Multiple sequence alignment - TraesCS7D01G108900

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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 TraesCS7D01G108900 chr7D 100.000 3534 0 0 1 3534 65602194 65598661 0.000000e+00 6527.0
1 TraesCS7D01G108900 chr7D 100.000 28 0 0 3391 3418 159710196 159710223 6.000000e-03 52.8
2 TraesCS7D01G108900 chrUn 91.336 2851 109 58 615 3386 84040539 84037748 0.000000e+00 3770.0
3 TraesCS7D01G108900 chrUn 90.359 446 17 8 1 430 84041099 84040664 2.380000e-156 562.0
4 TraesCS7D01G108900 chrUn 79.096 177 37 0 1395 1571 218154896 218155072 4.790000e-24 122.0
5 TraesCS7D01G108900 chrUn 79.096 177 37 0 1395 1571 246423473 246423297 4.790000e-24 122.0
6 TraesCS7D01G108900 chr7A 91.266 2370 132 40 686 3029 69901143 69903463 0.000000e+00 3160.0
7 TraesCS7D01G108900 chr7A 84.122 296 24 10 2131 2422 69904717 69904993 7.520000e-67 265.0
8 TraesCS7D01G108900 chr7A 79.941 339 40 17 3027 3347 69903595 69903923 1.280000e-54 224.0
9 TraesCS7D01G108900 chr7A 90.123 162 12 2 541 699 69895813 69895973 1.290000e-49 207.0
10 TraesCS7D01G108900 chr7A 87.500 144 16 2 3391 3534 33879015 33879156 7.850000e-37 165.0
11 TraesCS7D01G108900 chr7A 91.667 108 9 0 429 536 82206167 82206274 2.200000e-32 150.0
12 TraesCS7D01G108900 chr7A 79.661 177 25 6 1072 1238 69974796 69974971 2.230000e-22 117.0
13 TraesCS7D01G108900 chr1D 86.636 217 26 2 1378 1594 414775940 414776153 1.640000e-58 237.0
14 TraesCS7D01G108900 chr1D 90.000 110 11 0 427 536 392140976 392141085 3.680000e-30 143.0
15 TraesCS7D01G108900 chr1D 88.793 116 12 1 426 541 445194840 445194954 1.320000e-29 141.0
16 TraesCS7D01G108900 chr1A 85.845 219 28 2 1377 1595 511500328 511500543 2.740000e-56 230.0
17 TraesCS7D01G108900 chr1A 77.027 148 23 10 3391 3531 497214122 497213979 1.360000e-09 75.0
18 TraesCS7D01G108900 chr6D 92.517 147 10 1 3389 3534 411813794 411813940 3.570000e-50 209.0
19 TraesCS7D01G108900 chr4A 86.928 153 19 1 3382 3534 211389209 211389360 1.690000e-38 171.0
20 TraesCS7D01G108900 chr4A 85.185 81 11 1 1159 1238 621813321 621813401 8.130000e-12 82.4
21 TraesCS7D01G108900 chr3D 94.444 108 6 0 429 536 552962288 552962395 2.180000e-37 167.0
22 TraesCS7D01G108900 chr3D 82.069 145 24 2 1452 1595 110310573 110310430 4.790000e-24 122.0
23 TraesCS7D01G108900 chr3D 77.215 158 34 2 1087 1243 109967801 109967645 1.350000e-14 91.6
24 TraesCS7D01G108900 chr5D 90.984 122 9 2 421 542 509228112 509228231 2.820000e-36 163.0
25 TraesCS7D01G108900 chr3B 79.295 227 42 5 1372 1595 161461186 161460962 1.700000e-33 154.0
26 TraesCS7D01G108900 chr2D 90.598 117 10 1 421 536 548080220 548080336 1.700000e-33 154.0
27 TraesCS7D01G108900 chr2D 86.842 114 14 1 425 537 628843047 628842934 3.700000e-25 126.0
28 TraesCS7D01G108900 chr4D 91.589 107 9 0 429 535 100563732 100563838 7.900000e-32 148.0
29 TraesCS7D01G108900 chr3A 81.707 164 28 2 1433 1595 120175808 120175970 6.150000e-28 135.0
30 TraesCS7D01G108900 chr3A 84.800 125 19 0 425 549 53215406 53215282 3.700000e-25 126.0
31 TraesCS7D01G108900 chr3A 77.901 181 37 3 1063 1241 120223523 120223702 3.730000e-20 110.0
32 TraesCS7D01G108900 chr3A 77.222 180 37 4 1063 1240 120357289 120357466 6.240000e-18 102.0
33 TraesCS7D01G108900 chr7B 79.885 174 24 6 1075 1238 7358061 7357889 2.230000e-22 117.0
34 TraesCS7D01G108900 chr5A 80.137 146 22 7 3391 3531 271057503 271057646 6.240000e-18 102.0
35 TraesCS7D01G108900 chr5A 85.714 98 11 3 1162 1256 495028722 495028625 2.240000e-17 100.0
36 TraesCS7D01G108900 chr1B 79.730 148 23 7 3389 3531 47401197 47401052 2.240000e-17 100.0
37 TraesCS7D01G108900 chr2B 90.000 70 7 0 10 79 741494633 741494702 1.350000e-14 91.6
38 TraesCS7D01G108900 chr2A 79.775 89 18 0 3391 3479 602815154 602815242 8.190000e-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 TraesCS7D01G108900 chr7D 65598661 65602194 3533 True 6527.000000 6527 100.000000 1 3534 1 chr7D.!!$R1 3533
1 TraesCS7D01G108900 chrUn 84037748 84041099 3351 True 2166.000000 3770 90.847500 1 3386 2 chrUn.!!$R2 3385
2 TraesCS7D01G108900 chr7A 69901143 69904993 3850 False 1216.333333 3160 85.109667 686 3347 3 chr7A.!!$F5 2661

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
742 820 0.328592 GAACCAGGGAGGAAAGGGTC 59.671 60.0 0.00 0.0 41.22 4.46 F
1185 1296 0.531200 CCTACGGCGAGACCTTCTTT 59.469 55.0 16.62 0.0 35.61 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2207 2323 0.179045 GGAGGGACGTACCGTAGCTA 60.179 60.0 12.23 0.00 41.37 3.32 R
2853 2998 0.027194 CTACCGAATCGCGACTTCGA 59.973 55.0 34.18 23.03 46.36 3.71 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
23 24 0.904865 TGATCTCGGCTCCACCTTGT 60.905 55.000 0.00 0.00 35.61 3.16
42 43 5.047092 CCTTGTATTGAGGATTTGTTGCCTT 60.047 40.000 0.00 0.00 36.33 4.35
77 83 8.919777 ACACTATTACATAGAAATAAAGCCCC 57.080 34.615 0.00 0.00 36.68 5.80
78 84 7.942894 ACACTATTACATAGAAATAAAGCCCCC 59.057 37.037 0.00 0.00 36.68 5.40
79 85 7.119262 CACTATTACATAGAAATAAAGCCCCCG 59.881 40.741 0.00 0.00 36.68 5.73
80 86 3.945640 ACATAGAAATAAAGCCCCCGT 57.054 42.857 0.00 0.00 0.00 5.28
