Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000813.1 Kokia drynarioides strain JFW-HI SEQ_111898, 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: 3506
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Found at i:152 original size:9 final size:9
Alignment explanation
Indices: 140--174 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
130 AAAAAGAGTC
140 AAAAAAATA
1 AAAAAAATA
149 AAAAAAATA
1 AAAAAAATA
* *
158 AAAAAATTT
1 AAAAAAATA
167 AAAAAAAT
1 AAAAAAAT
175 TTTAAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (9 bp):
AAAAAAATA
Found at i:228 original size:22 final size:21
Alignment explanation
Indices: 180--228 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
170 AAAATTTTAA
* *
180 AAAAAAAAAAGAAAAAATGAG
1 AAAAAAAAAAGAAAAAAAGAC
*
201 ATAAAAAAGAAGAAGAAAAAGAC
1 A-AAAAAAAAAGAA-AAAAAGAC
224 AAAAA
1 AAAAA
229 TATGTTTGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 15 0.65
23 7 0.30
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.04
Consensus pattern (21 bp):
AAAAAAAAAAGAAAAAAAGAC
Found at i:1949 original size:11 final size:11
Alignment explanation
Indices: 1933--1957 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1923 TAGGAACATC
1933 AAAAAAAAAAG
1 AAAAAAAAAAG
1944 AAAAAAAAAAG
1 AAAAAAAAAAG
1955 AAA
1 AAA
1958 CGGGGTCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:2036 original size:31 final size:30
Alignment explanation
Indices: 2012--2077 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
2002 ATTTTCGAGG
* *
2012 AATTTGGGGGTCAAAATTGAAATTTTTGGAA
1 AATTT-GGGATCAAAATTGAAATTTTCGGAA
* *
2043 AATTTGGGATTAAAATTGAAATTTT-GAAA
1 AATTTGGGATCAAAATTGAAATTTTCGGAA
2072 AATTTG
1 AATTTG
2078 AGGTTGAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 9 0.28
30 18 0.56
31 5 0.16
ACGTcount: A:0.39, C:0.02, G:0.21, T:0.38
Consensus pattern (30 bp):
AATTTGGGATCAAAATTGAAATTTTCGGAA
Found at i:2144 original size:29 final size:27
Alignment explanation
Indices: 2112--2393 Score: 111
Period size: 30 Copynumber: 9.5 Consensus size: 27
2102 ATTTAGTGGT
*
2112 AAATGGTAATTTTTGGATGTTCAAGGGTA
1 AAAT-GTAATTTTTGGAAGTT-AAGGGTA
* * * *
2141 AAATCATAATTTTAGGGAAGTTTAGGGTC
1 AAAT-GTAATTTT-TGGAAGTTAAGGGTA
* * *
2170 AAATGTAATTTTTGAAAAGTTTAGGAGTT
1 AAATGTAATTTTTG-GAAGTTAAGG-GTA
** *
2199 AAATGGTAATTTCGGAGAAGTTTAGGGGTTA
1 AAAT-GTAATTTTTG-GAAG-TTAAGGG-TA
*
2230 AAATGTAA-TTTTGGAAAGGTTAGGGGGTTA
1 AAATGTAATTTTTGG-AA-GTTA-AGGG-TA
*
2260 AAATGTAA-TTTTGGAAAAGTTTATGGGTTA
1 AAATGTAATTTTTGG--AAG-TTAAGGG-TA
*
2290 AAATGTAA-TTTTGGAAAAGTTTAATGGTCA
1 AAATGTAATTTTTGG--AAG-TTAAGGGT-A
* *
