Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015174.1 Corchorus olitorius cultivar O-4 contig15207, 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: 28779
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:3462 original size:14 final size:14
Alignment explanation
Indices: 3440--3469 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3430 TTCAAGTACC
*
3440 AATTGTAAAAAAAA
1 AATTCTAAAAAAAA
3454 AATTCTAAAAAAAA
1 AATTCTAAAAAAAA
3468 AA
1 AA
3470 AGACACTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.20
Consensus pattern (14 bp):
AATTCTAAAAAAAA
Found at i:4405 original size:16 final size:17
Alignment explanation
Indices: 4386--4432 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
4376 TATGCATTTG
4386 TTTGTTTTAGTTTAGT-
1 TTTGTTTTAGTTTAGTC
*
4402 TTTGTTTAAGTTTTTAGTC
1 TTTGTTTTAG--TTTAGTC
4421 TTTGTTTT-GTTT
1 TTTGTTTTAGTTT
4433 TCTAGCTTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 12 0.46
18 7 0.27
19 7 0.27
ACGTcount: A:0.11, C:0.02, G:0.17, T:0.70
Consensus pattern (17 bp):
TTTGTTTTAGTTTAGTC
Found at i:8101 original size:38 final size:38
Alignment explanation
Indices: 8054--8127 Score: 148
Period size: 38 Copynumber: 1.9 Consensus size: 38
8044 TGTAATGAAA
8054 GAACATAAATTTGGATATTATATAATCAATATTTATTT
1 GAACATAAATTTGGATATTATATAATCAATATTTATTT
8092 GAACATAAATTTGGATATTATATAATCAATATTTAT
1 GAACATAAATTTGGATATTATATAATCAATATTTAT
8128 AACTTTAACC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.43
Consensus pattern (38 bp):
GAACATAAATTTGGATATTATATAATCAATATTTATTT
Found at i:8298 original size:16 final size:16
Alignment explanation
Indices: 8277--8310 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
8267 AGCCAAAAAA
*
8277 ACCCAAAATCCGAATG
1 ACCCAAAACCCGAATG
*
8293 ACCCAAAACCCGAGTG
1 ACCCAAAACCCGAATG
8309 AC
1 AC
8311 ATGAGGCCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.35, G:0.15, T:0.09
Consensus pattern (16 bp):
ACCCAAAACCCGAATG
Found at i:9029 original size:22 final size:22
Alignment explanation
Indices: 9004--9050 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
8994 TTTTTAGTTG
9004 AGTAAAACT-ATAAAAATAAAAT
1 AGTAAAA-TGATAAAAATAAAAT
*
9026 AGTAAAATGGTAAAAATAAAAT
1 AGTAAAATGATAAAAATAAAAT
9048 AGT
1 AGT
9051 TATAAGGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 1 0.04
22 22 0.96
ACGTcount: A:0.64, C:0.02, G:0.11, T:0.23
Consensus pattern (22 bp):
AGTAAAATGATAAAAATAAAAT
Found at i:9029 original size:93 final size:93
Alignment explanation
Indices: 8927--9113 Score: 311
Period size: 93 Copynumber: 2.0 Consensus size: 93
8917 ACTTTTTAAT
* * * *
8927 TAAATTAGTAATATTGTAAAAATAAAATAGGTATAAGGATATTTGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
*
8992 AATTTTTAGTTGAGTAAAACTATAAAAA
66 AATTTTTAGTTGACTAAAACTATAAAAA
*
9020 TAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
*
9085 AGTTTTTAGTTGACTAAAACTATAAAAA
66 AATTTTTAGTTGACTAAAACTATAAAAA
9113 T
1 T
9114 TTAAACAATA
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
93 87 1.00
ACGTcount: A:0.52, C:0.02, G:0.12, T:0.34
Consensus pattern (93 bp):
TAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
AATTTTTAGTTGACTAAAACTATAAAAA
Found at i:19297 original size:3 final size:3
Alignment explanation
Indices: 19289--19327 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
19279 AAAACACCAT
19289 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
19328 TTATTATTAT
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):
ATA
Found at i:19549 original size:16 final size:16
Alignment explanation
Indices: 19530--19584 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
19520 AACCCGCCCA
19530 AACCCGAAATTACCCG
1 AACCCGAAATTACCCG
19546 AACCCGAAATTACCCG
1 AACCCGAAATTACCCG
* *
19562 AGCCCGAAAATACCCG
1 AACCCGAAATTACCCG
19578 AACCCGA
1 AACCCGA
19585 GACAGCCCGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.38, C:0.38, G:0.15, T:0.09
Consensus pattern (16 bp):
AACCCGAAATTACCCG
Found at i:19594 original size:32 final size:32
Alignment explanation
Indices: 19530--19600 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
19520 AACCCGCCCA
* *
19530 AACCCGAAATTACCCGAACCCGAAATTACCCG
