Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008413.1 Kokia drynarioides strain JFW-HI SEQ_123084, 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: 2885
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.32
Found at i:1920 original size:29 final size:28
Alignment explanation
Indices: 1891--2206 Score: 175
Period size: 30 Copynumber: 10.8 Consensus size: 28
1881 AGTTTCAAAG
1891 AATTTAGGGTTAAAATGTAATTTTGGAA
1 AATTTAGGGTTAAAATGTAATTTTGGAA
* * **
1919 GAATTCGAGGGTTAAAAGGTAATTTTATCAA
1 -AATT-TAGGGTTAAAATGTAATTTT-GGAA
* * **
1950 AGTTT-GGGGTAAAATGGGATTTTGGGAA
1 AATTTAGGGTTAAAATGTAATTTT-GGAA
** * * * *
1978 GGTTTAGGGTCAAAATGTTATCTTGGGGA
1 AATTTAGGGTTAAAATGTAAT-TTTGGAA
* * * *
2007 AGTTTGGGGTCAAAATGTAGTTTTGGAA
1 AATTTAGGGTTAAAATGTAATTTTGGAA
* *
2035 AAGTTTGAGGGTGAAAATGTGATTTTGGAA
1 AA-TTT-AGGGTTAAAATGTAATTTTGGAA
* *
2065 ATGTTTGAGGGTTAAAATGTGATTTTGGGAA
1 A-ATTT-AGGGTTAAAATGTAATTTT-GGAA
* * * *
2096 AATTTGGGGTCAAAATGTGATTTTAGGGA
1 AATTTAGGGTTAAAATGTAATTTT-GGAA
* * * *
2125 AGTTTGGGGTTAAAATATGATTTTGGAA
1 AATTTAGGGTTAAAATGTAATTTTGGAA
* * *
2153 AAGTTTAGGGGTCAAATTGTAATTTTAGAA
1 AA-TTTA-GGGTTAAAATGTAATTTTGGAA
* *
2183 AAGTTTAAGGGTCAAAATGCAATT
1 AA-TTT-AGGGTTAAAATGTAATT
2207 GTTAAAATGT
Statistics
Matches: 225, Mismatches: 51, Indels: 21
0.76 0.17 0.07
Matches are distributed among these distances:
28 30 0.13
29 82 0.36
30 105 0.47
31 8 0.04
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (28 bp):
AATTTAGGGTTAAAATGTAATTTTGGAA
Found at i:1932 original size:30 final size:30
Alignment explanation
Indices: 1888--2152 Score: 175
Period size: 29 Copynumber: 9.1 Consensus size: 30
1878 TGAAGTTTCA
*
1888 AAGAATTT-AGGGTTAAAATGTAATTTTGG
1 AAGAATTTGAGGGTTAAAATGTGATTTTGG
* * * **
1917 AAGAATTCGAGGGTTAAAAGGTAATTTTATC
1 AAGAATTTGAGGGTTAAAATGTGATTTT-GG
* *
1948 AA-AGTTTG-GGG-TAAAATGGGATTTTGGG
1 AAGAATTTGAGGGTTAAAATGTGATTTT-GG
* * * *
1976 AAG-GTTT-AGGGTCAAAATGTTATCTTGG
1 AAGAATTTGAGGGTTAAAATGTGATTTTGG
* *
2004 -GGAAGTTTG-GGGTCAAAATGT-AGTTTTGG
1 AAGAA-TTTGAGGGTTAAAATGTGA-TTTTGG
*
2033 AA-AAGTTTGAGGGTGAAAATGTGATTTTGG
1 AAGAA-TTTGAGGGTTAAAATGTGATTTTGG
*
2063 AA-ATGTTTGAGGGTTAAAATGTGATTTTGGG
1 AAGA-ATTTGAGGGTTAAAATGTGATTTT-GG
*
2094 AA-AATTTG-GGGTCAAAATGTGATTTTAGG
1 AAGAATTTGAGGGTTAAAATGTGATTTT-GG
*
2123 --GAAGTTTG-GGGTTAAAATATGATTTTGG
1 AAGAA-TTTGAGGGTTAAAATGTGATTTTGG
2151 AA
1 AA
2153 AAGTTTAGGG
Statistics
Matches: 190, Mismatches: 28, Indels: 35
0.75 0.11 0.14
Matches are distributed among these distances:
