Multiple sequence alignment - TraesCS2A01G264000

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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 TraesCS2A01G264000 chr2A 100.000 2492 0 0 503 2994 418982922 418985413 0.000000e+00 4602.0
1 TraesCS2A01G264000 chr2A 100.000 273 0 0 1 273 418982420 418982692 3.440000e-139 505.0
2 TraesCS2A01G264000 chr2D 92.964 1947 73 29 727 2618 316269344 316267407 0.000000e+00 2778.0
3 TraesCS2A01G264000 chr2D 89.912 228 19 4 2638 2865 351283482 351283705 1.050000e-74 291.0
4 TraesCS2A01G264000 chr2D 88.158 228 25 2 2638 2865 293220928 293220703 1.370000e-68 270.0
5 TraesCS2A01G264000 chr2D 89.286 56 6 0 2939 2994 316161817 316161762 1.490000e-08 71.3
6 TraesCS2A01G264000 chr2B 89.858 1617 78 32 727 2308 384110794 384109229 0.000000e+00 1999.0
7 TraesCS2A01G264000 chr2B 90.467 514 46 3 2352 2865 384095712 384095202 0.000000e+00 675.0
8 TraesCS2A01G264000 chr2B 95.000 40 1 1 2319 2358 384105419 384105381 8.960000e-06 62.1
9 TraesCS2A01G264000 chr6A 91.244 434 36 2 1563 1995 573020464 573020896 9.240000e-165 590.0
10 TraesCS2A01G264000 chr6A 93.064 173 12 0 1239 1411 573019591 573019763 1.380000e-63 254.0
11 TraesCS2A01G264000 chr6A 92.754 69 5 0 504 572 155094420 155094352 1.900000e-17 100.0
12 TraesCS2A01G264000 chr6B 91.014 434 37 2 1563 1995 644382955 644383387 4.300000e-163 584.0
13 TraesCS2A01G264000 chr6B 92.941 170 12 0 1241 1410 644382221 644382390 6.410000e-62 248.0
14 TraesCS2A01G264000 chr6B 90.278 72 6 1 504 574 710954211 710954140 3.180000e-15 93.5
15 TraesCS2A01G264000 chr6D 90.783 434 38 2 1563 1995 428418152 428418584 2.000000e-161 579.0
16 TraesCS2A01G264000 chr6D 89.035 228 24 1 2638 2865 108032059 108032285 6.320000e-72 281.0
17 TraesCS2A01G264000 chr6D 93.714 175 11 0 1237 1411 428417323 428417497 2.290000e-66 263.0
18 TraesCS2A01G264000 chr4D 94.872 273 13 1 1 273 444521004 444520733 2.760000e-115 425.0
19 TraesCS2A01G264000 chr4D 93.846 65 2 2 508 572 111563522 111563460 2.460000e-16 97.1
20 TraesCS2A01G264000 chr3D 94.505 273 13 2 1 273 560256086 560256356 1.280000e-113 420.0
21 TraesCS2A01G264000 chr1A 94.161 274 15 1 1 273 453070709 453070982 1.660000e-112 416.0
22 TraesCS2A01G264000 chr1A 93.431 274 17 1 1 273 453066765 453067038 3.590000e-109 405.0
23 TraesCS2A01G264000 chr1D 93.773 273 17 0 1 273 445930801 445931073 7.720000e-111 411.0
24 TraesCS2A01G264000 chr1D 93.773 273 16 1 1 273 157985381 157985652 2.780000e-110 409.0
25 TraesCS2A01G264000 chr5D 93.066 274 17 2 1 273 275620024 275620296 1.670000e-107 399.0
26 TraesCS2A01G264000 chr5D 89.474 228 23 1 2638 2865 212032830 212033056 1.360000e-73 287.0
27 TraesCS2A01G264000 chr5D 89.474 228 23 1 2638 2865 462706701 462706927 1.360000e-73 287.0
28 TraesCS2A01G264000 chr5D 88.596 228 24 2 2638 2865 462701492 462701717 2.940000e-70 276.0
29 TraesCS2A01G264000 chr5B 89.668 271 28 0 1 271 425888718 425888448 2.210000e-91 346.0
30 TraesCS2A01G264000 chr7D 90.351 228 19 2 2638 2865 237603427 237603203 2.260000e-76 296.0
31 TraesCS2A01G264000 chr7D 93.846 65 2 2 508 572 376070529 376070467 2.460000e-16 97.1
32 TraesCS2A01G264000 chr7A 86.081 273 38 0 1 273 265731737 265732009 8.120000e-76 294.0
33 TraesCS2A01G264000 chr7A 94.286 70 4 0 504 573 265732032 265732101 1.130000e-19 108.0
34 TraesCS2A01G264000 chr1B 87.773 229 24 4 2638 2865 440194618 440194393 6.360000e-67 265.0
35 TraesCS2A01G264000 chr4B 92.857 70 3 2 508 576 10779013 10779081 1.900000e-17 100.0
36 TraesCS2A01G264000 chr3A 92.754 69 5 0 504 572 178183840 178183772 1.900000e-17 100.0
37 TraesCS2A01G264000 chr3A 92.647 68 1 4 508 573 558702773 558702838 8.840000e-16 95.3
38 TraesCS2A01G264000 chr5A 93.939 66 2 2 508 573 644156212 644156149 6.830000e-17 99.0
39 TraesCS2A01G264000 chr4A 87.342 79 4 4 2549 2623 614605523 614605447 5.320000e-13 86.1
40 TraesCS2A01G264000 chr7B 80.488 82 15 1 2543 2623 411063751 411063670 8.960000e-06 62.1


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 TraesCS2A01G264000 chr2A 418982420 418985413 2993 False 2553.50 4602 100.0000 1 2994 2 chr2A.!!$F1 2993
1 TraesCS2A01G264000 chr2D 316267407 316269344 1937 True 2778.00 2778 92.9640 727 2618 1 chr2D.!!$R3 1891
2 TraesCS2A01G264000 chr2B 384105381 384110794 5413 True 1030.55 1999 92.4290 727 2358 2 chr2B.!!$R2 1631
3 TraesCS2A01G264000 chr2B 384095202 384095712 510 True 675.00 675 90.4670 2352 2865 1 chr2B.!!$R1 513
4 TraesCS2A01G264000 chr6A 573019591 573020896 1305 False 422.00 590 92.1540 1239 1995 2 chr6A.!!$F1 756
5 TraesCS2A01G264000 chr6B 644382221 644383387 1166 False 416.00 584 91.9775 1241 1995 2 chr6B.!!$F1 754
6 TraesCS2A01G264000 chr6D 428417323 428418584 1261 False 421.00 579 92.2485 1237 1995 2 chr6D.!!$F2 758
7 TraesCS2A01G264000 chr1A 453066765 453070982 4217 False 410.50 416 93.7960 1 273 2 chr1A.!!$F1 272

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
