Multiple sequence alignment - TraesCS1D01G268600

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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 TraesCS1D01G268600 chr1D 100.000 4680 0 0 1 4680 364066268 364061589 0.000000e+00 8643.0
1 TraesCS1D01G268600 chr1D 90.426 564 41 9 1 554 59532478 59531918 0.000000e+00 730.0
2 TraesCS1D01G268600 chr1D 80.537 149 11 6 1462 1610 364064747 364064617 1.070000e-16 99.0
3 TraesCS1D01G268600 chr1D 80.537 149 11 6 1522 1652 364064807 364064659 1.070000e-16 99.0
4 TraesCS1D01G268600 chr1A 90.527 2143 95 38 640 2733 463291747 463289664 0.000000e+00 2734.0
5 TraesCS1D01G268600 chr1A 89.105 2001 130 28 2731 4674 463289598 463287629 0.000000e+00 2407.0
6 TraesCS1D01G268600 chr1B 91.957 1492 76 19 2731 4206 487490119 487488656 0.000000e+00 2050.0
7 TraesCS1D01G268600 chr1B 90.945 1259 71 15 873 2102 487497005 487495761 0.000000e+00 1653.0
8 TraesCS1D01G268600 chr1B 92.188 640 40 6 2097 2733 487490804 487490172 0.000000e+00 896.0
9 TraesCS1D01G268600 chr1B 92.874 421 19 3 4261 4680 487488654 487488244 6.700000e-168 601.0
10 TraesCS1D01G268600 chr1B 97.015 134 3 1 691 824 487497136 487497004 1.690000e-54 224.0
11 TraesCS1D01G268600 chr3A 80.626 1151 157 48 1177 2309 634935601 634936703 0.000000e+00 830.0
12 TraesCS1D01G268600 chr3A 89.739 575 44 10 1 564 81667879 81667309 0.000000e+00 721.0
13 TraesCS1D01G268600 chr3B 79.982 1119 167 39 1196 2305 654424077 654425147 0.000000e+00 773.0
14 TraesCS1D01G268600 chr5D 91.577 558 39 5 1 550 467426952 467427509 0.000000e+00 763.0
15 TraesCS1D01G268600 chr2D 90.442 565 43 7 1 554 620188692 620188128 0.000000e+00 734.0
16 TraesCS1D01G268600 chr2D 89.965 568 41 11 1 554 573909803 573910368 0.000000e+00 719.0
17 TraesCS1D01G268600 chr2D 89.858 562 48 6 1 554 34362295 34361735 0.000000e+00 713.0
18 TraesCS1D01G268600 chr3D 79.420 1137 150 55 1196 2305 495484896 495485975 0.000000e+00 726.0
19 TraesCS1D01G268600 chr3D 89.716 564 46 8 1 554 339453695 339453134 0.000000e+00 710.0
20 TraesCS1D01G268600 chr6D 90.106 566 44 8 1 554 42088768 42089333 0.000000e+00 725.0
21 TraesCS1D01G268600 chr4A 89.558 565 47 7 1 554 6014660 6014097 0.000000e+00 706.0
22 TraesCS1D01G268600 chr7A 86.047 86 4 5 1805 1883 663536915 663536831 8.340000e-13 86.1


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 TraesCS1D01G268600 chr1D 364061589 364066268 4679 True 2947.000000 8643 87.024667 1 4680 3 chr1D.!!$R2 4679
1 TraesCS1D01G268600 chr1D 59531918 59532478 560 True 730.000000 730 90.426000 1 554 1 chr1D.!!$R1 553
2 TraesCS1D01G268600 chr1A 463287629 463291747 4118 True 2570.500000 2734 89.816000 640 4674 2 chr1A.!!$R1 4034
3 TraesCS1D01G268600 chr1B 487488244 487490804 2560 True 1182.333333 2050 92.339667 2097 4680 3 chr1B.!!$R1 2583
4 TraesCS1D01G268600 chr1B 487495761 487497136 1375 True 938.500000 1653 93.980000 691 2102 2 chr1B.!!$R2 1411
5 TraesCS1D01G268600 chr3A 634935601 634936703 1102 False 830.000000 830 80.626000 1177 2309 1 chr3A.!!$F1 1132
6 TraesCS1D01G268600 chr3A 81667309 81667879 570 True 721.000000 721 89.739000 1 564 1 chr3A.!!$R1 563
7 TraesCS1D01G268600 chr3B 654424077 654425147 1070 False 773.000000 773 79.982000 1196 2305 1 chr3B.!!$F1 1109
8 TraesCS1D01G268600 chr5D 467426952 467427509 557 False 763.000000 763 91.577000 1 550 1 chr5D.!!$F1 549
9 TraesCS1D01G268600 chr2D 620188128 620188692 564 True 734.000000 734 90.442000 1 554 1 chr2D.!!$R2 553
10 TraesCS1D01G268600 chr2D 573909803 573910368 565 False 719.000000 719 89.965000 1 554 1 chr2D.!!$F1 553
11 TraesCS1D01G268600 chr2D 34361735 34362295 560 True 713.000000 713 89.858000 1 554 1 chr2D.!!$R1 553
12 TraesCS1D01G268600 chr3D 495484896 495485975 1079 False 726.000000 726 79.420000 1196 2305 1 chr3D.!!$F1 1109
13 TraesCS1D01G268600 chr3D 339453134 339453695 561 True 710.000000 710 89.716000 1 554 1 chr3D.!!$R1 553
14 TraesCS1D01G268600 chr6D 42088768 42089333 565 False 725.000000 725 90.106000 1 554 1 chr6D.!!$F1 553
15 TraesCS1D01G268600 chr4A 6014097 6014660 563 True 706.000000 706 89.558000 1 554 1 chr4A.!!$R1 553

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
596 617 0.036765 AAACCTCAGCGATGGCGTAA 60.037 50.0 0.00 0.00 46.35 3.18 F
867 898 0.037232 AACTAGCTGGTCGTTCTGCC 60.037 55.0 2.06 0.00 32.97 4.85 F
1260 1316 0.979665 TCAAGGAGGAGAGCAACCTG 59.020 55.0 0.00 0.00 37.93 4.00 F
1263 1319 1.197430 AGGAGGAGAGCAACCTGGTG 61.197 60.0 0.00 0.00 37.93 4.17 F
2667 2860 1.342074 TGAGACTGGGGTGACTTCAG 58.658 55.0 4.69 4.69 37.51 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2019 2207 2.033194 GTTGTAGCAGACGGGGTGC 61.033 63.158 0.00 0.00 41.54 5.01 R
