Multiple sequence alignment - TraesCS5A01G060900

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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 TraesCS5A01G060900 chr5A 100.000 5149 0 0 1 5149 64415668 64410520 0.000000e+00 9509.0
1 TraesCS5A01G060900 chr5A 87.121 264 21 5 3353 3603 64411882 64411619 2.350000e-73 287.0
2 TraesCS5A01G060900 chr5A 87.121 264 21 5 3787 4050 64412316 64412066 2.350000e-73 287.0
3 TraesCS5A01G060900 chr5D 92.678 5231 216 64 13 5149 71916055 71910898 0.000000e+00 7384.0
4 TraesCS5A01G060900 chr5D 90.187 214 14 3 3787 4000 71912708 71912502 6.570000e-69 272.0
5 TraesCS5A01G060900 chr5D 88.268 179 18 2 3135 3312 71912428 71912252 1.450000e-50 211.0
6 TraesCS5A01G060900 chr5D 94.915 59 3 0 4545 4603 357570614 357570672 5.490000e-15 93.5
7 TraesCS5A01G060900 chr5B 92.456 2850 144 34 1681 4490 82444166 82446984 0.000000e+00 4006.0
8 TraesCS5A01G060900 chr5B 89.095 1458 100 23 274 1698 82442720 82444151 0.000000e+00 1757.0
9 TraesCS5A01G060900 chr5B 90.123 567 34 8 4603 5149 82446993 82447557 0.000000e+00 717.0
10 TraesCS5A01G060900 chr5B 88.333 240 14 9 1 227 82442078 82442316 5.080000e-70 276.0
11 TraesCS5A01G060900 chr5B 85.328 259 22 8 3361 3603 82446274 82446532 2.380000e-63 254.0
12 TraesCS5A01G060900 chr5B 84.766 256 27 8 3787 4042 82445836 82446079 3.980000e-61 246.0
13 TraesCS5A01G060900 chr5B 87.709 179 19 2 3134 3311 82446085 82446261 6.760000e-49 206.0
14 TraesCS5A01G060900 chr2D 91.898 1802 100 19 489 2272 78792373 78794146 0.000000e+00 2477.0
15 TraesCS5A01G060900 chr2D 97.253 182 5 0 2209 2390 78794147 78794328 5.010000e-80 309.0
16 TraesCS5A01G060900 chr1A 87.826 575 48 13 489 1061 548315303 548315857 0.000000e+00 654.0
17 TraesCS5A01G060900 chr1A 92.500 200 9 2 1059 1252 548319716 548319915 1.090000e-71 281.0
18 TraesCS5A01G060900 chr1A 94.915 59 3 0 4545 4603 94757577 94757635 5.490000e-15 93.5
19 TraesCS5A01G060900 chr6B 90.355 394 30 2 1382 1767 88742955 88742562 1.280000e-140 510.0
20 TraesCS5A01G060900 chr6B 94.915 59 3 0 4545 4603 388349617 388349559 5.490000e-15 93.5
21 TraesCS5A01G060900 chrUn 94.915 59 3 0 4545 4603 45092700 45092758 5.490000e-15 93.5
22 TraesCS5A01G060900 chrUn 94.915 59 3 0 4545 4603 171042987 171043045 5.490000e-15 93.5
23 TraesCS5A01G060900 chrUn 94.915 59 3 0 4545 4603 420974490 420974548 5.490000e-15 93.5
24 TraesCS5A01G060900 chr4B 94.915 59 3 0 4545 4603 209319522 209319580 5.490000e-15 93.5
25 TraesCS5A01G060900 chr1D 94.915 59 3 0 4545 4603 351014945 351014887 5.490000e-15 93.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G060900 chr5A 64410520 64415668 5148 True 9509.000000 9509 100.000000 1 5149 1 chr5A.!!$R1 5148
