Multiple sequence alignment - TraesCS6B01G043400

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 TraesCS6B01G043400 chr6B 100.000 2618 0 0 1 2618 26390753 26393370 0.000000e+00 4835
1 TraesCS6B01G043400 chr6B 94.979 478 21 2 32 509 26792710 26792236 0.000000e+00 747
2 TraesCS6B01G043400 chr6B 95.349 172 5 2 602 770 26792197 26792026 1.190000e-68 270
3 TraesCS6B01G043400 chr6B 87.283 173 21 1 602 774 26514377 26514548 2.060000e-46 196
4 TraesCS6B01G043400 chr6A 84.267 1786 248 19 852 2618 108331255 108329484 0.000000e+00 1711
5 TraesCS6B01G043400 chr6A 84.702 889 125 7 852 1730 494037788 494036901 0.000000e+00 878
6 TraesCS6B01G043400 chr6A 85.882 170 23 1 605 774 15897764 15897596 2.070000e-41 180
7 TraesCS6B01G043400 chr6A 87.912 91 11 0 371 461 15702679 15702769 9.910000e-20 108
8 TraesCS6B01G043400 chr4A 81.517 1688 275 30 862 2527 325472452 325474124 0.000000e+00 1354
9 TraesCS6B01G043400 chr5B 83.800 1179 158 19 954 2119 641553621 641554779 0.000000e+00 1088
10 TraesCS6B01G043400 chr5B 88.832 394 42 2 2213 2604 641555072 641555465 1.410000e-132 483
11 TraesCS6B01G043400 chr5B 80.822 511 91 7 2078 2584 492254035 492253528 6.790000e-106 394
12 TraesCS6B01G043400 chr5D 75.505 1633 341 45 984 2584 263995807 263997412 0.000000e+00 745
13 TraesCS6B01G043400 chr5D 88.820 161 15 3 612 770 27977376 27977217 7.390000e-46 195
14 TraesCS6B01G043400 chr4B 73.926 1630 364 42 984 2578 567014674 567013071 1.340000e-167 599
15 TraesCS6B01G043400 chr4B 80.460 522 101 1 2078 2598 55767611 55767090 5.250000e-107 398
16 TraesCS6B01G043400 chr4B 87.805 164 14 5 612 770 575728663 575728825 1.240000e-43 187
17 TraesCS6B01G043400 chr4B 79.012 162 30 4 1988 2147 495077417 495077576 9.910000e-20 108
18 TraesCS6B01G043400 chr6D 89.974 379 28 8 116 492 14938721 14938351 5.070000e-132 481
19 TraesCS6B01G043400 chr6D 95.858 169 7 0 602 770 14938297 14938129 9.230000e-70 274
20 TraesCS6B01G043400 chr6D 94.083 169 10 0 602 770 15347417 15347249 9.300000e-65 257
21 TraesCS6B01G043400 chr6D 89.937 159 13 3 614 770 15350776 15350619 4.420000e-48 202
22 TraesCS6B01G043400 chr6D 86.747 166 21 1 599 764 14505524 14505688 1.600000e-42 183
23 TraesCS6B01G043400 chr6D 91.667 84 7 0 378 461 14505302 14505385 1.650000e-22 117
24 TraesCS6B01G043400 chr6D 86.813 91 12 0 371 461 14437100 14437190 4.610000e-18 102
25 TraesCS6B01G043400 chr4D 82.213 506 87 3 2078 2581 426793295 426793799 1.440000e-117 433
26 TraesCS6B01G043400 chr1B 75.585 598 135 10 1988 2581 401559569 401560159 4.260000e-73 285
27 TraesCS6B01G043400 chr1B 75.252 497 104 17 2101 2588 31658106 31658592 4.390000e-53 219
28 TraesCS6B01G043400 chr3B 78.998 419 79 9 2084 2498 790653389 790652976 7.140000e-71 278
29 TraesCS6B01G043400 chr3B 75.581 516 111 12 2080 2587 811554703 811554195 9.360000e-60 241
30 TraesCS6B01G043400 chr2A 87.597 129 15 1 2095 2222 770132633 770132761 5.840000e-32 148


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 TraesCS6B01G043400 chr6B 26390753 26393370 2617 False 4835.0 4835 100.000 1 2618 1 chr6B.!!$F1 2617
1 TraesCS6B01G043400 chr6B 26792026 26792710 684 True 508.5 747 95.164 32 770 2 chr6B.!!$R1 738
2 TraesCS6B01G043400 chr6A 108329484 108331255 1771 True 1711.0 1711 84.267 852 2618 1 chr6A.!!$R2 1766
3 TraesCS6B01G043400 chr6A 494036901 494037788 887 True 878.0 878 84.702 852 1730 1 chr6A.!!$R3 878
4 TraesCS6B01G043400 chr4A 325472452 325474124 1672 False 1354.0 1354 81.517 862 2527 1 chr4A.!!$F1 1665
5 TraesCS6B01G043400 chr5B 641553621 641555465 1844 False 785.5 1088 86.316 954 2604 2 chr5B.!!$F1 1650
6 TraesCS6B01G043400 chr5B 492253528 492254035 507 True 394.0 394 80.822 2078 2584 1 chr5B.!!$R1 506
7 TraesCS6B01G043400 chr5D 263995807 263997412 1605 False 745.0 745 75.505 984 2584 1 chr5D.!!$F1 1600
8 TraesCS6B01G043400 chr4B 567013071 567014674 1603 True 599.0 599 73.926 984 2578 1 chr4B.!!$R2 1594
9 TraesCS6B01G043400 chr4B 55767090 55767611 521 True 398.0 398 80.460 2078 2598 1 chr4B.!!$R1 520
10 TraesCS6B01G043400 chr6D 14938129 14938721 592 True 377.5 481 92.916 116 770 2 chr6D.!!$R1 654
11 TraesCS6B01G043400 chr6D 15347249 15350776 3527 True 229.5 257 92.010 602 770 2 chr6D.!!$R2 168
12 TraesCS6B01G043400 chr4D 426793295 426793799 504 False 433.0 433 82.213 2078 2581 1 chr4D.!!$F1 503
