Multiple sequence alignment - TraesCS6B01G111600

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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 TraesCS6B01G111600 chr6B 100.000 2896 0 0 1 2896 93437091 93434196 0 5349
1 TraesCS6B01G111600 chrUn 94.936 1402 62 5 1499 2896 19244325 19245721 0 2187
2 TraesCS6B01G111600 chrUn 89.101 1468 107 21 3 1433 19242846 19244297 0 1775
3 TraesCS6B01G111600 chr6A 94.306 1405 65 9 1499 2896 57691916 57690520 0 2137
4 TraesCS6B01G111600 chr6A 87.792 1499 128 21 1 1460 57693399 57691917 0 1703


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 TraesCS6B01G111600 chr6B 93434196 93437091 2895 True 5349 5349 100.0000 1 2896 1 chr6B.!!$R1 2895
1 TraesCS6B01G111600 chrUn 19242846 19245721 2875 False 1981 2187 92.0185 3 2896 2 chrUn.!!$F1 2893
2 TraesCS6B01G111600 chr6A 57690520 57693399 2879 True 1920 2137 91.0490 1 2896 2 chr6A.!!$R1 2895

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
769 822 0.036732 TGCAGGAACCCAACTAGCAG 59.963 55.0 0.0 0.0 0.0 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2282 2352 0.747255 GCAGCAGTCGGGAATCTAGA 59.253 55.0 0.0 0.0 0.0 2.43 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
30 31 3.569701 AGCCATATTATTTTGCTGGACCG 59.430 43.478 0.00 0.00 0.00 4.79
55 56 7.351223 GCAATATCTGAAGTGTAATCTTGCTC 58.649 38.462 0.00 0.00 34.12 4.26
90 91 2.907696 TCGGGTGGAAATTAAGGTGAGA 59.092 45.455 0.00 0.00 0.00 3.27
142 173 7.042925 GCCTGCAAGAATGAACATAAAATGATC 60.043 37.037 0.00 0.00 34.07 2.92
146 177 9.017669 GCAAGAATGAACATAAAATGATCTGAC 57.982 33.333 0.00 0.00 33.70 3.51
226 257 3.638627 TGAGCTCTTCTGAGTTCTGACAA 59.361 43.478 16.19 0.00 46.42 3.18
298 330 6.147821 ACGACTTGTATCAAAACTGGAATCTG 59.852 38.462 0.00 0.00 0.00 2.90
299 331 6.402550 CGACTTGTATCAAAACTGGAATCTGG 60.403 42.308 0.00 0.00 0.00 3.86
300 332 5.711976 ACTTGTATCAAAACTGGAATCTGGG 59.288 40.000 0.00 0.00 0.00 4.45
310 342 1.992557 TGGAATCTGGGTAAAGTGCCT 59.007 47.619 0.00 0.00 0.00 4.75
314 346 2.787473 TCTGGGTAAAGTGCCTGATG 57.213 50.000 0.00 0.00 0.00 3.07
315 347 1.281867 TCTGGGTAAAGTGCCTGATGG 59.718 52.381 0.00 0.00 0.00 3.51
323 355 4.313020 AAAGTGCCTGATGGATCTTCTT 57.687 40.909 0.00 0.00 34.57 2.52
336 368 7.767659 TGATGGATCTTCTTATTCAAGTGTCTG 59.232 37.037 0.00 0.00 33.20 3.51
563 595 7.609532 AGCAATGTTAGAAGTTAGAATGCTCTT 59.390 33.333 0.00 0.00 35.69 2.85
608 640 2.501316 AGCTTTTGAAGTTTGGCACCTT 59.499 40.909 0.00 0.00 0.00 3.50
614 646 7.387673 GCTTTTGAAGTTTGGCACCTTATTAAT 59.612 33.333 0.00 0.00 0.00 1.40
620 652 7.158099 AGTTTGGCACCTTATTAATCTCAAC 57.842 36.000 0.00 0.00 0.00 3.18
621 653 6.719370 AGTTTGGCACCTTATTAATCTCAACA 59.281 34.615 0.00 0.00 0.00 3.33
638 670 9.561069 AATCTCAACATATAAAATAGTCGGCTT 57.439 29.630 0.00 0.00 0.00 4.35
