Multiple sequence alignment - TraesCS3B01G182800

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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 TraesCS3B01G182800 chr3B 100.000 8647 0 0 1 8647 193613760 193622406 0.000000e+00 15969
1 TraesCS3B01G182800 chr3B 90.184 163 16 0 3067 3229 242601496 242601658 6.800000e-51 213
2 TraesCS3B01G182800 chr3B 90.184 163 16 0 3067 3229 369098022 369097860 6.800000e-51 213
3 TraesCS3B01G182800 chr3A 96.967 4187 80 17 3824 8000 150721219 150725368 0.000000e+00 6985
4 TraesCS3B01G182800 chr3A 97.143 1365 23 3 1707 3056 150719859 150721222 0.000000e+00 2290
5 TraesCS3B01G182800 chr3A 93.246 1140 45 11 576 1703 150718218 150719337 0.000000e+00 1650
6 TraesCS3B01G182800 chr3A 96.751 277 7 2 8372 8647 150725525 150725800 2.200000e-125 460
7 TraesCS3B01G182800 chr3A 87.829 304 30 3 275 578 137605361 137605065 4.970000e-92 350
8 TraesCS3B01G182800 chr3A 87.273 275 11 7 1 269 150717959 150718215 8.490000e-75 292
9 TraesCS3B01G182800 chr3A 94.118 119 7 0 8272 8390 150725366 150725484 1.920000e-41 182
10 TraesCS3B01G182800 chr3D 96.151 3196 88 17 4038 7221 135382170 135385342 0.000000e+00 5188
11 TraesCS3B01G182800 chr3D 92.406 1725 72 16 1 1703 135378597 135380284 0.000000e+00 2405
12 TraesCS3B01G182800 chr3D 93.564 1445 60 21 7219 8647 135385444 135386871 0.000000e+00 2122
13 TraesCS3B01G182800 chr3D 97.697 1042 23 1 1886 2926 135381113 135382154 0.000000e+00 1790
14 TraesCS3B01G182800 chr3D 93.578 109 6 1 1707 1815 135380888 135380995 2.500000e-35 161
15 TraesCS3B01G182800 chr1B 99.356 777 5 0 3054 3830 143631247 143630471 0.000000e+00 1408
16 TraesCS3B01G182800 chr1B 87.708 301 30 4 275 575 161567245 161566952 2.310000e-90 344
17 TraesCS3B01G182800 chr2B 99.048 735 3 2 3089 3823 23312273 23311543 0.000000e+00 1315
18 TraesCS3B01G182800 chr2B 87.043 301 32 4 272 572 717213945 717214238 5.000000e-87 333
19 TraesCS3B01G182800 chr6D 96.944 720 19 1 3107 3826 255020183 255019467 0.000000e+00 1205
20 TraesCS3B01G182800 chr6D 87.987 308 30 4 272 579 5905866 5906166 2.970000e-94 357
21 TraesCS3B01G182800 chr6D 87.582 306 32 5 275 579 5905101 5905401 4.970000e-92 350
22 TraesCS3B01G182800 chr7D 95.805 739 21 3 3089 3824 14550321 14549590 0.000000e+00 1184
23 TraesCS3B01G182800 chr7D 95.447 637 23 3 3187 3823 184482563 184483193 0.000000e+00 1011
24 TraesCS3B01G182800 chr6A 94.394 767 27 9 3058 3823 75913784 75914535 0.000000e+00 1164
25 TraesCS3B01G182800 chr7A 94.530 713 25 7 3111 3823 53626079 53625381 0.000000e+00 1088
26 TraesCS3B01G182800 chr7A 89.137 313 26 4 275 585 503449068 503448762 4.900000e-102 383
27 TraesCS3B01G182800 chr5A 93.733 734 29 6 3094 3823 533749301 533748581 0.000000e+00 1085
28 TraesCS3B01G182800 chr4A 91.612 763 23 18 3061 3823 210994355 210995076 0.000000e+00 1016
