Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold763
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: 17223
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.31
Found at i:1638 original size:16 final size:16
Alignment explanation
Indices: 1619--1651 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1609 ATTATAGTGG
1619 AATG-ACTTCATAACTA
1 AATGAACTT-ATAACTA
1635 AATGAACTTATAACTA
1 AATGAACTTATAACTA
1651 A
1 A
1652 TAGGTGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.30
Consensus pattern (16 bp):
AATGAACTTATAACTA
Found at i:5158 original size:27 final size:27
Alignment explanation
Indices: 5124--5301 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
5114 TAAATTGTAC
5124 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
5151 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
5177 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
5205 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
5233 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
5260 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
5287 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
5302 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:5238 original size:82 final size:81
Alignment explanation
Indices: 5125--5280 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
5115 AAATTGTACA
* *
5125 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
5189 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
5206 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
5271 TGCGAGTTGA
65 TGCGAATTGA
5281 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:5292 original size:82 final size:81
Alignment explanation
Indices: 5121--5301 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
5111 GAGTAAATTG
* *
5121 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
5186 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
5202 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
5266 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
5284 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
5302 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:13415 original size:27 final size:27
Alignment explanation
Indices: 13378--13582 Score: 259
Period size: 27 Copynumber: 7.6 Consensus size: 27
13368 TAAATTGTAC
13378 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
13405 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
13432 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
13458 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
13486 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
13514 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
13541 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
13568 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
13583 GACTCAATAT
Statistics
Matches: 156, Mismatches: 19, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
27 133 0.85
28 23 0.15
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:13517 original size:109 final size:108
Alignment explanation
Indices: 13379--13582 Score: 320
Period size: 109 Copynumber: 1.9 Consensus size: 108
13369 AAATTGTACA
* *
13379 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGT
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGATTTGACTACGTAGCACTAAGTGT
13444 GCGAAATGAATATGAT-GCACTAAGTGTGCGAATTGACCATGCG
66 GCGAAATGAATAT-ATAGCACTAAGTGTGCGAATTGACCATGCG
*
13487 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGATTTGACTACGTAGCACTAAGTG
** * *
13552 TGCGAGTTGATTATATAGCACTGAGTGTGCG
65 TGCGAAATGAATATATAGCACTAAGTGTGCG
13583 GACTCAATAT
Statistics
Matches: 87, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
108 17 0.20
109 70 0.80
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.30
Consensus pattern (108 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGATTTGACTACGTAGCACTAAGTGT
GCGAAATGAATATATAGCACTAAGTGTGCGAATTGACCATGCG
Found at i:15150 original size:7 final size:7
Alignment explanation
Indices: 15138--15242 Score: 65
Period size: 7 Copynumber: 14.0 Consensus size: 7
15128 TATATAAAAA
15138 TATATAT
1 TATATAT
15145 TATATAT
1 TATATAT
15152 TATATTAACT
1 TATA-T-A-T
15162 TA-ATAT
1 TATATAT
15168 T-TAAGTAT
1 TAT-A-TAT
15176 TAATATAT
1 T-ATATAT
*
15184 AATATAT
1 TATATAT
15191 TATTATAT
1 TA-TATAT
15199 TATAT-T
1 TATATAT
15205 ATATTATAT
1 -TA-TATAT
15214 TATAT-T
1 TATATAT
15220 ATATTATAT
1 -TA-TATAT
15229 TATATAT
1 TATATAT
*
15236 AATATAT
1 TATATAT
15243 AAAACATAAG
Statistics
Matches: 80, Mismatches: 3, Indels: 30
0.71 0.03 0.27
Matches are distributed among these distances:
6 4 0.05
7 41 0.51
8 26 0.32
9 5 0.06
10 4 0.05
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (7 bp):
TATATAT
Found at i:15197 original size:15 final size:15
Alignment explanation
Indices: 15138--15235 Score: 80
Period size: 15 Copynumber: 6.5 Consensus size: 15
15128 TATATAAAAA
15138 TATATATTA-TATAT
1 TATATATTATTATAT
*
15152 TATAT-TAACTTAATAT
1 TATATATTA-TT-ATAT
*
15168 T-TAAGTATTAATATAT
1 TAT-A-TATTATTATAT
*
15184 AATATATTATTATAT
1 TATATATTATTATAT
15199 TATAT-TATATTATAT
1 TATATAT-TATTATAT
15214 TATAT-TATATTATAT
1 TATATAT-TATTATAT
15229 TATATAT
1 TATATAT
15236 AATATATAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
13 2 0.03
14 6 0.09
15 44 0.64
16 12 0.17
17 3 0.04
18 2 0.03
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (15 bp):
TATATATTATTATAT
Found at i:15199 original size:5 final size:5
Alignment explanation
Indices: 15191--15242 Score: 88
Period size: 5 Copynumber: 10.6 Consensus size: 5
15181 TATAATATAT
*
15191 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TA-TA TAATA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
15240 TAT
1 TAT
15243 AAAACATAAG
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
4 4 0.09
5 41 0.91
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TATTA
Found at i:16454 original size:22 final size:22
Alignment explanation
Indices: 16425--16481 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
16415 TAGCACGTTA
16425 AGTGCTCTCTGTTTAGCACATCT
1 AGTGCTCTCTGTTTAGCAC-TCT
* *
16448 -GTGCTCTCTGTATAGCACTTT
1 AGTGCTCTCTGTTTAGCACTCT
16469 AGTGCTCTCTGTT
1 AGTGCTCTCTGTT
16482 CGTTTGTGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 2 0.07
22 28 0.93
ACGTcount: A:0.14, C:0.25, G:0.19, T:0.42
Consensus pattern (22 bp):
AGTGCTCTCTGTTTAGCACTCT
Found at i:16740 original size:13 final size:13
Alignment explanation
Indices: 16722--16748 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
16712 ATGGATTTAT
16722 TGCCTATTTATTC
1 TGCCTATTTATTC
16735 TGCCTATTTATTC
1 TGCCTATTTATTC
16748 T
1 T
16749 TGTAGTGCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.22, G:0.07, T:0.56
Consensus pattern (13 bp):
TGCCTATTTATTC
Done.