Multiple sequence alignment - TraesCS4B01G217400

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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 TraesCS4B01G217400 chr4B 100.000 4591 0 0 1 4591 458460993 458456403 0.000000e+00 8479.0
1 TraesCS4B01G217400 chr4B 89.157 249 25 2 4287 4534 328107851 328107604 4.460000e-80 309.0
2 TraesCS4B01G217400 chr4B 93.478 46 3 0 4087 4132 215918388 215918433 8.240000e-08 69.4
3 TraesCS4B01G217400 chr4A 93.980 3538 111 34 688 4154 91469536 91473042 0.000000e+00 5260.0
4 TraesCS4B01G217400 chr4A 90.469 682 23 22 1 659 91468881 91469543 0.000000e+00 861.0
5 TraesCS4B01G217400 chr4A 93.966 116 6 1 4186 4301 91473044 91473158 1.700000e-39 174.0
6 TraesCS4B01G217400 chr4D 93.292 3354 104 54 688 3962 373210670 373207359 0.000000e+00 4835.0
7 TraesCS4B01G217400 chr4D 94.198 655 21 6 1 646 373211316 373210670 0.000000e+00 983.0
8 TraesCS4B01G217400 chr4D 89.069 247 24 3 4287 4532 284102138 284102382 2.080000e-78 303.0
9 TraesCS4B01G217400 chr4D 89.916 238 21 2 4298 4534 362196457 362196692 2.080000e-78 303.0
10 TraesCS4B01G217400 chr4D 85.854 205 19 5 3964 4162 373207191 373206991 4.650000e-50 209.0
11 TraesCS4B01G217400 chr4D 93.966 116 6 1 4186 4301 373207005 373206891 1.700000e-39 174.0
12 TraesCS4B01G217400 chr4D 96.610 59 2 0 4533 4591 373206895 373206837 1.050000e-16 99.0
13 TraesCS4B01G217400 chr4D 93.478 46 3 0 4087 4132 169122940 169122895 8.240000e-08 69.4
14 TraesCS4B01G217400 chr4D 94.737 38 2 0 4090 4127 47553080 47553117 4.960000e-05 60.2
15 TraesCS4B01G217400 chr2B 90.123 243 23 1 4297 4538 162634432 162634190 9.590000e-82 315.0
16 TraesCS4B01G217400 chr3B 89.754 244 22 3 4295 4536 528516456 528516698 4.460000e-80 309.0
17 TraesCS4B01G217400 chr3B 93.478 46 3 0 4087 4132 665451146 665451101 8.240000e-08 69.4
18 TraesCS4B01G217400 chr7B 89.300 243 25 1 4297 4538 124341093 124340851 2.080000e-78 303.0
19 TraesCS4B01G217400 chr7B 90.909 44 3 1 4076 4118 53620850 53620893 1.780000e-04 58.4
20 TraesCS4B01G217400 chr5A 89.344 244 23 3 4297 4539 6147345 6147586 2.080000e-78 303.0
21 TraesCS4B01G217400 chr5A 87.500 144 18 0 1556 1699 445392218 445392361 2.840000e-37 167.0
22 TraesCS4B01G217400 chr5D 88.934 244 25 2 4297 4539 7946853 7947095 2.680000e-77 300.0
23 TraesCS4B01G217400 chr5D 87.075 147 17 2 1554 1699 345848407 345848262 1.020000e-36 165.0
24 TraesCS4B01G217400 chr5D 93.182 44 3 0 4077 4120 500648107 500648064 1.070000e-06 65.8
25 TraesCS4B01G217400 chr1D 88.618 246 24 4 4297 4542 113878191 113878432 3.470000e-76 296.0
26 TraesCS4B01G217400 chr5B 86.806 144 19 0 1556 1699 405768065 405768208 1.320000e-35 161.0
27 TraesCS4B01G217400 chr7A 89.231 65 7 0 4057 4121 689887712 689887776 1.060000e-11 82.4
28 TraesCS4B01G217400 chr3A 93.750 48 3 0 4085 4132 631305601 631305554 6.370000e-09 73.1
29 TraesCS4B01G217400 chr7D 100.000 37 0 0 819 855 185418984 185419020 8.240000e-08 69.4
30 TraesCS4B01G217400 chr6B 97.500 40 1 0 819 858 353088544 353088505 8.240000e-08 69.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G217400 chr4B 458456403 458460993 4590 True 8479.000000 8479 100.000 1 4591 1 chr4B.!!$R2 4590
1 TraesCS4B01G217400 chr4A 91468881 91473158 4277 False 2098.333333 5260 92.805 1 4301 3 chr4A.!!$F1 4300
2 TraesCS4B01G217400 chr4D 373206837 373211316 4479 True 1260.000000 4835 92.784 1 4591 5 chr4D.!!$R2 4590

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
670 700 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.0 0.0 0.0 0.00 3.82 F
1717 1750 0.393537 ACTGGCTCTGGCTGCATAAC 60.394 55.0 0.5 0.0 38.73 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2571 2712 1.078497 CCACTCTGCGCCCACATTA 60.078 57.895 4.18 0.0 0.0 1.90 R
3691 3870 0.237235 GTGGTGCATGTACGTTGTGG 59.763 55.000 7.89 0.0 0.0 4.17 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
23 24 1.047596 AGCTGCCCAGACGAGATGAT 61.048 55.000 0.00 0.00 0.00 2.45
144 160 4.998788 TGATTACTGCAGTAGCTAGTGTG 58.001 43.478 24.79 20.72 42.74 3.82
178 194 3.368190 CTGCGGCACCAGAGAGAGG 62.368 68.421 0.00 0.00 34.77 3.69
180 196 3.465403 CGGCACCAGAGAGAGGGG 61.465 72.222 0.00 0.00 0.00 4.79
185 201 2.285180 CCAGAGAGAGGGGGAGGG 59.715 72.222 0.00 0.00 0.00 4.30
186 202 2.285180 CAGAGAGAGGGGGAGGGG 59.715 72.222 0.00 0.00 0.00 4.79
187 203 3.039526 AGAGAGAGGGGGAGGGGG 61.040 72.222 0.00 0.00 0.00 5.40
188 204 3.036959 GAGAGAGGGGGAGGGGGA 61.037 72.222 0.00 0.00 0.00 4.81
189 205 3.039526 AGAGAGGGGGAGGGGGAG 61.040 72.222 0.00 0.00 0.00 4.30
350 379 6.358030 GCACATACGTACAAAGGTATACTACG 59.642 42.308 15.91 15.91 35.46 3.51
378 407 1.280142 CTATGTCGTCCCGCTCTCG 59.720 63.158 0.00 0.00 0.00 4.04
414 443 1.273267 TGCTCTCCTCTTTCCCTGCTA 60.273 52.381 0.00 0.00 0.00 3.49
470 500 4.426313 CCACGCCCCCTTTCTCCC 62.426 72.222 0.00 0.00 0.00 4.30
636 666 4.167319 AGCCTTTTCTCTTCCTCTCTCTT 58.833 43.478 0.00 0.00 0.00 2.85
638 668 4.622933 GCCTTTTCTCTTCCTCTCTCTTCC 60.623 50.000 0.00 0.00 0.00 3.46
639 669 4.777366 CCTTTTCTCTTCCTCTCTCTTCCT 59.223 45.833 0.00 0.00 0.00 3.36
640 670 5.248248 CCTTTTCTCTTCCTCTCTCTTCCTT 59.752 44.000 0.00 0.00 0.00 3.36
641 671 6.239858 CCTTTTCTCTTCCTCTCTCTTCCTTT 60.240 42.308 0.00 0.00 0.00 3.11
