Multiple sequence alignment - TraesCS6B01G301100

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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 TraesCS6B01G301100 chr6B 100.000 4279 0 0 1 4279 539619396 539615118 0.000000e+00 7902.0
1 TraesCS6B01G301100 chr6D 94.542 1814 76 17 41 1834 358220412 358218602 0.000000e+00 2780.0
2 TraesCS6B01G301100 chr6D 86.677 1261 66 48 3044 4234 357872249 357871021 0.000000e+00 1304.0
3 TraesCS6B01G301100 chr6D 89.940 994 57 26 2638 3605 358218026 358217050 0.000000e+00 1242.0
4 TraesCS6B01G301100 chr6D 92.797 472 21 6 1952 2418 358218591 358218128 0.000000e+00 671.0
5 TraesCS6B01G301100 chr6D 89.041 365 21 8 3625 3973 358214001 358213640 6.570000e-118 435.0
6 TraesCS6B01G301100 chr6D 91.026 312 7 4 3971 4274 358212824 358212526 6.660000e-108 401.0
7 TraesCS6B01G301100 chr6D 93.836 146 5 1 2468 2609 358218130 358217985 2.590000e-52 217.0
8 TraesCS6B01G301100 chr6D 85.938 192 17 2 2867 3048 357872478 357872287 3.380000e-46 196.0
9 TraesCS6B01G301100 chr6A 90.705 1958 97 38 544 2445 499800133 499802061 0.000000e+00 2529.0
10 TraesCS6B01G301100 chr6A 91.388 418 24 10 2643 3048 499802862 499803279 2.890000e-156 562.0
11 TraesCS6B01G301100 chr6A 85.276 489 45 13 3103 3575 499803301 499803778 2.990000e-131 479.0
12 TraesCS6B01G301100 chr6A 83.333 552 38 28 3746 4275 499804061 499804580 1.080000e-125 460.0
13 TraesCS6B01G301100 chr6A 96.970 33 0 1 2452 2483 499802828 499802860 2.000000e-03 54.7
14 TraesCS6B01G301100 chr2B 92.157 51 4 0 3146 3196 711166239 711166189 5.940000e-09 73.1
15 TraesCS6B01G301100 chr5D 87.755 49 5 1 141 189 334692573 334692620 5.980000e-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 TraesCS6B01G301100 chr6B 539615118 539619396 4278 True 7902.000000 7902 100.000000 1 4279 1 chr6B.!!$R1 4278
1 TraesCS6B01G301100 chr6D 358212526 358220412 7886 True 957.666667 2780 91.863667 41 4274 6 chr6D.!!$R2 4233
2 TraesCS6B01G301100 chr6D 357871021 357872478 1457 True 750.000000 1304 86.307500 2867 4234 2 chr6D.!!$R1 1367
3 TraesCS6B01G301100 chr6A 499800133 499804580 4447 False 816.940000 2529 89.534400 544 4275 5 chr6A.!!$F1 3731

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
725 735 0.530744 TCTCTGTTCCCGTTGGATCG 59.469 55.0 0.0 0.0 41.4 3.69 F
1963 2015 0.748367 TGCAGTGTTGGTTGGCGTAA 60.748 50.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2234 2291 0.243907 GGCAGTCACGCTCACTAGAA 59.756 55.0 0.0 0.0 0.0 2.10 R
3291 4209 0.248949 GGAACGGACGAGATAGTGGC 60.249 60.0 0.0 0.0 0.0 5.01 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
37 38 9.727859 TGGTTATAGCTTTTTGTTACTATCACA 57.272 29.630 0.00 0.00 0.00 3.58
51 52 5.762179 ACTATCACAAAAGTGGATGAGGA 57.238 39.130 0.00 0.00 0.00 3.71
57 58 1.523758 AAAGTGGATGAGGACAACGC 58.476 50.000 0.00 0.00 0.00 4.84
112 113 3.643792 GCTAGTTGGTCCATAGATCTGGT 59.356 47.826 5.18 0.00 37.57 4.00
113 114 4.101741 GCTAGTTGGTCCATAGATCTGGTT 59.898 45.833 5.18 0.00 37.57 3.67
