Multiple sequence alignment - TraesCS2A01G184500

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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 TraesCS2A01G184500 chr2A 100.000 4569 0 0 1 4569 144849046 144853614 0.000000e+00 8438
1 TraesCS2A01G184500 chr2D 90.909 1628 75 29 1 1593 155478618 155477029 0.000000e+00 2119
2 TraesCS2A01G184500 chr2D 96.154 1144 41 3 1642 2785 155477026 155475886 0.000000e+00 1866
3 TraesCS2A01G184500 chr2D 92.484 479 22 9 3321 3796 155475894 155475427 0.000000e+00 673
4 TraesCS2A01G184500 chr2D 78.041 888 145 30 1793 2660 1588832 1589689 8.770000e-142 514
5 TraesCS2A01G184500 chr2B 88.970 1641 85 41 1 1593 212774038 212772446 0.000000e+00 1940
6 TraesCS2A01G184500 chr2B 95.542 1144 48 3 1642 2785 212772444 212771304 0.000000e+00 1827
7 TraesCS2A01G184500 chr2B 79.454 915 140 32 1675 2580 10356934 10357809 5.060000e-169 604
8 TraesCS2A01G184500 chr2B 89.431 492 29 9 3321 3808 212771312 212770840 2.350000e-167 599
9 TraesCS2A01G184500 chr2B 77.178 964 172 30 1638 2576 10597924 10598864 6.780000e-143 518
10 TraesCS2A01G184500 chr1D 91.575 546 40 2 2785 3324 260959960 260960505 0.000000e+00 749
11 TraesCS2A01G184500 chr1D 83.562 584 83 9 3998 4569 112915832 112916414 6.730000e-148 534
12 TraesCS2A01G184500 chr3D 91.560 545 40 2 2785 3324 496940293 496940836 0.000000e+00 747
13 TraesCS2A01G184500 chr1B 91.544 544 41 1 2785 3323 666575891 666576434 0.000000e+00 745
14 TraesCS2A01G184500 chr1B 90.264 493 42 2 2786 3272 646559840 646559348 1.390000e-179 640
15 TraesCS2A01G184500 chr1B 85.474 475 63 5 4096 4569 684342469 684342938 1.480000e-134 490
16 TraesCS2A01G184500 chr7D 90.876 548 42 4 2785 3324 565242153 565242700 0.000000e+00 728
17 TraesCS2A01G184500 chr7D 85.237 569 80 3 4002 4569 236834567 236834002 2.370000e-162 582
18 TraesCS2A01G184500 chr7B 90.826 545 45 2 2784 3324 184304290 184304833 0.000000e+00 725
19 TraesCS2A01G184500 chr3B 92.476 412 23 3 2782 3187 678194871 678195280 2.370000e-162 582
20 TraesCS2A01G184500 chr3B 81.709 585 88 10 3998 4569 691483105 691482527 1.920000e-128 470
21 TraesCS2A01G184500 chr3B 90.476 210 16 3 2782 2990 678196234 678196440 1.620000e-69 274
22 TraesCS2A01G184500 chrUn 90.951 431 33 2 2902 3327 154519474 154519045 3.960000e-160 575
23 TraesCS2A01G184500 chrUn 90.654 428 34 2 2902 3324 323396785 323397211 8.580000e-157 564
24 TraesCS2A01G184500 chr1A 85.341 498 70 3 4073 4569 380260767 380261262 3.150000e-141 512
25 TraesCS2A01G184500 chr5A 85.178 506 63 11 4067 4569 591098466 591097970 4.080000e-140 508
26 TraesCS2A01G184500 chr4D 82.414 580 88 8 3999 4566 35361375 35361952 1.140000e-135 494
27 TraesCS2A01G184500 chr6D 84.694 490 69 6 4073 4560 387882219 387881734 6.870000e-133 484
28 TraesCS2A01G184500 chr4A 83.333 504 80 4 4068 4569 567224809 567224308 3.220000e-126 462
29 TraesCS2A01G184500 chr7A 85.165 182 26 1 2785 2966 521873419 521873239 7.810000e-43 185


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 TraesCS2A01G184500 chr2A 144849046 144853614 4568 False 8438.000000 8438 100.000000 1 4569 1 chr2A.!!$F1 4568
1 TraesCS2A01G184500 chr2D 155475427 155478618 3191 True 1552.666667 2119 93.182333 1 3796 3 chr2D.!!$R1 3795
2 TraesCS2A01G184500 chr2D 1588832 1589689 857 False 514.000000 514 78.041000 1793 2660 1 chr2D.!!$F1 867
3 TraesCS2A01G184500 chr2B 212770840 212774038 3198 True 1455.333333 1940 91.314333 1 3808 3 chr2B.!!$R1 3807
4 TraesCS2A01G184500 chr2B 10356934 10357809 875 False 604.000000 604 79.454000 1675 2580 1 chr2B.!!$F1 905
5 TraesCS2A01G184500 chr2B 10597924 10598864 940 False 518.000000 518 77.178000 1638 2576 1 chr2B.!!$F2 938
6 TraesCS2A01G184500 chr1D 260959960 260960505 545 False 749.000000 749 91.575000 2785 3324 1 chr1D.!!$F2 539
7 TraesCS2A01G184500 chr1D 112915832 112916414 582 False 534.000000 534 83.562000 3998 4569 1 chr1D.!!$F1 571
8 TraesCS2A01G184500 chr3D 496940293 496940836 543 False 747.000000 747 91.560000 2785 3324 1 chr3D.!!$F1 539
9 TraesCS2A01G184500 chr1B 666575891 666576434 543 False 745.000000 745 91.544000 2785 3323 1 chr1B.!!$F1 538
10 TraesCS2A01G184500 chr7D 565242153 565242700 547 False 728.000000 728 90.876000 2785 3324 1 chr7D.!!$F1 539
11 TraesCS2A01G184500 chr7D 236834002 236834567 565 True 582.000000 582 85.237000 4002 4569 1 chr7D.!!$R1 567
12 TraesCS2A01G184500 chr7B 184304290 184304833 543 False 725.000000 725 90.826000 2784 3324 1 chr7B.!!$F1 540
13 TraesCS2A01G184500 chr3B 691482527 691483105 578 True 470.000000 470 81.709000 3998 4569 1 chr3B.!!$R1 571
14 TraesCS2A01G184500 chr3B 678194871 678196440 1569 False 428.000000 582 91.476000 2782 3187 2 chr3B.!!$F1 405
15 TraesCS2A01G184500 chr4D 35361375 35361952 577 False 494.000000 494 82.414000 3999 4566 1 chr4D.!!$F1 567
16 TraesCS2A01G184500 chr4A 567224308 567224809 501 True 462.000000 462 83.333000 4068 4569 1 chr4A.!!$R1 501

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
985 1025 0.104855 TCGCATCGGCAGCTTCTTAT 59.895 50.000 0.00 0.0 41.24 1.73 F
1243 1283 1.447643 GGGATCCTGGACGATGGTG 59.552 63.158 12.58 0.0 0.00 4.17 F
2209 2277 0.457853 CGAAATCTCGGCTCGGTCAA 60.458 55.000 0.00 0.0 41.57 3.18 F
