Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016414.1 Corchorus olitorius cultivar O-4 contig16447, 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: 27929
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--32 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33 CTAAAAAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2969 original size:59 final size:59
Alignment explanation
Indices: 2849--2969 Score: 181
Period size: 59 Copynumber: 2.1 Consensus size: 59
2839 AACTTCACAA
* * * *
2849 GAATTGTCTTTAGATCCTTCTATGAGCAGTCTTCATACTCATCTCTCAAATTCTTTAAG
1 GAATTGTCTTCAGATCCGTCTATGAGCAGTCTTCATACTCATCTCTAAAATCCTTTAAG
*
2908 GAATTGTCTTCAGATCCGTCTATGAGCAGTCTTCATACTCATTTCTTAAAATCCTTT-AG
1 GAATTGTCTTCAGATCCGTCTATGAGCAGTCTTCATACTCATCTC-TAAAATCCTTTAAG
2967 GAA
1 GAA
2970 CTGCCTTCTA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
59 47 0.84
60 9 0.16
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.39
Consensus pattern (59 bp):
GAATTGTCTTCAGATCCGTCTATGAGCAGTCTTCATACTCATCTCTAAAATCCTTTAAG
Found at i:3054 original size:61 final size:60
Alignment explanation
Indices: 2987--3227 Score: 261
Period size: 61 Copynumber: 4.0 Consensus size: 60
2977 CTAAACCATT
* * *
2987 TTCGTGATCTGTC-TCTAGATTCACCCTTAAATATCATTCCGGAACTGTCTTCAGATCTGTC
1 TTCGTGAACTGTCTTC-AGATTCACTCTTAAATATCATTCAGGAACTGTCTTCAGATCT-TC
* * * * *
3048 TTCGTGAACTGTCTTCAGATTCACTCTTCAATATCATTCAGGAGCTGTCTTCAAAACCCATC
1 TTCGTGAACTGTCTTCAGATTCACTCTTAAATATCATTCAGGAACTGTCTTC-AGA-TCTTC
* * * * *
3110 TTCGTGAACTGTCTTCATATTCATTCTTAAAT-TCCTTTTAGAAACTGTCTTCAGATCCTTC
1 TTCGTGAACTGTCTTCAGATTCACTCTTAAATAT-CATTCAGGAACTGTCTTCAGAT-CTTC
* * * *
3171 TTCGTGAACTATCTTCAGTTTCACTCTTAAATATCATTTAGGAGCTGTCTTCAGATC
1 TTCGTGAACTGTCTTCAGATTCACTCTTAAATATCATTCAGGAACTGTCTTCAGATC
3228 CATGGACTAG
Statistics
Matches: 149, Mismatches: 25, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
60 1 0.01
61 97 0.65
62 50 0.34
63 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (60 bp):
TTCGTGAACTGTCTTCAGATTCACTCTTAAATATCATTCAGGAACTGTCTTCAGATCTTC
Found at i:3061 original size:13 final size:12
Alignment explanation
Indices: 3028--3066 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3018 TATCATTCCG
3028 GAACTGTCTTCA
1 GAACTGTCTTCA
* *
3040 GATCTGTCTTCGT
1 GAACTGTCTTC-A
3053 GAACTGTCTTCA
1 GAACTGTCTTCA
3065 GA
1 GA
3067 TTCACTCTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.36
Consensus pattern (12 bp):
GAACTGTCTTCA
Found at i:3158 original size:62 final size:61
Alignment explanation
Indices: 2936--3223 Score: 217
Period size: 61 Copynumber: 4.7 Consensus size: 61
2926 TCTATGAGCA
* * * * * * * *
2936 GTCTTCATACTCATTTCTTAAA-ATCCTTTAGGAACTGCCTTCTAAA-CCATTTTCGTGATCT
1 GTCTTCATATTCA-CTCTTAAATATCATTCAGAAACTGTCTTC-AAACCCATCTTCGTGAACT
* * * * * * **
2997 GTC-TCTAGATTCACCCTTAAATATCATTCCGGAACTGTCTTCAGATCTGTCTTCGTGAACT
1 GTCTTC-ATATTCACTCTTAAATATCATTCAGAAACTGTCTTCAAACCCATCTTCGTGAACT
* * * *
3058 GTCTTCAGATTCACTCTTCAATATCATTCAGGAGCTGTCTTCAAAACCCATCTTCGTGAACT
