Multiple sequence alignment - TraesCS2A01G290900

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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 TraesCS2A01G290900 chr2A 100.000 7297 0 0 1 7297 501316503 501323799 0.000000e+00 13476.0
1 TraesCS2A01G290900 chr2A 100.000 135 0 0 7099 7233 501323467 501323601 4.370000e-62 250.0
2 TraesCS2A01G290900 chr2A 100.000 135 0 0 6965 7099 501323601 501323735 4.370000e-62 250.0
3 TraesCS2A01G290900 chr2A 97.143 35 0 1 159 192 9056164 9056130 2.840000e-04 58.4
4 TraesCS2A01G290900 chr2D 95.284 6065 167 40 482 6523 370237068 370243036 0.000000e+00 9505.0
5 TraesCS2A01G290900 chr2D 87.117 489 23 11 6647 7096 370243541 370244028 1.090000e-142 518.0
6 TraesCS2A01G290900 chr2D 89.034 383 39 3 35 416 370236685 370237065 8.570000e-129 472.0
7 TraesCS2A01G290900 chr2D 94.949 198 10 0 7099 7296 370243897 370244094 1.980000e-80 311.0
8 TraesCS2A01G290900 chr2D 94.792 96 5 0 6552 6647 370243034 370243129 4.560000e-32 150.0
9 TraesCS2A01G290900 chr2B 92.993 2412 87 29 482 2840 439767104 439769486 0.000000e+00 3443.0
10 TraesCS2A01G290900 chr2B 94.062 1886 99 11 2839 4719 439769564 439771441 0.000000e+00 2850.0
11 TraesCS2A01G290900 chr2B 94.137 1808 65 15 4814 6612 439771814 439773589 0.000000e+00 2713.0
12 TraesCS2A01G290900 chr2B 91.843 331 21 1 6775 7099 439773858 439774188 2.400000e-124 457.0
13 TraesCS2A01G290900 chr2B 87.565 386 46 2 32 416 439766717 439767101 5.190000e-121 446.0
14 TraesCS2A01G290900 chr2B 94.444 198 11 0 7099 7296 439774054 439774251 9.200000e-79 305.0
15 TraesCS2A01G290900 chr5A 82.371 329 50 3 6777 7099 548991973 548991647 5.570000e-71 279.0
16 TraesCS2A01G290900 chr5A 82.178 101 17 1 6648 6748 7480734 7480833 1.300000e-12 86.1
17 TraesCS2A01G290900 chr5B 77.778 468 65 14 6671 7099 294080679 294080212 1.220000e-62 252.0
18 TraesCS2A01G290900 chr5B 79.775 267 49 5 6825 7090 9296711 9296973 9.660000e-44 189.0
19 TraesCS2A01G290900 chr7A 89.447 199 20 1 7099 7296 730885706 730885904 4.370000e-62 250.0
20 TraesCS2A01G290900 chr1D 88.889 198 22 0 7099 7296 367851017 367851214 2.030000e-60 244.0
21 TraesCS2A01G290900 chr1D 88.000 50 4 2 159 206 315618599 315618648 2.840000e-04 58.4
22 TraesCS2A01G290900 chr6B 75.373 536 101 29 4674 5195 699005527 699005009 5.690000e-56 230.0
23 TraesCS2A01G290900 chr6B 80.000 275 41 10 3543 3808 699007326 699007057 2.690000e-44 191.0
24 TraesCS2A01G290900 chr1A 86.935 199 26 0 7099 7297 45503778 45503976 2.650000e-54 224.0
25 TraesCS2A01G290900 chr6D 80.515 272 43 8 3544 3808 459697802 459697534 4.460000e-47 200.0
26 TraesCS2A01G290900 chr6A 84.848 198 30 0 7099 7296 85263703 85263506 4.460000e-47 200.0
27 TraesCS2A01G290900 chr6A 79.783 277 36 14 3543 3808 605379651 605379384 4.500000e-42 183.0
28 TraesCS2A01G290900 chr3B 83.920 199 31 1 7099 7297 501104019 501104216 9.660000e-44 189.0
29 TraesCS2A01G290900 chr3B 75.105 478 80 16 6660 7098 501103675 501104152 3.480000e-43 187.0
30 TraesCS2A01G290900 chr3B 87.719 57 3 4 159 211 679508918 679508862 6.110000e-06 63.9
31 TraesCS2A01G290900 chr7D 87.821 156 19 0 7141 7296 577320164 577320009 4.500000e-42 183.0
32 TraesCS2A01G290900 chr3A 77.528 267 50 9 6808 7069 507294875 507295136 1.270000e-32 152.0
33 TraesCS2A01G290900 chr3A 83.544 79 6 6 140 211 594867056 594867134 4.720000e-07 67.6
34 TraesCS2A01G290900 chr3D 92.045 88 7 0 6662 6749 384849724 384849811 2.760000e-24 124.0


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 TraesCS2A01G290900 chr2A 501316503 501323799 7296 False 4658.666667 13476 100.000000 1 7297 3 chr2A.!!$F1 7296
1 TraesCS2A01G290900 chr2D 370236685 370244094 7409 False 2191.200000 9505 92.235200 35 7296 5 chr2D.!!$F1 7261
2 TraesCS2A01G290900 chr2B 439766717 439774251 7534 False 1702.333333 3443 92.507333 32 7296 6 chr2B.!!$F1 7264
3 TraesCS2A01G290900 chr6B 699005009 699007326 2317 True 210.500000 230 77.686500 3543 5195 2 chr6B.!!$R1 1652

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
543 547 0.033781 TCGAAACCACCGGACGATTT 59.966 50.000 9.46 2.6 0.00 2.17 F
1383 1443 0.754472 TTGTCCTTCCGTTTCGAGGT 59.246 50.000 0.00 0.0 32.33 3.85 F
1390 1450 0.892755 TCCGTTTCGAGGTGCATAGT 59.107 50.000 0.00 0.0 0.00 2.12 F
1758 1821 2.180276 GAGCCCTGAGGAAGTCTGTAA 58.820 52.381 0.00 0.0 33.47 2.41 F
2292 2355 2.613977 CCCAGTCTGCACTTCCAGTTAG 60.614 54.545 0.00 0.0 34.47 2.34 F
3867 4019 1.684450 TCGCGGTATTATGGAAGCTGA 59.316 47.619 6.13 0.0 0.00 4.26 F
4849 6005 4.340894 TGAATCGAACTGTAATGCTTGC 57.659 40.909 0.00 0.0 0.00 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1551 1614 0.242825 TTCAACTCGGCGGTCAGTAG 59.757 55.000 7.21 0.00 0.00 2.57 R
