Multiple sequence alignment - TraesCS1A01G275600

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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 TraesCS1A01G275600 chr1A 100.000 2732 0 0 1 2732 469664683 469661952 0.000000e+00 5046.0
1 TraesCS1A01G275600 chr1A 80.034 591 93 11 145 713 234809137 234809724 5.440000e-112 414.0
2 TraesCS1A01G275600 chr1A 74.888 446 96 11 278 713 580928651 580929090 3.590000e-44 189.0
3 TraesCS1A01G275600 chr1D 94.089 2047 74 20 720 2732 370918486 370916453 0.000000e+00 3066.0
4 TraesCS1A01G275600 chr1D 80.402 398 59 10 150 532 159909759 159910152 4.450000e-73 285.0
5 TraesCS1A01G275600 chr1D 77.305 423 87 6 264 681 111517648 111518066 9.780000e-60 241.0
6 TraesCS1A01G275600 chr1B 93.285 1236 46 21 716 1923 494240852 494239626 0.000000e+00 1788.0
7 TraesCS1A01G275600 chr1B 93.292 805 27 11 1951 2730 494237543 494236741 0.000000e+00 1162.0
8 TraesCS1A01G275600 chr1B 89.607 356 29 4 370 722 494241488 494241138 1.930000e-121 446.0
9 TraesCS1A01G275600 chr1B 78.356 596 102 10 145 713 223141590 223140995 7.190000e-96 361.0
10 TraesCS1A01G275600 chr6D 76.361 588 110 20 145 713 10695463 10694886 3.440000e-74 289.0
11 TraesCS1A01G275600 chr6D 76.136 352 73 8 323 667 433474233 433473886 1.010000e-39 174.0
12 TraesCS1A01G275600 chr5D 77.315 432 76 18 147 561 525971620 525971194 4.550000e-58 235.0
13 TraesCS1A01G275600 chr5D 75.610 410 94 4 284 689 376684221 376683814 5.970000e-47 198.0
14 TraesCS1A01G275600 chr5D 92.000 50 4 0 86 135 77865229 77865278 1.360000e-08 71.3
15 TraesCS1A01G275600 chr7A 79.730 296 45 13 278 563 68234316 68234606 1.660000e-47 200.0
16 TraesCS1A01G275600 chr7A 77.391 115 22 3 24 136 727281417 727281305 6.310000e-07 65.8
17 TraesCS1A01G275600 chr2B 81.553 206 29 8 1428 1627 785271225 785271427 7.830000e-36 161.0
18 TraesCS1A01G275600 chr2B 79.907 214 27 12 1428 1627 785278582 785278793 2.840000e-30 143.0
19 TraesCS1A01G275600 chr2B 77.326 172 32 6 299 463 71879277 71879448 8.050000e-16 95.3
20 TraesCS1A01G275600 chr2B 95.455 44 1 1 98 140 731456497 731456540 4.880000e-08 69.4
21 TraesCS1A01G275600 chr2A 80.095 211 26 11 1431 1627 775272171 775271963 2.840000e-30 143.0
22 TraesCS1A01G275600 chr4D 79.500 200 32 8 518 713 467991436 467991242 1.710000e-27 134.0
23 TraesCS1A01G275600 chr2D 78.972 214 29 11 1428 1627 649585904 649586115 6.140000e-27 132.0
24 TraesCS1A01G275600 chr4A 92.157 51 2 2 97 146 553439667 553439618 1.360000e-08 71.3


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 TraesCS1A01G275600 chr1A 469661952 469664683 2731 True 5046 5046 100.000000 1 2732 1 chr1A.!!$R1 2731
1 TraesCS1A01G275600 chr1A 234809137 234809724 587 False 414 414 80.034000 145 713 1 chr1A.!!$F1 568
2 TraesCS1A01G275600 chr1D 370916453 370918486 2033 True 3066 3066 94.089000 720 2732 1 chr1D.!!$R1 2012
