Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008342.1 Corchorus capsularis cultivar CVL-1 contig08363, 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: 14381
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Found at i:2449 original size:209 final size:209
Alignment explanation
Indices: 2089--2507 Score: 820
Period size: 209 Copynumber: 2.0 Consensus size: 209
2079 TTGTTTTCTT
*
2089 GTGGTGGTTAGTTACTAGGTCTGCCAGGTGTAGTTTTAGGGTAATGGTAAATCGTTCCTTCACAC
1 GTGGTGGTTAGTTACTAGGTCTGCCAGGTGTAGTTTTAGGGTAATGGTAAATCGTTCCTTCAAAC
2154 ACTTCACTATTTGCATTCATGCATTGAGATCGCCTCAGACCCGGGCATACCCTAGTTTTGGGAGG
66 ACTTCACTATTTGCATTCATGCATTGAGATCGCCTCAGACCCGGGCATACCCTAGTTTTGGGAGG
*
2219 TATAATAGCAAGCCTTCGTGGGACTCGTTTGTCCCCGTGTAGGTTGTGCGAAAAACCTCCACCCA
131 TATAATAGCAAGCCTTCGTGGGACTCGTTTGTCCCCGTGTAGGTTGTGCAAAAAACCTCCACCCA
2284 AGGAAAATCTACTA
196 AGGAAAATCTACTA
2298 GTGGTGGTTAGTTACTAGGTCTGCCAGGTGTAGTTTTAGGGTAATGGTAAATCGTTCCTTCAAAC
1 GTGGTGGTTAGTTACTAGGTCTGCCAGGTGTAGTTTTAGGGTAATGGTAAATCGTTCCTTCAAAC
2363 ACTTCACTATTTGCATTCATGCATTGAGATCGCCTCAGACCCGGGCATACCCTAGTTTTGGGAGG
66 ACTTCACTATTTGCATTCATGCATTGAGATCGCCTCAGACCCGGGCATACCCTAGTTTTGGGAGG
2428 TATAATAGCAAGCCTTCGTGGGACTCGTTTGTCCCCGTGTAGGTTGTGCAAAAAACCTCCACCCA
131 TATAATAGCAAGCCTTCGTGGGACTCGTTTGTCCCCGTGTAGGTTGTGCAAAAAACCTCCACCCA
2493 AGGAAAATCTACTA
196 AGGAAAATCTACTA
2507 G
1 G
2508 CCCAGCGATG
Statistics
Matches: 208, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
209 208 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (209 bp):
GTGGTGGTTAGTTACTAGGTCTGCCAGGTGTAGTTTTAGGGTAATGGTAAATCGTTCCTTCAAAC
ACTTCACTATTTGCATTCATGCATTGAGATCGCCTCAGACCCGGGCATACCCTAGTTTTGGGAGG
TATAATAGCAAGCCTTCGTGGGACTCGTTTGTCCCCGTGTAGGTTGTGCAAAAAACCTCCACCCA
AGGAAAATCTACTA
Found at i:4056 original size:22 final size:22
Alignment explanation
Indices: 4008--4057 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
3998 TCAGGCCCAC
* *
4008 ATTCTTGTCTCATATCCTCTTT
1 ATTCTTGTCTCATATCCTATTG
* **
4030 TTTCTTGTCTCATATTTTATTG
1 ATTCTTGTCTCATATCCTATTG
4052 ATTCTT
1 ATTCTT
4058 TATTTATATC
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.14, C:0.20, G:0.06, T:0.60
Consensus pattern (22 bp):
ATTCTTGTCTCATATCCTATTG
Found at i:6952 original size:46 final size:48
Alignment explanation
Indices: 6853--6971 Score: 215
Period size: 46 Copynumber: 2.5 Consensus size: 48
6843 AAAAAACTGG
6853 GAAAGAGGTCGCAAAAAGAAAGAGAAACAAAAAACTGGGCCTAAAAAA
1 GAAAGAGGTCGCAAAAAGAAAGAGAAACAAAAAACTGGGCCTAAAAAA
*
6901 TAAAGAGGTCGCAAAAAGAAAGAGAAA-AAAAAA-TGGGCCTAAAAAA
1 GAAAGAGGTCGCAAAAAGAAAGAGAAACAAAAAACTGGGCCTAAAAAA
6947 GAAAGAGGTCGCAAAAAGAAAGAGA
1 GAAAGAGGTCGCAAAAAGAAAGAGA
6972 TATAAATGGA
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
46 37 0.54
47 6 0.09
48 26 0.38
ACGTcount: A:0.59, C:0.10, G:0.24, T:0.07
