Multiple sequence alignment - TraesCS5B01G310500

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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 TraesCS5B01G310500 chr5B 100.000 3685 0 0 1 3685 492539697 492536013 0.000000e+00 6806.0
1 TraesCS5B01G310500 chr5B 100.000 530 0 0 4027 4556 492535671 492535142 0.000000e+00 979.0
2 TraesCS5B01G310500 chr5D 94.421 1936 59 20 1753 3685 410422101 410420212 0.000000e+00 2931.0
3 TraesCS5B01G310500 chr5D 92.834 628 45 0 1096 1723 410422728 410422101 0.000000e+00 911.0
4 TraesCS5B01G310500 chr5D 92.557 618 35 7 475 1087 410423376 410422765 0.000000e+00 876.0
5 TraesCS5B01G310500 chr5D 94.159 428 20 4 1 427 410423942 410423519 0.000000e+00 647.0
6 TraesCS5B01G310500 chr5D 85.250 400 32 7 4106 4490 410420112 410419725 1.990000e-103 387.0
7 TraesCS5B01G310500 chr5A 95.831 1823 59 10 1804 3625 522058038 522056232 0.000000e+00 2929.0
8 TraesCS5B01G310500 chr5A 92.147 573 42 3 1092 1662 522058678 522058107 0.000000e+00 806.0
9 TraesCS5B01G310500 chr5A 90.845 426 27 6 3 427 522060156 522059742 1.110000e-155 560.0
10 TraesCS5B01G310500 chr5A 87.129 505 34 11 607 1087 522059207 522058710 1.110000e-150 544.0
11 TraesCS5B01G310500 chr5A 97.059 136 4 0 475 610 522059598 522059463 3.550000e-56 230.0
12 TraesCS5B01G310500 chrUn 98.000 50 0 1 438 487 396963090 396963138 8.120000e-13 86.1
13 TraesCS5B01G310500 chr3D 94.545 55 2 1 438 491 280387062 280387116 2.920000e-12 84.2
14 TraesCS5B01G310500 chr3D 94.545 55 2 1 438 491 365000869 365000815 2.920000e-12 84.2
15 TraesCS5B01G310500 chr3D 96.078 51 1 1 435 485 469375566 469375615 1.050000e-11 82.4
16 TraesCS5B01G310500 chr3D 92.727 55 3 1 438 491 13372333 13372387 1.360000e-10 78.7
17 TraesCS5B01G310500 chr2B 94.444 54 2 1 439 491 538373697 538373750 1.050000e-11 82.4
18 TraesCS5B01G310500 chr1A 94.340 53 1 2 438 489 47209938 47209887 3.780000e-11 80.5
19 TraesCS5B01G310500 chr6D 92.727 55 3 1 438 491 408737583 408737529 1.360000e-10 78.7
20 TraesCS5B01G310500 chr4D 97.778 45 1 0 438 482 203639879 203639923 1.360000e-10 78.7


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 TraesCS5B01G310500 chr5B 492535142 492539697 4555 True 3892.5 6806 100.0000 1 4556 2 chr5B.!!$R1 4555
1 TraesCS5B01G310500 chr5D 410419725 410423942 4217 True 1150.4 2931 91.8442 1 4490 5 chr5D.!!$R1 4489
2 TraesCS5B01G310500 chr5A 522056232 522060156 3924 True 1013.8 2929 92.6022 3 3625 5 chr5A.!!$R1 3622

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
286 287 0.602905 GTGCACCTGACTGTACCACC 60.603 60.0 5.22 0.0 0.00 4.61 F
1296 1710 0.174617 TATCGGCTTCACGCATCACA 59.825 50.0 0.00 0.0 41.67 3.58 F
2709 3127 0.034756 TCACCATCAACCAGGACACG 59.965 55.0 0.00 0.0 0.00 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2043 2458 0.037139 GGTGCCACCACATACGTACA 60.037 55.0 9.55 0.0 43.88 2.90 R
2826 3244 0.598680 CTAATCTTGAGGAGCCGCCG 60.599 60.0 0.00 0.0 43.43 6.46 R
4523 4968 0.032952 CCGTCGAAAACAGAGGGACA 59.967 55.0 0.00 0.0 44.02 4.02 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 8.919777 ATACTAAGCTCTTTTAGGTTGTTTGT 57.080 30.769 0.00 0.00 45.40 2.83
68 69 6.763610 ACTTGAAGTTCGTTTTCTTCTCAGAT 59.236 34.615 0.00 0.00 40.20 2.90
84 85 4.040339 TCTCAGATAGTCTGTTTGGTTGCA 59.960 41.667 6.83 0.00 44.58 4.08
178 179 5.961421 TCAATAAAATGGGGTAGGGGAAAAG 59.039 40.000 0.00 0.00 0.00 2.27
179 180 3.935240 AAAATGGGGTAGGGGAAAAGT 57.065 42.857 0.00 0.00 0.00 2.66
286 287 0.602905 GTGCACCTGACTGTACCACC 60.603 60.000 5.22 0.00 0.00 4.61
364 366 3.797451 TTTGTTTGTTTTCGTACCCCC 57.203 42.857 0.00 0.00 0.00 5.40
379 381 4.039488 CGTACCCCCAAGCACTACATTATA 59.961 45.833 0.00 0.00 0.00 0.98
380 382 4.432980 ACCCCCAAGCACTACATTATAC 57.567 45.455 0.00 0.00 0.00 1.47
394 397 7.012327 CACTACATTATACATTGTCAACCCCAG 59.988 40.741 0.00 0.00 0.00 4.45
410 413 2.350522 CCCAGTGGTCGATGAAAGAAG 58.649 52.381 8.74 0.00 0.00 2.85
427 430 5.956068 AAGAAGCATTTCTGAGTTTCTCC 57.044 39.130 0.00 0.00 42.80 3.71
428 431 4.978099 AGAAGCATTTCTGAGTTTCTCCA 58.022 39.130 0.00 0.00 42.04 3.86
429 432 5.002516 AGAAGCATTTCTGAGTTTCTCCAG 58.997 41.667 0.00 0.00 42.04 3.86
430 433 4.363991 AGCATTTCTGAGTTTCTCCAGT 57.636 40.909 0.00 0.00 0.00 4.00
431 434 4.070716 AGCATTTCTGAGTTTCTCCAGTG 58.929 43.478 0.00 0.00 0.00 3.66
432 435 3.190118 GCATTTCTGAGTTTCTCCAGTGG 59.810 47.826 1.40 1.40 0.00 4.00
433 436 3.492102 TTTCTGAGTTTCTCCAGTGGG 57.508 47.619 9.92 0.00 0.00 4.61
434 437 0.687354 TCTGAGTTTCTCCAGTGGGC 59.313 55.000 9.92 0.00 0.00 5.36
435 438 0.689623 CTGAGTTTCTCCAGTGGGCT 59.310 55.000 9.92 0.14 0.00 5.19
436 439 1.902508 CTGAGTTTCTCCAGTGGGCTA 59.097 52.381 9.92 0.00 0.00 3.93
438 441 2.303022 TGAGTTTCTCCAGTGGGCTAAG 59.697 50.000 9.92 0.00 0.00 2.18
440 443 2.303311 AGTTTCTCCAGTGGGCTAAGAC 59.697 50.000 9.92 1.54 0.00 3.01
441 444 2.024176 TTCTCCAGTGGGCTAAGACA 57.976 50.000 9.92 0.00 0.00 3.41
443 446 2.334977 TCTCCAGTGGGCTAAGACAAA 58.665 47.619 9.92 0.00 0.00 2.83
444 447 2.912956 TCTCCAGTGGGCTAAGACAAAT 59.087 45.455 9.92 0.00 0.00 2.32
445 448 3.055094 TCTCCAGTGGGCTAAGACAAATC 60.055 47.826 9.92 0.00 0.00 2.17
446 449 2.912956 TCCAGTGGGCTAAGACAAATCT 59.087 45.455 9.92 0.00 36.42 2.40
449 452 4.878397 CCAGTGGGCTAAGACAAATCTAAG 59.122 45.833 0.00 0.00 33.57 2.18
451 454 5.582665 CAGTGGGCTAAGACAAATCTAAGAC 59.417 44.000 0.00 0.00 33.57 3.01
