Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014967.1 Corchorus olitorius cultivar O-4 contig15000, 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: 21621
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Found at i:4302 original size:9 final size:9
Alignment explanation
Indices: 4288--4313 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
4278 AAATGGTTGC
4288 TTTGTTTTG
1 TTTGTTTTG
4297 TTTGTTTTG
1 TTTGTTTTG
4306 TTTGTTTT
1 TTTGTTTT
4314 AATGCTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (9 bp):
TTTGTTTTG
Found at i:7932 original size:22 final size:21
Alignment explanation
Indices: 7890--7948 Score: 57
Period size: 22 Copynumber: 2.8 Consensus size: 21
7880 AAGAAAAAGA
7890 AAAAGAAAAAAGAAA-ACTTGG
1 AAAA-AAAAAAGAAAGACTTGG
*** *
7911 CCCAAAAAAAGAAAGAGGTTGG
1 AAAAAAAAAAGAAAGA-CTTGG
7933 AAAAAAAAAAGAAAGA
1 AAAAAAAAAAGAAAGA
7949 AAAATAGCAC
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
20 10 0.34
21 2 0.07
22 17 0.59
ACGTcount: A:0.66, C:0.07, G:0.20, T:0.07
Consensus pattern (21 bp):
AAAAAAAAAAGAAAGACTTGG
Found at i:8046 original size:14 final size:13
Alignment explanation
Indices: 8029--8069 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
8019 ATTTTTCCAA
8029 AAAAATGGTTTTTC
1 AAAAATGG-TTTTC
8043 AAAAATGGTTTTC
1 AAAAATGGTTTTC
* *
8056 AAAATTTGTTTTC
1 AAAAATGGTTTTC
8069 A
1 A
8070 CGAGGATGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 17 0.68
14 8 0.32
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (13 bp):
AAAAATGGTTTTC
Found at i:8715 original size:16 final size:17
Alignment explanation
Indices: 8694--8730 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
8684 CAAGTGCACT
8694 AAAAAAA-GAAAAAAGA
1 AAAAAAAGGAAAAAAGA
*
8710 AAAAAAAGGAAAAATGA
1 AAAAAAAGGAAAAAAGA
8727 AAAA
1 AAAA
8731 TGATGAAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.03
Consensus pattern (17 bp):
AAAAAAAGGAAAAAAGA
Found at i:9812 original size:104 final size:104
Alignment explanation
Indices: 9614--9908 Score: 312
Period size: 104 Copynumber: 2.8 Consensus size: 104
9604 CTAAAGATTT
* * * *
9614 ATTTCAG-TTGACCCAGGGCGGTCTTTCTTCAATTCATTTCAGTTGATCCAGGAGGATCTTACCT
1 ATTTCAGATTGATCCAGGGCGATCTTTCTTCAATT-ATTTCAGTTGATCCAGG-GGATCTTTCTT
* * *
9678 CAATCTATATT-AGTTGACCGAGGGCAGTCTTTCTTTAGTTC
64 CAATATAT-TTCAGTTGACCGAGGGCAGTCTTTCTTCAATTC
* * *
9719 ATTTTA-ATTGATCCAGGGCGATCTTTCCTCAATTACTTCAGTTGATCCAGGGTGATCTTTCTTC
1 ATTTCAGATTGATCCAGGGCGATCTTTCTTCAATTATTTCAGTTGATCCAGGG-GATCTTTCTTC
* *
9783 AATATATTTCAGTTGATCC-AGGGCGGTCTTTCTTCAATTT
65 AATATATTTCAGTTGA-CCGAGGGCAGTCTTTCTTCAATTC
** *
9823 ATTTCAGA-TGATCTGGGGCGATCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTC
1 ATTTCAGATTGATCCAGGGCGATC-TTTCTTCA-ATTATTTCAGTTGATCCAGGG-GATC-TTTC
* * *
9887 TGCAGTTTATTTCAGTTGACCG
62 TTCAATATATTTCAGTTGACCG
9909 CAAATGGAGC
Statistics
Matches: 159, Mismatches: 22, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
