Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006693.1 Hibiscus syriacus cultivar Beakdansim tig00016651_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 54871
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:3156 original size:15 final size:13
Alignment explanation
Indices: 3113--3176 Score: 60
Period size: 13 Copynumber: 4.8 Consensus size: 13
3103 TGTGTGTATA
3113 TATAAACTATAAAG
1 TATAAA-TATAAAG
*
3127 TATAAATATAGAG
1 TATAAATATAAAG
3140 TATACATATATAAAG
1 TATA-A-ATATAAAG
*
3155 TAT-AA-GTAAAG
1 TATAAATATAAAG
*
3166 TATAAGTATAA
1 TATAAATATAA
3177 GTAAAAACTA
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
11 8 0.20
12 2 0.05
13 14 0.34
14 7 0.17
15 10 0.24
ACGTcount: A:0.55, C:0.03, G:0.11, T:0.31
Consensus pattern (13 bp):
TATAAATATAAAG
Found at i:3161 original size:6 final size:6
Alignment explanation
Indices: 3124--3179 Score: 51
Period size: 6 Copynumber: 8.8 Consensus size: 6
3114 ATAAACTATA
* *
3124 AAGTAT AAATAT AGAGTAT ACATATAT AAAGTAT AAGTA- AAGTAT AAGTAT
1 AAGTAT AAGTAT A-AGTAT A-A-GTAT -AAGTAT AAGTAT AAGTAT AAGTAT
3175 AAGTA
1 AAGTA
3180 AAAACTATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
5 5 0.12
6 22 0.54
7 9 0.22
8 4 0.10
9 1 0.02
ACGTcount: A:0.54, C:0.02, G:0.14, T:0.30
Consensus pattern (6 bp):
AAGTAT
Found at i:3166 original size:11 final size:11
Alignment explanation
Indices: 3150--3179 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
3140 TATACATATA
3150 TAAAGTATAAG
1 TAAAGTATAAG
3161 TAAAGTATAAG
1 TAAAGTATAAG
3172 TATAAGTA
1 TA-AAGTA
3180 AAAACTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.30
Consensus pattern (11 bp):
TAAAGTATAAG
Found at i:3189 original size:39 final size:37
Alignment explanation
Indices: 3122--3198 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 37
3112 ATATAAACTA
* *
3122 TAAAGTATAAATATAGAGTATACATATATAAAGTATAAG
1 TAAAGTATAAATATAGAGTAAAAATATAT-AA-TATAAG
*
3161 TAAAGTATAAGTATA-AGTAAAAACTATATAATATAAG
1 TAAAGTATAAATATAGAGTAAAAA-TATATAATATAAG
3198 T
1 T
3199 GGCAATGAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
37 7 0.21
38 8 0.24
39 19 0.56
ACGTcount: A:0.55, C:0.03, G:0.12, T:0.31
Consensus pattern (37 bp):
TAAAGTATAAATATAGAGTAAAAATATATAATATAAG
Found at i:4051 original size:21 final size:20
Alignment explanation
Indices: 4013--4065 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
4003 GGTTGAAACC
*
4013 ATTAATATTA-TTACTATTA
1 ATTATTATTATTTACTATTA
*
4032 ATTATTATTATTTAACTATTT
1 ATTATTATTATTT-ACTATTA
* *
4053 TTTATTTTTATTT
1 ATTATTATTATTT
4066 TATTTATTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 9 0.32
20 2 0.07
21 17 0.61
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (20 bp):
ATTATTATTATTTACTATTA
Found at i:4842 original size:21 final size:21
