Multiple sequence alignment - TraesCS7D01G383100

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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 TraesCS7D01G383100 chr7D 100.000 3248 0 0 1 3248 496784466 496787713 0.000000e+00 5999.0
1 TraesCS7D01G383100 chr7A 93.555 2948 136 24 348 3248 562214965 562217905 0.000000e+00 4342.0
2 TraesCS7D01G383100 chr7A 93.023 86 5 1 231 315 562175371 562175456 1.220000e-24 124.0
3 TraesCS7D01G383100 chr7B 91.522 2878 179 26 425 3248 524918644 524921510 0.000000e+00 3903.0
4 TraesCS7D01G383100 chr7B 83.562 219 14 9 102 314 524916762 524916964 5.530000e-43 185.0
5 TraesCS7D01G383100 chr1D 89.430 1457 124 16 1032 2461 436654306 436652853 0.000000e+00 1810.0
6 TraesCS7D01G383100 chr1A 88.595 1473 136 15 1032 2476 533733799 533732331 0.000000e+00 1760.0
7 TraesCS7D01G383100 chr1B 88.714 1400 123 15 1032 2399 591451883 591450487 0.000000e+00 1677.0
8 TraesCS7D01G383100 chr2D 81.579 190 22 9 604 790 586788911 586788732 9.390000e-31 145.0
9 TraesCS7D01G383100 chr2A 79.487 195 22 9 614 792 721598890 721598698 4.400000e-24 122.0
10 TraesCS7D01G383100 chr3A 84.783 92 9 5 603 693 556989602 556989689 1.610000e-13 87.9
11 TraesCS7D01G383100 chr6D 100.000 28 0 0 180 207 468007508 468007481 6.000000e-03 52.8


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 TraesCS7D01G383100 chr7D 496784466 496787713 3247 False 5999 5999 100.000 1 3248 1 chr7D.!!$F1 3247
1 TraesCS7D01G383100 chr7A 562214965 562217905 2940 False 4342 4342 93.555 348 3248 1 chr7A.!!$F2 2900
2 TraesCS7D01G383100 chr7B 524916762 524921510 4748 False 2044 3903 87.542 102 3248 2 chr7B.!!$F1 3146
3 TraesCS7D01G383100 chr1D 436652853 436654306 1453 True 1810 1810 89.430 1032 2461 1 chr1D.!!$R1 1429
4 TraesCS7D01G383100 chr1A 533732331 533733799 1468 True 1760 1760 88.595 1032 2476 1 chr1A.!!$R1 1444
5 TraesCS7D01G383100 chr1B 591450487 591451883 1396 True 1677 1677 88.714 1032 2399 1 chr1B.!!$R1 1367

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
926 2571 0.107654 GCAACCAACTAGATCCGCCT 60.108 55.0 0.0 0.0 0.00 5.52 F
1593 3256 0.647410 CACTTATCGAGGCTGTTGCG 59.353 55.0 0.0 0.0 40.82 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2181 3844 0.393537 CCTTCTCGATGCTGGCCTTT 60.394 55.000 3.32 0.0 0.0 3.11 R
2466 4153 1.302832 GCAGGTGGAACAGGACCAG 60.303 63.158 0.00 0.0 41.8 4.00 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
17 18 2.663196 GGCCTGCGTAAGTGTCCT 59.337 61.111 0.00 0.00 41.68 3.85
18 19 1.895238 GGCCTGCGTAAGTGTCCTA 59.105 57.895 0.00 0.00 41.68 2.94
19 20 0.464452 GGCCTGCGTAAGTGTCCTAT 59.536 55.000 0.00 0.00 41.68 2.57
20 21 1.571919 GCCTGCGTAAGTGTCCTATG 58.428 55.000 0.00 0.00 41.68 2.23
21 22 1.806623 GCCTGCGTAAGTGTCCTATGG 60.807 57.143 0.00 0.00 41.68 2.74
22 23 1.480954 CCTGCGTAAGTGTCCTATGGT 59.519 52.381 0.00 0.00 41.68 3.55
23 24 2.691526 CCTGCGTAAGTGTCCTATGGTA 59.308 50.000 0.00 0.00 41.68 3.25
24 25 3.321111 CCTGCGTAAGTGTCCTATGGTAT 59.679 47.826 0.00 0.00 41.68 2.73
