Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007659.1 Kokia drynarioides strain JFW-HI SEQ_122290, 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: 21800
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:1874 original size:7 final size:7
Alignment explanation
Indices: 1862--1888 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1852 AATCCTTTTG
1862 TCCCAAT
1 TCCCAAT
1869 TCCCAAT
1 TCCCAAT
1876 TCCCAAT
1 TCCCAAT
1883 TCCCAA
1 TCCCAA
1889 ACCCCAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.44, G:0.00, T:0.26
Consensus pattern (7 bp):
TCCCAAT
Found at i:2933 original size:20 final size:19
Alignment explanation
Indices: 2895--2933 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
2885 ACAATTATTA
* *
2895 TAGAATAAATTTATTAAAT
1 TAGAATAAATTGATAAAAT
2914 TAGAATTAAATTGATAAAAT
1 TAGAA-TAAATTGATAAAAT
2934 ATTTAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (19 bp):
TAGAATAAATTGATAAAAT
Found at i:10488 original size:435 final size:435
Alignment explanation
Indices: 9738--10609 Score: 1248
Period size: 435 Copynumber: 2.0 Consensus size: 435
9728 AGAGCTTCAA
* * *
9738 CTTTGTGATAAAATATGAGTAATTGAACCATTAGAAACATATAAAATGGCTACCTTTTTTCCTAT
1 CTTTGTGATAAAATATGAGTAATTGAACCATCAGAAACATATAAAATGACTACCGTTTTTCCTAT
* * * * *
9803 AAAGTGGTTACCCTTGAGGAAGCTTTAGCGATGAATTTCTTTAAGAATTATCTTTTGATAGTTAA
66 AAAATGGCTACCCTTGAGGAAGCTTTAGCAATGAATTTCTTTAAGAACTATATTTTGATAGTTAA
* * * *
9868 ACTTTGCAAATGGAGCTCTTGATATCTTAAAGACATGCCCAATTTTTGTTGCACAAAATTATGCT
131 ACTTTGCAAATGGAGCTCTTGATAACTTAAAGACATACCCAATTTTCGATGCACAAAATTATGCT
** * * *
9933 AATATTCCAGGCAATTAATAGTTTTCCATAAGTCTATCAATGCACCACAAGTGGACCCTCAATCT
196 AATATTCCAAACAATTAATAATCTTCAATAAGTCTATCAATGCACCACAAGTGGACCCTCAATCT
* * * * * *
9998 GACTCAAAGGAAACCATCCGTACATCTTTCAGGTTACTTTATCGGGATGAAAAAAAACTAGTTGA
261 GACTCAAAGGAAACCATCCGAACATCTTTCAAGTTACTTCATCGAGATAAAAAAAAACTACTTGA
* * *
10063 T-CTTACAAATCCTTGCCAAAGAAAATAGAGAGCATAAGGATTCGTAGCACTCTTTATTATCCTC
326 TCCTT-CAAATCCTCGCCAAAGAAAATAGAGAGCATAAAGATTCGTAGCACTCTTCATTATCCTC
* * *
10127 CACTAAGATAAATTCTTGAAGAAGTACTATTCATTGAGGGAACACT
390 CACCAAGATAAATTCTTGAAGAAGTACTACTCATTAAGGGAACACT
*
10173 CTTTGTGATAGAATATGAGTAATTGAACCATCAGAAACATATAAAATGACTACCGTTTTTCCTAT
1 CTTTGTGATAAAATATGAGTAATTGAACCATCAGAAACATATAAAATGACTACCGTTTTTCCTAT
* * *