675 726 1.067354 CATTCTTTCAGCAGTTGGGCC 60.067 52.381 0.00 0.00 0.00 5.80
676 727 0.106268 TTCTTTCAGCAGTTGGGCCA 60.106 50.000 0.00 0.00 0.00 5.36
677 728 0.106268 TCTTTCAGCAGTTGGGCCAA 60.106 50.000 16.66 16.66 0.00 4.52
703 754 5.820947 CCTAAGTCGCCTGGTAAATTATGTT 59.179 40.000 0.00 0.00 0.00 2.71
704 755 6.317893 CCTAAGTCGCCTGGTAAATTATGTTT 59.682 38.462 0.00 0.00 0.00 2.83
732 783 6.306987 ACATTCTTTAGGAGGCAAGAGAAAA 58.693 36.000 0.00 0.00 30.68 2.29
755 808 4.236527 AGACCTTAACCCTTATTGCAGG 57.763 45.455 0.00 0.00 0.00 4.85
769 822 0.036732 TGCAGGAACCCAACTAGCAG 59.963 55.000 0.00 0.00 0.00 4.24
770 823 0.036875 GCAGGAACCCAACTAGCAGT 59.963 55.000 0.00 0.00 0.00 4.40
786 849 1.200020 GCAGTGGTTTTCCCTCGAATG 59.800 52.381 0.00 0.00 39.73 2.67
804 867 2.398252 TGATTCCTGCAGCTCAAGAG 57.602 50.000 8.66 0.00 0.00 2.85
845 908 0.846427 TCCCAGGGCAGGAATCAACT 60.846 55.000 0.00 0.00 0.00 3.16
917 980 1.259609 TCCAAGCTTGCATTCCCTTG 58.740 50.000 21.43 4.12 35.61 3.61
925 988 2.496899 TGCATTCCCTTGGTTCTCTC 57.503 50.000 0.00 0.00 0.00 3.20
973 1036 7.751768 CCTTGATGGGTCTATCCTAAAAATC 57.248 40.000 0.00 0.00 36.25 2.17
989 1052 4.906747 AAAATCTCTCTGTCCTCTTGCT 57.093 40.909 0.00 0.00 0.00 3.91
1093 1156 1.226746 GTTCTATATGCCGGTGCCAC 58.773 55.000 1.90 0.00 36.33 5.01
1094 1157 0.833949 TTCTATATGCCGGTGCCACA 59.166 50.000 1.90 0.00 36.33 4.17
1095 1158 1.055849 TCTATATGCCGGTGCCACAT 58.944 50.000 1.90 0.00 36.33 3.21
1096 1159 1.159285 CTATATGCCGGTGCCACATG 58.841 55.000 1.90 0.00 36.33 3.21
1097 1160 0.761802 TATATGCCGGTGCCACATGA 59.238 50.000 1.90 0.00 36.33 3.07
1098 1161 0.111061 ATATGCCGGTGCCACATGAT 59.889 50.000 1.90 0.00 36.33 2.45
1099 1162 0.761802 TATGCCGGTGCCACATGATA 59.238 50.000 1.90 0.00 36.33 2.15
1117 1180 7.572523 CATGATATTACATGGTTCTTGTGGT 57.427 36.000 0.00 0.00 42.45 4.16
1123 1186 1.234615 ATGGTTCTTGTGGTTCCGCG 61.235 55.000 0.00 0.00 0.00 6.46
1133 1196 1.068816 GTGGTTCCGCGCTGTTTTATT 60.069 47.619 5.56 0.00 0.00 1.40
1141 1204 2.470999 CGCGCTGTTTTATTTGTTGCTT 59.529 40.909 5.56 0.00 0.00 3.91
1144 1207 4.375305 GCGCTGTTTTATTTGTTGCTTGAG 60.375 41.667 0.00 0.00 0.00 3.02
1151 1214 5.772825 TTATTTGTTGCTTGAGCTTCTGT 57.227 34.783 4.44 0.00 42.66 3.41
1152 1215 3.698029 TTTGTTGCTTGAGCTTCTGTC 57.302 42.857 4.44 0.00 42.66 3.51
1182 1245 5.685841 TCTAAATTTGTTAACTCGTGCTGC 58.314 37.500 7.22 0.00 0.00 5.25
1183 1246 4.568152 AAATTTGTTAACTCGTGCTGCT 57.432 36.364 7.22 0.00 0.00 4.24
1185 1248 0.586319 TTGTTAACTCGTGCTGCTGC 59.414 50.000 8.89 8.89 40.20 5.25
1188 1251 0.670546 TTAACTCGTGCTGCTGCTCC 60.671 55.000 17.00 6.46 40.48 4.70
1205 1268 1.305633 CCTCTCAGGAGTGCCAGGA 60.306 63.158 0.00 0.00 37.67 3.86
1220 1283 2.124860 GGATTGGGCGCGGTAACT 60.125 61.111 8.83 0.00 0.00 2.24