81 87 4.245251 ACATAGAAATAAAGCCCCCGTT 57.755 40.909 0.00 0.00 0.00 4.44
82 88 5.376756 ACATAGAAATAAAGCCCCCGTTA 57.623 39.130 0.00 0.00 0.00 3.18
83 89 5.757988 ACATAGAAATAAAGCCCCCGTTAA 58.242 37.500 0.00 0.00 0.00 2.01
84 90 6.370453 ACATAGAAATAAAGCCCCCGTTAAT 58.630 36.000 0.00 0.00 0.00 1.40
85 91 6.837048 ACATAGAAATAAAGCCCCCGTTAATT 59.163 34.615 0.00 0.00 0.00 1.40
87 93 4.337274 AGAAATAAAGCCCCCGTTAATTCG 59.663 41.667 0.00 0.00 33.13 3.34
88 94 1.381522 TAAAGCCCCCGTTAATTCGC 58.618 50.000 0.00 0.00 0.00 4.70
89 95 0.609681 AAAGCCCCCGTTAATTCGCA 60.610 50.000 0.00 0.00 0.00 5.10
90 96 0.609681 AAGCCCCCGTTAATTCGCAA 60.610 50.000 0.00 0.00 0.00 4.85
91 97 0.609681 AGCCCCCGTTAATTCGCAAA 60.610 50.000 0.00 0.00 0.00 3.68
149 155 2.125326 GCCGATTTACCCCCTTGGC 61.125 63.158 0.00 0.00 37.83 4.52
203 219 1.348775 CCCCCTCCTCCTCAACCATC 61.349 65.000 0.00 0.00 0.00 3.51
374 391 0.525668 CCCATCTTCGGACTCGTTCG 60.526 60.000 0.00 0.00 37.69 3.95
396 413 5.867174 TCGAAAATCGACTAACATGTGTGAT 59.133 36.000 0.00 0.00 44.82 3.06
430 447 6.625081 GCACCAGAGGAATACCAAATTTGTAC 60.625 42.308 16.73 0.00 38.94 2.90
432 449 6.884836 ACCAGAGGAATACCAAATTTGTACTC 59.115 38.462 16.73 12.82 38.94 2.59
433 450 6.318900 CCAGAGGAATACCAAATTTGTACTCC 59.681 42.308 16.73 15.61 38.94 3.85
434 451 6.318900 CAGAGGAATACCAAATTTGTACTCCC 59.681 42.308 16.73 11.51 38.94 4.30
435 452 6.217693 AGAGGAATACCAAATTTGTACTCCCT 59.782 38.462 16.73 15.44 38.94 4.20
436 453 6.424032 AGGAATACCAAATTTGTACTCCCTC 58.576 40.000 16.73 4.39 38.94 4.30
437 454 6.217693 AGGAATACCAAATTTGTACTCCCTCT 59.782 38.462 16.73 2.70 38.94 3.69
438 455 6.318900 GGAATACCAAATTTGTACTCCCTCTG 59.681 42.308 16.73 0.41 35.97 3.35
439 456 4.724279 ACCAAATTTGTACTCCCTCTGT 57.276 40.909 16.73 1.01 0.00 3.41
440 457 5.061721 ACCAAATTTGTACTCCCTCTGTT 57.938 39.130 16.73 0.00 0.00 3.16
441 458 5.070685 ACCAAATTTGTACTCCCTCTGTTC 58.929 41.667 16.73 0.00 0.00 3.18
442 459 5.070001 CCAAATTTGTACTCCCTCTGTTCA 58.930 41.667 16.73 0.00 0.00 3.18
443 460 5.048713 CCAAATTTGTACTCCCTCTGTTCAC 60.049 44.000 16.73 0.00 0.00 3.18
444 461 5.568620 AATTTGTACTCCCTCTGTTCACT 57.431 39.130 0.00 0.00 0.00 3.41
445 462 5.568620 ATTTGTACTCCCTCTGTTCACTT 57.431 39.130 0.00 0.00 0.00 3.16
446 463 5.367945 TTTGTACTCCCTCTGTTCACTTT 57.632 39.130 0.00 0.00 0.00 2.66
447 464 5.367945 TTGTACTCCCTCTGTTCACTTTT 57.632 39.130 0.00 0.00 0.00 2.27
448 465 6.488769 TTGTACTCCCTCTGTTCACTTTTA 57.511 37.500 0.00 0.00 0.00 1.52
449 466 6.681729 TGTACTCCCTCTGTTCACTTTTAT 57.318 37.500 0.00 0.00 0.00 1.40
450 467 7.786046 TGTACTCCCTCTGTTCACTTTTATA 57.214 36.000 0.00 0.00 0.00 0.98
451 468 8.197592 TGTACTCCCTCTGTTCACTTTTATAA 57.802 34.615 0.00 0.00 0.00 0.98
452 469 8.311836 TGTACTCCCTCTGTTCACTTTTATAAG 58.688 37.037 0.00 0.00 37.40 1.73
453 470 7.554959 ACTCCCTCTGTTCACTTTTATAAGA 57.445 36.000 0.00 0.00 35.30 2.10
454 471 7.387643 ACTCCCTCTGTTCACTTTTATAAGAC 58.612 38.462 0.00 0.00 35.30 3.01
455 472 7.016268 ACTCCCTCTGTTCACTTTTATAAGACA 59.984 37.037 0.00 0.00 35.30 3.41
456 473 7.918076 TCCCTCTGTTCACTTTTATAAGACAT 58.082 34.615 0.00 0.00 35.30 3.06
457 474 8.383175 TCCCTCTGTTCACTTTTATAAGACATT 58.617 33.333 0.00 0.00 35.30 2.71
458 475 9.014297 CCCTCTGTTCACTTTTATAAGACATTT 57.986 33.333 0.00 0.00 35.30 2.32
475 492 8.485976 AAGACATTTTAGATAGTTCAGACAGC 57.514 34.615 0.00 0.00 0.00 4.40
476 493 7.846066 AGACATTTTAGATAGTTCAGACAGCT 58.154 34.615 0.00 0.00 0.00 4.24
477 494 7.978975 AGACATTTTAGATAGTTCAGACAGCTC 59.021 37.037 0.00 0.00 0.00 4.09
478 495 7.044798 ACATTTTAGATAGTTCAGACAGCTCC 58.955 38.462 0.00 0.00 0.00 4.70
479 496 5.599999 TTTAGATAGTTCAGACAGCTCCC 57.400 43.478 0.00 0.00 0.00 4.30
480 497 3.107402 AGATAGTTCAGACAGCTCCCA 57.893 47.619 0.00 0.00 0.00 4.37
481 498 3.445008 AGATAGTTCAGACAGCTCCCAA 58.555 45.455 0.00 0.00 0.00 4.12
482 499 3.840666 AGATAGTTCAGACAGCTCCCAAA 59.159 43.478 0.00 0.00 0.00 3.28
483 500 4.287067 AGATAGTTCAGACAGCTCCCAAAA 59.713 41.667 0.00 0.00 0.00 2.44
484 501 2.576615 AGTTCAGACAGCTCCCAAAAC 58.423 47.619 0.00 0.00 0.00 2.43
485 502 2.092429 AGTTCAGACAGCTCCCAAAACA 60.092 45.455 0.00 0.00 0.00 2.83
486 503 2.260844 TCAGACAGCTCCCAAAACAG 57.739 50.000 0.00 0.00 0.00 3.16
487 504 1.490490 TCAGACAGCTCCCAAAACAGT 59.510 47.619 0.00 0.00 0.00 3.55
488 505 2.092429 TCAGACAGCTCCCAAAACAGTT 60.092 45.455 0.00 0.00 0.00 3.16
489 506 2.291741 CAGACAGCTCCCAAAACAGTTC 59.708 50.000 0.00 0.00 0.00 3.01
490 507 2.092429 AGACAGCTCCCAAAACAGTTCA 60.092 45.455 0.00 0.00 0.00 3.18
491 508 2.687935 GACAGCTCCCAAAACAGTTCAA 59.312 45.455 0.00 0.00 0.00 2.69
492 509 3.096092 ACAGCTCCCAAAACAGTTCAAA 58.904 40.909 0.00 0.00 0.00 2.69
493 510 3.513515 ACAGCTCCCAAAACAGTTCAAAA 59.486 39.130 0.00 0.00 0.00 2.44
494 511 4.162131 ACAGCTCCCAAAACAGTTCAAAAT 59.838 37.500 0.00 0.00 0.00 1.82
495 512 4.746611 CAGCTCCCAAAACAGTTCAAAATC 59.253 41.667 0.00 0.00 0.00 2.17
496 513 4.405358 AGCTCCCAAAACAGTTCAAAATCA 59.595 37.500 0.00 0.00 0.00 2.57
497 514 4.746611 GCTCCCAAAACAGTTCAAAATCAG 59.253 41.667 0.00 0.00 0.00 2.90
