Multiple sequence alignment - TraesCS5B01G362300

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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 TraesCS5B01G362300 chr5B 100.000 7310 0 0 1 7310 541623624 541616315 0.000000e+00 13500
1 TraesCS5B01G362300 chr5A 91.822 6334 302 92 956 7194 561666266 561660054 0.000000e+00 8628
2 TraesCS5B01G362300 chr5A 88.115 488 26 16 426 893 561666744 561666269 1.070000e-152 551
3 TraesCS5B01G362300 chr5A 96.552 87 2 1 7223 7308 561660053 561659967 7.640000e-30 143
4 TraesCS5B01G362300 chr5D 94.481 3660 134 24 1559 5187 444733589 444729967 0.000000e+00 5578
5 TraesCS5B01G362300 chr5D 89.735 2192 105 43 5189 7310 444729884 444727743 0.000000e+00 2691
6 TraesCS5B01G362300 chr5D 86.108 1562 102 43 1 1499 444735203 444733694 0.000000e+00 1576
7 TraesCS5B01G362300 chr4D 83.562 365 47 12 2736 3090 196235482 196235843 5.470000e-86 329
8 TraesCS5B01G362300 chrUn 82.787 366 49 11 2736 3090 35821555 35821193 1.530000e-81 315
9 TraesCS5B01G362300 chr2A 83.333 306 42 8 2748 3045 47360227 47360531 2.600000e-69 274


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 TraesCS5B01G362300 chr5B 541616315 541623624 7309 True 13500.000000 13500 100.000 1 7310 1 chr5B.!!$R1 7309
1 TraesCS5B01G362300 chr5A 561659967 561666744 6777 True 3107.333333 8628 92.163 426 7308 3 chr5A.!!$R1 6882
2 TraesCS5B01G362300 chr5D 444727743 444735203 7460 True 3281.666667 5578 90.108 1 7310 3 chr5D.!!$R1 7309

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
954 1027 0.030638 CGAGGGCCTTGTTGTTGTTG 59.969 55.000 7.89 0.00 0.00 3.33 F
1514 1657 0.036010 CTGAACTGACGCCCCTGAAT 60.036 55.000 0.00 0.00 0.00 2.57 F
1658 1815 0.037605 GAACCGACCACACCACCTAG 60.038 60.000 0.00 0.00 0.00 3.02 F
3274 3451 0.598419 GCCAAAGTTTGCTGGAGTGC 60.598 55.000 10.25 2.77 34.35 4.40 F
4139 4330 1.355971 TAAGGCTCGCGATTTGTCAC 58.644 50.000 10.36 0.00 0.00 3.67 F
5849 6147 1.461127 CTGTAAGCACCTCTGTTTCGC 59.539 52.381 0.00 0.00 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2118 2276 0.178973 ACAAGGGTAAACAGGTGCCC 60.179 55.000 0.00 0.0 41.36 5.36 R
3264 3441 0.251787 TACTCTCCAGCACTCCAGCA 60.252 55.000 0.00 0.0 36.85 4.41 R
3315 3492 0.898326 GCCATCCGTCCCCAAGTTTT 60.898 55.000 0.00 0.0 0.00 2.43 R
4830 5028 1.885887 GTCAACTTGCCAACATAGCCA 59.114 47.619 0.00 0.0 0.00 4.75 R
5897 6197 1.202348 CCTGCGGATTTTCAAACTCCC 59.798 52.381 1.03 0.0 0.00 4.30 R
6718 7038 0.462581 TCATCTGCAGCGATTGACCC 60.463 55.000 9.47 0.0 0.00 4.46 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 3.086600 CTCCCTCTGGCCAGACCC 61.087 72.222 32.00 0.00 37.83 4.46
53 54 1.960417 GGCATTCTACAAGCCCTCTC 58.040 55.000 0.00 0.00 42.58 3.20
54 55 1.475930 GGCATTCTACAAGCCCTCTCC 60.476 57.143 0.00 0.00 42.58 3.71
61 62 0.250513 ACAAGCCCTCTCCGATGTTC 59.749 55.000 0.00 0.00 0.00 3.18
64 65 1.045911 AGCCCTCTCCGATGTTCTCC 61.046 60.000 0.00 0.00 0.00 3.71
173 174 4.202223 GGGGATTCGATTACTGCTTCTACA 60.202 45.833 0.00 0.00 0.00 2.74
185 186 2.393271 CTTCTACAAGCTCCTGGGTG 57.607 55.000 0.00 0.00 0.00 4.61
186 187 0.984230 TTCTACAAGCTCCTGGGTGG 59.016 55.000 0.00 0.00 37.10 4.61
187 188 0.178903 TCTACAAGCTCCTGGGTGGT 60.179 55.000 0.00 0.00 37.07 4.16
188 189 0.693049 CTACAAGCTCCTGGGTGGTT 59.307 55.000 0.00 1.03 37.07 3.67
189 190 1.073923 CTACAAGCTCCTGGGTGGTTT 59.926 52.381 3.79 0.67 37.07 3.27
190 191 1.145571 ACAAGCTCCTGGGTGGTTTA 58.854 50.000 3.79 0.00 37.07 2.01
191 192 1.073923 ACAAGCTCCTGGGTGGTTTAG 59.926 52.381 3.79 0.00 37.07 1.85
204 205 3.004419 GGTGGTTTAGACAAGTTTGCTCC 59.996 47.826 0.00 0.00 0.00 4.70
205 206 2.875933 TGGTTTAGACAAGTTTGCTCCG 59.124 45.455 0.00 0.00 0.00 4.63
207 208 1.519408 TTAGACAAGTTTGCTCCGCC 58.481 50.000 0.00 0.00 0.00 6.13
210 211 3.737172 CAAGTTTGCTCCGCCGGG 61.737 66.667 1.90 0.00 0.00 5.73
212 213 4.699522 AGTTTGCTCCGCCGGGAC 62.700 66.667 1.90 0.00 37.43 4.46
218 219 3.827898 CTCCGCCGGGACAGAGAC 61.828 72.222 1.90 0.00 37.43 3.36
232 233 0.913451 AGAGACCCAGAGGCAGCAAT 60.913 55.000 0.00 0.00 36.11 3.56
313 315 3.694566 AGGAATGGGACGTATTTTTCAGC 59.305 43.478 0.00 0.00 0.00 4.26
317 319 2.817258 TGGGACGTATTTTTCAGCCTTG 59.183 45.455 0.00 0.00 0.00 3.61
