Multiple sequence alignment - TraesCS2A01G471400

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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 TraesCS2A01G471400 chr2A 100.000 3371 0 0 1 3371 713537546 713534176 0.000000e+00 6226.0
1 TraesCS2A01G471400 chr2A 87.500 48 3 3 13 57 713537510 713537463 6.000000e-03 52.8
2 TraesCS2A01G471400 chr2A 87.500 48 3 3 37 84 713537534 713537490 6.000000e-03 52.8
3 TraesCS2A01G471400 chr2D 94.542 1649 74 9 999 2646 575346955 575345322 0.000000e+00 2532.0
4 TraesCS2A01G471400 chr2D 94.249 539 23 1 73 611 575347825 575347295 0.000000e+00 817.0
5 TraesCS2A01G471400 chr2D 90.378 582 29 14 2813 3371 575242264 575241687 0.000000e+00 739.0
6 TraesCS2A01G471400 chr2D 88.718 585 36 7 2811 3371 634413164 634412586 0.000000e+00 688.0
7 TraesCS2A01G471400 chr2D 98.507 67 1 0 2692 2758 634413342 634413276 5.910000e-23 119.0
8 TraesCS2A01G471400 chr2D 96.825 63 2 0 2756 2818 634413248 634413186 4.600000e-19 106.0
9 TraesCS2A01G471400 chr2D 97.500 40 0 1 609 648 575347279 575347241 2.170000e-07 67.6
10 TraesCS2A01G471400 chr2B 92.775 1661 97 7 993 2652 691429364 691427726 0.000000e+00 2381.0
11 TraesCS2A01G471400 chr2B 92.298 1649 90 16 999 2646 691357628 691356016 0.000000e+00 2307.0
12 TraesCS2A01G471400 chr2B 93.144 423 20 6 69 490 691447139 691446725 2.220000e-171 612.0
13 TraesCS2A01G471400 chr2B 86.231 581 40 16 2817 3371 691308626 691308060 8.050000e-166 593.0
14 TraesCS2A01G471400 chr2B 94.833 329 17 0 283 611 691358306 691357978 6.450000e-142 514.0
15 TraesCS2A01G471400 chr2B 84.932 219 26 5 74 289 691362362 691362148 7.330000e-52 215.0
16 TraesCS2A01G471400 chr2B 96.032 126 5 0 486 611 691429761 691429636 4.410000e-49 206.0
17 TraesCS2A01G471400 chr2B 95.522 67 3 0 2692 2758 691315989 691315923 1.280000e-19 108.0
18 TraesCS2A01G471400 chr2B 97.500 40 0 1 609 648 691357962 691357924 2.170000e-07 67.6


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 TraesCS2A01G471400 chr2A 713534176 713537546 3370 True 2110.533333 6226 91.666667 1 3371 3 chr2A.!!$R1 3370
1 TraesCS2A01G471400 chr2D 575345322 575347825 2503 True 1138.866667 2532 95.430333 73 2646 3 chr2D.!!$R2 2573
2 TraesCS2A01G471400 chr2D 575241687 575242264 577 True 739.000000 739 90.378000 2813 3371 1 chr2D.!!$R1 558
3 TraesCS2A01G471400 chr2D 634412586 634413342 756 True 304.333333 688 94.683333 2692 3371 3 chr2D.!!$R3 679
4 TraesCS2A01G471400 chr2B 691427726 691429761 2035 True 1293.500000 2381 94.403500 486 2652 2 chr2B.!!$R5 2166
5 TraesCS2A01G471400 chr2B 691356016 691362362 6346 True 775.900000 2307 92.390750 74 2646 4 chr2B.!!$R4 2572
6 TraesCS2A01G471400 chr2B 691308060 691308626 566 True 593.000000 593 86.231000 2817 3371 1 chr2B.!!$R1 554

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
962 4912 0.101219 TCGATCGTGTCATGAGCCAG 59.899 55.0 15.94 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2695 6647 0.391263 GGACGAAAGGGCGTGATCTT 60.391 55.0 0.0 0.0 45.72 2.4 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
19 20 2.189594 TGGCTCAATGTCTTCACCTG 57.810 50.000 0.00 0.00 0.00 4.00
20 21 1.421268 TGGCTCAATGTCTTCACCTGT 59.579 47.619 0.00 0.00 0.00 4.00
21 22 1.808945 GGCTCAATGTCTTCACCTGTG 59.191 52.381 0.00 0.00 0.00 3.66
22 23 2.498167 GCTCAATGTCTTCACCTGTGT 58.502 47.619 0.00 0.00 0.00 3.72
23 24 2.880890 GCTCAATGTCTTCACCTGTGTT 59.119 45.455 0.00 0.00 0.00 3.32
24 25 3.058639 GCTCAATGTCTTCACCTGTGTTC 60.059 47.826 0.00 0.00 0.00 3.18
25 26 3.130633 TCAATGTCTTCACCTGTGTTCG 58.869 45.455 0.00 0.00 0.00 3.95
26 27 1.512926 ATGTCTTCACCTGTGTTCGC 58.487 50.000 0.00 0.00 0.00 4.70
27 28 0.531974 TGTCTTCACCTGTGTTCGCC 60.532 55.000 0.00 0.00 0.00 5.54
28 29 1.300620 TCTTCACCTGTGTTCGCCG 60.301 57.895 0.00 0.00 0.00 6.46
29 30 1.300620 CTTCACCTGTGTTCGCCGA 60.301 57.895 0.00 0.00 0.00 5.54
30 31 1.557443 CTTCACCTGTGTTCGCCGAC 61.557 60.000 0.00 0.00 0.00 4.79
31 32 3.403057 CACCTGTGTTCGCCGACG 61.403 66.667 0.00 0.00 42.01 5.12
40 41 4.395080 TCGCCGACGATGATTCAC 57.605 55.556 0.00 0.00 45.12 3.18
41 42 1.226859 TCGCCGACGATGATTCACC 60.227 57.895 0.00 0.00 45.12 4.02
42 43 1.226974 CGCCGACGATGATTCACCT 60.227 57.895 0.00 0.00 43.93 4.00
43 44 1.482621 CGCCGACGATGATTCACCTG 61.483 60.000 0.00 0.00 43.93 4.00
44 45 0.460284 GCCGACGATGATTCACCTGT 60.460 55.000 0.00 0.00 0.00 4.00
45 46 1.280982 CCGACGATGATTCACCTGTG 58.719 55.000 0.00 0.00 0.00 3.66
46 47 1.404181 CCGACGATGATTCACCTGTGT 60.404 52.381 0.00 0.00 0.00 3.72
47 48 2.337583 CGACGATGATTCACCTGTGTT 58.662 47.619 0.00 0.00 0.00 3.32
48 49 2.736721 CGACGATGATTCACCTGTGTTT 59.263 45.455 0.00 0.00 0.00 2.83
49 50 3.924073 CGACGATGATTCACCTGTGTTTA 59.076 43.478 0.00 0.00 0.00 2.01
50 51 4.201589 CGACGATGATTCACCTGTGTTTAC 60.202 45.833 0.00 0.00 0.00 2.01
51 52 4.637276 ACGATGATTCACCTGTGTTTACA 58.363 39.130 0.00 0.00 35.08 2.41
52 53 5.060506 ACGATGATTCACCTGTGTTTACAA 58.939 37.500 0.00 0.00 36.14 2.41
53 54 5.705441 ACGATGATTCACCTGTGTTTACAAT 59.295 36.000 0.00 0.00 36.14 2.71
54 55 6.023435 CGATGATTCACCTGTGTTTACAATG 58.977 40.000 0.00 0.00 36.14 2.82
