Multiple sequence alignment - TraesCS3A01G300700

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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 TraesCS3A01G300700 chr3A 100.000 3274 0 0 1 3274 534533756 534537029 0.000000e+00 6047.0
1 TraesCS3A01G300700 chr3A 76.214 597 94 30 1477 2035 709061766 709062352 4.160000e-69 272.0
2 TraesCS3A01G300700 chr3D 91.188 1827 96 39 734 2512 415647810 415646001 0.000000e+00 2422.0
3 TraesCS3A01G300700 chr3D 95.992 474 17 2 2801 3274 415644433 415643962 0.000000e+00 769.0
4 TraesCS3A01G300700 chr3D 93.224 487 26 4 1 482 415653025 415652541 0.000000e+00 710.0
5 TraesCS3A01G300700 chr3D 76.914 823 136 35 1477 2261 573907446 573908252 5.050000e-113 418.0
6 TraesCS3A01G300700 chr3D 85.479 303 21 7 2510 2803 415644760 415644472 8.880000e-76 294.0
7 TraesCS3A01G300700 chr3D 87.500 80 10 0 2173 2252 573879056 573879135 3.480000e-15 93.5
8 TraesCS3A01G300700 chr3B 89.944 1611 78 23 908 2475 542135099 542133530 0.000000e+00 2001.0
9 TraesCS3A01G300700 chr3B 91.942 484 17 8 2801 3274 542132456 542131985 0.000000e+00 658.0
10 TraesCS3A01G300700 chr3B 92.958 426 20 6 30 448 542162964 542162542 2.160000e-171 612.0
11 TraesCS3A01G300700 chr7D 94.490 1089 38 10 1189 2272 6136955 6135884 0.000000e+00 1659.0
12 TraesCS3A01G300700 chr7D 91.927 384 22 6 108 482 6140676 6140293 2.240000e-146 529.0
13 TraesCS3A01G300700 chr2A 92.157 51 2 2 1797 1846 731374498 731374547 1.630000e-08 71.3
14 TraesCS3A01G300700 chr5D 96.875 32 1 0 2169 2200 421984660 421984629 2.000000e-03 54.7


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 TraesCS3A01G300700 chr3A 534533756 534537029 3273 False 6047.000000 6047 100.000000 1 3274 1 chr3A.!!$F1 3273
1 TraesCS3A01G300700 chr3A 709061766 709062352 586 False 272.000000 272 76.214000 1477 2035 1 chr3A.!!$F2 558
2 TraesCS3A01G300700 chr3D 415643962 415647810 3848 True 1161.666667 2422 90.886333 734 3274 3 chr3D.!!$R2 2540
3 TraesCS3A01G300700 chr3D 573907446 573908252 806 False 418.000000 418 76.914000 1477 2261 1 chr3D.!!$F2 784
4 TraesCS3A01G300700 chr3B 542131985 542135099 3114 True 1329.500000 2001 90.943000 908 3274 2 chr3B.!!$R2 2366
5 TraesCS3A01G300700 chr7D 6135884 6140676 4792 True 1094.000000 1659 93.208500 108 2272 2 chr7D.!!$R1 2164

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
268 273 0.042274 GCAAACACGGTGCATTTTGC 60.042 50.0 23.12 23.12 44.95 3.68 F
611 624 0.106419 TTATGTTGGCCCCCGGATTC 60.106 55.0 0.73 0.00 0.00 2.52 F
914 2699 0.388659 ATTTGCTTTGCTGCACGGAA 59.611 45.0 0.00 0.99 43.20 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1092 2901 0.560688 GGATGGAGAGAGGGGAGACT 59.439 60.0 0.00 0.00 0.00 3.24 R
2060 5191 0.679505 CGAAGGACTGGTGGAAGACA 59.320 55.0 0.00 0.00 0.00 3.41 R
2912 8080 1.120437 GCTTTGCGCACAGTAAACAC 58.880 50.0 23.45 3.31 38.92 3.32 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
34 35 8.991243 TTAAGTTAAATACATCTACGCACAGT 57.009 30.769 0.00 0.00 0.00 3.55
35 36 6.887376 AGTTAAATACATCTACGCACAGTG 57.113 37.500 0.00 0.00 0.00 3.66
36 37 5.291128 AGTTAAATACATCTACGCACAGTGC 59.709 40.000 16.21 16.21 40.69 4.40
37 38 3.526931 AATACATCTACGCACAGTGCT 57.473 42.857 23.15 12.54 42.25 4.40
38 39 3.526931 ATACATCTACGCACAGTGCTT 57.473 42.857 23.15 16.68 42.25 3.91
39 40 1.714794 ACATCTACGCACAGTGCTTC 58.285 50.000 23.15 0.00 42.25 3.86
40 41 1.000843 ACATCTACGCACAGTGCTTCA 59.999 47.619 23.15 5.09 42.25 3.02
41 42 1.657594 CATCTACGCACAGTGCTTCAG 59.342 52.381 23.15 15.87 42.25 3.02
42 43 0.958822 TCTACGCACAGTGCTTCAGA 59.041 50.000 23.15 17.72 42.25 3.27
43 44 1.546029 TCTACGCACAGTGCTTCAGAT 59.454 47.619 23.15 4.53 42.25 2.90
44 45 2.029020 TCTACGCACAGTGCTTCAGATT 60.029 45.455 23.15 1.68 42.25 2.40
45 46 1.597742 ACGCACAGTGCTTCAGATTT 58.402 45.000 23.15 0.00 42.25 2.17
46 47 2.766313 ACGCACAGTGCTTCAGATTTA 58.234 42.857 23.15 0.00 42.25 1.40
47 48 3.338249 ACGCACAGTGCTTCAGATTTAT 58.662 40.909 23.15 0.00 42.25 1.40
48 49 3.372206 ACGCACAGTGCTTCAGATTTATC 59.628 43.478 23.15 0.00 42.25 1.75
49 50 3.620374 CGCACAGTGCTTCAGATTTATCT 59.380 43.478 23.15 0.00 42.25 1.98
50 51 4.093998 CGCACAGTGCTTCAGATTTATCTT 59.906 41.667 23.15 0.00 42.25 2.40
51 52 5.291858 CGCACAGTGCTTCAGATTTATCTTA 59.708 40.000 23.15 0.00 42.25 2.10
52 53 6.018425 CGCACAGTGCTTCAGATTTATCTTAT 60.018 38.462 23.15 0.00 42.25 1.73
53 54 7.351223 GCACAGTGCTTCAGATTTATCTTATC 58.649 38.462 18.92 0.00 40.96 1.75
54 55 7.011763 GCACAGTGCTTCAGATTTATCTTATCA 59.988 37.037 18.92 0.00 40.96 2.15
55 56 9.053840 CACAGTGCTTCAGATTTATCTTATCAT 57.946 33.333 0.00 0.00 34.22 2.45
56 57 9.624373 ACAGTGCTTCAGATTTATCTTATCATT 57.376 29.630 0.00 0.00 34.22 2.57
69 70 9.474313 TTTATCTTATCATTACCATTATGCCCC 57.526 33.333 0.00 0.00 0.00 5.80
70 71 6.461577 TCTTATCATTACCATTATGCCCCA 57.538 37.500 0.00 0.00 0.00 4.96
71 72 6.484288 TCTTATCATTACCATTATGCCCCAG 58.516 40.000 0.00 0.00 0.00 4.45
72 73 3.524095 TCATTACCATTATGCCCCAGG 57.476 47.619 0.00 0.00 0.00 4.45
85 86 1.560505 CCCCAGGCATTAAGTTTGCT 58.439 50.000 0.00 0.00 40.03 3.91
