Multiple sequence alignment - TraesCS6B01G100100

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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 TraesCS6B01G100100 chr6B 100.000 2864 0 0 1 2864 77988653 77991516 0.000000e+00 5289.0
1 TraesCS6B01G100100 chr6B 93.968 862 46 6 2007 2862 78318374 78319235 0.000000e+00 1299.0
2 TraesCS6B01G100100 chr6B 93.503 862 50 6 2007 2862 78273765 78274626 0.000000e+00 1277.0
3 TraesCS6B01G100100 chr6B 90.648 941 51 19 1020 1926 78312041 78312978 0.000000e+00 1216.0
4 TraesCS6B01G100100 chr6B 92.577 714 22 3 1 686 78239457 78240167 0.000000e+00 996.0
5 TraesCS6B01G100100 chr6B 93.740 623 36 2 2007 2627 78315722 78316343 0.000000e+00 931.0
6 TraesCS6B01G100100 chr6B 93.291 626 39 2 2007 2630 78271154 78271778 0.000000e+00 920.0
7 TraesCS6B01G100100 chr6B 95.606 569 21 3 1020 1585 78267512 78268079 0.000000e+00 909.0
8 TraesCS6B01G100100 chr6B 81.518 817 105 26 793 1595 59100330 59101114 5.210000e-177 630.0
9 TraesCS6B01G100100 chr6B 91.162 396 28 4 1537 1926 78267995 78268389 5.430000e-147 531.0
10 TraesCS6B01G100100 chr6B 93.333 345 19 3 682 1025 78264461 78264802 9.160000e-140 507.0
11 TraesCS6B01G100100 chr6B 92.754 345 21 3 682 1025 78308919 78309260 1.980000e-136 496.0
12 TraesCS6B01G100100 chr6B 86.284 401 40 6 828 1216 58812188 58812585 3.410000e-114 422.0
13 TraesCS6B01G100100 chr6B 82.748 313 40 6 1285 1586 58812622 58812931 1.690000e-67 267.0
14 TraesCS6B01G100100 chr6B 88.636 132 13 2 2071 2200 59824157 59824288 2.950000e-35 159.0
15 TraesCS6B01G100100 chr6B 87.805 82 4 3 1537 1612 78312524 78312605 1.090000e-14 91.6
16 TraesCS6B01G100100 chr6B 92.308 52 4 0 1635 1686 59101344 59101395 1.100000e-09 75.0
17 TraesCS6B01G100100 chrUn 88.561 1591 105 20 1 1586 112540646 112539128 0.000000e+00 1858.0
18 TraesCS6B01G100100 chrUn 88.288 777 50 16 1569 2336 112539175 112538431 0.000000e+00 893.0
19 TraesCS6B01G100100 chrUn 87.755 98 5 3 2343 2440 112538447 112538357 1.090000e-19 108.0
20 TraesCS6B01G100100 chrUn 100.000 30 0 0 420 449 112540353 112540324 3.990000e-04 56.5
21 TraesCS6B01G100100 chrUn 85.455 55 6 2 642 695 279457901 279457848 3.990000e-04 56.5
22 TraesCS6B01G100100 chr3D 88.150 1173 80 19 1693 2857 603322117 603323238 0.000000e+00 1341.0
23 TraesCS6B01G100100 chr3D 91.228 798 55 7 789 1585 603321283 603322066 0.000000e+00 1072.0
24 TraesCS6B01G100100 chr6A 90.299 835 63 8 747 1577 45407287 45408107 0.000000e+00 1077.0
25 TraesCS6B01G100100 chr6A 91.123 721 62 1 1 721 45374022 45374740 0.000000e+00 976.0