452 455 5.248477 AGTGGGCTAAGACAAATCTAAGACA 59.752 40.000 0.00 0.00 33.57 3.41
453 456 5.938125 GTGGGCTAAGACAAATCTAAGACAA 59.062 40.000 0.00 0.00 33.57 3.18
454 457 6.092807 GTGGGCTAAGACAAATCTAAGACAAG 59.907 42.308 0.00 0.00 33.57 3.16
455 458 6.013725 TGGGCTAAGACAAATCTAAGACAAGA 60.014 38.462 0.00 0.00 33.57 3.02
456 459 6.879458 GGGCTAAGACAAATCTAAGACAAGAA 59.121 38.462 0.00 0.00 33.57 2.52
458 461 8.951243 GGCTAAGACAAATCTAAGACAAGAATT 58.049 33.333 0.00 0.00 33.57 2.17
462 465 9.971922 AAGACAAATCTAAGACAAGAATTTTGG 57.028 29.630 0.00 0.00 33.04 3.28
463 466 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
465 468 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
466 469 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
467 470 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
468 471 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
469 472 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
470 473 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
471 474 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
472 475 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
473 476 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
490 590 5.297569 AGGGAGTATATTCTTTGCAGGTC 57.702 43.478 0.00 0.00 0.00 3.85
514 614 2.094762 ATCTGTTGCTGGTCGGTTAC 57.905 50.000 0.00 0.00 0.00 2.50
704 1065 4.565022 TGTGCGTATCAAACTTGATCTCA 58.435 39.130 8.19 3.41 44.17 3.27
763 1124 2.183478 ATCAGTTCATCCAACGTGCA 57.817 45.000 0.00 0.00 40.32 4.57
764 1125 1.960417 TCAGTTCATCCAACGTGCAA 58.040 45.000 0.00 0.00 40.32 4.08
1038 1423 3.005578 AGAAACTAACGACAGACCAGGTC 59.994 47.826 12.25 12.25 0.00 3.85
1076 1462 7.396540 AGTATGTGTGGAATTTCCTCATTTC 57.603 36.000 19.96 10.34 41.43 2.17
1087 1473 7.401955 AATTTCCTCATTTCCTGATCAACTC 57.598 36.000 0.00 0.00 32.10 3.01
1088 1474 5.503634 TTCCTCATTTCCTGATCAACTCA 57.496 39.130 0.00 0.00 32.10 3.41
1089 1475 4.836825 TCCTCATTTCCTGATCAACTCAC 58.163 43.478 0.00 0.00 32.10 3.51
1094 1508 7.309621 CCTCATTTCCTGATCAACTCACATTTT 60.310 37.037 0.00 0.00 32.10 1.82
1115 1529 9.941664 CATTTTAGTCCTGATGAAACATCATAC 57.058 33.333 13.54 13.87 0.00 2.39
1124 1538 5.643348 TGATGAAACATCATACGTCTGCTTT 59.357 36.000 9.88 0.00 0.00 3.51
1153 1567 8.358148 TCTTTCAGGTACTACTTCAACTACAAG 58.642 37.037 0.00 0.00 36.02 3.16
1154 1568 6.022163 TCAGGTACTACTTCAACTACAAGC 57.978 41.667 0.00 0.00 36.02 4.01
1183 1597 1.476110 GCAAGGGTGAAGGTGTACACA 60.476 52.381 26.51 3.97 38.57 3.72
1219 1633 1.702299 CAATCACGACCGAAGACGC 59.298 57.895 0.00 0.00 38.29 5.19
1225 1639 2.144680 CGACCGAAGACGCGTTCTC 61.145 63.158 15.53 12.41 38.29 2.87
1260 1674 1.674221 GCTGCTTGACGATGAGGTTCT 60.674 52.381 0.00 0.00 0.00 3.01
1263 1677 4.437239 CTGCTTGACGATGAGGTTCTAAT 58.563 43.478 0.00 0.00 0.00 1.73
1266 1680 6.403049 TGCTTGACGATGAGGTTCTAATTTA 58.597 36.000 0.00 0.00 0.00 1.40
1276 1690 9.279904 GATGAGGTTCTAATTTATCGATAGTCG 57.720 37.037 5.09 0.00 42.10 4.18
1277 1691 8.162878 TGAGGTTCTAATTTATCGATAGTCGT 57.837 34.615 5.09 0.00 41.35 4.34
1291 1705 1.515519 GTCGTATCGGCTTCACGCA 60.516 57.895 0.00 0.00 41.67 5.24
1295 1709 0.577269 GTATCGGCTTCACGCATCAC 59.423 55.000 0.00 0.00 41.67 3.06
1296 1710 0.174617 TATCGGCTTCACGCATCACA 59.825 50.000 0.00 0.00 41.67 3.58
1303 1717 2.476854 GCTTCACGCATCACAAATCTCC 60.477 50.000 0.00 0.00 38.92 3.71
1314 1728 7.322664 GCATCACAAATCTCCCATTTTAAGAA 58.677 34.615 0.00 0.00 0.00 2.52
1325 1739 8.331740 TCTCCCATTTTAAGAAGATCTCATGTT 58.668 33.333 0.00 0.00 0.00 2.71
1326 1740 9.618890 CTCCCATTTTAAGAAGATCTCATGTTA 57.381 33.333 0.00 0.00 0.00 2.41
1369 1784 6.279123 TGAGAAGATAGTGCTGTTCATGATC 58.721 40.000 0.00 0.00 0.00 2.92
1468 1883 4.935578 TCCAGGAGATAACTGAACTGAGA 58.064 43.478 0.00 0.00 38.20 3.27
1579 1994 1.009900 CGATGAGCGTCTCGGGTAC 60.010 63.158 3.08 0.00 32.35 3.34
1594 2009 3.448301 TCGGGTACAAGTTCACGGATTAT 59.552 43.478 1.77 0.00 0.00 1.28
1609 2024 4.248859 CGGATTATTATGTCAGGAGCAGG 58.751 47.826 0.00 0.00 0.00 4.85
1612 2027 2.898729 ATTATGTCAGGAGCAGGTCG 57.101 50.000 0.00 0.00 0.00 4.79
1680 2095 5.538053 TGAGTTAATTGGCCAACATCTTTCA 59.462 36.000 23.27 16.95 0.00 2.69
1682 2097 5.539955 AGTTAATTGGCCAACATCTTTCAGT 59.460 36.000 23.27 2.28 0.00 3.41
1701 2116 6.304356 TCAGTCTTGCTACTTTCACATTTG 57.696 37.500 0.00 0.00 0.00 2.32
1710 2125 7.362662 TGCTACTTTCACATTTGAATCTGAAC 58.637 34.615 0.00 0.00 41.50 3.18
1723 2138 7.528996 TTGAATCTGAACATGAATTCAACCT 57.471 32.000 13.09 0.00 38.12 3.50
1724 2139 7.528996 TGAATCTGAACATGAATTCAACCTT 57.471 32.000 13.09 3.86 38.12 3.50
1725 2140 8.634335 TGAATCTGAACATGAATTCAACCTTA 57.366 30.769 13.09 0.00 38.12 2.69
1726 2141 9.246670 TGAATCTGAACATGAATTCAACCTTAT 57.753 29.630 13.09 0.00 38.12 1.73
1768 2183 4.626604 TGCGAATCATTTCAAATTTGCCTC 59.373 37.500 13.54 1.68 40.21 4.70
1787 2202 7.765695 TGCCTCTGAACTTAAAATCTGAAAT 57.234 32.000 0.00 0.00 0.00 2.17
1862 2277 0.323360 GAGCTGTTGTGGGGGCATTA 60.323 55.000 0.00 0.00 0.00 1.90
1865 2280 1.024271 CTGTTGTGGGGGCATTATCG 58.976 55.000 0.00 0.00 0.00 2.92
1970 2385 5.525378 TCTTCAGTCTTGTGCTTTCTCTTTC 59.475 40.000 0.00 0.00 0.00 2.62
1980 2395 6.119536 TGTGCTTTCTCTTTCCAGTAGAAAA 58.880 36.000 0.00 0.00 43.84 2.29
1990 2405 5.828299 TTCCAGTAGAAAACCACAAACAG 57.172 39.130 0.00 0.00 0.00 3.16
1992 2407 5.123227 TCCAGTAGAAAACCACAAACAGAG 58.877 41.667 0.00 0.00 0.00 3.35
