Multiple sequence alignment - TraesCS6A01G250800

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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 TraesCS6A01G250800 chr6A 100.000 5208 0 0 1 5208 465226251 465231458 0.000000e+00 9618
1 TraesCS6A01G250800 chr6D 93.323 5257 188 63 9 5208 326534753 326539903 0.000000e+00 7613
2 TraesCS6A01G250800 chr6B 92.552 2645 129 29 104 2707 495813951 495811334 0.000000e+00 3731
3 TraesCS6A01G250800 chr6B 94.684 2088 63 18 2707 4781 495809762 495807710 0.000000e+00 3197
4 TraesCS6A01G250800 chr6B 88.128 438 22 11 4790 5208 495807584 495807158 1.300000e-135 494
5 TraesCS6A01G250800 chr1D 92.653 245 9 5 2139 2377 254439691 254439932 1.390000e-90 344
6 TraesCS6A01G250800 chr1D 91.903 247 11 4 2139 2377 491423743 491423498 2.320000e-88 337
7 TraesCS6A01G250800 chr1D 91.228 114 9 1 2668 2780 128528726 128528613 2.510000e-33 154
8 TraesCS6A01G250800 chr5D 92.245 245 12 3 2139 2377 503296555 503296798 1.800000e-89 340
9 TraesCS6A01G250800 chr5D 91.463 246 12 5 2139 2377 512413923 512414166 3.890000e-86 329
10 TraesCS6A01G250800 chr5D 91.020 245 12 7 2139 2377 6172258 6172018 6.510000e-84 322
11 TraesCS6A01G250800 chr2D 92.245 245 11 4 2139 2377 638429086 638429328 1.800000e-89 340
12 TraesCS6A01G250800 chr2D 91.228 114 9 1 2666 2778 141479466 141479579 2.510000e-33 154
13 TraesCS6A01G250800 chr3D 91.803 244 10 6 2139 2376 235621199 235621438 1.080000e-86 331
14 TraesCS6A01G250800 chr3D 92.523 107 8 0 2671 2777 450875186 450875292 2.510000e-33 154
15 TraesCS6A01G250800 chr3D 89.908 109 11 0 2670 2778 284818307 284818415 1.960000e-29 141
16 TraesCS6A01G250800 chr1A 90.517 116 9 2 2667 2780 188149105 188148990 9.030000e-33 152
17 TraesCS6A01G250800 chr1B 89.720 107 11 0 2671 2777 507850466 507850360 2.530000e-28 137


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 TraesCS6A01G250800 chr6A 465226251 465231458 5207 False 9618 9618 100.000 1 5208 1 chr6A.!!$F1 5207
1 TraesCS6A01G250800 chr6D 326534753 326539903 5150 False 7613 7613 93.323 9 5208 1 chr6D.!!$F1 5199
2 TraesCS6A01G250800 chr6B 495807158 495813951 6793 True 2474 3731 91.788 104 5208 3 chr6B.!!$R1 5104

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
158 161 0.110373 CACGCCTAAACAACCGAAGC 60.110 55.000 0.00 0.0 0.0 3.86 F
558 568 1.134694 GGCGAACGATTTCTGTGGC 59.865 57.895 0.00 0.0 0.0 5.01 F
1167 1180 1.008538 GAAGGTGTGTTGGCAAGCG 60.009 57.895 0.00 0.0 0.0 4.68 F
2571 2603 0.036164 ATGCGCACACTTCCCAGTTA 59.964 50.000 14.90 0.0 0.0 2.24 F
2572 2604 0.602638 TGCGCACACTTCCCAGTTAG 60.603 55.000 5.66 0.0 0.0 2.34 F
4027 5650 1.267574 TTGAGAAGATCCTGCCGCCT 61.268 55.000 0.00 0.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1158 1171 1.339610 ACATACAAAAGCGCTTGCCAA 59.660 42.857 25.80 10.68 40.41 4.52 R
2543 2574 1.656652 AGTGTGCGCATATCAAGGAC 58.343 50.000 15.91 0.00 0.00 3.85 R
