Multiple sequence alignment - TraesCS1B01G104300

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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 TraesCS1B01G104300 chr1B 100.000 2454 0 0 1 2454 114690532 114692985 0.000000e+00 4532.0
1 TraesCS1B01G104300 chr1B 84.783 92 6 5 2184 2273 392735753 392735838 4.350000e-13 86.1
2 TraesCS1B01G104300 chr1B 93.478 46 3 0 1872 1917 26834590 26834635 4.380000e-08 69.4
3 TraesCS1B01G104300 chr1A 90.719 668 47 10 433 1091 72754154 72754815 0.000000e+00 876.0
4 TraesCS1B01G104300 chr1A 91.555 521 32 8 1115 1633 72754812 72755322 0.000000e+00 708.0
5 TraesCS1B01G104300 chr1A 89.908 436 39 3 1 435 72753666 72754097 7.670000e-155 556.0
6 TraesCS1B01G104300 chr1D 86.914 512 39 13 460 952 72883417 72883919 1.280000e-152 549.0
7 TraesCS1B01G104300 chr1D 92.697 356 25 1 940 1294 72883968 72884323 1.680000e-141 512.0
8 TraesCS1B01G104300 chr1D 91.714 350 23 5 1285 1631 72884447 72884793 4.750000e-132 481.0
9 TraesCS1B01G104300 chr1D 88.718 390 35 5 2 387 72882608 72882992 3.690000e-128 468.0
10 TraesCS1B01G104300 chr5D 73.034 356 64 26 1920 2257 554154373 554154714 2.010000e-16 97.1
11 TraesCS1B01G104300 chr3A 84.694 98 9 5 2175 2268 57028925 57028830 2.600000e-15 93.5
12 TraesCS1B01G104300 chr3A 80.435 92 11 6 1939 2030 31655416 31655332 2.040000e-06 63.9
13 TraesCS1B01G104300 chr3A 100.000 30 0 0 1891 1920 621985932 621985961 3.410000e-04 56.5
14 TraesCS1B01G104300 chr4A 100.000 29 0 0 2189 2217 66890305 66890277 1.000000e-03 54.7
15 TraesCS1B01G104300 chr7B 100.000 28 0 0 1893 1920 591949026 591948999 4.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G104300 chr1B 114690532 114692985 2453 False 4532.000000 4532 100.000000 1 2454 1 chr1B.!!$F2 2453
1 TraesCS1B01G104300 chr1A 72753666 72755322 1656 False 713.333333 876 90.727333 1 1633 3 chr1A.!!$F1 1632
2 TraesCS1B01G104300 chr1D 72882608 72884793 2185 False 502.500000 549 90.010750 2 1631 4 chr1D.!!$F1 1629

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
530 887 0.042188 CGTGTTTTGCCTGTCACTCG 60.042 55.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2156 2763 0.036732 ACGAGAAAAGCAGGCATCCA 59.963 50.0 0.0 0.0 0.0 3.41 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
46 47 9.599322 GAAATATATTGTAAGCAATTCCGTCAG 57.401 33.333 0.00 0.00 42.19 3.51
117 120 4.202212 GGGTGTCAAAATAGTTTGTGCCTT 60.202 41.667 14.70 0.00 43.90 4.35
219 222 3.291101 GACAAGGGACGCCTACGCA 62.291 63.158 0.00 0.00 45.53 5.24
232 235 1.463674 CTACGCAGCAAAGGGGAATT 58.536 50.000 0.00 0.00 0.00 2.17
244 247 0.677842 GGGGAATTGGATGCATGAGC 59.322 55.000 2.46 0.00 42.57 4.26
255 258 0.321346 TGCATGAGCTCTTCGTCCAA 59.679 50.000 16.19 0.00 42.74 3.53
277 280 2.604139 TGGACACCATAGTCACTGTCA 58.396 47.619 0.00 0.00 40.29 3.58
290 293 5.138276 AGTCACTGTCACTAAGTCTACCAA 58.862 41.667 0.00 0.00 0.00 3.67
291 294 5.775701 AGTCACTGTCACTAAGTCTACCAAT 59.224 40.000 0.00 0.00 0.00 3.16
292 295 6.946583 AGTCACTGTCACTAAGTCTACCAATA 59.053 38.462 0.00 0.00 0.00 1.90
330 334 2.158871 GGCCAATGAGGTCACCGTAATA 60.159 50.000 0.00 0.00 43.39 0.98
338 342 2.626743 AGGTCACCGTAATATCCTTCGG 59.373 50.000 0.00 0.00 46.98 4.30
339 343 2.401351 GTCACCGTAATATCCTTCGGC 58.599 52.381 0.00 0.00 45.76 5.54
340 344 1.001048 TCACCGTAATATCCTTCGGCG 60.001 52.381 0.00 0.00 45.76 6.46
342 346 1.891150 ACCGTAATATCCTTCGGCGAT 59.109 47.619 11.76 0.00 45.76 4.58
343 347 3.084039 ACCGTAATATCCTTCGGCGATA 58.916 45.455 11.76 0.00 45.76 2.92
345 349 4.022068 ACCGTAATATCCTTCGGCGATAAA 60.022 41.667 11.76 0.00 45.76 1.40
348 352 5.285607 CGTAATATCCTTCGGCGATAAAGAC 59.714 44.000 11.76 1.15 0.00 3.01
349 353 4.866508 ATATCCTTCGGCGATAAAGACA 57.133 40.909 11.76 0.00 0.00 3.41
350 354 3.536956 ATCCTTCGGCGATAAAGACAA 57.463 42.857 11.76 0.00 0.00 3.18
410 628 8.988064 TTAATTTGCACACTAAACAAAGTTGA 57.012 26.923 0.00 0.00 36.78 3.18
435 653 0.893727 GGGATGTGTGGTGGGTTGAC 60.894 60.000 0.00 0.00 0.00 3.18
442 719 2.203437 GGTGGGTTGACGGGCTTT 60.203 61.111 0.00 0.00 0.00 3.51
455 732 4.407621 TGACGGGCTTTCTTATATCCTTCA 59.592 41.667 0.00 0.00 0.00 3.02
500 856 1.208776 GTTGTATAAGTGACGGGGCCT 59.791 52.381 0.84 0.00 0.00 5.19
503 859 0.748450 TATAAGTGACGGGGCCTTCG 59.252 55.000 15.43 15.43 0.00 3.79
530 887 0.042188 CGTGTTTTGCCTGTCACTCG 60.042 55.000 0.00 0.00 0.00 4.18
538 895 1.890489 TGCCTGTCACTCGTTAGCTTA 59.110 47.619 0.00 0.00 0.00 3.09
542 899 3.921021 CCTGTCACTCGTTAGCTTACTTG 59.079 47.826 0.85 0.00 0.00 3.16
563 920 3.071023 TGCAGTAGTTATATGGAGCACCC 59.929 47.826 0.00 0.00 34.81 4.61
595 952 6.837048 ACACCCCTTAAATGTTTTAGAGTTGT 59.163 34.615 0.00 0.00 0.00 3.32
607 964 8.241497 TGTTTTAGAGTTGTGTCCTAGTCTAA 57.759 34.615 0.00 0.00 36.90 2.10
612 969 9.970553 TTAGAGTTGTGTCCTAGTCTAAATCTA 57.029 33.333 0.00 0.00 36.24 1.98
613 970 8.880991 AGAGTTGTGTCCTAGTCTAAATCTAA 57.119 34.615 0.00 0.00 0.00 2.10
614 971 8.962679 AGAGTTGTGTCCTAGTCTAAATCTAAG 58.037 37.037 0.00 0.00 0.00 2.18
752 1119 6.151144 ACTTGCAAGGGATAAGTATTTGTGAC 59.849 38.462 29.18 0.00 33.22 3.67
770 1137 4.141367 TGTGACATAAACCCTCCTCACAAA 60.141 41.667 0.00 0.00 36.08 2.83
807 1175 2.823747 ACGTACATAGAGTGCTCACCAA 59.176 45.455 1.82 0.00 0.00 3.67
