Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2743
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: 6210
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.37
Found at i:321 original size:166 final size:166
Alignment explanation
Indices: 78--663 Score: 680
Period size: 166 Copynumber: 3.5 Consensus size: 166
68 ATTGATCCAA
* * * *
78 AATTTTTTAAATTTATC-AA-ATTATTATTT-ATTCATTCATTAAGTTAGTTTTTAAAAATTCAT
1 AATTTTTAAAATTCATCAAATATTATTATTTAATTCA-T-ATTAAATTAATTTTTAAAAATTCAT
* * *
140 TCATTTTCATGAGTTTGGAATTTTTTATTGGAAATTACCCTGTTTCCAAAATACAGAGTTTTCTA
64 TCATTTTCATGAGTTTGGAATTTTTTCTTGGAAATTTCCCTGTTTCTAAAATACAGAGTTTTCTA
* * * *
205 TTCCATAAATGTTTTCGAGGAAATTTTTCTTGGTTTTT
129 CTCCATAAATGTTTTCGGGGGAATTTTTCTTAGTTTTT
* *
243 AATTTTTAAAATTCATCAAATATTATTATTTAATTCATACTAAATCAATTTTTAAAAATTCATTC
1 AATTTTTAAAATTCATCAAATATTATTATTTAATTCATATTAAATTAATTTTTAAAAATTCATTC
* * * * * *
308 ATTTTCATGAGTTTGGAATTCTTTCTTGGAAATTTCCCTTATTTTTGAAATACTGAATTTTCTAC
66 ATTTTCATGAGTTTGGAATTTTTTCTTGGAAATTTCCC-TGTTTCTAAAATACAGAGTTTTCTAC
373 TCCATAAATGTTTTCGGGGGAATTTTTCTTAG-TTTT
130 TCCATAAATGTTTTCGGGGGAATTTTTCTTAGTTTTT
* * * *
409 AATTTTTAAAATTCATAAAATGTTATTATTTAATTCCTATTAAATTAGA-TTTAAAAAATTCATT
1 AATTTTTAAAATTCATCAAATATTATTATTTAATTCATATTAAATTA-ATTTTTAAAAATTCATT
* * * * * **
473 CATTTTCGTGAGTTTTGAATTTTTTCTTAGAAATTTTCTTGTTTCTAAAATATGGAGTTTTCTAC
65 CATTTTCATGAGTTTGGAATTTTTTCTTGGAAATTTCCCTGTTTCTAAAATACAGAGTTTTCTAC
* * *
538 TCCATAAATGTTTTTGGGGGGATTTTTTTTAGTTTTT
130 TCCATAAATGTTTTCGGGGGAATTTTTCTTAGTTTTT
* * * * * * * * * *
575 AATTTTTAAAATTCGTTAAATATTGTAATTAAATTTACATTAAATTAGTTTTGAGAAATTCAATT
1 AATTTTTAAAATTCATCAAATATTATTATTTAATTCATATTAAATTAATTTTTAAAAATTC-ATT
* *
640 TATTTT-ATGAGTTTTGAATTTTTT
65 CATTTTCATGAGTTTGGAATTTTTT
664 TAGTATATAT
Statistics
Matches: 359, Mismatches: 54, Indels: 15
0.84 0.13 0.04
Matches are distributed among these distances:
165 64 0.18
166 222 0.62
167 68 0.19
168 5 0.01
ACGTcount: A:0.31, C:0.09, G:0.10, T:0.50
Consensus pattern (166 bp):
AATTTTTAAAATTCATCAAATATTATTATTTAATTCATATTAAATTAATTTTTAAAAATTCATTC
ATTTTCATGAGTTTGGAATTTTTTCTTGGAAATTTCCCTGTTTCTAAAATACAGAGTTTTCTACT
CCATAAATGTTTTCGGGGGAATTTTTCTTAGTTTTT
Found at i:822 original size:5 final size:5
Alignment explanation
Indices: 812--836 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
802 GATTTTTGAA
812 AATTT AATTT AATTT AATTT AATTT
1 AATTT AATTT AATTT AATTT AATTT
837 GTACTATCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
AATTT
Found at i:1176 original size:23 final size:23
Alignment explanation
Indices: 1146--1197 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
1136 GAGTTTTGGC
1146 AAGAAAGAA-AAAGAGAAAAAAAA
1 AAGAAAGAAGAAAGAG-AAAAAAA
*
1169 AAGAAAGAAGAAAGAGAGAAAAA
1 AAGAAAGAAGAAAGAGAAAAAAA
1192 AAGAAA
1 AAGAAA
1198 ATTAAAGCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 21 0.78
24 6 0.22
