Multiple sequence alignment - TraesCS5D01G222000

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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 TraesCS5D01G222000 chr5D 100.000 2681 0 0 1 2681 329508607 329511287 0.000000e+00 4951.0
1 TraesCS5D01G222000 chr5D 93.939 132 7 1 725 856 329509201 329509331 5.850000e-47 198.0
2 TraesCS5D01G222000 chr5D 93.939 132 7 1 595 725 329509331 329509462 5.850000e-47 198.0
3 TraesCS5D01G222000 chr5A 91.178 1893 96 21 833 2681 427087927 427086062 0.000000e+00 2505.0
4 TraesCS5D01G222000 chr5A 92.015 263 18 3 6 267 427088442 427088182 1.520000e-97 366.0
5 TraesCS5D01G222000 chr5B 91.414 1153 68 10 810 1935 382700487 382701635 0.000000e+00 1552.0
6 TraesCS5D01G222000 chr5B 91.045 268 17 2 1 268 382699948 382700208 3.280000e-94 355.0
7 TraesCS5D01G222000 chr5B 79.532 171 13 10 2008 2166 382701636 382701796 4.720000e-18 102.0
8 TraesCS5D01G222000 chr2B 82.883 111 15 4 2374 2483 697975542 697975435 2.200000e-16 97.1
9 TraesCS5D01G222000 chr2A 100.000 28 0 0 345 372 14999493 14999466 5.000000e-03 52.8
10 TraesCS5D01G222000 chr2A 100.000 28 0 0 345 372 161948591 161948618 5.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G222000 chr5D 329508607 329511287 2680 False 1782.333333 4951 95.959333 1 2681 3 chr5D.!!$F1 2680
1 TraesCS5D01G222000 chr5A 427086062 427088442 2380 True 1435.500000 2505 91.596500 6 2681 2 chr5A.!!$R1 2675
2 TraesCS5D01G222000 chr5B 382699948 382701796 1848 False 669.666667 1552 87.330333 1 2166 3 chr5B.!!$F1 2165

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
268 269 0.942410 TGCACGCACCTCGAGTTTAC 60.942 55.000 12.31 0.00 41.67 2.01 F
272 273 1.000506 ACGCACCTCGAGTTTACATGT 59.999 47.619 12.31 2.69 41.67 3.21 F
1206 1231 0.321653 GCACCCTCTTGGACGACAAT 60.322 55.000 0.00 0.00 38.65 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1145 1164 0.323629 TAGTTTGTTGGAGGAGCCGG 59.676 55.0 0.00 0.0 40.66 6.13 R
1660 1694 0.533491 TATAGTGACAGGCGCGGTTT 59.467 50.0 8.83 0.0 0.00 3.27 R
2626 2694 0.462047 ATAAGCCGGCTTCGTCTTGG 60.462 55.0 43.34 0.0 32.94 3.61 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
99 100 2.125229 CATGCTGACGCTGGCTCT 60.125 61.111 0.00 0.00 36.97 4.09
121 122 2.508526 GCTGCGGAAATGGGATATCTT 58.491 47.619 0.00 0.00 0.00 2.40
135 136 1.413118 TATCTTGCAGCATCTCCCGA 58.587 50.000 0.00 0.00 0.00 5.14
147 148 3.200887 CTCCCGAGCTCGATTCCGG 62.201 68.421 36.59 26.86 43.02 5.14
201 202 2.123726 GGGCATCTTTCCCCGCAT 60.124 61.111 0.00 0.00 37.81 4.73
227 228 3.482436 ACGTTTGACAGCTCCCATTAAA 58.518 40.909 0.00 0.00 0.00 1.52
234 235 3.084786 ACAGCTCCCATTAAACTGAAGC 58.915 45.455 0.00 0.00 32.67 3.86
235 236 2.096496 CAGCTCCCATTAAACTGAAGCG 59.904 50.000 0.00 0.00 0.00 4.68
240 241 3.504520 TCCCATTAAACTGAAGCGTTTCC 59.495 43.478 9.65 0.00 38.08 3.13
263 264 3.857854 GCATGCACGCACCTCGAG 61.858 66.667 14.21 5.13 41.67 4.04
268 269 0.942410 TGCACGCACCTCGAGTTTAC 60.942 55.000 12.31 0.00 41.67 2.01
269 270 0.942410 GCACGCACCTCGAGTTTACA 60.942 55.000 12.31 0.00 41.67 2.41
272 273 1.000506 ACGCACCTCGAGTTTACATGT 59.999 47.619 12.31 2.69 41.67 3.21
273 274 2.066262 CGCACCTCGAGTTTACATGTT 58.934 47.619 12.31 0.00 41.67 2.71
274 275 2.478894 CGCACCTCGAGTTTACATGTTT 59.521 45.455 12.31 0.00 41.67 2.83
275 276 3.059188 CGCACCTCGAGTTTACATGTTTT 60.059 43.478 12.31 0.00 41.67 2.43
276 277 4.553938 CGCACCTCGAGTTTACATGTTTTT 60.554 41.667 12.31 0.00 41.67 1.94
301 302 5.467705 TCTTGAGGTAGCTTAGTTCGTTTC 58.532 41.667 0.00 0.00 0.00 2.78
302 303 5.243283 TCTTGAGGTAGCTTAGTTCGTTTCT 59.757 40.000 0.00 0.00 0.00 2.52
313 314 4.547406 AGTTCGTTTCTTGTTTACAGGC 57.453 40.909 0.00 0.00 0.00 4.85
318 319 3.005367 CGTTTCTTGTTTACAGGCCCAAT 59.995 43.478 0.00 0.00 0.00 3.16
349 350 9.333724 TCTTTATTTTGGGAAACGATATACTCC 57.666 33.333 0.00 0.00 0.00 3.85
350 351 8.454570 TTTATTTTGGGAAACGATATACTCCC 57.545 34.615 0.00 0.00 46.77 4.30
352 353 4.950205 TTGGGAAACGATATACTCCCTC 57.050 45.455 7.48 0.00 46.72 4.30
353 354 3.236896 TGGGAAACGATATACTCCCTCC 58.763 50.000 7.48 0.00 46.72 4.30
354 355 3.116862 TGGGAAACGATATACTCCCTCCT 60.117 47.826 7.48 0.00 46.72 3.69
355 356 4.106825 TGGGAAACGATATACTCCCTCCTA 59.893 45.833 7.48 0.00 46.72 2.94
357 358 5.541484 GGGAAACGATATACTCCCTCCTAAA 59.459 44.000 0.00 0.00 43.74 1.85
359 360 6.492772 GGAAACGATATACTCCCTCCTAAAGA 59.507 42.308 0.00 0.00 0.00 2.52
