Multiple sequence alignment - TraesCS7B01G489400

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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 TraesCS7B01G489400 chr7B 100.000 3361 0 0 1 3361 743452354 743448994 0.000000e+00 6207.0
1 TraesCS7B01G489400 chr7B 97.368 114 3 0 407 520 743451874 743451761 9.520000e-46 195.0
2 TraesCS7B01G489400 chr7B 97.368 114 3 0 481 594 743451948 743451835 9.520000e-46 195.0
3 TraesCS7B01G489400 chr7B 100.000 40 0 0 407 446 743451800 743451761 1.290000e-09 75.0
4 TraesCS7B01G489400 chr7B 100.000 40 0 0 555 594 743451948 743451909 1.290000e-09 75.0
5 TraesCS7B01G489400 chr7D 91.287 2571 157 36 817 3361 631925005 631922476 0.000000e+00 3445.0
6 TraesCS7B01G489400 chr7D 90.303 330 32 0 1 330 631925771 631925442 1.850000e-117 433.0
7 TraesCS7B01G489400 chr7D 85.294 68 9 1 66 132 442824619 442824686 6.020000e-08 69.4
8 TraesCS7B01G489400 chr7A 91.224 1732 95 23 783 2490 736492817 736494515 0.000000e+00 2303.0
9 TraesCS7B01G489400 chr7A 89.000 900 69 21 2484 3361 736494987 736495878 0.000000e+00 1086.0
10 TraesCS7B01G489400 chr7A 88.270 341 39 1 1 341 736488236 736488575 1.120000e-109 407.0
11 TraesCS7B01G489400 chr7A 78.049 123 24 3 13 132 674610683 674610805 1.290000e-09 75.0
12 TraesCS7B01G489400 chr6B 82.603 1529 180 41 993 2490 246677595 246676122 0.000000e+00 1271.0
13 TraesCS7B01G489400 chr6B 82.341 1529 184 40 993 2490 246773700 246772227 0.000000e+00 1249.0
14 TraesCS7B01G489400 chr6B 84.581 1109 137 16 1385 2490 246362070 246360993 0.000000e+00 1070.0
15 TraesCS7B01G489400 chr6B 85.059 763 101 10 1731 2490 246510322 246509570 0.000000e+00 765.0
16 TraesCS7B01G489400 chr6B 90.141 71 6 1 3091 3160 225937743 225937813 1.280000e-14 91.6
17 TraesCS7B01G489400 chrUn 82.472 1529 182 40 993 2490 190887399 190885926 0.000000e+00 1260.0
18 TraesCS7B01G489400 chr3B 82.432 370 51 11 2989 3354 160353504 160353145 9.060000e-81 311.0
19 TraesCS7B01G489400 chr3B 92.424 66 3 2 3097 3160 293628501 293628566 3.570000e-15 93.5
20 TraesCS7B01G489400 chr1D 79.273 275 46 11 2852 3121 75012600 75012868 7.410000e-42 182.0
21 TraesCS7B01G489400 chr1D 79.137 278 41 15 2852 3121 74957503 74957771 3.450000e-40 176.0
22 TraesCS7B01G489400 chr1B 85.621 153 18 4 2957 3107 506912829 506912979 1.250000e-34 158.0
23 TraesCS7B01G489400 chr5B 79.730 222 34 9 2888 3105 553358858 553358644 2.090000e-32 150.0
24 TraesCS7B01G489400 chr5B 100.000 29 0 0 110 138 117283551 117283523 2.000000e-03 54.7
25 TraesCS7B01G489400 chr2D 84.354 147 19 4 2989 3133 411261170 411261314 1.260000e-29 141.0
26 TraesCS7B01G489400 chr3A 79.775 178 30 6 2936 3109 147807207 147807032 1.270000e-24 124.0
27 TraesCS7B01G489400 chr3A 77.880 217 34 9 2911 3123 616775208 616775002 4.550000e-24 122.0
28 TraesCS7B01G489400 chr4A 81.690 142 20 6 587 724 740895486 740895625 2.740000e-21 113.0
29 TraesCS7B01G489400 chr4B 94.595 37 2 0 102 138 453075798 453075834 1.300000e-04 58.4


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 TraesCS7B01G489400 chr7B 743448994 743452354 3360 True 1349.4 6207 98.9472 1 3361 5 chr7B.!!$R1 3360
1 TraesCS7B01G489400 chr7D 631922476 631925771 3295 True 1939.0 3445 90.7950 1 3361 2 chr7D.!!$R1 3360
2 TraesCS7B01G489400 chr7A 736492817 736495878 3061 False 1694.5 2303 90.1120 783 3361 2 chr7A.!!$F3 2578
3 TraesCS7B01G489400 chr6B 246676122 246677595 1473 True 1271.0 1271 82.6030 993 2490 1 chr6B.!!$R3 1497
4 TraesCS7B01G489400 chr6B 246772227 246773700 1473 True 1249.0 1249 82.3410 993 2490 1 chr6B.!!$R4 1497
5 TraesCS7B01G489400 chr6B 246360993 246362070 1077 True 1070.0 1070 84.5810 1385 2490 1 chr6B.!!$R1 1105
6 TraesCS7B01G489400 chr6B 246509570 246510322 752 True 765.0 765 85.0590 1731 2490 1 chr6B.!!$R2 759
7 TraesCS7B01G489400 chrUn 190885926 190887399 1473 True 1260.0 1260 82.4720 993 2490 1 chrUn.!!$R1 1497

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
649 721 0.042581 TGTGCTCATAGGGACAGGGA 59.957 55.0 0.00 0.00 32.85 4.20 F
996 1074 0.240678 TGCCTACGTACGAGCGAAAA 59.759 50.0 24.41 3.05 35.59 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2310 2440 0.102481 TGGCTCGTTATCTCGAAGGC 59.898 55.0 0.00 0.0 39.34 4.35 R
2902 3536 0.773644 AGAGCTCCAAAAGGCCTGAA 59.226 50.0 5.69 0.0 0.00 3.02 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
58 59 2.814097 CGAAGGGTCAAGGTCCAATTGT 60.814 50.000 4.43 0.00 0.00 2.71