1251 1314 9.302345 GACAAGTCTATGATCGACATTTTAAGA 57.698 33.333 0.00 1.60 40.07 2.10
1255 1318 9.653287 AGTCTATGATCGACATTTTAAGAACAA 57.347 29.630 0.00 0.00 40.07 2.83
1259 1322 7.921786 TGATCGACATTTTAAGAACAAGGAT 57.078 32.000 0.00 0.00 0.00 3.24
1262 1325 7.605410 TCGACATTTTAAGAACAAGGATACC 57.395 36.000 0.00 0.00 37.17 2.73
1263 1326 6.596497 TCGACATTTTAAGAACAAGGATACCC 59.404 38.462 0.00 0.00 37.17 3.69
1272 1335 1.094785 CAAGGATACCCGCACCTTTG 58.905 55.000 0.00 0.00 41.33 2.77
1277 1340 2.617021 GGATACCCGCACCTTTGAAGAA 60.617 50.000 0.00 0.00 0.00 2.52
1298 1361 6.952743 AGAATTTCATCTTGCATATGTCGAC 58.047 36.000 9.11 9.11 0.00 4.20
1314 1377 3.254903 TGTCGACTTCTGCAAGTAAGCTA 59.745 43.478 17.92 0.00 43.37 3.32
1331 1398 3.139077 AGCTACCTGTTTGTGCAGTTAC 58.861 45.455 0.00 0.00 34.84 2.50
1332 1399 2.875933 GCTACCTGTTTGTGCAGTTACA 59.124 45.455 0.00 0.00 34.84 2.41
1350 1417 1.610522 ACATTGCCTGCACTTCTTGTC 59.389 47.619 0.00 0.00 0.00 3.18
1355 1423 1.691196 CCTGCACTTCTTGTCCCAAA 58.309 50.000 0.00 0.00 0.00 3.28
1364 1432 6.685368 GCACTTCTTGTCCCAAACCTTTTATT 60.685 38.462 0.00 0.00 0.00 1.40
1366 1434 6.609616 ACTTCTTGTCCCAAACCTTTTATTCA 59.390 34.615 0.00 0.00 0.00 2.57
1377 1445 7.707893 CCAAACCTTTTATTCATGTCATCATCC 59.292 37.037 0.00 0.00 31.15 3.51
1384 1452 7.622893 TTATTCATGTCATCATCCGAAAACA 57.377 32.000 0.00 0.00 31.15 2.83
1433 1501 4.272489 CTGGCCAAGATTTTGATACTCCA 58.728 43.478 7.01 0.00 36.36 3.86
1436 1504 5.136105 GGCCAAGATTTTGATACTCCAGAT 58.864 41.667 0.00 0.00 36.36 2.90
1438 1506 6.060788 GCCAAGATTTTGATACTCCAGATCT 58.939 40.000 0.00 0.00 36.36 2.75
1441 1509 7.772292 CCAAGATTTTGATACTCCAGATCTTGA 59.228 37.037 19.23 0.00 42.81 3.02
1442 1510 9.170734 CAAGATTTTGATACTCCAGATCTTGAA 57.829 33.333 14.67 0.00 42.81 2.69
1460 1528 8.344939 ATCTTGAAGATATAAGGGTAAACCCA 57.655 34.615 20.25 0.54 45.45 4.51
1461 1529 8.960064 ATCTTGAAGATATAAGGGTAAACCCAT 58.040 33.333 20.25 11.02 45.45 4.00
1472 1540 4.170468 GGTAAACCCATCATCCATCAGT 57.830 45.455 0.00 0.00 0.00 3.41
1473 1541 4.536765 GGTAAACCCATCATCCATCAGTT 58.463 43.478 0.00 0.00 0.00 3.16
1474 1542 4.956075 GGTAAACCCATCATCCATCAGTTT 59.044 41.667 0.00 0.00 0.00 2.66
1475 1543 5.422012 GGTAAACCCATCATCCATCAGTTTT 59.578 40.000 0.00 0.00 0.00 2.43
1476 1544 6.070824 GGTAAACCCATCATCCATCAGTTTTT 60.071 38.462 0.00 0.00 0.00 1.94
1477 1545 5.665916 AACCCATCATCCATCAGTTTTTC 57.334 39.130 0.00 0.00 0.00 2.29
1478 1546 4.939255 ACCCATCATCCATCAGTTTTTCT 58.061 39.130 0.00 0.00 0.00 2.52
1479 1547 5.336102 ACCCATCATCCATCAGTTTTTCTT 58.664 37.500 0.00 0.00 0.00 2.52
1480 1548 5.781818 ACCCATCATCCATCAGTTTTTCTTT 59.218 36.000 0.00 0.00 0.00 2.52
1481 1549 6.270695 ACCCATCATCCATCAGTTTTTCTTTT 59.729 34.615 0.00 0.00 0.00 2.27