26 TraesCS6B01G100100 chr6A 87.285 582 41 6 1762 2337 45408549 45409103 4.030000e-178 634.0
27 TraesCS6B01G100100 chr6A 91.324 438 35 2 2421 2858 45409218 45409652 1.900000e-166 595.0
28 TraesCS6B01G100100 chr6A 80.435 828 106 35 792 1595 33010573 33011368 5.320000e-162 580.0
29 TraesCS6B01G100100 chr6A 90.196 153 12 2 1570 1722 45408070 45408219 2.250000e-46 196.0
30 TraesCS6B01G100100 chr6A 97.222 36 1 0 1638 1673 33011544 33011579 8.570000e-06 62.1
31 TraesCS6B01G100100 chr3B 92.991 428 23 2 1569 1993 810520286 810519863 4.050000e-173 617.0
32 TraesCS6B01G100100 chr3B 90.802 424 33 3 789 1209 810520715 810520295 1.930000e-156 562.0
33 TraesCS6B01G100100 chr5A 90.323 465 44 1 2394 2858 535009615 535010078 2.440000e-170 608.0
34 TraesCS6B01G100100 chr5D 89.914 466 44 3 2394 2858 421397532 421397995 5.280000e-167 597.0
35 TraesCS6B01G100100 chr6D 80.135 740 88 35 875 1595 29089554 29090253 5.510000e-137 497.0
36 TraesCS6B01G100100 chr6D 81.734 323 44 8 1285 1595 24001799 24002118 3.660000e-64 255.0
37 TraesCS6B01G100100 chr6D 80.967 331 50 8 1275 1595 16529309 16528982 1.700000e-62 250.0
38 TraesCS6B01G100100 chr4D 76.201 437 104 0 2402 2838 64181215 64181651 6.170000e-57 231.0
39 TraesCS6B01G100100 chr7B 92.248 129 9 1 2209 2336 372327627 372327755 6.300000e-42 182.0
40 TraesCS6B01G100100 chr2D 92.188 128 8 2 2210 2336 556055812 556055686 2.270000e-41 180.0
41 TraesCS6B01G100100 chr2B 92.500 40 1 2 1987 2026 39336494 39336457 3.990000e-04 56.5


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G100100 chr6B 77988653 77991516 2863 False 5289.000 5289 100.0000 1 2864 1 chr6B.!!$F2 2863
1 TraesCS6B01G100100 chr6B 78239457 78240167 710 False 996.000 996 92.5770 1 686 1 chr6B.!!$F3 685
2 TraesCS6B01G100100 chr6B 78264461 78274626 10165 False 828.800 1277 93.3790 682 2862 5 chr6B.!!$F6 2180
3 TraesCS6B01G100100 chr6B 78308919 78319235 10316 False 806.720 1299 91.7830 682 2862 5 chr6B.!!$F7 2180
4 TraesCS6B01G100100 chr6B 59100330 59101395 1065 False 352.500 630 86.9130 793 1686 2 chr6B.!!$F5 893
5 TraesCS6B01G100100 chr6B 58812188 58812931 743 False 344.500 422 84.5160 828 1586 2 chr6B.!!$F4 758
6 TraesCS6B01G100100 chrUn 112538357 112540646 2289 True 728.875 1858 91.1510 1 2440 4 chrUn.!!$R2 2439
7 TraesCS6B01G100100 chr3D 603321283 603323238 1955 False 1206.500 1341 89.6890 789 2857 2 chr3D.!!$F1 2068
8 TraesCS6B01G100100 chr6A 45374022 45374740 718 False 976.000 976 91.1230 1 721 1 chr6A.!!$F1 720
9 TraesCS6B01G100100 chr6A 45407287 45409652 2365 False 625.500 1077 89.7760 747 2858 4 chr6A.!!$F3 2111
