Multiple sequence alignment - TraesCS4D01G291700

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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 TraesCS4D01G291700 chr4D 100.000 5149 0 0 1 5149 462832513 462837661 0.000000e+00 9509.0
1 TraesCS4D01G291700 chr4A 95.331 2249 55 17 686 2922 6884590 6886800 0.000000e+00 3526.0
2 TraesCS4D01G291700 chr4A 97.521 1210 21 3 2907 4107 6887420 6888629 0.000000e+00 2060.0
3 TraesCS4D01G291700 chr4A 90.637 1068 49 22 4106 5149 6888734 6889774 0.000000e+00 1371.0
4 TraesCS4D01G291700 chr4A 86.683 398 48 4 162 554 6876585 6876982 2.200000e-118 436.0
5 TraesCS4D01G291700 chr4A 86.683 398 48 4 162 554 6883245 6883642 2.200000e-118 436.0
6 TraesCS4D01G291700 chr4A 97.951 244 5 0 686 929 6878310 6878553 1.710000e-114 424.0
7 TraesCS4D01G291700 chr4A 100.000 177 0 0 2923 3099 6887216 6887392 1.380000e-85 327.0
8 TraesCS4D01G291700 chr4A 94.118 119 6 1 560 678 6877575 6877692 4.100000e-41 180.0
9 TraesCS4D01G291700 chr4A 94.118 119 6 1 560 678 6883855 6883972 4.100000e-41 180.0
10 TraesCS4D01G291700 chr4B 91.540 1903 103 37 2515 4383 578043795 578041917 0.000000e+00 2569.0
11 TraesCS4D01G291700 chr4B 86.713 1016 102 19 1510 2516 578044876 578043885 0.000000e+00 1098.0
12 TraesCS4D01G291700 chr4B 88.133 809 52 23 630 1435 578045807 578045040 0.000000e+00 922.0
13 TraesCS4D01G291700 chr4B 87.222 540 54 10 1 529 578046333 578045798 7.380000e-168 601.0
14 TraesCS4D01G291700 chr4B 83.505 582 52 16 4381 4943 578041888 578041332 2.140000e-138 503.0
15 TraesCS4D01G291700 chr6B 88.235 187 21 1 1 186 516474069 516473883 6.710000e-54 222.0
16 TraesCS4D01G291700 chr6D 87.895 190 20 2 1 187 425084383 425084194 2.410000e-53 220.0
17 TraesCS4D01G291700 chr7A 86.702 188 24 1 1 187 255584313 255584500 1.880000e-49 207.0
18 TraesCS4D01G291700 chr5B 87.709 179 18 4 1 177 43692511 43692687 6.760000e-49 206.0
19 TraesCS4D01G291700 chr5B 87.151 179 23 0 2047 2225 610132132 610131954 2.430000e-48 204.0
20 TraesCS4D01G291700 chr7B 84.892 139 16 4 42 178 713198219 713198354 8.990000e-28 135.0
21 TraesCS4D01G291700 chr1B 95.946 74 3 0 555 628 323977025 323976952 2.520000e-23 121.0
22 TraesCS4D01G291700 chr1D 94.667 75 4 0 554 628 224341385 224341311 3.260000e-22 117.0
23 TraesCS4D01G291700 chr3D 95.161 62 3 0 555 616 35815190 35815129 1.180000e-16 99.0
24 TraesCS4D01G291700 chr2A 94.444 36 2 0 5018 5053 61841995 61842030 7.200000e-04 56.5


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 TraesCS4D01G291700 chr4D 462832513 462837661 5148 False 9509.000000 9509 100.000000 1 5149 1 chr4D.!!$F1 5148
1 TraesCS4D01G291700 chr4A 6883245 6889774 6529 False 1316.666667 3526 94.048333 162 5149 6 chr4A.!!$F2 4987
