Multiple sequence alignment - TraesCS6A01G319800

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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 TraesCS6A01G319800 chr6A 100.000 4615 0 0 1 4615 555115039 555110425 0.000000e+00 8523.0
1 TraesCS6A01G319800 chr6D 92.713 2086 118 14 1765 3821 409667479 409665399 0.000000e+00 2979.0
2 TraesCS6A01G319800 chr6D 87.876 932 52 24 664 1555 409668751 409667841 0.000000e+00 1038.0
3 TraesCS6A01G319800 chr6D 86.314 738 89 8 3864 4590 409665046 409664310 0.000000e+00 793.0
4 TraesCS6A01G319800 chr6D 86.522 230 8 4 1552 1769 409667813 409667595 9.990000e-57 231.0
5 TraesCS6A01G319800 chr6D 85.106 188 15 8 743 923 409670841 409670660 3.670000e-41 180.0
6 TraesCS6A01G319800 chr6B 91.578 2078 127 24 1758 3828 615640781 615638745 0.000000e+00 2824.0
7 TraesCS6A01G319800 chr6B 88.860 772 72 9 3855 4615 615638566 615637798 0.000000e+00 937.0
8 TraesCS6A01G319800 chr6B 86.194 833 54 44 657 1462 615641991 615641193 0.000000e+00 845.0
9 TraesCS6A01G319800 chr6B 95.455 44 2 0 1512 1555 615641169 615641126 2.300000e-08 71.3
10 TraesCS6A01G319800 chr6B 96.970 33 0 1 1552 1583 615641099 615641067 2.000000e-03 54.7
11 TraesCS6A01G319800 chr4D 85.315 572 66 13 2 561 56734382 56734947 4.000000e-160 575.0
12 TraesCS6A01G319800 chr4B 83.566 572 73 13 2 561 83309597 83310159 2.460000e-142 516.0
13 TraesCS6A01G319800 chr4B 78.893 578 102 16 9 578 662460643 662460078 1.570000e-99 374.0
14 TraesCS6A01G319800 chr3A 83.392 566 81 8 2 558 56054390 56054951 3.180000e-141 512.0
15 TraesCS6A01G319800 chr4A 84.601 526 67 10 2 517 540063792 540063271 1.150000e-140 510.0
16 TraesCS6A01G319800 chr7D 82.542 590 79 19 2 573 528032556 528033139 8.920000e-137 497.0
17 TraesCS6A01G319800 chr5D 84.252 508 70 9 2 506 6370556 6370056 1.930000e-133 486.0
18 TraesCS6A01G319800 chr2B 85.867 467 46 13 3 456 680758962 680759421 3.230000e-131 479.0
19 TraesCS6A01G319800 chr7B 85.033 461 55 7 2 451 562985120 562985577 1.510000e-124 457.0


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 TraesCS6A01G319800 chr6A 555110425 555115039 4614 True 8523.0 8523 100.0000 1 4615 1 chr6A.!!$R1 4614
1 TraesCS6A01G319800 chr6D 409664310 409670841 6531 True 1044.2 2979 87.7062 664 4590 5 chr6D.!!$R1 3926
2 TraesCS6A01G319800 chr6B 615637798 615641991 4193 True 946.4 2824 91.8114 657 4615 5 chr6B.!!$R1 3958
3 TraesCS6A01G319800 chr4D 56734382 56734947 565 False 575.0 575 85.3150 2 561 1 chr4D.!!$F1 559
4 TraesCS6A01G319800 chr4B 83309597 83310159 562 False 516.0 516 83.5660 2 561 1 chr4B.!!$F1 559
5 TraesCS6A01G319800 chr4B 662460078 662460643 565 True 374.0 374 78.8930 9 578 1 chr4B.!!$R1 569
6 TraesCS6A01G319800 chr3A 56054390 56054951 561 False 512.0 512 83.3920 2 558 1 chr3A.!!$F1 556
7 TraesCS6A01G319800 chr4A 540063271 540063792 521 True 510.0 510 84.6010 2 517 1 chr4A.!!$R1 515
8 TraesCS6A01G319800 chr7D 528032556 528033139 583 False 497.0 497 82.5420 2 573 1 chr7D.!!$F1 571
9 TraesCS6A01G319800 chr5D 6370056 6370556 500 True 486.0 486 84.2520 2 506 1 chr5D.!!$R1 504

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
370 374 0.037697 CCGAGATGGTGTGGTCGAAA 60.038 55.0 0.00 0.00 34.28 3.46 F
502 554 0.038166 ACTTTGGACGATGGCATGGT 59.962 50.0 15.31 15.31 0.00 3.55 F
1874 3562 0.109412 ACGCTACTGTTACGTGCCTC 60.109 55.0 0.00 0.00 38.85 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1962 3653 0.179111 CAAATCTGAGGTAGGCGCGA 60.179 55.0 12.1 0.0 0.00 5.87 R
2236 3935 0.539986 TAGATGGAAAGTGGGGCGAC 59.460 55.0 0.0 0.0 0.00 5.19 R
3839 5601 0.317269 CGACATGGCATCATTTCGGC 60.317 55.0 0.0 0.0 44.91 5.54 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
33 34 0.449388 GAGCAAATGGACGCCTTCAG 59.551 55.000 0.00 0.00 0.00 3.02
113 114 2.046892 GAGGCGGAGAAGCAAGCA 60.047 61.111 0.00 0.00 39.27 3.91
154 155 0.899717 GCCAATGCCAAGACCAAGGA 60.900 55.000 0.00 0.00 0.00 3.36
172 173 4.950205 AGGAAAAAGAAGTGGTACTCGA 57.050 40.909 0.00 0.00 0.00 4.04
186 187 3.058155 GGTACTCGATAGCATGATGACGT 60.058 47.826 0.00 0.00 0.00 4.34
215 216 4.099633 AGATCATGAAGGTGGACTTGAGA 58.900 43.478 0.00 0.00 40.21 3.27
