Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023510.1 Corchorus olitorius cultivar O-4 contig23543, 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: 24051
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:2259 original size:45 final size:45
Alignment explanation
Indices: 2208--2337 Score: 224
Period size: 45 Copynumber: 2.9 Consensus size: 45
2198 CTAAATTCTA
*
2208 CTTCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTC
1 CTTCATCTCTAGGTAATTCATCAAAATAAAACTAATATTATACTC
*
2253 CTTCATCTCTAGGTAATTCATCAAAATAAAACTAATATTCTACTC
1 CTTCATCTCTAGGTAATTCATCAAAATAAAACTAATATTATACTC
* *
2298 CTCCATCTCTAGGTAATTCATCAAAATAAACCTAATATTA
1 CTTCATCTCTAGGTAATTCATCAAAATAAAACTAATATTA
2338 ATTGTTGCTT
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 80 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.35
Consensus pattern (45 bp):
CTTCATCTCTAGGTAATTCATCAAAATAAAACTAATATTATACTC
Found at i:4229 original size:85 final size:84
Alignment explanation
Indices: 4069--4326 Score: 335
Period size: 84 Copynumber: 3.1 Consensus size: 84
4059 ACAAATATAT
* * ** *
4069 TTAAAAAATTATAATATATCTAAGTTTTGCAATTAAAATAGTTTAATGGTAAAAATAAAATAGTT
1 TTAAAAAATTTTAATATATCTAAGTTTTGTAATTAAAATAGTAAAATGGTAAAAATCAAATAGTT
4134 ATAAAGAGATTAGATTTAA
66 ATAAAGAGATTAGATTTAA
4153 TTAAAAAATTTTAA-ATTATCTAAGTTTTGTAATTAAAATAGTAAAAATGGTAAAAATCAAATAG
1 TTAAAAAATTTTAATA-TATCTAAGTTTTGTAATTAAAATAGT-AAAATGGTAAAAATCAAATAG
* * *
4217 TTATAAAAAGATTTGACTTAA
64 TTATAAAGAGATTAGATTTAA
** *
4238 TTAAAATTTTTTAATATATCTAAGTTTT-T-TTTAATTAATAGTAAAATGGTAAAAA-CAAAATA
1 TTAAAAAATTTTAATATATCTAAGTTTTGTAATTAA--AATAGTAAAATGGTAAAAATC-AAATA
4300 GTTATAAAGAGATTAGATTTAA
63 GTTATAAAGAGATTAGATTTAA
*
4322 GTAAA
1 TTAAA
4327 TAAAAATAGA
Statistics
Matches: 153, Mismatches: 15, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
83 6 0.04
84 80 0.52
85 66 0.43
86 1 0.01
ACGTcount: A:0.49, C:0.03, G:0.10, T:0.38
Consensus pattern (84 bp):
TTAAAAAATTTTAATATATCTAAGTTTTGTAATTAAAATAGTAAAATGGTAAAAATCAAATAGTT
ATAAAGAGATTAGATTTAA
Found at i:4471 original size:42 final size:42
Alignment explanation
Indices: 4419--4503 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
4409 AATAATTGAT
*
4419 TCAAATGTTTTACAAAACTCGTACTTTTATATATAATATAGA
1 TCAAAAGTTTTACAAAACTCGTACTTTTATATATAATATAGA
* * *
4461 TCAAAAGTTTTGCAAAACTTGTACTTTTATATATAGTATAGA
1 TCAAAAGTTTTACAAAACTCGTACTTTTATATATAATATAGA
4503 T
1 T
4504 ATATAGTGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (42 bp):
TCAAAAGTTTTACAAAACTCGTACTTTTATATATAATATAGA
Found at i:8846 original size:4 final size:4
Alignment explanation
Indices: 8837--8868 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
8827 CATGTTTAAT
8837 TTTA TTTA TTTA TTTA TTTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTT
8869 TTTTTTTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:8857 original size:13 final size:13
Alignment explanation
Indices: 8837--8869 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
8827 CATGTTTAAT
8837 TTTA-TTTATTTA
1 TTTATTTTATTTA
8849 TTTATTTTATTTA
1 TTTATTTTATTTA
8862 TTTATTTT
1 TTTATTTT
8870 TTTTTTACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:8857 original size:17 final size:17
Alignment explanation
Indices: 8835--8876 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
8825 CTCATGTTTA
8835 ATTTTATTTATTTATTT
1 ATTTTATTTATTTATTT
8852 ATTTTATTTATTTATTT
1 ATTTTATTTATTTATTT
8869 -TTTT-TTTA
1 ATTTTATTTA
8877 CATAAGAGCG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.16
16 4 0.16
17 17 0.68
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (17 bp):
ATTTTATTTATTTATTT
Found at i:18894 original size:17 final size:16
Alignment explanation
Indices: 18872--18915 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 16
18862 ATGAGGCCCA
18872 CGCGCTGGCCTGGGCC
1 CGCGCTGGCCTGGGCC
*
18888 GCGCGCTGGCCTAGGCC
1 -CGCGCTGGCCTGGGCC
18905 CGC-CTGGCCTG
1 CGCGCTGGCCTG
18916 CTGGTTGGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 7 0.28
16 3 0.12
17 15 0.60
ACGTcount: A:0.02, C:0.43, G:0.41, T:0.14
Consensus pattern (16 bp):
CGCGCTGGCCTGGGCC
Found at i:19815 original size:21 final size:21
Alignment explanation
Indices: 19791--19857 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
19781 AATTCTCTGT
19791 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * ** *
19812 AAATCATAGAAA-ATTC-TTTGT
1 AAATTA-AGAAATACTCAACT-C
19833 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
19854 AAAT
1 AAAT
19858 CCTGATCCTT
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
20 6 0.19
21 20 0.62
22 6 0.19
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Found at i:19837 original size:42 final size:42
Alignment explanation
Indices: 19778--19858 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
19768 AATAAGTCTT
19778 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
*
19820 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATC
19859 CTGATCCTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.47, C:0.16, G:0.07, T:0.30
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:22073 original size:11 final size:11
Alignment explanation
Indices: 22043--22081 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
22033 AAAGTATATT
*
22043 TTATCTTCATA
1 TTATCTTTATA
22054 GTATATCTTTATA
1 -T-TATCTTTATA
22067 TTATCTTTATA
1 TTATCTTTATA
22078 TTAT
1 TTAT
22082 ATAAGTCTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 14 0.56
12 2 0.08
13 9 0.36
ACGTcount: A:0.28, C:0.10, G:0.03, T:0.59
Consensus pattern (11 bp):
TTATCTTTATA
Found at i:22192 original size:50 final size:49
Alignment explanation
Indices: 22133--22234 Score: 177
Period size: 50 Copynumber: 2.1 Consensus size: 49
22123 ATATCCTTCT
*
22133 TTATCTTTAACTTTTAAGGTTTAATATGTAATTTTTATTTATCAATTAAA
1 TTATCTTTAACTTTTAAAGTTTAATATGTAA-TTTTATTTATCAATTAAA
*
22183 TTATCTTTAACTTTTAAAGTTTCATATGTAATTTTATTTATCAATTAAA
1 TTATCTTTAACTTTTAAAGTTTAATATGTAATTTTATTTATCAATTAAA
22232 TTA
1 TTA
22235 AATATATTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
49 21 0.42
50 29 0.58
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.54
Consensus pattern (49 bp):
TTATCTTTAACTTTTAAAGTTTAATATGTAATTTTATTTATCAATTAAA
Done.