Multiple sequence alignment - TraesCS2A01G338600

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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 TraesCS2A01G338600 chr2A 100.000 3681 0 0 1 3681 572709153 572705473 0.000000e+00 6798.0
1 TraesCS2A01G338600 chr2A 77.605 643 110 28 1319 1943 572748090 572747464 3.500000e-95 359.0
2 TraesCS2A01G338600 chr2B 89.468 2630 134 57 707 3254 489028959 489031527 0.000000e+00 3190.0
3 TraesCS2A01G338600 chr2B 95.575 339 15 0 3343 3681 489031768 489032106 8.990000e-151 544.0
4 TraesCS2A01G338600 chr2B 76.287 641 122 24 1319 1943 489015902 489016528 7.670000e-82 315.0
5 TraesCS2A01G338600 chr2B 83.742 326 31 10 2 313 489028410 489028727 4.650000e-74 289.0
6 TraesCS2A01G338600 chr2B 85.714 98 2 5 3252 3349 489031650 489031735 3.910000e-15 93.5
7 TraesCS2A01G338600 chr2D 90.789 2432 122 45 574 2964 417209948 417212318 0.000000e+00 3157.0
8 TraesCS2A01G338600 chr2D 89.072 1638 79 54 2125 3681 417211490 417213108 0.000000e+00 1941.0
9 TraesCS2A01G338600 chr2D 77.138 643 119 23 1316 1943 417183828 417184457 7.570000e-92 348.0
10 TraesCS2A01G338600 chr2D 81.564 358 31 17 2 333 417209363 417209711 2.820000e-66 263.0
11 TraesCS2A01G338600 chr1B 88.548 620 71 0 1315 1934 41526840 41526221 0.000000e+00 752.0
12 TraesCS2A01G338600 chr1B 85.935 647 77 10 2160 2802 41526059 41525423 0.000000e+00 678.0
13 TraesCS2A01G338600 chr1B 86.577 149 17 1 1060 1205 41527587 41527439 1.060000e-35 161.0


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 TraesCS2A01G338600 chr2A 572705473 572709153 3680 True 6798.000000 6798 100.000000 1 3681 1 chr2A.!!$R1 3680
1 TraesCS2A01G338600 chr2A 572747464 572748090 626 True 359.000000 359 77.605000 1319 1943 1 chr2A.!!$R2 624
2 TraesCS2A01G338600 chr2B 489028410 489032106 3696 False 1029.125000 3190 88.624750 2 3681 4 chr2B.!!$F2 3679
3 TraesCS2A01G338600 chr2B 489015902 489016528 626 False 315.000000 315 76.287000 1319 1943 1 chr2B.!!$F1 624
4 TraesCS2A01G338600 chr2D 417209363 417213108 3745 False 1787.000000 3157 87.141667 2 3681 3 chr2D.!!$F2 3679
5 TraesCS2A01G338600 chr2D 417183828 417184457 629 False 348.000000 348 77.138000 1316 1943 1 chr2D.!!$F1 627
6 TraesCS2A01G338600 chr1B 41525423 41527587 2164 True 530.333333 752 87.020000 1060 2802 3 chr1B.!!$R1 1742

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
929 1041 0.037697 CCTGTTCCATCCGTCGTGAA 60.038 55.0 0.00 0.0 0.00 3.18 F
1663 2289 0.171455 ACCTCTTCATCGTGCTCGTC 59.829 55.0 8.17 0.0 38.33 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2392 3082 1.059584 TGAGGGACCTCTTGTTGCCA 61.060 55.0 18.48 0.0 43.12 4.92 R
3326 4200 0.252881 AGCTCCTCCTGGTTGGATCA 60.253 55.0 10.56 0.0 45.16 2.92 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
42 43 3.733344 GATTGCTCGCCACGCCCTA 62.733 63.158 0.00 0.00 0.00 3.53
75 82 5.334414 CCCGGTCACGTAGTTATAGTGATAC 60.334 48.000 0.00 0.00 45.13 2.24
79 86 6.018751 GGTCACGTAGTTATAGTGATACGACA 60.019 42.308 10.22 0.00 45.13 4.35
80 87 7.307632 GGTCACGTAGTTATAGTGATACGACAT 60.308 40.741 10.22 0.00 45.13 3.06
81 88 8.066595 GTCACGTAGTTATAGTGATACGACATT 58.933 37.037 10.22 0.00 45.13 2.71
82 89 8.066000 TCACGTAGTTATAGTGATACGACATTG 58.934 37.037 10.22 0.00 41.61 2.82
83 90 7.854422 CACGTAGTTATAGTGATACGACATTGT 59.146 37.037 10.22 0.00 41.61 2.71
84 91 8.400947 ACGTAGTTATAGTGATACGACATTGTT 58.599 33.333 10.22 0.00 37.78 2.83
85 92 9.868389 CGTAGTTATAGTGATACGACATTGTTA 57.132 33.333 0.00 0.00 42.66 2.41
123 130 7.598493 TGATTTTCCTTAGTTGCAAATAACAGC 59.402 33.333 14.91 1.89 33.02 4.40
131 138 4.739716 AGTTGCAAATAACAGCGAACTTTG 59.260 37.500 0.00 0.00 32.33 2.77
137 144 5.994887 AATAACAGCGAACTTTGTACACA 57.005 34.783 0.00 0.00 0.00 3.72
140 147 4.893424 ACAGCGAACTTTGTACACATTT 57.107 36.364 0.00 0.00 0.00 2.32
142 149 6.554334 ACAGCGAACTTTGTACACATTTAT 57.446 33.333 0.00 0.00 0.00 1.40
149 158 6.854496 ACTTTGTACACATTTATCACGTGT 57.146 33.333 16.51 5.66 45.42 4.49
263 296 0.243907 GAAGTAGCTCAGTGGTGCGA 59.756 55.000 0.00 0.00 38.51 5.10
264 297 0.679505 AAGTAGCTCAGTGGTGCGAA 59.320 50.000 0.00 0.00 38.51 4.70
265 298 0.038159 AGTAGCTCAGTGGTGCGAAC 60.038 55.000 0.00 0.00 38.51 3.95
283 320 4.504858 CGAACCACTAGGCTGATAAAACT 58.495 43.478 0.00 0.00 39.06 2.66
288 325 5.823045 ACCACTAGGCTGATAAAACTAATGC 59.177 40.000 0.00 0.00 39.06 3.56
290 327 6.543831 CCACTAGGCTGATAAAACTAATGCTT 59.456 38.462 0.00 0.00 0.00 3.91
314 351 4.899239 GAGCGCTAGCCACGGCAT 62.899 66.667 11.50 0.00 46.67 4.40
319 356 4.488136 CTAGCCACGGCATGCCCA 62.488 66.667 30.79 8.24 44.88 5.36
320 357 4.794648 TAGCCACGGCATGCCCAC 62.795 66.667 30.79 16.97 44.88 4.61
