Multiple sequence alignment - TraesCS1D01G423300

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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 TraesCS1D01G423300 chr1D 100.000 5962 0 0 1 5962 478348232 478342271 0.000000e+00 11010.0
1 TraesCS1D01G423300 chr1B 94.295 4417 170 32 1578 5962 666247030 666242664 0.000000e+00 6685.0
2 TraesCS1D01G423300 chr1B 87.230 556 50 8 1731 2285 77961654 77961119 1.100000e-171 614.0
3 TraesCS1D01G423300 chr1B 87.983 466 23 17 852 1295 666247523 666247069 2.460000e-143 520.0
4 TraesCS1D01G423300 chr1B 83.067 313 31 8 172 463 666248278 666247967 1.270000e-66 265.0
5 TraesCS1D01G423300 chr1B 91.083 157 14 0 1757 1913 10175755 10175911 4.680000e-51 213.0
6 TraesCS1D01G423300 chrUn 94.206 4418 173 33 1578 5962 227023498 227027865 0.000000e+00 6663.0
7 TraesCS1D01G423300 chrUn 87.554 466 25 17 852 1295 227023005 227023459 5.330000e-140 508.0
8 TraesCS1D01G423300 chrUn 84.293 382 32 10 1549 1911 56403277 56403649 1.230000e-91 348.0
9 TraesCS1D01G423300 chr1A 93.555 2312 105 17 3658 5960 574539790 574537514 0.000000e+00 3404.0
10 TraesCS1D01G423300 chr1A 95.382 1819 61 11 1616 3421 574541596 574539788 0.000000e+00 2872.0
11 TraesCS1D01G423300 chr1A 90.228 788 44 10 30 792 574570999 574570220 0.000000e+00 998.0
12 TraesCS1D01G423300 chr1A 92.593 405 16 13 833 1225 574542580 574542178 2.410000e-158 569.0
13 TraesCS1D01G423300 chr1A 87.637 364 21 5 1254 1610 574542179 574541833 9.310000e-108 401.0
14 TraesCS1D01G423300 chr4D 87.179 1365 110 33 1408 2731 144880910 144879570 0.000000e+00 1491.0
15 TraesCS1D01G423300 chr4D 88.670 203 13 5 1007 1209 144881320 144881128 7.720000e-59 239.0
16 TraesCS1D01G423300 chr4B 83.479 914 85 30 1409 2285 5022723 5021839 0.000000e+00 791.0
17 TraesCS1D01G423300 chr4B 85.960 755 75 18 1519 2254 199730036 199730778 0.000000e+00 778.0
18 TraesCS1D01G423300 chr4B 92.771 498 32 1 2234 2731 545093704 545094197 0.000000e+00 717.0
19 TraesCS1D01G423300 chr4B 90.776 477 38 1 2261 2731 199745938 199746414 3.030000e-177 632.0
20 TraesCS1D01G423300 chr4A 92.169 498 34 1 2234 2731 730776333 730776825 0.000000e+00 699.0
21 TraesCS1D01G423300 chr3A 92.804 403 28 1 2234 2635 401528336 401527934 3.100000e-162 582.0
22 TraesCS1D01G423300 chr3A 92.308 403 30 1 2234 2635 401474417 401474015 6.700000e-159 571.0
23 TraesCS1D01G423300 chr3A 94.245 139 8 0 2593 2731 401474021 401473883 4.680000e-51 213.0
24 TraesCS1D01G423300 chr3A 94.245 139 8 0 2593 2731 401527940 401527802 4.680000e-51 213.0
25 TraesCS1D01G423300 chr3A 80.870 115 21 1 1096 1209 431119558 431119672 8.230000e-14 89.8
26 TraesCS1D01G423300 chr5D 84.375 384 32 12 1549 1913 507308484 507308110 9.510000e-93 351.0