166 167 9.517609 GTTCTTTGTACTATCGTGACAGATTAT 57.482 33.333 0.00 0.00 32.39 1.28
285 287 9.657121 AAAACGTGCCATTTTTATAAATTTGTG 57.343 25.926 0.00 0.00 31.63 3.33
350 355 8.599774 GCAGTTTTAAAGTTTAGCATGTCAAAA 58.400 29.630 0.00 0.00 0.00 2.44
539 549 0.892755 TCGAGCGACAGTTATTGGGT 59.107 50.000 0.00 0.00 0.00 4.51
546 556 4.004982 GCGACAGTTATTGGGTCCTAAAA 58.995 43.478 0.00 0.00 0.00 1.52
620 630 1.821216 AGTAGGATGGGTTTGTTGCG 58.179 50.000 0.00 0.00 0.00 4.85
635 645 4.481112 GCGCCAAGCCACCAATCG 62.481 66.667 0.00 0.00 40.81 3.34
642 652 2.083774 CAAGCCACCAATCGAAGCTAA 58.916 47.619 0.00 0.00 32.39 3.09
725 735 0.530744 TCTCTGTTCCCGTTGGATCG 59.469 55.000 0.00 0.00 41.40 3.69
852 863 2.418333 CGTCGTCGCGTTCTCACAG 61.418 63.158 5.77 0.00 0.00 3.66
877 897 3.465403 CTGACCCCTGCTCCTCCG 61.465 72.222 0.00 0.00 0.00 4.63
991 1016 2.345991 GTAGGCACGGCAAGGTCA 59.654 61.111 0.00 0.00 0.00 4.02
1140 1165 2.668212 CACGCCGGCAAGAAAGGA 60.668 61.111 28.98 0.00 0.00 3.36
1161 1186 3.785859 ACCATCAGCCCGCACGAT 61.786 61.111 0.00 0.00 0.00 3.73
1491 1528 2.643232 GGTCGGGTTCAGCTACGGT 61.643 63.158 0.00 0.00 0.00 4.83
1662 1699 3.249189 ACGCTCCAGGGGCTCAAA 61.249 61.111 10.45 0.00 0.00 2.69
1759 1800 6.208988 TCAAGTTAGCACACCTATGTCTAG 57.791 41.667 0.00 0.00 36.72 2.43
1839 1882 9.444600 TTTTGGAATTGACATAGTAGTAGTTCC 57.555 33.333 0.00 0.00 34.61 3.62
1937 1987 6.785191 CACACATAGTGTTTTCTGTTTGTCT 58.215 36.000 0.00 0.00 45.08 3.41
1940 1990 5.299279 ACATAGTGTTTTCTGTTTGTCTGGG 59.701 40.000 0.00 0.00 0.00 4.45
1942 1992 4.340617 AGTGTTTTCTGTTTGTCTGGGAA 58.659 39.130 0.00 0.00 0.00 3.97
1959 2011 1.501169 GAAATGCAGTGTTGGTTGGC 58.499 50.000 0.00 0.00 0.00 4.52
1963 2015 0.748367 TGCAGTGTTGGTTGGCGTAA 60.748 50.000 0.00 0.00 0.00 3.18
1979 2031 4.009002 GGCGTAATTTGGGTGGTTAACTA 58.991 43.478 5.42 0.00 0.00 2.24
1985 2037 4.857509 TTTGGGTGGTTAACTAATGCAC 57.142 40.909 5.42 4.60 0.00 4.57
1989 2041 3.371898 GGGTGGTTAACTAATGCACGTAC 59.628 47.826 5.42 0.00 0.00 3.67
2128 2183 4.037565 GGTAAGTAAGCAGTGCCTTTGTTT 59.962 41.667 12.58 0.37 0.00 2.83
2189 2246 7.827236 CCTACCTATATTGTTCTGTTCACCAAA 59.173 37.037 0.00 0.00 0.00 3.28
2201 2258 4.590918 TGTTCACCAAACCTGTCTTACAA 58.409 39.130 0.00 0.00 37.03 2.41
2234 2291 2.256117 ACGAAAGCAGTTGCCTAGTT 57.744 45.000 0.00 0.00 43.38 2.24
2239 2296 4.092091 CGAAAGCAGTTGCCTAGTTTCTAG 59.908 45.833 11.99 0.00 43.38 2.43
2240 2297 4.625607 AAGCAGTTGCCTAGTTTCTAGT 57.374 40.909 0.00 0.00 43.38 2.57
2241 2298 3.931578 AGCAGTTGCCTAGTTTCTAGTG 58.068 45.455 0.00 0.00 43.38 2.74
2242 2299 3.578716 AGCAGTTGCCTAGTTTCTAGTGA 59.421 43.478 0.00 0.00 43.38 3.41
2243 2300 3.929610 GCAGTTGCCTAGTTTCTAGTGAG 59.070 47.826 0.00 0.00 34.31 3.51
2244 2301 3.929610 CAGTTGCCTAGTTTCTAGTGAGC 59.070 47.826 3.62 1.35 0.00 4.26
2349 2427 6.826893 TGCAAACTTTTCTTTAAGCATGTC 57.173 33.333 0.00 0.00 0.00 3.06
2380 2462 5.586243 TCAATGAGTTGCCTCTGTAATTAGC 59.414 40.000 0.00 0.00 38.61 3.09