1 TraesCS5A01G060900 chr5A 64411619 64412316 697 True 287.000000 287 87.121000 3353 4050 2 chr5A.!!$R2 697
2 TraesCS5A01G060900 chr5D 71910898 71916055 5157 True 2622.333333 7384 90.377667 13 5149 3 chr5D.!!$R1 5136
3 TraesCS5A01G060900 chr5B 82442078 82447557 5479 False 1066.000000 4006 88.258571 1 5149 7 chr5B.!!$F1 5148
4 TraesCS5A01G060900 chr2D 78792373 78794328 1955 False 1393.000000 2477 94.575500 489 2390 2 chr2D.!!$F1 1901
5 TraesCS5A01G060900 chr1A 548315303 548319915 4612 False 467.500000 654 90.163000 489 1252 2 chr1A.!!$F2 763

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
830 1237 0.036010 AGGGCATCCTGTTCTTGTCG 60.036 55.0 0.0 0.0 42.98 4.35 F
1901 6247 0.532115 AATTGCTCGGTTTCCATGCC 59.468 50.0 0.0 0.0 0.00 4.40 F
2398 6808 1.103398 AGCCAAAGTGAGCTTGCGTT 61.103 50.0 0.0 0.0 35.22 4.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2702 7112 0.240945 CGAACGCCCTCTGCAAATTT 59.759 50.0 0.00 0.0 41.33 1.82 R
2852 7262 2.403252 GATTGACCACGACAATCCCT 57.597 50.0 0.00 0.0 44.21 4.20 R
4235 8704 2.224523 TGATCCAGTGACACAAAGACCC 60.225 50.0 8.59 0.0 0.00 4.46 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
61 62 7.035612 CACCATTTCCTTCCTTTACATAAAGC 58.964 38.462 5.95 0.00 40.93 3.51
82 83 1.566298 ATCTCCTGGCCAGAACCACC 61.566 60.000 34.91 0.00 35.33 4.61
85 86 2.833913 CCTGGCCAGAACCACCACT 61.834 63.158 34.91 0.00 35.33 4.00
86 87 1.488705 CCTGGCCAGAACCACCACTA 61.489 60.000 34.91 0.00 35.33 2.74
88 89 0.766674 TGGCCAGAACCACCACTAGT 60.767 55.000 0.00 0.00 33.75 2.57
89 90 1.272807 GGCCAGAACCACCACTAGTA 58.727 55.000 0.00 0.00 0.00 1.82
90 91 1.838077 GGCCAGAACCACCACTAGTAT 59.162 52.381 0.00 0.00 0.00 2.12
97 107 7.122204 GCCAGAACCACCACTAGTATAAAAATT 59.878 37.037 0.00 0.00 0.00 1.82
98 108 8.674607 CCAGAACCACCACTAGTATAAAAATTC 58.325 37.037 0.00 0.00 0.00 2.17
192 210 8.964476 TCTACAAAATAGATCAACCAAGGATC 57.036 34.615 0.00 0.00 41.14 3.36
242 272 1.547372 CACCCTTGGGCTGAAGAATTG 59.453 52.381 5.46 0.00 0.00 2.32
274 389 5.109903 ACTGTATTATCCGAACTGCACTTC 58.890 41.667 0.00 0.00 0.00 3.01
409 795 2.443887 TCTTCTCGGTTACCCAAACG 57.556 50.000 0.00 0.00 46.44 3.60
415 801 1.301953 GGTTACCCAAACGGTCGCT 60.302 57.895 0.00 0.00 43.58 4.93
547 936 0.174617 GGTACTGCTCTGGAGTCTGC 59.825 60.000 0.00 0.00 0.00 4.26
616 1005 4.521062 CCCCTTCCGCTCGAGCTG 62.521 72.222 32.88 27.25 39.32 4.24
617 1006 4.521062 CCCTTCCGCTCGAGCTGG 62.521 72.222 32.88 31.35 39.32 4.85
618 1007 3.764466 CCTTCCGCTCGAGCTGGT 61.764 66.667 32.46 0.00 39.32 4.00
619 1008 2.202676 CTTCCGCTCGAGCTGGTC 60.203 66.667 32.46 11.41 39.32 4.02