362 363 8.493787 AACGATATACTCCCTCCTAAAGAAAT 57.506 34.615 0.00 0.00 0.00 2.17
363 364 9.597681 AACGATATACTCCCTCCTAAAGAAATA 57.402 33.333 0.00 0.00 0.00 1.40
370 371 7.969004 ACTCCCTCCTAAAGAAATATAAGAGC 58.031 38.462 0.00 0.00 0.00 4.09
371 372 6.994221 TCCCTCCTAAAGAAATATAAGAGCG 58.006 40.000 0.00 0.00 0.00 5.03
380 381 4.816925 AGAAATATAAGAGCGGAAAGTGGC 59.183 41.667 0.00 0.00 0.00 5.01
395 396 2.222019 AGTGGCCGAAAAATGCCTCTC 61.222 52.381 0.00 0.00 45.64 3.20
397 398 1.429423 GCCGAAAAATGCCTCTCCG 59.571 57.895 0.00 0.00 0.00 4.63
423 425 7.229530 GCTTAAAATTTGAAGCGGAAAGATTG 58.770 34.615 21.77 0.00 38.79 2.67
425 427 8.519492 TTAAAATTTGAAGCGGAAAGATTGAG 57.481 30.769 0.00 0.00 0.00 3.02
430 432 6.817765 TTGAAGCGGAAAGATTGAGTAATT 57.182 33.333 0.00 0.00 0.00 1.40
433 435 8.330466 TGAAGCGGAAAGATTGAGTAATTAAA 57.670 30.769 0.00 0.00 0.00 1.52
434 436 8.450964 TGAAGCGGAAAGATTGAGTAATTAAAG 58.549 33.333 0.00 0.00 0.00 1.85
486 497 2.340210 TTGTGTTCTGCCTAGCACAA 57.660 45.000 11.92 11.92 45.74 3.33
513 524 9.539825 TGTACATGTATCATTTTTGCAAAAAGT 57.460 25.926 33.47 25.81 40.78 2.66
556 568 6.245408 TCAATGCACTTGTTTACCTAATCCT 58.755 36.000 0.00 0.00 36.20 3.24
562 574 7.048512 GCACTTGTTTACCTAATCCTACATCT 58.951 38.462 0.00 0.00 0.00 2.90
563 575 7.224949 GCACTTGTTTACCTAATCCTACATCTC 59.775 40.741 0.00 0.00 0.00 2.75
565 577 7.402071 ACTTGTTTACCTAATCCTACATCTCCA 59.598 37.037 0.00 0.00 0.00 3.86
566 578 7.120923 TGTTTACCTAATCCTACATCTCCAC 57.879 40.000 0.00 0.00 0.00 4.02
567 579 6.901300 TGTTTACCTAATCCTACATCTCCACT 59.099 38.462 0.00 0.00 0.00 4.00
569 581 8.921205 GTTTACCTAATCCTACATCTCCACTAA 58.079 37.037 0.00 0.00 0.00 2.24
570 582 8.707796 TTACCTAATCCTACATCTCCACTAAG 57.292 38.462 0.00 0.00 0.00 2.18
571 583 5.540719 ACCTAATCCTACATCTCCACTAAGC 59.459 44.000 0.00 0.00 0.00 3.09
574 586 7.397476 CCTAATCCTACATCTCCACTAAGCATA 59.603 40.741 0.00 0.00 0.00 3.14
575 587 7.805083 AATCCTACATCTCCACTAAGCATAT 57.195 36.000 0.00 0.00 0.00 1.78
577 589 7.704578 TCCTACATCTCCACTAAGCATATAC 57.295 40.000 0.00 0.00 0.00 1.47
579 591 7.612244 TCCTACATCTCCACTAAGCATATACTC 59.388 40.741 0.00 0.00 0.00 2.59
580 592 6.597832 ACATCTCCACTAAGCATATACTCC 57.402 41.667 0.00 0.00 0.00 3.85
581 593 5.482175 ACATCTCCACTAAGCATATACTCCC 59.518 44.000 0.00 0.00 0.00 4.30
583 595 5.716979 TCTCCACTAAGCATATACTCCCTT 58.283 41.667 0.00 0.00 0.00 3.95
584 596 5.775701 TCTCCACTAAGCATATACTCCCTTC 59.224 44.000 0.00 0.00 0.00 3.46
585 597 5.464069 TCCACTAAGCATATACTCCCTTCA 58.536 41.667 0.00 0.00 0.00 3.02
586 598 6.084738 TCCACTAAGCATATACTCCCTTCAT 58.915 40.000 0.00 0.00 0.00 2.57
587 599 6.211584 TCCACTAAGCATATACTCCCTTCATC 59.788 42.308 0.00 0.00 0.00 2.92
588 600 6.212388 CCACTAAGCATATACTCCCTTCATCT 59.788 42.308 0.00 0.00 0.00 2.90
589 601 7.319646 CACTAAGCATATACTCCCTTCATCTC 58.680 42.308 0.00 0.00 0.00 2.75
590 602 5.398603 AAGCATATACTCCCTTCATCTCG 57.601 43.478 0.00 0.00 0.00 4.04
591 603 4.667573 AGCATATACTCCCTTCATCTCGA 58.332 43.478 0.00 0.00 0.00 4.04
592 604 5.080337 AGCATATACTCCCTTCATCTCGAA 58.920 41.667 0.00 0.00 0.00 3.71
593 605 5.719085 AGCATATACTCCCTTCATCTCGAAT 59.281 40.000 0.00 0.00 31.69 3.34
595 607 6.312426 GCATATACTCCCTTCATCTCGAATTG 59.688 42.308 0.00 0.00 31.69 2.32
596 608 2.911484 ACTCCCTTCATCTCGAATTGC 58.089 47.619 0.00 0.00 31.69 3.56
597 609 2.503356 ACTCCCTTCATCTCGAATTGCT 59.497 45.455 0.00 0.00 31.69 3.91
598 610 3.054802 ACTCCCTTCATCTCGAATTGCTT 60.055 43.478 0.00 0.00 31.69 3.91
599 611 3.273434 TCCCTTCATCTCGAATTGCTTG 58.727 45.455 0.00 0.00 31.69 4.01
600 612 3.012518 CCCTTCATCTCGAATTGCTTGT 58.987 45.455 0.00 0.00 31.69 3.16
601 613 3.064545 CCCTTCATCTCGAATTGCTTGTC 59.935 47.826 0.00 0.00 31.69 3.18
602 614 3.937706 CCTTCATCTCGAATTGCTTGTCT 59.062 43.478 0.00 0.00 31.69 3.41
603 615 4.201792 CCTTCATCTCGAATTGCTTGTCTG 60.202 45.833 0.00 0.00 31.69 3.51
604 616 4.192429 TCATCTCGAATTGCTTGTCTGA 57.808 40.909 0.00 0.00 0.00 3.27
605 617 4.179298 TCATCTCGAATTGCTTGTCTGAG 58.821 43.478 0.00 0.00 0.00 3.35
606 618 3.942130 TCTCGAATTGCTTGTCTGAGA 57.058 42.857 0.00 0.00 0.00 3.27
607 619 4.462508 TCTCGAATTGCTTGTCTGAGAT 57.537 40.909 0.00 0.00 0.00 2.75
608 620 4.825422 TCTCGAATTGCTTGTCTGAGATT 58.175 39.130 0.00 0.00 0.00 2.40
609 621 5.240891 TCTCGAATTGCTTGTCTGAGATTT 58.759 37.500 0.00 0.00 0.00 2.17
610 622 5.121298 TCTCGAATTGCTTGTCTGAGATTTG 59.879 40.000 0.00 0.00 0.00 2.32
