Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012993.1 Corchorus capsularis cultivar CVL-1 contig13014, 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: 72083
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4157 original size:58 final size:56
Alignment explanation
Indices: 4037--4180 Score: 139
Period size: 58 Copynumber: 2.5 Consensus size: 56
4027 CCGAAACCCG
* * **
4037 CCCGAACCCGCCCGTACCTGAACCCGAAATTACCCGAATTGACCAGAAAAGTCAACGT
1 CCCGAACCCGCCCG-ACCCGAACCCGAAATTACCCGAAATGACCAG-AAAGTCAACAA
* *
4095 CCCGAACCCGCCCGAACCCGAACCCGAAATTACCCGAAAAT-ACCCG-AATTCGAGACAA
1 CCCGAACCCGCCCG-ACCCGAACCCGAAATTACCCG-AAATGACCAGAAAGTC-A-ACAA
*
4153 CCCGAACCCGAACCCGACCCGAGCCCGA
1 CCCGAACCCG--CCCGACCCGAACCCGA
4181 GATCAAAATA
Statistics
Matches: 73, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
56 4 0.05
57 1 0.01
58 50 0.68
59 14 0.19
60 4 0.05
ACGTcount: A:0.33, C:0.41, G:0.17, T:0.09
Consensus pattern (56 bp):
CCCGAACCCGCCCGACCCGAACCCGAAATTACCCGAAATGACCAGAAAGTCAACAA
Found at i:4978 original size:16 final size:15
Alignment explanation
Indices: 4957--5012 Score: 67
Period size: 16 Copynumber: 3.6 Consensus size: 15
4947 CCGGGCCCGA
4957 ACCCGAACCTGAAAAT
1 ACCCGAACC-GAAAAT
4973 ACCCGAACACGAAAAT
1 ACCCGAAC-CGAAAAT
* * *
4989 ACCTGAACCCAAAGT
1 ACCCGAACCGAAAAT
5004 ACCCGAACC
1 ACCCGAACC
5013 CGAACCCGCC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
15 13 0.37
16 21 0.60
17 1 0.03
ACGTcount: A:0.43, C:0.36, G:0.12, T:0.09
Consensus pattern (15 bp):
ACCCGAACCGAAAAT
Found at i:21710 original size:18 final size:18
Alignment explanation
Indices: 21673--21708 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
21663 TTGAATTAAT
*
21673 TCTTCAATAATCTTCAAA
1 TCTTCAAAAATCTTCAAA
21691 TCTTCAAAATATCTTCAA
1 TCTTCAAAA-ATCTTCAA
21709 TCACGAACTT
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:0.39, C:0.22, G:0.00, T:0.39
Consensus pattern (18 bp):
TCTTCAAAAATCTTCAAA
Found at i:27114 original size:6 final size:6
Alignment explanation
Indices: 27098--27129 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
27088 GAAGCAAAGC
27098 AAATC- AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
27130 ACAGAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (6 bp):
AAATCT
Found at i:30852 original size:10 final size:9
Alignment explanation
Indices: 30836--30860 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
30826 TCTGGTCGAA
30836 ATTTTTTTT
1 ATTTTTTTT
30845 ATTTTTTTT
1 ATTTTTTTT
30854 ATTTTTT
1 ATTTTTT
30861 GATATTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:31934 original size:30 final size:30
Alignment explanation
Indices: 31898--31962 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
31888 AAGGATCCAT
*
31898 TGGCCGGTTGTGGCCGGTTGCCCCATGCGA
1 TGGCCGGTTGTGGCCGGTTGCCCCATCCGA
* *
31928 TGGCCGGTTGTGGCTGGTTGCTCCATCCGA
1 TGGCCGGTTGTGGCCGGTTGCCCCATCCGA
31958 TGGCC
1 TGGCC
31963 CATGCGATGG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.06, C:0.29, G:0.38, T:0.26
Consensus pattern (30 bp):
TGGCCGGTTGTGGCCGGTTGCCCCATCCGA
Found at i:34738 original size:23 final size:23
Alignment explanation
Indices: 34693--34742 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 23
34683 CATGAAACAT
34693 AAACAATACAACATTAAAATTTAG
1 AAACAATACAACA-TAAAATTTAG
*
34717 AAACAATACATAC-TAAAGTTTAG
1 AAACAATACA-ACATAAAATTTAG
34740 AAA
1 AAA
34743 GTTGCCCAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 12 0.50
24 10 0.42
25 2 0.08
ACGTcount: A:0.58, C:0.12, G:0.06, T:0.24
Consensus pattern (23 bp):
AAACAATACAACATAAAATTTAG
Found at i:35958 original size:9 final size:8
Alignment explanation
Indices: 35938--35971 Score: 59
Period size: 8 Copynumber: 4.1 Consensus size: 8
35928 CACCTTCTTG
35938 AAAAATTC
1 AAAAATTC
35946 AAAAATTC
1 AAAAATTC
35954 AAAAACTTC
1 AAAAA-TTC
35963 AAAAATTC
1 AAAAATTC
35971 A
1 A
35972 TAGCCGATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 17 0.68
9 8 0.32
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAAATTC
Found at i:35963 original size:17 final size:16
Alignment explanation
Indices: 35938--35971 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
35928 CACCTTCTTG
35938 AAAAATTCAAAAATTC
1 AAAAATTCAAAAATTC
35954 AAAAACTTCAAAAATTC
1 AAAAA-TTCAAAAATTC
35971 A
1 A
35972 TAGCCGATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAAATTCAAAAATTC
Found at i:37698 original size:33 final size:31
Alignment explanation
Indices: 37659--37772 Score: 131
Period size: 33 Copynumber: 3.6 Consensus size: 31
37649 CTAATTGTGA
37659 TGAAAACAATTCTGTTTTGGTTGAACATAGCAT
1 TGAAAACAATTCTGTTTTGGTTG-A-ATAGCAT
*
37692 TAAAAACAATTCTGTTTTGGTTGATTATAGCAT
1 TGAAAACAATTCTGTTTTGGTTGA--ATAGCAT
* * *
37725 TGCAAATAATCCTGTTTTGGTTG-ATAGCAT
1 TGAAAACAATTCTGTTTTGGTTGAATAGCAT
* *
37755 TGAAAATAAATCTGTTTT
1 TGAAAACAATTCTGTTTT
37773 TGGTGACGAG
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
30 22 0.31
32 1 0.01
33 48 0.68
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (31 bp):
TGAAAACAATTCTGTTTTGGTTGAATAGCAT
Found at i:62351 original size:21 final size:21
Alignment explanation
Indices: 62325--62374 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
62315 GCACTGGAGT
* * *
62325 ACATGGGTCGCGAGGCAAACC
1 ACATGGGCCGCCAAGCAAACC
62346 ACATGGGCCGCCAAGCAAACC
1 ACATGGGCCGCCAAGCAAACC
62367 ACATGGGC
1 ACATGGGC
62375 GCCCAGCGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.30, C:0.32, G:0.30, T:0.08
Consensus pattern (21 bp):
ACATGGGCCGCCAAGCAAACC
Done.