3129 3925 0.251033 AGACCAGCAATGCAAGCTCA 60.251 50.000 13.45 0.0 41.14 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1932 2000 1.686355 GGTGTCATGTTGTCACCCAA 58.314 50.0 11.36 0.0 46.23 4.12 R
3129 3925 0.539051 CATGGAGGAAGCGGAACTCT 59.461 55.0 0.00 0.0 0.00 3.24 R
3243 4080 0.312729 TGTCGACGCTAGCTTTGTGA 59.687 50.0 13.93 0.5 0.00 3.58 R
4022 4953 0.536460 GCGTTTGAGGAGGGTTTGGA 60.536 55.0 0.00 0.0 0.00 3.53 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
106 107 1.463444 GTGGCTGTGTTGGTAATCGAC 59.537 52.381 0.00 0.00 0.00 4.20
112 113 2.557924 TGTGTTGGTAATCGACGTAGGT 59.442 45.455 0.00 0.00 32.34 3.08
159 160 5.063880 AGTGTGTTCTAAACATGGGAAGTC 58.936 41.667 0.00 0.00 44.35 3.01
213 218 5.269459 CAACAGAATACTCGTTGGTGAAG 57.731 43.478 0.00 0.00 37.07 3.02
215 220 4.810790 ACAGAATACTCGTTGGTGAAGAG 58.189 43.478 0.00 0.00 37.96 2.85
223 228 1.140816 GTTGGTGAAGAGAGCGTGTC 58.859 55.000 0.00 0.00 0.00 3.67
230 235 2.750166 TGAAGAGAGCGTGTCCTTCTAG 59.250 50.000 0.00 0.00 35.28 2.43
237 242 1.813786 GCGTGTCCTTCTAGTCTGACT 59.186 52.381 15.57 15.57 0.00 3.41
238 243 2.229302 GCGTGTCCTTCTAGTCTGACTT 59.771 50.000 16.53 0.37 0.00 3.01
241 246 4.918583 CGTGTCCTTCTAGTCTGACTTTTC 59.081 45.833 16.53 1.60 0.00 2.29
247 252 8.338986 GTCCTTCTAGTCTGACTTTTCTTTTTG 58.661 37.037 16.53 0.00 0.00 2.44
275 280 1.927895 CTGACCGCAGTTCTATCACC 58.072 55.000 0.00 0.00 37.37 4.02
320 325 1.536766 TGCTCTTGCAGAAACCGAATG 59.463 47.619 0.00 0.00 45.31 2.67
322 327 2.030805 GCTCTTGCAGAAACCGAATGTT 60.031 45.455 0.00 0.00 37.76 2.71
327 332 2.890311 TGCAGAAACCGAATGTTGGATT 59.110 40.909 0.00 0.00 37.23 3.01
448 460 9.694520 CTGTCTCAGAAAATATATCGTTTTGTG 57.305 33.333 13.09 13.09 39.68 3.33
453 465 6.628856 CAGAAAATATATCGTTTTGTGAGCGG 59.371 38.462 13.66 0.00 40.33 5.52
473 496 4.036262 GCGGGATGCAAACATATTGAGTTA 59.964 41.667 0.00 0.00 45.45 2.24
475 498 5.971202 CGGGATGCAAACATATTGAGTTAAC 59.029 40.000 0.00 0.00 36.35 2.01
513 541 6.539324 CCAAAATGCATGATGTTTGATGAAC 58.461 36.000 18.76 0.00 38.78 3.18
564 592 7.985634 ATAAAATGCATGTGACCGAAATTAC 57.014 32.000 0.00 0.00 0.00 1.89
568 596 2.747446 GCATGTGACCGAAATTACCTGT 59.253 45.455 0.00 0.00 0.00 4.00
579 607 5.009210 CCGAAATTACCTGTTGACAAGGAAA 59.991 40.000 0.00 0.00 0.00 3.13
588 616 3.694072 TGTTGACAAGGAAACTGAACCAG 59.306 43.478 0.00 0.00 42.68 4.00
641 672 2.359975 GGCGGACCCAGGTGAAAG 60.360 66.667 0.00 0.00 0.00 2.62
642 673 2.747686 GCGGACCCAGGTGAAAGA 59.252 61.111 0.00 0.00 0.00 2.52
643 674 1.072505 GCGGACCCAGGTGAAAGAA 59.927 57.895 0.00 0.00 0.00 2.52
644 675 1.235281 GCGGACCCAGGTGAAAGAAC 61.235 60.000 0.00 0.00 0.00 3.01
645 676 0.107831 CGGACCCAGGTGAAAGAACA 59.892 55.000 0.00 0.00 0.00 3.18
646 677 1.271379 CGGACCCAGGTGAAAGAACAT 60.271 52.381 0.00 0.00 0.00 2.71
647 678 2.162681 GGACCCAGGTGAAAGAACATG 58.837 52.381 0.00 0.00 0.00 3.21
648 679 2.489073 GGACCCAGGTGAAAGAACATGT 60.489 50.000 0.00 0.00 29.97 3.21
649 680 3.222603 GACCCAGGTGAAAGAACATGTT 58.777 45.455 11.78 11.78 29.97 2.71
650 681 4.394729 GACCCAGGTGAAAGAACATGTTA 58.605 43.478 11.95 0.00 29.97 2.41
651 682 4.398319 ACCCAGGTGAAAGAACATGTTAG 58.602 43.478 11.95 0.00 29.97 2.34
682 713 4.115516 CAGTCAAGTCAACCGATCATAGG 58.884 47.826 0.00 0.00 0.00 2.57
764 797 3.137533 GGAGCAAGCAGTCTATTCATCC 58.862 50.000 0.00 0.00 0.00 3.51
805 838 1.152204 TCCCGGTGTTCTCTTCCCA 60.152 57.895 0.00 0.00 0.00 4.37
806 839 1.003718 CCCGGTGTTCTCTTCCCAC 60.004 63.158 0.00 0.00 0.00 4.61
825 858 1.764723 ACAGCTTGGATCCATCATCGA 59.235 47.619 17.06 0.00 31.26 3.59
912 952 4.154195 CAGCTTCCTTGTGCGTACTTAATT 59.846 41.667 4.97 0.00 0.00 1.40
963 1003 4.671880 TCGTAAATTGCACGCTGTAATT 57.328 36.364 7.74 7.74 42.93 1.40
985 1025 0.104855 TCGCATCGGCAGCTTCTTAT 59.895 50.000 0.00 0.00 41.24 1.73
1095 1135 3.380004 AGAACTTCTCCGATGAGCTACTG 59.620 47.826 0.00 0.00 38.58 2.74
1136 1176 5.594317 TCGGGTCAGTTTATAAGGTAGTACC 59.406 44.000 11.73 11.73 38.99 3.34
1154 1194 4.947388 AGTACCGTATGATTTTGCCACAAT 59.053 37.500 0.00 0.00 0.00 2.71
1242 1282 1.766461 GGGGATCCTGGACGATGGT 60.766 63.158 12.58 0.00 0.00 3.55
1243 1283 1.447643 GGGATCCTGGACGATGGTG 59.552 63.158 12.58 0.00 0.00 4.17
1244 1284 1.447643 GGATCCTGGACGATGGTGG 59.552 63.158 3.84 0.00 0.00 4.61
1416 1456 5.230306 GCAGAGCAACGGACGATATATTATC 59.770 44.000 0.00 0.00 0.00 1.75
1564 1629 5.674525 CATGACTTTGCATAAGGTCCTCTA 58.325 41.667 11.59 0.00 40.93 2.43
1567 1632 6.349300 TGACTTTGCATAAGGTCCTCTATTC 58.651 40.000 11.59 0.00 40.93 1.75
1569 1634 6.963322 ACTTTGCATAAGGTCCTCTATTCTT 58.037 36.000 11.59 0.00 0.00 2.52
1571 1636 6.560003 TTGCATAAGGTCCTCTATTCTTCA 57.440 37.500 0.00 0.00 0.00 3.02
1576 1641 2.761208 AGGTCCTCTATTCTTCACACCG 59.239 50.000 0.00 0.00 0.00 4.94
1584 1649 7.289317 TCCTCTATTCTTCACACCGGTAATATT 59.711 37.037 6.87 0.00 0.00 1.28
1585 1650 7.385205 CCTCTATTCTTCACACCGGTAATATTG 59.615 40.741 6.87 0.00 0.00 1.90
1586 1651 5.751243 ATTCTTCACACCGGTAATATTGC 57.249 39.130 6.87 0.00 0.00 3.56
1587 1652 4.481368 TCTTCACACCGGTAATATTGCT 57.519 40.909 6.87 0.00 0.00 3.91
1593 1658 4.024893 CACACCGGTAATATTGCTAGCAAG 60.025 45.833 31.88 19.20 39.47 4.01
1609 1674 6.586868 CTAGCAAGCAAGATTCTTCTACTG 57.413 41.667 0.00 0.00 0.00 2.74
1610 1675 5.157940 AGCAAGCAAGATTCTTCTACTGA 57.842 39.130 0.00 0.00 0.00 3.41
