Multiple sequence alignment - TraesCS3B01G602100

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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 TraesCS3B01G602100 chr3B 100.000 2684 0 0 1 2684 822116248 822113565 0.000000e+00 4957.0
1 TraesCS3B01G602100 chr3D 92.231 1197 44 17 784 1962 610208029 610206864 0.000000e+00 1650.0
2 TraesCS3B01G602100 chr3D 92.620 664 43 4 2022 2684 610206760 610206102 0.000000e+00 950.0
3 TraesCS3B01G602100 chr3D 89.908 545 47 6 1 541 610208621 610208081 0.000000e+00 695.0
4 TraesCS3B01G602100 chr3D 91.919 99 8 0 2104 2202 66523476 66523378 3.600000e-29 139.0
5 TraesCS3B01G602100 chr3A 90.756 1071 50 24 859 1922 744392794 744391766 0.000000e+00 1384.0
6 TraesCS3B01G602100 chr3A 90.369 488 34 8 2199 2682 744391627 744391149 1.750000e-176 628.0
7 TraesCS3B01G602100 chr3A 85.846 325 32 4 546 858 744393568 744393246 1.540000e-87 333.0
8 TraesCS3B01G602100 chr3A 96.739 92 2 1 2027 2118 744391715 744391625 4.630000e-33 152.0
9 TraesCS3B01G602100 chr1B 91.129 496 30 6 2197 2684 475148060 475147571 0.000000e+00 660.0
10 TraesCS3B01G602100 chr1B 100.000 36 0 0 2649 2684 8166529 8166564 1.720000e-07 67.6
11 TraesCS3B01G602100 chr1A 89.569 441 35 3 2241 2680 6550965 6550535 1.400000e-152 549.0
12 TraesCS3B01G602100 chr1A 88.616 448 33 7 2241 2680 6537398 6536961 1.830000e-146 529.0
13 TraesCS3B01G602100 chr1A 80.952 315 28 12 946 1246 6566184 6566480 1.250000e-53 220.0
14 TraesCS3B01G602100 chr1A 86.228 167 17 2 2265 2425 6566926 6567092 2.750000e-40 176.0
15 TraesCS3B01G602100 chr1A 90.909 121 10 1 2423 2543 6567185 6567304 7.690000e-36 161.0
16 TraesCS3B01G602100 chr5B 86.164 477 32 13 2211 2684 55501867 55502312 4.020000e-133 484.0
17 TraesCS3B01G602100 chr5B 81.224 474 49 20 1219 1685 55501292 55501732 1.980000e-91 346.0
18 TraesCS3B01G602100 chr1D 89.789 284 23 4 2262 2543 5397740 5398019 2.540000e-95 359.0
19 TraesCS3B01G602100 chr6B 95.506 89 4 0 2114 2202 472612058 472612146 2.790000e-30 143.0
20 TraesCS3B01G602100 chr6B 93.548 93 5 1 2117 2209 646750059 646750150 1.300000e-28 137.0
21 TraesCS3B01G602100 chr5A 96.512 86 3 0 2117 2202 443966873 443966788 2.790000e-30 143.0
22 TraesCS3B01G602100 chr5A 94.382 89 5 0 2114 2202 458796687 458796775 1.300000e-28 137.0
23 TraesCS3B01G602100 chr7D 93.407 91 6 0 2114 2204 423587103 423587193 4.660000e-28 135.0
24 TraesCS3B01G602100 chr7D 84.058 138 13 5 2270 2398 251446 251583 1.010000e-24 124.0
25 TraesCS3B01G602100 chr2A 87.387 111 10 3 2108 2214 43155317 43155207 1.010000e-24 124.0
26 TraesCS3B01G602100 chr5D 86.441 118 8 5 2110 2224 209317068 209316956 3.630000e-24 122.0


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 TraesCS3B01G602100 chr3B 822113565 822116248 2683 True 4957.000000 4957 100.000000 1 2684 1 chr3B.!!$R1 2683
1 TraesCS3B01G602100 chr3D 610206102 610208621 2519 True 1098.333333 1650 91.586333 1 2684 3 chr3D.!!$R2 2683
2 TraesCS3B01G602100 chr3A 744391149 744393568 2419 True 624.250000 1384 90.927500 546 2682 4 chr3A.!!$R1 2136