10 TraesCS6B01G100100 chr6A 33010573 33011579 1006 False 321.050 580 88.8285 792 1673 2 chr6A.!!$F2 881
11 TraesCS6B01G100100 chr3B 810519863 810520715 852 True 589.500 617 91.8965 789 1993 2 chr3B.!!$R1 1204
12 TraesCS6B01G100100 chr6D 29089554 29090253 699 False 497.000 497 80.1350 875 1595 1 chr6D.!!$F2 720

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
409 411 0.038159 CTTCTCGGGCTCAACTTCGT 60.038 55.0 0.0 0.0 0.00 3.85 F
441 443 0.391793 GCCAAGCTCGCTCTAGGTTT 60.392 55.0 0.0 0.0 35.08 3.27 F
1579 4502 0.321653 CCAAGTCCCCCAAGAAGACG 60.322 60.0 0.0 0.0 35.65 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1302 4151 0.028110 GAACGAAATCGGCCATCTGC 59.972 55.0 2.24 0.0 44.95 4.26 R
1594 4517 0.322906 CAGCCTTCTTCTTGGGGGAC 60.323 60.0 0.00 0.0 0.00 4.46 R
2699 14205 0.107831 GTACTTGGCGGGCCATATCA 59.892 55.0 14.03 0.0 46.64 2.15 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
21 22 1.841556 GCGGGGATGGGACTGGATA 60.842 63.158 0.00 0.00 0.00 2.59
239 240 3.062909 GCAACGAATCGGTATGTTTAGCA 59.937 43.478 7.80 0.00 0.00 3.49
251 252 5.240844 GGTATGTTTAGCAGTGGAAAGTTGT 59.759 40.000 0.00 0.00 0.00 3.32
257 258 4.632538 AGCAGTGGAAAGTTGTTGTAAC 57.367 40.909 0.00 0.00 0.00 2.50
409 411 0.038159 CTTCTCGGGCTCAACTTCGT 60.038 55.000 0.00 0.00 0.00 3.85
438 440 2.107953 GGCCAAGCTCGCTCTAGG 59.892 66.667 0.00 0.00 0.00 3.02
439 441 2.726351 GGCCAAGCTCGCTCTAGGT 61.726 63.158 0.00 0.00 0.00 3.08
440 442 1.219393 GCCAAGCTCGCTCTAGGTT 59.781 57.895 0.00 0.00 37.68 3.50
441 443 0.391793 GCCAAGCTCGCTCTAGGTTT 60.392 55.000 0.00 0.00 35.08 3.27
442 444 1.946283 GCCAAGCTCGCTCTAGGTTTT 60.946 52.381 0.00 0.00 35.08 2.43
443 445 2.427506 CCAAGCTCGCTCTAGGTTTTT 58.572 47.619 0.00 0.00 35.08 1.94
444 446 2.160417 CCAAGCTCGCTCTAGGTTTTTG 59.840 50.000 0.00 0.00 35.08 2.44
445 447 1.443802 AGCTCGCTCTAGGTTTTTGC 58.556 50.000 0.00 0.00 0.00 3.68
446 448 1.002544 AGCTCGCTCTAGGTTTTTGCT 59.997 47.619 0.00 0.00 0.00 3.91
447 449 1.395262 GCTCGCTCTAGGTTTTTGCTC 59.605 52.381 0.00 0.00 0.00 4.26
448 450 2.933056 GCTCGCTCTAGGTTTTTGCTCT 60.933 50.000 0.00 0.00 0.00 4.09
449 451 2.926838 CTCGCTCTAGGTTTTTGCTCTC 59.073 50.000 0.00 0.00 0.00 3.20
450 452 2.299013 TCGCTCTAGGTTTTTGCTCTCA 59.701 45.455 0.00 0.00 0.00 3.27
451 453 2.670414 CGCTCTAGGTTTTTGCTCTCAG 59.330 50.000 0.00 0.00 0.00 3.35
452 454 2.418280 GCTCTAGGTTTTTGCTCTCAGC 59.582 50.000 0.00 0.00 42.82 4.26
453 455 3.867984 GCTCTAGGTTTTTGCTCTCAGCT 60.868 47.826 0.00 0.00 42.97 4.24
454 456 3.931578 TCTAGGTTTTTGCTCTCAGCTC 58.068 45.455 0.00 0.00 42.97 4.09