13 TraesCS6B01G043400 chr1B 401559569 401560159 590 False 285.0 285 75.585 1988 2581 1 chr1B.!!$F2 593
14 TraesCS6B01G043400 chr3B 811554195 811554703 508 True 241.0 241 75.581 2080 2587 1 chr3B.!!$R2 507

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
778 3544 0.037046 TGATGTGTCAGCTGATGCGT 60.037 50.0 21.47 16.38 45.42 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1748 4531 0.034863 GTTTGATTCTACCCGGGGCA 60.035 55.0 27.92 11.59 0.0 5.36 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
19 20 1.438651 CAGCTTTACCACTGCGCTAA 58.561 50.000 9.73 0.00 0.00 3.09
208 209 4.519147 GTTGACTCTCTTTTCTTGAACGC 58.481 43.478 0.00 0.00 0.00 4.84
249 250 1.692519 ACTTAACAGACGCAAGAGGGT 59.307 47.619 0.00 0.00 44.44 4.34
250 251 2.069273 CTTAACAGACGCAAGAGGGTG 58.931 52.381 0.00 0.00 41.49 4.61
314 317 8.853077 TGATCTCTGCTTTATATTTGTATGGG 57.147 34.615 0.00 0.00 0.00 4.00
349 352 9.160496 GATTGGATGTTAGGTTCAGATATGATC 57.840 37.037 0.00 0.00 0.00 2.92
381 384 1.804748 GTCCGTTGCCACTAGGAAAAG 59.195 52.381 0.00 0.00 32.92 2.27
492 495 5.882557 ACTGGGATTAGACTTATGTTTGCTG 59.117 40.000 0.00 0.00 0.00 4.41
509 512 2.228138 CTGAGAAGATCCAGCTGAGC 57.772 55.000 17.39 4.17 0.00 4.26
511 514 2.957680 CTGAGAAGATCCAGCTGAGCTA 59.042 50.000 17.39 0.00 39.26 3.32
512 515 3.369175 TGAGAAGATCCAGCTGAGCTAA 58.631 45.455 17.39 0.00 39.26 3.09
513 516 3.131933 TGAGAAGATCCAGCTGAGCTAAC 59.868 47.826 17.39 7.64 39.26 2.34
514 517 3.373830 AGAAGATCCAGCTGAGCTAACT 58.626 45.455 17.39 9.58 39.26 2.24
515 518 3.132646 AGAAGATCCAGCTGAGCTAACTG 59.867 47.826 17.39 0.00 39.26 3.16
517 520 2.430332 AGATCCAGCTGAGCTAACTGTC 59.570 50.000 17.39 1.54 38.14 3.51
518 521 1.930251 TCCAGCTGAGCTAACTGTCT 58.070 50.000 17.39 0.00 36.40 3.41
519 522 1.821753 TCCAGCTGAGCTAACTGTCTC 59.178 52.381 17.39 0.00 36.40 3.36
520 523 1.824230 CCAGCTGAGCTAACTGTCTCT 59.176 52.381 17.39 0.00 36.40 3.10
521 524 2.159254 CCAGCTGAGCTAACTGTCTCTC 60.159 54.545 17.39 0.00 36.40 3.20
522 525 2.491298 CAGCTGAGCTAACTGTCTCTCA 59.509 50.000 8.42 6.48 36.40 3.27
523 526 3.056962 CAGCTGAGCTAACTGTCTCTCAA 60.057 47.826 8.42 0.00 36.40 3.02
524 527 3.193267 AGCTGAGCTAACTGTCTCTCAAG 59.807 47.826 4.49 4.70 36.99 3.02
525 528 3.675775 GCTGAGCTAACTGTCTCTCAAGG 60.676 52.174 0.00 1.10 35.44 3.61
526 529 3.501349 TGAGCTAACTGTCTCTCAAGGT 58.499 45.455 0.00 0.00 33.17 3.50
528 531 5.077564 TGAGCTAACTGTCTCTCAAGGTAA 58.922 41.667 0.00 0.00 33.17 2.85
530 533 6.031751 AGCTAACTGTCTCTCAAGGTAAAG 57.968 41.667 0.00 0.00 0.00 1.85
531 534 5.775701 AGCTAACTGTCTCTCAAGGTAAAGA 59.224 40.000 0.00 0.00 0.00 2.52
532 535 6.267928 AGCTAACTGTCTCTCAAGGTAAAGAA 59.732 38.462 0.00 0.00 0.00 2.52
533 536 6.929606 GCTAACTGTCTCTCAAGGTAAAGAAA 59.070 38.462 0.00 0.00 0.00 2.52
535 538 9.326413 CTAACTGTCTCTCAAGGTAAAGAAAAA 57.674 33.333 0.00 0.00 0.00 1.94
536 539 7.555306 ACTGTCTCTCAAGGTAAAGAAAAAC 57.445 36.000 0.00 0.00 0.00 2.43
537 540 6.258068 ACTGTCTCTCAAGGTAAAGAAAAACG 59.742 38.462 0.00 0.00 0.00 3.60
540 543 7.223387 TGTCTCTCAAGGTAAAGAAAAACGTAC 59.777 37.037 0.00 0.00 0.00 3.67
542 545 6.585416 TCTCAAGGTAAAGAAAAACGTACCT 58.415 36.000 0.00 0.00 42.20 3.08
543 546 7.725251 TCTCAAGGTAAAGAAAAACGTACCTA 58.275 34.615 2.94 0.00 40.74 3.08
544 547 8.203485 TCTCAAGGTAAAGAAAAACGTACCTAA 58.797 33.333 2.94 0.00 40.74 2.69
546 549 9.341078 TCAAGGTAAAGAAAAACGTACCTAATT 57.659 29.630 2.94 0.00 40.74 1.40
553 556 9.768662 AAAGAAAAACGTACCTAATTAGTCAGA 57.231 29.630 11.50 0.00 0.00 3.27
556 559 9.148104 GAAAAACGTACCTAATTAGTCAGATGT 57.852 33.333 11.50 3.79 0.00 3.06
559 562 9.578439 AAACGTACCTAATTAGTCAGATGTAAC 57.422 33.333 11.50 1.31 0.00 2.50
560 563 8.517062 ACGTACCTAATTAGTCAGATGTAACT 57.483 34.615 11.50 0.00 0.00 2.24
561 564 8.964772 ACGTACCTAATTAGTCAGATGTAACTT 58.035 33.333 11.50 0.00 0.00 2.66
562 565 9.798994 CGTACCTAATTAGTCAGATGTAACTTT 57.201 33.333 11.50 0.00 0.00 2.66
568 571 8.854614 AATTAGTCAGATGTAACTTTTCTGCT 57.145 30.769 0.00 0.00 37.41 4.24
569 572 8.854614 ATTAGTCAGATGTAACTTTTCTGCTT 57.145 30.769 0.00 0.00 37.41 3.91
570 573 6.793492 AGTCAGATGTAACTTTTCTGCTTC 57.207 37.500 0.00 0.00 37.41 3.86
571 574 6.291377 AGTCAGATGTAACTTTTCTGCTTCA 58.709 36.000 0.00 0.00 37.41 3.02
572 575 6.203723 AGTCAGATGTAACTTTTCTGCTTCAC 59.796 38.462 0.00 0.00 37.41 3.18
573 576 6.203723 GTCAGATGTAACTTTTCTGCTTCACT 59.796 38.462 0.00 0.00 37.41 3.41
