Multiple sequence alignment - TraesCS2D01G411900

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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 TraesCS2D01G411900 chr2D 100.000 4534 0 0 1 4534 526520506 526515973 0.000000e+00 8373.0
1 TraesCS2D01G411900 chr2D 92.388 959 38 10 1824 2780 274923326 274924251 0.000000e+00 1334.0
2 TraesCS2D01G411900 chr2A 94.122 2807 123 21 766 3553 671707659 671704876 0.000000e+00 4231.0
3 TraesCS2D01G411900 chr2A 95.546 696 25 5 3556 4246 671704836 671704142 0.000000e+00 1109.0
4 TraesCS2D01G411900 chr2A 90.687 451 28 8 1 449 671708093 671707655 5.050000e-164 588.0
5 TraesCS2D01G411900 chr2A 96.194 289 11 0 4245 4533 671704061 671703773 1.480000e-129 473.0
6 TraesCS2D01G411900 chr2B 93.954 2812 128 20 772 3554 622917664 622914866 0.000000e+00 4213.0
7 TraesCS2D01G411900 chr2B 94.628 726 35 3 3556 4279 622914827 622914104 0.000000e+00 1122.0
8 TraesCS2D01G411900 chr2B 92.035 452 24 4 1 452 622918104 622917665 3.850000e-175 625.0
9 TraesCS2D01G411900 chr2B 95.736 258 11 0 4277 4534 622914059 622913802 2.520000e-112 416.0
10 TraesCS2D01G411900 chr6B 93.014 959 40 7 1824 2780 27634227 27633294 0.000000e+00 1375.0
11 TraesCS2D01G411900 chr6B 86.076 79 11 0 3945 4023 496988445 496988523 8.080000e-13 86.1
12 TraesCS2D01G411900 chr6B 91.228 57 2 3 4269 4323 648175727 648175672 1.750000e-09 75.0
13 TraesCS2D01G411900 chr4D 93.014 959 32 11 1824 2780 455258961 455258036 0.000000e+00 1367.0
14 TraesCS2D01G411900 chr7B 92.451 967 38 8 1824 2780 145929508 145928567 0.000000e+00 1349.0
15 TraesCS2D01G411900 chr7B 91.980 611 31 3 2170 2780 4604450 4605042 0.000000e+00 841.0
16 TraesCS2D01G411900 chr5B 92.075 959 50 6 1824 2780 504043727 504044661 0.000000e+00 1327.0
17 TraesCS2D01G411900 chr6D 94.888 802 23 8 1824 2622 97558766 97559552 0.000000e+00 1238.0
18 TraesCS2D01G411900 chr6D 86.076 79 11 0 3945 4023 325819719 325819641 8.080000e-13 86.1
19 TraesCS2D01G411900 chr3B 94.306 562 24 3 1824 2383 85095477 85094922 0.000000e+00 854.0
20 TraesCS2D01G411900 chr3B 87.075 294 20 2 2487 2780 85094710 85094435 2.630000e-82 316.0
21 TraesCS2D01G411900 chr3B 88.043 184 20 1 3355 3538 586051334 586051515 2.750000e-52 217.0
22 TraesCS2D01G411900 chr3B 91.209 91 8 0 4077 4167 586051517 586051607 1.710000e-24 124.0
23 TraesCS2D01G411900 chr6A 86.076 79 11 0 3945 4023 464689285 464689207 8.080000e-13 86.1
24 TraesCS2D01G411900 chr6A 93.878 49 1 2 4277 4323 104118358 104118406 6.290000e-09 73.1
25 TraesCS2D01G411900 chr1D 97.727 44 1 0 4281 4324 59951889 59951846 4.860000e-10 76.8
26 TraesCS2D01G411900 chr1D 90.385 52 5 0 4270 4321 327989356 327989407 8.140000e-08 69.4
27 TraesCS2D01G411900 chr1B 90.741 54 5 0 4282 4335 10310817 10310764 6.290000e-09 73.1
28 TraesCS2D01G411900 chr5D 95.238 42 2 0 4282 4323 249531532 249531573 2.930000e-07 67.6
29 TraesCS2D01G411900 chr5D 87.719 57 6 1 4268 4324 441926037 441926092 1.050000e-06 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 TraesCS2D01G411900 chr2D 526515973 526520506 4533 True 8373.00 8373 100.00000 1 4534 1 chr2D.!!$R1 4533
1 TraesCS2D01G411900 chr2D 274923326 274924251 925 False 1334.00 1334 92.38800 1824 2780 1 chr2D.!!$F1 956
2 TraesCS2D01G411900 chr2A 671703773 671708093 4320 True 1600.25 4231 94.13725 1 4533 4 chr2A.!!$R1 4532
3 TraesCS2D01G411900 chr2B 622913802 622918104 4302 True 1594.00 4213 94.08825 1 4534 4 chr2B.!!$R1 4533
4 TraesCS2D01G411900 chr6B 27633294 27634227 933 True 1375.00 1375 93.01400 1824 2780 1 chr6B.!!$R1 956
5 TraesCS2D01G411900 chr4D 455258036 455258961 925 True 1367.00 1367 93.01400 1824 2780 1 chr4D.!!$R1 956
6 TraesCS2D01G411900 chr7B 145928567 145929508 941 True 1349.00 1349 92.45100 1824 2780 1 chr7B.!!$R1 956
7 TraesCS2D01G411900 chr7B 4604450 4605042 592 False 841.00 841 91.98000 2170 2780 1 chr7B.!!$F1 610
8 TraesCS2D01G411900 chr5B 504043727 504044661 934 False 1327.00 1327 92.07500 1824 2780 1 chr5B.!!$F1 956
9 TraesCS2D01G411900 chr6D 97558766 97559552 786 False 1238.00 1238 94.88800 1824 2622 1 chr6D.!!$F1 798
10 TraesCS2D01G411900 chr3B 85094435 85095477 1042 True 585.00 854 90.69050 1824 2780 2 chr3B.!!$R1 956

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
556 559 0.031994 ACAAAAACACATCGCCCAGC 59.968 50.000 0.00 0.00 0.00 4.85 F
686 689 0.036010 ACAGCTTATGTTGGAGCGCT 60.036 50.000 11.27 11.27 39.96 5.92 F
757 760 0.179134 AGCGCGTCTGTTGGAGATAC 60.179 55.000 8.43 0.00 31.63 2.24 F
758 761 0.179134 GCGCGTCTGTTGGAGATACT 60.179 55.000 8.43 0.00 31.63 2.12 F
1543 1558 0.966370 CGAAGACGGAGGAGAAGGGT 60.966 60.000 0.00 0.00 35.72 4.34 F
2740 2914 1.072965 AGAACAAGAAGCTGGACCCTG 59.927 52.381 0.00 0.00 0.00 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1404 1410 0.035439 GTGGCTGGCCTGCTTAGTAA 60.035 55.0 30.65 9.87 36.94 2.24 R
2671 2844 0.176449 TCGCAGCACAGCTATGTCAT 59.824 50.0 0.00 0.00 37.65 3.06 R
2672 2845 0.176449 ATCGCAGCACAGCTATGTCA 59.824 50.0 0.00 0.00 37.65 3.58 R
2673 2846 0.580578 CATCGCAGCACAGCTATGTC 59.419 55.0 0.00 0.00 37.65 3.06 R
2931 3106 0.313672 TCAATTGCCACCTGCGTTTC 59.686 50.0 0.00 0.00 45.60 2.78 R