498 515 5.451798 GCTCCCAAAACAGTTCAAAATCAGA 60.452 40.000 0.00 0.00 0.00 3.27
499 516 6.729690 TCCCAAAACAGTTCAAAATCAGAT 57.270 33.333 0.00 0.00 0.00 2.90
500 517 6.514947 TCCCAAAACAGTTCAAAATCAGATG 58.485 36.000 0.00 0.00 0.00 2.90
501 518 6.098124 TCCCAAAACAGTTCAAAATCAGATGT 59.902 34.615 0.00 0.00 0.00 3.06
502 519 6.421801 CCCAAAACAGTTCAAAATCAGATGTC 59.578 38.462 0.00 0.00 0.00 3.06
503 520 7.205297 CCAAAACAGTTCAAAATCAGATGTCT 58.795 34.615 0.00 0.00 0.00 3.41
504 521 8.352201 CCAAAACAGTTCAAAATCAGATGTCTA 58.648 33.333 0.00 0.00 0.00 2.59
505 522 9.734620 CAAAACAGTTCAAAATCAGATGTCTAA 57.265 29.630 0.00 0.00 0.00 2.10
508 525 9.736023 AACAGTTCAAAATCAGATGTCTAAAAC 57.264 29.630 0.00 0.00 0.00 2.43
509 526 8.070171 ACAGTTCAAAATCAGATGTCTAAAACG 58.930 33.333 0.00 0.00 0.00 3.60
510 527 8.070171 CAGTTCAAAATCAGATGTCTAAAACGT 58.930 33.333 0.00 0.00 0.00 3.99
511 528 8.283291 AGTTCAAAATCAGATGTCTAAAACGTC 58.717 33.333 0.00 0.00 43.19 4.34
526 543 9.934641 GTCTAAAACGTCTTATAAAAGAGAACG 57.065 33.333 0.00 0.00 42.40 3.95
527 544 9.132521 TCTAAAACGTCTTATAAAAGAGAACGG 57.867 33.333 0.00 0.00 42.40 4.44
528 545 7.951530 AAAACGTCTTATAAAAGAGAACGGA 57.048 32.000 0.00 0.00 42.40 4.69
529 546 7.578169 AAACGTCTTATAAAAGAGAACGGAG 57.422 36.000 0.00 0.00 42.40 4.63
530 547 5.648572 ACGTCTTATAAAAGAGAACGGAGG 58.351 41.667 0.00 0.00 42.40 4.30
531 548 5.041940 CGTCTTATAAAAGAGAACGGAGGG 58.958 45.833 0.00 0.00 42.40 4.30
532 549 5.163581 CGTCTTATAAAAGAGAACGGAGGGA 60.164 44.000 0.00 0.00 42.40 4.20
533 550 6.274579 GTCTTATAAAAGAGAACGGAGGGAG 58.725 44.000 0.00 0.00 42.40 4.30
534 551 5.956563 TCTTATAAAAGAGAACGGAGGGAGT 59.043 40.000 0.00 0.00 36.80 3.85
535 552 7.067981 GTCTTATAAAAGAGAACGGAGGGAGTA 59.932 40.741 0.00 0.00 42.40 2.59
536 553 5.855740 ATAAAAGAGAACGGAGGGAGTAG 57.144 43.478 0.00 0.00 0.00 2.57
537 554 2.903375 AAGAGAACGGAGGGAGTAGT 57.097 50.000 0.00 0.00 0.00 2.73
538 555 4.313020 AAAGAGAACGGAGGGAGTAGTA 57.687 45.455 0.00 0.00 0.00 1.82
539 556 4.313020 AAGAGAACGGAGGGAGTAGTAA 57.687 45.455 0.00 0.00 0.00 2.24
540 557 4.313020 AGAGAACGGAGGGAGTAGTAAA 57.687 45.455 0.00 0.00 0.00 2.01
541 558 4.670765 AGAGAACGGAGGGAGTAGTAAAA 58.329 43.478 0.00 0.00 0.00 1.52
542 559 5.082425 AGAGAACGGAGGGAGTAGTAAAAA 58.918 41.667 0.00 0.00 0.00 1.94
543 560 5.047448 AGAGAACGGAGGGAGTAGTAAAAAC 60.047 44.000 0.00 0.00 0.00 2.43
544 561 3.582714 ACGGAGGGAGTAGTAAAAACG 57.417 47.619 0.00 0.00 0.00 3.60
545 562 3.157087 ACGGAGGGAGTAGTAAAAACGA 58.843 45.455 0.00 0.00 0.00 3.85
566 583 7.246674 ACGAACATGTTAACATATTAGCCAG 57.753 36.000 20.39 8.51 34.26 4.85
572 589 5.874831 TGTTAACATATTAGCCAGCAAACG 58.125 37.500 3.59 0.00 0.00 3.60
607 680 9.635520 CAATCTACTTGCTTTCTTGATTTCATT 57.364 29.630 0.00 0.00 0.00 2.57
608 681 9.635520 AATCTACTTGCTTTCTTGATTTCATTG 57.364 29.630 0.00 0.00 0.00 2.82
609 682 7.086376 TCTACTTGCTTTCTTGATTTCATTGC 58.914 34.615 0.00 0.00 0.00 3.56
610 683 5.603596 ACTTGCTTTCTTGATTTCATTGCA 58.396 33.333 0.00 0.00 0.00 4.08
611 684 6.228258 ACTTGCTTTCTTGATTTCATTGCAT 58.772 32.000 0.00 0.00 0.00 3.96
612 685 7.380536 ACTTGCTTTCTTGATTTCATTGCATA 58.619 30.769 0.00 0.00 0.00 3.14
613 686 7.874016 ACTTGCTTTCTTGATTTCATTGCATAA 59.126 29.630 0.00 0.00 0.00 1.90
632 705 6.655003 TGCATAAAAAGATATGTAGCCTAGCC 59.345 38.462 0.00 0.00 36.00 3.93
633 706 6.881602 GCATAAAAAGATATGTAGCCTAGCCT 59.118 38.462 0.00 0.00 36.00 4.58
634 707 8.041323 GCATAAAAAGATATGTAGCCTAGCCTA 58.959 37.037 0.00 0.00 36.00 3.93
635 708 9.593134 CATAAAAAGATATGTAGCCTAGCCTAG 57.407 37.037 0.00 0.00 0.00 3.02
678 756 7.507277 GGATAAAAGCAGGGGAAGATAAAGATT 59.493 37.037 0.00 0.00 0.00 2.40
704 782 7.754625 TGATGTACTGACATGATTGAACATTG 58.245 34.615 0.00 0.00 46.64 2.82
742 820 0.328592 GAACCAGGGAGGAAAGGGTC 59.671 60.000 0.00 0.00 41.22 4.46
787 875 1.893801 ACAACAACCCGGTGACAAAAA 59.106 42.857 0.00 0.00 0.00 1.94
795 883 4.572909 ACCCGGTGACAAAAATACTAGTC 58.427 43.478 0.00 0.00 0.00 2.59
913 1020 0.801067 GGCGCCGTCTATATAAGCCG 60.801 60.000 12.58 0.00 33.43 5.52
953 1064 2.091720 CCTTCATCAACCCATCCATCCA 60.092 50.000 0.00 0.00 0.00 3.41
964 1075 2.147315 ATCCATCCACCGAGCGATCG 62.147 60.000 17.57 17.57 0.00 3.69
977 1088 2.418910 CGATCGGCACTCCCACTCT 61.419 63.158 7.38 0.00 0.00 3.24
978 1089 1.101635 CGATCGGCACTCCCACTCTA 61.102 60.000 7.38 0.00 0.00 2.43
1134 1245 2.030562 AACCTCTGCGTCAACGGG 59.969 61.111 4.54 0.00 40.23 5.28
1185 1296 0.531200 CCTACGGCGAGACCTTCTTT 59.469 55.000 16.62 0.00 35.61 2.52
1191 1302 1.004918 CGAGACCTTCTTTGGCCGT 60.005 57.895 0.00 0.00 0.00 5.68
1310 1421 4.202243 TGCATTTTCCCTCCAAAACAAGAG 60.202 41.667 0.00 0.00 0.00 2.85
1324 1436 1.802960 ACAAGAGAAACAGAGCATGCG 59.197 47.619 13.01 0.00 0.00 4.73
1677 1790 2.869503 ATTAACGCCGCCTGGTCCAG 62.870 60.000 12.40 12.40 37.67 3.86
1703 1816 5.418676 CAAGGCCAGAGAGAAAAACAAAAA 58.581 37.500 5.01 0.00 0.00 1.94
1704 1817 5.876651 AGGCCAGAGAGAAAAACAAAAAT 57.123 34.783 5.01 0.00 0.00 1.82
1706 1819 4.751600 GGCCAGAGAGAAAAACAAAAATGG 59.248 41.667 0.00 0.00 0.00 3.16