55 56 6.128309 CGATGATTCACCTGTGTTTACAATGA 60.128 38.462 0.00 0.00 36.14 2.57
56 57 6.951062 TGATTCACCTGTGTTTACAATGAA 57.049 33.333 8.38 8.38 41.96 2.57
57 58 6.734137 TGATTCACCTGTGTTTACAATGAAC 58.266 36.000 8.20 0.00 41.24 3.18
58 59 4.804608 TCACCTGTGTTTACAATGAACG 57.195 40.909 0.00 0.00 36.14 3.95
59 60 4.443621 TCACCTGTGTTTACAATGAACGA 58.556 39.130 0.00 0.00 36.14 3.85
60 61 5.060506 TCACCTGTGTTTACAATGAACGAT 58.939 37.500 0.00 0.00 36.14 3.73
61 62 5.049749 TCACCTGTGTTTACAATGAACGATG 60.050 40.000 0.00 0.00 36.14 3.84
62 63 5.049749 CACCTGTGTTTACAATGAACGATGA 60.050 40.000 0.00 0.00 36.14 2.92
63 64 5.705441 ACCTGTGTTTACAATGAACGATGAT 59.295 36.000 0.00 0.00 36.14 2.45
64 65 6.206634 ACCTGTGTTTACAATGAACGATGATT 59.793 34.615 0.00 0.00 36.14 2.57
65 66 6.742718 CCTGTGTTTACAATGAACGATGATTC 59.257 38.462 0.00 0.00 36.14 2.52
66 67 7.195839 TGTGTTTACAATGAACGATGATTCA 57.804 32.000 0.00 0.00 42.62 2.57
67 68 7.075121 TGTGTTTACAATGAACGATGATTCAC 58.925 34.615 0.00 0.00 41.29 3.18
68 69 6.523201 GTGTTTACAATGAACGATGATTCACC 59.477 38.462 0.00 0.00 41.29 4.02
69 70 6.429692 TGTTTACAATGAACGATGATTCACCT 59.570 34.615 0.00 0.00 41.29 4.00
70 71 4.952262 ACAATGAACGATGATTCACCTG 57.048 40.909 0.00 0.00 41.29 4.00
71 72 4.326826 ACAATGAACGATGATTCACCTGT 58.673 39.130 0.00 0.00 41.29 4.00
180 188 4.382754 CAGAAAGAAAATTGCTACAACGCC 59.617 41.667 0.00 0.00 0.00 5.68
181 189 4.278419 AGAAAGAAAATTGCTACAACGCCT 59.722 37.500 0.00 0.00 0.00 5.52
182 190 3.559238 AGAAAATTGCTACAACGCCTG 57.441 42.857 0.00 0.00 0.00 4.85
183 191 1.985684 GAAAATTGCTACAACGCCTGC 59.014 47.619 0.00 0.00 0.00 4.85
184 192 0.958091 AAATTGCTACAACGCCTGCA 59.042 45.000 0.00 0.00 0.00 4.41
185 193 0.240945 AATTGCTACAACGCCTGCAC 59.759 50.000 0.00 0.00 35.01 4.57
186 194 1.911293 ATTGCTACAACGCCTGCACG 61.911 55.000 0.00 0.00 35.01 5.34
187 195 3.788766 GCTACAACGCCTGCACGG 61.789 66.667 1.59 0.00 37.37 4.94
212 220 2.358582 CACTGTTGGCTTGTTGATGACA 59.641 45.455 0.00 0.00 36.19 3.58
269 277 0.536006 GCTTGGACTTGTGAGCCAGT 60.536 55.000 0.00 0.00 32.94 4.00
277 285 2.101582 ACTTGTGAGCCAGTCGGATATC 59.898 50.000 0.00 0.00 0.00 1.63
299 4155 3.122278 CGCCATAACCAATATTACCGTCG 59.878 47.826 0.00 0.00 0.00 5.12
308 4164 4.984161 CCAATATTACCGTCGGACGTAAAT 59.016 41.667 26.72 24.29 40.58 1.40
578 4434 3.277742 GACGACGAACTTGTGCGCC 62.278 63.158 4.18 0.00 0.00 6.53
644 4518 3.589288 AGCAAGAGTAGAAGTTCCCCATT 59.411 43.478 0.00 0.00 0.00 3.16
645 4519 3.691609 GCAAGAGTAGAAGTTCCCCATTG 59.308 47.826 0.00 0.75 0.00 2.82
646 4520 3.636153 AGAGTAGAAGTTCCCCATTGC 57.364 47.619 0.00 0.00 0.00 3.56
647 4521 3.185455 AGAGTAGAAGTTCCCCATTGCT 58.815 45.455 0.00 0.00 0.00 3.91
648 4522 3.589288 AGAGTAGAAGTTCCCCATTGCTT 59.411 43.478 0.00 0.00 0.00 3.91
649 4523 4.043435 AGAGTAGAAGTTCCCCATTGCTTT 59.957 41.667 0.00 0.00 0.00 3.51
666 4550 2.666994 GCTTTAGGTACGTCTTGACTGC 59.333 50.000 0.00 0.00 0.00 4.40
667 4551 3.614390 GCTTTAGGTACGTCTTGACTGCT 60.614 47.826 0.00 0.00 0.00 4.24
668 4552 3.844577 TTAGGTACGTCTTGACTGCTC 57.155 47.619 0.00 0.00 0.00 4.26
669 4553 1.912417 AGGTACGTCTTGACTGCTCT 58.088 50.000 0.00 0.00 0.00 4.09
671 4555 1.466024 GGTACGTCTTGACTGCTCTCG 60.466 57.143 0.00 0.00 0.00 4.04
675 4559 0.525761 GTCTTGACTGCTCTCGCTCT 59.474 55.000 0.00 0.00 36.97 4.09
676 4560 0.808125 TCTTGACTGCTCTCGCTCTC 59.192 55.000 0.00 0.00 36.97 3.20
677 4561 0.179140 CTTGACTGCTCTCGCTCTCC 60.179 60.000 0.00 0.00 36.97 3.71
678 4562 0.610509 TTGACTGCTCTCGCTCTCCT 60.611 55.000 0.00 0.00 36.97 3.69
679 4563 1.029408 TGACTGCTCTCGCTCTCCTC 61.029 60.000 0.00 0.00 36.97 3.71
680 4564 1.724582 GACTGCTCTCGCTCTCCTCC 61.725 65.000 0.00 0.00 36.97 4.30
681 4565 1.453745 CTGCTCTCGCTCTCCTCCT 60.454 63.158 0.00 0.00 36.97 3.69
682 4566 1.727511 CTGCTCTCGCTCTCCTCCTG 61.728 65.000 0.00 0.00 36.97 3.86
683 4567 2.489275 GCTCTCGCTCTCCTCCTGG 61.489 68.421 0.00 0.00 0.00 4.45
684 4568 1.827789 CTCTCGCTCTCCTCCTGGG 60.828 68.421 0.00 0.00 0.00 4.45
685 4569 2.043450 CTCGCTCTCCTCCTGGGT 60.043 66.667 0.00 0.00 36.25 4.51
686 4570 2.363018 TCGCTCTCCTCCTGGGTG 60.363 66.667 0.00 0.00 36.25 4.61
687 4571 2.681778 CGCTCTCCTCCTGGGTGT 60.682 66.667 0.00 0.00 36.25 4.16
688 4572 2.985456 GCTCTCCTCCTGGGTGTG 59.015 66.667 0.00 0.00 36.25 3.82
689 4573 1.915769 GCTCTCCTCCTGGGTGTGT 60.916 63.158 0.00 0.00 36.25 3.72
690 4574 1.893919 GCTCTCCTCCTGGGTGTGTC 61.894 65.000 0.00 0.00 36.25 3.67
691 4575 0.252012 CTCTCCTCCTGGGTGTGTCT 60.252 60.000 0.00 0.00 36.25 3.41
692 4576 1.006043 CTCTCCTCCTGGGTGTGTCTA 59.994 57.143 0.00 0.00 36.25 2.59
693 4577 1.006043 TCTCCTCCTGGGTGTGTCTAG 59.994 57.143 0.00 0.00 36.25 2.43
694 4578 1.006043 CTCCTCCTGGGTGTGTCTAGA 59.994 57.143 0.00 0.00 36.25 2.43
695 4579 1.187087 CCTCCTGGGTGTGTCTAGAC 58.813 60.000 16.32 16.32 0.00 2.59
696 4580 1.272760 CCTCCTGGGTGTGTCTAGACT 60.273 57.143 23.01 0.00 0.00 3.24
697 4581 2.096248 CTCCTGGGTGTGTCTAGACTC 58.904 57.143 23.01 19.55 0.00 3.36
698 4582 1.711375 TCCTGGGTGTGTCTAGACTCT 59.289 52.381 23.01 0.00 0.00 3.24
699 4583 2.917600 TCCTGGGTGTGTCTAGACTCTA 59.082 50.000 23.01 7.24 0.00 2.43