2445 2527 2.212812 TGTATGGGCAATGCTTGTGA 57.787 45.000 4.82 0.00 0.00 3.58
2446 2528 1.818060 TGTATGGGCAATGCTTGTGAC 59.182 47.619 4.82 0.00 0.00 3.67
2447 2529 2.094675 GTATGGGCAATGCTTGTGACT 58.905 47.619 4.82 0.00 0.00 3.41
2448 2530 1.636148 ATGGGCAATGCTTGTGACTT 58.364 45.000 4.82 0.00 0.00 3.01
2449 2531 2.284754 TGGGCAATGCTTGTGACTTA 57.715 45.000 4.82 0.00 0.00 2.24
2450 2532 1.885887 TGGGCAATGCTTGTGACTTAC 59.114 47.619 4.82 0.00 0.00 2.34
2451 2533 2.162681 GGGCAATGCTTGTGACTTACT 58.837 47.619 4.82 0.00 0.00 2.24
2452 2534 2.095059 GGGCAATGCTTGTGACTTACTG 60.095 50.000 4.82 0.00 0.00 2.74
2453 2535 2.095059 GGCAATGCTTGTGACTTACTGG 60.095 50.000 4.82 0.00 0.00 4.00
2454 2536 2.669391 GCAATGCTTGTGACTTACTGGC 60.669 50.000 0.00 0.00 0.00 4.85
2509 3352 2.304761 TCCATTTCTTTAGGGACTGCGT 59.695 45.455 0.00 0.00 41.52 5.24
2519 3362 1.568025 GGACTGCGTCCGTGTTTTC 59.432 57.895 11.11 0.00 43.14 2.29
2538 3385 6.644592 TGTTTTCTCTTGTTTGAAACCAACTG 59.355 34.615 5.50 0.00 32.72 3.16
2539 3386 4.370364 TCTCTTGTTTGAAACCAACTGC 57.630 40.909 5.50 0.00 0.00 4.40
2574 3421 2.288948 GGCATGCAAAATGGTCTGTTCA 60.289 45.455 21.36 0.00 0.00 3.18
2609 3456 7.694093 AGAAGAACAAAATGGTCTCTATTCCT 58.306 34.615 0.00 0.00 45.11 3.36
2610 3457 8.166726 AGAAGAACAAAATGGTCTCTATTCCTT 58.833 33.333 0.00 0.00 45.11 3.36
2611 3458 8.712228 AAGAACAAAATGGTCTCTATTCCTTT 57.288 30.769 0.00 0.00 45.11 3.11
2612 3459 8.712228 AGAACAAAATGGTCTCTATTCCTTTT 57.288 30.769 0.00 0.00 41.32 2.27
2613 3460 9.147732 AGAACAAAATGGTCTCTATTCCTTTTT 57.852 29.630 0.00 0.00 41.32 1.94
2644 3491 9.449719 TTTTGAGAAACTAATGGTCTCTATTCC 57.550 33.333 0.00 0.00 38.87 3.01
2645 3492 7.733773 TGAGAAACTAATGGTCTCTATTCCA 57.266 36.000 0.00 0.00 38.87 3.53
2646 3493 8.324191 TGAGAAACTAATGGTCTCTATTCCAT 57.676 34.615 0.00 0.00 45.06 3.41
2676 3523 9.847224 TTTTGAGGTAATAATGGTCTCTATTCC 57.153 33.333 0.00 0.00 0.00 3.01
2727 3574 1.545582 TGGGCTTTAAATCTGTGCTGC 59.454 47.619 0.00 0.00 0.00 5.25
2728 3575 1.821136 GGGCTTTAAATCTGTGCTGCT 59.179 47.619 0.00 0.00 0.00 4.24
2742 3589 0.673644 GCTGCTCGTGGGCTCTAAAA 60.674 55.000 0.00 0.00 0.00 1.52
2759 3606 1.568504 AAACTGAGATGGGCCGAGTA 58.431 50.000 0.00 0.00 0.00 2.59
2781 3628 3.269643 ACTTGGGCCCTTAATCTAAGCTT 59.730 43.478 25.70 3.48 34.46 3.74
2791 3638 6.291377 CCTTAATCTAAGCTTGGCATGTCTA 58.709 40.000 9.86 0.00 34.46 2.59
2817 3668 1.657804 AACTAAGCTAGGCCACCACT 58.342 50.000 5.01 0.00 0.00 4.00
2848 3699 1.468054 GCAACCTAGCGCTGAATTTGG 60.468 52.381 22.90 14.08 0.00 3.28
3030 3898 5.344884 AGATGAAAGAGTAAGCTTCTACGC 58.655 41.667 0.00 0.00 0.00 4.42
3053 3963 2.355444 CACGCATTCCAGTTCATGCATA 59.645 45.455 0.00 0.00 45.23 3.14
3125 4043 0.593128 AACAAAGCTGACGGTGCATC 59.407 50.000 0.00 0.00 0.00 3.91
3291 4209 0.987715 CAGTTGAGTCGATCACTGCG 59.012 55.000 3.01 0.00 37.77 5.18
3292 4210 0.734253 AGTTGAGTCGATCACTGCGC 60.734 55.000 0.00 0.00 37.77 6.09
