Multiple sequence alignment - TraesCS5B01G230400

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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 TraesCS5B01G230400 chr5B 100.000 4793 0 0 1 4793 407214291 407219083 0.000000e+00 8852.0
1 TraesCS5B01G230400 chr5D 95.994 3994 118 11 805 4793 344546623 344542667 0.000000e+00 6451.0
2 TraesCS5B01G230400 chr5D 88.735 648 54 12 1 633 344566199 344565556 0.000000e+00 774.0
3 TraesCS5B01G230400 chr5D 88.991 109 11 1 633 741 457999588 457999481 3.010000e-27 134.0
4 TraesCS5B01G230400 chr5A 95.275 4000 143 14 805 4780 447534942 447538919 0.000000e+00 6298.0
5 TraesCS5B01G230400 chr5A 96.319 163 5 1 4631 4793 447539029 447539190 2.840000e-67 267.0
6 TraesCS5B01G230400 chr5A 89.091 110 11 1 632 741 400418350 400418242 8.370000e-28 135.0
7 TraesCS5B01G230400 chr5A 89.091 110 11 1 632 741 400495265 400495373 8.370000e-28 135.0
8 TraesCS5B01G230400 chr5A 98.333 60 1 0 4573 4632 447538928 447538987 6.560000e-19 106.0
9 TraesCS5B01G230400 chr6B 93.548 2635 140 13 1026 3655 137380620 137383229 0.000000e+00 3897.0
10 TraesCS5B01G230400 chr6D 92.827 2635 144 13 1026 3655 63726130 63728724 0.000000e+00 3777.0
11 TraesCS5B01G230400 chr6D 87.500 120 13 2 623 741 382000348 382000466 2.330000e-28 137.0
12 TraesCS5B01G230400 chr6A 93.109 2554 149 11 1108 3655 80875868 80878400 0.000000e+00 3716.0
13 TraesCS5B01G230400 chr6A 92.308 78 6 0 1026 1103 80875808 80875885 1.410000e-20 111.0
14 TraesCS5B01G230400 chr1A 89.091 110 11 1 632 741 490890940 490890832 8.370000e-28 135.0
15 TraesCS5B01G230400 chr1A 89.091 110 11 1 632 741 505560915 505560807 8.370000e-28 135.0
16 TraesCS5B01G230400 chr1A 87.234 94 7 1 3567 3655 278128856 278128949 8.490000e-18 102.0
17 TraesCS5B01G230400 chr7A 88.991 109 11 1 633 741 144657928 144657821 3.010000e-27 134.0
18 TraesCS5B01G230400 chr4A 88.991 109 11 1 633 741 153778408 153778301 3.010000e-27 134.0
19 TraesCS5B01G230400 chr4A 88.991 109 11 1 633 741 702001251 702001144 3.010000e-27 134.0
20 TraesCS5B01G230400 chr2A 88.889 81 4 1 3567 3642 5609372 5609452 1.420000e-15 95.3
21 TraesCS5B01G230400 chr2B 79.562 137 15 9 1026 1162 324624044 324623921 8.550000e-13 86.1
22 TraesCS5B01G230400 chr2B 85.294 68 7 3 452 518 6984508 6984443 3.100000e-07 67.6
23 TraesCS5B01G230400 chr2B 85.294 68 7 3 452 518 7030993 7031058 3.100000e-07 67.6
24 TraesCS5B01G230400 chr2B 85.294 68 7 3 452 518 7069684 7069749 3.100000e-07 67.6
25 TraesCS5B01G230400 chr2B 85.294 68 7 3 452 518 7111353 7111418 3.100000e-07 67.6
26 TraesCS5B01G230400 chr2B 85.294 68 7 3 452 518 7125188 7125253 3.100000e-07 67.6
27 TraesCS5B01G230400 chr4B 77.083 144 19 13 389 522 588691812 588691951 2.390000e-08 71.3
28 TraesCS5B01G230400 chrUn 85.294 68 7 3 452 518 421241263 421241328 3.100000e-07 67.6
29 TraesCS5B01G230400 chr3D 82.278 79 10 4 423 499 560117037 560117113 1.110000e-06 65.8


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 TraesCS5B01G230400 chr5B 407214291 407219083 4792 False 8852.000000 8852 100.000000 1 4793 1 chr5B.!!$F1 4792
1 TraesCS5B01G230400 chr5D 344542667 344546623 3956 True 6451.000000 6451 95.994000 805 4793 1 chr5D.!!$R1 3988
2 TraesCS5B01G230400 chr5D 344565556 344566199 643 True 774.000000 774 88.735000 1 633 1 chr5D.!!$R2 632
3 TraesCS5B01G230400 chr5A 447534942 447539190 4248 False 2223.666667 6298 96.642333 805 4793 3 chr5A.!!$F2 3988
4 TraesCS5B01G230400 chr6B 137380620 137383229 2609 False 3897.000000 3897 93.548000 1026 3655 1 chr6B.!!$F1 2629
5 TraesCS5B01G230400 chr6D 63726130 63728724 2594 False 3777.000000 3777 92.827000 1026 3655 1 chr6D.!!$F1 2629
6 TraesCS5B01G230400 chr6A 80875808 80878400 2592 False 1913.500000 3716 92.708500 1026 3655 2 chr6A.!!$F1 2629

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
762 773 0.034089 ACCAGCCTGAAGTATTGGGC 60.034 55.000 0.00 0.00 41.85 5.36 F
1941 1961 0.249031 GTCTTGTTGTGTGGCTTGCC 60.249 55.000 4.43 4.43 0.00 4.52 F
2451 2471 1.948145 GCAGCCAAGAGGATTGATCAG 59.052 52.381 0.00 0.00 36.89 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2451 2471 1.463056 TGAATCACGTCCATCAAACGC 59.537 47.619 0.0 0.0 43.76 4.84 R