3 TraesCS1A01G275600 chr1B 494236741 494241488 4747 True 1132 1788 92.061333 370 2730 3 chr1B.!!$R2 2360
4 TraesCS1A01G275600 chr1B 223140995 223141590 595 True 361 361 78.356000 145 713 1 chr1B.!!$R1 568
5 TraesCS1A01G275600 chr6D 10694886 10695463 577 True 289 289 76.361000 145 713 1 chr6D.!!$R1 568

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
96 97 0.037326 TCTCAACTTCTTCGGCGCAT 60.037 50.0 10.83 0.00 0.00 4.73 F
102 103 0.097674 CTTCTTCGGCGCATCCAAAG 59.902 55.0 10.83 4.95 34.01 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1542 1897 0.548682 ACCACCCCAGCATCTTCTCT 60.549 55.000 0.0 0.0 0.0 3.10 R
2056 4477 1.668337 CGCATATTCTCTCTCGCTGGG 60.668 57.143 0.0 0.0 0.0 4.45 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
36 37 4.196971 GGATACCGGGATATGTAAATGGC 58.803 47.826 6.32 0.00 0.00 4.40
37 38 4.323945 GGATACCGGGATATGTAAATGGCA 60.324 45.833 6.32 0.00 0.00 4.92
38 39 3.586470 ACCGGGATATGTAAATGGCAA 57.414 42.857 6.32 0.00 0.00 4.52
39 40 3.904717 ACCGGGATATGTAAATGGCAAA 58.095 40.909 6.32 0.00 0.00 3.68
40 41 3.634910 ACCGGGATATGTAAATGGCAAAC 59.365 43.478 6.32 0.00 0.00 2.93
41 42 3.888930 CCGGGATATGTAAATGGCAAACT 59.111 43.478 0.00 0.00 0.00 2.66
42 43 5.067273 CCGGGATATGTAAATGGCAAACTA 58.933 41.667 0.00 0.00 0.00 2.24
43 44 5.048991 CCGGGATATGTAAATGGCAAACTAC 60.049 44.000 0.00 0.00 0.00 2.73
44 45 5.048991 CGGGATATGTAAATGGCAAACTACC 60.049 44.000 0.00 0.00 0.00 3.18
45 46 5.830991 GGGATATGTAAATGGCAAACTACCA 59.169 40.000 0.00 0.00 42.61 3.25
46 47 6.322712 GGGATATGTAAATGGCAAACTACCAA 59.677 38.462 0.00 0.00 41.49 3.67
47 48 7.015195 GGGATATGTAAATGGCAAACTACCAAT 59.985 37.037 0.00 0.00 41.49 3.16
48 49 8.421002 GGATATGTAAATGGCAAACTACCAATT 58.579 33.333 0.00 0.00 41.49 2.32
49 50 9.816354 GATATGTAAATGGCAAACTACCAATTT 57.184 29.630 0.00 0.00 41.49 1.82
50 51 9.816354 ATATGTAAATGGCAAACTACCAATTTC 57.184 29.630 0.00 0.00 41.49 2.17
51 52 7.055667 TGTAAATGGCAAACTACCAATTTCA 57.944 32.000 0.00 0.00 41.49 2.69
52 53 6.926272 TGTAAATGGCAAACTACCAATTTCAC 59.074 34.615 0.00 0.00 41.49 3.18
53 54 5.543507 AATGGCAAACTACCAATTTCACA 57.456 34.783 0.00 0.00 41.49 3.58
54 55 5.743636 ATGGCAAACTACCAATTTCACAT 57.256 34.783 0.00 0.00 41.49 3.21
55 56 5.132897 TGGCAAACTACCAATTTCACATC 57.867 39.130 0.00 0.00 33.12 3.06
56 57 4.021544 TGGCAAACTACCAATTTCACATCC 60.022 41.667 0.00 0.00 33.12 3.51
57 58 4.021544 GGCAAACTACCAATTTCACATCCA 60.022 41.667 0.00 0.00 0.00 3.41
58 59 5.337491 GGCAAACTACCAATTTCACATCCAT 60.337 40.000 0.00 0.00 0.00 3.41
59 60 6.127479 GGCAAACTACCAATTTCACATCCATA 60.127 38.462 0.00 0.00 0.00 2.74
60 61 6.751888 GCAAACTACCAATTTCACATCCATAC 59.248 38.462 0.00 0.00 0.00 2.39
61 62 7.576666 GCAAACTACCAATTTCACATCCATACA 60.577 37.037 0.00 0.00 0.00 2.29
62 63 8.303156 CAAACTACCAATTTCACATCCATACAA 58.697 33.333 0.00 0.00 0.00 2.41
63 64 8.593945 AACTACCAATTTCACATCCATACAAT 57.406 30.769 0.00 0.00 0.00 2.71
64 65 8.593945 ACTACCAATTTCACATCCATACAATT 57.406 30.769 0.00 0.00 0.00 2.32
