Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023186.1 Corchorus olitorius cultivar O-4 contig23219, 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: 19159
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Found at i:722 original size:20 final size:21
Alignment explanation
Indices: 687--725 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
677 AGTTATAATC
687 TTTCTTTTCTCTTTTCTTTTA
1 TTTCTTTTCTCTTTTCTTTTA
708 TTTCTTTTC-CTTTTCTTT
1 TTTCTTTTCTCTTTTCTTT
726 AAAATTGGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTCTTTTCTCTTTTCTTTTA
Found at i:837 original size:14 final size:14
Alignment explanation
Indices: 814--916 Score: 81
Period size: 14 Copynumber: 7.7 Consensus size: 14
804 AGCTGGGCCA
814 CGCG-CTGGCCCAG
1 CGCGCCTGGCCCAG
* **
827 CACGCCTGGCCTGG
1 CGCGCCTGGCCCAG
*
841 CGCGCCTGGGCC-G
1 CGCGCCTGGCCCAG
*
854 CTCG-CTGGCCCAG
1 CGCGCCTGGCCCAG
* **
867 CGTGCCTGGCCTGG
1 CGCGCCTGGCCCAG
*
881 CGCGCCTGGGCC-G
1 CGCGCCTGGCCCAG
894 CGCG-CTGGCCCAG
1 CGCGCCTGGCCCAG
*
907 CGTGCCTGGC
1 CGCGCCTGGC
917 TTGGCACGCC
Statistics
Matches: 68, Mismatches: 17, Indels: 9
0.72 0.18 0.10
Matches are distributed among these distances:
12 12 0.18
13 19 0.28
14 37 0.54
ACGTcount: A:0.04, C:0.44, G:0.40, T:0.13
Consensus pattern (14 bp):
CGCGCCTGGCCCAG
Found at i:851 original size:40 final size:40
Alignment explanation
Indices: 806--930 Score: 196
Period size: 40 Copynumber: 3.1 Consensus size: 40
796 GGCAAGGCAG
* **
806 CTGGGCCACGCGCTGGCCCAGCACGCCTGGCCTGGCGCGC
1 CTGGGCCGCGCGCTGGCCCAGCGTGCCTGGCCTGGCGCGC
*
846 CTGGGCCGCTCGCTGGCCCAGCGTGCCTGGCCTGGCGCGC
1 CTGGGCCGCGCGCTGGCCCAGCGTGCCTGGCCTGGCGCGC
* *
886 CTGGGCCGCGCGCTGGCCCAGCGTGCCTGGCTTGGCACGC
1 CTGGGCCGCGCGCTGGCCCAGCGTGCCTGGCCTGGCGCGC
926 CTGGG
1 CTGGG
931 GCAGGCCCAT
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 78 1.00
ACGTcount: A:0.05, C:0.42, G:0.40, T:0.14
Consensus pattern (40 bp):
CTGGGCCGCGCGCTGGCCCAGCGTGCCTGGCCTGGCGCGC
Found at i:13249 original size:23 final size:22
Alignment explanation
Indices: 13223--13276 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 22
13213 GCGAAAGAAA
*
13223 AAAGAAAAGCAAGCAAAAAAA-TG
1 AAAGAAAA--AAGAAAAAAAAGTG
13246 AAAGGAAAAAAGAAAAAAAATGTG
1 AAA-GAAAAAAGAAAAAAAA-GTG
13270 AAAGAAA
1 AAAGAAA
13277 TGAACTGATT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 10 0.37
23 7 0.26
24 10 0.37
ACGTcount: A:0.72, C:0.04, G:0.19, T:0.06
Consensus pattern (22 bp):
AAAGAAAAAAGAAAAAAAAGTG
Found at i:13719 original size:26 final size:28
Alignment explanation
Indices: 13690--13754 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 28
13680 AAAGAAGGAG
*
13690 AAAAGAAAAATGAAGA-AAAGAA-TTGA
1 AAAAGAAAAATGAAAAGAAAGAAGTTGA
13716 AAAAG-AAAA-GAAAAGAAAGAAGTTGA
1 AAAAGAAAAATGAAAAGAAAGAAGTTGA
*
13742 AAATGTAAAAATG
1 AAAAG-AAAAATG
13755 GAGGAAAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
24 4 0.12
25 10 0.31
26 13 0.41
28 4 0.12
29 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.20, T:0.12
Consensus pattern (28 bp):
AAAAGAAAAATGAAAAGAAAGAAGTTGA
Found at i:14041 original size:2 final size:2
Alignment explanation
Indices: 14034--14076 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
14024 TGCGTGACGA
14034 AG AG AG AG A- AG -G AG AG AG AG AG AG AG A- AG -G AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