216 217 3.969287 TCATGAAGGTGGACTTGAGAG 57.031 47.619 0.00 0.00 40.21 3.20
220 221 1.070758 GAAGGTGGACTTGAGAGCACA 59.929 52.381 0.00 0.00 40.21 4.57
222 223 0.681733 GGTGGACTTGAGAGCACAGA 59.318 55.000 0.00 0.00 0.00 3.41
239 240 1.889829 CAGAGTTGTCGAGGAAGAGGT 59.110 52.381 0.00 0.00 0.00 3.85
370 374 0.037697 CCGAGATGGTGTGGTCGAAA 60.038 55.000 0.00 0.00 34.28 3.46
378 383 3.192922 GTGGTCGAAATCCCGCCG 61.193 66.667 0.00 0.00 0.00 6.46
409 425 4.988598 CCGGCCGCTGACAAGTGT 62.989 66.667 22.85 0.00 31.58 3.55
411 427 2.591715 GGCCGCTGACAAGTGTGT 60.592 61.111 0.00 0.00 42.10 3.72
428 447 5.610398 AGTGTGTCAACATGAACTGTATGA 58.390 37.500 0.00 0.00 38.92 2.15
458 509 5.675684 TTTAGAGGCTGACATGTATGACA 57.324 39.130 0.00 0.00 0.00 3.58
462 513 4.162888 AGAGGCTGACATGTATGACAATCA 59.837 41.667 0.00 0.00 32.55 2.57
502 554 0.038166 ACTTTGGACGATGGCATGGT 59.962 50.000 15.31 15.31 0.00 3.55
532 587 0.249911 ATCTATGACCGCGGGCTTTC 60.250 55.000 34.65 19.78 0.00 2.62
564 619 1.507141 GCGGACATGAAATAGGCCGG 61.507 60.000 8.94 0.00 39.17 6.13
565 620 1.507141 CGGACATGAAATAGGCCGGC 61.507 60.000 21.18 21.18 35.42 6.13
567 622 1.507141 GACATGAAATAGGCCGGCGG 61.507 60.000 24.35 24.35 0.00 6.13
568 623 2.113139 ATGAAATAGGCCGGCGGG 59.887 61.111 29.48 9.71 0.00 6.13
569 624 2.752807 ATGAAATAGGCCGGCGGGT 61.753 57.895 29.48 10.32 34.97 5.28
570 625 2.124445 GAAATAGGCCGGCGGGTT 60.124 61.111 29.48 11.80 34.97 4.11
571 626 2.439519 AAATAGGCCGGCGGGTTG 60.440 61.111 29.48 1.53 34.97 3.77
572 627 4.499633 AATAGGCCGGCGGGTTGG 62.500 66.667 29.48 1.07 34.97 3.77
586 641 2.361104 TTGGACGCAGGGCCAATC 60.361 61.111 6.18 0.00 40.24 2.67
587 642 3.936772 TTGGACGCAGGGCCAATCC 62.937 63.158 6.18 7.39 40.24 3.01
589 644 2.361104 GACGCAGGGCCAATCCAA 60.361 61.111 6.18 0.00 36.21 3.53
591 646 2.212900 GACGCAGGGCCAATCCAAAC 62.213 60.000 6.18 0.00 36.21 2.93
593 648 1.606885 CGCAGGGCCAATCCAAACAT 61.607 55.000 6.18 0.00 36.21 2.71
595 650 1.830477 GCAGGGCCAATCCAAACATAA 59.170 47.619 6.18 0.00 36.21 1.90
597 652 3.307339 GCAGGGCCAATCCAAACATAAAA 60.307 43.478 6.18 0.00 36.21 1.52
598 653 4.252878 CAGGGCCAATCCAAACATAAAAC 58.747 43.478 6.18 0.00 36.21 2.43
600 655 4.535692 AGGGCCAATCCAAACATAAAACAT 59.464 37.500 6.18 0.00 36.21 2.71
602 657 5.815222 GGGCCAATCCAAACATAAAACATAC 59.185 40.000 4.39 0.00 36.21 2.39
603 658 5.518487 GGCCAATCCAAACATAAAACATACG 59.482 40.000 0.00 0.00 34.01 3.06
604 659 6.326375 GCCAATCCAAACATAAAACATACGA 58.674 36.000 0.00 0.00 0.00 3.43
605 660 6.809196 GCCAATCCAAACATAAAACATACGAA 59.191 34.615 0.00 0.00 0.00 3.85
607 662 9.197694 CCAATCCAAACATAAAACATACGAAAA 57.802 29.630 0.00 0.00 0.00 2.29
611 666 9.967346 TCCAAACATAAAACATACGAAAAATGA 57.033 25.926 0.00 0.00 0.00 2.57
624 679 3.001562 CGAAAAATGAACAAAACACGCGT 60.002 39.130 5.58 5.58 0.00 6.01
628 683 1.897641 TGAACAAAACACGCGTTTCC 58.102 45.000 10.22 0.00 44.65 3.13
629 684 1.469308 TGAACAAAACACGCGTTTCCT 59.531 42.857 10.22 0.00 44.65 3.36
630 685 2.095161 TGAACAAAACACGCGTTTCCTT 60.095 40.909 10.22 0.00 44.65 3.36
632 687 1.196200 CAAAACACGCGTTTCCTTGG 58.804 50.000 10.22 0.00 44.65 3.61
633 688 0.812549 AAAACACGCGTTTCCTTGGT 59.187 45.000 10.22 0.00 44.65 3.67
634 689 0.812549 AAACACGCGTTTCCTTGGTT 59.187 45.000 10.22 5.95 41.60 3.67
635 690 0.379316 AACACGCGTTTCCTTGGTTC 59.621 50.000 10.22 0.00 28.09 3.62
636 691 1.083015 CACGCGTTTCCTTGGTTCG 60.083 57.895 10.22 0.00 0.00 3.95
649 704 3.343421 GTTCGGCGCGTTGGAGTT 61.343 61.111 8.43 0.00 0.00 3.01
654 709 3.044305 GCGCGTTGGAGTTGCTCT 61.044 61.111 8.43 0.00 0.00 4.09
655 710 2.856032 CGCGTTGGAGTTGCTCTG 59.144 61.111 0.00 0.00 0.00 3.35
656 711 1.664649 CGCGTTGGAGTTGCTCTGA 60.665 57.895 0.00 0.00 0.00 3.27
658 713 1.569479 GCGTTGGAGTTGCTCTGACC 61.569 60.000 0.00 0.00 0.00 4.02
659 714 1.284982 CGTTGGAGTTGCTCTGACCG 61.285 60.000 0.00 0.00 0.00 4.79
660 715 1.301716 TTGGAGTTGCTCTGACCGC 60.302 57.895 0.00 0.00 0.00 5.68
661 716 2.435059 GGAGTTGCTCTGACCGCC 60.435 66.667 0.00 0.00 0.00 6.13
662 717 2.435059 GAGTTGCTCTGACCGCCC 60.435 66.667 0.00 0.00 0.00 6.13