611 612 0.10412 GATTTTAATGCGGGTGGGCC 59.896 55.0 0.0 0.0 0.0 5.8 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2422 9190 0.10412 TATTCGATCGGCCAGTGGTG 59.896 55.0 16.41 3.99 0.0 4.17 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 0.250513 GCCAAGAGATCCGTGGACTT 59.749 55.000 16.39 0.00 45.72 3.01
55 56 2.009042 GCCAAGAGATCCGTGGACTTG 61.009 57.143 16.39 9.60 45.72 3.16
71 72 2.854777 GACTTGGTCGTGATTCTCATCG 59.145 50.000 0.00 0.00 31.08 3.84
76 77 1.524355 GTCGTGATTCTCATCGCATGG 59.476 52.381 0.00 0.00 39.58 3.66
84 85 1.153309 TCATCGCATGGGCACTCTG 60.153 57.895 4.59 0.00 41.24 3.35
112 113 1.722751 CGCAATGCACGAGTCTTCAAC 60.723 52.381 5.91 0.00 0.00 3.18
135 136 2.336341 GATCGCGACAGAGATCCCT 58.664 57.895 12.93 0.00 44.52 4.20
141 142 1.739049 GACAGAGATCCCTCCTGCG 59.261 63.158 0.00 0.00 40.30 5.18
142 143 1.743321 GACAGAGATCCCTCCTGCGG 61.743 65.000 0.00 0.00 40.30 5.69
151 152 1.153549 CCTCCTGCGGCTTACAGAC 60.154 63.158 0.00 0.00 37.32 3.51
162 163 3.050619 GGCTTACAGACGATATCCAACG 58.949 50.000 0.00 0.00 0.00 4.10
233 234 7.627298 TTAGATGCTTTTACGAGAGAGTAGT 57.373 36.000 0.00 0.00 0.00 2.73
266 267 1.164041 GGTGTAGGTGTGGTGTGTGC 61.164 60.000 0.00 0.00 0.00 4.57
269 270 2.824880 TAGGTGTGGTGTGTGCCCC 61.825 63.158 0.00 0.00 0.00 5.80
594 595 8.655935 AAAAATTCTAAACACATCTCCCTGAT 57.344 30.769 0.00 0.00 35.40 2.90
595 596 8.655935 AAAATTCTAAACACATCTCCCTGATT 57.344 30.769 0.00 0.00 32.05 2.57
596 597 8.655935 AAATTCTAAACACATCTCCCTGATTT 57.344 30.769 0.00 0.00 32.05 2.17
597 598 8.655935 AATTCTAAACACATCTCCCTGATTTT 57.344 30.769 0.00 0.00 32.05 1.82
598 599 9.753674 AATTCTAAACACATCTCCCTGATTTTA 57.246 29.630 0.00 0.00 32.05 1.52
599 600 9.753674 ATTCTAAACACATCTCCCTGATTTTAA 57.246 29.630 0.00 0.00 32.05 1.52
600 601 9.753674 TTCTAAACACATCTCCCTGATTTTAAT 57.246 29.630 0.00 0.00 32.05 1.40
601 602 9.177608 TCTAAACACATCTCCCTGATTTTAATG 57.822 33.333 0.00 0.00 32.05 1.90
602 603 5.841957 ACACATCTCCCTGATTTTAATGC 57.158 39.130 0.00 0.00 32.05 3.56
603 604 4.336433 ACACATCTCCCTGATTTTAATGCG 59.664 41.667 0.00 0.00 32.05 4.73
604 605 3.885297 ACATCTCCCTGATTTTAATGCGG 59.115 43.478 0.00 0.00 32.05 5.69
605 606 2.930950 TCTCCCTGATTTTAATGCGGG 58.069 47.619 0.00 0.00 0.00 6.13
606 607 2.241176 TCTCCCTGATTTTAATGCGGGT 59.759 45.455 0.00 0.00 33.41 5.28
607 608 2.358898 CTCCCTGATTTTAATGCGGGTG 59.641 50.000 0.00 0.00 33.41 4.61
608 609 1.408702 CCCTGATTTTAATGCGGGTGG 59.591 52.381 0.00 0.00 0.00 4.61
609 610 1.408702 CCTGATTTTAATGCGGGTGGG 59.591 52.381 0.00 0.00 0.00 4.61
610 611 0.820871 TGATTTTAATGCGGGTGGGC 59.179 50.000 0.00 0.00 0.00 5.36
611 612 0.104120 GATTTTAATGCGGGTGGGCC 59.896 55.000 0.00 0.00 0.00 5.80
612 613 0.325203 ATTTTAATGCGGGTGGGCCT 60.325 50.000 4.53 0.00 34.45 5.19
613 614 1.254284 TTTTAATGCGGGTGGGCCTG 61.254 55.000 4.53 0.00 44.07 4.85
614 615 2.433646 TTTAATGCGGGTGGGCCTGT 62.434 55.000 4.53 0.00 43.16 4.00
615 616 3.636929 TAATGCGGGTGGGCCTGTG 62.637 63.158 4.53 0.00 43.16 3.66
626 627 2.269241 GCCTGTGCCTCTACACCC 59.731 66.667 0.00 0.00 39.93 4.61
627 628 2.592993 GCCTGTGCCTCTACACCCA 61.593 63.158 0.00 0.00 39.93 4.51
628 629 1.599047 CCTGTGCCTCTACACCCAG 59.401 63.158 0.00 0.00 39.93 4.45
629 630 1.194781 CCTGTGCCTCTACACCCAGT 61.195 60.000 0.00 0.00 39.93 4.00
630 631 1.557099 CTGTGCCTCTACACCCAGTA 58.443 55.000 0.00 0.00 39.93 2.74
631 632 1.899814 CTGTGCCTCTACACCCAGTAA 59.100 52.381 0.00 0.00 39.93 2.24
632 633 2.301870 CTGTGCCTCTACACCCAGTAAA 59.698 50.000 0.00 0.00 39.93 2.01
633 634 2.038033 TGTGCCTCTACACCCAGTAAAC 59.962 50.000 0.00 0.00 39.93 2.01
634 635 1.626825 TGCCTCTACACCCAGTAAACC 59.373 52.381 0.00 0.00 30.92 3.27
635 636 1.065636 GCCTCTACACCCAGTAAACCC 60.066 57.143 0.00 0.00 30.92 4.11
636 637 1.558294 CCTCTACACCCAGTAAACCCC 59.442 57.143 0.00 0.00 30.92 4.95
637 638 2.547990 CTCTACACCCAGTAAACCCCT 58.452 52.381 0.00 0.00 30.92 4.79
638 639 2.500504 CTCTACACCCAGTAAACCCCTC 59.499 54.545 0.00 0.00 30.92 4.30
639 640 2.158127 TCTACACCCAGTAAACCCCTCA 60.158 50.000 0.00 0.00 30.92 3.86
640 641 1.755200 ACACCCAGTAAACCCCTCAT 58.245 50.000 0.00 0.00 0.00 2.90
641 642 1.633945 ACACCCAGTAAACCCCTCATC 59.366 52.381 0.00 0.00 0.00 2.92
642 643 1.064685 CACCCAGTAAACCCCTCATCC 60.065 57.143 0.00 0.00 0.00 3.51
643 644 0.551396 CCCAGTAAACCCCTCATCCC 59.449 60.000 0.00 0.00 0.00 3.85
644 645 1.596496 CCAGTAAACCCCTCATCCCT 58.404 55.000 0.00 0.00 0.00 4.20
645 646 1.212935 CCAGTAAACCCCTCATCCCTG 59.787 57.143 0.00 0.00 0.00 4.45
646 647 1.916181 CAGTAAACCCCTCATCCCTGT 59.084 52.381 0.00 0.00 0.00 4.00
647 648 3.112263 CAGTAAACCCCTCATCCCTGTA 58.888 50.000 0.00 0.00 0.00 2.74
648 649 3.521937 CAGTAAACCCCTCATCCCTGTAA 59.478 47.826 0.00 0.00 0.00 2.41
649 650 3.522343 AGTAAACCCCTCATCCCTGTAAC 59.478 47.826 0.00 0.00 0.00 2.50
650 651 2.053747 AACCCCTCATCCCTGTAACA 57.946 50.000 0.00 0.00 0.00 2.41
651 652 2.286935 ACCCCTCATCCCTGTAACAT 57.713 50.000 0.00 0.00 0.00 2.71
