Multiple sequence alignment - TraesCS5B01G480400

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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 TraesCS5B01G480400 chr5B 100.000 3082 0 0 1 3082 652925076 652928157 0.000000e+00 5692
1 TraesCS5B01G480400 chr5B 97.756 2585 56 2 499 3082 513600648 513603231 0.000000e+00 4451
2 TraesCS5B01G480400 chr5B 90.356 477 29 12 167 635 513600268 513600735 7.310000e-171 610
3 TraesCS5B01G480400 chr4A 96.745 2949 59 11 167 3082 35615015 35612071 0.000000e+00 4879
4 TraesCS5B01G480400 chr4A 91.405 477 33 6 167 635 535873667 535873191 0.000000e+00 647
5 TraesCS5B01G480400 chr7B 96.707 2946 61 13 167 3082 263144460 263141521 0.000000e+00 4870
6 TraesCS5B01G480400 chr7B 97.795 2585 55 2 499 3082 446153227 446155810 0.000000e+00 4457
7 TraesCS5B01G480400 chr7B 97.756 2585 56 2 499 3082 446172041 446174624 0.000000e+00 4451
8 TraesCS5B01G480400 chr7B 91.368 475 34 7 167 635 446152841 446153314 0.000000e+00 643
9 TraesCS5B01G480400 chr7B 90.776 477 33 7 167 635 169298169 169298642 7.250000e-176 627
10 TraesCS5B01G480400 chr7B 92.170 447 26 6 167 611 582235322 582235761 9.380000e-175 623
11 TraesCS5B01G480400 chr7A 96.741 2946 54 21 167 3082 204164365 204167298 0.000000e+00 4870
12 TraesCS5B01G480400 chr2B 96.439 2949 71 6 167 3082 338772765 338769818 0.000000e+00 4833
13 TraesCS5B01G480400 chr2B 97.756 2585 56 2 499 3082 49093059 49095642 0.000000e+00 4451
14 TraesCS5B01G480400 chr6B 95.995 2921 103 8 167 3082 48489771 48486860 0.000000e+00 4734
15 TraesCS5B01G480400 chr6B 96.886 2762 54 16 353 3082 417231854 417234615 0.000000e+00 4595
16 TraesCS5B01G480400 chr1A 98.049 2563 48 2 521 3082 252511204 252508643 0.000000e+00 4455
17 TraesCS5B01G480400 chr4B 89.727 477 32 12 167 635 15939349 15938882 7.360000e-166 593
18 TraesCS5B01G480400 chr5A 96.386 166 6 0 1 166 645619212 645619377 1.090000e-69 274


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 TraesCS5B01G480400 chr5B 652925076 652928157 3081 False 5692.0 5692 100.0000 1 3082 1 chr5B.!!$F1 3081
1 TraesCS5B01G480400 chr5B 513600268 513603231 2963 False 2530.5 4451 94.0560 167 3082 2 chr5B.!!$F2 2915
2 TraesCS5B01G480400 chr4A 35612071 35615015 2944 True 4879.0 4879 96.7450 167 3082 1 chr4A.!!$R1 2915
3 TraesCS5B01G480400 chr7B 263141521 263144460 2939 True 4870.0 4870 96.7070 167 3082 1 chr7B.!!$R1 2915
4 TraesCS5B01G480400 chr7B 446172041 446174624 2583 False 4451.0 4451 97.7560 499 3082 1 chr7B.!!$F2 2583
5 TraesCS5B01G480400 chr7B 446152841 446155810 2969 False 2550.0 4457 94.5815 167 3082 2 chr7B.!!$F4 2915
6 TraesCS5B01G480400 chr7A 204164365 204167298 2933 False 4870.0 4870 96.7410 167 3082 1 chr7A.!!$F1 2915
7 TraesCS5B01G480400 chr2B 338769818 338772765 2947 True 4833.0 4833 96.4390 167 3082 1 chr2B.!!$R1 2915
8 TraesCS5B01G480400 chr2B 49093059 49095642 2583 False 4451.0 4451 97.7560 499 3082 1 chr2B.!!$F1 2583
9 TraesCS5B01G480400 chr6B 48486860 48489771 2911 True 4734.0 4734 95.9950 167 3082 1 chr6B.!!$R1 2915
10 TraesCS5B01G480400 chr6B 417231854 417234615 2761 False 4595.0 4595 96.8860 353 3082 1 chr6B.!!$F1 2729
11 TraesCS5B01G480400 chr1A 252508643 252511204 2561 True 4455.0 4455 98.0490 521 3082 1 chr1A.!!$R1 2561

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
