Multiple sequence alignment - TraesCS4A01G456200

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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 TraesCS4A01G456200 chr4A 100.000 2339 0 0 1 2339 720957854 720955516 0.000000e+00 4320.0
1 TraesCS4A01G456200 chr4A 89.497 457 42 2 1 457 721238217 721237767 7.250000e-160 573.0
2 TraesCS4A01G456200 chr4A 85.043 468 51 10 456 922 721237732 721237283 2.120000e-125 459.0
3 TraesCS4A01G456200 chr7D 86.720 1378 111 25 993 2339 14907346 14908682 0.000000e+00 1465.0
4 TraesCS4A01G456200 chr7D 91.904 457 36 1 1 457 14906393 14906848 2.530000e-179 638.0
5 TraesCS4A01G456200 chr7D 90.094 424 34 4 544 965 14906930 14907347 5.680000e-151 544.0
6 TraesCS4A01G456200 chr7D 95.833 48 2 0 458 505 14906885 14906932 6.930000e-11 78.7
7 TraesCS4A01G456200 chrUn 84.889 225 30 4 1899 2121 135321600 135321378 8.410000e-55 224.0
8 TraesCS4A01G456200 chrUn 84.889 225 30 4 1899 2121 135354754 135354532 8.410000e-55 224.0
9 TraesCS4A01G456200 chrUn 84.889 225 30 4 1899 2121 239422206 239421984 8.410000e-55 224.0
10 TraesCS4A01G456200 chrUn 84.889 225 30 4 1899 2121 245489241 245489019 8.410000e-55 224.0
11 TraesCS4A01G456200 chrUn 84.649 228 31 4 1896 2121 367976714 367976939 8.410000e-55 224.0
12 TraesCS4A01G456200 chrUn 84.211 228 32 4 1896 2121 91000243 91000468 3.910000e-53 219.0
13 TraesCS4A01G456200 chrUn 84.211 228 32 4 1896 2121 91056650 91056875 3.910000e-53 219.0
14 TraesCS4A01G456200 chrUn 83.700 227 34 3 1896 2121 91107478 91107702 6.550000e-51 211.0
15 TraesCS4A01G456200 chr3D 84.211 228 33 2 1895 2121 158362189 158361964 3.910000e-53 219.0


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 TraesCS4A01G456200 chr4A 720955516 720957854 2338 True 4320.000 4320 100.00000 1 2339 1 chr4A.!!$R1 2338
1 TraesCS4A01G456200 chr4A 721237283 721238217 934 True 516.000 573 87.27000 1 922 2 chr4A.!!$R2 921
2 TraesCS4A01G456200 chr7D 14906393 14908682 2289 False 681.425 1465 91.13775 1 2339 4 chr7D.!!$F1 2338

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
755 792 0.174389 CACACCCCTCTGTCATCTCG 59.826 60.0 0.0 0.0 0.0 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2081 2148 0.036022 AAGAAGCACTCTGGCCTGAC 59.964 55.0 8.48 0.0 33.37 3.51 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
31 32 9.659135 TCATAAGTCAATTTTGATCCCCATTAT 57.341 29.630 0.00 0.00 39.73 1.28
34 35 6.585416 AGTCAATTTTGATCCCCATTATTGC 58.415 36.000 0.00 0.00 39.73 3.56
40 41 0.251341 ATCCCCATTATTGCGCCTCC 60.251 55.000 4.18 0.00 0.00 4.30
50 51 0.248012 TTGCGCCTCCGAACAATCTA 59.752 50.000 4.18 0.00 36.29 1.98
68 69 8.000780 ACAATCTACTCCAAATTATCCAAAGC 57.999 34.615 0.00 0.00 0.00 3.51
86 87 1.000521 CCTGGGATGCAAGCTTGGA 60.001 57.895 27.10 25.42 0.00 3.53
186 187 9.319143 GTTAGCAGATTGAAAGAAGATTAGCTA 57.681 33.333 0.00 0.00 0.00 3.32
191 192 9.206870 CAGATTGAAAGAAGATTAGCTAGATCC 57.793 37.037 0.00 0.94 0.00 3.36
209 210 3.548745 TCCTCCACTATGCTCACATTG 57.451 47.619 0.00 0.00 37.74 2.82