27 1 0.01
28 27 0.14
29 86 0.45
30 68 0.36
31 8 0.04
ACGTcount: A:0.32, C:0.02, G:0.31, T:0.35
Consensus pattern (30 bp):
AAGAATTTGAGGGTTAAAATGTGATTTTGG
Found at i:2125 original size:118 final size:117
Alignment explanation
Indices: 1897--2201 Score: 341
Period size: 118 Copynumber: 2.6 Consensus size: 117
1887 AAAGAATTTA
* * * * *
1897 GGGTTAAAATGTAATTTTGGAAGAA-TTCGAGGGTTAAAAGGTAATTTTATCAAAGTTTG-GGG-
1 GGGTTAAAATGTAGTTTTGGAA-AAGTTTGAGGGTCAAAATGTAATTTTA-GAAAGTTTGAGGGT
** * *
1959 TAAAATGGGATTTTGGGAAGGTTTAGGGTCAAAATGTTATCTTGGGGAAGTTTG
64 TAAAATGGGATTTTGGGAAAATTTAGGGTCAAAATGTGATCTTAGGGAAGTTTG
* * * *
2013 GGGTCAAAATGTAGTTTTGGAAAAGTTTGAGGGTGAAAATGTGATTTTGGAAATGTTTGAGGGTT
1 GGGTTAAAATGTAGTTTTGGAAAAGTTTGAGGGTCAAAATGTAATTTTAGAAA-GTTTGAGGGTT
* * *
2078 AAAATGTGATTTTGGGAAAATTTGGGGTCAAAATGTGATTTTAGGGAAGTTTG
65 AAAATGGGATTTTGGGAAAATTTAGGGTCAAAATGTGATCTTAGGGAAGTTTG
* * *
2131 GGGTTAAAATAT-GATTTTGGAAAAGTTT-AGGGGTCAAATTGTAATTTTAGAAAAGTTTAAGGG
1 GGGTTAAAATGTAG-TTTTGGAAAAGTTTGA-GGGTCAAAATGTAATTTTAG-AAAGTTTGAGGG
*
2194 TCAAAATG
63 TTAAAATG
2202 CAATTGTTAA
Statistics
Matches: 159, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
115 5 0.03
116 44 0.28
117 5 0.03
118 102 0.64
119 3 0.02
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.35
Consensus pattern (117 bp):
GGGTTAAAATGTAGTTTTGGAAAAGTTTGAGGGTCAAAATGTAATTTTAGAAAGTTTGAGGGTTA
AAATGGGATTTTGGGAAAATTTAGGGTCAAAATGTGATCTTAGGGAAGTTTG
Found at i:2178 original size:30 final size:29
Alignment explanation
Indices: 1948--2201 Score: 255
Period size: 29 Copynumber: 8.7 Consensus size: 29
1938 TAATTTTATC
* *
1948 AAAGTTTGGGGT-AAAATGGGATTTTGGG
1 AAAGTTTGGGGTCAAAATGTGATTTTGGA
* * * * *
1976 AAGGTTTAGGGTCAAAATGTTATCTTGGG
1 AAAGTTTGGGGTCAAAATGTGATTTTGGA
*
2005 GAAGTTTGGGGTCAAAATGT-AGTTTTGGA
1 AAAGTTTGGGGTCAAAATGTGA-TTTTGGA
*
2034 AAAGTTTGAGGGTGAAAATGTGATTTTGGA
1 AAAGTTTG-GGGTCAAAATGTGATTTTGGA
* *
2064 AATGTTTGAGGGTTAAAATGTGATTTTGGGA
1 AAAGTTTG-GGGTCAAAATGTGATTTT-GGA
2095 AAA-TTTGGGGTCAAAATGTGATTTTAGG-
1 AAAGTTTGGGGTCAAAATGTGATTTT-GGA
* * *
2123 GAAGTTTGGGGTTAAAATATGATTTTGGA
1 AAAGTTTGGGGTCAAAATGTGATTTTGGA
* * *
2152 AAAGTTTAGGGGTCAAATTGTAATTTTAGA
1 AAAGTTT-GGGGTCAAAATGTGATTTTGGA
*
2182 AAAGTTTAAGGGTCAAAATG
1 AAAGTTT-GGGGTCAAAATG
2202 CAATTGTTAA
Statistics
Matches: 190, Mismatches: 28, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
28 15 0.08
29 87 0.46
30 82 0.43
31 6 0.03
ACGTcount: A:0.32, C:0.02, G:0.31, T:0.35
Consensus pattern (29 bp):
AAAGTTTGGGGTCAAAATGTGATTTTGGA