3 TraesCS3B01G602100 chr5B 55501292 55502312 1020 False 415.000000 484 83.694000 1219 2684 2 chr5B.!!$F1 1465

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
933 1400 0.179029 CTCCTCCTCCTCTCCGTCTC 60.179 65.0 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1965 2464 0.168788 GGCATGATGTGGTCAACGTG 59.831 55.0 0.0 0.0 40.97 4.49 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
42 44 9.590451 GAATGCATATAAAATACATGGGATTGG 57.410 33.333 0.00 0.00 0.00 3.16
77 79 5.359576 TGAAAGTTGTGCATAGGACAAAGTT 59.640 36.000 5.67 3.63 35.15 2.66
127 129 3.996150 ACATGAGTTTGGTTTGCTCAG 57.004 42.857 0.00 0.00 41.73 3.35
168 170 6.909550 ACCACCAGAAACATAGCAAAATTA 57.090 33.333 0.00 0.00 0.00 1.40
201 203 8.998377 AGAAACATAAACCATTTGCCAAATTAC 58.002 29.630 0.00 0.00 0.00 1.89
214 216 3.828786 CCAAATTACGTGCAAACCCTAC 58.171 45.455 0.00 0.00 0.00 3.18
225 227 2.386064 AAACCCTACGCACTGCCGAA 62.386 55.000 0.00 0.00 0.00 4.30
240 242 3.110358 TGCCGAATTATACTCAACGACG 58.890 45.455 0.00 0.00 0.00 5.12
242 244 3.699067 CCGAATTATACTCAACGACGGT 58.301 45.455 0.00 0.00 34.39 4.83
254 256 1.578583 ACGACGGTTTTGAAGTCCAG 58.421 50.000 0.00 0.00 0.00 3.86
273 275 4.080695 TCCAGGAATCTCAAGTTCATCCAG 60.081 45.833 0.00 0.00 0.00 3.86
285 287 0.179092 TCATCCAGTCATGCTCTGCG 60.179 55.000 10.76 6.23 0.00 5.18
286 288 1.145598 ATCCAGTCATGCTCTGCGG 59.854 57.895 10.76 0.00 0.00 5.69
304 306 1.734163 GGGAGGTTGAATGGTGTACG 58.266 55.000 0.00 0.00 0.00 3.67
315 317 4.202172 TGAATGGTGTACGTGAGTTTCTGA 60.202 41.667 0.00 0.00 46.40 3.27
316 318 3.804786 TGGTGTACGTGAGTTTCTGAA 57.195 42.857 0.00 0.00 46.40 3.02
317 319 4.126208 TGGTGTACGTGAGTTTCTGAAA 57.874 40.909 0.00 0.00 46.40 2.69
323 325 7.331193 GGTGTACGTGAGTTTCTGAAATCTATT 59.669 37.037 6.06 0.00 46.40 1.73
336 338 9.759473 TTCTGAAATCTATTCTTCAGGGAAATT 57.241 29.630 10.91 0.00 45.67 1.82
339 341 9.182214 TGAAATCTATTCTTCAGGGAAATTCAG 57.818 33.333 0.00 0.00 0.00 3.02
340 342 9.401058 GAAATCTATTCTTCAGGGAAATTCAGA 57.599 33.333 0.00 0.00 0.00 3.27
361 363 2.038975 TCTTGGGGTCCCTCTCCG 59.961 66.667 8.15 0.00 40.23 4.63
362 364 3.787001 CTTGGGGTCCCTCTCCGC 61.787 72.222 8.15 0.00 40.23 5.54
397 399 6.707440 TCTTGAGAATAGTCCAGAGATGAC 57.293 41.667 0.00 0.00 0.00 3.06
399 401 4.527944 TGAGAATAGTCCAGAGATGACGT 58.472 43.478 0.00 0.00 37.80 4.34
401 403 3.562141 AGAATAGTCCAGAGATGACGTCG 59.438 47.826 11.62 0.00 37.80 5.12
419 421 2.095718 GTCGTGGAAAATGCAGAACCTC 60.096 50.000 0.00 0.00 0.00 3.85
420 422 1.879380 CGTGGAAAATGCAGAACCTCA 59.121 47.619 0.00 0.00 0.00 3.86
423 425 4.301628 GTGGAAAATGCAGAACCTCAAAG 58.698 43.478 0.00 0.00 0.00 2.77
442 444 1.087501 GTTCTCAATCCTTGTCGGGC 58.912 55.000 0.00 0.00 0.00 6.13
443 445 0.984230 TTCTCAATCCTTGTCGGGCT 59.016 50.000 0.00 0.00 0.00 5.19
444 446 0.250234 TCTCAATCCTTGTCGGGCTG 59.750 55.000 0.00 0.00 0.00 4.85
445 447 1.372087 CTCAATCCTTGTCGGGCTGC 61.372 60.000 0.00 0.00 0.00 5.25
457 460 3.695606 GGCTGCACCCTCGACTGA 61.696 66.667 0.50 0.00 0.00 3.41
459 462 1.078848 GCTGCACCCTCGACTGAAT 60.079 57.895 0.00 0.00 0.00 2.57