63 64 2.293399 GGTCAAGGTCCAATTGTGTGTC 59.707 50.000 4.43 0.00 0.00 3.67
71 72 3.820467 GTCCAATTGTGTGTCAAGGATGA 59.180 43.478 4.43 0.00 39.55 2.92
73 74 4.520111 TCCAATTGTGTGTCAAGGATGAAG 59.480 41.667 4.43 0.00 39.55 3.02
96 97 1.478105 GCAACTAGGGCAAAGGATTGG 59.522 52.381 4.00 0.00 37.02 3.16
98 99 0.631212 ACTAGGGCAAAGGATTGGGG 59.369 55.000 0.00 0.00 37.02 4.96
109 110 0.318120 GGATTGGGGCAAGTTGTGTG 59.682 55.000 4.48 0.00 0.00 3.82
138 139 1.802508 GCACTTGCAACTGGGACAAAC 60.803 52.381 0.00 0.00 38.62 2.93
172 173 0.179032 TGTGTGTCGAGGGTGCATTT 60.179 50.000 0.00 0.00 0.00 2.32
173 174 0.238289 GTGTGTCGAGGGTGCATTTG 59.762 55.000 0.00 0.00 0.00 2.32
177 178 1.234821 GTCGAGGGTGCATTTGAACA 58.765 50.000 0.00 0.00 0.00 3.18
180 181 0.244721 GAGGGTGCATTTGAACAGGC 59.755 55.000 0.00 0.00 0.00 4.85
218 219 0.784178 CGATTGTGTGTCGAGTGTGG 59.216 55.000 0.00 0.00 41.40 4.17
227 228 1.069978 TGTCGAGTGTGGATTTGCAGA 59.930 47.619 0.00 0.00 0.00 4.26
232 233 3.430790 CGAGTGTGGATTTGCAGATAGGA 60.431 47.826 0.00 0.00 0.00 2.94
250 251 1.810755 GGACAAAAAGGTCGGGCTTAG 59.189 52.381 0.00 0.00 38.70 2.18
260 261 0.739462 TCGGGCTTAGTTGCATGTCG 60.739 55.000 0.00 0.00 34.04 4.35
283 284 3.642938 GGTGATACAACAGCCCACA 57.357 52.632 0.00 0.00 32.97 4.17
309 310 7.510675 ACAAAGGTGATTATCTCCTAGGAAA 57.489 36.000 13.77 4.77 39.27 3.13
330 331 5.559427 AAGAAACAAAAACCCAACAATGC 57.441 34.783 0.00 0.00 0.00 3.56
332 333 4.875536 AGAAACAAAAACCCAACAATGCTC 59.124 37.500 0.00 0.00 0.00 4.26
333 334 4.486125 AACAAAAACCCAACAATGCTCT 57.514 36.364 0.00 0.00 0.00 4.09
390 462 4.268720 GTGAAACCAGCCCACCAA 57.731 55.556 0.00 0.00 0.00 3.67
407 479 2.496899 CAAGGTCTTGGCACTGGTAT 57.503 50.000 2.94 0.00 36.95 2.73
409 481 2.749621 CAAGGTCTTGGCACTGGTATTC 59.250 50.000 2.94 0.00 36.95 1.75
410 482 1.282157 AGGTCTTGGCACTGGTATTCC 59.718 52.381 0.00 0.00 0.00 3.01
412 484 2.359900 GTCTTGGCACTGGTATTCCTG 58.640 52.381 0.00 0.00 38.41 3.86
413 485 1.985159 TCTTGGCACTGGTATTCCTGT 59.015 47.619 0.00 0.00 44.76 4.00
414 486 2.027192 TCTTGGCACTGGTATTCCTGTC 60.027 50.000 0.00 0.00 42.61 3.51
415 487 1.656587 TGGCACTGGTATTCCTGTCT 58.343 50.000 0.00 0.00 42.61 3.41
416 488 2.827755 TGGCACTGGTATTCCTGTCTA 58.172 47.619 0.00 0.00 42.61 2.59
417 489 3.178046 TGGCACTGGTATTCCTGTCTAA 58.822 45.455 0.00 0.00 42.61 2.10
418 490 3.055385 TGGCACTGGTATTCCTGTCTAAC 60.055 47.826 0.00 0.00 42.61 2.34
419 491 3.197983 GGCACTGGTATTCCTGTCTAACT 59.802 47.826 0.00 0.00 42.61 2.24
420 492 4.404715 GGCACTGGTATTCCTGTCTAACTA 59.595 45.833 0.00 0.00 42.61 2.24
421 493 5.070580 GGCACTGGTATTCCTGTCTAACTAT 59.929 44.000 0.00 0.00 42.61 2.12
422 494 5.986135 GCACTGGTATTCCTGTCTAACTATG 59.014 44.000 0.00 0.00 42.61 2.23
423 495 6.516718 CACTGGTATTCCTGTCTAACTATGG 58.483 44.000 0.00 0.00 42.61 2.74
424 496 6.323996 CACTGGTATTCCTGTCTAACTATGGA 59.676 42.308 0.00 0.00 42.61 3.41
425 497 6.551601 ACTGGTATTCCTGTCTAACTATGGAG 59.448 42.308 0.00 0.00 41.02 3.86
426 498 5.839063 TGGTATTCCTGTCTAACTATGGAGG 59.161 44.000 0.00 0.00 34.23 4.30
427 499 4.965200 ATTCCTGTCTAACTATGGAGGC 57.035 45.455 0.00 0.00 0.00 4.70
428 500 2.307768 TCCTGTCTAACTATGGAGGCG 58.692 52.381 0.00 0.00 0.00 5.52
429 501 1.341531 CCTGTCTAACTATGGAGGCGG 59.658 57.143 0.00 0.00 0.00 6.13
430 502 0.750850 TGTCTAACTATGGAGGCGGC 59.249 55.000 0.00 0.00 0.00 6.53
431 503 0.750850 GTCTAACTATGGAGGCGGCA 59.249 55.000 13.08 0.00 0.00 5.69
432 504 1.040646 TCTAACTATGGAGGCGGCAG 58.959 55.000 13.08 0.96 0.00 4.85
433 505 0.753262 CTAACTATGGAGGCGGCAGT 59.247 55.000 13.08 1.73 0.00 4.40
434 506 0.464036 TAACTATGGAGGCGGCAGTG 59.536 55.000 13.08 0.00 0.00 3.66
435 507 1.264749 AACTATGGAGGCGGCAGTGA 61.265 55.000 13.08 0.00 0.00 3.41
439 511 0.179045 ATGGAGGCGGCAGTGATAAC 60.179 55.000 13.08 0.00 0.00 1.89
442 514 1.291132 GAGGCGGCAGTGATAACTTC 58.709 55.000 13.08 0.00 0.00 3.01
447 519 3.429085 GCGGCAGTGATAACTTCATTTG 58.571 45.455 0.00 0.00 36.54 2.32
456 528 8.777413 CAGTGATAACTTCATTTGAGACTTTCA 58.223 33.333 0.00 0.00 36.54 2.69
463 535 9.831737 AACTTCATTTGAGACTTTCAATATTCG 57.168 29.630 0.00 0.00 44.90 3.34
464 536 9.003658 ACTTCATTTGAGACTTTCAATATTCGT 57.996 29.630 0.00 0.00 44.90 3.85
465 537 9.483062 CTTCATTTGAGACTTTCAATATTCGTC 57.517 33.333 0.00 0.00 44.90 4.20
466 538 7.974675 TCATTTGAGACTTTCAATATTCGTCC 58.025 34.615 0.00 0.00 44.90 4.79