210 211 3.106827 TCCTCCACTATGCTCACATTGA 58.893 45.455 0.00 0.00 37.74 2.57
212 213 3.624861 CCTCCACTATGCTCACATTGAAC 59.375 47.826 0.00 0.00 37.74 3.18
237 238 8.105197 ACGGGAGATTGGTTTTACTTAAGTATT 58.895 33.333 15.92 0.00 0.00 1.89
284 285 5.489792 TTCATGAGCACTTTACCTCTTCT 57.510 39.130 0.00 0.00 0.00 2.85
288 289 6.211584 TCATGAGCACTTTACCTCTTCTAGTT 59.788 38.462 0.00 0.00 0.00 2.24
290 291 5.538813 TGAGCACTTTACCTCTTCTAGTTGA 59.461 40.000 0.00 0.00 0.00 3.18
332 333 9.097257 CAACAAATTTTTGAGGCTTTTCTTCTA 57.903 29.630 9.88 0.00 40.55 2.10
376 377 0.688749 AGGGCCTGCATTGATTTCCC 60.689 55.000 4.50 0.00 0.00 3.97
435 436 2.299582 TGGCATTTTGGATGTGTCCTTG 59.700 45.455 0.00 0.00 45.32 3.61
448 449 1.824230 TGTCCTTGCACAACAAAGCTT 59.176 42.857 0.00 0.00 37.96 3.74
451 452 3.062504 GTCCTTGCACAACAAAGCTTTTG 59.937 43.478 9.53 9.18 37.96 2.44
493 530 9.758651 GTTTGATTTGGGAAAAATACTACACTT 57.241 29.630 0.00 0.00 0.00 3.16
500 537 7.284074 TGGGAAAAATACTACACTTCTCAACA 58.716 34.615 0.00 0.00 0.00 3.33
502 539 8.451748 GGGAAAAATACTACACTTCTCAACATC 58.548 37.037 0.00 0.00 0.00 3.06
508 545 6.518208 ACTACACTTCTCAACATCCTAGAC 57.482 41.667 0.00 0.00 0.00 2.59
526 563 6.890814 TCCTAGACTTAAAGTAGAGGGTTCTG 59.109 42.308 0.00 0.00 33.27 3.02
528 565 4.223255 AGACTTAAAGTAGAGGGTTCTGGC 59.777 45.833 0.00 0.00 34.79 4.85
530 567 5.339477 ACTTAAAGTAGAGGGTTCTGGCTA 58.661 41.667 0.00 0.00 34.79 3.93
557 594 3.299503 AGAACCACCTGAAATTGTTGCT 58.700 40.909 0.00 0.00 0.00 3.91
611 648 4.043596 AGGCAATGGGAGAGAAACTCTAT 58.956 43.478 1.12 0.00 41.35 1.98
615 652 6.267928 GGCAATGGGAGAGAAACTCTATAGTA 59.732 42.308 0.00 0.00 41.35 1.82
657 694 5.130311 ACCAACCTTTATGGCAAAAGTTTCT 59.870 36.000 15.84 0.00 41.89 2.52
659 696 7.016170 ACCAACCTTTATGGCAAAAGTTTCTAT 59.984 33.333 15.84 0.00 41.89 1.98
661 698 7.539034 ACCTTTATGGCAAAAGTTTCTATGT 57.461 32.000 15.84 6.71 40.22 2.29
689 726 7.362401 GCACTCCTTTGTGACAAATGATAATCT 60.362 37.037 11.58 0.00 40.12 2.40
710 747 8.682936 AATCTAATTGTGGCTACCTGAATAAG 57.317 34.615 0.00 0.00 0.00 1.73
719 756 5.163301 TGGCTACCTGAATAAGCTCTTAAGG 60.163 44.000 9.83 9.83 36.48 2.69
722 759 6.824196 GCTACCTGAATAAGCTCTTAAGGTTT 59.176 38.462 18.67 0.95 40.24 3.27
755 792 0.174389 CACACCCCTCTGTCATCTCG 59.826 60.000 0.00 0.00 0.00 4.04
771 808 5.408604 GTCATCTCGTACAACCAGTTCATTT 59.591 40.000 0.00 0.00 0.00 2.32
819 856 7.150783 AGAAAAGAGTTGCATGTTAAGGATC 57.849 36.000 0.00 0.00 0.00 3.36
821 858 8.103305 AGAAAAGAGTTGCATGTTAAGGATCTA 58.897 33.333 0.00 0.00 0.00 1.98
932 971 5.578727 AGTCGATCTAGAAATGTTCTTGCAC 59.421 40.000 0.00 0.00 41.14 4.57
933 972 5.348724 GTCGATCTAGAAATGTTCTTGCACA 59.651 40.000 0.00 0.00 41.14 4.57
965 1004 1.826096 GGTCTTTCTCCGGCTACTTCT 59.174 52.381 0.00 0.00 0.00 2.85
966 1005 3.022406 GGTCTTTCTCCGGCTACTTCTA 58.978 50.000 0.00 0.00 0.00 2.10
967 1006 3.637694 GGTCTTTCTCCGGCTACTTCTAT 59.362 47.826 0.00 0.00 0.00 1.98
968 1007 4.826183 GGTCTTTCTCCGGCTACTTCTATA 59.174 45.833 0.00 0.00 0.00 1.31
969 1008 5.477637 GGTCTTTCTCCGGCTACTTCTATAT 59.522 44.000 0.00 0.00 0.00 0.86