575 578 6.203530 CAGATGTAACTTTTCTGCTTCACTGA 59.796 38.462 0.00 0.00 31.35 3.41
576 579 6.767902 AGATGTAACTTTTCTGCTTCACTGAA 59.232 34.615 0.00 0.00 34.73 3.02
577 580 6.942532 TGTAACTTTTCTGCTTCACTGAAT 57.057 33.333 0.00 0.00 36.28 2.57
578 581 6.959361 TGTAACTTTTCTGCTTCACTGAATC 58.041 36.000 0.00 0.00 36.28 2.52
579 582 5.444663 AACTTTTCTGCTTCACTGAATCC 57.555 39.130 0.00 0.00 36.28 3.01
580 583 4.723309 ACTTTTCTGCTTCACTGAATCCT 58.277 39.130 0.00 0.00 36.28 3.24
583 586 6.097412 ACTTTTCTGCTTCACTGAATCCTTTT 59.903 34.615 0.00 0.00 36.28 2.27
584 587 6.469782 TTTCTGCTTCACTGAATCCTTTTT 57.530 33.333 0.00 0.00 36.28 1.94
610 613 8.511604 TTATTGAGGAAATCTTCACTGAATCC 57.488 34.615 0.00 2.08 31.40 3.01
704 3470 5.362430 TGCAAGTGGTTTGAGGTTTCTAATT 59.638 36.000 0.00 0.00 39.21 1.40
770 3536 3.482786 GTGTTTCGATTGATGTGTCAGC 58.517 45.455 0.00 0.00 35.39 4.26
771 3537 3.187227 GTGTTTCGATTGATGTGTCAGCT 59.813 43.478 0.00 0.00 35.39 4.24
772 3538 3.187022 TGTTTCGATTGATGTGTCAGCTG 59.813 43.478 7.63 7.63 35.39 4.24
773 3539 3.317603 TTCGATTGATGTGTCAGCTGA 57.682 42.857 13.74 13.74 35.39 4.26
774 3540 3.531934 TCGATTGATGTGTCAGCTGAT 57.468 42.857 21.47 2.86 35.39 2.90
775 3541 3.192466 TCGATTGATGTGTCAGCTGATG 58.808 45.455 21.47 0.00 35.39 3.07
776 3542 2.286242 CGATTGATGTGTCAGCTGATGC 60.286 50.000 21.47 15.80 35.39 3.91
777 3543 1.081094 TTGATGTGTCAGCTGATGCG 58.919 50.000 21.47 0.00 45.42 4.73
778 3544 0.037046 TGATGTGTCAGCTGATGCGT 60.037 50.000 21.47 16.38 45.42 5.24
779 3545 1.081892 GATGTGTCAGCTGATGCGTT 58.918 50.000 21.47 7.47 45.42 4.84
780 3546 1.466167 GATGTGTCAGCTGATGCGTTT 59.534 47.619 21.47 3.10 45.42 3.60
781 3547 0.867746 TGTGTCAGCTGATGCGTTTC 59.132 50.000 21.47 5.43 45.42 2.78
782 3548 0.166814 GTGTCAGCTGATGCGTTTCC 59.833 55.000 21.47 4.63 45.42 3.13
783 3549 0.250252 TGTCAGCTGATGCGTTTCCA 60.250 50.000 21.47 7.52 45.42 3.53
784 3550 0.874390 GTCAGCTGATGCGTTTCCAA 59.126 50.000 21.47 0.00 45.42 3.53
785 3551 1.470098 GTCAGCTGATGCGTTTCCAAT 59.530 47.619 21.47 0.00 45.42 3.16
786 3552 1.739466 TCAGCTGATGCGTTTCCAATC 59.261 47.619 13.74 0.00 45.42 2.67
787 3553 1.469703 CAGCTGATGCGTTTCCAATCA 59.530 47.619 8.42 0.00 45.42 2.57
788 3554 2.095110 CAGCTGATGCGTTTCCAATCAA 60.095 45.455 8.42 0.00 45.42 2.57
789 3555 2.163010 AGCTGATGCGTTTCCAATCAAG 59.837 45.455 0.00 0.00 45.42 3.02
790 3556 2.095059 GCTGATGCGTTTCCAATCAAGT 60.095 45.455 0.00 0.00 0.00 3.16
791 3557 3.612479 GCTGATGCGTTTCCAATCAAGTT 60.612 43.478 0.00 0.00 0.00 2.66
792 3558 3.899734 TGATGCGTTTCCAATCAAGTTG 58.100 40.909 0.00 0.00 37.57 3.16
793 3559 3.567585 TGATGCGTTTCCAATCAAGTTGA 59.432 39.130 8.27 8.27 40.37 3.18
794 3560 3.624326 TGCGTTTCCAATCAAGTTGAG 57.376 42.857 11.91 0.00 40.37 3.02
795 3561 2.287547 TGCGTTTCCAATCAAGTTGAGC 60.288 45.455 11.91 7.07 40.37 4.26
796 3562 2.030805 GCGTTTCCAATCAAGTTGAGCT 60.031 45.455 11.91 0.00 40.37 4.09
797 3563 3.550842 GCGTTTCCAATCAAGTTGAGCTT 60.551 43.478 11.91 0.00 40.37 3.74
798 3564 4.320202 GCGTTTCCAATCAAGTTGAGCTTA 60.320 41.667 11.91 0.00 40.37 3.09
799 3565 5.757886 CGTTTCCAATCAAGTTGAGCTTAA 58.242 37.500 11.91 1.07 40.37 1.85
800 3566 6.381801 CGTTTCCAATCAAGTTGAGCTTAAT 58.618 36.000 11.91 0.00 40.37 1.40
801 3567 6.524586 CGTTTCCAATCAAGTTGAGCTTAATC 59.475 38.462 11.91 2.75 40.37 1.75
802 3568 7.370383 GTTTCCAATCAAGTTGAGCTTAATCA 58.630 34.615 11.91 0.00 40.37 2.57
803 3569 7.707624 TTCCAATCAAGTTGAGCTTAATCAT 57.292 32.000 11.91 0.00 40.37 2.45
804 3570 7.092137 TCCAATCAAGTTGAGCTTAATCATG 57.908 36.000 11.91 0.00 40.37 3.07
805 3571 6.660521 TCCAATCAAGTTGAGCTTAATCATGT 59.339 34.615 11.91 0.00 40.37 3.21
806 3572 7.177216 TCCAATCAAGTTGAGCTTAATCATGTT 59.823 33.333 11.91 0.00 40.37 2.71
807 3573 7.487189 CCAATCAAGTTGAGCTTAATCATGTTC 59.513 37.037 11.91 0.00 40.37 3.18
808 3574 7.692460 ATCAAGTTGAGCTTAATCATGTTCA 57.308 32.000 11.91 0.00 35.27 3.18
809 3575 7.137490 TCAAGTTGAGCTTAATCATGTTCAG 57.863 36.000 0.08 0.00 35.27 3.02
810 3576 6.936335 TCAAGTTGAGCTTAATCATGTTCAGA 59.064 34.615 0.08 0.00 35.27 3.27
811 3577 7.445096 TCAAGTTGAGCTTAATCATGTTCAGAA 59.555 33.333 0.08 0.00 35.27 3.02
812 3578 7.375106 AGTTGAGCTTAATCATGTTCAGAAG 57.625 36.000 0.00 0.00 0.00 2.85
813 3579 6.373774 AGTTGAGCTTAATCATGTTCAGAAGG 59.626 38.462 0.00 0.00 0.00 3.46
