Multiple sequence alignment - TraesCS1A01G143300

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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 TraesCS1A01G143300 chr1A 100.000 4470 0 0 1 4470 246693935 246689466 0.000000e+00 8255.0
1 TraesCS1A01G143300 chr1B 92.492 2544 84 54 710 3214 272881417 272878942 0.000000e+00 3541.0
2 TraesCS1A01G143300 chr1B 93.417 881 40 3 3262 4125 272878867 272877988 0.000000e+00 1290.0
3 TraesCS1A01G143300 chr1B 87.024 578 29 17 181 727 272884804 272884242 1.060000e-170 610.0
4 TraesCS1A01G143300 chr1B 92.568 148 8 2 31 178 272895097 272894953 4.530000e-50 209.0
5 TraesCS1A01G143300 chr1B 95.918 49 2 0 4117 4165 272877020 272876972 3.710000e-11 80.5
6 TraesCS1A01G143300 chr1D 91.155 1515 55 25 622 2125 196611927 196610481 0.000000e+00 1982.0
7 TraesCS1A01G143300 chr1D 97.112 1108 27 1 2116 3218 196610455 196609348 0.000000e+00 1864.0
8 TraesCS1A01G143300 chr1D 95.048 929 41 3 3234 4161 196609362 196608438 0.000000e+00 1456.0
9 TraesCS1A01G143300 chr1D 88.969 553 26 11 55 607 196613011 196612494 0.000000e+00 651.0
10 TraesCS1A01G143300 chr1D 87.859 313 24 5 2315 2627 69689083 69688785 5.500000e-94 355.0
11 TraesCS1A01G143300 chr1D 89.531 277 23 5 4195 4470 196608439 196608168 3.310000e-91 346.0
12 TraesCS1A01G143300 chr1D 90.179 224 22 0 4247 4470 483058530 483058753 4.370000e-75 292.0
13 TraesCS1A01G143300 chr3A 89.776 313 29 1 2315 2627 411839275 411838966 9.010000e-107 398.0
14 TraesCS1A01G143300 chr3A 89.848 197 20 0 4271 4467 572961136 572961332 2.060000e-63 254.0
15 TraesCS1A01G143300 chr2B 89.189 259 25 1 2369 2627 143243870 143244125 2.010000e-83 320.0
16 TraesCS1A01G143300 chr5D 90.583 223 19 2 4249 4470 363125313 363125092 1.220000e-75 294.0
17 TraesCS1A01G143300 chr2D 90.594 202 18 1 4269 4470 430015201 430015001 2.650000e-67 267.0
18 TraesCS1A01G143300 chr5B 87.111 225 26 2 4246 4470 429801547 429801326 7.420000e-63 252.0
19 TraesCS1A01G143300 chr2A 86.607 224 27 3 4248 4470 772442669 772442448 1.240000e-60 244.0
20 TraesCS1A01G143300 chr6B 90.964 166 15 0 4246 4411 705509224 705509389 1.620000e-54 224.0
21 TraesCS1A01G143300 chr7A 75.342 219 50 4 4247 4463 653637857 653637641 7.910000e-18 102.0


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 TraesCS1A01G143300 chr1A 246689466 246693935 4469 True 8255.000 8255 100.00000 1 4470 1 chr1A.!!$R1 4469
1 TraesCS1A01G143300 chr1B 272876972 272884804 7832 True 1380.375 3541 92.21275 181 4165 4 chr1B.!!$R2 3984
2 TraesCS1A01G143300 chr1D 196608168 196613011 4843 True 1259.800 1982 92.36300 55 4470 5 chr1D.!!$R2 4415

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
823 4241 0.179234 TTCTCCTCCAACACGCACAA 59.821 50.0 0.0 0.0 0.0 3.33 F
1011 4443 0.546122 CCGGACAGATGGATTTGGGA 59.454 55.0 0.0 0.0 0.0 4.37 F
2020 5486 0.539051 CCATGTCCACCACCTCTCTC 59.461 60.0 0.0 0.0 0.0 3.20 F
2851 6363 2.403252 ATCAAGGCCCTAAACACTCG 57.597 50.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1674 5134 0.105964 CGGCGGGTCATCCAAAGATA 59.894 55.000 0.00 0.0 34.36 1.98 R
2587 6099 1.486310 TCTATGCCGCCAGTTCTGAAT 59.514 47.619 1.00 0.0 0.00 2.57 R
3223 6735 0.179015 TGGCTTACCACCTCGCAAAA 60.179 50.000 0.00 0.0 42.67 2.44 R