Alignment explanation
Indices: 4786--4846 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
4776 CACACTTATT
*
4786 GAAAAT-AAAA-ATAACAAAA
1 GAAAATAAAAAGATAATAAAA
* *
4805 GAAAATAAAGATG-TAATATAA
1 GAAAATAAA-AAGATAATAAAA
4826 GAAAATAAAAAGATAATAAAA
1 GAAAATAAAAAGATAATAAAA
4847 AATATTGGCA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
19 6 0.18
20 4 0.12
21 23 0.70
ACGTcount: A:0.72, C:0.02, G:0.10, T:0.16
Consensus pattern (21 bp):
GAAAATAAAAAGATAATAAAA
Found at i:6819 original size:11 final size:11
Alignment explanation
Indices: 6803--6832 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
6793 ATATGACTAA
6803 AATAAAATAAT
1 AATAAAATAAT
6814 AATAAAATAAT
1 AATAAAATAAT
6825 AATAAAAT
1 AATAAAAT
6833 TACTAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:8252 original size:3 final size:3
Alignment explanation
Indices: 8246--8274 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
8236 TATTTATTAT
8246 TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
8275 ACTATTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:9046 original size:220 final size:217
Alignment explanation
Indices: 8664--9344 Score: 848
Period size: 220 Copynumber: 3.2 Consensus size: 217
8654 GAAAATGTTG
* * *
8664 AAAACATTCTACCCAGAGGTCTTATGAATGGCCCGGAGGTCTTATCATCTTGCTCAGAAGGTTTA
1 AAAACATTCT-CCCA-AGGTCTTATGGATGGCCCGGAGGTCTTATCATCTTGCTCGGAAGGCTTA
* *
8729 CAGATAACTCGGAGGATTTAACATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAG-TTGTC
64 CAGAT-ACCCAGAGGATTTAACATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTT-GTTTGTC
* * * * *
8793 AAGGAACCCCTTCAAAGGCTTAGCTTCCTTTAACAACT-ATTTGAAATAATTAAAAAACCCCTGA
127 AAGGAACCCCTTAAAAGGCTTAGCTTCCTTTAACAACTCTTTTGAGATAATTAAGAAACCCCTTA
8857 AAGGCTTAGTTTCCAAAATCTCATTTA
192 AAGGCTTAGTTTCCAAAATCTCA-TTA
8884 AAAACATTCTGCCCTAAGGTCTTATGGATGGCCCGGAGGTCTTATCATCTTGCTCGGAAGGCTTA
1 AAAACATTCT-CCC-AAGGTCTTATGGATGGCCCGGAGGTCTTATCATCTTGCTCGGAAGGCTTA
8949 CAGATGACCCAGAGGATTTAACATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTGTTTGTCA
64 CAGAT-ACCCAGAGGATTTAACATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTGTTTGTCA
* * *
9014 AGGAACCCCTTAAAAGGGTTAGCTTTCTTTAACAACTCTTTTGAGGTAATTAAGAAACCCCTTAA
128 AGGAACCCCTTAAAAGGCTTAGCTTCCTTTAACAACTCTTTTGAGATAATTAAGAAACCCCTTAA
* *
9079 AGACTTAGTTTCCAAAATCTTATT-
193 AGGCTTAGTTTCCAAAATCTCATTA
* * *
9103 AAAA-A------C-A--TC--AT---T--CTCGAAGGTCTTATCATCTTGCTCGGAAGACTTATA
1 AAAACATTCTCCCAAGGTCTTATGGATGGCCCGGAGGTCTTATCATCTTGCTCGGAAGGC-T-TA
* * *
9151 GATGA-A-CCGGAGGATTTAAACATCAAGAAACTCTTGAAAATCAAGCTTAGTTTCTTGTTTGTC
64 CA-GATACCCAGAGGATTT-AACATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTGTTTGTC
*
9214 AAGGAACCCCTTAAAAGGCTTAGCTTCCTTTAACAACTCTTTTGCGATAATTAAGAAACCCCTTA
127 AAGGAACCCCTTAAAAGGCTTAGCTTCCTTTAACAACTCTTTTGAGATAATTAAGAAACCCCTTA