1611 1676 5.743117 AGCAAGCAAGATTCTTCTACTGAT 58.257 37.500 0.00 0.00 0.00 2.90
1612 1677 6.882656 AGCAAGCAAGATTCTTCTACTGATA 58.117 36.000 0.00 0.00 0.00 2.15
1613 1678 7.334090 AGCAAGCAAGATTCTTCTACTGATAA 58.666 34.615 0.00 0.00 0.00 1.75
1614 1679 7.279758 AGCAAGCAAGATTCTTCTACTGATAAC 59.720 37.037 0.00 0.00 0.00 1.89
1615 1680 7.616673 CAAGCAAGATTCTTCTACTGATAACG 58.383 38.462 0.00 0.00 0.00 3.18
1616 1681 6.868622 AGCAAGATTCTTCTACTGATAACGT 58.131 36.000 0.00 0.00 0.00 3.99
1617 1682 6.754209 AGCAAGATTCTTCTACTGATAACGTG 59.246 38.462 0.00 0.00 0.00 4.49
1618 1683 6.531948 GCAAGATTCTTCTACTGATAACGTGT 59.468 38.462 0.00 0.00 0.00 4.49
1619 1684 7.463383 GCAAGATTCTTCTACTGATAACGTGTG 60.463 40.741 0.00 0.00 0.00 3.82
1620 1685 7.392494 AGATTCTTCTACTGATAACGTGTGA 57.608 36.000 0.00 0.00 0.00 3.58
1621 1686 8.001881 AGATTCTTCTACTGATAACGTGTGAT 57.998 34.615 0.00 0.00 0.00 3.06
1622 1687 7.918033 AGATTCTTCTACTGATAACGTGTGATG 59.082 37.037 0.00 0.00 0.00 3.07
1623 1688 6.510879 TCTTCTACTGATAACGTGTGATGT 57.489 37.500 0.00 0.00 0.00 3.06
1624 1689 6.920817 TCTTCTACTGATAACGTGTGATGTT 58.079 36.000 0.00 0.00 0.00 2.71
1625 1690 8.047413 TCTTCTACTGATAACGTGTGATGTTA 57.953 34.615 0.00 0.00 34.45 2.41
1626 1691 8.683615 TCTTCTACTGATAACGTGTGATGTTAT 58.316 33.333 0.00 0.00 41.54 1.89
1633 1698 6.677781 ATAACGTGTGATGTTATCCTTTGG 57.322 37.500 0.00 0.00 35.93 3.28
1634 1699 4.280436 ACGTGTGATGTTATCCTTTGGA 57.720 40.909 0.00 0.00 35.55 3.53
1635 1700 4.253685 ACGTGTGATGTTATCCTTTGGAG 58.746 43.478 0.00 0.00 34.05 3.86
1636 1701 4.253685 CGTGTGATGTTATCCTTTGGAGT 58.746 43.478 0.00 0.00 34.05 3.85
1637 1702 5.046878 ACGTGTGATGTTATCCTTTGGAGTA 60.047 40.000 0.00 0.00 34.05 2.59
1638 1703 5.520288 CGTGTGATGTTATCCTTTGGAGTAG 59.480 44.000 0.00 0.00 34.05 2.57
1639 1704 6.627287 CGTGTGATGTTATCCTTTGGAGTAGA 60.627 42.308 0.00 0.00 34.05 2.59
1640 1705 6.535508 GTGTGATGTTATCCTTTGGAGTAGAC 59.464 42.308 0.00 0.00 34.05 2.59
1648 1713 8.483758 GTTATCCTTTGGAGTAGACAAGGATAA 58.516 37.037 20.81 20.81 40.60 1.75
1708 1773 5.772825 TTGGTGGAGATTTTTCACTTCAG 57.227 39.130 0.00 0.00 0.00 3.02
1775 1840 9.878599 CATTTTTATCCACCATCGTAGATAAAC 57.121 33.333 4.15 0.00 40.20 2.01
1932 2000 7.072454 TGGGTCTGAAGCCTCAAAATATACTAT 59.928 37.037 0.00 0.00 43.82 2.12
2041 2109 4.201980 TGTCGTGGGATCGATGTAAGTTAG 60.202 45.833 0.54 0.00 41.78 2.34
2209 2277 0.457853 CGAAATCTCGGCTCGGTCAA 60.458 55.000 0.00 0.00 41.57 3.18
2385 2457 9.459640 CTTAGTTGATTTCCTTGCATTATGATG 57.540 33.333 0.00 0.00 36.32 3.07
2614 2713 4.653341 TGAAATTCCCTTTGGACACATTGT 59.347 37.500 0.00 0.00 41.57 2.71
2700 2799 8.458843 TGTAGGCTGAGCATTTAAGATAAAAAC 58.541 33.333 6.82 0.00 0.00 2.43
2857 2961 5.937540 TCGTTCATTACAGAATTCACCACAT 59.062 36.000 8.44 0.00 0.00 3.21
2859 2963 7.604545 TCGTTCATTACAGAATTCACCACATAA 59.395 33.333 8.44 0.00 0.00 1.90
2890 2994 5.532406 ACATCATTAACAAGAATCCCATCCG 59.468 40.000 0.00 0.00 0.00 4.18
2930 3034 5.850046 AACTTAGCTATTAGATGGGCCAT 57.150 39.130 21.39 21.39 0.00 4.40
3006 3110 3.529319 AGATACCCCATGCTTCCTTCTTT 59.471 43.478 0.00 0.00 0.00 2.52
3054 3158 6.296365 TCAAATTCATTTGCAAAAATCGCA 57.704 29.167 17.19 0.00 45.06 5.10
3129 3925 0.251033 AGACCAGCAATGCAAGCTCA 60.251 50.000 13.45 0.00 41.14 4.26
3200 4037 4.789807 AGAGATCATAACTTTGCCAGCAT 58.210 39.130 0.00 0.00 0.00 3.79
3203 4040 6.261826 AGAGATCATAACTTTGCCAGCATAAC 59.738 38.462 0.00 0.00 0.00 1.89
3243 4080 3.818773 ACACTTGCCGCACTAATACTTTT 59.181 39.130 0.00 0.00 0.00 2.27
3253 4090 6.128391 CCGCACTAATACTTTTCACAAAGCTA 60.128 38.462 0.00 0.00 43.03 3.32
3269 4106 5.191059 CAAAGCTAGCGTCGACATTAATTC 58.809 41.667 17.16 0.00 0.00 2.17
3313 4150 0.909610 TCCAACCCATCCGAGCTTCT 60.910 55.000 0.00 0.00 0.00 2.85
3324 4161 5.297776 CCATCCGAGCTTCTGAAATATTTGT 59.702 40.000 5.17 0.00 0.00 2.83
3325 4162 6.483307 CCATCCGAGCTTCTGAAATATTTGTA 59.517 38.462 5.17 0.00 0.00 2.41
3328 4165 8.506168 TCCGAGCTTCTGAAATATTTGTATTT 57.494 30.769 5.17 0.00 32.81 1.40
3554 4483 5.535783 ACATGTGTCATCAAATTTCAGGTCA 59.464 36.000 0.00 0.00 0.00 4.02
3588 4517 4.097286 GTGAGCACAAAACTTCCCACTTTA 59.903 41.667 0.00 0.00 0.00 1.85
3590 4519 4.278310 AGCACAAAACTTCCCACTTTACT 58.722 39.130 0.00 0.00 0.00 2.24
3595 4524 5.357032 ACAAAACTTCCCACTTTACTGTGAG 59.643 40.000 0.00 0.00 40.12 3.51
3596 4525 5.367945 AAACTTCCCACTTTACTGTGAGA 57.632 39.130 0.00 0.00 40.12 3.27
3597 4526 4.608948 ACTTCCCACTTTACTGTGAGAG 57.391 45.455 0.00 0.00 40.12 3.20
3598 4527 4.223953 ACTTCCCACTTTACTGTGAGAGA 58.776 43.478 0.00 0.00 40.12 3.10
3599 4528 4.841246 ACTTCCCACTTTACTGTGAGAGAT 59.159 41.667 0.00 0.00 40.12 2.75
3600 4529 4.808414 TCCCACTTTACTGTGAGAGATG 57.192 45.455 0.00 0.00 40.12 2.90
3601 4530 4.160329 TCCCACTTTACTGTGAGAGATGT 58.840 43.478 0.00 0.00 40.12 3.06
3602 4531 4.220821 TCCCACTTTACTGTGAGAGATGTC 59.779 45.833 0.00 0.00 40.12 3.06
3603 4532 4.169508 CCACTTTACTGTGAGAGATGTCG 58.830 47.826 0.00 0.00 40.12 4.35
3604 4533 4.082733 CCACTTTACTGTGAGAGATGTCGA 60.083 45.833 0.00 0.00 40.12 4.20
3607 4536 5.473846 ACTTTACTGTGAGAGATGTCGAGAA 59.526 40.000 0.00 0.00 0.00 2.87
3691 4621 3.558418 GCATTCAATAAAGCAAGCCATGG 59.442 43.478 7.63 7.63 0.00 3.66
3692 4622 2.965572 TCAATAAAGCAAGCCATGGC 57.034 45.000 30.12 30.12 42.33 4.40
3808 4739 6.369629 TCCTTTGGAGATTTCTGTACCAAAA 58.630 36.000 0.00 0.00 45.59 2.44
