Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2276
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: 31272
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:6962 original size:15 final size:16
Alignment explanation
Indices: 6942--6971 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
6932 TTTTCTTTGA
6942 ATCACTC-TCTTTTTT
1 ATCACTCATCTTTTTT
6957 ATCACTCATCTTTTT
1 ATCACTCATCTTTTT
6972 GTTTTTCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.17, C:0.27, G:0.00, T:0.57
Consensus pattern (16 bp):
ATCACTCATCTTTTTT
Found at i:9920 original size:23 final size:22
Alignment explanation
Indices: 9868--9920 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
9858 TCCACGTCTT
*
9868 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
9890 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
9913 TTTCTTTT
1 TTTCTTTT
9921 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:18480 original size:30 final size:30
Alignment explanation
Indices: 18446--18542 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
18436 TAAACTAAAA
18446 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
18476 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* * *
18506 TGAGTTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
18536 TGAGCTA
1 TGAGCTA
18543 GGAGTGAGCT
Statistics
Matches: 48, Mismatches: 16, Indels: 6
0.69 0.23 0.09
Matches are distributed among these distances:
29 2 0.04
30 40 0.83
31 6 0.12
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:18595 original size:20 final size:21
Alignment explanation
Indices: 18572--18613 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
18562 TCAGGCACGA
18572 TGGA-TTGAGCTCGAATA-AGC
1 TGGATTTGAGCT-GAATAGAGC
18592 TGGATTTGAGCTGAATAGAGC
1 TGGATTTGAGCTGAATAGAGC
18613 T
1 T
18614 CGTGGAGCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.29, C:0.12, G:0.31, T:0.29
Consensus pattern (21 bp):
TGGATTTGAGCTGAATAGAGC
Found at i:20136 original size:20 final size:20
Alignment explanation
Indices: 20113--20159 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
20103 GGGTTAAGAT
*
20113 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
20133 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
20153 TGAGCTG
1 TGAGCTG
20160 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:23186 original size:13 final size:12
Alignment explanation
Indices: 23145--23189 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
23135 ATTGAGAGTG
23145 AAAAGAA-TGTGA
1 AAAAGAAGT-TGA
*
23157 AAAAGAAATTGA
1 AAAAGAAGTTGA
23169 AAAAGAAGTTGA
1 AAAAGAAGTTGA
23181 AGAAAGAAG
1 A-AAAGAAG
23190 AGAAAATGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 22 0.73
13 8 0.27
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.13
Consensus pattern (12 bp):
AAAAGAAGTTGA
Found at i:26797 original size:27 final size:27
Alignment explanation
Indices: 26767--26818 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
26757 TCAATTTCTT
*
26767 TTTTCGCTTT-TTCTTTTTCTTTTTCAA
1 TTTTC-CTTTCTTCATTTTCTTTTTCAA
*
26794 TTTTCTTTTCTTCATTTTCTTTTTC
1 TTTTCCTTTCTTCATTTTCTTTTTC
26819 TCTCACTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 3 0.14
27 19 0.86
ACGTcount: A:0.06, C:0.19, G:0.02, T:0.73
Consensus pattern (27 bp):
TTTTCCTTTCTTCATTTTCTTTTTCAA
Found at i:26810 original size:14 final size:14
Alignment explanation
Indices: 26781--26817 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
26771 CGCTTTTTCT
26781 TTTTC-TTTTTCAA
1 TTTTCTTTTTTCAA
26794 TTTTCTTTTCTTC-A
1 TTTTCTTTT-TTCAA
26808 TTTTCTTTTT
1 TTTTCTTTTT
26818 CTCTCACTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 6 0.27
14 13 0.59
15 3 0.14
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTCTTTTTTCAA
Found at i:26845 original size:18 final size:18
Alignment explanation
Indices: 26776--26899 Score: 86
Period size: 18 Copynumber: 6.6 Consensus size: 18
26766 TTTTTCGCTT
26776 TTTCTTTTTCTTTTTCAA
1 TTTCTTTTTCTTTTTCAA
* **
