Multiple sequence alignment - TraesCS6D01G090100

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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 TraesCS6D01G090100 chr6D 100.000 2604 0 0 1 2604 55935746 55933143 0.000000e+00 4809.0
1 TraesCS6D01G090100 chr6B 89.765 2042 94 24 1 2019 126150376 126148427 0.000000e+00 2507.0
2 TraesCS6D01G090100 chr6B 91.852 135 11 0 2088 2222 126145958 126145824 3.420000e-44 189.0
3 TraesCS6D01G090100 chr6B 91.111 135 4 2 2478 2604 126145704 126145570 2.660000e-40 176.0
4 TraesCS6D01G090100 chr6B 90.598 117 8 3 2277 2392 126145824 126145710 4.490000e-33 152.0
5 TraesCS6D01G090100 chr6A 89.599 1769 113 24 302 2049 70431160 70429442 0.000000e+00 2182.0
6 TraesCS6D01G090100 chr6A 87.694 772 45 22 1 770 70431924 70431201 0.000000e+00 854.0
7 TraesCS6D01G090100 chr6A 89.695 524 34 7 2090 2604 70428860 70428348 0.000000e+00 651.0
8 TraesCS6D01G090100 chr6A 84.324 185 29 0 2093 2277 592521791 592521975 5.720000e-42 182.0
9 TraesCS6D01G090100 chr7B 85.946 185 26 0 2093 2277 490894583 490894767 5.680000e-47 198.0
10 TraesCS6D01G090100 chr4D 85.946 185 26 0 2093 2277 196883398 196883214 5.680000e-47 198.0
11 TraesCS6D01G090100 chr3B 83.696 184 30 0 2094 2277 30522457 30522640 9.580000e-40 174.0
12 TraesCS6D01G090100 chr5A 79.670 182 31 5 2102 2277 20792692 20792873 2.720000e-25 126.0
13 TraesCS6D01G090100 chr5D 91.071 56 5 0 2135 2190 486824576 486824631 2.780000e-10 76.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G090100 chr6D 55933143 55935746 2603 True 4809 4809 100.0000 1 2604 1 chr6D.!!$R1 2603
1 TraesCS6D01G090100 chr6B 126145570 126150376 4806 True 756 2507 90.8315 1 2604 4 chr6B.!!$R1 2603
2 TraesCS6D01G090100 chr6A 70428348 70431924 3576 True 1229 2182 88.9960 1 2604 3 chr6A.!!$R1 2603

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
525 993 0.680061 TGCATGCCACATGAAGCAAA 59.32 45.0 16.68 5.21 43.36 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2252 5166 0.033504 AGTAGTGCCACACCTTGTCG 59.966 55.0 0.0 0.0 34.49 4.35 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
324 786 3.087031 AGATGCCATGAAACAACCTCTG 58.913 45.455 0.00 0.00 0.00 3.35
340 802 2.159282 CCTCTGAATGTTCAATGCAGCC 60.159 50.000 0.00 0.00 36.64 4.85
401 869 7.130681 AGCTATGCTGGTTAAGAGTATTTCT 57.869 36.000 0.00 0.00 37.57 2.52