2853 2998 0.249398 GCCGCAGAGAGTTTTAGGGA 59.751 55.000 0.00 0.00 0.00 4.20 R
2976 3121 2.785679 GCGCACATCTGGTAATTTCAC 58.214 47.619 0.30 0.00 0.00 3.18 R
3150 3296 7.651304 CCATGATCAAGAGTATACTGACACTTC 59.349 40.741 10.90 1.25 29.13 3.01 R
4104 4486 3.071874 TGGAGCCTACAAGTTCCATTG 57.928 47.619 0.00 0.00 34.90 2.82 R
5080 6238 0.750911 GGAAAGCTCCAGGCCATGAG 60.751 60.000 15.30 15.30 41.96 2.90 R
6823 8479 0.544833 TTGCCATTCATTGCCCCTGT 60.545 50.000 0.00 0.00 0.00 4.00 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 5.305644 AGTCAAACTGCCGATCTAAGGATAT 59.694 40.000 0.00 0.00 31.46 1.63
132 133 3.870538 AGCATGGCTTAGATGGATTGA 57.129 42.857 0.00 0.00 33.89 2.57
137 138 5.942236 GCATGGCTTAGATGGATTGAATCTA 59.058 40.000 5.03 0.00 35.92 1.98
240 242 9.484806 AAAAATATTCATTCAGTGGAAGGAGAT 57.515 29.630 0.00 0.00 43.81 2.75
252 254 4.216687 GTGGAAGGAGATATTCTCGTCGAT 59.783 45.833 0.00 0.00 44.28 3.59
275 277 7.464577 CGATTATGAGACGTTTGTGATGATGTT 60.465 37.037 0.00 0.00 0.00 2.71
367 371 7.812309 GCATATGCGACTATACTATGTTTCA 57.188 36.000 12.82 0.00 0.00 2.69
368 372 8.239681 GCATATGCGACTATACTATGTTTCAA 57.760 34.615 12.82 0.00 0.00 2.69
397 401 6.713762 TTGAGAAATTGGTGAGTGATTGTT 57.286 33.333 0.00 0.00 0.00 2.83
426 430 6.819397 AAGTTACAAAATAGTGCTCCTTCC 57.181 37.500 0.00 0.00 0.00 3.46
427 431 4.935808 AGTTACAAAATAGTGCTCCTTCCG 59.064 41.667 0.00 0.00 0.00 4.30
428 432 3.418684 ACAAAATAGTGCTCCTTCCGT 57.581 42.857 0.00 0.00 0.00 4.69
429 433 3.335579 ACAAAATAGTGCTCCTTCCGTC 58.664 45.455 0.00 0.00 0.00 4.79
430 434 3.008049 ACAAAATAGTGCTCCTTCCGTCT 59.992 43.478 0.00 0.00 0.00 4.18
431 435 3.528597 AAATAGTGCTCCTTCCGTCTC 57.471 47.619 0.00 0.00 0.00 3.36
432 436 2.145397 ATAGTGCTCCTTCCGTCTCA 57.855 50.000 0.00 0.00 0.00 3.27
433 437 1.464734 TAGTGCTCCTTCCGTCTCAG 58.535 55.000 0.00 0.00 0.00 3.35
434 438 0.251386 AGTGCTCCTTCCGTCTCAGA 60.251 55.000 0.00 0.00 0.00 3.27
435 439 0.603569 GTGCTCCTTCCGTCTCAGAA 59.396 55.000 0.00 0.00 0.00 3.02
436 440 1.205893 GTGCTCCTTCCGTCTCAGAAT 59.794 52.381 0.00 0.00 0.00 2.40
437 441 2.427453 GTGCTCCTTCCGTCTCAGAATA 59.573 50.000 0.00 0.00 0.00 1.75
438 442 3.096852 TGCTCCTTCCGTCTCAGAATAA 58.903 45.455 0.00 0.00 0.00 1.40
439 443 3.131223 TGCTCCTTCCGTCTCAGAATAAG 59.869 47.826 0.00 0.00 0.00 1.73
440 444 3.131400 GCTCCTTCCGTCTCAGAATAAGT 59.869 47.826 0.00 0.00 0.00 2.24
441 445 4.677584 CTCCTTCCGTCTCAGAATAAGTG 58.322 47.826 0.00 0.00 0.00 3.16
442 446 4.341487 TCCTTCCGTCTCAGAATAAGTGA 58.659 43.478 0.00 0.00 0.00 3.41
443 447 4.956700 TCCTTCCGTCTCAGAATAAGTGAT 59.043 41.667 0.00 0.00 0.00 3.06
444 448 5.046529 CCTTCCGTCTCAGAATAAGTGATG 58.953 45.833 0.00 0.00 0.00 3.07
445 449 5.394663 CCTTCCGTCTCAGAATAAGTGATGT 60.395 44.000 0.00 0.00 0.00 3.06
446 450 6.183360 CCTTCCGTCTCAGAATAAGTGATGTA 60.183 42.308 0.00 0.00 0.00 2.29
447 451 6.132791 TCCGTCTCAGAATAAGTGATGTAC 57.867 41.667 0.00 0.00 0.00 2.90
448 452 5.650703 TCCGTCTCAGAATAAGTGATGTACA 59.349 40.000 0.00 0.00 0.00 2.90
449 453 6.152154 TCCGTCTCAGAATAAGTGATGTACAA 59.848 38.462 0.00 0.00 0.00 2.41
450 454 6.811665 CCGTCTCAGAATAAGTGATGTACAAA 59.188 38.462 0.00 0.00 0.00 2.83
451 455 7.009631 CCGTCTCAGAATAAGTGATGTACAAAG 59.990 40.741 0.00 0.00 0.00 2.77
452 456 7.542477 CGTCTCAGAATAAGTGATGTACAAAGT 59.458 37.037 0.00 0.00 0.00 2.66
453 457 9.209175 GTCTCAGAATAAGTGATGTACAAAGTT 57.791 33.333 0.00 3.49 0.00 2.66
454 458 9.208022 TCTCAGAATAAGTGATGTACAAAGTTG 57.792 33.333 0.00 0.00 0.00 3.16
455 459 9.208022 CTCAGAATAAGTGATGTACAAAGTTGA 57.792 33.333 0.00 0.00 0.00 3.18
456 460 9.554395 TCAGAATAAGTGATGTACAAAGTTGAA 57.446 29.630 0.00 0.00 0.00 2.69
461 465 7.807977 AAGTGATGTACAAAGTTGAATCACT 57.192 32.000 21.98 21.98 46.34 3.41
462 466 7.807977 AGTGATGTACAAAGTTGAATCACTT 57.192 32.000 21.98 13.77 44.59 3.16
463 467 8.902540 AGTGATGTACAAAGTTGAATCACTTA 57.097 30.769 21.98 0.00 44.59 2.24
464 468 9.507329 AGTGATGTACAAAGTTGAATCACTTAT 57.493 29.630 21.98 11.09 44.59 1.73
474 478 9.893305 AAAGTTGAATCACTTATTTTAGAACGG 57.107 29.630 0.00 0.00 35.87 4.44
475 479 8.842358 AGTTGAATCACTTATTTTAGAACGGA 57.158 30.769 0.00 0.00 0.00 4.69
476 480 8.936864 AGTTGAATCACTTATTTTAGAACGGAG 58.063 33.333 0.00 0.00 0.00 4.63
477 481 8.932791 GTTGAATCACTTATTTTAGAACGGAGA 58.067 33.333 0.00 0.00 0.00 3.71
478 482 9.496873 TTGAATCACTTATTTTAGAACGGAGAA 57.503 29.630 0.00 0.00 0.00 2.87
479 483 9.496873 TGAATCACTTATTTTAGAACGGAGAAA 57.503 29.630 0.00 0.00 0.00 2.52
480 484 9.974750 GAATCACTTATTTTAGAACGGAGAAAG 57.025 33.333 0.00 0.00 0.00 2.62
512 516 8.331742 TGCAATTCGTTTTAAATTGTTCTTTCC 58.668 29.630 9.54 0.00 43.09 3.13
517 521 6.530534 TCGTTTTAAATTGTTCTTTCCGCAAA 59.469 30.769 0.00 0.00 0.00 3.68
523 527 6.822073 AATTGTTCTTTCCGCAAAAACTAC 57.178 33.333 0.00 0.00 0.00 2.73
