Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008601.1 Corchorus capsularis cultivar CVL-1 contig08622, 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: 44620
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:6614 original size:51 final size:50
Alignment explanation
Indices: 6538--6638 Score: 175
Period size: 51 Copynumber: 2.0 Consensus size: 50
6528 AATTTTACCA
*
6538 ATTTTGTTAAGAGTATAACATATGTAAGTTAGATTTTTGAGGACTCCCTCC
1 ATTTTGTTAAGAGTATAACATATGTAAGTTAGATTTTTCAGGAC-CCCTCC
*
6589 ATTTTGTTAATAGTATAACATATGTAAGTTAGATTTTTCAGGACCCCTCC
1 ATTTTGTTAAGAGTATAACATATGTAAGTTAGATTTTTCAGGACCCCTCC
6639 CTCCGCCCCT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
50 6 0.12
51 42 0.88
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.40
Consensus pattern (50 bp):
ATTTTGTTAAGAGTATAACATATGTAAGTTAGATTTTTCAGGACCCCTCC
Found at i:7278 original size:45 final size:45
Alignment explanation
Indices: 7210--7303 Score: 163
Period size: 45 Copynumber: 2.1 Consensus size: 45
7200 TGGGAGTTCC
*
7210 AGATGGTGTTCGCAACCAGGAGGTTGGAGATCTCGTGGAGGAAGA
1 AGATGGTGTCCGCAACCAGGAGGTTGGAGATCTCGTGGAGGAAGA
7255 AGATGGTGTCCGCAACC-GCGAGGTTGGAGATCTCGTGGAGGAAGA
1 AGATGGTGTCCGCAACCAG-GAGGTTGGAGATCTCGTGGAGGAAGA
7300 AGAT
1 AGAT
7304 CTTGAGGATG
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 1 0.02
45 46 0.98
ACGTcount: A:0.27, C:0.15, G:0.39, T:0.19
Consensus pattern (45 bp):
AGATGGTGTCCGCAACCAGGAGGTTGGAGATCTCGTGGAGGAAGA
Found at i:11198 original size:21 final size:19
Alignment explanation
Indices: 11143--11201 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 19
11133 TCTTTTGAGA
*
11143 TTTCTTCAGTTTTTCAGTCTT
1 TTTCTTC-GTTTTTC-TTCTT
11164 TTTCTTCG-TTTTCTTCTT
1 TTTCTTCGTTTTTCTTCTT
11182 GTTTCTTCGGTTTTTCTTCT
1 -TTTCTTC-GTTTTTCTTCT
11202 CCTTCTTTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
18 4 0.12
19 12 0.35
20 2 0.06
21 16 0.47
ACGTcount: A:0.03, C:0.20, G:0.10, T:0.66
Consensus pattern (19 bp):
TTTCTTCGTTTTTCTTCTT
Found at i:14070 original size:32 final size:31
Alignment explanation
Indices: 14008--14071 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 31
13998 GTAAGCTTAG
* * *
14008 GTTTTAATAATTATTATAGTTTGGGGAATAA
1 GTTTAAATAATTATTATAGTTTGAGAAATAA
14039 GTTTAAATATATTATTATA-TATTGAGAAATAA
1 GTTTAAATA-ATTATTATAGT-TTGAGAAATAA
14071 G
1 G
14072 ATTTTTAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 9 0.32
32 19 0.68
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.44
Consensus pattern (31 bp):
GTTTAAATAATTATTATAGTTTGAGAAATAA
Found at i:16899 original size:3 final size:3
Alignment explanation
Indices: 16891--16929 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
16881 ATAAAAATTT
16891 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
16930 ATACTCTATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:20396 original size:18 final size:19
Alignment explanation
Indices: 20370--20407 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
20360 TATTTTTACC
* *
20370 CCTATTCTCTTTCC-CCTA
1 CCTAGTCTCTCTCCTCCTA
20388 CCTAGTCTCTCTCCTCCTA
1 CCTAGTCTCTCTCCTCCTA
20407 C
1 C
20408 TCACTTTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.11, C:0.47, G:0.03, T:0.39
Consensus pattern (19 bp):
CCTAGTCTCTCTCCTCCTA
Found at i:22370 original size:20 final size:20
Alignment explanation
Indices: 22345--22389 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
22335 CACCTGGGGT
22345 GATCATGGGTGGTGATCTTA
1 GATCATGGGTGGTGATCTTA
22365 GATCATGGGTGGTGATCTTA
1 GATCATGGGTGGTGATCTTA
22385 GATCA
1 GATCA
22390 CCTGTTTGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.22, C:0.11, G:0.33, T:0.33
Consensus pattern (20 bp):
GATCATGGGTGGTGATCTTA
