Multiple sequence alignment - TraesCS5A01G107500

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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 TraesCS5A01G107500 chr5A 100.000 3813 0 0 852 4664 184017727 184021539 0.000000e+00 7042.0
1 TraesCS5A01G107500 chr5A 100.000 620 0 0 1 620 184016876 184017495 0.000000e+00 1146.0
2 TraesCS5A01G107500 chr5A 88.380 284 31 2 210 492 32738637 32738919 1.610000e-89 340.0
3 TraesCS5A01G107500 chr5A 86.713 286 36 2 210 494 585212043 585212327 2.710000e-82 316.0
4 TraesCS5A01G107500 chr5A 87.143 280 32 3 210 487 536261225 536261502 9.740000e-82 315.0
5 TraesCS5A01G107500 chr5A 85.714 287 40 1 210 495 510477983 510477697 7.580000e-78 302.0
6 TraesCS5A01G107500 chr5D 95.918 2940 87 17 1737 4660 138485581 138482659 0.000000e+00 4734.0
7 TraesCS5A01G107500 chr5D 96.089 895 21 1 862 1742 138491550 138490656 0.000000e+00 1447.0
8 TraesCS5A01G107500 chr5D 84.527 349 38 9 2684 3026 181613955 181614293 9.670000e-87 331.0
9 TraesCS5A01G107500 chr5D 85.593 236 10 10 1 212 493829858 493829623 4.700000e-55 226.0
10 TraesCS5A01G107500 chr5D 84.181 177 4 10 1 153 525765098 525765274 2.910000e-32 150.0
11 TraesCS5A01G107500 chr5D 75.940 266 50 10 2679 2936 334703611 334703870 1.760000e-24 124.0
12 TraesCS5A01G107500 chr5D 97.368 38 1 0 1998 2035 3146612 3146575 1.080000e-06 65.8
13 TraesCS5A01G107500 chr5B 89.945 2725 157 37 2037 4664 188019513 188016809 0.000000e+00 3406.0
14 TraesCS5A01G107500 chr5B 94.917 1141 40 6 873 1997 188020652 188019514 0.000000e+00 1770.0
15 TraesCS5A01G107500 chr5B 82.322 577 64 18 4045 4589 369487905 369488475 2.540000e-127 466.0
16 TraesCS5A01G107500 chr5B 85.960 349 38 7 2684 3026 163266195 163266538 3.430000e-96 363.0
17 TraesCS5A01G107500 chr5B 81.275 251 8 15 1 212 87238453 87238703 2.890000e-37 167.0
18 TraesCS5A01G107500 chr2B 81.879 745 67 21 3977 4664 361287982 361287249 2.440000e-157 566.0
19 TraesCS5A01G107500 chr2B 95.238 63 3 0 3979 4041 34592944 34593006 2.970000e-17 100.0
20 TraesCS5A01G107500 chr4B 81.586 744 71 20 3980 4664 644281074 644280338 5.270000e-154 555.0
21 TraesCS5A01G107500 chr4B 78.324 346 52 11 2699 3037 560241846 560241517 7.910000e-48 202.0
22 TraesCS5A01G107500 chr6B 85.680 412 52 6 4045 4452 545212972 545213380 1.200000e-115 427.0
23 TraesCS5A01G107500 chr3B 82.424 495 62 11 3980 4452 556033020 556032529 4.340000e-110 409.0
24 TraesCS5A01G107500 chr3B 83.122 237 27 8 2801 3035 341227212 341227437 2.200000e-48 204.0
25 TraesCS5A01G107500 chr3B 96.875 64 2 0 3979 4042 802598565 802598502 1.770000e-19 108.0
26 TraesCS5A01G107500 chr3B 95.385 65 3 0 3977 4041 166158882 166158818 2.300000e-18 104.0
27 TraesCS5A01G107500 chr1A 84.504 413 55 7 4045 4452 391946751 391946343 2.610000e-107 399.0
28 TraesCS5A01G107500 chr1A 85.169 236 11 1 1 212 28937977 28938212 2.180000e-53 220.0
29 TraesCS5A01G107500 chr7B 83.551 383 53 7 4074 4451 63019669 63020046 2.670000e-92 350.0
30 TraesCS5A01G107500 chr7B 96.875 64 1 1 3976 4038 169305814 169305751 6.380000e-19 106.0
31 TraesCS5A01G107500 chr2D 88.811 286 31 1 210 494 511532086 511532371 2.670000e-92 350.0
32 TraesCS5A01G107500 chr2D 86.441 236 8 7 1 212 429202397 429202632 2.170000e-58 237.0
33 TraesCS5A01G107500 chr2D 85.593 236 10 7 1 212 533090773 533090538 4.700000e-55 226.0
34 TraesCS5A01G107500 chr2D 85.714 224 17 9 1 212 543290187 543290407 6.070000e-54 222.0
35 TraesCS5A01G107500 chr1B 83.924 367 44 13 2679 3039 390427072 390427429 2.080000e-88 337.0
36 TraesCS5A01G107500 chr1B 97.368 38 1 0 1998 2035 49808808 49808771 1.080000e-06 65.8
37 TraesCS5A01G107500 chr3D 94.340 212 12 0 1 212 16255183 16254972 4.500000e-85 326.0
38 TraesCS5A01G107500 chr3D 83.122 237 27 8 2801 3035 239613003 239613228 2.200000e-48 204.0
39 TraesCS5A01G107500 chr3D 81.673 251 7 10 1 212 352946046 352945796 6.200000e-39 172.0
40 TraesCS5A01G107500 chr3D 95.455 44 2 0 1833 1876 513623259 513623302 2.330000e-08 71.3
41 TraesCS5A01G107500 chr2A 86.713 286 36 2 210 494 107404752 107404468 2.710000e-82 316.0
42 TraesCS5A01G107500 chr2A 86.972 284 34 3 210 492 751480314 751480595 2.710000e-82 316.0
43 TraesCS5A01G107500 chr2A 85.764 288 38 3 210 496 519533543 519533828 7.580000e-78 302.0
44 TraesCS5A01G107500 chr2A 86.121 281 36 2 215 494 446012353 446012075 2.730000e-77 300.0