611 623 4.756642 TCGAATTGCTTGTCTGAGATTTGT 59.243 37.500 0.00 0.00 0.00 2.83
612 624 5.084722 CGAATTGCTTGTCTGAGATTTGTC 58.915 41.667 0.00 0.00 0.00 3.18
613 625 5.106791 CGAATTGCTTGTCTGAGATTTGTCT 60.107 40.000 0.00 0.00 0.00 3.41
614 626 6.091305 CGAATTGCTTGTCTGAGATTTGTCTA 59.909 38.462 0.00 0.00 0.00 2.59
615 627 6.981762 ATTGCTTGTCTGAGATTTGTCTAG 57.018 37.500 0.00 0.00 0.00 2.43
616 628 5.728637 TGCTTGTCTGAGATTTGTCTAGA 57.271 39.130 0.00 0.00 0.00 2.43
617 629 5.473931 TGCTTGTCTGAGATTTGTCTAGAC 58.526 41.667 16.32 16.32 38.52 2.59
618 630 5.011023 TGCTTGTCTGAGATTTGTCTAGACA 59.989 40.000 21.74 21.74 44.12 3.41
619 631 5.347364 GCTTGTCTGAGATTTGTCTAGACAC 59.653 44.000 25.13 13.90 45.09 3.67
620 632 5.048153 TGTCTGAGATTTGTCTAGACACG 57.952 43.478 25.13 9.71 41.82 4.49
621 633 4.082733 TGTCTGAGATTTGTCTAGACACGG 60.083 45.833 25.13 17.19 41.82 4.94
622 634 4.156190 GTCTGAGATTTGTCTAGACACGGA 59.844 45.833 25.13 19.08 41.67 4.69
623 635 4.950475 TCTGAGATTTGTCTAGACACGGAT 59.050 41.667 25.13 17.97 41.67 4.18
624 636 4.998788 TGAGATTTGTCTAGACACGGATG 58.001 43.478 25.13 0.00 41.67 3.51
625 637 4.462834 TGAGATTTGTCTAGACACGGATGT 59.537 41.667 25.13 16.54 41.67 3.06
642 654 9.114952 ACACGGATGTCTAGATATATCTGTATG 57.885 37.037 23.03 11.49 37.12 2.39
643 655 9.114952 CACGGATGTCTAGATATATCTGTATGT 57.885 37.037 23.03 8.16 37.12 2.29
723 735 7.759489 AGTACTAAACTGCAAATTCCATCAA 57.241 32.000 0.00 0.00 36.93 2.57
724 736 8.353423 AGTACTAAACTGCAAATTCCATCAAT 57.647 30.769 0.00 0.00 36.93 2.57
725 737 8.246180 AGTACTAAACTGCAAATTCCATCAATG 58.754 33.333 0.00 0.00 36.93 2.82
726 738 7.230849 ACTAAACTGCAAATTCCATCAATGA 57.769 32.000 0.00 0.00 0.00 2.57
727 739 7.844009 ACTAAACTGCAAATTCCATCAATGAT 58.156 30.769 0.00 0.00 0.00 2.45
728 740 8.316214 ACTAAACTGCAAATTCCATCAATGATT 58.684 29.630 0.00 0.00 0.00 2.57
729 741 6.978343 AACTGCAAATTCCATCAATGATTG 57.022 33.333 0.00 0.00 0.00 2.67
730 742 6.045072 ACTGCAAATTCCATCAATGATTGT 57.955 33.333 4.93 0.00 0.00 2.71
731 743 6.103997 ACTGCAAATTCCATCAATGATTGTC 58.896 36.000 4.93 0.00 0.00 3.18
732 744 6.070995 ACTGCAAATTCCATCAATGATTGTCT 60.071 34.615 4.93 0.00 0.00 3.41
733 745 6.103330 TGCAAATTCCATCAATGATTGTCTG 58.897 36.000 4.93 4.58 0.00 3.51
734 746 6.071278 TGCAAATTCCATCAATGATTGTCTGA 60.071 34.615 4.93 0.00 0.00 3.27
735 747 6.475727 GCAAATTCCATCAATGATTGTCTGAG 59.524 38.462 4.93 0.53 0.00 3.35
736 748 7.629866 GCAAATTCCATCAATGATTGTCTGAGA 60.630 37.037 4.93 2.53 0.00 3.27
737 749 8.414003 CAAATTCCATCAATGATTGTCTGAGAT 58.586 33.333 4.93 0.68 0.00 2.75
738 750 8.534954 AATTCCATCAATGATTGTCTGAGATT 57.465 30.769 4.93 5.65 0.00 2.40
739 751 7.949690 TTCCATCAATGATTGTCTGAGATTT 57.050 32.000 4.93 0.00 0.00 2.17
740 752 7.329588 TCCATCAATGATTGTCTGAGATTTG 57.670 36.000 4.93 0.00 0.00 2.32
741 753 6.888088 TCCATCAATGATTGTCTGAGATTTGT 59.112 34.615 4.93 0.00 0.00 2.83
742 754 7.066645 TCCATCAATGATTGTCTGAGATTTGTC 59.933 37.037 4.93 0.00 0.00 3.18
743 755 7.148137 CCATCAATGATTGTCTGAGATTTGTCA 60.148 37.037 4.93 0.00 0.00 3.58
744 756 7.933215 TCAATGATTGTCTGAGATTTGTCAT 57.067 32.000 4.93 0.00 0.00 3.06
745 757 9.623000 ATCAATGATTGTCTGAGATTTGTCATA 57.377 29.630 4.93 0.00 0.00 2.15
746 758 9.623000 TCAATGATTGTCTGAGATTTGTCATAT 57.377 29.630 4.93 0.00 0.00 1.78
750 762 9.317936 TGATTGTCTGAGATTTGTCATATACAC 57.682 33.333 0.00 0.00 38.00 2.90
751 763 7.755582 TTGTCTGAGATTTGTCATATACACG 57.244 36.000 0.00 0.00 38.00 4.49
752 764 6.273071 TGTCTGAGATTTGTCATATACACGG 58.727 40.000 0.00 0.00 38.00 4.94
753 765 6.096282 TGTCTGAGATTTGTCATATACACGGA 59.904 38.462 0.00 0.00 38.00 4.69
754 766 7.148641 GTCTGAGATTTGTCATATACACGGAT 58.851 38.462 0.00 0.00 38.00 4.18
755 767 7.115520 GTCTGAGATTTGTCATATACACGGATG 59.884 40.741 0.00 0.00 38.00 3.51
756 768 6.816136 TGAGATTTGTCATATACACGGATGT 58.184 36.000 0.00 0.00 43.30 3.06
757 769 6.923508 TGAGATTTGTCATATACACGGATGTC 59.076 38.462 0.00 0.00 40.48 3.06
758 770 7.055667 AGATTTGTCATATACACGGATGTCT 57.944 36.000 0.00 0.00 40.48 3.41
759 771 8.178313 AGATTTGTCATATACACGGATGTCTA 57.822 34.615 0.00 0.00 40.48 2.59
760 772 8.300286 AGATTTGTCATATACACGGATGTCTAG 58.700 37.037 0.00 0.00 40.48 2.43
761 773 7.576861 TTTGTCATATACACGGATGTCTAGA 57.423 36.000 0.00 0.00 40.48 2.43
762 774 7.761038 TTGTCATATACACGGATGTCTAGAT 57.239 36.000 0.00 0.00 40.48 1.98
763 775 8.857694 TTGTCATATACACGGATGTCTAGATA 57.142 34.615 0.00 0.00 40.48 1.98