700 1106 2.409378 CCATTTGCATGCTGTTTTCGAC 59.591 45.455 20.33 0.00 0.00 4.20
830 1237 0.036010 AGGGCATCCTGTTCTTGTCG 60.036 55.000 0.00 0.00 42.98 4.35
849 1259 9.737427 TCTTGTCGTTCTGCATTTTTATTTTTA 57.263 25.926 0.00 0.00 0.00 1.52
869 1292 9.750125 ATTTTTATTTCTTTGGTCTGTGTTCTC 57.250 29.630 0.00 0.00 0.00 2.87
913 1336 1.227497 GGGAGGCTCTGATCTTGCG 60.227 63.158 15.23 0.00 0.00 4.85
1286 5580 4.148825 CCGGGAAGCTCCTGACGG 62.149 72.222 11.38 6.72 45.95 4.79
1374 5668 1.134075 GCAGCACAAGATCTGCGTG 59.866 57.895 17.35 17.35 44.94 5.34
1377 5671 1.375908 GCACAAGATCTGCGTGGGA 60.376 57.895 21.12 0.00 30.22 4.37
1395 5689 2.932130 GATTCGGGCAGCCTGAGACC 62.932 65.000 22.65 12.12 40.34 3.85
1563 5863 2.538512 TGGAGATCCATGATTGCGAG 57.461 50.000 0.00 0.00 42.01 5.03
1608 5908 1.068083 CGGGCTGATGTACTGCGAT 59.932 57.895 0.00 0.00 42.94 4.58
1691 5993 3.969117 TGCATGTTCAGAAACTCACAC 57.031 42.857 0.00 0.00 36.30 3.82
1745 6081 3.635331 CTCATGTTGCTTGGTTTGTCAG 58.365 45.455 0.00 0.00 0.00 3.51
1886 6232 5.390145 GCTAAATTTGCAGGTTGCTGAATTG 60.390 40.000 0.00 6.59 45.31 2.32
1901 6247 0.532115 AATTGCTCGGTTTCCATGCC 59.468 50.000 0.00 0.00 0.00 4.40
1949 6295 1.115326 AAGCAGTTCCTTGGGTTGGC 61.115 55.000 0.00 0.00 0.00 4.52
2247 6657 3.500299 GGAAAGACTTCAGCCACTCTTTC 59.500 47.826 9.52 9.52 44.10 2.62
2398 6808 1.103398 AGCCAAAGTGAGCTTGCGTT 61.103 50.000 0.00 0.00 35.22 4.84
2702 7112 5.092554 TGAAATTAGGCGATAACTGTCCA 57.907 39.130 0.00 0.00 0.00 4.02
2852 7262 6.767902 GTGATTGTAGCCCATAGATTCTTTCA 59.232 38.462 0.00 0.00 0.00 2.69
2872 7282 1.909302 AGGGATTGTCGTGGTCAATCT 59.091 47.619 15.07 0.00 45.79 2.40
2873 7283 2.009774 GGGATTGTCGTGGTCAATCTG 58.990 52.381 15.07 0.00 45.79 2.90
2874 7284 2.354704 GGGATTGTCGTGGTCAATCTGA 60.355 50.000 15.07 0.00 45.79 3.27
2875 7285 3.535561 GGATTGTCGTGGTCAATCTGAT 58.464 45.455 15.07 0.00 45.79 2.90
2952 7362 3.547868 CGTAAATGTCGATGACACAGGAG 59.452 47.826 1.11 0.00 45.65 3.69
3090 7500 9.906660 TTTCAAGTTGTTATCAAATATGACCAC 57.093 29.630 2.11 0.00 38.69 4.16
3107 7517 2.225117 ACCACCATTTCCCCTTCTTCTG 60.225 50.000 0.00 0.00 0.00 3.02
3123 7533 5.367945 TCTTCTGGTTAGTTGAAGGTTGT 57.632 39.130 0.00 0.00 38.10 3.32
3126 7536 3.118038 TCTGGTTAGTTGAAGGTTGTGCT 60.118 43.478 0.00 0.00 0.00 4.40
3127 7537 3.626930 TGGTTAGTTGAAGGTTGTGCTT 58.373 40.909 0.00 0.00 0.00 3.91
3133 7543 3.821033 AGTTGAAGGTTGTGCTTATGGAC 59.179 43.478 0.00 0.00 34.96 4.02
3160 7570 6.371548 GTCTAAGGACTGTGCACATTATTTCA 59.628 38.462 22.00 2.56 39.24 2.69
3188 7598 4.321230 CCAGCAGAAATTCAGGGTTGTAAC 60.321 45.833 0.00 0.00 0.00 2.50
