Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015156.1 Kokia drynarioides strain JFW-HI SEQ_130200, 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: 37575
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.32
Found at i:6623 original size:15 final size:16
Alignment explanation
Indices: 6584--6624 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
6574 TTAAGGAAAT
6584 AATTTTAATAATATTAA
1 AATTTTAA-AATATTAA
*
6601 CA-TTTAAAAT-TTAA
1 AATTTTAAAATATTAA
6615 AATTTTAAAA
1 AATTTTAAAA
6625 AATAAATAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
14 5 0.24
15 10 0.48
16 5 0.24
17 1 0.05
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTTTAAAATATTAA
Found at i:9992 original size:28 final size:28
Alignment explanation
Indices: 9952--10014 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
9942 GAGCAACAGG
*
9952 AATAAATATTAGATCACGGGGCAGCAGA
1 AATAAATATTAGATCAAGGGGCAGCAGA
9980 AATAAATATTAGATCAAGGGGCAGCAGA
1 AATAAATATTAGATCAAGGGGCAGCAGA
*
10008 AGTAAAT
1 AATAAAT
10015 GGGGGTCTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (28 bp):
AATAAATATTAGATCAAGGGGCAGCAGA
Found at i:31442 original size:6 final size:6
Alignment explanation
Indices: 31433--31457 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
31423 TTTCTTTTTA
31433 CTATTC CTATTC CTATTC CTATTC C
1 CTATTC CTATTC CTATTC CTATTC C
31458 CTTTATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.36, G:0.00, T:0.48
Consensus pattern (6 bp):
CTATTC
Found at i:33694 original size:21 final size:20
Alignment explanation
Indices: 33644--33696 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
33634 TTTTTCAAAA
33644 CTTCTCTCTTTTCTCCCTTCC
1 CTTCTC-CTTTTCTCCCTTCC
* * * *
33665 CATCCCCTTTTTTCCTTTCCC
1 CTTCTCCTTTTCTCCCTT-CC
33686 CTTCTCCTTTT
1 CTTCTCCTTTT
33697 GAGAGACTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.02, C:0.45, G:0.00, T:0.53
Consensus pattern (20 bp):
CTTCTCCTTTTCTCCCTTCC
Found at i:34481 original size:2 final size:2
Alignment explanation
Indices: 34474--34505 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
34464 CTCTTATAAG
34474 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
34506 CGCCATTGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:35551 original size:57 final size:58
Alignment explanation
Indices: 35456--35574 Score: 150
Period size: 57 Copynumber: 2.1 Consensus size: 58
35446 ACTGAAACTG
* *
35456 AAGTTGGCTGAAAAGAAGAAACATGAAGAGGTACCCAAGGAGGAAAATGTTGA-GAAA
1 AAGTTGGCTGAAAAGAAGAAACATGAAGAGGCACCCAAGGAGGAAAAGGTTGAGGAAA
* * * * * * *
35513 AAGTTGGTTGAGAAGAAGAAACCTGATGAGGCATCCAAGGAGGAGAGGGTTGAGGAAA
1 AAGTTGGCTGAAAAGAAGAAACATGAAGAGGCACCCAAGGAGGAAAAGGTTGAGGAAA
35571 AAGT
1 AAGT
35575 ACCAAAATCA
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