45 TraesCS5A01G107500 chr2A 87.288 236 6 7 1 212 559107475 559107710 1.000000e-61 248.0
46 TraesCS5A01G107500 chr2A 85.169 236 11 10 1 212 751480038 751480273 2.180000e-53 220.0
47 TraesCS5A01G107500 chr2A 96.970 33 1 0 1845 1877 668172961 668172929 6.520000e-04 56.5
48 TraesCS5A01G107500 chr6A 87.500 232 5 1 1 208 35253775 35254006 3.600000e-61 246.0
49 TraesCS5A01G107500 chr6A 95.556 135 6 0 78 212 415093351 415093217 2.830000e-52 217.0
50 TraesCS5A01G107500 chr6A 76.528 409 79 14 4045 4443 15880541 15880942 1.700000e-49 207.0
51 TraesCS5A01G107500 chr6A 81.609 174 23 6 2684 2850 559807788 559807959 8.140000e-28 135.0
52 TraesCS5A01G107500 chr6A 83.333 150 20 4 2679 2823 542731830 542731979 2.930000e-27 134.0
53 TraesCS5A01G107500 chr7A 86.441 236 8 3 1 212 207894463 207894698 2.170000e-58 237.0
54 TraesCS5A01G107500 chr4D 86.441 236 8 1 1 212 488494390 488494625 2.170000e-58 237.0
55 TraesCS5A01G107500 chr4D 97.368 38 1 0 1998 2035 123627716 123627753 1.080000e-06 65.8
56 TraesCS5A01G107500 chr4D 97.368 38 1 0 1998 2035 135017188 135017151 1.080000e-06 65.8
57 TraesCS5A01G107500 chr4D 97.368 38 1 0 1998 2035 295871701 295871664 1.080000e-06 65.8
58 TraesCS5A01G107500 chr7D 85.169 236 11 8 1 212 593681760 593681995 2.180000e-53 220.0
59 TraesCS5A01G107500 chr7D 72.079 505 98 31 3978 4452 204876347 204875856 1.370000e-20 111.0
60 TraesCS5A01G107500 chr7D 93.023 43 1 1 1849 1891 133326308 133326268 1.400000e-05 62.1
61 TraesCS5A01G107500 chr4A 72.320 513 93 32 3980 4452 67295541 67296044 1.060000e-21 115.0
62 TraesCS5A01G107500 chr4A 92.593 54 4 0 4537 4590 166303427 166303480 1.390000e-10 78.7
63 TraesCS5A01G107500 chr3A 95.238 63 3 0 3979 4041 1759616 1759554 2.970000e-17 100.0
64 TraesCS5A01G107500 chrUn 85.542 83 10 2 3960 4041 334641586 334641505 8.310000e-13 86.1
65 TraesCS5A01G107500 chrUn 97.368 38 1 0 1998 2035 40097589 40097552 1.080000e-06 65.8
66 TraesCS5A01G107500 chrUn 97.368 38 1 0 1998 2035 405103500 405103537 1.080000e-06 65.8
67 TraesCS5A01G107500 chr1D 97.368 38 1 0 1998 2035 380266746 380266709 1.080000e-06 65.8
68 TraesCS5A01G107500 chr1D 100.000 28 0 0 1838 1865 63377284 63377311 8.000000e-03 52.8


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 TraesCS5A01G107500 chr5A 184016876 184021539 4663 False 4094 7042 100.0000 1 4664 2 chr5A.!!$F4 4663
1 TraesCS5A01G107500 chr5D 138482659 138485581 2922 True 4734 4734 95.9180 1737 4660 1 chr5D.!!$R2 2923
2 TraesCS5A01G107500 chr5D 138490656 138491550 894 True 1447 1447 96.0890 862 1742 1 chr5D.!!$R3 880
3 TraesCS5A01G107500 chr5B 188016809 188020652 3843 True 2588 3406 92.4310 873 4664 2 chr5B.!!$R1 3791
4 TraesCS5A01G107500 chr5B 369487905 369488475 570 False 466 466 82.3220 4045 4589 1 chr5B.!!$F3 544
5 TraesCS5A01G107500 chr2B 361287249 361287982 733 True 566 566 81.8790 3977 4664 1 chr2B.!!$R1 687
6 TraesCS5A01G107500 chr4B 644280338 644281074 736 True 555 555 81.5860 3980 4664 1 chr4B.!!$R2 684
7 TraesCS5A01G107500 chr2A 751480038 751480595 557 False 268 316 86.0705 1 492 2 chr2A.!!$F3 491

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
270 338 0.104487 TGTAACGTGGACTTTCGCCA 59.896 50.0 0.00 0.00 0.00 5.69 F
425 493 0.179067 GGACATTTGTATCCGCCGGA 60.179 55.0 8.97 8.97 35.55 5.14 F
533 601 0.179111 TGCCGAAGATAGTCAAGGCG 60.179 55.0 0.00 0.00 46.85 5.52 F
552 620 0.179189 GGACAGAAAAATCGGCGCAG 60.179 55.0 10.83 5.07 0.00 5.18 F
555 623 0.179189 CAGAAAAATCGGCGCAGGTC 60.179 55.0 10.83 0.00 0.00 3.85 F
1084 1166 0.261991 TCCTTCCGCTATGTCCCTCT 59.738 55.0 0.00 0.00 0.00 3.69 F
2696 2794 1.026182 ATGACCGTGCGATGCAACAT 61.026 50.0 0.00 0.00 41.47 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2000 2083 0.041833 TCAGCTAGGAGGAAGGTGCT 59.958 55.000 0.00 0.00 41.22 4.40 R
2365 2449 0.396139 AGGGTGCATAACATGGCCAG 60.396 55.000 13.05 6.08 0.00 4.85 R
2467 2565 1.130561 CATCTCTGCAGCACACACATG 59.869 52.381 9.47 0.00 0.00 3.21 R
2604 2702 8.940768 TTTAAAAATTTCAGTGGACAGAAAGG 57.059 30.769 4.07 0.00 35.38 3.11 R
2752 2850 8.134895 CGGGCATGATTTATAAACATTTACACT 58.865 33.333 0.00 0.00 0.00 3.55 R
2940 3039 2.757314 CCCTTCCCTCTCTGCATTTTTC 59.243 50.000 0.00 0.00 0.00 2.29 R
4275 4427 0.391130 GCATCTTGTCGTGGTGGCTA 60.391 55.000 0.00 0.00 0.00 3.93 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
22 23 4.803426 CGAGTGGGTCAGCGCTCC 62.803 72.222 7.13 6.81 0.00 4.70
