57.539 40.909 0.00 0.00 0.00 3.16
798 966 1.838112 TATCCAAGCCAAGCACAAGG 58.162 50.000 0.00 0.00 0.00 3.61
801 969 2.919328 AAGCCAAGCACAAGGGGC 60.919 61.111 0.00 0.00 46.77 5.80
809 977 3.508840 CACAAGGGGCGCCGAATC 61.509 66.667 22.54 10.00 0.00 2.52
821 989 4.204891 CGAATCGCGGACGCCAAC 62.205 66.667 6.13 0.05 39.84 3.77
849 1017 2.819422 CACCATTCGTGCAAGATGAG 57.181 50.000 2.36 0.00 35.18 2.90
851 1019 2.743664 CACCATTCGTGCAAGATGAGAA 59.256 45.455 2.36 0.00 35.18 2.87
870 1038 3.423154 CCGCAGACGAAGGGCAAC 61.423 66.667 0.00 0.00 43.93 4.17
871 1039 2.664851 CGCAGACGAAGGGCAACA 60.665 61.111 0.00 0.00 43.93 3.33
872 1040 2.250939 CGCAGACGAAGGGCAACAA 61.251 57.895 0.00 0.00 43.93 2.83
873 1041 1.282875 GCAGACGAAGGGCAACAAC 59.717 57.895 0.00 0.00 39.74 3.32
911 1079 2.570135 GGAGACAATTGAGATCCAGCC 58.430 52.381 13.59 0.00 0.00 4.85
912 1080 2.172293 GGAGACAATTGAGATCCAGCCT 59.828 50.000 13.59 0.00 0.00 4.58
913 1081 3.204526 GAGACAATTGAGATCCAGCCTG 58.795 50.000 13.59 0.00 0.00 4.85
916 1084 4.012374 GACAATTGAGATCCAGCCTGAAA 58.988 43.478 13.59 0.00 0.00 2.69
923 1096 3.113824 AGATCCAGCCTGAAATCACTCT 58.886 45.455 0.00 0.00 0.00 3.24
924 1097 3.522750 AGATCCAGCCTGAAATCACTCTT 59.477 43.478 0.00 0.00 0.00 2.85
938 1111 1.684049 CTCTTCCTCCGGTGCCTCT 60.684 63.158 0.00 0.00 0.00 3.69
946 1119 2.104331 CGGTGCCTCTACGCGAAT 59.896 61.111 15.93 0.00 0.00 3.34
960 1133 2.860628 CGAATTCCGCTCGCTTCCG 61.861 63.158 0.00 0.00 0.00 4.30
967 1140 4.443266 GCTCGCTTCCGCTCACCT 62.443 66.667 0.00 0.00 0.00 4.00
997 1170 4.308458 CGTCCCTTGCGTCCCACA 62.308 66.667 0.00 0.00 0.00 4.17
1016 1189 4.248859 CACACTCCATATATACCAGCAGC 58.751 47.826 0.00 0.00 0.00 5.25
1044 1217 0.608640 CGCCCCTTTCACTAGTCAGT 59.391 55.000 0.00 0.00 34.42 3.41
1045 1218 1.002087 CGCCCCTTTCACTAGTCAGTT 59.998 52.381 0.00 0.00 30.46 3.16
1046 1219 2.427506 GCCCCTTTCACTAGTCAGTTG 58.572 52.381 0.00 0.00 30.46 3.16
1047 1220 2.427506 CCCCTTTCACTAGTCAGTTGC 58.572 52.381 0.00 0.00 30.46 4.17
1050 1223 3.330267 CCTTTCACTAGTCAGTTGCCTC 58.670 50.000 0.00 0.00 30.46 4.70
1081 1254 3.706373 CCTCACCCACCCACCTCG 61.706 72.222 0.00 0.00 0.00 4.63
1343 1538 3.549150 CTCAAGCTCTTCGCCGCG 61.549 66.667 6.39 6.39 40.39 6.46
1814 2009 3.681835 GACGTGTGGAGCCTCGGT 61.682 66.667 0.00 0.00 0.00 4.69
1830 2025 1.464376 CGGTATGGCGATCCTGGAGT 61.464 60.000 1.52 0.00 0.00 3.85
2148 2357 3.373220 GGAGGAGAGTTAGGAGTCCATCA 60.373 52.174 12.86 0.00 0.00 3.07
2170 2383 8.743085 ATCAAAGCTGATGTGTACATAATCTT 57.257 30.769 17.50 7.66 40.94 2.40
2209 2422 1.586154 CCTGTCCCATGTGGCGTTTC 61.586 60.000 0.00 0.00 0.00 2.78
2316 2536 8.434733 TTCTTCATCAGAATCAGAAGCATAAG 57.565 34.615 0.00 0.00 36.51 1.73
2317 2537 6.482641 TCTTCATCAGAATCAGAAGCATAAGC 59.517 38.462 0.00 0.00 37.86 3.09
2318 2538 5.677567 TCATCAGAATCAGAAGCATAAGCA 58.322 37.500 0.00 0.00 45.49 3.91
2319 2539 6.296803 TCATCAGAATCAGAAGCATAAGCAT 58.703 36.000 0.00 0.00 45.49 3.79
2404 2812 3.751621 CATTGCACAAGAGGAAATCGAC 58.248 45.455 0.00 0.00 0.00 4.20
2408 2816 3.932710 TGCACAAGAGGAAATCGACATAC 59.067 43.478 0.00 0.00 0.00 2.39
2409 2817 3.932710 GCACAAGAGGAAATCGACATACA 59.067 43.478 0.00 0.00 0.00 2.29