2920 2940 0.610232 ACAAACTGAGCCCTGATGCC 60.610 55.000 0.0 0.0 0.00 4.40 R
4412 4439 0.888736 CATTGAACGTGCAGTCCCCA 60.889 55.000 0.0 0.0 0.00 4.96 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
22 23 2.327325 TAGGGAGAAGCTGAGGTTGT 57.673 50.000 0.00 0.00 0.00 3.32
24 25 0.322008 GGGAGAAGCTGAGGTTGTGG 60.322 60.000 0.00 0.00 0.00 4.17
77 78 4.056125 TGCCGGCTCTGTCACTCG 62.056 66.667 29.70 0.00 0.00 4.18
86 87 3.321497 GCTCTGTCACTCGAATGTTCTT 58.679 45.455 0.00 0.00 0.00 2.52
87 88 4.486090 GCTCTGTCACTCGAATGTTCTTA 58.514 43.478 0.00 0.00 0.00 2.10
103 104 9.601217 GAATGTTCTTATAGGTGTAGATTGTGT 57.399 33.333 0.00 0.00 0.00 3.72
105 106 6.816640 TGTTCTTATAGGTGTAGATTGTGTGC 59.183 38.462 0.00 0.00 0.00 4.57
108 109 0.034756 AGGTGTAGATTGTGTGCGCA 59.965 50.000 5.66 5.66 0.00 6.09
125 126 2.912967 GCGCATGCATTCATAAGTATGC 59.087 45.455 19.57 3.97 46.13 3.14
147 148 5.405269 TGCGTGTATGTGAATATGTATGAGC 59.595 40.000 0.00 0.00 0.00 4.26
150 151 6.183359 CGTGTATGTGAATATGTATGAGCGTC 60.183 42.308 0.00 0.00 0.00 5.19
173 174 7.148573 CGTCTGCTTCTGTATTGTGTTAGAAAT 60.149 37.037 0.00 0.00 0.00 2.17
174 175 8.507249 GTCTGCTTCTGTATTGTGTTAGAAATT 58.493 33.333 0.00 0.00 0.00 1.82
175 176 9.719355 TCTGCTTCTGTATTGTGTTAGAAATTA 57.281 29.630 0.00 0.00 0.00 1.40
227 234 9.897744 CCATTTTTGCATATAAGACGATTATGT 57.102 29.630 0.00 0.00 0.00 2.29
253 261 7.932491 TGGGGCATGTAATATGAATTTGATTTG 59.068 33.333 0.00 0.00 0.00 2.32
254 262 7.388500 GGGGCATGTAATATGAATTTGATTTGG 59.612 37.037 0.00 0.00 0.00 3.28
272 280 6.718912 TGATTTGGATTGATGTTGTAAGTCCA 59.281 34.615 0.00 0.00 32.81 4.02
273 281 7.396907 TGATTTGGATTGATGTTGTAAGTCCAT 59.603 33.333 0.00 0.00 34.55 3.41
281 289 7.581213 TGATGTTGTAAGTCCATGTTTCTTT 57.419 32.000 0.00 0.00 0.00 2.52
282 290 8.684386 TGATGTTGTAAGTCCATGTTTCTTTA 57.316 30.769 0.00 0.00 0.00 1.85
343 351 0.321653 ATTCTCAACCCCACTCGCAC 60.322 55.000 0.00 0.00 0.00 5.34
344 352 2.709125 TTCTCAACCCCACTCGCACG 62.709 60.000 0.00 0.00 0.00 5.34
369 377 5.060506 ACAAATAACACATGACCTTCGACA 58.939 37.500 0.00 0.00 0.00 4.35
380 388 3.118555 TGACCTTCGACACTCCTTTTTCA 60.119 43.478 0.00 0.00 0.00 2.69
385 393 5.163652 CCTTCGACACTCCTTTTTCAAAGTT 60.164 40.000 0.00 0.00 0.00 2.66
386 394 5.229921 TCGACACTCCTTTTTCAAAGTTG 57.770 39.130 0.00 0.00 0.00 3.16
392 400 6.138761 CACTCCTTTTTCAAAGTTGATCGAG 58.861 40.000 0.00 0.00 37.00 4.04
395 403 5.588648 TCCTTTTTCAAAGTTGATCGAGTGT 59.411 36.000 0.00 0.00 37.00 3.55
405 413 5.542779 AGTTGATCGAGTGTCTTTAGCTTT 58.457 37.500 0.00 0.00 0.00 3.51
430 438 2.163211 GTCAGCTGATTTTGAGAAGGGC 59.837 50.000 21.47 0.00 0.00 5.19
448 456 3.017232 CGAGAAGTTCGTCGAAGGG 57.983 57.895 8.18 0.00 44.27 3.95
503 511 3.258372 GCTACCCCATCATCTATCGTTGA 59.742 47.826 0.00 0.00 0.00 3.18
505 513 4.277515 ACCCCATCATCTATCGTTGATG 57.722 45.455 10.06 10.06 45.66 3.07
535 546 3.093278 GCGGTAGCACAGTGATGC 58.907 61.111 4.15 0.35 46.50 3.91
558 569 2.594536 ATCTCTGGGGGAAATCTCCA 57.405 50.000 0.99 0.00 44.51 3.86
565 576 0.249911 GGGGAAATCTCCATCGACGG 60.250 60.000 0.00 0.00 44.51 4.79
566 577 0.464452 GGGAAATCTCCATCGACGGT 59.536 55.000 0.00 0.00 44.51 4.83
567 578 1.684983 GGGAAATCTCCATCGACGGTA 59.315 52.381 0.00 0.00 44.51 4.02
568 579 2.288273 GGGAAATCTCCATCGACGGTAG 60.288 54.545 0.00 0.00 44.51 3.18
574 585 2.727392 CCATCGACGGTAGGGCCAA 61.727 63.158 6.18 0.00 36.97 4.52
579 590 2.204029 ACGGTAGGGCCAAAGGGA 60.204 61.111 6.18 0.00 36.97 4.20
580 591 1.618447 ACGGTAGGGCCAAAGGGAT 60.618 57.895 6.18 0.00 36.97 3.85
581 592 1.152963 CGGTAGGGCCAAAGGGATG 60.153 63.158 6.18 0.00 36.97 3.51
582 593 1.230212 GGTAGGGCCAAAGGGATGG 59.770 63.158 6.18 0.00 43.70 3.51
588 599 2.124151 CCAAAGGGATGGCTCGGG 60.124 66.667 0.00 0.00 35.59 5.14
589 600 2.124151 CAAAGGGATGGCTCGGGG 60.124 66.667 0.00 0.00 0.00 5.73
590 601 4.129148 AAAGGGATGGCTCGGGGC 62.129 66.667 0.00 0.00 40.90 5.80
611 622 4.621832 AACACGACGTTGGGTTGT 57.378 50.000 22.63 7.17 44.35 3.32
614 625 2.585698 ACGACGTTGGGTTGTGGT 59.414 55.556 7.90 0.00 41.84 4.16
