Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012327.1 Kokia drynarioides strain JFW-HI SEQ_127329, 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: 4601
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.34
Found at i:1439 original size:22 final size:22
Alignment explanation
Indices: 1414--1460 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
1404 CTATAAAACA
*
1414 TTTGTAACTCTCTTCATAATGT
1 TTTGTAACTCTCCTCATAATGT
1436 TTTGTAACTCTCCTCATAATGT
1 TTTGTAACTCTCCTCATAATGT
1458 TTT
1 TTT
1461 ATTTTAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.09, T:0.51
Consensus pattern (22 bp):
TTTGTAACTCTCCTCATAATGT
Found at i:4143 original size:127 final size:129
Alignment explanation
Indices: 3890--4145 Score: 408
Period size: 127 Copynumber: 2.0 Consensus size: 129
3880 TTTCATTTGA
*
3890 TTAAACAACAATCACTACTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAAATC
1 TTAAACAACAATCACTACTTTACTTAAAAATCCAAACTTTTATTTCAAAATAGTTAAAAAAAATC
* *
3955 AAAATTTTGTTAAAAGCTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTTT
66 AAAACTTTGTTAAAAACTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTTT
* * * **
4019 TTAAAGAA-AATCACTACTTTGCTTAAAAATCGAAACTTTTATTTCAAAATAGTTTGAAAAAATC
1 TTAAACAACAATCACTACTTTACTTAAAAATCCAAACTTTTATTTCAAAATAGTTAAAAAAAATC
* *
4083 -AAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACATATTTTTATTTTTTT
66 AAAACTTTGTTAAAAACTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTTT
4146 AAAAATTTAA
Statistics
Matches: 117, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
127 59 0.50
128 51 0.44
129 7 0.06
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.41
Consensus pattern (129 bp):
TTAAACAACAATCACTACTTTACTTAAAAATCCAAACTTTTATTTCAAAATAGTTAAAAAAAATC
AAAACTTTGTTAAAAACTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTTT
Found at i:4189 original size:149 final size:149
Alignment explanation
Indices: 4014--4382 Score: 553
Period size: 150 Copynumber: 2.4 Consensus size: 149
4004 GATTTTTATT
* * *
4014 TTTTTTTAAAGAAAATCACTACTTTGCTTAAAAATCGAAACTTTTATTTCAAAATAGTTTGAAAA
1 TTTTTTTAAAGAAAATCACTATTTTGCTTAAAAATC-AAACTTTTATTTCGAAATAGTTAGAAAA
*
4079 AATC-AAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACATATTTTTATTTT
65 AATCAAAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACATATTTTT-TATT
*
4143 TTTAAAAATTTAAACTTTCTC
129 TTTAAAAATCTAAACTTTCTC
* *
4164 -TTTTTTAAAGAAAATCACCATTTTGCTTTAAAATCCAAACTTTTATTTCGAAATAGTTAGAAAA
1 TTTTTTTAAAGAAAATCACTATTTTGCTTAAAAAT-CAAACTTTTATTTCGAAATAGTTAGAAAA
4228 AATCAAAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACATATTTTTTATTT
65 AATCAAAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACATATTTTTTATTT
*
4293 TTAAAAATCTAAACTTTTTC
130 TTAAAAATCTAAACTTTCTC
* * * *
4313 TTTTTTTAAAGAAAATAATTATTTTACTTAAAAAATCAAAGCTTTTATTTCGAAATTATTTAAGA
1 TTTTTTTAAAGAAAATCACTATTTTGCTT-AAAAATCAAA-CTTTTATTTCGAAA-TAGTT-AGA
4378 AAAAA
62 AAAAA
4383 AACCAAAATA
Statistics
Matches: 198, Mismatches: 14, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
149 83 0.42
150 84 0.42
151 19 0.10
152 4 0.02
153 8 0.04
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.43
Consensus pattern (149 bp):
TTTTTTTAAAGAAAATCACTATTTTGCTTAAAAATCAAACTTTTATTTCGAAATAGTTAGAAAAA
ATCAAAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACATATTTTTTATTTT
TAAAAATCTAAACTTTCTC
Found at i:4273 original size:150 final size:149
Alignment explanation
Indices: 4014--4382 Score: 553
Period size: 149 Copynumber: 2.4 Consensus size: 149
4004 GATTTTTATT
* * * *
4014 TTTTTTTAAAGAAAATCACTACTTTGCTTAAAAATCGAAACTTTTATTTCAAAATAGTTTGAAAA
1 TTTTTTTAAAGAAAATCACTATTTTGCTTAAAAATCCAAACTTTTATTTCGAAATAGTTAGAAAA
*
4079 AATCAAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACATATTTTTATTTTT
66 AATCAAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACATATTTTT-TATTT
*
4144 TTAAAAATTTAAACTTTCTC
130 TTAAAAATCTAAACTTTCTC
* *
4164 -TTTTTTAAAGAAAATCACCATTTTGCTTTAAAATCCAAACTTTTATTTCGAAATAGTTAGAAAA
1 TTTTTTTAAAGAAAATCACTATTTTGCTTAAAAATCCAAACTTTTATTTCGAAATAGTTAGAAAA
4228 AATCAAAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACATATTTTTTATTT
66 AATC-AAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACATATTTTTTATTT
*
4293 TTAAAAATCTAAACTTTTTC
130 TTAAAAATCTAAACTTTCTC
* * * *
4313 TTTTTTTAAAGAAAATAATTATTTTACTTAAAAAAT-CAAAGCTTTTATTTCGAAATTATTTAAG
1 TTTTTTTAAAGAAAATCACTATTTTGCTT-AAAAATCCAAA-CTTTTATTTCGAAA-TAGTT-AG
4377 AAAAAA
62 AAAAAA
4383 AACCAAAATA
Statistics
Matches: 198, Mismatches: 15, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
149 84 0.42
150 83 0.42
151 19 0.10
152 4 0.02
153 8 0.04
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.43
Consensus pattern (149 bp):
TTTTTTTAAAGAAAATCACTATTTTGCTTAAAAATCCAAACTTTTATTTCGAAATAGTTAGAAAA
AATCAAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACATATTTTTTATTTT
TAAAAATCTAAACTTTCTC
Done.