493 961 8.557029 ACAAACTAGCTTGTTGACTAATACAAC 58.443 33.333 14.32 0.00 45.07 3.32
497 965 5.621193 AGCTTGTTGACTAATACAACCTGT 58.379 37.500 0.00 0.00 44.49 4.00
500 968 7.387948 AGCTTGTTGACTAATACAACCTGTTAG 59.612 37.037 0.00 0.00 44.49 2.34
502 970 8.967664 TTGTTGACTAATACAACCTGTTAGTT 57.032 30.769 0.00 0.00 44.49 2.24
504 972 9.701098 TGTTGACTAATACAACCTGTTAGTTAG 57.299 33.333 0.00 0.00 44.49 2.34
513 981 3.545703 ACCTGTTAGTTAGATGCATGCC 58.454 45.455 16.68 0.00 0.00 4.40
521 989 3.630769 AGTTAGATGCATGCCACATGAAG 59.369 43.478 16.68 0.00 0.00 3.02
525 993 0.680061 TGCATGCCACATGAAGCAAA 59.320 45.000 16.68 5.21 43.36 3.68
549 1017 4.616604 CGTCCAAATGTTCAATGCAGTCAT 60.617 41.667 0.00 0.00 33.53 3.06
550 1018 5.391843 CGTCCAAATGTTCAATGCAGTCATA 60.392 40.000 0.00 0.00 31.46 2.15
551 1019 6.567050 GTCCAAATGTTCAATGCAGTCATAT 58.433 36.000 0.00 0.00 31.46 1.78
552 1020 6.474427 GTCCAAATGTTCAATGCAGTCATATG 59.526 38.462 0.00 0.00 31.46 1.78
553 1021 6.153170 TCCAAATGTTCAATGCAGTCATATGT 59.847 34.615 1.90 0.00 31.46 2.29
554 1022 6.814644 CCAAATGTTCAATGCAGTCATATGTT 59.185 34.615 1.90 0.00 31.46 2.71
555 1023 7.975058 CCAAATGTTCAATGCAGTCATATGTTA 59.025 33.333 1.90 0.00 31.46 2.41
556 1024 8.800972 CAAATGTTCAATGCAGTCATATGTTAC 58.199 33.333 1.90 0.00 31.46 2.50
557 1025 7.628769 ATGTTCAATGCAGTCATATGTTACA 57.371 32.000 1.90 0.00 31.46 2.41
558 1026 6.841119 TGTTCAATGCAGTCATATGTTACAC 58.159 36.000 1.90 0.00 31.46 2.90
559 1027 6.128035 TGTTCAATGCAGTCATATGTTACACC 60.128 38.462 1.90 0.00 31.46 4.16
560 1028 4.881273 TCAATGCAGTCATATGTTACACCC 59.119 41.667 1.90 0.00 31.46 4.61
561 1029 4.778213 ATGCAGTCATATGTTACACCCT 57.222 40.909 1.90 0.00 0.00 4.34
562 1030 4.568072 TGCAGTCATATGTTACACCCTT 57.432 40.909 1.90 0.00 0.00 3.95
563 1031 4.917385 TGCAGTCATATGTTACACCCTTT 58.083 39.130 1.90 0.00 0.00 3.11
564 1032 4.699735 TGCAGTCATATGTTACACCCTTTG 59.300 41.667 1.90 0.00 0.00 2.77
565 1033 4.700213 GCAGTCATATGTTACACCCTTTGT 59.300 41.667 1.90 0.00 42.84 2.83
566 1034 5.163754 GCAGTCATATGTTACACCCTTTGTC 60.164 44.000 1.90 0.00 39.91 3.18
567 1035 5.063438 CAGTCATATGTTACACCCTTTGTCG 59.937 44.000 1.90 0.00 39.91 4.35
568 1036 5.046878 AGTCATATGTTACACCCTTTGTCGA 60.047 40.000 1.90 0.00 39.91 4.20
569 1037 5.640357 GTCATATGTTACACCCTTTGTCGAA 59.360 40.000 1.90 0.00 39.91 3.71
570 1038 6.148150 GTCATATGTTACACCCTTTGTCGAAA 59.852 38.462 1.90 0.00 39.91 3.46
