Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008433.1 Kokia drynarioides strain JFW-HI SEQ_123104, 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: 13611
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:2995 original size:11 final size:12
Alignment explanation
Indices: 2970--2998 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
2960 GATAATGCTT
2970 AATTCTTTCTGA
1 AATTCTTTCTGA
2982 AATTCTTT-TGA
1 AATTCTTTCTGA
2993 AATTCT
1 AATTCT
2999 ATCATTTGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.52
Consensus pattern (12 bp):
AATTCTTTCTGA
Found at i:7199 original size:30 final size:30
Alignment explanation
Indices: 7165--7231 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
7155 AATTTAATAG
* *
7165 TTAAACTCGACA-CTTTTCCTAATTTGGTAC
1 TTAAACTCGACACCTTTT-CTAAGTTGATAC
* *
7195 TTAAACTTGATACCTTTTCTAAGTTGATAC
1 TTAAACTCGACACCTTTTCTAAGTTGATAC
7225 TTAAACT
1 TTAAACT
7232 TTTGAGGTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 27 0.84
31 5 0.16
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.42
Consensus pattern (30 bp):
TTAAACTCGACACCTTTTCTAAGTTGATAC
Found at i:7528 original size:28 final size:27
Alignment explanation
Indices: 7494--7548 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
7484 AAAAAATGCC
*
7494 AAGTTCAAGTACCAAATTGGGTAAAAAA
1 AAGTTCAAGTACCAAATTAGG-AAAAAA
* *
7522 AAGTTCAGGTACTAAATTAGGAAAAAA
1 AAGTTCAAGTACCAAATTAGGAAAAAA
7549 TGTTAAGTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.51, C:0.09, G:0.18, T:0.22
Consensus pattern (27 bp):
AAGTTCAAGTACCAAATTAGGAAAAAA
Found at i:8182 original size:63 final size:63
Alignment explanation
Indices: 8083--8262 Score: 196
Period size: 63 Copynumber: 2.9 Consensus size: 63
8073 ATATATTAAA
* * *
8083 AAAATAAAAAATAATATTATATTAGTAGAGGGTTATCAAATGGTGACACTACAGGGAAAAAAAT
1 AAAA-AAAAAATAATATTATATTAGTAGAAGATTATCAAATGGTGGCACTACAGGGAAAAAAAT
**
8147 AAAAAAAAAATAATATTATATTAGTAGAAGATTATCAAATGACGGCA-TCACAGGG--AAAAAT
1 AAAAAAAAAATAATATTATATTAGTAGAAGATTATCAAATGGTGGCACT-ACAGGGAAAAAAAT
* * * *
8208 ----AAAAAATAATATTATATTAAT-GGAGAATTATTAAATGGTGGCACTATAGGGAAAA
1 AAAAAAAAAATAATATTATATTAGTAGAAG-ATTATCAAATGGTGGCACTACAGGGAAAA
8263 TTATACAAAA
Statistics
Matches: 100, Mismatches: 11, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
56 3 0.03
57 39 0.39
58 1 0.01
59 2 0.02
61 6 0.06
62 1 0.01
63 44 0.44
64 4 0.04
ACGTcount: A:0.52, C:0.06, G:0.17, T:0.26
Consensus pattern (63 bp):
AAAAAAAAAATAATATTATATTAGTAGAAGATTATCAAATGGTGGCACTACAGGGAAAAAAAT
Found at i:8395 original size:25 final size:25
Alignment explanation
Indices: 8317--8397 Score: 87
Period size: 25 Copynumber: 3.2 Consensus size: 25
8307 ATAAAATAAA
8317 TAAAAACATTAAATAACAAATCAAT
1 TAAAAACATTAAATAACAAATCAAT
* * *
8342 T-AAAA-ATTAAATTCACTCAA-CTAAA
1 TAAAAACATTAAA-TAAC-AAATC-AAT
8367 TAAAAACATTAAATAACAAATCAAT
1 TAAAAACATTAAATAACAAATCAAT
8392 TAAAAA
1 TAAAAA
8398 TTAAATTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