3544 3720 0.036010 AGATCTTTGTGTGCCTCCGG 60.036 55.0 0.00 0.00 0.00 5.14 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
69 70 1.250154 TTGCCTGGTGCTAATGGTGC 61.250 55.000 0.00 0.00 42.00 5.01
107 108 1.570813 CGAAGATGCCAATACGCTCA 58.429 50.000 0.00 0.00 0.00 4.26
137 138 1.290134 GTGGGGAGGACTGGATCTTT 58.710 55.000 0.00 0.00 0.00 2.52
222 225 7.917505 CCAAAATTCTGTGCTTATCAGGATTAC 59.082 37.037 0.00 0.00 39.38 1.89
249 252 6.264088 CGACCTTAATTAGTCAGTCAGTACC 58.736 44.000 5.89 0.00 33.08 3.34
262 265 2.735134 GTCAGTACCGTGATGTTCCAAC 59.265 50.000 0.00 0.00 0.00 3.77
263 266 2.365941 TCAGTACCGTGATGTTCCAACA 59.634 45.455 0.00 0.00 44.06 3.33
264 267 2.736721 CAGTACCGTGATGTTCCAACAG 59.263 50.000 0.00 0.00 43.04 3.16
265 268 2.631062 AGTACCGTGATGTTCCAACAGA 59.369 45.455 0.00 0.00 43.04 3.41
266 269 2.169832 ACCGTGATGTTCCAACAGAG 57.830 50.000 0.00 0.00 43.04 3.35
267 270 0.798776 CCGTGATGTTCCAACAGAGC 59.201 55.000 0.00 0.00 43.04 4.09
268 271 1.609061 CCGTGATGTTCCAACAGAGCT 60.609 52.381 0.00 0.00 43.04 4.09
269 272 2.146342 CGTGATGTTCCAACAGAGCTT 58.854 47.619 0.00 0.00 43.04 3.74
270 273 2.096069 CGTGATGTTCCAACAGAGCTTG 60.096 50.000 0.00 0.00 43.04 4.01
271 274 2.880890 GTGATGTTCCAACAGAGCTTGT 59.119 45.455 0.00 0.00 43.04 3.16
322 325 1.225376 TTTGTTCGACGCAAGCGGAT 61.225 50.000 19.30 0.00 44.69 4.18
341 344 3.181500 GGATTAACCGCATTTGGTGACTC 60.181 47.826 0.00 0.00 42.89 3.36
393 396 4.096382 CCAGAAATAACAACGATTCCCTGG 59.904 45.833 0.00 0.00 34.02 4.45
407 410 1.607467 CCTGGCCAAAACCCTCCAG 60.607 63.158 7.01 0.00 44.25 3.86
411 414 0.469144 GGCCAAAACCCTCCAGAACA 60.469 55.000 0.00 0.00 0.00 3.18
452 455 0.179134 CGCTCCAAACCTCTACTCCG 60.179 60.000 0.00 0.00 0.00 4.63
453 456 0.175989 GCTCCAAACCTCTACTCCGG 59.824 60.000 0.00 0.00 0.00 5.14
454 457 1.558233 CTCCAAACCTCTACTCCGGT 58.442 55.000 0.00 0.00 34.27 5.28
455 458 2.731572 CTCCAAACCTCTACTCCGGTA 58.268 52.381 0.00 0.00 32.07 4.02
456 459 3.094572 CTCCAAACCTCTACTCCGGTAA 58.905 50.000 0.00 0.00 32.07 2.85
457 460 3.509442 TCCAAACCTCTACTCCGGTAAA 58.491 45.455 0.00 0.00 32.07 2.01
458 461 3.903090 TCCAAACCTCTACTCCGGTAAAA 59.097 43.478 0.00 0.00 32.07 1.52
459 462 4.020839 TCCAAACCTCTACTCCGGTAAAAG 60.021 45.833 0.00 0.00 32.07 2.27
460 463 3.606595 AACCTCTACTCCGGTAAAAGC 57.393 47.619 0.00 0.00 32.07 3.51
461 464 2.532843 ACCTCTACTCCGGTAAAAGCA 58.467 47.619 0.00 0.00 0.00 3.91
462 465 3.105283 ACCTCTACTCCGGTAAAAGCAT 58.895 45.455 0.00 0.00 0.00 3.79
463 466 3.132467 ACCTCTACTCCGGTAAAAGCATC 59.868 47.826 0.00 0.00 0.00 3.91
464 467 3.385111 CCTCTACTCCGGTAAAAGCATCT 59.615 47.826 0.00 0.00 0.00 2.90
465 468 4.500035 CCTCTACTCCGGTAAAAGCATCTC 60.500 50.000 0.00 0.00 0.00 2.75
466 469 2.693267 ACTCCGGTAAAAGCATCTCC 57.307 50.000 0.00 0.00 0.00 3.71
467 470 1.134788 ACTCCGGTAAAAGCATCTCCG 60.135 52.381 0.00 0.00 40.72 4.63
468 471 1.136305 CTCCGGTAAAAGCATCTCCGA 59.864 52.381 0.00 0.00 43.22 4.55
469 472 1.134907 TCCGGTAAAAGCATCTCCGAC 60.135 52.381 0.00 0.00 43.22 4.79
470 473 1.404986 CCGGTAAAAGCATCTCCGACA 60.405 52.381 0.00 0.00 43.22 4.35
471 474 1.927174 CGGTAAAAGCATCTCCGACAG 59.073 52.381 0.00 0.00 43.22 3.51
472 475 2.416836 CGGTAAAAGCATCTCCGACAGA 60.417 50.000 0.00 0.00 43.22 3.41
473 476 2.930682 GGTAAAAGCATCTCCGACAGAC 59.069 50.000 0.00 0.00 32.26 3.51
474 477 1.714794 AAAAGCATCTCCGACAGACG 58.285 50.000 0.00 0.00 42.18 4.18
475 478 0.737715 AAAGCATCTCCGACAGACGC 60.738 55.000 0.00 0.00 40.90 5.19
476 479 2.874010 AAGCATCTCCGACAGACGCG 62.874 60.000 3.53 3.53 45.48 6.01
477 480 2.951745 CATCTCCGACAGACGCGC 60.952 66.667 5.73 0.00 41.07 6.86
478 481 4.538283 ATCTCCGACAGACGCGCG 62.538 66.667 30.96 30.96 41.07 6.86
481 484 3.656243 CTCCGACAGACGCGCGTTA 62.656 63.158 38.03 14.84 41.07 3.18
482 485 2.801996 CCGACAGACGCGCGTTAA 60.802 61.111 38.03 0.00 41.07 2.01
483 486 2.366584 CCGACAGACGCGCGTTAAA 61.367 57.895 38.03 0.00 41.07 1.52
484 487 1.483806 CGACAGACGCGCGTTAAAA 59.516 52.632 38.03 0.00 34.51 1.52
485 488 0.111617 CGACAGACGCGCGTTAAAAA 60.112 50.000 38.03 0.00 34.51 1.94
510 513 8.865590 AAAAATTACAGCGTTGAAATAGTGTT 57.134 26.923 6.16 0.00 0.00 3.32
511 514 8.865590 AAAATTACAGCGTTGAAATAGTGTTT 57.134 26.923 6.16 0.00 0.00 2.83
512 515 8.865590 AAATTACAGCGTTGAAATAGTGTTTT 57.134 26.923 6.16 0.00 0.00 2.43
513 516 8.865590 AATTACAGCGTTGAAATAGTGTTTTT 57.134 26.923 6.16 0.00 0.00 1.94
514 517 7.672351 TTACAGCGTTGAAATAGTGTTTTTG 57.328 32.000 6.16 0.00 0.00 2.44
515 518 5.646606 ACAGCGTTGAAATAGTGTTTTTGT 58.353 33.333 6.16 0.00 0.00 2.83
516 519 5.514914 ACAGCGTTGAAATAGTGTTTTTGTG 59.485 36.000 6.16 0.00 0.00 3.33
517 520 4.502645 AGCGTTGAAATAGTGTTTTTGTGC 59.497 37.500 0.00 0.00 0.00 4.57
518 521 4.602957 GCGTTGAAATAGTGTTTTTGTGCG 60.603 41.667 0.00 0.00 0.00 5.34
519 522 4.602957 CGTTGAAATAGTGTTTTTGTGCGC 60.603 41.667 0.00 0.00 0.00 6.09
520 523 3.039405 TGAAATAGTGTTTTTGTGCGCG 58.961 40.909 0.00 0.00 0.00 6.86
521 524 2.044888 AATAGTGTTTTTGTGCGCGG 57.955 45.000 8.83 0.00 0.00 6.46
522 525 0.239879 ATAGTGTTTTTGTGCGCGGG 59.760 50.000 8.83 0.00 0.00 6.13
523 526 0.814410 TAGTGTTTTTGTGCGCGGGA 60.814 50.000 8.83 0.00 0.00 5.14
524 527 1.657181 GTGTTTTTGTGCGCGGGAG 60.657 57.895 8.83 0.00 0.00 4.30
525 528 2.050442 GTTTTTGTGCGCGGGAGG 60.050 61.111 8.83 0.00 0.00 4.30
