Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021714.1 Corchorus olitorius cultivar O-4 contig21747, 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: 15234
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Found at i:5307 original size:41 final size:41
Alignment explanation
Indices: 5250--5334 Score: 152
Period size: 41 Copynumber: 2.1 Consensus size: 41
5240 GATGAGCTTG
*
5250 GGTATGTCCCTGTTTTGTTCCTGTATTCATGTATGCATATT
1 GGTATGTCCCTATTTTGTTCCTGTATTCATGTATGCATATT
*
5291 GGTATGTCCCTATTTTGTTCCTGTATTCATGTATGCATTTT
1 GGTATGTCCCTATTTTGTTCCTGTATTCATGTATGCATATT
5332 GGT
1 GGT
5335 CCTGCTTTGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.14, C:0.16, G:0.20, T:0.49
Consensus pattern (41 bp):
GGTATGTCCCTATTTTGTTCCTGTATTCATGTATGCATATT
Found at i:6943 original size:50 final size:50
Alignment explanation
Indices: 6862--6968 Score: 153
Period size: 50 Copynumber: 2.1 Consensus size: 50
6852 CGATCAACTT
* *
6862 CTTTGAATCGTCTTCTAATCCAATATAAAAAGGACTGTCTTCCGCTTATC
1 CTTTGAATCGTCTTCCAATCCAATATAAAAAGGACCGTCTTCCGCTTATC
* * *
6912 CTTTGAA-CTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAATC-GTCTTCCAATCCAATATAAAAAGGACCGTCTTCCGCTTATC
6962 CTTTGAA
1 CTTTGAA
6969 GAATTTCATT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
49 1 0.02
50 50 0.98
ACGTcount: A:0.26, C:0.25, G:0.12, T:0.36
Consensus pattern (50 bp):
CTTTGAATCGTCTTCCAATCCAATATAAAAAGGACCGTCTTCCGCTTATC
Found at i:7228 original size:64 final size:64
Alignment explanation
Indices: 7153--7562 Score: 507
Period size: 64 Copynumber: 6.4 Consensus size: 64
7143 CCGGTGCATC
* * * * * *
7153 TCTTAACAAGATCATCTTCCGATCAACTTCTGAAAATTTTTGAGAAACCCTCTTCTTGCATACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTATTGAGAAACCATCTTCTGGTATACT
* * * * * * *
7217 TCTTGACAAGATCGTCTTCCGATCAATTTCTAAAAACTATTGAGAAATCATCTTCCGATGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTATTGAGAAACCATCTTCTGGTATACT
* * *
7281 TCTTGACAAGATTGTCTTCCGATCAACTTCTGAAAATTATTGAGAAACCATCTTCCGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTATTGAGAAACCATCTTCTGGTATACT
* * * * * * * *
7345 TCATGATAAGGTCGTCTTCCGATCGACTTCTGAAAATTGTTGAGAAACCAGCTTCTGGTGTATT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTATTGAGAAACCATCTTCTGGTATACT
**
7409 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATCGTTGAGAAAACCATCTTCTGG-AGTAC
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTATTGAG-AAACCATCTTCTGGTA-TAC
7473 T
64 T
* * * * * *
7474 TCTTGACCAGATCGTCTTCTGGTCAACTTTTGAAAATTTTTGAGAAACCATCTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTATTGAGAAACCATCTTCTGGTATACT
7538 TCTTGACAAGATCGTCTTCCGATCA
1 TCTTGACAAGATCGTCTTCCGATCA
7563 TCTGAAAATT
Statistics
Matches: 297, Mismatches: 46, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
64 243 0.82
65 54 0.18
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.35
Consensus pattern (64 bp):
TCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTATTGAGAAACCATCTTCTGGTATACT
Found at i:7556 original size:193 final size:191
Alignment explanation
Indices: 7134--7575 Score: 561
Period size: 192 Copynumber: 2.3 Consensus size: 191
7124 ACTTCTAAAT
* * * * *
7134 AACCGTCTTCCGGTGCA-TCTCTTAACAAGATCATCTTCCGATCAACTTCTGAAAATTTTTGAGA
1 AACCATCTTCCGGTGTACT-TCTTGACAAGATCGTCTTCCGATC-ACTTCTGAAAATTGTTGAGA
** * *
7198 AACCCTCTTCTTGCATACTTCTTGACAAGATCGTCTTCCGATCAATTTCTAAAAACTATTGAGAA
64 AACCAGCTTCTGGCATACTTCTTGACAAGATCGTCTTCCGATCAACTTCTAAAAACTATTGAGAA
* *
7263 ATCATCTTCCGATGTACTTCTTGACAAGATTGTCTTCCGATCAACTTCTGAAAATTATTGAGA
129 ACCATCTTCCGATGTACTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTATTGAGA
* * *
7326 AACCATCTTCCGGTGTACTTCATGATAAGGTCGTCTTCCGATCGACTTCTGAAAATTGTTGAGAA
1 AACCATCTTCCGGTGTACTTCTTGACAAGATCGTCTTCCGATC-ACTTCTGAAAATTGTTGAGAA
** * * *
7391 ACCAGCTTCTGGTGTATTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAA-TCGTTGAGAA
65 ACCAGCTTCTGGCATACTTCTTGACAAGATCGTCTTCCGATCAACTTCTAAAAACT-ATTGAG-A
* * * * * *
7455 AACCATCTTCTGGA-GTACTTCTTGACCAGATCGTCTTCTGGTCAACTTTTGAAAATTTTTGAGA
128 AACCATCTTC-CGATGTACTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTATTGAGA
*
7519 AACCATCTTCTGGTGTACTTCTTGACAAGATCGTCTTCCGATCA--TCTGAAAATTGTT
1 AACCATCTTCCGGTGTACTTCTTGACAAGATCGTCTTCCGATCACTTCTGAAAATTGTT
7576 TCTAGCAAAC
Statistics
Matches: 216, Mismatches: 30, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
190 13 0.06
191 1 0.00
192 106 0.49
193 94 0.44
194 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (191 bp):
AACCATCTTCCGGTGTACTTCTTGACAAGATCGTCTTCCGATCACTTCTGAAAATTGTTGAGAAA
CCAGCTTCTGGCATACTTCTTGACAAGATCGTCTTCCGATCAACTTCTAAAAACTATTGAGAAAC
CATCTTCCGATGTACTTCTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTATTGAGA
Found at i:7621 original size:193 final size:192
Alignment explanation
Indices: 7222--7638 Score: 486
Period size: 193 Copynumber: 2.2 Consensus size: 192
7212 ATACTTCTTG
* * *
7222 ACAAGATCGTCTTCCGATCAATTTCT-AAAAACTATTGAGAAATCATCTTCCGATGTACTTCTTG
1 ACAAGATCGTCTTCCGATCAACTTCTGAAAATCTATTGAGAAACCATCTTCCGATGTACTTCTTG
*
7286 ACAAGATTGTCTTCCGATCAACTTCTGAAAATTATTGAGAAACCATCTTCCGGTGTACTTCATGA
66 ACAAGATCGTCTTCCGATCAACTTCTGAAAATTATTGAGAAACCATCTTCCGGTGTACTTCATGA
* * * * * * *
7351 TAAGGTCGTCTTCCGATCGACTTCTGAAAATTGTTGAGAAACCAGCTTCTGGTGTATTTCTTG
131 CAAGATCGTCTTCCGATCGAC-TCTGAAAATTGTTGAGAAACCAGCTTCCGATGTATTCCCTA
* *
7414 ACAAGATCGTCTTCCGATCAACTTCTGAAAATC-GTTGAGAAAACCATCTTCTGGA-GTACTTCT
1 ACAAGATCGTCTTCCGATCAACTTCTGAAAATCTATTGAG-AAACCATCTTC-CGATGTACTTCT
* * * * * * *
7477 TGACCAGATCGTCTTCTGGTCAACTTTTGAAAATTTTTGAGAAACCATCTTCTGGTGTACTTCTT
64 TGACAAGATCGTCTTCCGATCAACTTCTGAAAATTATTGAGAAACCATCTTCCGGTGTACTTCAT
*
7542 GACAAGATCGTCTTCCGATC-A-TCTGAAAATTGTTTCTAGCAAACC-GTCTTCCGATGTATTCC
129 GACAAGATCGTCTTCCGATCGACTCTGAAAATTG-TT-GAG-AAACCAG-CTTCCGATGTATTCC
7604 CTA
190 CTA
** * * * *
7607 ATGAGATTGTCTTCCAATCAGCATCTGAAAAT
1 ACAAGATCGTCTTCCGATCAACTTCTGAAAAT
7639 TCAATCTAGC
Statistics
Matches: 191, Mismatches: 27, Indels: 13
0.83 0.12 0.06
Matches are distributed among these distances:
190 11 0.06
191 2 0.01
192 34 0.18
193 142 0.74
194 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (192 bp):
ACAAGATCGTCTTCCGATCAACTTCTGAAAATCTATTGAGAAACCATCTTCCGATGTACTTCTTG
ACAAGATCGTCTTCCGATCAACTTCTGAAAATTATTGAGAAACCATCTTCCGGTGTACTTCATGA
CAAGATCGTCTTCCGATCGACTCTGAAAATTGTTGAGAAACCAGCTTCCGATGTATTCCCTA
Found at i:13866 original size:25 final size:25
Alignment explanation
Indices: 13828--13880 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
13818 CCAAGACATA
* *
13828 AATAAAAGGTCCAAATGCATAAAGG
1 AATAAAAGGCCCAAATGCACAAAGG
* *
13853 AATAAAAGGCCCAAGTGCACCAAGG
1 AATAAAAGGCCCAAATGCACAAAGG
13878 AAT
1 AAT
13881 TTAAAAGCCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.49, C:0.17, G:0.21, T:0.13
Consensus pattern (25 bp):
AATAAAAGGCCCAAATGCACAAAGG
Found at i:14581 original size:15 final size:16
Alignment explanation
Indices: 14557--14596 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
14547 AGAAGTTGAA
*
14557 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
14572 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
14588 AGAAAACAA
1 AGAAAACAA
14597 AACAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Done.