872 1240 7.123247 ACATTCAAGATTAATTAGCACAAGCCT 59.877 33.333 0.00 0.00 43.56 4.58
992 1429 7.500227 CCTCTATAAAAGACTCCATTTGCATGA 59.500 37.037 0.00 0.00 31.07 3.07
1005 1442 5.421277 CATTTGCATGACCCAAACACATAT 58.579 37.500 0.00 0.00 35.27 1.78
1053 1490 5.301805 CCAAACTCCCAAGTGTTGTAAGAAT 59.698 40.000 0.00 0.00 35.36 2.40
1091 1555 2.887152 ACACAAATTCTGCTCTTGGGTC 59.113 45.455 0.00 0.00 30.97 4.46
1092 1556 3.152341 CACAAATTCTGCTCTTGGGTCT 58.848 45.455 0.00 0.00 0.00 3.85
1093 1557 3.571401 CACAAATTCTGCTCTTGGGTCTT 59.429 43.478 0.00 0.00 0.00 3.01
1094 1558 3.571401 ACAAATTCTGCTCTTGGGTCTTG 59.429 43.478 0.00 0.00 0.00 3.02
1095 1559 1.831580 ATTCTGCTCTTGGGTCTTGC 58.168 50.000 0.00 0.00 0.00 4.01
1096 1560 0.250901 TTCTGCTCTTGGGTCTTGCC 60.251 55.000 0.00 0.00 0.00 4.52
1105 1569 4.326255 GGTCTTGCCCTCATGGTG 57.674 61.111 0.00 0.00 36.04 4.17
1106 1570 2.048603 GGTCTTGCCCTCATGGTGC 61.049 63.158 0.00 0.00 36.04 5.01
1107 1571 1.001641 GTCTTGCCCTCATGGTGCT 60.002 57.895 0.00 0.00 36.04 4.40
1108 1572 0.253044 GTCTTGCCCTCATGGTGCTA 59.747 55.000 0.00 0.00 36.04 3.49
1109 1573 1.133976 GTCTTGCCCTCATGGTGCTAT 60.134 52.381 0.00 0.00 36.04 2.97
1110 1574 1.141657 TCTTGCCCTCATGGTGCTATC 59.858 52.381 0.00 0.00 36.04 2.08
1111 1575 0.918258 TTGCCCTCATGGTGCTATCA 59.082 50.000 0.00 0.00 36.04 2.15
1112 1576 1.142936 TGCCCTCATGGTGCTATCAT 58.857 50.000 0.00 0.00 36.04 2.45
1113 1577 1.072806 TGCCCTCATGGTGCTATCATC 59.927 52.381 0.00 0.00 36.04 2.92
1114 1578 1.943046 GCCCTCATGGTGCTATCATCG 60.943 57.143 0.00 0.00 36.04 3.84
1115 1579 1.338484 CCCTCATGGTGCTATCATCGG 60.338 57.143 0.00 0.00 0.00 4.18
1116 1580 1.338484 CCTCATGGTGCTATCATCGGG 60.338 57.143 0.00 0.00 0.00 5.14
1117 1581 1.345741 CTCATGGTGCTATCATCGGGT 59.654 52.381 0.00 0.00 0.00 5.28
1167 1631 7.921786 ATACATATTACATGCGGCAATTACT 57.078 32.000 6.82 0.00 0.00 2.24
1179 1643 4.262506 GCGGCAATTACTCTATCCTAACCT 60.263 45.833 0.00 0.00 0.00 3.50
1225 1690 1.002017 ATGGCAACCATTGAGGGGG 59.998 57.895 0.00 0.00 42.23 5.40
1398 1996 2.556114 GCCATTATCAAGCTAGGGCCAT 60.556 50.000 6.18 0.00 39.73 4.40
1401 1999 5.513233 CCATTATCAAGCTAGGGCCATAAT 58.487 41.667 6.18 1.57 39.73 1.28
1418 2017 4.481195 TGGCACAAGAGTCTTGGC 57.519 55.556 31.20 28.22 31.92 4.52
1421 2020 0.595095 GGCACAAGAGTCTTGGCAAG 59.405 55.000 31.20 21.17 35.91 4.01
1442 2041 9.609346 GGCAAGAGTATTGTAAGATACCTTTTA 57.391 33.333 0.00 0.00 33.85 1.52
1476 2075 5.825507 AGCAAGTGATGTTGAGTCTTTTTC 58.174 37.500 0.00 0.00 0.00 2.29
1477 2076 5.591877 AGCAAGTGATGTTGAGTCTTTTTCT 59.408 36.000 0.00 0.00 0.00 2.52
1482 2084 6.753744 AGTGATGTTGAGTCTTTTTCTTTTGC 59.246 34.615 0.00 0.00 0.00 3.68
1484 2086 5.303747 TGTTGAGTCTTTTTCTTTTGCGA 57.696 34.783 0.00 0.00 0.00 5.10
1507 2109 3.431572 GTGAGTGATGTTGAGTCTTGAGC 59.568 47.826 0.00 0.00 0.00 4.26
1520 2122 3.179443 TCTTGAGCAGACAAGTTTCGT 57.821 42.857 14.53 0.00 44.96 3.85
1521 2123 2.866156 TCTTGAGCAGACAAGTTTCGTG 59.134 45.455 14.53 0.00 44.96 4.35
1552 2158 3.120041 CCGTTTGTCCATGGAAAACAAC 58.880 45.455 30.47 22.03 34.23 3.32
1592 2199 1.558233 AAAGGTCCTGACTACCTCGG 58.442 55.000 0.00 0.00 46.85 4.63
1593 2200 0.971447 AAGGTCCTGACTACCTCGGC 60.971 60.000 0.00 0.00 46.85 5.54
1594 2201 1.380112 GGTCCTGACTACCTCGGCT 60.380 63.158 0.00 0.00 33.97 5.52
1595 2202 1.385756 GGTCCTGACTACCTCGGCTC 61.386 65.000 0.00 0.00 33.97 4.70
1596 2203 1.076923 TCCTGACTACCTCGGCTCC 60.077 63.158 0.00 0.00 0.00 4.70
1597 2204 1.076632 CCTGACTACCTCGGCTCCT 60.077 63.158 0.00 0.00 0.00 3.69
1598 2205 1.104577 CCTGACTACCTCGGCTCCTC 61.105 65.000 0.00 0.00 0.00 3.71
1599 2206 1.440938 CTGACTACCTCGGCTCCTCG 61.441 65.000 0.00 0.00 0.00 4.63
1600 2207 1.451747 GACTACCTCGGCTCCTCGT 60.452 63.158 0.00 0.00 0.00 4.18
1602 2209 1.153127 CTACCTCGGCTCCTCGTCT 60.153 63.158 0.00 0.00 0.00 4.18
1603 2210 0.106335 CTACCTCGGCTCCTCGTCTA 59.894 60.000 0.00 0.00 0.00 2.59
1604 2211 0.763652 TACCTCGGCTCCTCGTCTAT 59.236 55.000 0.00 0.00 0.00 1.98
1620 2227 5.326900 TCGTCTATATATAGGGGTGTTGCA 58.673 41.667 17.81 0.00 0.00 4.08
1624 2231 7.450903 GTCTATATATAGGGGTGTTGCAACTT 58.549 38.462 28.61 12.38 0.00 2.66
1633 2240 4.382147 GGGGTGTTGCAACTTAAACTTTCA 60.382 41.667 28.61 3.04 0.00 2.69
1634 2241 4.803613 GGGTGTTGCAACTTAAACTTTCAG 59.196 41.667 28.61 0.00 0.00 3.02
1635 2242 4.803613 GGTGTTGCAACTTAAACTTTCAGG 59.196 41.667 28.61 0.00 0.00 3.86
1636 2243 5.393678 GGTGTTGCAACTTAAACTTTCAGGA 60.394 40.000 28.61 1.76 0.00 3.86
1637 2244 6.096695 GTGTTGCAACTTAAACTTTCAGGAA 58.903 36.000 28.61 1.09 0.00 3.36
1638 2245 6.034577 GTGTTGCAACTTAAACTTTCAGGAAC 59.965 38.462 28.61 10.02 0.00 3.62
1639 2246 6.071616 TGTTGCAACTTAAACTTTCAGGAACT 60.072 34.615 28.61 0.00 43.88 3.01
1656 2263 6.908870 AGGAACTGAAAATTGTTCAAAAGC 57.091 33.333 8.22 0.00 42.91 3.51
1657 2264 6.405538 AGGAACTGAAAATTGTTCAAAAGCA 58.594 32.000 8.22 0.00 42.91 3.91
1658 2265 7.049754 AGGAACTGAAAATTGTTCAAAAGCAT 58.950 30.769 8.22 0.00 42.91 3.79
1659 2266 8.203485 AGGAACTGAAAATTGTTCAAAAGCATA 58.797 29.630 8.22 0.00 42.91 3.14
1660 2267 8.825745 GGAACTGAAAATTGTTCAAAAGCATAA 58.174 29.630 8.22 0.00 42.91 1.90
1671 2278 8.939201 TGTTCAAAAGCATAAAAACATTCTCA 57.061 26.923 0.00 0.00 0.00 3.27