677 2105 2.772924 CCCCCACCATCCAAAGCT 59.227 61.111 0.00 0.00 0.00 3.74
695 2123 3.437795 GCATCAGCAGGCACGCTT 61.438 61.111 0.00 0.00 41.38 4.68
716 2145 2.433491 TCATCAACGCCGAACCCG 60.433 61.111 0.00 0.00 0.00 5.28
769 2198 2.283388 CACAGCAACCCAGGGCAT 60.283 61.111 4.91 0.00 0.00 4.40
804 2233 1.962822 CGCACAGAAAGCAGGAGCA 60.963 57.895 0.00 0.00 45.49 4.26
809 2238 1.419387 ACAGAAAGCAGGAGCAAGACT 59.581 47.619 0.00 0.00 45.49 3.24
859 2292 4.953868 CGACCACCGACAACGCCA 62.954 66.667 0.00 0.00 41.76 5.69
1035 2509 2.327244 CCGCGAGACGTAGGTAGC 59.673 66.667 8.23 0.00 41.42 3.58
1036 2510 2.053291 CGCGAGACGTAGGTAGCG 60.053 66.667 0.00 14.73 37.93 4.26
1037 2511 2.352115 GCGAGACGTAGGTAGCGC 60.352 66.667 15.50 15.50 40.11 5.92
1038 2512 2.327244 CGAGACGTAGGTAGCGCC 59.673 66.667 2.29 0.00 37.58 6.53
1060 2534 2.485122 CATCTTTTGACGCCGCCC 59.515 61.111 0.00 0.00 0.00 6.13
1081 2555 2.989881 GCCTTTTTCCGGCGGAAGG 61.990 63.158 36.44 33.82 43.06 3.46
1379 2875 1.853646 GCGAGATGGTACGTACGTGAC 60.854 57.143 30.25 21.62 0.00 3.67
1466 2962 2.223947 GGACCACGGCTTTTGTTTCAAT 60.224 45.455 0.00 0.00 0.00 2.57
1475 2971 5.865552 CGGCTTTTGTTTCAATTCTGATGAT 59.134 36.000 0.00 0.00 0.00 2.45
1496 2992 7.416154 TGATTTTTCTGAGTTGTAAGTACCG 57.584 36.000 0.00 0.00 0.00 4.02
1593 3120 2.995939 CGCTGATACTCAAGTTCTGCAA 59.004 45.455 16.34 0.00 33.88 4.08
1656 3183 9.740710 AGATTGTTTTTACCAGTTTATAGCTCT 57.259 29.630 0.00 0.00 0.00 4.09
1709 3259 2.420568 GCCGTCGGGGATGTAGTCA 61.421 63.158 14.38 0.00 38.47 3.41
1731 3281 2.611751 TCACTCAAAATGTGTCGTGTGG 59.388 45.455 0.00 0.00 36.83 4.17
1735 3297 1.065401 CAAAATGTGTCGTGTGGCACT 59.935 47.619 19.83 0.00 36.63 4.40
1738 3300 1.388547 ATGTGTCGTGTGGCACTTTT 58.611 45.000 19.83 0.00 36.63 2.27
1769 3453 0.716108 GTGTGCAGTATGAGCGTGAC 59.284 55.000 0.00 0.00 39.69 3.67
1821 3506 7.420184 AGTTACCTTTATTTTTGTTGCATGC 57.580 32.000 11.82 11.82 0.00 4.06
1828 3513 7.118101 CCTTTATTTTTGTTGCATGCTACACAT 59.882 33.333 30.25 23.28 40.66 3.21
1840 3525 2.805671 TGCTACACATTGTCGACTTTGG 59.194 45.455 17.92 10.20 0.00 3.28
1866 3551 7.062605 GCTAGTTTATGTTTCACGCTACTGTTA 59.937 37.037 0.00 0.00 0.00 2.41
1874 3562 0.109412 ACGCTACTGTTACGTGCCTC 60.109 55.000 0.00 0.00 38.85 4.70
1957 3648 7.331026 AGTGCATTATAGCTAACTGACTTGAA 58.669 34.615 0.00 0.00 34.99 2.69
1977 3668 1.395635 TAATTCGCGCCTACCTCAGA 58.604 50.000 0.00 0.00 0.00 3.27
1978 3669 0.753262 AATTCGCGCCTACCTCAGAT 59.247 50.000 0.00 0.00 0.00 2.90
1982 3673 0.460284 CGCGCCTACCTCAGATTTGT 60.460 55.000 0.00 0.00 0.00 2.83
1993 3684 4.641989 ACCTCAGATTTGTATTGGCATCAC 59.358 41.667 0.00 0.00 0.00 3.06
2053 3744 9.826574 TGTTTTTACTACAGTACAGATTGAAGT 57.173 29.630 0.00 0.00 0.00 3.01
2128 3827 2.099141 TTTCAGAAGATGGCACCTCG 57.901 50.000 0.00 0.00 0.00 4.63
2179 3878 0.328258 TTGGAGGCTTGCTAGTTCCC 59.672 55.000 14.58 6.64 30.65 3.97
2209 3908 6.057533 TGATGAACAATCATGCCTAAGTAGG 58.942 40.000 0.00 0.00 46.30 3.18
2236 3935 5.399596 CCAATCAGTACTGTATCGTCGAATG 59.600 44.000 21.99 4.18 0.00 2.67
2323 4022 0.958822 GTGGCCCACGAACTGAATTT 59.041 50.000 0.00 0.00 0.00 1.82
2371 4070 6.487299 AAGTCTGGTCAGGATATTAAGGTC 57.513 41.667 0.00 0.00 0.00 3.85
2413 4112 2.826128 CTGGACAGCTTACAGTGGTCTA 59.174 50.000 0.00 0.00 0.00 2.59
2474 4173 4.072131 TGCAATCCTTACAAACAGAGTCC 58.928 43.478 0.00 0.00 0.00 3.85
2545 4244 2.886523 TCCTGAAACTTCATGGTTGCTG 59.113 45.455 0.00 0.00 36.46 4.41
2636 4335 6.942532 TGCTGAAGAGTAAAGTTGTTCATT 57.057 33.333 0.00 0.00 0.00 2.57
2637 4336 6.959361 TGCTGAAGAGTAAAGTTGTTCATTC 58.041 36.000 0.00 0.00 0.00 2.67
2651 4353 3.758554 TGTTCATTCTAGCCCTGCTTTTC 59.241 43.478 0.00 0.00 40.44 2.29
2683 4385 6.519382 TCATTTGGCTCATGACTATAGTGAG 58.481 40.000 10.90 11.83 41.69 3.51
2719 4421 9.125906 CTTTTCTTTTGTGAAGATAATCAGCAG 57.874 33.333 0.00 0.00 0.00 4.24
2728 4430 6.867816 GTGAAGATAATCAGCAGTATCTCCAG 59.132 42.308 0.00 0.00 38.67 3.86
2845 4547 2.746362 CCAGAGAGATGCTGTTTTCCAC 59.254 50.000 0.00 0.00 0.00 4.02
3046 4748 3.832527 ACACTTGTTGCCAGAGGTTAAT 58.167 40.909 0.00 0.00 0.00 1.40
3093 4795 1.518903 AAGGCCAAGTCGAAAGCTGC 61.519 55.000 5.01 0.00 0.00 5.25
