Multiple sequence alignment - TraesCS6A01G352400

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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 TraesCS6A01G352400 chr6A 100.000 1433 0 0 1474 2906 584950261 584951693 0.000000e+00 2647.0
1 TraesCS6A01G352400 chr6A 100.000 1108 0 0 1 1108 584948788 584949895 0.000000e+00 2047.0
2 TraesCS6A01G352400 chr6A 89.062 192 19 2 422 612 85700384 85700194 1.350000e-58 237.0
3 TraesCS6A01G352400 chr6A 89.944 179 15 2 422 600 431069372 431069197 8.100000e-56 228.0
4 TraesCS6A01G352400 chr6B 92.141 1476 70 27 1474 2906 660242722 660244194 0.000000e+00 2041.0
5 TraesCS6A01G352400 chr6B 88.477 243 17 6 867 1108 660242412 660242644 1.700000e-72 283.0
6 TraesCS6A01G352400 chr6B 84.746 59 7 2 1051 1108 660242629 660242686 1.120000e-04 58.4
7 TraesCS6A01G352400 chr6D 88.366 1169 78 37 1474 2601 436757891 436759042 0.000000e+00 1352.0
8 TraesCS6A01G352400 chr6D 86.893 412 33 10 13 422 436756541 436756933 2.660000e-120 442.0
9 TraesCS6A01G352400 chr6D 87.243 243 8 8 889 1108 436757595 436757837 3.720000e-64 255.0
10 TraesCS6A01G352400 chr6D 88.268 179 14 4 605 782 436756927 436757099 1.060000e-49 207.0
11 TraesCS6A01G352400 chr2A 91.713 181 11 2 423 600 617757241 617757062 6.220000e-62 248.0
12 TraesCS6A01G352400 chr2A 89.730 185 10 7 422 600 13616101 13615920 8.100000e-56 228.0
13 TraesCS6A01G352400 chr1A 90.659 182 15 2 423 603 5131709 5131529 1.040000e-59 241.0
14 TraesCS6A01G352400 chr4D 91.011 178 14 2 423 600 481856471 481856646 3.740000e-59 239.0
15 TraesCS6A01G352400 chr3A 91.111 180 11 3 421 600 69643092 69642918 3.740000e-59 239.0
16 TraesCS6A01G352400 chr7D 89.674 184 13 4 423 604 13796456 13796635 2.250000e-56 230.0
17 TraesCS6A01G352400 chr1D 89.888 178 15 3 423 600 471826342 471826168 2.910000e-55 226.0


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 TraesCS6A01G352400 chr6A 584948788 584951693 2905 False 2347.000000 2647 100.000000 1 2906 2 chr6A.!!$F1 2905
1 TraesCS6A01G352400 chr6B 660242412 660244194 1782 False 794.133333 2041 88.454667 867 2906 3 chr6B.!!$F1 2039
2 TraesCS6A01G352400 chr6D 436756541 436759042 2501 False 564.000000 1352 87.692500 13 2601 4 chr6D.!!$F1 2588

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
502 505 0.03438 GGTTAAGGGGAAGGAGGTGC 60.034 60.0 0.0 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2158 2630 0.76489 AGCTGTGCCCTTGTTCTACA 59.235 50.0 0.0 0.0 0.0 2.74 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
45 46 5.392995 TGATTTCTCCAAATGTTTCTGGGA 58.607 37.500 0.00 0.00 31.94 4.37
79 80 5.917462 CAAAAAGTTGGAAGAAAGGTCCAT 58.083 37.500 0.00 0.00 44.62 3.41
81 82 5.791336 AAAGTTGGAAGAAAGGTCCATTC 57.209 39.130 0.00 0.00 44.62 2.67
86 87 4.766375 TGGAAGAAAGGTCCATTCGATAC 58.234 43.478 1.27 0.00 40.33 2.24
123 124 4.818546 GTGAAGCATCAATAGGTAGTGCAT 59.181 41.667 0.00 0.00 37.30 3.96
129 130 5.277683 GCATCAATAGGTAGTGCATCAACAG 60.278 44.000 0.00 0.00 35.93 3.16
149 150 8.137437 TCAACAGAGGAATTGTGAGAAAAATTC 58.863 33.333 0.00 0.00 40.51 2.17
191 192 5.561679 AGGTTGAAAAGTCTCTTGGGTATC 58.438 41.667 0.00 0.00 0.00 2.24
195 196 5.235516 TGAAAAGTCTCTTGGGTATCGTTC 58.764 41.667 0.00 0.00 0.00 3.95
353 356 6.961360 AGATATGGAAGTAATCACGTGAGA 57.039 37.500 24.41 11.59 0.00 3.27
369 372 3.068064 GATTTGGTGGCGGGGTGG 61.068 66.667 0.00 0.00 0.00 4.61
386 389 4.278310 GGGTGGTTATTGCATCCTAGTTT 58.722 43.478 0.00 0.00 0.00 2.66
395 398 3.954200 TGCATCCTAGTTTGAAGCATGA 58.046 40.909 0.00 0.00 32.12 3.07
401 404 1.160137 AGTTTGAAGCATGAGGTCGC 58.840 50.000 0.00 0.00 0.00 5.19
407 410 2.746277 GCATGAGGTCGCCGGTTT 60.746 61.111 1.90 0.00 0.00 3.27
411 414 3.119096 GAGGTCGCCGGTTTGAGC 61.119 66.667 1.90 8.95 0.00 4.26
420 423 2.607457 CGGTTTGAGCCGTAACACA 58.393 52.632 0.00 0.00 46.11 3.72
421 424 0.233848 CGGTTTGAGCCGTAACACAC 59.766 55.000 0.00 0.00 46.11 3.82
435 438 5.431650 GTAACACACGAGTAATGCTACAC 57.568 43.478 0.00 0.00 0.00 2.90
436 439 3.653539 ACACACGAGTAATGCTACACA 57.346 42.857 0.00 0.00 0.00 3.72
437 440 4.188247 ACACACGAGTAATGCTACACAT 57.812 40.909 0.00 0.00 42.30 3.21
438 441 5.319140 ACACACGAGTAATGCTACACATA 57.681 39.130 0.00 0.00 38.34 2.29
439 442 5.100259 ACACACGAGTAATGCTACACATAC 58.900 41.667 0.00 0.00 38.34 2.39
440 443 5.099575 CACACGAGTAATGCTACACATACA 58.900 41.667 0.00 0.00 38.34 2.29
441 444 5.748630 CACACGAGTAATGCTACACATACAT 59.251 40.000 0.00 0.00 38.34 2.29
442 445 6.915843 CACACGAGTAATGCTACACATACATA 59.084 38.462 0.00 0.00 38.34 2.29
