Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002819.1 Hibiscus syriacus cultivar Beakdansim tig00005799_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: 213166
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
File 2 of 2
Found at i:165596 original size:19 final size:19
Alignment explanation
Indices: 165574--165689 Score: 92
Period size: 19 Copynumber: 6.6 Consensus size: 19
165564 GAAACACAAA
165574 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
165593 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
165609 TCG--TTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
*
165625 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
165641 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
**
165658 TCGCATTGCGATAGTCATT
1 TCGCATTGCGATTTTCATT
*
165677 TCTGCGTTGCGAT
1 TC-GCATTGCGAT
165690 AGTCATTTTT
Statistics
Matches: 79, Mismatches: 8, Indels: 19
0.75 0.08 0.18
Matches are distributed among these distances:
14 15 0.19
15 3 0.04
16 12 0.15
17 4 0.05
18 12 0.15
19 24 0.30
20 9 0.11
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:165615 original size:14 final size:14
Alignment explanation
Indices: 165596--165653 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
165586 TTTCATTTCG
165596 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
165610 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
165626 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
165642 CGTTGCGATTTT
1 CGTTGCGATTTT
165654 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:165660 original size:33 final size:33
Alignment explanation
Indices: 165579--165669 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
165569 ACAAATCGCA
*
165579 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
165612 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
165644 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
165670 AGTCATTTCT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:165688 original size:20 final size:20
Alignment explanation
Indices: 165642--165708 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
165632 GCGATTTTGT
**
165642 CGTTGCGATTTTCATTTC-G
1 CGTTGCGATAGTCATTTCTG
*
165661 CATTGCGATAGTCATTTCTG
1 CGTTGCGATAGTCATTTCTG
*
165681 CGTTGCGATAGTCATTTTTG
1 CGTTGCGATAGTCATTTCTG
*
165701 TGTTGCGA
1 CGTTGCGA
165709 AAGTAAACTA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 15 0.37
20 26 0.63
ACGTcount: A:0.15, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCTG
Found at i:166233 original size:17 final size:18
Alignment explanation
Indices: 166190--166233 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
166180 GTCGATCAGA
*
166190 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
166208 TGATAGCTCTGGGCGA-G
1 TGATGGCTCTGGGCGAGG
166225 TGATGGCTC
1 TGATGGCTC
166234 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.14, C:0.16, G:0.43, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:167600 original size:20 final size:20
Alignment explanation
Indices: 167552--167610 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
167542 AATAGTTTCT
** *
167552 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
167572 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
167592 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
167611 AGATAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:167658 original size:19 final size:19
Alignment explanation
Indices: 167636--167686 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
167626 GAAACTAAAA
