Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004896.1 Kokia drynarioides strain JFW-HI SEQ_118586, 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: 40665
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:2268 original size:73 final size:69
Alignment explanation
Indices: 2145--2276 Score: 158
Period size: 73 Copynumber: 1.9 Consensus size: 69
2135 ATTTTGTCTT
* * **
2145 CACTTTAATTTTTTTTACTTATTTACTTAAGGAATAATTCATTTGTTTTATACCTATATAACACG
1 CACTTTAATTTTTTTTACTTATTTACTAAAAGAATAATTCATTTACTTTATA--TATATAACACG
2210 TGTCAC
64 TGTCAC
* *
2216 CACTTTAATTTCCTTTTTCCTTATTTA-TCAAAAGAATGATTCATTTACTTTATATATATAA
1 CACTTTAATTT--TTTTTACTTATTTACT-AAAAGAATAATTCATTTACTTTATATATATAA
2277 TATTATTATT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
71 18 0.35
72 1 0.02
73 33 0.63
ACGTcount: A:0.31, C:0.15, G:0.05, T:0.48
Consensus pattern (69 bp):
CACTTTAATTTTTTTTACTTATTTACTAAAAGAATAATTCATTTACTTTATATATATAACACGTG
TCAC
Found at i:5572 original size:25 final size:25
Alignment explanation
Indices: 5544--5644 Score: 112
Period size: 25 Copynumber: 4.0 Consensus size: 25
5534 AGACGATGAA
*
5544 GATATTTTGTCTGGCTCGTGAGAGC
1 GATATTCTGTCTGGCTCGTGAGAGC
*
5569 GATACTCTGTCTGGCTCGTGAGAGC
1 GATATTCTGTCTGGCTCGTGAGAGC
* * * *
5594 GATATTCTATCTGTCTCGTAAGAAC
1 GATATTCTGTCTGGCTCGTGAGAGC
* * *
5619 GTTATTCTATCTAGGCTCGTTAGAGC
1 GATATTCTGTCT-GGCTCGTGAGAGC
5645 TACATTTTGG
Statistics
Matches: 64, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
25 54 0.84
26 10 0.16
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.35
Consensus pattern (25 bp):
GATATTCTGTCTGGCTCGTGAGAGC
Found at i:8915 original size:6 final size:6
Alignment explanation
Indices: 8904--8930 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
8894 CTATTGACAA
8904 TTTCTT TTTCTT TTTCTT TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTT
8931 AATTATATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTCTT
Found at i:10218 original size:6 final size:6
Alignment explanation
Indices: 10207--10243 Score: 65
Period size: 6 Copynumber: 6.0 Consensus size: 6
10197 AATCCCCGAT
10207 TCTTGG TCTTGG TCTTGG TCTTGG TCTTTGG TCTTGG
1 TCTTGG TCTTGG TCTTGG TCTTGG TC-TTGG TCTTGG
10244 AATCACATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.00, C:0.16, G:0.32, T:0.51
Consensus pattern (6 bp):
TCTTGG
Found at i:22897 original size:18 final size:19
Alignment explanation
Indices: 22871--22906 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
22861 ACTATTGGAG
22871 ATATCTTTTTT-TTTTCTA
1 ATATCTTTTTTATTTTCTA
*
22889 ATATTTTTTTTATTTTCT
1 ATATCTTTTTTATTTTCT
22907 TACTATACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (19 bp):
ATATCTTTTTTATTTTCTA
Found at i:25514 original size:20 final size:21
Alignment explanation
Indices: 25484--25527 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
25474 ATGTCATGTA
*
25484 TAAATTTTCTCTGTAGAATAT
1 TAAATTTTCTCCGTAGAATAT
25505 TAAA-TTTCTCCGTAGAATAT
1 TAAATTTTCTCCGTAGAATAT
25525 TAA
1 TAA
25528 TTTAACGGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.43
Consensus pattern (21 bp):
TAAATTTTCTCCGTAGAATAT
Found at i:25823 original size:16 final size:16
Alignment explanation
