Multiple sequence alignment - TraesCS5D01G154500

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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 TraesCS5D01G154500 chr5D 100.000 3614 0 0 1 3614 242648173 242644560 0.000000e+00 6674.0
1 TraesCS5D01G154500 chr5D 84.351 524 65 15 1 515 242647894 242648409 6.970000e-137 497.0
2 TraesCS5D01G154500 chr5D 86.979 384 39 10 196 571 14645161 14644781 4.310000e-114 422.0
3 TraesCS5D01G154500 chr5D 84.713 314 26 9 2560 2858 8027834 8027528 9.810000e-76 294.0
4 TraesCS5D01G154500 chr5D 79.769 346 45 9 2566 2890 443802423 443802082 1.010000e-55 228.0
5 TraesCS5D01G154500 chr5D 85.000 120 14 3 2579 2696 8027466 8027583 6.340000e-23 119.0
6 TraesCS5D01G154500 chr5D 94.643 56 3 0 516 571 65949232 65949287 1.790000e-13 87.9
7 TraesCS5D01G154500 chr5B 92.096 2252 121 26 682 2891 255891386 255893622 0.000000e+00 3120.0
8 TraesCS5D01G154500 chr5B 87.246 690 69 10 2926 3614 255924243 255924914 0.000000e+00 769.0
9 TraesCS5D01G154500 chr5A 95.010 1944 70 8 682 2613 309594767 309596695 0.000000e+00 3027.0
10 TraesCS5D01G154500 chr5A 91.038 424 30 7 2903 3324 309597082 309597499 1.880000e-157 566.0
11 TraesCS5D01G154500 chr5A 93.243 296 16 1 3319 3614 309606246 309606537 1.990000e-117 433.0
12 TraesCS5D01G154500 chr5A 85.882 255 18 6 2612 2848 309596828 309597082 4.630000e-64 255.0
13 TraesCS5D01G154500 chr1D 91.615 322 24 3 196 515 58617185 58617505 3.310000e-120 442.0
14 TraesCS5D01G154500 chr1D 87.533 377 36 9 202 571 24118063 24117691 3.340000e-115 425.0
15 TraesCS5D01G154500 chr1D 87.071 379 39 6 196 566 326008843 326008467 1.550000e-113 420.0
16 TraesCS5D01G154500 chr1D 86.010 386 43 8 190 570 470919677 470920056 1.560000e-108 403.0
17 TraesCS5D01G154500 chr1D 85.514 214 21 8 9 222 31676481 31676278 7.860000e-52 215.0
18 TraesCS5D01G154500 chr3D 86.614 381 43 6 196 571 516387859 516387482 7.220000e-112 414.0
19 TraesCS5D01G154500 chr3D 88.385 353 29 8 166 514 556115341 556114997 7.220000e-112 414.0
20 TraesCS5D01G154500 chr3D 85.845 219 19 10 3 221 608802129 608801923 4.700000e-54 222.0
21 TraesCS5D01G154500 chr3D 79.139 302 37 14 2594 2872 536987679 536987381 6.160000e-43 185.0
22 TraesCS5D01G154500 chr2D 86.387 382 44 7 196 571 128372251 128371872 9.340000e-111 411.0
23 TraesCS5D01G154500 chr2D 85.648 216 20 7 3 217 649602854 649602649 2.190000e-52 217.0
24 TraesCS5D01G154500 chr2D 94.737 57 3 0 515 571 6531602 6531546 4.970000e-14 89.8
25 TraesCS5D01G154500 chr7B 83.333 330 34 10 2561 2872 593072028 593072354 5.910000e-73 285.0
26 TraesCS5D01G154500 chr3A 82.891 339 35 12 2553 2872 716965200 716965534 2.120000e-72 283.0
27 TraesCS5D01G154500 chrUn 82.006 339 32 14 2560 2872 323126520 323126855 9.950000e-66 261.0
28 TraesCS5D01G154500 chrUn 82.006 339 32 14 2560 2872 323129736 323130071 9.950000e-66 261.0
29 TraesCS5D01G154500 chrUn 82.006 339 32 14 2560 2872 353153025 353152690 9.950000e-66 261.0
30 TraesCS5D01G154500 chr6D 79.894 378 41 18 2557 2912 450357021 450357385 1.000000e-60 244.0
31 TraesCS5D01G154500 chr6D 86.124 209 18 8 9 217 126629640 126629443 7.860000e-52 215.0
32 TraesCS5D01G154500 chr7A 88.060 201 16 5 1 199 729059195 729059001 7.800000e-57 231.0
33 TraesCS5D01G154500 chr7A 87.065 201 18 7 1 199 729060427 729060233 1.690000e-53 220.0
34 TraesCS5D01G154500 chr6A 85.780 218 20 8 3 220 611518607 611518401 1.690000e-53 220.0
35 TraesCS5D01G154500 chr6A 85.648 216 19 7 3 218 602162276 602162479 2.190000e-52 217.0
36 TraesCS5D01G154500 chr6A 93.103 58 2 2 515 571 178074237 178074293 2.310000e-12 84.2
37 TraesCS5D01G154500 chr1A 85.581 215 19 9 3 217 521563012 521562810 7.860000e-52 215.0
38 TraesCS5D01G154500 chr1A 93.220 59 2 2 515 572 57739505 57739562 6.430000e-13 86.1
39 TraesCS5D01G154500 chr1A 91.525 59 3 2 515 572 57740092 57740149 2.990000e-11 80.5
40 TraesCS5D01G154500 chr1A 94.231 52 2 1 522 572 30495584 30495635 1.080000e-10 78.7
41 TraesCS5D01G154500 chr7D 77.469 324 44 16 2565 2866 39960748 39960432 2.230000e-37 167.0
42 TraesCS5D01G154500 chr7D 85.124 121 14 4 2579 2696 61746706 61746587 1.760000e-23 121.0
43 TraesCS5D01G154500 chr7D 94.737 57 3 0 515 571 32736597 32736541 4.970000e-14 89.8
44 TraesCS5D01G154500 chr6B 87.692 130 14 2 2744 2872 683550235 683550363 2.250000e-32 150.0
45 TraesCS5D01G154500 chr4A 84.259 108 15 2 573 679 543751439 543751545 1.770000e-18 104.0
46 TraesCS5D01G154500 chr4D 93.333 45 3 0 527 571 484922270 484922226 2.330000e-07 67.6


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 TraesCS5D01G154500 chr5D 242644560 242648173 3613 True 6674.000000 6674 100.000000 1 3614 1 chr5D.!!$R3 3613
