Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010749.1 Corchorus capsularis cultivar CVL-1 contig10770, 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: 23029
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Found at i:2251 original size:17 final size:18
Alignment explanation
Indices: 2224--2266 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
2214 AACCTAAGTA
* *
2224 ATGCTAAATGCAAGCTAT
1 ATGCAAAATGCAAACTAT
2242 ATG-AAAATGCAAACTAT
1 ATGCAAAATGCAAACTAT
2259 ATGCAAAA
1 ATGCAAAA
2267 CGAGAAAGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.23
Consensus pattern (18 bp):
ATGCAAAATGCAAACTAT
Found at i:8141 original size:17 final size:17
Alignment explanation
Indices: 8119--8166 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
8109 GATGACCCCC
**
8119 AGATCACCAGTGATTTA
1 AGATCACCAGTGATGCA
*
8136 AGATCACCAGTAATGCA
1 AGATCACCAGTGATGCA
*
8153 AGATCACCGGTGAT
1 AGATCACCAGTGAT
8167 ACCCTTAGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (17 bp):
AGATCACCAGTGATGCA
Found at i:16509 original size:15 final size:15
Alignment explanation
Indices: 16489--16561 Score: 96
Period size: 16 Copynumber: 4.7 Consensus size: 15
16479 ATTGGGCGGG
16489 TTCGGGTTCGAGTA-T
1 TTCGGGTTCG-GTATT
16504 TTCGGGTTCCGGTATT
1 TTCGGGTT-CGGTATT
16520 TTCGGGTTCGGGTA-T
1 TTCGGGTTC-GGTATT
16535 TTCGGGTTCGGATATT
1 TTCGGGTTCGG-TATT
16551 TTCGGGTTCGG
1 TTCGGGTTCGG
16562 GCTCGGATCG
Statistics
Matches: 53, Mismatches: 0, Indels: 9
0.85 0.00 0.15
Matches are distributed among these distances:
14 2 0.04
15 24 0.45
16 27 0.51
ACGTcount: A:0.08, C:0.15, G:0.36, T:0.41
Consensus pattern (15 bp):
TTCGGGTTCGGTATT
Found at i:16560 original size:16 final size:15
Alignment explanation
Indices: 16489--16561 Score: 87
Period size: 15 Copynumber: 4.7 Consensus size: 15
16479 ATTGGGCGGG
16489 TTCGGGTTC-GAGTAT
1 TTCGGGTTCGGA-TAT
16504 TTCGGGTTCCGG-TATT
1 TTCGGGTT-CGGATA-T
*
16520 TTCGGGTTCGGGTAT
1 TTCGGGTTCGGATAT
16535 TTCGGGTTCGGATATT
1 TTCGGGTTCGGATA-T
16551 TTCGGGTTCGG
1 TTCGGGTTCGG
16562 GCTCGGATCG
Statistics
Matches: 52, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
15 27 0.52
16 24 0.46
17 1 0.02
ACGTcount: A:0.08, C:0.15, G:0.36, T:0.41
Consensus pattern (15 bp):
TTCGGGTTCGGATAT
Found at i:16561 original size:31 final size:31
Alignment explanation
Indices: 16489--16562 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
16479 ATTGGGCGGG
*
16489 TTCGGGTTCGAGTATTTCGGGTTCCGGTATT
1 TTCGGGTTCGGGTATTTCGGGTTCCGGTATT
16520 TTCGGGTTCGGGTATTTCGGGTT-CGGATATT
1 TTCGGGTTCGGGTATTTCGGGTTCCGG-TATT
16551 TTCGGGTTCGGG
1 TTCGGGTTCGGG
16563 CTCGGATCGG
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
30 3 0.07
31 38 0.93
ACGTcount: A:0.08, C:0.15, G:0.36, T:0.41
Consensus pattern (31 bp):
TTCGGGTTCGGGTATTTCGGGTTCCGGTATT
Found at i:16582 original size:23 final size:23
Alignment explanation
Indices: 16552--16605 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
16542 TCGGATATTT
*
16552 TCGGGTTCGGGCTCGGATCGGGA
1 TCGGGTTCGGGCCCGGATCGGGA
* *
16575 TCGGGTTCGGGCCCGGGTCGGGT
1 TCGGGTTCGGGCCCGGATCGGGA
*
16598 TCGTGTTC
1 TCGGGTTC
16606 ACTTTCGATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.04, C:0.24, G:0.46, T:0.26
Consensus pattern (23 bp):
TCGGGTTCGGGCCCGGATCGGGA
Found at i:17326 original size:20 final size:20