Indices: 25802--25832 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25792 CATTAAAATT
25802 CAAAATCCAAAACTAC
1 CAAAATCCAAAACTAC
*
25818 CAAAATCCTAAACTA
1 CAAAATCCAAAACTA
25833 TCCATGACCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.29, G:0.00, T:0.16
Consensus pattern (16 bp):
CAAAATCCAAAACTAC
Found at i:26397 original size:15 final size:15
Alignment explanation
Indices: 26357--26403 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
26347 TTCATTTATT
*
26357 TTTTAAAAAAAATAA
1 TTTTAAAATAAATAA
*
26372 TATTTCGAAATAAATAA
1 T-TTT-AAAATAAATAA
26389 TTTTAAAATAAATAA
1 TTTTAAAATAAATAA
26404 AATAAAAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 11 0.41
16 6 0.22
17 10 0.37
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (15 bp):
TTTTAAAATAAATAA
Found at i:36371 original size:23 final size:23
Alignment explanation
Indices: 36345--36415 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
36335 AAGTTCACTG
36345 ATTGCGAGACAAGATATTCGCCC
1 ATTGCGAGACAAGATATTCGCCC
* * * * **
36368 ATT--GA-AAAACTATGTTCACTG
1 ATTGCGAGACAA-GATATTCGCCC
36389 ATTGCGAGACAAGATATTCGCCC
1 ATTGCGAGACAAGATATTCGCCC
36412 ATTG
1 ATTG
36416 AAAAACTATG
Statistics
Matches: 32, Mismatches: 12, Indels: 8
0.62 0.23 0.15
Matches are distributed among these distances:
20 3 0.09
21 11 0.34
23 15 0.47
24 3 0.09
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (23 bp):
ATTGCGAGACAAGATATTCGCCC
Found at i:36387 original size:44 final size:44
Alignment explanation
Indices: 36337--36427 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
36327 TTAGTAAGAA
36337 GTTCACTGATTGCGAGACAAGATATTCGCCCATTGAAAAACTAT
1 GTTCACTGATTGCGAGACAAGATATTCGCCCATTGAAAAACTAT
36381 GTTCACTGATTGCGAGACAAGATATTCGCCCATTGAAAAACTAT
1 GTTCACTGATTGCGAGACAAGATATTCGCCCATTGAAAAACTAT
36425 GTT
1 GTT
36428 GCGCCTTAGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.29
Consensus pattern (44 bp):
GTTCACTGATTGCGAGACAAGATATTCGCCCATTGAAAAACTAT
Found at i:39877 original size:47 final size:48
Alignment explanation
Indices: 39811--39912 Score: 127
Period size: 47 Copynumber: 2.1 Consensus size: 48
39801 TGGGTCAAAG
* * * *
39811 CAATAAAGCGATCACCTTCTT-GATGAGATATAGA-AAGTTGATTAGAT
1 CAATGAAGCGATCACCTTCTTAG-TGAGATACAGAGAAGTTGACTAAAT
* *
39858 CAATGAAGCGATTATCTTCTTAGTGAGATACAGAGAAGTTGACTAAAT
1 CAATGAAGCGATCACCTTCTTAGTGAGATACAGAGAAGTTGACTAAAT
39906 CAATGAA
1 CAATGAA
39913 ACAAAGATCG
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
47 28 0.60
48 19 0.40
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (48 bp):
CAATGAAGCGATCACCTTCTTAGTGAGATACAGAGAAGTTGACTAAAT
Found at i:40225 original size:16 final size:17
Alignment explanation
Indices: 40204--40237 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
40194 AAAATTTAAT
40204 ACTACCCA-AACCCTAA
1 ACTACCCATAACCCTAA
*
40220 ACTACCCATGACCCTAA
1 ACTACCCATAACCCTAA
40237 A
1 A
40238 TATACAAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.41, C:0.41, G:0.03, T:0.15
Consensus pattern (17 bp):
ACTACCCATAACCCTAA
Found at i:40648 original size:2 final size:2
Alignment explanation
Indices: 40641--40665 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40631 TGTACATACA
40641 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.