Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021953.1 Corchorus olitorius cultivar O-4 contig21986, 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: 25958
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:9630 original size:18 final size:18
Alignment explanation
Indices: 9607--9643 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
9597 AACATCAATA
9607 CAACTAAACCTTTCCAGC
1 CAACTAAACCTTTCCAGC
9625 CAACTAAACCTTTCCAGC
1 CAACTAAACCTTTCCAGC
9643 C
1 C
9644 TTTACAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.41, G:0.05, T:0.22
Consensus pattern (18 bp):
CAACTAAACCTTTCCAGC
Found at i:10334 original size:26 final size:26
Alignment explanation
Indices: 10303--10354 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
10293 ATATTCGTAG
10303 AGTTAATTTACGATCCGATCTTACCA
1 AGTTAATTTACGATCCGATCTTACCA
10329 AGTTAATTTACGATCCGATCTTACCA
1 AGTTAATTTACGATCCGATCTTACCA
10355 TGATTAGTTT
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:0.31, C:0.23, G:0.12, T:0.35
Consensus pattern (26 bp):
AGTTAATTTACGATCCGATCTTACCA
Found at i:11840 original size:22 final size:22
Alignment explanation
Indices: 11815--12617 Score: 234
Period size: 22 Copynumber: 37.0 Consensus size: 22
11805 GATAATTACA
*
11815 CTATGAAATTGTGATAACCTCT
1 CTATGAAATTTTGATAACCTCT
11837 CTATGAAATTTTGATAAACCT-T
1 CTATGAAATTTTGAT-AACCTCT
* *
11859 CCTATAAAATTTTGATAAACCTCC
1 -CTATGAAATTTTGAT-AACCTCT
*
11883 CTATAAAATTTTGATAACCTC-
1 CTATGAAATTTTGATAACCTCT
* *
11904 CTTATGAAATCTTGATAA-CT-A
1 C-TATGAAATTTTGATAACCTCT
*
11925 C-A-G--ATTTTGATAACCTCC
1 CTATGAAATTTTGATAACCTCT
**
11943 CTATGATTTTTTGATAACCTCAT
1 CTATGAAATTTTGATAACCTC-T
* * *
11966 -TATGAAATTTTGTTAATCTCC
1 CTATGAAATTTTGATAACCTCT
* * *
11987 CTATGAAATTTTGATCTACAT-A
1 CTATGAAATTTTGAT-AACCTCT
*
12009 CTATGAAATTTTGAGAACC-CT
1 CTATGAAATTTTGATAACCTCT
* **
12030 CTTATGAAATTTTGA-AAACTAAA
1 C-TATGAAATTTTGATAACCT-CT
12053 CTATGAAATTTTGATATATCCTC-
1 CTATGAAATTTTGATA-A-CCTCT
*
12076 CT-TGAAATTTTGATTA-CTCT
1 CTATGAAATTTTGATAACCTCT
* * * *
12096 ATAATAAAAGTTTAATAACCT-T
1 CT-ATGAAATTTTGATAACCTCT
* * *
12118 C-CT--AA-TTTGGTAACCATAT
1 CTATGAAATTTTGATAACC-TCT
* *
12137 -TATGAAATTTTGCTAACCTCC
1 CTATGAAATTTTGATAACCTCT
* **** **
12158 CCA-GAAATACCAATATGAAAT-T
1 CTATGAAATTTTGATA--ACCTCT
* *** * *
12180 -T-TGGTAA-TCACAT-GCAT-T
1 CTAT-GAAATTTTGATAACCTCT
*
12198 -T-TGAAAATTTGATAACCTCT
1 CTATGAAATTTTGATAACCTCT
* *
12218 TTATGAAATTTTGATAACCTTT
1 CTATGAAATTTTGATAACCTCT
* * *
12240 CTATAAAATTTTGTTGACC-CAT
1 CTATGAAATTTTGATAACCTC-T
* * * *
12262 CTATGAAATTTCGATAATCACA
1 CTATGAAATTTTGATAACCTCT
* *
12284 ATAT-ATAATTTTGATAACCTCG
1 CTATGA-AATTTTGATAACCTCT
* ** *
12306 CTTTGAAATTTTGATAACAACA
1 CTATGAAATTTTGATAACCTCT
*
12328 CTATGAAATTTTGATAATCT-T
1 CTATGAAATTTTGATAACCTCT
*
12349 CCTAT-AAATTTTGATAATCTGATCT
1 -CTATGAAATTTTGATAA-C--CTCT
* * *
12374 CTATGAAATTTCGATAATCACT
1 CTATGAAATTTTGATAACCTCT
* *
12396 CTATTAGA-TTTGATAACCT-T
1 CTATGAAATTTTGATAACCTCT
* *
12416 CTATCAAATTTTGGT-A-CTC-
1 CTATGAAATTTTGATAACCTCT
* *
12435 CTTATGAAATTGAGACTTTTATAAGCT-T
1 C-TATGAAA-T-----TTTGATAACCTCT
* * *
12463 CATGTGAAATTTTGATAACCACA
1 C-TATGAAATTTTGATAACCTCT
** * * *
12486 CTAAAAAATTTTGATTACCACA
1 CTATGAAATTTTGATAACCTCT
*
