Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008662.1 Corchorus capsularis cultivar CVL-1 contig08683, 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: 17275
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:251 original size:19 final size:19
Alignment explanation
Indices: 227--270 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
217 GTTCTGCACT
227 TGTGCATGTGTGTATGGCA
1 TGTGCATGTGTGTATGGCA
246 TGTGCATGTGTGTATGGCA
1 TGTGCATGTGTGTATGGCA
265 TGTGCA
1 TGTGCA
271 GGCCTGTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.16, C:0.11, G:0.36, T:0.36
Consensus pattern (19 bp):
TGTGCATGTGTGTATGGCA
Found at i:1524 original size:27 final size:27
Alignment explanation
Indices: 1487--1579 Score: 123
Period size: 27 Copynumber: 3.4 Consensus size: 27
1477 GAACTTAAAG
* * * *
1487 AATGACTAAAATGCCCCCGAGTGTAAA
1 AATGACCAAAATGCCCCTGAGCGCAAA
*
1514 AATGACCAAAATGCCCCTGAGCGCGAA
1 AATGACCAAAATGCCCCTGAGCGCAAA
* *
1541 AATGACCAAAATACCCCTGGGCGCAAA
1 AATGACCAAAATGCCCCTGAGCGCAAA
1568 AATGACCAAAAT
1 AATGACCAAAAT
1580 ACCCTTGGGC
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.42, C:0.26, G:0.18, T:0.14
Consensus pattern (27 bp):
AATGACCAAAATGCCCCTGAGCGCAAA
Found at i:1580 original size:27 final size:27
Alignment explanation
Indices: 1511--1590 Score: 124
Period size: 27 Copynumber: 3.0 Consensus size: 27
1501 CCCCGAGTGT
* *
1511 AAAAATGACCAAAATGCCCCTGAGCGC
1 AAAAATGACCAAAATACCCCTGGGCGC
*
1538 GAAAATGACCAAAATACCCCTGGGCGC
1 AAAAATGACCAAAATACCCCTGGGCGC
*
1565 AAAAATGACCAAAATACCCTTGGGCG
1 AAAAATGACCAAAATACCCCTGGGCG
1591 ACCCTAATGC
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.40, C:0.28, G:0.20, T:0.12
Consensus pattern (27 bp):
AAAAATGACCAAAATACCCCTGGGCGC
Found at i:5669 original size:17 final size:17
Alignment explanation
Indices: 5647--5680 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5637 TTGTGTTCTC
5647 TAGGGTTACATAAGGTG
1 TAGGGTTACATAAGGTG
5664 TAGGGTTACATAAGGTG
1 TAGGGTTACATAAGGTG
5681 GCTATTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.35, T:0.29
Consensus pattern (17 bp):
TAGGGTTACATAAGGTG
Found at i:5826 original size:16 final size:18
Alignment explanation
Indices: 5795--5833 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
5785 TCCTTGGGTT
5795 GAATCCTAGTGAAATTC-G
1 GAATCCTAG-GAAATTCTG
5813 GAATCCTA-GAAATTCTG
1 GAATCCTAGGAAATTCTG
5830 GAAT
1 GAAT
5834 TCTGCAGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 7 0.35
17 5 0.25
18 8 0.40
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (18 bp):
GAATCCTAGGAAATTCTG
Found at i:9288 original size:13 final size:13
Alignment explanation
Indices: 9270--9297 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
9260 TAAATAAGGG
9270 TATATTTGAAAAA
1 TATATTTGAAAAA
9283 TATATTTGAAAAA
1 TATATTTGAAAAA
9296 TA
1 TA
9298 AAGGGTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (13 bp):
TATATTTGAAAAA
Found at i:11090 original size:156 final size:155
Alignment explanation
Indices: 10590--11164 Score: 798
Period size: 155 Copynumber: 3.7 Consensus size: 155
