Multiple sequence alignment - TraesCS4D01G105400

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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 TraesCS4D01G105400 chr4D 100.000 2723 0 0 1 2723 84174703 84171981 0.000000e+00 5029.0
1 TraesCS4D01G105400 chr4D 88.155 515 58 3 1948 2460 374836209 374835696 6.450000e-171 610.0
2 TraesCS4D01G105400 chr4D 95.385 260 10 2 2461 2718 446410108 446409849 1.950000e-111 412.0
3 TraesCS4D01G105400 chr4D 93.985 266 12 4 2458 2719 484233291 484233026 1.520000e-107 399.0
4 TraesCS4D01G105400 chr4D 76.724 232 35 17 213 433 84982172 84981949 7.970000e-21 111.0
5 TraesCS4D01G105400 chr4D 100.000 29 0 0 1822 1850 6146668 6146696 1.000000e-03 54.7
6 TraesCS4D01G105400 chr4A 93.723 1593 61 11 241 1815 496115613 496114042 0.000000e+00 2351.0
7 TraesCS4D01G105400 chr4B 98.667 900 10 1 857 1756 119109688 119108791 0.000000e+00 1594.0
8 TraesCS4D01G105400 chr4B 88.639 889 64 19 3 870 119110719 119109847 0.000000e+00 1048.0
9 TraesCS4D01G105400 chr4B 76.042 384 67 19 83 449 145384584 145384209 2.790000e-40 176.0
10 TraesCS4D01G105400 chr1D 87.379 515 61 4 1948 2460 379491344 379490832 3.020000e-164 588.0
11 TraesCS4D01G105400 chr1D 93.985 266 14 2 2460 2723 106963965 106964230 4.220000e-108 401.0
12 TraesCS4D01G105400 chr7D 87.016 516 63 3 1948 2460 88026472 88025958 1.820000e-161 579.0
13 TraesCS4D01G105400 chr7D 86.914 512 64 3 1950 2459 503801493 503800983 3.040000e-159 571.0
14 TraesCS4D01G105400 chr7D 94.615 260 12 2 2461 2718 365382972 365382713 4.220000e-108 401.0
15 TraesCS4D01G105400 chr7D 79.954 439 71 13 2 431 174985409 174985839 9.470000e-80 307.0
16 TraesCS4D01G105400 chr2D 86.965 514 64 3 1948 2460 178779630 178779119 2.350000e-160 575.0
17 TraesCS4D01G105400 chr2D 95.019 261 11 2 2460 2718 272208862 272208602 2.520000e-110 409.0
18 TraesCS4D01G105400 chr2D 94.007 267 11 4 2458 2719 317984349 317984083 1.520000e-107 399.0
19 TraesCS4D01G105400 chr2D 80.791 354 61 6 2 352 326240766 326240417 1.240000e-68 270.0
20 TraesCS4D01G105400 chrUn 86.460 517 64 6 1948 2460 211005386 211004872 1.830000e-156 562.0
21 TraesCS4D01G105400 chr2B 82.905 661 72 18 1831 2460 756221421 756220771 8.520000e-155 556.0
22 TraesCS4D01G105400 chr2B 78.719 437 70 19 1 431 395657778 395657359 1.240000e-68 270.0
23 TraesCS4D01G105400 chr6D 86.240 516 66 4 1948 2459 107934573 107935087 3.060000e-154 555.0
24 TraesCS4D01G105400 chr6D 94.697 264 10 4 2458 2718 276661678 276661940 9.080000e-110 407.0
25 TraesCS4D01G105400 chr6D 94.318 264 11 4 2458 2718 276662295 276662033 4.220000e-108 401.0
26 TraesCS4D01G105400 chr6D 82.394 142 18 3 2 143 5102455 5102589 1.710000e-22 117.0
27 TraesCS4D01G105400 chr5D 86.600 500 62 4 1965 2460 546069264 546069762 5.130000e-152 547.0
28 TraesCS4D01G105400 chr5D 95.402 261 9 3 2460 2718 210825459 210825200 1.950000e-111 412.0
29 TraesCS4D01G105400 chr5D 96.774 31 1 0 1823 1853 476613625 476613595 5.000000e-03 52.8
30 TraesCS4D01G105400 chr1A 78.486 502 74 17 1819 2288 307494422 307493923 5.700000e-77 298.0
31 TraesCS4D01G105400 chr3A 76.682 446 78 17 2 436 204818641 204819071 9.810000e-55 224.0
32 TraesCS4D01G105400 chr7B 100.000 29 0 0 1822 1850 130132316 130132288 1.000000e-03 54.7
33 TraesCS4D01G105400 chr7B 100.000 28 0 0 1823 1850 130202727 130202700 5.000000e-03 52.8
34 TraesCS4D01G105400 chr3B 100.000 29 0 0 1822 1850 825272791 825272819 1.000000e-03 54.7


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 TraesCS4D01G105400 chr4D 84171981 84174703 2722 True 5029 5029 100.000 1 2723 1 chr4D.!!$R1 2722
1 TraesCS4D01G105400 chr4D 374835696 374836209 513 True 610 610 88.155 1948 2460 1 chr4D.!!$R3 512
2 TraesCS4D01G105400 chr4A 496114042 496115613 1571 True 2351 2351 93.723 241 1815 1 chr4A.!!$R1 1574
3 TraesCS4D01G105400 chr4B 119108791 119110719 1928 True 1321 1594 93.653 3 1756 2 chr4B.!!$R2 1753
4 TraesCS4D01G105400 chr1D 379490832 379491344 512 True 588 588 87.379 1948 2460 1 chr1D.!!$R1 512
5 TraesCS4D01G105400 chr7D 88025958 88026472 514 True 579 579 87.016 1948 2460 1 chr7D.!!$R1 512
6 TraesCS4D01G105400 chr7D 503800983 503801493 510 True 571 571 86.914 1950 2459 1 chr7D.!!$R3 509
7 TraesCS4D01G105400 chr2D 178779119 178779630 511 True 575 575 86.965 1948 2460 1 chr2D.!!$R1 512
8 TraesCS4D01G105400 chrUn 211004872 211005386 514 True 562 562 86.460 1948 2460 1 chrUn.!!$R1 512
9 TraesCS4D01G105400 chr2B 756220771 756221421 650 True 556 556 82.905 1831 2460 1 chr2B.!!$R2 629
10 TraesCS4D01G105400 chr6D 107934573 107935087 514 False 555 555 86.240 1948 2459 1 chr6D.!!$F2 511

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
70 71 0.237498 GTTCGCTTTTGAGGGTTCCG 59.763 55.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1856 2055 0.035881 CCATGAGTATGCGCTGGGAT 59.964 55.0 9.73 0.0 32.79 3.85 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