27 TraesCS1D01G423300 chr2D 77.665 394 65 16 5587 5960 23474514 23474124 1.010000e-52 219.0
28 TraesCS1D01G423300 chr3D 82.609 115 19 1 1096 1209 303407286 303407172 3.800000e-17 100.0
29 TraesCS1D01G423300 chr3B 80.992 121 20 3 1090 1209 418056285 418056403 6.360000e-15 93.5


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 TraesCS1D01G423300 chr1D 478342271 478348232 5961 True 11010.0 11010 100.000000 1 5962 1 chr1D.!!$R1 5961
1 TraesCS1D01G423300 chr1B 666242664 666248278 5614 True 2490.0 6685 88.448333 172 5962 3 chr1B.!!$R2 5790
2 TraesCS1D01G423300 chr1B 77961119 77961654 535 True 614.0 614 87.230000 1731 2285 1 chr1B.!!$R1 554
3 TraesCS1D01G423300 chrUn 227023005 227027865 4860 False 3585.5 6663 90.880000 852 5962 2 chrUn.!!$F2 5110
4 TraesCS1D01G423300 chr1A 574537514 574542580 5066 True 1811.5 3404 92.291750 833 5960 4 chr1A.!!$R2 5127
5 TraesCS1D01G423300 chr1A 574570220 574570999 779 True 998.0 998 90.228000 30 792 1 chr1A.!!$R1 762
6 TraesCS1D01G423300 chr4D 144879570 144881320 1750 True 865.0 1491 87.924500 1007 2731 2 chr4D.!!$R1 1724
7 TraesCS1D01G423300 chr4B 5021839 5022723 884 True 791.0 791 83.479000 1409 2285 1 chr4B.!!$R1 876
8 TraesCS1D01G423300 chr4B 199730036 199730778 742 False 778.0 778 85.960000 1519 2254 1 chr4B.!!$F1 735
9 TraesCS1D01G423300 chr3A 401527802 401528336 534 True 397.5 582 93.524500 2234 2731 2 chr3A.!!$R2 497
10 TraesCS1D01G423300 chr3A 401473883 401474417 534 True 392.0 571 93.276500 2234 2731 2 chr3A.!!$R1 497

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
819 864 0.526211 AAAAGAAATTCCCGCTCGCC 59.474 50.000 0.00 0.00 0.00 5.54 F
1226 1384 0.591236 TACGTAACGTAATCGGCCGC 60.591 55.000 23.51 5.12 39.44 6.53 F
2330 2863 0.246635 GGAAGACGGTTAGCAGAGCA 59.753 55.000 0.00 0.00 0.00 4.26 F
2619 3189 3.066342 CACAGTACACTACTATGGACGGG 59.934 52.174 0.00 0.00 38.57 5.28 F
2752 3329 5.910166 GTGTTGATCTATAGCACTAGTGTCG 59.090 44.000 23.44 8.36 0.00 4.35 F
4099 4687 4.262592 GCCTTTTCTGTTCCATCATTTGGT 60.263 41.667 0.00 0.00 46.52 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2286 2819 2.045340 GCACCCCACGCCTTGTAT 60.045 61.111 0.00 0.0 0.00 2.29 R
2836 3413 1.070445 GCCCTGCAGCTCGATGTAT 59.930 57.895 8.66 0.0 0.00 2.29 R
3370 3954 3.253230 CGAACATGTATCAGACACTGCA 58.747 45.455 0.00 0.0 42.17 4.41 R
3452 4036 6.233905 TGGTAGATGCTCTGCTTTTGTATA 57.766 37.500 0.00 0.0 29.49 1.47 R
4685 5273 1.555075 ACCAGCTTTATCCGAGCAAGA 59.445 47.619 0.00 0.0 42.56 3.02 R
5680 6279 0.035439 CCGCCACCTTCCTTGTATGT 60.035 55.000 0.00 0.0 0.00 2.29 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
21 22 4.942761 ATGCTCAAACCAATTGTCAACT 57.057 36.364 4.43 0.00 40.11 3.16
22 23 4.305989 TGCTCAAACCAATTGTCAACTC 57.694 40.909 4.43 0.00 40.11 3.01