543 547 0.033781 TCGAAACCACCGGACGATTT 59.966 50.000 9.46 2.60 0.00 2.17
590 594 3.434319 GTGAGCCGTCCGTCCGTA 61.434 66.667 0.00 0.00 0.00 4.02
591 595 2.438975 TGAGCCGTCCGTCCGTAT 60.439 61.111 0.00 0.00 0.00 3.06
592 596 2.025727 GAGCCGTCCGTCCGTATG 59.974 66.667 0.00 0.00 0.00 2.39
593 597 2.753043 AGCCGTCCGTCCGTATGT 60.753 61.111 0.00 0.00 0.00 2.29
594 598 2.182537 GCCGTCCGTCCGTATGTT 59.817 61.111 0.00 0.00 0.00 2.71
595 599 1.875364 GCCGTCCGTCCGTATGTTC 60.875 63.158 0.00 0.00 0.00 3.18
596 600 1.805254 CCGTCCGTCCGTATGTTCT 59.195 57.895 0.00 0.00 0.00 3.01
868 911 2.920912 TTCCACCTTCCGTCCGCT 60.921 61.111 0.00 0.00 0.00 5.52
869 912 2.939261 TTCCACCTTCCGTCCGCTC 61.939 63.158 0.00 0.00 0.00 5.03
870 913 4.452733 CCACCTTCCGTCCGCTCC 62.453 72.222 0.00 0.00 0.00 4.70
871 914 4.796231 CACCTTCCGTCCGCTCCG 62.796 72.222 0.00 0.00 0.00 4.63
1383 1443 0.754472 TTGTCCTTCCGTTTCGAGGT 59.246 50.000 0.00 0.00 32.33 3.85
1386 1446 1.301401 CCTTCCGTTTCGAGGTGCA 60.301 57.895 0.00 0.00 0.00 4.57
1390 1450 0.892755 TCCGTTTCGAGGTGCATAGT 59.107 50.000 0.00 0.00 0.00 2.12
1644 1707 3.968649 TGCTGTTTTTCTCAATGACTGC 58.031 40.909 0.00 0.00 36.24 4.40
1758 1821 2.180276 GAGCCCTGAGGAAGTCTGTAA 58.820 52.381 0.00 0.00 33.47 2.41
1971 2034 2.750888 GGACGGTGCGAAGATTGCC 61.751 63.158 0.00 0.00 0.00 4.52
2063 2126 6.389830 TTGCCAGGTAAATATGCTGTTATG 57.610 37.500 0.00 0.00 0.00 1.90
2064 2127 5.689835 TGCCAGGTAAATATGCTGTTATGA 58.310 37.500 0.00 0.00 0.00 2.15
2115 2178 8.744568 TGATGTATGCAGACATGGTTTAATTA 57.255 30.769 30.31 0.00 40.18 1.40
2122 2185 7.102346 TGCAGACATGGTTTAATTATTTTGGG 58.898 34.615 0.00 0.00 0.00 4.12
2123 2186 6.538381 GCAGACATGGTTTAATTATTTTGGGG 59.462 38.462 0.00 0.00 0.00 4.96
2163 2226 4.394920 GCCAATTATTTGAAGAGTGTCGGA 59.605 41.667 0.00 0.00 34.60 4.55
2277 2340 4.995487 CACTCTGTAAGTTTTACCCCAGTC 59.005 45.833 0.00 0.00 35.45 3.51
2292 2355 2.613977 CCCAGTCTGCACTTCCAGTTAG 60.614 54.545 0.00 0.00 34.47 2.34
2482 2546 8.397575 TCAAAGATATAGTAGATGCGTCTCTT 57.602 34.615 12.83 5.14 35.87 2.85
2603 2667 9.474313 TGCTACCTTCCTGATAAATGTTATTTT 57.526 29.630 0.00 0.00 0.00 1.82
2635 2699 6.860790 TTTCACCTACATATGTCCACACTA 57.139 37.500 12.68 0.00 0.00 2.74
2686 2750 5.119898 GCATTTGTATCCGAAAATTGCAACA 59.880 36.000 0.00 0.00 0.00 3.33
2941 3086 9.743581 ATTTGCAATCCAAAAATTAGATTTCCT 57.256 25.926 0.00 0.00 45.80 3.36
2962 3107 6.419791 TCCTTTTTCCAAACTCAGAAGTGTA 58.580 36.000 0.00 0.00 35.36 2.90
3150 3296 4.201891 GCCTTATGCAATGTCTGAACTCTG 60.202 45.833 0.00 0.00 40.77 3.35
3180 3326 6.589523 GTCAGTATACTCTTGATCATGGATGC 59.410 42.308 1.26 3.13 0.00 3.91
3459 3606 4.975631 TCCGGAAACTTCTTTATCAACCA 58.024 39.130 0.00 0.00 0.00 3.67
3490 3637 7.897864 TCTCCTTTCAACCTTTTTGTTTTGTA 58.102 30.769 0.00 0.00 0.00 2.41
3867 4019 1.684450 TCGCGGTATTATGGAAGCTGA 59.316 47.619 6.13 0.00 0.00 4.26
4104 4486 9.444600 TGGACTATGGTTGTAACTTATTTCTTC 57.555 33.333 0.00 0.00 0.00 2.87
4433 5232 6.128418 GCTCCCAAGCGAAATCTCTAATAATC 60.128 42.308 0.00 0.00 39.10 1.75
4495 5345 7.436320 AATTTTGCCCCACACATATATCTTT 57.564 32.000 0.00 0.00 0.00 2.52
4497 5347 6.463995 TTTGCCCCACACATATATCTTTTC 57.536 37.500 0.00 0.00 0.00 2.29
4664 5524 9.877178 ATCTCAATACGTTGAAAAGATCTTACT 57.123 29.630 8.75 0.00 43.39 2.24
4849 6005 4.340894 TGAATCGAACTGTAATGCTTGC 57.659 40.909 0.00 0.00 0.00 4.01
5080 6238 6.555315 CAGTGGATACCTTTGCATAAAGAAC 58.445 40.000 0.00 0.00 44.87 3.01
5101 6259 4.722700 TGGCCTGGAGCTTTCCGC 62.723 66.667 3.32 0.00 43.05 5.54
5152 6310 7.202016 TGAGACAACATACTTCAAACCATTC 57.798 36.000 0.00 0.00 0.00 2.67
5240 6398 7.060383 TGGCCAAAACTTCTTCATAATTGAA 57.940 32.000 0.61 0.00 39.54 2.69
5265 6423 8.877864 AGAGGATTGATAGTAGTCTGGAATAG 57.122 38.462 0.00 0.00 0.00 1.73
5291 6449 8.585471 AAATGTGATCCAGAATTACATGTTCT 57.415 30.769 2.30 0.00 42.13 3.01
5346 6506 2.308570 AGATGGTTACCATTGGCTGACA 59.691 45.455 18.78 0.00 45.26 3.58
5427 6587 7.156876 TCACGCTTCCTTGAATTGAAATTAT 57.843 32.000 0.00 0.00 0.00 1.28
5475 6639 7.838079 AGCTGCAAATATTTGACCCATATTA 57.162 32.000 28.33 4.92 40.55 0.98
5493 6657 7.669722 CCCATATTATAAAACTGTAGTGGGCAT 59.330 37.037 0.00 0.00 36.48 4.40
5918 7091 1.065636 TCTTGCCCTGCTGATCTGAAG 60.066 52.381 3.42 1.87 0.00 3.02
6359 7532 6.926826 TGTAGCACGTCTCATTTTCTTTCTTA 59.073 34.615 0.00 0.00 0.00 2.10
6385 7561 4.058817 CGGGTGCTAAATACAGAGAATCC 58.941 47.826 0.00 0.00 33.66 3.01
6432 7608 6.779049 CCTCATGATTCCCCTGATTTATTCAA 59.221 38.462 0.00 0.00 32.78 2.69
6763 8394 0.678395 TGGCGCCAAATGTTGATGTT 59.322 45.000 30.74 0.00 0.00 2.71
6795 8445 0.041238 AGGTCGATGGAGTGAGGGAA 59.959 55.000 0.00 0.00 0.00 3.97
6876 8532 0.037734 TCTAGAGTGAGGTCGCACCA 59.962 55.000 7.86 0.00 41.95 4.17
