Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013812.1 Kokia drynarioides strain JFW-HI SEQ_128840, 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: 43092
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Found at i:36 original size:12 final size:11
Alignment explanation
Indices: 11--49 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1 TTAAACTTAG
*
11 ATTTATTTTCA
1 ATTTATTTTAA
22 ATTTGATTTTAA
1 ATTT-ATTTTAA
*
34 ATTTAATTTAA
1 ATTTATTTTAA
45 ATTTA
1 ATTTA
50 AATTTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (11 bp):
ATTTATTTTAA
Found at i:41 original size:17 final size:17
Alignment explanation
Indices: 29--69 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
19 TCAATTTGAT
29 TTTAAATTTAATTTAAA
1 TTTAAATTTAATTTAAA
*
46 TTTAAATTTATTTTAAAA
1 TTTAAATTTAATTT-AAA
64 TTTAAA
1 TTTAAA
70 AGATTATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTAAATTTAATTTAAA
Found at i:43 original size:11 final size:12
Alignment explanation
Indices: 29--69 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
19 TCAATTTGAT
29 TTTAAATTT-AA
1 TTTAAATTTAAA
40 TTTAAATTTAAA
1 TTTAAATTTAAA
*
52 TTT-ATTTTAAAA
1 TTTAAATTT-AAA
64 TTTAAA
1 TTTAAA
70 AGATTATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 13 0.52
12 11 0.44
13 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:47 original size:6 final size:6
Alignment explanation
Indices: 29--69 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
19 TCAATTTGAT
*
29 TTTAAA TTT-AA TTTAAA TTTAAA TTT-AT TTTAAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
70 AGATTATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
5 9 0.30
6 17 0.57
7 4 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:99 original size:14 final size:15
Alignment explanation
Indices: 80--108 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
70 AGATTATTAT
80 AAAGT-CAAATTACA
1 AAAGTCCAAATTACA
94 AAAGTCCAAATTACA
1 AAAGTCCAAATTACA
109 TGTGCAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.55, C:0.17, G:0.07, T:0.21
Consensus pattern (15 bp):
AAAGTCCAAATTACA
Found at i:7253 original size:20 final size:21
Alignment explanation
Indices: 7207--7261 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 21
7197 CTTTCAATAG
7207 AAAACAATAGAATTTTAATTCCC
1 AAAA-AATAGAA-TTTAATTCCC
**
7230 AAAAAATAGAATTT-ATTCTT
1 AAAAAATAGAATTTAATTCCC
7250 AAAAAATA-AATT
1 AAAAAATAGAATT
7262 CTCACTACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.13
20 12 0.40
21 3 0.10
22 7 0.23
23 4 0.13
ACGTcount: A:0.55, C:0.09, G:0.04, T:0.33
Consensus pattern (21 bp):
AAAAAATAGAATTTAATTCCC
Found at i:14047 original size:27 final size:26
Alignment explanation
Indices: 14015--14102 Score: 77
Period size: 27 Copynumber: 3.3 Consensus size: 26
14005 TAGTCTGTTT
* *
14015 TTGGCTCGAATGAGTAATATTTTGTA
1 TTGGCTCAAATGAATAATATTTTGTA
* ** * *
14041 CTTGGCTCAAATAAACCATATTCTGCA
1 -TTGGCTCAAATGAATAATATTTTGTA
*
14068 TCTGGTTCAAATGAATAATATTTTGTA
1 T-TGGCTCAAATGAATAATATTTTGTA
14095 TTTGGCTC
1 -TTGGCTC
14103 GAATATGCTA
Statistics
Matches: 45, Mismatches: 14, Indels: 4
0.71 0.22 0.06
Matches are distributed among these distances:
26 1 0.02
27 43 0.96
28 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (26 bp):