320 322 4.879545 GGGACGTATTTTTCAGCCTTGATA 59.120 41.667 0.00 0.00 32.27 2.15
413 443 4.640771 AAGAGAAGGCATGGTTGAACTA 57.359 40.909 0.00 0.00 0.00 2.24
415 445 4.327680 AGAGAAGGCATGGTTGAACTAAC 58.672 43.478 0.00 0.00 38.60 2.34
456 487 2.159382 AGGTCCAAAACTAACCGCATG 58.841 47.619 0.00 0.00 38.14 4.06
561 595 2.715005 CAGAGCGAGCGAGAGAGG 59.285 66.667 0.00 0.00 0.00 3.69
746 805 3.202467 GAGAGACGCTCCACCCTC 58.798 66.667 0.00 0.00 37.69 4.30
747 806 2.363147 AGAGACGCTCCACCCTCC 60.363 66.667 3.66 0.00 0.00 4.30
951 1024 2.644992 GCGAGGGCCTTGTTGTTG 59.355 61.111 21.87 0.00 0.00 3.33
952 1025 2.193536 GCGAGGGCCTTGTTGTTGT 61.194 57.895 21.87 0.00 0.00 3.32
953 1026 1.734388 GCGAGGGCCTTGTTGTTGTT 61.734 55.000 21.87 0.00 0.00 2.83
954 1027 0.030638 CGAGGGCCTTGTTGTTGTTG 59.969 55.000 7.89 0.00 0.00 3.33
1184 1260 1.487231 CGTTCCGTTCGCTTCTGTG 59.513 57.895 0.00 0.00 0.00 3.66
1185 1261 1.204312 GTTCCGTTCGCTTCTGTGC 59.796 57.895 0.00 0.00 0.00 4.57
1251 1329 2.433145 CTCGATGCGCCAGTGTGT 60.433 61.111 4.18 0.00 0.00 3.72
1338 1416 1.934589 CCCGCGTCATGATGAGTTAA 58.065 50.000 19.30 0.00 0.00 2.01
1347 1425 3.876914 TCATGATGAGTTAATTGGTCGGC 59.123 43.478 0.00 0.00 0.00 5.54
1348 1426 2.276201 TGATGAGTTAATTGGTCGGCG 58.724 47.619 0.00 0.00 0.00 6.46
1350 1428 0.322322 TGAGTTAATTGGTCGGCGGT 59.678 50.000 7.21 0.00 0.00 5.68
1351 1429 0.725117 GAGTTAATTGGTCGGCGGTG 59.275 55.000 7.21 0.00 0.00 4.94
1352 1430 0.675522 AGTTAATTGGTCGGCGGTGG 60.676 55.000 7.21 0.00 0.00 4.61
1353 1431 0.956902 GTTAATTGGTCGGCGGTGGT 60.957 55.000 7.21 0.00 0.00 4.16
1354 1432 0.956410 TTAATTGGTCGGCGGTGGTG 60.956 55.000 7.21 0.00 0.00 4.17
1409 1513 0.446222 CAATGGCGTTTCCCGTACTG 59.554 55.000 0.00 0.00 39.32 2.74
1481 1589 1.970917 CTGCCCTGTTCATTCGCGTC 61.971 60.000 5.77 0.00 0.00 5.19
1504 1612 4.090642 CACGAGTTTATCTGCTGAACTGAC 59.909 45.833 0.00 0.00 34.09 3.51
1514 1657 0.036010 CTGAACTGACGCCCCTGAAT 60.036 55.000 0.00 0.00 0.00 2.57
1539 1686 1.678970 GTGATTCACCCCCACTGGC 60.679 63.158 5.44 0.00 0.00 4.85
1540 1687 2.438434 GATTCACCCCCACTGGCG 60.438 66.667 0.00 0.00 0.00 5.69
1544 1691 4.096003 CACCCCCACTGGCGGTAG 62.096 72.222 3.94 0.00 34.52 3.18
1557 1704 1.623973 GCGGTAGCGGTTTGTCAGAC 61.624 60.000 17.08 0.00 0.00 3.51
1562 1719 0.597637 AGCGGTTTGTCAGACTGTCG 60.598 55.000 1.59 2.43 0.00 4.35
1572 1729 0.870393 CAGACTGTCGCTTGCATTGT 59.130 50.000 1.52 0.00 0.00 2.71
1618 1775 3.557577 TTCATTTGCCTCGTGTGATTG 57.442 42.857 0.00 0.00 0.00 2.67
1654 1811 2.281276 GGGAACCGACCACACCAC 60.281 66.667 0.00 0.00 40.86 4.16
1655 1812 2.281276 GGAACCGACCACACCACC 60.281 66.667 0.00 0.00 0.00 4.61
1656 1813 2.814835 GGAACCGACCACACCACCT 61.815 63.158 0.00 0.00 0.00 4.00
1657 1814 1.474332 GGAACCGACCACACCACCTA 61.474 60.000 0.00 0.00 0.00 3.08
1658 1815 0.037605 GAACCGACCACACCACCTAG 60.038 60.000 0.00 0.00 0.00 3.02
1659 1816 0.761702 AACCGACCACACCACCTAGT 60.762 55.000 0.00 0.00 0.00 2.57
1660 1817 1.183676 ACCGACCACACCACCTAGTC 61.184 60.000 0.00 0.00 0.00 2.59
1749 1906 2.725641 GGTTTGTCGGTTGCCACC 59.274 61.111 0.00 0.00 40.16 4.61
1778 1936 5.168569 TGGTAGCTTTCTATCTGTTGTTCG 58.831 41.667 0.00 0.00 0.00 3.95
1870 2028 2.491693 GGAAATTCCATTGGTTCGCTCA 59.508 45.455 7.23 0.00 36.28 4.26
1918 2076 4.328983 CGAAAAGCTTGAGATAGCGGTTTA 59.671 41.667 0.00 0.00 45.82 2.01
1951 2109 2.624838 ACTTGCATTTGGGAGTTCACTG 59.375 45.455 0.00 0.00 0.00 3.66
1952 2110 0.961019 TGCATTTGGGAGTTCACTGC 59.039 50.000 0.00 0.00 0.00 4.40
1953 2111 1.251251 GCATTTGGGAGTTCACTGCT 58.749 50.000 0.00 0.00 34.50 4.24
1954 2112 2.224744 TGCATTTGGGAGTTCACTGCTA 60.225 45.455 0.00 0.00 34.50 3.49
1995 2153 5.689514 GGATTCTGATTCTGACGTATGACTG 59.310 44.000 0.00 0.00 0.00 3.51
2032 2190 4.344390 AGAGTGCTGCATCATATCTGAAGA 59.656 41.667 5.27 0.00 34.37 2.87
2071 2229 5.931441 AGAGTTGTTTGCTTGTGATACTC 57.069 39.130 0.00 0.00 0.00 2.59
2110 2268 7.976826 TCCGCATGTTTATTACTCGTTAAAAT 58.023 30.769 0.00 0.00 0.00 1.82
2214 2372 2.230660 GGCCATGGAGGTAAATACTGC 58.769 52.381 18.40 0.00 40.61 4.40
2290 2454 5.406649 TGTTCTGTTTGTTTCACAATGGTC 58.593 37.500 0.00 0.00 38.00 4.02
2373 2537 6.616577 ACCCTTTAAAACCTTCCATAGAACA 58.383 36.000 0.00 0.00 0.00 3.18
2407 2571 9.931210 GTATTGTTACCTTACACTAAATCATGC 57.069 33.333 0.00 0.00 0.00 4.06