86 87 1.901833 CCCCAGGCATTAAGTTTGCTT 59.098 47.619 0.00 0.00 40.03 3.91
87 88 2.302733 CCCCAGGCATTAAGTTTGCTTT 59.697 45.455 0.00 0.00 40.03 3.51
88 89 3.588955 CCCAGGCATTAAGTTTGCTTTC 58.411 45.455 0.00 0.00 40.03 2.62
89 90 3.006752 CCCAGGCATTAAGTTTGCTTTCA 59.993 43.478 0.00 0.00 40.03 2.69
90 91 4.502950 CCCAGGCATTAAGTTTGCTTTCAA 60.503 41.667 0.00 0.00 40.03 2.69
91 92 4.687483 CCAGGCATTAAGTTTGCTTTCAAG 59.313 41.667 0.00 0.00 40.03 3.02
95 96 5.237127 GGCATTAAGTTTGCTTTCAAGCTTT 59.763 36.000 12.65 5.16 46.86 3.51
96 97 6.238456 GGCATTAAGTTTGCTTTCAAGCTTTT 60.238 34.615 12.65 4.86 46.86 2.27
97 98 7.042119 GGCATTAAGTTTGCTTTCAAGCTTTTA 60.042 33.333 12.65 4.05 46.86 1.52
98 99 8.498358 GCATTAAGTTTGCTTTCAAGCTTTTAT 58.502 29.630 12.65 4.97 46.86 1.40
101 102 7.482654 AAGTTTGCTTTCAAGCTTTTATTCC 57.517 32.000 12.65 0.00 46.86 3.01
102 103 6.483307 AAGTTTGCTTTCAAGCTTTTATTCCC 59.517 34.615 12.65 0.00 46.86 3.97
103 104 8.383524 AAGTTTGCTTTCAAGCTTTTATTCCCC 61.384 37.037 12.65 0.00 46.86 4.81
106 107 5.467035 CTTTCAAGCTTTTATTCCCCACA 57.533 39.130 0.00 0.00 0.00 4.17
121 122 0.318445 CCACAGTGCTTCAAGCTTGC 60.318 55.000 21.99 10.95 42.97 4.01
131 132 4.093408 TGCTTCAAGCTTGCTATTAACTCG 59.907 41.667 21.99 0.54 42.97 4.18
132 133 4.330074 GCTTCAAGCTTGCTATTAACTCGA 59.670 41.667 21.99 0.00 38.45 4.04
133 134 5.007136 GCTTCAAGCTTGCTATTAACTCGAT 59.993 40.000 21.99 0.00 38.45 3.59
134 135 5.973651 TCAAGCTTGCTATTAACTCGATG 57.026 39.130 21.99 0.00 0.00 3.84
184 189 2.564947 GAGCAGAAGAAGAGAAGGTGGA 59.435 50.000 0.00 0.00 0.00 4.02
200 205 1.065928 GGATGCTACACCGACTCCG 59.934 63.158 0.00 0.00 0.00 4.63
202 207 2.005960 GATGCTACACCGACTCCGCT 62.006 60.000 0.00 0.00 0.00 5.52
267 272 0.581053 GGCAAACACGGTGCATTTTG 59.419 50.000 8.30 12.36 44.07 2.44
268 273 0.042274 GCAAACACGGTGCATTTTGC 60.042 50.000 23.12 23.12 44.95 3.68
278 285 0.109179 TGCATTTTGCTGATGTCGGC 60.109 50.000 6.87 6.87 45.31 5.54
288 295 0.538584 TGATGTCGGCTGCTGATTCT 59.461 50.000 15.18 2.31 0.00 2.40
291 298 0.737367 TGTCGGCTGCTGATTCTTCG 60.737 55.000 15.18 0.00 0.00 3.79
310 317 1.841103 TGTGGTGCTGGGAGCTGTA 60.841 57.895 0.00 0.00 42.97 2.74
320 327 1.007118 TGGGAGCTGTAGGAGACATCA 59.993 52.381 0.00 0.00 37.45 3.07
367 374 4.848357 AGATTTGGTGCTGTAGCTGTAAT 58.152 39.130 5.38 0.67 42.66 1.89
454 464 7.846107 GCATTTGACATTATTGTACTGTACTCG 59.154 37.037 17.98 4.08 35.79 4.18
462 472 5.972107 ATTGTACTGTACTCGTTACCTGT 57.028 39.130 17.98 0.00 0.00 4.00
467 477 3.009473 ACTGTACTCGTTACCTGTCCCTA 59.991 47.826 0.00 0.00 0.00 3.53
469 479 3.758554 TGTACTCGTTACCTGTCCCTAAC 59.241 47.826 0.00 0.00 0.00 2.34
470 480 1.815003 ACTCGTTACCTGTCCCTAACG 59.185 52.381 4.04 4.04 44.24 3.18
471 481 1.133790 CTCGTTACCTGTCCCTAACGG 59.866 57.143 9.39 0.00 43.46 4.44
472 482 0.890683 CGTTACCTGTCCCTAACGGT 59.109 55.000 2.71 0.00 40.89 4.83
473 483 1.403249 CGTTACCTGTCCCTAACGGTG 60.403 57.143 2.71 0.00 40.89 4.94
474 484 1.895131 GTTACCTGTCCCTAACGGTGA 59.105 52.381 0.00 0.00 36.11 4.02
475 485 2.299867 GTTACCTGTCCCTAACGGTGAA 59.700 50.000 0.00 0.00 36.11 3.18
476 486 1.426751 ACCTGTCCCTAACGGTGAAA 58.573 50.000 0.00 0.00 34.75 2.69
477 487 1.071228 ACCTGTCCCTAACGGTGAAAC 59.929 52.381 0.00 0.00 34.75 2.78
478 488 1.071071 CCTGTCCCTAACGGTGAAACA 59.929 52.381 0.00 0.00 39.98 2.83
479 489 2.413837 CTGTCCCTAACGGTGAAACAG 58.586 52.381 0.00 0.00 39.98 3.16
480 490 2.036733 CTGTCCCTAACGGTGAAACAGA 59.963 50.000 2.12 0.00 39.98 3.41
481 491 2.036733 TGTCCCTAACGGTGAAACAGAG 59.963 50.000 0.00 0.00 39.98 3.35
482 492 2.036862 GTCCCTAACGGTGAAACAGAGT 59.963 50.000 0.00 0.00 39.98 3.24
483 493 2.036733 TCCCTAACGGTGAAACAGAGTG 59.963 50.000 0.00 0.00 39.98 3.51
484 494 2.413837 CCTAACGGTGAAACAGAGTGG 58.586 52.381 0.00 0.00 39.98 4.00
485 495 2.224209 CCTAACGGTGAAACAGAGTGGT 60.224 50.000 0.00 0.00 39.98 4.16
486 496 2.413310 AACGGTGAAACAGAGTGGTT 57.587 45.000 0.00 0.00 39.98 3.67
487 497 2.413310 ACGGTGAAACAGAGTGGTTT 57.587 45.000 0.00 0.00 43.30 3.27
488 498 2.718563 ACGGTGAAACAGAGTGGTTTT 58.281 42.857 0.00 0.00 40.85 2.43
489 499 3.086282 ACGGTGAAACAGAGTGGTTTTT 58.914 40.909 0.00 0.00 40.85 1.94
490 500 3.128068 ACGGTGAAACAGAGTGGTTTTTC 59.872 43.478 0.00 0.00 40.85 2.29
491 501 3.377172 CGGTGAAACAGAGTGGTTTTTCT 59.623 43.478 0.00 0.00 40.85 2.52
492 502 4.142469 CGGTGAAACAGAGTGGTTTTTCTT 60.142 41.667 0.00 0.00 40.85 2.52
493 503 5.621329 CGGTGAAACAGAGTGGTTTTTCTTT 60.621 40.000 0.00 0.00 40.85 2.52
494 504 6.163476 GGTGAAACAGAGTGGTTTTTCTTTT 58.837 36.000 0.00 0.00 40.85 2.27
495 505 6.090763 GGTGAAACAGAGTGGTTTTTCTTTTG 59.909 38.462 0.00 0.00 40.85 2.44
496 506 6.645003 GTGAAACAGAGTGGTTTTTCTTTTGT 59.355 34.615 0.00 0.00 40.85 2.83
497 507 7.170828 GTGAAACAGAGTGGTTTTTCTTTTGTT 59.829 33.333 0.00 0.00 40.85 2.83
498 508 7.170658 TGAAACAGAGTGGTTTTTCTTTTGTTG 59.829 33.333 0.00 0.00 40.85 3.33
499 509 6.339587 ACAGAGTGGTTTTTCTTTTGTTGA 57.660 33.333 0.00 0.00 0.00 3.18
500 510 6.156519 ACAGAGTGGTTTTTCTTTTGTTGAC 58.843 36.000 0.00 0.00 0.00 3.18