1773 1889 4.828829 CCATTAACTAACTCCACGTCCTT 58.171 43.478 0.00 0.00 0.00 3.36
1925 2041 1.745115 CACCATCGTGGACGCCATT 60.745 57.895 10.46 0.00 40.96 3.16
2133 2249 3.201707 AAGGTGACCAGCCTGCAGG 62.202 63.158 29.34 29.34 36.30 4.85
2207 2323 3.011517 ATGGTCAAGAGCCCCGCT 61.012 61.111 0.00 0.00 43.88 5.52
2246 2362 2.661675 CCGTCACTGTTTGTACTGATCG 59.338 50.000 0.00 0.00 0.00 3.69
2255 2371 2.054232 TGTACTGATCGTCCTCCTCC 57.946 55.000 0.00 0.00 0.00 4.30
2256 2372 1.320507 GTACTGATCGTCCTCCTCCC 58.679 60.000 0.00 0.00 0.00 4.30
2260 2376 0.395862 TGATCGTCCTCCTCCCACTC 60.396 60.000 0.00 0.00 0.00 3.51
2263 2379 1.305381 CGTCCTCCTCCCACTCCTT 60.305 63.158 0.00 0.00 0.00 3.36
2295 2415 1.795286 CTCCGGCGAGCTGATTATTTC 59.205 52.381 9.30 0.00 0.00 2.17
2302 2422 3.788163 GCGAGCTGATTATTTCTTTGTGC 59.212 43.478 0.00 0.00 0.00 4.57
2306 2426 4.216257 AGCTGATTATTTCTTTGTGCGTGT 59.784 37.500 0.00 0.00 0.00 4.49
2307 2427 4.321745 GCTGATTATTTCTTTGTGCGTGTG 59.678 41.667 0.00 0.00 0.00 3.82
2309 2429 5.448438 TGATTATTTCTTTGTGCGTGTGTC 58.552 37.500 0.00 0.00 0.00 3.67
2310 2430 2.383298 ATTTCTTTGTGCGTGTGTCG 57.617 45.000 0.00 0.00 43.12 4.35
2311 2431 1.360820 TTTCTTTGTGCGTGTGTCGA 58.639 45.000 0.00 0.00 42.86 4.20
2312 2432 1.577468 TTCTTTGTGCGTGTGTCGAT 58.423 45.000 0.00 0.00 42.86 3.59
2313 2433 0.858583 TCTTTGTGCGTGTGTCGATG 59.141 50.000 0.00 0.00 42.86 3.84
2383 2509 3.323243 CAAGTACAACTACCAGAACGGG 58.677 50.000 0.00 0.00 40.22 5.28
2543 2669 1.503818 CCTCTCCTAGAGCGAGCGAC 61.504 65.000 0.00 0.00 40.98 5.19
2578 2708 2.098443 GTCGTTTGGTTGCTTCCTTTCA 59.902 45.455 0.00 0.00 0.00 2.69
2706 2844 0.392336 AATTTGCGCTTGGGCTGAAA 59.608 45.000 9.73 0.00 36.09 2.69
2787 2932 3.000041 GTTCATGATCCAGTGCGTACAA 59.000 45.455 6.38 0.00 0.00 2.41
2814 2959 4.220382 CAGGACCAAAACTAATCATTGGCA 59.780 41.667 3.79 0.00 45.99 4.92
2817 2962 3.900601 ACCAAAACTAATCATTGGCACCA 59.099 39.130 3.79 0.00 45.99 4.17
2818 2963 4.346418 ACCAAAACTAATCATTGGCACCAA 59.654 37.500 4.24 4.24 45.99 3.67
2819 2964 5.163258 ACCAAAACTAATCATTGGCACCAAA 60.163 36.000 6.14 0.00 45.99 3.28
2820 2965 5.179182 CCAAAACTAATCATTGGCACCAAAC 59.821 40.000 6.14 0.00 39.55 2.93
2821 2966 5.543507 AAACTAATCATTGGCACCAAACA 57.456 34.783 6.14 0.00 39.55 2.83
2853 2998 2.332063 AAATTGCCTCACCGATCGAT 57.668 45.000 18.66 0.00 0.00 3.59
2854 2999 1.871080 AATTGCCTCACCGATCGATC 58.129 50.000 18.66 15.68 0.00 3.69
2892 3037 1.590238 GCAGGAACTTGACGATCGATG 59.410 52.381 24.34 10.61 34.60 3.84
3074 3367 0.249120 TCGACTGGCCGATCATTTGT 59.751 50.000 0.00 0.00 33.14 2.83
3147 3440 4.191111 CGATCGGTCGTAGAAGCG 57.809 61.111 10.62 0.00 42.78 4.68
3148 3441 2.004489 CGATCGGTCGTAGAAGCGC 61.004 63.158 10.62 0.00 42.78 5.92
3150 3443 0.524816 GATCGGTCGTAGAAGCGCAA 60.525 55.000 11.47 0.00 39.69 4.85
3151 3444 0.801067 ATCGGTCGTAGAAGCGCAAC 60.801 55.000 11.47 2.34 39.69 4.17
3152 3445 1.443872 CGGTCGTAGAAGCGCAACT 60.444 57.895 11.47 11.06 39.69 3.16
3153 3446 1.674611 CGGTCGTAGAAGCGCAACTG 61.675 60.000 11.47 0.00 39.69 3.16
3364 3678 4.695455 CGCCACCTGGACCTATTATTATTG 59.305 45.833 0.00 0.00 37.39 1.90
3404 3718 7.978099 ATTATTTGATGGGAAAAGCTTACCT 57.022 32.000 18.01 4.04 36.34 3.08
3405 3719 7.790782 TTATTTGATGGGAAAAGCTTACCTT 57.209 32.000 18.01 11.14 36.34 3.50
3406 3720 5.722021 TTTGATGGGAAAAGCTTACCTTC 57.278 39.130 18.01 17.45 39.29 3.46
3407 3721 4.380843 TGATGGGAAAAGCTTACCTTCA 57.619 40.909 20.16 20.16 43.96 3.02
3408 3722 4.335416 TGATGGGAAAAGCTTACCTTCAG 58.665 43.478 20.16 0.00 42.23 3.02
3410 3724 1.819288 GGGAAAAGCTTACCTTCAGCC 59.181 52.381 18.01 5.96 38.09 4.85
3411 3725 1.468914 GGAAAAGCTTACCTTCAGCCG 59.531 52.381 0.00 0.00 38.09 5.52
3412 3726 1.468914 GAAAAGCTTACCTTCAGCCGG 59.531 52.381 0.00 0.00 38.09 6.13
3413 3727 0.960861 AAAGCTTACCTTCAGCCGGC 60.961 55.000 21.89 21.89 38.09 6.13
3415 3729 2.511600 CTTACCTTCAGCCGGCCG 60.512 66.667 26.15 21.04 0.00 6.13
3416 3730 2.998480 TTACCTTCAGCCGGCCGA 60.998 61.111 30.73 17.59 0.00 5.54
3445 3759 3.991051 CGTCCACTGCCTCCGTGT 61.991 66.667 0.00 0.00 0.00 4.49
3446 3760 2.048127 GTCCACTGCCTCCGTGTC 60.048 66.667 0.00 0.00 0.00 3.67
3447 3761 3.311110 TCCACTGCCTCCGTGTCC 61.311 66.667 0.00 0.00 0.00 4.02
3448 3762 3.625897 CCACTGCCTCCGTGTCCA 61.626 66.667 0.00 0.00 0.00 4.02
3451 3765 2.202797 CTGCCTCCGTGTCCATCG 60.203 66.667 0.00 0.00 0.00 3.84
3459 3773 2.420138 CGTGTCCATCGGATCCTCT 58.580 57.895 10.75 0.00 32.73 3.69
3460 3774 0.031314 CGTGTCCATCGGATCCTCTG 59.969 60.000 10.75 6.81 32.73 3.35
3461 3775 1.115467 GTGTCCATCGGATCCTCTGT 58.885 55.000 10.75 0.00 32.73 3.41
3462 3776 1.482593 GTGTCCATCGGATCCTCTGTT 59.517 52.381 10.75 0.00 32.73 3.16
3463 3777 1.482182 TGTCCATCGGATCCTCTGTTG 59.518 52.381 10.75 0.00 32.73 3.33
3464 3778 1.757118 GTCCATCGGATCCTCTGTTGA 59.243 52.381 10.75 0.00 32.73 3.18
3465 3779 2.366916 GTCCATCGGATCCTCTGTTGAT 59.633 50.000 10.75 0.70 32.73 2.57
3466 3780 2.630098 TCCATCGGATCCTCTGTTGATC 59.370 50.000 10.75 0.00 38.30 2.92
3467 3781 2.366590 CCATCGGATCCTCTGTTGATCA 59.633 50.000 10.75 0.00 40.32 2.92