2574 2606 1.048601 TCTTCTTTCCACCGCTGACT 58.951 50.000 0.00 0.00 0.00 3.41 R
3471 5094 1.101331 TGTGTGCATGCAAGTGTTGA 58.899 45.000 24.58 0.00 0.00 3.18 R
4150 5773 1.532090 CCTTCGTCATCGTCTTCCTCG 60.532 57.143 0.00 0.00 38.33 4.63 R
4847 6601 0.178992 TTCAACACCTTCCTGCAGGG 60.179 55.000 32.23 18.81 38.42 4.45 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
25 26 0.251341 GGTGTGCTGATTTCAGGGGT 60.251 55.000 9.49 0.00 43.94 4.95
27 28 1.963515 GTGTGCTGATTTCAGGGGTTT 59.036 47.619 9.49 0.00 43.94 3.27
31 32 4.462483 TGTGCTGATTTCAGGGGTTTAATC 59.538 41.667 9.49 0.00 43.94 1.75
44 45 3.688185 GGGTTTAATCTTCAGGGTTCGAC 59.312 47.826 0.00 0.00 0.00 4.20
46 47 5.001874 GGTTTAATCTTCAGGGTTCGACTT 58.998 41.667 0.00 0.00 0.00 3.01
53 54 5.295152 TCTTCAGGGTTCGACTTAGTTTTC 58.705 41.667 0.00 0.00 0.00 2.29
54 55 4.675976 TCAGGGTTCGACTTAGTTTTCA 57.324 40.909 0.00 0.00 0.00 2.69
55 56 5.223449 TCAGGGTTCGACTTAGTTTTCAT 57.777 39.130 0.00 0.00 0.00 2.57
57 58 6.761312 TCAGGGTTCGACTTAGTTTTCATTA 58.239 36.000 0.00 0.00 0.00 1.90
58 59 7.218614 TCAGGGTTCGACTTAGTTTTCATTAA 58.781 34.615 0.00 0.00 0.00 1.40
60 61 8.347035 CAGGGTTCGACTTAGTTTTCATTAAAA 58.653 33.333 0.00 0.00 32.15 1.52
158 161 0.110373 CACGCCTAAACAACCGAAGC 60.110 55.000 0.00 0.00 0.00 3.86
266 273 2.058913 ATTAAAGCCAAACAACCGCG 57.941 45.000 0.00 0.00 0.00 6.46
294 301 4.787280 CCCCCTCTCTCCCTGCGT 62.787 72.222 0.00 0.00 0.00 5.24
324 331 1.677052 GAGCCGTCTACGATTTCCTCT 59.323 52.381 3.65 0.00 43.02 3.69
325 332 1.677052 AGCCGTCTACGATTTCCTCTC 59.323 52.381 3.65 0.00 43.02 3.20
326 333 1.677052 GCCGTCTACGATTTCCTCTCT 59.323 52.381 3.65 0.00 43.02 3.10
391 401 1.520787 CCAGGTAACGATCCGCCAC 60.521 63.158 0.00 0.00 46.39 5.01
428 438 1.149148 GTGGTTTTCTCCGTCTCAGC 58.851 55.000 0.00 0.00 0.00 4.26
469 479 7.360101 CGGACGTGTTATCTTCAAGAGAAAATT 60.360 37.037 0.00 0.00 38.06 1.82
521 531 1.997928 GCTTTCGGATCTTGCCTGGC 61.998 60.000 12.87 12.87 0.00 4.85
558 568 1.134694 GGCGAACGATTTCTGTGGC 59.865 57.895 0.00 0.00 0.00 5.01
598 608 3.257393 GCTGTGCGGATAAGATAGATGG 58.743 50.000 0.00 0.00 0.00 3.51
601 611 3.511540 TGTGCGGATAAGATAGATGGAGG 59.488 47.826 0.00 0.00 0.00 4.30
645 655 5.221803 CCATGACTTAGTATCCTGATGCCTT 60.222 44.000 0.00 0.00 0.00 4.35
648 658 3.961408 ACTTAGTATCCTGATGCCTTCGT 59.039 43.478 0.00 0.00 0.00 3.85
660 670 2.653726 TGCCTTCGTATACCGTCCTTA 58.346 47.619 0.00 0.00 37.94 2.69
864 874 6.071952 TCCTTAAATGTGCTGCCTTTCTTTAG 60.072 38.462 0.00 0.00 0.00 1.85
902 912 6.145534 CGATGTTTAGAGTTGCAAGTCTTGTA 59.854 38.462 35.19 19.25 39.36 2.41
932 945 5.809719 TTCTTTTGGCAAAAATGTTGGAC 57.190 34.783 24.15 0.00 34.81 4.02
954 967 6.879458 GGACTTTAGTGCTTTTATCTCTTGGA 59.121 38.462 0.00 0.00 33.32 3.53
960 973 6.581712 AGTGCTTTTATCTCTTGGAGATCTC 58.418 40.000 14.75 14.75 45.03 2.75
970 983 6.580788 TCTCTTGGAGATCTCATTTAAGCTG 58.419 40.000 23.85 15.34 33.35 4.24
