Multiple sequence alignment - TraesCS3D01G285100

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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 TraesCS3D01G285100 chr3D 100.000 7252 0 0 1 7252 394747736 394754987 0.000000e+00 13393
1 TraesCS3D01G285100 chr3B 95.949 6517 136 45 796 7252 513990183 513996631 0.000000e+00 10455
2 TraesCS3D01G285100 chr3B 93.579 732 27 7 28 758 513989466 513990178 0.000000e+00 1074
3 TraesCS3D01G285100 chr3A 96.089 6009 178 27 1265 7252 514105527 514111499 0.000000e+00 9742
4 TraesCS3D01G285100 chr3A 85.983 478 13 21 780 1256 514105016 514105440 5.130000e-126 462
5 TraesCS3D01G285100 chr3A 88.116 345 16 12 31 367 514095952 514096279 3.170000e-103 387
6 TraesCS3D01G285100 chr7A 85.809 303 41 1 3083 3385 216341146 216340846 3.260000e-83 320


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 TraesCS3D01G285100 chr3D 394747736 394754987 7251 False 13393.0 13393 100.000 1 7252 1 chr3D.!!$F1 7251
1 TraesCS3D01G285100 chr3B 513989466 513996631 7165 False 5764.5 10455 94.764 28 7252 2 chr3B.!!$F1 7224
2 TraesCS3D01G285100 chr3A 514105016 514111499 6483 False 5102.0 9742 91.036 780 7252 2 chr3A.!!$F2 6472

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
963 965 0.099968 TGCTACTGCTACCGCTAACG 59.900 55.000 0.00 0.0 40.48 3.18 F
1574 1683 0.244178 TATGGACGCACGCACTTACA 59.756 50.000 0.00 0.0 0.00 2.41 F
2769 2918 0.036388 TTGGCTCCATCAAGACCGTC 60.036 55.000 0.00 0.0 0.00 4.79 F
3192 3341 0.392998 GTGTGCCCCAGATCAACGAT 60.393 55.000 0.00 0.0 0.00 3.73 F
4250 4401 1.003355 AAGTCCCATGCCACTCACG 60.003 57.895 0.00 0.0 0.00 4.35 F
5793 5944 0.109179 CTGCTAAAGCCGCAAATGCA 60.109 50.000 6.18 0.0 41.18 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2751 2900 0.904865 AGACGGTCTTGATGGAGCCA 60.905 55.000 4.45 0.00 0.00 4.75 R
3237 3386 0.824109 AGCGGATGGATTCGAACTCA 59.176 50.000 0.00 1.93 0.00 3.41 R
3809 3958 1.600356 TGCGCTTGTGGCTTCATCA 60.600 52.632 9.73 0.00 39.13 3.07 R
4496 4647 2.138542 ACAGCAATGGATACCAGGGAT 58.861 47.619 0.00 0.00 36.75 3.85 R
6218 6369 2.353704 GGTTGCCAGGTTAAAGAATGCC 60.354 50.000 0.00 0.00 0.00 4.40 R
6941 7092 1.805345 CTGAAGTGGCAGCTCAAAGAG 59.195 52.381 0.00 0.00 0.00 2.85 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
17 18 4.312052 TATTGCCCAGCGACAACC 57.688 55.556 0.00 0.00 0.00 3.77
18 19 1.743623 TATTGCCCAGCGACAACCG 60.744 57.895 0.00 0.00 42.21 4.44
27 28 3.550656 CGACAACCGCTTGACCTC 58.449 61.111 0.00 0.00 0.00 3.85
28 29 1.300620 CGACAACCGCTTGACCTCA 60.301 57.895 0.00 0.00 0.00 3.86
29 30 1.557443 CGACAACCGCTTGACCTCAC 61.557 60.000 0.00 0.00 0.00 3.51
97 98 6.742718 CGACAGATAATTTTGTGATGGACAAC 59.257 38.462 0.05 0.00 44.53 3.32
109 110 0.472352 TGGACAACCTCCTAACCGGT 60.472 55.000 0.00 0.00 40.26 5.28
194 195 3.005050 ACGACGTCACTTTTGTCCTGATA 59.995 43.478 17.16 0.00 0.00 2.15
195 196 3.985279 CGACGTCACTTTTGTCCTGATAA 59.015 43.478 17.16 0.00 0.00 1.75
