Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023782.1 Corchorus olitorius cultivar O-4 contig23815, 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: 48562
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Found at i:4763 original size:29 final size:30
Alignment explanation
Indices: 4720--4779 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
4710 GAAGTTTGTG
* *
4720 TTTGAAGACTCATTGAAGACTTATTTGAAGA
1 TTTGAAGAC-CATTGAAGAATTATTTCAAGA
4751 TTTGAAGA-CATTGAAGAATTATTTCAAGA
1 TTTGAAGACCATTGAAGAATTATTTCAAGA
4780 AGAAAGAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 19 0.70
31 8 0.30
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.35
Consensus pattern (30 bp):
TTTGAAGACCATTGAAGAATTATTTCAAGA
Found at i:11590 original size:29 final size:31
Alignment explanation
Indices: 11543--11602 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
11533 GAAGTTCGTG
* *
11543 TTTGAAGACTCATTGAAGACTTATTTGAAGA
1 TTTGAAGACTCATTGAAGAATTATTTCAAGA
11574 TTTGAAGA-T-ATTGAAGAATTATTTCAAGA
1 TTTGAAGACTCATTGAAGAATTATTTCAAGA
11603 AGAAAGAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 18 0.67
30 1 0.04
31 8 0.30
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.37
Consensus pattern (31 bp):
TTTGAAGACTCATTGAAGAATTATTTCAAGA
Found at i:12206 original size:18 final size:18
Alignment explanation
Indices: 12183--12218 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
12173 AGATGTTTTC
12183 TTTTCTTCTAGTTTTTAG
1 TTTTCTTCTAGTTTTTAG
12201 TTTTCTTCTAGTTTTTAG
1 TTTTCTTCTAGTTTTTAG
12219 GTAAGGGTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.11, T:0.67
Consensus pattern (18 bp):
TTTTCTTCTAGTTTTTAG
Found at i:21518 original size:131 final size:131
Alignment explanation
Indices: 21284--21535 Score: 443
Period size: 131 Copynumber: 1.9 Consensus size: 131
21274 TGATTGTTGA
* *
21284 TTGTAATTGATTGATTTGATAATGCAGATTTGTGGCATAGGTCCACAAGGAAATTTTGCTTTGTT
1 TTGTAATTGATTGATTTGATAATGCAGATTTGTGGCATAGGCCCACAAGGAAAATTTGCTTTGTT
21349 GTTTCCGCTTTAATTATTTGTTTGGTTAATTCCTGGGATATCCGAAGTTACAACAAGGATTAGTG
66 GTTTCCGCTTTAATTATTTGTTTGGTTAATTCCTGGGATATCCGAAGTTACAACAAGGATTAGTG
21414 C
131 C
* *
21415 TTGTAATTGATTGATTTGATAGTGGAGATTTGTGGCATAGGCCCACAA-GAAAATTTGCTTTGTT
1 TTGTAATTGATTGATTTGATAATGCAGATTTGTGGCATAGGCCCACAAGGAAAATTTGCTTTGTT
*
21479 GTTTTCCGCTTTAATTATTTGTTTGGTTAATTCTTGGGATATCCGAAGTTACAACAA
66 G-TTTCCGCTTTAATTATTTGTTTGGTTAATTCCTGGGATATCCGAAGTTACAACAA
21536 AAGATTGTGG
Statistics
Matches: 115, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
130 16 0.14
131 99 0.86
ACGTcount: A:0.25, C:0.12, G:0.22, T:0.41
Consensus pattern (131 bp):
TTGTAATTGATTGATTTGATAATGCAGATTTGTGGCATAGGCCCACAAGGAAAATTTGCTTTGTT
GTTTCCGCTTTAATTATTTGTTTGGTTAATTCCTGGGATATCCGAAGTTACAACAAGGATTAGTG
C
Found at i:22380 original size:29 final size:30
Alignment explanation
Indices: 22318--22388 Score: 108
Period size: 29 Copynumber: 2.4 Consensus size: 30
22308 GAAAGGCACT
*
22318 AAAACGTCCAAAATTAAGAGTTTAAGGGAC
1 AAAACGTCCAAAATTAAGAGTTCAAGGGAC
* *
22348 AAAACGTCCAAAATTAA-AGTTCACGGGGC
1 AAAACGTCCAAAATTAAGAGTTCAAGGGAC
22377 AAAACGTCCAAA
1 AAAACGTCCAAA
22389 CCATACAAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
29 21 0.55
30 17 0.45
ACGTcount: A:0.46, C:0.18, G:0.18, T:0.17
Consensus pattern (30 bp):
AAAACGTCCAAAATTAAGAGTTCAAGGGAC
Found at i:23329 original size:13 final size:13
Alignment explanation