2534 2705 2.221169 TGACAGGACTGCAATGTTCAC 58.779 47.619 0.00 0.00 0.00 3.18
2667 2841 7.500141 ACCTAAAAGATTGCTTCAACAACAAT 58.500 30.769 0.00 0.00 36.74 2.71
2731 2905 3.904136 AGCATTGACTAGTTGTTGTGC 57.096 42.857 0.00 4.35 33.69 4.57
2735 2909 4.142902 GCATTGACTAGTTGTTGTGCGTAT 60.143 41.667 0.00 0.00 0.00 3.06
2820 2994 3.944015 AGCCAATCAAATGACTCAGTAGC 59.056 43.478 0.00 0.00 0.00 3.58
2903 3077 6.809196 TCAGTTGAAAATTTACACGTGCTTTT 59.191 30.769 17.22 15.55 0.00 2.27
2955 3130 4.506288 TGTGTTGTCTTCTTATGTGTGACG 59.494 41.667 0.00 0.00 0.00 4.35
3001 3177 4.948341 AAAATTTACAGGGAAAGCGGTT 57.052 36.364 0.00 0.00 0.00 4.44
3157 3334 4.551410 GCTTTTTGCTTGAAACTGACATGC 60.551 41.667 0.00 0.00 38.95 4.06
3264 3441 2.047061 GGAGAAAAGGGGCCAAAGTTT 58.953 47.619 4.39 0.00 0.00 2.66
3271 3448 1.667722 GGGCCAAAGTTTGCTGGAG 59.332 57.895 10.25 0.00 34.35 3.86
3274 3451 0.598419 GCCAAAGTTTGCTGGAGTGC 60.598 55.000 10.25 2.77 34.35 4.40
3315 3492 1.615116 CCCAAAGCTGGAGATGCAGAA 60.615 52.381 5.44 0.00 46.92 3.02
3365 3542 3.948473 GAGGTAAAATTGCTTCCTCCTCC 59.052 47.826 0.00 0.00 38.81 4.30
3367 3544 4.044698 AGGTAAAATTGCTTCCTCCTCCTT 59.955 41.667 0.00 0.00 0.00 3.36
3385 3562 3.033184 CCTTCTCTCTCTGCTCAATCCT 58.967 50.000 0.00 0.00 0.00 3.24
3388 3565 4.734398 TCTCTCTCTGCTCAATCCTTTC 57.266 45.455 0.00 0.00 0.00 2.62
3408 3585 4.897509 TCTGCTGGATATGGAATCGAAT 57.102 40.909 0.00 0.00 0.00 3.34
3430 3607 8.746927 CGAATAGGTTACTTTTCATGGCACAGA 61.747 40.741 0.00 0.00 35.27 3.41
3621 3798 2.683475 GGATGGGTGGGAACTGGG 59.317 66.667 0.00 0.00 0.00 4.45
4105 4296 8.774586 AGTATAAATGCTAGCTTATGTTTTCCG 58.225 33.333 17.23 0.00 0.00 4.30
4128 4319 4.640789 ACTCATCTACTGTTAAGGCTCG 57.359 45.455 0.00 0.00 0.00 5.03
4139 4330 1.355971 TAAGGCTCGCGATTTGTCAC 58.644 50.000 10.36 0.00 0.00 3.67
4253 4444 2.076100 TGACAAGAGCAATTGGTAGCG 58.924 47.619 10.70 4.24 34.36 4.26
4273 4466 2.096909 CGCACACTCCTCAAGTAAAACG 60.097 50.000 0.00 0.00 36.07 3.60
4336 4529 2.042762 TCCCCAGGGGACATGGAG 59.957 66.667 25.51 0.00 46.17 3.86
4342 4535 1.565759 CCAGGGGACATGGAGATGAAA 59.434 52.381 0.00 0.00 40.51 2.69
4460 4654 8.735315 TGTTTGAACAAAATTACTCAACTCAGA 58.265 29.630 1.47 0.00 35.67 3.27
4504 4698 5.814705 GGTTACACTTTCTGAGGATGATGAG 59.185 44.000 0.00 0.00 0.00 2.90
4830 5028 7.160547 TGATGCATGTTAATCAAGAACACAT 57.839 32.000 2.46 0.00 39.51 3.21
4898 5096 7.204604 TCATTCATCAACATAATTGACATGGC 58.795 34.615 0.00 0.00 0.00 4.40
5005 5206 4.141855 ACAAGTACGCAATAGTTTGTGC 57.858 40.909 0.00 0.00 45.30 4.57
5171 5374 4.034048 CCTTATTTCAGATGCCACGTACAC 59.966 45.833 0.00 0.00 0.00 2.90
5187 5390 6.540914 CCACGTACACCCAGACAAATTATATT 59.459 38.462 0.00 0.00 0.00 1.28
5248 5532 9.355215 TCTTTAGAGAACTTAGTTATTTCAGCG 57.645 33.333 0.00 0.00 0.00 5.18
5276 5560 5.452496 CCTTGGATCTGTAGTGACCAGTATG 60.452 48.000 0.00 0.00 32.16 2.39
5317 5601 4.208666 CACACTCTTCTCGTATGCATCATG 59.791 45.833 0.19 0.00 0.00 3.07
5328 5612 4.965762 CGTATGCATCATGTTGTGATTGTC 59.034 41.667 0.19 0.00 45.25 3.18
5331 5615 3.501445 TGCATCATGTTGTGATTGTCGAA 59.499 39.130 5.69 0.00 45.25 3.71
5365 5649 1.887320 GCATTTAGCAAGCAGTGTCG 58.113 50.000 0.00 0.00 44.79 4.35
5381 5665 2.230508 GTGTCGGACATGGTTAGACTGA 59.769 50.000 14.78 0.00 33.40 3.41
5437 5721 5.066246 GCAGATACTACGAGACTTGGTTAGT 59.934 44.000 0.00 0.00 40.71 2.24
5438 5722 6.404513 GCAGATACTACGAGACTTGGTTAGTT 60.405 42.308 0.00 0.00 37.17 2.24
5439 5723 7.188157 CAGATACTACGAGACTTGGTTAGTTC 58.812 42.308 0.00 0.00 37.17 3.01
5440 5724 4.780275 ACTACGAGACTTGGTTAGTTCC 57.220 45.455 0.00 0.00 37.17 3.62
5441 5725 4.147321 ACTACGAGACTTGGTTAGTTCCA 58.853 43.478 0.00 0.00 37.17 3.53
5472 5756 3.140325 TGGAGTCAACACCTTTGATCC 57.860 47.619 0.00 0.00 32.11 3.36
5517 5801 3.974871 TTTAGGCTGTGGAACGTTTTC 57.025 42.857 0.46 0.00 42.39 2.29
5525 5809 5.506649 GGCTGTGGAACGTTTTCTTTTATCA 60.507 40.000 0.46 0.00 42.39 2.15
5555 5839 8.347771 TCATCTTAAATGCTATCACTGAAATGC 58.652 33.333 0.00 0.00 0.00 3.56
5633 5920 8.177119 ACTAGAATCTGAGGCTACTTTCATAG 57.823 38.462 0.00 0.00 0.00 2.23
5634 5921 8.001875 ACTAGAATCTGAGGCTACTTTCATAGA 58.998 37.037 0.00 0.00 0.00 1.98
5737 6035 7.975616 ACAATGCACATAATTACACTTTCCATC 59.024 33.333 0.00 0.00 0.00 3.51
