Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3193
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: 26735
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:5612 original size:10 final size:10
Alignment explanation
Indices: 5597--5627 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
5587 TAGTAGTTTC
5597 TTCAAAAAAA
1 TTCAAAAAAA
5607 TTCAAAAAAAA
1 TTC-AAAAAAA
5618 TTCAAAAAAA
1 TTCAAAAAAA
5628 AAAAAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.19
Consensus pattern (10 bp):
TTCAAAAAAA
Found at i:5629 original size:12 final size:11
Alignment explanation
Indices: 5600--5628 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
5590 TAGTTTCTTC
5600 AAAAAAATTCA
1 AAAAAAATTCA
5611 AAAAAAATTCA
1 AAAAAAATTCA
5622 AAAAAAA
1 AAAAAAA
5629 AAAAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:5699 original size:15 final size:15
Alignment explanation
Indices: 5679--5730 Score: 95
Period size: 15 Copynumber: 3.4 Consensus size: 15
5669 TATCAAGTTG
5679 AAAAAAAATTCGTGA
1 AAAAAAAATTCGTGA
5694 AAAAAAAATTCGTGA
1 AAAAAAAATTCGTGA
5709 AAAAAAAATTTCGTGA
1 AAAAAAAA-TTCGTGA
5725 AAAAAA
1 AAAAAA
5731 GAAGAAGCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 23 0.64
16 13 0.36
ACGTcount: A:0.63, C:0.06, G:0.12, T:0.19
Consensus pattern (15 bp):
AAAAAAAATTCGTGA
Found at i:5700 original size:16 final size:16
Alignment explanation
Indices: 5679--5730 Score: 88
Period size: 16 Copynumber: 3.3 Consensus size: 16
5669 TATCAAGTTG
5679 AAAAAAAATTCGTG-A
1 AAAAAAAATTCGTGAA
5694 AAAAAAAATTCGTGAA
1 AAAAAAAATTCGTGAA
*
5710 AAAAAAATTTCGTGAA
1 AAAAAAAATTCGTGAA
5726 AAAAA
1 AAAAA
5731 GAAGAAGCTA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
15 14 0.40
16 21 0.60
ACGTcount: A:0.63, C:0.06, G:0.12, T:0.19
Consensus pattern (16 bp):
AAAAAAAATTCGTGAA
Found at i:15667 original size:19 final size:18
Alignment explanation
Indices: 15631--15670 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
15621 TTTCCACTCG
*
15631 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
15649 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
15668 TTT
1 TTT
15671 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:16743 original size:14 final size:14
Alignment explanation
Indices: 16724--16777 Score: 85
Period size: 14 Copynumber: 3.9 Consensus size: 14
16714 CAAAACTAGC
16724 TTTTTTTTCACAAT
1 TTTTTTTTCACAAT
16738 TTTTTTTTCACAATT
1 TTTTTTTTCACAA-T
16753 TTTTTTTTCA-AA-
1 TTTTTTTTCACAAT
16765 TTTTTTTTCACAA
1 TTTTTTTTCACAA
16778 CTTGATATCC
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
12 10 0.26
13 2 0.05
14 15 0.39
15 11 0.29
ACGTcount: A:0.22, C:0.13, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTTTTTCACAAT
Found at i:16768 original size:27 final size:29
Alignment explanation
Indices: 16724--16777 Score: 94
Period size: 27 Copynumber: 1.9 Consensus size: 29
16714 CAAAACTAGC
16724 TTTTTTTTCACAATTTTTTTTTCACAATT
1 TTTTTTTTCACAATTTTTTTTTCACAATT
16753 TTTTTTTTCA-AA-TTTTTTTTCACAA
1 TTTTTTTTCACAATTTTTTTTTCACAA
16778 CTTGATATCC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 13 0.52
28 2 0.08
29 10 0.40
ACGTcount: A:0.22, C:0.13, G:0.00, T:0.65
Consensus pattern (29 bp):
TTTTTTTTCACAATTTTTTTTTCACAATT
Found at i:16833 original size:13 final size:13
Alignment explanation
Indices: 16815--16847 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
16805 TGGAAACTAG
16815 TTTTTTTTT-GAA
1 TTTTTTTTTCGAA
*
16827 TTTTTTTTTCGAG
1 TTTTTTTTTCGAA
16840 TTTTTTTT
1 TTTTTTTT
16848 CGAGAATCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.09, C:0.03, G:0.09, T:0.79
Consensus pattern (13 bp):
TTTTTTTTTCGAA
Found at i:16848 original size:12 final size:12
Alignment explanation
Indices: 16813--16851 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
16803 AATGGAAACT
*
16813 AGTTTTTTTTTG
1 AGTTTTTTTTCG
*
16825 AATTTTTTTTTCG
1 -AGTTTTTTTTCG
16838 AGTTTTTTTTCG
1 AGTTTTTTTTCG
16850 AG
1 AG
16852 AATCTACTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.13, C:0.05, G:0.15, T:0.67
Consensus pattern (12 bp):
AGTTTTTTTTCG
Found at i:18777 original size:79 final size:79
Alignment explanation
Indices: 18646--18800 Score: 310
Period size: 79 Copynumber: 2.0 Consensus size: 79
18636 CTGATATGTG
18646 ACGTATTTAGGTTCTACTATGTATTATGTGTGTATTTAAGTATGTTTTGGTATTGATTTGATGTT
1 ACGTATTTAGGTTCTACTATGTATTATGTGTGTATTTAAGTATGTTTTGGTATTGATTTGATGTT
18711 GTTTATGTTTTGTA
66 GTTTATGTTTTGTA
18725 ACGTATTTAGGTTCTACTATGTATTATGTGTGTATTTAAGTATGTTTTGGTATTGATTTGATGTT
1 ACGTATTTAGGTTCTACTATGTATTATGTGTGTATTTAAGTATGTTTTGGTATTGATTTGATGTT
18790 GTTTATGTTTT
66 GTTTATGTTTT
18801 AATGAATAAG
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 76 1.00
ACGTcount: A:0.20, C:0.04, G:0.21, T:0.55
Consensus pattern (79 bp):
ACGTATTTAGGTTCTACTATGTATTATGTGTGTATTTAAGTATGTTTTGGTATTGATTTGATGTT
GTTTATGTTTTGTA
Found at i:19088 original size:52 final size:52
Alignment explanation
Indices: 19004--19104 Score: 175
Period size: 52 Copynumber: 1.9 Consensus size: 52
18994 TAAGGCAACG
* *
19004 TAATGGACAACAGCTTAAGATCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
1 TAATAGACAACAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
*
19056 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
1 TAATAGACAACAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
19105 TATGTGCATG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.27
Consensus pattern (52 bp):
TAATAGACAACAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
Found at i:25416 original size:52 final size:52
Alignment explanation
Indices: 25333--25433 Score: 184
Period size: 52 Copynumber: 1.9 Consensus size: 52
25323 TAAGGCAACG
* *
25333 TAATGGACAGCAGCTTAAGATCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
25385 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
25434 TATGTGCATG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.27
Consensus pattern (52 bp):
TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
Done.