Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024825.1 Corchorus olitorius cultivar O-4 contig24858, 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: 99589
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:16913 original size:40 final size:40
Alignment explanation
Indices: 16868--16946 Score: 158
Period size: 40 Copynumber: 2.0 Consensus size: 40
16858 AAAGCCAAGC
16868 ATGAGGCATATATATTTGCATGTATTGTGCCCTCATTTGT
1 ATGAGGCATATATATTTGCATGTATTGTGCCCTCATTTGT
16908 ATGAGGCATATATATTTGCATGTATTGTGCCCTCATTTG
1 ATGAGGCATATATATTTGCATGTATTGTGCCCTCATTTG
16947 AATTGAACCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.23, C:0.15, G:0.20, T:0.42
Consensus pattern (40 bp):
ATGAGGCATATATATTTGCATGTATTGTGCCCTCATTTGT
Found at i:20159 original size:15 final size:15
Alignment explanation
Indices: 20139--20169 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
20129 TCTAATGGCG
20139 ACTTCAACTGATGCA
1 ACTTCAACTGATGCA
*
20154 ACTTCAACTGCTGCA
1 ACTTCAACTGATGCA
20169 A
1 A
20170 TACCTTACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.26
Consensus pattern (15 bp):
ACTTCAACTGATGCA
Found at i:21198 original size:1 final size:1
Alignment explanation
Indices: 21163--21189 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
21153 TGCATTTCAC
21163 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
21190 GCGGAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:22532 original size:13 final size:13
Alignment explanation
Indices: 22514--22539 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
22504 GCAGTGTAGG
22514 CTAATGCTGCTTA
1 CTAATGCTGCTTA
22527 CTAATGCTGCTTA
1 CTAATGCTGCTTA
22540 TGAACTGTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (13 bp):
CTAATGCTGCTTA
Found at i:30962 original size:26 final size:27
Alignment explanation
Indices: 30926--30987 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
30916 TGGCCCGGAG
*
30926 TCATATTTTAGT-GGAAAAAAAAAGAA
1 TCATATTTTAGTAGAAAAAAAAAAGAA
30952 TCATATTTTAGTAGAAAAAAAAAAGAA
1 TCATATTTTAGTAGAAAAAAAAAAGAA
30979 TCATATTTT
1 TCATATTTT
30988 TATTTCCTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 12 0.35
27 22 0.65
ACGTcount: A:0.52, C:0.05, G:0.11, T:0.32
Consensus pattern (27 bp):
TCATATTTTAGTAGAAAAAAAAAAGAA
Found at i:35023 original size:9 final size:9
Alignment explanation
Indices: 35009--35039 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
34999 CAAAGAAGAA
35009 GAGGATTTC
1 GAGGATTTC
35018 GAGGATTTC
1 GAGGATTTC
*
35027 GAGGATTTT
1 GAGGATTTC
35036 GAGG
1 GAGG
35040 TTTTGGGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.23, C:0.06, G:0.39, T:0.32
Consensus pattern (9 bp):
GAGGATTTC
Found at i:36793 original size:103 final size:103
Alignment explanation
Indices: 36605--36811 Score: 342
Period size: 103 Copynumber: 2.0 Consensus size: 103
36595 ACAATGTTCA
* ** *
36605 CAAAAATAAGCAACATTTAACCTATTTCCAAAATTCTCTTAGAGGTCTACTCTAAGTTGTTACTT
1 CAAAAATAAGCAACATTTAACATATACCCAAAATTCTCTTAGAGGTCTACTCTAAATTGTTACTT
*
36670 AGGATTTGATTACCTACAATTGCATATAGGAATCTCAT
66 AGGATTTGATTACCTACAATTCCATATAGGAATCTCAT
* * *
36708 CAAACATAGGCAACATTTAACATATACCCAAAATTCTCTTAGATGTCTACTCTAAATTGTTACTT
1 CAAAAATAAGCAACATTTAACATATACCCAAAATTCTCTTAGAGGTCTACTCTAAATTGTTACTT
36773 AGGATTTGATTACCTACAATTCCATATAGGAATCTCAT
66 AGGATTTGATTACCTACAATTCCATATAGGAATCTCAT
36811 C
1 C
36812 TAACTGTAGA
Statistics
Matches: 96, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
103 96 1.00
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.34
Consensus pattern (103 bp):
CAAAAATAAGCAACATTTAACATATACCCAAAATTCTCTTAGAGGTCTACTCTAAATTGTTACTT
AGGATTTGATTACCTACAATTCCATATAGGAATCTCAT
Found at i:41430 original size:21 final size:20
Alignment explanation
Indices: 41399--41445 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
41389 GTAGTTGAAA
* *
41399 GAGAGTCAGATGATTCAAAT
1 GAGATTCAGATCATTCAAAT
*
41419 GATGATTCAGATCATTCGAAT
1 GA-GATTCAGATCATTCAAAT
41440 GAGATT
1 GAGATT