652 653 2.573463 ACCCCTCATCCCTGTAACATT 58.427 47.619 0.00 0.00 0.00 2.71
653 654 3.743132 ACCCCTCATCCCTGTAACATTA 58.257 45.455 0.00 0.00 0.00 1.90
654 655 4.315993 ACCCCTCATCCCTGTAACATTAT 58.684 43.478 0.00 0.00 0.00 1.28
655 656 4.104738 ACCCCTCATCCCTGTAACATTATG 59.895 45.833 0.00 0.00 0.00 1.90
656 657 4.104738 CCCCTCATCCCTGTAACATTATGT 59.895 45.833 0.00 0.00 0.00 2.29
657 658 5.309543 CCCCTCATCCCTGTAACATTATGTA 59.690 44.000 0.00 0.00 0.00 2.29
658 659 6.012508 CCCCTCATCCCTGTAACATTATGTAT 60.013 42.308 0.00 0.00 0.00 2.29
659 660 6.881065 CCCTCATCCCTGTAACATTATGTATG 59.119 42.308 0.00 0.00 40.26 2.39
661 662 7.388776 CCTCATCCCTGTAACATTATGTATGTG 59.611 40.741 0.00 0.00 46.75 3.21
662 663 7.801104 TCATCCCTGTAACATTATGTATGTGT 58.199 34.615 0.00 0.00 46.75 3.72
663 664 8.929487 TCATCCCTGTAACATTATGTATGTGTA 58.071 33.333 0.00 0.00 46.75 2.90
664 665 9.208022 CATCCCTGTAACATTATGTATGTGTAG 57.792 37.037 0.00 0.00 46.75 2.74
665 666 7.214381 TCCCTGTAACATTATGTATGTGTAGC 58.786 38.462 0.00 0.00 46.75 3.58
666 667 6.989759 CCCTGTAACATTATGTATGTGTAGCA 59.010 38.462 0.00 0.00 46.75 3.49
667 668 7.497579 CCCTGTAACATTATGTATGTGTAGCAA 59.502 37.037 0.00 0.00 46.75 3.91
668 669 8.888716 CCTGTAACATTATGTATGTGTAGCAAA 58.111 33.333 0.00 0.00 46.75 3.68
669 670 9.920826 CTGTAACATTATGTATGTGTAGCAAAG 57.079 33.333 0.00 0.00 46.75 2.77
670 671 8.394877 TGTAACATTATGTATGTGTAGCAAAGC 58.605 33.333 0.00 0.00 46.75 3.51
671 672 7.630242 AACATTATGTATGTGTAGCAAAGCT 57.370 32.000 0.00 0.00 46.75 3.74
672 673 7.251704 ACATTATGTATGTGTAGCAAAGCTC 57.748 36.000 0.00 0.00 45.71 4.09
673 674 7.050377 ACATTATGTATGTGTAGCAAAGCTCT 58.950 34.615 0.00 0.00 45.71 4.09
674 675 7.554118 ACATTATGTATGTGTAGCAAAGCTCTT 59.446 33.333 0.00 0.00 45.71 2.85
675 676 7.921786 TTATGTATGTGTAGCAAAGCTCTTT 57.078 32.000 0.00 0.00 40.44 2.52
676 677 9.613428 ATTATGTATGTGTAGCAAAGCTCTTTA 57.387 29.630 0.00 0.00 40.44 1.85
677 678 9.613428 TTATGTATGTGTAGCAAAGCTCTTTAT 57.387 29.630 0.00 0.00 40.44 1.40
678 679 7.921786 TGTATGTGTAGCAAAGCTCTTTATT 57.078 32.000 0.00 0.00 40.44 1.40
679 680 7.974675 TGTATGTGTAGCAAAGCTCTTTATTC 58.025 34.615 0.00 0.00 40.44 1.75
680 681 5.880054 TGTGTAGCAAAGCTCTTTATTCC 57.120 39.130 0.00 0.00 40.44 3.01
681 682 5.560724 TGTGTAGCAAAGCTCTTTATTCCT 58.439 37.500 0.00 0.00 40.44 3.36
682 683 6.003950 TGTGTAGCAAAGCTCTTTATTCCTT 58.996 36.000 0.00 0.00 40.44 3.36
683 684 6.072508 TGTGTAGCAAAGCTCTTTATTCCTTG 60.073 38.462 0.00 0.00 40.44 3.61
684 685 5.415701 TGTAGCAAAGCTCTTTATTCCTTGG 59.584 40.000 0.00 0.00 40.44 3.61
685 686 4.411013 AGCAAAGCTCTTTATTCCTTGGT 58.589 39.130 0.00 0.00 30.62 3.67
686 687 4.219288 AGCAAAGCTCTTTATTCCTTGGTG 59.781 41.667 0.00 0.00 30.62 4.17
687 688 4.218417 GCAAAGCTCTTTATTCCTTGGTGA 59.782 41.667 0.00 0.00 0.00 4.02
688 689 5.105595 GCAAAGCTCTTTATTCCTTGGTGAT 60.106 40.000 0.00 0.00 0.00 3.06
689 690 6.573094 GCAAAGCTCTTTATTCCTTGGTGATT 60.573 38.462 0.00 0.00 0.00 2.57
690 691 7.381323 CAAAGCTCTTTATTCCTTGGTGATTT 58.619 34.615 0.00 0.00 0.00 2.17
691 692 6.765915 AGCTCTTTATTCCTTGGTGATTTC 57.234 37.500 0.00 0.00 0.00 2.17
695 1656 7.336931 GCTCTTTATTCCTTGGTGATTTCTGTA 59.663 37.037 0.00 0.00 0.00 2.74
697 1658 9.177608 TCTTTATTCCTTGGTGATTTCTGTATG 57.822 33.333 0.00 0.00 0.00 2.39
704 1665 7.942341 TCCTTGGTGATTTCTGTATGTTTTAGT 59.058 33.333 0.00 0.00 0.00 2.24
707 1668 9.787435 TTGGTGATTTCTGTATGTTTTAGTAGT 57.213 29.630 0.00 0.00 0.00 2.73
716 1677 9.146984 TCTGTATGTTTTAGTAGTTGTGTATGC 57.853 33.333 0.00 0.00 0.00 3.14
730 1691 7.707104 AGTTGTGTATGCTATCTTTTTATGGC 58.293 34.615 0.00 0.00 34.21 4.40
741 1702 0.322997 TTTTATGGCTGGACCCGTGG 60.323 55.000 0.00 0.00 37.83 4.94
939 2026 0.310854 CAACACCAACGGAAGCTTCC 59.689 55.000 32.12 32.12 44.05 3.46
988 2088 4.406456 ACCATCAATACAACCAGCAAAGA 58.594 39.130 0.00 0.00 0.00 2.52
1004 2104 3.306225 GCAAAGACATCCAAAGCCATGAA 60.306 43.478 0.00 0.00 0.00 2.57
1022 2122 3.368571 GTTGCAGTGCTCCCTGGC 61.369 66.667 17.60 0.00 32.92 4.85
1034 2134 3.554342 CCTGGCCCTCCTGATCGG 61.554 72.222 0.00 0.00 33.56 4.18
1145 2245 1.359459 GCCGGTTCAGTTCATCGGTC 61.359 60.000 1.90 0.00 42.35 4.79
1193 2293 0.661020 GTGTACGTGCTGCTTGGTTT 59.339 50.000 4.97 0.00 0.00 3.27
1491 3017 0.319555 TTGTTCCTTCTCGCACGAGG 60.320 55.000 19.09 5.41 42.20 4.63
1548 3739 4.025229 TCCAACGAAAAGTGACGAGAAATG 60.025 41.667 0.00 0.00 0.00 2.32
1549 3740 4.260620 CCAACGAAAAGTGACGAGAAATGT 60.261 41.667 0.00 0.00 0.00 2.71
1553 3744 5.175126 ACGAAAAGTGACGAGAAATGTACTG 59.825 40.000 0.00 0.00 0.00 2.74
1561 3756 3.807622 ACGAGAAATGTACTGTGTGTTGG 59.192 43.478 0.00 0.00 0.00 3.77
1940 4884 4.373116 GCTTCGTCGAGTGCCCCA 62.373 66.667 10.09 0.00 0.00 4.96
2014 4958 4.915809 TGATCATTATCTCCTCCAACCCAT 59.084 41.667 0.00 0.00 32.93 4.00
2058 5003 0.673985 TGCCTCCCGATTCGTAGATG 59.326 55.000 5.20 0.54 35.04 2.90
2129 5098 8.637281 TCGTTTTCTTTCTTTTTCCCATTAAC 57.363 30.769 0.00 0.00 0.00 2.01
2138 5107 9.541143 TTTCTTTTTCCCATTAACTTTCATGTC 57.459 29.630 0.00 0.00 0.00 3.06
