Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020089.1 Corchorus olitorius cultivar O-4 contig20122, 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: 22518
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:6224 original size:20 final size:20
Alignment explanation
Indices: 6199--6265 Score: 71
Period size: 22 Copynumber: 3.1 Consensus size: 20
6189 TTTTATGAAA
6199 TTTGATAAACACTATAAAAT
1 TTTGATAAACACTATAAAAT
* *
6219 TTTGATAATCTCCATATAAAAT
1 TTTGATAAAC-AC-TATAAAAT
*
6241 TTTGATAATTACACTATAAAGT
1 TTTGATAA--ACACTATAAAAT
6263 TTT
1 TTT
6266 TATGACGATA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 9 0.24
21 1 0.03
22 26 0.68
23 1 0.03
24 1 0.03
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (20 bp):
TTTGATAAACACTATAAAAT
Found at i:6239 original size:22 final size:22
Alignment explanation
Indices: 6211--6332 Score: 90
Period size: 22 Copynumber: 5.5 Consensus size: 22
6201 TGATAAACAC
6211 TATAAAATTTTGATAATCTCCA
1 TATAAAATTTTGATAATCTCCA
*
6233 TATAAAATTTTGATAAT-TACA
1 TATAAAATTTTGATAATCTCCA
* * * *
6254 CTATAAAGTTTTTATGA-CGATAC-
1 -TATAAAATTTTGATAATC--TCCA
* *
6277 TATAAAATTTCGAGAATCTCCA
1 TATAAAATTTTGATAATCTCCA
* * *
6299 TATGAAATTTTGTTAA-CTTCCC
1 TATAAAATTTTGATAATC-TCCA
6321 TATAAAATTTTG
1 TATAAAATTTTG
6333 TTACACTCCG
Statistics
Matches: 77, Mismatches: 16, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
21 6 0.08
22 67 0.87
23 1 0.01
24 3 0.04
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (22 bp):
TATAAAATTTTGATAATCTCCA
Found at i:6410 original size:22 final size:22
Alignment explanation
Indices: 6355--6424 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 22
6345 TCCCTAATAA
*
6355 AAATTTTAACAACCACCTAATG
1 AAATTTTAATAACCACCTAATG
* * *
6377 AAATTTTGATAACTACCTTATG
1 AAATTTTAATAACCACCTAATG
* * *
6399 AAATTTTAATAAACTCCCAATG
1 AAATTTTAATAACCACCTAATG
6421 AAAT
1 AAAT
6425 GTTGGTAAGC
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (22 bp):
AAATTTTAATAACCACCTAATG
Found at i:6421 original size:44 final size:43
Alignment explanation
Indices: 6374--6652 Score: 151
Period size: 44 Copynumber: 6.4 Consensus size: 43
6364 CAACCACCTA
*
6374 ATGAAATTTTGATAACTACCTTATGAAATTTTAATAAACTCCC
1 ATGAAATTTTGATAACTACCTTATGAAATTTTGATAAACTCCC
* * * * * * * *
6417 AATGAAATGTTGGTAAGCGCACATTATGATATTTTGGTAACCTTCCG
1 -ATGAAATTTTGATAA-C-TACCTTATGAAATTTTGATAAAC-TCCC
* * * * **
6464 ATAAAATATTGGTAA-TCACATTATGAAATTTTGATAAACATATC
1 ATGAAATTTTGATAACT-ACCTTATGAAATTTTGATAAAC-TCCC
* * *
6508 ATGAAATTGTGATACCT-CAC-TATGAAATTTTTATAAACCTCCC
1 ATGAAATTTTGATAACTAC-CTTATGAAATTTTGATAAA-CTCCC
* *
6551 TAT-AACATTTTGATAACCT-CCATT-TCAAATTTTGAT-AA-TCTC
1 -ATGAA-ATTTTGATAA-CTACC-TTATGAAATTTTGATAAACTCCC
* * * * **