489 492 3.736720 ACGGTGTTTCCTAAACCTCTTC 58.263 45.455 0.41 0.00 40.67 2.87
493 496 4.760715 GGTGTTTCCTAAACCTCTTCCTTC 59.239 45.833 0.41 0.00 40.67 3.46
494 497 4.451435 GTGTTTCCTAAACCTCTTCCTTCG 59.549 45.833 0.41 0.00 40.67 3.79
499 502 5.516984 TCCTAAACCTCTTCCTTCGAGTAT 58.483 41.667 0.00 0.00 0.00 2.12
513 516 5.817296 CCTTCGAGTATGATTTCAACATCCA 59.183 40.000 0.00 0.00 0.00 3.41
515 518 7.012704 CCTTCGAGTATGATTTCAACATCCAAT 59.987 37.037 0.00 0.00 0.00 3.16
541 544 0.940126 GCGAGATAGTTGTGCCCATG 59.060 55.000 0.00 0.00 0.00 3.66
543 546 2.808202 GCGAGATAGTTGTGCCCATGAT 60.808 50.000 0.00 0.00 0.00 2.45
544 547 2.804527 CGAGATAGTTGTGCCCATGATG 59.195 50.000 0.00 0.00 0.00 3.07
555 558 1.477558 GCCCATGATGAATCCGGTTCT 60.478 52.381 0.00 0.00 37.72 3.01
558 561 3.071602 CCCATGATGAATCCGGTTCTAGT 59.928 47.826 0.00 0.00 37.72 2.57
562 565 6.095440 CCATGATGAATCCGGTTCTAGTTTTT 59.905 38.462 0.00 0.00 37.72 1.94
565 568 6.884295 TGATGAATCCGGTTCTAGTTTTTCAT 59.116 34.615 0.00 0.00 37.72 2.57
573 576 6.036300 CCGGTTCTAGTTTTTCATGCGTATAA 59.964 38.462 0.00 0.00 0.00 0.98
674 677 8.807948 ATTAAGAGGCACTAGAAAGCATTTAA 57.192 30.769 0.00 4.81 41.55 1.52
675 678 8.807948 TTAAGAGGCACTAGAAAGCATTTAAT 57.192 30.769 0.00 0.00 41.55 1.40
737 740 7.614124 AAAACTTCACATTTGACTGCAATTT 57.386 28.000 0.00 0.00 33.25 1.82
740 743 3.899734 TCACATTTGACTGCAATTTCCG 58.100 40.909 0.00 0.00 33.25 4.30
742 745 3.670055 CACATTTGACTGCAATTTCCGAC 59.330 43.478 0.00 0.00 33.25 4.79
746 749 1.879380 TGACTGCAATTTCCGACAAGG 59.121 47.619 0.00 0.00 42.97 3.61
747 750 1.200020 GACTGCAATTTCCGACAAGGG 59.800 52.381 0.00 0.00 41.52 3.95
765 780 2.315386 GGTTTCACGCTGGTCGGAC 61.315 63.158 0.00 0.00 43.86 4.79
770 785 2.027625 CACGCTGGTCGGACCTTTC 61.028 63.158 26.41 14.43 43.86 2.62
771 786 2.434359 CGCTGGTCGGACCTTTCC 60.434 66.667 26.41 11.63 39.58 3.13
847 862 5.253330 TCTACACAAGAAAATAAGCCTGGG 58.747 41.667 0.00 0.00 0.00 4.45
926 1393 2.566708 AGATTTGCTCCTCCTCCTCT 57.433 50.000 0.00 0.00 0.00 3.69
927 1394 2.397597 AGATTTGCTCCTCCTCCTCTC 58.602 52.381 0.00 0.00 0.00 3.20
929 1396 0.972983 TTTGCTCCTCCTCCTCTCCG 60.973 60.000 0.00 0.00 0.00 4.63
930 1397 2.156496 TTGCTCCTCCTCCTCTCCGT 62.156 60.000 0.00 0.00 0.00 4.69
932 1399 1.919771 CTCCTCCTCCTCTCCGTCT 59.080 63.158 0.00 0.00 0.00 4.18
933 1400 0.179029 CTCCTCCTCCTCTCCGTCTC 60.179 65.000 0.00 0.00 0.00 3.36
934 1401 0.622154 TCCTCCTCCTCTCCGTCTCT 60.622 60.000 0.00 0.00 0.00 3.10
935 1402 0.179029 CCTCCTCCTCTCCGTCTCTC 60.179 65.000 0.00 0.00 0.00 3.20
937 1404 1.525077 CCTCCTCTCCGTCTCTCCG 60.525 68.421 0.00 0.00 0.00 4.63
1125 1606 1.331214 CTCTTGCCCCTTGCTCAAAA 58.669 50.000 0.00 0.00 42.00 2.44
1146 1628 4.525912 ATGCAAATCTTGGTTGTTCCTC 57.474 40.909 0.00 0.00 37.07 3.71
1165 1647 1.960689 TCCGCCGATGTTGATCTGATA 59.039 47.619 0.00 0.00 0.00 2.15
1168 1650 2.093310 CGCCGATGTTGATCTGATATGC 59.907 50.000 0.00 0.00 0.00 3.14
1297 1780 0.478072 AACCACCATCACCAGCTCAA 59.522 50.000 0.00 0.00 0.00 3.02
1309 1792 2.228343 ACCAGCTCAACTCACTACGTAC 59.772 50.000 0.00 0.00 0.00 3.67
1367 1854 6.770303 TGAAATTGAATCGAATGTATGCCCTA 59.230 34.615 0.00 0.00 0.00 3.53