23 24 3.953612 TGCTCAAACCAATTGTCAACTCT 59.046 39.130 4.43 0.00 40.11 3.24
24 25 4.036734 TGCTCAAACCAATTGTCAACTCTC 59.963 41.667 4.43 0.00 40.11 3.20
25 26 4.557496 GCTCAAACCAATTGTCAACTCTCC 60.557 45.833 4.43 0.00 40.11 3.71
26 27 4.792068 TCAAACCAATTGTCAACTCTCCT 58.208 39.130 4.43 0.00 40.11 3.69
27 28 4.821805 TCAAACCAATTGTCAACTCTCCTC 59.178 41.667 4.43 0.00 40.11 3.71
28 29 4.713792 AACCAATTGTCAACTCTCCTCT 57.286 40.909 4.43 0.00 0.00 3.69
45 46 7.098074 TCTCCTCTTCGTCCTAAAATAGTTC 57.902 40.000 0.00 0.00 0.00 3.01
48 49 8.223177 TCCTCTTCGTCCTAAAATAGTTCTAG 57.777 38.462 0.00 0.00 0.00 2.43
49 50 8.051535 TCCTCTTCGTCCTAAAATAGTTCTAGA 58.948 37.037 0.00 0.00 0.00 2.43
76 77 5.705441 AGTCTCGTCATAAAATGCCTCAAAA 59.295 36.000 0.00 0.00 0.00 2.44
77 78 6.024049 GTCTCGTCATAAAATGCCTCAAAAG 58.976 40.000 0.00 0.00 0.00 2.27
79 80 4.764823 TCGTCATAAAATGCCTCAAAAGGT 59.235 37.500 0.00 0.00 45.34 3.50
124 125 4.989279 ATAAAATGTGCACTCCATGTCC 57.011 40.909 19.41 0.00 0.00 4.02
125 126 1.167851 AAATGTGCACTCCATGTCCG 58.832 50.000 19.41 0.00 0.00 4.79
134 135 4.520874 TGCACTCCATGTCCGAAAAATAAA 59.479 37.500 0.00 0.00 0.00 1.40
212 219 7.038659 CCATTTTAACTGAAGTTCCAACAACA 58.961 34.615 0.00 0.00 39.31 3.33
231 239 1.178534 ATGACTTTGTTGGTGGCCCG 61.179 55.000 0.00 0.00 0.00 6.13
412 442 3.517602 TCATACCAATCGAAGTCAACCG 58.482 45.455 0.00 0.00 0.00 4.44
414 444 0.953960 ACCAATCGAAGTCAACCGGC 60.954 55.000 0.00 0.00 0.00 6.13
472 502 8.019669 CCATCTGTCAGATTTAGTGTCAAAAAG 58.980 37.037 12.88 0.00 31.32 2.27
477 507 8.181573 TGTCAGATTTAGTGTCAAAAAGTCAAC 58.818 33.333 0.00 0.00 0.00 3.18
479 509 8.181573 TCAGATTTAGTGTCAAAAAGTCAACAC 58.818 33.333 0.00 0.00 41.77 3.32
542 575 5.205821 TGATATTCTTTCGTGGAGTCCCTA 58.794 41.667 6.74 0.00 0.00 3.53
592 629 1.997606 CACCGTACGGACCTTTCATTC 59.002 52.381 39.52 0.00 38.96 2.67
617 654 4.920640 TTTGAAAAAGGGATGTACGCAA 57.079 36.364 0.00 0.00 0.00 4.85
662 699 6.432783 TGGGTATAAAATGTCACAGGTTCAAG 59.567 38.462 0.00 0.00 0.00 3.02
674 711 4.080919 CACAGGTTCAAGTCCTATCATCCA 60.081 45.833 0.00 0.00 33.54 3.41
735 780 8.780249 TGACAAGATAAGTTAAAGTAAAGTGGC 58.220 33.333 0.00 0.00 0.00 5.01
788 833 1.066002 CTCAACACAGGTGGTTTGCAG 59.934 52.381 4.24 0.00 34.19 4.41
790 835 1.476085 CAACACAGGTGGTTTGCAGAA 59.524 47.619 4.24 0.00 34.19 3.02
792 837 1.956477 ACACAGGTGGTTTGCAGAATC 59.044 47.619 4.24 0.00 34.19 2.52
793 838 1.955778 CACAGGTGGTTTGCAGAATCA 59.044 47.619 0.00 0.00 0.00 2.57
794 839 1.956477 ACAGGTGGTTTGCAGAATCAC 59.044 47.619 13.40 13.40 0.00 3.06
795 840 2.233271 CAGGTGGTTTGCAGAATCACT 58.767 47.619 18.24 7.53 0.00 3.41
818 863 2.347697 AAAAAGAAATTCCCGCTCGC 57.652 45.000 0.00 0.00 0.00 5.03
819 864 0.526211 AAAAGAAATTCCCGCTCGCC 59.474 50.000 0.00 0.00 0.00 5.54
