Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012123.1 Corchorus olitorius cultivar O-4 contig12156, 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: 63658
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Found at i:2260 original size:3 final size:3
Alignment explanation
Indices: 2252--2337 Score: 172
Period size: 3 Copynumber: 28.7 Consensus size: 3
2242 ATTTATTTAT
2252 ATA ATA ATA 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 ATA ATA ATA
2300 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2338 TTATAGTTAT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 83 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:7597 original size:13 final size:13
Alignment explanation
Indices: 7577--7614 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
7567 GCGTTTTGCT
7577 ACTTGACCCTCCA
1 ACTTGACCCTCCA
*
7590 ATTTGACCCTCCA
1 ACTTGACCCTCCA
7603 ACTTGACCCTCC
1 ACTTGACCCTCC
7615 TAACGTGTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.21, C:0.45, G:0.08, T:0.26
Consensus pattern (13 bp):
ACTTGACCCTCCA
Found at i:11497 original size:13 final size:13
Alignment explanation
Indices: 11479--11523 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
11469 TTTCCTTCCC
11479 TTTTATTTTTTAT
1 TTTTATTTTTTAT
11492 TTTTATTTTTTAT
1 TTTTATTTTTTAT
*
11505 ATTTATTATTATTAT
1 TTTTATT-TT-TTAT
11520 TTTT
1 TTTT
11524 TTCCTTTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 19 0.68
14 2 0.07
15 7 0.25
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTATTTTTTAT
Found at i:11754 original size:17 final size:16
Alignment explanation
Indices: 11732--11765 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
11722 CTTCACCCTC
11732 TTTTTTT-TTCTTTTCT
1 TTTTTTTCTTC-TTTCT
11748 TTTTTTTCTTCTTTCT
1 TTTTTTTCTTCTTTCT
11764 TT
1 TT
11766 CTCCTCCCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTTTTTCTTCTTTCT
Found at i:18832 original size:19 final size:19
Alignment explanation
Indices: 18807--18855 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
18797 CTGCATCTCA
18807 CACACACATATGAATATTC
1 CACACACATATGAATATTC
* *
18826 TACACACATACGAATATTC
1 CACACACATATGAATATTC
18845 CACACACATAT
1 CACACACATAT
18856 TCACATATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.43, C:0.29, G:0.04, T:0.24
Consensus pattern (19 bp):
CACACACATATGAATATTC
Found at i:18860 original size:27 final size:27
Alignment explanation
Indices: 18830--18881 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
18820 ATATTCTACA
18830 CACATACGAATATTCCACACACATATT
1 CACATACGAATATTCCACACACATATT
* *
18857 CACATATGAATATTCTACACACATA
1 CACATACGAATATTCCACACACATA
18882 CGAATATTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.42, C:0.27, G:0.04, T:0.27
Consensus pattern (27 bp):
CACATACGAATATTCCACACACATATT
Found at i:18868 original size:46 final size:46
Alignment explanation
Indices: 18811--18929 Score: 229
Period size: 46 Copynumber: 2.6 Consensus size: 46
18801 ATCTCACACA
18811 CACATATGAATATTCTACACACATACGAATATTCCACACACATATT
1 CACATATGAATATTCTACACACATACGAATATTCCACACACATATT
*
18857 CACATATGAATATTCTACACACATACGAATATTTCACACACATATT
1 CACATATGAATATTCTACACACATACGAATATTCCACACACATATT
18903 CACATATGAATATTCTACACACATACG
1 CACATATGAATATTCTACACACATACG
18930 GAGTACTCCA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
46 72 1.00
ACGTcount: A:0.41, C:0.25, G:0.05, T:0.29