1482 1550 6.815142 CCCATCATCCATCAGTTTTTCTTTTC 59.185 38.462 0.00 0.00 0.00 2.29
1483 1551 7.310237 CCCATCATCCATCAGTTTTTCTTTTCT 60.310 37.037 0.00 0.00 0.00 2.52
1484 1552 8.092687 CCATCATCCATCAGTTTTTCTTTTCTT 58.907 33.333 0.00 0.00 0.00 2.52
1485 1553 9.485206 CATCATCCATCAGTTTTTCTTTTCTTT 57.515 29.630 0.00 0.00 0.00 2.52
1487 1555 9.533253 TCATCCATCAGTTTTTCTTTTCTTTTC 57.467 29.630 0.00 0.00 0.00 2.29
1488 1556 7.985634 TCCATCAGTTTTTCTTTTCTTTTCG 57.014 32.000 0.00 0.00 0.00 3.46
1489 1557 7.767261 TCCATCAGTTTTTCTTTTCTTTTCGA 58.233 30.769 0.00 0.00 0.00 3.71
1490 1558 8.247562 TCCATCAGTTTTTCTTTTCTTTTCGAA 58.752 29.630 0.00 0.00 0.00 3.71
1491 1559 8.534778 CCATCAGTTTTTCTTTTCTTTTCGAAG 58.465 33.333 0.00 0.00 32.21 3.79
1492 1560 8.534778 CATCAGTTTTTCTTTTCTTTTCGAAGG 58.465 33.333 0.00 0.00 32.21 3.46
1493 1561 7.033185 TCAGTTTTTCTTTTCTTTTCGAAGGG 58.967 34.615 0.00 0.00 32.21 3.95
1494 1562 7.033185 CAGTTTTTCTTTTCTTTTCGAAGGGA 58.967 34.615 0.00 0.00 32.21 4.20
1495 1563 7.706607 CAGTTTTTCTTTTCTTTTCGAAGGGAT 59.293 33.333 0.00 0.00 32.21 3.85
1496 1564 7.706607 AGTTTTTCTTTTCTTTTCGAAGGGATG 59.293 33.333 0.00 0.00 32.21 3.51
1497 1565 6.709018 TTTCTTTTCTTTTCGAAGGGATGT 57.291 33.333 0.00 0.00 32.21 3.06
1503 1571 5.165961 TCTTTTCGAAGGGATGTGATTCT 57.834 39.130 0.00 0.00 0.00 2.40
1546 1614 9.265901 ACATCTAGCAATTGACTGTTACATATC 57.734 33.333 10.34 0.00 0.00 1.63
1547 1615 9.264719 CATCTAGCAATTGACTGTTACATATCA 57.735 33.333 10.34 0.00 0.00 2.15
1548 1616 8.648557 TCTAGCAATTGACTGTTACATATCAC 57.351 34.615 10.34 0.00 0.00 3.06
1550 1618 5.294306 AGCAATTGACTGTTACATATCACCG 59.706 40.000 10.34 0.00 0.00 4.94
1567 1635 3.375922 TCACCGAAAAACTCAACTGAACC 59.624 43.478 0.00 0.00 0.00 3.62
1587 1657 1.526464 CGTACATGCGCATATTGCAGA 59.474 47.619 24.84 0.00 46.98 4.26
1588 1658 2.410646 CGTACATGCGCATATTGCAGAG 60.411 50.000 24.84 10.64 46.98 3.35
1661 1731 5.290493 TCACCGAGTATATGCAGGAAAAT 57.710 39.130 11.20 0.00 0.00 1.82
1785 1855 3.319122 GGTCAAGAAGTTCAAGGTGCATT 59.681 43.478 5.50 0.00 0.00 3.56
1800 1870 1.740585 TGCATTTAATCCCCAACGTCG 59.259 47.619 0.00 0.00 0.00 5.12
1805 1875 2.660189 TAATCCCCAACGTCGTCTTC 57.340 50.000 0.00 0.00 0.00 2.87
1917 1987 1.284982 CCGTCTTGTTCCTGTCTGCG 61.285 60.000 0.00 0.00 0.00 5.18
1933 2003 6.417191 TGTCTGCGGTTTAAATAAGATGAC 57.583 37.500 0.00 0.00 0.00 3.06
2136 2206 6.403964 CCATATGTGATATGCCCATTTTCTCG 60.404 42.308 1.24 0.00 40.96 4.04
2222 2292 4.734398 TTGGTCAGAGTGCACAAATTTT 57.266 36.364 21.04 0.00 0.00 1.82
2292 2362 6.514048 GCACTTGCATGTAAATCTAGATTCCC 60.514 42.308 18.19 11.89 41.59 3.97
2504 2578 4.882671 TTCTCACAAGAACTTTCACAGC 57.117 40.909 0.00 0.00 36.59 4.40
2574 2648 4.380841 TCAGTACCACCACGTTCATATC 57.619 45.455 0.00 0.00 0.00 1.63
2633 2707 5.551233 TCTGAATTAAGCTAGCACAAGTGT 58.449 37.500 18.83 0.09 0.00 3.55