1672 2279 9.545105 TGTTCAAAAGCATAAAAACATTCTCAT 57.455 25.926 0.00 0.00 0.00 2.90
1673 2280 9.801714 GTTCAAAAGCATAAAAACATTCTCATG 57.198 29.630 0.00 0.00 36.34 3.07
1674 2281 9.761504 TTCAAAAGCATAAAAACATTCTCATGA 57.238 25.926 0.00 0.00 34.11 3.07
1675 2282 9.195411 TCAAAAGCATAAAAACATTCTCATGAC 57.805 29.630 0.00 0.00 34.11 3.06
1676 2283 9.199982 CAAAAGCATAAAAACATTCTCATGACT 57.800 29.630 0.00 0.00 34.11 3.41
1677 2284 9.768662 AAAAGCATAAAAACATTCTCATGACTT 57.231 25.926 0.00 0.00 34.11 3.01
1678 2285 8.976986 AAGCATAAAAACATTCTCATGACTTC 57.023 30.769 0.00 0.00 34.11 3.01
1679 2286 8.114331 AGCATAAAAACATTCTCATGACTTCA 57.886 30.769 0.00 0.00 34.11 3.02
1680 2287 8.579006 AGCATAAAAACATTCTCATGACTTCAA 58.421 29.630 0.00 0.00 34.11 2.69
1681 2288 9.195411 GCATAAAAACATTCTCATGACTTCAAA 57.805 29.630 0.00 0.00 34.11 2.69
1765 2372 9.713684 AAAATCCCATGTAGAATTATTCAGGAA 57.286 29.630 7.74 0.00 0.00 3.36
1766 2373 9.887862 AAATCCCATGTAGAATTATTCAGGAAT 57.112 29.630 7.74 0.00 34.93 3.01
1767 2374 9.887862 AATCCCATGTAGAATTATTCAGGAATT 57.112 29.630 7.74 0.00 32.50 2.17
1768 2375 9.887862 ATCCCATGTAGAATTATTCAGGAATTT 57.112 29.630 7.74 0.00 32.50 1.82
1769 2376 9.713684 TCCCATGTAGAATTATTCAGGAATTTT 57.286 29.630 7.74 0.00 32.50 1.82
1833 2440 7.938563 AAAAATTGCTCATTAGTTTAACGCA 57.061 28.000 0.00 0.00 0.00 5.24
1834 2441 8.532977 AAAAATTGCTCATTAGTTTAACGCAT 57.467 26.923 0.00 0.00 0.00 4.73
1835 2442 7.510428 AAATTGCTCATTAGTTTAACGCATG 57.490 32.000 3.99 3.99 0.00 4.06
1836 2443 5.621197 TTGCTCATTAGTTTAACGCATGT 57.379 34.783 8.62 0.00 0.00 3.21
1837 2444 5.621197 TGCTCATTAGTTTAACGCATGTT 57.379 34.783 8.62 0.00 42.19 2.71
1838 2445 6.007936 TGCTCATTAGTTTAACGCATGTTT 57.992 33.333 8.62 0.00 39.54 2.83
1839 2446 6.442952 TGCTCATTAGTTTAACGCATGTTTT 58.557 32.000 8.62 0.00 39.54 2.43
1840 2447 7.585867 TGCTCATTAGTTTAACGCATGTTTTA 58.414 30.769 8.62 0.00 39.54 1.52
1841 2448 7.748683 TGCTCATTAGTTTAACGCATGTTTTAG 59.251 33.333 8.62 2.48 39.54 1.85
1842 2449 7.960738 GCTCATTAGTTTAACGCATGTTTTAGA 59.039 33.333 8.62 0.00 39.54 2.10
1843 2450 9.988350 CTCATTAGTTTAACGCATGTTTTAGAT 57.012 29.630 8.62 0.00 39.54 1.98
1871 2478 8.713708 TTTTTAAAAATCATGTACTCCCTCCA 57.286 30.769 9.31 0.00 0.00 3.86
1872 2479 8.893563 TTTTAAAAATCATGTACTCCCTCCAT 57.106 30.769 0.00 0.00 0.00 3.41
1873 2480 9.983024 TTTTAAAAATCATGTACTCCCTCCATA 57.017 29.630 0.00 0.00 0.00 2.74
1874 2481 8.974060 TTAAAAATCATGTACTCCCTCCATAC 57.026 34.615 0.00 0.00 0.00 2.39
1875 2482 6.575244 AAAATCATGTACTCCCTCCATACA 57.425 37.500 0.00 0.00 33.54 2.29
1876 2483 5.815233 AATCATGTACTCCCTCCATACAG 57.185 43.478 0.00 0.00 32.58 2.74
1877 2484 2.965831 TCATGTACTCCCTCCATACAGC 59.034 50.000 0.00 0.00 32.58 4.40
1878 2485 2.848678 TGTACTCCCTCCATACAGCT 57.151 50.000 0.00 0.00 0.00 4.24
1879 2486 3.965470 TGTACTCCCTCCATACAGCTA 57.035 47.619 0.00 0.00 0.00 3.32
1880 2487 4.259933 TGTACTCCCTCCATACAGCTAA 57.740 45.455 0.00 0.00 0.00 3.09
1881 2488 4.616553 TGTACTCCCTCCATACAGCTAAA 58.383 43.478 0.00 0.00 0.00 1.85
1882 2489 5.027460 TGTACTCCCTCCATACAGCTAAAA 58.973 41.667 0.00 0.00 0.00 1.52
1883 2490 4.489306 ACTCCCTCCATACAGCTAAAAC 57.511 45.455 0.00 0.00 0.00 2.43
1884 2491 3.118738 ACTCCCTCCATACAGCTAAAACG 60.119 47.826 0.00 0.00 0.00 3.60
1885 2492 2.835764 TCCCTCCATACAGCTAAAACGT 59.164 45.455 0.00 0.00 0.00 3.99
1886 2493 3.262405 TCCCTCCATACAGCTAAAACGTT 59.738 43.478 0.00 0.00 0.00 3.99
1887 2494 4.007659 CCCTCCATACAGCTAAAACGTTT 58.992 43.478 7.96 7.96 0.00 3.60
1888 2495 4.142687 CCCTCCATACAGCTAAAACGTTTG 60.143 45.833 15.46 4.72 0.00 2.93
1889 2496 4.454504 CCTCCATACAGCTAAAACGTTTGT 59.545 41.667 15.46 10.97 0.00 2.83
1890 2497 5.048991 CCTCCATACAGCTAAAACGTTTGTT 60.049 40.000 15.46 1.98 40.98 2.83
1891 2498 6.148150 CCTCCATACAGCTAAAACGTTTGTTA 59.852 38.462 15.46 3.20 37.31 2.41
1892 2499 7.308109 CCTCCATACAGCTAAAACGTTTGTTAA 60.308 37.037 15.46 0.02 37.31 2.01
1893 2500 8.101654 TCCATACAGCTAAAACGTTTGTTAAT 57.898 30.769 15.46 0.34 37.31 1.40
1894 2501 9.217278 TCCATACAGCTAAAACGTTTGTTAATA 57.783 29.630 15.46 1.66 37.31 0.98
1895 2502 9.997482 CCATACAGCTAAAACGTTTGTTAATAT 57.003 29.630 15.46 6.27 37.31 1.28
1899 2506 9.223099 ACAGCTAAAACGTTTGTTAATATAGGT 57.777 29.630 15.46 12.61 37.31 3.08
1959 2566 9.617523 TGATGTTTCTTCATACACATCATACAT 57.382 29.630 9.27 0.00 46.73 2.29
2164 2771 9.866655 TTTTCTCATATATAAGTTTGGATGCCT 57.133 29.630 0.00 0.00 0.00 4.75
2165 2772 8.853077 TTCTCATATATAAGTTTGGATGCCTG 57.147 34.615 0.00 0.00 0.00 4.85
2166 2773 6.881065 TCTCATATATAAGTTTGGATGCCTGC 59.119 38.462 0.00 0.00 0.00 4.85
2167 2774 6.782986 TCATATATAAGTTTGGATGCCTGCT 58.217 36.000 0.00 0.00 0.00 4.24
2168 2775 7.233632 TCATATATAAGTTTGGATGCCTGCTT 58.766 34.615 0.00 0.00 0.00 3.91
2169 2776 7.725397 TCATATATAAGTTTGGATGCCTGCTTT 59.275 33.333 0.00 0.00 0.00 3.51
2170 2777 6.796785 ATATAAGTTTGGATGCCTGCTTTT 57.203 33.333 0.00 0.00 0.00 2.27
2171 2778 3.391506 AAGTTTGGATGCCTGCTTTTC 57.608 42.857 0.00 0.00 0.00 2.29
2172 2779 2.601905 AGTTTGGATGCCTGCTTTTCT 58.398 42.857 0.00 0.00 0.00 2.52
2173 2780 2.560105 AGTTTGGATGCCTGCTTTTCTC 59.440 45.455 0.00 0.00 0.00 2.87
2174 2781 1.167851 TTGGATGCCTGCTTTTCTCG 58.832 50.000 0.00 0.00 0.00 4.04