972 985 6.715280 TCTTGGAGATCTCATTTAAGCTGTT 58.285 36.000 23.85 0.00 0.00 3.16
1158 1171 1.343069 GAGACCCTGAGAAGGTGTGT 58.657 55.000 0.00 0.00 37.88 3.72
1164 1177 1.679139 CTGAGAAGGTGTGTTGGCAA 58.321 50.000 0.00 0.00 0.00 4.52
1167 1180 1.008538 GAAGGTGTGTTGGCAAGCG 60.009 57.895 0.00 0.00 0.00 4.68
1171 1184 1.226945 GTGTGTTGGCAAGCGCTTT 60.227 52.632 22.51 2.65 38.60 3.51
1216 1229 5.163302 TGTTAGATTGGTGTTTGTTGACG 57.837 39.130 0.00 0.00 0.00 4.35
1469 1489 5.336690 GCTTTGTTCCATTATCCTGCTTTGA 60.337 40.000 0.00 0.00 0.00 2.69
1471 1491 3.696051 TGTTCCATTATCCTGCTTTGAGC 59.304 43.478 0.00 0.00 42.82 4.26
1498 1518 8.034058 AGTTAAATAGTCATGCACTCACTTTC 57.966 34.615 0.00 0.00 36.43 2.62
1500 1520 9.151471 GTTAAATAGTCATGCACTCACTTTCTA 57.849 33.333 0.00 0.00 36.43 2.10
1696 1716 5.366482 AAATGCAAGGGGTAAGTTTTTGT 57.634 34.783 0.00 0.00 0.00 2.83
1725 1745 9.274206 GTTCTTAGTTGGTAATCTGTCTTTCTT 57.726 33.333 0.00 0.00 0.00 2.52
1727 1747 8.871125 TCTTAGTTGGTAATCTGTCTTTCTTCT 58.129 33.333 0.00 0.00 0.00 2.85
1793 1816 8.656806 TCTTAAGGAAGGAATTCTGACAAAGTA 58.343 33.333 5.23 0.00 33.09 2.24
1846 1872 4.437239 CTCTGACTTTGTGACACAGTTCT 58.563 43.478 8.55 0.00 0.00 3.01
1917 1943 2.301583 ACTTGCTCTCTTTCTGTCCTCC 59.698 50.000 0.00 0.00 0.00 4.30
1928 1954 7.020827 TCTTTCTGTCCTCCTGAAATATTGT 57.979 36.000 0.00 0.00 39.40 2.71
1943 1969 7.405292 TGAAATATTGTGGTGAAAGAGATCCT 58.595 34.615 0.00 0.00 0.00 3.24
2077 2105 7.612244 TGTATTGCCTGGTAGTATTGCTTTTTA 59.388 33.333 0.00 0.00 0.00 1.52
2091 2119 4.985413 TGCTTTTTATTTCATCAGCCGAG 58.015 39.130 0.00 0.00 0.00 4.63
2106 2134 1.531578 GCCGAGAAGTTGAACCTTGTC 59.468 52.381 0.00 0.00 32.84 3.18
2115 2143 7.514721 AGAAGTTGAACCTTGTCCTGTTTATA 58.485 34.615 0.00 0.00 0.00 0.98
2325 2356 8.621286 TCATCCTTTCTTACAAACAAAAGAGTC 58.379 33.333 0.00 0.00 33.49 3.36
2347 2378 6.887002 AGTCTTTTCTTATTGAAGGGTGGATC 59.113 38.462 0.00 0.00 35.89 3.36
2428 2459 6.265577 GTTGCTGAAAGATGTTAGTTGTTGT 58.734 36.000 0.00 0.00 34.07 3.32
2429 2460 6.449635 TGCTGAAAGATGTTAGTTGTTGTT 57.550 33.333 0.00 0.00 34.07 2.83
2430 2461 6.264832 TGCTGAAAGATGTTAGTTGTTGTTG 58.735 36.000 0.00 0.00 34.07 3.33
2431 2462 5.687285 GCTGAAAGATGTTAGTTGTTGTTGG 59.313 40.000 0.00 0.00 34.07 3.77
2432 2463 6.459573 GCTGAAAGATGTTAGTTGTTGTTGGA 60.460 38.462 0.00 0.00 34.07 3.53
2434 2465 8.006298 TGAAAGATGTTAGTTGTTGTTGGATT 57.994 30.769 0.00 0.00 0.00 3.01
2435 2466 9.126151 TGAAAGATGTTAGTTGTTGTTGGATTA 57.874 29.630 0.00 0.00 0.00 1.75
2437 2468 9.912634 AAAGATGTTAGTTGTTGTTGGATTATG 57.087 29.630 0.00 0.00 0.00 1.90
2438 2469 8.635765 AGATGTTAGTTGTTGTTGGATTATGT 57.364 30.769 0.00 0.00 0.00 2.29
2439 2470 9.733556 AGATGTTAGTTGTTGTTGGATTATGTA 57.266 29.630 0.00 0.00 0.00 2.29
2502 2533 2.231235 CAGTGGCTGTTAATTGGTTCCC 59.769 50.000 0.00 0.00 0.00 3.97
