Multiple sequence alignment - TraesCS7D01G352100

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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 TraesCS7D01G352100 chr7D 100.000 2417 0 0 1 2417 452976946 452979362 0.000000e+00 4464.0
1 TraesCS7D01G352100 chr7D 85.778 225 26 3 1 219 451886367 451886143 1.440000e-57 233.0
2 TraesCS7D01G352100 chr7D 97.674 43 1 0 2375 2417 623843762 623843804 9.270000e-10 75.0
3 TraesCS7D01G352100 chr7B 91.511 483 22 8 1 464 476220068 476220550 0.000000e+00 647.0
4 TraesCS7D01G352100 chr7B 85.941 505 24 20 1290 1772 476220547 476221026 1.670000e-136 496.0
5 TraesCS7D01G352100 chr7B 91.385 325 13 4 1958 2281 476221027 476221337 4.770000e-117 431.0
6 TraesCS7D01G352100 chr7B 84.889 225 28 3 1 219 474282169 474281945 3.130000e-54 222.0
7 TraesCS7D01G352100 chr7A 87.082 449 51 6 1048 1495 544249289 544248847 3.590000e-138 501.0
8 TraesCS7D01G352100 chr7A 89.431 369 33 3 1763 2130 544248290 544247927 6.090000e-126 460.0
9 TraesCS7D01G352100 chr7A 86.730 422 47 5 1 413 544255600 544255179 6.090000e-126 460.0
10 TraesCS7D01G352100 chr7A 85.381 472 36 14 607 1052 544255147 544254683 2.190000e-125 459.0
11 TraesCS7D01G352100 chr7A 84.444 225 29 3 1 219 545605793 545606017 1.460000e-52 217.0
12 TraesCS7D01G352100 chr6A 83.761 234 30 5 1 227 7370156 7369924 5.230000e-52 215.0
13 TraesCS7D01G352100 chr6D 81.974 233 36 3 1 227 7456366 7456134 2.450000e-45 193.0
14 TraesCS7D01G352100 chr6D 78.723 141 26 3 2280 2417 329963351 329963212 9.200000e-15 91.6
15 TraesCS7D01G352100 chr5A 87.255 102 13 0 2280 2381 454441994 454441893 1.520000e-22 117.0
16 TraesCS7D01G352100 chr2A 84.112 107 14 2 2275 2381 723849709 723849812 1.530000e-17 100.0
17 TraesCS7D01G352100 chr2A 79.137 139 28 1 2280 2417 382326154 382326016 7.110000e-16 95.3
18 TraesCS7D01G352100 chr4B 83.333 102 15 1 2280 2379 614717816 614717917 2.560000e-15 93.5
19 TraesCS7D01G352100 chr3D 97.674 43 1 0 2375 2417 105245520 105245562 9.270000e-10 75.0
20 TraesCS7D01G352100 chr3D 97.674 43 1 0 2375 2417 105272266 105272308 9.270000e-10 75.0
21 TraesCS7D01G352100 chr1B 97.674 43 1 0 2375 2417 161987978 161987936 9.270000e-10 75.0
22 TraesCS7D01G352100 chr2D 92.000 50 4 0 2368 2417 325346265 325346216 1.200000e-08 71.3
23 TraesCS7D01G352100 chr5D 88.889 54 4 2 2364 2417 425038280 425038331 5.580000e-07 65.8
24 TraesCS7D01G352100 chr3B 87.931 58 3 4 2362 2417 652492093 652492148 5.580000e-07 65.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G352100 chr7D 452976946 452979362 2416 False 4464.000000 4464 100.000000 1 2417 1 chr7D.!!$F1 2416
1 TraesCS7D01G352100 chr7B 476220068 476221337 1269 False 524.666667 647 89.612333 1 2281 3 chr7B.!!$F1 2280
2 TraesCS7D01G352100 chr7A 544247927 544249289 1362 True 480.500000 501 88.256500 1048 2130 2 chr7A.!!$R1 1082
3 TraesCS7D01G352100 chr7A 544254683 544255600 917 True 459.500000 460 86.055500 1 1052 2 chr7A.!!$R2 1051

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
496 525 0.101759 CACCACAGCAGCATATTGCC 59.898 55.0 0.0 0.0 46.52 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2284 2705 0.105658 TAAGAGGCCCGGCTGTAGAT 60.106 55.0 9.86 0.0 0.0 1.98 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
176 189 2.488153 GTTCTGGTGTTGTTAGGGATGC 59.512 50.000 0.00 0.00 0.00 3.91
255 271 1.211212 TGTCCCGATAGAAGACCGAGA 59.789 52.381 0.00 0.00 38.09 4.04
320 336 3.204827 CCTGGAAAGGCGATGGCG 61.205 66.667 0.00 0.00 41.24 5.69
333 352 0.855349 GATGGCGACGATGATGACAC 59.145 55.000 0.00 0.00 0.00 3.67
336 355 1.874019 GCGACGATGATGACACGCT 60.874 57.895 0.00 0.00 42.19 5.07
375 394 4.096681 TCTCAAGGTAATCTCCAGCAAGA 58.903 43.478 0.00 0.00 0.00 3.02
395 418 2.472059 CCGATTCGGCCACCACATG 61.472 63.158 12.95 0.00 41.17 3.21
402 425 1.978617 GGCCACCACATGACCCTTG 60.979 63.158 0.00 0.00 0.00 3.61
416 439 1.302271 CCTTGTCAGCAGCAGCAGA 60.302 57.895 3.17 0.00 45.49 4.26
417 440 0.677098 CCTTGTCAGCAGCAGCAGAT 60.677 55.000 3.17 0.00 45.49 2.90
427 456 3.188011 CAGCAGATGCAGTGCCAG 58.812 61.111 17.87 9.19 45.16 4.85
442 471 1.561076 TGCCAGTCCATGCTTCAGTAT 59.439 47.619 0.00 0.00 0.00 2.12
443 472 2.025981 TGCCAGTCCATGCTTCAGTATT 60.026 45.455 0.00 0.00 0.00 1.89
444 473 2.357009 GCCAGTCCATGCTTCAGTATTG 59.643 50.000 0.00 0.00 0.00 1.90
445 474 2.357009 CCAGTCCATGCTTCAGTATTGC 59.643 50.000 0.00 0.00 0.00 3.56
446 475 3.011818 CAGTCCATGCTTCAGTATTGCA 58.988 45.455 0.00 0.00 41.13 4.08
447 476 3.630769 CAGTCCATGCTTCAGTATTGCAT 59.369 43.478 0.00 0.00 46.74 3.96
452 481 4.627611 ATGCTTCAGTATTGCATGACAC 57.372 40.909 0.00 0.00 44.48 3.67
453 482 2.416202 TGCTTCAGTATTGCATGACACG 59.584 45.455 0.00 0.00 0.00 4.49
454 483 2.223112 GCTTCAGTATTGCATGACACGG 60.223 50.000 0.00 0.00 0.00 4.94
455 484 2.022764 TCAGTATTGCATGACACGGG 57.977 50.000 0.00 0.00 0.00 5.28
456 485 1.552792 TCAGTATTGCATGACACGGGA 59.447 47.619 0.00 0.00 0.00 5.14
457 486 2.027653 TCAGTATTGCATGACACGGGAA 60.028 45.455 0.00 0.00 0.00 3.97
458 487 2.945008 CAGTATTGCATGACACGGGAAT 59.055 45.455 0.00 2.12 0.00 3.01
459 488 3.002656 CAGTATTGCATGACACGGGAATC 59.997 47.826 0.00 0.00 0.00 2.52
460 489 1.016627 ATTGCATGACACGGGAATCG 58.983 50.000 0.00 0.00 45.88 3.34