9279 AAGGCTTAGTTTCCAAAATCTCATTA
192 AAGGCTTAGTTTCCAAAATCTCATTA
* ** *
9305 AAAACATCCTACCTGGAGGTCTTATAGATGGCCCGGAGGT
1 AAAACATTCT-CC-CAAGGTCTTATGGATGGCCCGGAGGT
9345 TTTAAATATC
Statistics
Matches: 402, Mismatches: 32, Indels: 53
0.83 0.07 0.11
Matches are distributed among these distances:
200 38 0.09
201 130 0.32
202 8 0.02
203 3 0.01
205 2 0.00
207 2 0.00
209 1 0.00
211 1 0.00
212 1 0.00
214 2 0.00
216 2 0.00
218 1 0.00
219 6 0.01
220 155 0.39
221 50 0.12
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (217 bp):
AAAACATTCTCCCAAGGTCTTATGGATGGCCCGGAGGTCTTATCATCTTGCTCGGAAGGCTTACA
GATACCCAGAGGATTTAACATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTGTTTGTCAAGG
AACCCCTTAAAAGGCTTAGCTTCCTTTAACAACTCTTTTGAGATAATTAAGAAACCCCTTAAAGG
CTTAGTTTCCAAAATCTCATTA
Found at i:9267 original size:201 final size:200
Alignment explanation
Indices: 8920--9312 Score: 678
Period size: 201 Copynumber: 2.0 Consensus size: 200
8910 GATGGCCCGG
* *
8920 AGGTCTTATCATCTTGCTCGGAAGGCTTACAGATGACCCAGAGGATTTAACATCAAGAAACCCTT
1 AGGTCTTATCATCTTGCTCGGAAGACTTACAGATGAACCAGAGGATTTAACATCAAGAAACCCTT
* *
8985 GAAAATCAAGCTTAGTTTCTTGTTTGTCAAGGAACCCCTTAAAAGGGTTAGCTTTCTTTAACAAC
66 GAAAATCAAGCTTAGTTTCTTGTTTGTCAAGGAACCCCTTAAAAGGCTTAGCTTCCTTTAACAAC
* *
9050 TCTTTTGAGGTAATTAAGAAACCCCTTAAAGACTTAGTTTCCAAAATCTTATTAAAAACATCATT
131 TCTTTTGAGATAATTAAGAAACCCCTTAAAGACTTAGTTTCCAAAATCTCATTAAAAACATCATT
9115 CTCGA
196 CTCGA
* * *
9120 AGGTCTTATCATCTTGCTCGGAAGACTTATAGATGAACCGGAGGATTTAAACATCAAGAAACTCT
1 AGGTCTTATCATCTTGCTCGGAAGACTTACAGATGAACCAGAGGATTT-AACATCAAGAAACCCT
9185 TGAAAATCAAGCTTAGTTTCTTGTTTGTCAAGGAACCCCTTAAAAGGCTTAGCTTCCTTTAACAA
65 TGAAAATCAAGCTTAGTTTCTTGTTTGTCAAGGAACCCCTTAAAAGGCTTAGCTTCCTTTAACAA
* *
9250 CTCTTTTGCGATAATTAAGAAACCCCTTAAAGGCTTAGTTTCCAAAATCTCATTAAAAACATC
130 CTCTTTTGAGATAATTAAGAAACCCCTTAAAGACTTAGTTTCCAAAATCTCATTAAAAACATC
9313 CTACCTGGAG
Statistics
Matches: 181, Mismatches: 11, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
200 44 0.24
201 137 0.76
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.31
Consensus pattern (200 bp):
AGGTCTTATCATCTTGCTCGGAAGACTTACAGATGAACCAGAGGATTTAACATCAAGAAACCCTT
GAAAATCAAGCTTAGTTTCTTGTTTGTCAAGGAACCCCTTAAAAGGCTTAGCTTCCTTTAACAAC
TCTTTTGAGATAATTAAGAAACCCCTTAAAGACTTAGTTTCCAAAATCTCATTAAAAACATCATT
CTCGA
Found at i:9410 original size:22 final size:22
Alignment explanation
Indices: 9382--9424 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
9372 TTTTTGAAAA
9382 CATCTTGCACTCTAGGTCTTAT
1 CATCTTGCACTCTAGGTCTTAT
*
9404 CATCTTGCACTGTAGGTCTTA
1 CATCTTGCACTCTAGGTCTTA
9425 CAGATGTGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.26, G:0.16, T:0.40
Consensus pattern (22 bp):
CATCTTGCACTCTAGGTCTTAT
Found at i:14117 original size:55 final size:54
