Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013297.1 Kokia drynarioides strain JFW-HI SEQ_128319, 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: 6217
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Warning! 69 characters in sequence are not A, C, G, or T
Found at i:110 original size:3 final size:3
Alignment explanation
Indices: 97--165 Score: 59
Period size: 3 Copynumber: 23.0 Consensus size: 3
87 CTTTCGGCTT
* *
97 TTA TT- TTA TTA TTA TTA ATA TTA CTAA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
** ** *
142 AAA GAA TTA TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
166 ATGCATTTAT
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
2 2 0.04
3 49 0.92
4 2 0.04
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:907 original size:23 final size:23
Alignment explanation
Indices: 888--938 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
878 CTTTTTAATA
* *
888 TTAAGTTTAAAATCAATTTAAAT
1 TTAAATTTAAAATAAATTTAAAT
*
911 TTAAATTTAAGATAAATTTAAAT
1 TTAAATTTAAAATAAATTTAAAT
934 TTAAA
1 TTAAA
939 AATAAATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (23 bp):
TTAAATTTAAAATAAATTTAAAT
Found at i:911 original size:6 final size:6
Alignment explanation
Indices: 902--951 Score: 59
Period size: 6 Copynumber: 8.5 Consensus size: 6
892 GTTTAAAATC
**
902 AATTTA AATTTA AATTTA AGA--TA AATTTA AATTTA AAAATA AATTTA
1 AATTTA AATTTA AATTTA A-ATTTA AATTTA AATTTA AATTTA AATTTA
949 AAT
1 AAT
952 CAATTTAAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
4 1 0.03
5 3 0.08
6 32 0.86
7 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (6 bp):
AATTTA
Found at i:913 original size:17 final size:18
Alignment explanation
Indices: 906--951 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
896 AAAATCAATT
*
906 TAAATTTAAATTT-AAGA
1 TAAATTTAAATTTAAAAA
923 TAAATTTAAATTTAAAAA
1 TAAATTTAAATTTAAAAA
941 TAAATTTAAAT
1 TAAATTTAAAT
952 CAATTTAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
TAAATTTAAATTTAAAAA
Found at i:934 original size:29 final size:28
Alignment explanation
Indices: 902--960 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 28
892 GTTTAAAATC
**
902 AATTTAAATTTAAATTTAAGATAAATTTA
1 AATTTAAAAATAAATTTAA-ATAAATTTA
*
931 AATTTAAAAATAAATTTAAATCAATTTA
1 AATTTAAAAATAAATTTAAATAAATTTA
959 AA
1 AA
961 CCCAACTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 10 0.37
29 17 0.63
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (28 bp):
AATTTAAAAATAAATTTAAATAAATTTA
Found at i:1492 original size:102 final size:102
Alignment explanation
Indices: 1237--1751 Score: 850
Period size: 102 Copynumber: 5.0 Consensus size: 102
1227 GACGTCGAGA
* *
1237 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACCTCCTATTGTTTTTAATCCAACTTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATTGTTTTTAATCCAACTTT
* ** *
1302 ACTGTAACTTCAAGAGGATATAAATTGACGTTTTTGAAG
66 ACTGCAACTTCAAGAGGATAGGAATTGA--TGTTTGAAG
* *
1341 CTTCATCCTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATTGTCTTTAATCCAACTTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATTGTTTTTAATCCAACTTT
*
1406 ACTGCAACTTCAAGAGGATAGGAATTGGTGTTTGAAG
66 ACTGCAACTTCAAGAGGATAGGAATTGATGTTTGAAG
* * *
1443 CTTTATCTTTCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATTGTTTTTAATCCCACTTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATTGTTTTTAATCCAACTTT
*
1508 ACTGCAACTTCAAGAGGATAGAAATTGATGTTTGAAG
66 ACTGCAACTTCAAGAGGATAGGAATTGATGTTTGAAG
*
1545 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAACACTTGCTATTGTTTTTAATCCAACTTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATTGTTTTTAATCCAACTTT
*
1610 ACTTCAACTTCAAGAGGATAGGAATTGATGTTTGAAG
66 ACTGCAACTTCAAGAGGATAGGAATTGATGTTTGAAG
* *
1647 CTTCATCTTGCTCTTACTACAACTTCAAAGAGATAAAGACTTGCTATTGTTTTTAATCCCACTTT
1 CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATTGTTTTTAATCCAACTTT
*
1712 ACTGCAACTTCAAGAGGATAGGAATTGATGTGTGAAG
66 ACTGCAACTTCAAGAGGATAGGAATTGATGTTTGAAG
1749 CTT
1 CTT
1752 TATCACCGTT
Statistics
Matches: 384, Mismatches: 27, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
102 299 0.78
104 85 0.22
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (102 bp):
CTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATTGTTTTTAATCCAACTTT
ACTGCAACTTCAAGAGGATAGGAATTGATGTTTGAAG
Done.