230 298 1.374343 CTAGGGCAGCACGTCGTCTA 61.374 60.000 0.00 0.00 0.00 2.59
270 338 0.104487 TGTAACGTGGACTTTCGCCA 59.896 50.000 0.00 0.00 0.00 5.69
281 349 3.469863 TTTCGCCAGCCTTCGTGGT 62.470 57.895 0.00 0.00 37.40 4.16
284 352 4.373116 GCCAGCCTTCGTGGTCGA 62.373 66.667 0.00 0.00 44.66 4.20
328 396 9.762933 ATGCATATATTTATTTTCAAACCGCTT 57.237 25.926 0.00 0.00 0.00 4.68
335 403 6.698359 TTATTTTCAAACCGCTTGCAATAC 57.302 33.333 0.00 0.00 34.76 1.89
340 408 5.440234 TCAAACCGCTTGCAATACTTTTA 57.560 34.783 0.00 0.00 34.76 1.52
342 410 6.451393 TCAAACCGCTTGCAATACTTTTATT 58.549 32.000 0.00 0.00 34.76 1.40
343 411 6.926272 TCAAACCGCTTGCAATACTTTTATTT 59.074 30.769 0.00 0.00 34.76 1.40
344 412 6.704512 AACCGCTTGCAATACTTTTATTTG 57.295 33.333 0.00 0.00 0.00 2.32
346 414 4.032786 CCGCTTGCAATACTTTTATTTGGC 59.967 41.667 0.00 0.00 0.00 4.52
348 416 4.492409 GCTTGCAATACTTTTATTTGGCGC 60.492 41.667 0.00 0.00 0.00 6.53
349 417 3.175152 TGCAATACTTTTATTTGGCGCG 58.825 40.909 0.00 0.00 0.00 6.86
350 418 3.119814 TGCAATACTTTTATTTGGCGCGA 60.120 39.130 12.10 0.00 0.00 5.87
354 422 1.136169 ACTTTTATTTGGCGCGACGAC 60.136 47.619 12.10 0.67 34.27 4.34
364 432 1.553654 CGCGACGACGAAATGGATC 59.446 57.895 12.29 0.00 42.66 3.36
369 437 2.244651 CGACGAAATGGATCGGGCC 61.245 63.158 0.00 0.00 46.82 5.80
372 440 2.546494 CGAAATGGATCGGGCCAGC 61.546 63.158 4.39 0.00 42.15 4.85
416 484 1.004320 ACAGCGCCGGACATTTGTA 60.004 52.632 5.05 0.00 0.00 2.41
425 493 0.179067 GGACATTTGTATCCGCCGGA 60.179 55.000 8.97 8.97 35.55 5.14
431 499 3.214845 GTATCCGCCGGACCGACT 61.215 66.667 17.49 0.00 32.98 4.18
432 500 2.440796 TATCCGCCGGACCGACTT 60.441 61.111 17.49 0.00 32.98 3.01
436 504 2.096442 CCGCCGGACCGACTTAAAC 61.096 63.158 17.49 0.00 0.00 2.01
438 506 1.080569 GCCGGACCGACTTAAACGA 60.081 57.895 17.49 0.00 0.00 3.85
440 508 2.000429 CCGGACCGACTTAAACGAAT 58.000 50.000 17.49 0.00 0.00 3.34
468 536 1.268184 GGACAAAAACACCGTCCGTTC 60.268 52.381 0.00 0.00 39.86 3.95
477 545 3.060615 CGTCCGTTCGGGTCTCCT 61.061 66.667 11.37 0.00 37.00 3.69
478 546 2.572284 GTCCGTTCGGGTCTCCTG 59.428 66.667 11.37 0.00 37.00 3.86
479 547 2.116772 TCCGTTCGGGTCTCCTGT 59.883 61.111 11.37 0.00 37.00 4.00
480 548 1.532316 TCCGTTCGGGTCTCCTGTT 60.532 57.895 11.37 0.00 37.00 3.16
481 549 1.374252 CCGTTCGGGTCTCCTGTTG 60.374 63.158 3.04 0.00 0.00 3.33
482 550 1.374252 CGTTCGGGTCTCCTGTTGG 60.374 63.158 0.00 0.00 0.00 3.77
483 551 1.812686 CGTTCGGGTCTCCTGTTGGA 61.813 60.000 0.00 0.00 40.69 3.53
495 563 3.173965 TCCTGTTGGAGTTCCTCTAAGG 58.826 50.000 0.00 2.36 37.46 2.69
496 564 2.237392 CCTGTTGGAGTTCCTCTAAGGG 59.763 54.545 0.00 0.00 31.92 3.95
497 565 3.173965 CTGTTGGAGTTCCTCTAAGGGA 58.826 50.000 0.00 0.00 35.59 4.20
498 566 3.173965 TGTTGGAGTTCCTCTAAGGGAG 58.826 50.000 0.00 0.00 41.51 4.30
506 574 1.369321 CTCTAAGGGAGGGCATCGC 59.631 63.158 8.26 8.26 41.11 4.58
507 575 1.382557 TCTAAGGGAGGGCATCGCA 60.383 57.895 18.44 0.00 43.20 5.10
508 576 1.227674 CTAAGGGAGGGCATCGCAC 60.228 63.158 18.44 0.00 43.20 5.34
509 577 2.978452 CTAAGGGAGGGCATCGCACG 62.978 65.000 18.44 2.37 43.20 5.34
513 581 4.521062 GAGGGCATCGCACGCTCT 62.521 66.667 8.34 1.53 44.95 4.09
514 582 4.087892 AGGGCATCGCACGCTCTT 62.088 61.111 0.00 0.00 36.59 2.85
515 583 3.869272 GGGCATCGCACGCTCTTG 61.869 66.667 0.00 0.00 0.00 3.02
516 584 4.527157 GGCATCGCACGCTCTTGC 62.527 66.667 0.00 0.00 39.28 4.01
517 585 4.527157 GCATCGCACGCTCTTGCC 62.527 66.667 0.00 0.00 39.53 4.52
518 586 4.214383 CATCGCACGCTCTTGCCG 62.214 66.667 0.00 0.00 39.53 5.69
519 587 4.435436 ATCGCACGCTCTTGCCGA 62.435 61.111 0.00 0.00 39.53 5.54
520 588 3.932580 ATCGCACGCTCTTGCCGAA 62.933 57.895 0.00 0.00 39.53 4.30
521 589 4.139420 CGCACGCTCTTGCCGAAG 62.139 66.667 0.00 0.00 39.53 3.79
522 590 2.738521 GCACGCTCTTGCCGAAGA 60.739 61.111 0.00 0.00 36.42 2.87
523 591 2.103042 GCACGCTCTTGCCGAAGAT 61.103 57.895 0.00 0.00 37.58 2.40
524 592 0.806102 GCACGCTCTTGCCGAAGATA 60.806 55.000 0.00 0.00 37.58 1.98
525 593 1.203928 CACGCTCTTGCCGAAGATAG 58.796 55.000 0.00 0.00 37.58 2.08
526 594 0.818296 ACGCTCTTGCCGAAGATAGT 59.182 50.000 0.00 0.00 37.58 2.12
527 595 1.202313 ACGCTCTTGCCGAAGATAGTC 60.202 52.381 0.00 0.00 37.58 2.59
528 596 1.202302 CGCTCTTGCCGAAGATAGTCA 60.202 52.381 0.00 0.00 37.58 3.41
529 597 2.735444 CGCTCTTGCCGAAGATAGTCAA 60.735 50.000 0.00 0.00 37.58 3.18
530 598 2.863137 GCTCTTGCCGAAGATAGTCAAG 59.137 50.000 0.00 0.00 37.58 3.02