333 370 0.403655 TGCCCACTCATGCAACCTAA 59.596 50.000 0.00 0.00 33.87 2.69
336 373 2.945440 GCCCACTCATGCAACCTAATCA 60.945 50.000 0.00 0.00 0.00 2.57
346 410 3.758554 TGCAACCTAATCAAGAGGCTTTC 59.241 43.478 0.00 0.00 37.63 2.62
353 417 7.414266 ACCTAATCAAGAGGCTTTCCTAAAAT 58.586 34.615 0.00 0.00 44.46 1.82
354 418 8.557450 ACCTAATCAAGAGGCTTTCCTAAAATA 58.443 33.333 0.00 0.00 44.46 1.40
379 451 6.168270 AGTAGTAGTACTCCTAGTTACGGG 57.832 45.833 5.96 0.00 34.00 5.28
392 464 1.728425 GTTACGGGAGCAACTAAACGG 59.272 52.381 0.00 0.00 33.35 4.44
395 467 1.017701 CGGGAGCAACTAAACGGACC 61.018 60.000 0.00 0.00 0.00 4.46
403 475 3.120442 GCAACTAAACGGACCATGTGTAC 60.120 47.826 0.00 0.00 0.00 2.90
405 477 5.472148 CAACTAAACGGACCATGTGTACTA 58.528 41.667 0.00 0.00 0.00 1.82
408 480 7.035840 ACTAAACGGACCATGTGTACTATAG 57.964 40.000 0.00 0.00 0.00 1.31
409 481 5.927281 AAACGGACCATGTGTACTATAGT 57.073 39.130 10.87 10.87 0.00 2.12
410 482 4.913335 ACGGACCATGTGTACTATAGTG 57.087 45.455 15.90 0.00 0.00 2.74
411 483 4.275810 ACGGACCATGTGTACTATAGTGT 58.724 43.478 15.90 2.57 0.00 3.55
412 484 5.439721 ACGGACCATGTGTACTATAGTGTA 58.560 41.667 15.90 1.30 0.00 2.90
413 485 5.530171 ACGGACCATGTGTACTATAGTGTAG 59.470 44.000 15.90 3.81 0.00 2.74
414 486 5.562307 CGGACCATGTGTACTATAGTGTAGC 60.562 48.000 15.90 4.01 0.00 3.58
415 487 5.535406 GGACCATGTGTACTATAGTGTAGCT 59.465 44.000 15.90 0.00 0.00 3.32
416 488 6.392625 ACCATGTGTACTATAGTGTAGCTG 57.607 41.667 15.90 7.46 0.00 4.24
417 489 5.221263 ACCATGTGTACTATAGTGTAGCTGC 60.221 44.000 15.90 0.00 0.00 5.25
418 490 5.221244 CCATGTGTACTATAGTGTAGCTGCA 60.221 44.000 15.90 0.00 0.00 4.41
419 491 6.450545 CATGTGTACTATAGTGTAGCTGCAT 58.549 40.000 15.90 7.21 0.00 3.96
420 492 5.831997 TGTGTACTATAGTGTAGCTGCATG 58.168 41.667 15.90 0.00 0.00 4.06
465 537 1.508088 ACGAAGGCTACGTTACCCG 59.492 57.895 0.00 0.00 41.18 5.28
493 565 2.117051 GAGGTTTCCTCGGATTACCCT 58.883 52.381 11.86 4.33 41.08 4.34
494 566 2.102757 GAGGTTTCCTCGGATTACCCTC 59.897 54.545 11.86 8.62 41.08 4.30
496 568 2.237893 GGTTTCCTCGGATTACCCTCAA 59.762 50.000 6.53 0.00 0.00 3.02
497 569 3.307904 GGTTTCCTCGGATTACCCTCAAA 60.308 47.826 6.53 0.00 0.00 2.69
498 570 4.329392 GTTTCCTCGGATTACCCTCAAAA 58.671 43.478 0.00 0.00 0.00 2.44
499 571 3.906720 TCCTCGGATTACCCTCAAAAG 57.093 47.619 0.00 0.00 0.00 2.27
500 572 3.446968 TCCTCGGATTACCCTCAAAAGA 58.553 45.455 0.00 0.00 0.00 2.52
501 573 3.841845 TCCTCGGATTACCCTCAAAAGAA 59.158 43.478 0.00 0.00 0.00 2.52
502 574 4.287585 TCCTCGGATTACCCTCAAAAGAAA 59.712 41.667 0.00 0.00 0.00 2.52
503 575 5.007682 CCTCGGATTACCCTCAAAAGAAAA 58.992 41.667 0.00 0.00 0.00 2.29
504 576 5.475564 CCTCGGATTACCCTCAAAAGAAAAA 59.524 40.000 0.00 0.00 0.00 1.94
505 577 6.349363 CCTCGGATTACCCTCAAAAGAAAAAG 60.349 42.308 0.00 0.00 0.00 2.27
506 578 6.300703 TCGGATTACCCTCAAAAGAAAAAGA 58.699 36.000 0.00 0.00 0.00 2.52
507 579 6.773685 TCGGATTACCCTCAAAAGAAAAAGAA 59.226 34.615 0.00 0.00 0.00 2.52
508 580 7.285858 TCGGATTACCCTCAAAAGAAAAAGAAA 59.714 33.333 0.00 0.00 0.00 2.52
509 581 7.923878 CGGATTACCCTCAAAAGAAAAAGAAAA 59.076 33.333 0.00 0.00 0.00 2.29
510 582 9.607988 GGATTACCCTCAAAAGAAAAAGAAAAA 57.392 29.630 0.00 0.00 0.00 1.94
512 584 9.613428 ATTACCCTCAAAAGAAAAAGAAAAAGG 57.387 29.630 0.00 0.00 0.00 3.11
513 585 7.016153 ACCCTCAAAAGAAAAAGAAAAAGGT 57.984 32.000 0.00 0.00 0.00 3.50
514 586 7.458397 ACCCTCAAAAGAAAAAGAAAAAGGTT 58.542 30.769 0.00 0.00 0.00 3.50
515 587 7.942341 ACCCTCAAAAGAAAAAGAAAAAGGTTT 59.058 29.630 0.00 0.00 0.00 3.27
516 588 8.450964 CCCTCAAAAGAAAAAGAAAAAGGTTTC 58.549 33.333 0.00 0.00 43.05 2.78
517 589 8.450964 CCTCAAAAGAAAAAGAAAAAGGTTTCC 58.549 33.333 0.00 0.00 43.65 3.13
518 590 9.219603 CTCAAAAGAAAAAGAAAAAGGTTTCCT 57.780 29.630 0.00 0.00 43.65 3.36
519 591 9.214957 TCAAAAGAAAAAGAAAAAGGTTTCCTC 57.785 29.630 0.00 0.00 43.65 3.71
520 592 7.827819 AAAGAAAAAGAAAAAGGTTTCCTCG 57.172 32.000 0.00 0.00 43.65 4.63
521 593 5.902681 AGAAAAAGAAAAAGGTTTCCTCGG 58.097 37.500 0.00 0.00 43.65 4.63
522 594 5.655090 AGAAAAAGAAAAAGGTTTCCTCGGA 59.345 36.000 0.00 0.00 43.65 4.55
523 595 6.323996 AGAAAAAGAAAAAGGTTTCCTCGGAT 59.676 34.615 0.00 0.00 43.65 4.18
524 596 5.707242 AAAGAAAAAGGTTTCCTCGGATC 57.293 39.130 0.00 0.00 43.65 3.36
525 597 3.687125 AGAAAAAGGTTTCCTCGGATCC 58.313 45.455 0.00 0.00 43.65 3.36
526 598 3.073946 AGAAAAAGGTTTCCTCGGATCCA 59.926 43.478 13.41 0.00 43.65 3.41
527 599 3.518992 AAAAGGTTTCCTCGGATCCAA 57.481 42.857 13.41 0.00 30.89 3.53
528 600 2.491675 AAGGTTTCCTCGGATCCAAC 57.508 50.000 13.41 7.94 30.89 3.77
529 601 1.657804 AGGTTTCCTCGGATCCAACT 58.342 50.000 13.41 0.00 0.00 3.16
