Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008379.1 Kokia drynarioides strain JFW-HI SEQ_123047, 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: 3527
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Found at i:1357 original size:28 final size:27
Alignment explanation
Indices: 1313--1389 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 27
1303 GTTTTTATAT
*
1313 TTTTTTAAATTTTAAAATTTAGCTCTT-A
1 TTTTTT-AATTTAAAAATTTAG-TCTTAA
1341 TATTTTTAATTTAAAAAATTTAGTCTTAA
1 T-TTTTTAATTT-AAAAATTTAGTCTTAA
* *
1370 TTTTTTTATTTCAAAATTTA
1 TTTTTTAATTTAAAAATTTA
1390 AATTCAACTG
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
27 8 0.19
28 19 0.44
29 16 0.37
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (27 bp):
TTTTTTAATTTAAAAATTTAGTCTTAA
Found at i:1841 original size:12 final size:12
Alignment explanation
Indices: 1824--1871 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
1814 GATATTTTTT
1824 TTTAATTTGGTA
1 TTTAATTTGGTA
**
1836 TTTAATTTTTTTTA
1 TTTAA--TTTGGTA
1850 TTTAATTTGGTA
1 TTTAATTTGGTA
1862 TTTAAATTTG
1 TTT-AATTTG
1872 ATAATTTTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
12 13 0.45
13 6 0.21
14 10 0.34
ACGTcount: A:0.25, C:0.00, G:0.10, T:0.65
Consensus pattern (12 bp):
TTTAATTTGGTA
Found at i:1878 original size:26 final size:26
Alignment explanation
Indices: 1824--1878 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
1814 GATATTTTTT
* ** *
1824 TTTAATTTGGTATTTAATTTTTTTTA
1 TTTAATTTGGTATTTAAATTTGATAA
1850 TTTAATTTGGTATTTAAATTTGATAA
1 TTTAATTTGGTATTTAAATTTGATAA
1876 TTT
1 TTT
1879 TTCTTAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (26 bp):
TTTAATTTGGTATTTAAATTTGATAA
Found at i:1880 original size:57 final size:57
Alignment explanation
Indices: 1797--1905 Score: 148
Period size: 57 Copynumber: 1.9 Consensus size: 57
1787 TTAATATAAT
* * * * *
1797 ATTTAGTATTTGAAATTGATATTTTTTTTTAATTTGGTATTTAATTTTTTTTATTTA
1 ATTTAGTATTTGAAATTGATAATTTTTCTTAATTTGATATCTAAATTTTTTTATTTA
*
1854 ATTTGGTATTT-AAATTTGATAATTTTTCTTAATTTGATATCTAAATTTTTTT
1 ATTTAGTATTTGAAA-TTGATAATTTTTCTTAATTTGATATCTAAATTTTTTT
1906 GGATCCAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
56 3 0.07
57 42 0.93
ACGTcount: A:0.28, C:0.02, G:0.08, T:0.62
Consensus pattern (57 bp):
ATTTAGTATTTGAAATTGATAATTTTTCTTAATTTGATATCTAAATTTTTTTATTTA
Found at i:1889 original size:31 final size:29
Alignment explanation
Indices: 1797--1901 Score: 94
Period size: 31 Copynumber: 3.6 Consensus size: 29
1787 TTAATATAAT
*
1797 ATTTAGTATTTGAAA-TTGATATTTTTTTTTA
1 ATTTGGTATTT-AAATTTGATA--TTTTTTTA
1828 ATTTGGTATTT-AATTT--T-TTTTATTTA
1 ATTTGGTATTTAAATTTGATATTTT-TTTA
1854 ATTTGGTATTTAAATTTGATAATTTTTCTTA
