Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3240
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: 26666
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Found at i:2654 original size:19 final size:20
Alignment explanation
Indices: 2609--2656 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
2599 GTTTGTATAT
2609 TTTTAATTAATTAATTAGATA
1 TTTT-ATTAATTAATTAGATA
* *
2630 -TATATTATTTAATTA-ATA
1 TTTTATTAATTAATTAGATA
2648 TTTTATTAA
1 TTTTATTAA
2657 GATTTTTAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
18 3 0.14
19 17 0.77
20 2 0.09
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTTATTAATTAATTAGATA
Found at i:9156 original size:52 final size:52
Alignment explanation
Indices: 9099--9202 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
9089 AGCAGAAAGT
*
9099 AAGGGAACAAACTTGACTATAGAGACATCATTGATGCACAAAATAAAACATA
1 AAGGGAACAAACTTGACTACAGAGACATCATTGATGCACAAAATAAAACATA
9151 AAGGGAACAAACTTGACTACAGAGACATCATTGATGCACAAAATAAAACATA
1 AAGGGAACAAACTTGACTACAGAGACATCATTGATGCACAAAATAAAACATA
9203 TCGAGAAGTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.50, C:0.16, G:0.15, T:0.18
Consensus pattern (52 bp):
AAGGGAACAAACTTGACTACAGAGACATCATTGATGCACAAAATAAAACATA
Found at i:9644 original size:15 final size:15
Alignment explanation
Indices: 9623--9657 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
9613 AAGGCCGAGG
9623 AAGAAAATACTAAGA
1 AAGAAAATACTAAGA
* *
9638 TAGAAAATGCTAAGA
1 AAGAAAATACTAAGA
9653 AAGAA
1 AAGAA
9658 TCTGTTGACC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.63, C:0.06, G:0.17, T:0.14
Consensus pattern (15 bp):
AAGAAAATACTAAGA
Found at i:9914 original size:72 final size:72
Alignment explanation
Indices: 9829--9975 Score: 240
Period size: 72 Copynumber: 2.0 Consensus size: 72
9819 ACCTAACTAA
* * ***
9829 TTTTTGTACATGGAAAATCCTAAACTAGATAACCTTATTGTGTGTGAAGTTGTTTAATTTTAGGT
1 TTTTTGCACATGGAAAATCCTAAACTAGATAAACTTATTCAATGTGAAGTTGTTTAATTTTAGGT
9894 GTTCAAT
66 GTTCAAT
*
9901 TTTTTGCACATGGAAAATCCTAAACTAGATAAACTTATTCAATGTGAAGTTGTTTAGTTTTAGGT
1 TTTTTGCACATGGAAAATCCTAAACTAGATAAACTTATTCAATGTGAAGTTGTTTAATTTTAGGT
9966 GTTCAAT
66 GTTCAAT
9973 TTT
1 TTT
9976 CACCCAACAA
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 69 1.00
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.43
Consensus pattern (72 bp):
TTTTTGCACATGGAAAATCCTAAACTAGATAAACTTATTCAATGTGAAGTTGTTTAATTTTAGGT
GTTCAAT
Found at i:22778 original size:2 final size:2
Alignment explanation
Indices: 22771--22807 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
22761 TCATGTTAGA
22771 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
22808 TCATATTCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:25926 original size:21 final size:20
Alignment explanation
Indices: 25902--25940 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
25892 TTTAAGATTT
*
25902 TTTAATTAAGAAATTAAAAAA
1 TTTAATTAA-AAAATAAAAAA
25923 TTTAATTAAAAAATAAAA
1 TTTAATTAAAAAATAAAA
25941 TTTTTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
TTTAATTAAAAAATAAAAAA
Found at i:25950 original size:21 final size:21
Alignment explanation
Indices: 25900--25947 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
25890 TTTTTAAGAT
*
25900 TTTTTAATTAAGAAATTAAAA
1 TTTTTAATTAAGAAAATAAAA
**
25921 AATTTAATTAA-AAAATAAAA
1 TTTTTAATTAAGAAAATAAAA
25941 TTTTTAA
1 TTTTTAA
25948 ATTTTTTTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
TTTTTAATTAAGAAAATAAAA
Found at i:25961 original size:20 final size:20
Alignment explanation
Indices: 25938--25977 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
25928 TTAAAAAATA
25938 AAATTTTTAAATTTTTTTTT
1 AAATTTTTAAATTTTTTTTT
25958 AAATTTTTAAATTTTTTTTT
1 AAATTTTTAAATTTTTTTTT
25978 TTTTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
AAATTTTTAAATTTTTTTTT