57 44 0.85
58 8 0.15
ACGTcount: A:0.43, C:0.08, G:0.34, T:0.15
Consensus pattern (58 bp):
AAGTTGGCTGAAAAGAAGAAACATGAAGAGGCACCCAAGGAGGAAAAGGTTGAGGAAA
Found at i:35630 original size:72 final size:72
Alignment explanation
Indices: 35512--35918 Score: 310
Period size: 72 Copynumber: 5.7 Consensus size: 72
35502 ATGTTGAGAA
* * * *
35512 AAAGTTGGTTGAGAAGAAGAAACCTGATGAGGCAT-CC-AAGGAGGAGAGGGTTGAGGAAAAAGT
1 AAAGTTGGTTGAGAAGAAGGAACCTGAAGA-G-ATACCTAAGGAGGAGAGTGTTGAGGAAAAGGT
*
35575 ACCAAAATC
64 ACCAAAACC
* * *
35584 AAAGTTGGTTGAGAAGAAGGAACTTGAAGAGATACCTAAGGTGGAGAGTGTTGA-GAAGAAGGCA
1 AAAGTTGGTTGAGAAGAAGGAACCTGAAGAGATACCTAAGGAGGAGAGTGTTGAGGAA-AAGGTA
***
35648 TGGAAACC
65 CCAAAACC
* * ** * * *
35656 AAAGTTGATCGAGAAGAAGGAACCT-AA-AGACGCGCTCAAGAAGGGGAGTGTTGAGGAAAATGT
1 AAAGTTGGTTGAGAAGAAGGAACCTGAAGAGATAC-CT-AAGGAGGAGAGTGTTGAGGAAAAGGT
**
35719 ACCAAAATT
64 ACCAAAACC
* * * * *
35728 AAGGCTGGTTGA-AACTAAGGAACCTGAAGAGGA-ACCCAAAGG-GGAGAGTATTGAGGAAAAGG
1 AAAGTTGGTTGAGAA-GAAGGAACCTGAAGA-GATA-CCTAAGGAGGAGAGTGTTGAGGAAAAGG
*
35790 TACCAAAACT
63 TACCAAAACC
* * * ** * * * * *
35800 AAAATTGGTTAAGAAGAAGGAACCTCG-GGAGGCACCCAAAGATGAGAGTCTTGAGGGAAAGGTA
1 AAAGTTGGTTGAGAAGAAGGAACCT-GAAGAGATACCTAAGGAGGAGAGTGTTGAGGAAAAGGTA
35864 CCAAAACC
65 CCAAAACC
* * * *
35872 AAAGTTGGTTGAAAATAAGGAACTTGAAGAGGTACCTAAGGAGGAGA
1 AAAGTTGGTTGAGAAGAAGGAACCTGAAGAGATACCTAAGGAGGAGA
35919 CTGTCGAGAA
Statistics
Matches: 258, Mismatches: 61, Indels: 32
0.74 0.17 0.09
Matches are distributed among these distances:
70 6 0.02
71 19 0.07
72 217 0.84
73 11 0.04
74 2 0.01
75 3 0.01
ACGTcount: A:0.41, C:0.12, G:0.31, T:0.16
Consensus pattern (72 bp):
AAAGTTGGTTGAGAAGAAGGAACCTGAAGAGATACCTAAGGAGGAGAGTGTTGAGGAAAAGGTAC
CAAAACC
Found at i:35918 original size:144 final size:142
Alignment explanation
Indices: 35511--35918 Score: 397
Period size: 144 Copynumber: 2.8 Consensus size: 142
35501 AATGTTGAGA
* * * *
35511 AAAAGTTGGTTGAGAAGAAGAAACCTGATGAGGCATCCAAGGAGGAGAGGGTTGAGGAAAAAGTA
1 AAAA-TTGGTTGAGAAGAAGGAACCTGA-GAGGCACCCAAAGAGGAGAGTGTTGAGGAAAAAGTA
* * * *
35576 CCAAAATCAAAGTTGGTTGAGAAGAAGGAACTTGAAGAGATACCTAAGGTGGAGAGTGTTGAGAA
64 CCAAAATCAAAGTTGGTTGAAAATAAGGAACTTGAAGAGGTACCTAAGG-GGAGAGTATTGAGAA
***
35641 GAAGGCATGGAAACC
128 GAAGGCACCAAAACC
* * * * * * * * *
35656 AAAGTTGATCGAGAAGAAGGAACCTAAAGACGCGCTC-AAGAAGGGGAGTGTTGAGGAAAATGTA
1 AAAATTGGTTGAGAAGAAGGAACCT-GAGAGGCACCCAAAG-AGGAGAGTGTTGAGGAAAAAGTA
* * * * * * *
35720 CCAAAATTAAGGCTGGTTGAAACTAAGGAACCTGAAGAGGAACCCAAAGGGGAGAGTATTGAGGA
64 CCAAAATCAAAGTTGGTTGAAAATAAGGAACTTGAAGAGGTA-CCTAAGGGGAGAGTATTGA-GA
* *
35785 A-AAGGTACCAAAACT
127 AGAAGGCACCAAAACC
* * * * * *
35800 AAAATTGGTTAAGAAGAAGGAACCTCGGGAGGCACCCAAAGATGAGAGTCTTGAGGGAAAGGTAC
