Multiple sequence alignment - TraesCS2B01G305700

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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 TraesCS2B01G305700 chr2B 100.000 3410 0 0 1 3410 436024597 436028006 0.000000e+00 6298.0
1 TraesCS2B01G305700 chr2D 91.689 2226 115 22 770 2970 367226338 367228518 0.000000e+00 3022.0
2 TraesCS2B01G305700 chr2D 76.522 345 70 6 382 715 608485103 608484759 9.720000e-41 178.0
3 TraesCS2B01G305700 chr2D 97.059 34 1 0 2849 2882 69267877 69267844 1.320000e-04 58.4
4 TraesCS2B01G305700 chr2D 96.970 33 1 0 2817 2849 313221572 313221604 4.750000e-04 56.5
5 TraesCS2B01G305700 chr2A 96.116 1828 62 2 932 2750 497439110 497440937 0.000000e+00 2974.0
6 TraesCS2B01G305700 chr2A 88.604 781 81 7 45 823 497420117 497420891 0.000000e+00 942.0
7 TraesCS2B01G305700 chr2A 94.737 38 2 0 2824 2861 346206978 346206941 3.670000e-05 60.2
8 TraesCS2B01G305700 chr4D 90.357 280 23 3 2987 3263 148518370 148518648 6.950000e-97 364.0
9 TraesCS2B01G305700 chr4D 90.476 147 13 1 3264 3410 148518731 148518876 3.470000e-45 193.0
10 TraesCS2B01G305700 chr3B 74.818 548 117 17 207 746 650063260 650063794 9.520000e-56 228.0
11 TraesCS2B01G305700 chr3B 74.020 408 80 17 384 777 395354067 395354462 3.550000e-30 143.0
12 TraesCS2B01G305700 chr3B 75.229 218 44 7 467 678 729667799 729667586 1.010000e-15 95.3
13 TraesCS2B01G305700 chr3B 90.909 44 3 1 2822 2864 728063464 728063421 1.320000e-04 58.4
14 TraesCS2B01G305700 chr5D 92.517 147 10 1 3264 3410 313103131 313102986 3.450000e-50 209.0
15 TraesCS2B01G305700 chr5D 76.989 352 64 15 375 712 56806880 56807228 5.810000e-43 185.0
16 TraesCS2B01G305700 chr6B 82.840 169 28 1 548 715 27809808 27809640 2.120000e-32 150.0
17 TraesCS2B01G305700 chr6B 88.636 44 4 1 2822 2864 456768725 456768768 6.000000e-03 52.8
18 TraesCS2B01G305700 chr5A 80.108 186 30 5 564 746 575712677 575712858 7.680000e-27 132.0
19 TraesCS2B01G305700 chr5A 90.909 44 3 1 2822 2864 511898593 511898636 1.320000e-04 58.4
20 TraesCS2B01G305700 chr5A 89.130 46 4 1 2817 2861 128433900 128433855 4.750000e-04 56.5
21 TraesCS2B01G305700 chr5B 73.727 373 78 11 382 742 541971297 541970933 9.930000e-26 128.0
22 TraesCS2B01G305700 chr5B 100.000 30 0 0 2853 2882 554824996 554825025 4.750000e-04 56.5
23 TraesCS2B01G305700 chr1B 76.503 183 39 4 559 740 645083336 645083515 2.800000e-16 97.1
24 TraesCS2B01G305700 chr7A 76.503 183 32 3 343 515 1511005 1511186 4.690000e-14 89.8
25 TraesCS2B01G305700 chr7B 100.000 29 0 0 2821 2849 670450582 670450610 2.000000e-03 54.7
26 TraesCS2B01G305700 chr7B 100.000 29 0 0 2821 2849 670486107 670486135 2.000000e-03 54.7
27 TraesCS2B01G305700 chr7B 100.000 29 0 0 2821 2849 670504573 670504601 2.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G305700 chr2B 436024597 436028006 3409 False 6298.0 6298 100.0000 1 3410 1 chr2B.!!$F1 3409
1 TraesCS2B01G305700 chr2D 367226338 367228518 2180 False 3022.0 3022 91.6890 770 2970 1 chr2D.!!$F2 2200
2 TraesCS2B01G305700 chr2A 497439110 497440937 1827 False 2974.0 2974 96.1160 932 2750 1 chr2A.!!$F2 1818
3 TraesCS2B01G305700 chr2A 497420117 497420891 774 False 942.0 942 88.6040 45 823 1 chr2A.!!$F1 778
4 TraesCS2B01G305700 chr4D 148518370 148518876 506 False 278.5 364 90.4165 2987 3410 2 chr4D.!!$F1 423
5 TraesCS2B01G305700 chr3B 650063260 650063794 534 False 228.0 228 74.8180 207 746 1 chr3B.!!$F2 539

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
682 687 0.037697 AATGCTTGTAGTCGTCGCCA 60.038 50.0 0.0 0.0 0.0 5.69 F
1234 1493 0.040499 ACTTCTCCTCCTCTTCCGCT 59.960 55.0 0.0 0.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2244 2503 0.108945 GGTTGAGCTCCAGCAAATGC 60.109 55.0 12.15 0.0 45.16 3.56 R
2989 3258 0.323178 CCAGCAATTCCAGAGTGCCT 60.323 55.0 0.00 0.0 39.13 4.75 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
18 19 3.379650 TAGGCGCCTATCAGTTTGC 57.620 52.632 32.24 0.00 0.00 3.68
19 20 0.539518 TAGGCGCCTATCAGTTTGCA 59.460 50.000 32.24 8.26 0.00 4.08
20 21 0.745845 AGGCGCCTATCAGTTTGCAG 60.746 55.000 31.86 0.00 0.00 4.41
21 22 0.744414 GGCGCCTATCAGTTTGCAGA 60.744 55.000 22.15 0.00 0.00 4.26
22 23 1.086696 GCGCCTATCAGTTTGCAGAA 58.913 50.000 0.00 0.00 0.00 3.02
23 24 1.063174 GCGCCTATCAGTTTGCAGAAG 59.937 52.381 0.00 0.00 0.00 2.85
24 25 2.350522 CGCCTATCAGTTTGCAGAAGT 58.649 47.619 0.00 0.00 0.00 3.01
25 26 2.744202 CGCCTATCAGTTTGCAGAAGTT 59.256 45.455 0.00 0.00 0.00 2.66
26 27 3.189287 CGCCTATCAGTTTGCAGAAGTTT 59.811 43.478 0.00 0.00 0.00 2.66
27 28 4.479619 GCCTATCAGTTTGCAGAAGTTTG 58.520 43.478 0.00 0.00 0.00 2.93
28 29 4.616835 GCCTATCAGTTTGCAGAAGTTTGG 60.617 45.833 0.00 0.00 0.00 3.28
29 30 2.869233 TCAGTTTGCAGAAGTTTGGC 57.131 45.000 0.00 0.00 0.00 4.52
30 31 1.408702 TCAGTTTGCAGAAGTTTGGCC 59.591 47.619 0.00 0.00 0.00 5.36