2175 2782 0.036732 TGGATGCCTGCTTTTCTCGT 59.963 50.000 0.00 0.00 0.00 4.18
2176 2783 1.277842 TGGATGCCTGCTTTTCTCGTA 59.722 47.619 0.00 0.00 0.00 3.43
2177 2784 1.666189 GGATGCCTGCTTTTCTCGTAC 59.334 52.381 0.00 0.00 0.00 3.67
2178 2785 2.346803 GATGCCTGCTTTTCTCGTACA 58.653 47.619 0.00 0.00 0.00 2.90
2179 2786 1.795768 TGCCTGCTTTTCTCGTACAG 58.204 50.000 0.00 0.00 0.00 2.74
2180 2787 1.343142 TGCCTGCTTTTCTCGTACAGA 59.657 47.619 0.00 0.00 0.00 3.41
2181 2788 2.028112 TGCCTGCTTTTCTCGTACAGAT 60.028 45.455 0.00 0.00 0.00 2.90
2182 2789 2.605366 GCCTGCTTTTCTCGTACAGATC 59.395 50.000 0.00 0.00 0.00 2.75
2183 2790 3.677424 GCCTGCTTTTCTCGTACAGATCT 60.677 47.826 0.00 0.00 0.00 2.75
2184 2791 4.440250 GCCTGCTTTTCTCGTACAGATCTA 60.440 45.833 0.00 0.00 0.00 1.98
2185 2792 5.038033 CCTGCTTTTCTCGTACAGATCTAC 58.962 45.833 0.00 0.00 0.00 2.59
2186 2793 5.393135 CCTGCTTTTCTCGTACAGATCTACA 60.393 44.000 0.00 0.00 0.00 2.74
2187 2794 6.208988 TGCTTTTCTCGTACAGATCTACAT 57.791 37.500 0.00 0.00 0.00 2.29
2188 2795 6.631016 TGCTTTTCTCGTACAGATCTACATT 58.369 36.000 0.00 0.00 0.00 2.71
2189 2796 7.097192 TGCTTTTCTCGTACAGATCTACATTT 58.903 34.615 0.00 0.00 0.00 2.32
2190 2797 7.602644 TGCTTTTCTCGTACAGATCTACATTTT 59.397 33.333 0.00 0.00 0.00 1.82
2191 2798 8.443937 GCTTTTCTCGTACAGATCTACATTTTT 58.556 33.333 0.00 0.00 0.00 1.94
2192 2799 9.959775 CTTTTCTCGTACAGATCTACATTTTTC 57.040 33.333 0.00 0.00 0.00 2.29
2193 2800 9.706691 TTTTCTCGTACAGATCTACATTTTTCT 57.293 29.630 0.00 0.00 0.00 2.52
2194 2801 9.706691 TTTCTCGTACAGATCTACATTTTTCTT 57.293 29.630 0.00 0.00 0.00 2.52
2239 2846 6.862944 ACACGTTTAACACTTGTTCAAATG 57.137 33.333 0.00 6.37 34.20 2.32
2240 2847 5.287513 ACACGTTTAACACTTGTTCAAATGC 59.712 36.000 0.00 0.00 34.20 3.56
2241 2848 5.287274 CACGTTTAACACTTGTTCAAATGCA 59.713 36.000 0.00 0.00 39.31 3.96
2242 2849 6.019961 CACGTTTAACACTTGTTCAAATGCAT 60.020 34.615 0.00 0.00 39.31 3.96
2243 2850 6.019961 ACGTTTAACACTTGTTCAAATGCATG 60.020 34.615 0.00 0.00 39.31 4.06
2244 2851 6.198029 CGTTTAACACTTGTTCAAATGCATGA 59.802 34.615 0.00 0.00 39.31 3.07
2245 2852 7.096106 CGTTTAACACTTGTTCAAATGCATGAT 60.096 33.333 0.00 0.00 39.31 2.45
2246 2853 8.550376 GTTTAACACTTGTTCAAATGCATGATT 58.450 29.630 0.00 0.00 39.31 2.57
2247 2854 9.755804 TTTAACACTTGTTCAAATGCATGATTA 57.244 25.926 0.00 0.00 39.31 1.75
2248 2855 9.755804 TTAACACTTGTTCAAATGCATGATTAA 57.244 25.926 0.00 0.00 39.31 1.40
2249 2856 7.642071 ACACTTGTTCAAATGCATGATTAAC 57.358 32.000 0.00 3.82 0.00 2.01
2250 2857 7.208777 ACACTTGTTCAAATGCATGATTAACA 58.791 30.769 0.00 6.52 0.00 2.41
2251 2858 7.874016 ACACTTGTTCAAATGCATGATTAACAT 59.126 29.630 0.00 0.00 40.17 2.71
2252 2859 8.714179 CACTTGTTCAAATGCATGATTAACATT 58.286 29.630 0.00 0.00 37.07 2.71
2253 2860 9.275398 ACTTGTTCAAATGCATGATTAACATTT 57.725 25.926 0.00 0.00 43.01 2.32
2378 2985 9.598517 ACAGAAGCAAAATAATGAAAAGAAACA 57.401 25.926 0.00 0.00 0.00 2.83
2379 2986 9.853921 CAGAAGCAAAATAATGAAAAGAAACAC 57.146 29.630 0.00 0.00 0.00 3.32
2380 2987 8.755018 AGAAGCAAAATAATGAAAAGAAACACG 58.245 29.630 0.00 0.00 0.00 4.49
2381 2988 6.876804 AGCAAAATAATGAAAAGAAACACGC 58.123 32.000 0.00 0.00 0.00 5.34
2382 2989 6.701400 AGCAAAATAATGAAAAGAAACACGCT 59.299 30.769 0.00 0.00 0.00 5.07
2383 2990 7.865385 AGCAAAATAATGAAAAGAAACACGCTA 59.135 29.630 0.00 0.00 0.00 4.26
2384 2991 8.155923 GCAAAATAATGAAAAGAAACACGCTAG 58.844 33.333 0.00 0.00 0.00 3.42
2385 2992 8.638565 CAAAATAATGAAAAGAAACACGCTAGG 58.361 33.333 0.00 0.00 0.00 3.02
2386 2993 7.448748 AATAATGAAAAGAAACACGCTAGGT 57.551 32.000 0.00 0.00 0.00 3.08
2387 2994 5.767816 AATGAAAAGAAACACGCTAGGTT 57.232 34.783 0.00 0.00 0.00 3.50
2388 2995 4.545823 TGAAAAGAAACACGCTAGGTTG 57.454 40.909 0.00 0.00 0.00 3.77
2389 2996 3.314080 TGAAAAGAAACACGCTAGGTTGG 59.686 43.478 0.00 0.00 0.00 3.77
2390 2997 1.235724 AAGAAACACGCTAGGTTGGC 58.764 50.000 0.00 0.00 0.00 4.52
2391 2998 0.396811 AGAAACACGCTAGGTTGGCT 59.603 50.000 0.00 0.00 0.00 4.75
2392 2999 1.621814 AGAAACACGCTAGGTTGGCTA 59.378 47.619 0.00 0.00 0.00 3.93
2393 3000 2.000447 GAAACACGCTAGGTTGGCTAG 59.000 52.381 0.00 0.00 0.00 3.42
2394 3001 1.263356 AACACGCTAGGTTGGCTAGA 58.737 50.000 0.00 0.00 0.00 2.43
2395 3002 1.486211 ACACGCTAGGTTGGCTAGAT 58.514 50.000 0.00 0.00 0.00 1.98
2396 3003 1.137086 ACACGCTAGGTTGGCTAGATG 59.863 52.381 0.00 0.00 0.00 2.90
2397 3004 1.137086 CACGCTAGGTTGGCTAGATGT 59.863 52.381 0.00 0.00 0.00 3.06
2398 3005 1.137086 ACGCTAGGTTGGCTAGATGTG 59.863 52.381 0.00 0.00 0.00 3.21
2399 3006 1.587547 GCTAGGTTGGCTAGATGTGC 58.412 55.000 0.00 0.00 0.00 4.57
2400 3007 1.858091 CTAGGTTGGCTAGATGTGCG 58.142 55.000 0.00 0.00 0.00 5.34
2401 3008 1.409064 CTAGGTTGGCTAGATGTGCGA 59.591 52.381 0.00 0.00 0.00 5.10
2402 3009 0.176680 AGGTTGGCTAGATGTGCGAG 59.823 55.000 0.00 0.00 0.00 5.03
2403 3010 0.108138 GGTTGGCTAGATGTGCGAGT 60.108 55.000 0.00 0.00 0.00 4.18
2404 3011 1.002366 GTTGGCTAGATGTGCGAGTG 58.998 55.000 0.00 0.00 0.00 3.51
2405 3012 0.740868 TTGGCTAGATGTGCGAGTGC 60.741 55.000 0.00 0.00 43.20 4.40
2441 3048 4.120331 GCCCGTGGTTGCATGCTC 62.120 66.667 20.33 11.78 0.00 4.26
2442 3049 2.360350 CCCGTGGTTGCATGCTCT 60.360 61.111 20.33 0.00 0.00 4.09
2443 3050 1.973281 CCCGTGGTTGCATGCTCTT 60.973 57.895 20.33 0.00 0.00 2.85