167636 TCGCGTTGCGATTTGCATT
1 TCGCGTTGCGATTTGCATT
167655 TCGCGTTGCGATTTGCATT
1 TCGCGTTGCGATTTGCATT
167674 TCGCGTTGCGATT
1 TCGCGTTGCGATT
167687 CTCGGTTGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.10, C:0.22, G:0.27, T:0.41
Consensus pattern (19 bp):
TCGCGTTGCGATTTGCATT
Found at i:168147 original size:20 final size:20
Alignment explanation
Indices: 168122--168193 Score: 99
Period size: 20 Copynumber: 3.6 Consensus size: 20
168112 ATTATGTATT
*
168122 ATCGCGTTGTGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGA
*
168142 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGA
* *
168162 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGAAAGTCAGA
*
168182 ATCTCGTTGCGA
1 ATCGCGTTGCGA
168194 TTTTGTATTA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.26
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGA
Found at i:168231 original size:20 final size:20
Alignment explanation
Indices: 168121--168235 Score: 97
Period size: 20 Copynumber: 5.7 Consensus size: 20
168111 GATTATGTAT
* *
168121 TATCGCGTTGTGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
168141 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
168161 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGATAGTCAG
* * *
168181 TATCTCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
* *
168202 TATTGCATTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
168222 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
168236 TTTCCCAATT
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
19 3 0.04
20 62 0.79
21 11 0.14
22 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:168253 original size:21 final size:21
Alignment explanation
Indices: 168224--168295 Score: 92
Period size: 21 Copynumber: 3.5 Consensus size: 21
168214 ATAGTCAGTA
168224 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
168245 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
168265 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
*
168286 TCGCGTTGCG
1 TCGCATTGCG
168296 CTTTACTTAT
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 16 0.39
21 25 0.61
ACGTcount: A:0.15, C:0.26, G:0.19, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:168254 original size:41 final size:41
Alignment explanation
Indices: 168224--168316 Score: 141
Period size: 41 Copynumber: 2.3 Consensus size: 41
168214 ATAGTCAGTA
* *
168224 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
* * *
168265 TCGCATTGCGATTTTCCCAATTCGCGTTGCGCTTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
168306 TCGCATTGCGA
1 TCGCATTGCGA
168317 ATTGGGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.16, C:0.26, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:168268 original size:20 final size:20
Alignment explanation
Indices: 168224--168316 Score: 87
Period size: 20 Copynumber: 4.5 Consensus size: 20
168214 ATAGTCAGTA
* **
168224 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
168245 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
168265 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
* *
168286 TCGCGTTGCGCTTTACTTAT
1 TCGCATTGCGATTTACTTAT
168306 TCGCATTGCGA
1 TCGCATTGCGA
168317 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 31 0.55
21 25 0.45
ACGTcount: A:0.16, C:0.26, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:168602 original size:9 final size:9
Alignment explanation
Indices: 168588--168615 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
168578 AGAATTGTCC
168588 TTATTTCCT
1 TTATTTCCT