2 TraesCS4D01G291700 chr4A 6876585 6878553 1968 False 346.666667 436 92.917333 162 929 3 chr4A.!!$F1 767
3 TraesCS4D01G291700 chr4B 578041332 578046333 5001 True 1138.600000 2569 87.422600 1 4943 5 chr4B.!!$R1 4942

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
359 373 0.178938 ATGGTTGGGCATTGTCCACA 60.179 50.000 10.12 6.26 36.87 4.17 F
1341 2577 0.178932 TGGACTGCTGGACTGGTAGT 60.179 55.000 0.00 0.00 32.67 2.73 F
1609 2949 0.108186 TGCTGCGAACTGTAGGATGG 60.108 55.000 0.00 0.00 0.00 3.51 F
1703 3045 2.100252 TGAAGGGAAATACTCGCCGTAG 59.900 50.000 0.00 0.00 37.73 3.51 F
1947 3299 2.423373 GCCAGAAAAGCATCCATCCCTA 60.423 50.000 0.00 0.00 0.00 3.53 F
2607 4054 3.821033 AGAAAGTTTGCATCACAGGTACC 59.179 43.478 2.73 2.73 0.00 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1409 2645 0.112995 TTCAAGCAGGCATGTCCCTT 59.887 50.000 0.00 0.00 31.24 3.95 R
2765 4216 0.900421 TCCTGCAGTGAGATGACTGG 59.100 55.000 13.81 0.00 43.17 4.00 R
3256 5347 5.542635 ACACAGACAGGAGTAATACAAAGGA 59.457 40.000 0.00 0.00 0.00 3.36 R
3676 5769 7.609532 ACATAAGAGCAATTCAACTTAGAGCTT 59.390 33.333 0.00 0.00 0.00 3.74 R
3739 5832 4.708909 AGTAAGCACAGATCTGATGACTGA 59.291 41.667 29.27 13.59 35.85 3.41 R
4202 6414 1.669115 CAGTTGGCCTGTCAGGTCG 60.669 63.158 18.59 0.21 44.85 4.79 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
44 45 0.602905 GTGTCCTTCACCCTGTTCGG 60.603 60.000 0.00 0.00 40.84 4.30
71 77 2.238521 CACCCTATCTCTCTCTGCTCC 58.761 57.143 0.00 0.00 0.00 4.70
116 122 4.725556 ACGTTCATGTCATGTGTTGTAC 57.274 40.909 12.54 0.00 0.00 2.90
118 124 3.120338 CGTTCATGTCATGTGTTGTACCC 60.120 47.826 12.54 0.00 0.00 3.69
123 133 5.240623 TCATGTCATGTGTTGTACCCTTTTC 59.759 40.000 12.54 0.00 0.00 2.29
124 134 3.562141 TGTCATGTGTTGTACCCTTTTCG 59.438 43.478 0.00 0.00 0.00 3.46
133 143 6.646240 GTGTTGTACCCTTTTCGTACTCATTA 59.354 38.462 0.00 0.00 37.55 1.90
136 146 6.576185 TGTACCCTTTTCGTACTCATTATCC 58.424 40.000 0.00 0.00 37.55 2.59
238 250 9.102757 CTTATTAATGTCCGATCCTATGAATGG 57.897 37.037 0.00 0.00 0.00 3.16
258 270 6.598753 ATGGTATGTGTTTATCTACGTTGC 57.401 37.500 0.00 0.00 0.00 4.17
259 271 4.871557 TGGTATGTGTTTATCTACGTTGCC 59.128 41.667 0.00 0.00 0.00 4.52
269 283 7.707893 TGTTTATCTACGTTGCCTTAATCTACC 59.292 37.037 0.00 0.00 0.00 3.18
359 373 0.178938 ATGGTTGGGCATTGTCCACA 60.179 50.000 10.12 6.26 36.87 4.17
403 417 1.506493 CTCATATCAGGCAAGTCCGC 58.494 55.000 0.00 0.00 40.77 5.54
414 428 2.163818 CAAGTCCGCTTGTAGAACCA 57.836 50.000 0.00 0.00 45.18 3.67
530 545 3.118075 TCCAAATATGTCAATCTGCCCGA 60.118 43.478 0.00 0.00 0.00 5.14
533 548 5.473162 CCAAATATGTCAATCTGCCCGATAA 59.527 40.000 0.00 0.00 0.00 1.75
543 558 2.832129 TCTGCCCGATAATCCTACATCC 59.168 50.000 0.00 0.00 0.00 3.51
