Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold5
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: 1536239
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.33
Warning! 124408 characters in sequence are not A, C, G, or T
File 14 of 14
Found at i:1526274 original size:20 final size:18
Alignment explanation
Indices: 1526244--1526294 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 18
1526234 TTAAATATTT
1526244 TTTTATATTTAATATTAAAA
1 TTTT-TATTTAATATT-AAA
*
1526264 TTATTTATTTAATATTTAA
1 TT-TTTATTTAATATTAAA
1526283 TTTTTATTTAAT
1 TTTTTATTTAAT
1526295 TAAATAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 10 0.34
19 4 0.14
20 13 0.45
21 2 0.07
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTTATTTAATATTAAA
Found at i:1526289 original size:22 final size:22
Alignment explanation
Indices: 1526240--1526309 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 22
1526230 TTTTTTAAAT
1526240 ATTTTT-TTATATTTAATA-TTA
1 ATTTTTATT-TATTTAATATTTA
**
1526261 A-AATTATTTATTTAATATTTA
1 ATTTTTATTTATTTAATATTTA
*
1526282 ATTTTTATTTAATTAAATAATTTA
1 ATTTTTATTT-ATTTAAT-ATTTA
1526306 ATTT
1 ATTT
1526310 AATTGATGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
20 11 0.28
21 7 0.18
22 6 0.15
23 6 0.15
24 9 0.23
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
ATTTTTATTTATTTAATATTTA
Found at i:1526302 original size:19 final size:19
Alignment explanation
Indices: 1526205--1526313 Score: 57
Period size: 18 Copynumber: 5.6 Consensus size: 19
1526195 ATCCATTAAA
*
1526205 TTTTATTTAATGT-AATATT
1 TTTTATTTAAT-TAAATAAT
* *
1526224 TTTTAATTT-TTTAAATATTTT
1 TTTT-ATTTAATTAAATA--AT
*
1526245 TTTATATTTAATATTAA-AAT
1 TTT-TATTTAAT-TAAATAAT
**
1526265 TATTTATTTAA-TATTTAAT
1 T-TTTATTTAATTAAATAAT
1526284 TTTTATTTAATTAAATAA-
1 TTTTATTTAATTAAATAAT
*
1526302 TTTAATTTAATT
1 TTTTATTTAATT
1526314 GATGGTTTGA
Statistics
Matches: 70, Mismatches: 10, Indels: 21
0.69 0.10 0.21
Matches are distributed among these distances:
18 22 0.31
19 18 0.26
20 13 0.19
21 11 0.16
22 3 0.04
23 3 0.04
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (19 bp):
TTTTATTTAATTAAATAAT
Found at i:1527588 original size:16 final size:16
Alignment explanation
Indices: 1527575--1527624 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
1527565 TGATTTTTTT
*
1527575 ATTTCAATTATTTTAA
1 ATTTAAATTATTTTAA
1527591 ATTTAAATTA-TTTAA
1 ATTTAAATTATTTTAA
*
1527606 TATTT-AATCATTTTAA
1 -ATTTAAATTATTTTAA
1527622 ATT
1 ATT
1527625 AATTAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 12 0.40
16 18 0.60
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTTAAATTATTTTAA
Found at i:1528032 original size:22 final size:22
Alignment explanation
Indices: 1527997--1528041 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1527987 AATATTTTTT
* *
1527997 TAAATTTAATTATAAAAATATA
1 TAAATATAAATATAAAAATATA
*
1528019 TAAATATAAATATAAATATATA
1 TAAATATAAATATAAAAATATA
1528041 T
1 T
1528042 TTTTAATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATATAAATATAAAAATATA
Found at i:1528877 original size:17 final size:18
Alignment explanation
Indices: 1528855--1528894 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
1528845 ATATAAATAT
1528855 TAATATAATTTTT-TAAA
1 TAATATAATTTTTGTAAA
1528872 TAATATAATTTTTGTAAA
1 TAATATAATTTTTGTAAA
*
1528890 AAATA
1 TAATA
1528895 AAATATATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
TAATATAATTTTTGTAAA
Found at i:1529309 original size:28 final size:27
Alignment explanation
Indices: 1529251--1529342 Score: 84
