Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014047.1 Corchorus capsularis cultivar CVL-1 contig14068, 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: 44410
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Found at i:7304 original size:155 final size:155
Alignment explanation
Indices: 7024--7306 Score: 347
Period size: 156 Copynumber: 1.8 Consensus size: 155
7014 TGTCAAAGAA
* * * * **
7024 CTTAGAATATCTCCACAAGACTATGGAAAAATTCTAAGTAAAACCGAGCTCCTCTTGATGGTGAA
1 CTTAGAATATCTCCACAAGACTATGGAAAAAATCTAAGTAAAACCGAACTCCTCTAGATAGAAAA
* * * * * *
7089 TTAGGTTTCTCTCCCTAAATTGTCCTTAAATGAAAAACTAGCACAAGCTTTTCATTCTAAGTCCA
66 TTAGGTTTCGCACCCCAAACTGTCCTTAAATGAAAAACTAACACAAGCTTTTCATACTAAGTCCA
7154 ACGAAGCTAATTTTCCACCAGTATG
131 ACGAAGCTAATTTTCCACCAGTATG
* * *
7179 CTTAGATTATCTCCATAAGGCTATGGGAAAAAATCTAAGTAAAACCGAACT-CTCTAGCATAGAA
1 CTTAGAATATCTCCACAAGACTAT-GGAAAAAATCTAAGTAAAACCGAACTCCTCTAG-ATAGAA
* * * *
7243 AAGTT-GGTTTGGCACCCCAAACTGTCCTTAACTGAAAAAC-AACATAAGTTTTTCATACTAAGT
64 AA-TTAGGTTTCGCACCCCAAACTGTCCTTAAATGAAAAACTAACACAAGCTTTTCATACTAAGT
7306 C
128 C
7307 TGCTTGAGAT
Statistics
Matches: 106, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
155 46 0.43
156 58 0.55
157 2 0.02
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.29
Consensus pattern (155 bp):
CTTAGAATATCTCCACAAGACTATGGAAAAAATCTAAGTAAAACCGAACTCCTCTAGATAGAAAA
TTAGGTTTCGCACCCCAAACTGTCCTTAAATGAAAAACTAACACAAGCTTTTCATACTAAGTCCA
ACGAAGCTAATTTTCCACCAGTATG
Found at i:10645 original size:21 final size:21
Alignment explanation
Indices: 10619--10659 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
10609 CGGAGGTAAA
10619 CGGAGAGTACAAAAAGAAATT
1 CGGAGAGTACAAAAAGAAATT
*
10640 CGGAGAGTACAAAGAGAAAT
1 CGGAGAGTACAAAAAGAAAT
10660 CCACAAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.10, G:0.27, T:0.12
Consensus pattern (21 bp):
CGGAGAGTACAAAAAGAAATT
Found at i:15056 original size:28 final size:28
Alignment explanation
Indices: 15016--15071 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
15006 AGCCTGTCTC
15016 ATGTTTGGGCAAAATGTTAAAATAAAAA
1 ATGTTTGGGCAAAATGTTAAAATAAAAA
*
15044 ATGTTTGGGCAAAATGTTAAAATCAAAA
1 ATGTTTGGGCAAAATGTTAAAATAAAAA
15072 GGGAAGGGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.29
Consensus pattern (28 bp):
ATGTTTGGGCAAAATGTTAAAATAAAAA
Found at i:21582 original size:14 final size:14
Alignment explanation
Indices: 21563--21589 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
21553 GATATATTAA
21563 TACATGCTATATAT
1 TACATGCTATATAT
21577 TACATGCTATATA
1 TACATGCTATATA
21590 CTCCCTCCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (14 bp):
TACATGCTATATAT
Found at i:25629 original size:23 final size:23
Alignment explanation
Indices: 25599--25645 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
25589 TCAGTTCTGA
25599 TATGATCTATCACTACTCGAAGC
1 TATGATCTATCACTACTCGAAGC
25622 TATGATCTATCACTACTCGAAGC
1 TATGATCTATCACTACTCGAAGC
25645 T
1 T
25646 CTCCATTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.32
Consensus pattern (23 bp):
TATGATCTATCACTACTCGAAGC
Found at i:29488 original size:99 final size:99
Alignment explanation
Indices: 29314--29492 Score: 286
Period size: 99 Copynumber: 1.8 Consensus size: 99
29304 TTATCGATGT
* ** *
29314 TGGGAATATGAGGGTTTGAAACTGACCAAGCCTTACAAACGGCTGTCATACGGATTCGATCGAGC
1 TGGGAATATGAGGGGTTGAAACTGACCAAGCCTTACAAACGAATCTCATACGGATTCGATCGAGC
*
29379 CAATCAAATCCCAACGGGAACTTATTGGTGGTGG
66 CAACCAAATCCCAACGGGAACTTATTGGTGGTGG
* *
29413 TGGGAATATGTGGGGTTGAAACTGACCAAGCCTTACAAACGAATCTCATACGGATTCGGTCGAGC
1 TGGGAATATGAGGGGTTGAAACTGACCAAGCCTTACAAACGAATCTCATACGGATTCGATCGAGC
*
29478 CAACCCAATCCCAAC
66 CAACCAAATCCCAAC
29493 CTGATCAATT
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
99 72 1.00
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.22
Consensus pattern (99 bp):
TGGGAATATGAGGGGTTGAAACTGACCAAGCCTTACAAACGAATCTCATACGGATTCGATCGAGC
CAACCAAATCCCAACGGGAACTTATTGGTGGTGG
Found at i:30133 original size:16 final size:16
Alignment explanation
Indices: 30112--30144 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
30102 TCTAGCCGAC
30112 TGATAATAAGAATAAA
1 TGATAATAAGAATAAA
*
30128 TGATAATAAGAGTAAA
1 TGATAATAAGAATAAA
30144 T
1 T
30145 AATTGTATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.15, T:0.27
Consensus pattern (16 bp):
TGATAATAAGAATAAA
Found at i:43898 original size:7 final size:7
Alignment explanation
Indices: 43886--43921 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
43876 AATTTTATTT
43886 TAATATA
1 TAATATA
43893 TAATATA
1 TAATATA
*
43900 TATTAT-
1 TAATATA
43906 TAATATA
1 TAATATA
43913 TAATATA
1 TAATATA
43920 TA
1 TA
43922 TATGTGTGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 5 0.19
7 21 0.81
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
TAATATA
Found at i:43910 original size:20 final size:19
Alignment explanation
Indices: 43881--43922 Score: 75
Period size: 20 Copynumber: 2.2 Consensus size: 19
43871 GTAAGAATTT
43881 TATTTTAATATATAATATA
1 TATTTTAATATATAATATA
43900 TATTATTAATATATAATATA
1 TATT-TTAATATATAATATA
43920 TAT
1 TAT
43923 ATGTGTGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TATTTTAATATATAATATA
Done.