2183 5152 1.335810 TGAAGTTACGACGAGCACTGT 59.664 47.619 0.00 0.00 0.00 3.55
2190 5159 1.278172 CGACGAGCACTGTTCAGTGG 61.278 60.000 26.98 16.55 39.97 4.00
2191 5160 1.560860 GACGAGCACTGTTCAGTGGC 61.561 60.000 26.98 20.38 39.97 5.01
2270 5239 1.880027 GTGGTTCACAGGTTCCATGTC 59.120 52.381 0.00 0.00 34.08 3.06
2422 9190 4.113354 GTTCATCCAACGACTCCAGATAC 58.887 47.826 0.00 0.00 0.00 2.24
2441 9209 0.104120 CACCACTGGCCGATCGAATA 59.896 55.000 18.66 0.58 0.00 1.75
2497 9265 0.620556 CTCTAACCACACTGGCCCAT 59.379 55.000 0.00 0.00 42.67 4.00
2498 9266 1.004745 CTCTAACCACACTGGCCCATT 59.995 52.381 0.00 0.00 42.67 3.16
2513 9281 2.896039 CCCATTAAAACCCTTCACCCA 58.104 47.619 0.00 0.00 0.00 4.51
2520 9288 2.035626 CCCTTCACCCACGCCATT 59.964 61.111 0.00 0.00 0.00 3.16
2588 9395 1.887242 GCAGCGGCCGACATTGATA 60.887 57.895 33.48 0.00 0.00 2.15
2658 9658 4.920640 TCTAGATTGGATCTCGTGGTTC 57.079 45.455 0.00 0.00 40.76 3.62
2674 9674 2.903547 TTCTGAAACTTGCGGCGGC 61.904 57.895 9.78 9.68 40.52 6.53
2696 9696 4.330620 GCGGAATAAGTATTTCGTCAACCA 59.669 41.667 12.19 0.00 44.45 3.67
2697 9697 5.725864 GCGGAATAAGTATTTCGTCAACCAC 60.726 44.000 12.19 0.00 44.45 4.16
2701 9701 2.409975 AGTATTTCGTCAACCACCGTG 58.590 47.619 0.00 0.00 0.00 4.94
2727 9727 9.787435 GGGGTTTTTGGAATTTTAGAGTATTTT 57.213 29.630 0.00 0.00 0.00 1.82
2751 9751 0.117340 AGCCAGAGGTAGGTCAAGGT 59.883 55.000 0.00 0.00 0.00 3.50
2779 9779 3.728373 GGCCCCACTACCCACCAG 61.728 72.222 0.00 0.00 0.00 4.00
2838 9838 2.896443 CCCCACGAGCCTCTTCTC 59.104 66.667 0.00 0.00 0.00 2.87
2856 9856 1.743252 CGTGGCCTCCAGAAGCTTC 60.743 63.158 19.11 19.11 32.34 3.86
2857 9857 1.376466 GTGGCCTCCAGAAGCTTCA 59.624 57.895 27.57 7.01 32.34 3.02
2865 9865 1.349026 TCCAGAAGCTTCAAGGGTCTG 59.651 52.381 27.57 14.89 0.00 3.51
2866 9866 1.612726 CCAGAAGCTTCAAGGGTCTGG 60.613 57.143 27.57 19.73 37.52 3.86
2867 9867 0.037447 AGAAGCTTCAAGGGTCTGGC 59.963 55.000 27.57 0.00 0.00 4.85
2868 9868 0.250901 GAAGCTTCAAGGGTCTGGCA 60.251 55.000 21.67 0.00 0.00 4.92
2869 9869 0.251077 AAGCTTCAAGGGTCTGGCAG 60.251 55.000 8.58 8.58 0.00 4.85
2870 9870 1.073897 GCTTCAAGGGTCTGGCAGT 59.926 57.895 15.27 0.00 0.00 4.40
2871 9871 1.239968 GCTTCAAGGGTCTGGCAGTG 61.240 60.000 15.27 4.99 0.00 3.66
2872 9872 1.228245 TTCAAGGGTCTGGCAGTGC 60.228 57.895 15.27 6.55 0.00 4.40
2884 9884 4.729918 CAGTGCCCCAGCTCCACC 62.730 72.222 0.00 0.00 40.80 4.61
2889 9889 4.133373 CCCCAGCTCCACCCCATG 62.133 72.222 0.00 0.00 0.00 3.66
2908 9908 4.357947 GACACCGGCGCTCAGTCA 62.358 66.667 7.64 0.00 0.00 3.41
2909 9909 3.649277 GACACCGGCGCTCAGTCAT 62.649 63.158 7.64 0.00 0.00 3.06
2910 9910 3.190849 CACCGGCGCTCAGTCATG 61.191 66.667 7.64 0.00 0.00 3.07
2911 9911 3.381983 ACCGGCGCTCAGTCATGA 61.382 61.111 7.64 0.00 0.00 3.07
2912 9912 2.887568 CCGGCGCTCAGTCATGAC 60.888 66.667 18.47 18.47 0.00 3.06
2913 9913 2.125952 CGGCGCTCAGTCATGACA 60.126 61.111 27.02 7.16 0.00 3.58
2914 9914 2.447887 CGGCGCTCAGTCATGACAC 61.448 63.158 27.02 12.43 0.00 3.67
2915 9915 2.447887 GGCGCTCAGTCATGACACG 61.448 63.158 27.02 22.76 34.53 4.49
2916 9916 1.444383 GCGCTCAGTCATGACACGA 60.444 57.895 27.02 20.34 33.68 4.35
2917 9917 1.678269 GCGCTCAGTCATGACACGAC 61.678 60.000 27.02 12.77 33.68 4.34
2918 9918 0.109551 CGCTCAGTCATGACACGACT 60.110 55.000 27.02 0.00 44.55 4.18
2927 9927 2.027024 GACACGACTGTCACGGCA 59.973 61.111 8.73 0.00 45.57 5.69
2928 9928 2.016704 GACACGACTGTCACGGCAG 61.017 63.158 8.73 0.00 45.57 4.85
2929 9929 3.406361 CACGACTGTCACGGCAGC 61.406 66.667 8.73 0.00 39.96 5.25
2930 9930 3.911698 ACGACTGTCACGGCAGCA 61.912 61.111 8.73 0.00 39.96 4.41
2931 9931 3.108289 CGACTGTCACGGCAGCAG 61.108 66.667 8.73 0.00 39.96 4.24
2932 9932 2.340078 GACTGTCACGGCAGCAGA 59.660 61.111 2.24 0.00 39.96 4.26
2933 9933 1.300931 GACTGTCACGGCAGCAGAA 60.301 57.895 2.24 0.00 39.96 3.02
2934 9934 1.287730 GACTGTCACGGCAGCAGAAG 61.288 60.000 2.24 0.00 39.96 2.85
2935 9935 2.031012 TGTCACGGCAGCAGAAGG 59.969 61.111 0.00 0.00 0.00 3.46
2936 9936 2.031163 GTCACGGCAGCAGAAGGT 59.969 61.111 0.00 0.00 0.00 3.50
2937 9937 2.029844 GTCACGGCAGCAGAAGGTC 61.030 63.158 0.00 0.00 0.00 3.85
2938 9938 3.114616 CACGGCAGCAGAAGGTCG 61.115 66.667 0.00 0.00 0.00 4.79
2939 9939 4.379243 ACGGCAGCAGAAGGTCGG 62.379 66.667 0.00 0.00 0.00 4.79
2942 9942 4.704833 GCAGCAGAAGGTCGGCCA 62.705 66.667 9.71 0.00 38.36 5.36
2943 9943 2.270205 CAGCAGAAGGTCGGCCAT 59.730 61.111 9.71 0.00 38.36 4.40
2944 9944 2.110967 CAGCAGAAGGTCGGCCATG 61.111 63.158 9.71 5.03 38.36 3.66
2945 9945 2.825836 GCAGAAGGTCGGCCATGG 60.826 66.667 9.71 7.63 37.19 3.66
2946 9946 2.671070 CAGAAGGTCGGCCATGGT 59.329 61.111 14.67 0.00 37.19 3.55
2947 9947 1.450312 CAGAAGGTCGGCCATGGTC 60.450 63.158 14.67 10.70 37.19 4.02
2948 9948 1.918293 AGAAGGTCGGCCATGGTCA 60.918 57.895 18.31 0.16 37.19 4.02
2949 9949 1.450312 GAAGGTCGGCCATGGTCAG 60.450 63.158 18.31 9.50 37.19 3.51
2950 9950 3.628646 AAGGTCGGCCATGGTCAGC 62.629 63.158 18.31 12.96 37.19 4.26
