Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1804
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: 12349
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Found at i:1550 original size:13 final size:13
Alignment explanation
Indices: 1532--1557 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1522 CATTTTTCTG
1532 TGTATCGATACAT
1 TGTATCGATACAT
1545 TGTATCGATACAT
1 TGTATCGATACAT
1558 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1554 original size:33 final size:33
Alignment explanation
Indices: 1512--1578 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1502 GCCAAGGAAA
***
1512 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1545 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1578 T
1 T
1579 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:4051 original size:56 final size:50
Alignment explanation
Indices: 3932--4317 Score: 166
Period size: 52 Copynumber: 7.3 Consensus size: 50
3922 CTCAATTCTC
* * * * *
3932 CACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAGACACTAATTTT
1 CACAATCGGGGATACTCAAACTCCGATTTTATTTCCAAAACACCAATTTT
*
3982 CTATAATCGGGGATACTCAAACTCCGATTTTATTTCCAAAAAAAAACACCAATTTTT
1 C-ACAATCGGGGATACTCAAACTCCGATTTTATTTCC-----AAAACACCAA-TTTT
* * * **** * * **
4039 CACAATCGGGGATACTCCAACCCCG-TTAATCATTGGGGATACTCCAACCCCGTT
1 CACAATCGGGGATACTCAAACTCCGATT--TTATTTCCAAAACACCAA---TTTT
*** * * * * ** *
4093 -ATTTTCGGGGGGATACTCCAACCCCGACTTTATTTCCAAAATATTGATTTTT
1 CACAATC--GGGGATACTCAAACTCCGATTTTATTTCCAAAACA-CCAATTTT
* * * * * * * *
4145 CATAATCGAGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTT
1 CACAATCGGGGATACTCAAACTCCGATTTTATTTCCAAAACACCAA-TTTT
* * * *
4196 CCACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTT
1 -CACAATCGGGGATACTCAAACTCCGATTTTATTTCCAAAACACCAATTTT
* * *
4247 C-CTTTAATCGGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTT
1 CAC---AATCGGGGATACTCAAACTCCGATTTTATTTCC-AAAACACCAA-TTTT
*
4301 CACAATCGAGGATACTC
1 CACAATCGGGGATACTC
4318 TAACCTCGTT
Statistics
Matches: 253, Mismatches: 59, Indels: 46
0.71 0.16 0.13
Matches are distributed among these distances:
49 1 0.00
50 3 0.01
51 68 0.27
52 91 0.36
53 16 0.06
54 13 0.05
55 22 0.09
56 30 0.12
57 9 0.04
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (50 bp):
CACAATCGGGGATACTCAAACTCCGATTTTATTTCCAAAACACCAATTTT
Found at i:4113 original size:28 final size:27
Alignment explanation
Indices: 4046--4118 Score: 96
Period size: 27 Copynumber: 2.7 Consensus size: 27
4036 TTTCACAATC
4046 GGGGATACTCCAACCCCGTTAATCATT
1 GGGGATACTCCAACCCCGTTAATCATT
*
4073 GGGGATACTCCAACCCCGTT-AT-TTT
1 GGGGATACTCCAACCCCGTTAATCATT
4098 CGGGGGGATACTCCAACCCCG
1 ---GGGGATACTCCAACCCCG
4119 ACTTTATTTC
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
25 2 0.05
26 2 0.05
27 20 0.48
28 18 0.43
ACGTcount: A:0.22, C:0.32, G:0.23, T:0.23
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATT
Found at i:4176 original size:51 final size:51
Alignment explanation
Indices: 4103--4322 Score: 224
Period size: 52 Copynumber: 4.3 Consensus size: 51
4093 ATTTTCGGGG
* * *** *
4103 GGATACTCCAACCCCGACTTTATTTCCAAAATATTGATTTTTCATAATCGA
1 GGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATCGA
* * * * *
4154 GGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTTCCACAATCGG
1 GGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTT-CACAATCGA
* * * ** *
4206 GGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGG
1 GGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTC-ACAATCGA
** *
4258 GGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGA
1 GGATACTCCAACCCCGATTTTATTTCC-AAAACACCAATTTTTCACAATCGA
*
4310 GGATACTCTAACC
1 GGATACTCCAACC
4323 TCGTTATCTC
Statistics
Matches: 138, Mismatches: 28, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
51 36 0.26
52 88 0.64
53 14 0.10
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.33
Consensus pattern (51 bp):
GGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATCGA
Found at i:4373 original size:27 final size:28
Alignment explanation
Indices: 4337--4408 Score: 110
Period size: 27 Copynumber: 2.6 Consensus size: 28
4327 TATCTCATCG
4337 GGGATACTCCAACCCCGTTACTTCCG-A
1 GGGATACTCCAACCCCGTTACTTCCGAA
* *
4364 GGGATACTCCAACCCCGTTATTTTCGAA
1 GGGATACTCCAACCCCGTTACTTCCGAA
*
4392 GGGATACTCCAATCCCG
1 GGGATACTCCAACCCCG
4409 ATTTTTTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 24 0.59
28 17 0.41
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.24
Consensus pattern (28 bp):
GGGATACTCCAACCCCGTTACTTCCGAA
Found at i:4415 original size:28 final size:27
Alignment explanation
Indices: 4306--4408 Score: 111
Period size: 28 Copynumber: 3.8 Consensus size: 27
4296 TTTTTCACAA
* * *
4306 TCGA-GGATACTCTAACCTCGTTATCTCA
1 TCGAGGGATACTCCAACCCCGTTAT-T-T
*
4334 TCG-GGGATACTCCAACCCCGTTACTT
1 TCGAGGGATACTCCAACCCCGTTATTT
*
4360 CCGAGGGATACTCCAACCCCGTTATTT
1 TCGAGGGATACTCCAACCCCGTTATTT
*
4387 TCGAAGGGATACTCCAATCCCG
1 TCG-AGGGATACTCCAACCCCG
4409 ATTTTTTTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
26 2 0.03
27 25 0.39
28 37 0.58
ACGTcount: A:0.23, C:0.32, G:0.18, T:0.26
Consensus pattern (27 bp):
TCGAGGGATACTCCAACCCCGTTATTT
Found at i:6431 original size:21 final size:20
Alignment explanation
Indices: 6384--6437 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
6374 CATTTAAGAC
**
6384 ATGTATCGATACATTCACTT
1 ATGTATCGATACATTCACCA
6404 ATGTATCGATACATTCACCA
1 ATGTATCGATACATTCACCA
6424 ATTGTATCGATACA
1 A-TGTATCGATACA
6438 AATTGTAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 19 0.61
21 12 0.39
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACATTCACCA
Found at i:9892 original size:13 final size:13
Alignment explanation
Indices: 9874--9899 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9864 CAATTTTTTG
9874 TGTATCGATACAT
1 TGTATCGATACAT
9887 TGTATCGATACAT
1 TGTATCGATACAT
9900 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:9984 original size:20 final size:20
Alignment explanation
Indices: 9959--10031 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
9949 CATCCTTTTT
9959 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
9979 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACA-TTGCAAC
10000 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
10020 ATGTATCGATAC
1 ATGTATCGATAC
10032 TTTGAATTGT
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:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:10004 original size:21 final size:21
Alignment explanation
Indices: 9938--10014 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
9928 CTGCCAAGAA
*
9938 ATGTATCGATACATCCTTTTT-
1 ATGTATCGATACAT-TTTTTTC
****
9959 ATGTATCGATACA-TTGCAAC
1 ATGTATCGATACATTTTTTTC
9979 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACATTTTTTTC
10000 ATGTATCGATACATT
1 ATGTATCGATACATT
10015 GCAACATGTA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
19 1 0.02
20 13 0.29
21 31 0.69
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.43
Consensus pattern (21 bp):
ATGTATCGATACATTTTTTTC
Found at i:10004 original size:41 final size:41
Alignment explanation
Indices: 9938--10031 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
9928 CTGCCAAGAA
9938 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
*
9979 ATGTATCGATACAT-TTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTT-ATGTATCGATACATTGCAAC
10020 ATGTATCGATAC
1 ATGTATCGATAC
10032 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 5 0.10
41 46 0.90
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
Found at i:10664 original size:21 final size:21
Alignment explanation
Indices: 10638--10688 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
10628 TCTCTCCTTT
10638 ATCTCCCCCGTTTATTAATAA
1 ATCTCCCCCGTTTATTAATAA
10659 ATCTCCCCCGTTTATTAATAA
1 ATCTCCCCCGTTTATTAATAA
10680 ATCTCCCCC
1 ATCTCCCCC
10689 TTAATCAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.25, C:0.35, G:0.04, T:0.35
Consensus pattern (21 bp):
ATCTCCCCCGTTTATTAATAA
Done.