Multiple sequence alignment - TraesCS5B01G237800

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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 TraesCS5B01G237800 chr5B 100.000 3542 0 0 1 3542 418560572 418557031 0.000000e+00 6541
1 TraesCS5B01G237800 chr5B 79.735 528 90 11 54 577 709231730 709232244 2.010000e-97 366
2 TraesCS5B01G237800 chr5D 91.524 2737 94 54 893 3542 354275867 354273182 0.000000e+00 3642
3 TraesCS5B01G237800 chr5D 95.897 195 8 0 685 879 354276280 354276086 2.050000e-82 316
4 TraesCS5B01G237800 chr5A 87.286 1400 100 33 936 2285 455282175 455280804 0.000000e+00 1528
5 TraesCS5B01G237800 chr5A 80.559 715 43 34 2454 3114 455280678 455280006 2.490000e-126 462
6 TraesCS5B01G237800 chr5A 87.042 355 18 13 3211 3542 455279939 455279590 3.340000e-100 375
7 TraesCS5B01G237800 chr5A 85.668 307 22 5 578 879 455292116 455291827 1.600000e-78 303
8 TraesCS5B01G237800 chr5A 76.937 555 105 19 37 576 647608488 647607942 9.620000e-76 294
9 TraesCS5B01G237800 chr7A 76.545 550 112 13 37 576 287210333 287210875 5.790000e-73 285
10 TraesCS5B01G237800 chr1D 79.592 392 72 7 189 576 168330635 168330248 1.250000e-69 274
11 TraesCS5B01G237800 chr1D 77.751 418 81 9 163 576 470887831 470887422 2.730000e-61 246
12 TraesCS5B01G237800 chr1D 76.471 391 85 6 190 577 479580300 479580686 4.630000e-49 206
13 TraesCS5B01G237800 chr7B 74.206 535 117 14 34 552 4610407 4610936 1.670000e-48 204
14 TraesCS5B01G237800 chr1B 75.414 423 93 10 160 576 325286672 325287089 1.000000e-45 195
15 TraesCS5B01G237800 chrUn 74.580 417 98 6 163 576 119057218 119056807 3.630000e-40 176


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 TraesCS5B01G237800 chr5B 418557031 418560572 3541 True 6541.000000 6541 100.000000 1 3542 1 chr5B.!!$R1 3541
1 TraesCS5B01G237800 chr5B 709231730 709232244 514 False 366.000000 366 79.735000 54 577 1 chr5B.!!$F1 523
2 TraesCS5B01G237800 chr5D 354273182 354276280 3098 True 1979.000000 3642 93.710500 685 3542 2 chr5D.!!$R1 2857
3 TraesCS5B01G237800 chr5A 455279590 455282175 2585 True 788.333333 1528 84.962333 936 3542 3 chr5A.!!$R3 2606
4 TraesCS5B01G237800 chr5A 647607942 647608488 546 True 294.000000 294 76.937000 37 576 1 chr5A.!!$R2 539
5 TraesCS5B01G237800 chr7A 287210333 287210875 542 False 285.000000 285 76.545000 37 576 1 chr7A.!!$F1 539
6 TraesCS5B01G237800 chr7B 4610407 4610936 529 False 204.000000 204 74.206000 34 552 1 chr7B.!!$F1 518

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
158 175 0.035439 CCCTGTGTTGTTCGCCCTAT 60.035 55.0 0.0 0.0 0.00 2.57 F
585 611 0.039798 TGTTTCGAGAACGTCCTCCG 60.040 55.0 0.0 0.0 44.03 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2142 2446 1.141019 CGGGTAGGTGATGGACGTG 59.859 63.158 0.0 0.0 0.00 4.49 R
2556 2893 0.110295 CACAAGGACCACACCATCCA 59.890 55.000 0.0 0.0 37.47 3.41 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 4.451900 CACCAGTGACAAAAAGGTCTAGT 58.548 43.478 0.00 0.00 38.61 2.57
23 24 5.607477 CACCAGTGACAAAAAGGTCTAGTA 58.393 41.667 0.00 0.00 38.61 1.82
24 25 5.465724 CACCAGTGACAAAAAGGTCTAGTAC 59.534 44.000 0.00 0.00 38.61 2.73
25 26 4.684703 CCAGTGACAAAAAGGTCTAGTACG 59.315 45.833 0.00 0.00 38.61 3.67
26 27 5.508489 CCAGTGACAAAAAGGTCTAGTACGA 60.508 44.000 0.00 0.00 38.61 3.43
27 28 6.157211 CAGTGACAAAAAGGTCTAGTACGAT 58.843 40.000 0.00 0.00 38.61 3.73
28 29 7.310664 CAGTGACAAAAAGGTCTAGTACGATA 58.689 38.462 0.00 0.00 38.61 2.92
29 30 7.485277 CAGTGACAAAAAGGTCTAGTACGATAG 59.515 40.741 0.00 0.00 38.61 2.08
30 31 6.253083 GTGACAAAAAGGTCTAGTACGATAGC 59.747 42.308 0.00 0.00 38.61 2.97
31 32 6.071784 TGACAAAAAGGTCTAGTACGATAGCA 60.072 38.462 0.00 0.00 38.61 3.49
32 33 6.331061 ACAAAAAGGTCTAGTACGATAGCAG 58.669 40.000 0.00 0.00 42.67 4.24
33 34 4.571372 AAAGGTCTAGTACGATAGCAGC 57.429 45.455 0.00 0.00 42.67 5.25
34 35 2.144730 AGGTCTAGTACGATAGCAGCG 58.855 52.381 0.00 0.00 42.67 5.18
35 36 2.141517 GGTCTAGTACGATAGCAGCGA 58.858 52.381 0.00 0.00 42.67 4.93
46 47 2.302199 TAGCAGCGATGGTGGCTCTG 62.302 60.000 16.76 0.00 39.08 3.35
49 50 2.060383 AGCGATGGTGGCTCTGCTA 61.060 57.895 0.00 0.00 35.37 3.49
51 52 1.819229 CGATGGTGGCTCTGCTACT 59.181 57.895 6.06 0.00 39.93 2.57
59 60 0.902531 GGCTCTGCTACTGGGTTGTA 59.097 55.000 0.00 0.00 0.00 2.41
113 130 2.574018 CGTGCTCCCTGGAGTGACA 61.574 63.158 14.45 1.85 43.70 3.58
123 140 0.117140 TGGAGTGACACCCTGATCCT 59.883 55.000 11.02 0.00 0.00 3.24
158 175 0.035439 CCCTGTGTTGTTCGCCCTAT 60.035 55.000 0.00 0.00 0.00 2.57
183 202 2.870372 GTGGTGGCACGAATGAGC 59.130 61.111 12.17 0.00 0.00 4.26
186 205 1.672356 GGTGGCACGAATGAGCTGT 60.672 57.895 12.17 0.00 31.76 4.40
232 252 2.431539 GACGACATCGACGCTTTGT 58.568 52.632 8.54 0.00 43.02 2.83