764 776 9.462606 TTGTCATATACACGGATGTCTAGATAT 57.537 33.333 0.96 0.96 40.48 1.63
777 789 9.961264 GGATGTCTAGATATATCCGTATATGGA 57.039 37.037 16.13 16.13 43.58 3.41
791 803 9.621629 ATCCGTATATGGACAAATTTAAGACAA 57.378 29.630 16.12 0.00 41.85 3.18
792 804 9.451002 TCCGTATATGGACAAATTTAAGACAAA 57.549 29.630 9.78 0.00 31.53 2.83
852 864 5.959618 AGTACTAAACTGCAAATTCCACC 57.040 39.130 0.00 0.00 36.93 4.61
853 865 5.381757 AGTACTAAACTGCAAATTCCACCA 58.618 37.500 0.00 0.00 36.93 4.17
854 866 5.830991 AGTACTAAACTGCAAATTCCACCAA 59.169 36.000 0.00 0.00 36.93 3.67
860 872 3.244181 ACTGCAAATTCCACCAATTCCAC 60.244 43.478 0.00 0.00 33.16 4.02
886 898 5.187186 CCGCCACCTATATATACACTTCCTT 59.813 44.000 0.00 0.00 0.00 3.36
972 985 1.404986 CCTATCTTGAACAACCGCCGA 60.405 52.381 0.00 0.00 0.00 5.54
1020 1039 1.598130 GGAGCTGCTCAACGTGGTT 60.598 57.895 28.95 0.00 31.08 3.67
1169 1188 0.688487 TCCTCCAACAAACTACCCGG 59.312 55.000 0.00 0.00 0.00 5.73
1206 1231 0.321653 GCACCCTCTTGGACGACAAT 60.322 55.000 0.00 0.00 38.65 2.71
1213 1238 0.445436 CTTGGACGACAATCAGCAGC 59.555 55.000 0.00 0.00 38.65 5.25
1239 1264 3.774702 GTTTCGTCGTCTGCCGCC 61.775 66.667 0.00 0.00 36.19 6.13
1359 1384 4.899239 GCCGGAGCTGACGATGGG 62.899 72.222 5.05 0.00 35.50 4.00
1440 1474 2.677979 CGACGACCAGAGCGAGACA 61.678 63.158 0.00 0.00 0.00 3.41
1442 1476 1.853114 GACGACCAGAGCGAGACACA 61.853 60.000 0.00 0.00 0.00 3.72
1565 1599 1.670083 GGTACCGCCACCTTGACAC 60.670 63.158 0.00 0.00 35.55 3.67
1660 1694 3.797353 GGCGGAGGGCAGGATTGA 61.797 66.667 0.00 0.00 46.16 2.57
1664 1698 1.032114 CGGAGGGCAGGATTGAAACC 61.032 60.000 0.00 0.00 0.00 3.27
1667 1701 2.485122 GGCAGGATTGAAACCGCG 59.515 61.111 0.00 0.00 0.00 6.46
1718 1762 8.608185 AATGTGGTTAGGATTATTGGATTGTT 57.392 30.769 0.00 0.00 0.00 2.83
1735 1779 5.699458 GGATTGTTATTAGGTGGGTATGACG 59.301 44.000 0.00 0.00 0.00 4.35
1736 1780 5.936187 TTGTTATTAGGTGGGTATGACGA 57.064 39.130 0.00 0.00 0.00 4.20
1777 1826 5.291858 GGGCATGTCATATGTATGTGTATCG 59.708 44.000 17.68 0.00 35.26 2.92
1780 1829 6.808704 GCATGTCATATGTATGTGTATCGTCT 59.191 38.462 17.68 0.00 35.26 4.18
1896 1945 1.272648 CCCTTCCCTGCTTCCATTTCA 60.273 52.381 0.00 0.00 0.00 2.69
1916 1965 0.314935 ATGGTTTGCACTGCTTTCCG 59.685 50.000 1.98 0.00 0.00 4.30
1935 1984 2.236395 CCGTTACATCCTTCTGACCCTT 59.764 50.000 0.00 0.00 0.00 3.95
1964 2013 9.967346 TGTTCTCTCGGTTTATTTATATCTGAG 57.033 33.333 0.00 0.00 34.14 3.35
1965 2014 9.413048 GTTCTCTCGGTTTATTTATATCTGAGG 57.587 37.037 0.00 0.00 33.79 3.86
1966 2015 8.935614 TCTCTCGGTTTATTTATATCTGAGGA 57.064 34.615 0.00 0.00 33.79 3.71
1969 2018 8.920174 TCTCGGTTTATTTATATCTGAGGAACA 58.080 33.333 0.00 0.00 33.79 3.18
1970 2019 9.542462 CTCGGTTTATTTATATCTGAGGAACAA 57.458 33.333 0.00 0.00 0.00 2.83
1972 2021 8.273557 CGGTTTATTTATATCTGAGGAACAACG 58.726 37.037 0.00 0.00 0.00 4.10
1987 2036 9.372369 TGAGGAACAACGTTTCAAAATAAATTT 57.628 25.926 0.00 0.00 0.00 1.82
2187 2249 4.100498 GTCATTCCCAGCATCCATGATTTT 59.900 41.667 0.00 0.00 0.00 1.82
2188 2250 5.302568 GTCATTCCCAGCATCCATGATTTTA 59.697 40.000 0.00 0.00 0.00 1.52
2246 2308 4.004196 TCAATATGAGATGCAGGCTCAG 57.996 45.455 21.83 11.87 44.75 3.35
2248 2310 1.421480 TATGAGATGCAGGCTCAGCT 58.579 50.000 21.83 12.21 44.75 4.24
2256 2318 1.801332 CAGGCTCAGCTGAATGCAC 59.199 57.895 24.41 15.69 45.94 4.57
2309 2371 2.302587 TGGGCTCCTGGGTTTTAAAG 57.697 50.000 0.00 0.00 0.00 1.85
2320 2382 5.652452 CCTGGGTTTTAAAGGAGTTCCATAG 59.348 44.000 0.28 0.00 38.89 2.23
2376 2438 6.655078 AGGATCACTTTGCACACTATTTTT 57.345 33.333 0.00 0.00 0.00 1.94
2391 2453 9.185192 CACACTATTTTTGAGGAGAATTTTCAC 57.815 33.333 0.00 0.00 0.00 3.18
2408 2470 4.464069 TTCACCCACTCAAACCTTTTTG 57.536 40.909 0.00 0.00 43.17 2.44
2414 2476 6.921307 CACCCACTCAAACCTTTTTGTATAAC 59.079 38.462 0.00 0.00 42.51 1.89
2463 2525 9.299963 CATTAAACGCTATTTGATCCAAATTCA 57.700 29.630 9.78 0.00 40.60 2.57
2621 2689 8.877779 GCCATATAATCATAGTGATGTGAAGAC 58.122 37.037 0.00 0.00 37.15 3.01
2625 2693 8.809159 ATAATCATAGTGATGTGAAGACGAAG 57.191 34.615 0.00 0.00 37.15 3.79
2626 2694 4.424626 TCATAGTGATGTGAAGACGAAGC 58.575 43.478 0.00 0.00 34.41 3.86
2627 2695 2.086054 AGTGATGTGAAGACGAAGCC 57.914 50.000 0.00 0.00 0.00 4.35
2628 2696 1.344438 AGTGATGTGAAGACGAAGCCA 59.656 47.619 0.00 0.00 0.00 4.75
2629 2697 2.143122 GTGATGTGAAGACGAAGCCAA 58.857 47.619 0.00 0.00 0.00 4.52