2320 AAATGTGATTTTTGGAAAATTTTAAGGGTCA
1 AAATGTAATTTTTGG--AA-GTTAAGGGT-A
* *
2351 AAATGTAATTTTGGAGAAGTTTAGGTGTTA
1 AAATGTAATTTTTG-GAAGTTAAGG-G-TA
*
2381 AAATGTGATTTTT
1 AAATGTAATTTTT
2394 AGAGAAAATA
Statistics
Matches: 206, Mismatches: 30, Indels: 33
0.77 0.11 0.12
Matches are distributed among these distances:
27 1 0.00
28 17 0.08
29 40 0.19
30 100 0.49
31 47 0.23
32 1 0.00
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.38
Consensus pattern (27 bp):
AAATGTAATTTTTGGAAGTTAAGGGTA
Found at i:2210 original size:30 final size:29
Alignment explanation
Indices: 2158--2392 Score: 251
Period size: 30 Copynumber: 7.9 Consensus size: 29
2148 AATTTTAGGG
* *
2158 AAGTTTAGGG-TCAAATGTAATTTTTGAA
1 AAGTTTAGGGTTAAAATGTAATTTTGGAA
* *
2186 AAGTTTAGGAGTT-AAATGGTAATTTCGGAG
1 AAGTTTAGG-GTTAAAAT-GTAATTTTGGAA
2216 AAGTTTAGGGGTTAAAATGTAATTTTGG-A
1 AAGTTTA-GGGTTAAAATGTAATTTTGGAA
*
2245 AAGGTTAGGGGGTTAAAATGTAATTTTGGAA
1 AAGTTTA--GGGTTAAAATGTAATTTTGGAA
2276 AAGTTTATGGGTTAAAATGTAATTTTGGAA
1 AAGTTTA-GGGTTAAAATGTAATTTTGGAA
* * *
2306 AAGTTTAATGGTCAAAATGTGATTTTTGGAA
1 AAGTTT-AGGGTTAAAATGT-AATTTTGGAA
* * *
2337 AATTTTAAGGGTCAAAATGTAATTTTGGAG
1 AAGTTT-AGGGTTAAAATGTAATTTTGGAA
*
2367 AAGTTTAGGTGTTAAAATGTGATTTT
1 AAGTTTAGG-GTTAAAATGTAATTTT
2393 TAGAGAAAAT
Statistics
Matches: 179, Mismatches: 18, Indels: 18
0.83 0.08 0.08
Matches are distributed among these distances:
28 9 0.05
29 14 0.08
30 115 0.64
31 41 0.23
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.38
Consensus pattern (29 bp):
AAGTTTAGGGTTAAAATGTAATTTTGGAA
Found at i:2363 original size:61 final size:61
Alignment explanation
Indices: 2158--2393 Score: 252
Period size: 61 Copynumber: 3.9 Consensus size: 61
2148 AATTTTAGGG
* * *
2158 AAGTTT-AGGGTC-AAATGTAATTTTTGAAAAGTTTAGGAGTT-AAATG-GTAATTTCGGAG
1 AAGTTTAAGGGTCAAAATGTAATTTTGGAAAAGTTTAGGAGTTAAAATGTG-AATTTTGGAA
* * * *
2216 AAGTTTAGGGGTTAAAATGTAATTTTGG-AAAGGTTAGGGGGTTAAAATGT-AATTTTGGAA
1 AAGTTTAAGGGTCAAAATGTAATTTTGGAAAAGTTTA-GGAGTTAAAATGTGAATTTTGGAA
* * * * *
2276 AAGTTTATGGGTTAAAATGTAATTTTGGAAAAGTTTAATG-GTCAAAATGTGATTTTTGGAA
1 AAGTTTAAGGGTCAAAATGTAATTTTGGAAAAGTTT-AGGAGTTAAAATGTGAATTTTGGAA
* * * *
2337 AATTTTAAGGGTCAAAATGTAATTTTGGAGAAGTTTAGGTGTTAAAATGTGATTTTT
1 AAGTTTAAGGGTCAAAATGTAATTTTGGAAAAGTTTAGGAGTTAAAATGTGAATTTT
2394 AGAGAAAATA
Statistics
Matches: 151, Mismatches: 18, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
58 6 0.04
59 11 0.07
60 64 0.42
61 69 0.46
62 1 0.01
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.38
Consensus pattern (61 bp):
AAGTTTAAGGGTCAAAATGTAATTTTGGAAAAGTTTAGGAGTTAAAATGTGAATTTTGGAA
Done.