Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012395.1 Corchorus olitorius cultivar O-4 contig12428, 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: 28706
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:6259 original size:11 final size:11
Alignment explanation
Indices: 6243--6268 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
6233 CCTTTGCCTA
6243 AAAACTAGAAG
1 AAAACTAGAAG
6254 AAAACTAGAAG
1 AAAACTAGAAG
6265 AAAA
1 AAAA
6269 GATCTAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:8775 original size:21 final size:21
Alignment explanation
Indices: 8751--8823 Score: 56
Period size: 21 Copynumber: 3.4 Consensus size: 21
8741 GGCATGGAAT
8751 GGTGATGGCACGGGCATGGCC
1 GGTGATGGCACGGGCATGGCC
* * * **
8772 GGTGGTGGCATGGGCTTAACC
1 GGTGATGGCACGGGCATGGCC
* * *
8793 GGTGGTGGCACGGTGAATGGGC
1 GGTGATGGCACGG-GCATGGCC
*
8815 GGTAATGGC
1 GGTGATGGC
8824 TTAGTAGTGG
Statistics
Matches: 38, Mismatches: 13, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
21 28 0.74
22 10 0.26
ACGTcount: A:0.15, C:0.18, G:0.48, T:0.19
Consensus pattern (21 bp):
GGTGATGGCACGGGCATGGCC
Found at i:12092 original size:25 final size:25
Alignment explanation
Indices: 12064--12113 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
12054 TAGAAAACGC
12064 AAAAACA-ACAATTTTTT-TTTTAGA
1 AAAAACACA-AATTTTTTCTTTTAGA
*
12088 AAAAACGCAAATTTTTTCTTTTAGA
1 AAAAACACAAATTTTTTCTTTTAGA
12113 A
1 A
12114 TAGAAACGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (25 bp):
AAAAACACAAATTTTTTCTTTTAGA
Found at i:12120 original size:27 final size:24
Alignment explanation
Indices: 12073--12123 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 24
12063 CAAAAACAAC
12073 AATTTTTTTTTTAGAAAAAACGCA
1 AATTTTTTTTTTAGAAAAAACGCA
12097 AATTTTTTCTTTTAGAATAGAAACGCA
1 AATTTTTT-TTTTAGAA-A-AAACGCA
12124 GAGACTAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 8 0.33
25 8 0.33
26 1 0.04
27 7 0.29
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (24 bp):
AATTTTTTTTTTAGAAAAAACGCA
Found at i:18271 original size:2 final size:2
Alignment explanation
Indices: 18264--18296 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
18254 TAGTTAGAAT
*
18264 TA TA TA TA TA TA TA TA TA TA T- TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18297 AGTGATGACG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:23889 original size:79 final size:79
Alignment explanation
Indices: 23752--23897 Score: 197
Period size: 79 Copynumber: 1.8 Consensus size: 79
23742 GCTCTATTCG
* ** *
23752 TTCCACTCCATTCTTTGCAAGGGACTCACCCTCACAATTAGCAGTTCTAGGGATATGGTGAATAG
1 TTCCACTCCATTCATTGCAAAAGACTCACCCTCACAATTAGCAGTTCTAGGGAAATGGTGAATAG
23817 CACCACTCTATCTA
66 CACCACTCTATCTA
* * *
23831 TTCCACTCCATTCATTGGAAAAGAGTCAGCCTCACAAATTAGCATGTT-T-GGGAAATGGTGAAT
1 TTCCACTCCATTCATTGCAAAAGACTCACCCTCAC-AATTAGCA-GTTCTAGGGAAATGGTGAAT
23894 AGCA
64 AGCA
23898 AAGCTCCTTA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
79 46 0.79
80 9 0.16
81 3 0.05
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.28
Consensus pattern (79 bp):
TTCCACTCCATTCATTGCAAAAGACTCACCCTCACAATTAGCAGTTCTAGGGAAATGGTGAATAG
CACCACTCTATCTA
Found at i:26537 original size:9 final size:9
Alignment explanation
Indices: 26523--26548 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
26513 TGAACAACTT
26523 ATTATTATA
1 ATTATTATA
26532 ATTATTATA
1 ATTATTATA
26541 ATTATTAT
1 ATTATTAT
26549 CAGTTATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
ATTATTATA
Found at i:26645 original size:3 final size:3
Alignment explanation
Indices: 26637--26723 Score: 59
Period size: 3 Copynumber: 29.0 Consensus size: 3
26627 TAATTTGGAC
* * * * * *
26637 TTA TTA TTA TTA TAA TAA TTA TTA TTA -AA CTTA TTA TTA GTG GTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
* ** * *
26682 TTA TAA TTA TTA AAA TTA TTA TTA TAA TAA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
26724 GTGGTATGTA
Statistics
Matches: 66, Mismatches: 16, Indels: 4
0.77 0.19 0.05
Matches are distributed among these distances:
2 1 0.02
3 64 0.97
4 1 0.02
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (3 bp):
TTA
Found at i:26659 original size:15 final size:15
Alignment explanation
Indices: 26639--26721 Score: 77
Period size: 15 Copynumber: 5.7 Consensus size: 15
26629 ATTTGGACTT
26639 ATTATTATTATAATA
1 ATTATTATTATAATA
26654 ATTATTA-T-TAA-A
1 ATTATTATTATAATA
* **
26666 CTTATTATTAGTGGT-
1 ATTATTATTA-TAATA
*
26681 ATTATAATTATTAA-A
1 ATTATTATTA-TAATA
26696 ATTATTATTATAATA
1 ATTATTATTATAATA
26711 ATTATTATTAT
1 ATTATTATTAT
26722 TAGTGGTATG
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
12 7 0.13
13 4 0.08
14 4 0.08
15 38 0.72
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (15 bp):
ATTATTATTATAATA
Found at i:26671 original size:30 final size:30
Alignment explanation
Indices: 26635--26723 Score: 103
Period size: 30 Copynumber: 3.0 Consensus size: 30
26625 GTTAATTTGG
26635 ACTTATTATTATTATAATAATTATTATTAA
1 ACTTATTATTATTATAATAATTATTATTAA
*
26665 ACTTATTATTAGTGGTATTATAATTATTA--AA
1 ACTTATTATTA-T--TATAATAATTATTATTAA
* *
26696 A-TTATTATTATAATAATTATTATTATTA
1 ACTTATTATTATTATAATAATTATTATTA
26724 GTGGTATGTA
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
27 11 0.22
29 2 0.04
30 20 0.40
31 4 0.08
33 13 0.26
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (30 bp):
ACTTATTATTATTATAATAATTATTATTAA
Done.