1 TraesCS5D01G154500 chr5D 242647894 242648409 515 False 497.000000 497 84.351000 1 515 1 chr5D.!!$F3 514
2 TraesCS5D01G154500 chr5B 255891386 255893622 2236 False 3120.000000 3120 92.096000 682 2891 1 chr5B.!!$F1 2209
3 TraesCS5D01G154500 chr5B 255924243 255924914 671 False 769.000000 769 87.246000 2926 3614 1 chr5B.!!$F2 688
4 TraesCS5D01G154500 chr5A 309594767 309597499 2732 False 1282.666667 3027 90.643333 682 3324 3 chr5A.!!$F2 2642
5 TraesCS5D01G154500 chrUn 323126520 323130071 3551 False 261.000000 261 82.006000 2560 2872 2 chrUn.!!$F1 312
6 TraesCS5D01G154500 chr7A 729059001 729060427 1426 True 225.500000 231 87.562500 1 199 2 chr7A.!!$R1 198

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
284 397 0.168128 GATTTCGTTTGAGGCACGGG 59.832 55.0 0.00 0.0 38.23 5.28 F
515 630 0.234884 GAAACTTCCAGGTTGCGACG 59.765 55.0 0.00 0.0 0.00 5.12 F
1902 2040 0.591659 CGACCTTCGAGACTGTGTCA 59.408 55.0 5.76 0.0 43.74 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1098 1236 0.820891 GCACGCCCATGATCTCCATT 60.821 55.0 0.00 0.0 31.94 3.16 R
2446 2584 1.014352 CAACCCATACACGCCTAAGC 58.986 55.0 0.00 0.0 0.00 3.09 R
3405 5265 0.252284 ACCCGACCTTGAGTCAGGAT 60.252 55.0 13.56 0.0 44.81 3.24 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
31 32 1.816863 ATCACAACCGTGCCTCTCGT 61.817 55.000 0.00 0.00 43.28 4.18
33 34 2.029073 CAACCGTGCCTCTCGTGT 59.971 61.111 0.00 0.00 0.00 4.49
37 38 1.153823 CCGTGCCTCTCGTGTAAGG 60.154 63.158 0.00 0.00 35.65 2.69
153 264 0.671781 AGCACAACCATGTCTCTCGC 60.672 55.000 0.00 0.00 37.82 5.03
176 287 2.440539 AGCAAAATCGTGACTCTCGT 57.559 45.000 0.76 0.00 0.00 4.18
246 359 3.362693 CGTGAGAGTTACGGTTTTGCTTC 60.363 47.826 0.00 0.00 37.86 3.86
273 386 1.082366 GCGCGGTTGTGATTTCGTT 60.082 52.632 8.83 0.00 0.00 3.85
274 387 0.659123 GCGCGGTTGTGATTTCGTTT 60.659 50.000 8.83 0.00 0.00 3.60
281 394 3.042887 GTTGTGATTTCGTTTGAGGCAC 58.957 45.455 0.00 0.00 0.00 5.01
284 397 0.168128 GATTTCGTTTGAGGCACGGG 59.832 55.000 0.00 0.00 38.23 5.28
296 409 2.047655 CACGGGCGTGCCTCTTTA 60.048 61.111 11.25 0.00 39.39 1.85
298 411 2.264794 CGGGCGTGCCTCTTTAGT 59.735 61.111 11.25 0.00 36.10 2.24
304 417 2.354403 GGCGTGCCTCTTTAGTAAAGGA 60.354 50.000 20.04 8.24 39.01 3.36
305 418 3.332034 GCGTGCCTCTTTAGTAAAGGAA 58.668 45.455 20.04 0.21 39.01 3.36
404 517 5.907207 TGGGATCTAGTTTTGAAGATCTCG 58.093 41.667 11.05 0.00 40.21 4.04
409 522 3.026630 AGTTTTGAAGATCTCGACGCA 57.973 42.857 0.00 0.00 0.00 5.24
412 525 3.297830 TTTGAAGATCTCGACGCAAGA 57.702 42.857 0.00 0.00 43.62 3.02
419 532 1.996292 TCTCGACGCAAGAAATCCAG 58.004 50.000 0.00 0.00 43.62 3.86
446 559 1.156736 AGCGGTTTGAGATTTGGACG 58.843 50.000 0.00 0.00 0.00 4.79
496 611 6.314400 TGAATAAACGGATCTACGAAAAAGGG 59.686 38.462 0.00 0.00 37.61 3.95
502 617 4.694037 CGGATCTACGAAAAAGGGAAACTT 59.306 41.667 0.00 0.00 37.18 2.66
515 630 0.234884 GAAACTTCCAGGTTGCGACG 59.765 55.000 0.00 0.00 0.00 5.12
516 631 1.782028 AAACTTCCAGGTTGCGACGC 61.782 55.000 14.19 14.19 0.00 5.19
517 632 2.664851 CTTCCAGGTTGCGACGCA 60.665 61.111 20.50 20.50 36.47 5.24
518 633 2.203084 TTCCAGGTTGCGACGCAA 60.203 55.556 30.11 30.11 46.80 4.85
525 640 2.047655 TTGCGACGCAACCTAGGG 60.048 61.111 30.11 0.00 43.99 3.53
526 641 2.575893 TTGCGACGCAACCTAGGGA 61.576 57.895 30.11 6.84 43.99 4.20
527 642 2.202756 GCGACGCAACCTAGGGAG 60.203 66.667 16.42 6.02 0.00 4.30
528 643 3.003113 GCGACGCAACCTAGGGAGT 62.003 63.158 16.42 3.72 0.00 3.85
529 644 1.590147 CGACGCAACCTAGGGAGTT 59.410 57.895 14.81 0.00 0.00 3.01
530 645 0.736325 CGACGCAACCTAGGGAGTTG 60.736 60.000 14.81 9.92 45.92 3.16
531 646 0.606604 GACGCAACCTAGGGAGTTGA 59.393 55.000 14.81 0.00 46.03 3.18
532 647 1.001633 GACGCAACCTAGGGAGTTGAA 59.998 52.381 14.81 0.00 46.03 2.69
533 648 1.002087 ACGCAACCTAGGGAGTTGAAG 59.998 52.381 14.81 8.90 46.03 3.02
534 649 1.002087 CGCAACCTAGGGAGTTGAAGT 59.998 52.381 14.81 0.00 46.03 3.01
535 650 2.427506 GCAACCTAGGGAGTTGAAGTG 58.572 52.381 14.81 0.00 46.03 3.16
536 651 2.038557 GCAACCTAGGGAGTTGAAGTGA 59.961 50.000 14.81 0.00 46.03 3.41
537 652 3.307762 GCAACCTAGGGAGTTGAAGTGAT 60.308 47.826 14.81 0.00 46.03 3.06
538 653 4.508662 CAACCTAGGGAGTTGAAGTGATC 58.491 47.826 14.81 0.00 46.03 2.92
539 654 4.067944 ACCTAGGGAGTTGAAGTGATCT 57.932 45.455 14.81 0.00 0.00 2.75
540 655 4.430441 ACCTAGGGAGTTGAAGTGATCTT 58.570 43.478 14.81 0.00 36.51 2.40
541 656 4.846940 ACCTAGGGAGTTGAAGTGATCTTT 59.153 41.667 14.81 0.00 33.64 2.52
542 657 5.181748 CCTAGGGAGTTGAAGTGATCTTTG 58.818 45.833 0.00 0.00 33.64 2.77