6593 ATGAAATTTTGAAAACCACCTCATGAAATTTTGATAACCATCTT
1 ATGAAATTTTGATAACTACCTTATGAAATTTTGATAAAC-TCCC
6637 ATGAAATTTTGATAAC
1 ATGAAATTTTGATAAC
6653 ATCCTATAAA
Statistics
Matches: 177, Mismatches: 40, Indels: 36
0.70 0.16 0.14
Matches are distributed among these distances:
40 2 0.01
41 24 0.14
42 6 0.03
43 21 0.12
44 75 0.42
45 15 0.08
46 31 0.18
47 3 0.02
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (43 bp):
ATGAAATTTTGATAACTACCTTATGAAATTTTGATAAACTCCC
Found at i:6617 original size:107 final size:106
Alignment explanation
Indices: 6486--6759 Score: 251
Period size: 107 Copynumber: 2.6 Consensus size: 106
6476 TAATCACATT
* * *
6486 ATGAAATTTTGATAAACATATCATGAAATTGTGAT-ACC-TCACTATGAAATTTTTATAAACCTC
1 ATGAAATTTTGATAAACACATCATGAAATTGTGATAACCATC-CTATGAAATTTTGAT-AACAT-
6549 CCTATAACA-TTTTGATAACCTCCATTTCAAATTTTGATAATCTC
63 CCTATAA-ATTTTTGATAACCTCCATTTCAAATTTTGATAATCTC
* * *
6593 ATGAAATTTTGA-AAACCACCTCATGAAATTTTGATAACCATCTTATGAAATTTTGATAACATCC
1 ATGAAATTTTGATAAA-CACATCATGAAATTGTGATAACCATCCTATGAAATTTTGATAACATCC
* * *
6657 TATAAATTTTTTATAACCTCC-TTAT-AAACTTTTGTTAACCTCC
65 TATAAATTTTTGATAACCTCCATT-TCAAA-TTTTGATAATCT-C
* * * * * *
6700 TACGAAATTATGATAAGA-ACA-CTATTAAATTTTGATAACC-CCCAATGAAATTTTGATAAC
1 -ATGAAATTTTGATAA-ACACATC-ATGAAATTGTGATAACCATCCTATGAAATTTTGATAAC
6760 CCCCAACAAA
Statistics
Matches: 140, Mismatches: 16, Indels: 22
0.79 0.09 0.12
Matches are distributed among these distances:
105 6 0.04
106 34 0.24
107 51 0.36
108 44 0.31
109 4 0.03
110 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.37
Consensus pattern (106 bp):
ATGAAATTTTGATAAACACATCATGAAATTGTGATAACCATCCTATGAAATTTTGATAACATCCT
ATAAATTTTTGATAACCTCCATTTCAAATTTTGATAATCTC
Found at i:6738 original size:65 final size:64
Alignment explanation
Indices: 6596--6760 Score: 167
Period size: 65 Copynumber: 2.6 Consensus size: 64
6586 TAATCTCATG
* * * * *
6596 AAATTTTGAAAACCACCTCATGAAATTTTGATAACCATCTTATGAAATTTTGATAACATCCTAT
1 AAATTTTGATAACCACCTCATGAAATTTTGATAACCATCCTACGAAATTATGATAACAACCTAT
* * * * *
6660 AAATTTTTTATAACCTCCTTAT-AAACTTTTGTTAACC-TCCTACGAAATTATGATAAGAACACT
1 AAA-TTTTGATAACCACCTCATGAAA-TTTTGATAACCATCCTACGAAATTATGATAACAAC-CT
6723 ATT
63 A-T
6726 AAATTTTGATAACC-CC-CAATGAAATTTTGATAACC
1 AAATTTTGATAACCACCTC-ATGAAATTTTGATAACC
6761 CCCAACAAAA
Statistics
Matches: 82, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
64 38 0.46
65 40 0.49
66 4 0.05
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.36
Consensus pattern (64 bp):
AAATTTTGATAACCACCTCATGAAATTTTGATAACCATCCTACGAAATTATGATAACAACCTAT
Found at i:6748 original size:129 final size:128
Alignment explanation
Indices: 6486--6760 Score: 303
Period size: 129 Copynumber: 2.1 Consensus size: 128