501 511 6.155827 CAGAGTGGTTTTTCTTTTGTTGACA 58.844 36.000 0.00 0.00 0.00 3.58
502 512 6.813152 CAGAGTGGTTTTTCTTTTGTTGACAT 59.187 34.615 0.00 0.00 0.00 3.06
503 513 6.813152 AGAGTGGTTTTTCTTTTGTTGACATG 59.187 34.615 0.00 0.00 0.00 3.21
507 517 6.070767 TGGTTTTTCTTTTGTTGACATGGGTA 60.071 34.615 0.00 0.00 0.00 3.69
510 520 8.722394 GTTTTTCTTTTGTTGACATGGGTAAAA 58.278 29.630 0.00 0.00 0.00 1.52
520 530 5.630121 TGACATGGGTAAAACAGAGATTGT 58.370 37.500 0.00 0.00 43.45 2.71
533 543 3.696051 CAGAGATTGTTGGTGGTATTGGG 59.304 47.826 0.00 0.00 0.00 4.12
534 544 2.427095 GAGATTGTTGGTGGTATTGGGC 59.573 50.000 0.00 0.00 0.00 5.36
535 545 2.175202 GATTGTTGGTGGTATTGGGCA 58.825 47.619 0.00 0.00 0.00 5.36
537 547 1.626686 TGTTGGTGGTATTGGGCAAG 58.373 50.000 0.00 0.00 0.00 4.01
538 548 1.133325 TGTTGGTGGTATTGGGCAAGT 60.133 47.619 0.00 0.00 0.00 3.16
540 550 3.158676 GTTGGTGGTATTGGGCAAGTTA 58.841 45.455 0.00 0.00 0.00 2.24
541 551 3.527507 TGGTGGTATTGGGCAAGTTAA 57.472 42.857 0.00 0.00 0.00 2.01
542 552 4.054359 TGGTGGTATTGGGCAAGTTAAT 57.946 40.909 0.00 0.00 0.00 1.40
543 553 4.020543 TGGTGGTATTGGGCAAGTTAATC 58.979 43.478 0.00 0.00 0.00 1.75
546 556 4.947388 GTGGTATTGGGCAAGTTAATCTCA 59.053 41.667 0.00 0.00 0.00 3.27
547 557 4.947388 TGGTATTGGGCAAGTTAATCTCAC 59.053 41.667 0.00 0.00 0.00 3.51
548 558 4.338400 GGTATTGGGCAAGTTAATCTCACC 59.662 45.833 0.00 0.00 0.00 4.02
550 560 1.707989 TGGGCAAGTTAATCTCACCCA 59.292 47.619 0.00 0.00 44.10 4.51
552 562 2.290960 GGGCAAGTTAATCTCACCCACT 60.291 50.000 0.00 0.00 39.57 4.00
555 565 4.081087 GGCAAGTTAATCTCACCCACTCTA 60.081 45.833 0.00 0.00 0.00 2.43
557 567 5.755861 GCAAGTTAATCTCACCCACTCTATC 59.244 44.000 0.00 0.00 0.00 2.08
558 568 5.776173 AGTTAATCTCACCCACTCTATCG 57.224 43.478 0.00 0.00 0.00 2.92
559 569 5.446860 AGTTAATCTCACCCACTCTATCGA 58.553 41.667 0.00 0.00 0.00 3.59
560 570 5.892119 AGTTAATCTCACCCACTCTATCGAA 59.108 40.000 0.00 0.00 0.00 3.71
561 571 6.551601 AGTTAATCTCACCCACTCTATCGAAT 59.448 38.462 0.00 0.00 0.00 3.34
562 572 5.878406 AATCTCACCCACTCTATCGAATT 57.122 39.130 0.00 0.00 0.00 2.17
565 578 5.446860 TCTCACCCACTCTATCGAATTAGT 58.553 41.667 0.00 0.00 0.00 2.24
569 582 6.323996 TCACCCACTCTATCGAATTAGTCATT 59.676 38.462 0.00 0.00 0.00 2.57
570 583 7.504574 TCACCCACTCTATCGAATTAGTCATTA 59.495 37.037 0.00 0.00 0.00 1.90
582 595 9.481340 TCGAATTAGTCATTATTCTCCTGATTG 57.519 33.333 0.00 0.00 0.00 2.67
583 596 9.481340 CGAATTAGTCATTATTCTCCTGATTGA 57.519 33.333 0.00 0.00 0.00 2.57
596 609 9.727859 ATTCTCCTGATTGATCTCTGAATTATG 57.272 33.333 0.00 0.00 0.00 1.90
597 610 8.260099 TCTCCTGATTGATCTCTGAATTATGT 57.740 34.615 0.00 0.00 0.00 2.29
599 612 8.672823 TCCTGATTGATCTCTGAATTATGTTG 57.327 34.615 0.00 0.00 0.00 3.33
600 613 7.718314 TCCTGATTGATCTCTGAATTATGTTGG 59.282 37.037 0.00 0.00 0.00 3.77
601 614 7.268199 TGATTGATCTCTGAATTATGTTGGC 57.732 36.000 0.00 0.00 0.00 4.52
602 615 6.263842 TGATTGATCTCTGAATTATGTTGGCC 59.736 38.462 0.00 0.00 0.00 5.36
603 616 4.464008 TGATCTCTGAATTATGTTGGCCC 58.536 43.478 0.00 0.00 0.00 5.80
604 617 3.297134 TCTCTGAATTATGTTGGCCCC 57.703 47.619 0.00 0.00 0.00 5.80
605 618 2.091885 TCTCTGAATTATGTTGGCCCCC 60.092 50.000 0.00 0.00 0.00 5.40
606 619 1.032014 CTGAATTATGTTGGCCCCCG 58.968 55.000 0.00 0.00 0.00 5.73
611 624 0.106419 TTATGTTGGCCCCCGGATTC 60.106 55.000 0.73 0.00 0.00 2.52
612 625 1.282653 TATGTTGGCCCCCGGATTCA 61.283 55.000 0.73 0.00 0.00 2.57
613 626 2.440247 GTTGGCCCCCGGATTCAG 60.440 66.667 0.73 0.00 0.00 3.02
614 627 2.612430 TTGGCCCCCGGATTCAGA 60.612 61.111 0.73 0.00 0.00 3.27
615 628 2.679342 TTGGCCCCCGGATTCAGAG 61.679 63.158 0.73 0.00 0.00 3.35
616 629 3.878667 GGCCCCCGGATTCAGAGG 61.879 72.222 0.73 0.00 0.00 3.69
617 630 3.090532 GCCCCCGGATTCAGAGGT 61.091 66.667 0.73 0.00 0.00 3.85
618 631 2.911143 CCCCCGGATTCAGAGGTG 59.089 66.667 0.73 0.00 0.00 4.00
619 632 1.995626 CCCCCGGATTCAGAGGTGT 60.996 63.158 0.73 0.00 0.00 4.16
621 634 1.264749 CCCCGGATTCAGAGGTGTCA 61.265 60.000 0.73 0.00 0.00 3.58
623 636 0.608130 CCGGATTCAGAGGTGTCACA 59.392 55.000 5.12 0.00 0.00 3.58
624 637 1.001974 CCGGATTCAGAGGTGTCACAA 59.998 52.381 5.12 0.00 0.00 3.33
625 638 2.069273 CGGATTCAGAGGTGTCACAAC 58.931 52.381 5.12 0.00 0.00 3.32
626 639 2.289072 CGGATTCAGAGGTGTCACAACT 60.289 50.000 0.00 0.00 32.17 3.16
627 640 3.744660 GGATTCAGAGGTGTCACAACTT 58.255 45.455 0.00 0.00 28.17 2.66
629 642 4.932200 GGATTCAGAGGTGTCACAACTTAG 59.068 45.833 0.00 0.00 28.17 2.18
630 643 5.511545 GGATTCAGAGGTGTCACAACTTAGT 60.512 44.000 0.00 0.00 28.17 2.24
631 644 4.322080 TCAGAGGTGTCACAACTTAGTG 57.678 45.455 0.00 0.00 40.85 2.74
632 645 3.704566 TCAGAGGTGTCACAACTTAGTGT 59.295 43.478 0.00 0.00 40.37 3.55
633 646 4.161565 TCAGAGGTGTCACAACTTAGTGTT 59.838 41.667 0.00 0.00 40.37 3.32
650 2426 8.312564 ACTTAGTGTTGTATTACCTTCCTTCTC 58.687 37.037 0.00 0.00 0.00 2.87
651 2427 6.051179 AGTGTTGTATTACCTTCCTTCTCC 57.949 41.667 0.00 0.00 0.00 3.71
658 2434 4.891992 TTACCTTCCTTCTCCAGTTCAG 57.108 45.455 0.00 0.00 0.00 3.02
661 2437 3.459969 ACCTTCCTTCTCCAGTTCAGTTT 59.540 43.478 0.00 0.00 0.00 2.66