3106 4808 4.217767 TCGAAAGCTGCTCTAGTTACTTCA 59.782 41.667 1.00 0.00 0.00 3.02
3115 4817 7.253817 GCTGCTCTAGTTACTTCATTAAACTCG 60.254 40.741 0.00 0.00 35.23 4.18
3124 4826 6.295719 ACTTCATTAAACTCGGGATACTGT 57.704 37.500 0.00 0.00 45.94 3.55
3127 4829 6.479972 TCATTAAACTCGGGATACTGTGAT 57.520 37.500 0.00 0.00 45.94 3.06
3128 4830 7.591421 TCATTAAACTCGGGATACTGTGATA 57.409 36.000 0.00 0.00 45.94 2.15
3211 4913 2.341257 CCAAGTCACGAGGAACATCAG 58.659 52.381 0.00 0.00 0.00 2.90
3212 4914 2.029020 CCAAGTCACGAGGAACATCAGA 60.029 50.000 0.00 0.00 0.00 3.27
3325 5027 3.096357 GGGTATGTTGCCCAGGGT 58.904 61.111 7.55 0.00 45.40 4.34
3449 5151 5.336690 GCTCCACCTTTCTATGATTGCAAAA 60.337 40.000 1.71 0.00 0.00 2.44
3537 5239 3.068307 GGGCTTAAGCTAGTCGATCAGAA 59.932 47.826 25.88 0.00 41.70 3.02
3572 5277 3.942748 GTGGTGCGTATTTCCTATCCAAA 59.057 43.478 0.00 0.00 0.00 3.28
3603 5316 3.996150 ACAGTGCAAGCCAATATATGC 57.004 42.857 0.00 0.00 39.22 3.14
3607 5320 5.240183 ACAGTGCAAGCCAATATATGCTTAG 59.760 40.000 9.32 6.48 45.59 2.18
3612 5325 5.916883 GCAAGCCAATATATGCTTAGTTGTG 59.083 40.000 9.32 0.65 45.59 3.33
3632 5345 2.903784 TGTGGTATAGGTGCAACTCTGT 59.096 45.455 8.04 0.00 36.74 3.41
3666 5379 2.473816 GAAAGTGTTTTCTGGCTTGGC 58.526 47.619 0.00 0.00 39.66 4.52
3761 5474 9.817809 TGCTAGTATTAATTTCCTTGTCTGTAG 57.182 33.333 0.00 0.00 0.00 2.74
3821 5583 0.965439 AAGCCATGGCAGCGTTTTTA 59.035 45.000 37.18 0.00 44.88 1.52
3839 5601 3.033184 TGCTGCCGCAGAGTTTTG 58.967 55.556 24.80 0.00 42.25 2.44
3840 5602 2.429739 GCTGCCGCAGAGTTTTGC 60.430 61.111 24.80 3.50 40.67 3.68
3841 5603 2.256461 CTGCCGCAGAGTTTTGCC 59.744 61.111 15.74 0.00 41.01 4.52
3842 5604 3.599792 CTGCCGCAGAGTTTTGCCG 62.600 63.158 15.74 0.00 41.01 5.69
3843 5605 3.353836 GCCGCAGAGTTTTGCCGA 61.354 61.111 0.00 0.00 41.01 5.54
3844 5606 2.903547 GCCGCAGAGTTTTGCCGAA 61.904 57.895 0.00 0.00 41.01 4.30
3845 5607 1.652012 CCGCAGAGTTTTGCCGAAA 59.348 52.632 0.00 0.00 41.01 3.46
3847 5609 1.330306 CGCAGAGTTTTGCCGAAATG 58.670 50.000 0.00 0.00 41.01 2.32
3848 5610 1.069296 CGCAGAGTTTTGCCGAAATGA 60.069 47.619 0.00 0.00 41.01 2.57
3850 5612 2.919229 GCAGAGTTTTGCCGAAATGATG 59.081 45.455 0.00 0.00 38.13 3.07
3851 5613 2.919229 CAGAGTTTTGCCGAAATGATGC 59.081 45.455 0.00 0.00 0.00 3.91
3871 5893 2.223340 GCCATGTCGGATAACTGCAAAG 60.223 50.000 0.00 0.00 36.56 2.77
3873 5895 3.879295 CCATGTCGGATAACTGCAAAGAT 59.121 43.478 0.00 0.00 36.56 2.40
3875 5897 3.270027 TGTCGGATAACTGCAAAGATGG 58.730 45.455 0.00 0.00 0.00 3.51
3957 5980 4.560108 GCAAGAACCAGAAGCATCATTGTT 60.560 41.667 0.00 0.00 0.00 2.83
3960 5983 4.828939 AGAACCAGAAGCATCATTGTTTCA 59.171 37.500 5.56 0.00 43.33 2.69
4002 6028 8.389603 TCTTGTTTGCATTTGAAGAAAATCAAC 58.610 29.630 0.00 0.00 38.95 3.18
4020 6046 8.599624 AAATCAACTTTTCATCCCATCTGTAT 57.400 30.769 0.00 0.00 0.00 2.29
4033 6060 3.873361 CCATCTGTATGGCAGTTGTGTAG 59.127 47.826 0.00 0.00 46.17 2.74
4041 6068 3.202906 TGGCAGTTGTGTAGTGAGTTTC 58.797 45.455 0.00 0.00 0.00 2.78
4042 6069 2.548480 GGCAGTTGTGTAGTGAGTTTCC 59.452 50.000 0.00 0.00 0.00 3.13
4045 6073 5.238583 GCAGTTGTGTAGTGAGTTTCCTAT 58.761 41.667 0.00 0.00 0.00 2.57
4055 6083 5.590818 AGTGAGTTTCCTATAGTTCCTCCA 58.409 41.667 0.00 0.00 0.00 3.86
4063 6091 4.406003 TCCTATAGTTCCTCCAACAGAAGC 59.594 45.833 0.00 0.00 37.48 3.86
4065 6093 2.849294 AGTTCCTCCAACAGAAGCTC 57.151 50.000 0.00 0.00 37.48 4.09
4079 6107 7.373493 CAACAGAAGCTCCATATTCAGTTTTT 58.627 34.615 0.00 0.00 34.23 1.94
4082 6110 6.805271 CAGAAGCTCCATATTCAGTTTTTGTG 59.195 38.462 0.00 0.00 0.00 3.33
4085 6113 6.006449 AGCTCCATATTCAGTTTTTGTGACT 58.994 36.000 0.00 0.00 0.00 3.41
4092 6120 4.066646 TCAGTTTTTGTGACTGATCGGA 57.933 40.909 9.00 0.00 46.21 4.55
4114 6142 1.800805 TTGCAAAGAAGAGAGCCGAG 58.199 50.000 0.00 0.00 0.00 4.63
4115 6143 0.681733 TGCAAAGAAGAGAGCCGAGT 59.318 50.000 0.00 0.00 0.00 4.18
4116 6144 1.893137 TGCAAAGAAGAGAGCCGAGTA 59.107 47.619 0.00 0.00 0.00 2.59
4117 6145 2.094494 TGCAAAGAAGAGAGCCGAGTAG 60.094 50.000 0.00 0.00 0.00 2.57
4119 6147 3.765026 CAAAGAAGAGAGCCGAGTAGAC 58.235 50.000 0.00 0.00 0.00 2.59
