Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011446.1 Corchorus capsularis cultivar CVL-1 contig11467, 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: 19372
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3830 original size:18 final size:18
Alignment explanation
Indices: 3807--3844 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
3797 ACTCCTTTAA
3807 GCTTGTCCATGCTTCCTT
1 GCTTGTCCATGCTTCCTT
*
3825 GCTTGTCCATGCTTGCTT
1 GCTTGTCCATGCTTCCTT
3843 GC
1 GC
3845 ACTCCTTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.32, G:0.21, T:0.42
Consensus pattern (18 bp):
GCTTGTCCATGCTTCCTT
Found at i:7268 original size:1 final size:1
Alignment explanation
Indices: 7262--7295 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
7252 AGTCTCCGCT
* *
7262 CCCCCCCCCGCCACCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
7296 TTTTTTTCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.03, C:0.94, G:0.03, T:0.00
Consensus pattern (1 bp):
C
Found at i:9939 original size:8 final size:8
Alignment explanation
Indices: 9928--10009 Score: 56
Period size: 8 Copynumber: 10.1 Consensus size: 8
9918 AAATTGGAGC
*
9928 ATTGAATA
1 ATTGAAGA
9936 ATTGAAGA
1 ATTGAAGA
* *
9944 ACTGAAGCG
1 ATTGAAG-A
* *
9953 TTTGAATA
1 ATTGAAGA
*
9961 ATTGAATA
1 ATTGAAGA
9969 ATTGAAGA
1 ATTGAAGA
*
9977 ATTGAAGC
1 ATTGAAGA
* *
9985 ATTGGATA
1 ATTGAAGA
* *
9993 GTTAAAGA
1 ATTGAAGA
10001 ATTGAAGA
1 ATTGAAGA
10009 A
1 A
10010 AGGCCACCCT
Statistics
Matches: 54, Mismatches: 19, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
8 50 0.93
9 4 0.07
ACGTcount: A:0.45, C:0.04, G:0.22, T:0.29
Consensus pattern (8 bp):
ATTGAAGA
Found at i:9988 original size:24 final size:24
Alignment explanation
Indices: 9961--10007 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
9951 CGTTTGAATA
*
9961 ATTGAATAATTGAAGAATTGAAGC
1 ATTGAATAATTAAAGAATTGAAGC
* *
9985 ATTGGATAGTTAAAGAATTGAAG
1 ATTGAATAATTAAAGAATTGAAG
10008 AAAGGCCACC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.45, C:0.02, G:0.23, T:0.30
Consensus pattern (24 bp):
ATTGAATAATTAAAGAATTGAAGC
Found at i:10045 original size:58 final size:58
Alignment explanation
Indices: 9879--10226 Score: 353
Period size: 58 Copynumber: 6.2 Consensus size: 58
9869 AGAAAATAAA
* * *
9879 TTGAAGAATTGAAGAAAGACCATCCTGGATCATTGAAGTAAATTGGAGCATTGAATAA
1 TTGAAGAATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGAAGCATTGAATAG
* *** ** ** * * *
9937 TTGAAGAACTGAAGCGTTTGAATA-ATTGAATAATTGAAG--AATTGAAGCATTGGATAG
1 TTGAAGAATTGAA--GAAAGACCACCCTGGATCATTGAAGTAAATTGAAGCATTGAATAG
* *
9994 TTAAAGAATTGAAGAAAGGCCACCCTGGATCATTGAAGTAAATTGAAGC-------A-
1 TTGAAGAATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGAAGCATTGAATAG
* *
10044 TTGAAGAATTGAAGAAAGACC-CCCTGGATCATTGAAGTAAATTGAAGCATTGGATAA
1 TTGAAGAATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGAAGCATTGAATAG
* * *
10101 TTGAAGAATTGAAGAAAGACCACCCTAGATCATTGAAGTAAATTGATGCTTTGAAT-G