461 490 1.643868 TTGCATGACACGGGAATCGC 61.644 55.000 0.00 0.00 43.89 4.58
462 491 2.106074 GCATGACACGGGAATCGCA 61.106 57.895 0.00 0.00 43.89 5.10
463 492 1.643868 GCATGACACGGGAATCGCAA 61.644 55.000 0.00 0.00 43.89 4.85
464 493 0.801872 CATGACACGGGAATCGCAAA 59.198 50.000 0.00 0.00 43.89 3.68
465 494 1.086696 ATGACACGGGAATCGCAAAG 58.913 50.000 0.00 0.00 43.89 2.77
466 495 1.134694 GACACGGGAATCGCAAAGC 59.865 57.895 0.00 0.00 43.89 3.51
467 496 2.253414 GACACGGGAATCGCAAAGCC 62.253 60.000 0.00 0.00 43.89 4.35
468 497 2.750237 ACGGGAATCGCAAAGCCC 60.750 61.111 0.00 0.00 43.89 5.19
469 498 2.749839 CGGGAATCGCAAAGCCCA 60.750 61.111 0.00 0.00 40.71 5.36
470 499 2.885113 GGGAATCGCAAAGCCCAC 59.115 61.111 0.00 0.00 40.39 4.61
471 500 1.678970 GGGAATCGCAAAGCCCACT 60.679 57.895 0.00 0.00 40.39 4.00
472 501 1.508088 GGAATCGCAAAGCCCACTG 59.492 57.895 0.00 0.00 0.00 3.66
473 502 1.508088 GAATCGCAAAGCCCACTGG 59.492 57.895 0.00 0.00 0.00 4.00
483 512 4.584518 CCCACTGGCAGCACCACA 62.585 66.667 15.89 0.00 46.36 4.17
484 513 2.981909 CCACTGGCAGCACCACAG 60.982 66.667 15.89 0.00 46.36 3.66
485 514 3.667282 CACTGGCAGCACCACAGC 61.667 66.667 15.89 0.00 46.36 4.40
486 515 4.193893 ACTGGCAGCACCACAGCA 62.194 61.111 15.89 0.00 46.36 4.41
487 516 3.362797 CTGGCAGCACCACAGCAG 61.363 66.667 0.00 0.00 46.36 4.24
490 519 3.371063 GCAGCACCACAGCAGCAT 61.371 61.111 0.00 0.00 45.12 3.79
491 520 2.042259 GCAGCACCACAGCAGCATA 61.042 57.895 0.00 0.00 45.12 3.14
492 521 1.381928 GCAGCACCACAGCAGCATAT 61.382 55.000 0.00 0.00 45.12 1.78
493 522 1.100510 CAGCACCACAGCAGCATATT 58.899 50.000 0.00 0.00 36.85 1.28
494 523 1.100510 AGCACCACAGCAGCATATTG 58.899 50.000 0.00 0.00 36.85 1.90
495 524 0.526954 GCACCACAGCAGCATATTGC 60.527 55.000 0.00 0.00 45.46 3.56
496 525 0.101759 CACCACAGCAGCATATTGCC 59.898 55.000 0.00 0.00 46.52 4.52
497 526 0.323633 ACCACAGCAGCATATTGCCA 60.324 50.000 0.00 0.00 46.52 4.92
498 527 1.037493 CCACAGCAGCATATTGCCAT 58.963 50.000 0.00 0.00 46.52 4.40
499 528 1.269569 CCACAGCAGCATATTGCCATG 60.270 52.381 0.00 0.00 46.52 3.66
504 533 4.667420 GCATATTGCCATGCCTGC 57.333 55.556 4.18 0.00 44.55 4.85
505 534 1.743391 GCATATTGCCATGCCTGCA 59.257 52.632 0.00 0.00 44.55 4.41
506 535 0.319555 GCATATTGCCATGCCTGCAG 60.320 55.000 6.78 6.78 44.55 4.41
507 536 0.319555 CATATTGCCATGCCTGCAGC 60.320 55.000 8.66 4.57 40.35 5.25
521 550 2.967397 CAGCATGCACAACCCCTG 59.033 61.111 21.98 2.32 0.00 4.45
522 551 1.604308 CAGCATGCACAACCCCTGA 60.604 57.895 21.98 0.00 0.00 3.86
523 552 1.604593 AGCATGCACAACCCCTGAC 60.605 57.895 21.98 0.00 0.00 3.51
524 553 1.604593 GCATGCACAACCCCTGACT 60.605 57.895 14.21 0.00 0.00 3.41
525 554 1.181098 GCATGCACAACCCCTGACTT 61.181 55.000 14.21 0.00 0.00 3.01
526 555 1.886222 GCATGCACAACCCCTGACTTA 60.886 52.381 14.21 0.00 0.00 2.24
527 556 1.812571 CATGCACAACCCCTGACTTAC 59.187 52.381 0.00 0.00 0.00 2.34
528 557 0.250124 TGCACAACCCCTGACTTACG 60.250 55.000 0.00 0.00 0.00 3.18
529 558 0.953960 GCACAACCCCTGACTTACGG 60.954 60.000 0.00 0.00 0.00 4.02
530 559 0.321298 CACAACCCCTGACTTACGGG 60.321 60.000 0.00 0.00 44.27 5.28
531 560 1.376812 CAACCCCTGACTTACGGGC 60.377 63.158 0.00 0.00 43.37 6.13
532 561 1.844289 AACCCCTGACTTACGGGCA 60.844 57.895 0.00 0.00 43.37 5.36
536 565 2.571757 CTGACTTACGGGCAGCGA 59.428 61.111 0.00 0.00 44.93 4.93
537 566 1.080093 CTGACTTACGGGCAGCGAA 60.080 57.895 0.00 0.00 44.93 4.70
538 567 1.352156 CTGACTTACGGGCAGCGAAC 61.352 60.000 0.00 0.00 44.93 3.95
539 568 2.431942 ACTTACGGGCAGCGAACG 60.432 61.111 0.00 1.74 0.00 3.95
540 569 3.849953 CTTACGGGCAGCGAACGC 61.850 66.667 11.31 11.31 42.33 4.84
541 570 4.666397 TTACGGGCAGCGAACGCA 62.666 61.111 20.66 0.00 44.88 5.24
551 580 3.485431 CGAACGCAGCCTGCTCAG 61.485 66.667 15.80 1.47 42.25 3.35
552 581 3.797546 GAACGCAGCCTGCTCAGC 61.798 66.667 15.80 0.00 42.25 4.26
553 582 4.631247 AACGCAGCCTGCTCAGCA 62.631 61.111 15.80 0.00 42.25 4.41
554 583 4.631247 ACGCAGCCTGCTCAGCAA 62.631 61.111 15.80 0.00 42.25 3.91
555 584 4.099170 CGCAGCCTGCTCAGCAAC 62.099 66.667 15.80 0.00 42.25 4.17
556 585 3.745803 GCAGCCTGCTCAGCAACC 61.746 66.667 10.04 0.00 40.96 3.77
557 586 3.060615 CAGCCTGCTCAGCAACCC 61.061 66.667 0.00 0.00 38.41 4.11
558 587 3.255397 AGCCTGCTCAGCAACCCT 61.255 61.111 0.00 0.00 38.41 4.34
559 588 1.920325 AGCCTGCTCAGCAACCCTA 60.920 57.895 0.00 0.00 38.41 3.53
560 589 1.746991 GCCTGCTCAGCAACCCTAC 60.747 63.158 0.00 0.00 38.41 3.18
561 590 1.986413 CCTGCTCAGCAACCCTACT 59.014 57.895 0.00 0.00 38.41 2.57
562 591 0.107945 CCTGCTCAGCAACCCTACTC 60.108 60.000 0.00 0.00 38.41 2.59
563 592 0.901124 CTGCTCAGCAACCCTACTCT 59.099 55.000 0.00 0.00 38.41 3.24
564 593 0.610174 TGCTCAGCAACCCTACTCTG 59.390 55.000 0.00 0.00 34.76 3.35
565 594 0.107945 GCTCAGCAACCCTACTCTGG 60.108 60.000 0.00 0.00 0.00 3.86
566 595 1.270907 CTCAGCAACCCTACTCTGGT 58.729 55.000 0.00 0.00 37.85 4.00
567 596 0.976641 TCAGCAACCCTACTCTGGTG 59.023 55.000 0.00 0.00 39.38 4.17
568 597 0.674895 CAGCAACCCTACTCTGGTGC 60.675 60.000 0.00 0.00 35.88 5.01
569 598 1.741770 GCAACCCTACTCTGGTGCG 60.742 63.158 0.00 0.00 35.88 5.34
570 599 1.741770 CAACCCTACTCTGGTGCGC 60.742 63.158 0.00 0.00 35.88 6.09
571 600 2.955881 AACCCTACTCTGGTGCGCC 61.956 63.158 10.11 10.11 35.88 6.53