2410 2818 4.033358 GCACAAGAGGAAATCGACATACAG 59.967 45.833 0.00 0.00 0.00 2.74
2455 3882 5.654209 GGGGAGATGAAATTTAAGAACTGCT 59.346 40.000 0.00 0.00 0.00 4.24
2465 3892 0.679505 AAGAACTGCTACAGGCGACA 59.320 50.000 0.00 0.00 45.43 4.35
2466 3893 0.679505 AGAACTGCTACAGGCGACAA 59.320 50.000 0.00 0.00 45.43 3.18
2467 3894 1.070134 AGAACTGCTACAGGCGACAAA 59.930 47.619 0.00 0.00 45.43 2.83
2488 3915 0.693049 TTCCTCCTGCTTCTTGTCCC 59.307 55.000 0.00 0.00 0.00 4.46
2503 3930 1.816835 TGTCCCGCAGTTGAGTAGTAG 59.183 52.381 0.00 0.00 0.00 2.57
2505 3932 3.012518 GTCCCGCAGTTGAGTAGTAGTA 58.987 50.000 0.00 0.00 0.00 1.82
2506 3933 3.012518 TCCCGCAGTTGAGTAGTAGTAC 58.987 50.000 0.00 0.00 0.00 2.73
2512 3939 7.201145 CCGCAGTTGAGTAGTAGTACAATAAT 58.799 38.462 10.33 0.00 0.00 1.28
2525 3952 6.119144 AGTACAATAATCGCAAACACATCC 57.881 37.500 0.00 0.00 0.00 3.51
2526 3953 5.880332 AGTACAATAATCGCAAACACATCCT 59.120 36.000 0.00 0.00 0.00 3.24
2527 3954 7.045416 AGTACAATAATCGCAAACACATCCTA 58.955 34.615 0.00 0.00 0.00 2.94
2528 3955 6.942532 ACAATAATCGCAAACACATCCTAT 57.057 33.333 0.00 0.00 0.00 2.57
2529 3956 8.984764 GTACAATAATCGCAAACACATCCTATA 58.015 33.333 0.00 0.00 0.00 1.31
2530 3957 8.087982 ACAATAATCGCAAACACATCCTATAG 57.912 34.615 0.00 0.00 0.00 1.31
2531 3958 7.173218 ACAATAATCGCAAACACATCCTATAGG 59.827 37.037 13.07 13.07 0.00 2.57
2561 3988 2.251642 GCGGTGCCACGTCTTCTTT 61.252 57.895 0.00 0.00 35.98 2.52
2573 4003 3.569701 ACGTCTTCTTTTCTACGGGTACA 59.430 43.478 0.00 0.00 39.57 2.90
2598 4028 2.721274 TGCCATTTTCAATGACGGTG 57.279 45.000 0.00 0.00 0.00 4.94
2602 4032 2.752354 CCATTTTCAATGACGGTGCCTA 59.248 45.455 0.00 0.00 0.00 3.93
2603 4033 3.181497 CCATTTTCAATGACGGTGCCTAG 60.181 47.826 0.00 0.00 0.00 3.02
2819 4288 1.366319 AGGGAACTGTTGAGATGGCT 58.634 50.000 0.00 0.00 41.13 4.75
2895 5408 1.300620 CAACACGGGACAGAGCGAA 60.301 57.895 0.00 0.00 0.00 4.70
2896 5409 0.878523 CAACACGGGACAGAGCGAAA 60.879 55.000 0.00 0.00 0.00 3.46
2923 5436 2.143876 ACAAAACCCAGCAGTTGTCT 57.856 45.000 0.00 0.00 28.08 3.41
2957 5470 2.527100 GTTGCGCTGATAACGTAGTCT 58.473 47.619 9.73 0.00 45.00 3.24
3057 9535 3.825611 GCGCGTGCAATGGGGAAT 61.826 61.111 17.66 0.00 42.15 3.01
3058 9536 2.102749 CGCGTGCAATGGGGAATG 59.897 61.111 0.00 0.00 31.21 2.67
3059 9537 2.202783 GCGTGCAATGGGGAATGC 60.203 61.111 0.00 0.00 42.86 3.56
3064 9542 3.390003 GCAATGGGGAATGCAATGG 57.610 52.632 0.00 0.00 42.12 3.16
3065 9543 0.831966 GCAATGGGGAATGCAATGGA 59.168 50.000 0.00 0.00 42.12 3.41
3066 9544 1.418637 GCAATGGGGAATGCAATGGAT 59.581 47.619 0.00 0.00 42.12 3.41
3067 9545 2.808933 GCAATGGGGAATGCAATGGATG 60.809 50.000 0.00 0.00 42.12 3.51
3177 9655 5.098211 GCATCCTTGATTTTCTGCAAGTAC 58.902 41.667 0.00 0.00 39.79 2.73
3178 9656 5.644644 CATCCTTGATTTTCTGCAAGTACC 58.355 41.667 0.00 0.00 39.79 3.34
3180 9658 5.136828 TCCTTGATTTTCTGCAAGTACCAA 58.863 37.500 0.00 0.00 39.79 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 4.776322 CGAGGGTCATGCGGCCAA 62.776 66.667 2.24 0.00 0.00 4.52
30 31 3.052082 CAGGCACAGAGGGCAACG 61.052 66.667 0.00 0.00 35.46 4.10
31 32 1.673665 CTCAGGCACAGAGGGCAAC 60.674 63.158 0.00 0.00 38.38 4.17