5738 6036 7.643569 ATGCACATAATTACACTTTCCATCA 57.356 32.000 0.00 0.00 0.00 3.07
5739 6037 7.643569 TGCACATAATTACACTTTCCATCAT 57.356 32.000 0.00 0.00 0.00 2.45
5849 6147 1.461127 CTGTAAGCACCTCTGTTTCGC 59.539 52.381 0.00 0.00 0.00 4.70
5897 6197 8.019669 GTGTAGTGTTATGGTACTCATATACCG 58.980 40.741 5.29 0.00 46.72 4.02
5900 6200 5.477984 GTGTTATGGTACTCATATACCGGGA 59.522 44.000 6.32 0.00 46.72 5.14
5902 6202 3.889859 TGGTACTCATATACCGGGAGT 57.110 47.619 6.32 11.07 46.72 3.85
5912 6212 6.059484 TCATATACCGGGAGTTTGAAAATCC 58.941 40.000 15.49 15.49 0.00 3.01
5934 6234 3.430453 GCAGGAGGATAGTCTATCTGCT 58.570 50.000 17.50 11.78 39.17 4.24
5946 6246 4.281941 AGTCTATCTGCTGTGTGTGAGAAA 59.718 41.667 0.00 0.00 0.00 2.52
5952 6252 1.672881 GCTGTGTGTGAGAAAGTGCTT 59.327 47.619 0.00 0.00 0.00 3.91
5979 6279 4.704833 TTGGCGCCTGAGAGTGGC 62.705 66.667 29.70 0.00 46.42 5.01
6036 6336 3.354131 GCTCAAGAAGCCTACCGAG 57.646 57.895 0.00 0.00 45.92 4.63
6038 6338 1.066787 GCTCAAGAAGCCTACCGAGTT 60.067 52.381 0.00 0.00 45.92 3.01
6091 6391 1.091771 CATGCCTACCAAGTCGGCTG 61.092 60.000 11.08 4.27 43.53 4.85
6092 6392 2.820037 GCCTACCAAGTCGGCTGC 60.820 66.667 0.00 0.00 40.58 5.25
6093 6393 2.662596 CCTACCAAGTCGGCTGCA 59.337 61.111 0.50 0.00 39.03 4.41
6156 6456 3.134127 CGGCCCAGGTAAGCAAGC 61.134 66.667 0.00 0.00 0.00 4.01
6157 6457 2.356667 GGCCCAGGTAAGCAAGCT 59.643 61.111 0.00 0.00 35.94 3.74
6167 6467 3.149981 GGTAAGCAAGCTTTTCCTCTGT 58.850 45.455 13.06 0.00 37.47 3.41
6168 6468 3.189495 GGTAAGCAAGCTTTTCCTCTGTC 59.811 47.826 13.06 0.00 37.47 3.51
6177 6477 2.910688 TTTCCTCTGTCGAAGCAACT 57.089 45.000 0.00 0.00 0.00 3.16
6178 6478 4.307432 CTTTTCCTCTGTCGAAGCAACTA 58.693 43.478 0.00 0.00 0.00 2.24
6179 6479 4.330944 TTTCCTCTGTCGAAGCAACTAA 57.669 40.909 0.00 0.00 0.00 2.24
6180 6480 3.577649 TCCTCTGTCGAAGCAACTAAG 57.422 47.619 0.00 0.00 0.00 2.18
6181 6481 3.154710 TCCTCTGTCGAAGCAACTAAGA 58.845 45.455 0.00 0.00 0.00 2.10
6182 6482 3.057456 TCCTCTGTCGAAGCAACTAAGAC 60.057 47.826 0.00 0.00 0.00 3.01
6188 6488 6.320418 TCTGTCGAAGCAACTAAGACCATATA 59.680 38.462 0.00 0.00 0.00 0.86
6215 6515 8.906867 ACAGATTATGAAATCCCACATTGTAAG 58.093 33.333 0.00 0.00 42.20 2.34
6295 6595 2.938798 ATGCCCCAAAGACCCCGA 60.939 61.111 0.00 0.00 0.00 5.14
6371 6671 3.521529 AAACAGCAGCGCTCCGAGT 62.522 57.895 7.13 0.00 36.40 4.18
6418 6719 5.174035 GTCTGATCGGTGATAGACAAAATCG 59.826 44.000 0.42 0.00 39.39 3.34
6548 6864 3.696051 TGGTGGATAAATTGCAGAGCTTC 59.304 43.478 0.00 0.00 0.00 3.86
6623 6939 6.703607 GGTCATTCATGAGTACATTCTACTGG 59.296 42.308 0.00 0.00 37.51 4.00
6634 6950 7.705214 AGTACATTCTACTGGTACTCGAAATC 58.295 38.462 0.00 0.00 42.94 2.17
6635 6951 5.579718 ACATTCTACTGGTACTCGAAATCG 58.420 41.667 0.00 0.00 41.45 3.34
6637 6953 4.871993 TCTACTGGTACTCGAAATCGAC 57.128 45.455 0.58 0.00 44.22 4.20
6639 6955 2.079158 ACTGGTACTCGAAATCGACGA 58.921 47.619 0.00 0.00 44.22 4.20
6640 6956 2.681848 ACTGGTACTCGAAATCGACGAT 59.318 45.455 4.05 4.05 44.22 3.73
6641 6957 3.036633 CTGGTACTCGAAATCGACGATG 58.963 50.000 11.83 0.59 44.22 3.84
6642 6958 1.779724 GGTACTCGAAATCGACGATGC 59.220 52.381 11.83 6.03 44.22 3.91
6643 6959 2.447250 GTACTCGAAATCGACGATGCA 58.553 47.619 11.83 0.00 44.22 3.96
6644 6960 1.550065 ACTCGAAATCGACGATGCAG 58.450 50.000 11.83 7.47 44.22 4.41
6645 6961 1.132453 ACTCGAAATCGACGATGCAGA 59.868 47.619 11.83 9.72 44.22 4.26
6646 6962 1.514811 CTCGAAATCGACGATGCAGAC 59.485 52.381 11.83 1.15 44.22 3.51
6647 6963 0.224746 CGAAATCGACGATGCAGACG 59.775 55.000 11.83 13.19 43.02 4.18
6648 6964 1.269166 GAAATCGACGATGCAGACGT 58.731 50.000 18.86 18.86 46.58 4.34
6649 6965 0.992072 AAATCGACGATGCAGACGTG 59.008 50.000 22.61 15.44 43.97 4.49
6686 7002 5.586243 CAGGAAAGCTAGCTAGTTAAATGCA 59.414 40.000 19.70 0.00 0.00 3.96
6705 7025 4.780815 TGCACCCCAATTAGACTAGATTG 58.219 43.478 0.00 0.00 33.97 2.67
6718 7038 4.648762 AGACTAGATTGGAGACCATGTCTG 59.351 45.833 0.69 8.02 43.53 3.51
6739 7059 1.263484 GGTCAATCGCTGCAGATGATG 59.737 52.381 20.43 10.64 0.00 3.07
6898 7236 1.068083 GCCGAGATCGAAGATGCCA 59.932 57.895 3.31 0.00 45.12 4.92
6899 7237 0.943359 GCCGAGATCGAAGATGCCAG 60.943 60.000 3.31 0.00 45.12 4.85
