Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002094.1 Kokia drynarioides strain JFW-HI SEQ_114012, whole genome shotgun sequence
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: 8146
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:1724 original size:93 final size:94
Alignment explanation
Indices: 1617--1793 Score: 248
Period size: 93 Copynumber: 1.9 Consensus size: 94
1607 AGAAGAAAAG
* * * * *
1617 AAAAAAATCAAGAAAATACCTTAATCCCTAAATTCTTTCCTCACGTATGGTGAATTGAAAAAAAG
1 AAAAAAATCAAGAAAATACCTTAATCCCTAAATCCCTTCCTAACGTATGATGAATTGAAAAAAAA
1682 ACTCAAAATTAAATATGAGATAGAGAAGA
66 ACTCAAAATTAAATATGAGATAGAGAAGA
* * * * *
1711 AAAAAAAT-GAGAAAATACTTTAATCCCTAAATCCCTTCTTAACTTCTGATGAATTGAAAAAAAA
1 AAAAAAATCAAGAAAATACCTTAATCCCTAAATCCCTTCCTAACGTATGATGAATTGAAAAAAAA
*
1775 ACTCAAAATTTAATATGAG
66 ACTCAAAATTAAATATGAG
1794 GTGGAAATTT
Statistics
Matches: 72, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
93 64 0.89
94 8 0.11
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.27
Consensus pattern (94 bp):
AAAAAAATCAAGAAAATACCTTAATCCCTAAATCCCTTCCTAACGTATGATGAATTGAAAAAAAA
ACTCAAAATTAAATATGAGATAGAGAAGA
Found at i:2219 original size:102 final size:102
Alignment explanation
Indices: 2043--2246 Score: 381
Period size: 102 Copynumber: 2.0 Consensus size: 102
2033 TGTGTGAATA
*
2043 GAAAACCTCACAAATTTAGGTTACATGATGAGAATTAGGACTACAAAATATATTCTCCTTATCTG
1 GAAAACCTCACAAATTTAGGTTACATGATGAGAATTAGGACTACAAAATATACTCTCCTTATCTG
2108 TATTGATAAGAGCTAAGACCTCTTCCGAAGGATTCTC
66 TATTGATAAGAGCTAAGACCTCTTCCGAAGGATTCTC
*
2145 GAAAACCTCACAAATTTAGGTTACATGATGAGAATTAGGACTACAAAATATCCTCTCCTTATCTG
1 GAAAACCTCACAAATTTAGGTTACATGATGAGAATTAGGACTACAAAATATACTCTCCTTATCTG
*
2210 TATTGATAAGAGCTAAGACCTCTTCCGAAGGGTTCTC
66 TATTGATAAGAGCTAAGACCTCTTCCGAAGGATTCTC
2247 AATCATACAA
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
102 99 1.00
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (102 bp):
GAAAACCTCACAAATTTAGGTTACATGATGAGAATTAGGACTACAAAATATACTCTCCTTATCTG
TATTGATAAGAGCTAAGACCTCTTCCGAAGGATTCTC
Found at i:7770 original size:14 final size:15
Alignment explanation
Indices: 7722--7768 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
7712 AATTTATCTT
* *
7722 AAATTTTTAAATTTGA
1 AAATTTTAAAAATT-A
*
7738 AAA-TTAAAAAATTA
1 AAATTTTAAAAATTA
7752 AAATTTTAAAAATTA
1 AAATTTTAAAAATTA
7767 AA
1 AA
7769 TTCTAAAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.15
15 19 0.73
16 3 0.12
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (15 bp):
AAATTTTAAAAATTA
Found at i:7775 original size:14 final size:15
Alignment explanation
Indices: 7744--7776 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
7734 TTGAAAATTA
*
7744 AAAAATTAAAATTTT
1 AAAAATTAAAATTCT
7759 AAAAATT-AAATTCT
1 AAAAATTAAAATTCT
7773 AAAA
1 AAAA
7777 TGTAATGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAAATTAAAATTCT
Found at i:8075 original size:35 final size:35
Alignment explanation
Indices: 8018--8130 Score: 111
Period size: 35 Copynumber: 3.1 Consensus size: 35
8008 ATCATTTTTA
*
8018 ATTTATAAAATTTTAAATTAATAATAATAAAATTAT
1 ATTT-TAAAATTTTAAAATAATAATAATAAAATTAT
* * ***
8054 ATTTTAATATTTTAAAATAATAAAAATTTCA-TAT
1 ATTTTAAAATTTTAAAATAATAATAATAAAATTAT
* *
8088 ATTTTAAAAATTATAAATTATAAAAATAATAAAATTAT
1 ATTTT-AAAATTTTAAA--ATAATAATAATAAAATTAT
8126 ATTTT
1 ATTTT
8131 TATTATTATA
Statistics
Matches: 60, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
34 8 0.13
35 30 0.50
36 4 0.07
37 10 0.17
38 8 0.13
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (35 bp):
ATTTTAAAATTTTAAAATAATAATAATAAAATTAT
Found at i:8113 original size:16 final size:16
Alignment explanation
Indices: 8068--8126 Score: 55
Period size: 16 Copynumber: 3.5 Consensus size: 16
8058 TAATATTTTA
*
8068 AAATAATAAAAATTTCAT
1 AAATTATAAAAA-TT-AT
* *
8086 ATATTTTAAAAATTAT
1 AAATTATAAAAATTAT
*
8102 AAATTATAAAAATAAT
1 AAATTATAAAAATTAT
8118 AAAATTATA
1 -AAATTATA
8127 TTTTTATTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
16 15 0.44
17 10 0.29
18 9 0.26
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (16 bp):
AAATTATAAAAATTAT
Done.