Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_22 ID=scaffold_22-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: 95467
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.30
Warning! 9657 characters in sequence are not A, C, G, or T
Found at i:2690 original size:13 final size:13
Alignment explanation
Indices: 2672--2697 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2662 GTTCGTAAGG
2672 GATGTGAGGCATT
1 GATGTGAGGCATT
2685 GATGTGAGGCATT
1 GATGTGAGGCATT
2698 CTTGGCCTAT
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:0.08, G:0.38, T:0.31
Consensus pattern (13 bp):
GATGTGAGGCATT
Found at i:15356 original size:20 final size:20
Alignment explanation
Indices: 15314--15356 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
15304 CTAACGAAAG
** *
15314 ATATACTATAAATATTAATA
1 ATATACTATAAATAGAAAAA
15334 ATATACTATAAATAGAAAAA
1 ATATACTATAAATAGAAAAA
15354 ATA
1 ATA
15357 AATGCAAACG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (20 bp):
ATATACTATAAATAGAAAAA
Found at i:29184 original size:10 final size:10
Alignment explanation
Indices: 29164--29199 Score: 51
Period size: 9 Copynumber: 3.9 Consensus size: 10
29154 AAGTCACCGA
29164 TTCTC-TTTT
1 TTCTCTTTTT
29173 TTCTCTTTTT
1 TTCTCTTTTT
29183 TTCT-TTTTT
1 TTCTCTTTTT
29192 TT-TCTTTT
1 TTCTCTTTT
29200 CAAGAGTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 1 0.04
9 16 0.64
10 8 0.32
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (10 bp):
TTCTCTTTTT
Found at i:44920 original size:14 final size:12
Alignment explanation
Indices: 44891--44928 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
44881 CACATTTGAC
44891 AATAAAAAATAA
1 AATAAAAAATAA
44903 AATAAAAGAATGAA
1 AATAAAA-AAT-AA
44917 AAT-AAAAATAA
1 AATAAAAAATAA
44928 A
1 A
44929 TTTCCTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 3 0.12
12 10 0.42
13 6 0.25
14 5 0.21
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (12 bp):
AATAAAAAATAA
Found at i:51922 original size:12 final size:12
Alignment explanation
Indices: 51905--51929 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
51895 GCCAAAGACG
51905 AAAGAAAGGAAA
1 AAAGAAAGGAAA
51917 AAAGAAAGGAAA
1 AAAGAAAGGAAA
51929 A
1 A
51930 TCAGCAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AAAGAAAGGAAA
Found at i:56435 original size:16 final size:16
Alignment explanation
Indices: 56411--56454 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 16
56401 AGTATGATGT
*
56411 AAATAATAACTACTAG
1 AAATCATAACTACTAG
*
56427 AAATCATAAATTACTAG
1 AAATCAT-AACTACTAG
56444 AAATCA-AACTA
1 AAATCATAACTA
56455 GAAATCATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 4 0.17
16 6 0.25
17 14 0.58
ACGTcount: A:0.57, C:0.14, G:0.05, T:0.25
Consensus pattern (16 bp):
AAATCATAACTACTAG
Found at i:58223 original size:28 final size:28
Alignment explanation
Indices: 58191--58246 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
58181 TTCTGACTAG
58191 TAGGAGTAATATTAGAGGTGAAAAAATT
1 TAGGAGTAATATTAGAGGTGAAAAAATT
*
58219 TAGGAGTAATATTAGAGGTGCAAAAATT
1 TAGGAGTAATATTAGAGGTGAAAAAATT
58247 AGTTTTTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.45, C:0.02, G:0.25, T:0.29
Consensus pattern (28 bp):
TAGGAGTAATATTAGAGGTGAAAAAATT
Found at i:61587 original size:21 final size:22
Alignment explanation
Indices: 61561--61601 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
61551 CAAGTCTATC
61561 AAATAAACATA-AAATTCAAAG
1 AAATAAACATACAAATTCAAAG
* *
61582 AAATAAGCATACTAATTCAA
1 AAATAAACATACAAATTCAA
61602 CCATTTAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.61, C:0.12, G:0.05, T:0.22
Consensus pattern (22 bp):
AAATAAACATACAAATTCAAAG
Found at i:62275 original size:42 final size:41
Alignment explanation
Indices: 62178--62279 Score: 132
Period size: 42 Copynumber: 2.5 Consensus size: 41
