Multiple sequence alignment - TraesCS4A01G270000

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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 TraesCS4A01G270000 chr4A 100.000 2219 0 0 859 3077 581455356 581457574 0.000000e+00 4098.0
1 TraesCS4A01G270000 chr4A 100.000 574 0 0 1 574 581454498 581455071 0.000000e+00 1061.0
2 TraesCS4A01G270000 chr4B 88.744 1990 123 29 860 2772 31973106 31971141 0.000000e+00 2340.0
3 TraesCS4A01G270000 chr4B 90.122 820 41 7 2288 3077 31971139 31970330 0.000000e+00 1029.0
4 TraesCS4A01G270000 chr4B 88.265 196 8 7 95 284 31974101 31973915 1.440000e-53 220.0
5 TraesCS4A01G270000 chr4B 81.648 267 13 19 278 511 31973563 31973300 4.050000e-44 189.0
6 TraesCS4A01G270000 chr4D 95.316 982 37 1 1557 2538 19461225 19460253 0.000000e+00 1550.0
7 TraesCS4A01G270000 chr4D 94.239 677 15 3 963 1615 19461873 19461197 0.000000e+00 1013.0
8 TraesCS4A01G270000 chr4D 95.294 170 8 0 2908 3077 19460192 19460023 1.410000e-68 270.0
9 TraesCS4A01G270000 chr4D 80.220 273 9 21 278 513 19462973 19462709 2.460000e-36 163.0
10 TraesCS4A01G270000 chr4D 100.000 38 0 0 2871 2908 19460255 19460218 1.530000e-08 71.3
11 TraesCS4A01G270000 chr4D 100.000 36 0 0 937 972 19461923 19461888 1.980000e-07 67.6


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 TraesCS4A01G270000 chr4A 581454498 581457574 3076 False 2579.500000 4098 100.000000 1 3077 2 chr4A.!!$F1 3076
1 TraesCS4A01G270000 chr4B 31970330 31974101 3771 True 944.500000 2340 87.194750 95 3077 4 chr4B.!!$R1 2982
2 TraesCS4A01G270000 chr4D 19460023 19462973 2950 True 522.483333 1550 94.178167 278 3077 6 chr4D.!!$R1 2799

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
455 854 0.040942 CCAATCAATCCACCCACCCA 59.959 55.0 0.0 0.0 0.0 4.51 F
458 857 0.041090 ATCAATCCACCCACCCAACC 59.959 55.0 0.0 0.0 0.0 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1676 2580 0.027979 CAAATACATCCAGCACGGCG 59.972 55.0 4.80 4.8 33.14 6.46 R
2199 3111 0.902531 CCACAGTGGTCGAACCCTAT 59.097 55.0 11.99 0.0 37.50 2.57 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 7.377766 GCTTCAACTAAATGTTCCTGTATGA 57.622 36.000 0.00 0.00 36.63 2.15
25 26 7.989826 GCTTCAACTAAATGTTCCTGTATGAT 58.010 34.615 0.00 0.00 36.63 2.45
26 27 7.912250 GCTTCAACTAAATGTTCCTGTATGATG 59.088 37.037 0.00 0.00 36.63 3.07
27 28 7.320443 TCAACTAAATGTTCCTGTATGATGC 57.680 36.000 0.00 0.00 36.63 3.91
28 29 6.883756 TCAACTAAATGTTCCTGTATGATGCA 59.116 34.615 0.00 0.00 36.63 3.96
29 30 6.683974 ACTAAATGTTCCTGTATGATGCAC 57.316 37.500 0.00 0.00 0.00 4.57
30 31 6.179756 ACTAAATGTTCCTGTATGATGCACA 58.820 36.000 0.00 0.00 0.00 4.57
31 32 6.830324 ACTAAATGTTCCTGTATGATGCACAT 59.170 34.615 0.00 0.00 42.39 3.21
32 33 5.509716 AATGTTCCTGTATGATGCACATG 57.490 39.130 10.77 0.00 39.77 3.21
33 34 3.281158 TGTTCCTGTATGATGCACATGG 58.719 45.455 10.77 5.38 39.77 3.66
34 35 2.620115 GTTCCTGTATGATGCACATGGG 59.380 50.000 10.77 0.00 39.77 4.00
35 36 0.956633 CCTGTATGATGCACATGGGC 59.043 55.000 14.67 14.67 39.77 5.36
36 37 0.589708 CTGTATGATGCACATGGGCG 59.410 55.000 16.66 0.00 39.77 6.13
37 38 0.107263 TGTATGATGCACATGGGCGT 60.107 50.000 16.24 16.24 39.77 5.68