108 109 0.108585 GGTCTCCTTGTTGCACTCCA 59.891 55.0 0.0 0.0 0.0 3.86 F
110 111 0.250467 TCTCCTTGTTGCACTCCAGC 60.250 55.0 0.0 0.0 0.0 4.85 F
887 1029 0.313672 GCCGATGAAACCAAGCAACA 59.686 50.0 0.0 0.0 0.0 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1185 1327 0.745845 CCAGAGAGTCCAATTGGCGG 60.746 60.0 20.33 5.95 34.44 6.13 R
1736 1878 0.892358 ACCTGACGAAGAGTGCGGTA 60.892 55.0 0.00 0.00 0.00 4.02 R
2708 2851 0.321122 AAAGAAGAGCCCGAGCAGTG 60.321 55.0 0.00 0.00 43.56 3.66 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
22 23 5.623551 TCTCCATATGAGTTATCTCCCCT 57.376 43.478 3.65 0.00 42.12 4.79
23 24 5.982391 TCTCCATATGAGTTATCTCCCCTT 58.018 41.667 3.65 0.00 42.12 3.95
24 25 7.116089 TCTCCATATGAGTTATCTCCCCTTA 57.884 40.000 3.65 0.00 42.12 2.69
25 26 7.544650 TCTCCATATGAGTTATCTCCCCTTAA 58.455 38.462 3.65 0.00 42.12 1.85
26 27 8.016652 TCTCCATATGAGTTATCTCCCCTTAAA 58.983 37.037 3.65 0.00 42.12 1.52
27 28 8.575736 TCCATATGAGTTATCTCCCCTTAAAA 57.424 34.615 3.65 0.00 39.75 1.52
28 29 8.660435 TCCATATGAGTTATCTCCCCTTAAAAG 58.340 37.037 3.65 0.00 39.75 2.27
29 30 8.440771 CCATATGAGTTATCTCCCCTTAAAAGT 58.559 37.037 3.65 0.00 39.75 2.66
30 31 9.853177 CATATGAGTTATCTCCCCTTAAAAGTT 57.147 33.333 0.00 0.00 39.75 2.66
33 34 9.601810 ATGAGTTATCTCCCCTTAAAAGTTTTT 57.398 29.630 6.10 0.00 39.75 1.94
62 63 8.853077 CTGAAAGCATTATATCAGGGATACAA 57.147 34.615 0.00 0.00 36.50 2.41
63 64 9.288576 CTGAAAGCATTATATCAGGGATACAAA 57.711 33.333 0.00 0.00 36.50 2.83
64 65 9.066892 TGAAAGCATTATATCAGGGATACAAAC 57.933 33.333 0.00 0.00 39.74 2.93
65 66 8.409358 AAAGCATTATATCAGGGATACAAACC 57.591 34.615 0.00 0.00 39.74 3.27
66 67 7.335127 AGCATTATATCAGGGATACAAACCT 57.665 36.000 0.00 0.00 37.66 3.50
67 68 7.759607 AGCATTATATCAGGGATACAAACCTT 58.240 34.615 0.00 0.00 34.05 3.50
68 69 7.667219 AGCATTATATCAGGGATACAAACCTTG 59.333 37.037 0.00 0.00 34.05 3.61
69 70 7.665559 GCATTATATCAGGGATACAAACCTTGA 59.334 37.037 0.00 0.00 45.01 3.02
70 71 9.003658 CATTATATCAGGGATACAAACCTTGAC 57.996 37.037 0.00 0.00 44.05 3.18
71 72 4.927267 ATCAGGGATACAAACCTTGACA 57.073 40.909 0.00 0.00 44.05 3.58
72 73 4.927267 TCAGGGATACAAACCTTGACAT 57.073 40.909 0.00 0.00 38.32 3.06
73 74 6.575244 ATCAGGGATACAAACCTTGACATA 57.425 37.500 0.00 0.00 44.05 2.29
74 75 6.381498 TCAGGGATACAAACCTTGACATAA 57.619 37.500 0.00 0.00 38.32 1.90
75 76 6.969043 TCAGGGATACAAACCTTGACATAAT 58.031 36.000 0.00 0.00 38.32 1.28
76 77 7.054124 TCAGGGATACAAACCTTGACATAATC 58.946 38.462 0.00 0.00 38.32 1.75
77 78 7.056635 CAGGGATACAAACCTTGACATAATCT 58.943 38.462 0.00 0.00 36.77 2.40
78 79 7.012704 CAGGGATACAAACCTTGACATAATCTG 59.987 40.741 0.00 0.00 36.77 2.90
79 80 6.263168 GGGATACAAACCTTGACATAATCTGG 59.737 42.308 0.00 0.00 39.74 3.86
80 81 7.054124 GGATACAAACCTTGACATAATCTGGA 58.946 38.462 0.00 0.00 0.00 3.86
81 82 7.556275 GGATACAAACCTTGACATAATCTGGAA 59.444 37.037 0.00 0.00 0.00 3.53
82 83 6.575162 ACAAACCTTGACATAATCTGGAAC 57.425 37.500 0.00 0.00 0.00 3.62
83 84 5.476945 ACAAACCTTGACATAATCTGGAACC 59.523 40.000 0.00 0.00 0.00 3.62
84 85 4.236527 ACCTTGACATAATCTGGAACCC 57.763 45.455 0.00 0.00 0.00 4.11
85 86 3.206150 CCTTGACATAATCTGGAACCCG 58.794 50.000 0.00 0.00 0.00 5.28
86 87 3.206150 CTTGACATAATCTGGAACCCGG 58.794 50.000 0.00 0.00 0.00 5.73