3304 4226 0.867753 CACTGCGCCACTATCTCGTC 60.868 60.000 4.18 0.00 0.00 4.20
3384 4316 0.028902 GTTGGTTCGTCTGCAACACC 59.971 55.000 0.00 0.00 0.00 4.16
3385 4317 1.433053 TTGGTTCGTCTGCAACACCG 61.433 55.000 0.00 0.00 28.55 4.94
3386 4318 2.248431 GTTCGTCTGCAACACCGC 59.752 61.111 0.00 0.00 0.00 5.68
3387 4319 2.202946 TTCGTCTGCAACACCGCA 60.203 55.556 0.00 0.00 40.32 5.69
3389 4321 4.012895 CGTCTGCAACACCGCACC 62.013 66.667 0.00 0.00 36.86 5.01
3390 4322 4.012895 GTCTGCAACACCGCACCG 62.013 66.667 0.00 0.00 36.86 4.94
3427 4359 0.257039 AGAGGTCAACCCATGGATGC 59.743 55.000 15.22 8.11 36.42 3.91
3455 4387 6.873076 AGCTAGCCATTACTACTACTACTACG 59.127 42.308 12.13 0.00 0.00 3.51
3456 4388 6.648725 GCTAGCCATTACTACTACTACTACGT 59.351 42.308 2.29 0.00 0.00 3.57
3459 4391 6.931840 AGCCATTACTACTACTACTACGTACC 59.068 42.308 0.00 0.00 0.00 3.34
3475 4421 2.191786 TACCACTGGCCACATTCCGG 62.192 60.000 0.00 0.00 36.07 5.14
3519 4465 1.515519 GTTGACGCCACGCTCGATA 60.516 57.895 0.00 0.00 0.00 2.92
3556 4503 5.333566 TTTATTTCCTCCTGTTCCTGGTT 57.666 39.130 0.00 0.00 0.00 3.67
3602 4559 0.040425 ACTTTTGTGGACGCGATTGC 60.040 50.000 15.93 0.00 37.91 3.56
3612 7603 3.486263 GCGATTGCGGTGCTACTT 58.514 55.556 0.00 0.00 38.16 2.24
3613 7604 1.794222 GCGATTGCGGTGCTACTTT 59.206 52.632 0.00 0.00 38.16 2.66
3614 7605 0.168128 GCGATTGCGGTGCTACTTTT 59.832 50.000 0.00 0.00 38.16 2.27
3615 7606 1.790481 GCGATTGCGGTGCTACTTTTC 60.790 52.381 0.00 0.00 38.16 2.29
3618 7609 3.492313 GATTGCGGTGCTACTTTTCTTG 58.508 45.455 0.00 0.00 0.00 3.02
3619 7610 1.961793 TGCGGTGCTACTTTTCTTGT 58.038 45.000 0.00 0.00 0.00 3.16
3620 7611 2.294074 TGCGGTGCTACTTTTCTTGTT 58.706 42.857 0.00 0.00 0.00 2.83
3621 7612 2.289547 TGCGGTGCTACTTTTCTTGTTC 59.710 45.455 0.00 0.00 0.00 3.18
3622 7613 2.548480 GCGGTGCTACTTTTCTTGTTCT 59.452 45.455 0.00 0.00 0.00 3.01
3623 7614 3.003378 GCGGTGCTACTTTTCTTGTTCTT 59.997 43.478 0.00 0.00 0.00 2.52
3649 7640 1.580942 CCGACGAGGAAACGGTACA 59.419 57.895 0.00 0.00 45.00 2.90
3651 7642 1.055338 CGACGAGGAAACGGTACAAC 58.945 55.000 0.00 0.00 37.61 3.32
3652 7643 1.600164 CGACGAGGAAACGGTACAACA 60.600 52.381 0.00 0.00 37.61 3.33
3653 7644 1.788886 GACGAGGAAACGGTACAACAC 59.211 52.381 0.00 0.00 37.61 3.32
3700 7700 4.060038 GGTGTGGGCATGCACAGC 62.060 66.667 26.16 22.55 41.53 4.40
3967 8094 1.377072 TCGATCGTACGGTCCACCA 60.377 57.895 22.21 1.65 35.14 4.17
4037 8990 2.180204 CATCCGATGTTGGGCCGTC 61.180 63.158 0.00 0.00 0.00 4.79
4223 9193 0.742990 CTCGTAAATTCGCCAGCCCA 60.743 55.000 0.00 0.00 0.00 5.36
4275 9245 0.685097 CCGGGAGAGAAACCAACAGA 59.315 55.000 0.00 0.00 0.00 3.41
4276 9246 1.338200 CCGGGAGAGAAACCAACAGAG 60.338 57.143 0.00 0.00 0.00 3.35
4277 9247 1.344763 CGGGAGAGAAACCAACAGAGT 59.655 52.381 0.00 0.00 0.00 3.24
4278 9248 2.772287 GGGAGAGAAACCAACAGAGTG 58.228 52.381 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 9.727859 TGTGATAGTAACAAAAAGCTATAACCA 57.272 29.630 0.00 0.00 28.72 3.67