700 4584 3.018149 CCTGGGTGTGTCTAGACTCTAC 58.982 54.545 23.01 17.26 0.00 2.59
701 4585 3.308545 CCTGGGTGTGTCTAGACTCTACT 60.309 52.174 23.01 0.00 0.00 2.57
702 4586 4.080469 CCTGGGTGTGTCTAGACTCTACTA 60.080 50.000 23.01 12.92 0.00 1.82
714 4604 5.728937 AGACTCTACTAGGGTGGTATGAA 57.271 43.478 0.00 0.00 0.00 2.57
716 4606 4.216708 ACTCTACTAGGGTGGTATGAAGC 58.783 47.826 0.00 0.00 0.00 3.86
726 4616 3.182967 GTGGTATGAAGCTTGACGAGAG 58.817 50.000 2.10 0.00 0.00 3.20
731 4621 1.357991 GAAGCTTGACGAGAGCCTGC 61.358 60.000 2.10 0.00 41.03 4.85
734 4624 2.922503 TTGACGAGAGCCTGCCCA 60.923 61.111 0.00 0.00 0.00 5.36
735 4625 3.240134 TTGACGAGAGCCTGCCCAC 62.240 63.158 0.00 0.00 0.00 4.61
740 4630 0.107703 CGAGAGCCTGCCCACATTTA 60.108 55.000 0.00 0.00 0.00 1.40
747 4643 2.936202 CCTGCCCACATTTATAGCTGT 58.064 47.619 0.00 0.00 0.00 4.40
753 4649 3.117512 CCCACATTTATAGCTGTTCCCCT 60.118 47.826 0.00 0.00 0.00 4.79
754 4650 3.885297 CCACATTTATAGCTGTTCCCCTG 59.115 47.826 0.00 0.00 0.00 4.45
755 4651 3.316308 CACATTTATAGCTGTTCCCCTGC 59.684 47.826 0.00 0.00 38.23 4.85
758 4654 1.407656 TATAGCTGTTCCCCTGCCCG 61.408 60.000 0.00 0.00 38.70 6.13
784 4680 1.521681 GCATACCCACAGTCGGAGC 60.522 63.158 0.00 0.00 0.00 4.70
787 4683 1.961180 ATACCCACAGTCGGAGCAGC 61.961 60.000 0.00 0.00 0.00 5.25
794 4690 3.127533 GTCGGAGCAGCGCCAAAT 61.128 61.111 16.28 0.00 0.00 2.32
798 4694 1.746615 GGAGCAGCGCCAAATCTGA 60.747 57.895 10.86 0.00 32.26 3.27
800 4696 0.523072 GAGCAGCGCCAAATCTGAAA 59.477 50.000 2.29 0.00 32.26 2.69
801 4697 0.961019 AGCAGCGCCAAATCTGAAAA 59.039 45.000 2.29 0.00 32.26 2.29
802 4698 1.340889 AGCAGCGCCAAATCTGAAAAA 59.659 42.857 2.29 0.00 32.26 1.94
803 4699 2.028748 AGCAGCGCCAAATCTGAAAAAT 60.029 40.909 2.29 0.00 32.26 1.82
804 4700 3.193267 AGCAGCGCCAAATCTGAAAAATA 59.807 39.130 2.29 0.00 32.26 1.40
807 4703 5.163513 CAGCGCCAAATCTGAAAAATAACT 58.836 37.500 2.29 0.00 32.26 2.24
808 4704 5.061311 CAGCGCCAAATCTGAAAAATAACTG 59.939 40.000 2.29 0.00 32.26 3.16
809 4705 5.048083 AGCGCCAAATCTGAAAAATAACTGA 60.048 36.000 2.29 0.00 0.00 3.41
810 4706 5.633182 GCGCCAAATCTGAAAAATAACTGAA 59.367 36.000 0.00 0.00 0.00 3.02
812 4708 7.148590 GCGCCAAATCTGAAAAATAACTGAATT 60.149 33.333 0.00 0.00 0.00 2.17
813 4709 8.375465 CGCCAAATCTGAAAAATAACTGAATTC 58.625 33.333 0.00 0.00 0.00 2.17
820 4716 9.965824 TCTGAAAAATAACTGAATTCAACTTCC 57.034 29.630 9.88 0.00 30.37 3.46
821 4717 9.971922 CTGAAAAATAACTGAATTCAACTTCCT 57.028 29.630 9.88 0.00 30.37 3.36
822 4718 9.748708 TGAAAAATAACTGAATTCAACTTCCTG 57.251 29.630 9.88 0.00 0.00 3.86
823 4719 9.750125 GAAAAATAACTGAATTCAACTTCCTGT 57.250 29.630 9.88 0.00 0.00 4.00
839 4735 2.298163 TCCTGTTTACTTCGGACTGGAC 59.702 50.000 0.00 0.00 36.76 4.02
848 4744 2.579738 GGACTGGACTTCCGAGCC 59.420 66.667 0.00 0.00 39.43 4.70
866 4816 2.885113 GGCCGGCTGGTTTTCATC 59.115 61.111 28.56 0.41 37.67 2.92
868 4818 2.038269 GCCGGCTGGTTTTCATCGA 61.038 57.895 22.15 0.00 37.67 3.59
871 4821 0.443869 CGGCTGGTTTTCATCGAGTG 59.556 55.000 0.00 0.00 0.00 3.51
873 4823 0.169009 GCTGGTTTTCATCGAGTGCC 59.831 55.000 0.00 0.00 0.00 5.01
878 4828 5.092554 TGGTTTTCATCGAGTGCCTATAA 57.907 39.130 0.00 0.00 0.00 0.98
881 4831 6.093495 TGGTTTTCATCGAGTGCCTATAAAAG 59.907 38.462 0.00 0.00 0.00 2.27
883 4833 7.148306 GGTTTTCATCGAGTGCCTATAAAAGAA 60.148 37.037 0.00 0.00 0.00 2.52
884 4834 7.539712 TTTCATCGAGTGCCTATAAAAGAAG 57.460 36.000 0.00 0.00 0.00 2.85
885 4835 5.601662 TCATCGAGTGCCTATAAAAGAAGG 58.398 41.667 0.00 0.00 35.86 3.46
886 4836 4.402056 TCGAGTGCCTATAAAAGAAGGG 57.598 45.455 0.00 0.00 33.17 3.95
887 4837 2.872858 CGAGTGCCTATAAAAGAAGGGC 59.127 50.000 0.00 0.00 42.73 5.19
888 4838 3.432326 CGAGTGCCTATAAAAGAAGGGCT 60.432 47.826 0.00 0.00 42.84 5.19
890 4840 3.783082 AGTGCCTATAAAAGAAGGGCTCT 59.217 43.478 0.00 0.00 42.84 4.09
891 4841 4.130857 GTGCCTATAAAAGAAGGGCTCTC 58.869 47.826 0.00 0.00 42.84 3.20
892 4842 3.136626 TGCCTATAAAAGAAGGGCTCTCC 59.863 47.826 0.00 0.00 42.84 3.71
930 4880 1.226831 GCCTGCAGCGACTAGAGAC 60.227 63.158 8.66 0.00 0.00 3.36
931 4881 1.938657 GCCTGCAGCGACTAGAGACA 61.939 60.000 8.66 0.00 0.00 3.41
932 4882 0.528017 CCTGCAGCGACTAGAGACAA 59.472 55.000 8.66 0.00 0.00 3.18
934 4884 2.458951 CTGCAGCGACTAGAGACAATC 58.541 52.381 0.00 0.00 0.00 2.67
935 4885 2.095461 TGCAGCGACTAGAGACAATCT 58.905 47.619 0.00 0.00 42.47 2.40
936 4886 3.279434 TGCAGCGACTAGAGACAATCTA 58.721 45.455 0.00 0.00 39.64 1.98
937 4887 3.885901 TGCAGCGACTAGAGACAATCTAT 59.114 43.478 0.00 0.00 39.82 1.98
938 4888 4.339530 TGCAGCGACTAGAGACAATCTATT 59.660 41.667 0.00 0.00 39.82 1.73
939 4889 5.163509 TGCAGCGACTAGAGACAATCTATTT 60.164 40.000 0.00 0.00 39.82 1.40
940 4890 5.401079 GCAGCGACTAGAGACAATCTATTTC 59.599 44.000 0.00 0.00 39.82 2.17
941 4891 5.918011 CAGCGACTAGAGACAATCTATTTCC 59.082 44.000 0.00 0.00 39.82 3.13
942 4892 5.594725 AGCGACTAGAGACAATCTATTTCCA 59.405 40.000 0.00 0.00 39.82 3.53
943 4893 6.266558 AGCGACTAGAGACAATCTATTTCCAT 59.733 38.462 0.00 0.00 39.82 3.41
944 4894 6.584563 GCGACTAGAGACAATCTATTTCCATC 59.415 42.308 0.00 0.00 39.82 3.51
945 4895 6.799441 CGACTAGAGACAATCTATTTCCATCG 59.201 42.308 0.00 0.00 39.82 3.84
