Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_367 ID=scaffold_367-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: 8183
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.30
Warning! 368 characters in sequence are not A, C, G, or T
Found at i:126 original size:21 final size:21
Alignment explanation
Indices: 100--141 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
90 TGTTTTAAAG
100 AACAAGAAAG-AAAATAAAGAA
1 AACAAGAAAGTAAAA-AAAGAA
*
121 AACAAGACAGTAAAAAAAGAA
1 AACAAGAAAGTAAAAAAAGAA
142 GAAAATAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.74, C:0.07, G:0.14, T:0.05
Consensus pattern (21 bp):
AACAAGAAAGTAAAAAAAGAA
Found at i:914 original size:40 final size:41
Alignment explanation
Indices: 847--1257 Score: 273
Period size: 44 Copynumber: 9.7 Consensus size: 41
837 CTATTTTTAG
*
847 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGATGCGA
* * ** **
888 TCTGCT-CTCTGCAACCTCAGAAAGATAAGATCTTGATGTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-CTTGATG-CGA
* * * *
930 TCCGCTACACTGCAACTTCAGGGAGATAGGA-TTGATTTCTTCTG-
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGA----TGC-GA
974 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGATGCGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGATGCGA
* * ** **
1015 TCTGCT-CTCTGCAACCTCAGAAAGATAAGATCTTGATGTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-CTTGATG-CGA
* * *
1057 TCCGCTCCACTGCAACTTCAGGGAGATAGGA-TTGATTTCTTCTG-
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGA----TGC-GA
*
1101 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGATGCGA
* * * * * ** **
1142 CCTACT-CTCTGTAACCTCAGAAAGATAAGATCTTGATGTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-CTTGATG-CGA
* * *
1184 TCCGCTCCACTGCAACTTCAGGGAGATAGGA-TTGATTTCTTCTG-
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGA----TGC-GA
1228 TCTGCTCCACTGCAACTTCAGGGAGATAAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAG
1258 TCTGTTTCAC
Statistics
Matches: 279, Mismatches: 63, Indels: 53
0.71 0.16 0.13
Matches are distributed among these distances:
40 61 0.22
41 51 0.18
42 16 0.06
43 56 0.20
44 85 0.30
45 10 0.04
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.28
Consensus pattern (41 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGATGCGA
Found at i:1072 original size:127 final size:127
Alignment explanation
Indices: 846--1257 Score: 779
Period size: 127 Copynumber: 3.2 Consensus size: 127
836 GCTATTTTTA
846 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTCTGCAACCTCAGAAA
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTCTGCAACCTCAGAAA
*
911 GATAAGATCTTGATGTTAATCCGCTACACTGCAACTTCAGGGAGATAGGATTGATTTCTTCT
66 GATAAGATCTTGATGTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCT
*
973 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGATGCGATCTGCTCTCTGCAACCTCAGAAA
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTCTGCAACCTCAGAAA
1038 GATAAGATCTTGATGTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCT
66 GATAAGATCTTGATGTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCT
* * *
1100 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGACCTACTCTCTGTAACCTCAGAAA
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTCTGCAACCTCAGAAA
1165 GATAAGATCTTGATGTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCT
66 GATAAGATCTTGATGTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCT
1227 GTCTGCTCCACTGCAACTTCAGGGAGATAAG
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAG
1258 TCTGTTTCAC
Statistics
Matches: 279, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
127 279 1.00
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (127 bp):
GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTCTGCAACCTCAGAAA
GATAAGATCTTGATGTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCT
Found at i:1201 original size:83 final size:83
Alignment explanation
Indices: 850--1211 Score: 281
Period size: 83 Copynumber: 4.3 Consensus size: 83
840 TTTTTAGTCT
* *
850 GCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCT-CTCTGCAACCTCAGAAAGAT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGACCTGCTCCACTGCAACCTCAGAAAGAT
914 AAGATCTTGATGTTAATCC
66 AAGA-CTTGATGTTAATCC
* * * * ** * **
933 GCTACACTGCAACTTCAGGGAGATAGGA-TTGATTTCTTCTGTCTGCTCCACTGCAACTTCAGGG
1 GCTCCACTGCAACTTCAGGGAGATAAGACTGGA-TGCGAC---CTGCTCCACTGCAACCTCAGAA
** *
997 AGATAAGACTTGATG-CGATCT
62 AGATAAGACTTGATGTTAATCC
* * ** * ** * **
1018 GCT-CTCTGCAACCTCAGAAAGATAAGATCTTGATGTTAATCC-GCTCCACTGCAACTTCAGGGA
1 GCTCCACTGCAACTTCAGGGAGATAAGA-CTGGATG-CGA-CCTGCTCCACTGCAACCTCAGAAA
* **
1081 GATAGGA-TTGAT-TTCTTCTGTC
63 GATAAGACTTGATGTTAATC---C
* * *
1103 TGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGACCTACT-CTCTGTAACCTCAGAAAGA
1 -GCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGACCTGCTCCACTGCAACCTCAGAAAGA
1167 TAAGATCTTGATGTTAATCC
65 TAAGA-CTTGATGTTAATCC
1187 GCTCCACTGCAACTTCAGGGAGATA
1 GCTCCACTGCAACTTCAGGGAGATA
1212 GGATTGATTT
Statistics
Matches: 216, Mismatches: 44, Indels: 38
0.72 0.15 0.13
Matches are distributed among these distances:
82 10 0.05
83 80 0.37
84 41 0.19
85 10 0.05
86 30 0.14
87 45 0.21
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (83 bp):
GCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGACCTGCTCCACTGCAACCTCAGAAAGAT
AAGACTTGATGTTAATCC
Found at i:6040 original size:28 final size:28
Alignment explanation
Indices: 5954--6028 Score: 150
Period size: 28 Copynumber: 2.7 Consensus size: 28
5944 AATGATGTAG
5954 AAAAAAGAATAAAAGAATAATTACTCGA
1 AAAAAAGAATAAAAGAATAATTACTCGA
5982 AAAAAAGAATAAAAGAATAATTACTCGA
1 AAAAAAGAATAAAAGAATAATTACTCGA
6010 AAAAAAGAATAAAAGAATA
1 AAAAAAGAATAAAAGAATA
6029 CTGGCTCAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.68, C:0.05, G:0.11, T:0.16
Consensus pattern (28 bp):
AAAAAAGAATAAAAGAATAATTACTCGA
Done.