Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018630.1 Corchorus olitorius cultivar O-4 contig18663, 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: 30511
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.28
Found at i:612 original size:76 final size:76
Alignment explanation
Indices: 475--625 Score: 175
Period size: 76 Copynumber: 2.0 Consensus size: 76
465 ACAAGGACCC
*
475 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCA-AG
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGA-
539 TGGGCAGTGTCA
65 TGGGCAGTGTCA
* * * **
551 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA
*
613 GATGGGCTGTGTC
63 GATGGGCAGTGTC
626 TTAGCTCATC
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
75 4 0.06
76 53 0.83
77 7 0.11
ACGTcount: A:0.17, C:0.30, G:0.28, T:0.25
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Found at i:1723 original size:28 final size:28
Alignment explanation
Indices: 1682--1755 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 28
1672 AGGTGTCCCT
*
1682 GAAATGACCGAAATGCCCCTAG-CCTAGC
1 GAAATGACCAAAATGCCCCTAGACCTA-C
**
1710 GAAATGACCAAAATGCCCCTAGATGTAC
1 GAAATGACCAAAATGCCCCTAGACCTAC
*
1738 AAAATGACCAAAATGCCC
1 GAAATGACCAAAATGCCC
1756 TTGGTCATGC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 39 0.95
29 2 0.05
ACGTcount: A:0.39, C:0.28, G:0.18, T:0.15
Consensus pattern (28 bp):
GAAATGACCAAAATGCCCCTAGACCTAC
Found at i:3339 original size:3 final size:3
Alignment explanation
Indices: 3314--3385 Score: 110
Period size: 3 Copynumber: 24.3 Consensus size: 3
3304 ACATTAGGGT
* * *
3314 TTC TTC TTT TTC TCC TTC CTC TTC TT- TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
3361 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
3386 CTAGCAAAGC
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
2 2 0.03
3 60 0.97
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:3779 original size:21 final size:21
Alignment explanation
Indices: 3728--3779 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 21
3718 ACAGGGAGAG
* * *
3728 AATGTTGTATAATGAAGCCAG
1 AATGTTGAAAAATGAAGCCAA
* * *
3749 ATTCTAGAAAAATGAAGCCAA
1 AATGTTGAAAAATGAAGCCAA
3770 AATGTTGAAA
1 AATGTTGAAA
3780 CAAAATGCTG
Statistics
Matches: 22, Mismatches: 9, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.25
Consensus pattern (21 bp):
AATGTTGAAAAATGAAGCCAA
Found at i:4024 original size:24 final size:24
Alignment explanation
Indices: 3992--4041 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
3982 GGCATTGCCA
*
3992 TGAGATTTAGGCTTGCTCTGTTTC
1 TGAGATTTAGGCATGCTCTGTTTC
*
4016 TGAGTTTTAGGCATGCTCTGTTTC
1 TGAGATTTAGGCATGCTCTGTTTC
4040 TG
1 TG
4042 TTAATTGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.12, C:0.16, G:0.26, T:0.46
Consensus pattern (24 bp):
TGAGATTTAGGCATGCTCTGTTTC
Found at i:7684 original size:12 final size:12
Alignment explanation
Indices: 7678--7849 Score: 236
Period size: 12 Copynumber: 14.3 Consensus size: 12
7668 TTCTTTCCTG
*
7678 AACTCTTTTTTC
1 AACTCTTTCTTC
7690 AACTCTTTCTTC
1 AACTCTTTCTTC