41446 GTTGTGGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (20 bp):
GAGATTCAGATCATTCAAAT
Found at i:48549 original size:20 final size:20
Alignment explanation
Indices: 48524--48563 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
48514 AATCCACATC
48524 AGGATTAAATAAGGTTTAGA
1 AGGATTAAATAAGGTTTAGA
48544 AGGATTAAATAAGGTTTAGA
1 AGGATTAAATAAGGTTTAGA
48564 CATAGAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.25, T:0.30
Consensus pattern (20 bp):
AGGATTAAATAAGGTTTAGA
Found at i:61094 original size:15 final size:16
Alignment explanation
Indices: 61070--61109 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
61060 AGAGGTTGAA
*
61070 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
61085 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
61101 AGAAAACAA
1 AGAAAACAA
61110 AACAAAATAA
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
Found at i:77039 original size:3 final size:3
Alignment explanation
Indices: 77033--77058 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
77023 TGTTGTTGTT
77033 GTA GTA GTA GTA GTA GTA GTA GTA GT
1 GTA GTA GTA GTA GTA GTA GTA GTA GT
77059 TTTTAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.35, T:0.35
Consensus pattern (3 bp):
GTA
Found at i:79983 original size:13 final size:13
Alignment explanation
Indices: 79965--79990 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
79955 AGTACCTTAG
79965 CCTACCTTTTCTA
1 CCTACCTTTTCTA
79978 CCTACCTTTTCTA
1 CCTACCTTTTCTA
79991 AATCAATTGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.38, G:0.00, T:0.46
Consensus pattern (13 bp):
CCTACCTTTTCTA
Found at i:88120 original size:28 final size:29
Alignment explanation
Indices: 88065--88120 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
88055 CGTTAGGCTG
*
88065 AGGGGCAAAACGTCCCAAAATTGGAGTTC
1 AGGGGCAAAACGTCCCAAAATTGAAGTTC
*
88094 AGGGGCAAAATGT-CCAAAATTGAAGTT
1 AGGGGCAAAACGTCCCAAAATTGAAGTT
88121 TAAGGGACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.38, C:0.16, G:0.27, T:0.20
Consensus pattern (29 bp):
AGGGGCAAAACGTCCCAAAATTGAAGTTC
Found at i:88126 original size:29 final size:28
Alignment explanation
Indices: 88065--88140 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 28
88055 CGTTAGGCTG
* * *
88065 AGGGGCAAAACGTCCCAAAATTGGAGTTC
1 AGGGGCAAAATGT-CCAAAATTGAAGTTA
88094 AGGGGCAAAATGTCCAAAATTGAAGTTTA
1 AGGGGCAAAATGTCCAAAATTGAAG-TTA
* * *
88123 AGGGACCAAATATCCAAA
1 AGGGGCAAAATGTCCAAA
88141 CCATAGAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
28 11 0.28
29 29 0.73
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.18
Consensus pattern (28 bp):
AGGGGCAAAATGTCCAAAATTGAAGTTA
Found at i:90015 original size:51 final size:51
Alignment explanation
Indices: 89944--90071 Score: 211
Period size: 51 Copynumber: 2.5 Consensus size: 51
89934 ACACGTGTAC
* *
89944 AGTGTTTGTATGTCCGGAGACAAGATTGAAACAAGAGAAAAACACTAAAAG
1 AGTGTTTGTTTGTCCTGAGACAAGATTGAAACAAGAGAAAAACACTAAAAG
*
89995 AGTGTTTGTTTATCCTGAGACAAGATTGAAACAAGAGAAAAACACTAAAAG
1 AGTGTTTGTTTGTCCTGAGACAAGATTGAAACAAGAGAAAAACACTAAAAG
* *
90046 AGTGTTTGTTTGTCTTGACACAAGAT
1 AGTGTTTGTTTGTCCTGAGACAAGAT
90072 CTAATCTAGG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 71 1.00
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.26
Consensus pattern (51 bp):
AGTGTTTGTTTGTCCTGAGACAAGATTGAAACAAGAGAAAAACACTAAAAG
Found at i:99010 original size:76 final size:76
Alignment explanation
Indices: 98860--99003 Score: 186
Period size: 76 Copynumber: 1.9 Consensus size: 76
98850 ACAAGGACCC
* *
98860 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
98925 GGGCAGTGTCA
66 GGGCAGTGTCA
* * **
98936 CGACTCCAGCTGGGTGCCCACATGGTTTGCC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA
98998 GATGGG
63 GATGGG
99004 TTGTGTCTTA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
75 4 0.07
76 48 0.81
77 7 0.12
ACGTcount: A:0.17, C:0.31, G:0.29, T:0.23
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Done.