196 197 4.143389 CGACGTCACTTTTGTCCTGATAAC 60.143 45.833 17.16 0.00 0.00 1.89
197 198 4.957296 ACGTCACTTTTGTCCTGATAACT 58.043 39.130 0.00 0.00 0.00 2.24
198 199 5.365619 ACGTCACTTTTGTCCTGATAACTT 58.634 37.500 0.00 0.00 0.00 2.66
199 200 5.820947 ACGTCACTTTTGTCCTGATAACTTT 59.179 36.000 0.00 0.00 0.00 2.66
200 201 6.987992 ACGTCACTTTTGTCCTGATAACTTTA 59.012 34.615 0.00 0.00 0.00 1.85
201 202 7.660208 ACGTCACTTTTGTCCTGATAACTTTAT 59.340 33.333 0.00 0.00 0.00 1.40
202 203 9.146984 CGTCACTTTTGTCCTGATAACTTTATA 57.853 33.333 0.00 0.00 0.00 0.98
204 205 9.444600 TCACTTTTGTCCTGATAACTTTATACC 57.555 33.333 0.00 0.00 0.00 2.73
205 206 8.674607 CACTTTTGTCCTGATAACTTTATACCC 58.325 37.037 0.00 0.00 0.00 3.69
227 228 1.146452 CTTTATACCCCCTCCCCCAC 58.854 60.000 0.00 0.00 0.00 4.61
387 388 6.914215 GCATTGGTAGTATTCAACATCACATG 59.086 38.462 0.00 0.00 0.00 3.21
479 480 3.366121 CACATACAGTTTCAGTCTCGCAG 59.634 47.826 0.00 0.00 0.00 5.18
498 499 2.749621 CAGGCCAACTTTCTCCATGTAC 59.250 50.000 5.01 0.00 0.00 2.90
499 500 2.644798 AGGCCAACTTTCTCCATGTACT 59.355 45.455 5.01 0.00 0.00 2.73
500 501 3.844211 AGGCCAACTTTCTCCATGTACTA 59.156 43.478 5.01 0.00 0.00 1.82
502 503 4.576463 GGCCAACTTTCTCCATGTACTATG 59.424 45.833 0.00 0.00 0.00 2.23
503 504 4.035675 GCCAACTTTCTCCATGTACTATGC 59.964 45.833 0.00 0.00 0.00 3.14
523 524 2.430694 GCTTTGAGTTTGAACCCCAACT 59.569 45.455 0.00 0.00 33.85 3.16
535 536 1.235724 CCCCAACTGGTTCTTTCGTC 58.764 55.000 0.00 0.00 0.00 4.20
537 538 0.865769 CCAACTGGTTCTTTCGTCGG 59.134 55.000 0.00 0.00 0.00 4.79
538 539 0.865769 CAACTGGTTCTTTCGTCGGG 59.134 55.000 0.00 0.00 0.00 5.14
542 543 2.322830 GGTTCTTTCGTCGGGGTGC 61.323 63.158 0.00 0.00 0.00 5.01
557 558 4.393155 TGCGATGCCTTGCGTCCT 62.393 61.111 2.90 0.00 41.05 3.85
601 602 9.413048 TGAAATTTGTTCAAACTTCTTACGTTT 57.587 25.926 16.42 4.91 35.12 3.60
666 667 5.621197 TGATATGGTGTTACAAAGTGCAC 57.379 39.130 9.40 9.40 0.00 4.57
729 730 1.875157 GCTTTTGCTTTCTGGGCCTTG 60.875 52.381 4.53 0.00 43.35 3.61
772 773 9.674824 TTAACTTAATTTATTTTTCGCAACCGA 57.325 25.926 0.00 0.00 42.66 4.69
773 774 7.790861 ACTTAATTTATTTTTCGCAACCGAG 57.209 32.000 0.00 0.00 45.35 4.63
774 775 6.804783 ACTTAATTTATTTTTCGCAACCGAGG 59.195 34.615 0.00 0.00 45.35 4.63
775 776 3.562567 TTTATTTTTCGCAACCGAGGG 57.437 42.857 0.00 0.00 45.35 4.30
776 777 2.476126 TATTTTTCGCAACCGAGGGA 57.524 45.000 0.00 0.00 45.35 4.20
777 778 1.165270 ATTTTTCGCAACCGAGGGAG 58.835 50.000 0.00 0.00 45.35 4.30
778 779 0.887387 TTTTTCGCAACCGAGGGAGG 60.887 55.000 0.00 0.00 45.35 4.30
794 795 2.277404 GGGAGGAGAGGACGCTCT 59.723 66.667 3.19 0.00 35.26 4.09
829 831 6.154534 ACTTTTCCAAGGCAAAGTTAAGAACT 59.845 34.615 10.45 0.00 39.69 3.01
917 919 1.299316 GCAGCAAGCGCAACAAAGA 60.299 52.632 11.47 0.00 42.27 2.52
960 962 0.738975 CAGTGCTACTGCTACCGCTA 59.261 55.000 3.83 0.00 39.62 4.26
961 963 1.134367 CAGTGCTACTGCTACCGCTAA 59.866 52.381 3.83 0.00 39.62 3.09