1 AACCCGAAAATACCCGAACCCGAAATCACCCG
* *
19562 AGCCCGAAAATACCCGAACCCGAGA-CAGCCCG
1 AACCCGAAAATACCCGAACCCGAAATCA-CCCG
19594 AACCCGA
1 AACCCGA
19601 CCCGAGACCG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
31 1 0.03
32 32 0.97
ACGTcount: A:0.37, C:0.39, G:0.17, T:0.07
Consensus pattern (32 bp):
AACCCGAAAATACCCGAACCCGAAATCACCCG
Found at i:19823 original size:2 final size:2
Alignment explanation
Indices: 19816--19850 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
19806 AAACTACTAA
19816 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19851 CTTAAATAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20126 original size:31 final size:31
Alignment explanation
Indices: 20055--20126 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
20045 GTCTATCAGC
*
20055 TTTTAATTTGTTTAATTTAAGACTTTCATTT
1 TTTTAATTTGTTTAATTTAAGACTTTAATTT
*
20086 TAATT-ATTTGTTTAATTTAATG-C-TTAATTT
1 T-TTTAATTTGTTTAATTTAA-GACTTTAATTT
20116 GTTTTAATTTG
1 -TTTTAATTTG
20127 CAATAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 8 0.24
31 23 0.68
32 3 0.09
ACGTcount: A:0.26, C:0.04, G:0.08, T:0.61
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGACTTTAATTT
Found at i:20568 original size:11 final size:11
Alignment explanation
Indices: 20552--20590 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
20542 TCGAAATCAA
20552 ACCCGAACCCG
1 ACCCGAACCCG
20563 ACCCG-ACCCG
1 ACCCGAACCCG
*
20573 AGCCCGAACCCT
1 A-CCCGAACCCG
20585 ACCCGA
1 ACCCGA
20591 GACCGAATCC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
10 6 0.24
11 14 0.56
12 5 0.20
ACGTcount: A:0.26, C:0.54, G:0.18, T:0.03
Consensus pattern (11 bp):
ACCCGAACCCG
Found at i:20588 original size:17 final size:17
Alignment explanation
Indices: 20552--20602 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
20542 TCGAAATCAA
*
20552 ACCCGAACCCG-ACCCG
1 ACCCGAGCCCGAACCCG
*
20568 ACCCGAGCCCGAACCCT
1 ACCCGAGCCCGAACCCG
* *
20585 ACCCGAGACCGAATCCG
1 ACCCGAGCCCGAACCCG
20602 A
1 A
20603 AAATACCCGA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 10 0.34
17 19 0.66
ACGTcount: A:0.27, C:0.49, G:0.20, T:0.04
Consensus pattern (17 bp):
ACCCGAGCCCGAACCCG
Found at i:20626 original size:16 final size:16
Alignment explanation
Indices: 20593--20712 Score: 104
Period size: 16 Copynumber: 7.6 Consensus size: 16
20583 CTACCCGAGA
*
20593 CCGAATCCGAAAATAC
1 CCGAACCCGAAAATAC
*
20609 CCGAACCC-AACATAAC
1 CCGAACCCGAAAAT-AC
*
20625 CCGAGCCCGAAAATAC
1 CCGAACCCGAAAATAC
**
20641 CCGAACCCG-ACTTAAC
1 CCGAACCCGAAAAT-AC
* *
20657 CGGAGCCCGAAAATAC
1 CCGAACCCGAAAATAC
20673 CCGAACCCGAAAA-AGC
1 CCGAACCCGAAAATA-C
* *
20689 CCAAACCCG-AAGTAC
1 CCGAACCCGAAAATAC
20704 CCGAACCCG
1 CCGAACCCG
20713 TCCGAGCCCG
Statistics
Matches: 82, Mismatches: 16, Indels: 13
0.74 0.14 0.12
Matches are distributed among these distances:
15 18 0.22
16 58 0.71
17 6 0.07
ACGTcount: A:0.38, C:0.39, G:0.16, T:0.07
Consensus pattern (16 bp):
CCGAACCCGAAAATAC
Found at i:20681 original size:32 final size:32
Alignment explanation
Indices: 20599--20712 Score: 142
Period size: 32 Copynumber: 3.6 Consensus size: 32
20589 GAGACCGAAT
*
20599 CCGAAAATACCCGAACCCAACATAACCCGAGC
1 CCGAAAATACCCGAACCCGACATAACCCGAGC
* *
20631 CCGAAAATACCCGAACCCGACTTAACCGGAGC
1 CCGAAAATACCCGAACCCGACATAACCCGAGC
* * *
20663 CCGAAAATACCCGAACCCGA-AAAAGCCCAAAC
1 CCGAAAATACCCGAACCCGACATAA-CCCGAGC
*
20695 CCG-AAGTACCCGAACCCG
1 CCGAAAATACCCGAACCCG
20713 TCCGAGCCCG
Statistics
Matches: 72, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
31 16 0.22
32 56 0.78
ACGTcount: A:0.39, C:0.39, G:0.16, T:0.06
Consensus pattern (32 bp):
CCGAAAATACCCGAACCCGACATAACCCGAGC
Found at i:20945 original size:30 final size:30
Alignment explanation
Indices: 20911--20987 Score: 154
Period size: 30 Copynumber: 2.6 Consensus size: 30
20901 TGAGAAAAGC
20911 AAAACATTATTTGATGCTTTAACCCAAAAA
1 AAAACATTATTTGATGCTTTAACCCAAAAA
20941 AAAACATTATTTGATGCTTTAACCCAAAAA
1 AAAACATTATTTGATGCTTTAACCCAAAAA
20971 AAAACATTATTTGATGC
1 AAAACATTATTTGATGC
20988 AATGTAATTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.31
Consensus pattern (30 bp):
AAAACATTATTTGATGCTTTAACCCAAAAA
Done.