455 457 2.947127 AGGTTTTTGCTCTCAGCTCT 57.053 45.000 0.00 0.00 42.97 4.09
456 458 4.772624 TCTAGGTTTTTGCTCTCAGCTCTA 59.227 41.667 0.00 0.00 42.97 2.43
457 459 3.936564 AGGTTTTTGCTCTCAGCTCTAG 58.063 45.455 0.00 0.00 42.97 2.43
506 528 6.023603 AGTTGATGGGGTTAGAAGTTAGAGA 58.976 40.000 0.00 0.00 0.00 3.10
607 629 1.382009 AGGCCGGTTTGGTTTTGGT 60.382 52.632 1.90 0.00 41.21 3.67
642 664 3.338250 GGCCTCCCCACATGGACA 61.338 66.667 0.00 0.00 37.39 4.02
652 674 3.545703 CCCACATGGACATACTTTCTCC 58.454 50.000 0.00 0.00 37.39 3.71
653 675 3.054434 CCCACATGGACATACTTTCTCCA 60.054 47.826 0.00 0.00 38.47 3.86
735 759 8.777413 TGAATGAATATATGCACTCTAAAGCAC 58.223 33.333 3.88 0.00 44.49 4.40
745 769 6.436261 TGCACTCTAAAGCACGTCTATATAC 58.564 40.000 0.00 0.00 35.51 1.47
958 1002 3.644399 CTCAGAGCAGAGCAGCGCA 62.644 63.158 11.47 0.00 40.15 6.09
1029 1083 3.939837 TTCGCCGGAGAAGCAGCAG 62.940 63.158 17.34 0.00 0.00 4.24
1192 4034 3.417275 CTACCTCGCTGCCGTCCTG 62.417 68.421 0.00 0.00 35.54 3.86
1302 4151 1.142870 TCCTGTTCCTCTTGTGTTGGG 59.857 52.381 0.00 0.00 0.00 4.12
1392 4246 1.639635 AAGAAGGCCCGCATCATCCT 61.640 55.000 0.00 0.00 0.00 3.24
1411 4265 2.107750 CGCCACCTGATGATCGCT 59.892 61.111 0.00 0.00 0.00 4.93
1577 4500 2.266279 CTACCAAGTCCCCCAAGAAGA 58.734 52.381 0.00 0.00 0.00 2.87
1578 4501 0.771755 ACCAAGTCCCCCAAGAAGAC 59.228 55.000 0.00 0.00 0.00 3.01
1579 4502 0.321653 CCAAGTCCCCCAAGAAGACG 60.322 60.000 0.00 0.00 35.65 4.18
1580 4503 0.321653 CAAGTCCCCCAAGAAGACGG 60.322 60.000 0.00 0.00 35.65 4.79
1581 4504 2.046217 GTCCCCCAAGAAGACGGC 60.046 66.667 0.00 0.00 0.00 5.68
1582 4505 3.327404 TCCCCCAAGAAGACGGCC 61.327 66.667 0.00 0.00 0.00 6.13
1583 4506 4.778143 CCCCCAAGAAGACGGCCG 62.778 72.222 26.86 26.86 0.00 6.13
1598 4521 4.832608 CCGCCGCTACCAAGTCCC 62.833 72.222 0.00 0.00 0.00 4.46
1599 4522 4.832608 CGCCGCTACCAAGTCCCC 62.833 72.222 0.00 0.00 0.00 4.81
1600 4523 4.484872 GCCGCTACCAAGTCCCCC 62.485 72.222 0.00 0.00 0.00 5.40
1601 4524 3.006728 CCGCTACCAAGTCCCCCA 61.007 66.667 0.00 0.00 0.00 4.96
1602 4525 2.598787 CCGCTACCAAGTCCCCCAA 61.599 63.158 0.00 0.00 0.00 4.12
1603 4526 1.078426 CGCTACCAAGTCCCCCAAG 60.078 63.158 0.00 0.00 0.00 3.61
1604 4527 1.550130 CGCTACCAAGTCCCCCAAGA 61.550 60.000 0.00 0.00 0.00 3.02
1605 4528 0.696501 GCTACCAAGTCCCCCAAGAA 59.303 55.000 0.00 0.00 0.00 2.52
1606 4529 1.340114 GCTACCAAGTCCCCCAAGAAG 60.340 57.143 0.00 0.00 0.00 2.85
1612 4535 0.476611 AGTCCCCCAAGAAGAAGGCT 60.477 55.000 0.00 0.00 0.00 4.58
1636 4779 3.378427 CAGCCACAAATTAAGGAGTAGCC 59.622 47.826 0.00 0.00 0.00 3.93