25 26 4.521639 CCTGCGTAAGTGTCCTATGGTATA 59.478 45.833 0.00 0.00 41.68 1.47
26 27 5.185249 CCTGCGTAAGTGTCCTATGGTATAT 59.815 44.000 0.00 0.00 41.68 0.86
27 28 6.020971 TGCGTAAGTGTCCTATGGTATATG 57.979 41.667 0.00 0.00 41.68 1.78
28 29 5.047590 TGCGTAAGTGTCCTATGGTATATGG 60.048 44.000 0.00 0.00 41.68 2.74
29 30 5.047519 GCGTAAGTGTCCTATGGTATATGGT 60.048 44.000 0.00 0.00 41.68 3.55
30 31 6.517864 GCGTAAGTGTCCTATGGTATATGGTT 60.518 42.308 0.00 0.00 41.68 3.67
31 32 7.439381 CGTAAGTGTCCTATGGTATATGGTTT 58.561 38.462 0.00 0.00 0.00 3.27
32 33 7.384115 CGTAAGTGTCCTATGGTATATGGTTTG 59.616 40.741 0.00 0.00 0.00 2.93
33 34 7.446106 AAGTGTCCTATGGTATATGGTTTGA 57.554 36.000 0.00 0.00 0.00 2.69
34 35 7.446106 AGTGTCCTATGGTATATGGTTTGAA 57.554 36.000 0.00 0.00 0.00 2.69
35 36 7.509546 AGTGTCCTATGGTATATGGTTTGAAG 58.490 38.462 0.00 0.00 0.00 3.02
36 37 7.347222 AGTGTCCTATGGTATATGGTTTGAAGA 59.653 37.037 0.00 0.00 0.00 2.87
37 38 7.990886 GTGTCCTATGGTATATGGTTTGAAGAA 59.009 37.037 0.00 0.00 0.00 2.52
38 39 8.553153 TGTCCTATGGTATATGGTTTGAAGAAA 58.447 33.333 0.00 0.00 0.00 2.52
39 40 9.574516 GTCCTATGGTATATGGTTTGAAGAAAT 57.425 33.333 0.00 0.00 0.00 2.17
40 41 9.573166 TCCTATGGTATATGGTTTGAAGAAATG 57.427 33.333 0.00 0.00 0.00 2.32
41 42 8.796475 CCTATGGTATATGGTTTGAAGAAATGG 58.204 37.037 0.00 0.00 0.00 3.16
42 43 9.354673 CTATGGTATATGGTTTGAAGAAATGGT 57.645 33.333 0.00 0.00 0.00 3.55
43 44 8.608185 ATGGTATATGGTTTGAAGAAATGGTT 57.392 30.769 0.00 0.00 0.00 3.67
44 45 8.062065 TGGTATATGGTTTGAAGAAATGGTTC 57.938 34.615 0.00 0.00 0.00 3.62
45 46 7.893302 TGGTATATGGTTTGAAGAAATGGTTCT 59.107 33.333 0.00 0.00 46.47 3.01
46 47 8.190784 GGTATATGGTTTGAAGAAATGGTTCTG 58.809 37.037 0.00 0.00 43.59 3.02
47 48 8.956426 GTATATGGTTTGAAGAAATGGTTCTGA 58.044 33.333 0.00 0.00 43.59 3.27
48 49 6.729690 ATGGTTTGAAGAAATGGTTCTGAA 57.270 33.333 0.00 0.00 43.59 3.02
49 50 6.537453 TGGTTTGAAGAAATGGTTCTGAAA 57.463 33.333 0.00 0.00 43.59 2.69
50 51 6.337356 TGGTTTGAAGAAATGGTTCTGAAAC 58.663 36.000 0.00 0.00 43.59 2.78
51 52 6.154363 TGGTTTGAAGAAATGGTTCTGAAACT 59.846 34.615 7.02 0.00 43.59 2.66
52 53 6.697455 GGTTTGAAGAAATGGTTCTGAAACTC 59.303 38.462 7.02 0.00 43.59 3.01
53 54 5.673337 TGAAGAAATGGTTCTGAAACTCG 57.327 39.130 7.02 0.00 43.59 4.18
54 55 4.515191 TGAAGAAATGGTTCTGAAACTCGG 59.485 41.667 7.02 0.00 43.59 4.63
55 56 4.086706 AGAAATGGTTCTGAAACTCGGT 57.913 40.909 7.02 0.00 42.73 4.69
56 57 4.461198 AGAAATGGTTCTGAAACTCGGTT 58.539 39.130 7.02 0.00 42.73 4.44
57 58 4.887655 AGAAATGGTTCTGAAACTCGGTTT 59.112 37.500 7.02 3.27 42.73 3.27
58 59 4.568152 AATGGTTCTGAAACTCGGTTTG 57.432 40.909 7.02 0.00 35.77 2.93
59 60 2.993937 TGGTTCTGAAACTCGGTTTGT 58.006 42.857 7.02 0.00 35.77 2.83
60 61 4.139859 TGGTTCTGAAACTCGGTTTGTA 57.860 40.909 7.02 0.00 35.77 2.41
61 62 4.710324 TGGTTCTGAAACTCGGTTTGTAT 58.290 39.130 7.02 0.00 35.77 2.29
62 63 4.513692 TGGTTCTGAAACTCGGTTTGTATG 59.486 41.667 7.02 0.00 35.77 2.39
63 64 4.753107 GGTTCTGAAACTCGGTTTGTATGA 59.247 41.667 6.73 0.00 35.77 2.15