87 88 2.193127 TGACATAATCTGGAACCCGGT 58.807 47.619 0.00 0.00 0.00 5.28
88 89 3.376636 TGACATAATCTGGAACCCGGTA 58.623 45.455 0.00 0.00 0.00 4.02
89 90 3.386726 TGACATAATCTGGAACCCGGTAG 59.613 47.826 0.00 0.00 0.00 3.18
90 91 2.704065 ACATAATCTGGAACCCGGTAGG 59.296 50.000 0.00 0.00 43.78 3.18
99 100 4.455366 CCCGGTAGGTCTCCTTGT 57.545 61.111 0.00 0.00 34.61 3.16
100 101 2.680066 CCCGGTAGGTCTCCTTGTT 58.320 57.895 0.00 0.00 34.61 2.83
101 102 0.249398 CCCGGTAGGTCTCCTTGTTG 59.751 60.000 0.00 0.00 34.61 3.33
102 103 0.391263 CCGGTAGGTCTCCTTGTTGC 60.391 60.000 0.00 0.00 34.61 4.17
103 104 0.320374 CGGTAGGTCTCCTTGTTGCA 59.680 55.000 0.00 0.00 34.61 4.08
104 105 1.809684 GGTAGGTCTCCTTGTTGCAC 58.190 55.000 0.00 0.00 34.61 4.57
105 106 1.348036 GGTAGGTCTCCTTGTTGCACT 59.652 52.381 0.00 0.00 34.61 4.40
106 107 2.613223 GGTAGGTCTCCTTGTTGCACTC 60.613 54.545 0.00 0.00 34.61 3.51
107 108 0.398318 AGGTCTCCTTGTTGCACTCC 59.602 55.000 0.00 0.00 0.00 3.85
108 109 0.108585 GGTCTCCTTGTTGCACTCCA 59.891 55.000 0.00 0.00 0.00 3.86
109 110 1.517242 GTCTCCTTGTTGCACTCCAG 58.483 55.000 0.00 0.00 0.00 3.86
110 111 0.250467 TCTCCTTGTTGCACTCCAGC 60.250 55.000 0.00 0.00 0.00 4.85
111 112 0.535780 CTCCTTGTTGCACTCCAGCA 60.536 55.000 0.00 0.00 43.99 4.41
118 119 3.238232 TGCACTCCAGCAACTGATC 57.762 52.632 0.00 0.00 42.46 2.92
119 120 0.321919 TGCACTCCAGCAACTGATCC 60.322 55.000 0.00 0.00 42.46 3.36
120 121 1.028868 GCACTCCAGCAACTGATCCC 61.029 60.000 0.00 0.00 32.44 3.85
121 122 0.617413 CACTCCAGCAACTGATCCCT 59.383 55.000 0.00 0.00 32.44 4.20
122 123 1.004044 CACTCCAGCAACTGATCCCTT 59.996 52.381 0.00 0.00 32.44 3.95
123 124 2.237143 CACTCCAGCAACTGATCCCTTA 59.763 50.000 0.00 0.00 32.44 2.69
124 125 3.118112 CACTCCAGCAACTGATCCCTTAT 60.118 47.826 0.00 0.00 32.44 1.73
125 126 3.135530 ACTCCAGCAACTGATCCCTTATC 59.864 47.826 0.00 0.00 32.44 1.75
126 127 3.387962 TCCAGCAACTGATCCCTTATCT 58.612 45.455 0.00 0.00 35.45 1.98
127 128 3.782523 TCCAGCAACTGATCCCTTATCTT 59.217 43.478 0.00 0.00 35.45 2.40
128 129 4.228210 TCCAGCAACTGATCCCTTATCTTT 59.772 41.667 0.00 0.00 35.45 2.52
129 130 4.952335 CCAGCAACTGATCCCTTATCTTTT 59.048 41.667 0.00 0.00 35.45 2.27
130 131 5.067023 CCAGCAACTGATCCCTTATCTTTTC 59.933 44.000 0.00 0.00 35.45 2.29
131 132 5.649395 CAGCAACTGATCCCTTATCTTTTCA 59.351 40.000 0.00 0.00 35.45 2.69
132 133 6.151648 CAGCAACTGATCCCTTATCTTTTCAA 59.848 38.462 0.00 0.00 35.45 2.69
133 134 6.151817 AGCAACTGATCCCTTATCTTTTCAAC 59.848 38.462 0.00 0.00 35.45 3.18
134 135 6.625960 GCAACTGATCCCTTATCTTTTCAACC 60.626 42.308 0.00 0.00 35.45 3.77
135 136 6.394345 ACTGATCCCTTATCTTTTCAACCT 57.606 37.500 0.00 0.00 35.45 3.50
136 137 6.794534 ACTGATCCCTTATCTTTTCAACCTT 58.205 36.000 0.00 0.00 35.45 3.50
137 138 7.928873 ACTGATCCCTTATCTTTTCAACCTTA 58.071 34.615 0.00 0.00 35.45 2.69
138 139 8.390921 ACTGATCCCTTATCTTTTCAACCTTAA 58.609 33.333 0.00 0.00 35.45 1.85
139 140 9.413734 CTGATCCCTTATCTTTTCAACCTTAAT 57.586 33.333 0.00 0.00 35.45 1.40
140 141 9.189156 TGATCCCTTATCTTTTCAACCTTAATG 57.811 33.333 0.00 0.00 35.45 1.90
141 142 9.408648 GATCCCTTATCTTTTCAACCTTAATGA 57.591 33.333 0.00 0.00 0.00 2.57
142 143 9.768215 ATCCCTTATCTTTTCAACCTTAATGAA 57.232 29.630 0.00 0.00 35.11 2.57
143 144 9.020731 TCCCTTATCTTTTCAACCTTAATGAAC 57.979 33.333 0.00 0.00 36.57 3.18