2630 2698 2.158449 GTGATGTGAAGACGAAGCCAAG 59.842 50.000 0.00 0.00 0.00 3.61
2631 2699 2.037121 TGATGTGAAGACGAAGCCAAGA 59.963 45.455 0.00 0.00 0.00 3.02
2632 2700 1.865865 TGTGAAGACGAAGCCAAGAC 58.134 50.000 0.00 0.00 0.00 3.01
2633 2701 0.784778 GTGAAGACGAAGCCAAGACG 59.215 55.000 0.00 0.00 0.00 4.18
2634 2702 0.671796 TGAAGACGAAGCCAAGACGA 59.328 50.000 0.00 0.00 0.00 4.20
2635 2703 1.067974 TGAAGACGAAGCCAAGACGAA 59.932 47.619 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 100 0.478072 ATATCCCATTTCCGCAGCCA 59.522 50.000 0.00 0.00 0.00 4.75
121 122 3.079478 AGCTCGGGAGATGCTGCA 61.079 61.111 4.13 4.13 40.25 4.41
135 136 2.093537 GAGATGCCCGGAATCGAGCT 62.094 60.000 0.73 0.00 40.85 4.09
147 148 1.005156 GATCTGCTCGGGAGATGCC 60.005 63.158 11.52 0.00 38.80 4.40
194 195 2.678836 TGTCAAACGTAATAATGCGGGG 59.321 45.455 0.00 0.00 39.13 5.73
201 202 4.274602 TGGGAGCTGTCAAACGTAATAA 57.725 40.909 0.00 0.00 0.00 1.40
227 228 1.067060 GCAAAAGGGAAACGCTTCAGT 59.933 47.619 0.35 0.00 35.61 3.41
234 235 1.139163 GTGCATGCAAAAGGGAAACG 58.861 50.000 24.58 0.00 0.00 3.60
235 236 1.139163 CGTGCATGCAAAAGGGAAAC 58.861 50.000 24.58 5.45 0.00 2.78
274 275 6.285990 ACGAACTAAGCTACCTCAAGAAAAA 58.714 36.000 0.00 0.00 0.00 1.94
275 276 5.850614 ACGAACTAAGCTACCTCAAGAAAA 58.149 37.500 0.00 0.00 0.00 2.29
276 277 5.464030 ACGAACTAAGCTACCTCAAGAAA 57.536 39.130 0.00 0.00 0.00 2.52
277 278 5.464030 AACGAACTAAGCTACCTCAAGAA 57.536 39.130 0.00 0.00 0.00 2.52
278 279 5.243283 AGAAACGAACTAAGCTACCTCAAGA 59.757 40.000 0.00 0.00 0.00 3.02
279 280 5.471257 AGAAACGAACTAAGCTACCTCAAG 58.529 41.667 0.00 0.00 0.00 3.02
280 281 5.464030 AGAAACGAACTAAGCTACCTCAA 57.536 39.130 0.00 0.00 0.00 3.02
281 282 5.221382 ACAAGAAACGAACTAAGCTACCTCA 60.221 40.000 0.00 0.00 0.00 3.86
282 283 5.228665 ACAAGAAACGAACTAAGCTACCTC 58.771 41.667 0.00 0.00 0.00 3.85
283 284 5.211174 ACAAGAAACGAACTAAGCTACCT 57.789 39.130 0.00 0.00 0.00 3.08
284 285 5.919272 AACAAGAAACGAACTAAGCTACC 57.081 39.130 0.00 0.00 0.00 3.18
285 286 7.844482 TGTAAACAAGAAACGAACTAAGCTAC 58.156 34.615 0.00 0.00 0.00 3.58
286 287 7.170320 CCTGTAAACAAGAAACGAACTAAGCTA 59.830 37.037 0.00 0.00 0.00 3.32
287 288 6.018180 CCTGTAAACAAGAAACGAACTAAGCT 60.018 38.462 0.00 0.00 0.00 3.74
288 289 6.134061 CCTGTAAACAAGAAACGAACTAAGC 58.866 40.000 0.00 0.00 0.00 3.09
289 290 6.134061 GCCTGTAAACAAGAAACGAACTAAG 58.866 40.000 0.00 0.00 0.00 2.18
290 291 5.007921 GGCCTGTAAACAAGAAACGAACTAA 59.992 40.000 0.00 0.00 0.00 2.24
291 292 4.512571 GGCCTGTAAACAAGAAACGAACTA 59.487 41.667 0.00 0.00 0.00 2.24
292 293 3.314357 GGCCTGTAAACAAGAAACGAACT 59.686 43.478 0.00 0.00 0.00 3.01
293 294 3.549423 GGGCCTGTAAACAAGAAACGAAC 60.549 47.826 0.84 0.00 0.00 3.95
294 295 2.619646 GGGCCTGTAAACAAGAAACGAA 59.380 45.455 0.84 0.00 0.00 3.85
295 296 2.223745 GGGCCTGTAAACAAGAAACGA 58.776 47.619 0.84 0.00 0.00 3.85
296 297 1.950909 TGGGCCTGTAAACAAGAAACG 59.049 47.619 4.53 0.00 0.00 3.60
301 302 4.806640 AATCATTGGGCCTGTAAACAAG 57.193 40.909 4.53 0.00 0.00 3.16
302 303 4.837860 AGAAATCATTGGGCCTGTAAACAA 59.162 37.500 4.53 0.00 0.00 2.83
344 345 9.091220 GCTCTTATATTTCTTTAGGAGGGAGTA 57.909 37.037 0.00 0.00 0.00 2.59
345 346 7.256012 CGCTCTTATATTTCTTTAGGAGGGAGT 60.256 40.741 0.00 0.00 35.51 3.85
346 347 7.093992 CGCTCTTATATTTCTTTAGGAGGGAG 58.906 42.308 0.00 0.00 35.51 4.30
348 349 6.014499 TCCGCTCTTATATTTCTTTAGGAGGG 60.014 42.308 0.00 0.00 34.05 4.30
349 350 6.994221 TCCGCTCTTATATTTCTTTAGGAGG 58.006 40.000 0.00 0.00 0.00 4.30
350 351 8.888579 TTTCCGCTCTTATATTTCTTTAGGAG 57.111 34.615 0.00 0.00 0.00 3.69
352 353 8.552034 CACTTTCCGCTCTTATATTTCTTTAGG 58.448 37.037 0.00 0.00 0.00 2.69
353 354 8.552034 CCACTTTCCGCTCTTATATTTCTTTAG 58.448 37.037 0.00 0.00 0.00 1.85
354 355 7.012044 GCCACTTTCCGCTCTTATATTTCTTTA 59.988 37.037 0.00 0.00 0.00 1.85
355 356 6.183360 GCCACTTTCCGCTCTTATATTTCTTT 60.183 38.462 0.00 0.00 0.00 2.52
357 358 4.816925 GCCACTTTCCGCTCTTATATTTCT 59.183 41.667 0.00 0.00 0.00 2.52
359 360 3.883489 GGCCACTTTCCGCTCTTATATTT 59.117 43.478 0.00 0.00 0.00 1.40
362 363 1.202486 CGGCCACTTTCCGCTCTTATA 60.202 52.381 2.24 0.00 40.46 0.98
363 364 0.462047 CGGCCACTTTCCGCTCTTAT 60.462 55.000 2.24 0.00 40.46 1.73
365 366 2.358737 CGGCCACTTTCCGCTCTT 60.359 61.111 2.24 0.00 40.46 2.85
366 367 2.391724 TTTCGGCCACTTTCCGCTCT 62.392 55.000 2.24 0.00 46.05 4.09