64 65 5.411669 GGTTCTGAAACTCGGTTTGTATGAT 59.588 40.000 6.73 0.00 35.77 2.45
65 66 6.592607 GGTTCTGAAACTCGGTTTGTATGATA 59.407 38.462 6.73 0.00 35.77 2.15
66 67 7.412672 GGTTCTGAAACTCGGTTTGTATGATAC 60.413 40.741 6.73 0.00 35.77 2.24
67 68 6.931838 TCTGAAACTCGGTTTGTATGATACT 58.068 36.000 4.03 0.00 35.77 2.12
68 69 6.811665 TCTGAAACTCGGTTTGTATGATACTG 59.188 38.462 4.03 0.00 35.77 2.74
69 70 5.350365 TGAAACTCGGTTTGTATGATACTGC 59.650 40.000 4.03 0.00 35.77 4.40
70 71 4.737855 ACTCGGTTTGTATGATACTGCT 57.262 40.909 4.03 0.00 0.00 4.24
71 72 5.847111 ACTCGGTTTGTATGATACTGCTA 57.153 39.130 4.03 0.00 0.00 3.49
72 73 6.406692 ACTCGGTTTGTATGATACTGCTAT 57.593 37.500 4.03 0.00 0.00 2.97
73 74 7.520451 ACTCGGTTTGTATGATACTGCTATA 57.480 36.000 4.03 0.00 0.00 1.31
74 75 7.594714 ACTCGGTTTGTATGATACTGCTATAG 58.405 38.462 4.03 0.00 0.00 1.31
75 76 7.447545 ACTCGGTTTGTATGATACTGCTATAGA 59.552 37.037 3.21 0.00 0.00 1.98
76 77 7.817641 TCGGTTTGTATGATACTGCTATAGAG 58.182 38.462 3.21 0.95 0.00 2.43
77 78 7.030165 CGGTTTGTATGATACTGCTATAGAGG 58.970 42.308 3.21 0.00 0.00 3.69
78 79 6.814146 GGTTTGTATGATACTGCTATAGAGGC 59.186 42.308 3.21 0.00 0.00 4.70
79 80 7.310113 GGTTTGTATGATACTGCTATAGAGGCT 60.310 40.741 3.21 0.00 0.00 4.58
80 81 8.740906 GTTTGTATGATACTGCTATAGAGGCTA 58.259 37.037 3.21 0.00 0.00 3.93
81 82 9.480861 TTTGTATGATACTGCTATAGAGGCTAT 57.519 33.333 3.21 0.00 0.00 2.97
83 84 9.785982 TGTATGATACTGCTATAGAGGCTATAG 57.214 37.037 14.27 14.27 0.00 1.31
124 125 5.355910 TGGAGTGGTTTTGTTAAGAGTGTTC 59.644 40.000 0.00 0.00 0.00 3.18
164 165 1.908619 TCACCATGCTTGAAGAGGCTA 59.091 47.619 0.00 0.00 0.00 3.93
165 166 2.093288 TCACCATGCTTGAAGAGGCTAG 60.093 50.000 0.00 0.00 0.00 3.42
190 191 1.350019 CCTGGTTTTTACTCCCTCCGT 59.650 52.381 0.00 0.00 0.00 4.69
192 193 1.348696 TGGTTTTTACTCCCTCCGTCC 59.651 52.381 0.00 0.00 0.00 4.79
193 194 1.348696 GGTTTTTACTCCCTCCGTCCA 59.651 52.381 0.00 0.00 0.00 4.02
194 195 2.224597 GGTTTTTACTCCCTCCGTCCAA 60.225 50.000 0.00 0.00 0.00 3.53
195 196 3.560668 GGTTTTTACTCCCTCCGTCCAAT 60.561 47.826 0.00 0.00 0.00 3.16
196 197 4.323715 GGTTTTTACTCCCTCCGTCCAATA 60.324 45.833 0.00 0.00 0.00 1.90
197 198 5.247862 GTTTTTACTCCCTCCGTCCAATAA 58.752 41.667 0.00 0.00 0.00 1.40
198 199 5.703730 TTTTACTCCCTCCGTCCAATAAT 57.296 39.130 0.00 0.00 0.00 1.28
199 200 6.811634 TTTTACTCCCTCCGTCCAATAATA 57.188 37.500 0.00 0.00 0.00 0.98
200 201 7.383156 TTTTACTCCCTCCGTCCAATAATAT 57.617 36.000 0.00 0.00 0.00 1.28
201 202 8.495160 TTTTACTCCCTCCGTCCAATAATATA 57.505 34.615 0.00 0.00 0.00 0.86
202 203 8.495160 TTTACTCCCTCCGTCCAATAATATAA 57.505 34.615 0.00 0.00 0.00 0.98
203 204 8.495160 TTACTCCCTCCGTCCAATAATATAAA 57.505 34.615 0.00 0.00 0.00 1.40
204 205 7.383156 ACTCCCTCCGTCCAATAATATAAAA 57.617 36.000 0.00 0.00 0.00 1.52
205 206 7.985589 ACTCCCTCCGTCCAATAATATAAAAT 58.014 34.615 0.00 0.00 0.00 1.82
206 207 7.883311 ACTCCCTCCGTCCAATAATATAAAATG 59.117 37.037 0.00 0.00 0.00 2.32
207 208 7.751646 TCCCTCCGTCCAATAATATAAAATGT 58.248 34.615 0.00 0.00 0.00 2.71