2764 3030 1.152589 TTGCACCACCAATCCAGCA 60.153 52.632 0.00 0.00 0.00 4.41 R
3014 3280 1.672356 GGTGCGCTGTGTGAGGAAT 60.672 57.895 9.73 0.00 0.00 3.01 R
3089 3355 3.064408 ACTTGCAGACATTATCATGTGCG 59.936 43.478 0.00 0.00 44.22 5.34 R
3862 4159 0.470080 CCTTCCGATCCCAGCTAGGA 60.470 60.000 2.45 2.45 41.22 2.94 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
137 138 1.289066 CGAGGCGTCTTCTTGGTCA 59.711 57.895 4.69 0.00 0.00 4.02
293 294 1.665442 GGCAAAAATGGGCGACAGT 59.335 52.632 0.00 0.00 0.00 3.55
316 318 4.689549 TGACGGAGAAGGCGGGGA 62.690 66.667 0.00 0.00 0.00 4.81
334 336 0.534203 GACGAGGGTTGCTTGTTGGA 60.534 55.000 0.00 0.00 0.00 3.53
436 448 2.690778 GCCGACGCAAATCAGGCTT 61.691 57.895 0.00 0.00 44.06 4.35
444 456 5.132897 ACGCAAATCAGGCTTAAAAATGA 57.867 34.783 0.00 0.00 0.00 2.57
460 472 1.821216 ATGAGCCGAAAATTGGTCGT 58.179 45.000 10.03 0.00 36.77 4.34
501 517 2.366584 CGTTTGAGTCGGCGCGTTA 61.367 57.895 8.43 0.00 0.00 3.18
505 521 4.493747 GAGTCGGCGCGTTAGGCT 62.494 66.667 8.43 6.16 40.44 4.58
512 528 2.785258 CGCGTTAGGCTGCCTTTC 59.215 61.111 28.55 18.17 40.44 2.62
521 537 2.032528 CTGCCTTTCCTGTCCGCA 59.967 61.111 0.00 0.00 0.00 5.69
523 539 3.423154 GCCTTTCCTGTCCGCACG 61.423 66.667 0.00 0.00 0.00 5.34
550 570 2.507547 GACCGCGCACGTAATGGA 60.508 61.111 8.75 0.00 37.70 3.41
564 585 3.004419 CGTAATGGATCGGAGTTGCTCTA 59.996 47.826 0.00 0.00 0.00 2.43
565 586 4.499188 CGTAATGGATCGGAGTTGCTCTAA 60.499 45.833 0.00 0.00 0.00 2.10
566 587 2.961526 TGGATCGGAGTTGCTCTAAC 57.038 50.000 0.00 0.00 39.65 2.34
577 598 4.945246 AGTTGCTCTAACTCTCAAAACGA 58.055 39.130 0.00 0.00 46.55 3.85
578 599 5.357257 AGTTGCTCTAACTCTCAAAACGAA 58.643 37.500 0.00 0.00 46.55 3.85
579 600 5.815740 AGTTGCTCTAACTCTCAAAACGAAA 59.184 36.000 0.00 0.00 46.55 3.46
580 601 5.652744 TGCTCTAACTCTCAAAACGAAAC 57.347 39.130 0.00 0.00 0.00 2.78
581 602 4.510340 TGCTCTAACTCTCAAAACGAAACC 59.490 41.667 0.00 0.00 0.00 3.27
582 603 4.750598 GCTCTAACTCTCAAAACGAAACCT 59.249 41.667 0.00 0.00 0.00 3.50
583 604 5.107414 GCTCTAACTCTCAAAACGAAACCTC 60.107 44.000 0.00 0.00 0.00 3.85
584 605 5.909477 TCTAACTCTCAAAACGAAACCTCA 58.091 37.500 0.00 0.00 0.00 3.86
585 606 5.983720 TCTAACTCTCAAAACGAAACCTCAG 59.016 40.000 0.00 0.00 0.00 3.35
586 607 2.872858 ACTCTCAAAACGAAACCTCAGC 59.127 45.455 0.00 0.00 0.00 4.26
587 608 1.864711 TCTCAAAACGAAACCTCAGCG 59.135 47.619 0.00 0.00 0.00 5.18
588 609 1.864711 CTCAAAACGAAACCTCAGCGA 59.135 47.619 0.00 0.00 0.00 4.93
589 610 2.480419 CTCAAAACGAAACCTCAGCGAT 59.520 45.455 0.00 0.00 0.00 4.58
590 611 2.223144 TCAAAACGAAACCTCAGCGATG 59.777 45.455 0.00 0.00 0.00 3.84
591 612 1.156736 AAACGAAACCTCAGCGATGG 58.843 50.000 0.00 0.00 0.00 3.51
592 613 1.298859 AACGAAACCTCAGCGATGGC 61.299 55.000 0.00 0.00 40.37 4.40
593 614 2.802667 CGAAACCTCAGCGATGGCG 61.803 63.158 0.00 0.00 46.35 5.69
594 615 1.741770 GAAACCTCAGCGATGGCGT 60.742 57.895 0.00 0.00 46.35 5.68
595 616 0.459585 GAAACCTCAGCGATGGCGTA 60.460 55.000 0.00 0.00 46.35 4.42
596 617 0.036765 AAACCTCAGCGATGGCGTAA 60.037 50.000 0.00 0.00 46.35 3.18
597 618 0.460284 AACCTCAGCGATGGCGTAAG 60.460 55.000 0.00 0.00 46.35 2.34
598 619 1.592669 CCTCAGCGATGGCGTAAGG 60.593 63.158 0.00 0.00 46.35 2.69
599 620 1.437573 CTCAGCGATGGCGTAAGGA 59.562 57.895 0.00 0.00 46.35 3.36
600 621 0.179111 CTCAGCGATGGCGTAAGGAA 60.179 55.000 0.00 0.00 46.35 3.36
601 622 0.248012 TCAGCGATGGCGTAAGGAAA 59.752 50.000 0.00 0.00 46.35 3.13
602 623 1.083489 CAGCGATGGCGTAAGGAAAA 58.917 50.000 0.00 0.00 46.35 2.29
603 624 1.670811 CAGCGATGGCGTAAGGAAAAT 59.329 47.619 0.00 0.00 46.35 1.82
604 625 1.670811 AGCGATGGCGTAAGGAAAATG 59.329 47.619 0.00 0.00 46.35 2.32
605 626 1.268539 GCGATGGCGTAAGGAAAATGG 60.269 52.381 0.00 0.00 40.36 3.16
606 627 1.268539 CGATGGCGTAAGGAAAATGGC 60.269 52.381 0.00 0.00 38.28 4.40
607 628 1.748493 GATGGCGTAAGGAAAATGGCA 59.252 47.619 0.00 0.00 41.91 4.92
608 629 1.173043 TGGCGTAAGGAAAATGGCAG 58.827 50.000 0.00 0.00 33.90 4.85
609 630 0.179137 GGCGTAAGGAAAATGGCAGC 60.179 55.000 0.00 0.00 38.28 5.25
610 631 0.811281 GCGTAAGGAAAATGGCAGCT 59.189 50.000 0.00 0.00 38.28 4.24
611 632 1.468054 GCGTAAGGAAAATGGCAGCTG 60.468 52.381 10.11 10.11 38.28 4.24
612 633 1.812571 CGTAAGGAAAATGGCAGCTGT 59.187 47.619 16.64 0.00 0.00 4.40
613 634 2.159517 CGTAAGGAAAATGGCAGCTGTC 60.160 50.000 12.53 12.53 0.00 3.51
614 635 1.260544 AAGGAAAATGGCAGCTGTCC 58.739 50.000 17.28 17.27 0.00 4.02
615 636 0.407139 AGGAAAATGGCAGCTGTCCT 59.593 50.000 17.28 15.38 0.00 3.85
