Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1921
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: 14941
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Found at i:235 original size:88 final size:89
Alignment explanation
Indices: 135--311 Score: 311
Period size: 88 Copynumber: 2.0 Consensus size: 89
125 CTGATCACAG
* * *
135 AAAAAGTTCGAAGAAGCTAAGGCTTTGAGAGAGAAAATAGTAATGGCATTAAGTAAATATGCA-A
1 AAAAAGTACGAAGAAGCTAAGGCTTTCAGAGAGAAAATAGTAATGGCATTAAGGAAATATGCACA
199 CCATATGGCTACCAACTTTACCAA
66 CCATATGGCTACCAACTTTACCAA
223 AAAAAGTACGAAGAAGCTAAGGCTTTCAGAGAGAAAATAGTAATGGCATTAAGGAAATATGCACA
1 AAAAAGTACGAAGAAGCTAAGGCTTTCAGAGAGAAAATAGTAATGGCATTAAGGAAATATGCACA
*
288 CCATATGGCTACCAAGTTTACCAA
66 CCATATGGCTACCAACTTTACCAA
312 GCTTAGGATT
Statistics
Matches: 84, Mismatches: 4, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
88 60 0.71
89 24 0.29
ACGTcount: A:0.44, C:0.15, G:0.20, T:0.21
Consensus pattern (89 bp):
AAAAAGTACGAAGAAGCTAAGGCTTTCAGAGAGAAAATAGTAATGGCATTAAGGAAATATGCACA
CCATATGGCTACCAACTTTACCAA
Found at i:2630 original size:70 final size:70
Alignment explanation
Indices: 2532--2667 Score: 263
Period size: 70 Copynumber: 1.9 Consensus size: 70
2522 TTTCAAGCTT
*
2532 TTTTTTTAAATATTTGAAGGTTGATACTTTCATCCTCACGTCCAAATATATGTTGAATATAGATA
1 TTTTTTTAAATATTTGAAGGTTGATACTTTCATCCTCACGTCCAAATATATGTTGAATACAGATA
2597 CAAGC
66 CAAGC
2602 TTTTTTTAAATATTTGAAGGTTGATACTTTCATCCTCACGTCCAAATATATGTTGAATACAGATA
1 TTTTTTTAAATATTTGAAGGTTGATACTTTCATCCTCACGTCCAAATATATGTTGAATACAGATA
2667 C
66 C
2668 TCTAGAGAAA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.40
Consensus pattern (70 bp):
TTTTTTTAAATATTTGAAGGTTGATACTTTCATCCTCACGTCCAAATATATGTTGAATACAGATA
CAAGC
Found at i:3309 original size:74 final size:78
Alignment explanation
Indices: 3231--3383 Score: 269
Period size: 74 Copynumber: 2.0 Consensus size: 78
3221 GAAATTTGAA
3231 AAAATAAAATGTAGAATCAAGCAATGAATACCGATTTG-AAACATTGT-A-AG-AGAAGAAGAAG
1 AAAATAAAATGTAGAATCAAGCAATGAATACCGATTTGAAAACATTGTAAGAGAAGAAGAAGAAG
3292 AAGCAGTGTAGTT
66 AAGCAGTGTAGTT
*
3305 AAAATAAAATGTATAATCAAGCAATGAATACCGATTTGAAAACATTGTAAGAGAAGAAGAAGAAG
1 AAAATAAAATGTAGAATCAAGCAATGAATACCGATTTGAAAACATTGTAAGAGAAGAAGAAGAAG
3370 AAGCAGTGTAGTT
66 AAGCAGTGTAGTT
3383 A
1 A
3384 GCTAAGTCGG
Statistics
Matches: 74, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
74 37 0.50
75 9 0.12
76 1 0.01
77 2 0.03
78 25 0.34
ACGTcount: A:0.50, C:0.08, G:0.21, T:0.22
Consensus pattern (78 bp):
AAAATAAAATGTAGAATCAAGCAATGAATACCGATTTGAAAACATTGTAAGAGAAGAAGAAGAAG
AAGCAGTGTAGTT
Found at i:8966 original size:3 final size:3
Alignment explanation
Indices: 8951--8985 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
8941 AGGTTTGCAA
* *
8951 GAT GAT GAA GAT GAT GAT GAT GAT GAT GAA GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
8986 CCTGCACATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.40, C:0.00, G:0.34, T:0.26
Consensus pattern (3 bp):
GAT
Found at i:9749 original size:21 final size:21
Alignment explanation
Indices: 9724--9778 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
9714 TTTAAAAAAT
9724 TATTTTATATTAATATT-TATA
1 TATTTTATATTAAT-TTATATA
9745 TATTTTTATAATTAATTTATATA
1 TA-TTTTAT-ATTAATTTATATA
* *
9768 AATTTTTTATT
1 TATTTTATATT
9779 TTAAATAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
21 5 0.17
22 13 0.45
23 11 0.38
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TATTTTATATTAATTTATATA
Found at i:9782 original size:23 final size:23
Alignment explanation
Indices: 9720--9782 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
9710 ATATTTTAAA
9720 AAATTATTTTATATTAATATTTAT
1 AAATT-TTTTATATTAATATTTAT
*
9744 ATA-TTTTTATAATTAAT-TTATAT
1 AAATTTTTTAT-ATTAATATT-TAT
*
9767 AAATTTTTTATTTTAA
1 AAATTTTTTATATTAA
9783 ATAATAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
22 8 0.24
23 16 0.48
24 9 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
AAATTTTTTATATTAATATTTAT
Found at i:13131 original size:1 final size:1
Alignment explanation
Indices: 13127--13171 Score: 72
Period size: 1 Copynumber: 45.0 Consensus size: 1
13117 TTTTGTTTTT
* *
13127 GGGGGGGGGGGGGTGGGGGGGTGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
13172 AGTGGGGAGG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.00, C:0.00, G:0.96, T:0.04
Consensus pattern (1 bp):
G
Found at i:13163 original size:26 final size:26
Alignment explanation
Indices: 13127--13178 Score: 88
Period size: 25 Copynumber: 2.0 Consensus size: 26
13117 TTTTGTTTTT
*
13127 GGGGGGGGGGGGGTGGGGGG-GTGGG
1 GGGGGGGGGGGGGGGGGGGGAGTGGG
13152 GGGGGGGGGGGGGGGGGGGGAGTGGG
1 GGGGGGGGGGGGGGGGGGGGAGTGGG
13178 G
1 G
13179 AGGGTGCTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 19 0.76
26 6 0.24
ACGTcount: A:0.02, C:0.00, G:0.92, T:0.06
Consensus pattern (26 bp):
GGGGGGGGGGGGGGGGGGGGAGTGGG
Done.