208 209 8.221944 TCCCTCCGTCCAATAATATAAAATGTT 58.778 33.333 0.00 0.00 0.00 2.71
257 266 7.056006 AGAAAGAAACATTGAAAGGGCATTTT 58.944 30.769 0.00 0.00 0.00 1.82
270 279 8.632679 TGAAAGGGCATTTTACATCTGATAATC 58.367 33.333 0.00 0.00 0.00 1.75
306 315 8.757982 ATAATAGTCAGTGCAATGGAAAGATT 57.242 30.769 15.06 9.47 0.00 2.40
307 316 4.778534 AGTCAGTGCAATGGAAAGATTG 57.221 40.909 15.06 0.00 36.55 2.67
308 317 3.508793 AGTCAGTGCAATGGAAAGATTGG 59.491 43.478 15.06 0.00 34.42 3.16
309 318 3.256631 GTCAGTGCAATGGAAAGATTGGT 59.743 43.478 15.06 0.00 34.42 3.67
310 319 4.458989 GTCAGTGCAATGGAAAGATTGGTA 59.541 41.667 15.06 0.00 34.42 3.25
311 320 5.048083 GTCAGTGCAATGGAAAGATTGGTAA 60.048 40.000 15.06 0.00 34.42 2.85
312 321 5.538053 TCAGTGCAATGGAAAGATTGGTAAA 59.462 36.000 15.06 0.00 34.42 2.01
313 322 6.041409 TCAGTGCAATGGAAAGATTGGTAAAA 59.959 34.615 15.06 0.00 34.42 1.52
314 323 6.705381 CAGTGCAATGGAAAGATTGGTAAAAA 59.295 34.615 6.18 0.00 34.42 1.94
315 324 7.388500 CAGTGCAATGGAAAGATTGGTAAAAAT 59.612 33.333 6.18 0.00 34.42 1.82
316 325 7.938490 AGTGCAATGGAAAGATTGGTAAAAATT 59.062 29.630 0.00 0.00 34.42 1.82
317 326 8.229811 GTGCAATGGAAAGATTGGTAAAAATTC 58.770 33.333 0.00 0.00 34.42 2.17
318 327 8.156165 TGCAATGGAAAGATTGGTAAAAATTCT 58.844 29.630 0.00 0.00 34.42 2.40
319 328 8.659491 GCAATGGAAAGATTGGTAAAAATTCTC 58.341 33.333 0.00 0.00 34.42 2.87
320 329 9.709495 CAATGGAAAGATTGGTAAAAATTCTCA 57.291 29.630 0.00 0.00 30.82 3.27
446 2073 5.460419 GGTTTATTCGTGCAAATGTTCAACA 59.540 36.000 0.00 0.00 0.00 3.33
450 2078 3.951306 TCGTGCAAATGTTCAACAGAAG 58.049 40.909 0.00 0.00 0.00 2.85
479 2107 2.128035 CATTATTCGGACTCTGACGCC 58.872 52.381 0.00 0.00 0.00 5.68
663 2302 2.445654 CCCCTCCTCCAGCCTCTC 60.446 72.222 0.00 0.00 0.00 3.20
807 2452 2.349886 CGAGCAACAGCTAGGTTGATTC 59.650 50.000 18.37 13.45 46.35 2.52
836 2481 2.857152 CGCAGCATCACTTCTCTTAGTC 59.143 50.000 0.00 0.00 0.00 2.59
848 2493 7.542477 TCACTTCTCTTAGTCGTTGAATCAATC 59.458 37.037 0.00 0.00 0.00 2.67
851 2496 6.028368 TCTCTTAGTCGTTGAATCAATCGAC 58.972 40.000 27.21 27.21 42.26 4.20
859 2504 2.469826 TGAATCAATCGACGAATCCCG 58.530 47.619 0.00 0.00 45.44 5.14
860 2505 1.792949 GAATCAATCGACGAATCCCGG 59.207 52.381 0.00 0.00 43.93 5.73
926 2571 0.107654 GCAACCAACTAGATCCGCCT 60.108 55.000 0.00 0.00 0.00 5.52
985 2630 2.506438 GCTCCCGTAGCGTGTCAC 60.506 66.667 0.00 0.00 42.53 3.67
999 2645 1.204941 GTGTCACCAGCCGTTCTATCT 59.795 52.381 0.00 0.00 0.00 1.98
1130 2781 2.295909 TGGTTTCAAAGCCAAGGAATCG 59.704 45.455 0.00 0.00 36.28 3.34
1206 2869 2.190578 CTGGGCAAGACCGGATCC 59.809 66.667 9.46 0.00 39.34 3.36
1398 3061 5.716228 TGATATTGCAAATGTCAAGGGAGTT 59.284 36.000 1.71 0.00 0.00 3.01
1593 3256 0.647410 CACTTATCGAGGCTGTTGCG 59.353 55.000 0.00 0.00 40.82 4.85
1674 3337 3.001431 CGATTGCTGCTGAGATTCTGAAG 59.999 47.826 0.00 0.00 0.00 3.02
1693 3356 4.530553 TGAAGCAGAAGGGTGTCTACAATA 59.469 41.667 0.00 0.00 0.00 1.90
1716 3379 3.123050 CAAGAAGCTTTTTGGGGTTTCG 58.877 45.455 19.39 0.00 0.00 3.46