3809 4740 6.836527 TCCTTTGGAGATTTCTGTACCAAAAA 59.163 34.615 0.00 0.00 45.59 1.94
3810 4741 7.014230 TCCTTTGGAGATTTCTGTACCAAAAAG 59.986 37.037 0.00 0.00 45.59 2.27
3811 4742 7.201911 CCTTTGGAGATTTCTGTACCAAAAAGT 60.202 37.037 0.00 0.00 45.59 2.66
3812 4743 7.654022 TTGGAGATTTCTGTACCAAAAAGTT 57.346 32.000 0.00 0.00 37.62 2.66
3813 4744 7.654022 TGGAGATTTCTGTACCAAAAAGTTT 57.346 32.000 0.00 0.00 0.00 2.66
3814 4745 8.073467 TGGAGATTTCTGTACCAAAAAGTTTT 57.927 30.769 0.00 0.00 0.00 2.43
3815 4746 8.536175 TGGAGATTTCTGTACCAAAAAGTTTTT 58.464 29.630 7.79 7.79 0.00 1.94
3847 4778 7.795482 CATGGCATGGATTTGAATTTGTATT 57.205 32.000 19.80 0.00 0.00 1.89
3848 4779 8.890124 CATGGCATGGATTTGAATTTGTATTA 57.110 30.769 19.80 0.00 0.00 0.98
3849 4780 9.327628 CATGGCATGGATTTGAATTTGTATTAA 57.672 29.630 19.80 0.00 0.00 1.40
3850 4781 8.715191 TGGCATGGATTTGAATTTGTATTAAC 57.285 30.769 0.00 0.00 0.00 2.01
3851 4782 7.768120 TGGCATGGATTTGAATTTGTATTAACC 59.232 33.333 0.00 0.00 0.00 2.85
3852 4783 7.768120 GGCATGGATTTGAATTTGTATTAACCA 59.232 33.333 0.00 0.00 0.00 3.67
3853 4784 9.160496 GCATGGATTTGAATTTGTATTAACCAA 57.840 29.630 0.00 0.00 0.00 3.67
3873 4804 8.415950 AACCAAATTTGTAATGTGATAGACCA 57.584 30.769 16.73 0.00 0.00 4.02
3874 4805 8.415950 ACCAAATTTGTAATGTGATAGACCAA 57.584 30.769 16.73 0.00 0.00 3.67
3875 4806 8.865090 ACCAAATTTGTAATGTGATAGACCAAA 58.135 29.630 16.73 0.00 0.00 3.28
3876 4807 9.703892 CCAAATTTGTAATGTGATAGACCAAAA 57.296 29.630 16.73 0.00 0.00 2.44
3893 4824 8.986477 AGACCAAAAACATAATTTAGATGCAC 57.014 30.769 0.00 0.00 0.00 4.57
3894 4825 8.806146 AGACCAAAAACATAATTTAGATGCACT 58.194 29.630 0.00 0.00 0.00 4.40
3896 4827 9.855021 ACCAAAAACATAATTTAGATGCACTAC 57.145 29.630 0.00 0.00 0.00 2.73
3897 4828 9.853555 CCAAAAACATAATTTAGATGCACTACA 57.146 29.630 0.00 0.00 0.00 2.74
3902 4833 9.836864 AACATAATTTAGATGCACTACATGAGA 57.163 29.630 0.00 0.00 39.84 3.27
3906 4837 8.969260 AATTTAGATGCACTACATGAGATCAA 57.031 30.769 0.00 0.00 39.84 2.57
3907 4838 9.570468 AATTTAGATGCACTACATGAGATCAAT 57.430 29.630 0.00 0.00 39.84 2.57
3908 4839 8.969260 TTTAGATGCACTACATGAGATCAATT 57.031 30.769 0.00 0.00 39.84 2.32
3909 4840 8.969260 TTAGATGCACTACATGAGATCAATTT 57.031 30.769 0.00 0.00 39.84 1.82
3910 4841 7.493743 AGATGCACTACATGAGATCAATTTC 57.506 36.000 0.00 0.00 39.84 2.17
3911 4842 6.485984 AGATGCACTACATGAGATCAATTTCC 59.514 38.462 0.00 0.00 39.84 3.13
3912 4843 5.748402 TGCACTACATGAGATCAATTTCCT 58.252 37.500 0.00 0.00 0.00 3.36
3913 4844 6.182627 TGCACTACATGAGATCAATTTCCTT 58.817 36.000 0.00 0.00 0.00 3.36
3914 4845 6.094464 TGCACTACATGAGATCAATTTCCTTG 59.906 38.462 0.00 0.00 36.09 3.61
3916 4847 7.678218 GCACTACATGAGATCAATTTCCTTGAC 60.678 40.741 0.00 0.00 46.37 3.18
3917 4848 7.335171 CACTACATGAGATCAATTTCCTTGACA 59.665 37.037 0.00 0.00 46.37 3.58
3918 4849 7.884877 ACTACATGAGATCAATTTCCTTGACAA 59.115 33.333 0.00 0.00 46.37 3.18
3919 4850 6.917533 ACATGAGATCAATTTCCTTGACAAC 58.082 36.000 0.00 0.00 46.37 3.32
3920 4851 6.491062 ACATGAGATCAATTTCCTTGACAACA 59.509 34.615 0.00 0.00 46.37 3.33
3921 4852 7.177921 ACATGAGATCAATTTCCTTGACAACAT 59.822 33.333 0.00 0.00 46.37 2.71
3922 4853 6.916440 TGAGATCAATTTCCTTGACAACATG 58.084 36.000 0.00 0.00 46.37 3.21
3923 4854 6.716173 TGAGATCAATTTCCTTGACAACATGA 59.284 34.615 0.00 0.00 46.37 3.07
3924 4855 7.231115 TGAGATCAATTTCCTTGACAACATGAA 59.769 33.333 0.00 0.00 46.37 2.57
3925 4856 8.130671 AGATCAATTTCCTTGACAACATGAAT 57.869 30.769 0.00 0.00 46.37 2.57
3926 4857 8.033038 AGATCAATTTCCTTGACAACATGAATG 58.967 33.333 0.00 0.09 46.37 2.67
3927 4858 5.927689 TCAATTTCCTTGACAACATGAATGC 59.072 36.000 0.00 0.00 38.97 3.56
3928 4859 4.933505 TTTCCTTGACAACATGAATGCA 57.066 36.364 0.00 0.00 0.00 3.96
3929 4860 4.933505 TTCCTTGACAACATGAATGCAA 57.066 36.364 0.00 6.38 0.00 4.08
3930 4861 4.933505 TCCTTGACAACATGAATGCAAA 57.066 36.364 0.00 0.00 0.00 3.68
3931 4862 4.619973 TCCTTGACAACATGAATGCAAAC 58.380 39.130 0.00 0.00 0.00 2.93
3932 4863 4.099113 TCCTTGACAACATGAATGCAAACA 59.901 37.500 0.00 0.00 0.00 2.83
3933 4864 4.209703 CCTTGACAACATGAATGCAAACAC 59.790 41.667 0.00 0.00 0.00 3.32
3934 4865 4.652421 TGACAACATGAATGCAAACACT 57.348 36.364 0.00 0.00 0.00 3.55
3935 4866 5.008619 TGACAACATGAATGCAAACACTT 57.991 34.783 0.00 0.00 0.00 3.16
3936 4867 5.417811 TGACAACATGAATGCAAACACTTT 58.582 33.333 0.00 0.00 0.00 2.66
3937 4868 5.519566 TGACAACATGAATGCAAACACTTTC 59.480 36.000 0.00 0.00 0.00 2.62
3938 4869 5.417811 ACAACATGAATGCAAACACTTTCA 58.582 33.333 0.00 0.95 37.88 2.69
3939 4870 5.521010 ACAACATGAATGCAAACACTTTCAG 59.479 36.000 0.00 0.77 37.20 3.02
3940 4871 4.624015 ACATGAATGCAAACACTTTCAGG 58.376 39.130 0.00 8.20 39.77 3.86
3941 4872 4.099881 ACATGAATGCAAACACTTTCAGGT 59.900 37.500 9.32 9.32 41.18 4.00
3942 4873 4.734398 TGAATGCAAACACTTTCAGGTT 57.266 36.364 0.00 0.00 32.03 3.50
3943 4874 4.681744 TGAATGCAAACACTTTCAGGTTC 58.318 39.130 0.00 0.00 32.03 3.62
3944 4875 4.402155 TGAATGCAAACACTTTCAGGTTCT 59.598 37.500 0.00 0.00 32.03 3.01
3945 4876 5.592282 TGAATGCAAACACTTTCAGGTTCTA 59.408 36.000 0.00 0.00 32.03 2.10
3946 4877 6.096141 TGAATGCAAACACTTTCAGGTTCTAA 59.904 34.615 0.00 0.00 32.03 2.10
3947 4878 5.906113 TGCAAACACTTTCAGGTTCTAAA 57.094 34.783 0.00 0.00 0.00 1.85