545 560 3.181329 TGCCCGATAATCCTACATCCAT 58.819 45.455 0.00 0.00 0.00 3.41
554 569 7.173907 CGATAATCCTACATCCATGAAGCTTTT 59.826 37.037 0.00 0.00 0.00 2.27
555 570 8.773033 ATAATCCTACATCCATGAAGCTTTTT 57.227 30.769 0.00 0.00 0.00 1.94
556 571 6.705863 ATCCTACATCCATGAAGCTTTTTC 57.294 37.500 0.00 0.00 0.00 2.29
557 572 5.819991 TCCTACATCCATGAAGCTTTTTCT 58.180 37.500 0.00 0.00 0.00 2.52
558 573 6.248433 TCCTACATCCATGAAGCTTTTTCTT 58.752 36.000 0.00 0.00 0.00 2.52
568 1170 6.455360 TGAAGCTTTTTCTTCAATCACACT 57.545 33.333 0.00 0.00 46.56 3.55
578 1180 9.513906 TTTTCTTCAATCACACTTATCCATGTA 57.486 29.630 0.00 0.00 0.00 2.29
579 1181 8.722480 TTCTTCAATCACACTTATCCATGTAG 57.278 34.615 0.00 0.00 0.00 2.74
628 1230 6.844696 ATTTACGTGGATGTAGCATTACTG 57.155 37.500 0.00 0.00 0.00 2.74
645 1247 2.203126 GCAATCTGCCCTCCCTCG 60.203 66.667 0.00 0.00 37.42 4.63
648 1250 0.253044 CAATCTGCCCTCCCTCGAAA 59.747 55.000 0.00 0.00 0.00 3.46
678 1280 4.407296 TGCCCCACCCAAAATACAAATATC 59.593 41.667 0.00 0.00 0.00 1.63
680 1282 4.647399 CCCCACCCAAAATACAAATATCGT 59.353 41.667 0.00 0.00 0.00 3.73
682 1284 5.504994 CCCACCCAAAATACAAATATCGTCG 60.505 44.000 0.00 0.00 0.00 5.12
811 2024 4.340950 TCATGTAGTCACTCACAAGTCACA 59.659 41.667 0.00 0.00 26.96 3.58
941 2154 2.328099 GCGTCAGGCCCACAGAAAG 61.328 63.158 0.00 0.00 34.80 2.62
944 2157 0.398318 GTCAGGCCCACAGAAAGAGT 59.602 55.000 0.00 0.00 0.00 3.24
947 2160 1.140312 AGGCCCACAGAAAGAGTGAA 58.860 50.000 0.00 0.00 39.30 3.18
959 2172 4.220821 AGAAAGAGTGAAACGGATAGAGCA 59.779 41.667 0.00 0.00 45.86 4.26
961 2174 3.357203 AGAGTGAAACGGATAGAGCAGA 58.643 45.455 0.00 0.00 45.86 4.26
962 2175 3.764434 AGAGTGAAACGGATAGAGCAGAA 59.236 43.478 0.00 0.00 45.86 3.02
964 2177 3.258372 AGTGAAACGGATAGAGCAGAACA 59.742 43.478 0.00 0.00 45.86 3.18
1285 2512 0.251916 TGTGAGCACCCTTTATCCGG 59.748 55.000 0.00 0.00 0.00 5.14
1301 2536 2.522638 CGGTTCCTATGTTCGCGGC 61.523 63.158 6.13 0.00 0.00 6.53
1331 2566 4.742201 CGGGTCCGTGGACTGCTG 62.742 72.222 17.99 4.58 44.04 4.41
1341 2577 0.178932 TGGACTGCTGGACTGGTAGT 60.179 55.000 0.00 0.00 32.67 2.73
1342 2578 1.076513 TGGACTGCTGGACTGGTAGTA 59.923 52.381 0.00 0.00 30.31 1.82
1343 2579 1.477295 GGACTGCTGGACTGGTAGTAC 59.523 57.143 0.00 0.00 30.31 2.73
1344 2580 2.448453 GACTGCTGGACTGGTAGTACT 58.552 52.381 0.00 0.00 27.92 2.73
1362 2598 7.387122 GGTAGTACTTTTTCTTGTTCGAGGAAT 59.613 37.037 0.00 0.00 0.00 3.01
1387 2623 5.866207 AGGGATTTCGTGTTCTTACTTCTT 58.134 37.500 0.00 0.00 0.00 2.52
1456 2692 3.071023 AGGAATTTAGGATCGGATTCGCA 59.929 43.478 0.00 0.00 36.13 5.10
1555 2895 8.406297 GTTTATTCCCAAGCGAAGAAGATAAAT 58.594 33.333 0.00 0.00 0.00 1.40
1584 2924 8.861086 ACTTCTCTGTTGTTCTACTAGAAATCA 58.139 33.333 0.00 0.86 35.75 2.57