543 658 3.416156 AGGGAGTTGAAGTGATCTTTGC 58.584 45.455 0.00 0.00 33.64 3.68
544 659 3.149196 GGGAGTTGAAGTGATCTTTGCA 58.851 45.455 0.00 0.00 33.64 4.08
545 660 3.569701 GGGAGTTGAAGTGATCTTTGCAA 59.430 43.478 0.00 0.00 33.64 4.08
546 661 4.540824 GGAGTTGAAGTGATCTTTGCAAC 58.459 43.478 0.00 11.00 38.01 4.17
547 662 4.214437 GAGTTGAAGTGATCTTTGCAACG 58.786 43.478 0.00 0.00 40.33 4.10
548 663 3.876914 AGTTGAAGTGATCTTTGCAACGA 59.123 39.130 8.20 8.20 40.33 3.85
549 664 4.024556 AGTTGAAGTGATCTTTGCAACGAG 60.025 41.667 11.57 1.70 40.33 4.18
550 665 3.466836 TGAAGTGATCTTTGCAACGAGT 58.533 40.909 11.57 0.34 33.64 4.18
551 666 4.627058 TGAAGTGATCTTTGCAACGAGTA 58.373 39.130 11.57 0.27 33.64 2.59
552 667 4.447724 TGAAGTGATCTTTGCAACGAGTAC 59.552 41.667 11.57 11.75 33.64 2.73
553 668 4.258702 AGTGATCTTTGCAACGAGTACT 57.741 40.909 11.57 13.57 0.00 2.73
554 669 4.632153 AGTGATCTTTGCAACGAGTACTT 58.368 39.130 11.57 0.00 0.00 2.24
555 670 4.686554 AGTGATCTTTGCAACGAGTACTTC 59.313 41.667 11.57 4.44 0.00 3.01
556 671 4.686554 GTGATCTTTGCAACGAGTACTTCT 59.313 41.667 11.57 0.00 0.00 2.85
557 672 4.923871 TGATCTTTGCAACGAGTACTTCTC 59.076 41.667 11.57 3.11 39.62 2.87
558 673 4.316205 TCTTTGCAACGAGTACTTCTCA 57.684 40.909 0.00 0.00 42.88 3.27
559 674 4.689071 TCTTTGCAACGAGTACTTCTCAA 58.311 39.130 0.00 0.00 42.88 3.02
560 675 5.297547 TCTTTGCAACGAGTACTTCTCAAT 58.702 37.500 0.00 0.00 42.88 2.57
561 676 5.758296 TCTTTGCAACGAGTACTTCTCAATT 59.242 36.000 0.00 0.00 42.88 2.32
562 677 6.926826 TCTTTGCAACGAGTACTTCTCAATTA 59.073 34.615 0.00 0.00 42.88 1.40
563 678 6.706055 TTGCAACGAGTACTTCTCAATTAG 57.294 37.500 0.00 0.00 42.88 1.73
564 679 5.779922 TGCAACGAGTACTTCTCAATTAGT 58.220 37.500 0.00 0.00 42.88 2.24
565 680 5.633601 TGCAACGAGTACTTCTCAATTAGTG 59.366 40.000 0.00 0.00 42.88 2.74
566 681 5.862323 GCAACGAGTACTTCTCAATTAGTGA 59.138 40.000 0.00 0.00 42.88 3.41
567 682 6.531948 GCAACGAGTACTTCTCAATTAGTGAT 59.468 38.462 0.00 0.00 42.88 3.06
568 683 7.063544 GCAACGAGTACTTCTCAATTAGTGATT 59.936 37.037 0.00 0.00 42.88 2.57
569 684 8.926710 CAACGAGTACTTCTCAATTAGTGATTT 58.073 33.333 0.00 0.00 42.88 2.17
570 685 8.690680 ACGAGTACTTCTCAATTAGTGATTTC 57.309 34.615 0.00 0.00 42.88 2.17
571 686 8.304596 ACGAGTACTTCTCAATTAGTGATTTCA 58.695 33.333 0.00 0.00 42.88 2.69
572 687 9.307121 CGAGTACTTCTCAATTAGTGATTTCAT 57.693 33.333 0.00 0.00 42.88 2.57
587 702 8.786826 AGTGATTTCATTAAAATAGTCCGTGA 57.213 30.769 0.00 0.00 37.70 4.35
588 703 9.396022 AGTGATTTCATTAAAATAGTCCGTGAT 57.604 29.630 0.00 0.00 37.70 3.06
589 704 9.651718 GTGATTTCATTAAAATAGTCCGTGATC 57.348 33.333 0.00 0.00 37.70 2.92
590 705 9.613428 TGATTTCATTAAAATAGTCCGTGATCT 57.387 29.630 0.00 0.00 37.70 2.75
591 706 9.869844 GATTTCATTAAAATAGTCCGTGATCTG 57.130 33.333 0.00 0.00 37.70 2.90
592 707 9.613428 ATTTCATTAAAATAGTCCGTGATCTGA 57.387 29.630 0.00 0.00 35.77 3.27
593 708 8.648557 TTCATTAAAATAGTCCGTGATCTGAG 57.351 34.615 0.00 0.00 0.00 3.35
594 709 8.007405 TCATTAAAATAGTCCGTGATCTGAGA 57.993 34.615 0.00 0.00 0.00 3.27
595 710 8.138074 TCATTAAAATAGTCCGTGATCTGAGAG 58.862 37.037 0.00 0.00 0.00 3.20
596 711 5.923733 AAAATAGTCCGTGATCTGAGAGT 57.076 39.130 0.00 0.00 0.00 3.24
597 712 5.923733 AAATAGTCCGTGATCTGAGAGTT 57.076 39.130 0.00 0.00 0.00 3.01
598 713 5.508200 AATAGTCCGTGATCTGAGAGTTC 57.492 43.478 0.00 0.00 0.00 3.01
599 714 1.740585 AGTCCGTGATCTGAGAGTTCG 59.259 52.381 0.00 0.00 0.00 3.95
600 715 1.095600 TCCGTGATCTGAGAGTTCGG 58.904 55.000 13.14 13.14 38.16 4.30
601 716 0.811915 CCGTGATCTGAGAGTTCGGT 59.188 55.000 11.75 0.00 33.20 4.69
602 717 2.014857 CCGTGATCTGAGAGTTCGGTA 58.985 52.381 11.75 0.00 33.20 4.02
603 718 2.619177 CCGTGATCTGAGAGTTCGGTAT 59.381 50.000 11.75 0.00 33.20 2.73
604 719 3.549019 CCGTGATCTGAGAGTTCGGTATG 60.549 52.174 11.75 0.00 33.20 2.39
605 720 3.376540 GTGATCTGAGAGTTCGGTATGC 58.623 50.000 0.00 0.00 0.00 3.14
606 721 3.067461 GTGATCTGAGAGTTCGGTATGCT 59.933 47.826 0.00 0.00 0.00 3.79
607 722 3.067320 TGATCTGAGAGTTCGGTATGCTG 59.933 47.826 0.00 0.00 0.00 4.41
608 723 2.723273 TCTGAGAGTTCGGTATGCTGA 58.277 47.619 0.00 0.00 0.00 4.26
609 724 3.291584 TCTGAGAGTTCGGTATGCTGAT 58.708 45.455 0.00 0.00 0.00 2.90
610 725 3.701542 TCTGAGAGTTCGGTATGCTGATT 59.298 43.478 0.00 0.00 0.00 2.57
611 726 4.160439 TCTGAGAGTTCGGTATGCTGATTT 59.840 41.667 0.00 0.00 0.00 2.17
612 727 4.832248 TGAGAGTTCGGTATGCTGATTTT 58.168 39.130 0.00 0.00 0.00 1.82
613 728 4.870426 TGAGAGTTCGGTATGCTGATTTTC 59.130 41.667 0.00 0.00 0.00 2.29
614 729 3.865745 AGAGTTCGGTATGCTGATTTTCG 59.134 43.478 0.00 0.00 0.00 3.46
615 730 3.857052 AGTTCGGTATGCTGATTTTCGA 58.143 40.909 0.00 0.00 0.00 3.71