Consensus pattern (46 bp):
CACATATGAATATTCTACACACATACGAATATTCCACACACATATT
Found at i:18881 original size:19 final size:19
Alignment explanation
Indices: 18857--18901 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
18847 CACACATATT
18857 CACATATGAATA-TTCTACA
1 CACATATGAATATTTC-ACA
*
18876 CACATACGAATATTTCACA
1 CACATATGAATATTTCACA
18895 CACATAT
1 CACATAT
18902 TCACATATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 20 0.87
20 3 0.13
ACGTcount: A:0.42, C:0.24, G:0.04, T:0.29
Consensus pattern (19 bp):
CACATATGAATATTTCACA
Found at i:18906 original size:27 final size:27
Alignment explanation
Indices: 18876--18927 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
18866 ATATTCTACA
18876 CACATACGAATATT-TCACACACATATT
1 CACATACGAATATTCT-ACACACATATT
*
18903 CACATATGAATATTCTACACACATA
1 CACATACGAATATTCTACACACATA
18928 CGGAGTACTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.42, C:0.25, G:0.04, T:0.29
Consensus pattern (27 bp):
CACATACGAATATTCTACACACATATT
Found at i:22374 original size:19 final size:20
Alignment explanation
Indices: 22327--22384 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
22317 GAAGAGAAAG
* *
22327 AAGATGAAAGAGAAGAAATAAA
1 AAGAAGAAAGAAAAG-AAT-AA
22349 AAGAAG-AAGAAACAGAATAA
1 AAGAAGAAAGAAA-AGAATAA
22369 AA-AAGAAAGAAAAGAA
1 AAGAAGAAAGAAAAGAA
22385 ACAGAATGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
19 7 0.22
20 10 0.31
21 8 0.25
22 7 0.22
ACGTcount: A:0.72, C:0.02, G:0.21, T:0.05
Consensus pattern (20 bp):
AAGAAGAAAGAAAAGAATAA
Found at i:22391 original size:25 final size:26
Alignment explanation
Indices: 22321--22391 Score: 92
Period size: 25 Copynumber: 2.8 Consensus size: 26
22311 AAGACTGAAG
* * * *
22321 AGAAAGAAGATGAAAGAGAAGAAATA
1 AGAAAGAAGAAGAAACAGAATAAAAA
22347 A-AAAGAAGAAGAAACAGAATAAAAA
1 AGAAAGAAGAAGAAACAGAATAAAAA
22372 AGAAAGAA-AAGAAACAGAAT
1 AGAAAGAAGAAGAAACAGAAT
22392 GGGCAAAAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
25 33 0.82
26 7 0.17
ACGTcount: A:0.70, C:0.03, G:0.21, T:0.06
Consensus pattern (26 bp):
AGAAAGAAGAAGAAACAGAATAAAAA
Found at i:25270 original size:1 final size:1
Alignment explanation
Indices: 25266--25294 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
25256 AGGGATTCGC
25266 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
25295 CCTAGCCCCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:28646 original size:19 final size:19
Alignment explanation
Indices: 28622--28658 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
28612 CTGTTTAGCA
28622 ACTGTACAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
*
28641 ACTGTACAGATTAGATTA
1 ACTGTACAGATGAGATTA
28659 GGTACTGTAT
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:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:28848 original size:2 final size:2
Alignment explanation
Indices: 28843--28891 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
28833 ACTACTACTA
28843 AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28882 AT AT AT AT AT
1 AT AT AT AT AT
28892 TAATTAAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 3 0.07
2 41 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:29068 original size:18 final size:19
Alignment explanation
Indices: 29047--29084 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
29037 TTTTCCTTCC
*