531 599 3.452474 CTCTTGCCGAAGATAGTCAAGG 58.548 50.000 0.00 0.00 37.58 3.61
532 600 1.936547 CTTGCCGAAGATAGTCAAGGC 59.063 52.381 0.00 0.00 44.38 4.35
533 601 0.179111 TGCCGAAGATAGTCAAGGCG 60.179 55.000 0.00 0.00 46.85 5.52
534 602 0.876342 GCCGAAGATAGTCAAGGCGG 60.876 60.000 0.00 0.00 40.17 6.13
535 603 0.744874 CCGAAGATAGTCAAGGCGGA 59.255 55.000 0.00 0.00 39.62 5.54
536 604 1.536284 CCGAAGATAGTCAAGGCGGAC 60.536 57.143 0.00 4.46 39.62 4.79
537 605 1.134367 CGAAGATAGTCAAGGCGGACA 59.866 52.381 13.46 2.27 40.29 4.02
538 606 2.796383 CGAAGATAGTCAAGGCGGACAG 60.796 54.545 13.46 0.00 40.29 3.51
539 607 2.145397 AGATAGTCAAGGCGGACAGA 57.855 50.000 13.46 3.14 40.29 3.41
540 608 2.457598 AGATAGTCAAGGCGGACAGAA 58.542 47.619 13.46 1.24 40.29 3.02
541 609 2.832129 AGATAGTCAAGGCGGACAGAAA 59.168 45.455 13.46 0.00 40.29 2.52
542 610 3.260884 AGATAGTCAAGGCGGACAGAAAA 59.739 43.478 13.46 0.00 40.29 2.29
543 611 2.341846 AGTCAAGGCGGACAGAAAAA 57.658 45.000 13.46 0.00 40.29 1.94
544 612 2.863809 AGTCAAGGCGGACAGAAAAAT 58.136 42.857 13.46 0.00 40.29 1.82
545 613 2.814336 AGTCAAGGCGGACAGAAAAATC 59.186 45.455 13.46 0.00 40.29 2.17
546 614 1.804151 TCAAGGCGGACAGAAAAATCG 59.196 47.619 0.00 0.00 0.00 3.34
547 615 1.135689 CAAGGCGGACAGAAAAATCGG 60.136 52.381 0.00 0.00 0.00 4.18
548 616 1.136774 GGCGGACAGAAAAATCGGC 59.863 57.895 0.00 0.00 39.67 5.54
549 617 1.226018 GCGGACAGAAAAATCGGCG 60.226 57.895 0.00 0.00 32.46 6.46
550 618 1.226018 CGGACAGAAAAATCGGCGC 60.226 57.895 0.00 0.00 0.00 6.53
551 619 1.873165 GGACAGAAAAATCGGCGCA 59.127 52.632 10.83 0.00 0.00 6.09
552 620 0.179189 GGACAGAAAAATCGGCGCAG 60.179 55.000 10.83 5.07 0.00 5.18
553 621 0.179189 GACAGAAAAATCGGCGCAGG 60.179 55.000 10.83 0.00 0.00 4.85
554 622 0.889186 ACAGAAAAATCGGCGCAGGT 60.889 50.000 10.83 0.00 0.00 4.00
555 623 0.179189 CAGAAAAATCGGCGCAGGTC 60.179 55.000 10.83 0.00 0.00 3.85
556 624 1.136774 GAAAAATCGGCGCAGGTCC 59.863 57.895 10.83 0.00 0.00 4.46
558 626 3.894547 AAAATCGGCGCAGGTCCGT 62.895 57.895 10.83 0.00 46.49 4.69
559 627 3.894547 AAATCGGCGCAGGTCCGTT 62.895 57.895 10.83 0.00 46.49 4.44
560 628 3.894547 AATCGGCGCAGGTCCGTTT 62.895 57.895 10.83 1.30 46.49 3.60
563 631 4.025401 GGCGCAGGTCCGTTTGTG 62.025 66.667 10.83 0.00 0.00 3.33
564 632 4.025401 GCGCAGGTCCGTTTGTGG 62.025 66.667 0.30 0.00 0.00 4.17
565 633 2.280524 CGCAGGTCCGTTTGTGGA 60.281 61.111 0.00 0.00 35.04 4.02
566 634 2.317609 CGCAGGTCCGTTTGTGGAG 61.318 63.158 0.00 0.00 39.14 3.86
567 635 1.070786 GCAGGTCCGTTTGTGGAGA 59.929 57.895 0.00 0.00 39.14 3.71
568 636 0.534203 GCAGGTCCGTTTGTGGAGAA 60.534 55.000 0.00 0.00 39.14 2.87
569 637 1.961793 CAGGTCCGTTTGTGGAGAAA 58.038 50.000 0.00 0.00 39.14 2.52
570 638 1.602377 CAGGTCCGTTTGTGGAGAAAC 59.398 52.381 0.00 0.00 39.14 2.78
571 639 1.489230 AGGTCCGTTTGTGGAGAAACT 59.511 47.619 0.00 0.00 39.14 2.66
572 640 2.092592 AGGTCCGTTTGTGGAGAAACTT 60.093 45.455 0.00 0.00 39.14 2.66
573 641 2.686405 GGTCCGTTTGTGGAGAAACTTT 59.314 45.455 0.00 0.00 39.14 2.66
574 642 3.488553 GGTCCGTTTGTGGAGAAACTTTG 60.489 47.826 0.00 0.00 39.14 2.77
575 643 2.685897 TCCGTTTGTGGAGAAACTTTGG 59.314 45.455 0.00 0.00 34.26 3.28
576 644 2.223711 CCGTTTGTGGAGAAACTTTGGG 60.224 50.000 0.00 0.00 34.26 4.12
577 645 2.798145 CGTTTGTGGAGAAACTTTGGGC 60.798 50.000 0.00 0.00 34.26 5.36
578 646 2.151502 TTGTGGAGAAACTTTGGGCA 57.848 45.000 0.00 0.00 0.00 5.36
579 647 2.380064 TGTGGAGAAACTTTGGGCAT 57.620 45.000 0.00 0.00 0.00 4.40
580 648 2.676748 TGTGGAGAAACTTTGGGCATT 58.323 42.857 0.00 0.00 0.00 3.56
581 649 3.037549 TGTGGAGAAACTTTGGGCATTT 58.962 40.909 0.00 0.00 0.00 2.32
582 650 3.454082 TGTGGAGAAACTTTGGGCATTTT 59.546 39.130 0.00 0.00 0.00 1.82
583 651 3.809279 GTGGAGAAACTTTGGGCATTTTG 59.191 43.478 0.00 0.00 0.00 2.44
584 652 3.454082 TGGAGAAACTTTGGGCATTTTGT 59.546 39.130 0.00 0.00 0.00 2.83
585 653 3.809279 GGAGAAACTTTGGGCATTTTGTG 59.191 43.478 0.00 0.00 0.00 3.33
586 654 3.807553 AGAAACTTTGGGCATTTTGTGG 58.192 40.909 0.00 0.00 0.00 4.17
587 655 2.636647 AACTTTGGGCATTTTGTGGG 57.363 45.000 0.00 0.00 0.00 4.61
588 656 1.506025 ACTTTGGGCATTTTGTGGGT 58.494 45.000 0.00 0.00 0.00 4.51
589 657 1.843206 ACTTTGGGCATTTTGTGGGTT 59.157 42.857 0.00 0.00 0.00 4.11
590 658 2.158827 ACTTTGGGCATTTTGTGGGTTC 60.159 45.455 0.00 0.00 0.00 3.62
591 659 0.761802 TTGGGCATTTTGTGGGTTCC 59.238 50.000 0.00 0.00 0.00 3.62