1953 3616 1.414158 GTGCTGGATCTGCTACCCTA 58.586 55.000 11.30 0.00 0.00 3.53
2214 3877 0.036732 AGAAGGGCATCGAGTTTGCA 59.963 50.000 11.32 0.00 41.95 4.08
2260 3924 4.753516 TCTGTTTGAAGTGAGGAGAACA 57.246 40.909 0.00 0.00 0.00 3.18
2342 4026 8.580720 CCTAGAGTATTGACATGTAGCAGTATT 58.419 37.037 0.00 0.00 0.00 1.89
2343 4027 9.404348 CTAGAGTATTGACATGTAGCAGTATTG 57.596 37.037 0.00 0.00 0.00 1.90
2466 4153 7.850492 GCCTTGTTTTGTTTGACACATAAATTC 59.150 33.333 0.00 0.00 34.43 2.17
2495 4182 3.211045 GTTCCACCTGCTGTTCTTGTAA 58.789 45.455 0.00 0.00 0.00 2.41
2880 4582 4.049186 CGTACTCTCGGGGAATAAATGTG 58.951 47.826 0.00 0.00 0.00 3.21
2936 4642 0.250901 TTTCAGAAGGCAGGGACAGC 60.251 55.000 0.00 0.00 41.34 4.40
2943 4649 2.439156 GCAGGGACAGCCATGGTC 60.439 66.667 14.67 5.80 45.86 4.02
2960 4666 5.697633 CCATGGTCAAATTCTCACCTTTTTG 59.302 40.000 2.57 0.00 0.00 2.44
2964 4670 6.071108 TGGTCAAATTCTCACCTTTTTGTTCA 60.071 34.615 2.95 0.00 32.33 3.18
3045 4771 4.941713 ACTGGTATAAAGAATTTGGGCCA 58.058 39.130 0.00 0.00 39.63 5.36
3111 4837 3.717392 AGGATTAGGGAAGAAAGTAGGGC 59.283 47.826 0.00 0.00 0.00 5.19
3188 4916 7.158099 AGCCTTGAATGTGTTAAAAGGATAC 57.842 36.000 3.98 0.00 39.88 2.24
3222 4952 5.178096 TGTCCTGATCAGCTTTATTTCCA 57.822 39.130 17.76 0.20 0.00 3.53
3223 4953 4.943705 TGTCCTGATCAGCTTTATTTCCAC 59.056 41.667 17.76 1.50 0.00 4.02
3224 4954 4.034510 GTCCTGATCAGCTTTATTTCCACG 59.965 45.833 17.76 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.464452 ATAGGACACTTACGCAGGCC 59.536 55.000 0.00 0.00 0.00 5.19
1 2 1.571919 CATAGGACACTTACGCAGGC 58.428 55.000 0.00 0.00 0.00 4.85
2 3 1.480954 ACCATAGGACACTTACGCAGG 59.519 52.381 0.00 0.00 0.00 4.85
3 4 2.961526 ACCATAGGACACTTACGCAG 57.038 50.000 0.00 0.00 0.00 5.18
4 5 5.047590 CCATATACCATAGGACACTTACGCA 60.048 44.000 0.00 0.00 0.00 5.24
5 6 5.047519 ACCATATACCATAGGACACTTACGC 60.048 44.000 0.00 0.00 0.00 4.42
6 7 6.585695 ACCATATACCATAGGACACTTACG 57.414 41.667 0.00 0.00 0.00 3.18
7 8 8.426489 TCAAACCATATACCATAGGACACTTAC 58.574 37.037 0.00 0.00 0.00 2.34
8 9 8.555896 TCAAACCATATACCATAGGACACTTA 57.444 34.615 0.00 0.00 0.00 2.24
9 10 7.446106 TCAAACCATATACCATAGGACACTT 57.554 36.000 0.00 0.00 0.00 3.16
10 11 7.347222 TCTTCAAACCATATACCATAGGACACT 59.653 37.037 0.00 0.00 0.00 3.55
11 12 7.506114 TCTTCAAACCATATACCATAGGACAC 58.494 38.462 0.00 0.00 0.00 3.67
12 13 7.684317 TCTTCAAACCATATACCATAGGACA 57.316 36.000 0.00 0.00 0.00 4.02
13 14 8.974060 TTTCTTCAAACCATATACCATAGGAC 57.026 34.615 0.00 0.00 0.00 3.85
14 15 9.573166 CATTTCTTCAAACCATATACCATAGGA 57.427 33.333 0.00 0.00 0.00 2.94
15 16 8.796475 CCATTTCTTCAAACCATATACCATAGG 58.204 37.037 0.00 0.00 0.00 2.57
16 17 9.354673 ACCATTTCTTCAAACCATATACCATAG 57.645 33.333 0.00 0.00 0.00 2.23
17 18 9.707957 AACCATTTCTTCAAACCATATACCATA 57.292 29.630 0.00 0.00 0.00 2.74
18 19 8.608185 AACCATTTCTTCAAACCATATACCAT 57.392 30.769 0.00 0.00 0.00 3.55
19 20 7.893302 AGAACCATTTCTTCAAACCATATACCA 59.107 33.333 0.00 0.00 39.17 3.25