2543 2574 2.736670 AAGGGGTAGCTAATTGCCTG 57.263 50.000 0.00 0.00 44.23 4.85
2558 2590 0.815213 GCCTGTCCTTGATATGCGCA 60.815 55.000 14.96 14.96 0.00 6.09
2571 2603 0.036164 ATGCGCACACTTCCCAGTTA 59.964 50.000 14.90 0.00 0.00 2.24
2572 2604 0.602638 TGCGCACACTTCCCAGTTAG 60.603 55.000 5.66 0.00 0.00 2.34
2574 2606 1.337447 GCGCACACTTCCCAGTTAGTA 60.337 52.381 0.30 0.00 0.00 1.82
2575 2607 2.607187 CGCACACTTCCCAGTTAGTAG 58.393 52.381 0.00 0.00 0.00 2.57
2599 2648 2.554032 AGCGGTGGAAAGAAGAAATGTG 59.446 45.455 0.00 0.00 0.00 3.21
2784 4406 3.312973 CGCACAGAGGGAGTACTAGTTAG 59.687 52.174 0.00 0.00 0.00 2.34
2806 4428 1.625315 TGATGGAGTGGAAGTGGAGTG 59.375 52.381 0.00 0.00 0.00 3.51
2814 4436 3.013921 GTGGAAGTGGAGTGTGTTGAAA 58.986 45.455 0.00 0.00 0.00 2.69
2815 4437 3.013921 TGGAAGTGGAGTGTGTTGAAAC 58.986 45.455 0.00 0.00 0.00 2.78
2817 4439 3.442273 GGAAGTGGAGTGTGTTGAAACAA 59.558 43.478 0.00 0.00 41.21 2.83
2831 4453 6.920758 GTGTTGAAACAAATAGCCATGTAACA 59.079 34.615 0.00 0.00 41.21 2.41
2961 4584 4.023707 ACTCTTGTCAATGTAGCTTGCAAC 60.024 41.667 0.00 0.00 0.00 4.17
3041 4664 4.135306 GTCGTAGGGATCTCACTGTATCA 58.865 47.826 0.00 0.00 0.00 2.15
3471 5094 2.149578 GTCTGCATCTGTTGAAGCACT 58.850 47.619 0.00 0.00 41.23 4.40
3749 5372 4.922206 TCAAGCCTGGTACATCAATTTCT 58.078 39.130 0.00 0.00 38.20 2.52
3823 5446 8.487028 AGTTCCTCTATCCTGTCGATAAAATTT 58.513 33.333 0.00 0.00 32.93 1.82
4027 5650 1.267574 TTGAGAAGATCCTGCCGCCT 61.268 55.000 0.00 0.00 0.00 5.52
4282 5905 6.524586 GCATTCTATTGTTCCTTTCTCGTTTG 59.475 38.462 0.00 0.00 0.00 2.93
4343 5969 6.322969 TCTTGGCGTCTTAAGATTATGAGGTA 59.677 38.462 8.75 0.00 0.00 3.08
4423 6049 3.003689 CCAGCAGTATTATTTTGGAGCCG 59.996 47.826 0.00 0.00 0.00 5.52
4428 6054 4.511826 CAGTATTATTTTGGAGCCGAGACC 59.488 45.833 0.00 0.00 0.00 3.85
4474 6100 0.463654 ATTGGTCGTGTGTGTGCTGT 60.464 50.000 0.00 0.00 0.00 4.40
4494 6120 4.880759 TGTTGCATTTTCCATGACGAAAT 58.119 34.783 0.00 0.00 32.00 2.17
4499 6125 5.105837 TGCATTTTCCATGACGAAATCATCA 60.106 36.000 0.00 0.00 45.52 3.07
4502 6128 7.811236 GCATTTTCCATGACGAAATCATCATAT 59.189 33.333 0.00 0.00 45.52 1.78
4505 6131 7.601073 TTCCATGACGAAATCATCATATAGC 57.399 36.000 0.00 0.00 45.52 2.97
4506 6132 6.700352 TCCATGACGAAATCATCATATAGCA 58.300 36.000 0.00 0.00 45.52 3.49
4507 6133 7.333323 TCCATGACGAAATCATCATATAGCAT 58.667 34.615 0.00 0.00 45.52 3.79
4509 6135 9.101655 CCATGACGAAATCATCATATAGCATTA 57.898 33.333 0.00 0.00 45.52 1.90
4545 6177 1.584380 CTGCTCAGCAACTTGAGGCC 61.584 60.000 0.00 0.00 43.80 5.19
4576 6208 4.860022 TGTATCAGATCTGTCAGTCAGGA 58.140 43.478 21.92 0.00 43.76 3.86
4671 6304 3.692791 AAGCGAAGACTTTGTGGAAAC 57.307 42.857 4.35 0.00 0.00 2.78
4705 6342 2.669569 CACCACCGTTCCTGGCTG 60.670 66.667 0.00 0.00 31.13 4.85
4723 6360 1.600916 GTTGCTTCCGGGTCTTGCT 60.601 57.895 0.00 0.00 0.00 3.91
4724 6361 1.302511 TTGCTTCCGGGTCTTGCTC 60.303 57.895 0.00 0.00 0.00 4.26