3341 7753 9.950496 TTTTCTCAGAAGCTTACAGATAGAAAT 57.050 29.630 0.00 0.00 32.34 2.17
4039 8485 6.569780 AGCACAGAAACGTTTAAAAGGAAAT 58.430 32.000 14.65 0.00 0.00 2.17
4040 8486 7.708998 AGCACAGAAACGTTTAAAAGGAAATA 58.291 30.769 14.65 0.00 0.00 1.40
4045 8492 9.341899 CAGAAACGTTTAAAAGGAAATAGGATG 57.658 33.333 14.65 0.00 0.00 3.51
4081 8528 8.074370 CAGAAGCATCCATATCAAAACTATGTG 58.926 37.037 0.00 0.00 0.00 3.21
4082 8529 7.776969 AGAAGCATCCATATCAAAACTATGTGT 59.223 33.333 0.00 0.00 0.00 3.72
4122 8577 7.488322 TCTTTTAACTGTCTTGGTTTTGGATG 58.512 34.615 0.00 0.00 0.00 3.51
4126 8581 3.117512 ACTGTCTTGGTTTTGGATGGAGT 60.118 43.478 0.00 0.00 0.00 3.85
4129 8584 3.888930 GTCTTGGTTTTGGATGGAGTTGA 59.111 43.478 0.00 0.00 0.00 3.18
4138 8593 4.801521 TGGATGGAGTTGATGGATGAAT 57.198 40.909 0.00 0.00 0.00 2.57
4147 8602 6.127647 GGAGTTGATGGATGAATTTGCAGTTA 60.128 38.462 0.00 0.00 0.00 2.24
4173 8629 1.458639 GCTGGGGCATGATTAGGTGC 61.459 60.000 0.00 0.00 40.55 5.01
4190 8646 2.609916 GGTGCGAAAGAAAGGAGCTATC 59.390 50.000 0.00 0.00 0.00 2.08
4191 8647 3.262420 GTGCGAAAGAAAGGAGCTATCA 58.738 45.455 0.00 0.00 0.00 2.15
4192 8648 3.308323 GTGCGAAAGAAAGGAGCTATCAG 59.692 47.826 0.00 0.00 0.00 2.90
4193 8649 2.869192 GCGAAAGAAAGGAGCTATCAGG 59.131 50.000 0.00 0.00 0.00 3.86
4235 8704 3.792956 GTGTGCATCAACTTGACACAAAG 59.207 43.478 13.88 0.00 42.39 2.77
4241 8710 3.963129 TCAACTTGACACAAAGGGTCTT 58.037 40.909 0.74 0.00 36.26 3.01
4242 8711 4.340617 TCAACTTGACACAAAGGGTCTTT 58.659 39.130 0.74 0.00 36.26 2.52
4277 8746 0.036388 TGGAAGCCGCACCTTAGAAG 60.036 55.000 7.86 0.00 0.00 2.85
4298 8767 0.179124 GCCACGGAAAGCAACACAAA 60.179 50.000 0.00 0.00 0.00 2.83
4330 8799 5.298989 TGTGATGGTGATGATGATGATGA 57.701 39.130 0.00 0.00 0.00 2.92
4331 8800 5.876357 TGTGATGGTGATGATGATGATGAT 58.124 37.500 0.00 0.00 0.00 2.45
4332 8801 5.705441 TGTGATGGTGATGATGATGATGATG 59.295 40.000 0.00 0.00 0.00 3.07
4333 8802 5.705905 GTGATGGTGATGATGATGATGATGT 59.294 40.000 0.00 0.00 0.00 3.06
4334 8803 5.705441 TGATGGTGATGATGATGATGATGTG 59.295 40.000 0.00 0.00 0.00 3.21
4335 8804 5.298989 TGGTGATGATGATGATGATGTGA 57.701 39.130 0.00 0.00 0.00 3.58
4336 8805 5.876357 TGGTGATGATGATGATGATGTGAT 58.124 37.500 0.00 0.00 0.00 3.06
4337 8806 5.705441 TGGTGATGATGATGATGATGTGATG 59.295 40.000 0.00 0.00 0.00 3.07
4342 8811 6.801539 TGATGATGATGATGTGATGTGATG 57.198 37.500 0.00 0.00 0.00 3.07
4353 8822 7.939782 TGATGTGATGTGATGTTTTGTTAAGT 58.060 30.769 0.00 0.00 0.00 2.24
4371 8840 7.204604 TGTTAAGTGTCTTTGTCGATGACTAA 58.795 34.615 7.44 0.00 34.44 2.24
4383 8852 7.761038 TGTCGATGACTAATGAGGTATATGT 57.239 36.000 0.00 0.00 33.15 2.29
