Multiple sequence alignment - TraesCS6B01G366100

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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 TraesCS6B01G366100 chr6B 100.000 5112 0 0 1 5112 638832686 638827575 0.000000e+00 9441
1 TraesCS6B01G366100 chr6A 88.410 4012 287 81 1161 5112 567936371 567932478 0.000000e+00 4669
2 TraesCS6B01G366100 chr6A 90.992 1099 63 14 9 1085 567937606 567936522 0.000000e+00 1448
3 TraesCS6B01G366100 chr6A 88.043 92 8 2 1077 1167 567936478 567936389 7.000000e-19 106
4 TraesCS6B01G366100 chr6D 88.116 2415 153 65 1227 3574 423750128 423752475 0.000000e+00 2747
5 TraesCS6B01G366100 chr6D 90.691 1128 67 16 57 1167 423748909 423750015 0.000000e+00 1467
6 TraesCS6B01G366100 chr6D 95.244 862 38 3 3626 4484 423752627 423753488 0.000000e+00 1362
7 TraesCS6B01G366100 chr6D 80.556 504 87 9 4547 5046 46942815 46943311 1.340000e-100 377
8 TraesCS6B01G366100 chr1A 80.919 566 85 11 4494 5041 572682195 572681635 4.730000e-115 425
9 TraesCS6B01G366100 chr7D 81.312 503 77 13 4547 5042 182613148 182613640 4.800000e-105 392
10 TraesCS6B01G366100 chr5B 81.391 489 83 6 4547 5032 690708231 690708714 4.800000e-105 392
11 TraesCS6B01G366100 chr5D 81.224 490 82 8 4556 5042 67952758 67952276 2.230000e-103 387
12 TraesCS6B01G366100 chr5D 80.561 499 87 7 4547 5042 446678563 446679054 4.830000e-100 375
13 TraesCS6B01G366100 chr3D 81.224 490 82 7 4556 5042 452573551 452573069 2.230000e-103 387
14 TraesCS6B01G366100 chr2B 80.924 498 84 9 4556 5050 626879110 626878621 2.890000e-102 383
15 TraesCS6B01G366100 chrUn 80.677 502 83 9 4547 5042 89532871 89532378 1.340000e-100 377


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 TraesCS6B01G366100 chr6B 638827575 638832686 5111 True 9441.000000 9441 100.000000 1 5112 1 chr6B.!!$R1 5111
1 TraesCS6B01G366100 chr6A 567932478 567937606 5128 True 2074.333333 4669 89.148333 9 5112 3 chr6A.!!$R1 5103
2 TraesCS6B01G366100 chr6D 423748909 423753488 4579 False 1858.666667 2747 91.350333 57 4484 3 chr6D.!!$F2 4427
3 TraesCS6B01G366100 chr1A 572681635 572682195 560 True 425.000000 425 80.919000 4494 5041 1 chr1A.!!$R1 547

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
641 657 1.286849 ACTATAAAACCACCCCCTGCC 59.713 52.381 0.0 0.0 0.00 4.85 F
1304 1461 0.105224 TCTTGACTTTTCGCCGTGGA 59.895 50.000 0.0 0.0 0.00 4.02 F
1621 1796 0.033504 TGTCGTTCTGGGTCTTCAGC 59.966 55.000 0.0 0.0 34.91 4.26 F
1958 2141 0.037590 TCTTTGATTCCGGGGTGTGG 59.962 55.000 0.0 0.0 0.00 4.17 F
2393 2586 0.045162 TCCCTCTCCCCCGGTAATTT 59.955 55.000 0.0 0.0 0.00 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1446 1606 0.038159 CAGGGCGTAGGTATGCTAGC 60.038 60.0 8.10 8.1 38.27 3.42 R
2374 2567 0.045162 AAATTACCGGGGGAGAGGGA 59.955 55.0 6.32 0.0 0.00 4.20 R
2594 2822 0.393537 GAATCAGACCCACCAGCTGG 60.394 60.0 31.60 31.6 40.26 4.85 R
2861 3089 0.466543 GGTACCACATACATCCGGCA 59.533 55.0 7.15 0.0 35.23 5.69 R
4235 4580 0.036010 ACCGAACATCAAGCCCAGAG 60.036 55.0 0.00 0.0 0.00 3.35 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
37 44 8.891671 AATATTGGTTTTAATCATGCATGGTC 57.108 30.769 25.97 6.94 0.00 4.02
72 79 3.119495 GCCTCCGTCATTGCTTTTATGTT 60.119 43.478 0.00 0.00 0.00 2.71
245 252 5.408909 CAGCATCATGATAATGTCTGTCTCC 59.591 44.000 8.15 0.00 0.00 3.71
259 266 5.070446 TGTCTGTCTCCATCACTGTTTAACT 59.930 40.000 0.00 0.00 0.00 2.24
267 274 4.152402 CCATCACTGTTTAACTGGTCTTCG 59.848 45.833 6.90 0.00 0.00 3.79
362 375 8.713271 GGCTCTTCTCCATAAGAAAATATAACG 58.287 37.037 0.00 0.00 43.39 3.18
384 397 4.492895 CGCATACGCAACTACGGTAAAAAT 60.493 41.667 0.00 0.00 38.40 1.82
390 403 6.723282 ACGCAACTACGGTAAAAATTAAACA 58.277 32.000 0.00 0.00 37.37 2.83
441 456 3.678289 TGTCACTAGCATCAACTTGCAT 58.322 40.909 0.00 0.00 45.23 3.96
484 499 2.613026 TCTCTCGAGCAAACCAACAA 57.387 45.000 7.81 0.00 0.00 2.83
501 516 2.615869 ACAACATGTTGCAACAACCAC 58.384 42.857 34.06 6.69 44.03 4.16
555 570 3.602483 GTTTAACCAGGCCTCACGAATA 58.398 45.455 0.00 0.00 0.00 1.75
568 583 5.523916 GCCTCACGAATAACAATGATGTAGT 59.476 40.000 0.00 0.00 39.40 2.73
577 592 8.492673 AATAACAATGATGTAGTATATGCCCG 57.507 34.615 0.00 0.00 39.40 6.13
634 649 6.664384 TCCATGGGTTAAACTATAAAACCACC 59.336 38.462 13.02 0.00 44.95 4.61
