Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_199 ID=scaffold_199-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: 9756
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.27
Warning! 320 characters in sequence are not A, C, G, or T
Found at i:7446 original size:1 final size:1
Alignment explanation
Indices: 7440--7552 Score: 91
Period size: 1 Copynumber: 113.0 Consensus size: 1
7430 TATTATGCCT
* * * * * * * *
7440 AAAAAAAAGAAAAAAAAGAAAAAAAACAACAAAAAAAACAAAAAACAAAAAAACAAAAAAACAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * ** ** *
7505 AAAACAAAAAAACAAAAAAGCAAAAAAGTAAAAAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
7553 TCAAGATGAA
Statistics
Matches: 84, Mismatches: 28, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 84 1.00
ACGTcount: A:0.87, C:0.08, G:0.04, T:0.01
Consensus pattern (1 bp):
A
Found at i:7489 original size:24 final size:23
Alignment explanation
Indices: 7441--7552 Score: 122
Period size: 24 Copynumber: 4.9 Consensus size: 23
7431 ATTATGCCTA
* *
7441 AAAAAAAGAAAAAAA-AGAAAA-
1 AAAAAAACAAAAAAACAAAAAAC
*
7462 AAAACAACAAAAAAAACAAAAAAC
1 AAAAAAAC-AAAAAAACAAAAAAC
7486 AAAAAAACAAAAAAACAAAAAAAC
1 AAAAAAACAAAAAAAC-AAAAAAC
* *
7510 AAAAAAACAAAAAAGCAAAAAAG
1 AAAAAAACAAAAAAACAAAAAAC
* *
7533 TAAAAAA-AAAAAAAGAAAAA
1 AAAAAAACAAAAAAACAAAAA
7553 TCAAGATGAA
Statistics
Matches: 78, Mismatches: 9, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
21 6 0.08
22 18 0.23
23 25 0.32
24 29 0.37
ACGTcount: A:0.87, C:0.08, G:0.04, T:0.01
Consensus pattern (23 bp):
AAAAAAACAAAAAAACAAAAAAC
Found at i:8689 original size:147 final size:146
Alignment explanation
Indices: 8434--8844 Score: 449
Period size: 151 Copynumber: 2.8 Consensus size: 146
8424 AATCTCTGTT
* * *
8434 TTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCC-TCGGTCATGCC-GAGGTATTTCT
1 TTTTTCAAAAATCAACTCATAATGCAGAAGTGAGTTGAGCCTTGGGTCAT-CCTGAGGTA--T-T
* *
8497 TTTAAATTTCCATTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGGTCATCCT
62 TTTAAATTTCCATTTTCAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGTCATCCT
* *
8562 GAGGTATTTTTCAATTT-TCG
127 GAGGT-CTTTTCAATTTCTAG
*
8582 TTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGGTCATCCTGAGGTATTTTT
1 TTTTTCAAAAATCAACTCATAATGC-AGAAGTGAGTTGAGCCTTGGGTCATCCTGAGGTATTTTT
** *
8647 AAATTTTCGTTTTTC-AAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCATCCTGA
65 AAA-TTTCCATTTTCAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGTCATCCTGA
*
8711 GGTCTTTTCAATTTCTAT
129 GGTCTTTTCAATTTCTAG
* * *
8729 TTTTTCAAAAAAAAATCAACTCATAATGCTAGAAGTTAGTTGAGCCTCGGGTTA-CGCTGAGGTA
1 TTTTTC----AAAAATCAACTCATAATGC-AGAAGTGAGTTGAGCCTTGGGTCATC-CTGAGGTA
* * * ** *
8793 -TTTTCAATATCTATTTTTCAAAGGTCAACTCACAAT-CTGAGAAGTGAGTTGA
60 TTTTTAAATTTCCA-TTTTCAAAAATCAACTCATAATGC-GAGAAGTGAGTTGA
8845 ACTTCGGATC
Statistics
Matches: 225, Mismatches: 25, Indels: 23
0.82 0.09 0.08
Matches are distributed among these distances:
146 10 0.04
147 63 0.28
148 33 0.15
149 20 0.09
150 26 0.12
151 73 0.32
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (146 bp):
TTTTTCAAAAATCAACTCATAATGCAGAAGTGAGTTGAGCCTTGGGTCATCCTGAGGTATTTTTA
AATTTCCATTTTCAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGTCATCCTGAGG
TCTTTTCAATTTCTAG
Found at i:8770 original size:78 final size:74
Alignment explanation
Indices: 8434--8844 Score: 444
Period size: 74 Copynumber: 5.5 Consensus size: 74
8424 AATCTCTGTT
* *
8434 TTTTTCAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTC-GGTCATGCC-GAGGTATTTC
1 TTTTTCAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGTCAT-CCTGAGGTA-TT-
* * **
8496 TTTTAAATTTCC
63 TTTCAATTTTAG
* * *
8508 ATTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGGTCATCCTGAGGTATTTTT
1 TTTTTCAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGTCATCCTGAGGTATTTTT
*
8573 CAATTTTCG
66 CAATTTTAG
* *
8582 TTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGGTCATCCTGAGGTATTTTT
1 TTTTTCAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGTCATCCTGAGGTATTTTT
* *
8647 AAATTTTCG
66 CAATTTTAG
* *
8656 TTTTTC-AAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCATCCTGAGGT-CTTTT
1 TTTTTCAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGTCATCCTGAGGTATTTTT
*
8719 CAATTTCTAT
66 CAATTT-TAG
* * *
8729 TTTTTCAAAAAAAAATCAACTCATAATGCTAGAAGTTAGTTGAGCCTCGGGTTA-CGCTGAGGTA
1 TTTTTC----AAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGTCATC-CTGAGGTA
*
8793 -TTTTCAATATCTA-
61 TTTTTCAAT-TTTAG
** *
8806 TTTTTCAAAGGTCAACTCACAAT-CTGAGAAGTGAGTTGA
1 TTTTTCAAAAATCAACTCATAATGC-GAGAAGTGAGTTGA
8845 ACTTCGGATC
Statistics
Matches: 297, Mismatches: 27, Indels: 27
0.85 0.08 0.08
Matches are distributed among these distances:
72 10 0.03
73 82 0.28
74 109 0.37
75 20 0.07
76 12 0.04
77 7 0.02
78 56 0.19
79 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (74 bp):
TTTTTCAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGTCATCCTGAGGTATTTTT
CAATTTTAG
Found at i:9146 original size:10 final size:10
Alignment explanation
Indices: 9121--9164 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
9111 AAAATAGTAG
*
9121 TAAAAAAATC
1 TAAAAAAATA
9131 TCAAAAAAATA
1 T-AAAAAAATA
9142 TAAAAAAATA
1 TAAAAAAATA
*
9152 -CAAAAAATA
1 TAAAAAAATA
9161 TAAA
1 TAAA
9165 TTACATTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 8 0.28
10 12 0.41
11 9 0.31
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (10 bp):
TAAAAAAATA
Found at i:9298 original size:29 final size:29
Alignment explanation
Indices: 9266--9330 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
9256 ACAGTCGGGC
9266 CCCCAAACTTTCC-AGAAATTACATTTTAG
1 CCCCAAACTTTCCTA-AAATTACATTTTAG
* * * *
9295 CCCCATATTTTCCTAAAATTACGTTTTTG
1 CCCCAAACTTTCCTAAAATTACATTTTAG
9324 CCCCAAA
1 CCCCAAA
9331 AACTTTGCAC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 29 0.97
30 1 0.03
ACGTcount: A:0.31, C:0.29, G:0.06, T:0.34
Consensus pattern (29 bp):
CCCCAAACTTTCCTAAAATTACATTTTAG
Found at i:9593 original size:21 final size:21
Alignment explanation
Indices: 9544--9584 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
9534 CGGCAACCAA
*
9544 AGAAACAA-AAAAAATAGCAG
1 AGAAAAAAGAAAAAATAGCAG
9564 AGAAAAAAGAAAAAATAGCAG
1 AGAAAAAAGAAAAAATAGCAG
9585 CAAGCAAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.71, C:0.07, G:0.17, T:0.05
Consensus pattern (21 bp):
AGAAAAAAGAAAAAATAGCAG
Done.