10580 ATGTATATCA
* * * *
10590 TCTTGGCTAAGTTTCATCTCAAACGGACTTTAGATGAAAAACTTATGCACGTTTTTCAGTTAAGG
1 TCTTGGCAAAGTTTCATCTCAATCAGACTTAAGATGAAAAACTTATGCACGTTTTTCAGTTAAGG
* *
10655 ACAGTTTGGGGTGAAAAACCAGTTCACTATGAAGGAGAGCTCGGTTTTACTTAGAATTTTTTCCA
66 ACAGTTTGGGGTGAGAAACCAGTTCACCATGAAGGAGAGCTCGGTTTTACTTAGAATTTTTTCCA
*
10720 TAGTGTTATGGAGATAATCTAAGTC
131 TAGTCTTATGGAGATAATCTAAGTC
* * * *
10745 CCTTGGCGAAGTTTCATCTCAATCAGACTTAAGGTGAAAAACTTATGCACATTTTTCAGTTAAGG
1 TCTTGGCAAAGTTTCATCTCAATCAGACTTAAGATGAAAAACTTATGCACGTTTTTCAGTTAAGG
* *
10810 ACAGTTTGGGGTGAGAAACCAGTTCACTATGAAGGAGTGCTCGGTTTTACTTAGAATTTTTTCCA
66 ACAGTTTGGGGTGAGAAACCAGTTCACCATGAAGGAGAGCTCGGTTTTACTTAGAATTTTTTCCA
* *
10875 TAGTCTTATGGAGATAACCTAAGCC
131 TAGTCTTATGGAGATAATCTAAGTC
* ** * * *
10900 TACTGGTGG-AAA--TTCAGCCTC-ATTGGACTGAAGATGAAAAACTTACGCATGTTTTTCAGTT
1 T-CT--TGGCAAAGTTTCA-TCTCAATCAGACTTAAGATGAAAAACTTATGCACGTTTTTCAGTT
* * *
10961 AAGGACAATTTGGGGTGAGAAACCAAGTTCACCATGAAGGAGAGCTCAGTTTTACTTAGAATTGT
62 AAGGACAGTTTGGGGTGAGAAACC-AGTTCACCATGAAGGAGAGCTCGGTTTTACTTAGAATTTT
*
11026 TTCCATAGTCTTATGGAGATTATCTAAGTC
126 TTCCATAGTCTTATGGAGATAATCTAAGTC
** *
11056 TCTTGGCAAAGTTTCATCTCAATCAGACTTAAGATGAAAAACTTATGCTTGTTTTTCACTTAAGG
1 TCTTGGCAAAGTTTCATCTCAATCAGACTTAAGATGAAAAACTTATGCACGTTTTTCAGTTAAGG
* *
11121 ACAGTTTGGGGTGTGAAACCTAGTTCACCATGAAGGAGGGCTCG
66 ACAGTTTGGGGTGAGAAACC-AGTTCACCATGAAGGAGAGCTCG
11165 AACCCAGCCA
Statistics
Matches: 369, Mismatches: 42, Indels: 17
0.86 0.10 0.04
Matches are distributed among these distances:
153 3 0.01
154 3 0.01
155 208 0.56
156 150 0.41
157 2 0.01
158 3 0.01
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (155 bp):
TCTTGGCAAAGTTTCATCTCAATCAGACTTAAGATGAAAAACTTATGCACGTTTTTCAGTTAAGG
ACAGTTTGGGGTGAGAAACCAGTTCACCATGAAGGAGAGCTCGGTTTTACTTAGAATTTTTTCCA
TAGTCTTATGGAGATAATCTAAGTC
Found at i:11505 original size:28 final size:28
Alignment explanation
Indices: 11473--11544 Score: 135
Period size: 28 Copynumber: 2.6 Consensus size: 28
11463 GCATGCTGTG
11473 TGACATATCAGAGGGAAGATTTTCCGCC
1 TGACATATCAGAGGGAAGATTTTCCGCC
*
11501 TGACATATCAGAGGGAAGATTTTTCGCC
1 TGACATATCAGAGGGAAGATTTTCCGCC
11529 TGACATATCAGAGGGA
1 TGACATATCAGAGGGA
11545 GACGTCCTGG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (28 bp):
TGACATATCAGAGGGAAGATTTTCCGCC
Found at i:15054 original size:16 final size:16
Alignment explanation
Indices: 15029--15063 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
15019 CTTATAATAA
*
15029 GGAACGGAGGGACTAG
1 GGAACAGAGGGACTAG
15045 GGAACAGAGGGACTAG
1 GGAACAGAGGGACTAG
15061 GGA
1 GGA
15064 GTAATTAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.49, T:0.06
Consensus pattern (16 bp):
GGAACAGAGGGACTAG
Found at i:16920 original size:15 final size:15
Alignment explanation
Indices: 16900--16931 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
16890 TTGGGATTTT
*
16900 CTAAATATTTGTTAA
1 CTAAATAATTGTTAA
16915 CTAAATAATTGTTAA
1 CTAAATAATTGTTAA
16930 CT
1 CT
16932 TTCGACCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (15 bp):
CTAAATAATTGTTAA
Done.