Multiple sequence alignment - TraesCS3B01G012100

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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 TraesCS3B01G012100 chr3B 100.000 2570 0 0 1 2570 5407351 5409920 0.000000e+00 4747.0
1 TraesCS3B01G012100 chr3B 89.936 1868 100 39 739 2570 3308357 3306542 0.000000e+00 2327.0
2 TraesCS3B01G012100 chr3B 82.529 601 42 31 157 735 3308960 3308401 1.080000e-128 470.0
3 TraesCS3B01G012100 chr3A 84.426 1708 113 68 734 2420 7655463 7657038 0.000000e+00 1539.0
4 TraesCS3B01G012100 chr3A 92.788 208 8 3 418 619 7655144 7655350 6.950000e-76 294.0
5 TraesCS3B01G012100 chr3A 78.730 315 33 17 16 307 7654685 7654988 2.030000e-41 180.0
6 TraesCS3B01G012100 chr3A 86.508 126 9 1 2445 2570 7657036 7657153 5.770000e-27 132.0
7 TraesCS3B01G012100 chr3D 83.488 1508 98 70 729 2176 1316017 1314601 0.000000e+00 1266.0
8 TraesCS3B01G012100 chr3D 85.984 371 28 10 2203 2570 1314602 1314253 2.410000e-100 375.0
9 TraesCS3B01G012100 chr3D 80.967 331 23 23 418 735 1316350 1316047 2.570000e-55 226.0
10 TraesCS3B01G012100 chr7A 88.660 97 2 4 641 734 273417663 273417573 2.700000e-20 110.0
11 TraesCS3B01G012100 chr7A 88.660 97 2 4 641 734 498035666 498035576 2.700000e-20 110.0
12 TraesCS3B01G012100 chr7A 88.889 81 4 3 657 734 577059904 577059826 7.570000e-16 95.3
13 TraesCS3B01G012100 chr2A 86.486 111 2 5 627 734 603379986 603380086 2.700000e-20 110.0
14 TraesCS3B01G012100 chr2A 85.586 111 3 5 627 734 686744579 686744479 1.260000e-18 104.0
15 TraesCS3B01G012100 chr4A 89.412 85 4 3 653 734 505194831 505194749 4.520000e-18 102.0
16 TraesCS3B01G012100 chr7D 100.000 29 0 0 846 874 38795009 38795037 1.000000e-03 54.7


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 TraesCS3B01G012100 chr3B 5407351 5409920 2569 False 4747.000000 4747 100.000000 1 2570 1 chr3B.!!$F1 2569
1 TraesCS3B01G012100 chr3B 3306542 3308960 2418 True 1398.500000 2327 86.232500 157 2570 2 chr3B.!!$R1 2413
2 TraesCS3B01G012100 chr3A 7654685 7657153 2468 False 536.250000 1539 85.613000 16 2570 4 chr3A.!!$F1 2554
3 TraesCS3B01G012100 chr3D 1314253 1316350 2097 True 622.333333 1266 83.479667 418 2570 3 chr3D.!!$R1 2152

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
998 1262 0.040425 GCTTTTCTTGCTTTCGGCGA 60.04 50.0 4.99 4.99 45.43 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2202 2557 1.003223 GGGTGCTCAACGTGTTAACAC 60.003 52.381 25.73 25.73 43.15 3.32 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
77 80 5.701290 AGAAAATGAAAACTCGACCTACAGG 59.299 40.000 0.00 0.00 42.17 4.00
115 130 7.491696 ACGTACTCATCAAAGTAAATTAGGAGC 59.508 37.037 0.00 0.00 33.68 4.70
127 142 9.620259 AAGTAAATTAGGAGCCTCATTAAGAAG 57.380 33.333 0.00 0.00 0.00 2.85
130 145 2.200081 AGGAGCCTCATTAAGAAGCCA 58.800 47.619 0.00 0.00 34.06 4.75
150 165 2.187073 CCATTGGGCTGAGAGTTGC 58.813 57.895 0.00 0.00 0.00 4.17
151 166 0.323178 CCATTGGGCTGAGAGTTGCT 60.323 55.000 0.00 0.00 0.00 3.91
152 167 1.093159 CATTGGGCTGAGAGTTGCTC 58.907 55.000 0.00 0.00 44.21 4.26