62168 TGAAATGGCC
* * *
62178 CTGCTCACACAAGCTGTGGGTCGGCATGTAGCTACACGATG
1 CTGCTCACACGAGCTGTGGGTCAGAATGTAGCTACACGATG
* * *
62219 CTACTCACAGGAGCTGTGGGTTAGAATGTAAGCTACACGATG
1 CTGCTCACACGAGCTGTGGGTCAGAATGT-AGCTACACGATG
*
62261 CTGCTTACACGAGCTGTGG
1 CTGCTCACACGAGCTGTGG
62280 AGAATTCACA
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
41 23 0.45
42 28 0.55
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.24
Consensus pattern (41 bp):
CTGCTCACACGAGCTGTGGGTCAGAATGTAGCTACACGATG
Found at i:66154 original size:26 final size:27
Alignment explanation
Indices: 66125--66175 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
66115 GACCGTAATG
66125 CCCCTAAAGGGTAAATGACT-ATTTTT
1 CCCCTAAAGGGTAAATGACTGATTTTT
**
66151 CCCCTCGAGGGTAAATGACTGATTT
1 CCCCTAAAGGGTAAATGACTGATTT
66176 GTGCTATGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (27 bp):
CCCCTAAAGGGTAAATGACTGATTTTT
Found at i:80289 original size:33 final size:32
Alignment explanation
Indices: 80247--80374 Score: 103
Period size: 33 Copynumber: 3.6 Consensus size: 32
80237 TCCCCCAAGG
80247 GGTTGCTAAGTGCTGATTCCTCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCC-CGAATCATTGGT
* * *
80280 GGTTGCTAAGTGCTGATCCCACCATATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CGA-ATC----AT-TG---GT
* *
80322 GGTTGCTAAGTGCTGATTCCCTGATTCATTGCT
1 GGTTGCTAAGTGCTGATTCCC-GAATCATTGGT
80355 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
80375 ACCGTATTTT
Statistics
Matches: 76, Mismatches: 9, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
33 41 0.54
34 3 0.04
36 2 0.03
37 2 0.03
38 2 0.03
39 2 0.03
41 3 0.04
42 21 0.28
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (32 bp):
GGTTGCTAAGTGCTGATTCCCGAATCATTGGT
Found at i:80289 original size:102 final size:102
Alignment explanation
Indices: 80113--80342 Score: 372
Period size: 102 Copynumber: 2.3 Consensus size: 102
80103 ATTGAATATA
* *
80113 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGTTGATTCCCTGATTCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCTGAATCATTGGT
* * *
80178 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTG
66 GGTTGCTAAGTGCTGATCCCACCATATCTTAAATGTG
* *
80215 AAGGGGGTTGCTAAGTGTTGGTTCCCCCAAGGGGTTGCTAAGTGCTGATT-CCTCGAATCATTGG
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCT-GAATCATTGG
80279 TGGTTGCTAAGTGCTGATCCCACCATATCTTAAATGTG
65 TGGTTGCTAAGTGCTGATCCCACCATATCTTAAATGTG
*
80317 AAAGGGGTTGCTAAGTGCTGATTCCC
1 AAGGGGGTTGCTAAGTGCTGATTCCC
80343 TGATTCATTG
Statistics
Matches: 117, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
101 3 0.03
102 114 0.97
ACGTcount: A:0.20, C:0.19, G:0.29, T:0.32
Consensus pattern (102 bp):
AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCTGAATCATTGGT
GGTTGCTAAGTGCTGATCCCACCATATCTTAAATGTG
Found at i:80366 original size:75 final size:77
Alignment explanation
Indices: 80243--80447 Score: 308
Period size: 75 Copynumber: 2.7 Consensus size: 77
80233 TGGTTCCCCC
80243 AAGGGGTTGCTAAGTGCTGATT-CCTCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCATA-
1 AAGGGGTTGCTAAGTGCTGATTCCCT-GAATCATTGGTGGTTGCTAAGTGCTGATCCCACCATAT
80306 TCTTAAATGTG-A
65 TCTTAAATGTGAA
* * * *
80318 AAGGGGTTGCTAAGTGCTGATTCCCTGATTCATTGCTGGTTGCTAAGTGCTGATTCCACCGTATT
1 AAGGGGTTGCTAAGTGCTGATTCCCTGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCATATT
* *
80383 TTTGAATGTGAA
66 CTTAAATGTGAA
* *
80395 AAGGGGTTGCTAAGTGTTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGA
1 AAGGGGTTGCTAAGTGCTGATTCCCTGAATCATTGGTGGTTGCTAAGTGCTGA
80448 ATCCACCGAA
Statistics
Matches: 117, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
75 55 0.47
76 12 0.10
77 50 0.43
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (77 bp):
AAGGGGTTGCTAAGTGCTGATTCCCTGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCATATT
CTTAAATGTGAA
Done.