234 254 1.282248 ACGACATCGACGCTTTGTGG 61.282 55.000 8.54 0.00 43.02 4.17
237 257 1.227999 ACATCGACGCTTTGTGGGTG 61.228 55.000 0.00 0.00 42.57 4.61
238 258 1.070786 ATCGACGCTTTGTGGGTGT 59.929 52.632 0.00 0.00 42.14 4.16
242 262 2.101209 GACGCTTTGTGGGTGTCGTG 62.101 60.000 0.00 0.00 42.14 4.35
256 276 1.372997 TCGTGCTTCCTGAAGACGC 60.373 57.895 11.00 7.67 40.79 5.19
258 278 1.004440 GTGCTTCCTGAAGACGCCT 60.004 57.895 11.00 0.00 38.97 5.52
259 279 1.016653 GTGCTTCCTGAAGACGCCTC 61.017 60.000 11.00 0.00 38.97 4.70
307 331 0.107831 CGGGTGAAGACCTTTGTCCA 59.892 55.000 0.00 0.00 42.81 4.02
308 332 1.271379 CGGGTGAAGACCTTTGTCCAT 60.271 52.381 0.00 0.00 42.81 3.41
310 334 3.230976 GGGTGAAGACCTTTGTCCATTT 58.769 45.455 0.00 0.00 42.81 2.32
400 424 0.541392 TAGGTCGTAGCGTGGAGGTA 59.459 55.000 0.00 0.00 0.00 3.08
403 427 0.594284 GTCGTAGCGTGGAGGTATGC 60.594 60.000 0.00 0.00 39.13 3.14
413 437 4.551388 CGTGGAGGTATGCTTAGATCTTC 58.449 47.826 0.00 0.00 0.00 2.87
416 440 5.775701 GTGGAGGTATGCTTAGATCTTCCTA 59.224 44.000 0.00 0.00 0.00 2.94
421 445 8.268878 AGGTATGCTTAGATCTTCCTATGTTT 57.731 34.615 0.00 0.00 0.00 2.83
442 466 2.879907 GCCGGTAGCGTAGTCACA 59.120 61.111 13.99 0.00 0.00 3.58
443 467 1.515736 GCCGGTAGCGTAGTCACAC 60.516 63.158 13.99 0.00 0.00 3.82
445 469 1.499056 CGGTAGCGTAGTCACACGT 59.501 57.895 6.07 0.00 43.79 4.49
471 496 7.282450 TGTTCTGCGTGATCTAGTTATCTTAGA 59.718 37.037 0.00 0.00 0.00 2.10
492 517 2.178912 TCGGCTTTGTAAGAGGGTTG 57.821 50.000 0.00 0.00 0.00 3.77
496 521 2.239400 GCTTTGTAAGAGGGTTGCCTT 58.761 47.619 0.00 0.00 0.00 4.35
505 530 2.644676 GAGGGTTGCCTTACCATCTTC 58.355 52.381 7.04 0.00 43.75 2.87
509 534 4.478686 AGGGTTGCCTTACCATCTTCTATT 59.521 41.667 0.00 0.00 40.09 1.73
515 540 6.480763 TGCCTTACCATCTTCTATTGTTCAA 58.519 36.000 0.00 0.00 0.00 2.69
544 569 7.378728 GTGTACTTTCTTTGATGGTTGCTTTAC 59.621 37.037 0.00 0.00 0.00 2.01
556 582 9.194972 TGATGGTTGCTTTACATATAAAATGGA 57.805 29.630 0.00 0.00 29.82 3.41
563 589 7.913297 TGCTTTACATATAAAATGGAGCGAAAC 59.087 33.333 0.00 0.00 29.82 2.78
565 591 7.867305 TTACATATAAAATGGAGCGAAACCA 57.133 32.000 0.00 0.00 41.83 3.67
579 605 3.872560 GAAACCATGTTTCGAGAACGT 57.127 42.857 4.16 0.00 40.69 3.99
580 606 3.795659 GAAACCATGTTTCGAGAACGTC 58.204 45.455 4.16 0.00 40.69 4.34
581 607 1.792006 ACCATGTTTCGAGAACGTCC 58.208 50.000 0.00 0.00 40.69 4.79
582 608 1.343465 ACCATGTTTCGAGAACGTCCT 59.657 47.619 0.00 0.00 40.69 3.85
583 609 1.993370 CCATGTTTCGAGAACGTCCTC 59.007 52.381 0.00 0.00 40.69 3.71
584 610 1.993370 CATGTTTCGAGAACGTCCTCC 59.007 52.381 0.00 0.00 40.69 4.30
585 611 0.039798 TGTTTCGAGAACGTCCTCCG 60.040 55.000 0.00 0.00 44.03 4.63
586 612 0.731855 GTTTCGAGAACGTCCTCCGG 60.732 60.000 0.00 0.00 42.24 5.14
587 613 0.890542 TTTCGAGAACGTCCTCCGGA 60.891 55.000 2.93 2.93 42.24 5.14
588 614 0.679002 TTCGAGAACGTCCTCCGGAT 60.679 55.000 3.57 0.00 42.24 4.18
589 615 1.064296 CGAGAACGTCCTCCGGATG 59.936 63.158 3.57 1.17 43.80 3.51
590 616 1.227002 GAGAACGTCCTCCGGATGC 60.227 63.158 3.57 0.00 42.09 3.91
591 617 1.945354 GAGAACGTCCTCCGGATGCA 61.945 60.000 3.57 0.00 42.09 3.96
592 618 1.144057 GAACGTCCTCCGGATGCAT 59.856 57.895 3.57 0.00 42.09 3.96
593 619 1.153369 AACGTCCTCCGGATGCATG 60.153 57.895 3.57 0.00 42.09 4.06
594 620 1.899437 AACGTCCTCCGGATGCATGT 61.899 55.000 3.57 0.00 42.09 3.21
595 621 1.153369 CGTCCTCCGGATGCATGTT 60.153 57.895 3.57 0.00 32.73 2.71
596 622 1.154205 CGTCCTCCGGATGCATGTTC 61.154 60.000 3.57 0.00 32.73 3.18
597 623 0.107703 GTCCTCCGGATGCATGTTCA 60.108 55.000 3.57 0.00 32.73 3.18
598 624 0.839277 TCCTCCGGATGCATGTTCAT 59.161 50.000 3.57 0.00 0.00 2.57
599 625 1.212688 TCCTCCGGATGCATGTTCATT 59.787 47.619 3.57 0.00 0.00 2.57
600 626 2.026641 CCTCCGGATGCATGTTCATTT 58.973 47.619 3.57 0.00 0.00 2.32
601 627 2.033801 CCTCCGGATGCATGTTCATTTC 59.966 50.000 3.57 0.00 0.00 2.17
602 628 2.947652 CTCCGGATGCATGTTCATTTCT 59.052 45.455 3.57 0.00 0.00 2.52
603 629 3.355378 TCCGGATGCATGTTCATTTCTT 58.645 40.909 2.46 0.00 0.00 2.52
604 630 3.763360 TCCGGATGCATGTTCATTTCTTT 59.237 39.130 2.46 0.00 0.00 2.52
605 631 4.220382 TCCGGATGCATGTTCATTTCTTTT 59.780 37.500 2.46 0.00 0.00 2.27
606 632 4.931002 CCGGATGCATGTTCATTTCTTTTT 59.069 37.500 2.46 0.00 0.00 1.94
607 633 5.163933 CCGGATGCATGTTCATTTCTTTTTG 60.164 40.000 2.46 0.00 0.00 2.44
608 634 5.624292 GGATGCATGTTCATTTCTTTTTGC 58.376 37.500 2.46 0.00 0.00 3.68
609 635 4.712191 TGCATGTTCATTTCTTTTTGCG 57.288 36.364 0.00 0.00 0.00 4.85
610 636 3.493877 TGCATGTTCATTTCTTTTTGCGG 59.506 39.130 0.00 0.00 0.00 5.69
611 637 3.120580 GCATGTTCATTTCTTTTTGCGGG 60.121 43.478 0.00 0.00 0.00 6.13
612 638 3.104843 TGTTCATTTCTTTTTGCGGGG 57.895 42.857 0.00 0.00 0.00 5.73
