Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013476.1 Corchorus capsularis cultivar CVL-1 contig13497, 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: 19963
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Found at i:8558 original size:18 final size:18
Alignment explanation
Indices: 8535--8570 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
8525 TCTTGCACAT
8535 GATCAGGAGCTGCTGACA
1 GATCAGGAGCTGCTGACA
*
8553 GATCAGGAGCTGTTGACA
1 GATCAGGAGCTGCTGACA
8571 AAAATAATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.19, G:0.33, T:0.19
Consensus pattern (18 bp):
GATCAGGAGCTGCTGACA
Found at i:9178 original size:108 final size:110
Alignment explanation
Indices: 8987--9221 Score: 327
Period size: 109 Copynumber: 2.2 Consensus size: 110
8977 CGTAGCCAAA
* * *
8987 AGTGCCTTTCCTT-TTGTTGATTCTGACTTATGTAGCCCATTTAAAAAATCTATATTTTGACTTG
1 AGTGCCCTTCCTTGTTGATGATTCTGACCTATGTAGCCCATTTAAAAAATCTATATTTTGACTTG
* *
9051 GAGTGAGTGCACCCATAGGAGTGTTGCACTG-GCGCACCTCCGGG
66 GAGAGAGTGCACCCATAGGAGTGTTGCACTGAGCGCACCTCCAGG
*
9095 AGTGCCCTTCCTTGTTGATGATTCTGGCCTATGTAGCCCATTTAAAAAAAT-T-TATTTTGACTT
1 AGTGCCCTTCCTTGTTGATGATTCTGACCTATGTAGCCCATTT-AAAAAATCTATATTTTGACTT
* **
9158 GGAGCAG-GTGCACCCTTAGGAGTGTTGCACTGATTGCACCTCCAGG
65 GGAG-AGAGTGCACCCATAGGAGTGTTGCACTGAGCGCACCTCCAGG
*
9204 AGTGCCCCTCCTTGTTGA
1 AGTGCCCTTCCTTGTTGA
9222 CACTTCTAGC
Statistics
Matches: 113, Mismatches: 10, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
108 51 0.45
109 55 0.49
110 7 0.06
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.34
Consensus pattern (110 bp):
AGTGCCCTTCCTTGTTGATGATTCTGACCTATGTAGCCCATTTAAAAAATCTATATTTTGACTTG
GAGAGAGTGCACCCATAGGAGTGTTGCACTGAGCGCACCTCCAGG
Found at i:9251 original size:109 final size:110
Alignment explanation
Indices: 9029--9253 Score: 269
Period size: 109 Copynumber: 2.1 Consensus size: 110
9019 TAGCCCATTT
* *
9029 AAAAAATCTATATTTTGACTTGGAGTGAGTGCACCCATAGGAGTGTTGCACTGGCGCACCTCCGG
1 AAAAAATCTATATTTTGACTTGGAGAGAGTGCACCCATAGGAGTGTTGCACTGGCGCACCTCCAG
* * * * * ***
9094 GAGTGCCCTTCCTTGTTGATGATTCTGGCCTATGTAGCCCATTTA
66 GAGTGCCCCTCCTTGTTGATCATTCTAGCCTATGCAGCCAAAAAA
* **
9139 AAAAAAT-T-TATTTTGACTTGGAGCAG-GTGCACCCTTAGGAGTGTTGCACTGATTGCACCTCC
1 AAAAAATCTATATTTTGACTTGGAG-AGAGTGCACCCATAGGAGTGTTGCACTG-GCGCACCTCC
*
9201 AGGAGTGCCCCTCCTTGTTGA-CACTTCTAGCCTATGCAGCTAAAAAA
64 AGGAGTGCCCCTCCTTGTTGATCA-TTCTAGCCTATGCAGCCAAAAAA
9248 AAAAAA
1 AAAAAA
9254 GGCTTACAAT
Statistics
Matches: 98, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
108 40 0.41
109 51 0.52
110 7 0.07
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (110 bp):
AAAAAATCTATATTTTGACTTGGAGAGAGTGCACCCATAGGAGTGTTGCACTGGCGCACCTCCAG
