Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024776.1 Corchorus olitorius cultivar O-4 contig24809, 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: 7968
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Found at i:1253 original size:15 final size:14
Alignment explanation
Indices: 1228--1257 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1218 CTTTTAAATT
1228 ATTCTGAAAAAAAA
1 ATTCTGAAAAAAAA
1242 ATTCTAGAAAAAAAA
1 ATTCT-GAAAAAAAA
1257 A
1 A
1258 AAAACAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.20
Consensus pattern (14 bp):
ATTCTGAAAAAAAA
Found at i:3639 original size:20 final size:22
Alignment explanation
Indices: 3614--3725 Score: 65
Period size: 22 Copynumber: 5.2 Consensus size: 22
3604 GAATTTCGAG
3614 AACCTT-TTAT-AAATATTT-TT
1 AACCTTCTTATGAAAT-TTTGTT
3634 AACCTTCTTATGAAATTTTGTT
1 AACCTTCTTATGAAATTTTGTT
* * * * *
3656 AACCTCCCTAAGGAATTTTG-A
1 AACCTTCTTATGAAATTTTGTT
*
3677 AGACC-TCATTATGAAATTTTGAT
1 A-ACCTTC-TTATGAAATTTTGTT
** *
3700 AA-CTTCCCAATGAAATTTTGAT
1 AACCTT-CTTATGAAATTTTGTT
3722 AACC
1 AACC
3726 AACACTATGA
Statistics
Matches: 71, Mismatches: 12, Indels: 15
0.72 0.12 0.15
Matches are distributed among these distances:
20 6 0.08
21 10 0.14
22 52 0.73
23 3 0.04
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (22 bp):
AACCTTCTTATGAAATTTTGTT
Found at i:3744 original size:45 final size:45
Alignment explanation
Indices: 3686--3771 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
3676 AAGACCTCAT
* * *
3686 TATGAAATTTTGATAACTTCCCA-ATGAAATTTTGATAACCAACAC
1 TATGAAATGTTGATAACCT-CCATATGAAATATTGATAACCAACAC
* *
3731 TATGAGATGTTGATAACCTCCATATGATATATTGATAACCA
1 TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCA
3772 TGTTATGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 3 0.09
45 32 0.91
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (45 bp):
TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCAACAC
Found at i:3765 original size:22 final size:22
Alignment explanation
Indices: 3633--3802 Score: 105
Period size: 22 Copynumber: 7.7 Consensus size: 22
3623 TAAATATTTT
* * *
3633 TAACCTTCTTATGAAATTTTGT
1 TAACCTCCATATGAAATTTTGA
* * *
3655 TAACCTCCCTAAGGAATTTTGA
1 TAACCTCCATATGAAATTTTGA
3677 -AGACCT-CATTATGAAATTTTGA
1 TA-ACCTCCA-TATGAAATTTTGA
*
3699 TAACTTCCCA-ATGAAATTTTGA
1 TAACCT-CCATATGAAATTTTGA
** * *
3721 TAACCAACACTATGAGATGTTGA
1 TAACCTCCA-TATGAAATTTTGA
* *
3744 TAACCTCCATATGATATATTGA
1 TAACCTCCATATGAAATTTTGA
** * *
3766 TAACCAT-GTTATGAAAATTTAA
1 TAACC-TCCATATGAAATTTTGA
*
3788 AAACCTCCATATGAA
1 TAACCTCCATATGAA
3803 TTGTTAGTAA
Statistics
Matches: 112, Mismatches: 27, Indels: 18
0.71 0.17 0.11
Matches are distributed among these distances:
21 5 0.04
22 86 0.77
23 19 0.17
24 2 0.02
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (22 bp):
TAACCTCCATATGAAATTTTGA
Found at i:3921 original size:22 final size:22
Alignment explanation
Indices: 3843--4647 Score: 227
Period size: 22 Copynumber: 36.3 Consensus size: 22
3833 AATCACACTA
*
3843 TGATAACCTCGCTATGAAATTT
1 TGATAACCTCCCTATGAAATTT
* *
3865 TGATAAACCTTCCTATAAAATTT
1 TGAT-AACCTCCCTATGAAATTT
*
3888 TGATAAACCTCCCTATAAAATTT
1 TGAT-AACCTCCCTATGAAATTT
* *
3911 TGATAACCTCCTTATGAAATCT
1 TGATAACCTCCCTATGAAATTT
*
3933 TGATAA-----CTA-CAAATTT
1 TGATAACCTCCCTATGAAATTT
