Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001058.1 Kokia drynarioides strain JFW-HI SEQ_112304, 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: 12153
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Warning! 24 characters in sequence are not A, C, G, or T
Found at i:8828 original size:207 final size:206
Alignment explanation
Indices: 8469--9043 Score: 841
Period size: 207 Copynumber: 2.8 Consensus size: 206
8459 GACCATCCAC
* *
8469 AAAC-AGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGCTC
1 AAACAAGCGATGCGGTCATCTTCATGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
* ** *
8533 AAAGCGAGCAAAATCTTCGAACCTCAACTTCCTGAGGAGATACTGAGAAGCAGGTTGAAGCAATA
66 AAAGCGAGCAAAATCTTCGAACC-CAACTTCCTGACGAGATACTGAGAAGCAGGTCAAAGTAATA
* *
8598 AAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAG
130 AAATGGTTAGCCTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAA
* *
8663 AGAAGCGGATTG
195 AGAAGCAGATTA
* *
8675 AAACAAGCGATGCGGCCATCTTCATGATGAGATACTGAAAAGAAGACCAAATCAAACCCACGCTC
1 AAACAAGCGATGCGGTCATCTTCATGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
* * *
8740 AAAACGAGCAAAATCTTCGAACTCCAACTTCTTGACGAGACACTGAGAAGCAGGTCAAAGTAATA
66 AAAGCGAGCAAAATCTTCGAAC-CCAACTTCCTGACGAGATACTGAGAAGCAGGTCAAAGTAATA
* * * *
8805 AAATGGTTAGCGTCCTGATGAGATACTAAGAAGTGAATCAAATTCGTCTTCTTGATGAGATACAA
130 AAATGGTTAGCCTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAA
8870 AGAAGCAGATTA
195 AGAAGCAGATTA
* *
8882 AAACAAGCGATGCGATCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
1 AAACAAGCGATGCGGTCATCTTCATGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
* * * * * *
8947 GATGTGAGC-AAATCTTCGAACCCAGCTTCCTGATGAGATACTGAGAAGCAGATCGAAA-TAATA
66 AAAGCGAGCAAAATCTTCGAACCCAACTTCCTGACGAGATACTGAGAAGCAGGTC-AAAGTAATA
* *
9010 AAATGGTTAGCCTCCTGATGAGACACAGAGAAGT
130 AAATGGTTAGCCTCCTGATGAGATACTGAGAAGT
9044 ATATCAACTC
Statistics
Matches: 331, Mismatches: 35, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
205 63 0.19
206 19 0.06
207 248 0.75
208 1 0.00
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.21
Consensus pattern (206 bp):
AAACAAGCGATGCGGTCATCTTCATGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTC
AAAGCGAGCAAAATCTTCGAACCCAACTTCCTGACGAGATACTGAGAAGCAGGTCAAAGTAATAA
AATGGTTAGCCTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAAA
GAAGCAGATTA
Found at i:9515 original size:23 final size:23
Alignment explanation
Indices: 9484--9544 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
9474 TTGGAATTTG
9484 AATTT-AATTTAAAATTAAGTTT
1 AATTTAAATTTAAAATTAAGTTT
* *
9506 -ATTTGAAATTT-AAATTTATTTT
1 AATTT-AAATTTAAAATTAAGTTT
9528 AAATTTAAATTTAAAAT
1 -AATTTAAATTTAAAAT
9545 GTCCAATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
21 4 0.12
22 9 0.28
23 11 0.34
24 8 0.25
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (23 bp):
AATTTAAATTTAAAATTAAGTTT
Found at i:9518 original size:17 final size:17
Alignment explanation
Indices: 9478--9540 Score: 74