467 539 7.606073 TCATTTGAGACTTTCAATATTCGTCCA 59.394 33.333 0.00 0.00 44.90 4.02
468 540 6.968131 TTGAGACTTTCAATATTCGTCCAG 57.032 37.500 0.00 0.00 40.82 3.86
469 541 4.870426 TGAGACTTTCAATATTCGTCCAGC 59.130 41.667 0.00 0.00 31.34 4.85
470 542 3.865745 AGACTTTCAATATTCGTCCAGCG 59.134 43.478 0.00 0.00 43.01 5.18
471 543 2.936498 ACTTTCAATATTCGTCCAGCGG 59.064 45.455 0.00 0.00 41.72 5.52
472 544 1.948104 TTCAATATTCGTCCAGCGGG 58.052 50.000 0.00 0.00 41.72 6.13
473 545 1.116308 TCAATATTCGTCCAGCGGGA 58.884 50.000 0.00 0.00 42.29 5.14
474 546 1.068588 TCAATATTCGTCCAGCGGGAG 59.931 52.381 5.57 0.69 46.12 4.30
475 547 0.393077 AATATTCGTCCAGCGGGAGG 59.607 55.000 18.13 18.13 46.12 4.30
481 553 4.804420 TCCAGCGGGAGGAGGCAT 62.804 66.667 0.00 0.00 38.64 4.40
482 554 3.801997 CCAGCGGGAGGAGGCATT 61.802 66.667 0.00 0.00 35.59 3.56
483 555 2.203126 CAGCGGGAGGAGGCATTC 60.203 66.667 0.00 0.00 0.00 2.67
495 567 4.965200 GGAGGCATTCCTGTCTAACTAT 57.035 45.455 0.00 0.00 44.46 2.12
496 568 4.636249 GGAGGCATTCCTGTCTAACTATG 58.364 47.826 0.00 0.00 44.46 2.23
497 569 4.503991 GGAGGCATTCCTGTCTAACTATGG 60.504 50.000 0.00 0.00 44.46 2.74
498 570 4.298626 AGGCATTCCTGTCTAACTATGGA 58.701 43.478 0.00 0.00 42.34 3.41
499 571 4.346418 AGGCATTCCTGTCTAACTATGGAG 59.654 45.833 0.00 0.00 42.34 3.86
500 572 4.101741 GGCATTCCTGTCTAACTATGGAGT 59.898 45.833 0.00 0.00 37.59 3.85
501 573 5.293560 GCATTCCTGTCTAACTATGGAGTC 58.706 45.833 0.00 0.00 33.58 3.36
502 574 5.524284 CATTCCTGTCTAACTATGGAGTCG 58.476 45.833 0.00 0.00 33.58 4.18
503 575 3.552875 TCCTGTCTAACTATGGAGTCGG 58.447 50.000 0.00 0.00 33.58 4.79
504 576 2.034812 CCTGTCTAACTATGGAGTCGGC 59.965 54.545 0.00 0.00 33.58 5.54
505 577 2.688446 CTGTCTAACTATGGAGTCGGCA 59.312 50.000 0.00 0.00 33.58 5.69
506 578 2.688446 TGTCTAACTATGGAGTCGGCAG 59.312 50.000 0.00 0.00 33.58 4.85
507 579 2.688958 GTCTAACTATGGAGTCGGCAGT 59.311 50.000 0.00 0.00 33.58 4.40
508 580 2.688446 TCTAACTATGGAGTCGGCAGTG 59.312 50.000 0.00 0.00 33.58 3.66
509 581 1.557099 AACTATGGAGTCGGCAGTGA 58.443 50.000 0.00 0.00 33.58 3.41
510 582 1.781786 ACTATGGAGTCGGCAGTGAT 58.218 50.000 0.00 0.00 0.00 3.06
511 583 2.945456 ACTATGGAGTCGGCAGTGATA 58.055 47.619 0.00 0.00 0.00 2.15
512 584 3.296854 ACTATGGAGTCGGCAGTGATAA 58.703 45.455 0.00 0.00 0.00 1.75
513 585 2.604046 ATGGAGTCGGCAGTGATAAC 57.396 50.000 0.00 0.00 0.00 1.89
514 586 1.557099 TGGAGTCGGCAGTGATAACT 58.443 50.000 0.00 0.00 0.00 2.24
515 587 1.899814 TGGAGTCGGCAGTGATAACTT 59.100 47.619 0.00 0.00 0.00 2.66
516 588 2.094182 TGGAGTCGGCAGTGATAACTTC 60.094 50.000 0.00 0.00 0.00 3.01
517 589 2.094182 GGAGTCGGCAGTGATAACTTCA 60.094 50.000 0.00 0.00 0.00 3.02
518 590 3.430929 GGAGTCGGCAGTGATAACTTCAT 60.431 47.826 0.00 0.00 36.54 2.57
519 591 4.184629 GAGTCGGCAGTGATAACTTCATT 58.815 43.478 0.00 0.00 36.54 2.57
520 592 4.579869 AGTCGGCAGTGATAACTTCATTT 58.420 39.130 0.00 0.00 36.54 2.32
521 593 5.730550 AGTCGGCAGTGATAACTTCATTTA 58.269 37.500 0.00 0.00 36.54 1.40
522 594 6.170506 AGTCGGCAGTGATAACTTCATTTAA 58.829 36.000 0.00 0.00 36.54 1.52
523 595 6.313905 AGTCGGCAGTGATAACTTCATTTAAG 59.686 38.462 0.00 0.00 41.33 1.85
524 596 6.312918 GTCGGCAGTGATAACTTCATTTAAGA 59.687 38.462 0.00 0.00 38.67 2.10
525 597 6.312918 TCGGCAGTGATAACTTCATTTAAGAC 59.687 38.462 0.00 0.00 38.67 3.01
526 598 6.313905 CGGCAGTGATAACTTCATTTAAGACT 59.686 38.462 0.00 0.00 38.67 3.24
527 599 7.148407 CGGCAGTGATAACTTCATTTAAGACTT 60.148 37.037 0.00 0.00 38.67 3.01
528 600 8.515414 GGCAGTGATAACTTCATTTAAGACTTT 58.485 33.333 0.00 0.00 38.67 2.66
544 616 3.865745 AGACTTTCAATATTCGTCCAGCG 59.134 43.478 0.00 0.00 43.01 5.18
545 617 2.936498 ACTTTCAATATTCGTCCAGCGG 59.064 45.455 0.00 0.00 41.72 5.52
548 620 1.068588 TCAATATTCGTCCAGCGGGAG 59.931 52.381 5.57 0.69 46.12 4.30
578 650 0.750850 TGTCTAACTATGGAGGCGGC 59.249 55.000 0.00 0.00 0.00 6.53
593 665 2.017049 GGCGGCAGTGATAACTTCATT 58.983 47.619 3.07 0.00 36.54 2.57
598 670 5.237344 GCGGCAGTGATAACTTCATTAATCT 59.763 40.000 0.00 0.00 36.54 2.40
612 684 8.900781 ACTTCATTAATCTCAAAGATGATGTGG 58.099 33.333 10.71 8.55 34.65 4.17
619 691 2.040145 TCAAAGATGATGTGGTGGCTCA 59.960 45.455 0.00 0.00 0.00 4.26
621 693 0.107312 AGATGATGTGGTGGCTCAGC 60.107 55.000 0.00 0.00 0.00 4.26
639 711 2.034878 AGCCTCTCGAATGTGCTCATA 58.965 47.619 0.93 0.00 33.49 2.15
641 713 2.865670 GCCTCTCGAATGTGCTCATAGG 60.866 54.545 0.93 5.98 33.49 2.57