616 637 0.813821 GGAAAATGGCAGCTGTCCTC 59.186 55.000 17.28 10.12 0.00 3.71
617 638 0.449388 GAAAATGGCAGCTGTCCTCG 59.551 55.000 17.28 0.00 0.00 4.63
618 639 1.589716 AAAATGGCAGCTGTCCTCGC 61.590 55.000 17.28 0.00 0.00 5.03
619 640 2.475371 AAATGGCAGCTGTCCTCGCT 62.475 55.000 17.28 1.56 38.49 4.93
623 644 2.508887 CAGCTGTCCTCGCTGCTC 60.509 66.667 5.25 0.00 46.98 4.26
624 645 2.679642 AGCTGTCCTCGCTGCTCT 60.680 61.111 0.00 0.00 38.96 4.09
625 646 2.264166 GCTGTCCTCGCTGCTCTT 59.736 61.111 0.00 0.00 0.00 2.85
626 647 2.099431 GCTGTCCTCGCTGCTCTTG 61.099 63.158 0.00 0.00 0.00 3.02
627 648 1.588597 CTGTCCTCGCTGCTCTTGA 59.411 57.895 0.00 0.00 0.00 3.02
628 649 0.735632 CTGTCCTCGCTGCTCTTGAC 60.736 60.000 0.00 0.07 0.00 3.18
629 650 1.181741 TGTCCTCGCTGCTCTTGACT 61.182 55.000 0.00 0.00 0.00 3.41
630 651 0.037790 GTCCTCGCTGCTCTTGACTT 60.038 55.000 0.00 0.00 0.00 3.01
631 652 0.244994 TCCTCGCTGCTCTTGACTTC 59.755 55.000 0.00 0.00 0.00 3.01
632 653 0.739112 CCTCGCTGCTCTTGACTTCC 60.739 60.000 0.00 0.00 0.00 3.46
633 654 0.246086 CTCGCTGCTCTTGACTTCCT 59.754 55.000 0.00 0.00 0.00 3.36
634 655 0.681733 TCGCTGCTCTTGACTTCCTT 59.318 50.000 0.00 0.00 0.00 3.36
635 656 1.074752 CGCTGCTCTTGACTTCCTTC 58.925 55.000 0.00 0.00 0.00 3.46
636 657 1.074752 GCTGCTCTTGACTTCCTTCG 58.925 55.000 0.00 0.00 0.00 3.79
637 658 1.719600 CTGCTCTTGACTTCCTTCGG 58.280 55.000 0.00 0.00 0.00 4.30
638 659 1.273606 CTGCTCTTGACTTCCTTCGGA 59.726 52.381 0.00 0.00 0.00 4.55
642 663 0.038159 CTTGACTTCCTTCGGAGCGT 60.038 55.000 0.00 0.00 31.21 5.07
676 701 1.157870 AAAGGTGGTGTCACGCGAAG 61.158 55.000 15.93 4.76 44.50 3.79
819 850 1.595109 GCAAAGCAAACACCAGCCC 60.595 57.895 0.00 0.00 0.00 5.19
820 851 1.821936 CAAAGCAAACACCAGCCCA 59.178 52.632 0.00 0.00 0.00 5.36
821 852 0.249573 CAAAGCAAACACCAGCCCAG 60.250 55.000 0.00 0.00 0.00 4.45
822 853 2.031674 AAAGCAAACACCAGCCCAGC 62.032 55.000 0.00 0.00 0.00 4.85
824 855 2.521465 CAAACACCAGCCCAGCCA 60.521 61.111 0.00 0.00 0.00 4.75
825 856 2.203538 AAACACCAGCCCAGCCAG 60.204 61.111 0.00 0.00 0.00 4.85
826 857 4.982701 AACACCAGCCCAGCCAGC 62.983 66.667 0.00 0.00 0.00 4.85
848 879 0.468400 CCAGGGGAAACGGAAACCAA 60.468 55.000 0.00 0.00 0.00 3.67
851 882 1.063492 AGGGGAAACGGAAACCAAACT 60.063 47.619 0.00 0.00 0.00 2.66
867 898 0.037232 AACTAGCTGGTCGTTCTGCC 60.037 55.000 2.06 0.00 32.97 4.85
868 899 1.153549 CTAGCTGGTCGTTCTGCCC 60.154 63.158 0.00 0.00 32.97 5.36
869 900 2.579684 CTAGCTGGTCGTTCTGCCCC 62.580 65.000 0.00 0.00 32.97 5.80
878 909 3.953652 TTCTGCCCCCTCCCTCCA 61.954 66.667 0.00 0.00 0.00 3.86
880 911 2.697644 CTGCCCCCTCCCTCCATT 60.698 66.667 0.00 0.00 0.00 3.16
881 912 2.696125 TGCCCCCTCCCTCCATTC 60.696 66.667 0.00 0.00 0.00 2.67
902 933 1.069358 CCCTACAAATCTCTCGCCTCC 59.931 57.143 0.00 0.00 0.00 4.30
903 934 1.069358 CCTACAAATCTCTCGCCTCCC 59.931 57.143 0.00 0.00 0.00 4.30
904 935 2.035632 CTACAAATCTCTCGCCTCCCT 58.964 52.381 0.00 0.00 0.00 4.20
967 998 2.284331 TCCTAGCTTCCACCGCCA 60.284 61.111 0.00 0.00 0.00 5.69
988 1019 3.853330 CGCGCACACTTCCATCCG 61.853 66.667 8.75 0.00 0.00 4.18
989 1020 4.166011 GCGCACACTTCCATCCGC 62.166 66.667 0.30 0.00 34.50 5.54
997 1028 1.078214 CTTCCATCCGCTTCCAGCA 60.078 57.895 0.00 0.00 42.58 4.41
1103 1153 4.452733 GGAGGACAAGGCCGTCGG 62.453 72.222 6.99 6.99 36.73 4.79
1260 1316 0.979665 TCAAGGAGGAGAGCAACCTG 59.020 55.000 0.00 0.00 37.93 4.00
1263 1319 1.197430 AGGAGGAGAGCAACCTGGTG 61.197 60.000 0.00 0.00 37.93 4.17
1426 1485 3.197790 CGGCCAAGAGCGATGTGG 61.198 66.667 2.24 0.00 45.17 4.17
1430 1489 3.869272 CAAGAGCGATGTGGCGGC 61.869 66.667 0.00 0.00 38.18 6.53
2305 2493 4.780815 TGAATTCATCGCCAAGAAGGTAT 58.219 39.130 3.38 0.00 40.61 2.73
2313 2501 5.873179 TCGCCAAGAAGGTATTAAACTTG 57.127 39.130 0.00 0.00 40.61 3.16
2315 2503 5.410439 TCGCCAAGAAGGTATTAAACTTGTC 59.590 40.000 0.00 0.00 40.61 3.18
2330 2518 4.762289 ACTTGTCTCTTCTCTTTGTGGT 57.238 40.909 0.00 0.00 0.00 4.16
2343 2531 5.421056 TCTCTTTGTGGTATCGTGTCCTAAT 59.579 40.000 0.00 0.00 0.00 1.73
2345 2533 6.103997 TCTTTGTGGTATCGTGTCCTAATTC 58.896 40.000 0.00 0.00 0.00 2.17
2349 2537 6.567050 TGTGGTATCGTGTCCTAATTCTTAC 58.433 40.000 0.00 0.00 0.00 2.34
2427 2617 2.724174 GCGATTTTGTGTTTGTAGTGGC 59.276 45.455 0.00 0.00 0.00 5.01
2446 2636 2.413371 GGCTTCAACTGAATTCGTCTGC 60.413 50.000 0.04 5.17 33.01 4.26
2457 2647 4.142447 TGAATTCGTCTGCTGTAGGTAGTC 60.142 45.833 0.04 0.00 0.00 2.59
2533 2726 7.113684 GCACTCGTAGCACAATAATCTAACTAG 59.886 40.741 0.00 0.00 0.00 2.57
2574 2767 3.384668 CAAGTAGGATGACATAGTGGCG 58.615 50.000 0.00 0.00 0.00 5.69