367 368 1.512156 TTTTCGGCCACTTTCCGCTC 61.512 55.000 2.24 0.00 46.05 5.03
368 369 1.104577 TTTTTCGGCCACTTTCCGCT 61.105 50.000 2.24 0.00 46.05 5.52
369 370 0.038618 ATTTTTCGGCCACTTTCCGC 60.039 50.000 2.24 0.00 46.05 5.54
371 372 1.428448 GCATTTTTCGGCCACTTTCC 58.572 50.000 2.24 0.00 0.00 3.13
380 381 2.098293 CCGGAGAGGCATTTTTCGG 58.902 57.895 0.00 0.00 0.00 4.30
395 396 2.094957 TCCGCTTCAAATTTTAAGCCGG 60.095 45.455 24.39 25.05 44.17 6.13
397 398 5.227152 TCTTTCCGCTTCAAATTTTAAGCC 58.773 37.500 24.39 11.79 44.17 4.35
409 411 8.665685 TCTTTAATTACTCAATCTTTCCGCTTC 58.334 33.333 0.00 0.00 0.00 3.86
433 435 9.061435 GCTACTGAAAATTATAGCCTTGAATCT 57.939 33.333 0.00 0.00 35.10 2.40
434 436 9.061435 AGCTACTGAAAATTATAGCCTTGAATC 57.939 33.333 0.00 0.00 40.80 2.52
445 447 9.113838 CACAATCCACTAGCTACTGAAAATTAT 57.886 33.333 2.27 0.00 0.00 1.28
447 449 6.942576 ACACAATCCACTAGCTACTGAAAATT 59.057 34.615 2.27 0.00 0.00 1.82
448 450 6.476378 ACACAATCCACTAGCTACTGAAAAT 58.524 36.000 2.27 0.00 0.00 1.82
519 530 7.889469 ACAAGTGCATTGATACAAGATTTTCT 58.111 30.769 13.53 0.00 41.83 2.52
525 537 6.714810 AGGTAAACAAGTGCATTGATACAAGA 59.285 34.615 13.53 0.00 41.83 3.02
527 539 6.892658 AGGTAAACAAGTGCATTGATACAA 57.107 33.333 13.53 0.00 41.83 2.41
535 547 6.717289 TGTAGGATTAGGTAAACAAGTGCAT 58.283 36.000 0.00 0.00 0.00 3.96
556 568 6.663953 GGGAGTATATGCTTAGTGGAGATGTA 59.336 42.308 0.00 0.00 0.00 2.29
562 574 5.464069 TGAAGGGAGTATATGCTTAGTGGA 58.536 41.667 0.00 0.00 0.00 4.02
563 575 5.808366 TGAAGGGAGTATATGCTTAGTGG 57.192 43.478 0.00 0.00 0.00 4.00
565 577 6.151985 CGAGATGAAGGGAGTATATGCTTAGT 59.848 42.308 0.00 0.00 0.00 2.24
566 578 6.375736 TCGAGATGAAGGGAGTATATGCTTAG 59.624 42.308 0.00 0.00 0.00 2.18
567 579 6.246163 TCGAGATGAAGGGAGTATATGCTTA 58.754 40.000 0.00 0.00 0.00 3.09
569 581 4.667573 TCGAGATGAAGGGAGTATATGCT 58.332 43.478 0.00 0.00 0.00 3.79
570 582 5.392767 TTCGAGATGAAGGGAGTATATGC 57.607 43.478 0.00 0.00 31.44 3.14
571 583 6.312426 GCAATTCGAGATGAAGGGAGTATATG 59.688 42.308 3.93 0.00 40.65 1.78
574 586 4.346418 AGCAATTCGAGATGAAGGGAGTAT 59.654 41.667 3.93 0.00 40.65 2.12
575 587 3.706594 AGCAATTCGAGATGAAGGGAGTA 59.293 43.478 3.93 0.00 40.65 2.59
577 589 3.191078 AGCAATTCGAGATGAAGGGAG 57.809 47.619 3.93 0.00 40.65 4.30
579 591 3.012518 ACAAGCAATTCGAGATGAAGGG 58.987 45.455 3.93 0.00 40.65 3.95
580 592 3.937706 AGACAAGCAATTCGAGATGAAGG 59.062 43.478 3.93 0.00 40.65 3.46
581 593 4.628766 TCAGACAAGCAATTCGAGATGAAG 59.371 41.667 3.93 0.00 40.65 3.02
583 595 4.082026 TCTCAGACAAGCAATTCGAGATGA 60.082 41.667 3.93 0.00 0.00 2.92
584 596 4.179298 TCTCAGACAAGCAATTCGAGATG 58.821 43.478 0.00 0.00 0.00 2.90
585 597 4.462508 TCTCAGACAAGCAATTCGAGAT 57.537 40.909 0.00 0.00 0.00 2.75
586 598 3.942130 TCTCAGACAAGCAATTCGAGA 57.058 42.857 0.00 0.00 0.00 4.04
587 599 5.106791 ACAAATCTCAGACAAGCAATTCGAG 60.107 40.000 0.00 0.00 0.00 4.04
588 600 4.756642 ACAAATCTCAGACAAGCAATTCGA 59.243 37.500 0.00 0.00 0.00 3.71
589 601 5.039480 ACAAATCTCAGACAAGCAATTCG 57.961 39.130 0.00 0.00 0.00 3.34
590 602 6.251655 AGACAAATCTCAGACAAGCAATTC 57.748 37.500 0.00 0.00 0.00 2.17
591 603 7.118971 GTCTAGACAAATCTCAGACAAGCAATT 59.881 37.037 18.20 0.00 36.54 2.32
592 604 6.593382 GTCTAGACAAATCTCAGACAAGCAAT 59.407 38.462 18.20 0.00 36.54 3.56
593 605 5.928839 GTCTAGACAAATCTCAGACAAGCAA 59.071 40.000 18.20 0.00 36.54 3.91
595 607 5.347364 GTGTCTAGACAAATCTCAGACAAGC 59.653 44.000 26.74 5.92 41.73 4.01
596 608 5.570973 CGTGTCTAGACAAATCTCAGACAAG 59.429 44.000 26.74 1.32 41.73 3.16
597 609 5.461526 CGTGTCTAGACAAATCTCAGACAA 58.538 41.667 26.74 0.00 41.73 3.18
598 610 4.082733 CCGTGTCTAGACAAATCTCAGACA 60.083 45.833 26.74 0.00 43.77 3.41
599 611 4.156190 TCCGTGTCTAGACAAATCTCAGAC 59.844 45.833 26.74 10.30 43.77 3.51
600 612 4.332828 TCCGTGTCTAGACAAATCTCAGA 58.667 43.478 26.74 9.40 43.77 3.27
601 613 4.703645 TCCGTGTCTAGACAAATCTCAG 57.296 45.455 26.74 7.18 43.77 3.35
602 614 4.462834 ACATCCGTGTCTAGACAAATCTCA 59.537 41.667 26.74 8.62 43.77 3.27
603 615 5.000012 ACATCCGTGTCTAGACAAATCTC 58.000 43.478 26.74 13.11 43.77 2.75
615 627 7.618502 ACAGATATATCTAGACATCCGTGTC 57.381 40.000 14.92 0.44 44.08 3.67
616 628 9.114952 CATACAGATATATCTAGACATCCGTGT 57.885 37.037 14.92 8.22 36.95 4.49
617 629 9.114952 ACATACAGATATATCTAGACATCCGTG 57.885 37.037 14.92 2.77 34.85 4.94
699 711 7.759489 TTGATGGAATTTGCAGTTTAGTACT 57.241 32.000 0.00 0.00 37.68 2.73