38 39 1.139853 TGTATGATGCACATGGGCGTA 59.860 47.619 16.27 3.54 39.77 4.42
39 40 2.217750 GTATGATGCACATGGGCGTAA 58.782 47.619 16.27 8.51 39.77 3.18
40 41 1.985473 ATGATGCACATGGGCGTAAT 58.015 45.000 16.27 10.98 37.87 1.89
41 42 2.629336 TGATGCACATGGGCGTAATA 57.371 45.000 16.27 1.57 36.28 0.98
42 43 3.138884 TGATGCACATGGGCGTAATAT 57.861 42.857 16.27 1.15 36.28 1.28
43 44 4.278975 TGATGCACATGGGCGTAATATA 57.721 40.909 16.27 0.00 36.28 0.86
44 45 4.252878 TGATGCACATGGGCGTAATATAG 58.747 43.478 16.27 0.00 36.28 1.31
45 46 3.052455 TGCACATGGGCGTAATATAGG 57.948 47.619 16.66 0.00 36.28 2.57
46 47 2.290008 TGCACATGGGCGTAATATAGGG 60.290 50.000 16.66 0.00 36.28 3.53
47 48 2.290071 GCACATGGGCGTAATATAGGGT 60.290 50.000 3.02 0.00 0.00 4.34
48 49 3.809324 GCACATGGGCGTAATATAGGGTT 60.809 47.826 3.02 0.00 0.00 4.11
49 50 4.394729 CACATGGGCGTAATATAGGGTTT 58.605 43.478 0.00 0.00 0.00 3.27
50 51 4.215399 CACATGGGCGTAATATAGGGTTTG 59.785 45.833 0.00 0.00 0.00 2.93
51 52 2.853705 TGGGCGTAATATAGGGTTTGC 58.146 47.619 0.00 0.00 0.00 3.68
52 53 2.156917 GGGCGTAATATAGGGTTTGCC 58.843 52.381 0.00 0.00 40.48 4.52
53 54 1.802365 GGCGTAATATAGGGTTTGCCG 59.198 52.381 0.00 0.00 34.97 5.69
54 55 2.548493 GGCGTAATATAGGGTTTGCCGA 60.548 50.000 0.00 0.00 34.97 5.54
55 56 2.477754 GCGTAATATAGGGTTTGCCGAC 59.522 50.000 0.00 0.00 34.97 4.79
56 57 2.727798 CGTAATATAGGGTTTGCCGACG 59.272 50.000 0.00 0.00 34.97 5.12
57 58 2.249844 AATATAGGGTTTGCCGACGG 57.750 50.000 10.29 10.29 34.97 4.79
58 59 1.125633 ATATAGGGTTTGCCGACGGT 58.874 50.000 16.73 0.00 34.97 4.83
59 60 0.903942 TATAGGGTTTGCCGACGGTT 59.096 50.000 16.73 0.00 34.97 4.44
60 61 0.675522 ATAGGGTTTGCCGACGGTTG 60.676 55.000 16.73 0.00 34.97 3.77
61 62 1.756408 TAGGGTTTGCCGACGGTTGA 61.756 55.000 16.73 0.00 34.97 3.18
62 63 1.969589 GGGTTTGCCGACGGTTGAT 60.970 57.895 16.73 0.00 34.97 2.57
63 64 1.209127 GGTTTGCCGACGGTTGATG 59.791 57.895 16.73 0.00 0.00 3.07
64 65 1.209127 GTTTGCCGACGGTTGATGG 59.791 57.895 16.73 0.00 0.00 3.51
65 66 1.969064 TTTGCCGACGGTTGATGGG 60.969 57.895 16.73 0.00 0.00 4.00
66 67 2.398840 TTTGCCGACGGTTGATGGGA 62.399 55.000 16.73 0.00 0.00 4.37
67 68 2.046700 GCCGACGGTTGATGGGAA 60.047 61.111 16.73 0.00 0.00 3.97
68 69 1.451387 GCCGACGGTTGATGGGAAT 60.451 57.895 16.73 0.00 0.00 3.01
69 70 1.714899 GCCGACGGTTGATGGGAATG 61.715 60.000 16.73 0.00 0.00 2.67
70 71 0.107897 CCGACGGTTGATGGGAATGA 60.108 55.000 5.48 0.00 0.00 2.57
71 72 1.290203 CGACGGTTGATGGGAATGAG 58.710 55.000 0.00 0.00 0.00 2.90
72 73 1.668419 GACGGTTGATGGGAATGAGG 58.332 55.000 0.00 0.00 0.00 3.86
73 74 0.394352 ACGGTTGATGGGAATGAGGC 60.394 55.000 0.00 0.00 0.00 4.70
74 75 1.439353 CGGTTGATGGGAATGAGGCG 61.439 60.000 0.00 0.00 0.00 5.52
75 76 0.107214 GGTTGATGGGAATGAGGCGA 60.107 55.000 0.00 0.00 0.00 5.54
76 77 1.303309 GTTGATGGGAATGAGGCGAG 58.697 55.000 0.00 0.00 0.00 5.03
77 78 1.134401 GTTGATGGGAATGAGGCGAGA 60.134 52.381 0.00 0.00 0.00 4.04
78 79 0.465705 TGATGGGAATGAGGCGAGAC 59.534 55.000 0.00 0.00 0.00 3.36
79 80 0.755686 GATGGGAATGAGGCGAGACT 59.244 55.000 0.00 0.00 0.00 3.24
80 81 1.964223 GATGGGAATGAGGCGAGACTA 59.036 52.381 0.00 0.00 0.00 2.59