592 660 0.399091 TGGGCATTTTGTGGGTTCCA 60.399 50.000 0.00 0.00 0.00 3.53
593 661 0.761802 GGGCATTTTGTGGGTTCCAA 59.238 50.000 0.00 0.00 34.18 3.53
594 662 1.542328 GGGCATTTTGTGGGTTCCAAC 60.542 52.381 0.00 0.00 34.18 3.77
595 663 1.416030 GGCATTTTGTGGGTTCCAACT 59.584 47.619 0.00 0.00 34.18 3.16
596 664 2.547855 GGCATTTTGTGGGTTCCAACTC 60.548 50.000 0.00 0.00 34.18 3.01
597 665 2.102252 GCATTTTGTGGGTTCCAACTCA 59.898 45.455 0.00 0.00 36.97 3.41
598 666 3.431486 GCATTTTGTGGGTTCCAACTCAA 60.431 43.478 0.00 0.00 41.88 3.02
599 667 4.764172 CATTTTGTGGGTTCCAACTCAAA 58.236 39.130 0.00 0.07 41.88 2.69
600 668 4.464069 TTTTGTGGGTTCCAACTCAAAG 57.536 40.909 0.00 0.00 41.88 2.77
601 669 2.065899 TGTGGGTTCCAACTCAAAGG 57.934 50.000 0.00 0.00 41.88 3.11
602 670 1.566703 TGTGGGTTCCAACTCAAAGGA 59.433 47.619 0.00 0.00 41.88 3.36
603 671 2.024846 TGTGGGTTCCAACTCAAAGGAA 60.025 45.455 0.00 0.00 41.88 3.36
604 672 2.623416 GTGGGTTCCAACTCAAAGGAAG 59.377 50.000 0.00 0.00 44.08 3.46
605 673 2.512056 TGGGTTCCAACTCAAAGGAAGA 59.488 45.455 0.00 0.00 44.08 2.87
606 674 2.885266 GGGTTCCAACTCAAAGGAAGAC 59.115 50.000 0.00 0.00 44.08 3.01
607 675 3.435169 GGGTTCCAACTCAAAGGAAGACT 60.435 47.826 0.00 0.00 44.08 3.24
608 676 4.207955 GGTTCCAACTCAAAGGAAGACTT 58.792 43.478 0.00 0.00 44.08 3.01
1075 1157 0.755698 AATCCTCGCTCCTTCCGCTA 60.756 55.000 0.00 0.00 0.00 4.26
1076 1158 0.540830 ATCCTCGCTCCTTCCGCTAT 60.541 55.000 0.00 0.00 0.00 2.97
1084 1166 0.261991 TCCTTCCGCTATGTCCCTCT 59.738 55.000 0.00 0.00 0.00 3.69
1206 1288 4.756642 CACACCACAAAATCAGAGCTAAGA 59.243 41.667 0.00 0.00 0.00 2.10
1232 1314 1.134699 TCTCTGCTTCCGCATCGATTT 60.135 47.619 0.00 0.00 46.74 2.17
1242 1324 3.689161 TCCGCATCGATTTCTTTCATTGT 59.311 39.130 0.00 0.00 0.00 2.71
1328 1410 2.269940 ACCTAGTGGGCTTGACATCTT 58.730 47.619 0.00 0.00 39.10 2.40
1460 1542 3.264947 TCCATCTCTTGTCTGATTTGCG 58.735 45.455 0.00 0.00 0.00 4.85
1666 1748 9.566624 CATAAATTTCGTGAACAATGTTTTGTC 57.433 29.630 0.00 0.00 45.30 3.18
1675 1757 7.219917 CGTGAACAATGTTTTGTCAACAGTTAT 59.780 33.333 0.00 0.00 45.30 1.89
1916 1999 5.610908 GCTAAAGCAGCGACAATTATTTG 57.389 39.130 0.00 0.00 41.37 2.32
1917 2000 4.027377 GCTAAAGCAGCGACAATTATTTGC 60.027 41.667 0.00 0.00 41.37 3.68
2000 2083 1.200760 AGCATGTGTCTAGCCACCCA 61.201 55.000 0.70 0.00 34.35 4.51
2039 2122 1.134280 AGTATGGATGCTGAAGCGCTT 60.134 47.619 25.35 25.35 45.83 4.68
2365 2449 7.494625 TGCTGCTTTATACCTGTTTACAGATAC 59.505 37.037 11.35 0.00 46.59 2.24
2448 2546 6.767902 CAGTATGACATAAGGTATTGGCTGTT 59.232 38.462 0.00 0.00 39.69 3.16
2467 2565 4.223953 TGTTGATCCTACTAGGGGTGATC 58.776 47.826 2.04 1.14 35.59 2.92
2492 2590 1.092348 TGTGCTGCAGAGATGCAATC 58.908 50.000 20.43 0.00 44.88 2.67
2604 2702 5.416271 TGGTGTTTCTTCCTACCATAGTC 57.584 43.478 0.00 0.00 38.23 2.59
2696 2794 1.026182 ATGACCGTGCGATGCAACAT 61.026 50.000 0.00 0.00 41.47 2.71
2752 2850 9.461312 GATTTACCTGCCCATATTAATGTCATA 57.539 33.333 0.00 0.00 0.00 2.15
3597 3699 2.878406 CGTTGGTGTTGACTTCAAGGAT 59.122 45.455 0.00 0.00 36.39 3.24
3683 3785 1.317431 TTCCTTGACCTAGCGCGCTA 61.317 55.000 36.12 36.12 0.00 4.26
3789 3892 9.829507 TCTTTCATTTGGTGTTTCATGTAATTT 57.170 25.926 0.00 0.00 0.00 1.82
3925 4029 2.373502 AGTTATATCCAGCTGCCCCTTC 59.626 50.000 8.66 0.00 0.00 3.46
4072 4213 0.586802 GACAAACCGTTGAGAGGCAC 59.413 55.000 0.00 0.00 38.20 5.01
4073 4214 0.107410 ACAAACCGTTGAGAGGCACA 60.107 50.000 0.00 0.00 38.20 4.57
4113 4256 0.250513 GTCACTCCAAAGAGGGCGAT 59.749 55.000 0.00 0.00 43.86 4.58
4181 4324 1.549203 GTCATTGCCATCCCACACTT 58.451 50.000 0.00 0.00 0.00 3.16
4189 4332 2.827921 GCCATCCCACACTTTGAGAAAT 59.172 45.455 0.00 0.00 0.00 2.17
4194 4337 5.560722 TCCCACACTTTGAGAAATGACTA 57.439 39.130 0.00 0.00 0.00 2.59
4195 4338 6.126863 TCCCACACTTTGAGAAATGACTAT 57.873 37.500 0.00 0.00 0.00 2.12
4275 4427 1.202879 TGAAGATCCACGCCAAACCTT 60.203 47.619 0.00 0.00 0.00 3.50
4288 4440 0.470766 AAACCTTAGCCACCACGACA 59.529 50.000 0.00 0.00 0.00 4.35
4292 4444 1.066143 CCTTAGCCACCACGACAAGAT 60.066 52.381 0.00 0.00 0.00 2.40
4293 4445 2.002586 CTTAGCCACCACGACAAGATG 58.997 52.381 0.00 0.00 0.00 2.90
4294 4446 0.391130 TAGCCACCACGACAAGATGC 60.391 55.000 0.00 0.00 0.00 3.91
4303 4459 2.507102 ACAAGATGCGCTCCGACG 60.507 61.111 9.73 0.00 0.00 5.12
4357 4513 0.179100 CTGGCGTCGTGGAAGATCAT 60.179 55.000 0.00 0.00 0.00 2.45