6918 8574 4.202121 GGAGATGGTCTTGCGATGTAAGTA 60.202 45.833 0.00 0.00 0.00 2.24
6944 8600 0.461516 CGTGCTCAGCCTGTCATGAT 60.462 55.000 0.00 0.00 0.00 2.45
6948 8604 2.092592 TGCTCAGCCTGTCATGATGAAT 60.093 45.455 0.00 0.00 0.00 2.57
6951 8607 4.760715 GCTCAGCCTGTCATGATGAATAAT 59.239 41.667 0.00 0.00 0.00 1.28
7087 8743 4.760047 CCGTGGGCGAGGAACCTG 62.760 72.222 0.00 0.00 41.33 4.00
7088 8744 4.003788 CGTGGGCGAGGAACCTGT 62.004 66.667 0.00 0.00 41.33 4.00
7089 8745 2.047179 GTGGGCGAGGAACCTGTC 60.047 66.667 0.00 0.00 0.00 3.51
7090 8746 2.525629 TGGGCGAGGAACCTGTCA 60.526 61.111 0.00 0.00 0.00 3.58
7091 8747 1.918293 TGGGCGAGGAACCTGTCAT 60.918 57.895 0.00 0.00 0.00 3.06
7092 8748 1.153349 GGGCGAGGAACCTGTCATC 60.153 63.158 0.00 0.00 33.56 2.92
7096 8752 1.153349 GAGGAACCTGTCATCGGGC 60.153 63.158 0.00 0.00 43.58 6.13
7097 8753 2.511600 GGAACCTGTCATCGGGCG 60.512 66.667 0.00 0.00 43.58 6.13
7098 8754 3.195698 GAACCTGTCATCGGGCGC 61.196 66.667 0.00 0.00 43.58 6.53
7099 8755 3.665675 GAACCTGTCATCGGGCGCT 62.666 63.158 7.64 0.00 43.58 5.92
7100 8756 3.254024 AACCTGTCATCGGGCGCTT 62.254 57.895 7.64 0.00 43.58 4.68
7101 8757 3.197790 CCTGTCATCGGGCGCTTG 61.198 66.667 7.64 0.00 32.93 4.01
7102 8758 2.125552 CTGTCATCGGGCGCTTGA 60.126 61.111 7.64 5.89 0.00 3.02
7103 8759 2.434185 TGTCATCGGGCGCTTGAC 60.434 61.111 20.02 20.02 40.10 3.18
7104 8760 3.195698 GTCATCGGGCGCTTGACC 61.196 66.667 17.55 0.00 37.46 4.02
7105 8761 3.390521 TCATCGGGCGCTTGACCT 61.391 61.111 7.64 0.00 39.40 3.85
7106 8762 2.436646 CATCGGGCGCTTGACCTT 60.437 61.111 7.64 0.00 39.40 3.50
7107 8763 2.436646 ATCGGGCGCTTGACCTTG 60.437 61.111 7.64 0.00 39.40 3.61
7108 8764 2.954684 ATCGGGCGCTTGACCTTGA 61.955 57.895 7.64 0.00 39.40 3.02
7109 8765 2.257409 ATCGGGCGCTTGACCTTGAT 62.257 55.000 7.64 0.00 39.40 2.57
7110 8766 1.153449 CGGGCGCTTGACCTTGATA 60.153 57.895 7.64 0.00 39.40 2.15
7111 8767 1.154205 CGGGCGCTTGACCTTGATAG 61.154 60.000 7.64 0.00 39.40 2.08
7122 8778 2.267174 CCTTGATAGGTGCCATGGAG 57.733 55.000 18.40 0.00 36.74 3.86
7123 8779 1.602311 CTTGATAGGTGCCATGGAGC 58.398 55.000 18.40 10.53 0.00 4.70
7124 8780 1.142465 CTTGATAGGTGCCATGGAGCT 59.858 52.381 18.40 17.22 0.00 4.09
7125 8781 0.761187 TGATAGGTGCCATGGAGCTC 59.239 55.000 18.40 4.71 0.00 4.09
7126 8782 0.036022 GATAGGTGCCATGGAGCTCC 59.964 60.000 26.78 26.78 44.92 4.70
7147 8803 5.815233 CCAGATATACCTGGTGTTGAGAT 57.185 43.478 10.23 0.00 46.62 2.75
7148 8804 5.788450 CCAGATATACCTGGTGTTGAGATC 58.212 45.833 10.23 1.62 46.62 2.75
7149 8805 5.305386 CCAGATATACCTGGTGTTGAGATCA 59.695 44.000 10.23 0.00 46.62 2.92
7150 8806 6.183361 CCAGATATACCTGGTGTTGAGATCAA 60.183 42.308 10.23 0.00 46.62 2.57
7151 8807 7.448420 CAGATATACCTGGTGTTGAGATCAAT 58.552 38.462 10.23 0.00 38.24 2.57
7152 8808 7.601886 CAGATATACCTGGTGTTGAGATCAATC 59.398 40.741 10.23 0.26 38.24 2.67
7153 8809 5.965033 ATACCTGGTGTTGAGATCAATCT 57.035 39.130 10.23 0.00 40.50 2.40
7162 8818 2.126914 GAGATCAATCTCGTGGTCGG 57.873 55.000 4.34 0.00 43.29 4.79
7163 8819 1.676529 GAGATCAATCTCGTGGTCGGA 59.323 52.381 4.34 0.00 43.29 4.55
7164 8820 1.678627 AGATCAATCTCGTGGTCGGAG 59.321 52.381 0.00 0.00 33.60 4.63
7165 8821 0.747255 ATCAATCTCGTGGTCGGAGG 59.253 55.000 0.00 0.00 37.69 4.30
7166 8822 0.323087 TCAATCTCGTGGTCGGAGGA 60.323 55.000 0.00 0.00 37.69 3.71
7167 8823 0.747255 CAATCTCGTGGTCGGAGGAT 59.253 55.000 0.00 0.00 37.69 3.24
7168 8824 1.954382 CAATCTCGTGGTCGGAGGATA 59.046 52.381 0.00 0.00 37.69 2.59
7169 8825 1.898902 ATCTCGTGGTCGGAGGATAG 58.101 55.000 0.00 0.00 37.69 2.08
7170 8826 0.818445 TCTCGTGGTCGGAGGATAGC 60.818 60.000 0.00 0.00 37.69 2.97
7171 8827 1.077285 TCGTGGTCGGAGGATAGCA 60.077 57.895 0.00 0.00 37.69 3.49
7172 8828 1.101635 TCGTGGTCGGAGGATAGCAG 61.102 60.000 0.00 0.00 37.69 4.24
7173 8829 1.384989 CGTGGTCGGAGGATAGCAGT 61.385 60.000 0.00 0.00 0.00 4.40
7174 8830 0.103208 GTGGTCGGAGGATAGCAGTG 59.897 60.000 0.00 0.00 0.00 3.66
7175 8831 0.033503 TGGTCGGAGGATAGCAGTGA 60.034 55.000 0.00 0.00 0.00 3.41
7176 8832 0.671251 GGTCGGAGGATAGCAGTGAG 59.329 60.000 0.00 0.00 0.00 3.51
7177 8833 1.394618 GTCGGAGGATAGCAGTGAGT 58.605 55.000 0.00 0.00 0.00 3.41
7178 8834 2.573369 GTCGGAGGATAGCAGTGAGTA 58.427 52.381 0.00 0.00 0.00 2.59
7179 8835 2.550606 GTCGGAGGATAGCAGTGAGTAG 59.449 54.545 0.00 0.00 0.00 2.57
7180 8836 1.883275 CGGAGGATAGCAGTGAGTAGG 59.117 57.143 0.00 0.00 0.00 3.18
7181 8837 2.750135 CGGAGGATAGCAGTGAGTAGGT 60.750 54.545 0.00 0.00 0.00 3.08
7182 8838 2.625790 GGAGGATAGCAGTGAGTAGGTG 59.374 54.545 0.00 0.00 0.00 4.00
7183 8839 2.035321 GAGGATAGCAGTGAGTAGGTGC 59.965 54.545 0.00 0.00 37.48 5.01
7184 8840 1.757118 GGATAGCAGTGAGTAGGTGCA 59.243 52.381 0.00 0.00 39.80 4.57