178 193 1.083015 CGTGCGTTTTCAGAACGGG 60.083 57.895 12.45 0.00 43.25 5.28
188 203 0.684535 TCAGAACGGGCATCACTGAA 59.315 50.000 0.00 0.00 35.20 3.02
196 226 1.089920 GGCATCACTGAAGCGTCAAT 58.910 50.000 3.39 0.00 31.88 2.57
203 233 1.699656 CTGAAGCGTCAATGCCTCGG 61.700 60.000 3.39 0.00 31.88 4.63
218 251 1.150567 CTCGGCCAAATCTCTCGCTG 61.151 60.000 2.24 0.00 0.00 5.18
225 258 1.728971 CAAATCTCTCGCTGTCACCAC 59.271 52.381 0.00 0.00 0.00 4.16
226 259 0.247736 AATCTCTCGCTGTCACCACC 59.752 55.000 0.00 0.00 0.00 4.61
227 260 1.938657 ATCTCTCGCTGTCACCACCG 61.939 60.000 0.00 0.00 0.00 4.94
233 266 2.258591 CTGTCACCACCGACGGAG 59.741 66.667 23.38 13.45 43.75 4.63
259 292 1.139853 AGGGCGGAAGATGAAGATGAC 59.860 52.381 0.00 0.00 0.00 3.06
263 296 2.736978 CGGAAGATGAAGATGACGAGG 58.263 52.381 0.00 0.00 0.00 4.63
264 297 2.478831 GGAAGATGAAGATGACGAGGC 58.521 52.381 0.00 0.00 0.00 4.70
265 298 2.159043 GGAAGATGAAGATGACGAGGCA 60.159 50.000 0.00 0.00 0.00 4.75
266 299 2.886862 AGATGAAGATGACGAGGCAG 57.113 50.000 0.00 0.00 0.00 4.85
324 357 7.415206 GCCGACATGACCTTTGATTAAGTTAAT 60.415 37.037 7.87 7.87 31.56 1.40
389 426 0.244994 CTCACAGTTCCCAGTCTCGG 59.755 60.000 0.00 0.00 0.00 4.63
408 445 5.932303 TCTCGGTTCCAAGAAGAATAACAAG 59.068 40.000 0.00 0.00 0.00 3.16
409 446 4.454504 TCGGTTCCAAGAAGAATAACAAGC 59.545 41.667 0.00 0.00 0.00 4.01
411 448 5.617751 CGGTTCCAAGAAGAATAACAAGCTG 60.618 44.000 0.00 0.00 0.00 4.24
414 451 5.376625 TCCAAGAAGAATAACAAGCTGTGT 58.623 37.500 0.00 0.00 44.64 3.72
440 608 8.801299 TGCATAGATACACCAAGAAATGAAAAA 58.199 29.630 0.00 0.00 0.00 1.94
503 675 1.421485 GGAGAAAGATGTGCGTGCG 59.579 57.895 0.00 0.00 0.00 5.34
508 680 0.661187 AAAGATGTGCGTGCGCTTTG 60.661 50.000 17.49 0.00 42.51 2.77
518 690 2.918131 GCGTGCGCTTTGATTTCTTTCT 60.918 45.455 9.73 0.00 38.26 2.52
523 695 3.848582 GCGCTTTGATTTCTTTCTAGTGC 59.151 43.478 0.00 0.00 32.03 4.40
525 697 5.693814 CGCTTTGATTTCTTTCTAGTGCTT 58.306 37.500 0.00 0.00 0.00 3.91
526 698 5.792468 CGCTTTGATTTCTTTCTAGTGCTTC 59.208 40.000 0.00 0.00 0.00 3.86
528 700 7.020602 GCTTTGATTTCTTTCTAGTGCTTCTC 58.979 38.462 0.00 0.00 0.00 2.87
529 701 7.094848 GCTTTGATTTCTTTCTAGTGCTTCTCT 60.095 37.037 0.00 0.00 0.00 3.10
530 702 7.664082 TTGATTTCTTTCTAGTGCTTCTCTG 57.336 36.000 0.00 0.00 0.00 3.35
555 745 0.945813 GGTAGGATCGACTCGACTGG 59.054 60.000 2.53 0.00 39.18 4.00
576 766 4.019591 TGGGATAATCATGCAGATCAGAGG 60.020 45.833 0.00 0.00 35.39 3.69
622 812 2.033424 GTCACCTTTTCTGCAAGGACAC 59.967 50.000 9.19 1.61 45.79 3.67
623 813 2.023673 CACCTTTTCTGCAAGGACACA 58.976 47.619 9.19 0.00 45.79 3.72
624 814 2.426738 CACCTTTTCTGCAAGGACACAA 59.573 45.455 9.19 0.00 45.79 3.33
625 815 2.427095 ACCTTTTCTGCAAGGACACAAC 59.573 45.455 9.19 0.00 45.79 3.32
645 835 3.806625 CCAAACATTGGTCCATCCATC 57.193 47.619 0.00 0.00 46.60 3.51
646 836 2.431782 CCAAACATTGGTCCATCCATCC 59.568 50.000 0.00 0.00 46.60 3.51
647 837 3.098377 CAAACATTGGTCCATCCATCCA 58.902 45.455 0.00 0.00 46.60 3.41
648 838 2.442236 ACATTGGTCCATCCATCCAC 57.558 50.000 0.00 0.00 46.60 4.02