4120 6148 1.658994 AGAAGAGAGCCGAGTAGACG 58.341 55.000 0.00 0.00 0.00 4.18
4121 6149 1.065998 AGAAGAGAGCCGAGTAGACGT 60.066 52.381 0.00 0.00 0.00 4.34
4122 6150 2.168106 AGAAGAGAGCCGAGTAGACGTA 59.832 50.000 0.00 0.00 0.00 3.57
4123 6151 1.938625 AGAGAGCCGAGTAGACGTAC 58.061 55.000 0.00 0.00 0.00 3.67
4124 6152 0.936600 GAGAGCCGAGTAGACGTACC 59.063 60.000 0.00 0.00 0.00 3.34
4135 6163 4.013050 AGTAGACGTACCCTTCCTGTAAC 58.987 47.826 0.00 0.00 0.00 2.50
4137 6165 3.233507 AGACGTACCCTTCCTGTAACAA 58.766 45.455 0.00 0.00 0.00 2.83
4139 6167 4.285260 AGACGTACCCTTCCTGTAACAAAT 59.715 41.667 0.00 0.00 0.00 2.32
4178 6209 6.206634 TGTGCTACACCTTTAGATGGAAAAAG 59.793 38.462 0.00 0.00 32.73 2.27
4250 6284 9.491675 AGTGCATGAATGATATTTTTGTTGAAA 57.508 25.926 0.00 0.00 0.00 2.69
4253 6287 9.153721 GCATGAATGATATTTTTGTTGAAAGGA 57.846 29.630 0.00 0.00 0.00 3.36
4280 6314 5.885352 TGAAAGATGTGTCAAAAGGTTCTCA 59.115 36.000 0.00 0.00 0.00 3.27
4292 6326 2.045045 TTCTCAATGGGCCCAGCG 60.045 61.111 31.97 23.15 0.00 5.18
4352 6386 0.331278 CCATTGCCAACCTCCCTGTA 59.669 55.000 0.00 0.00 0.00 2.74
4361 6395 4.137543 CCAACCTCCCTGTAATTGATAGC 58.862 47.826 0.00 0.00 0.00 2.97
4420 6455 6.844696 TTATCTTGCAATCCATCGTACTTC 57.155 37.500 0.00 0.00 0.00 3.01
4483 6518 7.093354 TCACTTCATTCGCATTCTCTATATCC 58.907 38.462 0.00 0.00 0.00 2.59
4604 6639 0.396060 TGCCATTTGCCAAGGGAAAC 59.604 50.000 7.98 0.00 38.20 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 4.276642 AGCATCCTTCTTTTGGATCTTCC 58.723 43.478 0.00 0.00 41.94 3.46
132 133 0.178967 TTGGTCTTGGCATTGGCAGA 60.179 50.000 13.02 10.01 43.71 4.26
134 135 1.186917 CCTTGGTCTTGGCATTGGCA 61.187 55.000 9.11 9.11 43.71 4.92
154 155 5.790593 TGCTATCGAGTACCACTTCTTTTT 58.209 37.500 0.00 0.00 0.00 1.94
172 173 1.762370 TCACCCACGTCATCATGCTAT 59.238 47.619 0.00 0.00 0.00 2.97
186 187 2.025981 CCACCTTCATGATCTTCACCCA 60.026 50.000 0.00 0.00 0.00 4.51
215 216 1.000283 CTTCCTCGACAACTCTGTGCT 60.000 52.381 0.00 0.00 35.30 4.40
216 217 1.000163 TCTTCCTCGACAACTCTGTGC 60.000 52.381 0.00 0.00 35.30 4.57
220 221 2.164338 GACCTCTTCCTCGACAACTCT 58.836 52.381 0.00 0.00 0.00 3.24
222 223 1.996798 TGACCTCTTCCTCGACAACT 58.003 50.000 0.00 0.00 0.00 3.16
239 240 2.419159 CCTGCATCTTCTCGAACCATGA 60.419 50.000 0.00 0.00 0.00 3.07
402 418 4.009675 ACAGTTCATGTTGACACACTTGT 58.990 39.130 0.00 0.00 39.96 3.16
409 425 5.559770 ACCATCATACAGTTCATGTTGACA 58.440 37.500 0.00 0.00 39.96 3.58
411 427 7.523293 AAAACCATCATACAGTTCATGTTGA 57.477 32.000 0.00 0.00 39.96 3.18
447 466 5.595133 TCATGCCAATGATTGTCATACATGT 59.405 36.000 19.12 2.69 40.22 3.21
462 513 2.661718 TCATGTCAGCATCATGCCAAT 58.338 42.857 5.84 0.00 46.52 3.16
502 554 2.162408 CGGTCATAGATCATGCTAGCGA 59.838 50.000 10.77 2.11 35.51 4.93
532 587 4.793071 TCATGTCCGCACACAAATTTTAG 58.207 39.130 0.00 0.00 34.48 1.85
567 622 4.966787 TTGGCCCTGCGTCCAACC 62.967 66.667 0.00 0.00 37.43 3.77
568 623 2.676471 ATTGGCCCTGCGTCCAAC 60.676 61.111 0.00 0.00 44.23 3.77
569 624 2.361104 GATTGGCCCTGCGTCCAA 60.361 61.111 0.00 0.00 45.35 3.53
570 625 4.424711 GGATTGGCCCTGCGTCCA 62.425 66.667 0.00 0.00 0.00 4.02
571 626 3.936772 TTGGATTGGCCCTGCGTCC 62.937 63.158 0.00 0.82 34.97 4.79
572 627 1.976474 TTTGGATTGGCCCTGCGTC 60.976 57.895 0.00 0.00 34.97 5.19
574 629 1.606885 ATGTTTGGATTGGCCCTGCG 61.607 55.000 0.00 0.00 34.97 5.18
575 630 1.484038 TATGTTTGGATTGGCCCTGC 58.516 50.000 0.00 0.00 34.97 4.85
579 634 5.518487 CGTATGTTTTATGTTTGGATTGGCC 59.482 40.000 0.00 0.00 37.10 5.36
580 635 6.326375 TCGTATGTTTTATGTTTGGATTGGC 58.674 36.000 0.00 0.00 0.00 4.52
581 636 8.749841 TTTCGTATGTTTTATGTTTGGATTGG 57.250 30.769 0.00 0.00 0.00 3.16
595 650 8.105135 CGTGTTTTGTTCATTTTTCGTATGTTT 58.895 29.630 0.00 0.00 0.00 2.83
597 652 6.291374 GCGTGTTTTGTTCATTTTTCGTATGT 60.291 34.615 0.00 0.00 0.00 2.29
598 653 6.055805 GCGTGTTTTGTTCATTTTTCGTATG 58.944 36.000 0.00 0.00 0.00 2.39
600 655 4.202558 CGCGTGTTTTGTTCATTTTTCGTA 59.797 37.500 0.00 0.00 0.00 3.43
602 657 3.001562 ACGCGTGTTTTGTTCATTTTTCG 60.002 39.130 12.93 0.00 0.00 3.46
603 658 4.493074 ACGCGTGTTTTGTTCATTTTTC 57.507 36.364 12.93 0.00 0.00 2.29