4725 6362 2.050836 TTGCTTCCGGGTCTTGCTCA 62.051 55.000 0.00 0.00 0.00 4.26
4726 6363 2.035442 GCTTCCGGGTCTTGCTCAC 61.035 63.158 0.00 0.00 0.00 3.51
4727 6364 1.376037 CTTCCGGGTCTTGCTCACC 60.376 63.158 0.00 0.00 0.00 4.02
4728 6365 2.111999 CTTCCGGGTCTTGCTCACCA 62.112 60.000 0.00 0.00 35.35 4.17
4729 6366 2.046892 CCGGGTCTTGCTCACCAG 60.047 66.667 0.00 0.00 35.35 4.00
4847 6601 1.607251 CGGAACAGTAACCACCACCTC 60.607 57.143 0.00 0.00 0.00 3.85
4868 6622 1.477558 CCTGCAGGAAGGTGTTGAACT 60.478 52.381 29.88 0.00 37.39 3.01
4954 6709 1.399089 GTGTAGTCCTCGTCTCTGAGC 59.601 57.143 0.00 0.00 34.56 4.26
4956 6711 1.399089 GTAGTCCTCGTCTCTGAGCAC 59.601 57.143 0.00 0.00 34.56 4.40
4969 6724 3.293901 GAGCACGACAGCTGCCTCT 62.294 63.158 15.27 3.87 46.75 3.69
4995 6750 3.550992 CGCGTGGCCGTGTGTATC 61.551 66.667 0.00 0.00 39.68 2.24
5061 6816 1.102978 GTTTGGCCGGACTGCATATT 58.897 50.000 9.82 0.00 0.00 1.28
5062 6817 2.294074 GTTTGGCCGGACTGCATATTA 58.706 47.619 9.82 0.00 0.00 0.98
5063 6818 2.884639 GTTTGGCCGGACTGCATATTAT 59.115 45.455 9.82 0.00 0.00 1.28
5096 6851 1.707427 ACTGGAGTTCTGAATTGGCCT 59.293 47.619 3.32 0.00 0.00 5.19
5120 6893 1.017177 GCATTTGGACGGTCGCTGTA 61.017 55.000 1.43 0.00 0.00 2.74
5142 6915 8.400184 TGTATGGTTATGTCTACTATAGCGTT 57.600 34.615 0.00 0.00 0.00 4.84
5143 6916 9.506018 TGTATGGTTATGTCTACTATAGCGTTA 57.494 33.333 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.304928 CCTGAAATCAGCACACCAAACTC 60.305 47.826 4.87 0.00 42.47 3.01
1 2 2.624838 CCTGAAATCAGCACACCAAACT 59.375 45.455 4.87 0.00 42.47 2.66
2 3 2.288395 CCCTGAAATCAGCACACCAAAC 60.288 50.000 4.87 0.00 42.47 2.93
3 4 1.962807 CCCTGAAATCAGCACACCAAA 59.037 47.619 4.87 0.00 42.47 3.28
4 5 1.619654 CCCTGAAATCAGCACACCAA 58.380 50.000 4.87 0.00 42.47 3.67
5 6 0.251297 CCCCTGAAATCAGCACACCA 60.251 55.000 4.87 0.00 42.47 4.17
6 7 0.251341 ACCCCTGAAATCAGCACACC 60.251 55.000 4.87 0.00 42.47 4.16
7 8 1.620822 AACCCCTGAAATCAGCACAC 58.379 50.000 4.87 0.00 42.47 3.82
8 9 2.380064 AAACCCCTGAAATCAGCACA 57.620 45.000 4.87 0.00 42.47 4.57
9 10 4.706962 AGATTAAACCCCTGAAATCAGCAC 59.293 41.667 4.87 0.00 42.47 4.40
10 11 4.934356 AGATTAAACCCCTGAAATCAGCA 58.066 39.130 4.87 0.00 42.47 4.41
11 12 5.418840 TGAAGATTAAACCCCTGAAATCAGC 59.581 40.000 4.87 0.00 42.47 4.26
12 13 6.096001 CCTGAAGATTAAACCCCTGAAATCAG 59.904 42.308 3.37 3.37 43.40 2.90
13 14 5.951747 CCTGAAGATTAAACCCCTGAAATCA 59.048 40.000 0.00 0.00 32.04 2.57
25 26 7.001099 ACTAAGTCGAACCCTGAAGATTAAA 57.999 36.000 0.00 0.00 0.00 1.52
27 28 6.600882 AACTAAGTCGAACCCTGAAGATTA 57.399 37.500 0.00 0.00 0.00 1.75
31 32 5.054477 TGAAAACTAAGTCGAACCCTGAAG 58.946 41.667 0.00 0.00 0.00 3.02
63 64 5.241662 TGAAAAAGTCCAAAACAAACCCTG 58.758 37.500 0.00 0.00 0.00 4.45
64 65 5.491323 TGAAAAAGTCCAAAACAAACCCT 57.509 34.783 0.00 0.00 0.00 4.34