4432 8995 0.034477 AACACTTATGGGAAGCCGGG 60.034 55.000 2.18 0.0 0.00 5.73 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
26 27 9.691362 GAATAGATTAACAGTTTTTCCTGCAAA 57.309 29.630 0.00 0.00 35.83 3.68
53 54 6.667007 AAAAGAAACACCAAAAAGATGCAG 57.333 33.333 0.00 0.00 0.00 4.41
54 55 5.596836 AAGAAACACCAAAAAGATGCAGA 57.403 34.783 0.00 0.00 0.00 4.26
55 56 5.596836 AGAAACACCAAAAAGATGCAGAA 57.403 34.783 0.00 0.00 0.00 3.02
56 57 6.165700 AGAAACACCAAAAAGATGCAGAAT 57.834 33.333 0.00 0.00 0.00 2.40
57 58 6.585416 AGAAACACCAAAAAGATGCAGAATT 58.415 32.000 0.00 0.00 0.00 2.17
136 137 0.250513 CTGGTCCTAGTTGGCAGGTC 59.749 60.000 0.00 0.00 34.56 3.85
170 171 0.533032 GCATCCTATCCGCTCCTACC 59.467 60.000 0.00 0.00 0.00 3.18
171 172 1.893210 GCATCCTATCCGCTCCTACCT 60.893 57.143 0.00 0.00 0.00 3.08
172 173 1.821753 CATCCTATCCGCTCCTACCTG 59.178 57.143 0.00 0.00 0.00 4.00
173 174 0.851469 TCCTATCCGCTCCTACCTGT 59.149 55.000 0.00 0.00 0.00 4.00
174 175 2.060275 TCCTATCCGCTCCTACCTGTA 58.940 52.381 0.00 0.00 0.00 2.74
175 176 2.444388 TCCTATCCGCTCCTACCTGTAA 59.556 50.000 0.00 0.00 0.00 2.41
176 177 2.820787 CCTATCCGCTCCTACCTGTAAG 59.179 54.545 0.00 0.00 0.00 2.34
234 235 1.529948 ACCGTCAGAACTGGTCCGA 60.530 57.895 1.93 0.00 29.93 4.55
418 426 2.139323 TCGGACAGTACTAGCCATGT 57.861 50.000 12.24 0.00 0.00 3.21
428 436 8.213518 ACAGTACTAGCCATGTCATTAAAATG 57.786 34.615 0.00 0.00 37.75 2.32
589 609 4.142600 GGTTATGTCCACTGCATCTCAAAC 60.143 45.833 0.00 0.00 0.00 2.93
599 619 2.491693 TGCATCTCAAACGGAAATTCCC 59.508 45.455 6.42 0.00 31.13 3.97
656 1231 5.501156 GGAGTATTGAACTTGGGATTCACT 58.499 41.667 0.00 0.00 39.07 3.41
707 1282 4.142182 ACATGTTGGAAGTTGGAACACAAG 60.142 41.667 0.00 0.00 40.38 3.16
727 4144 4.016113 AGCAAAACTTCAACTCGTGAAC 57.984 40.909 0.00 0.00 41.47 3.18
820 4238 1.301716 GCTTCTCCTCCAACACGCA 60.302 57.895 0.00 0.00 0.00 5.24
823 4241 0.179234 TTCTCCTCCAACACGCACAA 59.821 50.000 0.00 0.00 0.00 3.33
1011 4443 0.546122 CCGGACAGATGGATTTGGGA 59.454 55.000 0.00 0.00 0.00 4.37
1049 4481 6.147656 GGGTAAGCAAATCAAATCAAACCAAG 59.852 38.462 0.00 0.00 0.00 3.61
1053 4485 4.512571 GCAAATCAAATCAAACCAAGCAGT 59.487 37.500 0.00 0.00 0.00 4.40
1059 4491 6.169094 TCAAATCAAACCAAGCAGTTTTTCA 58.831 32.000 0.00 0.00 37.87 2.69
1079 4511 1.748493 AGTTCGAGACTCAGAGATGGC 59.252 52.381 3.79 0.00 31.20 4.40
1080 4512 1.474478 GTTCGAGACTCAGAGATGGCA 59.526 52.381 3.79 0.00 0.00 4.92
1214 4647 3.545703 CCATAACCAAGCTAAGGTCTGG 58.454 50.000 17.89 17.89 38.76 3.86
1300 4745 1.998315 CTGTGCTCTGAATTCGGACAG 59.002 52.381 13.13 14.90 39.95 3.51
1393 4842 2.046314 CCCCGCCACGAAATCAGT 60.046 61.111 0.00 0.00 0.00 3.41
1425 4878 3.512496 CTCCTTATCCCCCTCTCTTACC 58.488 54.545 0.00 0.00 0.00 2.85
1441 4894 3.073356 TCTTACCGAATTCAACCCCAGTT 59.927 43.478 6.22 0.00 36.33 3.16
1442 4895 1.905637 ACCGAATTCAACCCCAGTTC 58.094 50.000 6.22 0.00 32.45 3.01
1477 4936 2.832129 TGTATGCCTTCGACCTTCTTCT 59.168 45.455 0.00 0.00 0.00 2.85
1478 4937 3.260884 TGTATGCCTTCGACCTTCTTCTT 59.739 43.478 0.00 0.00 0.00 2.52
1479 4938 2.457366 TGCCTTCGACCTTCTTCTTC 57.543 50.000 0.00 0.00 0.00 2.87
1480 4939 1.971357 TGCCTTCGACCTTCTTCTTCT 59.029 47.619 0.00 0.00 0.00 2.85