20 21 8.190784 CAGAACCATTTCTTCAAACCATATACC 58.809 37.037 0.00 0.00 40.34 2.73
21 22 8.956426 TCAGAACCATTTCTTCAAACCATATAC 58.044 33.333 0.00 0.00 40.34 1.47
22 23 9.527157 TTCAGAACCATTTCTTCAAACCATATA 57.473 29.630 0.00 0.00 40.34 0.86
23 24 8.421249 TTCAGAACCATTTCTTCAAACCATAT 57.579 30.769 0.00 0.00 40.34 1.78
24 25 7.831691 TTCAGAACCATTTCTTCAAACCATA 57.168 32.000 0.00 0.00 40.34 2.74
25 26 6.729690 TTCAGAACCATTTCTTCAAACCAT 57.270 33.333 0.00 0.00 40.34 3.55
26 27 6.154363 AGTTTCAGAACCATTTCTTCAAACCA 59.846 34.615 11.65 0.00 40.34 3.67
27 28 6.573434 AGTTTCAGAACCATTTCTTCAAACC 58.427 36.000 11.65 0.00 40.34 3.27
28 29 6.414987 CGAGTTTCAGAACCATTTCTTCAAAC 59.585 38.462 9.08 9.08 40.34 2.93
29 30 6.459573 CCGAGTTTCAGAACCATTTCTTCAAA 60.460 38.462 0.00 0.00 40.34 2.69
30 31 5.008613 CCGAGTTTCAGAACCATTTCTTCAA 59.991 40.000 0.00 0.00 40.34 2.69
31 32 4.515191 CCGAGTTTCAGAACCATTTCTTCA 59.485 41.667 0.00 0.00 40.34 3.02
32 33 4.515567 ACCGAGTTTCAGAACCATTTCTTC 59.484 41.667 0.00 0.00 40.34 2.87
33 34 4.461198 ACCGAGTTTCAGAACCATTTCTT 58.539 39.130 0.00 0.00 40.34 2.52
34 35 4.086706 ACCGAGTTTCAGAACCATTTCT 57.913 40.909 0.00 0.00 43.35 2.52
35 36 4.830826 AACCGAGTTTCAGAACCATTTC 57.169 40.909 0.00 0.00 36.39 2.17
36 37 4.401202 ACAAACCGAGTTTCAGAACCATTT 59.599 37.500 0.00 0.00 36.39 2.32
37 38 3.951680 ACAAACCGAGTTTCAGAACCATT 59.048 39.130 0.00 0.00 36.39 3.16
38 39 3.551846 ACAAACCGAGTTTCAGAACCAT 58.448 40.909 0.00 0.00 36.39 3.55
39 40 2.993937 ACAAACCGAGTTTCAGAACCA 58.006 42.857 0.00 0.00 36.39 3.67
40 41 4.753107 TCATACAAACCGAGTTTCAGAACC 59.247 41.667 0.00 0.00 36.39 3.62
41 42 5.917541 TCATACAAACCGAGTTTCAGAAC 57.082 39.130 0.00 0.00 33.10 3.01
42 43 7.330946 CAGTATCATACAAACCGAGTTTCAGAA 59.669 37.037 0.00 0.00 33.10 3.02
43 44 6.811665 CAGTATCATACAAACCGAGTTTCAGA 59.188 38.462 0.00 0.00 33.10 3.27
44 45 6.455646 GCAGTATCATACAAACCGAGTTTCAG 60.456 42.308 0.00 0.00 33.10 3.02
45 46 5.350365 GCAGTATCATACAAACCGAGTTTCA 59.650 40.000 0.00 0.00 33.10 2.69
46 47 5.581085 AGCAGTATCATACAAACCGAGTTTC 59.419 40.000 0.00 0.00 33.10 2.78
47 48 5.488341 AGCAGTATCATACAAACCGAGTTT 58.512 37.500 0.00 0.00 36.05 2.66
48 49 5.086104 AGCAGTATCATACAAACCGAGTT 57.914 39.130 0.00 0.00 0.00 3.01
49 50 4.737855 AGCAGTATCATACAAACCGAGT 57.262 40.909 0.00 0.00 0.00 4.18
50 51 7.817641 TCTATAGCAGTATCATACAAACCGAG 58.182 38.462 0.00 0.00 0.00 4.63
51 52 7.094334 CCTCTATAGCAGTATCATACAAACCGA 60.094 40.741 0.00 0.00 0.00 4.69
52 53 7.030165 CCTCTATAGCAGTATCATACAAACCG 58.970 42.308 0.00 0.00 0.00 4.44
53 54 6.814146 GCCTCTATAGCAGTATCATACAAACC 59.186 42.308 0.00 0.00 0.00 3.27
54 55 7.607250 AGCCTCTATAGCAGTATCATACAAAC 58.393 38.462 0.00 0.00 0.00 2.93
55 56 7.782897 AGCCTCTATAGCAGTATCATACAAA 57.217 36.000 0.00 0.00 0.00 2.83
57 58 9.785982 CTATAGCCTCTATAGCAGTATCATACA 57.214 37.037 7.66 0.00 0.00 2.29
58 59 8.726988 GCTATAGCCTCTATAGCAGTATCATAC 58.273 40.741 27.77 6.55 46.99 2.39
59 60 8.856153 GCTATAGCCTCTATAGCAGTATCATA 57.144 38.462 27.77 0.00 46.99 2.15