3468 3782 3.554544 CCATCGGATCCTCTGTTGATCAG 60.555 52.174 10.75 0.00 44.85 2.90
3477 3791 3.790152 TCTGTTGATCAGATGGACGAG 57.210 47.619 0.00 0.00 46.77 4.18
3478 3792 3.356290 TCTGTTGATCAGATGGACGAGA 58.644 45.455 0.00 0.00 46.77 4.04
3479 3793 3.379688 TCTGTTGATCAGATGGACGAGAG 59.620 47.826 0.00 0.00 46.77 3.20
3481 3795 1.767759 TGATCAGATGGACGAGAGCA 58.232 50.000 0.00 0.00 0.00 4.26
3482 3796 1.406898 TGATCAGATGGACGAGAGCAC 59.593 52.381 0.00 0.00 0.00 4.40
3483 3797 0.749649 ATCAGATGGACGAGAGCACC 59.250 55.000 0.00 0.00 0.00 5.01
3484 3798 1.142748 CAGATGGACGAGAGCACCC 59.857 63.158 0.00 0.00 0.00 4.61
3485 3799 2.060980 AGATGGACGAGAGCACCCC 61.061 63.158 0.00 0.00 0.00 4.95
3486 3800 3.083997 ATGGACGAGAGCACCCCC 61.084 66.667 0.00 0.00 0.00 5.40
3489 3803 4.436998 GACGAGAGCACCCCCGTG 62.437 72.222 0.00 0.00 43.35 4.94
3492 3806 2.577593 GAGAGCACCCCCGTGTAC 59.422 66.667 0.00 0.00 42.39 2.90
3494 3808 1.612442 AGAGCACCCCCGTGTACAT 60.612 57.895 0.00 0.00 42.39 2.29
3495 3809 1.449601 GAGCACCCCCGTGTACATG 60.450 63.158 8.18 8.18 42.39 3.21
3496 3810 2.180159 GAGCACCCCCGTGTACATGT 62.180 60.000 13.91 2.69 42.39 3.21
3497 3811 2.038269 GCACCCCCGTGTACATGTG 61.038 63.158 9.11 10.23 42.39 3.21
3499 3813 0.953471 CACCCCCGTGTACATGTGTG 60.953 60.000 9.11 13.04 35.10 3.82
3500 3814 1.373435 CCCCCGTGTACATGTGTGT 59.627 57.895 9.11 0.00 42.39 3.72
3501 3815 0.672401 CCCCCGTGTACATGTGTGTC 60.672 60.000 9.11 0.00 39.77 3.67
3502 3816 0.320374 CCCCGTGTACATGTGTGTCT 59.680 55.000 9.11 0.00 39.77 3.41
3503 3817 1.428448 CCCGTGTACATGTGTGTCTG 58.572 55.000 9.11 0.00 39.77 3.51
3504 3818 0.790207 CCGTGTACATGTGTGTCTGC 59.210 55.000 9.11 0.00 39.77 4.26
3505 3819 1.496934 CGTGTACATGTGTGTCTGCA 58.503 50.000 9.11 0.00 39.77 4.41
3506 3820 1.864082 CGTGTACATGTGTGTCTGCAA 59.136 47.619 9.11 0.00 39.77 4.08
3507 3821 2.348498 CGTGTACATGTGTGTCTGCAAC 60.348 50.000 9.11 0.00 39.77 4.17
3508 3822 2.872245 GTGTACATGTGTGTCTGCAACT 59.128 45.455 9.11 0.00 39.77 3.16
3509 3823 2.871633 TGTACATGTGTGTCTGCAACTG 59.128 45.455 9.11 0.00 39.77 3.16
3510 3824 2.330440 ACATGTGTGTCTGCAACTGA 57.670 45.000 0.00 0.00 31.41 3.41
3512 3826 1.069432 CATGTGTGTCTGCAACTGAGC 60.069 52.381 0.00 0.00 0.00 4.26
3513 3827 0.815213 TGTGTGTCTGCAACTGAGCC 60.815 55.000 0.00 0.00 0.00 4.70
3517 3831 1.002033 GTGTCTGCAACTGAGCCTTTG 60.002 52.381 0.00 0.00 0.00 2.77
3528 4114 4.672409 ACTGAGCCTTTGTTTCGAAAAAG 58.328 39.130 13.10 13.15 33.95 2.27
3530 4116 4.920376 TGAGCCTTTGTTTCGAAAAAGAG 58.080 39.130 19.31 15.42 35.79 2.85
3531 4117 4.638421 TGAGCCTTTGTTTCGAAAAAGAGA 59.362 37.500 17.87 0.00 35.79 3.10
3532 4118 5.175090 AGCCTTTGTTTCGAAAAAGAGAG 57.825 39.130 17.87 10.24 35.79 3.20
3533 4119 4.640647 AGCCTTTGTTTCGAAAAAGAGAGT 59.359 37.500 17.87 4.09 35.79 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 6.267471 AGTCAAAAGGCAACAAATCCTCAATA 59.733 34.615 0.00 0.00 41.41 1.90
73 79 0.244178 TTTTGCGAATTAACGGGGGC 59.756 50.000 0.00 0.00 0.00 5.80
130 136 1.613061 CCAAGGGGGTAAATCGGCT 59.387 57.895 0.00 0.00 0.00 5.52
149 155 2.719739 ACAGAGCCAAATGTGATCTGG 58.280 47.619 17.48 0.00 40.21 3.86
222 238 4.217266 AAGGGTGTGGGAGGGGGT 62.217 66.667 0.00 0.00 0.00 4.95
234 250 1.535687 ACTAGCACGGGTCAAGGGT 60.536 57.895 0.00 0.00 0.00 4.34
348 365 1.304630 TCCGAAGATGGGGTCGACA 60.305 57.895 18.91 0.00 39.64 4.35
374 391 8.728088 AAAATCACACATGTTAGTCGATTTTC 57.272 30.769 19.58 0.00 37.12 2.29
430 447 7.386851 TGTCTTATAAAAGTGAACAGAGGGAG 58.613 38.462 0.00 0.00 34.13 4.30
432 449 8.567285 AATGTCTTATAAAAGTGAACAGAGGG 57.433 34.615 0.00 0.00 34.13 4.30
449 466 9.587772 GCTGTCTGAACTATCTAAAATGTCTTA 57.412 33.333 0.00 0.00 0.00 2.10
450 467 8.317679 AGCTGTCTGAACTATCTAAAATGTCTT 58.682 33.333 0.00 0.00 0.00 3.01
451 468 7.846066 AGCTGTCTGAACTATCTAAAATGTCT 58.154 34.615 0.00 0.00 0.00 3.41
452 469 7.223777 GGAGCTGTCTGAACTATCTAAAATGTC 59.776 40.741 0.00 0.00 0.00 3.06
453 470 7.044798 GGAGCTGTCTGAACTATCTAAAATGT 58.955 38.462 0.00 0.00 0.00 2.71
454 471 6.481644 GGGAGCTGTCTGAACTATCTAAAATG 59.518 42.308 0.00 0.00 0.00 2.32
455 472 6.156949 TGGGAGCTGTCTGAACTATCTAAAAT 59.843 38.462 0.00 0.00 0.00 1.82
456 473 5.483937 TGGGAGCTGTCTGAACTATCTAAAA 59.516 40.000 0.00 0.00 0.00 1.52
457 474 5.023452 TGGGAGCTGTCTGAACTATCTAAA 58.977 41.667 0.00 0.00 0.00 1.85
458 475 4.610333 TGGGAGCTGTCTGAACTATCTAA 58.390 43.478 0.00 0.00 0.00 2.10
459 476 4.251103 TGGGAGCTGTCTGAACTATCTA 57.749 45.455 0.00 0.00 0.00 1.98
460 477 3.107402 TGGGAGCTGTCTGAACTATCT 57.893 47.619 0.00 0.00 0.00 1.98
461 478 3.895232 TTGGGAGCTGTCTGAACTATC 57.105 47.619 0.00 0.00 0.00 2.08
462 479 4.202461 TGTTTTGGGAGCTGTCTGAACTAT 60.202 41.667 0.00 0.00 0.00 2.12
463 480 3.135712 TGTTTTGGGAGCTGTCTGAACTA 59.864 43.478 0.00 0.00 0.00 2.24
464 481 2.092429 TGTTTTGGGAGCTGTCTGAACT 60.092 45.455 0.00 0.00 0.00 3.01
465 482 2.291741 CTGTTTTGGGAGCTGTCTGAAC 59.708 50.000 0.00 0.00 0.00 3.18
466 483 2.092429 ACTGTTTTGGGAGCTGTCTGAA 60.092 45.455 0.00 0.00 0.00 3.02
467 484 1.490490 ACTGTTTTGGGAGCTGTCTGA 59.510 47.619 0.00 0.00 0.00 3.27