65 66 6.561737 TTTGAAAAAGTCCAAAACAAACCC 57.438 33.333 0.00 0.00 30.29 4.11
96 99 9.892444 TCTATCCCTACCATCTGTTTAATTCTA 57.108 33.333 0.00 0.00 0.00 2.10
98 101 8.871125 TCTCTATCCCTACCATCTGTTTAATTC 58.129 37.037 0.00 0.00 0.00 2.17
100 103 8.652290 GTTCTCTATCCCTACCATCTGTTTAAT 58.348 37.037 0.00 0.00 0.00 1.40
101 104 7.201884 CGTTCTCTATCCCTACCATCTGTTTAA 60.202 40.741 0.00 0.00 0.00 1.52
102 105 6.264744 CGTTCTCTATCCCTACCATCTGTTTA 59.735 42.308 0.00 0.00 0.00 2.01
103 106 5.069251 CGTTCTCTATCCCTACCATCTGTTT 59.931 44.000 0.00 0.00 0.00 2.83
104 107 4.585162 CGTTCTCTATCCCTACCATCTGTT 59.415 45.833 0.00 0.00 0.00 3.16
105 108 4.145807 CGTTCTCTATCCCTACCATCTGT 58.854 47.826 0.00 0.00 0.00 3.41
106 109 4.145807 ACGTTCTCTATCCCTACCATCTG 58.854 47.826 0.00 0.00 0.00 2.90
107 110 4.141228 TGACGTTCTCTATCCCTACCATCT 60.141 45.833 0.00 0.00 0.00 2.90
110 113 3.285484 GTGACGTTCTCTATCCCTACCA 58.715 50.000 0.00 0.00 0.00 3.25
116 119 1.132643 AGCGTGTGACGTTCTCTATCC 59.867 52.381 0.00 0.00 44.73 2.59
160 163 2.359478 AATCGGGTGTGGTTCGGC 60.359 61.111 0.00 0.00 0.00 5.54
204 207 1.269448 GCACGAATTGGTGGTGTGAAT 59.731 47.619 20.36 0.00 38.36 2.57
232 239 2.443887 TTAATACGGTCCGGCTATGC 57.556 50.000 17.28 0.00 0.00 3.14
233 240 2.735134 GCTTTAATACGGTCCGGCTATG 59.265 50.000 17.28 0.67 0.00 2.23
324 331 2.687566 GGGGGAGGAAGGCGAAGA 60.688 66.667 0.00 0.00 0.00 2.87
325 332 4.162690 CGGGGGAGGAAGGCGAAG 62.163 72.222 0.00 0.00 0.00 3.79
469 479 0.598562 GATCGAGCAGGAATCGGCTA 59.401 55.000 0.00 0.00 44.15 3.93
558 568 0.461339 CCACGAATCTAACCACCCCG 60.461 60.000 0.00 0.00 0.00 5.73
598 608 5.461526 GCAAATCAAGTTAAACCACTCCTC 58.538 41.667 0.00 0.00 0.00 3.71
601 611 5.195001 TGGCAAATCAAGTTAAACCACTC 57.805 39.130 0.00 0.00 0.00 3.51
839 849 3.766545 AGAAAGGCAGCACATTTAAGGA 58.233 40.909 0.00 0.00 0.00 3.36
840 850 4.525912 AAGAAAGGCAGCACATTTAAGG 57.474 40.909 0.00 0.00 0.00 2.69
864 874 0.951558 AACATCGGTTGGCAAGTGAC 59.048 50.000 0.00 0.00 35.46 3.67
907 920 5.707298 TCCAACATTTTTGCCAAAAGAAACA 59.293 32.000 2.46 0.00 35.30 2.83
932 945 8.729805 ATCTCCAAGAGATAAAAGCACTAAAG 57.270 34.615 5.30 0.00 46.15 1.85
954 967 7.071698 TGGGAGATAACAGCTTAAATGAGATCT 59.928 37.037 0.00 0.00 0.00 2.75
960 973 5.684704 TCCTGGGAGATAACAGCTTAAATG 58.315 41.667 0.00 0.00 33.43 2.32
970 983 1.213296 TGGGCTTCCTGGGAGATAAC 58.787 55.000 6.06 0.00 0.00 1.89
972 985 2.212752 AATGGGCTTCCTGGGAGATA 57.787 50.000 6.06 0.00 0.00 1.98
1158 1171 1.339610 ACATACAAAAGCGCTTGCCAA 59.660 42.857 25.80 10.68 40.41 4.52
1164 1177 1.737793 GTAGGCACATACAAAAGCGCT 59.262 47.619 2.64 2.64 0.00 5.92
1167 1180 4.385748 GCAAAAGTAGGCACATACAAAAGC 59.614 41.667 0.00 0.00 0.00 3.51
1171 1184 6.432783 ACAATAGCAAAAGTAGGCACATACAA 59.567 34.615 0.00 0.00 0.00 2.41
1216 1229 2.160417 ACTGCGCAAGATACAAAGAAGC 59.840 45.455 13.05 0.00 43.02 3.86
1469 1489 4.759782 AGTGCATGACTATTTAACTCGCT 58.240 39.130 0.00 0.00 30.86 4.93