613 639 2.432510 TGTTCATTTCTTTTTGCGGGGT 59.567 40.909 0.00 0.00 0.00 4.95
614 640 3.118592 TGTTCATTTCTTTTTGCGGGGTT 60.119 39.130 0.00 0.00 0.00 4.11
615 641 3.828875 TCATTTCTTTTTGCGGGGTTT 57.171 38.095 0.00 0.00 0.00 3.27
616 642 3.462021 TCATTTCTTTTTGCGGGGTTTG 58.538 40.909 0.00 0.00 0.00 2.93
617 643 2.317530 TTTCTTTTTGCGGGGTTTGG 57.682 45.000 0.00 0.00 0.00 3.28
618 644 0.466124 TTCTTTTTGCGGGGTTTGGG 59.534 50.000 0.00 0.00 0.00 4.12
619 645 0.688087 TCTTTTTGCGGGGTTTGGGT 60.688 50.000 0.00 0.00 0.00 4.51
620 646 0.531753 CTTTTTGCGGGGTTTGGGTG 60.532 55.000 0.00 0.00 0.00 4.61
621 647 1.265454 TTTTTGCGGGGTTTGGGTGT 61.265 50.000 0.00 0.00 0.00 4.16
622 648 0.396695 TTTTGCGGGGTTTGGGTGTA 60.397 50.000 0.00 0.00 0.00 2.90
623 649 0.178958 TTTGCGGGGTTTGGGTGTAT 60.179 50.000 0.00 0.00 0.00 2.29
624 650 0.896019 TTGCGGGGTTTGGGTGTATG 60.896 55.000 0.00 0.00 0.00 2.39
625 651 1.303806 GCGGGGTTTGGGTGTATGT 60.304 57.895 0.00 0.00 0.00 2.29
626 652 1.591504 GCGGGGTTTGGGTGTATGTG 61.592 60.000 0.00 0.00 0.00 3.21
627 653 1.591504 CGGGGTTTGGGTGTATGTGC 61.592 60.000 0.00 0.00 0.00 4.57
628 654 0.251608 GGGGTTTGGGTGTATGTGCT 60.252 55.000 0.00 0.00 0.00 4.40
629 655 1.627864 GGGTTTGGGTGTATGTGCTT 58.372 50.000 0.00 0.00 0.00 3.91
630 656 2.555670 GGGGTTTGGGTGTATGTGCTTA 60.556 50.000 0.00 0.00 0.00 3.09
631 657 3.158676 GGGTTTGGGTGTATGTGCTTAA 58.841 45.455 0.00 0.00 0.00 1.85
632 658 3.057104 GGGTTTGGGTGTATGTGCTTAAC 60.057 47.826 0.00 0.00 0.00 2.01
633 659 3.057104 GGTTTGGGTGTATGTGCTTAACC 60.057 47.826 0.00 0.00 0.00 2.85
634 660 2.102070 TGGGTGTATGTGCTTAACCG 57.898 50.000 0.00 0.00 0.00 4.44
635 661 1.348366 TGGGTGTATGTGCTTAACCGT 59.652 47.619 0.00 0.00 0.00 4.83
636 662 1.735571 GGGTGTATGTGCTTAACCGTG 59.264 52.381 0.00 0.00 0.00 4.94
637 663 1.735571 GGTGTATGTGCTTAACCGTGG 59.264 52.381 0.00 0.00 0.00 4.94
638 664 2.613474 GGTGTATGTGCTTAACCGTGGA 60.613 50.000 0.00 0.00 0.00 4.02
639 665 3.267483 GTGTATGTGCTTAACCGTGGAT 58.733 45.455 0.00 0.00 0.00 3.41
640 666 3.308866 GTGTATGTGCTTAACCGTGGATC 59.691 47.826 0.00 0.00 0.00 3.36
641 667 2.779755 ATGTGCTTAACCGTGGATCA 57.220 45.000 0.00 0.00 0.00 2.92
642 668 2.552599 TGTGCTTAACCGTGGATCAA 57.447 45.000 0.00 0.00 0.00 2.57
643 669 2.422597 TGTGCTTAACCGTGGATCAAG 58.577 47.619 0.00 0.00 0.00 3.02
644 670 2.224426 TGTGCTTAACCGTGGATCAAGT 60.224 45.455 0.00 0.00 0.00 3.16
645 671 2.159627 GTGCTTAACCGTGGATCAAGTG 59.840 50.000 0.00 0.00 0.00 3.16
646 672 1.737793 GCTTAACCGTGGATCAAGTGG 59.262 52.381 0.00 0.00 0.00 4.00
647 673 2.874457 GCTTAACCGTGGATCAAGTGGT 60.874 50.000 0.00 0.00 33.45 4.16
648 674 2.754946 TAACCGTGGATCAAGTGGTC 57.245 50.000 0.00 0.00 31.17 4.02
649 675 0.762418 AACCGTGGATCAAGTGGTCA 59.238 50.000 0.00 0.00 31.17 4.02
650 676 0.762418 ACCGTGGATCAAGTGGTCAA 59.238 50.000 0.00 0.00 0.00 3.18
651 677 1.142060 ACCGTGGATCAAGTGGTCAAA 59.858 47.619 0.00 0.00 0.00 2.69
652 678 2.226330 CCGTGGATCAAGTGGTCAAAA 58.774 47.619 0.00 0.00 0.00 2.44
653 679 2.031157 CCGTGGATCAAGTGGTCAAAAC 60.031 50.000 0.00 0.00 0.00 2.43
654 680 2.616376 CGTGGATCAAGTGGTCAAAACA 59.384 45.455 0.00 0.00 0.00 2.83
655 681 3.253188 CGTGGATCAAGTGGTCAAAACAT 59.747 43.478 0.00 0.00 0.00 2.71
656 682 4.549458 GTGGATCAAGTGGTCAAAACATG 58.451 43.478 0.00 0.00 0.00 3.21
657 683 4.037923 GTGGATCAAGTGGTCAAAACATGT 59.962 41.667 0.00 0.00 0.00 3.21
658 684 5.240623 GTGGATCAAGTGGTCAAAACATGTA 59.759 40.000 0.00 0.00 0.00 2.29
659 685 5.240623 TGGATCAAGTGGTCAAAACATGTAC 59.759 40.000 0.00 0.00 0.00 2.90
660 686 5.473504 GGATCAAGTGGTCAAAACATGTACT 59.526 40.000 0.00 0.00 0.00 2.73
661 687 6.348540 GGATCAAGTGGTCAAAACATGTACTC 60.349 42.308 0.00 0.00 0.00 2.59
662 688 4.819630 TCAAGTGGTCAAAACATGTACTCC 59.180 41.667 0.00 0.00 0.00 3.85
663 689 4.706842 AGTGGTCAAAACATGTACTCCT 57.293 40.909 0.00 0.00 0.00 3.69
664 690 5.818678 AGTGGTCAAAACATGTACTCCTA 57.181 39.130 0.00 0.00 0.00 2.94
665 691 5.548406 AGTGGTCAAAACATGTACTCCTAC 58.452 41.667 0.00 0.00 0.00 3.18
666 692 5.307196 AGTGGTCAAAACATGTACTCCTACT 59.693 40.000 0.00 0.00 0.00 2.57
667 693 6.495872 AGTGGTCAAAACATGTACTCCTACTA 59.504 38.462 0.00 0.00 0.00 1.82
668 694 6.589139 GTGGTCAAAACATGTACTCCTACTAC 59.411 42.308 0.00 0.00 0.00 2.73
669 695 6.495872 TGGTCAAAACATGTACTCCTACTACT 59.504 38.462 0.00 0.00 0.00 2.57
670 696 7.034397 GGTCAAAACATGTACTCCTACTACTC 58.966 42.308 0.00 0.00 0.00 2.59
671 697 7.093858 GGTCAAAACATGTACTCCTACTACTCT 60.094 40.741 0.00 0.00 0.00 3.24
672 698 8.954350 GTCAAAACATGTACTCCTACTACTCTA 58.046 37.037 0.00 0.00 0.00 2.43
673 699 9.524496 TCAAAACATGTACTCCTACTACTCTAA 57.476 33.333 0.00 0.00 0.00 2.10
674 700 9.570488 CAAAACATGTACTCCTACTACTCTAAC 57.430 37.037 0.00 0.00 0.00 2.34
675 701 9.531158 AAAACATGTACTCCTACTACTCTAACT 57.469 33.333 0.00 0.00 0.00 2.24