1993 2408 4.261197 CCAGTAGAAAACCACAAACAGAGC 60.261 45.833 0.00 0.00 0.00 4.09
2011 2426 1.526887 AGCGTGATCGTGTTGTTCTTG 59.473 47.619 0.00 0.00 39.49 3.02
2012 2427 1.260561 GCGTGATCGTGTTGTTCTTGT 59.739 47.619 0.00 0.00 39.49 3.16
2013 2428 2.473609 GCGTGATCGTGTTGTTCTTGTA 59.526 45.455 0.00 0.00 39.49 2.41
2014 2429 3.660904 GCGTGATCGTGTTGTTCTTGTAC 60.661 47.826 0.00 0.00 39.49 2.90
2026 2441 6.425721 TGTTGTTCTTGTACTATGTGGCTAAC 59.574 38.462 0.00 0.00 0.00 2.34
2035 2450 8.657074 TGTACTATGTGGCTAACAATGATAAC 57.343 34.615 0.00 0.00 43.61 1.89
2039 2454 9.845740 ACTATGTGGCTAACAATGATAACATAA 57.154 29.630 0.00 0.00 43.61 1.90
2042 2457 8.978874 TGTGGCTAACAATGATAACATAATCT 57.021 30.769 0.00 0.00 35.24 2.40
2043 2458 9.407380 TGTGGCTAACAATGATAACATAATCTT 57.593 29.630 0.00 0.00 35.24 2.40
2044 2459 9.669353 GTGGCTAACAATGATAACATAATCTTG 57.331 33.333 0.00 0.00 35.50 3.02
2045 2460 9.407380 TGGCTAACAATGATAACATAATCTTGT 57.593 29.630 0.00 0.00 35.50 3.16
2070 2485 1.380302 GTGGTGGCACCTGAAGGAT 59.620 57.895 34.69 0.00 39.58 3.24
2074 2489 2.190578 GGCACCTGAAGGATCCCG 59.809 66.667 8.55 0.00 38.94 5.14
2076 2491 1.450312 GCACCTGAAGGATCCCGTG 60.450 63.158 8.55 8.47 38.94 4.94
2709 3127 0.034756 TCACCATCAACCAGGACACG 59.965 55.000 0.00 0.00 0.00 4.49
2754 3172 3.296709 CTGGCTCGCGTACCTGGTT 62.297 63.158 18.40 0.00 0.00 3.67
2783 3201 0.741221 ATCTCGTTCAAAGAGCCGGC 60.741 55.000 21.89 21.89 35.79 6.13
3090 3508 3.134879 TGGAACACGAGCTCGGTT 58.865 55.556 36.93 33.11 44.95 4.44
3135 3553 1.224592 GACGGTGCTCCCCATCAAT 59.775 57.895 0.00 0.00 0.00 2.57
3141 3559 1.148273 GCTCCCCATCAATGCCGTA 59.852 57.895 0.00 0.00 0.00 4.02
3561 3979 1.028905 CGCTCTTCTACTAGCCAGCT 58.971 55.000 0.00 0.00 35.22 4.24
3564 3982 3.482436 GCTCTTCTACTAGCCAGCTAGA 58.518 50.000 28.73 9.79 46.56 2.43
3565 3983 3.502211 GCTCTTCTACTAGCCAGCTAGAG 59.498 52.174 28.73 20.75 46.56 2.43
3566 3984 4.714632 CTCTTCTACTAGCCAGCTAGAGT 58.285 47.826 28.73 15.42 46.56 3.24
3569 3987 1.611491 CTACTAGCCAGCTAGAGTGCC 59.389 57.143 28.73 0.00 46.56 5.01
3570 3988 0.324738 ACTAGCCAGCTAGAGTGCCA 60.325 55.000 28.73 0.00 46.56 4.92
3571 3989 0.388659 CTAGCCAGCTAGAGTGCCAG 59.611 60.000 19.80 0.00 46.56 4.85
3572 3990 1.045350 TAGCCAGCTAGAGTGCCAGG 61.045 60.000 0.00 0.00 33.50 4.45
3575 3993 1.153409 CAGCTAGAGTGCCAGGCAG 60.153 63.158 16.83 3.36 40.08 4.85
3617 4047 2.667137 CACGGTGTGTGTTTTGTGTTT 58.333 42.857 0.00 0.00 43.88 2.83
3618 4048 2.406691 CACGGTGTGTGTTTTGTGTTTG 59.593 45.455 0.00 0.00 43.88 2.93
3619 4049 2.034812 ACGGTGTGTGTTTTGTGTTTGT 59.965 40.909 0.00 0.00 0.00 2.83
3620 4050 2.406691 CGGTGTGTGTTTTGTGTTTGTG 59.593 45.455 0.00 0.00 0.00 3.33
3621 4051 3.385577 GGTGTGTGTTTTGTGTTTGTGT 58.614 40.909 0.00 0.00 0.00 3.72
3622 4052 3.804873 GGTGTGTGTTTTGTGTTTGTGTT 59.195 39.130 0.00 0.00 0.00 3.32
3623 4053 4.318404 GGTGTGTGTTTTGTGTTTGTGTTG 60.318 41.667 0.00 0.00 0.00 3.33
3624 4054 4.268884 GTGTGTGTTTTGTGTTTGTGTTGT 59.731 37.500 0.00 0.00 0.00 3.32
3625 4055 4.870426 TGTGTGTTTTGTGTTTGTGTTGTT 59.130 33.333 0.00 0.00 0.00 2.83
3626 4056 5.351465 TGTGTGTTTTGTGTTTGTGTTGTTT 59.649 32.000 0.00 0.00 0.00 2.83
3627 4057 5.899151 GTGTGTTTTGTGTTTGTGTTGTTTC 59.101 36.000 0.00 0.00 0.00 2.78
3628 4058 5.580691 TGTGTTTTGTGTTTGTGTTGTTTCA 59.419 32.000 0.00 0.00 0.00 2.69
3643 4073 2.942376 TGTTTCATGTTTGTGACTCGCT 59.058 40.909 0.00 0.00 0.00 4.93
3645 4075 4.754618 TGTTTCATGTTTGTGACTCGCTAT 59.245 37.500 0.00 0.00 0.00 2.97
3650 4080 4.245845 TGTTTGTGACTCGCTATGTGTA 57.754 40.909 0.00 0.00 0.00 2.90
3651 4081 3.985279 TGTTTGTGACTCGCTATGTGTAC 59.015 43.478 0.00 0.00 0.00 2.90
3659 4089 0.795358 CGCTATGTGTACGCGTGTGA 60.795 55.000 24.59 0.00 41.78 3.58
3665 4095 0.732880 GTGTACGCGTGTGATGCTCT 60.733 55.000 24.59 0.00 0.00 4.09
3672 4102 0.710567 CGTGTGATGCTCTGAACGTC 59.289 55.000 0.00 0.00 0.00 4.34
3673 4103 1.071605 GTGTGATGCTCTGAACGTCC 58.928 55.000 0.00 0.00 0.00 4.79
4043 4473 2.273776 CACACACACACACCCCCA 59.726 61.111 0.00 0.00 0.00 4.96
4044 4474 2.118404 CACACACACACACCCCCAC 61.118 63.158 0.00 0.00 0.00 4.61
4045 4475 2.273776 CACACACACACCCCCACA 59.726 61.111 0.00 0.00 0.00 4.17
4046 4476 2.118404 CACACACACACCCCCACAC 61.118 63.158 0.00 0.00 0.00 3.82
4047 4477 2.518349 CACACACACCCCCACACC 60.518 66.667 0.00 0.00 0.00 4.16
4048 4478 3.816090 ACACACACCCCCACACCC 61.816 66.667 0.00 0.00 0.00 4.61
4049 4479 4.596585 CACACACCCCCACACCCC 62.597 72.222 0.00 0.00 0.00 4.95
4051 4481 4.596585 CACACCCCCACACCCCAC 62.597 72.222 0.00 0.00 0.00 4.61
4053 4483 4.596585 CACCCCCACACCCCACAC 62.597 72.222 0.00 0.00 0.00 3.82
4055 4485 4.596585 CCCCCACACCCCACACAC 62.597 72.222 0.00 0.00 0.00 3.82
4056 4486 3.814906 CCCCACACCCCACACACA 61.815 66.667 0.00 0.00 0.00 3.72
4057 4487 2.518349 CCCACACCCCACACACAC 60.518 66.667 0.00 0.00 0.00 3.82
4058 4488 2.899838 CCACACCCCACACACACG 60.900 66.667 0.00 0.00 0.00 4.49
4059 4489 3.582120 CACACCCCACACACACGC 61.582 66.667 0.00 0.00 0.00 5.34
4060 4490 3.792736 ACACCCCACACACACGCT 61.793 61.111 0.00 0.00 0.00 5.07
4061 4491 3.279116 CACCCCACACACACGCTG 61.279 66.667 0.00 0.00 0.00 5.18
4062 4492 3.792736 ACCCCACACACACGCTGT 61.793 61.111 0.00 0.00 0.00 4.40
4070 4500 3.101209 CACACGCTGTGCAGTTGT 58.899 55.556 8.31 2.55 41.89 3.32
4071 4501 1.297819 CACACGCTGTGCAGTTGTG 60.298 57.895 18.21 18.21 41.89 3.33
