Multiple sequence alignment - TraesCS6D01G065300

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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 TraesCS6D01G065300 chr6D 100.000 2588 0 0 1 2588 31826686 31829273 0.000000e+00 4780.0
1 TraesCS6D01G065300 chr6B 87.303 1205 94 22 323 1496 67503883 67505059 0.000000e+00 1323.0
2 TraesCS6D01G065300 chr6B 86.855 1202 104 23 323 1496 68640337 68639162 0.000000e+00 1295.0
3 TraesCS6D01G065300 chr6B 81.575 749 66 31 1891 2588 68637982 68637255 1.050000e-153 553.0
4 TraesCS6D01G065300 chr6B 83.742 326 38 9 1495 1809 67505089 67505410 7.000000e-76 294.0
5 TraesCS6D01G065300 chr6B 89.610 231 17 5 100 324 68640611 68640382 1.170000e-73 287.0
6 TraesCS6D01G065300 chr6A 84.118 1020 86 32 1 969 36398102 36399096 0.000000e+00 917.0
7 TraesCS6D01G065300 chr6A 90.562 498 39 4 999 1496 36399098 36399587 0.000000e+00 652.0
8 TraesCS6D01G065300 chr6A 88.618 123 13 1 2466 2588 36403032 36403153 5.770000e-32 148.0
9 TraesCS6D01G065300 chr6A 86.667 60 8 0 10 69 595027915 595027856 1.660000e-07 67.6
10 TraesCS6D01G065300 chr2A 92.453 53 4 0 8 60 500525359 500525411 2.760000e-10 76.8
11 TraesCS6D01G065300 chr2A 92.453 53 4 0 8 60 500525816 500525868 2.760000e-10 76.8
12 TraesCS6D01G065300 chr2A 94.286 35 2 0 1326 1360 733583995 733584029 1.000000e-03 54.7
13 TraesCS6D01G065300 chr2D 92.157 51 4 0 10 60 369468554 369468604 3.570000e-09 73.1
14 TraesCS6D01G065300 chr2B 90.385 52 5 0 8 59 439218399 439218450 4.620000e-08 69.4
15 TraesCS6D01G065300 chr7B 90.196 51 5 0 7 57 192795170 192795220 1.660000e-07 67.6
16 TraesCS6D01G065300 chr7D 100.000 31 0 0 31 61 78182492 78182462 1.000000e-04 58.4


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 TraesCS6D01G065300 chr6D 31826686 31829273 2587 False 4780.000000 4780 100.000000 1 2588 1 chr6D.!!$F1 2587
1 TraesCS6D01G065300 chr6B 67503883 67505410 1527 False 808.500000 1323 85.522500 323 1809 2 chr6B.!!$F1 1486
2 TraesCS6D01G065300 chr6B 68637255 68640611 3356 True 711.666667 1295 86.013333 100 2588 3 chr6B.!!$R1 2488
3 TraesCS6D01G065300 chr6A 36398102 36403153 5051 False 572.333333 917 87.766000 1 2588 3 chr6A.!!$F1 2587

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
495 560 0.8501 TGGTTTGATCCCTGGTGTGT 59.15 50.0 0.0 0.0 0.0 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1644 1796 0.739112 GAGACGAGAAGGCAGCCAAG 60.739 60.0 15.8 2.04 0.0 3.61 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 38 2.447572 TGGGCTGACTCCACCACA 60.448 61.111 0.00 0.00 0.00 4.17
43 44 1.271597 GCTGACTCCACCACAAGGAAT 60.272 52.381 0.00 0.00 38.69 3.01
47 48 3.907474 TGACTCCACCACAAGGAATCTAA 59.093 43.478 0.00 0.00 32.80 2.10
61 62 5.211973 AGGAATCTAACCATCTGAGCTACA 58.788 41.667 0.00 0.00 0.00 2.74
62 63 5.069781 AGGAATCTAACCATCTGAGCTACAC 59.930 44.000 0.00 0.00 0.00 2.90