1677 4820 1.301165 GCTTGCCACCTGCTTTTGG 60.301 57.895 0.00 0.00 42.00 3.28
1681 4824 1.367471 GCCACCTGCTTTTGGTTCC 59.633 57.895 0.00 0.00 35.28 3.62
1697 4840 3.751175 TGGTTCCGAACATTTGTCATCTC 59.249 43.478 13.23 0.00 0.00 2.75
1722 4865 5.350504 TGAACTTCTCTCTTCCATCATCC 57.649 43.478 0.00 0.00 0.00 3.51
1754 4897 1.069636 CGCTCTTTGCTCACTGAAACC 60.070 52.381 0.00 0.00 40.11 3.27
1795 5228 5.843969 TCAGCCCCTCATCTTATGTTATGTA 59.156 40.000 0.00 0.00 0.00 2.29
1796 5229 6.014242 TCAGCCCCTCATCTTATGTTATGTAG 60.014 42.308 0.00 0.00 0.00 2.74
1829 5262 4.218312 TCATAGACCTATCAAGCTGCAGA 58.782 43.478 20.43 0.00 0.00 4.26
1905 5340 2.674754 CCTGCGGGGGAAGCTTAA 59.325 61.111 2.57 0.00 35.28 1.85
1941 5376 4.817517 TCCATCTTCTACGTTCTGAAACC 58.182 43.478 0.00 0.00 31.27 3.27
1978 7030 3.821033 GCGCTAAATTGGACCAGGAATAT 59.179 43.478 0.00 0.00 0.00 1.28
1979 7031 5.001232 GCGCTAAATTGGACCAGGAATATA 58.999 41.667 0.00 0.00 0.00 0.86
1980 7032 5.648092 GCGCTAAATTGGACCAGGAATATAT 59.352 40.000 0.00 0.00 0.00 0.86
1981 7033 6.821665 GCGCTAAATTGGACCAGGAATATATA 59.178 38.462 0.00 0.00 0.00 0.86
1992 7044 8.877195 GGACCAGGAATATATAGTTGAAAGGTA 58.123 37.037 0.00 0.00 0.00 3.08
1993 7045 9.708092 GACCAGGAATATATAGTTGAAAGGTAC 57.292 37.037 0.00 0.00 0.00 3.34
1995 7047 9.930693 CCAGGAATATATAGTTGAAAGGTACTC 57.069 37.037 0.00 0.00 38.49 2.59
1996 7048 9.930693 CAGGAATATATAGTTGAAAGGTACTCC 57.069 37.037 0.00 0.00 38.49 3.85
1997 7049 9.102453 AGGAATATATAGTTGAAAGGTACTCCC 57.898 37.037 0.00 0.00 38.49 4.30
2000 7052 6.997942 ATATAGTTGAAAGGTACTCCCTCC 57.002 41.667 0.00 0.00 45.47 4.30
2001 7053 2.267192 AGTTGAAAGGTACTCCCTCCC 58.733 52.381 0.00 0.00 45.47 4.30
2002 7054 2.157989 AGTTGAAAGGTACTCCCTCCCT 60.158 50.000 0.00 0.00 45.47 4.20
2003 7055 2.643304 GTTGAAAGGTACTCCCTCCCTT 59.357 50.000 0.00 0.00 45.47 3.95
2004 7056 2.547990 TGAAAGGTACTCCCTCCCTTC 58.452 52.381 0.00 0.00 45.47 3.46
2005 7057 1.838715 GAAAGGTACTCCCTCCCTTCC 59.161 57.143 0.00 0.00 45.47 3.46
2006 7058 1.102938 AAGGTACTCCCTCCCTTCCT 58.897 55.000 0.00 0.00 45.47 3.36
2007 7059 2.012168 AGGTACTCCCTCCCTTCCTA 57.988 55.000 0.00 0.00 40.71 2.94
2008 7060 2.304700 AGGTACTCCCTCCCTTCCTAA 58.695 52.381 0.00 0.00 40.71 2.69
2025 8173 9.603921 CCCTTCCTAAATATAAGACGTTTTGTA 57.396 33.333 0.83 0.00 0.00 2.41
2146 8299 8.696043 ATAGCTTGACCATGCTCAAAATATTA 57.304 30.769 12.72 0.00 41.32 0.98
2157 10962 8.537223 CATGCTCAAAATATTAATGCAGACAAC 58.463 33.333 0.00 0.00 32.42 3.32
2383 13828 6.896307 AGGTCTTATATTAGATAACGGAGGGG 59.104 42.308 0.00 0.00 0.00 4.79
2391 13836 4.701651 AGATAACGGAGGGGGTATTTTC 57.298 45.455 0.00 0.00 0.00 2.29