604 659 4.912528 AACGCGTGTTTTGTTCATTTTT 57.087 31.818 14.98 0.00 33.53 1.94
605 660 4.912528 AAACGCGTGTTTTGTTCATTTT 57.087 31.818 20.85 0.00 45.89 1.82
616 671 0.379316 GAACCAAGGAAACGCGTGTT 59.621 50.000 14.98 10.95 40.98 3.32
617 672 1.768112 CGAACCAAGGAAACGCGTGT 61.768 55.000 14.98 7.31 0.00 4.49
619 674 2.248835 CCGAACCAAGGAAACGCGT 61.249 57.895 5.58 5.58 0.00 6.01
624 679 3.350612 CGCGCCGAACCAAGGAAA 61.351 61.111 0.00 0.00 0.00 3.13
626 681 4.612412 AACGCGCCGAACCAAGGA 62.612 61.111 5.73 0.00 0.00 3.36
628 683 4.383602 CCAACGCGCCGAACCAAG 62.384 66.667 5.73 0.00 0.00 3.61
629 684 4.912485 TCCAACGCGCCGAACCAA 62.912 61.111 5.73 0.00 0.00 3.67
632 687 3.343421 AACTCCAACGCGCCGAAC 61.343 61.111 5.73 0.00 0.00 3.95
633 688 3.342627 CAACTCCAACGCGCCGAA 61.343 61.111 5.73 0.00 0.00 4.30
636 691 4.090057 GAGCAACTCCAACGCGCC 62.090 66.667 5.73 0.00 0.00 6.53
658 713 2.755469 CTTTGGATGGTGGGGGCG 60.755 66.667 0.00 0.00 0.00 6.13
659 714 3.076916 GCTTTGGATGGTGGGGGC 61.077 66.667 0.00 0.00 0.00 5.80
660 715 1.683365 CAGCTTTGGATGGTGGGGG 60.683 63.158 0.00 0.00 0.00 5.40
661 716 2.353610 GCAGCTTTGGATGGTGGGG 61.354 63.158 0.00 0.00 33.98 4.96
662 717 0.974010 ATGCAGCTTTGGATGGTGGG 60.974 55.000 0.00 0.00 33.98 4.61
664 719 1.134367 CTGATGCAGCTTTGGATGGTG 59.866 52.381 2.53 0.00 36.18 4.17
665 720 1.471119 CTGATGCAGCTTTGGATGGT 58.529 50.000 2.53 0.00 0.00 3.55
677 2105 4.710167 AGCGTGCCTGCTGATGCA 62.710 61.111 0.00 0.00 45.28 3.96
695 2123 2.032634 GTTCGGCGTTGATGAGGCA 61.033 57.895 6.85 0.00 40.86 4.75
787 2216 0.240411 CTTGCTCCTGCTTTCTGTGC 59.760 55.000 0.00 0.00 40.48 4.57
788 2217 1.534595 GTCTTGCTCCTGCTTTCTGTG 59.465 52.381 0.00 0.00 40.48 3.66
792 2221 3.045601 TGTAGTCTTGCTCCTGCTTTC 57.954 47.619 0.00 0.00 40.48 2.62
804 2233 1.235724 GGCGTGGCTTTTGTAGTCTT 58.764 50.000 0.00 0.00 0.00 3.01
809 2238 2.311701 CGTCGGCGTGGCTTTTGTA 61.312 57.895 6.85 0.00 0.00 2.41
1032 2506 3.338275 AAAAGATGGGCGGGCGCTA 62.338 57.895 7.64 0.00 41.60 4.26
1035 2509 2.749839 TCAAAAGATGGGCGGGCG 60.750 61.111 0.00 0.00 0.00 6.13
1036 2510 2.885113 GTCAAAAGATGGGCGGGC 59.115 61.111 0.00 0.00 0.00 6.13
1037 2511 3.051392 GCGTCAAAAGATGGGCGGG 62.051 63.158 0.00 0.00 0.00 6.13
1038 2512 2.485122 GCGTCAAAAGATGGGCGG 59.515 61.111 0.00 0.00 0.00 6.13
1260 2744 1.760480 GAGCAGGAGGAGGAGGACC 60.760 68.421 0.00 0.00 0.00 4.46
1379 2875 1.205657 GCGTATCCGTGGTATGTGTG 58.794 55.000 0.00 0.00 36.15 3.82
1428 2924 2.181777 CTAGCGCAGGCGAACTCA 59.818 61.111 18.96 0.00 46.35 3.41
1429 2925 2.583593 CCTAGCGCAGGCGAACTC 60.584 66.667 18.96 0.00 46.35 3.01
1430 2926 3.068691 TCCTAGCGCAGGCGAACT 61.069 61.111 18.96 8.40 45.10 3.01
1431 2927 2.886124 GTCCTAGCGCAGGCGAAC 60.886 66.667 18.96 5.39 45.10 3.95
1439 2935 3.952628 AAAGCCGTGGTCCTAGCGC 62.953 63.158 0.00 0.00 0.00 5.92
1466 2962 9.342308 ACTTACAACTCAGAAAAATCATCAGAA 57.658 29.630 0.00 0.00 0.00 3.02
1475 2971 5.524646 CACCGGTACTTACAACTCAGAAAAA 59.475 40.000 6.87 0.00 0.00 1.94
1496 2992 0.461339 ATGTAACGTCGCCATCCACC 60.461 55.000 0.00 0.00 0.00 4.61
1709 3259 3.250762 CCACACGACACATTTTGAGTGAT 59.749 43.478 0.00 0.00 40.16 3.06
1715 3265 1.065401 AGTGCCACACGACACATTTTG 59.935 47.619 0.00 0.00 39.64 2.44
1769 3453 4.485163 TCAACGCTGATACGATATGGATG 58.515 43.478 0.00 0.00 36.70 3.51
1821 3506 3.067106 AGCCAAAGTCGACAATGTGTAG 58.933 45.455 19.50 4.55 0.00 2.74
1828 3513 5.302360 ACATAAACTAGCCAAAGTCGACAA 58.698 37.500 19.50 0.00 0.00 3.18
1840 3525 5.347907 ACAGTAGCGTGAAACATAAACTAGC 59.652 40.000 0.00 0.00 35.74 3.42
1957 3648 1.961394 TCTGAGGTAGGCGCGAATTAT 59.039 47.619 12.10 0.00 0.00 1.28
1962 3653 0.179111 CAAATCTGAGGTAGGCGCGA 60.179 55.000 12.10 0.00 0.00 5.87
1993 3684 1.542915 CATCCTTTGGTCAAGTGGCAG 59.457 52.381 0.00 0.00 0.00 4.85
1996 3687 3.960571 AGATCATCCTTTGGTCAAGTGG 58.039 45.455 0.00 0.00 37.99 4.00
2078 3769 9.868277 AACAACAGAAAAACATTGTATCAGAAA 57.132 25.926 0.00 0.00 34.24 2.52
2128 3827 1.481871 TGACAACTACCGGAGATCCC 58.518 55.000 9.46 0.00 0.00 3.85
2179 3878 3.613737 GGCATGATTGTTCATCAAAACCG 59.386 43.478 0.00 0.00 45.45 4.44
