Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1598
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: 17952
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Found at i:2428 original size:2 final size:2
Alignment explanation
Indices: 2423--2460 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2413 ATATATATAT
2423 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2461 TTTATAGTGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3250 original size:17 final size:17
Alignment explanation
Indices: 3228--3283 Score: 78
Period size: 17 Copynumber: 3.4 Consensus size: 17
3218 TTAATTATTA
3228 TTTAATATAAATATAAT
1 TTTAATATAAATATAAT
* * *
3245 TTTAATATATATTTATT
1 TTTAATATAAATATAAT
3262 TTTAATATAAATAT-AT
1 TTTAATATAAATATAAT
3278 TTTAAT
1 TTTAAT
3284 TATTTATTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
16 7 0.21
17 26 0.79
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTAATATAAATATAAT
Found at i:3268 original size:28 final size:28
Alignment explanation
Indices: 3207--3271 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
3197 TAATTATAAA
*
3207 TTTAATA-ATTTTTAATTATTATTTAAT
1 TTTAATATAATTTTAATTATTATTTAAT
* * *
3234 ATAAATATAATTTTAA-TATATATTTATT
1 TTTAATATAATTTTAATTAT-TATTTAAT
3262 TTTAATATAA
1 TTTAATATAA
3272 ATATATTTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
27 8 0.27
28 22 0.73
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
TTTAATATAATTTTAATTATTATTTAAT
Found at i:5422 original size:2 final size:2
Alignment explanation
Indices: 5415--5444 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5405 TTAAAATAAA
5415 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5445 TACTCCAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10307 original size:2 final size:2
Alignment explanation
Indices: 10300--10326 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10290 CGGCTGGCAC
10300 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
10327 ATAAAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13216 original size:24 final size:23
Alignment explanation
Indices: 13177--13228 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 23
13167 ATAGCTATAC
13177 AATATAAATATAATATAAAAAATTA
1 AATATAAATATAATAT-AAAAA-TA
*
13202 AATAT-AATATGATATAAAAATA
1 AATATAAATATAATATAAAAATA
13224 AATAT
1 AATAT
13229 GATACGAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 7 0.27
23 5 0.19
24 9 0.35
25 5 0.19
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (23 bp):
AATATAAATATAATATAAAAATA
Found at i:13225 original size:22 final size:19
Alignment explanation
Indices: 13180--13228 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 19
13170 GCTATACAAT
13180 ATAAATATAATATAAAAAA
1 ATAAATATAATATAAAAAA
*
13199 TTAAATATAATATGATATAAAA
1 ATAAATATAATAT-A-A-AAAA
13221 ATAAATAT
1 ATAAATAT
13229 GATACGAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 12 0.48
20 1 0.04
21 1 0.04
22 11 0.44
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (19 bp):
ATAAATATAATATAAAAAA
Found at i:14514 original size:2 final size:2
Alignment explanation
Indices: 14509--14552 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
14499 CTTAAGACTA
* ** *
14509 AT AT AT AT AT GT GG AT AT AT AT AT AG AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14551 AT
1 AT
14553 CCCTTTAAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (2 bp):
AT
Found at i:15082 original size:2 final size:2
Alignment explanation
Indices: 15075--15128 Score: 54
Period size: 2 Copynumber: 27.0 Consensus size: 2
15065 TTTCACTAAG
* * * * * *
15075 AT AT AT AT AT AT AT AT AT AT AT AT AC AC AC AT AT AC AC AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15117 AT AT AT AT AT AT
1 AT AT AT AT AT AT
15129 CACGATCAAC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (2 bp):
AT
Found at i:15725 original size:14 final size:15
Alignment explanation
Indices: 15706--15736 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
15696 CCTCCCTTTA
15706 TTTATTTT-TATTTT
1 TTTATTTTATATTTT
15720 TTTATTTTATATTTT
1 TTTATTTTATATTTT
15735 TT
1 TT
15737 AAATGAGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTATTTTATATTTT
Found at i:17216 original size:77 final size:78
Alignment explanation
Indices: 17111--17254 Score: 220
Period size: 78 Copynumber: 1.9 Consensus size: 78
17101 TCTCAATAAA
* *
17111 ATTAAAGGGAAACCACATGAAACAACATTCAGTTGGTTTG-TCTTTGAAATTAAATTAGGTTAAA
1 ATTAAAGGGAAACCAAAAGAAACAACATTCAGTTGGTTTGTTCTTTGAAATTAAATTAGGTTAAA
17175 AATTCTTTGATTC
66 AATTCTTTGATTC
* * *
17188 ATTAAA-GGAAGCCAAAAGAAACATACATTCAGTTGGTTTGTTCTTTGAAATTAGATTATGTTAA
1 ATTAAAGGGAAACCAAAAGAAACA-ACATTCAGTTGGTTTGTTCTTTGAAATTAAATTAGGTTAA
17252 AAA
65 AAA
17255 ACTCTTTTGT
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
76 14 0.23
77 22 0.37
78 24 0.40
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (78 bp):
ATTAAAGGGAAACCAAAAGAAACAACATTCAGTTGGTTTGTTCTTTGAAATTAAATTAGGTTAAA
AATTCTTTGATTC
Found at i:17384 original size:20 final size:22
Alignment explanation
Indices: 17341--17386 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
17331 AATCATGGAC
17341 TTTAAGAAAGAATTTTTATTTT
1 TTTAAGAAAGAATTTTTATTTT
*
17363 TTTAA-AAA-AATGTTTTTTTTT
1 TTTAAGAAAGAAT-TTTTATTTT
17384 TTT
1 TTT
17387 TTGGAATTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 3 0.14
21 14 0.64
22 5 0.23
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTAAGAAAGAATTTTTATTTT
Found at i:17595 original size:2 final size:2
Alignment explanation
Indices: 17588--17620 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
17578 ATCTATATTA
17588 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17621 ATAAGAACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.