Multiple sequence alignment - TraesCS1B01G357800

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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 TraesCS1B01G357800 chr1B 100.000 2978 0 0 1 2978 587523895 587526872 0.000000e+00 5500.0
1 TraesCS1B01G357800 chr1B 83.944 2267 288 41 1 2219 587027120 587029358 0.000000e+00 2100.0
2 TraesCS1B01G357800 chr1B 86.553 409 41 9 2211 2610 587031066 587031469 3.520000e-119 438.0
3 TraesCS1B01G357800 chr1B 83.621 348 46 5 2624 2962 478055517 478055172 1.720000e-82 316.0
4 TraesCS1B01G357800 chr1B 90.608 181 8 2 2803 2977 587038903 587039080 6.420000e-57 231.0
5 TraesCS1B01G357800 chr1B 92.547 161 9 2 2622 2780 587035617 587035776 8.300000e-56 228.0
6 TraesCS1B01G357800 chr1A 83.560 1326 197 14 1 1309 532261194 532262515 0.000000e+00 1221.0
7 TraesCS1B01G357800 chr1A 84.082 1313 143 37 1315 2619 532262582 532263836 0.000000e+00 1206.0
8 TraesCS1B01G357800 chr1A 82.240 366 50 7 2622 2977 455606804 455606444 4.820000e-78 302.0
9 TraesCS1B01G357800 chr1A 93.855 179 11 0 2641 2819 532264378 532264556 1.360000e-68 270.0
10 TraesCS1B01G357800 chr1D 90.782 358 18 8 2622 2977 433979462 433979806 5.810000e-127 464.0
11 TraesCS1B01G357800 chr1D 90.782 358 18 8 2622 2977 434034448 434034792 5.810000e-127 464.0
12 TraesCS1B01G357800 chr1D 83.227 471 70 8 3 470 433954932 433955396 9.870000e-115 424.0
13 TraesCS1B01G357800 chr1D 83.152 368 46 8 2622 2978 355431200 355430838 3.700000e-84 322.0
14 TraesCS1B01G357800 chr3D 75.520 625 132 15 1349 1963 601221653 601221040 1.350000e-73 287.0
15 TraesCS1B01G357800 chr5D 73.871 731 140 34 616 1309 536880360 536879644 8.250000e-61 244.0
16 TraesCS1B01G357800 chr4A 73.871 731 140 33 616 1309 633069037 633069753 8.250000e-61 244.0
17 TraesCS1B01G357800 chr3B 75.556 450 90 15 1569 2013 808595798 808595364 1.400000e-48 204.0
18 TraesCS1B01G357800 chr7B 88.235 51 6 0 1748 1798 715252092 715252042 8.910000e-06 62.1


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 TraesCS1B01G357800 chr1B 587523895 587526872 2977 False 5500.0 5500 100.000000 1 2978 1 chr1B.!!$F1 2977
1 TraesCS1B01G357800 chr1B 587027120 587031469 4349 False 1269.0 2100 85.248500 1 2610 2 chr1B.!!$F2 2609
2 TraesCS1B01G357800 chr1B 587035617 587039080 3463 False 229.5 231 91.577500 2622 2977 2 chr1B.!!$F3 355
3 TraesCS1B01G357800 chr1A 532261194 532264556 3362 False 899.0 1221 87.165667 1 2819 3 chr1A.!!$F1 2818
4 TraesCS1B01G357800 chr3D 601221040 601221653 613 True 287.0 287 75.520000 1349 1963 1 chr3D.!!$R1 614
5 TraesCS1B01G357800 chr5D 536879644 536880360 716 True 244.0 244 73.871000 616 1309 1 chr5D.!!$R1 693
6 TraesCS1B01G357800 chr4A 633069037 633069753 716 False 244.0 244 73.871000 616 1309 1 chr4A.!!$F1 693

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
917 952 0.179145 ATGCGATGAAAAGCTGCAGC 60.179 50.0 31.53 31.53 39.17 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2328 4186 0.023732 CGTTAATGAGCACGTCAGCG 59.976 55.0 0.0 0.0 39.07 5.18 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
24 25 4.787598 TCGGACTACTTACTTGAAACGAC 58.212 43.478 0.00 0.00 0.00 4.34