66 67 1.198713 ACCATCTGAGCTACACCCAG 58.801 55.000 0.00 0.00 0.00 4.45
70 71 2.310779 TCTGAGCTACACCCAGTTCT 57.689 50.000 0.00 0.00 0.00 3.01
71 72 2.171840 TCTGAGCTACACCCAGTTCTC 58.828 52.381 0.00 0.00 32.54 2.87
72 73 2.175202 CTGAGCTACACCCAGTTCTCT 58.825 52.381 0.00 0.00 32.89 3.10
74 75 2.300152 TGAGCTACACCCAGTTCTCTTG 59.700 50.000 0.00 0.00 32.89 3.02
76 77 3.507411 AGCTACACCCAGTTCTCTTGTA 58.493 45.455 0.00 0.00 0.00 2.41
77 78 4.097418 AGCTACACCCAGTTCTCTTGTAT 58.903 43.478 0.00 0.00 0.00 2.29
78 79 4.532521 AGCTACACCCAGTTCTCTTGTATT 59.467 41.667 0.00 0.00 0.00 1.89
79 80 4.631813 GCTACACCCAGTTCTCTTGTATTG 59.368 45.833 0.00 0.00 0.00 1.90
87 88 5.513094 CCAGTTCTCTTGTATTGAAGGGTCA 60.513 44.000 0.00 0.00 0.00 4.02
94 95 7.016153 TCTTGTATTGAAGGGTCATTGTAGT 57.984 36.000 0.00 0.00 32.48 2.73
103 104 7.792032 TGAAGGGTCATTGTAGTCCTTATTAG 58.208 38.462 0.00 0.00 37.88 1.73
149 150 5.745312 AGACATCAGTGATGAAGTACCAA 57.255 39.130 34.38 0.00 42.09 3.67
168 171 3.256383 CCAAAACATGAACCTGATGCAGA 59.744 43.478 0.00 0.00 32.44 4.26
189 192 4.333649 AGAGATACATTGTTGTGCAATCCG 59.666 41.667 0.00 0.00 45.33 4.18
204 207 2.554032 CAATCCGCAAAACTCTTGTCCT 59.446 45.455 0.00 0.00 0.00 3.85
224 227 1.056700 AGCCCTGTCACACTGTCCTT 61.057 55.000 0.00 0.00 0.00 3.36
314 322 5.975693 AAATCACCCGAGCAATTTTTAGA 57.024 34.783 0.00 0.00 0.00 2.10
326 380 7.274250 CGAGCAATTTTTAGAAAATCCCTTGAG 59.726 37.037 0.00 0.00 0.00 3.02
363 417 6.478129 TGGACTTATCGGGTGATTAACTTTT 58.522 36.000 0.00 0.00 35.99 2.27
364 418 6.596497 TGGACTTATCGGGTGATTAACTTTTC 59.404 38.462 0.00 0.00 35.99 2.29
409 469 7.014615 TGCAGACATAGACACTCACATATATGT 59.985 37.037 12.75 12.75 42.84 2.29
442 506 8.818860 ACTTATAACCCTATAAAGACACACACA 58.181 33.333 0.00 0.00 31.11 3.72
443 507 9.095065 CTTATAACCCTATAAAGACACACACAC 57.905 37.037 0.00 0.00 31.11 3.82
495 560 0.850100 TGGTTTGATCCCTGGTGTGT 59.150 50.000 0.00 0.00 0.00 3.72
499 564 3.244770 GGTTTGATCCCTGGTGTGTTAGA 60.245 47.826 0.00 0.00 0.00 2.10
500 565 4.394729 GTTTGATCCCTGGTGTGTTAGAA 58.605 43.478 0.00 0.00 0.00 2.10
502 567 2.571653 TGATCCCTGGTGTGTTAGAAGG 59.428 50.000 0.00 0.00 0.00 3.46
508 573 3.181454 CCTGGTGTGTTAGAAGGACAACT 60.181 47.826 0.00 0.00 0.00 3.16
528 593 6.215636 ACAACTATCCTCTTAACCATCCAACT 59.784 38.462 0.00 0.00 0.00 3.16
545 610 5.551233 TCCAACTACAAGATGGTTCTCAAG 58.449 41.667 3.51 0.00 39.03 3.02
547 612 5.409826 CCAACTACAAGATGGTTCTCAAGAC 59.590 44.000 0.00 0.00 33.90 3.01
551 616 3.392616 ACAAGATGGTTCTCAAGACTGGT 59.607 43.478 0.00 0.00 0.00 4.00
557 622 8.783660 AGATGGTTCTCAAGACTGGTATAATA 57.216 34.615 0.00 0.00 0.00 0.98
562 627 8.429641 GGTTCTCAAGACTGGTATAATAATGGA 58.570 37.037 0.00 0.00 0.00 3.41
573 638 9.231297 CTGGTATAATAATGGATGGGTTTACAG 57.769 37.037 0.00 0.00 0.00 2.74