1 TTGAAGAATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGAAGCATTGAATAG
* * * *
10158 ATTGAAGAATTGAAGAAAGACCACCATGGATCATTGAAGTAAATTTATGCATTGAATAA
1 -TTGAAGAATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGAAGCATTGAATAG
10217 TTGAAGAATT
1 TTGAAGAATT
10227 AAAGCATTGA
Statistics
Matches: 237, Mismatches: 37, Indels: 32
0.77 0.12 0.10
Matches are distributed among these distances:
49 27 0.11
50 19 0.08
51 1 0.00
55 3 0.01
56 12 0.05
57 47 0.20
58 113 0.48
59 11 0.05
60 4 0.02
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.27
Consensus pattern (58 bp):
TTGAAGAATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGAAGCATTGAATAG
Found at i:10055 original size:16 final size:17
Alignment explanation
Indices: 10024--10057 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
10014 CACCCTGGAT
10024 CATTGAAGTAAATTGAAG
1 CATTGAAG-AAATTGAAG
10042 CATTGAAG-AATTGAAG
1 CATTGAAGAAATTGAAG
10058 AAAGACCCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
18 8 0.50
ACGTcount: A:0.44, C:0.06, G:0.24, T:0.26
Consensus pattern (17 bp):
CATTGAAGAAATTGAAG
Found at i:10087 original size:107 final size:109
Alignment explanation
Indices: 9969--10226 Score: 344
Period size: 107 Copynumber: 2.3 Consensus size: 109
9959 TAATTGAATA
* * * *
9969 ATTGAAG--AATTGAAGCATTGGATAGTTAAAGAATTGAAGAAAGGCCACCCTGGATCATTGAAG
1 ATTGAAGTAAATTGAAGCATTGGATAATTGAAGAATTGAAGAAAGACCACCCTAGATCATTGAAG
*
10032 TAAATTGAAGC-ATTGAAGAATTGAAGAAAGACC-CCCTGGATC
66 TAAATTGAAGCTATTGAAGAATTGAAGAAAGACCACCATGGATC
10074 ATTGAAGTAAATTGAAGCATTGGATAATTGAAGAATTGAAGAAAGACCACCCTAGATCATTGAAG
1 ATTGAAGTAAATTGAAGCATTGGATAATTGAAGAATTGAAGAAAGACCACCCTAGATCATTGAAG
*
10139 TAAATTGATGCTTTGAATGATTGAAGAATTGAAGAAAGACCACCATGGATC
66 TAAATTGAAGC------T-ATTGAAGAATTGAAGAAAGACCACCATGGATC
* * *
10190 ATTGAAGTAAATTTATGCATTGAATAATTGAAGAATT
1 ATTGAAGTAAATTGAAGCATTGGATAATTGAAGAATT
10227 AAAGCATTGA
Statistics
Matches: 133, Mismatches: 9, Indels: 11
0.87 0.06 0.07
Matches are distributed among these distances:
105 7 0.05
107 62 0.47
115 22 0.17
116 42 0.32
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.26
Consensus pattern (109 bp):
ATTGAAGTAAATTGAAGCATTGGATAATTGAAGAATTGAAGAAAGACCACCCTAGATCATTGAAG
TAAATTGAAGCTATTGAAGAATTGAAGAAAGACCACCATGGATC
Found at i:10087 original size:115 final size:111
Alignment explanation
Indices: 9877--10199 Score: 332
Period size: 115 Copynumber: 2.8 Consensus size: 111
9867 ATAGAAAATA
* * * *
9877 AATTGAAGAATTGAAGAAAGACCATCCTGGATCATTGAAGTAAATTGGAGCATTGAATAATTGAA
1 AATTAAAGAATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGAAGCATTGAAGAATTGAA
* * *** * *
9942 GAACTGAAGCGTTTGAATAATTGAA-TAATTGAAGAATTGAAGCATTGGAT
66 GAA-AG-ACCCCATGGATCATTGAAGTAATT--A-AATTGAAGCATTGGAT
* *
9992 AGTTAAAGAATTGAAGAAAGGCCACCCTGGATCATTGAAGTAAATTGAAGCATTGAAGAATTGAA
1 AATTAAAGAATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGAAGCATTGAAGAATTGAA
*
10057 GAAAGACCCCCTGGATCATTGAAG----TAAATTGAAGCATTGGAT
66 GAAAGACCCCATGGATCATTGAAGTAATTAAATTGAAGCATTGGAT
* * *
10099 AATTGAAGAATTGAAGAAAGACCACCCTAGATCATTGAAGTAAATTGATGCTTTGAATGATTGAA
1 AATTAAAGAATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGAAGC--------ATTGAA
10164 GAATTGAAGAAAGACCACCATGGATCATTGAAGTAA
58 GAATTGAAGAAAGACC-CCATGGATCATTGAAGTAA
10200 ATTTATGCAT
Statistics
Matches: 176, Mismatches: 19, Indels: 22
0.81 0.09 0.10
Matches are distributed among these distances:
107 62 0.35
108 1 0.01
110 1 0.01
113 12 0.07
114 1 0.01
115 84 0.48
116 15 0.09
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.25
Consensus pattern (111 bp):
AATTAAAGAATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGAAGCATTGAAGAATTGAA
GAAAGACCCCATGGATCATTGAAGTAATTAAATTGAAGCATTGGAT
Found at i:10219 original size:116 final size:117
Alignment explanation
Indices: 10035--10528 Score: 542
Period size: 116 Copynumber: 4.1 Consensus size: 117
10025 ATTGAAGTAA
* *
10035 ATTGAA-GCATTGAAGAATTGAAGAAAGACC-CCCTGGATCATTGAAGTAAATTGAAGCATTGGA
1 ATTGAATGAATTGAAGAATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGAAGCATTGAA
10098 TAATTGAAGAATTGAAGAAAGACCACCCTAGATCATTGAAGTAAATTGATGC
66 TAATTGAAGAATTGAAGAAAGACCACCCTAGATCATTGAAGTAAATTGATGC
* * * *
10150 TTTGAATG-ATTGAAGAATTGAAGAAAGACCACCATGGATCATTGAAGTAAATTTATGCATTGAA
1 ATTGAATGAATTGAAGAATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGAAGCATTGAA
* ** ** ** * *
10214 TAATTGAAGAATTAAAGCATTGAATA-GTTGAAGA--ATTGAAGAAAGACCACCCTGGAT-C
66 TAATTGAAGAATTGAAG-AAAGACCACCCT--AGATCATTGAAG-TA-A--A---TTGATGC
10272 ATTGAACTGAATTGAAGCATTGAAGAATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGA
1 A-T----TGAA-TG-A--ATTGAAGAATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGA
*
10337 AGCATTGAATAATTGAAGAATTGAAGAAAGACCACCCT-GTATCATTGAACTAAATTGATGC
57 AGCATTGAATAATTGAAGAATTGAAGAAAGACCACCCTAG-ATCATTGAAGTAAATTGATGC
* *
10398 ATTGAAT-AATTGAAGAATTGAAGAAAGATCACCCTGGATCATTGAAGTAAATTGATGCATTGAA
1 ATTGAATGAATTGAAGAATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGAAGCATTGAA
* *
10462 TAATTGAAGAATTGAAGAAAGACCACCCTGGATCATT-AGAGTAAATTGAAGC
66 TAATTGAAGAATTGAAGAAAGACCACCCTAGATCATTGA-AGTAAATTGATGC
10514 ATTGAA-GAATTGAAG
1 ATTGAATGAATTGAAG
10529 TTGAAGCATT
Statistics
Matches: 317, Mismatches: 32, Indels: 59
0.78 0.08 0.14
Matches are distributed among these distances:
115 28 0.09
116 168 0.53
117 6 0.02
118 5 0.02
120 2 0.01
121 4 0.01
122 1 0.00
123 5 0.02
125 5 0.02
126 2 0.01
127 4 0.01
128 3 0.01
129 1 0.00
130 2 0.01
131 5 0.02
132 76 0.24
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.26
Consensus pattern (117 bp):
ATTGAATGAATTGAAGAATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGAAGCATTGAA
TAATTGAAGAATTGAAGAAAGACCACCCTAGATCATTGAAGTAAATTGATGC
Found at i:10221 original size:8 final size:8
Alignment explanation
Indices: 10208--10256 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 8