970 1009 6.383415 GTCTTTCTCCGGCTACTTCTATATG 58.617 44.000 0.00 0.00 0.00 1.78
971 1010 6.207025 GTCTTTCTCCGGCTACTTCTATATGA 59.793 42.308 0.00 0.00 0.00 2.15
972 1011 6.948886 TCTTTCTCCGGCTACTTCTATATGAT 59.051 38.462 0.00 0.00 0.00 2.45
973 1012 8.107729 TCTTTCTCCGGCTACTTCTATATGATA 58.892 37.037 0.00 0.00 0.00 2.15
974 1013 7.867305 TTCTCCGGCTACTTCTATATGATAG 57.133 40.000 0.00 0.00 0.00 2.08
975 1014 7.196637 TCTCCGGCTACTTCTATATGATAGA 57.803 40.000 0.00 0.00 0.00 1.98
976 1015 7.276658 TCTCCGGCTACTTCTATATGATAGAG 58.723 42.308 0.00 0.00 0.00 2.43
977 1016 6.959904 TCCGGCTACTTCTATATGATAGAGT 58.040 40.000 0.00 1.76 0.00 3.24
978 1017 7.403671 TCCGGCTACTTCTATATGATAGAGTT 58.596 38.462 0.00 0.00 0.00 3.01
979 1018 8.546322 TCCGGCTACTTCTATATGATAGAGTTA 58.454 37.037 0.00 0.00 0.00 2.24
980 1019 9.175312 CCGGCTACTTCTATATGATAGAGTTAA 57.825 37.037 0.00 0.00 0.00 2.01
981 1020 9.991388 CGGCTACTTCTATATGATAGAGTTAAC 57.009 37.037 0.00 0.00 0.00 2.01
1006 1045 8.797438 ACTCCAGAAATCTCCTAAAAATGAAAC 58.203 33.333 0.00 0.00 0.00 2.78
1022 1061 7.855784 AAATGAAACCCTTCCATTTAGAGTT 57.144 32.000 0.00 0.00 0.00 3.01
1062 1113 6.146184 TCTCTAATGAAAGCACTGAAGAAACG 59.854 38.462 0.00 0.00 0.00 3.60
1069 1120 1.527311 GCACTGAAGAAACGTCCAGAC 59.473 52.381 0.00 0.00 0.00 3.51
1071 1122 3.194861 CACTGAAGAAACGTCCAGACAA 58.805 45.455 0.00 0.00 0.00 3.18
1084 1135 2.241176 TCCAGACAACTTTTGTGGGTCT 59.759 45.455 0.00 0.00 45.52 3.85
1097 1148 0.318441 TGGGTCTGTTGCTTCTCTCG 59.682 55.000 0.00 0.00 0.00 4.04
1125 1176 1.354368 TGGAACAACATCCTTCCTCCC 59.646 52.381 0.00 0.00 40.35 4.30
1157 1208 8.808092 ACTAGGTAGCTCTATTTTGGATGATAC 58.192 37.037 0.00 0.00 0.00 2.24
1188 1239 1.221293 CCAGCTGCTTCCCTCTCAG 59.779 63.158 8.66 0.00 0.00 3.35
1216 1267 6.845908 ACTATGGAAATAGTCATTCATGGCT 58.154 36.000 0.00 0.00 46.01 4.75
1275 1333 5.975988 ATGAGGTCCCTAATGTGTATTGT 57.024 39.130 0.00 0.00 0.00 2.71
1357 1417 5.061853 CCTAGTGGTCTTCATGAATGGATG 58.938 45.833 8.96 0.00 0.00 3.51
1369 1429 2.509131 TGAATGGATGGGTGCACATCTA 59.491 45.455 20.43 12.27 45.11 1.98
1374 1434 3.079578 GGATGGGTGCACATCTATGATG 58.920 50.000 20.43 6.06 45.11 3.07
1379 1439 3.562973 GGGTGCACATCTATGATGAACTG 59.437 47.826 20.43 3.99 0.00 3.16
1416 1476 5.104610 AGCAACTGGACTCTGAACATGATAT 60.105 40.000 0.00 0.00 0.00 1.63
1418 1478 6.763135 GCAACTGGACTCTGAACATGATATTA 59.237 38.462 0.00 0.00 0.00 0.98
1419 1479 7.443575 GCAACTGGACTCTGAACATGATATTAT 59.556 37.037 0.00 0.00 0.00 1.28
1420 1480 8.771766 CAACTGGACTCTGAACATGATATTATG 58.228 37.037 0.00 5.95 0.00 1.90
1421 1481 8.255111 ACTGGACTCTGAACATGATATTATGA 57.745 34.615 13.98 0.00 0.00 2.15
1422 1482 8.366401 ACTGGACTCTGAACATGATATTATGAG 58.634 37.037 13.98 3.53 0.00 2.90
1423 1483 8.482852 TGGACTCTGAACATGATATTATGAGA 57.517 34.615 13.98 5.97 0.00 3.27
1525 1592 7.552687 TGAAAAATATCATACAGTCTCGGCTTT 59.447 33.333 0.00 0.00 0.00 3.51
1567 1634 5.483811 TGTATCAGCGAATAAAGACACCAA 58.516 37.500 0.00 0.00 0.00 3.67
1603 1670 4.599047 AGGTCTATTAGAGCATGCTCAC 57.401 45.455 40.91 30.00 44.69 3.51