31 32 0.385390 AGTTTGCAGAAGTTTGGCCG 59.615 50.000 0.00 0.00 0.00 6.13
32 33 0.383949 GTTTGCAGAAGTTTGGCCGA 59.616 50.000 0.00 0.00 0.00 5.54
33 34 1.107114 TTTGCAGAAGTTTGGCCGAA 58.893 45.000 0.00 0.00 0.00 4.30
34 35 0.667993 TTGCAGAAGTTTGGCCGAAG 59.332 50.000 5.37 0.00 0.00 3.79
52 53 4.451900 CGAAGGCCCAATGTATATATCCC 58.548 47.826 0.00 0.00 0.00 3.85
75 76 6.660949 CCCTTCCACTTTCATCTAGTTTCAAT 59.339 38.462 0.00 0.00 0.00 2.57
77 78 7.148171 CCTTCCACTTTCATCTAGTTTCAATCC 60.148 40.741 0.00 0.00 0.00 3.01
78 79 7.020827 TCCACTTTCATCTAGTTTCAATCCT 57.979 36.000 0.00 0.00 0.00 3.24
79 80 6.881065 TCCACTTTCATCTAGTTTCAATCCTG 59.119 38.462 0.00 0.00 0.00 3.86
87 88 7.759886 TCATCTAGTTTCAATCCTGTAAAGTCG 59.240 37.037 0.00 0.00 0.00 4.18
108 109 6.044171 AGTCGTACCTAGGACCAGATATAAGT 59.956 42.308 17.98 0.00 40.82 2.24
123 124 9.888878 CCAGATATAAGTTTTGTGAAGCATATG 57.111 33.333 0.00 0.00 0.00 1.78
140 141 6.706295 AGCATATGAGACTAAATTAGAGGGC 58.294 40.000 6.97 0.00 0.00 5.19
158 159 2.352715 GGGCTTTGCACATTTGGAGTAC 60.353 50.000 0.00 0.00 0.00 2.73
163 164 5.437289 TTTGCACATTTGGAGTACAAGAG 57.563 39.130 0.00 0.00 40.82 2.85
246 248 2.264794 CAAAGGACCTCGGACCCG 59.735 66.667 1.31 1.31 41.35 5.28
248 250 1.840198 AAAGGACCTCGGACCCGTT 60.840 57.895 8.42 0.00 40.74 4.44
289 293 9.214953 CACTCTTATTCTTATTTGATTCAACGC 57.785 33.333 0.00 0.00 0.00 4.84
321 325 2.457743 TAAGTGGCGGCGGTGATGTT 62.458 55.000 9.78 0.00 0.00 2.71
326 330 2.885644 CGGCGGTGATGTTCCTCG 60.886 66.667 0.00 0.00 0.00 4.63
365 369 6.776887 ATAATGTCTCCCATCTTCAATCCT 57.223 37.500 0.00 0.00 31.75 3.24
393 397 0.654160 CGGTATGTCTAGCGTCGTCA 59.346 55.000 0.00 0.00 42.41 4.35
410 414 1.418637 GTCAAAGGGTGTGTGGAGGTA 59.581 52.381 0.00 0.00 0.00 3.08
411 415 2.039879 GTCAAAGGGTGTGTGGAGGTAT 59.960 50.000 0.00 0.00 0.00 2.73
412 416 2.039746 TCAAAGGGTGTGTGGAGGTATG 59.960 50.000 0.00 0.00 0.00 2.39
418 422 2.093973 GGTGTGTGGAGGTATGTCTCTG 60.094 54.545 0.00 0.00 34.39 3.35
420 424 2.826128 TGTGTGGAGGTATGTCTCTGTC 59.174 50.000 0.00 0.00 34.39 3.51
426 430 2.554893 GAGGTATGTCTCTGTCGGATCC 59.445 54.545 0.00 0.00 0.00 3.36
427 431 2.175931 AGGTATGTCTCTGTCGGATCCT 59.824 50.000 10.75 0.00 0.00 3.24
430 434 1.924731 TGTCTCTGTCGGATCCTGTT 58.075 50.000 10.75 0.00 0.00 3.16
476 480 4.273480 CGGTGGATATGTTTGGATCAAGTC 59.727 45.833 0.00 0.00 0.00 3.01
499 503 7.033185 GTCTTTGTTCATGTGTTTACAGGTTT 58.967 34.615 0.00 0.00 40.79 3.27
503 507 7.106439 TGTTCATGTGTTTACAGGTTTGATT 57.894 32.000 0.00 0.00 40.79 2.57
508 512 8.474025 TCATGTGTTTACAGGTTTGATTCTTTT 58.526 29.630 0.00 0.00 40.79 2.27
510 514 7.831753 TGTGTTTACAGGTTTGATTCTTTTGA 58.168 30.769 0.00 0.00 31.91 2.69
516 520 7.133891 ACAGGTTTGATTCTTTTGATCTACG 57.866 36.000 0.00 0.00 0.00 3.51
531 535 2.823984 TCTACGACTCTCTCCATCGAC 58.176 52.381 0.00 0.00 39.16 4.20
548 552 1.578583 GACGATGGTTGTTATCCCGG 58.421 55.000 0.00 0.00 0.00 5.73
559 563 0.402504 TTATCCCGGTGCACTGGTTT 59.597 50.000 36.69 26.83 40.86 3.27
566 570 1.227234 GTGCACTGGTTTTGTGGGC 60.227 57.895 10.32 0.00 36.08 5.36
574 579 0.317160 GGTTTTGTGGGCCTTAGCAC 59.683 55.000 4.53 2.24 45.43 4.40
584 589 2.033424 GGGCCTTAGCACGATGATTTTC 59.967 50.000 0.84 0.00 42.56 2.29
585 590 2.033424 GGCCTTAGCACGATGATTTTCC 59.967 50.000 0.00 0.00 42.56 3.13
594 599 2.742053 ACGATGATTTTCCGGTTGTCTG 59.258 45.455 0.00 0.00 0.00 3.51
596 601 1.974265 TGATTTTCCGGTTGTCTGCA 58.026 45.000 0.00 0.00 0.00 4.41
612 617 1.329171 TGCAACAACAAGGCTTGCCT 61.329 50.000 26.45 8.56 39.69 4.75
618 623 1.115326 AACAAGGCTTGCCTGGGTTC 61.115 55.000 26.45 0.00 0.00 3.62
619 624 2.282462 AAGGCTTGCCTGGGTTCG 60.282 61.111 15.52 0.00 0.00 3.95
636 641 1.075525 CGGTGAGGGAGGGGTGATA 60.076 63.158 0.00 0.00 0.00 2.15
640 645 0.689745 TGAGGGAGGGGTGATAACGG 60.690 60.000 0.00 0.00 0.00 4.44
641 646 2.041206 GAGGGAGGGGTGATAACGGC 62.041 65.000 0.00 0.00 0.00 5.68
666 671 1.712977 GCCTTCAGCTCGCTCCAATG 61.713 60.000 0.00 0.00 38.99 2.82
670 675 1.022982 TCAGCTCGCTCCAATGCTTG 61.023 55.000 0.00 0.00 33.03 4.01
674 679 2.009042 GCTCGCTCCAATGCTTGTAGT 61.009 52.381 0.00 0.00 0.00 2.73
675 680 1.929836 CTCGCTCCAATGCTTGTAGTC 59.070 52.381 0.00 0.00 0.00 2.59
676 681 0.647410 CGCTCCAATGCTTGTAGTCG 59.353 55.000 0.00 0.00 0.00 4.18
677 682 1.726853 GCTCCAATGCTTGTAGTCGT 58.273 50.000 0.00 0.00 0.00 4.34
678 683 1.661112 GCTCCAATGCTTGTAGTCGTC 59.339 52.381 0.00 0.00 0.00 4.20
679 684 1.920574 CTCCAATGCTTGTAGTCGTCG 59.079 52.381 0.00 0.00 0.00 5.12
681 686 0.370273 CAATGCTTGTAGTCGTCGCC 59.630 55.000 0.00 0.00 0.00 5.54
682 687 0.037697 AATGCTTGTAGTCGTCGCCA 60.038 50.000 0.00 0.00 0.00 5.69
683 688 0.458543 ATGCTTGTAGTCGTCGCCAG 60.459 55.000 0.00 0.00 0.00 4.85
721 726 7.936584 TCTGGTTGTAATTTTTGTTACCTCTG 58.063 34.615 0.00 0.00 34.43 3.35