2598 14100 3.055819 AGTCCACAATCAGTACTTCGCAT 60.056 43.478 0.00 0.00 0.00 4.73
2699 14205 3.767673 TCGATTTCCACCTTAGTACAGCT 59.232 43.478 0.00 0.00 0.00 4.24
2749 14255 5.928976 TCCTTATTGCAATTAGCTCTGCTA 58.071 37.500 18.75 8.81 45.94 3.49
2862 14368 5.937540 TGAGTGTGTTTCATAATGAACCGAT 59.062 36.000 0.00 0.00 35.89 4.18
2863 14369 6.128309 TGAGTGTGTTTCATAATGAACCGATG 60.128 38.462 0.00 0.00 35.89 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 1.220206 CCGACTGCAGATCCAGCTT 59.780 57.895 23.35 0.00 36.29 3.74
61 62 2.563798 CCACGCATGCCACCAGTTT 61.564 57.895 13.15 0.00 0.00 2.66
98 99 2.954684 CGAGTGCCAACCCTAGCCA 61.955 63.158 0.00 0.00 0.00 4.75
239 240 5.298527 GCCTAAGTTACAACAACTTTCCACT 59.701 40.000 7.61 0.00 40.58 4.00
251 252 8.685838 AAATGTAGAGTTTGCCTAAGTTACAA 57.314 30.769 0.00 0.00 0.00 2.41
257 258 9.346725 GATTGAAAAATGTAGAGTTTGCCTAAG 57.653 33.333 0.00 0.00 0.00 2.18
409 411 1.185315 GCTTGGCCCAGCTAAATTCA 58.815 50.000 21.29 0.00 36.79 2.57
438 440 3.669536 ACCTAGAGCTGAGAGCAAAAAC 58.330 45.455 0.00 0.00 45.56 2.43
439 441 4.357918 AACCTAGAGCTGAGAGCAAAAA 57.642 40.909 0.00 0.00 45.56 1.94
440 442 4.202357 TGAAACCTAGAGCTGAGAGCAAAA 60.202 41.667 0.00 0.00 45.56 2.44
441 443 3.324846 TGAAACCTAGAGCTGAGAGCAAA 59.675 43.478 0.00 0.00 45.56 3.68
442 444 2.899900 TGAAACCTAGAGCTGAGAGCAA 59.100 45.455 0.00 0.00 45.56 3.91
443 445 2.529632 TGAAACCTAGAGCTGAGAGCA 58.470 47.619 0.00 0.00 45.56 4.26
444 446 3.118811 ACATGAAACCTAGAGCTGAGAGC 60.119 47.826 0.00 0.00 42.84 4.09
445 447 4.159321 TGACATGAAACCTAGAGCTGAGAG 59.841 45.833 0.00 0.00 0.00 3.20
446 448 4.089361 TGACATGAAACCTAGAGCTGAGA 58.911 43.478 0.00 0.00 0.00 3.27
447 449 4.462508 TGACATGAAACCTAGAGCTGAG 57.537 45.455 0.00 0.00 0.00 3.35
448 450 4.890158 TTGACATGAAACCTAGAGCTGA 57.110 40.909 0.00 0.00 0.00 4.26
449 451 6.149973 TGAAATTGACATGAAACCTAGAGCTG 59.850 38.462 0.00 0.00 0.00 4.24
450 452 6.240894 TGAAATTGACATGAAACCTAGAGCT 58.759 36.000 0.00 0.00 0.00 4.09
451 453 6.500684 TGAAATTGACATGAAACCTAGAGC 57.499 37.500 0.00 0.00 0.00 4.09
452 454 8.396390 CAGATGAAATTGACATGAAACCTAGAG 58.604 37.037 0.00 0.00 0.00 2.43
453 455 7.884877 ACAGATGAAATTGACATGAAACCTAGA 59.115 33.333 0.00 0.00 0.00 2.43
454 456 7.966753 CACAGATGAAATTGACATGAAACCTAG 59.033 37.037 0.00 0.00 0.00 3.02
455 457 7.665145 TCACAGATGAAATTGACATGAAACCTA 59.335 33.333 0.00 0.00 0.00 3.08
456 458 6.491062 TCACAGATGAAATTGACATGAAACCT 59.509 34.615 0.00 0.00 0.00 3.50
457 459 6.680810 TCACAGATGAAATTGACATGAAACC 58.319 36.000 0.00 0.00 0.00 3.27