GAGTGCCCCTCCTTGTTGATCATTCTAGCCTATGCAGCCAAAAAA
Found at i:9368 original size:79 final size:77
Alignment explanation
Indices: 9246--9439 Score: 237
Period size: 79 Copynumber: 2.5 Consensus size: 77
9236 GCAGCTAAAA
* * *
9246 AAAAAAAAGGCTTACAATGCCTATAGCCTATGTAGCTTAAAAAGAAAAGGCTTACAATGCCTATA
1 AAAAAAAAGGCGTACAACGCCTATAGCCTATGCAGCTTAAAAAG-AAAGGCTTACAATGCC--TA
9311 TAGCCAATGTAGCTT
63 TAGCCAATGTAGCTT
* * * * *
9326 -GAAAGAGGGCGTACAACGCCTATAGCCTATGCAGCTTAAAAAGAATGGCTTACCATGCCTATAG
1 AAAAAAAAGGCGTACAACGCCTATAGCCTATGCAGCTTAAAAAGAAAGGCTTACAATGCCTATAG
*
9390 CCTATGTAGCTT
66 CCAATGTAGCTT
* * * *
9402 AAAAAAAAGGCTTACTACGCCTACAGTCTATGCAGCTT
1 AAAAAAAAGGCGTACAACGCCTATAGCCTATGCAGCTT
9440 TGCAACGCCT
Statistics
Matches: 97, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
76 16 0.16
77 30 0.31
78 14 0.14
79 37 0.38
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.24
Consensus pattern (77 bp):
AAAAAAAAGGCGTACAACGCCTATAGCCTATGCAGCTTAAAAAGAAAGGCTTACAATGCCTATAG
CCAATGTAGCTT
Found at i:9386 original size:39 final size:39
Alignment explanation
Indices: 9228--9439 Score: 214
Period size: 39 Copynumber: 5.4 Consensus size: 39
9218 TTGACACTTC
* *
9228 TAGCCTATGCAGCTAAAAAAAAAAAAGGCTTACAATGCCTA
1 TAGCCTATGCAGCT--TAAAAAGAAAGGCTTACAATGCCTA
*
9269 TAGCCTATGTAGCTTAAAAAGAAAAGGCTTACAATGCCTATA
1 TAGCCTATGCAGCTTAAAAAG-AAAGGCTTACAATGCC--TA
* * * * * *
9311 TAGCCAATGTAGCTT-GAAAG-AGGGCGTACAACGCCTA
1 TAGCCTATGCAGCTTAAAAAGAAAGGCTTACAATGCCTA
* *
9348 TAGCCTATGCAGCTTAAAAAGAATGGCTTACCATGCCTA
1 TAGCCTATGCAGCTTAAAAAGAAAGGCTTACAATGCCTA
* * *
9387 TAGCCTATGTAGCTTAAAAA-AAAGGCTTACTACGCCTA
1 TAGCCTATGCAGCTTAAAAAGAAAGGCTTACAATGCCTA
* *
9425 CAGTCTATGCAGCTT
1 TAGCCTATGCAGCTT
9440 TGCAACGCCT
Statistics
Matches: 144, Mismatches: 22, Indels: 13
0.80 0.12 0.07
Matches are distributed among these distances:
37 15 0.10
38 31 0.22
39 49 0.34
40 16 0.11
41 17 0.12
42 16 0.11
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24
Consensus pattern (39 bp):
TAGCCTATGCAGCTTAAAAAGAAAGGCTTACAATGCCTA
Found at i:10036 original size:47 final size:45
Alignment explanation
Indices: 9984--10346 Score: 243
Period size: 45 Copynumber: 8.2 Consensus size: 45
9974 ATCACCTTCC
*
9984 TCCAACAATGAAAATTTATACGCTCTTTCCAACATGATGGTGGCGCT
1 TCCAACAAT-AAAATTTATACGCGC-TTCCAACATGATGGTGGCGCT
* * *
10031 TCCAACAATAAAATTTATATGCGCTTCCAACACGGTGGGGTGGCGCT
1 TCCAACAATAAAATTTATACGCGCTTCCAACATGAT--GGTGGCGCT
* ** * * * * *
10078 TCCAACAGACAAAACCTATACTCACTTCCAAAATGATGGTGACGCC
1 TCCAACA-ATAAAATTTATACGCGCTTCCAACATGATGGTGGCGCT
* * *
10124 TCCAATCACAAAAAAAATTTATACGCTCTTTCCAACATGAGGGTGGCGCT