Alignment explanation
Indices: 13980--14136 Score: 242
Period size: 54 Copynumber: 2.9 Consensus size: 54
13970 ATAATCACTA
* * * *
13980 GTTCGTAAAACATTTGACAACACATTCGTCATTTCCTGAGGCTTTTGCCCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCCCAGAT
*
14034 GTTCGTAAAATATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCCCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCCCAGAT
* *
14088 GTTTTGTAAAACATTTGACAACACATTCATCCTTTCATGTGGCTTCTGC
1 G-TTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGC
14137 ACAAATATTT
Statistics
Matches: 94, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
54 50 0.53
55 44 0.47
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCCCAGAT
Found at i:15132 original size:75 final size:75
Alignment explanation
Indices: 15009--15188 Score: 254
Period size: 75 Copynumber: 2.4 Consensus size: 75
14999 ATAAGATGAT
*
15009 ATGGGCCTTCAACATGCCCCAACATTTGCTGATACAAACGTTCAAAATGCGA-CAATATTCCAAT
1 ATGGGCATTCAACATGCCCCAACATTTGCTGATACAAACGTTCAAAATGC-ATCAATATTCCAAT
15073 TTCTGATTGAA
65 TTCTGATTGAA
* *** * *
15084 ATGGGCATTCAACATTCCCCGGTATTTGCTGATACAAATGTTCAAAATGCATTAATATTCCAATT
1 ATGGGCATTCAACATGCCCCAACATTTGCTGATACAAACGTTCAAAATGCATCAATATTCCAATT
15149 TCTGATTGAA
66 TCTGATTGAA
* * *
15159 ATGGGCTTTCAGCATGCCCTAACATTTGCT
1 ATGGGCATTCAACATGCCCCAACATTTGCT
15189 TCTTGCTAAT
Statistics
Matches: 90, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
74 1 0.01
75 89 0.99
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.32
Consensus pattern (75 bp):
ATGGGCATTCAACATGCCCCAACATTTGCTGATACAAACGTTCAAAATGCATCAATATTCCAATT
TCTGATTGAA
Found at i:22145 original size:29 final size:27
Alignment explanation
Indices: 22060--22145 Score: 66
Period size: 28 Copynumber: 3.0 Consensus size: 27
22050 ATTAAATTGC
* *
22060 AAAATATATAAAATTCATGGTCAAAATTGA
1 AAAATATA-AAAATTAATGGAC-AAATT-A
* * *
22090 AAATTATAAAAATTAGT-GATTAAATTA
1 AAAATATAAAAATTAATGGA-CAAATTA
22117 TAAAATATAAAAATTAATGGACAACATTA
1 -AAAATATAAAAATTAATGGACAA-ATTA
22146 GATATATCAT
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
27 1 0.02
28 23 0.52
29 13 0.30
30 7 0.16
ACGTcount: A:0.56, C:0.05, G:0.08, T:0.31
Consensus pattern (27 bp):
AAAATATAAAAATTAATGGACAAATTA
Found at i:24393 original size:26 final size:26
Alignment explanation
Indices: 24357--24408 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
24347 TTTTCTACAA
24357 GAATTTTTTTATATAACATAAAATTT
1 GAATTTTTTTATATAACATAAAATTT
24383 GAATTTTTTTATATAACATAAAATTT
1 GAATTTTTTTATATAACATAAAATTT
24409 ACCTAGACTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (26 bp):
GAATTTTTTTATATAACATAAAATTT
Found at i:25171 original size:45 final size:44
Alignment explanation
Indices: 25064--25188 Score: 182
Period size: 43 Copynumber: 2.8 Consensus size: 44
25054 ACCTCTAAGA