724 729 9.575868 TGGTTGTAATTTTTGTTACCTCTGATA 57.424 29.630 0.00 0.00 34.43 2.15
739 745 5.843421 ACCTCTGATATTCTCTTACTGCCAT 59.157 40.000 0.00 0.00 0.00 4.40
744 750 7.234166 TCTGATATTCTCTTACTGCCATGATGA 59.766 37.037 0.00 0.00 0.00 2.92
750 756 7.974482 TCTCTTACTGCCATGATGAATTATG 57.026 36.000 0.00 0.00 0.00 1.90
752 758 6.005823 TCTTACTGCCATGATGAATTATGGG 58.994 40.000 14.08 3.45 42.42 4.00
765 771 6.418057 TGAATTATGGGTTGCAAGTTTCTT 57.582 33.333 0.00 0.00 0.00 2.52
768 774 1.408969 TGGGTTGCAAGTTTCTTCCC 58.591 50.000 11.22 11.22 0.00 3.97
802 808 6.205464 TCAGTTGAGAATAAGAACAAGGCAAG 59.795 38.462 0.00 0.00 0.00 4.01
805 811 5.072741 TGAGAATAAGAACAAGGCAAGCTT 58.927 37.500 0.00 0.00 0.00 3.74
816 822 3.659183 AGGCAAGCTTCAGGTGATTAT 57.341 42.857 0.00 0.00 0.00 1.28
823 829 4.273318 AGCTTCAGGTGATTATTCCCAAC 58.727 43.478 0.00 0.00 0.00 3.77
825 831 4.462483 GCTTCAGGTGATTATTCCCAACAA 59.538 41.667 0.00 0.00 0.00 2.83
872 878 2.436115 GTTTTCCCCTCCTCCGCG 60.436 66.667 0.00 0.00 0.00 6.46
874 880 2.522367 TTTTCCCCTCCTCCGCGTT 61.522 57.895 4.92 0.00 0.00 4.84
982 1003 3.539791 CAAATGCCCGCCATCCCC 61.540 66.667 0.00 0.00 31.43 4.81
990 1011 2.354729 CGCCATCCCCAAGTTCCA 59.645 61.111 0.00 0.00 0.00 3.53
1152 1399 3.756783 CTCTCCCTCCCCGACCCT 61.757 72.222 0.00 0.00 0.00 4.34
1228 1487 1.683629 CCTACGCACTTCTCCTCCTCT 60.684 57.143 0.00 0.00 0.00 3.69
1229 1488 2.096248 CTACGCACTTCTCCTCCTCTT 58.904 52.381 0.00 0.00 0.00 2.85
1230 1489 0.892063 ACGCACTTCTCCTCCTCTTC 59.108 55.000 0.00 0.00 0.00 2.87
1231 1490 0.174617 CGCACTTCTCCTCCTCTTCC 59.825 60.000 0.00 0.00 0.00 3.46
1232 1491 0.174617 GCACTTCTCCTCCTCTTCCG 59.825 60.000 0.00 0.00 0.00 4.30
1233 1492 0.174617 CACTTCTCCTCCTCTTCCGC 59.825 60.000 0.00 0.00 0.00 5.54
1234 1493 0.040499 ACTTCTCCTCCTCTTCCGCT 59.960 55.000 0.00 0.00 0.00 5.52
1235 1494 0.744281 CTTCTCCTCCTCTTCCGCTC 59.256 60.000 0.00 0.00 0.00 5.03
1236 1495 0.333312 TTCTCCTCCTCTTCCGCTCT 59.667 55.000 0.00 0.00 0.00 4.09
1237 1496 0.333312 TCTCCTCCTCTTCCGCTCTT 59.667 55.000 0.00 0.00 0.00 2.85
1238 1497 0.744281 CTCCTCCTCTTCCGCTCTTC 59.256 60.000 0.00 0.00 0.00 2.87
1239 1498 0.684805 TCCTCCTCTTCCGCTCTTCC 60.685 60.000 0.00 0.00 0.00 3.46
1293 1552 4.200283 CCTCTCGCTGTCTCCGCC 62.200 72.222 0.00 0.00 0.00 6.13
1307 1566 3.148279 CGCCGCCTCCTCCTTACT 61.148 66.667 0.00 0.00 0.00 2.24
1405 1664 1.592400 CGCCTTCGTCTCCCTGTACA 61.592 60.000 0.00 0.00 0.00 2.90
1494 1753 0.904649 ACAATGCTCTGATGGACGGA 59.095 50.000 0.00 0.00 0.00 4.69
1767 2026 4.660938 AGCAGGTCCCGGCCAAAC 62.661 66.667 2.24 0.00 37.86 2.93
1795 2054 0.675633 GTGCACAGGGCTTGTTGATT 59.324 50.000 13.17 0.00 45.15 2.57
2301 2560 1.457643 CTCTGTCCTGGCCGGGATA 60.458 63.158 36.01 31.26 37.73 2.59
2358 2617 4.540099 AGGGTTAGGAAACTGATGGATCAA 59.460 41.667 0.00 0.00 43.88 2.57
2397 2656 2.292016 TGTTGGTTGCAGTTCCATTACG 59.708 45.455 7.89 0.00 33.50 3.18
2510 2769 1.220477 GGCTCAGGAAGAGGACAGC 59.780 63.158 0.00 0.00 44.86 4.40
2634 2894 2.704190 TCTCCAAGAGTCCAAGACCT 57.296 50.000 0.00 0.00 32.18 3.85
2682 2949 0.436150 CGCGAGTGTGAACATGACAG 59.564 55.000 0.00 0.00 0.00 3.51
2703 2970 6.006449 ACAGTGCATATTCAAGGACTTCTTT 58.994 36.000 0.00 0.00 33.98 2.52
2725 2992 8.420222 TCTTTTCAAGTCAAAATGGATTAGCAA 58.580 29.630 0.00 0.00 0.00 3.91
2744 3011 4.853268 GCAATTAGGTGCAGCTTAGAATC 58.147 43.478 25.47 5.91 44.29 2.52
2750 3017 1.003116 GTGCAGCTTAGAATCCATGCG 60.003 52.381 0.00 0.00 36.47 4.73
2786 3053 3.161866 GGTCTTAATGTTTTCCCTGCCA 58.838 45.455 0.00 0.00 0.00 4.92
2790 3057 1.047801 AATGTTTTCCCTGCCACCAC 58.952 50.000 0.00 0.00 0.00 4.16
2793 3060 1.047801 GTTTTCCCTGCCACCACAAT 58.952 50.000 0.00 0.00 0.00 2.71
2797 3064 2.142356 TCCCTGCCACCACAATAATG 57.858 50.000 0.00 0.00 0.00 1.90
2803 3070 2.094675 GCCACCACAATAATGCTCACT 58.905 47.619 0.00 0.00 0.00 3.41
2810 3077 4.142534 CCACAATAATGCTCACTTGGTCTG 60.143 45.833 0.00 0.00 0.00 3.51
2817 3084 0.319900 CTCACTTGGTCTGGTCGGTG 60.320 60.000 0.00 0.00 0.00 4.94
2820 3087 0.106149 ACTTGGTCTGGTCGGTGTTC 59.894 55.000 0.00 0.00 0.00 3.18
2832 3099 2.622470 GTCGGTGTTCTATACTCCCTCC 59.378 54.545 0.00 0.00 37.15 4.30
2833 3100 1.607628 CGGTGTTCTATACTCCCTCCG 59.392 57.143 0.00 0.00 37.15 4.63
2834 3101 2.664015 GGTGTTCTATACTCCCTCCGT 58.336 52.381 0.00 0.00 34.91 4.69
2835 3102 2.622470 GGTGTTCTATACTCCCTCCGTC 59.378 54.545 0.00 0.00 34.91 4.79
2836 3103 2.622470 GTGTTCTATACTCCCTCCGTCC 59.378 54.545 0.00 0.00 0.00 4.79
2837 3104 2.237643 GTTCTATACTCCCTCCGTCCC 58.762 57.143 0.00 0.00 0.00 4.46
2838 3105 1.526315 TCTATACTCCCTCCGTCCCA 58.474 55.000 0.00 0.00 0.00 4.37
2839 3106 1.854939 TCTATACTCCCTCCGTCCCAA 59.145 52.381 0.00 0.00 0.00 4.12
2840 3107 2.245546 TCTATACTCCCTCCGTCCCAAA 59.754 50.000 0.00 0.00 0.00 3.28