7185 8841 2.482142 GGATAGCAGTGAGTAGGTGCAC 60.482 54.545 8.80 8.80 39.80 4.57
7186 8842 0.895530 TAGCAGTGAGTAGGTGCACC 59.104 55.000 29.22 29.22 39.80 5.01
7188 8844 0.390472 GCAGTGAGTAGGTGCACCTC 60.390 60.000 41.00 29.41 44.77 3.85
7189 8845 0.109086 CAGTGAGTAGGTGCACCTCG 60.109 60.000 41.00 17.86 44.77 4.63
7190 8846 0.251209 AGTGAGTAGGTGCACCTCGA 60.251 55.000 41.00 23.27 44.77 4.04
7191 8847 0.171455 GTGAGTAGGTGCACCTCGAG 59.829 60.000 41.00 5.13 44.77 4.04
7192 8848 0.965866 TGAGTAGGTGCACCTCGAGG 60.966 60.000 41.00 30.11 44.77 4.63
7193 8849 0.680280 GAGTAGGTGCACCTCGAGGA 60.680 60.000 41.00 21.63 44.77 3.71
7194 8850 0.681564 AGTAGGTGCACCTCGAGGAG 60.682 60.000 41.00 30.15 44.77 3.69
7195 8851 0.680280 GTAGGTGCACCTCGAGGAGA 60.680 60.000 41.00 20.02 44.77 3.71
7196 8852 0.039180 TAGGTGCACCTCGAGGAGAA 59.961 55.000 41.00 22.88 44.77 2.87
7197 8853 1.079750 GGTGCACCTCGAGGAGAAC 60.080 63.158 37.69 31.98 38.94 3.01
7198 8854 1.444553 GTGCACCTCGAGGAGAACG 60.445 63.158 37.69 19.37 38.94 3.95
7199 8855 1.602605 TGCACCTCGAGGAGAACGA 60.603 57.895 37.69 11.85 38.94 3.85
7204 8860 3.906718 TCGAGGAGAACGAGGAGC 58.093 61.111 0.00 0.00 34.85 4.70
7205 8861 1.749638 TCGAGGAGAACGAGGAGCC 60.750 63.158 0.00 0.00 34.85 4.70
7206 8862 2.802106 GAGGAGAACGAGGAGCCG 59.198 66.667 0.00 0.00 0.00 5.52
7207 8863 2.035940 AGGAGAACGAGGAGCCGT 59.964 61.111 0.00 0.00 45.64 5.68
7208 8864 2.182030 GGAGAACGAGGAGCCGTG 59.818 66.667 0.00 0.00 42.54 4.94
7209 8865 2.182030 GAGAACGAGGAGCCGTGG 59.818 66.667 0.00 0.00 42.54 4.94
7210 8866 3.358076 GAGAACGAGGAGCCGTGGG 62.358 68.421 0.00 0.00 42.54 4.61
7224 8880 2.525629 TGGGCGAGGAACCTGTCA 60.526 61.111 0.00 0.00 0.00 3.58
7296 8952 4.320788 GCAAGCTCTACAGAAGCAACATTT 60.321 41.667 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.872431 GGGTATCCCCGACCTCTG 58.128 66.667 0.00 0.00 42.41 3.35
27 28 6.575162 AGATCGGCAGTTTGACTAATTTTT 57.425 33.333 0.00 0.00 0.00 1.94
28 29 7.148239 CCTTAGATCGGCAGTTTGACTAATTTT 60.148 37.037 0.00 0.00 0.00 1.82
29 30 6.316390 CCTTAGATCGGCAGTTTGACTAATTT 59.684 38.462 0.00 0.00 0.00 1.82
30 31 5.817816 CCTTAGATCGGCAGTTTGACTAATT 59.182 40.000 0.00 0.00 0.00 1.40
33 34 4.021229 TCCTTAGATCGGCAGTTTGACTA 58.979 43.478 0.00 0.00 0.00 2.59
41 42 5.360999 TCCACATATATCCTTAGATCGGCAG 59.639 44.000 0.00 0.00 33.67 4.85
58 59 5.423704 TTCCGATTTGTAAGGTCCACATA 57.576 39.130 0.00 0.00 0.00 2.29
84 85 2.526046 CCCGGGGAAACACTCACCT 61.526 63.158 14.71 0.00 46.85 4.00
132 133 2.572104 GACTGGTTCCACCACCTAGATT 59.428 50.000 0.00 0.00 44.79 2.40
137 138 0.399949 TCTGACTGGTTCCACCACCT 60.400 55.000 0.00 0.00 44.79 4.00
214 216 8.884124 TCTCCTTCCACTGAATGAATATTTTT 57.116 30.769 0.00 0.00 0.00 1.94
223 225 5.925397 CGAGAATATCTCCTTCCACTGAATG 59.075 44.000 1.98 0.00 40.34 2.67
233 235 7.608376 TCTCATAATCGACGAGAATATCTCCTT 59.392 37.037 3.01 0.00 40.34 3.36
252 254 8.716646 ATAACATCATCACAAACGTCTCATAA 57.283 30.769 0.00 0.00 0.00 1.90
275 277 7.536964 CACGCACACAACATTTTTAGATTGATA 59.463 33.333 0.00 0.00 0.00 2.15
368 372 9.617523 AATCACTCACCAATTTCTCAAATTTTT 57.382 25.926 0.00 0.00 38.97 1.94
373 377 6.713762 ACAATCACTCACCAATTTCTCAAA 57.286 33.333 0.00 0.00 0.00 2.69
374 378 6.713762 AACAATCACTCACCAATTTCTCAA 57.286 33.333 0.00 0.00 0.00 3.02
416 420 0.603569 TTCTGAGACGGAAGGAGCAC 59.396 55.000 0.00 0.00 0.00 4.40
418 422 3.131400 ACTTATTCTGAGACGGAAGGAGC 59.869 47.826 0.00 0.00 31.92 4.70
419 423 4.399618 TCACTTATTCTGAGACGGAAGGAG 59.600 45.833 0.00 0.00 31.92 3.69
420 424 4.341487 TCACTTATTCTGAGACGGAAGGA 58.659 43.478 0.00 0.00 31.92 3.36
421 425 4.720649 TCACTTATTCTGAGACGGAAGG 57.279 45.455 0.00 0.00 31.92 3.46
422 426 5.655488 ACATCACTTATTCTGAGACGGAAG 58.345 41.667 0.00 0.00 31.92 3.46
423 427 5.661056 ACATCACTTATTCTGAGACGGAA 57.339 39.130 0.00 0.00 33.01 4.30
424 428 5.650703 TGTACATCACTTATTCTGAGACGGA 59.349 40.000 0.00 0.00 0.00 4.69
425 429 5.891451 TGTACATCACTTATTCTGAGACGG 58.109 41.667 0.00 0.00 0.00 4.79
426 430 7.542477 ACTTTGTACATCACTTATTCTGAGACG 59.458 37.037 0.00 0.00 0.00 4.18
427 431 8.764524 ACTTTGTACATCACTTATTCTGAGAC 57.235 34.615 0.00 0.00 0.00 3.36
428 432 9.208022 CAACTTTGTACATCACTTATTCTGAGA 57.792 33.333 0.00 0.00 0.00 3.27
429 433 9.208022 TCAACTTTGTACATCACTTATTCTGAG 57.792 33.333 0.00 0.00 0.00 3.35
430 434 9.554395 TTCAACTTTGTACATCACTTATTCTGA 57.446 29.630 0.00 0.00 0.00 3.27
435 439 9.507329 AGTGATTCAACTTTGTACATCACTTAT 57.493 29.630 15.40 0.00 42.22 1.73
436 440 8.902540 AGTGATTCAACTTTGTACATCACTTA 57.097 30.769 15.40 0.00 42.22 2.24
437 441 7.807977 AGTGATTCAACTTTGTACATCACTT 57.192 32.000 15.40 4.35 42.22 3.16
438 442 7.807977 AAGTGATTCAACTTTGTACATCACT 57.192 32.000 15.40 15.40 44.12 3.41