65 66 9.693739 ACTACCAATTTCACATCCATACAATTA 57.306 29.630 0.00 0.00 0.00 1.40
76 77 9.920826 CACATCCATACAATTATATGTAATCGC 57.079 33.333 3.17 0.00 39.12 4.58
77 78 9.890629 ACATCCATACAATTATATGTAATCGCT 57.109 29.630 3.17 0.00 39.12 4.93
80 81 9.803315 TCCATACAATTATATGTAATCGCTCTC 57.197 33.333 3.17 0.00 39.12 3.20
81 82 9.586435 CCATACAATTATATGTAATCGCTCTCA 57.414 33.333 3.17 0.00 39.12 3.27
85 86 9.547753 ACAATTATATGTAATCGCTCTCAACTT 57.452 29.630 0.00 0.00 30.28 2.66
87 88 9.988815 AATTATATGTAATCGCTCTCAACTTCT 57.011 29.630 0.00 0.00 30.28 2.85
88 89 9.988815 ATTATATGTAATCGCTCTCAACTTCTT 57.011 29.630 0.00 0.00 0.00 2.52
89 90 7.938563 ATATGTAATCGCTCTCAACTTCTTC 57.061 36.000 0.00 0.00 0.00 2.87
90 91 4.166523 TGTAATCGCTCTCAACTTCTTCG 58.833 43.478 0.00 0.00 0.00 3.79
91 92 2.285827 ATCGCTCTCAACTTCTTCGG 57.714 50.000 0.00 0.00 0.00 4.30
92 93 0.388649 TCGCTCTCAACTTCTTCGGC 60.389 55.000 0.00 0.00 0.00 5.54
93 94 1.678269 CGCTCTCAACTTCTTCGGCG 61.678 60.000 0.00 0.00 35.75 6.46
94 95 1.960994 GCTCTCAACTTCTTCGGCGC 61.961 60.000 0.00 0.00 0.00 6.53
95 96 0.667487 CTCTCAACTTCTTCGGCGCA 60.667 55.000 10.83 0.00 0.00 6.09
96 97 0.037326 TCTCAACTTCTTCGGCGCAT 60.037 50.000 10.83 0.00 0.00 4.73
97 98 0.371645 CTCAACTTCTTCGGCGCATC 59.628 55.000 10.83 0.00 0.00 3.91
98 99 1.019278 TCAACTTCTTCGGCGCATCC 61.019 55.000 10.83 0.00 0.00 3.51
99 100 1.003839 AACTTCTTCGGCGCATCCA 60.004 52.632 10.83 0.00 34.01 3.41
100 101 0.605319 AACTTCTTCGGCGCATCCAA 60.605 50.000 10.83 0.00 34.01 3.53
101 102 0.605319 ACTTCTTCGGCGCATCCAAA 60.605 50.000 10.83 0.00 34.01 3.28
102 103 0.097674 CTTCTTCGGCGCATCCAAAG 59.902 55.000 10.83 4.95 34.01 2.77
103 104 1.922135 TTCTTCGGCGCATCCAAAGC 61.922 55.000 10.83 0.00 34.01 3.51
104 105 2.671276 TTCGGCGCATCCAAAGCA 60.671 55.556 10.83 0.00 34.01 3.91
105 106 2.855728 CTTCGGCGCATCCAAAGCAC 62.856 60.000 10.83 0.00 34.01 4.40
106 107 3.736100 CGGCGCATCCAAAGCACA 61.736 61.111 10.83 0.00 34.01 4.57
107 108 2.650196 GGCGCATCCAAAGCACAA 59.350 55.556 10.83 0.00 34.01 3.33
108 109 1.734117 GGCGCATCCAAAGCACAAC 60.734 57.895 10.83 0.00 34.01 3.32
109 110 1.007502 GCGCATCCAAAGCACAACA 60.008 52.632 0.30 0.00 0.00 3.33
110 111 0.597118 GCGCATCCAAAGCACAACAA 60.597 50.000 0.30 0.00 0.00 2.83
111 112 1.936203 GCGCATCCAAAGCACAACAAT 60.936 47.619 0.30 0.00 0.00 2.71
112 113 2.406130 CGCATCCAAAGCACAACAATT 58.594 42.857 0.00 0.00 0.00 2.32
113 114 2.409378 CGCATCCAAAGCACAACAATTC 59.591 45.455 0.00 0.00 0.00 2.17
114 115 3.391965 GCATCCAAAGCACAACAATTCA 58.608 40.909 0.00 0.00 0.00 2.57
115 116 3.184986 GCATCCAAAGCACAACAATTCAC 59.815 43.478 0.00 0.00 0.00 3.18
116 117 4.624015 CATCCAAAGCACAACAATTCACT 58.376 39.130 0.00 0.00 0.00 3.41
117 118 4.305989 TCCAAAGCACAACAATTCACTC 57.694 40.909 0.00 0.00 0.00 3.51
118 119 3.953612 TCCAAAGCACAACAATTCACTCT 59.046 39.130 0.00 0.00 0.00 3.24
