Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002905.1 Kokia drynarioides strain JFW-HI SEQ_115325, 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: 61202
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:392 original size:18 final size:16
Alignment explanation
Indices: 369--416 Score: 64
Period size: 18 Copynumber: 3.0 Consensus size: 16
359 CTTTTTTTTC
369 CTTCTCCTTCTTCCTCTT
1 CTTCTCCTTCTT--TCTT
387 CTTCTCCTTCTTTCTT
1 CTTCTCCTTCTTTCTT
403 CTTCT--TTCTTTCTT
1 CTTCTCCTTCTTTCTT
417 TCTTTCTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.30
16 9 0.30
18 12 0.40
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (16 bp):
CTTCTCCTTCTTTCTT
Found at i:408 original size:22 final size:22
Alignment explanation
Indices: 365--423 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
355 TACCCTTTTT
365 TTTCCTTCTCCTTCTTCCTC-TTC
1 TTTCCTTCT--TTCTTCCTCTTTC
*
388 TTCTCCTTCTTTCTTCTTCTTTC
1 TT-TCCTTCTTTCTTCCTCTTTC
*
411 TTTCTTTCTTTCT
1 TTTCCTTCTTTCT
424 CTTTTTTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 18 0.56
23 7 0.22
24 7 0.22
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTCCTTCTTTCTTCCTCTTTC
Found at i:411 original size:4 final size:4
Alignment explanation
Indices: 394--434 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
384 CTTCTTCTCC
*
394 TTCT TTC- TTC- TTCT TTCT TTCT TTCT TTCT CTTTT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TT
435 ATTTTTTCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 6 0.18
4 24 0.73
5 3 0.09
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTCT
Found at i:24700 original size:23 final size:24
Alignment explanation
Indices: 24674--24729 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
24664 TTGAAATCCA
24674 AAATATAAATACTGCATG-CAAT-G
1 AAATATAAATACTG-ATGCCAATAG
* *
24697 AAATTTAAATATTGATGCCAATAG
1 AAATATAAATACTGATGCCAATAG
24721 AAA-ATAAAT
1 AAATATAAAT
24730 TATAATATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 3 0.11
23 21 0.75
24 4 0.14
ACGTcount: A:0.52, C:0.09, G:0.11, T:0.29
Consensus pattern (24 bp):
AAATATAAATACTGATGCCAATAG
Found at i:31977 original size:23 final size:23
Alignment explanation
Indices: 31934--31977 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
31924 GAAATTAAAT
*
31934 TGTAATTTTTAAAATAATAAAAA
1 TGTAATTTTTAAAAGAATAAAAA
*
31957 TGTAATTTTTAAAAGATTAAA
1 TGTAATTTTTAAAAGAATAAA
31978 TAAAAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (23 bp):
TGTAATTTTTAAAAGAATAAAAA
Found at i:37079 original size:20 final size:21
Alignment explanation
Indices: 37056--37099 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
37046 CAAGAAAGAG
* *
37056 AAATTAAAACAACATAAAC-A
1 AAATCAAAACAACAAAAACTA
*
37076 AAATCAAACCAACAAAAACTA
1 AAATCAAAACAACAAAAACTA
37097 AAA
1 AAA
37100 GACAGGATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.70, C:0.18, G:0.00, T:0.11
Consensus pattern (21 bp):
AAATCAAAACAACAAAAACTA
Found at i:49052 original size:35 final size:35
Alignment explanation
Indices: 49011--49085 Score: 150
Period size: 35 Copynumber: 2.1 Consensus size: 35
49001 AGTGGTATAC
49011 TATGTTATTTCAGCTTGTGAGCGTGTAGGATATGG
1 TATGTTATTTCAGCTTGTGAGCGTGTAGGATATGG
49046 TATGTTATTTCAGCTTGTGAGCGTGTAGGATATGG
1 TATGTTATTTCAGCTTGTGAGCGTGTAGGATATGG
49081 TATGT
1 TATGT
49086 GTCCACTACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.20, C:0.08, G:0.31, T:0.41
Consensus pattern (35 bp):
TATGTTATTTCAGCTTGTGAGCGTGTAGGATATGG