7702 AACTCTTTCTTC
1 AACTCTTTCTTC
7714 AACTCTTTCTTC
1 AACTCTTTCTTC
* *
7726 AACTCTTTCCTG
1 AACTCTTTCTTC
*
7738 AACTCGTTCTTC
1 AACTCTTTCTTC
* *
7750 AACTCTTTCCTG
1 AACTCTTTCTTC
* *
7762 AACTCTTTCCTG
1 AACTCTTTCTTC
7774 AACTCTTTCTTC
1 AACTCTTTCTTC
*
7786 AACTCTTTCCTC
1 AACTCTTTCTTC
7798 AACTCTTTCTTC
1 AACTCTTTCTTC
* *
7810 AACTCTTTCATG
1 AACTCTTTCTTC
*
7822 AACTCTTTCCTC
1 AACTCTTTCTTC
7834 AACTCTTTCTTC
1 AACTCTTTCTTC
7846 AACT
1 AACT
7850 GGATCTGGAG
Statistics
Matches: 142, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 142 1.00
ACGTcount: A:0.18, C:0.33, G:0.03, T:0.46
Consensus pattern (12 bp):
AACTCTTTCTTC
Found at i:7998 original size:12 final size:12
Alignment explanation
Indices: 7983--8067 Score: 50
Period size: 12 Copynumber: 7.3 Consensus size: 12
7973 TCTGCAGCAC
7983 TTTCTTCTACAT
1 TTTCTTCTACAT
** *
7995 TTTCCACAACAT
1 TTTCTTCTACAT
*
8007 TTTCTTCTGCA-
1 TTTCTTCTACAT
* *
8018 -TT-TTCAACAC
1 TTTCTTCTACAT
*
8028 TTTCATCTACAT
1 TTTCTTCTACAT
* ** *
8040 CTTCCACAACAT
1 TTTCTTCTACAT
8052 TTTCTTCTACAT
1 TTTCTTCTACAT
8064 TTTC
1 TTTC
8068 ACCCAAATTT
Statistics
Matches: 50, Mismatches: 20, Indels: 6
0.66 0.26 0.08
Matches are distributed among these distances:
9 5 0.10
10 2 0.04
11 2 0.04
12 41 0.82
ACGTcount: A:0.22, C:0.29, G:0.01, T:0.47
Consensus pattern (12 bp):
TTTCTTCTACAT
Found at i:8029 original size:45 final size:45
Alignment explanation
Indices: 7980--8068 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
7970 GCTTCTGCAG
* * *
7980 CACTTTCTTCTACATTTTCCACAACATTTTCTTCTGCATTTTCAA
1 CACTTTCATCTACATCTTCCACAACATTTTCTTCTACATTTTCAA
8025 CACTTTCATCTACATCTTCCACAACATTTTCTTCTACATTTTCA
1 CACTTTCATCTACATCTTCCACAACATTTTCTTCTACATTTTCA
8069 CCCAAATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.24, C:0.30, G:0.01, T:0.45
Consensus pattern (45 bp):
CACTTTCATCTACATCTTCCACAACATTTTCTTCTACATTTTCAA
Found at i:8078 original size:24 final size:24
Alignment explanation
Indices: 7983--8067 Score: 113
Period size: 24 Copynumber: 3.7 Consensus size: 24
7973 TCTGCAGCAC
7983 TTTCTTCTACATTTTCCACAACAT
1 TTTCTTCTACATTTTCCACAACAT
* *
8007 TTTCTTCTGCATTTT---CAACAC
1 TTTCTTCTACATTTTCCACAACAT
* *
8028 TTTCATCTACATCTTCCACAACAT
1 TTTCTTCTACATTTTCCACAACAT
8052 TTTCTTCTACATTTTC
1 TTTCTTCTACATTTTC
8068 ACCCAAATTT
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
21 17 0.34
24 33 0.66
ACGTcount: A:0.22, C:0.29, G:0.01, T:0.47
Consensus pattern (24 bp):
TTTCTTCTACATTTTCCACAACAT
Found at i:9184 original size:16 final size:16
Alignment explanation
Indices: 9163--9199 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
9153 GGTTAATGGG
9163 TTTTTACTTTATTTTC
1 TTTTTACTTTATTTTC
*
9179 TTTTTATTTTATTTTC
1 TTTTTACTTTATTTTC
9195 TTTTT
1 TTTTT
9200 CCGCCAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.11, C:0.08, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTACTTTATTTTC
Found at i:13939 original size:15 final size:15
Alignment explanation
Indices: 13909--13950 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
13899 TTACTTTGCT