4387 8856 6.309009 CGATGACTAATGAGGTATATGTGTGC 59.691 42.308 0.00 0.00 0.00 4.57
4396 8865 9.845740 AATGAGGTATATGTGTGCTAATTAACA 57.154 29.630 0.00 0.00 0.00 2.41
4423 8892 0.950836 CATGGAACCTGAAACACGCA 59.049 50.000 0.00 0.00 0.00 5.24
4490 8964 7.148440 TGCAAAGAATTTTCCTGAAAACAGTTG 60.148 33.333 7.18 9.96 42.32 3.16
4503 8977 7.973388 CCTGAAAACAGTTGAATTCAAAGTGTA 59.027 33.333 26.26 15.82 35.47 2.90
4504 8978 8.682128 TGAAAACAGTTGAATTCAAAGTGTAC 57.318 30.769 26.26 21.44 35.47 2.90
4511 8985 6.153680 AGTTGAATTCAAAGTGTACCACCAAA 59.846 34.615 22.07 0.00 37.63 3.28
4560 9034 3.813443 AGCTCCATGTCGATAAATTGCT 58.187 40.909 0.00 0.00 0.00 3.91
4563 9037 6.701340 AGCTCCATGTCGATAAATTGCTATA 58.299 36.000 0.00 0.00 0.00 1.31
4565 9039 6.813649 GCTCCATGTCGATAAATTGCTATAGA 59.186 38.462 3.21 0.00 0.00 1.98
4580 9054 4.284490 TGCTATAGAAAGTGGGGCTAGATG 59.716 45.833 3.21 0.00 0.00 2.90
4585 9059 1.501582 AAGTGGGGCTAGATGGAGAC 58.498 55.000 0.00 0.00 0.00 3.36
4599 9073 4.594920 AGATGGAGACTTCTGACCTTTTCA 59.405 41.667 0.00 0.00 42.72 2.69
4619 9098 6.601741 TTCATGGCATGAAACAAGAAAAAC 57.398 33.333 34.19 0.00 45.57 2.43
4623 9102 5.976458 TGGCATGAAACAAGAAAAACTCTT 58.024 33.333 0.00 0.00 45.80 2.85
4689 9168 4.483311 AGTACTTCCTCGTCGAAATCAAC 58.517 43.478 0.00 0.00 0.00 3.18
4704 9183 4.766404 AATCAACGAGAAAATGTGACCC 57.234 40.909 0.00 0.00 0.00 4.46
4747 9226 1.473258 TTTGGTATCATGGGCACAGC 58.527 50.000 0.00 0.00 0.00 4.40
4815 9298 5.392380 GGGACACAGCAGAAGTTCAATAATG 60.392 44.000 5.50 0.65 0.00 1.90
4909 9392 2.229792 CAGTGGAGCTTGCTTGGTTAA 58.770 47.619 0.00 0.00 0.00 2.01
5080 9577 5.245531 TCTAGTGGTGCTTAATTCAAGTGG 58.754 41.667 0.00 0.00 36.55 4.00
5118 9616 5.301045 ACAGGGCATGACTTGATGAATTATG 59.699 40.000 19.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 0.645868 GTATGCACTTTCGGCGTCTC 59.354 55.000 6.85 0.00 0.00 3.36
90 91 9.645059 TCCGTATGCATCAATTTTGAATTTTTA 57.355 25.926 0.19 0.00 41.13 1.52
97 107 4.157472 TGCTTCCGTATGCATCAATTTTGA 59.843 37.500 0.19 0.00 42.14 2.69
98 108 4.422840 TGCTTCCGTATGCATCAATTTTG 58.577 39.130 0.19 0.00 33.94 2.44
115 125 8.138074 GGAGGAAAGTTTTATATGGATTGCTTC 58.862 37.037 0.00 0.00 0.00 3.86
168 186 8.834465 CAGATCCTTGGTTGATCTATTTTGTAG 58.166 37.037 2.70 0.00 45.48 2.74
199 217 7.996644 GGTGGGGTTCTGATAGAAATATTACAA 59.003 37.037 0.00 0.00 35.75 2.41
222 244 7.787847 TAGACAATTCTTCAGCCCAAGGGTG 62.788 48.000 7.05 6.48 41.56 4.61
274 389 3.221771 ACGGATCCTCATCTTCTCTCAG 58.778 50.000 10.75 0.00 0.00 3.35
526 915 1.476085 CAGACTCCAGAGCAGTACCAG 59.524 57.143 0.00 0.00 0.00 4.00
529 918 0.891373 TGCAGACTCCAGAGCAGTAC 59.109 55.000 0.00 0.00 32.48 2.73