643 715 2.625314 CTCTCGAATGTGCTCATAGGGA 59.375 50.000 0.93 4.40 33.49 4.20
649 721 0.042581 TGTGCTCATAGGGACAGGGA 59.957 55.000 0.00 0.00 32.85 4.20
650 722 1.344393 TGTGCTCATAGGGACAGGGAT 60.344 52.381 0.00 0.00 32.85 3.85
656 728 0.759346 ATAGGGACAGGGATTGCGTC 59.241 55.000 0.00 0.00 0.00 5.19
657 729 1.672854 TAGGGACAGGGATTGCGTCG 61.673 60.000 0.00 0.00 0.00 5.12
681 756 3.319972 GCGTTCATAGGGGTGAGTGTATA 59.680 47.826 0.00 0.00 0.00 1.47
699 774 6.602009 AGTGTATATGGCTATGTATGAGCGTA 59.398 38.462 0.00 0.00 41.06 4.42
766 841 9.741647 AGAAGAGAATTGACAAAACTGAATTTC 57.258 29.630 0.00 0.00 0.00 2.17
804 879 8.561536 TCCTAGGATACATTTATTCAAGTCCA 57.438 34.615 7.62 0.00 41.41 4.02
845 923 5.371115 TTTCTTTTCCAGGTGCTTATTCG 57.629 39.130 0.00 0.00 0.00 3.34
880 958 4.393680 ACTCGTTTGTGCTTTGTCTTGTTA 59.606 37.500 0.00 0.00 0.00 2.41
887 965 3.498777 GTGCTTTGTCTTGTTAGGAGTCC 59.501 47.826 0.00 0.00 0.00 3.85
904 982 4.758165 GGAGTCCGGTTTTGTTTCTGATAA 59.242 41.667 0.00 0.00 0.00 1.75
912 990 7.439655 CCGGTTTTGTTTCTGATAAAAATTCCA 59.560 33.333 0.00 0.00 31.37 3.53
917 995 8.795786 TTGTTTCTGATAAAAATTCCAAGTCG 57.204 30.769 0.00 0.00 0.00 4.18
919 997 8.289618 TGTTTCTGATAAAAATTCCAAGTCGAG 58.710 33.333 0.00 0.00 0.00 4.04
920 998 7.979444 TTCTGATAAAAATTCCAAGTCGAGT 57.021 32.000 0.00 0.00 0.00 4.18
921 999 7.596749 TCTGATAAAAATTCCAAGTCGAGTC 57.403 36.000 0.00 0.00 0.00 3.36
922 1000 6.310467 TCTGATAAAAATTCCAAGTCGAGTCG 59.690 38.462 6.09 6.09 0.00 4.18
924 1002 3.396260 AAAATTCCAAGTCGAGTCGGA 57.604 42.857 13.54 0.00 0.00 4.55
925 1003 3.611766 AAATTCCAAGTCGAGTCGGAT 57.388 42.857 13.54 0.00 0.00 4.18
926 1004 3.611766 AATTCCAAGTCGAGTCGGATT 57.388 42.857 13.54 5.00 0.00 3.01
927 1005 4.730949 AATTCCAAGTCGAGTCGGATTA 57.269 40.909 13.54 0.00 0.00 1.75
928 1006 4.939052 ATTCCAAGTCGAGTCGGATTAT 57.061 40.909 13.54 0.00 0.00 1.28
929 1007 4.730949 TTCCAAGTCGAGTCGGATTATT 57.269 40.909 13.54 0.00 0.00 1.40
930 1008 5.840243 TTCCAAGTCGAGTCGGATTATTA 57.160 39.130 13.54 0.00 0.00 0.98
931 1009 5.840243 TCCAAGTCGAGTCGGATTATTAA 57.160 39.130 13.54 0.00 0.00 1.40
932 1010 6.401047 TCCAAGTCGAGTCGGATTATTAAT 57.599 37.500 13.54 0.00 0.00 1.40
945 1023 7.491696 GTCGGATTATTAATTATTAGGCGCTCT 59.508 37.037 7.64 5.38 0.00 4.09
946 1024 8.038944 TCGGATTATTAATTATTAGGCGCTCTT 58.961 33.333 7.64 0.00 0.00 2.85
959 1037 3.134804 AGGCGCTCTTATTTGACCACTAT 59.865 43.478 7.64 0.00 0.00 2.12
960 1038 3.877508 GGCGCTCTTATTTGACCACTATT 59.122 43.478 7.64 0.00 0.00 1.73
995 1073 0.452987 ATGCCTACGTACGAGCGAAA 59.547 50.000 24.41 6.48 35.59 3.46
996 1074 0.240678 TGCCTACGTACGAGCGAAAA 59.759 50.000 24.41 3.05 35.59 2.29
1008 1087 3.645975 CGAAAACGCAGGCACGGT 61.646 61.111 4.96 0.00 37.37 4.83
1023 1102 2.095853 GCACGGTCGATTCATGTTGATT 59.904 45.455 0.00 0.00 0.00 2.57
1029 1108 5.449041 CGGTCGATTCATGTTGATTGGAAAT 60.449 40.000 0.00 0.00 0.00 2.17
1031 1110 7.134815 GGTCGATTCATGTTGATTGGAAATAG 58.865 38.462 0.00 0.00 0.00 1.73
1032 1111 6.634436 GTCGATTCATGTTGATTGGAAATAGC 59.366 38.462 0.00 0.00 0.00 2.97
1033 1112 5.622448 CGATTCATGTTGATTGGAAATAGCG 59.378 40.000 0.00 0.00 0.00 4.26
1091 1173 2.896443 CCGGAGAGGCTGGAAGTC 59.104 66.667 0.00 0.00 46.81 3.01
1188 1282 3.875727 TCGAGATACTGGTACTTCTTCCG 59.124 47.826 0.00 0.00 0.00 4.30
1336 1457 0.528684 GGCCTCTCGATTCCTCAACG 60.529 60.000 0.00 0.00 0.00 4.10
1402 1523 1.497722 CGAAAGGAGTTTCAGCCGC 59.502 57.895 0.00 0.00 42.06 6.53
1666 1796 3.884774 GAGGCACCACCACCACCA 61.885 66.667 0.00 0.00 43.14 4.17
1667 1797 4.204028 AGGCACCACCACCACCAC 62.204 66.667 0.00 0.00 43.14 4.16
1698 1828 0.461516 ACAGCTGCGGACATGAGATG 60.462 55.000 15.27 0.00 0.00 2.90
1713 1843 1.398390 GAGATGTTGACATTCGGTGGC 59.602 52.381 0.00 0.00 36.57 5.01
1729 1859 3.774702 GCGACGTCGGCAAGGAAC 61.775 66.667 36.13 15.40 40.23 3.62
1733 1863 2.171489 GACGTCGGCAAGGAACAAGC 62.171 60.000 0.00 0.00 0.00 4.01
1930 2060 1.344438 CTAACCCTCCATGCAGCGATA 59.656 52.381 0.00 0.00 0.00 2.92
1931 2061 0.767375 AACCCTCCATGCAGCGATAT 59.233 50.000 0.00 0.00 0.00 1.63
1955 2085 3.185246 AGGCAGGAACGATTCACTATG 57.815 47.619 0.00 0.00 0.00 2.23
2025 2155 0.965439 TTTCCATTTGGTTGGCGGAG 59.035 50.000 0.00 0.00 36.66 4.63
2106 2236 2.697992 TTCTTGCCTTTGCTTGCGCC 62.698 55.000 4.18 0.00 38.71 6.53
2175 2305 1.153823 CCGGTGTGATCTCCGTGAC 60.154 63.158 17.84 0.00 45.58 3.67
2215 2345 0.730155 CAACATGCCACGTGACATGC 60.730 55.000 35.36 22.65 46.08 4.06
