Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011203.1 Kokia drynarioides strain JFW-HI SEQ_126180, 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: 12980
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.34
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:46 original size:34 final size:32
Alignment explanation
Indices: 7--75 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
1 TATTAA
*
7 ATAATAAATAGAT-AGTTAATGAACATATTAATAT
1 ATAATAAATA-ATAAGTAAAT--ACATATTAATAT
*
41 ATAATAAATAATAAGTAAATATATATTAATAT
1 ATAATAAATAATAAGTAAATACATATTAATAT
73 ATA
1 ATA
76 TTTATATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 14 0.44
33 2 0.06
34 16 0.50
ACGTcount: A:0.57, C:0.01, G:0.06, T:0.36
Consensus pattern (32 bp):
ATAATAAATAATAAGTAAATACATATTAATAT
Found at i:1506 original size:191 final size:192
Alignment explanation
Indices: 1182--1933 Score: 822
Period size: 201 Copynumber: 3.8 Consensus size: 192
1172 ACTTGGCCTT
* * * *
1182 CTTCTCAGTATCTCATCAGGAAGCTAACCGTTTATTGCTTCGACTTGCTTCTCTGTGTCTCATCA
1 CTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGTTTCTCAGTGTCTCATCA
*
1247 GGAAGCTGGGATTCGAAGATTTGCTCACGTCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTAT
66 GGAAGCTGGGATTCGAAGATTTGCTCACGTC-AGCGTGAGTTTGATTTGGTCTTCTTCTCAGTAT
* * *
1312 CTCATCAAGAAGATGACCGCGTCTTTTGTTTCAACTCGCTTCTCTG-T-ACGAATTTGGTCCA
130 CTCATCAGGAAGATGACCGCGTCTTTTGTTTCAATTCGCTTCTCTGTTAACGAATTTGGTCCG
* *
1373 CTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTCCTTCGACCTGTTTCTCGGTGTCTCATCA
1 CTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGTTTCTCAGTGTCTCATCA
** *
1438 GGAAGCTAAGATTCAAAGATTTGCTCACGTCGAGCGTGAGTTTGATTTGGTCTTCTTCTCAGTAT
66 GGAAGCTGGGATTCGAAGATTTGCTCACGTC-AGCGTGAGTTTGATTTGGTCTTCTTCTCAGTAT
*
1503 CTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATTCGCTTCTCTGTATCTCATCAAGAAGACGA
130 CTCATCAGGAAGATGACCGCGTCTTTTGTTTCAATTCGCTTCTCTG----T--T-----A-ACGA
*
1568 ATTTGGTTCG
183 ATTTGGTCCG
* * * *
1578 CTTCTAAGTATCTCATCAGGAAACTAACCTTTTATTGCTTCGACCTATTTCCCAGTGTCTCATCA
1 CTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGTTTCTCAGTGTCTCATCA
* * * * *
1643 GGAAGCTGGGGTTCGAAGATTTGTTCA---CATCGT-AGATTTGATTTGGTCTTCTTCTTAGTGT
66 GGAAGCTGGGATTCGAAGATTTGCTCACGTCAGCGTGAG-TTTGATTTGGTCTTCTTCTCAGTAT
* * *
1704 CTCATCACGAAGATGACTGCGT-TGTTTGTTTCAATTCGCTTCTCTGTATCTCATCAAGAAGACA
130 CTCATCAGGAAGATGACCGCGTCT-TTTGTTTCAATTCGCTTCTCTG----T--T-----A-ACG
1768 AATTTGGTCCG
182 AATTTGGTCCG
* * * * *
1779 CTTCTTAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACTTGTTCCTTAGTGTCTTATCA
1 CTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGTTTCTCAGTGTCTCATCA
* * * * * * *
1844 AGAAGCTGGGGTTCGAAGATTTGTTCACATCA-TG-GA-TTTGATTTGGTCTTATTCTCAGCATC
66 GGAAGCTGGGATTCGAAGATTTGCTCACGTCAGCGTGAGTTTGATTTGGTCTTCTTCTCAGTATC
*
1906 TCATCAGGAAGATGACCGCGTCATTTGT
131 TCATCAGGAAGATGACCGCGTCTTTTGT
1934 GGGTAATCAC
Statistics
Matches: 490, Mismatches: 50, Indels: 32
0.86 0.09 0.06
Matches are distributed among these distances:
191 164 0.33
198 1 0.00
200 2 0.00
201 225 0.46
202 1 0.00
203 2 0.00
204 2 0.00
205 93 0.19
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.37
Consensus pattern (192 bp):
CTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGTTTCTCAGTGTCTCATCA
GGAAGCTGGGATTCGAAGATTTGCTCACGTCAGCGTGAGTTTGATTTGGTCTTCTTCTCAGTATC
TCATCAGGAAGATGACCGCGTCTTTTGTTTCAATTCGCTTCTCTGTTAACGAATTTGGTCCG
Found at i:5073 original size:32 final size:32
Alignment explanation
Indices: 5032--5095 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
5022 GACATTCATC
5032 ATCCCATACACCCGGGTTACGCTTTCTAAGCA
1 ATCCCATACACCCGGGTTACGCTTTCTAAGCA
5064 ATCCCATACACCCGGGTTACGCTTTCTAAGCA
1 ATCCCATACACCCGGGTTACGCTTTCTAAGCA
5096 GGTGGAAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.25
Consensus pattern (32 bp):
ATCCCATACACCCGGGTTACGCTTTCTAAGCA
Done.