662 2438 4.068599 CCTTCCTTCTCCAGTTCAGTTTC 58.931 47.826 0.00 0.00 0.00 2.78
664 2440 5.372373 CTTCCTTCTCCAGTTCAGTTTCTT 58.628 41.667 0.00 0.00 0.00 2.52
666 2442 6.688073 TCCTTCTCCAGTTCAGTTTCTTAT 57.312 37.500 0.00 0.00 0.00 1.73
669 2445 8.656806 TCCTTCTCCAGTTCAGTTTCTTATAAA 58.343 33.333 0.00 0.00 0.00 1.40
670 2446 9.284968 CCTTCTCCAGTTCAGTTTCTTATAAAA 57.715 33.333 0.00 0.00 0.00 1.52
685 2461 6.408869 TCTTATAAAAGAAAACGATCCCGGT 58.591 36.000 0.00 0.00 38.81 5.28
689 2465 5.970317 AAAAGAAAACGATCCCGGTAAAT 57.030 34.783 0.00 0.00 40.78 1.40
697 2473 5.349061 ACGATCCCGGTAAATTTAAGACT 57.651 39.130 0.00 0.00 40.78 3.24
707 2483 7.388500 CCGGTAAATTTAAGACTCTGGTTAACA 59.612 37.037 8.10 0.00 0.00 2.41
714 2490 8.842358 TTTAAGACTCTGGTTAACATTACAGG 57.158 34.615 8.10 3.04 0.00 4.00
717 2493 6.702329 AGACTCTGGTTAACATTACAGGAAG 58.298 40.000 8.10 3.03 0.00 3.46
718 2494 5.805728 ACTCTGGTTAACATTACAGGAAGG 58.194 41.667 8.10 1.22 0.00 3.46
719 2495 5.309806 ACTCTGGTTAACATTACAGGAAGGT 59.690 40.000 8.10 1.73 32.12 3.50
720 2496 6.183361 ACTCTGGTTAACATTACAGGAAGGTT 60.183 38.462 8.10 0.18 44.02 3.50
721 2497 6.607019 TCTGGTTAACATTACAGGAAGGTTT 58.393 36.000 8.10 0.00 38.91 3.27
722 2498 7.747690 TCTGGTTAACATTACAGGAAGGTTTA 58.252 34.615 8.10 0.00 38.91 2.01
723 2499 8.219178 TCTGGTTAACATTACAGGAAGGTTTAA 58.781 33.333 8.10 0.00 38.91 1.52
725 2501 9.369672 TGGTTAACATTACAGGAAGGTTTAAAT 57.630 29.630 8.10 0.00 38.91 1.40
731 2507 9.462606 ACATTACAGGAAGGTTTAAATAGAAGG 57.537 33.333 0.00 0.00 0.00 3.46
732 2508 9.462606 CATTACAGGAAGGTTTAAATAGAAGGT 57.537 33.333 0.00 0.00 0.00 3.50
775 2551 9.732130 AGATTGGATAGTTTATCAGCCTAAATC 57.268 33.333 0.00 0.00 36.91 2.17
790 2566 4.320494 GCCTAAATCATAAGCAACCCATCG 60.320 45.833 0.00 0.00 0.00 3.84
801 2577 1.760479 AACCCATCGACGTGGAACCA 61.760 55.000 3.81 0.00 42.02 3.67
813 2597 1.059584 TGGAACCAGTGGAAGGCTCA 61.060 55.000 18.40 2.39 0.00 4.26
815 2599 1.272147 GGAACCAGTGGAAGGCTCATT 60.272 52.381 18.40 0.00 0.00 2.57
816 2600 2.087646 GAACCAGTGGAAGGCTCATTC 58.912 52.381 18.40 2.41 0.00 2.67
817 2601 1.067295 ACCAGTGGAAGGCTCATTCA 58.933 50.000 18.40 0.00 0.00 2.57
818 2602 1.004044 ACCAGTGGAAGGCTCATTCAG 59.996 52.381 18.40 0.00 0.00 3.02
819 2603 1.004044 CCAGTGGAAGGCTCATTCAGT 59.996 52.381 1.68 0.00 0.00 3.41
820 2604 2.354259 CAGTGGAAGGCTCATTCAGTC 58.646 52.381 0.00 0.00 0.00 3.51
821 2605 1.980765 AGTGGAAGGCTCATTCAGTCA 59.019 47.619 0.00 0.00 0.00 3.41
822 2606 2.575279 AGTGGAAGGCTCATTCAGTCAT 59.425 45.455 0.00 0.00 0.00 3.06
823 2607 3.009916 AGTGGAAGGCTCATTCAGTCATT 59.990 43.478 0.00 0.00 0.00 2.57
856 2641 2.798148 ATCCGAAGCGTCCCACCAAC 62.798 60.000 0.00 0.00 0.00 3.77
884 2669 2.029073 ACAACACCTCGCGTCCAG 59.971 61.111 5.77 0.00 0.00 3.86
914 2699 0.388659 ATTTGCTTTGCTGCACGGAA 59.611 45.000 0.00 0.99 43.20 4.30
918 2703 0.936297 GCTTTGCTGCACGGAACTTG 60.936 55.000 0.00 0.00 0.00 3.16
939 2724 2.568623 ACTACAGAGCCCAAAACCAG 57.431 50.000 0.00 0.00 0.00 4.00
1391 4467 2.353958 CATGGTGAGGCTGCCTGT 59.646 61.111 28.82 2.00 31.76 4.00
1392 4468 1.200760 ACATGGTGAGGCTGCCTGTA 61.201 55.000 28.82 12.29 31.76 2.74
1436 4512 0.814010 CGAAATTCGCCCCGGAATCT 60.814 55.000 0.73 0.00 35.65 2.40
1439 4515 3.809374 ATTCGCCCCGGAATCTCGC 62.809 63.158 0.73 0.00 31.06 5.03
1441 4517 4.830765 CGCCCCGGAATCTCGCAA 62.831 66.667 0.73 0.00 0.00 4.85
1442 4518 3.202706 GCCCCGGAATCTCGCAAC 61.203 66.667 0.73 0.00 0.00 4.17
1444 4520 2.183300 CCCGGAATCTCGCAACGA 59.817 61.111 0.73 0.00 0.00 3.85
1445 4521 1.227263 CCCGGAATCTCGCAACGAT 60.227 57.895 0.73 0.00 34.61 3.73
1446 4522 1.215655 CCCGGAATCTCGCAACGATC 61.216 60.000 0.73 0.00 34.61 3.69
1447 4523 1.540607 CCGGAATCTCGCAACGATCG 61.541 60.000 14.88 14.88 34.61 3.69
1448 4524 1.540607 CGGAATCTCGCAACGATCGG 61.541 60.000 20.98 3.26 34.61 4.18
1471 4547 2.215604 CGATTCGCGTCCGTGTCTC 61.216 63.158 5.77 0.00 35.54 3.36
1472 4548 2.202440 ATTCGCGTCCGTGTCTCG 60.202 61.111 5.77 0.00 39.52 4.04
1473 4549 2.573341 GATTCGCGTCCGTGTCTCGA 62.573 60.000 5.77 0.00 42.86 4.04
1521 4600 2.207924 AACCGGTGGTTCGAGAGCT 61.208 57.895 8.52 0.00 43.05 4.09
1756 4855 1.448540 CCGGCTACAAGGTGCTGAG 60.449 63.158 0.00 0.00 37.75 3.35
1930 5043 3.058160 CGCCTTCAAGGTGCCCAG 61.058 66.667 3.44 0.00 39.28 4.45
2171 5302 3.236003 GAGGACGCCGGTTCAGGTT 62.236 63.158 1.90 0.00 0.00 3.50
2246 5377 3.719144 GTCGTGGTTTTCGCCGGG 61.719 66.667 2.18 0.00 0.00 5.73
2280 5411 1.133025 CGTTGGTTCCATGAATCTGGC 59.867 52.381 0.00 0.00 36.16 4.85
2309 5440 8.462811 TGCAGACACAAAACAAAGTATCTTTTA 58.537 29.630 0.00 0.00 0.00 1.52
2310 5441 9.296400 GCAGACACAAAACAAAGTATCTTTTAA 57.704 29.630 0.00 0.00 0.00 1.52
2325 5456 5.941555 TCTTTTAACTTTTGGGGCTTTCA 57.058 34.783 0.00 0.00 0.00 2.69
2338 5469 4.222588 TGGGGCTTTCAGGATGTTATTTTG 59.777 41.667 0.00 0.00 37.40 2.44
2348 5481 8.402798 TCAGGATGTTATTTTGTGTAATGTGT 57.597 30.769 0.00 0.00 37.40 3.72
2437 5588 6.560003 TGTGTCCAGTACTCCAATATGATT 57.440 37.500 0.00 0.00 0.00 2.57