4393 4549 1.679680 CTACCCGTCATCGTACACCAT 59.320 52.381 0.00 0.00 35.01 3.55
4481 4663 0.316032 GTCGCGTCTCCTACATCGTC 60.316 60.000 5.77 0.00 0.00 4.20
4489 4671 0.750546 TCCTACATCGTCCCTCGTGG 60.751 60.000 0.00 0.00 40.80 4.94
4498 4680 2.034066 CCCTCGTGGCACCATTGT 59.966 61.111 12.86 0.00 0.00 2.71
4613 4803 2.091112 GCCATCATCCGATCGCTCG 61.091 63.158 10.32 0.78 44.62 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 4.162690 GTCGCCCCGAGCCAGATT 62.163 66.667 0.00 0.00 36.23 2.40
40 41 2.492090 CCTCCTGCTTCTCCGTCG 59.508 66.667 0.00 0.00 0.00 5.12
44 45 4.847444 GCCGCCTCCTGCTTCTCC 62.847 72.222 0.00 0.00 38.05 3.71
93 118 2.229589 GCTCGAGCATCTGCAGACG 61.230 63.158 31.91 18.03 45.16 4.18
221 289 6.892310 AAAACACTAAAAACTAGACGACGT 57.108 33.333 0.00 0.00 0.00 4.34
222 290 9.853921 AATAAAAACACTAAAAACTAGACGACG 57.146 29.630 0.00 0.00 0.00 5.12
256 324 3.423154 GGCTGGCGAAAGTCCACG 61.423 66.667 0.00 0.00 34.43 4.94
324 392 4.259371 CGCCAAATAAAAGTATTGCAAGCG 60.259 41.667 4.94 5.88 32.84 4.68
328 396 3.119814 TCGCGCCAAATAAAAGTATTGCA 60.120 39.130 0.00 0.00 30.04 4.08
335 403 1.520368 GTCGTCGCGCCAAATAAAAG 58.480 50.000 0.00 0.00 0.00 2.27
340 408 1.632046 ATTTCGTCGTCGCGCCAAAT 61.632 50.000 0.00 0.00 36.96 2.32
342 410 2.735478 ATTTCGTCGTCGCGCCAA 60.735 55.556 0.00 0.00 36.96 4.52
343 411 3.474904 CATTTCGTCGTCGCGCCA 61.475 61.111 0.00 0.00 36.96 5.69
344 412 4.204891 CCATTTCGTCGTCGCGCC 62.205 66.667 0.00 0.00 36.96 6.53
346 414 1.553654 GATCCATTTCGTCGTCGCG 59.446 57.895 0.00 0.00 36.96 5.87
348 416 1.206745 CCCGATCCATTTCGTCGTCG 61.207 60.000 0.00 0.00 37.42 5.12
349 417 1.488261 GCCCGATCCATTTCGTCGTC 61.488 60.000 0.00 0.00 37.42 4.20
350 418 1.520787 GCCCGATCCATTTCGTCGT 60.521 57.895 0.00 0.00 37.42 4.34
354 422 2.546494 GCTGGCCCGATCCATTTCG 61.546 63.158 0.00 0.00 38.83 3.46
387 455 1.866237 GGCGCTGTGTTTGAATCGA 59.134 52.632 7.64 0.00 0.00 3.59
388 456 1.509787 CGGCGCTGTGTTTGAATCG 60.510 57.895 8.45 0.00 0.00 3.34
391 459 2.203084 TCCGGCGCTGTGTTTGAA 60.203 55.556 16.49 0.00 0.00 2.69
392 460 2.970324 GTCCGGCGCTGTGTTTGA 60.970 61.111 16.49 1.24 0.00 2.69
416 484 1.606885 TTTAAGTCGGTCCGGCGGAT 61.607 55.000 33.54 17.56 36.23 4.18
420 488 0.667184 TTCGTTTAAGTCGGTCCGGC 60.667 55.000 8.12 8.12 0.00 6.13
488 556 1.369321 GCGATGCCCTCCCTTAGAG 59.631 63.158 0.00 0.00 42.83 2.43
489 557 1.382557 TGCGATGCCCTCCCTTAGA 60.383 57.895 0.00 0.00 0.00 2.10
490 558 1.227674 GTGCGATGCCCTCCCTTAG 60.228 63.158 0.00 0.00 0.00 2.18
491 559 2.908015 GTGCGATGCCCTCCCTTA 59.092 61.111 0.00 0.00 0.00 2.69
492 560 4.473520 CGTGCGATGCCCTCCCTT 62.474 66.667 0.00 0.00 0.00 3.95
496 564 4.521062 AGAGCGTGCGATGCCCTC 62.521 66.667 0.00 0.00 0.00 4.30
497 565 4.087892 AAGAGCGTGCGATGCCCT 62.088 61.111 0.00 0.00 0.00 5.19
498 566 3.869272 CAAGAGCGTGCGATGCCC 61.869 66.667 0.00 0.00 0.00 5.36
499 567 4.527157 GCAAGAGCGTGCGATGCC 62.527 66.667 7.89 0.00 34.21 4.40
500 568 4.527157 GGCAAGAGCGTGCGATGC 62.527 66.667 9.89 9.89 45.91 3.91
501 569 4.214383 CGGCAAGAGCGTGCGATG 62.214 66.667 2.52 0.00 45.91 3.84
502 570 3.932580 TTCGGCAAGAGCGTGCGAT 62.933 57.895 2.52 0.00 45.91 4.58
503 571 4.656117 TTCGGCAAGAGCGTGCGA 62.656 61.111 2.52 1.59 45.91 5.10
504 572 4.139420 CTTCGGCAAGAGCGTGCG 62.139 66.667 2.52 0.00 45.91 5.34
505 573 0.806102 TATCTTCGGCAAGAGCGTGC 60.806 55.000 0.00 0.00 42.13 5.34
506 574 1.203928 CTATCTTCGGCAAGAGCGTG 58.796 55.000 5.78 0.00 42.13 5.34
507 575 0.818296 ACTATCTTCGGCAAGAGCGT 59.182 50.000 5.78 3.19 42.13 5.07
508 576 1.202302 TGACTATCTTCGGCAAGAGCG 60.202 52.381 5.78 0.00 42.13 5.03
509 577 2.586258 TGACTATCTTCGGCAAGAGC 57.414 50.000 5.78 0.00 42.13 4.09
510 578 3.452474 CCTTGACTATCTTCGGCAAGAG 58.548 50.000 7.17 0.00 42.13 2.85
511 579 2.418746 GCCTTGACTATCTTCGGCAAGA 60.419 50.000 7.17 2.63 43.06 3.02
512 580 1.936547 GCCTTGACTATCTTCGGCAAG 59.063 52.381 0.00 0.00 37.48 4.01
513 581 1.739035 CGCCTTGACTATCTTCGGCAA 60.739 52.381 0.00 0.00 37.39 4.52
514 582 0.179111 CGCCTTGACTATCTTCGGCA 60.179 55.000 0.00 0.00 37.39 5.69
515 583 0.876342 CCGCCTTGACTATCTTCGGC 60.876 60.000 0.00 0.00 0.00 5.54
516 584 0.744874 TCCGCCTTGACTATCTTCGG 59.255 55.000 0.00 0.00 37.00 4.30
517 585 1.134367 TGTCCGCCTTGACTATCTTCG 59.866 52.381 0.00 0.00 36.21 3.79
518 586 2.427453 TCTGTCCGCCTTGACTATCTTC 59.573 50.000 0.00 0.00 36.21 2.87
519 587 2.457598 TCTGTCCGCCTTGACTATCTT 58.542 47.619 0.00 0.00 36.21 2.40