616 731 3.865745 AGTTCGGTATGCTGATTTTCGAG 59.134 43.478 0.00 0.00 0.00 4.04
617 732 3.793797 TCGGTATGCTGATTTTCGAGA 57.206 42.857 0.00 0.00 0.00 4.04
618 733 4.322080 TCGGTATGCTGATTTTCGAGAT 57.678 40.909 0.00 0.00 0.00 2.75
619 734 4.693283 TCGGTATGCTGATTTTCGAGATT 58.307 39.130 0.00 0.00 0.00 2.40
620 735 5.838529 TCGGTATGCTGATTTTCGAGATTA 58.161 37.500 0.00 0.00 0.00 1.75
621 736 5.690409 TCGGTATGCTGATTTTCGAGATTAC 59.310 40.000 0.00 0.00 0.00 1.89
622 737 5.462068 CGGTATGCTGATTTTCGAGATTACA 59.538 40.000 0.00 0.00 0.00 2.41
623 738 6.019075 CGGTATGCTGATTTTCGAGATTACAA 60.019 38.462 0.00 0.00 0.00 2.41
624 739 7.348201 GGTATGCTGATTTTCGAGATTACAAG 58.652 38.462 0.00 0.00 0.00 3.16
625 740 6.992063 ATGCTGATTTTCGAGATTACAAGT 57.008 33.333 0.00 0.00 0.00 3.16
626 741 6.801539 TGCTGATTTTCGAGATTACAAGTT 57.198 33.333 0.00 0.00 0.00 2.66
627 742 6.831769 TGCTGATTTTCGAGATTACAAGTTC 58.168 36.000 0.00 0.00 0.00 3.01
628 743 6.426633 TGCTGATTTTCGAGATTACAAGTTCA 59.573 34.615 0.00 0.00 0.00 3.18
629 744 6.958193 GCTGATTTTCGAGATTACAAGTTCAG 59.042 38.462 0.00 0.00 0.00 3.02
630 745 7.364522 TGATTTTCGAGATTACAAGTTCAGG 57.635 36.000 0.00 0.00 0.00 3.86
631 746 6.934645 TGATTTTCGAGATTACAAGTTCAGGT 59.065 34.615 0.00 0.00 0.00 4.00
632 747 7.444183 TGATTTTCGAGATTACAAGTTCAGGTT 59.556 33.333 0.00 0.00 0.00 3.50
633 748 7.562454 TTTTCGAGATTACAAGTTCAGGTTT 57.438 32.000 0.00 0.00 0.00 3.27
634 749 6.780706 TTCGAGATTACAAGTTCAGGTTTC 57.219 37.500 0.00 0.00 0.00 2.78
635 750 5.849510 TCGAGATTACAAGTTCAGGTTTCA 58.150 37.500 0.00 0.00 0.00 2.69
636 751 6.464222 TCGAGATTACAAGTTCAGGTTTCAT 58.536 36.000 0.00 0.00 0.00 2.57
637 752 6.934645 TCGAGATTACAAGTTCAGGTTTCATT 59.065 34.615 0.00 0.00 0.00 2.57
638 753 7.444183 TCGAGATTACAAGTTCAGGTTTCATTT 59.556 33.333 0.00 0.00 0.00 2.32
639 754 8.717821 CGAGATTACAAGTTCAGGTTTCATTTA 58.282 33.333 0.00 0.00 0.00 1.40
646 761 9.150348 ACAAGTTCAGGTTTCATTTAACTTTTG 57.850 29.630 0.00 0.00 35.57 2.44
647 762 9.150348 CAAGTTCAGGTTTCATTTAACTTTTGT 57.850 29.630 0.00 0.00 35.57 2.83
648 763 8.926715 AGTTCAGGTTTCATTTAACTTTTGTC 57.073 30.769 0.00 0.00 0.00 3.18
649 764 8.749354 AGTTCAGGTTTCATTTAACTTTTGTCT 58.251 29.630 0.00 0.00 0.00 3.41
652 767 9.179909 TCAGGTTTCATTTAACTTTTGTCTACA 57.820 29.630 0.00 0.00 0.00 2.74
653 768 9.796120 CAGGTTTCATTTAACTTTTGTCTACAA 57.204 29.630 0.00 0.00 0.00 2.41
655 770 9.797556 GGTTTCATTTAACTTTTGTCTACAAGT 57.202 29.630 0.00 0.00 37.15 3.16
662 777 8.570068 TTAACTTTTGTCTACAAGTTGAAGGT 57.430 30.769 10.54 1.98 42.09 3.50
663 778 7.462571 AACTTTTGTCTACAAGTTGAAGGTT 57.537 32.000 10.54 2.38 40.87 3.50
664 779 7.462571 ACTTTTGTCTACAAGTTGAAGGTTT 57.537 32.000 10.54 0.00 37.15 3.27
665 780 8.570068 ACTTTTGTCTACAAGTTGAAGGTTTA 57.430 30.769 10.54 0.00 37.15 2.01
666 781 9.185680 ACTTTTGTCTACAAGTTGAAGGTTTAT 57.814 29.630 10.54 0.00 37.15 1.40
671 786 9.226606 TGTCTACAAGTTGAAGGTTTATTATGG 57.773 33.333 10.54 0.00 0.00 2.74
672 787 9.444600 GTCTACAAGTTGAAGGTTTATTATGGA 57.555 33.333 10.54 0.00 0.00 3.41
675 790 8.706322 ACAAGTTGAAGGTTTATTATGGAACT 57.294 30.769 10.54 0.00 0.00 3.01
676 791 9.143155 ACAAGTTGAAGGTTTATTATGGAACTT 57.857 29.630 10.54 0.00 32.70 2.66
677 792 9.981114 CAAGTTGAAGGTTTATTATGGAACTTT 57.019 29.630 0.00 0.00 30.66 2.66
746 870 2.506061 CCCAGGCGATCTCTCCCTG 61.506 68.421 10.07 10.07 44.49 4.45
863 988 0.956410 ACTCGAGTCCTCAGGTGACG 60.956 60.000 13.58 0.00 37.80 4.35
882 1011 2.390599 CCCTTCGTACGACGTCCGA 61.391 63.158 19.36 11.82 43.14 4.55
993 1122 3.726595 TACGTGCCGCCCTACATGC 62.727 63.158 0.00 0.00 0.00 4.06
1137 1275 1.300697 GGTGCAGAGGACGTTCGTT 60.301 57.895 0.00 0.00 0.00 3.85
1356 1494 2.740714 GCGTCCATGCTTCGTCACC 61.741 63.158 0.00 0.00 0.00 4.02
1551 1689 2.792599 GTCATCGCCTCGTCGTCT 59.207 61.111 0.00 0.00 0.00 4.18
1731 1869 2.203015 GCCGAATTCCTGCCGCTA 60.203 61.111 0.00 0.00 0.00 4.26
1833 1971 2.744202 CACCAACATGCTCCTTCACTAC 59.256 50.000 0.00 0.00 0.00 2.73
1902 2040 0.591659 CGACCTTCGAGACTGTGTCA 59.408 55.000 5.76 0.00 43.74 3.58
1923 2061 1.741770 GCACGTCTGGCGGAAGATT 60.742 57.895 16.31 0.00 46.52 2.40
2065 2203 3.068064 TGCTCACGGCGATCTCCA 61.068 61.111 16.62 0.44 45.43 3.86
2070 2208 2.362503 ACGGCGATCTCCAGGACA 60.363 61.111 16.62 0.00 0.00 4.02
2208 2346 1.000359 TGACGAGGATCTGGAGCCA 60.000 57.895 7.64 0.00 39.89 4.75
2446 2584 1.349627 CTCAGCGCCATTGCTTACG 59.650 57.895 2.29 0.00 44.46 3.18
2469 2607 0.907704 AGGCGTGTATGGGTTGAGGA 60.908 55.000 0.00 0.00 0.00 3.71
2470 2608 0.180406 GGCGTGTATGGGTTGAGGAT 59.820 55.000 0.00 0.00 0.00 3.24
2471 2609 1.583054 GCGTGTATGGGTTGAGGATC 58.417 55.000 0.00 0.00 0.00 3.36