6476 TAATCACATT
* *
6486 ATGAAATTTTGATAAACATATCATGAAATTGTGATACCTCACTATGAAATTTTTATAAACCTCCC
1 ATGAAATTTTGATAACCATATCATGAAATTGTGATACATCACTATGAAATTTTTATAAACCTCCC
* * * *
6551 TATAACATTTTGATAACCTCCATTTCAAATTTTGATAATCTCATGAAATTTTGAAAACCACCTC
66 TATAACATTTTGATAACCTCCA-TACAAATTATGATAAACACATGAAATTTTGAAAACCACCTC
* * *
6615 ATGAAATTTTGATAACCATCTTATGAAATTTTGATAACATC-CTAT-AAATTTTT-TATAACCTC
1 ATGAAATTTTGATAACCATATCATGAAATTGTGAT-ACATCACTATGAAATTTTTATA-AACCTC
* * * *
6677 CTTATAA-ACTTTTGTTAACCTCC-TACGAAATTATGATAAGAACACTATTAAATTTTGATAACC
64 CCTATAACA-TTTTGATAACCTCCATAC-AAATTATGAT-A-AACAC-ATGAAATTTTGAAAACC
6740 -CC-C
124 ACCTC
6743 AATGAAATTTTGATAACC
1 -ATGAAATTTTGATAACC
6761 CCCAACAAAA
Statistics
Matches: 125, Mismatches: 13, Indels: 16
0.81 0.08 0.10
Matches are distributed among these distances:
126 2 0.02
127 12 0.10
128 35 0.28
129 57 0.46
130 19 0.15
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (128 bp):
ATGAAATTTTGATAACCATATCATGAAATTGTGATACATCACTATGAAATTTTTATAAACCTCCC
TATAACATTTTGATAACCTCCATACAAATTATGATAAACACATGAAATTTTGAAAACCACCTC
Found at i:6760 original size:21 final size:21
Alignment explanation
Indices: 6485--6779 Score: 152
Period size: 22 Copynumber: 13.8 Consensus size: 21
6475 GTAATCACAT
* ***
6485 TATGAAATTTTGATAAACATA
1 TATGAAATTTTGATAACCCCC
* *
6506 TCATGAAATTGTGAT-ACCTCAC
1 T-ATGAAATTTTGATAACC-CCC
*
6528 TATGAAATTTTTATAAACCTCCC
1 TATGAAATTTTGAT-AACC-CCC
*
6551 TAT-AACATTTTGATAACCTCCA
1 TATGAA-ATTTTGATAACC-CCC
* * * *
6573 TTTCAAATTTTGATAA-TCTC
1 TATGAAATTTTGATAACCCCC
* *
6593 -ATGAAATTTTGAAAACCACC
1 TATGAAATTTTGATAACCCCC
* *
6613 TCATGAAATTTTGATAACCATCT
1 T-ATGAAATTTTGATAACC-CCC
**
6636 TATGAAATTTTGATAACATCC
1 TATGAAATTTTGATAACCCCC
* *
6657 TAT-AAATTTTTTATAACCTCCT
1 TATGAAA-TTTTGATAACC-CCC
* *
6679 TAT-AAACTTTTGTTAACCTCC
1 TATGAAA-TTTTGATAACCCCC
* * ** *
6700 TACGAAATTATGATAAGAACAC
1 TATGAAATTTTGATAA-CCCCC
*
6722 TATTAAATTTTGATAACCCCC
1 TATGAAATTTTGATAACCCCC
*
6743 AATGAAATTTTGATAACCCCC
1 TATGAAATTTTGATAACCCCC
* **
6764 AACAAAATTTTGATAA
1 TATGAAATTTTGATAA
6780 TTAATTACAC
Statistics
Matches: 209, Mismatches: 51, Indels: 28
0.73 0.18 0.10
Matches are distributed among these distances:
19 12 0.06
20 5 0.02
21 73 0.35
22 99 0.47
23 20 0.10
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.37
Consensus pattern (21 bp):
TATGAAATTTTGATAACCCCC
Found at i:6835 original size:22 final size:21
Alignment explanation
Indices: 6811--6886 Score: 71
Period size: 22 Copynumber: 3.5 Consensus size: 21
6801 GATAACTTAC
*
6811 CTATGAAATTTTGTTAATCTCC
1 CTAT-AAATTTTGTTAATCTCA
** * *
6833 CTATAAAATTTTGAGAACCACA
1 CTAT-AAATTTTGTTAATCTCA
*
6855 CTATCAAATTTTGTTGATCTCA
1 CTAT-AAATTTTGTTAATCTCA
6877 CTATAAATTT
1 CTATAAATTT