10198 AAATTTATGC
*
10208 ATTGAATA
1 ATTGAAGA
10216 ATTGAAGA
1 ATTGAAGA
* *
10224 ATTAAAGC
1 ATTGAAGA
*
10232 ATTGAATA
1 ATTGAAGA
*
10240 GTTGAAGA
1 ATTGAAGA
10248 ATTGAAGA
1 ATTGAAGA
10256 A
1 A
10257 AGACCACCCT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.49, C:0.02, G:0.20, T:0.29
Consensus pattern (8 bp):
ATTGAAGA
Found at i:10284 original size:58 final size:58
Alignment explanation
Indices: 10223--10528 Score: 441
Period size: 58 Copynumber: 5.4 Consensus size: 58
10213 ATAATTGAAG
* * *
10223 AATTAAAGCATTGAATAGTTGAAGAATTGAAGAAAGACCACCCTGGATCATTGAACTG
1 AATTGAAGCATTGAATAATTGAAGAATTGAAGAAAGACCACCCTGGATCATTGAACTA
*
10281 AATTGAAGC--------ATTGAAGAATTGAAGAAAGACCACCCTGGATCATTGAAGTA
1 AATTGAAGCATTGAATAATTGAAGAATTGAAGAAAGACCACCCTGGATCATTGAACTA
*
10331 AATTGAAGCATTGAATAATTGAAGAATTGAAGAAAGACCACCCTGTATCATTGAACTA
1 AATTGAAGCATTGAATAATTGAAGAATTGAAGAAAGACCACCCTGGATCATTGAACTA
* * *
10389 AATTGATGCATTGAATAATTGAAGAATTGAAGAAAGATCACCCTGGATCATTGAAGTA
1 AATTGAAGCATTGAATAATTGAAGAATTGAAGAAAGACCACCCTGGATCATTGAACTA
* *
10447 AATTGATGCATTGAATAATTGAAGAATTGAAGAAAGACCACCCTGGATCATT-AGAGTA
1 AATTGAAGCATTGAATAATTGAAGAATTGAAGAAAGACCACCCTGGATCATTGA-ACTA
*
10505 AATTGAAGCATTGAAGAATTGAAG
1 AATTGAAGCATTGAATAATTGAAG
10529 TTGAAGCATT
Statistics
Matches: 226, Mismatches: 13, Indels: 18
0.88 0.05 0.07
Matches are distributed among these distances:
50 47 0.21
57 1 0.00
58 178 0.79
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (58 bp):
AATTGAAGCATTGAATAATTGAAGAATTGAAGAAAGACCACCCTGGATCATTGAACTA
Found at i:10294 original size:42 final size:42
Alignment explanation
Indices: 10158--10345 Score: 112
Period size: 50 Copynumber: 4.3 Consensus size: 42
10148 GCTTTGAATG
* * *
10158 ATTGAAGAATTGAAGAAAGACCACCATGGATCATTGAAGTAA
1 ATTGAAGCATTGAAGAAAGACCACCCTGGATCATTGAACTAA
* * * * ** ** ** *
10200 ATTTATGCATTGAATAATTGAAGA-ATTAAAGCATTGAA-T-A
1 ATTGAAGCATTGAAGAA-AGACCACCCTGGATCATTGAACTAA
* *
10240 GTTGAAGAATTGAAGAAAGACCACCCTGGATCATTGAACTGAATTGAA
1 ATTGAAGCATTGAAGAAAGACCACCCTGGATCATTGAAC-----T-AA
* *
10288 GCATTGAAGAATTGAAGAAAGACCACCCTGGATCATTGAAGTAA
1 --ATTGAAGCATTGAAGAAAGACCACCCTGGATCATTGAACTAA
10332 ATTGAAGCATTGAA
1 ATTGAAGCATTGAA
10346 TAATTGAAGA
Statistics
Matches: 106, Mismatches: 28, Indels: 24
0.67 0.18 0.15
Matches are distributed among these distances:
39 3 0.03
40 22 0.21
41 1 0.01
42 35 0.33
43 3 0.03
44 2 0.02
45 1 0.01
46 1 0.01
48 1 0.01
50 37 0.35
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.25
Consensus pattern (42 bp):
ATTGAAGCATTGAAGAAAGACCACCCTGGATCATTGAACTAA
Found at i:10328 original size:82 final size:80
Alignment explanation
Indices: 10152--10306 Score: 211
Period size: 82 Copynumber: 1.9 Consensus size: 80
10142 ATTGATGCTT
* * * *
10152 TGAATGATTGAAGAATTGAAGAAAGACCACCATGGATCATTGAAGTAAATTTATGCATTGAATAA
1 TGAAT-ATTGAAGAATTGAAGAAAGACCACCATGGATCATTGAACTAAATTGAAGCATTGAAGAA
* *
10217 TTGAAGAATTAAAGCAT
