Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2183
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: 17260
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Found at i:480 original size:14 final size:14
Alignment explanation
Indices: 461--491 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
451 TACAATATAT
461 ATAAGAATTATACG
1 ATAAGAATTATACG
475 ATAAGAATTATACG
1 ATAAGAATTATACG
489 ATA
1 ATA
492 TATATCCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.06, G:0.13, T:0.29
Consensus pattern (14 bp):
ATAAGAATTATACG
Found at i:5567 original size:20 final size:20
Alignment explanation
Indices: 5542--5619 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
5532 GTAAAAAGAT
*
5542 AGAATGTACCGATACATTGA
1 AGAATGTATCGATACATTGA
*
5562 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
* *
5582 TA-CATTTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
* *
5602 AAAATGTATCAATACATT
1 AGAATGTATCGATACATT
5620 TGGGTACTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
19 1 0.02
20 46 0.96
21 1 0.02
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:6850 original size:21 final size:21
Alignment explanation
Indices: 6824--6864 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
6814 AGTTGCCACT
*
6824 GACTTGTGGTCTTTGAAAGGG
1 GACTTGTGGGCTTTGAAAGGG
6845 GACTTGTGGGCTTTGAAAGG
1 GACTTGTGGGCTTTGAAAGG
6865 ATGCCATTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.10, G:0.39, T:0.32
Consensus pattern (21 bp):
GACTTGTGGGCTTTGAAAGGG
Found at i:6869 original size:79 final size:81
Alignment explanation
Indices: 6511--7003 Score: 446
Period size: 85 Copynumber: 5.9 Consensus size: 81
6501 CACTAACTTG
* * * * *
6511 TGTGGGCTTTGAAAAGAGTTGCCACCGACTCATGCGGGCTTTGAAAAGAGTTACCACCG-CTTGT
1 TGTGGGCTTTG-AAAG-GATGCCACTGACT--TGTGGGCTTTGAAAAGAG-TGCCACTGACTTGT
* *
6575 GGGCTTTGAAAAGAGTGCCACTAACT
61 GGGCTTTG-AAAGGGTG---C-GACT
* * *
6601 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTAACTTGTGGGCT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCT
*
6665 TTGAAAAGAGTGCCACTGACT
66 TTG-AAAGGGTG---C-GACT
* * *
6686 TGTGGGCTTTGAAACGG-TGCCATTGACTTGGGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGC
1 TGTGGGCTTTGAAA-GGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
6749 TTTGAAAGGGTGCCACTGACT
65 TTTGAAAGGGTG---C-GACT
* * * *
6770 TGTGGGCTTCGAAATGATGCCACTGACTTGTGGGTTTTGAAAAGAGTTGCCACTGACTTGTGGTC
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAG-TGCCACTGACTTGTGGGC
6835 TTTGAAA-GG-G-GACT
65 TTTGAAAGGGTGCGACT
* * *
6849 TGTGGGCTTTGAAAGGATGCCATTGACTTGTGGGCTTTGAAAGGA-TGCGACTGACTTGTGTGGG
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGAC-T-TGTGGG
6913 CTTTGAAAGGGTGCCACTGACT
64 CTTTGAAAGGGTG---C-GACT
* * * *
6935 TGTGGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAATGA-TGCCACTAACTTGGGGGC
1 TGT-GGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
6999 TTTGA
65 TTTGA
7004 GGAGATGAAC
Statistics
Matches: 353, Mismatches: 34, Indels: 37
0.83 0.08 0.09
Matches are distributed among these distances:
77 9 0.03
78 1 0.00
79 57 0.16
80 2 0.01
81 1 0.00
83 1 0.00
84 59 0.17
85 103 0.29
86 47 0.13
87 47 0.13
88 11 0.03
89 4 0.01
90 11 0.03
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (81 bp):
TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCT
TTGAAAGGGTGCGACT
Found at i:6952 original size:29 final size:28
Alignment explanation
Indices: 6497--7003 Score: 562
Period size: 28 Copynumber: 17.9 Consensus size: 28
6487 TTTTAAAAAT
*
6497 GTGCCACTAACTTGTGTGGGCTTTGAAAAGAG
1 GTGCCACTGAC-T-TGTGGGCTTTG-AAAG-G
* * *
6529 TTGCCACCGACTCATGCGGGCTTTGAAAAGAG