468 485 1.972872 ACTGTTTTGGGAGCTGTCTG 58.027 50.000 0.00 0.00 0.00 3.51
469 486 2.092429 TGAACTGTTTTGGGAGCTGTCT 60.092 45.455 0.00 0.00 0.00 3.41
470 487 2.297701 TGAACTGTTTTGGGAGCTGTC 58.702 47.619 0.00 0.00 0.00 3.51
471 488 2.435372 TGAACTGTTTTGGGAGCTGT 57.565 45.000 0.00 0.00 0.00 4.40
472 489 3.799281 TTTGAACTGTTTTGGGAGCTG 57.201 42.857 0.00 0.00 0.00 4.24
473 490 4.405358 TGATTTTGAACTGTTTTGGGAGCT 59.595 37.500 0.00 0.00 0.00 4.09
474 491 4.692228 TGATTTTGAACTGTTTTGGGAGC 58.308 39.130 0.00 0.00 0.00 4.70
475 492 6.147864 TCTGATTTTGAACTGTTTTGGGAG 57.852 37.500 0.00 0.00 0.00 4.30
476 493 6.098124 ACATCTGATTTTGAACTGTTTTGGGA 59.902 34.615 0.00 0.00 0.00 4.37
477 494 6.282930 ACATCTGATTTTGAACTGTTTTGGG 58.717 36.000 0.00 0.00 0.00 4.12
478 495 7.205297 AGACATCTGATTTTGAACTGTTTTGG 58.795 34.615 0.00 0.00 0.00 3.28
479 496 9.734620 TTAGACATCTGATTTTGAACTGTTTTG 57.265 29.630 0.00 0.00 0.00 2.44
482 499 9.736023 GTTTTAGACATCTGATTTTGAACTGTT 57.264 29.630 0.00 0.00 0.00 3.16
483 500 8.070171 CGTTTTAGACATCTGATTTTGAACTGT 58.930 33.333 0.00 0.00 0.00 3.55
484 501 8.070171 ACGTTTTAGACATCTGATTTTGAACTG 58.930 33.333 0.00 0.00 0.00 3.16
485 502 8.154649 ACGTTTTAGACATCTGATTTTGAACT 57.845 30.769 0.00 0.00 0.00 3.01
486 503 8.283291 AGACGTTTTAGACATCTGATTTTGAAC 58.717 33.333 0.00 0.00 27.88 3.18
487 504 8.378172 AGACGTTTTAGACATCTGATTTTGAA 57.622 30.769 0.00 0.00 27.88 2.69
488 505 7.962964 AGACGTTTTAGACATCTGATTTTGA 57.037 32.000 0.00 0.00 27.88 2.69
500 517 9.934641 CGTTCTCTTTTATAAGACGTTTTAGAC 57.065 33.333 4.75 0.00 35.49 2.59
501 518 9.132521 CCGTTCTCTTTTATAAGACGTTTTAGA 57.867 33.333 4.75 0.00 35.49 2.10
502 519 9.132521 TCCGTTCTCTTTTATAAGACGTTTTAG 57.867 33.333 4.75 0.00 35.49 1.85
503 520 9.132521 CTCCGTTCTCTTTTATAAGACGTTTTA 57.867 33.333 0.52 0.52 35.49 1.52
504 521 7.117379 CCTCCGTTCTCTTTTATAAGACGTTTT 59.883 37.037 0.00 0.00 35.49 2.43
505 522 6.589139 CCTCCGTTCTCTTTTATAAGACGTTT 59.411 38.462 0.00 0.00 35.49 3.60
506 523 6.098017 CCTCCGTTCTCTTTTATAAGACGTT 58.902 40.000 0.00 0.00 35.49 3.99
507 524 5.393896 CCCTCCGTTCTCTTTTATAAGACGT 60.394 44.000 0.00 0.00 35.49 4.34
508 525 5.041940 CCCTCCGTTCTCTTTTATAAGACG 58.958 45.833 0.00 0.00 35.49 4.18
509 526 6.127394 ACTCCCTCCGTTCTCTTTTATAAGAC 60.127 42.308 0.00 0.00 35.49 3.01
510 527 5.956563 ACTCCCTCCGTTCTCTTTTATAAGA 59.043 40.000 0.00 0.00 38.06 2.10
511 528 6.223351 ACTCCCTCCGTTCTCTTTTATAAG 57.777 41.667 0.00 0.00 0.00 1.73
512 529 6.894103 ACTACTCCCTCCGTTCTCTTTTATAA 59.106 38.462 0.00 0.00 0.00 0.98
513 530 6.430007 ACTACTCCCTCCGTTCTCTTTTATA 58.570 40.000 0.00 0.00 0.00 0.98
514 531 5.270794 ACTACTCCCTCCGTTCTCTTTTAT 58.729 41.667 0.00 0.00 0.00 1.40
515 532 4.670765 ACTACTCCCTCCGTTCTCTTTTA 58.329 43.478 0.00 0.00 0.00 1.52
516 533 3.508426 ACTACTCCCTCCGTTCTCTTTT 58.492 45.455 0.00 0.00 0.00 2.27
517 534 3.172471 ACTACTCCCTCCGTTCTCTTT 57.828 47.619 0.00 0.00 0.00 2.52
518 535 2.903375 ACTACTCCCTCCGTTCTCTT 57.097 50.000 0.00 0.00 0.00 2.85
519 536 4.313020 TTTACTACTCCCTCCGTTCTCT 57.687 45.455 0.00 0.00 0.00 3.10
520 537 5.167121 GTTTTTACTACTCCCTCCGTTCTC 58.833 45.833 0.00 0.00 0.00 2.87
521 538 4.321527 CGTTTTTACTACTCCCTCCGTTCT 60.322 45.833 0.00 0.00 0.00 3.01
522 539 3.922850 CGTTTTTACTACTCCCTCCGTTC 59.077 47.826 0.00 0.00 0.00 3.95
523 540 3.573967 TCGTTTTTACTACTCCCTCCGTT 59.426 43.478 0.00 0.00 0.00 4.44
524 541 3.157087 TCGTTTTTACTACTCCCTCCGT 58.843 45.455 0.00 0.00 0.00 4.69
525 542 3.855689 TCGTTTTTACTACTCCCTCCG 57.144 47.619 0.00 0.00 0.00 4.63
526 543 4.886579 TGTTCGTTTTTACTACTCCCTCC 58.113 43.478 0.00 0.00 0.00 4.30
527 544 5.930569 ACATGTTCGTTTTTACTACTCCCTC 59.069 40.000 0.00 0.00 0.00 4.30
528 545 5.861727 ACATGTTCGTTTTTACTACTCCCT 58.138 37.500 0.00 0.00 0.00 4.20
529 546 6.549912 AACATGTTCGTTTTTACTACTCCC 57.450 37.500 4.92 0.00 0.00 4.30
530 547 8.550376 TGTTAACATGTTCGTTTTTACTACTCC 58.450 33.333 15.85 0.00 0.00 3.85
538 555 9.349145 GGCTAATATGTTAACATGTTCGTTTTT 57.651 29.630 27.48 10.28 38.39 1.94
539 556 8.516234 TGGCTAATATGTTAACATGTTCGTTTT 58.484 29.630 27.48 10.89 38.39 2.43
540 557 8.046294 TGGCTAATATGTTAACATGTTCGTTT 57.954 30.769 27.48 11.50 38.39 3.60
541 558 7.618502 TGGCTAATATGTTAACATGTTCGTT 57.381 32.000 27.48 16.99 38.39 3.85
542 559 6.238374 GCTGGCTAATATGTTAACATGTTCGT 60.238 38.462 27.48 12.13 38.39 3.85
543 560 6.136071 GCTGGCTAATATGTTAACATGTTCG 58.864 40.000 27.48 23.02 38.39 3.95
544 561 7.026631 TGCTGGCTAATATGTTAACATGTTC 57.973 36.000 27.48 17.12 38.39 3.18
545 562 7.403312 TTGCTGGCTAATATGTTAACATGTT 57.597 32.000 27.01 27.01 40.15 2.71
566 583 7.603515 CAAGTAGATTGCATTATTTCGTTTGC 58.396 34.615 0.00 0.00 35.67 3.68
605 678 8.734386 GCTAGGCTACATATCTTTTTATGCAAT 58.266 33.333 0.00 0.00 33.67 3.56
606 679 7.174946 GGCTAGGCTACATATCTTTTTATGCAA 59.825 37.037 9.46 0.00 33.67 4.08
607 680 6.655003 GGCTAGGCTACATATCTTTTTATGCA 59.345 38.462 9.46 0.00 33.67 3.96
608 681 6.881602 AGGCTAGGCTACATATCTTTTTATGC 59.118 38.462 18.73 0.00 33.67 3.14
609 682 9.593134 CTAGGCTAGGCTACATATCTTTTTATG 57.407 37.037 21.36 3.79 35.98 1.90