639 655 5.419788 GGTTAAACTATAAAACCACCCCCTG 59.580 44.000 0.00 0.00 41.89 4.45
641 657 1.286849 ACTATAAAACCACCCCCTGCC 59.713 52.381 0.00 0.00 0.00 4.85
721 744 7.308710 CCAAACCATTTGCATTTTTCTATTGCT 60.309 33.333 0.00 0.00 39.31 3.91
788 811 1.669115 ACCAGATGCAGACACACGC 60.669 57.895 0.00 0.00 0.00 5.34
821 844 3.728385 AAATAAGAGCTGAGGGTGCTT 57.272 42.857 0.00 0.00 41.30 3.91
918 956 4.699522 GGGAGCGCAAAGGGACGT 62.700 66.667 11.47 0.00 0.00 4.34
1029 1067 1.133407 CCCTCTTCTTCGTCTTCCTCG 59.867 57.143 0.00 0.00 0.00 4.63
1062 1101 5.695424 AAGGTTTTCCCATCTACCTCTAC 57.305 43.478 0.00 0.00 40.03 2.59
1063 1102 4.038633 AGGTTTTCCCATCTACCTCTACC 58.961 47.826 0.00 0.00 36.25 3.18
1066 1105 3.614568 TTCCCATCTACCTCTACCTCC 57.385 52.381 0.00 0.00 0.00 4.30
1083 1175 2.171725 CCTTTCGATCGTTCCGCCC 61.172 63.158 15.94 0.00 0.00 6.13
1085 1177 2.845752 CTTTCGATCGTTCCGCCCCA 62.846 60.000 15.94 0.00 0.00 4.96
1087 1179 1.393487 TTCGATCGTTCCGCCCCATA 61.393 55.000 15.94 0.00 0.00 2.74
1096 1188 4.580551 CGCCCCATACGTCGTCCC 62.581 72.222 0.00 0.00 0.00 4.46
1172 1290 3.519107 TGGGAGAATCTTGCATGTCAGTA 59.481 43.478 0.00 0.00 33.73 2.74
1186 1304 2.047061 GTCAGTAGGTGGGCATGGATA 58.953 52.381 0.00 0.00 0.00 2.59
1214 1332 0.984961 TGGGCTTGAGGATCTCCCAG 60.985 60.000 0.00 0.00 42.05 4.45
1220 1338 3.307506 CTTGAGGATCTCCCAGTCTCAT 58.692 50.000 0.00 0.00 34.89 2.90
1223 1341 2.817258 GAGGATCTCCCAGTCTCATACG 59.183 54.545 0.00 0.00 37.41 3.06
1232 1350 2.534298 CAGTCTCATACGGTTGCTCTG 58.466 52.381 0.00 0.00 0.00 3.35
1244 1401 4.518970 ACGGTTGCTCTGTTAATTTGATGT 59.481 37.500 0.00 0.00 30.45 3.06
1255 1412 7.866898 TCTGTTAATTTGATGTTGTGTGGATTG 59.133 33.333 0.00 0.00 0.00 2.67
1259 1416 3.220674 TGATGTTGTGTGGATTGTGGA 57.779 42.857 0.00 0.00 0.00 4.02
1300 1457 1.660333 GCTGTTCTTGACTTTTCGCCG 60.660 52.381 0.00 0.00 0.00 6.46
1303 1460 0.941542 TTCTTGACTTTTCGCCGTGG 59.058 50.000 0.00 0.00 0.00 4.94
1304 1461 0.105224 TCTTGACTTTTCGCCGTGGA 59.895 50.000 0.00 0.00 0.00 4.02
1327 1484 1.332997 GCTCCTTGTCTACATGCATGC 59.667 52.381 26.53 11.82 0.00 4.06
1386 1543 1.000274 GCTTGGCCGGCTAATAATTGG 60.000 52.381 26.51 13.96 0.00 3.16
1387 1544 1.000274 CTTGGCCGGCTAATAATTGGC 60.000 52.381 26.51 5.29 44.98 4.52
1409 1569 4.458295 GCCCCTCTTCCTTTTGTTTACTAC 59.542 45.833 0.00 0.00 0.00 2.73
1412 1572 6.296803 CCCTCTTCCTTTTGTTTACTACAGT 58.703 40.000 0.00 0.00 38.19 3.55
1426 1586 7.437267 TGTTTACTACAGTTAGCAGAAACAGTC 59.563 37.037 0.00 0.00 34.22 3.51
1428 1588 5.533482 ACTACAGTTAGCAGAAACAGTCAG 58.467 41.667 0.00 0.00 32.23 3.51
1429 1589 4.408182 ACAGTTAGCAGAAACAGTCAGT 57.592 40.909 0.00 0.00 0.00 3.41
1432 1592 6.346096 ACAGTTAGCAGAAACAGTCAGTAAA 58.654 36.000 0.00 0.00 0.00 2.01
1433 1593 6.821665 ACAGTTAGCAGAAACAGTCAGTAAAA 59.178 34.615 0.00 0.00 0.00 1.52
1434 1594 7.126398 CAGTTAGCAGAAACAGTCAGTAAAAC 58.874 38.462 0.00 0.00 0.00 2.43
1435 1595 6.821665 AGTTAGCAGAAACAGTCAGTAAAACA 59.178 34.615 0.00 0.00 0.00 2.83
1436 1596 7.335924 AGTTAGCAGAAACAGTCAGTAAAACAA 59.664 33.333 0.00 0.00 0.00 2.83
1437 1597 6.509418 AGCAGAAACAGTCAGTAAAACAAA 57.491 33.333 0.00 0.00 0.00 2.83
1438 1598 6.555315 AGCAGAAACAGTCAGTAAAACAAAG 58.445 36.000 0.00 0.00 0.00 2.77
1440 1600 6.555315 CAGAAACAGTCAGTAAAACAAAGCT 58.445 36.000 0.00 0.00 0.00 3.74
1441 1601 7.029563 CAGAAACAGTCAGTAAAACAAAGCTT 58.970 34.615 0.00 0.00 0.00 3.74
1442 1602 7.008628 CAGAAACAGTCAGTAAAACAAAGCTTG 59.991 37.037 0.00 0.00 0.00 4.01
1443 1603 4.672409 ACAGTCAGTAAAACAAAGCTTGC 58.328 39.130 0.00 0.00 0.00 4.01
1444 1604 4.044426 CAGTCAGTAAAACAAAGCTTGCC 58.956 43.478 0.00 0.00 0.00 4.52
1445 1605 3.068165 AGTCAGTAAAACAAAGCTTGCCC 59.932 43.478 0.00 0.00 0.00 5.36
1446 1606 2.034053 TCAGTAAAACAAAGCTTGCCCG 59.966 45.455 0.00 0.00 0.00 6.13
1447 1607 1.136690 GTAAAACAAAGCTTGCCCGC 58.863 50.000 0.00 0.00 0.00 6.13
1448 1608 1.036707 TAAAACAAAGCTTGCCCGCT 58.963 45.000 0.00 0.00 43.31 5.52
1449 1609 1.036707 AAAACAAAGCTTGCCCGCTA 58.963 45.000 0.00 0.00 39.86 4.26
1450 1610 0.598065 AAACAAAGCTTGCCCGCTAG 59.402 50.000 0.00 0.00 39.86 3.42
1478 1638 3.019003 GCCCTGCGCTAGTTCCTCA 62.019 63.158 9.73 0.00 0.00 3.86
1483 1643 2.417719 CTGCGCTAGTTCCTCAGTTTT 58.582 47.619 9.73 0.00 0.00 2.43
1485 1645 2.806244 TGCGCTAGTTCCTCAGTTTTTC 59.194 45.455 9.73 0.00 0.00 2.29