**
3949 TGATAACCTCCCTATGATTTTT
1 TGATAACCTCCCTATGAAATTT
**
3971 TGATAACCTCATTATGAAATTT
1 TGATAACCTCCCTATGAAATTT
* *
3993 TGTTAATCTCCCTATGAAATTT
1 TGATAACCTCCCTATGAAATTT
* * *
4015 TGATCTACAT-ACTATGAAATTT
1 TGAT-AACCTCCCTATGAAATTT
* *
4037 TGATAACC-CTCTTATGAAAATT
1 TGATAACCTC-CCTATGAAATTT
* **
4059 TGA-AAACTAAACTATGAAATTT
1 TGATAACCT-CCCTATGAAATTT
* *
4081 TGATAACCTTCATATGAAATTT
1 TGATAACCTCCCTATGAAATTT
*
4103 TGATATCCTCGCTCCT-TGAAATTT
1 TGATAACCT--C-CCTATGAAATTT
* ** * *
4127 TGATTA-CTCTATAATAAAAGTT
1 TGATAACCTCCCT-ATGAAATTT
* **
4149 TAATAACCT---T-TCTAA-TT
1 TGATAACCTCCCTATGAAATTT
* *
4166 TGGTAACCAT-ACTATGAAATTT
1 TGATAACC-TCCCTATGAAATTT
* *
4188 TGATAACCTCCCCA-GAAATACCACTA
1 TGATAACCTCCCTATGAAAT-----TT
** ***
4214 TGA-AATTTTGGTAAT-AACATTT
1 TGATAACCTCCCT-ATGAA-ATTT
* **
4236 TGAAAATTTGATAACTCTTTATGAAATTT
1 TG---A--T-A-ACCTCCCTATGAAATTT
* *
4265 TGATAACCTCTCTATAAAATTT
1 TGATAACCTCCCTATGAAATTT
* * *
4287 TGTTGACC-CTTCTATGAAATTTT
1 TGATAACCTC-CCTATGAAA-TTT
* * ** *
4310 TGATAATCACATTATGTAATTT
1 TGATAACCTCCCTATGAAATTT
* *
4332 TGATAACCTCGCTTTGAAATTT
1 TGATAACCTCCCTATGAAATTT
** * *
4354 TGATAACAACACTATGGAATTT
1 TGATAACCTCCCTATGAAATTT
* ** *
4376 TAATAATTTTCCTAT-AAATTT
1 TGATAACCTCCCTATGAAATTT
*
4397 TGATAATCCGATCTCTATGAAATTT
1 TGATAA-CC--TCCCTATGAAATTT
* * *
4422 CGATAA--TCACTGCATGAGA-TT
1 TGATAACCTCCCT--ATGAAATTT
* *
4443 TGATAACCT-TCTATCAAATTT
1 TGATAACCTCCCTATGAAATTT
*
4464 TGAT-A-CTCCTTATGAAATTGAGACTT
1 TGATAACCTCCCTATGAAA-T-----TT
* * * *
4490 TTATAATCTTCATATGAAATTT
1 TGATAACCTCCCTATGAAATTT
* * *
4512 TGATAACCACACTA-AAAATTTT
1 TGATAACCTCCCTATGAAA-TTT
* * *
4534 TAATAACCACAC--TGAAATTT
1 TGATAACCTCCCTATGAAATTT
*
4554 TGATAACCTCCCCATGAAATATT
1 TGATAACCTCCCTATGAAAT-TT
*
4577 TG-TAACCTCCTTATGAAATTT
1 TGATAACCTCCCTATGAAATTT
* * *
4598 TGTTAACCACACTATGAAATTCT
1 TGATAACCTCCCTATGAAATT-T
* *
4621 T-ATAACCTCGCTATGACATTT
1 TGATAACCTCCCTATGAAATTT
4642 TGATAA
1 TGATAA
4648 TCTCTTTGAT
Statistics
Matches: 570, Mismatches: 142, Indels: 142
0.67 0.17 0.17
Matches are distributed among these distances:
16 11 0.02
17 10 0.02
18 4 0.01
19 2 0.00
20 30 0.05
21 55 0.10
22 308 0.54
23 73 0.13
24 19 0.03
25 17 0.03
26 13 0.02
27 4 0.01
28 10 0.02
29 9 0.02
30 5 0.01
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (22 bp):
TGATAACCTCCCTATGAAATTT
Found at i:4264 original size:20 final size:21
Alignment explanation
Indices: 4238--4286 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
4228 TAACATTTTG
*
4238 AAAATTTGATAA-CTCTTTAT
1 AAAATTTGATAACCTCTCTAT
*
4258 GAAATTTTGATAACCTCTCTAT
1 -AAAATTTGATAACCTCTCTAT
4280 AAAATTT
1 AAAATTT
4287 TGTTGACCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.43
Consensus pattern (21 bp):
AAAATTTGATAACCTCTCTAT
Found at i:4369 original size:67 final size:66
Alignment explanation
Indices: 4211--4376 Score: 156
Period size: 67 Copynumber: 2.5 Consensus size: 66
4201 AGAAATACCA
* * * * * * *
4211 CTATGAAATTTTGGTAATAACATTTTGAAA-ATTTGATAACTCTTTATGAAATTTTGATAACCTC
1 CTATGAAATTTTGATAACAACACTATGAAATTTTTGATAACACATTATGAAATTTTGATAACCTC
*
4275 T
66 G
* * * * * *
4276 CTATAAAATTTTGTTGAC-CCTTCTATGAAATTTTTGATAATCACATTATGTAATTTTGATAACC
1 CTATGAAATTTTGATAACAAC-ACTATGAAATTTTTGATAA-CACATTATGAAATTTTGATAACC
4340 TCG
64 TCG
* *
4343 CTTTGAAATTTTGATAACAACACTATGGAATTTT