29 30 2.218759 CGATTCGAAATAGAGGGTTGCG 59.781 50.000 0.00 0.00 0.00 4.85
30 31 3.454375 GATTCGAAATAGAGGGTTGCGA 58.546 45.455 0.00 0.00 0.00 5.10
32 33 1.134907 TCGAAATAGAGGGTTGCGACC 60.135 52.381 15.51 15.51 45.75 4.79
50 51 4.143389 GCGACCGTGATAATATTCTTTCGG 60.143 45.833 15.48 15.48 41.95 4.30
70 71 0.237498 GTTCGCTTTTGAGGGTTCCG 59.763 55.000 0.00 0.00 0.00 4.30
80 81 6.486993 GCTTTTGAGGGTTCCGAGAATTATAT 59.513 38.462 0.00 0.00 0.00 0.86
104 105 7.074653 TGATTTATAGGCGGAAGAATTAGGT 57.925 36.000 0.00 0.00 0.00 3.08
117 118 2.403252 ATTAGGTCAAACGGAGGCTG 57.597 50.000 0.00 0.00 0.00 4.85
238 241 5.104900 GCTTCTAGGGTCCTTCATTGTCTAA 60.105 44.000 0.00 0.00 0.00 2.10
258 261 9.360093 TGTCTAACAAAAATTGTCAAAAATCGT 57.640 25.926 0.00 0.00 44.59 3.73
263 266 8.417780 ACAAAAATTGTCAAAAATCGTCATCA 57.582 26.923 0.00 0.00 40.56 3.07
444 447 1.751924 GAGACGTATGAGCCACCTCTT 59.248 52.381 0.00 0.00 38.93 2.85
449 452 2.716217 GTATGAGCCACCTCTTGCTTT 58.284 47.619 0.00 0.00 38.11 3.51
453 456 0.326264 AGCCACCTCTTGCTTTCGAT 59.674 50.000 0.00 0.00 32.94 3.59
481 484 7.505258 TGCCATTAGCTATGTTGTGTATTCTA 58.495 34.615 0.00 0.00 44.23 2.10
516 525 7.448777 TCTCTCAAGTACTCTGATACAAACACT 59.551 37.037 0.00 0.00 0.00 3.55
517 526 7.952671 TCTCAAGTACTCTGATACAAACACTT 58.047 34.615 0.00 0.00 0.00 3.16
518 527 8.421784 TCTCAAGTACTCTGATACAAACACTTT 58.578 33.333 0.00 0.00 0.00 2.66
519 528 8.365399 TCAAGTACTCTGATACAAACACTTTG 57.635 34.615 0.00 0.00 45.95 2.77
520 529 8.201464 TCAAGTACTCTGATACAAACACTTTGA 58.799 33.333 0.00 0.00 43.26 2.69
521 530 7.948278 AGTACTCTGATACAAACACTTTGAC 57.052 36.000 1.75 0.00 43.26 3.18
546 555 4.156008 ACCGCAGTAGAAAATTTGACCATC 59.844 41.667 0.00 0.00 0.00 3.51
568 577 1.505151 TTTGAGGCATGTGGGGGCTA 61.505 55.000 0.00 0.00 41.74 3.93
576 585 2.490718 GCATGTGGGGGCTATTTGGATA 60.491 50.000 0.00 0.00 0.00 2.59
775 802 2.844451 GCAGCAACCAAACGGCTCA 61.844 57.895 0.00 0.00 35.27 4.26
796 823 6.350629 TCAGTGATTTCAGACATCAGAAGA 57.649 37.500 0.00 0.00 31.11 2.87
814 841 5.746245 CAGAAGATACTCGTCCACAAATCTC 59.254 44.000 0.00 0.00 0.00 2.75
832 859 7.177216 ACAAATCTCAAGGCATACTTTCATTGA 59.823 33.333 0.00 0.00 37.29 2.57
871 1070 2.235402 TGTCCTTGGGATCGTACTTTCC 59.765 50.000 3.03 3.03 32.73 3.13
1098 1297 2.563427 GGCAGAGGCGCAAAAGAC 59.437 61.111 10.83 0.00 42.47 3.01
1170 1369 2.108514 CATGTCGCTCGTGGCCAAT 61.109 57.895 7.24 0.00 37.74 3.16
1476 1675 0.109735 CTGCGCTGTTCGACTACTCA 60.110 55.000 9.73 0.00 41.67 3.41
1761 1960 6.951971 AGCTATGGGTGGATAATTAAGCTAG 58.048 40.000 1.61 0.00 36.10 3.42
1780 1979 2.996631 AGCCAGTAAAAGAGGATGCTG 58.003 47.619 0.00 0.00 0.00 4.41
1784 1983 4.583871 CCAGTAAAAGAGGATGCTGTCTT 58.416 43.478 0.00 0.00 34.37 3.01
1785 1984 5.006386 CCAGTAAAAGAGGATGCTGTCTTT 58.994 41.667 0.00 0.00 43.38 2.52
1786 1985 5.106396 CCAGTAAAAGAGGATGCTGTCTTTG 60.106 44.000 0.00 0.00 41.21 2.77
1787 1986 5.471456 CAGTAAAAGAGGATGCTGTCTTTGT 59.529 40.000 0.00 0.00 41.21 2.83
1788 1987 5.703130 AGTAAAAGAGGATGCTGTCTTTGTC 59.297 40.000 0.00 0.00 41.21 3.18
1800 1999 1.525619 GTCTTTGTCTTGTCCCGTTCG 59.474 52.381 0.00 0.00 0.00 3.95
1815 2014 3.168193 CCGTTCGTCCAAATGTTAATGC 58.832 45.455 0.00 0.00 0.00 3.56
1816 2015 3.168193 CGTTCGTCCAAATGTTAATGCC 58.832 45.455 0.00 0.00 0.00 4.40
1817 2016 3.119990 CGTTCGTCCAAATGTTAATGCCT 60.120 43.478 0.00 0.00 0.00 4.75
1818 2017 4.093703 CGTTCGTCCAAATGTTAATGCCTA 59.906 41.667 0.00 0.00 0.00 3.93
1819 2018 5.391097 CGTTCGTCCAAATGTTAATGCCTAA 60.391 40.000 0.00 0.00 0.00 2.69
1820 2019 6.383415 GTTCGTCCAAATGTTAATGCCTAAA 58.617 36.000 0.00 0.00 0.00 1.85
1821 2020 6.767524 TCGTCCAAATGTTAATGCCTAAAT 57.232 33.333 0.00 0.00 0.00 1.40
1822 2021 7.867305 TCGTCCAAATGTTAATGCCTAAATA 57.133 32.000 0.00 0.00 0.00 1.40
1823 2022 8.282455 TCGTCCAAATGTTAATGCCTAAATAA 57.718 30.769 0.00 0.00 0.00 1.40
1824 2023 8.740906 TCGTCCAAATGTTAATGCCTAAATAAA 58.259 29.630 0.00 0.00 0.00 1.40
1825 2024 9.528018 CGTCCAAATGTTAATGCCTAAATAAAT 57.472 29.630 0.00 0.00 0.00 1.40
1827 2026 9.323985 TCCAAATGTTAATGCCTAAATAAATGC 57.676 29.630 0.00 0.00 0.00 3.56
1828 2027 9.328845 CCAAATGTTAATGCCTAAATAAATGCT 57.671 29.630 0.00 0.00 0.00 3.79
1853 2052 3.034030 GCAGCTGCACTTTTCGGT 58.966 55.556 33.36 0.00 41.59 4.69
1854 2053 1.360192 GCAGCTGCACTTTTCGGTT 59.640 52.632 33.36 0.00 41.59 4.44
1855 2054 0.936297 GCAGCTGCACTTTTCGGTTG 60.936 55.000 33.36 0.00 41.59 3.77
1856 2055 0.662619 CAGCTGCACTTTTCGGTTGA 59.337 50.000 0.00 0.00 0.00 3.18
1857 2056 1.267806 CAGCTGCACTTTTCGGTTGAT 59.732 47.619 0.00 0.00 0.00 2.57
1860 2059 1.200020 CTGCACTTTTCGGTTGATCCC 59.800 52.381 0.00 0.00 0.00 3.85
1867 2066 2.514592 CGGTTGATCCCAGCGCAT 60.515 61.111 11.47 0.00 0.00 4.73
1868 2067 1.227527 CGGTTGATCCCAGCGCATA 60.228 57.895 11.47 0.00 0.00 3.14
