Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga13g01162.F1
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: 3224
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Found at i:147 original size:41 final size:40
Alignment explanation
Indices: 89--337 Score: 245
Period size: 41 Copynumber: 6.1 Consensus size: 40
79 GCAAAAATTA
* * *
89 TAAAACACAGAGCAATAGAGGCCTTTTTTGGTAAAACGTCGC
1 TAAAA-ACAGAGCATTAGCGGCC-TTTTTGGTAAAACGCCGC
* *
131 TAAAAACAGAGCAATAGCGGCATTTTTGGTAAAACGCCGC
1 TAAAAACAGAGCATTAGCGGCCTTTTTGGTAAAACGCCGC
*
171 TAAAAACCAGAGCATTAGCGGCGC-TTTTGGTAAAACGCTGC
1 TAAAAA-CAGAGCATTAGCGGC-CTTTTTGGTAAAACGCCGC
* * * * *
212 TAAAAATCAAAGCATTAGCTGCGC-TTTCGGTAAAATGTCGC
1 TAAAAA-CAGAGCATTAGCGGC-CTTTTTGGTAAAACGCCGC
* * *
253 TAAAAAAAGAGCATTAGTGG-CTTTTTTGTAAAACGCCGC
1 TAAAAACAGAGCATTAGCGGCCTTTTTGGTAAAACGCCGC
* * *
292 TAAAAACTAGAACATTAGCGGCGC-TTCTAGTAAAACGCCGC
1 TAAAAAC-AGAGCATTAGCGGC-CTTTTTGGTAAAACGCCGC
333 TAAAA
1 TAAAA
338 GTCATATAAC
Statistics
Matches: 175, Mismatches: 26, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
38 1 0.01
39 19 0.11
40 44 0.25
41 105 0.60
42 6 0.03
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (40 bp):
TAAAAACAGAGCATTAGCGGCCTTTTTGGTAAAACGCCGC
Found at i:172 original size:40 final size:40
Alignment explanation
Indices: 114--337 Score: 261
Period size: 41 Copynumber: 5.5 Consensus size: 40
104 TAGAGGCCTT
* * **
114 TTTTGGTAAAACGTCGCTAAAAACAGAGCAATAGCGGCAT
1 TTTTGGTAAAACGCCGCTAAAAACAGAGCATTAGCGGCGC
154 TTTTGGTAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGC
1 TTTTGGTAAAACGCCGCTAAAAA-CAGAGCATTAGCGGCGC
* * *
195 TTTTGGTAAAACGCTGCTAAAAATCAAAGCATTAGCTGCGC
1 TTTTGGTAAAACGCCGCTAAAAA-CAGAGCATTAGCGGCGC
* * * * * *
236 TTTCGGTAAAATGTCGCTAAAAAAAGAGCATTAGTGGC-T
1 TTTTGGTAAAACGCCGCTAAAAACAGAGCATTAGCGGCGC
* *
275 TTTTTGTAAAACGCCGCTAAAAACTAGAACATTAGCGGCGC
1 TTTTGGTAAAACGCCGCTAAAAAC-AGAGCATTAGCGGCGC
* *
316 TTCTAGTAAAACGCCGCTAAAA
1 TTTTGGTAAAACGCCGCTAAAA
338 GTCATATAAC
Statistics
Matches: 154, Mismatches: 27, Indels: 5
0.83 0.15 0.03
Matches are distributed among these distances:
39 19 0.12
40 45 0.29
41 90 0.58
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (40 bp):
TTTTGGTAAAACGCCGCTAAAAACAGAGCATTAGCGGCGC
Found at i:264 original size:81 final size:80
Alignment explanation
Indices: 90--337 Score: 225
Period size: 80 Copynumber: 3.0 Consensus size: 80
80 CAAAAATTAT
* * * *
90 AAAACACAGAGCAATAGAGGCCTTTTTTGGTAAAACG-TCGCTAAAAACAGAGCAATAGCGGCAT
1 AAAACA-AGAGCATTAGCGGCC--TTTTGGTAAAACGCT-GCTAAAAACAAAGCAATAGCGGCAC
*
154 TTTTGGTAAAACGCCGCTA
62 TTTCGGTAAAACGCCGCTA
* * * *
173 AAAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCTGCTAAAAATCAAAGCATTAGCTGCGCTT
1 AAAACAAGAGCATTAGCGGC-CTTTTGGTAAAACGCTGCTAAAAA-CAAAGCAATAGCGGCACTT
* *
238 TCGGTAAAATGTCGCTA
64 TCGGTAAAACGCCGCTA
* * * * * *
255 AAAA-AAGAGCATTAGTGGCTTTTTTGTAAAACGCCGCTAAAAACTAGAA-CATTAGCGGCGC-T
1 AAAACAAGAGCATTAGCGGCCTTTTGGTAAAACGCTGCTAAAAAC-A-AAGCAATAGCGGCACTT