119 120 4.402155 TCCAAAGCACAACAATTCACTCTT 59.598 37.500 0.00 0.00 0.00 2.85
120 121 5.592282 TCCAAAGCACAACAATTCACTCTTA 59.408 36.000 0.00 0.00 0.00 2.10
121 122 6.265196 TCCAAAGCACAACAATTCACTCTTAT 59.735 34.615 0.00 0.00 0.00 1.73
122 123 6.364165 CCAAAGCACAACAATTCACTCTTATG 59.636 38.462 0.00 0.00 0.00 1.90
123 124 6.882610 AAGCACAACAATTCACTCTTATGA 57.117 33.333 0.00 0.00 0.00 2.15
124 125 6.882610 AGCACAACAATTCACTCTTATGAA 57.117 33.333 0.00 0.00 42.62 2.57
125 126 7.275888 AGCACAACAATTCACTCTTATGAAA 57.724 32.000 0.00 0.00 41.78 2.69
126 127 7.715657 AGCACAACAATTCACTCTTATGAAAA 58.284 30.769 0.00 0.00 41.78 2.29
127 128 8.362639 AGCACAACAATTCACTCTTATGAAAAT 58.637 29.630 0.00 0.00 41.78 1.82
128 129 8.981647 GCACAACAATTCACTCTTATGAAAATT 58.018 29.630 0.00 0.00 41.78 1.82
163 164 5.635280 CGAGACATCATACTTGAAACAGTGT 59.365 40.000 0.00 0.00 34.96 3.55
167 168 7.663081 AGACATCATACTTGAAACAGTGTCATT 59.337 33.333 0.00 0.00 38.48 2.57
191 197 4.961438 AAGACTTGTGGATTTTGGCATT 57.039 36.364 0.00 0.00 0.00 3.56
200 209 5.990996 TGTGGATTTTGGCATTCTTTCTTTC 59.009 36.000 0.00 0.00 0.00 2.62
202 211 4.091945 GGATTTTGGCATTCTTTCTTTCGC 59.908 41.667 0.00 0.00 0.00 4.70
207 216 2.533266 GCATTCTTTCTTTCGCCATGG 58.467 47.619 7.63 7.63 0.00 3.66
218 227 2.361104 GCCATGGCGGGTTCTCAA 60.361 61.111 23.48 0.00 34.06 3.02
222 231 0.958091 CATGGCGGGTTCTCAAAACA 59.042 50.000 0.00 0.00 0.00 2.83
225 234 1.029681 GGCGGGTTCTCAAAACAACT 58.970 50.000 0.00 0.00 0.00 3.16
226 235 1.001706 GGCGGGTTCTCAAAACAACTC 60.002 52.381 0.00 0.00 0.00 3.01
250 260 2.571212 TGTGCTTCACAATCTCCGTTT 58.429 42.857 0.00 0.00 41.69 3.60
258 268 5.418310 TCACAATCTCCGTTTTTCAAGAC 57.582 39.130 0.00 0.00 0.00 3.01
263 273 4.875544 TCTCCGTTTTTCAAGACACTTG 57.124 40.909 5.29 5.29 0.00 3.16
287 304 1.447838 CTCCGGCGTGCAACTACAT 60.448 57.895 6.01 0.00 31.75 2.29
289 306 2.695055 CGGCGTGCAACTACATCG 59.305 61.111 0.00 0.00 31.75 3.84
310 334 2.029244 GTCAACGAGCATGAATACACCG 59.971 50.000 0.00 0.00 0.00 4.94
314 338 0.657840 GAGCATGAATACACCGTGGC 59.342 55.000 3.03 0.00 0.00 5.01
336 360 4.166523 CGTACTATCTTGCCGATGGTATG 58.833 47.826 10.87 11.27 44.56 2.39
353 378 2.766651 GTATCCTCGGTGGGGGCA 60.767 66.667 0.00 0.00 36.20 5.36
372 397 4.762251 GGGCATTTGTGAAGACTATATCCC 59.238 45.833 0.00 0.00 0.00 3.85
389 414 6.704056 ATATCCCATCCCTAAGGTAACAAG 57.296 41.667 0.00 0.00 41.41 3.16
472 500 1.528309 AAGCTCGTTGGGGTGTTGG 60.528 57.895 0.00 0.00 0.00 3.77
480 508 3.881104 GGGGTGTTGGTCGTGGGT 61.881 66.667 0.00 0.00 0.00 4.51
554 583 6.642131 GTGTAATCTTGCACAACATGATTGTT 59.358 34.615 0.00 0.00 46.81 2.83
602 637 4.436050 CGCACGCATGATTTTTAGAAGTCT 60.436 41.667 0.00 0.00 0.00 3.24
614 649 9.220767 GATTTTTAGAAGTCTGGAGTACATGTT 57.779 33.333 2.30 0.00 0.00 2.71
616 651 6.911250 TTAGAAGTCTGGAGTACATGTTCA 57.089 37.500 2.30 0.00 0.00 3.18
620 655 6.212388 AGAAGTCTGGAGTACATGTTCATCTT 59.788 38.462 2.30 6.19 0.00 2.40