534 923 1.153588 GAGCTGCAGACTCCAGAGC 60.154 63.158 20.43 0.00 32.03 4.09
540 929 2.125188 GGCTGGAGCTGCAGACTC 60.125 66.667 36.18 21.69 41.70 3.36
541 930 2.607134 AGGCTGGAGCTGCAGACT 60.607 61.111 35.74 35.74 41.70 3.24
542 931 2.436292 CAGGCTGGAGCTGCAGAC 60.436 66.667 36.18 34.28 41.70 3.51
620 1009 4.083862 AAGAACGAGCGGGAGGGC 62.084 66.667 0.00 0.00 0.00 5.19
621 1010 2.125512 CAAGAACGAGCGGGAGGG 60.126 66.667 0.00 0.00 0.00 4.30
622 1011 1.961180 ATCCAAGAACGAGCGGGAGG 61.961 60.000 0.00 0.00 0.00 4.30
623 1012 0.528684 GATCCAAGAACGAGCGGGAG 60.529 60.000 0.00 0.00 0.00 4.30
624 1013 1.515954 GATCCAAGAACGAGCGGGA 59.484 57.895 0.00 0.00 0.00 5.14
625 1014 1.878522 CGATCCAAGAACGAGCGGG 60.879 63.158 0.00 0.00 35.59 6.13
626 1015 2.517450 GCGATCCAAGAACGAGCGG 61.517 63.158 0.00 0.00 39.43 5.52
627 1016 1.475441 GAGCGATCCAAGAACGAGCG 61.475 60.000 0.00 0.00 41.83 5.03
628 1017 1.475441 CGAGCGATCCAAGAACGAGC 61.475 60.000 0.00 0.00 29.49 5.03
629 1018 0.179161 ACGAGCGATCCAAGAACGAG 60.179 55.000 0.00 0.00 29.49 4.18
630 1019 0.242825 AACGAGCGATCCAAGAACGA 59.757 50.000 0.00 0.00 29.49 3.85
631 1020 0.640768 GAACGAGCGATCCAAGAACG 59.359 55.000 0.00 0.00 0.00 3.95
775 1182 0.316841 ATGCAACAAAAATCCGCGGT 59.683 45.000 27.15 10.00 0.00 5.68
787 1194 0.317799 GCAACCACATCCATGCAACA 59.682 50.000 0.00 0.00 38.63 3.33
849 1259 4.451900 ACGAGAACACAGACCAAAGAAAT 58.548 39.130 0.00 0.00 0.00 2.17
861 1284 1.111116 ACCGGGAGAACGAGAACACA 61.111 55.000 6.32 0.00 35.47 3.72
869 1292 2.431942 CGGAACACCGGGAGAACG 60.432 66.667 6.32 0.26 42.66 3.95
913 1336 0.813210 CTTCTCCTCCTGCAATCCGC 60.813 60.000 0.00 0.00 42.89 5.54
1374 5668 3.764160 CTCAGGCTGCCCGAATCCC 62.764 68.421 16.57 0.00 35.76 3.85
1377 5671 2.586792 GTCTCAGGCTGCCCGAAT 59.413 61.111 16.57 0.00 35.76 3.34
1491 5791 1.886585 GCCGTCAGAGAGCTTCTCA 59.113 57.895 13.42 0.00 45.73 3.27
1563 5863 3.831333 TCTCCACATAGATCTCTGCATCC 59.169 47.826 7.96 0.00 0.00 3.51
1691 5993 1.959282 AGAAAGGCAAAGGCACTGAAG 59.041 47.619 0.00 0.00 40.86 3.02
1826 6162 5.181056 TGATCAAACATGCAAGTACGTGAAT 59.819 36.000 13.30 4.53 0.00 2.57
1886 6232 1.675641 ACAGGCATGGAAACCGAGC 60.676 57.895 2.31 0.00 0.00 5.03
1946 6292 1.293498 GCTGTCTTCTTCCTCGCCA 59.707 57.895 0.00 0.00 0.00 5.69
1949 6295 1.063806 CAACGCTGTCTTCTTCCTCG 58.936 55.000 0.00 0.00 0.00 4.63
2033 6379 0.601558 GTGAGTACGGGCTGTCAGAA 59.398 55.000 0.06 0.00 0.00 3.02
2166 6512 5.549347 ACAGATATCTGATGTTCCATCTGC 58.451 41.667 34.16 0.00 46.59 4.26
2247 6657 1.094073 CCGGCTTCAGATGCTTCCAG 61.094 60.000 8.14 0.00 0.00 3.86
2354 6764 3.510753 CCCACATGACCACAAAATCATCA 59.489 43.478 0.00 0.00 33.18 3.07