2586 2779 1.448985 TAGTGGCGCCATTTCACTTC 58.551 50.000 35.23 17.28 41.37 3.01
2589 2782 1.810151 GTGGCGCCATTTCACTTCTAA 59.190 47.619 35.23 0.00 0.00 2.10
2591 2784 3.088532 TGGCGCCATTTCACTTCTAATT 58.911 40.909 29.03 0.00 0.00 1.40
2592 2785 3.509575 TGGCGCCATTTCACTTCTAATTT 59.490 39.130 29.03 0.00 0.00 1.82
2593 2786 4.021544 TGGCGCCATTTCACTTCTAATTTT 60.022 37.500 29.03 0.00 0.00 1.82
2594 2787 4.562789 GGCGCCATTTCACTTCTAATTTTC 59.437 41.667 24.80 0.00 0.00 2.29
2595 2788 5.402398 GCGCCATTTCACTTCTAATTTTCT 58.598 37.500 0.00 0.00 0.00 2.52
2596 2789 5.513141 GCGCCATTTCACTTCTAATTTTCTC 59.487 40.000 0.00 0.00 0.00 2.87
2628 2821 5.818136 TGAGTTATGTTCCTTGCTATTGC 57.182 39.130 0.00 0.00 40.20 3.56
2651 2844 5.801947 GCAAATGGTACTTGCTTGTTATGAG 59.198 40.000 10.24 0.00 44.66 2.90
2657 2850 3.679389 ACTTGCTTGTTATGAGACTGGG 58.321 45.455 0.00 0.00 0.00 4.45
2659 2852 1.985159 TGCTTGTTATGAGACTGGGGT 59.015 47.619 0.00 0.00 0.00 4.95
2667 2860 1.342074 TGAGACTGGGGTGACTTCAG 58.658 55.000 4.69 4.69 37.51 3.02
2703 2901 4.627035 TCATCTGATGAACACGACATTGTC 59.373 41.667 17.56 6.73 36.11 3.18
2724 2922 4.693566 GTCGTGGGTTCAACTGAATTCATA 59.306 41.667 8.96 0.00 36.33 2.15
2727 2925 5.449041 CGTGGGTTCAACTGAATTCATATGG 60.449 44.000 8.96 0.00 36.33 2.74
2756 3022 5.459505 AGCACCTGTACCTCTGTAATCTAT 58.540 41.667 0.00 0.00 0.00 1.98
2790 3056 2.940994 TTGGTGGTGCAAGTAAGCTA 57.059 45.000 0.00 0.00 34.99 3.32
2795 3061 4.224147 TGGTGGTGCAAGTAAGCTAAGATA 59.776 41.667 0.00 0.00 34.99 1.98
2801 3067 3.491267 GCAAGTAAGCTAAGATAGTGGCG 59.509 47.826 0.00 0.00 0.00 5.69
2810 3076 4.025647 GCTAAGATAGTGGCGTCATTTCAC 60.026 45.833 0.00 0.00 0.00 3.18
2817 3083 3.258372 AGTGGCGTCATTTCACTTCTAGA 59.742 43.478 0.00 0.00 38.44 2.43
2822 3088 6.876789 TGGCGTCATTTCACTTCTAGATTTTA 59.123 34.615 0.00 0.00 0.00 1.52
2826 3092 8.596380 CGTCATTTCACTTCTAGATTTTACTCC 58.404 37.037 0.00 0.00 0.00 3.85
2830 3096 9.674068 ATTTCACTTCTAGATTTTACTCCCTTC 57.326 33.333 0.00 0.00 0.00 3.46
2831 3097 8.437274 TTCACTTCTAGATTTTACTCCCTTCT 57.563 34.615 0.00 0.00 0.00 2.85
2833 3099 8.532819 TCACTTCTAGATTTTACTCCCTTCTTC 58.467 37.037 0.00 0.00 0.00 2.87
2840 3106 6.651225 AGATTTTACTCCCTTCTTCGTTTGAG 59.349 38.462 0.00 0.00 0.00 3.02
2848 3114 4.392138 CCCTTCTTCGTTTGAGTTATGTCC 59.608 45.833 0.00 0.00 0.00 4.02
2849 3115 4.392138 CCTTCTTCGTTTGAGTTATGTCCC 59.608 45.833 0.00 0.00 0.00 4.46
2852 3118 4.994852 TCTTCGTTTGAGTTATGTCCCTTG 59.005 41.667 0.00 0.00 0.00 3.61
2855 3121 3.120199 CGTTTGAGTTATGTCCCTTGCTG 60.120 47.826 0.00 0.00 0.00 4.41
2886 3152 6.538945 TGGTATGTGCTTGTTATGAGACTA 57.461 37.500 0.00 0.00 0.00 2.59
2888 3154 5.986135 GGTATGTGCTTGTTATGAGACTAGG 59.014 44.000 0.00 0.00 0.00 3.02
2890 3156 3.197766 TGTGCTTGTTATGAGACTAGGGG 59.802 47.826 0.00 0.00 0.00 4.79
2948 3214 3.891366 GGGATCAATTTGGTCGGATCATT 59.109 43.478 3.65 0.00 38.27 2.57
2949 3215 4.261741 GGGATCAATTTGGTCGGATCATTG 60.262 45.833 3.65 0.00 38.27 2.82
3014 3280 1.820519 GCAAACAAGATGATGAGCCCA 59.179 47.619 0.00 0.00 0.00 5.36
3089 3355 2.482142 CGCAGAGACCCTATTCAGGTTC 60.482 54.545 0.00 0.00 40.79 3.62
3102 3368 4.880886 TTCAGGTTCGCACATGATAATG 57.119 40.909 2.93 0.00 43.09 1.90
3118 3384 6.974932 TGATAATGTCTGCAAGTCTTCTTC 57.025 37.500 0.00 0.00 33.76 2.87
3122 3388 4.679373 TGTCTGCAAGTCTTCTTCTCTT 57.321 40.909 0.00 0.00 33.76 2.85
3131 3397 6.907748 GCAAGTCTTCTTCTCTTGTTTAACAC 59.092 38.462 0.00 0.00 40.14 3.32
3132 3398 7.410485 CAAGTCTTCTTCTCTTGTTTAACACC 58.590 38.462 0.00 0.00 35.34 4.16
3259 3525 5.306678 AGAGGATGATACTGAATTCTCCACC 59.693 44.000 7.05 2.72 0.00 4.61
3271 3537 1.142748 CTCCACCTCTGATGGCGTC 59.857 63.158 0.00 0.00 37.13 5.19
3333 3599 3.445008 AGATTCCTGCTACTGAGGTTGA 58.555 45.455 0.00 0.00 31.85 3.18
3345 3613 2.768527 CTGAGGTTGATCCCTGCTTCTA 59.231 50.000 0.00 0.00 34.03 2.10
3346 3614 2.501723 TGAGGTTGATCCCTGCTTCTAC 59.498 50.000 0.00 0.00 34.03 2.59
3356 3624 3.019564 CCCTGCTTCTACCCTCAAATTG 58.980 50.000 0.00 0.00 0.00 2.32
3364 3632 5.068234 TCTACCCTCAAATTGACACTACG 57.932 43.478 0.00 0.00 0.00 3.51
3406 3675 7.477494 TCATAGTTCATTTCATCAATGTGCTG 58.523 34.615 0.00 0.00 42.79 4.41
3667 3936 1.216710 GGTGAAGAGCTCCACCGAG 59.783 63.158 21.67 0.00 42.73 4.63
3689 3958 2.202932 CCGCCTGATGAGGTTCCG 60.203 66.667 0.00 0.00 42.15 4.30
3693 3965 1.604378 CCTGATGAGGTTCCGGCTT 59.396 57.895 0.00 0.00 34.16 4.35
3762 4059 3.644966 TGATAGGAGATGGCCGTTTTT 57.355 42.857 0.00 0.00 0.00 1.94
3823 4120 4.202010 GGGGATCGGATTTGTATGTGTTTG 60.202 45.833 0.00 0.00 0.00 2.93