12508 CTATGAAATTTTGATAACCTCC
1 CTATGAAATTTTGATAACCTCT
*
12530 CTATGAAATATT-AGTAACCTC-
1 CTATGAAATTTTGA-TAACCTCT
* ***
12551 CTTATGAAATTTTGTTAACCAGA
1 C-TATGAAATTTTGATAACCTCT
*
12574 CTATGAAATTCTT-ATAACCTCG
1 CTATGAAATT-TTGATAACCTCT
* * *
12596 CTATCAGATTTTGATAATCTCT
1 CTATGAAATTTTGATAACCTCT
12618 TTGATAACCT
Statistics
Matches: 574, Mismatches: 137, Indels: 140
0.67 0.16 0.16
Matches are distributed among these distances:
16 9 0.02
17 13 0.02
18 13 0.02
19 12 0.02
20 18 0.03
21 56 0.10
22 362 0.63
23 56 0.10
24 6 0.01
25 14 0.02
26 4 0.01
27 2 0.00
28 9 0.02
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.39
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCTCT
Found at i:11992 original size:82 final size:84
Alignment explanation
Indices: 11844--12001 Score: 203
Period size: 82 Copynumber: 1.9 Consensus size: 84
11834 TCTCTATGAA
* * *
11844 ATTTTGATAAACCTTCCTATAAAATTTTGATAAACCTCCCTATAAAATTTTGATAACCTCCTTAT
1 ATTTTGATAAACCTCCCTATAAAATTTTGATAAACCTCACTATAAAATTTTGATAACCTCCCTAT
11909 GAAATCTTGATAACTACAG
66 GAAATCTTGATAACTACAG
* ** * * * *
11928 ATTTTGAT-AACCTCCCTATGATTTTTTGAT-AACCTCATTATGAAATTTTGTTAATCTCCCTAT
1 ATTTTGATAAACCTCCCTATAAAATTTTGATAAACCTCACTATAAAATTTTGATAACCTCCCTAT
*
11991 GAAATTTTGAT
66 GAAATCTTGAT
12002 CTACATACTA
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
82 37 0.59
83 18 0.29
84 8 0.13
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (84 bp):
ATTTTGATAAACCTCCCTATAAAATTTTGATAAACCTCACTATAAAATTTTGATAACCTCCCTAT
GAAATCTTGATAACTACAG
Found at i:12668 original size:22 final size:21
Alignment explanation
Indices: 12643--12850 Score: 101
Period size: 22 Copynumber: 9.4 Consensus size: 21
12633 TAAAATTGTG
*
12643 ATAACCACACTATGAAATTTCA
1 ATAACCAC-CTATGAAATTTTA
** **
12665 ATAATCTTCCTACAAAATTTTA
1 ATAA-CCACCTATGAAATTTTA
*
12687 ATAACCTGATCCTATGAAATTTTG
1 ATAACC--A-CCTATGAAATTTTA
* *
12711 GTAACCACACTATGAAATTTTG
1 ATAACCAC-CTATGAAATTTTA
* * * *
12733 ATAACCTTCCCATGAAGTTTTG
1 ATAACC-ACCTATGAAATTTTA
** *
12755 ATAACTTCCATATGAAATTTTG
1 ATAACCACC-TATGAAATTTTA
* * * *
12777 GTAATCACACTATGGAATTTTG
1 ATAACCAC-CTATGAAATTTTA
* * *
12799 ATAGCCTCCTCATGAAATTATA
1 ATAACCACCT-ATGAAATTTTA
* *
12821 ATAACCATCTTATGAAATTTTG
1 ATAACCA-CCTATGAAATTTTA
12843 ATAACCAC
1 ATAACCAC
12851 ACAGAGACTA
Statistics
Matches: 141, Mismatches: 35, Indels: 21
0.72 0.18 0.11
Matches are distributed among these distances:
21 8 0.06
22 111 0.79
23 6 0.04
24 16 0.11
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.35
Consensus pattern (21 bp):
ATAACCACCTATGAAATTTTA
Found at i:12825 original size:66 final size:66
Alignment explanation
Indices: 12635--12852 Score: 215
Period size: 66 Copynumber: 3.3 Consensus size: 66
12625 CCTTTCTATA
* * ** * * ** * *
12635 AAATTGTGATAACCACACTATGAAATTTCAATAATCTTCCTACAAAATTTTAATAACCTGATCCT
1 AAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAATTATAATAACC--ATCAT
12700 ATG
64 ATG
* * * *
12703 AAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAGTTTTGATAA-CTTCCATA
1 AAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAATTATAATAACCAT-CATA
12767 TG
65 TG
* * * *
12769 AAATTTTGGTAATCACACTATGGAATTTTGATAGCC-TCCTCATGAAATTATAATAACCATCTTA