1879 2078 0.179076 CAGCGCATACTCATGGACCA 60.179 55.000 11.47 0.00 32.36 4.02
1882 2081 1.742831 GCGCATACTCATGGACCAAAA 59.257 47.619 0.30 0.00 32.36 2.44
1891 2090 3.229293 TCATGGACCAAAAGATGCAACA 58.771 40.909 0.00 0.00 0.00 3.33
1894 2093 3.791245 TGGACCAAAAGATGCAACAAAC 58.209 40.909 0.00 0.00 0.00 2.93
1909 2108 5.163322 TGCAACAAACCTGATTCCAGATTTT 60.163 36.000 0.00 0.00 43.02 1.82
1924 2123 4.827284 CCAGATTTTGTAAACTGTCCACCT 59.173 41.667 0.00 0.00 33.61 4.00
1932 2131 8.983702 TTTGTAAACTGTCCACCTACTTATTT 57.016 30.769 0.00 0.00 0.00 1.40
1982 2206 1.153046 CCAACCGTGTCAACCCAGT 60.153 57.895 0.00 0.00 0.00 4.00
1985 2209 0.463116 AACCGTGTCAACCCAGTGAC 60.463 55.000 0.00 0.00 46.74 3.67
1995 2219 1.519408 ACCCAGTGACAATGTAACGC 58.481 50.000 1.77 0.00 0.00 4.84
1996 2220 1.202710 ACCCAGTGACAATGTAACGCA 60.203 47.619 1.77 0.00 0.00 5.24
2052 2276 2.202770 TTTCACACGGCGTGTCGT 60.203 55.556 39.67 19.20 43.92 4.34
2056 2280 0.318869 TCACACGGCGTGTCGTAATT 60.319 50.000 39.67 16.84 43.92 1.40
2106 2330 3.921021 CGTGACGAGCTCTTCAAAACTAT 59.079 43.478 23.05 0.00 0.00 2.12
2197 2429 5.238432 TGCTAAACATGAACAACTTCGATGT 59.762 36.000 0.00 0.00 33.33 3.06
2203 2435 6.888430 ACATGAACAACTTCGATGTTAGAAC 58.112 36.000 15.47 8.84 40.90 3.01
2234 2466 4.024048 CCATGTGTATAAGTGAATTCGCCC 60.024 45.833 15.29 0.00 0.00 6.13
2244 2476 0.876342 GAATTCGCCCAGTAGCCTCG 60.876 60.000 0.00 0.00 0.00 4.63
2251 2483 1.753073 GCCCAGTAGCCTCGTACTTAA 59.247 52.381 0.00 0.00 30.40 1.85
2258 2490 6.405065 CCAGTAGCCTCGTACTTAATTGTGTA 60.405 42.308 0.00 0.00 30.40 2.90
2267 2499 8.915871 TCGTACTTAATTGTGTACAATAGGTC 57.084 34.615 10.37 3.60 45.06 3.85
2282 2514 7.208064 ACAATAGGTCATAGGTGGTTACATT 57.792 36.000 0.00 0.00 0.00 2.71
2303 2535 6.600032 ACATTGTTTCGTTGCCTACCATATTA 59.400 34.615 0.00 0.00 0.00 0.98
2309 2541 6.854496 TCGTTGCCTACCATATTATGAAAC 57.146 37.500 5.21 0.64 0.00 2.78
2321 2553 4.685169 ATTATGAAACTTGCTCACCGTG 57.315 40.909 0.00 0.00 0.00 4.94
2352 2585 6.803154 AAGTGTCTAACATGGTTTCTTAGC 57.197 37.500 0.00 0.00 0.00 3.09
2364 2597 3.403038 GTTTCTTAGCTGTCTGCCTCAA 58.597 45.455 0.00 0.00 44.23 3.02
2372 2605 2.159114 GCTGTCTGCCTCAAAAACCAAA 60.159 45.455 0.00 0.00 35.15 3.28
2376 2609 4.081198 TGTCTGCCTCAAAAACCAAATTGT 60.081 37.500 0.00 0.00 0.00 2.71
2385 2618 8.090214 CCTCAAAAACCAAATTGTCTACATCAT 58.910 33.333 0.00 0.00 0.00 2.45
2421 2654 2.498167 GAGTGATCCGCAATTGCCTAT 58.502 47.619 24.24 17.10 37.91 2.57
2429 2662 6.816640 TGATCCGCAATTGCCTATAATACTAC 59.183 38.462 24.24 5.36 37.91 2.73
2465 2698 2.317530 GGGACCTGAGTTGCTGATAC 57.682 55.000 0.00 0.00 0.00 2.24
2466 2699 1.471676 GGGACCTGAGTTGCTGATACG 60.472 57.143 0.00 0.00 0.00 3.06
2467 2700 1.204941 GGACCTGAGTTGCTGATACGT 59.795 52.381 0.00 0.00 0.00 3.57
2468 2701 2.531206 GACCTGAGTTGCTGATACGTC 58.469 52.381 0.00 0.00 0.00 4.34
2469 2702 2.164624 GACCTGAGTTGCTGATACGTCT 59.835 50.000 0.00 0.00 0.00 4.18
2470 2703 2.164624 ACCTGAGTTGCTGATACGTCTC 59.835 50.000 0.00 0.00 0.00 3.36
2471 2704 2.480416 CCTGAGTTGCTGATACGTCTCC 60.480 54.545 0.00 0.00 0.00 3.71
2472 2705 2.164422 CTGAGTTGCTGATACGTCTCCA 59.836 50.000 0.00 0.00 0.00 3.86
2473 2706 2.560981 TGAGTTGCTGATACGTCTCCAA 59.439 45.455 0.00 0.00 0.00 3.53
2474 2707 2.924290 GAGTTGCTGATACGTCTCCAAC 59.076 50.000 12.20 12.20 36.84 3.77
2489 2722 7.734538 CGTCTCCAACGCATTTATAATTTTT 57.265 32.000 0.00 0.00 45.76 1.94
2490 2723 8.829514 CGTCTCCAACGCATTTATAATTTTTA 57.170 30.769 0.00 0.00 45.76 1.52
2491 2724 9.445786 CGTCTCCAACGCATTTATAATTTTTAT 57.554 29.630 0.00 0.00 45.76 1.40
2581 2814 9.916360 ATTTTTGGGACTAACCTATTAACCTAG 57.084 33.333 0.00 0.00 38.98 3.02
2582 2815 8.683776 TTTTGGGACTAACCTATTAACCTAGA 57.316 34.615 0.00 0.00 38.98 2.43
2583 2816 7.909485 TTGGGACTAACCTATTAACCTAGAG 57.091 40.000 0.00 0.00 38.98 2.43
2584 2817 5.837438 TGGGACTAACCTATTAACCTAGAGC 59.163 44.000 0.00 0.00 38.98 4.09
2585 2818 5.245751 GGGACTAACCTATTAACCTAGAGCC 59.754 48.000 0.00 0.00 38.98 4.70
2586 2819 5.245751 GGACTAACCTATTAACCTAGAGCCC 59.754 48.000 0.00 0.00 35.41 5.19
2587 2820 5.785123 ACTAACCTATTAACCTAGAGCCCA 58.215 41.667 0.00 0.00 0.00 5.36
2588 2821 5.839606 ACTAACCTATTAACCTAGAGCCCAG 59.160 44.000 0.00 0.00 0.00 4.45
2589 2822 4.282292 ACCTATTAACCTAGAGCCCAGT 57.718 45.455 0.00 0.00 0.00 4.00
2590 2823 3.967987 ACCTATTAACCTAGAGCCCAGTG 59.032 47.826 0.00 0.00 0.00 3.66
2591 2824 3.244249 CCTATTAACCTAGAGCCCAGTGC 60.244 52.174 0.00 0.00 41.71 4.40
2592 2825 0.909623 TTAACCTAGAGCCCAGTGCC 59.090 55.000 0.00 0.00 42.71 5.01
2593 2826 0.252513 TAACCTAGAGCCCAGTGCCA 60.253 55.000 0.00 0.00 42.71 4.92
2594 2827 1.557269 AACCTAGAGCCCAGTGCCAG 61.557 60.000 0.00 0.00 42.71 4.85
2595 2828 1.992277 CCTAGAGCCCAGTGCCAGT 60.992 63.158 0.00 0.00 42.71 4.00
2596 2829 1.557269 CCTAGAGCCCAGTGCCAGTT 61.557 60.000 0.00 0.00 42.71 3.16
2597 2830 0.326264 CTAGAGCCCAGTGCCAGTTT 59.674 55.000 0.00 0.00 42.71 2.66