1 CTATGAAATTTTGATAACAACACTATGAAATTTT
4377 AATAATTTTC
Statistics
Matches: 77, Mismatches: 20, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
64 1 0.01
65 20 0.26
66 8 0.10
67 47 0.61
68 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.43
Consensus pattern (66 bp):
CTATGAAATTTTGATAACAACACTATGAAATTTTTGATAACACATTATGAAATTTTGATAACCTC
G
Found at i:4741 original size:46 final size:44
Alignment explanation
Indices: 4686--4786 Score: 114
Period size: 46 Copynumber: 2.2 Consensus size: 44
4676 GATAACCACA
4686 CTATGAAATTTCAATAACCTTCAT-AAGAAATTTTAATAACTTGATC
1 CTATGAAATTTCAATAACCTTC-TCAAGAAATTTTAATAACTT--TC
** * * *
4732 CTATGAAATTTTGATAGCCTTCTCATGAAATTTTGATAACTTTC
1 CTATGAAATTTCAATAACCTTCTCAAGAAATTTTAATAACTTTC
*
4776 ATATGAAATTT
1 CTATGAAATTT
4787 TGGTAACCAC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
44 12 0.25
45 1 0.02
46 35 0.73
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.41
Consensus pattern (44 bp):
CTATGAAATTTCAATAACCTTCTCAAGAAATTTTAATAACTTTC
Found at i:4837 original size:66 final size:66
Alignment explanation
Indices: 4738--4864 Score: 182
Period size: 66 Copynumber: 1.9 Consensus size: 66
4728 GATCCTATGA
* * * * ** *
4738 AATTTTGATAGCCTTCTCATGAAATTTTGATAACTTTCATATGAAATTTTGGTAACCACACTAAG
1 AATTTTGATAACCTCCTCATGAAATTATAATAACCATCATATGAAATTTTGATAACCACACTAAG
4803 C
66 C
*
4804 AATTTTGATAACCTCCTCATGAAATTATAATAACCATCTTATGAAATTTTGATAACCACAC
1 AATTTTGATAACCTCCTCATGAAATTATAATAACCATCATATGAAATTTTGATAACCACAC
4865 AGAGACAAGA
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
66 53 1.00
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (66 bp):
AATTTTGATAACCTCCTCATGAAATTATAATAACCATCATATGAAATTTTGATAACCACACTAAG
C
Found at i:4861 original size:22 final size:22
Alignment explanation
Indices: 4664--4861 Score: 134
Period size: 22 Copynumber: 8.9 Consensus size: 22
4654 TGATAATTGT
* *
4664 CTATAAAATTGTGATAACCA-C
1 CTATGAAATTTTGATAACCATC
** *
4685 ACTATGAAATTTCAATAACCTTC
1 -CTATGAAATTTTGATAACCATC
* * * *
4708 ATAAGAAATTTTAATAACTTGATC
1 CTATGAAATTTTGATAAC--CATC
* *
4732 CTATGAAATTTTGATAGCC-TT
1 CTATGAAATTTTGATAACCATC
**
4753 CTCATGAAATTTTGATAACTTTC
1 CT-ATGAAATTTTGATAACCATC
* *
4776 ATATGAAATTTTGGTAACCA-C
1 CTATGAAATTTTGATAACCATC
* *
4797 ACTAAGCAATTTTGATAACC-TC
1 -CTATGAAATTTTGATAACCATC
* *
4819 CTCATGAAATTATAATAACCATC
1 CT-ATGAAATTTTGATAACCATC
*
4842 TTATGAAATTTTGATAACCA
1 CTATGAAATTTTGATAACCA
4862 CACAGAGACA
Statistics
Matches: 133, Mismatches: 34, Indels: 18
0.72 0.18 0.10
Matches are distributed among these distances:
21 6 0.05
22 105 0.79
23 6 0.05
24 16 0.12
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCATC
Found at i:6562 original size:17 final size:17
Alignment explanation
Indices: 6540--6589 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
6530 AATTTTTTCA
* *
6540 ATTTTTTTAAAGAAATT
1 ATTTTTTTAAAAAAAAT
*
6557 ATTTTTTGAAAAAAAAT
1 ATTTTTTTAAAAAAAAT
*
6574 ATTGTTTTAAAAAAAA
1 ATTTTTTTAAAAAAAA
6590 GTGACGTTGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
ATTTTTTTAAAAAAAAT
Found at i:6991 original size:3 final size:3
Alignment explanation
Indices: 6985--7017 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
6975 ATTATTATTA
6985 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
7018 GATTGTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Done.