25 26 4.275689 TCGGACTACTTACTTGAAACGACA 59.724 41.667 0.00 0.00 0.00 4.35
28 29 6.183359 CGGACTACTTACTTGAAACGACAATC 60.183 42.308 0.00 0.00 0.00 2.67
41 42 3.659786 ACGACAATCGGATGTGAAAAGA 58.340 40.909 2.97 0.00 45.59 2.52
46 47 1.803334 TCGGATGTGAAAAGAACCCG 58.197 50.000 0.00 0.00 37.08 5.28
85 86 2.879002 ACCTCGTCTCATATGCTGTG 57.121 50.000 0.00 0.00 0.00 3.66
91 92 2.544694 CGTCTCATATGCTGTGGACCTC 60.545 54.545 0.00 0.00 0.00 3.85
128 129 2.170607 CCTGATGACTATGTTTCCGGGT 59.829 50.000 0.00 0.00 0.00 5.28
149 150 4.464008 GTTAAGGATCCTGGATGCATTCA 58.536 43.478 27.01 7.63 32.78 2.57
178 179 4.723309 GAATGAAGATATCTGCCAAGGGT 58.277 43.478 5.86 0.00 0.00 4.34
180 181 4.591321 TGAAGATATCTGCCAAGGGTTT 57.409 40.909 5.86 0.00 0.00 3.27
181 182 4.934356 TGAAGATATCTGCCAAGGGTTTT 58.066 39.130 5.86 0.00 0.00 2.43
189 190 3.966665 TCTGCCAAGGGTTTTGAAGAAAT 59.033 39.130 0.00 0.00 0.00 2.17
192 193 5.852827 TGCCAAGGGTTTTGAAGAAATAAG 58.147 37.500 0.00 0.00 0.00 1.73
197 198 9.025041 CCAAGGGTTTTGAAGAAATAAGTATCT 57.975 33.333 0.00 0.00 0.00 1.98
227 229 6.036517 CACTAGGAGGAAATTGAAGATGTTCG 59.963 42.308 0.00 0.00 35.17 3.95
274 276 3.306613 TCTGATCATGTCTGCATCCTCT 58.693 45.455 0.00 0.00 31.99 3.69
277 279 4.221530 TGATCATGTCTGCATCCTCTACT 58.778 43.478 0.00 0.00 31.99 2.57
278 280 4.038883 TGATCATGTCTGCATCCTCTACTG 59.961 45.833 0.00 0.00 31.99 2.74
281 283 3.093057 TGTCTGCATCCTCTACTGACT 57.907 47.619 0.00 0.00 34.48 3.41
304 306 0.601046 TCCAGAAACTGCTGCAGACG 60.601 55.000 34.28 16.62 35.18 4.18
312 314 1.079819 TGCTGCAGACGTTAGGCTC 60.080 57.895 20.43 0.00 29.21 4.70
313 315 1.811679 GCTGCAGACGTTAGGCTCC 60.812 63.158 20.43 0.00 29.21 4.70
316 318 1.185618 TGCAGACGTTAGGCTCCAGT 61.186 55.000 0.00 0.00 29.21 4.00
319 321 2.093106 CAGACGTTAGGCTCCAGTAGT 58.907 52.381 0.00 0.00 29.21 2.73
322 324 5.061853 CAGACGTTAGGCTCCAGTAGTATA 58.938 45.833 0.00 0.00 29.21 1.47
346 348 2.363147 AGAGAGACGAGGGGGTGC 60.363 66.667 0.00 0.00 0.00 5.01
365 367 2.825836 CTGCGAGGATTGTGGCCC 60.826 66.667 0.00 0.00 0.00 5.80
375 377 1.610554 ATTGTGGCCCAGATTGCTGC 61.611 55.000 0.00 0.00 40.91 5.25
395 397 0.984230 AGGCATTCGTTTGGAGGAGA 59.016 50.000 0.00 0.00 0.00 3.71
420 422 3.764972 CCAACGGGGGTTGTTTACATATT 59.235 43.478 6.26 0.00 32.80 1.28
424 426 5.326900 ACGGGGGTTGTTTACATATTTTCT 58.673 37.500 0.00 0.00 0.00 2.52
443 445 7.728847 TTTTCTCTCATCAACTCATTCGAAA 57.271 32.000 0.00 0.00 0.00 3.46
470 472 4.261801 CAGTTTACTCCAACCATACCAGG 58.738 47.826 0.00 0.00 0.00 4.45
475 477 3.375699 ACTCCAACCATACCAGGTAGAG 58.624 50.000 5.31 7.51 42.25 2.43
493 495 2.079925 GAGTGGGCACAAGAGACATTC 58.920 52.381 0.00 0.00 0.00 2.67
496 498 1.071542 TGGGCACAAGAGACATTCGAA 59.928 47.619 0.00 0.00 0.00 3.71
497 499 2.151202 GGGCACAAGAGACATTCGAAA 58.849 47.619 0.00 0.00 0.00 3.46
519 521 5.560966 AAAAATTGGTACAGTATGGCTCG 57.439 39.130 0.00 0.00 43.62 5.03
545 547 4.026052 TCTGCAGTCACCAGATCTTGATA 58.974 43.478 14.67 0.00 34.59 2.15
546 548 4.099113 TCTGCAGTCACCAGATCTTGATAG 59.901 45.833 14.67 0.00 34.59 2.08
