Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010058.1 Kokia drynarioides strain JFW-HI SEQ_124832, 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: 107764
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 142 characters in sequence are not A, C, G, or T
Found at i:1771 original size:5 final size:5
Alignment explanation
Indices: 1763--1803 Score: 50
Period size: 5 Copynumber: 8.2 Consensus size: 5
1753 TCTGACCCAA
1763 ATATT ATATT ATATT A-ATT ATA-T ATAATT ATATTT ATATT A
1 ATATT ATATT ATATT ATATT ATATT AT-ATT ATA-TT ATATT A
1804 AATCACTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
4 7 0.22
5 17 0.53
6 8 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
ATATT
Found at i:1784 original size:14 final size:14
Alignment explanation
Indices: 1763--1804 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
1753 TCTGACCCAA
1763 ATATTATATTATATT
1 ATATTATATTA-ATT
1778 A-ATTATATATAATT
1 ATATTATAT-TAATT
1792 ATATTTATATTAA
1 ATA-TTATATTAA
1805 ATCACTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
14 11 0.46
15 7 0.29
16 6 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATATTATATTAATT
Found at i:9770 original size:31 final size:31
Alignment explanation
Indices: 9749--9813 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
9739 GTATTTTTTG
*
9749 ACTCAAAAATATTTTTAAAAAGTATTACTAA
1 ACTCAAAAACATTTTTAAAAAGTATTACTAA
*
9780 ACTCAAAAACATTTTTAAAAAGTATCACTAA
1 ACTCAAAAACATTTTTAAAAAGTATTACTAA
9811 ACT
1 ACT
9814 AACTTTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.51, C:0.14, G:0.03, T:0.32
Consensus pattern (31 bp):
ACTCAAAAACATTTTTAAAAAGTATTACTAA
Found at i:15576 original size:15 final size:17
Alignment explanation
Indices: 15545--15576 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
15535 TAAAAGATTT
15545 TATTATTATTGTTATCA
1 TATTATTATTGTTATCA
15562 TATT-TTATT-TTATCA
1 TATTATTATTGTTATCA
15577 ACTTCAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 5 0.33
17 4 0.27
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.62
Consensus pattern (17 bp):
TATTATTATTGTTATCA
Found at i:19405 original size:6 final size:6
Alignment explanation
Indices: 19394--19420 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
19384 GCCCATGATT
19394 TTTTTC TTTTTC TTTTTC TTTTTC TTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTT
19421 CCCTTTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTC
Found at i:32952 original size:13 final size:13
Alignment explanation
Indices: 32934--32961 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
32924 TCGGTTCCCT
32934 ACCGCTTTTTCTC
1 ACCGCTTTTTCTC
32947 ACCGCTTTTTCTC
1 ACCGCTTTTTCTC
32960 AC
1 AC
32962 TAGTCAAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.11, C:0.39, G:0.07, T:0.43
Consensus pattern (13 bp):
ACCGCTTTTTCTC
Found at i:46823 original size:15 final size:16
Alignment explanation
Indices: 46793--46826 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
46783 TTAAAAATCT
*
46793 ATTTTAATTATAATTA
1 ATTTGAATTATAATTA
46809 ATTTGAATT-TAATTA
1 ATTTGAATTATAATTA
46824 ATT
1 ATT
46827 ATTCAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
ATTTGAATTATAATTA
Found at i:57854 original size:52 final size:52
Alignment explanation