Consensus pattern (48 bp):
GAAAGAGGTCGCAAAAAGAAAGAGAAACAAAAAACTGGGCCTAAAAAA
Found at i:8962 original size:69 final size:69
Alignment explanation
Indices: 8876--9303 Score: 456
Period size: 69 Copynumber: 6.2 Consensus size: 69
8866 AATTCCTTGA
* * *
8876 CTTTTCCATAAGTCAAACTCGTTTCCATACGAGGTAGTTCAAGCTTTGGTTCCATCCAAGCAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCACACGAGGTAGTTCAAGCTTTGGTTCCATCCAAGCAGCA
*
8941 GGGG
66 GAGG
** * * * *
8945 CTTTTCCATGAGCCAAACTCGTTTCCATACGAGTTAGTT-TAGCATTGGTTCCATCCAAGCAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCACACGAGGTAGTTCAAGCTTTGGTTCCATCCAAGCAGCA
*
9009 GGGG
66 GAGG
* * *
9013 CTTTTCCACAAGCCAAACTCGTTTTCACACGA-GTCAGTTCAAGCTTTGGTTCCATCCAAGTATT
1 CTTTTCCACAAGCCAAACTCGTTTCCACACGAGGT-AGTTCAAGCTTTGGTTCCATCCAAGCA-G
*
9077 CAAAGG
64 CAGAGG
* * *
9083 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGATAGTTTAAGCTTTGGTTCCATCCAA--A-CA
1 CTTTTCCACAAGCCAAACTCGTTTCCACACGAGGTAGTTCAAGCTTTGGTTCCATCCAAGCAGCA
9145 GAGG
66 GAGG
* * * * * *
9149 ATTTTCCACAAGTCAAACTCGTTTCCACACGA-GTCAGATCCATCTTTGGTTCCATCCAGGCAAG
1 CTTTTCCACAAGCCAAACTCGTTTCCACACGAGGT-AGTTCAAGCTTTGGTTCCATCCAAGC-AG
9213 -AGAGG
64 CAGAGG
* * * * * * * *
9218 CTTTTCCACAAGCCAAACCCGCTTCCACGCGAGATAGTTTAAGATTTGGTTCCATCAAAGCATTC
1 CTTTTCCACAAGCCAAACTCGTTTCCACACGAGGTAGTTCAAGCTTTGGTTCCATCCAAGCA-GC
*
9283 AGGGG
65 AGAGG
*
9288 CTTTTCCATAAGCCAA
1 CTTTTCCACAAGCCAA
9304 GTTCAGTGAG
Statistics
Matches: 301, Mismatches: 46, Indels: 23
0.81 0.12 0.06
Matches are distributed among these distances:
65 1 0.00
66 53 0.18
67 1 0.00
68 61 0.20
69 107 0.36
70 77 0.26
71 1 0.00
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (69 bp):
CTTTTCCACAAGCCAAACTCGTTTCCACACGAGGTAGTTCAAGCTTTGGTTCCATCCAAGCAGCA
GAGG
Found at i:9268 original size:205 final size:206
Alignment explanation
Indices: 8876--9303 Score: 549
Period size: 205 Copynumber: 2.1 Consensus size: 206
8866 AATTCCTTGA
* *
8876 CTTTTCCATAAGTCAAACTCGTTTCCATACGAGGTAGTTCAAGCTTTGGTTCCATCCAAGCAGCA
1 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGATAGTTCAAGCTTTGGTTCCATCCAA-CAGCA
* * ** * * **
8941 GGGGCTTTTCCATGAGCCAAACTCGTTTCCATACGAGTTAGTTTAGCATTGGTTCCATCCAAGCA
65 GAGGATTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGTCCAGCATTGGTTCCATCCAAGCA
* * * * * *
9006 GCAGGGGCTTTTCCACAAGCCAAACTCGTTTTCACACGAGTCAGTTCAAGCTTTGGTTCCATCCA
130 GCAGAGGCTTTTCCACAAGCCAAACCCGCTTCCACACGAGTCAGTTCAAGATTTGGTTCCATCAA
*
9071 AGTATTCAAAGG
195 AGCATTCAAAGG
* *
9083 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGATAGTTTAAGCTTTGGTTCCATCCAA-A-CAG
1 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGATAGTTCAAGCTTTGGTTCCATCCAACAGCAG
* * * *
9146 AGGATTTTCCACAAGTCAAACTCGTTTCCACACGAGTCAGATCCATCTTTGGTTCCATCCAGGCA
66 AGGATTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAG-TCCAGCATTGGTTCCATCCAAGC-