Alignment explanation
Indices: 17303--17344 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
17293 AATTTTTTTA
17303 TTTTATAA-ATAATTCTTGAT
1 TTTTATAATATAATT-TTGAT
* *
17323 TTTTTTAATATTATTTTGAT
1 TTTTATAATATAATTTTGAT
17343 TT
1 TT
17345 CGGGCTCGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (20 bp):
TTTTATAATATAATTTTGAT
Found at i:17470 original size:11 final size:10
Alignment explanation
Indices: 17434--17470 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
17424 CAGGTTCGGA
17434 TTCGGGCGGG
1 TTCGGGCGGG
*
17444 TTCAGGCGGG
1 TTCGGGCGGG
17454 TTCGGGCGGG
1 TTCGGGCGGG
17464 TTTCGGG
1 -TTCGGG
17471 TTCATTTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 18 0.75
11 6 0.25
ACGTcount: A:0.03, C:0.19, G:0.54, T:0.24
Consensus pattern (10 bp):
TTCGGGCGGG
Found at i:19006 original size:21 final size:22
Alignment explanation
Indices: 18975--19015 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
18965 CATTCAATTA
18975 TATATTTTTTTGAAATATAAAT
1 TATATTTTTTTGAAATATAAAT
*
18997 TATATTTTTTT-ATATATAA
1 TATATTTTTTTGAAATATAA
19016 TTGGTACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
TATATTTTTTTGAAATATAAAT
Found at i:20189 original size:21 final size:21
Alignment explanation
Indices: 20163--20211 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
20153 ATTCTGTTAC
20163 AACAAATCGGTGACAACTATG
1 AACAAATCGGTGACAACTATG
20184 AACAAATCGGTGACAACTATG
1 AACAAATCGGTGACAACTATG
20205 AACAAAT
1 AACAAAT
20212 ATAAACAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.18
Consensus pattern (21 bp):
AACAAATCGGTGACAACTATG
Found at i:21495 original size:241 final size:241
Alignment explanation
Indices: 21072--21550 Score: 859
Period size: 241 Copynumber: 2.0 Consensus size: 241
21062 CCTCCCTTCT
*
21072 GAATCCATACAAGTAGCCATGTCCAATGCCTCCAACTAATTTGGACCATCTTTGGGGATCAATTT
1 GAATCCATACAAGTAGCCATGTCCAATGCCTCCAACTAATTTGGACCATATTTGGGGATCAATTT
**
21137 GGACCGAATTTAAACTAAGCTGCTGTTGTCATATTAAAATGCATGAACCAAGTTTTAAACATAGC
66 GGACCGAATCCAAACTAAGCTGCTGTTGTCATATTAAAATGCATGAACCAAGTTTTAAACATAGC
21202 TTCAATAACTAACGTTGTCAAACAAAAGTCCCAAAATGTAAACATTCAATGCTAGCAATATGCTA
131 TTCAATAACTAACGTTGTCAAACAAAAGTCCCAAAATGTAAACATTCAATGCTAGCAATATGCTA
*
21267 TATACATTATTAAGGCTGCTATATAGATGAAGATACCAACAGATTA
196 TATACACTATTAAGGCTGCTATATAGATGAAGATACCAACAGATTA
21313 GAATCCATACAAGTAGCCATGTCCAATGCCTCCAACTAATTTGGACCATATTTGGGGATCAATTT
1 GAATCCATACAAGTAGCCATGTCCAATGCCTCCAACTAATTTGGACCATATTTGGGGATCAATTT
* *
21378 GGACCGAATCCAAACTAAGCTGCTGTTGTCATATTAGAATGCATGAACCATGTTTTAAACATAGC
66 GGACCGAATCCAAACTAAGCTGCTGTTGTCATATTAAAATGCATGAACCAAGTTTTAAACATAGC
* * *
21443 TTCAATAACTCACGTTGTCAAACAAAAGTCCCATAATGTAAACATTCAATGCTAGCAATATGTTA
131 TTCAATAACTAACGTTGTCAAACAAAAGTCCCAAAATGTAAACATTCAATGCTAGCAATATGCTA
* *
21508 TATACACTATTAAGGCTGCTATATGGATGAAGATACCAGCAGA
196 TATACACTATTAAGGCTGCTATATAGATGAAGATACCAACAGA
21551 ATCATGTTTA
Statistics
Matches: 227, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
241 227 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (241 bp):
GAATCCATACAAGTAGCCATGTCCAATGCCTCCAACTAATTTGGACCATATTTGGGGATCAATTT
GGACCGAATCCAAACTAAGCTGCTGTTGTCATATTAAAATGCATGAACCAAGTTTTAAACATAGC
TTCAATAACTAACGTTGTCAAACAAAAGTCCCAAAATGTAAACATTCAATGCTAGCAATATGCTA
TATACACTATTAAGGCTGCTATATAGATGAAGATACCAACAGATTA
Done.