1609 2949 0.108186 TGCTGCGAACTGTAGGATGG 60.108 55.000 0.00 0.00 0.00 3.51
1649 2991 4.273005 ACTGCACAGTACTTTGAAAACG 57.727 40.909 13.23 0.00 40.43 3.60
1703 3045 2.100252 TGAAGGGAAATACTCGCCGTAG 59.900 50.000 0.00 0.00 37.73 3.51
1762 3104 7.365741 TGAATCTTGTGATTTCTTCTTGCTTC 58.634 34.615 0.00 0.00 42.43 3.86
1887 3239 3.071479 GAGCCCGTGATTTCTACAAACA 58.929 45.455 0.00 0.00 0.00 2.83
1947 3299 2.423373 GCCAGAAAAGCATCCATCCCTA 60.423 50.000 0.00 0.00 0.00 3.53
2607 4054 3.821033 AGAAAGTTTGCATCACAGGTACC 59.179 43.478 2.73 2.73 0.00 3.34
2765 4216 9.533983 CTTGTAATATGTCAAATGTATCATCGC 57.466 33.333 0.00 0.00 0.00 4.58
3256 5347 4.202111 GCGGTATGGAAAATAGCACCAATT 60.202 41.667 0.00 0.00 37.24 2.32
3739 5832 0.324614 TTGACATGGATGGTGCTCGT 59.675 50.000 0.00 0.00 0.00 4.18
3948 6041 3.371034 TCCTTGGAATCGTCTACATGGA 58.629 45.455 0.00 0.00 35.56 3.41
4082 6183 4.136796 TGGGTTCATTCTTGTGAGTCTTG 58.863 43.478 0.00 0.00 0.00 3.02
4199 6411 5.105513 TGAGTCTACAATTCTATGTTCGGCA 60.106 40.000 0.00 0.00 34.75 5.69
4200 6412 5.352284 AGTCTACAATTCTATGTTCGGCAG 58.648 41.667 0.00 0.00 34.75 4.85
4201 6413 4.025647 GTCTACAATTCTATGTTCGGCAGC 60.026 45.833 0.00 0.00 34.75 5.25
4202 6414 2.017049 ACAATTCTATGTTCGGCAGCC 58.983 47.619 0.00 0.00 0.00 4.85
4312 6542 9.807921 AATAATTTCCTTCCAAAACTCAGTAGA 57.192 29.630 0.00 0.00 0.00 2.59
4319 6549 7.336931 TCCTTCCAAAACTCAGTAGATTATTGC 59.663 37.037 0.00 0.00 0.00 3.56
4388 6649 9.090692 GTAACATGATTGCTTTGCATAAAATCT 57.909 29.630 0.00 0.00 38.76 2.40
4566 6827 2.621055 CTCTCTGGACTGTCCTTATCCG 59.379 54.545 26.03 9.81 37.46 4.18
4580 6841 3.430374 CCTTATCCGACCACTCGATGTTT 60.430 47.826 0.00 0.00 43.06 2.83
4673 6934 1.134551 TGGCTTTGAACCAAAACCTGC 60.135 47.619 11.62 3.97 39.49 4.85
4694 6955 2.143122 GCTCATCAGTTCGTGAAACCA 58.857 47.619 0.00 0.00 39.19 3.67
4726 6988 1.672854 CCGGATCCCGTTCTGTGCTA 61.673 60.000 6.06 0.00 46.80 3.49
4773 7035 3.836617 AGGCAAACCTCCCTACCC 58.163 61.111 0.00 0.00 46.34 3.69
4774 7036 1.163555 AGGCAAACCTCCCTACCCT 59.836 57.895 0.00 0.00 46.34 4.34
4775 7037 0.420272 AGGCAAACCTCCCTACCCTA 59.580 55.000 0.00 0.00 46.34 3.53
4776 7038 0.837940 GGCAAACCTCCCTACCCTAG 59.162 60.000 0.00 0.00 0.00 3.02
4777 7039 1.581223 GCAAACCTCCCTACCCTAGT 58.419 55.000 0.00 0.00 0.00 2.57
4778 7040 1.209747 GCAAACCTCCCTACCCTAGTG 59.790 57.143 0.00 0.00 0.00 2.74
4779 7041 2.829023 CAAACCTCCCTACCCTAGTGA 58.171 52.381 0.00 0.00 0.00 3.41
4780 7042 3.385115 CAAACCTCCCTACCCTAGTGAT 58.615 50.000 0.00 0.00 0.00 3.06
4781 7043 3.331718 AACCTCCCTACCCTAGTGATC 57.668 52.381 0.00 0.00 0.00 2.92
4782 7044 2.224077 ACCTCCCTACCCTAGTGATCA 58.776 52.381 0.00 0.00 0.00 2.92