572 601 4.162690 CCCTACTCTGGTGCGCCC 62.163 72.222 15.15 6.44 0.00 6.13
573 602 4.514577 CCTACTCTGGTGCGCCCG 62.515 72.222 15.15 7.79 35.15 6.13
574 603 3.449227 CTACTCTGGTGCGCCCGA 61.449 66.667 15.15 12.47 35.15 5.14
575 604 3.701604 CTACTCTGGTGCGCCCGAC 62.702 68.421 15.15 0.00 35.15 4.79
595 624 4.169696 CGGCGGTGGGCAATCCTA 62.170 66.667 0.00 0.00 46.16 2.94
596 625 2.515901 GGCGGTGGGCAATCCTAT 59.484 61.111 0.00 0.00 46.16 2.57
597 626 1.758592 GGCGGTGGGCAATCCTATA 59.241 57.895 0.00 0.00 46.16 1.31
598 627 0.605589 GGCGGTGGGCAATCCTATAC 60.606 60.000 0.00 0.00 46.16 1.47
599 628 0.949105 GCGGTGGGCAATCCTATACG 60.949 60.000 0.00 0.00 42.87 3.06
600 629 0.320421 CGGTGGGCAATCCTATACGG 60.320 60.000 0.00 0.00 36.20 4.02
601 630 0.605589 GGTGGGCAATCCTATACGGC 60.606 60.000 0.00 0.00 36.20 5.68
602 631 0.949105 GTGGGCAATCCTATACGGCG 60.949 60.000 4.80 4.80 36.20 6.46
603 632 1.375523 GGGCAATCCTATACGGCGG 60.376 63.158 13.24 0.00 0.00 6.13
604 633 1.370064 GGCAATCCTATACGGCGGT 59.630 57.895 13.24 1.39 0.00 5.68
605 634 0.949105 GGCAATCCTATACGGCGGTG 60.949 60.000 13.24 0.00 0.00 4.94
632 661 1.421268 GGGTCTGATGGCATGGTATCA 59.579 52.381 3.81 0.00 32.75 2.15
677 711 0.591170 CGTCCGTTTTGATGGTTGCT 59.409 50.000 0.00 0.00 0.00 3.91
679 713 2.661594 GTCCGTTTTGATGGTTGCTTC 58.338 47.619 0.00 0.00 0.00 3.86
684 718 1.243902 TTTGATGGTTGCTTCGTCCC 58.756 50.000 0.00 0.00 0.00 4.46
692 726 3.998672 GCTTCGTCCCACCCGTCA 61.999 66.667 0.00 0.00 0.00 4.35
712 746 7.362574 CCCGTCAATTCCATTGTTAGTTTGTAT 60.363 37.037 0.00 0.00 41.02 2.29
713 747 7.484641 CCGTCAATTCCATTGTTAGTTTGTATG 59.515 37.037 0.00 0.00 41.02 2.39
714 748 8.020819 CGTCAATTCCATTGTTAGTTTGTATGT 58.979 33.333 0.00 0.00 41.02 2.29
729 763 2.829720 TGTATGTAGTCCGAGTTGGCTT 59.170 45.455 0.00 0.00 37.80 4.35
732 766 2.799017 TGTAGTCCGAGTTGGCTTAGA 58.201 47.619 0.00 0.00 37.80 2.10
743 777 5.346181 AGTTGGCTTAGAATAGAGTGACC 57.654 43.478 0.00 0.00 0.00 4.02
748 782 3.243468 GCTTAGAATAGAGTGACCCCGAC 60.243 52.174 0.00 0.00 0.00 4.79
751 785 1.334243 GAATAGAGTGACCCCGACTCG 59.666 57.143 0.00 0.00 43.95 4.18
769 803 1.810606 CGGAGGTGAGGATGGATCGG 61.811 65.000 0.00 0.00 0.00 4.18
810 859 0.108329 GAACTGAAGATCCGGCCGAA 60.108 55.000 30.73 6.63 0.00 4.30
814 863 0.108329 TGAAGATCCGGCCGAAAGTC 60.108 55.000 30.73 18.00 0.00 3.01
830 879 3.770040 TCCACCGACCTGCCGATG 61.770 66.667 0.00 0.00 0.00 3.84
854 903 5.622346 CTATAAAAGGAGTCTCCAAGGCT 57.378 43.478 21.26 5.24 39.61 4.58
855 904 2.869101 AAAAGGAGTCTCCAAGGCTC 57.131 50.000 21.26 0.00 45.88 4.70
862 913 2.999591 GAGTCTCCAAGGCTCATGAAGC 61.000 54.545 3.76 2.68 45.89 3.86
874 925 0.675083 CATGAAGCCAACAACAGCCA 59.325 50.000 0.00 0.00 0.00 4.75
899 950 2.632377 GTCCTCGCAATCCAGATCAAA 58.368 47.619 0.00 0.00 0.00 2.69
906 957 2.286872 CAATCCAGATCAAAGCGAGCT 58.713 47.619 0.00 0.00 42.52 4.09
908 959 0.179127 TCCAGATCAAAGCGAGCTCG 60.179 55.000 31.37 31.37 38.68 5.03
909 960 0.459237 CCAGATCAAAGCGAGCTCGT 60.459 55.000 34.46 19.89 38.68 4.18
950 1002 1.612395 CCGCAAGAAGGAGAGGAGCT 61.612 60.000 0.00 0.00 43.02 4.09
957 1009 2.124653 GGAGAGGAGCTCGTCGGA 60.125 66.667 26.05 0.00 44.91 4.55
991 1046 1.339438 ACACTAAGGAGGCGACGAGTA 60.339 52.381 0.00 0.00 0.00 2.59
1004 1059 3.489398 GCGACGAGTAACAAGGAGATGAT 60.489 47.826 0.00 0.00 0.00 2.45
1008 1063 4.466370 ACGAGTAACAAGGAGATGATGGAA 59.534 41.667 0.00 0.00 0.00 3.53
1009 1064 5.046591 ACGAGTAACAAGGAGATGATGGAAA 60.047 40.000 0.00 0.00 0.00 3.13
1011 1066 7.147724 ACGAGTAACAAGGAGATGATGGAAATA 60.148 37.037 0.00 0.00 0.00 1.40
1018 1073 3.368427 GGAGATGATGGAAATATCGCCGA 60.368 47.826 0.00 0.00 32.51 5.54
1023 1078 0.677288 TGGAAATATCGCCGACGGAT 59.323 50.000 20.50 5.60 40.63 4.18
1030 1085 1.945354 ATCGCCGACGGATGTCTTGT 61.945 55.000 20.50 0.00 43.21 3.16
1098 1153 4.512484 CCAGAAAGAAGAGGATGAAGGTC 58.488 47.826 0.00 0.00 0.00 3.85
1111 1166 1.258676 GAAGGTCGTCAAGAGGAGGT 58.741 55.000 0.00 0.00 33.18 3.85
1114 1169 0.670854 GGTCGTCAAGAGGAGGTTGC 60.671 60.000 0.00 0.00 33.18 4.17
1136 1191 4.996976 GGCGCTCATCGACCATAT 57.003 55.556 7.64 0.00 41.34 1.78
1140 1195 1.923204 GCGCTCATCGACCATATCATC 59.077 52.381 0.00 0.00 41.67 2.92
1154 1209 1.339097 ATCATCGCCTACCCCTACAC 58.661 55.000 0.00 0.00 0.00 2.90
1206 1261 0.602905 AGCGTTCCAAGTTCTTCCGG 60.603 55.000 0.00 0.00 0.00 5.14
1218 1273 1.141234 CTTCCGGGAGTTCTACGCC 59.859 63.158 0.00 0.00 37.34 5.68
1224 1279 0.245813 GGGAGTTCTACGCCGAAAGT 59.754 55.000 0.00 0.00 39.10 2.66
1228 1283 3.177487 GAGTTCTACGCCGAAAGTAAGG 58.823 50.000 0.00 0.00 0.00 2.69
1242 1297 0.175073 GTAAGGAGACGGCCGACAAT 59.825 55.000 35.90 11.27 0.00 2.71
1281 1336 2.416972 GGGACTCATCGACCAGTACAAC 60.417 54.545 9.50 0.00 0.00 3.32
1282 1337 2.230508 GGACTCATCGACCAGTACAACA 59.769 50.000 3.35 0.00 0.00 3.33
1345 1400 1.679305 GAGGAGACGGTGGAGAGCA 60.679 63.158 0.00 0.00 0.00 4.26
1364 1419 2.549778 GCAAGGGCAGCAACCATTTTTA 60.550 45.455 0.00 0.00 40.72 1.52
1372 1430 7.503902 AGGGCAGCAACCATTTTTATTTTAAAA 59.496 29.630 2.51 2.51 0.00 1.52
1373 1431 8.138074 GGGCAGCAACCATTTTTATTTTAAAAA 58.862 29.630 4.44 7.42 34.15 1.94
1374 1432 9.179552 GGCAGCAACCATTTTTATTTTAAAAAG 57.820 29.630 4.44 2.43 33.28 2.27