575 640 9.802039 GGTATAATAATGGATGGGTTTACAGAA 57.198 33.333 0.00 0.00 0.00 3.02
671 759 8.666129 AACCGATCCTATATCCATCTTAAAGA 57.334 34.615 0.00 0.00 0.00 2.52
773 879 5.010012 GCTACCAAAGATTTACCATCATGGG 59.990 44.000 9.04 0.00 43.37 4.00
790 896 7.671398 CCATCATGGGTAATTTCCTAATTAGCT 59.329 37.037 6.99 0.00 46.49 3.32
869 976 7.255625 GCCTGTCTTAAAAATCATCCTTATCCC 60.256 40.741 0.00 0.00 0.00 3.85
870 977 7.231519 CCTGTCTTAAAAATCATCCTTATCCCC 59.768 40.741 0.00 0.00 0.00 4.81
875 982 1.958288 ATCATCCTTATCCCCGAGGG 58.042 55.000 0.00 0.00 46.11 4.30
948 1055 8.359875 TGTTAATGCTCCAATTGAATTCCTTA 57.640 30.769 7.12 0.00 0.00 2.69
949 1056 8.811017 TGTTAATGCTCCAATTGAATTCCTTAA 58.189 29.630 7.12 1.71 0.00 1.85
969 1076 7.707893 TCCTTAAATCTACGTTATTCGGGAAAG 59.292 37.037 0.00 0.00 44.69 2.62
970 1077 7.707893 CCTTAAATCTACGTTATTCGGGAAAGA 59.292 37.037 0.00 0.00 44.69 2.52
971 1078 8.638685 TTAAATCTACGTTATTCGGGAAAGAG 57.361 34.615 0.00 0.00 44.69 2.85
972 1079 4.644103 TCTACGTTATTCGGGAAAGAGG 57.356 45.455 0.00 0.00 44.69 3.69
973 1080 2.019948 ACGTTATTCGGGAAAGAGGC 57.980 50.000 0.00 0.00 44.69 4.70
974 1081 1.296727 CGTTATTCGGGAAAGAGGCC 58.703 55.000 0.00 0.00 35.71 5.19
975 1082 1.134491 CGTTATTCGGGAAAGAGGCCT 60.134 52.381 3.86 3.86 35.71 5.19
976 1083 2.562635 GTTATTCGGGAAAGAGGCCTC 58.437 52.381 26.22 26.22 0.00 4.70
977 1084 2.170817 GTTATTCGGGAAAGAGGCCTCT 59.829 50.000 30.40 30.40 42.75 3.69
978 1085 6.717986 CGTTATTCGGGAAAGAGGCCTCTT 62.718 50.000 37.44 37.44 42.54 2.85
984 1091 4.561155 AAGAGGCCTCTTCGGGAA 57.439 55.556 37.44 0.00 46.13 3.97
985 1092 2.773458 AAGAGGCCTCTTCGGGAAA 58.227 52.632 37.44 0.00 46.13 3.13
1014 1122 4.287067 TGCTCAAGGCTATAAATAGGAGGG 59.713 45.833 0.00 0.00 42.39 4.30
1016 1124 5.013183 GCTCAAGGCTATAAATAGGAGGGAA 59.987 44.000 0.00 0.00 38.06 3.97
1034 1145 3.279434 GGAACAAGACATCCATACCACC 58.721 50.000 0.00 0.00 35.71 4.61
1035 1146 3.308117 GGAACAAGACATCCATACCACCA 60.308 47.826 0.00 0.00 35.71 4.17
1036 1147 3.350219 ACAAGACATCCATACCACCAC 57.650 47.619 0.00 0.00 0.00 4.16
1037 1148 2.642311 ACAAGACATCCATACCACCACA 59.358 45.455 0.00 0.00 0.00 4.17
1038 1149 3.009723 CAAGACATCCATACCACCACAC 58.990 50.000 0.00 0.00 0.00 3.82
1039 1150 1.559682 AGACATCCATACCACCACACC 59.440 52.381 0.00 0.00 0.00 4.16
1080 1191 2.521451 TTGGCCCCGTAGCACAAGA 61.521 57.895 0.00 0.00 0.00 3.02
1087 1198 1.618861 CCGTAGCACAAGAGAGTTCG 58.381 55.000 0.00 0.00 0.00 3.95
1136 1247 1.108776 CCATGGCTTCCAAGATGGTG 58.891 55.000 0.00 0.00 39.03 4.17
1212 1323 2.031012 CGACTCCCTGCTGCAACA 59.969 61.111 3.02 0.00 0.00 3.33
1230 1341 3.153369 ACATCAAATGCTGTGGGTACA 57.847 42.857 0.00 0.00 35.08 2.90
1241 1352 2.339556 TGGGTACAATTGCTGCGGC 61.340 57.895 11.65 11.65 39.26 6.53
1302 1413 4.101448 CCCCGGAAGCAGGACCAG 62.101 72.222 0.73 0.00 0.00 4.00