547 549 3.129871 GCAGTCACCAGATCTTGATAGC 58.870 50.000 0.00 4.85 0.00 2.97
560 562 5.078411 TCTTGATAGCAAAGAGGACAGTC 57.922 43.478 0.00 0.00 32.73 3.51
565 567 3.777106 AGCAAAGAGGACAGTCATGAA 57.223 42.857 0.00 0.00 0.00 2.57
593 598 2.489073 GGGGACAGTGATGGTGAACTTT 60.489 50.000 0.00 0.00 0.00 2.66
610 615 5.766174 TGAACTTTTTAACGCCTACAAGGAT 59.234 36.000 0.00 0.00 37.67 3.24
611 616 6.263617 TGAACTTTTTAACGCCTACAAGGATT 59.736 34.615 0.00 0.00 37.67 3.01
629 634 6.686484 AGGATTTAATGGAGCAAGGTTTTT 57.314 33.333 0.00 0.00 0.00 1.94
635 640 7.531857 TTAATGGAGCAAGGTTTTTGTATCA 57.468 32.000 0.00 0.00 0.00 2.15
664 669 3.696051 AGCTCGCAACCAATAATGACAAT 59.304 39.130 0.00 0.00 0.00 2.71
750 755 5.072329 ACCTACTCCACCAAATAGATCATGG 59.928 44.000 0.00 0.27 40.16 3.66
761 793 1.328279 AGATCATGGTGCATGGCATG 58.672 50.000 22.99 22.99 41.91 4.06
786 818 5.008118 GCATAGTAGAGGGTTCAATGAAAGC 59.992 44.000 0.00 0.00 0.00 3.51
793 825 5.297776 AGAGGGTTCAATGAAAGCGATTATG 59.702 40.000 0.00 0.00 0.00 1.90
794 826 4.949856 AGGGTTCAATGAAAGCGATTATGT 59.050 37.500 0.00 0.00 0.00 2.29
886 921 2.092538 CAGCACCATGGAGAGGATTCTT 60.093 50.000 21.47 0.00 32.53 2.52
889 924 3.539604 CACCATGGAGAGGATTCTTGAC 58.460 50.000 21.47 0.00 32.53 3.18
917 952 0.179145 ATGCGATGAAAAGCTGCAGC 60.179 50.000 31.53 31.53 39.17 5.25
924 959 1.409790 TGAAAAGCTGCAGCAACATGT 59.590 42.857 38.24 17.76 45.16 3.21
993 1035 7.274447 TGGAGAATGCAAACAGAGAAAAATTT 58.726 30.769 0.00 0.00 28.48 1.82
1034 1079 7.935755 AGACATTATGACTGATGATAACAAGGG 59.064 37.037 0.00 0.00 0.00 3.95
1041 1086 3.620488 TGATGATAACAAGGGCAAGGAC 58.380 45.455 0.00 0.00 0.00 3.85
1049 1094 1.407656 AAGGGCAAGGACGACAGACA 61.408 55.000 0.00 0.00 0.00 3.41
1060 1105 1.002868 GACAGACAGGTGGCAGCAT 60.003 57.895 20.04 6.30 0.00 3.79
1075 1120 0.689055 AGCATCTCAAGCACTGGTGA 59.311 50.000 4.79 0.00 0.00 4.02
1083 1128 2.899900 TCAAGCACTGGTGACTCTATGT 59.100 45.455 4.79 0.00 0.00 2.29
1159 1204 9.889128 TTGTTAATAATCTCACTGTGATGATCA 57.111 29.630 11.45 0.00 0.00 2.92
1172 1217 5.856126 GTGATGATCACTGAAAACCGTAA 57.144 39.130 17.84 0.00 43.73 3.18
1174 1219 6.307155 GTGATGATCACTGAAAACCGTAAAG 58.693 40.000 17.84 0.00 43.73 1.85
1175 1220 4.742438 TGATCACTGAAAACCGTAAAGC 57.258 40.909 0.00 0.00 0.00 3.51
1183 1228 4.263435 TGAAAACCGTAAAGCCCGATTAT 58.737 39.130 0.00 0.00 0.00 1.28
1206 1251 4.454728 TGCAGCAAAAATCCTGGAATAC 57.545 40.909 0.00 0.00 0.00 1.89
1209 1254 4.440663 GCAGCAAAAATCCTGGAATACCTC 60.441 45.833 0.00 0.00 37.04 3.85
1253 1304 7.613022 TGATGATGAAAGTCTCAAAAGGCTAAT 59.387 33.333 0.00 0.00 36.07 1.73
1264 1315 6.151648 TCTCAAAAGGCTAATGAAAGTCATGG 59.848 38.462 4.05 0.00 37.15 3.66
1289 1340 5.523916 CAGATGTAGTTCCAAAGGTAATCGG 59.476 44.000 0.00 0.00 0.00 4.18
1296 1347 2.506231 TCCAAAGGTAATCGGTGCCATA 59.494 45.455 0.00 0.00 33.55 2.74
1371 1491 8.725405 TCAAACTGAATATATTCTTGCCGTTA 57.275 30.769 22.77 3.04 37.67 3.18
1383 1503 0.107410 TGCCGTTATAGGTGCTTGGG 60.107 55.000 0.00 0.00 0.00 4.12
1390 1510 4.039973 CGTTATAGGTGCTTGGGGAGATAA 59.960 45.833 0.00 0.00 0.00 1.75
1412 1532 5.549742 ATTTGTTGGGCATCAGAAGAAAA 57.450 34.783 0.00 0.00 0.00 2.29