2841 3108 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
2842 3109 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
2843 3110 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
2845 3112 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
2846 3113 1.064979 TCCCTCCGTCCCAAAATAAGC 60.065 52.381 0.00 0.00 0.00 3.09
2847 3114 1.014352 CCTCCGTCCCAAAATAAGCG 58.986 55.000 0.00 0.00 0.00 4.68
2848 3115 1.677820 CCTCCGTCCCAAAATAAGCGT 60.678 52.381 0.00 0.00 0.00 5.07
2849 3116 2.419021 CCTCCGTCCCAAAATAAGCGTA 60.419 50.000 0.00 0.00 0.00 4.42
2850 3117 2.606272 CTCCGTCCCAAAATAAGCGTAC 59.394 50.000 0.00 0.00 0.00 3.67
2851 3118 1.325338 CCGTCCCAAAATAAGCGTACG 59.675 52.381 11.84 11.84 0.00 3.67
2852 3119 2.261345 CGTCCCAAAATAAGCGTACGA 58.739 47.619 21.65 0.00 0.00 3.43
2853 3120 2.028404 CGTCCCAAAATAAGCGTACGAC 59.972 50.000 21.65 10.59 0.00 4.34
2854 3121 3.256558 GTCCCAAAATAAGCGTACGACT 58.743 45.455 21.65 12.91 0.00 4.18
2855 3122 3.681417 GTCCCAAAATAAGCGTACGACTT 59.319 43.478 21.65 22.00 0.00 3.01
2856 3123 4.152938 GTCCCAAAATAAGCGTACGACTTT 59.847 41.667 21.65 11.99 0.00 2.66
2857 3124 5.348451 GTCCCAAAATAAGCGTACGACTTTA 59.652 40.000 21.65 13.79 0.00 1.85
2858 3125 6.036408 GTCCCAAAATAAGCGTACGACTTTAT 59.964 38.462 21.65 15.37 0.00 1.40
2859 3126 7.222611 GTCCCAAAATAAGCGTACGACTTTATA 59.777 37.037 21.65 7.54 0.00 0.98
2862 3129 9.236691 CCAAAATAAGCGTACGACTTTATACTA 57.763 33.333 21.65 6.18 0.00 1.82
2877 3144 8.186178 ACTTTATACTAAATCAGCGACACTTG 57.814 34.615 0.00 0.00 0.00 3.16
2878 3145 7.817962 ACTTTATACTAAATCAGCGACACTTGT 59.182 33.333 0.00 0.00 0.00 3.16
2884 3153 4.836125 AATCAGCGACACTTGTTTTGAT 57.164 36.364 0.00 0.00 0.00 2.57
2889 3158 2.548057 GCGACACTTGTTTTGATGGAGA 59.452 45.455 0.00 0.00 0.00 3.71
2908 3177 5.191921 TGGAGAGAGTAGTTCAGGTCTATCA 59.808 44.000 0.00 0.00 30.41 2.15
2913 3182 6.249951 AGAGTAGTTCAGGTCTATCAGTGTT 58.750 40.000 0.00 0.00 0.00 3.32
2916 3185 2.654749 TCAGGTCTATCAGTGTTGCG 57.345 50.000 0.00 0.00 0.00 4.85
2927 3196 1.603802 CAGTGTTGCGGAAACTCATGT 59.396 47.619 0.00 0.00 39.70 3.21
2933 3202 0.370273 GCGGAAACTCATGTGCTACG 59.630 55.000 0.00 0.00 0.00 3.51
2937 3206 2.000447 GAAACTCATGTGCTACGGACC 59.000 52.381 0.00 0.00 0.00 4.46
2956 3225 2.504175 ACCACGGTTAGTCCATGCTTAT 59.496 45.455 0.00 0.00 35.57 1.73
2957 3226 3.707611 ACCACGGTTAGTCCATGCTTATA 59.292 43.478 0.00 0.00 35.57 0.98
2970 3239 8.168725 AGTCCATGCTTATAAAAGATGATGGAT 58.831 33.333 0.00 0.00 41.58 3.41
2971 3240 8.800332 GTCCATGCTTATAAAAGATGATGGATT 58.200 33.333 0.00 0.00 41.58 3.01
2972 3241 9.370930 TCCATGCTTATAAAAGATGATGGATTT 57.629 29.630 0.00 0.00 38.41 2.17
2973 3242 9.419297 CCATGCTTATAAAAGATGATGGATTTG 57.581 33.333 0.00 0.00 37.53 2.32
2974 3243 9.419297 CATGCTTATAAAAGATGATGGATTTGG 57.581 33.333 0.00 0.00 34.37 3.28
2975 3244 8.765488 TGCTTATAAAAGATGATGGATTTGGA 57.235 30.769 0.00 0.00 34.37 3.53
2976 3245 9.199645 TGCTTATAAAAGATGATGGATTTGGAA 57.800 29.630 0.00 0.00 34.37 3.53
2977 3246 9.688592 GCTTATAAAAGATGATGGATTTGGAAG 57.311 33.333 0.00 0.00 34.37 3.46
2982 3251 8.655935 AAAAGATGATGGATTTGGAAGTTAGT 57.344 30.769 0.00 0.00 0.00 2.24
2983 3252 9.753674 AAAAGATGATGGATTTGGAAGTTAGTA 57.246 29.630 0.00 0.00 0.00 1.82
2984 3253 9.927081 AAAGATGATGGATTTGGAAGTTAGTAT 57.073 29.630 0.00 0.00 0.00 2.12
2985 3254 8.915057 AGATGATGGATTTGGAAGTTAGTATG 57.085 34.615 0.00 0.00 0.00 2.39
2986 3255 6.942532 TGATGGATTTGGAAGTTAGTATGC 57.057 37.500 0.00 0.00 0.00 3.14
2987 3256 6.422333 TGATGGATTTGGAAGTTAGTATGCA 58.578 36.000 0.00 0.00 0.00 3.96
2988 3257 6.889177 TGATGGATTTGGAAGTTAGTATGCAA 59.111 34.615 0.00 0.00 0.00 4.08
2989 3258 7.395772 TGATGGATTTGGAAGTTAGTATGCAAA 59.604 33.333 0.00 0.00 40.38 3.68
2990 3259 7.156876 TGGATTTGGAAGTTAGTATGCAAAG 57.843 36.000 0.00 0.00 39.65 2.77
2991 3260 6.152661 TGGATTTGGAAGTTAGTATGCAAAGG 59.847 38.462 0.00 0.00 39.65 3.11
2992 3261 5.385509 TTTGGAAGTTAGTATGCAAAGGC 57.614 39.130 0.00 0.00 41.68 4.35
3011 3280 0.609957 CACTCTGGAATTGCTGGGCA 60.610 55.000 3.55 0.00 36.47 5.36
3044 3313 0.467844 AACTGTTCATGTGGCTGGCA 60.468 50.000 0.00 0.00 0.00 4.92
3048 3317 0.108520 GTTCATGTGGCTGGCAATGG 60.109 55.000 5.14 0.00 0.00 3.16
3067 3336 4.295141 TGGAACATAGGATTTGGACGTT 57.705 40.909 0.00 0.00 0.00 3.99
3068 3337 4.258543 TGGAACATAGGATTTGGACGTTC 58.741 43.478 0.00 0.00 0.00 3.95
3071 3340 3.518590 ACATAGGATTTGGACGTTCGAC 58.481 45.455 0.00 0.00 0.00 4.20
3098 3367 1.992519 GCAGACATGGGCTCCAGGAT 61.993 60.000 12.01 0.00 37.52 3.24
3100 3369 1.071385 CAGACATGGGCTCCAGGATAC 59.929 57.143 12.01 4.43 37.52 2.24
3101 3370 0.398318 GACATGGGCTCCAGGATACC 59.602 60.000 12.01 0.00 37.52 2.73
3102 3371 1.062488 ACATGGGCTCCAGGATACCC 61.062 60.000 17.79 17.79 37.52 3.69
