Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008462.1 Corchorus capsularis cultivar CVL-1 contig08483, 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: 22293
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.33
Found at i:142 original size:13 final size:13
Alignment explanation
Indices: 124--148 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
114 TAAATCTAAG
124 TTTTTTTTTTTGT
1 TTTTTTTTTTTGT
137 TTTTTTTTTTTG
1 TTTTTTTTTTTG
149 ACTAAAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (13 bp):
TTTTTTTTTTTGT
Found at i:208 original size:32 final size:31
Alignment explanation
Indices: 164--261 Score: 97
Period size: 33 Copynumber: 3.0 Consensus size: 31
154 AATTGCTCAT
*
164 GCCGCCCTAGGGGGCGGCTGAGCCATGGTAGG
1 GCCGCCCCAGGGGGCGGCTG-GCCATGGTAGG
* **
196 GCCGCCCCAGGGGAGAGGCCTGGCCATGGTAAT
1 GCCGCCCCAGGGG-GCGG-CTGGCCATGGTAGG
* *
229 GCCGCACCAGGGGGACGGCTTGCCATGGCTAGG
1 GCCGCCCCAGGGGG-CGGCTGGCCATGG-TAGG
262 CCATTCCCCT
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
32 22 0.42
33 28 0.53
34 3 0.06
ACGTcount: A:0.15, C:0.30, G:0.43, T:0.12
Consensus pattern (31 bp):
GCCGCCCCAGGGGGCGGCTGGCCATGGTAGG
Found at i:312 original size:33 final size:33
Alignment explanation
Indices: 268--378 Score: 88
Period size: 33 Copynumber: 3.4 Consensus size: 33
258 TAGGCCATTC
*
268 CCCTGGTGCGGCTAAGCCATGGCCAAGCCGCC-
1 CCCTGGGGCGGCTAAGCCATGGCCAAGCCGCCT
* *
300 CTCTTGGGGCGGC-ACTA-CCATGGCCAGGCCGCCT
1 C-CCTGGGGCGGCTA--AGCCATGGCCAAGCCGCCT
** *
334 CCCTGGGGCGGCTCTGCCATGG--ATAGACCGCCC
1 CCCTGGGGCGGCTAAGCCATGGCCA-AG-CCGCCT
367 CCCTGGGGCGGC
1 CCCTGGGGCGGC
379 ACCGGTACTA
Statistics
Matches: 63, Mismatches: 8, Indels: 15
0.73 0.09 0.17
Matches are distributed among these distances:
31 1 0.02
32 3 0.05
33 57 0.90
34 2 0.03
ACGTcount: A:0.12, C:0.40, G:0.34, T:0.14
Consensus pattern (33 bp):
CCCTGGGGCGGCTAAGCCATGGCCAAGCCGCCT
Found at i:491 original size:33 final size:33
Alignment explanation
Indices: 434--516 Score: 116
Period size: 33 Copynumber: 2.6 Consensus size: 33
424 CCGCCCTAAC
*
434 GGGGCGGCT-AGCCGTGGCAAAGCCGTCCTAGT
1 GGGGCGGCTCCGCCGTGGCAAAGCCGTCCTAGT
* *
466 GGGGCGGCTCCGCCGTGGTAGAGCCGTCCTAGT
1 GGGGCGGCTCCGCCGTGGCAAAGCCGTCCTAGT
*
499 GGGGAGGCTCCG-CGTGGC
1 GGGGCGGCTCCGCCGTGGC
517 TAAGGGCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
32 14 0.31
33 31 0.69
ACGTcount: A:0.11, C:0.29, G:0.45, T:0.16
Consensus pattern (33 bp):
GGGGCGGCTCCGCCGTGGCAAAGCCGTCCTAGT
Found at i:737 original size:18 final size:19
Alignment explanation
Indices: 714--749 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
704 ACTTAAAATG
714 AAAAAGAA-AAAAGAAAAA
1 AAAAAGAAGAAAAGAAAAA
*
732 AAAAAGAAGAAAGGAAAA
1 AAAAAGAAGAAAAGAAAA
750 TAAGAGCCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (19 bp):
AAAAAGAAGAAAAGAAAAA
Found at i:3211 original size:14 final size:14
Alignment explanation
Indices: 3194--3231 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
3184 CTTTCTATCC
3194 CTTAATGTCTAAAT
1 CTTAATGTCTAAAT
3208 CTTAATGTCTAAAT
1 CTTAATGTCTAAAT
3222 CTTAATGTCT
1 CTTAATGTCT
3232 TTCTTTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.45
Consensus pattern (14 bp):
CTTAATGTCTAAAT
Found at i:12221 original size:13 final size:13
Alignment explanation
Indices: 12199--12234 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
12189 AAAATTCTAT
12199 TTGACCCTCCAAA
1 TTGACCCTCCAAA
* *
12212 TTGTCCCTCCAAT
1 TTGACCCTCCAAA
12225 TTGACCCTCC
1 TTGACCCTCC
12235 TAATAATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.19, C:0.42, G:0.08, T:0.31
Consensus pattern (13 bp):
TTGACCCTCCAAA
Found at i:12863 original size:41 final size:41
Alignment explanation
Indices: 12805--12886 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
12795 TTTATAACTA
* *
12805 GGGGCTAAACTTAGATTTAATTTCTTACCTTAATTATTAGG
1 GGGGCTAAACCTAGATTTAATTTATTACCTTAATTATTAGG
* *
12846 GGGGCTAAACCTGGATTTAATTTATTTCCTTAATTATTAGG
1 GGGGCTAAACCTAGATTTAATTTATTACCTTAATTATTAGG
12887 AGGGTCATGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.41
Consensus pattern (41 bp):
GGGGCTAAACCTAGATTTAATTTATTACCTTAATTATTAGG
Found at i:14796 original size:25 final size:25
Alignment explanation
Indices: 14767--14814 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
14757 AAGGAGAATT
* *
14767 TTTCCATCGTCCATCAAGAGGGAAA
1 TTTCCATCCTCCATAAAGAGGGAAA
* *
14792 TTTCCTTCCTGCATAAAGAGGGA
1 TTTCCATCCTCCATAAAGAGGGA
14815 TGACGTCCTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (25 bp):
TTTCCATCCTCCATAAAGAGGGAAA
Found at i:18113 original size:2 final size:2
Alignment explanation
Indices: 18108--18140 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
18098 TGCTATAATT
18108 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18141 CACACACTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21540 original size:22 final size:22
Alignment explanation
Indices: 21484--21540 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 22
21474 GTACTTTAGG
21484 ATTAATTAGTGTATGGATCAAT
1 ATTAATTAGTGTATGGATCAAT
21506 ATTTTTTTAATTAGTGTATGGATCAAT
1 A-----TTAATTAGTGTATGGATCAAT
21533 ATTAATTA
1 ATTAATTA
21541 CTACTTAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
22 8 0.27
27 22 0.73
ACGTcount: A:0.35, C:0.04, G:0.14, T:0.47
Consensus pattern (22 bp):
ATTAATTAGTGTATGGATCAAT
Done.