946 4896 7.308049 CGACTAGAGACAATCTATTTCCATCGA 60.308 40.741 0.00 0.00 39.82 3.59
947 4897 8.415950 ACTAGAGACAATCTATTTCCATCGAT 57.584 34.615 0.00 0.00 39.82 3.59
948 4898 8.519526 ACTAGAGACAATCTATTTCCATCGATC 58.480 37.037 0.00 0.00 39.82 3.69
949 4899 6.385843 AGAGACAATCTATTTCCATCGATCG 58.614 40.000 9.36 9.36 36.10 3.69
950 4900 6.015856 AGAGACAATCTATTTCCATCGATCGT 60.016 38.462 15.94 0.00 36.10 3.73
951 4901 5.923114 AGACAATCTATTTCCATCGATCGTG 59.077 40.000 15.94 12.28 0.00 4.35
952 4902 5.601662 ACAATCTATTTCCATCGATCGTGT 58.398 37.500 15.94 4.17 0.00 4.49
953 4903 5.692204 ACAATCTATTTCCATCGATCGTGTC 59.308 40.000 15.94 0.00 0.00 3.67
954 4904 4.911514 TCTATTTCCATCGATCGTGTCA 57.088 40.909 15.94 0.00 0.00 3.58
955 4905 5.453567 TCTATTTCCATCGATCGTGTCAT 57.546 39.130 15.94 0.00 0.00 3.06
956 4906 5.222631 TCTATTTCCATCGATCGTGTCATG 58.777 41.667 15.94 11.02 0.00 3.07
957 4907 3.518634 TTTCCATCGATCGTGTCATGA 57.481 42.857 15.94 0.00 0.00 3.07
958 4908 2.781945 TCCATCGATCGTGTCATGAG 57.218 50.000 15.94 5.96 0.00 2.90
959 4909 1.135046 CCATCGATCGTGTCATGAGC 58.865 55.000 15.94 0.00 0.00 4.26
960 4910 1.135046 CATCGATCGTGTCATGAGCC 58.865 55.000 15.94 0.00 0.00 4.70
961 4911 0.746659 ATCGATCGTGTCATGAGCCA 59.253 50.000 15.94 0.00 0.00 4.75
962 4912 0.101219 TCGATCGTGTCATGAGCCAG 59.899 55.000 15.94 0.00 0.00 4.85
963 4913 1.485838 CGATCGTGTCATGAGCCAGC 61.486 60.000 7.03 0.00 0.00 4.85
964 4914 1.485838 GATCGTGTCATGAGCCAGCG 61.486 60.000 0.00 0.00 0.00 5.18
965 4915 1.948721 ATCGTGTCATGAGCCAGCGA 61.949 55.000 0.00 4.78 0.00 4.93
966 4916 2.447887 CGTGTCATGAGCCAGCGAC 61.448 63.158 0.00 0.00 0.00 5.19
967 4917 2.103042 GTGTCATGAGCCAGCGACC 61.103 63.158 0.00 0.00 0.00 4.79
968 4918 2.285773 TGTCATGAGCCAGCGACCT 61.286 57.895 0.00 0.00 0.00 3.85
969 4919 0.970427 TGTCATGAGCCAGCGACCTA 60.970 55.000 0.00 0.00 0.00 3.08
970 4920 0.249238 GTCATGAGCCAGCGACCTAG 60.249 60.000 0.00 0.00 0.00 3.02
971 4921 0.684479 TCATGAGCCAGCGACCTAGT 60.684 55.000 0.00 0.00 0.00 2.57
972 4922 1.032794 CATGAGCCAGCGACCTAGTA 58.967 55.000 0.00 0.00 0.00 1.82
973 4923 1.033574 ATGAGCCAGCGACCTAGTAC 58.966 55.000 0.00 0.00 0.00 2.73
974 4924 1.355916 GAGCCAGCGACCTAGTACG 59.644 63.158 0.00 2.19 0.00 3.67
975 4925 1.077930 AGCCAGCGACCTAGTACGA 60.078 57.895 9.42 0.00 0.00 3.43
976 4926 1.063811 GCCAGCGACCTAGTACGAC 59.936 63.158 9.42 2.44 0.00 4.34
977 4927 1.351012 CCAGCGACCTAGTACGACG 59.649 63.158 9.42 0.00 0.00 5.12
978 4928 1.086067 CCAGCGACCTAGTACGACGA 61.086 60.000 0.00 0.00 0.00 4.20
979 4929 0.935898 CAGCGACCTAGTACGACGAT 59.064 55.000 0.00 0.00 0.00 3.73
980 4930 1.070710 CAGCGACCTAGTACGACGATC 60.071 57.143 0.00 0.00 0.00 3.69
981 4931 0.933097 GCGACCTAGTACGACGATCA 59.067 55.000 0.00 0.00 0.00 2.92
982 4932 1.070710 GCGACCTAGTACGACGATCAG 60.071 57.143 0.00 0.00 0.00 2.90
983 4933 1.526041 CGACCTAGTACGACGATCAGG 59.474 57.143 0.00 4.98 0.00 3.86
984 4934 2.800985 CGACCTAGTACGACGATCAGGA 60.801 54.545 0.00 0.00 0.00 3.86
1023 4973 2.401195 GCGTCAGCCAAATCGCTC 59.599 61.111 0.00 0.00 44.28 5.03
1058 5008 3.046087 CCTCACCGTGCAGCAGTG 61.046 66.667 8.22 8.22 0.00 3.66
1067 5017 3.819188 GCAGCAGTGCCACTATCC 58.181 61.111 12.58 0.00 44.72 2.59
1075 5025 2.774351 GCCACTATCCCTGCCCCT 60.774 66.667 0.00 0.00 0.00 4.79
1100 5050 2.617308 ACGTCGAGTATGATGATTCGGT 59.383 45.455 0.00 0.00 34.08 4.69
1160 5110 1.683943 CTCATGGACGATTTGGGCAT 58.316 50.000 0.00 0.00 0.00 4.40
1161 5111 2.849942 CTCATGGACGATTTGGGCATA 58.150 47.619 0.00 0.00 0.00 3.14
1329 5279 0.734253 CAGAGCACGAGTACCAGCAC 60.734 60.000 0.00 0.00 0.00 4.40
1330 5280 1.179174 AGAGCACGAGTACCAGCACA 61.179 55.000 0.00 0.00 0.00 4.57
1521 5471 2.805353 CTCGCGGTCGTCCAAGTG 60.805 66.667 6.13 0.00 36.96 3.16
1560 5510 3.310860 GACCGTGCCCCTCGTCAAT 62.311 63.158 0.00 0.00 0.00 2.57
1608 5558 4.651008 GACGTGGTCGGGTGCGAA 62.651 66.667 0.00 0.00 41.85 4.70
2034 5984 2.588877 CGGGTGATCATGGCGACC 60.589 66.667 0.00 0.00 0.00 4.79
2340 6290 1.591594 CAAGCATATCGACCGCGGT 60.592 57.895 34.89 34.89 38.28 5.68
2479 6430 0.740164 AGAGACATGCTTGCTCGCTG 60.740 55.000 14.04 0.00 33.75 5.18
2501 6452 5.663456 TGTAGGTTGGGTGTTCGATTATAC 58.337 41.667 0.00 0.00 0.00 1.47
2504 6455 5.365619 AGGTTGGGTGTTCGATTATACATC 58.634 41.667 0.00 0.00 0.00 3.06
2533 6484 4.833380 TCGGTCCTCCTCTCATATTTTAGG 59.167 45.833 0.00 0.00 0.00 2.69
2539 6490 8.047310 GTCCTCCTCTCATATTTTAGGTCAAAA 58.953 37.037 0.00 0.00 40.34 2.44
2763 6745 5.018539 TCGACCTGAATAAAATGACCGAT 57.981 39.130 0.00 0.00 0.00 4.18
2859 6870 2.691011 TGCAACCGGTTTTAGCTCTTTT 59.309 40.909 19.55 0.00 0.00 2.27
2862 6873 3.891056 ACCGGTTTTAGCTCTTTTTCG 57.109 42.857 0.00 0.00 0.00 3.46
2863 6874 2.031420 ACCGGTTTTAGCTCTTTTTCGC 60.031 45.455 0.00 0.00 0.00 4.70
2864 6875 2.581637 CGGTTTTAGCTCTTTTTCGCC 58.418 47.619 0.00 0.00 0.00 5.54
2865 6876 2.581637 GGTTTTAGCTCTTTTTCGCCG 58.418 47.619 0.00 0.00 0.00 6.46
2893 6904 3.926821 GAGTCTCGTTCTTCAACTCCT 57.073 47.619 0.00 0.00 32.13 3.69
2925 6936 1.727880 GGTTGCAGCATACGTCGTTTA 59.272 47.619 1.78 0.00 0.00 2.01
2972 6983 2.563013 CTAGCTTGCTGCACCCCCAT 62.563 60.000 0.00 0.00 45.94 4.00
