Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007669.1 Corchorus capsularis cultivar CVL-1 contig07690, 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: 28539
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Found at i:2908 original size:43 final size:43
Alignment explanation
Indices: 2847--2933 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
2837 AATGAACAGT
* *
2847 ATTTCAGTTAAGAAATGAGATTTTGTTGTGAAATGTTAAGAAA
1 ATTTCAGTTAAGAAATGAGATTTTGTTGTGAAATGATAACAAA
2890 ATTTCAGTTAAGAAATGAGATTTTGTTGTGAAATGATAACAAA
1 ATTTCAGTTAAGAAATGAGATTTTGTTGTGAAATGATAACAAA
2933 A
1 A
2934 CAAACGAAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.41, C:0.03, G:0.20, T:0.36
Consensus pattern (43 bp):
ATTTCAGTTAAGAAATGAGATTTTGTTGTGAAATGATAACAAA
Found at i:3006 original size:23 final size:23
Alignment explanation
Indices: 2976--3023 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
2966 AAAGACAAGT
2976 GAATAGAGAGACAATAGAAAATG
1 GAATAGAGAGACAATAGAAAATG
2999 GAATAGAGAGACAATAGAAAATG
1 GAATAGAGAGACAATAGAAAATG
3022 GA
1 GA
3024 GAAGAAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.56, C:0.04, G:0.27, T:0.12
Consensus pattern (23 bp):
GAATAGAGAGACAATAGAAAATG
Found at i:3041 original size:23 final size:24
Alignment explanation
Indices: 2978--3048 Score: 85
Period size: 23 Copynumber: 3.0 Consensus size: 24
2968 AGACAAGTGA
*
2978 ATAGAGAGACAATAGAAAATGGA-
1 ATAGAGAGAAAATAGAAAATGGAG
*
3001 ATAGAGAGACAATAGAAAATGGAG
1 ATAGAGAGAAAATAGAAAATGGAG
*
3025 A-AGA-AGAAAATATGAAAAAGGAG
1 ATAGAGAGAAAATA-GAAAATGGAG
3048 A
1 A
3049 GAAATTGTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.16
23 36 0.82
24 1 0.02
ACGTcount: A:0.59, C:0.03, G:0.27, T:0.11
Consensus pattern (24 bp):
ATAGAGAGAAAATAGAAAATGGAG
Found at i:3258 original size:11 final size:11
Alignment explanation
Indices: 3244--3284 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
3234 ATTCATAACA
3244 AATTTATAATT
1 AATTTATAATT
3255 AATTTATAATT
1 AATTTATAATT
3266 -ATTTGATAATT
1 AATTT-ATAATT
*
3277 ATTTTATA
1 AATTTATA
3285 TAGGAAAGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
10 4 0.15
11 20 0.74
12 3 0.11
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (11 bp):
AATTTATAATT
Found at i:4485 original size:199 final size:198
Alignment explanation
Indices: 4143--4540 Score: 548
Period size: 199 Copynumber: 2.0 Consensus size: 198
4133 AGAAGTTGAC
* * * *
4143 ACATATTCCTTAAGGGGACACATGTCAACCCTTAAACCTTGCACGTGCAGTCTACTAAATGACTG
1 ACATATTCCCTAAAGGGACACATGTCAACCCTTAAACCTCGCACGTGCAGTCTACTAAATCACTG
* * * ** ** *
4208 GCAGTGTATAGTATAATTTTTCTTATAAGATTATTATATGATCCATTGTCAGTGTAAATTTTGGA
66 ACAGTGCATAATATAATTTTTCTTATAAGATTATTATACAATAAACTGTCAGTGTAAATTTTGGA
* * **
4273 CTCCATAAGCGGGTTAAGAAGTTGACATATACCCCATTTCATAA-TTAATTAAATATTTAATATT
131 CTCAATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAACAAAATTAAATATTTAATATT
4337 AAT
196 AAT
* *
4340 ACATATTCCCTAAAGGGACACATGTCAACCCTTAAACCTCGCACGTTCAGTCTGCTAAACTCCAC
1 ACATATTCCCTAAAGGGACACATGTCAACCCTTAAACCTCGCACGTGCAGTCTACTAAA-T-CAC
* *
4405 TTAC-GTTGCATAATATAATTTTTCTTATAGGATTATTATACAATAAACTGTCAGTGTAAATTTT
64 TGACAG-TGCATAATATAATTTTTCTTATAAGATTATTATACAATAAACTGTCAGTGTAAATTTT
* **