962 964 1.134560 AGTGCTACTGCTACCGCTAAC 59.865 52.381 0.00 0.00 40.48 2.34
963 965 0.099968 TGCTACTGCTACCGCTAACG 59.900 55.000 0.00 0.00 40.48 3.18
964 966 1.207377 GCTACTGCTACCGCTAACGC 61.207 60.000 0.00 0.00 35.38 4.84
965 967 0.381089 CTACTGCTACCGCTAACGCT 59.619 55.000 0.00 0.00 38.22 5.07
1013 1015 2.752807 TAAAGATGAGCCCCGGCCC 61.753 63.158 1.02 0.00 43.17 5.80
1256 1258 4.268884 GCATGACATCGAGAAGGTTAGTTC 59.731 45.833 0.00 0.00 0.00 3.01
1258 1260 3.830178 TGACATCGAGAAGGTTAGTTCCA 59.170 43.478 0.00 0.00 0.00 3.53
1260 1262 4.759782 ACATCGAGAAGGTTAGTTCCATG 58.240 43.478 0.00 0.00 0.00 3.66
1261 1263 4.223032 ACATCGAGAAGGTTAGTTCCATGT 59.777 41.667 0.00 0.00 0.00 3.21
1262 1264 4.451629 TCGAGAAGGTTAGTTCCATGTC 57.548 45.455 0.00 0.00 0.00 3.06
1263 1265 4.087182 TCGAGAAGGTTAGTTCCATGTCT 58.913 43.478 0.00 0.00 0.00 3.41
1494 1578 1.451387 GGTGGCGTCCATGGGTAAG 60.451 63.158 13.02 2.09 35.28 2.34
1509 1593 3.244284 TGGGTAAGCTTCGAGTTTTGCTA 60.244 43.478 0.00 0.00 35.09 3.49
1517 1617 5.751028 AGCTTCGAGTTTTGCTACATAGATC 59.249 40.000 0.00 0.00 33.64 2.75
1518 1618 5.520288 GCTTCGAGTTTTGCTACATAGATCA 59.480 40.000 0.00 0.00 0.00 2.92
1565 1672 1.066918 CGTACCCCTATGGACGCAC 59.933 63.158 0.00 0.00 38.00 5.34
1570 1679 2.184322 CCTATGGACGCACGCACT 59.816 61.111 0.00 0.00 0.00 4.40
1571 1680 1.447838 CCTATGGACGCACGCACTT 60.448 57.895 0.00 0.00 0.00 3.16
1573 1682 0.921347 CTATGGACGCACGCACTTAC 59.079 55.000 0.00 0.00 0.00 2.34
1574 1683 0.244178 TATGGACGCACGCACTTACA 59.756 50.000 0.00 0.00 0.00 2.41
1575 1684 0.601576 ATGGACGCACGCACTTACAA 60.602 50.000 0.00 0.00 0.00 2.41
1576 1685 0.601576 TGGACGCACGCACTTACAAT 60.602 50.000 0.00 0.00 0.00 2.71
1754 1863 0.252421 TCATCCAGGAGGTGCTCAGT 60.252 55.000 0.00 0.00 35.89 3.41
1854 1982 2.001361 TACGCGCTAGCCAGTCTTCC 62.001 60.000 5.73 0.00 41.18 3.46
1954 2084 7.279758 CCTTCTTCCTTCTTGATTCATGTACTC 59.720 40.741 0.00 0.00 0.00 2.59
1955 2085 6.644347 TCTTCCTTCTTGATTCATGTACTCC 58.356 40.000 0.00 0.00 0.00 3.85
1956 2086 6.441924 TCTTCCTTCTTGATTCATGTACTCCT 59.558 38.462 0.00 0.00 0.00 3.69
2002 2132 3.217626 CAAGGACAGGAGAAAAGTTGCT 58.782 45.455 0.00 0.00 0.00 3.91
2003 2133 4.389374 CAAGGACAGGAGAAAAGTTGCTA 58.611 43.478 0.00 0.00 0.00 3.49
2059 2193 1.740585 CCACTCTAGGTCGTCACTGAG 59.259 57.143 0.00 0.00 0.00 3.35
2204 2344 5.878406 ATCCCTGGTTCTGTGATTAGTAG 57.122 43.478 0.00 0.00 0.00 2.57
2207 2347 6.258354 TCCCTGGTTCTGTGATTAGTAGTAA 58.742 40.000 0.00 0.00 0.00 2.24
2208 2348 6.380274 TCCCTGGTTCTGTGATTAGTAGTAAG 59.620 42.308 0.00 0.00 0.00 2.34
2209 2349 6.154706 CCCTGGTTCTGTGATTAGTAGTAAGT 59.845 42.308 0.00 0.00 0.00 2.24
2210 2350 7.341256 CCCTGGTTCTGTGATTAGTAGTAAGTA 59.659 40.741 0.00 0.00 0.00 2.24
2211 2351 8.189460 CCTGGTTCTGTGATTAGTAGTAAGTAC 58.811 40.741 0.00 0.00 0.00 2.73
2212 2352 8.874744 TGGTTCTGTGATTAGTAGTAAGTACT 57.125 34.615 0.00 0.00 44.69 2.73