676 702 9.531158 AAACATGTACTCCTACTACTCTAACTT 57.469 33.333 0.00 0.00 0.00 2.66
735 761 1.354337 CCGACACTGTTCCTGCATCG 61.354 60.000 0.00 0.00 0.00 3.84
748 774 1.057361 GCATCGAGCGACAAACGTC 59.943 57.895 0.00 0.00 44.60 4.34
750 776 1.891178 CATCGAGCGACAAACGTCTA 58.109 50.000 0.00 0.00 44.60 2.59
756 782 1.002033 AGCGACAAACGTCTAACGACT 60.002 47.619 6.48 3.93 46.05 4.18
861 887 1.668151 GTCACGTCCCTGGAACTGC 60.668 63.158 0.00 0.00 0.00 4.40
879 905 2.124860 AGGCCGGAAACATACGCC 60.125 61.111 5.05 0.00 0.00 5.68
880 906 2.437002 GGCCGGAAACATACGCCA 60.437 61.111 5.05 0.00 0.00 5.69
881 907 1.822186 GGCCGGAAACATACGCCAT 60.822 57.895 5.05 0.00 0.00 4.40
882 908 1.647084 GCCGGAAACATACGCCATC 59.353 57.895 5.05 0.00 0.00 3.51
883 909 1.931551 CCGGAAACATACGCCATCG 59.068 57.895 0.00 0.00 42.43 3.84
884 910 1.275657 CGGAAACATACGCCATCGC 59.724 57.895 0.00 0.00 39.84 4.58
887 913 1.003866 GGAAACATACGCCATCGCTTC 60.004 52.381 0.00 0.00 39.84 3.86
888 914 1.003866 GAAACATACGCCATCGCTTCC 60.004 52.381 0.00 0.00 39.84 3.46
889 915 1.151777 AACATACGCCATCGCTTCCG 61.152 55.000 0.00 0.00 39.84 4.30
903 1134 1.772182 CTTCCGAATTCCGATCCTCG 58.228 55.000 0.00 0.00 41.76 4.63
1057 1289 2.038329 CGACCTCCACCCCCACTA 59.962 66.667 0.00 0.00 0.00 2.74
1069 1301 1.605058 CCCCACTACACTCCACTCCG 61.605 65.000 0.00 0.00 0.00 4.63
1070 1302 1.215647 CCACTACACTCCACTCCGC 59.784 63.158 0.00 0.00 0.00 5.54
1138 1385 2.202810 GGCACTCAGGCGAGCTAC 60.203 66.667 6.32 0.00 43.66 3.58
1571 1834 4.445545 GCGAACAAGAAGGCCGCG 62.446 66.667 0.00 0.00 36.53 6.46
1667 1947 2.190756 GCACCCAGCTCGTAGTAGT 58.809 57.895 0.00 0.00 41.15 2.73
1668 1948 0.531200 GCACCCAGCTCGTAGTAGTT 59.469 55.000 0.00 0.00 41.15 2.24
1669 1949 1.067071 GCACCCAGCTCGTAGTAGTTT 60.067 52.381 0.00 0.00 41.15 2.66
1696 1979 1.092348 ACACTGCATCGTACGCTCTA 58.908 50.000 11.24 0.00 0.00 2.43
1821 2108 8.074972 CGTAGTACAATCTAGAGTACATTTCCC 58.925 40.741 19.11 4.91 42.26 3.97
1827 2114 2.789409 AGAGTACATTTCCCCTGCAC 57.211 50.000 0.00 0.00 0.00 4.57
1963 2262 3.000041 CACAGAGTTTTAGCGGCACATA 59.000 45.455 1.45 0.00 0.00 2.29
1964 2263 3.062639 CACAGAGTTTTAGCGGCACATAG 59.937 47.826 1.45 0.00 0.00 2.23
2003 2303 3.482436 TCCGGTTTTAGTGACAGCAAAT 58.518 40.909 0.00 0.00 0.00 2.32
2078 2382 1.911293 GCGAGCGCTCATTCACCAAA 61.911 55.000 34.69 0.00 38.26 3.28
2142 2446 2.297033 TGGTGATTTGCCTTTCAGCTTC 59.703 45.455 9.50 0.00 40.22 3.86
2153 2461 1.795768 TTCAGCTTCACGTCCATCAC 58.204 50.000 0.00 0.00 0.00 3.06
2160 2468 1.141019 CACGTCCATCACCTACCCG 59.859 63.158 0.00 0.00 0.00 5.28
2161 2469 2.106332 CGTCCATCACCTACCCGC 59.894 66.667 0.00 0.00 0.00 6.13
2179 2487 1.162800 GCGGTGAAGATGGATCTGCC 61.163 60.000 0.00 0.00 37.19 4.85
2305 2613 1.620822 CCTGCTGCTTGTTACCCTTT 58.379 50.000 0.00 0.00 0.00 3.11
2383 2697 1.863662 GCTCTTGGTCTGGTCGTCGA 61.864 60.000 0.00 0.00 0.00 4.20
2430 2747 7.860918 TGTAGATGTAGTAGTAGTGGTCAAG 57.139 40.000 0.00 0.00 0.00 3.02
2454 2773 6.519382 GGTAACTCCTCTCTAGTCTCTAGTC 58.481 48.000 4.13 0.00 0.00 2.59
2455 2774 6.325804 GGTAACTCCTCTCTAGTCTCTAGTCT 59.674 46.154 4.13 0.00 0.00 3.24
2456 2775 6.481434 AACTCCTCTCTAGTCTCTAGTCTC 57.519 45.833 4.13 0.00 0.00 3.36
2457 2776 5.778542 ACTCCTCTCTAGTCTCTAGTCTCT 58.221 45.833 4.13 0.00 0.00 3.10
2458 2777 6.919158 ACTCCTCTCTAGTCTCTAGTCTCTA 58.081 44.000 4.13 0.00 0.00 2.43
2459 2778 7.005296 ACTCCTCTCTAGTCTCTAGTCTCTAG 58.995 46.154 4.13 9.70 33.41 2.43
2460 2779 6.919158 TCCTCTCTAGTCTCTAGTCTCTAGT 58.081 44.000 13.18 0.00 33.72 2.57
2461 2780 7.002879 TCCTCTCTAGTCTCTAGTCTCTAGTC 58.997 46.154 13.18 0.00 33.72 2.59
2462 2781 7.005296 CCTCTCTAGTCTCTAGTCTCTAGTCT 58.995 46.154 13.18 4.77 33.72 3.24
2463 2782 7.175293 CCTCTCTAGTCTCTAGTCTCTAGTCTC 59.825 48.148 13.18 0.00 33.72 3.36
2464 2783 7.813331 TCTCTAGTCTCTAGTCTCTAGTCTCT 58.187 42.308 13.18 4.25 33.72 3.10
2465 2784 8.942033 TCTCTAGTCTCTAGTCTCTAGTCTCTA 58.058 40.741 13.18 4.94 33.72 2.43
2466 2785 9.221933 CTCTAGTCTCTAGTCTCTAGTCTCTAG 57.778 44.444 13.18 15.62 33.72 2.43
2467 2786 8.721479 TCTAGTCTCTAGTCTCTAGTCTCTAGT 58.279 40.741 17.98 3.15 33.72 2.57
2472 2791 8.162085 TCTCTAGTCTCTAGTCTCTAGTCTAGG 58.838 44.444 7.05 0.00 35.48 3.02
2520 2842 1.478105 GAAGGGGCCAGTTAAATGCAG 59.522 52.381 4.39 0.00 0.00 4.41
2557 2894 5.648178 TTTTCTCACATGGTGATGGATTG 57.352 39.130 0.00 0.00 41.94 2.67
2558 2895 3.286329 TCTCACATGGTGATGGATTGG 57.714 47.619 0.00 0.00 41.94 3.16
2593 2945 3.009723 TGTGGTAGTAGTAGTACGTGCC 58.990 50.000 0.00 6.68 33.97 5.01
2722 3083 1.202915 TGAGTTCAATGAAGCCAGGCA 60.203 47.619 15.80 0.00 0.00 4.75
2894 3271 7.605410 GGAGATTCAAAATACTCCAACGTAA 57.395 36.000 0.00 0.00 45.53 3.18