35 36 2.878406 CGTTGTCCTCATCCACTTTTGT 59.122 45.455 0.00 0.00 0.00 2.83
36 37 2.350772 GCGTTGTCCTCATCCACTTTTG 60.351 50.000 0.00 0.00 0.00 2.44
37 38 1.880027 GCGTTGTCCTCATCCACTTTT 59.120 47.619 0.00 0.00 0.00 2.27
38 39 1.523758 GCGTTGTCCTCATCCACTTT 58.476 50.000 0.00 0.00 0.00 2.66
39 40 0.670546 CGCGTTGTCCTCATCCACTT 60.671 55.000 0.00 0.00 0.00 3.16
40 41 1.079819 CGCGTTGTCCTCATCCACT 60.080 57.895 0.00 0.00 0.00 4.00
41 42 1.352156 GACGCGTTGTCCTCATCCAC 61.352 60.000 15.53 0.00 42.04 4.02
42 43 1.080093 GACGCGTTGTCCTCATCCA 60.080 57.895 15.53 0.00 42.04 3.41
43 44 3.782042 GACGCGTTGTCCTCATCC 58.218 61.111 15.53 0.00 42.04 3.51
51 52 4.751098 TGGAATAAACTAAAGACGCGTTGT 59.249 37.500 15.53 0.00 0.00 3.32
57 58 7.127686 ACAAACGTTGGAATAAACTAAAGACG 58.872 34.615 10.33 0.00 34.12 4.18
87 88 4.219507 CAGATCTATGGACCAACTAGCGAT 59.780 45.833 0.00 0.00 0.00 4.58
152 153 8.045176 TCGATCTATTCATAATCTGTCACGAT 57.955 34.615 0.00 0.00 0.00 3.73
196 197 7.718753 ACTGCCATCCTCTAGATAAGATTTTTG 59.281 37.037 0.00 0.00 32.37 2.44
208 210 8.738645 ACTTTATAAAAACTGCCATCCTCTAG 57.261 34.615 0.00 0.00 0.00 2.43
210 212 7.283354 GCTACTTTATAAAAACTGCCATCCTCT 59.717 37.037 0.00 0.00 0.00 3.69
248 250 7.546778 AAATGGCACGTTTTGAAAAATTACT 57.453 28.000 0.00 0.00 0.00 2.24
249 251 8.608102 AAAAATGGCACGTTTTGAAAAATTAC 57.392 26.923 9.29 0.00 29.05 1.89
260 262 7.800847 GCACAAATTTATAAAAATGGCACGTTT 59.199 29.630 14.50 0.00 35.46 3.60
261 263 7.294473 GCACAAATTTATAAAAATGGCACGTT 58.706 30.769 14.50 0.00 35.46 3.99
262 264 6.400515 CGCACAAATTTATAAAAATGGCACGT 60.401 34.615 14.50 0.00 35.46 4.49
294 296 9.288576 CTTCTAGATATAAATGACATTGGCCAA 57.711 33.333 23.00 23.00 0.00 4.52
296 298 9.678260 ATCTTCTAGATATAAATGACATTGGCC 57.322 33.333 0.34 0.00 32.12 5.36
428 436 0.178947 AGCCCCGATTGACCCAAAAA 60.179 50.000 0.00 0.00 0.00 1.94
474 484 1.153349 CCTAGCGACCCTTTCTGGC 60.153 63.158 0.00 0.00 0.00 4.85
601 611 1.821216 CGCAACAAACCCATCCTACT 58.179 50.000 0.00 0.00 0.00 2.57
620 630 1.508088 CTTCGATTGGTGGCTTGGC 59.492 57.895 0.00 0.00 0.00 4.52
635 645 0.643820 ATGCGCGTACGTTTAGCTTC 59.356 50.000 17.90 0.00 42.83 3.86
642 652 2.663478 CCACACATGCGCGTACGTT 61.663 57.895 17.90 0.00 42.83 3.99
725 735 0.750911 ATAGGGCAGCAGCAAGAAGC 60.751 55.000 2.65 0.00 44.61 3.86
883 903 1.346722 CGGGCTTGTATTAGTAGGGGG 59.653 57.143 0.00 0.00 0.00 5.40
988 1013 2.039084 AGTTCACCATCTTCCCTGTGAC 59.961 50.000 0.00 0.00 37.46 3.67
991 1016 2.711009 TCAAGTTCACCATCTTCCCTGT 59.289 45.455 0.00 0.00 0.00 4.00
1095 1120 2.672996 GCCCAGACGTGCATGGTT 60.673 61.111 11.36 0.00 34.58 3.67
1140 1165 3.965258 TGCGGGCTGATGGTGGTT 61.965 61.111 0.00 0.00 0.00 3.67
1252 1289 2.112297 GACCACGTTGGGCTTGGA 59.888 61.111 8.57 0.00 44.12 3.53
1491 1528 2.203408 TTGAACGCCACCATGCCA 60.203 55.556 0.00 0.00 0.00 4.92
1588 1625 2.765807 CCGCTCCATGGTCTCCCT 60.766 66.667 12.58 0.00 0.00 4.20
1662 1699 2.411504 GGAGACGGAGAAGAGCGCT 61.412 63.158 11.27 11.27 0.00 5.92