820 865 1.644786 AAAGAAATTCCCGCTCGCCG 61.645 55.000 0.00 0.00 0.00 6.46
882 1030 2.677037 CGCTCGTCCACCTCCTAATTTT 60.677 50.000 0.00 0.00 0.00 1.82
886 1034 2.618045 CGTCCACCTCCTAATTTTGGCT 60.618 50.000 0.00 0.00 0.00 4.75
891 1042 4.195416 CACCTCCTAATTTTGGCTCTCTC 58.805 47.826 0.00 0.00 0.00 3.20
980 1138 3.535962 CTCTCGCTCCTGGCCTCC 61.536 72.222 3.32 0.00 37.74 4.30
1216 1374 1.002624 TCCCTCGGGTACGTAACGT 60.003 57.895 17.13 0.00 44.35 3.99
1218 1376 1.091537 CCCTCGGGTACGTAACGTAA 58.908 55.000 17.13 0.48 43.95 3.18
1219 1377 1.676006 CCCTCGGGTACGTAACGTAAT 59.324 52.381 17.13 0.00 43.95 1.89
1225 1383 1.112459 GTACGTAACGTAATCGGCCG 58.888 55.000 22.12 22.12 43.95 6.13
1226 1384 0.591236 TACGTAACGTAATCGGCCGC 60.591 55.000 23.51 5.12 39.44 6.53
1303 1558 1.084370 GGCGACGAACAGGAGAATGG 61.084 60.000 0.00 0.00 0.00 3.16
1329 1584 3.245754 GCATCACACCACACACAAATTTG 59.754 43.478 16.67 16.67 0.00 2.32
1362 1617 7.044117 CGATCCAAACATTTTCATTCCGTAATG 60.044 37.037 0.00 0.00 43.32 1.90
1363 1618 6.987386 TCCAAACATTTTCATTCCGTAATGT 58.013 32.000 0.32 0.00 42.66 2.71
1364 1619 7.087639 TCCAAACATTTTCATTCCGTAATGTC 58.912 34.615 0.32 0.00 42.66 3.06
1366 1621 6.582677 AACATTTTCATTCCGTAATGTCCA 57.417 33.333 0.32 0.00 42.66 4.02
1368 1623 7.873719 ACATTTTCATTCCGTAATGTCCATA 57.126 32.000 0.32 0.00 42.66 2.74
1369 1624 8.463930 ACATTTTCATTCCGTAATGTCCATAT 57.536 30.769 0.32 0.00 42.66 1.78
1370 1625 9.567776 ACATTTTCATTCCGTAATGTCCATATA 57.432 29.630 0.32 0.00 42.66 0.86
1404 1659 1.709147 GATGTGCGGCCAAGTGCTAG 61.709 60.000 2.24 0.00 40.92 3.42
1424 1679 2.169352 AGAGACCCCTGTGAATGATTCG 59.831 50.000 0.18 0.00 0.00 3.34
1520 1800 2.676839 CAAGCTCATTGCAGTGGAGTAG 59.323 50.000 9.56 0.38 45.94 2.57
1537 1817 9.403583 AGTGGAGTAGTTTTCAGTGAATTTAAA 57.596 29.630 6.36 0.00 0.00 1.52
1657 2174 4.411327 CGCATATATGGTATTTTTGCCCG 58.589 43.478 14.51 1.33 0.00 6.13
1658 2175 4.674101 CGCATATATGGTATTTTTGCCCGG 60.674 45.833 14.51 0.00 0.00 5.73
1667 2184 1.324383 TTTTTGCCCGGAAGAAGTCC 58.676 50.000 0.73 0.00 43.90 3.85
1855 2387 9.060347 GTTAGTTATCATCATGATGGTCACATT 57.940 33.333 30.54 15.52 37.70 2.71
1965 2497 9.326339 CTCATCATTTCTAACATATGCATTTCG 57.674 33.333 3.54 0.00 0.00 3.46
2286 2819 7.167535 TGTTGATGGTCATGATTCTGTTTAGA 58.832 34.615 0.00 0.00 0.00 2.10
2330 2863 0.246635 GGAAGACGGTTAGCAGAGCA 59.753 55.000 0.00 0.00 0.00 4.26
2453 2986 6.449635 TGCCTGGTTGATGAAATATGTAAC 57.550 37.500 0.00 0.00 0.00 2.50
2580 3113 7.093945 GGAGATCCTAATCAGTAAGTGATCCTC 60.094 44.444 0.00 0.00 45.89 3.71
2619 3189 3.066342 CACAGTACACTACTATGGACGGG 59.934 52.174 0.00 0.00 38.57 5.28
2752 3329 5.910166 GTGTTGATCTATAGCACTAGTGTCG 59.090 44.000 23.44 8.36 0.00 4.35
2784 3361 9.399797 ACTTAGATGATTGAAATGTATTCTGCA 57.600 29.630 0.00 0.00 0.00 4.41