642 672 5.993748 TTCTCTTCCTCTCTCTTCCTTTC 57.006 43.478 0.00 0.00 0.00 2.62
643 673 5.269554 TCTCTTCCTCTCTCTTCCTTTCT 57.730 43.478 0.00 0.00 0.00 2.52
644 674 5.261216 TCTCTTCCTCTCTCTTCCTTTCTC 58.739 45.833 0.00 0.00 0.00 2.87
645 675 5.015178 TCTCTTCCTCTCTCTTCCTTTCTCT 59.985 44.000 0.00 0.00 0.00 3.10
646 676 5.650283 TCTTCCTCTCTCTTCCTTTCTCTT 58.350 41.667 0.00 0.00 0.00 2.85
647 677 5.714806 TCTTCCTCTCTCTTCCTTTCTCTTC 59.285 44.000 0.00 0.00 0.00 2.87
648 678 4.349365 TCCTCTCTCTTCCTTTCTCTTCC 58.651 47.826 0.00 0.00 0.00 3.46
649 679 4.045334 TCCTCTCTCTTCCTTTCTCTTCCT 59.955 45.833 0.00 0.00 0.00 3.36
650 680 4.402474 CCTCTCTCTTCCTTTCTCTTCCTC 59.598 50.000 0.00 0.00 0.00 3.71
651 681 5.264395 CTCTCTCTTCCTTTCTCTTCCTCT 58.736 45.833 0.00 0.00 0.00 3.69
652 682 5.016173 TCTCTCTTCCTTTCTCTTCCTCTG 58.984 45.833 0.00 0.00 0.00 3.35
653 683 4.746466 TCTCTTCCTTTCTCTTCCTCTGT 58.254 43.478 0.00 0.00 0.00 3.41
654 684 4.526262 TCTCTTCCTTTCTCTTCCTCTGTG 59.474 45.833 0.00 0.00 0.00 3.66
655 685 4.227197 TCTTCCTTTCTCTTCCTCTGTGT 58.773 43.478 0.00 0.00 0.00 3.72
656 686 4.039730 TCTTCCTTTCTCTTCCTCTGTGTG 59.960 45.833 0.00 0.00 0.00 3.82
657 687 3.309296 TCCTTTCTCTTCCTCTGTGTGT 58.691 45.455 0.00 0.00 0.00 3.72
658 688 3.070159 TCCTTTCTCTTCCTCTGTGTGTG 59.930 47.826 0.00 0.00 0.00 3.82
659 689 3.181461 CCTTTCTCTTCCTCTGTGTGTGT 60.181 47.826 0.00 0.00 0.00 3.72
660 690 3.459232 TTCTCTTCCTCTGTGTGTGTG 57.541 47.619 0.00 0.00 0.00 3.82
661 691 2.388735 TCTCTTCCTCTGTGTGTGTGT 58.611 47.619 0.00 0.00 0.00 3.72
662 692 2.101415 TCTCTTCCTCTGTGTGTGTGTG 59.899 50.000 0.00 0.00 0.00 3.82
663 693 1.831106 TCTTCCTCTGTGTGTGTGTGT 59.169 47.619 0.00 0.00 0.00 3.72
664 694 1.935873 CTTCCTCTGTGTGTGTGTGTG 59.064 52.381 0.00 0.00 0.00 3.82
665 695 0.901827 TCCTCTGTGTGTGTGTGTGT 59.098 50.000 0.00 0.00 0.00 3.72
666 696 1.009078 CCTCTGTGTGTGTGTGTGTG 58.991 55.000 0.00 0.00 0.00 3.82
667 697 1.675714 CCTCTGTGTGTGTGTGTGTGT 60.676 52.381 0.00 0.00 0.00 3.72
668 698 1.394572 CTCTGTGTGTGTGTGTGTGTG 59.605 52.381 0.00 0.00 0.00 3.82
669 699 1.155889 CTGTGTGTGTGTGTGTGTGT 58.844 50.000 0.00 0.00 0.00 3.72
670 700 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
671 701 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
672 702 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
673 703 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
674 704 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
675 705 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
676 706 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
677 707 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
678 708 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
679 709 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
680 710 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
681 711 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
682 712 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
683 713 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
684 714 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
685 715 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
686 716 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
697 727 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
699 729 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
704 734 2.073056 GTGTGTGTGTGTGTGTGAGAA 58.927 47.619 0.00 0.00 0.00 2.87
754 784 1.678101 GGCCATAATTCTTGCGAGCTT 59.322 47.619 0.00 0.00 0.00 3.74
907 937 1.278127 ACACCACACCACCATAGCTAC 59.722 52.381 0.00 0.00 0.00 3.58
918 948 4.202161 CCACCATAGCTACACTAGAACCAG 60.202 50.000 0.00 0.00 33.29 4.00
922 952 5.452077 CCATAGCTACACTAGAACCAGAACC 60.452 48.000 0.00 0.00 33.29 3.62
1074 1107 0.408309 TGGACGAAGAGGAGGAGGAA 59.592 55.000 0.00 0.00 0.00 3.36
1176 1209 1.187567 GGGGCATGGTGTTTGAAGCT 61.188 55.000 0.00 0.00 0.00 3.74
1389 1422 1.084370 CGCCCTTCTTAGCCGACTTG 61.084 60.000 0.00 0.00 0.00 3.16
1519 1552 0.601046 CGTCCACGGGATGATGATGG 60.601 60.000 6.35 0.00 40.94 3.51
1521 1554 1.601759 CCACGGGATGATGATGGCC 60.602 63.158 0.00 0.00 0.00 5.36
1717 1750 0.393537 ACTGGCTCTGGCTGCATAAC 60.394 55.000 0.50 0.00 38.73 1.89
1852 1885 2.819595 ATGCGCGCGAACTCCAAT 60.820 55.556 37.18 2.82 0.00 3.16
1922 1964 2.100087 GTGAGCTACTAGGAGACAAGGC 59.900 54.545 6.02 0.00 0.00 4.35
2124 2171 3.385749 ATCCTGCTGGTTACCGCCG 62.386 63.158 9.73 8.60 34.23 6.46
2205 2258 2.038387 AACCATGCGAGTTATCCCAC 57.962 50.000 0.00 0.00 0.00 4.61
2283 2392 8.049117 TCTTTCATCTTTACCGGAGTAGTAGTA 58.951 37.037 9.46 0.00 0.00 1.82
2284 2393 7.798596 TTCATCTTTACCGGAGTAGTAGTAG 57.201 40.000 9.46 0.00 0.00 2.57
2285 2394 6.893583 TCATCTTTACCGGAGTAGTAGTAGT 58.106 40.000 9.46 0.00 0.00 2.73
2286 2395 8.023021 TCATCTTTACCGGAGTAGTAGTAGTA 57.977 38.462 9.46 0.00 0.00 1.82
2287 2396 8.147058 TCATCTTTACCGGAGTAGTAGTAGTAG 58.853 40.741 9.46 0.00 0.00 2.57
2288 2397 6.284459 TCTTTACCGGAGTAGTAGTAGTAGC 58.716 44.000 9.46 0.00 0.00 3.58
2289 2398 5.614324 TTACCGGAGTAGTAGTAGTAGCA 57.386 43.478 9.46 0.00 0.00 3.49
2290 2399 4.070630 ACCGGAGTAGTAGTAGTAGCAG 57.929 50.000 9.46 0.00 0.00 4.24
2291 2400 2.807392 CCGGAGTAGTAGTAGTAGCAGC 59.193 54.545 0.00 0.00 0.00 5.25