2598 2831 0.324943 TAGAGCCCAGTGCCAGTTTC 59.675 55.000 0.00 0.00 42.71 2.78
2599 2832 1.073897 GAGCCCAGTGCCAGTTTCT 59.926 57.895 0.00 0.00 42.71 2.52
2600 2833 1.228367 AGCCCAGTGCCAGTTTCTG 60.228 57.895 0.00 0.00 42.71 3.02
2601 2834 1.529244 GCCCAGTGCCAGTTTCTGT 60.529 57.895 0.00 0.00 0.00 3.41
2602 2835 1.109323 GCCCAGTGCCAGTTTCTGTT 61.109 55.000 0.00 0.00 0.00 3.16
2603 2836 1.402787 CCCAGTGCCAGTTTCTGTTT 58.597 50.000 0.00 0.00 0.00 2.83
2604 2837 1.756538 CCCAGTGCCAGTTTCTGTTTT 59.243 47.619 0.00 0.00 0.00 2.43
2605 2838 2.168313 CCCAGTGCCAGTTTCTGTTTTT 59.832 45.455 0.00 0.00 0.00 1.94
2628 2861 9.765795 TTTTTCCTTGTTTTTGAGTTTTACAGA 57.234 25.926 0.00 0.00 0.00 3.41
2629 2862 9.765795 TTTTCCTTGTTTTTGAGTTTTACAGAA 57.234 25.926 0.00 0.00 0.00 3.02
2630 2863 9.765795 TTTCCTTGTTTTTGAGTTTTACAGAAA 57.234 25.926 0.00 0.00 0.00 2.52
2631 2864 9.765795 TTCCTTGTTTTTGAGTTTTACAGAAAA 57.234 25.926 0.00 0.00 32.00 2.29
2632 2865 9.418045 TCCTTGTTTTTGAGTTTTACAGAAAAG 57.582 29.630 0.00 0.00 35.21 2.27
2633 2866 8.655970 CCTTGTTTTTGAGTTTTACAGAAAAGG 58.344 33.333 0.00 0.00 35.21 3.11
2634 2867 9.418045 CTTGTTTTTGAGTTTTACAGAAAAGGA 57.582 29.630 0.00 0.00 35.21 3.36
2635 2868 9.765795 TTGTTTTTGAGTTTTACAGAAAAGGAA 57.234 25.926 0.00 0.00 35.21 3.36
2636 2869 9.936759 TGTTTTTGAGTTTTACAGAAAAGGAAT 57.063 25.926 0.00 0.00 35.21 3.01
2638 2871 9.936759 TTTTTGAGTTTTACAGAAAAGGAATGT 57.063 25.926 0.00 0.00 35.21 2.71
2639 2872 9.581099 TTTTGAGTTTTACAGAAAAGGAATGTC 57.419 29.630 0.00 0.00 35.21 3.06
2640 2873 7.873719 TGAGTTTTACAGAAAAGGAATGTCA 57.126 32.000 0.00 0.00 35.21 3.58
2641 2874 8.287439 TGAGTTTTACAGAAAAGGAATGTCAA 57.713 30.769 0.00 0.00 35.21 3.18
2642 2875 8.744652 TGAGTTTTACAGAAAAGGAATGTCAAA 58.255 29.630 0.00 0.00 35.21 2.69
2643 2876 8.926715 AGTTTTACAGAAAAGGAATGTCAAAC 57.073 30.769 6.34 6.34 39.55 2.93
2644 2877 7.700656 AGTTTTACAGAAAAGGAATGTCAAACG 59.299 33.333 8.05 0.00 42.02 3.60
2645 2878 4.568152 ACAGAAAAGGAATGTCAAACGG 57.432 40.909 0.00 0.00 0.00 4.44
2646 2879 4.204012 ACAGAAAAGGAATGTCAAACGGA 58.796 39.130 0.00 0.00 0.00 4.69
2647 2880 4.275936 ACAGAAAAGGAATGTCAAACGGAG 59.724 41.667 0.00 0.00 0.00 4.63
2649 2882 4.515567 AGAAAAGGAATGTCAAACGGAGTC 59.484 41.667 0.00 0.00 45.00 3.36
2650 2883 2.474410 AGGAATGTCAAACGGAGTCC 57.526 50.000 0.00 0.00 45.00 3.85
2651 2884 1.697432 AGGAATGTCAAACGGAGTCCA 59.303 47.619 10.49 0.00 45.00 4.02
2652 2885 2.105821 AGGAATGTCAAACGGAGTCCAA 59.894 45.455 10.49 0.00 45.00 3.53
2653 2886 2.882137 GGAATGTCAAACGGAGTCCAAA 59.118 45.455 10.49 0.00 45.00 3.28
2654 2887 3.304458 GGAATGTCAAACGGAGTCCAAAC 60.304 47.826 10.49 0.00 45.00 2.93
2655 2888 1.292061 TGTCAAACGGAGTCCAAACG 58.708 50.000 10.49 0.00 45.00 3.60
2656 2889 0.584876 GTCAAACGGAGTCCAAACGG 59.415 55.000 10.49 0.00 45.00 4.44
2657 2890 0.464870 TCAAACGGAGTCCAAACGGA 59.535 50.000 10.49 0.00 45.00 4.69
2658 2891 1.134461 TCAAACGGAGTCCAAACGGAA 60.134 47.619 10.49 0.00 45.00 4.30
2659 2892 1.877443 CAAACGGAGTCCAAACGGAAT 59.123 47.619 10.49 0.00 45.00 3.01
2660 2893 3.068560 CAAACGGAGTCCAAACGGAATA 58.931 45.455 10.49 0.00 45.00 1.75
2661 2894 3.405823 AACGGAGTCCAAACGGAATAA 57.594 42.857 10.49 0.00 45.00 1.40
2662 2895 3.405823 ACGGAGTCCAAACGGAATAAA 57.594 42.857 10.49 0.00 29.74 1.40
2663 2896 3.742385 ACGGAGTCCAAACGGAATAAAA 58.258 40.909 10.49 0.00 29.74 1.52
2664 2897 3.499537 ACGGAGTCCAAACGGAATAAAAC 59.500 43.478 10.49 0.00 29.74 2.43
2665 2898 3.749609 CGGAGTCCAAACGGAATAAAACT 59.250 43.478 10.49 0.00 33.16 2.66
2666 2899 4.214758 CGGAGTCCAAACGGAATAAAACTT 59.785 41.667 10.49 0.00 33.16 2.66
2667 2900 5.278120 CGGAGTCCAAACGGAATAAAACTTT 60.278 40.000 10.49 0.00 33.16 2.66
2668 2901 6.073112 CGGAGTCCAAACGGAATAAAACTTTA 60.073 38.462 10.49 0.00 33.16 1.85
2669 2902 7.080099 GGAGTCCAAACGGAATAAAACTTTAC 58.920 38.462 3.60 0.00 33.16 2.01
2670 2903 6.661669 AGTCCAAACGGAATAAAACTTTACG 58.338 36.000 0.00 0.00 33.16 3.18
2671 2904 6.482973 AGTCCAAACGGAATAAAACTTTACGA 59.517 34.615 0.00 0.00 33.16 3.43
2672 2905 7.173735 AGTCCAAACGGAATAAAACTTTACGAT 59.826 33.333 0.00 0.00 33.16 3.73
2673 2906 7.269724 GTCCAAACGGAATAAAACTTTACGATG 59.730 37.037 0.00 0.00 33.16 3.84
2674 2907 7.172875 TCCAAACGGAATAAAACTTTACGATGA 59.827 33.333 0.00 0.00 0.00 2.92
2675 2908 7.966204 CCAAACGGAATAAAACTTTACGATGAT 59.034 33.333 0.00 0.00 0.00 2.45
2676 2909 9.337091 CAAACGGAATAAAACTTTACGATGATT 57.663 29.630 0.00 0.00 0.00 2.57
2677 2910 9.902196 AAACGGAATAAAACTTTACGATGATTT 57.098 25.926 0.00 0.00 0.00 2.17
2678 2911 9.902196 AACGGAATAAAACTTTACGATGATTTT 57.098 25.926 0.00 0.00 0.00 1.82
2679 2912 9.902196 ACGGAATAAAACTTTACGATGATTTTT 57.098 25.926 0.00 0.00 0.00 1.94
2686 2919 8.797266 AAACTTTACGATGATTTTTCTTGGAC 57.203 30.769 0.00 0.00 0.00 4.02
2687 2920 6.909909 ACTTTACGATGATTTTTCTTGGACC 58.090 36.000 0.00 0.00 0.00 4.46