2500 3119 6.933521 GTCCATCACATATTTGAGATGCTACT 59.066 38.462 14.92 0.00 44.71 2.57
2516 3135 5.280654 TGCTACTGATACAATGCTGATGA 57.719 39.130 0.00 0.00 0.00 2.92
2624 3243 3.373439 CAGAGTGCTTTAGAATCTGGTGC 59.627 47.826 0.00 0.00 34.97 5.01
2636 3255 2.871182 TCTGGTGCACATCGAGTATC 57.129 50.000 20.43 0.00 0.00 2.24
2641 3260 3.684305 TGGTGCACATCGAGTATCTTTTG 59.316 43.478 20.43 0.00 0.00 2.44
2656 3275 5.638530 ATCTTTTGTCTTCCTCCTATCCC 57.361 43.478 0.00 0.00 0.00 3.85
2669 3288 4.589374 CCTCCTATCCCCAACAAGTAGTAG 59.411 50.000 0.00 0.00 0.00 2.57
2717 3336 4.762251 GGTGTGTCTCCTTAGAGCAAAATT 59.238 41.667 0.00 0.00 40.22 1.82
2761 3380 6.755141 CGTTTTCTGAAGATACCTCCGAAATA 59.245 38.462 0.00 0.00 0.00 1.40
2771 3390 8.174733 AGATACCTCCGAAATAACTAAATCGA 57.825 34.615 0.00 0.00 37.48 3.59
2772 3391 8.804204 AGATACCTCCGAAATAACTAAATCGAT 58.196 33.333 0.00 0.00 37.48 3.59
2814 3433 9.258826 TGTGGTTATTCAAATTGATTTTGTCAG 57.741 29.630 0.00 0.00 44.25 3.51
2866 3496 1.056700 GCCTCCCATCTTCTGGCCTA 61.057 60.000 3.32 0.00 44.46 3.93
2963 3598 8.472007 TTCTGTACTTTATTTGGACCATGTTT 57.528 30.769 0.00 0.00 0.00 2.83
2979 3614 4.097741 CCATGTTTTCAGTTGTCTGGTGAA 59.902 41.667 0.00 0.00 41.59 3.18
3030 3665 2.220653 TGCAGATTGAAGGGGGAAAG 57.779 50.000 0.00 0.00 0.00 2.62
3043 3679 2.103094 GGGGGAAAGGCATTAGAATTGC 59.897 50.000 0.00 0.00 0.00 3.56
3123 3760 1.464376 ATGGACGTATCAGCTCCCCG 61.464 60.000 0.00 0.00 0.00 5.73
3134 3771 2.203806 GCTCCCCGAAGCTTAGACT 58.796 57.895 8.29 0.00 39.27 3.24
3175 3812 2.236395 AGCCGAGCTTAGTAAACATGGT 59.764 45.455 0.00 0.00 33.89 3.55
3283 3921 7.872113 AAGCAATCCCTTCTTATTCTTACAG 57.128 36.000 0.00 0.00 0.00 2.74
3285 3923 7.278875 AGCAATCCCTTCTTATTCTTACAGAG 58.721 38.462 0.00 0.00 0.00 3.35
3310 3948 4.527944 TCTGATGAGAAGGTCGTGATACT 58.472 43.478 0.00 0.00 0.00 2.12
3324 3962 7.336931 AGGTCGTGATACTTTTAGATGCAAAAT 59.663 33.333 0.00 0.00 0.00 1.82
3334 3972 9.791801 ACTTTTAGATGCAAAATTTTAACCCAT 57.208 25.926 2.44 4.49 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 2.929641 TGCAACTTCATCCTTGACACA 58.070 42.857 0.00 0.00 0.00 3.72
63 64 3.441572 CCCTAGTTGCAACTTCATCCTTG 59.558 47.826 35.20 15.00 40.37 3.61
92 93 1.039856 GACACACAACTTGCCCCAAT 58.960 50.000 0.00 0.00 0.00 3.16
96 97 1.507141 CCTCGACACACAACTTGCCC 61.507 60.000 0.00 0.00 0.00 5.36
98 99 0.814010 ACCCTCGACACACAACTTGC 60.814 55.000 0.00 0.00 0.00 4.01
138 139 1.234615 ACACAATTTGGCGTCGAGGG 61.235 55.000 7.31 0.00 0.00 4.30
189 190 1.003580 ACACACAATCGAGGCCTGATT 59.996 47.619 12.00 16.87 36.52 2.57
202 203 2.611751 CAAATCCACACTCGACACACAA 59.388 45.455 0.00 0.00 0.00 3.33
214 215 3.998913 TGTCCTATCTGCAAATCCACA 57.001 42.857 0.00 0.00 0.00 4.17
218 219 6.272822 ACCTTTTTGTCCTATCTGCAAATC 57.727 37.500 0.00 0.00 33.00 2.17
227 228 1.633945 AGCCCGACCTTTTTGTCCTAT 59.366 47.619 0.00 0.00 31.35 2.57
232 233 2.621526 CAACTAAGCCCGACCTTTTTGT 59.378 45.455 0.00 0.00 0.00 2.83
260 261 1.032114 GGCTGTTGTATCACCCCTGC 61.032 60.000 0.00 0.00 0.00 4.85
262 263 0.844661 TGGGCTGTTGTATCACCCCT 60.845 55.000 0.00 0.00 40.04 4.79
263 264 0.679960 GTGGGCTGTTGTATCACCCC 60.680 60.000 0.00 0.00 40.04 4.95
283 284 5.964477 TCCTAGGAGATAATCACCTTTGTGT 59.036 40.000 7.62 0.00 43.26 3.72
297 298 6.493802 GGGTTTTTGTTTCTTTCCTAGGAGAT 59.506 38.462 12.26 0.00 0.00 2.75
302 303 6.635755 TGTTGGGTTTTTGTTTCTTTCCTAG 58.364 36.000 0.00 0.00 0.00 3.02
309 310 4.842574 AGCATTGTTGGGTTTTTGTTTCT 58.157 34.783 0.00 0.00 0.00 2.52
319 320 3.577389 GCCTAGAGCATTGTTGGGT 57.423 52.632 0.00 0.00 42.97 4.51
390 462 1.282157 GGAATACCAGTGCCAAGACCT 59.718 52.381 0.00 0.00 35.97 3.85
401 473 6.015010 CCTCCATAGTTAGACAGGAATACCAG 60.015 46.154 0.00 0.00 38.94 4.00
406 478 3.322254 CGCCTCCATAGTTAGACAGGAAT 59.678 47.826 0.00 0.00 0.00 3.01
407 479 2.693591 CGCCTCCATAGTTAGACAGGAA 59.306 50.000 0.00 0.00 0.00 3.36
409 481 1.341531 CCGCCTCCATAGTTAGACAGG 59.658 57.143 0.00 0.00 0.00 4.00
410 482 1.269831 GCCGCCTCCATAGTTAGACAG 60.270 57.143 0.00 0.00 0.00 3.51
412 484 0.750850 TGCCGCCTCCATAGTTAGAC 59.249 55.000 0.00 0.00 0.00 2.59
413 485 1.040646 CTGCCGCCTCCATAGTTAGA 58.959 55.000 0.00 0.00 0.00 2.10
414 486 0.753262 ACTGCCGCCTCCATAGTTAG 59.247 55.000 0.00 0.00 0.00 2.34
415 487 0.464036 CACTGCCGCCTCCATAGTTA 59.536 55.000 0.00 0.00 0.00 2.24
416 488 1.221840 CACTGCCGCCTCCATAGTT 59.778 57.895 0.00 0.00 0.00 2.24