615 626 1.078285 ACGACGTTGGGTTGTGGTT 60.078 52.632 7.90 0.00 41.84 3.67
616 627 0.177604 ACGACGTTGGGTTGTGGTTA 59.822 50.000 7.90 0.00 41.84 2.85
617 628 0.863144 CGACGTTGGGTTGTGGTTAG 59.137 55.000 0.00 0.00 0.00 2.34
618 629 1.232119 GACGTTGGGTTGTGGTTAGG 58.768 55.000 0.00 0.00 0.00 2.69
619 630 0.179012 ACGTTGGGTTGTGGTTAGGG 60.179 55.000 0.00 0.00 0.00 3.53
620 631 0.891904 CGTTGGGTTGTGGTTAGGGG 60.892 60.000 0.00 0.00 0.00 4.79
621 632 0.541063 GTTGGGTTGTGGTTAGGGGG 60.541 60.000 0.00 0.00 0.00 5.40
622 633 0.701659 TTGGGTTGTGGTTAGGGGGA 60.702 55.000 0.00 0.00 0.00 4.81
623 634 1.137594 TGGGTTGTGGTTAGGGGGAG 61.138 60.000 0.00 0.00 0.00 4.30
624 635 1.689412 GGTTGTGGTTAGGGGGAGG 59.311 63.158 0.00 0.00 0.00 4.30
625 636 1.689412 GTTGTGGTTAGGGGGAGGG 59.311 63.158 0.00 0.00 0.00 4.30
626 637 2.235761 TTGTGGTTAGGGGGAGGGC 61.236 63.158 0.00 0.00 0.00 5.19
627 638 3.793888 GTGGTTAGGGGGAGGGCG 61.794 72.222 0.00 0.00 0.00 6.13
630 641 3.013327 GTTAGGGGGAGGGCGGTT 61.013 66.667 0.00 0.00 0.00 4.44
631 642 3.012722 TTAGGGGGAGGGCGGTTG 61.013 66.667 0.00 0.00 0.00 3.77
643 654 3.118454 CGGTTGGCAGTGGCGTAG 61.118 66.667 12.58 0.00 42.47 3.51
656 667 3.547513 CGTAGCTAGGGGGTGGCC 61.548 72.222 5.50 0.00 31.44 5.36
657 668 2.366435 GTAGCTAGGGGGTGGCCA 60.366 66.667 0.00 0.00 31.44 5.36
658 669 2.040884 TAGCTAGGGGGTGGCCAG 60.041 66.667 5.11 0.00 31.44 4.85
659 670 3.714078 TAGCTAGGGGGTGGCCAGG 62.714 68.421 5.11 0.00 31.44 4.45
661 672 2.039405 CTAGGGGGTGGCCAGGAT 60.039 66.667 5.11 0.00 0.00 3.24
662 673 2.368192 TAGGGGGTGGCCAGGATG 60.368 66.667 5.11 0.00 0.00 3.51
681 692 3.317280 GTCCATGGACCACCCTAGA 57.683 57.895 31.37 0.00 39.08 2.43
682 693 1.580059 GTCCATGGACCACCCTAGAA 58.420 55.000 31.37 0.00 39.08 2.10
683 694 2.127708 GTCCATGGACCACCCTAGAAT 58.872 52.381 31.37 0.00 39.08 2.40
684 695 2.509964 GTCCATGGACCACCCTAGAATT 59.490 50.000 31.37 0.00 39.08 2.17
685 696 3.053619 GTCCATGGACCACCCTAGAATTT 60.054 47.826 31.37 0.00 39.08 1.82
686 697 3.596046 TCCATGGACCACCCTAGAATTTT 59.404 43.478 11.44 0.00 35.38 1.82
687 698 3.701040 CCATGGACCACCCTAGAATTTTG 59.299 47.826 5.56 0.00 35.38 2.44
688 699 4.344104 CATGGACCACCCTAGAATTTTGT 58.656 43.478 0.00 0.00 35.38 2.83
689 700 5.505780 CATGGACCACCCTAGAATTTTGTA 58.494 41.667 0.00 0.00 35.38 2.41
690 701 5.789574 TGGACCACCCTAGAATTTTGTAT 57.210 39.130 0.00 0.00 35.38 2.29
691 702 6.894735 TGGACCACCCTAGAATTTTGTATA 57.105 37.500 0.00 0.00 35.38 1.47
692 703 7.460214 TGGACCACCCTAGAATTTTGTATAT 57.540 36.000 0.00 0.00 35.38 0.86
693 704 8.570038 TGGACCACCCTAGAATTTTGTATATA 57.430 34.615 0.00 0.00 35.38 0.86
694 705 8.656806 TGGACCACCCTAGAATTTTGTATATAG 58.343 37.037 0.00 0.00 35.38 1.31
695 706 8.657712 GGACCACCCTAGAATTTTGTATATAGT 58.342 37.037 0.00 0.00 0.00 2.12
696 707 9.490379 GACCACCCTAGAATTTTGTATATAGTG 57.510 37.037 0.00 0.00 0.00 2.74
697 708 8.999895 ACCACCCTAGAATTTTGTATATAGTGT 58.000 33.333 0.00 0.00 0.00 3.55
748 759 7.568199 AGTAAACATATGTAAATGGACCAGC 57.432 36.000 9.21 0.00 0.00 4.85
749 760 5.852282 AAACATATGTAAATGGACCAGCC 57.148 39.130 9.21 0.00 37.10 4.85
750 761 4.796110 ACATATGTAAATGGACCAGCCT 57.204 40.909 6.56 0.00 37.63 4.58
751 762 4.464008 ACATATGTAAATGGACCAGCCTG 58.536 43.478 6.56 0.00 37.63 4.85
752 763 4.165950 ACATATGTAAATGGACCAGCCTGA 59.834 41.667 6.56 0.00 37.63 3.86
753 764 3.737559 ATGTAAATGGACCAGCCTGAA 57.262 42.857 0.00 0.00 37.63 3.02
754 765 3.071874 TGTAAATGGACCAGCCTGAAG 57.928 47.619 0.00 0.00 37.63 3.02
755 766 2.375174 TGTAAATGGACCAGCCTGAAGT 59.625 45.455 0.00 0.00 37.63 3.01
756 767 3.585289 TGTAAATGGACCAGCCTGAAGTA 59.415 43.478 0.00 0.00 37.63 2.24
757 768 4.227300 TGTAAATGGACCAGCCTGAAGTAT 59.773 41.667 0.00 0.00 37.63 2.12
758 769 4.322057 AAATGGACCAGCCTGAAGTATT 57.678 40.909 0.00 0.00 37.63 1.89
759 770 2.787473 TGGACCAGCCTGAAGTATTG 57.213 50.000 0.00 0.00 37.63 1.90
760 771 1.281867 TGGACCAGCCTGAAGTATTGG 59.718 52.381 0.00 0.00 37.63 3.16
761 772 1.408822 GGACCAGCCTGAAGTATTGGG 60.409 57.143 0.00 0.00 33.20 4.12
762 773 0.034089 ACCAGCCTGAAGTATTGGGC 60.034 55.000 0.00 0.00 41.85 5.36