48 49 2.060980 TTGCCGTTTTTGGTGCCCT 61.061 52.632 0.00 0.00 0.00 5.19
94 95 0.750249 ATGCGACCATATCACGACCA 59.250 50.000 0.00 0.00 0.00 4.02
98 99 1.139989 GGACATGCGACCATATCACG 58.860 55.000 0.00 0.00 0.00 4.35
100 101 2.769893 CATGGACATGCGACCATATCA 58.230 47.619 15.86 0.00 44.49 2.15
129 130 4.899239 GTCCATCAGCGCCTCCCG 62.899 72.222 2.29 0.00 40.75 5.14
165 166 3.488569 GTCCGGGATCCCCATGCA 61.489 66.667 25.73 1.27 45.83 3.96
166 167 3.171388 AGTCCGGGATCCCCATGC 61.171 66.667 25.73 12.64 45.83 4.06
173 174 1.420430 TATCCAACCAGTCCGGGATC 58.580 55.000 0.00 0.00 40.49 3.36
177 178 0.469917 AGCATATCCAACCAGTCCGG 59.530 55.000 0.00 0.00 42.50 5.14
179 180 3.498774 ATGAGCATATCCAACCAGTCC 57.501 47.619 0.00 0.00 0.00 3.85
187 188 6.609212 GGATAGAGGAGTAATGAGCATATCCA 59.391 42.308 0.00 0.00 37.28 3.41
192 193 5.248020 CCTTGGATAGAGGAGTAATGAGCAT 59.752 44.000 0.00 0.00 36.33 3.79
218 219 2.430921 CTGCGACGGTGTCTGTCC 60.431 66.667 0.00 0.00 32.68 4.02
221 222 2.734723 CCACTGCGACGGTGTCTG 60.735 66.667 14.78 0.62 38.92 3.51
239 240 1.115467 AGATGGTGTAGAGGAAGCGG 58.885 55.000 0.00 0.00 0.00 5.52
267 269 0.977395 ACTAAGGTTGCGCTCCTTCT 59.023 50.000 29.85 18.65 43.26 2.85
298 300 1.706305 TCCAAATGGGTTAGACGGGTT 59.294 47.619 0.00 0.00 38.11 4.11
304 306 1.005450 GCCACCTCCAAATGGGTTAGA 59.995 52.381 0.00 0.00 36.41 2.10
310 312 3.451894 GCCGCCACCTCCAAATGG 61.452 66.667 0.00 0.00 39.16 3.16
314 316 3.706373 GAGAGCCGCCACCTCCAA 61.706 66.667 0.00 0.00 0.00 3.53
334 336 2.678836 CCTCTGTCTTATGTCGTCGAGT 59.321 50.000 0.00 0.00 0.00 4.18
375 377 0.981183 AATACCAGTCGCCACTTGGA 59.019 50.000 0.00 0.00 37.39 3.53
388 390 5.047660 GTGCCTTACAAATCAACCAATACCA 60.048 40.000 0.00 0.00 0.00 3.25
397 399 7.768120 ACAAATCAAAAGTGCCTTACAAATCAA 59.232 29.630 0.00 0.00 0.00 2.57
409 411 2.867647 GCCCTCCACAAATCAAAAGTGC 60.868 50.000 0.00 0.00 32.09 4.40
412 414 4.341366 AAAGCCCTCCACAAATCAAAAG 57.659 40.909 0.00 0.00 0.00 2.27
414 416 3.454082 ACAAAAGCCCTCCACAAATCAAA 59.546 39.130 0.00 0.00 0.00 2.69
416 418 2.627699 GACAAAAGCCCTCCACAAATCA 59.372 45.455 0.00 0.00 0.00 2.57
417 419 2.351738 CGACAAAAGCCCTCCACAAATC 60.352 50.000 0.00 0.00 0.00 2.17
419 421 1.028905 CGACAAAAGCCCTCCACAAA 58.971 50.000 0.00 0.00 0.00 2.83
420 422 0.821711 CCGACAAAAGCCCTCCACAA 60.822 55.000 0.00 0.00 0.00 3.33
421 423 1.228124 CCGACAAAAGCCCTCCACA 60.228 57.895 0.00 0.00 0.00 4.17
422 424 1.971695 CCCGACAAAAGCCCTCCAC 60.972 63.158 0.00 0.00 0.00 4.02
425 434 1.241990 GGAACCCGACAAAAGCCCTC 61.242 60.000 0.00 0.00 0.00 4.30
529 697 0.108945 GCCGACCTATACGTATGGGC 60.109 60.000 31.36 23.16 37.81 5.36
532 700 3.427638 CCTCATGCCGACCTATACGTATG 60.428 52.174 18.37 4.86 0.00 2.39
533 701 2.753452 CCTCATGCCGACCTATACGTAT 59.247 50.000 13.54 13.54 0.00 3.06
534 702 2.156917 CCTCATGCCGACCTATACGTA 58.843 52.381 0.00 0.00 0.00 3.57
535 703 0.959553 CCTCATGCCGACCTATACGT 59.040 55.000 0.00 0.00 0.00 3.57
536 704 0.388649 GCCTCATGCCGACCTATACG 60.389 60.000 0.00 0.00 0.00 3.06
537 705 0.388649 CGCCTCATGCCGACCTATAC 60.389 60.000 0.00 0.00 36.24 1.47
538 706 0.826256 ACGCCTCATGCCGACCTATA 60.826 55.000 7.14 0.00 36.24 1.31
539 707 2.088674 GACGCCTCATGCCGACCTAT 62.089 60.000 7.14 0.00 36.24 2.57
