Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_119 ID=scaffold_119-JGI_221_v2.0
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: 12265
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Found at i:1144 original size:87 final size:87
Alignment explanation
Indices: 998--1168 Score: 222
Period size: 87 Copynumber: 2.0 Consensus size: 87
988 TATGCTTCGG
* * *
998 TATATATAGAAATGAGACCATTTGCATACCTACTCATTAAAGGCAGAGTTCCAAACAAAACATCA
1 TATATATAGAAATGAGACCATATGCATACCAACTCATTAAAGACAGAGTTCCAAACAAAACATCA
* *
1063 TATATCGCATTCCGCAGTACGA
66 CATATCGCAATCCGCAGTACGA
* *
1085 TATATATA-AAAGTGAGACCATATGCATACCAATTTCGTT-AAGACAGAG-TCCAAAGCAAAACA
1 TATATATAGAAA-TGAGACCATATGCATACCAA-CTCATTAAAGACAGAGTTCCAAA-CAAAACA
*
1147 TCACATATCGCAATCTGCAGTA
63 TCACATATCGCAATCCGCAGTA
1169 TTGAGTAGAA
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
86 9 0.12
87 60 0.82
88 4 0.05
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.25
Consensus pattern (87 bp):
TATATATAGAAATGAGACCATATGCATACCAACTCATTAAAGACAGAGTTCCAAACAAAACATCA
CATATCGCAATCCGCAGTACGA
Found at i:6862 original size:21 final size:20
Alignment explanation
Indices: 6831--6885 Score: 85
Period size: 20 Copynumber: 2.7 Consensus size: 20
6821 AACACAAAAA
6831 TTTTGAAACACGAGATTTT-T
1 TTTTGAAACACGA-ATTTTCT
6851 TTTTGAAAACACGAATTTTCT
1 TTTTG-AAACACGAATTTTCT
6872 TTTTGAAACACGAA
1 TTTTGAAACACGAA
6886 AATTTTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 19 0.58
21 14 0.42
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (20 bp):
TTTTGAAACACGAATTTTCT
Found at i:6913 original size:38 final size:38
Alignment explanation
Indices: 6850--6930 Score: 101
Period size: 38 Copynumber: 2.1 Consensus size: 38
6840 ACGAGATTTT
* * *
6850 TTTTTGAAAACACGAATTTTCTTTTTGAAA-CACGAAAA
1 TTTTTAAAAACACAAAATTTCTTTTTGAAATCA-GAAAA
* *
6888 TTTTTAAAAACACAAAATTTGTTTTTGAAATCATAAAA
1 TTTTTAAAAACACAAAATTTCTTTTTGAAATCAGAAAA
6926 TTTTT
1 TTTTT
6931 GATAAAATAC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 35 0.95
39 2 0.05
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.42
Consensus pattern (38 bp):
TTTTTAAAAACACAAAATTTCTTTTTGAAATCAGAAAA
Found at i:6974 original size:36 final size:37
Alignment explanation
Indices: 6934--7008 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 37
6924 AATTTTTGAT
*
6934 AAAA-TACGAAACACGAGAAATTTTTTTTGAAAA-ACG
1 AAAATTACGAAACACGAG-AATTTTTTTCGAAAACACG
*
6970 AAAATTTCGAAACACGAGAATTTTTTTCGAAAACACG
1 AAAATTACGAAACACGAGAATTTTTTTCGAAAACACG
7007 AA
1 AA
7009 TTTTTTTGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
36 18 0.51
37 17 0.49
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.25
Consensus pattern (37 bp):
AAAATTACGAAACACGAGAATTTTTTTCGAAAACACG
Found at i:7005 original size:21 final size:21
Alignment explanation
Indices: 6942--7015 Score: 65
Period size: 19 Copynumber: 3.9 Consensus size: 21
6932 ATAAAATACG
*
6942 AAACACGAGAAATTTTTTTTGA
1 AAACACGAG-AATTTTTTTCGA
*
