Multiple sequence alignment - TraesCS7D01G411500

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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 TraesCS7D01G411500 chr7D 100.000 6706 0 0 1 6706 530132818 530126113 0.000000e+00 12384.0
1 TraesCS7D01G411500 chr7D 85.600 125 17 1 311 434 503703328 503703204 5.460000e-26 130.0
2 TraesCS7D01G411500 chr7B 94.392 3263 103 25 2146 5372 568683034 568679816 0.000000e+00 4939.0
3 TraesCS7D01G411500 chr7B 90.096 1464 90 27 1 1423 568685430 568683981 0.000000e+00 1849.0
4 TraesCS7D01G411500 chr7B 91.867 750 29 9 5406 6138 568679813 568679079 0.000000e+00 1018.0
5 TraesCS7D01G411500 chr7B 93.056 576 25 9 6139 6706 568679013 568678445 0.000000e+00 828.0
6 TraesCS7D01G411500 chr7B 90.343 466 27 9 1508 1964 568683952 568683496 4.480000e-166 595.0
7 TraesCS7D01G411500 chr7B 89.437 142 8 5 2009 2148 568683338 568683202 8.940000e-39 172.0
8 TraesCS7D01G411500 chr7A 94.011 2104 69 14 3283 5372 610452834 610450774 0.000000e+00 3134.0
9 TraesCS7D01G411500 chr7A 90.333 2069 104 44 4 2005 610456173 610454134 0.000000e+00 2625.0
10 TraesCS7D01G411500 chr7A 95.659 1267 33 8 5406 6670 610450771 610449525 0.000000e+00 2015.0
11 TraesCS7D01G411500 chr7A 91.304 437 16 6 2009 2437 610454025 610453603 1.620000e-160 577.0
12 TraesCS7D01G411500 chr7A 85.819 409 30 15 2603 3006 610453541 610453156 6.260000e-110 409.0
13 TraesCS7D01G411500 chr7A 96.392 194 6 1 3086 3279 610453155 610452963 1.090000e-82 318.0
14 TraesCS7D01G411500 chr6B 79.082 196 38 3 24 218 717670563 717670756 1.520000e-26 132.0
15 TraesCS7D01G411500 chr6B 100.000 31 0 0 374 404 123634452 123634422 2.610000e-04 58.4
16 TraesCS7D01G411500 chr4B 75.581 258 58 4 1 257 500109643 500109896 9.130000e-24 122.0
17 TraesCS7D01G411500 chr4A 75.385 260 56 7 1 257 60889969 60890223 1.180000e-22 119.0
18 TraesCS7D01G411500 chrUn 78.109 201 31 12 24 218 311363888 311364081 1.530000e-21 115.0
19 TraesCS7D01G411500 chr2A 78.523 149 27 5 28 174 17827440 17827585 7.160000e-15 93.5
20 TraesCS7D01G411500 chr5D 75.000 220 43 9 3 219 329437410 329437620 2.580000e-14 91.6


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 TraesCS7D01G411500 chr7D 530126113 530132818 6705 True 12384.000000 12384 100.000000 1 6706 1 chr7D.!!$R2 6705
1 TraesCS7D01G411500 chr7B 568678445 568685430 6985 True 1566.833333 4939 91.531833 1 6706 6 chr7B.!!$R1 6705
2 TraesCS7D01G411500 chr7A 610449525 610456173 6648 True 1513.000000 3134 92.253000 4 6670 6 chr7A.!!$R1 6666

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
329 332 0.034337 AAGTTTGCTTCGCCGAGGTA 59.966 50.000 0.00 0.0 0.00 3.08 F
811 842 0.107214 GCCTTGATTCCATCGTCCCA 60.107 55.000 0.00 0.0 0.00 4.37 F
872 913 0.179026 TCCTCGTCTCCCTCCATACG 60.179 60.000 0.00 0.0 36.71 3.06 F
2719 3129 0.317854 TCGACACTTGCTGACTGACG 60.318 55.000 0.00 0.0 0.00 4.35 F
2909 3327 0.688487 TGGTAAGTACACACCCCAGC 59.312 55.000 12.03 0.0 33.61 4.85 F
4342 4891 1.205655 TCCTTTGCTCTGATCCACGAG 59.794 52.381 0.00 0.0 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1622 1710 1.033574 GATCCGACAATCTCCCGTCT 58.966 55.000 0.00 0.0 0.00 4.18 R