765 776 2.799176 GCCTGAAGTATTGGGCTGG 58.201 57.895 0.00 0.00 39.50 4.85
766 777 1.387295 GCCTGAAGTATTGGGCTGGC 61.387 60.000 0.00 0.00 39.50 4.85
767 778 0.257039 CCTGAAGTATTGGGCTGGCT 59.743 55.000 0.00 0.00 0.00 4.75
768 779 1.490490 CCTGAAGTATTGGGCTGGCTA 59.510 52.381 0.00 0.00 0.00 3.93
769 780 2.565841 CTGAAGTATTGGGCTGGCTAC 58.434 52.381 0.00 0.00 0.00 3.58
770 781 1.134521 TGAAGTATTGGGCTGGCTACG 60.135 52.381 0.00 0.00 0.00 3.51
771 782 0.463833 AAGTATTGGGCTGGCTACGC 60.464 55.000 0.00 0.00 0.00 4.42
795 806 4.436998 CGGTGGGGCGAGACTGAC 62.437 72.222 0.00 0.00 0.00 3.51
796 807 3.311110 GGTGGGGCGAGACTGACA 61.311 66.667 0.00 0.00 0.00 3.58
797 808 2.741092 GTGGGGCGAGACTGACAA 59.259 61.111 0.00 0.00 0.00 3.18
798 809 1.296715 GTGGGGCGAGACTGACAAT 59.703 57.895 0.00 0.00 0.00 2.71
799 810 0.321653 GTGGGGCGAGACTGACAATT 60.322 55.000 0.00 0.00 0.00 2.32
800 811 0.321564 TGGGGCGAGACTGACAATTG 60.322 55.000 3.24 3.24 0.00 2.32
801 812 1.026718 GGGGCGAGACTGACAATTGG 61.027 60.000 10.83 0.00 0.00 3.16
802 813 0.321653 GGGCGAGACTGACAATTGGT 60.322 55.000 10.83 0.00 0.00 3.67
803 814 1.523758 GGCGAGACTGACAATTGGTT 58.476 50.000 10.83 0.00 0.00 3.67
828 839 1.351017 TGAAGGATGGACTGACCCAAC 59.649 52.381 0.00 0.00 40.04 3.77
838 849 3.242969 GGACTGACCCAACTTCGTTTTTC 60.243 47.826 0.00 0.00 0.00 2.29
913 925 2.700773 GCTGGAATTGCCCGTGACC 61.701 63.158 0.00 0.00 34.97 4.02
914 926 1.303236 CTGGAATTGCCCGTGACCA 60.303 57.895 0.00 0.00 34.97 4.02
925 937 1.683917 CCCGTGACCAAAATCCAAACA 59.316 47.619 0.00 0.00 0.00 2.83
959 973 5.055812 ACAAAACAAAGCAGAGAGAGAGAG 58.944 41.667 0.00 0.00 0.00 3.20
971 985 1.229209 GAGAGAGACCACCCACCCA 60.229 63.158 0.00 0.00 0.00 4.51
975 989 3.252284 AGACCACCCACCCAGCAG 61.252 66.667 0.00 0.00 0.00 4.24
980 994 0.331278 CCACCCACCCAGCAGAATTA 59.669 55.000 0.00 0.00 0.00 1.40
981 995 1.272425 CCACCCACCCAGCAGAATTAA 60.272 52.381 0.00 0.00 0.00 1.40
1630 1650 4.477975 GCAGCGACGCCTACGACT 62.478 66.667 17.79 0.00 43.93 4.18
1941 1961 0.249031 GTCTTGTTGTGTGGCTTGCC 60.249 55.000 4.43 4.43 0.00 4.52
2016 2036 4.473520 AGAGGCGGTGGAATGGCG 62.474 66.667 0.00 0.00 35.52 5.69
2233 2253 6.014156 GGGCTACCTTATTCAGTCTGATATGT 60.014 42.308 2.68 0.52 0.00 2.29
2292 2312 5.843019 TCCTTAGAACAGGGAAGTCAATT 57.157 39.130 0.00 0.00 34.24 2.32
2451 2471 1.948145 GCAGCCAAGAGGATTGATCAG 59.052 52.381 0.00 0.00 36.89 2.90
2475 2495 5.672570 GCGTTTGATGGACGTGATTCATAAA 60.673 40.000 0.00 0.00 42.22 1.40
2476 2496 6.310960 CGTTTGATGGACGTGATTCATAAAA 58.689 36.000 0.00 0.00 35.88 1.52
2890 2910 7.408756 AAGACAATGAAGCCTAATTGCATTA 57.591 32.000 0.00 0.00 37.30 1.90
2920 2940 4.662278 TCCATTTTACAAGGAAGGGACAG 58.338 43.478 0.00 0.00 31.42 3.51
2949 2969 4.134563 GGGCTCAGTTTGTTTCAGTTCTA 58.865 43.478 0.00 0.00 0.00 2.10
3326 3346 7.724305 TCACATCTACTGTTTGGTTTACTTC 57.276 36.000 0.00 0.00 35.29 3.01
3591 3611 4.451096 CACTGAATACTACAGCCGTGTTTT 59.549 41.667 0.00 0.00 38.19 2.43
3642 3667 5.734720 TGTGGAAGAAATAGGTGTCAGATC 58.265 41.667 0.00 0.00 0.00 2.75
3760 3785 4.217767 GTCCTGGGTTGTTGAAGGTAATTC 59.782 45.833 0.00 0.00 38.50 2.17
3782 3807 5.376625 TCCTAGCTGGGCTTAATACAAATG 58.623 41.667 12.10 0.00 40.44 2.32
4123 4148 7.214381 TGTTACCAAACTATCATAGGATTCCG 58.786 38.462 0.00 0.00 36.51 4.30
4125 4150 5.855045 ACCAAACTATCATAGGATTCCGTC 58.145 41.667 0.00 0.00 34.89 4.79
4126 4151 4.923871 CCAAACTATCATAGGATTCCGTCG 59.076 45.833 0.00 0.00 34.89 5.12
4133 4158 4.392047 TCATAGGATTCCGTCGCTACTTA 58.608 43.478 0.00 0.00 0.00 2.24
4134 4159 5.008331 TCATAGGATTCCGTCGCTACTTAT 58.992 41.667 0.00 0.00 0.00 1.73
4168 4193 6.256643 AGGAGAGTTACTTTTTGGTTACCA 57.743 37.500 0.00 0.00 0.00 3.25
4175 4200 8.417273 AGTTACTTTTTGGTTACCATAATGCT 57.583 30.769 4.38 0.00 31.53 3.79
4176 4201 8.866093 AGTTACTTTTTGGTTACCATAATGCTT 58.134 29.630 4.38 0.00 31.53 3.91
4177 4202 9.483916 GTTACTTTTTGGTTACCATAATGCTTT 57.516 29.630 4.38 0.00 31.53 3.51
4180 4205 7.817478 ACTTTTTGGTTACCATAATGCTTTAGC 59.183 33.333 4.38 0.00 35.80 3.09
4181 4206 5.845391 TTGGTTACCATAATGCTTTAGCC 57.155 39.130 4.38 0.00 34.81 3.93