3846 4143 0.389025 GGAACCAAAGTGGGCTTGTG 59.611 55.000 0.00 0.00 43.37 3.33
3862 4159 5.303971 GGCTTGTGCTATGAATGAGATACT 58.696 41.667 0.00 0.00 39.59 2.12
3876 4177 3.013921 GAGATACTCCTAGCTGGGATCG 58.986 54.545 20.41 11.52 34.56 3.69
3888 4189 2.444256 GGGATCGGAAGGTGGGGAG 61.444 68.421 0.00 0.00 0.00 4.30
3981 4282 2.693591 ACCTGTCTGTACATGGTATCCG 59.306 50.000 0.00 0.00 36.19 4.18
3988 4289 5.010314 GTCTGTACATGGTATCCGTGGATTA 59.990 44.000 6.72 0.00 44.23 1.75
4022 4323 7.328249 TCGGCATGTTGATTTTGTTTAGAAATC 59.672 33.333 0.00 3.33 41.59 2.17
4023 4324 7.447430 GGCATGTTGATTTTGTTTAGAAATCG 58.553 34.615 0.00 0.00 43.24 3.34
4125 4436 4.156664 GCATATGGCAATGATCTGTGAC 57.843 45.455 4.56 0.00 43.97 3.67
4129 4440 0.647410 GGCAATGATCTGTGACGTCG 59.353 55.000 11.62 0.00 0.00 5.12
4138 4449 3.052082 GTGACGTCGGGGTCTCGA 61.052 66.667 11.62 0.00 37.81 4.04
4156 4467 1.864082 CGACCATTGTTTTGTTTGCCC 59.136 47.619 0.00 0.00 0.00 5.36
4217 4532 3.427161 AGTTTTTGACTGAAGCAGTGC 57.573 42.857 7.13 7.13 45.44 4.40
4218 4533 2.111756 GTTTTTGACTGAAGCAGTGCG 58.888 47.619 10.00 0.00 45.44 5.34
4227 4542 0.787183 GAAGCAGTGCGACTCTTGTC 59.213 55.000 10.00 0.00 39.70 3.18
4233 4548 0.946221 GTGCGACTCTTGTCCACTGG 60.946 60.000 0.00 0.00 39.28 4.00
4259 4574 2.887152 CCATTGCATTCCTAGTTAGGCC 59.113 50.000 0.00 0.00 43.31 5.19
4263 4578 2.092429 TGCATTCCTAGTTAGGCCAAGG 60.092 50.000 5.01 3.48 43.31 3.61
4274 4589 2.816777 AGGCCAAGGGAGATTCTTTC 57.183 50.000 5.01 0.00 0.00 2.62
4320 4635 2.210116 GTTCTGAAAGTGGCAAGACGA 58.790 47.619 0.00 0.00 33.76 4.20
4327 4642 2.281484 TGGCAAGACGAACAGGGC 60.281 61.111 0.00 0.00 0.00 5.19
4409 4729 2.649129 GCCATGCTTGGGTTGGGTC 61.649 63.158 19.47 0.00 43.84 4.46
4465 4786 1.916697 GAACAGCGAGAAGGGCAAGC 61.917 60.000 0.00 0.00 0.00 4.01
4508 4829 1.518903 GGACAGTGCCAAGGAGCAAC 61.519 60.000 0.00 0.00 46.19 4.17
4526 4847 3.737972 GCAACAACTTTCCCTTTGACCAG 60.738 47.826 0.00 0.00 0.00 4.00
4538 4859 3.544684 CTTTGACCAGCATAGCATACCA 58.455 45.455 0.00 0.00 0.00 3.25
4539 4860 3.643199 TTGACCAGCATAGCATACCAA 57.357 42.857 0.00 0.00 0.00 3.67
4540 4861 3.643199 TGACCAGCATAGCATACCAAA 57.357 42.857 0.00 0.00 0.00 3.28
4541 4862 3.278574 TGACCAGCATAGCATACCAAAC 58.721 45.455 0.00 0.00 0.00 2.93
4542 4863 2.618709 GACCAGCATAGCATACCAAACC 59.381 50.000 0.00 0.00 0.00 3.27
4631 4961 3.328931 TGATCCCCTCTCTGAATAATGGC 59.671 47.826 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
289 290 1.105167 TTCTCCGTCACCGACACTGT 61.105 55.000 0.00 0.00 35.63 3.55
293 294 2.927580 GCCTTCTCCGTCACCGACA 61.928 63.158 0.00 0.00 35.63 4.35
316 318 0.818040 GTCCAACAAGCAACCCTCGT 60.818 55.000 0.00 0.00 0.00 4.18
334 336 4.995058 TGGCCTTCCTTCCCCCGT 62.995 66.667 3.32 0.00 0.00 5.28
399 408 2.250485 CGAACACGAGACGGACGT 59.750 61.111 0.00 0.00 44.83 4.34
436 448 5.157781 CGACCAATTTTCGGCTCATTTTTA 58.842 37.500 0.00 0.00 32.66 1.52
444 456 1.296056 CGGACGACCAATTTTCGGCT 61.296 55.000 11.04 0.00 44.40 5.52
449 461 1.301874 TCCGCGGACGACCAATTTT 60.302 52.632 27.28 0.00 43.93 1.82
460 472 3.037249 CCGTTTTTCGTCCGCGGA 61.037 61.111 27.28 27.28 44.57 5.54
489 505 4.796231 CAGCCTAACGCGCCGACT 62.796 66.667 5.73 0.00 44.76 4.18
501 517 2.759795 GGACAGGAAAGGCAGCCT 59.240 61.111 8.70 8.70 33.87 4.58
505 521 2.281484 GTGCGGACAGGAAAGGCA 60.281 61.111 0.63 0.00 0.00 4.75
528 544 4.644230 TACGTGCGCGGTCCGTTT 62.644 61.111 25.20 3.01 43.45 3.60
532 548 3.560278 CCATTACGTGCGCGGTCC 61.560 66.667 25.20 0.00 43.45 4.46
540 560 1.593006 GCAACTCCGATCCATTACGTG 59.407 52.381 0.00 0.00 0.00 4.49
544 564 4.649674 AGTTAGAGCAACTCCGATCCATTA 59.350 41.667 0.00 0.00 44.48 1.90
564 585 3.312697 GCTGAGGTTTCGTTTTGAGAGTT 59.687 43.478 0.00 0.00 0.00 3.01
565 586 2.872858 GCTGAGGTTTCGTTTTGAGAGT 59.127 45.455 0.00 0.00 0.00 3.24
566 587 2.096713 CGCTGAGGTTTCGTTTTGAGAG 60.097 50.000 0.00 0.00 0.00 3.20
567 588 1.864711 CGCTGAGGTTTCGTTTTGAGA 59.135 47.619 0.00 0.00 0.00 3.27
568 589 1.864711 TCGCTGAGGTTTCGTTTTGAG 59.135 47.619 0.00 0.00 0.00 3.02
569 590 1.942677 TCGCTGAGGTTTCGTTTTGA 58.057 45.000 0.00 0.00 0.00 2.69
570 591 2.574322 CATCGCTGAGGTTTCGTTTTG 58.426 47.619 0.00 0.00 0.00 2.44
571 592 1.535462 CCATCGCTGAGGTTTCGTTTT 59.465 47.619 0.00 0.00 0.00 2.43
572 593 1.156736 CCATCGCTGAGGTTTCGTTT 58.843 50.000 0.00 0.00 0.00 3.60
573 594 1.298859 GCCATCGCTGAGGTTTCGTT 61.299 55.000 0.00 0.00 0.00 3.85
574 595 1.741770 GCCATCGCTGAGGTTTCGT 60.742 57.895 0.00 0.00 0.00 3.85
575 596 2.802667 CGCCATCGCTGAGGTTTCG 61.803 63.158 0.00 0.00 0.00 3.46
576 597 0.459585 TACGCCATCGCTGAGGTTTC 60.460 55.000 0.00 0.00 39.84 2.78