60 61 7.759489 GCTATAGCCTCTATAGCAGTATCAT 57.241 40.000 27.77 0.00 46.99 2.45
68 69 4.396790 ACAAGACGCTATAGCCTCTATAGC 59.603 45.833 25.01 25.01 45.33 2.97
69 70 6.503589 AACAAGACGCTATAGCCTCTATAG 57.496 41.667 21.75 17.27 35.82 1.31
70 71 6.896021 AAACAAGACGCTATAGCCTCTATA 57.104 37.500 21.75 0.00 35.82 1.31
71 72 5.793030 AAACAAGACGCTATAGCCTCTAT 57.207 39.130 21.75 13.10 35.82 1.98
72 73 5.593679 AAAACAAGACGCTATAGCCTCTA 57.406 39.130 21.75 0.00 35.82 2.43
73 74 4.473477 AAAACAAGACGCTATAGCCTCT 57.527 40.909 19.00 18.15 37.89 3.69
96 97 7.093992 CACTCTTAACAAAACCACTCCAAAAA 58.906 34.615 0.00 0.00 0.00 1.94
97 98 6.209788 ACACTCTTAACAAAACCACTCCAAAA 59.790 34.615 0.00 0.00 0.00 2.44
98 99 5.712917 ACACTCTTAACAAAACCACTCCAAA 59.287 36.000 0.00 0.00 0.00 3.28
99 100 5.258051 ACACTCTTAACAAAACCACTCCAA 58.742 37.500 0.00 0.00 0.00 3.53
100 101 4.850680 ACACTCTTAACAAAACCACTCCA 58.149 39.130 0.00 0.00 0.00 3.86
124 125 3.882888 TGAGCTCACCTGTAAAAAGTTGG 59.117 43.478 13.74 0.00 0.00 3.77
164 165 4.500452 AGGGAGTAAAAACCAGGTACTCT 58.500 43.478 16.65 2.30 42.19 3.24
165 166 4.323333 GGAGGGAGTAAAAACCAGGTACTC 60.323 50.000 10.75 10.75 41.94 2.59
270 279 9.844790 TTGCACTGACTATTATTTTTCTTGATG 57.155 29.630 0.00 0.00 0.00 3.07
282 291 7.067372 CCAATCTTTCCATTGCACTGACTATTA 59.933 37.037 5.49 0.00 33.08 0.98
323 332 5.908341 TGCTTTTACCGATTGTTCCTTTTT 58.092 33.333 0.00 0.00 0.00 1.94
324 333 5.523438 TGCTTTTACCGATTGTTCCTTTT 57.477 34.783 0.00 0.00 0.00 2.27
325 334 5.523438 TTGCTTTTACCGATTGTTCCTTT 57.477 34.783 0.00 0.00 0.00 3.11
326 335 5.523438 TTTGCTTTTACCGATTGTTCCTT 57.477 34.783 0.00 0.00 0.00 3.36
327 336 5.722021 ATTTGCTTTTACCGATTGTTCCT 57.278 34.783 0.00 0.00 0.00 3.36
328 337 6.779115 AAATTTGCTTTTACCGATTGTTCC 57.221 33.333 0.00 0.00 0.00 3.62
329 338 8.288217 TGTAAATTTGCTTTTACCGATTGTTC 57.712 30.769 7.80 0.00 40.00 3.18
330 339 8.825667 ATGTAAATTTGCTTTTACCGATTGTT 57.174 26.923 7.80 0.00 40.00 2.83
331 340 8.707839 CAATGTAAATTTGCTTTTACCGATTGT 58.292 29.630 7.80 0.00 40.00 2.71
332 341 8.920665 TCAATGTAAATTTGCTTTTACCGATTG 58.079 29.630 7.80 15.16 40.00 2.67
333 342 9.482627 TTCAATGTAAATTTGCTTTTACCGATT 57.517 25.926 7.80 0.00 40.00 3.34
334 343 9.482627 TTTCAATGTAAATTTGCTTTTACCGAT 57.517 25.926 7.80 0.00 40.00 4.18
335 344 8.873215 TTTCAATGTAAATTTGCTTTTACCGA 57.127 26.923 7.80 0.00 40.00 4.69
422 2048 5.460419 TGTTGAACATTTGCACGAATAAACC 59.540 36.000 0.00 0.00 0.00 3.27
423 2049 6.416455 TCTGTTGAACATTTGCACGAATAAAC 59.584 34.615 0.00 0.00 0.00 2.01
446 2073 7.112779 AGTCCGAATAATGAACATTTCCTTCT 58.887 34.615 5.37 0.00 32.50 2.85
450 2078 6.538742 TCAGAGTCCGAATAATGAACATTTCC 59.461 38.462 5.37 0.00 32.50 3.13
479 2107 2.470821 GTACGATGGGAGTCATTTCCG 58.529 52.381 0.00 0.00 38.17 4.30
606 2239 1.067416 TGACGATGAGGTATGGCGC 59.933 57.895 0.00 0.00 0.00 6.53
607 2240 0.597637 GGTGACGATGAGGTATGGCG 60.598 60.000 0.00 0.00 0.00 5.69
646 2285 2.445654 GAGAGGCTGGAGGAGGGG 60.446 72.222 0.00 0.00 0.00 4.79
688 2333 2.754375 GGAAGAAGGGGAACGGCA 59.246 61.111 0.00 0.00 0.00 5.69