1488 1648 4.023963 GCGCTAGTTCCTCAGTTTTTCTTT 60.024 41.667 0.00 0.00 0.00 2.52
1489 1649 5.505819 GCGCTAGTTCCTCAGTTTTTCTTTT 60.506 40.000 0.00 0.00 0.00 2.27
1491 1651 7.636326 CGCTAGTTCCTCAGTTTTTCTTTTTA 58.364 34.615 0.00 0.00 0.00 1.52
1492 1652 8.126700 CGCTAGTTCCTCAGTTTTTCTTTTTAA 58.873 33.333 0.00 0.00 0.00 1.52
1493 1653 9.967346 GCTAGTTCCTCAGTTTTTCTTTTTAAT 57.033 29.630 0.00 0.00 0.00 1.40
1502 1676 8.619546 TCAGTTTTTCTTTTTAATTTGGCCATG 58.380 29.630 6.09 0.00 0.00 3.66
1503 1677 7.379262 CAGTTTTTCTTTTTAATTTGGCCATGC 59.621 33.333 6.09 0.00 0.00 4.06
1505 1679 6.557291 TTTCTTTTTAATTTGGCCATGCTG 57.443 33.333 6.09 0.00 0.00 4.41
1557 1732 3.650070 TGCTAGCTATTCCTGATGACG 57.350 47.619 17.23 0.00 0.00 4.35
1565 1740 0.321564 TTCCTGATGACGCTTGGTGG 60.322 55.000 0.00 0.00 0.00 4.61
1566 1741 1.191489 TCCTGATGACGCTTGGTGGA 61.191 55.000 0.00 0.00 0.00 4.02
1583 1758 3.305608 GGTGGAAGCTGAAAAAGACATGG 60.306 47.826 0.00 0.00 0.00 3.66
1611 1786 2.481568 AGCATTGTGATGTGTCGTTCTG 59.518 45.455 0.00 0.00 35.63 3.02
1613 1788 1.877637 TTGTGATGTGTCGTTCTGGG 58.122 50.000 0.00 0.00 0.00 4.45
1614 1789 0.756294 TGTGATGTGTCGTTCTGGGT 59.244 50.000 0.00 0.00 0.00 4.51
1621 1796 0.033504 TGTCGTTCTGGGTCTTCAGC 59.966 55.000 0.00 0.00 34.91 4.26
1646 1821 8.442632 CTGGTTAGCATGAGAAATATCAAGAA 57.557 34.615 0.00 0.00 31.76 2.52
1647 1822 8.442632 TGGTTAGCATGAGAAATATCAAGAAG 57.557 34.615 0.00 0.00 31.76 2.85
1648 1823 7.012704 TGGTTAGCATGAGAAATATCAAGAAGC 59.987 37.037 0.00 0.00 31.76 3.86
1649 1824 7.228308 GGTTAGCATGAGAAATATCAAGAAGCT 59.772 37.037 0.00 0.00 34.12 3.74
1650 1825 6.864360 AGCATGAGAAATATCAAGAAGCTC 57.136 37.500 0.00 0.00 31.76 4.09
1651 1826 5.466058 AGCATGAGAAATATCAAGAAGCTCG 59.534 40.000 0.00 0.00 31.76 5.03
1652 1827 5.236047 GCATGAGAAATATCAAGAAGCTCGT 59.764 40.000 0.00 0.00 31.76 4.18
1653 1828 6.422100 GCATGAGAAATATCAAGAAGCTCGTA 59.578 38.462 0.00 0.00 31.76 3.43
1656 1831 9.632807 ATGAGAAATATCAAGAAGCTCGTATAC 57.367 33.333 0.00 0.00 31.76 1.47
1701 1876 3.941483 GGTTTATCTGGTCTGGATGTGTG 59.059 47.826 0.00 0.00 0.00 3.82
1717 1892 3.684908 TGTGTGGGATCATTACTGTTGG 58.315 45.455 0.00 0.00 0.00 3.77
1720 1895 4.522789 GTGTGGGATCATTACTGTTGGTTT 59.477 41.667 0.00 0.00 0.00 3.27
1765 1940 5.751680 CAATAATACAGCGTCCCATTCTTG 58.248 41.667 0.00 0.00 0.00 3.02
1815 1990 4.322080 TGACGATCATATGAGGTCAACC 57.678 45.455 27.30 11.85 38.01 3.77
1888 2063 2.044123 CCACCCAATGGTAAGCTCTC 57.956 55.000 0.00 0.00 45.57 3.20
1892 2073 1.133976 CCCAATGGTAAGCTCTCAGGG 60.134 57.143 0.00 0.00 0.00 4.45
1958 2141 0.037590 TCTTTGATTCCGGGGTGTGG 59.962 55.000 0.00 0.00 0.00 4.17
1971 2154 2.643551 GGGTGTGGGACTGATAACATG 58.356 52.381 0.00 0.00 0.00 3.21
2086 2270 5.698089 TGTCTTTCAAACATGTTTTTGCACA 59.302 32.000 21.10 15.88 36.56 4.57
2110 2294 3.303881 TCAAGTTGTCAGACTCCGATG 57.696 47.619 2.11 0.00 0.00 3.84
2117 2301 6.045318 AGTTGTCAGACTCCGATGATATTTG 58.955 40.000 1.31 0.00 0.00 2.32
2120 2304 6.042777 TGTCAGACTCCGATGATATTTGAAC 58.957 40.000 1.31 0.00 0.00 3.18
2124 2308 6.420306 CAGACTCCGATGATATTTGAACTCAG 59.580 42.308 0.00 0.00 0.00 3.35
2148 2332 4.559704 CGCTGAGGGAGCTTATAAACCTAG 60.560 50.000 0.00 0.00 46.64 3.02
2149 2333 4.345547 GCTGAGGGAGCTTATAAACCTAGT 59.654 45.833 0.00 0.00 45.21 2.57
2150 2334 5.539193 GCTGAGGGAGCTTATAAACCTAGTA 59.461 44.000 0.00 0.00 45.21 1.82
2156 2340 8.868103 AGGGAGCTTATAAACCTAGTATAACAC 58.132 37.037 0.00 0.00 0.00 3.32
2158 2342 9.694137 GGAGCTTATAAACCTAGTATAACACTG 57.306 37.037 0.00 0.00 38.24 3.66
2171 2355 4.801147 ATAACACTGTAATCAGCGCATG 57.199 40.909 11.47 5.22 44.77 4.06
2228 2412 8.514594 TGTTATCATTCTTTCAACAGTTCATCC 58.485 33.333 0.00 0.00 0.00 3.51
2229 2413 8.514594 GTTATCATTCTTTCAACAGTTCATCCA 58.485 33.333 0.00 0.00 0.00 3.41
2230 2414 6.317789 TCATTCTTTCAACAGTTCATCCAC 57.682 37.500 0.00 0.00 0.00 4.02
2239 2427 7.049799 TCAACAGTTCATCCACGATATCATA 57.950 36.000 3.12 0.00 0.00 2.15
2250 2438 9.404348 CATCCACGATATCATATATGTAGAAGC 57.596 37.037 12.42 0.00 0.00 3.86
2271 2459 9.516314 AGAAGCTTAAAATGTGTTTAGTTTGTC 57.484 29.630 0.00 0.00 0.00 3.18
2272 2460 9.296400 GAAGCTTAAAATGTGTTTAGTTTGTCA 57.704 29.630 0.00 0.00 0.00 3.58
2319 2512 2.937149 GAGACGGCCTGGTTTAATCTTC 59.063 50.000 0.00 0.00 0.00 2.87