168597 TTATTTCCT
1 TTATTTCCT
168606 TTATTTCCT
1 TTATTTCCT
168615 T
1 T
168616 GTTTGATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.11, C:0.21, G:0.00, T:0.68
Consensus pattern (9 bp):
TTATTTCCT
Found at i:169239 original size:15 final size:17
Alignment explanation
Indices: 169208--169239 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
169198 TTTTTTTAAT
169208 TTGTGCTTTATATTTTA
1 TTGTGCTTTATATTTTA
169225 TTGTG-TTTA-ATTTTA
1 TTGTGCTTTATATTTTA
169240 GCCCTTCATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.19, C:0.03, G:0.12, T:0.66
Consensus pattern (17 bp):
TTGTGCTTTATATTTTA
Found at i:174981 original size:116 final size:117
Alignment explanation
Indices: 174776--175021 Score: 345
Period size: 116 Copynumber: 2.1 Consensus size: 117
174766 GCATAAACCC
* * * *
174776 ATCAGCATTTCCAGTGGAAGGGTTCATAATAAGAAGAACTCATCCGATGAGGAAGAAGAAGTTCC
1 ATCAGCATTTCCAGTAGAAGGATTCATAATAAGAAGAACTCATCAGATGAGGAAGAAGAACTTCC
*
174841 TAATGAGAAGAACTTGTTCGACC-TTGGCTCATCCATCACATAAGGAGTTGG
66 TAATGAGAAGAACTTGTTCAACCTTTGGCTCATCCATCACATAAGGAGTTGG
* * * *
174892 ATCAGCATTTCCAGTAGAAGGATTCTTGATGAGAA-AAGCTCGTCAGATGAAGG-AGAAGAACTT
1 ATCAGCATTTCCAGTAGAAGGATTCATAATAAGAAGAA-CTCATCAGATG-AGGAAGAAGAACTT
* *
174955 CCTAATGAGAATAACTTGTTCAACCTTTGGCTCATCTATCACATAAGGAGTTGG
64 CCTAATGAGAAGAACTTGTTCAACCTTTGGCTCATCCATCACATAAGGAGTTGG
*
175009 ATCAACATTTCCA
1 ATCAGCATTTCCA
175022 ATGAGGGAAA
Statistics
Matches: 115, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
115 2 0.02
116 71 0.62
117 42 0.37
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (117 bp):
ATCAGCATTTCCAGTAGAAGGATTCATAATAAGAAGAACTCATCAGATGAGGAAGAAGAACTTCC
TAATGAGAAGAACTTGTTCAACCTTTGGCTCATCCATCACATAAGGAGTTGG
Found at i:175166 original size:44 final size:44
Alignment explanation
Indices: 175073--175168 Score: 104
Period size: 44 Copynumber: 2.2 Consensus size: 44
175063 CTTGGTTCAT
* * * *
175073 CCATCATATAAGGAGTTGGACCAGCATCACCATTTCGCTCGATT
1 CCATCACATAAGGAGTTGGACCAGCATCACCATTTAGCTAGATC
* * * *
175117 TCATCACATAAGGAGTTGGATCAGCGTCACTCTTTTAG-TAGATC
1 CCATCACATAAGGAGTTGGACCAGCATCAC-CATTTAGCTAGATC
175161 CCATCACA
1 CCATCACA
175169 GAATGAGATG
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
44 37 0.88
45 5 0.12
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (44 bp):
CCATCACATAAGGAGTTGGACCAGCATCACCATTTAGCTAGATC
Found at i:182950 original size:66 final size:66
Alignment explanation
Indices: 182867--182994 Score: 238
Period size: 66 Copynumber: 1.9 Consensus size: 66
182857 TTATCTCTTT
* *
182867 GTTAGCCCATGTACACATGTGAGAACTAAAGATATGTGAGTATATAGAGGTTGTGCACCTATGCT
1 GTTAGCCCATATACACATGTGAGAACTAAAGATATGTGAGTACATAGAGGTTGTGCACCTATGCT
182932 G
66 G
182933 GTTAGCCCATATACACATGTGAGAACTAAAGATATGTGAGTACATAGAGGTTGTGCACCTAT
1 GTTAGCCCATATACACATGTGAGAACTAAAGATATGTGAGTACATAGAGGTTGTGCACCTAT
182995 ACTATCACCA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (66 bp):
GTTAGCCCATATACACATGTGAGAACTAAAGATATGTGAGTACATAGAGGTTGTGCACCTATGCT
G
Found at i:194119 original size:19 final size:19
Alignment explanation
Indices: 194095--194144 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
194085 CGGCCAAGAG
* *
194095 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATCAAAAT
194114 CATGTATTTTCATCAAAAT
1 CATGTATTTTCATCAAAAT
194133 CATGTATTTTCA
1 CATGTATTTTCA
194145 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.34, C:0.16, G:0.06, T:0.44
Consensus pattern (19 bp):
CATGTATTTTCATCAAAAT
Found at i:196750 original size:31 final size:31
Alignment explanation