81 82 1.112113 TGGGAATGAGGCGAGACTAC 58.888 55.000 0.00 0.00 0.00 2.73
82 83 0.389757 GGGAATGAGGCGAGACTACC 59.610 60.000 0.00 0.00 0.00 3.18
83 84 1.112113 GGAATGAGGCGAGACTACCA 58.888 55.000 0.00 0.00 0.00 3.25
84 85 1.480954 GGAATGAGGCGAGACTACCAA 59.519 52.381 0.00 0.00 0.00 3.67
85 86 2.541556 GAATGAGGCGAGACTACCAAC 58.458 52.381 0.00 0.00 0.00 3.77
86 87 0.824759 ATGAGGCGAGACTACCAACC 59.175 55.000 0.00 0.00 0.00 3.77
87 88 1.255667 TGAGGCGAGACTACCAACCC 61.256 60.000 0.00 0.00 0.00 4.11
88 89 0.971447 GAGGCGAGACTACCAACCCT 60.971 60.000 0.00 0.00 0.00 4.34
89 90 0.544595 AGGCGAGACTACCAACCCTT 60.545 55.000 0.00 0.00 0.00 3.95
90 91 0.108281 GGCGAGACTACCAACCCTTC 60.108 60.000 0.00 0.00 0.00 3.46
91 92 0.108281 GCGAGACTACCAACCCTTCC 60.108 60.000 0.00 0.00 0.00 3.46
92 93 1.558233 CGAGACTACCAACCCTTCCT 58.442 55.000 0.00 0.00 0.00 3.36
93 94 1.900486 CGAGACTACCAACCCTTCCTT 59.100 52.381 0.00 0.00 0.00 3.36
94 95 3.094572 CGAGACTACCAACCCTTCCTTA 58.905 50.000 0.00 0.00 0.00 2.69
95 96 3.512724 CGAGACTACCAACCCTTCCTTAA 59.487 47.826 0.00 0.00 0.00 1.85
96 97 4.020839 CGAGACTACCAACCCTTCCTTAAA 60.021 45.833 0.00 0.00 0.00 1.52
97 98 5.511888 CGAGACTACCAACCCTTCCTTAAAA 60.512 44.000 0.00 0.00 0.00 1.52
98 99 5.877491 AGACTACCAACCCTTCCTTAAAAG 58.123 41.667 0.00 0.00 0.00 2.27
220 225 0.696501 ACTACACCCGGGCTTTTCAT 59.303 50.000 24.08 0.00 0.00 2.57
276 281 1.414550 GCCCTGATTCTCCCTAGTCAC 59.585 57.143 0.00 0.00 0.00 3.67
350 716 1.292223 CCTACCGGTCACCACACAG 59.708 63.158 12.40 0.00 0.00 3.66
380 779 4.802051 CCCGTCCCGTCCCGTCTA 62.802 72.222 0.00 0.00 0.00 2.59
381 780 3.207669 CCGTCCCGTCCCGTCTAG 61.208 72.222 0.00 0.00 0.00 2.43
420 819 1.519751 CTAGCCGTCTCCATCCTCGG 61.520 65.000 0.00 0.00 44.86 4.63
455 854 0.040942 CCAATCAATCCACCCACCCA 59.959 55.000 0.00 0.00 0.00 4.51
456 855 1.552023 CCAATCAATCCACCCACCCAA 60.552 52.381 0.00 0.00 0.00 4.12
458 857 0.041090 ATCAATCCACCCACCCAACC 59.959 55.000 0.00 0.00 0.00 3.77
459 858 1.609210 CAATCCACCCACCCAACCC 60.609 63.158 0.00 0.00 0.00 4.11
525 946 1.225983 CTCGCCTCCCAGAGAGAGA 59.774 63.158 9.84 0.92 46.50 3.10
526 947 0.819259 CTCGCCTCCCAGAGAGAGAG 60.819 65.000 9.84 5.72 46.50 3.20
527 948 1.225983 CGCCTCCCAGAGAGAGAGA 59.774 63.158 0.00 0.00 46.50 3.10
528 949 0.819259 CGCCTCCCAGAGAGAGAGAG 60.819 65.000 0.00 0.00 46.50 3.20
529 950 0.468029 GCCTCCCAGAGAGAGAGAGG 60.468 65.000 0.00 0.00 46.50 3.69
530 951 0.185901 CCTCCCAGAGAGAGAGAGGG 59.814 65.000 0.00 0.00 46.50 4.30
531 952 1.221635 CTCCCAGAGAGAGAGAGGGA 58.778 60.000 0.00 0.00 46.50 4.20
1329 2149 2.662535 CCATGGCTACAATGGGATCA 57.337 50.000 0.00 0.00 0.00 2.92
1364 2187 2.514824 GCTGCCTTCCCCGATGAC 60.515 66.667 0.00 0.00 0.00 3.06
1391 2214 2.288457 CGCCGAGGATGTGATGTATCTT 60.288 50.000 0.00 0.00 0.00 2.40
1433 2256 2.280628 CTCTATTTTGACGAGGGTGCC 58.719 52.381 0.00 0.00 0.00 5.01
1502 2325 2.587247 GCTGGACCAGGCTGAGACA 61.587 63.158 23.09 10.22 31.21 3.41
1571 2475 0.529378 CAGCTCCCCAAAATGCTGTC 59.471 55.000 0.00 0.00 45.31 3.51
1586 2490 4.032960 TGCTGTCAACAATGGAGGTAAT 57.967 40.909 0.00 0.00 0.00 1.89
1587 2491 4.009675 TGCTGTCAACAATGGAGGTAATC 58.990 43.478 0.00 0.00 0.00 1.75