Indices: 57797--57901 Score: 174
Period size: 52 Copynumber: 2.0 Consensus size: 52
57787 AAATTTAAGC
*
57797 TCAAACAATATTTAAATAAAAACTTAATATTTCCTCATATCCAATTTTTAAA
1 TCAAACAATATTTAAATAAAAACTTAATATTTCCTCAAATCCAATTTTTAAA
* * *
57849 TCAAACAGTATTTAAATGAGAACTTAATATTTCCTCAAATCCAATTTTTAAA
1 TCAAACAATATTTAAATAAAAACTTAATATTTCCTCAAATCCAATTTTTAAA
57901 T
1 T
57902 TTAATATTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.38
Consensus pattern (52 bp):
TCAAACAATATTTAAATAAAAACTTAATATTTCCTCAAATCCAATTTTTAAA
Found at i:61078 original size:12 final size:12
Alignment explanation
Indices: 61063--61088 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
61053 AACTATAAAT
61063 AAAAGAAAAGAA
1 AAAAGAAAAGAA
61075 AAAAGAAAAGAA
1 AAAAGAAAAGAA
61087 AA
1 AA
61089 GAGGGAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAGAA
Found at i:75369 original size:21 final size:21
Alignment explanation
Indices: 75340--75383 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
75330 AGTAGGTTTG
75340 TTTTGTTTTTGTTCTTTAAAT
1 TTTTGTTTTTGTTCTTTAAAT
* * *
75361 TTTTTTTTTTTTTTTTTAAAT
1 TTTTGTTTTTGTTCTTTAAAT
75382 TT
1 TT
75384 GAATTTCGTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.80
Consensus pattern (21 bp):
TTTTGTTTTTGTTCTTTAAAT
Found at i:83558 original size:163 final size:163
Alignment explanation
Indices: 83288--83613 Score: 580
Period size: 163 Copynumber: 2.0 Consensus size: 163
83278 GATTTAGACA
*
83288 AAATATCAAAGAACCCAAAATGAAGGGGAAAAAAGAAACCTCTGTTTTCACTATTTTTTTTTCAT
1 AAATATCAAAGAACCCAAAATGAAGGGGAAAAAAGAAACCTCTGTTTTCACTAATTTTTTTTCAT
*
83353 CTTGCTGTAATTACACCAAGCTCTCTTGGTTCTTAGCTGAGAGCCGTTTGAGGAACTCGGAAGTA
66 CTTGATGTAATTACACCAAGCTCTCTTGGTTCTTAGCTGAGAGCCGTTTGAGGAACTCGGAAGTA
*
83418 GTGATCATTGTTGTTGCAGACTTGGACATGGAC
131 GTGATCATTGTTGTTGCAGACATGGACATGGAC
* * *
83451 AAATATCAAGGAACCTAAAATGAAGGGGAAAAAAGCAACCTCTGTTTTCACTAATTTTTTTTCAT
1 AAATATCAAAGAACCCAAAATGAAGGGGAAAAAAGAAACCTCTGTTTTCACTAATTTTTTTTCAT
* *
83516 CTTGATGTAATTATACCAAGCTCTCTTGGTTCTTAGCTGAGAGCCGTTTGAGGAACTCGTAAGTA
66 CTTGATGTAATTACACCAAGCTCTCTTGGTTCTTAGCTGAGAGCCGTTTGAGGAACTCGGAAGTA
83581 GTGATCATTGTTGTTGCAGACATGGACATGGAC
131 GTGATCATTGTTGTTGCAGACATGGACATGGAC
83614 GCCCACCTCG
Statistics
Matches: 155, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
163 155 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (163 bp):
AAATATCAAAGAACCCAAAATGAAGGGGAAAAAAGAAACCTCTGTTTTCACTAATTTTTTTTCAT
CTTGATGTAATTACACCAAGCTCTCTTGGTTCTTAGCTGAGAGCCGTTTGAGGAACTCGGAAGTA
GTGATCATTGTTGTTGCAGACATGGACATGGAC
Found at i:98353 original size:12 final size:11
Alignment explanation
Indices: 98318--98360 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
98308 CCATTTTCTA
*
98318 AATAAAATAAT
1 AATAAAATATT
98329 AAT-AAATATTT
1 AATAAAATA-TT
98340 AATTAAAATATT
1 AA-TAAAATATT
98352 AATAAAATA
1 AATAAAATA
98361 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 5 0.18
13 5 0.18
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AATAAAATATT
Found at i:98363 original size:27 final size:27
Alignment explanation
Indices: 98315--98390 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
98305 CTACCATTTT
98315 CTAAATAA--AATAATAATAAATATTTAA
1 CTAAATAATTAATAA-AAT-AATATTTAA
*
98342 TTAAA-ATATTAATAAAATAATATTTAA