*
317 TCTAGTAAAACGCCGCTA
64 TC-GGTAAAACGCCGCTA
335 AAA
1 AAA
338 GTCATATAAC
Statistics
Matches: 139, Mismatches: 20, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
79 4 0.03
80 48 0.35
81 36 0.26
82 45 0.32
83 6 0.04
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (80 bp):
AAAACAAGAGCATTAGCGGCCTTTTGGTAAAACGCTGCTAAAAACAAAGCAATAGCGGCACTTTC
GGTAAAACGCCGCTA
Found at i:309 original size:121 final size:122
Alignment explanation
Indices: 118--337 Score: 343
Period size: 121 Copynumber: 1.8 Consensus size: 122
108 GGCCTTTTTT
* *
118 GGTAAAACGTCGCTAAAAACAGAGCAATAGCGGCATTTTTGGTAAAACGCCGCTAAAAACCAGAG
1 GGTAAAACGTCGCTAAAAAAAGAGCAATAGCGGCATTTTTGGTAAAACGCCGCTAAAAACCAGAA
* * *
183 CATTAGCGGCGCTTTTGGTAAAACGCTGCTAAAAATCAAAGCATTAGCTGCGCTTTC
66 CATTAGCGGCGCTTCTAGTAAAACGCCGCTAAAAATCAAAGCATTAGCTGCGCTTTC
* * * * *
240 GGTAAAATGTCGCTAAAAAAAGAGCATTAGTGGC-TTTTTTGTAAAACGCCGCTAAAAACTAGAA
1 GGTAAAACGTCGCTAAAAAAAGAGCAATAGCGGCATTTTTGGTAAAACGCCGCTAAAAACCAGAA
304 CATTAGCGGCGCTTCTAGTAAAACGCCGCTAAAA
66 CATTAGCGGCGCTTCTAGTAAAACGCCGCTAAAA
338 GTCATATAAC
Statistics
Matches: 88, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
121 58 0.66
122 30 0.34
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (122 bp):
GGTAAAACGTCGCTAAAAAAAGAGCAATAGCGGCATTTTTGGTAAAACGCCGCTAAAAACCAGAA
CATTAGCGGCGCTTCTAGTAAAACGCCGCTAAAAATCAAAGCATTAGCTGCGCTTTC
Found at i:436 original size:17 final size:18
Alignment explanation
Indices: 408--442 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
398 TTAAAACATT
*
408 AAACCTCTAAACCCTAAA
1 AAACCTCTAAACACTAAA
426 AAACC-CTAAACACTAAA
1 AAACCTCTAAACACTAAA
443 CTATAACCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.14
Consensus pattern (18 bp):
AAACCTCTAAACACTAAA
Found at i:447 original size:56 final size:53
Alignment explanation
Indices: 357--471 Score: 158
Period size: 56 Copynumber: 2.1 Consensus size: 53
347 CCTCTAAAAT
* *
357 CCTAAACCCCAAAAAATCATAAACACTAATCTATATAACCCTTAAAACATTAAAC
1 CCTAAACCCCAAAAAACCATAAACACTAAAC--TATAACCCTTAAAACATTAAAC
* * *
412 CTCTAAACCCTAAAAAACCCTAAACACTAAACTATAACCCTTAAAACCTTAAAC
1 C-CTAAACCCCAAAAAACCATAAACACTAAACTATAACCCTTAAAACATTAAAC
466 CCTAAA
1 CCTAAA
472 AAACATCACA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
53 5 0.09
54 22 0.41
55 1 0.02
56 26 0.48
ACGTcount: A:0.50, C:0.30, G:0.00, T:0.21
Consensus pattern (53 bp):
CCTAAACCCCAAAAAACCATAAACACTAAACTATAACCCTTAAAACATTAAAC
Found at i:664 original size:15 final size:15
Alignment explanation
Indices: 641--700 Score: 54
Period size: 15 Copynumber: 4.1 Consensus size: 15
631 TAATTTAACT
*
641 TTTATGGATTATGGG
1 TTTAGGGATTATGGG
656 TTTAGGGATTAT-GG
1 TTTAGGGATTATGGG
*
670 TTTAAGGG-TT-GGGG
1 TTT-AGGGATTATGGG
* *
684 TTTAAGGTTTATGGG
1 TTTAGGGATTATGGG
699 TT
1 TT
701 ATGGGTTAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
13 3 0.08
14 14 0.38
15 20 0.54
ACGTcount: A:0.18, C:0.00, G:0.37, T:0.45
Consensus pattern (15 bp):
TTTAGGGATTATGGG