2998 7009 1.337635 CGCTTCTGGTCTTCAAGCTCT 60.338 52.381 0.00 0.00 40.40 4.09
3042 7076 2.666862 TGGCCGTTTGTAGCACCG 60.667 61.111 0.00 0.00 0.00 4.94
3093 7131 2.294791 CACCAAAAATTGCCACCTCGTA 59.705 45.455 0.00 0.00 0.00 3.43
3197 7235 2.915659 TCACCGTCGGGAGTTGCT 60.916 61.111 17.28 0.00 36.97 3.91
3275 7313 2.901840 CCACGGTTGCAGCACTGT 60.902 61.111 2.05 0.00 36.65 3.55
3283 7321 2.113986 GCAGCACTGTTGTCCCCT 59.886 61.111 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.421268 ACAGGTGAAGACATTGAGCCA 59.579 47.619 0.00 0.00 0.00 4.75
1 2 1.808945 CACAGGTGAAGACATTGAGCC 59.191 52.381 0.00 0.00 0.00 4.70
2 3 2.498167 ACACAGGTGAAGACATTGAGC 58.502 47.619 6.40 0.00 0.00 4.26
3 4 3.185188 CGAACACAGGTGAAGACATTGAG 59.815 47.826 6.40 0.00 0.00 3.02
4 5 3.130633 CGAACACAGGTGAAGACATTGA 58.869 45.455 6.40 0.00 0.00 2.57
5 6 2.349817 GCGAACACAGGTGAAGACATTG 60.350 50.000 6.40 0.00 0.00 2.82
6 7 1.873591 GCGAACACAGGTGAAGACATT 59.126 47.619 6.40 0.00 0.00 2.71
7 8 1.512926 GCGAACACAGGTGAAGACAT 58.487 50.000 6.40 0.00 0.00 3.06
8 9 0.531974 GGCGAACACAGGTGAAGACA 60.532 55.000 6.40 0.00 0.00 3.41
9 10 1.557443 CGGCGAACACAGGTGAAGAC 61.557 60.000 0.00 0.00 0.00 3.01
10 11 1.300620 CGGCGAACACAGGTGAAGA 60.301 57.895 0.00 0.00 0.00 2.87
11 12 1.300620 TCGGCGAACACAGGTGAAG 60.301 57.895 7.35 0.00 0.00 3.02
12 13 1.593209 GTCGGCGAACACAGGTGAA 60.593 57.895 12.92 0.00 0.00 3.18
13 14 2.028484 GTCGGCGAACACAGGTGA 59.972 61.111 12.92 0.00 0.00 4.02
14 15 3.403057 CGTCGGCGAACACAGGTG 61.403 66.667 12.92 0.00 41.33 4.00
15 16 3.598715 TCGTCGGCGAACACAGGT 61.599 61.111 10.97 0.00 44.92 4.00
24 25 1.226974 AGGTGAATCATCGTCGGCG 60.227 57.895 1.15 1.15 39.92 6.46
25 26 0.460284 ACAGGTGAATCATCGTCGGC 60.460 55.000 0.00 0.00 0.00 5.54
26 27 1.280982 CACAGGTGAATCATCGTCGG 58.719 55.000 0.00 0.00 0.00 4.79
27 28 1.996292 ACACAGGTGAATCATCGTCG 58.004 50.000 6.40 0.00 0.00 5.12
28 29 4.688879 TGTAAACACAGGTGAATCATCGTC 59.311 41.667 6.40 0.00 0.00 4.20
29 30 4.637276 TGTAAACACAGGTGAATCATCGT 58.363 39.130 6.40 0.00 0.00 3.73
30 31 5.605564 TTGTAAACACAGGTGAATCATCG 57.394 39.130 6.40 0.00 0.00 3.84
31 32 7.144722 TCATTGTAAACACAGGTGAATCATC 57.855 36.000 6.40 0.00 0.00 2.92
32 33 7.370383 GTTCATTGTAAACACAGGTGAATCAT 58.630 34.615 6.40 0.00 32.70 2.45
33 34 6.512578 CGTTCATTGTAAACACAGGTGAATCA 60.513 38.462 6.40 0.00 32.70 2.57
34 35 5.851177 CGTTCATTGTAAACACAGGTGAATC 59.149 40.000 6.40 0.00 32.70 2.52
35 36 5.529430 TCGTTCATTGTAAACACAGGTGAAT 59.471 36.000 6.40 0.00 32.70 2.57
36 37 4.876679 TCGTTCATTGTAAACACAGGTGAA 59.123 37.500 6.40 0.00 0.00 3.18
37 38 4.443621 TCGTTCATTGTAAACACAGGTGA 58.556 39.130 6.40 0.00 0.00 4.02
38 39 4.804608 TCGTTCATTGTAAACACAGGTG 57.195 40.909 0.00 0.00 0.00 4.00
39 40 5.060506 TCATCGTTCATTGTAAACACAGGT 58.939 37.500 0.00 0.00 0.00 4.00
40 41 5.605564 TCATCGTTCATTGTAAACACAGG 57.394 39.130 0.00 0.00 0.00 4.00
41 42 7.269084 GTGAATCATCGTTCATTGTAAACACAG 59.731 37.037 0.00 0.00 39.99 3.66
42 43 7.075121 GTGAATCATCGTTCATTGTAAACACA 58.925 34.615 0.00 0.00 39.99 3.72
43 44 6.523201 GGTGAATCATCGTTCATTGTAAACAC 59.477 38.462 0.00 0.00 39.99 3.32
44 45 6.429692 AGGTGAATCATCGTTCATTGTAAACA 59.570 34.615 0.00 0.00 39.99 2.83
45 46 6.742718 CAGGTGAATCATCGTTCATTGTAAAC 59.257 38.462 0.00 0.00 39.99 2.01
46 47 6.429692 ACAGGTGAATCATCGTTCATTGTAAA 59.570 34.615 7.50 0.00 39.99 2.01
47 48 5.937540 ACAGGTGAATCATCGTTCATTGTAA 59.062 36.000 7.50 0.00 39.99 2.41
48 49 5.351189 CACAGGTGAATCATCGTTCATTGTA 59.649 40.000 0.00 0.00 39.99 2.41
49 50 4.154737 CACAGGTGAATCATCGTTCATTGT 59.845 41.667 0.00 0.00 39.99 2.71
50 51 4.154737 ACACAGGTGAATCATCGTTCATTG 59.845 41.667 6.40 0.00 39.99 2.82
51 52 4.326826 ACACAGGTGAATCATCGTTCATT 58.673 39.130 6.40 0.00 39.99 2.57
52 53 3.942829 ACACAGGTGAATCATCGTTCAT 58.057 40.909 6.40 0.00 39.99 2.57
53 54 3.401033 ACACAGGTGAATCATCGTTCA 57.599 42.857 6.40 0.00 35.84 3.18
54 55 4.749245 AAACACAGGTGAATCATCGTTC 57.251 40.909 6.40 0.00 0.00 3.95
55 56 5.060506 TGTAAACACAGGTGAATCATCGTT 58.939 37.500 6.40 0.00 0.00 3.85
56 57 4.637276 TGTAAACACAGGTGAATCATCGT 58.363 39.130 6.40 0.00 0.00 3.73
57 58 5.605564 TTGTAAACACAGGTGAATCATCG 57.394 39.130 6.40 0.00 0.00 3.84
58 59 7.144722 TCATTGTAAACACAGGTGAATCATC 57.855 36.000 6.40 0.00 0.00 2.92
59 60 7.523293 TTCATTGTAAACACAGGTGAATCAT 57.477 32.000 6.40 0.00 0.00 2.45
60 61 6.951062 TTCATTGTAAACACAGGTGAATCA 57.049 33.333 6.40 0.00 0.00 2.57
61 62 9.906660 TTTATTCATTGTAAACACAGGTGAATC 57.093 29.630 16.73 0.00 37.63 2.52
64 65 9.906660 GATTTTATTCATTGTAAACACAGGTGA 57.093 29.630 6.40 0.00 0.00 4.02
65 66 9.689976 TGATTTTATTCATTGTAAACACAGGTG 57.310 29.630 0.00 0.00 0.00 4.00
183 191 4.332637 GCCAACAGTGCAGCCGTG 62.333 66.667 0.00 0.00 0.00 4.94
184 192 4.569180 AGCCAACAGTGCAGCCGT 62.569 61.111 0.00 0.00 0.00 5.68
185 193 3.289834 AAGCCAACAGTGCAGCCG 61.290 61.111 0.00 0.00 0.00 5.52
186 194 2.019897 AACAAGCCAACAGTGCAGCC 62.020 55.000 0.00 0.00 0.00 4.85
187 195 0.872881 CAACAAGCCAACAGTGCAGC 60.873 55.000 0.00 0.00 0.00 5.25
212 220 2.951642 CACCATCAAGTGTGAGTTGGTT 59.048 45.455 0.29 0.00 42.18 3.67