526 529 2.517402 TTTTTGTGCGCGGGAGGT 60.517 55.556 8.83 0.00 0.00 3.85
527 530 2.122167 TTTTTGTGCGCGGGAGGTT 61.122 52.632 8.83 0.00 0.00 3.50
528 531 1.668101 TTTTTGTGCGCGGGAGGTTT 61.668 50.000 8.83 0.00 0.00 3.27
529 532 0.818445 TTTTGTGCGCGGGAGGTTTA 60.818 50.000 8.83 0.00 0.00 2.01
530 533 1.508808 TTTGTGCGCGGGAGGTTTAC 61.509 55.000 8.83 0.00 0.00 2.01
531 534 2.357760 GTGCGCGGGAGGTTTACA 60.358 61.111 8.83 0.00 0.00 2.41
532 535 2.047655 TGCGCGGGAGGTTTACAG 60.048 61.111 8.83 0.00 0.00 2.74
533 536 2.263540 GCGCGGGAGGTTTACAGA 59.736 61.111 8.83 0.00 0.00 3.41
534 537 2.098831 GCGCGGGAGGTTTACAGAC 61.099 63.158 8.83 0.00 0.00 3.51
535 538 1.804326 CGCGGGAGGTTTACAGACG 60.804 63.158 0.00 0.00 0.00 4.18
536 539 2.098831 GCGGGAGGTTTACAGACGC 61.099 63.158 0.00 0.00 38.70 5.19
537 540 1.290955 CGGGAGGTTTACAGACGCA 59.709 57.895 0.00 0.00 0.00 5.24
538 541 1.012486 CGGGAGGTTTACAGACGCAC 61.012 60.000 0.00 0.00 0.00 5.34
539 542 0.034337 GGGAGGTTTACAGACGCACA 59.966 55.000 0.00 0.00 0.00 4.57
540 543 1.541670 GGGAGGTTTACAGACGCACAA 60.542 52.381 0.00 0.00 0.00 3.33
541 544 2.215196 GGAGGTTTACAGACGCACAAA 58.785 47.619 0.00 0.00 0.00 2.83
542 545 2.614983 GGAGGTTTACAGACGCACAAAA 59.385 45.455 0.00 0.00 0.00 2.44
543 546 3.065648 GGAGGTTTACAGACGCACAAAAA 59.934 43.478 0.00 0.00 0.00 1.94
544 547 4.023739 AGGTTTACAGACGCACAAAAAC 57.976 40.909 0.00 0.00 0.00 2.43
545 548 3.440872 AGGTTTACAGACGCACAAAAACA 59.559 39.130 0.00 0.00 0.00 2.83
546 549 3.544682 GGTTTACAGACGCACAAAAACAC 59.455 43.478 0.00 0.00 0.00 3.32
547 550 4.159857 GTTTACAGACGCACAAAAACACA 58.840 39.130 0.00 0.00 0.00 3.72
548 551 4.624336 TTACAGACGCACAAAAACACAT 57.376 36.364 0.00 0.00 0.00 3.21
549 552 3.065019 ACAGACGCACAAAAACACATC 57.935 42.857 0.00 0.00 0.00 3.06
550 553 2.036217 CAGACGCACAAAAACACATCG 58.964 47.619 0.00 0.00 0.00 3.84
551 554 0.770008 GACGCACAAAAACACATCGC 59.230 50.000 0.00 0.00 0.00 4.58
552 555 0.593773 ACGCACAAAAACACATCGCC 60.594 50.000 0.00 0.00 0.00 5.54
553 556 1.274798 CGCACAAAAACACATCGCCC 61.275 55.000 0.00 0.00 0.00 6.13
554 557 0.249238 GCACAAAAACACATCGCCCA 60.249 50.000 0.00 0.00 0.00 5.36
555 558 1.769733 CACAAAAACACATCGCCCAG 58.230 50.000 0.00 0.00 0.00 4.45
556 559 0.031994 ACAAAAACACATCGCCCAGC 59.968 50.000 0.00 0.00 0.00 4.85
557 560 0.667184 CAAAAACACATCGCCCAGCC 60.667 55.000 0.00 0.00 0.00 4.85
558 561 1.815817 AAAAACACATCGCCCAGCCC 61.816 55.000 0.00 0.00 0.00 5.19
577 580 2.282391 GTGGTCCCACATGCAGCA 60.282 61.111 11.57 0.00 45.53 4.41
578 581 2.034532 TGGTCCCACATGCAGCAG 59.965 61.111 0.00 0.00 0.00 4.24
579 582 3.446570 GGTCCCACATGCAGCAGC 61.447 66.667 0.00 0.00 42.57 5.25
580 583 3.446570 GTCCCACATGCAGCAGCC 61.447 66.667 0.00 0.00 41.13 4.85
581 584 4.746309 TCCCACATGCAGCAGCCC 62.746 66.667 0.00 0.00 41.13 5.19
606 609 4.054825 CAAGCCGGCGCACCAAAT 62.055 61.111 23.20 0.00 37.52 2.32
607 610 3.302344 AAGCCGGCGCACCAAATT 61.302 55.556 23.20 3.74 37.52 1.82
608 611 3.572196 AAGCCGGCGCACCAAATTG 62.572 57.895 23.20 0.00 37.52 2.32
610 613 4.354939 CCGGCGCACCAAATTGCA 62.355 61.111 10.83 0.00 43.15 4.08
611 614 2.806198 CGGCGCACCAAATTGCAG 60.806 61.111 10.83 0.00 43.15 4.41
612 615 3.113979 GGCGCACCAAATTGCAGC 61.114 61.111 10.83 0.40 43.15 5.25
613 616 3.113979 GCGCACCAAATTGCAGCC 61.114 61.111 0.30 0.00 43.15 4.85
614 617 2.432972 CGCACCAAATTGCAGCCC 60.433 61.111 0.00 0.00 43.15 5.19
615 618 2.046988 GCACCAAATTGCAGCCCC 60.047 61.111 0.00 0.00 42.49 5.80
616 619 2.262292 CACCAAATTGCAGCCCCG 59.738 61.111 0.00 0.00 0.00 5.73
617 620 3.694538 ACCAAATTGCAGCCCCGC 61.695 61.111 0.00 0.00 0.00 6.13
618 621 3.693471 CCAAATTGCAGCCCCGCA 61.693 61.111 0.00 0.00 41.03 5.69
619 622 2.125832 CAAATTGCAGCCCCGCAG 60.126 61.111 0.00 0.00 44.14 5.18
620 623 4.073200 AAATTGCAGCCCCGCAGC 62.073 61.111 0.00 0.00 44.14 5.25
633 636 3.055719 GCAGCCTTGGTGCGCTAA 61.056 61.111 9.73 0.00 46.66 3.09
634 637 2.625823 GCAGCCTTGGTGCGCTAAA 61.626 57.895 9.73 0.00 46.66 1.85
635 638 1.937546 GCAGCCTTGGTGCGCTAAAT 61.938 55.000 9.73 0.00 46.66 1.40
636 639 0.527565 CAGCCTTGGTGCGCTAAATT 59.472 50.000 9.73 0.00 36.02 1.82
637 640 1.067635 CAGCCTTGGTGCGCTAAATTT 60.068 47.619 9.73 0.00 36.02 1.82
638 641 1.618343 AGCCTTGGTGCGCTAAATTTT 59.382 42.857 9.73 0.00 36.02 1.82
639 642 1.992667 GCCTTGGTGCGCTAAATTTTC 59.007 47.619 9.73 0.00 0.00 2.29
640 643 2.609244 GCCTTGGTGCGCTAAATTTTCA 60.609 45.455 9.73 0.00 0.00 2.69
641 644 3.648009 CCTTGGTGCGCTAAATTTTCAA 58.352 40.909 9.73 1.02 0.00 2.69
642 645 3.428534 CCTTGGTGCGCTAAATTTTCAAC 59.571 43.478 9.73 0.00 0.00 3.18
643 646 4.298332 CTTGGTGCGCTAAATTTTCAACT 58.702 39.130 9.73 0.00 0.00 3.16
644 647 4.314740 TGGTGCGCTAAATTTTCAACTT 57.685 36.364 9.73 0.00 0.00 2.66
645 648 4.295051 TGGTGCGCTAAATTTTCAACTTC 58.705 39.130 9.73 0.00 0.00 3.01
646 649 3.360758 GGTGCGCTAAATTTTCAACTTCG 59.639 43.478 9.73 0.00 0.00 3.79
647 650 3.972502 GTGCGCTAAATTTTCAACTTCGT 59.027 39.130 9.73 0.00 0.00 3.85
648 651 4.439776 GTGCGCTAAATTTTCAACTTCGTT 59.560 37.500 9.73 0.00 0.00 3.85
649 652 5.038033 TGCGCTAAATTTTCAACTTCGTTT 58.962 33.333 9.73 0.00 0.00 3.60
650 653 5.517054 TGCGCTAAATTTTCAACTTCGTTTT 59.483 32.000 9.73 0.00 0.00 2.43