2287 2429 0.773014 TATGGGATGGGAGCACATGG 59.227 55.000 0.00 0.00 30.74 3.66
2433 2582 8.478877 TGTGGTTAGTTAATTTTGGAAACACAT 58.521 29.630 8.70 0.00 39.03 3.21
2751 2900 1.302033 CCTCGTGGAGCAAGCACTT 60.302 57.895 0.00 0.00 34.57 3.16
2769 2918 0.036388 TTGGCTCCATCAAGACCGTC 60.036 55.000 0.00 0.00 0.00 4.79
3010 3159 1.959710 TCTGGGTGGCCTGTATGTTA 58.040 50.000 3.32 0.00 0.00 2.41
3192 3341 0.392998 GTGTGCCCCAGATCAACGAT 60.393 55.000 0.00 0.00 0.00 3.73
3237 3386 4.703379 GGATCAAGTCCATGGAGAGATT 57.297 45.455 16.81 5.12 46.96 2.40
3243 3392 4.751767 AGTCCATGGAGAGATTGAGTTC 57.248 45.455 16.81 0.00 0.00 3.01
3254 3403 3.722147 AGATTGAGTTCGAATCCATCCG 58.278 45.455 0.00 0.00 31.22 4.18
3267 3416 1.366111 CCATCCGCTTTGTGTACCCG 61.366 60.000 0.00 0.00 0.00 5.28
3285 3434 1.691976 CCGTCCAGGCCTAATATGACA 59.308 52.381 3.98 0.00 0.00 3.58
3653 3802 8.511604 AAGGTATGTTCATCATAAGGAAACAG 57.488 34.615 0.00 0.00 40.21 3.16
3664 3813 5.415701 TCATAAGGAAACAGAACATTCAGGC 59.584 40.000 0.00 0.00 0.00 4.85
3809 3958 4.923415 AGAACCCTGCTATACTTTTGCTT 58.077 39.130 0.00 0.00 0.00 3.91
3878 4027 2.798499 GCATGCACTTGATCAAGCATCC 60.798 50.000 30.95 18.90 45.14 3.51
3990 4141 9.765795 ACTGTAGCACTCATTATTTATACCTTC 57.234 33.333 0.00 0.00 0.00 3.46
4064 4215 4.603946 GCGGTAGTCGATGGGGGC 62.604 72.222 0.00 0.00 42.43 5.80
4250 4401 1.003355 AAGTCCCATGCCACTCACG 60.003 57.895 0.00 0.00 0.00 4.35
4496 4647 6.238566 GCTATGCATTGATCTTTTGCTCACTA 60.239 38.462 12.54 0.00 37.28 2.74
4589 4740 1.674441 CGTATCCGAGTCCAAGTGCTA 59.326 52.381 0.00 0.00 35.63 3.49
4952 5103 4.701651 GTGACCTCATTTGGATGTTCATCA 59.298 41.667 13.64 0.00 34.77 3.07
5045 5196 0.618458 GGATAACCACAGGGCTGTCA 59.382 55.000 0.00 0.00 42.83 3.58
5614 5765 7.566879 AGAGGTTCTATGATGTTGATAGAGGTT 59.433 37.037 0.00 0.00 34.61 3.50
5625 5776 8.783660 ATGTTGATAGAGGTTCTGTAAGGATA 57.216 34.615 0.00 0.00 0.00 2.59
5793 5944 0.109179 CTGCTAAAGCCGCAAATGCA 60.109 50.000 6.18 0.00 41.18 3.96
5819 5970 7.436673 ACATGAATTCATCTCGTAAGTCTTAGC 59.563 37.037 18.16 0.00 33.61 3.09
6218 6369 2.089980 CAGCTCATGAACAAGAAGGGG 58.910 52.381 0.00 0.00 0.00 4.79
6400 6551 5.582689 ACAAAAGAAAACAAGGAGGAGTG 57.417 39.130 0.00 0.00 0.00 3.51
6790 6941 7.613585 TGATGCACCAATTTCTGTATTTCATT 58.386 30.769 0.00 0.00 0.00 2.57
6941 7092 0.804989 AAGTGCATACGCTTTCCAGC 59.195 50.000 0.00 0.00 44.17 4.85
7213 7364 6.204688 GTGATGGTCTTCATAAAGTTGTCACA 59.795 38.462 0.00 0.00 35.97 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.743623 CGGTTGTCGCTGGGCAATA 60.744 57.895 5.28 0.00 0.00 1.90
10 11 1.300620 TGAGGTCAAGCGGTTGTCG 60.301 57.895 25.18 1.90 42.76 4.35
11 12 1.228657 GGTGAGGTCAAGCGGTTGTC 61.229 60.000 25.18 19.92 34.98 3.18
12 13 1.227853 GGTGAGGTCAAGCGGTTGT 60.228 57.895 25.18 7.94 34.98 3.32
13 14 0.606401 ATGGTGAGGTCAAGCGGTTG 60.606 55.000 21.02 21.02 34.67 3.77
14 15 0.110486 AATGGTGAGGTCAAGCGGTT 59.890 50.000 0.00 0.00 0.00 4.44