2783 3193 0.103572 TCACCGCGGCCTCTATTAAC 59.896 55.000 28.58 0.0 0.00 2.01 R
2893 3303 1.202769 GGGGCTGGGGTGTGTACTTA 61.203 60.000 0.00 0.0 0.00 2.24 R
4202 4751 2.297701 GTGCTTTCCAGAAACCTGTCA 58.702 47.619 0.00 0.0 0.00 3.58 R
4805 5381 0.039256 CTGCAAACATGTTGGTCCCG 60.039 55.000 12.82 0.0 0.00 5.14 R
6080 6674 1.000163 TCACAGTCCGAGCAGACTTTC 60.000 52.381 1.68 0.0 44.83 2.62 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
90 92 2.390599 CCCGTTGGTGTGCTCATCG 61.391 63.158 0.00 0.00 0.00 3.84
113 115 3.311110 GGAGGGCGTGTGGAGTCA 61.311 66.667 0.00 0.00 0.00 3.41
156 158 3.684788 AGATCCGAGTGATTTGGTTTTCG 59.315 43.478 0.00 0.00 32.41 3.46
212 215 1.886886 TCAAAGTTTCTACACGCCCC 58.113 50.000 0.00 0.00 0.00 5.80
216 219 3.538634 AAGTTTCTACACGCCCCTATC 57.461 47.619 0.00 0.00 0.00 2.08
237 240 3.055458 TCGGTGTATTCTTCTTCATGGCA 60.055 43.478 0.00 0.00 0.00 4.92
262 265 4.595762 ATTTGCTTTGCAGATCACAGTT 57.404 36.364 0.00 0.00 40.61 3.16
319 322 2.418060 CCGGGTTCAAACAAGTTTGCTT 60.418 45.455 18.29 0.00 46.92 3.91
328 331 1.227853 AAGTTTGCTTCGCCGAGGT 60.228 52.632 0.00 0.00 0.00 3.85
329 332 0.034337 AAGTTTGCTTCGCCGAGGTA 59.966 50.000 0.00 0.00 0.00 3.08
692 719 1.407656 TTCGCCTGGTCCAACTGACT 61.408 55.000 0.00 0.00 43.89 3.41
811 842 0.107214 GCCTTGATTCCATCGTCCCA 60.107 55.000 0.00 0.00 0.00 4.37
865 906 1.562783 CTTTTCCTCCTCGTCTCCCT 58.437 55.000 0.00 0.00 0.00 4.20
872 913 0.179026 TCCTCGTCTCCCTCCATACG 60.179 60.000 0.00 0.00 36.71 3.06
888 929 6.161855 TCCATACGAGTCAAATCATAAGCT 57.838 37.500 0.00 0.00 0.00 3.74
892 933 7.116948 CCATACGAGTCAAATCATAAGCTTAGG 59.883 40.741 11.88 11.88 0.00 2.69
893 934 6.222038 ACGAGTCAAATCATAAGCTTAGGA 57.778 37.500 21.90 21.90 0.00 2.94
965 1030 4.173043 ACAAATATACCCCTCCCTCTCTCT 59.827 45.833 0.00 0.00 0.00 3.10
1041 1106 2.046507 CTCCCTCACAGCCACAGC 60.047 66.667 0.00 0.00 40.32 4.40
1215 1280 2.672996 CCAACAAGGCCGGTGAGG 60.673 66.667 15.55 12.25 44.97 3.86
1325 1393 1.227853 AAGCTTCCGGTTCGTGCTT 60.228 52.632 0.00 8.68 38.88 3.91
1363 1434 2.686118 GCCAGCTTTGGAATGATCCTCT 60.686 50.000 0.00 0.00 46.70 3.69
1394 1470 3.886505 TGTGGTTTTACCCATGTGAGTTC 59.113 43.478 0.00 0.00 37.50 3.01
1398 1474 4.394729 GTTTTACCCATGTGAGTTCCTGA 58.605 43.478 0.00 0.00 0.00 3.86
1482 1560 3.945640 AATGGTAACGGAGCCCTATTT 57.054 42.857 0.00 0.00 42.51 1.40
1492 1570 5.308825 ACGGAGCCCTATTTTGATGATAAG 58.691 41.667 0.00 0.00 0.00 1.73
1541 1626 0.456142 TCACGATCTTTGCCTCGACG 60.456 55.000 0.00 0.00 38.24 5.12
1555 1640 2.107141 GACGAGGAAGATGGCCGG 59.893 66.667 0.00 0.00 0.00 6.13
1622 1710 7.475137 TGGAAGGTCTTTTTCTTTTTCAGAA 57.525 32.000 0.00 0.00 39.99 3.02
1623 1711 7.547227 TGGAAGGTCTTTTTCTTTTTCAGAAG 58.453 34.615 0.00 0.00 42.76 2.85
1624 1712 7.396055 TGGAAGGTCTTTTTCTTTTTCAGAAGA 59.604 33.333 0.00 0.00 42.76 2.87
1625 1713 7.702772 GGAAGGTCTTTTTCTTTTTCAGAAGAC 59.297 37.037 5.69 5.69 42.76 3.01
1633 1721 5.228945 TCTTTTTCAGAAGACGGGAGATT 57.771 39.130 0.00 0.00 30.98 2.40
1657 1747 5.243283 TGTCGGATCTAGGGAGTATAAAAGC 59.757 44.000 0.00 0.00 0.00 3.51