1303 1414 4.785453 CCCGGAAGCAGGACCAGC 62.785 72.222 0.73 0.00 0.00 4.85
1306 1417 4.785453 GGAAGCAGGACCAGCGGG 62.785 72.222 0.00 0.00 41.29 6.13
1496 1607 5.766150 TTTGTTCTGTTCCATCGAAACAT 57.234 34.783 1.83 0.00 36.14 2.71
1497 1608 5.766150 TTGTTCTGTTCCATCGAAACATT 57.234 34.783 1.83 0.00 36.14 2.71
1498 1609 5.766150 TGTTCTGTTCCATCGAAACATTT 57.234 34.783 1.83 0.00 36.14 2.32
1548 1692 6.385843 CAATGATAAACCATGTTCGGAACAA 58.614 36.000 25.64 10.07 45.86 2.83
1562 1706 6.418226 TGTTCGGAACAAAAATAATTCAACCG 59.582 34.615 20.52 0.00 38.72 4.44
1564 1708 5.915758 TCGGAACAAAAATAATTCAACCGTG 59.084 36.000 0.00 0.00 38.17 4.94
1603 1755 3.947834 CCTCCAATTAAATCTGCCGAACT 59.052 43.478 0.00 0.00 0.00 3.01
1612 1764 2.839486 TCTGCCGAACTTGAATCAGT 57.161 45.000 0.00 0.00 0.00 3.41
1621 1773 5.812642 CCGAACTTGAATCAGTTATAGCTGT 59.187 40.000 15.27 0.00 37.11 4.40
1626 1778 8.934507 ACTTGAATCAGTTATAGCTGTTCTAC 57.065 34.615 15.27 5.99 37.70 2.59
1630 1782 9.628500 TGAATCAGTTATAGCTGTTCTACTCTA 57.372 33.333 15.27 0.00 37.70 2.43
1635 1787 8.440059 CAGTTATAGCTGTTCTACTCTAGATCG 58.560 40.741 8.34 0.00 34.22 3.69
1642 1794 4.079901 TGTTCTACTCTAGATCGGTCCCTT 60.080 45.833 0.00 0.00 34.22 3.95
1643 1795 4.088056 TCTACTCTAGATCGGTCCCTTG 57.912 50.000 0.00 0.00 0.00 3.61
1644 1796 1.404843 ACTCTAGATCGGTCCCTTGC 58.595 55.000 0.00 0.00 0.00 4.01
1645 1797 1.063567 ACTCTAGATCGGTCCCTTGCT 60.064 52.381 0.00 0.00 0.00 3.91
1674 1827 3.257393 CTTCTCGTCTCCCAGAACAATG 58.743 50.000 0.00 0.00 0.00 2.82
1693 1847 5.241728 ACAATGTTGTTTCCTAGAAAGGAGC 59.758 40.000 0.00 0.00 42.15 4.70
1711 3619 4.141181 AGGAGCCATGCATATGTTTCCTTA 60.141 41.667 0.00 0.00 39.93 2.69
1712 3620 4.768968 GGAGCCATGCATATGTTTCCTTAT 59.231 41.667 0.00 0.00 34.53 1.73
1730 3639 5.723887 TCCTTATGTGGCCAAAATTTATGGT 59.276 36.000 7.24 0.00 40.23 3.55
1744 3653 6.753107 AATTTATGGTCGGTTTAGGAACTG 57.247 37.500 0.00 0.00 41.52 3.16
1757 3666 3.629142 AGGAACTGCGCCTACTAAAAT 57.371 42.857 4.18 0.00 37.18 1.82
1768 3677 5.177142 GCGCCTACTAAAATTAGCTTAGGAC 59.823 44.000 15.74 9.25 34.10 3.85
1845 3757 5.468072 GTCGAAAGTATAGATCTGGTCCGTA 59.532 44.000 5.18 0.00 0.00 4.02
2220 4311 9.213819 GCAAAGAAAAATGAAGAAACAAATCAC 57.786 29.630 0.00 0.00 0.00 3.06
2252 4344 8.925161 TTGAGAAAGAACAAACAAAATGGTAG 57.075 30.769 0.00 0.00 0.00 3.18
2255 4347 8.062065 AGAAAGAACAAACAAAATGGTAGACA 57.938 30.769 0.00 0.00 0.00 3.41
2275 4367 7.637709 AGACAACAAAGAAAAACAGAACAAC 57.362 32.000 0.00 0.00 0.00 3.32
2388 4482 4.392754 ACAGCCAAAAACAAAAGCAAAGAG 59.607 37.500 0.00 0.00 0.00 2.85
2394 4488 7.358830 CCAAAAACAAAAGCAAAGAGAAACAA 58.641 30.769 0.00 0.00 0.00 2.83
2424 5198 6.735678 AAAAACAGCGAAACCAAAGAAAAT 57.264 29.167 0.00 0.00 0.00 1.82
2426 5200 3.628017 ACAGCGAAACCAAAGAAAATCG 58.372 40.909 0.00 0.00 0.00 3.34