2642 2716 3.120511 GCTAGCACAAGTGTTAAGCTCAC 60.121 47.826 10.63 0.00 36.80 3.51
2653 2727 4.979197 GTGTTAAGCTCACGATCTGGATAG 59.021 45.833 0.00 0.00 0.00 2.08
2753 2828 1.278238 GAACATCTGTTACGGCCTCG 58.722 55.000 0.00 0.00 38.56 4.63
2781 2856 3.309296 CAACCCTAGGAGCTCAGGATAA 58.691 50.000 19.32 0.00 33.42 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.566545 TGCGGTCCAGCAAAATAATATG 57.433 40.909 6.01 0.00 45.06 1.78
30 31 7.011763 TGAGCAAGATTACACTTCAGATATTGC 59.988 37.037 6.46 6.46 43.35 3.56
55 56 0.537188 ACCCGACTATCTTGTGCCTG 59.463 55.000 0.00 0.00 0.00 4.85
67 68 2.640826 TCACCTTAATTTCCACCCGACT 59.359 45.455 0.00 0.00 0.00 4.18
68 69 3.007635 CTCACCTTAATTTCCACCCGAC 58.992 50.000 0.00 0.00 0.00 4.79
142 173 0.790207 CGGTTCAATGACGGTGTCAG 59.210 55.000 5.80 0.00 46.04 3.51
146 177 0.511221 GTCACGGTTCAATGACGGTG 59.489 55.000 13.17 13.17 46.25 4.94
260 291 4.273005 ACAAGTCGTTGTACTGCAAAAG 57.727 40.909 0.00 0.00 45.48 2.27
298 330 2.173569 AGATCCATCAGGCACTTTACCC 59.826 50.000 0.00 0.00 34.60 3.69
299 331 3.567478 AGATCCATCAGGCACTTTACC 57.433 47.619 0.00 0.00 34.60 2.85
300 332 4.775236 AGAAGATCCATCAGGCACTTTAC 58.225 43.478 0.00 0.00 34.60 2.01
310 342 7.767659 CAGACACTTGAATAAGAAGATCCATCA 59.232 37.037 0.00 0.00 37.36 3.07
314 346 5.877012 TGCAGACACTTGAATAAGAAGATCC 59.123 40.000 0.00 0.00 37.36 3.36
315 347 6.974932 TGCAGACACTTGAATAAGAAGATC 57.025 37.500 0.00 0.00 37.36 2.75
323 355 3.501828 ACGCAATTGCAGACACTTGAATA 59.498 39.130 28.77 0.00 38.39 1.75
336 368 1.190763 CAAGAAACAGCACGCAATTGC 59.809 47.619 20.76 20.76 43.34 3.56
582 614 5.352846 GGTGCCAAACTTCAAAAGCTTTAAA 59.647 36.000 13.10 9.23 0.00 1.52
585 617 3.055167 AGGTGCCAAACTTCAAAAGCTTT 60.055 39.130 5.69 5.69 0.00 3.51
586 618 2.501316 AGGTGCCAAACTTCAAAAGCTT 59.499 40.909 0.00 0.00 0.00 3.74
614 646 8.958119 AAAGCCGACTATTTTATATGTTGAGA 57.042 30.769 0.00 0.00 0.00 3.27
626 658 8.095937 GGCTGTATAATAAAAGCCGACTATTT 57.904 34.615 0.00 0.00 45.30 1.40
638 670 9.237187 TGAAAGAATGTGTGGCTGTATAATAAA 57.763 29.630 0.00 0.00 0.00 1.40
644 676 3.441572 GCTGAAAGAATGTGTGGCTGTAT 59.558 43.478 0.00 0.00 34.07 2.29
645 677 2.813754 GCTGAAAGAATGTGTGGCTGTA 59.186 45.455 0.00 0.00 34.07 2.74
646 678 1.610522 GCTGAAAGAATGTGTGGCTGT 59.389 47.619 0.00 0.00 34.07 4.40
675 726 0.535335 TACCAGGCGACTTAGGCTTG 59.465 55.000 0.00 0.00 45.21 4.01
676 727 1.272807 TTACCAGGCGACTTAGGCTT 58.727 50.000 0.00 0.00 45.21 4.35
703 754 7.016153 TCTTGCCTCCTAAAGAATGTTCTAA 57.984 36.000 0.00 0.00 36.28 2.10
704 755 6.440647 TCTCTTGCCTCCTAAAGAATGTTCTA 59.559 38.462 0.00 0.00 36.28 2.10
732 783 5.670361 TCCTGCAATAAGGGTTAAGGTCTAT 59.330 40.000 0.00 0.00 37.96 1.98
755 808 2.271944 AACCACTGCTAGTTGGGTTC 57.728 50.000 10.73 0.00 31.21 3.62