1 TCC-A--AC-AATAAAATTTATACGCGC-TTCCAACATGATGGTGGCGCT
* * * *
10174 TCCAGCGATAAAATTTATATGCGCTTCCAAC---ATGGTTGCG--
1 TCCAACAATAAAATTTATACGCGCTTCCAACATGATGGTGGCGCT
* * *
10214 -----CAAT-AAATTTATATGCGCTTCCAACATGATTGTGGCGCC
1 TCCAACAATAAAATTTATACGCGCTTCCAACATGATGGTGGCGCT
* * * *
10253 TCCAATC-ACAAAATTTATACACTCTTCCAACATGAGGGTGGCGCT
1 TCCAA-CAATAAAATTTATACGCGCTTCCAACATGATGGTGGCGCT
* * * * *
10298 TCCAGCGATGAAATTTATATGCGCTTCCAAC---ATGGTTGCGCT
1 TCCAACAATAAAATTTATACGCGCTTCCAACATGATGGTGGCGCT
10340 TCCAACA
1 TCCAACA
10347 TGATGCTGAC
Statistics
Matches: 244, Mismatches: 51, Indels: 47
0.71 0.15 0.14
Matches are distributed among these distances:
34 21 0.09
35 3 0.01
37 7 0.03
42 21 0.09
44 2 0.01
45 70 0.29
46 37 0.15
47 27 0.11
48 20 0.08
49 15 0.06
50 21 0.09
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (45 bp):
TCCAACAATAAAATTTATACGCGCTTCCAACATGATGGTGGCGCT
Found at i:10270 original size:79 final size:80
Alignment explanation
Indices: 10138--10286 Score: 185
Period size: 79 Copynumber: 1.9 Consensus size: 80
10128 ATCACAAAAA
* * * **
10138 AAATTTATACGCTCTTTCCAACATGAGGGTGGCGCTTCCAGCGATAAAATTTATATGCGCTTCCA
1 AAATTTATACGCGCTTTCCAACATGAGGGTGGCGCCTCCAGCGACAAAATTTATACACGCTTCCA
10203 ACATGGTTGCGCAAT
66 ACATGGTTGCGCAAT
* ** * *
10218 AAATTTATATGCGC-TTCCAACATGATTGTGGCGCCTCCAATC-ACAAAATTTATACACTCTTCC
1 AAATTTATACGCGCTTTCCAACATGAGGGTGGCGCCTCC-AGCGACAAAATTTATACACGCTTCC
10281 AACATG
65 AACATG
10287 AGGGTGGCGC
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
79 44 0.76
80 14 0.24
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (80 bp):
AAATTTATACGCGCTTTCCAACATGAGGGTGGCGCCTCCAGCGACAAAATTTATACACGCTTCCA
ACATGGTTGCGCAAT
Found at i:10305 original size:124 final size:126
Alignment explanation
Indices: 10102--10338 Score: 388
Period size: 124 Copynumber: 1.9 Consensus size: 126
10092 CCTATACTCA
*
10102 CTTCCAAAATGATGGTGACGCCTCCAATCACAAAAAAAATTTATACGCTCTTTCCAACATGAGGG
1 CTTCCAAAATGATGGTGACGCCTCCAATCAC---AAAAATTTATACACTCTTTCCAACATGAGGG
10167 TGGCGCTTCCAGCGATAAAATTTATATGCGCTTCCAACATGGTTGCGCAATAAATTTATATGCG
63 TGGCGCTTCCAGCGATAAAATTTATATGCGCTTCCAACATGGTTGCGCAATAAATTTATATGCG
* * *
10231 CTTCCAACATGATTGTGGCGCCTCCAATCAC-AAAATTTATACACTC-TTCCAACATGAGGGTGG
1 CTTCCAAAATGATGGTGACGCCTCCAATCACAAAAATTTATACACTCTTTCCAACATGAGGGTGG
*
10294 CGCTTCCAGCGATGAAATTTATATGCGCTTCCAACATGGTTGCGC
66 CGCTTCCAGCGATAAAATTTATATGCGCTTCCAACATGGTTGCGC
10339 TTCCAACATG
Statistics
Matches: 103, Mismatches: 5, Indels: 5
0.91 0.04 0.04
Matches are distributed among these distances:
124 61 0.59
125 14 0.14
129 28 0.27
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (126 bp):
CTTCCAAAATGATGGTGACGCCTCCAATCACAAAAATTTATACACTCTTTCCAACATGAGGGTGG