15 16 0.606401 CAATGGTGAGGTCAAGCGGT 60.606 55.000 0.00 0.00 0.00 5.68
16 17 0.321564 TCAATGGTGAGGTCAAGCGG 60.322 55.000 0.00 0.00 0.00 5.52
17 18 0.798776 GTCAATGGTGAGGTCAAGCG 59.201 55.000 0.00 0.00 33.27 4.68
18 19 1.896220 TGTCAATGGTGAGGTCAAGC 58.104 50.000 0.00 0.00 33.27 4.01
19 20 4.578871 TGTATGTCAATGGTGAGGTCAAG 58.421 43.478 0.00 0.00 33.27 3.02
20 21 4.565444 CCTGTATGTCAATGGTGAGGTCAA 60.565 45.833 0.00 0.00 33.27 3.18
21 22 3.055167 CCTGTATGTCAATGGTGAGGTCA 60.055 47.826 0.00 0.00 33.27 4.02
22 23 3.535561 CCTGTATGTCAATGGTGAGGTC 58.464 50.000 0.00 0.00 33.27 3.85
23 24 2.356125 GCCTGTATGTCAATGGTGAGGT 60.356 50.000 0.00 0.00 33.27 3.85
24 25 2.292267 GCCTGTATGTCAATGGTGAGG 58.708 52.381 0.00 0.00 33.27 3.86
25 26 2.679837 GTGCCTGTATGTCAATGGTGAG 59.320 50.000 0.00 0.00 33.27 3.51
26 27 2.710377 GTGCCTGTATGTCAATGGTGA 58.290 47.619 0.00 0.00 0.00 4.02
27 28 1.398041 CGTGCCTGTATGTCAATGGTG 59.602 52.381 0.00 0.00 0.00 4.17
28 29 1.737838 CGTGCCTGTATGTCAATGGT 58.262 50.000 0.00 0.00 0.00 3.55
29 30 0.378257 GCGTGCCTGTATGTCAATGG 59.622 55.000 0.00 0.00 0.00 3.16
60 61 9.599322 CAAAATTATCTGTCGCCTATTACAATC 57.401 33.333 0.00 0.00 0.00 2.67
97 98 4.648307 ACTTGAATACTACCGGTTAGGAGG 59.352 45.833 15.04 0.00 45.00 4.30
109 110 6.468333 TTACCGTGCCATACTTGAATACTA 57.532 37.500 0.00 0.00 0.00 1.82
194 195 7.186965 AGGGGGTATAAAGTTGGGTATAAAGTT 59.813 37.037 0.00 0.00 0.00 2.66
195 196 6.684243 AGGGGGTATAAAGTTGGGTATAAAGT 59.316 38.462 0.00 0.00 0.00 2.66
196 197 7.157947 AGGGGGTATAAAGTTGGGTATAAAG 57.842 40.000 0.00 0.00 0.00 1.85
197 198 6.103057 GGAGGGGGTATAAAGTTGGGTATAAA 59.897 42.308 0.00 0.00 0.00 1.40
198 199 5.612261 GGAGGGGGTATAAAGTTGGGTATAA 59.388 44.000 0.00 0.00 0.00 0.98
199 200 5.164897 GGAGGGGGTATAAAGTTGGGTATA 58.835 45.833 0.00 0.00 0.00 1.47
200 201 3.985452 GGAGGGGGTATAAAGTTGGGTAT 59.015 47.826 0.00 0.00 0.00 2.73
201 202 3.396565 GGAGGGGGTATAAAGTTGGGTA 58.603 50.000 0.00 0.00 0.00 3.69
202 203 2.211532 GGAGGGGGTATAAAGTTGGGT 58.788 52.381 0.00 0.00 0.00 4.51
203 204 1.497716 GGGAGGGGGTATAAAGTTGGG 59.502 57.143 0.00 0.00 0.00 4.12
204 205 1.497716 GGGGAGGGGGTATAAAGTTGG 59.502 57.143 0.00 0.00 0.00 3.77
205 206 1.497716 GGGGGAGGGGGTATAAAGTTG 59.502 57.143 0.00 0.00 0.00 3.16
227 228 9.552114 CTATCTTAGTCAAGTGAAATTGCTTTG 57.448 33.333 0.00 0.00 33.20 2.77
367 368 8.492673 TCTTTCATGTGATGTTGAATACTACC 57.507 34.615 0.00 0.00 32.27 3.18
376 377 6.831727 TTGCTTTTCTTTCATGTGATGTTG 57.168 33.333 0.00 0.00 0.00 3.33
387 388 6.704512 TCACAGTGTTTTTGCTTTTCTTTC 57.295 33.333 0.00 0.00 0.00 2.62
419 420 4.121317 CGAGGGTGGTTATGCGTTTAATA 58.879 43.478 0.00 0.00 0.00 0.98
434 435 4.436998 GCCTGGTCGACGAGGGTG 62.437 72.222 37.57 19.78 41.51 4.61
456 457 2.092838 GCGAGACTGAAACTGTATGTGC 59.907 50.000 0.00 0.00 0.00 4.57
479 480 3.073274 AGTACATGGAGAAAGTTGGCC 57.927 47.619 0.00 0.00 0.00 5.36