540 708 2.758327 ACGCCTCATGCCGACCTA 60.758 61.111 7.14 0.00 36.24 3.08
541 709 4.148825 GACGCCTCATGCCGACCT 62.149 66.667 7.14 0.00 36.24 3.85
542 710 4.148825 AGACGCCTCATGCCGACC 62.149 66.667 7.14 0.48 36.24 4.79
543 711 2.887568 CAGACGCCTCATGCCGAC 60.888 66.667 7.14 2.04 36.24 4.79
544 712 3.068064 TCAGACGCCTCATGCCGA 61.068 61.111 7.14 0.00 36.24 5.54
545 713 2.584418 CTCAGACGCCTCATGCCG 60.584 66.667 0.00 0.00 36.24 5.69
546 714 1.812922 CACTCAGACGCCTCATGCC 60.813 63.158 0.00 0.00 36.24 4.40
547 715 0.805322 CTCACTCAGACGCCTCATGC 60.805 60.000 0.00 0.00 0.00 4.06
548 716 0.529833 ACTCACTCAGACGCCTCATG 59.470 55.000 0.00 0.00 0.00 3.07
549 717 0.814457 GACTCACTCAGACGCCTCAT 59.186 55.000 0.00 0.00 0.00 2.90
550 718 0.537371 TGACTCACTCAGACGCCTCA 60.537 55.000 0.00 0.00 0.00 3.86
551 719 2.258317 TGACTCACTCAGACGCCTC 58.742 57.895 0.00 0.00 0.00 4.70
552 720 4.502187 TGACTCACTCAGACGCCT 57.498 55.556 0.00 0.00 0.00 5.52
558 726 3.188048 GCACAAAATCCTGACTCACTCAG 59.812 47.826 0.00 0.00 45.63 3.35
559 727 3.141398 GCACAAAATCCTGACTCACTCA 58.859 45.455 0.00 0.00 0.00 3.41
560 728 2.485814 GGCACAAAATCCTGACTCACTC 59.514 50.000 0.00 0.00 0.00 3.51
561 729 2.508526 GGCACAAAATCCTGACTCACT 58.491 47.619 0.00 0.00 0.00 3.41
562 730 1.541588 GGGCACAAAATCCTGACTCAC 59.458 52.381 0.00 0.00 0.00 3.51
563 731 1.547675 GGGGCACAAAATCCTGACTCA 60.548 52.381 0.00 0.00 0.00 3.41
564 732 1.177401 GGGGCACAAAATCCTGACTC 58.823 55.000 0.00 0.00 0.00 3.36
565 733 0.609131 CGGGGCACAAAATCCTGACT 60.609 55.000 0.00 0.00 0.00 3.41
566 734 1.595093 CCGGGGCACAAAATCCTGAC 61.595 60.000 0.00 0.00 0.00 3.51
567 735 1.304052 CCGGGGCACAAAATCCTGA 60.304 57.895 0.00 0.00 0.00 3.86
568 736 3.005540 GCCGGGGCACAAAATCCTG 62.006 63.158 2.18 0.00 41.49 3.86
569 737 2.679996 GCCGGGGCACAAAATCCT 60.680 61.111 2.18 0.00 41.49 3.24
579 747 1.313091 CCTAAAAGAACTGCCGGGGC 61.313 60.000 2.18 1.86 42.35 5.80
580 748 0.326927 TCCTAAAAGAACTGCCGGGG 59.673 55.000 2.18 0.00 0.00 5.73
581 749 1.679032 CCTCCTAAAAGAACTGCCGGG 60.679 57.143 2.18 0.00 0.00 5.73
582 750 1.679032 CCCTCCTAAAAGAACTGCCGG 60.679 57.143 0.00 0.00 0.00 6.13
583 751 1.739067 CCCTCCTAAAAGAACTGCCG 58.261 55.000 0.00 0.00 0.00 5.69
584 752 1.464734 GCCCTCCTAAAAGAACTGCC 58.535 55.000 0.00 0.00 0.00 4.85
585 753 1.464734 GGCCCTCCTAAAAGAACTGC 58.535 55.000 0.00 0.00 0.00 4.40
586 754 1.679032 CCGGCCCTCCTAAAAGAACTG 60.679 57.143 0.00 0.00 0.00 3.16
587 755 0.618981 CCGGCCCTCCTAAAAGAACT 59.381 55.000 0.00 0.00 0.00 3.01
588 756 0.327259 ACCGGCCCTCCTAAAAGAAC 59.673 55.000 0.00 0.00 0.00 3.01
589 757 1.069775 AACCGGCCCTCCTAAAAGAA 58.930 50.000 0.00 0.00 0.00 2.52
590 758 1.069775 AAACCGGCCCTCCTAAAAGA 58.930 50.000 0.00 0.00 0.00 2.52
591 759 1.173913 CAAACCGGCCCTCCTAAAAG 58.826 55.000 0.00 0.00 0.00 2.27
592 760 0.896479 GCAAACCGGCCCTCCTAAAA 60.896 55.000 0.00 0.00 0.00 1.52
593 761 1.303806 GCAAACCGGCCCTCCTAAA 60.304 57.895 0.00 0.00 0.00 1.85
594 762 2.353573 GCAAACCGGCCCTCCTAA 59.646 61.111 0.00 0.00 0.00 2.69
595 763 4.090588 CGCAAACCGGCCCTCCTA 62.091 66.667 0.00 0.00 0.00 2.94
611 779 3.991051 ATCTACATCGGGCCGGCG 61.991 66.667 27.98 19.58 0.00 6.46