4072 4502 1.745115 ACACGCTGTGCAGTTGTGT 60.745 52.632 19.13 19.13 41.67 3.72
4073 4503 1.010797 CACGCTGTGCAGTTGTGTC 60.011 57.895 14.24 0.00 34.50 3.67
4074 4504 1.449423 ACGCTGTGCAGTTGTGTCA 60.449 52.632 0.00 0.00 0.00 3.58
4075 4505 0.815213 ACGCTGTGCAGTTGTGTCAT 60.815 50.000 0.00 0.00 0.00 3.06
4076 4506 0.308684 CGCTGTGCAGTTGTGTCATT 59.691 50.000 0.00 0.00 0.00 2.57
4077 4507 1.762419 GCTGTGCAGTTGTGTCATTG 58.238 50.000 0.00 0.00 0.00 2.82
4078 4508 1.334556 GCTGTGCAGTTGTGTCATTGA 59.665 47.619 0.00 0.00 0.00 2.57
4079 4509 2.855953 GCTGTGCAGTTGTGTCATTGAC 60.856 50.000 9.93 9.93 0.00 3.18
4080 4510 2.355444 CTGTGCAGTTGTGTCATTGACA 59.645 45.455 15.41 15.41 40.50 3.58
4081 4511 2.950975 TGTGCAGTTGTGTCATTGACAT 59.049 40.909 21.60 3.86 44.63 3.06
4082 4512 3.243134 TGTGCAGTTGTGTCATTGACATG 60.243 43.478 21.60 16.21 44.63 3.21
4083 4513 2.950975 TGCAGTTGTGTCATTGACATGT 59.049 40.909 21.60 0.00 44.63 3.21
4084 4514 3.243134 TGCAGTTGTGTCATTGACATGTG 60.243 43.478 21.60 16.21 44.63 3.21
4085 4515 3.854414 GCAGTTGTGTCATTGACATGTGG 60.854 47.826 21.60 11.93 44.63 4.17
4086 4516 2.886523 AGTTGTGTCATTGACATGTGGG 59.113 45.455 21.60 0.00 44.63 4.61
4087 4517 1.246649 TGTGTCATTGACATGTGGGC 58.753 50.000 21.60 8.98 44.63 5.36
4088 4518 0.527565 GTGTCATTGACATGTGGGCC 59.472 55.000 21.60 0.00 44.63 5.80
4089 4519 0.405198 TGTCATTGACATGTGGGCCT 59.595 50.000 15.41 0.00 37.67 5.19
4090 4520 1.098050 GTCATTGACATGTGGGCCTC 58.902 55.000 1.15 0.49 32.09 4.70
4091 4521 0.034186 TCATTGACATGTGGGCCTCC 60.034 55.000 1.15 0.00 0.00 4.30
4092 4522 1.039233 CATTGACATGTGGGCCTCCC 61.039 60.000 1.15 0.00 45.71 4.30
4093 4523 1.217057 ATTGACATGTGGGCCTCCCT 61.217 55.000 1.15 0.00 45.70 4.20
4094 4524 1.852157 TTGACATGTGGGCCTCCCTC 61.852 60.000 1.15 0.16 45.70 4.30
4095 4525 3.391665 GACATGTGGGCCTCCCTCG 62.392 68.421 1.15 0.00 45.70 4.63
4096 4526 3.402681 CATGTGGGCCTCCCTCGT 61.403 66.667 4.53 0.00 45.70 4.18
4097 4527 3.402681 ATGTGGGCCTCCCTCGTG 61.403 66.667 4.53 0.00 45.70 4.35
4098 4528 3.924013 ATGTGGGCCTCCCTCGTGA 62.924 63.158 4.53 0.00 45.70 4.35
4099 4529 3.775654 GTGGGCCTCCCTCGTGAG 61.776 72.222 4.53 0.00 45.70 3.51
4103 4533 4.500116 GCCTCCCTCGTGAGCGAC 62.500 72.222 0.00 0.00 42.81 5.19
4104 4534 3.062466 CCTCCCTCGTGAGCGACA 61.062 66.667 0.00 0.00 42.81 4.35
4109 4539 2.335011 CTCGTGAGCGACACCACA 59.665 61.111 10.48 0.00 45.73 4.17
4112 4542 2.421739 GTGAGCGACACCACAGGT 59.578 61.111 5.93 0.00 43.05 4.00
4156 4586 1.529948 TGGAGTGGGACGACGTCTT 60.530 57.895 25.87 3.52 32.47 3.01
4179 4610 3.858238 GTCGAATATATAGCCGCTGTTCC 59.142 47.826 2.16 0.00 0.00 3.62
4180 4611 3.762288 TCGAATATATAGCCGCTGTTCCT 59.238 43.478 2.16 0.00 0.00 3.36
4222 4667 1.146358 GGCAGTCGGCTTGATCGTAC 61.146 60.000 0.00 0.00 44.01 3.67
4227 4672 1.135489 GTCGGCTTGATCGTACAGTCA 60.135 52.381 0.00 0.00 0.00 3.41
4249 4694 2.877043 TTTCGGATAGGCGGTCTTAC 57.123 50.000 0.00 0.00 0.00 2.34
4270 4715 1.620819 GATATGGTGATCGGCTCCTGT 59.379 52.381 0.00 0.00 0.00 4.00
4271 4716 0.752658 TATGGTGATCGGCTCCTGTG 59.247 55.000 0.00 0.00 0.00 3.66
4278 4723 3.710722 CGGCTCCTGTGGAAGGCT 61.711 66.667 0.00 0.00 46.92 4.58
4294 4739 2.378038 AGGCTTTGTTGTCTTGAAGCA 58.622 42.857 8.89 0.00 44.69 3.91
4300 4745 4.454728 TTGTTGTCTTGAAGCAAGCTTT 57.545 36.364 8.91 0.00 40.84 3.51
4301 4746 3.772932 TGTTGTCTTGAAGCAAGCTTTG 58.227 40.909 8.91 3.37 40.84 2.77
4321 4766 0.679640 CTATTGAAGGTTGGCGGCCA 60.680 55.000 19.77 19.77 0.00 5.36
4338 4783 1.933247 CCATGCTCTTCTTCCTCGAC 58.067 55.000 0.00 0.00 0.00 4.20
4347 4792 1.835494 TCTTCCTCGACGAAGATGGT 58.165 50.000 19.04 0.00 42.58 3.55
4359 4804 0.322187 AAGATGGTGGTGCCGGTAAC 60.322 55.000 0.00 0.00 41.21 2.50
4371 4816 1.597797 CCGGTAACTGGCGGACACTA 61.598 60.000 0.00 0.00 0.00 2.74
4378 4823 0.103208 CTGGCGGACACTAGGATGAC 59.897 60.000 0.00 0.00 0.00 3.06
4387 4832 0.120377 ACTAGGATGACCCCCAACCA 59.880 55.000 0.00 0.00 39.93 3.67
4405 4850 2.573462 ACCAACATGCCACATAGACTCT 59.427 45.455 0.00 0.00 0.00 3.24
4410 4855 5.207110 ACATGCCACATAGACTCTATGTC 57.793 43.478 23.56 16.05 45.67 3.06
4423 4868 3.568853 ACTCTATGTCATACACTACGGCC 59.431 47.826 0.00 0.00 0.00 6.13
4435 4880 1.161843 CTACGGCCGGTTGTTTCATT 58.838 50.000 31.76 6.43 0.00 2.57
4436 4881 1.538075 CTACGGCCGGTTGTTTCATTT 59.462 47.619 31.76 5.83 0.00 2.32
4441 4886 1.934849 GCCGGTTGTTTCATTTGCTCC 60.935 52.381 1.90 0.00 0.00 4.70
4449 4894 6.200854 GGTTGTTTCATTTGCTCCAAAAGTAG 59.799 38.462 0.00 0.00 36.90 2.57
4450 4895 5.288804 TGTTTCATTTGCTCCAAAAGTAGC 58.711 37.500 0.00 0.00 36.90 3.58
4451 4896 5.163468 TGTTTCATTTGCTCCAAAAGTAGCA 60.163 36.000 0.00 0.00 46.59 3.49
4456 4901 2.930950 TGCTCCAAAAGTAGCACAAGT 58.069 42.857 0.00 0.00 43.56 3.16
4457 4902 2.878406 TGCTCCAAAAGTAGCACAAGTC 59.122 45.455 0.00 0.00 43.56 3.01
4458 4903 3.142174 GCTCCAAAAGTAGCACAAGTCT 58.858 45.455 0.00 0.00 38.63 3.24
4490 4935 4.715297 GGTCCTCCAGTTCTAGGTTTGATA 59.285 45.833 0.00 0.00 34.30 2.15
4491 4936 5.395435 GGTCCTCCAGTTCTAGGTTTGATAC 60.395 48.000 0.00 0.00 34.30 2.24
4525 4970 7.418337 AAAAGTTCTAGGTTTGATGGTTTGT 57.582 32.000 0.00 0.00 0.00 2.83
4526 4971 6.635030 AAGTTCTAGGTTTGATGGTTTGTC 57.365 37.500 0.00 0.00 0.00 3.18
4527 4972 5.070685 AGTTCTAGGTTTGATGGTTTGTCC 58.929 41.667 0.00 0.00 0.00 4.02
4528 4973 4.028993 TCTAGGTTTGATGGTTTGTCCC 57.971 45.455 0.00 0.00 34.77 4.46