2427 5201 2.979813 CAGCGAAACCAAAGAAAATCGG 59.020 45.455 0.00 0.00 0.00 4.18
2463 5237 8.648557 ATGAAACAAAAGTAGAAGAAAAAGGC 57.351 30.769 0.00 0.00 0.00 4.35
2464 5238 6.750039 TGAAACAAAAGTAGAAGAAAAAGGCG 59.250 34.615 0.00 0.00 0.00 5.52
2465 5239 6.445357 AACAAAAGTAGAAGAAAAAGGCGA 57.555 33.333 0.00 0.00 0.00 5.54
2466 5240 6.445357 ACAAAAGTAGAAGAAAAAGGCGAA 57.555 33.333 0.00 0.00 0.00 4.70
2467 5241 6.859017 ACAAAAGTAGAAGAAAAAGGCGAAA 58.141 32.000 0.00 0.00 0.00 3.46
2468 5242 7.317390 ACAAAAGTAGAAGAAAAAGGCGAAAA 58.683 30.769 0.00 0.00 0.00 2.29
2469 5243 7.979537 ACAAAAGTAGAAGAAAAAGGCGAAAAT 59.020 29.630 0.00 0.00 0.00 1.82
2470 5244 9.458374 CAAAAGTAGAAGAAAAAGGCGAAAATA 57.542 29.630 0.00 0.00 0.00 1.40
2472 5246 9.841880 AAAGTAGAAGAAAAAGGCGAAAATATC 57.158 29.630 0.00 0.00 0.00 1.63
2521 5295 1.160137 GCATGACCGAGAAAACAGCT 58.840 50.000 0.00 0.00 0.00 4.24
2525 5299 1.610038 TGACCGAGAAAACAGCTACGA 59.390 47.619 0.00 0.00 0.00 3.43
2531 5305 3.251571 GAGAAAACAGCTACGACCGAAT 58.748 45.455 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 2.338809 AGATTCCTTGTGGTGGAGTCA 58.661 47.619 7.76 0.00 41.13 3.41
29 30 2.983192 TGGTTAGATTCCTTGTGGTGGA 59.017 45.455 0.00 0.00 34.23 4.02
37 38 5.663106 TGTAGCTCAGATGGTTAGATTCCTT 59.337 40.000 0.00 0.00 0.00 3.36
43 44 3.031736 GGGTGTAGCTCAGATGGTTAGA 58.968 50.000 0.00 0.00 0.00 2.10
47 48 3.399234 TGGGTGTAGCTCAGATGGT 57.601 52.632 0.00 0.00 0.00 3.55
61 62 4.263506 CCCTTCAATACAAGAGAACTGGGT 60.264 45.833 0.00 0.00 0.00 4.51
62 63 4.263506 ACCCTTCAATACAAGAGAACTGGG 60.264 45.833 0.00 0.00 34.57 4.45
66 67 6.431234 ACAATGACCCTTCAATACAAGAGAAC 59.569 38.462 0.00 0.00 34.61 3.01
70 71 7.016153 ACTACAATGACCCTTCAATACAAGA 57.984 36.000 0.00 0.00 34.61 3.02
71 72 6.316390 GGACTACAATGACCCTTCAATACAAG 59.684 42.308 0.00 0.00 34.61 3.16
72 73 6.012858 AGGACTACAATGACCCTTCAATACAA 60.013 38.462 0.00 0.00 34.61 2.41
74 75 5.990668 AGGACTACAATGACCCTTCAATAC 58.009 41.667 0.00 0.00 34.61 1.89
76 77 5.520748 AAGGACTACAATGACCCTTCAAT 57.479 39.130 0.00 0.00 34.61 2.57
77 78 4.993705 AAGGACTACAATGACCCTTCAA 57.006 40.909 0.00 0.00 34.61 2.69
78 79 6.636454 AATAAGGACTACAATGACCCTTCA 57.364 37.500 0.00 0.00 38.16 3.02
79 80 7.793036 ACTAATAAGGACTACAATGACCCTTC 58.207 38.462 0.00 0.00 38.16 3.46
119 120 8.627208 ACTTCATCACTGATGTCTTATTTGTT 57.373 30.769 16.96 0.00 40.55 2.83
135 136 6.016276 AGGTTCATGTTTTGGTACTTCATCAC 60.016 38.462 0.00 0.00 0.00 3.06
149 150 4.025040 TCTCTGCATCAGGTTCATGTTT 57.975 40.909 0.00 0.00 31.51 2.83
189 192 1.813178 GGGCTAGGACAAGAGTTTTGC 59.187 52.381 0.00 0.00 0.00 3.68
191 194 2.711547 ACAGGGCTAGGACAAGAGTTTT 59.288 45.455 0.00 0.00 0.00 2.43
204 207 0.178932 AGGACAGTGTGACAGGGCTA 60.179 55.000 0.00 0.00 0.00 3.93
224 227 5.047021 TCTGATTTGTGTTGGTTTGTGGAAA 60.047 36.000 0.00 0.00 0.00 3.13