29 TraesCS3B01G182800 chr6B 88.449 303 26 5 276 577 636485836 636486130 2.970000e-94 357
30 TraesCS3B01G182800 chr1A 87.375 301 31 3 275 575 497195442 497195149 1.080000e-88 339


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 TraesCS3B01G182800 chr3B 193613760 193622406 8646 False 15969.0 15969 100.000000 1 8647 1 chr3B.!!$F1 8646
1 TraesCS3B01G182800 chr3A 150717959 150725800 7841 False 1976.5 6985 94.249667 1 8647 6 chr3A.!!$F1 8646
2 TraesCS3B01G182800 chr3D 135378597 135386871 8274 False 2333.2 5188 94.679200 1 8647 5 chr3D.!!$F1 8646
3 TraesCS3B01G182800 chr1B 143630471 143631247 776 True 1408.0 1408 99.356000 3054 3830 1 chr1B.!!$R1 776
4 TraesCS3B01G182800 chr2B 23311543 23312273 730 True 1315.0 1315 99.048000 3089 3823 1 chr2B.!!$R1 734
5 TraesCS3B01G182800 chr6D 255019467 255020183 716 True 1205.0 1205 96.944000 3107 3826 1 chr6D.!!$R1 719
6 TraesCS3B01G182800 chr6D 5905101 5906166 1065 False 353.5 357 87.784500 272 579 2 chr6D.!!$F1 307
7 TraesCS3B01G182800 chr7D 14549590 14550321 731 True 1184.0 1184 95.805000 3089 3824 1 chr7D.!!$R1 735
8 TraesCS3B01G182800 chr7D 184482563 184483193 630 False 1011.0 1011 95.447000 3187 3823 1 chr7D.!!$F1 636
9 TraesCS3B01G182800 chr6A 75913784 75914535 751 False 1164.0 1164 94.394000 3058 3823 1 chr6A.!!$F1 765
10 TraesCS3B01G182800 chr7A 53625381 53626079 698 True 1088.0 1088 94.530000 3111 3823 1 chr7A.!!$R1 712
11 TraesCS3B01G182800 chr5A 533748581 533749301 720 True 1085.0 1085 93.733000 3094 3823 1 chr5A.!!$R1 729
12 TraesCS3B01G182800 chr4A 210994355 210995076 721 False 1016.0 1016 91.612000 3061 3823 1 chr4A.!!$F1 762

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
80 81 1.537135 GGCTCTCGCTGTCATACCTTC 60.537 57.143 0.00 0.00 36.09 3.46 F
1279 2070 1.749258 GGGGACGAGGATTGGTTGC 60.749 63.158 0.00 0.00 0.00 4.17 F
1571 2382 0.109458 TGTTGCTGTACCTACTCGCG 60.109 55.000 0.00 0.00 0.00 5.87 F
1856 3271 1.002900 GCTTTGCTGAGCGTTTGTACA 60.003 47.619 0.00 0.00 32.23 2.90 F
2074 3585 1.407575 GCCCTAGGCTTGAGTTTCTCC 60.408 57.143 2.05 0.00 46.69 3.71 F
3832 5372 1.192980 CGAAAACATTGCAAGCAAGGC 59.807 47.619 18.05 2.59 40.83 4.35 F
4510 6067 2.223665 GGTTTGCATGAAGGCTATCTGC 60.224 50.000 0.00 7.83 41.94 4.26 F
5716 7273 3.329386 TCAAGTAGCTGTGATGAGCAAC 58.671 45.455 0.00 0.00 41.83 4.17 F
7082 8648 2.760374 ACTTTGTCCTTCAGAAGCTCG 58.240 47.619 4.41 0.00 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1552 2363 0.109458 CGCGAGTAGGTACAGCAACA 60.109 55.000 0.00 0.00 33.68 3.33 R
2190 3701 0.321564 AACAAGCTGACGCATAGCCA 60.322 50.000 0.00 0.00 42.07 4.75 R
2954 4479 1.617850 CTGTCACTTGTCAGAGGAGCT 59.382 52.381 0.00 0.00 33.96 4.09 R
3745 5285 5.347620 AGTCGTGACTAGTCTAGACTCAT 57.652 43.478 30.45 17.59 40.26 2.90 R
3981 5524 5.670149 CATCTATTGATGTTGAGCAGTCC 57.330 43.478 8.76 0.00 43.68 3.85 R
5640 7197 1.971481 CATCCCAGATGCATTTCCGA 58.029 50.000 0.00 0.00 0.00 4.55 R