612 780 2.357517 CATCTACATCGGGCCGGC 60.358 66.667 27.98 21.18 0.00 6.13
613 781 2.357517 GCATCTACATCGGGCCGG 60.358 66.667 27.98 13.85 0.00 6.13
614 782 1.373497 GAGCATCTACATCGGGCCG 60.373 63.158 22.51 22.51 0.00 6.13
615 783 4.683432 GAGCATCTACATCGGGCC 57.317 61.111 0.00 0.00 0.00 5.80
620 788 9.692820 ACGAAGTGAAGTGAGAGCATCTACATC 62.693 44.444 0.00 0.00 45.48 3.06
621 789 8.019448 ACGAAGTGAAGTGAGAGCATCTACAT 62.019 42.308 0.00 0.00 45.48 2.29
622 790 6.778225 ACGAAGTGAAGTGAGAGCATCTACA 61.778 44.000 0.00 0.00 45.48 2.74
623 791 4.380023 ACGAAGTGAAGTGAGAGCATCTAC 60.380 45.833 0.00 0.00 45.48 2.59
624 792 3.759086 ACGAAGTGAAGTGAGAGCATCTA 59.241 43.478 0.00 0.00 45.48 1.98
626 794 2.953020 ACGAAGTGAAGTGAGAGCATC 58.047 47.619 0.00 0.00 42.51 3.91
627 795 4.081972 ACATACGAAGTGAAGTGAGAGCAT 60.082 41.667 0.00 0.00 45.73 3.79
628 796 3.255888 ACATACGAAGTGAAGTGAGAGCA 59.744 43.478 0.00 0.00 45.73 4.26
629 797 3.839293 ACATACGAAGTGAAGTGAGAGC 58.161 45.455 0.00 0.00 45.73 4.09
630 798 6.184580 AGTACATACGAAGTGAAGTGAGAG 57.815 41.667 0.00 0.00 45.73 3.20
631 799 6.570672 AAGTACATACGAAGTGAAGTGAGA 57.429 37.500 0.00 0.00 45.73 3.27
632 800 7.303261 TGTAAGTACATACGAAGTGAAGTGAG 58.697 38.462 3.98 0.00 45.73 3.51
633 801 7.205737 TGTAAGTACATACGAAGTGAAGTGA 57.794 36.000 3.98 0.00 45.73 3.41
634 802 7.462856 GCATGTAAGTACATACGAAGTGAAGTG 60.463 40.741 3.69 0.00 44.57 3.16
635 803 6.530534 GCATGTAAGTACATACGAAGTGAAGT 59.469 38.462 3.69 0.00 44.57 3.01
636 804 6.752351 AGCATGTAAGTACATACGAAGTGAAG 59.248 38.462 3.69 0.00 44.57 3.02
637 805 6.627243 AGCATGTAAGTACATACGAAGTGAA 58.373 36.000 3.69 0.00 44.57 3.18
638 806 6.203808 AGCATGTAAGTACATACGAAGTGA 57.796 37.500 3.69 0.00 44.57 3.41
639 807 6.887376 AAGCATGTAAGTACATACGAAGTG 57.113 37.500 3.69 2.30 44.57 3.16
640 808 9.245962 GAATAAGCATGTAAGTACATACGAAGT 57.754 33.333 3.69 0.00 44.57 3.01
641 809 8.417928 CGAATAAGCATGTAAGTACATACGAAG 58.582 37.037 3.69 0.00 44.57 3.79
642 810 7.096353 GCGAATAAGCATGTAAGTACATACGAA 60.096 37.037 3.69 0.00 44.57 3.85
643 811 6.361481 GCGAATAAGCATGTAAGTACATACGA 59.639 38.462 3.69 0.00 44.57 3.43
644 812 6.143278 TGCGAATAAGCATGTAAGTACATACG 59.857 38.462 3.69 0.00 44.57 3.06
645 813 7.402811 TGCGAATAAGCATGTAAGTACATAC 57.597 36.000 3.69 1.26 44.57 2.39
683 851 9.158233 ACAAAAATATAAGCACGTACTGTATGT 57.842 29.630 6.85 6.85 0.00 2.29
684 852 9.982291 AACAAAAATATAAGCACGTACTGTATG 57.018 29.630 5.51 5.51 0.00 2.39
687 855 9.389570 GAAAACAAAAATATAAGCACGTACTGT 57.610 29.630 0.00 0.00 0.00 3.55
688 856 9.388346 TGAAAACAAAAATATAAGCACGTACTG 57.612 29.630 0.00 0.00 0.00 2.74
689 857 9.607285 CTGAAAACAAAAATATAAGCACGTACT 57.393 29.630 0.00 0.00 0.00 2.73
690 858 9.601971 TCTGAAAACAAAAATATAAGCACGTAC 57.398 29.630 0.00 0.00 0.00 3.67
691 859 9.820229 CTCTGAAAACAAAAATATAAGCACGTA 57.180 29.630 0.00 0.00 0.00 3.57
692 860 8.564574 TCTCTGAAAACAAAAATATAAGCACGT 58.435 29.630 0.00 0.00 0.00 4.49
693 861 8.948853 TCTCTGAAAACAAAAATATAAGCACG 57.051 30.769 0.00 0.00 0.00 5.34
702 870 9.545105 TGCATACATTTCTCTGAAAACAAAAAT 57.455 25.926 0.00 0.00 0.00 1.82
703 871 8.939201 TGCATACATTTCTCTGAAAACAAAAA 57.061 26.923 0.00 0.00 0.00 1.94