520 588 2.145397 TCTGTCCGCCTTGACTATCT 57.855 50.000 0.00 0.00 36.21 1.98
521 589 2.961526 TTCTGTCCGCCTTGACTATC 57.038 50.000 0.00 0.00 36.21 2.08
522 590 3.695830 TTTTCTGTCCGCCTTGACTAT 57.304 42.857 0.00 0.00 36.21 2.12
523 591 3.478857 TTTTTCTGTCCGCCTTGACTA 57.521 42.857 0.00 0.00 36.21 2.59
524 592 2.341846 TTTTTCTGTCCGCCTTGACT 57.658 45.000 0.00 0.00 36.21 3.41
525 593 2.412847 CGATTTTTCTGTCCGCCTTGAC 60.413 50.000 0.00 0.00 35.77 3.18
526 594 1.804151 CGATTTTTCTGTCCGCCTTGA 59.196 47.619 0.00 0.00 0.00 3.02
527 595 1.135689 CCGATTTTTCTGTCCGCCTTG 60.136 52.381 0.00 0.00 0.00 3.61
528 596 1.165270 CCGATTTTTCTGTCCGCCTT 58.835 50.000 0.00 0.00 0.00 4.35
529 597 1.305930 GCCGATTTTTCTGTCCGCCT 61.306 55.000 0.00 0.00 0.00 5.52
530 598 1.136774 GCCGATTTTTCTGTCCGCC 59.863 57.895 0.00 0.00 0.00 6.13
531 599 1.226018 CGCCGATTTTTCTGTCCGC 60.226 57.895 0.00 0.00 0.00 5.54
532 600 1.226018 GCGCCGATTTTTCTGTCCG 60.226 57.895 0.00 0.00 0.00 4.79
533 601 0.179189 CTGCGCCGATTTTTCTGTCC 60.179 55.000 4.18 0.00 0.00 4.02
534 602 0.179189 CCTGCGCCGATTTTTCTGTC 60.179 55.000 4.18 0.00 0.00 3.51
535 603 0.889186 ACCTGCGCCGATTTTTCTGT 60.889 50.000 4.18 0.00 0.00 3.41
536 604 0.179189 GACCTGCGCCGATTTTTCTG 60.179 55.000 4.18 0.00 0.00 3.02
537 605 1.305930 GGACCTGCGCCGATTTTTCT 61.306 55.000 4.18 0.00 0.00 2.52
538 606 1.136774 GGACCTGCGCCGATTTTTC 59.863 57.895 4.18 0.00 0.00 2.29
539 607 3.274067 GGACCTGCGCCGATTTTT 58.726 55.556 4.18 0.00 0.00 1.94
546 614 4.025401 CACAAACGGACCTGCGCC 62.025 66.667 4.18 0.00 0.00 6.53
547 615 4.025401 CCACAAACGGACCTGCGC 62.025 66.667 0.00 0.00 0.00 6.09
548 616 2.280524 TCCACAAACGGACCTGCG 60.281 61.111 0.00 0.00 0.00 5.18
549 617 0.534203 TTCTCCACAAACGGACCTGC 60.534 55.000 0.00 0.00 0.00 4.85
550 618 1.602377 GTTTCTCCACAAACGGACCTG 59.398 52.381 0.00 0.00 0.00 4.00
551 619 1.489230 AGTTTCTCCACAAACGGACCT 59.511 47.619 0.00 0.00 40.60 3.85
552 620 1.963172 AGTTTCTCCACAAACGGACC 58.037 50.000 0.00 0.00 40.60 4.46
553 621 3.488553 CCAAAGTTTCTCCACAAACGGAC 60.489 47.826 0.00 0.00 40.60 4.79
554 622 2.685897 CCAAAGTTTCTCCACAAACGGA 59.314 45.455 0.00 0.00 40.60 4.69
555 623 2.223711 CCCAAAGTTTCTCCACAAACGG 60.224 50.000 0.00 0.00 40.60 4.44
556 624 2.798145 GCCCAAAGTTTCTCCACAAACG 60.798 50.000 0.00 0.00 40.60 3.60
557 625 2.167487 TGCCCAAAGTTTCTCCACAAAC 59.833 45.455 0.00 0.00 36.64 2.93
558 626 2.461695 TGCCCAAAGTTTCTCCACAAA 58.538 42.857 0.00 0.00 0.00 2.83
559 627 2.151502 TGCCCAAAGTTTCTCCACAA 57.848 45.000 0.00 0.00 0.00 3.33
560 628 2.380064 ATGCCCAAAGTTTCTCCACA 57.620 45.000 0.00 0.00 0.00 4.17
561 629 3.751479 AAATGCCCAAAGTTTCTCCAC 57.249 42.857 0.00 0.00 0.00 4.02
562 630 3.454082 ACAAAATGCCCAAAGTTTCTCCA 59.546 39.130 0.00 0.00 0.00 3.86
563 631 3.809279 CACAAAATGCCCAAAGTTTCTCC 59.191 43.478 0.00 0.00 0.00 3.71
564 632 3.809279 CCACAAAATGCCCAAAGTTTCTC 59.191 43.478 0.00 0.00 0.00 2.87
565 633 3.433456 CCCACAAAATGCCCAAAGTTTCT 60.433 43.478 0.00 0.00 0.00 2.52
566 634 2.877786 CCCACAAAATGCCCAAAGTTTC 59.122 45.455 0.00 0.00 0.00 2.78
567 635 2.240921 ACCCACAAAATGCCCAAAGTTT 59.759 40.909 0.00 0.00 0.00 2.66
568 636 1.843206 ACCCACAAAATGCCCAAAGTT 59.157 42.857 0.00 0.00 0.00 2.66
569 637 1.506025 ACCCACAAAATGCCCAAAGT 58.494 45.000 0.00 0.00 0.00 2.66
570 638 2.493035 GAACCCACAAAATGCCCAAAG 58.507 47.619 0.00 0.00 0.00 2.77
571 639 1.141858 GGAACCCACAAAATGCCCAAA 59.858 47.619 0.00 0.00 0.00 3.28
572 640 0.761802 GGAACCCACAAAATGCCCAA 59.238 50.000 0.00 0.00 0.00 4.12
573 641 0.399091 TGGAACCCACAAAATGCCCA 60.399 50.000 0.00 0.00 0.00 5.36
574 642 0.761802 TTGGAACCCACAAAATGCCC 59.238 50.000 0.00 0.00 30.78 5.36
575 643 1.416030 AGTTGGAACCCACAAAATGCC 59.584 47.619 0.00 0.00 30.78 4.40
576 644 2.102252 TGAGTTGGAACCCACAAAATGC 59.898 45.455 0.00 0.00 30.78 3.56
577 645 4.399004 TTGAGTTGGAACCCACAAAATG 57.601 40.909 0.00 0.00 30.78 2.32
578 646 4.141733 CCTTTGAGTTGGAACCCACAAAAT 60.142 41.667 0.00 0.00 30.78 1.82
579 647 3.196685 CCTTTGAGTTGGAACCCACAAAA 59.803 43.478 0.00 0.00 30.78 2.44
580 648 2.763448 CCTTTGAGTTGGAACCCACAAA 59.237 45.455 0.00 0.00 30.78 2.83
581 649 2.024846 TCCTTTGAGTTGGAACCCACAA 60.025 45.455 0.00 0.00 30.78 3.33
582 650 1.566703 TCCTTTGAGTTGGAACCCACA 59.433 47.619 0.00 0.00 30.78 4.17
583 651 2.358322 TCCTTTGAGTTGGAACCCAC 57.642 50.000 0.00 0.00 30.78 4.61