530 602 1.555533 AGGTTTCCTCGGATCCAACTC 59.444 52.381 13.41 2.97 0.00 3.01
531 603 1.555533 GGTTTCCTCGGATCCAACTCT 59.444 52.381 13.41 0.00 0.00 3.24
532 604 2.027100 GGTTTCCTCGGATCCAACTCTT 60.027 50.000 13.41 0.00 0.00 2.85
533 605 3.559384 GGTTTCCTCGGATCCAACTCTTT 60.559 47.826 13.41 0.00 0.00 2.52
534 606 4.072839 GTTTCCTCGGATCCAACTCTTTT 58.927 43.478 13.41 0.00 0.00 2.27
535 607 4.367039 TTCCTCGGATCCAACTCTTTTT 57.633 40.909 13.41 0.00 0.00 1.94
565 637 1.150827 ACGAGACGTGACATCGTACA 58.849 50.000 11.55 0.00 46.95 2.90
567 639 2.031769 ACGAGACGTGACATCGTACAAA 60.032 45.455 11.55 0.00 46.95 2.83
568 640 2.588539 CGAGACGTGACATCGTACAAAG 59.411 50.000 0.00 0.00 44.21 2.77
571 643 0.719465 CGTGACATCGTACAAAGCCC 59.281 55.000 0.00 0.00 0.00 5.19
616 715 7.499563 AGAAAGAAGGGTGAAAAGAAACTCTAC 59.500 37.037 0.00 0.00 0.00 2.59
617 716 6.502074 AGAAGGGTGAAAAGAAACTCTACT 57.498 37.500 0.00 0.00 0.00 2.57
619 718 5.230323 AGGGTGAAAAGAAACTCTACTCC 57.770 43.478 0.00 0.00 0.00 3.85
621 720 5.132144 AGGGTGAAAAGAAACTCTACTCCAA 59.868 40.000 0.00 0.00 0.00 3.53
629 733 6.293004 AGAAACTCTACTCCAAATCTCCAG 57.707 41.667 0.00 0.00 0.00 3.86
636 740 0.620556 TCCAAATCTCCAGTCCCTGC 59.379 55.000 0.00 0.00 0.00 4.85
639 743 0.909610 AAATCTCCAGTCCCTGCGGA 60.910 55.000 0.00 0.00 35.01 5.54
641 745 1.617947 ATCTCCAGTCCCTGCGGAAC 61.618 60.000 0.00 0.00 40.92 3.62
642 746 2.525629 TCCAGTCCCTGCGGAACA 60.526 61.111 0.00 0.00 40.92 3.18
643 747 2.358737 CCAGTCCCTGCGGAACAC 60.359 66.667 0.00 0.00 40.92 3.32
644 748 2.358737 CAGTCCCTGCGGAACACC 60.359 66.667 0.00 0.00 40.92 4.16
645 749 2.847234 AGTCCCTGCGGAACACCA 60.847 61.111 0.00 0.00 40.92 4.17
646 750 2.358737 GTCCCTGCGGAACACCAG 60.359 66.667 0.00 0.00 40.92 4.00
647 751 2.525629 TCCCTGCGGAACACCAGA 60.526 61.111 0.00 0.00 34.19 3.86
648 752 2.046892 CCCTGCGGAACACCAGAG 60.047 66.667 0.00 0.00 0.00 3.35
649 753 2.743928 CCTGCGGAACACCAGAGC 60.744 66.667 0.00 0.00 0.00 4.09
653 757 2.031012 CGGAACACCAGAGCAGCA 59.969 61.111 0.00 0.00 0.00 4.41
679 783 2.202878 GGCAGATCTAACGCCGCA 60.203 61.111 6.79 0.00 35.79 5.69
687 791 4.884257 TAACGCCGCAGATCCCGC 62.884 66.667 0.00 0.00 0.00 6.13
700 804 3.764466 CCCGCGGAGTCTTGCTCT 61.764 66.667 30.73 0.00 43.62 4.09
705 809 1.137825 CGGAGTCTTGCTCTCGGAC 59.862 63.158 0.00 0.00 43.62 4.79
711 815 0.541998 TCTTGCTCTCGGACTTCCCA 60.542 55.000 0.00 0.00 34.14 4.37
749 853 2.738695 GCAGCGCACAAGAGAGAGC 61.739 63.158 11.47 0.00 0.00 4.09
750 854 1.079956 CAGCGCACAAGAGAGAGCT 60.080 57.895 11.47 0.00 41.58 4.09
751 855 1.077645 CAGCGCACAAGAGAGAGCTC 61.078 60.000 11.47 5.27 39.20 4.09
752 856 1.809209 GCGCACAAGAGAGAGCTCC 60.809 63.158 10.93 1.70 42.30 4.70
754 858 1.153667 GCACAAGAGAGAGCTCCCG 60.154 63.158 10.93 0.00 42.30 5.14
755 859 1.599606 GCACAAGAGAGAGCTCCCGA 61.600 60.000 10.93 0.00 42.30 5.14
849 961 1.329599 GTTCCCTTTTATACAGCCGCG 59.670 52.381 0.00 0.00 0.00 6.46
850 962 0.179067 TCCCTTTTATACAGCCGCGG 60.179 55.000 24.05 24.05 0.00 6.46
851 963 0.179067 CCCTTTTATACAGCCGCGGA 60.179 55.000 33.48 8.40 0.00 5.54
852 964 1.542547 CCCTTTTATACAGCCGCGGAT 60.543 52.381 33.48 23.90 0.00 4.18
853 965 1.798813 CCTTTTATACAGCCGCGGATC 59.201 52.381 33.48 12.91 0.00 3.36
854 966 2.479837 CTTTTATACAGCCGCGGATCA 58.520 47.619 33.48 13.96 0.00 2.92
855 967 2.148916 TTTATACAGCCGCGGATCAG 57.851 50.000 33.48 15.38 0.00 2.90
856 968 0.317160 TTATACAGCCGCGGATCAGG 59.683 55.000 33.48 14.48 0.00 3.86
883 995 3.425713 CAGCGCCACATGCTCGTT 61.426 61.111 2.29 0.00 41.72 3.85
884 996 3.425713 AGCGCCACATGCTCGTTG 61.426 61.111 2.29 0.00 38.62 4.10
886 998 4.799473 CGCCACATGCTCGTTGCG 62.799 66.667 9.42 9.42 46.63 4.85
888 1000 3.425713 CCACATGCTCGTTGCGCT 61.426 61.111 9.73 0.00 46.63 5.92
890 1002 2.047844 ACATGCTCGTTGCGCTCT 60.048 55.556 9.73 0.00 46.63 4.09
892 1004 2.510238 ATGCTCGTTGCGCTCTCC 60.510 61.111 9.73 0.00 46.63 3.71
896 1008 4.742201 TCGTTGCGCTCTCCCTGC 62.742 66.667 9.73 0.00 0.00 4.85
897 1009 4.749310 CGTTGCGCTCTCCCTGCT 62.749 66.667 9.73 0.00 0.00 4.24
898 1010 2.817396 GTTGCGCTCTCCCTGCTC 60.817 66.667 9.73 0.00 0.00 4.26
899 1011 4.087892 TTGCGCTCTCCCTGCTCC 62.088 66.667 9.73 0.00 0.00 4.70
902 1014 3.847602 CGCTCTCCCTGCTCCCTG 61.848 72.222 0.00 0.00 0.00 4.45
903 1015 4.173924 GCTCTCCCTGCTCCCTGC 62.174 72.222 0.00 0.00 43.25 4.85
926 1038 2.264794 GCCTGTTCCATCCGTCGT 59.735 61.111 0.00 0.00 0.00 4.34
928 1040 1.589630 CCTGTTCCATCCGTCGTGA 59.410 57.895 0.00 0.00 0.00 4.35
929 1041 0.037697 CCTGTTCCATCCGTCGTGAA 60.038 55.000 0.00 0.00 0.00 3.18
930 1042 1.606994 CCTGTTCCATCCGTCGTGAAA 60.607 52.381 0.00 0.00 0.00 2.69
931 1043 2.139917 CTGTTCCATCCGTCGTGAAAA 58.860 47.619 0.00 0.00 0.00 2.29