4469 GGACTCAATGAGCGGGTTAAGAAGTTGACACATACCTTATTTCATAACAAAATTAAATATTTAAT
128 GGACTCAATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAACAAAATTAAATATTTAAT
4534 ATTAAT
193 ATTAAT
4540 A
1 A
4541 AAATTATACC
Statistics
Matches: 174, Mismatches: 23, Indels: 5
0.86 0.11 0.02
Matches are distributed among these distances:
197 54 0.31
198 2 0.01
199 96 0.55
200 22 0.13
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (198 bp):
ACATATTCCCTAAAGGGACACATGTCAACCCTTAAACCTCGCACGTGCAGTCTACTAAATCACTG
ACAGTGCATAATATAATTTTTCTTATAAGATTATTATACAATAAACTGTCAGTGTAAATTTTGGA
CTCAATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAACAAAATTAAATATTTAATATT
AAT
Found at i:4976 original size:26 final size:27
Alignment explanation
Indices: 4925--4976 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
4915 CCACTCTTCC
* *
4925 TTAGAAAATTTTACTTACTTTACATTT
1 TTAGAAAATTTTACTAACTATACATTT
4952 TTAG-AAATTTTACTAAGCTAT-CATT
1 TTAGAAAATTTTACTAA-CTATACATT
4977 AATATTGAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.48
Consensus pattern (27 bp):
TTAGAAAATTTTACTAACTATACATTT
Found at i:4989 original size:18 final size:18
Alignment explanation
Indices: 4962--5004 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
4952 TTAGAAATTT
4962 TACT-AAGCTATCATTAA
1 TACTGAAGCTATCATTAA
*
4979 TATTGAAGCTATCATTAA
1 TACTGAAGCTATCATTAA
4997 TACTGAAG
1 TACTGAAG
5005 GTTACCGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.35
Consensus pattern (18 bp):
TACTGAAGCTATCATTAA
Found at i:9912 original size:130 final size:130
Alignment explanation
Indices: 9679--9934 Score: 512
Period size: 130 Copynumber: 2.0 Consensus size: 130
9669 TAGTGAATAT
9679 TAGAATTATTGATGATTATTACGTGTTAATTAACTGGGCATGACACGTGTCGAGATTTGGAGGCC
1 TAGAATTATTGATGATTATTACGTGTTAATTAACTGGGCATGACACGTGTCGAGATTTGGAGGCC
9744 TCAACATTTAATGAGTTACCATACTCGTAGTGTACATTGTTTTAAATATATATATAAGATAGTAG
66 TCAACATTTAATGAGTTACCATACTCGTAGTGTACATTGTTTTAAATATATATATAAGATAGTAG
9809 TAGAATTATTGATGATTATTACGTGTTAATTAACTGGGCATGACACGTGTCGAGATTTGGAGGCC
1 TAGAATTATTGATGATTATTACGTGTTAATTAACTGGGCATGACACGTGTCGAGATTTGGAGGCC
9874 TCAACATTTAATGAGTTACCATACTCGTAGTGTACATTGTTTTAAATATATATATAAGATA
66 TCAACATTTAATGAGTTACCATACTCGTAGTGTACATTGTTTTAAATATATATATAAGATA
9935 AGATGCTCAG
Statistics
Matches: 126, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
130 126 1.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (130 bp):
TAGAATTATTGATGATTATTACGTGTTAATTAACTGGGCATGACACGTGTCGAGATTTGGAGGCC
TCAACATTTAATGAGTTACCATACTCGTAGTGTACATTGTTTTAAATATATATATAAGATAGTAG
Found at i:10192 original size:55 final size:55
Alignment explanation
Indices: 10108--10241 Score: 217
Period size: 49 Copynumber: 2.5 Consensus size: 55
10098 TCAACTGATG
*
10108 AGTGCACAGTGCCTGGACCTGGGTTCAAGTTCAAGTCTCACGGAATGTGAGTTTA
1 AGTGCACGGTGCCTGGACCTGGGTTCAAGTTCAAGTCTCACGGAATGTGAGTTTA
10163 AGTGCACGGTGCCTGGACCT-GG-----GTTCAAGTCTCACGGAATGTGAGTTTA
1 AGTGCACGGTGCCTGGACCTGGGTTCAAGTTCAAGTCTCACGGAATGTGAGTTTA
10212 AGTGCACGGTGCCTGGACCTGGGTTCAAGT
1 AGTGCACGGTGCCTGGACCTGGGTTCAAGT
10242 CTCACGGAAT
Statistics
Matches: 72, Mismatches: 1, Indels: 12
0.85 0.01 0.14
Matches are distributed among these distances:
49 47 0.65
50 2 0.03
54 2 0.03
55 21 0.29
ACGTcount: A:0.21, C:0.21, G:0.32, T:0.26