4529 4974 3.655777 TCTAGGTTTGATGGTTTGTCCCT 59.344 43.478 0.00 0.00 34.77 4.20
4530 4975 2.876581 AGGTTTGATGGTTTGTCCCTC 58.123 47.619 0.00 0.00 34.77 4.30
4531 4976 2.447047 AGGTTTGATGGTTTGTCCCTCT 59.553 45.455 0.00 0.00 33.02 3.69
4532 4977 2.558359 GGTTTGATGGTTTGTCCCTCTG 59.442 50.000 0.00 0.00 33.02 3.35
4533 4978 3.222603 GTTTGATGGTTTGTCCCTCTGT 58.777 45.455 0.00 0.00 33.02 3.41
4534 4979 3.593442 TTGATGGTTTGTCCCTCTGTT 57.407 42.857 0.00 0.00 33.02 3.16
4535 4980 3.593442 TGATGGTTTGTCCCTCTGTTT 57.407 42.857 0.00 0.00 33.02 2.83
4536 4981 3.909732 TGATGGTTTGTCCCTCTGTTTT 58.090 40.909 0.00 0.00 33.02 2.43
4537 4982 3.888930 TGATGGTTTGTCCCTCTGTTTTC 59.111 43.478 0.00 0.00 33.02 2.29
4538 4983 2.294074 TGGTTTGTCCCTCTGTTTTCG 58.706 47.619 0.00 0.00 34.77 3.46
4539 4984 2.092861 TGGTTTGTCCCTCTGTTTTCGA 60.093 45.455 0.00 0.00 34.77 3.71
4540 4985 2.289820 GGTTTGTCCCTCTGTTTTCGAC 59.710 50.000 0.00 0.00 0.00 4.20
4541 4986 1.860676 TTGTCCCTCTGTTTTCGACG 58.139 50.000 0.00 0.00 0.00 5.12
4542 4987 0.032952 TGTCCCTCTGTTTTCGACGG 59.967 55.000 0.00 0.00 35.87 4.79
4543 4988 0.033090 GTCCCTCTGTTTTCGACGGT 59.967 55.000 0.00 0.00 36.00 4.83
4544 4989 0.032952 TCCCTCTGTTTTCGACGGTG 59.967 55.000 0.00 0.00 36.00 4.94
4545 4990 1.566018 CCCTCTGTTTTCGACGGTGC 61.566 60.000 0.00 0.00 36.00 5.01
4546 4991 0.600255 CCTCTGTTTTCGACGGTGCT 60.600 55.000 0.00 0.00 36.00 4.40
4547 4992 1.336517 CCTCTGTTTTCGACGGTGCTA 60.337 52.381 0.00 0.00 36.00 3.49
4548 4993 2.607187 CTCTGTTTTCGACGGTGCTAT 58.393 47.619 0.00 0.00 36.00 2.97
4549 4994 3.428452 CCTCTGTTTTCGACGGTGCTATA 60.428 47.826 0.00 0.00 36.00 1.31
4550 4995 3.504863 TCTGTTTTCGACGGTGCTATAC 58.495 45.455 0.00 0.00 36.00 1.47
4551 4996 3.192001 TCTGTTTTCGACGGTGCTATACT 59.808 43.478 0.00 0.00 36.00 2.12
4552 4997 3.916761 TGTTTTCGACGGTGCTATACTT 58.083 40.909 0.00 0.00 0.00 2.24
4553 4998 3.676172 TGTTTTCGACGGTGCTATACTTG 59.324 43.478 0.00 0.00 0.00 3.16
4554 4999 1.917273 TTCGACGGTGCTATACTTGC 58.083 50.000 0.00 0.00 0.00 4.01
4555 5000 0.248336 TCGACGGTGCTATACTTGCG 60.248 55.000 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 6.116806 TCAAGTTCCTAGCAACTACAAACAA 58.883 36.000 0.00 0.00 35.45 2.83
68 69 3.181445 ACCTCATGCAACCAAACAGACTA 60.181 43.478 0.00 0.00 0.00 2.59
84 85 2.117156 GCCAGCATCGCAACCTCAT 61.117 57.895 0.00 0.00 0.00 2.90
201 202 4.732065 ACCTTTCCACGGAAGGATTTTTA 58.268 39.130 16.50 0.00 37.56 1.52
205 206 3.585732 TCTTACCTTTCCACGGAAGGATT 59.414 43.478 16.50 4.91 37.56 3.01
206 207 3.178865 TCTTACCTTTCCACGGAAGGAT 58.821 45.455 16.50 1.37 37.56 3.24
207 208 2.565834 CTCTTACCTTTCCACGGAAGGA 59.434 50.000 16.50 3.22 33.75 3.36
208 209 2.935676 GCTCTTACCTTTCCACGGAAGG 60.936 54.545 10.84 10.84 35.38 3.46
286 287 9.956720 AGAAAATGTCATCTTACACTGAAAAAG 57.043 29.630 0.00 0.00 30.75 2.27
364 366 7.910162 GGTTGACAATGTATAATGTAGTGCTTG 59.090 37.037 0.00 0.00 0.00 4.01
379 381 3.437642 CCACTGGGGTTGACAATGT 57.562 52.632 0.00 0.00 0.00 2.71
394 397 4.154918 AGAAATGCTTCTTTCATCGACCAC 59.845 41.667 0.00 0.00 38.89 4.16
410 413 3.190118 CCACTGGAGAAACTCAGAAATGC 59.810 47.826 0.00 0.00 31.08 3.56
427 430 5.582665 GTCTTAGATTTGTCTTAGCCCACTG 59.417 44.000 0.00 0.00 0.00 3.66
428 431 5.248477 TGTCTTAGATTTGTCTTAGCCCACT 59.752 40.000 0.00 0.00 0.00 4.00
429 432 5.488341 TGTCTTAGATTTGTCTTAGCCCAC 58.512 41.667 0.00 0.00 0.00 4.61
430 433 5.755409 TGTCTTAGATTTGTCTTAGCCCA 57.245 39.130 0.00 0.00 0.00 5.36
431 434 6.407202 TCTTGTCTTAGATTTGTCTTAGCCC 58.593 40.000 0.00 0.00 0.00 5.19
432 435 7.907214 TTCTTGTCTTAGATTTGTCTTAGCC 57.093 36.000 0.00 0.00 0.00 3.93
436 439 9.971922 CCAAAATTCTTGTCTTAGATTTGTCTT 57.028 29.630 0.00 0.00 28.79 3.01
438 441 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
440 443 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
441 444 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
443 446 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
444 447 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
445 448 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
446 449 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
449 452 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
451 454 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
452 455 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
453 456 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
454 457 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
455 458 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
456 459 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
458 461 2.852714 TATACTCCCTCCGTCCCAAA 57.147 50.000 0.00 0.00 0.00 3.28
462 465 4.799917 GCAAAGAATATACTCCCTCCGTCC 60.800 50.000 0.00 0.00 0.00 4.79
463 466 4.202223 TGCAAAGAATATACTCCCTCCGTC 60.202 45.833 0.00 0.00 0.00 4.79
465 468 4.310769 CTGCAAAGAATATACTCCCTCCG 58.689 47.826 0.00 0.00 0.00 4.63
466 469 4.103311 ACCTGCAAAGAATATACTCCCTCC 59.897 45.833 0.00 0.00 0.00 4.30
467 470 5.071115 AGACCTGCAAAGAATATACTCCCTC 59.929 44.000 0.00 0.00 0.00 4.30
468 471 4.971924 AGACCTGCAAAGAATATACTCCCT 59.028 41.667 0.00 0.00 0.00 4.20
469 472 5.059833 CAGACCTGCAAAGAATATACTCCC 58.940 45.833 0.00 0.00 0.00 4.30
470 473 5.675538 ACAGACCTGCAAAGAATATACTCC 58.324 41.667 0.00 0.00 0.00 3.85
471 474 8.894768 ATTACAGACCTGCAAAGAATATACTC 57.105 34.615 0.00 0.00 0.00 2.59