1471 1491 5.807520 AGTGAGTGCATGACTATTTAACTCG 59.192 40.000 0.00 0.00 36.26 4.18
1714 1734 6.291377 AGCACAATAACAGAAGAAAGACAGA 58.709 36.000 0.00 0.00 0.00 3.41
1725 1745 6.647334 TCCAAATTTGAGCACAATAACAGA 57.353 33.333 19.86 0.62 35.85 3.41
1727 1747 5.221402 TGCTCCAAATTTGAGCACAATAACA 60.221 36.000 27.08 12.45 45.62 2.41
1756 1776 9.945904 AATTCCTTCCTTAAGAAAGTAGTACTG 57.054 33.333 5.39 0.00 34.37 2.74
1785 1808 7.769044 ACACCAGATAACCATGTATACTTTGTC 59.231 37.037 4.17 1.17 0.00 3.18
1805 1830 8.424918 AGTCAGAGGTAATGATATTAACACCAG 58.575 37.037 0.10 0.00 0.00 4.00
1816 1841 5.934625 GTGTCACAAAGTCAGAGGTAATGAT 59.065 40.000 0.00 0.00 0.00 2.45
1827 1852 2.677836 GCAGAACTGTGTCACAAAGTCA 59.322 45.455 0.00 0.00 29.55 3.41
1846 1872 9.276590 CATCATGGTTTTATATTAGACAGAGCA 57.723 33.333 0.00 0.00 0.00 4.26
1917 1943 7.555554 AGGATCTCTTTCACCACAATATTTCAG 59.444 37.037 0.00 0.00 0.00 3.02
1928 1954 6.213397 TCTGAAACATAGGATCTCTTTCACCA 59.787 38.462 0.00 0.00 29.87 4.17
1943 1969 7.099764 TGCAAAACCAAGTTTTCTGAAACATA 58.900 30.769 1.58 0.00 46.01 2.29
2077 2105 3.942829 TCAACTTCTCGGCTGATGAAAT 58.057 40.909 0.00 0.00 0.00 2.17
2091 2119 4.983671 AAACAGGACAAGGTTCAACTTC 57.016 40.909 0.00 0.00 0.00 3.01
2115 2143 9.809096 TTGTACATACAACAAAAACATGTGAAT 57.191 25.926 0.00 0.00 40.93 2.57
2325 2356 5.648092 ACGATCCACCCTTCAATAAGAAAAG 59.352 40.000 0.00 0.00 35.40 2.27
2347 2378 7.470289 TTTTTATCACCAAAAATGGACAACG 57.530 32.000 1.10 0.00 33.57 4.10
2467 2498 4.284490 ACAGCCACTGAGAACAATAAGAGA 59.716 41.667 0.78 0.00 35.18 3.10
2502 2533 8.552034 CCCTTAAGAGCAAAAGAATAGAATACG 58.448 37.037 3.36 0.00 0.00 3.06
2543 2574 1.656652 AGTGTGCGCATATCAAGGAC 58.343 50.000 15.91 0.00 0.00 3.85
2558 2590 3.258622 GCTGACTACTAACTGGGAAGTGT 59.741 47.826 0.00 0.00 0.00 3.55
2571 2603 1.629043 TCTTTCCACCGCTGACTACT 58.371 50.000 0.00 0.00 0.00 2.57
2572 2604 2.029290 TCTTCTTTCCACCGCTGACTAC 60.029 50.000 0.00 0.00 0.00 2.73
2574 2606 1.048601 TCTTCTTTCCACCGCTGACT 58.951 50.000 0.00 0.00 0.00 3.41
2575 2607 1.878953 TTCTTCTTTCCACCGCTGAC 58.121 50.000 0.00 0.00 0.00 3.51
2599 2648 7.641411 CCATGAATAAAATCAAGTCACGTCATC 59.359 37.037 0.00 0.00 32.06 2.92
2680 2729 7.201732 CCATTTTAGCGACAACTAATTCCAGAT 60.202 37.037 0.00 0.00 32.35 2.90
2784 4406 2.039084 ACTCCACTTCCACTCCATCAAC 59.961 50.000 0.00 0.00 0.00 3.18
2806 4428 6.920758 TGTTACATGGCTATTTGTTTCAACAC 59.079 34.615 0.00 0.00 38.92 3.32
2814 4436 6.128007 GCAGTAGTTGTTACATGGCTATTTGT 60.128 38.462 0.00 0.00 34.56 2.83
2815 4437 6.094048 AGCAGTAGTTGTTACATGGCTATTTG 59.906 38.462 0.00 0.00 35.80 2.32
2817 4439 5.586243 CAGCAGTAGTTGTTACATGGCTATT 59.414 40.000 0.00 0.00 35.80 1.73
2953 4576 4.527564 CAGTACAAGTACAAGTTGCAAGC 58.472 43.478 12.43 0.00 38.48 4.01
2961 4584 3.393800 ACAGCTGCAGTACAAGTACAAG 58.606 45.455 15.27 7.89 38.48 3.16