2209 3908 5.007039 TCGACGATACAGTACTGATTGGTAC 59.993 44.000 29.30 12.66 41.47 3.34
2236 3935 0.539986 TAGATGGAAAGTGGGGCGAC 59.460 55.000 0.00 0.00 0.00 5.19
2279 3978 1.149101 TTCTGGAGGGCCTCTTGTTT 58.851 50.000 31.39 0.00 34.31 2.83
2371 4070 3.118482 AGACCAGATAGTTGCAGTCCATG 60.118 47.826 0.00 0.00 0.00 3.66
2413 4112 3.369892 CGATTGTCAAGATCCTGTTCCCT 60.370 47.826 0.00 0.00 0.00 4.20
2474 4173 2.983402 TTGTCTCCGTCGACAAGTAG 57.017 50.000 17.16 6.73 45.92 2.57
2545 4244 2.341846 TAATGGGGAAATCTGACGGC 57.658 50.000 0.00 0.00 0.00 5.68
2605 4304 5.376625 ACTTTACTCTTCAGCATGTTTCCA 58.623 37.500 0.00 0.00 37.40 3.53
2613 4312 6.767902 AGAATGAACAACTTTACTCTTCAGCA 59.232 34.615 0.00 0.00 0.00 4.41
2636 4335 4.551671 AGATAGAGAAAAGCAGGGCTAGA 58.448 43.478 0.00 0.00 38.25 2.43
2637 4336 4.953940 AGATAGAGAAAAGCAGGGCTAG 57.046 45.455 0.00 0.00 38.25 3.42
2651 4353 6.289834 AGTCATGAGCCAAATGAAGATAGAG 58.710 40.000 0.00 0.00 35.87 2.43
2701 4403 7.147672 TGGAGATACTGCTGATTATCTTCACAA 60.148 37.037 7.66 0.00 36.00 3.33
2719 4421 3.808618 GCCATGGGATTGTCTGGAGATAC 60.809 52.174 15.13 0.00 0.00 2.24
2728 4430 1.144503 AGGATCAGCCATGGGATTGTC 59.855 52.381 15.13 0.00 40.02 3.18
2845 4547 2.249844 ACAAGTAACGTCCCAAGTGG 57.750 50.000 0.00 0.00 0.00 4.00
3093 4795 7.769220 TCCCGAGTTTAATGAAGTAACTAGAG 58.231 38.462 0.00 0.00 32.58 2.43
3106 4808 9.847224 AATTTATCACAGTATCCCGAGTTTAAT 57.153 29.630 0.00 0.00 0.00 1.40
3115 4817 8.506168 TGTTTCTGAATTTATCACAGTATCCC 57.494 34.615 0.00 0.00 33.47 3.85
3123 4825 8.184192 CCCAGTACATGTTTCTGAATTTATCAC 58.816 37.037 23.32 5.25 33.47 3.06
3124 4826 8.106462 TCCCAGTACATGTTTCTGAATTTATCA 58.894 33.333 23.32 0.00 36.38 2.15
3127 4829 7.721842 TGTTCCCAGTACATGTTTCTGAATTTA 59.278 33.333 23.32 10.31 0.00 1.40
3128 4830 6.549364 TGTTCCCAGTACATGTTTCTGAATTT 59.451 34.615 23.32 0.00 0.00 1.82
3211 4913 5.173774 TGTGCATTTTCTTGTCTGAGTTC 57.826 39.130 0.00 0.00 0.00 3.01
3212 4914 5.105797 TGTTGTGCATTTTCTTGTCTGAGTT 60.106 36.000 0.00 0.00 0.00 3.01
3325 5027 2.507484 CATGGCTTCAAACCACTGAGA 58.493 47.619 0.00 0.00 40.82 3.27
3361 5063 4.329545 GGGGCAGTGCGGTTCTCA 62.330 66.667 9.45 0.00 0.00 3.27
3364 5066 3.628646 ATCAGGGGCAGTGCGGTTC 62.629 63.158 9.45 0.00 0.00 3.62
3449 5151 4.079901 TCCCGTATCAGTTCCTCTCTTAGT 60.080 45.833 0.00 0.00 0.00 2.24
3537 5239 2.500098 ACGCACCACATCTACCACTAAT 59.500 45.455 0.00 0.00 0.00 1.73
3572 5277 5.868454 TGGCTTGCACTGTACATATATGAT 58.132 37.500 19.63 6.41 0.00 2.45
3603 5316 4.827692 TGCACCTATACCACACAACTAAG 58.172 43.478 0.00 0.00 0.00 2.18
3607 5320 3.408634 AGTTGCACCTATACCACACAAC 58.591 45.455 0.00 0.00 36.93 3.32
3612 5325 3.611766 ACAGAGTTGCACCTATACCAC 57.388 47.619 0.00 0.00 0.00 4.16
3632 5345 9.077885 AGAAAACACTTTCCTGCAATATAGAAA 57.922 29.630 0.00 0.00 41.72 2.52
3761 5474 4.554973 GCAAGTCGCAGAACATGAAAATAC 59.445 41.667 0.00 0.00 39.69 1.89
3788 5501 3.311322 CCATGGCTTTTTGCATATGCTTG 59.689 43.478 27.13 13.60 45.15 4.01
3803 5516 1.135024 CATAAAAACGCTGCCATGGCT 60.135 47.619 35.53 14.65 42.51 4.75
3828 5590 1.069296 TCATTTCGGCAAAACTCTGCG 60.069 47.619 0.00 0.00 43.60 5.18
3836 5598 1.549620 ACATGGCATCATTTCGGCAAA 59.450 42.857 0.00 0.00 41.43 3.68
3837 5599 1.134753 GACATGGCATCATTTCGGCAA 59.865 47.619 0.00 0.00 41.43 4.52
3839 5601 0.317269 CGACATGGCATCATTTCGGC 60.317 55.000 0.00 0.00 44.91 5.54
3840 5602 3.831729 CGACATGGCATCATTTCGG 57.168 52.632 0.00 0.00 44.91 4.30
3841 5603 1.298602 TCCGACATGGCATCATTTCG 58.701 50.000 0.00 3.73 46.90 3.46
3842 5604 4.516698 AGTTATCCGACATGGCATCATTTC 59.483 41.667 0.00 0.00 37.80 2.17
3843 5605 4.276678 CAGTTATCCGACATGGCATCATTT 59.723 41.667 0.00 0.00 37.80 2.32
3844 5606 3.817084 CAGTTATCCGACATGGCATCATT 59.183 43.478 0.00 0.00 37.80 2.57
3845 5607 3.405831 CAGTTATCCGACATGGCATCAT 58.594 45.455 0.00 0.00 37.80 2.45
3847 5609 1.532868 GCAGTTATCCGACATGGCATC 59.467 52.381 0.00 0.00 37.80 3.91
3848 5610 1.134128 TGCAGTTATCCGACATGGCAT 60.134 47.619 0.00 0.00 37.80 4.40
3850 5612 1.378531 TTGCAGTTATCCGACATGGC 58.621 50.000 0.00 0.00 37.80 4.40
3851 5613 3.270027 TCTTTGCAGTTATCCGACATGG 58.730 45.455 0.00 0.00 40.09 3.66