314 322 8.785946 CAAATTTAAATGTGCTCAAGGGATTTT 58.214 29.630 5.42 0.00 0.00 1.82
326 380 6.475402 CCCGATAAGTCCAAATTTAAATGTGC 59.525 38.462 12.25 1.10 0.00 4.57
363 417 4.202000 TGCATTGCGTTTCTCAAGAAAAGA 60.202 37.500 18.53 3.36 44.58 2.52
364 418 4.043750 TGCATTGCGTTTCTCAAGAAAAG 58.956 39.130 12.30 12.30 44.58 2.27
379 439 3.063180 GTGAGTGTCTATGTCTGCATTGC 59.937 47.826 0.46 0.46 36.58 3.56
442 506 3.872603 TGCCGAAGTGCCAGTGGT 61.873 61.111 11.74 0.00 0.00 4.16
443 507 3.357079 GTGCCGAAGTGCCAGTGG 61.357 66.667 4.20 4.20 0.00 4.00
487 552 4.073293 AGTTGTCCTTCTAACACACCAG 57.927 45.455 0.00 0.00 0.00 4.00
502 567 6.235231 TGGATGGTTAAGAGGATAGTTGTC 57.765 41.667 0.00 0.00 0.00 3.18
508 573 7.622081 TCTTGTAGTTGGATGGTTAAGAGGATA 59.378 37.037 0.00 0.00 0.00 2.59
513 578 6.414732 CCATCTTGTAGTTGGATGGTTAAGA 58.585 40.000 11.66 0.00 46.61 2.10
528 593 4.593206 ACCAGTCTTGAGAACCATCTTGTA 59.407 41.667 0.00 0.00 35.54 2.41
545 610 9.227777 GTAAACCCATCCATTATTATACCAGTC 57.772 37.037 0.00 0.00 0.00 3.51
547 612 9.231297 CTGTAAACCCATCCATTATTATACCAG 57.769 37.037 0.00 0.00 0.00 4.00
562 627 7.875554 ACGCATTTTTATTTTCTGTAAACCCAT 59.124 29.630 0.00 0.00 0.00 4.00
573 638 4.201618 GGCAGAGCACGCATTTTTATTTTC 60.202 41.667 0.00 0.00 0.00 2.29
575 640 3.056607 AGGCAGAGCACGCATTTTTATTT 60.057 39.130 0.00 0.00 0.00 1.40
576 641 2.493278 AGGCAGAGCACGCATTTTTATT 59.507 40.909 0.00 0.00 0.00 1.40
577 642 2.094675 AGGCAGAGCACGCATTTTTAT 58.905 42.857 0.00 0.00 0.00 1.40
578 643 1.533625 AGGCAGAGCACGCATTTTTA 58.466 45.000 0.00 0.00 0.00 1.52
747 853 6.266103 CCATGATGGTAAATCTTTGGTAGCAT 59.734 38.462 2.54 0.00 38.35 3.79
790 896 6.584471 TCCAAAGGTGGCTAATATAAGGAA 57.416 37.500 0.00 0.00 45.54 3.36
836 942 6.331369 TGATTTTTAAGACAGGCTCCAAAG 57.669 37.500 0.00 0.00 0.00 2.77
869 976 0.760567 TCATCCAGATGACCCCTCGG 60.761 60.000 6.24 0.00 42.42 4.63
870 977 2.826337 TCATCCAGATGACCCCTCG 58.174 57.895 6.24 0.00 42.42 4.63
882 989 5.056480 GTGGTCAAATCGTGATATCATCCA 58.944 41.667 9.02 5.48 38.90 3.41
894 1001 5.851177 GCCATATAAAATCGTGGTCAAATCG 59.149 40.000 0.00 0.00 34.23 3.34
948 1055 6.047231 CCTCTTTCCCGAATAACGTAGATTT 58.953 40.000 0.00 0.00 40.78 2.17
949 1056 5.598769 CCTCTTTCCCGAATAACGTAGATT 58.401 41.667 0.00 0.00 40.78 2.40
969 1076 1.078356 GGTTTCCCGAAGAGGCCTC 60.078 63.158 26.22 26.22 39.21 4.70
970 1077 1.539124 AGGTTTCCCGAAGAGGCCT 60.539 57.895 3.86 3.86 39.21 5.19
971 1078 1.377333 CAGGTTTCCCGAAGAGGCC 60.377 63.158 0.00 0.00 39.21 5.19
972 1079 2.041115 GCAGGTTTCCCGAAGAGGC 61.041 63.158 0.00 0.00 39.21 4.70
973 1080 0.674895 CAGCAGGTTTCCCGAAGAGG 60.675 60.000 0.00 0.00 40.63 3.69
974 1081 1.301677 GCAGCAGGTTTCCCGAAGAG 61.302 60.000 0.00 0.00 35.12 2.85
975 1082 1.302511 GCAGCAGGTTTCCCGAAGA 60.303 57.895 0.00 0.00 35.12 2.87
976 1083 1.301677 GAGCAGCAGGTTTCCCGAAG 61.302 60.000 0.00 0.00 35.12 3.79