1414 1534 4.589216 TGTTGGGCATCAGAAGAAAAAG 57.411 40.909 0.00 0.00 0.00 2.27
1442 1565 4.287067 AGGAATAGAAGCTGACCAAGTCAA 59.713 41.667 0.00 0.00 42.26 3.18
1457 1580 0.106149 GTCAAGTCCACGGAACCAGT 59.894 55.000 0.00 0.00 0.00 4.00
1480 1603 9.219603 CAGTAACTGATCTTGAAAACCAATCTA 57.780 33.333 0.00 0.00 31.55 1.98
1485 1608 7.173907 ACTGATCTTGAAAACCAATCTAGTGTG 59.826 37.037 0.00 0.00 33.68 3.82
1559 1688 2.094494 AGCTGAACGAGTATGTGGTGAG 60.094 50.000 0.00 0.00 0.00 3.51
1587 1719 4.133820 TGTTATCCCTTTGTGTCACAGTG 58.866 43.478 5.67 0.00 0.00 3.66
1595 1727 0.179086 TGTGTCACAGTGTGCGACAT 60.179 50.000 18.80 0.00 40.88 3.06
1839 1974 0.320374 TGTCCACCGCTTCGAAAGAT 59.680 50.000 0.00 0.00 41.60 2.40
1849 1984 6.035650 CACCGCTTCGAAAGATATGTTTCTTA 59.964 38.462 19.67 8.04 41.60 2.10
1892 2027 1.949525 CATTAAGGAAGATGGTGGCGG 59.050 52.381 0.00 0.00 0.00 6.13
1894 2029 0.251916 TAAGGAAGATGGTGGCGGTG 59.748 55.000 0.00 0.00 0.00 4.94
1901 2036 4.858680 TGGTGGCGGTGCAACGAA 62.859 61.111 31.65 12.82 38.12 3.85
1925 2060 0.892063 GAGCCTTTCAGGAGTCTCGT 59.108 55.000 0.00 0.00 37.67 4.18
2095 2230 8.918202 ATACCATCTTTGAAACTTTGTGAGTA 57.082 30.769 0.00 0.00 37.72 2.59
2101 2236 4.846779 TGAAACTTTGTGAGTATTGCCC 57.153 40.909 0.00 0.00 37.72 5.36
2172 2307 3.084039 GCACTCCTTTGGATCAACATCA 58.916 45.455 0.00 0.00 0.00 3.07
2177 2312 4.582869 TCCTTTGGATCAACATCAGAGTG 58.417 43.478 0.00 0.00 0.00 3.51
2200 2335 2.762535 TGCCAGTTTCCTAGCAGTAC 57.237 50.000 0.00 0.00 29.99 2.73
2207 2342 3.057456 AGTTTCCTAGCAGTACAGTCACG 60.057 47.826 0.00 0.00 0.00 4.35
2239 4090 9.208022 TCACACAAACACAAAATTTAACATTGA 57.792 25.926 0.00 0.00 0.00 2.57
2321 4179 1.317613 AAACATGTGTGATGTGCCGT 58.682 45.000 0.00 0.00 31.80 5.68
2326 4184 2.031919 TGTGATGTGCCGTGGGAC 59.968 61.111 3.27 3.27 36.97 4.46
2346 4204 0.247301 GCGCTGACGTGCTCATTAAC 60.247 55.000 0.00 0.00 43.21 2.01
2367 4225 0.872388 GCTCGTTTGGTTTCATCGGT 59.128 50.000 0.00 0.00 0.00 4.69
2379 4237 0.109532 TCATCGGTGGCAAACTCCAA 59.890 50.000 0.00 0.00 37.96 3.53
2384 4242 0.893727 GGTGGCAAACTCCAATCGGT 60.894 55.000 0.00 0.00 37.96 4.69
2385 4243 1.612199 GGTGGCAAACTCCAATCGGTA 60.612 52.381 0.00 0.00 37.96 4.02
2388 4246 2.238646 TGGCAAACTCCAATCGGTAGAT 59.761 45.455 0.00 0.00 39.12 1.98
2404 4262 1.075601 AGATTTTGAGGGGCAGGTGA 58.924 50.000 0.00 0.00 0.00 4.02
2460 4318 2.086869 CCTACTGCCATTTGGTGACAG 58.913 52.381 0.00 0.31 44.54 3.51
2462 4320 0.185901 ACTGCCATTTGGTGACAGGT 59.814 50.000 0.00 0.00 44.54 4.00
2463 4321 0.599558 CTGCCATTTGGTGACAGGTG 59.400 55.000 0.00 0.00 44.54 4.00
2464 4322 0.184692 TGCCATTTGGTGACAGGTGA 59.815 50.000 0.00 0.00 44.54 4.02
2494 4352 3.384789 GGGAAACTGAATAATTCCAGCCC 59.615 47.826 6.16 0.00 43.56 5.19
2506 4364 1.002069 TCCAGCCCCTTGATTCACAT 58.998 50.000 0.00 0.00 0.00 3.21
2507 4365 1.108776 CCAGCCCCTTGATTCACATG 58.891 55.000 0.00 0.00 0.00 3.21
2508 4366 0.458669 CAGCCCCTTGATTCACATGC 59.541 55.000 0.00 0.00 0.00 4.06
2509 4367 0.685458 AGCCCCTTGATTCACATGCC 60.685 55.000 0.00 0.00 0.00 4.40
2510 4368 0.971959 GCCCCTTGATTCACATGCCA 60.972 55.000 0.00 0.00 0.00 4.92