2688 2921 6.488683 ACTTTACGATGATTTTTCTTGGACCA 59.511 34.615 0.00 0.00 0.00 4.02
2689 2922 6.494893 TTACGATGATTTTTCTTGGACCAG 57.505 37.500 0.00 0.00 0.00 4.00
2690 2923 4.651778 ACGATGATTTTTCTTGGACCAGA 58.348 39.130 0.00 0.00 0.00 3.86
2691 2924 5.070001 ACGATGATTTTTCTTGGACCAGAA 58.930 37.500 0.00 0.00 0.00 3.02
2692 2925 5.182001 ACGATGATTTTTCTTGGACCAGAAG 59.818 40.000 0.00 0.00 34.22 2.85
2693 2926 5.412594 CGATGATTTTTCTTGGACCAGAAGA 59.587 40.000 0.00 0.00 34.22 2.87
2694 2927 6.581171 ATGATTTTTCTTGGACCAGAAGAC 57.419 37.500 0.00 0.00 34.22 3.01
2695 2928 5.445069 TGATTTTTCTTGGACCAGAAGACA 58.555 37.500 0.00 0.00 34.22 3.41
2696 2929 6.070656 TGATTTTTCTTGGACCAGAAGACAT 58.929 36.000 0.00 0.00 34.22 3.06
2697 2930 6.207417 TGATTTTTCTTGGACCAGAAGACATC 59.793 38.462 0.00 5.11 34.22 3.06
2698 2931 3.703001 TTCTTGGACCAGAAGACATCC 57.297 47.619 0.00 0.00 0.00 3.51
2699 2932 2.619931 TCTTGGACCAGAAGACATCCA 58.380 47.619 0.00 0.00 39.50 3.41
2700 2933 2.303022 TCTTGGACCAGAAGACATCCAC 59.697 50.000 0.00 0.00 40.96 4.02
2701 2934 0.608130 TGGACCAGAAGACATCCACG 59.392 55.000 0.00 0.00 36.30 4.94
2702 2935 0.108138 GGACCAGAAGACATCCACGG 60.108 60.000 0.00 0.00 0.00 4.94
2703 2936 0.895530 GACCAGAAGACATCCACGGA 59.104 55.000 0.00 0.00 0.00 4.69
2704 2937 0.898320 ACCAGAAGACATCCACGGAG 59.102 55.000 0.00 0.00 0.00 4.63
2705 2938 0.460987 CCAGAAGACATCCACGGAGC 60.461 60.000 0.00 0.00 0.00 4.70
2706 2939 0.534412 CAGAAGACATCCACGGAGCT 59.466 55.000 0.00 0.00 0.00 4.09
2707 2940 1.066573 CAGAAGACATCCACGGAGCTT 60.067 52.381 0.00 0.00 0.00 3.74
2708 2941 1.066573 AGAAGACATCCACGGAGCTTG 60.067 52.381 0.00 0.00 0.00 4.01
2709 2942 0.036010 AAGACATCCACGGAGCTTGG 60.036 55.000 0.00 0.00 35.18 3.61
2711 2944 0.460987 GACATCCACGGAGCTTGGAG 60.461 60.000 11.20 6.37 46.46 3.86
2712 2945 1.194781 ACATCCACGGAGCTTGGAGT 61.195 55.000 11.20 6.90 46.46 3.85
2713 2946 0.742281 CATCCACGGAGCTTGGAGTG 60.742 60.000 11.20 7.99 46.46 3.51
2714 2947 2.046892 CCACGGAGCTTGGAGTGG 60.047 66.667 13.68 13.68 46.52 4.00
2715 2948 2.046892 CACGGAGCTTGGAGTGGG 60.047 66.667 0.00 0.00 0.00 4.61
2716 2949 3.322466 ACGGAGCTTGGAGTGGGG 61.322 66.667 0.00 0.00 0.00 4.96
2717 2950 4.101448 CGGAGCTTGGAGTGGGGG 62.101 72.222 0.00 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.482908 CCTCTATTTCGAATCGATCCCATT 58.517 41.667 6.06 0.00 35.23 3.16
1 2 4.081420 CCCTCTATTTCGAATCGATCCCAT 60.081 45.833 6.06 0.00 35.23 4.00
29 30 5.295152 ACCCGAAAGAATATTATCACGGTC 58.705 41.667 19.11 0.00 37.87 4.79
30 31 5.286267 ACCCGAAAGAATATTATCACGGT 57.714 39.130 19.11 10.42 37.87 4.83
32 33 5.611844 GCGAACCCGAAAGAATATTATCACG 60.612 44.000 0.00 0.00 38.22 4.35
34 35 5.607477 AGCGAACCCGAAAGAATATTATCA 58.393 37.500 0.00 0.00 38.22 2.15
50 51 0.596577 GGAACCCTCAAAAGCGAACC 59.403 55.000 0.00 0.00 0.00 3.62
80 81 7.074653 ACCTAATTCTTCCGCCTATAAATCA 57.925 36.000 0.00 0.00 0.00 2.57
96 97 2.678336 CAGCCTCCGTTTGACCTAATTC 59.322 50.000 0.00 0.00 0.00 2.17
104 105 2.592993 CCCCTCAGCCTCCGTTTGA 61.593 63.158 0.00 0.00 0.00 2.69
117 118 4.512914 GCTCATGTGGGGCCCCTC 62.513 72.222 40.66 36.41 36.94 4.30
407 410 6.251655 ACGTCTCCACCGTATCTATAATTC 57.748 41.667 0.00 0.00 36.65 2.17
421 424 0.179108 GGTGGCTCATACGTCTCCAC 60.179 60.000 13.02 13.02 44.71 4.02
433 436 0.320771 TCGAAAGCAAGAGGTGGCTC 60.321 55.000 0.00 0.00 40.01 4.70
444 447 2.291465 GCTAATGGCATCATCGAAAGCA 59.709 45.455 0.00 0.00 41.35 3.91
449 452 4.541973 ACATAGCTAATGGCATCATCGA 57.458 40.909 0.00 0.00 44.79 3.59
453 456 4.525996 ACACAACATAGCTAATGGCATCA 58.474 39.130 0.00 0.00 44.79 3.07
481 484 8.367660 TCAGAGTACTTGAGAGAACCAAATAT 57.632 34.615 0.00 0.00 0.00 1.28
516 525 2.623878 TTTCTACTGCGGTGGTCAAA 57.376 45.000 8.92 0.00 0.00 2.69
517 526 2.623878 TTTTCTACTGCGGTGGTCAA 57.376 45.000 8.92 0.25 0.00 3.18
518 527 2.851263 ATTTTCTACTGCGGTGGTCA 57.149 45.000 8.92 0.00 0.00 4.02
519 528 3.500680 TCAAATTTTCTACTGCGGTGGTC 59.499 43.478 8.92 0.00 0.00 4.02
520 529 3.252458 GTCAAATTTTCTACTGCGGTGGT 59.748 43.478 8.92 0.00 0.00 4.16
521 530 3.365969 GGTCAAATTTTCTACTGCGGTGG 60.366 47.826 8.92 5.33 0.00 4.61
546 555 2.703798 CCCCACATGCCTCAAAGCG 61.704 63.158 0.00 0.00 34.65 4.68
568 577 4.026052 CAACCCTTGGCTCTTATCCAAAT 58.974 43.478 0.00 0.00 42.45 2.32
606 615 3.934521 CAACACGTTGGTCAATGCA 57.065 47.368 1.83 0.00 36.95 3.96
665 674 6.572519 CCAATATTTTGGTTACAGATGGGTG 58.427 40.000 6.76 0.00 46.27 4.61
754 781 3.222855 CCGTTTGGTTGCTGCCCA 61.223 61.111 0.00 0.00 0.00 5.36
775 802 8.076910 AGTATCTTCTGATGTCTGAAATCACT 57.923 34.615 6.42 0.00 34.24 3.41
796 823 4.759782 CCTTGAGATTTGTGGACGAGTAT 58.240 43.478 0.00 0.00 0.00 2.12
814 841 4.460382 ACCTGTCAATGAAAGTATGCCTTG 59.540 41.667 0.00 0.00 32.32 3.61
832 859 2.283529 ATCTCCAACGCGGACCTGT 61.284 57.895 12.47 0.00 39.64 4.00
852 879 2.829023 AGGAAAGTACGATCCCAAGGA 58.171 47.619 14.21 0.00 36.31 3.36