1413 1471 5.116084 TGATAATTTGCAAGGAGCCTACT 57.884 39.130 0.00 0.00 44.83 2.57
1419 1477 5.693769 TTTGCAAGGAGCCTACTTAGTAT 57.306 39.130 0.00 0.00 44.83 2.12
1440 1503 2.280592 GTCCGTGTTTGGTCCGCT 60.281 61.111 0.00 0.00 0.00 5.52
1645 2039 9.703892 ATCGACAATGTAAATCAAAATCCAAAA 57.296 25.926 0.00 0.00 0.00 2.44
1687 2081 8.843885 ATATCAAACATGATCAGATGTGTAGG 57.156 34.615 0.00 0.00 36.66 3.18
1719 2113 9.798885 GCAAAATGTTTTAGCGAGATATAGTAG 57.201 33.333 0.00 0.00 0.00 2.57
1761 2155 2.027192 GGGATGAAACCACACAGAGCTA 60.027 50.000 0.00 0.00 0.00 3.32
1785 2204 3.499918 ACTGAATTCTTTTGCTCTCCACG 59.500 43.478 7.05 0.00 0.00 4.94
1786 2205 2.813754 TGAATTCTTTTGCTCTCCACGG 59.186 45.455 7.05 0.00 0.00 4.94
1793 2212 1.691195 TTGCTCTCCACGGTTCACCA 61.691 55.000 0.00 0.00 35.14 4.17
1836 2255 1.539388 TGTGCTTTTGCCCGAGTATTG 59.461 47.619 0.00 0.00 46.87 1.90
1845 2264 2.037641 TGCCCGAGTATTGATCATCCTG 59.962 50.000 0.00 0.00 0.00 3.86
1869 2288 5.929697 TCTTATTTGTGCTGTGTTCAGAG 57.070 39.130 0.00 0.00 43.76 3.35
1883 2302 5.163561 TGTGTTCAGAGCACATATACATCGA 60.164 40.000 15.59 0.00 41.32 3.59
1909 2328 7.394016 TGGTGAGTTCAGAGCAATTTAATAGA 58.606 34.615 0.00 0.00 0.00 1.98
1922 2341 8.049721 AGCAATTTAATAGAAGAAGCTACACCT 58.950 33.333 0.00 0.00 0.00 4.00
1954 2373 6.212791 ACAAACAGAACTAGTAGCCCAAGATA 59.787 38.462 0.00 0.00 0.00 1.98
1956 2375 6.869206 ACAGAACTAGTAGCCCAAGATAAA 57.131 37.500 0.00 0.00 0.00 1.40
2084 2504 5.630680 CACTGTCCTAAAAATGTGTGCAATC 59.369 40.000 0.00 0.00 0.00 2.67
2091 2511 0.245539 AATGTGTGCAATCTGCTGCC 59.754 50.000 0.00 0.00 45.31 4.85
2094 2514 1.531128 TGTGCAATCTGCTGCCCAA 60.531 52.632 0.00 0.00 45.31 4.12
2100 2520 0.681175 AATCTGCTGCCCAACAAACC 59.319 50.000 0.00 0.00 0.00 3.27
2178 2598 5.769662 AGTTTTTCATCAGTTCTACATGGCA 59.230 36.000 0.00 0.00 0.00 4.92
2199 2619 5.867174 GGCAATTGTTTTATATTATCCCGCC 59.133 40.000 7.40 0.00 0.00 6.13
2223 2643 3.196469 AGGTATCAGATATGCACCGATGG 59.804 47.826 0.00 0.00 34.36 3.51
2228 2648 2.731451 CAGATATGCACCGATGGTAACG 59.269 50.000 0.00 0.00 42.51 3.18
2283 2704 8.549338 AAAAGAGTTAATACCACACTTAGAGC 57.451 34.615 0.00 0.00 0.00 4.09
2284 2705 6.852420 AGAGTTAATACCACACTTAGAGCA 57.148 37.500 0.00 0.00 0.00 4.26
2285 2706 7.425224 AGAGTTAATACCACACTTAGAGCAT 57.575 36.000 0.00 0.00 0.00 3.79
2286 2707 7.493367 AGAGTTAATACCACACTTAGAGCATC 58.507 38.462 0.00 0.00 0.00 3.91
2297 2718 2.280457 GAGCATCTACAGCCGGGC 60.280 66.667 12.11 12.11 0.00 6.13
2298 2719 3.816367 GAGCATCTACAGCCGGGCC 62.816 68.421 17.02 0.00 0.00 5.80
2299 2720 3.866582 GCATCTACAGCCGGGCCT 61.867 66.667 17.02 3.41 0.00 5.19
2300 2721 2.423446 CATCTACAGCCGGGCCTC 59.577 66.667 17.02 0.00 0.00 4.70
2301 2722 2.136878 CATCTACAGCCGGGCCTCT 61.137 63.158 17.02 0.11 0.00 3.69
2302 2723 1.383248 ATCTACAGCCGGGCCTCTT 60.383 57.895 17.02 0.00 0.00 2.85
2303 2724 0.105658 ATCTACAGCCGGGCCTCTTA 60.106 55.000 17.02 0.00 0.00 2.10
2304 2725 0.105658 TCTACAGCCGGGCCTCTTAT 60.106 55.000 17.02 0.00 0.00 1.73
2305 2726 1.146359 TCTACAGCCGGGCCTCTTATA 59.854 52.381 17.02 0.00 0.00 0.98
2306 2727 1.272769 CTACAGCCGGGCCTCTTATAC 59.727 57.143 17.02 0.00 0.00 1.47
2307 2728 1.371558 CAGCCGGGCCTCTTATACC 59.628 63.158 17.02 0.00 0.00 2.73
2308 2729 1.842010 AGCCGGGCCTCTTATACCC 60.842 63.158 17.02 0.00 40.51 3.69
2312 2733 3.144613 GGGCCTCTTATACCCGTCT 57.855 57.895 0.84 0.00 32.92 4.18
2313 2734 0.967662 GGGCCTCTTATACCCGTCTC 59.032 60.000 0.84 0.00 32.92 3.36
2314 2735 1.700955 GGCCTCTTATACCCGTCTCA 58.299 55.000 0.00 0.00 0.00 3.27
2315 2736 2.037144 GGCCTCTTATACCCGTCTCAA 58.963 52.381 0.00 0.00 0.00 3.02
2316 2737 2.433239 GGCCTCTTATACCCGTCTCAAA 59.567 50.000 0.00 0.00 0.00 2.69
2317 2738 3.071167 GGCCTCTTATACCCGTCTCAAAT 59.929 47.826 0.00 0.00 0.00 2.32
2318 2739 4.058817 GCCTCTTATACCCGTCTCAAATG 58.941 47.826 0.00 0.00 0.00 2.32
2319 2740 4.058817 CCTCTTATACCCGTCTCAAATGC 58.941 47.826 0.00 0.00 0.00 3.56
2320 2741 4.058817 CTCTTATACCCGTCTCAAATGCC 58.941 47.826 0.00 0.00 0.00 4.40
2321 2742 2.922740 TATACCCGTCTCAAATGCCC 57.077 50.000 0.00 0.00 0.00 5.36
2322 2743 0.179056 ATACCCGTCTCAAATGCCCG 60.179 55.000 0.00 0.00 0.00 6.13
2323 2744 2.246761 TACCCGTCTCAAATGCCCGG 62.247 60.000 0.00 0.00 38.39 5.73
2324 2745 2.824041 CCGTCTCAAATGCCCGGG 60.824 66.667 19.09 19.09 35.11 5.73
2325 2746 3.508840 CGTCTCAAATGCCCGGGC 61.509 66.667 39.40 39.40 42.35 6.13
2342 2763 4.742201 CAGGCCGTCCGACCACTG 62.742 72.222 0.00 0.00 37.47 3.66
2353 2774 2.598467 ACCACTGGCCGGTCAAAA 59.402 55.556 16.42 0.00 27.30 2.44
2354 2775 1.076632 ACCACTGGCCGGTCAAAAA 60.077 52.632 16.42 0.00 27.30 1.94
2370 2791 3.852558 AAAAATCCACCCAACCGGA 57.147 47.368 9.46 0.00 35.27 5.14
2371 2792 1.334160 AAAAATCCACCCAACCGGAC 58.666 50.000 9.46 0.00 33.05 4.79
2372 2793 0.541063 AAAATCCACCCAACCGGACC 60.541 55.000 9.46 0.00 33.05 4.46
2373 2794 1.432023 AAATCCACCCAACCGGACCT 61.432 55.000 9.46 0.00 33.05 3.85
2374 2795 1.848886 AATCCACCCAACCGGACCTC 61.849 60.000 9.46 0.00 33.05 3.85
2375 2796 2.765705 ATCCACCCAACCGGACCTCT 62.766 60.000 9.46 0.00 33.05 3.69
2376 2797 2.663196 CACCCAACCGGACCTCTC 59.337 66.667 9.46 0.00 34.64 3.20
2377 2798 2.203182 ACCCAACCGGACCTCTCA 59.797 61.111 9.46 0.00 34.64 3.27