651 654 6.035112 TGCGCTAAATTTTCAACTTCGTTTTT 59.965 30.769 9.73 0.00 0.00 1.94
652 655 6.350743 GCGCTAAATTTTCAACTTCGTTTTTG 59.649 34.615 0.00 0.00 0.00 2.44
653 656 7.387945 CGCTAAATTTTCAACTTCGTTTTTGT 58.612 30.769 0.00 0.00 0.00 2.83
654 657 7.366972 CGCTAAATTTTCAACTTCGTTTTTGTG 59.633 33.333 0.00 0.00 0.00 3.33
655 658 7.161900 GCTAAATTTTCAACTTCGTTTTTGTGC 59.838 33.333 0.00 0.00 0.00 4.57
656 659 4.554162 TTTTCAACTTCGTTTTTGTGCG 57.446 36.364 0.00 0.00 0.00 5.34
657 660 2.904011 TCAACTTCGTTTTTGTGCGT 57.096 40.000 0.00 0.00 0.00 5.24
658 661 2.510874 TCAACTTCGTTTTTGTGCGTG 58.489 42.857 0.00 0.00 0.00 5.34
659 662 2.095668 TCAACTTCGTTTTTGTGCGTGT 60.096 40.909 0.00 0.00 0.00 4.49
660 663 2.622546 ACTTCGTTTTTGTGCGTGTT 57.377 40.000 0.00 0.00 0.00 3.32
661 664 2.936316 ACTTCGTTTTTGTGCGTGTTT 58.064 38.095 0.00 0.00 0.00 2.83
662 665 3.310246 ACTTCGTTTTTGTGCGTGTTTT 58.690 36.364 0.00 0.00 0.00 2.43
663 666 3.736759 ACTTCGTTTTTGTGCGTGTTTTT 59.263 34.783 0.00 0.00 0.00 1.94
684 687 4.678509 TTTTACAGCTTATGTTGGAGCG 57.321 40.909 0.00 0.00 39.96 5.03
685 688 1.651987 TACAGCTTATGTTGGAGCGC 58.348 50.000 0.00 0.00 39.96 5.92
686 689 0.036010 ACAGCTTATGTTGGAGCGCT 60.036 50.000 11.27 11.27 39.96 5.92
687 690 0.376152 CAGCTTATGTTGGAGCGCTG 59.624 55.000 18.48 0.00 43.53 5.18
688 691 0.036010 AGCTTATGTTGGAGCGCTGT 60.036 50.000 18.48 0.00 43.53 4.40
689 692 0.804989 GCTTATGTTGGAGCGCTGTT 59.195 50.000 18.48 0.00 0.00 3.16
690 693 1.200020 GCTTATGTTGGAGCGCTGTTT 59.800 47.619 18.48 0.00 0.00 2.83
691 694 2.351738 GCTTATGTTGGAGCGCTGTTTT 60.352 45.455 18.48 0.00 0.00 2.43
692 695 3.857010 GCTTATGTTGGAGCGCTGTTTTT 60.857 43.478 18.48 0.00 0.00 1.94
693 696 4.614993 GCTTATGTTGGAGCGCTGTTTTTA 60.615 41.667 18.48 0.00 0.00 1.52
694 697 5.637006 TTATGTTGGAGCGCTGTTTTTAT 57.363 34.783 18.48 4.69 0.00 1.40
695 698 3.552604 TGTTGGAGCGCTGTTTTTATC 57.447 42.857 18.48 0.00 0.00 1.75
696 699 2.095969 TGTTGGAGCGCTGTTTTTATCG 60.096 45.455 18.48 0.00 0.00 2.92
697 700 0.446222 TGGAGCGCTGTTTTTATCGC 59.554 50.000 18.48 0.00 46.95 4.58
700 703 4.735620 CGCTGTTTTTATCGCGCA 57.264 50.000 8.75 0.00 39.11 6.09
701 704 2.256247 CGCTGTTTTTATCGCGCAC 58.744 52.632 8.75 0.00 39.11 5.34
702 705 1.445224 CGCTGTTTTTATCGCGCACG 61.445 55.000 8.75 0.00 39.11 5.34
703 706 1.720330 GCTGTTTTTATCGCGCACGC 61.720 55.000 8.75 4.64 39.84 5.34
704 707 0.179225 CTGTTTTTATCGCGCACGCT 60.179 50.000 13.70 0.00 39.84 5.07
705 708 1.059979 CTGTTTTTATCGCGCACGCTA 59.940 47.619 13.70 2.04 39.84 4.26
706 709 1.661617 TGTTTTTATCGCGCACGCTAT 59.338 42.857 13.70 10.29 39.84 2.97
707 710 2.858941 TGTTTTTATCGCGCACGCTATA 59.141 40.909 13.70 9.23 39.84 1.31
708 711 3.491639 TGTTTTTATCGCGCACGCTATAT 59.508 39.130 13.70 6.55 39.84 0.86
709 712 4.680567 TGTTTTTATCGCGCACGCTATATA 59.319 37.500 13.70 4.70 39.84 0.86
710 713 5.175308 TGTTTTTATCGCGCACGCTATATAA 59.825 36.000 13.70 10.24 39.84 0.98
711 714 5.430220 TTTTATCGCGCACGCTATATAAG 57.570 39.130 13.70 0.00 39.84 1.73
729 732 9.608617 CTATATAAGCATCTTTTTCAGCACATG 57.391 33.333 0.00 0.00 0.00 3.21
730 733 3.587797 AGCATCTTTTTCAGCACATGG 57.412 42.857 0.00 0.00 0.00 3.66
731 734 1.997606 GCATCTTTTTCAGCACATGGC 59.002 47.619 0.00 0.00 45.30 4.40
754 757 2.049156 CAGCGCGTCTGTTGGAGA 60.049 61.111 18.43 0.00 38.02 3.71
755 758 1.446792 CAGCGCGTCTGTTGGAGAT 60.447 57.895 18.43 0.00 38.02 2.75
756 759 0.179137 CAGCGCGTCTGTTGGAGATA 60.179 55.000 18.43 0.00 38.02 1.98
757 760 0.179134 AGCGCGTCTGTTGGAGATAC 60.179 55.000 8.43 0.00 31.63 2.24
758 761 0.179134 GCGCGTCTGTTGGAGATACT 60.179 55.000 8.43 0.00 31.63 2.12
759 762 1.828832 CGCGTCTGTTGGAGATACTC 58.171 55.000 0.00 0.00 31.63 2.59
760 763 1.402259 CGCGTCTGTTGGAGATACTCT 59.598 52.381 0.00 0.00 31.63 3.24
761 764 2.612672 CGCGTCTGTTGGAGATACTCTA 59.387 50.000 0.00 0.00 31.63 2.43
762 765 3.064958 CGCGTCTGTTGGAGATACTCTAA 59.935 47.826 0.00 0.00 31.63 2.10
763 766 4.602995 GCGTCTGTTGGAGATACTCTAAG 58.397 47.826 0.00 0.00 31.92 2.18
764 767 4.335874 GCGTCTGTTGGAGATACTCTAAGA 59.664 45.833 0.00 0.00 31.92 2.10
770 773 6.728411 TGTTGGAGATACTCTAAGACCTACA 58.272 40.000 0.00 0.00 31.92 2.74
788 791 8.370940 AGACCTACATATACCATCTGATGTTTG 58.629 37.037 15.95 6.33 34.46 2.93
850 853 5.122239 TGCGCTCCTTGCAATTATACATATC 59.878 40.000 9.73 0.00 43.06 1.63
855 858 7.148340 GCTCCTTGCAATTATACATATCAGACC 60.148 40.741 0.00 0.00 42.31 3.85
975 978 3.697045 CACAAGGAACCAAGTAACCAACA 59.303 43.478 0.00 0.00 0.00 3.33
1147 1153 4.039357 CGACGGAGCCAGACACGT 62.039 66.667 0.00 0.00 42.88 4.49
1543 1558 0.966370 CGAAGACGGAGGAGAAGGGT 60.966 60.000 0.00 0.00 35.72 4.34
1924 1941 4.961511 TCGTTGCGCACCGAGCTT 62.962 61.111 26.61 0.00 42.61 3.74
2192 2242 4.415332 GCAGAGTTCGACGCCGGA 62.415 66.667 5.05 0.00 36.24 5.14
2213 2263 3.630013 AGGCTGGTGCAGAAGCGA 61.630 61.111 13.00 0.00 46.23 4.93
2632 2799 2.951726 TCAGTTGATCTTCGTCTGCAG 58.048 47.619 7.63 7.63 0.00 4.41
2633 2800 1.392853 CAGTTGATCTTCGTCTGCAGC 59.607 52.381 9.47 3.23 0.00 5.25
2639 2806 2.812358 TCTTCGTCTGCAGCTTTACA 57.188 45.000 9.47 0.00 0.00 2.41
2670 2843 2.223900 GCGATGATGATCCAGTGACTGA 60.224 50.000 15.33 0.37 32.44 3.41
2671 2844 3.739209 GCGATGATGATCCAGTGACTGAA 60.739 47.826 15.33 0.00 32.44 3.02