5737 7294 3.092334 ACCGACACAAAATCAAAAGCC 57.908 42.857 0.00 0.00 0.00 4.35 R
7559 9235 2.807967 TCTGAACATGCCGTTTCTCTTG 59.192 45.455 0.00 0.00 38.19 3.02 R
8602 10350 0.251916 CTATCACCGCCCAAGAACCA 59.748 55.000 0.00 0.00 0.00 3.67 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
80 81 1.537135 GGCTCTCGCTGTCATACCTTC 60.537 57.143 0.00 0.00 36.09 3.46
98 99 2.842208 TCAGTTTTTGACACGCCTTG 57.158 45.000 0.00 0.00 0.00 3.61
114 118 2.544267 GCCTTGTGCGAGTTATATGTCC 59.456 50.000 0.00 0.00 0.00 4.02
117 121 4.202161 CCTTGTGCGAGTTATATGTCCTCT 60.202 45.833 0.00 0.00 0.00 3.69
269 276 7.445945 AGAATTGGAGTAGACTGGTTATATGC 58.554 38.462 0.00 0.00 0.00 3.14
273 280 5.661312 TGGAGTAGACTGGTTATATGCAAGT 59.339 40.000 0.00 0.00 0.00 3.16
510 518 2.950309 AGAATGAAGCTGCATGTCATCC 59.050 45.455 8.32 0.00 30.76 3.51
699 1478 3.914579 CTCCTGGCTGTGGCTGGTG 62.915 68.421 14.51 9.83 44.94 4.17
701 1480 4.655647 CTGGCTGTGGCTGGTGCT 62.656 66.667 0.00 0.00 39.59 4.40
702 1481 4.960866 TGGCTGTGGCTGGTGCTG 62.961 66.667 0.00 0.00 39.59 4.41
704 1483 4.962836 GCTGTGGCTGGTGCTGGT 62.963 66.667 0.00 0.00 39.59 4.00
763 1542 1.919240 AAAGCCTTAAAACTCCCCGG 58.081 50.000 0.00 0.00 0.00 5.73
1279 2070 1.749258 GGGGACGAGGATTGGTTGC 60.749 63.158 0.00 0.00 0.00 4.17
1280 2071 2.106683 GGGACGAGGATTGGTTGCG 61.107 63.158 0.00 0.00 0.00 4.85
1281 2072 2.106683 GGACGAGGATTGGTTGCGG 61.107 63.158 0.00 0.00 0.00 5.69
1287 2078 3.053291 GATTGGTTGCGGCGGTGA 61.053 61.111 9.78 0.00 0.00 4.02
1382 2190 5.331902 GGTCGTGGTTATGAATTTGTGATG 58.668 41.667 0.00 0.00 0.00 3.07
1386 2194 5.104374 GTGGTTATGAATTTGTGATGCCTG 58.896 41.667 0.00 0.00 0.00 4.85
1504 2315 9.958180 TTCAAGTGTTGAAAGAATGGATATAGA 57.042 29.630 0.00 0.00 45.94 1.98
1505 2316 9.605275 TCAAGTGTTGAAAGAATGGATATAGAG 57.395 33.333 0.00 0.00 36.59 2.43
1550 2361 4.207891 CATAGGTATGGATGGCTACCAC 57.792 50.000 5.48 0.00 39.94 4.16
1551 2362 2.190398 AGGTATGGATGGCTACCACA 57.810 50.000 5.48 0.00 39.94 4.17
1552 2363 2.706350 AGGTATGGATGGCTACCACAT 58.294 47.619 5.48 0.00 39.94 3.21
1553 2364 2.373169 AGGTATGGATGGCTACCACATG 59.627 50.000 5.48 0.00 39.94 3.21
1554 2365 2.106511 GGTATGGATGGCTACCACATGT 59.893 50.000 0.00 0.00 40.36 3.21
1555 2366 3.435026 GGTATGGATGGCTACCACATGTT 60.435 47.826 0.00 0.00 40.36 2.71
1556 2367 2.127271 TGGATGGCTACCACATGTTG 57.873 50.000 0.00 0.00 35.80 3.33
1557 2368 0.740737 GGATGGCTACCACATGTTGC 59.259 55.000 0.00 0.00 43.79 4.17
1558 2369 1.683011 GGATGGCTACCACATGTTGCT 60.683 52.381 0.00 0.00 43.95 3.91
1559 2370 1.402968 GATGGCTACCACATGTTGCTG 59.597 52.381 0.00 0.00 43.95 4.41
1570 2381 1.927174 CATGTTGCTGTACCTACTCGC 59.073 52.381 0.00 0.00 0.00 5.03
1571 2382 0.109458 TGTTGCTGTACCTACTCGCG 60.109 55.000 0.00 0.00 0.00 5.87
1624 2435 2.070654 AAAAACTGGTTGCCGCTCCG 62.071 55.000 0.00 0.00 0.00 4.63
1703 2514 1.760613 GTATGTAGCTACTGCCACCCA 59.239 52.381 23.84 2.16 40.80 4.51