1605 1672 3.070159 GGTCTATTAGAGCATGCTCACCA 59.930 47.826 40.91 27.37 44.99 4.17
1666 1733 1.473677 CCGATGCCATTGCTTGAGAAA 59.526 47.619 0.00 0.00 38.71 2.52
1677 1744 2.494471 TGCTTGAGAAAATCCATGCCTG 59.506 45.455 0.00 0.00 33.97 4.85
1712 1779 7.039011 TGGGTAATACATGTGGATGAGATAGAC 60.039 40.741 9.11 0.00 33.36 2.59
1731 1798 3.327757 AGACCAATGCAGAAGGAACTACA 59.672 43.478 8.66 0.00 38.49 2.74
1732 1799 4.072131 GACCAATGCAGAAGGAACTACAA 58.928 43.478 8.66 0.00 38.49 2.41
1737 1804 4.365514 TGCAGAAGGAACTACAATGGAA 57.634 40.909 0.00 0.00 38.49 3.53
1757 1824 4.021544 GGAATTGTAAGGCAACCACATTCA 60.022 41.667 0.00 0.00 40.28 2.57
1772 1839 1.538512 CATTCACCAGACAAGCACCTG 59.461 52.381 0.00 0.00 0.00 4.00
1781 1848 3.190118 CAGACAAGCACCTGGAAATTCTC 59.810 47.826 0.00 0.00 0.00 2.87
1812 1879 6.183360 ACGACTAGGATGTATAGCGATGAATC 60.183 42.308 0.00 0.00 0.00 2.52
1813 1880 6.037720 CGACTAGGATGTATAGCGATGAATCT 59.962 42.308 0.00 0.00 0.00 2.40
1871 1938 2.896685 TGGGTTGAGCTTTGGTATTTGG 59.103 45.455 0.00 0.00 0.00 3.28
1877 1944 6.152831 GGTTGAGCTTTGGTATTTGGTATTCT 59.847 38.462 0.00 0.00 0.00 2.40
1933 2000 3.741707 TGTGGCATGAACACATGGA 57.258 47.368 16.66 0.00 43.35 3.41
1970 2037 5.973899 TTTATGGCAAGTTTAGTGATGCA 57.026 34.783 0.00 0.00 40.51 3.96
1977 2044 4.156556 GCAAGTTTAGTGATGCAAGGATGA 59.843 41.667 0.00 0.00 38.63 2.92
1985 2052 5.316167 AGTGATGCAAGGATGACAACTTTA 58.684 37.500 0.00 0.00 0.00 1.85
1986 2053 5.413833 AGTGATGCAAGGATGACAACTTTAG 59.586 40.000 0.00 0.00 0.00 1.85
1987 2054 4.701651 TGATGCAAGGATGACAACTTTAGG 59.298 41.667 0.00 0.00 0.00 2.69
1988 2055 2.819608 TGCAAGGATGACAACTTTAGGC 59.180 45.455 0.00 0.00 0.00 3.93
1989 2056 2.159517 GCAAGGATGACAACTTTAGGCG 60.160 50.000 0.00 0.00 0.00 5.52
1990 2057 2.403252 AGGATGACAACTTTAGGCGG 57.597 50.000 0.00 0.00 0.00 6.13
1991 2058 0.733150 GGATGACAACTTTAGGCGGC 59.267 55.000 0.00 0.00 0.00 6.53
1992 2059 1.448985 GATGACAACTTTAGGCGGCA 58.551 50.000 13.08 0.00 0.00 5.69
1993 2060 1.810151 GATGACAACTTTAGGCGGCAA 59.190 47.619 13.08 0.11 0.00 4.52
1994 2061 1.234821 TGACAACTTTAGGCGGCAAG 58.765 50.000 13.08 9.77 0.00 4.01
2006 2073 3.871775 CGGCAAGCATGACAACTTT 57.128 47.368 0.00 0.00 32.33 2.66
2007 2074 2.987413 CGGCAAGCATGACAACTTTA 57.013 45.000 0.00 0.00 32.33 1.85
2019 2086 8.806146 AGCATGACAACTTTATTTTTGGATAGT 58.194 29.630 0.00 0.00 0.00 2.12
2071 2138 1.909700 TTGGGATGGCAACTTCAGTC 58.090 50.000 0.00 0.00 42.34 3.51
2078 2145 4.156008 GGATGGCAACTTCAGTCGTAAAAT 59.844 41.667 0.00 0.00 42.34 1.82
2080 2147 5.600908 TGGCAACTTCAGTCGTAAAATAC 57.399 39.130 0.00 0.00 37.61 1.89
2081 2148 4.150980 TGGCAACTTCAGTCGTAAAATACG 59.849 41.667 3.63 3.63 46.05 3.06
2099 2167 1.676384 GTCAGGCCAGAGTGCTTCT 59.324 57.895 5.01 0.00 36.25 2.85
2101 2169 0.767375 TCAGGCCAGAGTGCTTCTTT 59.233 50.000 5.01 0.00 32.41 2.52
2102 2170 0.879765 CAGGCCAGAGTGCTTCTTTG 59.120 55.000 5.01 0.00 32.41 2.77
2103 2171 0.892814 AGGCCAGAGTGCTTCTTTGC 60.893 55.000 5.01 0.00 32.41 3.68