2449 5600 6.139679 TCCAATATGATTGGAGGGAATACC 57.860 41.667 15.42 0.00 43.17 2.73
2457 5608 3.297134 TGGAGGGAATACCATCTTTGC 57.703 47.619 0.00 0.00 45.10 3.68
2481 5673 4.123497 TGTGGATCCAAGATACACTTCG 57.877 45.455 18.20 0.00 36.61 3.79
2582 7079 3.620488 ACACAGACCTGAAAACACACAT 58.380 40.909 3.76 0.00 0.00 3.21
2630 7127 7.374228 CGCATATAAACAGTAAACATTGAGCTG 59.626 37.037 0.00 0.00 0.00 4.24
2636 7134 4.339247 ACAGTAAACATTGAGCTGCAGTTT 59.661 37.500 16.64 9.24 36.49 2.66
2638 7136 5.750067 CAGTAAACATTGAGCTGCAGTTTTT 59.250 36.000 16.64 8.84 34.58 1.94
2661 7778 1.938585 TGGTTTCAGGAGGACGAGAT 58.061 50.000 0.00 0.00 0.00 2.75
2664 7781 3.384789 TGGTTTCAGGAGGACGAGATATG 59.615 47.826 0.00 0.00 0.00 1.78
2766 7883 1.552337 AGATCCTGTCATCGTGCAGTT 59.448 47.619 0.00 0.00 0.00 3.16
2839 7997 2.936202 ACGCATGGGAAGAATGCTTAT 58.064 42.857 17.76 0.00 46.65 1.73
2845 8003 5.751990 GCATGGGAAGAATGCTTATTTTCAG 59.248 40.000 0.00 0.00 45.62 3.02
2912 8080 4.383052 CGCCATACTAATAGACGCAAGAAG 59.617 45.833 0.00 0.00 43.62 2.85
2956 8124 4.512944 AGCAGCGACAAGGATTATTACATG 59.487 41.667 0.00 0.00 0.00 3.21
3112 8280 2.901975 CTCGGATGTGGGAGGAAGA 58.098 57.895 0.00 0.00 0.00 2.87
3270 8438 9.468532 ACTTTATCATGAAGTTTCAAAAGAAGC 57.531 29.630 17.24 0.00 41.13 3.86
3272 8440 9.814899 TTTATCATGAAGTTTCAAAAGAAGCAA 57.185 25.926 0.00 0.00 41.13 3.91
3273 8441 9.985730 TTATCATGAAGTTTCAAAAGAAGCAAT 57.014 25.926 0.00 0.00 41.13 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 9.595823 ACTGTGCGTAGATGTATTTAACTTAAT 57.404 29.630 0.00 0.00 0.00 1.40
9 10 8.865978 CACTGTGCGTAGATGTATTTAACTTAA 58.134 33.333 0.00 0.00 0.00 1.85
10 11 7.009815 GCACTGTGCGTAGATGTATTTAACTTA 59.990 37.037 17.93 0.00 31.71 2.24
11 12 6.183360 GCACTGTGCGTAGATGTATTTAACTT 60.183 38.462 17.93 0.00 31.71 2.66
12 13 5.291128 GCACTGTGCGTAGATGTATTTAACT 59.709 40.000 17.93 0.00 31.71 2.24
13 14 5.490213 GCACTGTGCGTAGATGTATTTAAC 58.510 41.667 17.93 0.00 31.71 2.01
14 15 5.712217 GCACTGTGCGTAGATGTATTTAA 57.288 39.130 17.93 0.00 31.71 1.52
23 24 9.448686 AGATAAATCTGAAGCACTGTGCGTAGA 62.449 40.741 26.36 26.36 41.46 2.59
24 25 7.391288 AGATAAATCTGAAGCACTGTGCGTAG 61.391 42.308 25.39 22.40 41.46 3.51
25 26 5.624509 AGATAAATCTGAAGCACTGTGCGTA 60.625 40.000 25.39 15.08 41.46 4.42
26 27 4.860916 AGATAAATCTGAAGCACTGTGCGT 60.861 41.667 25.39 23.16 41.46 5.24
27 28 3.620374 AGATAAATCTGAAGCACTGTGCG 59.380 43.478 25.39 12.51 41.46 5.34
28 29 5.557891 AAGATAAATCTGAAGCACTGTGC 57.442 39.130 24.59 24.59 39.53 4.57
29 30 8.429493 TGATAAGATAAATCTGAAGCACTGTG 57.571 34.615 2.76 2.76 37.19 3.66
30 31 9.624373 AATGATAAGATAAATCTGAAGCACTGT 57.376 29.630 0.00 0.00 37.19 3.55
43 44 9.474313 GGGGCATAATGGTAATGATAAGATAAA 57.526 33.333 0.00 0.00 0.00 1.40
44 45 8.619281 TGGGGCATAATGGTAATGATAAGATAA 58.381 33.333 0.00 0.00 0.00 1.75
45 46 8.168905 TGGGGCATAATGGTAATGATAAGATA 57.831 34.615 0.00 0.00 0.00 1.98
46 47 7.043300 TGGGGCATAATGGTAATGATAAGAT 57.957 36.000 0.00 0.00 0.00 2.40
47 48 6.461577 TGGGGCATAATGGTAATGATAAGA 57.538 37.500 0.00 0.00 0.00 2.10
48 49 5.653769 CCTGGGGCATAATGGTAATGATAAG 59.346 44.000 0.00 0.00 0.00 1.73
49 50 5.579047 CCTGGGGCATAATGGTAATGATAA 58.421 41.667 0.00 0.00 0.00 1.75
50 51 5.191727 CCTGGGGCATAATGGTAATGATA 57.808 43.478 0.00 0.00 0.00 2.15
51 52 4.051661 CCTGGGGCATAATGGTAATGAT 57.948 45.455 0.00 0.00 0.00 2.45
52 53 3.524095 CCTGGGGCATAATGGTAATGA 57.476 47.619 0.00 0.00 0.00 2.57
65 66 3.996696 AAGCAAACTTAATGCCTGGGGC 61.997 50.000 1.07 1.07 44.91 5.80
66 67 1.560505 AGCAAACTTAATGCCTGGGG 58.439 50.000 0.00 0.00 44.91 4.96
67 68 3.006752 TGAAAGCAAACTTAATGCCTGGG 59.993 43.478 0.00 0.00 44.91 4.45
68 69 4.255833 TGAAAGCAAACTTAATGCCTGG 57.744 40.909 0.00 0.00 44.91 4.45
69 70 5.834239 CTTGAAAGCAAACTTAATGCCTG 57.166 39.130 0.00 0.00 44.91 4.85
84 85 5.011023 ACTGTGGGGAATAAAAGCTTGAAAG 59.989 40.000 0.00 0.00 0.00 2.62
85 86 4.898861 ACTGTGGGGAATAAAAGCTTGAAA 59.101 37.500 0.00 0.00 0.00 2.69
86 87 4.280677 CACTGTGGGGAATAAAAGCTTGAA 59.719 41.667 0.00 0.00 0.00 2.69
87 88 3.826157 CACTGTGGGGAATAAAAGCTTGA 59.174 43.478 0.00 0.00 0.00 3.02
88 89 3.614870 GCACTGTGGGGAATAAAAGCTTG 60.615 47.826 10.21 0.00 0.00 4.01
89 90 2.562738 GCACTGTGGGGAATAAAAGCTT 59.437 45.455 10.21 0.00 0.00 3.74
90 91 2.171003 GCACTGTGGGGAATAAAAGCT 58.829 47.619 10.21 0.00 0.00 3.74
91 92 2.171003 AGCACTGTGGGGAATAAAAGC 58.829 47.619 10.21 0.00 0.00 3.51
92 93 3.826157 TGAAGCACTGTGGGGAATAAAAG 59.174 43.478 10.21 0.00 0.00 2.27
93 94 3.838565 TGAAGCACTGTGGGGAATAAAA 58.161 40.909 10.21 0.00 0.00 1.52
94 95 3.517296 TGAAGCACTGTGGGGAATAAA 57.483 42.857 10.21 0.00 0.00 1.40
95 96 3.420893 CTTGAAGCACTGTGGGGAATAA 58.579 45.455 10.21 0.00 0.00 1.40
96 97 2.879756 GCTTGAAGCACTGTGGGGAATA 60.880 50.000 13.09 0.00 41.89 1.75
97 98 1.915141 CTTGAAGCACTGTGGGGAAT 58.085 50.000 10.21 0.00 0.00 3.01
98 99 0.823356 GCTTGAAGCACTGTGGGGAA 60.823 55.000 13.09 0.00 41.89 3.97
99 100 1.228245 GCTTGAAGCACTGTGGGGA 60.228 57.895 13.09 0.00 41.89 4.81
100 101 0.825010 AAGCTTGAAGCACTGTGGGG 60.825 55.000 20.45 0.00 45.56 4.96