1598 2502 3.032265 GGAGGTAATCCCCAAAATGCT 57.968 47.619 0.00 0.00 43.01 3.79
1599 2503 4.178956 GGAGGTAATCCCCAAAATGCTA 57.821 45.455 0.00 0.00 43.01 3.49
1600 2504 4.740902 GGAGGTAATCCCCAAAATGCTAT 58.259 43.478 0.00 0.00 43.01 2.97
1601 2505 4.524328 GGAGGTAATCCCCAAAATGCTATG 59.476 45.833 0.00 0.00 43.01 2.23
1602 2506 5.385198 GAGGTAATCCCCAAAATGCTATGA 58.615 41.667 0.00 0.00 0.00 2.15
1603 2507 5.776358 AGGTAATCCCCAAAATGCTATGAA 58.224 37.500 0.00 0.00 0.00 2.57
1604 2508 5.598417 AGGTAATCCCCAAAATGCTATGAAC 59.402 40.000 0.00 0.00 0.00 3.18
1605 2509 5.362430 GGTAATCCCCAAAATGCTATGAACA 59.638 40.000 0.00 0.00 0.00 3.18
1606 2510 6.127196 GGTAATCCCCAAAATGCTATGAACAA 60.127 38.462 0.00 0.00 0.00 2.83
1607 2511 6.564557 AATCCCCAAAATGCTATGAACAAT 57.435 33.333 0.00 0.00 0.00 2.71
1608 2512 5.341872 TCCCCAAAATGCTATGAACAATG 57.658 39.130 0.00 0.00 0.00 2.82
1609 2513 4.161942 TCCCCAAAATGCTATGAACAATGG 59.838 41.667 0.00 0.00 0.00 3.16
1610 2514 4.161942 CCCCAAAATGCTATGAACAATGGA 59.838 41.667 0.00 0.00 0.00 3.41
1611 2515 5.353938 CCCAAAATGCTATGAACAATGGAG 58.646 41.667 0.00 0.00 0.00 3.86
1612 2516 5.353938 CCAAAATGCTATGAACAATGGAGG 58.646 41.667 0.00 0.00 0.00 4.30
1613 2517 5.105228 CCAAAATGCTATGAACAATGGAGGT 60.105 40.000 0.00 0.00 0.00 3.85
1614 2518 6.096705 CCAAAATGCTATGAACAATGGAGGTA 59.903 38.462 0.00 0.00 0.00 3.08
1615 2519 6.699575 AAATGCTATGAACAATGGAGGTAC 57.300 37.500 0.00 0.00 0.00 3.34
1616 2520 4.150897 TGCTATGAACAATGGAGGTACC 57.849 45.455 2.73 2.73 39.54 3.34
1617 2521 3.131396 GCTATGAACAATGGAGGTACCG 58.869 50.000 6.18 0.00 42.61 4.02
1676 2580 2.025727 GAGCATCGCATGGCAAGC 59.974 61.111 4.29 4.29 0.00 4.01
1844 2748 3.817647 GGTTGATCATTGAGGATGCTACC 59.182 47.826 0.00 0.00 35.64 3.18
1989 2893 3.930848 GCTTTAGCCGCTCTAGTTACAAA 59.069 43.478 0.00 0.00 34.31 2.83
2096 3000 7.637631 TTCCAGCATTGTTGTTTATATAGCA 57.362 32.000 0.00 0.00 0.00 3.49
2113 3017 0.950116 GCATGCTTCTGCCACTATCC 59.050 55.000 11.37 0.00 38.71 2.59
2123 3027 4.985538 TCTGCCACTATCCTTTTCAGTTT 58.014 39.130 0.00 0.00 0.00 2.66
2162 3066 3.772025 AGTAGTTCATGTAGCTTCAGCCT 59.228 43.478 0.00 0.00 43.38 4.58
2173 3077 4.143986 AGCTTCAGCCTTCCACTATTAC 57.856 45.455 0.00 0.00 43.38 1.89
2189 3093 7.333423 TCCACTATTACATGTTGTTCTAACTGC 59.667 37.037 2.30 0.00 0.00 4.40
2199 3111 3.070748 TGTTCTAACTGCGCAAATAGCA 58.929 40.909 13.05 4.39 46.13 3.49
2269 3181 4.096682 TGCGGGGCAAATAAACTATTGTAC 59.903 41.667 0.00 0.00 34.76 2.90
2277 3189 8.921670 GGCAAATAAACTATTGTACCTTGTTTG 58.078 33.333 12.20 7.53 33.63 2.93
2342 3755 6.432107 TCGTTATTTTGAACCTACAAACTGC 58.568 36.000 0.00 0.00 39.08 4.40
2376 3789 0.466555 CTGTTTCCCCACGGACCAAA 60.467 55.000 0.00 0.00 38.14 3.28
2479 3892 3.070590 AGGTGCCACGGTATAGGAAATAC 59.929 47.826 0.00 0.00 0.00 1.89
2566 3979 1.144691 TTGGTGTCACTGGGATTGGA 58.855 50.000 2.35 0.00 0.00 3.53
2578 3991 2.158475 TGGGATTGGATGGAATAGGTGC 60.158 50.000 0.00 0.00 0.00 5.01
2581 3994 0.916086 TTGGATGGAATAGGTGCGGT 59.084 50.000 0.00 0.00 0.00 5.68
2603 4016 7.173562 GCGGTAATGGTATTACATTGGTATTGA 59.826 37.037 12.26 0.00 40.97 2.57
2642 4055 9.696917 GATGAAGATTTGTGTTTGAACCTAATT 57.303 29.630 0.00 0.00 0.00 1.40