472 475 8.709308 AGATTACAGACCTGCAAAGAATATACT 58.291 33.333 0.00 0.00 0.00 2.12
473 476 8.768955 CAGATTACAGACCTGCAAAGAATATAC 58.231 37.037 0.00 0.00 0.00 1.47
490 590 2.002586 CCGACCAGCAACAGATTACAG 58.997 52.381 0.00 0.00 0.00 2.74
514 614 7.881751 TCATCCTATTGAGAAATAGCCATCAAG 59.118 37.037 0.80 0.00 35.31 3.02
653 1014 8.767436 TGGGCAGCAGATAATTATATACATGTA 58.233 33.333 8.27 8.27 0.00 2.29
654 1015 7.632861 TGGGCAGCAGATAATTATATACATGT 58.367 34.615 2.69 2.69 0.00 3.21
655 1016 8.151141 CTGGGCAGCAGATAATTATATACATG 57.849 38.462 0.00 0.00 0.00 3.21
742 1103 2.226200 TGCACGTTGGATGAACTGATTG 59.774 45.455 0.00 0.00 31.70 2.67
1076 1462 6.093219 CAGGACTAAAATGTGAGTTGATCAGG 59.907 42.308 0.00 0.00 39.07 3.86
1087 1473 7.819644 TGATGTTTCATCAGGACTAAAATGTG 58.180 34.615 8.14 0.00 0.00 3.21
1088 1474 8.585471 ATGATGTTTCATCAGGACTAAAATGT 57.415 30.769 15.78 0.00 38.18 2.71
1089 1475 9.941664 GTATGATGTTTCATCAGGACTAAAATG 57.058 33.333 15.78 0.00 41.73 2.32
1094 1508 6.321435 AGACGTATGATGTTTCATCAGGACTA 59.679 38.462 15.78 3.55 41.73 2.59
1124 1538 9.538508 GTAGTTGAAGTAGTACCTGAAAGAAAA 57.461 33.333 0.00 0.00 34.07 2.29
1168 1582 1.070134 TGCTCTGTGTACACCTTCACC 59.930 52.381 22.91 7.41 34.14 4.02
1183 1597 0.767375 TGCCTTCCTTTGTCTGCTCT 59.233 50.000 0.00 0.00 0.00 4.09
1219 1633 5.850128 CAGCTTTGAGAAATCTTTGAGAACG 59.150 40.000 0.00 0.00 0.00 3.95
1225 1639 5.401674 GTCAAGCAGCTTTGAGAAATCTTTG 59.598 40.000 4.38 0.00 37.72 2.77
1291 1705 8.884124 TCTTCTTAAAATGGGAGATTTGTGAT 57.116 30.769 0.00 0.00 0.00 3.06
1295 1709 9.182214 TGAGATCTTCTTAAAATGGGAGATTTG 57.818 33.333 0.00 0.00 0.00 2.32
1296 1710 9.933240 ATGAGATCTTCTTAAAATGGGAGATTT 57.067 29.630 0.00 0.00 0.00 2.17
1314 1728 6.332976 ACAAAGGGGAATAACATGAGATCT 57.667 37.500 0.00 0.00 0.00 2.75
1325 1739 6.789268 TCTCAATCTGAAACAAAGGGGAATA 58.211 36.000 0.00 0.00 0.00 1.75
1326 1740 5.644188 TCTCAATCTGAAACAAAGGGGAAT 58.356 37.500 0.00 0.00 0.00 3.01
1468 1883 0.681564 CGACTGCCCTGTAGTCCTCT 60.682 60.000 6.73 0.00 41.12 3.69
1579 1994 6.761242 TCCTGACATAATAATCCGTGAACTTG 59.239 38.462 0.00 0.00 0.00 3.16
1594 2009 1.847328 TCGACCTGCTCCTGACATAA 58.153 50.000 0.00 0.00 0.00 1.90
1609 2024 0.816373 GAGAGTAGGGGTGGTTCGAC 59.184 60.000 0.00 0.00 0.00 4.20
1612 2027 0.537653 GCTGAGAGTAGGGGTGGTTC 59.462 60.000 0.00 0.00 0.00 3.62
1680 2095 6.942532 TTCAAATGTGAAAGTAGCAAGACT 57.057 33.333 0.00 0.00 40.87 3.24
1682 2097 7.445096 TCAGATTCAAATGTGAAAGTAGCAAGA 59.555 33.333 1.55 0.00 46.66 3.02
1740 2155 8.124199 GGCAAATTTGAAATGATTCGCAATAAT 58.876 29.630 22.31 0.00 38.46 1.28
1741 2156 7.333921 AGGCAAATTTGAAATGATTCGCAATAA 59.666 29.630 22.31 0.00 38.46 1.40
1742 2157 6.817641 AGGCAAATTTGAAATGATTCGCAATA 59.182 30.769 22.31 0.00 38.46 1.90
1743 2158 5.644636 AGGCAAATTTGAAATGATTCGCAAT 59.355 32.000 22.31 0.00 38.46 3.56
1744 2159 4.996122 AGGCAAATTTGAAATGATTCGCAA 59.004 33.333 22.31 0.00 38.46 4.85
1745 2160 4.567971 AGGCAAATTTGAAATGATTCGCA 58.432 34.783 22.31 0.00 38.46 5.10
1746 2161 4.866486 AGAGGCAAATTTGAAATGATTCGC 59.134 37.500 22.31 1.88 38.46 4.70
1747 2162 6.094719 TCAGAGGCAAATTTGAAATGATTCG 58.905 36.000 22.31 0.96 38.46 3.34
1748 2163 7.601508 AGTTCAGAGGCAAATTTGAAATGATTC 59.398 33.333 22.31 13.34 31.98 2.52
1749 2164 7.447594 AGTTCAGAGGCAAATTTGAAATGATT 58.552 30.769 22.31 8.08 31.98 2.57
1750 2165 7.001099 AGTTCAGAGGCAAATTTGAAATGAT 57.999 32.000 22.31 3.56 31.98 2.45
1751 2166 6.409524 AGTTCAGAGGCAAATTTGAAATGA 57.590 33.333 22.31 15.05 31.98 2.57
1752 2167 8.592105 TTAAGTTCAGAGGCAAATTTGAAATG 57.408 30.769 22.31 13.16 31.98 2.32
1819 2234 5.046591 CCAATACCCTACTCACAGTTCAAGA 60.047 44.000 0.00 0.00 0.00 3.02
1970 2385 4.261197 GCTCTGTTTGTGGTTTTCTACTGG 60.261 45.833 0.00 0.00 32.36 4.00
1980 2395 1.512926 GATCACGCTCTGTTTGTGGT 58.487 50.000 0.00 0.00 34.43 4.16
1990 2405 1.419374 AGAACAACACGATCACGCTC 58.581 50.000 0.00 0.00 43.96 5.03
1992 2407 1.260561 ACAAGAACAACACGATCACGC 59.739 47.619 0.00 0.00 43.96 5.34
1993 2408 3.734231 AGTACAAGAACAACACGATCACG 59.266 43.478 0.00 0.00 45.75 4.35
2011 2426 8.657074 TGTTATCATTGTTAGCCACATAGTAC 57.343 34.615 0.00 0.00 34.43 2.73
2013 2428 9.845740 TTATGTTATCATTGTTAGCCACATAGT 57.154 29.630 0.00 0.00 34.43 2.12
2035 2450 5.050363 GCCACCACATACGTACAAGATTATG 60.050 44.000 0.00 0.00 0.00 1.90
2038 2453 3.267483 GCCACCACATACGTACAAGATT 58.733 45.455 0.00 0.00 0.00 2.40
2039 2454 2.235155 TGCCACCACATACGTACAAGAT 59.765 45.455 0.00 0.00 0.00 2.40
2041 2456 1.730064 GTGCCACCACATACGTACAAG 59.270 52.381 0.00 0.00 41.67 3.16
2042 2457 1.608542 GGTGCCACCACATACGTACAA 60.609 52.381 9.55 0.00 43.88 2.41
2043 2458 0.037139 GGTGCCACCACATACGTACA 60.037 55.000 9.55 0.00 43.88 2.90
2044 2459 0.248289 AGGTGCCACCACATACGTAC 59.752 55.000 17.80 0.00 43.88 3.67
2045 2460 0.248012 CAGGTGCCACCACATACGTA 59.752 55.000 17.80 0.00 43.88 3.57
2046 2461 1.003839 CAGGTGCCACCACATACGT 60.004 57.895 17.80 0.00 43.88 3.57
2047 2462 0.321210 TTCAGGTGCCACCACATACG 60.321 55.000 17.80 0.00 43.88 3.06
2709 3127 2.036256 ATGACCCAGCCAGGCAAC 59.964 61.111 15.80 0.25 35.39 4.17
2754 3172 0.684535 TGAACGAGATCCACAGCCAA 59.315 50.000 0.00 0.00 0.00 4.52
2802 3220 1.458777 ACCCTGACGGTGACCTTCA 60.459 57.895 10.56 10.56 46.09 3.02
2826 3244 0.598680 CTAATCTTGAGGAGCCGCCG 60.599 60.000 0.00 0.00 43.43 6.46
2838 3256 4.202367 CCTTGCTTCCGGTATCCTAATCTT 60.202 45.833 0.00 0.00 0.00 2.40