704 872 7.169645 GCTGCATACATTTCTCTGAAAACAAAA 59.830 33.333 0.00 0.00 0.00 2.44
705 873 6.642131 GCTGCATACATTTCTCTGAAAACAAA 59.358 34.615 0.00 0.00 0.00 2.83
706 874 6.151691 GCTGCATACATTTCTCTGAAAACAA 58.848 36.000 0.00 0.00 0.00 2.83
707 875 5.335897 GGCTGCATACATTTCTCTGAAAACA 60.336 40.000 0.50 0.00 0.00 2.83
708 876 5.098211 GGCTGCATACATTTCTCTGAAAAC 58.902 41.667 0.50 0.00 0.00 2.43
709 877 4.158394 GGGCTGCATACATTTCTCTGAAAA 59.842 41.667 0.50 0.00 0.00 2.29
710 878 3.696051 GGGCTGCATACATTTCTCTGAAA 59.304 43.478 0.50 0.00 0.00 2.69
711 879 3.282021 GGGCTGCATACATTTCTCTGAA 58.718 45.455 0.50 0.00 0.00 3.02
712 880 2.421952 GGGGCTGCATACATTTCTCTGA 60.422 50.000 0.50 0.00 0.00 3.27
713 881 1.952296 GGGGCTGCATACATTTCTCTG 59.048 52.381 0.50 0.00 0.00 3.35
714 882 1.565759 TGGGGCTGCATACATTTCTCT 59.434 47.619 0.50 0.00 0.00 3.10
715 883 2.057137 TGGGGCTGCATACATTTCTC 57.943 50.000 0.50 0.00 0.00 2.87
716 884 2.176364 AGATGGGGCTGCATACATTTCT 59.824 45.455 0.50 0.00 0.00 2.52
717 885 2.590821 AGATGGGGCTGCATACATTTC 58.409 47.619 0.50 0.00 0.00 2.17
718 886 2.761786 AGATGGGGCTGCATACATTT 57.238 45.000 0.50 0.00 0.00 2.32
719 887 2.713167 ACTAGATGGGGCTGCATACATT 59.287 45.455 0.50 0.00 0.00 2.71
720 888 2.342659 ACTAGATGGGGCTGCATACAT 58.657 47.619 0.50 2.13 0.00 2.29
721 889 1.806496 ACTAGATGGGGCTGCATACA 58.194 50.000 0.50 0.00 0.00 2.29
722 890 3.165875 TCTACTAGATGGGGCTGCATAC 58.834 50.000 0.50 0.00 0.00 2.39
723 891 3.542969 TCTACTAGATGGGGCTGCATA 57.457 47.619 0.50 0.00 0.00 3.14
724 892 2.405618 TCTACTAGATGGGGCTGCAT 57.594 50.000 0.50 0.00 0.00 3.96
725 893 2.174685 TTCTACTAGATGGGGCTGCA 57.825 50.000 0.50 0.00 0.00 4.41
726 894 2.808567 GCTTTCTACTAGATGGGGCTGC 60.809 54.545 0.00 0.00 0.00 5.25
727 895 2.703007 AGCTTTCTACTAGATGGGGCTG 59.297 50.000 0.00 0.00 0.00 4.85
728 896 3.053359 AGCTTTCTACTAGATGGGGCT 57.947 47.619 0.00 0.00 0.00 5.19
731 899 8.861086 TCATTAGTTAGCTTTCTACTAGATGGG 58.139 37.037 0.00 0.00 0.00 4.00
737 905 7.926555 GTGCCATCATTAGTTAGCTTTCTACTA 59.073 37.037 0.00 0.00 0.00 1.82
738 906 6.763610 GTGCCATCATTAGTTAGCTTTCTACT 59.236 38.462 0.00 0.00 0.00 2.57
739 907 6.538742 TGTGCCATCATTAGTTAGCTTTCTAC 59.461 38.462 0.00 0.00 0.00 2.59
741 909 5.500234 TGTGCCATCATTAGTTAGCTTTCT 58.500 37.500 0.00 0.00 0.00 2.52
745 913 5.887598 TCAAATGTGCCATCATTAGTTAGCT 59.112 36.000 0.00 0.00 37.09 3.32
755 923 5.781210 TTTTAGTGTCAAATGTGCCATCA 57.219 34.783 0.00 0.00 0.00 3.07
756 924 8.931385 ATATTTTTAGTGTCAAATGTGCCATC 57.069 30.769 0.00 0.00 0.00 3.51
758 926 7.039434 TGGATATTTTTAGTGTCAAATGTGCCA 60.039 33.333 0.00 0.00 0.00 4.92
759 927 7.319646 TGGATATTTTTAGTGTCAAATGTGCC 58.680 34.615 0.00 0.00 0.00 5.01
760 928 8.755696 TTGGATATTTTTAGTGTCAAATGTGC 57.244 30.769 0.00 0.00 0.00 4.57
761 929 8.863049 GCTTGGATATTTTTAGTGTCAAATGTG 58.137 33.333 0.00 0.00 0.00 3.21
762 930 8.034804 GGCTTGGATATTTTTAGTGTCAAATGT 58.965 33.333 0.00 0.00 0.00 2.71
763 931 8.034215 TGGCTTGGATATTTTTAGTGTCAAATG 58.966 33.333 0.00 0.00 0.00 2.32
764 932 8.133024 TGGCTTGGATATTTTTAGTGTCAAAT 57.867 30.769 0.00 0.00 0.00 2.32
768 936 6.036470 GCTTGGCTTGGATATTTTTAGTGTC 58.964 40.000 0.00 0.00 0.00 3.67