722 2367 4.341783 GGTGGAGGCAGCAGCAGT 62.342 66.667 2.65 0.00 44.61 4.40
743 2388 3.322466 AGTGGCCGAAGACTGGGG 61.322 66.667 0.00 0.00 0.00 4.96
807 2452 2.515290 TGATGCTGCGCTGGATGG 60.515 61.111 25.02 1.74 0.00 3.51
836 2481 3.302480 GGGATTCGTCGATTGATTCAACG 60.302 47.826 0.15 7.93 0.00 4.10
848 2493 2.025156 CCGTACCGGGATTCGTCG 59.975 66.667 6.32 0.00 44.15 5.12
859 2504 0.398948 TCCCCAATCCCTACCGTACC 60.399 60.000 0.00 0.00 0.00 3.34
860 2505 1.139654 GTTCCCCAATCCCTACCGTAC 59.860 57.143 0.00 0.00 0.00 3.67
872 2517 3.640967 CCAGAAATTGTGAAGTTCCCCAA 59.359 43.478 0.00 4.11 36.20 4.12
926 2571 8.078060 TCTTGAACACTAATACATGATCCAGA 57.922 34.615 0.00 0.00 0.00 3.86
935 2580 8.078060 TGATCCAGATCTTGAACACTAATACA 57.922 34.615 8.99 0.00 38.60 2.29
978 2623 0.108804 ATAGAACGGCTGGTGACACG 60.109 55.000 0.00 0.00 36.07 4.49
985 2630 3.062763 CAAGCATAGATAGAACGGCTGG 58.937 50.000 0.00 0.00 0.00 4.85
999 2645 9.709495 AAAACATAAAAATCTCTTGCAAGCATA 57.291 25.926 21.99 9.44 0.00 3.14
1043 2694 0.890996 GTCCAACTGCAGGAACAGGG 60.891 60.000 19.93 9.67 42.21 4.45
1044 2695 0.179020 TGTCCAACTGCAGGAACAGG 60.179 55.000 19.93 11.78 42.21 4.00
1130 2781 0.524862 CTTCAAGCCACTGATGCCAC 59.475 55.000 0.00 0.00 0.00 5.01
1146 2806 4.396522 AGCTAATTGATGAGGATGCCTTC 58.603 43.478 0.00 0.00 31.76 3.46
1206 2869 4.574722 TGTGGTTACAGATGCCCGAAGG 62.575 54.545 0.00 0.00 38.99 3.46
1674 3337 3.055385 TGGTATTGTAGACACCCTTCTGC 60.055 47.826 0.00 0.00 0.00 4.26
1693 3356 2.174685 ACCCCAAAAAGCTTCTTGGT 57.825 45.000 26.12 9.49 40.51 3.67
1716 3379 2.763448 AGCTCTGACAACATCTAGGGTC 59.237 50.000 0.00 0.00 0.00 4.46
2181 3844 0.393537 CCTTCTCGATGCTGGCCTTT 60.394 55.000 3.32 0.00 0.00 3.11
2214 3877 1.529244 GGCTCCCTGCTGTTTGTGT 60.529 57.895 0.00 0.00 42.39 3.72
2260 3924 4.683832 CCTTCTCTTCGTATGGAATCGTT 58.316 43.478 0.00 0.00 33.26 3.85
2343 4027 6.882656 TGAGAAATATATAGATGCTCCAGGC 58.117 40.000 7.59 0.00 42.22 4.85
2466 4153 1.302832 GCAGGTGGAACAGGACCAG 60.303 63.158 0.00 0.00 41.80 4.00
2495 4182 2.771943 TCCACAGTTGAACTCCAGAAGT 59.228 45.455 0.00 0.00 41.10 3.01
2609 4302 2.813754 TGGCTCATCTTACAACAGCAAC 59.186 45.455 0.00 0.00 0.00 4.17
2832 4534 8.772705 GGAATGCAAACAAATGAAACTTATCAA 58.227 29.630 0.00 0.00 32.06 2.57
2880 4582 2.550606 TCCCAGATTACGCACAAACAAC 59.449 45.455 0.00 0.00 0.00 3.32
2936 4642 5.473066 AAAAGGTGAGAATTTGACCATGG 57.527 39.130 11.19 11.19 31.61 3.66
2943 4649 7.761249 AGAACTGAACAAAAAGGTGAGAATTTG 59.239 33.333 0.00 0.00 38.42 2.32
2960 4666 3.010420 GGTGCATAGGGAAGAACTGAAC 58.990 50.000 0.00 0.00 0.00 3.18
2964 4670 1.972588 AGGGTGCATAGGGAAGAACT 58.027 50.000 0.00 0.00 0.00 3.01
3045 4771 2.936202 ACAGCAGGAACAAGACAACAT 58.064 42.857 0.00 0.00 0.00 2.71
3099 4825 5.827326 ACTAACTCTTGCCCTACTTTCTT 57.173 39.130 0.00 0.00 0.00 2.52
3111 4837 5.765182 ACCCAAGAACATCAACTAACTCTTG 59.235 40.000 0.00 0.00 39.51 3.02
3214 4942 3.365164 GCGCACCTAAAACGTGGAAATAA 60.365 43.478 0.30 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.