1 AAAATTGGTTGAGAAGAAGGAACCT-GAGAGGCACCCAAAGAGGAGAGTGTTGAGGAAAAAGTAC
*
35865 CAAAACCAAAGTTGGTTGAAAATAAGGAACTTGAAGAGGTACCTAAGGAGGAGA
65 CAAAATCAAAGTTGGTTGAAAATAAGGAACTTGAAGAGGTACCTAAGG-GGAGA
35919 CTGTCGAGAA
Statistics
Matches: 205, Mismatches: 52, Indels: 13
0.76 0.19 0.05
Matches are distributed among these distances:
143 8 0.04
144 181 0.88
145 16 0.08
ACGTcount: A:0.41, C:0.12, G:0.31, T:0.16
Consensus pattern (142 bp):
AAAATTGGTTGAGAAGAAGGAACCTGAGAGGCACCCAAAGAGGAGAGTGTTGAGGAAAAAGTACC
AAAATCAAAGTTGGTTGAAAATAAGGAACTTGAAGAGGTACCTAAGGGGAGAGTATTGAGAAGAA
GGCACCAAAACC
Found at i:36662 original size:135 final size:135
Alignment explanation
Indices: 36504--36764 Score: 335
Period size: 135 Copynumber: 1.9 Consensus size: 135
36494 GAGAAGGTAT
* * * * * * *
36504 CAAAACGAAAGTTGATCGAGAAGAAGGAAA-CTGAGGATGCATCCAAGGGGGTCAGTGTTGAGGA
1 CAAAACCAAAGTTGATCGAGAAGAA-GAAACCTGAGGAGGCACCCAAGGAGGACAGGGTTGAGAA
* * * *
36568 AAAGGTATCAAAACCAAAGTTGGTTGAGAAGAAGGAACCTAAAGAGGTACCTGAGGTGGAGACCG
65 AAAAGTACCAAAACCAAAGTTGGTTGAGAAGAAGGAACCTAAAGAGATACCTAAGGTGGAGACCG
36633 ATGAGC
130 ATGAGC
* * * *
36639 CAAAACCAAAGTTGGTTGAGAAGAAGAAACCTGATGAGGCACCCAAGGAGGAGAGGGTTGAGAAA
1 CAAAACCAAAGTTGATCGAGAAGAAGAAACCTGAGGAGGCACCCAAGGAGGACAGGGTTGAGAAA
* * * *
36704 AAAGTGCCAAAATCAAAGTTGGTTGAGAAGAAGGAACTTGAAGAGATACCTAAGGTGGAGA
66 AAAGTACCAAAACCAAAGTTGGTTGAGAAGAAGGAACCTAAAGAGATACCTAAGGTGGAGA
36765 GTATTGAGAA
Statistics
Matches: 106, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
134 4 0.04
135 102 0.96
ACGTcount: A:0.40, C:0.13, G:0.32, T:0.15
Consensus pattern (135 bp):
CAAAACCAAAGTTGATCGAGAAGAAGAAACCTGAGGAGGCACCCAAGGAGGACAGGGTTGAGAAA
AAAGTACCAAAACCAAAGTTGGTTGAGAAGAAGGAACCTAAAGAGATACCTAAGGTGGAGACCGA
TGAGC
Found at i:36722 original size:72 final size:72
Alignment explanation
Indices: 36638--37052 Score: 341
Period size: 72 Copynumber: 5.8 Consensus size: 72
36628 GACCGATGAG
* * ** *
36638 CCAAAACCAAAGTTGGTTGAGAAGAAGAAACCTGATGAGGCACCCAAGGAGGAGAGGGTTGAGAA
1 CCAAAACCAAAGTTGGTTGAGAAGAAGGAACCTGAAGAGGCACCCAAGGAGGAGAGTATTGAGGA
*
36703 AAAAGTG
66 AAAAGTA
* * ** * *
36710 CCAAAATCAAAGTTGGTTGAGAAGAAGGAACTTGAAGAGATACCTAAGGTGGAGAGTATTGA-GA
1 CCAAAACCAAAGTTGGTTGAGAAGAAGGAACCTGAAGAGGCACCCAAGGAGGAGAGTATTGAGGA
*
36774 AGAAAGCA
66 A-AAAGTA
*** * * * * ** * * *
36782 TGGAAACCAAAGTTGATCGAGAAGAAGGAACCTAAAGATGTGCCCAAGAAGGGGAGTGTTGAGGA
1 CCAAAACCAAAGTTGGTTGAGAAGAAGGAACCTGAAGAGGCACCCAAGGAGGAGAGTATTGAGGA
*
36847 AAATGTA
66 AAAAGTA
** * * * *
36854 CCAAAATTAAGGCTGGTTGA-AACTAAGGAACCTGAAGAGGAACCCAAAGG-GGAGAGTATTGAG
1 CCAAAACCAAAGTTGGTTGAGAA-GAAGGAACCTGAAGAGGCACCC-AAGGAGGAGAGTATTGAG
**
36917 GAAACGGTA
64 GAAAAAGTA
* * * * * * **
36926 CCAAAACTAAAATTGGTTAAGAAGAAGGAACCTGGAGAGGCACCCAAAGATGAGAGTCCTGAGGA