977 1084 1.302511 GAGCAGCAGGTTTCCCGAA 60.303 57.895 0.00 0.00 35.12 4.30
978 1085 2.050836 TTGAGCAGCAGGTTTCCCGA 62.051 55.000 0.00 0.00 35.12 5.14
979 1086 1.580845 CTTGAGCAGCAGGTTTCCCG 61.581 60.000 0.00 0.00 35.12 5.14
980 1087 1.246737 CCTTGAGCAGCAGGTTTCCC 61.247 60.000 0.00 0.00 0.00 3.97
981 1088 1.871126 GCCTTGAGCAGCAGGTTTCC 61.871 60.000 0.00 0.00 42.97 3.13
982 1089 1.583477 GCCTTGAGCAGCAGGTTTC 59.417 57.895 0.00 0.00 42.97 2.78
983 1090 3.769201 GCCTTGAGCAGCAGGTTT 58.231 55.556 0.00 0.00 42.97 3.27
997 1104 6.043358 GTCTTGTTCCCTCCTATTTATAGCCT 59.957 42.308 0.00 0.00 0.00 4.58
1014 1122 3.689649 GTGGTGGTATGGATGTCTTGTTC 59.310 47.826 0.00 0.00 0.00 3.18
1016 1124 2.642311 TGTGGTGGTATGGATGTCTTGT 59.358 45.455 0.00 0.00 0.00 3.16
1034 1145 1.517257 GATGCGAGAGACGGGTGTG 60.517 63.158 0.00 0.00 42.83 3.82
1035 1146 1.977009 TGATGCGAGAGACGGGTGT 60.977 57.895 0.00 0.00 42.83 4.16
1036 1147 1.517257 GTGATGCGAGAGACGGGTG 60.517 63.158 0.00 0.00 42.83 4.61
1037 1148 1.532604 TTGTGATGCGAGAGACGGGT 61.533 55.000 0.00 0.00 42.83 5.28
1038 1149 0.389817 TTTGTGATGCGAGAGACGGG 60.390 55.000 0.00 0.00 42.83 5.28
1039 1150 0.994995 CTTTGTGATGCGAGAGACGG 59.005 55.000 0.00 0.00 42.83 4.79
1080 1191 1.940613 GCTGGTTTTGTGACGAACTCT 59.059 47.619 0.00 0.00 0.00 3.24
1087 1198 2.195922 CTTTGCAGCTGGTTTTGTGAC 58.804 47.619 17.12 0.00 0.00 3.67
1118 1229 1.108776 CCACCATCTTGGAAGCCATG 58.891 55.000 0.00 0.00 40.96 3.66
1175 1286 4.988598 AACACCTGGGCGTCGCTG 62.989 66.667 18.11 9.52 0.00 5.18
1212 1323 4.621274 GCAATTGTACCCACAGCATTTGAT 60.621 41.667 7.40 0.00 35.67 2.57
1498 1609 9.261180 GCATACACTTTATAGCTGTAGAATTGA 57.739 33.333 0.00 0.00 0.00 2.57
1521 1665 4.644234 TCCGAACATGGTTTATCATTGCAT 59.356 37.500 0.00 0.00 0.00 3.96
1548 1692 6.325919 TCTGAAGCACGGTTGAATTATTTT 57.674 33.333 0.00 0.00 0.00 1.82
1562 1706 4.333926 GGAGGATTATGTGTTCTGAAGCAC 59.666 45.833 12.91 12.91 36.26 4.40
1564 1708 4.517285 TGGAGGATTATGTGTTCTGAAGC 58.483 43.478 0.00 0.00 0.00 3.86
1603 1755 8.972127 AGAGTAGAACAGCTATAACTGATTCAA 58.028 33.333 10.11 0.00 40.25 2.69
1612 1764 7.451732 ACCGATCTAGAGTAGAACAGCTATAA 58.548 38.462 0.00 0.00 38.50 0.98
1621 1773 4.462133 CAAGGGACCGATCTAGAGTAGAA 58.538 47.826 0.00 0.00 38.50 2.10
1626 1778 1.698506 AGCAAGGGACCGATCTAGAG 58.301 55.000 0.00 0.00 0.00 2.43
1630 1782 1.604378 CCAAGCAAGGGACCGATCT 59.396 57.895 0.00 0.00 0.00 2.75
1635 1787 3.376918 GCAGCCAAGCAAGGGACC 61.377 66.667 0.00 0.00 0.00 4.46
1642 1794 2.359107 CGAGAAGGCAGCCAAGCA 60.359 61.111 15.80 0.00 35.83 3.91
1643 1795 2.359230 ACGAGAAGGCAGCCAAGC 60.359 61.111 15.80 1.72 0.00 4.01
1644 1796 0.739112 GAGACGAGAAGGCAGCCAAG 60.739 60.000 15.80 2.04 0.00 3.61
1645 1797 1.293498 GAGACGAGAAGGCAGCCAA 59.707 57.895 15.80 0.00 0.00 4.52