771 939 5.480073 TGTGCTTGGCTTGGATATTTTTAGT 59.520 36.000 0.00 0.00 0.00 2.24
804 972 4.204891 GTTGGCGTCCGCGATTCG 62.205 66.667 8.23 10.52 43.06 3.34
806 974 2.435938 ATGTTGGCGTCCGCGATT 60.436 55.556 8.23 0.00 43.06 3.34
807 975 3.195002 CATGTTGGCGTCCGCGAT 61.195 61.111 8.23 0.00 43.06 4.58
817 985 0.250793 AATGGTGCATGGCATGTTGG 59.749 50.000 26.94 3.70 41.91 3.77
821 989 0.526739 CACGAATGGTGCATGGCATG 60.527 55.000 22.99 22.99 41.91 4.06
849 1017 2.815647 CCCTTCGTCTGCGGCTTC 60.816 66.667 0.00 0.00 38.89 3.86
869 1037 2.967076 CGTCCGCTGTGCTGTTGT 60.967 61.111 0.00 0.00 0.00 3.32
870 1038 4.374702 GCGTCCGCTGTGCTGTTG 62.375 66.667 4.10 0.00 38.26 3.33
871 1039 4.908687 TGCGTCCGCTGTGCTGTT 62.909 61.111 13.31 0.00 42.51 3.16
892 1060 3.118482 TCAGGCTGGATCTCAATTGTCTC 60.118 47.826 15.73 1.17 0.00 3.36
896 1064 4.643334 TGATTTCAGGCTGGATCTCAATTG 59.357 41.667 23.00 0.00 0.00 2.32
988 1161 3.368116 GGTATATATGGAGTGTGGGACGC 60.368 52.174 0.00 0.00 40.62 5.19
989 1162 3.830178 TGGTATATATGGAGTGTGGGACG 59.170 47.826 0.00 0.00 0.00 4.79
990 1163 4.322801 GCTGGTATATATGGAGTGTGGGAC 60.323 50.000 0.00 0.00 0.00 4.46
991 1164 3.838317 GCTGGTATATATGGAGTGTGGGA 59.162 47.826 0.00 0.00 0.00 4.37
992 1165 3.582647 TGCTGGTATATATGGAGTGTGGG 59.417 47.826 0.00 0.00 0.00 4.61
993 1166 4.825422 CTGCTGGTATATATGGAGTGTGG 58.175 47.826 0.00 0.00 0.00 4.17
994 1167 4.248859 GCTGCTGGTATATATGGAGTGTG 58.751 47.826 0.00 0.00 0.00 3.82
995 1168 3.056536 CGCTGCTGGTATATATGGAGTGT 60.057 47.826 0.00 0.00 0.00 3.55
996 1169 3.193479 TCGCTGCTGGTATATATGGAGTG 59.807 47.826 0.00 0.00 0.00 3.51
997 1170 3.431415 TCGCTGCTGGTATATATGGAGT 58.569 45.455 0.00 0.00 0.00 3.85
1060 1233 2.750350 GTGGGTGGGTGAGGTGAG 59.250 66.667 0.00 0.00 0.00 3.51
1096 1279 0.538977 CATGAGATGGGATGGGTGGC 60.539 60.000 0.00 0.00 0.00 5.01
1764 1959 1.817099 CGTAGTCGCCGGAGTAGGT 60.817 63.158 5.05 0.00 32.08 3.08
1814 2009 1.496060 ACAACTCCAGGATCGCCATA 58.504 50.000 0.00 0.00 36.29 2.74
1830 2025 1.765074 GGAAGTGGCCCAGGTACAA 59.235 57.895 0.00 0.00 0.00 2.41
2148 2357 6.238211 GCGAAGATTATGTACACATCAGCTTT 60.238 38.462 15.89 4.88 36.63 3.51
2170 2383 1.266160 TTTATTCCTCCCCGTGGCGA 61.266 55.000 0.00 0.00 0.00 5.54
2209 2422 1.138069 ACGGCAAAAAGGTGAAAAGGG 59.862 47.619 0.00 0.00 0.00 3.95
2268 2485 6.727824 AGGTATCAATTCTCAAAACTGTCG 57.272 37.500 0.00 0.00 0.00 4.35
2316 2536 2.354821 CTGAGCCTTTTACGGGTTATGC 59.645 50.000 0.00 0.00 34.32 3.14
2317 2537 3.606687 ACTGAGCCTTTTACGGGTTATG 58.393 45.455 0.00 0.00 34.32 1.90
2318 2538 3.994931 ACTGAGCCTTTTACGGGTTAT 57.005 42.857 0.00 0.00 34.32 1.89
2319 2539 3.557686 GGAACTGAGCCTTTTACGGGTTA 60.558 47.826 0.00 0.00 34.32 2.85
2356 2639 0.510359 CTTGTGTCTGCTGTTCGCTC 59.490 55.000 0.00 0.00 40.11 5.03
2366 2649 3.427528 GCAATGCATGTTTCTTGTGTCTG 59.572 43.478 0.00 0.00 0.00 3.51
2367 2650 3.068448 TGCAATGCATGTTTCTTGTGTCT 59.932 39.130 2.72 0.00 31.71 3.41
2368 2651 3.182972 GTGCAATGCATGTTTCTTGTGTC 59.817 43.478 12.38 0.00 41.91 3.67
2369 2652 3.125316 GTGCAATGCATGTTTCTTGTGT 58.875 40.909 12.38 0.00 41.91 3.72
2404 2812 3.377346 AAGAGCTATGTCGCCTGTATG 57.623 47.619 0.00 0.00 0.00 2.39
2408 2816 3.265791 AGAAAAAGAGCTATGTCGCCTG 58.734 45.455 0.00 0.00 0.00 4.85