956 1086 2.371910 GGTCTTTGCTAGAGCTTCGT 57.628 50.000 2.72 0.00 45.79 3.85
957 1087 2.689646 GGTCTTTGCTAGAGCTTCGTT 58.310 47.619 2.72 0.00 45.79 3.85
995 1125 4.463050 AGAGGTGGAGGTAGGATAAGAG 57.537 50.000 0.00 0.00 0.00 2.85
1250 1390 3.689347 TGCCTGCAACAATCTGTATCTT 58.311 40.909 0.00 0.00 0.00 2.40
1252 1392 3.242543 GCCTGCAACAATCTGTATCTTCG 60.243 47.826 0.00 0.00 0.00 3.79
1309 1935 0.179161 CTGACTGACCGGTCGATGTC 60.179 60.000 31.04 31.04 38.91 3.06
1663 2289 0.171455 ACCTCTTCATCGTGCTCGTC 59.829 55.000 8.17 0.00 38.33 4.20
1670 2296 0.932123 CATCGTGCTCGTCTCCATCG 60.932 60.000 8.17 0.00 38.33 3.84
1822 2448 0.244721 GGAAAGGCACCATGCTCAAC 59.755 55.000 0.13 0.00 44.28 3.18
1973 2605 2.287608 GCCTATCATTTTAACGCCAGCC 60.288 50.000 0.00 0.00 0.00 4.85
2021 2653 8.756864 TCATTGTATTTTTCTTGGCGTTTTAAC 58.243 29.630 0.00 0.00 0.00 2.01
2098 2788 2.232452 CTGAACGATGTCTCACTTCCCT 59.768 50.000 0.00 0.00 0.00 4.20
2100 2790 1.924731 ACGATGTCTCACTTCCCTCA 58.075 50.000 0.00 0.00 0.00 3.86
2101 2791 2.248248 ACGATGTCTCACTTCCCTCAA 58.752 47.619 0.00 0.00 0.00 3.02
2104 2794 3.444034 CGATGTCTCACTTCCCTCAACTA 59.556 47.826 0.00 0.00 0.00 2.24
2105 2795 4.082190 CGATGTCTCACTTCCCTCAACTAA 60.082 45.833 0.00 0.00 0.00 2.24
2107 2797 5.623956 TGTCTCACTTCCCTCAACTAAAA 57.376 39.130 0.00 0.00 0.00 1.52
2108 2798 5.996644 TGTCTCACTTCCCTCAACTAAAAA 58.003 37.500 0.00 0.00 0.00 1.94
2109 2799 6.055588 TGTCTCACTTCCCTCAACTAAAAAG 58.944 40.000 0.00 0.00 0.00 2.27
2110 2800 6.056236 GTCTCACTTCCCTCAACTAAAAAGT 58.944 40.000 0.00 0.00 0.00 2.66
2111 2801 7.147620 TGTCTCACTTCCCTCAACTAAAAAGTA 60.148 37.037 0.00 0.00 0.00 2.24
2112 2802 7.171167 GTCTCACTTCCCTCAACTAAAAAGTAC 59.829 40.741 0.00 0.00 0.00 2.73
2113 2803 6.891388 TCACTTCCCTCAACTAAAAAGTACA 58.109 36.000 0.00 0.00 0.00 2.90
2114 2804 6.990349 TCACTTCCCTCAACTAAAAAGTACAG 59.010 38.462 0.00 0.00 0.00 2.74
2115 2805 6.766467 CACTTCCCTCAACTAAAAAGTACAGT 59.234 38.462 0.00 0.00 0.00 3.55
2116 2806 7.929785 CACTTCCCTCAACTAAAAAGTACAGTA 59.070 37.037 0.00 0.00 0.00 2.74
2117 2807 8.148999 ACTTCCCTCAACTAAAAAGTACAGTAG 58.851 37.037 0.00 0.00 0.00 2.57
2118 2808 7.844493 TCCCTCAACTAAAAAGTACAGTAGA 57.156 36.000 0.00 0.00 0.00 2.59
2119 2809 8.431910 TCCCTCAACTAAAAAGTACAGTAGAT 57.568 34.615 0.00 0.00 0.00 1.98
2120 2810 8.877195 TCCCTCAACTAAAAAGTACAGTAGATT 58.123 33.333 0.00 0.00 0.00 2.40
2121 2811 8.936864 CCCTCAACTAAAAAGTACAGTAGATTG 58.063 37.037 0.00 0.00 0.00 2.67
2122 2812 9.706691 CCTCAACTAAAAAGTACAGTAGATTGA 57.293 33.333 0.00 0.00 0.00 2.57
2188 2878 3.123804 GGTACTGGTCATATGCTTCGTG 58.876 50.000 0.00 0.00 0.00 4.35
2462 3152 4.873129 CGGTCATCGTGGCCCTCG 62.873 72.222 0.00 5.57 39.48 4.63
2542 3232 2.044650 ATGCTGCTCCCGTGCATT 60.045 55.556 0.00 0.00 43.85 3.56
2683 3373 5.398603 AGATCATTCACGAGTTCTGAAGT 57.601 39.130 0.00 0.00 31.22 3.01
2684 3374 5.788450 AGATCATTCACGAGTTCTGAAGTT 58.212 37.500 0.00 0.00 31.22 2.66
2685 3375 5.866633 AGATCATTCACGAGTTCTGAAGTTC 59.133 40.000 0.00 0.00 31.22 3.01
2686 3376 5.201713 TCATTCACGAGTTCTGAAGTTCT 57.798 39.130 4.17 0.00 31.22 3.01
2688 3378 4.649088 TTCACGAGTTCTGAAGTTCTGA 57.351 40.909 8.27 8.27 0.00 3.27
2689 3379 4.649088 TCACGAGTTCTGAAGTTCTGAA 57.351 40.909 18.19 18.19 32.96 3.02
2690 3380 4.611943 TCACGAGTTCTGAAGTTCTGAAG 58.388 43.478 21.45 14.20 35.48 3.02
2691 3381 4.338400 TCACGAGTTCTGAAGTTCTGAAGA 59.662 41.667 21.45 13.70 35.48 2.87
2695 3385 6.098679 CGAGTTCTGAAGTTCTGAAGATCAT 58.901 40.000 21.45 8.79 35.48 2.45
2696 3386 6.589523 CGAGTTCTGAAGTTCTGAAGATCATT 59.410 38.462 21.45 7.14 35.48 2.57
2702 3392 5.635280 TGAAGTTCTGAAGATCATTCACGAC 59.365 40.000 4.17 2.62 0.00 4.34
2716 3406 3.236632 TCACGACTTCAGATGATGGTG 57.763 47.619 0.00 0.00 0.00 4.17
2717 3407 2.094026 TCACGACTTCAGATGATGGTGG 60.094 50.000 0.00 0.54 0.00 4.61
2720 3410 0.107508 ACTTCAGATGATGGTGGCGG 60.108 55.000 1.41 0.00 0.00 6.13
2721 3411 1.442526 CTTCAGATGATGGTGGCGGC 61.443 60.000 0.00 0.00 0.00 6.53
2722 3412 2.124612 CAGATGATGGTGGCGGCA 60.125 61.111 7.97 7.97 0.00 5.69
2748 3438 0.813610 TGTCCGTCTGCTTGGTGTTG 60.814 55.000 0.00 0.00 0.00 3.33
2810 3504 1.887198 AGCAGCTACGTAGTGTTGTCT 59.113 47.619 22.98 15.58 45.73 3.41
2811 3505 2.095161 AGCAGCTACGTAGTGTTGTCTC 60.095 50.000 22.98 4.61 45.73 3.36
2812 3506 2.506865 CAGCTACGTAGTGTTGTCTCG 58.493 52.381 22.98 3.43 45.73 4.04
2824 3518 0.392706 TTGTCTCGTGTCATGGCAGT 59.607 50.000 0.00 0.00 0.00 4.40
2854 3548 2.032620 AGGCAGGGATAGTACAGAACG 58.967 52.381 0.00 0.00 0.00 3.95
2873 3567 4.445452 ACGGATAGTTCTACGCTCAAAA 57.555 40.909 0.00 0.00 0.00 2.44
2874 3568 5.007385 ACGGATAGTTCTACGCTCAAAAT 57.993 39.130 0.00 0.00 0.00 1.82