3948 4879 6.463995 TGCAAACACTTTCAGGTTCTAAAT 57.536 33.333 0.00 0.00 0.00 1.40
3949 4880 6.872920 TGCAAACACTTTCAGGTTCTAAATT 58.127 32.000 0.00 0.00 0.00 1.82
3950 4881 6.978080 TGCAAACACTTTCAGGTTCTAAATTC 59.022 34.615 0.00 0.00 0.00 2.17
3951 4882 7.147915 TGCAAACACTTTCAGGTTCTAAATTCT 60.148 33.333 0.00 0.00 0.00 2.40
3952 4883 7.706607 GCAAACACTTTCAGGTTCTAAATTCTT 59.293 33.333 0.00 0.00 0.00 2.52
3953 4884 9.586435 CAAACACTTTCAGGTTCTAAATTCTTT 57.414 29.630 0.00 0.00 0.00 2.52
3989 4920 6.344572 GTCAATAATGACGTCTAATGTGCA 57.655 37.500 17.92 0.00 45.94 4.57
3990 4921 6.948353 GTCAATAATGACGTCTAATGTGCAT 58.052 36.000 17.92 0.00 45.94 3.96
3991 4922 6.847792 GTCAATAATGACGTCTAATGTGCATG 59.152 38.462 17.92 4.77 45.94 4.06
3992 4923 6.760770 TCAATAATGACGTCTAATGTGCATGA 59.239 34.615 17.92 6.91 0.00 3.07
3993 4924 6.775939 ATAATGACGTCTAATGTGCATGAG 57.224 37.500 17.92 0.00 0.00 2.90
3994 4925 2.892374 TGACGTCTAATGTGCATGAGG 58.108 47.619 17.92 0.00 0.00 3.86
3995 4926 2.495669 TGACGTCTAATGTGCATGAGGA 59.504 45.455 17.92 0.00 0.00 3.71
3996 4927 3.056179 TGACGTCTAATGTGCATGAGGAA 60.056 43.478 17.92 0.00 0.00 3.36
4008 4939 3.711190 TGCATGAGGAACCTAAGAGCATA 59.289 43.478 0.00 0.00 0.00 3.14
4048 4979 3.551496 CTCCTCAAACGCCCAGGCA 62.551 63.158 9.78 0.00 42.06 4.75
4052 4983 2.281761 CAAACGCCCAGGCAGTCT 60.282 61.111 9.78 0.00 42.06 3.24
4057 4999 3.009115 GCCCAGGCAGTCTACCCA 61.009 66.667 3.12 0.00 41.49 4.51
4058 5000 2.602676 GCCCAGGCAGTCTACCCAA 61.603 63.158 3.12 0.00 41.49 4.12
4083 5036 2.629051 GATTTTTCGACCCAGACGGAT 58.371 47.619 0.00 0.00 34.64 4.18
4154 5108 2.084546 GCCCAAATATGAGGCGGATAC 58.915 52.381 0.00 0.00 34.59 2.24
4255 5210 1.681076 GCCGGACCAAACCCTAGAA 59.319 57.895 5.05 0.00 0.00 2.10
4293 5248 3.846405 TTCACTCCCTCCGCCACCT 62.846 63.158 0.00 0.00 0.00 4.00
4305 5260 2.289532 GCCACCTGAGCTCACCTCT 61.290 63.158 13.74 0.00 41.35 3.69
4411 5368 1.384191 GGGTTGGAGGAGGCAATGT 59.616 57.895 0.00 0.00 0.00 2.71
4413 5370 0.038166 GGTTGGAGGAGGCAATGTCA 59.962 55.000 0.00 0.00 0.00 3.58
4436 5393 2.629656 GCATTGCACTCCACCGCTT 61.630 57.895 3.15 0.00 0.00 4.68
4440 5397 4.681978 GCACTCCACCGCTTCCGT 62.682 66.667 0.00 0.00 0.00 4.69
4501 5458 1.078497 TCCATTGCGTCGGCTCAAT 60.078 52.632 0.00 0.00 40.82 2.57
4562 5519 1.668237 GCAGCCGAAAAATCTCTCCTC 59.332 52.381 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 5.693769 TTCTGGTATAGAACTGGGGAAAG 57.306 43.478 0.00 0.00 40.43 2.62
159 160 1.526464 GAACCAGCATTTTTGGCAACG 59.474 47.619 0.00 0.00 39.39 4.10
210 215 2.750712 ACTAGAAGGACACGCTCTCTTC 59.249 50.000 0.00 0.00 36.73 2.87
213 218 2.096819 CAGACTAGAAGGACACGCTCTC 59.903 54.545 0.00 0.00 0.00 3.20
215 220 2.085320 TCAGACTAGAAGGACACGCTC 58.915 52.381 0.00 0.00 0.00 5.03
223 228 7.283354 ACCAAAAAGAAAAGTCAGACTAGAAGG 59.717 37.037 2.64 0.02 0.00 3.46
230 235 5.028375 CGTGACCAAAAAGAAAAGTCAGAC 58.972 41.667 0.00 0.00 38.09 3.51
263 268 1.115467 AGGGAGCGGTGATAGAACTG 58.885 55.000 0.00 0.00 0.00 3.16
274 279 1.077068 TATGCCCAAAAGGGAGCGG 60.077 57.895 4.37 0.00 40.68 5.52
275 280 1.728490 GCTATGCCCAAAAGGGAGCG 61.728 60.000 4.37 0.00 40.68 5.03
352 357 5.191426 AGCATGCAGTTCTTCATCTTATGT 58.809 37.500 21.98 0.00 0.00 2.29
353 358 5.558463 CGAGCATGCAGTTCTTCATCTTATG 60.558 44.000 21.98 0.00 0.00 1.90
354 359 4.510711 CGAGCATGCAGTTCTTCATCTTAT 59.489 41.667 21.98 0.00 0.00 1.73
355 360 3.867493 CGAGCATGCAGTTCTTCATCTTA 59.133 43.478 21.98 0.00 0.00 2.10
448 460 2.618241 TCAATATGTTTGCATCCCGCTC 59.382 45.455 0.00 0.00 43.06 5.03
453 465 6.781138 TCGTTAACTCAATATGTTTGCATCC 58.219 36.000 3.71 0.00 36.58 3.51
534 562 8.994429 TTCGGTCACATGCATTTTATTTTATT 57.006 26.923 0.00 0.00 0.00 1.40
535 563 8.994429 TTTCGGTCACATGCATTTTATTTTAT 57.006 26.923 0.00 0.00 0.00 1.40
536 564 8.994429 ATTTCGGTCACATGCATTTTATTTTA 57.006 26.923 0.00 0.00 0.00 1.52
564 592 3.066760 GGTTCAGTTTCCTTGTCAACAGG 59.933 47.826 0.00 0.00 0.00 4.00
568 596 4.229304 TCTGGTTCAGTTTCCTTGTCAA 57.771 40.909 0.00 0.00 32.61 3.18
579 607 5.998363 GGTCTGATTTTACTTCTGGTTCAGT 59.002 40.000 0.00 0.00 33.31 3.41
588 616 4.473199 GCGGTTTGGTCTGATTTTACTTC 58.527 43.478 0.00 0.00 0.00 3.01
638 669 3.933332 GTCGCTAGCCTAACATGTTCTTT 59.067 43.478 15.85 2.35 0.00 2.52
639 670 3.056107 TGTCGCTAGCCTAACATGTTCTT 60.056 43.478 15.85 1.99 0.00 2.52
640 671 2.496070 TGTCGCTAGCCTAACATGTTCT 59.504 45.455 15.85 8.91 0.00 3.01
641 672 2.860735 CTGTCGCTAGCCTAACATGTTC 59.139 50.000 15.85 0.42 0.00 3.18
642 673 2.233922 ACTGTCGCTAGCCTAACATGTT 59.766 45.455 16.68 16.68 0.00 2.71
643 674 1.825474 ACTGTCGCTAGCCTAACATGT 59.175 47.619 9.66 8.48 0.00 3.21
644 675 2.159240 TGACTGTCGCTAGCCTAACATG 60.159 50.000 9.66 7.93 0.00 3.21
645 676 2.100197 TGACTGTCGCTAGCCTAACAT 58.900 47.619 9.66 2.41 0.00 2.71
646 677 1.541379 TGACTGTCGCTAGCCTAACA 58.459 50.000 9.66 10.30 0.00 2.41
647 678 2.094649 ACTTGACTGTCGCTAGCCTAAC 60.095 50.000 9.66 5.88 0.00 2.34
648 679 2.163815 GACTTGACTGTCGCTAGCCTAA 59.836 50.000 9.66 0.00 0.00 2.69
649 680 1.743958 GACTTGACTGTCGCTAGCCTA 59.256 52.381 9.66 0.00 0.00 3.93
650 681 0.528470 GACTTGACTGTCGCTAGCCT 59.472 55.000 9.66 0.00 0.00 4.58
651 682 0.243907 TGACTTGACTGTCGCTAGCC 59.756 55.000 9.66 0.00 39.64 3.93
682 713 6.971756 GCAAAGAAGCAAAGGAGAGATATTTC 59.028 38.462 0.00 0.00 0.00 2.17