1676 5136 8.701908 TCAGATAACTGATACGTAGGGTTTAT 57.298 34.615 13.16 8.28 46.55 1.40
1677 5137 8.790718 TCAGATAACTGATACGTAGGGTTTATC 58.209 37.037 15.40 15.40 46.55 1.75
1678 5138 8.794553 CAGATAACTGATACGTAGGGTTTATCT 58.205 37.037 17.93 17.93 46.03 1.98
1875 5336 4.262463 GGGGAAAGTGGAAGAAATGGAAAC 60.262 45.833 0.00 0.00 0.00 2.78
2020 5486 0.539051 CCATGTCCACCACCTCTCTC 59.461 60.000 0.00 0.00 0.00 3.20
2046 5512 9.554724 CGTCACATAATTATATTGGGCAATTAC 57.445 33.333 0.00 0.00 32.50 1.89
2070 5536 6.377146 ACAGTGGACTTCTTATTCTCTCTCTC 59.623 42.308 0.00 0.00 0.00 3.20
2122 5623 9.416794 CAGTAGGAATCATATGAACTCACATAC 57.583 37.037 9.99 12.17 35.91 2.39
2428 5935 3.681417 TCATTTTCGATGTCTGACAGCTG 59.319 43.478 21.98 13.48 31.24 4.24
2525 6037 7.335924 CCTAATTTACGGTCATCCTTCTTTTCA 59.664 37.037 0.00 0.00 0.00 2.69
2528 6040 4.286297 ACGGTCATCCTTCTTTTCATCA 57.714 40.909 0.00 0.00 0.00 3.07
2851 6363 2.403252 ATCAAGGCCCTAAACACTCG 57.597 50.000 0.00 0.00 0.00 4.18
2919 6431 3.181499 CGCAGTACCTATTTGACTCGACT 60.181 47.826 0.00 0.00 0.00 4.18
3013 6525 4.999950 ACCAGTAAGCATTTCTTCAGACAG 59.000 41.667 0.00 0.00 36.25 3.51
3135 6647 4.451150 TCGGCCTGCGACATGACC 62.451 66.667 0.00 0.00 0.00 4.02
3241 6753 0.955905 TTTTTGCGAGGTGGTAAGCC 59.044 50.000 0.00 0.00 0.00 4.35
3252 6764 2.719531 TGGTAAGCCACAAACTGACA 57.280 45.000 0.00 0.00 40.46 3.58
3497 7069 2.492484 GGAGGAGACGACAGTACAACAT 59.508 50.000 0.00 0.00 0.00 2.71
3589 7161 1.238439 GCTTGTAGGTTGAAGCTGCA 58.762 50.000 11.03 11.03 41.21 4.41
3590 7162 1.198637 GCTTGTAGGTTGAAGCTGCAG 59.801 52.381 14.30 10.11 39.34 4.41
3614 7186 0.606401 TTGCTGCAGTAGGAAGCACC 60.606 55.000 16.64 0.00 46.11 5.01
3660 7233 3.062370 AAGCCAGGAATTGCTTGCT 57.938 47.368 18.23 18.23 45.60 3.91
3661 7234 2.220653 AAGCCAGGAATTGCTTGCTA 57.779 45.000 23.00 0.00 45.60 3.49
3706 7279 2.093216 GCTCATTGCAGTTCGGAGG 58.907 57.895 0.00 0.00 42.31 4.30
3739 7312 2.774044 TGCGCTTGCATAAATCCGA 58.226 47.368 9.73 0.00 45.56 4.55
3742 7315 1.330521 GCGCTTGCATAAATCCGAAGA 59.669 47.619 0.00 0.00 38.92 2.87
3859 7446 7.608761 ACAACTACACACCAGAAAGAAAACTTA 59.391 33.333 0.00 0.00 0.00 2.24
3893 7480 5.488341 TGTTAGAACTCCATTGCTACTTCC 58.512 41.667 0.00 0.00 0.00 3.46
3944 7531 2.694628 ACTGATGCACACCAAAACATGT 59.305 40.909 0.00 0.00 0.00 3.21
3964 7551 7.389232 ACATGTTTCTGTGATCTGTCTGATAA 58.611 34.615 0.00 0.00 35.14 1.75
3974 7561 6.930164 GTGATCTGTCTGATAATCTGATTGCT 59.070 38.462 13.01 0.39 35.14 3.91
4125 8688 0.976641 CTTCTACACTGGGCCACTCA 59.023 55.000 0.00 0.00 0.00 3.41
4158 8721 2.558359 CAAACGAGAGGAAAAGGCCATT 59.442 45.455 5.01 0.00 0.00 3.16
4159 8722 2.586648 ACGAGAGGAAAAGGCCATTT 57.413 45.000 5.46 5.46 0.00 2.32
4160 8723 2.876581 ACGAGAGGAAAAGGCCATTTT 58.123 42.857 7.50 9.73 43.88 1.82
4161 8724 3.230976 ACGAGAGGAAAAGGCCATTTTT 58.769 40.909 7.50 4.84 41.24 1.94
4162 8725 3.255888 ACGAGAGGAAAAGGCCATTTTTC 59.744 43.478 17.74 17.74 41.24 2.29
4163 8726 3.255642 CGAGAGGAAAAGGCCATTTTTCA 59.744 43.478 24.00 0.00 44.82 2.69
4164 8727 4.261994 CGAGAGGAAAAGGCCATTTTTCAA 60.262 41.667 24.00 0.00 44.82 2.69
4165 8728 4.960938 AGAGGAAAAGGCCATTTTTCAAC 58.039 39.130 24.00 18.16 44.82 3.18