269 277 3.973206 ATTGGTTATGGCGATATCCGA 57.027 42.857 7.91 7.91 41.76 4.55
277 285 3.122278 CGACGGTAATATTGGTTATGGCG 59.878 47.826 0.00 0.00 0.00 5.69
299 4155 5.054390 TGCTGATCCAAAAATTTACGTCC 57.946 39.130 0.00 0.00 0.00 4.79
308 4164 0.316841 GGCCGTTGCTGATCCAAAAA 59.683 50.000 0.00 0.00 37.74 1.94
374 4230 4.265056 ACGGGGGTCAAGGTGTGC 62.265 66.667 0.00 0.00 0.00 4.57
455 4311 1.760192 TCTACTTCTACCCTGACGGC 58.240 55.000 0.00 0.00 33.26 5.68
644 4518 3.859627 GCAGTCAAGACGTACCTAAAGCA 60.860 47.826 0.00 0.00 36.20 3.91
645 4519 2.666994 GCAGTCAAGACGTACCTAAAGC 59.333 50.000 0.00 0.00 36.20 3.51
646 4520 4.082679 AGAGCAGTCAAGACGTACCTAAAG 60.083 45.833 0.00 0.00 36.20 1.85
647 4521 3.825014 AGAGCAGTCAAGACGTACCTAAA 59.175 43.478 0.00 0.00 36.20 1.85
648 4522 3.418995 AGAGCAGTCAAGACGTACCTAA 58.581 45.455 0.00 0.00 36.20 2.69
649 4523 3.008330 GAGAGCAGTCAAGACGTACCTA 58.992 50.000 0.00 0.00 36.20 3.08
666 4550 1.827789 CCCAGGAGGAGAGCGAGAG 60.828 68.421 0.00 0.00 38.24 3.20
667 4551 2.277072 CCCAGGAGGAGAGCGAGA 59.723 66.667 0.00 0.00 38.24 4.04
668 4552 2.043450 ACCCAGGAGGAGAGCGAG 60.043 66.667 0.00 0.00 39.89 5.03
669 4553 2.363018 CACCCAGGAGGAGAGCGA 60.363 66.667 0.00 0.00 39.89 4.93
671 4555 1.893919 GACACACCCAGGAGGAGAGC 61.894 65.000 0.00 0.00 39.89 4.09
675 4559 1.081481 TCTAGACACACCCAGGAGGA 58.919 55.000 0.00 0.00 39.89 3.71
676 4560 1.187087 GTCTAGACACACCCAGGAGG 58.813 60.000 18.20 0.00 43.78 4.30
677 4561 2.096248 GAGTCTAGACACACCCAGGAG 58.904 57.143 24.44 0.00 0.00 3.69
678 4562 1.711375 AGAGTCTAGACACACCCAGGA 59.289 52.381 24.44 0.00 0.00 3.86
679 4563 2.223803 AGAGTCTAGACACACCCAGG 57.776 55.000 24.44 0.00 0.00 4.45
680 4564 3.958018 AGTAGAGTCTAGACACACCCAG 58.042 50.000 24.44 0.00 0.00 4.45
681 4565 4.080469 CCTAGTAGAGTCTAGACACACCCA 60.080 50.000 24.44 8.78 39.57 4.51
682 4566 4.453751 CCTAGTAGAGTCTAGACACACCC 58.546 52.174 24.44 10.03 39.57 4.61
683 4567 4.080413 ACCCTAGTAGAGTCTAGACACACC 60.080 50.000 24.44 12.31 39.57 4.16
684 4568 4.877251 CACCCTAGTAGAGTCTAGACACAC 59.123 50.000 24.44 17.14 39.57 3.82
685 4569 4.080469 CCACCCTAGTAGAGTCTAGACACA 60.080 50.000 24.44 6.34 39.57 3.72
686 4570 4.080413 ACCACCCTAGTAGAGTCTAGACAC 60.080 50.000 24.44 18.23 39.57 3.67
687 4571 4.110072 ACCACCCTAGTAGAGTCTAGACA 58.890 47.826 24.44 1.16 39.57 3.41
688 4572 4.776435 ACCACCCTAGTAGAGTCTAGAC 57.224 50.000 15.41 15.41 39.57 2.59
689 4573 6.148901 TCATACCACCCTAGTAGAGTCTAGA 58.851 44.000 0.00 0.00 39.57 2.43
690 4574 6.436738 TCATACCACCCTAGTAGAGTCTAG 57.563 45.833 0.00 0.00 37.66 2.43
691 4575 6.690975 GCTTCATACCACCCTAGTAGAGTCTA 60.691 46.154 0.00 0.00 0.00 2.59
692 4576 5.697067 CTTCATACCACCCTAGTAGAGTCT 58.303 45.833 0.00 0.00 0.00 3.24
693 4577 4.278919 GCTTCATACCACCCTAGTAGAGTC 59.721 50.000 0.00 0.00 0.00 3.36
694 4578 4.079096 AGCTTCATACCACCCTAGTAGAGT 60.079 45.833 0.00 0.00 0.00 3.24
695 4579 4.475345 AGCTTCATACCACCCTAGTAGAG 58.525 47.826 0.00 0.00 0.00 2.43
696 4580 4.537945 AGCTTCATACCACCCTAGTAGA 57.462 45.455 0.00 0.00 0.00 2.59
697 4581 4.649674 TCAAGCTTCATACCACCCTAGTAG 59.350 45.833 0.00 0.00 0.00 2.57
698 4582 4.404715 GTCAAGCTTCATACCACCCTAGTA 59.595 45.833 0.00 0.00 0.00 1.82
699 4583 3.197983 GTCAAGCTTCATACCACCCTAGT 59.802 47.826 0.00 0.00 0.00 2.57
700 4584 3.738281 CGTCAAGCTTCATACCACCCTAG 60.738 52.174 0.00 0.00 0.00 3.02
701 4585 2.167693 CGTCAAGCTTCATACCACCCTA 59.832 50.000 0.00 0.00 0.00 3.53
702 4586 1.066143 CGTCAAGCTTCATACCACCCT 60.066 52.381 0.00 0.00 0.00 4.34
714 4604 2.264166 GCAGGCTCTCGTCAAGCT 59.736 61.111 6.44 0.00 39.75 3.74
716 4606 2.125350 GGGCAGGCTCTCGTCAAG 60.125 66.667 0.00 0.00 0.00 3.02
726 4616 1.610522 CAGCTATAAATGTGGGCAGGC 59.389 52.381 0.00 0.00 0.00 4.85
731 4621 3.117512 AGGGGAACAGCTATAAATGTGGG 60.118 47.826 0.00 0.00 0.00 4.61
734 4624 3.555966 GCAGGGGAACAGCTATAAATGT 58.444 45.455 0.00 0.00 0.00 2.71
735 4625 2.887152 GGCAGGGGAACAGCTATAAATG 59.113 50.000 0.00 0.00 33.88 2.32
740 4630 2.746375 CGGGCAGGGGAACAGCTAT 61.746 63.158 0.00 0.00 33.88 2.97
747 4643 2.137177 CTTTCCTTCGGGCAGGGGAA 62.137 60.000 8.31 8.31 36.25 3.97
753 4649 0.393808 GGTATGCTTTCCTTCGGGCA 60.394 55.000 0.00 0.00 39.06 5.36
754 4650 1.101635 GGGTATGCTTTCCTTCGGGC 61.102 60.000 0.00 0.00 34.44 6.13
755 4651 0.254747 TGGGTATGCTTTCCTTCGGG 59.745 55.000 0.00 0.00 0.00 5.14
758 4654 3.010420 GACTGTGGGTATGCTTTCCTTC 58.990 50.000 0.00 0.00 0.00 3.46
769 4665 2.646175 GCTGCTCCGACTGTGGGTA 61.646 63.158 8.75 0.00 0.00 3.69
784 4680 5.061311 CAGTTATTTTTCAGATTTGGCGCTG 59.939 40.000 7.64 0.00 0.00 5.18
787 4683 7.816945 ATTCAGTTATTTTTCAGATTTGGCG 57.183 32.000 0.00 0.00 0.00 5.69
788 4684 9.206870 TGAATTCAGTTATTTTTCAGATTTGGC 57.793 29.630 3.38 0.00 0.00 4.52
794 4690 9.965824 GGAAGTTGAATTCAGTTATTTTTCAGA 57.034 29.630 8.41 0.00 0.00 3.27
802 4698 9.574516 AGTAAACAGGAAGTTGAATTCAGTTAT 57.425 29.630 8.41 0.00 41.19 1.89
803 4699 8.974060 AGTAAACAGGAAGTTGAATTCAGTTA 57.026 30.769 8.41 0.00 41.19 2.24
804 4700 7.881775 AGTAAACAGGAAGTTGAATTCAGTT 57.118 32.000 8.41 6.54 41.19 3.16
807 4703 6.017440 CCGAAGTAAACAGGAAGTTGAATTCA 60.017 38.462 3.38 3.38 42.95 2.57
