Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold526
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: 9920
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.38
Found at i:991 original size:9 final size:8
Alignment explanation
Indices: 972--1009 Score: 53
Period size: 7 Copynumber: 4.9 Consensus size: 8
962 AAAGTTCAAT
972 GCCCCCCC
1 GCCCCCCC
980 GCCCCTCCC
1 GCCCC-CCC
989 GCCCCCCC
1 GCCCCCCC
997 -CCCCCCC
1 GCCCCCCC
1004 -CCCCCC
1 GCCCCCC
1010 TTCCCTCCGA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 13 0.45
8 8 0.28
9 8 0.28
ACGTcount: A:0.00, C:0.89, G:0.08, T:0.03
Consensus pattern (8 bp):
GCCCCCCC
Found at i:3144 original size:33 final size:33
Alignment explanation
Indices: 3107--3173 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3097 TTTCAACGAT
3107 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
3140 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
3173 T
1 T
3174 TTAAGCTACT
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:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:3145 original size:13 final size:13
Alignment explanation
Indices: 3127--3151 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3117 CATAAAGTGT
3127 TGTATCGATACAA
1 TGTATCGATACAA
3140 TGTATCGATACA
1 TGTATCGATACA
3152 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3232 original size:13 final size:13
Alignment explanation
Indices: 3214--3238 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3204 ATCACTTAAA
3214 TGTATCGATACAT
1 TGTATCGATACAT
3227 TGTATCGATACA
1 TGTATCGATACA
3239 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3340 original size:52 final size:52
Alignment explanation
Indices: 3247--3375 Score: 197
Period size: 52 Copynumber: 2.5 Consensus size: 52
3237 CACTGATCTT
* *
3247 TGTATCGATACATGCA-GAAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
3298 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
3350 TGTATCGATACATTACAGGCAAATTT
1 TGTATCGATACA-TGCAGGCAAATTT
3376 TCATATTTCG
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
51 16 0.23
52 43 0.61
53 12 0.17
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:6763 original size:19 final size:19
Alignment explanation
Indices: 6741--6814 Score: 67
Period size: 19 Copynumber: 3.7 Consensus size: 19
6731 ATATTCTAAC
*
6741 ATATTTATATATTTATATT
1 ATATTTATATTTTTATATT
*
6760 ATATTCTATTATTTTTTATATA
1 ATATT-TA-TA-TTTTTATATT
*
6782 ATATTTTATTTTTTTATATT
1 ATA-TTTATATTTTTATATT
* *
6802 TTATTCATATTTT
1 ATATTTATATTTT
6815 ATCTCAATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
19 13 0.30
20 13 0.30
21 3 0.07
22 13 0.30
23 2 0.05
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (19 bp):
ATATTTATATTTTTATATT
Found at i:6780 original size:22 final size:21
Alignment explanation
Indices: 6752--6814 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 21
6742 TATTTATATA
6752 TTTATATTATATTCTATTATTT
1 TTTATATTATATTCTATT-TTT
* *
6774 TTTATATAATATTTTA-TTTT
1 TTTATATTATATTCTATTTTT
*
6794 TTTATATTTTATTCATATTTT
1 TTTATATTATATTC-TATTTT
6815 ATCTCAATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 14 0.41
21 3 0.09
22 17 0.50
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTATATTATATTCTATTTTT
Found at i:6814 original size:20 final size:20
Alignment explanation
Indices: 6752--6814 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 20
6742 TATTTATATA
6752 TTTATATTATATTCTATTATTT
1 TTTATATTATATTC-A-TATTT
* *
6774 TTTATATAATATT-TTATTTT
1 TTTATATTATATTCATA-TTT
*
6794 TTTATATTTTATTCATATTT
1 TTTATATTATATTCATATTT
6814 T
1 T
6815 ATCTCAATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
19 2 0.06
20 18 0.53
21 2 0.06
22 12 0.35