Period size: 28 Copynumber: 3.4 Consensus size: 27
1529241 GTTACTTATT
*
1529251 TATTTGTCAAAAATGATAGTTATTTTG
1 TATTTGTCAAAAATGATAGTTATTTTA
* *
1529278 TATTTATCAAAAAT-AGTAGTTTCTTTTA
1 TATTTGTCAAAAATGA-TAG-TTATTTTA
* *
1529306 TATTTGTCAAATATGA-A-TGATTGTT-
1 TATTTGTCAAAAATGATAGTTATT-TTA
1529331 TATTTGTCAAAA
1 TATTTGTCAAAA
1529343 TTTATGGCTA
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
25 14 0.26
26 3 0.06
27 17 0.32
28 18 0.34
29 1 0.02
ACGTcount: A:0.35, C:0.05, G:0.12, T:0.48
Consensus pattern (27 bp):
TATTTGTCAAAAATGATAGTTATTTTA
Found at i:1532843 original size:160 final size:160
Alignment explanation
Indices: 1532579--1532909 Score: 644
Period size: 160 Copynumber: 2.1 Consensus size: 160
1532569 AAAAATGGGT
1532579 TTGTAAGTTGAACAAATCGCTATATGGATTGAAGCAATCTTCGAGGCAGTGGTACAAGCGATTTG
1 TTGTAAGTTGAACAAATCGCTATATGGATTGAAGCAATCTTCGAGGCAGTGGTACAAGCGATTTG
1532644 ATAGCTTTATGAGAAGACAGAAGTACACTAGAAGCAAATACGACCATTGTGTGTATTTGCGTAAG
66 ATAGCTTTATGAGAAGACAGAAGTACACTAGAAGCAAATACGACCATTGTGTGTATTTGCGTAAG
1532709 CTACAAGATGGATCTTTCATTTATCTCCTC
131 CTACAAGATGGATCTTTCATTTATCTCCTC
*
1532739 TTGTAAGTTGAACAAATCGCTATATGGATTGAAGCAATCTTCGAGGCAGTGGTATAAGCGATTTG
1 TTGTAAGTTGAACAAATCGCTATATGGATTGAAGCAATCTTCGAGGCAGTGGTACAAGCGATTTG
1532804 ATAGCTTTATGAGAAGACAGAAGTACACTAGAAGCAAATACGACCATTGTGTGTATTTGCGTAAG
66 ATAGCTTTATGAGAAGACAGAAGTACACTAGAAGCAAATACGACCATTGTGTGTATTTGCGTAAG
1532869 CTACAAGATGGATCTTTCATTTATCTCCTC
131 CTACAAGATGGATCTTTCATTTATCTCCTC
*
1532899 TTGTATGTTGA
1 TTGTAAGTTGA
1532910 TGATATGCTA
Statistics
Matches: 169, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
160 169 1.00
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.31
Consensus pattern (160 bp):
TTGTAAGTTGAACAAATCGCTATATGGATTGAAGCAATCTTCGAGGCAGTGGTACAAGCGATTTG
ATAGCTTTATGAGAAGACAGAAGTACACTAGAAGCAAATACGACCATTGTGTGTATTTGCGTAAG
CTACAAGATGGATCTTTCATTTATCTCCTC
Found at i:1533788 original size:28 final size:27
Alignment explanation
Indices: 1533739--1533824 Score: 88
Period size: 28 Copynumber: 3.2 Consensus size: 27
1533729 CATTTGTTTA
*
1533739 TCAAAAATGATGGTTATTTTGTATTTG
1 TCAAAAATGGTGGTTATTTTGTATTTG
1533766 TCAAAAATGGTGGTT-TCCTTTGTATTTG
1 TCAAAAATGGTGGTTAT--TTTGTATTTG
* * * *
1533794 TCAAATATGGAGGCT-TGTT-TATTTG
1 TCAAAAATGGTGGTTATTTTGTATTTG
1533819 TCAAAA
1 TCAAAA
1533825 TTTATGGCTA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
25 11 0.22
26 3 0.06
27 14 0.27
28 23 0.45
ACGTcount: A:0.28, C:0.08, G:0.20, T:0.44
Consensus pattern (27 bp):
TCAAAAATGGTGGTTATTTTGTATTTG
Found at i:1536056 original size:14 final size:14
Alignment explanation
Indices: 1536004--1536059 Score: 51
Period size: 14 Copynumber: 3.8 Consensus size: 14
1535994 AAAATATCTT
*
1536004 AAATATAAT-TTTA
1 AAATATAATAATTA
1536017 AAATATAATTATTATATA
1 AAATATAA-TA--AT-TA
*
1536035 AAACATAATAATTA
1 AAATATAATAATTA
1536049 AAATATAATAA
1 AAATATAATAA
1536060 AAATTATAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
13 8 0.23
14 13 0.37
15 2 0.06
17 3 0.09
18 9 0.26
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATATAATAATTA
Found at i:1536163 original size:25 final size:24
Alignment explanation
Indices: 1536121--1536170 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 24
1536111 CATCAAAATT
1536121 TTTAAAATAAAATAAAATATTATA
1 TTTAAAATAAAATAAAATATTATA
*
1536145 TTTATAATAAAAATAAAATATTATA
1 TTTAAAAT-AAAATAAAATATTATA
1536170 T
1 T
1536171 AATACTTACG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
TTTAAAATAAAATAAAATATTATA
Done.