4166 8729 3.727726 AGGAAAAGGCCATTTTTCAACG 58.272 40.909 24.00 0.00 44.82 4.10
4167 8730 2.223144 GGAAAAGGCCATTTTTCAACGC 59.777 45.455 24.00 9.34 44.82 4.84
4168 8731 1.496934 AAAGGCCATTTTTCAACGCG 58.503 45.000 5.01 3.53 0.00 6.01
4169 8732 0.943835 AAGGCCATTTTTCAACGCGC 60.944 50.000 5.73 0.00 0.00 6.86
4170 8733 1.663074 GGCCATTTTTCAACGCGCA 60.663 52.632 5.73 0.00 0.00 6.09
4171 8734 1.616872 GGCCATTTTTCAACGCGCAG 61.617 55.000 5.73 2.42 0.00 5.18
4172 8735 0.662970 GCCATTTTTCAACGCGCAGA 60.663 50.000 5.73 0.13 0.00 4.26
4173 8736 1.981254 CCATTTTTCAACGCGCAGAT 58.019 45.000 5.73 0.00 0.00 2.90
4174 8737 1.913403 CCATTTTTCAACGCGCAGATC 59.087 47.619 5.73 0.00 0.00 2.75
4175 8738 1.574477 CATTTTTCAACGCGCAGATCG 59.426 47.619 5.73 0.00 42.12 3.69
4176 8739 0.110419 TTTTTCAACGCGCAGATCGG 60.110 50.000 5.73 0.00 38.94 4.18
4177 8740 0.946700 TTTTCAACGCGCAGATCGGA 60.947 50.000 5.73 0.00 38.94 4.55
4178 8741 0.739462 TTTCAACGCGCAGATCGGAT 60.739 50.000 5.73 0.00 38.94 4.18
4179 8742 1.145759 TTCAACGCGCAGATCGGATC 61.146 55.000 5.73 10.02 38.94 3.36
4180 8743 2.655364 AACGCGCAGATCGGATCG 60.655 61.111 5.73 8.53 38.94 3.69
4181 8744 3.120979 AACGCGCAGATCGGATCGA 62.121 57.895 5.73 0.00 41.13 3.59
4182 8745 3.094058 CGCGCAGATCGGATCGAC 61.094 66.667 8.75 7.62 39.18 4.20
4183 8746 3.094058 GCGCAGATCGGATCGACG 61.094 66.667 22.81 22.81 39.18 5.12
4184 8747 3.094058 CGCAGATCGGATCGACGC 61.094 66.667 18.08 16.81 39.18 5.19
4185 8748 2.731348 GCAGATCGGATCGACGCC 60.731 66.667 12.08 0.00 39.18 5.68
4186 8749 3.034878 CAGATCGGATCGACGCCT 58.965 61.111 12.08 0.00 39.18 5.52
4187 8750 1.853114 GCAGATCGGATCGACGCCTA 61.853 60.000 12.08 0.00 39.18 3.93
4188 8751 0.805614 CAGATCGGATCGACGCCTAT 59.194 55.000 12.08 0.00 39.18 2.57
4189 8752 1.088306 AGATCGGATCGACGCCTATC 58.912 55.000 12.08 10.86 39.18 2.08
4190 8753 1.088306 GATCGGATCGACGCCTATCT 58.912 55.000 1.62 0.00 39.18 1.98
4191 8754 0.805614 ATCGGATCGACGCCTATCTG 59.194 55.000 4.80 0.00 39.18 2.90
4192 8755 0.250166 TCGGATCGACGCCTATCTGA 60.250 55.000 3.17 3.17 35.60 3.27
4193 8756 0.805614 CGGATCGACGCCTATCTGAT 59.194 55.000 4.80 0.00 31.30 2.90
4313 8876 0.612744 AGTCAAGAGGCAAGAGCTCC 59.387 55.000 10.93 0.00 41.70 4.70
4323 8886 3.831911 AGGCAAGAGCTCCTCTATACATC 59.168 47.826 10.93 0.00 40.28 3.06
4329 8892 1.819903 GCTCCTCTATACATCGGGGTC 59.180 57.143 0.00 0.00 0.00 4.46
4335 8898 1.546476 CTATACATCGGGGTCCTCTGC 59.454 57.143 0.00 0.00 0.00 4.26
4340 8903 2.569218 ATCGGGGTCCTCTGCGTAGT 62.569 60.000 0.00 0.00 0.00 2.73
4347 8910 2.033550 GGTCCTCTGCGTAGTCATACAG 59.966 54.545 0.00 0.00 31.76 2.74
4377 8940 6.202379 GCTACACTCAGTACGACTATATGTCA 59.798 42.308 0.00 0.00 45.60 3.58
4414 8977 5.245584 ACCCTATTTTGTTCCCTACGAAA 57.754 39.130 0.00 0.00 42.78 3.46
4422 8985 3.986277 TGTTCCCTACGAAACTTCTGAC 58.014 45.455 0.00 0.00 30.39 3.51
4432 8995 6.449448 ACGAAACTTCTGACGAATAAACTC 57.551 37.500 0.00 0.00 0.00 3.01
4437 9000 1.134907 TCTGACGAATAAACTCCCGGC 60.135 52.381 0.00 0.00 0.00 6.13
4445 9008 1.882308 TAAACTCCCGGCTTCCCATA 58.118 50.000 0.00 0.00 0.00 2.74
4447 9010 0.546598 AACTCCCGGCTTCCCATAAG 59.453 55.000 0.00 0.00 0.00 1.73
4450 9013 0.912487 TCCCGGCTTCCCATAAGTGT 60.912 55.000 0.00 0.00 0.00 3.55