2111 2179 2.476772 TGCTTCTTTGCACACGTGT 58.523 47.368 17.22 17.22 38.12 4.49
2130 2198 9.865321 ACACGTGTGATACTTATTACACTTATT 57.135 29.630 22.71 0.00 45.52 1.40
2207 2276 5.465532 AGATCTACATGCATCGATCAACT 57.534 39.130 22.35 7.99 35.81 3.16
2211 2280 3.257469 ACATGCATCGATCAACTCAGT 57.743 42.857 0.00 0.00 0.00 3.41
2265 2334 2.587522 GCCAGGTTTTCTTCTGTTCCT 58.412 47.619 0.00 0.00 0.00 3.36
2269 2338 3.316308 CAGGTTTTCTTCTGTTCCTGGTG 59.684 47.826 0.00 0.00 38.81 4.17
2272 2341 2.930826 TTCTTCTGTTCCTGGTGGAC 57.069 50.000 0.00 0.00 43.06 4.02
2331 2400 0.252197 AAGGTATGAAGTCGGTGCCC 59.748 55.000 0.00 0.00 0.00 5.36
2332 2401 0.907704 AGGTATGAAGTCGGTGCCCA 60.908 55.000 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 0.478072 AGGCGCAATAATGGGGATCA 59.522 50.000 10.83 0.00 39.74 2.92
31 32 0.248012 TAGATTGTTCGGAGGCGCAA 59.752 50.000 10.83 0.00 0.00 4.85
34 35 1.536284 GGAGTAGATTGTTCGGAGGCG 60.536 57.143 0.00 0.00 0.00 5.52
40 41 7.786178 TGGATAATTTGGAGTAGATTGTTCG 57.214 36.000 0.00 0.00 0.00 3.95
67 68 2.718073 CCAAGCTTGCATCCCAGGC 61.718 63.158 21.43 0.00 46.08 4.85
68 69 0.612732 TTCCAAGCTTGCATCCCAGG 60.613 55.000 21.43 4.85 0.00 4.45
86 87 5.012893 CCCAGATAAGTGAAAGGAAAGCTT 58.987 41.667 0.00 0.00 0.00 3.74
106 107 1.295423 GTGCTAAGACGAAGGCCCA 59.705 57.895 0.00 0.00 0.00 5.36
186 187 3.037851 TGTGAGCATAGTGGAGGATCT 57.962 47.619 0.00 0.00 33.73 2.75
191 192 3.308053 CGTTCAATGTGAGCATAGTGGAG 59.692 47.826 0.00 0.00 34.39 3.86
209 210 6.429078 ACTTAAGTAAAACCAATCTCCCGTTC 59.571 38.462 6.26 0.00 0.00 3.95
210 211 6.301486 ACTTAAGTAAAACCAATCTCCCGTT 58.699 36.000 6.26 0.00 0.00 4.44
212 213 8.502105 AATACTTAAGTAAAACCAATCTCCCG 57.498 34.615 18.88 0.00 33.76 5.14
241 242 9.199645 CATGAATATGATAGGGAGAGTACAGAT 57.800 37.037 0.00 0.00 36.36 2.90
242 243 8.394040 TCATGAATATGATAGGGAGAGTACAGA 58.606 37.037 0.00 0.00 38.37 3.41
243 244 8.586879 TCATGAATATGATAGGGAGAGTACAG 57.413 38.462 0.00 0.00 38.37 2.74
244 245 7.123397 GCTCATGAATATGATAGGGAGAGTACA 59.877 40.741 0.00 0.00 42.19 2.90
245 246 7.123397 TGCTCATGAATATGATAGGGAGAGTAC 59.877 40.741 0.00 0.00 42.19 2.73
261 262 6.059787 AGAAGAGGTAAAGTGCTCATGAAT 57.940 37.500 0.00 0.00 0.00 2.57
448 449 0.251297 CTGACCCAGGGCATCACAAA 60.251 55.000 4.91 0.00 0.00 2.83
451 452 0.251341 AAACTGACCCAGGGCATCAC 60.251 55.000 4.91 0.00 35.51 3.06
493 530 9.179909 CTCTACTTTAAGTCTAGGATGTTGAGA 57.820 37.037 0.00 0.00 31.40 3.27
500 537 7.562088 CAGAACCCTCTACTTTAAGTCTAGGAT 59.438 40.741 20.60 12.40 34.07 3.24
502 539 6.097129 CCAGAACCCTCTACTTTAAGTCTAGG 59.903 46.154 14.99 14.99 32.76 3.02
508 545 4.828072 AGCCAGAACCCTCTACTTTAAG 57.172 45.455 0.00 0.00 0.00 1.85
611 648 8.771521 TGGTCATAGCAATTACCTTACTACTA 57.228 34.615 0.00 0.00 31.60 1.82
615 652 6.069615 AGGTTGGTCATAGCAATTACCTTACT 60.070 38.462 0.00 0.00 37.94 2.24
628 665 5.913137 TTTGCCATAAAGGTTGGTCATAG 57.087 39.130 0.00 0.00 40.61 2.23
657 694 3.814625 TGTCACAAAGGAGTGCAACATA 58.185 40.909 0.00 0.00 41.43 2.29
659 696 2.121291 TGTCACAAAGGAGTGCAACA 57.879 45.000 0.00 0.00 41.43 3.33