2409 2817 3.618690 AGAAAAAGAGCTATGTCGCCT 57.381 42.857 0.00 0.00 0.00 5.52
2410 2818 3.804873 CCTAGAAAAAGAGCTATGTCGCC 59.195 47.826 0.00 0.00 0.00 5.54
2415 3841 5.878406 TCTCCCCTAGAAAAAGAGCTATG 57.122 43.478 0.00 0.00 0.00 2.23
2455 3882 1.001633 GGAGGAACTTTGTCGCCTGTA 59.998 52.381 0.00 0.00 41.55 2.74
2465 3892 3.481453 GACAAGAAGCAGGAGGAACTTT 58.519 45.455 0.00 0.00 41.55 2.66
2466 3893 2.224646 GGACAAGAAGCAGGAGGAACTT 60.225 50.000 0.00 0.00 41.55 2.66
2488 3915 7.111732 CGATTATTGTACTACTACTCAACTGCG 59.888 40.741 0.00 0.00 0.00 5.18
2503 3930 6.119144 AGGATGTGTTTGCGATTATTGTAC 57.881 37.500 0.00 0.00 0.00 2.90
2505 3932 6.942532 ATAGGATGTGTTTGCGATTATTGT 57.057 33.333 0.00 0.00 0.00 2.71
2506 3933 7.521529 CCTATAGGATGTGTTTGCGATTATTG 58.478 38.462 14.11 0.00 37.39 1.90
2512 3939 2.434336 AGCCTATAGGATGTGTTTGCGA 59.566 45.455 23.61 0.00 37.39 5.10
2525 3952 2.355132 CCGCACCGTCTATAGCCTATAG 59.645 54.545 11.82 11.82 39.57 1.31
2526 3953 2.290514 ACCGCACCGTCTATAGCCTATA 60.291 50.000 0.00 0.00 0.00 1.31
2527 3954 1.174783 CCGCACCGTCTATAGCCTAT 58.825 55.000 0.00 0.00 0.00 2.57
2528 3955 0.179009 ACCGCACCGTCTATAGCCTA 60.179 55.000 0.00 0.00 0.00 3.93
2529 3956 1.455217 ACCGCACCGTCTATAGCCT 60.455 57.895 0.00 0.00 0.00 4.58
2530 3957 1.299926 CACCGCACCGTCTATAGCC 60.300 63.158 0.00 0.00 0.00 3.93
2531 3958 1.949631 GCACCGCACCGTCTATAGC 60.950 63.158 0.00 0.00 0.00 2.97
2561 3988 3.055021 TGGCAAATCATGTACCCGTAGAA 60.055 43.478 0.00 0.00 0.00 2.10
2573 4003 4.871557 CCGTCATTGAAAATGGCAAATCAT 59.128 37.500 5.52 0.00 0.00 2.45
2623 4054 9.778993 CATCGTTCATCAAGATTAGAAAATTGT 57.221 29.630 0.00 0.00 0.00 2.71
2624 4055 9.992910 TCATCGTTCATCAAGATTAGAAAATTG 57.007 29.630 0.00 0.00 0.00 2.32
2627 4058 9.382275 TGATCATCGTTCATCAAGATTAGAAAA 57.618 29.630 0.00 0.00 0.00 2.29
2690 4121 3.193479 CCTTTGTTTAAGCCATCTCCACC 59.807 47.826 0.00 0.00 32.19 4.61
2696 4127 3.676291 TTGGCCTTTGTTTAAGCCATC 57.324 42.857 3.32 0.00 38.75 3.51
2802 4271 1.066858 TCGAGCCATCTCAACAGTTCC 60.067 52.381 0.00 0.00 39.30 3.62
2819 4288 0.806102 GGCTAGCGCACTGATTTCGA 60.806 55.000 11.47 0.00 38.10 3.71
2895 5408 3.100671 TGCTGGGTTTTGTACACCTTTT 58.899 40.909 0.00 0.00 34.36 2.27
2896 5409 2.693074 CTGCTGGGTTTTGTACACCTTT 59.307 45.455 0.00 0.00 34.36 3.11
2923 5436 2.817258 AGCGCAACCAATACTTTTAGCA 59.183 40.909 11.47 0.00 0.00 3.49
3008 9486 3.876300 GCAAGTACTCCGTGCAGG 58.124 61.111 12.19 0.00 46.33 4.85
3059 9537 2.440796 AGGCGGTGGCATCCATTG 60.441 61.111 0.00 0.00 42.47 2.82
3060 9538 2.124151 GAGGCGGTGGCATCCATT 60.124 61.111 0.00 0.00 43.89 3.16
3068 9546 4.530857 GATCGGGTGAGGCGGTGG 62.531 72.222 0.00 0.00 0.00 4.61
3069 9547 4.873129 CGATCGGGTGAGGCGGTG 62.873 72.222 7.38 0.00 0.00 4.94
3130 9608 2.309528 TATGCCCAAGTACTTGAGCG 57.690 50.000 32.50 20.69 45.61 5.03
3177 9655 5.282510 GTGTGCTGCTAGTACTATACTTGG 58.717 45.833 2.33 0.00 40.14 3.61
3178 9656 4.970611 CGTGTGCTGCTAGTACTATACTTG 59.029 45.833 2.33 0.00 40.14 3.16
3180 9658 3.003482 GCGTGTGCTGCTAGTACTATACT 59.997 47.826 2.33 0.00 39.40 2.12


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

AutoCloner maintained by Alex Coulton.