1 CCAAAACCAAAGTTGGTTGAGAAGAAGGAACCTGAAGAGGCACCCAAGGAGGAGAGTATTGAGGA
*
36991 AAAGGTA
66 AAAAGTA
* * * ** *
36998 CCAAAACCAAAGTTGGTTGAAAATAAGGAACATGAAGAGGTGCCTAAGGAGGAGA
1 CCAAAACCAAAGTTGGTTGAGAAGAAGGAACCTGAAGAGGCACCCAAGGAGGAGA
37053 CTGTCGAGAA
Statistics
Matches: 262, Mismatches: 75, Indels: 12
0.75 0.21 0.03
Matches are distributed among these distances:
71 7 0.03
72 247 0.94
73 8 0.03
ACGTcount: A:0.42, C:0.13, G:0.30, T:0.15
Consensus pattern (72 bp):
CCAAAACCAAAGTTGGTTGAGAAGAAGGAACCTGAAGAGGCACCCAAGGAGGAGAGTATTGAGGA
AAAAGTA
Found at i:37052 original size:144 final size:141
Alignment explanation
Indices: 36441--37052 Score: 409
Period size: 144 Copynumber: 4.3 Consensus size: 141
36431 TCAGAATTAC
* * * * * * * * * * *
36441 CAAAGTTGGTCGAAAAGAAGGAACTTGAAGTGATACCCAAGGTGGAGA--ATGGTGAGAAGGTAT
1 CAAAGTTGGTTGAAAATAAGGAACATGAAGAGGTACCTAAGG-GGAGAGTATTGAGAGAAAGCAC
* * * * * * * * **
36504 CAAAACGAAAGTTGATCGAGAAGAAGGAAACTGAGGATGCATCCAAGGGGGTCAGTGTTGAGGAA
65 CAAAACCAAAGTTGGTTGAGAAGAAGGAACCTGA-GAGGCACCCAAAGAGGAGAGTGTTGAGGAA
* * *
36569 AAGGTATCAAAAC
129 AAAGTACCAAAAT
* * * * * * ** *
36582 CAAAGTTGGTTGAGAAGAAGGAACCTAAAGAGGTACCTGAGGTG-GAG-ACCGA-TG--AG--CC
1 CAAAGTTGGTTGAAAATAAGGAACATGAAGAGGTACCTAAGGGGAGAGTATTGAGAGAAAGCACC
* * * *
36640 AAAACCAAAGTTGGTTGAGAAGAAGAAACCTGATGAGGCACCCAAGGAGGAGAGGGTTGAGAAAA
66 AAAACCAAAGTTGGTTGAGAAGAAGGAACCTGA-GAGGCACCCAAAGAGGAGAGTGTTGAGGAAA
*
36705 AAGTGCCAAAAT
130 AAGTACCAAAAT
* * * *
36717 CAAAGTTGGTTGAGAAGAAGGAACTTGAAGAGATACCTAAGGTGGAGAGTATTGAGAAGAAAGCA
1 CAAAGTTGGTTGAAAATAAGGAACATGAAGAGGTACCTAAGG-GGAGAGTATTGAG-AGAAAGCA
*** * * * * ** *
36782 TGGAAACCAAAGTTGATCGAGAAGAAGGAACCTAAAGATGTGCCC-AAGAAGGGGAGTGTTGAGG
64 CCAAAACCAAAGTTGGTTGAGAAGAAGGAACCT-GAGAGGCACCCAAAG-AGGAGAGTGTTGAGG
*
36846 AAAATGTACCAAAAT
127 AAAAAGTACCAAAAT
* * * * * * * *
36861 TAAGGCTGGTTGAAACTAAGGAACCTGAAGAGGAACCCAAAGGGGAGAGTATTGAG-GAAACGGT
1 CAAAGTTGGTTGAAAATAAGGAACATGAAGAGGTA-CCTAAGGGGAGAGTATTGAGAGAAA--GC
* * * * **
36925 ACCAAAACTAAAATTGGTTAAGAAGAAGGAACCTGGAGAGGCACCCAAAGATGAGAGTCCTGAGG
63 ACCAAAACCAAAGTTGGTTGAGAAGAAGGAACCT-GAGAGGCACCCAAAGAGGAGAGTGTTGAGG
* *
36990 AAAAGGTACCAAAAC
127 AAAAAGTACCAAAAT
*
37005 CAAAGTTGGTTGAAAATAAGGAACATGAAGAGGTGCCTAAGGAGGAGA
1 CAAAGTTGGTTGAAAATAAGGAACATGAAGAGGTACCTAAGG-GGAGA
37053 CTGTCGAGAA
Statistics
Matches: 360, Mismatches: 94, Indels: 31
0.74 0.19 0.06
Matches are distributed among these distances:
135 99 0.28
136 1 0.00
137 4 0.01
138 3 0.01
139 3 0.01
140 4 0.01
141 34 0.09
142 6 0.02
143 8 0.02
144 188 0.52
145 10 0.03
ACGTcount: A:0.41, C:0.12, G:0.31, T:0.16
Consensus pattern (141 bp):
CAAAGTTGGTTGAAAATAAGGAACATGAAGAGGTACCTAAGGGGAGAGTATTGAGAGAAAGCACC
AAAACCAAAGTTGGTTGAGAAGAAGGAACCTGAGAGGCACCCAAAGAGGAGAGTGTTGAGGAAAA
AGTACCAAAAT
Done.