448 452 9.893305 CCGTTCTAAAATAAGTGATTCAACTTT 57.107 29.630 6.76 0.00 40.77 2.66
449 453 9.280174 TCCGTTCTAAAATAAGTGATTCAACTT 57.720 29.630 0.00 0.00 42.89 2.66
450 454 8.842358 TCCGTTCTAAAATAAGTGATTCAACT 57.158 30.769 0.00 0.00 0.00 3.16
451 455 8.932791 TCTCCGTTCTAAAATAAGTGATTCAAC 58.067 33.333 0.00 0.00 0.00 3.18
452 456 9.496873 TTCTCCGTTCTAAAATAAGTGATTCAA 57.503 29.630 0.00 0.00 0.00 2.69
453 457 9.496873 TTTCTCCGTTCTAAAATAAGTGATTCA 57.503 29.630 0.00 0.00 0.00 2.57
454 458 9.974750 CTTTCTCCGTTCTAAAATAAGTGATTC 57.025 33.333 0.00 0.00 0.00 2.52
455 459 9.503399 ACTTTCTCCGTTCTAAAATAAGTGATT 57.497 29.630 0.00 0.00 0.00 2.57
457 461 9.415544 GTACTTTCTCCGTTCTAAAATAAGTGA 57.584 33.333 0.00 0.00 0.00 3.41
458 462 9.199982 TGTACTTTCTCCGTTCTAAAATAAGTG 57.800 33.333 0.00 0.00 0.00 3.16
459 463 9.939802 ATGTACTTTCTCCGTTCTAAAATAAGT 57.060 29.630 0.00 0.00 0.00 2.24
462 466 8.662141 GCAATGTACTTTCTCCGTTCTAAAATA 58.338 33.333 0.00 0.00 0.00 1.40
463 467 7.174253 TGCAATGTACTTTCTCCGTTCTAAAAT 59.826 33.333 0.00 0.00 0.00 1.82
464 468 6.483974 TGCAATGTACTTTCTCCGTTCTAAAA 59.516 34.615 0.00 0.00 0.00 1.52
465 469 5.992829 TGCAATGTACTTTCTCCGTTCTAAA 59.007 36.000 0.00 0.00 0.00 1.85
466 470 5.543714 TGCAATGTACTTTCTCCGTTCTAA 58.456 37.500 0.00 0.00 0.00 2.10
467 471 5.142061 TGCAATGTACTTTCTCCGTTCTA 57.858 39.130 0.00 0.00 0.00 2.10
468 472 4.002906 TGCAATGTACTTTCTCCGTTCT 57.997 40.909 0.00 0.00 0.00 3.01
469 473 4.742438 TTGCAATGTACTTTCTCCGTTC 57.258 40.909 0.00 0.00 0.00 3.95
470 474 5.616866 CGAATTGCAATGTACTTTCTCCGTT 60.617 40.000 13.82 0.00 0.00 4.44
471 475 4.142902 CGAATTGCAATGTACTTTCTCCGT 60.143 41.667 13.82 0.00 0.00 4.69
472 476 4.142902 ACGAATTGCAATGTACTTTCTCCG 60.143 41.667 13.82 6.60 0.00 4.63
473 477 5.296813 ACGAATTGCAATGTACTTTCTCC 57.703 39.130 13.82 0.00 0.00 3.71
474 478 7.623268 AAAACGAATTGCAATGTACTTTCTC 57.377 32.000 13.82 3.04 0.00 2.87
475 479 9.522804 TTTAAAACGAATTGCAATGTACTTTCT 57.477 25.926 13.82 0.00 0.00 2.52
479 483 9.255304 ACAATTTAAAACGAATTGCAATGTACT 57.745 25.926 13.82 0.00 44.42 2.73
480 484 9.856803 AACAATTTAAAACGAATTGCAATGTAC 57.143 25.926 13.82 7.05 44.42 2.90
502 506 5.570234 AGTAGTTTTTGCGGAAAGAACAA 57.430 34.783 20.43 5.52 0.00 2.83
512 516 3.285745 GTGGTTTCGAGTAGTTTTTGCG 58.714 45.455 0.00 0.00 0.00 4.85
517 521 1.688197 TCCGGTGGTTTCGAGTAGTTT 59.312 47.619 0.00 0.00 0.00 2.66
523 527 0.389426 AATCGTCCGGTGGTTTCGAG 60.389 55.000 0.00 0.00 34.20 4.04
543 547 3.349808 TTTGCATCGCCGTTCGCA 61.350 55.556 0.00 0.00 37.30 5.10
588 592 5.473504 ACCATTGGAACAGAACAGAACATAC 59.526 40.000 10.37 0.00 42.39 2.39
589 593 5.473162 CACCATTGGAACAGAACAGAACATA 59.527 40.000 10.37 0.00 42.39 2.29
590 594 4.279169 CACCATTGGAACAGAACAGAACAT 59.721 41.667 10.37 0.00 42.39 2.71
591 595 3.631686 CACCATTGGAACAGAACAGAACA 59.368 43.478 10.37 0.00 42.39 3.18
592 596 4.228912 CACCATTGGAACAGAACAGAAC 57.771 45.455 10.37 0.00 42.39 3.01
872 915 2.891941 TAAATCAGCAGGCAGGCGGG 62.892 60.000 0.00 0.00 39.27 6.13
1098 1158 3.848391 GAGCGGCGATCGAGACGAG 62.848 68.421 21.57 11.04 39.91 4.18
1269 1329 2.250741 GAGAGGAGACAAGGGCCTGC 62.251 65.000 6.92 0.00 30.70 4.85
1386 1446 4.322049 GGATCACAACTAGCCGCATACTAT 60.322 45.833 0.00 0.00 0.00 2.12
1390 1450 1.760029 TGGATCACAACTAGCCGCATA 59.240 47.619 0.00 0.00 0.00 3.14
1397 1457 3.553096 GGGTAGCGATGGATCACAACTAG 60.553 52.174 0.00 0.00 0.00 2.57
1398 1458 2.364324 GGGTAGCGATGGATCACAACTA 59.636 50.000 0.00 0.00 0.00 2.24
1399 1459 1.139058 GGGTAGCGATGGATCACAACT 59.861 52.381 0.00 0.00 0.00 3.16
1400 1460 1.134521 TGGGTAGCGATGGATCACAAC 60.135 52.381 0.00 0.00 0.00 3.32
1401 1461 1.134521 GTGGGTAGCGATGGATCACAA 60.135 52.381 0.00 0.00 0.00 3.33
1551 1614 0.242825 TTCAACTCGGCGGTCAGTAG 59.757 55.000 7.21 0.00 0.00 2.57
1758 1821 4.763793 CCTTTGTGACATCAAGGTTCTCAT 59.236 41.667 7.70 0.00 0.00 2.90
1971 2034 3.759581 CTCATTCCCCTCCCAATACATG 58.240 50.000 0.00 0.00 0.00 3.21
2063 2126 6.151691 ACATGTTACATGCAGTTGTTTCATC 58.848 36.000 23.43 0.00 0.00 2.92
2064 2127 6.088016 ACATGTTACATGCAGTTGTTTCAT 57.912 33.333 23.43 2.11 0.00 2.57
2073 2136 3.943381 ACATCAGGACATGTTACATGCAG 59.057 43.478 23.43 11.74 32.81 4.41
2115 2178 1.211457 TGCAACAAAGCACCCCAAAAT 59.789 42.857 0.00 0.00 40.11 1.82
2122 2185 1.300388 CCAGCTGCAACAAAGCACC 60.300 57.895 8.66 0.00 43.37 5.01
2123 2186 1.952635 GCCAGCTGCAACAAAGCAC 60.953 57.895 8.66 0.00 43.37 4.40
2163 2226 3.068590 CCACAGCATCACCTTTTTCAACT 59.931 43.478 0.00 0.00 0.00 3.16
2253 2316 3.746940 TGGGGTAAAACTTACAGAGTGC 58.253 45.455 0.00 0.00 39.00 4.40
2292 2355 8.426489 TGGTAACATGTATAGGGTAAATCAGAC 58.574 37.037 0.00 0.00 46.17 3.51
2347 2411 1.856265 CGGAGAAGCCAGCAAACACC 61.856 60.000 0.00 0.00 35.94 4.16