769 822 3.128764 GGAATCATTCGAGGGAAAACCAC 59.871 47.826 0.00 0.00 43.89 4.16
770 823 3.010138 AGGAATCATTCGAGGGAAAACCA 59.990 43.478 0.00 0.00 43.89 3.67
786 849 1.015868 GCTCTTGAGCTGCAGGAATC 58.984 55.000 17.12 0.00 31.64 2.52
804 867 1.271379 TGAAGTTAGAGTTGGCCTGGC 60.271 52.381 11.05 11.05 0.00 4.85
813 876 2.541466 CCCTGGGAGTGAAGTTAGAGT 58.459 52.381 7.01 0.00 0.00 3.24
845 908 5.163195 ACAAGTTCTCTTTCTGCCCTTTCTA 60.163 40.000 0.00 0.00 0.00 2.10
917 980 7.274603 AGTGTTTATATAGTCCGAGAGAACC 57.725 40.000 0.00 0.00 0.00 3.62
925 988 6.141462 GGAACTCGAGTGTTTATATAGTCCG 58.859 44.000 20.85 0.00 0.00 4.79
972 1035 1.274728 GCAAGCAAGAGGACAGAGAGA 59.725 52.381 0.00 0.00 0.00 3.10
973 1036 1.001746 TGCAAGCAAGAGGACAGAGAG 59.998 52.381 0.00 0.00 0.00 3.20
989 1052 1.830477 GAAGGCCCATTATTGGTGCAA 59.170 47.619 0.00 0.00 41.91 4.08
1005 1068 2.178912 TTAACGCACTGAAGGGAAGG 57.821 50.000 0.00 0.00 0.00 3.46
1093 1156 7.572523 ACCACAAGAACCATGTAATATCATG 57.427 36.000 0.00 0.00 43.14 3.07
1094 1157 7.285401 GGAACCACAAGAACCATGTAATATCAT 59.715 37.037 0.00 0.00 0.00 2.45
1095 1158 6.601613 GGAACCACAAGAACCATGTAATATCA 59.398 38.462 0.00 0.00 0.00 2.15
1096 1159 6.238374 CGGAACCACAAGAACCATGTAATATC 60.238 42.308 0.00 0.00 0.00 1.63
1097 1160 5.588648 CGGAACCACAAGAACCATGTAATAT 59.411 40.000 0.00 0.00 0.00 1.28
1098 1161 4.938832 CGGAACCACAAGAACCATGTAATA 59.061 41.667 0.00 0.00 0.00 0.98
1099 1162 3.756434 CGGAACCACAAGAACCATGTAAT 59.244 43.478 0.00 0.00 0.00 1.89
1117 1180 3.046390 CAACAAATAAAACAGCGCGGAA 58.954 40.909 16.26 0.00 0.00 4.30
1123 1186 4.746611 AGCTCAAGCAACAAATAAAACAGC 59.253 37.500 4.59 0.00 45.16 4.40
1133 1196 1.949525 GGACAGAAGCTCAAGCAACAA 59.050 47.619 4.59 0.00 45.16 2.83
1151 1214 9.675464 ACGAGTTAACAAATTTAGAATATGGGA 57.325 29.630 8.61 0.00 0.00 4.37
1152 1215 9.716507 CACGAGTTAACAAATTTAGAATATGGG 57.283 33.333 8.61 0.00 0.00 4.00
1175 1238 2.508887 GAGAGGAGCAGCAGCACG 60.509 66.667 3.17 0.00 45.49 5.34
1188 1251 1.134461 CAATCCTGGCACTCCTGAGAG 60.134 57.143 0.22 0.00 46.36 3.20
1205 1268 1.153309 GGTAGTTACCGCGCCCAAT 60.153 57.895 0.00 0.00 36.50 3.16
1214 1277 4.641989 TCATAGACTTGTCCGGTAGTTACC 59.358 45.833 0.00 0.00 42.98 2.85
1220 1283 3.562973 GTCGATCATAGACTTGTCCGGTA 59.437 47.826 0.00 0.00 35.84 4.02
1232 1295 9.098355 TCCTTGTTCTTAAAATGTCGATCATAG 57.902 33.333 0.00 0.00 35.48 2.23
1251 1314 0.696501 AAGGTGCGGGTATCCTTGTT 59.303 50.000 0.00 0.00 39.68 2.83
1255 1318 0.988832 TTCAAAGGTGCGGGTATCCT 59.011 50.000 0.00 0.00 0.00 3.24
1259 1322 2.871096 ATTCTTCAAAGGTGCGGGTA 57.129 45.000 0.00 0.00 0.00 3.69
1262 1325 3.641437 TGAAATTCTTCAAAGGTGCGG 57.359 42.857 0.00 0.00 38.65 5.69
1263 1326 5.051891 AGATGAAATTCTTCAAAGGTGCG 57.948 39.130 10.80 0.00 44.64 5.34