6964 AAA-ACGA-AA---ATTTCG-
1 AAACACGAGAATTTTTTTCGA
6979 AAACACGAGAATTTTTTTCGA
1 AAACACGAGAATTTTTTTCGA
7000 AAACAC--GAATTTTTTT
1 AAACACGAGAATTTTTTT
7016 GAATATTTAC
Statistics
Matches: 43, Mismatches: 3, Indels: 15
0.70 0.05 0.25
Matches are distributed among these distances:
15 3 0.07
16 8 0.19
17 2 0.05
19 12 0.28
20 5 0.12
21 10 0.23
22 3 0.07
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (21 bp):
AAACACGAGAATTTTTTTCGA
Found at i:7153 original size:5 final size:5
Alignment explanation
Indices: 7143--7170 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
7133 AAATTATTTA
7143 AAATT AAATT AAATT AAATT AAATT AAA
1 AAATT AAATT AAATT AAATT AAATT AAA
7171 AACATAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
AAATT
Found at i:7386 original size:18 final size:18
Alignment explanation
Indices: 7344--7388 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
7334 TTTCTTTTAC
7344 TTTTTTTTCTTTTTTCCT
1 TTTTTTTTCTTTTTTCCT
* *
7362 CTCTTTTTCTTTTTT-CT
1 TTTTTTTTCTTTTTTCCT
7379 TTTTTTTTCT
1 TTTTTTTTCT
7389 GGATTGGGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTTTTCTTTTTTCCT
Found at i:7712 original size:3 final size:3
Alignment explanation
Indices: 7701--7752 Score: 59
Period size: 3 Copynumber: 15.7 Consensus size: 3
7691 TTTTTTTCCC
7701 TCT TCCT TCT TCT TCT CTCTT TCTT TCT TCT TCT TCT TCT TCCT TCT
1 TCT T-CT TCT TCT TCT -TC-T TC-T TCT TCT TCT TCT TCT T-CT TCT
7748 TCT TC
1 TCT TC
7753 AAAACCGAGC
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
3 30 0.67
4 14 0.31
5 1 0.02
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:7714 original size:10 final size:10
Alignment explanation
Indices: 7701--7752 Score: 58
Period size: 10 Copynumber: 5.5 Consensus size: 10
7691 TTTTTTTCCC
7701 TCTTCCTTCT
1 TCTTCCTTCT
7711 TCTT-C-TC-
1 TCTTCCTTCT
*
7718 TCTTTCTTTCT
1 TC-TTCCTTCT
7729 TCTT-CTTCT
1 TCTTCCTTCT
7738 TCTTCCTTCT
1 TCTTCCTTCT
7748 TCTTC
1 TCTTC
7753 AAAACCGAGC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
7 2 0.06
8 4 0.11
9 9 0.26
10 18 0.51
11 2 0.06
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (10 bp):
TCTTCCTTCT
Found at i:7746 original size:16 final size:17
Alignment explanation
Indices: 7709--7752 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
7699 CCTCTTCCTT
*
7709 CTTCTTCTCTCTTTCTTT
1 CTTCTTCT-TCTTTCTTC
7727 CTTCTTCTTC-TTCTTC
1 CTTCTTCTTCTTTCTTC
7743 CTTCTTCTTC
1 CTTCTTCTTC
7753 AAAACCGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 15 0.60
17 2 0.08
18 8 0.32
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (17 bp):
CTTCTTCTTCTTTCTTC
Found at i:8139 original size:29 final size:29
Alignment explanation
Indices: 8097--8201 Score: 122
Period size: 29 Copynumber: 3.6 Consensus size: 29
8087 GGCCGAAACA
*
8097 AATTTCGAATAAGTTTATGGGTCAAAATGT
1 AATTTC-AAAAAGTTTATGGGTCAAAATGT
8127 AATTTCAAAAAGTTTATGGGTCAAAATGT
1 AATTTCAAAAAGTTTATGGGTCAAAATGT
* * * *
8156 AATTTTAGGAAAA-TTTAGGGGTTAAAATGC