4864 7144 6.770785 TGTCACTTAAGCAACCTTACTGATTT 59.229 34.615 1.29 0.00 33.43 2.17
4968 7248 6.923199 AACTAACTAAACAGTACCCTAGCA 57.077 37.500 0.00 0.00 0.00 3.49
4973 7253 5.915175 ACTAAACAGTACCCTAGCATTAGC 58.085 41.667 0.00 0.00 42.56 3.09
4974 7254 4.837093 AAACAGTACCCTAGCATTAGCA 57.163 40.909 0.00 0.00 45.49 3.49
4978 7258 2.630580 AGTACCCTAGCATTAGCAGCTC 59.369 50.000 0.00 0.00 45.49 4.09
4982 7262 2.555199 CCTAGCATTAGCAGCTCGTTT 58.445 47.619 0.00 0.00 45.49 3.60
4983 7263 2.541762 CCTAGCATTAGCAGCTCGTTTC 59.458 50.000 0.00 0.00 45.49 2.78
4987 7267 1.421410 ATTAGCAGCTCGTTTCGGCG 61.421 55.000 0.00 0.00 0.00 6.46
5009 7289 1.878953 GACAATGGTCGTTCACTGGT 58.121 50.000 0.00 0.00 33.68 4.00
5015 7295 1.202964 TGGTCGTTCACTGGTCTAGGA 60.203 52.381 0.00 0.00 0.00 2.94
5019 7299 2.094182 TCGTTCACTGGTCTAGGAATGC 60.094 50.000 0.00 0.00 0.00 3.56
5038 7318 5.886960 ATGCTTTGTACTTCTGATGAACC 57.113 39.130 0.00 0.00 0.00 3.62
5052 7332 9.829507 CTTCTGATGAACCTTTATAACAGATCT 57.170 33.333 0.00 0.00 34.07 2.75
5076 7356 9.877178 TCTGAATCCTTTTCATAAGAGAAGTAC 57.123 33.333 0.00 0.00 34.94 2.73
5077 7357 9.658799 CTGAATCCTTTTCATAAGAGAAGTACA 57.341 33.333 0.00 0.00 34.94 2.90
5091 7371 6.520272 AGAGAAGTACAGTATTGCCATCATC 58.480 40.000 0.00 0.00 0.00 2.92
5105 7385 2.158711 CCATCATCACACTGGTGCCTAT 60.159 50.000 0.17 0.00 44.87 2.57
5108 7388 4.341366 TCATCACACTGGTGCCTATATG 57.659 45.455 0.17 0.00 44.87 1.78
5123 7404 4.534103 GCCTATATGAGGGGTTCTTGAGAT 59.466 45.833 0.00 0.00 46.81 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.951602 GGACACAACTAAACCCACCAC 59.048 52.381 0.00 0.00 0.00 4.16
44 45 2.560981 GAGAGAGATAGGGTGCTTAGCC 59.439 54.545 0.29 0.00 0.00 3.93
71 77 3.896133 GCATGAGCATGGTGCCCG 61.896 66.667 0.00 0.00 46.52 6.13
86 92 1.621317 TGACATGAACGTAAGGAGGCA 59.379 47.619 0.00 0.00 46.39 4.75
116 122 7.048512 AGAAAGGATAATGAGTACGAAAAGGG 58.951 38.462 0.00 0.00 0.00 3.95
118 124 9.372369 AGAAGAAAGGATAATGAGTACGAAAAG 57.628 33.333 0.00 0.00 0.00 2.27
123 133 9.967346 TTGATAGAAGAAAGGATAATGAGTACG 57.033 33.333 0.00 0.00 0.00 3.67
150 160 9.686683 AATACACAAAGCTTGTATATCCTTTCT 57.313 29.630 9.42 0.00 43.23 2.52
155 165 6.363473 GCGAATACACAAAGCTTGTATATCC 58.637 40.000 9.42 3.26 43.23 2.59
160 170 3.318886 TCGCGAATACACAAAGCTTGTA 58.681 40.909 6.20 0.00 43.23 2.41
238 250 6.657836 AAGGCAACGTAGATAAACACATAC 57.342 37.500 0.00 0.00 46.39 2.39
258 270 6.732154 CAATCACATGCAAGGTAGATTAAGG 58.268 40.000 0.00 0.00 31.09 2.69
259 271 6.204359 GCAATCACATGCAAGGTAGATTAAG 58.796 40.000 0.00 0.00 45.70 1.85
291 305 2.724117 CCCCTCATATTCAAATCCCCCT 59.276 50.000 0.00 0.00 0.00 4.79
330 344 6.541907 ACAATGCCCAACCATTAATTCTTTT 58.458 32.000 0.00 0.00 33.86 2.27