4335 4362 8.684386 TTTGTTTATGATAACTTGGACAGTCA 57.316 30.769 2.17 0.00 32.94 3.41
4406 4433 5.356190 AGTTTAATCTGAGATGCATGGTGTG 59.644 40.000 2.46 0.00 0.00 3.82
4407 4434 2.343484 ATCTGAGATGCATGGTGTGG 57.657 50.000 2.46 0.00 0.00 4.17
4408 4435 0.393402 TCTGAGATGCATGGTGTGGC 60.393 55.000 2.46 0.00 0.00 5.01
4409 4436 1.712018 CTGAGATGCATGGTGTGGCG 61.712 60.000 2.46 0.00 0.00 5.69
4410 4437 1.450134 GAGATGCATGGTGTGGCGA 60.450 57.895 2.46 0.00 0.00 5.54
4411 4438 1.434622 GAGATGCATGGTGTGGCGAG 61.435 60.000 2.46 0.00 0.00 5.03
4412 4439 1.746615 GATGCATGGTGTGGCGAGT 60.747 57.895 2.46 0.00 0.00 4.18
4426 4453 2.426023 GAGTGGGGACTGCACGTT 59.574 61.111 0.00 0.00 0.00 3.99
4439 4466 4.072131 ACTGCACGTTCAATGGTATCTTT 58.928 39.130 0.00 0.00 0.00 2.52
4460 4487 6.655003 TCTTTTGTTAACTGGGCAGATCTAAG 59.345 38.462 7.22 0.00 0.00 2.18
4466 4493 0.461548 TGGGCAGATCTAAGTCGCTG 59.538 55.000 0.00 0.00 0.00 5.18
4565 4596 9.470399 AGTATAATTAAGGGAATTCAACCGTTT 57.530 29.630 7.93 0.00 38.70 3.60
4610 4870 0.684535 TTGGATGTCACGCCTCTGAA 59.315 50.000 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.886124 GTACTCTTGCCGCGCCTC 60.886 66.667 0.00 0.00 0.00 4.70
38 39 4.722203 CATCATCTTGATGCCTTCGTAC 57.278 45.455 4.68 0.00 46.37 3.67
77 78 9.601217 ACACAATCTACACCTATAAGAACATTC 57.399 33.333 0.00 0.00 0.00 2.67
86 87 3.131400 TGCGCACACAATCTACACCTATA 59.869 43.478 5.66 0.00 0.00 1.31
87 88 2.093711 TGCGCACACAATCTACACCTAT 60.094 45.455 5.66 0.00 0.00 2.57
103 104 3.609879 GCATACTTATGAATGCATGCGCA 60.610 43.478 14.96 14.96 46.19 6.09
125 126 5.629435 ACGCTCATACATATTCACATACACG 59.371 40.000 0.00 0.00 0.00 4.49
147 148 5.161358 TCTAACACAATACAGAAGCAGACG 58.839 41.667 0.00 0.00 0.00 4.18
214 221 3.135712 ACATGCCCCACATAATCGTCTTA 59.864 43.478 0.00 0.00 36.64 2.10
219 226 5.879777 TCATATTACATGCCCCACATAATCG 59.120 40.000 0.00 0.00 36.64 3.34
222 229 8.366401 CAAATTCATATTACATGCCCCACATAA 58.634 33.333 0.00 0.00 36.64 1.90
223 230 7.727634 TCAAATTCATATTACATGCCCCACATA 59.272 33.333 0.00 0.00 36.64 2.29
227 234 7.615039 AATCAAATTCATATTACATGCCCCA 57.385 32.000 0.00 0.00 0.00 4.96
228 235 7.388500 CCAAATCAAATTCATATTACATGCCCC 59.612 37.037 0.00 0.00 0.00 5.80
253 261 6.515272 AACATGGACTTACAACATCAATCC 57.485 37.500 0.00 0.00 0.00 3.01
254 262 7.820648 AGAAACATGGACTTACAACATCAATC 58.179 34.615 0.00 0.00 0.00 2.67
272 280 7.504926 TGGGGTGTAGTCTATAAAGAAACAT 57.495 36.000 0.00 0.00 34.29 2.71
273 281 6.938698 TGGGGTGTAGTCTATAAAGAAACA 57.061 37.500 0.00 0.00 32.16 2.83
281 289 4.713321 GTGGAGTTTGGGGTGTAGTCTATA 59.287 45.833 0.00 0.00 0.00 1.31
282 290 3.518303 GTGGAGTTTGGGGTGTAGTCTAT 59.482 47.826 0.00 0.00 0.00 1.98
284 292 1.697982 GTGGAGTTTGGGGTGTAGTCT 59.302 52.381 0.00 0.00 0.00 3.24
343 351 4.435518 CGAAGGTCATGTGTTATTTGTCCG 60.436 45.833 0.00 0.00 0.00 4.79
344 352 4.693566 TCGAAGGTCATGTGTTATTTGTCC 59.306 41.667 0.00 0.00 0.00 4.02
369 377 5.823045 ACTCGATCAACTTTGAAAAAGGAGT 59.177 36.000 4.86 2.78 41.13 3.85
380 388 5.542779 AGCTAAAGACACTCGATCAACTTT 58.457 37.500 0.00 0.00 0.00 2.66
385 393 4.690748 CCAAAAGCTAAAGACACTCGATCA 59.309 41.667 0.00 0.00 0.00 2.92
386 394 4.093556 CCCAAAAGCTAAAGACACTCGATC 59.906 45.833 0.00 0.00 0.00 3.69
392 400 3.304726 GCTGACCCAAAAGCTAAAGACAC 60.305 47.826 0.00 0.00 36.47 3.67
405 413 3.507162 TCTCAAAATCAGCTGACCCAA 57.493 42.857 20.97 2.98 0.00 4.12
444 452 2.204090 TTTCCTCCGGCCTCCCTT 60.204 61.111 0.00 0.00 0.00 3.95
448 456 1.147153 CATCCTTTCCTCCGGCCTC 59.853 63.158 0.00 0.00 0.00 4.70
459 467 1.279271 CTCCGGTGAGTTCCATCCTTT 59.721 52.381 0.00 0.00 33.70 3.11
465 473 2.449967 TAGCCCTCCGGTGAGTTCCA 62.450 60.000 4.76 0.00 36.86 3.53
503 511 2.370445 CCGCCCTCACTCCCTTCAT 61.370 63.158 0.00 0.00 0.00 2.57
505 513 1.677637 CTACCGCCCTCACTCCCTTC 61.678 65.000 0.00 0.00 0.00 3.46
506 514 1.686110 CTACCGCCCTCACTCCCTT 60.686 63.158 0.00 0.00 0.00 3.95
527 535 2.426024 CCCCAGAGATTTTGCATCACTG 59.574 50.000 6.33 6.33 36.79 3.66
532 543 2.925966 TTCCCCCAGAGATTTTGCAT 57.074 45.000 0.00 0.00 0.00 3.96