2672 2845 4.629092 CGATGATGATCCAGTGACTGAAT 58.371 43.478 15.33 0.00 32.44 2.57
2673 2846 4.448060 CGATGATGATCCAGTGACTGAATG 59.552 45.833 15.33 0.00 32.44 2.67
2679 2852 5.910614 TGATCCAGTGACTGAATGACATAG 58.089 41.667 15.33 0.00 32.44 2.23
2740 2914 1.072965 AGAACAAGAAGCTGGACCCTG 59.927 52.381 0.00 0.00 0.00 4.45
2787 2961 2.238847 AAATGCTGCCTCGCCTCGTA 62.239 55.000 0.00 0.00 0.00 3.43
2863 3038 5.841810 TCAGCAGGTTTCAGTTAAATTTGG 58.158 37.500 0.00 0.00 0.00 3.28
2906 3081 3.452990 TCGGGCCTATGACAATTTGACTA 59.547 43.478 0.84 0.00 0.00 2.59
2985 3160 0.470833 AGGAGCATACCGGAGATGCT 60.471 55.000 33.89 33.89 38.68 3.79
2997 3172 1.202359 GGAGATGCTCCGTGAAGAGAC 60.202 57.143 0.00 0.00 41.08 3.36
3002 3177 0.885196 GCTCCGTGAAGAGACTGTCT 59.115 55.000 10.66 10.66 35.82 3.41
3257 3432 3.126831 GGATCACGGCTATGTTCTTCTG 58.873 50.000 0.00 0.00 0.00 3.02
3327 3502 8.902806 TCGAAGCTATTATTGGAATTCAACAAT 58.097 29.630 7.93 10.83 36.54 2.71
3350 3525 2.778299 TCAAGGATTCCAGGTGTTTCG 58.222 47.619 5.29 0.00 0.00 3.46
3363 3538 2.474526 GGTGTTTCGAACATCTGCATCG 60.475 50.000 0.00 0.20 44.35 3.84
3373 3548 0.391661 ATCTGCATCGTTTGACGCCT 60.392 50.000 0.00 0.00 42.21 5.52
3374 3549 0.602638 TCTGCATCGTTTGACGCCTT 60.603 50.000 0.00 0.00 42.21 4.35
3375 3550 0.238289 CTGCATCGTTTGACGCCTTT 59.762 50.000 0.00 0.00 42.21 3.11
3376 3551 0.040514 TGCATCGTTTGACGCCTTTG 60.041 50.000 0.00 0.00 42.21 2.77
3380 3556 2.512485 TCGTTTGACGCCTTTGTCTA 57.488 45.000 0.00 0.00 42.21 2.59
3382 3558 1.862201 CGTTTGACGCCTTTGTCTACA 59.138 47.619 0.00 0.00 39.64 2.74
3455 3631 4.324641 GCAAGGAAGATAGGGAAAAGAGGT 60.325 45.833 0.00 0.00 0.00 3.85
3528 3704 1.643286 TCCATGGGTTTTGGGCTGATA 59.357 47.619 13.02 0.00 34.85 2.15
3544 3720 5.065090 GGGCTGATAAATGAATGGCAAAAAC 59.935 40.000 0.00 0.00 0.00 2.43
3547 3723 5.174395 TGATAAATGAATGGCAAAAACCGG 58.826 37.500 0.00 0.00 0.00 5.28
3644 3859 6.469410 TCCGTTCTTATACAACAACCATTCT 58.531 36.000 0.00 0.00 0.00 2.40
3647 3862 8.723311 CCGTTCTTATACAACAACCATTCTTAA 58.277 33.333 0.00 0.00 0.00 1.85
3696 3912 4.247258 TGAACCGTTCGTACTGCATTTAT 58.753 39.130 6.78 0.00 0.00 1.40
3706 3924 5.411361 TCGTACTGCATTTATTTTCACAGCT 59.589 36.000 0.00 0.00 0.00 4.24
3714 3932 6.476706 GCATTTATTTTCACAGCTGGATAACC 59.523 38.462 19.93 2.98 0.00 2.85
3812 4030 6.968131 TTGAATTTCCACTGAGAATCGTAG 57.032 37.500 0.00 0.00 38.61 3.51
3817 4035 1.478510 CCACTGAGAATCGTAGCACCT 59.521 52.381 0.00 0.00 38.61 4.00
3855 4073 5.836898 TGTTCTAGACCTGGAAACTAAGACA 59.163 40.000 0.00 6.15 31.87 3.41
3898 4116 7.177744 ACAACCATAAGAAACCCATACGAAATT 59.822 33.333 0.00 0.00 0.00 1.82
4030 4248 3.262660 AGAGCATGAAGGACATTCTCACA 59.737 43.478 0.00 0.00 46.40 3.58
4137 4355 1.701031 TTCGCCTGGGTGTTCTCCAA 61.701 55.000 0.00 0.00 33.36 3.53
4171 4389 1.853963 TTCCAGGAGGAGCACTAGAC 58.146 55.000 0.00 0.00 46.74 2.59
4202 4420 7.148340 CCTTGTTATCAGTTTCCTTAGCTGAAG 60.148 40.741 0.00 0.00 41.75 3.02
4313 4660 7.984422 AATCAGCGACAATTAATATGGATCA 57.016 32.000 0.00 0.00 0.00 2.92
4317 4664 6.870439 CAGCGACAATTAATATGGATCAGAGA 59.130 38.462 0.00 0.00 0.00 3.10
4324 4671 9.566530 CAATTAATATGGATCAGAGAGAGTACG 57.433 37.037 0.00 0.00 0.00 3.67
4331 4678 4.035909 GGATCAGAGAGAGTACGGAAGTTC 59.964 50.000 0.00 0.00 46.40 3.01
4492 4839 1.257750 TGACAGCGTCCCATACAGCT 61.258 55.000 6.30 0.00 38.10 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 1.070577 CGCTTGAGGAAACTGAACACG 60.071 52.381 0.00 0.00 44.43 4.49
107 108 1.481056 CCTCCCCACCGTTCTGTCTT 61.481 60.000 0.00 0.00 0.00 3.01
137 138 0.835971 TCAGTTCCACTGGGCTGCTA 60.836 55.000 12.84 0.00 45.94 3.49
222 225 4.744570 TGACTGACTAATTAAGGTCGCAG 58.255 43.478 0.00 0.00 35.45 5.18
249 252 1.800805 AGCTCTGTTGGAACATCACG 58.199 50.000 0.00 0.00 39.30 4.35
262 265 8.654230 TCTGCTTATTCTATAAACAAGCTCTG 57.346 34.615 6.23 0.00 41.65 3.35
263 266 7.930865 CCTCTGCTTATTCTATAAACAAGCTCT 59.069 37.037 6.23 0.00 41.65 4.09
264 267 7.307692 GCCTCTGCTTATTCTATAAACAAGCTC 60.308 40.741 6.23 0.00 41.65 4.09
265 268 6.484977 GCCTCTGCTTATTCTATAAACAAGCT 59.515 38.462 6.23 0.00 41.65 3.74
266 269 6.260936 TGCCTCTGCTTATTCTATAAACAAGC 59.739 38.462 0.00 0.00 41.51 4.01
267 270 7.254932 GGTGCCTCTGCTTATTCTATAAACAAG 60.255 40.741 0.00 0.00 38.71 3.16
268 271 6.542370 GGTGCCTCTGCTTATTCTATAAACAA 59.458 38.462 0.00 0.00 38.71 2.83
269 272 6.055588 GGTGCCTCTGCTTATTCTATAAACA 58.944 40.000 0.00 0.00 38.71 2.83
270 273 6.017852 GTGGTGCCTCTGCTTATTCTATAAAC 60.018 42.308 0.00 0.00 38.71 2.01
271 274 6.055588 GTGGTGCCTCTGCTTATTCTATAAA 58.944 40.000 0.00 0.00 38.71 1.40
272 275 5.366768 AGTGGTGCCTCTGCTTATTCTATAA 59.633 40.000 0.00 0.00 38.71 0.98
273 276 4.901849 AGTGGTGCCTCTGCTTATTCTATA 59.098 41.667 0.00 0.00 38.71 1.31
274 277 3.713764 AGTGGTGCCTCTGCTTATTCTAT 59.286 43.478 0.00 0.00 38.71 1.98
322 325 2.811431 CAGAGTCACCAAATGCGGTTAA 59.189 45.455 0.00 0.00 37.07 2.01
341 344 1.528309 AAGGGGTGTTCGTTGGCAG 60.528 57.895 0.00 0.00 0.00 4.85
393 396 0.673985 GTGTTCTGGAGGGTTTTGGC 59.326 55.000 0.00 0.00 0.00 4.52
407 410 2.478879 CCAACGGTTTTGTGAGGTGTTC 60.479 50.000 0.00 0.00 0.00 3.18
411 414 1.720694 CGCCAACGGTTTTGTGAGGT 61.721 55.000 0.00 0.00 34.97 3.85