6900 7238 0.319383 CCGAGATCGAAGATGCCAGG 60.319 60.000 3.31 0.00 45.12 4.45
6901 7239 0.319383 CGAGATCGAAGATGCCAGGG 60.319 60.000 0.00 0.00 45.12 4.45
6902 7240 0.034616 GAGATCGAAGATGCCAGGGG 59.965 60.000 0.00 0.00 45.12 4.79
6903 7241 1.599240 GATCGAAGATGCCAGGGGC 60.599 63.158 0.00 0.00 45.16 5.80
6970 7308 2.093235 GCAGATGAAGAAGTAGGTGCCT 60.093 50.000 0.00 0.00 0.00 4.75
6975 7313 0.984995 AAGAAGTAGGTGCCTGGGTC 59.015 55.000 0.12 0.00 0.00 4.46
7121 7464 2.686915 GCAAATCAGGAATGAGTGAGGG 59.313 50.000 0.00 0.00 0.00 4.30
7122 7465 3.875369 GCAAATCAGGAATGAGTGAGGGT 60.875 47.826 0.00 0.00 0.00 4.34
7124 7467 1.279496 TCAGGAATGAGTGAGGGTGG 58.721 55.000 0.00 0.00 0.00 4.61
7128 7471 0.107459 GAATGAGTGAGGGTGGAGGC 60.107 60.000 0.00 0.00 0.00 4.70
7129 7472 1.903877 AATGAGTGAGGGTGGAGGCG 61.904 60.000 0.00 0.00 0.00 5.52
7130 7473 3.775654 GAGTGAGGGTGGAGGCGG 61.776 72.222 0.00 0.00 0.00 6.13
7197 7559 3.333804 GCAGAGGTGAAGAAAAGAGAGG 58.666 50.000 0.00 0.00 0.00 3.69
7198 7560 3.244387 GCAGAGGTGAAGAAAAGAGAGGT 60.244 47.826 0.00 0.00 0.00 3.85
7199 7561 4.565022 CAGAGGTGAAGAAAAGAGAGGTC 58.435 47.826 0.00 0.00 0.00 3.85
7215 7584 1.202770 AGGTCGAGGTGAGGGTTTTTG 60.203 52.381 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 3.827634 GGCTTGTAGAATGCCCCG 58.172 61.111 0.00 0.00 40.71 5.73
37 38 2.160721 TCGGAGAGGGCTTGTAGAAT 57.839 50.000 0.00 0.00 0.00 2.40
53 54 0.752009 TCCGGAGAGGAGAACATCGG 60.752 60.000 0.00 0.00 45.98 4.18
54 55 2.795165 TCCGGAGAGGAGAACATCG 58.205 57.895 0.00 0.00 45.98 3.84
74 75 5.196341 ACGATCTATGTAGAAAATCGCCA 57.804 39.130 10.01 0.00 36.40 5.69
146 147 6.017192 AGAAGCAGTAATCGAATCCCCTATA 58.983 40.000 0.00 0.00 0.00 1.31
173 174 1.351350 GTCTAAACCACCCAGGAGCTT 59.649 52.381 0.00 0.00 41.22 3.74
179 180 3.243401 GCAAACTTGTCTAAACCACCCAG 60.243 47.826 0.00 0.00 0.00 4.45
182 183 3.004419 GGAGCAAACTTGTCTAAACCACC 59.996 47.826 0.00 0.00 0.00 4.61
185 186 3.537793 CGGAGCAAACTTGTCTAAACC 57.462 47.619 0.00 0.00 0.00 3.27
210 211 1.896694 CTGCCTCTGGGTCTCTGTC 59.103 63.158 0.00 0.00 34.45 3.51
212 213 1.834856 TTGCTGCCTCTGGGTCTCTG 61.835 60.000 0.00 0.00 34.45 3.35
218 219 2.119655 GCTCATTGCTGCCTCTGGG 61.120 63.158 0.00 0.00 38.95 4.45
232 233 1.725641 CATGCCGTGACTAAAGCTCA 58.274 50.000 0.00 0.00 0.00 4.26
417 447 0.953471 TAGTGGACCGTGCACAATGC 60.953 55.000 23.22 9.76 41.46 3.56
419 449 0.036388 CCTAGTGGACCGTGCACAAT 60.036 55.000 23.22 7.90 41.46 2.71
420 450 1.369692 CCTAGTGGACCGTGCACAA 59.630 57.895 23.22 0.00 41.46 3.33
423 454 2.280552 GGACCTAGTGGACCGTGCA 61.281 63.158 0.00 0.00 38.31 4.57
430 461 3.007182 CGGTTAGTTTTGGACCTAGTGGA 59.993 47.826 0.00 0.00 37.04 4.02
456 487 2.764314 CCGGCATGCTAGTTGTGGC 61.764 63.158 18.92 0.00 35.34 5.01
523 555 0.179134 CGTGGACGGTTCTGATCTCC 60.179 60.000 0.00 0.00 35.37 3.71
543 577 2.024588 CTCTCTCGCTCGCTCTGC 59.975 66.667 0.00 0.00 0.00 4.26
549 583 3.591835 GCTCCCCTCTCTCGCTCG 61.592 72.222 0.00 0.00 0.00 5.03
553 587 4.507916 TCGGGCTCCCCTCTCTCG 62.508 72.222 0.00 0.00 42.67 4.04
745 804 2.387772 CGGAGGAGGAGGAGGAGGA 61.388 68.421 0.00 0.00 0.00 3.71
746 805 2.197324 CGGAGGAGGAGGAGGAGG 59.803 72.222 0.00 0.00 0.00 4.30
747 806 2.520741 GCGGAGGAGGAGGAGGAG 60.521 72.222 0.00 0.00 0.00 3.69
822 889 3.038417 CGATTCGGCGGATGAGGC 61.038 66.667 4.83 0.00 0.00 4.70
941 1014 2.270047 CCAGCAACAACAACAACAAGG 58.730 47.619 0.00 0.00 0.00 3.61
942 1015 2.958213 ACCAGCAACAACAACAACAAG 58.042 42.857 0.00 0.00 0.00 3.16
944 1017 2.297315 TCAACCAGCAACAACAACAACA 59.703 40.909 0.00 0.00 0.00 3.33
945 1018 2.666022 GTCAACCAGCAACAACAACAAC 59.334 45.455 0.00 0.00 0.00 3.32
946 1019 2.669670 CGTCAACCAGCAACAACAACAA 60.670 45.455 0.00 0.00 0.00 2.83
947 1020 1.135546 CGTCAACCAGCAACAACAACA 60.136 47.619 0.00 0.00 0.00 3.33
948 1021 1.544686 CGTCAACCAGCAACAACAAC 58.455 50.000 0.00 0.00 0.00 3.32
949 1022 0.179150 GCGTCAACCAGCAACAACAA 60.179 50.000 0.00 0.00 0.00 2.83
950 1023 1.308783 TGCGTCAACCAGCAACAACA 61.309 50.000 0.00 0.00 40.78 3.33
951 1024 0.592247 CTGCGTCAACCAGCAACAAC 60.592 55.000 0.00 0.00 43.31 3.32
952 1025 1.723608 CCTGCGTCAACCAGCAACAA 61.724 55.000 0.00 0.00 43.31 2.83
953 1026 2.186160 CCTGCGTCAACCAGCAACA 61.186 57.895 0.00 0.00 43.31 3.33