417 489 1.050988 ATCACTGCCGCCTCCATAGT 61.051 55.000 0.00 0.00 0.00 2.12
418 490 0.969149 TATCACTGCCGCCTCCATAG 59.031 55.000 0.00 0.00 0.00 2.23
419 491 1.070134 GTTATCACTGCCGCCTCCATA 59.930 52.381 0.00 0.00 0.00 2.74
420 492 0.179045 GTTATCACTGCCGCCTCCAT 60.179 55.000 0.00 0.00 0.00 3.41
421 493 1.220749 GTTATCACTGCCGCCTCCA 59.779 57.895 0.00 0.00 0.00 3.86
422 494 0.107654 AAGTTATCACTGCCGCCTCC 60.108 55.000 0.00 0.00 31.60 4.30
423 495 1.291132 GAAGTTATCACTGCCGCCTC 58.709 55.000 0.00 0.00 31.60 4.70
424 496 0.613260 TGAAGTTATCACTGCCGCCT 59.387 50.000 0.00 0.00 31.60 5.52
425 497 1.668419 ATGAAGTTATCACTGCCGCC 58.332 50.000 0.00 0.00 41.93 6.13
426 498 3.126858 TCAAATGAAGTTATCACTGCCGC 59.873 43.478 0.00 0.00 41.93 6.53
427 499 4.631377 TCTCAAATGAAGTTATCACTGCCG 59.369 41.667 0.00 0.00 41.93 5.69
428 500 5.645497 AGTCTCAAATGAAGTTATCACTGCC 59.355 40.000 0.00 0.00 41.93 4.85
429 501 6.734104 AGTCTCAAATGAAGTTATCACTGC 57.266 37.500 0.00 0.00 41.93 4.40
430 502 8.777413 TGAAAGTCTCAAATGAAGTTATCACTG 58.223 33.333 0.00 0.00 41.93 3.66
431 503 8.908786 TGAAAGTCTCAAATGAAGTTATCACT 57.091 30.769 0.00 0.00 41.93 3.41
447 519 5.396750 GCTGGACGAATATTGAAAGTCTC 57.603 43.478 0.00 0.00 32.86 3.36
464 536 4.804420 ATGCCTCCTCCCGCTGGA 62.804 66.667 0.00 0.00 38.75 3.86
465 537 3.764160 GAATGCCTCCTCCCGCTGG 62.764 68.421 0.00 0.00 0.00 4.85
466 538 2.203126 GAATGCCTCCTCCCGCTG 60.203 66.667 0.00 0.00 0.00 5.18
467 539 3.483869 GGAATGCCTCCTCCCGCT 61.484 66.667 0.00 0.00 41.61 5.52
474 546 4.503991 CCATAGTTAGACAGGAATGCCTCC 60.504 50.000 0.00 0.00 44.80 4.30
475 547 4.345257 TCCATAGTTAGACAGGAATGCCTC 59.655 45.833 0.00 0.00 44.80 4.70
476 548 6.110773 ACTCCATAGTTAGACAGGAATGCCT 61.111 44.000 0.00 0.00 37.64 4.75
477 549 4.101741 ACTCCATAGTTAGACAGGAATGCC 59.898 45.833 0.00 0.00 29.00 4.40
478 550 5.283457 ACTCCATAGTTAGACAGGAATGC 57.717 43.478 0.00 0.00 29.00 3.56
479 551 5.508153 CCGACTCCATAGTTAGACAGGAATG 60.508 48.000 0.00 0.00 35.56 2.67
480 552 4.585162 CCGACTCCATAGTTAGACAGGAAT 59.415 45.833 0.00 0.00 35.56 3.01
481 553 3.952323 CCGACTCCATAGTTAGACAGGAA 59.048 47.826 0.00 0.00 35.56 3.36
482 554 3.552875 CCGACTCCATAGTTAGACAGGA 58.447 50.000 0.00 0.00 35.56 3.86
483 555 2.034812 GCCGACTCCATAGTTAGACAGG 59.965 54.545 0.00 0.00 35.56 4.00
484 556 2.688446 TGCCGACTCCATAGTTAGACAG 59.312 50.000 0.00 0.00 35.56 3.51
485 557 2.688446 CTGCCGACTCCATAGTTAGACA 59.312 50.000 0.00 0.00 35.56 3.41
486 558 2.688958 ACTGCCGACTCCATAGTTAGAC 59.311 50.000 0.00 0.00 35.56 2.59
487 559 2.688446 CACTGCCGACTCCATAGTTAGA 59.312 50.000 0.00 0.00 35.56 2.10
488 560 2.688446 TCACTGCCGACTCCATAGTTAG 59.312 50.000 0.00 0.00 35.56 2.34
489 561 2.730382 TCACTGCCGACTCCATAGTTA 58.270 47.619 0.00 0.00 35.56 2.24
490 562 1.557099 TCACTGCCGACTCCATAGTT 58.443 50.000 0.00 0.00 35.56 2.24
491 563 1.781786 ATCACTGCCGACTCCATAGT 58.218 50.000 0.00 0.00 39.21 2.12
492 564 3.319405 AGTTATCACTGCCGACTCCATAG 59.681 47.826 0.00 0.00 0.00 2.23
493 565 3.296854 AGTTATCACTGCCGACTCCATA 58.703 45.455 0.00 0.00 0.00 2.74
494 566 2.111384 AGTTATCACTGCCGACTCCAT 58.889 47.619 0.00 0.00 0.00 3.41
495 567 1.557099 AGTTATCACTGCCGACTCCA 58.443 50.000 0.00 0.00 0.00 3.86
496 568 2.094182 TGAAGTTATCACTGCCGACTCC 60.094 50.000 0.00 0.00 31.60 3.85
497 569 3.232213 TGAAGTTATCACTGCCGACTC 57.768 47.619 0.00 0.00 31.60 3.36
498 570 3.895232 ATGAAGTTATCACTGCCGACT 57.105 42.857 0.00 0.00 41.93 4.18
499 571 4.946784 AAATGAAGTTATCACTGCCGAC 57.053 40.909 0.00 0.00 41.93 4.79
500 572 6.312918 GTCTTAAATGAAGTTATCACTGCCGA 59.687 38.462 0.00 0.00 41.93 5.54
501 573 6.313905 AGTCTTAAATGAAGTTATCACTGCCG 59.686 38.462 0.00 0.00 41.93 5.69
502 574 7.617041 AGTCTTAAATGAAGTTATCACTGCC 57.383 36.000 0.00 0.00 41.93 4.85
503 575 9.548208 GAAAGTCTTAAATGAAGTTATCACTGC 57.452 33.333 0.00 0.00 41.93 4.40
515 587 9.443323 TGGACGAATATTGAAAGTCTTAAATGA 57.557 29.630 0.00 0.00 32.86 2.57
516 588 9.708222 CTGGACGAATATTGAAAGTCTTAAATG 57.292 33.333 0.00 0.00 32.86 2.32
517 589 8.398665 GCTGGACGAATATTGAAAGTCTTAAAT 58.601 33.333 0.00 0.00 32.86 1.40
518 590 7.748847 GCTGGACGAATATTGAAAGTCTTAAA 58.251 34.615 0.00 0.00 32.86 1.52
519 591 7.303634 GCTGGACGAATATTGAAAGTCTTAA 57.696 36.000 0.00 0.00 32.86 1.85
520 592 6.903883 GCTGGACGAATATTGAAAGTCTTA 57.096 37.500 0.00 0.00 32.86 2.10
521 593 5.803020 GCTGGACGAATATTGAAAGTCTT 57.197 39.130 0.00 0.00 32.86 3.01