Consensus pattern (55 bp):
AGTGCACGGTGCCTGGACCTGGGTTCAAGTTCAAGTCTCACGGAATGTGAGTTTA
Found at i:10276 original size:49 final size:49
Alignment explanation
Indices: 10136--10260 Score: 250
Period size: 49 Copynumber: 2.6 Consensus size: 49
10126 CTGGGTTCAA
10136 GTTCAAGTCTCACGGAATGTGAGTTTAAGTGCACGGTGCCTGGACCTGG
1 GTTCAAGTCTCACGGAATGTGAGTTTAAGTGCACGGTGCCTGGACCTGG
10185 GTTCAAGTCTCACGGAATGTGAGTTTAAGTGCACGGTGCCTGGACCTGG
1 GTTCAAGTCTCACGGAATGTGAGTTTAAGTGCACGGTGCCTGGACCTGG
10234 GTTCAAGTCTCACGGAATGTGAGTTTA
1 GTTCAAGTCTCACGGAATGTGAGTTTA
10261 GCGTGTCTGG
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 76 1.00
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (49 bp):
GTTCAAGTCTCACGGAATGTGAGTTTAAGTGCACGGTGCCTGGACCTGG
Found at i:10610 original size:21 final size:21
Alignment explanation
Indices: 10585--10628 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
10575 AAAATTTTAC
10585 TTAGAATTGAAATTACTTAAT
1 TTAGAATTGAAATTACTTAAT
10606 TTAGAATTGAAATTACTTAAT
1 TTAGAATTGAAATTACTTAAT
10627 TT
1 TT
10629 CAATCATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (21 bp):
TTAGAATTGAAATTACTTAAT
Found at i:24404 original size:10 final size:10
Alignment explanation
Indices: 24386--24415 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
24376 GACCGCGCAC
*
24386 CAACTGGCCA
1 CAACCGGCCA
24396 CAACCGGCCA
1 CAACCGGCCA
24406 CAACCGGCCA
1 CAACCGGCCA
24416 ATGGATCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.30, C:0.47, G:0.20, T:0.03
Consensus pattern (10 bp):
CAACCGGCCA
Found at i:26076 original size:238 final size:238
Alignment explanation
Indices: 25658--26135 Score: 956
Period size: 238 Copynumber: 2.0 Consensus size: 238
25648 GGGATTAGGG
25658 TTTTCTTGTGCAATTGATCTACTTAGTTGCAATTAGCCCTAATTGATTGTGTGATTGAGATTCTT
1 TTTTCTTGTGCAATTGATCTACTTAGTTGCAATTAGCCCTAATTGATTGTGTGATTGAGATTCTT
25723 GGGCTGCTTTTGCTGTGAGTTAAGATCTATTTTGAATAATTTCAGGTTACAAACCCTATTGGATT
66 GGGCTGCTTTTGCTGTGAGTTAAGATCTATTTTGAATAATTTCAGGTTACAAACCCTATTGGATT
25788 CAAGTGGTACAAAATAGGAGCTAATCGATTGAAAATTGTTTGAATTGTGCAGCAAGTTTGGAGAA
131 CAAGTGGTACAAAATAGGAGCTAATCGATTGAAAATTGTTTGAATTGTGCAGCAAGTTTGGAGAA
25853 GGATTTCGACAACAAGAGCCTGCATAAGTGGTTTGGTTTTGGT
196 GGATTTCGACAACAAGAGCCTGCATAAGTGGTTTGGTTTTGGT
25896 TTTTCTTGTGCAATTGATCTACTTAGTTGCAATTAGCCCTAATTGATTGTGTGATTGAGATTCTT
1 TTTTCTTGTGCAATTGATCTACTTAGTTGCAATTAGCCCTAATTGATTGTGTGATTGAGATTCTT
25961 GGGCTGCTTTTGCTGTGAGTTAAGATCTATTTTGAATAATTTCAGGTTACAAACCCTATTGGATT
66 GGGCTGCTTTTGCTGTGAGTTAAGATCTATTTTGAATAATTTCAGGTTACAAACCCTATTGGATT
26026 CAAGTGGTACAAAATAGGAGCTAATCGATTGAAAATTGTTTGAATTGTGCAGCAAGTTTGGAGAA
131 CAAGTGGTACAAAATAGGAGCTAATCGATTGAAAATTGTTTGAATTGTGCAGCAAGTTTGGAGAA
26091 GGATTTCGACAACAAGAGCCTGCATAAGTGGTTTGGTTTTGGT
196 GGATTTCGACAACAAGAGCCTGCATAAGTGGTTTGGTTTTGGT
26134 TT
1 TT
26136 AGATCACTTT
Statistics
Matches: 240, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
238 240 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (238 bp):
TTTTCTTGTGCAATTGATCTACTTAGTTGCAATTAGCCCTAATTGATTGTGTGATTGAGATTCTT
GGGCTGCTTTTGCTGTGAGTTAAGATCTATTTTGAATAATTTCAGGTTACAAACCCTATTGGATT
CAAGTGGTACAAAATAGGAGCTAATCGATTGAAAATTGTTTGAATTGTGCAGCAAGTTTGGAGAA
GGATTTCGACAACAAGAGCCTGCATAAGTGGTTTGGTTTTGGT
Done.