2967 3547 6.849588 AAACTTTGCAGCTTTATTTCCTTG 57.150 33.333 0.00 0.00 0.00 3.61
2970 3550 6.681777 ACTTTGCAGCTTTATTTCCTTGTAG 58.318 36.000 0.00 0.00 0.00 2.74
2973 3553 7.753309 TTGCAGCTTTATTTCCTTGTAGTTA 57.247 32.000 0.00 0.00 0.00 2.24
3370 3954 8.687292 TCTTAAGACCGTAGTCATACATGTAT 57.313 34.615 12.75 12.75 46.15 2.29
3452 4036 6.661304 ATCACAAGCATTTTCCTCTTCTTT 57.339 33.333 0.00 0.00 0.00 2.52
3512 4096 5.886960 AGTCACAACCATTTTAGAGCATC 57.113 39.130 0.00 0.00 0.00 3.91
3981 4568 6.898041 TGAGATTGTACTTTTTCATGGAACG 58.102 36.000 0.00 0.00 0.00 3.95
4099 4687 4.262592 GCCTTTTCTGTTCCATCATTTGGT 60.263 41.667 0.00 0.00 46.52 3.67
4100 4688 5.742838 GCCTTTTCTGTTCCATCATTTGGTT 60.743 40.000 0.00 0.00 46.52 3.67
4703 5291 4.685169 TTTTCTTGCTCGGATAAAGCTG 57.315 40.909 0.00 0.00 40.50 4.24
4880 5469 3.430862 GCAGATGCACGCCGGAAA 61.431 61.111 5.05 0.00 41.59 3.13
4974 5563 4.452114 GCCCATTTTGAACAGGTTTTGATC 59.548 41.667 0.00 0.00 0.00 2.92
5018 5607 3.127548 TGCGCTCTCAAAATGATCTTTCC 59.872 43.478 9.73 0.00 0.00 3.13
5036 5625 1.065600 CGCCCAGTGTTGGTGTTTG 59.934 57.895 0.00 0.00 43.40 2.93
5303 5897 1.446792 CCTCTCGCAGCATGTTCGT 60.447 57.895 0.00 0.00 39.31 3.85
5304 5898 1.016130 CCTCTCGCAGCATGTTCGTT 61.016 55.000 0.00 0.00 39.31 3.85
5342 5941 8.879427 AGGTTGTAGGTAATAGCAAAAATTCT 57.121 30.769 0.00 0.00 0.00 2.40
5356 5955 8.345724 AGCAAAAATTCTGTGAACATAGATCT 57.654 30.769 0.00 0.00 0.00 2.75
5438 6037 5.190992 TGCTTTCGTACACAAGAGACTTA 57.809 39.130 5.41 0.00 0.00 2.24
5530 6129 8.812513 AATTGAATGATACTTGATGGAAGTGA 57.187 30.769 0.00 0.00 45.05 3.41
5550 6149 5.370880 AGTGAGCCACATTTATATTCTCCCT 59.629 40.000 7.86 0.00 36.74 4.20
5571 6170 9.482627 CTCCCTAAATATCATATTTATCCTCGC 57.517 37.037 9.82 0.00 0.00 5.03
5680 6279 0.179048 CGCCAGCCATATCTGAACCA 60.179 55.000 0.00 0.00 36.19 3.67
5684 6283 3.496692 GCCAGCCATATCTGAACCACATA 60.497 47.826 0.00 0.00 36.19 2.29
5754 6353 2.194326 GGGCCCTGGATCTGAAGC 59.806 66.667 17.04 0.00 0.00 3.86
5774 6373 1.478837 CGGTGGCTCTATCTGGTCCTA 60.479 57.143 0.00 0.00 0.00 2.94
5791 6390 0.763652 CTATGCTGCTCCCTCATGGT 59.236 55.000 0.00 0.00 34.77 3.55
5847 6463 3.809374 CTCCCCTATTCGGTGGCGC 62.809 68.421 0.00 0.00 0.00 6.53
5850 6466 4.524318 CCTATTCGGTGGCGCGGT 62.524 66.667 8.83 0.00 0.00 5.68
5851 6467 3.261951 CTATTCGGTGGCGCGGTG 61.262 66.667 8.83 0.00 0.00 4.94
5882 6498 4.408821 GTGGCTGGCGATCCACCA 62.409 66.667 10.35 2.33 45.26 4.17
5883 6499 3.645660 TGGCTGGCGATCCACCAA 61.646 61.111 3.85 0.00 39.18 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.586001 AGAGTTGACAATTGGTTTGAGCAT 59.414 37.500 10.83 0.00 38.76 3.79
1 2 3.953612 AGAGTTGACAATTGGTTTGAGCA 59.046 39.130 10.83 0.00 38.76 4.26