2321 2514 3.078837 GACGGCCTGGTTTAATCTTCAA 58.921 45.455 0.00 0.00 0.00 2.69
2331 2524 8.872845 CCTGGTTTAATCTTCAAATAAACATGC 58.127 33.333 9.14 0.00 39.90 4.06
2332 2525 9.421806 CTGGTTTAATCTTCAAATAAACATGCA 57.578 29.630 9.14 0.00 39.90 3.96
2389 2582 3.436028 CCTCCCTCTCCCCCGGTA 61.436 72.222 0.00 0.00 0.00 4.02
2393 2586 0.045162 TCCCTCTCCCCCGGTAATTT 59.955 55.000 0.00 0.00 0.00 1.82
2395 2588 0.472898 CCTCTCCCCCGGTAATTTCC 59.527 60.000 0.00 0.00 0.00 3.13
2396 2589 1.508256 CTCTCCCCCGGTAATTTCCT 58.492 55.000 0.00 0.00 0.00 3.36
2397 2590 2.686119 CTCTCCCCCGGTAATTTCCTA 58.314 52.381 0.00 0.00 0.00 2.94
2398 2591 3.043418 CTCTCCCCCGGTAATTTCCTAA 58.957 50.000 0.00 0.00 0.00 2.69
2401 2594 4.479425 TCTCCCCCGGTAATTTCCTAAAAT 59.521 41.667 0.00 0.00 36.64 1.82
2404 2597 6.128486 TCCCCCGGTAATTTCCTAAAATAAC 58.872 40.000 0.00 0.00 33.93 1.89
2444 2660 9.056005 TCCATGCATACTAAAAATCATCAGTAC 57.944 33.333 0.00 0.00 0.00 2.73
2570 2798 4.481463 GTTATGCGCAATTACAGTGGTTT 58.519 39.130 17.11 0.00 0.00 3.27
2584 2812 4.183101 CAGTGGTTTGAAAAATGTGCTGT 58.817 39.130 0.00 0.00 0.00 4.40
2585 2813 4.630940 CAGTGGTTTGAAAAATGTGCTGTT 59.369 37.500 0.00 0.00 0.00 3.16
2586 2814 5.809562 CAGTGGTTTGAAAAATGTGCTGTTA 59.190 36.000 0.00 0.00 0.00 2.41
2587 2815 5.810074 AGTGGTTTGAAAAATGTGCTGTTAC 59.190 36.000 0.00 0.00 0.00 2.50
2588 2816 5.810074 GTGGTTTGAAAAATGTGCTGTTACT 59.190 36.000 0.00 0.00 0.00 2.24
2589 2817 5.809562 TGGTTTGAAAAATGTGCTGTTACTG 59.190 36.000 0.00 0.00 0.00 2.74
2590 2818 6.039616 GGTTTGAAAAATGTGCTGTTACTGA 58.960 36.000 0.00 0.00 0.00 3.41
2591 2819 6.701400 GGTTTGAAAAATGTGCTGTTACTGAT 59.299 34.615 0.00 0.00 0.00 2.90
2592 2820 7.865385 GGTTTGAAAAATGTGCTGTTACTGATA 59.135 33.333 0.00 0.00 0.00 2.15
2593 2821 8.905702 GTTTGAAAAATGTGCTGTTACTGATAG 58.094 33.333 0.00 0.00 0.00 2.08
2594 2822 6.611381 TGAAAAATGTGCTGTTACTGATAGC 58.389 36.000 0.00 0.00 42.33 2.97
2595 2823 5.567138 AAAATGTGCTGTTACTGATAGCC 57.433 39.130 0.00 0.00 41.40 3.93
2596 2824 3.912496 ATGTGCTGTTACTGATAGCCA 57.088 42.857 0.00 0.00 41.40 4.75
2598 2826 1.936547 GTGCTGTTACTGATAGCCAGC 59.063 52.381 0.00 0.00 46.81 4.85
2599 2827 1.833630 TGCTGTTACTGATAGCCAGCT 59.166 47.619 10.80 0.00 46.60 4.24
2600 2828 2.208431 GCTGTTACTGATAGCCAGCTG 58.792 52.381 6.78 6.78 46.81 4.24
2700 2928 2.610219 TCATTCGTTTGCATGAACCG 57.390 45.000 0.00 0.00 30.37 4.44
2753 2981 6.239800 CCCACTAGTTTTATATACCCAGTCCC 60.240 46.154 0.00 0.00 0.00 4.46
2779 3007 2.087646 GCCTTAGGCTGTTCTTCCTTG 58.912 52.381 17.16 0.00 46.69 3.61
2830 3058 1.140816 GTGTGAACTCTCGTGGCTTC 58.859 55.000 0.00 0.00 0.00 3.86
2861 3089 7.038445 AGGCTCAATGCATCTAGTTATGTAGAT 60.038 37.037 0.00 0.00 45.15 1.98
2884 3112 1.540363 CGGATGTATGTGGTACCAGCC 60.540 57.143 16.93 5.03 32.03 4.85
2933 3161 2.025887 AGTGGTAATTGCTCTGGAAGGG 60.026 50.000 0.00 0.00 37.64 3.95
2978 3207 6.422776 AACCTTGCTTTCGTAATCACATAG 57.577 37.500 0.00 0.00 0.00 2.23
3092 3329 2.245028 ACCTGTCCTGCTCCTGTATAGA 59.755 50.000 0.00 0.00 0.00 1.98
3167 3404 5.593095 TGTACAGCCTGAGTACCAATAGTAG 59.407 44.000 0.00 0.00 40.79 2.57
3191 3428 4.314961 TGTGCAGTGTTACCTTGTCATAG 58.685 43.478 0.00 0.00 0.00 2.23
3259 3497 2.419851 GCAGCTAGACAGGCAAAGAGAT 60.420 50.000 0.00 0.00 0.00 2.75
3313 3551 3.397482 GCACTACATGAGGCATTCCTAG 58.603 50.000 0.00 0.00 44.46 3.02
3335 3574 8.872845 CCTAGGTACATTTTCAATTTTTCATGC 58.127 33.333 0.00 0.00 0.00 4.06
3382 3621 1.751927 CAGTTCCAGCCCCTCATGC 60.752 63.158 0.00 0.00 0.00 4.06
3551 3790 4.869861 CACCAAAAACAGAAAGGTTCTTGG 59.130 41.667 9.04 9.04 39.20 3.61
3552 3791 4.530553 ACCAAAAACAGAAAGGTTCTTGGT 59.469 37.500 10.18 10.18 40.38 3.67
3553 3792 5.109210 CCAAAAACAGAAAGGTTCTTGGTC 58.891 41.667 3.57 0.00 38.11 4.02
3554 3793 5.337169 CCAAAAACAGAAAGGTTCTTGGTCA 60.337 40.000 3.57 0.00 38.11 4.02
3575 3814 6.349860 GGTCACTTGTCCTTTGTTTACTTTGT 60.350 38.462 0.00 0.00 0.00 2.83
3576 3815 7.088272 GTCACTTGTCCTTTGTTTACTTTGTT 58.912 34.615 0.00 0.00 0.00 2.83
3577 3816 7.061789 GTCACTTGTCCTTTGTTTACTTTGTTG 59.938 37.037 0.00 0.00 0.00 3.33
3608 3908 8.560374 GTTAATTAATATTTCTTGCCTCTCGCT 58.440 33.333 0.31 0.00 38.78 4.93
3624 3967 4.926244 TCTCGCTACTTAAGAAGCTCATG 58.074 43.478 10.09 0.00 36.56 3.07