814 3580 4.637534 TGAGCTTAATCATGTTCAGAAGGC 59.362 41.667 0.00 0.00 0.00 4.35
815 3581 4.592942 AGCTTAATCATGTTCAGAAGGCA 58.407 39.130 0.00 0.00 0.00 4.75
816 3582 5.198965 AGCTTAATCATGTTCAGAAGGCAT 58.801 37.500 0.00 0.00 0.00 4.40
817 3583 6.359804 AGCTTAATCATGTTCAGAAGGCATA 58.640 36.000 0.00 0.00 0.00 3.14
818 3584 6.830324 AGCTTAATCATGTTCAGAAGGCATAA 59.170 34.615 0.00 0.00 0.00 1.90
819 3585 7.504911 AGCTTAATCATGTTCAGAAGGCATAAT 59.495 33.333 0.00 0.00 0.00 1.28
820 3586 8.139989 GCTTAATCATGTTCAGAAGGCATAATT 58.860 33.333 0.00 0.00 0.00 1.40
824 3590 9.807649 AATCATGTTCAGAAGGCATAATTAAAC 57.192 29.630 0.00 0.00 0.00 2.01
825 3591 8.347004 TCATGTTCAGAAGGCATAATTAAACA 57.653 30.769 0.00 0.00 0.00 2.83
826 3592 8.243426 TCATGTTCAGAAGGCATAATTAAACAC 58.757 33.333 0.00 0.00 0.00 3.32
827 3593 6.607689 TGTTCAGAAGGCATAATTAAACACG 58.392 36.000 0.00 0.00 0.00 4.49
828 3594 6.205853 TGTTCAGAAGGCATAATTAAACACGT 59.794 34.615 0.00 0.00 0.00 4.49
829 3595 6.417191 TCAGAAGGCATAATTAAACACGTC 57.583 37.500 0.00 0.00 0.00 4.34
830 3596 5.353123 TCAGAAGGCATAATTAAACACGTCC 59.647 40.000 0.00 0.00 0.00 4.79
831 3597 5.123186 CAGAAGGCATAATTAAACACGTCCA 59.877 40.000 0.00 0.00 0.00 4.02
832 3598 5.708230 AGAAGGCATAATTAAACACGTCCAA 59.292 36.000 0.00 0.00 0.00 3.53
833 3599 5.968528 AGGCATAATTAAACACGTCCAAA 57.031 34.783 0.00 0.00 0.00 3.28
834 3600 6.334102 AGGCATAATTAAACACGTCCAAAA 57.666 33.333 0.00 0.00 0.00 2.44
835 3601 6.386654 AGGCATAATTAAACACGTCCAAAAG 58.613 36.000 0.00 0.00 0.00 2.27
836 3602 5.575218 GGCATAATTAAACACGTCCAAAAGG 59.425 40.000 0.00 0.00 0.00 3.11
837 3603 5.575218 GCATAATTAAACACGTCCAAAAGGG 59.425 40.000 0.00 0.00 38.37 3.95
838 3604 3.653539 ATTAAACACGTCCAAAAGGGC 57.346 42.857 0.00 0.00 36.21 5.19
839 3605 2.054232 TAAACACGTCCAAAAGGGCA 57.946 45.000 0.00 0.00 36.21 5.36
840 3606 0.744281 AAACACGTCCAAAAGGGCAG 59.256 50.000 0.00 0.00 36.21 4.85
841 3607 0.106918 AACACGTCCAAAAGGGCAGA 60.107 50.000 0.00 0.00 36.21 4.26
842 3608 0.106918 ACACGTCCAAAAGGGCAGAA 60.107 50.000 0.00 0.00 36.21 3.02
843 3609 1.247567 CACGTCCAAAAGGGCAGAAT 58.752 50.000 0.00 0.00 36.21 2.40
844 3610 1.613437 CACGTCCAAAAGGGCAGAATT 59.387 47.619 0.00 0.00 36.21 2.17
845 3611 1.613437 ACGTCCAAAAGGGCAGAATTG 59.387 47.619 0.00 0.00 36.21 2.32
846 3612 1.885887 CGTCCAAAAGGGCAGAATTGA 59.114 47.619 0.00 0.00 36.21 2.57
847 3613 2.095059 CGTCCAAAAGGGCAGAATTGAG 60.095 50.000 0.00 0.00 36.21 3.02
848 3614 3.157087 GTCCAAAAGGGCAGAATTGAGA 58.843 45.455 0.00 0.00 36.21 3.27
849 3615 3.057245 GTCCAAAAGGGCAGAATTGAGAC 60.057 47.826 0.00 0.00 36.21 3.36
850 3616 2.892852 CCAAAAGGGCAGAATTGAGACA 59.107 45.455 0.00 0.00 0.00 3.41
854 3620 0.038166 GGGCAGAATTGAGACACCCA 59.962 55.000 0.00 0.00 35.84 4.51
897 3663 0.314302 CCTCGTAGGCGATTCCGATT 59.686 55.000 0.00 0.00 46.80 3.34
909 3675 0.108329 TTCCGATTGCCTTCGAGTCC 60.108 55.000 6.94 0.00 41.62 3.85
910 3676 1.521681 CCGATTGCCTTCGAGTCCC 60.522 63.158 6.94 0.00 41.62 4.46
911 3677 1.517832 CGATTGCCTTCGAGTCCCT 59.482 57.895 0.00 0.00 41.62 4.20
944 3710 1.879796 CGAAGCCCTAATCTGCATCCC 60.880 57.143 0.00 0.00 0.00 3.85
948 3714 0.321122 CCCTAATCTGCATCCCTCGC 60.321 60.000 0.00 0.00 0.00 5.03
955 3721 4.537433 GCATCCCTCGCCGCTCTT 62.537 66.667 0.00 0.00 0.00 2.85
1062 3836 3.986277 TCTGGAAAACTACTTCGACCAC 58.014 45.455 0.00 0.00 0.00 4.16
1073 3850 2.632996 ACTTCGACCACTTGGATCTCAA 59.367 45.455 1.14 0.00 38.94 3.02
1074 3851 2.743636 TCGACCACTTGGATCTCAAC 57.256 50.000 1.14 0.00 38.94 3.18
1075 3852 1.067846 TCGACCACTTGGATCTCAACG 60.068 52.381 1.14 0.00 38.94 4.10
1241 4022 2.243957 CGCAGCACGTGAGGTTTCA 61.244 57.895 22.23 0.00 36.87 2.69
1260 4041 2.027192 TCAGCCTGTTGGACCTAATCAC 60.027 50.000 0.00 0.00 34.57 3.06
1292 4073 1.322538 GCGTCATGCTTGGGGGATTT 61.323 55.000 0.00 0.00 41.73 2.17
1307 4088 1.677576 GGATTTGGAGCGCATGATGAA 59.322 47.619 11.47 0.00 0.00 2.57
1317 4098 1.442526 GCATGATGAAGCAGGGTCCG 61.443 60.000 0.00 0.00 0.00 4.79
1326 4107 2.113139 CAGGGTCCGTGGCTGTTT 59.887 61.111 3.47 0.00 0.00 2.83
1470 4251 6.603201 AGAACATTGTGGAGAAACTCTTGAAA 59.397 34.615 0.00 0.00 0.00 2.69
1501 4282 1.343789 AGATCATGGAGATGCGTCTGG 59.656 52.381 14.59 0.14 37.00 3.86
1579 4361 6.073222 ACAGCCTCTTACGAAATTTGTTAGTG 60.073 38.462 0.00 0.00 0.00 2.74
1656 4439 1.674764 TTTGCAAGGTGTGTGGCCTG 61.675 55.000 3.32 0.00 36.30 4.85
