Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2115
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: 30180
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:3650 original size:14 final size:14
Alignment explanation
Indices: 3631--3679 Score: 57
Period size: 15 Copynumber: 3.6 Consensus size: 14
3621 TTTTATTATC
3631 TCTTTTTTC--CTT
1 TCTTTTTTCTTCTT
*
3643 TCTTTTTTCTTTTT
1 TCTTTTTTCTTCTT
*
3657 TCTTTTTTGTTTCTT
1 TCTTTTTT-CTTCTT
3672 TCTTTTTT
1 TCTTTTTT
3680 GTTTTGTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
12 9 0.29
14 10 0.32
15 12 0.39
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (14 bp):
TCTTTTTTCTTCTT
Found at i:3653 original size:7 final size:7
Alignment explanation
Indices: 3641--3684 Score: 61
Period size: 7 Copynumber: 6.1 Consensus size: 7
3631 TCTTTTTTCC
3641 TTTCTTT
1 TTTCTTT
3648 TTTCTTT
1 TTTCTTT
3655 TTTCTTT
1 TTTCTTT
*
3662 TTTGTTT
1 TTTCTTT
3669 CTTTCTTT
1 -TTTCTTT
*
3677 TTTGTTT
1 TTTCTTT
3684 T
1 T
3685 GTTAATATGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
7 27 0.82
8 6 0.18
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (7 bp):
TTTCTTT
Found at i:3661 original size:18 final size:19
Alignment explanation
Indices: 3631--3672 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
3621 TTTTATTATC
3631 TCTTTTTTCCTTTCTTT-TT
1 TCTTTTTTCCTTT-TTTGTT
3650 TCTTTTTT-CTTTTTTGTT
1 TCTTTTTTCCTTTTTTGTT
3668 TCTTT
1 TCTTT
3673 CTTTTTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 3 0.14
18 11 0.50
19 8 0.36
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (19 bp):
TCTTTTTTCCTTTTTTGTT
Found at i:3673 original size:15 final size:15
Alignment explanation
Indices: 3640--3683 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
3630 CTCTTTTTTC
*
3640 CTTTCTTTTTTCTTT
1 CTTTCTTTTTTGTTT
3655 -TTTCTTTTTTGTTT
1 CTTTCTTTTTTGTTT
3669 CTTTCTTTTTTGTTT
1 CTTTCTTTTTTGTTT
3684 TGTTAATATG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 13 0.48
15 14 0.52
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.82
Consensus pattern (15 bp):
CTTTCTTTTTTGTTT
Found at i:3721 original size:15 final size:14
Alignment explanation
Indices: 3701--3835 Score: 60
Period size: 14 Copynumber: 10.0 Consensus size: 14
3691 ATGGCACTAC
3701 ATTTTTTCCCTTTTT
1 ATTTTTT-CCTTTTT
3716 ATTTTTTCC--TTT
1 ATTTTTTCCTTTTT
3728 -TTTTTT-CTTTTT
1 ATTTTTTCCTTTTT
3740 ATTTTTT--TTATTT
1 ATTTTTTCCTT-TTT
*
3753 CTTGTTTT--TTTTT
1 ATT-TTTTCCTTTTT
**
3766 -TTTTTTTTTTTTT
1 ATTTTTTCCTTTTT
* *
3779 TTTTTTTCTTTTTT
1 ATTTTTTCCTTTTT
* *
3793 TTTATTCTTCCCTTTT
1 ATT-TT-TTCCTTTTT
3809 -TTTTTT--TTTTT
1 ATTTTTTCCTTTTT
3820 ATTTTTCTCTCTTTTT
1 ATTTTT-TC-CTTTTT
3836 TTTGGGTGGT
Statistics
Matches: 100, Mismatches: 5, Indels: 29
0.75 0.04 0.22
Matches are distributed among these distances:
10 1 0.01
11 14 0.14
12 15 0.15
13 22 0.22
14 25 0.25
15 11 0.11
16 12 0.12
ACGTcount: A:0.04, C:0.11, G:0.01, T:0.84
Consensus pattern (14 bp):
ATTTTTTCCTTTTT
Found at i:3748 original size:33 final size:30
Alignment explanation
Indices: 3711--3795 Score: 116
Period size: 30 Copynumber: 2.7 Consensus size: 30
3701 ATTTTTTCCC
3711 TTTTTATTTTTTCCTTTTTTTTTCTTTTTATTT
1 TTTTTATTTTTT-CTTTTTTTTT-TTTTT-TTT
* *
3744 TTTTTATTTCTTGTTTTTTTTTTTTTTTTT
1 TTTTTATTTTTTCTTTTTTTTTTTTTTTTT
*
3774 TTTTTTTTTTTTCTTTTTTTTT
1 TTTTTATTTTTTCTTTTTTTTT
3796 ATTCTTCCCT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
30 22 0.47
31 5 0.11
32 9 0.19
33 11 0.23
ACGTcount: A:0.04, C:0.06, G:0.01, T:0.89
Consensus pattern (30 bp):
TTTTTATTTTTTCTTTTTTTTTTTTTTTTT
Found at i:3817 original size:46 final size:46
Alignment explanation
Indices: 3701--3827 Score: 148
Period size: 46 Copynumber: 2.7 Consensus size: 46
3691 ATGGCACTAC
* *
3701 ATTTTTTCCCTTTTTATTTTTTCCTTTTTTTTTCTTTTTATTTTTTTT
1 ATTTCTTCCCTTTTT-TTTTTT-TTTTTTTTTTCTTTTTATTTTTTTT
