Multiple sequence alignment - TraesCS2D01G497200

Loading Multiple Alignment...

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 TraesCS2D01G497200 chr2D 100.000 4004 0 0 1 4004 593217658 593221661 0.000000e+00 7395.0
1 TraesCS2D01G497200 chr2D 91.899 395 29 2 3390 3781 542742509 542742903 2.100000e-152 549.0
2 TraesCS2D01G497200 chr2D 84.291 522 60 11 37 536 531894132 531894653 1.290000e-134 490.0
3 TraesCS2D01G497200 chr2D 87.755 98 10 2 3907 4004 194823355 194823450 3.270000e-21 113.0
4 TraesCS2D01G497200 chr2A 93.455 2460 119 17 787 3210 727956594 727959047 0.000000e+00 3613.0
5 TraesCS2D01G497200 chr2A 95.208 480 22 1 3318 3796 732236512 732236033 0.000000e+00 758.0
6 TraesCS2D01G497200 chr2A 90.780 141 8 4 3865 4004 727959048 727959184 2.460000e-42 183.0
7 TraesCS2D01G497200 chr2B 91.787 2496 133 39 679 3138 719472029 719474488 0.000000e+00 3408.0
8 TraesCS2D01G497200 chr2B 95.867 871 33 2 3135 4004 719491935 719492803 0.000000e+00 1406.0
9 TraesCS2D01G497200 chr2B 77.390 659 105 24 43 672 86206489 86207132 6.370000e-93 351.0
10 TraesCS2D01G497200 chr2B 93.750 192 12 0 3318 3509 464822575 464822766 5.060000e-74 289.0
11 TraesCS2D01G497200 chr4A 89.381 565 55 4 1762 2326 692656908 692656349 0.000000e+00 706.0
12 TraesCS2D01G497200 chr4A 85.741 533 55 11 43 556 429401989 429402519 9.790000e-151 544.0
13 TraesCS2D01G497200 chr4A 89.267 382 35 3 43 418 540063756 540063375 1.300000e-129 473.0
14 TraesCS2D01G497200 chr4A 87.755 98 10 1 3907 4004 538483033 538483128 3.270000e-21 113.0
15 TraesCS2D01G497200 chr4D 91.387 476 37 3 3318 3792 168198262 168198734 0.000000e+00 649.0
16 TraesCS2D01G497200 chr4D 85.565 478 49 11 43 500 298116797 298117274 2.160000e-132 483.0
17 TraesCS2D01G497200 chr4D 88.542 384 37 4 43 419 304743472 304743089 3.650000e-125 459.0
18 TraesCS2D01G497200 chr4D 86.905 84 9 1 3921 4004 466808781 466808700 4.260000e-15 93.5
19 TraesCS2D01G497200 chr4D 100.000 45 0 0 1 45 3370935 3370979 2.560000e-12 84.2
20 TraesCS2D01G497200 chr4D 100.000 45 0 0 1 45 121073686 121073642 2.560000e-12 84.2
21 TraesCS2D01G497200 chr4D 100.000 45 0 0 1 45 474862299 474862255 2.560000e-12 84.2
22 TraesCS2D01G497200 chr6B 90.269 483 43 4 3315 3793 474270957 474271439 2.630000e-176 628.0
23 TraesCS2D01G497200 chr6B 74.407 1180 286 14 1814 2985 668777850 668776679 3.600000e-135 492.0
24 TraesCS2D01G497200 chr6B 76.177 361 75 8 1079 1435 668778579 668778226 3.180000e-41 180.0
25 TraesCS2D01G497200 chr4B 88.660 485 49 6 3318 3799 497161646 497162127 1.600000e-163 586.0
26 TraesCS2D01G497200 chr4B 90.000 330 26 7 3472 3796 288994569 288994896 1.720000e-113 420.0
27 TraesCS2D01G497200 chr7D 88.589 482 45 4 3318 3796 82898047 82897573 9.650000e-161 577.0
28 TraesCS2D01G497200 chr1A 82.576 660 89 12 43 676 309396282 309395623 3.500000e-155 558.0
29 TraesCS2D01G497200 chr1A 100.000 45 0 0 1 45 312863759 312863715 2.560000e-12 84.2
30 TraesCS2D01G497200 chr6A 74.979 1183 274 19 1814 2985 591733157 591731986 3.540000e-145 525.0
31 TraesCS2D01G497200 chr6D 74.788 1182 278 17 1814 2985 444137559 444136388 7.670000e-142 514.0
32 TraesCS2D01G497200 chr6D 76.177 361 75 8 1079 1435 444138288 444137935 3.180000e-41 180.0
33 TraesCS2D01G497200 chr6D 100.000 45 0 0 1 45 446533372 446533328 2.560000e-12 84.2
34 TraesCS2D01G497200 chr5B 86.100 482 51 10 3318 3792 493482526 493482054 4.620000e-139 505.0
35 TraesCS2D01G497200 chr5D 84.230 539 62 13 43 562 75271272 75271806 1.660000e-138 503.0
36 TraesCS2D01G497200 chr5A 83.144 528 74 15 43 561 607689135 607689656 6.060000e-128 468.0
37 TraesCS2D01G497200 chr5A 81.628 479 68 14 92 561 440671559 440672026 2.920000e-101 379.0
38 TraesCS2D01G497200 chr7B 88.342 386 36 6 43 419 562985156 562985541 4.720000e-124 455.0
39 TraesCS2D01G497200 chr7A 86.957 391 28 4 1762 2152 32953520 32953153 6.190000e-113 418.0
40 TraesCS2D01G497200 chrUn 100.000 45 0 0 1 45 112299363 112299319 2.560000e-12 84.2
41 TraesCS2D01G497200 chr1D 100.000 45 0 0 1 45 102756213 102756169 2.560000e-12 84.2
42 TraesCS2D01G497200 chr1D 100.000 45 0 0 1 45 199866984 199866940 2.560000e-12 84.2
43 TraesCS2D01G497200 chr1D 100.000 45 0 0 1 45 459929394 459929438 2.560000e-12 84.2


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 TraesCS2D01G497200 chr2D 593217658 593221661 4003 False 7395 7395 100.0000 1 4004 1 chr2D.!!$F4 4003
1 TraesCS2D01G497200 chr2D 531894132 531894653 521 False 490 490 84.2910 37 536 1 chr2D.!!$F2 499
2 TraesCS2D01G497200 chr2A 727956594 727959184 2590 False 1898 3613 92.1175 787 4004 2 chr2A.!!$F1 3217
3 TraesCS2D01G497200 chr2B 719472029 719474488 2459 False 3408 3408 91.7870 679 3138 1 chr2B.!!$F3 2459
4 TraesCS2D01G497200 chr2B 719491935 719492803 868 False 1406 1406 95.8670 3135 4004 1 chr2B.!!$F4 869
5 TraesCS2D01G497200 chr2B 86206489 86207132 643 False 351 351 77.3900 43 672 1 chr2B.!!$F1 629
6 TraesCS2D01G497200 chr4A 692656349 692656908 559 True 706 706 89.3810 1762 2326 1 chr4A.!!$R2 564
7 TraesCS2D01G497200 chr4A 429401989 429402519 530 False 544 544 85.7410 43 556 1 chr4A.!!$F1 513
