Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018840.1 Corchorus olitorius cultivar O-4 contig18873, 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: 4516
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Found at i:83 original size:12 final size:12
Alignment explanation
Indices: 66--95 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
56 CCAACGTAAA
66 AAATTTTTCAAT
1 AAATTTTTCAAT
78 AAATTTTTCAAT
1 AAATTTTTCAAT
90 AAATTT
1 AAATTT
96 GTATGTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (12 bp):
AAATTTTTCAAT
Found at i:234 original size:22 final size:22
Alignment explanation
Indices: 187--235 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
177 CCACTCTGCG
* *
187 AAATTTTGATAATCTTCCTATG
1 AAATTTTGATAATCTACCTATA
*
209 AAATTTTGATAGTC-ACACTATA
1 AAATTTTGATAATCTAC-CTATA
231 AAATT
1 AAATT
236 GGTAAGCGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 1 0.04
22 22 0.96
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (22 bp):
AAATTTTGATAATCTACCTATA
Found at i:1973 original size:12 final size:12
Alignment explanation
Indices: 1956--1985 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
1946 CCAACGTAAA
1956 AAATTTTTCAAT
1 AAATTTTTCAAT
1968 AAATTTTTCAAT
1 AAATTTTTCAAT
1980 AAATTT
1 AAATTT
1986 GTATGTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (12 bp):
AAATTTTTCAAT
Found at i:2119 original size:22 final size:22
Alignment explanation
Indices: 2048--2109 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
2038 AATTTCGATA
** *
2048 ACCTATGAAAACTTGATAA-CC
1 ACCTATGAAATTTTGATAATCT
*
2069 ACTCTGTGAAATTTTGATAATCT
1 AC-CTATGAAATTTTGATAATCT
*
2092 TCCTATGAAATTTTGATA
1 ACCTATGAAATTTTGATA
2110 GTCACACTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 2 0.06
22 29 0.88
23 2 0.06
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.37
Consensus pattern (22 bp):
ACCTATGAAATTTTGATAATCT
Found at i:2124 original size:22 final size:22
Alignment explanation
Indices: 2077--2125 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
2067 CCACTCTGTG
* *
2077 AAATTTTGATAATCTTCCTATG
1 AAATTTTGATAATCTACCTATA
*
2099 AAATTTTGATAGTC-ACACTATA
1 AAATTTTGATAATCTAC-CTATA
2121 AAATT
1 AAATT
2126 GGTAAGCGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 1 0.04
22 22 0.96
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (22 bp):
AAATTTTGATAATCTACCTATA
Found at i:2955 original size:119 final size:118
Alignment explanation
Indices: 2714--3065 Score: 598
Period size: 118 Copynumber: 3.0 Consensus size: 118
2704 TGTTAACACA
2714 TTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGGA
1 TTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGGA
* * *
2779 AAATTTAAGGATTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGATCG
66 AAATTTAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGAGCC
*
2832 TTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTT-GTGGAAGAGTTGGTTTGAAGTGGA
1 TTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGGA
2896 AAATTTAAGGACTTGAGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGAGCC
66 AAATTTAAGGACTT--GAAATTCCTCAAAACAATATTCATGGTTGTGGTGGAGCC
* * *
2951 TTTGGGATCTAAGGATTAAGGATTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAATGGA
1 TTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGGA
* *
3016 AAAATGAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGA
66 AAATTTAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGA
3066 TGTTCTTTCA
Statistics
Matches: 221, Mismatches: 10, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
117 36 0.16
118 76 0.34
119 75 0.34
120 34 0.15
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.36
Consensus pattern (118 bp):
TTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGGA
AAATTTAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGAGCC
Found at i:3282 original size:17 final size:19
Alignment explanation
Indices: 3262--3308 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 19
3252 TATCTTTTTA
3262 TAATTAATAAAAA-AAT-T
1 TAATTAATAAAAAGAATAT
* *
3279 TAATGACTAAAAAGAATAT
1 TAATTAATAAAAAGAATAT
3298 TAATTAA-AAAA
1 TAATTAATAAAA
3309 TTATTATACT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 11 0.46
18 7 0.29
19 6 0.25
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (19 bp):
TAATTAATAAAAAGAATAT
Found at i:3389 original size:9 final size:9
Alignment explanation
Indices: 3375--3405 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
3365 TACGTGATTT
*
3375 TATATAGTA
1 TATATAATA
3384 TATATAATA
1 TATATAATA
3393 TATATAATA
1 TATATAATA
3402 TATA
1 TATA
3406 ATATAATGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (9 bp):
TATATAATA
Found at i:3430 original size:130 final size:130
Alignment explanation
Indices: 3279--3513 Score: 409
Period size: 130 Copynumber: 1.8 Consensus size: 130
3269 TAAAAAAATT
* *
3279 TAATGACTAAAAAGAATATTAATTAAAAAATTATTATACTATAATACTAAGAGTGTTTTAGAAAT
1 TAATGACTAAAAAGAATATTAATTAAAAAATTATTATACTATAACACTAAGAGTATTTTAGAAAT
*
3344 TTCCCAATTAAGATTTTTGA-TTACGTGATTTTATATAGTATATATAATATATATAATATATAAT
66 TTCCCAATTAAAATTTTTGAGTT-CGTGATTTTATATAGTATATATAATATATATAATATATAAT
3408 A
130 A
* *
3409 TAATGACTAATAAGAATATTAATTAAAAAATTATTATACTATAACACTAAGGGTATTTTAGAAAT
1 TAATGACTAAAAAGAATATTAATTAAAAAATTATTATACTATAACACTAAGAGTATTTTAGAAAT
3474 TTCCCAATTAAAATTTTTGAGTTCGTGATTTTATATAGTA
66 TTCCCAATTAAAATTTTTGAGTTCGTGATTTTATATAGTA
3514 GTAAGATAGT
Statistics
Matches: 99, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
130 97 0.98
131 2 0.02
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.40
Consensus pattern (130 bp):
TAATGACTAAAAAGAATATTAATTAAAAAATTATTATACTATAACACTAAGAGTATTTTAGAAAT
TTCCCAATTAAAATTTTTGAGTTCGTGATTTTATATAGTATATATAATATATATAATATATAATA
Found at i:3833 original size:18 final size:17
Alignment explanation
Indices: 3791--3836 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
3781 ATGTAATTTC
3791 ATTTATCAATTAAATTAA
1 ATTTAT-AATTAAATTAA
* *
3809 ATATATAATTATATTAAA
1 ATTTATAATTAAATT-AA
3827 ATTTATAATT
1 ATTTATAATT
3837 TCTTTTACCG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
ATTTATAATTAAATTAA
Done.