1668 4451 4.841441 GGCCTGGTTGGTCATGAA 57.159 55.556 0.00 0.00 40.97 2.57
1684 4467 5.431765 GTCATGAACATAAGGAGTGTGGAT 58.568 41.667 0.00 0.00 0.00 3.41
1738 4521 4.009675 TGGAAACTGGTTGTATGCAGATC 58.990 43.478 0.00 0.00 0.00 2.75
1748 4531 5.455326 GGTTGTATGCAGATCCTCCTAACAT 60.455 44.000 0.00 0.00 0.00 2.71
1809 4593 4.102113 CCTTCACAGGCAAAGGGG 57.898 61.111 0.00 0.00 38.72 4.79
1834 4618 0.535780 CCAAGCTGCTCCAACTGACA 60.536 55.000 1.00 0.00 0.00 3.58
1873 4657 0.834612 TCCAGAAACCTTGGACACGT 59.165 50.000 0.00 0.00 39.74 4.49
1894 4678 2.094675 CATCAAGCCCGGTGAAGAATT 58.905 47.619 0.00 0.00 0.00 2.17
1910 4694 2.441001 AGAATTCTAGTGGCAGGATGGG 59.559 50.000 6.06 0.00 35.86 4.00
1949 4733 3.588842 AGGAAGAGGTTGAACATGGATGA 59.411 43.478 0.00 0.00 0.00 2.92
1959 4743 1.076559 CATGGATGAGGCTGGGCAA 60.077 57.895 0.00 0.00 0.00 4.52
1970 4766 0.964358 GCTGGGCAAGATGCTTCAGT 60.964 55.000 19.09 0.00 44.28 3.41
1971 4767 1.093159 CTGGGCAAGATGCTTCAGTC 58.907 55.000 13.76 0.00 44.28 3.51
1981 4777 0.473755 TGCTTCAGTCCAGCCAAAGA 59.526 50.000 0.00 0.00 36.33 2.52
1998 4794 4.082625 CCAAAGATGTTGCTTGCTATCACA 60.083 41.667 0.00 0.00 0.00 3.58
1999 4795 5.393787 CCAAAGATGTTGCTTGCTATCACAT 60.394 40.000 0.00 0.00 0.00 3.21
2033 4829 7.001073 GGCATGGATCTAAAGGAGACTAATTT 58.999 38.462 0.00 0.00 42.68 1.82
2042 4838 4.388378 AGGAGACTAATTTGCCTACGAC 57.612 45.455 0.00 0.00 40.61 4.34
2104 4900 6.535150 GGACAGTGAAAACAATGAGATATCGA 59.465 38.462 0.00 0.00 0.00 3.59
2339 5337 1.217916 TGGAAGGAGTGGTGGTTTGA 58.782 50.000 0.00 0.00 0.00 2.69
2428 5426 0.625316 TTGATGATGTGGGTGGAGGG 59.375 55.000 0.00 0.00 0.00 4.30
2531 5529 0.038709 AGCTATCTCGCAGGATTCGC 60.039 55.000 0.00 0.00 0.00 4.70
2572 5570 0.742281 ACGAAGCTATGTGGCAGCAG 60.742 55.000 0.00 0.00 41.66 4.24
2588 5586 0.750911 GCAGGAGCATCTTTCCAGGG 60.751 60.000 0.00 0.00 41.58 4.45
2599 5597 0.677731 TTTCCAGGGCTCTGCAATCG 60.678 55.000 8.54 0.00 39.61 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.128692 GTTAGCGCAGTGGTAAAGCTG 59.871 52.381 11.47 0.00 41.85 4.24
1 2 1.439679 GTTAGCGCAGTGGTAAAGCT 58.560 50.000 11.47 0.00 41.85 3.74
2 3 0.094730 CGTTAGCGCAGTGGTAAAGC 59.905 55.000 11.47 0.00 41.85 3.51
15 16 2.577593 ACGAAGGGGAGCGTTAGC 59.422 61.111 0.00 0.00 45.58 3.09
19 20 1.827399 ATGACAACGAAGGGGAGCGT 61.827 55.000 0.00 0.00 43.39 5.07
22 23 1.831736 AGGTATGACAACGAAGGGGAG 59.168 52.381 0.00 0.00 0.00 4.30
23 24 1.946984 AGGTATGACAACGAAGGGGA 58.053 50.000 0.00 0.00 0.00 4.81
24 25 2.781681 AAGGTATGACAACGAAGGGG 57.218 50.000 0.00 0.00 0.00 4.79
25 26 4.401519 TCTCTAAGGTATGACAACGAAGGG 59.598 45.833 0.00 0.00 0.00 3.95
26 27 5.578005 TCTCTAAGGTATGACAACGAAGG 57.422 43.478 0.00 0.00 0.00 3.46
27 28 6.853720 TCTTCTCTAAGGTATGACAACGAAG 58.146 40.000 0.00 0.00 33.22 3.79
28 29 6.829229 TCTTCTCTAAGGTATGACAACGAA 57.171 37.500 0.00 0.00 33.22 3.85
29 30 6.829298 AGATCTTCTCTAAGGTATGACAACGA 59.171 38.462 0.00 0.00 33.22 3.85
30 31 7.033530 AGATCTTCTCTAAGGTATGACAACG 57.966 40.000 0.00 0.00 33.22 4.10
123 124 3.802862 AGCCAAGATCTGCTGATGG 57.197 52.632 11.21 8.93 36.23 3.51
249 250 5.860941 TTGCTAAGTGTTTCATTTTCCCA 57.139 34.783 0.00 0.00 0.00 4.37
250 251 6.280643 ACTTTGCTAAGTGTTTCATTTTCCC 58.719 36.000 12.87 0.00 42.91 3.97
314 317 3.815401 CCTAACATCCAATCCATTCGTCC 59.185 47.826 0.00 0.00 0.00 4.79
349 352 6.223852 AGTGGCAACGGACTTAGATATATTG 58.776 40.000 0.00 0.00 42.51 1.90
381 384 4.449131 TCAATCTGAACAGCAGGATGATC 58.551 43.478 0.00 0.00 44.98 2.92
492 495 3.384467 AGTTAGCTCAGCTGGATCTTCTC 59.616 47.826 10.31 0.00 40.10 2.87
506 509 5.646577 TTACCTTGAGAGACAGTTAGCTC 57.353 43.478 0.00 0.00 0.00 4.09
507 510 5.775701 TCTTTACCTTGAGAGACAGTTAGCT 59.224 40.000 0.00 0.00 0.00 3.32
508 511 6.026947 TCTTTACCTTGAGAGACAGTTAGC 57.973 41.667 0.00 0.00 0.00 3.09
509 512 8.888579 TTTTCTTTACCTTGAGAGACAGTTAG 57.111 34.615 0.00 0.00 0.00 2.34
511 514 7.201617 CGTTTTTCTTTACCTTGAGAGACAGTT 60.202 37.037 0.00 0.00 0.00 3.16
512 515 6.258068 CGTTTTTCTTTACCTTGAGAGACAGT 59.742 38.462 0.00 0.00 0.00 3.55
513 516 6.258068 ACGTTTTTCTTTACCTTGAGAGACAG 59.742 38.462 0.00 0.00 0.00 3.51
514 517 6.110707 ACGTTTTTCTTTACCTTGAGAGACA 58.889 36.000 0.00 0.00 0.00 3.41
515 518 6.600246 ACGTTTTTCTTTACCTTGAGAGAC 57.400 37.500 0.00 0.00 0.00 3.36
517 520 6.704937 AGGTACGTTTTTCTTTACCTTGAGAG 59.295 38.462 0.00 0.00 41.33 3.20