571 1039 6.711194 TCATATGTTACACCCTTTGTCGAAAA 59.289 34.615 1.90 0.00 39.91 2.29
572 1040 5.838531 ATGTTACACCCTTTGTCGAAAAA 57.161 34.783 0.00 0.00 39.91 1.94
599 1067 4.430007 TGTTACACTCGTCTTATCATGGC 58.570 43.478 0.00 0.00 0.00 4.40
607 1075 2.810274 CGTCTTATCATGGCCATCCTTG 59.190 50.000 17.61 6.48 38.49 3.61
617 1085 2.224992 TGGCCATCCTTGAGCTTGTTAA 60.225 45.455 0.00 0.00 0.00 2.01
618 1086 2.424956 GGCCATCCTTGAGCTTGTTAAG 59.575 50.000 0.00 0.00 0.00 1.85
620 1088 3.758554 GCCATCCTTGAGCTTGTTAAGAA 59.241 43.478 0.00 0.00 0.00 2.52
621 1089 4.400567 GCCATCCTTGAGCTTGTTAAGAAT 59.599 41.667 0.00 0.00 0.00 2.40
622 1090 5.678107 GCCATCCTTGAGCTTGTTAAGAATG 60.678 44.000 0.00 0.00 0.00 2.67
623 1091 5.416952 CCATCCTTGAGCTTGTTAAGAATGT 59.583 40.000 0.00 0.00 0.00 2.71
624 1092 6.404074 CCATCCTTGAGCTTGTTAAGAATGTC 60.404 42.308 0.00 0.00 0.00 3.06
625 1093 4.690748 TCCTTGAGCTTGTTAAGAATGTCG 59.309 41.667 0.00 0.00 0.00 4.35
664 1137 7.159322 TCTACTTCACTGAGTCTGTAAATCC 57.841 40.000 1.95 0.00 0.00 3.01
688 1161 5.826737 CCCATAAATTGCTCTGACTTCTGAT 59.173 40.000 0.00 0.00 0.00 2.90
690 1163 6.318144 CCATAAATTGCTCTGACTTCTGATGT 59.682 38.462 0.00 0.00 0.00 3.06
704 1177 4.115401 TCTGATGTACTAGCTTGCTGTG 57.885 45.455 5.26 1.08 0.00 3.66
705 1178 3.511540 TCTGATGTACTAGCTTGCTGTGT 59.488 43.478 5.26 6.82 0.00 3.72
706 1179 4.705023 TCTGATGTACTAGCTTGCTGTGTA 59.295 41.667 5.26 5.91 0.00 2.90
707 1180 4.998788 TGATGTACTAGCTTGCTGTGTAG 58.001 43.478 5.26 0.00 0.00 2.74
708 1181 3.868757 TGTACTAGCTTGCTGTGTAGG 57.131 47.619 5.26 0.00 0.00 3.18
709 1182 3.427573 TGTACTAGCTTGCTGTGTAGGA 58.572 45.455 5.26 0.00 0.00 2.94
738 1211 3.118531 AGAATGTGCCATTCTCCCTAGT 58.881 45.455 18.97 2.70 33.43 2.57
766 1239 4.472108 ACCTCCATTCCCTGTAATAAACGA 59.528 41.667 0.00 0.00 0.00 3.85
802 1275 6.653020 TCACTGGTACTCTGATATGCATTTT 58.347 36.000 3.54 0.00 0.00 1.82
806 1279 6.888105 TGGTACTCTGATATGCATTTTCTGA 58.112 36.000 3.54 11.00 0.00 3.27
826 1299 9.533831 TTTCTGATGTATATATACAGCTCTCCA 57.466 33.333 30.85 16.32 46.63 3.86
863 1339 3.814005 ACACTCTGTTTCGTAACCTGT 57.186 42.857 2.26 0.00 33.15 4.00
869 1345 4.362279 TCTGTTTCGTAACCTGTGTACAC 58.638 43.478 19.36 19.36 33.15 2.90
918 1394 7.652300 TTATTAATGTAGTGATTAGCTGCCG 57.348 36.000 0.00 0.00 0.00 5.69
919 1395 3.543680 AATGTAGTGATTAGCTGCCGT 57.456 42.857 0.00 0.00 0.00 5.68