1740 1777 6.095720 AGAGTTCTAGACATAGGTGTGCTAAC 59.904 42.308 0.00 0.00 39.09 2.34
1741 1778 6.188407 AGAGTTCTAGACATAGGTGTGCTAA 58.812 40.000 0.00 0.00 39.09 3.09
1742 1779 5.756918 AGAGTTCTAGACATAGGTGTGCTA 58.243 41.667 0.00 0.00 39.09 3.49
1857 1900 9.545105 ACAACAATTCAAGAAAATCAGCATTTA 57.455 25.926 0.00 0.00 31.51 1.40
1915 1965 6.201517 CCAGACAAACAGAAAACACTATGTG 58.798 40.000 0.00 0.00 39.75 3.21
1917 1967 5.530915 TCCCAGACAAACAGAAAACACTATG 59.469 40.000 0.00 0.00 0.00 2.23
1918 1968 5.690865 TCCCAGACAAACAGAAAACACTAT 58.309 37.500 0.00 0.00 0.00 2.12
1924 1974 4.161189 TGCATTTCCCAGACAAACAGAAAA 59.839 37.500 0.00 0.00 30.86 2.29
1925 1975 3.703556 TGCATTTCCCAGACAAACAGAAA 59.296 39.130 0.00 0.00 0.00 2.52
1928 1978 2.624838 ACTGCATTTCCCAGACAAACAG 59.375 45.455 0.00 0.00 34.47 3.16
1930 1980 2.362077 ACACTGCATTTCCCAGACAAAC 59.638 45.455 0.00 0.00 34.47 2.93
1935 1985 1.133513 ACCAACACTGCATTTCCCAGA 60.134 47.619 0.00 0.00 34.47 3.86
1936 1986 1.331214 ACCAACACTGCATTTCCCAG 58.669 50.000 0.00 0.00 36.41 4.45
1937 1987 1.411977 CAACCAACACTGCATTTCCCA 59.588 47.619 0.00 0.00 0.00 4.37
1940 1990 1.501169 GCCAACCAACACTGCATTTC 58.499 50.000 0.00 0.00 0.00 2.17
1942 1992 1.363443 CGCCAACCAACACTGCATT 59.637 52.632 0.00 0.00 0.00 3.56
1959 2011 6.031471 GCATTAGTTAACCACCCAAATTACG 58.969 40.000 0.88 0.00 0.00 3.18
1963 2015 4.082463 CGTGCATTAGTTAACCACCCAAAT 60.082 41.667 0.88 0.00 0.00 2.32
1979 2031 3.049206 GCAAAACACATGTACGTGCATT 58.951 40.909 16.99 6.78 40.73 3.56
1985 2037 3.485378 CACCAAAGCAAAACACATGTACG 59.515 43.478 0.00 0.00 0.00 3.67
1989 2041 4.370049 TCATCACCAAAGCAAAACACATG 58.630 39.130 0.00 0.00 0.00 3.21
2128 2183 3.626930 AGGTGTTGCTTGGTTTGACTTA 58.373 40.909 0.00 0.00 0.00 2.24
2178 2235 4.196193 TGTAAGACAGGTTTGGTGAACAG 58.804 43.478 0.00 0.00 40.13 3.16
2189 2246 2.054799 TCAGGCCTTTGTAAGACAGGT 58.945 47.619 0.00 0.00 0.00 4.00
2201 2258 2.222027 CTTTCGTTTCAGTCAGGCCTT 58.778 47.619 0.00 0.00 0.00 4.35
2234 2291 0.243907 GGCAGTCACGCTCACTAGAA 59.756 55.000 0.00 0.00 0.00 2.10
2239 2296 0.593128 AATTTGGCAGTCACGCTCAC 59.407 50.000 0.00 0.00 0.00 3.51
2240 2297 0.592637 CAATTTGGCAGTCACGCTCA 59.407 50.000 0.00 0.00 0.00 4.26
2241 2298 0.730494 GCAATTTGGCAGTCACGCTC 60.730 55.000 0.00 0.00 0.00 5.03
2242 2299 1.286880 GCAATTTGGCAGTCACGCT 59.713 52.632 0.00 0.00 0.00 5.07
2243 2300 0.597118 TTGCAATTTGGCAGTCACGC 60.597 50.000 0.00 0.00 45.88 5.34
2244 2301 1.850377 TTTGCAATTTGGCAGTCACG 58.150 45.000 0.00 0.00 45.88 4.35
2380 2462 1.359459 GCCTAACGGGAGCAAAGTCG 61.359 60.000 0.00 0.00 37.23 4.18
2445 2527 0.977395 GTCCCTGACTGCCAGTAAGT 59.023 55.000 8.43 0.00 41.33 2.24
2446 2528 1.270907 AGTCCCTGACTGCCAGTAAG 58.729 55.000 1.80 1.80 41.76 2.34
2447 2529 3.475932 AGTCCCTGACTGCCAGTAA 57.524 52.632 0.00 0.00 41.76 2.24
2509 3352 5.395642 GTTTCAAACAAGAGAAAACACGGA 58.604 37.500 0.00 0.00 35.71 4.69
2519 3362 3.108144 CGCAGTTGGTTTCAAACAAGAG 58.892 45.455 1.93 0.00 34.28 2.85