610 683 8.261522 GCTAGGCTAGGCTACATATCTTTTTAT 58.738 37.037 21.36 0.00 0.00 1.40
611 684 7.455008 AGCTAGGCTAGGCTACATATCTTTTTA 59.545 37.037 21.36 0.00 36.99 1.52
612 685 6.271159 AGCTAGGCTAGGCTACATATCTTTTT 59.729 38.462 21.36 0.00 36.99 1.94
613 686 5.782845 AGCTAGGCTAGGCTACATATCTTTT 59.217 40.000 21.36 0.00 36.99 2.27
632 705 4.824289 TCCGGTTACCACTTTTTAGCTAG 58.176 43.478 0.00 0.00 0.00 3.42
633 706 4.888326 TCCGGTTACCACTTTTTAGCTA 57.112 40.909 0.00 0.00 0.00 3.32
634 707 3.775261 TCCGGTTACCACTTTTTAGCT 57.225 42.857 0.00 0.00 0.00 3.32
635 708 6.499234 TTTATCCGGTTACCACTTTTTAGC 57.501 37.500 0.00 0.00 0.00 3.09
678 756 7.926674 ATGTTCAATCATGTCAGTACATCAA 57.073 32.000 0.00 0.00 44.70 2.57
704 782 1.278127 TCCCTTTCATCCTCGTGTTCC 59.722 52.381 0.00 0.00 0.00 3.62
730 808 1.900486 TCTTTCTCGACCCTTTCCTCC 59.100 52.381 0.00 0.00 0.00 4.30
739 817 4.143009 GCATGAACTCTTTCTTTCTCGACC 60.143 45.833 0.00 0.00 32.36 4.79
742 820 4.997905 TGCATGAACTCTTTCTTTCTCG 57.002 40.909 0.00 0.00 32.36 4.04
964 1075 0.176910 GCTCTTAGAGTGGGAGTGCC 59.823 60.000 11.18 0.00 31.39 5.01
966 1077 1.754226 GGAGCTCTTAGAGTGGGAGTG 59.246 57.143 14.64 0.00 31.39 3.51
968 1079 1.028905 CGGAGCTCTTAGAGTGGGAG 58.971 60.000 14.64 0.00 31.39 4.30
974 1085 0.667993 CTGGCTCGGAGCTCTTAGAG 59.332 60.000 27.47 21.56 41.99 2.43
977 1088 2.427245 GGCTGGCTCGGAGCTCTTA 61.427 63.158 27.47 12.04 41.99 2.10
978 1089 3.780173 GGCTGGCTCGGAGCTCTT 61.780 66.667 27.47 0.00 41.99 2.85
1107 1218 2.358737 CAGAGGTTGCCGGTGTCC 60.359 66.667 1.90 2.83 0.00 4.02
1677 1790 0.251341 TTTTCTCTCTGGCCTTGGCC 60.251 55.000 22.91 22.91 0.00 5.36
1729 1845 1.526686 GCGTGATCATGCATGGGGA 60.527 57.895 30.58 7.98 42.66 4.81
1773 1889 1.808546 CTGCAGTGCACCAACAACA 59.191 52.632 15.37 2.12 33.79 3.33
2133 2249 2.187896 TTGGCGTAGGGGTACTTGCC 62.188 60.000 0.00 0.00 45.03 4.52
2207 2323 0.179045 GGAGGGACGTACCGTAGCTA 60.179 60.000 12.23 0.00 41.37 3.32
2222 2338 2.035449 TCAGTACAAACAGTGACGGAGG 59.965 50.000 0.00 0.00 0.00 4.30
2246 2362 0.545548 ACAAGGAGTGGGAGGAGGAC 60.546 60.000 0.00 0.00 0.00 3.85
2255 2371 0.247736 CCGGAGAAGACAAGGAGTGG 59.752 60.000 0.00 0.00 0.00 4.00
2256 2372 0.390472 GCCGGAGAAGACAAGGAGTG 60.390 60.000 5.05 0.00 0.00 3.51
2260 2376 1.219393 GGAGCCGGAGAAGACAAGG 59.781 63.158 5.05 0.00 0.00 3.61
2289 2409 3.556365 TCGACACACGCACAAAGAAATAA 59.444 39.130 0.00 0.00 42.26 1.40
2291 2411 1.937223 TCGACACACGCACAAAGAAAT 59.063 42.857 0.00 0.00 42.26 2.17
2295 2415 0.581529 ACATCGACACACGCACAAAG 59.418 50.000 0.00 0.00 42.26 2.77
2302 2422 2.382746 CCCTGCACATCGACACACG 61.383 63.158 0.00 0.00 44.09 4.49
2306 2426 0.320683 CTGAACCCTGCACATCGACA 60.321 55.000 0.00 0.00 0.00 4.35
2307 2427 1.639298 GCTGAACCCTGCACATCGAC 61.639 60.000 0.00 0.00 37.23 4.20
2309 2429 1.672030 TGCTGAACCCTGCACATCG 60.672 57.895 0.00 0.00 41.38 3.84
2310 2430 4.402851 TGCTGAACCCTGCACATC 57.597 55.556 0.00 0.00 41.38 3.06
2383 2509 2.897350 GACATGCCGCACCTAGCC 60.897 66.667 0.00 0.00 41.38 3.93
2425 2551 2.101185 CAGCTCAGCGACGACGAT 59.899 61.111 12.29 0.40 42.66 3.73
2556 2686 0.661020 AAGGAAGCAACCAAACGACG 59.339 50.000 0.00 0.00 0.00 5.12
2578 2708 1.341156 CCTCCCCAGCTTCGAGGAAT 61.341 60.000 13.16 0.00 45.15 3.01
2706 2844 4.750098 CACATAAATAACCGCCGAATCTCT 59.250 41.667 0.00 0.00 0.00 3.10
2787 2932 6.239572 CCAATGATTAGTTTTGGTCCTGGTTT 60.240 38.462 0.00 0.00 36.08 3.27
2853 2998 0.027194 CTACCGAATCGCGACTTCGA 59.973 55.000 34.18 23.03 46.36 3.71
2854 2999 1.529883 GCTACCGAATCGCGACTTCG 61.530 60.000 29.76 29.76 44.57 3.79
2855 3000 0.524816 TGCTACCGAATCGCGACTTC 60.525 55.000 12.93 15.31 44.57 3.01
2856 3001 0.525668 CTGCTACCGAATCGCGACTT 60.526 55.000 12.93 7.28 44.57 3.01
2857 3002 1.064296 CTGCTACCGAATCGCGACT 59.936 57.895 12.93 0.00 44.57 4.18
2858 3003 1.944676 CCTGCTACCGAATCGCGAC 60.945 63.158 12.93 0.00 44.57 5.19
2859 3004 1.659622 TTCCTGCTACCGAATCGCGA 61.660 55.000 13.09 13.09 44.57 5.87
2865 3010 1.336517 CGTCAAGTTCCTGCTACCGAA 60.337 52.381 0.00 0.00 0.00 4.30
2892 3037 6.599638 AGCTCAGGTGTTGAAAGGTTATTATC 59.400 38.462 0.00 0.00 34.81 1.75
3074 3367 1.981853 GGCCGGGGAAGCAATCAAA 60.982 57.895 2.18 0.00 0.00 2.69
3142 3435 0.661483 GCAAAGTCCAGTTGCGCTTC 60.661 55.000 9.73 0.98 41.74 3.86
3150 3443 2.949644 GGTACAAACTGCAAAGTCCAGT 59.050 45.455 0.00 0.00 44.92 4.00
3151 3444 2.032030 CGGTACAAACTGCAAAGTCCAG 60.032 50.000 0.00 0.00 36.41 3.86
3152 3445 1.944024 CGGTACAAACTGCAAAGTCCA 59.056 47.619 0.00 0.00 0.00 4.02
3153 3446 1.944709 ACGGTACAAACTGCAAAGTCC 59.055 47.619 0.00 0.00 35.17 3.85
3338 3652 1.802553 AATAGGTCCAGGTGGCGTAT 58.197 50.000 0.00 0.00 34.44 3.06
3386 3700 4.335416 CTGAAGGTAAGCTTTTCCCATCA 58.665 43.478 3.20 13.45 0.00 3.07
3387 3701 3.129462 GCTGAAGGTAAGCTTTTCCCATC 59.871 47.826 3.20 9.89 37.69 3.51
3388 3702 3.092301 GCTGAAGGTAAGCTTTTCCCAT 58.908 45.455 3.20 0.28 37.69 4.00
3389 3703 2.514803 GCTGAAGGTAAGCTTTTCCCA 58.485 47.619 3.20 2.18 37.69 4.37
3390 3704 1.819288 GGCTGAAGGTAAGCTTTTCCC 59.181 52.381 3.20 2.56 40.64 3.97
3391 3705 1.468914 CGGCTGAAGGTAAGCTTTTCC 59.531 52.381 3.20 8.30 40.64 3.13