2381 2496 6.582636 TGTTACTGATCTGTTGACTGTTCTT 58.417 36.000 10.76 0.00 0.00 2.52
2382 2497 6.701841 TGTTACTGATCTGTTGACTGTTCTTC 59.298 38.462 10.76 0.00 0.00 2.87
2390 2505 6.273825 TCTGTTGACTGTTCTTCTAGTGTTC 58.726 40.000 0.00 0.00 0.00 3.18
2399 2517 6.053005 TGTTCTTCTAGTGTTCGGTTCAAAT 58.947 36.000 0.00 0.00 0.00 2.32
2402 2520 6.751157 TCTTCTAGTGTTCGGTTCAAATGTA 58.249 36.000 0.00 0.00 0.00 2.29
2518 2659 4.437587 GCCCCAGGAGCACTGCAT 62.438 66.667 3.30 0.00 46.14 3.96
2565 2706 1.435577 GGCGTGATAACGGAACAAGT 58.564 50.000 4.40 0.00 0.00 3.16
2571 2712 6.018507 GGCGTGATAACGGAACAAGTATAAAT 60.019 38.462 4.40 0.00 0.00 1.40
2779 2933 1.566703 CTGGTAGGAGGAGAGTGGAGA 59.433 57.143 0.00 0.00 0.00 3.71
2907 3065 3.099170 CCAGCCTACCCCCTGCAT 61.099 66.667 0.00 0.00 0.00 3.96
2908 3066 2.194056 CAGCCTACCCCCTGCATG 59.806 66.667 0.00 0.00 0.00 4.06
2909 3067 3.813724 AGCCTACCCCCTGCATGC 61.814 66.667 11.82 11.82 0.00 4.06
2910 3068 4.127744 GCCTACCCCCTGCATGCA 62.128 66.667 21.29 21.29 0.00 3.96
2954 3116 1.292992 TGCATGTTAGCGAGCTGATG 58.707 50.000 7.99 8.22 37.31 3.07
3040 3214 3.129113 TGTGATTTACTCCATGCATGCAC 59.871 43.478 25.37 19.21 0.00 4.57
3041 3215 2.355444 TGATTTACTCCATGCATGCACG 59.645 45.455 25.37 16.18 0.00 5.34
3042 3216 0.451383 TTTACTCCATGCATGCACGC 59.549 50.000 25.37 0.00 0.00 5.34
3043 3217 1.704387 TTACTCCATGCATGCACGCG 61.704 55.000 25.37 14.44 33.35 6.01
3044 3218 2.850806 TACTCCATGCATGCACGCGT 62.851 55.000 25.37 18.68 33.35 6.01
3045 3219 3.728267 CTCCATGCATGCACGCGTG 62.728 63.158 34.01 34.01 46.42 5.34
3188 3362 2.792599 GACGAGCTCACCGTCGAT 59.207 61.111 15.40 0.00 45.23 3.59
3407 3581 4.135153 CAGCAGGACGAGGACGGG 62.135 72.222 0.00 0.00 44.46 5.28
3408 3582 4.361971 AGCAGGACGAGGACGGGA 62.362 66.667 0.00 0.00 44.46 5.14
3409 3583 3.379445 GCAGGACGAGGACGGGAA 61.379 66.667 0.00 0.00 44.46 3.97
3410 3584 2.572284 CAGGACGAGGACGGGAAC 59.428 66.667 0.00 0.00 44.46 3.62
3657 3836 1.268999 GCTGATGTGCAAAACGGAACA 60.269 47.619 0.00 0.00 0.00 3.18
3691 3870 4.888038 ACGGAAGGAAACAACAGTAAAC 57.112 40.909 0.00 0.00 0.00 2.01
3905 4087 1.824230 CTCTCCATGGGATCGATCTCC 59.176 57.143 22.41 21.06 34.31 3.71
3933 4115 6.456501 GTCAGTACAAGGCTTCTCTTTTCTA 58.543 40.000 0.00 0.00 0.00 2.10
3959 4141 7.657336 TCCTTGCTGGAGTTTAACATTTTAAG 58.343 34.615 0.00 0.00 40.56 1.85
3998 4346 0.385390 CTCAGGCTGCCAACGTTTTT 59.615 50.000 22.65 0.00 0.00 1.94
4001 4349 2.034053 TCAGGCTGCCAACGTTTTTAAG 59.966 45.455 22.65 0.00 0.00 1.85
4012 4360 5.334879 CCAACGTTTTTAAGCTGCAGATACT 60.335 40.000 20.43 1.42 0.00 2.12
4043 4391 4.080807 TGCATGTTTATTACTCCCTCCGAA 60.081 41.667 0.00 0.00 0.00 4.30
4045 4393 4.476628 TGTTTATTACTCCCTCCGAACC 57.523 45.455 0.00 0.00 0.00 3.62
4046 4394 4.098894 TGTTTATTACTCCCTCCGAACCT 58.901 43.478 0.00 0.00 0.00 3.50
4047 4395 5.271598 TGTTTATTACTCCCTCCGAACCTA 58.728 41.667 0.00 0.00 0.00 3.08
4065 4419 6.129062 CGAACCTATGTCGCTCAAATAGATTC 60.129 42.308 0.00 0.00 0.00 2.52
4073 4427 7.890515 TGTCGCTCAAATAGATTCATCTAGAT 58.109 34.615 0.00 0.00 42.20 1.98
4110 4464 1.588674 ACATCCGTTTGAGCGACAAA 58.411 45.000 7.75 7.75 44.79 2.83
4127 4481 7.680730 AGCGACAAATAATATAGATTGGAGGT 58.319 34.615 0.00 0.00 0.00 3.85
4154 4508 9.383519 AGTAACTGATTTGACATGTAAGTATGG 57.616 33.333 0.00 0.00 32.32 2.74
4155 4509 9.378551 GTAACTGATTTGACATGTAAGTATGGA 57.621 33.333 0.00 0.00 32.32 3.41
4156 4510 7.849804 ACTGATTTGACATGTAAGTATGGAC 57.150 36.000 0.00 0.00 32.32 4.02
4157 4511 7.624549 ACTGATTTGACATGTAAGTATGGACT 58.375 34.615 0.00 0.00 37.59 3.85
4158 4512 7.766278 ACTGATTTGACATGTAAGTATGGACTC 59.234 37.037 0.00 0.00 33.58 3.36
4159 4513 7.619965 TGATTTGACATGTAAGTATGGACTCA 58.380 34.615 0.00 0.00 33.58 3.41
4160 4514 8.267183 TGATTTGACATGTAAGTATGGACTCAT 58.733 33.333 0.00 0.00 33.58 2.90
4161 4515 9.113838 GATTTGACATGTAAGTATGGACTCATT 57.886 33.333 0.00 0.00 33.58 2.57
4162 4516 8.862325 TTTGACATGTAAGTATGGACTCATTT 57.138 30.769 0.00 0.00 33.58 2.32
4163 4517 8.862325 TTGACATGTAAGTATGGACTCATTTT 57.138 30.769 0.00 0.00 33.58 1.82
4164 4518 8.862325 TGACATGTAAGTATGGACTCATTTTT 57.138 30.769 0.00 0.00 33.58 1.94
4302 4656 9.614792 AATGTATGTTCCAAAAGAGATACTACC 57.385 33.333 0.00 0.00 0.00 3.18
4303 4657 8.375493 TGTATGTTCCAAAAGAGATACTACCT 57.625 34.615 0.00 0.00 0.00 3.08
4304 4658 8.475639 TGTATGTTCCAAAAGAGATACTACCTC 58.524 37.037 0.00 0.00 0.00 3.85
4305 4659 6.295719 TGTTCCAAAAGAGATACTACCTCC 57.704 41.667 0.00 0.00 0.00 4.30
4306 4660 5.105473 TGTTCCAAAAGAGATACTACCTCCG 60.105 44.000 0.00 0.00 0.00 4.63
4307 4661 4.607239 TCCAAAAGAGATACTACCTCCGT 58.393 43.478 0.00 0.00 0.00 4.69
4308 4662 4.643784 TCCAAAAGAGATACTACCTCCGTC 59.356 45.833 0.00 0.00 0.00 4.79
4309 4663 4.202131 CCAAAAGAGATACTACCTCCGTCC 60.202 50.000 0.00 0.00 0.00 4.79
4310 4664 4.523168 AAAGAGATACTACCTCCGTCCT 57.477 45.455 0.00 0.00 0.00 3.85
4311 4665 3.495434 AGAGATACTACCTCCGTCCTG 57.505 52.381 0.00 0.00 0.00 3.86
4312 4666 2.106857 AGAGATACTACCTCCGTCCTGG 59.893 54.545 0.00 0.00 40.09 4.45
4313 4667 1.851653 AGATACTACCTCCGTCCTGGT 59.148 52.381 0.00 0.00 39.52 4.00
4314 4668 2.244252 AGATACTACCTCCGTCCTGGTT 59.756 50.000 0.00 0.00 39.52 3.67
4315 4669 2.610438 TACTACCTCCGTCCTGGTTT 57.390 50.000 0.00 0.00 39.52 3.27