144 145 8.251026 CCCTTATCTTTTCAACCTTAATGAACC 58.749 37.037 0.00 0.00 36.57 3.62
145 146 9.025041 CCTTATCTTTTCAACCTTAATGAACCT 57.975 33.333 0.00 0.00 36.57 3.50
150 151 9.681062 TCTTTTCAACCTTAATGAACCTATAGG 57.319 33.333 17.73 17.73 36.57 2.57
151 152 9.681062 CTTTTCAACCTTAATGAACCTATAGGA 57.319 33.333 26.01 3.17 36.57 2.94
155 156 9.457436 TCAACCTTAATGAACCTATAGGAAAAC 57.543 33.333 26.01 12.71 38.94 2.43
156 157 9.462606 CAACCTTAATGAACCTATAGGAAAACT 57.537 33.333 26.01 8.92 38.94 2.66
157 158 9.682465 AACCTTAATGAACCTATAGGAAAACTC 57.318 33.333 26.01 12.71 38.94 3.01
158 159 9.059023 ACCTTAATGAACCTATAGGAAAACTCT 57.941 33.333 26.01 5.90 38.94 3.24
159 160 9.907229 CCTTAATGAACCTATAGGAAAACTCTT 57.093 33.333 26.01 7.02 38.94 2.85
163 164 9.454859 AATGAACCTATAGGAAAACTCTTTCAG 57.545 33.333 26.01 0.00 42.44 3.02
164 165 7.394816 TGAACCTATAGGAAAACTCTTTCAGG 58.605 38.462 26.01 0.00 42.44 3.86
165 166 7.236847 TGAACCTATAGGAAAACTCTTTCAGGA 59.763 37.037 26.01 0.00 42.44 3.86
176 177 8.519799 AAAACTCTTTCAGGATGTTAGAACAA 57.480 30.769 0.00 0.00 43.03 2.83
215 216 9.610104 TGTGTAGTTATCATATTGTATAGGGGT 57.390 33.333 0.00 0.00 0.00 4.95
295 296 5.615289 AGGCTCACTTCATAACATGGTATC 58.385 41.667 0.00 0.00 0.00 2.24
305 306 6.077993 TCATAACATGGTATCAGAGCTAGGT 58.922 40.000 0.00 0.00 0.00 3.08
318 320 2.838813 GAGCTAGGTTTAGTTCCCCAGT 59.161 50.000 0.00 0.00 32.68 4.00
388 399 1.819229 GCCGCTCCTCTCTTCATCA 59.181 57.895 0.00 0.00 0.00 3.07
445 456 3.953775 CTGGTCCAGGCCACCGTT 61.954 66.667 11.46 0.00 36.61 4.44
459 470 3.423154 CGTTGTTCCAGGCCGCTC 61.423 66.667 0.00 0.00 0.00 5.03
460 471 2.032681 GTTGTTCCAGGCCGCTCT 59.967 61.111 0.00 0.00 0.00 4.09
461 472 2.032528 TTGTTCCAGGCCGCTCTG 59.967 61.111 0.00 0.00 34.70 3.35
462 473 2.818169 TTGTTCCAGGCCGCTCTGT 61.818 57.895 0.00 0.00 33.14 3.41
528 571 2.645730 CTCTTCAACGAGCTGCTACT 57.354 50.000 0.15 0.00 0.00 2.57
529 572 2.257894 CTCTTCAACGAGCTGCTACTG 58.742 52.381 0.15 0.09 0.00 2.74
530 573 0.718343 CTTCAACGAGCTGCTACTGC 59.282 55.000 0.15 0.00 40.20 4.40
531 574 0.318441 TTCAACGAGCTGCTACTGCT 59.682 50.000 0.15 0.00 41.16 4.24
532 575 0.389037 TCAACGAGCTGCTACTGCTG 60.389 55.000 0.15 0.00 38.70 4.41
538 581 4.831698 CTGCTACTGCTGCTCCTC 57.168 61.111 0.00 0.00 40.48 3.71
539 582 2.200989 CTGCTACTGCTGCTCCTCT 58.799 57.895 0.00 0.00 40.48 3.69
540 583 0.536260 CTGCTACTGCTGCTCCTCTT 59.464 55.000 0.00 0.00 40.48 2.85
541 584 0.534412 TGCTACTGCTGCTCCTCTTC 59.466 55.000 0.00 0.00 40.48 2.87
542 585 0.823460 GCTACTGCTGCTCCTCTTCT 59.177 55.000 0.00 0.00 36.03 2.85
543 586 1.202405 GCTACTGCTGCTCCTCTTCTC 60.202 57.143 0.00 0.00 36.03 2.87
544 587 2.378038 CTACTGCTGCTCCTCTTCTCT 58.622 52.381 0.00 0.00 0.00 3.10
545 588 0.896923 ACTGCTGCTCCTCTTCTCTG 59.103 55.000 0.00 0.00 0.00 3.35
546 589 0.896923 CTGCTGCTCCTCTTCTCTGT 59.103 55.000 0.00 0.00 0.00 3.41
618 760 0.959372 GTCTGCTGCTGCCATCAAGT 60.959 55.000 13.47 0.00 38.71 3.16
704 846 1.225983 CCACCACCAGTGTTGTCCA 59.774 57.895 0.00 0.00 45.74 4.02
719 861 0.608640 GTCCAAGTCCCACGATGTCT 59.391 55.000 0.00 0.00 0.00 3.41
744 886 6.931838 TGTTATCTTCAACGGACAGAACTAT 58.068 36.000 0.00 0.00 0.00 2.12
887 1029 0.313672 GCCGATGAAACCAAGCAACA 59.686 50.000 0.00 0.00 0.00 3.33
907 1049 6.238566 GCAACATGAGATGCTAGATGCTTTTA 60.239 38.462 0.00 0.00 40.09 1.52