103 3 0.02
104 72 0.45
105 39 0.25
106 25 0.16
107 20 0.13
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (104 bp):
ATTTCAGATTGATCCAGGGCGATCTTTCTTCAATTATTTCAGTTGATCCAGGGGATCTTTCTTCA
ATATATTTCAGTTGACCGAGGGCAGTCTTTCTTCAATTC
Found at i:9848 original size:139 final size:140
Alignment explanation
Indices: 9616--9907 Score: 335
Period size: 139 Copynumber: 2.1 Consensus size: 140
9606 AAAGATTTAT
*
9616 TTCAGTTGACCCAGGGCGGTCTTTCTTCAATTCATTTCAGTTGATCCAGGAGGATCTTACCTCAA
1 TTCAGTTGACCCAGGGCGATCTTTCTTCAATTCATTTCAGTTGATCCAGGAGGATCTTACCTCAA
* * *
9681 TCTATATTAGTTGACCGAGGGCAGTC-TTTCTTTAGTTCATTTTAATTGATCCAGGGCGATCTTT
66 TCTATATTAGATGACCGAGGGCAGTCTTTTCTTCAGTTCATTTCAATTGATCCAGGGCGATCTTT
9745 CCTCAATTAC
131 CCTCAATTAC
* * * * *
9755 TTCAGTTGATCCAGGGTGATCTTTCTTCAATAT-ATTTCAGTTGATCCAGG-GCGGTCTTTCTTC
1 TTCAGTTGACCCAGGGCGATCTTTCTTCAAT-TCATTTCAGTTGATCCAGGAG-GATCTTACCTC
* * * *
9818 AATTTAT-TTCAGATGATCTG-GGGC-GATCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGA
64 AATCTATATT-AGATGA-CCGAGGGCAG-TCTTTTCTTCAGTTCATTTCAATTGATCCAGGGCGA
* * *
9880 TCTTTTCTGCAGTTTAT
126 TCTTTCCT-CA-ATTAC
9897 TTCAGTTGACC
1 TTCAGTTGACC
9908 GCAAATGGAG
Statistics
Matches: 128, Mismatches: 17, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
138 4 0.03
139 70 0.55
140 39 0.30
141 2 0.02
142 13 0.10
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.40
Consensus pattern (140 bp):
TTCAGTTGACCCAGGGCGATCTTTCTTCAATTCATTTCAGTTGATCCAGGAGGATCTTACCTCAA
TCTATATTAGATGACCGAGGGCAGTCTTTTCTTCAGTTCATTTCAATTGATCCAGGGCGATCTTT
CCTCAATTAC
Found at i:9860 original size:36 final size:35
Alignment explanation
Indices: 9610--9905 Score: 305
Period size: 35 Copynumber: 8.4 Consensus size: 35
9600 GTTGCTAAAG
* *
9610 ATTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCA
1 ATTTATTTCAGTTGATCCAGGGCGATCTTTCTTCA
* * *
9645 ATTCATTTCAGTTGATCCAGGAG-GATCTTACCTCA
1 ATTTATTTCAGTTGATCCAGG-GCGATCTTTCTTCA
* *
9680 ATCTATATT-AGTTGA-CCGAGGGC-AGTCTTTCTTTA
1 ATTTAT-TTCAGTTGATCC-AGGGCGA-TCTTTCTTCA
* * * * *
9715 GTTCATTTTAATTGATCCAGGGCGATCTTTCCTCA
1 ATTTATTTCAGTTGATCCAGGGCGATCTTTCTTCA
* *
9750 A-TTACTTCAGTTGATCCAGGGTGATCTTTCTTCA
1 ATTTATTTCAGTTGATCCAGGGCGATCTTTCTTCA
* *
9784 ATATATTTCAGTTGATCCAGGGCGGTCTTTCTTCA
1 ATTTATTTCAGTTGATCCAGGGCGATCTTTCTTCA
* **
9819 ATTTATTTCAGATGATCTGGGGCGATCTTTTCTTCA
1 ATTTATTTCAGTTGATCCAGGGCGATC-TTTCTTCA
* *
9855 GTTTATTTCAGTTGATCCAGGGCGATCTTTTCTGCA
1 ATTTATTTCAGTTGATCCAGGGCGATC-TTTCTTCA
*
9891 GTTTATTTCAGTTGA
1 ATTTATTTCAGTTGA
9906 CCGCAAATGG
Statistics
Matches: 214, Mismatches: 37, Indels: 19
0.79 0.14 0.07
Matches are distributed among these distances:
34 34 0.16
35 120 0.56
36 60 0.28
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.41
Consensus pattern (35 bp):
ATTTATTTCAGTTGATCCAGGGCGATCTTTCTTCA
Found at i:10152 original size:69 final size:69
Alignment explanation
Indices: 10059--10305 Score: 431
Period size: 69 Copynumber: 3.6 Consensus size: 69
