Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000898.1 Kokia drynarioides strain JFW-HI SEQ_112025, 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: 23394
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34
Warning! 78 characters in sequence are not A, C, G, or T
Found at i:1242 original size:30 final size:29
Alignment explanation
Indices: 1208--1322 Score: 88
Period size: 29 Copynumber: 3.9 Consensus size: 29
1198 AATTTAAAAG
*
1208 AATTGAATCAAATCAAAATTTCATGTATAA
1 AATTGCATCAAATCAAAATTT-ATGTATAA
* *
1238 AATTGCA-CAAAATCAAAGTTTATGTATAC
1 AATTGCATC-AAATCAAAATTTATGTATAA
* * * * *
1267 AATTGCATCACGATTCAAATTTTATATGTAT
1 AATTGCATCA--AATCAAAATTTATGTATAA
* * *
1298 AATTACATCAAATTAAAATTCATGT
1 AATTGCATCAAATCAAAATTTATGT
1323 TTTAATTTAC
Statistics
Matches: 67, Mismatches: 14, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
29 26 0.39
30 18 0.27
31 23 0.34
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.36
Consensus pattern (29 bp):
AATTGCATCAAATCAAAATTTATGTATAA
Found at i:1263 original size:29 final size:30
Alignment explanation
Indices: 1217--1273 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
1207 GAATTGAATC
1217 AAATCAAAATTTCATGTATAAAATTGCACA
1 AAATCAAAATTTCATGTATAAAATTGCACA
* *
1247 AAATCAAAGTTT-ATGTATACAATTGCA
1 AAATCAAAATTTCATGTATAAAATTGCA
1274 TCACGATTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.32
Consensus pattern (30 bp):
AAATCAAAATTTCATGTATAAAATTGCACA
Found at i:10231 original size:6 final size:6
Alignment explanation
Indices: 10220--10244 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
10210 TCAAGAAATG
10220 CAAAAA CAAAAA CAAAAA CAAAAA C
1 CAAAAA CAAAAA CAAAAA CAAAAA C
10245 CCATTGAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (6 bp):
CAAAAA
Found at i:13132 original size:30 final size:29
Alignment explanation
Indices: 13088--13167 Score: 76
Period size: 30 Copynumber: 2.7 Consensus size: 29
13078 AAATTTTAAA
13088 TTAATAAA-AATAAAATTATACTTTAA-CTT
1 TTAA-AAATAATAAAATTATA-TTTAATCTT
13117 TCTAAAAATAATAAAAATT-TGATTTAATCTT
1 T-TAAAAATAAT-AAAATTAT-ATTTAATCTT
* *
13148 TTAAAAATTATAAAAATATA
1 TTAAAAATAATAAAATTATA
13168 AATAATTTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
29 10 0.23
30 22 0.51
31 11 0.26
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (29 bp):
TTAAAAATAATAAAATTATATTTAATCTT
Found at i:13192 original size:39 final size:39
Alignment explanation
Indices: 13119--13195 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
13109 TTTAACTTTC
* **
13119 TAAAAATAATAAAAATTTGATTTAATCTTTTAAAAATTA
1 TAAAAATAATAAAAATTTAATTTAATCTCCTAAAAATTA
13158 TAAAAAT-ATAAATAATTTAATTTCAA-CTCCTAAAAATT
1 TAAAAATAATAAA-AATTTAATTT-AATCTCCTAAAAATT
13196 TTTCTTGGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 5 0.15
39 26 0.79
40 2 0.06
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.39
Consensus pattern (39 bp):
TAAAAATAATAAAAATTTAATTTAATCTCCTAAAAATTA
Found at i:15892 original size:26 final size:27
Alignment explanation
Indices: 15860--15918 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
15850 TGCTAAACAA
** *
15860 AGAGCACTTTACGTGCTAATAAT-CGG
1 AGAGCACAATACGTGCTAAAAATACGG
15886 AGAGCACAATACGTGCTAAAAATAACGG
1 AGAGCACAATACGTGCTAAAAAT-ACGG
15914 AGAGC
1 AGAGC
15919 GCGCTAGTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 20 0.71
28 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.19
Consensus pattern (27 bp):
AGAGCACAATACGTGCTAAAAATACGG
Done.