2606 2755 2.093447 GGGACACCCTCTATGAACAGTG 60.093 54.545 0.00 0.00 41.34 3.66
2700 2990 5.473504 AGGTGCTTACAAGTTTTCATGTAGG 59.526 40.000 0.00 0.00 35.80 3.18
2709 2999 8.871686 ACAAGTTTTCATGTAGGAAAAACATC 57.128 30.769 17.16 0.00 45.37 3.06
2794 3101 6.380274 TGGGTACACCTTTCTCTACTTGATAG 59.620 42.308 0.00 0.00 41.11 2.08
2797 3104 7.975058 GGTACACCTTTCTCTACTTGATAGTTC 59.025 40.741 0.00 0.00 35.78 3.01
2818 3125 8.816640 AGTTCGTTATGAAAATTTGCAAGAAT 57.183 26.923 2.14 0.00 38.60 2.40
2829 3136 9.590088 GAAAATTTGCAAGAATCTCAAATGTTC 57.410 29.630 17.28 17.28 42.35 3.18
2831 3138 4.424061 TGCAAGAATCTCAAATGTTCGG 57.576 40.909 0.00 0.00 0.00 4.30
2894 3221 7.563724 TTACTGTTTATAGAGGGTGTCCTTT 57.436 36.000 0.00 0.00 45.05 3.11
2895 3222 5.805728 ACTGTTTATAGAGGGTGTCCTTTG 58.194 41.667 0.00 0.00 45.05 2.77
2896 3223 5.174037 TGTTTATAGAGGGTGTCCTTTGG 57.826 43.478 0.00 0.00 45.05 3.28
2899 3226 0.178873 TAGAGGGTGTCCTTTGGCCT 60.179 55.000 3.32 0.00 45.05 5.19
2912 3239 1.971505 TTGGCCTGGGAGCTATCACG 61.972 60.000 3.32 0.00 0.00 4.35
2913 3240 2.435693 GGCCTGGGAGCTATCACGT 61.436 63.158 0.00 0.00 0.00 4.49
2915 3242 1.676678 GCCTGGGAGCTATCACGTCA 61.677 60.000 0.00 0.00 0.00 4.35
2972 3656 1.064952 GTGTTTGGTTGAAGACACGGG 59.935 52.381 0.00 0.00 33.88 5.28
3149 4953 9.884465 GAAGCACTTAACAAATATATGATCACC 57.116 33.333 0.00 0.00 0.00 4.02
3152 4956 7.805071 GCACTTAACAAATATATGATCACCTGC 59.195 37.037 0.00 0.00 0.00 4.85
3183 4987 9.912634 AACAACACATATAACAGATTTTTCCAG 57.087 29.630 0.00 0.00 0.00 3.86
3266 5071 7.905604 TTTACATTCTCAACATCTCGTTCAT 57.094 32.000 0.00 0.00 34.86 2.57
3279 5084 4.476862 TCTCGTTCATGAGAGACTTTTCG 58.523 43.478 9.92 0.69 40.01 3.46
3312 5146 1.407936 CCCGATCTGACATCAGGACT 58.592 55.000 8.99 0.00 43.91 3.85
3320 5154 4.935578 TCTGACATCAGGACTAGAGGAAA 58.064 43.478 8.99 0.00 43.91 3.13
3330 5164 6.070538 TCAGGACTAGAGGAAATTTCTCCAAG 60.071 42.308 17.42 12.22 38.02 3.61
3332 5166 6.070481 AGGACTAGAGGAAATTTCTCCAAGAC 60.070 42.308 17.42 10.30 38.02 3.01
3334 5168 4.308526 AGAGGAAATTTCTCCAAGACCC 57.691 45.455 17.42 0.00 38.02 4.46
3353 5187 1.367840 GATCGGGAATGGACCTCGG 59.632 63.158 0.00 0.00 0.00 4.63
3364 5224 1.825474 TGGACCTCGGATCTTTGTCTC 59.175 52.381 0.00 0.00 0.00 3.36
3376 5236 0.250234 TTTGTCTCTGGCCCGATCTG 59.750 55.000 0.00 0.00 0.00 2.90
3475 5342 3.206150 CCTAGATTTGACATCGGGGTTG 58.794 50.000 0.00 0.00 0.00 3.77
3491 5358 0.818040 GTTGGGGCAAGTGTCTCGTT 60.818 55.000 0.00 0.00 0.00 3.85
3492 5359 0.534203 TTGGGGCAAGTGTCTCGTTC 60.534 55.000 0.00 0.00 0.00 3.95
3493 5360 1.371558 GGGGCAAGTGTCTCGTTCT 59.628 57.895 0.00 0.00 0.00 3.01
3495 5362 0.033504 GGGCAAGTGTCTCGTTCTGA 59.966 55.000 0.00 0.00 0.00 3.27
3496 5363 1.338200 GGGCAAGTGTCTCGTTCTGAT 60.338 52.381 0.00 0.00 0.00 2.90
3500 5367 3.506810 CAAGTGTCTCGTTCTGATCCTC 58.493 50.000 0.00 0.00 0.00 3.71
3504 5371 4.109050 GTGTCTCGTTCTGATCCTCAATC 58.891 47.826 0.00 0.00 34.72 2.67
3517 5784 5.485353 TGATCCTCAATCTAGTTTGACACCT 59.515 40.000 11.42 0.00 35.24 4.00
3518 5785 6.667848 TGATCCTCAATCTAGTTTGACACCTA 59.332 38.462 11.42 0.00 35.24 3.08
3570 5837 1.207089 GCTGTGTACTCCATGCTACCA 59.793 52.381 0.00 0.00 0.00 3.25
3573 5840 4.517285 CTGTGTACTCCATGCTACCAAAT 58.483 43.478 0.00 0.00 0.00 2.32
3583 5850 4.452455 CCATGCTACCAAATCTAACGATCC 59.548 45.833 0.00 0.00 0.00 3.36
3584 5851 4.746535 TGCTACCAAATCTAACGATCCA 57.253 40.909 0.00 0.00 0.00 3.41
3587 5854 2.919228 ACCAAATCTAACGATCCAGCC 58.081 47.619 0.00 0.00 0.00 4.85
3610 6592 5.006386 CAGGAGCAAAACTATCTTGACCTT 58.994 41.667 0.00 0.00 33.19 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 3.551454 CGAGAGTCACGGTTTTCCTTACA 60.551 47.826 1.62 0.00 37.95 2.41
33 34 2.608752 GCGAGAGTCACGGTTTTCCTTA 60.609 50.000 11.95 0.00 37.95 2.69
37 38 1.615107 CCGCGAGAGTCACGGTTTTC 61.615 60.000 8.23 0.00 42.01 2.29
99 102 2.342279 CGTGCCTCCTCGGAAACA 59.658 61.111 0.00 0.00 33.16 2.83
120 123 0.939577 TGTGCTTTCGCGAGAGTCAC 60.940 55.000 29.56 29.56 43.69 3.67
140 143 1.513158 CTTCCGCGAGAGACATGGT 59.487 57.895 8.23 0.00 0.00 3.55
143 146 0.037326 TTTGCTTCCGCGAGAGACAT 60.037 50.000 8.23 0.00 39.65 3.06
146 149 1.359848 GATTTTGCTTCCGCGAGAGA 58.640 50.000 8.23 0.00 39.65 3.10
153 264 2.069273 AGAGTCACGATTTTGCTTCCG 58.931 47.619 0.00 0.00 0.00 4.30
226 339 3.135994 GGAAGCAAAACCGTAACTCTCA 58.864 45.455 0.00 0.00 0.00 3.27
257 370 2.307049 CTCAAACGAAATCACAACCGC 58.693 47.619 0.00 0.00 0.00 5.68
281 394 0.108520 TTACTAAAGAGGCACGCCCG 60.109 55.000 3.95 0.00 39.21 6.13
284 397 2.968675 TCCTTTACTAAAGAGGCACGC 58.031 47.619 9.76 0.00 41.02 5.34
404 517 1.298859 ACCGCTGGATTTCTTGCGTC 61.299 55.000 0.00 0.00 45.90 5.19
