Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019647.1 Corchorus olitorius cultivar O-4 contig19680, 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: 29654
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:725 original size:71 final size:71
Alignment explanation
Indices: 642--784 Score: 277
Period size: 71 Copynumber: 2.0 Consensus size: 71
632 TCCACCACGT
642 CATCCGTGGTCCCGACCAATAAAATTTTGAGAAGTCAGATTTCTTCCCAAAATTTAGGCACAAAT
1 CATCCGTGGTCCCGACCAATAAAATTTTGAGAAGTCAGATTTCTTCCCAAAATTTAGGCACAAAT
707 TTAGCA
66 TTAGCA
*
713 CATCCGTGGTCCCGACCAATAGAATTTTGAGAAGTCAGATTTCTTCCCAAAATTTAGGCACAAAT
1 CATCCGTGGTCCCGACCAATAAAATTTTGAGAAGTCAGATTTCTTCCCAAAATTTAGGCACAAAT
778 TTAGCA
66 TTAGCA
784 C
1 C
785 CAGGTTTAGC
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (71 bp):
CATCCGTGGTCCCGACCAATAAAATTTTGAGAAGTCAGATTTCTTCCCAAAATTTAGGCACAAAT
TTAGCA
Found at i:1001 original size:8 final size:8
Alignment explanation
Indices: 988--1017 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
978 GTATGAAATA
988 TTTCCTTG
1 TTTCCTTG
996 TTTCCTTG
1 TTTCCTTG
1004 TTTCCTTG
1 TTTCCTTG
1012 TTTCCT
1 TTTCCT
1018 ACCCTAGTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.00, C:0.27, G:0.10, T:0.63
Consensus pattern (8 bp):
TTTCCTTG
Found at i:11529 original size:90 final size:89
Alignment explanation
Indices: 11376--11557 Score: 346
Period size: 90 Copynumber: 2.0 Consensus size: 89
11366 TAAAGATCAG
11376 TCACTGTCAAGAACAGTCATCCACTCCATCTCCAATTATCTGGCTTTGTTTTTCATTCAAAATGA
1 TCACTGTCAAGAACAGTCATCCACTCCATCTCCAATTATCTGGCTTTGTTTTTCATTCAAAATGA
11441 TATTACTCCAAGCTAGAAAAAATTT
66 TATTACTCCAAGCTAG-AAAAATTT
*
11466 TCACTGTCAAGAACAGTCATCCACTCCATCTCCAATTATCTGGCTTTGTTTTTTATTCAAAATGA
1 TCACTGTCAAGAACAGTCATCCACTCCATCTCCAATTATCTGGCTTTGTTTTTCATTCAAAATGA
11531 TATTACTCCAAGCTAGAAAAATTT
66 TATTACTCCAAGCTAGAAAAATTT
11555 TCA
1 TCA
11558 ACAAAACTTT
Statistics
Matches: 91, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
89 11 0.12
90 80 0.88
ACGTcount: A:0.32, C:0.23, G:0.10, T:0.35
Consensus pattern (89 bp):
TCACTGTCAAGAACAGTCATCCACTCCATCTCCAATTATCTGGCTTTGTTTTTCATTCAAAATGA
TATTACTCCAAGCTAGAAAAATTT
Found at i:16228 original size:22 final size:22
Alignment explanation
Indices: 16202--16283 Score: 110
Period size: 22 Copynumber: 3.7 Consensus size: 22
16192 AAAATGGCAT
*
16202 GGCACGGCACGACCCACGTGTC
1 GGCACGGCACGACCCACGTGCC
16224 GGCACGGCACGACCCACGTGCC
1 GGCACGGCACGACCCACGTGCC
* *
16246 GGCACAGCACGACCCACATGCC
1 GGCACGGCACGACCCACGTGCC
* * *
16268 GACGCAGCACGACCCA
1 GGCACGGCACGACCCA
16284 TTTATAATGT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 55 1.00
ACGTcount: A:0.23, C:0.44, G:0.28, T:0.05
Consensus pattern (22 bp):
GGCACGGCACGACCCACGTGCC
Found at i:18465 original size:66 final size:66
Alignment explanation
Indices: 18373--18496 Score: 230