3861 5725 2.284754 TGGCACCATCTTTGCAGTTA 57.715 45.000 0.00 0.00 42.12 2.24
3910 5933 7.102346 GCAATTGATCCTAGTCTGCAGTATAT 58.898 38.462 14.67 0.83 0.00 0.86
3923 5946 5.178096 TCTGGTTCTTGCAATTGATCCTA 57.822 39.130 10.34 3.72 0.00 2.94
4020 6046 3.202906 GAAACTCACTACACAACTGCCA 58.797 45.455 0.00 0.00 0.00 4.92
4025 6052 7.544915 GGAACTATAGGAAACTCACTACACAAC 59.455 40.741 4.43 0.00 43.67 3.32
4026 6053 7.453752 AGGAACTATAGGAAACTCACTACACAA 59.546 37.037 4.43 0.00 38.77 3.33
4033 6060 5.934402 TGGAGGAACTATAGGAAACTCAC 57.066 43.478 4.43 2.42 41.55 3.51
4041 6068 4.407296 AGCTTCTGTTGGAGGAACTATAGG 59.593 45.833 4.43 0.00 41.55 2.57
4042 6069 5.452636 GGAGCTTCTGTTGGAGGAACTATAG 60.453 48.000 0.00 0.00 41.55 1.31
4045 6073 2.567615 GGAGCTTCTGTTGGAGGAACTA 59.432 50.000 0.00 0.00 41.55 2.24
4055 6083 7.014615 ACAAAAACTGAATATGGAGCTTCTGTT 59.985 33.333 0.00 0.00 42.00 3.16
4079 6107 0.037326 GCAAGGTCCGATCAGTCACA 60.037 55.000 0.00 0.00 0.00 3.58
4082 6110 1.734465 CTTTGCAAGGTCCGATCAGTC 59.266 52.381 0.00 0.00 0.00 3.51
4085 6113 2.038426 TCTTCTTTGCAAGGTCCGATCA 59.962 45.455 8.56 0.00 0.00 2.92
4089 6117 2.072298 CTCTCTTCTTTGCAAGGTCCG 58.928 52.381 8.56 0.00 0.00 4.79
4091 6119 1.809547 GGCTCTCTTCTTTGCAAGGTC 59.190 52.381 8.56 0.00 0.00 3.85
4092 6120 1.879796 CGGCTCTCTTCTTTGCAAGGT 60.880 52.381 8.56 0.00 0.00 3.50
4104 6132 1.473080 GGTACGTCTACTCGGCTCTCT 60.473 57.143 0.00 0.00 34.94 3.10
4106 6134 0.463474 GGGTACGTCTACTCGGCTCT 60.463 60.000 0.00 0.00 34.94 4.09
4108 6136 0.034670 AAGGGTACGTCTACTCGGCT 60.035 55.000 0.00 0.00 34.94 5.52
4109 6137 0.380024 GAAGGGTACGTCTACTCGGC 59.620 60.000 0.00 0.00 34.94 5.54
4110 6138 1.020437 GGAAGGGTACGTCTACTCGG 58.980 60.000 0.00 0.00 34.94 4.63
4111 6139 1.669779 CAGGAAGGGTACGTCTACTCG 59.330 57.143 0.00 0.00 0.00 4.18
4112 6140 2.720915 ACAGGAAGGGTACGTCTACTC 58.279 52.381 0.00 0.00 0.00 2.59
4113 6141 2.895242 ACAGGAAGGGTACGTCTACT 57.105 50.000 0.00 0.00 0.00 2.57
4114 6142 3.758554 TGTTACAGGAAGGGTACGTCTAC 59.241 47.826 0.00 0.00 0.00 2.59
4115 6143 4.032960 TGTTACAGGAAGGGTACGTCTA 57.967 45.455 0.00 0.00 0.00 2.59
4116 6144 2.880443 TGTTACAGGAAGGGTACGTCT 58.120 47.619 0.00 0.00 0.00 4.18
4117 6145 3.665745 TTGTTACAGGAAGGGTACGTC 57.334 47.619 0.00 0.00 0.00 4.34
4119 6147 4.571919 TGATTTGTTACAGGAAGGGTACG 58.428 43.478 0.00 0.00 0.00 3.67
4120 6148 6.433093 ACAATGATTTGTTACAGGAAGGGTAC 59.567 38.462 0.00 0.00 43.57 3.34
4121 6149 6.432783 CACAATGATTTGTTACAGGAAGGGTA 59.567 38.462 0.00 0.00 43.57 3.69
4122 6150 5.243730 CACAATGATTTGTTACAGGAAGGGT 59.756 40.000 0.00 0.00 43.57 4.34
4123 6151 5.476599 TCACAATGATTTGTTACAGGAAGGG 59.523 40.000 0.00 0.00 43.57 3.95
4124 6152 6.573664 TCACAATGATTTGTTACAGGAAGG 57.426 37.500 0.00 0.00 43.57 3.46
4149 6177 6.065374 TCCATCTAAAGGTGTAGCACAAAAA 58.935 36.000 1.61 0.00 35.86 1.94
4151 6179 5.235850 TCCATCTAAAGGTGTAGCACAAA 57.764 39.130 1.61 0.00 35.86 2.83
4152 6180 4.901197 TCCATCTAAAGGTGTAGCACAA 57.099 40.909 1.61 0.00 35.86 3.33
4250 6284 5.709164 CCTTTTGACACATCTTTCAGATCCT 59.291 40.000 0.00 0.00 31.32 3.24
4253 6287 6.774656 AGAACCTTTTGACACATCTTTCAGAT 59.225 34.615 0.00 0.00 34.74 2.90
4274 6308 2.409870 CGCTGGGCCCATTGAGAAC 61.410 63.158 28.82 8.02 0.00 3.01
4280 6314 3.628646 GACTCACGCTGGGCCCATT 62.629 63.158 28.82 10.30 0.00 3.16
4292 6326 0.875908 TGCAAGCGTCTGTGACTCAC 60.876 55.000 1.86 1.86 34.56 3.51
4378 6413 9.888878 CAAGATAATCCTGCAGTAATATTTGTG 57.111 33.333 13.81 4.22 0.00 3.33
4408 6443 3.754850 TCACTTTCTCGAAGTACGATGGA 59.245 43.478 0.00 0.00 46.75 3.41
4410 6445 4.323868 GGTTCACTTTCTCGAAGTACGATG 59.676 45.833 0.00 0.00 46.75 3.84
4413 6448 3.898529 AGGTTCACTTTCTCGAAGTACG 58.101 45.455 0.00 0.00 46.75 3.67
4420 6455 4.822026 AGAATGGTAGGTTCACTTTCTCG 58.178 43.478 0.00 0.00 0.00 4.04
4425 6460 9.588096 AAGAAATTAAGAATGGTAGGTTCACTT 57.412 29.630 0.00 0.00 0.00 3.16
4427 6462 9.841880 GAAAGAAATTAAGAATGGTAGGTTCAC 57.158 33.333 0.00 0.00 0.00 3.18
4483 6518 3.909662 CCAATGGGACTCGCCAAG 58.090 61.111 0.00 0.00 38.95 3.61


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

AutoCloner maintained by Alex Coulton.