2444 3051 1.526575 CCCGTGGTTGCATGCTCTTT 61.527 55.000 20.33 0.00 0.00 2.52
2445 3052 0.314935 CCGTGGTTGCATGCTCTTTT 59.685 50.000 20.33 0.00 0.00 2.27
2446 3053 1.411394 CGTGGTTGCATGCTCTTTTG 58.589 50.000 20.33 1.09 0.00 2.44
2447 3054 1.001487 CGTGGTTGCATGCTCTTTTGA 60.001 47.619 20.33 0.00 0.00 2.69
2449 3056 1.614903 TGGTTGCATGCTCTTTTGAGG 59.385 47.619 20.33 0.00 46.30 3.86
2450 3057 1.670967 GGTTGCATGCTCTTTTGAGGC 60.671 52.381 20.33 0.00 46.30 4.70
2451 3058 0.604578 TTGCATGCTCTTTTGAGGCC 59.395 50.000 20.33 0.00 46.30 5.19
2452 3059 0.540133 TGCATGCTCTTTTGAGGCCA 60.540 50.000 20.33 0.00 46.30 5.36
2453 3060 0.172803 GCATGCTCTTTTGAGGCCAG 59.827 55.000 11.37 0.00 46.30 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 1.594862 GATACCTCGCATGTTGCTGAC 59.405 52.381 0.00 0.00 42.25 3.51
46 47 1.064060 GGTTGATACCTCGCATGTTGC 59.936 52.381 0.00 0.00 41.53 4.17
72 75 5.277925 CCCATCAAAAGCACCAAAATTTCAC 60.278 40.000 0.00 0.00 0.00 3.18
117 120 3.243359 AGAATCTGGGCCAAAAGTTCA 57.757 42.857 8.04 0.00 0.00 3.18
156 159 5.424895 TGCATTCAACCCCTATAAAAAGCAT 59.575 36.000 0.00 0.00 0.00 3.79
159 162 5.186797 TGGTGCATTCAACCCCTATAAAAAG 59.813 40.000 0.00 0.00 0.00 2.27
163 166 3.897239 CTGGTGCATTCAACCCCTATAA 58.103 45.455 0.00 0.00 0.00 0.98
219 222 1.197812 GCATCCAATTCCCCTTTGCT 58.802 50.000 0.00 0.00 0.00 3.91
232 235 0.538584 ACGAAGAGCTCATGCATCCA 59.461 50.000 17.77 0.00 42.74 3.41
255 258 3.582647 TGACAGTGACTATGGTGTCCAAT 59.417 43.478 0.00 0.00 38.86 3.16
269 272 6.152323 GGTATTGGTAGACTTAGTGACAGTGA 59.848 42.308 0.00 0.00 0.00 3.41
277 280 5.889853 TCGTCATGGTATTGGTAGACTTAGT 59.110 40.000 0.00 0.00 0.00 2.24
290 293 1.134098 CCTTGCCCTTCGTCATGGTAT 60.134 52.381 0.00 0.00 0.00 2.73
291 294 0.251916 CCTTGCCCTTCGTCATGGTA 59.748 55.000 0.00 0.00 0.00 3.25
292 295 1.002134 CCTTGCCCTTCGTCATGGT 60.002 57.895 0.00 0.00 0.00 3.55
387 391 6.312672 GGTCAACTTTGTTTAGTGTGCAAATT 59.687 34.615 0.00 0.00 32.61 1.82
389 393 5.164954 GGTCAACTTTGTTTAGTGTGCAAA 58.835 37.500 0.00 0.00 0.00 3.68
391 395 3.181505 CGGTCAACTTTGTTTAGTGTGCA 60.182 43.478 0.00 0.00 0.00 4.57
392 396 3.064271 TCGGTCAACTTTGTTTAGTGTGC 59.936 43.478 0.00 0.00 0.00 4.57
394 398 4.274950 CCATCGGTCAACTTTGTTTAGTGT 59.725 41.667 0.00 0.00 0.00 3.55
395 399 4.320202 CCCATCGGTCAACTTTGTTTAGTG 60.320 45.833 0.00 0.00 0.00 2.74
410 628 1.299648 CACCACACATCCCATCGGT 59.700 57.895 0.00 0.00 0.00 4.69
435 653 4.752101 CAGTGAAGGATATAAGAAAGCCCG 59.248 45.833 0.00 0.00 0.00 6.13
455 732 6.315393 CGCCAGTTCTACAAAAATATACCAGT 59.685 38.462 0.00 0.00 0.00 4.00
503 859 2.237066 GGCAAAACACGCAACCAGC 61.237 57.895 0.00 0.00 40.87 4.85
511 867 0.042188 CGAGTGACAGGCAAAACACG 60.042 55.000 0.00 0.00 38.15 4.49
538 895 8.589493 GGGTGCTCCATATAACTACTGCAAGT 62.589 46.154 7.20 0.00 43.18 3.16
542 899 3.557264 GGGGTGCTCCATATAACTACTGC 60.557 52.174 7.20 0.00 37.22 4.40
563 920 1.810151 CATTTAAGGGGTGTGTCACGG 59.190 52.381 0.00 0.00 34.83 4.94
595 952 6.432581 TGAGGCTTAGATTTAGACTAGGACA 58.567 40.000 0.00 0.00 28.87 4.02
607 964 6.512514 AGATGGATCTTTGAGGCTTAGATT 57.487 37.500 8.50 0.00 31.97 2.40
612 969 5.189180 GTTGTAGATGGATCTTTGAGGCTT 58.811 41.667 0.00 0.00 38.32 4.35
613 970 4.225942 TGTTGTAGATGGATCTTTGAGGCT 59.774 41.667 0.00 0.00 38.32 4.58
614 971 4.517285 TGTTGTAGATGGATCTTTGAGGC 58.483 43.478 0.00 0.00 38.32 4.70
728 1095 6.150976 TGTCACAAATACTTATCCCTTGCAAG 59.849 38.462 19.93 19.93 0.00 4.01
746 1113 3.392947 TGTGAGGAGGGTTTATGTCACAA 59.607 43.478 0.61 0.00 40.89 3.33
749 1116 4.715534 TTTGTGAGGAGGGTTTATGTCA 57.284 40.909 0.00 0.00 0.00 3.58
752 1119 6.447162 GTTCTTTTTGTGAGGAGGGTTTATG 58.553 40.000 0.00 0.00 0.00 1.90
770 1137 8.308931 TCTATGTACGTCAAGTTATGGTTCTTT 58.691 33.333 0.00 0.00 0.00 2.52
807 1175 7.279313 GCCAAAATTAGATTCAAAGTGCATGAT 59.721 33.333 0.00 0.00 0.00 2.45
929 1304 6.903883 AAACATACACGATGATAAGGACAC 57.096 37.500 0.00 0.00 39.06 3.67
992 1429 6.411376 TCTACGAATTCATATGTGTTTGGGT 58.589 36.000 6.22 2.73 0.00 4.51
1005 1442 7.145985 GGACTATATGTTGCTCTACGAATTCA 58.854 38.462 6.22 0.00 0.00 2.57
1053 1490 7.595819 ATTTGTGTGGTCCTCATTTCTTTTA 57.404 32.000 0.00 0.00 0.00 1.52
1068 1505 2.029649 CCCAAGAGCAGAATTTGTGTGG 60.030 50.000 0.00 0.00 0.00 4.17
1091 1555 1.134007 TGATAGCACCATGAGGGCAAG 60.134 52.381 10.48 0.00 42.05 4.01
1092 1556 0.918258 TGATAGCACCATGAGGGCAA 59.082 50.000 10.48 0.00 42.05 4.52
1093 1557 1.072806 GATGATAGCACCATGAGGGCA 59.927 52.381 10.48 0.00 42.05 5.36
1094 1558 1.818642 GATGATAGCACCATGAGGGC 58.181 55.000 0.00 0.00 42.05 5.19
1095 1559 1.338484 CCGATGATAGCACCATGAGGG 60.338 57.143 0.00 0.00 44.81 4.30
1096 1560 1.338484 CCCGATGATAGCACCATGAGG 60.338 57.143 0.00 0.00 42.21 3.86
1097 1561 1.345741 ACCCGATGATAGCACCATGAG 59.654 52.381 0.00 0.00 0.00 2.90
1098 1562 1.423584 ACCCGATGATAGCACCATGA 58.576 50.000 0.00 0.00 0.00 3.07
1099 1563 3.006859 TCTTACCCGATGATAGCACCATG 59.993 47.826 0.00 0.00 0.00 3.66
1100 1564 3.239449 TCTTACCCGATGATAGCACCAT 58.761 45.455 0.00 0.00 0.00 3.55
1101 1565 2.673258 TCTTACCCGATGATAGCACCA 58.327 47.619 0.00 0.00 0.00 4.17
1102 1566 3.963428 ATCTTACCCGATGATAGCACC 57.037 47.619 0.00 0.00 0.00 5.01
1103 1567 9.035607 CATATTAATCTTACCCGATGATAGCAC 57.964 37.037 0.00 0.00 0.00 4.40