3106 3375 1.843832 GGCTCCAGGATACCCCCTC 60.844 68.421 0.00 0.00 33.38 4.30
3107 3376 1.074471 GCTCCAGGATACCCCCTCA 60.074 63.158 0.00 0.00 33.38 3.86
3121 3390 0.809385 CCCTCAGCATGCTTCTTGTG 59.191 55.000 19.98 6.76 34.76 3.33
3170 3441 6.688578 TCACATTCTCCTAAACTGTGTACTC 58.311 40.000 0.00 0.00 38.61 2.59
3212 3484 6.008960 AGTTTTCAGCAAGAGGAGAATCAAT 58.991 36.000 0.00 0.00 36.25 2.57
3214 3486 4.148128 TCAGCAAGAGGAGAATCAATCC 57.852 45.455 0.00 0.00 36.25 3.01
3217 3489 2.216898 CAAGAGGAGAATCAATCCGGC 58.783 52.381 0.00 0.00 42.02 6.13
3218 3490 1.799933 AGAGGAGAATCAATCCGGCT 58.200 50.000 0.00 0.00 42.02 5.52
3263 3535 2.132996 CCAACCTTGGTGGCTTGCA 61.133 57.895 0.00 0.00 43.43 4.08
3265 3537 1.833934 AACCTTGGTGGCTTGCAGG 60.834 57.895 0.00 0.00 40.22 4.85
3266 3538 2.115910 CCTTGGTGGCTTGCAGGA 59.884 61.111 0.00 0.00 0.00 3.86
3290 3644 2.753966 CGGGTGCTTGGCAATCGAG 61.754 63.158 0.00 0.00 41.47 4.04
3298 3652 2.793933 GCTTGGCAATCGAGCTTCAATC 60.794 50.000 0.00 0.00 46.85 2.67
3308 3662 2.353704 CGAGCTTCAATCTGTACCACCA 60.354 50.000 0.00 0.00 0.00 4.17
3316 3670 4.132336 CAATCTGTACCACCATGGATCTG 58.868 47.826 21.47 6.27 40.96 2.90
3351 3705 1.490490 AGAGGAAATGCGGCTATGGAA 59.510 47.619 0.00 0.00 0.00 3.53
3352 3706 1.604278 GAGGAAATGCGGCTATGGAAC 59.396 52.381 0.00 0.00 0.00 3.62
3401 3755 9.255304 GCTGATTTTAGCATATAGAGTATAGCC 57.745 37.037 0.00 0.00 43.17 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.539518 TGCAAACTGATAGGCGCCTA 59.460 50.000 36.88 36.88 0.00 3.93
2 3 0.744414 TCTGCAAACTGATAGGCGCC 60.744 55.000 21.89 21.89 0.00 6.53
3 4 1.063174 CTTCTGCAAACTGATAGGCGC 59.937 52.381 0.00 0.00 0.00 6.53
4 5 2.350522 ACTTCTGCAAACTGATAGGCG 58.649 47.619 0.00 0.00 0.00 5.52
6 7 4.616835 GCCAAACTTCTGCAAACTGATAGG 60.617 45.833 0.00 0.00 0.00 2.57
7 8 4.479619 GCCAAACTTCTGCAAACTGATAG 58.520 43.478 0.00 0.00 0.00 2.08
8 9 3.255642 GGCCAAACTTCTGCAAACTGATA 59.744 43.478 0.00 0.00 0.00 2.15
9 10 2.036346 GGCCAAACTTCTGCAAACTGAT 59.964 45.455 0.00 0.00 0.00 2.90
10 11 1.408702 GGCCAAACTTCTGCAAACTGA 59.591 47.619 0.00 0.00 0.00 3.41
11 12 1.856802 GGCCAAACTTCTGCAAACTG 58.143 50.000 0.00 0.00 0.00 3.16
12 13 0.385390 CGGCCAAACTTCTGCAAACT 59.615 50.000 2.24 0.00 0.00 2.66
13 14 0.383949 TCGGCCAAACTTCTGCAAAC 59.616 50.000 2.24 0.00 0.00 2.93
14 15 1.066908 CTTCGGCCAAACTTCTGCAAA 59.933 47.619 2.24 0.00 0.00 3.68
15 16 0.667993 CTTCGGCCAAACTTCTGCAA 59.332 50.000 2.24 0.00 0.00 4.08
16 17 1.172180 CCTTCGGCCAAACTTCTGCA 61.172 55.000 2.24 0.00 0.00 4.41
17 18 1.581447 CCTTCGGCCAAACTTCTGC 59.419 57.895 2.24 0.00 0.00 4.26
18 19 1.581447 GCCTTCGGCCAAACTTCTG 59.419 57.895 2.24 0.00 44.06 3.02
19 20 4.081050 GCCTTCGGCCAAACTTCT 57.919 55.556 2.24 0.00 44.06 2.85
29 30 4.451900 GGATATATACATTGGGCCTTCGG 58.548 47.826 4.53 0.00 0.00 4.30
30 31 4.164221 AGGGATATATACATTGGGCCTTCG 59.836 45.833 4.53 0.00 0.00 3.79
31 32 5.717119 AGGGATATATACATTGGGCCTTC 57.283 43.478 4.53 0.00 0.00 3.46
32 33 5.044105 GGAAGGGATATATACATTGGGCCTT 60.044 44.000 4.53 0.00 0.00 4.35
33 34 4.478686 GGAAGGGATATATACATTGGGCCT 59.521 45.833 4.53 0.00 0.00 5.19
34 35 4.229582 TGGAAGGGATATATACATTGGGCC 59.770 45.833 0.00 0.00 0.00 5.80
35 36 5.044846 AGTGGAAGGGATATATACATTGGGC 60.045 44.000 0.00 0.00 0.00 5.36
36 37 6.642733 AGTGGAAGGGATATATACATTGGG 57.357 41.667 0.00 0.00 0.00 4.12
37 38 8.163408 TGAAAGTGGAAGGGATATATACATTGG 58.837 37.037 0.00 0.00 0.00 3.16
38 39 9.745018 ATGAAAGTGGAAGGGATATATACATTG 57.255 33.333 0.00 0.00 0.00 2.82
39 40 9.965902 GATGAAAGTGGAAGGGATATATACATT 57.034 33.333 0.00 0.00 0.00 2.71
40 41 9.343994 AGATGAAAGTGGAAGGGATATATACAT 57.656 33.333 0.00 0.00 0.00 2.29
41 42 8.742125 AGATGAAAGTGGAAGGGATATATACA 57.258 34.615 0.00 0.00 0.00 2.29
44 45 8.980832 ACTAGATGAAAGTGGAAGGGATATAT 57.019 34.615 0.00 0.00 0.00 0.86
45 46 8.798975 AACTAGATGAAAGTGGAAGGGATATA 57.201 34.615 0.00 0.00 0.00 0.86
46 47 7.698163 AACTAGATGAAAGTGGAAGGGATAT 57.302 36.000 0.00 0.00 0.00 1.63
47 48 7.182026 TGAAACTAGATGAAAGTGGAAGGGATA 59.818 37.037 0.00 0.00 0.00 2.59
48 49 6.012508 TGAAACTAGATGAAAGTGGAAGGGAT 60.013 38.462 0.00 0.00 0.00 3.85
49 50 5.309543 TGAAACTAGATGAAAGTGGAAGGGA 59.690 40.000 0.00 0.00 0.00 4.20
52 53 7.609532 AGGATTGAAACTAGATGAAAGTGGAAG 59.390 37.037 0.00 0.00 0.00 3.46
68 69 5.930569 AGGTACGACTTTACAGGATTGAAAC 59.069 40.000 0.00 0.00 0.00 2.78
75 76 4.265073 GTCCTAGGTACGACTTTACAGGA 58.735 47.826 9.08 0.00 0.00 3.86
77 78 4.012374 TGGTCCTAGGTACGACTTTACAG 58.988 47.826 9.08 0.00 0.00 2.74
78 79 4.012374 CTGGTCCTAGGTACGACTTTACA 58.988 47.826 9.08 0.00 0.00 2.41
79 80 4.265073 TCTGGTCCTAGGTACGACTTTAC 58.735 47.826 9.08 0.00 0.00 2.01
87 88 8.702819 ACAAAACTTATATCTGGTCCTAGGTAC 58.297 37.037 9.08 5.76 0.00 3.34
123 124 5.065346 GTGCAAAGCCCTCTAATTTAGTCTC 59.935 44.000 3.45 0.00 0.00 3.36