518 521 6.585416 AGGTACGTTTTTCTTTACCTTGAGA 58.415 36.000 0.00 0.00 41.33 3.27
519 522 6.856135 AGGTACGTTTTTCTTTACCTTGAG 57.144 37.500 0.00 0.00 41.33 3.02
520 523 8.907222 ATTAGGTACGTTTTTCTTTACCTTGA 57.093 30.769 7.64 0.00 41.33 3.02
528 531 9.939802 ATCTGACTAATTAGGTACGTTTTTCTT 57.060 29.630 16.73 0.00 0.00 2.52
530 533 9.148104 ACATCTGACTAATTAGGTACGTTTTTC 57.852 33.333 16.73 2.74 0.00 2.29
533 536 9.578439 GTTACATCTGACTAATTAGGTACGTTT 57.422 33.333 16.73 0.00 0.00 3.60
535 538 8.517062 AGTTACATCTGACTAATTAGGTACGT 57.483 34.615 16.73 8.20 0.00 3.57
536 539 9.798994 AAAGTTACATCTGACTAATTAGGTACG 57.201 33.333 16.73 2.82 0.00 3.67
542 545 9.944376 AGCAGAAAAGTTACATCTGACTAATTA 57.056 29.630 14.08 0.00 42.48 1.40
543 546 8.854614 AGCAGAAAAGTTACATCTGACTAATT 57.145 30.769 14.08 0.00 42.48 1.40
544 547 8.854614 AAGCAGAAAAGTTACATCTGACTAAT 57.145 30.769 14.08 0.00 42.48 1.73
546 549 7.385205 GTGAAGCAGAAAAGTTACATCTGACTA 59.615 37.037 14.08 0.00 42.48 2.59
547 550 6.203723 GTGAAGCAGAAAAGTTACATCTGACT 59.796 38.462 14.08 9.13 42.48 3.41
548 551 6.203723 AGTGAAGCAGAAAAGTTACATCTGAC 59.796 38.462 14.08 7.58 42.48 3.51
549 552 6.203530 CAGTGAAGCAGAAAAGTTACATCTGA 59.796 38.462 14.08 0.00 42.48 3.27
551 554 6.291377 TCAGTGAAGCAGAAAAGTTACATCT 58.709 36.000 0.00 0.00 0.00 2.90
552 555 6.545504 TCAGTGAAGCAGAAAAGTTACATC 57.454 37.500 0.00 0.00 0.00 3.06
553 556 6.942532 TTCAGTGAAGCAGAAAAGTTACAT 57.057 33.333 0.08 0.00 0.00 2.29
556 559 6.299141 AGGATTCAGTGAAGCAGAAAAGTTA 58.701 36.000 21.76 0.00 28.65 2.24
557 560 5.136105 AGGATTCAGTGAAGCAGAAAAGTT 58.864 37.500 21.76 0.00 28.65 2.66
559 562 5.702349 AAGGATTCAGTGAAGCAGAAAAG 57.298 39.130 21.76 0.00 28.65 2.27
560 563 6.469782 AAAAGGATTCAGTGAAGCAGAAAA 57.530 33.333 21.76 0.00 28.65 2.29
561 564 6.469782 AAAAAGGATTCAGTGAAGCAGAAA 57.530 33.333 21.76 0.00 28.65 2.52
584 587 8.960591 GGATTCAGTGAAGATTTCCTCAATAAA 58.039 33.333 11.91 0.00 0.00 1.40
586 589 7.865820 AGGATTCAGTGAAGATTTCCTCAATA 58.134 34.615 16.74 0.00 29.39 1.90
588 591 6.131972 AGGATTCAGTGAAGATTTCCTCAA 57.868 37.500 16.74 0.00 29.39 3.02
589 592 5.768980 AGGATTCAGTGAAGATTTCCTCA 57.231 39.130 16.74 0.00 29.39 3.86
591 594 9.790344 CATATTAGGATTCAGTGAAGATTTCCT 57.210 33.333 23.03 23.03 35.72 3.36
592 595 9.007901 CCATATTAGGATTCAGTGAAGATTTCC 57.992 37.037 11.91 12.70 0.00 3.13
593 596 9.566432 ACCATATTAGGATTCAGTGAAGATTTC 57.434 33.333 11.91 3.78 0.00 2.17
595 598 8.717717 TCACCATATTAGGATTCAGTGAAGATT 58.282 33.333 11.91 1.78 30.56 2.40
596 599 8.153550 GTCACCATATTAGGATTCAGTGAAGAT 58.846 37.037 11.91 2.40 35.02 2.40
597 600 7.500992 GTCACCATATTAGGATTCAGTGAAGA 58.499 38.462 11.91 0.00 35.02 2.87
598 601 6.422100 CGTCACCATATTAGGATTCAGTGAAG 59.578 42.308 11.91 0.00 35.02 3.02
600 603 5.739070 GCGTCACCATATTAGGATTCAGTGA 60.739 44.000 0.00 0.00 0.00 3.41
601 604 4.449068 GCGTCACCATATTAGGATTCAGTG 59.551 45.833 0.00 0.00 0.00 3.66
602 605 4.345257 AGCGTCACCATATTAGGATTCAGT 59.655 41.667 0.00 0.00 0.00 3.41
603 606 4.687948 CAGCGTCACCATATTAGGATTCAG 59.312 45.833 0.00 0.00 0.00 3.02
606 609 4.955811 TCAGCGTCACCATATTAGGATT 57.044 40.909 0.00 0.00 0.00 3.01
608 611 4.955811 ATTCAGCGTCACCATATTAGGA 57.044 40.909 0.00 0.00 0.00 2.94
609 612 5.408604 GGTAATTCAGCGTCACCATATTAGG 59.591 44.000 0.00 0.00 0.00 2.69
610 613 5.989168 TGGTAATTCAGCGTCACCATATTAG 59.011 40.000 0.00 0.00 34.40 1.73
770 3536 3.837213 ACTTGATTGGAAACGCATCAG 57.163 42.857 0.00 0.00 34.96 2.90
771 3537 3.567585 TCAACTTGATTGGAAACGCATCA 59.432 39.130 0.00 0.00 38.98 3.07
772 3538 4.159377 TCAACTTGATTGGAAACGCATC 57.841 40.909 0.00 0.00 38.98 3.91
773 3539 3.612479 GCTCAACTTGATTGGAAACGCAT 60.612 43.478 0.00 0.00 38.98 4.73
774 3540 2.287547 GCTCAACTTGATTGGAAACGCA 60.288 45.455 0.00 0.00 38.98 5.24
775 3541 2.030805 AGCTCAACTTGATTGGAAACGC 60.031 45.455 0.00 0.00 38.98 4.84
776 3542 3.904136 AGCTCAACTTGATTGGAAACG 57.096 42.857 0.00 0.00 38.98 3.60
777 3543 7.370383 TGATTAAGCTCAACTTGATTGGAAAC 58.630 34.615 0.00 0.00 39.58 2.78
778 3544 7.523293 TGATTAAGCTCAACTTGATTGGAAA 57.477 32.000 0.00 0.00 39.58 3.13
779 3545 7.177216 ACATGATTAAGCTCAACTTGATTGGAA 59.823 33.333 0.00 0.00 39.58 3.53
780 3546 6.660521 ACATGATTAAGCTCAACTTGATTGGA 59.339 34.615 0.00 0.00 39.58 3.53
781 3547 6.860080 ACATGATTAAGCTCAACTTGATTGG 58.140 36.000 0.00 0.00 39.58 3.16