649 839 1.311859 CATTGGTCCATCCATCCACG 58.688 55.000 0.00 0.00 46.60 4.94
650 840 1.134128 CATTGGTCCATCCATCCACGA 60.134 52.381 0.00 0.00 46.60 4.35
651 841 1.212375 TTGGTCCATCCATCCACGAT 58.788 50.000 0.00 0.00 46.60 3.73
671 861 7.015289 CACGATCGACATGATTACAAAAGTTT 58.985 34.615 24.34 0.00 37.47 2.66
672 862 8.166066 CACGATCGACATGATTACAAAAGTTTA 58.834 33.333 24.34 0.00 37.47 2.01
673 863 8.380644 ACGATCGACATGATTACAAAAGTTTAG 58.619 33.333 24.34 0.00 37.47 1.85
676 866 7.802738 TCGACATGATTACAAAAGTTTAGTGG 58.197 34.615 0.00 0.00 0.00 4.00
677 867 6.523201 CGACATGATTACAAAAGTTTAGTGGC 59.477 38.462 0.00 0.00 0.00 5.01
678 868 7.283625 ACATGATTACAAAAGTTTAGTGGCA 57.716 32.000 0.00 0.00 0.00 4.92
679 869 7.895759 ACATGATTACAAAAGTTTAGTGGCAT 58.104 30.769 0.00 0.00 0.00 4.40
680 870 9.019656 ACATGATTACAAAAGTTTAGTGGCATA 57.980 29.630 0.00 0.00 0.00 3.14
683 873 9.853555 TGATTACAAAAGTTTAGTGGCATAATG 57.146 29.630 0.00 0.00 0.00 1.90
684 874 8.702163 ATTACAAAAGTTTAGTGGCATAATGC 57.298 30.769 0.00 0.00 44.08 3.56
715 910 2.937149 GCTTAACTTAGTAGCCACCAGC 59.063 50.000 0.00 0.00 44.25 4.85
747 986 2.275318 CCGCTTAGAGCAGAGGAAAAG 58.725 52.381 0.50 0.00 42.58 2.27
749 988 2.093973 CGCTTAGAGCAGAGGAAAAGGA 60.094 50.000 0.50 0.00 42.58 3.36
750 989 3.266636 GCTTAGAGCAGAGGAAAAGGAC 58.733 50.000 0.00 0.00 41.89 3.85
759 998 0.240411 AGGAAAAGGACGACGAGACG 59.760 55.000 0.00 0.00 39.31 4.18
760 999 0.239347 GGAAAAGGACGACGAGACGA 59.761 55.000 0.00 0.00 37.03 4.20
761 1000 1.325647 GAAAAGGACGACGAGACGAC 58.674 55.000 0.00 0.00 37.03 4.34
809 1049 1.071471 ACTCCACTCCACAAAGCCG 59.929 57.895 0.00 0.00 0.00 5.52
811 1051 0.671781 CTCCACTCCACAAAGCCGAG 60.672 60.000 0.00 0.00 0.00 4.63
835 1075 0.907704 TAAAGCGCCCAAGGAGAGGA 60.908 55.000 2.29 0.00 0.00 3.71
836 1076 2.190488 AAAGCGCCCAAGGAGAGGAG 62.190 60.000 2.29 0.00 0.00 3.69
837 1077 3.077556 GCGCCCAAGGAGAGGAGA 61.078 66.667 0.00 0.00 0.00 3.71
838 1078 3.087666 GCGCCCAAGGAGAGGAGAG 62.088 68.421 0.00 0.00 0.00 3.20
839 1079 2.430610 CGCCCAAGGAGAGGAGAGG 61.431 68.421 0.00 0.00 0.00 3.69
998 1262 0.040425 GCTTTTCTTGCTTTCGGCGA 60.040 50.000 4.99 4.99 45.43 5.54
1043 1307 4.087892 CGGGCTGCTACTGCTGGT 62.088 66.667 0.00 0.00 40.48 4.00
1050 1314 2.510238 CTACTGCTGGTGGCGCTC 60.510 66.667 7.64 0.23 45.43 5.03
1051 1315 4.435436 TACTGCTGGTGGCGCTCG 62.435 66.667 7.64 0.00 45.43 5.03
1446 1713 1.214325 CATGCCGTCGTACCTGACA 59.786 57.895 2.46 0.00 38.84 3.58
1573 1840 2.885644 CCGTCGCCTTGTGATCGG 60.886 66.667 0.00 0.00 33.45 4.18
1575 1842 3.195698 GTCGCCTTGTGATCGGCC 61.196 66.667 0.00 0.00 43.38 6.13
1577 1844 4.776322 CGCCTTGTGATCGGCCCA 62.776 66.667 0.00 0.00 43.38 5.36
1578 1845 2.124151 GCCTTGTGATCGGCCCAT 60.124 61.111 0.00 0.00 40.43 4.00
1579 1846 2.189499 GCCTTGTGATCGGCCCATC 61.189 63.158 2.94 2.94 40.43 3.51
1580 1847 1.224315 CCTTGTGATCGGCCCATCA 59.776 57.895 9.21 9.21 0.00 3.07
1581 1848 0.394216 CCTTGTGATCGGCCCATCAA 60.394 55.000 15.18 0.00 34.50 2.57
1582 1849 0.734889 CTTGTGATCGGCCCATCAAC 59.265 55.000 15.18 9.80 34.50 3.18