29047 CTGAAAC-TTTTCTTCTTT
1 CTGAAACATTTTCTGCTTT
*
29065 CTGAATCATTTTCTGCTTT
1 CTGAAACATTTTCTGCTTT
29084 C
1 C
29085 CTGTTTTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.16, C:0.24, G:0.08, T:0.53
Consensus pattern (19 bp):
CTGAAACATTTTCTGCTTT
Found at i:36514 original size:53 final size:54
Alignment explanation
Indices: 36437--36540 Score: 201
Period size: 53 Copynumber: 1.9 Consensus size: 54
36427 ACAACGAACT
36437 TTAATTGCATATAATTTGTAATAGAAAATAAAAAAAT-TATACTCCATATATAA
1 TTAATTGCATATAATTTGTAATAGAAAATAAAAAAATATATACTCCATATATAA
36490 TTAATTGCATATAATTTGTAATAGAAAATAAAAAAATATATACTCCATATA
1 TTAATTGCATATAATTTGTAATAGAAAATAAAAAAATATATACTCCATATA
36541 ATTAATCCAA
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
53 37 0.74
54 13 0.26
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.36
Consensus pattern (54 bp):
TTAATTGCATATAATTTGTAATAGAAAATAAAAAAATATATACTCCATATATAA
Found at i:38490 original size:69 final size:68
Alignment explanation
Indices: 38379--38518 Score: 192
Period size: 69 Copynumber: 2.0 Consensus size: 68
38369 AGACTTGAAA
** * * * *
38379 TGCATTGTCTTTATATGTAATTTTAGTATTTGGATGTAATTAATGGTGTTCCTATAATTTTTTCC
1 TGCATTGTCTTTATATGTAATTTTACCATTTGGATGTAATTAAT-GAGATCCCACAATTTTTTCC
38444 TTAG
65 TTAG
*
38448 TGCATTGTCTTTATATGTAATTTTACCA-TTGAGATGTAATTAATGAGATCCCACCATTTTTTCC
1 TGCATTGTCTTTATATGTAATTTTACCATTTG-GATGTAATTAATGAGATCCCACAATTTTTTCC
38512 TTAG
65 TTAG
38516 TGC
1 TGC
38519 TTAGTTTTGG
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
68 25 0.40
69 38 0.60
ACGTcount: A:0.24, C:0.13, G:0.15, T:0.48
Consensus pattern (68 bp):
TGCATTGTCTTTATATGTAATTTTACCATTTGGATGTAATTAATGAGATCCCACAATTTTTTCCT
TAG
Found at i:43506 original size:2 final size:2
Alignment explanation
Indices: 43501--43541 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
43491 TCGAATATAT
43501 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
43542 TTAAACCCAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:46238 original size:43 final size:41
Alignment explanation
Indices: 46175--46261 Score: 120
Period size: 41 Copynumber: 2.1 Consensus size: 41
46165 CCTGTATATA
* ** *
46175 ATTTATTTTGGTTGGGGAGTCTTTAAGTAATTTGATTTTACGT
1 ATTTATCTTGGTTGAAGAGTC-TT-AGTAATTTGATTTTACAT
46218 ATTTATCTTGGTTGAAGAGTCTTAGTAATTTGATTTTACAT
1 ATTTATCTTGGTTGAAGAGTCTTAGTAATTTGATTTTACAT
46259 ATT
1 ATT
46262 CCTGCTACAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 20 0.50
42 2 0.05
43 18 0.45
ACGTcount: A:0.24, C:0.06, G:0.20, T:0.51
Consensus pattern (41 bp):
ATTTATCTTGGTTGAAGAGTCTTAGTAATTTGATTTTACAT
Found at i:46561 original size:22 final size:22
Alignment explanation
Indices: 46520--46562 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
46510 TAACAAGCCA
*
46520 AAAAATAAATTAGGAGAAAATT
1 AAAAATAAATTAGCAGAAAATT
46542 AAAAATAATATTAGCA-AAAAT
1 AAAAATAA-ATTAGCAGAAAAT
46563 CAAACCTGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.65, C:0.02, G:0.09, T:0.23
Consensus pattern (22 bp):
AAAAATAAATTAGCAGAAAATT
Found at i:60750 original size:2 final size:2
Alignment explanation
Indices: 60743--60810 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
60733 AACAAGTTAT
60743 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
60785 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
60811 TTGTGAGGAA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Done.