2841 3259 2.372172 CCCTTGCTTCCGGTATCCTAAT 59.628 50.000 0.00 0.00 0.00 1.73
2896 3314 4.200283 CTGGTCGCTCTCGCCCTC 62.200 72.222 0.00 0.00 35.26 4.30
3141 3559 1.200760 TGCTGATGTAGGTGCCCACT 61.201 55.000 0.00 0.00 0.00 4.00
3561 3979 2.607442 TGGCTGCCTGGCACTCTA 60.607 61.111 19.30 7.72 46.76 2.43
3589 4007 3.213264 ACACACCGTGACGAAGGT 58.787 55.556 6.54 0.00 42.34 3.50
3612 4042 6.070196 CACAAACATGAAACAACACAAACAC 58.930 36.000 0.00 0.00 0.00 3.32
3613 4043 5.985530 TCACAAACATGAAACAACACAAACA 59.014 32.000 0.00 0.00 0.00 2.83
3614 4044 6.145371 AGTCACAAACATGAAACAACACAAAC 59.855 34.615 0.00 0.00 0.00 2.93
3615 4045 6.219473 AGTCACAAACATGAAACAACACAAA 58.781 32.000 0.00 0.00 0.00 2.83
3617 4047 5.384063 AGTCACAAACATGAAACAACACA 57.616 34.783 0.00 0.00 0.00 3.72
3618 4048 4.495472 CGAGTCACAAACATGAAACAACAC 59.505 41.667 0.00 0.00 0.00 3.32
3619 4049 4.657055 CGAGTCACAAACATGAAACAACA 58.343 39.130 0.00 0.00 0.00 3.33
3620 4050 3.482110 GCGAGTCACAAACATGAAACAAC 59.518 43.478 0.00 0.00 0.00 3.32
3621 4051 3.376859 AGCGAGTCACAAACATGAAACAA 59.623 39.130 0.00 0.00 0.00 2.83
3622 4052 2.942376 AGCGAGTCACAAACATGAAACA 59.058 40.909 0.00 0.00 0.00 2.83
3623 4053 3.609103 AGCGAGTCACAAACATGAAAC 57.391 42.857 0.00 0.00 0.00 2.78
3624 4054 4.754618 ACATAGCGAGTCACAAACATGAAA 59.245 37.500 0.00 0.00 0.00 2.69
3625 4055 4.152223 CACATAGCGAGTCACAAACATGAA 59.848 41.667 0.00 0.00 0.00 2.57
3626 4056 3.679502 CACATAGCGAGTCACAAACATGA 59.320 43.478 0.00 0.00 0.00 3.07
3627 4057 3.433274 ACACATAGCGAGTCACAAACATG 59.567 43.478 0.00 0.00 0.00 3.21
3628 4058 3.664107 ACACATAGCGAGTCACAAACAT 58.336 40.909 0.00 0.00 0.00 2.71
3643 4073 1.135228 AGCATCACACGCGTACACATA 60.135 47.619 13.44 0.00 0.00 2.29
3645 4075 1.006688 AGCATCACACGCGTACACA 60.007 52.632 13.44 0.00 0.00 3.72
3650 4080 1.006220 TTCAGAGCATCACACGCGT 60.006 52.632 5.58 5.58 37.82 6.01
3651 4081 1.417592 GTTCAGAGCATCACACGCG 59.582 57.895 3.53 3.53 37.82 6.01
3659 4089 0.179100 CCATCGGACGTTCAGAGCAT 60.179 55.000 0.00 0.00 0.00 3.79
3665 4095 2.180769 CGAGCCATCGGACGTTCA 59.819 61.111 0.00 0.00 45.39 3.18
4026 4456 2.118404 GTGGGGGTGTGTGTGTGTG 61.118 63.158 0.00 0.00 0.00 3.82
4027 4457 2.274104 GTGGGGGTGTGTGTGTGT 59.726 61.111 0.00 0.00 0.00 3.72
4028 4458 2.118404 GTGTGGGGGTGTGTGTGTG 61.118 63.158 0.00 0.00 0.00 3.82
4029 4459 2.274104 GTGTGGGGGTGTGTGTGT 59.726 61.111 0.00 0.00 0.00 3.72
4030 4460 2.518349 GGTGTGGGGGTGTGTGTG 60.518 66.667 0.00 0.00 0.00 3.82
4031 4461 3.816090 GGGTGTGGGGGTGTGTGT 61.816 66.667 0.00 0.00 0.00 3.72
4032 4462 4.596585 GGGGTGTGGGGGTGTGTG 62.597 72.222 0.00 0.00 0.00 3.82
4034 4464 4.596585 GTGGGGTGTGGGGGTGTG 62.597 72.222 0.00 0.00 0.00 3.82
4036 4466 4.596585 GTGTGGGGTGTGGGGGTG 62.597 72.222 0.00 0.00 0.00 4.61
4038 4468 4.596585 GTGTGTGGGGTGTGGGGG 62.597 72.222 0.00 0.00 0.00 5.40
4039 4469 3.814906 TGTGTGTGGGGTGTGGGG 61.815 66.667 0.00 0.00 0.00 4.96
4040 4470 2.518349 GTGTGTGTGGGGTGTGGG 60.518 66.667 0.00 0.00 0.00 4.61
4041 4471 2.899838 CGTGTGTGTGGGGTGTGG 60.900 66.667 0.00 0.00 0.00 4.17
4042 4472 3.582120 GCGTGTGTGTGGGGTGTG 61.582 66.667 0.00 0.00 0.00 3.82
4043 4473 3.792736 AGCGTGTGTGTGGGGTGT 61.793 61.111 0.00 0.00 0.00 4.16
4044 4474 3.279116 CAGCGTGTGTGTGGGGTG 61.279 66.667 0.00 0.00 0.00 4.61
4045 4475 3.792736 ACAGCGTGTGTGTGGGGT 61.793 61.111 0.00 0.00 38.28 4.95
4054 4484 1.705337 GACACAACTGCACAGCGTGT 61.705 55.000 20.31 20.31 45.35 4.49
4055 4485 1.010797 GACACAACTGCACAGCGTG 60.011 57.895 15.51 15.51 39.59 5.34
4056 4486 0.815213 ATGACACAACTGCACAGCGT 60.815 50.000 0.00 0.00 0.00 5.07
4057 4487 0.308684 AATGACACAACTGCACAGCG 59.691 50.000 0.00 0.00 0.00 5.18
4058 4488 1.334556 TCAATGACACAACTGCACAGC 59.665 47.619 0.00 0.00 0.00 4.40
4059 4489 2.355444 TGTCAATGACACAACTGCACAG 59.645 45.455 12.63 0.00 37.67 3.66
4060 4490 2.363683 TGTCAATGACACAACTGCACA 58.636 42.857 12.63 0.00 37.67 4.57
4061 4491 3.243168 ACATGTCAATGACACAACTGCAC 60.243 43.478 19.17 0.00 45.65 4.57
4062 4492 2.950975 ACATGTCAATGACACAACTGCA 59.049 40.909 19.17 0.00 45.65 4.41
4063 4493 3.302555 CACATGTCAATGACACAACTGC 58.697 45.455 19.17 0.00 45.65 4.40
4064 4494 3.304861 CCCACATGTCAATGACACAACTG 60.305 47.826 19.17 14.89 45.65 3.16
4065 4495 2.886523 CCCACATGTCAATGACACAACT 59.113 45.455 19.17 0.00 45.65 3.16
4066 4496 2.607771 GCCCACATGTCAATGACACAAC 60.608 50.000 19.17 1.88 45.65 3.32
4067 4497 1.612950 GCCCACATGTCAATGACACAA 59.387 47.619 19.17 0.00 45.65 3.33
4068 4498 1.246649 GCCCACATGTCAATGACACA 58.753 50.000 19.17 0.00 45.65 3.72
4069 4499 0.527565 GGCCCACATGTCAATGACAC 59.472 55.000 19.17 4.56 45.65 3.67
4070 4500 0.405198 AGGCCCACATGTCAATGACA 59.595 50.000 19.08 19.08 46.90 3.58
4071 4501 1.098050 GAGGCCCACATGTCAATGAC 58.902 55.000 6.41 6.41 37.24 3.06
4072 4502 0.034186 GGAGGCCCACATGTCAATGA 60.034 55.000 0.00 0.00 37.24 2.57
4073 4503 1.039233 GGGAGGCCCACATGTCAATG 61.039 60.000 0.00 0.00 44.65 2.82
4074 4504 1.307647 GGGAGGCCCACATGTCAAT 59.692 57.895 0.00 0.00 44.65 2.57
4075 4505 2.763215 GGGAGGCCCACATGTCAA 59.237 61.111 0.00 0.00 44.65 3.18
4095 4525 1.664965 GACCTGTGGTGTCGCTCAC 60.665 63.158 0.00 2.71 45.47 3.51
4096 4526 2.734591 GACCTGTGGTGTCGCTCA 59.265 61.111 0.00 0.00 35.25 4.26
4097 4527 2.048127 GGACCTGTGGTGTCGCTC 60.048 66.667 0.00 0.00 35.25 5.03