1 ATTTGGTATTTAAATTTGAT-ATTTTT-TTA
* *
1885 ATTTGATATCTAAATTT
1 ATTTGGTATTTAAATTT
1902 TTTTGGATCC
Statistics
Matches: 63, Mismatches: 3, Indels: 16
0.77 0.04 0.20
Matches are distributed among these distances:
25 4 0.06
26 15 0.24
27 5 0.08
28 1 0.02
29 3 0.05
30 3 0.05
31 32 0.51
ACGTcount: A:0.29, C:0.02, G:0.09, T:0.61
Consensus pattern (29 bp):
ATTTGGTATTTAAATTTGATATTTTTTTA
Found at i:2202 original size:31 final size:30
Alignment explanation
Indices: 2167--2262 Score: 74
Period size: 31 Copynumber: 3.2 Consensus size: 30
2157 ATCAAGGTAC
2167 CAAATTAAGAAAAAATGTCAAGTTTAAGTGT
1 CAAATTAAGAAAAAAT-TCAAGTTTAAGTGT
* * *
2198 CAAATT-AGACCAAAAA--AAAGTTTAGGTGC
1 CAAATTAAGA--AAAAATTCAAGTTTAAGTGT
* *
2227 CAAATTAA-AAAAAAGTATCAAGTTTAAATAT
1 CAAATTAAGAAAAAA-T-TCAAGTTTAAGTGT
2258 CAAAT
1 CAAAT
2263 GTTATATTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 14
0.69 0.11 0.19
Matches are distributed among these distances:
27 5 0.10
29 17 0.34
30 4 0.08
31 19 0.38
32 5 0.10
ACGTcount: A:0.52, C:0.09, G:0.12, T:0.26
Consensus pattern (30 bp):
CAAATTAAGAAAAAATTCAAGTTTAAGTGT
Found at i:3397 original size:10 final size:10
Alignment explanation
Indices: 3222--3409 Score: 74
Period size: 9 Copynumber: 19.0 Consensus size: 10
3212 TATTTTTCTC
*
3222 ATAAAAAATC
1 ATAAAAAATT
*
3232 AT-ATAAATT
1 ATAAAAAATT
3241 ATAAAAAA--
1 ATAAAAAATT
3249 AT-AAAAA-T
1 ATAAAAAATT
* * *
3257 ATTAAAACTA
1 ATAAAAAATT
*
3267 ATATAAAATT
1 ATAAAAAATT
**
3277 AT-ACCAATT
1 ATAAAAAATT
*
3286 AT-AAAACTT
1 ATAAAAAATT
*
3295 ATAAAAAATC
1 ATAAAAAATT
3305 ATAAAAAACTT
1 ATAAAAAA-TT
3316 ATAAAAAAATTCT
1 AT-AAAAAA-T-T
3329 ACTAGTAATAAATT
1 A-TA--AA-AAATT
*
3343 ATAAAACATT
1 ATAAAAAATT
**
3353 -TAAAATTTT
1 ATAAAAAATT
*
3362 ATAAAAACTT
1 ATAAAAAATT
* *
3372 GT-AAGAATT
1 ATAAAAAATT
3381 CATAAAAAATT
1 -ATAAAAAATT
3392 AT-AAAAA-T
1 ATAAAAAATT
3400 ATAAAAAATT
1 ATAAAAAATT
3410 CTAATAAGAT
Statistics
Matches: 132, Mismatches: 29, Indels: 34
0.68 0.15 0.17
Matches are distributed among these distances:
7 5 0.04
8 7 0.05
9 45 0.34
10 43 0.33
11 11 0.08
12 7 0.05
13 5 0.04
14 3 0.02
15 3 0.02
16 3 0.02
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.31
Consensus pattern (10 bp):
ATAAAAAATT
Found at i:3405 original size:18 final size:20
Alignment explanation
Indices: 3382--3425 Score: 65
Period size: 18 Copynumber: 2.3 Consensus size: 20
3372 GTAAGAATTC
3382 ATAAAAAATTATAA-AA-AT
1 ATAAAAAATTATAATAAGAT
*
3400 ATAAAAAATTCTAATAAGAT
1 ATAAAAAATTATAATAAGAT
3420 ATAAAA
1 ATAAAA
3426 GTTAGAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 13 0.57
19 2 0.09
20 8 0.35
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (20 bp):
ATAAAAAATTATAATAAGAT
Done.