2681 4095 3.182887 TGGTACCCAATTCAAGCCAAT 57.817 42.857 10.07 0.00 0.00 3.16
2732 4146 6.093633 GGATAACAATGTAGAAAAGCGTCCTT 59.906 38.462 0.00 0.00 0.00 3.36
2752 4166 4.261741 CCTTGTTTTGTGATTCTGACCCTG 60.262 45.833 0.00 0.00 0.00 4.45
2764 4178 1.349026 CTGACCCTGACCAAGTGATGT 59.651 52.381 0.00 0.00 0.00 3.06
2795 4209 9.303537 GTTGGAGTATTAGATAACTTGTCAGAC 57.696 37.037 0.00 0.00 0.00 3.51
2834 4251 6.695245 CAATTTGAGACCGTTGTTCTTTTTG 58.305 36.000 0.00 0.00 0.00 2.44
2856 4273 7.800155 TTGATCAACTATAATCATTCCGCAA 57.200 32.000 3.38 0.00 32.24 4.85
2950 4393 3.906218 AGCATTATGTCTCTATGCCCTGA 59.094 43.478 0.00 0.00 44.35 3.86
3009 4452 7.120051 GCATACCTGATAGGGTTCTAGATCTA 58.880 42.308 1.69 1.69 40.58 1.98
3011 4454 5.894653 ACCTGATAGGGTTCTAGATCTACC 58.105 45.833 4.75 4.75 40.58 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.377766 TCATACAGGAACATTTAGTTGAAGC 57.622 36.000 0.00 0.00 41.51 3.86
1 2 7.912250 GCATCATACAGGAACATTTAGTTGAAG 59.088 37.037 0.00 0.00 41.51 3.02
2 3 7.392953 TGCATCATACAGGAACATTTAGTTGAA 59.607 33.333 0.00 0.00 41.51 2.69
3 4 6.883756 TGCATCATACAGGAACATTTAGTTGA 59.116 34.615 0.00 0.00 41.51 3.18
4 5 6.968904 GTGCATCATACAGGAACATTTAGTTG 59.031 38.462 0.00 0.00 41.51 3.16
5 6 6.658816 TGTGCATCATACAGGAACATTTAGTT 59.341 34.615 0.00 0.00 44.93 2.24
6 7 6.179756 TGTGCATCATACAGGAACATTTAGT 58.820 36.000 0.00 0.00 0.00 2.24
7 8 6.682423 TGTGCATCATACAGGAACATTTAG 57.318 37.500 0.00 0.00 0.00 1.85
8 9 6.039605 CCATGTGCATCATACAGGAACATTTA 59.960 38.462 0.00 0.00 34.67 1.40
9 10 5.163488 CCATGTGCATCATACAGGAACATTT 60.163 40.000 0.00 0.00 34.67 2.32
10 11 4.340097 CCATGTGCATCATACAGGAACATT 59.660 41.667 0.00 0.00 34.67 2.71
11 12 3.887110 CCATGTGCATCATACAGGAACAT 59.113 43.478 0.00 0.00 34.67 2.71
12 13 3.281158 CCATGTGCATCATACAGGAACA 58.719 45.455 0.00 0.00 34.67 3.18
13 14 2.620115 CCCATGTGCATCATACAGGAAC 59.380 50.000 0.00 0.00 34.67 3.62
14 15 2.934887 CCCATGTGCATCATACAGGAA 58.065 47.619 0.00 0.00 34.67 3.36
15 16 1.477377 GCCCATGTGCATCATACAGGA 60.477 52.381 0.00 0.00 34.67 3.86
16 17 0.956633 GCCCATGTGCATCATACAGG 59.043 55.000 0.00 0.00 34.67 4.00
17 18 0.589708 CGCCCATGTGCATCATACAG 59.410 55.000 0.00 0.00 34.67 2.74
18 19 0.107263 ACGCCCATGTGCATCATACA 60.107 50.000 0.00 0.00 34.67 2.29
19 20 1.877637 TACGCCCATGTGCATCATAC 58.122 50.000 0.00 0.00 34.67 2.39
20 21 2.629336 TTACGCCCATGTGCATCATA 57.371 45.000 0.00 0.00 34.67 2.15
21 22 1.985473 ATTACGCCCATGTGCATCAT 58.015 45.000 0.00 0.00 37.22 2.45
22 23 2.629336 TATTACGCCCATGTGCATCA 57.371 45.000 0.00 0.00 0.00 3.07
23 24 3.623060 CCTATATTACGCCCATGTGCATC 59.377 47.826 0.00 0.00 0.00 3.91
24 25 3.609853 CCTATATTACGCCCATGTGCAT 58.390 45.455 0.00 0.00 0.00 3.96
25 26 2.290008 CCCTATATTACGCCCATGTGCA 60.290 50.000 0.00 0.00 0.00 4.57
26 27 2.290071 ACCCTATATTACGCCCATGTGC 60.290 50.000 0.00 0.00 0.00 4.57
27 28 3.695830 ACCCTATATTACGCCCATGTG 57.304 47.619 0.00 0.00 0.00 3.21
28 29 4.394729 CAAACCCTATATTACGCCCATGT 58.605 43.478 0.00 0.00 0.00 3.21
29 30 3.190535 GCAAACCCTATATTACGCCCATG 59.809 47.826 0.00 0.00 0.00 3.66
30 31 3.418047 GCAAACCCTATATTACGCCCAT 58.582 45.455 0.00 0.00 0.00 4.00