Found at i:25973 original size:1 final size:1
Alignment explanation
Indices: 25969--26016 Score: 60
Period size: 1 Copynumber: 48.0 Consensus size: 1
25959 AATTTTTAAA
* * **
25969 TTTTTTTTTTTTTTTATTTTTTTTTTTTTTTATTTTAATTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
26017 AAAATGAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (1 bp):
T
Found at i:25998 original size:16 final size:16
Alignment explanation
Indices: 25968--26017 Score: 82
Period size: 16 Copynumber: 3.1 Consensus size: 16
25958 AAATTTTTAA
25968 ATTTTTTTTTTTTTTT
1 ATTTTTTTTTTTTTTT
25984 ATTTTTTTTTTTTTTT
1 ATTTTTTTTTTTTTTT
*
26000 ATTTTAATTTTTTTTTT
1 ATTTT-TTTTTTTTTTT
26017 A
1 A
26018 AAATGAATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 21 0.66
17 11 0.34
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (16 bp):
ATTTTTTTTTTTTTTT
Found at i:26075 original size:13 final size:13
Alignment explanation
Indices: 26057--26082 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
26047 TAAAATTAAA
26057 TTTTTTTTAATAT
1 TTTTTTTTAATAT
26070 TTTTTTTTAATAT
1 TTTTTTTTAATAT
26083 AATAAAATGT
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTTTTAATAT
Found at i:26188 original size:21 final size:19
Alignment explanation
Indices: 26163--26209 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
26153 AGAATAATAA
26163 TTTTTAATTAAAATTTTTTTT
1 TTTTTAATT--AATTTTTTTT
**
26184 TTTTTAATTTTTTTTTTTT
1 TTTTTAATTAATTTTTTTT
26203 TTTTTAA
1 TTTTTAA
26210 ATTTTATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 15 0.62
21 9 0.38
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTAATTAATTTTTTTT
Found at i:26199 original size:20 final size:20
Alignment explanation
Indices: 26176--26214 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
26166 TTAATTAAAA
26176 TTTTTTTTTTTTT-AATTTT
1 TTTTTTTTTTTTTAAATTTT
26195 TTTTTTTTTTTTTAAATTTT
1 TTTTTTTTTTTTTAAATTTT
26215 ATTTATGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (20 bp):
TTTTTTTTTTTTTAAATTTT
Found at i:26214 original size:16 final size:15
Alignment explanation
Indices: 26174--26203 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
26164 TTTTAATTAA
26174 AATTTTTTTTTTTTT
1 AATTTTTTTTTTTTT
26189 AATTTTTTTTTTTTT
1 AATTTTTTTTTTTTT
26204 TTTTAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (15 bp):
AATTTTTTTTTTTTT
Found at i:26289 original size:14 final size:16
Alignment explanation
Indices: 26272--26310 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
26262 TTTGTTTTTG
26272 ATTTTTTTTAA-AT-T
1 ATTTTTTTTAAGATAT
*
26286 ATTTTTTATAAGATAT
1 ATTTTTTTTAAGATAT
26302 ATTTTTTTT
1 ATTTTTTTT
26311 TTAAAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 10 0.48
15 2 0.10
16 9 0.43
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (16 bp):
ATTTTTTTTAAGATAT
Found at i:26465 original size:17 final size:16
Alignment explanation
Indices: 26443--26503 Score: 56
Period size: 15 Copynumber: 3.9 Consensus size: 16
26433 TTTAAAAAAA
26443 TTATTAATTATTAATAT
1 TTATTAA-TATTAATAT
*
26460 TTATTAAT-TTAAAAT
1 TTATTAATATTAATAT
** *
26475 TTATTTTTTTTAAT-T
1 TTATTAATATTAATAT
26490 TT-TTAATATTAATA
1 TTATTAATATTAATA
26504 ATTTTTTTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
14 8 0.23
15 15 0.43
16 5 0.14
17 7 0.20
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTATTAATATTAATAT
Found at i:26488 original size:31 final size:30
Alignment explanation
Indices: 26453--26512 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
26443 TTATTAATTA
26453 TTAATATTTATTAAT-TTAA-AATTTATTTTTT
1 TTAAT-TTT-TTAATATTAATAATTT-TTTTTT
26484 TTAATTTTTTAATATTAATAATTTTTTTT
1 TTAATTTTTTAATATTAATAATTTTTTTT
26513 AAAATTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 5 0.19
30 12 0.44
31 10 0.37
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (30 bp):
TTAATTTTTTAATATTAATAATTTTTTTTT
Done.