2895 3272 7.685594 GGAGATTCAAAATACTCCAACGTAAG 58.314 38.462 0.00 0.00 45.53 2.34
2896 3273 7.333672 GGAGATTCAAAATACTCCAACGTAAGT 59.666 37.037 0.00 0.00 45.57 2.24
2926 3303 3.018149 GTGGAGTAGAGTGGAGTGGTAG 58.982 54.545 0.00 0.00 0.00 3.18
2977 3354 3.368323 CCAAAGCTGGCGGATTTGTTAAT 60.368 43.478 29.04 0.00 46.26 1.40
2982 3359 3.380320 GCTGGCGGATTTGTTAATAACCT 59.620 43.478 0.00 0.00 0.00 3.50
3087 3492 0.735978 CGATCACCAGCACAGCGTTA 60.736 55.000 0.00 0.00 0.00 3.18
3118 3523 2.558795 GAGGTGACTTAGCTGTCTGTCA 59.441 50.000 0.00 2.61 44.43 3.58
3122 3527 4.560128 GTGACTTAGCTGTCTGTCAATCA 58.440 43.478 12.21 0.00 40.47 2.57
3132 3537 4.166011 GTCAATCACTGCCGCGCC 62.166 66.667 0.00 0.00 0.00 6.53
3254 3676 3.234353 GGGGGAAATGGAAATGGAGATC 58.766 50.000 0.00 0.00 0.00 2.75
3366 3798 1.833630 ACCGCTCTGGATGAATTCTGA 59.166 47.619 7.05 0.00 42.00 3.27
3401 3841 2.242043 CAGCCAACTGGTCCAAAAGAT 58.758 47.619 0.00 0.00 40.48 2.40
3402 3842 2.029649 CAGCCAACTGGTCCAAAAGATG 60.030 50.000 0.00 0.00 40.48 2.90
3403 3843 1.963515 GCCAACTGGTCCAAAAGATGT 59.036 47.619 0.00 0.00 37.57 3.06
3404 3844 3.153919 GCCAACTGGTCCAAAAGATGTA 58.846 45.455 0.00 0.00 37.57 2.29
3405 3845 3.763897 GCCAACTGGTCCAAAAGATGTAT 59.236 43.478 0.00 0.00 37.57 2.29
3406 3846 4.380867 GCCAACTGGTCCAAAAGATGTATG 60.381 45.833 0.00 0.00 37.57 2.39
3407 3847 4.158394 CCAACTGGTCCAAAAGATGTATGG 59.842 45.833 0.00 0.00 35.49 2.74
3408 3848 3.356290 ACTGGTCCAAAAGATGTATGGC 58.644 45.455 0.00 0.00 34.13 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.772886 ACTAGACCTTTTTGTCACTGGT 57.227 40.909 0.00 0.00 37.73 4.00
2 3 4.684703 CGTACTAGACCTTTTTGTCACTGG 59.315 45.833 0.00 0.00 37.73 4.00
3 4 5.526115 TCGTACTAGACCTTTTTGTCACTG 58.474 41.667 0.00 0.00 37.73 3.66
4 5 5.779529 TCGTACTAGACCTTTTTGTCACT 57.220 39.130 0.00 0.00 37.73 3.41
5 6 6.253083 GCTATCGTACTAGACCTTTTTGTCAC 59.747 42.308 0.00 0.00 37.73 3.67
6 7 6.071784 TGCTATCGTACTAGACCTTTTTGTCA 60.072 38.462 0.00 0.00 37.73 3.58
7 8 6.327934 TGCTATCGTACTAGACCTTTTTGTC 58.672 40.000 0.00 0.00 35.43 3.18
8 9 6.276832 TGCTATCGTACTAGACCTTTTTGT 57.723 37.500 0.00 0.00 0.00 2.83
9 10 5.232414 GCTGCTATCGTACTAGACCTTTTTG 59.768 44.000 0.00 0.00 0.00 2.44
10 11 5.349809 GCTGCTATCGTACTAGACCTTTTT 58.650 41.667 0.00 0.00 0.00 1.94
11 12 4.497674 CGCTGCTATCGTACTAGACCTTTT 60.498 45.833 0.00 0.00 0.00 2.27
12 13 3.003482 CGCTGCTATCGTACTAGACCTTT 59.997 47.826 0.00 0.00 0.00 3.11
13 14 2.548904 CGCTGCTATCGTACTAGACCTT 59.451 50.000 0.00 0.00 0.00 3.50
14 15 2.144730 CGCTGCTATCGTACTAGACCT 58.855 52.381 0.00 0.00 0.00 3.85
15 16 2.141517 TCGCTGCTATCGTACTAGACC 58.858 52.381 0.00 0.00 0.00 3.85
16 17 3.425094 CCATCGCTGCTATCGTACTAGAC 60.425 52.174 0.00 0.00 0.00 2.59
17 18 2.742589 CCATCGCTGCTATCGTACTAGA 59.257 50.000 0.00 0.00 0.00 2.43
18 19 2.484651 ACCATCGCTGCTATCGTACTAG 59.515 50.000 0.00 0.00 0.00 2.57
19 20 2.225727 CACCATCGCTGCTATCGTACTA 59.774 50.000 0.00 0.00 0.00 1.82
20 21 1.001268 CACCATCGCTGCTATCGTACT 60.001 52.381 0.00 0.00 0.00 2.73
21 22 1.409412 CACCATCGCTGCTATCGTAC 58.591 55.000 0.00 0.00 0.00 3.67
22 23 0.313987 CCACCATCGCTGCTATCGTA 59.686 55.000 0.00 0.00 0.00 3.43
23 24 1.068083 CCACCATCGCTGCTATCGT 59.932 57.895 0.00 0.00 0.00 3.73
24 25 2.313172 GCCACCATCGCTGCTATCG 61.313 63.158 0.00 0.00 0.00 2.92
25 26 0.948141 GAGCCACCATCGCTGCTATC 60.948 60.000 0.00 0.00 36.48 2.08
26 27 1.070445 GAGCCACCATCGCTGCTAT 59.930 57.895 0.00 0.00 36.48 2.97
27 28 2.060383 AGAGCCACCATCGCTGCTA 61.060 57.895 0.00 0.00 36.48 3.49
28 29 3.397439 AGAGCCACCATCGCTGCT 61.397 61.111 0.00 0.00 36.48 4.24
29 30 3.200593 CAGAGCCACCATCGCTGC 61.201 66.667 0.00 0.00 36.48 5.25
30 31 2.302199 TAGCAGAGCCACCATCGCTG 62.302 60.000 0.00 0.00 36.48 5.18
31 32 2.060383 TAGCAGAGCCACCATCGCT 61.060 57.895 0.00 0.00 39.95 4.93
32 33 1.884926 GTAGCAGAGCCACCATCGC 60.885 63.158 0.00 0.00 0.00 4.58
33 34 0.529337 CAGTAGCAGAGCCACCATCG 60.529 60.000 0.00 0.00 0.00 3.84
34 35 0.179062 CCAGTAGCAGAGCCACCATC 60.179 60.000 0.00 0.00 0.00 3.51
35 36 1.630126 CCCAGTAGCAGAGCCACCAT 61.630 60.000 0.00 0.00 0.00 3.55
46 47 0.814010 CGCCCATACAACCCAGTAGC 60.814 60.000 0.00 0.00 0.00 3.58
49 50 1.298667 GTCGCCCATACAACCCAGT 59.701 57.895 0.00 0.00 0.00 4.00
51 52 2.266372 CGTCGCCCATACAACCCA 59.734 61.111 0.00 0.00 0.00 4.51
102 103 0.539051 GATCAGGGTGTCACTCCAGG 59.461 60.000 0.00 0.00 0.00 4.45
107 124 2.260639 ATCAGGATCAGGGTGTCACT 57.739 50.000 2.35 0.00 0.00 3.41
109 126 2.025981 CCAAATCAGGATCAGGGTGTCA 60.026 50.000 0.00 0.00 0.00 3.58
113 130 0.929244 CCCCAAATCAGGATCAGGGT 59.071 55.000 14.35 0.00 34.68 4.34
123 140 1.620259 GGGCCAGATCCCCAAATCA 59.380 57.895 4.39 0.00 42.36 2.57
138 155 2.741486 TAGGGCGAACAACACAGGGC 62.741 60.000 0.00 0.00 0.00 5.19