1104 1568 8.758829 ACATATTAATCTTACCCGATGATAGCA 58.241 33.333 0.00 0.00 0.00 3.49
1105 1569 9.035607 CACATATTAATCTTACCCGATGATAGC 57.964 37.037 0.00 0.00 0.00 2.97
1108 1572 7.766278 GCTCACATATTAATCTTACCCGATGAT 59.234 37.037 0.00 0.00 0.00 2.45
1109 1573 7.097192 GCTCACATATTAATCTTACCCGATGA 58.903 38.462 0.00 0.00 0.00 2.92
1110 1574 6.873605 TGCTCACATATTAATCTTACCCGATG 59.126 38.462 0.00 0.00 0.00 3.84
1111 1575 7.004555 TGCTCACATATTAATCTTACCCGAT 57.995 36.000 0.00 0.00 0.00 4.18
1112 1576 6.413783 TGCTCACATATTAATCTTACCCGA 57.586 37.500 0.00 0.00 0.00 5.14
1113 1577 8.771920 TTATGCTCACATATTAATCTTACCCG 57.228 34.615 0.00 0.00 38.55 5.28
1141 1605 8.879759 AGTAATTGCCGCATGTAATATGTATAC 58.120 33.333 0.00 0.00 0.00 1.47
1200 1665 3.317149 CCTCAATGGTTGCCATGTCTATG 59.683 47.826 0.96 0.00 44.40 2.23
1225 1690 3.064324 AGGGCCGCAATGCACTTC 61.064 61.111 5.91 0.00 44.30 3.01
1278 1743 2.159531 CCTACACCATGTCGTGCAATTG 60.160 50.000 0.00 0.00 37.25 2.32
1398 1996 2.224744 TGCCAAGACTCTTGTGCCATTA 60.225 45.455 20.56 7.40 0.00 1.90
1401 1999 0.106769 TTGCCAAGACTCTTGTGCCA 60.107 50.000 20.56 12.53 0.00 4.92
1408 2006 4.899352 ACAATACTCTTGCCAAGACTCT 57.101 40.909 2.24 0.00 33.12 3.24
1409 2007 6.398918 TCTTACAATACTCTTGCCAAGACTC 58.601 40.000 2.24 0.00 33.12 3.36
1412 2010 7.125811 AGGTATCTTACAATACTCTTGCCAAGA 59.874 37.037 7.00 7.00 33.48 3.02
1413 2011 7.275920 AGGTATCTTACAATACTCTTGCCAAG 58.724 38.462 0.00 0.00 33.48 3.61
1442 2041 8.114331 TCAACATCACTTGCTTTATTTGAGAT 57.886 30.769 0.00 0.00 0.00 2.75
1443 2042 7.229306 ACTCAACATCACTTGCTTTATTTGAGA 59.771 33.333 13.02 0.00 39.76 3.27
1446 2045 7.365741 AGACTCAACATCACTTGCTTTATTTG 58.634 34.615 0.00 0.00 0.00 2.32
1476 2075 3.248363 TCAACATCACTCACTCGCAAAAG 59.752 43.478 0.00 0.00 0.00 2.27
1477 2076 3.202097 TCAACATCACTCACTCGCAAAA 58.798 40.909 0.00 0.00 0.00 2.44
1482 2084 3.567576 AGACTCAACATCACTCACTCG 57.432 47.619 0.00 0.00 0.00 4.18
1484 2086 4.798924 GCTCAAGACTCAACATCACTCACT 60.799 45.833 0.00 0.00 0.00 3.41
1507 2109 0.927537 TCACGCACGAAACTTGTCTG 59.072 50.000 0.00 0.00 0.00 3.51
1518 2120 0.179250 CAAACGGATCTTCACGCACG 60.179 55.000 0.00 0.00 0.00 5.34
1519 2121 0.865769 ACAAACGGATCTTCACGCAC 59.134 50.000 0.00 0.00 0.00 5.34
1520 2122 1.144969 GACAAACGGATCTTCACGCA 58.855 50.000 0.00 0.00 0.00 5.24
1521 2123 0.442699 GGACAAACGGATCTTCACGC 59.557 55.000 0.00 0.00 0.00 5.34
1592 2199 4.822896 CACCCCTATATATAGACGAGGAGC 59.177 50.000 19.51 0.00 32.05 4.70
1593 2200 6.003859 ACACCCCTATATATAGACGAGGAG 57.996 45.833 19.51 14.25 32.05 3.69
1594 2201 6.185511 CAACACCCCTATATATAGACGAGGA 58.814 44.000 19.51 0.00 32.05 3.71
1595 2202 5.163540 GCAACACCCCTATATATAGACGAGG 60.164 48.000 19.51 15.52 32.05 4.63
1596 2203 5.417894 TGCAACACCCCTATATATAGACGAG 59.582 44.000 19.51 10.36 32.05 4.18
1597 2204 5.326900 TGCAACACCCCTATATATAGACGA 58.673 41.667 19.51 0.00 32.05 4.20
1598 2205 5.654603 TGCAACACCCCTATATATAGACG 57.345 43.478 19.51 11.55 32.05 4.18
1599 2206 7.005709 AGTTGCAACACCCCTATATATAGAC 57.994 40.000 30.11 6.97 32.05 2.59
1600 2207 7.626999 AAGTTGCAACACCCCTATATATAGA 57.373 36.000 30.11 0.00 32.05 1.98
1602 2209 9.563748 GTTTAAGTTGCAACACCCCTATATATA 57.436 33.333 30.11 4.28 0.00 0.86
1603 2210 8.279361 AGTTTAAGTTGCAACACCCCTATATAT 58.721 33.333 30.11 3.00 0.00 0.86
1604 2211 7.635648 AGTTTAAGTTGCAACACCCCTATATA 58.364 34.615 30.11 7.06 0.00 0.86
1633 2240 6.405538 TGCTTTTGAACAATTTTCAGTTCCT 58.594 32.000 0.00 0.00 42.57 3.36
1634 2241 6.660887 TGCTTTTGAACAATTTTCAGTTCC 57.339 33.333 0.00 0.00 42.57 3.62
1645 2252 9.376075 TGAGAATGTTTTTATGCTTTTGAACAA 57.624 25.926 0.00 0.00 31.69 2.83
1646 2253 8.939201 TGAGAATGTTTTTATGCTTTTGAACA 57.061 26.923 0.00 0.00 0.00 3.18
1647 2254 9.801714 CATGAGAATGTTTTTATGCTTTTGAAC 57.198 29.630 0.00 0.00 0.00 3.18
1648 2255 9.761504 TCATGAGAATGTTTTTATGCTTTTGAA 57.238 25.926 0.00 0.00 0.00 2.69
1649 2256 9.195411 GTCATGAGAATGTTTTTATGCTTTTGA 57.805 29.630 0.00 0.00 0.00 2.69
1650 2257 9.199982 AGTCATGAGAATGTTTTTATGCTTTTG 57.800 29.630 0.00 0.00 0.00 2.44
1651 2258 9.768662 AAGTCATGAGAATGTTTTTATGCTTTT 57.231 25.926 0.00 0.00 0.00 2.27
1652 2259 9.415544 GAAGTCATGAGAATGTTTTTATGCTTT 57.584 29.630 0.00 0.00 0.00 3.51
1653 2260 8.579006 TGAAGTCATGAGAATGTTTTTATGCTT 58.421 29.630 0.00 0.00 0.00 3.91
1654 2261 8.114331 TGAAGTCATGAGAATGTTTTTATGCT 57.886 30.769 0.00 0.00 0.00 3.79
1655 2262 8.746922 TTGAAGTCATGAGAATGTTTTTATGC 57.253 30.769 0.00 0.00 0.00 3.14
1739 2346 9.713684 TTCCTGAATAATTCTACATGGGATTTT 57.286 29.630 0.00 0.00 0.00 1.82
1740 2347 9.887862 ATTCCTGAATAATTCTACATGGGATTT 57.112 29.630 0.00 1.08 0.00 2.17
1741 2348 9.887862 AATTCCTGAATAATTCTACATGGGATT 57.112 29.630 0.00 0.00 0.00 3.01
1742 2349 9.887862 AAATTCCTGAATAATTCTACATGGGAT 57.112 29.630 0.00 0.00 0.00 3.85
1743 2350 9.713684 AAAATTCCTGAATAATTCTACATGGGA 57.286 29.630 0.00 0.00 0.00 4.37
1809 2416 7.938563 TGCGTTAAACTAATGAGCAATTTTT 57.061 28.000 0.00 0.00 0.00 1.94
1810 2417 7.598493 ACATGCGTTAAACTAATGAGCAATTTT 59.402 29.630 0.00 0.00 36.69 1.82
1811 2418 7.090173 ACATGCGTTAAACTAATGAGCAATTT 58.910 30.769 0.00 0.00 36.69 1.82
1812 2419 6.620678 ACATGCGTTAAACTAATGAGCAATT 58.379 32.000 0.00 0.00 36.69 2.32