1704 2515 1.511613 ATGTAGCTACTGCCACCCAT 58.488 50.000 23.84 4.54 40.80 4.00
1708 3123 1.806496 AGCTACTGCCACCCATCATA 58.194 50.000 0.00 0.00 40.80 2.15
1856 3271 1.002900 GCTTTGCTGAGCGTTTGTACA 60.003 47.619 0.00 0.00 32.23 2.90
2025 3535 7.687941 ACATTACCTTATGTCCAAGTTCAAG 57.312 36.000 0.00 0.00 33.58 3.02
2026 3536 6.659242 ACATTACCTTATGTCCAAGTTCAAGG 59.341 38.462 0.00 0.00 33.58 3.61
2074 3585 1.407575 GCCCTAGGCTTGAGTTTCTCC 60.408 57.143 2.05 0.00 46.69 3.71
2190 3701 1.873591 GGAAATGCAACGACACTCAGT 59.126 47.619 0.00 0.00 0.00 3.41
2572 4083 7.236432 ACAGAAACTGATAGATATGGCAGGTAT 59.764 37.037 5.76 0.00 35.18 2.73
2587 4098 4.276926 GGCAGGTATGATCCAAGTGAAATC 59.723 45.833 0.00 0.00 0.00 2.17
2675 4186 1.612462 CCTCAAGTTCAGCATCAGCCA 60.612 52.381 0.00 0.00 43.56 4.75
2993 4518 3.436704 ACAGTGACGAGTGCATATTTTGG 59.563 43.478 0.00 0.00 0.00 3.28
3830 5370 3.374745 ACTCGAAAACATTGCAAGCAAG 58.625 40.909 13.35 7.90 39.47 4.01
3832 5372 1.192980 CGAAAACATTGCAAGCAAGGC 59.807 47.619 18.05 2.59 40.83 4.35
3848 5388 8.567948 GCAAGCAAGGCATTAGTATATAAGAAA 58.432 33.333 0.00 0.00 0.00 2.52
3965 5508 3.981071 TCAGAACTGTATGAAGTGGGG 57.019 47.619 1.73 0.00 0.00 4.96
3981 5524 7.902087 TGAAGTGGGGGTTTGATTTATAAAAG 58.098 34.615 1.21 0.00 0.00 2.27
4042 5585 6.924060 CCATTGTACTTACCATACTGTAGAGC 59.076 42.308 0.00 0.00 0.00 4.09
4111 5654 2.650778 GGCTTTGCCCAAGGAACG 59.349 61.111 0.00 0.00 44.06 3.95
4315 5870 6.116126 GGGTTAGTGATAGTGAGCATTCTTT 58.884 40.000 0.00 0.00 0.00 2.52
4316 5871 6.599638 GGGTTAGTGATAGTGAGCATTCTTTT 59.400 38.462 0.00 0.00 0.00 2.27
4317 5872 7.121315 GGGTTAGTGATAGTGAGCATTCTTTTT 59.879 37.037 0.00 0.00 0.00 1.94
4379 5934 6.128145 TGGTACACCATTTATTCACATCGTTG 60.128 38.462 0.00 0.00 42.01 4.10
4510 6067 2.223665 GGTTTGCATGAAGGCTATCTGC 60.224 50.000 0.00 7.83 41.94 4.26
4590 6147 4.825546 ATTTCAGTGAGAACAGTGCTTG 57.174 40.909 0.00 0.00 44.42 4.01
4721 6278 8.109705 TCCATCGATGAAAGAGAATTTTGAAA 57.890 30.769 26.86 0.00 0.00 2.69
4722 6279 8.742777 TCCATCGATGAAAGAGAATTTTGAAAT 58.257 29.630 26.86 0.00 0.00 2.17
5278 6835 7.309621 CCATTGTTCCAAGAAAGAGTTGATGAT 60.310 37.037 0.00 0.00 0.00 2.45
5292 6849 7.102346 AGAGTTGATGATAAAGGAACTGTCAG 58.898 38.462 0.00 0.00 40.86 3.51
5487 7044 3.895232 ACAGGTTCCTATGCAGTACAG 57.105 47.619 0.00 0.00 0.00 2.74
5640 7197 4.828939 TCCTGCTTTCAATTCAATGAGTGT 59.171 37.500 0.00 0.00 0.00 3.55
5716 7273 3.329386 TCAAGTAGCTGTGATGAGCAAC 58.671 45.455 0.00 0.00 41.83 4.17
5737 7294 9.213799 AGCAACTCTAAGAAAGATGAAACTAAG 57.786 33.333 0.00 0.00 32.41 2.18
5752 7309 7.769272 TGAAACTAAGGCTTTTGATTTTGTG 57.231 32.000 4.45 0.00 0.00 3.33
6474 8034 9.444600 GGATTAAATATTTGGACGGCTTAGATA 57.555 33.333 11.05 0.00 0.00 1.98
6862 8428 9.626045 GCTTGTATGGATTTAATGGTATTTAGC 57.374 33.333 0.00 0.00 0.00 3.09
