Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014592.1 Kokia drynarioides strain JFW-HI SEQ_129631, 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: 33390
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:1410 original size:14 final size:14
Alignment explanation
Indices: 1391--1418 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1381 TTATTTATTT
1391 GGTTATATGATCTA
1 GGTTATATGATCTA
1405 GGTTATATGATCTA
1 GGTTATATGATCTA
1419 CATTTCAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.43
Consensus pattern (14 bp):
GGTTATATGATCTA
Found at i:3777 original size:24 final size:23
Alignment explanation
Indices: 3740--3786 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
3730 TTTTCCTAAA
3740 AAAGAGAGAAAAGGAAGGTGAGAG
1 AAAGAGAGAAAAGG-AGGTGAGAG
*
3764 AAAGAGA-AATAAGGTGGTGAGAG
1 AAAGAGAGAA-AAGGAGGTGAGAG
3787 GGAATGAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.51, C:0.00, G:0.40, T:0.09
Consensus pattern (23 bp):
AAAGAGAGAAAAGGAGGTGAGAG
Found at i:12647 original size:13 final size:13
Alignment explanation
Indices: 12629--12662 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
12619 ATACATCATT
12629 AAAAAAAGAGAAA
1 AAAAAAAGAGAAA
12642 AAAAAAAGAGAAA
1 AAAAAAAGAGAAA
12655 AAGAAAAA
1 AA-AAAAA
12663 AAATTGACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAGAAA
Found at i:15101 original size:37 final size:37
Alignment explanation
Indices: 15060--15204 Score: 227
Period size: 37 Copynumber: 3.9 Consensus size: 37
15050 CATCTAAATT
*
15060 TTCAGGCTATGTGCCTAGTAGGCTTTGTGTCGGTGTA
1 TTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTGTA
* *
15097 TTCAGGCTATGTGCCTAGTAGGCTTTGTGCTGGTGTT
1 TTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTGTA
*
15134 TTCAAGCTATGTGCCTAGTAGGCTTTGTGCCGGTGTA
1 TTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTGTA
* * *
15171 TTCGGGCTATGTGCCTAGCAAGCTTTGTGCCGGT
1 TTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGT
15205 AATCCAAGAA
Statistics
Matches: 98, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 98 1.00
ACGTcount: A:0.13, C:0.19, G:0.32, T:0.37
Consensus pattern (37 bp):
TTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTGTA
Found at i:19970 original size:29 final size:29
Alignment explanation
Indices: 19889--20017 Score: 127
Period size: 28 Copynumber: 4.5 Consensus size: 29
19879 AACTGCCACT
* * * *
19889 ATTTTACAATTTTGCCACTGGTTTTCTAG
1 ATTTTACAGTTTTGCCACTAGTTTTCCAA
* *
19918 ATTTTACAGTTTTCCCATTA-TTTTCCAA
1 ATTTTACAGTTTTGCCACTAGTTTTCCAA
* * ** *
19946 ATTTTACGGTTTTTCCACTAGTTTTTTAG
1 ATTTTACAGTTTTGCCACTAGTTTTCCAA
*
19975 A-TTTATAGTTTTGCCACTAGTTTTCCAA
1 ATTTTACAGTTTTGCCACTAGTTTTCCAA
*
20003 ATTGTACAGTTTTGC
1 ATTTTACAGTTTTGC
20018 GGATTTTACA
Statistics
Matches: 78, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
28 45 0.58
29 33 0.42
ACGTcount: A:0.22, C:0.17, G:0.12, T:0.50
Consensus pattern (29 bp):
ATTTTACAGTTTTGCCACTAGTTTTCCAA
Found at i:19977 original size:57 final size:57
Alignment explanation
Indices: 19889--20017 Score: 161
Period size: 57 Copynumber: 2.3 Consensus size: 57
19879 AACTGCCACT
* * *
19889 ATTTTACAATTTTGCCACTGGTTTTCTAGATTTTACAGTTTTCCCATTA-TTTTCCAA
1 ATTTTACAGTTTTGCCACTAGTTTTCTAGA-TTTACAGTTTTCCCACTAGTTTTCCAA
* * * * *
19946 ATTTTACGGTTTTTCCACTAGTTTTTTAGATTTATAGTTTTGCCACTAGTTTTCCAA
1 ATTTTACAGTTTTGCCACTAGTTTTCTAGATTTACAGTTTTCCCACTAGTTTTCCAA
*
20003 ATTGTACAGTTTTGC
1 ATTTTACAGTTTTGC
20018 GGATTTTACA
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
56 15 0.25
57 45 0.75
ACGTcount: A:0.22, C:0.17, G:0.12, T:0.50
Consensus pattern (57 bp):
ATTTTACAGTTTTGCCACTAGTTTTCTAGATTTACAGTTTTCCCACTAGTTTTCCAA
Found at i:20785 original size:21 final size:21