14072 AG AG A
1 AG AG A
14077 AGGAAATGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
1 4 0.11
2 33 0.89
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:14055 original size:16 final size:16
Alignment explanation
Indices: 14034--14080 Score: 76
Period size: 16 Copynumber: 2.8 Consensus size: 16
14024 TGCGTGACGA
14034 AGAGAGAGAAGGAGAGAG
1 AGAGAGAGAA-G-GAGAG
14052 AGAGAGAGAAGGAGAG
1 AGAGAGAGAAGGAGAG
14068 AGAGAGAGAAGGA
1 AGAGAGAGAAGGA
14081 AATGATACGG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
16 18 0.62
17 1 0.03
18 10 0.34
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (16 bp):
AGAGAGAGAAGGAGAG
Found at i:14057 original size:18 final size:18
Alignment explanation
Indices: 14034--14076 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
14024 TGCGTGACGA
14034 AGAGAGAGAAGGAGAGAG
1 AGAGAGAGAAGGAGAGAG
14052 AGAGAGAGAAGGAGAGAG
1 AGAGAGAGAAGGAGAGAG
14070 AGAGAGA
1 AGAGAGA
14077 AGGAAATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (18 bp):
AGAGAGAGAAGGAGAGAG
Found at i:15194 original size:54 final size:53
Alignment explanation
Indices: 15130--15366 Score: 223
Period size: 54 Copynumber: 4.4 Consensus size: 53
15120 TCTTTTAAAT
* *
15130 TTTTCAGAGATCTAAGCTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAG
1 TTTTCAGAGATCTAAGTTGATCTTAAGATGACCCA-TGCGGTCTTTCATAGAAG
* * * *
15184 TTTTCAGAGATCTAAGTTGATTTTAAGATG-CCCTGTGCGATCTTTCACAGAAG
1 TTTTCAGAGATCTAAGTTGATCTTAAGATGACCC-ATGCGGTCTTTCATAGAAG
* * * * * *
15237 CTTTAAGATATCATAA-TTGATATTCAGATGACCCTATGCGGTCTTTTATAGAAG
1 TTTTCAGAGATC-TAAGTTGATCTTAAGATGACCC-ATGCGGTCTTTCATAGAAG
* *
15291 TTTTC-GATGATC-AGAGTTGATCTTAAGTTGATCCCATGCGGTCTTTCAAAGAAG
1 TTTTCAGA-GATCTA-AGTTGATCTTAAGATGA-CCCATGCGGTCTTTCATAGAAG
* *
15345 TTTTTAGATATC-AGAGTTGATC
1 TTTTCAGAGATCTA-AGTTGATC
15367 CCCAGATGAT
Statistics
Matches: 150, Mismatches: 25, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
52 1 0.01
53 42 0.28
54 102 0.68
55 5 0.03
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (53 bp):
TTTTCAGAGATCTAAGTTGATCTTAAGATGACCCATGCGGTCTTTCATAGAAG
Found at i:15309 original size:107 final size:107
Alignment explanation
Indices: 15155--15402 Score: 252
Period size: 107 Copynumber: 2.3 Consensus size: 107
15145 GCTGATCTTA
* * *
15155 AGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATTTTAAGATG-CCCTG
1 AGATGACCCAGTGCGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATCTTAAGATGACCC-A
*
15219 TGCGATCTTTCACAGAAGCTTTAAGATATCATAATTGATATTC
65 TGCGATCTTTCAAAGAAGCTTTAAGATATCATAATTGATATTC
* *
15262 AGATGACCCTA-TGCGGTCTTTTATAGAAGTTTTC-GATGATC-AGAGTTGATCTTAAGTTGATC
1 AGATGACCC-AGTGCGGTCTTTCATAGAAGTTTTCAGA-GATCTA-AGTTGATCTTAAGATGA-C
* * * * * ***
15324 CCATGCGGTCTTTCAAAGAAGTTTTTAGATATCAGAGTTGATCCCC
62 CCATGCGATCTTTCAAAGAAGCTTTAAGATATCATAATTGATATTC
* * * *
15370 AGATGATCCAGTACGGTCATTCCAAAGAAGTTT
1 AGATGACCCAGTGCGGTC-TTTCATAGAAGTTT
15403 CCTGTGATCA
Statistics
Matches: 115, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
106 3 0.03
107 49 0.43
108 49 0.43
109 14 0.12
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (107 bp):
AGATGACCCAGTGCGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATCTTAAGATGACCCAT
GCGATCTTTCAAAGAAGCTTTAAGATATCATAATTGATATTC
Found at i:15377 original size:54 final size:55
Alignment explanation
Indices: 15273--15583 Score: 300