443 446 7.434013 CACACGAGTAATGCTACACATACATAA 59.566 37.037 0.00 0.00 38.34 1.90
444 447 7.648112 ACACGAGTAATGCTACACATACATAAG 59.352 37.037 0.00 0.00 38.34 1.73
445 448 7.648112 CACGAGTAATGCTACACATACATAAGT 59.352 37.037 0.00 0.00 38.34 2.24
446 449 8.195436 ACGAGTAATGCTACACATACATAAGTT 58.805 33.333 0.00 0.00 38.34 2.66
447 450 9.031360 CGAGTAATGCTACACATACATAAGTTT 57.969 33.333 0.00 0.00 38.34 2.66
453 456 8.432110 TGCTACACATACATAAGTTTACATGG 57.568 34.615 0.00 0.00 0.00 3.66
454 457 7.497579 TGCTACACATACATAAGTTTACATGGG 59.502 37.037 0.00 0.00 0.00 4.00
455 458 7.497909 GCTACACATACATAAGTTTACATGGGT 59.502 37.037 0.00 0.00 34.57 4.51
456 459 9.391006 CTACACATACATAAGTTTACATGGGTT 57.609 33.333 0.00 0.00 32.57 4.11
457 460 8.644374 ACACATACATAAGTTTACATGGGTTT 57.356 30.769 0.00 0.00 25.53 3.27
458 461 8.736244 ACACATACATAAGTTTACATGGGTTTC 58.264 33.333 0.00 0.00 25.53 2.78
459 462 8.735315 CACATACATAAGTTTACATGGGTTTCA 58.265 33.333 0.00 0.00 0.00 2.69
460 463 8.736244 ACATACATAAGTTTACATGGGTTTCAC 58.264 33.333 0.00 0.00 0.00 3.18
461 464 8.735315 CATACATAAGTTTACATGGGTTTCACA 58.265 33.333 0.00 0.00 0.00 3.58
462 465 7.589958 ACATAAGTTTACATGGGTTTCACAA 57.410 32.000 0.00 0.00 0.00 3.33
463 466 8.012957 ACATAAGTTTACATGGGTTTCACAAA 57.987 30.769 0.00 0.00 0.00 2.83
464 467 7.923878 ACATAAGTTTACATGGGTTTCACAAAC 59.076 33.333 0.00 0.00 40.65 2.93
465 468 5.923733 AGTTTACATGGGTTTCACAAACA 57.076 34.783 0.00 0.00 43.15 2.83
466 469 5.901552 AGTTTACATGGGTTTCACAAACAG 58.098 37.500 0.00 0.00 43.15 3.16
467 470 5.654650 AGTTTACATGGGTTTCACAAACAGA 59.345 36.000 0.00 0.00 43.15 3.41
468 471 6.323739 AGTTTACATGGGTTTCACAAACAGAT 59.676 34.615 0.00 0.00 43.15 2.90
469 472 4.589216 ACATGGGTTTCACAAACAGATG 57.411 40.909 0.00 5.20 43.15 2.90
470 473 3.321682 ACATGGGTTTCACAAACAGATGG 59.678 43.478 0.00 0.00 43.15 3.51
471 474 2.315176 TGGGTTTCACAAACAGATGGG 58.685 47.619 1.78 0.00 43.15 4.00
472 475 2.316108 GGGTTTCACAAACAGATGGGT 58.684 47.619 1.78 0.00 43.15 4.51
473 476 2.698274 GGGTTTCACAAACAGATGGGTT 59.302 45.455 1.78 0.00 43.15 4.11
474 477 3.492482 GGGTTTCACAAACAGATGGGTTG 60.492 47.826 1.78 0.00 43.15 3.77
475 478 3.132111 GGTTTCACAAACAGATGGGTTGT 59.868 43.478 1.78 0.00 43.15 3.32
476 479 4.111916 GTTTCACAAACAGATGGGTTGTG 58.888 43.478 16.81 16.81 41.04 3.33
477 480 3.289407 TCACAAACAGATGGGTTGTGA 57.711 42.857 20.42 20.42 36.93 3.58
478 481 3.831323 TCACAAACAGATGGGTTGTGAT 58.169 40.909 20.42 0.00 35.70 3.06
479 482 4.214310 TCACAAACAGATGGGTTGTGATT 58.786 39.130 20.42 0.00 35.70 2.57
480 483 4.037803 TCACAAACAGATGGGTTGTGATTG 59.962 41.667 20.42 4.95 35.70 2.67
481 484 3.321682 ACAAACAGATGGGTTGTGATTGG 59.678 43.478 0.00 0.00 0.00 3.16
482 485 3.524095 AACAGATGGGTTGTGATTGGA 57.476 42.857 0.00 0.00 0.00 3.53
483 486 3.077484 ACAGATGGGTTGTGATTGGAG 57.923 47.619 0.00 0.00 0.00 3.86
484 487 2.291153 ACAGATGGGTTGTGATTGGAGG 60.291 50.000 0.00 0.00 0.00 4.30
485 488 1.995542 AGATGGGTTGTGATTGGAGGT 59.004 47.619 0.00 0.00 0.00 3.85
486 489 2.379907 AGATGGGTTGTGATTGGAGGTT 59.620 45.455 0.00 0.00 0.00 3.50
487 490 3.591527 AGATGGGTTGTGATTGGAGGTTA 59.408 43.478 0.00 0.00 0.00 2.85
488 491 3.885976 TGGGTTGTGATTGGAGGTTAA 57.114 42.857 0.00 0.00 0.00 2.01
489 492 3.761897 TGGGTTGTGATTGGAGGTTAAG 58.238 45.455 0.00 0.00 0.00 1.85
490 493 3.089284 GGGTTGTGATTGGAGGTTAAGG 58.911 50.000 0.00 0.00 0.00 2.69
491 494 3.089284 GGTTGTGATTGGAGGTTAAGGG 58.911 50.000 0.00 0.00 0.00 3.95
492 495 3.089284 GTTGTGATTGGAGGTTAAGGGG 58.911 50.000 0.00 0.00 0.00 4.79
493 496 2.638325 TGTGATTGGAGGTTAAGGGGA 58.362 47.619 0.00 0.00 0.00 4.81
494 497 2.990284 TGTGATTGGAGGTTAAGGGGAA 59.010 45.455 0.00 0.00 0.00 3.97
495 498 3.010138 TGTGATTGGAGGTTAAGGGGAAG 59.990 47.826 0.00 0.00 0.00 3.46
496 499 2.580783 TGATTGGAGGTTAAGGGGAAGG 59.419 50.000 0.00 0.00 0.00 3.46
497 500 2.444033 TTGGAGGTTAAGGGGAAGGA 57.556 50.000 0.00 0.00 0.00 3.36
498 501 1.966845 TGGAGGTTAAGGGGAAGGAG 58.033 55.000 0.00 0.00 0.00 3.69
499 502 1.214217 GGAGGTTAAGGGGAAGGAGG 58.786 60.000 0.00 0.00 0.00 4.30
500 503 1.557426 GGAGGTTAAGGGGAAGGAGGT 60.557 57.143 0.00 0.00 0.00 3.85
501 504 1.560146 GAGGTTAAGGGGAAGGAGGTG 59.440 57.143 0.00 0.00 0.00 4.00
502 505 0.034380 GGTTAAGGGGAAGGAGGTGC 60.034 60.000 0.00 0.00 0.00 5.01
503 506 0.034380 GTTAAGGGGAAGGAGGTGCC 60.034 60.000 0.00 0.00 0.00 5.01
515 518 3.897122 GGTGCCCACCCCTGTGAA 61.897 66.667 6.16 0.00 45.76 3.18
516 519 2.197324 GTGCCCACCCCTGTGAAA 59.803 61.111 0.00 0.00 45.76 2.69
517 520 1.456705 GTGCCCACCCCTGTGAAAA 60.457 57.895 0.00 0.00 45.76 2.29