8 TraesCS2D01G497200 chr6B 668776679 668778579 1900 True 336 492 75.2920 1079 2985 2 chr6B.!!$R1 1906
9 TraesCS2D01G497200 chr1A 309395623 309396282 659 True 558 558 82.5760 43 676 1 chr1A.!!$R1 633
10 TraesCS2D01G497200 chr6A 591731986 591733157 1171 True 525 525 74.9790 1814 2985 1 chr6A.!!$R1 1171
11 TraesCS2D01G497200 chr6D 444136388 444138288 1900 True 347 514 75.4825 1079 2985 2 chr6D.!!$R2 1906
12 TraesCS2D01G497200 chr5D 75271272 75271806 534 False 503 503 84.2300 43 562 1 chr5D.!!$F1 519
13 TraesCS2D01G497200 chr5A 607689135 607689656 521 False 468 468 83.1440 43 561 1 chr5A.!!$F2 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
851 894 0.035458 GGTTCAGTGGAGTGGAGTGG 59.965 60.0 0.0 0.0 0.00 4.00 F
868 911 0.108585 TGGAGCTTGCTCGTTCCTTT 59.891 50.0 15.3 0.0 35.55 3.11 F
945 991 0.949397 CCACATCATCTGATTGCCCG 59.051 55.0 0.0 0.0 31.21 6.13 F
1160 1256 1.014044 GTGAATTCGCTCACCTCGCA 61.014 55.0 11.8 0.0 39.93 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1812 1926 1.445582 CACGAAGGCCACCTCGTAC 60.446 63.158 22.24 0.0 36.08 3.67 R
2718 2835 3.591254 GAGCACCACCGACACCTCC 62.591 68.421 0.00 0.0 0.00 4.30 R
2949 3066 3.612247 GAAGCAGAAGGAGGCGCCA 62.612 63.158 31.54 0.0 40.02 5.69 R
3227 3345 5.973899 TCTTCTCTCTTATCATCCCATCG 57.026 43.478 0.00 0.0 0.00 3.84 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
41 42 9.901724 GACATTTCAAATAGACTACAACATACG 57.098 33.333 0.00 0.00 0.00 3.06
70 71 1.323412 GAGGAGGCTTGAGCTCGATA 58.677 55.000 9.64 0.00 41.70 2.92
90 91 1.271597 ACGGAGAAGCAAGCCAAGATT 60.272 47.619 0.00 0.00 0.00 2.40
124 125 1.074405 TGGAGAAGCAAGCCAAGATGT 59.926 47.619 0.00 0.00 0.00 3.06
133 134 3.264947 CAAGCCAAGATGTTCGAGATCA 58.735 45.455 8.69 0.46 0.00 2.92
137 138 3.866651 CCAAGATGTTCGAGATCAAGGT 58.133 45.455 8.69 0.00 0.00 3.50
227 229 0.463116 GTGGACCTGAACACCGTGTT 60.463 55.000 16.83 16.83 44.37 3.32
229 231 0.179067 GGACCTGAACACCGTGTTGA 60.179 55.000 21.49 12.42 41.28 3.18
255 257 1.207791 AGAGGCCATGGTTCGAGAAT 58.792 50.000 14.67 0.00 0.00 2.40
258 260 3.007398 AGAGGCCATGGTTCGAGAATATC 59.993 47.826 14.67 0.00 0.00 1.63
273 275 0.767375 ATATCCAGGCCGACATGCTT 59.233 50.000 0.00 0.00 0.00 3.91
393 404 3.826524 TCCTTTTTGTGTGCTGGATGTA 58.173 40.909 0.00 0.00 0.00 2.29
397 408 2.495155 TTGTGTGCTGGATGTATGCT 57.505 45.000 0.00 0.00 0.00 3.79
453 488 3.652057 AGGCTAACATTGTATGCCAGT 57.348 42.857 25.09 10.56 45.42 4.00
454 489 3.968265 AGGCTAACATTGTATGCCAGTT 58.032 40.909 25.09 10.03 45.42 3.16
471 507 0.748005 GTTGCTGGCATGATACCGGT 60.748 55.000 13.98 13.98 35.84 5.28
513 551 3.697166 TGGCCGCTAGTATGATCTATGA 58.303 45.455 0.00 0.00 0.00 2.15
514 552 4.281657 TGGCCGCTAGTATGATCTATGAT 58.718 43.478 0.00 0.00 0.00 2.45
520 558 5.294552 CGCTAGTATGATCTATGATCGTGGA 59.705 44.000 3.18 3.18 0.00 4.02
536 574 7.254852 TGATCGTGGACCTTTTAAATTTATGC 58.745 34.615 0.00 0.00 0.00 3.14
537 575 5.632959 TCGTGGACCTTTTAAATTTATGCG 58.367 37.500 0.00 0.00 0.00 4.73
538 576 4.264380 CGTGGACCTTTTAAATTTATGCGC 59.736 41.667 0.00 0.00 0.00 6.09
539 577 4.264380 GTGGACCTTTTAAATTTATGCGCG 59.736 41.667 0.00 0.00 0.00 6.86
540 578 3.794564 GGACCTTTTAAATTTATGCGCGG 59.205 43.478 8.83 0.00 0.00 6.46
541 579 4.439016 GGACCTTTTAAATTTATGCGCGGA 60.439 41.667 8.83 5.00 0.00 5.54
542 580 4.417506 ACCTTTTAAATTTATGCGCGGAC 58.582 39.130 8.83 0.00 0.00 4.79
543 581 4.082679 ACCTTTTAAATTTATGCGCGGACA 60.083 37.500 8.83 0.00 0.00 4.02
544 582 5.040635 CCTTTTAAATTTATGCGCGGACAT 58.959 37.500 8.83 6.32 0.00 3.06
545 583 5.051774 CCTTTTAAATTTATGCGCGGACATG 60.052 40.000 8.83 0.00 0.00 3.21
546 584 4.884458 TTAAATTTATGCGCGGACATGA 57.116 36.364 8.83 0.00 0.00 3.07
547 585 2.755836 AATTTATGCGCGGACATGAC 57.244 45.000 8.83 0.00 0.00 3.06
548 586 1.662517 ATTTATGCGCGGACATGACA 58.337 45.000 8.83 0.00 0.00 3.58
549 587 1.662517 TTTATGCGCGGACATGACAT 58.337 45.000 8.83 3.03 0.00 3.06
550 588 2.517650 TTATGCGCGGACATGACATA 57.482 45.000 8.83 1.92 0.00 2.29
551 589 2.064573 TATGCGCGGACATGACATAG 57.935 50.000 8.83 0.00 0.00 2.23
552 590 0.601046 ATGCGCGGACATGACATAGG 60.601 55.000 8.83 0.00 0.00 2.57
553 591 1.227263 GCGCGGACATGACATAGGT 60.227 57.895 8.83 0.00 0.00 3.08
554 592 1.215655 GCGCGGACATGACATAGGTC 61.216 60.000 8.83 0.00 44.57 3.85
562 600 3.617538 GACATAGGTCGTGCGCGC 61.618 66.667 27.26 27.26 38.14 6.86
565 603 4.444838 ATAGGTCGTGCGCGCCAA 62.445 61.111 30.77 8.12 36.97 4.52
572 610 4.577246 GTGCGCGCCAACCCAAAA 62.577 61.111 30.77 2.53 0.00 2.44
573 611 4.577246 TGCGCGCCAACCCAAAAC 62.577 61.111 30.77 0.00 0.00 2.43
574 612 4.577246 GCGCGCCAACCCAAAACA 62.577 61.111 23.24 0.00 0.00 2.83
575 613 2.105128 CGCGCCAACCCAAAACAA 59.895 55.556 0.00 0.00 0.00 2.83
576 614 1.519455 CGCGCCAACCCAAAACAAA 60.519 52.632 0.00 0.00 0.00 2.83
577 615 1.084370 CGCGCCAACCCAAAACAAAA 61.084 50.000 0.00 0.00 0.00 2.44
578 616 0.375454 GCGCCAACCCAAAACAAAAC 59.625 50.000 0.00 0.00 0.00 2.43
579 617 1.726853 CGCCAACCCAAAACAAAACA 58.273 45.000 0.00 0.00 0.00 2.83
