Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017354.1 Corchorus olitorius cultivar O-4 contig17387, 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: 70273
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:1524 original size:32 final size:32
Alignment explanation
Indices: 1483--1545 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
1473 CCTGCCTATT
1483 TAAAACTATTCAAATCATATCATATATATTTG
1 TAAAACTATTCAAATCATATCATATATATTTG
1515 TAAAACTATTCAAATCATATCATATATATTT
1 TAAAACTATTCAAATCATATCATATATATTT
1546 TTCTCTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.44, C:0.13, G:0.02, T:0.41
Consensus pattern (32 bp):
TAAAACTATTCAAATCATATCATATATATTTG
Found at i:7758 original size:42 final size:42
Alignment explanation
Indices: 7706--7795 Score: 137
Period size: 45 Copynumber: 2.1 Consensus size: 42
7696 AGTGCATTAC
*
7706 CTAAATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAAATTCTATCTCCATCTCTAGATAATTCATCAAAATAAAG
7747 CTAATATTCTACTTCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAA-ATTCTA--TCTCCATCTCTAGATAATTCATCAAAATAAAG
7792 CTAA
1 CTAA
7796 CATTAATTGT
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.14
45 34 0.77
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.33
Consensus pattern (42 bp):
CTAAATTCTATCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:14802 original size:10 final size:10
Alignment explanation
Indices: 14787--14843 Score: 96
Period size: 10 Copynumber: 5.6 Consensus size: 10
14777 ATACCTTGAT
14787 ATATCCGTAA
1 ATATCCGTAA
14797 ATATCCCGTAA
1 ATAT-CCGTAA
*
14808 ATATCAGTAA
1 ATATCCGTAA
14818 ATATCCGTAA
1 ATATCCGTAA
14828 ATATCCGTAA
1 ATATCCGTAA
14838 ATATCC
1 ATATCC
14844 ATATTAAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
10 34 0.77
11 10 0.23
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (10 bp):
ATATCCGTAA
Found at i:15377 original size:17 final size:17
Alignment explanation
Indices: 15355--15408 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
15345 AAAATATCTA
15355 TTTCAATTAAGTATGGG
1 TTTCAATTAAGTATGGG
* **
15372 TTTCAACTTAA-AATTTG
1 TTTCAA-TTAAGTATGGG
*
15389 TTTCAATTAAGTCTGGG
1 TTTCAATTAAGTATGGG
15406 TTT
1 TTT
15409 TGGTCATCTC
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
16 4 0.14
17 20 0.71
18 4 0.14
ACGTcount: A:0.28, C:0.09, G:0.17, T:0.46
Consensus pattern (17 bp):
TTTCAATTAAGTATGGG
Found at i:15434 original size:40 final size:38
Alignment explanation
Indices: 15343--15450 Score: 116
Period size: 40 Copynumber: 2.9 Consensus size: 38
15333 CACATTGTTG
* *
15343 TCAAAATATCTATTTCAATTAAGTATGGG--TT-TCAAC
1 TCAAAATAT-TGTTTCAATTAAGTCTGGGTTTTGTCAAC
* *
15379 TTAAAAT-TTGTTTCAATTAAGTCTGGGTTTTGGTCATC
1 TCAAAATATTGTTTCAATTAAGTCTGGGTTTT-GTCAAC
*
15417 TCAAAATATATGTTTCAATTAACTCTGGGTTTTG
1 TCAAAATAT-TGTTTCAATTAAGTCTGGGTTTTG
15451 CATTTAATGA
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
34 17 0.28
35 1 0.02
36 8 0.13
38 10 0.17
39 2 0.03
40 22 0.37
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.44
Consensus pattern (38 bp):
TCAAAATATTGTTTCAATTAAGTCTGGGTTTTGTCAAC
Found at i:22918 original size:18 final size:19
Alignment explanation
Indices: 22895--22932 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
22885 TAAGTCCCAT
22895 AAACTT-TGCTAACGTGGC
1 AAACTTATGCTAACGTGGC
22913 AAACTTATGCTAACGTGGC
1 AAACTTATGCTAACGTGGC
22932 A
1 A