634 670 1.742761 CATCTTCCGGCACAAGATGT 58.257 50.000 25.58 4.51 46.67 3.06
689 725 5.815581 TGACAACTTTAAGATACCCATGCT 58.184 37.500 0.00 0.00 0.00 3.79
705 741 1.229975 TGCTCACATGCAACCACTCG 61.230 55.000 0.00 0.00 40.29 4.18
717 753 2.151502 ACCACTCGATGATCTGGAGT 57.848 50.000 6.24 5.88 42.99 3.85
722 758 4.038522 CCACTCGATGATCTGGAGTATGTT 59.961 45.833 11.68 0.00 40.57 2.71
723 759 5.241728 CCACTCGATGATCTGGAGTATGTTA 59.758 44.000 11.68 0.00 40.57 2.41
1221 1576 2.482296 TTTTCGTCGACTCCTCCGCC 62.482 60.000 14.70 0.00 0.00 6.13
1466 1821 4.353437 GGTGGCGTTCGAGTCCGT 62.353 66.667 0.00 0.00 37.05 4.69
1542 1897 3.075005 GGCGACTGGGACTGGCTA 61.075 66.667 0.00 0.00 30.97 3.93
1643 1998 2.740055 CACCACGACAGCCAGCTC 60.740 66.667 0.00 0.00 0.00 4.09
1735 2090 2.725203 TTTCCGCCTGAGGTGAACCG 62.725 60.000 14.80 0.44 42.08 4.44
1776 2131 1.514443 GCTCAGCTACGTGTCCGAC 60.514 63.158 0.00 0.00 37.88 4.79
1866 2231 7.225538 CAGCTCCAGATTAATTAACCTGTACTG 59.774 40.741 16.78 15.47 0.00 2.74
1908 2274 1.079819 GCTGCGTTACTGCTCCTGA 60.080 57.895 1.68 0.00 39.94 3.86
2000 4421 0.905839 CGTAACAGCTAACGACGAGC 59.094 55.000 0.00 0.12 41.55 5.03
2056 4477 1.740025 GCCTCTCAGTAATTGTGGCAC 59.260 52.381 11.55 11.55 38.04 5.01
2074 4495 2.865670 GCACCCAGCGAGAGAGAATATG 60.866 54.545 0.00 0.00 0.00 1.78
2228 4649 1.891178 CGAACGTCTTATCGTCAGCA 58.109 50.000 0.00 0.00 43.38 4.41
2230 4651 2.728225 CGAACGTCTTATCGTCAGCAGT 60.728 50.000 0.00 0.00 43.38 4.40
2539 4979 1.619057 TCTCATGTGGATGGGGGCA 60.619 57.895 0.00 0.00 29.98 5.36
2571 5011 0.662970 GCTCCGCAGATCTGATCGAC 60.663 60.000 27.04 7.05 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.777463 CCATTTACATATCCCGGTATCCC 58.223 47.826 0.00 0.00 0.00 3.85
14 15 4.196971 GCCATTTACATATCCCGGTATCC 58.803 47.826 0.00 0.00 0.00 2.59
15 16 4.839121 TGCCATTTACATATCCCGGTATC 58.161 43.478 0.00 0.00 0.00 2.24
16 17 4.919774 TGCCATTTACATATCCCGGTAT 57.080 40.909 0.00 0.00 0.00 2.73
17 18 4.708576 TTGCCATTTACATATCCCGGTA 57.291 40.909 0.00 0.00 0.00 4.02
18 19 3.586470 TTGCCATTTACATATCCCGGT 57.414 42.857 0.00 0.00 0.00 5.28
19 20 3.888930 AGTTTGCCATTTACATATCCCGG 59.111 43.478 0.00 0.00 0.00 5.73
20 21 5.048991 GGTAGTTTGCCATTTACATATCCCG 60.049 44.000 0.00 0.00 0.00 5.14
21 22 5.830991 TGGTAGTTTGCCATTTACATATCCC 59.169 40.000 0.00 0.00 0.00 3.85
22 23 6.952773 TGGTAGTTTGCCATTTACATATCC 57.047 37.500 0.00 0.00 0.00 2.59
23 24 9.816354 AAATTGGTAGTTTGCCATTTACATATC 57.184 29.630 0.00 0.00 35.71 1.63
24 25 9.816354 GAAATTGGTAGTTTGCCATTTACATAT 57.184 29.630 0.00 0.00 35.71 1.78
25 26 8.807118 TGAAATTGGTAGTTTGCCATTTACATA 58.193 29.630 0.00 0.00 35.71 2.29
26 27 7.602265 GTGAAATTGGTAGTTTGCCATTTACAT 59.398 33.333 0.00 0.00 35.71 2.29
27 28 6.926272 GTGAAATTGGTAGTTTGCCATTTACA 59.074 34.615 0.00 0.00 35.71 2.41
28 29 6.926272 TGTGAAATTGGTAGTTTGCCATTTAC 59.074 34.615 0.00 0.00 35.71 2.01