808 4704 6.204108 TCCGAAGTAAACAGGAAGTTGAATTC 59.796 38.462 0.00 0.00 40.61 2.17
809 4705 6.017357 GTCCGAAGTAAACAGGAAGTTGAATT 60.017 38.462 0.00 0.00 41.19 2.17
810 4706 5.469084 GTCCGAAGTAAACAGGAAGTTGAAT 59.531 40.000 0.00 0.00 41.19 2.57
812 4708 4.100498 AGTCCGAAGTAAACAGGAAGTTGA 59.900 41.667 0.00 0.00 41.19 3.18
813 4709 4.211374 CAGTCCGAAGTAAACAGGAAGTTG 59.789 45.833 0.00 0.00 41.19 3.16
815 4711 3.244112 CCAGTCCGAAGTAAACAGGAAGT 60.244 47.826 0.00 0.00 34.17 3.01
817 4713 2.967201 TCCAGTCCGAAGTAAACAGGAA 59.033 45.455 0.00 0.00 34.17 3.36
818 4714 2.298163 GTCCAGTCCGAAGTAAACAGGA 59.702 50.000 0.00 0.00 0.00 3.86
819 4715 2.299297 AGTCCAGTCCGAAGTAAACAGG 59.701 50.000 0.00 0.00 0.00 4.00
820 4716 3.662247 AGTCCAGTCCGAAGTAAACAG 57.338 47.619 0.00 0.00 0.00 3.16
821 4717 3.243975 GGAAGTCCAGTCCGAAGTAAACA 60.244 47.826 0.00 0.00 35.64 2.83
822 4718 3.324117 GGAAGTCCAGTCCGAAGTAAAC 58.676 50.000 0.00 0.00 35.64 2.01
823 4719 3.672767 GGAAGTCCAGTCCGAAGTAAA 57.327 47.619 0.00 0.00 35.64 2.01
848 4744 3.051392 GATGAAAACCAGCCGGCCG 62.051 63.158 26.15 21.04 34.57 6.13
852 4802 0.443869 CACTCGATGAAAACCAGCCG 59.556 55.000 0.00 0.00 0.00 5.52
855 4805 1.813513 AGGCACTCGATGAAAACCAG 58.186 50.000 0.00 0.00 0.00 4.00
856 4806 3.627395 ATAGGCACTCGATGAAAACCA 57.373 42.857 0.00 0.00 41.75 3.67
860 4810 6.538742 CCTTCTTTTATAGGCACTCGATGAAA 59.461 38.462 0.00 0.00 41.75 2.69
866 4816 2.872858 GCCCTTCTTTTATAGGCACTCG 59.127 50.000 0.00 0.00 43.32 4.18
868 4818 3.783082 AGAGCCCTTCTTTTATAGGCACT 59.217 43.478 1.74 0.00 46.35 4.40
871 4821 3.745799 GGAGAGCCCTTCTTTTATAGGC 58.254 50.000 0.00 0.00 44.20 3.93
885 4835 1.065418 TGAAAATCGGAAGGGAGAGCC 60.065 52.381 0.00 0.00 0.00 4.70
886 4836 2.403252 TGAAAATCGGAAGGGAGAGC 57.597 50.000 0.00 0.00 0.00 4.09
887 4837 3.126831 CGATGAAAATCGGAAGGGAGAG 58.873 50.000 0.20 0.00 40.12 3.20
888 4838 2.764010 TCGATGAAAATCGGAAGGGAGA 59.236 45.455 8.13 0.00 43.64 3.71
890 4840 2.500098 ACTCGATGAAAATCGGAAGGGA 59.500 45.455 8.13 0.00 43.64 4.20
891 4841 2.609459 CACTCGATGAAAATCGGAAGGG 59.391 50.000 8.13 0.00 43.64 3.95
892 4842 2.030946 GCACTCGATGAAAATCGGAAGG 59.969 50.000 8.13 0.70 43.64 3.46
893 4843 2.030946 GGCACTCGATGAAAATCGGAAG 59.969 50.000 8.13 2.49 43.64 3.46
894 4844 2.006888 GGCACTCGATGAAAATCGGAA 58.993 47.619 8.13 0.00 43.64 4.30
895 4845 1.207089 AGGCACTCGATGAAAATCGGA 59.793 47.619 8.13 0.00 43.64 4.55
897 4847 1.267732 GCAGGCACTCGATGAAAATCG 60.268 52.381 1.75 1.75 44.73 3.34
898 4848 1.739466 TGCAGGCACTCGATGAAAATC 59.261 47.619 0.00 0.00 34.60 2.17
900 4850 1.159285 CTGCAGGCACTCGATGAAAA 58.841 50.000 5.57 0.00 34.60 2.29
914 4864 2.098934 AGATTGTCTCTAGTCGCTGCAG 59.901 50.000 10.11 10.11 30.26 4.41
921 4871 7.877003 TCGATGGAAATAGATTGTCTCTAGTC 58.123 38.462 0.00 0.00 39.82 2.59
922 4872 7.825331 TCGATGGAAATAGATTGTCTCTAGT 57.175 36.000 0.00 0.00 39.82 2.57
924 4874 7.175119 ACGATCGATGGAAATAGATTGTCTCTA 59.825 37.037 24.34 0.00 40.73 2.43
925 4875 6.015856 ACGATCGATGGAAATAGATTGTCTCT 60.016 38.462 24.34 0.00 33.74 3.10
926 4876 6.088749 CACGATCGATGGAAATAGATTGTCTC 59.911 42.308 24.34 0.00 36.03 3.36
927 4877 5.923114 CACGATCGATGGAAATAGATTGTCT 59.077 40.000 24.34 0.00 36.03 3.41
928 4878 5.692204 ACACGATCGATGGAAATAGATTGTC 59.308 40.000 24.34 0.00 36.03 3.18
930 4880 5.691754 TGACACGATCGATGGAAATAGATTG 59.308 40.000 24.34 7.05 0.00 2.67
931 4881 5.842907 TGACACGATCGATGGAAATAGATT 58.157 37.500 24.34 0.00 0.00 2.40
932 4882 5.453567 TGACACGATCGATGGAAATAGAT 57.546 39.130 24.34 0.00 0.00 1.98
934 4884 5.222631 TCATGACACGATCGATGGAAATAG 58.777 41.667 24.34 3.17 0.00 1.73
935 4885 5.195001 TCATGACACGATCGATGGAAATA 57.805 39.130 24.34 0.00 0.00 1.40
936 4886 4.053983 CTCATGACACGATCGATGGAAAT 58.946 43.478 24.34 8.68 0.00 2.17
937 4887 3.447742 CTCATGACACGATCGATGGAAA 58.552 45.455 24.34 6.86 0.00 3.13
938 4888 2.799562 GCTCATGACACGATCGATGGAA 60.800 50.000 24.34 9.16 0.00 3.53
939 4889 1.269257 GCTCATGACACGATCGATGGA 60.269 52.381 24.34 9.00 0.00 3.41
940 4890 1.135046 GCTCATGACACGATCGATGG 58.865 55.000 24.34 13.03 0.00 3.51
941 4891 1.135046 GGCTCATGACACGATCGATG 58.865 55.000 24.34 17.90 0.00 3.84
942 4892 0.746659 TGGCTCATGACACGATCGAT 59.253 50.000 24.34 9.45 0.00 3.59
943 4893 0.101219 CTGGCTCATGACACGATCGA 59.899 55.000 24.34 0.00 0.00 3.59
944 4894 1.485838 GCTGGCTCATGACACGATCG 61.486 60.000 14.88 14.88 0.00 3.69
945 4895 1.485838 CGCTGGCTCATGACACGATC 61.486 60.000 0.00 0.00 30.93 3.69
946 4896 1.520120 CGCTGGCTCATGACACGAT 60.520 57.895 0.00 0.00 30.93 3.73
947 4897 2.125952 CGCTGGCTCATGACACGA 60.126 61.111 0.00 0.00 30.93 4.35
948 4898 2.125952 TCGCTGGCTCATGACACG 60.126 61.111 0.00 0.00 0.00 4.49
949 4899 2.103042 GGTCGCTGGCTCATGACAC 61.103 63.158 0.00 0.00 33.04 3.67
950 4900 0.970427 TAGGTCGCTGGCTCATGACA 60.970 55.000 0.00 0.00 33.04 3.58
951 4901 0.249238 CTAGGTCGCTGGCTCATGAC 60.249 60.000 0.00 0.00 0.00 3.06
952 4902 0.684479 ACTAGGTCGCTGGCTCATGA 60.684 55.000 0.00 0.00 0.00 3.07
953 4903 1.032794 TACTAGGTCGCTGGCTCATG 58.967 55.000 0.00 0.00 0.00 3.07