2511 4369 1.108776 CCCCTTGATTCACATGCCAG 58.891 55.000 0.00 0.00 0.00 4.85
2518 4378 5.808540 CCTTGATTCACATGCCAGTAATTTG 59.191 40.000 0.00 0.00 0.00 2.32
2527 4387 9.421806 TCACATGCCAGTAATTTGAAATAAAAG 57.578 29.630 0.00 0.00 0.00 2.27
2638 5009 5.535333 CACAGATGTTTTCCAAAGCTGAAT 58.465 37.500 0.00 0.00 0.00 2.57
2685 5065 5.128827 GGTATGGGAGAGTCATGTACTTCAA 59.871 44.000 0.00 0.00 39.07 2.69
2706 5086 0.822164 AAGGCTGGATTCATGCTTGC 59.178 50.000 0.00 0.00 0.00 4.01
2752 5132 3.744719 CTCCCGTCGCCGTTCAGA 61.745 66.667 0.00 0.00 0.00 3.27
2792 5172 6.876789 TGTCTGTCGGATACAAATTAACATGT 59.123 34.615 0.00 0.00 37.74 3.21
2833 8317 0.243365 TGCACGGCAACATTTCATCC 59.757 50.000 0.00 0.00 34.76 3.51
2836 8320 0.322098 ACGGCAACATTTCATCCGGA 60.322 50.000 6.61 6.61 43.93 5.14
2871 8361 0.439985 CAACCATCTGTTCGACAGCG 59.560 55.000 9.34 0.00 45.54 5.18
2901 8391 8.037758 TCAGAAAGAAGTAGGTCTGATTCATTC 58.962 37.037 0.00 0.00 41.13 2.67
2933 8423 2.082231 CACCATCTCCTTCAACTGCAG 58.918 52.381 13.48 13.48 0.00 4.41
2952 8442 4.937620 TGCAGAAATGATCAGGTTCAGTAC 59.062 41.667 19.00 9.19 0.00 2.73
2962 8452 5.717078 TCAGGTTCAGTACGTACTCAAAT 57.283 39.130 25.10 8.76 33.46 2.32
2963 8453 5.466819 TCAGGTTCAGTACGTACTCAAATG 58.533 41.667 25.10 19.40 33.46 2.32
2964 8454 5.242171 TCAGGTTCAGTACGTACTCAAATGA 59.758 40.000 25.10 21.15 33.46 2.57
2977 8467 4.858935 ACTCAAATGACCGTCAAATTGTG 58.141 39.130 20.91 20.47 32.51 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.426159 CGGGTTCTTTTCACATCCGATTG 60.426 47.826 0.00 0.00 38.42 2.67
25 26 2.747446 CGGGTTCTTTTCACATCCGATT 59.253 45.455 0.00 0.00 38.42 3.34
28 29 1.463444 GACGGGTTCTTTTCACATCCG 59.537 52.381 0.00 0.00 41.45 4.18
41 42 3.569049 CTCCAGCGAACGACGGGTT 62.569 63.158 0.00 0.00 42.96 4.11
46 47 0.038526 TTCTTCCTCCAGCGAACGAC 60.039 55.000 0.00 0.00 0.00 4.34
71 72 2.432146 TGAGGTCCACAGCATATGAGAC 59.568 50.000 6.97 4.55 35.98 3.36
74 75 2.105306 CCATGAGGTCCACAGCATATGA 59.895 50.000 6.97 0.00 0.00 2.15
105 106 3.386726 CCCGGAAACATAGTCATCAGGTA 59.613 47.826 0.73 0.00 0.00 3.08
128 129 4.464008 GTGAATGCATCCAGGATCCTTAA 58.536 43.478 13.00 2.99 0.00 1.85
149 150 4.502259 GGCAGATATCTTCATTCGTCTGGT 60.502 45.833 1.33 0.00 34.99 4.00
161 162 4.934356 TCAAAACCCTTGGCAGATATCTT 58.066 39.130 1.33 0.00 0.00 2.40
167 168 2.746279 TCTTCAAAACCCTTGGCAGA 57.254 45.000 0.00 0.00 0.00 4.26
168 169 3.817709 TTTCTTCAAAACCCTTGGCAG 57.182 42.857 0.00 0.00 0.00 4.85
192 193 9.449719 TCAATTTCCTCCTAGTGAAAAAGATAC 57.550 33.333 4.16 0.00 34.43 2.24
197 198 8.796475 CATCTTCAATTTCCTCCTAGTGAAAAA 58.204 33.333 4.16 0.00 34.43 1.94
199 200 7.461749 ACATCTTCAATTTCCTCCTAGTGAAA 58.538 34.615 2.89 2.89 35.17 2.69
201 202 6.627087 ACATCTTCAATTTCCTCCTAGTGA 57.373 37.500 0.00 0.00 0.00 3.41
203 204 6.109359 CGAACATCTTCAATTTCCTCCTAGT 58.891 40.000 0.00 0.00 0.00 2.57
204 205 6.036517 CACGAACATCTTCAATTTCCTCCTAG 59.963 42.308 0.00 0.00 0.00 3.02
206 207 4.697352 CACGAACATCTTCAATTTCCTCCT 59.303 41.667 0.00 0.00 0.00 3.69
241 243 6.366604 CAGACATGATCAGATACTTCATGAGC 59.633 42.308 15.71 8.90 46.16 4.26