Found at i:684 original size:28 final size:28
Alignment explanation
Indices: 653--707 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
643 TATGGATTAT
* *
653 GGGTTTAGGGATTATGGTTTAAGGGTTG
1 GGGTTTAAGGATTATGGGTTAAGGGTTG
* *
681 GGGTTTAAGGTTTATGGGTTATGGGTT
1 GGGTTTAAGGATTATGGGTTAAGGGTT
708 AAGGGTTAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.16, C:0.00, G:0.42, T:0.42
Consensus pattern (28 bp):
GGGTTTAAGGATTATGGGTTAAGGGTTG
Found at i:709 original size:21 final size:21
Alignment explanation
Indices: 649--775 Score: 89
Period size: 21 Copynumber: 6.0 Consensus size: 21
639 CTTTTATGGA
*
649 TTATGGGTTTAGGGATTATGGT
1 TTATGGGTTT-GGGATTAAGGT
* * *
671 TTAAGGGTTGGGGTTTAAGGT
1 TTATGGGTTTGGGATTAAGGT
*
692 TTATGGGTTATGGG-TTAAGGG
1 TTATGGGTT-TGGGATTAAGGT
* * *
713 TTAGGGGTCTAGGATTAAGAGT
1 TTATGGGTTTGGGATTAAG-GT
* * *
735 TTAT-GTTTTAGGATTTAGGGT
1 TTATGGGTTTGGGA-TTAAGGT
756 TTAT-GGTTTAGGGATTAAGG
1 TTATGGGTTT-GGGATTAAGG
776 ATTAGTAGTT
Statistics
Matches: 82, Mismatches: 18, Indels: 11
0.74 0.16 0.10
Matches are distributed among these distances:
20 3 0.04
21 57 0.70
22 22 0.27
ACGTcount: A:0.21, C:0.01, G:0.37, T:0.41
Consensus pattern (21 bp):
TTATGGGTTTGGGATTAAGGT
Found at i:793 original size:7 final size:7
Alignment explanation
Indices: 653--795 Score: 67
Period size: 7 Copynumber: 20.1 Consensus size: 7
643 TATGGATTAT
653 GGGTTTA
1 GGGTTTA
*
660 GGGATTA
1 GGGTTTA
*
667 TGGTTTAA
1 GGGTTT-A
*
675 GGG-TTG
1 GGGTTTA
681 GGGTTTA
1 GGGTTTA
*
688 AGGTTTA
1 GGGTTTA
695 TGGG-TTA
1 -GGGTTTA
*
702 TGGGTTAA
1 -GGGTTTA
710 GGG-TTA
1 GGGTTTA
*
716 GGGGTCTA
1 -GGGTTTA
* *
724 GGATTAA
1 GGGTTTA
*
731 GAGTTTA
1 GGGTTTA
* *
738 TGTTTTA
1 GGGTTTA
*
745 GGATTTA
1 GGGTTTA
752 GGGTTTA
1 GGGTTTA
*
759 TGGTTTA
1 GGGTTTA
*
766 GGGATTA
1 GGGTTTA
* *
773 AGGATTA
1 GGGTTTA
*
780 GTAGTTTA
1 G-GGTTTA
788 GGGTTTA
1 GGGTTTA
795 G
1 G
796 TTAATTAGTG
Statistics
Matches: 98, Mismatches: 31, Indels: 14
0.69 0.22 0.10
Matches are distributed among these distances:
6 5 0.05
7 79 0.81
8 14 0.14
ACGTcount: A:0.22, C:0.01, G:0.37, T:0.41
Consensus pattern (7 bp):
GGGTTTA
Found at i:1744 original size:60 final size:59
Alignment explanation
Indices: 1607--1755 Score: 153
Period size: 60 Copynumber: 2.5 Consensus size: 59
1597 CTATTCAGAA
* * *
1607 ATCAGAGT-TAACTAGGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCCCTTACAG
1 ATCAGAGTAT-ACTGGGCC-TAGCCCATATCAATATCAATCTGGGCCATAGCCCATTACAG
* *
1667 TATCAGAGTATACTGGGCCTAGCCCATGTCAGTATCAATCTGGGCCATAGCCCTATTACA-
1 -ATCAGAGTATACTGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCC-ATTACAG
*
1727 AGTC-GAG-ATACATTGGGCCTTGCCCATAT
1 A-TCAGAGTATAC--TGGGCCTAGCCCATAT
1756 TAACACAGTT
Statistics
Matches: 76, Mismatches: 7, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
58 4 0.05
59 4 0.05
60 47 0.62
61 20 0.26
62 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (59 bp):
ATCAGAGTATACTGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCATTACAG
Done.