10049 CCGGATGCTT
* *
10059 TAGGCTTTTCCAGAAGCCAAACTCGTTTCCATATGAGTCAGTTTAAGCCTTGGTTCCATCCAAGC
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGC
10124 CACA
66 CACA
* *
10128 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGACTTGGATCCATCCAAGC
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGC
10193 CACA
66 CACA
*
10197 TAGGCTTTTCCACAAGCCAAACTCGTTTACATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGC
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGC
*
10262 CATA
66 CACA
*
10266 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATATGAGTCA
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCA
10306 AGCCTTACTT
Statistics
Matches: 168, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 168 1.00
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (69 bp):
TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGC
CACA
Found at i:10765 original size:30 final size:30
Alignment explanation
Indices: 10726--11383 Score: 1070
Period size: 30 Copynumber: 22.0 Consensus size: 30
10716 TGGCAATTTA
* *
10726 ATTTAAATCCTGGTTTAGGATCATTGCTTT
1 ATTTTAATCCTGGTTGAGGATCATTGCTTT
*
10756 ATTTTAATCCTGGTTGAGGATAATTGCTTT
1 ATTTTAATCCTGGTTGAGGATCATTGCTTT
* *
10786 ATTTTAATCCAGGTTGAGGATCATTGCTTC
1 ATTTTAATCCTGGTTGAGGATCATTGCTTT
*
10816 ATTTTAATCCTGGTTGAGGATCATTGCTTC
1 ATTTTAATCCTGGTTGAGGATCATTGCTTT
*
10846 A-TTTAATCCTGGTTGAGGATCATTGCTTC
1 ATTTTAATCCTGGTTGAGGATCATTGCTTT
*
10875 ATTTTAATCCTAGTTGAGGATCATTGCTTT
1 ATTTTAATCCTGGTTGAGGATCATTGCTTT
*
10905 ATTTTAATCCTGGTTGAGGATCATTGCTTC
1 ATTTTAATCCTGGTTGAGGATCATTGCTTT
10935 ATTTTAATCCTGGTTGAGGATCATTGCTTT
1 ATTTTAATCCTGGTTGAGGATCATTGCTTT
10965 ATTTTAATCCTGGTTGAGGATCATTGCTTT
1 ATTTTAATCCTGGTTGAGGATCATTGCTTT
*
10995 ATTTTAATCCTGGTTGAGGGTCATTGCTTT
1 ATTTTAATCCTGGTTGAGGATCATTGCTTT
*
11025 ATTTTAATCCTGGGTGAGGATCATTGCTTT
1 ATTTTAATCCTGGTTGAGGATCATTGCTTT
*
11055 ATTTTAATCCTGGTTGAGGATCATTGCTTC
1 ATTTTAATCCTGGTTGAGGATCATTGCTTT
*
11085 ATTTTAATCCTAGTTGAGGATCATTGCTTT
1 ATTTTAATCCTGGTTGAGGATCATTGCTTT
* *
11115 A-TTTAATCCTGTTTGAGGATCATTGCTTC
1 ATTTTAATCCTGGTTGAGGATCATTGCTTT
*
11144 ATTTTAATCCTGTTTGAGGATCATTGCTTT
1 ATTTTAATCCTGGTTGAGGATCATTGCTTT
11174 AGTTTTAATCCTGGTTGAGGATCATTGCTTT
1 A-TTTTAATCCTGGTTGAGGATCATTGCTTT
*
11205 ATTTTAATCCTGGTTGAGGGTCATTGCTTT
1 ATTTTAATCCTGGTTGAGGATCATTGCTTT
*
11235 ATTTTAATCCTGGGTGAGGATCATTGCTTT
1 ATTTTAATCCTGGTTGAGGATCATTGCTTT
*
11265 ATTTTAATCCTGGTTGAGGATCATTGCTTC
1 ATTTTAATCCTGGTTGAGGATCATTGCTTT
*
11295 ATTTTAATCCTGGTTGAGGATCATTGCTTC
1 ATTTTAATCCTGGTTGAGGATCATTGCTTT
*
11325 ATTTTAATCCTGGTCT-AAGATCATTGCTTT
1 ATTTTAATCCTGGT-TGAGGATCATTGCTTT
* *
11355 ATTTTAATCCTGATTTAGGATCATTGCTT
1 ATTTTAATCCTGGTTGAGGATCATTGCTT
11384 ATTAGTTAAT
Statistics
Matches: 590, Mismatches: 33, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
29 56 0.09
30 504 0.85
31 30 0.05
ACGTcount: A:0.21, C:0.15, G:0.19, T:0.45
Consensus pattern (30 bp):
ATTTTAATCCTGGTTGAGGATCATTGCTTT
Done.