101 102 0.313043 CAAGCTTGAAGCACTGTGGG 59.687 55.000 22.31 0.00 45.56 4.61
102 103 0.318445 GCAAGCTTGAAGCACTGTGG 60.318 55.000 30.39 0.00 45.56 4.17
103 104 0.666913 AGCAAGCTTGAAGCACTGTG 59.333 50.000 30.39 12.09 45.56 3.66
104 105 2.260844 TAGCAAGCTTGAAGCACTGT 57.739 45.000 30.39 9.10 45.56 3.55
105 106 3.844577 AATAGCAAGCTTGAAGCACTG 57.155 42.857 30.39 16.25 45.56 3.66
106 107 5.006386 AGTTAATAGCAAGCTTGAAGCACT 58.994 37.500 30.39 18.20 45.56 4.40
147 152 1.970640 TGCTCTTGCAGTCTCCTGTTA 59.029 47.619 0.00 0.00 45.31 2.41
184 189 2.052690 AGCGGAGTCGGTGTAGCAT 61.053 57.895 0.00 0.00 45.98 3.79
200 205 2.171489 GACGGTTTGAACGCCTCAGC 62.171 60.000 0.00 0.00 34.81 4.26
202 207 0.599204 GAGACGGTTTGAACGCCTCA 60.599 55.000 0.00 0.00 34.00 3.86
249 254 0.042274 GCAAAATGCACCGTGTTTGC 60.042 50.000 17.34 17.34 46.21 3.68
267 272 1.094073 AATCAGCAGCCGACATCAGC 61.094 55.000 0.00 0.00 0.00 4.26
268 273 0.935898 GAATCAGCAGCCGACATCAG 59.064 55.000 0.00 0.00 0.00 2.90
278 285 1.462283 CACCACACGAAGAATCAGCAG 59.538 52.381 0.00 0.00 0.00 4.24
279 286 1.511850 CACCACACGAAGAATCAGCA 58.488 50.000 0.00 0.00 0.00 4.41
288 295 2.425592 CTCCCAGCACCACACGAA 59.574 61.111 0.00 0.00 0.00 3.85
291 298 2.111999 TACAGCTCCCAGCACCACAC 62.112 60.000 0.00 0.00 45.56 3.82
310 317 4.466726 GGTTACAACTAGGTGATGTCTCCT 59.533 45.833 16.48 8.52 42.06 3.69
367 374 6.652062 GCAAGCCTTTTACACTAGTTAACCTA 59.348 38.462 0.88 0.00 0.00 3.08
383 390 1.134729 CCAAACACACTGCAAGCCTTT 60.135 47.619 0.00 0.00 37.60 3.11
454 464 1.895131 TCACCGTTAGGGACAGGTAAC 59.105 52.381 0.00 0.00 43.47 2.50
462 472 2.036733 CACTCTGTTTCACCGTTAGGGA 59.963 50.000 0.00 0.00 43.47 4.20
467 477 2.413310 AACCACTCTGTTTCACCGTT 57.587 45.000 0.00 0.00 0.00 4.44
469 479 3.377172 AGAAAAACCACTCTGTTTCACCG 59.623 43.478 0.00 0.00 37.46 4.94
470 480 4.983671 AGAAAAACCACTCTGTTTCACC 57.016 40.909 0.00 0.00 37.46 4.02
471 481 6.645003 ACAAAAGAAAAACCACTCTGTTTCAC 59.355 34.615 0.00 0.00 37.46 3.18
472 482 6.754193 ACAAAAGAAAAACCACTCTGTTTCA 58.246 32.000 0.00 0.00 37.46 2.69
473 483 7.383843 TCAACAAAAGAAAAACCACTCTGTTTC 59.616 33.333 0.00 0.00 37.46 2.78
474 484 7.170828 GTCAACAAAAGAAAAACCACTCTGTTT 59.829 33.333 0.00 0.00 40.05 2.83
475 485 6.645003 GTCAACAAAAGAAAAACCACTCTGTT 59.355 34.615 0.00 0.00 0.00 3.16
476 486 6.156519 GTCAACAAAAGAAAAACCACTCTGT 58.843 36.000 0.00 0.00 0.00 3.41
477 487 6.155827 TGTCAACAAAAGAAAAACCACTCTG 58.844 36.000 0.00 0.00 0.00 3.35
478 488 6.339587 TGTCAACAAAAGAAAAACCACTCT 57.660 33.333 0.00 0.00 0.00 3.24
479 489 6.035975 CCATGTCAACAAAAGAAAAACCACTC 59.964 38.462 0.00 0.00 0.00 3.51
480 490 5.874261 CCATGTCAACAAAAGAAAAACCACT 59.126 36.000 0.00 0.00 0.00 4.00
481 491 5.064579 CCCATGTCAACAAAAGAAAAACCAC 59.935 40.000 0.00 0.00 0.00 4.16
482 492 5.181748 CCCATGTCAACAAAAGAAAAACCA 58.818 37.500 0.00 0.00 0.00 3.67
483 493 5.182487 ACCCATGTCAACAAAAGAAAAACC 58.818 37.500 0.00 0.00 0.00 3.27
484 494 7.835634 TTACCCATGTCAACAAAAGAAAAAC 57.164 32.000 0.00 0.00 0.00 2.43
485 495 8.722394 GTTTTACCCATGTCAACAAAAGAAAAA 58.278 29.630 0.00 0.00 0.00 1.94
486 496 7.878127 TGTTTTACCCATGTCAACAAAAGAAAA 59.122 29.630 0.00 0.00 29.36 2.29
487 497 7.386851 TGTTTTACCCATGTCAACAAAAGAAA 58.613 30.769 0.00 0.00 29.36 2.52
488 498 6.936279 TGTTTTACCCATGTCAACAAAAGAA 58.064 32.000 0.00 0.00 29.36 2.52
489 499 6.378564 TCTGTTTTACCCATGTCAACAAAAGA 59.621 34.615 0.00 0.00 31.10 2.52
490 500 6.568869 TCTGTTTTACCCATGTCAACAAAAG 58.431 36.000 0.00 0.00 31.10 2.27
491 501 6.378564 TCTCTGTTTTACCCATGTCAACAAAA 59.621 34.615 0.00 0.00 31.10 2.44
492 502 5.888724 TCTCTGTTTTACCCATGTCAACAAA 59.111 36.000 0.00 0.00 31.10 2.83
493 503 5.441500 TCTCTGTTTTACCCATGTCAACAA 58.558 37.500 0.00 0.00 31.10 2.83
494 504 5.042463 TCTCTGTTTTACCCATGTCAACA 57.958 39.130 0.00 0.00 0.00 3.33
495 505 6.016276 ACAATCTCTGTTTTACCCATGTCAAC 60.016 38.462 0.00 0.00 32.99 3.18
496 506 6.068010 ACAATCTCTGTTTTACCCATGTCAA 58.932 36.000 0.00 0.00 32.99 3.18
497 507 5.630121 ACAATCTCTGTTTTACCCATGTCA 58.370 37.500 0.00 0.00 32.99 3.58
498 508 6.381801 CAACAATCTCTGTTTTACCCATGTC 58.618 40.000 0.00 0.00 46.49 3.06
499 509 5.243730 CCAACAATCTCTGTTTTACCCATGT 59.756 40.000 0.00 0.00 46.49 3.21
500 510 5.243730 ACCAACAATCTCTGTTTTACCCATG 59.756 40.000 0.00 0.00 46.49 3.66
501 511 5.243730 CACCAACAATCTCTGTTTTACCCAT 59.756 40.000 0.00 0.00 46.49 4.00
502 512 4.582656 CACCAACAATCTCTGTTTTACCCA 59.417 41.667 0.00 0.00 46.49 4.51
503 513 4.022329 CCACCAACAATCTCTGTTTTACCC 60.022 45.833 0.00 0.00 46.49 3.69
507 517 6.239289 CCAATACCACCAACAATCTCTGTTTT 60.239 38.462 0.00 0.00 46.49 2.43
510 520 4.335416 CCAATACCACCAACAATCTCTGT 58.665 43.478 0.00 0.00 41.27 3.41
520 530 2.390225 AACTTGCCCAATACCACCAA 57.610 45.000 0.00 0.00 0.00 3.67
525 535 4.338400 GGTGAGATTAACTTGCCCAATACC 59.662 45.833 0.00 0.00 0.00 2.73
526 536 4.338400 GGGTGAGATTAACTTGCCCAATAC 59.662 45.833 0.00 0.00 40.26 1.89
527 537 4.017958 TGGGTGAGATTAACTTGCCCAATA 60.018 41.667 0.00 0.00 43.99 1.90
528 538 3.245586 TGGGTGAGATTAACTTGCCCAAT 60.246 43.478 0.00 0.00 43.99 3.16