Found at i:51376 original size:31 final size:31
Alignment explanation
Indices: 51341--51400 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
51331 ACGGAATTGG
51341 CCCTAAGTTGTTGATTATTGGTTAATTATCC
1 CCCTAAGTTGTTGATTATTGGTTAATTATCC
51372 CCCTAAGTTGTTGATTATTGGTTAATTAT
1 CCCTAAGTTGTTGATTATTGGTTAATTAT
51401 TCATGTCAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (31 bp):
CCCTAAGTTGTTGATTATTGGTTAATTATCC
Found at i:53777 original size:170 final size:170
Alignment explanation
Indices: 53494--53803 Score: 523
Period size: 170 Copynumber: 1.8 Consensus size: 170
53484 GTAAAAATCC
* *
53494 CTTATTAATCCCGCGTATAAGCCTAATGGCATGTCATACGTATCCTAACCTTTTACAAAGTTCAC
1 CTTATTAATCCCGCATATAAGCCTAATGGCATGCCATACGTATCCTAACCTTTTACAAAGTTCAC
* *
53559 TCGGCTATCATTTTCGTATAAATGTCAAAACCAATTCCTATGCATAATTTCATTTCTCATTTTCG
66 TCGGCTATCATTTTCGTATAAATGTCAAAACCAATTCCTATACATAATTTCATTTCTCACTTTCG
53624 AGACAAATAATCAGTTAACAATCACTTTTACATCTTGCGT
131 AGACAAATAATCAGTTAACAATCACTTTTACATCTTGCGT
* * *
53664 CTTATTAATCGCGCATATAA-CCTTGATGGCATGCCATACGTATCCTAACCTTTTACGAAGTTCA
1 CTTATTAATCCCGCATATAAGCC-TAATGGCATGCCATACGTATCCTAACCTTTTACAAAGTTCA
* *
53728 CTCGGGTATCATTTTCGTATAAATGTCAAAACCAATTCCTGTACATAATTTCATTTCTCACTTTC
65 CTCGGCTATCATTTTCGTATAAATGTCAAAACCAATTCCTATACATAATTTCATTTCTCACTTTC
53793 GAGACAAATAA
130 GAGACAAATAA
53804 CCAATATTTA
Statistics
Matches: 130, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
169 2 0.02
170 128 0.98
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35
Consensus pattern (170 bp):
CTTATTAATCCCGCATATAAGCCTAATGGCATGCCATACGTATCCTAACCTTTTACAAAGTTCAC
TCGGCTATCATTTTCGTATAAATGTCAAAACCAATTCCTATACATAATTTCATTTCTCACTTTCG
AGACAAATAATCAGTTAACAATCACTTTTACATCTTGCGT
Found at i:53885 original size:2 final size:2
Alignment explanation
Indices: 53878--53903 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
53868 TACTTAGTTC
53878 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
53904 CAGTATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56401 original size:77 final size:77
Alignment explanation
Indices: 56274--56428 Score: 283
Period size: 77 Copynumber: 2.0 Consensus size: 77
56264 AAGACAAGTG
56274 TTGAGCCTCTTCATCACATGAAGTACATGTTTTACTTCATCAAGTCCACTTAATCTAATCGAAGC
1 TTGAGCCTCTTCATCACATGAAGTACATGTTTTACTTCATCAAGTCCACTTAATCTAATCGAAGC
56339 TAGATTGCTAAA
66 TAGATTGCTAAA
** *
56351 TTGAGCCTCTTCATTGCATGAAGTACATGTTTTACTTCATCAAGTGCACTTAATCTAATCGAAGC
1 TTGAGCCTCTTCATCACATGAAGTACATGTTTTACTTCATCAAGTCCACTTAATCTAATCGAAGC
56416 TAGATTGCTAAA
66 TAGATTGCTAAA
56428 T
1 T
56429 CCTTCAATCT
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 75 1.00
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (77 bp):
TTGAGCCTCTTCATCACATGAAGTACATGTTTTACTTCATCAAGTCCACTTAATCTAATCGAAGC
TAGATTGCTAAA
Found at i:56979 original size:20 final size:20
Alignment explanation
Indices: 56954--56994 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
56944 CTTCAGTATT
56954 AAAGAGGTGGTAGGGGATAC
1 AAAGAGGTGGTAGGGGATAC
56974 AAAGAGGTGGTAGGGGATAC
1 AAAGAGGTGGTAGGGGATAC
56994 A
1 A
56995 GAAAGGGACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.05, G:0.44, T:0.15
Consensus pattern (20 bp):
AAAGAGGTGGTAGGGGATAC
Found at i:60964 original size:2 final size:2
Alignment explanation
Indices: 60959--61000 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
60949 TTTCAATTTG
60959 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61001 TAAATTTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.