539 611 3.764160 GAATGCCTCCTCCCGCTGG 62.764 68.421 0.00 0.00 0.00 4.85
548 620 4.503991 CCATAGTTAGACAGGAATGCCTCC 60.504 50.000 0.00 0.00 44.80 4.30
554 626 3.322254 CGCCTCCATAGTTAGACAGGAAT 59.678 47.826 0.00 0.00 0.00 3.01
564 636 1.221840 CACTGCCGCCTCCATAGTT 59.778 57.895 0.00 0.00 0.00 2.24
593 665 4.883585 GCCACCACATCATCTTTGAGATTA 59.116 41.667 0.00 0.00 31.32 1.75
598 670 2.040145 TGAGCCACCACATCATCTTTGA 59.960 45.455 0.00 0.00 36.00 2.69
619 691 0.829333 ATGAGCACATTCGAGAGGCT 59.171 50.000 3.13 3.13 37.56 4.58
621 693 2.288702 CCCTATGAGCACATTCGAGAGG 60.289 54.545 0.83 2.50 37.87 3.69
630 702 0.042581 TCCCTGTCCCTATGAGCACA 59.957 55.000 0.00 0.00 0.00 4.57
639 711 2.990479 GACGCAATCCCTGTCCCT 59.010 61.111 0.00 0.00 0.00 4.20
641 713 2.100631 CACGACGCAATCCCTGTCC 61.101 63.158 0.00 0.00 0.00 4.02
643 715 2.742372 GCACGACGCAATCCCTGT 60.742 61.111 0.00 0.00 41.79 4.00
656 728 0.806102 CTCACCCCTATGAACGCACG 60.806 60.000 0.00 0.00 0.00 5.34
657 729 0.249398 ACTCACCCCTATGAACGCAC 59.751 55.000 0.00 0.00 0.00 5.34
661 736 5.794894 CCATATACACTCACCCCTATGAAC 58.205 45.833 0.00 0.00 0.00 3.18
681 756 3.525537 GCATACGCTCATACATAGCCAT 58.474 45.455 0.00 0.00 36.60 4.40
736 811 9.784531 TTCAGTTTTGTCAATTCTCTTCTAGAT 57.215 29.630 0.00 0.00 33.05 1.98
779 854 8.561536 TGGACTTGAATAAATGTATCCTAGGA 57.438 34.615 15.46 15.46 0.00 2.94
780 855 9.799106 ATTGGACTTGAATAAATGTATCCTAGG 57.201 33.333 0.82 0.82 0.00 3.02
794 869 7.466746 TTTGCTTAGCTAATTGGACTTGAAT 57.533 32.000 6.64 0.00 0.00 2.57
800 875 5.644977 ACCTTTTGCTTAGCTAATTGGAC 57.355 39.130 20.06 0.00 0.00 4.02
801 876 6.664428 AAACCTTTTGCTTAGCTAATTGGA 57.336 33.333 20.06 0.00 0.00 3.53
831 908 2.883574 TCGTAACGAATAAGCACCTGG 58.116 47.619 0.00 0.00 31.06 4.45
833 910 5.049198 TCGATATCGTAACGAATAAGCACCT 60.049 40.000 23.61 0.00 39.99 4.00
880 958 2.171870 TCAGAAACAAAACCGGACTCCT 59.828 45.455 9.46 0.00 0.00 3.69
887 965 8.359060 TGGAATTTTTATCAGAAACAAAACCG 57.641 30.769 0.00 0.00 0.00 4.44
904 982 3.396260 TCCGACTCGACTTGGAATTTT 57.604 42.857 0.00 0.00 0.00 1.82
917 995 7.491696 AGCGCCTAATAATTAATAATCCGACTC 59.508 37.037 2.29 0.00 0.00 3.36
919 997 7.491696 AGAGCGCCTAATAATTAATAATCCGAC 59.508 37.037 2.29 0.00 0.00 4.79
920 998 7.553334 AGAGCGCCTAATAATTAATAATCCGA 58.447 34.615 2.29 0.00 0.00 4.55
921 999 7.772332 AGAGCGCCTAATAATTAATAATCCG 57.228 36.000 2.29 0.00 0.00 4.18
928 1006 8.780249 GGTCAAATAAGAGCGCCTAATAATTAA 58.220 33.333 2.29 0.00 0.00 1.40
929 1007 7.934665 TGGTCAAATAAGAGCGCCTAATAATTA 59.065 33.333 2.29 0.00 38.81 1.40
930 1008 6.770785 TGGTCAAATAAGAGCGCCTAATAATT 59.229 34.615 2.29 0.00 38.81 1.40
931 1009 6.204882 GTGGTCAAATAAGAGCGCCTAATAAT 59.795 38.462 2.29 0.00 39.81 1.28
932 1010 5.526111 GTGGTCAAATAAGAGCGCCTAATAA 59.474 40.000 2.29 0.00 39.81 1.40
966 1044 8.815189 CGCTCGTACGTAGGCATATATATATAT 58.185 37.037 16.05 9.12 0.00 0.86
967 1045 8.028938 TCGCTCGTACGTAGGCATATATATATA 58.971 37.037 16.05 4.92 0.00 0.86
968 1046 6.870439 TCGCTCGTACGTAGGCATATATATAT 59.130 38.462 16.05 0.00 0.00 0.86
970 1048 5.052481 TCGCTCGTACGTAGGCATATATAT 58.948 41.667 16.05 0.00 0.00 0.86
971 1049 4.432712 TCGCTCGTACGTAGGCATATATA 58.567 43.478 16.05 0.00 0.00 0.86
972 1050 3.264947 TCGCTCGTACGTAGGCATATAT 58.735 45.455 16.05 0.00 0.00 0.86
973 1051 2.687370 TCGCTCGTACGTAGGCATATA 58.313 47.619 16.05 2.47 0.00 0.86
974 1052 1.516161 TCGCTCGTACGTAGGCATAT 58.484 50.000 16.05 0.00 0.00 1.78
975 1053 1.298602 TTCGCTCGTACGTAGGCATA 58.701 50.000 16.05 6.82 0.00 3.14
976 1054 0.452987 TTTCGCTCGTACGTAGGCAT 59.547 50.000 16.05 0.00 0.00 4.40
995 1073 3.876589 AATCGACCGTGCCTGCGTT 62.877 57.895 0.00 0.00 0.00 4.84
996 1074 4.373116 AATCGACCGTGCCTGCGT 62.373 61.111 0.00 0.00 0.00 5.24
1008 1087 6.511605 CGCTATTTCCAATCAACATGAATCGA 60.512 38.462 0.00 0.00 0.00 3.59
1023 1102 7.543756 TCATCATATCGTTATCGCTATTTCCA 58.456 34.615 0.00 0.00 36.96 3.53
1029 1108 5.340803 GGCTTCATCATATCGTTATCGCTA 58.659 41.667 0.00 0.00 36.96 4.26
1031 1110 3.307242 GGGCTTCATCATATCGTTATCGC 59.693 47.826 0.00 0.00 36.96 4.58
1032 1111 3.865745 GGGGCTTCATCATATCGTTATCG 59.134 47.826 0.00 0.00 38.55 2.92
1033 1112 4.192317 GGGGGCTTCATCATATCGTTATC 58.808 47.826 0.00 0.00 0.00 1.75
1188 1282 2.266055 CGCAGGAGGGACTTGACC 59.734 66.667 0.00 0.00 41.55 4.02
1401 1522 4.875713 AACGCCGGGATCCCATGC 62.876 66.667 30.42 27.77 35.37 4.06