764 797 4.163839 AGAGGGAATGAACTTCAGATCTGG 59.836 45.833 22.42 9.99 35.41 3.86
805 838 1.764723 TCGATGATGGATCCAAGCTGT 59.235 47.619 20.67 0.30 0.00 4.40
806 839 2.414806 CTCGATGATGGATCCAAGCTG 58.585 52.381 20.67 8.23 0.00 4.24
818 851 0.309302 CGCTTCTCGTCCTCGATGAT 59.691 55.000 0.00 0.00 45.21 2.45
842 882 0.109342 AAGTGCACTGACCTTGGAGG 59.891 55.000 22.49 0.00 42.49 4.30
944 984 5.169561 CGATCAATTACAGCGTGCAATTTAC 59.830 40.000 0.00 0.00 0.00 2.01
963 1003 1.884464 GAAGCTGCCGATGCGATCA 60.884 57.895 0.00 0.00 41.78 2.92
985 1025 4.523943 GGTGGCCATTAATTGCTGATGATA 59.476 41.667 9.72 0.00 0.00 2.15
1024 1064 0.966370 AGCTCGTTCGGTAGGCTCTT 60.966 55.000 0.00 0.00 0.00 2.85
1242 1282 0.836606 TCTTCACAGCAACCACTCCA 59.163 50.000 0.00 0.00 0.00 3.86
1243 1283 1.876156 CTTCTTCACAGCAACCACTCC 59.124 52.381 0.00 0.00 0.00 3.85
1244 1284 1.265365 GCTTCTTCACAGCAACCACTC 59.735 52.381 0.00 0.00 37.22 3.51
1416 1456 1.067985 ACAGTGTCAGTGATCTCTGCG 60.068 52.381 18.01 7.77 35.63 5.18
1564 1629 5.437060 AGCAATATTACCGGTGTGAAGAAT 58.563 37.500 19.93 10.42 0.00 2.40
1567 1632 4.211374 GCTAGCAATATTACCGGTGTGAAG 59.789 45.833 19.93 3.77 0.00 3.02
1569 1634 3.133183 TGCTAGCAATATTACCGGTGTGA 59.867 43.478 19.93 3.07 0.00 3.58
1571 1636 3.830744 TGCTAGCAATATTACCGGTGT 57.169 42.857 19.93 8.60 0.00 4.16
1585 1650 5.006552 CAGTAGAAGAATCTTGCTTGCTAGC 59.993 44.000 13.56 13.56 41.29 3.42
1586 1651 6.336566 TCAGTAGAAGAATCTTGCTTGCTAG 58.663 40.000 0.00 0.00 37.10 3.42
1587 1652 6.286240 TCAGTAGAAGAATCTTGCTTGCTA 57.714 37.500 0.00 0.00 37.10 3.49
1593 1658 6.531948 ACACGTTATCAGTAGAAGAATCTTGC 59.468 38.462 0.00 0.00 37.10 4.01
1594 1659 7.755373 TCACACGTTATCAGTAGAAGAATCTTG 59.245 37.037 0.00 0.00 37.10 3.02
1595 1660 7.827701 TCACACGTTATCAGTAGAAGAATCTT 58.172 34.615 0.00 0.00 37.10 2.40
1596 1661 7.392494 TCACACGTTATCAGTAGAAGAATCT 57.608 36.000 0.00 0.00 39.82 2.40
1597 1662 7.702772 ACATCACACGTTATCAGTAGAAGAATC 59.297 37.037 0.00 0.00 0.00 2.52
1598 1663 7.548097 ACATCACACGTTATCAGTAGAAGAAT 58.452 34.615 0.00 0.00 0.00 2.40
1599 1664 6.920817 ACATCACACGTTATCAGTAGAAGAA 58.079 36.000 0.00 0.00 0.00 2.52
1600 1665 6.510879 ACATCACACGTTATCAGTAGAAGA 57.489 37.500 0.00 0.00 0.00 2.87
1601 1666 8.858003 ATAACATCACACGTTATCAGTAGAAG 57.142 34.615 0.00 0.00 35.15 2.85
1610 1675 6.411376 TCCAAAGGATAACATCACACGTTAT 58.589 36.000 0.00 0.00 41.19 1.89
1611 1676 5.795972 TCCAAAGGATAACATCACACGTTA 58.204 37.500 0.00 0.00 33.59 3.18
1612 1677 4.647611 TCCAAAGGATAACATCACACGTT 58.352 39.130 0.00 0.00 0.00 3.99
1613 1678 4.253685 CTCCAAAGGATAACATCACACGT 58.746 43.478 0.00 0.00 0.00 4.49
1614 1679 4.253685 ACTCCAAAGGATAACATCACACG 58.746 43.478 0.00 0.00 0.00 4.49
1615 1680 6.535508 GTCTACTCCAAAGGATAACATCACAC 59.464 42.308 0.00 0.00 0.00 3.82
1616 1681 6.212589 TGTCTACTCCAAAGGATAACATCACA 59.787 38.462 0.00 0.00 0.00 3.58
1617 1682 6.640518 TGTCTACTCCAAAGGATAACATCAC 58.359 40.000 0.00 0.00 0.00 3.06
1618 1683 6.867519 TGTCTACTCCAAAGGATAACATCA 57.132 37.500 0.00 0.00 0.00 3.07
1619 1684 6.763610 CCTTGTCTACTCCAAAGGATAACATC 59.236 42.308 0.00 0.00 0.00 3.06
1620 1685 6.443849 TCCTTGTCTACTCCAAAGGATAACAT 59.556 38.462 0.00 0.00 0.00 2.71
1621 1686 5.783360 TCCTTGTCTACTCCAAAGGATAACA 59.217 40.000 0.00 0.00 0.00 2.41
1622 1687 6.295719 TCCTTGTCTACTCCAAAGGATAAC 57.704 41.667 0.00 0.00 0.00 1.89
1623 1688 8.483758 GTTATCCTTGTCTACTCCAAAGGATAA 58.516 37.037 22.71 22.71 38.29 1.75
1624 1689 7.622081 TGTTATCCTTGTCTACTCCAAAGGATA 59.378 37.037 15.64 15.64 34.54 2.59
1625 1690 6.443849 TGTTATCCTTGTCTACTCCAAAGGAT 59.556 38.462 17.33 17.33 35.69 3.24
1626 1691 5.783360 TGTTATCCTTGTCTACTCCAAAGGA 59.217 40.000 5.52 5.52 0.00 3.36
1627 1692 6.049955 TGTTATCCTTGTCTACTCCAAAGG 57.950 41.667 0.00 0.00 0.00 3.11
1628 1693 7.278868 GTGATGTTATCCTTGTCTACTCCAAAG 59.721 40.741 0.00 0.00 0.00 2.77
1629 1694 7.103641 GTGATGTTATCCTTGTCTACTCCAAA 58.896 38.462 0.00 0.00 0.00 3.28
1630 1695 6.212589 TGTGATGTTATCCTTGTCTACTCCAA 59.787 38.462 0.00 0.00 0.00 3.53
1631 1696 5.719563 TGTGATGTTATCCTTGTCTACTCCA 59.280 40.000 0.00 0.00 0.00 3.86
1632 1697 6.043411 GTGTGATGTTATCCTTGTCTACTCC 58.957 44.000 0.00 0.00 0.00 3.85
1633 1698 6.631016 TGTGTGATGTTATCCTTGTCTACTC 58.369 40.000 0.00 0.00 0.00 2.59
1634 1699 6.605471 TGTGTGATGTTATCCTTGTCTACT 57.395 37.500 0.00 0.00 0.00 2.57
1635 1700 7.849804 AATGTGTGATGTTATCCTTGTCTAC 57.150 36.000 0.00 0.00 0.00 2.59
1636 1701 9.764363 GATAATGTGTGATGTTATCCTTGTCTA 57.236 33.333 0.00 0.00 31.69 2.59
1637 1702 8.267183 TGATAATGTGTGATGTTATCCTTGTCT 58.733 33.333 0.00 0.00 35.15 3.41
1638 1703 8.437360 TGATAATGTGTGATGTTATCCTTGTC 57.563 34.615 0.00 0.00 35.15 3.18
1639 1704 8.806429 TTGATAATGTGTGATGTTATCCTTGT 57.194 30.769 0.00 0.00 35.15 3.16
1675 1740 2.451490 TCTCCACCAAAACAACAGCAA 58.549 42.857 0.00 0.00 0.00 3.91
1862 1930 7.174426 GGCAAGGTATGTAGAAAATGTATACCC 59.826 40.741 0.00 0.00 42.59 3.69
1932 2000 1.686355 GGTGTCATGTTGTCACCCAA 58.314 50.000 11.36 0.00 46.23 4.12
2136 2204 4.036027 CCACTAACAGCATTAGCATCAAGG 59.964 45.833 7.48 0.00 45.49 3.61
2144 2212 4.816385 CCATGTACCCACTAACAGCATTAG 59.184 45.833 6.29 6.29 0.00 1.73
2614 2713 8.826765 AGAAATTAACTATTCTCAACAGGGAGA 58.173 33.333 0.00 0.00 41.99 3.71