7082 8648 2.760374 ACTTTGTCCTTCAGAAGCTCG 58.240 47.619 4.41 0.00 0.00 5.03
7138 8705 3.955471 AGTGTGTGGACAGAATAATGGG 58.045 45.455 0.00 0.00 30.74 4.00
7423 9096 4.159135 TCGACTAATTTGGGACCTCAGTAC 59.841 45.833 0.00 0.00 0.00 2.73
7559 9235 3.409570 GTGGTTCAAAGAAGTAGACCCC 58.590 50.000 0.00 0.00 0.00 4.95
7562 9238 4.072839 GGTTCAAAGAAGTAGACCCCAAG 58.927 47.826 0.00 0.00 0.00 3.61
7686 9366 1.067354 GCTGGTTTTGCTTAGCATGCT 60.067 47.619 25.99 25.99 38.76 3.79
7687 9367 2.611224 GCTGGTTTTGCTTAGCATGCTT 60.611 45.455 28.02 10.27 38.76 3.91
7688 9368 3.248266 CTGGTTTTGCTTAGCATGCTTC 58.752 45.455 28.02 15.66 38.76 3.86
8006 9687 4.237724 CGGGAGCTTTCTTTCATTTTTCC 58.762 43.478 0.00 0.00 0.00 3.13
8007 9688 4.021981 CGGGAGCTTTCTTTCATTTTTCCT 60.022 41.667 0.00 0.00 0.00 3.36
8043 9725 4.261825 GGCTATCGAGTCAGCTATTCTGTT 60.262 45.833 14.01 0.00 43.32 3.16
8044 9726 5.048643 GGCTATCGAGTCAGCTATTCTGTTA 60.049 44.000 14.01 0.00 43.32 2.41
8094 9777 7.252708 TGCATGCTGAGTCTTAATATTGTTTG 58.747 34.615 20.33 0.00 0.00 2.93
8182 9865 2.814919 AGGACGGAGCTATATTGAGTCG 59.185 50.000 0.00 0.00 0.00 4.18
8189 9872 2.560542 AGCTATATTGAGTCGAGCAGGG 59.439 50.000 0.00 0.00 35.55 4.45
8206 9889 2.757099 GGCCATGACCCAGCCTTG 60.757 66.667 0.00 0.00 43.62 3.61
8207 9890 2.356278 GCCATGACCCAGCCTTGA 59.644 61.111 0.00 0.00 0.00 3.02
8208 9891 1.304381 GCCATGACCCAGCCTTGAA 60.304 57.895 0.00 0.00 0.00 2.69
8209 9892 0.685458 GCCATGACCCAGCCTTGAAT 60.685 55.000 0.00 0.00 0.00 2.57
8213 9896 1.075601 TGACCCAGCCTTGAATCCTT 58.924 50.000 0.00 0.00 0.00 3.36
8214 9897 1.272092 TGACCCAGCCTTGAATCCTTG 60.272 52.381 0.00 0.00 0.00 3.61
8217 9900 2.029623 CCCAGCCTTGAATCCTTGATG 58.970 52.381 0.00 0.00 0.00 3.07
8223 9906 6.460676 CCAGCCTTGAATCCTTGATGAAATAC 60.461 42.308 0.00 0.00 0.00 1.89
8224 9907 6.095860 CAGCCTTGAATCCTTGATGAAATACA 59.904 38.462 0.00 0.00 0.00 2.29
8228 9911 8.857098 CCTTGAATCCTTGATGAAATACATGAT 58.143 33.333 0.00 0.00 39.56 2.45
8281 9967 0.958091 TTGTGGCCCTCAAACATTCG 59.042 50.000 0.00 0.00 0.00 3.34
8297 9983 5.248870 ACATTCGTATTTGCAAAGGATCC 57.751 39.130 18.19 2.48 0.00 3.36
8329 10015 1.654220 CCAGTGAGGCCACAAAACG 59.346 57.895 3.76 0.00 45.54 3.60
8355 10041 8.878769 GCATTTTCAAAAATATTACAATCCCGT 58.121 29.630 0.63 0.00 36.52 5.28
8547 10295 0.238289 GGTTGTCGATGCACCAACTG 59.762 55.000 13.50 0.00 38.74 3.16
8558 10306 1.743394 GCACCAACTGCCAATACTACC 59.257 52.381 0.00 0.00 40.42 3.18
8596 10344 4.706962 TCTGCATCTACAACTCTTAGCTCA 59.293 41.667 0.00 0.00 0.00 4.26
8601 10349 7.391554 TGCATCTACAACTCTTAGCTCATTTTT 59.608 33.333 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 2.184448 CACAAGGCGTGTCAAAAACTG 58.816 47.619 2.20 0.00 38.92 3.16
98 99 4.569761 TCAGAGGACATATAACTCGCAC 57.430 45.455 0.00 0.00 36.40 5.34
105 106 7.418337 TTGCAGTACTTCAGAGGACATATAA 57.582 36.000 0.00 0.00 39.36 0.98
114 118 5.233225 TCACAGATTTGCAGTACTTCAGAG 58.767 41.667 0.00 0.00 0.00 3.35