1402 1523 2.591715 GAACGCCGGGATCCCATG 60.592 66.667 30.42 20.87 35.37 3.66
1662 1792 3.378742 AGCTGTATTCTCTACTCGTGGTG 59.621 47.826 0.00 0.00 0.00 4.17
1663 1793 3.378742 CAGCTGTATTCTCTACTCGTGGT 59.621 47.826 5.25 0.00 0.00 4.16
1664 1794 3.793801 GCAGCTGTATTCTCTACTCGTGG 60.794 52.174 16.64 0.00 0.00 4.94
1665 1795 3.367607 GCAGCTGTATTCTCTACTCGTG 58.632 50.000 16.64 0.00 0.00 4.35
1666 1796 2.032302 CGCAGCTGTATTCTCTACTCGT 59.968 50.000 16.64 0.00 0.00 4.18
1667 1797 2.603412 CCGCAGCTGTATTCTCTACTCG 60.603 54.545 16.64 5.30 0.00 4.18
1668 1798 2.619177 TCCGCAGCTGTATTCTCTACTC 59.381 50.000 16.64 0.00 0.00 2.59
1698 1828 1.495951 GTCGCCACCGAATGTCAAC 59.504 57.895 0.00 0.00 46.34 3.18
1713 1843 1.886861 CTTGTTCCTTGCCGACGTCG 61.887 60.000 30.33 30.33 39.44 5.12
1724 1854 0.771127 TACCCAAGCTGCTTGTTCCT 59.229 50.000 33.16 18.27 39.58 3.36
1725 1855 1.474077 CATACCCAAGCTGCTTGTTCC 59.526 52.381 33.16 0.00 39.58 3.62
1726 1856 1.474077 CCATACCCAAGCTGCTTGTTC 59.526 52.381 33.16 0.00 39.58 3.18
1729 1859 1.747355 CTTCCATACCCAAGCTGCTTG 59.253 52.381 30.44 30.44 40.75 4.01
1733 1863 0.753111 GGCCTTCCATACCCAAGCTG 60.753 60.000 0.00 0.00 0.00 4.24
1767 1897 1.416772 GTCCTGGCCTTGATAGGGTAC 59.583 57.143 3.32 0.00 42.25 3.34
1930 2060 3.452627 AGTGAATCGTTCCTGCCTAGAAT 59.547 43.478 0.00 0.00 0.00 2.40
1931 2061 2.832129 AGTGAATCGTTCCTGCCTAGAA 59.168 45.455 0.00 0.00 0.00 2.10
1955 2085 3.727970 GCATAACTTTTCACCTAGCGCAC 60.728 47.826 11.47 0.00 0.00 5.34
2025 2155 1.753073 CAAGCCAGATTTGGTCCATCC 59.247 52.381 3.90 0.00 46.80 3.51
2106 2236 1.213013 CTTGTCCCGGTCAGTCGAG 59.787 63.158 0.00 0.00 0.00 4.04
2175 2305 6.318648 TGTTGATTATTTCTTCAAGGGATCCG 59.681 38.462 5.45 0.00 32.79 4.18
2310 2440 0.102481 TGGCTCGTTATCTCGAAGGC 59.898 55.000 0.00 0.00 39.34 4.35
2364 2498 3.908382 GCTGCAACACAAGAAATTAGACG 59.092 43.478 0.00 0.00 0.00 4.18
2500 3119 6.430000 CAGGATCAATCATCAGCATTGTATCA 59.570 38.462 0.00 0.00 33.61 2.15
2516 3135 9.101655 GCATTTTTATAAACAAGCAGGATCAAT 57.898 29.630 6.68 0.00 0.00 2.57
2539 3158 5.663456 AGCGATAATTTGTCAATTTGGCAT 58.337 33.333 4.24 0.00 34.29 4.40
2579 3198 7.707464 TCTGTGAGTCAAAACAACGAGTTAATA 59.293 33.333 0.00 0.00 40.26 0.98
2580 3199 6.537301 TCTGTGAGTCAAAACAACGAGTTAAT 59.463 34.615 0.00 0.00 40.26 1.40
2624 3243 6.102663 AGGAAGACAAAAGATACTCGATGTG 58.897 40.000 0.00 0.00 0.00 3.21
2636 3255 3.523564 TGGGGATAGGAGGAAGACAAAAG 59.476 47.826 0.00 0.00 0.00 2.27
2641 3260 2.478292 TGTTGGGGATAGGAGGAAGAC 58.522 52.381 0.00 0.00 0.00 3.01
2656 3275 7.667043 TTGCTCATAAACTACTACTTGTTGG 57.333 36.000 0.00 0.00 0.00 3.77
2669 3288 7.365741 CCATCACCATAAGATTGCTCATAAAC 58.634 38.462 0.00 0.00 0.00 2.01
2717 3336 0.944386 GCGTTTGAGTTGCTCTGGAA 59.056 50.000 0.00 0.00 0.00 3.53
2761 3380 5.812642 CACTCTTGTGCCTATCGATTTAGTT 59.187 40.000 1.71 0.00 37.38 2.24
2895 3529 4.202212 GCTCCAAAAGGCCTGAAAAGTTTA 60.202 41.667 5.69 0.00 0.00 2.01
2899 3533 1.966354 AGCTCCAAAAGGCCTGAAAAG 59.034 47.619 5.69 1.62 0.00 2.27
2900 3534 1.963515 GAGCTCCAAAAGGCCTGAAAA 59.036 47.619 5.69 0.00 0.00 2.29
2901 3535 1.145738 AGAGCTCCAAAAGGCCTGAAA 59.854 47.619 5.69 0.00 0.00 2.69
2902 3536 0.773644 AGAGCTCCAAAAGGCCTGAA 59.226 50.000 5.69 0.00 0.00 3.02
2933 3568 8.528044 TGGTCCAAATAAAGTACAGAAAAAGT 57.472 30.769 0.00 0.00 0.00 2.66
2934 3569 9.410556 CATGGTCCAAATAAAGTACAGAAAAAG 57.589 33.333 0.00 0.00 0.00 2.27
2937 3572 8.472007 AACATGGTCCAAATAAAGTACAGAAA 57.528 30.769 0.00 0.00 0.00 2.52
2944 3579 7.360113 ACTGAAAACATGGTCCAAATAAAGT 57.640 32.000 0.00 0.00 0.00 2.66
2953 3588 3.004734 CCAGACAACTGAAAACATGGTCC 59.995 47.826 0.00 0.00 46.03 4.46
2963 3598 7.732025 TCTTAGTAATTCACCAGACAACTGAA 58.268 34.615 0.00 0.00 46.03 3.02
2979 3614 7.284034 CACATGCAGAGGGAAATTCTTAGTAAT 59.716 37.037 0.00 0.00 0.00 1.89
3030 3665 4.984161 ACATTAATGCGCAATTCTAATGCC 59.016 37.500 27.29 0.00 40.72 4.40
3123 3760 3.997681 GGGACAAGTGAAGTCTAAGCTTC 59.002 47.826 0.00 0.00 43.68 3.86
3151 3788 3.955650 TGTTTACTAAGCTCGGCTTCT 57.044 42.857 13.37 4.74 46.77 2.85
3152 3789 3.309954 CCATGTTTACTAAGCTCGGCTTC 59.690 47.826 13.37 1.37 46.77 3.86
3175 3812 8.554835 TCGACTCCACATTTCATAAAATTGTA 57.445 30.769 0.00 0.00 32.69 2.41
3189 3826 9.085645 TGGTATTATTTACTATCGACTCCACAT 57.914 33.333 0.00 0.00 0.00 3.21
3224 3861 9.958180 TTTGATCAGGAAAGTAAATAGTGATGA 57.042 29.630 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.