10238 AAAATGGCTACCCTTTAGGAAGCTTTAGCAACT-AATTTCTTTAAGACCTATATTTTGGTAGTTA
66 AAAATGGCTACCCTTGAGGAAGCTTTAGCAA-TGAATTTCTTTAAGAACTATATTTTGATAGTTA
* * *
10302 AATTTTGCATATGGAGCTCTTGATAACTTAAAGATC-TACCCAATTTTCGATGCACGAAATTATG
130 AACTTTGCAAATGGAGCTCTTGATAACTTAAAGA-CATACCCAATTTTCGATGCACAAAATTATG
* *
10366 CTCATATTCCAAACAATTAATAATCTTCAATAAGTCTATCAATGCACCACATGTGGACCC-CTAA
194 CTAATATTCCAAACAATTAATAATCTTCAATAAGTCTATCAATGCACCACAAGTGGACCCTC-AA
* * * * * *
10430 TCTGGCTCAAAGGTAACCATCTGAACATTTTTCAAGTTAGTTCATCTAGATAAAAAAAAACTACT
258 TCTGACTCAAAGGAAACCATCCGAACATCTTTCAAGTTACTTCATCGAGATAAAAAAAAACTACT
*
10495 TGATCCTTCAAATCCTCGCCAAAGAAAATAGCGAGCATAAAGATTCGTAGCACTCTTCATTATCC
323 TGATCCTTCAAATCCTCGCCAAAGAAAATAGAGAGCATAAAGATTCGTAGCACTCTTCATTATCC
* * *
10560 TCCACCAATATAGATTCTTGAAGAAGTACTACTCATTAAGGGAATACT
388 TCCACCAAGATAAATTCTTGAAGAAGTACTACTCATTAAGGGAACACT
10608 CT
1 CT
10610 AAGATAGATT
Statistics
Matches: 385, Mismatches: 48, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
434 1 0.00
435 379 0.98
436 5 0.01
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (435 bp):
CTTTGTGATAAAATATGAGTAATTGAACCATCAGAAACATATAAAATGACTACCGTTTTTCCTAT
AAAATGGCTACCCTTGAGGAAGCTTTAGCAATGAATTTCTTTAAGAACTATATTTTGATAGTTAA
ACTTTGCAAATGGAGCTCTTGATAACTTAAAGACATACCCAATTTTCGATGCACAAAATTATGCT
AATATTCCAAACAATTAATAATCTTCAATAAGTCTATCAATGCACCACAAGTGGACCCTCAATCT
GACTCAAAGGAAACCATCCGAACATCTTTCAAGTTACTTCATCGAGATAAAAAAAAACTACTTGA
TCCTTCAAATCCTCGCCAAAGAAAATAGAGAGCATAAAGATTCGTAGCACTCTTCATTATCCTCC
ACCAAGATAAATTCTTGAAGAAGTACTACTCATTAAGGGAACACT
Found at i:14711 original size:77 final size:77
Alignment explanation
Indices: 14578--14722 Score: 211
Period size: 77 Copynumber: 1.9 Consensus size: 77
14568 AGACCTGCTC
* * * * *
14578 ATGGGCTGGGCCACTCTACCTGGTCCAGAGGCTCACTCGAAAAGTGGGAGGATTTGGGTAAAAAT
1 ATGGGCTGAGCCACTCGACCTGGTCCAAAGGCCCACTCGAAAAGTGAGAGGATTTGGGTAAAAAT
14643 ATAGGCTCGAAA
66 ATAGGCTCGAAA
* *
14655 ATGGGCTGAGCCACTCGACCTGG-CCTAAAGGCCCACTTGAAAAGTGAGAGGGTTTGGGTAAAAA
1 ATGGGCTGAGCCACTCGACCTGGTCC-AAAGGCCCACTCGAAAAGTGAGAGGATTTGGGTAAAAA
14719 TATA
65 TATA
14723 AACCTGAAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
76 2 0.03
77 58 0.97
ACGTcount: A:0.30, C:0.19, G:0.30, T:0.21
Consensus pattern (77 bp):
ATGGGCTGAGCCACTCGACCTGGTCCAAAGGCCCACTCGAAAAGTGAGAGGATTTGGGTAAAAAT
ATAGGCTCGAAA
Done.