409 522 1.541588 GCTTTCACCGCTGGATTTCTT 59.458 47.619 1.50 0.00 0.00 2.52
412 525 1.586154 CCGCTTTCACCGCTGGATTT 61.586 55.000 1.50 0.00 0.00 2.17
419 532 1.082104 CTCAAACCGCTTTCACCGC 60.082 57.895 0.00 0.00 0.00 5.68
431 544 1.399727 CCGTGCGTCCAAATCTCAAAC 60.400 52.381 0.00 0.00 0.00 2.93
434 547 0.250124 AACCGTGCGTCCAAATCTCA 60.250 50.000 0.00 0.00 0.00 3.27
446 559 3.185797 ACGTTTTATCTCTCAAACCGTGC 59.814 43.478 0.00 0.00 30.37 5.34
496 611 0.234884 CGTCGCAACCTGGAAGTTTC 59.765 55.000 0.00 0.00 0.00 2.78
515 630 2.038557 TCACTTCAACTCCCTAGGTTGC 59.961 50.000 8.29 0.00 42.40 4.17
516 631 4.223923 AGATCACTTCAACTCCCTAGGTTG 59.776 45.833 8.29 6.14 43.57 3.77
517 632 4.430441 AGATCACTTCAACTCCCTAGGTT 58.570 43.478 8.29 0.00 0.00 3.50
518 633 4.067944 AGATCACTTCAACTCCCTAGGT 57.932 45.455 8.29 0.00 0.00 3.08
519 634 5.181748 CAAAGATCACTTCAACTCCCTAGG 58.818 45.833 0.06 0.06 35.05 3.02
520 635 4.633565 GCAAAGATCACTTCAACTCCCTAG 59.366 45.833 0.00 0.00 35.05 3.02
521 636 4.041567 TGCAAAGATCACTTCAACTCCCTA 59.958 41.667 0.00 0.00 35.05 3.53
522 637 3.181440 TGCAAAGATCACTTCAACTCCCT 60.181 43.478 0.00 0.00 35.05 4.20
523 638 3.149196 TGCAAAGATCACTTCAACTCCC 58.851 45.455 0.00 0.00 35.05 4.30
524 639 4.540824 GTTGCAAAGATCACTTCAACTCC 58.459 43.478 0.00 0.00 37.61 3.85
525 640 4.024893 TCGTTGCAAAGATCACTTCAACTC 60.025 41.667 11.22 0.00 38.03 3.01
526 641 3.876914 TCGTTGCAAAGATCACTTCAACT 59.123 39.130 11.22 0.00 38.03 3.16
527 642 4.209452 TCGTTGCAAAGATCACTTCAAC 57.791 40.909 11.22 3.45 37.42 3.18
528 643 3.876914 ACTCGTTGCAAAGATCACTTCAA 59.123 39.130 15.52 0.00 35.05 2.69
529 644 3.466836 ACTCGTTGCAAAGATCACTTCA 58.533 40.909 15.52 0.00 35.05 3.02
530 645 4.686554 AGTACTCGTTGCAAAGATCACTTC 59.313 41.667 15.52 4.33 35.05 3.01
531 646 4.632153 AGTACTCGTTGCAAAGATCACTT 58.368 39.130 15.52 4.70 38.05 3.16
532 647 4.258702 AGTACTCGTTGCAAAGATCACT 57.741 40.909 15.52 16.67 0.00 3.41
533 648 4.686554 AGAAGTACTCGTTGCAAAGATCAC 59.313 41.667 15.52 14.91 0.00 3.06
534 649 4.883083 AGAAGTACTCGTTGCAAAGATCA 58.117 39.130 15.52 3.95 0.00 2.92
535 650 5.443142 GAGAAGTACTCGTTGCAAAGATC 57.557 43.478 15.52 9.76 35.84 2.75
561 676 9.878667 TCACGGACTATTTTAATGAAATCACTA 57.121 29.630 0.00 0.00 38.80 2.74
562 677 8.786826 TCACGGACTATTTTAATGAAATCACT 57.213 30.769 0.00 0.00 38.80 3.41
563 678 9.651718 GATCACGGACTATTTTAATGAAATCAC 57.348 33.333 0.00 0.00 38.80 3.06
564 679 9.613428 AGATCACGGACTATTTTAATGAAATCA 57.387 29.630 0.00 0.00 38.80 2.57
565 680 9.869844 CAGATCACGGACTATTTTAATGAAATC 57.130 33.333 0.00 0.00 38.80 2.17
566 681 9.613428 TCAGATCACGGACTATTTTAATGAAAT 57.387 29.630 0.00 0.00 40.88 2.17
567 682 9.098355 CTCAGATCACGGACTATTTTAATGAAA 57.902 33.333 0.00 0.00 0.00 2.69
568 683 8.474831 TCTCAGATCACGGACTATTTTAATGAA 58.525 33.333 0.00 0.00 0.00 2.57
569 684 8.007405 TCTCAGATCACGGACTATTTTAATGA 57.993 34.615 0.00 0.00 0.00 2.57
570 685 7.923344 ACTCTCAGATCACGGACTATTTTAATG 59.077 37.037 0.00 0.00 0.00 1.90
571 686 8.012957 ACTCTCAGATCACGGACTATTTTAAT 57.987 34.615 0.00 0.00 0.00 1.40
572 687 7.406031 ACTCTCAGATCACGGACTATTTTAA 57.594 36.000 0.00 0.00 0.00 1.52
573 688 7.406031 AACTCTCAGATCACGGACTATTTTA 57.594 36.000 0.00 0.00 0.00 1.52
574 689 5.923733 ACTCTCAGATCACGGACTATTTT 57.076 39.130 0.00 0.00 0.00 1.82
575 690 5.449314 CGAACTCTCAGATCACGGACTATTT 60.449 44.000 0.00 0.00 0.00 1.40
576 691 4.035792 CGAACTCTCAGATCACGGACTATT 59.964 45.833 0.00 0.00 0.00 1.73
577 692 3.562141 CGAACTCTCAGATCACGGACTAT 59.438 47.826 0.00 0.00 0.00 2.12
578 693 2.937149 CGAACTCTCAGATCACGGACTA 59.063 50.000 0.00 0.00 0.00 2.59
579 694 1.740585 CGAACTCTCAGATCACGGACT 59.259 52.381 0.00 0.00 0.00 3.85
580 695 1.202200 CCGAACTCTCAGATCACGGAC 60.202 57.143 7.51 0.00 41.09 4.79
581 696 1.095600 CCGAACTCTCAGATCACGGA 58.904 55.000 7.51 0.00 41.09 4.69
582 697 0.811915 ACCGAACTCTCAGATCACGG 59.188 55.000 10.63 10.63 43.61 4.94
583 698 3.622828 CATACCGAACTCTCAGATCACG 58.377 50.000 0.00 0.00 0.00 4.35
584 699 3.067461 AGCATACCGAACTCTCAGATCAC 59.933 47.826 0.00 0.00 0.00 3.06
585 700 3.067320 CAGCATACCGAACTCTCAGATCA 59.933 47.826 0.00 0.00 0.00 2.92
586 701 3.316588 TCAGCATACCGAACTCTCAGATC 59.683 47.826 0.00 0.00 0.00 2.75
587 702 3.291584 TCAGCATACCGAACTCTCAGAT 58.708 45.455 0.00 0.00 0.00 2.90
588 703 2.723273 TCAGCATACCGAACTCTCAGA 58.277 47.619 0.00 0.00 0.00 3.27
589 704 3.724508 ATCAGCATACCGAACTCTCAG 57.275 47.619 0.00 0.00 0.00 3.35
590 705 4.471904 AAATCAGCATACCGAACTCTCA 57.528 40.909 0.00 0.00 0.00 3.27
591 706 4.026475 CGAAAATCAGCATACCGAACTCTC 60.026 45.833 0.00 0.00 0.00 3.20