871 1070 2.945008 TCTCTTGTGTGGCTTTGACAAG 59.055 45.455 0.00 0.00 45.27 3.16
1170 1369 2.697761 GCGTCCTCTGAGGTGCGTA 61.698 63.158 28.74 10.48 37.25 4.42
1605 1804 2.992689 TTCGCGTAGGACAGCCCA 60.993 61.111 5.77 0.00 37.41 5.36
1761 1960 2.680339 GACAGCATCCTCTTTTACTGGC 59.320 50.000 0.00 0.00 0.00 4.85
1780 1979 1.525619 CGAACGGGACAAGACAAAGAC 59.474 52.381 0.00 0.00 0.00 3.01
1784 1983 0.249573 GGACGAACGGGACAAGACAA 60.250 55.000 0.00 0.00 0.00 3.18
1785 1984 1.364901 GGACGAACGGGACAAGACA 59.635 57.895 0.00 0.00 0.00 3.41
1786 1985 0.249573 TTGGACGAACGGGACAAGAC 60.250 55.000 0.00 0.00 0.00 3.01
1787 1986 0.464870 TTTGGACGAACGGGACAAGA 59.535 50.000 0.00 0.00 0.00 3.02
1788 1987 1.196808 CATTTGGACGAACGGGACAAG 59.803 52.381 0.00 0.00 0.00 3.16
1815 2014 7.761249 AGCTGCACTTTTTAGCATTTATTTAGG 59.239 33.333 1.02 0.00 40.42 2.69
1816 2015 8.589629 CAGCTGCACTTTTTAGCATTTATTTAG 58.410 33.333 0.00 0.00 40.42 1.85
1817 2016 7.063308 GCAGCTGCACTTTTTAGCATTTATTTA 59.937 33.333 33.36 0.00 40.42 1.40
1818 2017 6.128472 GCAGCTGCACTTTTTAGCATTTATTT 60.128 34.615 33.36 0.00 40.42 1.40
1819 2018 5.349543 GCAGCTGCACTTTTTAGCATTTATT 59.650 36.000 33.36 0.00 40.42 1.40
1820 2019 4.866486 GCAGCTGCACTTTTTAGCATTTAT 59.134 37.500 33.36 0.00 40.42 1.40
1821 2020 4.236935 GCAGCTGCACTTTTTAGCATTTA 58.763 39.130 33.36 0.00 40.42 1.40
1822 2021 3.062042 GCAGCTGCACTTTTTAGCATTT 58.938 40.909 33.36 0.00 40.42 2.32
1823 2022 2.680577 GCAGCTGCACTTTTTAGCATT 58.319 42.857 33.36 0.00 40.42 3.56
1824 2023 2.358939 GCAGCTGCACTTTTTAGCAT 57.641 45.000 33.36 0.00 40.42 3.79
1825 2024 3.871775 GCAGCTGCACTTTTTAGCA 57.128 47.368 33.36 0.00 39.84 3.49
1850 2049 1.227527 TATGCGCTGGGATCAACCG 60.228 57.895 9.73 0.00 40.11 4.44
1851 2050 0.179045 AGTATGCGCTGGGATCAACC 60.179 55.000 9.73 0.00 38.08 3.77
1852 2051 1.221414 GAGTATGCGCTGGGATCAAC 58.779 55.000 9.73 0.00 0.00 3.18
1853 2052 0.829990 TGAGTATGCGCTGGGATCAA 59.170 50.000 9.73 0.00 0.00 2.57
1854 2053 1.051008 ATGAGTATGCGCTGGGATCA 58.949 50.000 9.73 7.16 0.00 2.92
1855 2054 1.436600 CATGAGTATGCGCTGGGATC 58.563 55.000 9.73 0.85 0.00 3.36
1856 2055 0.035881 CCATGAGTATGCGCTGGGAT 59.964 55.000 9.73 0.00 32.79 3.85
1857 2056 1.048160 TCCATGAGTATGCGCTGGGA 61.048 55.000 9.73 0.84 32.79 4.37
1860 2059 0.179076 TGGTCCATGAGTATGCGCTG 60.179 55.000 9.73 0.00 32.79 5.18
1867 2066 4.299586 TGCATCTTTTGGTCCATGAGTA 57.700 40.909 0.00 0.00 0.00 2.59
1868 2067 3.159213 TGCATCTTTTGGTCCATGAGT 57.841 42.857 0.00 0.00 0.00 3.41
1879 2078 5.163322 TGGAATCAGGTTTGTTGCATCTTTT 60.163 36.000 0.00 0.00 0.00 2.27
1882 2081 3.499338 TGGAATCAGGTTTGTTGCATCT 58.501 40.909 0.00 0.00 0.00 2.90
1894 2093 7.219484 ACAGTTTACAAAATCTGGAATCAGG 57.781 36.000 0.00 0.00 41.23 3.86
1936 2135 8.480853 CGGACGAAATGAAGAATCTTTCTATAC 58.519 37.037 0.00 0.00 39.61 1.47
1940 2139 5.348997 GTCGGACGAAATGAAGAATCTTTCT 59.651 40.000 0.00 0.00 43.15 2.52
1955 2179 2.027897 CACGGTTGGTCGGACGAA 59.972 61.111 1.15 1.15 0.00 3.85
2043 2267 2.407361 CGGATCATAATTACGACACGCC 59.593 50.000 0.00 0.00 0.00 5.68
2052 2276 6.183360 CCAACGGTGAAAACGGATCATAATTA 60.183 38.462 0.00 0.00 35.23 1.40
2056 2280 3.004171 CCAACGGTGAAAACGGATCATA 58.996 45.455 0.00 0.00 35.23 2.15
2172 2404 5.940192 TCGAAGTTGTTCATGTTTAGCAT 57.060 34.783 0.00 0.00 38.60 3.79
2185 2417 6.142817 GCAATTGTTCTAACATCGAAGTTGT 58.857 36.000 15.86 0.00 38.95 3.32
2197 2429 6.832520 ATACACATGGTGCAATTGTTCTAA 57.167 33.333 7.40 0.00 36.98 2.10
2203 2435 6.193514 TCACTTATACACATGGTGCAATTG 57.806 37.500 0.00 0.00 36.98 2.32
2234 2466 5.408356 ACACAATTAAGTACGAGGCTACTG 58.592 41.667 0.00 0.00 0.00 2.74
2258 2490 6.824958 ATGTAACCACCTATGACCTATTGT 57.175 37.500 0.00 0.00 0.00 2.71
2267 2499 5.873179 ACGAAACAATGTAACCACCTATG 57.127 39.130 0.00 0.00 0.00 2.23
2282 2514 6.350103 TCATAATATGGTAGGCAACGAAACA 58.650 36.000 0.00 0.00 46.39 2.83
2303 2535 2.254546 TCACGGTGAGCAAGTTTCAT 57.745 45.000 6.76 0.00 0.00 2.57
2309 2541 0.249868 TCCACTTCACGGTGAGCAAG 60.250 55.000 11.14 8.69 39.34 4.01
2321 2553 5.063880 ACCATGTTAGACACTTTCCACTTC 58.936 41.667 0.00 0.00 0.00 3.01
2352 2585 3.799281 TTTGGTTTTTGAGGCAGACAG 57.201 42.857 0.00 0.00 0.00 3.51
2364 2597 8.788806 TCGTAATGATGTAGACAATTTGGTTTT 58.211 29.630 0.78 0.00 0.00 2.43
2372 2605 6.480320 GGAAGCTTCGTAATGATGTAGACAAT 59.520 38.462 19.91 0.00 0.00 2.71
2376 2609 5.854010 AGGAAGCTTCGTAATGATGTAGA 57.146 39.130 19.63 0.00 0.00 2.59
2385 2618 3.076621 TCACTCGTAGGAAGCTTCGTAA 58.923 45.455 25.91 13.62 30.38 3.18
2421 2654 7.262772 CCTGATGGACAACTTTCGTAGTATTA 58.737 38.462 0.00 0.00 33.17 0.98
2429 2662 1.003118 TCCCCTGATGGACAACTTTCG 59.997 52.381 0.00 0.00 35.39 3.46
2453 2686 2.924290 GTTGGAGACGTATCAGCAACTC 59.076 50.000 18.89 6.58 0.00 3.01
2555 2788 9.916360 CTAGGTTAATAGGTTAGTCCCAAAAAT 57.084 33.333 0.00 0.00 36.75 1.82