577 598 0.036765 TTACGCCATCGCTGAGGTTT 60.037 50.000 0.00 0.00 39.84 3.27
578 599 0.460284 CTTACGCCATCGCTGAGGTT 60.460 55.000 0.00 0.00 39.84 3.50
579 600 1.141881 CTTACGCCATCGCTGAGGT 59.858 57.895 0.00 0.00 39.84 3.85
580 601 1.592669 CCTTACGCCATCGCTGAGG 60.593 63.158 0.00 0.00 39.84 3.86
581 602 0.179111 TTCCTTACGCCATCGCTGAG 60.179 55.000 0.00 0.00 39.84 3.35
582 603 0.248012 TTTCCTTACGCCATCGCTGA 59.752 50.000 0.00 0.00 39.84 4.26
583 604 1.083489 TTTTCCTTACGCCATCGCTG 58.917 50.000 0.00 0.00 39.84 5.18
584 605 1.670811 CATTTTCCTTACGCCATCGCT 59.329 47.619 0.00 0.00 39.84 4.93
585 606 1.268539 CCATTTTCCTTACGCCATCGC 60.269 52.381 0.00 0.00 39.84 4.58
586 607 1.268539 GCCATTTTCCTTACGCCATCG 60.269 52.381 0.00 0.00 42.43 3.84
587 608 1.748493 TGCCATTTTCCTTACGCCATC 59.252 47.619 0.00 0.00 0.00 3.51
588 609 1.750778 CTGCCATTTTCCTTACGCCAT 59.249 47.619 0.00 0.00 0.00 4.40
589 610 1.173043 CTGCCATTTTCCTTACGCCA 58.827 50.000 0.00 0.00 0.00 5.69
590 611 0.179137 GCTGCCATTTTCCTTACGCC 60.179 55.000 0.00 0.00 0.00 5.68
591 612 0.811281 AGCTGCCATTTTCCTTACGC 59.189 50.000 0.00 0.00 0.00 4.42
592 613 1.812571 ACAGCTGCCATTTTCCTTACG 59.187 47.619 15.27 0.00 0.00 3.18
593 614 2.164422 GGACAGCTGCCATTTTCCTTAC 59.836 50.000 15.27 0.00 0.00 2.34
594 615 2.041620 AGGACAGCTGCCATTTTCCTTA 59.958 45.455 23.46 0.00 28.60 2.69
595 616 1.203100 AGGACAGCTGCCATTTTCCTT 60.203 47.619 23.46 7.23 28.60 3.36
596 617 0.407139 AGGACAGCTGCCATTTTCCT 59.593 50.000 23.46 19.07 0.00 3.36
597 618 0.813821 GAGGACAGCTGCCATTTTCC 59.186 55.000 23.46 17.38 0.00 3.13
598 619 0.449388 CGAGGACAGCTGCCATTTTC 59.551 55.000 23.46 13.85 0.00 2.29
599 620 1.589716 GCGAGGACAGCTGCCATTTT 61.590 55.000 23.46 7.83 0.00 1.82
600 621 2.042831 GCGAGGACAGCTGCCATTT 61.043 57.895 23.46 8.13 0.00 2.32
601 622 2.437359 GCGAGGACAGCTGCCATT 60.437 61.111 23.46 8.73 0.00 3.16
602 623 3.397439 AGCGAGGACAGCTGCCAT 61.397 61.111 23.46 8.45 44.22 4.40
608 629 2.099431 CAAGAGCAGCGAGGACAGC 61.099 63.158 0.00 0.00 0.00 4.40
609 630 0.735632 GTCAAGAGCAGCGAGGACAG 60.736 60.000 0.00 0.00 0.00 3.51
610 631 1.181741 AGTCAAGAGCAGCGAGGACA 61.182 55.000 10.70 0.00 0.00 4.02
611 632 0.037790 AAGTCAAGAGCAGCGAGGAC 60.038 55.000 0.00 2.48 0.00 3.85
612 633 0.244994 GAAGTCAAGAGCAGCGAGGA 59.755 55.000 0.00 0.00 0.00 3.71
613 634 0.739112 GGAAGTCAAGAGCAGCGAGG 60.739 60.000 0.00 0.00 0.00 4.63
614 635 0.246086 AGGAAGTCAAGAGCAGCGAG 59.754 55.000 0.00 0.00 0.00 5.03
615 636 0.681733 AAGGAAGTCAAGAGCAGCGA 59.318 50.000 0.00 0.00 0.00 4.93
616 637 1.074752 GAAGGAAGTCAAGAGCAGCG 58.925 55.000 0.00 0.00 0.00 5.18
617 638 1.074752 CGAAGGAAGTCAAGAGCAGC 58.925 55.000 0.00 0.00 0.00 5.25
632 653 1.416813 CTGCTGCTTACGCTCCGAAG 61.417 60.000 0.00 0.00 36.97 3.79
633 654 1.446099 CTGCTGCTTACGCTCCGAA 60.446 57.895 0.00 0.00 36.97 4.30
634 655 2.181777 CTGCTGCTTACGCTCCGA 59.818 61.111 0.00 0.00 36.97 4.55
635 656 1.875813 CTCTGCTGCTTACGCTCCG 60.876 63.158 0.00 0.00 36.97 4.63
636 657 2.170434 GCTCTGCTGCTTACGCTCC 61.170 63.158 0.00 0.00 36.97 4.70
637 658 1.016130 TTGCTCTGCTGCTTACGCTC 61.016 55.000 0.00 0.00 36.97 5.03
638 659 0.603707 TTTGCTCTGCTGCTTACGCT 60.604 50.000 0.00 0.00 36.97 5.07
642 663 2.294233 CACCTTTTTGCTCTGCTGCTTA 59.706 45.455 0.00 0.00 0.00 3.09
821 852 4.299796 TTTCCCCTGGTGGCTGGC 62.300 66.667 0.00 0.00 0.00 4.85
822 853 2.283173 GTTTCCCCTGGTGGCTGG 60.283 66.667 0.00 0.00 0.00 4.85
824 855 3.966543 CCGTTTCCCCTGGTGGCT 61.967 66.667 0.00 0.00 0.00 4.75
825 856 2.987355 TTTCCGTTTCCCCTGGTGGC 62.987 60.000 0.00 0.00 0.00 5.01
826 857 1.151908 TTTCCGTTTCCCCTGGTGG 59.848 57.895 0.00 0.00 0.00 4.61
828 859 1.152138 GGTTTCCGTTTCCCCTGGT 59.848 57.895 0.00 0.00 0.00 4.00
848 879 0.037232 GGCAGAACGACCAGCTAGTT 60.037 55.000 0.00 0.00 0.00 2.24
851 882 2.978824 GGGCAGAACGACCAGCTA 59.021 61.111 0.00 0.00 45.64 3.32
867 898 1.985473 TAGGGGAATGGAGGGAGGGG 61.985 65.000 0.00 0.00 0.00 4.79
868 899 0.768609 GTAGGGGAATGGAGGGAGGG 60.769 65.000 0.00 0.00 0.00 4.30
869 900 0.030092 TGTAGGGGAATGGAGGGAGG 60.030 60.000 0.00 0.00 0.00 4.30
870 901 1.893315 TTGTAGGGGAATGGAGGGAG 58.107 55.000 0.00 0.00 0.00 4.30
878 909 2.104963 GGCGAGAGATTTGTAGGGGAAT 59.895 50.000 0.00 0.00 0.00 3.01
880 911 1.120530 GGCGAGAGATTTGTAGGGGA 58.879 55.000 0.00 0.00 0.00 4.81
881 912 1.069358 GAGGCGAGAGATTTGTAGGGG 59.931 57.143 0.00 0.00 0.00 4.79
902 933 2.612251 GAGAGGGAGGGAGGGAGG 59.388 72.222 0.00 0.00 0.00 4.30
903 934 2.612251 GGAGAGGGAGGGAGGGAG 59.388 72.222 0.00 0.00 0.00 4.30
904 935 3.036959 GGGAGAGGGAGGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