580 618 2.076863 CGCCAACCCAAAACAAAACAA 58.923 42.857 0.00 0.00 0.00 2.83
581 619 2.484264 CGCCAACCCAAAACAAAACAAA 59.516 40.909 0.00 0.00 0.00 2.83
582 620 3.058224 CGCCAACCCAAAACAAAACAAAA 60.058 39.130 0.00 0.00 0.00 2.44
583 621 4.556699 CGCCAACCCAAAACAAAACAAAAA 60.557 37.500 0.00 0.00 0.00 1.94
584 622 4.681942 GCCAACCCAAAACAAAACAAAAAC 59.318 37.500 0.00 0.00 0.00 2.43
585 623 5.736207 GCCAACCCAAAACAAAACAAAAACA 60.736 36.000 0.00 0.00 0.00 2.83
586 624 5.917447 CCAACCCAAAACAAAACAAAAACAG 59.083 36.000 0.00 0.00 0.00 3.16
587 625 5.697473 ACCCAAAACAAAACAAAAACAGG 57.303 34.783 0.00 0.00 0.00 4.00
588 626 5.377478 ACCCAAAACAAAACAAAAACAGGA 58.623 33.333 0.00 0.00 0.00 3.86
589 627 5.239744 ACCCAAAACAAAACAAAAACAGGAC 59.760 36.000 0.00 0.00 0.00 3.85
590 628 5.378180 CCAAAACAAAACAAAAACAGGACG 58.622 37.500 0.00 0.00 0.00 4.79
591 629 5.378180 CAAAACAAAACAAAAACAGGACGG 58.622 37.500 0.00 0.00 0.00 4.79
592 630 4.522722 AACAAAACAAAAACAGGACGGA 57.477 36.364 0.00 0.00 0.00 4.69
593 631 4.729227 ACAAAACAAAAACAGGACGGAT 57.271 36.364 0.00 0.00 0.00 4.18
594 632 4.429108 ACAAAACAAAAACAGGACGGATG 58.571 39.130 0.00 0.00 0.00 3.51
595 633 2.793278 AACAAAAACAGGACGGATGC 57.207 45.000 0.00 0.00 0.00 3.91
596 634 1.981256 ACAAAAACAGGACGGATGCT 58.019 45.000 0.00 0.00 0.00 3.79
598 636 1.879380 CAAAAACAGGACGGATGCTGA 59.121 47.619 2.60 0.00 46.84 4.26
599 637 1.813513 AAAACAGGACGGATGCTGAG 58.186 50.000 2.60 0.00 46.84 3.35
600 638 0.674895 AAACAGGACGGATGCTGAGC 60.675 55.000 0.00 0.00 46.84 4.26
601 639 2.584418 CAGGACGGATGCTGAGCG 60.584 66.667 0.00 0.00 46.84 5.03
602 640 3.842923 AGGACGGATGCTGAGCGG 61.843 66.667 0.00 0.00 0.00 5.52
603 641 3.838271 GGACGGATGCTGAGCGGA 61.838 66.667 0.00 0.00 0.00 5.54
604 642 2.419198 GACGGATGCTGAGCGGAT 59.581 61.111 0.00 0.00 0.00 4.18
605 643 1.953138 GACGGATGCTGAGCGGATG 60.953 63.158 0.00 0.00 0.00 3.51
606 644 2.355445 GACGGATGCTGAGCGGATGA 62.355 60.000 0.00 0.00 0.00 2.92
607 645 1.953138 CGGATGCTGAGCGGATGAC 60.953 63.158 0.00 0.00 0.00 3.06
608 646 1.445095 GGATGCTGAGCGGATGACT 59.555 57.895 0.00 0.00 0.00 3.41
609 647 0.879400 GGATGCTGAGCGGATGACTG 60.879 60.000 0.00 0.00 0.00 3.51
610 648 0.103755 GATGCTGAGCGGATGACTGA 59.896 55.000 0.00 0.00 0.00 3.41
611 649 0.104487 ATGCTGAGCGGATGACTGAG 59.896 55.000 0.00 0.00 0.00 3.35
612 650 1.882167 GCTGAGCGGATGACTGAGC 60.882 63.158 0.00 0.00 37.22 4.26
613 651 1.588403 CTGAGCGGATGACTGAGCG 60.588 63.158 0.00 0.00 34.34 5.03
614 652 1.997928 CTGAGCGGATGACTGAGCGA 61.998 60.000 0.00 0.00 34.34 4.93
615 653 1.139734 GAGCGGATGACTGAGCGAA 59.860 57.895 0.00 0.00 34.34 4.70
616 654 0.458543 GAGCGGATGACTGAGCGAAA 60.459 55.000 0.00 0.00 34.34 3.46
617 655 0.737715 AGCGGATGACTGAGCGAAAC 60.738 55.000 0.00 0.00 34.34 2.78
618 656 1.014044 GCGGATGACTGAGCGAAACA 61.014 55.000 0.00 0.00 0.00 2.83
619 657 1.428448 CGGATGACTGAGCGAAACAA 58.572 50.000 0.00 0.00 0.00 2.83
620 658 1.798223 CGGATGACTGAGCGAAACAAA 59.202 47.619 0.00 0.00 0.00 2.83
621 659 2.411547 CGGATGACTGAGCGAAACAAAC 60.412 50.000 0.00 0.00 0.00 2.93
622 660 2.411547 GGATGACTGAGCGAAACAAACG 60.412 50.000 0.00 0.00 0.00 3.60
623 661 1.929230 TGACTGAGCGAAACAAACGA 58.071 45.000 0.00 0.00 0.00 3.85
624 662 2.272678 TGACTGAGCGAAACAAACGAA 58.727 42.857 0.00 0.00 0.00 3.85
625 663 2.673862 TGACTGAGCGAAACAAACGAAA 59.326 40.909 0.00 0.00 0.00 3.46
626 664 3.125487 TGACTGAGCGAAACAAACGAAAA 59.875 39.130 0.00 0.00 0.00 2.29
627 665 3.680789 ACTGAGCGAAACAAACGAAAAG 58.319 40.909 0.00 0.00 0.00 2.27
628 666 2.446282 TGAGCGAAACAAACGAAAAGC 58.554 42.857 0.00 0.00 0.00 3.51
630 668 0.496851 GCGAAACAAACGAAAAGCGG 59.503 50.000 0.00 0.00 46.49 5.52
631 669 1.856807 GCGAAACAAACGAAAAGCGGA 60.857 47.619 0.00 0.00 46.49 5.54
632 670 1.771291 CGAAACAAACGAAAAGCGGAC 59.229 47.619 0.00 0.00 46.49 4.79
633 671 2.788030 GAAACAAACGAAAAGCGGACA 58.212 42.857 0.00 0.00 46.49 4.02
634 672 2.923605 AACAAACGAAAAGCGGACAA 57.076 40.000 0.00 0.00 46.49 3.18
635 673 2.923605 ACAAACGAAAAGCGGACAAA 57.076 40.000 0.00 0.00 46.49 2.83
636 674 2.792749 ACAAACGAAAAGCGGACAAAG 58.207 42.857 0.00 0.00 46.49 2.77
637 675 2.162809 ACAAACGAAAAGCGGACAAAGT 59.837 40.909 0.00 0.00 46.49 2.66
638 676 3.374678 ACAAACGAAAAGCGGACAAAGTA 59.625 39.130 0.00 0.00 46.49 2.24
639 677 4.035909 ACAAACGAAAAGCGGACAAAGTAT 59.964 37.500 0.00 0.00 46.49 2.12
640 678 3.806316 ACGAAAAGCGGACAAAGTATG 57.194 42.857 0.00 0.00 46.49 2.39
641 679 3.135994 ACGAAAAGCGGACAAAGTATGT 58.864 40.909 0.00 0.00 46.49 2.29
642 680 3.059188 ACGAAAAGCGGACAAAGTATGTG 60.059 43.478 0.00 0.00 46.49 3.21
643 681 2.989422 AAAGCGGACAAAGTATGTGC 57.011 45.000 0.00 0.00 44.12 4.57
644 682 1.165270 AAGCGGACAAAGTATGTGCC 58.835 50.000 0.00 0.00 46.76 5.01
645 683 0.324943 AGCGGACAAAGTATGTGCCT 59.675 50.000 0.00 0.00 46.76 4.75
646 684 0.447801 GCGGACAAAGTATGTGCCTG 59.552 55.000 0.00 0.00 46.76 4.85
647 685 1.808411 CGGACAAAGTATGTGCCTGT 58.192 50.000 0.00 0.00 46.76 4.00
648 686 2.151202 CGGACAAAGTATGTGCCTGTT 58.849 47.619 0.00 0.00 46.76 3.16
649 687 2.159627 CGGACAAAGTATGTGCCTGTTC 59.840 50.000 0.00 0.00 46.76 3.18