1379 1866 2.689034 GCCCTACCCTGCTGTCCT 60.689 66.667 0.00 0.00 0.00 3.85
1380 1867 3.036429 GCCCTACCCTGCTGTCCTG 62.036 68.421 0.00 0.00 0.00 3.86
1381 1868 1.613630 CCCTACCCTGCTGTCCTGT 60.614 63.158 0.00 0.00 0.00 4.00
1382 1869 0.325296 CCCTACCCTGCTGTCCTGTA 60.325 60.000 0.00 0.00 0.00 2.74
1446 1933 2.556287 GACGCGTTCCTGCAAAGG 59.444 61.111 15.53 0.00 34.15 3.11
1688 2181 6.948886 GGAAAGGGGAAGAAGAAGTAAGAAAT 59.051 38.462 0.00 0.00 0.00 2.17
1778 2272 4.379499 GCTGATACTGCACAAAGTTTACCC 60.379 45.833 0.00 0.00 0.00 3.69
1791 2285 3.761897 AGTTTACCCTTGCTGCATTGTA 58.238 40.909 1.84 2.78 0.00 2.41
1792 2286 3.758554 AGTTTACCCTTGCTGCATTGTAG 59.241 43.478 1.84 0.00 0.00 2.74
1793 2287 1.750193 TACCCTTGCTGCATTGTAGC 58.250 50.000 18.52 18.52 41.49 3.58
1862 2361 6.020201 GCGGGTGGAAATAATAAAAACATTCG 60.020 38.462 0.00 0.00 0.00 3.34
1935 2434 2.307098 AGCTTCCAGCCTAACTTGTGAT 59.693 45.455 0.00 0.00 43.77 3.06
1965 2464 4.342665 TGGAACACAGGACAAAAATAACCC 59.657 41.667 0.00 0.00 0.00 4.11
1967 2466 4.929819 ACACAGGACAAAAATAACCCAC 57.070 40.909 0.00 0.00 0.00 4.61
1968 2467 3.316868 ACACAGGACAAAAATAACCCACG 59.683 43.478 0.00 0.00 0.00 4.94
1970 2469 3.955551 ACAGGACAAAAATAACCCACGTT 59.044 39.130 0.00 0.00 35.90 3.99
1971 2470 4.202070 ACAGGACAAAAATAACCCACGTTG 60.202 41.667 0.00 0.00 33.17 4.10
1972 2471 4.036971 CAGGACAAAAATAACCCACGTTGA 59.963 41.667 0.00 0.00 33.17 3.18
1973 2472 4.037089 AGGACAAAAATAACCCACGTTGAC 59.963 41.667 0.00 0.00 33.17 3.18
1974 2473 4.292599 GACAAAAATAACCCACGTTGACC 58.707 43.478 0.00 0.00 33.17 4.02
1975 2474 3.700038 ACAAAAATAACCCACGTTGACCA 59.300 39.130 0.00 0.00 33.17 4.02
1976 2475 3.994204 AAAATAACCCACGTTGACCAC 57.006 42.857 0.00 0.00 33.17 4.16
1977 2476 2.642154 AATAACCCACGTTGACCACA 57.358 45.000 0.00 0.00 33.17 4.17
1978 2477 2.871096 ATAACCCACGTTGACCACAT 57.129 45.000 0.00 0.00 33.17 3.21
1979 2478 2.172851 TAACCCACGTTGACCACATC 57.827 50.000 0.00 0.00 33.17 3.06
1980 2479 0.181587 AACCCACGTTGACCACATCA 59.818 50.000 0.00 0.00 34.65 3.07
1981 2480 0.400213 ACCCACGTTGACCACATCAT 59.600 50.000 0.00 0.00 37.11 2.45
1982 2481 0.804364 CCCACGTTGACCACATCATG 59.196 55.000 0.00 0.00 37.11 3.07
1983 2482 0.168788 CCACGTTGACCACATCATGC 59.831 55.000 0.00 0.00 37.11 4.06
1984 2483 0.168788 CACGTTGACCACATCATGCC 59.831 55.000 0.00 0.00 37.11 4.40
1985 2484 0.036732 ACGTTGACCACATCATGCCT 59.963 50.000 0.00 0.00 37.11 4.75
1986 2485 1.167851 CGTTGACCACATCATGCCTT 58.832 50.000 0.00 0.00 37.11 4.35
1987 2486 1.541147 CGTTGACCACATCATGCCTTT 59.459 47.619 0.00 0.00 37.11 3.11
1988 2487 2.669113 CGTTGACCACATCATGCCTTTG 60.669 50.000 0.00 0.00 37.11 2.77
1989 2488 0.889994 TGACCACATCATGCCTTTGC 59.110 50.000 0.00 0.00 32.43 3.68
1990 2489 1.180029 GACCACATCATGCCTTTGCT 58.820 50.000 0.00 0.00 38.71 3.91
1991 2490 2.290832 TGACCACATCATGCCTTTGCTA 60.291 45.455 0.00 0.00 32.86 3.49
1992 2491 2.954318 GACCACATCATGCCTTTGCTAT 59.046 45.455 0.00 0.00 38.71 2.97
1993 2492 2.954318 ACCACATCATGCCTTTGCTATC 59.046 45.455 0.00 0.00 38.71 2.08