251 253 5.085219 AGAGGATGCAGACATGATCAGATA 58.915 41.667 0.00 0.00 36.35 1.98
274 276 4.833380 AGCAGTTTCTGGAGTAAGTCAGTA 59.167 41.667 0.00 0.00 33.13 2.74
277 279 3.803715 GCAGCAGTTTCTGGAGTAAGTCA 60.804 47.826 0.00 0.00 34.74 3.41
278 280 2.739379 GCAGCAGTTTCTGGAGTAAGTC 59.261 50.000 0.00 0.00 34.74 3.01
281 283 2.771089 CTGCAGCAGTTTCTGGAGTAA 58.229 47.619 14.90 0.00 44.36 2.24
304 306 8.577048 TGTCATATATACTACTGGAGCCTAAC 57.423 38.462 0.00 0.00 0.00 2.34
312 314 8.035984 TCGTCTCTCTGTCATATATACTACTGG 58.964 40.741 0.00 0.00 0.00 4.00
313 315 8.989653 TCGTCTCTCTGTCATATATACTACTG 57.010 38.462 0.00 0.00 0.00 2.74
316 318 7.364851 CCCCTCGTCTCTCTGTCATATATACTA 60.365 44.444 0.00 0.00 0.00 1.82
319 321 5.339282 CCCCCTCGTCTCTCTGTCATATATA 60.339 48.000 0.00 0.00 0.00 0.86
322 324 2.489985 CCCCCTCGTCTCTCTGTCATAT 60.490 54.545 0.00 0.00 0.00 1.78
346 348 3.869272 GCCACAATCCTCGCAGCG 61.869 66.667 9.06 9.06 0.00 5.18
375 377 1.089920 CTCCTCCAAACGAATGCCTG 58.910 55.000 0.00 0.00 0.00 4.85
382 384 1.278127 GTTGGGATCTCCTCCAAACGA 59.722 52.381 3.08 0.00 45.89 3.85
402 404 5.650703 AGAGAAAATATGTAAACAACCCCCG 59.349 40.000 0.00 0.00 0.00 5.73
420 422 6.705825 TGTTTCGAATGAGTTGATGAGAGAAA 59.294 34.615 0.00 0.00 0.00 2.52
424 426 7.096551 TGTATGTTTCGAATGAGTTGATGAGA 58.903 34.615 0.00 0.00 0.00 3.27
443 445 6.013206 TGGTATGGTTGGAGTAAACTGTATGT 60.013 38.462 0.00 0.00 0.00 2.29
470 472 1.618837 TGTCTCTTGTGCCCACTCTAC 59.381 52.381 0.00 0.00 0.00 2.59
475 477 0.798776 CGAATGTCTCTTGTGCCCAC 59.201 55.000 0.00 0.00 0.00 4.61
497 499 4.142469 GCGAGCCATACTGTACCAATTTTT 60.142 41.667 0.00 0.00 0.00 1.94
519 521 0.107312 ATCTGGTGACTGCAGATGGC 60.107 55.000 23.35 7.19 45.13 4.40
528 530 5.188555 TCTTTGCTATCAAGATCTGGTGACT 59.811 40.000 0.00 0.00 33.12 3.41
545 547 3.326006 TCTTCATGACTGTCCTCTTTGCT 59.674 43.478 5.17 0.00 0.00 3.91
546 548 3.668447 TCTTCATGACTGTCCTCTTTGC 58.332 45.455 5.17 0.00 0.00 3.68
547 549 3.683822 GCTCTTCATGACTGTCCTCTTTG 59.316 47.826 5.17 0.00 0.00 2.77
560 562 0.179089 CTGTCCCCTCGCTCTTCATG 60.179 60.000 0.00 0.00 0.00 3.07
565 567 1.000993 ATCACTGTCCCCTCGCTCT 59.999 57.895 0.00 0.00 0.00 4.09
593 598 6.885376 TCCATTAAATCCTTGTAGGCGTTAAA 59.115 34.615 0.00 0.00 34.61 1.52
610 615 7.957002 TGATACAAAAACCTTGCTCCATTAAA 58.043 30.769 0.00 0.00 0.00 1.52
611 616 7.531857 TGATACAAAAACCTTGCTCCATTAA 57.468 32.000 0.00 0.00 0.00 1.40
629 634 1.136110 TGCGAGCTTCCGAATGATACA 59.864 47.619 0.00 0.00 0.00 2.29
635 640 0.605319 TTGGTTGCGAGCTTCCGAAT 60.605 50.000 4.48 0.00 0.00 3.34
664 669 1.733912 GTGTCGAGCATGATTCTGCAA 59.266 47.619 0.00 0.00 44.77 4.08
750 755 1.538512 CTACTATGCCATGCCATGCAC 59.461 52.381 0.00 0.00 43.04 4.57
761 793 4.689612 TCATTGAACCCTCTACTATGCC 57.310 45.455 0.00 0.00 0.00 4.40
786 818 0.530650 AGCCACGAGCCACATAATCG 60.531 55.000 0.00 0.00 45.47 3.34
793 825 2.815647 GTAGCAGCCACGAGCCAC 60.816 66.667 0.00 0.00 45.47 5.01
794 826 2.997315 AGTAGCAGCCACGAGCCA 60.997 61.111 0.00 0.00 45.47 4.75
820 855 3.490759 CTACGCAGCTTGGTGCCG 61.491 66.667 17.42 14.54 44.23 5.69
886 921 3.317603 TCATCGCATTCTTCACAGTCA 57.682 42.857 0.00 0.00 0.00 3.41