1272 1335 7.585573 GTCGACATATGCAAGATGAAATTCTTC 59.414 37.037 11.55 1.11 33.69 2.87
1277 1340 6.765036 AGAAGTCGACATATGCAAGATGAAAT 59.235 34.615 19.50 0.00 0.00 2.17
1298 1361 3.931578 ACAGGTAGCTTACTTGCAGAAG 58.068 45.455 0.00 0.00 39.14 2.85
1314 1377 3.490761 GCAATGTAACTGCACAAACAGGT 60.491 43.478 0.00 0.00 42.21 4.00
1331 1398 1.068055 GGACAAGAAGTGCAGGCAATG 60.068 52.381 0.00 0.00 38.62 2.82
1332 1399 1.251251 GGACAAGAAGTGCAGGCAAT 58.749 50.000 0.00 0.00 38.62 3.56
1350 1417 6.934056 TGATGACATGAATAAAAGGTTTGGG 58.066 36.000 0.00 0.00 0.00 4.12
1355 1423 6.356556 TCGGATGATGACATGAATAAAAGGT 58.643 36.000 0.00 0.00 36.82 3.50
1364 1432 4.392754 CAGTGTTTTCGGATGATGACATGA 59.607 41.667 0.00 0.00 36.82 3.07
1366 1434 4.326826 ACAGTGTTTTCGGATGATGACAT 58.673 39.130 0.00 0.00 39.67 3.06
1377 1445 6.849305 GTGTTGAAATACCTACAGTGTTTTCG 59.151 38.462 0.00 0.00 39.62 3.46
1384 1452 5.925509 ACACAGTGTTGAAATACCTACAGT 58.074 37.500 0.00 0.00 0.00 3.55
1461 1529 9.533253 GAAAAGAAAAGAAAAACTGATGGATGA 57.467 29.630 0.00 0.00 0.00 2.92
1462 1530 8.482429 CGAAAAGAAAAGAAAAACTGATGGATG 58.518 33.333 0.00 0.00 0.00 3.51
1463 1531 8.413229 TCGAAAAGAAAAGAAAAACTGATGGAT 58.587 29.630 0.00 0.00 0.00 3.41
1464 1532 7.767261 TCGAAAAGAAAAGAAAAACTGATGGA 58.233 30.769 0.00 0.00 0.00 3.41
1465 1533 7.985634 TCGAAAAGAAAAGAAAAACTGATGG 57.014 32.000 0.00 0.00 0.00 3.51
1466 1534 8.534778 CCTTCGAAAAGAAAAGAAAAACTGATG 58.465 33.333 0.00 0.00 38.57 3.07
1467 1535 7.706607 CCCTTCGAAAAGAAAAGAAAAACTGAT 59.293 33.333 0.00 0.00 38.57 2.90
1468 1536 7.033185 CCCTTCGAAAAGAAAAGAAAAACTGA 58.967 34.615 0.00 0.00 38.57 3.41
1469 1537 7.033185 TCCCTTCGAAAAGAAAAGAAAAACTG 58.967 34.615 0.00 0.00 38.57 3.16
1470 1538 7.165460 TCCCTTCGAAAAGAAAAGAAAAACT 57.835 32.000 0.00 0.00 38.57 2.66
1471 1539 7.491372 ACATCCCTTCGAAAAGAAAAGAAAAAC 59.509 33.333 0.00 0.00 38.57 2.43
1472 1540 7.491048 CACATCCCTTCGAAAAGAAAAGAAAAA 59.509 33.333 0.00 0.00 38.57 1.94
1473 1541 6.978080 CACATCCCTTCGAAAAGAAAAGAAAA 59.022 34.615 0.00 0.00 38.57 2.29
1474 1542 6.320164 TCACATCCCTTCGAAAAGAAAAGAAA 59.680 34.615 0.00 0.00 38.57 2.52
1475 1543 5.825679 TCACATCCCTTCGAAAAGAAAAGAA 59.174 36.000 0.00 0.00 38.57 2.52
1476 1544 5.373222 TCACATCCCTTCGAAAAGAAAAGA 58.627 37.500 0.00 0.00 38.57 2.52
1477 1545 5.689383 TCACATCCCTTCGAAAAGAAAAG 57.311 39.130 0.00 0.00 38.57 2.27
1478 1546 6.490040 AGAATCACATCCCTTCGAAAAGAAAA 59.510 34.615 0.00 0.00 38.57 2.29
1479 1547 6.003950 AGAATCACATCCCTTCGAAAAGAAA 58.996 36.000 0.00 0.00 38.57 2.52
1480 1548 5.412594 CAGAATCACATCCCTTCGAAAAGAA 59.587 40.000 0.00 0.00 34.14 2.52
1481 1549 4.937620 CAGAATCACATCCCTTCGAAAAGA 59.062 41.667 0.00 0.00 34.14 2.52
1482 1550 4.697352 ACAGAATCACATCCCTTCGAAAAG 59.303 41.667 0.00 0.00 0.00 2.27