1583 1850 1.024046 TTGTGATCGGCCCATCAACG 61.024 55.000 15.18 0.00 34.50 4.10
1585 1852 2.513666 GATCGGCCCATCAACGCA 60.514 61.111 5.34 0.00 0.00 5.24
1586 1853 2.514592 ATCGGCCCATCAACGCAG 60.515 61.111 0.00 0.00 0.00 5.18
1592 1862 2.108514 CCCATCAACGCAGCATCGT 61.109 57.895 0.00 0.00 45.58 3.73
1613 1883 2.032634 CATGCCAAGGTACACGCGT 61.033 57.895 5.58 5.58 0.00 6.01
1614 1884 1.740296 ATGCCAAGGTACACGCGTC 60.740 57.895 9.86 0.00 0.00 5.19
1615 1885 3.475774 GCCAAGGTACACGCGTCG 61.476 66.667 9.86 8.08 0.00 5.12
1616 1886 3.475774 CCAAGGTACACGCGTCGC 61.476 66.667 9.86 7.29 0.00 5.19
1618 1888 3.677648 AAGGTACACGCGTCGCCT 61.678 61.111 9.86 14.55 33.52 5.52
1619 1889 3.909258 AAGGTACACGCGTCGCCTG 62.909 63.158 21.55 13.12 32.76 4.85
1649 1926 4.007644 CCACCAGCTGCACCGAGA 62.008 66.667 8.66 0.00 0.00 4.04
1650 1927 2.433838 CACCAGCTGCACCGAGAG 60.434 66.667 8.66 0.00 0.00 3.20
1651 1928 4.385405 ACCAGCTGCACCGAGAGC 62.385 66.667 8.66 0.00 35.28 4.09
1653 1930 4.426112 CAGCTGCACCGAGAGCGA 62.426 66.667 0.00 0.00 40.34 4.93
1706 1987 1.011968 CGTACGTGGTGACCATGGTG 61.012 60.000 25.52 9.32 44.23 4.17
1742 2035 1.976045 CTTGCATGGCGTACGTTTTTC 59.024 47.619 17.90 4.71 0.00 2.29
1743 2036 0.238817 TGCATGGCGTACGTTTTTCC 59.761 50.000 17.90 9.49 0.00 3.13
1745 2038 1.465187 GCATGGCGTACGTTTTTCCTC 60.465 52.381 17.90 0.00 0.00 3.71
1928 2235 3.362304 CGTAAGTTGGGTCTCGTTTTTCG 60.362 47.826 0.00 0.00 41.41 3.46
2076 2408 5.757320 CCATGTCTCATCTTCTTGGTATGTC 59.243 44.000 0.00 0.00 0.00 3.06
2099 2454 2.956333 CCATGATCACCAACTCATGCAT 59.044 45.455 0.00 0.00 44.75 3.96
2101 2456 2.282407 TGATCACCAACTCATGCATCG 58.718 47.619 0.00 0.00 0.00 3.84
2110 2465 2.101575 CATGCATCGTGGTGCTGC 59.898 61.111 6.66 0.00 45.27 5.25
2124 2479 2.028748 GGTGCTGCCTGATGAATTGTTT 60.029 45.455 0.00 0.00 0.00 2.83
2143 2498 5.192927 TGTTTCTTTTGCTATCCCGATCAT 58.807 37.500 0.00 0.00 0.00 2.45
2159 2514 3.426159 CGATCATTGTGTGCAACCTAACC 60.426 47.826 0.00 0.00 37.44 2.85
2165 2520 2.028876 GTGTGCAACCTAACCAACCTT 58.971 47.619 0.00 0.00 34.36 3.50
2184 2539 6.790285 ACCTTTGTGTTAGGTACATTAACG 57.210 37.500 12.21 0.00 44.11 3.18
2185 2540 6.523840 ACCTTTGTGTTAGGTACATTAACGA 58.476 36.000 12.21 2.79 44.11 3.85
2186 2541 6.991531 ACCTTTGTGTTAGGTACATTAACGAA 59.008 34.615 12.21 7.08 44.11 3.85
2187 2542 7.041848 ACCTTTGTGTTAGGTACATTAACGAAC 60.042 37.037 12.21 8.15 44.11 3.95
2188 2543 7.172019 CCTTTGTGTTAGGTACATTAACGAACT 59.828 37.037 12.21 0.00 39.39 3.01
2189 2544 9.195411 CTTTGTGTTAGGTACATTAACGAACTA 57.805 33.333 12.21 3.99 39.39 2.24
2190 2545 8.746922 TTGTGTTAGGTACATTAACGAACTAG 57.253 34.615 12.21 0.00 39.39 2.57
2191 2546 6.808212 TGTGTTAGGTACATTAACGAACTAGC 59.192 38.462 12.21 0.00 39.39 3.42
2192 2547 7.031975 GTGTTAGGTACATTAACGAACTAGCT 58.968 38.462 12.21 0.00 39.39 3.32
2193 2548 7.008992 GTGTTAGGTACATTAACGAACTAGCTG 59.991 40.741 0.00 0.00 39.39 4.24
2194 2549 5.007385 AGGTACATTAACGAACTAGCTGG 57.993 43.478 0.00 0.00 0.00 4.85
2195 2550 4.465305 AGGTACATTAACGAACTAGCTGGT 59.535 41.667 0.00 0.00 0.00 4.00