2 3 4.540824 GAGAGTTGACAATTGGTTTGAGC 58.459 43.478 10.83 0.00 38.76 4.26
3 4 4.823989 AGGAGAGTTGACAATTGGTTTGAG 59.176 41.667 10.83 0.00 38.76 3.02
4 5 4.792068 AGGAGAGTTGACAATTGGTTTGA 58.208 39.130 10.83 0.00 38.76 2.69
5 6 4.823989 AGAGGAGAGTTGACAATTGGTTTG 59.176 41.667 10.83 0.00 41.36 2.93
6 7 5.053978 AGAGGAGAGTTGACAATTGGTTT 57.946 39.130 10.83 0.00 0.00 3.27
7 8 4.713792 AGAGGAGAGTTGACAATTGGTT 57.286 40.909 10.83 0.00 0.00 3.67
8 9 4.646572 GAAGAGGAGAGTTGACAATTGGT 58.353 43.478 10.83 0.00 0.00 3.67
9 10 3.681897 CGAAGAGGAGAGTTGACAATTGG 59.318 47.826 10.83 0.00 0.00 3.16
10 11 4.310769 ACGAAGAGGAGAGTTGACAATTG 58.689 43.478 3.24 3.24 0.00 2.32
11 12 4.561105 GACGAAGAGGAGAGTTGACAATT 58.439 43.478 0.00 0.00 0.00 2.32
12 13 3.056465 GGACGAAGAGGAGAGTTGACAAT 60.056 47.826 0.00 0.00 0.00 2.71
13 14 2.296471 GGACGAAGAGGAGAGTTGACAA 59.704 50.000 0.00 0.00 0.00 3.18
14 15 1.887198 GGACGAAGAGGAGAGTTGACA 59.113 52.381 0.00 0.00 0.00 3.58
15 16 2.164338 AGGACGAAGAGGAGAGTTGAC 58.836 52.381 0.00 0.00 0.00 3.18
16 17 2.588464 AGGACGAAGAGGAGAGTTGA 57.412 50.000 0.00 0.00 0.00 3.18
17 18 4.785511 TTTAGGACGAAGAGGAGAGTTG 57.214 45.455 0.00 0.00 0.00 3.16
18 19 6.664384 ACTATTTTAGGACGAAGAGGAGAGTT 59.336 38.462 0.00 0.00 0.00 3.01
19 20 6.189133 ACTATTTTAGGACGAAGAGGAGAGT 58.811 40.000 0.00 0.00 0.00 3.24
20 21 6.702716 ACTATTTTAGGACGAAGAGGAGAG 57.297 41.667 0.00 0.00 0.00 3.20
21 22 6.890814 AGAACTATTTTAGGACGAAGAGGAGA 59.109 38.462 0.00 0.00 0.00 3.71
22 23 7.102847 AGAACTATTTTAGGACGAAGAGGAG 57.897 40.000 0.00 0.00 0.00 3.69
23 24 8.051535 TCTAGAACTATTTTAGGACGAAGAGGA 58.948 37.037 0.00 0.00 0.00 3.71
24 25 8.223177 TCTAGAACTATTTTAGGACGAAGAGG 57.777 38.462 0.00 0.00 0.00 3.69
45 46 7.278868 AGGCATTTTATGACGAGACTTTTCTAG 59.721 37.037 0.00 0.00 45.18 2.43
48 49 6.128282 TGAGGCATTTTATGACGAGACTTTTC 60.128 38.462 0.00 0.00 45.18 2.29
49 50 5.705441 TGAGGCATTTTATGACGAGACTTTT 59.295 36.000 0.00 0.00 45.18 2.27
53 54 5.545658 TTTGAGGCATTTTATGACGAGAC 57.454 39.130 0.00 0.00 45.18 3.36
112 113 4.695217 TTATTTTTCGGACATGGAGTGC 57.305 40.909 0.00 0.00 34.85 4.40
118 119 6.254281 AGGAGTGTTTATTTTTCGGACATG 57.746 37.500 0.00 0.00 0.00 3.21
124 125 4.076394 TGGGGAGGAGTGTTTATTTTTCG 58.924 43.478 0.00 0.00 0.00 3.46
125 126 5.303333 TGTTGGGGAGGAGTGTTTATTTTTC 59.697 40.000 0.00 0.00 0.00 2.29
134 135 0.986019 TGTGTGTTGGGGAGGAGTGT 60.986 55.000 0.00 0.00 0.00 3.55
212 219 1.178534 CGGGCCACCAACAAAGTCAT 61.179 55.000 4.39 0.00 36.13 3.06
329 353 4.833938 CCTCTCTCTCATCTCCATCATTGA 59.166 45.833 0.00 0.00 0.00 2.57
402 431 0.872388 AATTCACGCCGGTTGACTTC 59.128 50.000 1.90 0.00 0.00 3.01
412 442 2.287909 TGTGGCAAGTAAAATTCACGCC 60.288 45.455 0.00 0.00 38.56 5.68
414 444 3.974401 CAGTGTGGCAAGTAAAATTCACG 59.026 43.478 0.00 0.00 0.00 4.35