650 688 2.159627 GGACAAAGTATGTGCCTGTTCG 59.840 50.000 0.00 0.00 43.99 3.95
651 689 2.151202 ACAAAGTATGTGCCTGTTCGG 58.849 47.619 0.00 0.00 41.93 4.30
652 690 1.468520 CAAAGTATGTGCCTGTTCGGG 59.531 52.381 0.00 0.00 0.00 5.14
653 691 0.690762 AAGTATGTGCCTGTTCGGGT 59.309 50.000 0.00 0.00 0.00 5.28
654 692 0.249398 AGTATGTGCCTGTTCGGGTC 59.751 55.000 0.00 0.00 0.00 4.46
655 693 1.082117 GTATGTGCCTGTTCGGGTCG 61.082 60.000 0.00 0.00 0.00 4.79
656 694 1.252215 TATGTGCCTGTTCGGGTCGA 61.252 55.000 0.00 0.00 0.00 4.20
657 695 2.737376 GTGCCTGTTCGGGTCGAC 60.737 66.667 7.13 7.13 34.89 4.20
658 696 4.351938 TGCCTGTTCGGGTCGACG 62.352 66.667 9.92 0.00 34.89 5.12
667 705 2.433664 GGGTCGACGCGTTGGAAT 60.434 61.111 25.66 0.00 0.00 3.01
668 706 2.030958 GGGTCGACGCGTTGGAATT 61.031 57.895 25.66 0.00 0.00 2.17
669 707 1.131826 GGTCGACGCGTTGGAATTG 59.868 57.895 25.66 0.00 0.00 2.32
670 708 1.509162 GTCGACGCGTTGGAATTGC 60.509 57.895 25.66 3.32 0.00 3.56
671 709 1.666553 TCGACGCGTTGGAATTGCT 60.667 52.632 25.66 0.00 0.00 3.91
672 710 1.225745 CGACGCGTTGGAATTGCTC 60.226 57.895 19.10 0.00 0.00 4.26
673 711 1.134694 GACGCGTTGGAATTGCTCC 59.865 57.895 15.53 0.00 45.64 4.70
674 712 1.298859 GACGCGTTGGAATTGCTCCT 61.299 55.000 15.53 0.00 45.64 3.69
675 713 0.036765 ACGCGTTGGAATTGCTCCTA 60.037 50.000 5.58 0.00 45.64 2.94
676 714 0.373716 CGCGTTGGAATTGCTCCTAC 59.626 55.000 0.00 0.00 45.64 3.18
677 715 1.448985 GCGTTGGAATTGCTCCTACA 58.551 50.000 0.00 0.00 46.84 2.74
695 733 3.728076 ACAAGCAGTAAGTCGTCTCAA 57.272 42.857 0.00 0.00 0.00 3.02
696 734 3.381949 ACAAGCAGTAAGTCGTCTCAAC 58.618 45.455 0.00 0.00 0.00 3.18
697 735 6.614847 CTACAAGCAGTAAGTCGTCTCAACG 61.615 48.000 0.00 0.00 40.26 4.10
698 736 8.899570 CTACAAGCAGTAAGTCGTCTCAACGT 62.900 46.154 0.00 0.00 40.02 3.99
747 785 0.437295 CGGACGTGCCTTTTCGTAAG 59.563 55.000 0.00 0.00 40.39 2.34
754 792 2.619646 GTGCCTTTTCGTAAGTTTGGGA 59.380 45.455 0.00 0.00 39.48 4.37
756 794 2.228103 GCCTTTTCGTAAGTTTGGGAGG 59.772 50.000 0.00 0.00 39.48 4.30
757 795 3.483421 CCTTTTCGTAAGTTTGGGAGGT 58.517 45.455 0.00 0.00 39.48 3.85
771 809 1.069668 GGGAGGTATAAATCGTGGCGT 59.930 52.381 0.00 0.00 0.00 5.68
772 810 2.132762 GGAGGTATAAATCGTGGCGTG 58.867 52.381 0.00 0.00 0.00 5.34
773 811 2.132762 GAGGTATAAATCGTGGCGTGG 58.867 52.381 0.00 0.00 0.00 4.94
774 812 0.584876 GGTATAAATCGTGGCGTGGC 59.415 55.000 0.00 0.00 0.00 5.01
775 813 0.231279 GTATAAATCGTGGCGTGGCG 59.769 55.000 0.00 0.00 0.00 5.69
776 814 0.179105 TATAAATCGTGGCGTGGCGT 60.179 50.000 0.00 0.00 0.00 5.68
777 815 1.701545 ATAAATCGTGGCGTGGCGTG 61.702 55.000 0.00 0.00 0.00 5.34
778 816 2.766875 TAAATCGTGGCGTGGCGTGA 62.767 55.000 0.00 0.00 0.00 4.35
782 820 4.012895 GTGGCGTGGCGTGACTTG 62.013 66.667 0.00 0.00 0.00 3.16
785 823 2.356553 GCGTGGCGTGACTTGGTA 60.357 61.111 0.00 0.00 0.00 3.25
800 838 0.035534 TGGTATGGCGTGCATGAGTT 60.036 50.000 10.93 0.00 0.00 3.01
815 853 4.033817 GCATGAGTTATGTCAACTCTCAGC 59.966 45.833 15.86 12.99 45.13 4.26
817 855 5.474578 TGAGTTATGTCAACTCTCAGCTT 57.525 39.130 15.86 0.00 45.13 3.74
833 876 2.486982 CAGCTTTTGGACTGATGAGTGG 59.513 50.000 0.00 0.00 35.90 4.00
849 892 0.759346 GTGGTTCAGTGGAGTGGAGT 59.241 55.000 0.00 0.00 0.00 3.85
850 893 0.758734 TGGTTCAGTGGAGTGGAGTG 59.241 55.000 0.00 0.00 0.00 3.51
851 894 0.035458 GGTTCAGTGGAGTGGAGTGG 59.965 60.000 0.00 0.00 0.00 4.00
852 895 1.048601 GTTCAGTGGAGTGGAGTGGA 58.951 55.000 0.00 0.00 0.00 4.02
853 896 1.001406 GTTCAGTGGAGTGGAGTGGAG 59.999 57.143 0.00 0.00 0.00 3.86
856 899 0.472734 AGTGGAGTGGAGTGGAGCTT 60.473 55.000 0.00 0.00 0.00 3.74
858 901 1.376553 GGAGTGGAGTGGAGCTTGC 60.377 63.158 0.00 0.00 0.00 4.01
868 911 0.108585 TGGAGCTTGCTCGTTCCTTT 59.891 50.000 15.30 0.00 35.55 3.11
880 923 2.158667 TCGTTCCTTTCCTTTCCTTGCT 60.159 45.455 0.00 0.00 0.00 3.91
900 946 7.308109 CCTTGCTTAGTACGGTAATCAACAAAA 60.308 37.037 0.00 0.00 0.00 2.44
908 954 5.757886 ACGGTAATCAACAAAACAGACATG 58.242 37.500 0.00 0.00 0.00 3.21
909 955 4.616802 CGGTAATCAACAAAACAGACATGC 59.383 41.667 0.00 0.00 0.00 4.06
910 956 5.527951 GGTAATCAACAAAACAGACATGCA 58.472 37.500 0.00 0.00 0.00 3.96
911 957 6.158598 GGTAATCAACAAAACAGACATGCAT 58.841 36.000 0.00 0.00 0.00 3.96
923 969 6.862711 ACAGACATGCATCATCAATAAGAG 57.137 37.500 0.00 0.00 0.00 2.85
924 970 6.354938 ACAGACATGCATCATCAATAAGAGT 58.645 36.000 0.00 0.00 0.00 3.24
925 971 6.827251 ACAGACATGCATCATCAATAAGAGTT 59.173 34.615 0.00 0.00 0.00 3.01
926 972 7.012138 ACAGACATGCATCATCAATAAGAGTTC 59.988 37.037 0.00 0.00 0.00 3.01
928 974 6.124340 ACATGCATCATCAATAAGAGTTCCA 58.876 36.000 0.00 0.00 0.00 3.53
929 975 6.039047 ACATGCATCATCAATAAGAGTTCCAC 59.961 38.462 0.00 0.00 0.00 4.02
930 976 5.499313 TGCATCATCAATAAGAGTTCCACA 58.501 37.500 0.00 0.00 0.00 4.17
931 977 6.124340 TGCATCATCAATAAGAGTTCCACAT 58.876 36.000 0.00 0.00 0.00 3.21
934 980 7.040617 GCATCATCAATAAGAGTTCCACATCAT 60.041 37.037 0.00 0.00 0.00 2.45
936 982 7.799081 TCATCAATAAGAGTTCCACATCATCT 58.201 34.615 0.00 0.00 0.00 2.90
937 983 7.713942 TCATCAATAAGAGTTCCACATCATCTG 59.286 37.037 0.00 0.00 0.00 2.90