Indices: 196710--196782 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
196700 ACTCGGGGTG
* * *
196710 ACCACATCTTAATTAAATAAAAATGAAAATG
1 ACCATATCTTAATAAAATAAAAATGAAAATA
* *
196741 ATCATATCTTAATAAAATAAAAATGAAAGTA
1 ACCATATCTTAATAAAATAAAAATGAAAATA
196772 ACCATATCTTA
1 ACCATATCTTA
196783 TGTTTTTTGA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.53, C:0.12, G:0.05, T:0.29
Consensus pattern (31 bp):
ACCATATCTTAATAAAATAAAAATGAAAATA
Found at i:197245 original size:50 final size:49
Alignment explanation
Indices: 197175--197357 Score: 158
Period size: 50 Copynumber: 3.7 Consensus size: 49
197165 TAAATATATG
* *
197175 TTAAAATTCACTAG-AGTAATTATGTGTTAAGTTGATTGACATGATATGTA
1 TTAAAGTTCACTAGTA-TAATTATGTGTTAAGTTCATTGA-ATGATATGTA
* * * *
197225 TTTAAGTTCAC-ATGTATAATTATGTATTAAGTTCACT-AAT-ATTATGTG
1 TTAAAGTTCACTA-GTATAATTATGTGTTAAGTTCATTGAATGA-TATGTA
* * * *
197273 TTAAAGTTGACTAGTGTAATTATATGTTAAGTTCATTGATATGATATGTG
1 TTAAAGTTCACTAGTATAATTATGTGTTAAGTTCATTGA-ATGATATGTA
* * * * *
197323 TTAAATTTTACTGGTGTAATTATGTGATAAGTTCA
1 TTAAAGTTCACTAGTATAATTATGTGTTAAGTTCA
197358 ATGGTATAAT
Statistics
Matches: 109, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
47 1 0.01
48 36 0.33
49 4 0.04
50 66 0.61
51 2 0.02
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44
Consensus pattern (49 bp):
TTAAAGTTCACTAGTATAATTATGTGTTAAGTTCATTGAATGATATGTA
Found at i:197271 original size:22 final size:23
Alignment explanation
Indices: 197219--197285 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 23
197209 ATTGACATGA
*
197219 TATGTATTTAAGTTCACATGTATAAT
1 TATGTA-TTAAGTTCAC-T-AATAAT
197245 TATGTATTAAGTTCACTAAT-AT
1 TATGTATTAAGTTCACTAATAAT
* *
197267 TATGTGTTAAAGTTGACTA
1 TATGTATT-AAGTTCACTA
197286 GTGTAATTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
22 9 0.24
23 11 0.30
24 1 0.03
25 10 0.27
26 6 0.16
ACGTcount: A:0.34, C:0.07, G:0.13, T:0.45
Consensus pattern (23 bp):
TATGTATTAAGTTCACTAATAAT
Found at i:197343 original size:98 final size:98
Alignment explanation
Indices: 197173--197357 Score: 239
Period size: 98 Copynumber: 1.9 Consensus size: 98
197163 TGTAAATATA
* * *
197173 TGTTAAAATTCACTAGAGTAATTATGTGTTAAGTTGATTGACATGATATGTATTTAAGTTCACAT
1 TGTTAAAATTCACTAGAGTAATTATATGTTAAGTTCATTGACATGATATGTATTAAAGTTCACAT
197238 GTATAATTATGT-ATTAAGTTCACTAATATTATG
66 GTATAATTATGTGA-TAAGTTCACTAATATTATG
* * * * * * *
197271 TGTTAAAGTTGACTAGTGTAATTATATGTTAAGTTCATTGATATGATATGTGTTAAATTTTAC-T
1 TGTTAAAATTCACTAGAGTAATTATATGTTAAGTTCATTGACATGATATGTATTAAAGTTCACAT
*
197335 GGTGTAATTATGTGATAAGTTCA
66 -GTATAATTATGTGATAAGTTCA
197358 ATGGTATAAT
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
97 1 0.01
98 72 0.97
99 1 0.01
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44
Consensus pattern (98 bp):
TGTTAAAATTCACTAGAGTAATTATATGTTAAGTTCATTGACATGATATGTATTAAAGTTCACAT
GTATAATTATGTGATAAGTTCACTAATATTATG
Found at i:197348 original size:26 final size:26
Alignment explanation
Indices: 197147--197367 Score: 77
Period size: 25 Copynumber: 8.9 Consensus size: 26
197137 ATCATAAGTC
* * *
197147 GTGTT-AAGTTTACTAGTGTAAATAT
1 GTGTTAAAGTTCACTGGTGTAATTAT
* * * *
197172 ATGTTAAAATTCACTAGAGTAATTAT
1 GTGTTAAAGTTCACTGGTGTAATTAT
* * *** *
197198 GTGTT-AAGTTGATTGACATGA-TAT
1 GTGTTAAAGTTCACTGGTGTAATTAT
* * *
197222 GTATTTAAGTTCACAT-GTATAATTAT
1 GTGTTAAAGTTCAC-TGGTGTAATTAT
* **
197248 GTATT-AAGTTCACT--AAT-ATTAT
1 GTGTTAAAGTTCACTGGTGTAATTAT
* *
197270 GTGTTAAAGTTGACTAGTGTAATTAT
1 GTGTTAAAGTTCACTGGTGTAATTAT
* * * * *
197296 ATGTT-AAGTTCATTGATATGA-TAT