29 30 7.055667 TGTGAAATTGGTAGTTTGCCATTTA 57.944 32.000 0.00 0.00 35.71 1.40
30 31 5.923204 TGTGAAATTGGTAGTTTGCCATTT 58.077 33.333 0.00 0.00 35.71 2.32
31 32 5.543507 TGTGAAATTGGTAGTTTGCCATT 57.456 34.783 0.00 0.00 35.71 3.16
32 33 5.337491 GGATGTGAAATTGGTAGTTTGCCAT 60.337 40.000 0.00 0.00 35.71 4.40
33 34 4.021544 GGATGTGAAATTGGTAGTTTGCCA 60.022 41.667 0.00 0.00 0.00 4.92
34 35 4.021544 TGGATGTGAAATTGGTAGTTTGCC 60.022 41.667 0.00 0.00 0.00 4.52
35 36 5.132897 TGGATGTGAAATTGGTAGTTTGC 57.867 39.130 0.00 0.00 0.00 3.68
36 37 7.825681 TGTATGGATGTGAAATTGGTAGTTTG 58.174 34.615 0.00 0.00 0.00 2.93
37 38 8.415950 TTGTATGGATGTGAAATTGGTAGTTT 57.584 30.769 0.00 0.00 0.00 2.66
38 39 8.593945 ATTGTATGGATGTGAAATTGGTAGTT 57.406 30.769 0.00 0.00 0.00 2.24
39 40 8.593945 AATTGTATGGATGTGAAATTGGTAGT 57.406 30.769 0.00 0.00 0.00 2.73
50 51 9.920826 GCGATTACATATAATTGTATGGATGTG 57.079 33.333 21.79 11.99 36.58 3.21
51 52 9.890629 AGCGATTACATATAATTGTATGGATGT 57.109 29.630 21.79 9.53 36.58 3.06
54 55 9.803315 GAGAGCGATTACATATAATTGTATGGA 57.197 33.333 21.79 13.73 36.58 3.41
55 56 9.586435 TGAGAGCGATTACATATAATTGTATGG 57.414 33.333 21.79 8.46 36.58 2.74
59 60 9.547753 AAGTTGAGAGCGATTACATATAATTGT 57.452 29.630 0.00 0.00 35.37 2.71
61 62 9.988815 AGAAGTTGAGAGCGATTACATATAATT 57.011 29.630 0.00 0.00 30.77 1.40
62 63 9.988815 AAGAAGTTGAGAGCGATTACATATAAT 57.011 29.630 0.00 0.00 33.47 1.28
63 64 9.464714 GAAGAAGTTGAGAGCGATTACATATAA 57.535 33.333 0.00 0.00 0.00 0.98
64 65 7.803659 CGAAGAAGTTGAGAGCGATTACATATA 59.196 37.037 0.00 0.00 0.00 0.86
65 66 6.638873 CGAAGAAGTTGAGAGCGATTACATAT 59.361 38.462 0.00 0.00 0.00 1.78
66 67 5.971792 CGAAGAAGTTGAGAGCGATTACATA 59.028 40.000 0.00 0.00 0.00 2.29
67 68 4.800993 CGAAGAAGTTGAGAGCGATTACAT 59.199 41.667 0.00 0.00 0.00 2.29
68 69 4.166523 CGAAGAAGTTGAGAGCGATTACA 58.833 43.478 0.00 0.00 0.00 2.41
69 70 3.548268 CCGAAGAAGTTGAGAGCGATTAC 59.452 47.826 0.00 0.00 0.00 1.89
70 71 3.770666 CCGAAGAAGTTGAGAGCGATTA 58.229 45.455 0.00 0.00 0.00 1.75
71 72 2.611518 CCGAAGAAGTTGAGAGCGATT 58.388 47.619 0.00 0.00 0.00 3.34
72 73 1.737363 GCCGAAGAAGTTGAGAGCGAT 60.737 52.381 0.00 0.00 0.00 4.58
73 74 0.388649 GCCGAAGAAGTTGAGAGCGA 60.389 55.000 0.00 0.00 0.00 4.93
74 75 1.678269 CGCCGAAGAAGTTGAGAGCG 61.678 60.000 0.00 0.00 36.06 5.03
75 76 1.960994 GCGCCGAAGAAGTTGAGAGC 61.961 60.000 0.00 0.00 0.00 4.09
76 77 0.667487 TGCGCCGAAGAAGTTGAGAG 60.667 55.000 4.18 0.00 0.00 3.20
77 78 0.037326 ATGCGCCGAAGAAGTTGAGA 60.037 50.000 4.18 0.00 0.00 3.27
78 79 0.371645 GATGCGCCGAAGAAGTTGAG 59.628 55.000 4.18 0.00 0.00 3.02
79 80 1.019278 GGATGCGCCGAAGAAGTTGA 61.019 55.000 4.18 0.00 0.00 3.18
80 81 1.298157 TGGATGCGCCGAAGAAGTTG 61.298 55.000 4.18 0.00 40.66 3.16
81 82 0.605319 TTGGATGCGCCGAAGAAGTT 60.605 50.000 4.18 0.00 40.66 2.66
82 83 0.605319 TTTGGATGCGCCGAAGAAGT 60.605 50.000 4.18 0.00 40.66 3.01