3632 3975 2.409948 AAGAAGCTCATGTAGTGCCC 57.590 50.000 0.00 0.00 37.44 5.36
3649 3992 2.765135 TGCCCATGGTTATGTGAAATGG 59.235 45.455 11.73 0.00 38.01 3.16
3698 4042 9.758651 ATAACATAACATTTGTATCGCTACTCA 57.241 29.630 0.00 0.00 0.00 3.41
3725 4069 1.781025 TTGGCCTGACTTTGAACGCG 61.781 55.000 3.53 3.53 0.00 6.01
3982 4326 1.349026 TCCCAAGAGAACAGCAAGAGG 59.651 52.381 0.00 0.00 0.00 3.69
3988 4332 1.004440 GAACAGCAAGAGGGTCGCT 60.004 57.895 0.00 0.00 36.10 4.93
4057 4401 0.687354 ACTTCTTCCACCATCACGCT 59.313 50.000 0.00 0.00 0.00 5.07
4195 4539 6.326375 GTGTTAGGACTTCAGAGATAGTGTG 58.674 44.000 0.00 0.00 0.00 3.82
4202 4546 6.206395 ACTTCAGAGATAGTGTGTCTCATG 57.794 41.667 5.99 0.00 43.57 3.07
4225 4569 4.689345 GGTACTACTGTTGTACTGCTTTGG 59.311 45.833 24.36 0.00 39.89 3.28
4449 4794 2.125512 GCCACGACGCCTCTTCAT 60.126 61.111 0.00 0.00 0.00 2.57
4462 4807 2.044650 TTCATGCAGCTGCCTCCC 60.045 61.111 34.64 8.86 41.18 4.30
4552 4913 1.293498 GCGAGAGGGCTGTTTCAGA 59.707 57.895 0.66 0.00 32.44 3.27
4584 4945 4.079253 GTTTGTATCTTGCCCAGGAAGAA 58.921 43.478 2.58 0.00 33.22 2.52
4590 4951 3.181329 TCTTGCCCAGGAAGAATAGACA 58.819 45.455 0.00 0.00 0.00 3.41
4626 4987 6.404734 CCTGAAAATGGAATAAAGTTCTCCCG 60.405 42.308 0.00 0.00 0.00 5.14
4634 4996 0.910088 AAAGTTCTCCCGGCTAGCCT 60.910 55.000 30.55 7.15 0.00 4.58
4635 4997 0.910088 AAGTTCTCCCGGCTAGCCTT 60.910 55.000 30.55 13.17 0.00 4.35
4650 5012 1.375396 CCTTCGTCCCGATGTTGCA 60.375 57.895 0.00 0.00 35.23 4.08
4695 5058 1.153349 GGTTGTCTCCGGCAGATCC 60.153 63.158 0.00 2.39 32.08 3.36
4706 5069 2.961526 GGCAGATCCGTCTTTAGTGA 57.038 50.000 0.00 0.00 30.42 3.41
4727 5090 1.153353 TTTGCTCGGATTTGGTCGTC 58.847 50.000 0.00 0.00 0.00 4.20
4767 5130 5.420421 TGTGTTTTCAGTTTGGATCCTTTCA 59.580 36.000 14.23 0.00 0.00 2.69
4775 5138 7.405292 TCAGTTTGGATCCTTTCAATCTATGT 58.595 34.615 14.23 0.00 0.00 2.29
4800 5163 0.320858 TTCATCGGCGGCAGTTGTTA 60.321 50.000 10.53 0.00 0.00 2.41
4802 5165 0.732571 CATCGGCGGCAGTTGTTATT 59.267 50.000 10.53 0.00 0.00 1.40
4808 5171 3.202906 GGCGGCAGTTGTTATTCTGATA 58.797 45.455 3.07 0.00 34.02 2.15
4829 5192 0.033109 GCTGGTTCTATGGGGCCTTT 60.033 55.000 0.84 0.00 0.00 3.11
4838 5201 0.402504 ATGGGGCCTTTAACACGACA 59.597 50.000 0.84 0.00 0.00 4.35
4845 5208 3.314357 GGCCTTTAACACGACAACTTCTT 59.686 43.478 0.00 0.00 0.00 2.52
4872 5235 7.328737 ACTGTCTACTACAACAAGTTTTGTCT 58.671 34.615 6.68 0.00 44.59 3.41
4883 5246 1.021968 GTTTTGTCTGGTTCCAGCGT 58.978 50.000 13.44 0.00 34.33 5.07
4913 5276 2.747460 GATGGCAGCGCACCTTCA 60.747 61.111 22.55 9.96 32.87 3.02
4943 5306 3.003585 TCAGTGTTTGTAGTCGTCGCTAA 59.996 43.478 0.00 0.00 0.00 3.09
4957 5320 3.361414 GTCGCTAAGTGGTCTACGAATC 58.639 50.000 0.00 0.00 0.00 2.52
4970 5333 5.921408 GGTCTACGAATCTGGATGTACATTC 59.079 44.000 10.30 8.72 0.00 2.67
5024 5387 9.152595 CATGATGATTGAAGATGAATAGATCGT 57.847 33.333 0.00 0.00 0.00 3.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 6.090783 GCTAACATTATCATGACCATGCATG 58.909 40.000 20.19 20.19 45.41 4.06
28 29 5.184479 GGCTAACATTATCATGACCATGCAT 59.816 40.000 13.58 0.00 38.65 3.96
29 30 4.520111 GGCTAACATTATCATGACCATGCA 59.480 41.667 13.58 0.00 38.65 3.96
31 32 5.413833 GGAGGCTAACATTATCATGACCATG 59.586 44.000 12.49 12.49 40.09 3.66
32 33 5.564550 GGAGGCTAACATTATCATGACCAT 58.435 41.667 0.00 0.00 34.11 3.55
37 44 4.631131 TGACGGAGGCTAACATTATCATG 58.369 43.478 0.00 0.00 36.34 3.07
72 79 7.491682 AGTGTACTTTTTGTTTACGAGGACTA 58.508 34.615 0.00 0.00 0.00 2.59
223 230 5.303165 TGGAGACAGACATTATCATGATGC 58.697 41.667 18.72 2.80 32.92 3.91
245 252 4.377431 GCGAAGACCAGTTAAACAGTGATG 60.377 45.833 0.00 0.00 0.00 3.07
259 266 4.142337 TGTCATAGTTATTCGCGAAGACCA 60.142 41.667 27.20 16.66 0.00 4.02
330 343 4.040047 TCTTATGGAGAAGAGCCCAATGA 58.960 43.478 0.00 0.00 35.85 2.57
362 375 3.995412 TTTTACCGTAGTTGCGTATGC 57.005 42.857 0.00 0.00 43.20 3.14
384 397 6.482308 GTGGAGACTTTTACTGCTCTGTTTAA 59.518 38.462 0.00 0.00 0.00 1.52
390 403 2.610727 GCGTGGAGACTTTTACTGCTCT 60.611 50.000 0.00 0.00 0.00 4.09
441 456 9.802039 AGAAAGTAATGGGTGAATTTGTAACTA 57.198 29.630 0.00 0.00 0.00 2.24
484 499 1.547820 TGTGTGGTTGTTGCAACATGT 59.452 42.857 31.48 0.00 38.95 3.21
501 516 6.053650 AGACAGACATTATGATGACCATGTG 58.946 40.000 4.20 0.00 36.71 3.21
512 527 6.078202 ACCGTGATAGAGACAGACATTATG 57.922 41.667 0.00 0.00 0.00 1.90