661 698 3.698539 TCATTTGTCACAAAGGAGTGCAA 59.301 39.130 13.51 0.00 39.35 4.08
689 726 6.001449 AGCTTATTCAGGTAGCCACAATTA 57.999 37.500 0.00 0.00 35.53 1.40
710 747 4.460731 AGGATTGAGCAAAACCTTAAGAGC 59.539 41.667 3.36 0.20 30.89 4.09
719 756 3.552890 GGTGTGGAAGGATTGAGCAAAAC 60.553 47.826 0.00 0.00 0.00 2.43
722 759 1.547675 GGGTGTGGAAGGATTGAGCAA 60.548 52.381 0.00 0.00 0.00 3.91
794 831 8.103305 AGATCCTTAACATGCAACTCTTTTCTA 58.897 33.333 0.00 0.00 0.00 2.10
796 833 7.150783 AGATCCTTAACATGCAACTCTTTTC 57.849 36.000 0.00 0.00 0.00 2.29
801 838 6.291377 TCCATAGATCCTTAACATGCAACTC 58.709 40.000 0.00 0.00 0.00 3.01
819 856 1.065199 TCTGCCTTGGCACTTCCATAG 60.065 52.381 10.65 0.00 46.04 2.23
821 858 0.323178 CTCTGCCTTGGCACTTCCAT 60.323 55.000 10.65 0.00 46.04 3.41
833 870 2.896039 ACAGAACTTAGGTCTCTGCCT 58.104 47.619 0.00 0.00 40.23 4.75
875 914 3.749665 TGTGATTTTCCTTTGGGCAAG 57.250 42.857 0.00 0.00 0.00 4.01
889 928 9.988350 GATCGACTTAAATAACACATTGTGATT 57.012 29.630 23.12 14.74 32.88 2.57
911 950 5.349817 AGTGTGCAAGAACATTTCTAGATCG 59.650 40.000 0.00 0.00 39.61 3.69
955 994 9.991388 GTTAACTCTATCATATAGAAGTAGCCG 57.009 37.037 0.00 0.00 0.00 5.52
968 1007 8.646900 GGAGATTTCTGGAGTTAACTCTATCAT 58.353 37.037 29.66 17.62 42.48 2.45
969 1008 7.841729 AGGAGATTTCTGGAGTTAACTCTATCA 59.158 37.037 29.66 19.99 42.48 2.15
970 1009 8.245195 AGGAGATTTCTGGAGTTAACTCTATC 57.755 38.462 29.66 19.72 42.48 2.08
971 1010 9.716556 TTAGGAGATTTCTGGAGTTAACTCTAT 57.283 33.333 29.66 13.04 42.48 1.98
972 1011 9.543231 TTTAGGAGATTTCTGGAGTTAACTCTA 57.457 33.333 29.66 24.64 42.48 2.43
973 1012 8.437274 TTTAGGAGATTTCTGGAGTTAACTCT 57.563 34.615 29.66 13.09 42.48 3.24
974 1013 9.503399 TTTTTAGGAGATTTCTGGAGTTAACTC 57.497 33.333 24.73 24.73 42.14 3.01
979 1018 8.940397 TTCATTTTTAGGAGATTTCTGGAGTT 57.060 30.769 0.00 0.00 0.00 3.01
980 1019 8.797438 GTTTCATTTTTAGGAGATTTCTGGAGT 58.203 33.333 0.00 0.00 0.00 3.85
981 1020 8.246871 GGTTTCATTTTTAGGAGATTTCTGGAG 58.753 37.037 0.00 0.00 0.00 3.86
982 1021 7.178451 GGGTTTCATTTTTAGGAGATTTCTGGA 59.822 37.037 0.00 0.00 0.00 3.86
983 1022 7.179160 AGGGTTTCATTTTTAGGAGATTTCTGG 59.821 37.037 0.00 0.00 0.00 3.86
984 1023 8.127150 AGGGTTTCATTTTTAGGAGATTTCTG 57.873 34.615 0.00 0.00 0.00 3.02
985 1024 8.727100 AAGGGTTTCATTTTTAGGAGATTTCT 57.273 30.769 0.00 0.00 0.00 2.52
986 1025 8.035394 GGAAGGGTTTCATTTTTAGGAGATTTC 58.965 37.037 0.00 0.00 34.90 2.17
987 1026 7.512402 TGGAAGGGTTTCATTTTTAGGAGATTT 59.488 33.333 0.00 0.00 34.90 2.17
988 1027 7.016296 TGGAAGGGTTTCATTTTTAGGAGATT 58.984 34.615 0.00 0.00 34.90 2.40
989 1028 6.561294 TGGAAGGGTTTCATTTTTAGGAGAT 58.439 36.000 0.00 0.00 34.90 2.75
990 1029 5.959512 TGGAAGGGTTTCATTTTTAGGAGA 58.040 37.500 0.00 0.00 34.90 3.71
991 1030 6.857437 ATGGAAGGGTTTCATTTTTAGGAG 57.143 37.500 0.00 0.00 34.90 3.69
992 1031 7.625498 AAATGGAAGGGTTTCATTTTTAGGA 57.375 32.000 0.79 0.00 34.90 2.94
993 1032 8.811994 TCTAAATGGAAGGGTTTCATTTTTAGG 58.188 33.333 10.45 2.05 34.89 2.69
1002 1041 8.047310 TCATAGAACTCTAAATGGAAGGGTTTC 58.953 37.037 0.00 0.00 37.79 2.78