498 499 3.826157 TGGGGTTCAAACTCAAAGCATAG 59.174 43.478 0.00 0.00 0.00 2.23
499 500 3.838565 TGGGGTTCAAACTCAAAGCATA 58.161 40.909 0.00 0.00 0.00 3.14
500 501 2.676748 TGGGGTTCAAACTCAAAGCAT 58.323 42.857 0.00 0.00 0.00 3.79
502 503 2.430694 AGTTGGGGTTCAAACTCAAAGC 59.569 45.455 0.00 0.00 37.08 3.51
503 504 3.181476 CCAGTTGGGGTTCAAACTCAAAG 60.181 47.826 0.00 0.00 37.08 2.77
523 524 1.070105 CACCCCGACGAAAGAACCA 59.930 57.895 0.00 0.00 0.00 3.67
598 599 6.529463 ACCGCCGTTTACATATGTATAAAC 57.471 37.500 16.16 17.47 37.74 2.01
601 602 5.048154 TGCTACCGCCGTTTACATATGTATA 60.048 40.000 16.16 9.03 34.43 1.47
602 603 4.240096 GCTACCGCCGTTTACATATGTAT 58.760 43.478 16.16 1.87 0.00 2.29
652 653 2.719531 TCCTGGTGCACTTTGTAACA 57.280 45.000 17.98 3.04 0.00 2.41
655 656 3.357203 TGTTTTCCTGGTGCACTTTGTA 58.643 40.909 17.98 0.00 0.00 2.41
656 657 2.166254 CTGTTTTCCTGGTGCACTTTGT 59.834 45.455 17.98 0.00 0.00 2.83
666 667 5.066505 GGAGTATACATTGCTGTTTTCCTGG 59.933 44.000 5.50 0.00 36.79 4.45
669 670 6.699575 ATGGAGTATACATTGCTGTTTTCC 57.300 37.500 5.50 0.00 36.79 3.13
758 759 1.165270 CTCCCTCGGTTGCGAAAAAT 58.835 50.000 0.00 0.00 0.00 1.82
759 760 0.887387 CCTCCCTCGGTTGCGAAAAA 60.887 55.000 0.00 0.00 0.00 1.94
760 761 1.302192 CCTCCCTCGGTTGCGAAAA 60.302 57.895 0.00 0.00 0.00 2.29
761 762 2.345991 CCTCCCTCGGTTGCGAAA 59.654 61.111 0.00 0.00 0.00 3.46
762 763 3.702048 CCCTCCCTCGGTTGCGAA 61.702 66.667 0.00 0.00 0.00 4.70
763 764 4.689549 TCCCTCCCTCGGTTGCGA 62.690 66.667 0.00 0.00 0.00 5.10
764 765 4.148825 CTCCCTCCCTCGGTTGCG 62.149 72.222 0.00 0.00 0.00 4.85
765 766 3.787001 CCTCCCTCCCTCGGTTGC 61.787 72.222 0.00 0.00 0.00 4.17
766 767 2.038975 TCCTCCCTCCCTCGGTTG 59.961 66.667 0.00 0.00 0.00 3.77
767 768 2.231540 CTCTCCTCCCTCCCTCGGTT 62.232 65.000 0.00 0.00 0.00 4.44
768 769 2.617538 TCTCCTCCCTCCCTCGGT 60.618 66.667 0.00 0.00 0.00 4.69
769 770 2.197324 CTCTCCTCCCTCCCTCGG 59.803 72.222 0.00 0.00 0.00 4.63
770 771 2.197324 CCTCTCCTCCCTCCCTCG 59.803 72.222 0.00 0.00 0.00 4.63
771 772 1.231928 GTCCTCTCCTCCCTCCCTC 59.768 68.421 0.00 0.00 0.00 4.30
772 773 2.695970 CGTCCTCTCCTCCCTCCCT 61.696 68.421 0.00 0.00 0.00 4.20
773 774 2.123640 CGTCCTCTCCTCCCTCCC 60.124 72.222 0.00 0.00 0.00 4.30
774 775 2.835895 GCGTCCTCTCCTCCCTCC 60.836 72.222 0.00 0.00 0.00 4.30
775 776 1.826487 GAGCGTCCTCTCCTCCCTC 60.826 68.421 0.00 0.00 35.16 4.30
776 777 0.989212 TAGAGCGTCCTCTCCTCCCT 60.989 60.000 0.00 0.00 45.21 4.20
777 778 0.106619 TTAGAGCGTCCTCTCCTCCC 60.107 60.000 0.00 0.00 45.21 4.30
778 779 1.026584 GTTAGAGCGTCCTCTCCTCC 58.973 60.000 0.00 0.00 45.21 4.30
794 795 3.215975 CCTTGGAAAAGTTGGTCGGTTA 58.784 45.455 0.00 0.00 0.00 2.85
829 831 1.138883 GCGTGTGTGCTCTCCGATA 59.861 57.895 0.00 0.00 0.00 2.92
917 919 1.064296 CACCGATCGCTTCGCTACT 59.936 57.895 10.32 0.00 46.71 2.57
932 934 2.747855 GTAGCACTGGCCAGCACC 60.748 66.667 33.06 20.00 42.56 5.01