1813 2420 6.194796 ACATGCGTTAAACTAATGAGCAAT 57.805 33.333 0.00 0.00 36.69 3.56
1814 2421 5.621197 ACATGCGTTAAACTAATGAGCAA 57.379 34.783 0.00 0.00 36.69 3.91
1815 2422 5.621197 AACATGCGTTAAACTAATGAGCA 57.379 34.783 0.00 0.00 37.54 4.26
1816 2423 6.927933 AAAACATGCGTTAAACTAATGAGC 57.072 33.333 0.00 0.00 33.99 4.26
1817 2424 9.988350 ATCTAAAACATGCGTTAAACTAATGAG 57.012 29.630 0.00 0.00 33.99 2.90
1845 2452 9.320295 TGGAGGGAGTACATGATTTTTAAAAAT 57.680 29.630 22.95 22.95 41.06 1.82
1846 2453 8.713708 TGGAGGGAGTACATGATTTTTAAAAA 57.286 30.769 15.38 15.38 0.00 1.94
1847 2454 8.893563 ATGGAGGGAGTACATGATTTTTAAAA 57.106 30.769 0.00 0.00 0.00 1.52
1848 2455 9.403583 GTATGGAGGGAGTACATGATTTTTAAA 57.596 33.333 0.00 0.00 0.00 1.52
1849 2456 8.553153 TGTATGGAGGGAGTACATGATTTTTAA 58.447 33.333 0.00 0.00 0.00 1.52
1850 2457 8.096621 TGTATGGAGGGAGTACATGATTTTTA 57.903 34.615 0.00 0.00 0.00 1.52
1851 2458 6.969043 TGTATGGAGGGAGTACATGATTTTT 58.031 36.000 0.00 0.00 0.00 1.94
1852 2459 6.575244 TGTATGGAGGGAGTACATGATTTT 57.425 37.500 0.00 0.00 0.00 1.82
1853 2460 5.455326 GCTGTATGGAGGGAGTACATGATTT 60.455 44.000 0.00 0.00 0.00 2.17
1854 2461 4.040952 GCTGTATGGAGGGAGTACATGATT 59.959 45.833 0.00 0.00 0.00 2.57
1855 2462 3.580458 GCTGTATGGAGGGAGTACATGAT 59.420 47.826 0.00 0.00 0.00 2.45
1856 2463 2.965831 GCTGTATGGAGGGAGTACATGA 59.034 50.000 0.00 0.00 0.00 3.07
1857 2464 2.968574 AGCTGTATGGAGGGAGTACATG 59.031 50.000 0.00 0.00 0.00 3.21
1858 2465 3.336509 AGCTGTATGGAGGGAGTACAT 57.663 47.619 0.00 0.00 0.00 2.29
1859 2466 2.848678 AGCTGTATGGAGGGAGTACA 57.151 50.000 0.00 0.00 0.00 2.90
1860 2467 5.358090 GTTTTAGCTGTATGGAGGGAGTAC 58.642 45.833 0.00 0.00 0.00 2.73
1861 2468 4.098960 CGTTTTAGCTGTATGGAGGGAGTA 59.901 45.833 0.00 0.00 0.00 2.59
1862 2469 3.118738 CGTTTTAGCTGTATGGAGGGAGT 60.119 47.826 0.00 0.00 0.00 3.85
1863 2470 3.118738 ACGTTTTAGCTGTATGGAGGGAG 60.119 47.826 0.00 0.00 0.00 4.30
1864 2471 2.835764 ACGTTTTAGCTGTATGGAGGGA 59.164 45.455 0.00 0.00 0.00 4.20
1865 2472 3.261981 ACGTTTTAGCTGTATGGAGGG 57.738 47.619 0.00 0.00 0.00 4.30
1866 2473 4.454504 ACAAACGTTTTAGCTGTATGGAGG 59.545 41.667 11.66 0.00 0.00 4.30
1867 2474 5.607119 ACAAACGTTTTAGCTGTATGGAG 57.393 39.130 11.66 0.00 0.00 3.86
1868 2475 7.493743 TTAACAAACGTTTTAGCTGTATGGA 57.506 32.000 11.66 0.00 0.00 3.41
1869 2476 9.997482 ATATTAACAAACGTTTTAGCTGTATGG 57.003 29.630 11.66 0.00 0.00 2.74
1873 2480 9.223099 ACCTATATTAACAAACGTTTTAGCTGT 57.777 29.630 11.66 3.50 0.00 4.40
2138 2745 9.866655 AGGCATCCAAACTTATATATGAGAAAA 57.133 29.630 11.24 0.00 0.00 2.29
2139 2746 9.288576 CAGGCATCCAAACTTATATATGAGAAA 57.711 33.333 11.24 0.00 0.00 2.52
2140 2747 7.391554 GCAGGCATCCAAACTTATATATGAGAA 59.608 37.037 11.24 0.00 0.00 2.87
2141 2748 6.881065 GCAGGCATCCAAACTTATATATGAGA 59.119 38.462 11.24 0.00 0.00 3.27
2142 2749 6.883217 AGCAGGCATCCAAACTTATATATGAG 59.117 38.462 3.05 3.05 0.00 2.90
2143 2750 6.782986 AGCAGGCATCCAAACTTATATATGA 58.217 36.000 2.80 0.00 0.00 2.15
2144 2751 7.458409 AAGCAGGCATCCAAACTTATATATG 57.542 36.000 0.00 0.00 0.00 1.78
2145 2752 8.482852 AAAAGCAGGCATCCAAACTTATATAT 57.517 30.769 0.00 0.00 0.00 0.86
2146 2753 7.779798 AGAAAAGCAGGCATCCAAACTTATATA 59.220 33.333 0.00 0.00 0.00 0.86
2147 2754 6.608808 AGAAAAGCAGGCATCCAAACTTATAT 59.391 34.615 0.00 0.00 0.00 0.86
2148 2755 5.951747 AGAAAAGCAGGCATCCAAACTTATA 59.048 36.000 0.00 0.00 0.00 0.98
2149 2756 4.774200 AGAAAAGCAGGCATCCAAACTTAT 59.226 37.500 0.00 0.00 0.00 1.73
2150 2757 4.151883 AGAAAAGCAGGCATCCAAACTTA 58.848 39.130 0.00 0.00 0.00 2.24
2151 2758 2.967887 AGAAAAGCAGGCATCCAAACTT 59.032 40.909 0.00 0.00 0.00 2.66
2152 2759 2.560105 GAGAAAAGCAGGCATCCAAACT 59.440 45.455 0.00 0.00 0.00 2.66
2153 2760 2.669391 CGAGAAAAGCAGGCATCCAAAC 60.669 50.000 0.00 0.00 0.00 2.93
2154 2761 1.541147 CGAGAAAAGCAGGCATCCAAA 59.459 47.619 0.00 0.00 0.00 3.28
2155 2762 1.167851 CGAGAAAAGCAGGCATCCAA 58.832 50.000 0.00 0.00 0.00 3.53
2156 2763 0.036732 ACGAGAAAAGCAGGCATCCA 59.963 50.000 0.00 0.00 0.00 3.41
2157 2764 1.666189 GTACGAGAAAAGCAGGCATCC 59.334 52.381 0.00 0.00 0.00 3.51
2158 2765 2.346803 TGTACGAGAAAAGCAGGCATC 58.653 47.619 0.00 0.00 0.00 3.91
2159 2766 2.028112 TCTGTACGAGAAAAGCAGGCAT 60.028 45.455 0.00 0.00 0.00 4.40
2160 2767 1.343142 TCTGTACGAGAAAAGCAGGCA 59.657 47.619 0.00 0.00 0.00 4.75
2161 2768 2.080286 TCTGTACGAGAAAAGCAGGC 57.920 50.000 0.00 0.00 0.00 4.85
2162 2769 4.116747 AGATCTGTACGAGAAAAGCAGG 57.883 45.455 0.00 0.00 33.12 4.85
2163 2770 5.641709 TGTAGATCTGTACGAGAAAAGCAG 58.358 41.667 5.18 0.00 33.12 4.24
2164 2771 5.638596 TGTAGATCTGTACGAGAAAAGCA 57.361 39.130 5.18 0.00 33.12 3.91
2165 2772 7.527084 AAATGTAGATCTGTACGAGAAAAGC 57.473 36.000 5.18 0.00 33.12 3.51
2166 2773 9.959775 GAAAAATGTAGATCTGTACGAGAAAAG 57.040 33.333 5.18 0.00 33.12 2.27
2167 2774 9.706691 AGAAAAATGTAGATCTGTACGAGAAAA 57.293 29.630 5.18 0.00 33.12 2.29
2168 2775 9.706691 AAGAAAAATGTAGATCTGTACGAGAAA 57.293 29.630 5.18 0.00 33.12 2.52
2217 2824 5.287274 TGCATTTGAACAAGTGTTAAACGTG 59.713 36.000 10.66 0.14 43.18 4.49
2218 2825 5.403246 TGCATTTGAACAAGTGTTAAACGT 58.597 33.333 10.66 0.00 38.56 3.99
2219 2826 5.940603 TGCATTTGAACAAGTGTTAAACG 57.059 34.783 10.66 0.00 38.56 3.60