142 159 2.684001 CCTATAGGGCGAACAACACA 57.316 50.000 11.33 0.00 0.00 3.72
220 239 0.949105 GACACCCACAAAGCGTCGAT 60.949 55.000 0.00 0.00 0.00 3.59
221 240 1.593209 GACACCCACAAAGCGTCGA 60.593 57.895 0.00 0.00 0.00 4.20
232 252 1.691195 TTCAGGAAGCACGACACCCA 61.691 55.000 0.00 0.00 0.00 4.51
234 254 0.033504 TCTTCAGGAAGCACGACACC 59.966 55.000 4.15 0.00 38.28 4.16
237 257 1.618640 GCGTCTTCAGGAAGCACGAC 61.619 60.000 24.48 16.78 46.12 4.34
238 258 1.372997 GCGTCTTCAGGAAGCACGA 60.373 57.895 24.48 2.66 46.12 4.35
242 262 1.448717 GGAGGCGTCTTCAGGAAGC 60.449 63.158 6.34 0.00 46.13 3.86
256 276 2.683867 ACGTAGAGAAGAATCACGGAGG 59.316 50.000 0.00 0.00 36.95 4.30
258 278 3.079578 ACACGTAGAGAAGAATCACGGA 58.920 45.455 0.00 0.00 36.95 4.69
259 279 3.119955 TGACACGTAGAGAAGAATCACGG 60.120 47.826 0.00 0.00 36.95 4.94
264 284 3.511934 AGCCTTGACACGTAGAGAAGAAT 59.488 43.478 0.00 0.00 0.00 2.40
265 285 2.891580 AGCCTTGACACGTAGAGAAGAA 59.108 45.455 0.00 0.00 0.00 2.52
266 286 2.488545 GAGCCTTGACACGTAGAGAAGA 59.511 50.000 0.00 0.00 0.00 2.87
267 287 2.416162 GGAGCCTTGACACGTAGAGAAG 60.416 54.545 0.00 0.00 0.00 2.85
307 331 1.871039 CACCGTTGTCGAGTCCAAAAT 59.129 47.619 0.00 0.00 39.71 1.82
308 332 1.134759 TCACCGTTGTCGAGTCCAAAA 60.135 47.619 0.00 0.00 39.71 2.44
310 334 0.249155 GTCACCGTTGTCGAGTCCAA 60.249 55.000 0.00 0.00 39.71 3.53
334 358 2.938956 CCAAGAGGGAGAACAACACT 57.061 50.000 0.00 0.00 40.01 3.55
421 445 0.317799 TGACTACGCTACCGGCAAAA 59.682 50.000 0.00 0.00 41.91 2.44
426 450 1.226211 CGTGTGACTACGCTACCGG 60.226 63.158 0.00 0.00 37.24 5.28
442 466 1.540267 ACTAGATCACGCAGAACACGT 59.460 47.619 0.00 0.00 46.42 4.49
443 467 2.264109 ACTAGATCACGCAGAACACG 57.736 50.000 0.00 0.00 0.00 4.49
445 469 5.836821 AGATAACTAGATCACGCAGAACA 57.163 39.130 0.00 0.00 0.00 3.18
459 483 9.745880 CTTACAAAGCCGATTCTAAGATAACTA 57.254 33.333 0.00 0.00 0.00 2.24
471 496 3.081804 CAACCCTCTTACAAAGCCGATT 58.918 45.455 0.00 0.00 0.00 3.34
492 517 6.183360 GGTTGAACAATAGAAGATGGTAAGGC 60.183 42.308 0.00 0.00 0.00 4.35
496 521 5.872617 CACGGTTGAACAATAGAAGATGGTA 59.127 40.000 0.00 0.00 0.00 3.25
505 530 6.780706 AGAAAGTACACGGTTGAACAATAG 57.219 37.500 0.00 0.00 0.00 1.73
509 534 4.936411 TCAAAGAAAGTACACGGTTGAACA 59.064 37.500 0.00 0.00 0.00 3.18
515 540 4.081322 ACCATCAAAGAAAGTACACGGT 57.919 40.909 0.00 0.00 0.00 4.83
544 569 6.738114 ACATGGTTTCGCTCCATTTTATATG 58.262 36.000 0.00 0.00 42.92 1.78
552 578 1.468520 CGAAACATGGTTTCGCTCCAT 59.531 47.619 25.11 0.00 45.29 3.41
563 589 1.993370 GAGGACGTTCTCGAAACATGG 59.007 52.381 8.41 0.00 40.62 3.66
565 591 1.402456 CGGAGGACGTTCTCGAAACAT 60.402 52.381 17.65 0.00 40.62 2.71
581 607 2.947652 AGAAATGAACATGCATCCGGAG 59.052 45.455 11.34 3.17 0.00 4.63
582 608 3.003394 AGAAATGAACATGCATCCGGA 57.997 42.857 6.61 6.61 0.00 5.14
583 609 3.788333 AAGAAATGAACATGCATCCGG 57.212 42.857 0.00 0.00 0.00 5.14
584 610 5.669357 GCAAAAAGAAATGAACATGCATCCG 60.669 40.000 0.00 0.00 33.00 4.18
585 611 5.624292 GCAAAAAGAAATGAACATGCATCC 58.376 37.500 0.00 0.00 33.00 3.51
586 612 5.310489 CGCAAAAAGAAATGAACATGCATC 58.690 37.500 0.00 0.00 33.00 3.91
587 613 4.152759 CCGCAAAAAGAAATGAACATGCAT 59.847 37.500 0.00 0.00 33.00 3.96
588 614 3.493877 CCGCAAAAAGAAATGAACATGCA 59.506 39.130 0.00 0.00 33.00 3.96
589 615 3.120580 CCCGCAAAAAGAAATGAACATGC 60.121 43.478 0.00 0.00 0.00 4.06
590 616 3.432933 CCCCGCAAAAAGAAATGAACATG 59.567 43.478 0.00 0.00 0.00 3.21
591 617 3.070878 ACCCCGCAAAAAGAAATGAACAT 59.929 39.130 0.00 0.00 0.00 2.71
592 618 2.432510 ACCCCGCAAAAAGAAATGAACA 59.567 40.909 0.00 0.00 0.00 3.18
593 619 3.106242 ACCCCGCAAAAAGAAATGAAC 57.894 42.857 0.00 0.00 0.00 3.18
594 620 3.828875 AACCCCGCAAAAAGAAATGAA 57.171 38.095 0.00 0.00 0.00 2.57
595 621 3.462021 CAAACCCCGCAAAAAGAAATGA 58.538 40.909 0.00 0.00 0.00 2.57
596 622 2.547634 CCAAACCCCGCAAAAAGAAATG 59.452 45.455 0.00 0.00 0.00 2.32
597 623 2.486370 CCCAAACCCCGCAAAAAGAAAT 60.486 45.455 0.00 0.00 0.00 2.17
598 624 1.134371 CCCAAACCCCGCAAAAAGAAA 60.134 47.619 0.00 0.00 0.00 2.52
599 625 0.466124 CCCAAACCCCGCAAAAAGAA 59.534 50.000 0.00 0.00 0.00 2.52
600 626 0.688087 ACCCAAACCCCGCAAAAAGA 60.688 50.000 0.00 0.00 0.00 2.52
601 627 0.531753 CACCCAAACCCCGCAAAAAG 60.532 55.000 0.00 0.00 0.00 2.27
602 628 1.265454 ACACCCAAACCCCGCAAAAA 61.265 50.000 0.00 0.00 0.00 1.94
603 629 0.396695 TACACCCAAACCCCGCAAAA 60.397 50.000 0.00 0.00 0.00 2.44
604 630 0.178958 ATACACCCAAACCCCGCAAA 60.179 50.000 0.00 0.00 0.00 3.68
605 631 0.896019 CATACACCCAAACCCCGCAA 60.896 55.000 0.00 0.00 0.00 4.85
606 632 1.303724 CATACACCCAAACCCCGCA 60.304 57.895 0.00 0.00 0.00 5.69
607 633 1.303806 ACATACACCCAAACCCCGC 60.304 57.895 0.00 0.00 0.00 6.13
