Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2041
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: 26248
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1143 original size:17 final size:18
Alignment explanation
Indices: 1123--1156 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1113 TTAAAGATGC
1123 AATTATATT-TTTATTTT
1 AATTATATTATTTATTTT
1140 AATTATATTATTTATTT
1 AATTATATTATTTATTT
1157 ATTTAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
AATTATATTATTTATTTT
Found at i:3205 original size:21 final size:21
Alignment explanation
Indices: 3181--3221 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3171 TTTATTATAT
3181 TTATAAATATAATAAATATTA
1 TTATAAATATAATAAATATTA
* * *
3202 TTATAATTATTATAATTATT
1 TTATAAATATAATAAATATT
3222 GTAATTGTGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTATAAATATAATAAATATTA
Found at i:3226 original size:9 final size:9
Alignment explanation
Indices: 3198--3227 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
3188 TATAATAAAT
3198 ATTATTATA
1 ATTATTATA
3207 ATTATTATA
1 ATTATTATA
*
3216 ATTATTGTA
1 ATTATTATA
3225 ATT
1 ATT
3228 GTGAATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (9 bp):
ATTATTATA
Found at i:11785 original size:48 final size:48
Alignment explanation
Indices: 11729--11826 Score: 178
Period size: 48 Copynumber: 2.0 Consensus size: 48
11719 TTGCACCTGA
*
11729 CCAGATATTTGCTATGTAGTTAGTATTTTAAGTTGATATTAGTCAAAC
1 CCAGATATTTGCTATGTAGTCAGTATTTTAAGTTGATATTAGTCAAAC
*
11777 CCAGATATTTGTTATGTAGTCAGTATTTTAAGTTGATATTAGTCAAAC
1 CCAGATATTTGCTATGTAGTCAGTATTTTAAGTTGATATTAGTCAAAC
11825 CC
1 CC
11827 TCGTAACAAG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (48 bp):
CCAGATATTTGCTATGTAGTCAGTATTTTAAGTTGATATTAGTCAAAC
Found at i:17948 original size:19 final size:20
Alignment explanation
Indices: 17908--17948 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
17898 GACTTGATTT
*
17908 AAATGAAAATAAAATTAGGA
1 AAATGAAAATAAAATTAAGA
17928 AAAT-AAAA-AAAATTTAAGA
1 AAATGAAAATAAAA-TTAAGA
17947 AA
1 AA
17949 TTTGGTCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
18 4 0.21
19 11 0.58
20 4 0.21
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.20
Consensus pattern (20 bp):
AAATGAAAATAAAATTAAGA
Found at i:19359 original size:15 final size:16
Alignment explanation
Indices: 19341--19374 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
19331 TTTAAAAAAA
19341 TTAAATTC-AAAATGT
1 TTAAATTCAAAAATGT
19356 TT-AATTCAAAAATGT
1 TTAAATTCAAAAATGT
19371 TTAA
1 TTAA
19375 GGGAAAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
14 5 0.29
15 11 0.65
16 1 0.06
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (16 bp):
TTAAATTCAAAAATGT
Found at i:25501 original size:51 final size:49
Alignment explanation
Indices: 25424--25541 Score: 166
Period size: 51 Copynumber: 2.4 Consensus size: 49
25414 TCAATTTTCT
* *
25424 TAATCGGGGATACTCCAACTCTGATTTTATTTCTAAAACACCCATTCTCCA
1 TAATCGGGGATACTCCAACTCCGA-TTTATTTCCAAAACACCCATT-TCCA
* *
25475 TAATCGGGGATACTCCAACTCCGATTTATTTCCAAAACACCGATTTTCA