2702 7112 0.240945 CGAACGCCCTCTGCAAATTT 59.759 50.000 0.00 0.00 41.33 1.82
2852 7262 2.403252 GATTGACCACGACAATCCCT 57.597 50.000 0.00 0.00 44.21 4.20
2872 7282 5.192927 GGGTTTCATGTCCACTATCAATCA 58.807 41.667 0.00 0.00 0.00 2.57
2873 7283 4.273480 CGGGTTTCATGTCCACTATCAATC 59.727 45.833 0.00 0.00 0.00 2.67
2874 7284 4.199310 CGGGTTTCATGTCCACTATCAAT 58.801 43.478 0.00 0.00 0.00 2.57
2875 7285 3.605634 CGGGTTTCATGTCCACTATCAA 58.394 45.455 0.00 0.00 0.00 2.57
2952 7362 5.508224 GCTAAAACGTGCAGTCATACAAATC 59.492 40.000 0.00 0.00 0.00 2.17
3090 7500 2.907458 ACCAGAAGAAGGGGAAATGG 57.093 50.000 0.00 0.00 0.00 3.16
3107 7517 5.335661 CCATAAGCACAACCTTCAACTAACC 60.336 44.000 0.00 0.00 0.00 2.85
3123 7533 4.160439 CAGTCCTTAGACAGTCCATAAGCA 59.840 45.833 0.00 0.00 46.15 3.91
3126 7536 4.081642 GCACAGTCCTTAGACAGTCCATAA 60.082 45.833 0.00 0.00 46.15 1.90
3127 7537 3.447586 GCACAGTCCTTAGACAGTCCATA 59.552 47.826 0.00 0.00 46.15 2.74
3133 7543 2.820059 TGTGCACAGTCCTTAGACAG 57.180 50.000 17.42 0.00 46.15 3.51
3148 7558 5.066893 TCTGCTGGAGAATGAAATAATGTGC 59.933 40.000 0.00 0.00 0.00 4.57
3160 7570 3.011032 ACCCTGAATTTCTGCTGGAGAAT 59.989 43.478 12.50 0.00 40.53 2.40
3188 7598 5.733620 AATTTGATTGCTATATGGGCTGG 57.266 39.130 4.57 0.00 0.00 4.85
3341 7753 6.888088 AGATGCATGCATAAGAGCCATAATTA 59.112 34.615 32.27 0.00 36.70 1.40
3349 7761 3.683822 GGACTAGATGCATGCATAAGAGC 59.316 47.826 33.27 25.90 36.70 4.09
4039 8485 3.432749 GCTTCTGGTCAGCATTCATCCTA 60.433 47.826 0.00 0.00 37.22 2.94
4040 8486 2.683152 GCTTCTGGTCAGCATTCATCCT 60.683 50.000 0.00 0.00 37.22 3.24
4096 8549 7.469537 TCCAAAACCAAGACAGTTAAAAGAA 57.530 32.000 0.00 0.00 0.00 2.52
4098 8551 6.701400 CCATCCAAAACCAAGACAGTTAAAAG 59.299 38.462 0.00 0.00 0.00 2.27
4101 8554 5.450453 TCCATCCAAAACCAAGACAGTTAA 58.550 37.500 0.00 0.00 0.00 2.01
4116 8571 4.589647 TTCATCCATCAACTCCATCCAA 57.410 40.909 0.00 0.00 0.00 3.53
4122 8577 4.159135 ACTGCAAATTCATCCATCAACTCC 59.841 41.667 0.00 0.00 0.00 3.85
4126 8581 6.095860 CCTCTAACTGCAAATTCATCCATCAA 59.904 38.462 0.00 0.00 0.00 2.57
4129 8584 5.513233 ACCTCTAACTGCAAATTCATCCAT 58.487 37.500 0.00 0.00 0.00 3.41
4138 8593 2.229792 CCAGCAACCTCTAACTGCAAA 58.770 47.619 0.00 0.00 38.58 3.68
4173 8629 4.130286 ACCTGATAGCTCCTTTCTTTCG 57.870 45.455 0.00 0.00 0.00 3.46
4193 8649 5.923114 CACACATGTCATAGGTAGCTGATAC 59.077 44.000 4.27 0.00 0.00 2.24
4235 8704 2.224523 TGATCCAGTGACACAAAGACCC 60.225 50.000 8.59 0.00 0.00 4.46
4277 8746 3.959975 TGTTGCTTTCCGTGGCGC 61.960 61.111 0.00 0.00 0.00 6.53
4298 8767 5.795972 TCATCACCATCACAAAATGCAAAT 58.204 33.333 0.00 0.00 0.00 2.32
