Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007349.1 Corchorus capsularis cultivar CVL-1 contig07370, 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: 21708
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Found at i:4235 original size:197 final size:196
Alignment explanation
Indices: 3871--4241 Score: 437
Period size: 197 Copynumber: 1.9 Consensus size: 196
3861 TGGTTGTTTG
* * *
3871 TGAAACTTGTGATCTTAGGTGTTCAAGTGCAGGTCGACTTGGAGGTCTAAGGCCGACGAACGAAG
1 TGAAACTTGTGATCTTAGGTGTTCAAGTGCAGGTCGAATTGAAGGTCTAAGGCCAACGAACGAAG
* * *** *
3936 GAAGATTTATCAAGTGAAGATTGTCGACATACACATCTAGAAGTTTGGTGATTCAAGTTGATCTT
66 GAAGATTGATCAAGTAAAGATTGTCGACATACACATCTA-AAGTTTAAAGATTCAAGTAGATCTT
* *
4001 AGGCGGGTCTCTAAGGTGGATTTGGACCAATTACAACTAAATTCGTATCAGATTGCTTAATTTTT
130 AGGCGGGTCTCTAAGGTAGATTTGAACCAATTACAACTAAATTCGTATCAGATTGCTTAATTTTT
4066 TA
195 TA
* * * *
4068 TGAATCTTGTGATCTTAGGTGTTCAATTGCAGGTCTAATTGAAGGTCTACGGCCAACGAACGAA-
1 TGAAACTTGTGATCTTAGGTGTTCAAGTGCAGGTCGAATTGAAGGTCTAAGGCCAACGAACGAAG
* * * * **
4132 GAGGATTGCTTAAGTAAAGGTTGTCGACATACTTATCT-AAGTGTTAAAGAAGTTCAAGTAGATT
66 GAAGATTGATCAAGTAAAGATTGTCGACATACACATCTAAAGT-TTAAAG-A-TTCAAGTAGA-T
* *
4196 CTT-GGCGGGTCT-TAAGGATAGATTTGAATCTAA-TACAACTAGATTC
127 CTTAGGCGGGTCTCTAAGG-TAGATTTGAA-CCAATTACAACTAAATTC
4242 ATATGAATTA
Statistics
Matches: 145, Mismatches: 23, Indels: 12
0.81 0.13 0.07
Matches are distributed among these distances:
194 4 0.03
195 3 0.02
196 36 0.25
197 95 0.66
198 7 0.05
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (196 bp):
TGAAACTTGTGATCTTAGGTGTTCAAGTGCAGGTCGAATTGAAGGTCTAAGGCCAACGAACGAAG
GAAGATTGATCAAGTAAAGATTGTCGACATACACATCTAAAGTTTAAAGATTCAAGTAGATCTTA
GGCGGGTCTCTAAGGTAGATTTGAACCAATTACAACTAAATTCGTATCAGATTGCTTAATTTTTT
A
Found at i:6575 original size:313 final size:312
Alignment explanation
Indices: 5983--6597 Score: 989
Period size: 313 Copynumber: 2.0 Consensus size: 312
5973 TTGCAAAAGA
* * * *
5983 ATTACCCTTCGTGGGTCTCATTCTCCATAAAGAAATATTTTTTTTGTTGGATTATTTATCAAATG
1 ATTACCCTCCGTGGGGCCCATTCTCCATAAAAAAATATTTTTTTTGTTGGATTATTTATCAAATG
*
6048 ATCCTCATACTTTTATGCTTTATGCTATTTAATCCTTTACAACTATGGGTTGGACAATTTAACGC
66 ATCCTCATACTTTTATGCTTTATGCTATCTAATCCTTTACAACTATGGGTTGGACAATTTAACGC
* *
6113 TTCGGCTTTTATTTTTTATTTTTTGTTCTATTTGTCAGATTAAGGTGATTCAAGTGTCTATTAAA
131 GTCGGCTTATATTTTTTATTTTTTGTTCTATTTGTCAGATTAAGGTGATTCAAGTGTCTATTAAA
* * * * *
6178 ATGTGATTTCATGATCTACAACTTTTATGAAGAACTCAGAAGCCAATTTTAATGTTTTGGTTCTA
196 AGGTAATTTCATGATCTACAACTTTCATGAAGAACTCAGAAGCCAATTTTAATATTTTGATTCTA
* * *
6243 AAAAATGCTTCCGAAATTTTGTGGTTTCGATTGACGATCTATTTATTGAATG
261 AAAAATGCTTACGAAATTTTATGGTCTCGATTGACGATCTATTTATTGAATG
**
6295 ATTACCCTCCGTGGGGCCCATTCTCCATAAAAAAATATTTTTTTTGTTGGATTATTTATTGAATG
1 ATTACCCTCCGTGGGGCCCATTCTCCATAAAAAAATATTTTTTTTGTTGGATTATTTATCAAATG