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (23 bp):
AAGAAAGAAGAAAGAGAAAAAAA
Found at i:2693 original size:156 final size:156
Alignment explanation
Indices: 2408--2717 Score: 442
Period size: 156 Copynumber: 2.0 Consensus size: 156
2398 CATTCCTTTC
* *
2408 ATTTTTCAAGTCCTTTAGGGATATCAGGCACTTTTAAGTCAAAGGTATCCCCTAAGGGTTTTTTT
1 ATTTTTCAAGTCCTTTAGGGATATCAGACACTTTTAAGTCAAAGGTATCCCCTAAGGGTTATTTT
*
2473 TGTAATTTTCTAAAATCAAGTCCAAAGTTGTCACCGAGTCTGCTTTTATGCCGAAGGTGAGTATT
66 TGTAATTTTCTAAAAGCAAGTCCAAAGTTGTCACCGAGTCTGCTTTTATGCCGAAGGTGAGTATT
*
2538 TAGGATAGGTTATCCCATCTATAATA
131 TAGCATAGGTTATCCCATCTATAATA
* *
2564 ATTTTTCAAGTCCTTTAGGGGTATCAGACACTTTTAAGTCAAAGGTATCCCTTAAGGG-TATTTT
1 ATTTTTCAAGTCCTTTAGGGATATCAGACACTTTTAAGTCAAAGGTATCCCCTAAGGGTTATTTT
* * * * * * * * ** *
2628 TGTGATTTTTTTAAAGCTAAGTCCTAGGTTGTCACTGGGTTTGCTTTTATGTTGAAGGTGGGTAT
66 TGTAATTTTCTAAAAGC-AAGTCCAAAGTTGTCACCGAGTCTGCTTTTATGCCGAAGGTGAGTAT
*
2693 TTAGCATAGGTTATCCCATTTATAA
130 TTAGCATAGGTTATCCCATCTATAA
2718 CCTTTTTAAG
Statistics
Matches: 135, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
155 18 0.13
156 117 0.87
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (156 bp):
ATTTTTCAAGTCCTTTAGGGATATCAGACACTTTTAAGTCAAAGGTATCCCCTAAGGGTTATTTT
TGTAATTTTCTAAAAGCAAGTCCAAAGTTGTCACCGAGTCTGCTTTTATGCCGAAGGTGAGTATT
TAGCATAGGTTATCCCATCTATAATA
Found at i:4592 original size:20 final size:20
Alignment explanation
Indices: 4569--4641 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
4559 ACAATTCAAA
4569 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
4589 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
4610 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
4630 GTATCGATACAT
1 GTATCGATACAT
4642 AAAAAAGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:4613 original size:21 final size:21
Alignment explanation
Indices: 4587--4662 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
4577 ACATGTTGCA
4587 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
4608 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
4628 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
*
4649 TTGTATCGATACAT
1 ATGTATCGATACAT
4663 TTCTTGGCAG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:4620 original size:41 final size:41
Alignment explanation
Indices: 4569--4662 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
4559 ACAATTCAAA
*
4569 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
*
4610 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
4651 GTATCGATACAT
1 GTATCGATACAT
4663 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:4719 original size:13 final size:13
Alignment explanation
Indices: 4701--4726 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4691 TACAGCAAGT
4701 ATGTATCGATACA
1 ATGTATCGATACA
4714 ATGTATCGATACA
1 ATGTATCGATACA
4727 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Done.