CGCTTCCAGCGATAAAATTTATATGCGCTTCCAACATGGTTGCGCAATAAATTTATATGCG
Found at i:10361 original size:20 final size:17
Alignment explanation
Indices: 10317--10366 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
10307 GAAATTTATA
*
10317 TGCGCTTCCAACATGGT
1 TGCGCTTCCAACATGGC
10334 TGCGCTTCCAACATGATGC
1 TGCGCTTCCAACATG--GC
10353 TGACGCTTCCAACA
1 TG-CGCTTCCAACA
10367 GAGAGAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 15 0.52
19 3 0.10
20 11 0.38
ACGTcount: A:0.22, C:0.32, G:0.20, T:0.26
Consensus pattern (17 bp):
TGCGCTTCCAACATGGC
Found at i:10554 original size:41 final size:42
Alignment explanation
Indices: 10481--10689 Score: 176
Period size: 45 Copynumber: 4.8 Consensus size: 42
10471 TATGGTAACA
**
10481 GCGCTTCCAATCTCAA-AATT-TACACCGTCTTCCA-GGTGGTG
1 GCGCTTCCAATGACAAGAATTATAC-CC-TCTTCCATGGTGGTG
* *
10522 GCGCTTCCAATGACAA-AATTTATACCCACTTCCAACATAGTGGTG
1 GCGCTTCCAATGACAAGAA-TTATACCCTCTT-C--CATGGTGGTG
* *
10567 GCGCTTCCAATGACAAGAATTATACTCTCTTCCAATATGATGGTG
1 GCGCTTCCAATGACAAGAATTATACCCTCTTCC---ATGGTGGTG
* * *
10612 GCGCTTCCAATGGCAAGAATTATATCCTCTTCCAACATAGTGGT-
1 GCGCTTCCAATGACAAGAATTATACCCTCTT-C--CATGGTGGTG
* *
10656 GTGCTTCCAATGACAAGAATTATACTCTCTTCCA
1 GCGCTTCCAATGACAAGAATTATACCCTCTTCCA
10690 CATGGTGTTG
Statistics
Matches: 138, Mismatches: 17, Indels: 26
0.76 0.09 0.14
Matches are distributed among these distances:
41 21 0.15
42 6 0.04
43 4 0.03
44 30 0.22
45 73 0.53
46 3 0.02
48 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.30
Consensus pattern (42 bp):
GCGCTTCCAATGACAAGAATTATACCCTCTTCCATGGTGGTG
Found at i:10575 original size:45 final size:45
Alignment explanation
Indices: 10516--10689 Score: 246
Period size: 45 Copynumber: 3.9 Consensus size: 45
10506 CGTCTTCCAG
*
10516 GTGGTGGCGCTTCCAATGACAA-AATTTATACCCACTTCCAACATA
1 GTGGTGGCGCTTCCAATGACAAGAA-TTATACCCTCTTCCAACATA
* *
10561 GTGGTGGCGCTTCCAATGACAAGAATTATACTCTCTTCCAATAT-
1 GTGGTGGCGCTTCCAATGACAAGAATTATACCCTCTTCCAACATA
* *
10605 GATGGTGGCGCTTCCAATGGCAAGAATTATATCCTCTTCCAACATA
1 G-TGGTGGCGCTTCCAATGACAAGAATTATACCCTCTTCCAACATA
* *
10651 GTGGT-GTGCTTCCAATGACAAGAATTATACTCTCTTCCA
1 GTGGTGGCGCTTCCAATGACAAGAATTATACCCTCTTCCA
10690 CATGGTGTTG
Statistics
Matches: 115, Mismatches: 11, Indels: 7
0.86 0.08 0.05
Matches are distributed among these distances:
44 31 0.27
45 81 0.70
46 3 0.03
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (45 bp):
GTGGTGGCGCTTCCAATGACAAGAATTATACCCTCTTCCAACATA
Found at i:10644 original size:90 final size:89
Alignment explanation
Indices: 10517--10689 Score: 285
Period size: 90 Copynumber: 1.9 Consensus size: 89
10507 GTCTTCCAGG
