Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011013.1 Corchorus capsularis cultivar CVL-1 contig11034, 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: 15539
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:315 original size:4 final size:4
Alignment explanation
Indices: 306--334 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
296 ATGTATGAAG
306 GGAA GGAA GGAA GGAA GGAA GGAA GGAA G
1 GGAA GGAA GGAA GGAA GGAA GGAA GGAA G
335 AAAAGGAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (4 bp):
GGAA
Found at i:981 original size:27 final size:27
Alignment explanation
Indices: 951--1003 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
941 GTCTCATGTT
951 TATAGGATGTAATGATAAGCCTGAATC
1 TATAGGATGTAATGATAAGCCTGAATC
* *
978 TATATGATGTACTGATAAGCCTGAAT
1 TATAGGATGTAATGATAAGCCTGAAT
1004 AGGCCTGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (27 bp):
TATAGGATGTAATGATAAGCCTGAATC
Found at i:1019 original size:37 final size:37
Alignment explanation
Indices: 969--1040 Score: 119
Period size: 37 Copynumber: 1.9 Consensus size: 37
959 GTAATGATAA
*
969 GCCTGAATCTATATGATGT-ACTGATAAGCCTGAATAG
1 GCCTGAATCTATATGATGTAAC-GATAAGCCCGAATAG
1006 GCCTGAATCTATATGATGTAACGATAAGCCCGAAT
1 GCCTGAATCTATATGATGTAACGATAAGCCCGAAT
1041 TTATATGATG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
37 31 0.94
38 2 0.06
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (37 bp):
GCCTGAATCTATATGATGTAACGATAAGCCCGAATAG
Found at i:1146 original size:59 final size:59
Alignment explanation
Indices: 1009--1148 Score: 181
Period size: 59 Copynumber: 2.4 Consensus size: 59
999 TGAATAGGCC
* * * *
1009 TGAATCTATATGATGTAACGATAAGCCCGAATTTATATGATGTAACGATAATCTTGAAAA
1 TGAA-CTATATGATGTAACAATAAACCCGAATCTATATGATGTAACGATAAACTTGAAAA
* * * *
1069 TGAAGTATATAATGTAACAATAAACCTGAATCTATGTGATGTAACGATAAACTTGAAAA
1 TGAACTATATGATGTAACAATAAACCCGAATCTATATGATGTAACGATAAACTTGAAAA
**
1128 TGAACTATATGACCTAACAAT
1 TGAACTATATGATGTAACAAT
1149 GAGCTATATG
Statistics
Matches: 68, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
59 64 0.94
60 4 0.06
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.30
Consensus pattern (59 bp):
TGAACTATATGATGTAACAATAAACCCGAATCTATATGATGTAACGATAAACTTGAAAA
Found at i:3060 original size:14 final size:14
Alignment explanation
Indices: 3040--3075 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3030 CGGAGAGTGG
3040 CTTTTTTTCGTTTTT
1 CTTTTTTTC-TTTTT
3055 -TTTTTTTCTTTTT
1 CTTTTTTTCTTTTT
3068 CTTTTTTT
1 CTTTTTTT
3076 ATTGCTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (14 bp):
CTTTTTTTCTTTTT
Found at i:3074 original size:18 final size:18
Alignment explanation
Indices: 3051--3085 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3041 TTTTTTTCGT
* *
3051 TTTTTTTTTTTCTTTTTC
1 TTTTTTTATTGCTTTTTC
3069 TTTTTTTATTGCTTTTT
1 TTTTTTTATTGCTTTTT
3086 GGACTAAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.03, C:0.09, G:0.03, T:0.86
Consensus pattern (18 bp):
TTTTTTTATTGCTTTTTC
Found at i:5776 original size:31 final size:31
Alignment explanation