* * *
25064 TTTTTCTACTAGAGCCAGATAGGCACCTCTAGTATTTTTTTCGT
1 TTTTTCTACTAGAGCCAGATAGGCACCTCTAGTATTTGTTCCCT
25108 TTTTT-TACTAGAGCCAGATAGGCACCTCTAGTAATTTGTTCCCT
1 TTTTTCTACTAGAGCCAGATAGGCACCTCTAGT-ATTTGTTCCCT
*
25152 TTTTTCCT-CTAGAGCCAGATAGGCACCTCTAGCATTT
1 TTTTT-CTACTAGAGCCAGATAGGCACCTCTAGTATTT
25189 TTTTATAGGA
Statistics
Matches: 74, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
43 27 0.36
44 22 0.30
45 24 0.32
46 1 0.01
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.39
Consensus pattern (44 bp):
TTTTTCTACTAGAGCCAGATAGGCACCTCTAGTATTTGTTCCCT
Found at i:29342 original size:32 final size:32
Alignment explanation
Indices: 29306--29420 Score: 86
Period size: 32 Copynumber: 3.2 Consensus size: 32
29296 TTTTAATTAA
29306 GTTTTAGGATATTATTTTTATATTTTATCTTT
1 GTTTTAGGATATTATTTTTATATTTTATCTTT
* ** *
29338 GTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATT
1 GTTTTAGG-ATATTA-TTTTTATA---TTT--TA-TCT--TT
29380 AAGTTTTAGGATATTATTTTTATATTTTATCTTT
1 --GTTTTAGGATATTATTTTTATATTTTATCTTT
29414 GTTTTAG
1 GTTTTAG
29421 TTATTTTAGT
Statistics
Matches: 63, Mismatches: 8, Indels: 24
0.66 0.08 0.25
Matches are distributed among these distances:
32 15 0.24
33 5 0.08
34 8 0.13
36 2 0.03
37 5 0.08
39 5 0.08
40 2 0.03
42 8 0.13
43 5 0.08
44 8 0.13
ACGTcount: A:0.24, C:0.02, G:0.13, T:0.61
Consensus pattern (32 bp):
GTTTTAGGATATTATTTTTATATTTTATCTTT
Found at i:29484 original size:76 final size:76
Alignment explanation
Indices: 29269--29456 Score: 333
Period size: 76 Copynumber: 2.5 Consensus size: 76
29259 TTTTATCTTT
*
29269 GTATTTTAGTTTAAATAGGGTTTAGTATTTTAATTAAGTTTTAGGATATTATTTTTATATTTTAT
1 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAGGATATTATTTTTATATTTTAT
29334 CTTTGTTTTAG
66 CTTTGTTTTAG
29345 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAGGATATTATTTTTATATTTTAT
1 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAGGATATTATTTTTATATTTTAT
29410 CTTTGTTTTAG
66 CTTTGTTTTAG
* *
29421 TTATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTA
1 GTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTA
29457 GGATTTAAGA
Statistics
Matches: 108, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
75 5 0.05
76 103 0.95
ACGTcount: A:0.27, C:0.01, G:0.13, T:0.59
Consensus pattern (76 bp):
GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAGGATATTATTTTTATATTTTAT
CTTTGTTTTAG
Found at i:30085 original size:10 final size:11
Alignment explanation
Indices: 30072--30100 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
30062 AATTTAGTTA
30072 TTTTATTT-AT
1 TTTTATTTAAT
30082 TTTTATTTAAT
1 TTTTATTTAAT
30093 TTTTATTT
1 TTTTATTT
30101 CATTATACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.44
11 10 0.56
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTATTTAAT
Found at i:38973 original size:30 final size:30
Alignment explanation
Indices: 38909--38975 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
38899 CGTCTGGCAA
* * *
38909 TGAACCGGCTGAAAACCTATAAAATCGGGG
1 TGAACCGGCTGAAAACCGACAAAACCGGGG
**
38939 TGAACCGGCTGAAAACCGACAAAACCGGTT
1 TGAACCGGCTGAAAACCGACAAAACCGGGG
38969 TGAACCG
1 TGAACCG
38976 CCGGTTCACT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.36, C:0.24, G:0.25, T:0.15
Consensus pattern (30 bp):
TGAACCGGCTGAAAACCGACAAAACCGGGG
Found at i:40922 original size:17 final size:16
Alignment explanation
Indices: 40891--40934 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 16
40881 TACTTTCTTA
* *
40891 ATTTTTGCTTTAAATT
1 ATTTTTCCTTAAAATT
40907 ATTTTTTCCTTAAAATT
1 A-TTTTTCCTTAAAATT
40924 ATTTTTCCTTA
1 ATTTTTCCTTA
40935 TTCAATGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 11 0.44
17 14 0.56
ACGTcount: A:0.25, C:0.11, G:0.02, T:0.61
Consensus pattern (16 bp):
ATTTTTCCTTAAAATT
Found at i:44337 original size:27 final size:27
Alignment explanation
Indices: 44247--44398 Score: 171
Period size: 27 Copynumber: 5.5 Consensus size: 27
44237 ACCATTTTAC
* *
44247 AAATAATTCTCAAATGTCATCGTTTT-A
1 AAATAATTCCCAAATGTCA-CTTTTTCA
** *
44274 AAATAATTAACAGAATGTCACTATTTTTA
1 AAATAATTCCCA-AATGTCACT-TTTTCA
*
44303 AAAAAATTCCCAAATGTCACTTTTTCA
1 AAATAATTCCCAAATGTCACTTTTTCA
* *
44330 AAATAATTCCCAAAATGTTACTTTTTTA
1 AAATAATTCCC-AAATGTCACTTTTTCA
*
44358 AAATAATTCCCAAATGTCACCTTTTCA
1 AAATAATTCCCAAATGTCACTTTTTCA
*
44385 AAATAATTCTCAAA
1 AAATAATTCCCAAA
44399 ATCGCTGGGT
Statistics
Matches: 107, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
27 52 0.49
28 45 0.42
29 10 0.09
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (27 bp):
AAATAATTCCCAAATGTCACTTTTTCA
Found at i:44375 original size:55 final size:56
Alignment explanation
Indices: 44217--44400 Score: 214
Period size: 56 Copynumber: 3.3 Consensus size: 56
44207 ACCTTTATTA
* * * *
44217 AAAATAATT-ATCAAAATTTCACCA-TTTTACAAATAATTCTCAAATGTCATCGTTTT-
1 AAAATAATTCA-CAAAATGTCACTATTTTTA-AAATAATTCCCAAATGTCA-CCTTTTC
* * * *
44273 AAAATAATTAACAGAATGTCACTATTTTTAAAAAAATTCCCAAATGTCACTTTTTC
1 AAAATAATTCACAAAATGTCACTATTTTTAAAATAATTCCCAAATGTCACCTTTTC
* *
44329 AAAATAATTCCCAAAATGTTACT-TTTTTAAAATAATTCCCAAATGTCACCTTTTC
1 AAAATAATTCACAAAATGTCACTATTTTTAAAATAATTCCCAAATGTCACCTTTTC
*
44384 AAAATAATTCTCAAAAT
1 AAAATAATTCACAAAAT
44401 CGCTGGGTCG
Statistics
Matches: 112, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
55 51 0.46
56 55 0.49
57 6 0.05
ACGTcount: A:0.42, C:0.17, G:0.04, T:0.37
Consensus pattern (56 bp):
AAAATAATTCACAAAATGTCACTATTTTTAAAATAATTCCCAAATGTCACCTTTTC
Found at i:44400 original size:28 final size:27
Alignment explanation
Indices: 44217--44400 Score: 149
