Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014232.1 Kokia drynarioides strain JFW-HI SEQ_129265, 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: 20596
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:5702 original size:11 final size:11
Alignment explanation
Indices: 5686--5714 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
5676 TTTGTTTATG
5686 TTTTTTTTTTC
1 TTTTTTTTTTC
5697 TTTTTTTTTTC
1 TTTTTTTTTTC
5708 TTTTTTT
1 TTTTTTT
5715 AAAAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:7243 original size:26 final size:25
Alignment explanation
Indices: 7205--7278 Score: 96
Period size: 26 Copynumber: 2.8 Consensus size: 25
7195 ATGTCACTGG
*
7205 CTCAAGGCCTGCTACTTAATCACCGA
1 CTCAAGGCTTGCTA-TTAATCACCGA
7231 CTCGAA-GCTTGCTATTTAATCACCGA
1 CTC-AAGGCTTGCTA-TTAATCACCGA
7257 CTCAAGGCTTGCTATATAATCA
1 CTCAAGGCTTGCTAT-TAATCA
7279 TCTCTTTTCT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
25 3 0.07
26 38 0.88
27 2 0.05
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.28
Consensus pattern (25 bp):
CTCAAGGCTTGCTATTAATCACCGA
Found at i:10471 original size:401 final size:400
Alignment explanation
Indices: 9723--10516 Score: 1318
Period size: 401 Copynumber: 2.0 Consensus size: 400
9713 TCTCCTATTT
*
9723 GGGTGTTCTTGTTGCTCAATTCCAAATCAATCTTCTAAGCCTCACAAATTTCTTGGAAAAACATC
1 GGGTCTTCTTGTTGCTCAATTCCAAATCAATCTTCTAAGCCTCACAAATTTCTTGGAAAAACATC
* *
9788 ACTTTAGCTTTTTATTCGGCTAAAACAAAACCGTCATGATTGCATGACAACTGCGTACACATAGC
66 ACTTTAGCTTTTCATTCGGCTAAAACAAAACCGTCATGATTCCATGACAACTGCGTACACATAGC
* * *
9853 TCGTAAAGAAAATAAAGACTTTTGGCTCAAAGCGTCAGTAACAATATTGGCCTTGCCCGGATGAT
131 TCATAAAGAAAATAAAGACTTTCGGCTCAAAGCGTCAGCAACAATATTGGCCTTGCCCGGATGAT
* * *
9918 ATTCGATAACTGAGTCATAATCTTTCAACAATTCTAACCATCTCCGTTACCGTAGATTAAGCTCT
196 ATTCGATAACCGAGTCATAATATTTCAACAATTCTAACCATCTCCGTTACCATAGATTAAGCTCT
** **
9983 TTTTGCGACATCAAATATTTCAATCTTTTATGATTTGTAAAAATACAACATTTTTCTCCGTACAA
261 TTTTGCGACATCAAATATTTCAAGATTTTATGATTTGTAAAAATACAACATTTTTCTCCACACAA
* *
10048 ATAATGTCGCCATATTTTTAATGCAAAAACTATTGCCGCAAGTTCCAAATCATGTGTAGGGTAAT
326 ATAATGTCGCCATATTTTTAATGCAAAAACTATTGCCCCAAGTTCCAAATCATATG-AGGGTAAT
10113 TTCTCGTATCC
390 TTCTCGTATCC
* * *
10124 GGGTCTTCTTGTTGCTCAATTCCAAATCATTCTTTTGAGCCTCACAAATTTCTTGGAAAAACATC
1 GGGTCTTCTTGTTGCTCAATTCCAAATCAATCTTCTAAGCCTCACAAATTTCTTGGAAAAACATC
* * * *
10189 GCTTTAGCTTTTCATTCGTCTAAAACAAAACCGTCTTGATTCCATGACAACTGCTTACACATAGC
66 ACTTTAGCTTTTCATTCGGCTAAAACAAAACCGTCATGATTCCATGACAACTGCGTACACATAGC
* *
10254 TCATAAAGAAAATAAAGACTTTCGGCTCAAGGTGTCAGCAACAATATTGGCCTTGCCCGGATGAT
131 TCATAAAGAAAATAAAGACTTTCGGCTCAAAGCGTCAGCAACAATATTGGCCTTGCCCGGATGAT
* *
10319 ATTTGATAACCGAGTCATAATATTTCAACAATTCTAACCATCTCCGTTGCCATAGATTAAGCTCT
196 ATTCGATAACCGAGTCATAATATTTCAACAATTCTAACCATCTCCGTTACCATAGATTAAGCTCT
*
10384 TTTTGCGACATCAAATATTTCAAGATTTTATGATTTGTAAAAATACGACATTTTTCTCCACACAA