518 521 0.831711 GTGCCCACCCCTGTGAAAAT 60.832 55.000 0.00 0.00 45.76 1.82
519 522 0.541764 TGCCCACCCCTGTGAAAATC 60.542 55.000 0.00 0.00 45.76 2.17
520 523 0.541764 GCCCACCCCTGTGAAAATCA 60.542 55.000 0.00 0.00 45.76 2.57
521 524 1.549203 CCCACCCCTGTGAAAATCAG 58.451 55.000 0.00 0.00 45.76 2.90
527 530 2.134789 CCTGTGAAAATCAGGGAGGG 57.865 55.000 4.27 0.00 46.03 4.30
528 531 1.635487 CCTGTGAAAATCAGGGAGGGA 59.365 52.381 4.27 0.00 46.03 4.20
529 532 2.356535 CCTGTGAAAATCAGGGAGGGAG 60.357 54.545 4.27 0.00 46.03 4.30
530 533 2.307098 CTGTGAAAATCAGGGAGGGAGT 59.693 50.000 0.00 0.00 0.00 3.85
531 534 2.040278 TGTGAAAATCAGGGAGGGAGTG 59.960 50.000 0.00 0.00 0.00 3.51
532 535 1.635487 TGAAAATCAGGGAGGGAGTGG 59.365 52.381 0.00 0.00 0.00 4.00
533 536 1.636003 GAAAATCAGGGAGGGAGTGGT 59.364 52.381 0.00 0.00 0.00 4.16
534 537 1.760405 AAATCAGGGAGGGAGTGGTT 58.240 50.000 0.00 0.00 0.00 3.67
535 538 2.661176 AATCAGGGAGGGAGTGGTTA 57.339 50.000 0.00 0.00 0.00 2.85
536 539 2.182516 ATCAGGGAGGGAGTGGTTAG 57.817 55.000 0.00 0.00 0.00 2.34
537 540 0.790993 TCAGGGAGGGAGTGGTTAGT 59.209 55.000 0.00 0.00 0.00 2.24
538 541 1.151413 TCAGGGAGGGAGTGGTTAGTT 59.849 52.381 0.00 0.00 0.00 2.24
539 542 2.384375 TCAGGGAGGGAGTGGTTAGTTA 59.616 50.000 0.00 0.00 0.00 2.24
540 543 2.766828 CAGGGAGGGAGTGGTTAGTTAG 59.233 54.545 0.00 0.00 0.00 2.34
541 544 2.658489 AGGGAGGGAGTGGTTAGTTAGA 59.342 50.000 0.00 0.00 0.00 2.10
542 545 3.078612 AGGGAGGGAGTGGTTAGTTAGAA 59.921 47.826 0.00 0.00 0.00 2.10
543 546 3.842436 GGGAGGGAGTGGTTAGTTAGAAA 59.158 47.826 0.00 0.00 0.00 2.52
544 547 4.081031 GGGAGGGAGTGGTTAGTTAGAAAG 60.081 50.000 0.00 0.00 0.00 2.62
545 548 4.776308 GGAGGGAGTGGTTAGTTAGAAAGA 59.224 45.833 0.00 0.00 0.00 2.52
546 549 5.247792 GGAGGGAGTGGTTAGTTAGAAAGAA 59.752 44.000 0.00 0.00 0.00 2.52
547 550 6.239800 GGAGGGAGTGGTTAGTTAGAAAGAAA 60.240 42.308 0.00 0.00 0.00 2.52
548 551 7.145474 AGGGAGTGGTTAGTTAGAAAGAAAA 57.855 36.000 0.00 0.00 0.00 2.29
549 552 7.580007 AGGGAGTGGTTAGTTAGAAAGAAAAA 58.420 34.615 0.00 0.00 0.00 1.94
571 574 6.382869 AAATCCTAGTCAGCATGTAATTGC 57.617 37.500 0.00 0.00 43.09 3.56
581 584 4.600012 GCATGTAATTGCGTGTAACTCT 57.400 40.909 15.87 0.00 32.06 3.24
582 585 4.969816 GCATGTAATTGCGTGTAACTCTT 58.030 39.130 15.87 0.00 32.06 2.85
583 586 5.390613 GCATGTAATTGCGTGTAACTCTTT 58.609 37.500 15.87 0.00 32.06 2.52
584 587 5.283717 GCATGTAATTGCGTGTAACTCTTTG 59.716 40.000 15.87 0.00 32.06 2.77
585 588 5.994887 TGTAATTGCGTGTAACTCTTTGT 57.005 34.783 0.00 0.00 31.75 2.83
586 589 7.514805 CATGTAATTGCGTGTAACTCTTTGTA 58.485 34.615 7.52 0.00 31.75 2.41
587 590 7.661127 TGTAATTGCGTGTAACTCTTTGTAT 57.339 32.000 0.00 0.00 31.75 2.29
588 591 7.514805 TGTAATTGCGTGTAACTCTTTGTATG 58.485 34.615 0.00 0.00 31.75 2.39
589 592 6.554334 AATTGCGTGTAACTCTTTGTATGT 57.446 33.333 0.00 0.00 31.75 2.29
590 593 5.994887 TTGCGTGTAACTCTTTGTATGTT 57.005 34.783 0.00 0.00 31.75 2.71
591 594 5.994887 TGCGTGTAACTCTTTGTATGTTT 57.005 34.783 0.00 0.00 31.75 2.83
592 595 7.479897 TTGCGTGTAACTCTTTGTATGTTTA 57.520 32.000 0.00 0.00 31.75 2.01
593 596 7.112528 TGCGTGTAACTCTTTGTATGTTTAG 57.887 36.000 0.00 0.00 31.75 1.85
594 597 6.013689 GCGTGTAACTCTTTGTATGTTTAGC 58.986 40.000 0.00 0.00 31.75 3.09
595 598 6.347079 GCGTGTAACTCTTTGTATGTTTAGCA 60.347 38.462 0.00 0.00 31.75 3.49
596 599 7.623506 GCGTGTAACTCTTTGTATGTTTAGCAT 60.624 37.037 0.00 0.00 36.70 3.79
597 600 8.227791 CGTGTAACTCTTTGTATGTTTAGCATT 58.772 33.333 0.00 0.00 35.02 3.56
603 606 7.769044 ACTCTTTGTATGTTTAGCATTATCGGT 59.231 33.333 0.00 0.00 38.94 4.69
614 617 2.353579 GCATTATCGGTAACACACACCC 59.646 50.000 0.00 0.00 31.96 4.61
615 618 3.601435 CATTATCGGTAACACACACCCA 58.399 45.455 0.00 0.00 31.96 4.51
616 619 2.747396 TATCGGTAACACACACCCAC 57.253 50.000 0.00 0.00 31.96 4.61
621 624 2.371306 GGTAACACACACCCACACTTT 58.629 47.619 0.00 0.00 0.00 2.66
661 664 5.153950 ACAGAAAAGAGTAGATGGGTCAC 57.846 43.478 0.00 0.00 0.00 3.67
715 718 1.510776 ACGAAAACGCCAATAACGGA 58.489 45.000 0.00 0.00 34.00 4.69
742 745 3.107447 CGCCGAATAGGGTTTGCC 58.893 61.111 0.00 0.00 41.48 4.52
800 888 5.514274 TTTTAAACAGCCCAAACTCAGAG 57.486 39.130 0.00 0.00 0.00 3.35
805 893 3.500635 CCCAAACTCAGAGGGGCT 58.499 61.111 1.53 0.00 38.98 5.19
808 896 1.763770 CAAACTCAGAGGGGCTGGT 59.236 57.895 1.53 0.00 44.98 4.00
827 915 2.675075 GGCCGGCCTGTTTGCTTA 60.675 61.111 38.76 0.00 0.00 3.09
828 916 2.052104 GGCCGGCCTGTTTGCTTAT 61.052 57.895 38.76 0.00 0.00 1.73
830 918 0.246360 GCCGGCCTGTTTGCTTATTT 59.754 50.000 18.11 0.00 0.00 1.40