4330 8799 7.715657 ACACTTAACAAAACATCACATCACAT 58.284 30.769 0.00 0.00 0.00 3.21
4331 8800 7.066887 AGACACTTAACAAAACATCACATCACA 59.933 33.333 0.00 0.00 0.00 3.58
4332 8801 7.417612 AGACACTTAACAAAACATCACATCAC 58.582 34.615 0.00 0.00 0.00 3.06
4333 8802 7.566760 AGACACTTAACAAAACATCACATCA 57.433 32.000 0.00 0.00 0.00 3.07
4334 8803 8.745837 CAAAGACACTTAACAAAACATCACATC 58.254 33.333 0.00 0.00 0.00 3.06
4335 8804 8.250332 ACAAAGACACTTAACAAAACATCACAT 58.750 29.630 0.00 0.00 0.00 3.21
4336 8805 7.598278 ACAAAGACACTTAACAAAACATCACA 58.402 30.769 0.00 0.00 0.00 3.58
4337 8806 7.044966 CGACAAAGACACTTAACAAAACATCAC 60.045 37.037 0.00 0.00 0.00 3.06
4342 8811 7.163682 GTCATCGACAAAGACACTTAACAAAAC 59.836 37.037 0.00 0.00 32.09 2.43
4353 8822 5.047306 ACCTCATTAGTCATCGACAAAGACA 60.047 40.000 10.49 0.00 34.60 3.41
4413 8882 2.675844 CGAGGGATTTATGCGTGTTTCA 59.324 45.455 0.00 0.00 0.00 2.69
4423 8892 4.356405 TCATCATGTGCGAGGGATTTAT 57.644 40.909 0.00 0.00 0.00 1.40
4526 9000 7.840931 TCGACATGGAGCTATCATACAAATAT 58.159 34.615 0.00 0.00 0.00 1.28
4535 9009 5.409520 GCAATTTATCGACATGGAGCTATCA 59.590 40.000 0.00 0.00 0.00 2.15
4543 9017 8.993121 ACTTTCTATAGCAATTTATCGACATGG 58.007 33.333 0.00 0.00 0.00 3.66
4560 9034 5.087323 CTCCATCTAGCCCCACTTTCTATA 58.913 45.833 0.00 0.00 0.00 1.31
4563 9037 2.122768 CTCCATCTAGCCCCACTTTCT 58.877 52.381 0.00 0.00 0.00 2.52
4565 9039 1.840635 GTCTCCATCTAGCCCCACTTT 59.159 52.381 0.00 0.00 0.00 2.66
4580 9054 4.006319 CCATGAAAAGGTCAGAAGTCTCC 58.994 47.826 0.00 0.00 40.43 3.71
4585 9059 3.760151 TCATGCCATGAAAAGGTCAGAAG 59.240 43.478 4.55 0.00 40.43 2.85
4599 9073 6.165700 AGAGTTTTTCTTGTTTCATGCCAT 57.834 33.333 0.00 0.00 29.61 4.40
4623 9102 9.342308 CTTCCTGACTTTTTATAAGATATGGCA 57.658 33.333 0.00 0.00 0.00 4.92
4625 9104 9.289782 CCCTTCCTGACTTTTTATAAGATATGG 57.710 37.037 0.00 0.00 0.00 2.74
4635 9114 5.656549 TTCTTCCCCTTCCTGACTTTTTA 57.343 39.130 0.00 0.00 0.00 1.52
4643 9122 2.593925 AAGCTTTCTTCCCCTTCCTG 57.406 50.000 0.00 0.00 0.00 3.86
4689 9168 2.488153 GGGAAAGGGTCACATTTTCTCG 59.512 50.000 3.99 0.00 32.74 4.04
4704 9183 5.272402 AGAAAACCTGGATAATGGGGAAAG 58.728 41.667 0.00 0.00 0.00 2.62
4747 9226 7.918643 ACAAGTTTAACATGCCAAAAATTCAG 58.081 30.769 0.00 0.00 0.00 3.02
4815 9298 2.025887 ACACCAACCCAGAATCCAGATC 60.026 50.000 0.00 0.00 0.00 2.75
5080 9577 1.404315 GCCCTGTAGTACTCTGCACAC 60.404 57.143 0.00 0.00 33.13 3.82
5118 9616 4.689812 CAGCTCACAGTGATATCCAATAGC 59.310 45.833 2.97 0.49 0.00 2.97
5130 9628 2.621763 GGTTCACCAGCTCACAGTG 58.378 57.895 0.00 0.00 35.64 3.66


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

AutoCloner maintained by Alex Coulton.