1666 1756 3.451526 GGAGTATAAAAGCCGCTACGTT 58.548 45.455 0.00 0.00 0.00 3.99
1686 1776 4.258860 CGTTGACAAAAGAAAAGTTCGTGC 60.259 41.667 0.00 0.00 34.02 5.34
1698 1792 3.202829 AGTTCGTGCTTAAGTTGGGAA 57.797 42.857 4.02 0.92 0.00 3.97
1701 1795 4.583073 AGTTCGTGCTTAAGTTGGGAAAAT 59.417 37.500 4.02 0.00 0.00 1.82
1926 2024 3.248363 TGATCACGTAATGCTATGCTTGC 59.752 43.478 0.00 0.00 0.00 4.01
1974 2072 3.258123 ACGGCAAATTTTCTACCATTGCT 59.742 39.130 8.47 0.00 44.30 3.91
2023 2253 1.979855 TGCCCCACATGCATGTATAC 58.020 50.000 30.92 20.06 39.39 1.47
2074 2304 6.774656 AGATTAGTGATGGCAGAATAAAAGGG 59.225 38.462 0.00 0.00 0.00 3.95
2099 2329 7.857885 GGAAAATATCAGACGATCAAACCAATC 59.142 37.037 0.00 0.00 32.73 2.67
2119 2349 7.994911 ACCAATCTGATAATATGTTGAAGAGCA 59.005 33.333 0.00 0.00 0.00 4.26
2123 2353 9.887629 ATCTGATAATATGTTGAAGAGCATAGG 57.112 33.333 0.00 0.00 32.02 2.57
2222 2621 1.539496 GGCCATAACTTGCCGATCGTA 60.539 52.381 15.09 0.00 38.00 3.43
2223 2622 2.413837 GCCATAACTTGCCGATCGTAT 58.586 47.619 15.09 0.99 0.00 3.06
2224 2623 3.581755 GCCATAACTTGCCGATCGTATA 58.418 45.455 15.09 0.00 0.00 1.47
2225 2624 3.991773 GCCATAACTTGCCGATCGTATAA 59.008 43.478 15.09 5.16 0.00 0.98
2226 2625 4.143179 GCCATAACTTGCCGATCGTATAAC 60.143 45.833 15.09 0.00 0.00 1.89
2227 2626 4.986034 CCATAACTTGCCGATCGTATAACA 59.014 41.667 15.09 1.24 0.00 2.41
2338 2746 6.097554 TGGTAATGGACAAGTCAAACAAACAT 59.902 34.615 2.29 0.00 0.00 2.71
2440 2848 5.008415 GGCACTGATCAGATTTTTCGATGAT 59.992 40.000 29.27 0.00 35.16 2.45
2507 2915 7.340487 TGAGCTATCTCAGAAACAATGACTAGA 59.660 37.037 0.00 0.00 43.95 2.43
2520 2928 2.793933 TGACTAGACACGCGAATTAGC 58.206 47.619 15.93 0.00 0.00 3.09
2526 2934 1.252015 GACACGCGAATTAGCACGTAG 59.748 52.381 15.93 0.00 36.91 3.51
2542 2950 1.952296 CGTAGCTATGACGTACCCCTT 59.048 52.381 7.19 0.00 35.58 3.95
2592 3000 8.801882 TGGTACCCAAGAAAAAGTAGATATTG 57.198 34.615 10.07 0.00 0.00 1.90
2620 3028 3.358118 AGACTAGCTAGAGGAAAGCGTT 58.642 45.455 27.45 0.00 44.87 4.84
2626 3034 5.441709 AGCTAGAGGAAAGCGTTAGTATC 57.558 43.478 0.00 0.00 44.87 2.24
2702 3112 3.377172 GTGGTCCAAATTAAGGATGGTCG 59.623 47.826 0.00 0.00 37.52 4.79
2719 3129 0.317854 TCGACACTTGCTGACTGACG 60.318 55.000 0.00 0.00 0.00 4.35
2734 3144 4.864247 TGACTGACGTGAACATCATGTATG 59.136 41.667 5.26 4.59 45.80 2.39
2783 3193 1.824852 GGAAAACATGGCTACCAAGGG 59.175 52.381 0.00 0.00 36.95 3.95
2893 3303 3.002791 CAAGCTACATCGTCACAATGGT 58.997 45.455 0.00 0.00 0.00 3.55
2902 3320 4.587584 TCGTCACAATGGTAAGTACACA 57.412 40.909 0.00 0.00 0.00 3.72
2903 3321 4.300803 TCGTCACAATGGTAAGTACACAC 58.699 43.478 0.00 0.00 0.00 3.82
2904 3322 3.430895 CGTCACAATGGTAAGTACACACC 59.569 47.826 8.57 8.57 35.24 4.16
2905 3323 3.749609 GTCACAATGGTAAGTACACACCC 59.250 47.826 12.03 0.00 33.61 4.61
2906 3324 3.078837 CACAATGGTAAGTACACACCCC 58.921 50.000 12.03 0.00 33.61 4.95
2907 3325 2.712087 ACAATGGTAAGTACACACCCCA 59.288 45.455 12.03 3.48 33.61 4.96
2908 3326 3.244770 ACAATGGTAAGTACACACCCCAG 60.245 47.826 12.03 5.61 33.61 4.45
2909 3327 0.688487 TGGTAAGTACACACCCCAGC 59.312 55.000 12.03 0.00 33.61 4.85