831 919 1.337728 GCCGGCCTGTTTGCTTATTTT 60.338 47.619 18.11 0.00 0.00 1.82
832 920 2.336667 CCGGCCTGTTTGCTTATTTTG 58.663 47.619 0.00 0.00 0.00 2.44
842 930 0.458370 GCTTATTTTGCCGTGCCTGG 60.458 55.000 0.00 0.00 0.00 4.45
843 931 1.173043 CTTATTTTGCCGTGCCTGGA 58.827 50.000 0.00 0.00 0.00 3.86
845 933 0.963355 TATTTTGCCGTGCCTGGACC 60.963 55.000 0.00 0.00 0.00 4.46
946 1343 0.828762 TCTTTGGAACCCCGACGAGA 60.829 55.000 0.00 0.00 34.29 4.04
983 1394 1.759459 CTAGCTGGTCCGAATCCCCC 61.759 65.000 0.00 0.00 0.00 5.40
1662 2095 2.579738 GAGGACAGGAAGCCGGAC 59.420 66.667 5.05 0.00 0.00 4.79
1785 2221 1.752833 GTTCGACTCCACCAAGGGT 59.247 57.895 0.00 0.00 38.24 4.34
1919 2356 1.826709 GCTGAGGAGGTAGGCTTCC 59.173 63.158 1.23 1.23 40.80 3.46
1933 2370 1.205655 GGCTTCCTGATTTTCCTTGCC 59.794 52.381 0.00 0.00 0.00 4.52
1939 2376 3.973305 TCCTGATTTTCCTTGCCCTTTTT 59.027 39.130 0.00 0.00 0.00 1.94
1940 2377 4.040339 TCCTGATTTTCCTTGCCCTTTTTC 59.960 41.667 0.00 0.00 0.00 2.29
1983 2422 1.042229 TTCTGCATTTGCTTGCCTGT 58.958 45.000 3.94 0.00 42.06 4.00
1986 2425 0.244450 TGCATTTGCTTGCCTGTAGC 59.756 50.000 3.94 0.00 42.06 3.58
1999 2438 1.299541 CTGTAGCTTACGGCCCAATG 58.700 55.000 0.00 0.00 43.05 2.82
2005 2444 1.202290 GCTTACGGCCCAATGTGAATG 60.202 52.381 0.00 0.00 34.27 2.67
2033 2473 6.503616 CGAAAAGCATGTACTGTAGATCTC 57.496 41.667 0.00 0.00 0.00 2.75
2124 2595 8.814038 ATTGTGCAAAGAACTCTTTATATCCT 57.186 30.769 4.43 0.00 43.72 3.24
2125 2596 7.615582 TGTGCAAAGAACTCTTTATATCCTG 57.384 36.000 4.43 0.00 43.72 3.86
2126 2597 7.394016 TGTGCAAAGAACTCTTTATATCCTGA 58.606 34.615 4.43 0.00 43.72 3.86
2128 2599 8.730680 GTGCAAAGAACTCTTTATATCCTGAAA 58.269 33.333 4.43 0.00 43.72 2.69
2158 2630 4.586884 ACAGAGCATCATGTTGAACTGAT 58.413 39.130 24.05 1.02 37.82 2.90
2169 2641 6.427853 TCATGTTGAACTGATGTAGAACAAGG 59.572 38.462 0.00 0.00 33.77 3.61
2185 2657 1.342174 CAAGGGCACAGCTCAAATTGT 59.658 47.619 0.00 0.00 0.00 2.71
2186 2658 2.557924 CAAGGGCACAGCTCAAATTGTA 59.442 45.455 0.00 0.00 0.00 2.41
2187 2659 2.440409 AGGGCACAGCTCAAATTGTAG 58.560 47.619 0.00 0.00 0.00 2.74
2188 2660 1.135286 GGGCACAGCTCAAATTGTAGC 60.135 52.381 8.63 8.63 39.08 3.58
2189 2661 1.466360 GGCACAGCTCAAATTGTAGCG 60.466 52.381 10.22 8.59 43.63 4.26
2190 2662 1.464608 GCACAGCTCAAATTGTAGCGA 59.535 47.619 10.22 0.00 43.63 4.93
2191 2663 2.726066 GCACAGCTCAAATTGTAGCGAC 60.726 50.000 10.22 0.00 43.63 5.19
2192 2664 1.726791 ACAGCTCAAATTGTAGCGACG 59.273 47.619 10.22 0.00 43.63 5.12
2193 2665 1.992667 CAGCTCAAATTGTAGCGACGA 59.007 47.619 0.00 0.00 43.63 4.20
2240 2716 0.322098 TTACTGAATGGGGTGCACCG 60.322 55.000 29.08 15.85 41.60 4.94
2251 2727 2.485835 GGGGTGCACCGTATAAATGCTA 60.486 50.000 29.08 0.00 41.60 3.49
2252 2728 3.207778 GGGTGCACCGTATAAATGCTAA 58.792 45.455 29.08 0.00 40.13 3.09
2265 2741 8.050750 CGTATAAATGCTAAACTTTCTGACTCG 58.949 37.037 0.00 0.00 0.00 4.18
2284 2760 7.792925 TGACTCGTATGTTAAATGTCTGTTTG 58.207 34.615 0.00 0.00 0.00 2.93
2317 2793 1.481363 TCGGGTACATACAAATGCGGA 59.519 47.619 0.00 0.00 36.50 5.54
2351 2827 6.814954 AGAAATTGTAGAGCCATAGAAGGA 57.185 37.500 0.00 0.00 0.00 3.36
2521 2998 7.147976 GTCTGCTTCACCTGTCAAAAATTTAT 58.852 34.615 0.00 0.00 0.00 1.40
2548 3026 5.916318 ACATGTCTGCTTTCCAAAATTCAA 58.084 33.333 0.00 0.00 0.00 2.69
2551 3029 5.976458 TGTCTGCTTTCCAAAATTCAACTT 58.024 33.333 0.00 0.00 0.00 2.66
2702 3187 9.573166 TGACAAGGTTATGCTTAATTGCTATAT 57.427 29.630 5.89 0.00 0.00 0.86
2782 3267 5.545588 AGCGTGACAGCATATCTGATATTT 58.454 37.500 7.43 0.00 45.72 1.40
2794 3279 9.066892 GCATATCTGATATTTGTAAACCCTTCA 57.933 33.333 7.43 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.798710 TCAATATGCTAGCCTACCTAAATCT 57.201 36.000 13.29 0.00 0.00 2.40
1 2 9.454859 AAATCAATATGCTAGCCTACCTAAATC 57.545 33.333 13.29 0.00 0.00 2.17
2 3 9.454859 GAAATCAATATGCTAGCCTACCTAAAT 57.545 33.333 13.29 0.00 0.00 1.40
3 4 8.660435 AGAAATCAATATGCTAGCCTACCTAAA 58.340 33.333 13.29 0.00 0.00 1.85
4 5 8.207350 AGAAATCAATATGCTAGCCTACCTAA 57.793 34.615 13.29 0.00 0.00 2.69
5 6 7.093289 GGAGAAATCAATATGCTAGCCTACCTA 60.093 40.741 13.29 0.00 0.00 3.08
6 7 6.296145 GGAGAAATCAATATGCTAGCCTACCT 60.296 42.308 13.29 0.00 0.00 3.08
7 8 5.877564 GGAGAAATCAATATGCTAGCCTACC 59.122 44.000 13.29 0.00 0.00 3.18
8 9 6.467677 TGGAGAAATCAATATGCTAGCCTAC 58.532 40.000 13.29 0.00 0.00 3.18
9 10 6.686484 TGGAGAAATCAATATGCTAGCCTA 57.314 37.500 13.29 7.29 0.00 3.93
10 11 5.573380 TGGAGAAATCAATATGCTAGCCT 57.427 39.130 13.29 4.74 0.00 4.58