2875 3569 4.804139 ACGGATAGTTCTACGCTCAAAATG 59.196 41.667 0.00 0.00 0.00 2.32
2876 3570 4.804139 CGGATAGTTCTACGCTCAAAATGT 59.196 41.667 0.00 0.00 0.00 2.71
2877 3571 5.975344 CGGATAGTTCTACGCTCAAAATGTA 59.025 40.000 0.00 0.00 0.00 2.29
2878 3572 6.074994 CGGATAGTTCTACGCTCAAAATGTAC 60.075 42.308 0.00 0.00 0.00 2.90
2879 3573 6.979238 GGATAGTTCTACGCTCAAAATGTACT 59.021 38.462 0.00 0.00 0.00 2.73
2881 3575 9.512435 GATAGTTCTACGCTCAAAATGTACTTA 57.488 33.333 0.00 0.00 0.00 2.24
2882 3576 7.578169 AGTTCTACGCTCAAAATGTACTTAC 57.422 36.000 0.00 0.00 0.00 2.34
2883 3577 6.307318 AGTTCTACGCTCAAAATGTACTTACG 59.693 38.462 0.00 0.00 0.00 3.18
2885 3579 6.151691 TCTACGCTCAAAATGTACTTACGTT 58.848 36.000 0.00 0.00 37.03 3.99
2886 3580 5.260027 ACGCTCAAAATGTACTTACGTTC 57.740 39.130 0.00 0.00 34.53 3.95
2947 3643 1.553248 TGCTATTGTAGGACGGCACTT 59.447 47.619 0.00 0.00 0.00 3.16
2955 3651 2.434185 GACGGCACTTCATCGGCA 60.434 61.111 0.00 0.00 31.36 5.69
2961 3657 1.027357 GCACTTCATCGGCATTCCAT 58.973 50.000 0.00 0.00 0.00 3.41
2962 3658 1.268896 GCACTTCATCGGCATTCCATG 60.269 52.381 0.00 0.00 0.00 3.66
2999 3722 4.357142 CGGATTTCATTTCCTGATGCTTG 58.643 43.478 0.00 0.00 32.72 4.01
3038 3770 6.710597 AACACTAGACTGTCTCTTGTACAA 57.289 37.500 14.62 8.28 33.68 2.41
3048 3780 8.868635 ACTGTCTCTTGTACAAAAAGTAGTAC 57.131 34.615 10.03 5.33 40.68 2.73
3049 3781 7.646922 ACTGTCTCTTGTACAAAAAGTAGTACG 59.353 37.037 10.03 0.00 42.62 3.67
3050 3782 7.706159 TGTCTCTTGTACAAAAAGTAGTACGA 58.294 34.615 10.03 0.00 42.62 3.43
3051 3783 8.190122 TGTCTCTTGTACAAAAAGTAGTACGAA 58.810 33.333 10.03 0.00 42.62 3.85
3086 3818 8.051901 AGTACATTAAGTCAACCATTTTAGGC 57.948 34.615 0.00 0.00 0.00 3.93
3099 3832 4.823989 CCATTTTAGGCGAATGATTCTCCT 59.176 41.667 19.43 19.43 46.15 3.69
3104 3837 2.025887 AGGCGAATGATTCTCCTTTGGT 60.026 45.455 10.78 0.00 41.98 3.67
3112 3845 3.010138 TGATTCTCCTTTGGTGGTTAGGG 59.990 47.826 0.00 0.00 0.00 3.53
3195 3944 1.838913 AATCAGCGCACAACAACAAC 58.161 45.000 11.47 0.00 0.00 3.32
3237 3986 2.354510 CCACGCTTCAAGACAGACAAAA 59.645 45.455 0.00 0.00 0.00 2.44
3297 4171 7.907214 ACAGAATACAAGATACAACCACTTC 57.093 36.000 0.00 0.00 0.00 3.01
3301 4175 7.707035 AGAATACAAGATACAACCACTTCGATC 59.293 37.037 0.00 0.00 0.00 3.69
3302 4176 5.407407 ACAAGATACAACCACTTCGATCT 57.593 39.130 0.00 0.00 0.00 2.75
3303 4177 5.171476 ACAAGATACAACCACTTCGATCTG 58.829 41.667 0.00 0.00 0.00 2.90
3304 4178 3.786635 AGATACAACCACTTCGATCTGC 58.213 45.455 0.00 0.00 0.00 4.26
3305 4179 3.195610 AGATACAACCACTTCGATCTGCA 59.804 43.478 0.00 0.00 0.00 4.41
3306 4180 1.800805 ACAACCACTTCGATCTGCAG 58.199 50.000 7.63 7.63 0.00 4.41
3307 4181 0.445436 CAACCACTTCGATCTGCAGC 59.555 55.000 9.47 0.00 0.00 5.25
3308 4182 0.035317 AACCACTTCGATCTGCAGCA 59.965 50.000 9.47 0.00 0.00 4.41
3309 4183 0.035317 ACCACTTCGATCTGCAGCAA 59.965 50.000 9.47 0.00 0.00 3.91
3310 4184 1.339438 ACCACTTCGATCTGCAGCAAT 60.339 47.619 9.47 0.00 0.00 3.56
3311 4185 1.329906 CCACTTCGATCTGCAGCAATC 59.670 52.381 9.47 7.10 0.00 2.67
3312 4186 2.004733 CACTTCGATCTGCAGCAATCA 58.995 47.619 9.47 0.00 0.00 2.57
3368 4281 7.669722 AGCTACAAAGGAATATGGAAACTGAAA 59.330 33.333 0.00 0.00 0.00 2.69
3372 4285 4.270008 AGGAATATGGAAACTGAAACCGG 58.730 43.478 0.00 0.00 0.00 5.28
3373 4286 3.181490 GGAATATGGAAACTGAAACCGGC 60.181 47.826 0.00 0.00 0.00 6.13
3375 4288 1.698506 ATGGAAACTGAAACCGGCAA 58.301 45.000 0.00 0.00 0.00 4.52
3382 4295 0.385390 CTGAAACCGGCAAAAGCTGT 59.615 50.000 0.00 0.00 0.00 4.40
3384 4297 1.215014 GAAACCGGCAAAAGCTGTGC 61.215 55.000 13.08 13.08 41.45 4.57
3593 4506 2.182030 CTCGGTCGTCTCTTGGCC 59.818 66.667 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 2.008268 ATAACTACGTGACCGGGGCG 62.008 60.000 6.32 9.85 38.78 6.13
50 51 2.033801 CACTATAACTACGTGACCGGGG 59.966 54.545 6.32 0.00 38.78 5.73
53 54 5.175673 TCGTATCACTATAACTACGTGACCG 59.824 44.000 0.00 0.00 40.11 4.79
94 101 9.860898 GTTATTTGCAACTAAGGAAAATCAGAT 57.139 29.630 9.30 0.00 32.55 2.90
99 106 6.586082 CGCTGTTATTTGCAACTAAGGAAAAT 59.414 34.615 9.30 0.00 32.55 1.82
111 118 4.300189 ACAAAGTTCGCTGTTATTTGCA 57.700 36.364 0.00 0.00 34.90 4.08
123 130 6.515002 CACGTGATAAATGTGTACAAAGTTCG 59.485 38.462 10.90 2.99 40.39 3.95
174 183 0.179076 TGATATGCCGTCACAGCTGG 60.179 55.000 19.93 7.28 0.00 4.85
263 296 6.318900 GCATTAGTTTTATCAGCCTAGTGGTT 59.681 38.462 0.00 0.00 35.27 3.67
264 297 5.823045 GCATTAGTTTTATCAGCCTAGTGGT 59.177 40.000 0.00 0.00 35.27 4.16
265 298 6.058183 AGCATTAGTTTTATCAGCCTAGTGG 58.942 40.000 0.00 0.00 0.00 4.00
283 320 1.787215 CGCTCACGTGCAAGCATTA 59.213 52.632 23.95 0.07 38.45 1.90