65 TTGAAGAA-TAAACCAC
* *
10234 TGAATAGTTGAAGAATTGAAGAAAGACCACCCTGGATCATTGAACTGAATTGAAGCATTGAAGAA
1 TGAATA-TTGAAGAATTGAAGAAAGACCACCATGGATCATTGAACTAAATTGAAGCATTGAAGAA
10299 TTGAAGAA
65 TTGAAGAA
10307 AGACCACCCT
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
81 1 0.02
82 65 0.98
ACGTcount: A:0.43, C:0.10, G:0.21, T:0.26
Consensus pattern (80 bp):
TGAATATTGAAGAATTGAAGAAAGACCACCATGGATCATTGAACTAAATTGAAGCATTGAAGAAT
TGAAGAATAAACCAC
Found at i:10330 original size:190 final size:190
Alignment explanation
Indices: 10044--10416 Score: 577
Period size: 190 Copynumber: 1.9 Consensus size: 190
10034 AATTGAAGCA
*
10044 TTGAAGAATTGAAGAAAGACCCCCTGGATCATTGAAGTAAATTGAAGCATTGGATAATTGAAGAA
1 TTGAAGAATTGAAGAAAGACCCCCTGGATCATTGAACTAAATTGAAGC-------AATTGAAGAA
* * *
10109 TTGAAGAAAGACCACCCTAGATCATTGAAGTAAATTGATGCTTTGAATGATTGAAGAATTGAAGA
59 TTGAAGAAAGACCACCCTAGATCATTGAAGTAAATTGAAGCATTGAATAATTGAAGAATTGAAGA
* *
10174 AAGACCACCATGGATCATTGAAGTAAATTTATGCATTGAATAATTGAAGAATTAAAGCATTGAAT
124 AAGACCACCATGGATCATTGAACTAAATTGATGCATTGAATAATTGAAGAATTAAAGCATTGAAT
10239 AG
189 AG
*
10241 TTGAAGAATTGAAGAAAGACCACCCTGGATCATTGAACTGAATTGAAGC-ATTGAAGAATTGAAG
1 TTGAAGAATTGAAGAAAGACC-CCCTGGATCATTGAACTAAATTGAAGCAATTGAAGAATTGAAG
*
10305 AAAGACCACCCTGGATCATTGAAGTAAATTGAAGCATTGAATAATTGAAGAATTGAAGAAAGACC
65 AAAGACCACCCTAGATCATTGAAGTAAATTGAAGCATTGAATAATTGAAGAATTGAAGAAAGACC
* *
10370 ACCCTGTATCATTGAACTAAATTGATGCATTGAATAATTGAAGAATT
130 ACCATGGATCATTGAACTAAATTGATGCATTGAATAATTGAAGAATT
10417 GAAGAAAGAT
Statistics
Matches: 165, Mismatches: 10, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
190 119 0.72
197 21 0.13
198 25 0.15
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (190 bp):
TTGAAGAATTGAAGAAAGACCCCCTGGATCATTGAACTAAATTGAAGCAATTGAAGAATTGAAGA
AAGACCACCCTAGATCATTGAAGTAAATTGAAGCATTGAATAATTGAAGAATTGAAGAAAGACCA
CCATGGATCATTGAACTAAATTGATGCATTGAATAATTGAAGAATTAAAGCATTGAATAG
Found at i:10345 original size:8 final size:8
Alignment explanation
Indices: 10331--10364 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
10321 CATTGAAGTA
10331 AATTGAAG
1 AATTGAAG
* *
10339 CATTGAAT
1 AATTGAAG
10347 AATTGAAG
1 AATTGAAG
10355 AATTGAAG
1 AATTGAAG
10363 AA
1 AA
10365 AGACCACCCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.50, C:0.03, G:0.21, T:0.26
Consensus pattern (8 bp):
AATTGAAG
Found at i:10352 original size:16 final size:18
Alignment explanation
Indices: 10321--10362 Score: 61
Period size: 16 Copynumber: 2.4 Consensus size: 18
10311 CACCCTGGAT
10321 CATTGAAGTAAATTGAAG
1 CATTGAAGTAAATTGAAG
10339 CATTGAA-T-AATTGAAG
1 CATTGAAGTAAATTGAAG
*
10355 AATTGAAG
1 CATTGAAG
10363 AAAGACCACC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 14 0.64
17 1 0.05
18 7 0.32
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.29
Consensus pattern (18 bp):
CATTGAAGTAAATTGAAG
Found at i:10384 original size:248 final size:247
Alignment explanation
Indices: 9961--10474 Score: 886