986 1465 2.571212 TCTGCCGAATGCCGAAATATT 58.429 42.857 0.00 0.00 41.76 1.28
1022 1501 4.512914 GGAGGCCCTGGTGGATGC 62.513 72.222 0.00 0.00 35.39 3.91
1023 1502 4.512914 GAGGCCCTGGTGGATGCC 62.513 72.222 0.00 3.01 39.88 4.40
1040 1519 2.297895 CCACGGGTTCAGGGATGGA 61.298 63.158 0.00 0.00 0.00 3.41
1049 1528 0.548031 TCAGGGATGGAGGATTGTGC 59.452 55.000 0.00 0.00 0.00 4.57
1065 1544 1.134367 TGTGCGAGCATACTAGTGGAC 59.866 52.381 5.39 0.00 0.00 4.02
1155 1634 0.600057 CTTCCAGTTTGGCAAGGCTC 59.400 55.000 0.00 0.00 37.47 4.70
1156 1635 0.106268 TTCCAGTTTGGCAAGGCTCA 60.106 50.000 0.00 0.00 37.47 4.26
1157 1636 0.112995 TCCAGTTTGGCAAGGCTCAT 59.887 50.000 0.00 0.00 37.47 2.90
1158 1637 0.971386 CCAGTTTGGCAAGGCTCATT 59.029 50.000 0.00 0.00 0.00 2.57
1159 1638 1.337447 CCAGTTTGGCAAGGCTCATTG 60.337 52.381 0.00 0.00 0.00 2.82
1357 1841 9.558648 ACGAAATTTACTTTTTCACGTTTTAGT 57.441 25.926 0.00 0.00 33.61 2.24
1393 1881 4.499037 TCGTCGAGAAAAGTTCATCTCA 57.501 40.909 15.21 4.24 41.73 3.27
1525 2013 2.299013 TCTTGTACACTTGGACATCGCT 59.701 45.455 0.00 0.00 0.00 4.93
1651 2139 1.771255 CATTCCTTCCTACTCCAGGGG 59.229 57.143 0.00 0.00 45.58 4.79
1687 2176 1.512926 GCGATAGTGGATGCCGAATT 58.487 50.000 0.00 0.00 39.35 2.17
1688 2177 2.611971 GGCGATAGTGGATGCCGAATTA 60.612 50.000 0.00 0.00 37.81 1.40
1775 2264 4.442753 GGAGGCATCAAAAGTTCAAAACCA 60.443 41.667 0.00 0.00 0.00 3.67
1820 2309 9.587772 GAGCACTTGAAGTTCATCTATTAGTTA 57.412 33.333 6.36 0.00 0.00 2.24
1861 2350 4.499019 CCCTAACTGTTGTTGCAATCGTTT 60.499 41.667 0.59 0.00 37.59 3.60
1893 2382 1.799548 GCACTAGCTACTCGGTCTTGC 60.800 57.143 0.00 0.00 37.91 4.01
1900 2390 0.388134 TACTCGGTCTTGCGAACTGC 60.388 55.000 0.00 0.00 46.70 4.40
1933 2426 8.729805 TGAAATATCTTGTTTTGGTTTGCTTT 57.270 26.923 0.00 0.00 0.00 3.51
1942 2439 1.006337 GGTTTGCTTTCCATGCGCA 60.006 52.632 14.96 14.96 0.00 6.09
1970 2467 8.789762 TGATATATCCATGCTCATTCTGTTTTG 58.210 33.333 10.25 0.00 0.00 2.44
1973 2470 2.613691 CATGCTCATTCTGTTTTGCCC 58.386 47.619 0.00 0.00 0.00 5.36
2079 4970 4.460382 AGAATTGACCTTATGCACAACCAG 59.540 41.667 0.00 0.00 0.00 4.00
2106 5020 2.828520 TCTGGTCTCTTCGAAGCAGAAT 59.171 45.455 22.86 0.00 44.51 2.40
2156 5070 1.000274 GCCCGACATTTGCTCAAAAGT 60.000 47.619 3.28 3.28 35.28 2.66
2175 5089 6.515272 AAAGTTGAAAGCAAGAGTTTCAGA 57.485 33.333 0.00 0.00 43.11 3.27