535 546 3.956848 GGAGATTTCCCCCAGAGATTTTG 59.043 47.826 0.00 0.00 37.53 2.44
558 569 1.520666 CTTTGGCCCTACCGTCGAT 59.479 57.895 0.00 0.00 43.94 3.59
594 605 1.370587 CCACAACCCAACGTCGTGTT 61.371 55.000 0.00 0.00 43.09 3.32
595 606 1.816259 CCACAACCCAACGTCGTGT 60.816 57.895 0.00 0.00 0.00 4.49
596 607 1.370587 AACCACAACCCAACGTCGTG 61.371 55.000 0.00 0.00 0.00 4.35
597 608 0.177604 TAACCACAACCCAACGTCGT 59.822 50.000 0.00 0.00 0.00 4.34
598 609 0.863144 CTAACCACAACCCAACGTCG 59.137 55.000 0.00 0.00 0.00 5.12
599 610 1.232119 CCTAACCACAACCCAACGTC 58.768 55.000 0.00 0.00 0.00 4.34
600 611 0.179012 CCCTAACCACAACCCAACGT 60.179 55.000 0.00 0.00 0.00 3.99
601 612 0.891904 CCCCTAACCACAACCCAACG 60.892 60.000 0.00 0.00 0.00 4.10
602 613 0.541063 CCCCCTAACCACAACCCAAC 60.541 60.000 0.00 0.00 0.00 3.77
603 614 0.701659 TCCCCCTAACCACAACCCAA 60.702 55.000 0.00 0.00 0.00 4.12
604 615 1.072852 TCCCCCTAACCACAACCCA 60.073 57.895 0.00 0.00 0.00 4.51
605 616 1.689412 CTCCCCCTAACCACAACCC 59.311 63.158 0.00 0.00 0.00 4.11
606 617 1.689412 CCTCCCCCTAACCACAACC 59.311 63.158 0.00 0.00 0.00 3.77
607 618 1.689412 CCCTCCCCCTAACCACAAC 59.311 63.158 0.00 0.00 0.00 3.32
608 619 2.235761 GCCCTCCCCCTAACCACAA 61.236 63.158 0.00 0.00 0.00 3.33
609 620 2.612746 GCCCTCCCCCTAACCACA 60.613 66.667 0.00 0.00 0.00 4.17
610 621 3.793888 CGCCCTCCCCCTAACCAC 61.794 72.222 0.00 0.00 0.00 4.16
613 624 3.013327 AACCGCCCTCCCCCTAAC 61.013 66.667 0.00 0.00 0.00 2.34
614 625 3.012722 CAACCGCCCTCCCCCTAA 61.013 66.667 0.00 0.00 0.00 2.69
626 637 3.118454 CTACGCCACTGCCAACCG 61.118 66.667 0.00 0.00 0.00 4.44
627 638 2.515996 TAGCTACGCCACTGCCAACC 62.516 60.000 0.00 0.00 0.00 3.77
628 639 1.079405 TAGCTACGCCACTGCCAAC 60.079 57.895 0.00 0.00 0.00 3.77
629 640 1.218047 CTAGCTACGCCACTGCCAA 59.782 57.895 0.00 0.00 0.00 4.52
630 641 2.721167 CCTAGCTACGCCACTGCCA 61.721 63.158 0.00 0.00 0.00 4.92
631 642 2.107141 CCTAGCTACGCCACTGCC 59.893 66.667 0.00 0.00 0.00 4.85
632 643 2.107141 CCCTAGCTACGCCACTGC 59.893 66.667 0.00 0.00 0.00 4.40
633 644 2.797278 CCCCCTAGCTACGCCACTG 61.797 68.421 0.00 0.00 0.00 3.66
634 645 2.444140 CCCCCTAGCTACGCCACT 60.444 66.667 0.00 0.00 0.00 4.00
635 646 2.762875 ACCCCCTAGCTACGCCAC 60.763 66.667 0.00 0.00 0.00 5.01
636 647 2.762459 CACCCCCTAGCTACGCCA 60.762 66.667 0.00 0.00 0.00 5.69
637 648 3.547513 CCACCCCCTAGCTACGCC 61.548 72.222 0.00 0.00 0.00 5.68
638 649 4.237207 GCCACCCCCTAGCTACGC 62.237 72.222 0.00 0.00 0.00 4.42
639 650 3.547513 GGCCACCCCCTAGCTACG 61.548 72.222 0.00 0.00 0.00 3.51
640 651 2.366435 TGGCCACCCCCTAGCTAC 60.366 66.667 0.00 0.00 0.00 3.58
641 652 2.040884 CTGGCCACCCCCTAGCTA 60.041 66.667 0.00 0.00 0.00 3.32
644 655 2.039405 ATCCTGGCCACCCCCTAG 60.039 66.667 0.00 0.00 0.00 3.02
645 656 2.368192 CATCCTGGCCACCCCCTA 60.368 66.667 0.00 0.00 0.00 3.53
648 659 4.129148 GACCATCCTGGCCACCCC 62.129 72.222 0.00 0.00 42.67 4.95
649 660 4.129148 GGACCATCCTGGCCACCC 62.129 72.222 0.00 0.00 42.67 4.61
650 661 2.693871 ATGGACCATCCTGGCCACC 61.694 63.158 0.00 0.00 43.14 4.61
651 662 1.454479 CATGGACCATCCTGGCCAC 60.454 63.158 0.00 0.00 43.14 5.01
652 663 2.692824 CCATGGACCATCCTGGCCA 61.693 63.158 5.56 4.71 43.97 5.36
653 664 2.196776 CCATGGACCATCCTGGCC 59.803 66.667 5.56 0.00 42.67 5.36
654 665 1.152881 GTCCATGGACCATCCTGGC 60.153 63.158 31.37 5.53 42.67 4.85
663 674 1.580059 TTCTAGGGTGGTCCATGGAC 58.420 55.000 33.14 33.14 43.87 4.02
664 675 2.587060 ATTCTAGGGTGGTCCATGGA 57.413 50.000 11.44 11.44 38.24 3.41
665 676 3.669939 AAATTCTAGGGTGGTCCATGG 57.330 47.619 4.97 4.97 38.24 3.66
666 677 4.344104 ACAAAATTCTAGGGTGGTCCATG 58.656 43.478 0.00 0.00 38.24 3.66
667 678 4.675063 ACAAAATTCTAGGGTGGTCCAT 57.325 40.909 0.00 0.00 38.24 3.41
668 679 5.789574 ATACAAAATTCTAGGGTGGTCCA 57.210 39.130 0.00 0.00 38.24 4.02
669 680 8.657712 ACTATATACAAAATTCTAGGGTGGTCC 58.342 37.037 0.00 0.00 0.00 4.46
670 681 9.490379 CACTATATACAAAATTCTAGGGTGGTC 57.510 37.037 0.00 0.00 0.00 4.02
671 682 8.999895 ACACTATATACAAAATTCTAGGGTGGT 58.000 33.333 0.00 0.00 0.00 4.16
722 733 9.116067 GCTGGTCCATTTACATATGTTTACTTA 57.884 33.333 14.77 0.00 0.00 2.24