517 550 4.811557 GGGACTCCACGAAAGAATATCAAG 59.188 45.833 0.00 0.00 0.00 3.02
579 616 4.678509 TCAAAATCGAATGAAAGGTCCG 57.321 40.909 0.00 0.00 0.00 4.79
592 629 4.557301 GCGTACATCCCTTTTTCAAAATCG 59.443 41.667 0.00 0.00 0.00 3.34
617 654 1.675552 AAGCAAACACGCTACCAAGT 58.324 45.000 0.00 0.00 42.89 3.16
662 699 0.687354 ACGGGCATGGATGATAGGAC 59.313 55.000 0.00 0.00 0.00 3.85
674 711 4.287766 AGAAGAAAGAAGTAACGGGCAT 57.712 40.909 0.00 0.00 0.00 4.40
800 845 0.526211 GGCGAGCGGGAATTTCTTTT 59.474 50.000 0.00 0.00 0.00 2.27
801 846 1.644786 CGGCGAGCGGGAATTTCTTT 61.645 55.000 0.00 0.00 0.00 2.52
803 848 2.511600 CGGCGAGCGGGAATTTCT 60.512 61.111 0.00 0.00 0.00 2.52
882 1030 1.938596 AGAGGGAGGGAGAGAGCCA 60.939 63.158 0.00 0.00 0.00 4.75
886 1034 0.253868 TGGAGAGAGGGAGGGAGAGA 60.254 60.000 0.00 0.00 0.00 3.10
891 1042 1.081092 TGGTTGGAGAGAGGGAGGG 59.919 63.158 0.00 0.00 0.00 4.30
950 1108 4.070552 GAGAGCTTCCGGTGGCGT 62.071 66.667 0.00 0.19 0.00 5.68
1225 1383 2.189784 GAAGCCTAACCCTCCGGC 59.810 66.667 0.00 0.00 44.09 6.13
1226 1384 1.265454 ACTGAAGCCTAACCCTCCGG 61.265 60.000 0.00 0.00 0.00 5.14
1303 1558 0.030638 GTGTGTGGTGTGATGCCAAC 59.969 55.000 0.00 0.00 37.81 3.77
1329 1584 3.934457 AAATGTTTGGATCGGTTGGAC 57.066 42.857 0.00 0.00 0.00 4.02
1366 1621 9.230122 CGCACATCAGAGATCTCCTATATATAT 57.770 37.037 19.30 0.00 0.00 0.86
1368 1623 6.489700 CCGCACATCAGAGATCTCCTATATAT 59.510 42.308 19.30 1.71 0.00 0.86
1369 1624 5.825151 CCGCACATCAGAGATCTCCTATATA 59.175 44.000 19.30 0.00 0.00 0.86
1370 1625 4.644234 CCGCACATCAGAGATCTCCTATAT 59.356 45.833 19.30 5.14 0.00 0.86
1371 1626 4.013050 CCGCACATCAGAGATCTCCTATA 58.987 47.826 19.30 2.88 0.00 1.31
1384 1639 2.462125 TAGCACTTGGCCGCACATCA 62.462 55.000 0.00 0.00 46.50 3.07
1385 1640 1.709147 CTAGCACTTGGCCGCACATC 61.709 60.000 0.00 0.00 46.50 3.06
1404 1659 2.093447 ACGAATCATTCACAGGGGTCTC 60.093 50.000 0.00 0.00 0.00 3.36
1443 1698 7.460071 ACGTACTGGGAGAGTAGATATTGTAT 58.540 38.462 0.00 0.00 37.87 2.29
1520 1800 8.690840 CACCGAAGATTTAAATTCACTGAAAAC 58.309 33.333 1.43 0.00 0.00 2.43
1537 1817 7.687941 ACATAACAGAAAAATCACCGAAGAT 57.312 32.000 0.00 0.00 0.00 2.40
1538 1818 7.118680 GGTACATAACAGAAAAATCACCGAAGA 59.881 37.037 0.00 0.00 0.00 2.87
1539 1819 7.241376 GGTACATAACAGAAAAATCACCGAAG 58.759 38.462 0.00 0.00 0.00 3.79
1541 1821 5.644636 GGGTACATAACAGAAAAATCACCGA 59.355 40.000 0.00 0.00 0.00 4.69
1542 1822 5.413213 TGGGTACATAACAGAAAAATCACCG 59.587 40.000 0.00 0.00 0.00 4.94
1657 2174 3.944015 CCTCAATCATGTGGACTTCTTCC 59.056 47.826 0.00 0.00 46.13 3.46
1658 2175 4.583871 ACCTCAATCATGTGGACTTCTTC 58.416 43.478 4.11 0.00 41.74 2.87
1667 2184 5.395682 AAATGGTCAACCTCAATCATGTG 57.604 39.130 0.10 0.00 36.82 3.21