140 141 5.437289 TCTTGTACTCCAAATGTGCAAAG 57.563 39.130 0.00 0.00 38.95 2.77
158 159 3.275143 TCTCTACGAGGAAGAGCTCTTG 58.725 50.000 33.07 20.20 40.30 3.02
163 164 3.440872 TCTTGTTCTCTACGAGGAAGAGC 59.559 47.826 0.00 0.00 40.30 4.09
224 226 0.744771 GTCCGAGGTCCTTTGCATCC 60.745 60.000 0.00 0.00 0.00 3.51
289 293 1.185315 CCACTTATGCCCAACCAAGG 58.815 55.000 0.00 0.00 0.00 3.61
304 308 4.329545 AACATCACCGCCGCCACT 62.330 61.111 0.00 0.00 0.00 4.00
340 344 8.460317 AGGATTGAAGATGGGAGACATTATAT 57.540 34.615 0.00 0.00 40.72 0.86
341 345 7.310052 CGAGGATTGAAGATGGGAGACATTATA 60.310 40.741 0.00 0.00 40.72 0.98
378 382 1.135083 CCCTTTGACGACGCTAGACAT 60.135 52.381 0.00 0.00 0.00 3.06
387 391 0.179067 TCCACACACCCTTTGACGAC 60.179 55.000 0.00 0.00 0.00 4.34
393 397 2.039879 GACATACCTCCACACACCCTTT 59.960 50.000 0.00 0.00 0.00 3.11
410 414 2.151502 ACAGGATCCGACAGAGACAT 57.848 50.000 5.98 0.00 0.00 3.06
411 415 1.546029 CAACAGGATCCGACAGAGACA 59.454 52.381 5.98 0.00 0.00 3.41
412 416 1.134965 CCAACAGGATCCGACAGAGAC 60.135 57.143 5.98 0.00 0.00 3.36
418 422 1.136305 TCGAATCCAACAGGATCCGAC 59.864 52.381 5.98 0.00 42.67 4.79
420 424 2.533266 ATCGAATCCAACAGGATCCG 57.467 50.000 5.98 3.99 40.58 4.18
426 430 2.086869 AGCACCAATCGAATCCAACAG 58.913 47.619 0.00 0.00 0.00 3.16
427 431 2.198827 AGCACCAATCGAATCCAACA 57.801 45.000 0.00 0.00 0.00 3.33
430 434 2.766263 AGACTAGCACCAATCGAATCCA 59.234 45.455 0.00 0.00 0.00 3.41
440 444 0.541063 TCCACCGAAGACTAGCACCA 60.541 55.000 0.00 0.00 0.00 4.17
476 480 7.032580 TCAAACCTGTAAACACATGAACAAAG 58.967 34.615 0.00 0.00 0.00 2.77
499 503 7.397892 AGAGAGTCGTAGATCAAAAGAATCA 57.602 36.000 11.70 0.00 40.67 2.57
503 507 5.254115 TGGAGAGAGTCGTAGATCAAAAGA 58.746 41.667 0.00 0.00 40.67 2.52
508 512 3.069729 TCGATGGAGAGAGTCGTAGATCA 59.930 47.826 0.00 0.00 40.67 2.92
510 514 3.395639 GTCGATGGAGAGAGTCGTAGAT 58.604 50.000 0.00 0.00 40.67 1.98
516 520 2.679355 CATCGTCGATGGAGAGAGTC 57.321 55.000 24.59 0.00 36.51 3.36
531 535 1.295792 CACCGGGATAACAACCATCG 58.704 55.000 6.32 0.00 0.00 3.84
548 552 1.227234 GCCCACAAAACCAGTGCAC 60.227 57.895 9.40 9.40 35.69 4.57
559 563 0.676466 CATCGTGCTAAGGCCCACAA 60.676 55.000 0.00 0.00 37.74 3.33
566 570 2.287915 CCGGAAAATCATCGTGCTAAGG 59.712 50.000 0.00 0.00 0.00 2.69
574 579 2.476185 GCAGACAACCGGAAAATCATCG 60.476 50.000 9.46 0.00 0.00 3.84
594 599 0.877213 CAGGCAAGCCTTGTTGTTGC 60.877 55.000 11.67 0.00 45.70 4.17
596 601 1.402107 CCCAGGCAAGCCTTGTTGTT 61.402 55.000 11.67 0.00 45.70 2.83
604 609 4.660938 ACCGAACCCAGGCAAGCC 62.661 66.667 2.02 2.02 0.00 4.35
612 617 2.606519 CCTCCCTCACCGAACCCA 60.607 66.667 0.00 0.00 0.00 4.51
618 623 0.689745 TTATCACCCCTCCCTCACCG 60.690 60.000 0.00 0.00 0.00 4.94
619 624 0.837940 GTTATCACCCCTCCCTCACC 59.162 60.000 0.00 0.00 0.00 4.02
666 671 1.805945 CCTGGCGACGACTACAAGC 60.806 63.158 0.65 0.00 0.00 4.01
670 675 1.308069 TACCACCTGGCGACGACTAC 61.308 60.000 0.65 0.00 39.32 2.73
674 679 1.980232 ATGTACCACCTGGCGACGA 60.980 57.895 0.00 0.00 39.32 4.20
675 680 1.809619 CATGTACCACCTGGCGACG 60.810 63.158 0.00 0.00 39.32 5.12
676 681 1.449601 CCATGTACCACCTGGCGAC 60.450 63.158 0.00 0.00 39.32 5.19
677 682 0.980754 ATCCATGTACCACCTGGCGA 60.981 55.000 0.00 0.00 34.41 5.54
678 683 0.532862 GATCCATGTACCACCTGGCG 60.533 60.000 0.00 0.00 34.41 5.69
679 684 0.839946 AGATCCATGTACCACCTGGC 59.160 55.000 0.00 0.00 34.41 4.85
681 686 1.839994 ACCAGATCCATGTACCACCTG 59.160 52.381 0.00 0.00 0.00 4.00
682 687 2.239654 CAACCAGATCCATGTACCACCT 59.760 50.000 0.00 0.00 0.00 4.00
683 688 2.026262 ACAACCAGATCCATGTACCACC 60.026 50.000 0.00 0.00 0.00 4.61
721 726 8.789825 ATTCATCATGGCAGTAAGAGAATATC 57.210 34.615 0.00 0.00 0.00 1.63
724 729 9.011095 CATAATTCATCATGGCAGTAAGAGAAT 57.989 33.333 0.00 0.00 0.00 2.40
729 734 5.771666 ACCCATAATTCATCATGGCAGTAAG 59.228 40.000 0.00 0.00 40.41 2.34
739 745 5.999205 AACTTGCAACCCATAATTCATCA 57.001 34.783 0.00 0.00 0.00 3.07
744 750 5.279960 GGGAAGAAACTTGCAACCCATAATT 60.280 40.000 12.84 0.00 36.27 1.40
750 756 1.408969 TGGGAAGAAACTTGCAACCC 58.591 50.000 11.22 11.22 36.72 4.11
777 783 5.620206 TGCCTTGTTCTTATTCTCAACTGA 58.380 37.500 0.00 0.00 0.00 3.41
779 785 5.048434 GCTTGCCTTGTTCTTATTCTCAACT 60.048 40.000 0.00 0.00 0.00 3.16
782 788 4.655963 AGCTTGCCTTGTTCTTATTCTCA 58.344 39.130 0.00 0.00 0.00 3.27
788 794 3.149196 CCTGAAGCTTGCCTTGTTCTTA 58.851 45.455 2.10 0.00 32.78 2.10
802 808 4.016444 TGTTGGGAATAATCACCTGAAGC 58.984 43.478 0.00 0.00 0.00 3.86
805 811 7.178573 TGTATTTGTTGGGAATAATCACCTGA 58.821 34.615 0.00 0.00 0.00 3.86
816 822 4.141135 TGGAGGTCTTGTATTTGTTGGGAA 60.141 41.667 0.00 0.00 0.00 3.97
823 829 7.052873 AGATCAGAATGGAGGTCTTGTATTTG 58.947 38.462 0.00 0.00 36.16 2.32