723 734 7.068226 GGCTGGTCCATTTACATATGTTTACTT 59.932 37.037 14.77 0.00 34.01 2.24
724 735 6.546034 GGCTGGTCCATTTACATATGTTTACT 59.454 38.462 14.77 0.00 34.01 2.24
725 736 6.546034 AGGCTGGTCCATTTACATATGTTTAC 59.454 38.462 14.77 3.92 37.29 2.01
726 737 6.545666 CAGGCTGGTCCATTTACATATGTTTA 59.454 38.462 14.77 2.80 37.29 2.01
727 738 5.360714 CAGGCTGGTCCATTTACATATGTTT 59.639 40.000 14.77 0.00 37.29 2.83
728 739 4.889409 CAGGCTGGTCCATTTACATATGTT 59.111 41.667 14.77 0.00 37.29 2.71
729 740 4.165950 TCAGGCTGGTCCATTTACATATGT 59.834 41.667 15.73 13.93 37.29 2.29
730 741 4.717877 TCAGGCTGGTCCATTTACATATG 58.282 43.478 15.73 0.00 37.29 1.78
731 742 5.103940 ACTTCAGGCTGGTCCATTTACATAT 60.104 40.000 15.73 0.00 37.29 1.78
732 743 4.227300 ACTTCAGGCTGGTCCATTTACATA 59.773 41.667 15.73 0.00 37.29 2.29
733 744 3.010584 ACTTCAGGCTGGTCCATTTACAT 59.989 43.478 15.73 0.00 37.29 2.29
734 745 2.375174 ACTTCAGGCTGGTCCATTTACA 59.625 45.455 15.73 0.00 37.29 2.41
735 746 3.073274 ACTTCAGGCTGGTCCATTTAC 57.927 47.619 15.73 0.00 37.29 2.01
736 747 5.192927 CAATACTTCAGGCTGGTCCATTTA 58.807 41.667 15.73 0.00 37.29 1.40
737 748 4.019174 CAATACTTCAGGCTGGTCCATTT 58.981 43.478 15.73 0.00 37.29 2.32
738 749 3.624777 CAATACTTCAGGCTGGTCCATT 58.375 45.455 15.73 7.03 37.29 3.16
739 750 2.092212 CCAATACTTCAGGCTGGTCCAT 60.092 50.000 15.73 0.77 37.29 3.41
740 751 1.281867 CCAATACTTCAGGCTGGTCCA 59.718 52.381 15.73 0.00 37.29 4.02
741 752 1.408822 CCCAATACTTCAGGCTGGTCC 60.409 57.143 15.73 0.00 0.00 4.46
742 753 2.019156 GCCCAATACTTCAGGCTGGTC 61.019 57.143 15.73 0.00 42.34 4.02
743 754 0.034089 GCCCAATACTTCAGGCTGGT 60.034 55.000 15.73 8.17 42.34 4.00
744 755 2.799176 GCCCAATACTTCAGGCTGG 58.201 57.895 15.73 1.44 42.34 4.85
747 758 1.387295 GCCAGCCCAATACTTCAGGC 61.387 60.000 0.00 0.00 46.13 4.85
748 759 0.257039 AGCCAGCCCAATACTTCAGG 59.743 55.000 0.00 0.00 0.00 3.86
749 760 2.565841 GTAGCCAGCCCAATACTTCAG 58.434 52.381 0.00 0.00 0.00 3.02
750 761 1.134521 CGTAGCCAGCCCAATACTTCA 60.135 52.381 0.00 0.00 0.00 3.02
751 762 1.583054 CGTAGCCAGCCCAATACTTC 58.417 55.000 0.00 0.00 0.00 3.01
752 763 3.780624 CGTAGCCAGCCCAATACTT 57.219 52.632 0.00 0.00 0.00 2.24
778 789 4.436998 GTCAGTCTCGCCCCACCG 62.437 72.222 0.00 0.00 0.00 4.94
779 790 2.185310 ATTGTCAGTCTCGCCCCACC 62.185 60.000 0.00 0.00 0.00 4.61
780 791 0.321653 AATTGTCAGTCTCGCCCCAC 60.322 55.000 0.00 0.00 0.00 4.61
781 792 0.321564 CAATTGTCAGTCTCGCCCCA 60.322 55.000 0.00 0.00 0.00 4.96
782 793 1.026718 CCAATTGTCAGTCTCGCCCC 61.027 60.000 4.43 0.00 0.00 5.80
783 794 0.321653 ACCAATTGTCAGTCTCGCCC 60.322 55.000 4.43 0.00 0.00 6.13
784 795 1.197721 CAACCAATTGTCAGTCTCGCC 59.802 52.381 4.43 0.00 0.00 5.54
785 796 1.197721 CCAACCAATTGTCAGTCTCGC 59.802 52.381 4.43 0.00 33.60 5.03
786 797 1.197721 GCCAACCAATTGTCAGTCTCG 59.802 52.381 4.43 0.00 33.60 4.04
787 798 2.508526 AGCCAACCAATTGTCAGTCTC 58.491 47.619 4.43 0.00 33.60 3.36
788 799 2.624838 CAAGCCAACCAATTGTCAGTCT 59.375 45.455 4.43 0.00 33.60 3.24
789 800 2.622942 TCAAGCCAACCAATTGTCAGTC 59.377 45.455 4.43 0.00 33.60 3.51
790 801 2.665165 TCAAGCCAACCAATTGTCAGT 58.335 42.857 4.43 0.00 33.60 3.41
791 802 3.553508 CCTTCAAGCCAACCAATTGTCAG 60.554 47.826 4.43 0.00 33.60 3.51
792 803 2.364970 CCTTCAAGCCAACCAATTGTCA 59.635 45.455 4.43 0.00 33.60 3.58
793 804 2.627699 TCCTTCAAGCCAACCAATTGTC 59.372 45.455 4.43 0.00 33.60 3.18
794 805 2.676748 TCCTTCAAGCCAACCAATTGT 58.323 42.857 4.43 0.00 33.60 2.71
795 806 3.592059 CATCCTTCAAGCCAACCAATTG 58.408 45.455 0.00 0.00 35.40 2.32
796 807 2.568509 CCATCCTTCAAGCCAACCAATT 59.431 45.455 0.00 0.00 0.00 2.32
797 808 2.181975 CCATCCTTCAAGCCAACCAAT 58.818 47.619 0.00 0.00 0.00 3.16
798 809 1.146774 TCCATCCTTCAAGCCAACCAA 59.853 47.619 0.00 0.00 0.00 3.67
799 810 0.776810 TCCATCCTTCAAGCCAACCA 59.223 50.000 0.00 0.00 0.00 3.67
800 811 1.177401 GTCCATCCTTCAAGCCAACC 58.823 55.000 0.00 0.00 0.00 3.77
801 812 1.815003 CAGTCCATCCTTCAAGCCAAC 59.185 52.381 0.00 0.00 0.00 3.77
802 813 1.704628 TCAGTCCATCCTTCAAGCCAA 59.295 47.619 0.00 0.00 0.00 4.52