715 727 7.395206 ACAAATCTCAGACAATCATTGATGGAA 59.605 33.333 3.79 0.00 0.00 3.53
724 736 9.317936 GTGTATATGACAAATCTCAGACAATCA 57.682 33.333 0.00 0.00 40.66 2.57
725 737 8.483218 CGTGTATATGACAAATCTCAGACAATC 58.517 37.037 0.00 0.00 40.66 2.67
726 738 7.439356 CCGTGTATATGACAAATCTCAGACAAT 59.561 37.037 0.00 0.00 40.66 2.71
727 739 6.756542 CCGTGTATATGACAAATCTCAGACAA 59.243 38.462 0.00 0.00 40.66 3.18
728 740 6.096282 TCCGTGTATATGACAAATCTCAGACA 59.904 38.462 0.00 0.00 40.66 3.41
729 741 6.504398 TCCGTGTATATGACAAATCTCAGAC 58.496 40.000 0.00 0.00 40.66 3.51
730 742 6.709018 TCCGTGTATATGACAAATCTCAGA 57.291 37.500 0.00 0.00 40.66 3.27
731 743 6.925718 ACATCCGTGTATATGACAAATCTCAG 59.074 38.462 0.00 0.00 40.66 3.35
732 744 6.816136 ACATCCGTGTATATGACAAATCTCA 58.184 36.000 0.00 0.00 40.66 3.27
733 745 7.148641 AGACATCCGTGTATATGACAAATCTC 58.851 38.462 0.00 0.00 40.66 2.75
734 746 7.055667 AGACATCCGTGTATATGACAAATCT 57.944 36.000 0.00 0.00 40.66 2.40
735 747 8.297426 TCTAGACATCCGTGTATATGACAAATC 58.703 37.037 0.00 0.00 40.66 2.17
736 748 8.178313 TCTAGACATCCGTGTATATGACAAAT 57.822 34.615 0.00 0.00 40.66 2.32
737 749 7.576861 TCTAGACATCCGTGTATATGACAAA 57.423 36.000 0.00 0.00 40.66 2.83
738 750 7.761038 ATCTAGACATCCGTGTATATGACAA 57.239 36.000 0.00 0.00 40.66 3.18
751 763 9.961264 TCCATATACGGATATATCTAGACATCC 57.039 37.037 12.42 15.41 32.54 3.51
765 777 9.621629 TTGTCTTAAATTTGTCCATATACGGAT 57.378 29.630 0.00 0.00 37.41 4.18
766 778 9.451002 TTTGTCTTAAATTTGTCCATATACGGA 57.549 29.630 0.00 0.00 0.00 4.69
830 842 5.381757 TGGTGGAATTTGCAGTTTAGTACT 58.618 37.500 0.00 0.00 37.68 2.73
831 843 5.699097 TGGTGGAATTTGCAGTTTAGTAC 57.301 39.130 0.00 0.00 0.00 2.73
832 844 6.909550 ATTGGTGGAATTTGCAGTTTAGTA 57.090 33.333 0.00 0.00 0.00 1.82
833 845 5.806654 ATTGGTGGAATTTGCAGTTTAGT 57.193 34.783 0.00 0.00 0.00 2.24
834 846 5.639082 GGAATTGGTGGAATTTGCAGTTTAG 59.361 40.000 0.00 0.00 34.18 1.85
835 847 5.070981 TGGAATTGGTGGAATTTGCAGTTTA 59.929 36.000 0.00 0.00 34.18 2.01
836 848 4.141528 TGGAATTGGTGGAATTTGCAGTTT 60.142 37.500 0.00 0.00 34.18 2.66
837 849 3.390639 TGGAATTGGTGGAATTTGCAGTT 59.609 39.130 0.00 0.00 34.18 3.16
838 850 2.971330 TGGAATTGGTGGAATTTGCAGT 59.029 40.909 0.00 0.00 34.18 4.40
839 851 3.007182 AGTGGAATTGGTGGAATTTGCAG 59.993 43.478 0.00 0.00 34.18 4.41
840 852 2.971330 AGTGGAATTGGTGGAATTTGCA 59.029 40.909 0.00 0.00 34.18 4.08
841 853 3.588955 GAGTGGAATTGGTGGAATTTGC 58.411 45.455 0.00 0.00 34.18 3.68
842 854 3.367292 CGGAGTGGAATTGGTGGAATTTG 60.367 47.826 0.00 0.00 34.18 2.32
843 855 2.825532 CGGAGTGGAATTGGTGGAATTT 59.174 45.455 0.00 0.00 34.18 1.82
844 856 2.446435 CGGAGTGGAATTGGTGGAATT 58.554 47.619 0.00 0.00 36.94 2.17
845 857 1.955208 GCGGAGTGGAATTGGTGGAAT 60.955 52.381 0.00 0.00 0.00 3.01
846 858 0.608035 GCGGAGTGGAATTGGTGGAA 60.608 55.000 0.00 0.00 0.00 3.53
847 859 1.002624 GCGGAGTGGAATTGGTGGA 60.003 57.895 0.00 0.00 0.00 4.02
848 860 2.046285 GGCGGAGTGGAATTGGTGG 61.046 63.158 0.00 0.00 0.00 4.61
849 861 1.303236 TGGCGGAGTGGAATTGGTG 60.303 57.895 0.00 0.00 0.00 4.17
850 862 1.303317 GTGGCGGAGTGGAATTGGT 60.303 57.895 0.00 0.00 0.00 3.67
851 863 2.046285 GGTGGCGGAGTGGAATTGG 61.046 63.158 0.00 0.00 0.00 3.16
852 864 0.251916 TAGGTGGCGGAGTGGAATTG 59.748 55.000 0.00 0.00 0.00 2.32
853 865 1.213296 ATAGGTGGCGGAGTGGAATT 58.787 50.000 0.00 0.00 0.00 2.17
854 866 2.097110 TATAGGTGGCGGAGTGGAAT 57.903 50.000 0.00 0.00 0.00 3.01
860 872 5.163540 GGAAGTGTATATATAGGTGGCGGAG 60.164 48.000 0.00 0.00 0.00 4.63
886 898 4.285790 AGGAGGGTGGGCTTGGGA 62.286 66.667 0.00 0.00 0.00 4.37
1145 1164 0.323629 TAGTTTGTTGGAGGAGCCGG 59.676 55.000 0.00 0.00 40.66 6.13
1195 1220 0.955428 GGCTGCTGATTGTCGTCCAA 60.955 55.000 0.00 0.00 37.49 3.53
1279 1304 2.201022 GCTCGCTAATCGGGGAGGA 61.201 63.158 9.82 0.00 43.54 3.71
1281 1306 2.340443 GGCTCGCTAATCGGGGAG 59.660 66.667 0.00 0.00 45.28 4.30
1355 1380 3.467226 CGCCGTCCACTACCCCAT 61.467 66.667 0.00 0.00 0.00 4.00
1359 1384 2.181021 CTGACGCCGTCCACTACC 59.819 66.667 15.60 0.00 0.00 3.18
1507 1541 1.306141 TCACGGCCATCTCCCTCTT 60.306 57.895 2.24 0.00 0.00 2.85
1587 1621 3.065306 CCGTCCCACAGCCTTACA 58.935 61.111 0.00 0.00 0.00 2.41
1645 1679 1.032114 GGTTTCAATCCTGCCCTCCG 61.032 60.000 0.00 0.00 0.00 4.63
1660 1694 0.533491 TATAGTGACAGGCGCGGTTT 59.467 50.000 8.83 0.00 0.00 3.27
1664 1698 0.945099 TCTCTATAGTGACAGGCGCG 59.055 55.000 0.00 0.00 0.00 6.86