584 652 2.512056 TCTTCCTTTGAGTTGGAACCCA 59.488 45.455 0.00 0.00 37.42 4.51
585 653 2.885266 GTCTTCCTTTGAGTTGGAACCC 59.115 50.000 0.00 0.00 37.42 4.11
586 654 3.821748 AGTCTTCCTTTGAGTTGGAACC 58.178 45.455 0.00 0.00 37.42 3.62
587 655 5.836821 AAAGTCTTCCTTTGAGTTGGAAC 57.163 39.130 0.00 0.00 41.86 3.62
588 656 5.949354 TGAAAAGTCTTCCTTTGAGTTGGAA 59.051 36.000 0.00 0.00 42.62 3.53
589 657 5.505780 TGAAAAGTCTTCCTTTGAGTTGGA 58.494 37.500 0.00 0.00 42.62 3.53
590 658 5.835113 TGAAAAGTCTTCCTTTGAGTTGG 57.165 39.130 0.00 0.00 42.62 3.77
591 659 8.532977 TTTTTGAAAAGTCTTCCTTTGAGTTG 57.467 30.769 0.00 0.00 42.62 3.16
851 919 2.167693 AGTCTCCAACACGTCAGTTCAA 59.832 45.455 0.00 0.00 0.00 2.69
852 920 1.754803 AGTCTCCAACACGTCAGTTCA 59.245 47.619 0.00 0.00 0.00 3.18
853 921 2.510768 AGTCTCCAACACGTCAGTTC 57.489 50.000 0.00 0.00 0.00 3.01
854 922 2.550978 CAAGTCTCCAACACGTCAGTT 58.449 47.619 0.00 0.00 0.00 3.16
855 923 1.202533 CCAAGTCTCCAACACGTCAGT 60.203 52.381 0.00 0.00 0.00 3.41
856 924 1.068588 TCCAAGTCTCCAACACGTCAG 59.931 52.381 0.00 0.00 0.00 3.51
857 925 1.068588 CTCCAAGTCTCCAACACGTCA 59.931 52.381 0.00 0.00 0.00 4.35
858 926 1.068741 ACTCCAAGTCTCCAACACGTC 59.931 52.381 0.00 0.00 0.00 4.34
859 927 1.120530 ACTCCAAGTCTCCAACACGT 58.879 50.000 0.00 0.00 0.00 4.49
860 928 2.135933 GAACTCCAAGTCTCCAACACG 58.864 52.381 0.00 0.00 0.00 4.49
919 987 4.170256 CCTTCTCTTTTCTGTCTAGACGC 58.830 47.826 17.85 0.00 31.21 5.19
1232 1314 3.652869 AGACTCCCAAGGACAATGAAAGA 59.347 43.478 0.00 0.00 0.00 2.52
1242 1324 4.453480 AATTCAAACAGACTCCCAAGGA 57.547 40.909 0.00 0.00 0.00 3.36
1328 1410 2.761559 ACCGAATCGACACAACATTGA 58.238 42.857 3.36 0.00 0.00 2.57
1460 1542 1.239347 AGCTGAAAAGGGCGAGAAAC 58.761 50.000 0.00 0.00 0.00 2.78
1477 1559 5.753921 ACACTACAGACAAGAAGTACAAAGC 59.246 40.000 0.00 0.00 0.00 3.51
1913 1996 0.458669 GTACTCCCTCCGATCGCAAA 59.541 55.000 10.32 0.00 0.00 3.68
1916 1999 1.823797 ATAGTACTCCCTCCGATCGC 58.176 55.000 10.32 0.00 0.00 4.58
1917 2000 5.066246 GGAAATATAGTACTCCCTCCGATCG 59.934 48.000 8.51 8.51 0.00 3.69
2000 2083 0.041833 TCAGCTAGGAGGAAGGTGCT 59.958 55.000 0.00 0.00 41.22 4.40
2039 2122 7.288810 AGTTCTTCATTTTATGTTCCTTGCA 57.711 32.000 0.00 0.00 0.00 4.08
2365 2449 0.396139 AGGGTGCATAACATGGCCAG 60.396 55.000 13.05 6.08 0.00 4.85
2425 2523 6.765989 TCAACAGCCAATACCTTATGTCATAC 59.234 38.462 0.00 0.00 0.00 2.39
2448 2546 4.140686 ACATGATCACCCCTAGTAGGATCA 60.141 45.833 18.43 17.34 45.74 2.92
2467 2565 1.130561 CATCTCTGCAGCACACACATG 59.869 52.381 9.47 0.00 0.00 3.21
2604 2702 8.940768 TTTAAAAATTTCAGTGGACAGAAAGG 57.059 30.769 4.07 0.00 35.38 3.11
2752 2850 8.134895 CGGGCATGATTTATAAACATTTACACT 58.865 33.333 0.00 0.00 0.00 3.55
2935 3034 6.463472 CCTTCCCTCTCTGCATTTTTCTTTTT 60.463 38.462 0.00 0.00 0.00 1.94
2940 3039 2.757314 CCCTTCCCTCTCTGCATTTTTC 59.243 50.000 0.00 0.00 0.00 2.29
3597 3699 7.125659 TCAACATTACCAGATGATTCTCCAGTA 59.874 37.037 0.00 0.00 0.00 2.74
3683 3785 3.055094 AGAGGCGATAAGGAACACAACAT 60.055 43.478 0.00 0.00 0.00 2.71
3789 3892 9.695526 CACCTCATGAACAAAATTCTAAAATCA 57.304 29.630 0.00 0.00 0.00 2.57
3925 4029 5.178797 CCTCCAAAGACATTACACACTAGG 58.821 45.833 0.00 0.00 0.00 3.02
4072 4213 2.548057 GTGTGTGGGTATCTTGTGTGTG 59.452 50.000 0.00 0.00 0.00 3.82
4073 4214 2.805295 CGTGTGTGGGTATCTTGTGTGT 60.805 50.000 0.00 0.00 0.00 3.72
4113 4256 3.708890 ACGTTGTTGTATTGTCTCGACA 58.291 40.909 0.00 0.00 39.98 4.35
4181 4324 6.003326 TGGCAAAGTCATAGTCATTTCTCAA 58.997 36.000 0.00 0.00 0.00 3.02
4189 4332 3.745975 CGTCTTTGGCAAAGTCATAGTCA 59.254 43.478 32.46 13.50 39.52 3.41
4194 4337 2.416547 CGATCGTCTTTGGCAAAGTCAT 59.583 45.455 32.46 23.44 39.52 3.06
4195 4338 1.798223 CGATCGTCTTTGGCAAAGTCA 59.202 47.619 32.46 20.51 39.52 3.41
4275 4427 0.391130 GCATCTTGTCGTGGTGGCTA 60.391 55.000 0.00 0.00 0.00 3.93
4303 4459 1.411493 CTTCGTAGCTTTCCGTCGGC 61.411 60.000 6.34 0.00 0.00 5.54
4357 4513 2.029623 GGTAGCAGGTGGTCTATTCGA 58.970 52.381 0.00 0.00 0.00 3.71
4481 4663 2.034066 ACAATGGTGCCACGAGGG 59.966 61.111 0.00 0.00 40.85 4.30
4489 4671 2.615912 GAGGCTTCTATGACAATGGTGC 59.384 50.000 0.00 0.00 0.00 5.01
4498 4680 3.834813 AGTTGTCACTGAGGCTTCTATGA 59.165 43.478 0.00 0.00 0.00 2.15
4590 4772 3.573772 GATCGGATGATGGCGGCGA 62.574 63.158 12.98 0.00 34.09 5.54


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

AutoCloner maintained by Alex Coulton.