31 32 2.487625 GGCAAACCCTATATTACGCCCA 60.488 50.000 0.00 0.00 32.01 5.36
32 33 2.156917 GGCAAACCCTATATTACGCCC 58.843 52.381 0.00 0.00 32.01 6.13
33 34 1.802365 CGGCAAACCCTATATTACGCC 59.198 52.381 0.00 0.00 34.91 5.68
34 35 2.477754 GTCGGCAAACCCTATATTACGC 59.522 50.000 0.00 0.00 0.00 4.42
35 36 2.727798 CGTCGGCAAACCCTATATTACG 59.272 50.000 0.00 0.00 0.00 3.18
36 37 3.062042 CCGTCGGCAAACCCTATATTAC 58.938 50.000 0.00 0.00 0.00 1.89
37 38 2.699846 ACCGTCGGCAAACCCTATATTA 59.300 45.455 12.28 0.00 0.00 0.98
38 39 1.487558 ACCGTCGGCAAACCCTATATT 59.512 47.619 12.28 0.00 0.00 1.28
39 40 1.125633 ACCGTCGGCAAACCCTATAT 58.874 50.000 12.28 0.00 0.00 0.86
40 41 0.903942 AACCGTCGGCAAACCCTATA 59.096 50.000 12.28 0.00 0.00 1.31
41 42 0.675522 CAACCGTCGGCAAACCCTAT 60.676 55.000 12.28 0.00 0.00 2.57
42 43 1.301874 CAACCGTCGGCAAACCCTA 60.302 57.895 12.28 0.00 0.00 3.53
43 44 2.406002 ATCAACCGTCGGCAAACCCT 62.406 55.000 12.28 0.00 0.00 4.34
44 45 1.969589 ATCAACCGTCGGCAAACCC 60.970 57.895 12.28 0.00 0.00 4.11
45 46 1.209127 CATCAACCGTCGGCAAACC 59.791 57.895 12.28 0.00 0.00 3.27
46 47 1.209127 CCATCAACCGTCGGCAAAC 59.791 57.895 12.28 0.00 0.00 2.93
47 48 1.969064 CCCATCAACCGTCGGCAAA 60.969 57.895 12.28 0.00 0.00 3.68
48 49 2.359354 CCCATCAACCGTCGGCAA 60.359 61.111 12.28 0.00 0.00 4.52
49 50 2.191786 ATTCCCATCAACCGTCGGCA 62.192 55.000 12.28 0.00 0.00 5.69
50 51 1.451387 ATTCCCATCAACCGTCGGC 60.451 57.895 12.28 0.00 0.00 5.54
51 52 0.107897 TCATTCCCATCAACCGTCGG 60.108 55.000 10.48 10.48 0.00 4.79
52 53 1.290203 CTCATTCCCATCAACCGTCG 58.710 55.000 0.00 0.00 0.00 5.12
53 54 1.668419 CCTCATTCCCATCAACCGTC 58.332 55.000 0.00 0.00 0.00 4.79
54 55 0.394352 GCCTCATTCCCATCAACCGT 60.394 55.000 0.00 0.00 0.00 4.83
55 56 1.439353 CGCCTCATTCCCATCAACCG 61.439 60.000 0.00 0.00 0.00 4.44
56 57 0.107214 TCGCCTCATTCCCATCAACC 60.107 55.000 0.00 0.00 0.00 3.77
57 58 1.134401 TCTCGCCTCATTCCCATCAAC 60.134 52.381 0.00 0.00 0.00 3.18
58 59 1.134401 GTCTCGCCTCATTCCCATCAA 60.134 52.381 0.00 0.00 0.00 2.57
59 60 0.465705 GTCTCGCCTCATTCCCATCA 59.534 55.000 0.00 0.00 0.00 3.07
60 61 0.755686 AGTCTCGCCTCATTCCCATC 59.244 55.000 0.00 0.00 0.00 3.51
61 62 1.689273 GTAGTCTCGCCTCATTCCCAT 59.311 52.381 0.00 0.00 0.00 4.00
62 63 1.112113 GTAGTCTCGCCTCATTCCCA 58.888 55.000 0.00 0.00 0.00 4.37
63 64 0.389757 GGTAGTCTCGCCTCATTCCC 59.610 60.000 0.00 0.00 0.00 3.97
64 65 1.112113 TGGTAGTCTCGCCTCATTCC 58.888 55.000 0.00 0.00 0.00 3.01
65 66 2.541556 GTTGGTAGTCTCGCCTCATTC 58.458 52.381 0.00 0.00 0.00 2.67
66 67 1.207329 GGTTGGTAGTCTCGCCTCATT 59.793 52.381 0.00 0.00 0.00 2.57
67 68 0.824759 GGTTGGTAGTCTCGCCTCAT 59.175 55.000 0.00 0.00 0.00 2.90
68 69 1.255667 GGGTTGGTAGTCTCGCCTCA 61.256 60.000 0.00 0.00 0.00 3.86
69 70 0.971447 AGGGTTGGTAGTCTCGCCTC 60.971 60.000 0.00 0.00 0.00 4.70
70 71 0.544595 AAGGGTTGGTAGTCTCGCCT 60.545 55.000 0.00 0.00 0.00 5.52
71 72 0.108281 GAAGGGTTGGTAGTCTCGCC 60.108 60.000 0.00 0.00 0.00 5.54
72 73 0.108281 GGAAGGGTTGGTAGTCTCGC 60.108 60.000 0.00 0.00 0.00 5.03
73 74 1.558233 AGGAAGGGTTGGTAGTCTCG 58.442 55.000 0.00 0.00 0.00 4.04
74 75 5.494390 TTTAAGGAAGGGTTGGTAGTCTC 57.506 43.478 0.00 0.00 0.00 3.36