782 3548 8.024865 TGAACATGATTAAGCTCAACTTGATTG 58.975 33.333 0.00 0.00 39.58 2.67
783 3549 8.114331 TGAACATGATTAAGCTCAACTTGATT 57.886 30.769 0.00 0.00 39.58 2.57
784 3550 7.609146 TCTGAACATGATTAAGCTCAACTTGAT 59.391 33.333 0.00 0.00 39.58 2.57
785 3551 6.936335 TCTGAACATGATTAAGCTCAACTTGA 59.064 34.615 0.00 0.00 39.58 3.02
786 3552 7.137490 TCTGAACATGATTAAGCTCAACTTG 57.863 36.000 0.00 0.00 39.58 3.16
787 3553 7.094463 CCTTCTGAACATGATTAAGCTCAACTT 60.094 37.037 0.00 0.00 42.76 2.66
788 3554 6.373774 CCTTCTGAACATGATTAAGCTCAACT 59.626 38.462 0.00 0.00 0.00 3.16
789 3555 6.549952 CCTTCTGAACATGATTAAGCTCAAC 58.450 40.000 0.00 0.00 0.00 3.18
790 3556 5.124457 GCCTTCTGAACATGATTAAGCTCAA 59.876 40.000 0.00 0.00 0.00 3.02
791 3557 4.637534 GCCTTCTGAACATGATTAAGCTCA 59.362 41.667 0.00 0.00 0.00 4.26
792 3558 4.637534 TGCCTTCTGAACATGATTAAGCTC 59.362 41.667 0.00 0.00 0.00 4.09
793 3559 4.592942 TGCCTTCTGAACATGATTAAGCT 58.407 39.130 0.00 0.00 0.00 3.74
794 3560 4.970662 TGCCTTCTGAACATGATTAAGC 57.029 40.909 0.00 0.00 0.00 3.09
798 3564 9.807649 GTTTAATTATGCCTTCTGAACATGATT 57.192 29.630 0.00 12.43 35.16 2.57
799 3565 8.970020 TGTTTAATTATGCCTTCTGAACATGAT 58.030 29.630 0.00 0.00 0.00 2.45
800 3566 8.243426 GTGTTTAATTATGCCTTCTGAACATGA 58.757 33.333 0.00 0.00 0.00 3.07
801 3567 7.218773 CGTGTTTAATTATGCCTTCTGAACATG 59.781 37.037 4.32 0.00 0.00 3.21
802 3568 7.094377 ACGTGTTTAATTATGCCTTCTGAACAT 60.094 33.333 0.00 0.13 0.00 2.71
803 3569 6.205853 ACGTGTTTAATTATGCCTTCTGAACA 59.794 34.615 0.00 0.00 0.00 3.18
804 3570 6.608610 ACGTGTTTAATTATGCCTTCTGAAC 58.391 36.000 0.00 0.00 0.00 3.18
805 3571 6.128117 GGACGTGTTTAATTATGCCTTCTGAA 60.128 38.462 0.00 0.00 0.00 3.02
806 3572 5.353123 GGACGTGTTTAATTATGCCTTCTGA 59.647 40.000 0.00 0.00 0.00 3.27
807 3573 5.123186 TGGACGTGTTTAATTATGCCTTCTG 59.877 40.000 0.00 0.00 0.00 3.02
808 3574 5.250200 TGGACGTGTTTAATTATGCCTTCT 58.750 37.500 0.00 0.00 0.00 2.85
809 3575 5.554822 TGGACGTGTTTAATTATGCCTTC 57.445 39.130 0.00 0.00 0.00 3.46
810 3576 5.968528 TTGGACGTGTTTAATTATGCCTT 57.031 34.783 0.00 0.00 0.00 4.35
811 3577 5.968528 TTTGGACGTGTTTAATTATGCCT 57.031 34.783 0.00 0.00 0.00 4.75
812 3578 5.575218 CCTTTTGGACGTGTTTAATTATGCC 59.425 40.000 0.00 0.00 44.07 4.40
813 3579 5.575218 CCCTTTTGGACGTGTTTAATTATGC 59.425 40.000 0.00 0.00 44.07 3.14
814 3580 5.575218 GCCCTTTTGGACGTGTTTAATTATG 59.425 40.000 0.00 0.00 44.07 1.90
815 3581 5.244178 TGCCCTTTTGGACGTGTTTAATTAT 59.756 36.000 0.00 0.00 44.07 1.28
816 3582 4.583489 TGCCCTTTTGGACGTGTTTAATTA 59.417 37.500 0.00 0.00 44.07 1.40
817 3583 3.385111 TGCCCTTTTGGACGTGTTTAATT 59.615 39.130 0.00 0.00 44.07 1.40
818 3584 2.959707 TGCCCTTTTGGACGTGTTTAAT 59.040 40.909 0.00 0.00 44.07 1.40
819 3585 2.359531 CTGCCCTTTTGGACGTGTTTAA 59.640 45.455 0.00 0.00 44.07 1.52
820 3586 1.950909 CTGCCCTTTTGGACGTGTTTA 59.049 47.619 0.00 0.00 44.07 2.01
821 3587 0.744281 CTGCCCTTTTGGACGTGTTT 59.256 50.000 0.00 0.00 44.07 2.83
822 3588 0.106918 TCTGCCCTTTTGGACGTGTT 60.107 50.000 0.00 0.00 44.07 3.32
823 3589 0.106918 TTCTGCCCTTTTGGACGTGT 60.107 50.000 0.00 0.00 44.07 4.49
824 3590 1.247567 ATTCTGCCCTTTTGGACGTG 58.752 50.000 0.00 0.00 44.07 4.49
825 3591 1.613437 CAATTCTGCCCTTTTGGACGT 59.387 47.619 0.00 0.00 44.07 4.34
826 3592 1.885887 TCAATTCTGCCCTTTTGGACG 59.114 47.619 0.00 0.00 44.07 4.79
827 3593 3.057245 GTCTCAATTCTGCCCTTTTGGAC 60.057 47.826 0.00 0.00 44.07 4.02
828 3594 3.157087 GTCTCAATTCTGCCCTTTTGGA 58.843 45.455 0.00 0.00 44.07 3.53
829 3595 2.892852 TGTCTCAATTCTGCCCTTTTGG 59.107 45.455 0.00 0.00 39.97 3.28
830 3596 3.305608 GGTGTCTCAATTCTGCCCTTTTG 60.306 47.826 0.00 0.00 0.00 2.44
831 3597 2.893489 GGTGTCTCAATTCTGCCCTTTT 59.107 45.455 0.00 0.00 0.00 2.27
832 3598 2.519013 GGTGTCTCAATTCTGCCCTTT 58.481 47.619 0.00 0.00 0.00 3.11
833 3599 1.272147 GGGTGTCTCAATTCTGCCCTT 60.272 52.381 0.00 0.00 0.00 3.95
834 3600 0.329596 GGGTGTCTCAATTCTGCCCT 59.670 55.000 0.00 0.00 0.00 5.19
835 3601 0.038166 TGGGTGTCTCAATTCTGCCC 59.962 55.000 0.00 0.00 35.37 5.36
836 3602 2.134789 ATGGGTGTCTCAATTCTGCC 57.865 50.000 0.00 0.00 0.00 4.85
837 3603 2.609459 CGTATGGGTGTCTCAATTCTGC 59.391 50.000 0.00 0.00 0.00 4.26
838 3604 2.609459 GCGTATGGGTGTCTCAATTCTG 59.391 50.000 0.00 0.00 0.00 3.02
839 3605 2.501723 AGCGTATGGGTGTCTCAATTCT 59.498 45.455 0.00 0.00 0.00 2.40
840 3606 2.866762 GAGCGTATGGGTGTCTCAATTC 59.133 50.000 0.00 0.00 0.00 2.17