967 998 4.908687 TGGAAGTGTGCGCGTGCT 62.909 61.111 23.16 0.00 43.34 4.40
989 1020 3.515286 CGGCCATGCTGCTGGAAG 61.515 66.667 18.30 9.40 38.69 3.46
997 1028 3.474570 GGTCTCCTCGGCCATGCT 61.475 66.667 2.24 0.00 0.00 3.79
1103 1153 3.732849 CAGCCTTCTCCCCCACCC 61.733 72.222 0.00 0.00 0.00 4.61
1146 1199 0.105709 CCTCCTCCTCCTCCTCCTTC 60.106 65.000 0.00 0.00 0.00 3.46
1389 1445 2.915659 TCGTCGGTCTTGGCAGGT 60.916 61.111 0.00 0.00 0.00 4.00
1444 1503 2.107953 GCTGCTCTCGGCCTTAGG 59.892 66.667 0.00 0.00 40.92 2.69
1445 1504 2.279120 CGCTGCTCTCGGCCTTAG 60.279 66.667 0.00 0.00 41.54 2.18
1446 1505 2.754254 TCGCTGCTCTCGGCCTTA 60.754 61.111 0.00 0.00 41.54 2.69
1447 1506 4.140599 CTCGCTGCTCTCGGCCTT 62.141 66.667 0.00 0.00 41.54 4.35
1521 1580 3.154473 TCCTCGGCCTTGGGATCG 61.154 66.667 0.00 0.00 0.00 3.69
2019 2207 2.033194 GTTGTAGCAGACGGGGTGC 61.033 63.158 0.00 0.00 41.54 5.01
2305 2493 7.110155 ACCACAAAGAGAAGAGACAAGTTTAA 58.890 34.615 0.00 0.00 0.00 1.52
2313 2501 4.859798 CACGATACCACAAAGAGAAGAGAC 59.140 45.833 0.00 0.00 0.00 3.36
2315 2503 4.810790 ACACGATACCACAAAGAGAAGAG 58.189 43.478 0.00 0.00 0.00 2.85
2330 2518 7.649533 TTGGAGTAAGAATTAGGACACGATA 57.350 36.000 0.00 0.00 0.00 2.92
2427 2617 3.496130 ACAGCAGACGAATTCAGTTGAAG 59.504 43.478 6.22 0.00 37.48 3.02
2446 2636 5.836821 TCACAGCATTAGACTACCTACAG 57.163 43.478 0.00 0.00 0.00 2.74
2457 2647 3.308053 CACAGGACGAATCACAGCATTAG 59.692 47.826 0.00 0.00 0.00 1.73
2503 2696 6.153067 AGATTATTGTGCTACGAGTGCTATC 58.847 40.000 0.00 0.00 0.00 2.08
2533 2726 3.023119 TGCACCAACAATCCACCATATC 58.977 45.455 0.00 0.00 0.00 1.63
2547 2740 3.719268 ATGTCATCCTACTTGCACCAA 57.281 42.857 0.00 0.00 0.00 3.67
2574 2767 9.133627 GAAAGAGAAAATTAGAAGTGAAATGGC 57.866 33.333 0.00 0.00 0.00 4.40
2592 2785 8.621286 GGAACATAACTCAAACAAGAAAGAGAA 58.379 33.333 0.00 0.00 32.59 2.87
2593 2786 7.993183 AGGAACATAACTCAAACAAGAAAGAGA 59.007 33.333 0.00 0.00 32.59 3.10
2594 2787 8.159344 AGGAACATAACTCAAACAAGAAAGAG 57.841 34.615 0.00 0.00 0.00 2.85
2595 2788 8.405531 CAAGGAACATAACTCAAACAAGAAAGA 58.594 33.333 0.00 0.00 0.00 2.52
2596 2789 7.168135 GCAAGGAACATAACTCAAACAAGAAAG 59.832 37.037 0.00 0.00 0.00 2.62
2628 2821 7.023575 GTCTCATAACAAGCAAGTACCATTTG 58.976 38.462 0.00 0.00 0.00 2.32
2637 2830 3.012518 CCCCAGTCTCATAACAAGCAAG 58.987 50.000 0.00 0.00 0.00 4.01
2648 2841 1.342074 CTGAAGTCACCCCAGTCTCA 58.658 55.000 0.00 0.00 0.00 3.27
2651 2844 4.649674 TCATATACTGAAGTCACCCCAGTC 59.350 45.833 3.19 0.00 41.01 3.51
2657 2850 8.893219 TGAATTCATCATATACTGAAGTCACC 57.107 34.615 18.26 3.13 45.85 4.02
2703 2901 5.449041 CCATATGAATTCAGTTGAACCCACG 60.449 44.000 14.54 0.00 36.80 4.94
2706 2904 5.418840 ACACCATATGAATTCAGTTGAACCC 59.581 40.000 14.54 0.00 36.80 4.11
2743 3009 8.849168 CCAGCATATCTAGATAGATTACAGAGG 58.151 40.741 17.22 6.47 42.66 3.69
2756 3022 4.040829 CACCACCAATCCAGCATATCTAGA 59.959 45.833 0.00 0.00 0.00 2.43
2764 3030 1.152589 TTGCACCACCAATCCAGCA 60.153 52.632 0.00 0.00 0.00 4.41
2766 3032 2.198827 TACTTGCACCACCAATCCAG 57.801 50.000 0.00 0.00 0.00 3.86
2773 3039 3.053831 TCTTAGCTTACTTGCACCACC 57.946 47.619 0.00 0.00 34.99 4.61
2790 3056 4.207891 AGTGAAATGACGCCACTATCTT 57.792 40.909 0.00 0.00 39.15 2.40
2795 3061 2.550830 AGAAGTGAAATGACGCCACT 57.449 45.000 0.00 0.00 42.34 4.00
2801 3067 8.884726 GGGAGTAAAATCTAGAAGTGAAATGAC 58.115 37.037 0.00 0.00 0.00 3.06
2810 3076 7.548967 ACGAAGAAGGGAGTAAAATCTAGAAG 58.451 38.462 0.00 0.00 0.00 2.85
2817 3083 6.296803 ACTCAAACGAAGAAGGGAGTAAAAT 58.703 36.000 0.00 0.00 34.13 1.82
2822 3088 3.840124 AACTCAAACGAAGAAGGGAGT 57.160 42.857 0.00 0.00 37.21 3.85
2826 3092 4.392138 GGGACATAACTCAAACGAAGAAGG 59.608 45.833 0.00 0.00 0.00 3.46
2830 3096 4.378459 GCAAGGGACATAACTCAAACGAAG 60.378 45.833 0.00 0.00 0.00 3.79
2831 3097 3.500680 GCAAGGGACATAACTCAAACGAA 59.499 43.478 0.00 0.00 0.00 3.85
2833 3099 3.074412 AGCAAGGGACATAACTCAAACG 58.926 45.455 0.00 0.00 0.00 3.60
2840 3106 6.460123 CCATATTCAACAGCAAGGGACATAAC 60.460 42.308 0.00 0.00 0.00 1.89
2848 3114 5.734220 GCACATACCATATTCAACAGCAAGG 60.734 44.000 0.00 0.00 0.00 3.61
2849 3115 5.066893 AGCACATACCATATTCAACAGCAAG 59.933 40.000 0.00 0.00 0.00 4.01
2852 3118 5.163622 ACAAGCACATACCATATTCAACAGC 60.164 40.000 0.00 0.00 0.00 4.40
2855 3121 8.620416 TCATAACAAGCACATACCATATTCAAC 58.380 33.333 0.00 0.00 0.00 3.18
2886 3152 5.041695 TCATCATATATCCAAGTCCCCCT 57.958 43.478 0.00 0.00 0.00 4.79
2888 3154 7.405292 TCAATTCATCATATATCCAAGTCCCC 58.595 38.462 0.00 0.00 0.00 4.81
2890 3156 8.944029 CACTCAATTCATCATATATCCAAGTCC 58.056 37.037 0.00 0.00 0.00 3.85