* * * *
6360 ATCCTCATACTTTTATGCTTTATGCTATCTAATCCTTTACAATTATGGGTTGGTCGATTTAACGG
66 ATCCTCATACTTTTATGCTTTATGCTATCTAATCCTTTACAACTATGGGTTGGACAATTTAACGC
6425 GTCGGCTTATATTTTTGTATTTTTTGTTCTATTTGTTC-GATTAAGGTGATTCAAGTGTCTATTA
131 GTCGGCTTATATTTTT-TATTTTTTGTTCTATTTG-TCAGATTAAGGTGATTCAAGTGTCTATTA
6489 AAAGGTAATTTCATGATCTACAACTTTCATGAAGAACTCAGAAGCCAATTTTAATATTTTGATTC
194 AAAGGTAATTTCATGATCTACAACTTTCATGAAGAACTCAGAAGCCAATTTTAATATTTTGATTC
* * *
6554 TAAAAAATGCTTATGAAATTTTATGGTCTCGATTGTCGGTCTAT
259 TAAAAAATGCTTACGAAATTTTATGGTCTCGATTGACGATCTAT
6598 CTAGTACTGT
Statistics
Matches: 277, Mismatches: 24, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
312 133 0.48
313 142 0.51
314 2 0.01
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (312 bp):
ATTACCCTCCGTGGGGCCCATTCTCCATAAAAAAATATTTTTTTTGTTGGATTATTTATCAAATG
ATCCTCATACTTTTATGCTTTATGCTATCTAATCCTTTACAACTATGGGTTGGACAATTTAACGC
GTCGGCTTATATTTTTTATTTTTTGTTCTATTTGTCAGATTAAGGTGATTCAAGTGTCTATTAAA
AGGTAATTTCATGATCTACAACTTTCATGAAGAACTCAGAAGCCAATTTTAATATTTTGATTCTA
AAAAATGCTTACGAAATTTTATGGTCTCGATTGACGATCTATTTATTGAATG
Found at i:8350 original size:49 final size:47
Alignment explanation
Indices: 8263--8403 Score: 151
Period size: 49 Copynumber: 3.0 Consensus size: 47
8253 AACGTGCCAA
* * * *
8263 TCAATTTTTTC-TAAAAATTGATAAAAAGTGCAAGGAAAAGTAAATAT
1 TCAATTTTGTCTTAAAAATTGAGAAAAAGTGC-ATGAAAAGTAAAGAT
* *
8310 TCAATTTTGTCTTAAAAATTGAGAAAAAAGTGCATTGAAAATTAAAGGT
1 TCAATTTTGTCTTAAAAATTGAG-AAAAAGTGCA-TGAAAAGTAAAGAT
* * *
8359 TCAATTTTGT-TGTAAAAATTTAGAAAAAGTTCATGAAACGTAAAG
1 TCAATTTTGTCT-TAAAAATTGAGAAAAAGTGCATGAAAAGTAAAG
8404 GATTGCTTTG
Statistics
Matches: 80, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
47 20 0.25
48 21 0.26
49 39 0.49
ACGTcount: A:0.46, C:0.06, G:0.15, T:0.33
Consensus pattern (47 bp):
TCAATTTTGTCTTAAAAATTGAGAAAAAGTGCATGAAAAGTAAAGAT
Found at i:14062 original size:28 final size:27
Alignment explanation
Indices: 14002--14089 Score: 104
Period size: 27 Copynumber: 3.2 Consensus size: 27
13992 TAGTTGCGAC
* **
14002 AATTTTGGCTAGTTACGGGGTTTTTGT
1 AATTTTGGCTAGTTGCGGCATTTTTGT
*
14029 AATTTTGGCTAGTTGCGGCAATTTTTGG
1 AATTTTGGCTAGTTGCGGC-ATTTTTGT
* * *
14057 AATTTTGGGTACTTGCGGCAGTTTTGT
1 AATTTTGGCTAGTTGCGGCATTTTTGT
14084 AATTTT
1 AATTTT
14090 TGGGTTGCTG
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
27 29 0.56
28 23 0.44
ACGTcount: A:0.17, C:0.09, G:0.27, T:0.47
Consensus pattern (27 bp):
AATTTTGGCTAGTTGCGGCATTTTTGT
Found at i:14090 original size:28 final size:28
Alignment explanation
Indices: 14023--14094 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
14013 GTTACGGGGT
* * *
14023 TTTTGTAATTTTGGCTAGTTGCGGCAAT
1 TTTTGTAATTTTGGGTACTTGCGGCAAG
*
14051 TTTTGGAATTTTGGGTACTTGCGGC-AG
1 TTTTGTAATTTTGGGTACTTGCGGCAAG