506 528 3.495434 TTAAGGGTGTGTTCGGATGTT 57.505 42.857 0.00 0.00 0.00 2.71
579 601 2.376109 CAAACCGGCCTCTCTCTACTA 58.624 52.381 0.00 0.00 0.00 1.82
583 605 1.128188 AACCAAACCGGCCTCTCTCT 61.128 55.000 0.00 0.00 39.03 3.10
584 606 0.250770 AAACCAAACCGGCCTCTCTC 60.251 55.000 0.00 0.00 39.03 3.20
607 629 1.204467 GCCGCTTGGAATTGAATTGGA 59.796 47.619 0.00 0.00 33.02 3.53
722 746 6.436261 TGTATATAGACGTGCTTTAGAGTGC 58.564 40.000 0.00 0.00 0.00 4.40
723 747 8.508062 AGATGTATATAGACGTGCTTTAGAGTG 58.492 37.037 0.00 0.00 0.00 3.51
786 813 2.828520 TGGTCAACTTTGCTTGGTTTCA 59.171 40.909 0.00 0.00 0.00 2.69
958 1002 2.369633 TGCTGGATCGGGATGCTGT 61.370 57.895 8.40 0.00 32.29 4.40
1029 1083 3.687321 TTCCTGGCAGCCATCTCGC 62.687 63.158 16.64 0.00 30.82 5.03
1030 1084 1.523258 CTTCCTGGCAGCCATCTCG 60.523 63.158 16.64 2.46 30.82 4.04
1031 1085 1.153005 CCTTCCTGGCAGCCATCTC 60.153 63.158 16.64 0.00 30.82 2.75
1183 4025 2.443781 AGGTACTCCAGGACGGCA 59.556 61.111 0.00 0.00 35.89 5.69
1271 4120 0.898326 GGAACAGGACCGGGCAAAAT 60.898 55.000 11.00 0.00 0.00 1.82
1302 4151 0.028110 GAACGAAATCGGCCATCTGC 59.972 55.000 2.24 0.00 44.95 4.26
1392 4246 2.202919 CGATCATCAGGTGGCGCA 60.203 61.111 10.83 0.00 0.00 6.09
1536 4390 3.702048 CGGCCGTCTTCTTGGGGA 61.702 66.667 19.50 0.00 0.00 4.81
1581 4504 4.832608 GGGACTTGGTAGCGGCGG 62.833 72.222 9.78 0.00 0.00 6.13
1582 4505 4.832608 GGGGACTTGGTAGCGGCG 62.833 72.222 0.51 0.51 0.00 6.46
1583 4506 4.484872 GGGGGACTTGGTAGCGGC 62.485 72.222 0.00 0.00 0.00 6.53
1584 4507 2.536997 CTTGGGGGACTTGGTAGCGG 62.537 65.000 0.00 0.00 0.00 5.52
1585 4508 1.078426 CTTGGGGGACTTGGTAGCG 60.078 63.158 0.00 0.00 0.00 4.26
1586 4509 0.696501 TTCTTGGGGGACTTGGTAGC 59.303 55.000 0.00 0.00 0.00 3.58
1587 4510 2.266279 TCTTCTTGGGGGACTTGGTAG 58.734 52.381 0.00 0.00 0.00 3.18
1588 4511 2.426431 TCTTCTTGGGGGACTTGGTA 57.574 50.000 0.00 0.00 0.00 3.25
1589 4512 1.425448 CTTCTTCTTGGGGGACTTGGT 59.575 52.381 0.00 0.00 0.00 3.67
1590 4513 1.272147 CCTTCTTCTTGGGGGACTTGG 60.272 57.143 0.00 0.00 0.00 3.61
1591 4514 1.888391 GCCTTCTTCTTGGGGGACTTG 60.888 57.143 0.00 0.00 0.00 3.16
1592 4515 0.405973 GCCTTCTTCTTGGGGGACTT 59.594 55.000 0.00 0.00 0.00 3.01
1593 4516 0.476611 AGCCTTCTTCTTGGGGGACT 60.477 55.000 0.00 0.00 0.00 3.85
1594 4517 0.322906 CAGCCTTCTTCTTGGGGGAC 60.323 60.000 0.00 0.00 0.00 4.46
1595 4518 2.078452 CAGCCTTCTTCTTGGGGGA 58.922 57.895 0.00 0.00 0.00 4.81
1596 4519 1.680314 GCAGCCTTCTTCTTGGGGG 60.680 63.158 0.00 0.00 0.00 5.40
1597 4520 0.964358 CTGCAGCCTTCTTCTTGGGG 60.964 60.000 0.00 0.00 0.00 4.96
