Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008673.1 Kokia drynarioides strain JFW-HI SEQ_123355, 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: 9228
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Found at i:1344 original size:14 final size:14
Alignment explanation
Indices: 1327--1365 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1317 TTCAATATTA
*
1327 TTAAACATATATAT
1 TTAATCATATATAT
* *
1341 TTAATTATTTATAT
1 TTAATCATATATAT
1355 TTAATCATATA
1 TTAATCATATA
1366 ATAAATTATT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (14 bp):
TTAATCATATATAT
Found at i:1412 original size:16 final size:19
Alignment explanation
Indices: 1364--1413 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 19
1354 TTTAATCATA
1364 TAATAAATTATTAGTATAAT
1 TAATAAATTATTAGTAT-AT
1384 TAATATAATTTATTA-T-T-T
1 TAATA-AA-TTATTAGTATAT
1402 TAATAAATTATT
1 TAATAAATTATT
1414 TAATATTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
16 5 0.18
17 2 0.07
18 6 0.21
20 6 0.21
21 3 0.11
22 6 0.21
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TAATAAATTATTAGTATAT
Found at i:1522 original size:15 final size:15
Alignment explanation
Indices: 1502--1559 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
1492 ATTCAATATT
1502 AATATTTTAATAATA
1 AATATTTTAATAATA
*
1517 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
* *
1536 AATATATTCATAATA
1 AATATTTTAATAATA
1551 AATATTTTA
1 AATATTTTA
1560 TAGTATAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:2333 original size:7 final size:7
Alignment explanation
Indices: 2323--2368 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
2313 TAGATTTTGG
*
2323 ATTTCGA
1 ATTTCAA
2330 ATTTCAA
1 ATTTCAA
2337 ATTTCAA
1 ATTTCAA
**
2344 ATTTTGA
1 ATTTCAA
*
2351 ATTTTAA
1 ATTTCAA
2358 ATTTCAA
1 ATTTCAA
2365 ATTT
1 ATTT
2369 TTGATGTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.37, C:0.09, G:0.04, T:0.50
Consensus pattern (7 bp):
ATTTCAA
Found at i:2369 original size:21 final size:21
Alignment explanation
Indices: 2323--2369 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
2313 TAGATTTTGG
*
2323 ATTTCGAATTTCAAATTTCAA
1 ATTTTGAATTTCAAATTTCAA
*
2344 ATTTTGAATTTTAAATTTCAA
1 ATTTTGAATTTCAAATTTCAA
2365 ATTTT
1 ATTTT
2370 TGATGTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.51
Consensus pattern (21 bp):
ATTTTGAATTTCAAATTTCAA
Found at i:5310 original size:12 final size:12
Alignment explanation
Indices: 5293--5317 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5283 TTTCATCATC
5293 ACCATTGCCATT
1 ACCATTGCCATT
5305 ACCATTGCCATT
1 ACCATTGCCATT
5317 A
1 A
5318 TCGTATGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.32, G:0.08, T:0.32
Consensus pattern (12 bp):
ACCATTGCCATT
Done.