Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019812.1 Corchorus olitorius cultivar O-4 contig19845, 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: 30915
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:966 original size:17 final size:18
Alignment explanation
Indices: 944--979 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
934 AAAGGGTAAT
*
944 TAAAAA-AATTGTTTTCA
1 TAAAAAGAAGTGTTTTCA
961 TAAAAAGAAGTGTTTTCA
1 TAAAAAGAAGTGTTTTCA
979 T
1 T
980 GATAGAGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (18 bp):
TAAAAAGAAGTGTTTTCA
Found at i:1859 original size:19 final size:18
Alignment explanation
Indices: 1835--1870 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1825 TGAAGACTTA
1835 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
1854 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
1871 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:1877 original size:30 final size:30
Alignment explanation
Indices: 1823--1882 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1813 GAAGTTCGTG
* *
1823 TTTGAAGACTTATTGAAGACAATTTGAAGA
1 TTTGAAGACTCATTGAAGACAATTTCAAGA
*
1853 TTTGAAGAC-CATTGAAGAATAATTTCAAGA
1 TTTGAAGACTCATTGAAG-ACAATTTCAAGA
1883 AGCAAGAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (30 bp):
TTTGAAGACTCATTGAAGACAATTTCAAGA
Found at i:3374 original size:76 final size:72
Alignment explanation
Indices: 3293--3440 Score: 181
Period size: 76 Copynumber: 2.0 Consensus size: 72
3283 TGTGGGATCG
* * * *
3293 ACCCCTACTTGCCCTAGCTATCTTTAGTTAGTA-ATTGTTGGGATTTTTATTTTTATGATTTGCT
1 ACCCCTACTTACCCTAGCTA-C-TTAGTTAGGATATTGTGGGGA--ATTATTTTTATGA-TTGCT
3357 GACGACCAATCA
61 GACGACCAATCA
* *
3369 ACCCCTACTTACCCTATCTACTTAGTTAGGATTTTGTGGGGAATTATTTTTATGATTGCTGACGA
1 ACCCCTACTTACCCTAGCTACTTAGTTAGGATATTGTGGGGAATTATTTTTATGATTGCTGACGA
*
3434 CCGATCA
66 CCAATCA
3441 TTAATGCATA
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
72 16 0.25
73 12 0.19
74 9 0.14
75 9 0.14
76 18 0.28
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (72 bp):
ACCCCTACTTACCCTAGCTACTTAGTTAGGATATTGTGGGGAATTATTTTTATGATTGCTGACGA
CCAATCA
Found at i:7027 original size:21 final size:20
Alignment explanation
Indices: 7003--7053 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 20
6993 AAGTTCGTGT
7003 TTGAAGATTTATTGAAGATAA
1 TTGAAGA-TTATTGAAGATAA
*
7024 TTGAAGA-T-TTGAAGATCA
1 TTGAAGATTATTGAAGATAA
7042 TTGAAGAATTAT
1 TTGAAG-ATTAT
7054 CTCGAGAAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 15 0.58
19 2 0.08
20 1 0.04
21 8 0.31
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.37
Consensus pattern (20 bp):
TTGAAGATTATTGAAGATAA
Found at i:17352 original size:19 final size:19
Alignment explanation
Indices: 17328--17364 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
17318 TTTTAATCCC
*
17328 TCATCTCCTCTTTCCTGAT
1 TCATCTCATCTTTCCTGAT
17347 TCATCTCATCTTTCCTGA
1 TCATCTCATCTTTCCTGA
17365 GTTTATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.14, C:0.35, G:0.05, T:0.46
Consensus pattern (19 bp):
TCATCTCATCTTTCCTGAT
Found at i:26665 original size:13 final size:13
Alignment explanation
Indices: 26646--26690 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
26636 AATATTTAAA
26646 ACTCCCCCACCCT
1 ACTCCCCCACCCT
* *
26659 CCTCCCCCTCCCT
1 ACTCCCCCACCCT
*
26672 ACTCTCCCCACCCC
1 ACTC-CCCCACCCT
26686 ACTCC
1 ACTCC
26691 TCCCCACCCC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.11, C:0.71, G:0.00, T:0.18
Consensus pattern (13 bp):
ACTCCCCCACCCT
Found at i:26693 original size:15 final size:16
Alignment explanation
Indices: 26657--26700 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
26647 CTCCCCCACC
26657 CTCCTCCCC-CTCCCTA
1 CTCCTCCCCAC-CCCTA
26673 CT-CTCCCCACCCC-A
1 CTCCTCCCCACCCCTA
26687 CTCCTCCCCACCCC
1 CTCCTCCCCACCCC
26701 CCTTGAACGA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 3 0.12
15 20 0.77
16 3 0.12
ACGTcount: A:0.09, C:0.73, G:0.00, T:0.18
Consensus pattern (16 bp):
CTCCTCCCCACCCCTA
Found at i:29181 original size:17 final size:17
Alignment explanation
Indices: 29156--29196 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
29146 ATTTTTATAA
*
29156 AAACTAAAATTGTTCAT
1 AAACAAAAATTGTTCAT
29173 AAACAAAAAATTGTTCAT
1 AAAC-AAAAATTGTTCAT
*
29191 GAACAA
1 AAACAA
29197 TGTAATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.54, C:0.12, G:0.07, T:0.27
Consensus pattern (17 bp):
AAACAAAAATTGTTCAT
Found at i:29184 original size:18 final size:18
Alignment explanation
Indices: 29161--29196 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
29151 TATAAAAACT
29161 AAAATTGTTCATAAACAA
1 AAAATTGTTCATAAACAA
*
29179 AAAATTGTTCATGAACAA
1 AAAATTGTTCATAAACAA
29197 TGTAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.11, G:0.08, T:0.28
Consensus pattern (18 bp):
AAAATTGTTCATAAACAA
Found at i:29448 original size:35 final size:35
Alignment explanation
Indices: 29402--29470 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
29392 ATAAACGAAC
*
29402 ACTTAAATGAACAATAAACGAGTCTGTTCGTGAAG
1 ACTTAAATGAACAATAAACGAGCCTGTTCGTGAAG
29437 ACTTAAATGAACAATAAACGAGCCTGTTCGTGAA
1 ACTTAAATGAACAATAAACGAGCCTGTTCGTGAA
29471 CATAAACGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.25
Consensus pattern (35 bp):
ACTTAAATGAACAATAAACGAGCCTGTTCGTGAAG
Done.