2959 3377 2.569059 TCAGATTTCAGCTGGCTATGC 58.431 47.619 15.13 0.00 34.20 3.14
2977 3395 5.513094 GCTATGCTATCCCACCAGTGATTTA 60.513 44.000 0.00 0.00 0.00 1.40
2978 3396 5.589367 ATGCTATCCCACCAGTGATTTAT 57.411 39.130 0.00 0.00 0.00 1.40
2979 3397 5.387113 TGCTATCCCACCAGTGATTTATT 57.613 39.130 0.00 0.00 0.00 1.40
2980 3398 5.765510 TGCTATCCCACCAGTGATTTATTT 58.234 37.500 0.00 0.00 0.00 1.40
3061 3479 6.770303 TCAAATTTAAAGGCCTTCTTTTTGGG 59.230 34.615 26.32 14.13 42.62 4.12
3071 3490 2.692709 TCTTTTTGGGCATGGAGGAA 57.307 45.000 0.00 0.00 0.00 3.36
3662 4207 7.282450 GGTAATTCAATCATAACCGAGGAACTT 59.718 37.037 0.00 0.00 41.55 2.66
3998 4547 2.371841 ACACTCCACAAACTGCCTATGA 59.628 45.455 0.00 0.00 0.00 2.15
4005 4554 4.818546 CCACAAACTGCCTATGAGAATAGG 59.181 45.833 7.32 7.32 45.05 2.57
4051 4600 7.823745 AAGAAGAAATGAAAAGTAAGAGGCA 57.176 32.000 0.00 0.00 0.00 4.75
4066 4615 2.756760 AGAGGCAAATGCAACATACCAG 59.243 45.455 7.80 0.00 44.36 4.00
4078 4627 4.383770 GCAACATACCAGTACTACCCATGT 60.384 45.833 0.00 0.54 0.00 3.21
4104 4653 5.249622 TGAGACACTATCCCAATTAACACCA 59.750 40.000 0.00 0.00 0.00 4.17
4286 4835 5.569355 TCCCAGAAGTTTATGCAAGATTCA 58.431 37.500 0.00 0.00 0.00 2.57
4342 4891 1.205655 TCCTTTGCTCTGATCCACGAG 59.794 52.381 0.00 0.00 0.00 4.18
4382 4931 4.403113 TGAGTATATCAGTGGGTACGCAAA 59.597 41.667 14.92 3.87 32.77 3.68
4391 4940 3.066203 AGTGGGTACGCAAAAACTGAAAG 59.934 43.478 14.92 0.00 42.29 2.62
4418 4967 7.837202 AATCGGTTCGAATACAAGTGAAATA 57.163 32.000 0.00 0.00 39.99 1.40
4501 5050 8.515414 ACTTAAGATATTGAAACCTGAAAGTGC 58.485 33.333 10.09 0.00 0.00 4.40
4509 5058 6.899393 TGAAACCTGAAAGTGCATCTTAAT 57.101 33.333 0.00 0.00 35.02 1.40
4583 5135 6.017934 TGTTGACTTCAGTGAACTTAGAATGC 60.018 38.462 10.15 0.00 41.63 3.56
4674 5226 7.450014 TGAAGGGAAATGTTAACTCAAAGCATA 59.550 33.333 7.22 0.00 0.00 3.14
4750 5319 7.015064 GGACCTTTCCATCTATACCTAGGTTA 58.985 42.308 22.11 11.20 42.30 2.85
4805 5381 1.070134 GGGAACAAAAAGGGTTGGAGC 59.930 52.381 0.00 0.00 32.50 4.70
4868 5444 4.265856 TGGACAGAAATAGGGCTAGAGA 57.734 45.455 0.00 0.00 0.00 3.10
4874 5450 4.656112 CAGAAATAGGGCTAGAGAAAGGGA 59.344 45.833 0.00 0.00 0.00 4.20
4888 5464 1.504275 AAGGGAGGCTGGCAGACAAT 61.504 55.000 24.81 1.34 0.00 2.71
4986 5562 5.535333 CAGGGCCATCATGTTTCAAATATC 58.465 41.667 6.18 0.00 0.00 1.63
4987 5563 5.069383 CAGGGCCATCATGTTTCAAATATCA 59.931 40.000 6.18 0.00 0.00 2.15
4988 5564 5.069516 AGGGCCATCATGTTTCAAATATCAC 59.930 40.000 6.18 0.00 0.00 3.06
4989 5565 5.069516 GGGCCATCATGTTTCAAATATCACT 59.930 40.000 4.39 0.00 0.00 3.41
4990 5566 6.265196 GGGCCATCATGTTTCAAATATCACTA 59.735 38.462 4.39 0.00 0.00 2.74
4991 5567 7.039504 GGGCCATCATGTTTCAAATATCACTAT 60.040 37.037 4.39 0.00 0.00 2.12
4992 5568 9.013229 GGCCATCATGTTTCAAATATCACTATA 57.987 33.333 0.00 0.00 0.00 1.31
5151 5727 2.749621 CACCCAACTAGGATCAACTTGC 59.250 50.000 0.00 0.00 41.22 4.01
5190 5766 4.624452 GCATGATTCTCCTTTTGTGCTTTC 59.376 41.667 0.00 0.00 0.00 2.62
5286 5862 3.136443 TGGGGCTTCACTCCTGTATATTG 59.864 47.826 0.00 0.00 0.00 1.90
5330 5906 1.270550 GTCTGATGCCCACAAAACCAG 59.729 52.381 0.00 0.00 0.00 4.00