2196 2551 5.046807 AGGTACATTAACGAACTAGCTGGTT 60.047 40.000 16.13 16.13 0.00 3.67
2197 2552 6.153340 AGGTACATTAACGAACTAGCTGGTTA 59.847 38.462 16.16 0.00 0.00 2.85
2198 2553 6.813152 GGTACATTAACGAACTAGCTGGTTAA 59.187 38.462 16.16 13.61 38.68 2.01
2199 2554 6.716898 ACATTAACGAACTAGCTGGTTAAC 57.283 37.500 16.16 3.51 37.58 2.01
2200 2555 5.640783 ACATTAACGAACTAGCTGGTTAACC 59.359 40.000 16.16 18.27 37.58 2.85
2201 2556 3.756933 AACGAACTAGCTGGTTAACCA 57.243 42.857 25.58 25.58 45.30 3.67
2257 2633 3.279116 CCGGCCGGTACATGCATG 61.279 66.667 36.64 25.09 0.00 4.06
2258 2634 2.203001 CGGCCGGTACATGCATGA 60.203 61.111 32.75 13.72 0.00 3.07
2259 2635 1.817520 CGGCCGGTACATGCATGAA 60.818 57.895 32.75 0.00 0.00 2.57
2260 2636 1.727467 GGCCGGTACATGCATGAAC 59.273 57.895 32.75 19.26 0.00 3.18
2261 2637 1.029408 GGCCGGTACATGCATGAACA 61.029 55.000 32.75 14.25 0.00 3.18
2262 2638 0.808125 GCCGGTACATGCATGAACAA 59.192 50.000 32.75 12.10 0.00 2.83
2324 2700 3.825014 GCATATCCATCCATGAACAAGCT 59.175 43.478 0.00 0.00 0.00 3.74
2325 2701 5.005740 GCATATCCATCCATGAACAAGCTA 58.994 41.667 0.00 0.00 0.00 3.32
2396 2781 1.291184 GGCGAAAAAGCAATGTGCCC 61.291 55.000 0.00 0.00 46.52 5.36
2421 2806 0.380024 TGCGGAAATGTGTGTGTGTG 59.620 50.000 0.00 0.00 0.00 3.82
2422 2807 0.380378 GCGGAAATGTGTGTGTGTGT 59.620 50.000 0.00 0.00 0.00 3.72
2423 2808 1.859597 GCGGAAATGTGTGTGTGTGTG 60.860 52.381 0.00 0.00 0.00 3.82
2424 2809 1.400142 CGGAAATGTGTGTGTGTGTGT 59.600 47.619 0.00 0.00 0.00 3.72
2425 2810 2.790812 CGGAAATGTGTGTGTGTGTGTG 60.791 50.000 0.00 0.00 0.00 3.82
2426 2811 2.163412 GGAAATGTGTGTGTGTGTGTGT 59.837 45.455 0.00 0.00 0.00 3.72
2427 2812 2.917701 AATGTGTGTGTGTGTGTGTG 57.082 45.000 0.00 0.00 0.00 3.82
2428 2813 1.093972 ATGTGTGTGTGTGTGTGTGG 58.906 50.000 0.00 0.00 0.00 4.17
2429 2814 0.957888 TGTGTGTGTGTGTGTGTGGG 60.958 55.000 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.659668 ACAGAAGAGCATAGTACTGAGTGTAA 59.340 38.462 5.39 0.00 32.25 2.41
1 2 6.181190 ACAGAAGAGCATAGTACTGAGTGTA 58.819 40.000 5.39 0.00 0.00 2.90
2 3 5.013547 ACAGAAGAGCATAGTACTGAGTGT 58.986 41.667 5.39 0.00 0.00 3.55
3 4 5.124617 TGACAGAAGAGCATAGTACTGAGTG 59.875 44.000 5.39 3.09 0.00 3.51
4 5 5.257262 TGACAGAAGAGCATAGTACTGAGT 58.743 41.667 5.39 0.00 0.00 3.41
5 6 5.588246 TCTGACAGAAGAGCATAGTACTGAG 59.412 44.000 5.39 0.00 0.00 3.35
6 7 5.501156 TCTGACAGAAGAGCATAGTACTGA 58.499 41.667 5.39 0.00 0.00 3.41
7 8 5.826601 TCTGACAGAAGAGCATAGTACTG 57.173 43.478 5.39 0.00 0.00 2.74
8 9 6.842437 TTTCTGACAGAAGAGCATAGTACT 57.158 37.500 17.06 0.00 35.37 2.73
9 10 7.891183 TTTTTCTGACAGAAGAGCATAGTAC 57.109 36.000 17.06 0.00 35.37 2.73
34 35 7.920160 TTTTCTTCTTTCAATTGCTTTGGTT 57.080 28.000 0.00 0.00 35.92 3.67
35 36 7.769970 TCATTTTCTTCTTTCAATTGCTTTGGT 59.230 29.630 0.00 0.00 35.92 3.67
36 37 8.145316 TCATTTTCTTCTTTCAATTGCTTTGG 57.855 30.769 0.00 0.00 35.92 3.28
37 38 9.991388 TTTCATTTTCTTCTTTCAATTGCTTTG 57.009 25.926 0.00 0.00 36.61 2.77
40 41 9.387257 AGTTTTCATTTTCTTCTTTCAATTGCT 57.613 25.926 0.00 0.00 0.00 3.91