1006 1045 7.995488 ACAATCATAGAACTCTAAATGGAAGGG 59.005 37.037 0.00 0.00 31.39 3.95
1062 1113 2.357952 GACCCACAAAAGTTGTCTGGAC 59.642 50.000 11.33 4.07 43.23 4.02
1069 1120 2.166254 AGCAACAGACCCACAAAAGTTG 59.834 45.455 0.00 0.00 39.32 3.16
1071 1122 2.143876 AGCAACAGACCCACAAAAGT 57.856 45.000 0.00 0.00 0.00 2.66
1084 1135 3.667497 ACAATCTCGAGAGAAGCAACA 57.333 42.857 21.52 0.00 41.36 3.33
1131 1182 7.863901 ATCATCCAAAATAGAGCTACCTAGT 57.136 36.000 0.00 0.00 0.00 2.57
1139 1190 9.606631 CTAATAGGGTATCATCCAAAATAGAGC 57.393 37.037 0.00 0.00 0.00 4.09
1144 1195 7.885399 GTGAGCTAATAGGGTATCATCCAAAAT 59.115 37.037 0.00 0.00 0.00 1.82
1210 1261 4.931002 CCTTTGAAACCAAATGTAGCCATG 59.069 41.667 0.00 0.00 33.55 3.66
1212 1263 4.219115 TCCTTTGAAACCAAATGTAGCCA 58.781 39.130 0.00 0.00 33.55 4.75
1216 1267 5.841237 TCCCATTCCTTTGAAACCAAATGTA 59.159 36.000 0.00 0.00 33.55 2.29
1275 1333 3.504520 CCCGCTTTAGCTTAAACTTCCAA 59.495 43.478 0.00 0.00 39.32 3.53
1317 1376 5.221422 CCACTAGGTTTTTGCCTTGATTTCA 60.221 40.000 0.00 0.00 39.94 2.69
1318 1377 5.230182 CCACTAGGTTTTTGCCTTGATTTC 58.770 41.667 0.00 0.00 39.94 2.17
1348 1408 1.285667 AGATGTGCACCCATCCATTCA 59.714 47.619 15.69 0.00 41.79 2.57
1357 1417 3.562973 CAGTTCATCATAGATGTGCACCC 59.437 47.826 15.69 6.29 0.00 4.61
1379 1439 1.126846 CAGTTGCTACGTTGCTAGTGC 59.873 52.381 22.42 6.42 33.87 4.40
1390 1450 3.386768 TGTTCAGAGTCCAGTTGCTAC 57.613 47.619 0.00 0.00 0.00 3.58
1416 1476 8.593945 AAAGTTATCCAAAGCCATTCTCATAA 57.406 30.769 0.00 0.00 0.00 1.90
1418 1478 7.486407 AAAAGTTATCCAAAGCCATTCTCAT 57.514 32.000 0.00 0.00 0.00 2.90
1419 1479 6.916360 AAAAGTTATCCAAAGCCATTCTCA 57.084 33.333 0.00 0.00 0.00 3.27
1501 1568 7.865706 AAAGCCGAGACTGTATGATATTTTT 57.134 32.000 0.00 0.00 0.00 1.94
1543 1610 5.670485 TGGTGTCTTTATTCGCTGATACAT 58.330 37.500 0.00 0.00 0.00 2.29
1544 1611 5.079689 TGGTGTCTTTATTCGCTGATACA 57.920 39.130 0.00 0.00 0.00 2.29
1644 1711 2.105528 CAAGCAATGGCATCGGGC 59.894 61.111 0.00 5.51 44.61 6.13
1647 1714 2.925578 TTTCTCAAGCAATGGCATCG 57.074 45.000 0.00 0.00 44.61 3.84
1656 1723 2.494471 CAGGCATGGATTTTCTCAAGCA 59.506 45.455 0.00 0.00 0.00 3.91
1660 1727 3.438216 TGTCAGGCATGGATTTTCTCA 57.562 42.857 0.00 0.00 0.00 3.27
1666 1733 3.245158 CCATCCTATGTCAGGCATGGATT 60.245 47.826 13.39 1.71 45.65 3.01
1677 1744 6.013725 TCCACATGTATTACCCATCCTATGTC 60.014 42.308 0.00 0.00 0.00 3.06
1684 1751 6.114187 TCTCATCCACATGTATTACCCATC 57.886 41.667 0.00 0.00 0.00 3.51
1696 1763 4.103627 TGCATTGGTCTATCTCATCCACAT 59.896 41.667 0.00 0.00 0.00 3.21
1712 1779 4.142315 CCATTGTAGTTCCTTCTGCATTGG 60.142 45.833 9.75 9.75 41.31 3.16
1731 1798 3.900601 TGTGGTTGCCTTACAATTCCATT 59.099 39.130 0.00 0.00 41.27 3.16
1732 1799 3.505386 TGTGGTTGCCTTACAATTCCAT 58.495 40.909 0.00 0.00 41.27 3.41
1737 1804 3.258123 GGTGAATGTGGTTGCCTTACAAT 59.742 43.478 0.00 0.00 41.27 2.71
1744 1811 0.598065 GTCTGGTGAATGTGGTTGCC 59.402 55.000 0.00 0.00 0.00 4.52
1772 1839 3.336138 AGTCGTGAAGGGAGAATTTCC 57.664 47.619 0.00 0.00 46.00 3.13