1994 2493 2.295349 CCACATCATGCCTTTGCTATCC 59.705 50.000 0.00 0.00 38.71 2.59
1995 2494 3.220110 CACATCATGCCTTTGCTATCCT 58.780 45.455 0.00 0.00 38.71 3.24
1996 2495 3.252701 CACATCATGCCTTTGCTATCCTC 59.747 47.826 0.00 0.00 38.71 3.71
1997 2496 3.117776 ACATCATGCCTTTGCTATCCTCA 60.118 43.478 0.00 0.00 38.71 3.86
2000 2499 4.903054 TCATGCCTTTGCTATCCTCATAG 58.097 43.478 0.00 0.00 38.71 2.23
2006 2505 5.874261 GCCTTTGCTATCCTCATAGATCTTC 59.126 44.000 0.00 0.00 34.82 2.87
2012 2511 4.862902 ATCCTCATAGATCTTCGTGTGG 57.137 45.455 0.00 8.62 0.00 4.17
2126 2718 8.658840 ATTCCTATTAGATTGTACTCCCTCTC 57.341 38.462 0.00 0.00 0.00 3.20
2128 2720 7.235079 TCCTATTAGATTGTACTCCCTCTCTG 58.765 42.308 0.00 0.00 0.00 3.35
2143 2735 8.065007 ACTCCCTCTCTGAAGAAATATAAGAGT 58.935 37.037 0.00 0.00 36.56 3.24
2144 2736 8.243961 TCCCTCTCTGAAGAAATATAAGAGTG 57.756 38.462 0.00 0.00 36.56 3.51
2268 2864 5.677319 TGGTTGGGTAGATCAGAAGTTAG 57.323 43.478 0.00 0.00 0.00 2.34
2271 2867 3.039011 TGGGTAGATCAGAAGTTAGGGC 58.961 50.000 0.00 0.00 0.00 5.19
2272 2868 3.039011 GGGTAGATCAGAAGTTAGGGCA 58.961 50.000 0.00 0.00 0.00 5.36
2273 2869 3.070302 GGGTAGATCAGAAGTTAGGGCAG 59.930 52.174 0.00 0.00 0.00 4.85
2279 2876 2.563179 TCAGAAGTTAGGGCAGTCTGAC 59.437 50.000 3.32 0.00 39.73 3.51
2289 2886 0.871057 GCAGTCTGACTTCAACCTGC 59.129 55.000 7.77 11.79 40.21 4.85
2355 2952 6.655078 ATCTTGTAGCACAATTTCAACCTT 57.345 33.333 2.83 0.00 37.48 3.50
2380 2977 9.517868 TTTGGGCATGATTGAATTAAATTTTCT 57.482 25.926 0.00 0.00 0.00 2.52
2473 3072 2.628178 AGAGAGGTGACGTGTCAAATCA 59.372 45.455 3.92 0.00 41.85 2.57
2494 3094 8.958119 AATCATAGGAGCGTGTCTTTTATTTA 57.042 30.769 0.00 0.00 0.00 1.40
2495 3095 8.958119 ATCATAGGAGCGTGTCTTTTATTTAA 57.042 30.769 0.00 0.00 0.00 1.52
2635 3235 6.716628 AGGTGACTGTGATGTTCAATATTTGT 59.283 34.615 0.00 0.00 41.13 2.83
2641 3241 8.456471 ACTGTGATGTTCAATATTTGTGATCAG 58.544 33.333 0.00 0.00 30.41 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 5.772672 TGTATTTTATATGCATTCGGGCCTT 59.227 36.000 3.54 0.00 0.00 4.35
16 17 9.590451 CCAATCCCATGTATTTTATATGCATTC 57.410 33.333 3.54 0.00 0.00 2.67
42 44 5.042593 TGCACAACTTTCACATCATTTGTC 58.957 37.500 0.00 0.00 36.00 3.18
48 50 4.455533 GTCCTATGCACAACTTTCACATCA 59.544 41.667 0.00 0.00 0.00 3.07
144 146 6.909550 AATTTTGCTATGTTTCTGGTGGTA 57.090 33.333 0.00 0.00 0.00 3.25
168 170 6.650390 GCAAATGGTTTATGTTTCTTGACCAT 59.350 34.615 0.22 0.22 46.68 3.55
184 186 3.063485 GCACGTAATTTGGCAAATGGTT 58.937 40.909 24.96 13.52 0.00 3.67
209 211 0.179094 TAATTCGGCAGTGCGTAGGG 60.179 55.000 9.45 0.00 0.00 3.53
214 216 2.469826 TGAGTATAATTCGGCAGTGCG 58.530 47.619 9.45 4.79 0.00 5.34
218 220 3.179795 CGTCGTTGAGTATAATTCGGCAG 59.820 47.826 0.00 0.00 0.00 4.85
225 227 6.647895 ACTTCAAAACCGTCGTTGAGTATAAT 59.352 34.615 0.00 0.00 35.29 1.28
240 242 4.398319 TGAGATTCCTGGACTTCAAAACC 58.602 43.478 0.00 0.00 0.00 3.27
242 244 5.694995 ACTTGAGATTCCTGGACTTCAAAA 58.305 37.500 14.11 5.95 0.00 2.44
254 256 4.836825 TGACTGGATGAACTTGAGATTCC 58.163 43.478 0.00 0.00 0.00 3.01