117 121 9.836864 AATATATCACAGATTTGCAGTACTTCA 57.163 29.630 0.00 0.00 0.00 3.02
232 239 5.446143 ACTCCAATTCTAGCTCATACTCG 57.554 43.478 0.00 0.00 0.00 4.18
269 276 3.821033 CCTACAAACCAAAGGAGGACTTG 59.179 47.826 0.00 0.00 39.96 3.16
273 280 4.601857 AGAATCCTACAAACCAAAGGAGGA 59.398 41.667 0.00 0.00 42.53 3.71
330 337 5.547666 ACCAAAGGGCTCCATAGAAATTTTT 59.452 36.000 0.00 0.00 37.90 1.94
485 493 6.429078 GGATGACATGCAGCTTCATTCTTATA 59.571 38.462 0.00 0.00 32.29 0.98
489 497 2.950309 GGATGACATGCAGCTTCATTCT 59.050 45.455 0.00 0.00 32.29 2.40
498 506 2.719739 AGAAAGTGGGATGACATGCAG 58.280 47.619 9.33 0.00 0.00 4.41
544 1321 7.798710 TCTTTGGTTCATAGGATAGGATAGG 57.201 40.000 0.00 0.00 28.27 2.57
545 1322 8.317679 CCTTCTTTGGTTCATAGGATAGGATAG 58.682 40.741 0.00 0.00 28.27 2.08
546 1323 7.256691 GCCTTCTTTGGTTCATAGGATAGGATA 60.257 40.741 0.00 0.00 28.27 2.59
547 1324 6.466470 GCCTTCTTTGGTTCATAGGATAGGAT 60.466 42.308 0.00 0.00 28.27 3.24
548 1325 5.163195 GCCTTCTTTGGTTCATAGGATAGGA 60.163 44.000 0.00 0.00 0.00 2.94
549 1326 5.066593 GCCTTCTTTGGTTCATAGGATAGG 58.933 45.833 0.00 0.00 0.00 2.57
594 1371 0.253160 TCCAGTAGGACAGGGGCAAT 60.253 55.000 0.00 0.00 39.61 3.56
699 1478 1.377856 GGGAGGAAGAAGCACCAGC 60.378 63.158 0.00 0.00 42.56 4.85
700 1479 1.078848 CGGGAGGAAGAAGCACCAG 60.079 63.158 0.00 0.00 0.00 4.00
701 1480 3.068881 CGGGAGGAAGAAGCACCA 58.931 61.111 0.00 0.00 0.00 4.17
702 1481 2.436824 GCGGGAGGAAGAAGCACC 60.437 66.667 0.00 0.00 0.00 5.01
703 1482 2.815647 CGCGGGAGGAAGAAGCAC 60.816 66.667 0.00 0.00 0.00 4.40
704 1483 2.994995 TCGCGGGAGGAAGAAGCA 60.995 61.111 6.13 0.00 0.00 3.91
866 1650 3.436028 TACGGGGGAGGAGGAGGG 61.436 72.222 0.00 0.00 0.00 4.30
867 1651 2.123382 GTACGGGGGAGGAGGAGG 60.123 72.222 0.00 0.00 0.00 4.30
1216 2004 3.073503 TCCCAAATCATCAGAGGCCATAG 59.926 47.826 5.01 0.00 0.00 2.23
1280 2071 4.773117 GTCGTCCTCGTCACCGCC 62.773 72.222 0.00 0.00 38.33 6.13
1382 2190 1.140452 TCAGATCAGAATGCTCCAGGC 59.860 52.381 0.00 0.00 42.22 4.85
1412 2220 4.651778 TCACTGGAAAATCCCTGTAACTG 58.348 43.478 0.00 0.00 36.74 3.16
1447 2258 0.466189 CCCTGCAAACCACACTGACT 60.466 55.000 0.00 0.00 0.00 3.41
1458 2269 2.435372 ATCGCCTATTTCCCTGCAAA 57.565 45.000 0.00 0.00 0.00 3.68
1504 2315 6.120220 GCTTGGTATACACTACCCAAATTCT 58.880 40.000 5.01 0.00 36.58 2.40
1505 2316 5.298527 GGCTTGGTATACACTACCCAAATTC 59.701 44.000 5.01 0.00 36.58 2.17
1547 2358 3.262420 GAGTAGGTACAGCAACATGTGG 58.738 50.000 0.00 0.00 34.56 4.17
1550 2361 1.927174 GCGAGTAGGTACAGCAACATG 59.073 52.381 0.00 0.00 34.05 3.21
1551 2362 1.469251 CGCGAGTAGGTACAGCAACAT 60.469 52.381 0.00 0.00 33.68 2.71
1552 2363 0.109458 CGCGAGTAGGTACAGCAACA 60.109 55.000 0.00 0.00 33.68 3.33
1553 2364 0.801067 CCGCGAGTAGGTACAGCAAC 60.801 60.000 8.23 0.00 33.68 4.17
1554 2365 1.246056 ACCGCGAGTAGGTACAGCAA 61.246 55.000 8.23 0.00 40.80 3.91