841 3607 2.420129 GGAGCGTATGGGTGTCTCAATT 60.420 50.000 0.00 0.00 0.00 2.32
842 3608 1.139058 GGAGCGTATGGGTGTCTCAAT 59.861 52.381 0.00 0.00 0.00 2.57
843 3609 0.535335 GGAGCGTATGGGTGTCTCAA 59.465 55.000 0.00 0.00 0.00 3.02
844 3610 1.327690 GGGAGCGTATGGGTGTCTCA 61.328 60.000 0.00 0.00 0.00 3.27
845 3611 1.442148 GGGAGCGTATGGGTGTCTC 59.558 63.158 0.00 0.00 0.00 3.36
846 3612 2.423898 CGGGAGCGTATGGGTGTCT 61.424 63.158 0.00 0.00 0.00 3.41
847 3613 2.106332 CGGGAGCGTATGGGTGTC 59.894 66.667 0.00 0.00 0.00 3.67
909 3675 2.343163 CTTCGCTCGTAGCTGGGAGG 62.343 65.000 15.15 7.59 39.60 4.30
910 3676 1.064946 CTTCGCTCGTAGCTGGGAG 59.935 63.158 10.55 10.55 39.60 4.30
911 3677 3.064987 GCTTCGCTCGTAGCTGGGA 62.065 63.158 12.51 0.00 39.60 4.37
927 3693 1.063183 GAGGGATGCAGATTAGGGCT 58.937 55.000 0.00 0.00 0.00 5.19
928 3694 0.321122 CGAGGGATGCAGATTAGGGC 60.321 60.000 0.00 0.00 0.00 5.19
929 3695 0.321122 GCGAGGGATGCAGATTAGGG 60.321 60.000 0.00 0.00 0.00 3.53
933 3699 2.109799 CGGCGAGGGATGCAGATT 59.890 61.111 0.00 0.00 0.00 2.40
958 3724 4.271816 CGATCTGGAGGGTCCGCG 62.272 72.222 0.00 0.00 40.17 6.46
967 3733 1.486310 CCATCAGGGAAACGATCTGGA 59.514 52.381 0.00 0.00 40.01 3.86
1029 3795 5.489792 AGTTTTCCAGATCAGACTTAGCA 57.510 39.130 0.00 0.00 0.00 3.49
1032 3806 7.176165 TCGAAGTAGTTTTCCAGATCAGACTTA 59.824 37.037 0.00 0.00 0.00 2.24
1062 3836 1.472878 TCCTCGTCGTTGAGATCCAAG 59.527 52.381 8.00 0.00 38.28 3.61
1118 3898 3.124636 CCACCGGACACTTTCTTTAATCG 59.875 47.826 9.46 0.00 0.00 3.34
1241 4022 2.269940 AGTGATTAGGTCCAACAGGCT 58.730 47.619 0.00 0.00 0.00 4.58
1260 4041 0.179100 ATGACGCCTGGACGATGAAG 60.179 55.000 15.53 0.00 36.70 3.02
1292 4073 1.078285 TGCTTCATCATGCGCTCCA 60.078 52.632 9.73 0.00 0.00 3.86
1317 4098 1.402325 GCCCAATTACGAAACAGCCAC 60.402 52.381 0.00 0.00 0.00 5.01
1326 4107 3.196901 ACATCAGTACAGCCCAATTACGA 59.803 43.478 0.00 0.00 0.00 3.43
1470 4251 1.129917 CCATGATCTCTCCTGCACCT 58.870 55.000 0.00 0.00 0.00 4.00
1579 4361 1.595794 TCGTTCCTTTGCTCGAACAAC 59.404 47.619 0.00 0.00 38.63 3.32
1656 4439 4.396166 CACTCCTTATGTTCATGACCAACC 59.604 45.833 0.00 0.00 0.00 3.77
1668 4451 3.189606 TCCCAATCCACACTCCTTATGT 58.810 45.455 0.00 0.00 0.00 2.29
1738 4521 2.510906 CCGGGGCATGTTAGGAGG 59.489 66.667 0.00 0.00 0.00 4.30
1748 4531 0.034863 GTTTGATTCTACCCGGGGCA 60.035 55.000 27.92 11.59 0.00 5.36
1809 4593 0.323725 TTGGAGCAGCTTGGATTCCC 60.324 55.000 0.00 0.00 0.00 3.97
1815 4599 0.535780 TGTCAGTTGGAGCAGCTTGG 60.536 55.000 0.00 0.00 0.00 3.61
1834 4618 2.519780 GATCCTCTCCCGCTCGGT 60.520 66.667 7.59 0.00 0.00 4.69
1860 4644 2.494059 CTTGATGACGTGTCCAAGGTT 58.506 47.619 0.00 0.00 34.11 3.50
1873 4657 0.690192 TTCTTCACCGGGCTTGATGA 59.310 50.000 6.32 5.71 0.00 2.92
1894 4678 0.339859 ACTCCCATCCTGCCACTAGA 59.660 55.000 0.00 0.00 0.00 2.43
1910 4694 1.679898 CTGGGGTCCTTGTCCACTC 59.320 63.158 0.00 0.00 0.00 3.51
1949 4733 1.379576 GAAGCATCTTGCCCAGCCT 60.380 57.895 0.00 0.00 46.52 4.58
1959 4743 0.694771 TTGGCTGGACTGAAGCATCT 59.305 50.000 0.00 0.00 42.69 2.90
1970 4766 1.614903 CAAGCAACATCTTTGGCTGGA 59.385 47.619 0.00 0.00 36.58 3.86
1971 4767 1.938016 GCAAGCAACATCTTTGGCTGG 60.938 52.381 0.00 0.00 36.58 4.85
1981 4777 5.135383 ACCATATGTGATAGCAAGCAACAT 58.865 37.500 1.24 1.96 0.00 2.71
1998 4794 2.191400 AGATCCATGCCGCTACCATAT 58.809 47.619 0.00 0.00 0.00 1.78
1999 4795 1.644509 AGATCCATGCCGCTACCATA 58.355 50.000 0.00 0.00 0.00 2.74
2033 4829 1.480789 TGAGCTATTGGTCGTAGGCA 58.519 50.000 2.04 0.00 43.09 4.75
2042 4838 2.286294 CGCTTACTGCTTGAGCTATTGG 59.714 50.000 4.44 0.00 42.66 3.16
2176 4975 0.393077 CACCTCTTGAACTGTCCGGT 59.607 55.000 0.00 0.00 0.00 5.28
2428 5426 0.612453 AGGTTCCTCTCCACGAGTCC 60.612 60.000 0.00 0.00 38.11 3.85
2484 5482 5.311649 AGCCTAGTCAAATGATCCCACATAT 59.688 40.000 0.00 0.00 0.00 1.78
2528 5526 2.165641 AGTCTCCACATACAAATCGCGA 59.834 45.455 13.09 13.09 0.00 5.87
2531 5529 5.004440 CGTTGTAGTCTCCACATACAAATCG 59.996 44.000 0.00 0.00 40.14 3.34
2533 5531 6.032956 TCGTTGTAGTCTCCACATACAAAT 57.967 37.500 0.00 0.00 40.14 2.32
2572 5570 0.465278 GAGCCCTGGAAAGATGCTCC 60.465 60.000 8.62 0.00 41.95 4.70
2599 5597 4.243383 GCCAACATCCGTGTTTGC 57.757 55.556 2.31 2.31 46.07 3.68


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

AutoCloner maintained by Alex Coulton.