2951 9951 4.101448 GGTCGGCCATGGTCAGCT 62.101 66.667 18.31 0.00 34.09 4.24
2952 9952 2.512515 GTCGGCCATGGTCAGCTC 60.513 66.667 18.31 0.00 0.00 4.09
2953 9953 3.785859 TCGGCCATGGTCAGCTCC 61.786 66.667 18.31 5.40 0.00 4.70
2954 9954 4.100084 CGGCCATGGTCAGCTCCA 62.100 66.667 18.31 0.00 42.01 3.86
2955 9955 2.124403 GGCCATGGTCAGCTCCAG 60.124 66.667 12.68 0.00 41.05 3.86
2956 9956 2.673523 GCCATGGTCAGCTCCAGT 59.326 61.111 14.67 0.00 41.05 4.00
2957 9957 1.451028 GCCATGGTCAGCTCCAGTC 60.451 63.158 14.67 0.00 41.05 3.51
2958 9958 1.222936 CCATGGTCAGCTCCAGTCC 59.777 63.158 2.57 0.00 41.05 3.85
2959 9959 1.153489 CATGGTCAGCTCCAGTCCG 60.153 63.158 0.18 0.00 41.05 4.79
2960 9960 2.362369 ATGGTCAGCTCCAGTCCGG 61.362 63.158 0.00 0.00 41.05 5.14
2961 9961 4.459089 GGTCAGCTCCAGTCCGGC 62.459 72.222 0.00 0.00 33.14 6.13
2962 9962 3.386237 GTCAGCTCCAGTCCGGCT 61.386 66.667 0.00 0.00 36.70 5.52
2970 9970 4.463879 CAGTCCGGCTGCTGGGAG 62.464 72.222 26.46 13.10 38.52 4.30
2975 9975 4.093291 CGGCTGCTGGGAGCTCTT 62.093 66.667 14.64 0.00 42.97 2.85
2976 9976 2.124778 GGCTGCTGGGAGCTCTTC 60.125 66.667 14.64 7.16 42.97 2.87
2977 9977 2.124778 GCTGCTGGGAGCTCTTCC 60.125 66.667 14.64 7.93 42.97 3.46
2984 9984 4.625800 GGAGCTCTTCCGCAATGT 57.374 55.556 14.64 0.00 35.91 2.71
2985 9985 2.388347 GGAGCTCTTCCGCAATGTC 58.612 57.895 14.64 0.00 35.91 3.06
2986 9986 1.424493 GGAGCTCTTCCGCAATGTCG 61.424 60.000 14.64 0.00 35.91 4.35
2987 9987 0.737715 GAGCTCTTCCGCAATGTCGT 60.738 55.000 6.43 0.00 0.00 4.34
2988 9988 0.737715 AGCTCTTCCGCAATGTCGTC 60.738 55.000 0.00 0.00 0.00 4.20
2989 9989 1.014044 GCTCTTCCGCAATGTCGTCA 61.014 55.000 0.00 0.00 0.00 4.35
2990 9990 1.645034 CTCTTCCGCAATGTCGTCAT 58.355 50.000 0.00 0.00 35.59 3.06
2991 9991 1.590238 CTCTTCCGCAATGTCGTCATC 59.410 52.381 0.00 0.00 32.56 2.92
2992 9992 0.652592 CTTCCGCAATGTCGTCATCC 59.347 55.000 0.00 0.00 32.56 3.51
2993 9993 0.249120 TTCCGCAATGTCGTCATCCT 59.751 50.000 0.00 0.00 32.56 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.440880 CCTCTGAATCTACTCCTTTGCTG 58.559 47.826 0.00 0.00 0.00 4.41
71 72 2.413142 GCTTCCAGAGTGCCCATGC 61.413 63.158 0.00 0.00 38.26 4.06
76 77 2.970974 GCGTTGCTTCCAGAGTGCC 61.971 63.158 0.00 0.00 0.00 5.01
84 85 2.082366 CGTGCATTGCGTTGCTTCC 61.082 57.895 11.41 0.50 43.18 3.46
112 113 2.115595 GATCTCTGTCGCGATCTGTTG 58.884 52.381 14.06 1.05 34.59 3.33
141 142 3.050619 CGTTGGATATCGTCTGTAAGCC 58.949 50.000 0.00 0.00 0.00 4.35
142 143 3.050619 CCGTTGGATATCGTCTGTAAGC 58.949 50.000 0.00 0.00 0.00 3.09
151 152 2.069273 GCAATCTCCCGTTGGATATCG 58.931 52.381 0.00 0.00 40.80 2.92
162 163 1.134098 TCTTCCAATCCGCAATCTCCC 60.134 52.381 0.00 0.00 0.00 4.30
169 170 1.378514 GGCCTTCTTCCAATCCGCA 60.379 57.895 0.00 0.00 0.00 5.69
171 172 1.819632 CCGGCCTTCTTCCAATCCG 60.820 63.158 0.00 0.00 36.90 4.18
201 202 5.242434 TCGTAAAAGCATCTAAAGCTCCAA 58.758 37.500 0.00 0.00 42.53 3.53
233 234 5.546499 ACACCTACACCCTAGAAATCAAAGA 59.454 40.000 0.00 0.00 0.00 2.52
502 503 6.812160 GGTAGAATAATATGTACAAGAGCCCG 59.188 42.308 0.00 0.00 0.00 6.13
503 504 7.908453 AGGTAGAATAATATGTACAAGAGCCC 58.092 38.462 0.00 0.00 0.00 5.19
504 505 9.425577 GAAGGTAGAATAATATGTACAAGAGCC 57.574 37.037 0.00 0.00 0.00 4.70
547 548 0.389426 TTCGAGAGTACGCCAAAGGC 60.389 55.000 0.00 0.00 46.75 4.35
572 573 8.655935 AAAATCAGGGAGATGTGTTTAGAATT 57.344 30.769 0.00 0.00 36.96 2.17
574 575 9.753674 ATTAAAATCAGGGAGATGTGTTTAGAA 57.246 29.630 0.00 0.00 36.96 2.10
576 577 7.917505 GCATTAAAATCAGGGAGATGTGTTTAG 59.082 37.037 0.00 0.00 36.96 1.85
577 578 7.415095 CGCATTAAAATCAGGGAGATGTGTTTA 60.415 37.037 0.00 0.00 36.96 2.01
579 580 5.163622 CGCATTAAAATCAGGGAGATGTGTT 60.164 40.000 0.00 0.00 36.96 3.32
580 581 4.336433 CGCATTAAAATCAGGGAGATGTGT 59.664 41.667 0.00 0.00 36.96 3.72
581 582 4.261322 CCGCATTAAAATCAGGGAGATGTG 60.261 45.833 0.00 0.00 36.96 3.21
582 583 3.885297 CCGCATTAAAATCAGGGAGATGT 59.115 43.478 0.00 0.00 36.96 3.06
583 584 3.254166 CCCGCATTAAAATCAGGGAGATG 59.746 47.826 6.26 0.00 41.26 2.90
584 585 3.117512 ACCCGCATTAAAATCAGGGAGAT 60.118 43.478 15.29 0.00 41.26 2.75
585 586 2.241176 ACCCGCATTAAAATCAGGGAGA 59.759 45.455 15.29 0.00 41.26 3.71
586 587 2.358898 CACCCGCATTAAAATCAGGGAG 59.641 50.000 15.29 6.90 41.26 4.30
587 588 2.374184 CACCCGCATTAAAATCAGGGA 58.626 47.619 15.29 0.00 41.26 4.20
588 589 1.408702 CCACCCGCATTAAAATCAGGG 59.591 52.381 9.37 9.37 44.17 4.45
589 590 1.408702 CCCACCCGCATTAAAATCAGG 59.591 52.381 0.00 0.00 0.00 3.86
590 591 1.202405 GCCCACCCGCATTAAAATCAG 60.202 52.381 0.00 0.00 0.00 2.90
591 592 0.820871 GCCCACCCGCATTAAAATCA 59.179 50.000 0.00 0.00 0.00 2.57
592 593 0.104120 GGCCCACCCGCATTAAAATC 59.896 55.000 0.00 0.00 0.00 2.17
593 594 0.325203 AGGCCCACCCGCATTAAAAT 60.325 50.000 0.00 0.00 39.21 1.82
594 595 1.077625 AGGCCCACCCGCATTAAAA 59.922 52.632 0.00 0.00 39.21 1.52
595 596 1.680651 CAGGCCCACCCGCATTAAA 60.681 57.895 0.00 0.00 39.21 1.52