11 12 6.639632 TTTGGAGAAATCAATATGCTAGCC 57.360 37.500 13.29 0.00 0.00 3.93
79 80 5.865013 TCACATCTAAAGCAAACGTATCGAA 59.135 36.000 0.00 0.00 0.00 3.71
81 82 5.696260 TCACATCTAAAGCAAACGTATCG 57.304 39.130 0.00 0.00 0.00 2.92
113 114 2.540383 TCCTCTGTTGATGCACTACCT 58.460 47.619 0.00 0.00 0.00 3.08
123 124 7.587037 ATTTTTCTCACAATTCCTCTGTTGA 57.413 32.000 0.00 0.00 0.00 3.18
129 130 8.239998 CCTACTGAATTTTTCTCACAATTCCTC 58.760 37.037 0.00 0.00 38.23 3.71
166 167 4.715713 ACCCAAGAGACTTTTCAACCTAC 58.284 43.478 0.00 0.00 0.00 3.18
259 262 9.738832 TTTTCTATTTTCTTTTTACTGGTTCGG 57.261 29.630 0.00 0.00 0.00 4.30
326 329 9.698309 CTCACGTGATTACTTCCATATCTTTAT 57.302 33.333 20.40 0.00 0.00 1.40
327 330 8.909923 TCTCACGTGATTACTTCCATATCTTTA 58.090 33.333 20.40 0.00 0.00 1.85
328 331 7.782049 TCTCACGTGATTACTTCCATATCTTT 58.218 34.615 20.40 0.00 0.00 2.52
329 332 7.348080 TCTCACGTGATTACTTCCATATCTT 57.652 36.000 20.40 0.00 0.00 2.40
330 333 6.961360 TCTCACGTGATTACTTCCATATCT 57.039 37.500 20.40 0.00 0.00 1.98
331 334 8.491152 CAAATCTCACGTGATTACTTCCATATC 58.509 37.037 20.40 0.00 35.82 1.63
332 335 7.442364 CCAAATCTCACGTGATTACTTCCATAT 59.558 37.037 20.40 0.00 35.82 1.78
333 336 6.761242 CCAAATCTCACGTGATTACTTCCATA 59.239 38.462 20.40 0.00 35.82 2.74
337 340 5.163854 CCACCAAATCTCACGTGATTACTTC 60.164 44.000 20.40 0.00 35.82 3.01
353 356 2.082836 TAACCACCCCGCCACCAAAT 62.083 55.000 0.00 0.00 0.00 2.32
369 372 6.194796 TGCTTCAAACTAGGATGCAATAAC 57.805 37.500 0.00 0.00 40.91 1.89
386 389 2.125552 CGGCGACCTCATGCTTCA 60.126 61.111 0.00 0.00 0.00 3.02
395 398 4.699522 GGCTCAAACCGGCGACCT 62.700 66.667 9.30 0.00 0.00 3.85
413 416 4.919168 TGTGTAGCATTACTCGTGTGTTAC 59.081 41.667 0.00 0.00 32.39 2.50
414 417 5.123805 TGTGTAGCATTACTCGTGTGTTA 57.876 39.130 0.00 0.00 0.00 2.41
415 418 3.985008 TGTGTAGCATTACTCGTGTGTT 58.015 40.909 0.00 0.00 0.00 3.32
416 419 3.653539 TGTGTAGCATTACTCGTGTGT 57.346 42.857 0.00 0.00 0.00 3.72
417 420 5.099575 TGTATGTGTAGCATTACTCGTGTG 58.900 41.667 0.00 0.00 38.94 3.82
418 421 5.319140 TGTATGTGTAGCATTACTCGTGT 57.681 39.130 0.00 0.00 38.94 4.49
419 422 7.648112 ACTTATGTATGTGTAGCATTACTCGTG 59.352 37.037 0.00 0.00 38.94 4.35
420 423 7.713750 ACTTATGTATGTGTAGCATTACTCGT 58.286 34.615 0.00 0.00 38.94 4.18
421 424 8.575565 AACTTATGTATGTGTAGCATTACTCG 57.424 34.615 0.00 0.00 38.94 4.18
427 430 9.056005 CCATGTAAACTTATGTATGTGTAGCAT 57.944 33.333 0.00 0.00 41.42 3.79
428 431 7.497579 CCCATGTAAACTTATGTATGTGTAGCA 59.502 37.037 0.00 0.00 0.00 3.49
429 432 7.497909 ACCCATGTAAACTTATGTATGTGTAGC 59.502 37.037 0.00 0.00 0.00 3.58
430 433 8.958119 ACCCATGTAAACTTATGTATGTGTAG 57.042 34.615 0.00 0.00 0.00 2.74
431 434 9.742144 AAACCCATGTAAACTTATGTATGTGTA 57.258 29.630 0.00 0.00 0.00 2.90
432 435 8.644374 AAACCCATGTAAACTTATGTATGTGT 57.356 30.769 0.00 0.00 0.00 3.72
433 436 8.735315 TGAAACCCATGTAAACTTATGTATGTG 58.265 33.333 0.00 0.00 0.00 3.21
434 437 8.736244 GTGAAACCCATGTAAACTTATGTATGT 58.264 33.333 0.00 0.00 0.00 2.29
435 438 8.735315 TGTGAAACCCATGTAAACTTATGTATG 58.265 33.333 0.00 0.00 34.36 2.39
436 439 8.871629 TGTGAAACCCATGTAAACTTATGTAT 57.128 30.769 0.00 0.00 34.36 2.29
437 440 8.693120 TTGTGAAACCCATGTAAACTTATGTA 57.307 30.769 0.00 0.00 34.36 2.29
438 441 7.589958 TTGTGAAACCCATGTAAACTTATGT 57.410 32.000 0.00 0.00 34.36 2.29
439 442 7.923344 TGTTTGTGAAACCCATGTAAACTTATG 59.077 33.333 0.00 0.00 40.67 1.90
440 443 8.012957 TGTTTGTGAAACCCATGTAAACTTAT 57.987 30.769 0.00 0.00 40.67 1.73
441 444 7.339721 TCTGTTTGTGAAACCCATGTAAACTTA 59.660 33.333 0.00 0.00 40.67 2.24
442 445 6.153680 TCTGTTTGTGAAACCCATGTAAACTT 59.846 34.615 0.00 0.00 40.67 2.66
443 446 5.654650 TCTGTTTGTGAAACCCATGTAAACT 59.345 36.000 0.00 0.00 40.67 2.66
444 447 5.897050 TCTGTTTGTGAAACCCATGTAAAC 58.103 37.500 0.00 0.00 40.67 2.01
445 448 6.462207 CCATCTGTTTGTGAAACCCATGTAAA 60.462 38.462 0.00 0.00 40.67 2.01
446 449 5.010516 CCATCTGTTTGTGAAACCCATGTAA 59.989 40.000 0.00 0.00 40.67 2.41
447 450 4.522405 CCATCTGTTTGTGAAACCCATGTA 59.478 41.667 0.00 0.00 40.67 2.29
448 451 3.321682 CCATCTGTTTGTGAAACCCATGT 59.678 43.478 0.00 0.00 40.67 3.21
449 452 3.306225 CCCATCTGTTTGTGAAACCCATG 60.306 47.826 0.00 0.00 40.67 3.66
450 453 2.899256 CCCATCTGTTTGTGAAACCCAT 59.101 45.455 0.00 0.00 40.67 4.00
451 454 2.315176 CCCATCTGTTTGTGAAACCCA 58.685 47.619 0.00 0.00 40.67 4.51
452 455 2.316108 ACCCATCTGTTTGTGAAACCC 58.684 47.619 0.00 0.00 40.67 4.11
453 456 3.132111 ACAACCCATCTGTTTGTGAAACC 59.868 43.478 0.00 0.00 40.67 3.27
454 457 4.111916 CACAACCCATCTGTTTGTGAAAC 58.888 43.478 7.74 0.00 41.73 2.78