5344 5920 8.408601 CCCACAAAACCAGATAATCTATTCTTG 58.591 37.037 0.00 0.00 0.00 3.02
5387 5963 9.771534 TTATTTGAAATTAAAAACCCACAGAGG 57.228 29.630 0.00 0.00 37.03 3.69
5442 6018 8.152898 CCCTTAAGGCCGTTACTAGTTAATTAT 58.847 37.037 16.70 0.00 0.00 1.28
5443 6019 8.985805 CCTTAAGGCCGTTACTAGTTAATTATG 58.014 37.037 9.00 0.00 0.00 1.90
5444 6020 9.538508 CTTAAGGCCGTTACTAGTTAATTATGT 57.461 33.333 0.00 0.00 0.00 2.29
5447 6023 9.485206 AAGGCCGTTACTAGTTAATTATGTATG 57.515 33.333 0.00 0.00 0.00 2.39
5625 6210 6.457392 CCCAAATGAGACATTCAACATACTCG 60.457 42.308 0.00 0.00 39.77 4.18
6080 6674 6.486657 TGGTTCAATCTTTGTAAGACCAAGAG 59.513 38.462 0.00 0.00 41.01 2.85
6109 6703 3.244422 TGCTCGGACTGTGAAGGTTAAAT 60.244 43.478 0.00 0.00 0.00 1.40
6196 6855 2.408271 TTGGTAGATGGCAAGAGCAG 57.592 50.000 0.00 0.00 44.61 4.24
6276 6935 9.778741 CCTTCATAATACTACTCCATTTTGCTA 57.221 33.333 0.00 0.00 0.00 3.49
6296 6955 9.893305 TTTGCTATTTCTTTAGTTTCTTGTAGC 57.107 29.630 0.00 0.00 33.37 3.58
6479 7140 5.583854 TCTGTTTTGAAGAGCAGCATATCTC 59.416 40.000 0.00 0.00 0.00 2.75
6569 7232 7.148188 CCAGCAAGAAATAAATAGAGAAGTGCA 60.148 37.037 0.00 0.00 0.00 4.57
6571 7234 6.684555 GCAAGAAATAAATAGAGAAGTGCACG 59.315 38.462 12.01 0.00 0.00 5.34
6626 7289 1.115467 CCATGGAAGAGCCTAGTCGT 58.885 55.000 5.56 0.00 37.63 4.34
6630 7293 1.654954 GGAAGAGCCTAGTCGTGCGA 61.655 60.000 0.00 0.00 0.00 5.10
6631 7294 0.382515 GAAGAGCCTAGTCGTGCGAT 59.617 55.000 0.00 0.00 0.00 4.58
6632 7295 0.382515 AAGAGCCTAGTCGTGCGATC 59.617 55.000 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
113 115 2.232941 TCGAAAGACCCGCTAGAAACAT 59.767 45.455 0.00 0.00 33.31 2.71
141 143 4.399303 GGATCCATCGAAAACCAAATCACT 59.601 41.667 6.95 0.00 0.00 3.41
212 215 5.406780 GCCATGAAGAAGAATACACCGATAG 59.593 44.000 0.00 0.00 0.00 2.08
216 219 3.270027 TGCCATGAAGAAGAATACACCG 58.730 45.455 0.00 0.00 0.00 4.94
257 260 0.321653 GGGAAGACGCCATCAACTGT 60.322 55.000 0.00 0.00 0.00 3.55
262 265 4.467084 GCCGGGAAGACGCCATCA 62.467 66.667 2.18 0.00 0.00 3.07
370 373 4.552365 CCGCCTGCATCCACCGAT 62.552 66.667 0.00 0.00 0.00 4.18
449 459 7.670364 GCCCAAAGCCATAAATTAAGTATCAT 58.330 34.615 0.00 0.00 34.35 2.45
692 719 3.073062 GCCTATTGATGCTCCCTCCTTTA 59.927 47.826 0.00 0.00 0.00 1.85
730 757 0.319383 ACAAGAGCGAGCTGTGTCAG 60.319 55.000 0.84 0.00 34.12 3.51
811 842 2.440599 GGGGCATCTTGGTGTGGT 59.559 61.111 0.00 0.00 0.00 4.16
865 906 6.161855 AGCTTATGATTTGACTCGTATGGA 57.838 37.500 0.00 0.00 0.00 3.41
893 934 9.326413 CGAAGGAGTATTTGTAGGATGTTAATT 57.674 33.333 0.00 0.00 0.00 1.40
965 1030 4.079253 TCTAGCTATGAGTGTGTGTGTGA 58.921 43.478 0.00 0.00 0.00 3.58
1314 1382 1.556564 ATACGATCAAGCACGAACCG 58.443 50.000 0.00 0.00 0.00 4.44
1325 1393 5.793817 AGCTGGCAAATATGTATACGATCA 58.206 37.500 0.00 0.00 0.00 2.92
1363 1434 5.522315 TGGGTAAAACCACATGAAGGATA 57.478 39.130 14.40 3.87 41.02 2.59
1394 1470 2.981898 TGTCTCTTCACATGCATCAGG 58.018 47.619 0.00 0.00 0.00 3.86
1398 1474 8.743085 ATAAAACTATGTCTCTTCACATGCAT 57.257 30.769 0.00 0.00 37.57 3.96
1456 1534 3.394606 AGGGCTCCGTTACCATTAATGAT 59.605 43.478 17.23 1.50 0.00 2.45