4453 9016 1.472480 CCGGCTTCCCATAAGTGTTTG 59.528 52.381 0.00 0.00 0.00 2.93
4466 9029 3.733443 AGTGTTTGGATTTCAGCAACC 57.267 42.857 0.00 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.691362 TTTGCAGGAAAAACTGTTAATCTATTC 57.309 29.630 0.00 0.00 40.59 1.75
29 30 6.878389 TCTGCATCTTTTTGGTGTTTCTTTTT 59.122 30.769 0.00 0.00 0.00 1.94
30 31 6.405538 TCTGCATCTTTTTGGTGTTTCTTTT 58.594 32.000 0.00 0.00 0.00 2.27
31 32 5.976458 TCTGCATCTTTTTGGTGTTTCTTT 58.024 33.333 0.00 0.00 0.00 2.52
32 33 5.596836 TCTGCATCTTTTTGGTGTTTCTT 57.403 34.783 0.00 0.00 0.00 2.52
33 34 5.596836 TTCTGCATCTTTTTGGTGTTTCT 57.403 34.783 0.00 0.00 0.00 2.52
34 35 6.849588 AATTCTGCATCTTTTTGGTGTTTC 57.150 33.333 0.00 0.00 0.00 2.78
35 36 7.442062 CCTAAATTCTGCATCTTTTTGGTGTTT 59.558 33.333 0.00 0.00 0.00 2.83
36 37 6.930722 CCTAAATTCTGCATCTTTTTGGTGTT 59.069 34.615 0.00 0.00 0.00 3.32
37 38 6.041979 ACCTAAATTCTGCATCTTTTTGGTGT 59.958 34.615 15.44 3.73 36.36 4.16
38 39 6.458210 ACCTAAATTCTGCATCTTTTTGGTG 58.542 36.000 15.44 0.00 36.36 4.17
39 40 6.670695 ACCTAAATTCTGCATCTTTTTGGT 57.329 33.333 12.40 12.40 34.05 3.67
40 41 6.930722 ACAACCTAAATTCTGCATCTTTTTGG 59.069 34.615 11.51 11.51 32.52 3.28
41 42 7.951530 ACAACCTAAATTCTGCATCTTTTTG 57.048 32.000 0.00 0.00 0.00 2.44
42 43 8.962884 AAACAACCTAAATTCTGCATCTTTTT 57.037 26.923 0.00 0.00 0.00 1.94
81 82 6.445786 ACCATTCAAGGTTACCCTACTCATAA 59.554 38.462 0.00 0.00 41.56 1.90
86 87 3.197116 CGACCATTCAAGGTTACCCTACT 59.803 47.826 0.00 0.00 43.38 2.57
170 171 0.037975 ACGGCGGTTACACCTTACAG 60.038 55.000 13.24 0.00 35.66 2.74
171 172 0.038343 GACGGCGGTTACACCTTACA 60.038 55.000 13.24 0.00 35.66 2.41
172 173 0.038343 TGACGGCGGTTACACCTTAC 60.038 55.000 13.24 0.00 35.66 2.34
173 174 0.896923 ATGACGGCGGTTACACCTTA 59.103 50.000 13.24 0.00 35.66 2.69
174 175 0.390735 GATGACGGCGGTTACACCTT 60.391 55.000 13.24 0.00 35.66 3.50
175 176 1.217244 GATGACGGCGGTTACACCT 59.783 57.895 13.24 0.00 35.66 4.00
176 177 1.812507 GGATGACGGCGGTTACACC 60.813 63.158 13.24 3.02 34.05 4.16
216 217 1.524863 CTCGGACCAGTTCTGACGGT 61.525 60.000 1.00 0.00 34.38 4.83
222 223 3.382832 CGGCCTCGGACCAGTTCT 61.383 66.667 0.00 0.00 0.00 3.01
275 276 2.789249 GCGCCCACGGAAACATAC 59.211 61.111 0.00 0.00 40.57 2.39
277 278 2.862674 ATACGCGCCCACGGAAACAT 62.863 55.000 5.73 0.00 40.57 2.71
278 279 3.592856 ATACGCGCCCACGGAAACA 62.593 57.895 5.73 0.00 40.57 2.83
300 301 2.282701 AATAATGCAAGTTGCCAGCG 57.717 45.000 24.59 0.00 44.23 5.18
478 498 1.251527 TGCTCCTCCCTCACGACTTC 61.252 60.000 0.00 0.00 0.00 3.01
610 630 8.523915 TCCGTATAATGTACTACTCCAAAAGA 57.476 34.615 0.00 0.00 0.00 2.52
611 631 8.411683 ACTCCGTATAATGTACTACTCCAAAAG 58.588 37.037 0.00 0.00 0.00 2.27
612 632 8.297470 ACTCCGTATAATGTACTACTCCAAAA 57.703 34.615 0.00 0.00 0.00 2.44
613 633 7.886629 ACTCCGTATAATGTACTACTCCAAA 57.113 36.000 0.00 0.00 0.00 3.28
615 635 9.006839 CAATACTCCGTATAATGTACTACTCCA 57.993 37.037 0.00 0.00 0.00 3.86
616 636 9.224267 TCAATACTCCGTATAATGTACTACTCC 57.776 37.037 0.00 0.00 0.00 3.85
656 1231 1.533625 CGCCACCTTCTTTCCATGAA 58.466 50.000 0.00 0.00 0.00 2.57
685 1260 4.362279 CTTGTGTTCCAACTTCCAACATG 58.638 43.478 0.00 0.00 32.80 3.21