1 GTCTTCATATTCACTCTTAAATATCATTCAGAAACTGTCTTC-AAACCCATCTTCGTGAACT
* * * * * *
3120 GTCTTCATATTCATTCTTAAAT-TCCTTTTAGAAACTGTCTTCAGATCCTTCTTCGTGAACT
1 GTCTTCATATTCACTCTTAAATAT-CATTCAGAAACTGTCTTCAAACCCATCTTCGTGAACT
* * * *
3181 ATCTTCAGT-TTCACTCTTAAATATCATTTAGGAGCTGTCTTCA
1 GTCTTCA-TATTCACTCTTAAATATCATTCAGAAACTGTCTTCA
3224 GATCCATGGA
Statistics
Matches: 183, Mismatches: 36, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
60 10 0.05
61 121 0.66
62 52 0.28
ACGTcount: A:0.24, C:0.25, G:0.12, T:0.39
Consensus pattern (61 bp):
GTCTTCATATTCACTCTTAAATATCATTCAGAAACTGTCTTCAAACCCATCTTCGTGAACT
Found at i:13574 original size:15 final size:15
Alignment explanation
Indices: 13554--13591 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
13544 TTAAGTAATT
13554 CAAATTAACAGAAAG
1 CAAATTAACAGAAAG
*
13569 CAAATTAAATAGAAAG
1 CAAATT-AACAGAAAG
13585 C-AATTAA
1 CAAATTAA
13592 AATAGAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 2 0.10
15 10 0.48
16 9 0.43
ACGTcount: A:0.61, C:0.11, G:0.11, T:0.18
Consensus pattern (15 bp):
CAAATTAACAGAAAG
Found at i:13584 original size:16 final size:16
Alignment explanation
Indices: 13554--13604 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
13544 TTAAGTAATT
*
13554 CAAATT-AACAGAAAG
1 CAAATTAAATAGAAAG
13569 CAAATTAAATAGAAAG
1 CAAATTAAATAGAAAG
13585 C-AATTAAAATAGAAAAG
1 CAAATT-AAATAG-AAAG
13602 CAA
1 CAA
13605 TAAATAATCA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
15 10 0.32
16 15 0.48
17 5 0.16
18 1 0.03
ACGTcount: A:0.63, C:0.10, G:0.12, T:0.16
Consensus pattern (16 bp):
CAAATTAAATAGAAAG
Found at i:13603 original size:17 final size:15
Alignment explanation
Indices: 13563--13610 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
13553 TCAAATTAAC
13563 AGAAAGCAAATTAAAT
1 AGAAAGC-AATTAAAT
13579 AGAAAGCAATTAAAAT
1 AGAAAGCAATT-AAAT
13595 AGAAAAGCAA-TAAAT
1 AG-AAAGCAATTAAAT
13610 A
1 A
13611 ATCAACATCC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.30
16 14 0.47
17 7 0.23
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.17
Consensus pattern (15 bp):
AGAAAGCAATTAAAT
Found at i:18954 original size:11 final size:10
Alignment explanation
Indices: 18938--18984 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
18928 AAGTTCGTTT
18938 TTGAAGACTCA
1 TTGAAGA-TCA
*
18949 TTGAAGATAA
1 TTGAAGATCA
18959 TTTGAAGAT--
1 -TTGAAGATCA
18968 TTGAAGATCA
1 TTGAAGATCA
18978 TTGAAGA
1 TTGAAGA
18985 ATTATTTCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
8 8 0.25
10 9 0.28
11 15 0.47
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.32
Consensus pattern (10 bp):
TTGAAGATCA
Found at i:18973 original size:19 final size:18
Alignment explanation
Indices: 18949--18984 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
18939 TGAAGACTCA
18949 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
18968 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
18985 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Done.