1466 1544 4.448210 TCATCAAAATAGGGCTCCGTTAC 58.552 43.478 0.00 0.00 0.00 2.50
1482 1560 1.405105 GGCGGCTTTGCTTATCATCAA 59.595 47.619 0.00 0.00 34.52 2.57
1541 1626 4.918201 CGGCCGGCCATCTTCCTC 62.918 72.222 42.78 14.89 35.37 3.71
1596 1681 7.547227 TCTGAAAAAGAAAAAGACCTTCCAAG 58.453 34.615 0.00 0.00 29.54 3.61
1622 1710 1.033574 GATCCGACAATCTCCCGTCT 58.966 55.000 0.00 0.00 0.00 4.18
1623 1711 1.033574 AGATCCGACAATCTCCCGTC 58.966 55.000 0.00 0.00 29.89 4.79
1624 1712 2.231529 CTAGATCCGACAATCTCCCGT 58.768 52.381 0.00 0.00 37.24 5.28
1625 1713 1.542030 CCTAGATCCGACAATCTCCCG 59.458 57.143 0.00 0.00 37.24 5.14
1633 1721 5.243283 GCTTTTATACTCCCTAGATCCGACA 59.757 44.000 0.00 0.00 0.00 4.35
1657 1747 3.595709 TTTCTTTTGTCAACGTAGCGG 57.404 42.857 0.00 0.00 0.00 5.52
1666 1756 4.695217 AGCACGAACTTTTCTTTTGTCA 57.305 36.364 0.00 0.00 0.00 3.58
1686 1776 9.855021 ACGATCATTTTATTTTCCCAACTTAAG 57.145 29.630 0.00 0.00 0.00 1.85
1926 2024 1.659098 GTACGGACGAAAGCATCAAGG 59.341 52.381 0.00 0.00 0.00 3.61
1987 2108 8.664669 TGTGGGGCATATATGATCGTATATAT 57.335 34.615 21.74 11.68 36.91 0.86
2004 2224 1.213926 TGTATACATGCATGTGGGGCA 59.786 47.619 36.72 26.04 46.66 5.36
2023 2253 6.576313 CGAGTGAATTTTGTTCTCTCACATTG 59.424 38.462 15.72 0.00 39.08 2.82
2061 2291 7.857885 CGTCTGATATTTTCCCTTTTATTCTGC 59.142 37.037 0.00 0.00 0.00 4.26
2074 2304 8.616076 AGATTGGTTTGATCGTCTGATATTTTC 58.384 33.333 0.00 0.00 34.09 2.29
2222 2621 7.088589 GTGCACCTCACATTCTTATTGTTAT 57.911 36.000 5.22 0.00 44.98 1.89
2223 2622 6.494893 GTGCACCTCACATTCTTATTGTTA 57.505 37.500 5.22 0.00 44.98 2.41
2224 2623 5.376854 GTGCACCTCACATTCTTATTGTT 57.623 39.130 5.22 0.00 44.98 2.83
2338 2746 2.163412 GGCGAAACCATTTGCTACATGA 59.837 45.455 0.00 0.00 44.14 3.07
2440 2848 1.253100 TCGCATGTCTAGTCACACCA 58.747 50.000 0.00 0.00 0.00 4.17
2470 2878 3.432051 ATAGCTCACCACTCGCGCC 62.432 63.158 0.00 0.00 0.00 6.53
2526 2934 4.763073 ACTAAAAAGGGGTACGTCATAGC 58.237 43.478 0.00 0.00 0.00 2.97
2542 2950 4.674475 GACGAACTGGGCAAAAACTAAAA 58.326 39.130 0.00 0.00 0.00 1.52
2597 3005 4.131596 ACGCTTTCCTCTAGCTAGTCTAG 58.868 47.826 20.10 10.43 44.90 2.43
2598 3006 4.153673 ACGCTTTCCTCTAGCTAGTCTA 57.846 45.455 20.10 4.32 36.49 2.59
2599 3007 3.007473 ACGCTTTCCTCTAGCTAGTCT 57.993 47.619 20.10 0.00 36.49 3.24
2600 3008 3.786516 AACGCTTTCCTCTAGCTAGTC 57.213 47.619 20.10 2.31 36.49 2.59
2601 3009 4.271661 ACTAACGCTTTCCTCTAGCTAGT 58.728 43.478 20.10 0.00 36.49 2.57
2602 3010 4.904253 ACTAACGCTTTCCTCTAGCTAG 57.096 45.455 15.01 15.01 36.49 3.42
2603 3011 6.060136 TGATACTAACGCTTTCCTCTAGCTA 58.940 40.000 0.00 0.00 36.49 3.32
2604 3012 4.888239 TGATACTAACGCTTTCCTCTAGCT 59.112 41.667 0.00 0.00 36.49 3.32
2605 3013 5.184340 TGATACTAACGCTTTCCTCTAGC 57.816 43.478 0.00 0.00 35.29 3.42
2677 3087 4.711355 ACCATCCTTAATTTGGACCACATG 59.289 41.667 0.00 0.00 36.30 3.21
2702 3112 0.855349 CACGTCAGTCAGCAAGTGTC 59.145 55.000 0.00 0.00 0.00 3.67
2783 3193 0.103572 TCACCGCGGCCTCTATTAAC 59.896 55.000 28.58 0.00 0.00 2.01
2893 3303 1.202769 GGGGCTGGGGTGTGTACTTA 61.203 60.000 0.00 0.00 0.00 2.24