707 1282 2.776225 CGTTCACGAGTTGAAGTTTTGC 59.224 45.455 0.00 0.00 45.23 3.68
820 4238 0.251341 GAATGGGGAGCCTGTGTTGT 60.251 55.000 0.00 0.00 0.00 3.32
823 4241 0.779997 AAAGAATGGGGAGCCTGTGT 59.220 50.000 0.00 0.00 0.00 3.72
944 4369 2.177669 CTCTGGGAGAGGAGAAGGAGAT 59.822 54.545 0.00 0.00 38.67 2.75
1011 4443 2.513026 CTTACCCGTGCTGCTCTGCT 62.513 60.000 0.00 0.00 0.00 4.24
1049 4481 3.555956 TGAGTCTCGAACTGAAAAACTGC 59.444 43.478 5.20 0.00 38.74 4.40
1053 4485 5.515797 TCTCTGAGTCTCGAACTGAAAAA 57.484 39.130 4.32 0.00 38.74 1.94
1059 4491 1.748493 GCCATCTCTGAGTCTCGAACT 59.252 52.381 4.32 0.71 42.42 3.01
1214 4647 4.568760 CGAGAAAGGAAAAGGCACTCTATC 59.431 45.833 0.00 0.00 38.49 2.08
1300 4745 1.970640 AGGCCCAAATGTTTCAGAACC 59.029 47.619 0.00 0.00 34.80 3.62
1372 4821 1.453197 GATTTCGTGGCGGGGGATT 60.453 57.895 0.00 0.00 0.00 3.01
1425 4878 2.488153 GGAAGAACTGGGGTTGAATTCG 59.512 50.000 0.04 0.00 35.58 3.34
1441 4894 2.225491 GCATACAGCAAAACACGGAAGA 59.775 45.455 0.00 0.00 44.79 2.87
1442 4895 2.584791 GCATACAGCAAAACACGGAAG 58.415 47.619 0.00 0.00 44.79 3.46
1477 4936 0.614979 CCCGAGTGGAGGAGGAAGAA 60.615 60.000 0.00 0.00 37.49 2.52
1478 4937 1.000486 CCCGAGTGGAGGAGGAAGA 60.000 63.158 0.00 0.00 37.49 2.87
1479 4938 0.033405 TACCCGAGTGGAGGAGGAAG 60.033 60.000 0.00 0.00 37.49 3.46
1480 4939 0.324091 GTACCCGAGTGGAGGAGGAA 60.324 60.000 0.00 0.00 37.49 3.36
1665 5125 4.814771 GGTCATCCAAAGATAAACCCTACG 59.185 45.833 0.00 0.00 33.96 3.51
1667 5127 4.141574 CGGGTCATCCAAAGATAAACCCTA 60.142 45.833 17.30 0.00 46.40 3.53
1668 5128 3.371595 CGGGTCATCCAAAGATAAACCCT 60.372 47.826 17.30 0.00 46.40 4.34
1669 5129 2.949644 CGGGTCATCCAAAGATAAACCC 59.050 50.000 12.61 12.61 45.76 4.11
1670 5130 2.357952 GCGGGTCATCCAAAGATAAACC 59.642 50.000 0.00 0.00 37.03 3.27
1671 5131 2.357952 GGCGGGTCATCCAAAGATAAAC 59.642 50.000 0.00 0.00 34.36 2.01
1673 5133 1.474320 CGGCGGGTCATCCAAAGATAA 60.474 52.381 0.00 0.00 34.36 1.75
1674 5134 0.105964 CGGCGGGTCATCCAAAGATA 59.894 55.000 0.00 0.00 34.36 1.98
1675 5135 1.153168 CGGCGGGTCATCCAAAGAT 60.153 57.895 0.00 0.00 34.36 2.40
1676 5136 2.267642 CGGCGGGTCATCCAAAGA 59.732 61.111 0.00 0.00 34.36 2.52
1677 5137 2.824041 CCGGCGGGTCATCCAAAG 60.824 66.667 20.56 0.00 34.36 2.77
1678 5138 4.418328 CCCGGCGGGTCATCCAAA 62.418 66.667 36.52 0.00 38.25 3.28
1759 5220 2.579787 GAGTCGATGACCACGCCG 60.580 66.667 0.00 0.00 32.18 6.46
1760 5221 2.202756 GGAGTCGATGACCACGCC 60.203 66.667 0.00 0.00 32.18 5.68
1761 5222 1.805945 GTGGAGTCGATGACCACGC 60.806 63.158 17.82 2.95 43.21 5.34
1762 5223 4.478195 GTGGAGTCGATGACCACG 57.522 61.111 17.82 0.00 43.21 4.94
1875 5336 2.599082 GACAGCGAAGTATCCTTTGTCG 59.401 50.000 0.00 0.00 34.93 4.35
2020 5486 9.554724 GTAATTGCCCAATATAATTATGTGACG 57.445 33.333 8.28 2.24 31.33 4.35
2046 5512 6.603201 AGAGAGAGAGAATAAGAAGTCCACTG 59.397 42.308 0.00 0.00 0.00 3.66
2428 5935 8.997621 TGAGATCTGTAATAACAAGGTAACAC 57.002 34.615 0.00 0.00 41.41 3.32
2525 6037 9.285770 GAAGAGAAAAACAGTAAACGTTTTGAT 57.714 29.630 20.19 4.21 43.82 2.57
2528 6040 7.595604 TGGAAGAGAAAAACAGTAAACGTTTT 58.404 30.769 20.19 0.00 45.90 2.43
2587 6099 1.486310 TCTATGCCGCCAGTTCTGAAT 59.514 47.619 1.00 0.00 0.00 2.57