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTATATTATATTCATATTT
Found at i:7036 original size:24 final size:23
Alignment explanation
Indices: 7008--7057 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
6998 ATTTTTTTTG
7008 TTTAAAATATAAATTATATAAAAT
1 TTTAAAATATAAATTATAT-AAAT
* **
7032 TTTAAAATTTATTTTATATAAAT
1 TTTAAAATATAAATTATATAAAT
7055 TTT
1 TTT
7058 GAACATTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTAAAATATAAATTATATAAAT
Found at i:7265 original size:27 final size:27
Alignment explanation
Indices: 7235--7307 Score: 75
Period size: 26 Copynumber: 2.8 Consensus size: 27
7225 TTTTAATAAA
*
7235 TAAATAATTATTTAA-TA-TAATTTAATT
1 TAAAT-ATTATATAATTATTAATTTAA-T
7262 TAAAT-TTATATAATTATTAATTTAAT
1 TAAATATTATATAATTATTAATTTAAT
7288 TAAATATT-TATAGA-TATTAA
1 TAAATATTATATA-ATTATTAA
7308 AATTTTTTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
25 7 0.17
26 18 0.44
27 16 0.39
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (27 bp):
TAAATATTATATAATTATTAATTTAAT
Found at i:7284 original size:22 final size:21
Alignment explanation
Indices: 7244--7294 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
7234 ATAAATAATT
7244 ATTTAATATAATTTAATTTAA
1 ATTTAATATAATTTAATTTAA
7265 ATTT-ATATAATTATTAATTT-A
1 ATTTAATATAA-T-TTAATTTAA
*
7286 ATTAAATAT
1 ATTTAATAT
7295 TTATAGATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 6 0.23
21 9 0.35
22 11 0.42
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTAATATAATTTAATTTAA
Found at i:8780 original size:7 final size:7
Alignment explanation
Indices: 8768--8822 Score: 51
Period size: 7 Copynumber: 7.9 Consensus size: 7
8758 ATCAATATAA
8768 AAAAATT
1 AAAAATT
8775 AAAAATT
1 AAAAATT
**
8782 -AATTTT
1 AAAAATT
8788 AAAAATT
1 AAAAATT
8795 AAATAA-T
1 AAA-AATT
*
8802 AAAATTT
1 AAAAATT
8809 AATAAATT
1 AA-AAATT
8817 AAAAAT
1 AAAAAT
8823 CTTATAACAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
6 5 0.13
7 25 0.66
8 8 0.21
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (7 bp):
AAAAATT
Found at i:8785 original size:35 final size:35
Alignment explanation
Indices: 8740--8818 Score: 90
Period size: 35 Copynumber: 2.2 Consensus size: 35
8730 ATTTTATTTT
8740 TAAATGTAATTATAAAATATCAATATAA-AAAAATTAA
1 TAAAT-TAATTATAAAA-ATCAA-ATAATAAAAATTAA
* * *
8777 -AAATTAATTTTAAAAATTAAATAATAAAATTTAA
1 TAAATTAATTATAAAAATCAAATAATAAAAATTAA
8811 TAAATTAA
1 TAAATTAA
8819 AAATCTTATA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
33 4 0.11
34 12 0.32
35 17 0.46
36 4 0.11
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (35 bp):
TAAATTAATTATAAAAATCAAATAATAAAAATTAA
Found at i:8862 original size:28 final size:27
Alignment explanation
Indices: 8798--8869 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 27
8788 AAAAATTAAA
*
8798 TAATAAAATTTA-ATAAATTAAAAATC
1 TAATAAAATTTATATAAATGAAAAATC
*
8824 TTATAACAATTTATATAAATGAAAAGTATC
1 TAATAA-AATTTATATAAATGAAAA--ATC
*
8854 -AATAAAATTGATATAA
1 TAATAAAATTTATATAA
8870 TCAAAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
26 5 0.13
27 6 0.16
28 20 0.53
29 4 0.11
30 3 0.08
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (27 bp):
TAATAAAATTTATATAAATGAAAAATC
Found at i:9137 original size:13 final size:13
Alignment explanation
Indices: 9088--9142 Score: 58
Period size: 13 Copynumber: 4.1 Consensus size: 13
9078 AAAATTTTAA
9088 ATTTATTAAATATT
1 ATTT-TTAAATATT
*
9102 ATTTTTATAATAAAT
1 ATTTTTA-AAT-ATT
*
9117 AATTTTAAATATT
1 ATTTTTAAATATT
9130 ATTTTTAAA-ATT
1 ATTTTTAAATATT
9142 A
1 A
9143 ATTTATAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
12 4 0.11
13 13 0.37
14 10 0.29
15 8 0.23
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATTTTTAAATATT
Done.