Alignment explanation
Indices: 20758--20813 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
20748 CAAAGTGAAG
20758 ACTTCTACCGATACAAGTGACT
1 ACTTCTACCGATACAAGT-ACT
* * *
20780 -CTTCTATCGAAACAAGTATT
1 ACTTCTACCGATACAAGTACT
20800 ACTTCTACCGATAC
1 ACTTCTACCGATAC
20814 TAAAAACTCT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.32, C:0.27, G:0.11, T:0.30
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTACT
Found at i:21114 original size:14 final size:14
Alignment explanation
Indices: 21095--21124 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
21085 CACAAAATAC
21095 ATAGTTTCCAAGTT
1 ATAGTTTCCAAGTT
21109 ATAGTTTCCAAGTT
1 ATAGTTTCCAAGTT
21123 AT
1 AT
21125 TACATAGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (14 bp):
ATAGTTTCCAAGTT
Found at i:21616 original size:52 final size:51
Alignment explanation
Indices: 21492--21730 Score: 291
Period size: 52 Copynumber: 4.6 Consensus size: 51
21482 TGCATATTTA
* * * * * *
21492 ATACTCATGATGACACAAAGTCATTGGACCTT-TAATTCGTTAAAGAATCAC
1 ATACTCACGATGACACATAGTCATCGGACCTTATAATCCG-TAAAGATTCAT
*
21543 ATACTCACGATGACACTTAGTCATCGGACCTTATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTATAATCCGTAAA-GATTCAT
* * *
21595 ATACTCACGATGACACATAGTCATCGTACCTCATAATCCGTAAGGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTATAATCCGTAA-AGATTCAT
* ** *
21647 ATACTCACGATGACACATAGTCATCAGACCTCGTAATCCATAACAGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTATAATCCGTAA-AGATTCAT
**
21699 ATACTCACGATGACATGTAGTCATCGGACCTT
1 ATACTCACGATGACACATAGTCATCGGACCTT
21731 TTTCATTTAT
Statistics
Matches: 164, Mismatches: 21, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
51 32 0.20
52 132 0.80
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.28
Consensus pattern (51 bp):
ATACTCACGATGACACATAGTCATCGGACCTTATAATCCGTAAAGATTCAT
Found at i:28055 original size:21 final size:21
Alignment explanation
Indices: 28030--28081 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
28020 AGTGATAGGC
28030 CTACCGATACAAGTGACT-CTT
1 CTACCGATACAAGT-ACTACTT
* * *
28051 TTACCGAAACAAGTATTACTT
1 CTACCGATACAAGTACTACTT
28072 CTACCGATAC
1 CTACCGATAC
28082 TAAAAACTCC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.29
Consensus pattern (21 bp):
CTACCGATACAAGTACTACTT
Found at i:28835 original size:52 final size:52
Alignment explanation
Indices: 28722--28959 Score: 289
Period size: 52 Copynumber: 4.6 Consensus size: 52
28712 TGCATATTTA
* ** * * * * *
28722 ATACTCATGATGACACAAAGTCATCAAACCT-TTAATTCGTTAAAGAATCAC
1 ATACTCACGATGACACGTAGTCATCAAACCTCATAATCCGTAAAAGATTCAT
* *
28773 ATACTCACGATGACACCTAGTCATCAGACCTCATAATCCGTAAAAGATTCAT
1 ATACTCACGATGACACGTAGTCATCAAACCTCATAATCCGTAAAAGATTCAT
** **
28825 ATACTCACGATGACACGTAGTCATCGGACCTCATAATCCGTAAGGGATTCAT
1 ATACTCACGATGACACGTAGTCATCAAACCTCATAATCCGTAAAAGATTCAT
* **
28877 ATACTCACGATGACACGTAGTCATCAAACCTCATAATCCATAACTGATTCAT
1 ATACTCACGATGACACGTAGTCATCAAACCTCATAATCCGTAAAAGATTCAT
* * *
28929 ATACTTACGATGACACGTAATCATCGAACCT
1 ATACTCACGATGACACGTAGTCATCAAACCT
28960 TTCTCGTTTA
Statistics
Matches: 165, Mismatches: 21, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
51 27 0.16
52 138 0.84
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACGTAGTCATCAAACCTCATAATCCGTAAAAGATTCAT
Found at i:29934 original size:25 final size:25
Alignment explanation
Indices: 29906--29954 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
29896 ACTAAATACA
29906 TTATGTTAATTTGGTCCTTTGGTCT
1 TTATGTTAATTTGGTCCTTTGGTCT
*
29931 TTATGTTAATTTGTTCCTTTGGTC
1 TTATGTTAATTTGGTCCTTTGGTC
29955 CTTCTAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.12, C:0.12, G:0.18, T:0.57
Consensus pattern (25 bp):
TTATGTTAATTTGGTCCTTTGGTCT
Done.