1555 2366 1.676635 ACCGCGAGTAGGTACAGCA 60.677 57.895 8.23 0.00 40.80 4.41
1556 2367 1.226603 CACCGCGAGTAGGTACAGC 60.227 63.158 8.23 0.00 40.59 4.40
1557 2368 0.377554 CTCACCGCGAGTAGGTACAG 59.622 60.000 8.23 0.00 40.59 2.74
1558 2369 1.028330 CCTCACCGCGAGTAGGTACA 61.028 60.000 8.23 0.00 40.59 2.90
1559 2370 1.028868 ACCTCACCGCGAGTAGGTAC 61.029 60.000 20.15 0.00 40.57 3.34
1570 2381 1.300971 CTGATTGCCACACCTCACCG 61.301 60.000 0.00 0.00 0.00 4.94
1571 2382 1.589716 GCTGATTGCCACACCTCACC 61.590 60.000 0.00 0.00 35.15 4.02
1610 2421 2.173669 CATACGGAGCGGCAACCAG 61.174 63.158 14.51 10.19 0.00 4.00
1657 2468 1.559682 CTTAGCCTTCAAGCCCACCTA 59.440 52.381 0.00 0.00 0.00 3.08
1856 3271 8.985315 TCAATAAATACATTCTGGAGCATTCT 57.015 30.769 0.00 0.00 0.00 2.40
1884 3299 9.931210 GGATTACAGAAAACCTAATTTCATACG 57.069 33.333 2.99 0.00 40.89 3.06
2190 3701 0.321564 AACAAGCTGACGCATAGCCA 60.322 50.000 0.00 0.00 42.07 4.75
2266 3777 0.749818 TGGCCTCGTTTGCAGTTTCA 60.750 50.000 3.32 0.00 0.00 2.69
2311 3822 3.876914 CTGTCACAACAACTGCTTTAGGA 59.123 43.478 0.00 0.00 34.24 2.94
2479 3990 6.527057 TCATTTGGCATCATTGAATGTGTA 57.473 33.333 4.93 0.00 0.00 2.90
2572 4083 4.081406 CACCTTGGATTTCACTTGGATCA 58.919 43.478 0.00 0.00 0.00 2.92
2587 4098 1.888436 TAGCACGGCTCTCACCTTGG 61.888 60.000 1.46 0.00 40.44 3.61
2653 4164 1.747709 CTGATGCTGAACTTGAGGGG 58.252 55.000 0.00 0.00 0.00 4.79
2675 4186 6.114187 TGGTTGACTTGATTCAGTATCACT 57.886 37.500 0.00 0.00 42.88 3.41
2936 4461 6.815089 AGGAGCTAAGAGACATAATTCACAG 58.185 40.000 0.00 0.00 0.00 3.66
2949 4474 3.761218 TCACTTGTCAGAGGAGCTAAGAG 59.239 47.826 0.00 0.00 0.00 2.85
2954 4479 1.617850 CTGTCACTTGTCAGAGGAGCT 59.382 52.381 0.00 0.00 33.96 4.09
3745 5285 5.347620 AGTCGTGACTAGTCTAGACTCAT 57.652 43.478 30.45 17.59 40.26 2.90
3965 5508 7.826690 TGAGCAGTCCTTTTATAAATCAAACC 58.173 34.615 0.00 0.00 0.00 3.27
3981 5524 5.670149 CATCTATTGATGTTGAGCAGTCC 57.330 43.478 8.76 0.00 43.68 3.85
4013 5556 9.661563 CTACAGTATGGTAAGTACAATGGAAAA 57.338 33.333 0.00 0.00 43.62 2.29
4111 5654 7.172190 ACTGCAATATCACTGATACTTGTATGC 59.828 37.037 0.58 6.42 0.00 3.14
4323 5878 6.249035 TCAAATAAGATCAACAAACGTCCC 57.751 37.500 0.00 0.00 0.00 4.46
4379 5934 5.765182 CCCATGTGACCTAACCAATAGAATC 59.235 44.000 0.00 0.00 33.04 2.52
4493 6050 0.178767 ACGCAGATAGCCTTCATGCA 59.821 50.000 0.00 0.00 41.38 3.96
4510 6067 1.990563 CTTACAACCGCTTCCAGTACG 59.009 52.381 0.00 0.00 0.00 3.67
4590 6147 4.591202 CAGTTCACAACATCTGACAACAC 58.409 43.478 0.00 0.00 0.00 3.32
4721 6278 8.798859 ACAGAAAACAGAGCATGACTTATTAT 57.201 30.769 0.00 0.00 0.00 1.28
4722 6279 9.719355 TTACAGAAAACAGAGCATGACTTATTA 57.281 29.630 0.00 0.00 0.00 0.98
4723 6280 8.621532 TTACAGAAAACAGAGCATGACTTATT 57.378 30.769 0.00 0.00 0.00 1.40
4972 6529 3.944055 TGAGCTGAACTCTGAGTTACC 57.056 47.619 22.08 11.91 46.41 2.85