596 597 2.044451 CAGGCCCACCCGCATTAA 60.044 61.111 0.00 0.00 39.21 1.40
597 598 3.334891 ACAGGCCCACCCGCATTA 61.335 61.111 0.00 0.00 39.21 1.90
609 610 2.269241 GGGTGTAGAGGCACAGGC 59.731 66.667 0.00 0.00 40.89 4.85
610 611 1.194781 ACTGGGTGTAGAGGCACAGG 61.195 60.000 0.00 0.00 40.89 4.00
611 612 1.557099 TACTGGGTGTAGAGGCACAG 58.443 55.000 0.00 0.00 40.89 3.66
612 613 2.018355 TTACTGGGTGTAGAGGCACA 57.982 50.000 0.00 0.00 40.89 4.57
613 614 2.614734 GGTTTACTGGGTGTAGAGGCAC 60.615 54.545 0.00 0.00 38.56 5.01
614 615 1.626825 GGTTTACTGGGTGTAGAGGCA 59.373 52.381 0.00 0.00 32.08 4.75
615 616 1.065636 GGGTTTACTGGGTGTAGAGGC 60.066 57.143 0.00 0.00 32.08 4.70
616 617 1.558294 GGGGTTTACTGGGTGTAGAGG 59.442 57.143 0.00 0.00 32.08 3.69
617 618 2.500504 GAGGGGTTTACTGGGTGTAGAG 59.499 54.545 0.00 0.00 32.08 2.43
618 619 2.158127 TGAGGGGTTTACTGGGTGTAGA 60.158 50.000 0.00 0.00 32.08 2.59
619 620 2.262637 TGAGGGGTTTACTGGGTGTAG 58.737 52.381 0.00 0.00 32.08 2.74
620 621 2.419457 TGAGGGGTTTACTGGGTGTA 57.581 50.000 0.00 0.00 0.00 2.90
621 622 1.633945 GATGAGGGGTTTACTGGGTGT 59.366 52.381 0.00 0.00 0.00 4.16
622 623 1.064685 GGATGAGGGGTTTACTGGGTG 60.065 57.143 0.00 0.00 0.00 4.61
623 624 1.296002 GGATGAGGGGTTTACTGGGT 58.704 55.000 0.00 0.00 0.00 4.51
624 625 0.551396 GGGATGAGGGGTTTACTGGG 59.449 60.000 0.00 0.00 0.00 4.45
625 626 1.212935 CAGGGATGAGGGGTTTACTGG 59.787 57.143 0.00 0.00 0.00 4.00
626 627 1.916181 ACAGGGATGAGGGGTTTACTG 59.084 52.381 0.00 0.00 0.00 2.74
627 628 2.361085 ACAGGGATGAGGGGTTTACT 57.639 50.000 0.00 0.00 0.00 2.24
628 629 3.264964 TGTTACAGGGATGAGGGGTTTAC 59.735 47.826 0.00 0.00 0.00 2.01
629 630 3.533146 TGTTACAGGGATGAGGGGTTTA 58.467 45.455 0.00 0.00 0.00 2.01
630 631 2.354328 TGTTACAGGGATGAGGGGTTT 58.646 47.619 0.00 0.00 0.00 3.27
631 632 2.053747 TGTTACAGGGATGAGGGGTT 57.946 50.000 0.00 0.00 0.00 4.11
632 633 2.286935 ATGTTACAGGGATGAGGGGT 57.713 50.000 0.00 0.00 0.00 4.95
633 634 4.104738 ACATAATGTTACAGGGATGAGGGG 59.895 45.833 9.79 0.00 0.00 4.79
634 635 5.310409 ACATAATGTTACAGGGATGAGGG 57.690 43.478 9.79 0.00 0.00 4.30
635 636 7.912056 CATACATAATGTTACAGGGATGAGG 57.088 40.000 9.79 0.00 0.00 3.86
645 646 8.612619 AGCTTTGCTACACATACATAATGTTAC 58.387 33.333 0.00 0.00 40.93 2.50
646 647 8.731275 AGCTTTGCTACACATACATAATGTTA 57.269 30.769 0.00 0.00 40.93 2.41
647 648 7.554118 AGAGCTTTGCTACACATACATAATGTT 59.446 33.333 0.00 0.00 42.17 2.71
648 649 7.050377 AGAGCTTTGCTACACATACATAATGT 58.950 34.615 0.00 0.00 44.30 2.71
649 650 7.488187 AGAGCTTTGCTACACATACATAATG 57.512 36.000 0.00 0.00 39.88 1.90
650 651 8.511604 AAAGAGCTTTGCTACACATACATAAT 57.488 30.769 0.00 0.00 39.88 1.28
651 652 7.921786 AAAGAGCTTTGCTACACATACATAA 57.078 32.000 0.00 0.00 39.88 1.90
652 653 9.613428 AATAAAGAGCTTTGCTACACATACATA 57.387 29.630 5.76 0.00 39.88 2.29
653 654 8.511604 AATAAAGAGCTTTGCTACACATACAT 57.488 30.769 5.76 0.00 39.88 2.29
654 655 7.065803 GGAATAAAGAGCTTTGCTACACATACA 59.934 37.037 5.76 0.00 39.88 2.29
655 656 7.281100 AGGAATAAAGAGCTTTGCTACACATAC 59.719 37.037 5.76 0.00 39.88 2.39
656 657 7.338710 AGGAATAAAGAGCTTTGCTACACATA 58.661 34.615 5.76 0.00 39.88 2.29
657 658 6.183347 AGGAATAAAGAGCTTTGCTACACAT 58.817 36.000 5.76 0.00 39.88 3.21
658 659 5.560724 AGGAATAAAGAGCTTTGCTACACA 58.439 37.500 5.76 0.00 39.88 3.72
659 660 6.317857 CAAGGAATAAAGAGCTTTGCTACAC 58.682 40.000 5.76 0.00 39.88 2.90
660 661 5.415701 CCAAGGAATAAAGAGCTTTGCTACA 59.584 40.000 5.76 0.00 39.88 2.74
661 662 5.416013 ACCAAGGAATAAAGAGCTTTGCTAC 59.584 40.000 5.76 0.00 39.88 3.58
662 663 5.415701 CACCAAGGAATAAAGAGCTTTGCTA 59.584 40.000 5.76 0.00 39.88 3.49
663 664 4.219288 CACCAAGGAATAAAGAGCTTTGCT 59.781 41.667 5.76 0.00 43.88 3.91
664 665 4.218417 TCACCAAGGAATAAAGAGCTTTGC 59.782 41.667 5.76 0.00 34.23 3.68
665 666 5.964958 TCACCAAGGAATAAAGAGCTTTG 57.035 39.130 5.76 0.00 34.23 2.77
666 667 7.452813 AGAAATCACCAAGGAATAAAGAGCTTT 59.547 33.333 0.74 0.74 36.63 3.51
667 668 6.950619 AGAAATCACCAAGGAATAAAGAGCTT 59.049 34.615 0.00 0.00 0.00 3.74
668 669 6.376581 CAGAAATCACCAAGGAATAAAGAGCT 59.623 38.462 0.00 0.00 0.00 4.09
669 670 6.151817 ACAGAAATCACCAAGGAATAAAGAGC 59.848 38.462 0.00 0.00 0.00 4.09
670 671 7.693969 ACAGAAATCACCAAGGAATAAAGAG 57.306 36.000 0.00 0.00 0.00 2.85
671 672 9.177608 CATACAGAAATCACCAAGGAATAAAGA 57.822 33.333 0.00 0.00 0.00 2.52
672 673 8.960591 ACATACAGAAATCACCAAGGAATAAAG 58.039 33.333 0.00 0.00 0.00 1.85
673 674 8.877864 ACATACAGAAATCACCAAGGAATAAA 57.122 30.769 0.00 0.00 0.00 1.40
674 675 8.877864 AACATACAGAAATCACCAAGGAATAA 57.122 30.769 0.00 0.00 0.00 1.40
675 676 8.877864 AAACATACAGAAATCACCAAGGAATA 57.122 30.769 0.00 0.00 0.00 1.75
676 677 7.781324 AAACATACAGAAATCACCAAGGAAT 57.219 32.000 0.00 0.00 0.00 3.01
677 678 7.595819 AAAACATACAGAAATCACCAAGGAA 57.404 32.000 0.00 0.00 0.00 3.36
678 679 7.942341 ACTAAAACATACAGAAATCACCAAGGA 59.058 33.333 0.00 0.00 0.00 3.36
