Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017595.1 Corchorus olitorius cultivar O-4 contig17628, 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: 19657
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Found at i:2505 original size:119 final size:122
Alignment explanation
Indices: 2217--2533 Score: 346
Period size: 119 Copynumber: 2.6 Consensus size: 122
2207 TAAAGTGCGT
*
2217 TGCACTCTTTTTCCCTTTATGATTGGTTTTGTCCCACAGGGTTTTCCGACTAAGG-TTTTAATGA
1 TGCACTCTTTTTCCC-TTATGATTGGTTTTGTCCCACTGGGTTTTCCGACTAAGGTTTTTAATGA
* * *
2281 GGCAACAATAGCACATTTAGATGTAATTGTCCTGAAGACATTTACATGGACTTAAATTGCTC
65 GGCAACAAGAGCACATGTAGA-GTAATTGTCCAGAAGACA--TACATGGACTTAAATTGC-C
*
2343 TAGCACTCTTTTTCCCTTTTG-TTCGGTTTTGTCCCACTGGGTTTTCCGACATAAGGTTTTTAAT
1 T-GCACTCTTTTTCCCTTATGATT-GGTTTTGTCCCACTGGGTTTTCCGAC-TAAGGTTTTTAAT
* * * *
2407 GAGGCAATGAAGAGCACATGTA-A-TATTTGTTCAGAAGACA-A-ATGGACTT-GATATG-C
63 GAGGCAA-CAAGAGCACATGTAGAGTAATTGTCCAGAAGACATACATGGACTTAAAT-TGCC
* * * *
2463 TGCACTCTTTTTTCCTTATGACTGGTTTTGTCCCATTGGGTTTTCC-AGCTTAAGGTTTTTAACG
1 TGCACTCTTTTTCCCTTATGATTGGTTTTGTCCCACTGGGTTTTCCGA-C-TAAGGTTTTTAATG
2527 AGGCAAC
64 AGGCAAC
2534 CATAATACGT
Statistics
Matches: 167, Mismatches: 16, Indels: 24
0.81 0.08 0.12
Matches are distributed among these distances:
118 1 0.01
119 59 0.35
120 3 0.02
121 2 0.01
122 10 0.06
123 1 0.01
125 2 0.01
126 44 0.26
127 19 0.11
128 15 0.09
129 11 0.07
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.38
Consensus pattern (122 bp):
TGCACTCTTTTTCCCTTATGATTGGTTTTGTCCCACTGGGTTTTCCGACTAAGGTTTTTAATGAG
GCAACAAGAGCACATGTAGAGTAATTGTCCAGAAGACATACATGGACTTAAATTGCC
Found at i:2985 original size:26 final size:26
Alignment explanation
Indices: 2946--2997 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
2936 TTTCTTTTTC
*
2946 TTTTTTGGGCTAAA-TGAAATTAGTT
1 TTTTTTGGGCTAAACTAAAATTAGTT
*
2971 TTTTTTTGGCATAAACTAAAATTAGTT
1 TTTTTTGGGC-TAAACTAAAATTAGTT
2998 ACTCGTACGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 9 0.39
26 4 0.17
27 10 0.43
ACGTcount: A:0.31, C:0.06, G:0.15, T:0.48
Consensus pattern (26 bp):
TTTTTTGGGCTAAACTAAAATTAGTT
Found at i:6063 original size:20 final size:20
Alignment explanation
Indices: 6038--6077 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
6028 TAATTAGGCC
6038 GAAAATTAGCAATAATTATT
1 GAAAATTAGCAATAATTATT
6058 GAAAATTAGCAATAATTATT
1 GAAAATTAGCAATAATTATT
6078 TCAATAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (20 bp):
GAAAATTAGCAATAATTATT
Found at i:10476 original size:8 final size:9
Alignment explanation
Indices: 10440--10477 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
10430 CCCAAATTAC
10440 TTATGGAAA
1 TTATGGAAA
*
10449 TTAAGGAAA
1 TTATGGAAA
10458 TTATGGAAA
1 TTATGGAAA
10467 TTAT-GAAA
1 TTATGGAAA
10475 TTA
1 TTA
10478 AATGAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 7 0.26
9 20 0.74
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.34
Consensus pattern (9 bp):
TTATGGAAA
Found at i:11820 original size:49 final size:47
Alignment explanation
Indices: 11743--11883 Score: 160
Period size: 49 Copynumber: 2.9 Consensus size: 47
11733 CAAGCAATCC
* *
11743 TTTACTTTTCACTGCACTTTTTCTCAATTTTTACTACAAAATTGAACT
1 TTTAATTTTCATTGCACTTTTTCTCAATTTTTA-TACAAAATTGAACT
* * *
11791 TTT-ATTTTTACTTGCATCTTTTTCTCAATTTTTAAGACAAAATTGATCT
1 TTTAATTTTCA-TTGCA-CTTTTTCTCAATTTTT-ATACAAAATTGAACT
* *
11840 TTTAATTTTCATCGCACTTTTTATCAATTTTT-TGACAAAATTGA
1 TTTAATTTTCATTGCACTTTTTCTCAATTTTTAT-ACAAAATTGA
11884 TTGGCACGCT
Statistics
Matches: 79, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
47 15 0.19
48 22 0.28
49 35 0.44
50 7 0.09
ACGTcount: A:0.28, C:0.16, G:0.06, T:0.50
Consensus pattern (47 bp):
TTTAATTTTCATTGCACTTTTTCTCAATTTTTATACAAAATTGAACT
Found at i:12743 original size:15 final size:15
Alignment explanation
Indices: 12702--12751 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
12692 TGCTAGGGTG
*
12702 AATGGTGCAAACAAC
1 AATGGTGCGAACAAC
12717 AATGGTGCGAACAAC
1 AATGGTGCGAACAAC
* *
12732 AATGGTGTGAACAAT
1 AATGGTGCGAACAAC
12747 AATGG
1 AATGG
12752 AAACGGTGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.42, C:0.14, G:0.26, T:0.18
Consensus pattern (15 bp):
AATGGTGCGAACAAC
Done.