1781 1848 4.082679 GCTATACATCCTAGTCGTGAAGGG 60.083 50.000 0.00 0.00 33.40 3.95
1830 1897 4.142315 CCCACCTGATTCATCATGTTTCAC 60.142 45.833 0.00 0.00 34.16 3.18
1848 1915 2.215942 ATACCAAAGCTCAACCCACC 57.784 50.000 0.00 0.00 0.00 4.61
1850 1917 2.896685 CCAAATACCAAAGCTCAACCCA 59.103 45.455 0.00 0.00 0.00 4.51
1899 1966 1.507562 CACACGTGTGGCACTTATCA 58.492 50.000 35.65 0.00 42.10 2.15
1922 1989 3.058570 CGTTCGGATTTTCCATGTGTTCA 60.059 43.478 0.00 0.00 35.91 3.18
1950 2017 4.398988 CCTTGCATCACTAAACTTGCCATA 59.601 41.667 0.00 0.00 34.20 2.74
1958 2025 5.182001 AGTTGTCATCCTTGCATCACTAAAC 59.818 40.000 0.00 0.00 0.00 2.01
1967 2034 2.819608 GCCTAAAGTTGTCATCCTTGCA 59.180 45.455 0.00 0.00 0.00 4.08
1970 2037 2.711542 CCGCCTAAAGTTGTCATCCTT 58.288 47.619 0.00 0.00 0.00 3.36
1977 2044 0.821711 TGCTTGCCGCCTAAAGTTGT 60.822 50.000 0.00 0.00 38.05 3.32
1985 2052 2.282391 TTGTCATGCTTGCCGCCT 60.282 55.556 0.00 0.00 38.05 5.52
1986 2053 2.126346 GTTGTCATGCTTGCCGCC 60.126 61.111 0.00 0.00 38.05 6.13
1987 2054 0.318955 AAAGTTGTCATGCTTGCCGC 60.319 50.000 0.00 0.00 39.77 6.53
1988 2055 2.987413 TAAAGTTGTCATGCTTGCCG 57.013 45.000 0.00 0.00 0.00 5.69
1989 2056 6.365050 CAAAAATAAAGTTGTCATGCTTGCC 58.635 36.000 0.00 0.00 0.00 4.52
1990 2057 6.202570 TCCAAAAATAAAGTTGTCATGCTTGC 59.797 34.615 0.00 0.00 0.00 4.01
1991 2058 7.712264 TCCAAAAATAAAGTTGTCATGCTTG 57.288 32.000 0.00 0.00 0.00 4.01
1992 2059 9.643693 CTATCCAAAAATAAAGTTGTCATGCTT 57.356 29.630 0.00 0.00 0.00 3.91
1993 2060 8.806146 ACTATCCAAAAATAAAGTTGTCATGCT 58.194 29.630 0.00 0.00 0.00 3.79
1994 2061 8.986477 ACTATCCAAAAATAAAGTTGTCATGC 57.014 30.769 0.00 0.00 0.00 4.06
2054 2121 0.321653 ACGACTGAAGTTGCCATCCC 60.322 55.000 0.00 0.00 32.66 3.85
2078 2145 1.185618 AAGCACTCTGGCCTGACGTA 61.186 55.000 8.48 0.00 0.00 3.57
2080 2147 1.739562 GAAGCACTCTGGCCTGACG 60.740 63.158 8.48 7.76 0.00 4.35
2081 2148 0.036022 AAGAAGCACTCTGGCCTGAC 59.964 55.000 8.48 0.00 33.37 3.51
2099 2167 5.933187 AATAAGTATCACACGTGTGCAAA 57.067 34.783 37.70 24.57 45.25 3.68
2101 2169 5.346551 GTGTAATAAGTATCACACGTGTGCA 59.653 40.000 37.70 27.43 45.25 4.57
2102 2170 5.575606 AGTGTAATAAGTATCACACGTGTGC 59.424 40.000 37.70 25.87 44.65 4.57
2103 2171 7.576750 AAGTGTAATAAGTATCACACGTGTG 57.423 36.000 37.04 37.04 44.65 3.82
2186 2255 5.225642 TGAGTTGATCGATGCATGTAGATC 58.774 41.667 20.73 20.73 39.74 2.75
2193 2262 4.511527 AGAAACTGAGTTGATCGATGCAT 58.488 39.130 0.54 0.00 0.00 3.96
2207 2276 5.186198 GCAGGCCTAGAATTAAGAAACTGA 58.814 41.667 3.98 0.00 0.00 3.41
2211 2280 4.862641 AGGCAGGCCTAGAATTAAGAAA 57.137 40.909 11.95 0.00 46.14 2.52
2244 2313 1.266989 GGAACAGAAGAAAACCTGGCG 59.733 52.381 0.00 0.00 34.85 5.69
2265 2334 2.232941 GGAGATTACTTGTCGTCCACCA 59.767 50.000 0.00 0.00 0.00 4.17
2269 2338 2.738964 GCCTGGAGATTACTTGTCGTCC 60.739 54.545 0.00 0.00 0.00 4.79
2272 2341 2.166459 TCTGCCTGGAGATTACTTGTCG 59.834 50.000 0.00 0.00 0.00 4.35
2308 2377 3.592059 GCACCGACTTCATACCTTAACA 58.408 45.455 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.