2190 5104 6.254589 AGAGTTTCAGATTTCGAGCTTTATCG 59.745 38.462 0.00 0.00 44.07 2.92
2252 5166 2.417787 GCAAGATTGAAAGGCCACCATC 60.418 50.000 5.01 3.11 0.00 3.51
2279 5193 0.035317 TGTGGCACTACTCCTGCTTG 59.965 55.000 19.83 0.00 34.84 4.01
2318 5232 6.096423 GGATAGCCAACATATAGGACGACATA 59.904 42.308 0.00 0.00 0.00 2.29
2385 5299 8.826546 CAAGTTTGCATGTATATACTTGACAC 57.173 34.615 25.27 18.26 42.99 3.67
2386 5300 8.668353 CAAGTTTGCATGTATATACTTGACACT 58.332 33.333 25.27 19.61 42.99 3.55
2387 5301 8.201554 AGTTTGCATGTATATACTTGACACTG 57.798 34.615 25.27 9.22 34.39 3.66
2388 5302 8.040727 AGTTTGCATGTATATACTTGACACTGA 58.959 33.333 25.27 10.37 34.39 3.41
2389 5303 7.770801 TTGCATGTATATACTTGACACTGAC 57.229 36.000 25.27 11.13 34.39 3.51
2390 5304 6.872920 TGCATGTATATACTTGACACTGACA 58.127 36.000 25.27 12.99 34.39 3.58
2411 5325 4.771684 GCACAATCATGCGGACAC 57.228 55.556 0.00 0.00 35.50 3.67
2422 5336 1.655484 TGCGGACACAAGCTGATATG 58.345 50.000 0.00 0.00 0.00 1.78
2433 5347 6.025896 CACAAGCTGATATGTAAAAGCACAG 58.974 40.000 0.00 0.00 38.14 3.66
2459 5374 4.144297 TGAAGCTGCAAGTAAAGGTGATT 58.856 39.130 1.02 0.00 35.30 2.57
2469 5384 0.696501 AAAGGTGATTGGTACCGCCT 59.303 50.000 7.57 6.68 44.47 5.52
2471 5386 1.575419 AGGTGATTGGTACCGCCTTA 58.425 50.000 7.57 0.00 40.09 2.69
2472 5387 1.910671 AGGTGATTGGTACCGCCTTAA 59.089 47.619 7.57 0.00 40.09 1.85
2473 5388 2.093128 AGGTGATTGGTACCGCCTTAAG 60.093 50.000 7.57 0.00 40.09 1.85
2474 5389 2.093341 GGTGATTGGTACCGCCTTAAGA 60.093 50.000 7.57 0.00 38.35 2.10
2475 5390 3.602483 GTGATTGGTACCGCCTTAAGAA 58.398 45.455 7.57 0.00 38.35 2.52
2476 5391 4.004982 GTGATTGGTACCGCCTTAAGAAA 58.995 43.478 7.57 0.00 38.35 2.52
2554 5469 0.749454 AGCCGGTCATCATTTCCAGC 60.749 55.000 1.90 0.00 0.00 4.85
2559 5474 3.003689 CCGGTCATCATTTCCAGCAATAC 59.996 47.826 0.00 0.00 0.00 1.89
2560 5475 3.627123 CGGTCATCATTTCCAGCAATACA 59.373 43.478 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
263 264 1.224592 GGCACATGTAGGTCCAGGG 59.775 63.158 0.00 0.00 0.00 4.45
293 294 3.920231 TCATGGCATCTGAAGCTTAGT 57.080 42.857 0.00 0.00 0.00 2.24
295 296 4.334552 TGTTTCATGGCATCTGAAGCTTA 58.665 39.130 15.55 0.00 35.58 3.09
298 299 3.248266 GTTGTTTCATGGCATCTGAAGC 58.752 45.455 9.82 9.82 34.33 3.86
299 300 3.508793 AGGTTGTTTCATGGCATCTGAAG 59.491 43.478 0.00 0.00 34.33 3.02
300 301 3.499338 AGGTTGTTTCATGGCATCTGAA 58.501 40.909 0.00 0.00 0.00 3.02