Period size: 54 Copynumber: 5.7 Consensus size: 55
15263 GATGACCCTA
* * * *** *
15273 TGCGGTC-TTTTATAGAAGTTTTCGATGATCAGAGTTGATCTTAAGTTGATCCCA-
1 TGCGGTCATTTCAAAGAAGTTTTAGATGATCAGAGTTGATCCCCAGATGAT-CCAG
15327 TGCGGTC-TTTCAAAGAAGTTTTTAGAT-ATCAGAGTTGATCCCCAGATGATCCAG
1 TGCGGTCATTTCAAAGAAG-TTTTAGATGATCAGAGTTGATCCCCAGATGATCCAG
* * * * * *
15381 TACGGTCATTCCAAAGAAGTTTCCT-G-TGATCAGAGTTGGTCCCCAGATAACCCAA
1 TGCGGTCATTTCAAAGAAGTTT--TAGATGATCAGAGTTGATCCCCAGATGATCCAG
**
15436 TGCATTCATTTC-AAGAAGTTTTTAG-TGATCAGAGTTGATCCCCAGATGATCCAG
1 TGCGGTCATTTCAAAGAAG-TTTTAGATGATCAGAGTTGATCCCCAGATGATCCAG
* *** *
15490 TGCGGTCATTTC-AAGAAGTTCTAGATGATCAGAGTTGATCCTTGGATAATCCAG
1 TGCGGTCATTTCAAAGAAGTTTTAGATGATCAGAGTTGATCCCCAGATGATCCAG
* * *
15544 TGCGGTCGTTTC-AAGAAGTTTTCGATGATCATAGTTGATC
1 TGCGGTCATTTCAAAGAAGTTTTAGATGATCAGAGTTGATC
15584 TCATTTCAAG
Statistics
Matches: 216, Mismatches: 32, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
53 9 0.04
54 154 0.71
55 52 0.24
56 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (55 bp):
TGCGGTCATTTCAAAGAAGTTTTAGATGATCAGAGTTGATCCCCAGATGATCCAG
Found at i:15598 original size:35 final size:35
Alignment explanation
Indices: 15552--15715 Score: 285
Period size: 35 Copynumber: 4.7 Consensus size: 35
15542 AGTGCGGTCG
*
15552 TTTCAAGAAGTTTTCGATGATCATAGTTGATCTCA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
**
15587 TTTCAAGAAGTTTTTAATGATCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
*
15622 TTTCAAGAAGTTTT-TATGATCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
15656 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
15691 TTTCAAGAAGTTTTCGATGATCAGA
1 TTTCAAGAAGTTTTCGATGATCAGA
15716 TGTCACGCCC
Statistics
Matches: 123, Mismatches: 5, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
34 33 0.27
35 90 0.73
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.39
Consensus pattern (35 bp):
TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
Found at i:15664 original size:69 final size:70
Alignment explanation
Indices: 15552--15715 Score: 285
Period size: 69 Copynumber: 2.4 Consensus size: 70
15542 AGTGCGGTCG
* *
15552 TTTCAAGAAGTTTTCGATGATCATAGTTGATCTCATTTCAAGAAGTTTTTAATGATCAGAGTTGA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCAATGATCAGAGTTGA
15617 TCTCA
66 TCTCA
* *
15622 TTTCAAGAAGTTTT-TATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCAATGATCAGAGTTGA
15686 TCTCA
66 TCTCA
15691 TTTCAAGAAGTTTTCGATGATCAGA
1 TTTCAAGAAGTTTTCGATGATCAGA
15716 TGTCACGCCC
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
69 65 0.74
70 23 0.26
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.39
Consensus pattern (70 bp):
TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCAATGATCAGAGTTGA
TCTCA
Found at i:17205 original size:28 final size:27
Alignment explanation
Indices: 17141--17215 Score: 64
Period size: 28 Copynumber: 2.7 Consensus size: 27
17131 TCCGGCATTT
17141 AAGGGCAAAACTGTAA-TTTAGTCAACC
1 AAGGGCAAAA-TGTAATTTTAGTCAACC
* * *
17168 AGGGGTAAAATGGTAATTTTAG-CTGACC
1 AAGGGCAAAAT-GTAATTTTAGTC-AACC
*
17196 AAGGGCAAAACAGTAATTTT
1 AAGGGCAAAA-TGTAATTTT
17216 GACATCTTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
26 1 0.03
27 13 0.34
28 24 0.63
ACGTcount: A:0.39, C:0.13, G:0.23, T:0.25
Consensus pattern (27 bp):
AAGGGCAAAATGTAATTTTAGTCAACC
Done.