Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010160.1 Kokia drynarioides strain JFW-HI SEQ_124965, 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: 32136
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Found at i:550 original size:59 final size:59
Alignment explanation
Indices: 466--811 Score: 384
Period size: 59 Copynumber: 5.8 Consensus size: 59
456 AAACTTTTCG
* * *
466 AAAATCCCA-TTTTATCCCCGAACCTTTCAAAAATTACCATTTTACCCTCGAAC-TCTCA
1 AAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCTCAAACTTC-CA
* * *
524 AAAATCCCATTTTTAACCTCGAACCTTCCAAAAATTACCATTTTACCCCCCCAAACTTTCA
1 AAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTA--CCCTCAAACTTCCA
*
585 AAAATCCCATTTTAAACCCCGAACCTTCCAAAAATTA-CATTTTACCC-CTAAACTTCCA
1 AAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCTC-AAACTTCCA
* * * * * *
643 AAAATCTCATTTTTAACCCCAAATCTTCCAAAAATCACCATTTTACCTTCGAACTTCCA
1 AAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCTCAAACTTCCA
* *
702 AAAATCCCATTTTAAACCCCAAACCTTCC-AAAATTACCATTTTTGACCC-CAAACCTTCCA
1 AAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCA-TTTT-ACCCTCAAA-CTTCCA
* * * *
762 AAAATCCCATTTTTGACCTCGAAAC-TCTC-AAAATTGCCATTTTTACCCTC
1 AAAATCCCATTTTTAACCCCGAACCTTC-CAAAAATTACCA-TTTTACCCTC
812 GAATGTTTTA
Statistics
Matches: 248, Mismatches: 28, Indels: 22
0.83 0.09 0.07
Matches are distributed among these distances:
57 1 0.00
58 61 0.25
59 88 0.35
60 53 0.21
61 44 0.18
62 1 0.00
ACGTcount: A:0.35, C:0.33, G:0.03, T:0.30
Consensus pattern (59 bp):
AAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTTACCCTCAAACTTCCA
Found at i:654 original size:119 final size:120
Alignment explanation
Indices: 456--809 Score: 415
Period size: 119 Copynumber: 3.0 Consensus size: 120
446 GAAGGTCCCT
* * * *
456 AAACTTTTCGAAAATCCCATTTT-ATCCCCGAACCTTTCAAAAATTACCATTTTA-CCCTCGAAC
1 AAAC-TTTCAAAAATCCCATTTTAAACCCCGAACCTTCCAAAAATTACCATTTTACCCCT-AAAC
*
519 -TCTCAAAAATCCCATTTTTAACCTCGAACCTTCCAAAAATTACCATTTTACCCCCCC
64 TTC-CAAAAATCCCATTTTTAACCTCGAAACTTCCAAAAATTACCATTTTACCCCCCC
576 AAACTTTCAAAAATCCCATTTTAAACCCCGAACCTTCCAAAAATTA-CATTTTACCCCTAAACTT
1 AAACTTTCAAAAATCCCATTTTAAACCCCGAACCTTCCAAAAATTACCATTTTACCCCTAAACTT
* * * **
640 CCAAAAATCTCATTTTTAACC-CCAAATCTTCCAAAAATCACCATTTTA--CCTTC
66 CCAAAAATCCCATTTTTAACCTCGAAA-CTTCCAAAAATTACCATTTTACCCCCCC
* * *
693 GAACTTCCAAAAATCCCATTTTAAACCCCAAACCTTCC-AAAATTACCATTTTTGACCCC-AAAC
1 AAACTTTCAAAAATCCCATTTTAAACCCCGAACCTTCCAAAAATTACCA-TTTT-ACCCCTAAA-
* *
756 CTTCCAAAAATCCCATTTTTGACCTCGAAAC-TCTC-AAAATTGCCATTTTTACCC
63 CTTCCAAAAATCCCATTTTTAACCTCGAAACTTC-CAAAAATTACCA-TTTTACCC
810 TCGAATGTTT
Statistics
Matches: 203, Mismatches: 18, Indels: 25
0.83 0.07 0.10
Matches are distributed among these distances:
116 7 0.03
117 40 0.20
118 20 0.10
119 100 0.49
120 35 0.17
121 1 0.00
ACGTcount: A:0.35, C:0.32, G:0.03, T:0.30
Consensus pattern (120 bp):
AAACTTTCAAAAATCCCATTTTAAACCCCGAACCTTCCAAAAATTACCATTTTACCCCTAAACTT
CCAAAAATCCCATTTTTAACCTCGAAACTTCCAAAAATTACCATTTTACCCCCCC
Found at i:779 original size:30 final size:30
Alignment explanation