83 84 2.170738 TTTGGATGCGCCGAAGAAG 58.829 52.632 4.18 0.00 40.66 2.85
84 85 4.388229 TTTGGATGCGCCGAAGAA 57.612 50.000 4.18 0.00 40.66 2.52
87 88 2.671276 TGCTTTGGATGCGCCGAA 60.671 55.556 4.18 0.00 40.66 4.30
88 89 3.430862 GTGCTTTGGATGCGCCGA 61.431 61.111 4.18 0.00 40.66 5.54
89 90 3.266230 TTGTGCTTTGGATGCGCCG 62.266 57.895 4.18 0.00 40.66 6.46
90 91 1.734117 GTTGTGCTTTGGATGCGCC 60.734 57.895 4.18 0.00 39.88 6.53
91 92 0.597118 TTGTTGTGCTTTGGATGCGC 60.597 50.000 0.00 0.00 40.87 6.09
92 93 2.068837 ATTGTTGTGCTTTGGATGCG 57.931 45.000 0.00 0.00 0.00 4.73
93 94 3.184986 GTGAATTGTTGTGCTTTGGATGC 59.815 43.478 0.00 0.00 0.00 3.91
94 95 4.624015 AGTGAATTGTTGTGCTTTGGATG 58.376 39.130 0.00 0.00 0.00 3.51
95 96 4.586001 AGAGTGAATTGTTGTGCTTTGGAT 59.414 37.500 0.00 0.00 0.00 3.41
96 97 3.953612 AGAGTGAATTGTTGTGCTTTGGA 59.046 39.130 0.00 0.00 0.00 3.53
97 98 4.311816 AGAGTGAATTGTTGTGCTTTGG 57.688 40.909 0.00 0.00 0.00 3.28
98 99 7.140705 TCATAAGAGTGAATTGTTGTGCTTTG 58.859 34.615 0.00 0.00 0.00 2.77
99 100 7.275888 TCATAAGAGTGAATTGTTGTGCTTT 57.724 32.000 0.00 0.00 0.00 3.51
100 101 6.882610 TCATAAGAGTGAATTGTTGTGCTT 57.117 33.333 0.00 0.00 0.00 3.91
101 102 6.882610 TTCATAAGAGTGAATTGTTGTGCT 57.117 33.333 0.00 0.00 33.41 4.40
102 103 7.928908 TTTTCATAAGAGTGAATTGTTGTGC 57.071 32.000 0.00 0.00 37.88 4.57
133 134 9.430623 TGTTTCAAGTATGATGTCTCGAATTAA 57.569 29.630 0.00 0.00 34.96 1.40
134 135 8.996024 TGTTTCAAGTATGATGTCTCGAATTA 57.004 30.769 0.00 0.00 34.96 1.40
135 136 7.604164 ACTGTTTCAAGTATGATGTCTCGAATT 59.396 33.333 0.00 0.00 34.96 2.17
136 137 7.063898 CACTGTTTCAAGTATGATGTCTCGAAT 59.936 37.037 0.00 0.00 34.96 3.34
137 138 6.366061 CACTGTTTCAAGTATGATGTCTCGAA 59.634 38.462 0.00 0.00 34.96 3.71
138 139 5.863935 CACTGTTTCAAGTATGATGTCTCGA 59.136 40.000 0.00 0.00 34.96 4.04
139 140 5.635280 ACACTGTTTCAAGTATGATGTCTCG 59.365 40.000 0.00 0.00 34.96 4.04
140 141 6.646653 TGACACTGTTTCAAGTATGATGTCTC 59.353 38.462 9.55 0.00 39.57 3.36
141 142 6.524734 TGACACTGTTTCAAGTATGATGTCT 58.475 36.000 9.55 0.00 39.57 3.41
142 143 6.785488 TGACACTGTTTCAAGTATGATGTC 57.215 37.500 0.00 0.00 39.42 3.06
143 144 7.750229 AATGACACTGTTTCAAGTATGATGT 57.250 32.000 0.18 0.00 34.96 3.06
157 158 6.119536 TCCACAAGTCTTTTAATGACACTGT 58.880 36.000 12.41 11.42 36.94 3.55
163 164 6.928492 GCCAAAATCCACAAGTCTTTTAATGA 59.072 34.615 0.00 0.00 0.00 2.57
167 168 5.860941 TGCCAAAATCCACAAGTCTTTTA 57.139 34.783 0.00 0.00 0.00 1.52
171 172 4.154942 AGAATGCCAAAATCCACAAGTCT 58.845 39.130 0.00 0.00 0.00 3.24
202 211 0.243636 GTTTTGAGAACCCGCCATGG 59.756 55.000 7.63 7.63 37.55 3.66
207 216 1.001706 GGAGTTGTTTTGAGAACCCGC 60.002 52.381 0.00 0.00 0.00 6.13
209 218 4.099419 ACATTGGAGTTGTTTTGAGAACCC 59.901 41.667 0.00 0.00 0.00 4.11
218 227 3.446873 TGTGAAGCACATTGGAGTTGTTT 59.553 39.130 0.00 0.00 39.62 2.83
222 231 4.147321 AGATTGTGAAGCACATTGGAGTT 58.853 39.130 0.62 0.00 44.16 3.01