1 TAATCGGGGATACTCCAACTCCGATTTATTTCCAAAACACCCATTTCCA
*
25524 CAATCGGGG-TACTCCAAC
1 TAATCGGGGATACTCCAAC
25542 CCCGTTATTT
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
48 9 0.15
49 11 0.18
50 19 0.31
51 23 0.37
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.30
Consensus pattern (49 bp):
TAATCGGGGATACTCCAACTCCGATTTATTTCCAAAACACCCATTTCCA
Found at i:25616 original size:78 final size:79
Alignment explanation
Indices: 25480--25726 Score: 294
Period size: 77 Copynumber: 3.2 Consensus size: 79
25470 CTCCATAATC
* * * *
25480 GGGGATACTCCAACTC-C-GATTTATTTCCAAAACACCGA-TTTTCACAATCGGGGTACTCCAAC
1 GGGGATACTCCAAC-CACGGTTTTATTTCTAAAACACCAATTTTTCACAATCGGGATACTCCAAC
25542 CCCGTTATTTCT-GA
65 CCCGTTATTTCTCGA
* * *
25556 GGGGATACTCTAACCACGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGATACTCCAACC
1 GGGGATACTCCAACCACGGTTTTATTTCTAAAACACCAATTTTTCACAATCGGGATACTCCAACC
25621 CCG-TATTT-TCGA
66 CCGTTATTTCTCGA
* * * *
25633 GGGGATACTCCAACCCCGGTTTTATTTTTAAAACACCAATTCTCCACAATCAGGGATACTCCAAC
1 GGGGATACTCCAACCACGGTTTTATTTCTAAAACACCAATTTTTCACAATC-GGGATACTCCAAC
*
25698 CCCGTTTTTTCATC--
65 CCCGTTATTTC-TCGA
*
25712 TGGGATACTCCAACC
1 GGGGATACTCCAACC
25727 CCGTTATTTC
Statistics
Matches: 147, Mismatches: 16, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
75 1 0.01
76 15 0.10
77 68 0.46
78 43 0.29
79 18 0.12
81 2 0.01
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (79 bp):
GGGGATACTCCAACCACGGTTTTATTTCTAAAACACCAATTTTTCACAATCGGGATACTCCAACC
CCGTTATTTCTCGA
Found at i:25717 original size:28 final size:27
Alignment explanation
Indices: 25682--25762 Score: 99
Period size: 28 Copynumber: 2.9 Consensus size: 27
25672 TTCTCCACAA
25682 TCAGGGATACTCCAACCCCGTTTTTTC
1 TCAGGGATACTCCAACCCCGTTTTTTC
* *
25709 ATCTGGGATACTCCAACCCCGTTATTTC
1 -TCAGGGATACTCCAACCCCGTTTTTTC
* * *
25737 TGAGGAGATACTTCAACCCCGATTTT
1 TCAGG-GATACTCCAACCCCGTTTTT
25763 ATTTTCAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 3 0.07
28 42 0.93
ACGTcount: A:0.22, C:0.30, G:0.16, T:0.32
Consensus pattern (27 bp):
TCAGGGATACTCCAACCCCGTTTTTTC
Found at i:25754 original size:107 final size:106
Alignment explanation
Indices: 25607--25799 Score: 282
Period size: 107 Copynumber: 1.8 Consensus size: 106
25597 TTTCATAATC
* * *
25607 GGGATACTCCAACCCCGTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTTTAAAACACCAA
1 GGGATACTCCAACCCCGTATTTTCGAGGAGATACTCCAACCCCGATTTTATTTTCAAAACACCAA
25672 -TTCTCCACAATCAGGGATACTCCAACCCCGTTTTTTCATCT
66 TTTCT-CACAATCAGGGATACTCCAACCCCGTTTTTTCATCT
* * **
25713 GGGATACTCCAACCCCGT-TATTTCTGAGGAGATACTTCAACCCCGATTTTATTTTCAAAATATT
1 GGGATACTCCAACCCCGTAT-TTTC-GAGGAGATACTCCAACCCCGATTTTATTTTCAAAACACC
25777 AATTTCTCACAATCAGGGATACT
64 AATTTCTCACAATCAGGGATACT
25800 TAAACCCCTG
Statistics
Matches: 77, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
105 1 0.01
106 22 0.29
107 50 0.65
108 4 0.05
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (106 bp):
GGGATACTCCAACCCCGTATTTTCGAGGAGATACTCCAACCCCGATTTTATTTTCAAAACACCAA
TTTCTCACAATCAGGGATACTCCAACCCCGTTTTTTCATCT
Done.