954 1027 2.186826 ACCTGCGTCAACCAGCAAC 61.187 57.895 0.00 0.00 43.31 4.17
1249 1327 1.451207 CGCGGATTCATTCCCCACA 60.451 57.895 0.00 0.00 42.06 4.17
1251 1329 2.191908 CCGCGGATTCATTCCCCA 59.808 61.111 24.07 0.00 42.06 4.96
1253 1331 3.649986 CGCCGCGGATTCATTCCC 61.650 66.667 33.48 6.41 42.06 3.97
1256 1334 4.856801 AGCCGCCGCGGATTCATT 62.857 61.111 35.54 9.54 45.97 2.57
1331 1409 0.322322 ACCGCCGACCAATTAACTCA 59.678 50.000 0.00 0.00 0.00 3.41
1350 1428 2.794820 TTCATCGCACCATCGCACCA 62.795 55.000 0.00 0.00 0.00 4.17
1351 1429 1.439353 ATTCATCGCACCATCGCACC 61.439 55.000 0.00 0.00 0.00 5.01
1352 1430 0.378257 AATTCATCGCACCATCGCAC 59.622 50.000 0.00 0.00 0.00 5.34
1353 1431 0.657312 GAATTCATCGCACCATCGCA 59.343 50.000 0.00 0.00 0.00 5.10
1354 1432 0.040958 GGAATTCATCGCACCATCGC 60.041 55.000 7.93 0.00 0.00 4.58
1357 1457 0.107214 ACGGGAATTCATCGCACCAT 60.107 50.000 16.76 0.00 40.89 3.55
1420 1524 0.178975 TCCCGATGCAAACCAAACCT 60.179 50.000 0.00 0.00 0.00 3.50
1481 1589 4.090642 GTCAGTTCAGCAGATAAACTCGTG 59.909 45.833 0.00 0.00 31.04 4.35
1486 1594 2.094417 GGCGTCAGTTCAGCAGATAAAC 59.906 50.000 0.00 0.00 0.00 2.01
1504 1612 0.457035 CACAATGGAATTCAGGGGCG 59.543 55.000 7.93 0.00 31.22 6.13
1514 1657 1.430853 TGGGGGTGAATCACAATGGAA 59.569 47.619 15.86 0.00 35.86 3.53
1539 1686 0.038526 AGTCTGACAAACCGCTACCG 60.039 55.000 10.88 0.00 0.00 4.02
1540 1687 1.270147 ACAGTCTGACAAACCGCTACC 60.270 52.381 10.88 0.00 0.00 3.18
1544 1691 1.853319 CGACAGTCTGACAAACCGC 59.147 57.895 10.88 0.00 0.00 5.68
1557 1704 0.870393 ACTCACAATGCAAGCGACAG 59.130 50.000 0.00 0.00 0.00 3.51
1562 1719 0.239347 AGCGAACTCACAATGCAAGC 59.761 50.000 0.00 0.00 0.00 4.01
1572 1729 1.540363 GGGTCAGAAACAGCGAACTCA 60.540 52.381 0.00 0.00 0.00 3.41
1618 1775 3.265995 TCCCAAATAACAGGAAGAGACCC 59.734 47.826 0.00 0.00 0.00 4.46
1650 1807 6.838382 ACAACTTTAATTCTGACTAGGTGGT 58.162 36.000 0.00 0.00 0.00 4.16
1651 1808 7.745620 AACAACTTTAATTCTGACTAGGTGG 57.254 36.000 0.00 0.00 0.00 4.61
1652 1809 9.490379 AGTAACAACTTTAATTCTGACTAGGTG 57.510 33.333 0.00 0.00 0.00 4.00
1653 1810 9.708092 GAGTAACAACTTTAATTCTGACTAGGT 57.292 33.333 0.00 0.00 0.00 3.08
1654 1811 9.706691 TGAGTAACAACTTTAATTCTGACTAGG 57.293 33.333 0.00 0.00 0.00 3.02
1660 1817 9.612620 GGTGAATGAGTAACAACTTTAATTCTG 57.387 33.333 0.00 0.00 0.00 3.02
1749 1906 5.121811 ACAGATAGAAAGCTACCAATGCAG 58.878 41.667 0.00 0.00 0.00 4.41
1848 2006 1.472480 AGCGAACCAATGGAATTTCCG 59.528 47.619 6.16 1.06 40.17 4.30
1918 2076 1.302752 TGCAAGTCAGCAAGCCGAT 60.303 52.632 0.00 0.00 42.46 4.18
1952 2110 5.720371 ATCCACTTACATGAGCTAGCTAG 57.280 43.478 19.38 16.84 0.00 3.42
1953 2111 5.835819 AGAATCCACTTACATGAGCTAGCTA 59.164 40.000 19.38 6.79 0.00 3.32
1954 2112 4.653341 AGAATCCACTTACATGAGCTAGCT 59.347 41.667 19.45 19.45 0.00 3.32
1969 2127 5.460419 GTCATACGTCAGAATCAGAATCCAC 59.540 44.000 0.00 0.00 0.00 4.02
1995 2153 4.094146 GCAGCACTCTAAATCTCCAACTTC 59.906 45.833 0.00 0.00 0.00 3.01
2032 2190 7.589958 ACAACTCTTATCCTCGACAAGATAT 57.410 36.000 0.00 0.00 0.00 1.63
2071 2229 3.436704 ACATGCGGATACACTCAAACTTG 59.563 43.478 0.00 0.00 0.00 3.16
2087 2245 8.933955 CAGATTTTAACGAGTAATAAACATGCG 58.066 33.333 0.00 0.00 0.00 4.73
2110 2268 0.550914 AAACAGGTGCCCAAGTCAGA 59.449 50.000 0.00 0.00 0.00 3.27
2118 2276 0.178973 ACAAGGGTAAACAGGTGCCC 60.179 55.000 0.00 0.00 41.36 5.36
2196 2354 3.117888 ACAGGCAGTATTTACCTCCATGG 60.118 47.826 4.97 4.97 42.93 3.66
2214 2372 6.846325 AGTTAAACGAGAAGAGAAAACAGG 57.154 37.500 0.00 0.00 0.00 4.00
2290 2454 6.433093 ACCAGCTTAAACCAAAATAGGTACAG 59.567 38.462 0.00 0.00 42.25 2.74
2425 2589 5.587289 TGTTGAACAGAATAACAGCAAACC 58.413 37.500 0.00 0.00 31.34 3.27
2467 2631 9.613428 CTGTATGAAAGTACCAGGATGATAAAA 57.387 33.333 0.00 0.00 39.69 1.52
2476 2640 6.884832 TCCAATACTGTATGAAAGTACCAGG 58.115 40.000 0.22 0.00 33.11 4.45
2513 2684 2.618241 GTGAACATTGCAGTCCTGTCAA 59.382 45.455 6.61 6.61 33.59 3.18
2534 2705 1.878953 ACAAGTCCTGCCAGTTAACG 58.121 50.000 0.00 0.00 0.00 3.18
2667 2841 8.100791 AGAGTTAATAAAGCCAGTGAACACATA 58.899 33.333 7.68 0.00 0.00 2.29
2731 2905 3.377346 AGCTAATCTCCACAGCATACG 57.623 47.619 0.00 0.00 37.78 3.06
2735 2909 4.162131 TCAACATAGCTAATCTCCACAGCA 59.838 41.667 0.00 0.00 37.78 4.41