2378 2799 1.460689 ACCCAACCGGACCTCTCAA 60.461 57.895 9.46 0.00 34.64 3.02
2379 2800 1.057851 ACCCAACCGGACCTCTCAAA 61.058 55.000 9.46 0.00 34.64 2.69
2380 2801 0.605589 CCCAACCGGACCTCTCAAAC 60.606 60.000 9.46 0.00 0.00 2.93
2381 2802 0.949105 CCAACCGGACCTCTCAAACG 60.949 60.000 9.46 0.00 0.00 3.60
2382 2803 1.301479 AACCGGACCTCTCAAACGC 60.301 57.895 9.46 0.00 0.00 4.84
2383 2804 2.434359 CCGGACCTCTCAAACGCC 60.434 66.667 0.00 0.00 0.00 5.68
2384 2805 2.434359 CGGACCTCTCAAACGCCC 60.434 66.667 0.00 0.00 0.00 6.13
2385 2806 2.434359 GGACCTCTCAAACGCCCG 60.434 66.667 0.00 0.00 0.00 6.13
2386 2807 2.434359 GACCTCTCAAACGCCCGG 60.434 66.667 0.00 0.00 0.00 5.73
2387 2808 3.952628 GACCTCTCAAACGCCCGGG 62.953 68.421 19.09 19.09 0.00 5.73
2389 2810 4.394712 CTCTCAAACGCCCGGGCT 62.395 66.667 41.01 26.06 39.32 5.19
2390 2811 4.697756 TCTCAAACGCCCGGGCTG 62.698 66.667 41.01 33.95 39.32 4.85
2391 2812 4.697756 CTCAAACGCCCGGGCTGA 62.698 66.667 41.01 34.10 39.32 4.26
2403 2824 2.682494 GGCTGACCGACACCCCTA 60.682 66.667 0.00 0.00 0.00 3.53
2404 2825 2.288025 GGCTGACCGACACCCCTAA 61.288 63.158 0.00 0.00 0.00 2.69
2405 2826 1.623542 GGCTGACCGACACCCCTAAT 61.624 60.000 0.00 0.00 0.00 1.73
2406 2827 1.117150 GCTGACCGACACCCCTAATA 58.883 55.000 0.00 0.00 0.00 0.98
2407 2828 1.692519 GCTGACCGACACCCCTAATAT 59.307 52.381 0.00 0.00 0.00 1.28
2408 2829 2.288886 GCTGACCGACACCCCTAATATC 60.289 54.545 0.00 0.00 0.00 1.63
2409 2830 2.299297 CTGACCGACACCCCTAATATCC 59.701 54.545 0.00 0.00 0.00 2.59
2410 2831 2.322658 GACCGACACCCCTAATATCCA 58.677 52.381 0.00 0.00 0.00 3.41
2411 2832 2.299297 GACCGACACCCCTAATATCCAG 59.701 54.545 0.00 0.00 0.00 3.86
2412 2833 1.002087 CCGACACCCCTAATATCCAGC 59.998 57.143 0.00 0.00 0.00 4.85
2413 2834 1.002087 CGACACCCCTAATATCCAGCC 59.998 57.143 0.00 0.00 0.00 4.85
2414 2835 1.351350 GACACCCCTAATATCCAGCCC 59.649 57.143 0.00 0.00 0.00 5.19
2415 2836 1.346046 ACACCCCTAATATCCAGCCCA 60.346 52.381 0.00 0.00 0.00 5.36
2416 2837 1.780309 CACCCCTAATATCCAGCCCAA 59.220 52.381 0.00 0.00 0.00 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
188 201 9.982291 TTGAGACGCTAATAAAAATGTATTCAC 57.018 29.630 0.00 0.00 0.00 3.18
255 271 1.073923 ACTTGCGAACCAATTCCCTCT 59.926 47.619 0.00 0.00 31.91 3.69
320 336 2.757686 TCTAGCGTGTCATCATCGTC 57.242 50.000 0.00 0.00 0.00 4.20
333 352 3.193691 AGAATACGGATCCCATTCTAGCG 59.806 47.826 24.85 7.38 37.27 4.26
336 355 5.246203 CCTTGAGAATACGGATCCCATTCTA 59.754 44.000 25.60 15.81 38.74 2.10
395 418 2.331132 GCTGCTGCTGACAAGGGTC 61.331 63.158 10.92 0.00 44.57 4.46
416 439 2.050350 GCATGGACTGGCACTGCAT 61.050 57.895 2.82 0.00 33.13 3.96
417 440 2.674033 GCATGGACTGGCACTGCA 60.674 61.111 2.82 0.00 33.13 4.41
422 445 0.983467 TACTGAAGCATGGACTGGCA 59.017 50.000 0.00 0.00 0.00 4.92
423 446 2.338577 ATACTGAAGCATGGACTGGC 57.661 50.000 0.00 0.00 0.00 4.85
442 471 1.643868 GCGATTCCCGTGTCATGCAA 61.644 55.000 0.00 0.00 41.15 4.08
443 472 2.106074 GCGATTCCCGTGTCATGCA 61.106 57.895 0.00 0.00 41.15 3.96
444 473 1.643868 TTGCGATTCCCGTGTCATGC 61.644 55.000 0.00 0.00 41.15 4.06
445 474 0.801872 TTTGCGATTCCCGTGTCATG 59.198 50.000 0.00 0.00 41.15 3.07
446 475 1.086696 CTTTGCGATTCCCGTGTCAT 58.913 50.000 0.00 0.00 41.15 3.06
447 476 1.573829 GCTTTGCGATTCCCGTGTCA 61.574 55.000 0.00 0.00 41.15 3.58
448 477 1.134694 GCTTTGCGATTCCCGTGTC 59.865 57.895 0.00 0.00 41.15 3.67
449 478 2.332654 GGCTTTGCGATTCCCGTGT 61.333 57.895 0.00 0.00 41.15 4.49
450 479 2.485122 GGCTTTGCGATTCCCGTG 59.515 61.111 0.00 0.00 41.15 4.94
451 480 2.750237 GGGCTTTGCGATTCCCGT 60.750 61.111 0.00 0.00 41.15 5.28
452 481 2.749839 TGGGCTTTGCGATTCCCG 60.750 61.111 6.56 0.00 41.65 5.14
453 482 1.678970 AGTGGGCTTTGCGATTCCC 60.679 57.895 4.45 4.45 39.22 3.97
454 483 1.508088 CAGTGGGCTTTGCGATTCC 59.492 57.895 0.00 0.00 0.00 3.01
455 484 1.508088 CCAGTGGGCTTTGCGATTC 59.492 57.895 0.00 0.00 0.00 2.52
456 485 3.685435 CCAGTGGGCTTTGCGATT 58.315 55.556 0.00 0.00 0.00 3.34
474 503 1.100510 AATATGCTGCTGTGGTGCTG 58.899 50.000 0.00 0.00 35.44 4.41
475 504 1.100510 CAATATGCTGCTGTGGTGCT 58.899 50.000 0.00 0.00 0.00 4.40
476 505 0.526954 GCAATATGCTGCTGTGGTGC 60.527 55.000 0.00 0.77 40.96 5.01
477 506 0.101759 GGCAATATGCTGCTGTGGTG 59.898 55.000 0.00 0.00 44.28 4.17
478 507 0.323633 TGGCAATATGCTGCTGTGGT 60.324 50.000 0.00 0.00 44.28 4.16
479 508 1.037493 ATGGCAATATGCTGCTGTGG 58.963 50.000 0.00 0.00 44.28 4.17
480 509 2.134201 CATGGCAATATGCTGCTGTG 57.866 50.000 0.00 0.00 44.28 3.66
488 517 0.319555 GCTGCAGGCATGGCAATATG 60.320 55.000 22.64 11.82 41.39 1.78
489 518 2.046938 GCTGCAGGCATGGCAATAT 58.953 52.632 22.64 0.00 41.39 1.28
490 519 3.528853 GCTGCAGGCATGGCAATA 58.471 55.556 22.64 5.64 41.39 1.90
503 532 2.993264 AGGGGTTGTGCATGCTGC 60.993 61.111 20.33 12.29 45.29 5.25
504 533 1.604308 TCAGGGGTTGTGCATGCTG 60.604 57.895 20.33 6.09 0.00 4.41
505 534 1.604593 GTCAGGGGTTGTGCATGCT 60.605 57.895 20.33 0.00 0.00 3.79
506 535 1.181098 AAGTCAGGGGTTGTGCATGC 61.181 55.000 11.82 11.82 0.00 4.06
507 536 1.812571 GTAAGTCAGGGGTTGTGCATG 59.187 52.381 0.00 0.00 0.00 4.06
508 537 1.610624 CGTAAGTCAGGGGTTGTGCAT 60.611 52.381 0.00 0.00 0.00 3.96
509 538 0.250124 CGTAAGTCAGGGGTTGTGCA 60.250 55.000 0.00 0.00 0.00 4.57