Period size: 248 Copynumber: 2.1 Consensus size: 247
9951 CGTTTGAATA
* * *
9961 ATTGAATAATTGAAGAATTGAAGCATTGGATAGTTAAAGAATTGAAGAAAGGCCACCCTGGATCA
1 ATTGAATAATTGAAGAATTAAAGCATTGAATAGTTAAAGAATTGAAGAAAGACCACCCTGGATCA
*
10026 TTGAAGTAAATTGAAGCATTGAAGAATTGAAGAAAGACCCCCTGGATCATTGAAGTAAATTGAAG
66 TTGAACTAAATTGAAGCATTGAAGAATTGAAGAAAGACCCCCTGGATCATTGAAGTAAATTGAAG
* * *
10091 CATTGGATAATTGAAGAATTGAAGAAAGACCACCCTAGATCATTGAAGTAAATTGATGCTTTGAA
131 CATTGAATAATTGAAGAATTGAAGAAAGACCACCCTAGATCATTGAACTAAATTGATGCATTGAA
* *
10156 TGATTGAAGAATTGAAGAAAGACCACCATGGATCATTGAAGTAAATTTATGC
196 TAATTGAAGAATTGAAGAAAGACCACCATGGATCATTGAAGTAAATTGATGC
*
10208 ATTGAATAATTGAAGAATTAAAGCATTGAATAGTTGAAGAATTGAAGAAAGACCACCCTGGATCA
1 ATTGAATAATTGAAGAATTAAAGCATTGAATAGTTAAAGAATTGAAGAAAGACCACCCTGGATCA
*
10273 TTGAACTGAATTGAAGCATTGAAGAATTGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGAA
66 TTGAACTAAATTGAAGCATTGAAGAATTGAAGAAAGACC-CCCTGGATCATTGAAGTAAATTGAA
10338 GCATTGAATAATTGAAGAATTGAAGAAAGACCACCCT-GTATCATTGAACTAAATTGATGCATTG
130 GCATTGAATAATTGAAGAATTGAAGAAAGACCACCCTAG-ATCATTGAACTAAATTGATGCATTG
* *
10402 AATAATTGAAGAATTGAAGAAAGATCACCCTGGATCATTGAAGTAAATTGATGC
194 AATAATTGAAGAATTGAAGAAAGACCACCATGGATCATTGAAGTAAATTGATGC
10456 ATTGAATAATTGAAGAATT
1 ATTGAATAATTGAAGAATT
10475 GAAGAAAGAC
Statistics
Matches: 252, Mismatches: 13, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
247 99 0.39
248 153 0.61
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.26
Consensus pattern (247 bp):
ATTGAATAATTGAAGAATTAAAGCATTGAATAGTTAAAGAATTGAAGAAAGACCACCCTGGATCA
TTGAACTAAATTGAAGCATTGAAGAATTGAAGAAAGACCCCCTGGATCATTGAAGTAAATTGAAG
CATTGAATAATTGAAGAATTGAAGAAAGACCACCCTAGATCATTGAACTAAATTGATGCATTGAA
TAATTGAAGAATTGAAGAAAGACCACCATGGATCATTGAAGTAAATTGATGC
Found at i:10519 original size:8 final size:8
Alignment explanation
Indices: 10506--10811 Score: 165
Period size: 8 Copynumber: 40.8 Consensus size: 8
10496 ATTAGAGTAA
10506 ATTGAAGC
1 ATTGAAGC
*
10514 ATTGAAGA
1 ATTGAAGC
10522 ATTGAAG-
1 ATTGAAGC
10529 -TTGAAGC
1 ATTGAAGC
**
10536 ATTGAAAT
1 ATTGAAGC
10544 ATTGAA--
1 ATTGAAGC
10550 ATTGAAGC
1 ATTGAAGC
*
10558 ATTGAAGA
1 ATTGAAGC
10566 ATTGAA--
1 ATTGAAGC
*
10572 ATTGAATC
1 ATTGAAGC
*
10580 ATT-AGAGA
1 ATTGA-AGC
10588 ATTGAA--
1 ATTGAAGC
*
10594 AGTGAAGC
1 ATTGAAGC
*
10602 ATTGAAGT
1 ATTGAAGC
10610 ATTGAA--
1 ATTGAAGC
**
10616 ATTGAAAT
1 ATTGAAGC
*
10624 ATTGAAGA
1 ATTGAAGC
10632 ATTGAA--
1 ATTGAAGC
10638 ATTGAAGC
1 ATTGAAGC
* *
10646 GTTGAAGA
1 ATTGAAGC
*
10654 ATGGAAATTGC
1 ATTG-AA--GC
*
10665 ATTGAAGA
1 ATTGAAGC
10673 ATTGAA--
1 ATTGAAGC
10679 ATTGAAGC
1 ATTGAAGC
* *
10687 ATTAAAGA
1 ATTGAAGC
*
10695 ATTGAA-A
1 ATTGAAGC
* *
10702 AGTGAAAC
1 ATTGAAGC
*
10710 ATTGAAGT
1 ATTGAAGC
10718 ATTGAA--
1 ATTGAAGC
10724 ATTGAAGC
1 ATTGAAGC
*
10732 ATTGAAGA
1 ATTGAAGC
10740 ATTGAA--
1 ATTGAAGC
10746 ATTGAAGC
1 ATTGAAGC
**
10754 ATTGAAAT
1 ATTGAAGC
10762 ATTGAA--
1 ATTGAAGC