529 539 2.109128 TGGGTGAGATTAACTTGCCCAA 59.891 45.455 0.00 0.00 43.99 4.12
531 541 2.092323 GTGGGTGAGATTAACTTGCCC 58.908 52.381 0.00 0.00 40.63 5.36
533 543 3.944087 AGAGTGGGTGAGATTAACTTGC 58.056 45.455 0.00 0.00 0.00 4.01
534 544 5.980116 CGATAGAGTGGGTGAGATTAACTTG 59.020 44.000 0.00 0.00 39.76 3.16
535 545 5.892119 TCGATAGAGTGGGTGAGATTAACTT 59.108 40.000 0.00 0.00 42.67 2.66
537 547 5.769484 TCGATAGAGTGGGTGAGATTAAC 57.231 43.478 0.00 0.00 42.67 2.01
557 567 9.481340 TCAATCAGGAGAATAATGACTAATTCG 57.519 33.333 0.00 0.00 37.22 3.34
562 572 9.599056 AGAGATCAATCAGGAGAATAATGACTA 57.401 33.333 0.00 0.00 0.00 2.59
565 578 8.488308 TCAGAGATCAATCAGGAGAATAATGA 57.512 34.615 0.00 0.00 0.00 2.57
570 583 9.727859 CATAATTCAGAGATCAATCAGGAGAAT 57.272 33.333 0.00 0.00 0.00 2.40
582 595 3.823304 GGGGCCAACATAATTCAGAGATC 59.177 47.826 4.39 0.00 0.00 2.75
583 596 3.437052 GGGGGCCAACATAATTCAGAGAT 60.437 47.826 4.39 0.00 0.00 2.75
587 600 1.032014 CGGGGGCCAACATAATTCAG 58.968 55.000 4.39 0.00 0.00 3.02
596 609 2.440247 CTGAATCCGGGGGCCAAC 60.440 66.667 4.39 0.00 0.00 3.77
597 610 2.612430 TCTGAATCCGGGGGCCAA 60.612 61.111 4.39 0.00 0.00 4.52
599 612 3.878667 CCTCTGAATCCGGGGGCC 61.879 72.222 0.00 0.00 31.31 5.80
600 613 3.090532 ACCTCTGAATCCGGGGGC 61.091 66.667 0.00 0.00 43.48 5.80
601 614 1.972660 GACACCTCTGAATCCGGGGG 61.973 65.000 0.00 0.00 45.27 5.40
602 615 1.264749 TGACACCTCTGAATCCGGGG 61.265 60.000 0.00 0.00 0.00 5.73
603 616 0.108138 GTGACACCTCTGAATCCGGG 60.108 60.000 0.00 0.00 0.00 5.73
604 617 0.608130 TGTGACACCTCTGAATCCGG 59.392 55.000 2.45 0.00 0.00 5.14
605 618 2.069273 GTTGTGACACCTCTGAATCCG 58.931 52.381 2.45 0.00 0.00 4.18
606 619 3.409026 AGTTGTGACACCTCTGAATCC 57.591 47.619 2.45 0.00 0.00 3.01
611 624 4.060038 ACACTAAGTTGTGACACCTCTG 57.940 45.455 2.45 0.00 40.12 3.35
612 625 4.755266 AACACTAAGTTGTGACACCTCT 57.245 40.909 2.45 0.00 39.49 3.69
623 636 8.657712 AGAAGGAAGGTAATACAACACTAAGTT 58.342 33.333 0.00 0.00 42.42 2.66
624 637 8.203681 AGAAGGAAGGTAATACAACACTAAGT 57.796 34.615 0.00 0.00 0.00 2.24
625 638 7.764901 GGAGAAGGAAGGTAATACAACACTAAG 59.235 40.741 0.00 0.00 0.00 2.18
626 639 7.236019 TGGAGAAGGAAGGTAATACAACACTAA 59.764 37.037 0.00 0.00 0.00 2.24
627 640 6.727231 TGGAGAAGGAAGGTAATACAACACTA 59.273 38.462 0.00 0.00 0.00 2.74
629 642 5.801380 TGGAGAAGGAAGGTAATACAACAC 58.199 41.667 0.00 0.00 0.00 3.32
630 643 5.546499 ACTGGAGAAGGAAGGTAATACAACA 59.454 40.000 0.00 0.00 0.00 3.33
631 644 6.051179 ACTGGAGAAGGAAGGTAATACAAC 57.949 41.667 0.00 0.00 0.00 3.32
632 645 6.271391 TGAACTGGAGAAGGAAGGTAATACAA 59.729 38.462 0.00 0.00 0.00 2.41
633 646 5.783360 TGAACTGGAGAAGGAAGGTAATACA 59.217 40.000 0.00 0.00 0.00 2.29
634 647 6.070710 ACTGAACTGGAGAAGGAAGGTAATAC 60.071 42.308 0.00 0.00 0.00 1.89
635 648 6.023603 ACTGAACTGGAGAAGGAAGGTAATA 58.976 40.000 0.00 0.00 0.00 0.98
636 649 4.846940 ACTGAACTGGAGAAGGAAGGTAAT 59.153 41.667 0.00 0.00 0.00 1.89
640 2416 3.778954 AACTGAACTGGAGAAGGAAGG 57.221 47.619 0.00 0.00 0.00 3.46
661 2437 6.408869 ACCGGGATCGTTTTCTTTTATAAGA 58.591 36.000 6.32 0.00 35.13 2.10
662 2438 6.673154 ACCGGGATCGTTTTCTTTTATAAG 57.327 37.500 6.32 0.00 33.95 1.73
664 2440 8.735692 ATTTACCGGGATCGTTTTCTTTTATA 57.264 30.769 6.32 0.00 33.95 0.98
666 2442 7.451501 AATTTACCGGGATCGTTTTCTTTTA 57.548 32.000 6.32 0.00 33.95 1.52
669 2445 5.970317 AAATTTACCGGGATCGTTTTCTT 57.030 34.783 6.32 0.00 33.95 2.52
670 2446 6.880529 TCTTAAATTTACCGGGATCGTTTTCT 59.119 34.615 6.32 0.00 33.95 2.52
671 2447 6.963242 GTCTTAAATTTACCGGGATCGTTTTC 59.037 38.462 6.32 0.00 33.95 2.29
672 2448 6.656270 AGTCTTAAATTTACCGGGATCGTTTT 59.344 34.615 6.32 0.45 33.95 2.43
673 2449 6.175471 AGTCTTAAATTTACCGGGATCGTTT 58.825 36.000 6.32 1.30 33.95 3.60
674 2450 5.737860 AGTCTTAAATTTACCGGGATCGTT 58.262 37.500 6.32 0.00 33.95 3.85
675 2451 5.128335 AGAGTCTTAAATTTACCGGGATCGT 59.872 40.000 6.32 0.00 33.95 3.73
676 2452 5.462398 CAGAGTCTTAAATTTACCGGGATCG 59.538 44.000 6.32 0.00 0.00 3.69
677 2453 5.758784 CCAGAGTCTTAAATTTACCGGGATC 59.241 44.000 6.32 0.00 0.00 3.36
678 2454 5.191124 ACCAGAGTCTTAAATTTACCGGGAT 59.809 40.000 6.32 0.00 0.00 3.85
679 2455 4.533311 ACCAGAGTCTTAAATTTACCGGGA 59.467 41.667 6.32 0.00 0.00 5.14
682 2458 8.314143 TGTTAACCAGAGTCTTAAATTTACCG 57.686 34.615 2.48 0.00 0.00 4.02
689 2465 8.653191 TCCTGTAATGTTAACCAGAGTCTTAAA 58.347 33.333 10.18 0.00 0.00 1.52
697 2473 5.836024 ACCTTCCTGTAATGTTAACCAGA 57.164 39.130 10.18 0.00 0.00 3.86
710 2486 7.523415 TGAACCTTCTATTTAAACCTTCCTGT 58.477 34.615 0.00 0.00 0.00 4.00
711 2487 7.996098 TGAACCTTCTATTTAAACCTTCCTG 57.004 36.000 0.00 0.00 0.00 3.86
712 2488 9.601810 ATTTGAACCTTCTATTTAAACCTTCCT 57.398 29.630 0.00 0.00 0.00 3.36
725 2501 9.627123 TCTTTTCTCAGAAATTTGAACCTTCTA 57.373 29.630 0.00 0.00 0.00 2.10
727 2503 9.755804 AATCTTTTCTCAGAAATTTGAACCTTC 57.244 29.630 0.00 0.00 0.00 3.46
729 2505 8.146412 CCAATCTTTTCTCAGAAATTTGAACCT 58.854 33.333 14.87 0.00 0.00 3.50
731 2507 9.702494 ATCCAATCTTTTCTCAGAAATTTGAAC 57.298 29.630 14.87 0.00 0.00 3.18