2919 6431 1.754226 TGCAGTACGCTGATGTCCATA 59.246 47.619 10.27 0.00 45.28 2.74
3013 6525 4.445385 GTCCATTTCATGTGAACAAACAGC 59.555 41.667 0.00 0.00 33.13 4.40
3135 6647 1.647629 GAGCTTCTGCCATGCATCG 59.352 57.895 0.00 0.00 38.13 3.84
3222 6734 0.955905 GGCTTACCACCTCGCAAAAA 59.044 50.000 0.00 0.00 35.26 1.94
3223 6735 0.179015 TGGCTTACCACCTCGCAAAA 60.179 50.000 0.00 0.00 42.67 2.44
3224 6736 1.452368 TGGCTTACCACCTCGCAAA 59.548 52.632 0.00 0.00 42.67 3.68
3225 6737 3.152865 TGGCTTACCACCTCGCAA 58.847 55.556 0.00 0.00 42.67 4.85
3233 6745 2.685897 GTTGTCAGTTTGTGGCTTACCA 59.314 45.455 0.00 0.00 46.51 3.25
3234 6746 2.034179 GGTTGTCAGTTTGTGGCTTACC 59.966 50.000 0.00 0.00 31.76 2.85
3235 6747 2.685897 TGGTTGTCAGTTTGTGGCTTAC 59.314 45.455 0.00 0.00 0.00 2.34
3236 6748 2.685897 GTGGTTGTCAGTTTGTGGCTTA 59.314 45.455 0.00 0.00 0.00 3.09
3237 6749 1.476488 GTGGTTGTCAGTTTGTGGCTT 59.524 47.619 0.00 0.00 0.00 4.35
3238 6750 1.102978 GTGGTTGTCAGTTTGTGGCT 58.897 50.000 0.00 0.00 0.00 4.75
3239 6751 0.814457 TGTGGTTGTCAGTTTGTGGC 59.186 50.000 0.00 0.00 0.00 5.01
3240 6752 1.134175 GGTGTGGTTGTCAGTTTGTGG 59.866 52.381 0.00 0.00 0.00 4.17
3241 6753 1.815613 TGGTGTGGTTGTCAGTTTGTG 59.184 47.619 0.00 0.00 0.00 3.33
3248 6760 2.092375 TGGTTACATGGTGTGGTTGTCA 60.092 45.455 0.00 0.00 0.00 3.58
3252 6764 3.806949 AGATGGTTACATGGTGTGGTT 57.193 42.857 0.00 0.00 37.47 3.67
3497 7069 5.354513 GCTGTGACTATGAGTGAGTAGTGTA 59.645 44.000 0.00 0.00 31.61 2.90
3614 7186 2.098680 GAGACGCGTCACTCTCCG 59.901 66.667 37.85 0.00 0.00 4.63
3660 7233 3.224324 GCCTCCCTGTCGGCGATA 61.224 66.667 14.79 10.14 36.45 2.92
3694 7267 0.179234 TTGTTGTCCTCCGAACTGCA 59.821 50.000 0.00 0.00 0.00 4.41
3698 7271 2.033151 CGAGTTTTGTTGTCCTCCGAAC 60.033 50.000 0.00 0.00 0.00 3.95
3706 7279 2.770818 CGCAGCGAGTTTTGTTGTC 58.229 52.632 9.98 0.00 0.00 3.18
3739 7312 6.757897 TGATCAAGCGGTAAATCATTTCTT 57.242 33.333 7.52 0.00 0.00 2.52
3742 7315 5.010012 GGGATGATCAAGCGGTAAATCATTT 59.990 40.000 19.55 5.81 38.60 2.32
3837 7424 9.057089 AGAATAAGTTTTCTTTCTGGTGTGTAG 57.943 33.333 0.00 0.00 40.91 2.74
3859 7446 9.007901 CAATGGAGTTCTAACAGAAAGAAGAAT 57.992 33.333 0.00 0.00 35.75 2.40
3893 7480 3.181503 GCAATCTGGTGCTTGTAGACATG 60.182 47.826 0.00 0.00 41.51 3.21
3944 7531 8.071177 TCAGATTATCAGACAGATCACAGAAA 57.929 34.615 0.00 0.00 38.19 2.52
4026 7613 4.398358 GTGTATTTCTAGAAAACTGGCCCC 59.602 45.833 21.26 4.88 33.56 5.80
4035 7622 3.869065 CTGGCCCGTGTATTTCTAGAAA 58.131 45.455 19.83 19.83 34.46 2.52
4125 8688 3.879295 CCTCTCGTTTGGACATAATGCAT 59.121 43.478 0.00 0.00 0.00 3.96
4158 8721 0.946700 TCCGATCTGCGCGTTGAAAA 60.947 50.000 8.43 0.00 39.11 2.29
4159 8722 0.739462 ATCCGATCTGCGCGTTGAAA 60.739 50.000 8.43 0.00 39.11 2.69
4160 8723 1.145759 GATCCGATCTGCGCGTTGAA 61.146 55.000 8.43 0.00 39.11 2.69
4161 8724 1.588932 GATCCGATCTGCGCGTTGA 60.589 57.895 8.43 6.83 39.11 3.18
4162 8725 2.920964 CGATCCGATCTGCGCGTTG 61.921 63.158 8.43 0.25 39.11 4.10
4163 8726 2.655364 CGATCCGATCTGCGCGTT 60.655 61.111 8.43 0.00 39.11 4.84
4164 8727 3.583086 TCGATCCGATCTGCGCGT 61.583 61.111 8.43 0.00 39.11 6.01
4165 8728 3.094058 GTCGATCCGATCTGCGCG 61.094 66.667 0.00 0.00 38.42 6.86