2948 3214 3.054508 TGATGAACACCTGCATATGGTCA 60.055 43.478 17.62 17.62 46.18 4.02
2949 3215 3.544684 TGATGAACACCTGCATATGGTC 58.455 45.455 4.56 8.16 35.28 4.02
3014 3280 1.672356 GGTGCGCTGTGTGAGGAAT 60.672 57.895 9.73 0.00 0.00 3.01
3089 3355 3.064408 ACTTGCAGACATTATCATGTGCG 59.936 43.478 0.00 0.00 44.22 5.34
3102 3368 4.376146 ACAAGAGAAGAAGACTTGCAGAC 58.624 43.478 0.00 0.00 42.93 3.51
3118 3384 7.745620 AGAAAGTATGGGTGTTAAACAAGAG 57.254 36.000 0.00 0.00 0.00 2.85
3122 3388 7.288560 TGGTAAGAAAGTATGGGTGTTAAACA 58.711 34.615 0.00 0.00 0.00 2.83
3131 3397 6.316390 GTGAGAACATGGTAAGAAAGTATGGG 59.684 42.308 0.00 0.00 0.00 4.00
3132 3398 6.316390 GGTGAGAACATGGTAAGAAAGTATGG 59.684 42.308 0.00 0.00 0.00 2.74
3271 3537 0.861837 GTTTGACAGTGAGCTCGGTG 59.138 55.000 9.64 11.25 0.00 4.94
3333 3599 2.270434 TTGAGGGTAGAAGCAGGGAT 57.730 50.000 0.00 0.00 0.00 3.85
3345 3613 4.253685 CATCGTAGTGTCAATTTGAGGGT 58.746 43.478 0.00 0.00 0.00 4.34
3346 3614 3.063997 GCATCGTAGTGTCAATTTGAGGG 59.936 47.826 0.00 0.00 0.00 4.30
3356 3624 6.973474 AGTGTTTATTCTAGCATCGTAGTGTC 59.027 38.462 0.00 0.00 0.00 3.67
3364 3632 9.534565 TGAACTATGAGTGTTTATTCTAGCATC 57.465 33.333 0.00 0.00 0.00 3.91
3394 3663 7.310664 AGTTCTAAAATGACAGCACATTGATG 58.689 34.615 0.00 0.00 39.88 3.07
3395 3664 7.362401 GGAGTTCTAAAATGACAGCACATTGAT 60.362 37.037 0.00 0.00 39.88 2.57
3406 3675 3.367025 CGACCGTGGAGTTCTAAAATGAC 59.633 47.826 0.00 0.00 0.00 3.06
3448 3717 1.742768 GTAGCTCACCTCCCATCCG 59.257 63.158 0.00 0.00 0.00 4.18
3693 3965 2.158871 GGACCTGGTTGGCGATTGTATA 60.159 50.000 0.00 0.00 40.22 1.47
3762 4059 5.450688 CCAACAAATTAAAGAACCCGACACA 60.451 40.000 0.00 0.00 0.00 3.72
3804 4101 5.401550 CAAGCAAACACATACAAATCCGAT 58.598 37.500 0.00 0.00 0.00 4.18
3823 4120 1.115326 AGCCCACTTTGGTTCCAAGC 61.115 55.000 4.44 4.82 35.17 4.01
3862 4159 0.470080 CCTTCCGATCCCAGCTAGGA 60.470 60.000 2.45 2.45 41.22 2.94
3876 4177 0.991920 TCAACATCTCCCCACCTTCC 59.008 55.000 0.00 0.00 0.00 3.46
3888 4189 6.992063 ACAAACCATCACTATCTCAACATC 57.008 37.500 0.00 0.00 0.00 3.06
3960 4261 2.693591 CGGATACCATGTACAGACAGGT 59.306 50.000 14.12 14.12 39.50 4.00
3981 4282 2.546778 TGCCGACGAAAGATAATCCAC 58.453 47.619 0.00 0.00 0.00 4.02
3988 4289 2.093306 TCAACATGCCGACGAAAGAT 57.907 45.000 0.00 0.00 0.00 2.40
4022 4323 4.757799 TGGTGACCACAAAATATGAACG 57.242 40.909 0.00 0.00 0.00 3.95
4138 4449 3.574354 ATGGGCAAACAAAACAATGGT 57.426 38.095 0.00 0.00 0.00 3.55
4173 4485 1.133513 TGCTCCCAAACAAGATGGTGT 60.134 47.619 0.00 0.00 36.14 4.16
4174 4486 1.619654 TGCTCCCAAACAAGATGGTG 58.380 50.000 0.00 0.00 36.14 4.17
4175 4487 2.450476 GATGCTCCCAAACAAGATGGT 58.550 47.619 0.00 0.00 36.14 3.55
4176 4488 1.753073 GGATGCTCCCAAACAAGATGG 59.247 52.381 0.00 0.00 37.71 3.51
4178 4490 2.042162 ACTGGATGCTCCCAAACAAGAT 59.958 45.455 0.00 0.00 35.03 2.40
4206 4521 0.788995 CAAGAGTCGCACTGCTTCAG 59.211 55.000 0.00 0.00 37.52 3.02
4209 4524 0.601311 GGACAAGAGTCGCACTGCTT 60.601 55.000 0.00 0.00 45.92 3.91
4211 4526 1.300931 TGGACAAGAGTCGCACTGC 60.301 57.895 0.00 0.00 45.92 4.40
4233 4548 5.992217 CCTAACTAGGAATGCAATGGTAGTC 59.008 44.000 0.00 0.00 46.63 2.59
4236 4551 4.445735 GGCCTAACTAGGAATGCAATGGTA 60.446 45.833 6.98 0.00 46.63 3.25
4237 4552 3.555966 GCCTAACTAGGAATGCAATGGT 58.444 45.455 6.98 0.00 46.63 3.55
4238 4553 2.887152 GGCCTAACTAGGAATGCAATGG 59.113 50.000 6.98 0.00 46.63 3.16
4239 4554 3.554934 TGGCCTAACTAGGAATGCAATG 58.445 45.455 3.32 0.00 46.63 2.82
4240 4555 3.951563 TGGCCTAACTAGGAATGCAAT 57.048 42.857 3.32 0.00 46.63 3.56
4241 4556 3.620488 CTTGGCCTAACTAGGAATGCAA 58.380 45.455 3.32 0.00 46.63 4.08
4259 4574 4.592942 TGGATGTGAAAGAATCTCCCTTG 58.407 43.478 0.00 0.00 0.00 3.61
4263 4578 5.653769 TCCAAATGGATGTGAAAGAATCTCC 59.346 40.000 0.00 0.00 39.78 3.71
4409 4729 3.251487 CCTTTTGTTAACTGTACCACCCG 59.749 47.826 7.22 0.00 0.00 5.28
4465 4786 1.199327 CATCTGTCCACAGCTTGCTTG 59.801 52.381 1.49 0.00 43.46 4.01
4508 4829 2.031120 TGCTGGTCAAAGGGAAAGTTG 58.969 47.619 0.00 0.00 0.00 3.16
4526 4847 2.358898 CCTGTGGTTTGGTATGCTATGC 59.641 50.000 0.00 0.00 0.00 3.14
4538 4859 2.203538 CCTGCCTGCCTGTGGTTT 60.204 61.111 0.00 0.00 0.00 3.27
4539 4860 3.177884 TCCTGCCTGCCTGTGGTT 61.178 61.111 0.00 0.00 0.00 3.67
4540 4861 3.958860 GTCCTGCCTGCCTGTGGT 61.959 66.667 0.00 0.00 0.00 4.16
4541 4862 4.729918 GGTCCTGCCTGCCTGTGG 62.730 72.222 0.00 0.00 0.00 4.17
4542 4863 3.278072 ATGGTCCTGCCTGCCTGTG 62.278 63.158 0.00 0.00 38.35 3.66


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

AutoCloner maintained by Alex Coulton.