Indices: 23311--23335 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23301 TCTCATAAAT
23311 ATTTTTATTTATA
1 ATTTTTATTTATA
23324 ATTTTTATTTAT
1 ATTTTTATTTAT
23336 TTATTTATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTTTATTTATA
Found at i:23969 original size:3 final size:3
Alignment explanation
Indices: 23961--24013 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
23951 TCATTTAACT
23961 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
24009 TTA TT
1 TTA TT
24014 TAATTTTTTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:24197 original size:88 final size:87
Alignment explanation
Indices: 24036--24200 Score: 197
Period size: 88 Copynumber: 1.9 Consensus size: 87
24026 CATGCTTGGA
* * * * **
24036 TTTTCTTAAAAATTGGAGATTTGAGTTAGCACATTATTGTTATATGAATTCATCACATGAGTACG
1 TTTTCTTAAAAATTGAAAATTTGACTTAGCACATAATTG-TATATGAATTCATCACATGAGTAAA
*
24101 GCATTTTTTTTAAACCGATAACT
65 ACATTTTTTTTAAACCGATAACT
* * * *
24124 TTTTCTTAAAAATTGAAAATTTGACTTAGTACGTAATTG-ATATGAATTCATGATATGAGTAAAA
1 TTTTCTTAAAAATTGAAAATTTGACTTAGCACATAATTGTATATGAATTCATCACATGAGTAAAA
*
24188 CATCATTTTTTAA
66 CAT-TTTTTTTAA
24201 CCCCGCAAAC
Statistics
Matches: 64, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
86 23 0.36
87 8 0.12
88 33 0.52
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.41
Consensus pattern (87 bp):
TTTTCTTAAAAATTGAAAATTTGACTTAGCACATAATTGTATATGAATTCATCACATGAGTAAAA
CATTTTTTTTAAACCGATAACT
Found at i:26907 original size:30 final size:29
Alignment explanation
Indices: 26835--26907 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 29
26825 TAAACAAATA
26835 GACAATTTGCACCCTAAACTTTAATTTTG
1 GACAATTTGCACCCTAAACTTTAATTTTG
*
26864 GACAATTTACACCCTAAA-TTATAATTTATG
1 GACAATTTGCACCCTAAACTT-TAATTT-TG
*
26894 GACAATATGCACCC
1 GACAATTTGCACCC
26908 CAATTGGATG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
28 2 0.05
29 23 0.59
30 14 0.36
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.33
Consensus pattern (29 bp):
GACAATTTGCACCCTAAACTTTAATTTTG
Found at i:27062 original size:29 final size:29
Alignment explanation
Indices: 27025--27080 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
27015 TTGTCCCTAT
* *
27025 ATTATAGTTAAAGGTGCAAATTGTCCAAA
1 ATTAAAGTTAAAGGTGCAAAGTGTCCAAA
* *
27054 ATTAAAGTTTAGGGTGCAAAGTGTCCA
1 ATTAAAGTTAAAGGTGCAAAGTGTCCA
27081 TTTGCATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (29 bp):
ATTAAAGTTAAAGGTGCAAAGTGTCCAAA
Found at i:31015 original size:2 final size:2
Alignment explanation
Indices: 31008--31046 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
30998 GATTGTTAGT
*
31008 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31047 GTATTGTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31047 original size:12 final size:12
Alignment explanation
Indices: 31012--31050 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
31002 GTTAGTTATA
*
31012 TATATATATATA
1 TATATATATATG
31024 TATATATATATG
1 TATATATATATG
31036 TATATATATATG
1 TATATATATATG
31048 TAT
1 TAT
31051 TGTTTATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (12 bp):
TATATATATATG
Found at i:37954 original size:2 final size:2
Alignment explanation
Indices: 37947--37983 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
37937 ATTGTATGTG
37947 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
37984 AAATTATTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.