Period size: 17 Copynumber: 3.7 Consensus size: 17
9468 GGCTTATTGG
*
9478 AATTTGAATTTAATTT-A
1 AATTTAAATTT-ATTTGA
* *
9495 AAATTAAGTTTATTTGA
1 AATTTAAATTTATTTGA
*
9512 AATTTAAATTTATTTTA
1 AATTTAAATTTATTTGA
9529 AATTTAAATTTA
1 AATTTAAATTTA
9541 AAATGTCCAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
16 4 0.10
17 35 0.90
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (17 bp):
AATTTAAATTTATTTGA
Found at i:9544 original size:7 final size:6
Alignment explanation
Indices: 9478--9542 Score: 57
Period size: 6 Copynumber: 11.3 Consensus size: 6
9468 GGCTTATTGG
* * *
9478 AATTTG AATTT- AATTTA AAATTA AGTTT- -ATTTGA AATTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTT-A AATTTA AATTTA
*
9523 ATTTTA AATTTA AATTTA AA
1 AATTTA AATTTA AATTTA AA
9543 ATGTCCAATT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
4 3 0.06
5 9 0.19
6 32 0.67
7 4 0.08
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.51
Consensus pattern (6 bp):
AATTTA
Found at i:11216 original size:29 final size:28
Alignment explanation
Indices: 11181--11447 Score: 232
Period size: 29 Copynumber: 9.2 Consensus size: 28
11171 AAATTCCGTC
*
11181 TTTACCCCCAAACTTCCAAAAATCCCAT
1 TTTACCCCAAAACTTCCAAAAATCCCAT
* *
11209 TTTGACCCCAAAACTTCTAAAAATTCCAT
1 TTT-ACCCCAAAACTTCCAAAAATCCCAT
*
11238 TTTACCCCTAAACTTCCAAAAATCCCAT
1 TTTACCCCAAAACTTCCAAAAATCCCAT
* *
11266 TTTAACCCCAAAACTTCTAAAAATTCCAAT
1 TTT-ACCCCAAAACTTCCAAAAA-TCCCAT
* *
11296 TTTATCCCTAAACTTCCAAAAATCCCATT
1 TTTACCCCAAAACTTCCAAAAATCCCA-T
**
11325 TTTGACCCCAAAACTTCCAAAAAT-TTAGTT
1 TTT-ACCCCAAAACTTCCAAAAATCCCA--T
* *
11355 TTTACCTCC-GAACTTCCAAAAATTCCATT
1 TTTACC-CCAAAACTTCCAAAAATCCCA-T
* ** **
11384 TTTAGCCCTGAACTTCCAAAAATTTCATT
1 TTTACCCCAAAACTTCCAAAAATCCCA-T
* * *
11413 TTTAACCTCGAAACTTCCAAAAATTACCAT
1 TTT-ACCCCAAAACTTCCAAAAA-TCCCAT
11443 TTTAC
1 TTTAC
11448 TCCCGGACAT
Statistics
Matches: 200, Mismatches: 28, Indels: 21
0.80 0.11 0.08
Matches are distributed among these distances:
28 34 0.17
29 110 0.55
30 53 0.26
31 3 0.01
ACGTcount: A:0.36, C:0.29, G:0.03, T:0.32
Consensus pattern (28 bp):
TTTACCCCAAAACTTCCAAAAATCCCAT
Found at i:11325 original size:58 final size:58
Alignment explanation
Indices: 11166--11446 Score: 298
Period size: 58 Copynumber: 4.8 Consensus size: 58
11156 CCCTAAATTG
* *
11166 TCTAAAAATTCC-GTCTTTACCCCCAAACTTCCAAAAATCCCATTTTGACCCCAAAACT
1 TCTAAAAATTCCAAT-TTTACCCCCAAACTTCCAAAAATCCCATTTTAACCCCAAAACT
*
11224 TCTAAAAATTCC-ATTTTACCCCTAAACTTCCAAAAATCCCATTTTAACCCCAAAACT
1 TCTAAAAATTCCAATTTTACCCCCAAACTTCCAAAAATCCCATTTTAACCCCAAAACT
* * *
11281 TCTAAAAATTCCAATTTTATCCCTAAACTTCCAAAAATCCCATTTTTGACCCCAAAACT
1 TCTAAAAATTCCAATTTTACCCCCAAACTTCCAAAAATCCCA-TTTTAACCCCAAAACT
* * * * * * * * **
11340 TCCAAAAATT-TAGTTTTTACCTCCGAACTTCCAAAAATTCCATTTTTAGCCCTGAACT
1 TCTAAAAATTCCA-ATTTTACCCCCAAACTTCCAAAAATCCCATTTTAACCCCAAAACT
* * * * * *
11398 TCCAAAAATTTCATTTTTAACCTCGAAACTTCCAAAAATTACCATTTTA
1 TCTAAAAATTCCAATTTT-ACCCCCAAACTTCCAAAAA-TCCCATTTTA