2666 2765 6.840780 AAATGCTCAGCCTACAAAAACTAT 57.159 33.333 0.00 0.00 0.00 2.12
2674 2773 8.458843 GTTTTTATCTTAAATGCTCAGCCTACA 58.541 33.333 0.00 0.00 0.00 2.74
2709 2808 5.815581 AGGCACCACTGTTAATCTATTCAA 58.184 37.500 0.00 0.00 0.00 2.69
2857 2961 5.979993 TCTTGTTAATGATGTACCGCCTTA 58.020 37.500 0.00 0.00 0.00 2.69
2859 2963 4.481368 TCTTGTTAATGATGTACCGCCT 57.519 40.909 0.00 0.00 0.00 5.52
2940 3044 4.695928 AGAGTTTCAAAGATTAGGCGTTCC 59.304 41.667 0.00 0.00 0.00 3.62
2985 3089 3.584733 AAGAAGGAAGCATGGGGTATC 57.415 47.619 0.00 0.00 0.00 2.24
2990 3094 3.812053 CGATCTAAAGAAGGAAGCATGGG 59.188 47.826 0.00 0.00 0.00 4.00
3006 3110 2.580962 AGATCAGCTCTGCACGATCTA 58.419 47.619 17.10 0.00 43.32 1.98
3054 3158 7.573968 ATTTTAGAGACTGACTTTTGTTGCT 57.426 32.000 0.00 0.00 0.00 3.91
3101 3897 6.670695 TTGCATTGCTGGTCTCTATATAGA 57.329 37.500 11.94 11.94 0.00 1.98
3129 3925 0.539051 CATGGAGGAAGCGGAACTCT 59.461 55.000 0.00 0.00 0.00 3.24
3187 3983 1.203174 AGGGGTTATGCTGGCAAAGTT 60.203 47.619 0.00 0.00 0.00 2.66
3200 4037 1.202769 GGTGTGGTGGCTAGGGGTTA 61.203 60.000 0.00 0.00 0.00 2.85
3203 4040 3.728373 GGGTGTGGTGGCTAGGGG 61.728 72.222 0.00 0.00 0.00 4.79
3243 4080 0.312729 TGTCGACGCTAGCTTTGTGA 59.687 50.000 13.93 0.50 0.00 3.58
3253 4090 7.328737 GGTTATATCAGAATTAATGTCGACGCT 59.671 37.037 11.62 2.55 0.00 5.07
3588 4517 4.219507 ACATTTCTCGACATCTCTCACAGT 59.780 41.667 0.00 0.00 0.00 3.55
3590 4519 4.672801 CGACATTTCTCGACATCTCTCACA 60.673 45.833 0.00 0.00 35.58 3.58
3595 4524 3.238570 CGTTCGACATTTCTCGACATCTC 59.761 47.826 0.00 0.00 42.30 2.75
3596 4525 3.172050 CGTTCGACATTTCTCGACATCT 58.828 45.455 0.00 0.00 42.30 2.90
3597 4526 2.915463 ACGTTCGACATTTCTCGACATC 59.085 45.455 0.00 0.00 42.30 3.06
3598 4527 2.915463 GACGTTCGACATTTCTCGACAT 59.085 45.455 0.00 0.00 42.30 3.06
3599 4528 2.287129 TGACGTTCGACATTTCTCGACA 60.287 45.455 0.00 0.00 42.30 4.35
3600 4529 2.313234 TGACGTTCGACATTTCTCGAC 58.687 47.619 0.00 0.00 42.30 4.20
3601 4530 2.691984 TGACGTTCGACATTTCTCGA 57.308 45.000 0.00 0.00 40.91 4.04
3602 4531 2.724690 ACTTGACGTTCGACATTTCTCG 59.275 45.455 0.00 0.00 34.83 4.04
3603 4532 5.817616 TTACTTGACGTTCGACATTTCTC 57.182 39.130 0.00 0.00 0.00 2.87
3604 4533 6.036300 TGTTTTACTTGACGTTCGACATTTCT 59.964 34.615 0.00 0.00 0.00 2.52
3607 4536 5.721876 TGTTTTACTTGACGTTCGACATT 57.278 34.783 0.00 0.00 0.00 2.71
3617 4546 8.289618 TGTAGCATTGATCTTGTTTTACTTGAC 58.710 33.333 0.00 0.00 0.00 3.18
3710 4640 6.866248 CCCACAACACACTTTTCATTAATACC 59.134 38.462 0.00 0.00 0.00 2.73
3788 4719 7.654022 AACTTTTTGGTACAGAAATCTCCAA 57.346 32.000 0.00 0.00 41.55 3.53
3812 4743 3.123157 CCATGCCATGGTTGTGAAAAA 57.877 42.857 15.89 0.00 45.54 1.94
3813 4744 2.835580 CCATGCCATGGTTGTGAAAA 57.164 45.000 15.89 0.00 45.54 2.29
3814 4745 8.374126 TTCAAATCCATGCCATGGTTGTGAAA 62.374 38.462 27.20 16.30 46.12 2.69
3815 4746 6.974465 TTCAAATCCATGCCATGGTTGTGAA 61.974 40.000 26.25 26.25 46.55 3.18
3823 4754 7.795482 AATACAAATTCAAATCCATGCCATG 57.205 32.000 0.00 0.00 0.00 3.66
3824 4755 9.328845 GTTAATACAAATTCAAATCCATGCCAT 57.671 29.630 0.00 0.00 0.00 4.40
3825 4756 7.768120 GGTTAATACAAATTCAAATCCATGCCA 59.232 33.333 0.00 0.00 0.00 4.92
3826 4757 7.768120 TGGTTAATACAAATTCAAATCCATGCC 59.232 33.333 0.00 0.00 0.00 4.40
3827 4758 8.715191 TGGTTAATACAAATTCAAATCCATGC 57.285 30.769 0.00 0.00 0.00 4.06
3847 4778 9.521841 TGGTCTATCACATTACAAATTTGGTTA 57.478 29.630 21.74 7.29 0.00 2.85
3848 4779 8.415950 TGGTCTATCACATTACAAATTTGGTT 57.584 30.769 21.74 4.90 0.00 3.67
3849 4780 8.415950 TTGGTCTATCACATTACAAATTTGGT 57.584 30.769 21.74 7.48 0.00 3.67
3850 4781 9.703892 TTTTGGTCTATCACATTACAAATTTGG 57.296 29.630 21.74 6.85 0.00 3.28
3868 4799 8.806146 AGTGCATCTAAATTATGTTTTTGGTCT 58.194 29.630 0.00 0.00 0.00 3.85
3869 4800 8.986477 AGTGCATCTAAATTATGTTTTTGGTC 57.014 30.769 0.00 0.00 0.00 4.02
3870 4801 9.855021 GTAGTGCATCTAAATTATGTTTTTGGT 57.145 29.630 0.00 0.00 0.00 3.67
3871 4802 9.853555 TGTAGTGCATCTAAATTATGTTTTTGG 57.146 29.630 0.00 0.00 0.00 3.28
3876 4807 9.836864 TCTCATGTAGTGCATCTAAATTATGTT 57.163 29.630 0.00 0.00 35.19 2.71
3881 4812 8.969260 TTGATCTCATGTAGTGCATCTAAATT 57.031 30.769 0.00 0.00 35.19 1.82
3882 4813 9.570468 AATTGATCTCATGTAGTGCATCTAAAT 57.430 29.630 0.00 0.00 35.19 1.40
3883 4814 8.969260 AATTGATCTCATGTAGTGCATCTAAA 57.031 30.769 0.00 0.00 35.19 1.85
3884 4815 8.969260 AAATTGATCTCATGTAGTGCATCTAA 57.031 30.769 0.00 0.00 35.19 2.10
3885 4816 7.658982 GGAAATTGATCTCATGTAGTGCATCTA 59.341 37.037 0.00 0.00 35.19 1.98
3886 4817 6.485984 GGAAATTGATCTCATGTAGTGCATCT 59.514 38.462 0.00 0.00 35.19 2.90
3887 4818 6.485984 AGGAAATTGATCTCATGTAGTGCATC 59.514 38.462 0.00 0.00 35.19 3.91
3888 4819 6.363065 AGGAAATTGATCTCATGTAGTGCAT 58.637 36.000 0.00 0.00 38.60 3.96
3889 4820 5.748402 AGGAAATTGATCTCATGTAGTGCA 58.252 37.500 0.00 0.00 0.00 4.57
3890 4821 6.317140 TCAAGGAAATTGATCTCATGTAGTGC 59.683 38.462 0.00 0.00 43.09 4.40
3891 4822 7.854557 TCAAGGAAATTGATCTCATGTAGTG 57.145 36.000 0.00 0.00 43.09 2.74
3903 4834 5.927689 GCATTCATGTTGTCAAGGAAATTGA 59.072 36.000 0.00 0.00 45.79 2.57
3904 4835 5.697178 TGCATTCATGTTGTCAAGGAAATTG 59.303 36.000 0.00 0.00 40.52 2.32
3905 4836 5.856156 TGCATTCATGTTGTCAAGGAAATT 58.144 33.333 0.00 0.00 0.00 1.82
3906 4837 5.471556 TGCATTCATGTTGTCAAGGAAAT 57.528 34.783 0.00 0.00 0.00 2.17