3041 4664 5.888161 GGATCCCTTTCTGAATGTACAACAT 59.112 40.000 0.00 0.00 41.31 2.71
3243 4866 7.308435 CCTGGACAGATGAAGAATTACAAAAC 58.692 38.462 0.00 0.00 0.00 2.43
3471 5094 1.101331 TGTGTGCATGCAAGTGTTGA 58.899 45.000 24.58 0.00 0.00 3.18
3749 5372 5.451798 GCAAGGAAAAACAGATCCACAAGAA 60.452 40.000 0.00 0.00 38.23 2.52
4150 5773 1.532090 CCTTCGTCATCGTCTTCCTCG 60.532 57.143 0.00 0.00 38.33 4.63
4282 5905 5.389307 GCGCATCAGATCAGCTACTTTAATC 60.389 44.000 0.30 0.00 0.00 1.75
4343 5969 8.664079 AGGATGAATGATACTTTATGGCTAACT 58.336 33.333 0.00 0.00 0.00 2.24
4353 5979 7.099120 GCCAACAAAAGGATGAATGATACTTT 58.901 34.615 0.00 0.00 45.89 2.66
4423 6049 6.410540 ACCAAGTCTGAAATATCAAGGTCTC 58.589 40.000 0.00 0.00 34.49 3.36
4428 6054 5.711976 ACCCAACCAAGTCTGAAATATCAAG 59.288 40.000 0.00 0.00 34.49 3.02
4474 6100 5.131594 TGATTTCGTCATGGAAAATGCAA 57.868 34.783 0.00 0.00 39.19 4.08
4503 6129 9.252962 GCAGCACAAAGATTAAATAATAATGCT 57.747 29.630 0.00 0.00 0.00 3.79
4504 6130 9.252962 AGCAGCACAAAGATTAAATAATAATGC 57.747 29.630 0.00 0.00 0.00 3.56
4545 6177 8.420222 ACTGACAGATCTGATACAAATAGGAAG 58.580 37.037 29.27 12.37 0.00 3.46
4576 6208 3.250744 CACGTTCCAGTCATACAACGAT 58.749 45.455 9.81 0.00 43.39 3.73
4637 6270 2.032680 TCGCTTTACTATTGGTGCCC 57.967 50.000 0.00 0.00 0.00 5.36
4683 6316 4.309950 AGGAACGGTGGTGCGTCC 62.310 66.667 0.00 0.00 0.00 4.79
4705 6342 1.578206 GAGCAAGACCCGGAAGCAAC 61.578 60.000 0.73 0.00 0.00 4.17
4723 6360 3.936203 GGCCGTGGTGACTGGTGA 61.936 66.667 0.00 0.00 0.00 4.02
4829 6583 1.271217 GGGAGGTGGTGGTTACTGTTC 60.271 57.143 0.00 0.00 0.00 3.18
4847 6601 0.178992 TTCAACACCTTCCTGCAGGG 60.179 55.000 32.23 18.81 38.42 4.45
4868 6622 2.708216 TCAATCAATCGGGCTGCTTA 57.292 45.000 0.00 0.00 0.00 3.09
4954 6709 1.739562 GGAAGAGGCAGCTGTCGTG 60.740 63.158 16.64 0.00 0.00 4.35
4956 6711 0.603707 TTTGGAAGAGGCAGCTGTCG 60.604 55.000 16.64 0.00 0.00 4.35
4969 6724 2.975799 GGCCACGCGAGTTTGGAA 60.976 61.111 15.93 0.00 46.40 3.53
5023 6778 7.910683 GGCCAAACGATAATTTTCTTCTTCTAG 59.089 37.037 0.00 0.00 0.00 2.43
5024 6779 7.413657 CGGCCAAACGATAATTTTCTTCTTCTA 60.414 37.037 2.24 0.00 35.47 2.10
5025 6780 6.621613 GGCCAAACGATAATTTTCTTCTTCT 58.378 36.000 0.00 0.00 0.00 2.85
5042 6797 1.102978 AATATGCAGTCCGGCCAAAC 58.897 50.000 2.24 0.00 0.00 2.93
5061 6816 6.611642 AGAACTCCAGTTGTATAGGAAGCATA 59.388 38.462 0.00 0.00 38.56 3.14
5062 6817 5.426833 AGAACTCCAGTTGTATAGGAAGCAT 59.573 40.000 0.00 0.00 38.56 3.79
5063 6818 4.777896 AGAACTCCAGTTGTATAGGAAGCA 59.222 41.667 0.00 0.00 38.56 3.91
5069 6824 6.037610 GCCAATTCAGAACTCCAGTTGTATAG 59.962 42.308 0.00 0.00 38.56 1.31
5096 6851 1.602323 GACCGTCCAAATGCCACCA 60.602 57.895 0.00 0.00 0.00 4.17
5142 6915 3.591695 TGGATGGCTTGCATTGGTATA 57.408 42.857 0.00 0.00 0.00 1.47
5143 6916 2.457813 TGGATGGCTTGCATTGGTAT 57.542 45.000 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.