Indices: 466--775 Score: 250
Period size: 30 Copynumber: 10.5 Consensus size: 30
456 AAACTTTTCG
* * *
466 AAAATCCCA-TTTTATCCCCGAACCTTTCA
1 AAAATCCCATTTTTAACCCCAAACCTTCCA
* *
495 AAAATTACCA-TTTT-ACCCTCGAA-C-TCTCA
1 AAAA-TCCCATTTTTAACCC-CAAACCTTC-CA
* *
524 AAAATCCCATTTTTAACCTCGAACCTTCCA
1 AAAATCCCATTTTTAACCCCAAACCTTCCA
* * *
554 AAAATTACCA-TTTTACCCCCCCAAA-CTTTCA
1 AAAA-TCCCATTTTTA--ACCCCAAACCTTCCA
* *
585 AAAATCCCATTTTAAACCCCGAACCTTCCA
1 AAAATCCCATTTTTAACCCCAAACCTTCCA
**
615 AAAATTACA-TTTT-ACCCCTAAA-CTTCCA
1 AAAATCCCATTTTTAACCCC-AAACCTTCCA
* *
643 AAAATCTCATTTTTAACCCCAAATCTTCCA
1 AAAATCCCATTTTTAACCCCAAACCTTCCA
* *
673 AAAATCACCA-TTTT-ACCTTCGAA-CTTCCA
1 AAAATC-CCATTTTTAACC-CCAAACCTTCCA
*
702 AAAATCCCATTTTAAACCCCAAACCTTCCA
1 AAAATCCCATTTTTAACCCCAAACCTTCCA
* * *
732 AAATTACCATTTTTGACCCCAAACCTTCCA
1 AAAATCCCATTTTTAACCCCAAACCTTCCA
762 AAAATCCCATTTTT
1 AAAATCCCATTTTT
776 GACCTCGAAA
Statistics
Matches: 227, Mismatches: 33, Indels: 41
0.75 0.11 0.14
Matches are distributed among these distances:
28 26 0.11
29 61 0.27
30 114 0.50
31 21 0.09
32 5 0.02
ACGTcount: A:0.35, C:0.33, G:0.02, T:0.30
Consensus pattern (30 bp):
AAAATCCCATTTTTAACCCCAAACCTTCCA
Found at i:794 original size:30 final size:31
Alignment explanation
Indices: 466--814 Score: 186
Period size: 30 Copynumber: 11.7 Consensus size: 31
456 AAACTTTTCG
* * * *
466 AAAATCCCA-TTTTATCCCCGAACCT-TTCA
1 AAAATCCCATTTTTAACCTCGAAACTCTCCA
* *
495 AAAATTACCA-TTTTACCCTCG-AACTCT-CA
1 AAAA-TCCCATTTTTAACCTCGAAACTCTCCA
*
524 AAAATCCCATTTTTAACCTCGAACCT-TCCA
1 AAAATCCCATTTTTAACCTCGAAACTCTCCA
* * * * *
554 AAAATTACCA-TTTTACCCCCCCAAACT-TTCA
1 AAAA-TCCCATTTTTA-ACCTCGAAACTCTCCA
* * *
585 AAAATCCCATTTTAAACCCCGAACCT-TCCA
1 AAAATCCCATTTTTAACCTCGAAACTCTCCA
** * *
615 AAAATTACA-TTTT-ACCCCTAAACT-TCCA
1 AAAATCCCATTTTTAACCTCGAAACTCTCCA
* *
643 AAAATCTCATTTTTAACC-CCAAA-TCTTCCA
1 AAAATCCCATTTTTAACCTCGAAACTC-TCCA
673 AAAATCACCA-TTTT-ACCTTCG-AACT-TCCA
1 AAAATC-CCATTTTTAACC-TCGAAACTCTCCA
* *
702 AAAATCCCATTTTAAACC-CCAAAC-CTTCCA
1 AAAATCCCATTTTTAACCTCGAAACTC-TCCA
* * * *
732 AAATTACCATTTTTGACC-CCAAAC-CTTCCA
1 AAAATCCCATTTTTAACCTCGAAACTC-TCCA
*
762 AAAATCCCATTTTTGACCTCGAAACTCT-CA
1 AAAATCCCATTTTTAACCTCGAAACTCTCCA
* * *
792 AAATTGCCATTTTTACCCTCGAA
1 AAAATCCCATTTTTAACCTCGAA
815 TGTTTTAAAT
Statistics
Matches: 255, Mismatches: 42, Indels: 45
0.75 0.12 0.13
Matches are distributed among these distances:
28 29 0.11
29 54 0.21
30 139 0.55
31 32 0.13
32 1 0.00
ACGTcount: A:0.35, C:0.32, G:0.03, T:0.30
Consensus pattern (31 bp):
AAAATCCCATTTTTAACCTCGAAACTCTCCA
Found at i:795 original size:89 final size:86
Alignment explanation
Indices: 475--784 Score: 299
Period size: 89 Copynumber: 3.5 Consensus size: 86
465 GAAAATCCCA
* * * *
475 TTTTATCCCCGAACCTTTCAAAAATTACCATTTTACCCTCGAAC-TCTCAAAAATCCCATTTTTA
1 TTTTAACCCCAAACCTTCCAAAAA-TCCCATTTTA-CCTCGAACTTC-CAAAAATCCCA-TTTTA
* *
539 ACCTCGAACCTTCCAAAAATTACCA-
62 ACCCCAAACCTTCC-AAAATTACCAT
* * * **
564 TTTTACCCCCCCAAA-CTTTCAAAAATCCCATTTTAAACCCCGAACCTTCCAAAAATTACATTTT