889 924 3.850273 GCTTTTCATCGCATTCTTCACAG 59.150 43.478 0.00 0.00 0.00 3.66
966 1007 3.777106 TCTCTGTTTGCATTCTCCAGT 57.223 42.857 0.00 0.00 0.00 4.00
969 1011 7.719778 AAATTTTTCTCTGTTTGCATTCTCC 57.280 32.000 0.00 0.00 0.00 3.71
1034 1079 0.946221 CACCTGTCTGTCGTCCTTGC 60.946 60.000 0.00 0.00 0.00 4.01
1041 1086 2.740055 GCTGCCACCTGTCTGTCG 60.740 66.667 0.00 0.00 0.00 4.35
1049 1094 1.378250 GCTTGAGATGCTGCCACCT 60.378 57.895 0.00 0.00 0.00 4.00
1060 1105 1.709578 AGAGTCACCAGTGCTTGAGA 58.290 50.000 0.00 0.00 0.00 3.27
1075 1120 5.238650 CCGTTTCAGTTTTGGAACATAGAGT 59.761 40.000 0.21 0.00 42.03 3.24
1083 1128 1.135333 GCACCCGTTTCAGTTTTGGAA 59.865 47.619 0.00 0.00 0.00 3.53
1152 1197 5.324697 GCTTTACGGTTTTCAGTGATCATC 58.675 41.667 0.00 0.00 0.00 2.92
1158 1203 1.069500 CGGGCTTTACGGTTTTCAGTG 60.069 52.381 0.00 0.00 0.00 3.66
1159 1204 1.202675 TCGGGCTTTACGGTTTTCAGT 60.203 47.619 0.00 0.00 0.00 3.41
1160 1205 1.515081 TCGGGCTTTACGGTTTTCAG 58.485 50.000 0.00 0.00 0.00 3.02
1167 1212 2.356382 TGCAAATAATCGGGCTTTACGG 59.644 45.455 0.00 0.00 0.00 4.02
1172 1217 1.473258 TGCTGCAAATAATCGGGCTT 58.527 45.000 0.00 0.00 0.00 4.35
1174 1219 2.292103 TTTGCTGCAAATAATCGGGC 57.708 45.000 22.84 0.00 0.00 6.13
1175 1220 4.270808 GGATTTTTGCTGCAAATAATCGGG 59.729 41.667 29.89 0.00 35.01 5.14
1183 1228 3.834489 TTCCAGGATTTTTGCTGCAAA 57.166 38.095 22.84 22.84 0.00 3.68
1253 1304 4.558226 ACTACATCTGCCATGACTTTCA 57.442 40.909 0.00 0.00 0.00 2.69
1264 1315 5.006746 CGATTACCTTTGGAACTACATCTGC 59.993 44.000 0.00 0.00 0.00 4.26
1371 1491 5.103515 ACAAATTATCTCCCCAAGCACCTAT 60.104 40.000 0.00 0.00 0.00 2.57
1383 1503 4.889409 TCTGATGCCCAACAAATTATCTCC 59.111 41.667 0.00 0.00 0.00 3.71
1390 1510 5.549742 TTTTCTTCTGATGCCCAACAAAT 57.450 34.783 0.00 0.00 0.00 2.32
1412 1532 4.162509 GGTCAGCTTCTATTCCTGTACCTT 59.837 45.833 0.00 0.00 30.77 3.50
1414 1534 3.451178 TGGTCAGCTTCTATTCCTGTACC 59.549 47.826 0.00 0.00 32.41 3.34
1442 1565 1.343465 CAGTTACTGGTTCCGTGGACT 59.657 52.381 4.14 0.00 0.00 3.85
1457 1580 9.219603 CACTAGATTGGTTTTCAAGATCAGTTA 57.780 33.333 0.00 0.00 38.95 2.24
1480 1603 3.244875 TGGCCATTATCTTGTGACACACT 60.245 43.478 8.05 0.00 35.11 3.55
1485 1608 2.301346 CCCTGGCCATTATCTTGTGAC 58.699 52.381 5.51 0.00 0.00 3.67
1536 1665 2.668457 CACCACATACTCGTTCAGCTTC 59.332 50.000 0.00 0.00 0.00 3.86
1559 1688 4.037446 TGACACAAAGGGATAACAAGCAAC 59.963 41.667 0.00 0.00 0.00 4.17
1587 1719 1.464687 GCACTGATCAACATGTCGCAC 60.465 52.381 0.00 0.00 0.00 5.34
1806 1941 3.618752 CGGTGGACAGTGTATCCATCAAA 60.619 47.826 13.21 0.00 46.25 2.69
1839 1974 6.491062 CCATGGAGCCATCAATAAGAAACATA 59.509 38.462 5.56 0.00 33.90 2.29
1849 1984 3.839490 TCAAAAACCATGGAGCCATCAAT 59.161 39.130 21.47 0.00 33.90 2.57
1892 2027 4.090057 GCTCCGGCTTCGTTGCAC 62.090 66.667 0.00 0.00 35.22 4.57
1925 2060 3.360867 TGTGCTTCTTTCACAAGGGAAA 58.639 40.909 0.00 0.00 41.01 3.13
1957 2092 9.434420 TCAACATCAAAGTTCATTTCTTTTGTT 57.566 25.926 0.00 0.00 36.83 2.83
2015 2150 6.258068 CCGACAGAAGGTGAATAATAAGTTCC 59.742 42.308 0.00 0.00 0.00 3.62
2031 2166 2.093973 ACATGAAGGCTACCGACAGAAG 60.094 50.000 0.00 0.00 0.00 2.85