1598 4521 1.593296 GCTGCAGCCTTCTTCTTGGG 61.593 60.000 28.76 0.00 34.31 4.12
1599 4522 1.881602 GCTGCAGCCTTCTTCTTGG 59.118 57.895 28.76 0.00 34.31 3.61
1612 4535 2.875296 ACTCCTTAATTTGTGGCTGCA 58.125 42.857 0.50 0.00 0.00 4.41
1636 4779 4.408993 TTCACAAGATCAATTGCAGACG 57.591 40.909 0.00 0.00 33.28 4.18
1677 4820 6.535150 TCATAGAGATGACAAATGTTCGGAAC 59.465 38.462 13.86 13.86 37.15 3.62
1681 4824 7.531280 AGTTCATAGAGATGACAAATGTTCG 57.469 36.000 0.00 0.00 41.92 3.95
1697 4840 7.153985 GGATGATGGAAGAGAGAAGTTCATAG 58.846 42.308 5.50 0.00 0.00 2.23
1754 4897 3.191371 GGCTGAAATTGAGTACCCTGTTG 59.809 47.826 0.00 0.00 0.00 3.33
1795 5228 6.784473 TGATAGGTCTATGATTGGTGTGATCT 59.216 38.462 0.00 0.00 0.00 2.75
1796 5229 6.997655 TGATAGGTCTATGATTGGTGTGATC 58.002 40.000 0.00 0.00 0.00 2.92
1829 5262 8.932791 GCATGATTCATTCAAAGATTCAGTTTT 58.067 29.630 0.00 0.00 38.03 2.43
1905 5340 7.225538 CGTAGAAGATGGAAATATGCAAACTCT 59.774 37.037 0.00 0.00 0.00 3.24
1941 5376 0.813184 AGCGCCACCATCATTTCTTG 59.187 50.000 2.29 0.00 0.00 3.02
1992 7044 6.788456 GTCTTATATTTAGGAAGGGAGGGAGT 59.212 42.308 0.00 0.00 0.00 3.85
1993 7045 6.071278 CGTCTTATATTTAGGAAGGGAGGGAG 60.071 46.154 0.00 0.00 0.00 4.30
1994 7046 5.778750 CGTCTTATATTTAGGAAGGGAGGGA 59.221 44.000 0.00 0.00 0.00 4.20
1995 7047 5.543020 ACGTCTTATATTTAGGAAGGGAGGG 59.457 44.000 0.00 0.00 0.00 4.30
1996 7048 6.667558 ACGTCTTATATTTAGGAAGGGAGG 57.332 41.667 0.00 0.00 0.00 4.30
1997 7049 8.827677 CAAAACGTCTTATATTTAGGAAGGGAG 58.172 37.037 0.00 0.00 0.00 4.30
1998 7050 8.323567 ACAAAACGTCTTATATTTAGGAAGGGA 58.676 33.333 0.00 0.00 0.00 4.20
1999 7051 8.502105 ACAAAACGTCTTATATTTAGGAAGGG 57.498 34.615 0.00 0.00 0.00 3.95
2045 8193 7.095017 CCCTCTGTTTCTGAATGTTAGAGTTTC 60.095 40.741 14.18 0.00 0.00 2.78
2049 8197 5.641209 CACCCTCTGTTTCTGAATGTTAGAG 59.359 44.000 10.92 10.92 0.00 2.43
2146 8299 3.502211 CGGAAGGTTAAGTTGTCTGCATT 59.498 43.478 0.00 0.00 0.00 3.56
2157 10962 3.004002 GGTTTGTGGTTCGGAAGGTTAAG 59.996 47.826 0.00 0.00 0.00 1.85
2203 11008 0.535797 GGACGGAGGGAGTAGTTTGG 59.464 60.000 0.00 0.00 0.00 3.28
2383 13828 9.710900 ATCTTTTTGATGTCAAAGGAAAATACC 57.289 29.630 8.07 0.00 45.34 2.73
2391 13836 9.196552 GGAGTAAAATCTTTTTGATGTCAAAGG 57.803 33.333 8.07 6.33 45.34 3.11
2523 14025 0.333993 AGGCAAATCAGGTGGCAGAT 59.666 50.000 0.00 0.00 43.68 2.90
2699 14205 0.107831 GTACTTGGCGGGCCATATCA 59.892 55.000 14.03 0.00 46.64 2.15
2749 14255 4.590222 GCCCAATATCCTTGATGTGGATTT 59.410 41.667 0.38 0.00 41.13 2.17
2830 14336 6.486253 TTATGAAACACACTCAGATGCTTC 57.514 37.500 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.