Indices: 5733--5818 Score: 102
Period size: 31 Copynumber: 2.8 Consensus size: 31
5723 AATGACTAAG
5733 AATGCCATGTGGCAATGCCACGTCGG-ACAAA
1 AATGCCATGTGGCAATGCCACGTCGGAAC-AA
* * *
5764 AATGTCATGTGGCAATGCCATGTTGGAACAA
1 AATGCCATGTGGCAATGCCACGTCGGAACAA
** *
5795 AATGCCACATGGCAAGGCCACGTC
1 AATGCCATGTGGCAATGCCACGTC
5819 AGACCAAGGC
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
31 43 0.96
32 2 0.04
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (31 bp):
AATGCCATGTGGCAATGCCACGTCGGAACAA
Found at i:7299 original size:29 final size:28
Alignment explanation
Indices: 7233--7309 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 28
7223 TTTCCCCTTG
* *
7233 TTTGGACGTTTTGCCTTCTGAACTTCAAT
1 TTTGGACATTTTGCC-CCTGAACTTCAAT
**
7262 TTTTTACATTTTGCCCCTGAACTTCAAT
1 TTTGGACATTTTGCCCCTGAACTTCAAT
7290 TTTGGGACATTTTGTCCCCT
1 TTT-GGACATTTTG-CCCCT
7310 TAACCTAACA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
28 15 0.38
29 20 0.50
30 5 0.12
ACGTcount: A:0.17, C:0.23, G:0.14, T:0.45
Consensus pattern (28 bp):
TTTGGACATTTTGCCCCTGAACTTCAAT
Found at i:10892 original size:105 final size:105
Alignment explanation
Indices: 10640--10901 Score: 402
Period size: 107 Copynumber: 2.5 Consensus size: 105
10630 TTTAGTCTTG
**
10640 ATTTCACTAAGTTTAGCTCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTTATAATTAA
1 ATTTCACTAAGTTTAGC-CCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATTAA
10705 TAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAACTA
65 TAA-TTATTGTTATAGGGTTTTAGAAATAAAATACAAAACTA
10747 ATTTCACTAAGTTTAGTCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATTAA
1 ATTTCACTAAGTTTAG-CCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATTAA
* *
10812 TAA-TATTGTTATAGGGTTTTAGAAATAAAATATATAACTA
65 TAATTATTGTTATAGGGTTTTAGAAATAAAATACAAAACTA
* **
10852 A-TTCACTAAGTTTAGCCCAAATTTAAATTAAAATTGTTTATTTTAAGGGT
1 ATTTCACTAAGTTTAGCCCAAATTAAAATT-TTATT-TTTATTTTAAGGGT
10902 TAGAAAAATT
Statistics
Matches: 145, Mismatches: 7, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
103 13 0.09
104 17 0.12
105 50 0.34
107 64 0.44
108 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.43
Consensus pattern (105 bp):
ATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATTAAT
AATTATTGTTATAGGGTTTTAGAAATAAAATACAAAACTA
Found at i:12842 original size:76 final size:76
Alignment explanation
Indices: 12752--12897 Score: 238
Period size: 76 Copynumber: 1.9 Consensus size: 76
12742 TAACCTCCAT
* * * * *
12752 AAATTAATACTCGATAAATTAATAACATCTCTAAATTATTAATTTTTCATGGTCTCAACCTTAAT
1 AAATTAATACTCGATAAATTAATAACATCTCTAAATTAATAATGTTTCATGATCCCAACATTAAT
12817 AATTTGCATAA
66 AATTTGCATAA
*
12828 AAATTAATACTCGATAAATTAATAACCTCTCTAAATTAATAATGTTTCATGATCCCAACATTAAT
1 AAATTAATACTCGATAAATTAATAACATCTCTAAATTAATAATGTTTCATGATCCCAACATTAAT
12893 AATTT
66 AATTT
12898 ATAGAGGTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
76 64 1.00
ACGTcount: A:0.42, C:0.15, G:0.05, T:0.38
Consensus pattern (76 bp):
AAATTAATACTCGATAAATTAATAACATCTCTAAATTAATAATGTTTCATGATCCCAACATTAAT
AATTTGCATAA
Done.