75 76 5.371769 ACTTTTAAGGAAGGGTTGGTAGTCT 59.628 40.000 0.00 0.00 0.00 3.24
76 77 5.628130 ACTTTTAAGGAAGGGTTGGTAGTC 58.372 41.667 0.00 0.00 0.00 2.59
77 78 5.658198 ACTTTTAAGGAAGGGTTGGTAGT 57.342 39.130 0.00 0.00 0.00 2.73
78 79 7.012661 TCTACTTTTAAGGAAGGGTTGGTAG 57.987 40.000 0.00 0.00 0.00 3.18
79 80 6.788957 TCTCTACTTTTAAGGAAGGGTTGGTA 59.211 38.462 0.00 0.00 0.00 3.25
80 81 5.609708 TCTCTACTTTTAAGGAAGGGTTGGT 59.390 40.000 0.00 0.00 0.00 3.67
81 82 6.123045 TCTCTACTTTTAAGGAAGGGTTGG 57.877 41.667 0.00 0.00 0.00 3.77
82 83 9.734984 TTTATCTCTACTTTTAAGGAAGGGTTG 57.265 33.333 0.00 0.00 0.00 3.77
167 172 6.864165 GCCCGACAACATAGATTAAAACAAAA 59.136 34.615 0.00 0.00 0.00 2.44
168 173 6.383415 GCCCGACAACATAGATTAAAACAAA 58.617 36.000 0.00 0.00 0.00 2.83
201 206 0.696501 ATGAAAAGCCCGGGTGTAGT 59.303 50.000 24.63 3.64 0.00 2.73
203 208 0.988832 AGATGAAAAGCCCGGGTGTA 59.011 50.000 24.63 3.26 0.00 2.90
205 210 0.527565 CAAGATGAAAAGCCCGGGTG 59.472 55.000 24.63 3.89 0.00 4.61
220 225 3.706373 GCAGAGCCGACCCCAAGA 61.706 66.667 0.00 0.00 0.00 3.02
276 281 1.669115 CCACTGGGTTGCTCGTGAG 60.669 63.158 0.00 0.00 0.00 3.51
334 700 1.798234 CGTCTGTGTGGTGACCGGTA 61.798 60.000 7.34 0.00 0.00 4.02
379 778 7.174253 GCTAGACCTAGACGAGTAGTAGTACTA 59.826 44.444 10.28 5.90 36.12 1.82
380 779 6.016276 GCTAGACCTAGACGAGTAGTAGTACT 60.016 46.154 10.09 10.09 37.50 2.73
381 780 6.149633 GCTAGACCTAGACGAGTAGTAGTAC 58.850 48.000 8.16 0.00 35.21 2.73
424 823 2.683572 GATTGGGTTGGGGGTGCC 60.684 66.667 0.00 0.00 0.00 5.01
459 858 4.171103 GATTGGGTCCGGACGGGG 62.171 72.222 27.68 0.00 36.01 5.73
525 946 3.756783 CCCCCGACCTCTCCCTCT 61.757 72.222 0.00 0.00 0.00 3.69
1349 2169 1.002624 GTTGTCATCGGGGAAGGCA 60.003 57.895 0.00 0.00 0.00 4.75
1502 2325 1.003580 ACATCGGTGAGAACAGCCATT 59.996 47.619 0.65 0.00 40.87 3.16
1571 2475 3.380471 TGGGGATTACCTCCATTGTTG 57.620 47.619 0.00 0.00 46.98 3.33
1586 2490 4.161942 CCATTGTTCATAGCATTTTGGGGA 59.838 41.667 0.00 0.00 0.00 4.81
1587 2491 4.161942 TCCATTGTTCATAGCATTTTGGGG 59.838 41.667 0.00 0.00 0.00 4.96
1588 2492 5.341872 TCCATTGTTCATAGCATTTTGGG 57.658 39.130 0.00 0.00 0.00 4.12
1589 2493 5.105228 ACCTCCATTGTTCATAGCATTTTGG 60.105 40.000 0.00 0.00 0.00 3.28
1590 2494 5.969423 ACCTCCATTGTTCATAGCATTTTG 58.031 37.500 0.00 0.00 0.00 2.44
1591 2495 6.096846 GGTACCTCCATTGTTCATAGCATTTT 59.903 38.462 4.06 0.00 35.97 1.82
1592 2496 5.594317 GGTACCTCCATTGTTCATAGCATTT 59.406 40.000 4.06 0.00 35.97 2.32
1593 2497 5.133221 GGTACCTCCATTGTTCATAGCATT 58.867 41.667 4.06 0.00 35.97 3.56
1594 2498 4.718961 GGTACCTCCATTGTTCATAGCAT 58.281 43.478 4.06 0.00 35.97 3.79
1595 2499 3.431626 CGGTACCTCCATTGTTCATAGCA 60.432 47.826 10.90 0.00 35.57 3.49
1596 2500 3.131396 CGGTACCTCCATTGTTCATAGC 58.869 50.000 10.90 0.00 35.57 2.97
1597 2501 3.134081 ACCGGTACCTCCATTGTTCATAG 59.866 47.826 4.49 0.00 35.57 2.23
1598 2502 3.109151 ACCGGTACCTCCATTGTTCATA 58.891 45.455 4.49 0.00 35.57 2.15
1599 2503 1.913419 ACCGGTACCTCCATTGTTCAT 59.087 47.619 4.49 0.00 35.57 2.57
1600 2504 1.276989 GACCGGTACCTCCATTGTTCA 59.723 52.381 7.34 0.00 35.57 3.18
1601 2505 1.276989 TGACCGGTACCTCCATTGTTC 59.723 52.381 7.34 0.00 35.57 3.18