2902 3320 1.667935 ATTATGCATGGGGCTGGGGT 61.668 55.000 10.16 0.00 45.15 4.95
2903 3321 0.472352 AATTATGCATGGGGCTGGGG 60.472 55.000 10.16 0.00 45.15 4.96
2904 3322 2.299867 GTTAATTATGCATGGGGCTGGG 59.700 50.000 10.16 0.00 45.15 4.45
2905 3323 3.233507 AGTTAATTATGCATGGGGCTGG 58.766 45.455 10.16 0.00 45.15 4.85
2906 3324 4.341806 TGAAGTTAATTATGCATGGGGCTG 59.658 41.667 10.16 0.00 45.15 4.85
2907 3325 4.545678 TGAAGTTAATTATGCATGGGGCT 58.454 39.130 10.16 0.00 45.15 5.19
2908 3326 4.935352 TGAAGTTAATTATGCATGGGGC 57.065 40.909 10.16 0.00 45.13 5.80
2959 3377 7.775093 TGAGAAAATAAATCACTGGTGGGATAG 59.225 37.037 0.70 0.00 0.00 2.08
3027 3445 6.226052 AGGCCTTTAAATTTGAAAGCAGAAG 58.774 36.000 15.65 4.77 33.38 2.85
3030 3448 6.226052 AGAAGGCCTTTAAATTTGAAAGCAG 58.774 36.000 21.54 5.77 33.38 4.24
3045 3463 1.348696 CATGCCCAAAAAGAAGGCCTT 59.651 47.619 20.65 20.65 46.55 4.35
3047 3465 0.036105 CCATGCCCAAAAAGAAGGCC 60.036 55.000 0.00 0.00 46.55 5.19
3061 3479 0.039618 TGTTTCCCCTTCCTCCATGC 59.960 55.000 0.00 0.00 0.00 4.06
3064 3482 1.982958 GTACTGTTTCCCCTTCCTCCA 59.017 52.381 0.00 0.00 0.00 3.86
3071 3490 4.351111 AGAGACATTTGTACTGTTTCCCCT 59.649 41.667 0.00 0.00 30.24 4.79
3691 4236 8.140677 TCCACAATTTGTTTTCTTGCATTTAG 57.859 30.769 0.00 0.00 0.00 1.85
3998 4547 6.650120 TCAGAAGGTATTTTTCGCCTATTCT 58.350 36.000 0.00 0.00 31.43 2.40
4005 4554 9.620660 TTCTTATTTTCAGAAGGTATTTTTCGC 57.379 29.630 0.00 0.00 0.00 4.70
4051 4600 5.190677 GGGTAGTACTGGTATGTTGCATTT 58.809 41.667 5.39 0.00 0.00 2.32
4066 4615 5.148651 AGTGTCTCAAACATGGGTAGTAC 57.851 43.478 0.00 0.00 40.80 2.73
4179 4728 9.148104 GTCACCGAGTAAGATAACAAATTAAGT 57.852 33.333 0.00 0.00 0.00 2.24
4202 4751 2.297701 GTGCTTTCCAGAAACCTGTCA 58.702 47.619 0.00 0.00 0.00 3.58
4286 4835 3.321111 ACATGTACACAGAAACTCCGAGT 59.679 43.478 0.00 0.00 0.00 4.18
4342 4891 8.760980 ATATACTCACTATTCAGGATAGCCTC 57.239 38.462 0.00 0.00 44.80 4.70
4382 4931 7.611213 ATTCGAACCGATTATCTTTCAGTTT 57.389 32.000 0.00 0.00 35.23 2.66
4391 4940 7.459394 TTCACTTGTATTCGAACCGATTATC 57.541 36.000 0.00 0.00 35.23 1.75
4418 4967 7.232534 TCAGCAGGCCGGAATATTAATTTTATT 59.767 33.333 5.05 0.00 0.00 1.40
4501 5050 5.817816 GTCACTGACCAGGGTAATTAAGATG 59.182 44.000 0.00 0.00 32.51 2.90
4554 5103 8.589335 TCTAAGTTCACTGAAGTCAACATTAC 57.411 34.615 0.00 0.00 31.08 1.89
4583 5135 5.940470 AGCACTACTTAAAGTGGAAAGATGG 59.060 40.000 8.92 0.00 45.75 3.51
4712 5264 9.225682 AGATGGAAAGGTCCTATTTAAGTATCA 57.774 33.333 0.00 0.00 45.22 2.15
4725 5294 5.404395 ACCTAGGTATAGATGGAAAGGTCC 58.596 45.833 14.41 0.00 45.21 4.46
4785 5361 1.070134 GCTCCAACCCTTTTTGTTCCC 59.930 52.381 0.00 0.00 0.00 3.97
4805 5381 0.039256 CTGCAAACATGTTGGTCCCG 60.039 55.000 12.82 0.00 0.00 5.14
4868 5444 1.719063 TTGTCTGCCAGCCTCCCTTT 61.719 55.000 0.00 0.00 0.00 3.11
4874 5450 2.162681 GTACAAATTGTCTGCCAGCCT 58.837 47.619 0.22 0.00 0.00 4.58
4888 5464 6.708949 GGAACAGTTGGAATAGACAGTACAAA 59.291 38.462 0.00 0.00 0.00 2.83
4986 5562 6.226052 TGAACCATATTGCTCTGCTATAGTG 58.774 40.000 0.84 0.00 30.97 2.74
4987 5563 6.042552 ACTGAACCATATTGCTCTGCTATAGT 59.957 38.462 0.84 0.00 30.97 2.12