Period size: 28 Copynumber: 6.6 Consensus size: 27
44207 ACCTTTATTA
* *
44217 AAAATAATTATCAAAATTTCACCATTTT
1 AAAATAATTCTCAAAATGTCACC-TTTT
*
44245 ACAAATAATTCTC-AAATGTCATCGTTTT
1 A-AAATAATTCTCAAAATGTCA-CCTTTT
** * *
44273 AAAATAATTAACAGAATGTCACTATTTTT
1 AAAATAATTCTCAAAATGTCAC--CTTTT
* * *
44302 AAAAAAATTC-CCAAATGTCACTTTTT
1 AAAATAATTCTCAAAATGTCACCTTTT
* * *
44328 CAAAATAATTCCCAAAATGTTACTTTTTT
1 -AAAATAATTCTCAAAATGTCAC-CTTTT
*
44357 AAAATAATTC-CCAAATGTCACCTTTT
1 AAAATAATTCTCAAAATGTCACCTTTT
44383 CAAAATAATTCTCAAAAT
1 -AAAATAATTCTCAAAAT
44401 CGCTGGGTCG
Statistics
Matches: 128, Mismatches: 18, Indels: 20
0.77 0.11 0.12
Matches are distributed among these distances:
26 9 0.07
27 38 0.30
28 53 0.41
29 28 0.22
ACGTcount: A:0.42, C:0.17, G:0.04, T:0.37
Consensus pattern (27 bp):
AAAATAATTCTCAAAATGTCACCTTTT
Found at i:51604 original size:28 final size:27
Alignment explanation
Indices: 51549--51679 Score: 108
Period size: 27 Copynumber: 4.7 Consensus size: 27
51539 CCTTTATTAA
* *
51549 AAATAATTCCCAAAATATCACCATTTTAT
1 AAATAATT-CCAAAATGTCATC-TTTTAT
* *
51578 AAATAATTCCTAAATGTCATCGTTTTAA
1 AAATAATTCCAAAATGTCATC-TTTTAT
*
51606 AAAT-ATTACCAAAATGTCA-CTATTTTT
1 AAATAATT-CCAAAATGTCATCT-TTTAT
*
51633 AAAAAATTCCAAAATGTCAT-TTTTCA-
1 AAATAATTCCAAAATGTCATCTTTT-AT
*
51659 AAATAATTCCCAAAATATCAT
1 AAATAATT-CCAAAATGTCAT
51680 GGGTCGGGTC
Statistics
Matches: 84, Mismatches: 12, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
26 11 0.13
27 33 0.39
28 32 0.38
29 8 0.10
ACGTcount: A:0.44, C:0.17, G:0.03, T:0.36
Consensus pattern (27 bp):
AAATAATTCCAAAATGTCATCTTTTAT
Found at i:51651 original size:55 final size:55
Alignment explanation
Indices: 51545--51678 Score: 182
Period size: 55 Copynumber: 2.4 Consensus size: 55
51535 ATCACCTTTA
* *
51545 TTAAAAATAATTCCCAAAATATCACCATTTTATAAATAATTCCTAAATGTCATCGTT
1 TTAAAAATAATTCCCAAAATATCACCATTTTATAAAAAATTCCAAAATGTCAT--TT
* * *
51602 TTAAAAAT-ATTACCAAAATGTCACTATTTT-TAAAAAATTCCAAAATGTCATTT
1 TTAAAAATAATTCCCAAAATATCACCATTTTATAAAAAATTCCAAAATGTCATTT
*
51655 TTCAAAATAATTCCCAAAATATCA
1 TTAAAAATAATTCCCAAAATATCA
51679 TGGGTCGGGT
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
53 9 0.13
54 13 0.19
55 19 0.28
56 19 0.28
57 8 0.12
ACGTcount: A:0.45, C:0.16, G:0.03, T:0.36
Consensus pattern (55 bp):
TTAAAAATAATTCCCAAAATATCACCATTTTATAAAAAATTCCAAAATGTCATTT
Found at i:51725 original size:17 final size:18
Alignment explanation
Indices: 51701--51745 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
51691 GGTTGGGTCT
*
51701 GGTCAGACGGTCAA-CCG
1 GGTCAGACCGTCAACCCG
*
51718 GTTCAGACCGTCAACCCG
1 GGTCAGACCGTCAACCCG
51736 GGTCAGACCG
1 GGTCAGACCG
51746 GTTTGGATCG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.22, C:0.33, G:0.31, T:0.13
Consensus pattern (18 bp):
GGTCAGACCGTCAACCCG
Done.