825 831 6.821616 AGATCAGAATGGAGGTCTTGTATT 57.178 37.500 0.00 0.00 36.16 1.89
982 1003 3.568538 CCATTTTCGCTCTTGGAACTTG 58.431 45.455 0.00 0.00 0.00 3.16
986 1007 0.521291 CGCCATTTTCGCTCTTGGAA 59.479 50.000 0.00 0.00 0.00 3.53
1152 1399 1.669440 GAGGAGCGTGTGGGTGTAA 59.331 57.895 0.00 0.00 0.00 2.41
1203 1450 2.284699 AGAAGTGCGTAGGGGCCT 60.285 61.111 0.84 0.00 0.00 5.19
1213 1460 0.174617 CGGAAGAGGAGGAGAAGTGC 59.825 60.000 0.00 0.00 0.00 4.40
1228 1487 3.771160 GCGGAGGGAAGAGCGGAA 61.771 66.667 0.00 0.00 0.00 4.30
1231 1490 4.214327 GAGGCGGAGGGAAGAGCG 62.214 72.222 0.00 0.00 0.00 5.03
1232 1491 2.762043 AGAGGCGGAGGGAAGAGC 60.762 66.667 0.00 0.00 0.00 4.09
1233 1492 2.485795 CGAGAGGCGGAGGGAAGAG 61.486 68.421 0.00 0.00 36.03 2.85
1234 1493 2.440430 CGAGAGGCGGAGGGAAGA 60.440 66.667 0.00 0.00 36.03 2.87
1293 1552 1.110518 GGAGGAGTAAGGAGGAGGCG 61.111 65.000 0.00 0.00 0.00 5.52
1401 1660 4.695560 AGCCCGTTCTTGCTGTAC 57.304 55.556 0.00 0.00 36.23 2.90
1405 1664 4.269523 TGGCAGCCCGTTCTTGCT 62.270 61.111 9.64 0.00 38.67 3.91
1494 1753 0.179045 GTCGCCCAGCCTTGATGTAT 60.179 55.000 0.00 0.00 0.00 2.29
1713 1972 2.039137 ACCTCCCGTCCCTTCTCC 59.961 66.667 0.00 0.00 0.00 3.71
1767 2026 1.648720 CCCTGTGCACAAGAACACG 59.351 57.895 21.98 7.01 39.71 4.49
1795 2054 3.386078 ACACACCCACATTTTGCATACAA 59.614 39.130 0.00 0.00 0.00 2.41
2043 2302 1.488812 ACGCCATACTTGCCTTCCATA 59.511 47.619 0.00 0.00 0.00 2.74
2199 2458 1.016627 CATTCCCGTGCATTCGACAT 58.983 50.000 0.00 0.00 0.00 3.06
2244 2503 0.108945 GGTTGAGCTCCAGCAAATGC 60.109 55.000 12.15 0.00 45.16 3.56
2301 2560 0.477204 ACCTGCCAGCATCTGCATAT 59.523 50.000 4.79 0.00 45.16 1.78
2358 2617 4.263506 CCAACATTTCTCCTACCAGTCCTT 60.264 45.833 0.00 0.00 0.00 3.36
2397 2656 5.163540 ACTCAGTATGTCTTATTGGTCCGTC 60.164 44.000 0.00 0.00 37.40 4.79
2441 2700 7.737869 TCTAGGTAGAATCTACTACACTCAGG 58.262 42.308 18.64 4.00 42.91 3.86
2634 2894 5.643777 GCAGCATAAAGTTCAAAGAGGTCTA 59.356 40.000 0.00 0.00 0.00 2.59
2682 2949 6.913170 TGAAAAGAAGTCCTTGAATATGCAC 58.087 36.000 0.00 0.00 34.79 4.57
2703 2970 9.859427 CTAATTGCTAATCCATTTTGACTTGAA 57.141 29.630 0.00 0.00 0.00 2.69
2718 2985 5.684704 TCTAAGCTGCACCTAATTGCTAAT 58.315 37.500 1.02 0.00 43.41 1.73
2725 2992 4.778213 TGGATTCTAAGCTGCACCTAAT 57.222 40.909 1.02 0.00 0.00 1.73
2744 3011 3.496130 CCAGAGAATAGCTAAACGCATGG 59.504 47.826 0.00 0.00 42.61 3.66
2750 3017 8.950208 ACATTAAGACCAGAGAATAGCTAAAC 57.050 34.615 0.00 0.00 0.00 2.01
2766 3033 3.056821 GGTGGCAGGGAAAACATTAAGAC 60.057 47.826 0.00 0.00 0.00 3.01
2786 3053 3.758554 GACCAAGTGAGCATTATTGTGGT 59.241 43.478 0.00 0.00 40.76 4.16
2790 3057 4.012374 ACCAGACCAAGTGAGCATTATTG 58.988 43.478 0.00 0.00 0.00 1.90
2793 3060 2.353704 CGACCAGACCAAGTGAGCATTA 60.354 50.000 0.00 0.00 0.00 1.90
2797 3064 1.374758 CCGACCAGACCAAGTGAGC 60.375 63.158 0.00 0.00 0.00 4.26
2803 3070 1.707106 TAGAACACCGACCAGACCAA 58.293 50.000 0.00 0.00 0.00 3.67
2810 3077 2.622470 GAGGGAGTATAGAACACCGACC 59.378 54.545 0.00 0.00 39.58 4.79
2817 3084 2.237643 GGGACGGAGGGAGTATAGAAC 58.762 57.143 0.00 0.00 0.00 3.01
2820 3087 2.376695 TTGGGACGGAGGGAGTATAG 57.623 55.000 0.00 0.00 0.00 1.31
2832 3099 2.028404 GTCGTACGCTTATTTTGGGACG 59.972 50.000 11.24 0.00 0.00 4.79
2833 3100 3.256558 AGTCGTACGCTTATTTTGGGAC 58.743 45.455 11.24 0.00 0.00 4.46
2834 3101 3.598019 AGTCGTACGCTTATTTTGGGA 57.402 42.857 11.24 0.00 0.00 4.37
2835 3102 4.673534 AAAGTCGTACGCTTATTTTGGG 57.326 40.909 20.05 0.00 0.00 4.12
2836 3103 8.123445 AGTATAAAGTCGTACGCTTATTTTGG 57.877 34.615 20.05 0.00 0.00 3.28
2842 3109 9.655769 CTGATTTAGTATAAAGTCGTACGCTTA 57.344 33.333 20.05 13.48 0.00 3.09
2843 3110 7.167136 GCTGATTTAGTATAAAGTCGTACGCTT 59.833 37.037 11.24 14.16 0.00 4.68
2845 3112 6.397274 CGCTGATTTAGTATAAAGTCGTACGC 60.397 42.308 11.24 5.97 0.00 4.42
2846 3113 6.847792 TCGCTGATTTAGTATAAAGTCGTACG 59.152 38.462 9.53 9.53 0.00 3.67
2847 3114 7.641411 TGTCGCTGATTTAGTATAAAGTCGTAC 59.359 37.037 0.00 0.00 0.00 3.67
2848 3115 7.641411 GTGTCGCTGATTTAGTATAAAGTCGTA 59.359 37.037 0.00 0.00 0.00 3.43
2849 3116 6.471519 GTGTCGCTGATTTAGTATAAAGTCGT 59.528 38.462 0.00 0.00 0.00 4.34
2850 3117 6.691818 AGTGTCGCTGATTTAGTATAAAGTCG 59.308 38.462 0.00 0.00 0.00 4.18
2851 3118 7.988904 AGTGTCGCTGATTTAGTATAAAGTC 57.011 36.000 0.00 0.00 0.00 3.01
2852 3119 7.817962 ACAAGTGTCGCTGATTTAGTATAAAGT 59.182 33.333 0.00 0.00 0.00 2.66
2853 3120 8.186178 ACAAGTGTCGCTGATTTAGTATAAAG 57.814 34.615 0.00 0.00 0.00 1.85
2854 3121 8.542497 AACAAGTGTCGCTGATTTAGTATAAA 57.458 30.769 0.00 0.00 0.00 1.40
2855 3122 8.542497 AAACAAGTGTCGCTGATTTAGTATAA 57.458 30.769 0.00 0.00 0.00 0.98
2856 3123 8.440059 CAAAACAAGTGTCGCTGATTTAGTATA 58.560 33.333 0.00 0.00 0.00 1.47
2857 3124 7.172532 TCAAAACAAGTGTCGCTGATTTAGTAT 59.827 33.333 0.00 0.00 0.00 2.12