333 347 4.162131 GGACAATGCCCAACCATTAATTCT 59.838 41.667 0.00 0.00 33.86 2.40
334 348 4.081198 TGGACAATGCCCAACCATTAATTC 60.081 41.667 0.00 0.00 33.86 2.17
338 352 2.175202 GTGGACAATGCCCAACCATTA 58.825 47.619 0.00 0.00 33.86 1.90
340 354 0.178938 TGTGGACAATGCCCAACCAT 60.179 50.000 0.00 0.00 35.12 3.55
350 364 1.374252 GGACGCGTCTGTGGACAAT 60.374 57.895 35.50 0.00 42.21 2.71
371 385 5.352284 CCTGATATGAGCCCATATACGTTC 58.648 45.833 0.03 0.00 43.89 3.95
403 417 8.567948 ACATTTGTTGTCTAATGGTTCTACAAG 58.432 33.333 0.00 0.00 39.68 3.16
411 425 8.855110 TCAATTGTACATTTGTTGTCTAATGGT 58.145 29.630 23.03 0.00 39.68 3.55
412 426 9.689976 TTCAATTGTACATTTGTTGTCTAATGG 57.310 29.630 23.03 0.00 39.68 3.16
414 428 9.912634 CCTTCAATTGTACATTTGTTGTCTAAT 57.087 29.630 23.03 0.00 39.87 1.73
459 474 7.812669 GGAAAAACAAACATACTACTTCATGGG 59.187 37.037 0.00 0.00 0.00 4.00
530 545 8.773033 AAAAAGCTTCATGGATGTAGGATTAT 57.227 30.769 0.00 0.00 0.00 1.28
533 548 6.430007 AGAAAAAGCTTCATGGATGTAGGAT 58.570 36.000 0.00 0.00 0.00 3.24
554 569 7.280876 GCTACATGGATAAGTGTGATTGAAGAA 59.719 37.037 0.00 0.00 0.00 2.52
555 570 6.763135 GCTACATGGATAAGTGTGATTGAAGA 59.237 38.462 0.00 0.00 0.00 2.87
556 571 6.539826 TGCTACATGGATAAGTGTGATTGAAG 59.460 38.462 0.00 0.00 0.00 3.02
557 572 6.413892 TGCTACATGGATAAGTGTGATTGAA 58.586 36.000 0.00 0.00 0.00 2.69
558 573 5.988287 TGCTACATGGATAAGTGTGATTGA 58.012 37.500 0.00 0.00 0.00 2.57
568 1170 2.963101 ACGTAGGCTGCTACATGGATAA 59.037 45.455 0.00 0.00 0.00 1.75
628 1230 2.203126 CGAGGGAGGGCAGATTGC 60.203 66.667 0.00 0.00 44.08 3.56
639 1241 1.677552 GCAAGAGGGTTTCGAGGGA 59.322 57.895 0.00 0.00 0.00 4.20
645 1247 1.606601 GGTGGGGCAAGAGGGTTTC 60.607 63.158 0.00 0.00 0.00 2.78
648 1250 4.938756 TGGGTGGGGCAAGAGGGT 62.939 66.667 0.00 0.00 0.00 4.34
678 1280 0.510790 TTTGTAGCACATGCACGACG 59.489 50.000 6.64 0.00 45.16 5.12
680 1282 0.871722 GGTTTGTAGCACATGCACGA 59.128 50.000 6.64 0.00 45.16 4.35
682 1284 2.811431 TGTAGGTTTGTAGCACATGCAC 59.189 45.455 6.64 3.37 45.16 4.57
775 1987 8.885693 AGTGACTACATGATTGGCTATATAGA 57.114 34.615 14.16 0.00 0.00 1.98
891 2104 4.079269 TGCTGGATTGGGATCTATTTTCCA 60.079 41.667 0.00 0.00 34.77 3.53
941 2154 3.784701 TCTGCTCTATCCGTTTCACTC 57.215 47.619 0.00 0.00 0.00 3.51
944 2157 3.953712 TGTTCTGCTCTATCCGTTTCA 57.046 42.857 0.00 0.00 0.00 2.69
947 2160 3.589988 CAGTTGTTCTGCTCTATCCGTT 58.410 45.455 0.00 0.00 37.36 4.44
979 2193 1.333636 GCCTTGGGCTCTCTGCTAGA 61.334 60.000 0.00 0.00 46.69 2.43
1285 2512 2.522638 CGGCCGCGAACATAGGAAC 61.523 63.158 14.67 0.00 0.00 3.62
1331 2566 6.073927 CGAACAAGAAAAAGTACTACCAGTCC 60.074 42.308 0.00 0.00 0.00 3.85
1341 2577 6.426937 CCTCATTCCTCGAACAAGAAAAAGTA 59.573 38.462 0.00 0.00 0.00 2.24