1667 1701 4.098654 ACACACATCTCTATAGTGACAGGC 59.901 45.833 6.65 0.00 37.05 4.85
1714 1758 5.936187 TCGTCATACCCACCTAATAACAA 57.064 39.130 0.00 0.00 0.00 2.83
1718 1762 6.891388 ACAAAATCGTCATACCCACCTAATA 58.109 36.000 0.00 0.00 0.00 0.98
1735 1779 4.640364 TGCCCAAATTGAAGGACAAAATC 58.360 39.130 0.00 0.00 42.03 2.17
1736 1780 4.703379 TGCCCAAATTGAAGGACAAAAT 57.297 36.364 0.00 0.00 42.03 1.82
1777 1826 1.758906 AGCCTCGGCCCTCTTAGAC 60.759 63.158 3.92 0.00 43.17 2.59
1780 1829 0.907704 TTTCAGCCTCGGCCCTCTTA 60.908 55.000 3.92 0.00 43.17 2.10
1896 1945 1.269726 CGGAAAGCAGTGCAAACCATT 60.270 47.619 19.20 0.00 0.00 3.16
1916 1965 5.535030 ACAAAAAGGGTCAGAAGGATGTAAC 59.465 40.000 0.00 0.00 0.00 2.50
1958 2007 5.828299 TTTTGAAACGTTGTTCCTCAGAT 57.172 34.783 0.00 0.00 0.00 2.90
1960 2009 7.979115 TTTATTTTGAAACGTTGTTCCTCAG 57.021 32.000 0.00 0.00 0.00 3.35
1961 2010 8.934507 AATTTATTTTGAAACGTTGTTCCTCA 57.065 26.923 0.00 0.00 0.00 3.86
1987 2036 7.720515 GGAGAACTGAAGCTAAGTAGGAGTATA 59.279 40.741 2.59 0.00 0.00 1.47
1990 2039 4.707934 GGAGAACTGAAGCTAAGTAGGAGT 59.292 45.833 2.59 0.00 0.00 3.85
1991 2040 4.201970 CGGAGAACTGAAGCTAAGTAGGAG 60.202 50.000 2.59 0.00 0.00 3.69
1992 2041 3.695060 CGGAGAACTGAAGCTAAGTAGGA 59.305 47.826 2.59 0.00 0.00 2.94
1993 2042 3.181485 CCGGAGAACTGAAGCTAAGTAGG 60.181 52.174 0.00 0.00 0.00 3.18
1994 2043 3.444388 ACCGGAGAACTGAAGCTAAGTAG 59.556 47.826 9.46 0.00 0.00 2.57
1995 2044 3.192844 CACCGGAGAACTGAAGCTAAGTA 59.807 47.826 9.46 0.00 0.00 2.24
1996 2045 2.028930 CACCGGAGAACTGAAGCTAAGT 60.029 50.000 9.46 0.00 0.00 2.24
2145 2207 5.389859 TGACCTGCAAAACTCCATAAATG 57.610 39.130 0.00 0.00 0.00 2.32
2256 2318 4.333649 TGAGAACTGAGAGCACAAGTTTTG 59.666 41.667 4.27 0.00 0.00 2.44
2267 2329 6.348295 CCATTGTGATTTGTGAGAACTGAGAG 60.348 42.308 0.00 0.00 0.00 3.20
2309 2371 5.602978 TCCTCTACAAATCCTATGGAACTCC 59.397 44.000 0.00 0.00 34.34 3.85
2346 2408 6.006449 AGTGTGCAAAGTGATCCTAAATTCT 58.994 36.000 0.00 0.00 0.00 2.40
2357 2419 5.592282 TCCTCAAAAATAGTGTGCAAAGTGA 59.408 36.000 0.00 0.00 0.00 3.41
2376 2438 3.394274 TGAGTGGGTGAAAATTCTCCTCA 59.606 43.478 12.51 7.19 39.97 3.86
2391 2453 7.284919 AGTTATACAAAAAGGTTTGAGTGGG 57.715 36.000 6.21 0.00 45.99 4.61
2428 2490 8.039603 TCAAATAGCGTTTAATGTCACAGAAT 57.960 30.769 0.00 0.00 0.00 2.40
2430 2492 7.201609 GGATCAAATAGCGTTTAATGTCACAGA 60.202 37.037 0.00 0.00 0.00 3.41
2431 2493 6.907212 GGATCAAATAGCGTTTAATGTCACAG 59.093 38.462 0.00 0.00 0.00 3.66
2432 2494 6.372937 TGGATCAAATAGCGTTTAATGTCACA 59.627 34.615 0.00 0.00 0.00 3.58
2433 2495 6.781138 TGGATCAAATAGCGTTTAATGTCAC 58.219 36.000 0.00 0.00 0.00 3.67
2463 2525 9.533831 AAGAAACATAGGATTAGAAAACCACAT 57.466 29.630 0.00 0.00 0.00 3.21
2531 2593 8.904099 AGGCATTGGTTATATACTTGTAGTTC 57.096 34.615 0.00 0.00 0.00 3.01
2593 2655 9.392259 CTTCACATCACTATGATTATATGGCAT 57.608 33.333 4.88 4.88 34.28 4.40
2595 2657 8.877779 GTCTTCACATCACTATGATTATATGGC 58.122 37.037 0.00 0.00 34.28 4.40
2596 2658 9.080915 CGTCTTCACATCACTATGATTATATGG 57.919 37.037 0.00 0.00 34.28 2.74
2597 2659 9.846248 TCGTCTTCACATCACTATGATTATATG 57.154 33.333 0.00 0.00 34.28 1.78
2599 2661 9.899226 CTTCGTCTTCACATCACTATGATTATA 57.101 33.333 0.00 0.00 34.28 0.98
2600 2662 7.383572 GCTTCGTCTTCACATCACTATGATTAT 59.616 37.037 0.00 0.00 34.28 1.28
2607 2675 2.560981 TGGCTTCGTCTTCACATCACTA 59.439 45.455 0.00 0.00 0.00 2.74
2621 2689 2.730672 CGGCTTCGTCTTGGCTTCG 61.731 63.158 0.00 0.00 0.00 3.79
2626 2694 0.462047 ATAAGCCGGCTTCGTCTTGG 60.462 55.000 43.34 0.00 32.94 3.61
2627 2695 0.931005 GATAAGCCGGCTTCGTCTTG 59.069 55.000 43.34 0.00 32.94 3.02
2628 2696 0.535335 TGATAAGCCGGCTTCGTCTT 59.465 50.000 43.34 23.09 36.09 3.01
2629 2697 0.535335 TTGATAAGCCGGCTTCGTCT 59.465 50.000 43.34 26.10 37.47 4.18
2630 2698 1.583054 ATTGATAAGCCGGCTTCGTC 58.417 50.000 43.34 36.55 37.47 4.20
2631 2699 1.670811 CAATTGATAAGCCGGCTTCGT 59.329 47.619 43.34 32.10 37.47 3.85
2632 2700 1.597937 GCAATTGATAAGCCGGCTTCG 60.598 52.381 43.34 23.42 37.47 3.79
2633 2701 1.405105 TGCAATTGATAAGCCGGCTTC 59.595 47.619 43.34 30.80 37.47 3.86
2634 2702 1.134946 GTGCAATTGATAAGCCGGCTT 59.865 47.619 41.05 41.05 39.83 4.35
2635 2703 0.740737 GTGCAATTGATAAGCCGGCT 59.259 50.000 27.08 27.08 0.00 5.52


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

AutoCloner maintained by Alex Coulton.