4098 4528 3.991051 CGGACCTGTGGTGTCGCT 61.991 66.667 0.00 0.00 35.25 4.93
4156 4586 4.482386 GAACAGCGGCTATATATTCGACA 58.518 43.478 0.26 0.00 0.00 4.35
4179 4610 2.673523 CACAAGCTGGAGGGGGAG 59.326 66.667 0.00 0.00 0.00 4.30
4180 4611 2.935481 CCACAAGCTGGAGGGGGA 60.935 66.667 0.00 0.00 43.95 4.81
4202 4647 1.320344 TACGATCAAGCCGACTGCCT 61.320 55.000 0.00 0.00 42.71 4.75
4214 4659 4.811908 TCCGAAAATTGACTGTACGATCA 58.188 39.130 0.00 0.00 0.00 2.92
4222 4667 2.287915 CCGCCTATCCGAAAATTGACTG 59.712 50.000 0.00 0.00 0.00 3.51
4227 4672 3.277142 AAGACCGCCTATCCGAAAATT 57.723 42.857 0.00 0.00 0.00 1.82
4249 4694 0.891373 AGGAGCCGATCACCATATCG 59.109 55.000 0.00 0.00 46.51 2.92
4270 4715 3.011566 TCAAGACAACAAAGCCTTCCA 57.988 42.857 0.00 0.00 0.00 3.53
4271 4716 3.796844 GCTTCAAGACAACAAAGCCTTCC 60.797 47.826 0.00 0.00 38.51 3.46
4278 4723 4.454728 AAGCTTGCTTCAAGACAACAAA 57.545 36.364 10.44 0.00 43.42 2.83
4294 4739 3.306294 GCCAACCTTCAATAGCAAAGCTT 60.306 43.478 0.00 0.00 40.44 3.74
4300 4745 1.312371 GCCGCCAACCTTCAATAGCA 61.312 55.000 0.00 0.00 0.00 3.49
4301 4746 1.433471 GCCGCCAACCTTCAATAGC 59.567 57.895 0.00 0.00 0.00 2.97
4304 4749 1.305213 ATGGCCGCCAACCTTCAAT 60.305 52.632 18.00 0.00 36.95 2.57
4321 4766 1.464734 TCGTCGAGGAAGAAGAGCAT 58.535 50.000 5.12 0.00 0.00 3.79
4338 4783 2.233605 TACCGGCACCACCATCTTCG 62.234 60.000 0.00 0.00 39.03 3.79
4359 4804 0.103208 GTCATCCTAGTGTCCGCCAG 59.897 60.000 0.00 0.00 0.00 4.85
4371 4816 1.071314 TGTTGGTTGGGGGTCATCCT 61.071 55.000 0.00 0.00 36.44 3.24
4378 4823 2.203758 TGGCATGTTGGTTGGGGG 60.204 61.111 0.00 0.00 0.00 5.40
4387 4832 5.605534 GACATAGAGTCTATGTGGCATGTT 58.394 41.667 38.40 19.21 44.09 2.71
4405 4850 1.610038 CCGGCCGTAGTGTATGACATA 59.390 52.381 26.12 0.00 0.00 2.29
4410 4855 0.108520 ACAACCGGCCGTAGTGTATG 60.109 55.000 26.12 13.12 0.00 2.39
4411 4856 0.609662 AACAACCGGCCGTAGTGTAT 59.390 50.000 26.12 11.93 0.00 2.29
4419 4864 1.281566 GCAAATGAAACAACCGGCCG 61.282 55.000 21.04 21.04 0.00 6.13
4423 4868 2.791383 TGGAGCAAATGAAACAACCG 57.209 45.000 0.00 0.00 0.00 4.44
4436 4881 2.878406 GACTTGTGCTACTTTTGGAGCA 59.122 45.455 0.00 0.00 46.24 4.26
4450 4895 3.130351 GGACCACCATCACAGACTTGTG 61.130 54.545 1.35 1.35 44.59 3.33
4451 4896 1.072331 GGACCACCATCACAGACTTGT 59.928 52.381 0.00 0.00 35.37 3.16
4452 4897 1.349026 AGGACCACCATCACAGACTTG 59.651 52.381 0.00 0.00 38.94 3.16
4453 4898 1.625818 GAGGACCACCATCACAGACTT 59.374 52.381 0.00 0.00 38.94 3.01
4454 4899 1.270907 GAGGACCACCATCACAGACT 58.729 55.000 0.00 0.00 38.94 3.24
4455 4900 0.250513 GGAGGACCACCATCACAGAC 59.749 60.000 2.58 0.00 38.94 3.51
4456 4901 0.178906 TGGAGGACCACCATCACAGA 60.179 55.000 6.55 0.00 41.77 3.41
4457 4902 0.251354 CTGGAGGACCACCATCACAG 59.749 60.000 11.45 0.00 41.77 3.66
4458 4903 0.473694 ACTGGAGGACCACCATCACA 60.474 55.000 11.45 0.00 41.77 3.58
4468 4913 4.828072 ATCAAACCTAGAACTGGAGGAC 57.172 45.455 0.00 0.00 36.61 3.85
4500 4945 7.847096 ACAAACCATCAAACCTAGAACTTTTT 58.153 30.769 0.00 0.00 0.00 1.94
4501 4946 7.417456 GGACAAACCATCAAACCTAGAACTTTT 60.417 37.037 0.00 0.00 38.79 2.27
4502 4947 6.040504 GGACAAACCATCAAACCTAGAACTTT 59.959 38.462 0.00 0.00 38.79 2.66
4503 4948 5.535030 GGACAAACCATCAAACCTAGAACTT 59.465 40.000 0.00 0.00 38.79 2.66
4504 4949 5.070685 GGACAAACCATCAAACCTAGAACT 58.929 41.667 0.00 0.00 38.79 3.01
4505 4950 4.217767 GGGACAAACCATCAAACCTAGAAC 59.782 45.833 0.00 0.00 41.20 3.01
4506 4951 4.105697 AGGGACAAACCATCAAACCTAGAA 59.894 41.667 0.00 0.00 41.20 2.10
4507 4952 3.655777 AGGGACAAACCATCAAACCTAGA 59.344 43.478 0.00 0.00 41.20 2.43
4508 4953 4.034285 AGGGACAAACCATCAAACCTAG 57.966 45.455 0.00 0.00 41.20 3.02
4517 4962 2.884639 CGAAAACAGAGGGACAAACCAT 59.115 45.455 0.00 0.00 41.20 3.55
4518 4963 2.092861 TCGAAAACAGAGGGACAAACCA 60.093 45.455 0.00 0.00 41.20 3.67
4519 4964 2.289820 GTCGAAAACAGAGGGACAAACC 59.710 50.000 0.00 0.00 38.08 3.27
4520 4965 2.033151 CGTCGAAAACAGAGGGACAAAC 60.033 50.000 0.00 0.00 0.00 2.93
4521 4966 2.206750 CGTCGAAAACAGAGGGACAAA 58.793 47.619 0.00 0.00 0.00 2.83
4522 4967 1.539496 CCGTCGAAAACAGAGGGACAA 60.539 52.381 0.00 0.00 44.02 3.18
4523 4968 0.032952 CCGTCGAAAACAGAGGGACA 59.967 55.000 0.00 0.00 44.02 4.02
4524 4969 0.033090 ACCGTCGAAAACAGAGGGAC 59.967 55.000 11.26 0.00 44.02 4.46
4525 4970 0.032952 CACCGTCGAAAACAGAGGGA 59.967 55.000 11.26 0.00 44.02 4.20
4526 4971 1.566018 GCACCGTCGAAAACAGAGGG 61.566 60.000 0.00 3.73 45.99 4.30
4527 4972 0.600255 AGCACCGTCGAAAACAGAGG 60.600 55.000 0.00 0.00 0.00 3.69
4528 4973 2.060326 TAGCACCGTCGAAAACAGAG 57.940 50.000 0.00 0.00 0.00 3.35
4529 4974 2.736144 ATAGCACCGTCGAAAACAGA 57.264 45.000 0.00 0.00 0.00 3.41
4530 4975 3.508762 AGTATAGCACCGTCGAAAACAG 58.491 45.455 0.00 0.00 0.00 3.16
4531 4976 3.581024 AGTATAGCACCGTCGAAAACA 57.419 42.857 0.00 0.00 0.00 2.83
4532 4977 3.483085 GCAAGTATAGCACCGTCGAAAAC 60.483 47.826 0.00 0.00 0.00 2.43
4533 4978 2.669434 GCAAGTATAGCACCGTCGAAAA 59.331 45.455 0.00 0.00 0.00 2.29
4534 4979 2.264813 GCAAGTATAGCACCGTCGAAA 58.735 47.619 0.00 0.00 0.00 3.46
4535 4980 1.796253 CGCAAGTATAGCACCGTCGAA 60.796 52.381 0.00 0.00 0.00 3.71
4536 4981 0.248336 CGCAAGTATAGCACCGTCGA 60.248 55.000 0.00 0.00 0.00 4.20
4537 4982 2.204491 CGCAAGTATAGCACCGTCG 58.796 57.895 0.00 0.00 0.00 5.12


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

AutoCloner maintained by Alex Coulton.