14078 TTTTGTAATTTTTGGGT
1 TTTTGTAA-TTTTGGGT
14095 TGCTGCGGCT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
27 8 0.21
28 30 0.79
ACGTcount: A:0.15, C:0.08, G:0.28, T:0.49
Consensus pattern (28 bp):
TTTTGTAATTTTGGGTACTTGCGGCAAG
Found at i:14101 original size:28 final size:28
Alignment explanation
Indices: 14023--14103 Score: 76
Period size: 28 Copynumber: 2.9 Consensus size: 28
14013 GTTACGGGGT
* * * *
14023 TTTTGTAATTTTGGCTAGTTGCGGCAAT
1 TTTTGTAATTTTGGGTTGCTGCGGCAAG
* *
14051 TTTTGGAATTTTGGG-TACTTGCGGC-AG
1 TTTTGTAATTTTGGGTTGC-TGCGGCAAG
14078 TTTTGTAATTTTTGGGTTGCTGCGGC
1 TTTTGTAA-TTTTGGGTTGCTGCGGC
14104 TTCTTTGACT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
27 8 0.19
28 32 0.76
29 2 0.05
ACGTcount: A:0.14, C:0.11, G:0.30, T:0.46
Consensus pattern (28 bp):
TTTTGTAATTTTGGGTTGCTGCGGCAAG
Found at i:14316 original size:25 final size:25
Alignment explanation
Indices: 14288--14341 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
14278 GTGCCGCATC
14288 TCATTATGTTGTGTTGCACCACATT
1 TCATTATGTTGTGTTGCACCACATT
* **
14313 TCATTGTGTTGTGTTGTGCCACATT
1 TCATTATGTTGTGTTGCACCACATT
14338 TCAT
1 TCAT
14342 GTCTGATGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.17, C:0.19, G:0.19, T:0.46
Consensus pattern (25 bp):
TCATTATGTTGTGTTGCACCACATT
Found at i:19114 original size:14 final size:13
Alignment explanation
Indices: 19088--19188 Score: 53
Period size: 12 Copynumber: 8.1 Consensus size: 13
19078 AAAGATTGCT
19088 CTTACAT-ATTTC
1 CTTACATAATTTC
19100 CTTACCATAATTTC
1 CTTA-CATAATTTC
19114 C--A-ATCAATATT-
1 CTTACAT-AAT-TTC
19125 CTTACAT-ATTTC
1 CTTACATAATTTC
19137 CTTACCATAATTTC
1 CTTA-CATAATTTC
19151 C--A-ATCAATATT-
1 CTTACAT-AAT-TTC
*
19162 CTTACAT-ATGTC
1 CTTACATAATTTC
19174 CTTACCATAATTTC
1 CTTA-CATAATTTC
19188 C
1 C
19189 AATCAATATT
Statistics
Matches: 69, Mismatches: 2, Indels: 34
0.66 0.02 0.32
Matches are distributed among these distances:
10 4 0.06
11 11 0.16
12 22 0.32
13 11 0.16
14 21 0.30
ACGTcount: A:0.31, C:0.26, G:0.01, T:0.43
Consensus pattern (13 bp):
CTTACATAATTTC
Found at i:19137 original size:37 final size:37
Alignment explanation
Indices: 19087--19204 Score: 218
Period size: 37 Copynumber: 3.2 Consensus size: 37
19077 AAAAGATTGC
19087 TCTTACATATTTCCTTACCATAATTTCCAATCAATAT
1 TCTTACATATTTCCTTACCATAATTTCCAATCAATAT
19124 TCTTACATATTTCCTTACCATAATTTCCAATCAATAT
1 TCTTACATATTTCCTTACCATAATTTCCAATCAATAT
*
19161 TCTTACATATGTCCTTACCATAATTTCCAATCAATAT
1 TCTTACATATTTCCTTACCATAATTTCCAATCAATAT
19198 TCATTAC
1 TC-TTAC
19205 TAAGTACCGT
Statistics
Matches: 79, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
37 75 0.95
38 4 0.05
ACGTcount: A:0.32, C:0.25, G:0.01, T:0.42
Consensus pattern (37 bp):
TCTTACATATTTCCTTACCATAATTTCCAATCAATAT
Done.