225 234 3.084039 GGAGATTGTGAAGCACATTGGA 58.916 45.455 0.62 0.00 44.16 3.53
226 235 2.159476 CGGAGATTGTGAAGCACATTGG 60.159 50.000 0.62 0.00 44.16 3.16
240 250 5.221048 CCAAGTGTCTTGAAAAACGGAGATT 60.221 40.000 10.54 0.00 0.00 2.40
250 260 3.149196 GAGCATCCCAAGTGTCTTGAAA 58.851 45.455 10.54 0.02 0.00 2.69
289 306 2.029244 CGGTGTATTCATGCTCGTTGAC 59.971 50.000 0.00 0.00 0.00 3.18
303 327 2.579873 AGATAGTACGCCACGGTGTAT 58.420 47.619 12.39 0.00 42.10 2.29
310 334 0.101759 TCGGCAAGATAGTACGCCAC 59.898 55.000 7.79 0.00 45.14 5.01
314 338 2.795175 ACCATCGGCAAGATAGTACG 57.205 50.000 0.00 0.00 37.52 3.67
336 360 1.705997 AATGCCCCCACCGAGGATAC 61.706 60.000 0.00 0.00 41.22 2.24
353 378 6.564152 AGGGATGGGATATAGTCTTCACAAAT 59.436 38.462 0.00 0.00 0.00 2.32
389 414 1.875514 TGCAGTGCAAAGAGACATCAC 59.124 47.619 17.26 0.00 34.76 3.06
431 459 1.372087 GCACTCCAAATGCCCTCTCG 61.372 60.000 0.00 0.00 37.08 4.04
472 500 4.481463 CCACATATTTGAAAACCCACGAC 58.519 43.478 0.00 0.00 0.00 4.34
480 508 4.887071 CCTCGGATCCCACATATTTGAAAA 59.113 41.667 6.06 0.00 0.00 2.29
554 583 2.854736 TCCCTCTGTCATCATCCTCA 57.145 50.000 0.00 0.00 0.00 3.86
584 619 6.749923 ACTCCAGACTTCTAAAAATCATGC 57.250 37.500 0.00 0.00 0.00 4.06
602 637 3.118775 CCGGAAGATGAACATGTACTCCA 60.119 47.826 0.00 0.00 0.00 3.86
616 651 2.766263 TCTACATCTTGTGCCGGAAGAT 59.234 45.455 5.05 8.52 40.16 2.40
620 655 0.175760 GCTCTACATCTTGTGCCGGA 59.824 55.000 5.05 0.00 0.00 5.14
634 670 2.028112 AGGAAGTTCGCAACATGCTCTA 60.028 45.455 0.00 0.00 42.25 2.43
689 725 1.001860 TCATCGAGTGGTTGCATGTGA 59.998 47.619 0.00 0.00 0.00 3.58
705 741 7.035004 GCATCTCTAACATACTCCAGATCATC 58.965 42.308 0.00 0.00 0.00 2.92
742 1070 3.009473 TGAAGGGAAAGATCTTCTGTGGG 59.991 47.826 8.78 0.00 39.85 4.61
1221 1576 3.792047 CAGTCGTGGTGCATGCGG 61.792 66.667 14.09 0.00 0.00 5.69
1494 1849 1.071385 GCCGTCATCATCTCCTCCATT 59.929 52.381 0.00 0.00 0.00 3.16
1542 1897 0.548682 ACCACCCCAGCATCTTCTCT 60.549 55.000 0.00 0.00 0.00 3.10
1684 2039 2.579201 GGCGCTACTGCTCTCCAA 59.421 61.111 7.64 0.00 36.97 3.53
1778 2133 4.338539 ACACGCAGTCGGTCGGAC 62.339 66.667 0.00 0.00 41.61 4.79
1779 2134 4.337060 CACACGCAGTCGGTCGGA 62.337 66.667 0.00 0.00 41.61 4.55
1781 2136 3.604494 TAGCACACGCAGTCGGTCG 62.604 63.158 0.00 0.00 41.61 4.79
1782 2137 2.087009 GTAGCACACGCAGTCGGTC 61.087 63.158 0.00 0.00 41.61 4.79
1783 2138 2.049433 GTAGCACACGCAGTCGGT 60.049 61.111 0.00 0.00 41.61 4.69
1866 2231 2.007608 GATTACGAACAACCAGAGGCC 58.992 52.381 0.00 0.00 0.00 5.19
1908 2274 5.306394 GGGTTACAGCTTAGTTTCACTTCT 58.694 41.667 0.00 0.00 0.00 2.85
2038 4459 2.290260 TGGGTGCCACAATTACTGAGAG 60.290 50.000 0.00 0.00 0.00 3.20
2056 4477 1.668337 CGCATATTCTCTCTCGCTGGG 60.668 57.143 0.00 0.00 0.00 4.45
2452 4890 1.270907 TCCTTTCACCTGAGAGGCTC 58.729 55.000 6.34 6.34 43.85 4.70
2539 4979 2.263741 CGGAGCAGGCAAAGCAGTT 61.264 57.895 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.