301 302 3.084039 GAGGTTGTTTCATGGCATCTGA 58.916 45.455 0.00 0.00 0.00 3.27
302 303 3.087031 AGAGGTTGTTTCATGGCATCTG 58.913 45.455 0.00 0.00 0.00 2.90
303 304 3.087031 CAGAGGTTGTTTCATGGCATCT 58.913 45.455 0.00 0.00 0.00 2.90
306 307 2.655090 TCAGAGGTTGTTTCATGGCA 57.345 45.000 0.00 0.00 0.00 4.92
307 308 3.256631 ACATTCAGAGGTTGTTTCATGGC 59.743 43.478 0.00 0.00 0.00 4.40
308 309 5.009911 TGAACATTCAGAGGTTGTTTCATGG 59.990 40.000 0.00 0.00 33.92 3.66
324 786 6.913873 AATTTATGGCTGCATTGAACATTC 57.086 33.333 0.50 0.00 0.00 2.67
493 961 3.313526 GTGGCATGCATCTAACTAACAGG 59.686 47.826 21.36 0.00 0.00 4.00
497 965 4.779696 TCATGTGGCATGCATCTAACTAA 58.220 39.130 21.36 0.00 0.00 2.24
500 968 3.794475 GCTTCATGTGGCATGCATCTAAC 60.794 47.826 21.36 9.61 0.00 2.34
502 970 1.951602 GCTTCATGTGGCATGCATCTA 59.048 47.619 21.36 2.63 0.00 1.98
504 972 0.458260 TGCTTCATGTGGCATGCATC 59.542 50.000 21.36 12.03 33.23 3.91
513 981 2.772568 TTGGACGTTTGCTTCATGTG 57.227 45.000 0.00 0.00 0.00 3.21
521 989 3.362888 GCATTGAACATTTGGACGTTTGC 60.363 43.478 0.00 0.00 0.00 3.68
525 993 2.622942 ACTGCATTGAACATTTGGACGT 59.377 40.909 0.00 0.00 0.00 4.34
549 1017 6.939132 TTTTTCGACAAAGGGTGTAACATA 57.061 33.333 0.00 0.00 41.96 2.29
550 1018 5.838531 TTTTTCGACAAAGGGTGTAACAT 57.161 34.783 0.00 0.00 41.96 2.71
572 1040 9.261180 CCATGATAAGACGAGTGTAACATATTT 57.739 33.333 0.00 0.00 41.43 1.40
573 1041 7.385205 GCCATGATAAGACGAGTGTAACATATT 59.615 37.037 0.00 0.00 41.43 1.28
574 1042 6.868864 GCCATGATAAGACGAGTGTAACATAT 59.131 38.462 0.00 0.00 41.43 1.78
575 1043 6.213677 GCCATGATAAGACGAGTGTAACATA 58.786 40.000 0.00 0.00 41.43 2.29
599 1067 5.416952 ACATTCTTAACAAGCTCAAGGATGG 59.583 40.000 16.74 5.66 38.90 3.51
607 1075 5.635700 ACTTCTCGACATTCTTAACAAGCTC 59.364 40.000 0.00 0.00 0.00 4.09
655 1128 6.547141 TCAGAGCAATTTATGGGGATTTACAG 59.453 38.462 0.00 0.00 0.00 2.74
664 1137 5.188434 TCAGAAGTCAGAGCAATTTATGGG 58.812 41.667 0.00 0.00 0.00 4.00
688 1161 3.427573 TCCTACACAGCAAGCTAGTACA 58.572 45.455 0.00 0.00 0.00 2.90
690 1163 3.698289 ACTCCTACACAGCAAGCTAGTA 58.302 45.455 0.00 0.61 0.00 1.82
738 1211 9.027202 GTTTATTACAGGGAATGGAGGTTTAAA 57.973 33.333 0.00 0.00 0.00 1.52
766 1239 6.596888 CAGAGTACCAGTGATCATTGACAAAT 59.403 38.462 18.99 3.82 0.00 2.32
802 1275 9.533831 TTTGGAGAGCTGTATATATACATCAGA 57.466 33.333 22.72 9.28 41.92 3.27