2538 3385 2.353030 GCCAACAAACACGGACGC 60.353 61.111 0.00 0.00 0.00 5.19
2539 3386 0.660005 CATGCCAACAAACACGGACG 60.660 55.000 0.00 0.00 0.00 4.79
2618 3465 9.449719 GGAATAGAGACCATTAGTTTCTCAAAA 57.550 33.333 0.00 0.00 39.13 2.44
2619 3466 8.602424 TGGAATAGAGACCATTAGTTTCTCAAA 58.398 33.333 0.00 0.00 39.13 2.69
2620 3467 8.146053 TGGAATAGAGACCATTAGTTTCTCAA 57.854 34.615 0.00 0.00 39.13 3.02
2621 3468 7.733773 TGGAATAGAGACCATTAGTTTCTCA 57.266 36.000 0.00 0.00 39.13 3.27
2650 3497 9.847224 GGAATAGAGACCATTATTACCTCAAAA 57.153 33.333 0.00 0.00 0.00 2.44
2651 3498 8.998814 TGGAATAGAGACCATTATTACCTCAAA 58.001 33.333 0.00 0.00 0.00 2.69
2652 3499 8.561536 TGGAATAGAGACCATTATTACCTCAA 57.438 34.615 0.00 0.00 0.00 3.02
2653 3500 8.561536 TTGGAATAGAGACCATTATTACCTCA 57.438 34.615 0.00 0.00 36.02 3.86
2654 3501 8.097662 CCTTGGAATAGAGACCATTATTACCTC 58.902 40.741 0.00 0.00 36.02 3.85
2655 3502 7.794683 TCCTTGGAATAGAGACCATTATTACCT 59.205 37.037 0.00 0.00 36.02 3.08
2656 3503 7.974504 TCCTTGGAATAGAGACCATTATTACC 58.025 38.462 0.00 0.00 36.02 2.85
2657 3504 8.097662 CCTCCTTGGAATAGAGACCATTATTAC 58.902 40.741 0.00 0.00 38.35 1.89
2658 3505 7.237679 CCCTCCTTGGAATAGAGACCATTATTA 59.762 40.741 0.00 0.00 38.35 0.98
2659 3506 6.044871 CCCTCCTTGGAATAGAGACCATTATT 59.955 42.308 0.00 0.00 38.35 1.40
2660 3507 5.549619 CCCTCCTTGGAATAGAGACCATTAT 59.450 44.000 0.00 0.00 38.35 1.28
2661 3508 4.907875 CCCTCCTTGGAATAGAGACCATTA 59.092 45.833 0.00 0.00 38.35 1.90
2662 3509 3.718956 CCCTCCTTGGAATAGAGACCATT 59.281 47.826 0.00 0.00 38.35 3.16
2663 3510 3.311702 ACCCTCCTTGGAATAGAGACCAT 60.312 47.826 0.00 0.00 38.35 3.55
2664 3511 2.045885 ACCCTCCTTGGAATAGAGACCA 59.954 50.000 0.00 0.00 38.35 4.02
2665 3512 2.765502 ACCCTCCTTGGAATAGAGACC 58.234 52.381 0.00 0.00 38.35 3.85
2666 3513 4.471747 AGAAACCCTCCTTGGAATAGAGAC 59.528 45.833 0.00 0.00 38.35 3.36
2667 3514 4.699994 AGAAACCCTCCTTGGAATAGAGA 58.300 43.478 0.00 0.00 38.35 3.10
2668 3515 5.432645 GAAGAAACCCTCCTTGGAATAGAG 58.567 45.833 0.00 0.00 38.35 2.43
2669 3516 4.081087 CGAAGAAACCCTCCTTGGAATAGA 60.081 45.833 0.00 0.00 38.35 1.98
2670 3517 4.192317 CGAAGAAACCCTCCTTGGAATAG 58.808 47.826 0.00 0.00 38.35 1.73
2671 3518 3.054655 CCGAAGAAACCCTCCTTGGAATA 60.055 47.826 0.00 0.00 38.35 1.75
2672 3519 2.290960 CCGAAGAAACCCTCCTTGGAAT 60.291 50.000 0.00 0.00 38.35 3.01
2673 3520 1.073284 CCGAAGAAACCCTCCTTGGAA 59.927 52.381 0.00 0.00 38.35 3.53
2674 3521 0.690762 CCGAAGAAACCCTCCTTGGA 59.309 55.000 0.00 0.00 38.35 3.53
2675 3522 0.400594 ACCGAAGAAACCCTCCTTGG 59.599 55.000 0.00 0.00 0.00 3.61
2676 3523 3.412237 TTACCGAAGAAACCCTCCTTG 57.588 47.619 0.00 0.00 0.00 3.61
2727 3574 2.231478 TCTCAGTTTTAGAGCCCACGAG 59.769 50.000 0.00 0.00 33.15 4.18
2728 3575 2.244695 TCTCAGTTTTAGAGCCCACGA 58.755 47.619 0.00 0.00 33.15 4.35
2742 3589 0.033011 AGTACTCGGCCCATCTCAGT 60.033 55.000 0.00 0.00 0.00 3.41
2759 3606 2.853077 AGCTTAGATTAAGGGCCCAAGT 59.147 45.455 27.56 11.59 36.31 3.16