938 984 7.186570 TCAATAAGAGTTCCACATCATCTGA 57.813 36.000 0.00 0.00 0.00 3.27
939 985 7.799081 TCAATAAGAGTTCCACATCATCTGAT 58.201 34.615 0.00 0.00 34.56 2.90
940 986 8.270030 TCAATAAGAGTTCCACATCATCTGATT 58.730 33.333 0.00 0.00 31.21 2.57
941 987 8.343366 CAATAAGAGTTCCACATCATCTGATTG 58.657 37.037 0.00 0.00 34.25 2.67
943 989 3.285484 AGTTCCACATCATCTGATTGCC 58.715 45.455 0.00 0.00 31.21 4.52
945 991 0.949397 CCACATCATCTGATTGCCCG 59.051 55.000 0.00 0.00 31.21 6.13
991 1063 3.752339 GGCGGCCTCTTTGCAAGG 61.752 66.667 12.87 1.35 36.95 3.61
1012 1099 3.224007 AAGGCAATGGCGTCCCCTT 62.224 57.895 0.00 5.33 42.47 3.95
1027 1114 1.553690 CCCTTCCACGTCCACCATCT 61.554 60.000 0.00 0.00 0.00 2.90
1160 1256 1.014044 GTGAATTCGCTCACCTCGCA 61.014 55.000 11.80 0.00 39.93 5.10
1173 1269 1.447489 CTCGCAGTCCTCCAAGCTG 60.447 63.158 0.00 0.00 0.00 4.24
1176 1272 2.435586 CAGTCCTCCAAGCTGCCG 60.436 66.667 0.00 0.00 0.00 5.69
1458 1554 2.781595 ATAATCCCATCGCGCCGGAC 62.782 60.000 5.05 0.00 0.00 4.79
1575 1671 2.425592 CAGAGGAACGGCACCACA 59.574 61.111 0.00 0.00 0.00 4.17
1671 1785 2.126580 GTCGTCGGGTTCGAGGTG 60.127 66.667 8.04 0.00 46.91 4.00
2715 2832 4.935495 CTGCTGGTGGCGGTGTGT 62.935 66.667 0.00 0.00 45.43 3.72
3234 3352 0.692756 TTGGGCCACTATCGATGGGA 60.693 55.000 5.23 0.00 37.73 4.37
3266 3384 7.987458 AGAGAGAAGAACTAACAATGACACAAA 59.013 33.333 0.00 0.00 0.00 2.83
3272 3390 8.225603 AGAACTAACAATGACACAAATCACTT 57.774 30.769 0.00 0.00 0.00 3.16
3344 3462 2.646799 AAGTGCTCGTGCGTTGCAAC 62.647 55.000 19.89 19.89 41.47 4.17
3345 3463 3.198489 TGCTCGTGCGTTGCAACA 61.198 55.556 28.01 8.05 41.47 3.33
3366 3484 7.301054 CAACAGGAGAAAAGAATATGACACAC 58.699 38.462 0.00 0.00 0.00 3.82
3461 3580 4.432712 ACAAAAGCGCAAGTTCAAGATTT 58.567 34.783 11.47 0.00 41.68 2.17
3548 3667 7.588854 CGGATAATGCACTGTTGATTAAGATTG 59.411 37.037 0.00 0.00 0.00 2.67
3719 3838 0.519519 CGCTGCGGGTTTAATGTCAA 59.480 50.000 15.40 0.00 0.00 3.18
3747 3866 5.871324 TCAGGGGGTTTTCTATAAAAGGT 57.129 39.130 0.00 0.00 35.29 3.50
3755 3874 6.238566 GGGTTTTCTATAAAAGGTATGACGGC 60.239 42.308 0.00 0.00 35.29 5.68
3761 3880 2.327200 AAAGGTATGACGGCCTAAGC 57.673 50.000 0.00 0.00 34.15 3.09
3765 3884 2.299297 AGGTATGACGGCCTAAGCATAC 59.701 50.000 18.23 18.23 42.56 2.39
3854 3973 5.668558 ACTTTGAAATGTGGAGTCGTTAC 57.331 39.130 0.00 0.00 0.00 2.50
3886 4005 9.706529 ATCTAGCATGATCACTATATCAACCTA 57.293 33.333 0.00 0.00 39.25 3.08
3887 4006 9.706529 TCTAGCATGATCACTATATCAACCTAT 57.293 33.333 0.00 0.00 39.25 2.57
3890 4009 8.819845 AGCATGATCACTATATCAACCTATTCA 58.180 33.333 0.00 0.00 39.25 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 9.901724 CGTATGTTGTAGTCTATTTGAAATGTC 57.098 33.333 0.00 0.00 0.00 3.06
16 17 8.879759 CCGTATGTTGTAGTCTATTTGAAATGT 58.120 33.333 0.00 0.00 0.00 2.71
17 18 9.093970 TCCGTATGTTGTAGTCTATTTGAAATG 57.906 33.333 0.00 0.00 0.00 2.32
18 19 9.832445 ATCCGTATGTTGTAGTCTATTTGAAAT 57.168 29.630 0.00 0.00 0.00 2.17
19 20 9.309516 GATCCGTATGTTGTAGTCTATTTGAAA 57.690 33.333 0.00 0.00 0.00 2.69
20 21 7.924412 GGATCCGTATGTTGTAGTCTATTTGAA 59.076 37.037 0.00 0.00 0.00 2.69
21 22 7.068962 TGGATCCGTATGTTGTAGTCTATTTGA 59.931 37.037 7.39 0.00 0.00 2.69
22 23 7.207383 TGGATCCGTATGTTGTAGTCTATTTG 58.793 38.462 7.39 0.00 0.00 2.32
23 24 7.356089 TGGATCCGTATGTTGTAGTCTATTT 57.644 36.000 7.39 0.00 0.00 1.40
24 25 6.971726 TGGATCCGTATGTTGTAGTCTATT 57.028 37.500 7.39 0.00 0.00 1.73
25 26 6.971726 TTGGATCCGTATGTTGTAGTCTAT 57.028 37.500 7.39 0.00 0.00 1.98
26 27 6.183360 CCTTTGGATCCGTATGTTGTAGTCTA 60.183 42.308 7.39 0.00 0.00 2.59
27 28 5.395324 CCTTTGGATCCGTATGTTGTAGTCT 60.395 44.000 7.39 0.00 0.00 3.24
28 29 4.809426 CCTTTGGATCCGTATGTTGTAGTC 59.191 45.833 7.39 0.00 0.00 2.59
29 30 4.468510 TCCTTTGGATCCGTATGTTGTAGT 59.531 41.667 7.39 0.00 0.00 2.73
30 31 5.018539 TCCTTTGGATCCGTATGTTGTAG 57.981 43.478 7.39 0.00 0.00 2.74
31 32 4.141801 CCTCCTTTGGATCCGTATGTTGTA 60.142 45.833 7.39 0.00 0.00 2.41
32 33 3.370527 CCTCCTTTGGATCCGTATGTTGT 60.371 47.826 7.39 0.00 0.00 3.32
33 34 3.118408 TCCTCCTTTGGATCCGTATGTTG 60.118 47.826 7.39 0.00 0.00 3.33
34 35 3.112263 TCCTCCTTTGGATCCGTATGTT 58.888 45.455 7.39 0.00 0.00 2.71
35 36 2.700897 CTCCTCCTTTGGATCCGTATGT 59.299 50.000 7.39 0.00 35.30 2.29
40 41 1.147153 GCCTCCTCCTTTGGATCCG 59.853 63.158 7.39 0.00 35.30 4.18
41 42 0.922626 AAGCCTCCTCCTTTGGATCC 59.077 55.000 4.20 4.20 35.30 3.36
70 71 0.326264 ATCTTGGCTTGCTTCTCCGT 59.674 50.000 0.00 0.00 0.00 4.69
90 91 2.928036 TCTCCACCTCCATCTCAAGA 57.072 50.000 0.00 0.00 0.00 3.02
124 125 0.606096 TTGGCGACCTTGATCTCGAA 59.394 50.000 6.30 0.00 31.24 3.71
133 134 1.074775 TCTTGGCATTGGCGACCTT 59.925 52.632 5.68 0.00 42.47 3.50
137 138 1.228398 TTGGTCTTGGCATTGGCGA 60.228 52.632 5.68 2.64 42.47 5.54
227 229 1.617018 CCATGGCCTCTTCCTCGTCA 61.617 60.000 3.32 0.00 0.00 4.35
229 231 1.201429 AACCATGGCCTCTTCCTCGT 61.201 55.000 13.04 0.00 0.00 4.18
255 257 1.419381 TAAGCATGTCGGCCTGGATA 58.581 50.000 0.00 0.00 0.00 2.59
258 260 0.392998 ACTTAAGCATGTCGGCCTGG 60.393 55.000 0.00 0.00 0.00 4.45