4316 4670 2.610438 ACTACCTCCGTCCTGGTTTA 57.390 50.000 0.00 0.00 39.52 2.01
4317 4671 3.111741 ACTACCTCCGTCCTGGTTTAT 57.888 47.619 0.00 0.00 39.52 1.40
4318 4672 4.255510 ACTACCTCCGTCCTGGTTTATA 57.744 45.455 0.00 0.00 39.52 0.98
4319 4673 4.613437 ACTACCTCCGTCCTGGTTTATAA 58.387 43.478 0.00 0.00 39.52 0.98
4320 4674 4.648307 ACTACCTCCGTCCTGGTTTATAAG 59.352 45.833 0.00 0.00 39.52 1.73
4321 4675 3.447950 ACCTCCGTCCTGGTTTATAAGT 58.552 45.455 0.00 0.00 39.52 2.24
4322 4676 3.450096 ACCTCCGTCCTGGTTTATAAGTC 59.550 47.826 0.00 0.00 39.52 3.01
4323 4677 3.181468 CCTCCGTCCTGGTTTATAAGTCC 60.181 52.174 0.00 2.91 39.52 3.85
4324 4678 3.705072 CTCCGTCCTGGTTTATAAGTCCT 59.295 47.826 0.00 0.00 39.52 3.85
4325 4679 4.098894 TCCGTCCTGGTTTATAAGTCCTT 58.901 43.478 0.00 0.00 39.52 3.36
4326 4680 4.533311 TCCGTCCTGGTTTATAAGTCCTTT 59.467 41.667 0.00 0.00 39.52 3.11
4327 4681 5.013391 TCCGTCCTGGTTTATAAGTCCTTTT 59.987 40.000 0.00 0.00 39.52 2.27
4328 4682 5.708697 CCGTCCTGGTTTATAAGTCCTTTTT 59.291 40.000 0.00 0.00 0.00 1.94
4329 4683 6.349033 CCGTCCTGGTTTATAAGTCCTTTTTG 60.349 42.308 0.00 0.41 0.00 2.44
4330 4684 6.206048 CGTCCTGGTTTATAAGTCCTTTTTGT 59.794 38.462 0.00 0.00 0.00 2.83
4331 4685 7.388500 CGTCCTGGTTTATAAGTCCTTTTTGTA 59.612 37.037 0.00 0.00 0.00 2.41
4332 4686 9.239551 GTCCTGGTTTATAAGTCCTTTTTGTAT 57.760 33.333 0.00 0.00 0.00 2.29
4333 4687 9.816787 TCCTGGTTTATAAGTCCTTTTTGTATT 57.183 29.630 0.00 0.00 0.00 1.89
4344 4698 9.665719 AAGTCCTTTTTGTATTTTGTGTCAAAT 57.334 25.926 0.00 0.00 31.45 2.32
4345 4699 9.665719 AGTCCTTTTTGTATTTTGTGTCAAATT 57.334 25.926 0.00 0.00 31.45 1.82
4390 4744 9.887629 AATAAAATATTGATGCATGTCACCAAA 57.112 25.926 2.46 0.00 30.60 3.28
4391 4745 9.887629 ATAAAATATTGATGCATGTCACCAAAA 57.112 25.926 2.46 0.00 30.60 2.44
4392 4746 8.795842 AAAATATTGATGCATGTCACCAAAAT 57.204 26.923 2.46 0.00 30.60 1.82
4393 4747 8.795842 AAATATTGATGCATGTCACCAAAATT 57.204 26.923 2.46 0.00 30.60 1.82
4394 4748 8.795842 AATATTGATGCATGTCACCAAAATTT 57.204 26.923 2.46 0.00 30.60 1.82
4395 4749 9.887629 AATATTGATGCATGTCACCAAAATTTA 57.112 25.926 2.46 0.00 30.60 1.40
4399 4753 9.531942 TTGATGCATGTCACCAAAATTTATATC 57.468 29.630 2.46 0.00 0.00 1.63
4400 4754 7.861872 TGATGCATGTCACCAAAATTTATATCG 59.138 33.333 2.46 0.00 0.00 2.92
4401 4755 7.094508 TGCATGTCACCAAAATTTATATCGT 57.905 32.000 0.00 0.00 0.00 3.73
4402 4756 7.542890 TGCATGTCACCAAAATTTATATCGTT 58.457 30.769 0.00 0.00 0.00 3.85
4403 4757 7.487509 TGCATGTCACCAAAATTTATATCGTTG 59.512 33.333 0.00 0.00 0.00 4.10
4404 4758 7.043458 GCATGTCACCAAAATTTATATCGTTGG 60.043 37.037 0.00 0.00 43.60 3.77
4405 4759 7.689446 TGTCACCAAAATTTATATCGTTGGA 57.311 32.000 9.30 0.00 41.05 3.53
4406 4760 8.287439 TGTCACCAAAATTTATATCGTTGGAT 57.713 30.769 9.30 0.00 41.05 3.41
4407 4761 8.744652 TGTCACCAAAATTTATATCGTTGGATT 58.255 29.630 9.30 0.00 41.05 3.01
4408 4762 9.233232 GTCACCAAAATTTATATCGTTGGATTC 57.767 33.333 9.30 0.00 41.05 2.52
4409 4763 9.184523 TCACCAAAATTTATATCGTTGGATTCT 57.815 29.630 9.30 0.00 41.05 2.40
4410 4764 9.801873 CACCAAAATTTATATCGTTGGATTCTT 57.198 29.630 9.30 0.00 41.05 2.52
4423 4777 8.786826 TCGTTGGATTCTTATTTGAACATAGT 57.213 30.769 0.00 0.00 0.00 2.12
4424 4778 9.226606 TCGTTGGATTCTTATTTGAACATAGTT 57.773 29.630 0.00 0.00 0.00 2.24
4425 4779 9.840427 CGTTGGATTCTTATTTGAACATAGTTT 57.160 29.630 0.00 0.00 0.00 2.66
4428 4782 9.527157 TGGATTCTTATTTGAACATAGTTTCCA 57.473 29.630 0.00 0.00 0.00 3.53
4491 4845 8.965986 AGTTAAATTTAAGATCGAACTTTGGC 57.034 30.769 13.50 0.00 0.00 4.52
4492 4846 8.573035 AGTTAAATTTAAGATCGAACTTTGGCA 58.427 29.630 13.50 0.00 0.00 4.92
4493 4847 8.635983 GTTAAATTTAAGATCGAACTTTGGCAC 58.364 33.333 13.50 0.00 0.00 5.01
4494 4848 5.957842 ATTTAAGATCGAACTTTGGCACA 57.042 34.783 13.50 0.00 0.00 4.57
4495 4849 5.957842 TTTAAGATCGAACTTTGGCACAT 57.042 34.783 13.50 0.00 39.30 3.21
4496 4850 7.624360 ATTTAAGATCGAACTTTGGCACATA 57.376 32.000 13.50 0.00 39.30 2.29
4497 4851 7.441890 TTTAAGATCGAACTTTGGCACATAA 57.558 32.000 13.50 0.00 39.30 1.90
4498 4852 7.624360 TTAAGATCGAACTTTGGCACATAAT 57.376 32.000 13.50 0.00 39.30 1.28
4499 4853 8.725405 TTAAGATCGAACTTTGGCACATAATA 57.275 30.769 13.50 0.00 39.30 0.98
4500 4854 6.604735 AGATCGAACTTTGGCACATAATAC 57.395 37.500 0.00 0.00 39.30 1.89
4501 4855 6.112734 AGATCGAACTTTGGCACATAATACA 58.887 36.000 0.00 0.00 39.30 2.29
4502 4856 6.597672 AGATCGAACTTTGGCACATAATACAA 59.402 34.615 0.00 0.00 39.30 2.41
4503 4857 6.561737 TCGAACTTTGGCACATAATACAAA 57.438 33.333 0.00 0.00 39.30 2.83
4507 4861 5.009854 CTTTGGCACATAATACAAAGGGG 57.990 43.478 7.83 0.00 43.56 4.79
4508 4862 4.323569 TTGGCACATAATACAAAGGGGA 57.676 40.909 0.00 0.00 39.30 4.81
4509 4863 3.626930 TGGCACATAATACAAAGGGGAC 58.373 45.455 0.00 0.00 0.00 4.46
4510 4864 4.264172 TTGGCACATAATACAAAGGGGACT 60.264 41.667 0.00 0.00 41.01 3.85
4511 4865 4.475381 TGGCACATAATACAAAGGGGACTA 59.525 41.667 0.00 0.00 42.68 2.59
4512 4866 5.044772 TGGCACATAATACAAAGGGGACTAA 60.045 40.000 0.00 0.00 42.68 2.24
4513 4867 5.531287 GGCACATAATACAAAGGGGACTAAG 59.469 44.000 0.00 0.00 42.68 2.18
4514 4868 6.354130 GCACATAATACAAAGGGGACTAAGA 58.646 40.000 0.00 0.00 42.68 2.10