3392 3706 1.468914 CCGGCTGAAGGTAAGCTTTTC 59.531 52.381 3.20 3.03 40.64 2.29
3393 3707 1.534729 CCGGCTGAAGGTAAGCTTTT 58.465 50.000 3.20 0.00 40.64 2.27
3394 3708 0.960861 GCCGGCTGAAGGTAAGCTTT 60.961 55.000 22.15 0.00 40.64 3.51
3395 3709 1.377333 GCCGGCTGAAGGTAAGCTT 60.377 57.895 22.15 3.48 40.64 3.74
3397 3711 2.824489 GGCCGGCTGAAGGTAAGC 60.824 66.667 28.56 0.41 40.06 3.09
3398 3712 2.311688 ATCGGCCGGCTGAAGGTAAG 62.312 60.000 39.93 13.43 34.70 2.34
3399 3713 2.306255 GATCGGCCGGCTGAAGGTAA 62.306 60.000 39.93 18.49 34.70 2.85
3400 3714 2.762459 ATCGGCCGGCTGAAGGTA 60.762 61.111 39.93 19.30 34.70 3.08
3428 3742 3.916392 GACACGGAGGCAGTGGACG 62.916 68.421 11.35 0.00 43.41 4.79
3429 3743 2.048127 GACACGGAGGCAGTGGAC 60.048 66.667 11.35 3.30 43.41 4.02
3431 3745 2.859273 GATGGACACGGAGGCAGTGG 62.859 65.000 11.35 0.00 43.41 4.00
3432 3746 1.448540 GATGGACACGGAGGCAGTG 60.449 63.158 6.29 6.29 44.57 3.66
3433 3747 2.982130 GATGGACACGGAGGCAGT 59.018 61.111 0.00 0.00 0.00 4.40
3434 3748 2.202797 CGATGGACACGGAGGCAG 60.203 66.667 0.00 0.00 0.00 4.85
3441 3755 0.031314 CAGAGGATCCGATGGACACG 59.969 60.000 5.98 0.00 32.98 4.49
3442 3756 1.115467 ACAGAGGATCCGATGGACAC 58.885 55.000 19.56 2.03 32.98 3.67
3444 3758 1.757118 TCAACAGAGGATCCGATGGAC 59.243 52.381 19.56 4.65 32.98 4.02
3445 3759 2.159179 TCAACAGAGGATCCGATGGA 57.841 50.000 19.56 8.49 33.66 3.41
3446 3760 2.366590 TGATCAACAGAGGATCCGATGG 59.633 50.000 19.56 8.69 40.32 3.51
3447 3761 3.740631 TGATCAACAGAGGATCCGATG 57.259 47.619 15.39 15.39 40.32 3.84
3458 3772 3.704512 CTCTCGTCCATCTGATCAACAG 58.295 50.000 0.00 0.00 46.97 3.16
3459 3773 2.159184 GCTCTCGTCCATCTGATCAACA 60.159 50.000 0.00 0.00 0.00 3.33
3460 3774 2.159184 TGCTCTCGTCCATCTGATCAAC 60.159 50.000 0.00 0.00 0.00 3.18
3461 3775 2.102578 TGCTCTCGTCCATCTGATCAA 58.897 47.619 0.00 0.00 0.00 2.57
3462 3776 1.406898 GTGCTCTCGTCCATCTGATCA 59.593 52.381 0.00 0.00 0.00 2.92
3463 3777 1.269517 GGTGCTCTCGTCCATCTGATC 60.270 57.143 0.00 0.00 0.00 2.92
3464 3778 0.749649 GGTGCTCTCGTCCATCTGAT 59.250 55.000 0.00 0.00 0.00 2.90
3465 3779 1.323271 GGGTGCTCTCGTCCATCTGA 61.323 60.000 0.00 0.00 0.00 3.27
3466 3780 1.142748 GGGTGCTCTCGTCCATCTG 59.857 63.158 0.00 0.00 0.00 2.90
3467 3781 2.060980 GGGGTGCTCTCGTCCATCT 61.061 63.158 0.00 0.00 0.00 2.90
3468 3782 2.501610 GGGGTGCTCTCGTCCATC 59.498 66.667 0.00 0.00 0.00 3.51
3469 3783 3.083997 GGGGGTGCTCTCGTCCAT 61.084 66.667 0.00 0.00 0.00 3.41
3472 3786 4.436998 CACGGGGGTGCTCTCGTC 62.437 72.222 0.00 0.00 33.31 4.20
3474 3788 3.066190 TACACGGGGGTGCTCTCG 61.066 66.667 0.00 0.00 0.00 4.04
3477 3791 1.449601 CATGTACACGGGGGTGCTC 60.450 63.158 0.00 0.00 0.00 4.26
3478 3792 2.221299 ACATGTACACGGGGGTGCT 61.221 57.895 0.00 0.00 0.00 4.40
3479 3793 2.038269 CACATGTACACGGGGGTGC 61.038 63.158 0.00 0.00 0.00 5.01
3481 3795 1.373435 CACACATGTACACGGGGGT 59.627 57.895 0.00 0.00 0.00 4.95
3482 3796 0.672401 GACACACATGTACACGGGGG 60.672 60.000 0.00 0.00 39.95 5.40
3483 3797 0.320374 AGACACACATGTACACGGGG 59.680 55.000 0.00 0.00 39.95 5.73
3484 3798 1.428448 CAGACACACATGTACACGGG 58.572 55.000 0.00 0.00 39.95 5.28
3485 3799 0.790207 GCAGACACACATGTACACGG 59.210 55.000 0.00 0.00 39.95 4.94
3486 3800 1.496934 TGCAGACACACATGTACACG 58.503 50.000 0.00 0.00 39.95 4.49
3487 3801 2.872245 AGTTGCAGACACACATGTACAC 59.128 45.455 0.00 0.00 39.95 2.90
3488 3802 2.871633 CAGTTGCAGACACACATGTACA 59.128 45.455 0.00 0.00 39.95 2.90
3489 3803 3.130633 TCAGTTGCAGACACACATGTAC 58.869 45.455 0.00 0.00 39.95 2.90
3490 3804 3.392882 CTCAGTTGCAGACACACATGTA 58.607 45.455 0.00 0.00 39.95 2.29
3492 3806 1.069432 GCTCAGTTGCAGACACACATG 60.069 52.381 0.00 0.00 0.00 3.21
3494 3808 0.815213 GGCTCAGTTGCAGACACACA 60.815 55.000 0.00 0.00 34.04 3.72
3495 3809 0.533755 AGGCTCAGTTGCAGACACAC 60.534 55.000 0.00 0.00 34.04 3.82
3496 3810 0.181114 AAGGCTCAGTTGCAGACACA 59.819 50.000 0.00 0.00 34.04 3.72
3497 3811 1.002033 CAAAGGCTCAGTTGCAGACAC 60.002 52.381 0.00 0.00 34.04 3.67
3499 3813 1.312815 ACAAAGGCTCAGTTGCAGAC 58.687 50.000 0.00 0.00 34.04 3.51
3500 3814 2.057137 AACAAAGGCTCAGTTGCAGA 57.943 45.000 4.02 0.00 34.04 4.26
3501 3815 2.735823 GAAACAAAGGCTCAGTTGCAG 58.264 47.619 5.45 0.00 34.04 4.41
3502 3816 1.065401 CGAAACAAAGGCTCAGTTGCA 59.935 47.619 9.76 0.00 34.04 4.08
3503 3817 1.333619 TCGAAACAAAGGCTCAGTTGC 59.666 47.619 5.45 3.17 0.00 4.17
3504 3818 3.691049 TTCGAAACAAAGGCTCAGTTG 57.309 42.857 0.00 0.97 0.00 3.16
3505 3819 4.712122 TTTTCGAAACAAAGGCTCAGTT 57.288 36.364 10.79 0.00 0.00 3.16
3506 3820 4.398044 TCTTTTTCGAAACAAAGGCTCAGT 59.602 37.500 17.88 0.00 31.86 3.41
3507 3821 4.920376 TCTTTTTCGAAACAAAGGCTCAG 58.080 39.130 17.88 3.09 31.86 3.35
3508 3822 4.638421 TCTCTTTTTCGAAACAAAGGCTCA 59.362 37.500 17.88 3.13 31.86 4.26
3509 3823 5.169836 TCTCTTTTTCGAAACAAAGGCTC 57.830 39.130 17.88 0.00 31.86 4.70
3510 3824 4.640647 ACTCTCTTTTTCGAAACAAAGGCT 59.359 37.500 17.88 0.00 31.86 4.58


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

AutoCloner maintained by Alex Coulton.