Found at i:23077 original size:115 final size:115
Alignment explanation
Indices: 22867--23096 Score: 397
Period size: 115 Copynumber: 2.0 Consensus size: 115
22857 TTGCTACACA
* *
22867 AATTCGATGGAAATTGGACTTCTTGGATTAGTAGAATCTTTTGCTGATTTATAATTAATCCATAT
1 AATTCGATGGAAATTGGACTTCTTGGATTAGCAGAATCTTTTGCTGATATATAATTAATCCATAT
* *
22932 ATGATTTAAATGGAAAAATTCATAGGAAGTGTTAAAGAAATGGATAAATT
66 ATGATTTAAATGGAAAAATTCATAGAAAGTGTTAAAGAAATGGAAAAATT
22982 AATTCGATGGAAATTGGACTTCTTGGATTAGCAGAATCTTTTGCTGATATATAATTAATCCATAT
1 AATTCGATGGAAATTGGACTTCTTGGATTAGCAGAATCTTTTGCTGATATATAATTAATCCATAT
* * *
23047 ATGATTTAAATGGAAAAATTGATCGAAAGTGTTAAGGAAATGGAAAAATT
66 ATGATTTAAATGGAAAAATTCATAGAAAGTGTTAAAGAAATGGAAAAATT
23097 TGGTTAAGTC
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
115 108 1.00
ACGTcount: A:0.39, C:0.07, G:0.19, T:0.35
Consensus pattern (115 bp):
AATTCGATGGAAATTGGACTTCTTGGATTAGCAGAATCTTTTGCTGATATATAATTAATCCATAT
ATGATTTAAATGGAAAAATTCATAGAAAGTGTTAAAGAAATGGAAAAATT
Found at i:30171 original size:15 final size:15
Alignment explanation
Indices: 30151--30179 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
30141 CATTGCTTTT
30151 TGCATAACAAAGTTA
1 TGCATAACAAAGTTA
30166 TGCATAACAAAGTT
1 TGCATAACAAAGTT
30180 CAATTCAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.28
Consensus pattern (15 bp):
TGCATAACAAAGTTA
Found at i:38100 original size:27 final size:27
Alignment explanation
Indices: 38065--38133 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 27
38055 ATCCTAGGGA
* *
38065 ACTAATTTTGAATG-GGAAACTGTTTTG
1 ACTAATTTTGAATGAAG-AACTGTCTTG
*
38092 ACTAGTTTTGAATGAAGAACTGTCTTG
1 ACTAATTTTGAATGAAGAACTGTCTTG
* *
38119 ACTAACTTGGAATGA
1 ACTAATTTTGAATGA
38134 GAGTCTGACT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 34 0.97
28 1 0.03
ACGTcount: A:0.32, C:0.10, G:0.22, T:0.36
Consensus pattern (27 bp):
ACTAATTTTGAATGAAGAACTGTCTTG
Found at i:38400 original size:26 final size:26
Alignment explanation
Indices: 38364--38415 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
38354 TTATTAATCT
38364 CTCCTTTTAAAAAAAAATTCCATCAA
1 CTCCTTTTAAAAAAAAATTCCATCAA
38390 CTCCTTTTAAAAAAAAATTCCATCAA
1 CTCCTTTTAAAAAAAAATTCCATCAA
38416 TTCGAACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (26 bp):
CTCCTTTTAAAAAAAAATTCCATCAA
Found at i:38512 original size:81 final size:82
Alignment explanation
Indices: 38398--38569 Score: 328
Period size: 81 Copynumber: 2.1 Consensus size: 82
38388 AACTCCTTTT
38398 AAAAAAAAATTCCATCAATTCGAACAAAGCTTTTCGATTTAGGGTGAAGCTCTATCCATCAATTC
1 AAAAAAAAATTCCATCAATTCGAACAAAGCTTTTCGATTTAGGGTGAAGCTCTATCCATCAATTC
38463 GTTGAGACAATTGAATG
66 GTTGAGACAATTGAATG
38480 AAAAAAAAA-TCCATCAATTCGAACAAAGCTTTTCGATTTAGGGTGAAGCTCTATCCATCAATTC
1 AAAAAAAAATTCCATCAATTCGAACAAAGCTTTTCGATTTAGGGTGAAGCTCTATCCATCAATTC
*
38544 GTTGAGGCAATTGAATG
66 GTTGAGACAATTGAATG
38561 AAAAAAAAA
1 AAAAAAAAA
38570 AGAACTATAC
Statistics
Matches: 89, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
81 80 0.90
82 9 0.10
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (82 bp):
AAAAAAAAATTCCATCAATTCGAACAAAGCTTTTCGATTTAGGGTGAAGCTCTATCCATCAATTC
GTTGAGACAATTGAATG
Found at i:38752 original size:47 final size:47
Alignment explanation
Indices: 38683--38776 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 47
38673 AAATTCCAAC
*
38683 AATTTCGAATTCCAATACTGAAACTAGAAGTCAAGGATTTGTGGTAA
1 AATTTCGAATTCCAATACTGAAACTAGAAGTCAAGCATTTGTGGTAA
* *
38730 AATTTTGAATTCCAATAGTGAAACTAGAAGTCAAGCATTTGTGGTAA
1 AATTTCGAATTCCAATACTGAAACTAGAAGTCAAGCATTTGTGGTAA
38777 GCCTTGGTTG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (47 bp):
AATTTCGAATTCCAATACTGAAACTAGAAGTCAAGCATTTGTGGTAA
Done.