956 1098 9.109393 GAATCAACTCCACTTATACAAGCAATA 57.891 33.333 0.00 0.00 34.94 1.90
1185 1327 3.188786 GAGATGTCGGCGGTGTGC 61.189 66.667 7.21 0.00 45.38 4.57
1864 2006 5.946972 CCTTCTCCTCTTACAGTTCAGACTA 59.053 44.000 0.00 0.00 33.90 2.59
1884 2026 3.777106 ACAGATGGCACTTCTCTTTCA 57.223 42.857 0.00 0.00 0.00 2.69
2148 2290 0.820074 CGTCCTCTAGCCAGTCGGAT 60.820 60.000 0.00 0.00 33.43 4.18
2213 2355 1.146637 GCTCAGTGGCATCATCGATC 58.853 55.000 0.00 0.00 0.00 3.69
2281 2423 5.198965 GTGTTCTAGGGTCTGTATCTGGTA 58.801 45.833 0.00 0.00 0.00 3.25
2570 2712 5.611374 TGATTCCTCTGTTCGAGTTTTTCT 58.389 37.500 0.00 0.00 38.11 2.52
2622 2765 1.519408 GCTTCGTGGTTTCCTTGCTA 58.481 50.000 0.00 0.00 0.00 3.49
2708 2851 1.779569 AACATCGTCACGTCCTTGAC 58.220 50.000 0.00 0.00 42.24 3.18
2778 2922 0.255033 TGAGGCTGTCTCTACCGCTA 59.745 55.000 11.02 0.00 42.86 4.26
2890 3034 1.169661 CGCCTGTTTGGTTGTGCCTA 61.170 55.000 0.00 0.00 38.35 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 8.575736 TTTTAAGGGGAGATAACTCATATGGA 57.424 34.615 2.13 0.00 44.22 3.41
4 5 9.853177 AACTTTTAAGGGGAGATAACTCATATG 57.147 33.333 2.13 0.00 44.22 1.78
7 8 9.601810 AAAAACTTTTAAGGGGAGATAACTCAT 57.398 29.630 2.13 0.00 44.22 2.90
37 38 8.853077 TTGTATCCCTGATATAATGCTTTCAG 57.147 34.615 0.00 0.00 36.26 3.02
38 39 9.066892 GTTTGTATCCCTGATATAATGCTTTCA 57.933 33.333 0.00 0.00 28.73 2.69
39 40 8.515414 GGTTTGTATCCCTGATATAATGCTTTC 58.485 37.037 0.00 0.00 28.73 2.62
40 41 8.227507 AGGTTTGTATCCCTGATATAATGCTTT 58.772 33.333 0.00 0.00 28.73 3.51
41 42 7.759607 AGGTTTGTATCCCTGATATAATGCTT 58.240 34.615 0.00 0.00 28.73 3.91
42 43 7.335127 AGGTTTGTATCCCTGATATAATGCT 57.665 36.000 0.00 0.00 28.73 3.79
43 44 7.665559 TCAAGGTTTGTATCCCTGATATAATGC 59.334 37.037 0.00 0.00 28.73 3.56
44 45 9.003658 GTCAAGGTTTGTATCCCTGATATAATG 57.996 37.037 0.00 0.00 28.73 1.90
45 46 8.723365 TGTCAAGGTTTGTATCCCTGATATAAT 58.277 33.333 0.00 0.00 28.73 1.28
46 47 8.096621 TGTCAAGGTTTGTATCCCTGATATAA 57.903 34.615 0.00 0.00 0.00 0.98
47 48 7.684317 TGTCAAGGTTTGTATCCCTGATATA 57.316 36.000 0.00 0.00 0.00 0.86
48 49 6.575244 TGTCAAGGTTTGTATCCCTGATAT 57.425 37.500 0.00 0.00 0.00 1.63
49 50 6.575244 ATGTCAAGGTTTGTATCCCTGATA 57.425 37.500 0.00 0.00 0.00 2.15
50 51 4.927267 TGTCAAGGTTTGTATCCCTGAT 57.073 40.909 0.00 0.00 0.00 2.90
51 52 4.927267 ATGTCAAGGTTTGTATCCCTGA 57.073 40.909 0.00 0.00 0.00 3.86
52 53 7.012704 CAGATTATGTCAAGGTTTGTATCCCTG 59.987 40.741 0.00 0.00 0.00 4.45
53 54 7.056635 CAGATTATGTCAAGGTTTGTATCCCT 58.943 38.462 0.00 0.00 0.00 4.20
54 55 6.263168 CCAGATTATGTCAAGGTTTGTATCCC 59.737 42.308 0.00 0.00 0.00 3.85
55 56 7.054124 TCCAGATTATGTCAAGGTTTGTATCC 58.946 38.462 0.00 0.00 0.00 2.59
56 57 8.398665 GTTCCAGATTATGTCAAGGTTTGTATC 58.601 37.037 0.00 0.00 0.00 2.24
57 58 7.339466 GGTTCCAGATTATGTCAAGGTTTGTAT 59.661 37.037 0.00 0.00 0.00 2.29
58 59 6.657541 GGTTCCAGATTATGTCAAGGTTTGTA 59.342 38.462 0.00 0.00 0.00 2.41
59 60 5.476945 GGTTCCAGATTATGTCAAGGTTTGT 59.523 40.000 0.00 0.00 0.00 2.83
60 61 5.105756 GGGTTCCAGATTATGTCAAGGTTTG 60.106 44.000 0.00 0.00 0.00 2.93
61 62 5.016831 GGGTTCCAGATTATGTCAAGGTTT 58.983 41.667 0.00 0.00 0.00 3.27
62 63 4.600062 GGGTTCCAGATTATGTCAAGGTT 58.400 43.478 0.00 0.00 0.00 3.50
63 64 3.370527 CGGGTTCCAGATTATGTCAAGGT 60.371 47.826 0.00 0.00 0.00 3.50