1668 2185 6.423776 AAAAATGGTCAACCTCAATCATGT 57.576 33.333 0.10 0.00 36.82 3.21
2286 2819 2.045340 GCACCCCACGCCTTGTAT 60.045 61.111 0.00 0.00 0.00 2.29
2330 2863 3.728845 ACGCAAGCGACTATAATTCCAT 58.271 40.909 22.30 0.00 42.83 3.41
2453 2986 6.070656 TGGGGGAAATTTCTGCAAGATATAG 58.929 40.000 17.42 0.00 46.36 1.31
2501 3034 3.442625 TGAAATTGCCTCAGAAGCATCAG 59.557 43.478 0.00 0.00 40.59 2.90
2619 3189 7.226325 AGCTGTCTATCTGATGTTTCAAATAGC 59.774 37.037 0.00 0.00 34.28 2.97
2836 3413 1.070445 GCCCTGCAGCTCGATGTAT 59.930 57.895 8.66 0.00 0.00 2.29
2944 3524 6.348498 ACAAGGAAATAAAGCTGCAAAGTTT 58.652 32.000 1.02 0.00 0.00 2.66
2973 3553 9.725019 TCATGACTTGACAAAACTCATTAGTAT 57.275 29.630 0.00 0.00 33.75 2.12
3022 3602 4.019860 TGCAGAGCTCAAAGAGTAAATCCT 60.020 41.667 17.77 0.00 31.39 3.24
3320 3904 5.355910 GGCGGTTAAGGATAAGTTGATTGAA 59.644 40.000 0.00 0.00 0.00 2.69
3370 3954 3.253230 CGAACATGTATCAGACACTGCA 58.747 45.455 0.00 0.00 42.17 4.41
3429 4013 6.661304 AAAGAAGAGGAAAATGCTTGTGAT 57.339 33.333 0.00 0.00 0.00 3.06
3452 4036 6.233905 TGGTAGATGCTCTGCTTTTGTATA 57.766 37.500 0.00 0.00 29.49 1.47
4685 5273 1.555075 ACCAGCTTTATCCGAGCAAGA 59.445 47.619 0.00 0.00 42.56 3.02
4876 5465 4.074970 AGGTGCCGAATCATCATATTTCC 58.925 43.478 0.00 0.00 0.00 3.13
4880 5469 3.866651 GCTAGGTGCCGAATCATCATAT 58.133 45.455 0.00 0.00 35.15 1.78
4904 5493 1.289066 CTCGGAAACCAGACGCTCA 59.711 57.895 0.00 0.00 0.00 4.26
4910 5499 2.342279 CGCCACTCGGAAACCAGA 59.658 61.111 0.00 0.00 33.78 3.86
4974 5563 2.134789 AAGGCTGGCATGTAAAGAGG 57.865 50.000 3.38 0.00 0.00 3.69
5288 5882 0.094216 CAGAACGAACATGCTGCGAG 59.906 55.000 9.07 0.00 0.00 5.03
5356 5955 9.999660 TGTAATTGTACCAACTATACAAACTCA 57.000 29.630 2.02 0.42 43.74 3.41
5407 6006 8.942338 TCTTGTGTACGAAAGCAATATATCTT 57.058 30.769 0.00 0.00 0.00 2.40
5550 6149 7.166970 GCGACGCGAGGATAAATATGATATTTA 59.833 37.037 15.93 17.21 0.00 1.40
5626 6225 2.123854 CGAGGGATCGGGTGGAGA 60.124 66.667 0.00 0.00 0.00 3.71
5670 6269 5.487488 ACCTTCCTTGTATGTGGTTCAGATA 59.513 40.000 0.00 0.00 0.00 1.98
5671 6270 4.289672 ACCTTCCTTGTATGTGGTTCAGAT 59.710 41.667 0.00 0.00 0.00 2.90
5680 6279 0.035439 CCGCCACCTTCCTTGTATGT 60.035 55.000 0.00 0.00 0.00 2.29
5754 6353 0.757188 AGGACCAGATAGAGCCACCG 60.757 60.000 0.00 0.00 0.00 4.94
5763 6362 2.251818 GGAGCAGCATAGGACCAGATA 58.748 52.381 0.00 0.00 0.00 1.98
5764 6363 1.055040 GGAGCAGCATAGGACCAGAT 58.945 55.000 0.00 0.00 0.00 2.90
5774 6373 0.763652 CTACCATGAGGGAGCAGCAT 59.236 55.000 0.00 0.00 39.57 3.79
5791 6390 0.400525 CCTGGATCCAAGGCCCTCTA 60.401 60.000 17.00 0.00 0.00 2.43
5891 6507 2.187946 GTCAGCTAGCCACGGCAT 59.812 61.111 12.13 0.00 44.88 4.40


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

AutoCloner maintained by Alex Coulton.