2556 2789 9.114938 TCTAGGTTAATAGGTTAGTCCCAAAAA 57.885 33.333 0.00 0.00 36.75 1.94
2557 2790 8.683776 TCTAGGTTAATAGGTTAGTCCCAAAA 57.316 34.615 0.00 0.00 36.75 2.44
2558 2791 7.147602 GCTCTAGGTTAATAGGTTAGTCCCAAA 60.148 40.741 0.00 0.00 36.75 3.28
2559 2792 6.325804 GCTCTAGGTTAATAGGTTAGTCCCAA 59.674 42.308 0.00 0.00 36.75 4.12
2560 2793 5.837438 GCTCTAGGTTAATAGGTTAGTCCCA 59.163 44.000 0.00 0.00 36.75 4.37
2561 2794 5.245751 GGCTCTAGGTTAATAGGTTAGTCCC 59.754 48.000 0.00 0.00 36.75 4.46
2562 2795 5.245751 GGGCTCTAGGTTAATAGGTTAGTCC 59.754 48.000 0.00 0.00 0.00 3.85
2563 2796 5.837438 TGGGCTCTAGGTTAATAGGTTAGTC 59.163 44.000 0.00 0.00 0.00 2.59
2564 2797 5.785123 TGGGCTCTAGGTTAATAGGTTAGT 58.215 41.667 0.00 0.00 0.00 2.24
2565 2798 5.839606 ACTGGGCTCTAGGTTAATAGGTTAG 59.160 44.000 0.00 0.00 0.00 2.34
2566 2799 5.601313 CACTGGGCTCTAGGTTAATAGGTTA 59.399 44.000 0.00 0.00 0.00 2.85
2567 2800 4.409247 CACTGGGCTCTAGGTTAATAGGTT 59.591 45.833 0.00 0.00 0.00 3.50
2568 2801 3.967987 CACTGGGCTCTAGGTTAATAGGT 59.032 47.826 0.00 0.00 0.00 3.08
2569 2802 3.244249 GCACTGGGCTCTAGGTTAATAGG 60.244 52.174 0.00 0.00 40.25 2.57
2570 2803 3.244249 GGCACTGGGCTCTAGGTTAATAG 60.244 52.174 0.21 0.00 44.01 1.73
2571 2804 2.704065 GGCACTGGGCTCTAGGTTAATA 59.296 50.000 0.21 0.00 44.01 0.98
2572 2805 1.490910 GGCACTGGGCTCTAGGTTAAT 59.509 52.381 0.21 0.00 44.01 1.40
2573 2806 0.909623 GGCACTGGGCTCTAGGTTAA 59.090 55.000 0.21 0.00 44.01 2.01
2574 2807 0.252513 TGGCACTGGGCTCTAGGTTA 60.253 55.000 0.21 0.00 44.01 2.85
2575 2808 1.538876 TGGCACTGGGCTCTAGGTT 60.539 57.895 0.21 0.00 44.01 3.50
2576 2809 1.992277 CTGGCACTGGGCTCTAGGT 60.992 63.158 0.21 0.00 44.01 3.08
2577 2810 1.557269 AACTGGCACTGGGCTCTAGG 61.557 60.000 0.21 0.00 44.01 3.02
2578 2811 0.326264 AAACTGGCACTGGGCTCTAG 59.674 55.000 0.21 0.73 44.01 2.43
2579 2812 0.324943 GAAACTGGCACTGGGCTCTA 59.675 55.000 0.21 0.00 44.01 2.43
2580 2813 1.073897 GAAACTGGCACTGGGCTCT 59.926 57.895 0.21 0.00 44.01 4.09
2581 2814 1.073897 AGAAACTGGCACTGGGCTC 59.926 57.895 0.21 0.00 44.01 4.70
2582 2815 1.228367 CAGAAACTGGCACTGGGCT 60.228 57.895 0.21 0.00 44.01 5.19
2583 2816 1.109323 AACAGAAACTGGCACTGGGC 61.109 55.000 7.62 0.00 43.74 5.36
2584 2817 1.402787 AAACAGAAACTGGCACTGGG 58.597 50.000 7.62 0.00 35.51 4.45
2585 2818 3.525268 AAAAACAGAAACTGGCACTGG 57.475 42.857 7.62 0.00 35.51 4.00
2602 2835 9.765795 TCTGTAAAACTCAAAAACAAGGAAAAA 57.234 25.926 0.00 0.00 0.00 1.94
2603 2836 9.765795 TTCTGTAAAACTCAAAAACAAGGAAAA 57.234 25.926 0.00 0.00 0.00 2.29
2604 2837 9.765795 TTTCTGTAAAACTCAAAAACAAGGAAA 57.234 25.926 0.00 0.00 0.00 3.13
2605 2838 9.765795 TTTTCTGTAAAACTCAAAAACAAGGAA 57.234 25.926 0.00 0.00 29.59 3.36
2606 2839 9.418045 CTTTTCTGTAAAACTCAAAAACAAGGA 57.582 29.630 0.00 0.00 31.37 3.36
2607 2840 8.655970 CCTTTTCTGTAAAACTCAAAAACAAGG 58.344 33.333 0.00 0.00 31.37 3.61
2608 2841 9.418045 TCCTTTTCTGTAAAACTCAAAAACAAG 57.582 29.630 0.00 0.00 31.37 3.16
2609 2842 9.765795 TTCCTTTTCTGTAAAACTCAAAAACAA 57.234 25.926 0.00 0.00 31.37 2.83
2610 2843 9.936759 ATTCCTTTTCTGTAAAACTCAAAAACA 57.063 25.926 0.00 0.00 31.37 2.83
2612 2845 9.936759 ACATTCCTTTTCTGTAAAACTCAAAAA 57.063 25.926 0.00 0.00 31.37 1.94
2613 2846 9.581099 GACATTCCTTTTCTGTAAAACTCAAAA 57.419 29.630 0.00 0.00 31.37 2.44
2614 2847 8.744652 TGACATTCCTTTTCTGTAAAACTCAAA 58.255 29.630 0.00 0.00 31.37 2.69
2615 2848 8.287439 TGACATTCCTTTTCTGTAAAACTCAA 57.713 30.769 0.00 0.00 31.37 3.02
2616 2849 7.873719 TGACATTCCTTTTCTGTAAAACTCA 57.126 32.000 0.00 0.00 31.37 3.41
2617 2850 9.020813 GTTTGACATTCCTTTTCTGTAAAACTC 57.979 33.333 7.36 0.00 39.54 3.01
2618 2851 7.700656 CGTTTGACATTCCTTTTCTGTAAAACT 59.299 33.333 11.22 0.00 40.08 2.66
2619 2852 7.043656 CCGTTTGACATTCCTTTTCTGTAAAAC 60.044 37.037 5.25 5.25 39.38 2.43
2620 2853 6.975772 CCGTTTGACATTCCTTTTCTGTAAAA 59.024 34.615 0.00 0.00 33.58 1.52
2621 2854 6.319152 TCCGTTTGACATTCCTTTTCTGTAAA 59.681 34.615 0.00 0.00 0.00 2.01
2622 2855 5.823570 TCCGTTTGACATTCCTTTTCTGTAA 59.176 36.000 0.00 0.00 0.00 2.41
2623 2856 5.369833 TCCGTTTGACATTCCTTTTCTGTA 58.630 37.500 0.00 0.00 0.00 2.74
2624 2857 4.204012 TCCGTTTGACATTCCTTTTCTGT 58.796 39.130 0.00 0.00 0.00 3.41
2625 2858 4.275936 ACTCCGTTTGACATTCCTTTTCTG 59.724 41.667 0.00 0.00 0.00 3.02
2626 2859 4.461198 ACTCCGTTTGACATTCCTTTTCT 58.539 39.130 0.00 0.00 0.00 2.52
2627 2860 4.320275 GGACTCCGTTTGACATTCCTTTTC 60.320 45.833 0.00 0.00 0.00 2.29
2628 2861 3.568430 GGACTCCGTTTGACATTCCTTTT 59.432 43.478 0.00 0.00 0.00 2.27
2629 2862 3.146847 GGACTCCGTTTGACATTCCTTT 58.853 45.455 0.00 0.00 0.00 3.11
2630 2863 2.105821 TGGACTCCGTTTGACATTCCTT 59.894 45.455 0.00 0.00 0.00 3.36
2631 2864 1.697432 TGGACTCCGTTTGACATTCCT 59.303 47.619 0.00 0.00 0.00 3.36
2632 2865 2.178912 TGGACTCCGTTTGACATTCC 57.821 50.000 0.00 0.00 0.00 3.01
2633 2866 3.606153 CGTTTGGACTCCGTTTGACATTC 60.606 47.826 0.00 0.00 0.00 2.67
