Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007493.1 Corchorus capsularis cultivar CVL-1 contig07514, 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: 20154
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:944 original size:10 final size:10
Alignment explanation
Indices: 929--1004 Score: 77
Period size: 10 Copynumber: 7.4 Consensus size: 10
919 AAGTTTATTG
929 ATAATATAAT
1 ATAATATAAT
939 ATAATATAAT
1 ATAATATAAT
949 AT-ATAATAAT
1 ATAAT-ATAAT
959 AATAATATAAT
1 -ATAATATAAT
*
970 ATAACATAATT
1 ATAATATAA-T
981 ATCAATAT-AT
1 AT-AATATAAT
991 AT-ATATATAT
1 ATAATATA-AT
1001 ATAA
1 ATAA
1005 AGATTGAATA
Statistics
Matches: 56, Mismatches: 2, Indels: 15
0.77 0.03 0.21
Matches are distributed among these distances:
8 4 0.07
9 2 0.04
10 32 0.57
11 12 0.21
12 6 0.11
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (10 bp):
ATAATATAAT
Found at i:965 original size:21 final size:21
Alignment explanation
Indices: 934--1004 Score: 78
Period size: 21 Copynumber: 3.4 Consensus size: 21
924 TATTGATAAT
934 ATAATATAATATAATATATA-
1 ATAATATAATATAATATATAC
954 ATAATAATAATATAATATA-AC
1 ATAAT-ATAATATAATATATAC
*
975 ATAATTATCAATAT-ATATATAT
1 ATAA-TAT-AATATAATATATAC
997 AT-ATATAA
1 ATAATATAA
1005 AGATTGAATA
Statistics
Matches: 45, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
19 2 0.04
20 9 0.20
21 25 0.56
22 9 0.20
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (21 bp):
ATAATATAATATAATATATAC
Found at i:967 original size:31 final size:29
Alignment explanation
Indices: 929--1004 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 29
919 AAGTTTATTG
*
929 ATAATATAATATAATATAATATAT-AATAAT
1 ATAATATAATATAACATAAT-TATCAAT-AT
959 AATAATATAATATAACATAATTATCAATAT
1 -ATAATATAATATAACATAATTATCAATAT
989 ATATATATATATATAA
1 ATA-ATATA-ATATAA
1005 AGATTGAATA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
29 3 0.07
30 10 0.24
31 28 0.68
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (29 bp):
ATAATATAATATAACATAATTATCAATAT
Found at i:1217 original size:21 final size:20
Alignment explanation
Indices: 1192--1238 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
1182 AATTTAAATT
* *
1192 AATTAATGCTAATTAATACTA
1 AATTAATGCAAATTAAAAC-A
*
1213 AATTATTGCAAATTAAAACA
1 AATTAATGCAAATTAAAACA
1233 AATTAA
1 AATTAA
1239 ACATTAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.34
Consensus pattern (20 bp):
AATTAATGCAAATTAAAACA
Found at i:3443 original size:36 final size:36
Alignment explanation
Indices: 3396--3468 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
3386 TAACCTAATG
3396 AAGCAAAGGGTACAACCAAACTCACATAAACTAACC
1 AAGCAAAGGGTACAACCAAACTCACATAAACTAACC
*
3432 AAGCAAAGGGTACAACCAAACTCACATAAACTGACC
1 AAGCAAAGGGTACAACCAAACTCACATAAACTAACC
3468 A
1 A
3469 GCTCTAGACT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.49, C:0.27, G:0.12, T:0.11
Consensus pattern (36 bp):
AAGCAAAGGGTACAACCAAACTCACATAAACTAACC
Found at i:5921 original size:8 final size:8
Alignment explanation
Indices: 5908--5933 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
5898 AATCTCCCCA
5908 TGAAATTT
1 TGAAATTT
5916 TGAAATTT
1 TGAAATTT
5924 TGAAATTT
1 TGAAATTT