*
10768 ATTGAAGT
1 ATTGAAGC
*
10776 ATTGAAGA
1 ATTGAAGC
10784 ATTGAA--
1 ATTGAAGC
10790 ATTGAAGC
1 ATTGAAGC
*
10798 ATTGAAGA
1 ATTGAAGC
10806 ATTGAA
1 ATTGAA
10812 ATTGAGATCA
Statistics
Matches: 239, Mismatches: 31, Indels: 56
0.73 0.10 0.17
Matches are distributed among these distances:
6 65 0.27
7 7 0.03
8 158 0.66
9 3 0.01
10 2 0.01
11 4 0.02
ACGTcount: A:0.45, C:0.04, G:0.22, T:0.29
Consensus pattern (8 bp):
ATTGAAGC
Found at i:10535 original size:22 final size:22
Alignment explanation
Indices: 10504--10816 Score: 431
Period size: 22 Copynumber: 14.3 Consensus size: 22
10494 TCATTAGAGT
10504 AAATTGAAGCATTGAAGAATTG
1 AAATTGAAGCATTGAAGAATTG
*
10526 AAGTTGAAGCATTGAA-ATATTG
1 AAATTGAAGCATTGAAGA-ATTG
10548 AAATTGAAGCATTGAAGAATTG
1 AAATTGAAGCATTGAAGAATTG
*
10570 AAATTGAATCATT-AGAGAATTG
1 AAATTGAAGCATTGA-AGAATTG
* *
10592 AAAGTGAAGCATTGAAGTATTG
1 AAATTGAAGCATTGAAGAATTG
**
10614 AAATTGAAATATTGAAGAATTG
1 AAATTGAAGCATTGAAGAATTG
* *
10636 AAATTGAAGCGTTGAAGAATGG
1 AAATTGAAGCATTGAAGAATTG
10658 AAATT---GCATTGAAGAATTG
1 AAATTGAAGCATTGAAGAATTG
*
10677 AAATTGAAGCATTAAAGAATTG
1 AAATTGAAGCATTGAAGAATTG
* * *
10699 AAAAGTGAAACATTGAAGTATTG
1 -AAATTGAAGCATTGAAGAATTG
10722 AAATTGAAGCATTGAAGAATTG
1 AAATTGAAGCATTGAAGAATTG
10744 AAATTGAAGCATTGAA-ATATTG
1 AAATTGAAGCATTGAAGA-ATTG
*
10766 AAATTGAAGTATTGAAGAATTG
1 AAATTGAAGCATTGAAGAATTG
10788 AAATTGAAGCATTGAAGAATTG
1 AAATTGAAGCATTGAAGAATTG
10810 AAATTGA
1 AAATTGA
10817 GATCATATTG
Statistics
Matches: 255, Mismatches: 26, Indels: 20
0.85 0.09 0.07
Matches are distributed among these distances:
19 17 0.07
21 3 0.01
22 214 0.84
23 21 0.08
ACGTcount: A:0.45, C:0.04, G:0.22, T:0.29
Consensus pattern (22 bp):
AAATTGAAGCATTGAAGAATTG
Found at i:10927 original size:47 final size:47
Alignment explanation
Indices: 10858--10953 Score: 131
Period size: 47 Copynumber: 2.0 Consensus size: 47
10848 AATTGAAGAG
* *
10858 AGACCAACTATGGTCACCAAATTGGAGACACGCATGGAA-GCGAGAAA
1 AGACCAACTATGGTCACCAAATTGCAAACACGCAT-GAAGGCGAGAAA
* * *
10905 AGACCAACTTTGGTCACTAAATTGCAAACTCGCATGAAGGCGAGAAA
1 AGACCAACTATGGTCACCAAATTGCAAACACGCATGAAGGCGAGAAA
10952 AG
1 AG
10954 GTTACCTGGA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
46 3 0.07
47 40 0.93
ACGTcount: A:0.40, C:0.21, G:0.24, T:0.16
Consensus pattern (47 bp):
AGACCAACTATGGTCACCAAATTGCAAACACGCATGAAGGCGAGAAA
Found at i:11161 original size:70 final size:70
Alignment explanation
Indices: 11075--11518 Score: 493
Period size: 70 Copynumber: 6.5 Consensus size: 70
11065 TTAGCTTATA
* *
11075 GAAAAGCCCCCT-AATGCTTGGGA-GGAACCAAAGCTTGAACT-ACCTTGTATGGAAATGAGTTT
1 GAAAAG-CCCCTGAATGCTT-GGATGGAACCAAAGCTTGAACTGA-CTCGTATGGAAACGAGTTT
11137 GGCTTGTG
63 GGCTTGTG
* * * *
11145 GAAAAGCCCCTGAATGCTCGGATGG----AAA---TGAACTGACTCGTACGGAGATGAGTTTGGC
1 GAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGTTTGGC
11203 TTGTG
66 TTGTG
* * ** * * *
11208 GAAAAGCCTCT-ATTGCTTGGATGGAATAAAAGCTTGAACTAACTCGTATGAAAACAAGTTTGGC