1483 1551 4.455533 CACAGAATCACATCCCTTCGAAAA 59.544 41.667 0.00 0.00 0.00 2.29
1484 1552 4.002982 CACAGAATCACATCCCTTCGAAA 58.997 43.478 0.00 0.00 0.00 3.46
1485 1553 3.007940 ACACAGAATCACATCCCTTCGAA 59.992 43.478 0.00 0.00 0.00 3.71
1486 1554 2.567169 ACACAGAATCACATCCCTTCGA 59.433 45.455 0.00 0.00 0.00 3.71
1487 1555 2.977914 ACACAGAATCACATCCCTTCG 58.022 47.619 0.00 0.00 0.00 3.79
1488 1556 8.682936 ATATTTACACAGAATCACATCCCTTC 57.317 34.615 0.00 0.00 0.00 3.46
1489 1557 9.479549 AAATATTTACACAGAATCACATCCCTT 57.520 29.630 0.00 0.00 0.00 3.95
1517 1585 4.833478 ACAGTCAATTGCTAGATGTCCT 57.167 40.909 0.00 0.00 0.00 3.85
1526 1594 5.294306 CGGTGATATGTAACAGTCAATTGCT 59.706 40.000 0.00 0.00 0.00 3.91
1546 1614 3.691498 GGTTCAGTTGAGTTTTTCGGTG 58.309 45.455 0.00 0.00 0.00 4.94
1547 1615 2.353579 CGGTTCAGTTGAGTTTTTCGGT 59.646 45.455 0.00 0.00 0.00 4.69
1548 1616 2.353579 ACGGTTCAGTTGAGTTTTTCGG 59.646 45.455 0.00 0.00 0.00 4.30
1550 1618 5.473796 TGTACGGTTCAGTTGAGTTTTTC 57.526 39.130 0.00 0.00 0.00 2.29
1642 1712 4.452455 GGACATTTTCCTGCATATACTCGG 59.548 45.833 0.00 0.00 41.95 4.63
1785 1855 2.671914 CGAAGACGACGTTGGGGATTAA 60.672 50.000 7.90 0.00 42.66 1.40
1812 1882 3.297620 GGCAACCAGGGTGCACAG 61.298 66.667 31.06 7.70 0.00 3.66
1820 1890 1.000739 ACCCATGATGGCAACCAGG 59.999 57.895 5.79 0.00 36.75 4.45
1933 2003 6.075280 CGTTCCAGGTTTCTTGTTTATTACG 58.925 40.000 0.00 0.00 0.00 3.18
1990 2060 2.173519 CCCATGACTTGCATCTTGGTT 58.826 47.619 16.77 0.00 40.63 3.67
1993 2063 5.389859 TTTAACCCATGACTTGCATCTTG 57.610 39.130 0.00 0.00 34.15 3.02
2043 2113 0.887933 TTGCTTTCTTTCCATCGGCC 59.112 50.000 0.00 0.00 0.00 6.13
2136 2206 4.743493 TCAAAGAACACCAAAGAAAGTGC 58.257 39.130 0.00 0.00 37.51 4.40
2282 2352 0.747255 GCAGCAGTCGGGAATCTAGA 59.253 55.000 0.00 0.00 0.00 2.43
2292 2362 1.461127 GTAGGTTTCTTGCAGCAGTCG 59.539 52.381 0.00 0.00 0.00 4.18
2341 2411 5.503662 TTTCTTGTAGCGGTCATACGATA 57.496 39.130 0.00 0.00 35.47 2.92
2342 2412 4.360563 CTTTCTTGTAGCGGTCATACGAT 58.639 43.478 0.00 0.00 35.47 3.73
2343 2413 3.766151 CTTTCTTGTAGCGGTCATACGA 58.234 45.455 0.00 0.00 35.47 3.43
2344 2414 2.281762 GCTTTCTTGTAGCGGTCATACG 59.718 50.000 0.00 0.00 0.00 3.06
2504 2578 8.345565 GCCCTTGTGTAAGATAAAAGTATCATG 58.654 37.037 0.00 0.00 38.95 3.07
2574 2648 2.227388 GGTGGTTTGTGCTCTCATTGAG 59.773 50.000 7.38 7.38 45.33 3.02
2633 2707 3.636764 TGCTATCCAGATCGTGAGCTTAA 59.363 43.478 0.00 0.00 0.00 1.85
2642 2716 4.508124 GGTAAAAGTGTGCTATCCAGATCG 59.492 45.833 0.00 0.00 0.00 3.69
2653 2727 2.224314 GCTCTGTGAGGTAAAAGTGTGC 59.776 50.000 0.00 0.00 0.00 4.57
2716 2791 3.057245 TGTTCCTCTCTGTGTTCTCATCG 60.057 47.826 0.00 0.00 0.00 3.84
2781 2856 5.381757 TGCAAGGATAACTAACAACCAACT 58.618 37.500 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.