41 42 9.642312 GAGTTTTCATTTTCTTCTTTCAATTGC 57.358 29.630 0.00 0.00 0.00 3.56
42 43 9.839589 CGAGTTTTCATTTTCTTCTTTCAATTG 57.160 29.630 0.00 0.00 0.00 2.32
51 54 7.186021 TGTAGGTCGAGTTTTCATTTTCTTC 57.814 36.000 0.00 0.00 0.00 2.87
54 57 5.928153 CCTGTAGGTCGAGTTTTCATTTTC 58.072 41.667 0.00 0.00 0.00 2.29
77 80 6.174451 TGATGAGTACGTACTGTTCAGTAC 57.826 41.667 31.91 24.61 40.73 2.73
82 85 8.511465 TTTACTTTGATGAGTACGTACTGTTC 57.489 34.615 31.91 24.87 36.50 3.18
83 86 9.485206 AATTTACTTTGATGAGTACGTACTGTT 57.515 29.630 31.91 18.45 36.50 3.16
115 130 2.425143 TGGCTGGCTTCTTAATGAGG 57.575 50.000 2.00 0.00 0.00 3.86
153 168 2.127232 GAAAACGCACGCTCCTGC 60.127 61.111 0.00 0.00 0.00 4.85
154 169 1.205064 CTGAAAACGCACGCTCCTG 59.795 57.895 0.00 0.00 0.00 3.86
178 193 1.792993 GCATTGACGCTTCAGTGATGC 60.793 52.381 18.16 18.58 40.99 3.91
196 226 1.221840 GAGAGATTTGGCCGAGGCA 59.778 57.895 16.65 0.00 44.11 4.75
203 233 0.723981 GTGACAGCGAGAGATTTGGC 59.276 55.000 0.00 0.00 0.00 4.52
218 251 0.942884 GTTTCTCCGTCGGTGGTGAC 60.943 60.000 11.88 5.22 31.60 3.67
225 258 2.033194 GCCCTTGTTTCTCCGTCGG 61.033 63.158 4.39 4.39 0.00 4.79
226 259 2.380410 CGCCCTTGTTTCTCCGTCG 61.380 63.158 0.00 0.00 0.00 5.12
227 260 2.033194 CCGCCCTTGTTTCTCCGTC 61.033 63.158 0.00 0.00 0.00 4.79
233 266 1.821216 TCATCTTCCGCCCTTGTTTC 58.179 50.000 0.00 0.00 0.00 2.78
264 297 3.423154 GAACGTTGGAGGCGCCTG 61.423 66.667 38.41 22.22 37.63 4.85
265 298 3.591254 GAGAACGTTGGAGGCGCCT 62.591 63.158 33.48 33.48 37.63 5.52
266 299 3.119096 GAGAACGTTGGAGGCGCC 61.119 66.667 21.89 21.89 37.10 6.53
324 357 2.355108 GCCTCTAGTTCATGGTGCAGAA 60.355 50.000 0.00 0.00 0.00 3.02
389 426 6.145535 CACAGCTTGTTATTCTTCTTGGAAC 58.854 40.000 0.00 0.00 0.00 3.62
408 445 2.905075 TGGTGTATCTATGCACACAGC 58.095 47.619 12.31 7.17 45.49 4.40
409 446 4.758688 TCTTGGTGTATCTATGCACACAG 58.241 43.478 12.31 7.67 45.49 3.66
411 448 6.316140 TCATTTCTTGGTGTATCTATGCACAC 59.684 38.462 12.31 1.99 43.87 3.82
414 451 7.936496 TTTCATTTCTTGGTGTATCTATGCA 57.064 32.000 0.00 0.00 0.00 3.96
440 608 1.880027 GCTGAAAGTGACCGGAATGTT 59.120 47.619 9.46 0.00 35.30 2.71
503 675 6.907741 AGAAGCACTAGAAAGAAATCAAAGC 58.092 36.000 0.00 0.00 0.00 3.51
508 680 6.648725 ACACAGAGAAGCACTAGAAAGAAATC 59.351 38.462 0.00 0.00 0.00 2.17
518 690 3.170991 ACCCTACACAGAGAAGCACTA 57.829 47.619 0.00 0.00 0.00 2.74
523 695 3.566322 CGATCCTACCCTACACAGAGAAG 59.434 52.174 0.00 0.00 0.00 2.85
525 697 2.775960 TCGATCCTACCCTACACAGAGA 59.224 50.000 0.00 0.00 0.00 3.10
526 698 2.879646 GTCGATCCTACCCTACACAGAG 59.120 54.545 0.00 0.00 0.00 3.35
528 700 2.879646 GAGTCGATCCTACCCTACACAG 59.120 54.545 0.00 0.00 0.00 3.66
529 701 2.744166 CGAGTCGATCCTACCCTACACA 60.744 54.545 6.73 0.00 0.00 3.72
530 702 1.872313 CGAGTCGATCCTACCCTACAC 59.128 57.143 6.73 0.00 0.00 2.90
555 745 5.187381 TCTCCTCTGATCTGCATGATTATCC 59.813 44.000 0.00 0.00 35.14 2.59
576 766 2.386661 TCAAACGGCTCCATCTTCTC 57.613 50.000 0.00 0.00 0.00 2.87
644 834 4.379339 TTGTAATCATGTCGATCGTGGA 57.621 40.909 15.94 8.89 31.11 4.02