TTGGCTCAAATGAATAATATTTTGTA
Found at i:15101 original size:22 final size:22
Alignment explanation
Indices: 15047--15101 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
15037 AACTAAAGAC
* * *
15047 ACGGGCGTATGGATGAGGGCAC
1 ACGGCCGTGTGGATGAGGGCAA
*
15069 ACGGCCATGTGGATGAGGGCAA
1 ACGGCCGTGTGGATGAGGGCAA
*
15091 ACGGTCGTGTG
1 ACGGCCGTGTG
15102 ACCCCTGTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.18, G:0.44, T:0.16
Consensus pattern (22 bp):
ACGGCCGTGTGGATGAGGGCAA
Found at i:17896 original size:29 final size:29
Alignment explanation
Indices: 17864--17933 Score: 131
Period size: 29 Copynumber: 2.4 Consensus size: 29
17854 GTAGAATATG
*
17864 AAATAATTTATTTAATTTAAAATCAATCA
1 AAATAATTTATTTAATTTAAAATCAATAA
17893 AAATAATTTATTTAATTTAAAATCAATAA
1 AAATAATTTATTTAATTTAAAATCAATAA
17922 AAATAATTTATT
1 AAATAATTTATT
17934 CAATCAATTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (29 bp):
AAATAATTTATTTAATTTAAAATCAATAA
Found at i:17941 original size:22 final size:22
Alignment explanation
Indices: 17913--17981 Score: 102
Period size: 22 Copynumber: 3.1 Consensus size: 22
17903 TTTAATTTAA
17913 AATCAATAAAAATAATTTATTC
1 AATCAATAAAAATAATTTATTC
*
17935 AATCAATTAAAATAATTTATTC
1 AATCAATAAAAATAATTTATTC
* * *
17957 AATTAATCAGAATAATTTATTC
1 AATCAATAAAAATAATTTATTC
17979 AAT
1 AAT
17982 TTAAAAGCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.51, C:0.09, G:0.01, T:0.39
Consensus pattern (22 bp):
AATCAATAAAAATAATTTATTC
Found at i:17960 original size:18 final size:18
Alignment explanation
Indices: 17937--17987 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 18
17927 ATTTATTCAA
17937 TCAATTAAAATAATTTAT
1 TCAATTAAAATAATTTAT
17955 TCAATTAATCAGAATAATTTAT
1 TCAATT-A--A-AATAATTTAT
17977 TCAATTTAAAA
1 TCAA-TTAAAA
17988 GCAATCAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
18 6 0.21
19 3 0.11
20 1 0.04
21 1 0.04
22 15 0.54
23 2 0.07
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (18 bp):
TCAATTAAAATAATTTAT
Found at i:28104 original size:20 final size:19
Alignment explanation
Indices: 28053--28111 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
28043 TTACTTTACA
* *
28053 AAGAAAATTGTATTATTTT
1 AAGAATATTTTATTATTTT
*
28072 GAGAATATTTTATTATTTT
1 AAGAATATTTTATTATTTT
* *
28091 AAGAGTATTTTTATCATTTT
1 AAGAATA-TTTTATTATTTT
28111 A
1 A
28112 TATTAATTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 21 0.64
20 12 0.36
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.53
Consensus pattern (19 bp):
AAGAATATTTTATTATTTT
Found at i:31397 original size:89 final size:89
Alignment explanation
Indices: 31246--31417 Score: 344
Period size: 89 Copynumber: 1.9 Consensus size: 89
31236 TGTGTGTGTG
31246 TTGCGTAAGGTTAAGAAAGTATAAACACTGATTACCTATTGAAACCTAAAAACATGAAAACAAAA
1 TTGCGTAAGGTTAAGAAAGTATAAACACTGATTACCTATTGAAACCTAAAAACATGAAAACAAAA
31311 GGTGAAACTAAAATGCAAGATAAA
66 GGTGAAACTAAAATGCAAGATAAA
31335 TTGCGTAAGGTTAAGAAAGTATAAACACTGATTACCTATTGAAACCTAAAAACATGAAAACAAAA
1 TTGCGTAAGGTTAAGAAAGTATAAACACTGATTACCTATTGAAACCTAAAAACATGAAAACAAAA
31400 GGTGAAACTAAAATGCAA
66 GGTGAAACTAAAATGCAA
31418 AATTTCCAAA
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 83 1.00