* *
9211 AG-AGAGGCTTTTCCACAAGCCAAACCCGCTTCCACGCGAGAT-AGTTTAAGATTTGGTTCCATC
129 AGCAGAGGCTTTTCCACAAGCCAAACCCGCTTCCACACGAG-TCAGTTCAAGATTTGGTTCCATC
**
9274 AAAGCATTCAGGGG
193 AAAGCATTCAAAGG
9288 CTTTTCCATAAGCCAA
1 CTTTTCCATAAGCCAA
9304 GTTCAGTGAG
Statistics
Matches: 190, Mismatches: 28, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
204 36 0.19
205 96 0.51
206 3 0.02
207 55 0.29
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (206 bp):
CTTTTCCATAAGCCAAACTCGTTTCCATACGAGATAGTTCAAGCTTTGGTTCCATCCAACAGCAG
AGGATTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGTCCAGCATTGGTTCCATCCAAGCAG
CAGAGGCTTTTCCACAAGCCAAACCCGCTTCCACACGAGTCAGTTCAAGATTTGGTTCCATCAAA
GCATTCAAAGG
Found at i:9485 original size:47 final size:47
Alignment explanation
Indices: 9412--9695 Score: 388
Period size: 47 Copynumber: 6.0 Consensus size: 47
9402 ATCCAGGAAA
* *
9412 TCTTCTCTCGCTTCCACGCGAGTTTTCAATTTAGTGACCAAAGATGG
1 TCTTTTCTCGCTTCCACGCGAGTTTTCAATCTAGTGACCAAAGATGG
**
9459 TCTTTTCTCGCTTCCACGCGAGTTTTCAATCCGGTGACCAAAGATGG
1 TCTTTTCTCGCTTCCACGCGAGTTTTCAATCTAGTGACCAAAGATGG
* * *
9506 TCTTTTCTTGCTTCCATGCGAGCTTTCAATCTAGTGACCAAAGATGG
1 TCTTTTCTCGCTTCCACGCGAGTTTTCAATCTAGTGACCAAAGATGG
* *
9553 TCTTTTCTCGCTTCCATGCGAGCTTTCAATCTAGTGACCAAAGATGG
1 TCTTTTCTCGCTTCCACGCGAGTTTTCAATCTAGTGACCAAAGATGG
* * * * *
9600 TCTTTTCTCACTTCCACACGGGTTTTCAATTTAGTCACCAAAGATGG
1 TCTTTTCTCGCTTCCACGCGAGTTTTCAATCTAGTGACCAAAGATGG
* * * * * *
9647 TCTTCTCTCGCTTCCATGCGAGTCTGCAATTTAGTGACCAAAGTTGG
1 TCTTTTCTCGCTTCCACGCGAGTTTTCAATCTAGTGACCAAAGATGG
9694 TC
1 TC
9696 AACGGGTTTT
Statistics
Matches: 211, Mismatches: 26, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 211 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.35
Consensus pattern (47 bp):
TCTTTTCTCGCTTCCACGCGAGTTTTCAATCTAGTGACCAAAGATGG
Found at i:10069 original size:28 final size:27
Alignment explanation
Indices: 10030--10107 Score: 108
Period size: 28 Copynumber: 2.9 Consensus size: 27
10020 GCATTAGGGT
10030 CATCTAAG-GGCATTTTGGTCATTTTCA
1 CATCTAAGAGGCATTTTGGTCATTTT-A
*
10057 CATCTAGGAGGCATTTTGGTCATCTTTA
1 CATCTAAGAGGCATTTTGGTCAT-TTTA
10085 CA-CTAAGA-GCATTTTGGTCATTT
1 CATCTAAGAGGCATTTTGGTCATTT
10108 GCATATTCAT
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
25 2 0.04
26 13 0.28
27 12 0.26
28 17 0.36
29 3 0.06
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (27 bp):
CATCTAAGAGGCATTTTGGTCATTTTA
Found at i:10770 original size:17 final size:19
Alignment explanation
Indices: 10727--10768 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
10717 AGTTTTTAAG
*
10727 TAAAAATGTAATATATAAA
1 TAAAAATTTAATATATAAA
10746 TAAAAATTTAATAT-TAAAA
1 TAAAAATTTAATATAT-AAA
10765 TAAA
1 TAAA
10769 TTAATAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (19 bp):
TAAAAATTTAATATATAAA
Done.