444 447 3.383825 GGAGATGCTTTTACCGGAGTAGA 59.616 47.826 9.46 0.00 0.00 2.59
452 455 2.930682 GTCTGTCGGAGATGCTTTTACC 59.069 50.000 0.00 0.00 40.67 2.85
453 456 2.599082 CGTCTGTCGGAGATGCTTTTAC 59.401 50.000 0.00 0.00 40.67 2.01
454 457 2.876091 CGTCTGTCGGAGATGCTTTTA 58.124 47.619 0.00 0.00 40.67 1.52
455 458 1.714794 CGTCTGTCGGAGATGCTTTT 58.285 50.000 0.00 0.00 40.67 2.27
456 459 3.425578 CGTCTGTCGGAGATGCTTT 57.574 52.632 0.00 0.00 40.67 3.51
460 463 2.951745 GCGCGTCTGTCGGAGATG 60.952 66.667 8.43 0.00 40.67 2.90
461 464 4.538283 CGCGCGTCTGTCGGAGAT 62.538 66.667 24.19 0.00 40.67 2.75
463 466 3.656243 TAACGCGCGTCTGTCGGAG 62.656 63.158 37.77 2.38 40.26 4.63
464 467 2.730006 TTTAACGCGCGTCTGTCGGA 62.730 55.000 37.77 14.89 40.26 4.55
465 468 1.878524 TTTTAACGCGCGTCTGTCGG 61.879 55.000 37.77 4.15 40.26 4.79
466 469 0.111617 TTTTTAACGCGCGTCTGTCG 60.112 50.000 37.77 5.05 43.12 4.35
467 470 3.713968 TTTTTAACGCGCGTCTGTC 57.286 47.368 37.77 0.00 0.00 3.51
485 488 8.865590 AACACTATTTCAACGCTGTAATTTTT 57.134 26.923 0.00 0.00 0.00 1.94
486 489 8.865590 AAACACTATTTCAACGCTGTAATTTT 57.134 26.923 0.00 0.00 0.00 1.82
487 490 8.865590 AAAACACTATTTCAACGCTGTAATTT 57.134 26.923 0.00 0.00 0.00 1.82
488 491 8.751335 CAAAAACACTATTTCAACGCTGTAATT 58.249 29.630 0.00 0.00 0.00 1.40
489 492 7.918562 ACAAAAACACTATTTCAACGCTGTAAT 59.081 29.630 0.00 0.00 0.00 1.89
490 493 7.219154 CACAAAAACACTATTTCAACGCTGTAA 59.781 33.333 0.00 0.00 0.00 2.41
491 494 6.689241 CACAAAAACACTATTTCAACGCTGTA 59.311 34.615 0.00 0.00 0.00 2.74
492 495 5.514914 CACAAAAACACTATTTCAACGCTGT 59.485 36.000 0.00 0.00 0.00 4.40
493 496 5.554324 GCACAAAAACACTATTTCAACGCTG 60.554 40.000 0.00 0.00 0.00 5.18
494 497 4.502645 GCACAAAAACACTATTTCAACGCT 59.497 37.500 0.00 0.00 0.00 5.07
495 498 4.602957 CGCACAAAAACACTATTTCAACGC 60.603 41.667 0.00 0.00 0.00 4.84
496 499 4.602957 GCGCACAAAAACACTATTTCAACG 60.603 41.667 0.30 0.00 0.00 4.10
497 500 4.602957 CGCGCACAAAAACACTATTTCAAC 60.603 41.667 8.75 0.00 0.00 3.18
498 501 3.483922 CGCGCACAAAAACACTATTTCAA 59.516 39.130 8.75 0.00 0.00 2.69
499 502 3.039405 CGCGCACAAAAACACTATTTCA 58.961 40.909 8.75 0.00 0.00 2.69
500 503 2.403698 CCGCGCACAAAAACACTATTTC 59.596 45.455 8.75 0.00 0.00 2.17
501 504 2.389998 CCGCGCACAAAAACACTATTT 58.610 42.857 8.75 0.00 0.00 1.40
502 505 1.335506 CCCGCGCACAAAAACACTATT 60.336 47.619 8.75 0.00 0.00 1.73
503 506 0.239879 CCCGCGCACAAAAACACTAT 59.760 50.000 8.75 0.00 0.00 2.12
504 507 0.814410 TCCCGCGCACAAAAACACTA 60.814 50.000 8.75 0.00 0.00 2.74
505 508 2.058829 CTCCCGCGCACAAAAACACT 62.059 55.000 8.75 0.00 0.00 3.55
506 509 1.657181 CTCCCGCGCACAAAAACAC 60.657 57.895 8.75 0.00 0.00 3.32
507 510 2.718731 CTCCCGCGCACAAAAACA 59.281 55.556 8.75 0.00 0.00 2.83
508 511 2.050442 CCTCCCGCGCACAAAAAC 60.050 61.111 8.75 0.00 0.00 2.43
509 512 1.668101 AAACCTCCCGCGCACAAAAA 61.668 50.000 8.75 0.00 0.00 1.94
510 513 0.818445 TAAACCTCCCGCGCACAAAA 60.818 50.000 8.75 0.00 0.00 2.44
511 514 1.227883 TAAACCTCCCGCGCACAAA 60.228 52.632 8.75 0.00 0.00 2.83
512 515 1.962306 GTAAACCTCCCGCGCACAA 60.962 57.895 8.75 0.00 0.00 3.33
513 516 2.357760 GTAAACCTCCCGCGCACA 60.358 61.111 8.75 0.00 0.00 4.57
514 517 2.357760 TGTAAACCTCCCGCGCAC 60.358 61.111 8.75 0.00 0.00 5.34
515 518 2.047655 CTGTAAACCTCCCGCGCA 60.048 61.111 8.75 0.00 0.00 6.09
516 519 2.098831 GTCTGTAAACCTCCCGCGC 61.099 63.158 0.00 0.00 0.00 6.86
517 520 1.804326 CGTCTGTAAACCTCCCGCG 60.804 63.158 0.00 0.00 0.00 6.46
518 521 2.098831 GCGTCTGTAAACCTCCCGC 61.099 63.158 0.00 0.00 0.00 6.13
519 522 1.012486 GTGCGTCTGTAAACCTCCCG 61.012 60.000 0.00 0.00 0.00 5.14
520 523 0.034337 TGTGCGTCTGTAAACCTCCC 59.966 55.000 0.00 0.00 0.00 4.30
521 524 1.873698 TTGTGCGTCTGTAAACCTCC 58.126 50.000 0.00 0.00 0.00 4.30
522 525 3.955771 TTTTGTGCGTCTGTAAACCTC 57.044 42.857 0.00 0.00 0.00 3.85
523 526 3.440872 TGTTTTTGTGCGTCTGTAAACCT 59.559 39.130 0.00 0.00 0.00 3.50
524 527 3.544682 GTGTTTTTGTGCGTCTGTAAACC 59.455 43.478 0.00 0.00 0.00 3.27
525 528 4.159857 TGTGTTTTTGTGCGTCTGTAAAC 58.840 39.130 0.00 0.00 0.00 2.01
526 529 4.421033 TGTGTTTTTGTGCGTCTGTAAA 57.579 36.364 0.00 0.00 0.00 2.01
527 530 4.593157 GATGTGTTTTTGTGCGTCTGTAA 58.407 39.130 0.00 0.00 0.00 2.41
528 531 3.302805 CGATGTGTTTTTGTGCGTCTGTA 60.303 43.478 0.00 0.00 0.00 2.74
529 532 2.538737 CGATGTGTTTTTGTGCGTCTGT 60.539 45.455 0.00 0.00 0.00 3.41
530 533 2.036217 CGATGTGTTTTTGTGCGTCTG 58.964 47.619 0.00 0.00 0.00 3.51
531 534 1.596954 GCGATGTGTTTTTGTGCGTCT 60.597 47.619 0.00 0.00 0.00 4.18
532 535 0.770008 GCGATGTGTTTTTGTGCGTC 59.230 50.000 0.00 0.00 0.00 5.19
533 536 0.593773 GGCGATGTGTTTTTGTGCGT 60.594 50.000 0.00 0.00 0.00 5.24
534 537 1.274798 GGGCGATGTGTTTTTGTGCG 61.275 55.000 0.00 0.00 0.00 5.34
535 538 0.249238 TGGGCGATGTGTTTTTGTGC 60.249 50.000 0.00 0.00 0.00 4.57
536 539 1.769733 CTGGGCGATGTGTTTTTGTG 58.230 50.000 0.00 0.00 0.00 3.33
537 540 0.031994 GCTGGGCGATGTGTTTTTGT 59.968 50.000 0.00 0.00 0.00 2.83
538 541 0.667184 GGCTGGGCGATGTGTTTTTG 60.667 55.000 0.00 0.00 0.00 2.44
539 542 1.665442 GGCTGGGCGATGTGTTTTT 59.335 52.632 0.00 0.00 0.00 1.94
540 543 2.275380 GGGCTGGGCGATGTGTTTT 61.275 57.895 0.00 0.00 0.00 2.43
541 544 2.676471 GGGCTGGGCGATGTGTTT 60.676 61.111 0.00 0.00 0.00 2.83