4166 8729 3.094058 CGTCGATCCGATCTGCGC 61.094 66.667 0.00 0.00 38.42 6.09
4167 8730 3.094058 GCGTCGATCCGATCTGCG 61.094 66.667 6.81 10.84 38.42 5.18
4168 8731 1.853114 TAGGCGTCGATCCGATCTGC 61.853 60.000 6.81 7.50 38.42 4.26
4169 8732 0.805614 ATAGGCGTCGATCCGATCTG 59.194 55.000 6.81 1.12 38.42 2.90
4170 8733 1.088306 GATAGGCGTCGATCCGATCT 58.912 55.000 16.75 8.74 38.42 2.75
4171 8734 1.088306 AGATAGGCGTCGATCCGATC 58.912 55.000 16.47 16.47 38.42 3.69
4172 8735 0.805614 CAGATAGGCGTCGATCCGAT 59.194 55.000 6.50 1.10 38.42 4.18
4173 8736 0.250166 TCAGATAGGCGTCGATCCGA 60.250 55.000 6.50 0.00 0.00 4.55
4174 8737 0.805614 ATCAGATAGGCGTCGATCCG 59.194 55.000 6.50 0.00 0.00 4.18
4175 8738 2.989840 CAAATCAGATAGGCGTCGATCC 59.010 50.000 6.50 0.00 0.00 3.36
4176 8739 2.410053 GCAAATCAGATAGGCGTCGATC 59.590 50.000 1.42 1.42 0.00 3.69
4177 8740 2.036475 AGCAAATCAGATAGGCGTCGAT 59.964 45.455 0.00 0.00 0.00 3.59
4178 8741 1.409064 AGCAAATCAGATAGGCGTCGA 59.591 47.619 0.00 0.00 0.00 4.20
4179 8742 1.524355 CAGCAAATCAGATAGGCGTCG 59.476 52.381 0.00 0.00 0.00 5.12
4180 8743 1.262683 GCAGCAAATCAGATAGGCGTC 59.737 52.381 0.00 0.00 0.00 5.19
4181 8744 1.303309 GCAGCAAATCAGATAGGCGT 58.697 50.000 0.00 0.00 0.00 5.68
4182 8745 0.234106 CGCAGCAAATCAGATAGGCG 59.766 55.000 0.00 0.00 37.17 5.52
4183 8746 1.262683 GACGCAGCAAATCAGATAGGC 59.737 52.381 0.00 0.00 0.00 3.93
4184 8747 2.543012 CTGACGCAGCAAATCAGATAGG 59.457 50.000 11.34 0.00 42.07 2.57
4185 8748 3.856104 CTGACGCAGCAAATCAGATAG 57.144 47.619 11.34 0.00 42.07 2.08
4254 8817 5.961421 TGAAATAAAACTATTTCCCCCTGGG 59.039 40.000 5.50 5.50 42.68 4.45
4256 8819 9.958180 ATTTTGAAATAAAACTATTTCCCCCTG 57.042 29.630 12.69 0.00 42.68 4.45
4257 8820 9.958180 CATTTTGAAATAAAACTATTTCCCCCT 57.042 29.630 12.69 0.00 42.68 4.79
4276 8839 7.685481 TCTTGACTGTAACCCTATCATTTTGA 58.315 34.615 0.00 0.00 0.00 2.69
4295 8858 0.612744 AGGAGCTCTTGCCTCTTGAC 59.387 55.000 14.64 0.00 40.80 3.18
4297 8860 3.457099 GAGGAGCTCTTGCCTCTTG 57.543 57.895 14.64 0.00 45.72 3.02
4313 8876 3.085533 CAGAGGACCCCGATGTATAGAG 58.914 54.545 0.00 0.00 0.00 2.43
4323 8886 2.754658 ACTACGCAGAGGACCCCG 60.755 66.667 0.00 0.00 0.00 5.73
4329 8892 1.405463 TGCTGTATGACTACGCAGAGG 59.595 52.381 0.00 0.00 34.65 3.69
4335 8898 2.568696 AGCACTGCTGTATGACTACG 57.431 50.000 1.67 0.00 37.57 3.51
4340 8903 2.825532 TGAGTGTAGCACTGCTGTATGA 59.174 45.455 14.15 0.00 45.44 2.15
4347 8910 1.199327 TCGTACTGAGTGTAGCACTGC 59.801 52.381 6.50 0.00 45.44 4.40
4350 8913 4.879104 ATAGTCGTACTGAGTGTAGCAC 57.121 45.455 0.00 0.00 34.10 4.40
4377 8940 1.794714 AGGGTAGCAGATCGATTGGT 58.205 50.000 0.00 8.28 0.00 3.67
4414 8977 3.368116 CCGGGAGTTTATTCGTCAGAAGT 60.368 47.826 0.00 0.00 40.09 3.01
4422 8985 1.296727 GGAAGCCGGGAGTTTATTCG 58.703 55.000 2.18 0.00 0.00 3.34
4432 8995 0.034477 AACACTTATGGGAAGCCGGG 60.034 55.000 2.18 0.00 0.00 5.73
4437 9000 6.588719 TGAAATCCAAACACTTATGGGAAG 57.411 37.500 0.00 0.00 37.31 3.46
4445 9008 3.450457 TGGTTGCTGAAATCCAAACACTT 59.550 39.130 0.00 0.00 34.02 3.16
4447 9010 3.068024 TCTGGTTGCTGAAATCCAAACAC 59.932 43.478 0.00 0.00 34.02 3.32


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

AutoCloner maintained by Alex Coulton.