555 570 5.865085 ACGGGCATATACTACATCATTGTT 58.135 37.500 0.00 0.00 37.28 2.83
568 583 5.948162 CCTAGTTCTAGGTTACGGGCATATA 59.052 44.000 15.52 0.00 32.60 0.86
577 592 6.750963 CGATGTGTTTCCTAGTTCTAGGTTAC 59.249 42.308 20.92 18.92 38.38 2.50
634 649 1.580066 TTTGTATGGAGGGGCAGGGG 61.580 60.000 0.00 0.00 0.00 4.79
788 811 5.961843 CAGCTCTTATTTTATTGTGCGTCTG 59.038 40.000 0.00 0.00 0.00 3.51
821 844 5.022787 CCCCTTTTATCCATTGTTCCAAGA 58.977 41.667 0.00 0.00 0.00 3.02
895 933 1.449246 CCTTTGCGCTCCCTCTCTG 60.449 63.158 9.73 0.00 0.00 3.35
896 934 2.664081 CCCTTTGCGCTCCCTCTCT 61.664 63.158 9.73 0.00 0.00 3.10
897 935 2.124942 CCCTTTGCGCTCCCTCTC 60.125 66.667 9.73 0.00 0.00 3.20
898 936 2.607750 TCCCTTTGCGCTCCCTCT 60.608 61.111 9.73 0.00 0.00 3.69
918 956 1.517832 GAAGCTAGCTTGCCTCCGA 59.482 57.895 33.91 0.00 36.26 4.55
968 1006 2.018086 CTCCTCCCTCCCTCCCTCT 61.018 68.421 0.00 0.00 0.00 3.69
1029 1067 2.751259 GGGAAAACCTTTGGGATCGTAC 59.249 50.000 0.00 0.00 35.85 3.67
1096 1188 1.781429 CGACCACGAAATCATCTAGCG 59.219 52.381 0.00 0.00 42.66 4.26
1172 1290 1.064463 CAACTGTATCCATGCCCACCT 60.064 52.381 0.00 0.00 0.00 4.00
1186 1304 0.109342 CCTCAAGCCCAGTCAACTGT 59.891 55.000 9.19 0.00 42.27 3.55
1214 1332 2.656560 ACAGAGCAACCGTATGAGAC 57.343 50.000 0.00 0.00 0.00 3.36
1220 1338 5.703592 ACATCAAATTAACAGAGCAACCGTA 59.296 36.000 0.00 0.00 0.00 4.02
1223 1341 6.144402 CACAACATCAAATTAACAGAGCAACC 59.856 38.462 0.00 0.00 0.00 3.77
1232 1350 7.095691 CCACAATCCACACAACATCAAATTAAC 60.096 37.037 0.00 0.00 0.00 2.01
1244 1401 2.627221 CACCATTCCACAATCCACACAA 59.373 45.455 0.00 0.00 0.00 3.33
1255 1412 0.536724 GCCCAAATCCACCATTCCAC 59.463 55.000 0.00 0.00 0.00 4.02
1259 1416 0.618393 CCCAGCCCAAATCCACCATT 60.618 55.000 0.00 0.00 0.00 3.16
1300 1457 1.618837 TGTAGACAAGGAGCTGTCCAC 59.381 52.381 0.00 0.00 46.80 4.02
1303 1460 2.275318 GCATGTAGACAAGGAGCTGTC 58.725 52.381 0.00 0.00 45.10 3.51
1304 1461 1.625315 TGCATGTAGACAAGGAGCTGT 59.375 47.619 0.00 0.00 0.00 4.40
1327 1484 1.342275 TGGCATCCCAATTCCCAAGAG 60.342 52.381 0.00 0.00 38.46 2.85
1386 1543 3.497332 AGTAAACAAAAGGAAGAGGGGC 58.503 45.455 0.00 0.00 0.00 5.80
1387 1544 5.627135 TGTAGTAAACAAAAGGAAGAGGGG 58.373 41.667 0.00 0.00 34.29 4.79
1391 1548 7.988599 TGCTAACTGTAGTAAACAAAAGGAAGA 59.011 33.333 0.00 0.00 37.74 2.87
1394 1551 7.502696 TCTGCTAACTGTAGTAAACAAAAGGA 58.497 34.615 0.00 0.00 37.74 3.36
1409 1569 6.844696 TTTACTGACTGTTTCTGCTAACTG 57.155 37.500 0.00 0.00 34.35 3.16
1412 1572 7.618502 TTGTTTTACTGACTGTTTCTGCTAA 57.381 32.000 0.00 0.00 0.00 3.09
1426 1586 2.393764 CGGGCAAGCTTTGTTTTACTG 58.606 47.619 0.00 0.00 0.00 2.74
1428 1588 1.136690 GCGGGCAAGCTTTGTTTTAC 58.863 50.000 0.00 0.00 0.00 2.01
1429 1589 1.036707 AGCGGGCAAGCTTTGTTTTA 58.963 45.000 0.00 0.00 46.80 1.52
1432 1592 1.866853 GCTAGCGGGCAAGCTTTGTT 61.867 55.000 11.78 0.00 46.80 2.83
1433 1593 2.335712 GCTAGCGGGCAAGCTTTGT 61.336 57.895 11.78 0.00 46.80 2.83
1434 1594 1.660560 ATGCTAGCGGGCAAGCTTTG 61.661 55.000 10.77 7.14 46.80 2.77
1435 1595 0.107214 TATGCTAGCGGGCAAGCTTT 60.107 50.000 10.77 0.00 46.80 3.51
1436 1596 0.815615 GTATGCTAGCGGGCAAGCTT 60.816 55.000 10.77 0.00 46.80 3.74
1438 1598 2.254464 GGTATGCTAGCGGGCAAGC 61.254 63.158 10.77 6.64 45.68 4.01
1440 1600 0.391597 GTAGGTATGCTAGCGGGCAA 59.608 55.000 10.77 0.00 45.68 4.52
1441 1601 1.802337 CGTAGGTATGCTAGCGGGCA 61.802 60.000 10.77 8.89 46.63 5.36
1442 1602 1.080705 CGTAGGTATGCTAGCGGGC 60.081 63.158 10.77 1.88 0.00 6.13
1443 1603 1.080705 GCGTAGGTATGCTAGCGGG 60.081 63.158 10.77 0.00 35.39 6.13
1444 1604 1.080705 GGCGTAGGTATGCTAGCGG 60.081 63.158 10.77 0.00 38.27 5.52
1445 1605 1.080705 GGGCGTAGGTATGCTAGCG 60.081 63.158 10.77 0.00 38.27 4.26
1446 1606 0.038159 CAGGGCGTAGGTATGCTAGC 60.038 60.000 8.10 8.10 38.27 3.42
1447 1607 0.038159 GCAGGGCGTAGGTATGCTAG 60.038 60.000 1.37 0.00 38.27 3.42
1448 1608 2.046938 GCAGGGCGTAGGTATGCTA 58.953 57.895 1.37 0.00 38.27 3.49
1449 1609 2.822399 GCAGGGCGTAGGTATGCT 59.178 61.111 1.37 0.00 38.27 3.79
1478 1638 7.285172 AGCATGGCCAAATTAAAAAGAAAAACT 59.715 29.630 10.96 0.00 0.00 2.66
1483 1643 5.619220 ACAGCATGGCCAAATTAAAAAGAA 58.381 33.333 10.96 0.00 43.62 2.52
1485 1645 7.614124 ATTACAGCATGGCCAAATTAAAAAG 57.386 32.000 10.96 0.00 43.62 2.27