4515 4869 6.826741 GCACATAATACAAAGGGGACTAAGAA 59.173 38.462 0.00 0.00 42.68 2.52
4516 4870 7.338449 GCACATAATACAAAGGGGACTAAGAAA 59.662 37.037 0.00 0.00 42.68 2.52
4517 4871 9.408648 CACATAATACAAAGGGGACTAAGAAAT 57.591 33.333 0.00 0.00 42.68 2.17
4518 4872 9.628500 ACATAATACAAAGGGGACTAAGAAATC 57.372 33.333 0.00 0.00 42.68 2.17
4519 4873 9.627123 CATAATACAAAGGGGACTAAGAAATCA 57.373 33.333 0.00 0.00 42.68 2.57
4520 4874 9.853177 ATAATACAAAGGGGACTAAGAAATCAG 57.147 33.333 0.00 0.00 42.68 2.90
4521 4875 4.923415 ACAAAGGGGACTAAGAAATCAGG 58.077 43.478 0.00 0.00 42.68 3.86
4522 4876 4.601857 ACAAAGGGGACTAAGAAATCAGGA 59.398 41.667 0.00 0.00 42.68 3.86
4523 4877 4.846168 AAGGGGACTAAGAAATCAGGAC 57.154 45.455 0.00 0.00 42.68 3.85
4524 4878 3.803340 AGGGGACTAAGAAATCAGGACA 58.197 45.455 0.00 0.00 40.61 4.02
4525 4879 3.777522 AGGGGACTAAGAAATCAGGACAG 59.222 47.826 0.00 0.00 40.61 3.51
4526 4880 3.775316 GGGGACTAAGAAATCAGGACAGA 59.225 47.826 0.00 0.00 0.00 3.41
4527 4881 4.141824 GGGGACTAAGAAATCAGGACAGAG 60.142 50.000 0.00 0.00 0.00 3.35
4528 4882 4.141824 GGGACTAAGAAATCAGGACAGAGG 60.142 50.000 0.00 0.00 0.00 3.69
4529 4883 4.468153 GGACTAAGAAATCAGGACAGAGGT 59.532 45.833 0.00 0.00 0.00 3.85
4530 4884 5.657302 GGACTAAGAAATCAGGACAGAGGTA 59.343 44.000 0.00 0.00 0.00 3.08
4531 4885 6.183360 GGACTAAGAAATCAGGACAGAGGTAG 60.183 46.154 0.00 0.00 0.00 3.18
4572 4926 7.170828 TGTTTGCACCTATATACGATCAATGTC 59.829 37.037 0.00 0.00 0.00 3.06
4585 4939 4.090498 CGATCAATGTCTATACATGCACCG 59.910 45.833 0.00 0.00 45.79 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.293924 GCACCAATCATCTCGTCTGG 58.706 55.000 0.00 0.00 0.00 3.86
11 12 2.014335 TGCACCAATCATCTCGTCTG 57.986 50.000 0.00 0.00 0.00 3.51
185 201 0.029989 AATACACTCCTCCCCCTCCC 60.030 60.000 0.00 0.00 0.00 4.30
186 202 1.425694 GAATACACTCCTCCCCCTCC 58.574 60.000 0.00 0.00 0.00 4.30
187 203 1.344087 TGGAATACACTCCTCCCCCTC 60.344 57.143 0.00 0.00 36.35 4.30
188 204 0.722676 TGGAATACACTCCTCCCCCT 59.277 55.000 0.00 0.00 36.35 4.79
189 205 1.490910 CTTGGAATACACTCCTCCCCC 59.509 57.143 0.00 0.00 36.35 5.40
350 379 3.140623 GGGACGACATAGGAGAGTAGTC 58.859 54.545 0.00 0.00 38.93 2.59
414 443 2.270352 TCGACACCAGGCAAAAAGAT 57.730 45.000 0.00 0.00 0.00 2.40
610 640 0.615850 AGGAAGAGAAAAGGCTCCGG 59.384 55.000 0.00 0.00 35.49 5.14
611 641 1.552792 AGAGGAAGAGAAAAGGCTCCG 59.447 52.381 0.00 0.00 35.49 4.63
612 642 2.837591 AGAGAGGAAGAGAAAAGGCTCC 59.162 50.000 0.00 0.00 35.49 4.70
636 666 3.070159 CACACACAGAGGAAGAGAAAGGA 59.930 47.826 0.00 0.00 0.00 3.36
638 668 3.806521 CACACACACAGAGGAAGAGAAAG 59.193 47.826 0.00 0.00 0.00 2.62
639 669 3.197766 ACACACACACAGAGGAAGAGAAA 59.802 43.478 0.00 0.00 0.00 2.52
640 670 2.766263 ACACACACACAGAGGAAGAGAA 59.234 45.455 0.00 0.00 0.00 2.87
641 671 2.101415 CACACACACACAGAGGAAGAGA 59.899 50.000 0.00 0.00 0.00 3.10
642 672 2.159043 ACACACACACACAGAGGAAGAG 60.159 50.000 0.00 0.00 0.00 2.85
643 673 1.831106 ACACACACACACAGAGGAAGA 59.169 47.619 0.00 0.00 0.00 2.87
644 674 1.935873 CACACACACACACAGAGGAAG 59.064 52.381 0.00 0.00 0.00 3.46
645 675 1.277842 ACACACACACACACAGAGGAA 59.722 47.619 0.00 0.00 0.00 3.36
646 676 0.901827 ACACACACACACACAGAGGA 59.098 50.000 0.00 0.00 0.00 3.71
647 677 1.009078 CACACACACACACACAGAGG 58.991 55.000 0.00 0.00 0.00 3.69
648 678 1.394572 CACACACACACACACACAGAG 59.605 52.381 0.00 0.00 0.00 3.35
649 679 1.270571 ACACACACACACACACACAGA 60.271 47.619 0.00 0.00 0.00 3.41
650 680 1.136000 CACACACACACACACACACAG 60.136 52.381 0.00 0.00 0.00 3.66
651 681 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
652 682 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
653 683 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
654 684 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
655 685 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
656 686 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
657 687 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
658 688 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
659 689 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
660 690 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
661 691 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
662 692 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
663 693 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
664 694 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
665 695 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
666 696 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
667 697 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
668 698 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
669 699 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
670 700 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
671 701 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
672 702 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
673 703 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
674 704 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
675 705 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
676 706 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
677 707 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