3030 3898 1.730121 GCATGAACTGGAATGCGTGTG 60.730 52.381 0.00 0.00 39.78 3.82
3070 3980 3.916035 TGCTCATGGTCATAGTCCTACT 58.084 45.455 0.00 0.00 0.00 2.57
3071 3981 4.672587 TTGCTCATGGTCATAGTCCTAC 57.327 45.455 0.00 0.00 0.00 3.18
3072 3982 5.894298 ATTTGCTCATGGTCATAGTCCTA 57.106 39.130 0.00 0.00 0.00 2.94
3084 4002 5.484173 TTAGCCGAGTTAATTTGCTCATG 57.516 39.130 8.87 0.00 33.63 3.07
3291 4209 0.248949 GGAACGGACGAGATAGTGGC 60.249 60.000 0.00 0.00 0.00 5.01
3292 4210 1.065701 CTGGAACGGACGAGATAGTGG 59.934 57.143 0.00 0.00 36.31 4.00
3304 4226 5.746990 ATAATTATCCTCCTCTGGAACGG 57.253 43.478 0.00 0.00 39.85 4.44
3427 4359 5.692613 AGTAGTAGTAATGGCTAGCTTCG 57.307 43.478 15.72 0.00 0.00 3.79
3455 4387 1.024579 CGGAATGTGGCCAGTGGTAC 61.025 60.000 5.11 11.09 0.00 3.34
3456 4388 1.298340 CGGAATGTGGCCAGTGGTA 59.702 57.895 5.11 0.00 0.00 3.25
3475 4421 2.031682 CACTTAATAATCTGCAGGGCGC 60.032 50.000 15.13 0.00 42.89 6.53
3519 4465 1.388547 ATAAAACGCCATCACGCCAT 58.611 45.000 0.00 0.00 36.19 4.40
3556 4503 6.227522 TGTAGTAGCATCAAAGCAAACAGTA 58.772 36.000 0.00 0.00 36.85 2.74
3602 4559 4.035208 ACAAGAACAAGAAAAGTAGCACCG 59.965 41.667 0.00 0.00 0.00 4.94
3608 7599 6.096695 GGCAACAACAAGAACAAGAAAAGTA 58.903 36.000 0.00 0.00 0.00 2.24
3610 7601 4.031652 CGGCAACAACAAGAACAAGAAAAG 59.968 41.667 0.00 0.00 0.00 2.27
3612 7603 3.191581 TCGGCAACAACAAGAACAAGAAA 59.808 39.130 0.00 0.00 0.00 2.52
3613 7604 2.750166 TCGGCAACAACAAGAACAAGAA 59.250 40.909 0.00 0.00 0.00 2.52
3614 7605 2.096819 GTCGGCAACAACAAGAACAAGA 59.903 45.455 0.00 0.00 0.00 3.02
3615 7606 2.450160 GTCGGCAACAACAAGAACAAG 58.550 47.619 0.00 0.00 0.00 3.16
3618 7609 0.653636 TCGTCGGCAACAACAAGAAC 59.346 50.000 0.00 0.00 0.00 3.01
3619 7610 0.934496 CTCGTCGGCAACAACAAGAA 59.066 50.000 0.00 0.00 0.00 2.52
3620 7611 0.878523 CCTCGTCGGCAACAACAAGA 60.879 55.000 0.00 0.00 0.00 3.02
3621 7612 0.878523 TCCTCGTCGGCAACAACAAG 60.879 55.000 0.00 0.00 0.00 3.16
3622 7613 0.462225 TTCCTCGTCGGCAACAACAA 60.462 50.000 0.00 0.00 0.00 2.83
3623 7614 0.462225 TTTCCTCGTCGGCAACAACA 60.462 50.000 0.00 0.00 0.00 3.33
3649 7640 3.264947 CATCATCATCCACGACTGTGTT 58.735 45.455 0.00 0.00 44.92 3.32
3651 7642 1.596260 GCATCATCATCCACGACTGTG 59.404 52.381 0.00 0.00 46.00 3.66
3652 7643 1.483827 AGCATCATCATCCACGACTGT 59.516 47.619 0.00 0.00 0.00 3.55
3653 7644 1.865340 CAGCATCATCATCCACGACTG 59.135 52.381 0.00 0.00 0.00 3.51
3700 7700 4.374702 GCGCGCTCTGTGTTGTGG 62.375 66.667 26.67 0.00 0.00 4.17
3705 7705 4.889856 TGTGTGCGCGCTCTGTGT 62.890 61.111 33.29 0.00 0.00 3.72
3967 8094 2.901840 CACTGTTGGTGGTGCGCT 60.902 61.111 9.73 0.00 41.90 5.92
4032 8985 2.281276 AAAACTGTCCCGGACGGC 60.281 61.111 24.15 0.00 42.17 5.68
4037 8990 1.602605 GGGTGGAAAACTGTCCCGG 60.603 63.158 0.00 0.00 36.80 5.73
4223 9193 2.394632 TGTAGATGCGGGAGTACCATT 58.605 47.619 0.00 0.00 40.22 3.16


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

AutoCloner maintained by Alex Coulton.