1 CTAAATA-ATTAATAAAATAATATTTAA
*
98369 CTAATTAATTAATAAAA-AATAT
1 CTAAATAATTAATAAAATAATAT
98391 CTCCAAAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
26 6 0.14
27 27 0.64
28 4 0.10
29 5 0.12
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (27 bp):
CTAAATAATTAATAAAATAATATTTAA
Found at i:98368 original size:23 final size:23
Alignment explanation
Indices: 98320--98390 Score: 56
Period size: 23 Copynumber: 3.0 Consensus size: 23
98310 ATTTTCTAAA
* * *
98320 TAAAATAATAAT-AAATATTTAAT
1 TAAAATATTAATAAAATA-ATATT
98343 TAAAATATTAATAAAATAATATT
1 TAAAATATTAATAAAATAATATT
98366 TAACTAATTAATTAATAAAA-AATAT
1 TAA--AA-T-ATTAATAAAATAATAT
98391 CTCCAAAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
23 17 0.43
24 5 0.12
25 2 0.05
26 6 0.15
27 10 0.25
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (23 bp):
TAAAATATTAATAAAATAATATT
Found at i:99104 original size:17 final size:17
Alignment explanation
Indices: 99071--99103 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
99061 TTGCATTGTC
99071 ATTTTTTTTACTTTTTT
1 ATTTTTTTTACTTTTTT
99088 ATTTTTTTTA-TTTTTT
1 ATTTTTTTTACTTTTTT
99104 TCGAATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (17 bp):
ATTTTTTTTACTTTTTT
Found at i:100002 original size:30 final size:29
Alignment explanation
Indices: 99938--100040 Score: 118
Period size: 30 Copynumber: 3.5 Consensus size: 29
99928 ATTTTGTTTA
*
99938 AAAAATTATATTTTAACCTCAAACTTTGC-
1 AAAAATTATATTTTAACCTTAAACTTT-CT
* * *
99967 CAAAATTATATTTTTACCTTTAAAGTTTCT
1 AAAAATTATATTTTAACC-TTAAACTTTCT
99997 AAAAATTATATTTTAACCCTTAAACTTTCT
1 AAAAATTATATTTTAA-CCTTAAACTTTCT
* *
100027 AATAATTACATTTT
1 AAAAATTATATTTT
100041 GTCCCCCAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
29 17 0.27
30 43 0.69
31 2 0.03
ACGTcount: A:0.39, C:0.15, G:0.02, T:0.45
Consensus pattern (29 bp):
AAAAATTATATTTTAACCTTAAACTTTCT
Found at i:100056 original size:60 final size:59
Alignment explanation
Indices: 99938--100090 Score: 148
Period size: 60 Copynumber: 2.6 Consensus size: 59
99928 ATTTTGTTTA
* * * *** *
99938 AAAAATTATATTTTAA-CCTCAAACTTTGCCAAAATTATATTTTTACCTTTAAAGTTTCT
1 AAAAATTATATTTTAACCCTTAAACTTT-CTAAAATTACATTTTTACCCCCAAAATTTCT
99997 AAAAATTATATTTTAACCCTTAAACTTTCTAATAATTACATTTTGT-CCCCCAAAATTTCT
1 AAAAATTATATTTTAACCCTTAAACTTTCTAA-AATTACATTTT-TACCCCCAAAATTTCT
*** * * *
100057 AAAAATGGCATTATAGCCCCTAAACTTTCTAAAA
1 AAAAATTATATTTTAACCCTTAAACTTTCTAAAA
100091 ATTAAAATTT
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
59 21 0.27
60 56 0.72
61 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.04, T:0.39
Consensus pattern (59 bp):
AAAAATTATATTTTAACCCTTAAACTTTCTAAAATTACATTTTTACCCCCAAAATTTCT
Found at i:100086 original size:30 final size:30
Alignment explanation
Indices: 100017--100092 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
100007 TTTTAACCCT
* * *
100017 TAAACTTTCTAATAATTACATTTTGTCCCC
1 TAAACTTTCTAAAAATGACATTTAGTCCCC
* * *
100047 CAAAATTTCTAAAAATGGCATTATAG-CCCC
1 TAAACTTTCTAAAAATGACATT-TAGTCCCC
100077 TAAACTTTCTAAAAAT
1 TAAACTTTCTAAAAAT
100093 TAAAATTTGA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
30 35 0.95
31 2 0.05
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (30 bp):
TAAACTTTCTAAAAATGACATTTAGTCCCC
Done.