592 707 3.865745 CGAAAATCAGCATACCGAACTCT 59.134 43.478 0.00 0.00 0.00 3.24
593 708 3.863424 TCGAAAATCAGCATACCGAACTC 59.137 43.478 0.00 0.00 0.00 3.01
594 709 3.857052 TCGAAAATCAGCATACCGAACT 58.143 40.909 0.00 0.00 0.00 3.01
595 710 3.863424 TCTCGAAAATCAGCATACCGAAC 59.137 43.478 0.00 0.00 0.00 3.95
596 711 4.118093 TCTCGAAAATCAGCATACCGAA 57.882 40.909 0.00 0.00 0.00 4.30
597 712 3.793797 TCTCGAAAATCAGCATACCGA 57.206 42.857 0.00 0.00 0.00 4.69
598 713 5.462068 TGTAATCTCGAAAATCAGCATACCG 59.538 40.000 0.00 0.00 0.00 4.02
599 714 6.844696 TGTAATCTCGAAAATCAGCATACC 57.155 37.500 0.00 0.00 0.00 2.73
600 715 7.910304 ACTTGTAATCTCGAAAATCAGCATAC 58.090 34.615 0.00 0.00 0.00 2.39
601 716 8.492673 AACTTGTAATCTCGAAAATCAGCATA 57.507 30.769 0.00 0.00 0.00 3.14
602 717 6.992063 ACTTGTAATCTCGAAAATCAGCAT 57.008 33.333 0.00 0.00 0.00 3.79
603 718 6.426633 TGAACTTGTAATCTCGAAAATCAGCA 59.573 34.615 0.00 0.00 0.00 4.41
604 719 6.831769 TGAACTTGTAATCTCGAAAATCAGC 58.168 36.000 0.00 0.00 0.00 4.26
605 720 7.118390 ACCTGAACTTGTAATCTCGAAAATCAG 59.882 37.037 0.00 0.00 0.00 2.90
606 721 6.934645 ACCTGAACTTGTAATCTCGAAAATCA 59.065 34.615 0.00 0.00 0.00 2.57
607 722 7.365840 ACCTGAACTTGTAATCTCGAAAATC 57.634 36.000 0.00 0.00 0.00 2.17
608 723 7.745620 AACCTGAACTTGTAATCTCGAAAAT 57.254 32.000 0.00 0.00 0.00 1.82
609 724 7.281324 TGAAACCTGAACTTGTAATCTCGAAAA 59.719 33.333 0.00 0.00 0.00 2.29
610 725 6.764085 TGAAACCTGAACTTGTAATCTCGAAA 59.236 34.615 0.00 0.00 0.00 3.46
611 726 6.285224 TGAAACCTGAACTTGTAATCTCGAA 58.715 36.000 0.00 0.00 0.00 3.71
612 727 5.849510 TGAAACCTGAACTTGTAATCTCGA 58.150 37.500 0.00 0.00 0.00 4.04
613 728 6.727824 ATGAAACCTGAACTTGTAATCTCG 57.272 37.500 0.00 0.00 0.00 4.04
620 735 9.150348 CAAAAGTTAAATGAAACCTGAACTTGT 57.850 29.630 0.00 0.00 37.24 3.16
621 736 9.150348 ACAAAAGTTAAATGAAACCTGAACTTG 57.850 29.630 0.00 0.00 37.24 3.16
622 737 9.366216 GACAAAAGTTAAATGAAACCTGAACTT 57.634 29.630 0.00 0.00 38.43 2.66
623 738 8.749354 AGACAAAAGTTAAATGAAACCTGAACT 58.251 29.630 0.00 0.00 0.00 3.01
624 739 8.926715 AGACAAAAGTTAAATGAAACCTGAAC 57.073 30.769 0.00 0.00 0.00 3.18
626 741 9.179909 TGTAGACAAAAGTTAAATGAAACCTGA 57.820 29.630 0.00 0.00 0.00 3.86
627 742 9.796120 TTGTAGACAAAAGTTAAATGAAACCTG 57.204 29.630 0.00 0.00 32.11 4.00
629 744 9.797556 ACTTGTAGACAAAAGTTAAATGAAACC 57.202 29.630 0.00 0.00 32.75 3.27
636 751 9.016438 ACCTTCAACTTGTAGACAAAAGTTAAA 57.984 29.630 0.84 0.00 43.09 1.52
637 752 8.570068 ACCTTCAACTTGTAGACAAAAGTTAA 57.430 30.769 0.84 0.00 43.09 2.01
638 753 8.570068 AACCTTCAACTTGTAGACAAAAGTTA 57.430 30.769 0.84 0.00 43.09 2.24
639 754 7.462571 AACCTTCAACTTGTAGACAAAAGTT 57.537 32.000 0.00 0.00 45.22 2.66
640 755 7.462571 AAACCTTCAACTTGTAGACAAAAGT 57.537 32.000 0.00 0.00 38.25 2.66
645 760 9.226606 CCATAATAAACCTTCAACTTGTAGACA 57.773 33.333 0.00 0.00 0.00 3.41
646 761 9.444600 TCCATAATAAACCTTCAACTTGTAGAC 57.555 33.333 0.00 0.00 0.00 2.59
649 764 9.802039 AGTTCCATAATAAACCTTCAACTTGTA 57.198 29.630 0.00 0.00 0.00 2.41
650 765 8.706322 AGTTCCATAATAAACCTTCAACTTGT 57.294 30.769 0.00 0.00 0.00 3.16
651 766 9.981114 AAAGTTCCATAATAAACCTTCAACTTG 57.019 29.630 0.00 0.00 33.09 3.16
670 785 2.561373 CTGGCGCGGAAAAGTTCC 59.439 61.111 8.83 0.00 46.62 3.62
671 786 2.126850 GCTGGCGCGGAAAAGTTC 60.127 61.111 8.83 0.00 0.00 3.01
672 787 3.670377 GGCTGGCGCGGAAAAGTT 61.670 61.111 8.83 0.00 36.88 2.66
673 788 4.947147 TGGCTGGCGCGGAAAAGT 62.947 61.111 8.83 0.00 36.88 2.66
674 789 3.443045 ATGGCTGGCGCGGAAAAG 61.443 61.111 8.83 0.00 36.88 2.27
675 790 3.746889 CATGGCTGGCGCGGAAAA 61.747 61.111 8.83 0.00 36.88 2.29
841 966 1.979693 ACCTGAGGACTCGAGTGCC 60.980 63.158 30.48 24.69 37.04 5.01
863 988 2.202531 GGACGTCGTACGAAGGGC 60.203 66.667 29.83 21.94 46.05 5.19
936 1065 1.188138 CTCGCTCGTAATTTAGCTGCG 59.812 52.381 0.00 0.00 42.70 5.18
945 1074 2.509052 TAGCATTGCTCGCTCGTAAT 57.491 45.000 15.81 0.00 40.44 1.89
995 1124 2.645281 AATGTGTGTGTGTGTGCGCG 62.645 55.000 0.00 0.00 0.00 6.86
996 1125 0.929824 GAATGTGTGTGTGTGTGCGC 60.930 55.000 0.00 0.00 0.00 6.09
997 1126 0.654184 CGAATGTGTGTGTGTGTGCG 60.654 55.000 0.00 0.00 0.00 5.34
998 1127 0.655208 TCGAATGTGTGTGTGTGTGC 59.345 50.000 0.00 0.00 0.00 4.57
999 1128 3.740832 AGTATCGAATGTGTGTGTGTGTG 59.259 43.478 0.00 0.00 0.00 3.82
1000 1129 3.987868 GAGTATCGAATGTGTGTGTGTGT 59.012 43.478 0.00 0.00 0.00 3.72
1001 1130 4.568229 GAGTATCGAATGTGTGTGTGTG 57.432 45.455 0.00 0.00 0.00 3.82
1064 1202 1.064296 CAGTAGCACTCGCGGTAGG 59.936 63.158 6.13 0.00 45.49 3.18
1098 1236 0.820891 GCACGCCCATGATCTCCATT 60.821 55.000 0.00 0.00 31.94 3.16