1342 2578 5.239525 CCTCATTCCTCGAACAAGAAAAAGT 59.760 40.000 0.00 0.00 0.00 2.66
1343 2579 5.335191 CCCTCATTCCTCGAACAAGAAAAAG 60.335 44.000 0.00 0.00 0.00 2.27
1344 2580 4.518970 CCCTCATTCCTCGAACAAGAAAAA 59.481 41.667 0.00 0.00 0.00 1.94
1362 2598 4.884668 AGTAAGAACACGAAATCCCTCA 57.115 40.909 0.00 0.00 0.00 3.86
1409 2645 0.112995 TTCAAGCAGGCATGTCCCTT 59.887 50.000 0.00 0.00 31.24 3.95
1456 2692 6.287525 CAACAACAATTCCACAAATAAGGGT 58.712 36.000 0.00 0.00 0.00 4.34
1501 2841 3.583806 CAAAATGCTGGCGAATAAACCA 58.416 40.909 0.00 0.00 0.00 3.67
1649 2991 7.549134 TCACAACCACATGATAAGTAATGAGAC 59.451 37.037 0.00 0.00 0.00 3.36
1703 3045 8.738645 ATCCAGATAAAATTGTGTTCTAGTCC 57.261 34.615 0.00 0.00 0.00 3.85
1809 3161 9.315525 CATGAAAATAATGCACAACATGGATAA 57.684 29.630 0.00 0.00 38.67 1.75
1887 3239 3.119352 GCAATCATTTCCTCTTTTCCGCT 60.119 43.478 0.00 0.00 0.00 5.52
1947 3299 7.935755 CCTATTGGATATGTTTGATGAGACACT 59.064 37.037 0.00 0.00 34.57 3.55
2314 3669 9.906660 TTACAGTTCATGATTTGGAATGTAAAC 57.093 29.630 12.51 0.00 31.71 2.01
2336 3691 7.987750 TCATAGCACCAACTAAATTGTTACA 57.012 32.000 0.00 0.00 36.47 2.41
2388 3743 7.618019 TGGTAAGAAGAGATGTAAGGCATAT 57.382 36.000 0.00 0.00 38.06 1.78
2765 4216 0.900421 TCCTGCAGTGAGATGACTGG 59.100 55.000 13.81 0.00 43.17 4.00
3256 5347 5.542635 ACACAGACAGGAGTAATACAAAGGA 59.457 40.000 0.00 0.00 0.00 3.36
3676 5769 7.609532 ACATAAGAGCAATTCAACTTAGAGCTT 59.390 33.333 0.00 0.00 0.00 3.74
3739 5832 4.708909 AGTAAGCACAGATCTGATGACTGA 59.291 41.667 29.27 13.59 35.85 3.41
3948 6041 2.633509 GGACACCGGTACTGTCGCT 61.634 63.158 6.87 0.00 39.23 4.93
4200 6412 4.329545 TTGGCCTGTCAGGTCGGC 62.330 66.667 18.59 5.64 44.85 5.54
4201 6413 2.358737 GTTGGCCTGTCAGGTCGG 60.359 66.667 18.59 0.00 44.85 4.79
4202 6414 1.669115 CAGTTGGCCTGTCAGGTCG 60.669 63.158 18.59 0.21 44.85 4.79
4204 6416 2.833913 CCCAGTTGGCCTGTCAGGT 61.834 63.158 20.24 0.00 39.74 4.00
4206 6418 2.034687 CCCCAGTTGGCCTGTCAG 59.965 66.667 3.32 0.00 39.74 3.51
4411 6672 9.710900 GAATTTTCCATGTTTTCCATTCTTAGT 57.289 29.630 0.00 0.00 0.00 2.24
4451 6712 7.754851 TGTACTTTTTCCAGTTTAGGGATTC 57.245 36.000 0.00 0.00 33.63 2.52
4566 6827 3.560068 ACTTGTCAAAACATCGAGTGGTC 59.440 43.478 0.00 0.00 34.73 4.02
4580 6841 5.253330 AGGTTTCAGAAGTGAACTTGTCAA 58.747 37.500 0.00 0.00 42.60 3.18
4617 6878 9.696917 ATCAACATAAACAAAGAAATGGACTTC 57.303 29.630 0.00 0.00 0.00 3.01
4673 6934 1.126846 GGTTTCACGAACTGATGAGCG 59.873 52.381 0.00 0.00 38.35 5.03
4694 6955 2.552373 GGGATCCGGTCTGAACTTGTTT 60.552 50.000 5.45 0.00 0.00 2.83
4720 6982 4.050553 GCATTGCTCAAACTTTTAGCACA 58.949 39.130 9.46 3.47 45.41 4.57
4726 6988 2.807837 GCCCAGCATTGCTCAAACTTTT 60.808 45.455 8.54 0.00 36.40 2.27