273 275 2.998670 AGATCACTCGTCGTCGAACTTA 59.001 45.455 6.19 0.00 45.61 2.24
432 467 4.771114 ACTGGCATACAATGTTAGCCTA 57.229 40.909 22.86 12.49 45.42 3.93
439 474 1.820519 CCAGCAACTGGCATACAATGT 59.179 47.619 0.00 0.00 45.13 2.71
453 488 0.833949 TACCGGTATCATGCCAGCAA 59.166 50.000 11.16 0.00 0.00 3.91
454 489 1.055849 ATACCGGTATCATGCCAGCA 58.944 50.000 21.72 0.00 0.00 4.41
466 502 0.675522 CGCCCAAAGTTCATACCGGT 60.676 55.000 13.98 13.98 0.00 5.28
471 507 3.342377 TGTCATCGCCCAAAGTTCATA 57.658 42.857 0.00 0.00 0.00 2.15
513 551 6.262601 CGCATAAATTTAAAAGGTCCACGAT 58.737 36.000 1.21 0.00 0.00 3.73
514 552 5.632959 CGCATAAATTTAAAAGGTCCACGA 58.367 37.500 1.21 0.00 0.00 4.35
520 558 4.082679 TGTCCGCGCATAAATTTAAAAGGT 60.083 37.500 8.75 0.00 0.00 3.50
536 574 0.934901 CGACCTATGTCATGTCCGCG 60.935 60.000 0.00 0.00 41.85 6.46
537 575 0.102481 ACGACCTATGTCATGTCCGC 59.898 55.000 0.00 0.00 41.85 5.54
538 576 1.840181 CACGACCTATGTCATGTCCG 58.160 55.000 0.00 0.00 41.85 4.79
539 577 1.571919 GCACGACCTATGTCATGTCC 58.428 55.000 0.00 0.00 41.85 4.02
540 578 1.200483 CGCACGACCTATGTCATGTC 58.800 55.000 0.00 0.00 41.85 3.06
541 579 0.806102 GCGCACGACCTATGTCATGT 60.806 55.000 0.30 0.00 41.85 3.21
542 580 1.811217 CGCGCACGACCTATGTCATG 61.811 60.000 8.75 0.00 43.93 3.07
543 581 1.588932 CGCGCACGACCTATGTCAT 60.589 57.895 8.75 0.00 43.93 3.06
544 582 2.202557 CGCGCACGACCTATGTCA 60.203 61.111 8.75 0.00 43.93 3.58
545 583 3.617538 GCGCGCACGACCTATGTC 61.618 66.667 29.10 0.00 43.93 3.06
555 593 4.577246 TTTTGGGTTGGCGCGCAC 62.577 61.111 34.42 23.13 0.00 5.34
556 594 4.577246 GTTTTGGGTTGGCGCGCA 62.577 61.111 34.42 16.55 0.00 6.09
557 595 4.577246 TGTTTTGGGTTGGCGCGC 62.577 61.111 25.94 25.94 0.00 6.86
558 596 1.084370 TTTTGTTTTGGGTTGGCGCG 61.084 50.000 0.00 0.00 0.00 6.86
559 597 0.375454 GTTTTGTTTTGGGTTGGCGC 59.625 50.000 0.00 0.00 0.00 6.53
560 598 1.726853 TGTTTTGTTTTGGGTTGGCG 58.273 45.000 0.00 0.00 0.00 5.69
561 599 4.505313 TTTTGTTTTGTTTTGGGTTGGC 57.495 36.364 0.00 0.00 0.00 4.52
562 600 5.831997 TGTTTTTGTTTTGTTTTGGGTTGG 58.168 33.333 0.00 0.00 0.00 3.77
563 601 5.917447 CCTGTTTTTGTTTTGTTTTGGGTTG 59.083 36.000 0.00 0.00 0.00 3.77
564 602 5.828328 TCCTGTTTTTGTTTTGTTTTGGGTT 59.172 32.000 0.00 0.00 0.00 4.11
565 603 5.239744 GTCCTGTTTTTGTTTTGTTTTGGGT 59.760 36.000 0.00 0.00 0.00 4.51
566 604 5.615764 CGTCCTGTTTTTGTTTTGTTTTGGG 60.616 40.000 0.00 0.00 0.00 4.12
567 605 5.378180 CGTCCTGTTTTTGTTTTGTTTTGG 58.622 37.500 0.00 0.00 0.00 3.28
568 606 5.177696 TCCGTCCTGTTTTTGTTTTGTTTTG 59.822 36.000 0.00 0.00 0.00 2.44
569 607 5.298347 TCCGTCCTGTTTTTGTTTTGTTTT 58.702 33.333 0.00 0.00 0.00 2.43
570 608 4.884247 TCCGTCCTGTTTTTGTTTTGTTT 58.116 34.783 0.00 0.00 0.00 2.83
571 609 4.522722 TCCGTCCTGTTTTTGTTTTGTT 57.477 36.364 0.00 0.00 0.00 2.83
572 610 4.429108 CATCCGTCCTGTTTTTGTTTTGT 58.571 39.130 0.00 0.00 0.00 2.83
573 611 3.245048 GCATCCGTCCTGTTTTTGTTTTG 59.755 43.478 0.00 0.00 0.00 2.44
574 612 3.132111 AGCATCCGTCCTGTTTTTGTTTT 59.868 39.130 0.00 0.00 0.00 2.43
575 613 2.693074 AGCATCCGTCCTGTTTTTGTTT 59.307 40.909 0.00 0.00 0.00 2.83
576 614 2.034558 CAGCATCCGTCCTGTTTTTGTT 59.965 45.455 0.00 0.00 0.00 2.83
577 615 1.608590 CAGCATCCGTCCTGTTTTTGT 59.391 47.619 0.00 0.00 0.00 2.83
578 616 1.879380 TCAGCATCCGTCCTGTTTTTG 59.121 47.619 0.00 0.00 0.00 2.44
579 617 2.154462 CTCAGCATCCGTCCTGTTTTT 58.846 47.619 0.00 0.00 0.00 1.94
580 618 1.813513 CTCAGCATCCGTCCTGTTTT 58.186 50.000 0.00 0.00 0.00 2.43
581 619 0.674895 GCTCAGCATCCGTCCTGTTT 60.675 55.000 0.00 0.00 0.00 2.83
582 620 1.078848 GCTCAGCATCCGTCCTGTT 60.079 57.895 0.00 0.00 0.00 3.16
583 621 2.581354 GCTCAGCATCCGTCCTGT 59.419 61.111 0.00 0.00 0.00 4.00
584 622 2.584418 CGCTCAGCATCCGTCCTG 60.584 66.667 0.00 0.00 0.00 3.86
585 623 3.842923 CCGCTCAGCATCCGTCCT 61.843 66.667 0.00 0.00 0.00 3.85
586 624 3.157217 ATCCGCTCAGCATCCGTCC 62.157 63.158 0.00 0.00 0.00 4.79
587 625 1.953138 CATCCGCTCAGCATCCGTC 60.953 63.158 0.00 0.00 0.00 4.79
588 626 2.107750 CATCCGCTCAGCATCCGT 59.892 61.111 0.00 0.00 0.00 4.69
589 627 1.953138 GTCATCCGCTCAGCATCCG 60.953 63.158 0.00 0.00 0.00 4.18
590 628 0.879400 CAGTCATCCGCTCAGCATCC 60.879 60.000 0.00 0.00 0.00 3.51
591 629 0.103755 TCAGTCATCCGCTCAGCATC 59.896 55.000 0.00 0.00 0.00 3.91
592 630 0.104487 CTCAGTCATCCGCTCAGCAT 59.896 55.000 0.00 0.00 0.00 3.79
593 631 1.514553 CTCAGTCATCCGCTCAGCA 59.485 57.895 0.00 0.00 0.00 4.41
594 632 1.882167 GCTCAGTCATCCGCTCAGC 60.882 63.158 0.00 0.00 0.00 4.26
595 633 1.588403 CGCTCAGTCATCCGCTCAG 60.588 63.158 0.00 0.00 0.00 3.35
596 634 1.595093 TTCGCTCAGTCATCCGCTCA 61.595 55.000 0.00 0.00 0.00 4.26
597 635 0.458543 TTTCGCTCAGTCATCCGCTC 60.459 55.000 0.00 0.00 0.00 5.03
598 636 0.737715 GTTTCGCTCAGTCATCCGCT 60.738 55.000 0.00 0.00 0.00 5.52
599 637 1.014044 TGTTTCGCTCAGTCATCCGC 61.014 55.000 0.00 0.00 0.00 5.54
600 638 1.428448 TTGTTTCGCTCAGTCATCCG 58.572 50.000 0.00 0.00 0.00 4.18
601 639 2.411547 CGTTTGTTTCGCTCAGTCATCC 60.412 50.000 0.00 0.00 0.00 3.51
602 640 2.475111 TCGTTTGTTTCGCTCAGTCATC 59.525 45.455 0.00 0.00 0.00 2.92