273 275 2.202987 CCTCCCGCAGAGCATGAC 60.203 66.667 0.00 0.00 41.74 3.06
285 287 1.002773 ACGTACACCATTCAACCTCCC 59.997 52.381 0.00 0.00 0.00 4.30
286 288 2.073816 CACGTACACCATTCAACCTCC 58.926 52.381 0.00 0.00 0.00 4.30
315 317 9.406113 CTCTGAATTTCCCTGAAGAATAGATTT 57.594 33.333 0.00 0.00 0.00 2.17
316 318 8.776119 TCTCTGAATTTCCCTGAAGAATAGATT 58.224 33.333 0.00 0.00 0.00 2.40
317 319 8.329346 TCTCTGAATTTCCCTGAAGAATAGAT 57.671 34.615 0.00 0.00 0.00 1.98
323 325 5.090139 AGACTCTCTGAATTTCCCTGAAGA 58.910 41.667 0.00 0.00 0.00 2.87
336 338 0.252284 GGGACCCCAAGACTCTCTGA 60.252 60.000 0.00 0.00 35.81 3.27
339 341 0.041982 AGAGGGACCCCAAGACTCTC 59.958 60.000 7.00 0.00 33.52 3.20
340 342 0.041982 GAGAGGGACCCCAAGACTCT 59.958 60.000 7.00 1.52 40.93 3.24
387 389 0.526211 TTCCACGACGTCATCTCTGG 59.474 55.000 17.16 10.99 0.00 3.86
388 390 2.347697 TTTCCACGACGTCATCTCTG 57.652 50.000 17.16 0.00 0.00 3.35
397 399 1.399727 GGTTCTGCATTTTCCACGACG 60.400 52.381 0.00 0.00 0.00 5.12
399 401 2.151202 GAGGTTCTGCATTTTCCACGA 58.849 47.619 0.00 0.00 0.00 4.35
401 403 4.202151 ACTTTGAGGTTCTGCATTTTCCAC 60.202 41.667 0.00 0.00 0.00 4.02
429 431 1.675641 GTGCAGCCCGACAAGGATT 60.676 57.895 0.00 0.00 45.00 3.01
430 432 2.045926 GTGCAGCCCGACAAGGAT 60.046 61.111 0.00 0.00 45.00 3.24
442 444 0.534412 AGATTCAGTCGAGGGTGCAG 59.466 55.000 0.00 0.00 0.00 4.41
443 445 0.976641 AAGATTCAGTCGAGGGTGCA 59.023 50.000 0.00 0.00 0.00 4.57
444 446 1.646189 GAAGATTCAGTCGAGGGTGC 58.354 55.000 0.00 0.00 0.00 5.01
445 447 1.469940 CCGAAGATTCAGTCGAGGGTG 60.470 57.143 10.35 0.00 39.64 4.61
457 460 0.601841 AAACACCGTCGCCGAAGATT 60.602 50.000 0.45 0.00 35.63 2.40
459 462 1.662446 GAAACACCGTCGCCGAAGA 60.662 57.895 0.45 0.00 35.63 2.87
470 473 4.368565 AGGAAGAGGTTTAGGAAACACC 57.631 45.455 4.60 0.00 43.15 4.16
479 482 7.419711 AATCATACTCGAAGGAAGAGGTTTA 57.580 36.000 0.00 0.00 39.90 2.01
489 492 5.817296 TGGATGTTGAAATCATACTCGAAGG 59.183 40.000 0.00 0.00 0.00 3.46
493 496 7.307632 GGAGATTGGATGTTGAAATCATACTCG 60.308 40.741 0.00 0.00 33.61 4.18
494 497 7.500227 TGGAGATTGGATGTTGAAATCATACTC 59.500 37.037 0.00 0.00 33.61 2.59
499 502 4.951715 CCTGGAGATTGGATGTTGAAATCA 59.048 41.667 0.00 0.00 33.61 2.57
527 530 4.147321 GGATTCATCATGGGCACAACTAT 58.853 43.478 0.00 0.00 0.00 2.12
541 544 6.737254 TGAAAAACTAGAACCGGATTCATC 57.263 37.500 9.46 0.00 40.09 2.92
543 546 5.106317 GCATGAAAAACTAGAACCGGATTCA 60.106 40.000 9.46 4.81 40.09 2.57
544 547 5.332707 GCATGAAAAACTAGAACCGGATTC 58.667 41.667 9.46 8.67 37.62 2.52
562 565 8.288689 TGCTAGTAATCCTATTATACGCATGA 57.711 34.615 0.00 0.00 0.00 3.07
652 655 8.807948 TTATTAAATGCTTTCTAGTGCCTCTT 57.192 30.769 0.00 0.00 0.00 2.85
717 720 4.383649 CGGAAATTGCAGTCAAATGTGAAG 59.616 41.667 0.00 0.00 34.87 3.02
722 725 3.899734 TGTCGGAAATTGCAGTCAAATG 58.100 40.909 0.00 0.00 35.56 2.32
729 732 0.527565 CCCCTTGTCGGAAATTGCAG 59.472 55.000 0.00 0.00 33.16 4.41
737 740 1.070105 CGTGAAACCCCTTGTCGGA 59.930 57.895 0.00 0.00 33.16 4.55
740 743 1.515521 CCAGCGTGAAACCCCTTGTC 61.516 60.000 0.00 0.00 0.00 3.18
742 745 1.515521 GACCAGCGTGAAACCCCTTG 61.516 60.000 0.00 0.00 0.00 3.61