26794 TTTTCTTTTCTTCATTTTCTT
1 -TTTC-TTT-TTCTTTTTCAA
* ** *
26815 TTTCTCTCACTTTTTCGA
1 TTTCTTTTTCTTTTTCAA
*
26833 TTTCTTTTTCTTTTGCAA
1 TTTCTTTTTCTTTTTCAA
* **
26851 TTTCTTTTTCTTCTTCGT
1 TTTCTTTTTCTTTTTCAA
*
26869 TTTCTTTTTGTTTTCTTTCAA
1 TTTC-TTTT-TCTT-TTTCAA
26890 TTTCTTTTTC
1 TTTCTTTTTC
26900 AATCTCTTTC
Statistics
Matches: 77, Mismatches: 23, Indels: 10
0.70 0.21 0.09
Matches are distributed among these distances:
18 37 0.48
19 11 0.14
20 14 0.18
21 15 0.19
ACGTcount: A:0.07, C:0.19, G:0.03, T:0.70
Consensus pattern (18 bp):
TTTCTTTTTCTTTTTCAA
Found at i:26893 original size:57 final size:55
Alignment explanation
Indices: 26776--26899 Score: 135
Period size: 57 Copynumber: 2.2 Consensus size: 55
26766 TTTTTCGCTT
* *
26776 TTTCTTTTTCTTTTTCAATTTTCTTTTCTTCATTTTCTTTTTCTCTCACTTTTTCGA
1 TTTCTTTTTCTTTTGCAATTTTCTTTTCTTCATTTTCTTTTTCTCT--CTTTTTCAA
* * *
26833 TTTCTTTTTCTTTTGCAATTTCTTTTTCTTCTTCGTTTTCTTTTTGT-T-TTCTTTCAA
1 TTTCTTTTTCTTTTGCAA-TT-TTCTT-TTCTTCATTTTCTTTTTCTCTCTT-TTTCAA
26890 TTTCTTTTTC
1 TTTCTTTTTC
26900 AATCTCTTTC
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
56 2 0.03
57 32 0.55
58 2 0.03
59 5 0.09
60 17 0.29
ACGTcount: A:0.07, C:0.19, G:0.03, T:0.70
Consensus pattern (55 bp):
TTTCTTTTTCTTTTGCAATTTTCTTTTCTTCATTTTCTTTTTCTCTCTTTTTCAA
Found at i:26899 original size:6 final size:6
Alignment explanation
Indices: 26773--26886 Score: 77
Period size: 6 Copynumber: 18.7 Consensus size: 6
26763 TCTTTTTTCG
* * * **
26773 CTTTTT CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA
1 CTTTTT CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT
** * ** * *
26824 CTTTTT CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTCTT CGTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
26872 CTTTTT -GTTTT CTTT
1 CTTTTT CTTTTT CTTT
26887 CAATTTCTTT
Statistics
Matches: 78, Mismatches: 27, Indels: 6
0.70 0.24 0.05
Matches are distributed among these distances:
5 4 0.05
6 62 0.79
7 9 0.12
8 3 0.04
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:27977 original size:28 final size:27
Alignment explanation
Indices: 27923--27980 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 27
27913 TAAACTTGAT
*
27923 TTTTTTTGCTCACCTTTTTTTTCTTTTC
1 TTTTTTTGCTCA-CTTTTTTTACTTTTC
27951 TTTTTTTGCTCA-TTTTTTTCACTTTT-
1 TTTTTTTGCTCACTTTTTTT-ACTTTTC
27977 TTTT
1 TTTT
27981 GATTTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 11 0.39
27 5 0.18
28 12 0.43
ACGTcount: A:0.05, C:0.17, G:0.03, T:0.74
Consensus pattern (27 bp):
TTTTTTTGCTCACTTTTTTTACTTTTC
Found at i:28705 original size:13 final size:13
Alignment explanation
Indices: 28687--28714 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
28677 TGTAACCTTT
28687 TACAATAAACAAG
1 TACAATAAACAAG
28700 TACAATAAACAAG
1 TACAATAAACAAG
28713 TA
1 TA
28715 AGCTATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.61, C:0.14, G:0.07, T:0.18
Consensus pattern (13 bp):
TACAATAAACAAG
Found at i:29633 original size:29 final size:27
Alignment explanation
Indices: 29570--29634 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 27
29560 TTAAACTTGA
*
29570 TTTTTTTTTGCTCACCTTTTTTTTTCTT
1 TTTTTTTTTGCTCA-CTTTTTTTTACTT
29598 TTCTTTTTTTGCTCGA-TTTTTTTCTCACTT
1 TT-TTTTTTTGCTC-ACTTTTTTT-T-ACTT
29628 TTTTTTT
1 TTTTTTT
29635 GACTTTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
28 9 0.28
29 17 0.53
30 6 0.19
ACGTcount: A:0.05, C:0.17, G:0.05, T:0.74
Consensus pattern (27 bp):
TTTTTTTTTGCTCACTTTTTTTTACTT
Found at i:31246 original size:28 final size:26
Alignment explanation
Indices: 31215--31272 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
31205 TTAAACTTGA
31215 TTTTTTTGCTCACCTTTTTTTTC-CTTT
1 TTTTTTTGCTCA--TTTTTTTTCACTTT
31242 CTTTTTTTGCTCATTTTTTTTCACTTT
1 -TTTTTTTGCTCATTTTTTTTCACTTT
31269 TTTT
1 TTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
26 13 0.45
27 4 0.14
28 12 0.41
ACGTcount: A:0.05, C:0.19, G:0.03, T:0.72
Consensus pattern (26 bp):
TTTTTTTGCTCATTTTTTTTCACTTT
Done.