510 539 0.953960 CCGTAAGTCAGGGGTTGTGC 60.954 60.000 0.00 0.00 0.00 4.57
511 540 0.321298 CCCGTAAGTCAGGGGTTGTG 60.321 60.000 0.00 0.00 45.85 3.33
512 541 2.063774 CCCGTAAGTCAGGGGTTGT 58.936 57.895 0.00 0.00 45.85 3.32
518 547 2.501223 TTCGCTGCCCGTAAGTCAGG 62.501 60.000 0.00 0.00 38.35 3.86
519 548 1.080093 TTCGCTGCCCGTAAGTCAG 60.080 57.895 0.00 0.00 38.35 3.51
520 549 1.373748 GTTCGCTGCCCGTAAGTCA 60.374 57.895 0.00 0.00 38.35 3.41
521 550 2.442188 CGTTCGCTGCCCGTAAGTC 61.442 63.158 0.00 0.00 38.35 3.01
522 551 2.431942 CGTTCGCTGCCCGTAAGT 60.432 61.111 0.00 0.00 38.35 2.24
523 552 3.849953 GCGTTCGCTGCCCGTAAG 61.850 66.667 9.99 0.00 38.35 2.34
524 553 4.666397 TGCGTTCGCTGCCCGTAA 62.666 61.111 17.63 0.00 38.35 3.18
539 568 3.745803 GGTTGCTGAGCAGGCTGC 61.746 66.667 31.56 31.56 45.46 5.25
540 569 2.189191 TAGGGTTGCTGAGCAGGCTG 62.189 60.000 10.94 10.94 40.61 4.85
541 570 1.920325 TAGGGTTGCTGAGCAGGCT 60.920 57.895 7.39 0.00 40.61 4.58
542 571 1.746991 GTAGGGTTGCTGAGCAGGC 60.747 63.158 7.39 4.84 40.61 4.85
543 572 0.107945 GAGTAGGGTTGCTGAGCAGG 60.108 60.000 7.39 0.00 40.61 4.85
544 573 0.901124 AGAGTAGGGTTGCTGAGCAG 59.099 55.000 7.39 0.00 40.61 4.24
545 574 0.610174 CAGAGTAGGGTTGCTGAGCA 59.390 55.000 1.40 1.40 36.47 4.26
546 575 0.107945 CCAGAGTAGGGTTGCTGAGC 60.108 60.000 0.00 0.00 0.00 4.26
547 576 1.066573 CACCAGAGTAGGGTTGCTGAG 60.067 57.143 0.00 0.00 36.19 3.35
548 577 0.976641 CACCAGAGTAGGGTTGCTGA 59.023 55.000 0.00 0.00 36.19 4.26
549 578 0.674895 GCACCAGAGTAGGGTTGCTG 60.675 60.000 0.00 0.00 36.19 4.41
550 579 1.679898 GCACCAGAGTAGGGTTGCT 59.320 57.895 0.00 0.00 36.19 3.91
551 580 1.741770 CGCACCAGAGTAGGGTTGC 60.742 63.158 0.00 0.00 36.19 4.17
552 581 1.741770 GCGCACCAGAGTAGGGTTG 60.742 63.158 0.30 0.00 36.19 3.77
553 582 2.663196 GCGCACCAGAGTAGGGTT 59.337 61.111 0.30 0.00 36.19 4.11
554 583 3.391382 GGCGCACCAGAGTAGGGT 61.391 66.667 10.83 0.00 39.88 4.34
555 584 4.162690 GGGCGCACCAGAGTAGGG 62.163 72.222 10.83 0.00 39.85 3.53
556 585 4.514577 CGGGCGCACCAGAGTAGG 62.515 72.222 10.83 0.00 40.22 3.18
557 586 3.449227 TCGGGCGCACCAGAGTAG 61.449 66.667 10.83 0.00 40.22 2.57
558 587 3.755628 GTCGGGCGCACCAGAGTA 61.756 66.667 10.83 0.00 41.16 2.59
578 607 2.107041 TATAGGATTGCCCACCGCCG 62.107 60.000 0.00 0.00 37.41 6.46
579 608 0.605589 GTATAGGATTGCCCACCGCC 60.606 60.000 0.00 0.00 37.41 6.13
580 609 0.949105 CGTATAGGATTGCCCACCGC 60.949 60.000 0.00 0.00 37.41 5.68
581 610 0.320421 CCGTATAGGATTGCCCACCG 60.320 60.000 0.00 0.00 45.00 4.94
582 611 0.605589 GCCGTATAGGATTGCCCACC 60.606 60.000 0.00 0.00 45.00 4.61
583 612 0.949105 CGCCGTATAGGATTGCCCAC 60.949 60.000 0.00 0.00 45.00 4.61
584 613 1.369692 CGCCGTATAGGATTGCCCA 59.630 57.895 0.00 0.00 45.00 5.36
585 614 1.375523 CCGCCGTATAGGATTGCCC 60.376 63.158 0.00 0.00 45.00 5.36
586 615 0.949105 CACCGCCGTATAGGATTGCC 60.949 60.000 0.00 0.00 45.00 4.52
587 616 0.949105 CCACCGCCGTATAGGATTGC 60.949 60.000 0.00 0.00 45.00 3.56
588 617 0.677288 TCCACCGCCGTATAGGATTG 59.323 55.000 0.00 0.00 45.00 2.67
589 618 1.069668 GTTCCACCGCCGTATAGGATT 59.930 52.381 0.00 0.00 45.00 3.01
590 619 0.677842 GTTCCACCGCCGTATAGGAT 59.322 55.000 0.00 0.00 45.00 3.24
591 620 1.394266 GGTTCCACCGCCGTATAGGA 61.394 60.000 0.00 0.00 45.00 2.94
592 621 1.068585 GGTTCCACCGCCGTATAGG 59.931 63.158 0.00 0.00 44.97 2.57
593 622 0.249322 CTGGTTCCACCGCCGTATAG 60.249 60.000 0.00 0.00 42.58 1.31
594 623 1.678598 CCTGGTTCCACCGCCGTATA 61.679 60.000 0.00 0.00 42.58 1.47
595 624 2.582436 CTGGTTCCACCGCCGTAT 59.418 61.111 0.00 0.00 42.58 3.06
596 625 3.697747 CCTGGTTCCACCGCCGTA 61.698 66.667 0.00 0.00 42.58 4.02
599 628 4.717313 GACCCTGGTTCCACCGCC 62.717 72.222 0.00 0.00 42.58 6.13
600 629 3.637273 AGACCCTGGTTCCACCGC 61.637 66.667 0.00 0.00 42.58 5.68
601 630 1.553690 ATCAGACCCTGGTTCCACCG 61.554 60.000 0.00 0.00 42.58 4.94
602 631 0.035056 CATCAGACCCTGGTTCCACC 60.035 60.000 0.00 0.00 39.22 4.61
603 632 0.035056 CCATCAGACCCTGGTTCCAC 60.035 60.000 0.00 0.00 31.51 4.02
604 633 1.852157 GCCATCAGACCCTGGTTCCA 61.852 60.000 0.00 0.00 34.86 3.53
605 634 1.077429 GCCATCAGACCCTGGTTCC 60.077 63.158 0.00 0.00 34.86 3.62
632 661 1.408702 AGATTGCACAAAACTGCCGTT 59.591 42.857 0.00 0.00 36.21 4.44
677 711 0.320946 GAATTGACGGGTGGGACGAA 60.321 55.000 0.00 0.00 34.93 3.85
679 713 1.743995 GGAATTGACGGGTGGGACG 60.744 63.158 0.00 0.00 37.36 4.79
712 746 2.799017 TCTAAGCCAACTCGGACTACA 58.201 47.619 0.00 0.00 36.56 2.74
713 747 3.863142 TTCTAAGCCAACTCGGACTAC 57.137 47.619 0.00 0.00 36.56 2.73
714 748 5.443283 TCTATTCTAAGCCAACTCGGACTA 58.557 41.667 0.00 0.00 36.56 2.59
729 763 3.743584 CGAGTCGGGGTCACTCTATTCTA 60.744 52.174 4.10 0.00 38.55 2.10
732 766 1.390565 CGAGTCGGGGTCACTCTATT 58.609 55.000 4.10 0.00 38.55 1.73
748 782 0.965439 GATCCATCCTCACCTCCGAG 59.035 60.000 0.00 0.00 0.00 4.63
751 785 0.470080 TCCGATCCATCCTCACCTCC 60.470 60.000 0.00 0.00 0.00 4.30
769 803 1.576421 GCCAATTCGGATCGGCATC 59.424 57.895 0.00 0.00 44.25 3.91
790 832 1.521681 CGGCCGGATCTTCAGTTCC 60.522 63.158 20.10 0.00 0.00 3.62
810 859 4.003788 CGGCAGGTCGGTGGACTT 62.004 66.667 0.00 0.00 42.97 3.01
830 879 4.709250 CCTTGGAGACTCCTTTTATAGGC 58.291 47.826 22.14 0.00 44.37 3.93