313 350 0.625316 TAGGTTGCATGAGTGGGCAT 59.375 50.000 0.00 0.00 40.17 4.40
314 351 0.403655 TTAGGTTGCATGAGTGGGCA 59.596 50.000 0.00 0.00 38.46 5.36
315 352 1.678101 GATTAGGTTGCATGAGTGGGC 59.322 52.381 0.00 0.00 0.00 5.36
316 353 3.003394 TGATTAGGTTGCATGAGTGGG 57.997 47.619 0.00 0.00 0.00 4.61
317 354 4.264253 TCTTGATTAGGTTGCATGAGTGG 58.736 43.478 0.00 0.00 0.00 4.00
319 356 4.521146 CCTCTTGATTAGGTTGCATGAGT 58.479 43.478 0.00 0.00 34.09 3.41
320 357 3.314635 GCCTCTTGATTAGGTTGCATGAG 59.685 47.826 0.00 0.00 36.43 2.90
353 417 9.026121 CCCGTAACTAGGAGTACTACTACTATA 57.974 40.741 11.03 2.25 40.66 1.31
354 418 7.730784 TCCCGTAACTAGGAGTACTACTACTAT 59.269 40.741 11.03 3.16 40.66 2.12
359 423 5.289083 CTCCCGTAACTAGGAGTACTACT 57.711 47.826 13.42 13.42 44.01 2.57
369 441 3.855950 CGTTTAGTTGCTCCCGTAACTAG 59.144 47.826 0.00 0.00 45.05 2.57
371 443 2.611224 CCGTTTAGTTGCTCCCGTAACT 60.611 50.000 1.74 1.74 45.95 2.24
372 444 1.728425 CCGTTTAGTTGCTCCCGTAAC 59.272 52.381 0.00 0.00 36.18 2.50
374 446 1.067635 GTCCGTTTAGTTGCTCCCGTA 60.068 52.381 0.00 0.00 0.00 4.02
376 448 1.017701 GGTCCGTTTAGTTGCTCCCG 61.018 60.000 0.00 0.00 0.00 5.14
377 449 0.035739 TGGTCCGTTTAGTTGCTCCC 59.964 55.000 0.00 0.00 0.00 4.30
379 451 2.159627 CACATGGTCCGTTTAGTTGCTC 59.840 50.000 0.00 0.00 0.00 4.26
381 453 1.877443 ACACATGGTCCGTTTAGTTGC 59.123 47.619 0.00 0.00 0.00 4.17
382 454 4.312443 AGTACACATGGTCCGTTTAGTTG 58.688 43.478 0.00 0.00 0.00 3.16
386 458 6.377996 ACACTATAGTACACATGGTCCGTTTA 59.622 38.462 4.74 0.00 0.00 2.01
392 464 6.439599 CAGCTACACTATAGTACACATGGTC 58.560 44.000 4.74 0.00 0.00 4.02
395 467 5.831997 TGCAGCTACACTATAGTACACATG 58.168 41.667 4.74 3.92 0.00 3.21
403 475 1.723542 GCGCATGCAGCTACACTATAG 59.276 52.381 19.57 0.00 42.61 1.31
405 477 2.609825 GCGCATGCAGCTACACTAT 58.390 52.632 19.57 0.00 42.61 2.12
415 487 3.302031 CCGTTTACGTGCGCATGCA 62.302 57.895 28.93 14.71 42.30 3.96
416 488 2.573167 CCGTTTACGTGCGCATGC 60.573 61.111 28.93 7.91 37.89 4.06
417 489 1.225637 GACCGTTTACGTGCGCATG 60.226 57.895 27.53 27.53 37.74 4.06
418 490 2.722731 CGACCGTTTACGTGCGCAT 61.723 57.895 15.91 0.00 37.74 4.73
419 491 3.396502 CGACCGTTTACGTGCGCA 61.397 61.111 5.66 5.66 37.74 6.09
420 492 4.125097 CCGACCGTTTACGTGCGC 62.125 66.667 0.00 0.00 37.74 6.09
423 495 2.090524 GCTCCCGACCGTTTACGTG 61.091 63.158 0.00 0.00 37.74 4.49
442 514 4.573162 ACGTAGCCTTCGTTGCTC 57.427 55.556 0.00 0.00 40.23 4.26
447 519 1.508088 CGGGTAACGTAGCCTTCGT 59.492 57.895 8.02 0.00 44.03 3.85
490 562 7.921786 AACCTTTTTCTTTTTCTTTTGAGGG 57.078 32.000 0.00 0.00 0.00 4.30
493 565 9.214957 GAGGAAACCTTTTTCTTTTTCTTTTGA 57.785 29.630 0.00 0.00 40.98 2.69
494 566 8.168626 CGAGGAAACCTTTTTCTTTTTCTTTTG 58.831 33.333 0.00 0.00 40.98 2.44
496 568 6.816640 CCGAGGAAACCTTTTTCTTTTTCTTT 59.183 34.615 0.00 0.00 40.98 2.52
497 569 6.153851 TCCGAGGAAACCTTTTTCTTTTTCTT 59.846 34.615 0.00 0.00 40.98 2.52
498 570 5.655090 TCCGAGGAAACCTTTTTCTTTTTCT 59.345 36.000 0.00 0.00 40.98 2.52
499 571 5.898174 TCCGAGGAAACCTTTTTCTTTTTC 58.102 37.500 0.00 0.00 40.98 2.29
500 572 5.925506 TCCGAGGAAACCTTTTTCTTTTT 57.074 34.783 0.00 0.00 40.98 1.94
501 573 5.010719 GGATCCGAGGAAACCTTTTTCTTTT 59.989 40.000 0.00 0.00 40.98 2.27
502 574 4.523173 GGATCCGAGGAAACCTTTTTCTTT 59.477 41.667 0.00 0.00 40.98 2.52
503 575 4.079970 GGATCCGAGGAAACCTTTTTCTT 58.920 43.478 0.00 0.00 40.98 2.52
504 576 3.073946 TGGATCCGAGGAAACCTTTTTCT 59.926 43.478 7.39 0.00 40.98 2.52
505 577 3.418047 TGGATCCGAGGAAACCTTTTTC 58.582 45.455 7.39 0.00 40.54 2.29
506 578 3.518992 TGGATCCGAGGAAACCTTTTT 57.481 42.857 7.39 0.00 31.76 1.94
507 579 3.154710 GTTGGATCCGAGGAAACCTTTT 58.845 45.455 7.39 0.00 31.76 2.27
508 580 2.375509 AGTTGGATCCGAGGAAACCTTT 59.624 45.455 7.39 0.00 31.76 3.11
509 581 1.985895 AGTTGGATCCGAGGAAACCTT 59.014 47.619 7.39 0.00 31.76 3.50
510 582 1.555533 GAGTTGGATCCGAGGAAACCT 59.444 52.381 7.39 0.00 36.03 3.50
511 583 1.555533 AGAGTTGGATCCGAGGAAACC 59.444 52.381 7.39 10.36 0.00 3.27
512 584 3.336138 AAGAGTTGGATCCGAGGAAAC 57.664 47.619 7.39 5.52 0.00 2.78
513 585 4.367039 AAAAGAGTTGGATCCGAGGAAA 57.633 40.909 7.39 0.00 0.00 3.13
514 586 4.367039 AAAAAGAGTTGGATCCGAGGAA 57.633 40.909 7.39 0.00 0.00 3.36
535 607 5.283294 TGTCACGTCTCGTCTTATCAAAAA 58.717 37.500 0.00 0.00 38.32 1.94
536 608 4.862350 TGTCACGTCTCGTCTTATCAAAA 58.138 39.130 0.00 0.00 38.32 2.44
537 609 4.492791 TGTCACGTCTCGTCTTATCAAA 57.507 40.909 0.00 0.00 38.32 2.69
538 610 4.659088 GATGTCACGTCTCGTCTTATCAA 58.341 43.478 0.00 0.00 38.32 2.57
539 611 3.242316 CGATGTCACGTCTCGTCTTATCA 60.242 47.826 0.00 0.00 38.32 2.15
540 612 3.242349 ACGATGTCACGTCTCGTCTTATC 60.242 47.826 6.26 0.00 41.42 1.75