775 2551 1.327460 CACGTCGATGGGTTGCTTATG 59.673 52.381 9.90 0.00 0.00 1.90
790 2566 0.602905 CCTTCCACTGGTTCCACGTC 60.603 60.000 0.00 0.00 0.00 4.34
801 2577 1.980765 TGACTGAATGAGCCTTCCACT 59.019 47.619 0.00 0.00 0.00 4.00
813 2597 3.094572 CCCTTCTGCCAAATGACTGAAT 58.905 45.455 0.00 0.00 0.00 2.57
815 2599 1.704628 TCCCTTCTGCCAAATGACTGA 59.295 47.619 0.00 0.00 0.00 3.41
816 2600 2.205022 TCCCTTCTGCCAAATGACTG 57.795 50.000 0.00 0.00 0.00 3.51
817 2601 2.978156 TTCCCTTCTGCCAAATGACT 57.022 45.000 0.00 0.00 0.00 3.41
818 2602 3.118992 GGATTTCCCTTCTGCCAAATGAC 60.119 47.826 0.00 0.00 0.00 3.06
819 2603 3.099141 GGATTTCCCTTCTGCCAAATGA 58.901 45.455 0.00 0.00 0.00 2.57
820 2604 2.159198 CGGATTTCCCTTCTGCCAAATG 60.159 50.000 0.00 0.00 0.00 2.32
821 2605 2.102578 CGGATTTCCCTTCTGCCAAAT 58.897 47.619 0.00 0.00 0.00 2.32
822 2606 1.074727 TCGGATTTCCCTTCTGCCAAA 59.925 47.619 0.00 0.00 0.00 3.28
823 2607 0.695924 TCGGATTTCCCTTCTGCCAA 59.304 50.000 0.00 0.00 0.00 4.52
901 2686 1.098869 TTCAAGTTCCGTGCAGCAAA 58.901 45.000 0.00 0.00 0.00 3.68
914 2699 3.857157 TTTGGGCTCTGTAGTTCAAGT 57.143 42.857 0.00 0.00 0.00 3.16
918 2703 2.814336 CTGGTTTTGGGCTCTGTAGTTC 59.186 50.000 0.00 0.00 0.00 3.01
1092 2901 0.560688 GGATGGAGAGAGGGGAGACT 59.439 60.000 0.00 0.00 0.00 3.24
1391 4467 1.668826 AATGTTGCAGAGGGAGGGTA 58.331 50.000 0.00 0.00 0.00 3.69
1392 4468 0.779997 AAATGTTGCAGAGGGAGGGT 59.220 50.000 0.00 0.00 0.00 4.34
1436 4512 2.506217 GTGAGCCGATCGTTGCGA 60.506 61.111 15.09 0.99 41.13 5.10
1458 4534 2.944557 CATCGAGACACGGACGCG 60.945 66.667 3.53 3.53 42.82 6.01
1469 4545 1.067749 CTCCTCTGGCTGCATCGAG 59.932 63.158 0.50 3.63 0.00 4.04
1471 4547 2.108566 CCTCCTCTGGCTGCATCG 59.891 66.667 0.50 0.00 0.00 3.84
1907 5020 4.699522 ACCTTGAAGGCGCCGACC 62.700 66.667 23.20 14.70 39.63 4.79
1930 5043 0.798776 CTTGCACGAGATGGTGAACC 59.201 55.000 0.00 0.00 40.38 3.62
2060 5191 0.679505 CGAAGGACTGGTGGAAGACA 59.320 55.000 0.00 0.00 0.00 3.41
2119 5250 2.331019 AAAGGACGCAACAACGGCAC 62.331 55.000 0.00 0.00 45.15 5.01
2120 5251 2.115911 AAAGGACGCAACAACGGCA 61.116 52.632 0.00 0.00 45.15 5.69
2199 5330 3.006247 GCTCCTCCTTGATCAAGAACAC 58.994 50.000 32.49 14.95 40.79 3.32
2246 5377 1.812571 ACCAACGGATTGATCACTTGC 59.187 47.619 0.00 0.00 38.15 4.01
2293 5424 9.607988 CCCCAAAAGTTAAAAGATACTTTGTTT 57.392 29.630 0.00 0.00 42.17 2.83
2298 5429 7.612065 AAGCCCCAAAAGTTAAAAGATACTT 57.388 32.000 0.00 0.00 36.20 2.24
2299 5430 7.289084 TGAAAGCCCCAAAAGTTAAAAGATACT 59.711 33.333 0.00 0.00 0.00 2.12
2309 5440 2.470057 TCCTGAAAGCCCCAAAAGTT 57.530 45.000 0.00 0.00 0.00 2.66
2310 5441 2.250924 CATCCTGAAAGCCCCAAAAGT 58.749 47.619 0.00 0.00 0.00 2.66
2311 5442 2.250924 ACATCCTGAAAGCCCCAAAAG 58.749 47.619 0.00 0.00 0.00 2.27
2316 5447 4.222810 ACAAAATAACATCCTGAAAGCCCC 59.777 41.667 0.00 0.00 0.00 5.80
2318 5449 5.783111 ACACAAAATAACATCCTGAAAGCC 58.217 37.500 0.00 0.00 0.00 4.35
2325 5456 9.515226 ACTACACATTACACAAAATAACATCCT 57.485 29.630 0.00 0.00 0.00 3.24
2338 5469 7.492352 AGAAAAAGGACACTACACATTACAC 57.508 36.000 0.00 0.00 0.00 2.90
2348 5481 9.675464 TTCACTAAAAGAAGAAAAAGGACACTA 57.325 29.630 0.00 0.00 0.00 2.74
2437 5588 2.852449 AGCAAAGATGGTATTCCCTCCA 59.148 45.455 0.00 0.00 34.98 3.86
2449 5600 5.128205 TCTTGGATCCACATAGCAAAGATG 58.872 41.667 15.91 0.00 0.00 2.90
2457 5608 5.923114 CGAAGTGTATCTTGGATCCACATAG 59.077 44.000 15.91 9.98 36.40 2.23
2481 5673 3.507622 CCTTCATTTCTGGTGTCCCTTTC 59.492 47.826 0.00 0.00 0.00 2.62
2574 7067 3.923461 CCGTTGTTTTTGACATGTGTGTT 59.077 39.130 1.15 0.00 39.09 3.32
2575 7068 3.506810 CCGTTGTTTTTGACATGTGTGT 58.493 40.909 1.15 0.00 42.49 3.72
2576 7069 2.281234 GCCGTTGTTTTTGACATGTGTG 59.719 45.455 1.15 0.00 38.26 3.82
2582 7079 2.685388 TCTGATGCCGTTGTTTTTGACA 59.315 40.909 0.00 0.00 36.19 3.58
2636 7134 4.975631 TCGTCCTCCTGAAACCATTAAAA 58.024 39.130 0.00 0.00 0.00 1.52
2638 7136 3.835978 TCTCGTCCTCCTGAAACCATTAA 59.164 43.478 0.00 0.00 0.00 1.40
2639 7137 3.437213 TCTCGTCCTCCTGAAACCATTA 58.563 45.455 0.00 0.00 0.00 1.90
2650 7148 1.957177 TGCTGACATATCTCGTCCTCC 59.043 52.381 0.00 0.00 32.15 4.30
2652 7150 3.225940 TCATGCTGACATATCTCGTCCT 58.774 45.455 0.00 0.00 33.67 3.85
2654 7152 4.615949 ACTTCATGCTGACATATCTCGTC 58.384 43.478 0.00 0.00 33.67 4.20
2661 7778 7.404671 TCAGTAGTAACTTCATGCTGACATA 57.595 36.000 0.00 0.00 31.42 2.29
2664 7781 5.926542 TGTTCAGTAGTAACTTCATGCTGAC 59.073 40.000 0.00 0.00 31.97 3.51
2839 7997 7.669722 ACATTAGAATGTTAGCCCTTCTGAAAA 59.330 33.333 1.96 0.00 46.95 2.29
2845 8003 8.732746 TTTCTACATTAGAATGTTAGCCCTTC 57.267 34.615 12.85 0.00 46.95 3.46
2869 8037 3.555547 GCGCTGTGATTCCTTTTGTTTTT 59.444 39.130 0.00 0.00 0.00 1.94
2912 8080 1.120437 GCTTTGCGCACAGTAAACAC 58.880 50.000 23.45 3.31 38.92 3.32
2946 8114 8.432110 TGATTGTAGAACGTGCATGTAATAAT 57.568 30.769 12.96 10.63 0.00 1.28
2956 8124 4.483476 AAACCTTGATTGTAGAACGTGC 57.517 40.909 0.00 0.00 0.00 5.34
3112 8280 2.224548 GGGGTCGAGGCTGCTATTTATT 60.225 50.000 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.