2033 2168 1.557099 ACATGAAGGCTACCGACAGA 58.443 50.000 0.00 0.00 0.00 3.41
2095 2230 4.998051 ACCCATAGAAATATTCGGGCAAT 58.002 39.130 0.00 0.00 37.16 3.56
2172 2307 5.091261 CTAGGAAACTGGCAATACACTCT 57.909 43.478 0.00 0.00 43.88 3.24
2200 2335 3.942539 TTGTGTGAATGAACGTGACTG 57.057 42.857 0.00 0.00 0.00 3.51
2257 4110 1.732683 GGCGGACGCACAATTTTGG 60.733 57.895 18.95 0.00 44.11 3.28
2302 4160 1.001487 CACGGCACATCACACATGTTT 60.001 47.619 0.00 0.00 0.00 2.83
2326 4184 1.682867 TTAATGAGCACGTCAGCGCG 61.683 55.000 0.00 0.00 39.07 6.86
2328 4186 0.023732 CGTTAATGAGCACGTCAGCG 59.976 55.000 0.00 0.00 39.07 5.18
2329 4187 0.370273 CCGTTAATGAGCACGTCAGC 59.630 55.000 0.00 0.00 39.07 4.26
2333 4191 1.076533 CGAGCCGTTAATGAGCACGT 61.077 55.000 14.83 0.00 36.15 4.49
2346 4204 0.179225 CGATGAAACCAAACGAGCCG 60.179 55.000 0.00 0.00 0.00 5.52
2360 4218 0.109532 TTGGAGTTTGCCACCGATGA 59.890 50.000 0.00 0.00 37.75 2.92
2367 4225 1.626321 TCTACCGATTGGAGTTTGCCA 59.374 47.619 5.81 0.00 39.21 4.92
2379 4237 1.843851 TGCCCCTCAAAATCTACCGAT 59.156 47.619 0.00 0.00 0.00 4.18
2384 4242 2.239654 CTCACCTGCCCCTCAAAATCTA 59.760 50.000 0.00 0.00 0.00 1.98
2385 4243 1.005215 CTCACCTGCCCCTCAAAATCT 59.995 52.381 0.00 0.00 0.00 2.40
2388 4246 1.004745 GATCTCACCTGCCCCTCAAAA 59.995 52.381 0.00 0.00 0.00 2.44
2404 4262 1.233369 CCGTGGTAGGAGGGGATCT 59.767 63.158 0.00 0.00 0.00 2.75
2460 4318 2.838202 TCAGTTTCCCCATCTACTCACC 59.162 50.000 0.00 0.00 0.00 4.02
2462 4320 6.884472 TTATTCAGTTTCCCCATCTACTCA 57.116 37.500 0.00 0.00 0.00 3.41
2463 4321 7.445707 GGAATTATTCAGTTTCCCCATCTACTC 59.554 40.741 7.29 0.00 34.15 2.59
2464 4322 7.091993 TGGAATTATTCAGTTTCCCCATCTACT 60.092 37.037 7.29 0.00 38.51 2.57
2494 4352 5.587388 AATTACTGGCATGTGAATCAAGG 57.413 39.130 0.00 0.00 0.00 3.61
2556 4416 3.713826 TTTTGCTAGGACCTTCGGAAT 57.286 42.857 0.00 0.00 0.00 3.01
2610 4470 4.616835 GCTTTGGAAAACATCTGTGCTAGG 60.617 45.833 0.00 0.00 0.00 3.02
2615 4475 4.572985 TCAGCTTTGGAAAACATCTGTG 57.427 40.909 0.00 0.00 0.00 3.66
2619 4479 7.917505 CCACTATATTCAGCTTTGGAAAACATC 59.082 37.037 0.00 0.00 0.00 3.06
2620 4480 7.147846 CCCACTATATTCAGCTTTGGAAAACAT 60.148 37.037 0.00 0.00 0.00 2.71
2638 5009 7.128077 ACCTAAAGTAAGTAGTGCCCACTATA 58.872 38.462 10.97 0.00 44.73 1.31
2685 5065 1.822990 CAAGCATGAATCCAGCCTTGT 59.177 47.619 0.00 0.00 33.41 3.16
2752 5132 4.260170 GACAGACATTCAAAGAGGCAGAT 58.740 43.478 0.00 0.00 0.00 2.90
2792 5172 5.672570 GCAACAAGCGTTAACACTATGCATA 60.673 40.000 17.28 6.20 32.75 3.14
2833 8317 0.597637 GATCAGGTACGCCACATCCG 60.598 60.000 0.00 0.00 37.19 4.18
2836 8320 1.406887 GGTTGATCAGGTACGCCACAT 60.407 52.381 0.00 0.00 37.19 3.21
2871 8361 4.215827 TCAGACCTACTTCTTTCTGACGAC 59.784 45.833 0.00 0.00 39.62 4.34
2901 8391 0.322277 AGATGGTGCTTGCAGTCCTG 60.322 55.000 0.00 0.00 0.00 3.86
2906 8396 1.093159 GAAGGAGATGGTGCTTGCAG 58.907 55.000 0.00 0.00 36.86 4.41
2933 8423 6.331061 AGTACGTACTGAACCTGATCATTTC 58.669 40.000 26.87 3.03 34.72 2.17
2952 8442 4.921470 ATTTGACGGTCATTTGAGTACG 57.079 40.909 12.26 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.