1 AATTTCA--AAAAGTTTATGGGTCAAAATGT
*
8186 AATTTTAAAAAGTTTA
1 AATTTCAAAAAGTTTA
8202 GGGGGGTCAA
Statistics
Matches: 67, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
28 4 0.06
29 32 0.48
30 27 0.40
31 4 0.06
ACGTcount: A:0.41, C:0.05, G:0.18, T:0.36
Consensus pattern (29 bp):
AATTTCAAAAAGTTTATGGGTCAAAATGT
Found at i:8221 original size:30 final size:29
Alignment explanation
Indices: 8107--8222 Score: 108
Period size: 29 Copynumber: 3.9 Consensus size: 29
8097 AATTTCGAAT
* * *
8107 AAGTTTATGGGTCAAAATGTAATTTCAAA
1 AAGTTTAGGGGTCAAAATATAATTTTAAA
* *
8136 AAGTTTATGGGTCAAAATGTAATTTTAGGAA
1 AAGTTTAGGGGTCAAAATATAATTTTA--AA
* **
8167 AA-TTTAGGGGTTAAAATGCAATTTTAAA
1 AAGTTTAGGGGTCAAAATATAATTTTAAA
*
8195 AAGTTTAGGGGGGTCAAAATATATTTTT
1 AAGTTTA--GGGGTCAAAATATAATTTT
8223 TTATTTTTTG
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
28 4 0.05
29 30 0.41
30 21 0.28
31 19 0.26
ACGTcount: A:0.39, C:0.04, G:0.21, T:0.36
Consensus pattern (29 bp):
AAGTTTAGGGGTCAAAATATAATTTTAAA
Found at i:8274 original size:18 final size:20
Alignment explanation
Indices: 8240--8279 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
8230 TTGTATTTTT
8240 TATTTTTATATATATATATA
1 TATTTTTATATATATATATA
*
8260 TATTTTTAAATATATATATA
1 TATTTTTATATATATATATA
8280 AACACGACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTTTTATATATATATATA
Found at i:8701 original size:82 final size:79
Alignment explanation
Indices: 8427--8859 Score: 583
Period size: 82 Copynumber: 5.6 Consensus size: 79
8417 ACAGAAATTG
* * * * *
8427 AAAATAGCTCGGCGTGA-CCAAAGCTCAACTCACCTTTGTA-TATGAGTTGA--TTTT-AAAAAA
1 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAA
*
8487 -AGACATAAATT-A
66 CAGAAATAAATTAA
* *
8499 AAAATACCTCAGTGTGACCCGAGGCTCAATTCACCTCTGTATTATGAGTTGA---TTT-AAAAAA
1 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAA
* *
8560 -AGACAGAAATT-A
66 CAGAAATAAATTAA
*
8572 AAAATACCTCAGTGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTTGAAAAA
1 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTTTGAAAAA
8637 ACAGAAATTAAATTAAA
65 ACAGAAA-TAAATT-AA
8654 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAA
1 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTG--AAAA
8719 AACAGAAATTAAATTAA
64 AACAGAAA-TAAATTAA
8736 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAA
1 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAA
8801 GCAGAAAT---TTAA
66 -CAGAAATAAATTAA
*
8813 AAAATACATCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGA
1 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGA
8860 AAAATGGGCA
Statistics
Matches: 334, Mismatches: 13, Indels: 23
0.90 0.04 0.06
Matches are distributed among these distances:
72 14 0.04
73 90 0.27
74 10 0.03
77 53 0.16
78 6 0.02
79 4 0.01
80 12 0.04
81 13 0.04
82 113 0.34
83 19 0.06
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (79 bp):
AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAA
CAGAAATAAATTAA
Done.