1258 1260 6.653526 TTCATTCATGTGTTCCAAAGACAT 57.346 33.333 0.00 0.00 45.16 3.06
1260 1262 7.652909 TGAAATTCATTCATGTGTTCCAAAGAC 59.347 33.333 0.00 0.00 43.08 3.01
1261 1263 7.724287 TGAAATTCATTCATGTGTTCCAAAGA 58.276 30.769 0.00 0.00 43.08 2.52
1262 1264 7.117236 CCTGAAATTCATTCATGTGTTCCAAAG 59.883 37.037 0.00 0.00 46.62 2.77
1263 1265 6.930164 CCTGAAATTCATTCATGTGTTCCAAA 59.070 34.615 0.00 0.00 46.62 3.28
1301 1384 9.698309 TTGTTTTTGTTTCTTAAGTGTGAATCA 57.302 25.926 1.63 0.00 0.00 2.57
1313 1397 6.073494 CCTGTTCCGTTTTGTTTTTGTTTCTT 60.073 34.615 0.00 0.00 0.00 2.52
1494 1578 5.520288 TGATCTATGTAGCAAAACTCGAAGC 59.480 40.000 0.00 0.00 0.00 3.86
1509 1593 6.942005 TGTTGAAACAATCTGGTGATCTATGT 59.058 34.615 0.00 0.00 35.67 2.29
1537 1637 4.413520 TCCATAGGGGTACGAGTTAGTACT 59.586 45.833 0.00 0.00 44.59 2.73
1539 1639 4.718961 GTCCATAGGGGTACGAGTTAGTA 58.281 47.826 0.00 0.00 38.11 1.82
1540 1640 3.560105 GTCCATAGGGGTACGAGTTAGT 58.440 50.000 0.00 0.00 38.11 2.24
1541 1641 2.551459 CGTCCATAGGGGTACGAGTTAG 59.449 54.545 1.72 0.00 40.41 2.34
1545 1650 1.105167 TGCGTCCATAGGGGTACGAG 61.105 60.000 11.37 0.00 40.41 4.18
1547 1654 1.066918 GTGCGTCCATAGGGGTACG 59.933 63.158 3.50 3.50 40.71 3.67
1565 1672 0.647410 CCTCTGCGATTGTAAGTGCG 59.353 55.000 0.00 0.00 0.00 5.34
1570 1679 2.167693 CAGTACCCCTCTGCGATTGTAA 59.832 50.000 0.00 0.00 0.00 2.41
1571 1680 1.754803 CAGTACCCCTCTGCGATTGTA 59.245 52.381 0.00 0.00 0.00 2.41
1573 1682 0.811616 GCAGTACCCCTCTGCGATTG 60.812 60.000 2.28 0.00 46.39 2.67
1574 1683 1.522569 GCAGTACCCCTCTGCGATT 59.477 57.895 2.28 0.00 46.39 3.34
1575 1684 3.221222 GCAGTACCCCTCTGCGAT 58.779 61.111 2.28 0.00 46.39 4.58
1854 1982 3.414700 GAGGCGTGCGTGACTTGG 61.415 66.667 0.00 0.00 0.00 3.61
1899 2027 5.300752 AGTTCCAAGGCGAATCTACATATG 58.699 41.667 0.00 0.00 0.00 1.78
1900 2028 5.552870 AGTTCCAAGGCGAATCTACATAT 57.447 39.130 0.00 0.00 0.00 1.78
1901 2029 5.116180 CAAGTTCCAAGGCGAATCTACATA 58.884 41.667 0.00 0.00 0.00 2.29
1954 2084 5.705441 TCATCTTAAACAAACCACTGCTAGG 59.295 40.000 0.00 0.00 0.00 3.02
1955 2085 6.801539 TCATCTTAAACAAACCACTGCTAG 57.198 37.500 0.00 0.00 0.00 3.42
1956 2086 6.016610 GGTTCATCTTAAACAAACCACTGCTA 60.017 38.462 0.00 0.00 39.33 3.49
2002 2132 2.304470 TGCCACCATGACAAAGCTAGTA 59.696 45.455 0.00 0.00 0.00 1.82
2003 2133 1.073763 TGCCACCATGACAAAGCTAGT 59.926 47.619 0.00 0.00 0.00 2.57
2059 2193 6.798959 GTCAAACAATTAGATTCAGCACTGAC 59.201 38.462 0.00 0.00 39.66 3.51
2145 2279 7.587037 TCAGTGTTTCATCTGGATTTTCTTT 57.413 32.000 0.00 0.00 33.13 2.52
2204 2344 9.341078 AGAGCTTAAGGTAGATACAGTACTTAC 57.659 37.037 7.26 0.00 0.00 2.34
2207 2347 7.808218 AGAGAGCTTAAGGTAGATACAGTACT 58.192 38.462 7.26 0.00 0.00 2.73
2208 2348 8.347035 CAAGAGAGCTTAAGGTAGATACAGTAC 58.653 40.741 7.26 0.00 31.81 2.73
2209 2349 8.272889 TCAAGAGAGCTTAAGGTAGATACAGTA 58.727 37.037 7.26 0.00 31.81 2.74
2210 2350 7.120051 TCAAGAGAGCTTAAGGTAGATACAGT 58.880 38.462 7.26 0.00 31.81 3.55