1 GTGCCACTGACT--TGTGGGCTTTG-AAAG-G
* * * *
6561 TTACCACCG-CTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTG-AAAGG
*
6589 GTGCCACTAACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
6617 GTGCCACTGACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* *
6645 GTGCCACTAACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTG-AAAGG
*
6674 GTGCCACTGACTTGTGGGCTTTGAAACG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* *
6702 GTGCCATTGACTTGGGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
*
6730 ATGCCACTGACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* *
6758 GTGCCACTGACTTGTGGGCTTCGAAATG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* *
6786 ATGCCACTGACTTGTGGGTTTTGAAAAGAG
1 GTGCCACTGACTTGTGGGCTTTG-AAAG-G
* *
6816 TTGCCACTGACTTGTGGTCTTTGAAA-G
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
6843 G-G-----GACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* *
6865 ATGCCATTGACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* *
6893 ATGCGACTGACTTGTGTGGGCTTTGAAAGG
1 GTGCCACTGAC-T-TGTGGGCTTTGAAAGG
6923 GTGCCACTGACTTGTGGGGCTTTGAAAGG
1 GTGCCACTGACTTGT-GGGCTTTGAAAGG
*
6952 GTGCCACTGACTTGTGGGCTTTGAAATG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
* * *
6980 ATGCCACTAACTTGGGGGCTTTGA
1 GTGCCACTGACTTGTGGGCTTTGA
7004 GGAGATGAAC
Statistics
Matches: 414, Mismatches: 46, Indels: 34
0.84 0.09 0.07
Matches are distributed among these distances:
21 17 0.04
22 1 0.00
23 1 0.00
26 1 0.00
27 1 0.00
28 221 0.53
29 90 0.22
30 46 0.11
31 3 0.01
32 33 0.08
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (28 bp):
GTGCCACTGACTTGTGGGCTTTGAAAGG
Found at i:8250 original size:1 final size:1
Alignment explanation
Indices: 8246--8310 Score: 58
Period size: 1 Copynumber: 65.0 Consensus size: 1
8236 TTTTATTGGG
* ** * * * **
8246 TTTTTGTTTTTTTTTTGGTTTTTTTTATTTTTTTTTTGTTTTTTTTGTTTTTTGGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
8311 GGGTTGTAAA
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.02, C:0.00, G:0.11, T:0.88
Consensus pattern (1 bp):
T
Found at i:8269 original size:20 final size:21
Alignment explanation
Indices: 8246--8298 Score: 90
Period size: 20 Copynumber: 2.6 Consensus size: 21
8236 TTTTATTGGG
8246 TTTTTGTTTTTTTTTTGGTTT
1 TTTTTGTTTTTTTTTTGGTTT
*
8267 TTTTTATTTTTTTTTT-GTTT
1 TTTTTGTTTTTTTTTTGGTTT
8287 TTTTTGTTTTTT
1 TTTTTGTTTTTT
8299 GGTTTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.02, C:0.00, G:0.09, T:0.89
Consensus pattern (21 bp):
TTTTTGTTTTTTTTTTGGTTT
Found at i:8307 original size:20 final size:19
Alignment explanation
Indices: 8235--8310 Score: 84
Period size: 19 Copynumber: 4.1 Consensus size: 19
8225 TTTTTTGCTA
* * *
8235 TTTTTATTGGGTTTTTGTT
1 TTTTTTTTGGTTTTTTTTT
8254 TTTTTTTTGGTTTTTTTTAT
1 TTTTTTTTGGTTTTTTTT-T
*
8274 TTTTTTTT--TGTTTTTTT
1 TTTTTTTTGGTTTTTTTTT
*
8291 TGTTTTTTGGTTTTTTTTT
1 TTTTTTTTGGTTTTTTTTT
8310 T
1 T
8311 GGGTTGTAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
17 8 0.17
18 7 0.15
19 24 0.50
20 9 0.19
ACGTcount: A:0.03, C:0.00, G:0.13, T:0.84
Consensus pattern (19 bp):
TTTTTTTTGGTTTTTTTTT
Found at i:8308 original size:21 final size:20
Alignment explanation
Indices: 8246--8311 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
8236 TTTTATTGGG
8246 TTTTTGTTTTTTTTTTGGTTT
1 TTTTTGTTTTTTTTTT-GTTT
*
8267 TTTTTATTTTTTTTTTGTTT
1 TTTTTGTTTTTTTTTTGTTT
**
8287 TTTTTGTTTTTTGGTT-TTT
1 TTTTTGTTTTTTTTTTGTTT
8306 TTTTTG
1 TTTTTG
8312 GGTTGTAAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.22
20 17 0.41
21 15 0.37
ACGTcount: A:0.02, C:0.00, G:0.12, T:0.86
Consensus pattern (20 bp):
TTTTTGTTTTTTTTTTGTTT
Done.