1602 2506 1.278127 CTGACCGGTACCTCCATTGTT 59.722 52.381 7.34 0.00 35.57 2.83
1603 2507 0.902531 CTGACCGGTACCTCCATTGT 59.097 55.000 7.34 0.00 35.57 2.71
1604 2508 1.191535 TCTGACCGGTACCTCCATTG 58.808 55.000 7.34 0.00 35.57 2.82
1605 2509 1.553704 GTTCTGACCGGTACCTCCATT 59.446 52.381 7.34 0.00 35.57 3.16
1606 2510 1.192428 GTTCTGACCGGTACCTCCAT 58.808 55.000 7.34 0.00 35.57 3.41
1607 2511 1.246056 CGTTCTGACCGGTACCTCCA 61.246 60.000 7.34 0.00 35.57 3.86
1608 2512 1.509923 CGTTCTGACCGGTACCTCC 59.490 63.158 7.34 0.00 0.00 4.30
1609 2513 1.509923 CCGTTCTGACCGGTACCTC 59.490 63.158 7.34 1.91 40.59 3.85
1610 2514 3.690745 CCGTTCTGACCGGTACCT 58.309 61.111 7.34 0.00 40.59 3.08
1616 2520 0.319211 TGCAGTTACCGTTCTGACCG 60.319 55.000 7.35 0.00 34.02 4.79
1617 2521 1.873698 TTGCAGTTACCGTTCTGACC 58.126 50.000 7.35 0.00 34.02 4.02
1676 2580 0.027979 CAAATACATCCAGCACGGCG 59.972 55.000 4.80 4.80 33.14 6.46
1858 2762 4.618912 CACGTCATCGGATACATCTCATTC 59.381 45.833 0.00 0.00 41.85 2.67
1989 2893 6.376299 CCATAGCAATGTCACATAGGCATAAT 59.624 38.462 14.79 4.76 43.07 1.28
2096 3000 3.659183 AAAGGATAGTGGCAGAAGCAT 57.341 42.857 0.00 0.00 44.61 3.79
2162 3066 9.214957 CAGTTAGAACAACATGTAATAGTGGAA 57.785 33.333 0.00 0.00 0.00 3.53
2173 3077 2.967459 TGCGCAGTTAGAACAACATG 57.033 45.000 5.66 0.00 0.00 3.21
2189 3093 2.221055 GTCGAACCCTATGCTATTTGCG 59.779 50.000 0.00 0.00 46.63 4.85
2199 3111 0.902531 CCACAGTGGTCGAACCCTAT 59.097 55.000 11.99 0.00 37.50 2.57
2269 3181 7.062605 CAGCACATAATTAAGAAGCAAACAAGG 59.937 37.037 10.67 0.00 0.00 3.61
2277 3189 3.319122 CCCCCAGCACATAATTAAGAAGC 59.681 47.826 0.00 0.00 0.00 3.86
2342 3755 5.506317 GGGGAAACAGCATATTCATCTTTCG 60.506 44.000 0.00 0.00 0.00 3.46
2376 3789 7.986889 AGTCAACAAAAAGCAACCAGAATAAAT 59.013 29.630 0.00 0.00 0.00 1.40
2479 3892 4.489737 TCCTAGTCCATACATAGGGTTGG 58.510 47.826 0.00 0.00 37.31 3.77
2534 3947 5.403166 CAGTGACACCAAAATTGCACAATAG 59.597 40.000 0.84 0.00 0.00 1.73
2566 3979 2.441750 ACCATTACCGCACCTATTCCAT 59.558 45.455 0.00 0.00 0.00 3.41
2578 3991 8.500773 GTCAATACCAATGTAATACCATTACCG 58.499 37.037 6.60 0.00 33.37 4.02
2614 4027 6.742109 AGGTTCAAACACAAATCTTCATCTG 58.258 36.000 0.00 0.00 0.00 2.90
2629 4042 9.406828 GTCTTAAATGGTCAATTAGGTTCAAAC 57.593 33.333 0.00 0.00 0.00 2.93
2642 4055 6.601613 GGTACCATGAATGTCTTAAATGGTCA 59.398 38.462 7.15 0.00 46.25 4.02
2727 4141 4.261614 GGGTCAGAATCACAAAACAAGGAC 60.262 45.833 0.00 0.00 0.00 3.85
2732 4146 3.882888 GTCAGGGTCAGAATCACAAAACA 59.117 43.478 0.00 0.00 0.00 2.83
2764 4178 8.380099 ACAAGTTATCTAATACTCCAACCAACA 58.620 33.333 0.00 0.00 0.00 3.33
2818 4232 5.866503 GTTGATCAAAAAGAACAACGGTC 57.133 39.130 10.35 0.00 45.82 4.79
2834 4251 8.173775 CAGATTGCGGAATGATTATAGTTGATC 58.826 37.037 6.97 0.00 0.00 2.92
2856 4273 1.759881 GGATAGGCCTGCTGCAGAT 59.240 57.895 30.10 15.68 43.89 2.90
2950 4393 3.072211 CCAGCATCATATCACGAAGCAT 58.928 45.455 0.00 0.00 29.67 3.79
3009 4452 3.367703 GCAGCAATGCAACTAATTCAGGT 60.368 43.478 8.35 0.00 34.41 4.00
3011 4454 3.184541 GGCAGCAATGCAACTAATTCAG 58.815 45.455 8.35 0.00 36.33 3.02


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

AutoCloner maintained by Alex Coulton.