1336 1474 2.809601 GACGAAGCATGGACGCGT 60.810 61.111 13.85 13.85 37.97 6.01
1747 1885 4.731503 CTCGCGTCCGTCGTCGTT 62.732 66.667 5.77 0.00 42.13 3.85
2139 2277 2.981560 GAAGTACCCGCCGTCGACA 61.982 63.158 17.16 0.00 38.10 4.35
2307 2445 2.893398 GGCAGGATTCCGACGAGT 59.107 61.111 0.00 0.00 0.00 4.18
2446 2584 1.014352 CAACCCATACACGCCTAAGC 58.986 55.000 0.00 0.00 0.00 3.09
2458 2596 3.784763 ACTTCTGATGATCCTCAACCCAT 59.215 43.478 2.19 0.00 0.00 4.00
2462 2600 4.272991 GCATGACTTCTGATGATCCTCAAC 59.727 45.833 0.00 0.00 0.00 3.18
2469 2607 5.190677 TGACATTGCATGACTTCTGATGAT 58.809 37.500 0.00 0.00 0.00 2.45
2470 2608 4.581868 TGACATTGCATGACTTCTGATGA 58.418 39.130 0.00 0.00 0.00 2.92
2471 2609 4.957759 TGACATTGCATGACTTCTGATG 57.042 40.909 0.00 0.00 0.00 3.07
2476 2614 4.418392 GAACCATGACATTGCATGACTTC 58.582 43.478 17.26 13.82 46.64 3.01
2700 2990 5.408604 TGTTTAGAGCTCCTCGATGTTTTTC 59.591 40.000 10.93 0.00 35.36 2.29
2709 2999 5.924475 TTTTTCTTGTTTAGAGCTCCTCG 57.076 39.130 10.93 0.00 35.36 4.63
2733 3024 3.951037 TCAGTGCTAAAAGTGCTTTGGAA 59.049 39.130 0.00 0.00 32.36 3.53
2735 3026 3.988379 TCAGTGCTAAAAGTGCTTTGG 57.012 42.857 0.00 0.00 32.36 3.28
2737 3028 6.039717 TCTGATTTCAGTGCTAAAAGTGCTTT 59.960 34.615 7.42 0.00 44.12 3.51
2794 3101 8.915654 AGATTCTTGCAAATTTTCATAACGAAC 58.084 29.630 0.00 0.00 31.73 3.95
2797 3104 8.451687 TGAGATTCTTGCAAATTTTCATAACG 57.548 30.769 0.00 0.00 0.00 3.18
2818 3125 5.304778 TCAAAGATGACCGAACATTTGAGA 58.695 37.500 0.00 0.00 29.49 3.27
2829 3136 1.731709 TGCGAACATCAAAGATGACCG 59.268 47.619 13.46 14.69 38.69 4.79
2892 3219 0.255890 GTGATAGCTCCCAGGCCAAA 59.744 55.000 5.01 0.00 0.00 3.28
2894 3221 2.434843 CGTGATAGCTCCCAGGCCA 61.435 63.158 5.01 0.00 0.00 5.36
2895 3222 2.370647 GACGTGATAGCTCCCAGGCC 62.371 65.000 0.00 0.00 0.00 5.19
2896 3223 1.068250 GACGTGATAGCTCCCAGGC 59.932 63.158 0.00 0.00 0.00 4.85
2899 3226 3.627395 AAAATGACGTGATAGCTCCCA 57.373 42.857 0.00 0.00 0.00 4.37
2969 3653 8.383318 AGTAAAATCATATTCTTCACATCCCG 57.617 34.615 0.00 0.00 0.00 5.14
3090 4894 8.791327 AAATAAAAAGGAAATCATGCCGAAAT 57.209 26.923 0.00 0.00 0.00 2.17
3161 4965 8.514594 CACACTGGAAAAATCTGTTATATGTGT 58.485 33.333 0.00 0.00 33.52 3.72
3208 5013 8.028354 CCATTGTTGATTTTTCTACAGTATGCA 58.972 33.333 0.00 0.00 42.53 3.96
3266 5071 1.865865 AAAGCGCGAAAAGTCTCTCA 58.134 45.000 12.10 0.00 0.00 3.27
3279 5084 1.648467 ATCGGGCTCAAGAAAAGCGC 61.648 55.000 0.00 0.00 46.06 5.92
3312 5146 4.081087 CGGGTCTTGGAGAAATTTCCTCTA 60.081 45.833 14.61 7.01 38.12 2.43
3320 5154 1.139058 CCGATCGGGTCTTGGAGAAAT 59.861 52.381 26.95 0.00 0.00 2.17
3334 5168 1.007271 CGAGGTCCATTCCCGATCG 60.007 63.158 8.51 8.51 0.00 3.69
3353 5187 0.537188 TCGGGCCAGAGACAAAGATC 59.463 55.000 4.39 0.00 0.00 2.75
3396 5256 3.781770 GAGTCAGGATCAGGCGGCG 62.782 68.421 0.51 0.51 0.00 6.46
3397 5257 2.107953 GAGTCAGGATCAGGCGGC 59.892 66.667 0.00 0.00 0.00 6.53
3400 5260 0.908198 ACCTTGAGTCAGGATCAGGC 59.092 55.000 13.56 0.00 37.39 4.85
3401 5261 1.135915 CGACCTTGAGTCAGGATCAGG 59.864 57.143 13.56 10.18 46.69 3.86
3402 5262 1.135915 CCGACCTTGAGTCAGGATCAG 59.864 57.143 13.56 0.00 46.69 2.90
3404 5264 0.461961 CCCGACCTTGAGTCAGGATC 59.538 60.000 13.56 1.28 44.81 3.36
3405 5265 0.252284 ACCCGACCTTGAGTCAGGAT 60.252 55.000 13.56 0.00 44.81 3.24
3408 5268 1.592223 GGACCCGACCTTGAGTCAG 59.408 63.158 0.00 0.00 46.69 3.51
3452 5319 2.434702 ACCCCGATGTCAAATCTAGGTC 59.565 50.000 0.00 0.00 0.00 3.85
3475 5342 0.951040 CAGAACGAGACACTTGCCCC 60.951 60.000 0.00 0.00 0.00 5.80
3493 5360 7.147828 CTAGGTGTCAAACTAGATTGAGGATCA 60.148 40.741 15.06 7.51 40.55 2.92
3495 5362 6.407525 GCTAGGTGTCAAACTAGATTGAGGAT 60.408 42.308 15.06 5.56 39.84 3.24
3496 5363 5.105310 GCTAGGTGTCAAACTAGATTGAGGA 60.105 44.000 15.06 3.42 39.84 3.71
3504 5371 4.883083 TCACAAGCTAGGTGTCAAACTAG 58.117 43.478 15.63 7.98 39.68 2.57
3517 5784 2.169352 GGGAGCTGATCTTCACAAGCTA 59.831 50.000 3.19 0.00 32.34 3.32
3518 5785 1.065564 GGGAGCTGATCTTCACAAGCT 60.066 52.381 2.83 2.83 35.13 3.74
3548 5815 0.459899 TAGCATGGAGTACACAGCGG 59.540 55.000 0.00 0.00 38.20 5.52
3550 5817 1.207089 TGGTAGCATGGAGTACACAGC 59.793 52.381 0.00 0.00 34.62 4.40
3570 5837 2.771943 TCCTGGCTGGATCGTTAGATTT 59.228 45.455 9.30 0.00 40.56 2.17
3573 5840 1.403814 CTCCTGGCTGGATCGTTAGA 58.596 55.000 13.94 0.00 45.16 2.10
3583 5850 2.996631 AGATAGTTTTGCTCCTGGCTG 58.003 47.619 0.00 0.00 42.39 4.85
3584 5851 3.009473 TCAAGATAGTTTTGCTCCTGGCT 59.991 43.478 0.00 0.00 42.39 4.75
3587 5854 4.583871 AGGTCAAGATAGTTTTGCTCCTG 58.416 43.478 0.00 0.00 32.60 3.86


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

AutoCloner maintained by Alex Coulton.