850 1326 5.521372 AGAAAGTGTACACAGGTTACGAAAC 59.479 40.000 27.06 6.08 34.66 2.78
863 1339 6.640518 ACTGAAGACAGAAAGAAAGTGTACA 58.359 36.000 0.00 0.00 46.03 2.90
869 1345 7.326968 AGGAAAACTGAAGACAGAAAGAAAG 57.673 36.000 0.00 0.00 46.03 2.62
918 1394 5.864418 TTGGGGTACATGTCTCAGTATAC 57.136 43.478 0.00 0.00 0.00 1.47
919 1395 6.687901 GCATTTGGGGTACATGTCTCAGTATA 60.688 42.308 0.00 0.00 0.00 1.47
986 1465 3.643320 CTCCCTCATATACTGCACAAGGA 59.357 47.826 0.00 0.00 0.00 3.36
1022 1501 2.257409 CTCCATCCCTGAACCCGTGG 62.257 65.000 0.00 0.00 0.00 4.94
1023 1502 1.221840 CTCCATCCCTGAACCCGTG 59.778 63.158 0.00 0.00 0.00 4.94
1040 1519 2.695666 ACTAGTATGCTCGCACAATCCT 59.304 45.455 0.00 0.00 0.00 3.24
1049 1528 1.669265 TGTCGTCCACTAGTATGCTCG 59.331 52.381 0.00 0.00 0.00 5.03
1065 1544 4.740268 TGTTAAGTAGCTGTGGTATGTCG 58.260 43.478 0.00 0.00 0.00 4.35
1159 1638 2.357327 TCAAGATTGCTGCATTGTGC 57.643 45.000 1.84 0.00 45.29 4.57
1280 1764 0.667993 ACCAATTTGGACGCACACAG 59.332 50.000 22.19 0.00 40.96 3.66
1349 1833 3.997021 AGAGCCATGAGACAACTAAAACG 59.003 43.478 0.00 0.00 0.00 3.60
1356 1840 1.996191 GACGAAGAGCCATGAGACAAC 59.004 52.381 0.00 0.00 0.00 3.32
1357 1841 1.402852 CGACGAAGAGCCATGAGACAA 60.403 52.381 0.00 0.00 0.00 3.18
1359 1843 0.452184 TCGACGAAGAGCCATGAGAC 59.548 55.000 0.00 0.00 0.00 3.36
1393 1881 4.142182 CCAAACGGTCAATAATCAAGCCAT 60.142 41.667 0.00 0.00 0.00 4.40
1504 1992 2.299013 AGCGATGTCCAAGTGTACAAGA 59.701 45.455 0.00 0.00 0.00 3.02
1559 2047 2.163509 GCCCGCTAGTATCATCTGAGA 58.836 52.381 0.00 0.00 0.00 3.27
1651 2139 1.210155 GCCACAAGTGATCCAACGC 59.790 57.895 0.94 0.00 0.00 4.84
1687 2176 7.569016 GAGATGGTCTCATGCGTCTAGCTATA 61.569 46.154 0.00 0.00 43.95 1.31
1688 2177 6.831899 GAGATGGTCTCATGCGTCTAGCTAT 61.832 48.000 0.00 0.00 43.95 2.97
1775 2264 3.270877 CTCGACGAAAATTCCCATCCTT 58.729 45.455 0.00 0.00 0.00 3.36
1820 2309 0.035630 GGCACAGGCATGAGAAGACT 60.036 55.000 4.84 0.00 43.71 3.24
1861 2350 3.417069 AGCTAGTGCAACATACACCAA 57.583 42.857 0.00 0.00 41.43 3.67
1893 2382 1.221466 TTTCAGCTCACCGCAGTTCG 61.221 55.000 0.00 0.00 42.61 3.95
1900 2390 5.551760 AAACAAGATATTTCAGCTCACCG 57.448 39.130 0.00 0.00 0.00 4.94
1933 2426 4.219264 TGGATATATCAATGCGCATGGA 57.781 40.909 28.89 28.89 0.00 3.41
1942 2439 9.529823 AAACAGAATGAGCATGGATATATCAAT 57.470 29.630 14.60 5.91 39.69 2.57