1 AAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCC-CATGAAATTATAATAACCATCATA
12833 TG
65 TG
*
12835 AAATTTTGATAACCACAC
1 AAATTTTGGTAACCACAC
12853 AGAGACTACA
Statistics
Matches: 125, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
65 4 0.03
66 72 0.58
67 3 0.02
68 46 0.37
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (66 bp):
AAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAATTATAATAACCATCATAT
G
Found at i:14463 original size:21 final size:22
Alignment explanation
Indices: 14420--14476 Score: 80
Period size: 21 Copynumber: 2.6 Consensus size: 22
14410 TATTGCCTTA
*
14420 CAAAAATATATTATTTCTCAGTG
1 CAAAAATA-AATATTTCTCAGTG
14443 CAAAAATAAATATTT-TCAGTG
1 CAAAAATAAATATTTCTCAGTG
*
14464 CAAAAAAAAATAT
1 CAAAAATAAATAT
14477 ATTATTTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 18 0.56
22 6 0.19
23 8 0.25
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.32
Consensus pattern (22 bp):
CAAAAATAAATATTTCTCAGTG
Found at i:14478 original size:23 final size:23
Alignment explanation
Indices: 14421--14479 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 23
14411 ATTGCCTTAC
*
14421 AAAAATATATTATTTCTCAGTGCA
1 AAAAAAATA-TATTTCTCAGTGCA
*
14445 AAAATAA-ATATTT-TCAGTGCAA
1 AAAAAAATATATTTCTCAGTGC-A
14467 AAAAAAATATATT
1 AAAAAAATATATT
14480 ATTTCAAACC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 7 0.23
22 12 0.40
23 6 0.20
24 5 0.17
ACGTcount: A:0.51, C:0.08, G:0.07, T:0.34
Consensus pattern (23 bp):
AAAAAAATATATTTCTCAGTGCA
Found at i:19175 original size:87 final size:86
Alignment explanation
Indices: 18965--19186 Score: 227
Period size: 87 Copynumber: 2.6 Consensus size: 86
18955 GACCACTCTG
* * * * *
18965 ATTTAAATTCAAAATA-TCCTCCACC-ACATCAGTTTCCAAAGATTTTGCAATATTACTAGCCAT
1 ATTTGAATTCAAACTACT-CTCCACCTA-ATCAGTTTCCAAAGATTTTGCAACATAACTACCCAT
19028 AACTCCATTAGGAAGATCACTAA
64 AACTCCATTAGGAAGATCACTAA
* * * *
19051 ATTTTGAATTCAAACTACTCTCTATCATAAT-ATTTTCCAAAGATTTTGCACCATAACTACCCAT
1 A-TTTGAATTCAAACTACTCTCCA-CCTAATCAGTTTCCAAAGATTTTGCAACATAACTACCCAT
*
19115 AACTCCATTAGGAAGATCACATTCA
64 AACTCCATTAGGAAGATCAC--TAA
** * * *
19140 A-TTGAATTCAAACTGTTCTCCACCTTATCAGTTTCCACAGAATTTGC
1 ATTTGAATTCAAACTACTCTCCACCTAATCAGTTTCCAAAGATTTTGC
19187 GCCTAAAAAT
Statistics
Matches: 111, Mismatches: 18, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
86 5 0.05
87 98 0.88
88 4 0.04
89 4 0.04
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.33
Consensus pattern (86 bp):
ATTTGAATTCAAACTACTCTCCACCTAATCAGTTTCCAAAGATTTTGCAACATAACTACCCATAA
CTCCATTAGGAAGATCACTAA
Found at i:23586 original size:38 final size:38
Alignment explanation
Indices: 23491--23599 Score: 116
Period size: 38 Copynumber: 2.9 Consensus size: 38
23481 TGGGCAACAC
*** *
23491 TGTTGGAAATTGCAATCACCCCAAGTTGGGGTGACGTGT
1 TGTTGGAAATTTTGATCACCCCAAGTTAGGGTGA-GTGT
** *
23530 T-TTGG-AATTTTGGCCACCCCATGTTAGGGTG-GTGCT
1 TGTTGGAAATTTTGATCACCCCAAGTTAGGGTGAGTG-T
23566 TGTTGGAAATTTTGATCACCCCAAGTTAGGGTGA
1 TGTTGGAAATTTTGATCACCCCAAGTTAGGGTGA
23600 TGACGATGAA
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
35 3 0.05
36 2 0.04
37 23 0.41
38 27 0.48
39 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.29, T:0.32
Consensus pattern (38 bp):
TGTTGGAAATTTTGATCACCCCAAGTTAGGGTGAGTGT
Done.