3907 4838 4.933505 TGCATTCATGTTGTCAAGGAAA 57.066 36.364 0.00 0.00 0.00 3.13
3908 4839 4.933505 TTGCATTCATGTTGTCAAGGAA 57.066 36.364 0.00 0.00 0.00 3.36
3909 4840 4.099113 TGTTTGCATTCATGTTGTCAAGGA 59.901 37.500 0.00 0.00 0.00 3.36
3910 4841 4.209703 GTGTTTGCATTCATGTTGTCAAGG 59.790 41.667 0.00 0.00 0.00 3.61
3911 4842 5.045215 AGTGTTTGCATTCATGTTGTCAAG 58.955 37.500 0.00 0.00 0.00 3.02
3912 4843 5.008619 AGTGTTTGCATTCATGTTGTCAA 57.991 34.783 0.00 0.00 0.00 3.18
3913 4844 4.652421 AGTGTTTGCATTCATGTTGTCA 57.348 36.364 0.00 0.00 0.00 3.58
3914 4845 5.519566 TGAAAGTGTTTGCATTCATGTTGTC 59.480 36.000 0.00 0.00 0.00 3.18
3915 4846 5.417811 TGAAAGTGTTTGCATTCATGTTGT 58.582 33.333 0.00 0.00 0.00 3.32
3916 4847 5.050634 CCTGAAAGTGTTTGCATTCATGTTG 60.051 40.000 0.00 0.00 31.92 3.33
3917 4848 5.051816 CCTGAAAGTGTTTGCATTCATGTT 58.948 37.500 0.00 0.00 31.92 2.71
3918 4849 4.099881 ACCTGAAAGTGTTTGCATTCATGT 59.900 37.500 0.00 0.59 31.92 3.21
3919 4850 4.624015 ACCTGAAAGTGTTTGCATTCATG 58.376 39.130 0.00 0.03 31.92 3.07
3920 4851 4.942761 ACCTGAAAGTGTTTGCATTCAT 57.057 36.364 0.00 0.00 31.92 2.57
3921 4852 4.402155 AGAACCTGAAAGTGTTTGCATTCA 59.598 37.500 0.00 0.00 29.45 2.57
3922 4853 4.936891 AGAACCTGAAAGTGTTTGCATTC 58.063 39.130 0.00 0.00 29.45 2.67
3923 4854 6.463995 TTAGAACCTGAAAGTGTTTGCATT 57.536 33.333 0.00 0.00 29.45 3.56
3924 4855 6.463995 TTTAGAACCTGAAAGTGTTTGCAT 57.536 33.333 0.00 0.00 29.45 3.96
3925 4856 5.906113 TTTAGAACCTGAAAGTGTTTGCA 57.094 34.783 0.00 0.00 29.45 4.08
3926 4857 7.203218 AGAATTTAGAACCTGAAAGTGTTTGC 58.797 34.615 0.00 0.00 29.45 3.68
3927 4858 9.586435 AAAGAATTTAGAACCTGAAAGTGTTTG 57.414 29.630 0.00 0.00 35.86 2.93
3967 4898 6.760770 TCATGCACATTAGACGTCATTATTGA 59.239 34.615 19.50 5.95 0.00 2.57
3968 4899 6.947258 TCATGCACATTAGACGTCATTATTG 58.053 36.000 19.50 11.01 0.00 1.90
3969 4900 6.203530 CCTCATGCACATTAGACGTCATTATT 59.796 38.462 19.50 0.00 0.00 1.40
3970 4901 5.698089 CCTCATGCACATTAGACGTCATTAT 59.302 40.000 19.50 4.79 0.00 1.28
3971 4902 5.049828 CCTCATGCACATTAGACGTCATTA 58.950 41.667 19.50 2.29 0.00 1.90
3972 4903 3.873361 CCTCATGCACATTAGACGTCATT 59.127 43.478 19.50 0.00 0.00 2.57
3973 4904 3.132824 TCCTCATGCACATTAGACGTCAT 59.867 43.478 19.50 5.54 0.00 3.06
3974 4905 2.495669 TCCTCATGCACATTAGACGTCA 59.504 45.455 19.50 0.00 0.00 4.35
3975 4906 3.165058 TCCTCATGCACATTAGACGTC 57.835 47.619 7.70 7.70 0.00 4.34
3976 4907 3.262420 GTTCCTCATGCACATTAGACGT 58.738 45.455 0.00 0.00 0.00 4.34
3977 4908 2.609459 GGTTCCTCATGCACATTAGACG 59.391 50.000 0.00 0.00 0.00 4.18
3978 4909 3.878778 AGGTTCCTCATGCACATTAGAC 58.121 45.455 0.00 0.00 0.00 2.59
3979 4910 5.425217 TCTTAGGTTCCTCATGCACATTAGA 59.575 40.000 0.00 0.00 0.00 2.10
3980 4911 5.674525 TCTTAGGTTCCTCATGCACATTAG 58.325 41.667 0.00 0.00 0.00 1.73
3981 4912 5.674525 CTCTTAGGTTCCTCATGCACATTA 58.325 41.667 0.00 0.00 0.00 1.90
3982 4913 4.521146 CTCTTAGGTTCCTCATGCACATT 58.479 43.478 0.00 0.00 0.00 2.71
3983 4914 3.683847 GCTCTTAGGTTCCTCATGCACAT 60.684 47.826 0.00 0.00 0.00 3.21
3984 4915 2.355108 GCTCTTAGGTTCCTCATGCACA 60.355 50.000 0.00 0.00 0.00 4.57
3985 4916 2.284190 GCTCTTAGGTTCCTCATGCAC 58.716 52.381 0.00 0.00 0.00 4.57
3986 4917 1.908619 TGCTCTTAGGTTCCTCATGCA 59.091 47.619 0.00 0.00 0.00 3.96
3987 4918 2.698855 TGCTCTTAGGTTCCTCATGC 57.301 50.000 0.00 0.00 0.00 4.06
3988 4919 6.997655 TGTATATGCTCTTAGGTTCCTCATG 58.002 40.000 0.00 0.00 0.00 3.07
3989 4920 6.295575 GCTGTATATGCTCTTAGGTTCCTCAT 60.296 42.308 0.00 0.00 0.00 2.90
3990 4921 5.011125 GCTGTATATGCTCTTAGGTTCCTCA 59.989 44.000 0.00 0.00 0.00 3.86
3991 4922 5.474825 GCTGTATATGCTCTTAGGTTCCTC 58.525 45.833 0.00 0.00 0.00 3.71
3992 4923 4.284746 GGCTGTATATGCTCTTAGGTTCCT 59.715 45.833 0.00 0.00 0.00 3.36
3993 4924 4.570930 GGCTGTATATGCTCTTAGGTTCC 58.429 47.826 0.00 0.00 0.00 3.62
3994 4925 4.238514 CGGCTGTATATGCTCTTAGGTTC 58.761 47.826 0.00 0.00 0.00 3.62
3995 4926 3.006967 CCGGCTGTATATGCTCTTAGGTT 59.993 47.826 0.00 0.00 0.00 3.50
3996 4927 2.563179 CCGGCTGTATATGCTCTTAGGT 59.437 50.000 0.00 0.00 0.00 3.08
4022 4953 0.536460 GCGTTTGAGGAGGGTTTGGA 60.536 55.000 0.00 0.00 0.00 3.53
4048 4979 4.630069 CGAAAAATCGTGATTGGGTAGACT 59.370 41.667 0.00 0.00 0.00 3.24
4052 4983 3.685756 GGTCGAAAAATCGTGATTGGGTA 59.314 43.478 0.00 0.00 0.00 3.69
4057 4999 3.435671 GTCTGGGTCGAAAAATCGTGATT 59.564 43.478 0.00 0.00 0.00 2.57
4058 5000 3.000727 GTCTGGGTCGAAAAATCGTGAT 58.999 45.455 0.00 0.00 0.00 3.06
4083 5036 2.223745 GTTTGAGGCCCGTTTAAGACA 58.776 47.619 0.00 0.00 0.00 3.41
4088 5041 0.603439 GGACGTTTGAGGCCCGTTTA 60.603 55.000 0.00 0.00 34.51 2.01
4161 5115 2.359354 TGACAAACGCATCCGGGG 60.359 61.111 0.00 0.00 39.22 5.73
4173 5127 3.980989 CCGGGTCCGACGTGACAA 61.981 66.667 11.39 0.00 42.83 3.18
4255 5210 1.132689 AGGGGAGAGGAGTGTGAAGTT 60.133 52.381 0.00 0.00 0.00 2.66
4293 5248 1.260538 AATCGCCAGAGGTGAGCTCA 61.261 55.000 13.74 13.74 45.82 4.26
4305 5260 1.077787 AGATGGCCGAAAATCGCCA 60.078 52.632 14.80 14.80 45.02 5.69
4334 5291 3.453070 GAGTCAGATCCGCTGCCCC 62.453 68.421 0.00 0.00 44.52 5.80
4436 5393 3.749064 GAGCGCTGTCCTCACGGA 61.749 66.667 18.48 0.00 36.83 4.69


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

AutoCloner maintained by Alex Coulton.