746 749 3.047877 CCGACCAGCGTGAAACCC 61.048 66.667 0.00 0.00 38.67 4.11
747 750 2.029964 TCCGACCAGCGTGAAACC 59.970 61.111 0.00 0.00 38.67 3.27
765 780 5.294552 GGACTTCTCATGAATTACGGAAAGG 59.705 44.000 0.00 0.00 0.00 3.11
770 785 4.122776 CCTGGACTTCTCATGAATTACGG 58.877 47.826 0.00 0.00 0.00 4.02
771 786 4.122776 CCCTGGACTTCTCATGAATTACG 58.877 47.826 0.00 0.00 0.00 3.18
840 855 1.229359 CATGAAGATGGCCCAGGCT 59.771 57.895 8.89 0.00 41.60 4.58
885 1351 1.508632 CTTACCGGAACCACACTGTG 58.491 55.000 9.46 6.19 0.00 3.66
929 1396 3.053849 GCGTGGAGACCGGAGAGAC 62.054 68.421 9.46 0.00 0.00 3.36
930 1397 2.750637 GCGTGGAGACCGGAGAGA 60.751 66.667 9.46 0.00 0.00 3.10
1125 1606 3.259123 GGAGGAACAACCAAGATTTGCAT 59.741 43.478 0.00 0.00 42.04 3.96
1146 1628 2.438868 TATCAGATCAACATCGGCGG 57.561 50.000 7.21 0.00 33.75 6.13
1168 1650 2.637025 CGCGGTGGAACAAACCAG 59.363 61.111 0.00 0.00 44.16 4.00
1290 1772 2.095869 ACGTACGTAGTGAGTTGAGCTG 60.096 50.000 21.41 0.00 45.73 4.24
1297 1780 0.946528 TGTGCACGTACGTAGTGAGT 59.053 50.000 22.34 7.85 45.73 3.41
1309 1792 3.150848 TCAGCTAGTTATCTGTGCACG 57.849 47.619 13.13 7.36 0.00 5.34
1367 1854 0.615331 CACATACAGGACAGCAGGGT 59.385 55.000 0.00 0.00 0.00 4.34
1379 1866 0.943673 GCTGCACACACACACATACA 59.056 50.000 0.00 0.00 0.00 2.29
1380 1867 1.195448 GAGCTGCACACACACACATAC 59.805 52.381 1.02 0.00 0.00 2.39
1381 1868 1.202627 TGAGCTGCACACACACACATA 60.203 47.619 1.02 0.00 0.00 2.29
1382 1869 0.464193 TGAGCTGCACACACACACAT 60.464 50.000 1.02 0.00 0.00 3.21
1446 1933 6.056090 AGGTTCTCCCTCTTGTTCTTTATC 57.944 41.667 0.00 0.00 40.71 1.75
1688 2181 3.047280 GACGCACGCACATTCCCA 61.047 61.111 0.00 0.00 0.00 4.37
1791 2285 3.760684 CAGGATAACAAAAGAGCCTTGCT 59.239 43.478 0.00 0.00 43.88 3.91
1792 2286 3.758554 TCAGGATAACAAAAGAGCCTTGC 59.241 43.478 0.00 0.00 0.00 4.01
1793 2287 5.964958 TTCAGGATAACAAAAGAGCCTTG 57.035 39.130 0.00 0.00 0.00 3.61
1825 2324 1.669760 CACCCGCCGCAACTAAAGA 60.670 57.895 0.00 0.00 0.00 2.52
1862 2361 1.862602 CGCCCAAGTTAGCACCAACC 61.863 60.000 0.00 0.00 0.00 3.77
1890 2389 7.061094 GCTAAATACAAGCAACACAGATTGTTC 59.939 37.037 2.84 0.00 46.05 3.18
1935 2434 6.968263 TTTTGTCCTGTGTTCCATCATTTA 57.032 33.333 0.00 0.00 0.00 1.40
1959 2458 2.039216 TGATGTGGTCAACGTGGGTTAT 59.961 45.455 0.00 0.00 33.72 1.89
1960 2459 1.416772 TGATGTGGTCAACGTGGGTTA 59.583 47.619 0.00 0.00 33.72 2.85
1961 2460 0.181587 TGATGTGGTCAACGTGGGTT 59.818 50.000 0.00 0.00 36.63 4.11
1962 2461 0.400213 ATGATGTGGTCAACGTGGGT 59.600 50.000 0.00 0.00 40.97 4.51
1965 2464 0.168788 GGCATGATGTGGTCAACGTG 59.831 55.000 0.00 0.00 40.97 4.49
1967 2466 1.167851 AAGGCATGATGTGGTCAACG 58.832 50.000 0.00 0.00 40.97 4.10
1968 2467 2.927871 GCAAAGGCATGATGTGGTCAAC 60.928 50.000 0.00 0.00 40.97 3.18
1970 2469 0.889994 GCAAAGGCATGATGTGGTCA 59.110 50.000 0.00 0.00 42.06 4.02
1971 2470 1.180029 AGCAAAGGCATGATGTGGTC 58.820 50.000 0.00 0.00 44.61 4.02
1972 2471 2.512692 TAGCAAAGGCATGATGTGGT 57.487 45.000 0.00 0.00 44.61 4.16
1973 2472 2.295349 GGATAGCAAAGGCATGATGTGG 59.705 50.000 0.00 0.00 44.61 4.17