2634 2867 2.289547 CGTTTGGACTCCGTTTGACATT 59.710 45.455 0.00 0.00 0.00 2.71
2635 2868 1.871039 CGTTTGGACTCCGTTTGACAT 59.129 47.619 0.00 0.00 0.00 3.06
2636 2869 1.292061 CGTTTGGACTCCGTTTGACA 58.708 50.000 0.00 0.00 0.00 3.58
2637 2870 0.584876 CCGTTTGGACTCCGTTTGAC 59.415 55.000 0.00 0.00 37.49 3.18
2638 2871 0.464870 TCCGTTTGGACTCCGTTTGA 59.535 50.000 0.00 0.00 40.17 2.69
2639 2872 1.301423 TTCCGTTTGGACTCCGTTTG 58.699 50.000 0.00 0.00 46.45 2.93
2640 2873 2.265589 ATTCCGTTTGGACTCCGTTT 57.734 45.000 0.00 0.00 46.45 3.60
2641 2874 3.405823 TTATTCCGTTTGGACTCCGTT 57.594 42.857 0.00 0.00 46.45 4.44
2642 2875 3.405823 TTTATTCCGTTTGGACTCCGT 57.594 42.857 0.00 0.00 46.45 4.69
2643 2876 3.749609 AGTTTTATTCCGTTTGGACTCCG 59.250 43.478 0.00 0.00 46.45 4.63
2644 2877 5.700722 AAGTTTTATTCCGTTTGGACTCC 57.299 39.130 0.00 0.00 46.45 3.85
2645 2878 6.793680 CGTAAAGTTTTATTCCGTTTGGACTC 59.206 38.462 0.00 0.00 46.45 3.36
2646 2879 6.482973 TCGTAAAGTTTTATTCCGTTTGGACT 59.517 34.615 0.00 0.00 46.45 3.85
2647 2880 6.657888 TCGTAAAGTTTTATTCCGTTTGGAC 58.342 36.000 0.00 0.00 46.45 4.02
2648 2881 6.857777 TCGTAAAGTTTTATTCCGTTTGGA 57.142 33.333 0.00 0.00 44.61 3.53
2649 2882 7.299586 TCATCGTAAAGTTTTATTCCGTTTGG 58.700 34.615 0.00 0.00 0.00 3.28
2650 2883 8.889849 ATCATCGTAAAGTTTTATTCCGTTTG 57.110 30.769 0.00 0.00 0.00 2.93
2651 2884 9.902196 AAATCATCGTAAAGTTTTATTCCGTTT 57.098 25.926 0.00 0.00 0.00 3.60
2652 2885 9.902196 AAAATCATCGTAAAGTTTTATTCCGTT 57.098 25.926 0.00 0.00 0.00 4.44
2653 2886 9.902196 AAAAATCATCGTAAAGTTTTATTCCGT 57.098 25.926 0.00 0.00 0.00 4.69
2660 2893 9.244799 GTCCAAGAAAAATCATCGTAAAGTTTT 57.755 29.630 0.00 0.00 0.00 2.43
2661 2894 7.865889 GGTCCAAGAAAAATCATCGTAAAGTTT 59.134 33.333 0.00 0.00 0.00 2.66
2662 2895 7.013846 TGGTCCAAGAAAAATCATCGTAAAGTT 59.986 33.333 0.00 0.00 0.00 2.66
2663 2896 6.488683 TGGTCCAAGAAAAATCATCGTAAAGT 59.511 34.615 0.00 0.00 0.00 2.66
2664 2897 6.908825 TGGTCCAAGAAAAATCATCGTAAAG 58.091 36.000 0.00 0.00 0.00 1.85
2665 2898 6.712998 TCTGGTCCAAGAAAAATCATCGTAAA 59.287 34.615 0.00 0.00 0.00 2.01
2666 2899 6.234920 TCTGGTCCAAGAAAAATCATCGTAA 58.765 36.000 0.00 0.00 0.00 3.18
2667 2900 5.800296 TCTGGTCCAAGAAAAATCATCGTA 58.200 37.500 0.00 0.00 0.00 3.43
2668 2901 4.651778 TCTGGTCCAAGAAAAATCATCGT 58.348 39.130 0.00 0.00 0.00 3.73
2669 2902 5.412594 TCTTCTGGTCCAAGAAAAATCATCG 59.587 40.000 0.00 0.00 35.79 3.84
2670 2903 6.207417 TGTCTTCTGGTCCAAGAAAAATCATC 59.793 38.462 0.00 0.00 35.79 2.92
2671 2904 6.070656 TGTCTTCTGGTCCAAGAAAAATCAT 58.929 36.000 0.00 0.00 35.79 2.45
2672 2905 5.445069 TGTCTTCTGGTCCAAGAAAAATCA 58.555 37.500 0.00 0.00 35.79 2.57
2673 2906 6.349694 GGATGTCTTCTGGTCCAAGAAAAATC 60.350 42.308 0.00 0.00 35.79 2.17
2674 2907 5.478332 GGATGTCTTCTGGTCCAAGAAAAAT 59.522 40.000 0.00 0.00 35.79 1.82
2675 2908 4.827284 GGATGTCTTCTGGTCCAAGAAAAA 59.173 41.667 0.00 0.00 35.79 1.94
2676 2909 4.141274 TGGATGTCTTCTGGTCCAAGAAAA 60.141 41.667 0.00 0.00 37.78 2.29
2677 2910 3.394274 TGGATGTCTTCTGGTCCAAGAAA 59.606 43.478 0.00 0.00 37.78 2.52
2678 2911 2.978978 TGGATGTCTTCTGGTCCAAGAA 59.021 45.455 0.00 0.00 37.78 2.52
2679 2912 2.303022 GTGGATGTCTTCTGGTCCAAGA 59.697 50.000 0.00 0.00 42.01 3.02
2680 2913 2.704572 GTGGATGTCTTCTGGTCCAAG 58.295 52.381 0.00 0.00 42.01 3.61
2681 2914 1.001974 CGTGGATGTCTTCTGGTCCAA 59.998 52.381 0.00 0.00 42.01 3.53
2682 2915 0.608130 CGTGGATGTCTTCTGGTCCA 59.392 55.000 0.00 0.00 38.37 4.02
2683 2916 0.108138 CCGTGGATGTCTTCTGGTCC 60.108 60.000 0.00 0.00 0.00 4.46
2684 2917 0.895530 TCCGTGGATGTCTTCTGGTC 59.104 55.000 0.00 0.00 0.00 4.02
2685 2918 0.898320 CTCCGTGGATGTCTTCTGGT 59.102 55.000 0.00 0.00 0.00 4.00
2686 2919 0.460987 GCTCCGTGGATGTCTTCTGG 60.461 60.000 0.00 0.00 0.00 3.86
2687 2920 0.534412 AGCTCCGTGGATGTCTTCTG 59.466 55.000 0.00 0.00 0.00 3.02
2688 2921 1.066573 CAAGCTCCGTGGATGTCTTCT 60.067 52.381 0.00 0.00 0.00 2.85
2689 2922 1.363744 CAAGCTCCGTGGATGTCTTC 58.636 55.000 0.00 0.00 0.00 2.87
2690 2923 0.036010 CCAAGCTCCGTGGATGTCTT 60.036 55.000 0.00 0.00 38.54 3.01
2691 2924 0.904865 TCCAAGCTCCGTGGATGTCT 60.905 55.000 1.25 0.00 40.33 3.41
2692 2925 0.460987 CTCCAAGCTCCGTGGATGTC 60.461 60.000 6.08 0.00 44.19 3.06
2693 2926 1.194781 ACTCCAAGCTCCGTGGATGT 61.195 55.000 6.08 4.58 44.19 3.06
2694 2927 0.742281 CACTCCAAGCTCCGTGGATG 60.742 60.000 6.08 4.13 44.19 3.51
2695 2928 1.599047 CACTCCAAGCTCCGTGGAT 59.401 57.895 6.08 0.00 44.19 3.41
2696 2929 3.059982 CACTCCAAGCTCCGTGGA 58.940 61.111 5.51 5.51 43.03 4.02
2697 2930 2.046892 CCACTCCAAGCTCCGTGG 60.047 66.667 8.63 8.63 40.71 4.94
2698 2931 2.046892 CCCACTCCAAGCTCCGTG 60.047 66.667 0.00 0.00 0.00 4.94
2699 2932 3.322466 CCCCACTCCAAGCTCCGT 61.322 66.667 0.00 0.00 0.00 4.69
2700 2933 4.101448 CCCCCACTCCAAGCTCCG 62.101 72.222 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.