1 GTGTTAAAGTTCACTGGTGTAATTAT
* *
197320 GTGTTAAATTTTACTGGTGTAATTAT
1 GTGTTAAAGTTCACTGGTGTAATTAT
* * *
197346 GTGAT-AAGTTCAATGGTATAAT
1 GTGTTAAAGTTCACTGGTGTAAT
197368 ATATTAATAC
Statistics
Matches: 142, Mismatches: 44, Indels: 20
0.69 0.21 0.10
Matches are distributed among these distances:
22 9 0.06
23 10 0.07
24 15 0.11
25 63 0.44
26 45 0.32
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.43
Consensus pattern (26 bp):
GTGTTAAAGTTCACTGGTGTAATTAT
Found at i:197609 original size:51 final size:51
Alignment explanation
Indices: 197508--197612 Score: 131
Period size: 51 Copynumber: 2.1 Consensus size: 51
197498 GCATGAATGC
* ** *
197508 AAACTATATGAATGATAAGATGCTACAACTCACTTGGTACATTAAGATAAG
1 AAACTATATGAATGAAAAGATGCTACAACTCACTTGGTACACAAAAATAAG
* * *
197559 AAACTATGTGAATGAAAAGGA-GCTACGACTCATTTGGTACACAAAAATAAG
1 AAACTATATGAATGAAAA-GATGCTACAACTCACTTGGTACACAAAAATAAG
197610 AAA
1 AAA
197613 TCATGGGGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
51 44 0.96
52 2 0.04
ACGTcount: A:0.46, C:0.13, G:0.17, T:0.24
Consensus pattern (51 bp):
AAACTATATGAATGAAAAGATGCTACAACTCACTTGGTACACAAAAATAAG
Found at i:198071 original size:33 final size:33
Alignment explanation
Indices: 198018--198119 Score: 127
Period size: 33 Copynumber: 3.1 Consensus size: 33
198008 TTATGATTTA
* * *
198018 TATGAGATAA-TTCTTGCCATGAAAATTCATGT
1 TATGATATAAGTTCTTACCATGAAAGTTCATGT
198050 TATGATATAAGTTCATT-CCATGAAAGTTCATGT
1 TATGATATAAGTTC-TTACCATGAAAGTTCATGT
* * *
198083 TACGATACAAGTTCTTACCTTGAAAGTTCATGT
1 TATGATATAAGTTCTTACCATGAAAGTTCATGT
198116 TATG
1 TATG
198120 TTATGTTCAT
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
32 11 0.18
33 48 0.79
34 2 0.03
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (33 bp):
TATGATATAAGTTCTTACCATGAAAGTTCATGT
Found at i:201220 original size:11 final size:11
Alignment explanation
Indices: 201197--201231 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
201187 AATAGAAATC
*
201197 AAAGA-GAATA
1 AAAGAGGAAGA
201207 AAAGAGGAAGA
1 AAAGAGGAAGA
201218 AAAGAGGAAGA
1 AAAGAGGAAGA
201229 AAA
1 AAA
201232 TTGCTCATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 5 0.22
11 18 0.78
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.03
Consensus pattern (11 bp):
AAAGAGGAAGA
Found at i:212370 original size:29 final size:29
Alignment explanation
Indices: 212337--212392 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
212327 CTATGACTTT
*
212337 ATTCTAAATTAATCATTAAACTTTTAAAC
1 ATTCTAAATTAATCATTAAACTATTAAAC
* * *
212366 ATTCTAATTTCATCCTTAAACTATTAA
1 ATTCTAAATTAATCATTAAACTATTAA
212393 CTTTTTTTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.41, C:0.16, G:0.00, T:0.43
Consensus pattern (29 bp):
ATTCTAAATTAATCATTAAACTATTAAAC
Found at i:212674 original size:60 final size:60
Alignment explanation
Indices: 212593--212733 Score: 153
Period size: 60 Copynumber: 2.4 Consensus size: 60
212583 GAATGTTTAA
* * * **
212593 AAAAGTTTAGGGGAC-AGTTTAGAATGA-AGGTTAAAGTTTGGGGATAAAATTGAAATATTC
1 AAAAGTTT-GAGGACTAATTTAGAATGATA-GTCAAAGTTTAAGGATAAAATTGAAATATTC
* * * *
212653 AAAAGTTTGAGGACTAATTTAGAATGATAGTCATAGTTTAAGGATGAAATTGGAATATTT
1 AAAAGTTTGAGGACTAATTTAGAATGATAGTCAAAGTTTAAGGATAAAATTGAAATATTC
212713 AAAAGTTT-AGAGACTAATTTA
1 AAAAGTTTGAG-GACTAATTTA
212734 AAATAGAGTC
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
59 7 0.10
60 61 0.88
61 1 0.01
ACGTcount: A:0.41, C:0.04, G:0.23, T:0.33
Consensus pattern (60 bp):
AAAAGTTTGAGGACTAATTTAGAATGATAGTCAAAGTTTAAGGATAAAATTGAAATATTC
Done.