803 814 1.003580 GTCAGTCCATCCTTCAAGCCA 59.996 52.381 0.00 0.00 0.00 4.75
828 839 2.036933 GCAAGTCGCTGAAAAACGAAG 58.963 47.619 0.00 0.00 40.47 3.79
838 849 4.759564 GCAAGATGCAAGTCGCTG 57.240 55.556 0.00 0.00 44.26 5.18
952 964 1.079438 GGGTGGGTGGTCTCTCTCT 59.921 63.158 0.00 0.00 0.00 3.10
959 973 2.142292 ATTCTGCTGGGTGGGTGGTC 62.142 60.000 0.00 0.00 0.00 4.02
971 985 4.706962 GGATGGAGGTTTGTTAATTCTGCT 59.293 41.667 0.00 0.00 0.00 4.24
975 989 6.208599 TGAGTTGGATGGAGGTTTGTTAATTC 59.791 38.462 0.00 0.00 0.00 2.17
980 994 3.490348 CTGAGTTGGATGGAGGTTTGTT 58.510 45.455 0.00 0.00 0.00 2.83
981 995 2.815589 GCTGAGTTGGATGGAGGTTTGT 60.816 50.000 0.00 0.00 0.00 2.83
1459 1479 1.486726 GTTGTCCGGATCCTTGGAGAT 59.513 52.381 7.81 0.00 34.21 2.75
1941 1961 1.565305 GCATTCTCACTGTAGGCTCG 58.435 55.000 0.00 0.00 0.00 5.03
2016 2036 4.504596 TGCCCATGGATCGCACCC 62.505 66.667 15.22 0.00 0.00 4.61
2233 2253 3.007182 ACCGGAGAAATGAAACTCGGTAA 59.993 43.478 9.46 0.00 45.88 2.85
2292 2312 5.670485 TCACAGCAAACTCTGAGAAAGTTA 58.330 37.500 12.44 0.00 35.96 2.24
2451 2471 1.463056 TGAATCACGTCCATCAAACGC 59.537 47.619 0.00 0.00 43.76 4.84
2475 2495 8.209917 GACAATGGTCTTTAAATCGGTATCTT 57.790 34.615 0.00 0.00 40.99 2.40
2476 2496 7.787725 GACAATGGTCTTTAAATCGGTATCT 57.212 36.000 0.00 0.00 40.99 1.98
2890 2910 7.179160 CCCTTCCTTGTAAAATGGAGAAGAAAT 59.821 37.037 0.00 0.00 33.81 2.17
2920 2940 0.610232 ACAAACTGAGCCCTGATGCC 60.610 55.000 0.00 0.00 0.00 4.40
2949 2969 1.981256 ACAGAACTTGGCATTTCCGT 58.019 45.000 5.90 0.34 37.80 4.69
3108 3128 4.392940 ACTTCTCCACAATTGAAGTGAGG 58.607 43.478 13.59 11.23 45.67 3.86
3591 3611 2.618241 GCACTCACTCATTTGTTGGACA 59.382 45.455 0.00 0.00 0.00 4.02
3642 3667 6.155475 TCACAAATCCAAACCAAAAGGTAG 57.845 37.500 0.00 0.00 0.00 3.18
3760 3785 5.133221 ACATTTGTATTAAGCCCAGCTAGG 58.867 41.667 0.00 0.00 38.25 3.02
3782 3807 6.855836 TGGCAATGATGAATAACTTGAGAAC 58.144 36.000 0.00 0.00 0.00 3.01
3912 3937 8.034804 GCCAAATCAAGGTAAACTTACATCAAT 58.965 33.333 2.25 0.00 37.29 2.57
4007 4032 3.995636 AGCTGGTAAGGATAACTCTCCA 58.004 45.455 0.00 0.00 37.81 3.86
4013 4038 7.048512 ACAGAATACAAGCTGGTAAGGATAAC 58.951 38.462 4.72 0.00 36.47 1.89
4123 4148 9.609950 CTCCTTGTAAGTTATATAAGTAGCGAC 57.390 37.037 3.21 0.00 0.00 5.19
4125 4150 9.828852 CTCTCCTTGTAAGTTATATAAGTAGCG 57.171 37.037 3.21 0.00 0.00 4.26
4168 4193 8.624776 GTCTTGACATAAAGGCTAAAGCATTAT 58.375 33.333 1.88 4.69 44.88 1.28
4175 4200 6.599244 CAGGATGTCTTGACATAAAGGCTAAA 59.401 38.462 15.21 0.00 32.82 1.85
4176 4201 6.115446 CAGGATGTCTTGACATAAAGGCTAA 58.885 40.000 15.21 0.00 32.82 3.09
4177 4202 5.674525 CAGGATGTCTTGACATAAAGGCTA 58.325 41.667 15.21 0.00 32.82 3.93
4178 4203 4.521146 CAGGATGTCTTGACATAAAGGCT 58.479 43.478 15.21 0.00 32.82 4.58
4179 4204 4.889832 CAGGATGTCTTGACATAAAGGC 57.110 45.455 15.21 4.04 32.22 4.35
4274 4299 7.827701 TGACCGTTTCCAGATATATATCAGTC 58.172 38.462 21.95 14.56 35.17 3.51
4285 4312 9.847224 AATTAGTAAATATGACCGTTTCCAGAT 57.153 29.630 0.00 0.00 0.00 2.90
4370 4397 4.463539 TCAGATTAAACTTGCACATGCCAT 59.536 37.500 0.49 0.00 41.18 4.40
4408 4435 3.515316 AACGTGCAGTCCCCACTCG 62.515 63.158 0.00 0.00 0.00 4.18
4409 4436 1.668151 GAACGTGCAGTCCCCACTC 60.668 63.158 0.00 0.00 0.00 3.51
4410 4437 1.978455 TTGAACGTGCAGTCCCCACT 61.978 55.000 0.00 0.00 0.00 4.00
4411 4438 0.889186 ATTGAACGTGCAGTCCCCAC 60.889 55.000 0.00 0.00 0.00 4.61
4412 4439 0.888736 CATTGAACGTGCAGTCCCCA 60.889 55.000 0.00 0.00 0.00 4.96
4426 4453 6.071616 GCCCAGTTAACAAAAGATACCATTGA 60.072 38.462 8.61 0.00 0.00 2.57
4439 4466 5.488341 GACTTAGATCTGCCCAGTTAACAA 58.512 41.667 5.18 0.00 0.00 2.83
4460 4487 1.140816 GTTCAGGTCTTCACAGCGAC 58.859 55.000 0.00 0.00 0.00 5.19
4466 4493 3.991121 GAGCAACTAGTTCAGGTCTTCAC 59.009 47.826 4.77 0.00 0.00 3.18
4562 4593 5.086727 GCAGTTTGAAGCTATTACGGAAAC 58.913 41.667 0.00 0.00 0.00 2.78
4565 4596 4.202245 AGCAGTTTGAAGCTATTACGGA 57.798 40.909 0.00 0.00 39.78 4.69
4729 5033 2.094597 TGCACAGCAATTTGTAGATGGC 60.095 45.455 0.00 0.00 34.76 4.40


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

AutoCloner maintained by Alex Coulton.