603 641 2.479837 TCGTTTGTTTCGCTCAGTCAT 58.520 42.857 0.00 0.00 0.00 3.06
604 642 1.929230 TCGTTTGTTTCGCTCAGTCA 58.071 45.000 0.00 0.00 0.00 3.41
605 643 3.313274 TTTCGTTTGTTTCGCTCAGTC 57.687 42.857 0.00 0.00 0.00 3.51
606 644 3.680789 CTTTTCGTTTGTTTCGCTCAGT 58.319 40.909 0.00 0.00 0.00 3.41
607 645 2.464016 GCTTTTCGTTTGTTTCGCTCAG 59.536 45.455 0.00 0.00 0.00 3.35
608 646 2.446282 GCTTTTCGTTTGTTTCGCTCA 58.554 42.857 0.00 0.00 0.00 4.26
609 647 1.443176 CGCTTTTCGTTTGTTTCGCTC 59.557 47.619 0.00 0.00 0.00 5.03
610 648 1.462791 CGCTTTTCGTTTGTTTCGCT 58.537 45.000 0.00 0.00 0.00 4.93
611 649 0.496851 CCGCTTTTCGTTTGTTTCGC 59.503 50.000 0.00 0.00 36.19 4.70
612 650 1.771291 GTCCGCTTTTCGTTTGTTTCG 59.229 47.619 0.00 0.00 36.19 3.46
613 651 2.788030 TGTCCGCTTTTCGTTTGTTTC 58.212 42.857 0.00 0.00 36.19 2.78
614 652 2.923605 TGTCCGCTTTTCGTTTGTTT 57.076 40.000 0.00 0.00 36.19 2.83
615 653 2.923605 TTGTCCGCTTTTCGTTTGTT 57.076 40.000 0.00 0.00 36.19 2.83
616 654 2.162809 ACTTTGTCCGCTTTTCGTTTGT 59.837 40.909 0.00 0.00 36.19 2.83
617 655 2.792749 ACTTTGTCCGCTTTTCGTTTG 58.207 42.857 0.00 0.00 36.19 2.93
618 656 4.035909 ACATACTTTGTCCGCTTTTCGTTT 59.964 37.500 0.00 0.00 30.89 3.60
619 657 3.562557 ACATACTTTGTCCGCTTTTCGTT 59.437 39.130 0.00 0.00 30.89 3.85
620 658 3.059188 CACATACTTTGTCCGCTTTTCGT 60.059 43.478 0.00 0.00 36.00 3.85
621 659 3.479006 CACATACTTTGTCCGCTTTTCG 58.521 45.455 0.00 0.00 36.00 3.46
622 660 3.234386 GCACATACTTTGTCCGCTTTTC 58.766 45.455 0.00 0.00 36.00 2.29
623 661 2.030274 GGCACATACTTTGTCCGCTTTT 60.030 45.455 0.00 0.00 36.00 2.27
624 662 1.539827 GGCACATACTTTGTCCGCTTT 59.460 47.619 0.00 0.00 36.00 3.51
625 663 1.165270 GGCACATACTTTGTCCGCTT 58.835 50.000 0.00 0.00 36.00 4.68
626 664 0.324943 AGGCACATACTTTGTCCGCT 59.675 50.000 0.00 0.00 36.00 5.52
627 665 0.447801 CAGGCACATACTTTGTCCGC 59.552 55.000 0.00 0.00 36.00 5.54
628 666 1.808411 ACAGGCACATACTTTGTCCG 58.192 50.000 0.00 0.00 36.00 4.79
629 667 2.159627 CGAACAGGCACATACTTTGTCC 59.840 50.000 0.00 0.00 36.00 4.02
630 668 2.159627 CCGAACAGGCACATACTTTGTC 59.840 50.000 0.00 0.00 36.00 3.18
631 669 2.151202 CCGAACAGGCACATACTTTGT 58.849 47.619 0.00 0.00 39.91 2.83
632 670 1.468520 CCCGAACAGGCACATACTTTG 59.531 52.381 0.00 0.00 39.21 2.77
633 671 1.073284 ACCCGAACAGGCACATACTTT 59.927 47.619 0.00 0.00 39.21 2.66
634 672 0.690762 ACCCGAACAGGCACATACTT 59.309 50.000 0.00 0.00 39.21 2.24
635 673 0.249398 GACCCGAACAGGCACATACT 59.751 55.000 0.00 0.00 39.21 2.12
636 674 1.082117 CGACCCGAACAGGCACATAC 61.082 60.000 0.00 0.00 39.21 2.39
637 675 1.216977 CGACCCGAACAGGCACATA 59.783 57.895 0.00 0.00 39.21 2.29
638 676 2.047274 CGACCCGAACAGGCACAT 60.047 61.111 0.00 0.00 39.21 3.21
639 677 3.228017 TCGACCCGAACAGGCACA 61.228 61.111 0.00 0.00 39.21 4.57
640 678 2.737376 GTCGACCCGAACAGGCAC 60.737 66.667 3.51 0.00 37.72 5.01
641 679 4.351938 CGTCGACCCGAACAGGCA 62.352 66.667 10.58 0.00 37.72 4.75
644 682 4.695231 ACGCGTCGACCCGAACAG 62.695 66.667 27.72 4.81 37.72 3.16
645 683 4.268939 AACGCGTCGACCCGAACA 62.269 61.111 27.72 0.00 37.72 3.18
646 684 3.759828 CAACGCGTCGACCCGAAC 61.760 66.667 27.72 3.57 37.72 3.95
650 688 2.030958 AATTCCAACGCGTCGACCC 61.031 57.895 14.44 0.00 0.00 4.46
651 689 1.131826 CAATTCCAACGCGTCGACC 59.868 57.895 14.44 1.77 0.00 4.79
652 690 1.509162 GCAATTCCAACGCGTCGAC 60.509 57.895 14.44 5.18 0.00 4.20
653 691 1.623081 GAGCAATTCCAACGCGTCGA 61.623 55.000 14.44 8.80 0.00 4.20
654 692 1.225745 GAGCAATTCCAACGCGTCG 60.226 57.895 14.44 0.00 0.00 5.12
655 693 1.134694 GGAGCAATTCCAACGCGTC 59.865 57.895 14.44 0.00 46.01 5.19
656 694 3.263941 GGAGCAATTCCAACGCGT 58.736 55.556 5.58 5.58 46.01 6.01
669 707 2.094649 ACGACTTACTGCTTGTAGGAGC 60.095 50.000 0.00 0.00 37.15 4.70
670 708 3.440872 AGACGACTTACTGCTTGTAGGAG 59.559 47.826 0.00 0.00 39.79 3.69
671 709 3.418995 AGACGACTTACTGCTTGTAGGA 58.581 45.455 0.00 0.00 33.16 2.94
672 710 3.190744 TGAGACGACTTACTGCTTGTAGG 59.809 47.826 0.00 0.00 34.79 3.18
673 711 4.421033 TGAGACGACTTACTGCTTGTAG 57.579 45.455 0.00 0.00 32.08 2.74
674 712 4.543692 GTTGAGACGACTTACTGCTTGTA 58.456 43.478 0.00 0.00 0.00 2.41
675 713 3.381949 GTTGAGACGACTTACTGCTTGT 58.618 45.455 0.00 0.00 0.00 3.16
747 785 3.314357 GCCACGATTTATACCTCCCAAAC 59.686 47.826 0.00 0.00 0.00 2.93
754 792 1.808891 GCCACGCCACGATTTATACCT 60.809 52.381 0.00 0.00 0.00 3.08
756 794 0.231279 CGCCACGCCACGATTTATAC 59.769 55.000 0.00 0.00 0.00 1.47
757 795 0.179105 ACGCCACGCCACGATTTATA 60.179 50.000 0.00 0.00 0.00 0.98
771 809 1.376683 GCCATACCAAGTCACGCCA 60.377 57.895 0.00 0.00 0.00 5.69
772 810 2.461110 CGCCATACCAAGTCACGCC 61.461 63.158 0.00 0.00 0.00 5.68
773 811 1.740296 ACGCCATACCAAGTCACGC 60.740 57.895 0.00 0.00 0.00 5.34
774 812 1.966493 GCACGCCATACCAAGTCACG 61.966 60.000 0.00 0.00 0.00 4.35
775 813 0.953471 TGCACGCCATACCAAGTCAC 60.953 55.000 0.00 0.00 0.00 3.67
776 814 0.035534 ATGCACGCCATACCAAGTCA 60.036 50.000 0.00 0.00 30.69 3.41
777 815 0.378257 CATGCACGCCATACCAAGTC 59.622 55.000 0.00 0.00 31.47 3.01
778 816 0.035534 TCATGCACGCCATACCAAGT 60.036 50.000 0.00 0.00 31.47 3.16