2801 2975 7.279536 ACATGTAGCTACTGAGTCATTTGATTG 59.720 37.037 23.84 0.76 0.00 2.67
2981 3156 3.554129 GCAACCGCTTTCCCTGTAAATTT 60.554 43.478 0.00 0.00 34.30 1.82
3001 3177 1.611006 TGTTTGGCGCAGAATTTAGCA 59.389 42.857 10.83 0.00 0.00 3.49
3049 3225 5.300286 AGCTAAATCACCAGAACAATATGCC 59.700 40.000 0.00 0.00 0.00 4.40
3094 3270 7.560368 AGAAAGAACATGGTAGATACCTCAAG 58.440 38.462 10.30 1.03 46.58 3.02
3264 3441 0.251787 TACTCTCCAGCACTCCAGCA 60.252 55.000 0.00 0.00 36.85 4.41
3271 3448 5.675538 AGACCAAATTATACTCTCCAGCAC 58.324 41.667 0.00 0.00 0.00 4.40
3315 3492 0.898326 GCCATCCGTCCCCAAGTTTT 60.898 55.000 0.00 0.00 0.00 2.43
3365 3542 4.741321 AAGGATTGAGCAGAGAGAGAAG 57.259 45.455 0.00 0.00 0.00 2.85
3367 3544 4.160065 CAGAAAGGATTGAGCAGAGAGAGA 59.840 45.833 0.00 0.00 0.00 3.10
3385 3562 4.687901 TCGATTCCATATCCAGCAGAAA 57.312 40.909 0.00 0.00 0.00 2.52
3388 3565 5.114780 CCTATTCGATTCCATATCCAGCAG 58.885 45.833 0.00 0.00 0.00 4.24
3408 3585 5.235850 TCTGTGCCATGAAAAGTAACCTA 57.764 39.130 0.00 0.00 0.00 3.08
3514 3691 8.417106 TGCTTAACAACATCACCAATTTAAAGA 58.583 29.630 0.00 0.00 0.00 2.52
3621 3798 1.153086 ATCTGAGCAATCCACCGGC 60.153 57.895 0.00 0.00 0.00 6.13
4105 4296 5.038033 CGAGCCTTAACAGTAGATGAGTTC 58.962 45.833 0.00 0.00 0.00 3.01
4128 4319 1.992667 TGTGATCTCGTGACAAATCGC 59.007 47.619 0.00 0.00 0.00 4.58
4139 4330 2.376808 AGTTCTGGCTTGTGATCTCG 57.623 50.000 0.00 0.00 0.00 4.04
4253 4444 2.870411 ACGTTTTACTTGAGGAGTGTGC 59.130 45.455 0.00 0.00 39.48 4.57
4330 4523 9.649167 AAAAGCTTATTTTCTTTCATCTCCATG 57.351 29.630 0.00 0.00 31.91 3.66
4336 4529 8.864024 GCTGGTAAAAGCTTATTTTCTTTCATC 58.136 33.333 0.00 0.00 40.20 2.92
4342 4535 5.007682 TCGGCTGGTAAAAGCTTATTTTCT 58.992 37.500 0.00 0.00 43.06 2.52
4460 4654 4.151883 ACCTGACCAACAGTAATGCAATT 58.848 39.130 0.00 0.00 44.40 2.32
4504 4698 3.451141 TCACAGGCCAAAACAATGAAC 57.549 42.857 5.01 0.00 0.00 3.18
4631 4829 5.589831 ACAATTGGGAAGCCCTTTACTATT 58.410 37.500 10.83 0.00 45.70 1.73
4640 4838 2.231716 AAGGTACAATTGGGAAGCCC 57.768 50.000 10.83 0.00 45.71 5.19
4736 4934 6.976934 TTTTCTTTCCCTCTATGCTTTTGT 57.023 33.333 0.00 0.00 0.00 2.83
4738 4936 7.603180 AGTTTTTCTTTCCCTCTATGCTTTT 57.397 32.000 0.00 0.00 0.00 2.27
4830 5028 1.885887 GTCAACTTGCCAACATAGCCA 59.114 47.619 0.00 0.00 0.00 4.75
5005 5206 6.513180 TGTTATGCTTTCGGTCTATCCTTAG 58.487 40.000 0.00 0.00 0.00 2.18
5152 5355 2.356135 GGTGTACGTGGCATCTGAAAT 58.644 47.619 0.00 0.00 0.00 2.17
5248 5532 3.368531 GGTCACTACAGATCCAAGGACAC 60.369 52.174 0.00 0.00 0.00 3.67
5276 5560 5.713025 AGTGTGATCAACATTATTTGTGCC 58.287 37.500 0.00 0.00 41.97 5.01
5317 5601 4.312443 TCTAACCCTTCGACAATCACAAC 58.688 43.478 0.00 0.00 0.00 3.32
5328 5612 4.701956 ATGCACAAAATCTAACCCTTCG 57.298 40.909 0.00 0.00 0.00 3.79
5331 5615 5.965922 GCTAAATGCACAAAATCTAACCCT 58.034 37.500 0.00 0.00 42.31 4.34
5365 5649 6.239064 CCACTAGTATCAGTCTAACCATGTCC 60.239 46.154 0.00 0.00 0.00 4.02
5381 5665 3.515502 TGCAACTGAGCTTCCACTAGTAT 59.484 43.478 0.00 0.00 34.99 2.12
5525 5809 7.041721 TCAGTGATAGCATTTAAGATGACGTT 58.958 34.615 0.00 0.00 0.00 3.99
5555 5839 8.970691 AATTCATCCGTCTTAATTTTGAACAG 57.029 30.769 0.00 0.00 0.00 3.16
5584 5868 2.003301 GAACCTCTGTTGCCTTCGATC 58.997 52.381 0.00 0.00 33.97 3.69
5633 5920 7.278868 ACATACAAAAGTAGCATGCTAAGAGTC 59.721 37.037 28.44 15.70 0.00 3.36
5634 5921 7.065085 CACATACAAAAGTAGCATGCTAAGAGT 59.935 37.037 28.44 21.86 0.00 3.24
5737 6035 6.209391 AGGGAGTTAATGAAAACCAAGTCATG 59.791 38.462 0.00 0.00 34.70 3.07
5738 6036 6.314917 AGGGAGTTAATGAAAACCAAGTCAT 58.685 36.000 0.00 0.00 36.00 3.06
5739 6037 5.701224 AGGGAGTTAATGAAAACCAAGTCA 58.299 37.500 0.00 0.00 0.00 3.41
5849 6147 8.689251 ACACGATATCAATAATCTATGTTCGG 57.311 34.615 3.12 0.00 0.00 4.30
5897 6197 1.202348 CCTGCGGATTTTCAAACTCCC 59.798 52.381 1.03 0.00 0.00 4.30
5900 6200 2.162681 CCTCCTGCGGATTTTCAAACT 58.837 47.619 0.00 0.00 0.00 2.66
5902 6202 2.577606 TCCTCCTGCGGATTTTCAAA 57.422 45.000 0.00 0.00 0.00 2.69
5912 6212 2.163412 GCAGATAGACTATCCTCCTGCG 59.837 54.545 17.23 1.57 35.16 5.18
5934 6234 2.677836 GTCAAGCACTTTCTCACACACA 59.322 45.455 0.00 0.00 0.00 3.72
5946 6246 1.893808 CAAGCACCGGTCAAGCACT 60.894 57.895 16.80 1.69 0.00 4.40