455 458 4.019858 TCACAACCCATCTGTTTGTGAAA 58.980 39.130 12.68 0.00 35.42 2.69
456 459 3.625853 TCACAACCCATCTGTTTGTGAA 58.374 40.909 12.68 0.00 35.42 3.18
457 460 3.289407 TCACAACCCATCTGTTTGTGA 57.711 42.857 11.36 11.36 35.69 3.58
458 461 4.300803 CAATCACAACCCATCTGTTTGTG 58.699 43.478 7.25 7.25 32.97 3.33
459 462 3.321682 CCAATCACAACCCATCTGTTTGT 59.678 43.478 0.00 0.00 0.00 2.83
460 463 3.573538 TCCAATCACAACCCATCTGTTTG 59.426 43.478 0.00 0.00 0.00 2.93
461 464 3.828451 CTCCAATCACAACCCATCTGTTT 59.172 43.478 0.00 0.00 0.00 2.83
462 465 3.424703 CTCCAATCACAACCCATCTGTT 58.575 45.455 0.00 0.00 0.00 3.16
463 466 2.291153 CCTCCAATCACAACCCATCTGT 60.291 50.000 0.00 0.00 0.00 3.41
464 467 2.291153 ACCTCCAATCACAACCCATCTG 60.291 50.000 0.00 0.00 0.00 2.90
465 468 1.995542 ACCTCCAATCACAACCCATCT 59.004 47.619 0.00 0.00 0.00 2.90
466 469 2.514458 ACCTCCAATCACAACCCATC 57.486 50.000 0.00 0.00 0.00 3.51
467 470 2.999185 AACCTCCAATCACAACCCAT 57.001 45.000 0.00 0.00 0.00 4.00
468 471 3.499563 CCTTAACCTCCAATCACAACCCA 60.500 47.826 0.00 0.00 0.00 4.51
469 472 3.089284 CCTTAACCTCCAATCACAACCC 58.911 50.000 0.00 0.00 0.00 4.11
470 473 3.089284 CCCTTAACCTCCAATCACAACC 58.911 50.000 0.00 0.00 0.00 3.77
471 474 3.089284 CCCCTTAACCTCCAATCACAAC 58.911 50.000 0.00 0.00 0.00 3.32
472 475 2.990284 TCCCCTTAACCTCCAATCACAA 59.010 45.455 0.00 0.00 0.00 3.33
473 476 2.638325 TCCCCTTAACCTCCAATCACA 58.362 47.619 0.00 0.00 0.00 3.58
474 477 3.621558 CTTCCCCTTAACCTCCAATCAC 58.378 50.000 0.00 0.00 0.00 3.06
475 478 2.580783 CCTTCCCCTTAACCTCCAATCA 59.419 50.000 0.00 0.00 0.00 2.57
476 479 2.850568 TCCTTCCCCTTAACCTCCAATC 59.149 50.000 0.00 0.00 0.00 2.67
477 480 2.853077 CTCCTTCCCCTTAACCTCCAAT 59.147 50.000 0.00 0.00 0.00 3.16
478 481 2.275466 CTCCTTCCCCTTAACCTCCAA 58.725 52.381 0.00 0.00 0.00 3.53
479 482 1.557188 CCTCCTTCCCCTTAACCTCCA 60.557 57.143 0.00 0.00 0.00 3.86
480 483 1.214217 CCTCCTTCCCCTTAACCTCC 58.786 60.000 0.00 0.00 0.00 4.30
481 484 1.560146 CACCTCCTTCCCCTTAACCTC 59.440 57.143 0.00 0.00 0.00 3.85
482 485 1.670059 CACCTCCTTCCCCTTAACCT 58.330 55.000 0.00 0.00 0.00 3.50
483 486 0.034380 GCACCTCCTTCCCCTTAACC 60.034 60.000 0.00 0.00 0.00 2.85
484 487 0.034380 GGCACCTCCTTCCCCTTAAC 60.034 60.000 0.00 0.00 0.00 2.01
485 488 2.394514 GGCACCTCCTTCCCCTTAA 58.605 57.895 0.00 0.00 0.00 1.85
486 489 4.164264 GGCACCTCCTTCCCCTTA 57.836 61.111 0.00 0.00 0.00 2.69
499 502 0.831711 ATTTTCACAGGGGTGGGCAC 60.832 55.000 0.00 0.00 45.32 5.01
500 503 0.541764 GATTTTCACAGGGGTGGGCA 60.542 55.000 0.00 0.00 45.32 5.36
501 504 0.541764 TGATTTTCACAGGGGTGGGC 60.542 55.000 0.00 0.00 45.32 5.36
502 505 1.549203 CTGATTTTCACAGGGGTGGG 58.451 55.000 0.00 0.00 45.32 4.61
509 512 2.307098 ACTCCCTCCCTGATTTTCACAG 59.693 50.000 0.00 0.00 35.43 3.66
510 513 2.040278 CACTCCCTCCCTGATTTTCACA 59.960 50.000 0.00 0.00 0.00 3.58
511 514 2.619074 CCACTCCCTCCCTGATTTTCAC 60.619 54.545 0.00 0.00 0.00 3.18
512 515 1.635487 CCACTCCCTCCCTGATTTTCA 59.365 52.381 0.00 0.00 0.00 2.69
513 516 1.636003 ACCACTCCCTCCCTGATTTTC 59.364 52.381 0.00 0.00 0.00 2.29
514 517 1.760405 ACCACTCCCTCCCTGATTTT 58.240 50.000 0.00 0.00 0.00 1.82
515 518 1.760405 AACCACTCCCTCCCTGATTT 58.240 50.000 0.00 0.00 0.00 2.17
516 519 2.225908 ACTAACCACTCCCTCCCTGATT 60.226 50.000 0.00 0.00 0.00 2.57
517 520 1.366435 ACTAACCACTCCCTCCCTGAT 59.634 52.381 0.00 0.00 0.00 2.90
518 521 0.790993 ACTAACCACTCCCTCCCTGA 59.209 55.000 0.00 0.00 0.00 3.86
519 522 1.657804 AACTAACCACTCCCTCCCTG 58.342 55.000 0.00 0.00 0.00 4.45
520 523 2.658489 TCTAACTAACCACTCCCTCCCT 59.342 50.000 0.00 0.00 0.00 4.20
521 524 3.111741 TCTAACTAACCACTCCCTCCC 57.888 52.381 0.00 0.00 0.00 4.30
522 525 4.776308 TCTTTCTAACTAACCACTCCCTCC 59.224 45.833 0.00 0.00 0.00 4.30
523 526 5.997384 TCTTTCTAACTAACCACTCCCTC 57.003 43.478 0.00 0.00 0.00 4.30
524 527 6.758806 TTTCTTTCTAACTAACCACTCCCT 57.241 37.500 0.00 0.00 0.00 4.20
525 528 7.812690 TTTTTCTTTCTAACTAACCACTCCC 57.187 36.000 0.00 0.00 0.00 4.30
546 549 7.260603 GCAATTACATGCTGACTAGGATTTTT 58.739 34.615 0.00 0.00 43.06 1.94
547 550 6.458751 CGCAATTACATGCTGACTAGGATTTT 60.459 38.462 0.00 0.00 44.21 1.82
548 551 5.008019 CGCAATTACATGCTGACTAGGATTT 59.992 40.000 0.00 0.00 44.21 2.17
549 552 4.512944 CGCAATTACATGCTGACTAGGATT 59.487 41.667 0.00 0.00 44.21 3.01
550 553 4.060900 CGCAATTACATGCTGACTAGGAT 58.939 43.478 0.00 0.00 44.21 3.24
551 554 3.118775 ACGCAATTACATGCTGACTAGGA 60.119 43.478 0.00 0.00 44.21 2.94