Found at i:2241 original size:30 final size:30
Alignment explanation
Indices: 2207--2315 Score: 100
Period size: 29 Copynumber: 3.7 Consensus size: 30
2197 AAATGCAATT
*
2207 GTTAAAATGTAATTTTGGAAAAATTTAGGG
1 GTTAAAATGTAATTTTGGAAAAATATAGGG
* * *
2237 GTTAAAATATAATTTTGGAGAAGTAT-GGG
1 GTTAAAATGTAATTTTGGAAAAATATAGGG
* * *
2266 GTCAAAAT-TCAGTTTT-GAAAAAGTAT-GAG
1 GTTAAAATGT-AATTTTGGAAAAA-TATAGGG
*
2295 GTTAAAATGTGATTTTGGAAA
1 GTTAAAATGTAATTTTGGAAA
2316 GGTTTGAAGG
Statistics
Matches: 63, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
28 5 0.08
29 31 0.49
30 27 0.43
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.35
Consensus pattern (30 bp):
GTTAAAATGTAATTTTGGAAAAATATAGGG
Found at i:2310 original size:29 final size:29
Alignment explanation
Indices: 2207--2345 Score: 93
Period size: 29 Copynumber: 4.7 Consensus size: 29
2197 AAATGCAATT
* * *
2207 GTTAAAATGTAATTTTGGAAAAA-TTTAGGG
1 GTTAAAATATAATTTT-GAAAAAGTAT-GAG
* * *
2237 GTTAAAATATAATTTTGGAGAAGTATGGG
1 GTTAAAATATAATTTTGAAAAAGTATGAG
* *
2266 GTCAAAAT-TCAGTTTTGAAAAAGTATGAG
1 GTTAAAATAT-AATTTTGAAAAAGTATGAG
* * * * *
2295 GTTAAAATGTGATTTTGGAAAGGTTTGAAG
1 GTTAAAATATAATTTTGAAAAAGTATG-AG
*
2325 GTTAAAATATGATTTTAGAAA
1 GTTAAAATATAATTTT-GAAA
2346 GGTTTGAGAG
Statistics
Matches: 87, Mismatches: 17, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
28 1 0.01
29 48 0.55
30 35 0.40
31 3 0.03
ACGTcount: A:0.40, C:0.01, G:0.24, T:0.35
Consensus pattern (29 bp):
GTTAAAATATAATTTTGAAAAAGTATGAG
Found at i:2329 original size:30 final size:30
Alignment explanation
Indices: 2293--2352 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
2283 AAAAAGTATG
* *
2293 AGGTTAAAATGTGATTTTGGAAAGGTTTGA
1 AGGTTAAAATATGATTTTAGAAAGGTTTGA
2323 AGGTTAAAATATGATTTTAGAAAGGTTTGA
1 AGGTTAAAATATGATTTTAGAAAGGTTTGA
2353 GAGTCAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.37, C:0.00, G:0.27, T:0.37
Consensus pattern (30 bp):
AGGTTAAAATATGATTTTAGAAAGGTTTGA
Found at i:2362 original size:30 final size:30
Alignment explanation
Indices: 2293--2364 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
2283 AAAAAGTATG
* * *
2293 AGGTTAAAATGTGATTTTGGAAAGGTTTGA
1 AGGTCAAAATATGATTTTAGAAAGGTTTGA
*
2323 AGGTTAAAATATGATTTTAGAAAGGTTTG-
1 AGGTCAAAATATGATTTTAGAAAGGTTTGA
2352 AGAGTCAAAATAT
1 AG-GTCAAAATAT
2365 AGTTTTTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 2 0.05
30 36 0.95
ACGTcount: A:0.39, C:0.01, G:0.25, T:0.35
Consensus pattern (30 bp):
AGGTCAAAATATGATTTTAGAAAGGTTTGA
Done.