6887 CGATACACTC
Statistics
Matches: 42, Mismatches: 12, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
21 6 0.14
22 36 0.86
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.41
Consensus pattern (21 bp):
CTATAAATTTTGTTAATCTCA
Found at i:6979 original size:61 final size:60
Alignment explanation
Indices: 6896--7012 Score: 164
Period size: 61 Copynumber: 1.9 Consensus size: 60
6886 TCGATACACT
* *
6896 CATTATGAAATTTTAACTACCACACAATGAAAATTTGATAATCTCTCCCTCTGAAATACCA
1 CATTATAAAATTTTAACTACCACACAATGAAAATTTGATAATCTC-CCCTCTAAAATACCA
* * *
6957 CATTATAAAATTTT-ATTAACCACACTATGAAATTTTGATAATCTCCCCTCTAAAAT
1 CATTATAAAATTTTAACT-ACCACACAATGAAAATTTGATAATCTCCCCTCTAAAAT
7013 TTCGATAACT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
60 12 0.24
61 38 0.76
ACGTcount: A:0.39, C:0.21, G:0.05, T:0.34
Consensus pattern (60 bp):
CATTATAAAATTTTAACTACCACACAATGAAAATTTGATAATCTCCCCTCTAAAATACCA
Found at i:7034 original size:22 final size:23
Alignment explanation
Indices: 6981--7036 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
6971 ATTAACCACA
*
6981 CTATGAAATTTTGATAATCTCCC
1 CTATGAAATTTCGATAATCTCCC
* * *
7004 CTCTAAAATTTCGATAA-CTTCC
1 CTATGAAATTTCGATAATCTCCC
7026 CTATGAAATTT
1 CTATGAAATTT
7037 TGTTACCTCT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 13 0.48
23 14 0.52
ACGTcount: A:0.32, C:0.21, G:0.07, T:0.39
Consensus pattern (23 bp):
CTATGAAATTTCGATAATCTCCC
Found at i:7111 original size:21 final size:22
Alignment explanation
Indices: 6964--7104 Score: 76
Period size: 22 Copynumber: 6.5 Consensus size: 22
6954 CCACATTATA
*
6964 AAATTTT-ATTAACCACACTATG
1 AAATTTTGA-TAACAACACTATG
** * * *
6986 AAATTTTGATAATCTCCCCTCTA
1 AAATTTTGATAA-CAACACTATG
* ** *
7009 AAATTTCGATAACTTCCCTATG
1 AAATTTTGATAACAACACTATG
* *
7031 AAATTTTG-TTAC--CTCTATG
1 AAATTTTGATAACAACACTATG
* * **
7050 AAATTGTGATTATTACACTATG
1 AAATTTTGATAACAACACTATG
*
7072 AAATTTTGGTAACAACACT-TG
1 AAATTTTGATAACAACACTATG
7093 AAATTTTGATAA
1 AAATTTTGATAA
7105 GCTCACTCTA
Statistics
Matches: 93, Mismatches: 21, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
19 13 0.14
20 3 0.03
21 16 0.17
22 44 0.47
23 17 0.18
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.39
Consensus pattern (22 bp):
AAATTTTGATAACAACACTATG
Found at i:7157 original size:22 final size:22
Alignment explanation
Indices: 7126--7282 Score: 106
Period size: 22 Copynumber: 7.2 Consensus size: 22
7116 CTCACTATGT
7126 ATTTTGATAATCTTCCTATGAA
1 ATTTTGATAATCTTCCTATGAA
*
7148 ATTTTAATAA-CTTCCATAT-AA
1 ATTTTGATAATCTTCC-TATGAA
* **
7169 GATTTCGATAATCGCCCTATGAA
1 -ATTTTGATAATCTTCCTATGAA
* ****
7192 ATTTTGATAACCAGAATATGAA
1 ATTTTGATAATCTTCCTATGAA
* * *
7214 ATTTTGGTAATCTCCCTGTGAA
1 ATTTTGATAATCTTCCTATGAA