1545 1720 1.679944 CCACCAAGCGTCATCAGGAAT 60.680 52.381 0.00 0.00 0.00 3.01
1565 1740 4.516698 TCTGTCCATGTCTTTTTCAGCTTC 59.483 41.667 0.00 0.00 0.00 3.86
1566 1741 4.276926 GTCTGTCCATGTCTTTTTCAGCTT 59.723 41.667 0.00 0.00 0.00 3.74
1583 1758 2.810274 ACACATCACAATGCTGTCTGTC 59.190 45.455 0.00 0.00 36.26 3.51
1603 1778 0.318762 AGCTGAAGACCCAGAACGAC 59.681 55.000 0.00 0.00 36.29 4.34
1604 1779 0.318441 CAGCTGAAGACCCAGAACGA 59.682 55.000 8.42 0.00 36.29 3.85
1611 1786 3.160872 GCTAACCAGCTGAAGACCC 57.839 57.895 17.39 0.00 44.93 4.46
1621 1796 8.442632 TTCTTGATATTTCTCATGCTAACCAG 57.557 34.615 0.00 0.00 0.00 4.00
1668 1843 7.931948 CCAGACCAGATAAACCGAGTTATAAAT 59.068 37.037 0.00 0.00 0.00 1.40
1671 1846 6.131264 TCCAGACCAGATAAACCGAGTTATA 58.869 40.000 0.00 0.00 0.00 0.98
1680 1855 3.941483 CCACACATCCAGACCAGATAAAC 59.059 47.826 0.00 0.00 0.00 2.01
1701 1876 7.093509 ACCAAATAAACCAACAGTAATGATCCC 60.094 37.037 0.00 0.00 0.00 3.85
1717 1892 7.992180 CAGAATGCCAGATAACCAAATAAAC 57.008 36.000 0.00 0.00 0.00 2.01
1815 1990 6.805271 CAGAATGCTTATCACCAAAAGTCAAG 59.195 38.462 0.00 0.00 0.00 3.02
1888 2063 2.153913 CGAAGTTCAGTTCGCCCTG 58.846 57.895 3.32 0.00 42.57 4.45
1958 2141 7.498900 TGATATGTGGAAACATGTTATCAGTCC 59.501 37.037 12.39 14.73 46.14 3.85
1971 2154 5.585390 CAAGCCTGAATGATATGTGGAAAC 58.415 41.667 0.00 0.00 0.00 2.78
2086 2270 4.079970 TCGGAGTCTGACAACTTGATAGT 58.920 43.478 10.88 0.00 35.68 2.12
2156 2340 7.116805 TCAGATTATTACATGCGCTGATTACAG 59.883 37.037 9.73 0.00 45.91 2.74
2158 2342 7.351414 TCAGATTATTACATGCGCTGATTAC 57.649 36.000 9.73 0.00 0.00 1.89
2171 2355 6.020281 CACTCAGCGTGTCTTCAGATTATTAC 60.020 42.308 0.00 0.00 38.84 1.89
2202 2386 8.514594 GGATGAACTGTTGAAAGAATGATAACA 58.485 33.333 0.00 0.00 0.00 2.41
2203 2387 8.514594 TGGATGAACTGTTGAAAGAATGATAAC 58.485 33.333 0.00 0.00 0.00 1.89
2293 2486 2.226962 AAACCAGGCCGTCTCTACTA 57.773 50.000 0.00 0.00 0.00 1.82
2374 2567 0.045162 AAATTACCGGGGGAGAGGGA 59.955 55.000 6.32 0.00 0.00 4.20
2418 2611 9.056005 GTACTGATGATTTTTAGTATGCATGGA 57.944 33.333 10.16 0.00 0.00 3.41
2420 2613 9.655769 GTGTACTGATGATTTTTAGTATGCATG 57.344 33.333 10.16 0.00 0.00 4.06
2421 2614 9.618890 AGTGTACTGATGATTTTTAGTATGCAT 57.381 29.630 3.79 3.79 0.00 3.96
2422 2615 8.882736 CAGTGTACTGATGATTTTTAGTATGCA 58.117 33.333 6.15 0.00 46.59 3.96
2438 2654 5.566826 GCCATTAGAGTTCACAGTGTACTGA 60.567 44.000 16.91 2.94 46.59 3.41
2444 2660 3.005554 CCTGCCATTAGAGTTCACAGTG 58.994 50.000 0.00 0.00 0.00 3.66
2554 2781 5.957910 TTTTTCAAACCACTGTAATTGCG 57.042 34.783 0.00 0.00 0.00 4.85
2570 2798 6.349280 GGCTATCAGTAACAGCACATTTTTCA 60.349 38.462 0.00 0.00 37.02 2.69
2584 2812 1.486310 CCACCAGCTGGCTATCAGTAA 59.514 52.381 33.06 0.00 45.08 2.24
2585 2813 1.123077 CCACCAGCTGGCTATCAGTA 58.877 55.000 33.06 0.00 45.08 2.74
2586 2814 1.630126 CCCACCAGCTGGCTATCAGT 61.630 60.000 33.06 8.48 45.08 3.41
2587 2815 1.147824 CCCACCAGCTGGCTATCAG 59.852 63.158 33.06 14.76 46.03 2.90
2588 2816 1.616327 ACCCACCAGCTGGCTATCA 60.616 57.895 33.06 0.00 39.01 2.15
2589 2817 1.147153 GACCCACCAGCTGGCTATC 59.853 63.158 33.06 20.20 39.01 2.08
2590 2818 1.307343 AGACCCACCAGCTGGCTAT 60.307 57.895 33.06 15.83 39.01 2.97
2591 2819 2.122729 AGACCCACCAGCTGGCTA 59.877 61.111 33.06 0.00 39.01 3.93
2592 2820 3.644606 CAGACCCACCAGCTGGCT 61.645 66.667 33.06 18.08 39.01 4.75
2593 2821 2.490270 AATCAGACCCACCAGCTGGC 62.490 60.000 33.06 15.91 39.01 4.85
2594 2822 0.393537 GAATCAGACCCACCAGCTGG 60.394 60.000 31.60 31.60 40.26 4.85
2595 2823 0.617413 AGAATCAGACCCACCAGCTG 59.383 55.000 6.78 6.78 0.00 4.24
2596 2824 1.004044 CAAGAATCAGACCCACCAGCT 59.996 52.381 0.00 0.00 0.00 4.24
2597 2825 1.003580 TCAAGAATCAGACCCACCAGC 59.996 52.381 0.00 0.00 0.00 4.85
2598 2826 3.423539 TTCAAGAATCAGACCCACCAG 57.576 47.619 0.00 0.00 0.00 4.00
2599 2827 4.043310 AGAATTCAAGAATCAGACCCACCA 59.957 41.667 8.44 0.00 0.00 4.17
2600 2828 4.593956 AGAATTCAAGAATCAGACCCACC 58.406 43.478 8.44 0.00 0.00 4.61
2686 2914 2.250188 GAAATCCGGTTCATGCAAACG 58.750 47.619 0.00 7.95 45.52 3.60
2700 2928 7.605449 TGTGGATGAGAAAGAAATTGAAATCC 58.395 34.615 0.00 0.00 33.23 3.01
2779 3007 3.603770 GCACATGACATTCTTTAACGCAC 59.396 43.478 0.00 0.00 0.00 5.34