4988 5564 6.462500 ACTGAACCATATTGCTCTGCTATAG 58.538 40.000 0.00 0.00 30.97 1.31
4989 5565 6.268617 AGACTGAACCATATTGCTCTGCTATA 59.731 38.462 0.00 0.00 31.85 1.31
4990 5566 5.071519 AGACTGAACCATATTGCTCTGCTAT 59.928 40.000 0.00 0.00 0.00 2.97
4991 5567 4.406972 AGACTGAACCATATTGCTCTGCTA 59.593 41.667 0.00 0.00 0.00 3.49
4992 5568 3.199508 AGACTGAACCATATTGCTCTGCT 59.800 43.478 0.00 0.00 0.00 4.24
4993 5569 3.539604 AGACTGAACCATATTGCTCTGC 58.460 45.455 0.00 0.00 0.00 4.26
5123 5699 0.178903 TCCTAGTTGGGTGGACTGCT 60.179 55.000 0.00 0.00 36.20 4.24
5151 5727 2.792500 TGCCTTGCATATCCCAACG 58.208 52.632 0.00 0.00 31.71 4.10
5190 5766 1.202698 GCCCCTGGAGCTATGTACTTG 60.203 57.143 0.00 0.00 0.00 3.16
5216 5792 3.855689 GTGGCAGTAAGCAACATTCAT 57.144 42.857 0.00 0.00 46.95 2.57
5387 5963 3.117663 TGAACCTAACTTGATATGCCCCC 60.118 47.826 0.00 0.00 0.00 5.40
5388 5964 4.164843 TGAACCTAACTTGATATGCCCC 57.835 45.455 0.00 0.00 0.00 5.80
5389 5965 5.417580 TGTTTGAACCTAACTTGATATGCCC 59.582 40.000 0.00 0.00 0.00 5.36
5390 5966 6.509418 TGTTTGAACCTAACTTGATATGCC 57.491 37.500 0.00 0.00 0.00 4.40
5391 5967 6.528072 GCTTGTTTGAACCTAACTTGATATGC 59.472 38.462 0.00 0.00 0.00 3.14
5392 5968 7.029563 GGCTTGTTTGAACCTAACTTGATATG 58.970 38.462 0.00 0.00 0.00 1.78
5393 5969 6.152831 GGGCTTGTTTGAACCTAACTTGATAT 59.847 38.462 0.00 0.00 0.00 1.63
5394 5970 5.475564 GGGCTTGTTTGAACCTAACTTGATA 59.524 40.000 0.00 0.00 0.00 2.15
5395 5971 4.280929 GGGCTTGTTTGAACCTAACTTGAT 59.719 41.667 0.00 0.00 0.00 2.57
5396 5972 3.634910 GGGCTTGTTTGAACCTAACTTGA 59.365 43.478 0.00 0.00 0.00 3.02
5397 5973 3.636764 AGGGCTTGTTTGAACCTAACTTG 59.363 43.478 0.00 0.00 0.00 3.16
5398 5974 3.910989 AGGGCTTGTTTGAACCTAACTT 58.089 40.909 0.00 0.00 0.00 2.66
5399 5975 3.595190 AGGGCTTGTTTGAACCTAACT 57.405 42.857 0.00 0.00 0.00 2.24
5400 5976 5.278808 CCTTAAGGGCTTGTTTGAACCTAAC 60.279 44.000 14.25 0.00 0.00 2.34
5401 5977 4.830600 CCTTAAGGGCTTGTTTGAACCTAA 59.169 41.667 14.25 0.00 0.00 2.69
5404 5980 3.660501 CCTTAAGGGCTTGTTTGAACC 57.339 47.619 14.25 0.00 0.00 3.62
5584 6160 5.656416 TCATTTGGGGACTTCCATACATTTC 59.344 40.000 0.00 0.00 36.58 2.17
5658 6244 4.310357 TCGCGATACCTGCATAAAAGTA 57.690 40.909 3.71 0.00 0.00 2.24
6080 6674 1.000163 TCACAGTCCGAGCAGACTTTC 60.000 52.381 1.68 0.00 44.83 2.62
6109 6703 6.047231 CAGAGCTCATTGATGATTACACTCA 58.953 40.000 17.77 0.00 36.02 3.41
6196 6855 2.932614 CACACAACTCCCTCGATCATTC 59.067 50.000 0.00 0.00 0.00 2.67
6296 6955 7.413657 GCCAGATAGACGAGATAAGCTAGTAAG 60.414 44.444 0.00 0.00 32.22 2.34
6382 7041 4.327680 ACACCAACCTTAGCTGAGAATTC 58.672 43.478 7.16 0.00 0.00 2.17
6589 7252 2.482326 GCCATAACGCAAGGCTCTT 58.518 52.632 0.00 0.00 44.92 2.85
6626 7289 1.600413 CGTCCTCAATCGATGATCGCA 60.600 52.381 10.45 0.00 40.21 5.10
6630 7293 1.959985 AGCTCGTCCTCAATCGATGAT 59.040 47.619 0.00 0.00 37.44 2.45
6631 7294 1.335182 GAGCTCGTCCTCAATCGATGA 59.665 52.381 0.00 0.00 35.57 2.92
6632 7295 1.336440 AGAGCTCGTCCTCAATCGATG 59.664 52.381 8.37 0.00 35.57 3.84


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

AutoCloner maintained by Alex Coulton.