23 6 0.14
24 8 0.18
25 16 0.36
26 8 0.18
27 6 0.14
ACGTcount: A:0.63, C:0.12, G:0.00, T:0.25
Consensus pattern (25 bp):
TAAAAACATTAAATAACAAATCAAT
Found at i:8411 original size:25 final size:24
Alignment explanation
Indices: 8310--8403 Score: 93
Period size: 24 Copynumber: 3.9 Consensus size: 24
8300 AAATTATATA
8310 AAATAAATAAAAACATTAAATAAC
1 AAATAAATAAAAACATTAAATAAC
* * *
8334 AAATCAATTAAAA-ATTAAATTCACTC
1 AAATAAATAAAAACATTAAA-T-A-AC
*
8360 AACTAAATAAAAACATTAAATAAC
1 AAATAAATAAAAACATTAAATAAC
* *
8384 AAATCAATTAAAA-ATTAAAT
1 AAATAAATAAAAACATTAAAT
8404 TAAACAAAAC
Statistics
Matches: 56, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
23 13 0.23
24 23 0.41
25 2 0.04
26 12 0.21
27 6 0.11
ACGTcount: A:0.64, C:0.11, G:0.00, T:0.26
Consensus pattern (24 bp):
AAATAAATAAAAACATTAAATAAC
Found at i:8417 original size:30 final size:32
Alignment explanation
Indices: 8381--8445 Score: 82
Period size: 30 Copynumber: 2.1 Consensus size: 32
8371 AACATTAAAT
*
8381 AACAAATCAA-TTAAAA-ATTAAAT-TAAACAA
1 AACAAAT-AACTTAAAACAATAAATATAAACAA
8411 AACAAATAACTTAAAACAATAAATACTAAACAA
1 AACAAATAACTTAAAACAATAAATA-TAAACAA
8444 AA
1 AA
8446 TATAACTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 2 0.07
30 13 0.43
31 6 0.20
33 9 0.30
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.20
Consensus pattern (32 bp):
AACAAATAACTTAAAACAATAAATATAAACAA
Found at i:8418 original size:50 final size:50
Alignment explanation
Indices: 8300--8419 Score: 170
Period size: 50 Copynumber: 2.4 Consensus size: 50
8290 GAACACTGAA
* * *
8300 AAATTATATAAAATAAATAAAAACATTAAATAACAAATCAATTAAAAATT
1 AAATTAAACAAAACAAATAAAAACATTAAATAACAAATCAATTAAAAATT
* **
8350 AAATT-CACTCAACTAAATAAAAACATTAAATAACAAATCAATTAAAAATT
1 AAATTAAACAAAAC-AAATAAAAACATTAAATAACAAATCAATTAAAAATT
8400 AAATTAAACAAAACAAATAA
1 AAATTAAACAAAACAAATAA
8420 CTTAAAACAA
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
49 3 0.05
50 52 0.87
51 5 0.08
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.25
Consensus pattern (50 bp):
AAATTAAACAAAACAAATAAAAACATTAAATAACAAATCAATTAAAAATT
Found at i:8838 original size:78 final size:81
Alignment explanation
Indices: 8697--8850 Score: 233
Period size: 78 Copynumber: 1.9 Consensus size: 81
8687 TTTTCTCTGT
* *
8697 AGTGTCGCCATTTGATAACCCTCCATTAATATAATAATAATATTATTTATTTATTTAATATATAA
1 AGTGCCGCCATTTGATAACCATCCATTAATATAATAAT-ATATTATTTATTTATTTAATATATAA
8762 ATATAAAAAAACCCCGG
65 ATATAAAAAAACCCCGG
* * *
8779 AGTGCCGCCATTTGAT-ACCATCTATTAATATAAT-AT-TATTTTTTATTTTTTTAATATATAAA
1 AGTGCCGCCATTTGATAACCATCCATTAATATAATAATATATTATTTATTTATTTAATATATAAA
8841 TATAAAAAAA
66 TATAAAAAAA
8851 TTCGTGTCAA
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
78 34 0.51
80 2 0.03
81 16 0.24
82 15 0.22
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.40
Consensus pattern (81 bp):
AGTGCCGCCATTTGATAACCATCCATTAATATAATAATATATTATTTATTTATTTAATATATAAA
TATAAAAAAACCCCGG
Done.