Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007180.1 Kokia drynarioides strain JFW-HI SEQ_121793, 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: 12390
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:1464 original size:21 final size:21
Alignment explanation
Indices: 1438--1479 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1428 AAGATTGACA
1438 ATCTTAGATTTGATATGTAAT
1 ATCTTAGATTTGATATGTAAT
*
1459 ATCTTAGATTTGATATTTAAT
1 ATCTTAGATTTGATATGTAAT
1480 CTTTAGAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.50
Consensus pattern (21 bp):
ATCTTAGATTTGATATGTAAT
Found at i:4554 original size:25 final size:25
Alignment explanation
Indices: 4503--4554 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
4493 TATATATTAA
* *
4503 TTTGAATATAATATATTTTTAATAT
1 TTTGAATATAATATATTTATAAAAT
*
4528 TTTGAATATACTATA-TTATAACAAT
1 TTTGAATATAATATATTTATAA-AAT
4553 TT
1 TT
4555 GCTGCAGATC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (25 bp):
TTTGAATATAATATATTTATAAAAT
Found at i:8811 original size:24 final size:24
Alignment explanation
Indices: 8776--8823 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
8766 GATCTTTTGT
*
8776 TGGTAAAGACAGCTTCCAATGGAA
1 TGGTAAAAACAGCTTCCAATGGAA
8800 TGGTAAAAACAGCTTCCAATGGAA
1 TGGTAAAAACAGCTTCCAATGGAA
8824 GGGTTGTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.21
Consensus pattern (24 bp):
TGGTAAAAACAGCTTCCAATGGAA
Found at i:10223 original size:208 final size:208
Alignment explanation
Indices: 9781--10585 Score: 1087
Period size: 208 Copynumber: 3.9 Consensus size: 208
9771 TCTACTTGTT
* * * *
9781 TGTATCTCATCAGGAAGACGAATTTGGTTAATTTCTCTGCATCTCATCAGGAAGATGACCACTTT
1 TGTATCTCATCAAGAAGACGGATTTGGTTAACTTCTCTACATCTCATCAGGAAGATGACCACTTT
* * *
9846 ATTGATTTGACCCACTTCTCTGTATCTCATCAGGAAGATAGGGTTTGGAAGTTTCACTCACATTG
66 ATTGATTTGACCCACTTCTCTATATCTCATCAAGAAGATGGGGTTTGGAAGTTTCACTCACATTG
* * * * *
9911 AGCTTCACTTCGTTGACTTGGTCTACTTCTTTGTATCTCATCAAGACGATGACCACTTCATTGAT
131 AGCTTCACTTCGTTGAATTGGTCTACTTCTCTGTATCTCATCAGGAAGATGA-CGCTTCATTGAT
*
9976 TTAATCCACTTCTA
195 TTAATCCACTTCTC
* * * * *
9990 TGTATCTCATCAGGAAGAAGGATTTGGTTCACTTCTCTACATCTCGTTAGGAAGATGACCACTTT
1 TGTATCTCATCAAGAAGACGGATTTGGTTAACTTCTCTACATCTCATCAGGAAGATGACCACTTT
*
10055 ATTGATTTGACCCACTTCTCTGTATCTCATCAAGAAGATGGGGTTTGGAAG-TTCACTCACATTG
66 ATTGATTTGACCCACTTCTCTATATCTCATCAAGAAGATGGGGTTTGGAAGTTTCACTCACATTG
* * * *
10119 AGCTTAACTTCGTTTAATTGGTCTACTTTTTTGTATCTCATCAGGAAGATGATCGCTTCATTGAT
131 AGCTTCACTTCGTTGAATTGGTCTACTTCTCTGTATCTCATCAGGAAGATGA-CGCTTCATTGAT
*
10184 TTAATCCCCTTCTC
195 TTAATCCACTTCTC
* * * * *
10198 TGTATCTCATCAAGAAGATGGATTTGGTTAACTTATCTGCATCTCGTCAGGAAGATGTCCACTTT
1 TGTATCTCATCAAGAAGACGGATTTGGTTAACTTCTCTACATCTCATCAGGAAGATGACCACTTT
* * *
10263 ATTGATTTGA-CCACTTCTCTATATCTCATCAGGAAGATGGGGTTTGAAAGTTTCATTCACATTG
66 ATTGATTTGACCCACTTCTCTATATCTCATCAAGAAGATGGGGTTTGGAAGTTTCACTCACATTG
* *
10327 AGCTTCACTTCGTTGAATTAGTCTACTTTTCTGTATCTCATCAGGAAGATGACTGCTTCATTGAT
131 AGCTTCACTTCGTTGAATTGGTCTACTTCTCTGTATCTCATCAGGAAGATGAC-GCTTCATTGAT
10392 TTAATCCACTTCTC
195 TTAATCCACTTCTC
* * *
10406 TGTATCTCATC-AGAAAGACGGATTT-GTTCTACTTCTCTATATCTCATCAGGAAGATGACCTCT
1 TGTATCTCATCAAG-AAGACGGATTTGGTT-AACTTCTCTACATCTCATCAGGAAGATGACCACT
* * * * **
10469 TAATTGCTTTGACCCACTTCTTTATATCTCATCAAGAAGATGGGGTTTCGAAGTTTCACTCGTAT
64 TTATTGATTTGACCCACTTCTCTATATCTCATCAAGAAGATGGGGTTTGGAAGTTTCACTCACAT
** * * ** *
10534 TGAGCTTTTCATCATTGTTTTGGTCTGCTTCTCTGTATCTCATCAGGAAGAT
129 TGAGCTTCACTTCGTTGAATTGGTCTACTTCTCTGTATCTCATCAGGAAGAT
10586 TACCTTTTGA
Statistics
Matches: 530, Mismatches: 61, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
207 43 0.08
208 292 0.55
209 195 0.37
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (208 bp):
TGTATCTCATCAAGAAGACGGATTTGGTTAACTTCTCTACATCTCATCAGGAAGATGACCACTTT
ATTGATTTGACCCACTTCTCTATATCTCATCAAGAAGATGGGGTTTGGAAGTTTCACTCACATTG
AGCTTCACTTCGTTGAATTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACGCTTCATTGATT
TAATCCACTTCTC
Done.