5932 TG
1 TG
5934 GTAAGCACAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (8 bp):
TGAAATTT
Found at i:8944 original size:37 final size:37
Alignment explanation
Indices: 8894--8989 Score: 185
Period size: 37 Copynumber: 2.6 Consensus size: 37
8884 TCAAAATCAT
8894 GAGGTAATCTTATTCAATATCAATATAAGAAAGTTAG
1 GAGGTAATCTTATTCAATATCAATATAAGAAAGTTAG
8931 GAGGTAATCTTATTCAATATCAATATAAGAAAGTTAG
1 GAGGTAATCTTATTCAATATCAATATAAGAAAGTTAG
8968 GAGGTAATCTTATTCAA-ATCAA
1 GAGGTAATCTTATTCAATATCAA
8990 CTCGTAAAAT
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 5 0.08
37 54 0.92
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.32
Consensus pattern (37 bp):
GAGGTAATCTTATTCAATATCAATATAAGAAAGTTAG
Found at i:11398 original size:32 final size:31
Alignment explanation
Indices: 11362--11434 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
11352 TGTCAGGCGT
**
11362 AAAATGTCTTAAATTTTTTAAGTTTAGG-GGAC
1 AAAATGTCTTAAA-TTTAAAAGTTTAGGAGG-C
* *
11394 AAAATGTCCTGAATTTAAAAGTTTAGGAGGC
1 AAAATGTCTTAAATTTAAAAGTTTAGGAGGC
11425 AAAATGTCTT
1 AAAATGTCTT
11435 GATTTGAAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
31 22 0.63
32 13 0.37
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.36
Consensus pattern (31 bp):
AAAATGTCTTAAATTTAAAAGTTTAGGAGGC
Found at i:11419 original size:31 final size:29
Alignment explanation
Indices: 11381--11462 Score: 87
Period size: 31 Copynumber: 2.8 Consensus size: 29
11371 TAAATTTTTT
11381 AAGTTTAGGGGACAAAATGTCCTGAATTTAA
1 AAGTTTAGGGGACAAAATGTCCTG-ATTT-A
* *
11412 AAGTTTAGGAGG-CAAAATGTCTTGATTTG
1 AAGTTTAGG-GGACAAAATGTCCTGATTTA
* *
11441 AAGTTTA-GGTACAAAACGTCCT
1 AAGTTTAGGGGACAAAATGTCCT
11463 TGACGCAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
27 1 0.02
28 10 0.23
29 7 0.16
30 4 0.09
31 20 0.45
32 2 0.05
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.30
Consensus pattern (29 bp):
AAGTTTAGGGGACAAAATGTCCTGATTTA
Found at i:11464 original size:29 final size:29
Alignment explanation
Indices: 11381--11465 Score: 77
Period size: 29 Copynumber: 2.8 Consensus size: 29
11371 TAAATTTTTT
11381 AAGTTTAGGGGACAAAATGTCC-TGAATTTAA
1 AAGTTTA--GGACAAAATGTCCTTG-ATTTAA
*
11412 AAGTTTAGGAGGCAAAATGT-CTTGATTT-G
1 AAGTTTAGGA--CAAAATGTCCTTGATTTAA
*
11441 AAGTTTAGGTACAAAACGTCCTTGA
1 AAGTTTAGG-ACAAAATGTCCTTGA
11466 CGCAATTGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
28 7 0.15
29 17 0.36
30 6 0.13
31 17 0.36
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.31
Consensus pattern (29 bp):
AAGTTTAGGACAAAATGTCCTTGATTTAA
Found at i:12983 original size:32 final size:32
Alignment explanation
Indices: 12910--12986 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 32
12900 TGCCCCATTC
* * * *
12910 TTCAGGGGGC-AAAATGTCTTTAATTTGGAAG
1 TTCAAGGGGCAAAAATGTCCTAAATTTGGAAA
*
12941 TT-TAGAGGGCAAAAATGTCCTAAATTTGGAAA
1 TTCAAG-GGGCAAAAATGTCCTAAATTTGGAAA
12973 TTCAAGGGGCAAAA
1 TTCAAGGGGCAAAA
12987 CATTGTGATT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
30 1 0.03
31 6 0.16
32 28 0.76
33 2 0.05
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.27
Consensus pattern (32 bp):
TTCAAGGGGCAAAAATGTCCTAAATTTGGAAA
Done.