833 882 5.030147 TGAGCCTTGGAGACTCCTTTTATA 58.970 41.667 22.14 0.00 37.46 0.98
854 903 0.961019 GGCTGTTGTTGGCTTCATGA 59.039 50.000 0.00 0.00 0.00 3.07
855 904 0.675083 TGGCTGTTGTTGGCTTCATG 59.325 50.000 0.00 0.00 0.00 3.07
857 906 1.391157 GGTGGCTGTTGTTGGCTTCA 61.391 55.000 0.00 0.00 0.00 3.02
862 913 4.326766 CGCGGTGGCTGTTGTTGG 62.327 66.667 0.00 0.00 36.88 3.77
919 971 4.953868 TTGCGGTGGTCACGACGG 62.954 66.667 0.00 0.00 0.00 4.79
927 979 1.674057 CTCTCCTTCTTGCGGTGGT 59.326 57.895 0.00 0.00 0.00 4.16
928 980 1.078848 CCTCTCCTTCTTGCGGTGG 60.079 63.158 0.00 0.00 0.00 4.61
929 981 0.108424 CTCCTCTCCTTCTTGCGGTG 60.108 60.000 0.00 0.00 0.00 4.94
970 1022 0.099082 CTCGTCGCCTCCTTAGTGTC 59.901 60.000 0.00 0.00 0.00 3.67
971 1023 0.608582 ACTCGTCGCCTCCTTAGTGT 60.609 55.000 0.00 0.00 0.00 3.55
973 1025 1.742268 GTTACTCGTCGCCTCCTTAGT 59.258 52.381 0.00 0.00 0.00 2.24
974 1026 1.741706 TGTTACTCGTCGCCTCCTTAG 59.258 52.381 0.00 0.00 0.00 2.18
975 1027 1.825090 TGTTACTCGTCGCCTCCTTA 58.175 50.000 0.00 0.00 0.00 2.69
991 1046 5.471456 GCGATATTTCCATCATCTCCTTGTT 59.529 40.000 0.00 0.00 0.00 2.83
1004 1059 0.677288 ATCCGTCGGCGATATTTCCA 59.323 50.000 12.93 0.00 41.33 3.53
1008 1063 3.491581 GACATCCGTCGGCGATATT 57.508 52.632 12.93 0.00 41.33 1.28
1018 1073 0.606401 CTGCCCAACAAGACATCCGT 60.606 55.000 0.00 0.00 0.00 4.69
1023 1078 0.179020 CCAGTCTGCCCAACAAGACA 60.179 55.000 5.68 0.00 32.23 3.41
1030 1085 3.970410 CCTGCCCAGTCTGCCCAA 61.970 66.667 0.00 0.00 0.00 4.12
1070 1125 1.078143 CTCTTCTTTCTGGCCCCGG 60.078 63.158 0.00 0.00 0.00 5.73
1071 1126 1.078143 CCTCTTCTTTCTGGCCCCG 60.078 63.158 0.00 0.00 0.00 5.73
1076 1131 4.512484 GACCTTCATCCTCTTCTTTCTGG 58.488 47.826 0.00 0.00 0.00 3.86
1080 1135 3.578716 TGACGACCTTCATCCTCTTCTTT 59.421 43.478 0.00 0.00 0.00 2.52
1082 1137 2.808919 TGACGACCTTCATCCTCTTCT 58.191 47.619 0.00 0.00 0.00 2.85
1098 1153 1.738099 CGGCAACCTCCTCTTGACG 60.738 63.158 0.00 0.00 43.36 4.35
1130 1185 1.203313 AGGGGTAGGCGATGATATGGT 60.203 52.381 0.00 0.00 0.00 3.55
1134 1189 2.522185 GTGTAGGGGTAGGCGATGATA 58.478 52.381 0.00 0.00 0.00 2.15
1136 1191 1.105167 CGTGTAGGGGTAGGCGATGA 61.105 60.000 0.00 0.00 0.00 2.92
1140 1195 1.362717 CATCGTGTAGGGGTAGGCG 59.637 63.158 0.00 0.00 0.00 5.52
1190 1245 1.071857 ACTCCCGGAAGAACTTGGAAC 59.928 52.381 0.73 0.00 0.00 3.62
1191 1246 1.430992 ACTCCCGGAAGAACTTGGAA 58.569 50.000 0.73 0.00 0.00 3.53
1206 1261 2.927553 TACTTTCGGCGTAGAACTCC 57.072 50.000 6.85 0.00 0.00 3.85
1218 1273 0.801067 CGGCCGTCTCCTTACTTTCG 60.801 60.000 19.50 0.00 0.00 3.46
1224 1279 1.766494 TATTGTCGGCCGTCTCCTTA 58.234 50.000 27.15 8.04 0.00 2.69
1228 1283 2.797515 CGATATTGTCGGCCGTCTC 58.202 57.895 27.15 16.95 46.47 3.36
1242 1297 2.495409 CCGCTGGTAGGCCACGATA 61.495 63.158 5.01 0.00 40.46 2.92
1345 1400 4.639078 AATAAAAATGGTTGCTGCCCTT 57.361 36.364 0.00 0.00 0.00 3.95
1364 1419 8.040727 ACCACTTTGACTGAAGCTTTTTAAAAT 58.959 29.630 0.00 0.00 0.00 1.82
1372 1430 3.620488 TCAACCACTTTGACTGAAGCTT 58.380 40.909 0.00 0.00 39.45 3.74
1373 1431 3.281727 TCAACCACTTTGACTGAAGCT 57.718 42.857 0.00 0.00 39.45 3.74
1387 1445 3.195396 GGCTCCTTGCAAATTATCAACCA 59.805 43.478 0.00 0.00 45.15 3.67
1413 1471 3.071312 ACCAAACACGGACACCATACTAA 59.929 43.478 0.00 0.00 0.00 2.24
1419 1477 1.153127 GGACCAAACACGGACACCA 60.153 57.895 0.00 0.00 0.00 4.17
1616 2010 9.703892 TGGATTTTGATTTACATTGTCGATTTT 57.296 25.926 0.00 0.00 0.00 1.82
1617 2011 9.703892 TTGGATTTTGATTTACATTGTCGATTT 57.296 25.926 0.00 0.00 0.00 2.17
1618 2012 9.703892 TTTGGATTTTGATTTACATTGTCGATT 57.296 25.926 0.00 0.00 0.00 3.34
1619 2013 9.703892 TTTTGGATTTTGATTTACATTGTCGAT 57.296 25.926 0.00 0.00 0.00 3.59
1661 2055 9.933723 CCTACACATCTGATCATGTTTGATATA 57.066 33.333 5.07 0.00 42.73 0.86
1678 2072 5.772521 ACATTTTGCAAGAACCTACACATC 58.227 37.500 0.00 0.00 0.00 3.06
1687 2081 5.685511 TCTCGCTAAAACATTTTGCAAGAAC 59.314 36.000 0.00 0.00 0.00 3.01
1719 2113 6.414732 TCCCAACCATGCATAGCTTATATAC 58.585 40.000 0.00 0.00 0.00 1.47
1761 2155 5.352569 CGTGGAGAGCAAAAGAATTCAGTAT 59.647 40.000 8.44 0.00 0.00 2.12
1785 2204 1.102978 AACACTGCTTGTGGTGAACC 58.897 50.000 13.33 0.00 46.28 3.62
1793 2212 0.819582 AGCTGCAAAACACTGCTTGT 59.180 45.000 1.02 0.00 43.07 3.16
1803 2222 0.536260 AAGCACACCAAGCTGCAAAA 59.464 45.000 1.02 0.00 42.53 2.44
1845 2264 6.486253 TCTGAACACAGCACAAATAAGATC 57.514 37.500 0.00 0.00 0.00 2.75
1849 2268 3.882288 TGCTCTGAACACAGCACAAATAA 59.118 39.130 0.99 0.00 40.80 1.40
1851 2270 2.300433 TGCTCTGAACACAGCACAAAT 58.700 42.857 0.99 0.00 40.80 2.32
1869 2288 4.560128 ACTCACCATCGATGTATATGTGC 58.440 43.478 23.27 0.00 0.00 4.57
1883 2302 8.049117 TCTATTAAATTGCTCTGAACTCACCAT 58.951 33.333 0.00 0.00 0.00 3.55
1909 2328 6.368779 TTGTATTGGTAGGTGTAGCTTCTT 57.631 37.500 0.00 0.00 0.00 2.52
1922 2341 7.325694 GGCTACTAGTTCTGTTTGTATTGGTA 58.674 38.462 0.00 0.00 0.00 3.25
1954 2373 9.844257 AAATCTAGCAATATGAAGCTACTCTTT 57.156 29.630 0.00 0.00 42.05 2.52
1994 2414 1.134175 CACAAAAACTTCAGGCACCGT 59.866 47.619 0.00 0.00 0.00 4.83
2035 2455 7.228507 TGAAAAGCTGTGTAGAAGCAAAGATAA 59.771 33.333 0.00 0.00 43.37 1.75
2040 2460 4.640201 AGTGAAAAGCTGTGTAGAAGCAAA 59.360 37.500 0.00 0.00 43.37 3.68