64 65 3.206150 CGGGTTCCAGATTATGTCAAGG 58.794 50.000 0.00 0.00 0.00 3.61
65 66 3.206150 CCGGGTTCCAGATTATGTCAAG 58.794 50.000 0.00 0.00 0.00 3.02
66 67 2.574369 ACCGGGTTCCAGATTATGTCAA 59.426 45.455 6.32 0.00 0.00 3.18
67 68 2.193127 ACCGGGTTCCAGATTATGTCA 58.807 47.619 6.32 0.00 0.00 3.58
68 69 3.244112 CCTACCGGGTTCCAGATTATGTC 60.244 52.174 4.31 0.00 0.00 3.06
69 70 2.704065 CCTACCGGGTTCCAGATTATGT 59.296 50.000 4.31 0.00 0.00 2.29
70 71 3.402628 CCTACCGGGTTCCAGATTATG 57.597 52.381 4.31 0.00 0.00 1.90
82 83 0.249398 CAACAAGGAGACCTACCGGG 59.751 60.000 6.32 0.00 41.89 5.73
83 84 0.391263 GCAACAAGGAGACCTACCGG 60.391 60.000 0.00 0.00 31.13 5.28
84 85 0.320374 TGCAACAAGGAGACCTACCG 59.680 55.000 0.00 0.00 31.13 4.02
85 86 1.348036 AGTGCAACAAGGAGACCTACC 59.652 52.381 0.00 0.00 41.43 3.18
86 87 2.613223 GGAGTGCAACAAGGAGACCTAC 60.613 54.545 0.00 0.00 41.43 3.18
87 88 1.623811 GGAGTGCAACAAGGAGACCTA 59.376 52.381 0.00 0.00 41.43 3.08
88 89 0.398318 GGAGTGCAACAAGGAGACCT 59.602 55.000 0.00 0.00 41.43 3.85
89 90 0.108585 TGGAGTGCAACAAGGAGACC 59.891 55.000 0.00 0.00 41.43 3.85
90 91 1.517242 CTGGAGTGCAACAAGGAGAC 58.483 55.000 0.00 0.00 41.43 3.36
91 92 0.250467 GCTGGAGTGCAACAAGGAGA 60.250 55.000 0.00 0.00 41.43 3.71
92 93 0.535780 TGCTGGAGTGCAACAAGGAG 60.536 55.000 0.00 0.00 41.43 3.69
93 94 0.106769 TTGCTGGAGTGCAACAAGGA 60.107 50.000 0.00 0.00 46.43 3.36
94 95 2.417978 TTGCTGGAGTGCAACAAGG 58.582 52.632 0.00 0.00 46.43 3.61
100 101 0.321919 GGATCAGTTGCTGGAGTGCA 60.322 55.000 0.00 0.00 41.65 4.57
101 102 1.028868 GGGATCAGTTGCTGGAGTGC 61.029 60.000 0.00 0.00 31.51 4.40
102 103 0.617413 AGGGATCAGTTGCTGGAGTG 59.383 55.000 0.00 0.00 31.51 3.51
103 104 1.366319 AAGGGATCAGTTGCTGGAGT 58.634 50.000 0.00 0.00 31.51 3.85
104 105 3.390639 AGATAAGGGATCAGTTGCTGGAG 59.609 47.826 0.00 0.00 36.98 3.86
105 106 3.387962 AGATAAGGGATCAGTTGCTGGA 58.612 45.455 0.00 0.00 36.98 3.86
106 107 3.853355 AGATAAGGGATCAGTTGCTGG 57.147 47.619 0.00 0.00 36.98 4.85
107 108 5.649395 TGAAAAGATAAGGGATCAGTTGCTG 59.351 40.000 0.00 0.00 36.98 4.41
108 109 5.819991 TGAAAAGATAAGGGATCAGTTGCT 58.180 37.500 0.00 0.00 36.98 3.91
109 110 6.325596 GTTGAAAAGATAAGGGATCAGTTGC 58.674 40.000 0.00 0.00 36.98 4.17
110 111 6.660949 AGGTTGAAAAGATAAGGGATCAGTTG 59.339 38.462 0.00 0.00 36.98 3.16
111 112 6.794534 AGGTTGAAAAGATAAGGGATCAGTT 58.205 36.000 0.00 0.00 36.98 3.16
112 113 6.394345 AGGTTGAAAAGATAAGGGATCAGT 57.606 37.500 0.00 0.00 36.98 3.41
113 114 8.807948 TTAAGGTTGAAAAGATAAGGGATCAG 57.192 34.615 0.00 0.00 36.98 2.90
114 115 9.189156 CATTAAGGTTGAAAAGATAAGGGATCA 57.811 33.333 0.00 0.00 36.98 2.92
115 116 9.408648 TCATTAAGGTTGAAAAGATAAGGGATC 57.591 33.333 0.00 0.00 34.40 3.36
116 117 9.768215 TTCATTAAGGTTGAAAAGATAAGGGAT 57.232 29.630 0.00 0.00 30.44 3.85
117 118 9.020731 GTTCATTAAGGTTGAAAAGATAAGGGA 57.979 33.333 0.00 0.00 35.03 4.20
118 119 8.251026 GGTTCATTAAGGTTGAAAAGATAAGGG 58.749 37.037 0.00 0.00 35.03 3.95
119 120 9.025041 AGGTTCATTAAGGTTGAAAAGATAAGG 57.975 33.333 0.00 0.00 35.03 2.69
124 125 9.681062 CCTATAGGTTCATTAAGGTTGAAAAGA 57.319 33.333 10.96 0.00 35.03 2.52
125 126 9.681062 TCCTATAGGTTCATTAAGGTTGAAAAG 57.319 33.333 18.51 0.00 35.03 2.27
129 130 9.457436 GTTTTCCTATAGGTTCATTAAGGTTGA 57.543 33.333 18.51 0.00 36.34 3.18