608 634 1.591504 GCACATACACCCAAACCCCG 61.592 60.000 0.00 0.00 0.00 5.73
609 635 0.251608 AGCACATACACCCAAACCCC 60.252 55.000 0.00 0.00 0.00 4.95
610 636 1.627864 AAGCACATACACCCAAACCC 58.372 50.000 0.00 0.00 0.00 4.11
611 637 3.057104 GGTTAAGCACATACACCCAAACC 60.057 47.826 0.00 0.00 0.00 3.27
612 638 3.365565 CGGTTAAGCACATACACCCAAAC 60.366 47.826 5.38 0.00 0.00 2.93
613 639 2.814919 CGGTTAAGCACATACACCCAAA 59.185 45.455 5.38 0.00 0.00 3.28
614 640 2.224572 ACGGTTAAGCACATACACCCAA 60.225 45.455 5.38 0.00 0.00 4.12
615 641 1.348366 ACGGTTAAGCACATACACCCA 59.652 47.619 5.38 0.00 0.00 4.51
616 642 1.735571 CACGGTTAAGCACATACACCC 59.264 52.381 5.38 0.00 0.00 4.61
617 643 1.735571 CCACGGTTAAGCACATACACC 59.264 52.381 5.38 0.00 0.00 4.16
618 644 2.690786 TCCACGGTTAAGCACATACAC 58.309 47.619 5.38 0.00 0.00 2.90
619 645 3.055747 TGATCCACGGTTAAGCACATACA 60.056 43.478 5.38 0.00 0.00 2.29
620 646 3.527533 TGATCCACGGTTAAGCACATAC 58.472 45.455 5.38 0.00 0.00 2.39
621 647 3.897141 TGATCCACGGTTAAGCACATA 57.103 42.857 5.38 0.00 0.00 2.29
622 648 2.779755 TGATCCACGGTTAAGCACAT 57.220 45.000 5.38 0.00 0.00 3.21
623 649 2.224426 ACTTGATCCACGGTTAAGCACA 60.224 45.455 5.38 0.00 0.00 4.57
624 650 2.159627 CACTTGATCCACGGTTAAGCAC 59.840 50.000 5.38 0.00 0.00 4.40
625 651 2.422597 CACTTGATCCACGGTTAAGCA 58.577 47.619 5.38 0.00 0.00 3.91
626 652 1.737793 CCACTTGATCCACGGTTAAGC 59.262 52.381 0.00 0.00 0.00 3.09
627 653 3.000727 GACCACTTGATCCACGGTTAAG 58.999 50.000 0.00 0.00 0.00 1.85
628 654 2.369203 TGACCACTTGATCCACGGTTAA 59.631 45.455 0.00 0.00 0.00 2.01
629 655 1.972075 TGACCACTTGATCCACGGTTA 59.028 47.619 0.00 0.00 0.00 2.85
630 656 0.762418 TGACCACTTGATCCACGGTT 59.238 50.000 0.00 0.00 0.00 4.44
631 657 0.762418 TTGACCACTTGATCCACGGT 59.238 50.000 0.00 0.00 0.00 4.83
632 658 1.890876 TTTGACCACTTGATCCACGG 58.109 50.000 0.00 0.00 0.00 4.94
633 659 2.616376 TGTTTTGACCACTTGATCCACG 59.384 45.455 0.00 0.00 0.00 4.94
634 660 4.037923 ACATGTTTTGACCACTTGATCCAC 59.962 41.667 0.00 0.00 0.00 4.02
635 661 4.214310 ACATGTTTTGACCACTTGATCCA 58.786 39.130 0.00 0.00 0.00 3.41
636 662 4.853924 ACATGTTTTGACCACTTGATCC 57.146 40.909 0.00 0.00 0.00 3.36
637 663 6.348540 GGAGTACATGTTTTGACCACTTGATC 60.349 42.308 2.30 0.00 0.00 2.92
638 664 5.473504 GGAGTACATGTTTTGACCACTTGAT 59.526 40.000 2.30 0.00 0.00 2.57
639 665 4.819630 GGAGTACATGTTTTGACCACTTGA 59.180 41.667 2.30 0.00 0.00 3.02
640 666 4.821805 AGGAGTACATGTTTTGACCACTTG 59.178 41.667 2.30 0.00 0.00 3.16
641 667 5.048846 AGGAGTACATGTTTTGACCACTT 57.951 39.130 2.30 0.00 0.00 3.16
642 668 4.706842 AGGAGTACATGTTTTGACCACT 57.293 40.909 2.30 0.00 0.00 4.00
643 669 5.548406 AGTAGGAGTACATGTTTTGACCAC 58.452 41.667 2.30 0.00 0.00 4.16
644 670 5.818678 AGTAGGAGTACATGTTTTGACCA 57.181 39.130 2.30 0.00 0.00 4.02
645 671 6.932947 AGTAGTAGGAGTACATGTTTTGACC 58.067 40.000 2.30 1.45 0.00 4.02
646 672 7.828712 AGAGTAGTAGGAGTACATGTTTTGAC 58.171 38.462 2.30 0.00 0.00 3.18
647 673 9.524496 TTAGAGTAGTAGGAGTACATGTTTTGA 57.476 33.333 2.30 0.00 0.00 2.69
648 674 9.570488 GTTAGAGTAGTAGGAGTACATGTTTTG 57.430 37.037 2.30 0.00 0.00 2.44
649 675 9.531158 AGTTAGAGTAGTAGGAGTACATGTTTT 57.469 33.333 2.30 0.00 0.00 2.43
650 676 9.531158 AAGTTAGAGTAGTAGGAGTACATGTTT 57.469 33.333 2.30 0.00 0.00 2.83
676 702 9.623000 TCTGCTGTATGACTTTACTGTACTATA 57.377 33.333 0.00 0.00 0.00 1.31
677 703 8.521170 TCTGCTGTATGACTTTACTGTACTAT 57.479 34.615 0.00 0.00 0.00 2.12
678 704 7.933215 TCTGCTGTATGACTTTACTGTACTA 57.067 36.000 0.00 0.00 0.00 1.82
679 705 6.835819 TCTGCTGTATGACTTTACTGTACT 57.164 37.500 0.00 0.00 0.00 2.73
680 706 7.884816 TTTCTGCTGTATGACTTTACTGTAC 57.115 36.000 0.00 0.00 0.00 2.90
682 708 9.319143 GATATTTCTGCTGTATGACTTTACTGT 57.681 33.333 0.00 0.00 0.00 3.55
683 709 8.768955 GGATATTTCTGCTGTATGACTTTACTG 58.231 37.037 0.00 0.00 0.00 2.74
687 713 8.757982 AATGGATATTTCTGCTGTATGACTTT 57.242 30.769 0.00 0.00 0.00 2.66
697 723 6.428159 GTGTCGGATAAATGGATATTTCTGCT 59.572 38.462 0.00 0.00 37.64 4.24
748 774 3.937079 GGGGGTGTTTTATGAGTCGTTAG 59.063 47.826 0.00 0.00 0.00 2.34
750 776 2.106857 TGGGGGTGTTTTATGAGTCGTT 59.893 45.455 0.00 0.00 0.00 3.85
756 782 2.494073 GCGAAATGGGGGTGTTTTATGA 59.506 45.455 0.00 0.00 0.00 2.15
798 824 0.252197 GTACGCTTCATTGGAGGGGT 59.748 55.000 13.15 4.72 45.94 4.95
861 887 2.469516 GGCGTATGTTTCCGGCCTG 61.470 63.158 0.00 0.00 43.02 4.85
879 905 1.457303 GATCGGAATTCGGAAGCGATG 59.543 52.381 18.30 0.00 39.77 3.84
880 906 1.605712 GGATCGGAATTCGGAAGCGAT 60.606 52.381 18.30 15.96 39.77 4.58
881 907 0.249322 GGATCGGAATTCGGAAGCGA 60.249 55.000 18.30 12.14 39.77 4.93
882 908 0.249489 AGGATCGGAATTCGGAAGCG 60.249 55.000 18.30 7.20 39.77 4.68
883 909 1.503294 GAGGATCGGAATTCGGAAGC 58.497 55.000 18.30 13.27 39.77 3.86