679 680 8.110860 ACTAAAACATACAGAAATCACCAAGG 57.889 34.615 0.00 0.00 0.00 3.61
681 682 9.787435 ACTACTAAAACATACAGAAATCACCAA 57.213 29.630 0.00 0.00 0.00 3.67
682 683 9.787435 AACTACTAAAACATACAGAAATCACCA 57.213 29.630 0.00 0.00 0.00 4.17
690 691 9.146984 GCATACACAACTACTAAAACATACAGA 57.853 33.333 0.00 0.00 0.00 3.41
691 692 9.151471 AGCATACACAACTACTAAAACATACAG 57.849 33.333 0.00 0.00 0.00 2.74
704 1665 8.836413 GCCATAAAAAGATAGCATACACAACTA 58.164 33.333 0.00 0.00 0.00 2.24
707 1668 7.201812 CCAGCCATAAAAAGATAGCATACACAA 60.202 37.037 0.00 0.00 0.00 3.33
709 1670 6.486657 TCCAGCCATAAAAAGATAGCATACAC 59.513 38.462 0.00 0.00 0.00 2.90
711 1672 6.072452 GGTCCAGCCATAAAAAGATAGCATAC 60.072 42.308 0.00 0.00 37.17 2.39
713 1674 4.829492 GGTCCAGCCATAAAAAGATAGCAT 59.171 41.667 0.00 0.00 37.17 3.79
715 1676 3.570125 GGGTCCAGCCATAAAAAGATAGC 59.430 47.826 0.00 0.00 39.65 2.97
716 1677 3.815401 CGGGTCCAGCCATAAAAAGATAG 59.185 47.826 0.00 0.00 39.65 2.08
718 1679 2.025321 ACGGGTCCAGCCATAAAAAGAT 60.025 45.455 0.00 0.00 39.65 2.40
720 1681 1.472480 CACGGGTCCAGCCATAAAAAG 59.528 52.381 0.00 0.00 39.65 2.27
724 1685 0.986019 ATCCACGGGTCCAGCCATAA 60.986 55.000 0.00 0.00 39.65 1.90
725 1686 0.986019 AATCCACGGGTCCAGCCATA 60.986 55.000 0.00 0.00 39.65 2.74
730 1691 1.191535 TGTAGAATCCACGGGTCCAG 58.808 55.000 0.00 0.00 0.00 3.86
741 1702 3.487544 GCAGCCGAACCAATTGTAGAATC 60.488 47.826 4.43 0.00 0.00 2.52
933 2020 4.224762 TGAGATGAGATGAGATGGAAGCT 58.775 43.478 0.00 0.00 30.44 3.74
939 2026 4.701171 TCGGAGATGAGATGAGATGAGATG 59.299 45.833 0.00 0.00 0.00 2.90
940 2027 4.920999 TCGGAGATGAGATGAGATGAGAT 58.079 43.478 0.00 0.00 0.00 2.75
941 2028 4.363991 TCGGAGATGAGATGAGATGAGA 57.636 45.455 0.00 0.00 0.00 3.27
942 2029 4.761227 TCTTCGGAGATGAGATGAGATGAG 59.239 45.833 0.00 0.00 35.73 2.90
943 2030 4.723309 TCTTCGGAGATGAGATGAGATGA 58.277 43.478 0.00 0.00 35.73 2.92
988 2088 2.028748 GCAACTTCATGGCTTTGGATGT 60.029 45.455 0.00 0.00 0.00 3.06
1004 2104 2.433446 CCAGGGAGCACTGCAACT 59.567 61.111 3.30 0.00 37.16 3.16
1022 2122 2.444706 TCAGGCCGATCAGGAGGG 60.445 66.667 0.00 0.00 45.00 4.30
1193 2293 0.107703 GGCACGAACCATCCATCAGA 60.108 55.000 0.00 0.00 0.00 3.27
1361 2699 1.574702 GGTTGCAGTTCTGCGGGTAC 61.575 60.000 17.95 12.96 37.69 3.34
1504 3030 1.608283 CCGTCCCTCTCGCTTCTTTTT 60.608 52.381 0.00 0.00 0.00 1.94
1509 3036 2.490685 GACCGTCCCTCTCGCTTC 59.509 66.667 0.00 0.00 0.00 3.86
1548 3739 0.944386 CTGCACCCAACACACAGTAC 59.056 55.000 0.00 0.00 0.00 2.73
1549 3740 0.179032 CCTGCACCCAACACACAGTA 60.179 55.000 0.00 0.00 0.00 2.74
1553 3744 1.447317 CTCACCTGCACCCAACACAC 61.447 60.000 0.00 0.00 0.00 3.82
1561 3756 2.046892 ATGTCGCTCACCTGCACC 60.047 61.111 0.00 0.00 0.00 5.01
2014 4958 1.338107 AGGAACACACGATGACTCCA 58.662 50.000 14.38 0.00 36.71 3.86
2024 4969 3.056821 GGGAGGCAAATTAAGGAACACAC 60.057 47.826 0.00 0.00 0.00 3.82
2058 5003 7.568679 GCGGTAAGAAATGAAAACCAAATGAAC 60.569 37.037 0.00 0.00 0.00 3.18
2080 5025 0.321298 ACGTTTATTCTGCCAGCGGT 60.321 50.000 0.00 0.00 0.00 5.68
2183 5152 3.626930 AGTTTGTTTAGTGGCCACTGAA 58.373 40.909 42.35 37.48 42.52 3.02
2222 5191 5.801531 TCACGGATGGCAAATACTAGTAT 57.198 39.130 9.71 9.71 0.00 2.12
2223 5192 5.597806 CTTCACGGATGGCAAATACTAGTA 58.402 41.667 4.77 4.77 0.00 1.82
2224 5193 4.442706 CTTCACGGATGGCAAATACTAGT 58.557 43.478 0.00 0.00 0.00 2.57
2225 5194 3.248602 GCTTCACGGATGGCAAATACTAG 59.751 47.826 0.00 0.00 0.00 2.57
2358 9126 2.455674 TCGGAGTTCACAACCATGAG 57.544 50.000 0.00 0.00 0.00 2.90
2401 9169 3.767131 TGTATCTGGAGTCGTTGGATGAA 59.233 43.478 0.00 0.00 0.00 2.57
2422 9190 0.104120 TATTCGATCGGCCAGTGGTG 59.896 55.000 16.41 3.99 0.00 4.17
2441 9209 7.530426 AGCAGTGTCCTAGAAAATTTCATTT 57.470 32.000 8.55 0.00 0.00 2.32
2497 9265 1.320507 GCGTGGGTGAAGGGTTTTAA 58.679 50.000 0.00 0.00 0.00 1.52
2498 9266 0.537828 GGCGTGGGTGAAGGGTTTTA 60.538 55.000 0.00 0.00 0.00 1.52
2520 9288 4.786507 CATGCATCAGAAAGAAAACACGA 58.213 39.130 0.00 0.00 0.00 4.35
2523 9291 3.004629 ACGCATGCATCAGAAAGAAAACA 59.995 39.130 19.57 0.00 0.00 2.83
2578 9385 1.275471 ATCGCGCGGTATCAATGTCG 61.275 55.000 31.69 0.00 0.00 4.35
2658 9658 4.741781 CGCCGCCGCAAGTTTCAG 62.742 66.667 0.00 0.00 34.03 3.02
2674 9674 5.220529 GGTGGTTGACGAAATACTTATTCCG 60.221 44.000 0.00 0.00 0.00 4.30
2679 9679 3.989167 CACGGTGGTTGACGAAATACTTA 59.011 43.478 0.00 0.00 0.00 2.24
2697 9697 2.920724 AAATTCCAAAAACCCCACGG 57.079 45.000 0.00 0.00 0.00 4.94
2701 9701 9.787435 AAAATACTCTAAAATTCCAAAAACCCC 57.213 29.630 0.00 0.00 0.00 4.95
2727 9727 4.447908 CCTTGACCTACCTCTGGCTCTATA 60.448 50.000 0.00 0.00 0.00 1.31
2736 9736 1.645710 CACCACCTTGACCTACCTCT 58.354 55.000 0.00 0.00 0.00 3.69
2737 9737 0.036294 GCACCACCTTGACCTACCTC 60.036 60.000 0.00 0.00 0.00 3.85
2821 9821 2.896443 GAGAAGAGGCTCGTGGGG 59.104 66.667 7.92 0.00 0.00 4.96
2838 9838 1.743252 GAAGCTTCTGGAGGCCACG 60.743 63.158 19.44 0.00 33.44 4.94
2867 9867 4.729918 GGTGGAGCTGGGGCACTG 62.730 72.222 0.00 0.00 41.70 3.66