2830 3058 4.122776 ACTAGATGCATTGAGCCTTTACG 58.877 43.478 0.00 0.00 44.83 3.18
2861 3089 0.466543 GGTACCACATACATCCGGCA 59.533 55.000 7.15 0.00 35.23 5.69
3125 3362 6.690098 GCTGTACATGATTGCAATAACAGAAG 59.310 38.462 26.20 15.98 34.99 2.85
3167 3404 2.680841 TGACAAGGTAACACTGCACAAC 59.319 45.455 0.00 0.00 41.41 3.32
3191 3428 2.558378 GTTAAGGCATCTTCCGTACCC 58.442 52.381 0.00 0.00 34.59 3.69
3259 3497 6.213679 ATGATTTACATATGGCCTTGCCGAA 61.214 40.000 3.32 0.00 44.13 4.30
3313 3551 8.938906 AGATGCATGAAAAATTGAAAATGTACC 58.061 29.630 2.46 0.00 0.00 3.34
3335 3574 5.056480 TGTACAACTGGTCAGTCAAAGATG 58.944 41.667 3.93 0.97 41.58 2.90
3340 3579 3.389656 TCCATGTACAACTGGTCAGTCAA 59.610 43.478 13.88 0.00 41.58 3.18
3382 3621 4.888325 AGATGCCCCTCCTCCCGG 62.888 72.222 0.00 0.00 0.00 5.73
3551 3790 6.617879 ACAAAGTAAACAAAGGACAAGTGAC 58.382 36.000 0.00 0.00 0.00 3.67
3552 3791 6.827586 ACAAAGTAAACAAAGGACAAGTGA 57.172 33.333 0.00 0.00 0.00 3.41
3553 3792 6.183360 GCAACAAAGTAAACAAAGGACAAGTG 60.183 38.462 0.00 0.00 0.00 3.16
3554 3793 5.867174 GCAACAAAGTAAACAAAGGACAAGT 59.133 36.000 0.00 0.00 0.00 3.16
3608 3908 5.395324 GGGCACTACATGAGCTTCTTAAGTA 60.395 44.000 0.00 0.00 32.77 2.24
3624 3967 3.275617 TCACATAACCATGGGCACTAC 57.724 47.619 18.09 0.00 35.36 2.73
3632 3975 8.497554 CAAAAGTTTCCATTTCACATAACCATG 58.502 33.333 0.00 0.00 38.21 3.66
3698 4042 2.629617 CAAAGTCAGGCCAACCAGAAAT 59.370 45.455 5.01 0.00 39.06 2.17
3725 4069 1.001860 GTAGGGCTGCAGATGGAGATC 59.998 57.143 20.43 0.00 35.31 2.75
4057 4401 0.820226 CGGAGAAGCTGAGATGGTGA 59.180 55.000 0.00 0.00 0.00 4.02
4093 4437 2.693797 ATTACGTATACCGGTCGCTG 57.306 50.000 12.40 2.22 42.24 5.18
4195 4539 6.323266 CAGTACAACAGTAGTACCATGAGAC 58.677 44.000 0.00 0.00 42.09 3.36
4202 4546 4.689345 CCAAAGCAGTACAACAGTAGTACC 59.311 45.833 0.00 0.00 42.09 3.34
4235 4580 0.036010 ACCGAACATCAAGCCCAGAG 60.036 55.000 0.00 0.00 0.00 3.35
4239 4584 0.663153 GCATACCGAACATCAAGCCC 59.337 55.000 0.00 0.00 0.00 5.19
4370 4715 6.358118 TGATTACACAGCATTTACGGAATC 57.642 37.500 0.00 0.00 0.00 2.52
4475 4820 1.265454 GGGAGACGAGGTGGACCAAT 61.265 60.000 0.00 0.00 38.89 3.16
4513 4858 4.738998 CAAGGGCCGGCATCCACA 62.739 66.667 30.85 0.00 0.00 4.17
4532 4877 2.347490 GAAACAGCCCTCTCGCCA 59.653 61.111 0.00 0.00 0.00 5.69
4537 4882 1.701847 ACACATCTGAAACAGCCCTCT 59.298 47.619 0.00 0.00 0.00 3.69
4552 4913 4.262420 GGCAAGATACAAACCCAAACACAT 60.262 41.667 0.00 0.00 0.00 3.21
4650 5012 6.183360 CCACACGTTCACTTATGATGCTAAAT 60.183 38.462 0.00 0.00 33.85 1.40
4690 5053 5.491982 AGCAAATTCACTAAAGACGGATCT 58.508 37.500 0.00 0.00 36.42 2.75
4695 5058 3.678072 TCCGAGCAAATTCACTAAAGACG 59.322 43.478 0.00 0.00 0.00 4.18
4706 5069 2.159382 ACGACCAAATCCGAGCAAATT 58.841 42.857 0.00 0.00 0.00 1.82
4727 5090 7.671827 TGAAAACACATAAACGTAGATGATCG 58.328 34.615 14.66 6.71 0.00 3.69
4767 5130 5.223382 CGCCGATGAAGAGTAACATAGATT 58.777 41.667 0.00 0.00 0.00 2.40
4775 5138 0.179111 CTGCCGCCGATGAAGAGTAA 60.179 55.000 0.00 0.00 0.00 2.24
4800 5163 4.262635 CCCATAGAACCAGCGTATCAGAAT 60.263 45.833 0.00 0.00 0.00 2.40
4802 5165 2.628178 CCCATAGAACCAGCGTATCAGA 59.372 50.000 0.00 0.00 0.00 3.27
4808 5171 2.590092 GCCCCATAGAACCAGCGT 59.410 61.111 0.00 0.00 0.00 5.07
4829 5192 4.751060 ACAGTCAAGAAGTTGTCGTGTTA 58.249 39.130 0.00 0.00 37.08 2.41
4838 5201 7.108841 TGTTGTAGTAGACAGTCAAGAAGTT 57.891 36.000 2.66 0.00 39.88 2.66
4845 5208 7.101054 ACAAAACTTGTTGTAGTAGACAGTCA 58.899 34.615 2.66 0.00 42.22 3.41
4872 5235 3.636231 CCTCCCACGCTGGAACCA 61.636 66.667 5.71 0.00 40.96 3.67
4883 5246 3.170672 CCATCATCGCCCCTCCCA 61.171 66.667 0.00 0.00 0.00 4.37
4913 5276 2.224066 ACTACAAACACTGAAGCGAGCT 60.224 45.455 0.00 0.00 0.00 4.09
4943 5306 3.366396 ACATCCAGATTCGTAGACCACT 58.634 45.455 0.00 0.00 34.32 4.00
4988 5351 8.837389 CATCTTCAATCATCATGACAGTACAAT 58.163 33.333 0.00 0.00 0.00 2.71
4997 5360 9.367444 CGATCTATTCATCTTCAATCATCATGA 57.633 33.333 0.00 0.00 0.00 3.07
4998 5361 9.152595 ACGATCTATTCATCTTCAATCATCATG 57.847 33.333 0.00 0.00 0.00 3.07
5064 5427 3.138304 TGCAGCAATTTTACTCGTCAGT 58.862 40.909 0.00 0.00 36.55 3.41
5066 5429 3.609175 GCTTGCAGCAATTTTACTCGTCA 60.609 43.478 8.67 0.00 41.89 4.35


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

AutoCloner maintained by Alex Coulton.