11447 CTCCCGGACA
Statistics
Matches: 195, Mismatches: 22, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
57 53 0.27
58 69 0.35
59 65 0.33
60 8 0.04
ACGTcount: A:0.36, C:0.29, G:0.03, T:0.32
Consensus pattern (58 bp):
TCTAAAAATTCCAATTTTACCCCCAAACTTCCAAAAATCCCATTTTAACCCCAAAACT
Found at i:11446 original size:59 final size:60
Alignment explanation
Indices: 11190--11561 Score: 276
Period size: 59 Copynumber: 6.4 Consensus size: 60
11180 CTTTACCCCC
* * * *
11190 AAACTTCCAAAAA-TCCCATTTTGACCCCAAAACTTCTAAAAATTCCA-TTTT-ACCCCT
1 AAACTTCCAAAAATTACCATTTTGACCCCAAAACTTCCAAAAATTCCATTTTTAACCTCG
* * * * * *
11247 AAACTTCCAAAAA-TCCCATTTTAACCCCAAAACTTCTAAAAATTCCAATTTTATCC-CT
1 AAACTTCCAAAAATTACCATTTTGACCCCAAAACTTCCAAAAATTCCATTTTTAACCTCG
* *
11305 AAACTTCCAAAAA-TCCCATTTTTGACCCCAAAACTTCCAAAAATT-TAGTTTTT-ACCTCCG
1 AAACTTCCAAAAATTACCA-TTTTGACCCCAAAACTTCCAAAAATTCCA-TTTTTAACCT-CG
* * ** *
11365 -AACTTCCAAAAATT-CCATTTTTAGCCCTGAACTTCCAAAAATTTCATTTTTAACCTCG
1 AAACTTCCAAAAATTACCATTTTGACCCCAAAACTTCCAAAAATTCCATTTTTAACCTCG
** * * * * *
11423 AAACTTCCAAAAATTACCATTTT-ACTCCC-GGACATCCAAAAACTCTATTTTTGACTTCG
1 AAACTTCCAAAAATTACCATTTTGAC-CCCAAAACTTCCAAAAATTCCATTTTTAACCTCG
* *
11482 AAAC-TCTC-AAAATTAGCC-TTTT-ACCCTC-AAA-TGTCTAAAAATTCCATTTTTAACCCCG
1 AAACTTC-CAAAAATTA-CCATTTTGACCC-CAAAACT-TCCAAAAATTCCATTTTTAACCTCG
** * *
11540 AATTTTCCCAAAATTACAATTT
1 AAACTTCCAAAAATTACCATTT
11562 CACCCCCGAG
Statistics
Matches: 263, Mismatches: 33, Indels: 36
0.79 0.10 0.11
Matches are distributed among these distances:
57 48 0.18
58 96 0.37
59 107 0.41
60 12 0.05
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.33
Consensus pattern (60 bp):
AAACTTCCAAAAATTACCATTTTGACCCCAAAACTTCCAAAAATTCCATTTTTAACCTCG
Found at i:11446 original size:88 final size:87
Alignment explanation
Indices: 11181--11447 Score: 290
Period size: 88 Copynumber: 3.1 Consensus size: 87
11171 AAATTCCGTC
* * * * *
11181 TTTACCCCCAAACTTCCAAAAATCCCATTTTGACCCCAAAACTTCTAAAAATTCCA-TTTTACCC
1 TTTACCTCCAAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTACCC
* *
11245 CTAAACTTCCAAAAA-TCCCAT
66 CAAAACTTCCAAAAATTACCAT
* * * *
11266 TTTAACC-CCAAAACTTCTAAAAATTCCAATTTTATCCCTAAACTTCCAAAAATCCCATTTTTGA
1 TTT-ACCTCC-AAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATTCCATTTTT-A
**
11330 CCCCAAAACTTCCAAAAATTTA-GTT
63 CCCCAAAACTTCCAAAAA-TTACCAT
* * * *
11355 TTTACCTCCGAACTTCCAAAAATTCCATTTTTAGCCCTGAACTTCCAAAAATTTCATTTTTAACC
1 TTTACCTCCAAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATTCCATTTTT-ACC
* *
11420 TCGAAACTTCCAAAAATTACCAT
65 CCAAAACTTCCAAAAATTACCAT
11443 TTTAC
1 TTTAC
11448 TCCCGGACAT
Statistics
Matches: 150, Mismatches: 24, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
85 5 0.03
86 42 0.28
87 7 0.05
88 89 0.59
89 6 0.04
90 1 0.01
ACGTcount: A:0.36, C:0.29, G:0.03, T:0.32
Consensus pattern (87 bp):
TTTACCTCCAAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTACCC
CAAAACTTCCAAAAATTACCAT
Done.