645 835 5.063438 ACTTTTGTAATCATGTCGATCGTGG 59.937 40.000 15.94 3.51 31.11 4.94
646 836 6.094739 ACTTTTGTAATCATGTCGATCGTG 57.905 37.500 15.94 6.43 31.11 4.35
647 837 6.721571 AACTTTTGTAATCATGTCGATCGT 57.278 33.333 15.94 0.00 31.11 3.73
648 838 8.380644 ACTAAACTTTTGTAATCATGTCGATCG 58.619 33.333 9.36 9.36 31.11 3.69
649 839 9.478019 CACTAAACTTTTGTAATCATGTCGATC 57.522 33.333 0.00 0.00 31.11 3.69
650 840 8.450964 CCACTAAACTTTTGTAATCATGTCGAT 58.549 33.333 0.00 0.00 35.12 3.59
651 841 7.572353 GCCACTAAACTTTTGTAATCATGTCGA 60.572 37.037 0.00 0.00 0.00 4.20
684 874 6.425504 GCTACTAAGTTAAGCATGCTTGATG 58.574 40.000 37.21 22.88 37.47 3.07
685 875 5.529060 GGCTACTAAGTTAAGCATGCTTGAT 59.471 40.000 37.21 23.28 38.01 2.57
686 876 4.876107 GGCTACTAAGTTAAGCATGCTTGA 59.124 41.667 37.21 29.12 38.01 3.02
688 878 4.636206 GTGGCTACTAAGTTAAGCATGCTT 59.364 41.667 33.70 33.70 38.01 3.91
699 889 1.348064 TGTGCTGGTGGCTACTAAGT 58.652 50.000 0.00 0.00 42.39 2.24
703 893 3.200825 AGAATATTGTGCTGGTGGCTACT 59.799 43.478 0.00 0.00 42.39 2.57
704 894 3.313526 CAGAATATTGTGCTGGTGGCTAC 59.686 47.826 0.00 0.00 42.39 3.58
705 895 3.544684 CAGAATATTGTGCTGGTGGCTA 58.455 45.455 0.00 0.00 42.39 3.93
706 896 2.372264 CAGAATATTGTGCTGGTGGCT 58.628 47.619 0.00 0.00 42.39 4.75
715 910 3.059325 GCTCTAAGCGGCAGAATATTGTG 60.059 47.826 8.21 8.21 0.00 3.33
747 986 3.114616 TCCGTCGTCTCGTCGTCC 61.115 66.667 7.75 0.00 36.79 4.79
749 988 3.771491 CGTCCGTCGTCTCGTCGT 61.771 66.667 7.75 0.00 36.79 4.34
750 989 3.473166 TCGTCCGTCGTCTCGTCG 61.473 66.667 2.43 2.43 40.80 5.12
835 1075 0.104934 ATAATGGTCGGCCTCCCTCT 60.105 55.000 7.97 0.00 35.27 3.69
836 1076 1.640917 TATAATGGTCGGCCTCCCTC 58.359 55.000 7.97 0.00 35.27 4.30
837 1077 1.697982 GTTATAATGGTCGGCCTCCCT 59.302 52.381 7.97 0.00 35.27 4.20
838 1078 1.271217 GGTTATAATGGTCGGCCTCCC 60.271 57.143 7.97 0.00 35.27 4.30
839 1079 1.271217 GGGTTATAATGGTCGGCCTCC 60.271 57.143 7.97 3.76 35.27 4.30
924 1177 5.047377 ACTCTCTAGCTTCTTCTTCCTTGTG 60.047 44.000 0.00 0.00 0.00 3.33
925 1178 5.083821 ACTCTCTAGCTTCTTCTTCCTTGT 58.916 41.667 0.00 0.00 0.00 3.16
926 1179 5.650543 GACTCTCTAGCTTCTTCTTCCTTG 58.349 45.833 0.00 0.00 0.00 3.61
998 1262 4.082523 CCGTCCACCTCGCCATGT 62.083 66.667 0.00 0.00 0.00 3.21
1332 1599 4.814294 GGCGTCGCAGGGGTGTAG 62.814 72.222 20.50 0.00 0.00 2.74
1553 1820 2.434884 ATCACAAGGCGACGGCTG 60.435 61.111 25.70 19.68 38.81 4.85
1573 1840 2.410469 GATGCTGCGTTGATGGGC 59.590 61.111 0.00 0.00 0.00 5.36
1575 1842 3.489731 ACGATGCTGCGTTGATGG 58.510 55.556 15.83 0.00 42.71 3.51
1582 1849 2.023741 GCATGGAACGATGCTGCG 59.976 61.111 13.00 0.00 44.57 5.18
1583 1850 1.936436 TTGGCATGGAACGATGCTGC 61.936 55.000 17.96 0.00 46.74 5.25
1585 1852 1.033746 CCTTGGCATGGAACGATGCT 61.034 55.000 13.94 0.00 46.74 3.79
1586 1853 1.315257 ACCTTGGCATGGAACGATGC 61.315 55.000 24.70 12.11 46.82 3.91
1587 1854 1.670811 GTACCTTGGCATGGAACGATG 59.329 52.381 24.70 0.00 0.00 3.84
1592 1862 0.958382 GCGTGTACCTTGGCATGGAA 60.958 55.000 24.70 8.04 0.00 3.53