552 555 3.001634 CACGCAATTACATGCTGACTAGG 59.998 47.826 0.00 0.00 44.21 3.02
553 556 3.618594 ACACGCAATTACATGCTGACTAG 59.381 43.478 0.00 0.00 44.21 2.57
554 557 3.595173 ACACGCAATTACATGCTGACTA 58.405 40.909 0.00 0.00 44.21 2.59
555 558 2.426522 ACACGCAATTACATGCTGACT 58.573 42.857 0.00 0.00 44.21 3.41
556 559 2.900122 ACACGCAATTACATGCTGAC 57.100 45.000 0.00 0.00 44.21 3.51
557 560 4.000325 AGTTACACGCAATTACATGCTGA 59.000 39.130 0.00 0.00 44.21 4.26
558 561 4.093408 AGAGTTACACGCAATTACATGCTG 59.907 41.667 0.00 0.00 44.21 4.41
559 562 4.253685 AGAGTTACACGCAATTACATGCT 58.746 39.130 0.00 0.00 44.21 3.79
560 563 4.600012 AGAGTTACACGCAATTACATGC 57.400 40.909 0.00 0.00 42.94 4.06
561 564 6.370593 ACAAAGAGTTACACGCAATTACATG 58.629 36.000 0.00 0.00 0.00 3.21
562 565 6.554334 ACAAAGAGTTACACGCAATTACAT 57.446 33.333 0.00 0.00 0.00 2.29
563 566 5.994887 ACAAAGAGTTACACGCAATTACA 57.005 34.783 0.00 0.00 0.00 2.41
564 567 7.515643 ACATACAAAGAGTTACACGCAATTAC 58.484 34.615 0.00 0.00 0.00 1.89
565 568 7.661127 ACATACAAAGAGTTACACGCAATTA 57.339 32.000 0.00 0.00 0.00 1.40
566 569 6.554334 ACATACAAAGAGTTACACGCAATT 57.446 33.333 0.00 0.00 0.00 2.32
567 570 6.554334 AACATACAAAGAGTTACACGCAAT 57.446 33.333 0.00 0.00 0.00 3.56
568 571 5.994887 AACATACAAAGAGTTACACGCAA 57.005 34.783 0.00 0.00 0.00 4.85
569 572 5.994887 AAACATACAAAGAGTTACACGCA 57.005 34.783 0.00 0.00 0.00 5.24
570 573 6.013689 GCTAAACATACAAAGAGTTACACGC 58.986 40.000 0.00 0.00 0.00 5.34
571 574 7.112528 TGCTAAACATACAAAGAGTTACACG 57.887 36.000 0.00 0.00 0.00 4.49
576 579 8.612619 CCGATAATGCTAAACATACAAAGAGTT 58.387 33.333 0.00 0.00 38.34 3.01
577 580 7.769044 ACCGATAATGCTAAACATACAAAGAGT 59.231 33.333 0.00 0.00 38.34 3.24
578 581 8.142994 ACCGATAATGCTAAACATACAAAGAG 57.857 34.615 0.00 0.00 38.34 2.85
579 582 9.602568 TTACCGATAATGCTAAACATACAAAGA 57.397 29.630 0.00 0.00 38.34 2.52
580 583 9.646336 GTTACCGATAATGCTAAACATACAAAG 57.354 33.333 0.00 0.00 38.34 2.77
581 584 9.163899 TGTTACCGATAATGCTAAACATACAAA 57.836 29.630 0.00 0.00 38.34 2.83
582 585 8.605746 GTGTTACCGATAATGCTAAACATACAA 58.394 33.333 0.00 0.00 38.34 2.41
583 586 7.764901 TGTGTTACCGATAATGCTAAACATACA 59.235 33.333 0.00 0.00 38.34 2.29
584 587 8.060090 GTGTGTTACCGATAATGCTAAACATAC 58.940 37.037 0.00 0.00 38.34 2.39
585 588 7.764901 TGTGTGTTACCGATAATGCTAAACATA 59.235 33.333 0.00 0.00 38.34 2.29
586 589 6.596106 TGTGTGTTACCGATAATGCTAAACAT 59.404 34.615 0.00 0.00 42.30 2.71
587 590 5.932883 TGTGTGTTACCGATAATGCTAAACA 59.067 36.000 0.00 0.00 0.00 2.83
588 591 6.245724 GTGTGTGTTACCGATAATGCTAAAC 58.754 40.000 0.00 0.00 0.00 2.01
589 592 5.352016 GGTGTGTGTTACCGATAATGCTAAA 59.648 40.000 0.00 0.00 0.00 1.85
590 593 4.871557 GGTGTGTGTTACCGATAATGCTAA 59.128 41.667 0.00 0.00 0.00 3.09
591 594 4.435425 GGTGTGTGTTACCGATAATGCTA 58.565 43.478 0.00 0.00 0.00 3.49
592 595 3.267483 GGTGTGTGTTACCGATAATGCT 58.733 45.455 0.00 0.00 0.00 3.79
593 596 2.353579 GGGTGTGTGTTACCGATAATGC 59.646 50.000 0.00 0.00 39.14 3.56
594 597 3.372822 GTGGGTGTGTGTTACCGATAATG 59.627 47.826 0.00 0.00 39.14 1.90
595 598 3.008157 TGTGGGTGTGTGTTACCGATAAT 59.992 43.478 0.00 0.00 39.14 1.28
596 599 2.367894 TGTGGGTGTGTGTTACCGATAA 59.632 45.455 0.00 0.00 39.14 1.75
597 600 1.969208 TGTGGGTGTGTGTTACCGATA 59.031 47.619 0.00 0.00 39.14 2.92
598 601 0.759959 TGTGGGTGTGTGTTACCGAT 59.240 50.000 0.00 0.00 39.14 4.18
599 602 0.179078 GTGTGGGTGTGTGTTACCGA 60.179 55.000 0.00 0.00 39.14 4.69
600 603 0.179067 AGTGTGGGTGTGTGTTACCG 60.179 55.000 0.00 0.00 39.14 4.02
601 604 2.047002 AAGTGTGGGTGTGTGTTACC 57.953 50.000 0.00 0.00 37.48 2.85
629 632 9.237846 CATCTACTCTTTTCTGTTTTCCAAAAC 57.762 33.333 7.81 7.81 46.40 2.43
635 638 6.710744 TGACCCATCTACTCTTTTCTGTTTTC 59.289 38.462 0.00 0.00 0.00 2.29
715 718 0.882042 CTATTCGGCGCTGAAGGCAT 60.882 55.000 32.94 20.55 41.91 4.40
751 754 4.465512 CGGTGCATGCTGGCGAAC 62.466 66.667 20.33 7.16 36.28 3.95
813 901 1.726248 GCAAAATAAGCAAACAGGCCG 59.274 47.619 0.00 0.00 0.00 6.13
815 903 1.726248 CGGCAAAATAAGCAAACAGGC 59.274 47.619 0.00 0.00 0.00 4.85
817 905 2.155539 GCACGGCAAAATAAGCAAACAG 59.844 45.455 0.00 0.00 0.00 3.16
819 907 1.459209 GGCACGGCAAAATAAGCAAAC 59.541 47.619 0.00 0.00 0.00 2.93
820 908 1.342819 AGGCACGGCAAAATAAGCAAA 59.657 42.857 0.00 0.00 0.00 3.68
821 909 0.965439 AGGCACGGCAAAATAAGCAA 59.035 45.000 0.00 0.00 0.00 3.91
823 911 0.458370 CCAGGCACGGCAAAATAAGC 60.458 55.000 0.00 0.00 0.00 3.09
824 912 1.135402 GTCCAGGCACGGCAAAATAAG 60.135 52.381 0.00 0.00 0.00 1.73
825 913 0.885196 GTCCAGGCACGGCAAAATAA 59.115 50.000 0.00 0.00 0.00 1.40