1 GAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGTTTGGC
*
11272 ATGTG
66 TTGTG
* * * *
11277 GAAAAGCCTCTG-TTGCTTGGATGGAACCAAAGCTTGAATTGACTTGTATGGAAACGAGTTTGGC
1 GAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGTTTGGC
11341 TTGTG
66 TTGTG
* * * *
11346 GAAAAGCCCCTAAATGCTTGGATGGAACAAAAGTTTAAACT-ACCTCGTATGGAAACGAGTTTGG
1 GAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTTGAACTGA-CTCGTATGGAAACGAGTTTGG
11410 CTTGTG
65 CTTGTG
* * * * *
11416 GACAAGCCCCTGAATGCTTTGATGGAACCAAAGCTTGATCTGATTCGAATGGAAACGAGTTTGGC
1 GAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGTTTGGC
11481 TTGTG
66 TTGTG
* *
11486 AAAAAGCCCCTG-CTGCTTGGATGGAACCAAAGC
1 GAAAAGCCCCTGAATGCTTGGATGGAACCAAAGC
11519 AAAATCTTCA
Statistics
Matches: 317, Mismatches: 43, Indels: 29
0.81 0.11 0.07
Matches are distributed among these distances:
62 11 0.03
63 40 0.13
64 1 0.00
66 6 0.02
69 126 0.40
70 132 0.42
71 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.26
Consensus pattern (70 bp):
GAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGTTTGGC
TTGTG
Found at i:12419 original size:9 final size:10
Alignment explanation
Indices: 12389--12422 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
12379 ACCCTAGAGC
12389 TTCTTTTCTTCT
1 TTCTTTT-TT-T
12401 TTCTTTTTTT
1 TTCTTTTTTT
12411 TTCTTTTTTT
1 TTCTTTTTTT
12421 TT
1 TT
12423 ACTTACTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 13 0.59
11 2 0.09
12 7 0.32
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:14300 original size:12 final size:13
Alignment explanation
Indices: 14259--14303 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
14249 AATTATTGTT
14259 TGCTTTATTAATC
1 TGCTTTATTAATC
*
14272 TGCTTTATTAATT
1 TGCTTTATTAATC
14285 TGCTTTA-TAATC
1 TGCTTTATTAATC
14297 TGCTTTA
1 TGCTTTA
14304 GATTTAGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.56
Consensus pattern (13 bp):
TGCTTTATTAATC
Found at i:14651 original size:10 final size:9
Alignment explanation
Indices: 14637--14661 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
14627 AAAAAAAAAA
14637 ATTTTTCCG
1 ATTTTTCCG
14646 ATTTTTCCG
1 ATTTTTCCG
14655 ATTTTTC
1 ATTTTTC
14662 TAAAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.20, G:0.08, T:0.60
Consensus pattern (9 bp):
ATTTTTCCG
Found at i:14667 original size:39 final size:39
Alignment explanation
Indices: 14608--14689 Score: 130
Period size: 39 Copynumber: 2.1 Consensus size: 39
14598 TAATTTTTGA
*
14608 TTTTCCGTTTTTTCTAAAAAAAAAAAAAAATTTTTCCGAT
1 TTTTCCGATTTTTCTAAAAAAAAAAAAAAATTTTTCCG-T
*
14648 TTTTCCGATTTTTCT-AAAAAAAAAAAATATTTTTCCGT
1 TTTTCCGATTTTTCTAAAAAAAAAAAAAAATTTTTCCGT
14686 TTTT
1 TTTT
14690 AAAATTAGGG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
38 5 0.12
39 21 0.52
40 14 0.35
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.46
Consensus pattern (39 bp):
TTTTCCGATTTTTCTAAAAAAAAAAAAAAATTTTTCCGT
Done.