* * *
7236 ATTTTGACAACCTTCCCATG-A
1 ATTTTGATAATCTTCCTATGAA
* *
7257 ATTTCGATAA-CCTCCTTATGAA
1 ATTTTGATAATCTTCC-TATGAA
7279 ATTT
1 ATTT
7283 AACATCCCAT
Statistics
Matches: 101, Mismatches: 28, Indels: 12
0.72 0.20 0.09
Matches are distributed among these distances:
20 4 0.04
21 19 0.19
22 73 0.72
23 5 0.05
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (22 bp):
ATTTTGATAATCTTCCTATGAA
Found at i:7386 original size:44 final size:44
Alignment explanation
Indices: 7294--7399 Score: 117
Period size: 44 Copynumber: 2.4 Consensus size: 44
7284 ACATCCCATG
* * * * * *
7294 AAATTGTGATAACTACACTATAAAATTTTAACATCCTACCTATG
1 AAATTTTGGTAACCACACTATAAAATTTTAACAACCCACCTATA
7338 AAATTTTGGTAACCACACTATAAAATTTTGAA-AACCGCA-CTATA
1 AAATTTTGGTAACCACACTATAAAATTTT-AACAACC-CACCTATA
*
7382 AAATTTTAGTAACCACAC
1 AAATTTTGGTAACCACAC
7400 AATGAATTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
44 50 0.94
45 3 0.06
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (44 bp):
AAATTTTGGTAACCACACTATAAAATTTTAACAACCCACCTATA
Found at i:7415 original size:21 final size:22
Alignment explanation
Indices: 7294--7415 Score: 106
Period size: 22 Copynumber: 5.6 Consensus size: 22
7284 ACATCCCATG
* *
7294 AAATTGTGATAACTACACTATA
1 AAATTTTGATAACCACACTATA
* * * *
7316 AAATTTTAACATCCTAC-CTATG
1 AAATTTTGATAACC-ACACTATA
*
7338 AAATTTTGGTAACCACACTATA
1 AAATTTTGATAACCACACTATA
* *
7360 AAATTTTGAAAACCGCACTATA
1 AAATTTTGATAACCACACTATA
*
7382 AAATTTT-AGTAACCACACAAT-
1 AAATTTTGA-TAACCACACTATA
*
7403 GAATTTTGATAAC
1 AAATTTTGATAAC
7416 TTCCAAAATT
Statistics
Matches: 78, Mismatches: 18, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
21 13 0.17
22 63 0.81
23 2 0.03
ACGTcount: A:0.43, C:0.17, G:0.08, T:0.32
Consensus pattern (22 bp):
AAATTTTGATAACCACACTATA
Found at i:7758 original size:10 final size:10
Alignment explanation
Indices: 7728--7765 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
7718 CGTACTTTTT
7728 ATATAGTATAG
1 ATATAG-ATAG
7739 ATA-A-ATAG
1 ATATAGATAG
7747 ATATAGATAG
1 ATATAGATAG
7757 ATATAGATA
1 ATATAGATA
7766 TATTTCTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
8 7 0.28
9 1 0.04
10 14 0.56
11 3 0.12
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.32
Consensus pattern (10 bp):
ATATAGATAG
Found at i:17496 original size:25 final size:25
Alignment explanation
Indices: 17468--17518 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
17458 CTTCTTAAAT
17468 ATATATAGTAATACTAATACAATTG
1 ATATATAGTAATACTAATACAATTG
* *
17493 ATATATAGTAATTCTAATATAATTG
1 ATATATAGTAATACTAATACAATTG
17518 A
1 A
17519 GGTTGGTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.39
Consensus pattern (25 bp):
ATATATAGTAATACTAATACAATTG
Done.