22933 CTTCCACGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (19 bp):
AAACTTATGCTAACGTGGC
Found at i:23962 original size:25 final size:25
Alignment explanation
Indices: 23934--23984 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
23924 AAGGCAAAGT
23934 TTAG-AATTGAAGAAGAATAATCAAG
1 TTAGCAATTG-AGAAGAATAATCAAG
* * *
23959 TTAGCATTTGAGAATAATACTCAAG
1 TTAGCAATTGAGAAGAATAATCAAG
23984 T
1 T
23985 CAAGACAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (25 bp):
TTAGCAATTGAGAAGAATAATCAAG
Found at i:25607 original size:60 final size:60
Alignment explanation
Indices: 25514--25634 Score: 224
Period size: 60 Copynumber: 2.0 Consensus size: 60
25504 ATTTTAATGG
25514 AGGCTCCACCACACAAAAGCACAATAATTTGACCAACCCTAATTGGGTTTCACTAGAGGC
1 AGGCTCCACCACACAAAAGCACAATAATTTGACCAACCCTAATTGGGTTTCACTAGAGGC
* *
25574 AGGCTCCACCACACAAAAGCACAATAATTTGACCAATCCTAATTGGGTTTTACTAGAGGC
1 AGGCTCCACCACACAAAAGCACAATAATTTGACCAACCCTAATTGGGTTTCACTAGAGGC
25634 A
1 A
25635 TTGGGCAATT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (60 bp):
AGGCTCCACCACACAAAAGCACAATAATTTGACCAACCCTAATTGGGTTTCACTAGAGGC
Found at i:28210 original size:24 final size:24
Alignment explanation
Indices: 28164--28210 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
28154 TAATTTATCT
*
28164 TTCTTCCTCCTCGACGTTTTTCCC
1 TTCTTCCTCCTCGACGTTCTTCCC
*
28188 TTCTTCTTCCTCGA-GCTTCTTCC
1 TTCTTCCTCCTCGACG-TTCTTCC
28211 TTCACCAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.04, C:0.40, G:0.09, T:0.47
Consensus pattern (24 bp):
TTCTTCCTCCTCGACGTTCTTCCC
Found at i:30412 original size:27 final size:27
Alignment explanation
Indices: 30381--30452 Score: 74
Period size: 26 Copynumber: 2.7 Consensus size: 27
30371 AATTGGACTT
30381 AAAATGACCAAAATGCCCCTGAATGTG
1 AAAATGACCAAAATGCCCCTGAATGTG
* ** * * *
30408 CAAATGACCAGGATG-CCCTTAGTGTT
1 AAAATGACCAAAATGCCCCTGAATGTG
*
30434 AAAATGACCGAAATGCCCC
1 AAAATGACCAAAATGCCCC
30453 CAAGGTGACC
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
26 19 0.56
27 15 0.44
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.19
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGAATGTG
Found at i:41824 original size:1 final size:1
Alignment explanation
Indices: 41818--41855 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
41808 AGAAAATGAG
41818 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
41856 GGAAAGACAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:53377 original size:31 final size:31
Alignment explanation
Indices: 53339--53446 Score: 114
Period size: 31 Copynumber: 3.5 Consensus size: 31
53329 TTAGGTTAAT
*
53339 TGCTCAAATAAGGGCCTAATGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAATATTTGCCAAAA
** * * **
53370 TGCTCAAATAAGGGCCCGATCTTT--TAATT
1 TGCTCAAATAAGGGCCTAATATTTGCCAAAA
*
53399 TGGC-CAAATAAGGGCCTAACATTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAATATTTGCCAAAA
53430 TGCTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
53447 GGCATCAGTT
Statistics
Matches: 60, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
29 19 0.32
30 4 0.07
31 37 0.62
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.26
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAATATTTGCCAAAA
Found at i:53522 original size:31 final size:31
Alignment explanation
Indices: 53487--53588 Score: 104
Period size: 31 Copynumber: 3.4 Consensus size: 31
53477 TCGATGCCAA
*
53487 GCCCTTATTTGAGCATTTTGGCCAACGTTAG