2368 2432 1.679139 TCCTTTGGGCTATTGCATCG 58.321 50.000 0.66 0.00 41.91 3.84
2610 2674 6.721318 AGTGTGGACATATGTAGGTGAAAAT 58.279 36.000 8.71 0.00 0.00 1.82
2656 2720 5.412526 TTTTCGGATACAAATGCGGTATC 57.587 39.130 0.00 0.00 45.92 2.24
2686 2750 7.362920 GGAATTCAAATTGCACCTATGTACACT 60.363 37.037 7.93 0.00 36.81 3.55
2792 2858 9.974980 TTTTTATTGTAGGAAAGAAATGGACAC 57.025 29.630 0.00 0.00 0.00 3.67
2853 2998 0.249398 GCCGCAGAGAGTTTTAGGGA 59.751 55.000 0.00 0.00 0.00 4.20
2933 3078 7.343057 ACTTCTGAGTTTGGAAAAAGGAAATCT 59.657 33.333 0.00 0.00 29.87 2.40
2941 3086 7.392113 TCAGTTACACTTCTGAGTTTGGAAAAA 59.608 33.333 0.00 0.00 36.04 1.94
2976 3121 2.785679 GCGCACATCTGGTAATTTCAC 58.214 47.619 0.30 0.00 0.00 3.18
3150 3296 7.651304 CCATGATCAAGAGTATACTGACACTTC 59.349 40.741 10.90 1.25 29.13 3.01
3867 4019 6.896883 ACAGGGAAACTACAGTAAGAAAACT 58.103 36.000 0.00 0.00 0.00 2.66
4104 4486 3.071874 TGGAGCCTACAAGTTCCATTG 57.928 47.619 0.00 0.00 34.90 2.82
4466 5265 9.073475 GATATATGTGTGGGGCAAAATTAACTA 57.927 33.333 0.00 0.00 0.00 2.24
4664 5524 4.041567 ACCACCTGACATGAACAATAGTGA 59.958 41.667 0.00 0.00 0.00 3.41
4849 6005 7.549488 CCAGGTAAAGGTGTAATCTAACAAGAG 59.451 40.741 0.00 0.00 0.00 2.85
5080 6238 0.750911 GGAAAGCTCCAGGCCATGAG 60.751 60.000 15.30 15.30 41.96 2.90
5101 6259 5.830457 TCTGTCCTTATCTCCATACAGAGTG 59.170 44.000 0.00 0.00 38.64 3.51
5152 6310 6.166984 TCACCAGAGAAATAATAGCCAGAG 57.833 41.667 0.00 0.00 0.00 3.35
5195 6353 9.566432 TGGCCAAAGTTTAAATAAATGTTTGAT 57.434 25.926 0.61 0.00 35.82 2.57
5240 6398 8.674173 TCTATTCCAGACTACTATCAATCCTCT 58.326 37.037 0.00 0.00 0.00 3.69
5251 6409 7.345653 TGGATCACATTTCTATTCCAGACTACT 59.654 37.037 0.00 0.00 31.12 2.57
5265 6423 8.680903 AGAACATGTAATTCTGGATCACATTTC 58.319 33.333 0.00 2.18 35.06 2.17
5346 6506 6.566079 TTGATAACATCATCCACTCTTCCT 57.434 37.500 0.00 0.00 39.39 3.36
5427 6587 6.909550 TCAAAGCCTTTTAAAGCCATCTAA 57.090 33.333 0.00 0.00 0.00 2.10
5475 6639 3.199071 TCCGATGCCCACTACAGTTTTAT 59.801 43.478 0.00 0.00 0.00 1.40
5493 6657 0.824109 CCTCTGCTGTACCAATCCGA 59.176 55.000 0.00 0.00 0.00 4.55
5918 7091 8.497554 TCATTGAAAAAGCACAAGCATTATTTC 58.502 29.630 0.00 0.00 45.49 2.17
6359 7532 2.431057 CTCTGTATTTAGCACCCGAGGT 59.569 50.000 0.00 0.00 35.62 3.85
6385 7561 2.601979 CCATGCGTGGCACATATAAACG 60.602 50.000 19.09 1.65 43.04 3.60
6657 8274 4.626042 AGATACTCTTCGCAACATCATCC 58.374 43.478 0.00 0.00 0.00 3.51
6696 8313 0.927537 TGCTCGTGTCTTTCACAACG 59.072 50.000 0.00 0.00 46.44 4.10
6701 8318 2.416747 CAGGAATGCTCGTGTCTTTCA 58.583 47.619 0.00 0.00 33.61 2.69
6795 8445 1.607467 GTCTGGTTGGGGCTGCAAT 60.607 57.895 0.50 0.00 0.00 3.56
6823 8479 0.544833 TTGCCATTCATTGCCCCTGT 60.545 50.000 0.00 0.00 0.00 4.00
6841 8497 0.892358 TAGAGGACGCGACACACCTT 60.892 55.000 15.93 6.95 32.53 3.50
6876 8532 1.066143 CCTCTGTTACGGCATGTCCTT 60.066 52.381 0.00 0.00 0.00 3.36
6944 8600 6.765036 GTCAAGATCTTCAGCTGGATTATTCA 59.235 38.462 15.13 0.00 0.00 2.57
6948 8604 4.718774 AGGTCAAGATCTTCAGCTGGATTA 59.281 41.667 10.49 0.00 0.00 1.75
6951 8607 2.544721 AGGTCAAGATCTTCAGCTGGA 58.455 47.619 10.49 3.47 0.00 3.86
7077 8733 1.141881 CCCGATGACAGGTTCCTCG 59.858 63.158 0.00 0.00 40.85 4.63
7078 8734 1.153349 GCCCGATGACAGGTTCCTC 60.153 63.158 0.00 0.00 0.00 3.71
7079 8735 2.990479 GCCCGATGACAGGTTCCT 59.010 61.111 0.00 0.00 0.00 3.36
7080 8736 2.511600 CGCCCGATGACAGGTTCC 60.512 66.667 0.00 0.00 0.00 3.62
7081 8737 3.195698 GCGCCCGATGACAGGTTC 61.196 66.667 0.00 0.00 0.00 3.62
7082 8738 3.254024 AAGCGCCCGATGACAGGTT 62.254 57.895 2.29 0.00 0.00 3.50
7083 8739 3.706373 AAGCGCCCGATGACAGGT 61.706 61.111 2.29 0.00 0.00 4.00
7084 8740 3.197790 CAAGCGCCCGATGACAGG 61.198 66.667 2.29 0.00 0.00 4.00
7085 8741 2.125552 TCAAGCGCCCGATGACAG 60.126 61.111 2.29 0.00 0.00 3.51
7086 8742 2.434185 GTCAAGCGCCCGATGACA 60.434 61.111 21.19 0.00 42.31 3.58
7087 8743 3.195698 GGTCAAGCGCCCGATGAC 61.196 66.667 19.13 19.13 42.08 3.06
7088 8744 2.954684 AAGGTCAAGCGCCCGATGA 61.955 57.895 2.29 0.48 0.00 2.92
7089 8745 2.436646 AAGGTCAAGCGCCCGATG 60.437 61.111 2.29 0.00 0.00 3.84
7090 8746 2.257409 ATCAAGGTCAAGCGCCCGAT 62.257 55.000 2.29 0.00 0.00 4.18
7091 8747 1.609635 TATCAAGGTCAAGCGCCCGA 61.610 55.000 2.29 0.00 0.00 5.14
7092 8748 1.153449 TATCAAGGTCAAGCGCCCG 60.153 57.895 2.29 0.00 0.00 6.13
7093 8749 0.815615 CCTATCAAGGTCAAGCGCCC 60.816 60.000 2.29 0.00 38.19 6.13
7094 8750 2.695314 CCTATCAAGGTCAAGCGCC 58.305 57.895 2.29 0.00 38.19 6.53
7104 8760 1.142465 AGCTCCATGGCACCTATCAAG 59.858 52.381 6.96 0.00 34.17 3.02
7105 8761 1.141657 GAGCTCCATGGCACCTATCAA 59.858 52.381 6.96 0.00 34.17 2.57
7106 8762 0.761187 GAGCTCCATGGCACCTATCA 59.239 55.000 6.96 0.00 34.17 2.15