678 708 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
679 709 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
680 710 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
681 711 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
682 712 1.128507 CTCACACACACACACACACAC 59.871 52.381 0.00 0.00 0.00 3.82
683 713 1.001406 TCTCACACACACACACACACA 59.999 47.619 0.00 0.00 0.00 3.72
684 714 1.720805 TCTCACACACACACACACAC 58.279 50.000 0.00 0.00 0.00 3.82
685 715 2.345876 CTTCTCACACACACACACACA 58.654 47.619 0.00 0.00 0.00 3.72
686 716 1.665679 CCTTCTCACACACACACACAC 59.334 52.381 0.00 0.00 0.00 3.82
697 727 4.022603 CTGATTCCTCTCTCCTTCTCACA 58.977 47.826 0.00 0.00 0.00 3.58
699 729 3.629539 CCCTGATTCCTCTCTCCTTCTCA 60.630 52.174 0.00 0.00 0.00 3.27
704 734 0.267356 CCCCCTGATTCCTCTCTCCT 59.733 60.000 0.00 0.00 0.00 3.69
754 784 3.527253 TCTTTCCCTTATGATCTTGCCCA 59.473 43.478 0.00 0.00 0.00 5.36
794 824 0.177141 GGCATGTGGCAGCATGATTT 59.823 50.000 24.52 0.00 46.65 2.17
907 937 4.608948 AGTTCTGGTTCTGGTTCTAGTG 57.391 45.455 0.00 0.00 0.00 2.74
918 948 7.086230 TCGATCTAGTTCTAAGTTCTGGTTC 57.914 40.000 0.00 0.00 0.00 3.62
922 952 6.566942 CGGGATCGATCTAGTTCTAAGTTCTG 60.567 46.154 23.96 4.84 39.00 3.02
992 1025 2.202756 GAGCACCCATCGACCGAC 60.203 66.667 0.00 0.00 0.00 4.79
1074 1107 4.363990 CTGGCGTGGTGCTCGAGT 62.364 66.667 15.13 0.00 45.43 4.18
1176 1209 2.423898 GCTCCCCACGCTACTGCTA 61.424 63.158 0.00 0.00 36.97 3.49
1546 1579 4.514577 CATCCGGCCGAAGTCGCT 62.515 66.667 30.73 0.00 38.18 4.93
1717 1750 5.589855 TGAATTTATATGTCAGGGTGCACTG 59.410 40.000 17.98 8.37 39.84 3.66
1812 1845 1.484240 ACACACATGTTTTGGGTTGGG 59.516 47.619 0.00 0.00 39.64 4.12
1852 1885 1.635817 GGGGAGCCAGCAATGGAGTA 61.636 60.000 0.00 0.00 0.00 2.59
2124 2171 3.495276 GGGCTAGAATTCTTGGGAGTAGC 60.495 52.174 14.36 13.80 0.00 3.58
2158 2206 1.803555 GCTAGCTAGCTAAAGGCATGC 59.196 52.381 33.71 17.82 45.62 4.06
2205 2258 2.283298 AGCATGGATAACTCAGTTGCG 58.717 47.619 0.00 0.00 0.00 4.85
2283 2392 1.153208 GCTCCATGCTGCTGCTACT 60.153 57.895 17.00 0.00 40.48 2.57
2284 2393 2.532256 CGCTCCATGCTGCTGCTAC 61.532 63.158 17.00 0.00 40.48 3.58
2285 2394 2.202974 CGCTCCATGCTGCTGCTA 60.203 61.111 17.00 3.79 40.48 3.49
2286 2395 4.091939 TCGCTCCATGCTGCTGCT 62.092 61.111 17.00 0.00 40.48 4.24
2287 2396 3.574445 CTCGCTCCATGCTGCTGC 61.574 66.667 8.89 8.89 40.11 5.25
2288 2397 2.125229 ACTCGCTCCATGCTGCTG 60.125 61.111 0.00 0.00 40.11 4.41
2289 2398 2.186384 GACTCGCTCCATGCTGCT 59.814 61.111 0.00 0.00 40.11 4.24
2290 2399 3.260483 CGACTCGCTCCATGCTGC 61.260 66.667 0.00 0.00 40.11 5.25
2291 2400 2.584418 CCGACTCGCTCCATGCTG 60.584 66.667 0.00 0.00 40.11 4.41
2381 2496 7.972832 AAATACATTTGAACCGAACACTAGA 57.027 32.000 0.00 0.00 0.00 2.43
2425 2556 7.061673 CGGTCTAGTCGTAGTAGTATATGTCAC 59.938 44.444 0.00 0.00 0.00 3.67
2440 2571 2.621998 CCATGGATTACGGTCTAGTCGT 59.378 50.000 5.56 15.47 43.64 4.34
2441 2572 2.882761 TCCATGGATTACGGTCTAGTCG 59.117 50.000 11.44 6.68 0.00 4.18
2442 2573 6.015688 TGTTATCCATGGATTACGGTCTAGTC 60.016 42.308 31.70 8.65 37.07 2.59
2448 2579 4.080807 TGTGTGTTATCCATGGATTACGGT 60.081 41.667 31.70 10.61 37.07 4.83
2518 2659 3.704566 TCAAATCCTTCTTAGCTAGCCGA 59.295 43.478 12.13 2.75 0.00 5.54
2565 2706 4.754618 CACTCTGCGCCCACATTATTTATA 59.245 41.667 4.18 0.00 0.00 0.98
2571 2712 1.078497 CCACTCTGCGCCCACATTA 60.078 57.895 4.18 0.00 0.00 1.90
2576 2717 3.315142 GATCACCACTCTGCGCCCA 62.315 63.158 4.18 0.00 0.00 5.36
2779 2933 0.674269 GACTCACTCGACGTCTCCCT 60.674 60.000 14.70 0.00 0.00 4.20
2908 3066 1.957562 GGAGGATGATGCATGCTGC 59.042 57.895 20.33 11.20 42.36 5.25
2909 3067 1.524848 GAGGAGGATGATGCATGCTG 58.475 55.000 20.33 0.00 42.36 4.41
2910 3068 0.400975 GGAGGAGGATGATGCATGCT 59.599 55.000 20.33 4.11 44.85 3.79
2954 3116 9.211485 TGCCAGTAGTTGATTAGTAGTTAAAAC 57.789 33.333 0.00 0.00 0.00 2.43
3008 3173 4.017126 GGAGTAAATCACAAGGAAAGGGG 58.983 47.826 0.00 0.00 0.00 4.79
3009 3174 4.662278 TGGAGTAAATCACAAGGAAAGGG 58.338 43.478 0.00 0.00 0.00 3.95
3040 3214 0.387112 ACCAAACATTCATGCACGCG 60.387 50.000 3.53 3.53 0.00 6.01
3041 3215 1.062258 CACCAAACATTCATGCACGC 58.938 50.000 0.00 0.00 0.00 5.34
3042 3216 1.062258 GCACCAAACATTCATGCACG 58.938 50.000 0.00 0.00 36.30 5.34
3043 3217 1.062258 CGCACCAAACATTCATGCAC 58.938 50.000 0.00 0.00 36.02 4.57
3044 3218 0.666880 GCGCACCAAACATTCATGCA 60.667 50.000 0.30 0.00 36.02 3.96
3045 3219 0.666880 TGCGCACCAAACATTCATGC 60.667 50.000 5.66 0.00 0.00 4.06
3046 3220 1.068402 TCTGCGCACCAAACATTCATG 60.068 47.619 5.66 0.00 0.00 3.07
3047 3221 1.068333 GTCTGCGCACCAAACATTCAT 60.068 47.619 5.66 0.00 0.00 2.57
3407 3581 3.142838 ATGGGCGCCTGCATGTTC 61.143 61.111 28.56 7.32 45.35 3.18
3408 3582 3.454573 CATGGGCGCCTGCATGTT 61.455 61.111 27.89 4.79 45.35 2.71
3409 3583 4.746309 ACATGGGCGCCTGCATGT 62.746 61.111 32.91 32.91 45.35 3.21
3410 3584 3.896133 GACATGGGCGCCTGCATG 61.896 66.667 31.85 31.85 45.35 4.06
3657 3836 2.677337 TCCTTCCGTTTCGTTTCGTTTT 59.323 40.909 0.00 0.00 0.00 2.43
3691 3870 0.237235 GTGGTGCATGTACGTTGTGG 59.763 55.000 7.89 0.00 0.00 4.17
3905 4087 1.352156 GAAGCCTTGTACTGACCGCG 61.352 60.000 0.00 0.00 0.00 6.46