1685 1838 4.500375 GGAAACATATGCATGGCTCCTTTC 60.500 45.833 10.16 7.30 35.57 2.62
1693 1847 5.775686 CCACATAAGGAAACATATGCATGG 58.224 41.667 10.16 3.88 43.93 3.66
1697 1851 3.636300 TGGCCACATAAGGAAACATATGC 59.364 43.478 0.00 0.00 43.93 3.14
1711 3619 3.118811 CCGACCATAAATTTTGGCCACAT 60.119 43.478 3.88 0.00 37.81 3.21
1712 3620 2.232452 CCGACCATAAATTTTGGCCACA 59.768 45.455 3.88 0.00 37.81 4.17
1730 3639 1.375013 GGCGCAGTTCCTAAACCGA 60.375 57.895 10.83 0.00 35.92 4.69
1744 3653 5.177142 GTCCTAAGCTAATTTTAGTAGGCGC 59.823 44.000 0.00 0.00 33.10 6.53
1757 3666 4.578871 GGTTAAAACCCGTCCTAAGCTAA 58.421 43.478 0.02 0.00 43.43 3.09
1768 3677 7.036829 TTTCAAGAGAAAAAGGTTAAAACCCG 58.963 34.615 8.27 0.00 44.01 5.28
1807 3719 4.204012 ACTTTCGACAAATTTGAGGGACA 58.796 39.130 24.64 9.99 0.00 4.02
1810 3722 7.843490 TCTATACTTTCGACAAATTTGAGGG 57.157 36.000 24.64 12.31 0.00 4.30
2252 4344 7.401484 TGTTGTTCTGTTTTTCTTTGTTGTC 57.599 32.000 0.00 0.00 0.00 3.18
2255 4347 8.655651 TCTTTGTTGTTCTGTTTTTCTTTGTT 57.344 26.923 0.00 0.00 0.00 2.83
2275 4367 7.575332 TTTGTTTCTTTCTCGGTTTTCTTTG 57.425 32.000 0.00 0.00 0.00 2.77
2409 5183 6.432107 TCTTTACCGATTTTCTTTGGTTTCG 58.568 36.000 0.00 0.00 35.00 3.46
2411 5185 9.438228 TTTTTCTTTACCGATTTTCTTTGGTTT 57.562 25.926 0.00 0.00 35.00 3.27
2439 5213 6.750039 CGCCTTTTTCTTCTACTTTTGTTTCA 59.250 34.615 0.00 0.00 0.00 2.69
2440 5214 6.970613 TCGCCTTTTTCTTCTACTTTTGTTTC 59.029 34.615 0.00 0.00 0.00 2.78
2443 5217 6.445357 TTCGCCTTTTTCTTCTACTTTTGT 57.555 33.333 0.00 0.00 0.00 2.83
2448 5222 7.685594 CGATATTTTCGCCTTTTTCTTCTACT 58.314 34.615 0.00 0.00 41.69 2.57
2449 5223 7.878408 CGATATTTTCGCCTTTTTCTTCTAC 57.122 36.000 0.00 0.00 41.69 2.59
2464 5238 6.516739 GCTGTTGTTTTGCTTCGATATTTTC 58.483 36.000 0.00 0.00 0.00 2.29
2465 5239 5.116983 CGCTGTTGTTTTGCTTCGATATTTT 59.883 36.000 0.00 0.00 0.00 1.82
2466 5240 4.616802 CGCTGTTGTTTTGCTTCGATATTT 59.383 37.500 0.00 0.00 0.00 1.40
2467 5241 4.083537 TCGCTGTTGTTTTGCTTCGATATT 60.084 37.500 0.00 0.00 0.00 1.28
2468 5242 3.435327 TCGCTGTTGTTTTGCTTCGATAT 59.565 39.130 0.00 0.00 0.00 1.63
2469 5243 2.803386 TCGCTGTTGTTTTGCTTCGATA 59.197 40.909 0.00 0.00 0.00 2.92
2470 5244 1.601903 TCGCTGTTGTTTTGCTTCGAT 59.398 42.857 0.00 0.00 0.00 3.59
2471 5245 1.010580 TCGCTGTTGTTTTGCTTCGA 58.989 45.000 0.00 0.00 0.00 3.71
2472 5246 1.112459 GTCGCTGTTGTTTTGCTTCG 58.888 50.000 0.00 0.00 0.00 3.79
2473 5247 1.202245 TGGTCGCTGTTGTTTTGCTTC 60.202 47.619 0.00 0.00 0.00 3.86
2476 5250 1.634702 TTTGGTCGCTGTTGTTTTGC 58.365 45.000 0.00 0.00 0.00 3.68
2521 5295 5.276270 GCTAAGTATGTTCATTCGGTCGTA 58.724 41.667 0.00 0.00 0.00 3.43
2525 5299 3.131577 TCGGCTAAGTATGTTCATTCGGT 59.868 43.478 0.00 0.00 0.00 4.69
2531 5305 2.181125 TGGGTCGGCTAAGTATGTTCA 58.819 47.619 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.