*** * *
3749 ATTTCTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTT
1 ATTTCTTCCCTTTTTTTTTTTTTTTTTTTTTCTTTTTATTTTTTTT
*
3795 -TATTCTTCCCTTTTTTTTTTTTTTTATTTTTCT
1 AT-TTCTTCCCTTTTTTTTTTTTTTTTTTTTTCT
3828 CTCTTTTTTT
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
45 1 0.02
46 48 0.73
47 6 0.09
48 11 0.17
ACGTcount: A:0.05, C:0.10, G:0.01, T:0.84
Consensus pattern (46 bp):
ATTTCTTCCCTTTTTTTTTTTTTTTTTTTTTCTTTTTATTTTTTTT
Found at i:3834 original size:24 final size:24
Alignment explanation
Indices: 3701--3838 Score: 104
Period size: 24 Copynumber: 5.8 Consensus size: 24
3691 ATGGCACTAC
* * *
3701 ATTTTT-TCCCTTTTTATTTTTTC
1 ATTTTTCTCTCTTTTTTTTTTTTT
* * *
3724 CTTTTTTTTTCTTTTTATTTTTTTT
1 ATTTTTCTCTCTTTTT-TTTTTTTT
*
3749 ATTTCTTGT-T-TTTTTTTTTTTTT
1 ATTT-TTCTCTCTTTTTTTTTTTTT
* * *
3772 -TTTTTTTTTTTTTTCTTTTTTTTT
1 ATTTTTCTCTCTTTT-TTTTTTTTT
* * *
3796 ATTCTTCCCTTTTTTTTTTTTTTT
1 ATTTTTCTCTCTTTTTTTTTTTTT
3820 ATTTTTCTCTCTTTTTTTT
1 ATTTTTCTCTCTTTTTTTT
3839 GGGTGGTGAT
Statistics
Matches: 93, Mismatches: 15, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
21 3 0.03
22 4 0.04
23 17 0.18
24 46 0.49
25 20 0.22
26 3 0.03
ACGTcount: A:0.04, C:0.11, G:0.01, T:0.84
Consensus pattern (24 bp):
ATTTTTCTCTCTTTTTTTTTTTTT
Found at i:3837 original size:46 final size:45
Alignment explanation
Indices: 3701--3838 Score: 143
Period size: 47 Copynumber: 3.0 Consensus size: 45
3691 ATGGCACTAC
* *
3701 ATTTTTTCCCTTTTTATTTTTTCCTTTTTTTTTCTTTTTATTTTTTTT
1 ATTTCTTCCCTTTTT-TTTTTT-TTTTTTTTTTCTTTTT-TTTTTTTT
** *
3749 ATTTCTT-GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTT
1 ATTTCTTCCCTTTTTTTTTTTTTTTTTTTTTCTTTTTT-TTTTTTT
* * * *
3794 TTATTCTTCCCTTTTTTTTTTTTTTTATTTTTCTCTCTTTTTTTT
1 AT-TTCTTCCCTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTT
3839 GGGTGGTGAT
Statistics
Matches: 75, Mismatches: 12, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
44 1 0.01
45 22 0.29
46 17 0.23
47 29 0.39
48 6 0.08
ACGTcount: A:0.04, C:0.11, G:0.01, T:0.84
Consensus pattern (45 bp):
ATTTCTTCCCTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTT
Found at i:3838 original size:1 final size:1
Alignment explanation
Indices: 3711--3825 Score: 95
Period size: 1 Copynumber: 115.0 Consensus size: 1
3701 ATTTTTTCCC
* ** * * * * *
3711 TTTTTATTTTTTCCTTTTTTTTTCTTTTTATTTTTTTTATTTCTTGTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * *** *
3776 TTTTTTTTTTCTTTTTTTTTATTCTTCCCTTTTTTTTTTTTTTTATTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3826 CTCTCTTTTT
Statistics
Matches: 90, Mismatches: 24, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 90 1.00
ACGTcount: A:0.04, C:0.08, G:0.01, T:0.87
Consensus pattern (1 bp):
T
Found at i:19597 original size:30 final size:30
Alignment explanation
Indices: 19563--19659 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
19553 TAAACTAAAA
*
19563 TGAGCTAAGCTTTAGCTCATGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCATGAGCTAAAGT
* * * * *
19593 TGAGCTGAGGTTAAACTCCTAAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCATGAGCTAAAGT
* *
19623 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGGTTTAGCTCATGAGCT-AAAGT
19653 TGAGCTA
1 TGAGCTA
19660 GGAGTGAGCT
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
30 50 0.93
31 4 0.07
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCATGAGCTAAAGT
Found at i:20121 original size:20 final size:20
Alignment explanation
Indices: 20098--20144 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
20088 GAACTCAAAC
20098 GAGCTGAATTGAGCTCAAGT
1 GAGCTGAATTGAGCTCAAGT
*
20118 GAGCTAAATTGAGCTCAAGT
1 GAGCTGAATTGAGCTCAAGT
*
20138 GTGCTGA
1 GAGCTGA
20145 TGGGAGCTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.26
Consensus pattern (20 bp):
GAGCTGAATTGAGCTCAAGT
Found at i:24581 original size:24 final size:24
Alignment explanation
Indices: 24554--24599 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