2211 2351 7.575414 TCAAGAGAGCTTAAGGTAGATACAG 57.425 40.000 7.26 0.00 31.81 2.74
2212 2352 8.540507 AATCAAGAGAGCTTAAGGTAGATACA 57.459 34.615 7.26 0.00 31.81 2.29
2287 2429 1.659098 CTTTGTCGCATACGGAACTCC 59.341 52.381 0.00 0.00 40.63 3.85
2319 2461 8.928448 TGCAGACATTATTATAGGAAGTCTCTT 58.072 33.333 0.00 0.00 33.01 2.85
2321 2463 9.717942 AATGCAGACATTATTATAGGAAGTCTC 57.282 33.333 0.00 0.00 44.78 3.36
2338 2487 9.995003 ATTTTTGGACTTAATTTAATGCAGACA 57.005 25.926 0.00 0.00 0.00 3.41
2385 2534 7.444183 CCACAACAGGAAGTTTCTGTCTTAATA 59.556 37.037 17.33 0.00 43.82 0.98
2751 2900 0.904865 AGACGGTCTTGATGGAGCCA 60.905 55.000 4.45 0.00 0.00 4.75
2769 2918 4.493547 CTTTCTCTGCAGTGAAGGAGTAG 58.506 47.826 27.30 18.93 29.65 2.57
3010 3159 2.293598 AAGGGAGGAGGGACATGAAT 57.706 50.000 0.00 0.00 0.00 2.57
3227 3376 4.406972 TGGATTCGAACTCAATCTCTCCAT 59.593 41.667 0.00 0.00 31.82 3.41
3237 3386 0.824109 AGCGGATGGATTCGAACTCA 59.176 50.000 0.00 1.93 0.00 3.41
3243 3392 1.086696 ACACAAAGCGGATGGATTCG 58.913 50.000 0.00 0.00 0.00 3.34
3254 3403 0.953960 CCTGGACGGGTACACAAAGC 60.954 60.000 0.00 0.00 0.00 3.51
3267 3416 3.244249 GGACTGTCATATTAGGCCTGGAC 60.244 52.174 17.99 14.88 39.13 4.02
3653 3802 4.497507 GGTTATTAAGGCGCCTGAATGTTC 60.498 45.833 39.03 28.44 30.26 3.18
3664 3813 2.434702 AGGGAGACAGGTTATTAAGGCG 59.565 50.000 0.00 0.00 0.00 5.52
3809 3958 1.600356 TGCGCTTGTGGCTTCATCA 60.600 52.632 9.73 0.00 39.13 3.07
3878 4027 2.586425 ACCAGTGTTGTTCTTCCCATG 58.414 47.619 0.00 0.00 0.00 3.66
3990 4141 2.025155 AGCTACGACCTGGTCAGTATG 58.975 52.381 25.42 18.85 32.09 2.39
4022 4173 2.349590 TGATCGGCATTCTTCACAGTG 58.650 47.619 0.00 0.00 0.00 3.66
4025 4176 4.621068 GATTTGATCGGCATTCTTCACA 57.379 40.909 0.00 0.00 0.00 3.58
4081 4232 4.190001 GTTGATCAGCTCATCATGTGTCT 58.810 43.478 0.00 0.00 32.69 3.41
4181 4332 2.669849 CTTGCTGCTGAGGAGGCT 59.330 61.111 2.44 0.00 0.00 4.58
4496 4647 2.138542 ACAGCAATGGATACCAGGGAT 58.861 47.619 0.00 0.00 36.75 3.85
4589 4740 5.249393 TGCCTCAAAGGTTAAGATCTTCTCT 59.751 40.000 12.24 5.33 37.80 3.10
4712 4863 2.224606 CAGGCTGTTTGAAGAAGCAGA 58.775 47.619 6.28 0.00 41.64 4.26
5045 5196 2.236146 TGATAAGAATGTGAGGCACGGT 59.764 45.455 0.00 0.00 37.14 4.83
5614 5765 7.179160 CACATCCATACCATCTATCCTTACAGA 59.821 40.741 0.00 0.00 0.00 3.41
5625 5776 3.116590 TCTCCCTCACATCCATACCATCT 60.117 47.826 0.00 0.00 0.00 2.90
5793 5944 7.436673 GCTAAGACTTACGAGATGAATTCATGT 59.563 37.037 25.37 21.31 36.57 3.21
5858 6009 8.208718 TGTAAGTTTCATATGTTGGATACTGC 57.791 34.615 1.90 0.00 37.61 4.40
6218 6369 2.353704 GGTTGCCAGGTTAAAGAATGCC 60.354 50.000 0.00 0.00 0.00 4.40
6320 6471 6.366877 CGAGAATTGCTCCAAAATTTGTCAAT 59.633 34.615 4.92 8.20 40.70 2.57
6400 6551 3.815401 AGGAGAACAACATTAGTGCACAC 59.185 43.478 21.04 0.00 0.00 3.82
6941 7092 1.805345 CTGAAGTGGCAGCTCAAAGAG 59.195 52.381 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.