954 4904 1.033574 GTACTAGGTCGCTGGCTCAT 58.966 55.000 0.00 0.00 0.00 2.90
955 4905 1.374343 CGTACTAGGTCGCTGGCTCA 61.374 60.000 0.00 0.00 0.00 4.26
956 4906 1.094073 TCGTACTAGGTCGCTGGCTC 61.094 60.000 0.00 0.00 0.00 4.70
957 4907 1.077930 TCGTACTAGGTCGCTGGCT 60.078 57.895 0.00 0.00 0.00 4.75
958 4908 1.063811 GTCGTACTAGGTCGCTGGC 59.936 63.158 0.00 0.00 0.00 4.85
959 4909 1.086067 TCGTCGTACTAGGTCGCTGG 61.086 60.000 0.00 0.00 0.00 4.85
960 4910 0.935898 ATCGTCGTACTAGGTCGCTG 59.064 55.000 0.00 0.00 0.00 5.18
961 4911 1.216122 GATCGTCGTACTAGGTCGCT 58.784 55.000 0.00 0.00 0.00 4.93
962 4912 0.933097 TGATCGTCGTACTAGGTCGC 59.067 55.000 0.00 0.00 0.00 5.19
963 4913 1.526041 CCTGATCGTCGTACTAGGTCG 59.474 57.143 0.00 0.00 0.00 4.79
964 4914 2.831333 TCCTGATCGTCGTACTAGGTC 58.169 52.381 0.00 0.00 0.00 3.85
965 4915 2.941720 GTTCCTGATCGTCGTACTAGGT 59.058 50.000 0.00 0.00 0.00 3.08
966 4916 3.204526 AGTTCCTGATCGTCGTACTAGG 58.795 50.000 0.00 0.00 0.00 3.02
967 4917 4.094590 ACAAGTTCCTGATCGTCGTACTAG 59.905 45.833 0.00 0.00 0.00 2.57
968 4918 4.005650 ACAAGTTCCTGATCGTCGTACTA 58.994 43.478 0.00 0.00 0.00 1.82
969 4919 2.818432 ACAAGTTCCTGATCGTCGTACT 59.182 45.455 0.00 0.00 0.00 2.73
970 4920 3.213249 ACAAGTTCCTGATCGTCGTAC 57.787 47.619 0.00 0.00 0.00 3.67
971 4921 4.005650 ACTACAAGTTCCTGATCGTCGTA 58.994 43.478 0.00 0.00 0.00 3.43
972 4922 2.818432 ACTACAAGTTCCTGATCGTCGT 59.182 45.455 0.00 0.00 0.00 4.34
973 4923 3.489180 ACTACAAGTTCCTGATCGTCG 57.511 47.619 0.00 0.00 0.00 5.12
974 4924 4.341099 CGTACTACAAGTTCCTGATCGTC 58.659 47.826 0.00 0.00 0.00 4.20
975 4925 3.427233 GCGTACTACAAGTTCCTGATCGT 60.427 47.826 0.00 0.00 0.00 3.73
976 4926 3.106672 GCGTACTACAAGTTCCTGATCG 58.893 50.000 0.00 0.00 0.00 3.69
977 4927 3.445857 GGCGTACTACAAGTTCCTGATC 58.554 50.000 0.00 0.00 0.00 2.92
978 4928 2.159282 CGGCGTACTACAAGTTCCTGAT 60.159 50.000 0.00 0.00 0.00 2.90
979 4929 1.200716 CGGCGTACTACAAGTTCCTGA 59.799 52.381 0.00 0.00 0.00 3.86
980 4930 1.200716 TCGGCGTACTACAAGTTCCTG 59.799 52.381 6.85 0.00 0.00 3.86
981 4931 1.538047 TCGGCGTACTACAAGTTCCT 58.462 50.000 6.85 0.00 0.00 3.36
982 4932 2.190981 CATCGGCGTACTACAAGTTCC 58.809 52.381 6.85 0.00 0.00 3.62
983 4933 2.190981 CCATCGGCGTACTACAAGTTC 58.809 52.381 6.85 0.00 0.00 3.01
984 4934 1.738030 GCCATCGGCGTACTACAAGTT 60.738 52.381 6.85 0.00 39.62 2.66
1058 5008 2.774351 AGGGGCAGGGATAGTGGC 60.774 66.667 0.00 0.00 39.71 5.01
1075 5025 1.011333 TCATCATACTCGACGTCGCA 58.989 50.000 32.19 19.55 39.60 5.10
1083 5033 3.643159 TCCACCGAATCATCATACTCG 57.357 47.619 0.00 0.00 0.00 4.18
1085 5035 4.162320 ACAGTTCCACCGAATCATCATACT 59.838 41.667 0.00 0.00 0.00 2.12
1086 5036 4.442706 ACAGTTCCACCGAATCATCATAC 58.557 43.478 0.00 0.00 0.00 2.39
1087 5037 4.442893 GGACAGTTCCACCGAATCATCATA 60.443 45.833 0.00 0.00 42.30 2.15
1100 5050 1.761174 GGAGGCAAGGACAGTTCCA 59.239 57.895 0.00 0.00 45.72 3.53
1160 5110 2.208619 TCGCCGGTGTCCAAACCTA 61.209 57.895 16.01 0.00 38.14 3.08
1161 5111 3.552384 TCGCCGGTGTCCAAACCT 61.552 61.111 16.01 0.00 38.14 3.50
1329 5279 3.726517 CCGCCGCACTTGGTCTTG 61.727 66.667 0.00 0.00 0.00 3.02
1395 5345 4.961511 GCGCTGGTGGTCACGACA 62.962 66.667 0.00 0.00 0.00 4.35
1608 5558 2.284258 ACCTCCCGCTTCTGCTCT 60.284 61.111 0.00 0.00 36.97 4.09
2319 6269 2.607892 GCGGTCGATATGCTTGGCC 61.608 63.158 0.00 0.00 0.00 5.36
2340 6290 1.954146 GAACGCGAACTGGTCAGCA 60.954 57.895 15.93 0.00 0.00 4.41
2479 6430 5.663456 TGTATAATCGAACACCCAACCTAC 58.337 41.667 0.00 0.00 0.00 3.18
2501 6452 4.258543 GAGAGGAGGACCGAGTATAGATG 58.741 52.174 0.00 0.00 41.83 2.90
2504 6455 3.773418 TGAGAGGAGGACCGAGTATAG 57.227 52.381 0.00 0.00 41.83 1.31
2539 6490 9.677567 GCAATTTCGTTATATACATGACCAAAT 57.322 29.630 0.00 0.00 27.60 2.32
2560 6511 7.361286 GGACTGAGAAGTCGAAATTTAGCAATT 60.361 37.037 0.00 0.00 39.57 2.32
2688 6640 2.286365 AGGGCGTGATCTTCCAAAAA 57.714 45.000 0.00 0.00 0.00 1.94
2689 6641 2.286365 AAGGGCGTGATCTTCCAAAA 57.714 45.000 0.00 0.00 0.00 2.44
2690 6642 2.159382 GAAAGGGCGTGATCTTCCAAA 58.841 47.619 0.00 0.00 0.00 3.28
2695 6647 0.391263 GGACGAAAGGGCGTGATCTT 60.391 55.000 0.00 0.00 45.72 2.40
2841 6852 3.549423 GCGAAAAAGAGCTAAAACCGGTT 60.549 43.478 15.86 15.86 0.00 4.44
2849 6860 1.303091 GGCCGGCGAAAAAGAGCTAA 61.303 55.000 22.54 0.00 0.00 3.09
2874 6885 2.959707 ACAGGAGTTGAAGAACGAGACT 59.040 45.455 0.00 0.00 37.15 3.24
2881 6892 1.540363 GGCGACACAGGAGTTGAAGAA 60.540 52.381 0.00 0.00 0.00 2.52
2893 6904 2.345991 GCAACCTAGGGCGACACA 59.654 61.111 14.81 0.00 0.00 3.72
2972 6983 1.827399 GAAGACCAGAAGCGGGACCA 61.827 60.000 0.00 0.00 0.00 4.02
2998 7009 2.196925 ACGGGCGGCATTTTTGTCA 61.197 52.632 12.47 0.00 0.00 3.58
3042 7076 3.552604 TTTTGCTAGAACGGCATCAAC 57.447 42.857 0.00 0.00 39.54 3.18
3067 7103 2.012673 GTGGCAATTTTTGGTGCAACA 58.987 42.857 0.00 0.00 39.98 3.33
3093 7131 1.592223 GCTGGAACTCGGTGCTACT 59.408 57.895 0.00 0.00 0.00 2.57
3275 7313 1.223501 TGGTAACCACAAGGGGACAA 58.776 50.000 0.00 0.00 42.91 3.18
3283 7321 2.790433 GAGCTTCCATGGTAACCACAA 58.210 47.619 12.58 0.00 35.80 3.33


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

AutoCloner maintained by Alex Coulton.