10517 TGGTGGCGCTTCCAATGACAAAATTTATACCCACTTCCAACATAGTGGTGGCGCTTCCAATGACA
1 TGGTGGCGCTTCCAATGACAAAATTTATACCCACTTCCAACATAGTGGT-GCGCTTCCAATGACA
10582 AGAATTATACTCTCTTCCAATATGA
65 AGAATTATACTCTCTTCCAATATGA
* * * *
10607 TGGTGGCGCTTCCAATGGCAAGAA-TTATATCCTCTTCCAACATAGTGGTGTGCTTCCAATGACA
1 TGGTGGCGCTTCCAATGACAA-AATTTATACCCACTTCCAACATAGTGGTGCGCTTCCAATGACA
10671 AGAATTATACTCTCTTCCA
65 AGAATTATACTCTCTTCCA
10690 CATGGTGTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
89 33 0.42
90 43 0.55
91 2 0.03
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.30
Consensus pattern (89 bp):
TGGTGGCGCTTCCAATGACAAAATTTATACCCACTTCCAACATAGTGGTGCGCTTCCAATGACAA
GAATTATACTCTCTTCCAATATGA
Found at i:10985 original size:36 final size:36
Alignment explanation
Indices: 10935--11052 Score: 139
Period size: 36 Copynumber: 3.3 Consensus size: 36
10925 CTGTTTCTGC
** * *
10935 CTATAATGTTGATGGCCTAAGTCGCCTAATCTTTGG
1 CTATAATGCCGATGGCCTAAGTCGCCCAATATTTGG
* *
10971 CTATAATGCCGATGGCCTAAGTCGCCCAAAAATTGG
1 CTATAATGCCGATGGCCTAAGTCGCCCAATATTTGG
* * *
11007 CTATAAAGTCGCTGGCC-ATAGTCGCCCAATATTTGG
1 CTATAATGCCGATGGCCTA-AGTCGCCCAATATTTGG
11043 CTATAATGCC
1 CTATAATGCC
11053 ACTGACCTTT
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
35 1 0.01
36 67 0.99
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (36 bp):
CTATAATGCCGATGGCCTAAGTCGCCCAATATTTGG
Found at i:11340 original size:46 final size:45
Alignment explanation
Indices: 11204--11346 Score: 171
Period size: 46 Copynumber: 3.1 Consensus size: 45
11194 AGGAGATGCA
* *
11204 TCTTATGTGAGCGCCCTTCTTCAGAAAG-ATTACTCTATAGAATAGC
1 TCTTATGTGAGCACCCTTCTTCAGAAAGAATT-CTCTATAG-GTAGC
* * *
11250 TCTTATGTGAGCACACTTCTTCAGAAAGAATACTCTACATGGTAGC
1 TCTTATGTGAGCACCCTTCTTCAGAAAGAATTCTCTATA-GGTAGC
* *
11296 TCTTATGTGAGCACCCATCTCCAGAAAGAATTCTCTATACGGTAGCC
1 TCTTATGTGAGCACCCTTCTTCAGAAAGAATTCTCTATA-GGTAG-C
11343 TCTT
1 TCTT
11347 GCAACGCATT
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
46 75 0.90
47 8 0.10
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (45 bp):
TCTTATGTGAGCACCCTTCTTCAGAAAGAATTCTCTATAGGTAGC
Found at i:16178 original size:48 final size:48
Alignment explanation
Indices: 16107--16206 Score: 182
Period size: 48 Copynumber: 2.1 Consensus size: 48
16097 ACTAAGGAAA
*
16107 ATATTTGCATTGTTAGAAGAGTGGTCTAATTCTCAAGTGGATAAAAGT
1 ATATTTGCATTGTTAGAAGAGTGGTCTAATTCTCAACTGGATAAAAGT
*
16155 ATATTTGCATTGTTAGAAGAGTGGTCTAATTCTCAACTGGATAAAGGT
1 ATATTTGCATTGTTAGAAGAGTGGTCTAATTCTCAACTGGATAAAAGT
16203 ATAT
1 ATAT
16207 GTAGTAAACA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.33, C:0.09, G:0.22, T:0.36
Consensus pattern (48 bp):
ATATTTGCATTGTTAGAAGAGTGGTCTAATTCTCAACTGGATAAAAGT
Done.