ACGTcount: A:0.50, C:0.13, G:0.16, T:0.22
Consensus pattern (89 bp):
TTGCGTAAGGTTAAGAAAGTATAAACACTGATTACCTATTGAAACCTAAAAACATGAAAACAAAA
GGTGAAACTAAAATGCAAGATAAA
Found at i:40533 original size:29 final size:29
Alignment explanation
Indices: 40479--40534 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
40469 TAAATTTAAC
*
40479 TAAAAAAATAAAAATAAAAGTCAAATTGA
1 TAAAAAAATAAAAATAAAACTCAAATTGA
*
40508 TAAAAAAATAAATATTAAAACT-AAATT
1 TAAAAAAATAAA-AATAAAACTCAAATT
40535 TTTCATTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.25
Consensus pattern (29 bp):
TAAAAAAATAAAAATAAAACTCAAATTGA
Found at i:40621 original size:12 final size:12
Alignment explanation
Indices: 40604--40632 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
40594 GAACACACTG
40604 TTTTTTCTTTTT
1 TTTTTTCTTTTT
40616 TTTTTTCTTTTT
1 TTTTTTCTTTTT
40628 TTTTT
1 TTTTT
40633 GCATTACTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (12 bp):
TTTTTTCTTTTT
Found at i:41555 original size:15 final size:15
Alignment explanation
Indices: 41523--41562 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
41513 TTCTTAATGA
* *
41523 TTTTTATAATTTATAT
1 TTTTTA-AAATTAAAT
41539 TTTTTAAAATTAAAT
1 TTTTTAAAATTAAAT
41554 TTTTTAAAA
1 TTTTTAAAA
41563 ATCTAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTTTAAAATTAAAT
Found at i:41563 original size:16 final size:16
Alignment explanation
Indices: 41523--41574 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
41513 TTCTTAATGA
* * *
41523 TTTTTATAATTTATAT
1 TTTTTAAAAATTAAAT
41539 TTTTT-AAAATTAAAT
1 TTTTTAAAAATTAAAT
41554 TTTTTAAAAATCT-AAT
1 TTTTTAAAAAT-TAAAT
41570 TTTTT
1 TTTTT
41575 TTACTTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
15 12 0.39
16 18 0.58
17 1 0.03
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTTAAAAATTAAAT
Found at i:42375 original size:23 final size:23
Alignment explanation
Indices: 42339--42460 Score: 108
Period size: 23 Copynumber: 5.3 Consensus size: 23
42329 GCTGGGGAAA
*
42339 CAGTAAGCATACACAGTGC-AAT
1 CAGTAAGCACACACAGTGCAAAT
* *
42361 CCAGTAGGCACACACAATGC-AAT
1 -CAGTAAGCACACACAGTGCAAAT
* * *
42384 CAGTAAGCGCACATAGCGCAAAT
1 CAGTAAGCACACACAGTGCAAAT
* * *
42407 CAGTAGGCACACAAAGTGCGAAT
1 CAGTAAGCACACACAGTGCAAAT
42430 CAGTAAGCACACGA-AGTGCGAAA-
1 CAGTAAGCACAC-ACAGTGC-AAAT
42453 CAGTAAGC
1 CAGTAAGC
42461 GCGCTAGCGT
Statistics
Matches: 81, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
22 14 0.17
23 64 0.79
24 3 0.04
ACGTcount: A:0.40, C:0.25, G:0.22, T:0.13
Consensus pattern (23 bp):
CAGTAAGCACACACAGTGCAAAT
Found at i:42457 original size:46 final size:45
Alignment explanation
Indices: 42339--42441 Score: 129
Period size: 45 Copynumber: 2.3 Consensus size: 45
42329 GCTGGGGAAA
* * *
42339 CAGTAAGCATACACAGTGC-AATCCAGTAGGCACACACAATGCAAT
1 CAGTAAGCACACATAGCGCAAAT-CAGTAGGCACACACAATGCAAT
*
42384 CAGTAAGCGCACATAGCGCAAATCAGTAGGCACACA-AAGTGCGAAT
1 CAGTAAGCACACATAGCGCAAATCAGTAGGCACACACAA-TGC-AAT
42430 CAGTAAGCACAC
1 CAGTAAGCACAC
42442 GAAGTGCGAA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
44 2 0.04
45 31 0.62
46 17 0.34
ACGTcount: A:0.40, C:0.26, G:0.20, T:0.14
Consensus pattern (45 bp):
CAGTAAGCACACATAGCGCAAATCAGTAGGCACACACAATGCAAT
Done.