557 560 4.343323 TGCATGTGGGACCACCGG 62.343 66.667 18.18 0.00 45.63 5.28
558 561 2.747460 CTGCATGTGGGACCACCG 60.747 66.667 18.18 10.71 45.63 4.94
559 562 3.064324 GCTGCATGTGGGACCACC 61.064 66.667 18.18 4.35 45.63 4.61
560 563 2.282391 TGCTGCATGTGGGACCAC 60.282 61.111 14.45 14.45 46.33 4.16
561 564 2.034532 CTGCTGCATGTGGGACCA 59.965 61.111 1.31 0.00 0.00 4.02
562 565 3.446570 GCTGCTGCATGTGGGACC 61.447 66.667 11.11 0.00 39.41 4.46
563 566 3.446570 GGCTGCTGCATGTGGGAC 61.447 66.667 17.89 0.00 41.91 4.46
564 567 4.746309 GGGCTGCTGCATGTGGGA 62.746 66.667 17.89 0.00 41.91 4.37
589 592 3.572196 AATTTGGTGCGCCGGCTTG 62.572 57.895 26.68 11.41 40.82 4.01
590 593 3.302344 AATTTGGTGCGCCGGCTT 61.302 55.556 26.68 6.12 40.82 4.35
591 594 4.054825 CAATTTGGTGCGCCGGCT 62.055 61.111 26.68 0.00 40.82 5.52
598 601 2.046988 GGGGCTGCAATTTGGTGC 60.047 61.111 0.50 0.00 45.15 5.01
599 602 2.262292 CGGGGCTGCAATTTGGTG 59.738 61.111 0.50 0.00 0.00 4.17
600 603 3.694538 GCGGGGCTGCAATTTGGT 61.695 61.111 0.50 0.00 34.15 3.67
601 604 3.652539 CTGCGGGGCTGCAATTTGG 62.653 63.158 0.50 0.00 45.74 3.28
602 605 2.125832 CTGCGGGGCTGCAATTTG 60.126 61.111 0.50 0.00 45.74 2.32
616 619 1.937546 ATTTAGCGCACCAAGGCTGC 61.938 55.000 11.47 0.00 40.32 5.25
617 620 0.527565 AATTTAGCGCACCAAGGCTG 59.472 50.000 11.47 0.00 40.32 4.85
618 621 1.256812 AAATTTAGCGCACCAAGGCT 58.743 45.000 11.47 0.00 43.12 4.58
619 622 1.992667 GAAAATTTAGCGCACCAAGGC 59.007 47.619 11.47 0.00 0.00 4.35
620 623 3.296322 TGAAAATTTAGCGCACCAAGG 57.704 42.857 11.47 0.00 0.00 3.61
621 624 4.298332 AGTTGAAAATTTAGCGCACCAAG 58.702 39.130 11.47 0.00 0.00 3.61
622 625 4.314740 AGTTGAAAATTTAGCGCACCAA 57.685 36.364 11.47 0.00 0.00 3.67
623 626 4.295051 GAAGTTGAAAATTTAGCGCACCA 58.705 39.130 11.47 0.00 0.00 4.17
624 627 3.360758 CGAAGTTGAAAATTTAGCGCACC 59.639 43.478 11.47 0.00 0.00 5.01
625 628 3.972502 ACGAAGTTGAAAATTTAGCGCAC 59.027 39.130 11.47 0.00 37.78 5.34
626 629 4.217754 ACGAAGTTGAAAATTTAGCGCA 57.782 36.364 11.47 0.00 37.78 6.09
642 645 3.963340 AAAACACGCACAAAAACGAAG 57.037 38.095 0.00 0.00 0.00 3.79
662 665 4.614993 GCGCTCCAACATAAGCTGTAAAAA 60.615 41.667 0.00 0.00 36.98 1.94
663 666 3.119990 GCGCTCCAACATAAGCTGTAAAA 60.120 43.478 0.00 0.00 36.98 1.52
664 667 2.418628 GCGCTCCAACATAAGCTGTAAA 59.581 45.455 0.00 0.00 36.98 2.01
665 668 2.006888 GCGCTCCAACATAAGCTGTAA 58.993 47.619 0.00 0.00 36.98 2.41
666 669 1.207089 AGCGCTCCAACATAAGCTGTA 59.793 47.619 2.64 0.00 36.98 2.74
667 670 0.036010 AGCGCTCCAACATAAGCTGT 60.036 50.000 2.64 0.00 40.84 4.40
668 671 0.376152 CAGCGCTCCAACATAAGCTG 59.624 55.000 7.13 0.80 44.51 4.24
669 672 0.036010 ACAGCGCTCCAACATAAGCT 60.036 50.000 7.13 0.00 36.35 3.74
670 673 0.804989 AACAGCGCTCCAACATAAGC 59.195 50.000 7.13 0.00 35.13 3.09
671 674 3.559238 AAAACAGCGCTCCAACATAAG 57.441 42.857 7.13 0.00 0.00 1.73
672 675 5.636837 GATAAAAACAGCGCTCCAACATAA 58.363 37.500 7.13 0.00 0.00 1.90
673 676 4.201773 CGATAAAAACAGCGCTCCAACATA 60.202 41.667 7.13 0.00 0.00 2.29
674 677 3.426159 CGATAAAAACAGCGCTCCAACAT 60.426 43.478 7.13 0.00 0.00 2.71
675 678 2.095969 CGATAAAAACAGCGCTCCAACA 60.096 45.455 7.13 0.00 0.00 3.33
676 679 2.505866 CGATAAAAACAGCGCTCCAAC 58.494 47.619 7.13 0.00 0.00 3.77
677 680 2.892373 CGATAAAAACAGCGCTCCAA 57.108 45.000 7.13 0.00 0.00 3.53
684 687 1.720330 GCGTGCGCGATAAAAACAGC 61.720 55.000 26.19 0.00 41.33 4.40
685 688 2.256247 GCGTGCGCGATAAAAACAG 58.744 52.632 26.19 0.00 41.33 3.16
686 689 4.426029 GCGTGCGCGATAAAAACA 57.574 50.000 26.19 0.00 41.33 2.83
703 706 9.608617 CATGTGCTGAAAAAGATGCTTATATAG 57.391 33.333 0.00 0.00 0.00 1.31
704 707 8.570488 CCATGTGCTGAAAAAGATGCTTATATA 58.430 33.333 0.00 0.00 0.00 0.86
705 708 7.431249 CCATGTGCTGAAAAAGATGCTTATAT 58.569 34.615 0.00 0.00 0.00 0.86
706 709 6.681120 GCCATGTGCTGAAAAAGATGCTTATA 60.681 38.462 0.00 0.00 36.87 0.98
707 710 5.657474 CCATGTGCTGAAAAAGATGCTTAT 58.343 37.500 0.00 0.00 0.00 1.73
708 711 4.618927 GCCATGTGCTGAAAAAGATGCTTA 60.619 41.667 0.00 0.00 36.87 3.09
709 712 3.863400 GCCATGTGCTGAAAAAGATGCTT 60.863 43.478 0.00 0.00 36.87 3.91
710 713 2.353406 GCCATGTGCTGAAAAAGATGCT 60.353 45.455 0.00 0.00 36.87 3.79
711 714 1.997606 GCCATGTGCTGAAAAAGATGC 59.002 47.619 0.00 0.00 36.87 3.91
738 741 0.179134 GTATCTCCAACAGACGCGCT 60.179 55.000 5.73 0.50 32.26 5.92
739 742 0.179134 AGTATCTCCAACAGACGCGC 60.179 55.000 5.73 0.00 32.26 6.86
740 743 1.828832 GAGTATCTCCAACAGACGCG 58.171 55.000 3.53 3.53 32.26 6.01
755 758 9.961264 CAGATGGTATATGTAGGTCTTAGAGTA 57.039 37.037 0.00 0.00 0.00 2.59
756 759 8.670490 TCAGATGGTATATGTAGGTCTTAGAGT 58.330 37.037 0.00 0.00 0.00 3.24
757 760 9.693739 ATCAGATGGTATATGTAGGTCTTAGAG 57.306 37.037 0.00 0.00 0.00 2.43
758 761 9.467796 CATCAGATGGTATATGTAGGTCTTAGA 57.532 37.037 1.95 0.00 0.00 2.10
759 762 9.249053 ACATCAGATGGTATATGTAGGTCTTAG 57.751 37.037 15.13 0.00 30.99 2.18
760 763 9.601810 AACATCAGATGGTATATGTAGGTCTTA 57.398 33.333 15.13 0.00 32.44 2.10
761 764 8.497910 AACATCAGATGGTATATGTAGGTCTT 57.502 34.615 15.13 0.00 32.44 3.01
762 765 8.370940 CAAACATCAGATGGTATATGTAGGTCT 58.629 37.037 15.13 0.00 32.44 3.85
763 766 8.150945 ACAAACATCAGATGGTATATGTAGGTC 58.849 37.037 15.13 0.00 32.44 3.85