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAG
** * **
53518 GCCCTTATTTG-GCCAAATT---AAAAGATCGG
1 GCCCTTATTTGAG-CATTTTGGCAAACG-TTAG
53547 GCCCTTATTTGAGCATTTTGGCAAACGTTAG
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAG
53578 GCCCTTATTTG
1 GCCCTTATTTG
53589 GCCAAATTAA
Statistics
Matches: 54, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
28 3 0.06
29 17 0.31
30 2 0.04
31 28 0.52
32 4 0.07
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.34
Consensus pattern (31 bp):
GCCCTTATTTGAGCATTTTGGCAAACGTTAG
Found at i:53556 original size:29 final size:29
Alignment explanation
Indices: 53517--53610 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 29
53507 GCCAACGTTA
53517 GGCCCTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGGCCAAATTAAAAGATCG
** * **
53546 GGCCCTTATTTGAG-CATTTTGGCAAACG-TTA
1 GGCCCTTATTTG-GCCAAATT---AAAAGATCG
53577 GGCCCTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGGCCAAATTAAAAGATCG
*
53606 AGCCC
1 GGCCC
53611 CTTTTTAGCA
Statistics
Matches: 48, Mismatches: 11, Indels: 12
0.68 0.15 0.17
Matches are distributed among these distances:
28 4 0.08
29 21 0.44
30 2 0.04
31 17 0.35
32 4 0.08
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (29 bp):
GGCCCTTATTTGGCCAAATTAAAAGATCG
Found at i:53580 original size:60 final size:61
Alignment explanation
Indices: 53487--53647 Score: 265
Period size: 60 Copynumber: 2.7 Consensus size: 61
53477 TCGATGCCAA
*
53487 GCCCTTATTTGAGCATTTTGGCCAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG-G
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGAG
53547 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGAG
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGAG
* * *
53608 CCCCTT-TTT-AGCATTTTGACAAACGTTAGACCCTTATTTG
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
53648 AGCAATTAGC
Statistics
Matches: 96, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
59 29 0.30
60 61 0.64
61 6 0.06
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (61 bp):
GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGAG
Found at i:62227 original size:21 final size:21
Alignment explanation
Indices: 62203--62252 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
62193 AAAGTTACTA
62203 AAAAATCTACTAAGCTTATTG
1 AAAAATCTACTAAGCTTATTG
62224 AAAAATCTACTAAGCTTATTG
1 AAAAATCTACTAAGCTTATTG
*
62245 AAAGATCT
1 AAAAATCT
62253 TATCAAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (21 bp):
AAAAATCTACTAAGCTTATTG
Found at i:62835 original size:14 final size:14
Alignment explanation
Indices: 62818--62851 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
62808 TTTATCAACC
62818 TATTTTTAATTTTA
1 TATTTTTAATTTTA
*
62832 TATTTTTATTTTTA
1 TATTTTTAATTTTA
62846 TCATTT
1 T-ATTT
62852 ATTCCATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (14 bp):
TATTTTTAATTTTA
Found at i:69593 original size:13 final size:12
Alignment explanation
Indices: 69550--69604 Score: 51
Period size: 13 Copynumber: 4.5 Consensus size: 12
69540 TCATGCACCC
*
69550 AAAACATTTTATT
1 AAAACA-TTTAAT
69563 AAAACCATTT-AT
1 AAAA-CATTTAAT
69575 AAAACATATTAAT
1 AAAACAT-TTAAT
*
69588 AAAACA-GTAAT
1 AAAACATTTAAT
69599 AAAACA
1 AAAACA
69605 GTTCCTCAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
11 13 0.35
12 7 0.19
13 15 0.41
14 2 0.05
ACGTcount: A:0.58, C:0.11, G:0.02, T:0.29
Consensus pattern (12 bp):
AAAACATTTAAT
Done.