Period size: 66 Copynumber: 1.9 Consensus size: 66
18363 CAGCTTCACC
* *
18373 TGAAACGGTGCCGGATTTTTCAAAAGAACCTGATATGGCCTTAGAACCCTTTGAAGCACTTGAAC
1 TGAAACGGCGCCAGATTTTTCAAAAGAACCTGATATGGCCTTAGAACCCTTTGAAGCACTTGAAC
18438 T
66 T
18439 TGAAACGGCGCCAGATTTTTCAAAAGAACCTGATATGGCCTTAGAACCCTTTGAAGCA
1 TGAAACGGCGCCAGATTTTTCAAAAGAACCTGATATGGCCTTAGAACCCTTTGAAGCA
18497 TTTTCACCTG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 56 1.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (66 bp):
TGAAACGGCGCCAGATTTTTCAAAAGAACCTGATATGGCCTTAGAACCCTTTGAAGCACTTGAAC
T
Found at i:18676 original size:36 final size:37
Alignment explanation
Indices: 18627--18718 Score: 87
Period size: 42 Copynumber: 2.4 Consensus size: 37
18617 TTGGAATCGG
**
18627 CGCTTGAACTTGAA-ACAGAGCCAGAGCCTTTGGAAT
1 CGCTTGATGTTGAATACAGAGCCAGAGCCTTTGGAAT
* * *
18663 CGCTTGATGTTGAACCTGATACGGTGGCAGAGCCTTTGGAAT
1 CGCTTGATGTTG-A----ATACAGAGCCAGAGCCTTTGGAAT
18705 CGCTTGATGTTGAA
1 CGCTTGATGTTGAA
18719 CCTGATACGG
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
36 10 0.22
37 2 0.04
41 2 0.04
42 31 0.69
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (37 bp):
CGCTTGATGTTGAATACAGAGCCAGAGCCTTTGGAAT
Found at i:18694 original size:42 final size:42
Alignment explanation
Indices: 18648--18816 Score: 232
Period size: 42 Copynumber: 4.0 Consensus size: 42
18638 GAAACAGAGC
*
18648 CAGAGCCTTTGGAATCGCTTGATGTTGAACCTGATACGGTGG
1 CAGAGCCTTTGGAATCGCTTGAAGTTGAACCTGATACGGTGG
*
18690 CAGAGCCTTTGGAATCGCTTGATGTTGAACCTGATACGGTGG
1 CAGAGCCTTTGGAATCGCTTGAAGTTGAACCTGATACGGTGG
** * ** *
18732 CAGAGCCTTTGGAATC-CTTTGAAGTTGATGCAGAGGCGGCGG
1 CAGAGCCTTTGGAATCGC-TTGAAGTTGAACCTGATACGGTGG
* *
18774 CGGAGCCTTTGGAATCACTTGAAGTTGAACCTGATACGGTGG
1 CAGAGCCTTTGGAATCGCTTGAAGTTGAACCTGATACGGTGG
18816 C
1 C
18817 GCCGGCGGCA
Statistics
Matches: 111, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
41 1 0.01
42 109 0.98
43 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.32, T:0.27
Consensus pattern (42 bp):
CAGAGCCTTTGGAATCGCTTGAAGTTGAACCTGATACGGTGG
Found at i:19897 original size:14 final size:14
Alignment explanation
Indices: 19875--19904 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19865 AATAAGGTAT
*
19875 TATTGTAATTTAAA
1 TATTATAATTTAAA
19889 TATTATAATTTAAA
1 TATTATAATTTAAA
19903 TA
1 TA
19905 ACATATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (14 bp):
TATTATAATTTAAA
Found at i:28026 original size:21 final size:19
Alignment explanation
Indices: 28000--28058 Score: 82
Period size: 19 Copynumber: 3.0 Consensus size: 19
27990 CGCTGCTCTA
28000 ATAATCTCATCTGTACAGT
1 ATAATCTCATCTGTACAGT
* *
28019 ACCTAATCTAATTTGTACAGT
1 A--TAATCTCATCTGTACAGT
28040 ATAATCTCATCTGTACAGT
1 ATAATCTCATCTGTACAGT
28059 TGATAAACAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.37
Consensus pattern (19 bp):
ATAATCTCATCTGTACAGT
Done.