1593 1863 1.376683 GCGTGTACCTTGGCATGGA 60.377 57.895 24.70 6.90 0.00 3.41
1657 1934 0.673022 GGCTCCATGGATCGATCAGC 60.673 60.000 25.93 23.00 0.00 4.26
1659 1936 1.667722 CGGCTCCATGGATCGATCA 59.332 57.895 25.93 13.02 0.00 2.92
1687 1968 1.011968 CACCATGGTCACCACGTACG 61.012 60.000 16.53 15.01 35.80 3.67
1688 1969 0.319083 TCACCATGGTCACCACGTAC 59.681 55.000 16.53 0.00 35.80 3.67
1689 1970 0.319083 GTCACCATGGTCACCACGTA 59.681 55.000 16.53 0.00 35.80 3.57
1690 1971 1.070786 GTCACCATGGTCACCACGT 59.929 57.895 16.53 0.00 35.80 4.49
1723 2004 1.335142 GGAAAAACGTACGCCATGCAA 60.335 47.619 16.72 0.00 0.00 4.08
1742 2035 4.496341 CGGAATCAACGGAATTCAATGAGG 60.496 45.833 7.93 0.00 0.00 3.86
1743 2036 4.094887 ACGGAATCAACGGAATTCAATGAG 59.905 41.667 7.93 0.04 35.23 2.90
1745 2038 4.097714 CACGGAATCAACGGAATTCAATG 58.902 43.478 7.93 3.08 35.23 2.82
1928 2235 4.517285 TCCTATGATTGACTGACCAAAGC 58.483 43.478 0.00 0.00 0.00 3.51
2099 2454 2.046988 CATCAGGCAGCACCACGA 60.047 61.111 0.00 0.00 43.14 4.35
2101 2456 1.135199 CAATTCATCAGGCAGCACCAC 60.135 52.381 0.00 0.00 43.14 4.16
2110 2465 7.490402 GGATAGCAAAAGAAACAATTCATCAGG 59.510 37.037 0.00 0.00 38.06 3.86
2124 2479 4.576053 CACAATGATCGGGATAGCAAAAGA 59.424 41.667 0.00 0.00 0.00 2.52
2143 2498 1.751924 GGTTGGTTAGGTTGCACACAA 59.248 47.619 0.00 0.00 0.00 3.33
2159 2514 7.041916 TCGTTAATGTACCTAACACAAAGGTTG 60.042 37.037 12.78 0.00 45.26 3.77
2165 2520 7.329226 GCTAGTTCGTTAATGTACCTAACACAA 59.671 37.037 12.78 4.89 42.09 3.33
2195 2550 4.034279 GCTCAACGTGTTAACACTGGTTAA 59.966 41.667 30.47 16.56 44.88 2.01
2196 2551 3.556775 GCTCAACGTGTTAACACTGGTTA 59.443 43.478 30.47 16.26 44.34 2.85
2197 2552 2.353579 GCTCAACGTGTTAACACTGGTT 59.646 45.455 30.47 24.85 44.34 3.67
2198 2553 1.937899 GCTCAACGTGTTAACACTGGT 59.062 47.619 30.47 21.25 44.34 4.00
2199 2554 1.937223 TGCTCAACGTGTTAACACTGG 59.063 47.619 30.47 20.67 44.34 4.00
2200 2555 2.286184 GGTGCTCAACGTGTTAACACTG 60.286 50.000 30.47 25.37 44.34 3.66
2201 2556 1.937899 GGTGCTCAACGTGTTAACACT 59.062 47.619 30.47 17.83 44.34 3.55
2202 2557 1.003223 GGGTGCTCAACGTGTTAACAC 60.003 52.381 25.73 25.73 43.15 3.32
2203 2558 1.301423 GGGTGCTCAACGTGTTAACA 58.699 50.000 3.59 3.59 0.00 2.41
2256 2632 1.514678 GGATGGCGTGTGCTTGTTCA 61.515 55.000 0.00 0.00 42.25 3.18
2257 2633 1.210155 GGATGGCGTGTGCTTGTTC 59.790 57.895 0.00 0.00 42.25 3.18
2258 2634 2.616330 CGGATGGCGTGTGCTTGTT 61.616 57.895 0.00 0.00 42.25 2.83
2259 2635 2.803155 ATCGGATGGCGTGTGCTTGT 62.803 55.000 0.00 0.00 42.25 3.16
2260 2636 2.040213 GATCGGATGGCGTGTGCTTG 62.040 60.000 0.00 0.00 42.25 4.01
2261 2637 1.815421 GATCGGATGGCGTGTGCTT 60.815 57.895 0.00 0.00 42.25 3.91
2262 2638 2.202932 GATCGGATGGCGTGTGCT 60.203 61.111 0.00 0.00 42.25 4.40
2324 2700 2.711711 GACCTCGTCGGCCACTATA 58.288 57.895 2.24 0.00 35.61 1.31
2325 2701 3.522808 GACCTCGTCGGCCACTAT 58.477 61.111 2.24 0.00 35.61 2.12
2396 2781 4.459331 CACATTTCCGCACCGCCG 62.459 66.667 0.00 0.00 0.00 6.46


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

AutoCloner maintained by Alex Coulton.