13909 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
13925 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
13940 TTGTTTTCTGT
1 TTGTTTTCTGT
13951 CAACCTCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:16193 original size:81 final size:81
Alignment explanation
Indices: 16053--16344 Score: 388
Period size: 81 Copynumber: 3.6 Consensus size: 81
16043 TCCAAATATA
* *
16053 TCTATAACGGTTGAACACCTAAATTGGTGTCCCCGTATAACAAATAAAGAGGAAAGACATCCCCT
1 TCTATAACGGTTGAACACCTAAATTGGTGTCCCCGTATAACTAATAAAGAGGAAGGACATCCCCT
16118 AATGAGACGTCCTCCC
66 AATGAGACGTCCTCCC
16134 TCTATAACGGTTGAACACCTAAATTGGTGTCCCCGTATAACTAATAAAGAGGAAGGACATCCCCT
1 TCTATAACGGTTGAACACCTAAATTGGTGTCCCCGTATAACTAATAAAGAGGAAGGACATCCCCT
16199 AATGAGACGTCCTCCC
66 AATGAGACGTCCTCCC
* * * * * * * * **
16215 TCTATAATGGTTGTACACCTCAATCGGCGTCCCCATATAACCAATAAA-AGGGACGGACGCCCCC
1 TCTATAACGGTTGAACACCTAAATTGGTGTCCCCGTATAACTAATAAAGA-GGAAGGACATCCCC
*
16279 TAATGAGACGTCCCCCC
65 TAATGAGACGTCCTCCC
* * * * * *
16296 TCTACAACGGTCGAACACCTCAGTTGGTGTCTCCCGCATAAATAATAAA
1 TCTATAACGGTTGAACACCTAAATTGGTGTC-CCCGTATAACTAATAAA
16345 AAGAATGAAA
Statistics
Matches: 185, Mismatches: 24, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
80 1 0.01
81 171 0.92
82 13 0.07
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (81 bp):
TCTATAACGGTTGAACACCTAAATTGGTGTCCCCGTATAACTAATAAAGAGGAAGGACATCCCCT
AATGAGACGTCCTCCC
Found at i:19497 original size:20 final size:21
Alignment explanation
Indices: 19462--19500 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
19452 TTTCCTTTCT
*
19462 TTTCTTTTCTCTTTTCTTTTA
1 TTTCTTTTCACTTTTCTTTTA
19483 TTTCTTTT-ACTTTTCTTT
1 TTTCTTTTCACTTTTCTTT
19501 AAAATTGGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTCTTTTCACTTTTCTTTTA
Found at i:24330 original size:38 final size:38
Alignment explanation
Indices: 24279--24389 Score: 213
Period size: 38 Copynumber: 2.9 Consensus size: 38
24269 ACTAGCACTT
24279 AACTCTTCATTCAGATCCATTATTAGAATTAACATTTA
1 AACTCTTCATTCAGATCCATTATTAGAATTAACATTTA
24317 AACTCTTCATTCAGATCCATTATTAGAATTAACATTTA
1 AACTCTTCATTCAGATCCATTATTAGAATTAACATTTA
*
24355 AACTCTTCATTCAGATCCATTATTAGAATCAACAT
1 AACTCTTCATTCAGATCCATTATTAGAATTAACAT
24390 GAGATGAGGA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
38 72 1.00
ACGTcount: A:0.37, C:0.20, G:0.05, T:0.38
Consensus pattern (38 bp):
AACTCTTCATTCAGATCCATTATTAGAATTAACATTTA
Found at i:28658 original size:2 final size:2
Alignment explanation
Indices: 28651--28677 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28641 TGGAAATCAA
28651 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
28678 GGCAGGCTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30277 original size:17 final size:18
Alignment explanation
Indices: 30257--30298 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
30247 AAGAGATCAC
*
30257 AAATATTCAATTAA-AAT
1 AAATATTCAAATAATAAT
*
30274 AAATATTTAAATAATAAT
1 AAATATTCAAATAATAAT
30292 AAATATT
1 AAATATT
30299 AAACATTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATATTCAAATAATAAT
Done.