764 767 8.034313 ACAAACATCAGATGGTATATGTAGGT 57.966 34.615 15.13 0.00 32.44 3.08
788 791 7.375544 GGAAGAATCGACGTTCAATAGTACTAC 59.624 40.741 4.31 0.00 0.00 2.73
850 853 7.040478 TGGAATACTTCATTTTTGTCTGGTCTG 60.040 37.037 0.00 0.00 0.00 3.51
855 858 7.116805 GCCTTTGGAATACTTCATTTTTGTCTG 59.883 37.037 0.00 0.00 0.00 3.51
914 917 2.047655 CGCCCGCTGGTACTTTCA 60.048 61.111 0.00 0.00 0.00 2.69
916 919 0.251073 ATAACGCCCGCTGGTACTTT 59.749 50.000 0.00 0.00 0.00 2.66
975 978 0.883370 GGCGTTGGTCTCTTTCGGTT 60.883 55.000 0.00 0.00 0.00 4.44
1049 1055 3.155167 GGACGTGGAGGCTAGGGG 61.155 72.222 0.00 0.00 0.00 4.79
1147 1153 1.301401 CCCAGAACGCCTTCGACAA 60.301 57.895 0.00 0.00 39.41 3.18
1404 1410 0.035439 GTGGCTGGCCTGCTTAGTAA 60.035 55.000 30.65 9.87 36.94 2.24
1924 1941 0.246360 AACGTCAGATCATCCACGCA 59.754 50.000 6.65 0.00 35.64 5.24
2192 2242 0.964358 GCTTCTGCACCAGCCTGAAT 60.964 55.000 0.00 0.00 41.13 2.57
2592 2759 0.892755 ATGTTTGGTGCCATGCTGAG 59.107 50.000 0.00 0.00 0.00 3.35
2595 2762 1.274167 CTGAATGTTTGGTGCCATGCT 59.726 47.619 0.00 0.00 0.00 3.79
2632 2799 2.158330 GCGCCCGCAATTGTAAAGC 61.158 57.895 7.40 4.74 41.49 3.51
2633 2800 1.867373 CGCGCCCGCAATTGTAAAG 60.867 57.895 13.42 0.00 42.06 1.85
2639 2806 2.901840 ATCATCGCGCCCGCAATT 60.902 55.556 13.42 0.00 42.06 2.32
2670 2843 1.012086 CGCAGCACAGCTATGTCATT 58.988 50.000 0.00 0.00 37.65 2.57
2671 2844 0.176449 TCGCAGCACAGCTATGTCAT 59.824 50.000 0.00 0.00 37.65 3.06
2672 2845 0.176449 ATCGCAGCACAGCTATGTCA 59.824 50.000 0.00 0.00 37.65 3.58
2673 2846 0.580578 CATCGCAGCACAGCTATGTC 59.419 55.000 0.00 0.00 37.65 3.06
2679 2852 4.471726 GCACCATCGCAGCACAGC 62.472 66.667 0.00 0.00 0.00 4.40
2740 2914 0.800012 TTTACCGCGTTCATGAAGGC 59.200 50.000 33.00 33.00 45.57 4.35
2787 2961 4.385358 AAACAAGCATTCGTTCACCTTT 57.615 36.364 0.00 0.00 0.00 3.11
2837 3012 7.254421 CCAAATTTAACTGAAACCTGCTGAAAC 60.254 37.037 0.00 0.00 0.00 2.78
2863 3038 0.868406 CAAGCAGTTCGAACAGGACC 59.132 55.000 28.78 9.54 0.00 4.46
2931 3106 0.313672 TCAATTGCCACCTGCGTTTC 59.686 50.000 0.00 0.00 45.60 2.78
2985 3160 2.271944 TCAGACAGTCTCTTCACGGA 57.728 50.000 0.00 0.00 0.00 4.69
2997 3172 3.949842 TCTGTTCCACTGATCAGACAG 57.050 47.619 29.27 27.05 40.65 3.51
3002 3177 0.608130 CCGGTCTGTTCCACTGATCA 59.392 55.000 0.00 0.00 28.97 2.92
3257 3432 5.047235 CAGGGCATATGTAGTTACCTCTACC 60.047 48.000 4.29 0.00 39.39 3.18
3327 3502 4.037446 CGAAACACCTGGAATCCTTGAAAA 59.963 41.667 0.00 0.00 0.00 2.29
3334 3509 2.500229 TGTTCGAAACACCTGGAATCC 58.500 47.619 0.00 0.00 36.25 3.01
3350 3525 2.762472 CGTCAAACGATGCAGATGTTC 58.238 47.619 0.00 0.00 46.05 3.18
3363 3538 4.483476 AATGTAGACAAAGGCGTCAAAC 57.517 40.909 0.00 0.00 38.43 2.93
3373 3548 4.142708 CCGCATACTGCAAATGTAGACAAA 60.143 41.667 5.49 0.00 45.36 2.83
3374 3549 3.373748 CCGCATACTGCAAATGTAGACAA 59.626 43.478 5.49 0.00 45.36 3.18
3375 3550 2.935849 CCGCATACTGCAAATGTAGACA 59.064 45.455 5.49 0.00 45.36 3.41
3376 3551 2.936498 ACCGCATACTGCAAATGTAGAC 59.064 45.455 5.49 0.00 45.36 2.59
3380 3556 2.878406 GGATACCGCATACTGCAAATGT 59.122 45.455 9.71 0.00 45.36 2.71
3382 3558 2.143122 CGGATACCGCATACTGCAAAT 58.857 47.619 0.00 0.00 45.36 2.32
3395 3571 3.005578 GGTTACATCTGTCCTCGGATACC 59.994 52.174 0.00 0.00 37.56 2.73
3455 3631 1.547820 TCAAGTTTTGCCACAAGTGCA 59.452 42.857 0.00 0.00 36.84 4.57
3528 3704 3.556843 CCTCCGGTTTTTGCCATTCATTT 60.557 43.478 0.00 0.00 0.00 2.32
3544 3720 0.036010 AGATCTTTGTGTGCCTCCGG 60.036 55.000 0.00 0.00 0.00 5.14
3547 3723 2.606725 CGATCAGATCTTTGTGTGCCTC 59.393 50.000 8.82 0.00 0.00 4.70
3554 3730 7.551974 ACTCATCAAAATCGATCAGATCTTTGT 59.448 33.333 17.15 7.58 38.98 2.83
3559 3771 6.841443 ACACTCATCAAAATCGATCAGATC 57.159 37.500 0.00 0.00 38.98 2.75
3644 3859 6.207221 TGATGCAAGATTTGACAAGCTCTTAA 59.793 34.615 12.25 6.98 0.00 1.85
3647 3862 4.077108 TGATGCAAGATTTGACAAGCTCT 58.923 39.130 0.00 0.00 0.00 4.09
3706 3924 3.812262 CATCAGTCATGCTGGTTATCCA 58.188 45.455 14.50 0.00 45.08 3.41
3773 3991 9.513906 TGGAAATTCAATATGTTTACTCTGTCA 57.486 29.630 0.00 0.00 0.00 3.58
3808 4026 0.949105 AAAGTTGCCGAGGTGCTACG 60.949 55.000 0.00 0.00 41.04 3.51
3812 4030 2.030274 ACATTAAAAGTTGCCGAGGTGC 60.030 45.455 0.00 0.00 0.00 5.01
3817 4035 5.410439 GGTCTAGAACATTAAAAGTTGCCGA 59.590 40.000 1.90 0.00 0.00 5.54
3855 4073 2.015456 TGTGATCAGGGACAGTGTCT 57.985 50.000 22.18 2.25 32.47 3.41
3898 4116 8.942033 TGTACAGGATCAGTTATAGTCCTAGTA 58.058 37.037 0.00 0.00 39.01 1.82
4030 4248 4.806330 ACTACGATTTGTCTGACGATGTT 58.194 39.130 2.98 0.00 0.00 2.71
4114 4332 0.693049 AGAACACCCAGGCGAAGATT 59.307 50.000 0.00 0.00 0.00 2.40
4137 4355 2.662866 CTGGAATGATGCAATGGGTCT 58.337 47.619 0.00 0.00 0.00 3.85
4171 4389 3.267031 AGGAAACTGATAACAAGGGGAGG 59.733 47.826 0.00 0.00 41.13 4.30
4231 4449 4.100963 AGTCGCATCTATTATGTTGGGTGA 59.899 41.667 0.00 0.00 0.00 4.02
4313 4660 7.463961 TTTTATGAACTTCCGTACTCTCTCT 57.536 36.000 0.00 0.00 0.00 3.10
4317 4664 8.718734 GTCAAATTTTATGAACTTCCGTACTCT 58.281 33.333 0.00 0.00 0.00 3.24
4324 4671 9.673454 AGTTAACGTCAAATTTTATGAACTTCC 57.327 29.630 0.00 0.00 0.00 3.46
4492 4839 5.417580 GGTTATGGCCTTGTCAACTGATAAA 59.582 40.000 3.32 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.