3959 4141 6.708054 CCTGAGAAGTTGAATGTATATGGGTC 59.292 42.308 0.00 0.00 0.00 4.46
4043 4391 6.161855 TGAATCTATTTGAGCGACATAGGT 57.838 37.500 0.00 0.00 0.00 3.08
4045 4393 9.288124 CTAGATGAATCTATTTGAGCGACATAG 57.712 37.037 0.58 0.00 38.60 2.23
4046 4394 9.014297 TCTAGATGAATCTATTTGAGCGACATA 57.986 33.333 0.58 0.00 38.60 2.29
4047 4395 7.890515 TCTAGATGAATCTATTTGAGCGACAT 58.109 34.615 0.58 0.00 38.60 3.06
4082 4436 6.807230 GTCGCTCAAACGGATGTATCTAATAT 59.193 38.462 0.00 0.00 0.00 1.28
4084 4438 4.982916 GTCGCTCAAACGGATGTATCTAAT 59.017 41.667 0.00 0.00 0.00 1.73
4085 4439 4.142337 TGTCGCTCAAACGGATGTATCTAA 60.142 41.667 0.00 0.00 0.00 2.10
4117 4471 7.038302 TGTCAAATCAGTTACTACCTCCAATCT 60.038 37.037 0.00 0.00 0.00 2.40
4166 4520 8.716909 CCATACTTCAACCGCAAAAATAAAAAT 58.283 29.630 0.00 0.00 0.00 1.82
4167 4521 7.926555 TCCATACTTCAACCGCAAAAATAAAAA 59.073 29.630 0.00 0.00 0.00 1.94
4168 4522 7.382759 GTCCATACTTCAACCGCAAAAATAAAA 59.617 33.333 0.00 0.00 0.00 1.52
4169 4523 6.864165 GTCCATACTTCAACCGCAAAAATAAA 59.136 34.615 0.00 0.00 0.00 1.40
4170 4524 6.207810 AGTCCATACTTCAACCGCAAAAATAA 59.792 34.615 0.00 0.00 29.00 1.40
4171 4525 5.708230 AGTCCATACTTCAACCGCAAAAATA 59.292 36.000 0.00 0.00 29.00 1.40
4172 4526 4.522789 AGTCCATACTTCAACCGCAAAAAT 59.477 37.500 0.00 0.00 29.00 1.82
4173 4527 3.886505 AGTCCATACTTCAACCGCAAAAA 59.113 39.130 0.00 0.00 29.00 1.94
4174 4528 3.482436 AGTCCATACTTCAACCGCAAAA 58.518 40.909 0.00 0.00 29.00 2.44
4175 4529 3.071479 GAGTCCATACTTCAACCGCAAA 58.929 45.455 0.00 0.00 35.56 3.68
4176 4530 2.037902 TGAGTCCATACTTCAACCGCAA 59.962 45.455 0.00 0.00 35.56 4.85
4177 4531 1.621317 TGAGTCCATACTTCAACCGCA 59.379 47.619 0.00 0.00 35.56 5.69
4178 4532 2.380084 TGAGTCCATACTTCAACCGC 57.620 50.000 0.00 0.00 35.56 5.68
4179 4533 6.049149 ACATAATGAGTCCATACTTCAACCG 58.951 40.000 0.00 0.00 35.56 4.44
4180 4534 7.275920 AGACATAATGAGTCCATACTTCAACC 58.724 38.462 0.00 0.00 35.56 3.77
4181 4535 8.723942 AAGACATAATGAGTCCATACTTCAAC 57.276 34.615 0.00 0.00 35.56 3.18
4183 4537 8.144478 GCTAAGACATAATGAGTCCATACTTCA 58.856 37.037 0.00 0.00 35.56 3.02
4184 4538 8.364142 AGCTAAGACATAATGAGTCCATACTTC 58.636 37.037 0.00 0.00 35.56 3.01
4280 4634 7.201884 CGGAGGTAGTATCTCTTTTGGAACATA 60.202 40.741 10.27 0.00 39.30 2.29
4289 4643 4.208746 CAGGACGGAGGTAGTATCTCTTT 58.791 47.826 10.27 0.00 0.00 2.52
4296 4650 2.610438 AAACCAGGACGGAGGTAGTA 57.390 50.000 0.00 0.00 37.07 1.82
4301 4655 3.181468 GGACTTATAAACCAGGACGGAGG 60.181 52.174 0.00 0.00 38.63 4.30
4302 4656 3.705072 AGGACTTATAAACCAGGACGGAG 59.295 47.826 0.00 0.00 38.63 4.63
4303 4657 3.716431 AGGACTTATAAACCAGGACGGA 58.284 45.455 0.00 0.00 38.63 4.69
4304 4658 4.482952 AAGGACTTATAAACCAGGACGG 57.517 45.455 0.00 0.00 42.50 4.79
4305 4659 6.206048 ACAAAAAGGACTTATAAACCAGGACG 59.794 38.462 0.00 0.00 0.00 4.79
4306 4660 7.520451 ACAAAAAGGACTTATAAACCAGGAC 57.480 36.000 0.00 0.00 0.00 3.85
4307 4661 9.816787 AATACAAAAAGGACTTATAAACCAGGA 57.183 29.630 0.00 0.00 0.00 3.86
4318 4672 9.665719 ATTTGACACAAAATACAAAAAGGACTT 57.334 25.926 0.00 0.00 36.19 3.01
4319 4673 9.665719 AATTTGACACAAAATACAAAAAGGACT 57.334 25.926 0.00 0.00 36.19 3.85
4364 4718 9.887629 TTTGGTGACATGCATCAATATTTTATT 57.112 25.926 13.99 0.00 46.39 1.40
4365 4719 9.887629 TTTTGGTGACATGCATCAATATTTTAT 57.112 25.926 13.99 0.00 46.39 1.40
4366 4720 9.887629 ATTTTGGTGACATGCATCAATATTTTA 57.112 25.926 13.99 0.00 46.39 1.52
4367 4721 8.795842 ATTTTGGTGACATGCATCAATATTTT 57.204 26.923 13.99 0.00 46.39 1.82
4368 4722 8.795842 AATTTTGGTGACATGCATCAATATTT 57.204 26.923 17.45 10.20 46.39 1.40
4369 4723 8.795842 AAATTTTGGTGACATGCATCAATATT 57.204 26.923 17.45 17.45 46.39 1.28
4373 4727 9.531942 GATATAAATTTTGGTGACATGCATCAA 57.468 29.630 10.53 10.53 45.55 2.57
4374 4728 7.861872 CGATATAAATTTTGGTGACATGCATCA 59.138 33.333 0.00 0.00 42.32 3.07
4375 4729 7.862372 ACGATATAAATTTTGGTGACATGCATC 59.138 33.333 0.00 0.00 42.32 3.91
4376 4730 7.715657 ACGATATAAATTTTGGTGACATGCAT 58.284 30.769 0.00 0.00 42.32 3.96
4377 4731 7.094508 ACGATATAAATTTTGGTGACATGCA 57.905 32.000 0.00 0.00 42.32 3.96
4378 4732 7.043458 CCAACGATATAAATTTTGGTGACATGC 60.043 37.037 0.00 0.00 42.32 4.06
4379 4733 8.187480 TCCAACGATATAAATTTTGGTGACATG 58.813 33.333 0.00 0.00 42.32 3.21
4380 4734 8.287439 TCCAACGATATAAATTTTGGTGACAT 57.713 30.769 0.00 0.00 42.32 3.06
4381 4735 7.689446 TCCAACGATATAAATTTTGGTGACA 57.311 32.000 0.00 0.00 38.32 3.58
4382 4736 9.233232 GAATCCAACGATATAAATTTTGGTGAC 57.767 33.333 0.00 0.00 38.32 3.67
4383 4737 9.184523 AGAATCCAACGATATAAATTTTGGTGA 57.815 29.630 0.00 0.00 38.32 4.02
4384 4738 9.801873 AAGAATCCAACGATATAAATTTTGGTG 57.198 29.630 0.00 0.00 38.32 4.17
4397 4751 9.396022 ACTATGTTCAAATAAGAATCCAACGAT 57.604 29.630 0.00 0.00 0.00 3.73
4398 4752 8.786826 ACTATGTTCAAATAAGAATCCAACGA 57.213 30.769 0.00 0.00 0.00 3.85
4399 4753 9.840427 AAACTATGTTCAAATAAGAATCCAACG 57.160 29.630 0.00 0.00 0.00 4.10
4402 4756 9.527157 TGGAAACTATGTTCAAATAAGAATCCA 57.473 29.630 0.00 0.00 0.00 3.41
4466 4820 8.573035 TGCCAAAGTTCGATCTTAAATTTAACT 58.427 29.630 9.09 0.87 0.00 2.24
4467 4821 8.635983 GTGCCAAAGTTCGATCTTAAATTTAAC 58.364 33.333 9.09 0.00 0.00 2.01
4468 4822 8.353684 TGTGCCAAAGTTCGATCTTAAATTTAA 58.646 29.630 9.09 10.16 0.00 1.52
