Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011049.1 Corchorus capsularis cultivar CVL-1 contig11070, 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: 42201
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:2618 original size:6 final size:6
Alignment explanation
Indices: 2595--2634 Score: 50
Period size: 5 Copynumber: 7.0 Consensus size: 6
2585 ATGTCATTGA
2595 ACATACT ACATA- ACATAT ACATAT -CATA- ACATAT ACATAT
1 ACATA-T ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
2635 CATCATAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
5 13 0.43
6 12 0.40
7 5 0.17
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (6 bp):
ACATAT
Found at i:2624 original size:16 final size:16
Alignment explanation
Indices: 2603--2637 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
2593 GAACATACTA
2603 CATAACATATACATAT
1 CATAACATATACATAT
2619 CATAACATATACATAT
1 CATAACATATACATAT
2635 CAT
1 CAT
2638 CATAATATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (16 bp):
CATAACATATACATAT
Found at i:3192 original size:9 final size:10
Alignment explanation
Indices: 3180--3234 Score: 53
Period size: 9 Copynumber: 5.5 Consensus size: 10
3170 TTGTCTATAT
3180 ATATATAATA
1 ATATATAATA
*
3190 TATTTATTACATA
1 -ATATA-TA-ATA
3203 ATA-ATAATA
1 ATATATAATA
3212 ATA-ATAATA
1 ATATATAATA
3221 ATA-ATAATA
1 ATATATAATA
3230 ATATA
1 ATATA
3235 GTAAAAATGT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
9 24 0.62
10 3 0.08
11 5 0.13
12 4 0.10
13 3 0.08
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (10 bp):
ATATATAATA
Found at i:3208 original size:3 final size:3
Alignment explanation
Indices: 3200--3232 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3190 TATTTATTAC
3200 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3233 TAGTAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:16940 original size:30 final size:30
Alignment explanation
Indices: 16904--17024 Score: 161
Period size: 30 Copynumber: 4.0 Consensus size: 30
16894 TACTACCGTT
* * *
16904 TGAGAAGACTGGACCGTTGATGAAGGTGCA
1 TGAGAAGATTGGACAGTTGATGCAGGTGCA
* * *
16934 TGAGAAGAATGGGCAGTTGATGCAGGTACA
1 TGAGAAGATTGGACAGTTGATGCAGGTGCA
* *
16964 TGAGATGATTGGACAGTTGATGCTGGTGCA
1 TGAGAAGATTGGACAGTTGATGCAGGTGCA
*
16994 TGAGAAGATTGGACAGTTGAAGCAGGTGCA
1 TGAGAAGATTGGACAGTTGATGCAGGTGCA
17024 T
1 T
17025 TAGCTGTCAA
Statistics
Matches: 78, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 78 1.00
ACGTcount: A:0.30, C:0.11, G:0.36, T:0.23
Consensus pattern (30 bp):
TGAGAAGATTGGACAGTTGATGCAGGTGCA
Found at i:22451 original size:16 final size:18
Alignment explanation
Indices: 22429--22468 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
22419 GCTTAGGGTT
22429 AAATTATTT-TTTA-AAG
1 AAATTATTTGTTTATAAG
*
22445 TAATTATTTGTTTATAAG
1 AAATTATTTGTTTATAAG
22463 AAATTA
1 AAATTA
22469 GAAAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 8 0.40
17 4 0.20
18 8 0.40
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (18 bp):
AAATTATTTGTTTATAAG
Found at i:24231 original size:31 final size:31
Alignment explanation
Indices: 24193--24252 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
24183 ACAACTATAA
24193 ACTTTCAACATGTGTCATACTTATAATCAAC
1 ACTTTCAACATGTGTCATACTTATAATCAAC
24224 ACTTTCAACATGTGTCATACTTATAATCA
1 ACTTTCAACATGTGTCATACTTATAATCA
24253 TCGGATCACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.35, C:0.22, G:0.07, T:0.37
Consensus pattern (31 bp):
ACTTTCAACATGTGTCATACTTATAATCAAC
Found at i:38330 original size:22 final size:22
Alignment explanation
Indices: 38302--38345 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
38292 GAAATATATA
38302 GTGTTCCCTGCTTGCAATTGCT
1 GTGTTCCCTGCTTGCAATTGCT
38324 GTGTTCCCTGCTTGCAATTGCT
1 GTGTTCCCTGCTTGCAATTGCT
38346 TCTTTTTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.09, C:0.27, G:0.23, T:0.41
Consensus pattern (22 bp):
GTGTTCCCTGCTTGCAATTGCT
Done.