1970 2467 5.337578 TGTGCTTTGGAAAAATATAGGGC 57.662 39.130 0.00 0.00 0.00 5.19
1973 2470 5.127682 AGGCCTGTGCTTTGGAAAAATATAG 59.872 40.000 3.11 0.00 37.74 1.31
2079 4970 4.202060 TGCTTCGAAGAGACCAGACATATC 60.202 45.833 28.95 6.06 38.43 1.63
2156 5070 6.038161 TCGAAATCTGAAACTCTTGCTTTCAA 59.962 34.615 0.51 0.00 37.22 2.69
2175 5089 4.386867 TGACCTCGATAAAGCTCGAAAT 57.613 40.909 0.00 0.00 46.14 2.17
2213 5127 2.217750 TGCAATATGCCGGTGATACAC 58.782 47.619 1.90 0.00 44.23 2.90
2214 5128 2.629336 TGCAATATGCCGGTGATACA 57.371 45.000 1.90 0.00 44.23 2.29
2215 5129 3.138304 TCTTGCAATATGCCGGTGATAC 58.862 45.455 1.90 0.00 44.23 2.24
2221 5135 3.713858 TTCAATCTTGCAATATGCCGG 57.286 42.857 0.00 0.00 44.23 6.13
2238 5152 0.109532 TTGTCGATGGTGGCCTTTCA 59.890 50.000 3.32 0.00 0.00 2.69
2241 5155 1.002134 CCTTGTCGATGGTGGCCTT 60.002 57.895 3.32 0.00 0.00 4.35
2252 5166 0.033504 AGTAGTGCCACACCTTGTCG 59.966 55.000 0.00 0.00 34.49 4.35
2262 5176 1.679311 CCAAGCAGGAGTAGTGCCA 59.321 57.895 0.00 0.00 42.24 4.92
2279 5193 1.506493 CTATCCTGATTGAGTGCGCC 58.494 55.000 4.18 0.00 0.00 6.53
2318 5232 5.502079 TGTGGTACAAAATTATCCATCCGT 58.498 37.500 0.00 0.00 44.16 4.69
2325 5239 7.881775 AGAATCCCTGTGGTACAAAATTATC 57.118 36.000 0.00 0.00 44.16 1.75
2385 5299 1.201998 GCATGATTGTGCTCGTGTCAG 60.202 52.381 0.00 0.00 41.82 3.51
2386 5300 0.798159 GCATGATTGTGCTCGTGTCA 59.202 50.000 0.00 0.00 41.82 3.58
2387 5301 0.247419 CGCATGATTGTGCTCGTGTC 60.247 55.000 0.00 0.00 42.88 3.67
2388 5302 1.638388 CCGCATGATTGTGCTCGTGT 61.638 55.000 0.00 0.00 42.88 4.49
2389 5303 1.061411 CCGCATGATTGTGCTCGTG 59.939 57.895 0.00 0.00 42.88 4.35
2390 5304 1.079197 TCCGCATGATTGTGCTCGT 60.079 52.632 0.00 0.00 42.88 4.18
2411 5325 6.426980 TCTGTGCTTTTACATATCAGCTTG 57.573 37.500 0.00 0.00 33.15 4.01
2422 5336 4.671250 GCAGCTTCAGATCTGTGCTTTTAC 60.671 45.833 29.32 20.05 38.53 2.01
2433 5347 4.006319 ACCTTTACTTGCAGCTTCAGATC 58.994 43.478 0.00 0.00 0.00 2.75
2459 5374 4.289238 TGAATTTCTTAAGGCGGTACCA 57.711 40.909 13.54 0.00 43.14 3.25
2554 5469 4.119136 TGTGCGGATCACTGTATGTATTG 58.881 43.478 0.00 0.00 45.81 1.90
2559 5474 1.869132 CCATGTGCGGATCACTGTATG 59.131 52.381 0.00 0.00 45.81 2.39
2560 5475 1.486310 ACCATGTGCGGATCACTGTAT 59.514 47.619 0.00 0.00 45.81 2.29


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

AutoCloner maintained by Alex Coulton.