4766 7028 4.528596 CCTAACATGATCACTAGGGTAGGG 59.471 50.000 16.37 6.16 0.00 3.53
4767 7029 4.021016 GCCTAACATGATCACTAGGGTAGG 60.021 50.000 20.89 19.69 32.95 3.18
4769 7031 4.552674 TGCCTAACATGATCACTAGGGTA 58.447 43.478 20.89 8.90 32.95 3.69
4770 7032 3.384168 TGCCTAACATGATCACTAGGGT 58.616 45.455 20.89 5.68 32.95 4.34
4771 7033 4.422073 TTGCCTAACATGATCACTAGGG 57.578 45.455 20.89 11.96 32.95 3.53
4772 7034 5.471456 GGATTTGCCTAACATGATCACTAGG 59.529 44.000 17.48 17.48 35.06 3.02
4773 7035 6.057533 TGGATTTGCCTAACATGATCACTAG 58.942 40.000 0.00 0.00 37.63 2.57
4774 7036 6.000246 TGGATTTGCCTAACATGATCACTA 58.000 37.500 0.00 0.00 37.63 2.74
4775 7037 4.858850 TGGATTTGCCTAACATGATCACT 58.141 39.130 0.00 0.00 37.63 3.41
4776 7038 4.641989 ACTGGATTTGCCTAACATGATCAC 59.358 41.667 0.00 0.00 37.63 3.06
4777 7039 4.858850 ACTGGATTTGCCTAACATGATCA 58.141 39.130 0.00 0.00 37.63 2.92
4778 7040 5.049129 GCTACTGGATTTGCCTAACATGATC 60.049 44.000 0.00 0.00 37.63 2.92
4779 7041 4.823989 GCTACTGGATTTGCCTAACATGAT 59.176 41.667 0.00 0.00 37.63 2.45
4780 7042 4.199310 GCTACTGGATTTGCCTAACATGA 58.801 43.478 0.00 0.00 37.63 3.07
4781 7043 3.316308 GGCTACTGGATTTGCCTAACATG 59.684 47.826 0.00 0.00 41.92 3.21
4782 7044 3.053693 TGGCTACTGGATTTGCCTAACAT 60.054 43.478 0.00 0.00 45.11 2.71
4968 7248 1.421410 CGCCGAAACGAGCTGCTAAT 61.421 55.000 0.15 0.00 34.06 1.73
4973 7253 3.777925 CACCGCCGAAACGAGCTG 61.778 66.667 0.00 0.00 34.06 4.24
4974 7254 3.986006 TCACCGCCGAAACGAGCT 61.986 61.111 0.00 0.00 34.06 4.09
4978 7258 1.154488 CATTGTCACCGCCGAAACG 60.154 57.895 0.00 0.00 0.00 3.60
4982 7262 2.047655 GACCATTGTCACCGCCGA 60.048 61.111 0.00 0.00 41.37 5.54
4983 7263 3.487202 CGACCATTGTCACCGCCG 61.487 66.667 0.00 0.00 41.85 6.46
4987 7267 1.531149 CAGTGAACGACCATTGTCACC 59.469 52.381 0.00 0.00 41.85 4.02
5006 7286 5.248477 AGAAGTACAAAGCATTCCTAGACCA 59.752 40.000 0.00 0.00 0.00 4.02
5009 7289 6.605471 TCAGAAGTACAAAGCATTCCTAGA 57.395 37.500 0.00 0.00 0.00 2.43
5015 7295 6.006449 AGGTTCATCAGAAGTACAAAGCATT 58.994 36.000 0.00 0.00 33.63 3.56
5046 7326 9.610705 TTCTCTTATGAAAAGGATTCAGATCTG 57.389 33.333 17.07 17.07 32.66 2.90
5047 7327 9.835389 CTTCTCTTATGAAAAGGATTCAGATCT 57.165 33.333 0.00 0.00 32.66 2.75
5052 7332 9.658799 CTGTACTTCTCTTATGAAAAGGATTCA 57.341 33.333 0.00 0.00 0.00 2.57
5076 7356 3.314357 CCAGTGTGATGATGGCAATACTG 59.686 47.826 6.16 6.16 34.83 2.74
5077 7357 3.054139 ACCAGTGTGATGATGGCAATACT 60.054 43.478 0.00 0.00 37.64 2.12
5091 7371 2.224378 CCCTCATATAGGCACCAGTGTG 60.224 54.545 0.00 0.00 45.03 3.82
5105 7385 3.895656 CCGTATCTCAAGAACCCCTCATA 59.104 47.826 0.00 0.00 0.00 2.15
5108 7388 2.108970 ACCGTATCTCAAGAACCCCTC 58.891 52.381 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.