826 914 0.963355 GGTCCAGGCACGGCAAAATA 60.963 55.000 0.00 0.00 0.00 1.40
827 915 2.275380 GGTCCAGGCACGGCAAAAT 61.275 57.895 0.00 0.00 0.00 1.82
828 916 2.909965 GGTCCAGGCACGGCAAAA 60.910 61.111 0.00 0.00 0.00 2.44
861 949 2.741759 AATTCATTTTGGGACCGTGC 57.258 45.000 0.00 0.00 0.00 5.34
862 950 3.584834 GGAAATTCATTTTGGGACCGTG 58.415 45.455 0.00 0.00 0.00 4.94
863 951 2.565391 GGGAAATTCATTTTGGGACCGT 59.435 45.455 0.00 0.00 0.00 4.83
865 953 2.909662 TGGGGAAATTCATTTTGGGACC 59.090 45.455 0.00 0.00 0.00 4.46
926 1321 0.389948 CTCGTCGGGGTTCCAAAGAG 60.390 60.000 0.00 0.00 0.00 2.85
946 1343 4.416738 GGCTTGCTCCTTCGGCCT 62.417 66.667 0.00 0.00 39.68 5.19
951 1362 4.549793 GCTAGGGCTTGCTCCTTC 57.450 61.111 7.69 0.00 35.92 3.46
983 1394 1.078426 ATTTGTTCGGCGAGGAGGG 60.078 57.895 10.46 0.00 0.00 4.30
985 1396 0.721718 GACATTTGTTCGGCGAGGAG 59.278 55.000 10.46 1.05 0.00 3.69
986 1397 0.672401 GGACATTTGTTCGGCGAGGA 60.672 55.000 10.46 0.00 0.00 3.71
1704 2140 4.918278 TCCACGTCCCCGTCACCA 62.918 66.667 0.00 0.00 46.28 4.17
1919 2356 3.989817 CGAAAAAGGGCAAGGAAAATCAG 59.010 43.478 0.00 0.00 0.00 2.90
1921 2358 3.990092 ACGAAAAAGGGCAAGGAAAATC 58.010 40.909 0.00 0.00 0.00 2.17
1922 2359 4.415881 AACGAAAAAGGGCAAGGAAAAT 57.584 36.364 0.00 0.00 0.00 1.82
1923 2360 3.897141 AACGAAAAAGGGCAAGGAAAA 57.103 38.095 0.00 0.00 0.00 2.29
1933 2370 7.979115 TCAATTACAGTTGAAACGAAAAAGG 57.021 32.000 0.00 0.00 35.31 3.11
1939 2376 7.925993 ACTGAAATCAATTACAGTTGAAACGA 58.074 30.769 0.00 0.00 41.09 3.85
1940 2377 8.560576 AACTGAAATCAATTACAGTTGAAACG 57.439 30.769 0.00 0.00 46.87 3.60
1983 2422 0.906066 TCACATTGGGCCGTAAGCTA 59.094 50.000 0.00 0.00 43.05 3.32
1986 2425 2.364632 TCATTCACATTGGGCCGTAAG 58.635 47.619 0.00 0.00 0.00 2.34
1999 2438 4.913376 ACATGCTTTTCGCTATCATTCAC 58.087 39.130 0.00 0.00 40.11 3.18
2005 2444 5.977725 TCTACAGTACATGCTTTTCGCTATC 59.022 40.000 0.00 0.00 40.11 2.08
2026 2466 5.536538 ACTCCACGCATATTCAAGAGATCTA 59.463 40.000 0.00 0.00 0.00 1.98
2033 2473 4.870426 AGTTACACTCCACGCATATTCAAG 59.130 41.667 0.00 0.00 0.00 3.02
2128 2599 7.275888 TCAACATGATGCTCTGTAACTTTTT 57.724 32.000 0.00 0.00 0.00 1.94
2137 2608 4.909894 CATCAGTTCAACATGATGCTCTG 58.090 43.478 13.60 15.49 44.43 3.35
2144 2615 6.427853 CCTTGTTCTACATCAGTTCAACATGA 59.572 38.462 0.00 0.00 31.82 3.07
2158 2630 0.764890 AGCTGTGCCCTTGTTCTACA 59.235 50.000 0.00 0.00 0.00 2.74
2159 2631 1.270839 TGAGCTGTGCCCTTGTTCTAC 60.271 52.381 0.00 0.00 0.00 2.59
2169 2641 1.466360 CGCTACAATTTGAGCTGTGCC 60.466 52.381 2.79 0.00 36.50 5.01
2185 2657 5.310720 ACATGATTATATGCTCGTCGCTA 57.689 39.130 0.00 0.00 40.11 4.26
2186 2658 4.179926 ACATGATTATATGCTCGTCGCT 57.820 40.909 0.00 0.00 40.11 4.93
2187 2659 4.910746 AACATGATTATATGCTCGTCGC 57.089 40.909 0.00 0.00 39.77 5.19
2188 2660 8.864024 AGAATTAACATGATTATATGCTCGTCG 58.136 33.333 0.00 0.00 0.00 5.12
2189 2661 9.964253 CAGAATTAACATGATTATATGCTCGTC 57.036 33.333 0.00 0.00 0.00 4.20
2190 2662 9.710900 TCAGAATTAACATGATTATATGCTCGT 57.289 29.630 0.00 0.00 0.00 4.18
2191 2663 9.964253 GTCAGAATTAACATGATTATATGCTCG 57.036 33.333 0.00 0.00 0.00 5.03
2202 2674 9.996554 TTCAGTAAAGAGTCAGAATTAACATGA 57.003 29.630 0.00 0.00 0.00 3.07
2205 2677 9.219603 CCATTCAGTAAAGAGTCAGAATTAACA 57.780 33.333 0.00 0.00 0.00 2.41
2206 2678 8.669243 CCCATTCAGTAAAGAGTCAGAATTAAC 58.331 37.037 0.00 0.00 0.00 2.01
2212 2687 4.020218 CACCCCATTCAGTAAAGAGTCAGA 60.020 45.833 0.00 0.00 0.00 3.27
2240 2716 8.870879 ACGAGTCAGAAAGTTTAGCATTTATAC 58.129 33.333 0.00 0.00 0.00 1.47
2251 2727 9.052759 ACATTTAACATACGAGTCAGAAAGTTT 57.947 29.630 0.00 0.00 0.00 2.66
2252 2728 8.603242 ACATTTAACATACGAGTCAGAAAGTT 57.397 30.769 0.00 0.00 0.00 2.66
2265 2741 7.584987 AGACAGCAAACAGACATTTAACATAC 58.415 34.615 0.00 0.00 0.00 2.39
2284 2760 2.029290 TGTACCCGAAAGAGAAGACAGC 60.029 50.000 0.00 0.00 0.00 4.40
2317 2793 6.409349 GGCTCTACAATTTCTAACCCCACTAT 60.409 42.308 0.00 0.00 0.00 2.12
2351 2827 7.397192 ACTTCAAAGTATATGCCCAAGATGTTT 59.603 33.333 0.00 0.00 37.52 2.83
2521 2998 2.655090 TGGAAAGCAGACATGTTCCA 57.345 45.000 10.07 10.07 0.00 3.53
2782 3267 2.955660 CAAGGCAAGTGAAGGGTTTACA 59.044 45.455 0.00 0.00 0.00 2.41
2794 3279 8.752005 TTATGATAATAAGCTTCAAGGCAAGT 57.248 30.769 0.00 0.00 34.17 3.16
2852 3337 6.038161 CACTGAGTTGTGTCAAGGAACAAATA 59.962 38.462 0.00 0.00 37.99 1.40
2854 3339 4.155826 CACTGAGTTGTGTCAAGGAACAAA 59.844 41.667 0.00 0.00 37.99 2.83


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

AutoCloner maintained by Alex Coulton.