2872 9872 4.133373 CATGGGGTGGAGCTGGGG 62.133 72.222 0.00 0.00 0.00 4.96
2881 9881 4.424711 CCGGTGTCCCATGGGGTG 62.425 72.222 30.93 15.08 44.74 4.61
2891 9891 3.649277 ATGACTGAGCGCCGGTGTC 62.649 63.158 17.91 13.10 33.70 3.67
2892 9892 3.695606 ATGACTGAGCGCCGGTGT 61.696 61.111 17.91 3.07 33.70 4.16
2893 9893 3.190849 CATGACTGAGCGCCGGTG 61.191 66.667 11.67 11.67 33.70 4.94
2894 9894 3.381983 TCATGACTGAGCGCCGGT 61.382 61.111 2.29 6.96 37.00 5.28
2895 9895 2.887568 GTCATGACTGAGCGCCGG 60.888 66.667 18.83 0.00 30.18 6.13
2896 9896 2.125952 TGTCATGACTGAGCGCCG 60.126 61.111 25.55 0.00 30.18 6.46
2897 9897 2.447887 CGTGTCATGACTGAGCGCC 61.448 63.158 25.55 0.00 30.18 6.53
2898 9898 1.444383 TCGTGTCATGACTGAGCGC 60.444 57.895 25.55 0.00 33.53 5.92
2899 9899 0.109551 AGTCGTGTCATGACTGAGCG 60.110 55.000 23.97 21.63 42.49 5.03
2900 9900 3.802613 AGTCGTGTCATGACTGAGC 57.197 52.632 23.97 16.18 42.49 4.26
2911 9911 2.027605 CTGCCGTGACAGTCGTGT 59.972 61.111 0.00 0.00 40.71 4.49
2912 9912 3.406361 GCTGCCGTGACAGTCGTG 61.406 66.667 0.00 0.00 39.96 4.35
2913 9913 3.848347 CTGCTGCCGTGACAGTCGT 62.848 63.158 0.00 0.00 39.96 4.34
2914 9914 3.108289 CTGCTGCCGTGACAGTCG 61.108 66.667 0.00 0.00 39.96 4.18
2915 9915 1.287730 CTTCTGCTGCCGTGACAGTC 61.288 60.000 0.00 0.00 39.96 3.51
2916 9916 1.301244 CTTCTGCTGCCGTGACAGT 60.301 57.895 0.00 0.00 39.96 3.55
2917 9917 2.031516 CCTTCTGCTGCCGTGACAG 61.032 63.158 0.00 0.00 40.80 3.51
2918 9918 2.031012 CCTTCTGCTGCCGTGACA 59.969 61.111 0.00 0.00 0.00 3.58
2919 9919 2.029844 GACCTTCTGCTGCCGTGAC 61.030 63.158 0.00 0.00 0.00 3.67
2920 9920 2.343758 GACCTTCTGCTGCCGTGA 59.656 61.111 0.00 0.00 0.00 4.35
2921 9921 3.114616 CGACCTTCTGCTGCCGTG 61.115 66.667 0.00 0.00 0.00 4.94
2922 9922 4.379243 CCGACCTTCTGCTGCCGT 62.379 66.667 0.00 0.00 0.00 5.68
2925 9925 3.984193 ATGGCCGACCTTCTGCTGC 62.984 63.158 0.00 0.00 36.63 5.25
2926 9926 2.110967 CATGGCCGACCTTCTGCTG 61.111 63.158 0.00 0.00 36.63 4.41
2927 9927 2.270205 CATGGCCGACCTTCTGCT 59.730 61.111 0.00 0.00 36.63 4.24
2928 9928 2.825836 CCATGGCCGACCTTCTGC 60.826 66.667 0.00 0.00 36.63 4.26
2929 9929 1.450312 GACCATGGCCGACCTTCTG 60.450 63.158 13.04 0.00 36.63 3.02
2930 9930 1.903877 CTGACCATGGCCGACCTTCT 61.904 60.000 13.04 0.00 36.63 2.85
2931 9931 1.450312 CTGACCATGGCCGACCTTC 60.450 63.158 13.04 0.00 36.63 3.46
2932 9932 2.671070 CTGACCATGGCCGACCTT 59.329 61.111 13.04 0.00 36.63 3.50
2933 9933 4.101448 GCTGACCATGGCCGACCT 62.101 66.667 13.04 0.00 36.63 3.85
2934 9934 4.101448 AGCTGACCATGGCCGACC 62.101 66.667 13.04 0.00 0.00 4.79
2935 9935 2.512515 GAGCTGACCATGGCCGAC 60.513 66.667 13.04 0.00 0.00 4.79
2936 9936 3.785859 GGAGCTGACCATGGCCGA 61.786 66.667 13.04 0.00 0.00 5.54
2937 9937 4.100084 TGGAGCTGACCATGGCCG 62.100 66.667 13.04 0.88 34.77 6.13
2938 9938 2.124403 CTGGAGCTGACCATGGCC 60.124 66.667 13.04 0.00 39.34 5.36
2939 9939 1.451028 GACTGGAGCTGACCATGGC 60.451 63.158 13.04 5.35 39.34 4.40
2940 9940 1.222936 GGACTGGAGCTGACCATGG 59.777 63.158 11.19 11.19 39.34 3.66
2941 9941 1.153489 CGGACTGGAGCTGACCATG 60.153 63.158 0.00 0.00 39.34 3.66
2942 9942 2.362369 CCGGACTGGAGCTGACCAT 61.362 63.158 0.00 0.00 42.00 3.55
2943 9943 2.997315 CCGGACTGGAGCTGACCA 60.997 66.667 0.00 0.00 42.00 4.02
2944 9944 4.459089 GCCGGACTGGAGCTGACC 62.459 72.222 5.05 0.00 42.00 4.02
2945 9945 3.386237 AGCCGGACTGGAGCTGAC 61.386 66.667 5.05 0.00 42.00 3.51
2958 9958 4.093291 AAGAGCTCCCAGCAGCCG 62.093 66.667 10.93 0.00 45.56 5.52
2959 9959 2.124778 GAAGAGCTCCCAGCAGCC 60.125 66.667 10.93 0.00 45.56 4.85
2960 9960 2.124778 GGAAGAGCTCCCAGCAGC 60.125 66.667 10.93 0.00 45.56 5.25
2961 9961 2.186384 CGGAAGAGCTCCCAGCAG 59.814 66.667 10.93 0.00 45.56 4.24
2962 9962 4.087892 GCGGAAGAGCTCCCAGCA 62.088 66.667 18.84 0.00 45.56 4.41
2963 9963 2.883267 ATTGCGGAAGAGCTCCCAGC 62.883 60.000 10.93 15.13 41.87 4.85
2964 9964 1.094073 CATTGCGGAAGAGCTCCCAG 61.094 60.000 10.93 4.79 41.87 4.45
2965 9965 1.078214 CATTGCGGAAGAGCTCCCA 60.078 57.895 10.93 0.00 41.87 4.37
2966 9966 1.078143 ACATTGCGGAAGAGCTCCC 60.078 57.895 10.93 4.33 41.87 4.30
2967 9967 1.424493 CGACATTGCGGAAGAGCTCC 61.424 60.000 10.93 0.00 41.40 4.70
2968 9968 0.737715 ACGACATTGCGGAAGAGCTC 60.738 55.000 5.27 5.27 38.13 4.09
2969 9969 0.737715 GACGACATTGCGGAAGAGCT 60.738 55.000 0.00 0.00 38.13 4.09
2970 9970 1.014044 TGACGACATTGCGGAAGAGC 61.014 55.000 0.00 0.00 35.12 4.09
2971 9971 1.590238 GATGACGACATTGCGGAAGAG 59.410 52.381 1.10 0.00 36.82 2.85
2972 9972 1.640428 GATGACGACATTGCGGAAGA 58.360 50.000 1.10 0.00 36.82 2.87
2973 9973 0.652592 GGATGACGACATTGCGGAAG 59.347 55.000 1.10 0.00 36.82 3.46
2974 9974 0.249120 AGGATGACGACATTGCGGAA 59.751 50.000 1.10 0.00 36.82 4.30
2975 9975 1.897423 AGGATGACGACATTGCGGA 59.103 52.632 1.10 0.00 36.82 5.54
2976 9976 4.521075 AGGATGACGACATTGCGG 57.479 55.556 1.10 0.00 36.82 5.69


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

AutoCloner maintained by Alex Coulton.