130 131 9.462606 AGTTTTCCTATAGGTTCATTAAGGTTG 57.537 33.333 18.51 0.00 36.34 3.77
131 132 9.682465 GAGTTTTCCTATAGGTTCATTAAGGTT 57.318 33.333 18.51 0.00 36.34 3.50
132 133 9.059023 AGAGTTTTCCTATAGGTTCATTAAGGT 57.941 33.333 18.51 0.00 36.34 3.50
133 134 9.907229 AAGAGTTTTCCTATAGGTTCATTAAGG 57.093 33.333 18.51 0.00 36.34 2.69
137 138 9.454859 CTGAAAGAGTTTTCCTATAGGTTCATT 57.545 33.333 18.51 8.77 41.62 2.57
138 139 8.049721 CCTGAAAGAGTTTTCCTATAGGTTCAT 58.950 37.037 18.51 2.64 41.62 2.57
139 140 7.236847 TCCTGAAAGAGTTTTCCTATAGGTTCA 59.763 37.037 18.51 15.54 41.62 3.18
140 141 7.621796 TCCTGAAAGAGTTTTCCTATAGGTTC 58.378 38.462 18.51 12.07 41.62 3.62
141 142 7.569599 TCCTGAAAGAGTTTTCCTATAGGTT 57.430 36.000 18.51 2.74 41.62 3.50
142 143 7.182930 ACATCCTGAAAGAGTTTTCCTATAGGT 59.817 37.037 18.51 0.00 41.62 3.08
143 144 7.569240 ACATCCTGAAAGAGTTTTCCTATAGG 58.431 38.462 13.07 13.07 41.62 2.57
146 147 8.826765 TCTAACATCCTGAAAGAGTTTTCCTAT 58.173 33.333 0.00 0.00 41.62 2.57
147 148 8.202461 TCTAACATCCTGAAAGAGTTTTCCTA 57.798 34.615 0.00 0.00 41.62 2.94
148 149 7.079451 TCTAACATCCTGAAAGAGTTTTCCT 57.921 36.000 0.00 0.00 41.62 3.36
149 150 7.228706 TGTTCTAACATCCTGAAAGAGTTTTCC 59.771 37.037 0.00 0.00 36.96 3.13
150 151 8.154649 TGTTCTAACATCCTGAAAGAGTTTTC 57.845 34.615 0.00 0.00 37.61 2.29
151 152 8.519799 TTGTTCTAACATCCTGAAAGAGTTTT 57.480 30.769 0.00 0.00 38.95 2.43
152 153 7.229506 CCTTGTTCTAACATCCTGAAAGAGTTT 59.770 37.037 0.00 0.00 38.95 2.66
153 154 6.712547 CCTTGTTCTAACATCCTGAAAGAGTT 59.287 38.462 0.00 0.00 38.95 3.01
154 155 6.183361 ACCTTGTTCTAACATCCTGAAAGAGT 60.183 38.462 0.00 0.00 38.95 3.24
155 156 6.234177 ACCTTGTTCTAACATCCTGAAAGAG 58.766 40.000 0.00 0.00 38.95 2.85
156 157 6.187727 ACCTTGTTCTAACATCCTGAAAGA 57.812 37.500 0.00 0.00 38.95 2.52
157 158 6.263168 ACAACCTTGTTCTAACATCCTGAAAG 59.737 38.462 0.00 0.00 38.47 2.62
158 159 6.039270 CACAACCTTGTTCTAACATCCTGAAA 59.961 38.462 0.00 0.00 39.91 2.69
159 160 5.530915 CACAACCTTGTTCTAACATCCTGAA 59.469 40.000 0.00 0.00 39.91 3.02
160 161 5.063204 CACAACCTTGTTCTAACATCCTGA 58.937 41.667 0.00 0.00 39.91 3.86
161 162 4.320494 GCACAACCTTGTTCTAACATCCTG 60.320 45.833 0.00 0.00 39.91 3.86
162 163 3.821033 GCACAACCTTGTTCTAACATCCT 59.179 43.478 0.00 0.00 39.91 3.24
163 164 3.821033 AGCACAACCTTGTTCTAACATCC 59.179 43.478 0.00 0.00 39.91 3.51
164 165 4.275936 ACAGCACAACCTTGTTCTAACATC 59.724 41.667 0.00 0.00 39.91 3.06
165 166 4.036734 CACAGCACAACCTTGTTCTAACAT 59.963 41.667 0.00 0.00 39.91 2.71
176 177 1.209504 ACTACACACACAGCACAACCT 59.790 47.619 0.00 0.00 0.00 3.50
215 216 7.301868 ACATGAAGGGAAATAAGCAAAGAAA 57.698 32.000 0.00 0.00 0.00 2.52
295 296 2.838202 TGGGGAACTAAACCTAGCTCTG 59.162 50.000 0.00 0.00 0.00 3.35
305 306 0.035739 GTGGCGACTGGGGAACTAAA 59.964 55.000 0.00 0.00 0.00 1.85
388 399 1.578897 GAAGAAGAGGGGAGAGGCTT 58.421 55.000 0.00 0.00 0.00 4.35
444 455 2.032528 CAGAGCGGCCTGGAACAA 59.967 61.111 0.00 0.00 38.70 2.83
445 456 3.240134 GACAGAGCGGCCTGGAACA 62.240 63.158 18.39 0.00 38.44 3.18
459 470 2.178521 CGGGAAGGACGTCGACAG 59.821 66.667 17.16 10.90 0.00 3.51
460 471 3.367743 CCGGGAAGGACGTCGACA 61.368 66.667 17.16 0.00 45.00 4.35
461 472 4.790861 GCCGGGAAGGACGTCGAC 62.791 72.222 9.92 5.18 45.00 4.20
525 568 2.098614 CAGAGAAGAGGAGCAGCAGTA 58.901 52.381 0.00 0.00 0.00 2.74