7107 8763 0.036022 GGAGCTCCATGGCACCTATC 59.964 60.000 28.43 0.00 39.33 2.08
7108 8764 0.695462 TGGAGCTCCATGGCACCTAT 60.695 55.000 32.00 0.00 42.01 2.57
7109 8765 1.306911 TGGAGCTCCATGGCACCTA 60.307 57.895 32.00 5.33 42.01 3.08
7110 8766 2.611800 TGGAGCTCCATGGCACCT 60.612 61.111 32.00 2.30 42.01 4.00
7111 8767 1.992519 ATCTGGAGCTCCATGGCACC 61.993 60.000 35.11 6.37 46.46 5.01
7112 8768 0.761187 TATCTGGAGCTCCATGGCAC 59.239 55.000 35.11 6.42 46.46 5.01
7113 8769 1.738474 ATATCTGGAGCTCCATGGCA 58.262 50.000 35.11 20.30 46.46 4.92
7114 8770 2.093235 GGTATATCTGGAGCTCCATGGC 60.093 54.545 35.11 20.18 46.46 4.40
7115 8771 3.197333 CAGGTATATCTGGAGCTCCATGG 59.803 52.174 35.11 24.20 46.46 3.66
7116 8772 4.468765 CAGGTATATCTGGAGCTCCATG 57.531 50.000 35.11 26.46 46.46 3.66
7126 8782 6.410942 TGATCTCAACACCAGGTATATCTG 57.589 41.667 5.98 5.98 34.70 2.90
7127 8783 7.512058 AGATTGATCTCAACACCAGGTATATCT 59.488 37.037 0.00 0.00 38.86 1.98
7128 8784 7.675062 AGATTGATCTCAACACCAGGTATATC 58.325 38.462 0.00 0.00 38.86 1.63
7129 8785 7.623999 AGATTGATCTCAACACCAGGTATAT 57.376 36.000 0.00 0.00 38.86 0.86
7131 8787 5.965033 AGATTGATCTCAACACCAGGTAT 57.035 39.130 0.00 0.00 38.86 2.73
7144 8800 1.678627 CTCCGACCACGAGATTGATCT 59.321 52.381 0.00 0.00 42.66 2.75
7145 8801 1.269309 CCTCCGACCACGAGATTGATC 60.269 57.143 0.00 0.00 42.66 2.92
7146 8802 0.747255 CCTCCGACCACGAGATTGAT 59.253 55.000 0.00 0.00 42.66 2.57
7147 8803 0.323087 TCCTCCGACCACGAGATTGA 60.323 55.000 0.00 0.00 42.66 2.57
7148 8804 0.747255 ATCCTCCGACCACGAGATTG 59.253 55.000 0.00 0.00 42.66 2.67
7149 8805 2.231529 CTATCCTCCGACCACGAGATT 58.768 52.381 0.00 0.00 42.66 2.40
7150 8806 1.898902 CTATCCTCCGACCACGAGAT 58.101 55.000 0.00 0.00 42.66 2.75
7151 8807 0.818445 GCTATCCTCCGACCACGAGA 60.818 60.000 0.00 0.00 42.66 4.04
7152 8808 1.101635 TGCTATCCTCCGACCACGAG 61.102 60.000 0.00 0.00 42.66 4.18
7153 8809 1.077285 TGCTATCCTCCGACCACGA 60.077 57.895 0.00 0.00 42.66 4.35
7154 8810 1.360551 CTGCTATCCTCCGACCACG 59.639 63.158 0.00 0.00 39.43 4.94
7155 8811 0.103208 CACTGCTATCCTCCGACCAC 59.897 60.000 0.00 0.00 0.00 4.16
7156 8812 0.033503 TCACTGCTATCCTCCGACCA 60.034 55.000 0.00 0.00 0.00 4.02
7157 8813 0.671251 CTCACTGCTATCCTCCGACC 59.329 60.000 0.00 0.00 0.00 4.79
7158 8814 1.394618 ACTCACTGCTATCCTCCGAC 58.605 55.000 0.00 0.00 0.00 4.79
7159 8815 2.487445 CCTACTCACTGCTATCCTCCGA 60.487 54.545 0.00 0.00 0.00 4.55
7160 8816 1.883275 CCTACTCACTGCTATCCTCCG 59.117 57.143 0.00 0.00 0.00 4.63
7161 8817 2.625790 CACCTACTCACTGCTATCCTCC 59.374 54.545 0.00 0.00 0.00 4.30
7162 8818 2.035321 GCACCTACTCACTGCTATCCTC 59.965 54.545 0.00 0.00 0.00 3.71
7163 8819 2.035632 GCACCTACTCACTGCTATCCT 58.964 52.381 0.00 0.00 0.00 3.24
7164 8820 1.757118 TGCACCTACTCACTGCTATCC 59.243 52.381 0.00 0.00 0.00 2.59
7165 8821 2.482142 GGTGCACCTACTCACTGCTATC 60.482 54.545 29.12 0.00 33.91 2.08
7166 8822 1.482593 GGTGCACCTACTCACTGCTAT 59.517 52.381 29.12 0.00 33.91 2.97
7167 8823 0.895530 GGTGCACCTACTCACTGCTA 59.104 55.000 29.12 0.00 33.91 3.49
7168 8824 0.833834 AGGTGCACCTACTCACTGCT 60.834 55.000 37.12 9.06 46.48 4.24
7169 8825 1.674057 AGGTGCACCTACTCACTGC 59.326 57.895 37.12 5.37 46.48 4.40
7179 8835 1.079750 GTTCTCCTCGAGGTGCACC 60.080 63.158 30.17 29.22 36.34 5.01
7180 8836 1.444553 CGTTCTCCTCGAGGTGCAC 60.445 63.158 30.17 25.43 36.34 4.57
7181 8837 1.602605 TCGTTCTCCTCGAGGTGCA 60.603 57.895 30.17 16.55 36.34 4.57
7182 8838 3.275088 TCGTTCTCCTCGAGGTGC 58.725 61.111 30.17 14.99 36.34 5.01
7187 8843 1.749638 GGCTCCTCGTTCTCCTCGA 60.750 63.158 0.00 0.00 35.96 4.04
7188 8844 2.802106 GGCTCCTCGTTCTCCTCG 59.198 66.667 0.00 0.00 0.00 4.63
7189 8845 2.047443 ACGGCTCCTCGTTCTCCTC 61.047 63.158 0.00 0.00 40.85 3.71
7190 8846 2.035940 ACGGCTCCTCGTTCTCCT 59.964 61.111 0.00 0.00 40.85 3.69
7191 8847 2.182030 CACGGCTCCTCGTTCTCC 59.818 66.667 0.00 0.00 41.86 3.71
7192 8848 2.182030 CCACGGCTCCTCGTTCTC 59.818 66.667 0.00 0.00 41.86 2.87
7193 8849 3.382832 CCCACGGCTCCTCGTTCT 61.383 66.667 0.00 0.00 41.86 3.01
7204 8860 4.760047 CAGGTTCCTCGCCCACGG 62.760 72.222 0.00 0.00 40.63 4.94
7205 8861 3.934391 GACAGGTTCCTCGCCCACG 62.934 68.421 0.00 0.00 42.01 4.94
7206 8862 2.047179 GACAGGTTCCTCGCCCAC 60.047 66.667 0.00 0.00 0.00 4.61
7207 8863 1.899437 GATGACAGGTTCCTCGCCCA 61.899 60.000 0.00 0.00 0.00 5.36
7208 8864 1.153349 GATGACAGGTTCCTCGCCC 60.153 63.158 0.00 0.00 0.00 6.13
7209 8865 1.519455 CGATGACAGGTTCCTCGCC 60.519 63.158 0.00 0.00 35.88 5.54
7210 8866 1.519455 CCGATGACAGGTTCCTCGC 60.519 63.158 0.00 0.00 40.10 5.03
7253 8909 5.493133 TGCGTCTGTTTTGTCTTTATTGT 57.507 34.783 0.00 0.00 0.00 2.71
7257 8913 3.625764 AGCTTGCGTCTGTTTTGTCTTTA 59.374 39.130 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.