2858 3125 6.480651 TCAAAACAAGTGTCGCTGATTTAGTA 59.519 34.615 0.00 0.00 0.00 1.82
2859 3126 5.295787 TCAAAACAAGTGTCGCTGATTTAGT 59.704 36.000 0.00 0.00 0.00 2.24
2862 3129 4.630894 TCAAAACAAGTGTCGCTGATTT 57.369 36.364 0.00 0.00 0.00 2.17
2877 3144 5.872070 CCTGAACTACTCTCTCCATCAAAAC 59.128 44.000 0.00 0.00 0.00 2.43
2878 3145 5.544176 ACCTGAACTACTCTCTCCATCAAAA 59.456 40.000 0.00 0.00 0.00 2.44
2884 3153 5.191921 TGATAGACCTGAACTACTCTCTCCA 59.808 44.000 0.00 0.00 0.00 3.86
2889 3158 5.822204 ACACTGATAGACCTGAACTACTCT 58.178 41.667 0.00 0.00 0.00 3.24
2908 3177 1.603802 CACATGAGTTTCCGCAACACT 59.396 47.619 0.00 0.00 37.93 3.55
2913 3182 1.438651 GTAGCACATGAGTTTCCGCA 58.561 50.000 0.00 0.00 0.00 5.69
2916 3185 2.000447 GTCCGTAGCACATGAGTTTCC 59.000 52.381 0.00 0.00 0.00 3.13
2927 3196 0.895100 ACTAACCGTGGTCCGTAGCA 60.895 55.000 0.00 0.00 33.66 3.49
2956 3225 9.753674 ACTAACTTCCAAATCCATCATCTTTTA 57.246 29.630 0.00 0.00 0.00 1.52
2957 3226 8.655935 ACTAACTTCCAAATCCATCATCTTTT 57.344 30.769 0.00 0.00 0.00 2.27
2970 3239 4.830046 TGCCTTTGCATACTAACTTCCAAA 59.170 37.500 0.00 0.00 44.23 3.28
2971 3240 4.402829 TGCCTTTGCATACTAACTTCCAA 58.597 39.130 0.00 0.00 44.23 3.53
2972 3241 4.027674 TGCCTTTGCATACTAACTTCCA 57.972 40.909 0.00 0.00 44.23 3.53
2985 3254 1.670967 GCAATTCCAGAGTGCCTTTGC 60.671 52.381 0.00 0.00 38.26 3.68
2986 3255 1.891150 AGCAATTCCAGAGTGCCTTTG 59.109 47.619 0.00 0.00 39.13 2.77
2987 3256 1.891150 CAGCAATTCCAGAGTGCCTTT 59.109 47.619 0.00 0.00 39.13 3.11
2988 3257 1.542492 CAGCAATTCCAGAGTGCCTT 58.458 50.000 0.00 0.00 39.13 4.35
2989 3258 0.323178 CCAGCAATTCCAGAGTGCCT 60.323 55.000 0.00 0.00 39.13 4.75
2990 3259 1.318158 CCCAGCAATTCCAGAGTGCC 61.318 60.000 0.00 0.00 39.13 5.01
2991 3260 1.941999 GCCCAGCAATTCCAGAGTGC 61.942 60.000 0.00 0.00 38.59 4.40
2992 3261 0.609957 TGCCCAGCAATTCCAGAGTG 60.610 55.000 0.00 0.00 34.76 3.51
3011 3280 2.519302 AGTTTGCAAGCCAGCGGT 60.519 55.556 9.92 0.00 37.31 5.68
3015 3284 2.223876 ACATGAACAGTTTGCAAGCCAG 60.224 45.455 9.92 5.77 0.00 4.85
3044 3313 4.855340 ACGTCCAAATCCTATGTTCCATT 58.145 39.130 0.00 0.00 0.00 3.16
3048 3317 4.032558 GTCGAACGTCCAAATCCTATGTTC 59.967 45.833 0.00 0.00 36.32 3.18
3067 3336 2.417787 CCATGTCTGCATCTTCTGTCGA 60.418 50.000 0.00 0.00 31.99 4.20
3068 3337 1.931841 CCATGTCTGCATCTTCTGTCG 59.068 52.381 0.00 0.00 31.99 4.35
3071 3340 1.022735 GCCCATGTCTGCATCTTCTG 58.977 55.000 0.00 0.00 31.99 3.02
3098 3367 0.621571 AGAAGCATGCTGAGGGGGTA 60.622 55.000 23.48 0.00 0.00 3.69
3100 3369 1.035932 CAAGAAGCATGCTGAGGGGG 61.036 60.000 23.48 5.46 0.00 5.40
3101 3370 0.323178 ACAAGAAGCATGCTGAGGGG 60.323 55.000 23.48 12.63 0.00 4.79
3102 3371 0.809385 CACAAGAAGCATGCTGAGGG 59.191 55.000 23.48 14.09 0.00 4.30
3106 3375 1.068748 GGTCACACAAGAAGCATGCTG 60.069 52.381 23.48 12.31 0.00 4.41
3107 3376 1.242076 GGTCACACAAGAAGCATGCT 58.758 50.000 16.30 16.30 0.00 3.79
3121 3390 3.744660 ACATTGTCTTCCTCTTGGTCAC 58.255 45.455 0.00 0.00 34.23 3.67
3152 3421 4.008330 CCGAGAGTACACAGTTTAGGAGA 58.992 47.826 0.00 0.00 0.00 3.71
3170 3441 1.066143 ACTGATACCAAACCTGCCGAG 60.066 52.381 0.00 0.00 0.00 4.63
3212 3484 0.468214 CTGTAGGGATGAGAGCCGGA 60.468 60.000 5.05 0.00 0.00 5.14
3214 3486 1.365633 GCTGTAGGGATGAGAGCCG 59.634 63.158 0.00 0.00 0.00 5.52
3217 3489 2.762887 TCAGTTGCTGTAGGGATGAGAG 59.237 50.000 0.00 0.00 32.61 3.20
3218 3490 2.497675 GTCAGTTGCTGTAGGGATGAGA 59.502 50.000 0.00 0.00 32.61 3.27
3263 3535 3.626924 AAGCACCCGAGCGTTCCT 61.627 61.111 0.00 0.00 40.15 3.36
3265 3537 3.423154 CCAAGCACCCGAGCGTTC 61.423 66.667 0.00 0.00 40.15 3.95
3278 3632 2.681848 AGATTGAAGCTCGATTGCCAAG 59.318 45.455 0.00 0.00 0.00 3.61
3290 3644 2.684881 CCATGGTGGTACAGATTGAAGC 59.315 50.000 2.57 0.00 41.80 3.86
3292 3646 4.474651 AGATCCATGGTGGTACAGATTGAA 59.525 41.667 12.58 0.00 41.80 2.69
3298 3652 2.627515 CCAGATCCATGGTGGTACAG 57.372 55.000 12.58 0.00 41.80 2.74
3308 3662 2.165234 CGATGATCGCTACCAGATCCAT 59.835 50.000 0.41 0.00 42.73 3.41
3316 3670 1.880675 TCCTCTTCGATGATCGCTACC 59.119 52.381 10.45 0.00 40.21 3.18
3322 3676 2.478134 CCGCATTTCCTCTTCGATGATC 59.522 50.000 0.95 0.00 0.00 2.92
3351 3705 0.757188 CCTCTCCATCCGGCTAGTGT 60.757 60.000 0.00 0.00 0.00 3.55
3352 3706 0.468214 TCCTCTCCATCCGGCTAGTG 60.468 60.000 0.00 0.00 0.00 2.74
3353 3707 0.178975 CTCCTCTCCATCCGGCTAGT 60.179 60.000 0.00 0.00 0.00 2.57
3354 3708 1.531739 GCTCCTCTCCATCCGGCTAG 61.532 65.000 0.00 0.00 0.00 3.42
3355 3709 1.531840 GCTCCTCTCCATCCGGCTA 60.532 63.158 0.00 0.00 0.00 3.93
3356 3710 2.841988 GCTCCTCTCCATCCGGCT 60.842 66.667 0.00 0.00 0.00 5.52
3357 3711 3.157252 TGCTCCTCTCCATCCGGC 61.157 66.667 0.00 0.00 0.00 6.13
3358 3712 3.136750 CTGCTCCTCTCCATCCGG 58.863 66.667 0.00 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.