5278 6835 7.094377 GCCATTAAATCACTGACAGTTCCTTTA 60.094 37.037 5.04 7.49 0.00 1.85
5487 7044 2.865551 CCAAACATTTGTGGTGACAAGC 59.134 45.455 3.79 0.00 46.06 4.01
5640 7197 1.971481 CATCCCAGATGCATTTCCGA 58.029 50.000 0.00 0.00 0.00 4.55
5716 7273 8.785329 AAGCCTTAGTTTCATCTTTCTTAGAG 57.215 34.615 0.00 0.00 36.02 2.43
5737 7294 3.092334 ACCGACACAAAATCAAAAGCC 57.908 42.857 0.00 0.00 0.00 4.35
5752 7309 4.449068 CACTAGATGGAAATGCATACCGAC 59.551 45.833 15.09 11.94 0.00 4.79
6474 8034 7.781324 ACATGAGTTGATTGGGATACTTTTT 57.219 32.000 0.00 0.00 0.00 1.94
6862 8428 3.317993 TCAATGATGCAATCTGGAGCATG 59.682 43.478 4.46 0.00 43.86 4.06
7082 8648 5.473066 AATTGCAATATCCCAAGGCATAC 57.527 39.130 13.39 0.00 34.03 2.39
7559 9235 2.807967 TCTGAACATGCCGTTTCTCTTG 59.192 45.455 0.00 0.00 38.19 3.02
7562 9238 4.425577 AATTCTGAACATGCCGTTTCTC 57.574 40.909 0.00 0.00 38.19 2.87
7686 9366 4.628766 CGAGAATCTTCAACATCTGCTGAA 59.371 41.667 0.00 0.00 0.00 3.02
7687 9367 4.179298 CGAGAATCTTCAACATCTGCTGA 58.821 43.478 0.00 0.00 0.00 4.26
7688 9368 3.242349 GCGAGAATCTTCAACATCTGCTG 60.242 47.826 0.00 0.00 0.00 4.41
8016 9698 1.300542 GCTGACTCGATAGCCCTGC 60.301 63.158 5.44 0.00 33.89 4.85
8043 9725 2.961741 TGCCAAACAGCACAAAGGATTA 59.038 40.909 0.00 0.00 38.00 1.75
8044 9726 1.761784 TGCCAAACAGCACAAAGGATT 59.238 42.857 0.00 0.00 38.00 3.01
8074 9756 9.372369 AGAGTACAAACAATATTAAGACTCAGC 57.628 33.333 0.00 0.00 34.57 4.26
8112 9795 3.558931 TTCCACATGCGAGTATGGAAT 57.441 42.857 8.68 0.00 44.43 3.01
8122 9805 0.806868 AGATGCACTTTCCACATGCG 59.193 50.000 0.00 0.00 42.44 4.73
8182 9865 4.512914 GGGTCATGGCCCCTGCTC 62.513 72.222 26.11 0.00 42.89 4.26
8189 9872 2.757099 CAAGGCTGGGTCATGGCC 60.757 66.667 8.19 8.19 45.57 5.36
8200 9883 6.189859 TGTATTTCATCAAGGATTCAAGGCT 58.810 36.000 0.00 0.00 0.00 4.58
8201 9884 6.455360 TGTATTTCATCAAGGATTCAAGGC 57.545 37.500 0.00 0.00 0.00 4.35
8202 9885 8.229253 TCATGTATTTCATCAAGGATTCAAGG 57.771 34.615 0.00 0.00 34.09 3.61
8240 9923 7.611855 CACAAGACTATTTTCCTAATCAACCCT 59.388 37.037 0.00 0.00 0.00 4.34
8241 9924 7.148069 CCACAAGACTATTTTCCTAATCAACCC 60.148 40.741 0.00 0.00 0.00 4.11
8281 9967 3.448660 AGGCAAGGATCCTTTGCAAATAC 59.551 43.478 31.92 21.58 34.32 1.89
8297 9983 0.392193 CACTGGCAGACCTAGGCAAG 60.392 60.000 23.66 0.00 41.25 4.01
8329 10015 8.878769 ACGGGATTGTAATATTTTTGAAAATGC 58.121 29.630 11.02 0.00 38.90 3.56
8355 10041 6.474140 TCTGTTTTCTGTTGTACTACTCCA 57.526 37.500 8.88 0.00 0.00 3.86
8558 10306 7.922811 TGTAGATGCAGAATATAATATCAGCCG 59.077 37.037 0.00 0.00 0.00 5.52
8601 10349 0.693622 TATCACCGCCCAAGAACCAA 59.306 50.000 0.00 0.00 0.00 3.67
8602 10350 0.251916 CTATCACCGCCCAAGAACCA 59.748 55.000 0.00 0.00 0.00 3.67
8603 10351 0.539986 TCTATCACCGCCCAAGAACC 59.460 55.000 0.00 0.00 0.00 3.62
8604 10352 1.207329 ACTCTATCACCGCCCAAGAAC 59.793 52.381 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.