Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_328 ID=scaffold_328-JGI_221_v2.0
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: 10305
ACGTcount: A:0.27, C:0.11, G:0.13, T:0.28
Warning! 2165 characters in sequence are not A, C, G, or T
Found at i:1008 original size:14 final size:14
Alignment explanation
Indices: 991--1032 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
981 ATTTAGTGTT
*
991 CGAGATTTGAGGTA
1 CGAGATTTAAGGTA
* *
1005 CGAGGTTTAAGGTC
1 CGAGATTTAAGGTA
1019 CGAGATTTAAGGTA
1 CGAGATTTAAGGTA
1033 TGATGTTTAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.29, C:0.10, G:0.33, T:0.29
Consensus pattern (14 bp):
CGAGATTTAAGGTA
Found at i:1013 original size:28 final size:27
Alignment explanation
Indices: 968--1053 Score: 91
Period size: 28 Copynumber: 3.1 Consensus size: 27
958 AGGTTTGGGG
* *
968 TTTGAGGTACAATATTTAGTGTTCGAGA
1 TTTGAGGTACGATGTTTAG-GTTCGAGA
* *
996 TTTGAGGTACGAGGTTTAAGGTCCGAGA
1 TTTGAGGTACGATGTTT-AGGTTCGAGA
* *
1024 TTTAAGGTATGATGTTTAGGGTTCGAGA
1 TTTGAGGTACGATGTTTA-GGTTCGAGA
1052 TT
1 TT
1054 CACGATTTAA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
27 1 0.02
28 45 0.94
29 2 0.04
ACGTcount: A:0.26, C:0.07, G:0.30, T:0.37
Consensus pattern (27 bp):
TTTGAGGTACGATGTTTAGGTTCGAGA
Found at i:1520 original size:2 final size:2
Alignment explanation
Indices: 1513--1553 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1503 ATGATACATG
1513 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1554 TTAATGCATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2930 original size:60 final size:59
Alignment explanation
Indices: 2814--2945 Score: 183
Period size: 60 Copynumber: 2.2 Consensus size: 59
2804 AATTTAACAC
*
2814 TCACCCAACTATTAATAAATTTATTTTTGGTCACTCAACTATGAAATGTGACAAAATGA
1 TCACCCAACTATTAATAAATTTATTTTTGGTCACTCAACTATGAAAAGTGACAAAATGA
* * * * * * *
2873 TCTCTCAACTATTAGTAAATTTATTTTTTGGTCACTTAACTATGAAAAGTTATAAAATGG
1 TCACCCAACTATTAATAAATTTA-TTTTTGGTCACTCAACTATGAAAAGTGACAAAATGA
2933 TCACCCAACTATT
1 TCACCCAACTATT
2946 CAATTTCTTA
Statistics
Matches: 62, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
59 20 0.32
60 42 0.68
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (59 bp):
TCACCCAACTATTAATAAATTTATTTTTGGTCACTCAACTATGAAAAGTGACAAAATGA
Found at i:3274 original size:20 final size:20
Alignment explanation
Indices: 3233--3275 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
3223 ACCGCATTAG
*
3233 AAATTTTGGTATTAAGTTAA
1 AAATTTTGGTATTAAGTAAA
*
3253 AAATTTTGGATATT-TGTAAA
1 AAATTTTGG-TATTAAGTAAA
3273 AAA
1 AAA
3276 AAAAAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (20 bp):
AAATTTTGGTATTAAGTAAA
Found at i:4023 original size:12 final size:12
Alignment explanation
Indices: 4006--4030 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3996 GGTGTTCATT
4006 CGGTTAACCGAC
1 CGGTTAACCGAC
4018 CGGTTAACCGAC
1 CGGTTAACCGAC
4030 C
1 C
4031 CGAAATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:4204 original size:9 final size:9
Alignment explanation
Indices: 4190--4284 Score: 120
Period size: 9 Copynumber: 10.4 Consensus size: 9
4180 TTTGGTTAAA
4190 AATTACCCG
1 AATTACCCG
4199 AATTACCCG
1 AATTACCCG
*
4208 AATTAACCG
1 AATTACCCG
4217 AATTACCCG
1 AATTACCCG
*
4226 AATTAACCG
1 AATTACCCG
*
4235 AATTAACCG
1 AATTACCCG
*
4244 AATTAACCG
1 AATTACCCG
4253 AATTA-CCG
1 AATTACCCG
*
4261 AAAAATACCCG
1 --AATTACCCG
4272 AATTACCCG
1 AATTACCCG
4281 AATT
1 AATT
4285 TTTTTATTTT
Statistics
Matches: 78, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
8 3 0.04
9 68 0.87
10 4 0.05
11 3 0.04
ACGTcount: A:0.41, C:0.26, G:0.11, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Done.