4469 4823 7.877003 TGTGCCAAAGTTCGATCTTAAATTTA 58.123 30.769 9.09 0.00 0.00 1.40
4470 4824 6.744112 TGTGCCAAAGTTCGATCTTAAATTT 58.256 32.000 9.09 0.00 0.00 1.82
4471 4825 6.325919 TGTGCCAAAGTTCGATCTTAAATT 57.674 33.333 9.09 0.00 0.00 1.82
4472 4826 5.957842 TGTGCCAAAGTTCGATCTTAAAT 57.042 34.783 9.09 0.00 0.00 1.40
4473 4827 5.957842 ATGTGCCAAAGTTCGATCTTAAA 57.042 34.783 9.09 0.00 0.00 1.52
4474 4828 7.624360 ATTATGTGCCAAAGTTCGATCTTAA 57.376 32.000 9.09 0.00 0.00 1.85
4475 4829 7.766738 TGTATTATGTGCCAAAGTTCGATCTTA 59.233 33.333 9.09 0.00 0.00 2.10
4476 4830 6.597672 TGTATTATGTGCCAAAGTTCGATCTT 59.402 34.615 2.83 2.83 0.00 2.40
4477 4831 6.112734 TGTATTATGTGCCAAAGTTCGATCT 58.887 36.000 0.00 0.00 0.00 2.75
4478 4832 6.358118 TGTATTATGTGCCAAAGTTCGATC 57.642 37.500 0.00 0.00 0.00 3.69
4479 4833 6.751514 TTGTATTATGTGCCAAAGTTCGAT 57.248 33.333 0.00 0.00 0.00 3.59
4480 4834 6.348950 CCTTTGTATTATGTGCCAAAGTTCGA 60.349 38.462 9.36 0.00 41.23 3.71
4481 4835 5.799936 CCTTTGTATTATGTGCCAAAGTTCG 59.200 40.000 9.36 0.00 41.23 3.95
4482 4836 6.099341 CCCTTTGTATTATGTGCCAAAGTTC 58.901 40.000 9.36 0.00 41.23 3.01
4483 4837 5.046663 CCCCTTTGTATTATGTGCCAAAGTT 60.047 40.000 9.36 0.00 41.23 2.66
4484 4838 4.466015 CCCCTTTGTATTATGTGCCAAAGT 59.534 41.667 9.36 0.00 41.23 2.66
4485 4839 4.709397 TCCCCTTTGTATTATGTGCCAAAG 59.291 41.667 0.00 0.00 42.03 2.77
4486 4840 4.464597 GTCCCCTTTGTATTATGTGCCAAA 59.535 41.667 0.00 0.00 0.00 3.28
4487 4841 4.020543 GTCCCCTTTGTATTATGTGCCAA 58.979 43.478 0.00 0.00 0.00 4.52
4488 4842 3.268334 AGTCCCCTTTGTATTATGTGCCA 59.732 43.478 0.00 0.00 0.00 4.92
4489 4843 3.898482 AGTCCCCTTTGTATTATGTGCC 58.102 45.455 0.00 0.00 0.00 5.01
4490 4844 6.354130 TCTTAGTCCCCTTTGTATTATGTGC 58.646 40.000 0.00 0.00 0.00 4.57
4491 4845 8.801882 TTTCTTAGTCCCCTTTGTATTATGTG 57.198 34.615 0.00 0.00 0.00 3.21
4492 4846 9.628500 GATTTCTTAGTCCCCTTTGTATTATGT 57.372 33.333 0.00 0.00 0.00 2.29
4493 4847 9.627123 TGATTTCTTAGTCCCCTTTGTATTATG 57.373 33.333 0.00 0.00 0.00 1.90
4494 4848 9.853177 CTGATTTCTTAGTCCCCTTTGTATTAT 57.147 33.333 0.00 0.00 0.00 1.28
4495 4849 8.272173 CCTGATTTCTTAGTCCCCTTTGTATTA 58.728 37.037 0.00 0.00 0.00 0.98
4496 4850 7.036863 TCCTGATTTCTTAGTCCCCTTTGTATT 60.037 37.037 0.00 0.00 0.00 1.89
4497 4851 6.447084 TCCTGATTTCTTAGTCCCCTTTGTAT 59.553 38.462 0.00 0.00 0.00 2.29
4498 4852 5.788533 TCCTGATTTCTTAGTCCCCTTTGTA 59.211 40.000 0.00 0.00 0.00 2.41
4499 4853 4.601857 TCCTGATTTCTTAGTCCCCTTTGT 59.398 41.667 0.00 0.00 0.00 2.83
4500 4854 4.944317 GTCCTGATTTCTTAGTCCCCTTTG 59.056 45.833 0.00 0.00 0.00 2.77
4501 4855 4.601857 TGTCCTGATTTCTTAGTCCCCTTT 59.398 41.667 0.00 0.00 0.00 3.11
4502 4856 4.175962 TGTCCTGATTTCTTAGTCCCCTT 58.824 43.478 0.00 0.00 0.00 3.95
4503 4857 3.777522 CTGTCCTGATTTCTTAGTCCCCT 59.222 47.826 0.00 0.00 0.00 4.79
4504 4858 3.775316 TCTGTCCTGATTTCTTAGTCCCC 59.225 47.826 0.00 0.00 0.00 4.81
4505 4859 4.141824 CCTCTGTCCTGATTTCTTAGTCCC 60.142 50.000 0.00 0.00 0.00 4.46
4506 4860 4.468153 ACCTCTGTCCTGATTTCTTAGTCC 59.532 45.833 0.00 0.00 0.00 3.85
4507 4861 5.669164 ACCTCTGTCCTGATTTCTTAGTC 57.331 43.478 0.00 0.00 0.00 2.59
4508 4862 6.257586 ACTACCTCTGTCCTGATTTCTTAGT 58.742 40.000 0.00 0.00 0.00 2.24
4509 4863 6.783708 ACTACCTCTGTCCTGATTTCTTAG 57.216 41.667 0.00 0.00 0.00 2.18
4510 4864 7.411808 AGTACTACCTCTGTCCTGATTTCTTA 58.588 38.462 0.00 0.00 0.00 2.10
4511 4865 6.257586 AGTACTACCTCTGTCCTGATTTCTT 58.742 40.000 0.00 0.00 0.00 2.52
4512 4866 5.833340 AGTACTACCTCTGTCCTGATTTCT 58.167 41.667 0.00 0.00 0.00 2.52
4513 4867 7.502895 TCATAGTACTACCTCTGTCCTGATTTC 59.497 40.741 4.31 0.00 0.00 2.17
4514 4868 7.355101 TCATAGTACTACCTCTGTCCTGATTT 58.645 38.462 4.31 0.00 0.00 2.17
4515 4869 6.912426 TCATAGTACTACCTCTGTCCTGATT 58.088 40.000 4.31 0.00 0.00 2.57
4516 4870 6.517013 TCATAGTACTACCTCTGTCCTGAT 57.483 41.667 4.31 0.00 0.00 2.90
4517 4871 5.970501 TCATAGTACTACCTCTGTCCTGA 57.029 43.478 4.31 0.00 0.00 3.86
4518 4872 6.547880 ACATTCATAGTACTACCTCTGTCCTG 59.452 42.308 4.31 0.00 0.00 3.86
4519 4873 6.674573 ACATTCATAGTACTACCTCTGTCCT 58.325 40.000 4.31 0.00 0.00 3.85
4520 4874 6.016108 GGACATTCATAGTACTACCTCTGTCC 60.016 46.154 25.39 25.39 41.30 4.02
4521 4875 6.773685 AGGACATTCATAGTACTACCTCTGTC 59.226 42.308 19.47 19.47 0.00 3.51
4522 4876 6.547880 CAGGACATTCATAGTACTACCTCTGT 59.452 42.308 4.31 7.17 0.00 3.41
4523 4877 6.547880 ACAGGACATTCATAGTACTACCTCTG 59.452 42.308 4.31 0.00 0.00 3.35
4524 4878 6.674573 ACAGGACATTCATAGTACTACCTCT 58.325 40.000 4.31 0.00 0.00 3.69
4525 4879 6.963083 ACAGGACATTCATAGTACTACCTC 57.037 41.667 4.31 0.00 0.00 3.85
4526 4880 7.556844 CAAACAGGACATTCATAGTACTACCT 58.443 38.462 4.31 2.43 0.00 3.08
4527 4881 6.258068 GCAAACAGGACATTCATAGTACTACC 59.742 42.308 4.31 0.00 0.00 3.18
4528 4882 6.816640 TGCAAACAGGACATTCATAGTACTAC 59.183 38.462 4.31 0.00 0.00 2.73
4529 4883 6.816640 GTGCAAACAGGACATTCATAGTACTA 59.183 38.462 4.77 4.77 38.62 1.82
4530 4884 5.643777 GTGCAAACAGGACATTCATAGTACT 59.356 40.000 0.00 0.00 38.62 2.73
4531 4885 5.163754 GGTGCAAACAGGACATTCATAGTAC 60.164 44.000 0.00 0.00 40.89 2.73


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

AutoCloner maintained by Alex Coulton.