5979 6279 1.599797 GTTGTCACAACCCTCCCCG 60.600 63.158 9.76 0.00 0.00 5.73
6036 6336 2.679199 GCTAGAAGTAGCGGCCAAC 58.321 57.895 2.24 0.00 42.41 3.77
6156 6456 3.134458 AGTTGCTTCGACAGAGGAAAAG 58.866 45.455 0.00 0.00 0.00 2.27
6157 6457 3.194005 AGTTGCTTCGACAGAGGAAAA 57.806 42.857 0.00 0.00 0.00 2.29
6167 6467 6.869695 TGTTATATGGTCTTAGTTGCTTCGA 58.130 36.000 0.00 0.00 0.00 3.71
6168 6468 6.978659 TCTGTTATATGGTCTTAGTTGCTTCG 59.021 38.462 0.00 0.00 0.00 3.79
6179 6479 9.965902 GGGATTTCATAATCTGTTATATGGTCT 57.034 33.333 0.00 0.00 40.07 3.85
6180 6480 9.739276 TGGGATTTCATAATCTGTTATATGGTC 57.261 33.333 0.00 0.00 40.07 4.02
6181 6481 9.520515 GTGGGATTTCATAATCTGTTATATGGT 57.479 33.333 0.00 0.00 40.07 3.55
6182 6482 9.519191 TGTGGGATTTCATAATCTGTTATATGG 57.481 33.333 0.00 0.00 40.07 2.74
6188 6488 7.722949 ACAATGTGGGATTTCATAATCTGTT 57.277 32.000 0.00 0.00 40.07 3.16
6215 6515 2.093106 TCTGAAAGAGTAGCTCGGGTC 58.907 52.381 0.00 0.00 38.67 4.46
6295 6595 2.202272 GCGCTACTTCGACGACGT 60.202 61.111 11.93 11.93 40.69 4.34
6371 6671 0.770499 TCTGAACCATGTGGCTTGGA 59.230 50.000 7.86 0.00 39.32 3.53
6418 6719 4.184629 CACCACTTCACTTACTGCTATCC 58.815 47.826 0.00 0.00 0.00 2.59
6570 6886 7.351223 GCTAGTTGCAATTCATCAAGATAGAC 58.649 38.462 0.59 0.00 42.31 2.59
6634 6950 0.796870 TAAGCACGTCTGCATCGTCG 60.797 55.000 12.86 10.28 46.97 5.12
6635 6951 0.640768 GTAAGCACGTCTGCATCGTC 59.359 55.000 12.86 9.01 46.97 4.20
6637 6953 1.280982 ATGTAAGCACGTCTGCATCG 58.719 50.000 9.35 9.35 46.97 3.84
6639 6955 3.595173 TGTAATGTAAGCACGTCTGCAT 58.405 40.909 0.52 0.00 46.97 3.96
6640 6956 3.033368 TGTAATGTAAGCACGTCTGCA 57.967 42.857 0.52 0.00 46.97 4.41
6641 6957 3.616821 TGATGTAATGTAAGCACGTCTGC 59.383 43.478 0.00 0.00 44.63 4.26
6642 6958 4.268644 CCTGATGTAATGTAAGCACGTCTG 59.731 45.833 0.00 0.00 0.00 3.51
6643 6959 4.159693 TCCTGATGTAATGTAAGCACGTCT 59.840 41.667 0.00 0.00 0.00 4.18
6644 6960 4.430007 TCCTGATGTAATGTAAGCACGTC 58.570 43.478 0.00 0.00 0.00 4.34
6645 6961 4.465632 TCCTGATGTAATGTAAGCACGT 57.534 40.909 0.00 0.00 0.00 4.49
6646 6962 5.727791 GCTTTCCTGATGTAATGTAAGCACG 60.728 44.000 0.00 0.00 37.34 5.34
6647 6963 5.355350 AGCTTTCCTGATGTAATGTAAGCAC 59.645 40.000 0.00 0.00 39.24 4.40
6648 6964 5.500234 AGCTTTCCTGATGTAATGTAAGCA 58.500 37.500 0.00 0.00 39.24 3.91
6649 6965 6.293135 GCTAGCTTTCCTGATGTAATGTAAGC 60.293 42.308 7.70 0.00 37.58 3.09
6650 6966 6.989169 AGCTAGCTTTCCTGATGTAATGTAAG 59.011 38.462 12.68 0.00 0.00 2.34
6718 7038 0.462581 TCATCTGCAGCGATTGACCC 60.463 55.000 9.47 0.00 0.00 4.46
6746 7066 4.230745 TCATTGCCCTTTAGGTCCTAAC 57.769 45.455 11.09 0.69 38.26 2.34
6747 7067 4.386312 CCATCATTGCCCTTTAGGTCCTAA 60.386 45.833 7.29 7.29 38.26 2.69
6748 7068 3.138283 CCATCATTGCCCTTTAGGTCCTA 59.862 47.826 0.00 0.00 38.26 2.94
6749 7069 2.091665 CCATCATTGCCCTTTAGGTCCT 60.092 50.000 0.00 0.00 38.26 3.85
6753 7073 1.684983 CTGCCATCATTGCCCTTTAGG 59.315 52.381 0.00 0.00 39.47 2.69
6876 7214 0.598680 CATCTTCGATCTCGGCCCAC 60.599 60.000 0.00 0.00 40.29 4.61
6903 7241 3.642778 AAGGTCGCCATCACCGTCG 62.643 63.158 0.00 0.00 39.13 5.12
7025 7363 0.953471 TACGACAACTGCACCATGGC 60.953 55.000 13.04 0.00 0.00 4.40
7124 7467 4.208686 CTACGTCCCTGCCGCCTC 62.209 72.222 0.00 0.00 0.00 4.70
7128 7471 0.592148 GATCTACTACGTCCCTGCCG 59.408 60.000 0.00 0.00 0.00 5.69
7129 7472 1.609555 CAGATCTACTACGTCCCTGCC 59.390 57.143 0.00 0.00 0.00 4.85
7130 7473 1.609555 CCAGATCTACTACGTCCCTGC 59.390 57.143 0.00 0.00 0.00 4.85
7131 7474 2.619177 CACCAGATCTACTACGTCCCTG 59.381 54.545 0.00 0.00 0.00 4.45
7134 7477 2.879646 CTCCACCAGATCTACTACGTCC 59.120 54.545 0.00 0.00 0.00 4.79
7137 7480 2.292016 CAGCTCCACCAGATCTACTACG 59.708 54.545 0.00 0.00 0.00 3.51
7166 7516 3.615811 ACCTCTGCCTCCCCTCCA 61.616 66.667 0.00 0.00 0.00 3.86
7197 7559 1.963172 ACAAAAACCCTCACCTCGAC 58.037 50.000 0.00 0.00 0.00 4.20
7198 7560 2.685897 CAAACAAAAACCCTCACCTCGA 59.314 45.455 0.00 0.00 0.00 4.04
7199 7561 2.223711 CCAAACAAAAACCCTCACCTCG 60.224 50.000 0.00 0.00 0.00 4.63
7215 7584 2.945668 GACCTCATCTGTATGCCCAAAC 59.054 50.000 0.00 0.00 32.76 2.93
7269 7638 1.278127 ACCCCAACATCAACTACTCCG 59.722 52.381 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.