261 TTTTGCGACATCAAATATTTCAAGATTTTATGATTTGTAAAAATACAACATTTTTCTCCACACAA
* *
10449 ATAATGTCGCCATATTTTTAATGTAAAAACTATTGCCCCAAGTTCCAAATCATATGGGGGTAATT
326 ATAATGTCGCCATATTTTTAATGCAAAAACTATTGCCCCAAGTTCCAAATCATATGAGGGTAATT
10514 TCT
391 TCT
10517 TTCATGCGAT
Statistics
Matches: 364, Mismatches: 29, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
400 11 0.03
401 353 0.97
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (400 bp):
GGGTCTTCTTGTTGCTCAATTCCAAATCAATCTTCTAAGCCTCACAAATTTCTTGGAAAAACATC
ACTTTAGCTTTTCATTCGGCTAAAACAAAACCGTCATGATTCCATGACAACTGCGTACACATAGC
TCATAAAGAAAATAAAGACTTTCGGCTCAAAGCGTCAGCAACAATATTGGCCTTGCCCGGATGAT
ATTCGATAACCGAGTCATAATATTTCAACAATTCTAACCATCTCCGTTACCATAGATTAAGCTCT
TTTTGCGACATCAAATATTTCAAGATTTTATGATTTGTAAAAATACAACATTTTTCTCCACACAA
ATAATGTCGCCATATTTTTAATGCAAAAACTATTGCCCCAAGTTCCAAATCATATGAGGGTAATT
TCTCGTATCC
Found at i:14727 original size:26 final size:26
Alignment explanation
Indices: 14666--14747 Score: 103
Period size: 26 Copynumber: 3.2 Consensus size: 26
14656 CACCAACTGT
* * * *
14666 TCACCGACTCAAAGCCTGCTAAAT-G
1 TCACCGGCTCGAAGCCTGCTATATAA
* *
14691 TCACTGGCTCGAAGCCTGCTATTTAA
1 TCACCGGCTCGAAGCCTGCTATATAA
14717 TCACCGGCTCGAAGCCTGCTATATAA
1 TCACCGGCTCGAAGCCTGCTATATAA
14743 TCACC
1 TCACC
14748 TCTTTTCTAA
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
25 19 0.40
26 29 0.60
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.24
Consensus pattern (26 bp):
TCACCGGCTCGAAGCCTGCTATATAA
Found at i:16381 original size:30 final size:30
Alignment explanation
Indices: 16340--16433 Score: 82
Period size: 30 Copynumber: 3.4 Consensus size: 30
16330 TGGAGTCGTT
16340 GTATCGGTAGAACTCTGAGGGTTTCATTTG
1 GTATCGGTAGAACTCTGAGGGTTTCATTTG
* *
16370 GTATTGGTAGAAC-C-CA-----TCA---G
1 GTATCGGTAGAACTCTGAGGGTTTCATTTG
16390 AGTATCGGTAGAACTCTGAGGGTTTCATTTG
1 -GTATCGGTAGAACTCTGAGGGTTTCATTTG
*
16421 GTATTGGTAGAAC
1 GTATCGGTAGAAC
16434 CCATCAGAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 22
0.64 0.07 0.29
Matches are distributed among these distances:
20 1 0.02
21 12 0.25
22 1 0.02
23 4 0.08
28 4 0.08
29 1 0.02
30 24 0.50
31 1 0.02
ACGTcount: A:0.24, C:0.14, G:0.29, T:0.33
Consensus pattern (30 bp):
GTATCGGTAGAACTCTGAGGGTTTCATTTG
Found at i:16416 original size:51 final size:51
Alignment explanation
Indices: 16340--16453 Score: 219
Period size: 51 Copynumber: 2.2 Consensus size: 51
16330 TGGAGTCGTT
16340 GTATCGGTAGAACTCTGAGGGTTTCATTTGGTATTGGTAGAACCCATCAGA
1 GTATCGGTAGAACTCTGAGGGTTTCATTTGGTATTGGTAGAACCCATCAGA
16391 GTATCGGTAGAACTCTGAGGGTTTCATTTGGTATTGGTAGAACCCATCAGA
1 GTATCGGTAGAACTCTGAGGGTTTCATTTGGTATTGGTAGAACCCATCAGA
*
16442 GTATCAGTAGAA
1 GTATCGGTAGAA
16454 GTGCAAAGGA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 62 1.00
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (51 bp):
GTATCGGTAGAACTCTGAGGGTTTCATTTGGTATTGGTAGAACCCATCAGA
Done.