2220 2827 7.462109 TCATGCATTTGAACAAGTGTTAAAC 57.538 32.000 0.00 0.00 38.56 2.01
2221 2828 8.659925 AATCATGCATTTGAACAAGTGTTAAA 57.340 26.923 0.00 0.00 38.56 1.52
2222 2829 9.755804 TTAATCATGCATTTGAACAAGTGTTAA 57.244 25.926 0.00 5.72 38.56 2.01
2223 2830 9.190858 GTTAATCATGCATTTGAACAAGTGTTA 57.809 29.630 0.00 3.04 38.56 2.41
2224 2831 7.710044 TGTTAATCATGCATTTGAACAAGTGTT 59.290 29.630 0.00 0.00 41.64 3.32
2225 2832 7.208777 TGTTAATCATGCATTTGAACAAGTGT 58.791 30.769 0.00 0.00 31.63 3.55
2226 2833 7.640616 TGTTAATCATGCATTTGAACAAGTG 57.359 32.000 0.00 5.83 0.00 3.16
2227 2834 8.836268 AATGTTAATCATGCATTTGAACAAGT 57.164 26.923 11.59 3.31 36.81 3.16
2352 2959 9.598517 TGTTTCTTTTCATTATTTTGCTTCTGT 57.401 25.926 0.00 0.00 0.00 3.41
2353 2960 9.853921 GTGTTTCTTTTCATTATTTTGCTTCTG 57.146 29.630 0.00 0.00 0.00 3.02
2354 2961 8.755018 CGTGTTTCTTTTCATTATTTTGCTTCT 58.245 29.630 0.00 0.00 0.00 2.85
2355 2962 7.527183 GCGTGTTTCTTTTCATTATTTTGCTTC 59.473 33.333 0.00 0.00 0.00 3.86
2356 2963 7.224557 AGCGTGTTTCTTTTCATTATTTTGCTT 59.775 29.630 0.00 0.00 0.00 3.91
2357 2964 6.701400 AGCGTGTTTCTTTTCATTATTTTGCT 59.299 30.769 0.00 0.00 0.00 3.91
2358 2965 6.876804 AGCGTGTTTCTTTTCATTATTTTGC 58.123 32.000 0.00 0.00 0.00 3.68
2359 2966 8.638565 CCTAGCGTGTTTCTTTTCATTATTTTG 58.361 33.333 0.00 0.00 0.00 2.44
2360 2967 8.357402 ACCTAGCGTGTTTCTTTTCATTATTTT 58.643 29.630 0.00 0.00 0.00 1.82
2361 2968 7.882179 ACCTAGCGTGTTTCTTTTCATTATTT 58.118 30.769 0.00 0.00 0.00 1.40
2362 2969 7.448748 ACCTAGCGTGTTTCTTTTCATTATT 57.551 32.000 0.00 0.00 0.00 1.40
2363 2970 7.305474 CAACCTAGCGTGTTTCTTTTCATTAT 58.695 34.615 0.00 0.00 0.00 1.28
2364 2971 6.293735 CCAACCTAGCGTGTTTCTTTTCATTA 60.294 38.462 0.00 0.00 0.00 1.90
2365 2972 5.507315 CCAACCTAGCGTGTTTCTTTTCATT 60.507 40.000 0.00 0.00 0.00 2.57
2366 2973 4.023193 CCAACCTAGCGTGTTTCTTTTCAT 60.023 41.667 0.00 0.00 0.00 2.57
2367 2974 3.314080 CCAACCTAGCGTGTTTCTTTTCA 59.686 43.478 0.00 0.00 0.00 2.69
2368 2975 3.852205 GCCAACCTAGCGTGTTTCTTTTC 60.852 47.826 0.00 0.00 0.00 2.29
2369 2976 2.034179 GCCAACCTAGCGTGTTTCTTTT 59.966 45.455 0.00 0.00 0.00 2.27
2370 2977 1.607148 GCCAACCTAGCGTGTTTCTTT 59.393 47.619 0.00 0.00 0.00 2.52
2371 2978 1.202770 AGCCAACCTAGCGTGTTTCTT 60.203 47.619 0.00 0.00 34.64 2.52
2372 2979 0.396811 AGCCAACCTAGCGTGTTTCT 59.603 50.000 0.00 0.00 34.64 2.52
2373 2980 2.000447 CTAGCCAACCTAGCGTGTTTC 59.000 52.381 0.00 0.00 37.34 2.78
2374 2981 1.621814 TCTAGCCAACCTAGCGTGTTT 59.378 47.619 0.00 0.00 42.73 2.83
2375 2982 1.263356 TCTAGCCAACCTAGCGTGTT 58.737 50.000 0.00 0.00 42.73 3.32
2376 2983 1.137086 CATCTAGCCAACCTAGCGTGT 59.863 52.381 0.00 0.00 42.73 4.49
2377 2984 1.137086 ACATCTAGCCAACCTAGCGTG 59.863 52.381 0.00 0.00 42.73 5.34
2378 2985 1.137086 CACATCTAGCCAACCTAGCGT 59.863 52.381 0.00 0.00 42.73 5.07
2379 2986 1.858091 CACATCTAGCCAACCTAGCG 58.142 55.000 0.00 0.00 42.73 4.26
2380 2987 1.587547 GCACATCTAGCCAACCTAGC 58.412 55.000 0.00 0.00 42.73 3.42
2381 2988 1.409064 TCGCACATCTAGCCAACCTAG 59.591 52.381 0.00 0.00 44.09 3.02
2382 2989 1.409064 CTCGCACATCTAGCCAACCTA 59.591 52.381 0.00 0.00 0.00 3.08
2383 2990 0.176680 CTCGCACATCTAGCCAACCT 59.823 55.000 0.00 0.00 0.00 3.50
2384 2991 0.108138 ACTCGCACATCTAGCCAACC 60.108 55.000 0.00 0.00 0.00 3.77
2385 2992 1.002366 CACTCGCACATCTAGCCAAC 58.998 55.000 0.00 0.00 0.00 3.77
2386 2993 0.740868 GCACTCGCACATCTAGCCAA 60.741 55.000 0.00 0.00 38.36 4.52
2387 2994 1.153568 GCACTCGCACATCTAGCCA 60.154 57.895 0.00 0.00 38.36 4.75
2388 2995 1.150567 CTGCACTCGCACATCTAGCC 61.151 60.000 0.00 0.00 45.36 3.93
2389 2996 0.459237 ACTGCACTCGCACATCTAGC 60.459 55.000 0.00 0.00 45.36 3.42
2390 2997 1.554392 GACTGCACTCGCACATCTAG 58.446 55.000 0.00 0.00 45.36 2.43
2391 2998 0.179163 CGACTGCACTCGCACATCTA 60.179 55.000 2.79 0.00 45.36 1.98
2392 2999 1.445066 CGACTGCACTCGCACATCT 60.445 57.895 2.79 0.00 45.36 2.90
2393 3000 1.734477 ACGACTGCACTCGCACATC 60.734 57.895 14.57 0.00 45.36 3.06
2394 3001 2.023771 CACGACTGCACTCGCACAT 61.024 57.895 14.57 0.00 45.36 3.21
2395 3002 2.658268 CACGACTGCACTCGCACA 60.658 61.111 14.57 0.00 45.36 4.57
2396 3003 4.064491 GCACGACTGCACTCGCAC 62.064 66.667 14.57 4.61 45.36 5.34
2400 3007 3.771491 CAGCGCACGACTGCACTC 61.771 66.667 11.47 0.00 44.50 3.51
2424 3031 4.120331 GAGCATGCAACCACGGGC 62.120 66.667 21.98 0.00 0.00 6.13
2425 3032 1.526575 AAAGAGCATGCAACCACGGG 61.527 55.000 21.98 0.00 0.00 5.28
2426 3033 0.314935 AAAAGAGCATGCAACCACGG 59.685 50.000 21.98 0.00 0.00 4.94
2427 3034 1.001487 TCAAAAGAGCATGCAACCACG 60.001 47.619 21.98 4.08 0.00 4.94
2428 3035 2.608752 CCTCAAAAGAGCATGCAACCAC 60.609 50.000 21.98 5.65 0.00 4.16
2429 3036 1.614903 CCTCAAAAGAGCATGCAACCA 59.385 47.619 21.98 0.00 0.00 3.67
2430 3037 1.670967 GCCTCAAAAGAGCATGCAACC 60.671 52.381 21.98 8.56 0.00 3.77
2431 3038 1.670967 GGCCTCAAAAGAGCATGCAAC 60.671 52.381 21.98 13.47 0.00 4.17
2432 3039 0.604578 GGCCTCAAAAGAGCATGCAA 59.395 50.000 21.98 0.00 0.00 4.08
2433 3040 0.540133 TGGCCTCAAAAGAGCATGCA 60.540 50.000 21.98 0.00 0.00 3.96
2434 3041 0.172803 CTGGCCTCAAAAGAGCATGC 59.827 55.000 10.51 10.51 0.00 4.06


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

AutoCloner maintained by Alex Coulton.