24544 ACACTTTTTC
* *
24554 CTTTCTTTTTTTCATTTTTCTTGA
1 CTTTCTATTTTTCAATTTTCTTGA
24578 CTTTCTATTTTTCAATTTTCTT
1 CTTTCTATTTTTCAATTTTCTT
24600 TTTCTTGTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.11, C:0.17, G:0.02, T:0.70
Consensus pattern (24 bp):
CTTTCTATTTTTCAATTTTCTTGA
Found at i:24604 original size:30 final size:30
Alignment explanation
Indices: 24562--24624 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 30
24552 TCCTTTCTTT
*
24562 TTTTCATTTTTCTTG-ACTTTCTATTTTTCAA
1 TTTTCATTTTTCTTGTACTTT-T-TCTTTCAA
24593 TTTTC-TTTTTCTTGTACTTTTTCTTTCAA
1 TTTTCATTTTTCTTGTACTTTTTCTTTCAA
24622 TTT
1 TTT
24625 CAGTTGATCG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 10 0.33
30 10 0.33
31 10 0.33
ACGTcount: A:0.13, C:0.16, G:0.03, T:0.68
Consensus pattern (30 bp):
TTTTCATTTTTCTTGTACTTTTTCTTTCAA
Found at i:26210 original size:46 final size:46
Alignment explanation
Indices: 26143--26316 Score: 169
Period size: 46 Copynumber: 3.8 Consensus size: 46
26133 TTTGGGCATC
* *
26143 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTT
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGAT
* *
26189 CGAACTCGTTGAGTTGAGTCCGAGTTCGA--GA-GG-TG-TAACCAGGCAT
1 CGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGCGAA-C--G-AT
* * **
26235 CAGAGCTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAACGCC
1 C-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGAT
* *
26282 CGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
26317 GCGGGTTACA
Statistics
Matches: 105, Mismatches: 12, Indels: 22
0.76 0.09 0.16
Matches are distributed among these distances:
42 2 0.02
43 2 0.02
44 2 0.02
45 2 0.02
46 62 0.59
47 26 0.25
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.29
Consensus pattern (46 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGAT
Found at i:26296 original size:93 final size:93
Alignment explanation
Indices: 26137--26309 Score: 283
Period size: 93 Copynumber: 1.9 Consensus size: 93
26127 ACCGGATTTG
* * **
26137 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAG
1 GGCATCAGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
26202 TTGAGTCCGAGTTCGAGAGGTGTAACCA
66 TTGAGTCCGAGTTCGAGAGGTGTAACCA
* * *
26230 GGCATCAGAGCTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCAGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
26295 TTGAGTCCGAGTTCG
66 TTGAGTCCGAGTTCG
26310 CTTATGGGCG
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.28
Consensus pattern (93 bp):
GGCATCAGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGGTGTAACCA
Found at i:29252 original size:15 final size:15
Alignment explanation
Indices: 29213--29291 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
29203 GTATCTTGGG
*
29213 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
29228 TATCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
29243 TTTCTTTATTC-GGG
1 TTTCTTTATTCTGGA
*
29257 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
29272 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
29286 TTTCTT
1 TTTCTT
29292 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
13 2 0.04
14 17 0.32
15 32 0.60
16 2 0.04
ACGTcount: A:0.11, C:0.16, G:0.14, T:0.58
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:29276 original size:29 final size:29
Alignment explanation
Indices: 29204--29290 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
29194 CATAGTATCG
* * * *
29204 TATCTTGGGTTTCTTTATCCTGGATATCTT
1 TATCTTGGATTTCTTTATTC-GGATTTCTC
*
29234 TAT-TCTGGATTTCTTTATTCGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCGGATTTCTC
*
29263 TATCTTGGATTTCTTTATTCGGTTTTCT
1 TATCTTGGATTTCTTTATTCGGATTTCT
29291 TGTTATCTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 32 0.65
30 17 0.35
ACGTcount: A:0.11, C:0.16, G:0.16, T:0.56
Consensus pattern (29 bp):
TATCTTGGATTTCTTTATTCGGATTTCTC
Done.