903 1134 1.067250 GGGAGACTGATGAGCGAGC 59.933 63.158 0.00 0.00 0.00 5.03
945 1176 2.266279 GGGGCTGGGAGTTATATAGCA 58.734 52.381 0.00 0.00 36.15 3.49
1034 1265 2.030562 GGGTGGAGGTCGTGTGTG 59.969 66.667 0.00 0.00 0.00 3.82
1057 1289 1.303074 TACTCGCGGAGTGGAGTGT 60.303 57.895 17.67 2.88 43.30 3.55
1696 1979 4.207165 GGGACAATGCATACCACTATTGT 58.793 43.478 15.84 8.39 44.00 2.71
1827 2114 2.193248 GAGAAATCCGGCCCTGGG 59.807 66.667 8.86 8.86 0.00 4.45
1963 2262 2.354805 GGAAAGGAACGCAGGTGATACT 60.355 50.000 0.00 0.00 0.00 2.12
1964 2263 2.007608 GGAAAGGAACGCAGGTGATAC 58.992 52.381 0.00 0.00 0.00 2.24
2003 2303 1.406898 TCCTGAAAAATGTTGCACGCA 59.593 42.857 0.00 0.00 0.00 5.24
2113 2417 1.203162 AGGCAAATCACCACCCAATCA 60.203 47.619 0.00 0.00 0.00 2.57
2142 2446 1.141019 CGGGTAGGTGATGGACGTG 59.859 63.158 0.00 0.00 0.00 4.49
2153 2461 1.227263 CATCTTCACCGCGGGTAGG 60.227 63.158 31.76 17.23 32.11 3.18
2160 2468 1.162800 GGCAGATCCATCTTCACCGC 61.163 60.000 0.00 0.00 34.22 5.68
2161 2469 0.178767 TGGCAGATCCATCTTCACCG 59.821 55.000 0.00 0.00 40.72 4.94
2179 2487 2.372264 CTGATGGATGTTGGGTTCCTG 58.628 52.381 0.00 0.00 32.95 3.86
2182 2490 0.734889 CGCTGATGGATGTTGGGTTC 59.265 55.000 0.00 0.00 0.00 3.62
2264 2572 5.870978 AGGCAGTAAAATGAAATGCACATTC 59.129 36.000 7.04 7.04 38.63 2.67
2383 2697 0.965363 GATGCAATGGAACCACCCGT 60.965 55.000 0.00 0.00 38.00 5.28
2430 2747 6.325804 AGACTAGAGACTAGAGAGGAGTTACC 59.674 46.154 11.94 0.00 39.35 2.85
2454 2773 5.607477 CCACACCTAGACTAGAGACTAGAG 58.393 50.000 11.27 10.45 40.95 2.43
2455 2774 4.141665 GCCACACCTAGACTAGAGACTAGA 60.142 50.000 11.27 0.00 40.95 2.43
2456 2775 4.131596 GCCACACCTAGACTAGAGACTAG 58.868 52.174 11.27 8.53 39.16 2.57
2457 2776 3.781407 AGCCACACCTAGACTAGAGACTA 59.219 47.826 11.27 0.00 0.00 2.59
2458 2777 2.578940 AGCCACACCTAGACTAGAGACT 59.421 50.000 11.27 0.00 0.00 3.24
2459 2778 2.946990 GAGCCACACCTAGACTAGAGAC 59.053 54.545 11.27 0.34 0.00 3.36
2460 2779 2.847449 AGAGCCACACCTAGACTAGAGA 59.153 50.000 11.27 0.00 0.00 3.10
2461 2780 2.948979 CAGAGCCACACCTAGACTAGAG 59.051 54.545 11.27 5.81 0.00 2.43
2462 2781 2.576648 TCAGAGCCACACCTAGACTAGA 59.423 50.000 11.27 0.00 0.00 2.43
2463 2782 3.006112 TCAGAGCCACACCTAGACTAG 57.994 52.381 2.18 2.18 0.00 2.57
2464 2783 3.451402 TTCAGAGCCACACCTAGACTA 57.549 47.619 0.00 0.00 0.00 2.59
2465 2784 2.310779 TTCAGAGCCACACCTAGACT 57.689 50.000 0.00 0.00 0.00 3.24
2466 2785 2.234908 ACATTCAGAGCCACACCTAGAC 59.765 50.000 0.00 0.00 0.00 2.59
2467 2786 2.540383 ACATTCAGAGCCACACCTAGA 58.460 47.619 0.00 0.00 0.00 2.43
2472 2791 3.715628 ACAAAACATTCAGAGCCACAC 57.284 42.857 0.00 0.00 0.00 3.82
2554 2891 1.428912 ACAAGGACCACACCATCCAAT 59.571 47.619 0.00 0.00 37.47 3.16
2555 2892 0.850100 ACAAGGACCACACCATCCAA 59.150 50.000 0.00 0.00 37.47 3.53
2556 2893 0.110295 CACAAGGACCACACCATCCA 59.890 55.000 0.00 0.00 37.47 3.41
2557 2894 0.609131 CCACAAGGACCACACCATCC 60.609 60.000 0.00 0.00 36.89 3.51
2558 2895 0.110486 ACCACAAGGACCACACCATC 59.890 55.000 0.00 0.00 38.69 3.51
2593 2945 2.227968 GAACAGCTAGCGCACAACCG 62.228 60.000 11.47 0.00 39.10 4.44
2651 3006 0.922626 GAGGGGAGGGATTCAAAGCT 59.077 55.000 0.00 0.00 0.00 3.74
2701 3062 1.888512 GCCTGGCTTCATTGAACTCAA 59.111 47.619 12.43 0.00 40.51 3.02
2704 3065 1.542492 CTGCCTGGCTTCATTGAACT 58.458 50.000 21.03 0.00 0.00 3.01
2722 3083 0.036388 TCGATCGAAAGCAAAGGCCT 60.036 50.000 16.99 0.00 42.56 5.19
2775 3136 0.449388 GCATGCACTTCTGTACCAGC 59.551 55.000 14.21 0.00 0.00 4.85
2811 3172 1.303155 TCCGTGCATGCATTCACCA 60.303 52.632 25.64 7.64 0.00 4.17
2899 3276 3.165875 CTCCACTCTACTCCACTTTGGA 58.834 50.000 0.00 0.00 45.98 3.53
2900 3277 2.900546 ACTCCACTCTACTCCACTTTGG 59.099 50.000 0.00 0.00 39.43 3.28
2901 3278 3.306364 CCACTCCACTCTACTCCACTTTG 60.306 52.174 0.00 0.00 0.00 2.77
2902 3279 2.900546 CCACTCCACTCTACTCCACTTT 59.099 50.000 0.00 0.00 0.00 2.66
2903 3280 2.158295 ACCACTCCACTCTACTCCACTT 60.158 50.000 0.00 0.00 0.00 3.16
2906 3283 2.648304 ACTACCACTCCACTCTACTCCA 59.352 50.000 0.00 0.00 0.00 3.86
2908 3285 3.942748 CTCACTACCACTCCACTCTACTC 59.057 52.174 0.00 0.00 0.00 2.59
2926 3303 0.386985 GTTCGGTCTCACGGTCTCAC 60.387 60.000 0.00 0.00 0.00 3.51
2977 3354 0.974010 CCCCGCTAGTGGACAGGTTA 60.974 60.000 24.31 0.00 0.00 2.85
2982 3359 4.715130 AGCCCCCGCTAGTGGACA 62.715 66.667 24.31 0.00 46.08 4.02
3087 3492 8.409358 ACAGCTAAGTCACCTCAATAAATTTT 57.591 30.769 0.00 0.00 0.00 1.82
3366 3798 2.811410 TGGCTGGCTTCAAATCAGAAT 58.189 42.857 2.00 0.00 0.00 2.40
3402 3842 4.586235 ATGCCCCGCCAGCCATAC 62.586 66.667 0.00 0.00 0.00 2.39
3403 3843 4.584518 CATGCCCCGCCAGCCATA 62.585 66.667 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.