546 618 1.150827 TGTACGATGTCACGTCTCGT 58.849 50.000 14.03 14.03 46.38 4.18
585 676 8.467598 GTTTCTTTTCACCCTTCTTTCTTTAGT 58.532 33.333 0.00 0.00 0.00 2.24
636 740 1.376424 ATGCTGCTCTGGTGTTCCG 60.376 57.895 0.00 0.00 36.30 4.30
639 743 1.975407 GGCATGCTGCTCTGGTGTT 60.975 57.895 18.92 0.00 44.28 3.32
641 745 2.360726 TGGCATGCTGCTCTGGTG 60.361 61.111 18.92 0.00 44.28 4.17
642 746 2.360852 GTGGCATGCTGCTCTGGT 60.361 61.111 18.92 0.00 44.28 4.00
643 747 1.753078 ATGTGGCATGCTGCTCTGG 60.753 57.895 18.92 0.00 44.28 3.86
644 748 1.433471 CATGTGGCATGCTGCTCTG 59.567 57.895 18.92 5.60 44.28 3.35
645 749 1.753078 CCATGTGGCATGCTGCTCT 60.753 57.895 18.92 0.00 44.28 4.09
646 750 2.805546 CCATGTGGCATGCTGCTC 59.194 61.111 18.92 0.53 44.28 4.26
679 783 3.082579 GCAAGACTCCGCGGGATCT 62.083 63.158 27.83 24.32 0.00 2.75
693 797 0.321671 TTGGGAAGTCCGAGAGCAAG 59.678 55.000 0.00 0.00 38.76 4.01
700 804 2.031465 GCGGTTTGGGAAGTCCGA 59.969 61.111 6.63 0.00 44.86 4.55
800 908 0.177836 GCTTCTTCCTCCTCTCCTGC 59.822 60.000 0.00 0.00 0.00 4.85
801 909 0.829990 GGCTTCTTCCTCCTCTCCTG 59.170 60.000 0.00 0.00 0.00 3.86
802 910 0.686112 CGGCTTCTTCCTCCTCTCCT 60.686 60.000 0.00 0.00 0.00 3.69
803 911 0.684805 TCGGCTTCTTCCTCCTCTCC 60.685 60.000 0.00 0.00 0.00 3.71
804 912 0.744281 CTCGGCTTCTTCCTCCTCTC 59.256 60.000 0.00 0.00 0.00 3.20
805 913 0.686112 CCTCGGCTTCTTCCTCCTCT 60.686 60.000 0.00 0.00 0.00 3.69
806 914 0.973496 ACCTCGGCTTCTTCCTCCTC 60.973 60.000 0.00 0.00 0.00 3.71
807 915 0.335361 TACCTCGGCTTCTTCCTCCT 59.665 55.000 0.00 0.00 0.00 3.69
881 993 2.817396 GAGCAGGGAGAGCGCAAC 60.817 66.667 11.47 2.78 37.01 4.17
885 997 3.847602 CAGGGAGCAGGGAGAGCG 61.848 72.222 0.00 0.00 37.01 5.03
886 998 4.173924 GCAGGGAGCAGGGAGAGC 62.174 72.222 0.00 0.00 44.79 4.09
926 1038 7.394359 AGCTCTAGCAAAGACCAAATATTTTCA 59.606 33.333 4.54 0.00 45.16 2.69
928 1040 7.709149 AGCTCTAGCAAAGACCAAATATTTT 57.291 32.000 4.54 0.00 45.16 1.82
929 1041 7.414540 CGAAGCTCTAGCAAAGACCAAATATTT 60.415 37.037 4.54 0.00 45.16 1.40
930 1042 6.037610 CGAAGCTCTAGCAAAGACCAAATATT 59.962 38.462 4.54 0.00 45.16 1.28
931 1043 5.525378 CGAAGCTCTAGCAAAGACCAAATAT 59.475 40.000 4.54 0.00 45.16 1.28
954 1084 2.278013 GCGACGCCTCCTCTAACG 60.278 66.667 9.14 0.00 0.00 3.18
955 1085 2.104530 GGCGACGCCTCCTCTAAC 59.895 66.667 31.30 0.96 46.69 2.34
980 1110 5.186215 GCCATCTTACTCTTATCCTACCTCC 59.814 48.000 0.00 0.00 0.00 4.30
1049 1179 2.817396 GGAGTGGCTGCTCGAAGC 60.817 66.667 0.20 0.20 42.82 3.86
1210 1343 1.130561 CAACGGAAGAAAGATTCGGGC 59.869 52.381 0.00 0.00 34.72 6.13
1259 1399 1.542915 CACTGTCAAGAAAGGGCATGG 59.457 52.381 0.00 0.00 0.00 3.66
1309 1935 2.742372 CCCACGCCTGAAACCTCG 60.742 66.667 0.00 0.00 0.00 4.63
1663 2289 4.766970 GGCAGGATGACGATGGAG 57.233 61.111 0.00 0.00 39.69 3.86
1693 2319 4.335647 AGCACGCCCAGGTTCCTG 62.336 66.667 11.52 11.52 0.00 3.86
1783 2409 4.287781 TGAAAGCCGACGCCGTCA 62.288 61.111 18.40 0.00 34.57 4.35
1822 2448 4.814294 GTGGGTAGGCCGCTGACG 62.814 72.222 0.00 0.00 39.67 4.35
1973 2605 4.916983 TGAACAGTTTGGGAATGTCTTG 57.083 40.909 0.00 0.00 0.00 3.02
2055 2742 3.933332 GCATAGAACACTGTTAGGTCACC 59.067 47.826 0.00 0.00 0.00 4.02
2104 2794 9.778741 TCAGTCATTCAATCTACTGTACTTTTT 57.221 29.630 8.58 0.00 40.18 1.94
2105 2795 9.778741 TTCAGTCATTCAATCTACTGTACTTTT 57.221 29.630 8.58 0.00 40.18 2.27
2107 2797 8.807118 TCTTCAGTCATTCAATCTACTGTACTT 58.193 33.333 8.58 0.00 40.18 2.24
2108 2798 8.354711 TCTTCAGTCATTCAATCTACTGTACT 57.645 34.615 8.58 0.00 40.18 2.73
2109 2799 9.593134 AATCTTCAGTCATTCAATCTACTGTAC 57.407 33.333 8.58 0.00 40.18 2.90
2111 2801 8.944029 CAAATCTTCAGTCATTCAATCTACTGT 58.056 33.333 8.58 0.00 40.18 3.55
2112 2802 8.396390 CCAAATCTTCAGTCATTCAATCTACTG 58.604 37.037 3.77 3.77 40.54 2.74
2113 2803 7.066766 GCCAAATCTTCAGTCATTCAATCTACT 59.933 37.037 0.00 0.00 0.00 2.57
2114 2804 7.148188 TGCCAAATCTTCAGTCATTCAATCTAC 60.148 37.037 0.00 0.00 0.00 2.59
2115 2805 6.885918 TGCCAAATCTTCAGTCATTCAATCTA 59.114 34.615 0.00 0.00 0.00 1.98
2116 2806 5.713389 TGCCAAATCTTCAGTCATTCAATCT 59.287 36.000 0.00 0.00 0.00 2.40
2117 2807 5.957798 TGCCAAATCTTCAGTCATTCAATC 58.042 37.500 0.00 0.00 0.00 2.67
2118 2808 5.988310 TGCCAAATCTTCAGTCATTCAAT 57.012 34.783 0.00 0.00 0.00 2.57
2119 2809 5.244402 ACATGCCAAATCTTCAGTCATTCAA 59.756 36.000 0.00 0.00 0.00 2.69
2120 2810 4.768448 ACATGCCAAATCTTCAGTCATTCA 59.232 37.500 0.00 0.00 0.00 2.57
2121 2811 5.125097 AGACATGCCAAATCTTCAGTCATTC 59.875 40.000 0.00 0.00 0.00 2.67
2122 2812 5.014858 AGACATGCCAAATCTTCAGTCATT 58.985 37.500 0.00 0.00 0.00 2.57
2123 2813 4.398358 CAGACATGCCAAATCTTCAGTCAT 59.602 41.667 0.00 0.00 0.00 3.06