779 817 0.659427 CTCATGCACGCCATACCAAG 59.341 55.000 0.00 0.00 31.47 3.61
780 818 0.035534 ACTCATGCACGCCATACCAA 60.036 50.000 0.00 0.00 31.47 3.67
781 819 0.035534 AACTCATGCACGCCATACCA 60.036 50.000 0.00 0.00 31.47 3.25
782 820 1.948104 TAACTCATGCACGCCATACC 58.052 50.000 0.00 0.00 31.47 2.73
783 821 2.872245 ACATAACTCATGCACGCCATAC 59.128 45.455 0.00 0.00 38.29 2.39
784 822 3.130633 GACATAACTCATGCACGCCATA 58.869 45.455 0.00 0.00 38.29 2.74
785 823 1.942657 GACATAACTCATGCACGCCAT 59.057 47.619 0.00 0.00 38.29 4.40
800 838 4.997395 GTCCAAAAGCTGAGAGTTGACATA 59.003 41.667 0.00 0.00 0.00 2.29
815 853 4.136796 TGAACCACTCATCAGTCCAAAAG 58.863 43.478 0.00 0.00 0.00 2.27
817 855 3.743521 CTGAACCACTCATCAGTCCAAA 58.256 45.455 0.00 0.00 38.57 3.28
833 876 1.001406 CTCCACTCCACTCCACTGAAC 59.999 57.143 0.00 0.00 0.00 3.18
849 892 0.108585 AAAGGAACGAGCAAGCTCCA 59.891 50.000 15.81 0.00 39.77 3.86
850 893 0.799393 GAAAGGAACGAGCAAGCTCC 59.201 55.000 15.81 3.37 39.77 4.70
851 894 0.799393 GGAAAGGAACGAGCAAGCTC 59.201 55.000 11.94 11.94 39.55 4.09
852 895 0.398318 AGGAAAGGAACGAGCAAGCT 59.602 50.000 0.00 0.00 0.00 3.74
853 896 1.239347 AAGGAAAGGAACGAGCAAGC 58.761 50.000 0.00 0.00 0.00 4.01
856 899 1.420138 AGGAAAGGAAAGGAACGAGCA 59.580 47.619 0.00 0.00 0.00 4.26
858 901 2.226674 GCAAGGAAAGGAAAGGAACGAG 59.773 50.000 0.00 0.00 0.00 4.18
868 911 2.901839 ACCGTACTAAGCAAGGAAAGGA 59.098 45.455 0.00 0.00 0.00 3.36
880 923 7.710044 TGTCTGTTTTGTTGATTACCGTACTAA 59.290 33.333 0.00 0.00 0.00 2.24
900 946 6.354938 ACTCTTATTGATGATGCATGTCTGT 58.645 36.000 2.46 0.00 0.00 3.41
908 954 6.261603 TGATGTGGAACTCTTATTGATGATGC 59.738 38.462 0.00 0.00 38.04 3.91
909 955 7.797038 TGATGTGGAACTCTTATTGATGATG 57.203 36.000 0.00 0.00 38.04 3.07
910 956 8.438373 AGATGATGTGGAACTCTTATTGATGAT 58.562 33.333 0.00 0.00 38.04 2.45
911 957 7.713942 CAGATGATGTGGAACTCTTATTGATGA 59.286 37.037 0.00 0.00 38.04 2.92
923 969 2.360165 GGGCAATCAGATGATGTGGAAC 59.640 50.000 0.00 0.00 34.49 3.62
924 970 2.658285 GGGCAATCAGATGATGTGGAA 58.342 47.619 0.00 0.00 34.49 3.53
925 971 1.475571 CGGGCAATCAGATGATGTGGA 60.476 52.381 0.00 0.00 34.49 4.02
926 972 0.949397 CGGGCAATCAGATGATGTGG 59.051 55.000 0.00 0.00 34.49 4.17
928 974 0.820891 GCCGGGCAATCAGATGATGT 60.821 55.000 15.62 0.00 34.49 3.06
929 975 0.820482 TGCCGGGCAATCAGATGATG 60.820 55.000 21.55 0.00 34.76 3.07
930 976 0.106569 TTGCCGGGCAATCAGATGAT 60.107 50.000 29.66 0.00 43.99 2.45
931 977 1.302617 TTGCCGGGCAATCAGATGA 59.697 52.632 29.66 5.96 43.99 2.92
943 989 2.040213 CTATCGCTGCTGTTTGCCGG 62.040 60.000 0.00 0.00 42.00 6.13
945 991 0.654683 CTCTATCGCTGCTGTTTGCC 59.345 55.000 0.00 0.00 42.00 4.52
1005 1092 2.346365 GTGGACGTGGAAGGGGAC 59.654 66.667 0.00 0.00 0.00 4.46
1012 1099 0.895530 GAGAAGATGGTGGACGTGGA 59.104 55.000 0.00 0.00 0.00 4.02
1027 1114 2.907042 GGAAGAGAAGAAGGGTGGAGAA 59.093 50.000 0.00 0.00 0.00 2.87
1146 1242 2.258591 GACTGCGAGGTGAGCGAA 59.741 61.111 0.00 0.00 37.44 4.70
1160 1256 2.456287 GAACGGCAGCTTGGAGGACT 62.456 60.000 0.00 0.00 0.00 3.85
1173 1269 1.398174 GGGAGTAGTAGGGGAACGGC 61.398 65.000 0.00 0.00 0.00 5.68
1176 1272 1.412793 GGGAGGGAGTAGTAGGGGAAC 60.413 61.905 0.00 0.00 0.00 3.62
1562 1658 2.983592 CCCTTGTGGTGCCGTTCC 60.984 66.667 0.00 0.00 0.00 3.62
1575 1671 1.693640 CATCAAGGCCTCCACCCTT 59.306 57.895 5.23 0.00 43.29 3.95
1812 1926 1.445582 CACGAAGGCCACCTCGTAC 60.446 63.158 22.24 0.00 36.08 3.67
2265 2382 4.980805 TGCCGCACCGTCTTCCAC 62.981 66.667 0.00 0.00 0.00 4.02
2718 2835 3.591254 GAGCACCACCGACACCTCC 62.591 68.421 0.00 0.00 0.00 4.30
2949 3066 3.612247 GAAGCAGAAGGAGGCGCCA 62.612 63.158 31.54 0.00 40.02 5.69
3227 3345 5.973899 TCTTCTCTCTTATCATCCCATCG 57.026 43.478 0.00 0.00 0.00 3.84
3266 3384 3.411446 TCATGCTTCCGTGAAAAGTGAT 58.589 40.909 0.00 0.00 34.16 3.06
3272 3390 3.145286 TGTGAATCATGCTTCCGTGAAA 58.855 40.909 6.82 0.00 40.20 2.69
3297 3415 8.758829 TGCTAGTCTTCTGTTTATAATTCTCCA 58.241 33.333 0.00 0.00 0.00 3.86
3331 3449 2.202946 TCCTGTTGCAACGCACGA 60.203 55.556 23.79 13.22 38.71 4.35
3337 3455 6.803807 GTCATATTCTTTTCTCCTGTTGCAAC 59.196 38.462 22.83 22.83 0.00 4.17
3344 3462 7.102346 AGAGTGTGTCATATTCTTTTCTCCTG 58.898 38.462 0.00 0.00 0.00 3.86
3345 3463 7.251321 AGAGTGTGTCATATTCTTTTCTCCT 57.749 36.000 0.00 0.00 0.00 3.69
3461 3580 7.665559 AGCCTTGTTTAAATAGAAGACATGTGA 59.334 33.333 1.15 0.00 0.00 3.58
3636 3755 8.291740 ACCGTAACTCCAAATTTAACATGTTAC 58.708 33.333 17.85 3.73 36.73 2.50
3691 3810 1.029408 AACCCGCAGCGCATATCAAA 61.029 50.000 11.47 0.00 0.00 2.69
3701 3820 2.715737 TTTGACATTAAACCCGCAGC 57.284 45.000 0.00 0.00 0.00 5.25
3719 3838 8.499288 TTTTATAGAAAACCCCCTGATGTTTT 57.501 30.769 0.00 0.00 44.82 2.43
3747 3866 2.605257 AGGTATGCTTAGGCCGTCATA 58.395 47.619 0.00 1.09 37.74 2.15
3854 3973 8.923609 ATATAGTGATCATGCTAGATTTGTCG 57.076 34.615 0.00 0.00 0.00 4.35
3969 4089 7.551035 AAATTGCAAACACAAGCAGATAAAA 57.449 28.000 1.71 0.00 42.39 1.52


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

AutoCloner maintained by Alex Coulton.