526 569 0.896923 CAGAGAAGAGGAGCAGCAGT 59.103 55.000 0.00 0.00 0.00 4.40
527 570 0.896923 ACAGAGAAGAGGAGCAGCAG 59.103 55.000 0.00 0.00 0.00 4.24
528 571 1.001746 CAACAGAGAAGAGGAGCAGCA 59.998 52.381 0.00 0.00 0.00 4.41
529 572 1.724429 CAACAGAGAAGAGGAGCAGC 58.276 55.000 0.00 0.00 0.00 5.25
530 573 1.275856 AGCAACAGAGAAGAGGAGCAG 59.724 52.381 0.00 0.00 0.00 4.24
531 574 1.001746 CAGCAACAGAGAAGAGGAGCA 59.998 52.381 0.00 0.00 0.00 4.26
532 575 1.724429 CAGCAACAGAGAAGAGGAGC 58.276 55.000 0.00 0.00 0.00 4.70
533 576 1.275856 AGCAGCAACAGAGAAGAGGAG 59.724 52.381 0.00 0.00 0.00 3.69
534 577 1.001746 CAGCAGCAACAGAGAAGAGGA 59.998 52.381 0.00 0.00 0.00 3.71
535 578 1.440708 CAGCAGCAACAGAGAAGAGG 58.559 55.000 0.00 0.00 0.00 3.69
536 579 0.797542 GCAGCAGCAACAGAGAAGAG 59.202 55.000 0.00 0.00 41.58 2.85
537 580 0.395686 AGCAGCAGCAACAGAGAAGA 59.604 50.000 3.17 0.00 45.49 2.87
538 581 0.517755 CAGCAGCAGCAACAGAGAAG 59.482 55.000 3.17 0.00 45.49 2.85
539 582 1.512996 GCAGCAGCAGCAACAGAGAA 61.513 55.000 4.63 0.00 45.49 2.87
540 583 1.964891 GCAGCAGCAGCAACAGAGA 60.965 57.895 4.63 0.00 45.49 3.10
541 584 1.913451 GAGCAGCAGCAGCAACAGAG 61.913 60.000 12.92 0.00 45.49 3.35
542 585 1.964891 GAGCAGCAGCAGCAACAGA 60.965 57.895 12.92 0.00 45.49 3.41
543 586 1.516365 AAGAGCAGCAGCAGCAACAG 61.516 55.000 12.92 0.00 45.49 3.16
544 587 1.512996 GAAGAGCAGCAGCAGCAACA 61.513 55.000 12.92 0.00 45.49 3.33
545 588 1.209640 GAAGAGCAGCAGCAGCAAC 59.790 57.895 12.92 5.77 45.49 4.17
546 589 0.536687 AAGAAGAGCAGCAGCAGCAA 60.537 50.000 12.92 0.00 45.49 3.91
694 836 0.179056 CGTGGGACTTGGACAACACT 60.179 55.000 0.00 0.00 0.00 3.55
704 846 2.930826 AACAAGACATCGTGGGACTT 57.069 45.000 0.00 0.00 0.00 3.01
719 861 5.607477 AGTTCTGTCCGTTGAAGATAACAA 58.393 37.500 0.00 0.00 0.00 2.83
744 886 2.203922 TGCTGCACCCAGTCCCTA 60.204 61.111 0.00 0.00 41.26 3.53
816 958 3.650950 GGCAGCAGGGGACAAGGA 61.651 66.667 0.00 0.00 0.00 3.36
907 1049 3.840666 TGATACTCTTCAGTGGCCTCTTT 59.159 43.478 4.10 0.00 33.62 2.52
956 1098 2.871022 GCTCGAGCATCATCATTTGTCT 59.129 45.455 31.91 0.00 41.59 3.41
1185 1327 0.745845 CCAGAGAGTCCAATTGGCGG 60.746 60.000 20.33 5.95 34.44 6.13
1553 1695 1.003696 GACCCTGTTTCCTCCTCTTGG 59.996 57.143 0.00 0.00 0.00 3.61
1736 1878 0.892358 ACCTGACGAAGAGTGCGGTA 60.892 55.000 0.00 0.00 0.00 4.02
1864 2006 3.072184 ACTGAAAGAGAAGTGCCATCTGT 59.928 43.478 0.00 0.00 37.43 3.41
1884 2026 2.032681 GTCCCTCTTGCGGCAACT 59.967 61.111 12.11 0.00 0.00 3.16
1910 2052 3.149196 GCAGGGACATGAAAAGAAGACA 58.851 45.455 0.00 0.00 0.00 3.41
2148 2290 2.109128 TGAAGCAAAAGGGGTGGTGATA 59.891 45.455 0.00 0.00 0.00 2.15
2281 2423 8.161425 ACAACCCATACAAGTTAGTGAACTATT 58.839 33.333 0.00 0.00 45.50 1.73
2353 2495 6.127730 ACAAGTTCAAAAGGTCGTTGAGAAAT 60.128 34.615 0.00 0.00 36.41 2.17
2407 2549 2.235891 GTGACCCCCTTTCGAAACAAT 58.764 47.619 6.47 0.00 0.00 2.71
2570 2712 3.126879 CGCCAGCCGAATCAGCAA 61.127 61.111 0.00 0.00 40.02 3.91
2708 2851 0.321122 AAAGAAGAGCCCGAGCAGTG 60.321 55.000 0.00 0.00 43.56 3.66
2890 3034 4.453480 TGAGGGTGGAGAAGAACAAAAT 57.547 40.909 0.00 0.00 0.00 1.82
2990 3134 1.209504 CTTCGAGCAATAGGGTCCCAA 59.790 52.381 11.55 0.00 40.99 4.12


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

AutoCloner maintained by Alex Coulton.