2173 2863 3.079131 TGCCACGAAGCATATGACC 57.921 52.632 6.97 0.00 38.00 4.02
2188 2878 1.369091 CGTAGTTGAGGGTGCATGCC 61.369 60.000 16.68 6.42 0.00 4.40
2392 3082 1.059584 TGAGGGACCTCTTGTTGCCA 61.060 55.000 18.48 0.00 43.12 4.92
2506 3196 2.202987 GAGGCCATGACGCTGAGG 60.203 66.667 5.01 0.00 0.00 3.86
2542 3232 2.747446 GCCGAAGATTTTGAGGTAGCAA 59.253 45.455 0.00 0.00 0.00 3.91
2584 3274 4.538283 ACGATCAGCGCGACCTCG 62.538 66.667 12.10 14.57 46.04 4.63
2683 3373 5.783111 TGAAGTCGTGAATGATCTTCAGAA 58.217 37.500 7.56 0.00 39.27 3.02
2684 3374 5.391312 TGAAGTCGTGAATGATCTTCAGA 57.609 39.130 7.56 5.82 39.27 3.27
2686 3376 5.391312 TCTGAAGTCGTGAATGATCTTCA 57.609 39.130 12.68 12.68 41.00 3.02
2688 3378 5.970592 TCATCTGAAGTCGTGAATGATCTT 58.029 37.500 0.00 0.00 0.00 2.40
2689 3379 5.588958 TCATCTGAAGTCGTGAATGATCT 57.411 39.130 0.00 0.00 0.00 2.75
2690 3380 5.177142 CCATCATCTGAAGTCGTGAATGATC 59.823 44.000 0.00 0.00 0.00 2.92
2691 3381 5.055144 CCATCATCTGAAGTCGTGAATGAT 58.945 41.667 0.00 0.00 0.00 2.45
2695 3385 3.588955 CACCATCATCTGAAGTCGTGAA 58.411 45.455 0.00 0.00 0.00 3.18
2696 3386 2.094026 CCACCATCATCTGAAGTCGTGA 60.094 50.000 0.00 0.00 0.00 4.35
2702 3392 1.442526 GCCGCCACCATCATCTGAAG 61.443 60.000 0.00 0.00 0.00 3.02
2720 3410 2.997897 AGACGGACAGAGGGGTGC 60.998 66.667 0.00 0.00 0.00 5.01
2721 3411 2.973899 CAGACGGACAGAGGGGTG 59.026 66.667 0.00 0.00 0.00 4.61
2722 3412 2.997897 GCAGACGGACAGAGGGGT 60.998 66.667 0.00 0.00 0.00 4.95
2748 3438 1.136000 GGAAATTTTGCATTGCCGCAC 60.136 47.619 6.12 0.00 42.87 5.34
2810 3504 2.036604 TCTACAAACTGCCATGACACGA 59.963 45.455 0.00 0.00 0.00 4.35
2811 3505 2.412870 TCTACAAACTGCCATGACACG 58.587 47.619 0.00 0.00 0.00 4.49
2812 3506 4.002982 TCATCTACAAACTGCCATGACAC 58.997 43.478 0.00 0.00 0.00 3.67
2824 3518 4.298626 ACTATCCCTGCCTCATCTACAAA 58.701 43.478 0.00 0.00 0.00 2.83
2854 3548 6.979238 AGTACATTTTGAGCGTAGAACTATCC 59.021 38.462 0.00 0.00 0.00 2.59
2879 3573 6.849502 ACAGAAATACTCATCTCGAACGTAA 58.150 36.000 0.00 0.00 0.00 3.18
2881 3575 5.312120 ACAGAAATACTCATCTCGAACGT 57.688 39.130 0.00 0.00 0.00 3.99
2882 3576 6.528423 AGAAACAGAAATACTCATCTCGAACG 59.472 38.462 0.00 0.00 0.00 3.95
2883 3577 7.820044 AGAAACAGAAATACTCATCTCGAAC 57.180 36.000 0.00 0.00 0.00 3.95
2885 3579 8.282455 ACTAGAAACAGAAATACTCATCTCGA 57.718 34.615 0.00 0.00 0.00 4.04
2931 3627 2.738643 CGATGAAGTGCCGTCCTACAAT 60.739 50.000 0.00 0.00 0.00 2.71
2955 3651 5.163663 CCGCACAACTACAATAACATGGAAT 60.164 40.000 0.00 0.00 0.00 3.01
2961 3657 5.470437 TGAAATCCGCACAACTACAATAACA 59.530 36.000 0.00 0.00 0.00 2.41
2962 3658 5.933790 TGAAATCCGCACAACTACAATAAC 58.066 37.500 0.00 0.00 0.00 1.89
3023 3746 7.646922 CGTACTACTTTTTGTACAAGAGACAGT 59.353 37.037 21.14 21.35 39.00 3.55
3024 3747 7.859377 TCGTACTACTTTTTGTACAAGAGACAG 59.141 37.037 21.14 18.43 39.00 3.51
3038 3770 6.485648 ACTCCATTGCTTTTCGTACTACTTTT 59.514 34.615 0.00 0.00 0.00 2.27
3048 3780 6.842163 ACTTAATGTACTCCATTGCTTTTCG 58.158 36.000 0.00 0.00 43.63 3.46
3049 3781 7.816640 TGACTTAATGTACTCCATTGCTTTTC 58.183 34.615 0.00 0.00 43.63 2.29
3050 3782 7.759489 TGACTTAATGTACTCCATTGCTTTT 57.241 32.000 0.00 0.00 43.63 2.27
3051 3783 7.309194 GGTTGACTTAATGTACTCCATTGCTTT 60.309 37.037 0.00 0.00 43.63 3.51
3086 3818 3.347216 ACCACCAAAGGAGAATCATTCG 58.653 45.455 0.00 0.00 38.69 3.34
3099 3832 3.141272 AGTCAAATCCCCTAACCACCAAA 59.859 43.478 0.00 0.00 0.00 3.28
3104 3837 2.354328 ACCAGTCAAATCCCCTAACCA 58.646 47.619 0.00 0.00 0.00 3.67
3112 3845 4.202050 GGATGCATACAACCAGTCAAATCC 60.202 45.833 3.28 0.00 38.58 3.01
3183 3918 4.683781 TCTCTTTTGTTGTTGTTGTTGTGC 59.316 37.500 0.00 0.00 0.00 4.57
3184 3919 6.670452 GCATCTCTTTTGTTGTTGTTGTTGTG 60.670 38.462 0.00 0.00 0.00 3.33
3195 3944 3.924686 GGCTGATTGCATCTCTTTTGTTG 59.075 43.478 0.00 0.00 45.15 3.33
3297 4171 2.474032 CGCATATGATTGCTGCAGATCG 60.474 50.000 20.43 1.04 40.54 3.69
3301 4175 1.232119 TCCGCATATGATTGCTGCAG 58.768 50.000 10.11 10.11 40.54 4.41
3302 4176 1.808343 GATCCGCATATGATTGCTGCA 59.192 47.619 6.97 0.00 40.54 4.41
3303 4177 1.808343 TGATCCGCATATGATTGCTGC 59.192 47.619 6.97 0.00 40.54 5.25
3304 4178 3.332034 TCTGATCCGCATATGATTGCTG 58.668 45.455 6.97 0.00 40.54 4.41
3305 4179 3.690475 TCTGATCCGCATATGATTGCT 57.310 42.857 6.97 0.00 40.54 3.91
3306 4180 3.937079 TCATCTGATCCGCATATGATTGC 59.063 43.478 6.97 0.00 35.80 3.56
3307 4181 6.288426 GATCATCTGATCCGCATATGATTG 57.712 41.667 6.97 0.00 45.46 2.67
3326 4200 0.252881 AGCTCCTCCTGGTTGGATCA 60.253 55.000 10.56 0.00 45.16 2.92
3541 4454 2.124695 GGAACATGACGGGGCTCC 60.125 66.667 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.