1974 2473 3.220110 AGGATAGCAAAGGCATGATGTG 58.780 45.455 0.00 0.00 44.61 3.21
1975 2474 3.117776 TGAGGATAGCAAAGGCATGATGT 60.118 43.478 0.00 0.00 44.61 3.06
1976 2475 3.483421 TGAGGATAGCAAAGGCATGATG 58.517 45.455 0.00 0.00 44.61 3.07
1977 2476 3.870538 TGAGGATAGCAAAGGCATGAT 57.129 42.857 0.00 0.00 44.61 2.45
1978 2477 3.870538 ATGAGGATAGCAAAGGCATGA 57.129 42.857 0.00 0.00 44.61 3.07
1979 2478 4.903054 TCTATGAGGATAGCAAAGGCATG 58.097 43.478 0.00 0.00 44.61 4.06
1980 2479 5.488203 AGATCTATGAGGATAGCAAAGGCAT 59.512 40.000 0.00 0.00 44.61 4.40
1981 2480 4.842948 AGATCTATGAGGATAGCAAAGGCA 59.157 41.667 0.00 0.00 44.61 4.75
1982 2481 5.419239 AGATCTATGAGGATAGCAAAGGC 57.581 43.478 0.00 0.00 41.61 4.35
1983 2482 6.098679 CGAAGATCTATGAGGATAGCAAAGG 58.901 44.000 0.00 0.00 32.78 3.11
1984 2483 6.585702 CACGAAGATCTATGAGGATAGCAAAG 59.414 42.308 0.00 0.00 32.78 2.77
1985 2484 6.040955 ACACGAAGATCTATGAGGATAGCAAA 59.959 38.462 0.00 0.00 32.78 3.68
1986 2485 5.536538 ACACGAAGATCTATGAGGATAGCAA 59.463 40.000 0.00 0.00 32.78 3.91
1987 2486 5.048434 CACACGAAGATCTATGAGGATAGCA 60.048 44.000 0.00 0.00 32.78 3.49
1988 2487 5.398169 CACACGAAGATCTATGAGGATAGC 58.602 45.833 0.00 0.00 32.78 2.97
1989 2488 5.621104 GCCACACGAAGATCTATGAGGATAG 60.621 48.000 17.02 0.00 33.90 2.08
1990 2489 4.218635 GCCACACGAAGATCTATGAGGATA 59.781 45.833 17.02 0.00 0.00 2.59
1991 2490 3.006323 GCCACACGAAGATCTATGAGGAT 59.994 47.826 17.02 0.00 0.00 3.24
1992 2491 2.362397 GCCACACGAAGATCTATGAGGA 59.638 50.000 17.02 0.00 0.00 3.71
1993 2492 2.363680 AGCCACACGAAGATCTATGAGG 59.636 50.000 0.00 4.75 0.00 3.86
1994 2493 3.724508 AGCCACACGAAGATCTATGAG 57.275 47.619 0.00 0.00 0.00 2.90
1995 2494 5.073428 AGATAGCCACACGAAGATCTATGA 58.927 41.667 0.00 0.00 0.00 2.15
1996 2495 5.384063 AGATAGCCACACGAAGATCTATG 57.616 43.478 0.00 0.00 0.00 2.23
1997 2496 6.412362 AAAGATAGCCACACGAAGATCTAT 57.588 37.500 0.00 0.00 0.00 1.98
2000 2499 5.050702 GCTAAAAGATAGCCACACGAAGATC 60.051 44.000 0.00 0.00 34.65 2.75
2006 2505 6.924060 ACTAATAGCTAAAAGATAGCCACACG 59.076 38.462 11.53 0.00 41.25 4.49
2105 2697 8.698973 TTCAGAGAGGGAGTACAATCTAATAG 57.301 38.462 0.00 0.00 0.00 1.73
2188 2780 7.931015 AATGAAAGTACATACTCCCTCCATA 57.069 36.000 0.00 0.00 34.99 2.74
2205 2797 9.793252 CTGATCTTTTTGGTATGGTAATGAAAG 57.207 33.333 0.00 0.00 0.00 2.62
2268 2864 0.398318 AGGTTGAAGTCAGACTGCCC 59.602 55.000 3.05 0.00 0.00 5.36
2271 2867 2.036992 AGAGCAGGTTGAAGTCAGACTG 59.963 50.000 3.05 0.00 35.73 3.51
2272 2868 2.298729 GAGAGCAGGTTGAAGTCAGACT 59.701 50.000 0.00 0.00 0.00 3.24
2273 2869 2.611722 GGAGAGCAGGTTGAAGTCAGAC 60.612 54.545 0.00 0.00 0.00 3.51
2279 2876 1.805869 CACAGGAGAGCAGGTTGAAG 58.194 55.000 0.00 0.00 0.00 3.02
2289 2886 3.883830 ACAGAGTAATGCACAGGAGAG 57.116 47.619 0.00 0.00 0.00 3.20
2355 2952 9.517868 AAGAAAATTTAATTCAATCATGCCCAA 57.482 25.926 0.00 0.00 0.00 4.12
2622 3222 8.052141 TGGGATACTGATCACAAATATTGAACA 58.948 33.333 0.00 0.00 42.74 3.18


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

AutoCloner maintained by Alex Coulton.