2084 2504 1.662044 GAGGTTTGTTGGGCAGCAG 59.338 57.895 0.00 0.00 0.00 4.24
2091 2511 4.815846 CCTTCAAAAATGGAGGTTTGTTGG 59.184 41.667 0.00 0.00 36.36 3.77
2094 2514 4.469586 ACACCTTCAAAAATGGAGGTTTGT 59.530 37.500 6.06 0.36 36.36 2.83
2100 2520 5.220643 GCAAAACACACCTTCAAAAATGGAG 60.221 40.000 0.00 0.00 0.00 3.86
2178 2598 6.150474 CCTCGGCGGGATAATATAAAACAATT 59.850 38.462 9.18 0.00 0.00 2.32
2199 2619 2.488153 TCGGTGCATATCTGATACCTCG 59.512 50.000 0.00 1.41 32.16 4.63
2251 2671 9.349713 AGTGTGGTATTAACTCTTTTTCATCAA 57.650 29.630 0.00 0.00 0.00 2.57
2262 2683 7.493367 AGATGCTCTAAGTGTGGTATTAACTC 58.507 38.462 0.00 0.00 0.00 3.01
2281 2702 3.866582 GGCCCGGCTGTAGATGCT 61.867 66.667 9.86 0.00 0.00 3.79
2282 2703 3.816367 GAGGCCCGGCTGTAGATGC 62.816 68.421 9.86 0.00 0.00 3.91
2283 2704 1.690219 AAGAGGCCCGGCTGTAGATG 61.690 60.000 9.86 0.00 0.00 2.90
2284 2705 0.105658 TAAGAGGCCCGGCTGTAGAT 60.106 55.000 9.86 0.00 0.00 1.98
2285 2706 0.105658 ATAAGAGGCCCGGCTGTAGA 60.106 55.000 9.86 0.00 0.00 2.59
2286 2707 1.272769 GTATAAGAGGCCCGGCTGTAG 59.727 57.143 9.86 0.00 0.00 2.74
2287 2708 1.335145 GTATAAGAGGCCCGGCTGTA 58.665 55.000 9.86 0.00 0.00 2.74
2288 2709 1.408453 GGTATAAGAGGCCCGGCTGT 61.408 60.000 9.86 0.00 0.00 4.40
2289 2710 1.371558 GGTATAAGAGGCCCGGCTG 59.628 63.158 9.86 0.00 0.00 4.85
2290 2711 1.842010 GGGTATAAGAGGCCCGGCT 60.842 63.158 9.86 0.00 32.16 5.52
2291 2712 2.748350 GGGTATAAGAGGCCCGGC 59.252 66.667 0.00 0.00 32.16 6.13
2294 2715 0.967662 GAGACGGGTATAAGAGGCCC 59.032 60.000 0.00 0.00 39.03 5.80
2295 2716 1.700955 TGAGACGGGTATAAGAGGCC 58.299 55.000 0.00 0.00 0.00 5.19
2296 2717 3.814005 TTTGAGACGGGTATAAGAGGC 57.186 47.619 0.00 0.00 0.00 4.70
2297 2718 4.058817 GCATTTGAGACGGGTATAAGAGG 58.941 47.826 0.00 0.00 0.00 3.69
2298 2719 4.058817 GGCATTTGAGACGGGTATAAGAG 58.941 47.826 0.00 0.00 0.00 2.85
2299 2720 3.181458 GGGCATTTGAGACGGGTATAAGA 60.181 47.826 0.00 0.00 0.00 2.10
2300 2721 3.139077 GGGCATTTGAGACGGGTATAAG 58.861 50.000 0.00 0.00 0.00 1.73
2301 2722 2.484065 CGGGCATTTGAGACGGGTATAA 60.484 50.000 0.00 0.00 0.00 0.98
2302 2723 1.069513 CGGGCATTTGAGACGGGTATA 59.930 52.381 0.00 0.00 0.00 1.47
2303 2724 0.179056 CGGGCATTTGAGACGGGTAT 60.179 55.000 0.00 0.00 0.00 2.73
2304 2725 1.219664 CGGGCATTTGAGACGGGTA 59.780 57.895 0.00 0.00 0.00 3.69
2305 2726 2.046314 CGGGCATTTGAGACGGGT 60.046 61.111 0.00 0.00 0.00 5.28
2306 2727 2.824041 CCGGGCATTTGAGACGGG 60.824 66.667 0.00 0.00 40.79 5.28
2307 2728 2.824041 CCCGGGCATTTGAGACGG 60.824 66.667 8.08 0.00 43.89 4.79
2308 2729 3.508840 GCCCGGGCATTTGAGACG 61.509 66.667 40.73 0.15 41.49 4.18
2325 2746 4.742201 CAGTGGTCGGACGGCCTG 62.742 72.222 16.89 3.53 41.25 4.85
2336 2757 1.076632 TTTTTGACCGGCCAGTGGT 60.077 52.632 11.74 0.78 44.10 4.16
2337 2758 3.849064 TTTTTGACCGGCCAGTGG 58.151 55.556 4.20 4.20 0.00 4.00
2352 2773 1.334160 GTCCGGTTGGGTGGATTTTT 58.666 50.000 0.00 0.00 36.48 1.94
2353 2774 0.541063 GGTCCGGTTGGGTGGATTTT 60.541 55.000 0.00 0.00 36.48 1.82
2354 2775 1.076014 GGTCCGGTTGGGTGGATTT 59.924 57.895 0.00 0.00 36.48 2.17
2355 2776 1.848886 GAGGTCCGGTTGGGTGGATT 61.849 60.000 0.00 0.00 36.48 3.01
2356 2777 2.204090 AGGTCCGGTTGGGTGGAT 60.204 61.111 0.00 0.00 36.48 3.41
2357 2778 2.926242 GAGGTCCGGTTGGGTGGA 60.926 66.667 0.00 0.00 37.00 4.02
2358 2779 2.928396 AGAGGTCCGGTTGGGTGG 60.928 66.667 0.00 0.00 37.00 4.61
2359 2780 1.764571 TTGAGAGGTCCGGTTGGGTG 61.765 60.000 0.00 0.00 37.00 4.61
2360 2781 1.057851 TTTGAGAGGTCCGGTTGGGT 61.058 55.000 0.00 0.00 37.00 4.51
2361 2782 0.605589 GTTTGAGAGGTCCGGTTGGG 60.606 60.000 0.00 0.00 35.24 4.12
2362 2783 0.949105 CGTTTGAGAGGTCCGGTTGG 60.949 60.000 0.00 0.00 0.00 3.77
2363 2784 1.566018 GCGTTTGAGAGGTCCGGTTG 61.566 60.000 0.00 0.00 0.00 3.77
2364 2785 1.301479 GCGTTTGAGAGGTCCGGTT 60.301 57.895 0.00 0.00 0.00 4.44
2365 2786 2.342648 GCGTTTGAGAGGTCCGGT 59.657 61.111 0.00 0.00 0.00 5.28
2366 2787 2.434359 GGCGTTTGAGAGGTCCGG 60.434 66.667 0.00 0.00 0.00 5.14
2367 2788 2.434359 GGGCGTTTGAGAGGTCCG 60.434 66.667 0.00 0.00 0.00 4.79
2368 2789 2.434359 CGGGCGTTTGAGAGGTCC 60.434 66.667 0.00 0.00 34.56 4.46
2369 2790 2.434359 CCGGGCGTTTGAGAGGTC 60.434 66.667 0.00 0.00 0.00 3.85
2370 2791 4.016706 CCCGGGCGTTTGAGAGGT 62.017 66.667 8.08 0.00 0.00 3.85
2387 2808 1.117150 TATTAGGGGTGTCGGTCAGC 58.883 55.000 0.00 0.00 43.02 4.26
2388 2809 2.299297 GGATATTAGGGGTGTCGGTCAG 59.701 54.545 0.00 0.00 0.00 3.51
2389 2810 2.322658 GGATATTAGGGGTGTCGGTCA 58.677 52.381 0.00 0.00 0.00 4.02
2390 2811 2.299297 CTGGATATTAGGGGTGTCGGTC 59.701 54.545 0.00 0.00 0.00 4.79
2391 2812 2.326428 CTGGATATTAGGGGTGTCGGT 58.674 52.381 0.00 0.00 0.00 4.69
2392 2813 1.002087 GCTGGATATTAGGGGTGTCGG 59.998 57.143 0.00 0.00 0.00 4.79
2393 2814 1.002087 GGCTGGATATTAGGGGTGTCG 59.998 57.143 0.00 0.00 0.00 4.35
2394 2815 1.351350 GGGCTGGATATTAGGGGTGTC 59.649 57.143 0.00 0.00 0.00 3.67
2395 2816 1.346046 TGGGCTGGATATTAGGGGTGT 60.346 52.381 0.00 0.00 0.00 4.16
2396 2817 1.444933 TGGGCTGGATATTAGGGGTG 58.555 55.000 0.00 0.00 0.00 4.61
2397 2818 2.222461 TTGGGCTGGATATTAGGGGT 57.778 50.000 0.00 0.00 0.00 4.95


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

AutoCloner maintained by Alex Coulton.