1 TTTTA--ACCCCAAACCTTCCAAAAATCCCATTTT--ACCTCGAA-CTTCCAAAAATCCCATTTT
*
628 -ACCCCTAAA-CTTCCAAAAAT-CTCAT
61 AACCCC-AAACCTTCCAAAATTAC-CAT
*
653 TTTTAACCCCAAATCTTCCAAAAATCACCATTTTACCTTCGAACTTCCAAAAATCCCATTTTAAA
1 TTTTAACCCCAAACCTTCCAAAAATC-CCATTTTACC-TCGAACTTCCAAAAATCCCATTTT-AA
718 CCCCAAACCTTCCAAAATTACCAT
63 CCCCAAACCTTCCAAAATTACCAT
*
742 TTTTGACCCCAAACCTTCCAAAAATCCCATTTTTGACCTCGAA
1 TTTTAACCCCAAACCTTCCAAAAATCCCA-TTTT-ACCTCGAA
785 ACTCTCAAAA
Statistics
Matches: 186, Mismatches: 17, Indels: 36
0.78 0.07 0.15
Matches are distributed among these distances:
87 28 0.15
88 28 0.15
89 85 0.46
90 26 0.14
91 17 0.09
92 2 0.01
ACGTcount: A:0.35, C:0.33, G:0.03, T:0.30
Consensus pattern (86 bp):
TTTTAACCCCAAACCTTCCAAAAATCCCATTTTACCTCGAACTTCCAAAAATCCCATTTTAACCC
CAAACCTTCCAAAATTACCAT
Found at i:5754 original size:47 final size:47
Alignment explanation
Indices: 5685--5774 Score: 171
Period size: 47 Copynumber: 1.9 Consensus size: 47
5675 CTAAAACAAG
5685 GTAGAATGTCTATCATGGAGTATGAGCATGAATTCCTTCGGCTTAGT
1 GTAGAATGTCTATCATGGAGTATGAGCATGAATTCCTTCGGCTTAGT
*
5732 GTAGAATGTCTATCATGGAGTATGAGCGTGAATTCCTTCGGCT
1 GTAGAATGTCTATCATGGAGTATGAGCATGAATTCCTTCGGCT
5775 CAGTCGTTAC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (47 bp):
GTAGAATGTCTATCATGGAGTATGAGCATGAATTCCTTCGGCTTAGT
Found at i:12185 original size:25 final size:23
Alignment explanation
Indices: 12142--12203 Score: 65
Period size: 25 Copynumber: 2.7 Consensus size: 23
12132 GGGCAAACAA
*
12142 AATTATTAA-ACAAAATAATATGAT
1 AATTATTAATA-AAATTAATAT-AT
12166 AATTTATTAATAAAATTAATATAT
1 AA-TTATTAATAAAATTAATATAT
*
12190 TATT-TTAATAAAAT
1 AATTATTAATAAAAT
12204 CATTTAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
22 10 0.29
23 2 0.06
24 5 0.15
25 16 0.47
26 1 0.03
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
AATTATTAATAAAATTAATATAT
Found at i:12282 original size:25 final size:24
Alignment explanation
Indices: 12254--12323 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 24
12244 AATTTAATTT
12254 TTAAATAATATTTTTAATATTTTTA
1 TTAAAT-ATATTTTTAATATTTTTA
*
12279 TTAAATATATATATTAATATTTTTA
1 TTAAATATAT-TTTTAATATTTTTA
*
12304 ATAAATATATTTTATAATAT
1 TTAAATATATTTT-TAATAT
12324 AAAATATTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
24 6 0.15
25 34 0.85
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TTAAATATATTTTTAATATTTTTA
Found at i:12285 original size:13 final size:13
Alignment explanation
Indices: 12269--12318 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
12259 TAATATTTTT
12269 AATATTTTTATTA
1 AATATTTTTATTA
* *
12282 AATATATATATT-
1 AATATTTTTATTA
*
12294 AATATTTTTAATA
1 AATATTTTTATTA
12307 AATATATTTTAT
1 AATAT-TTTTAT
12319 AATATAAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
12 9 0.31
13 15 0.52
14 5 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
AATATTTTTATTA
Found at i:12320 original size:13 final size:13
Alignment explanation
Indices: 12250--12324 Score: 56
Period size: 13 Copynumber: 6.1 Consensus size: 13
12240 CAATAATTTA
12250 ATTTT-TAAATAAT
1 ATTTTATAAAT-AT
12263 ATTTT-T-AATAT
1 ATTTTATAAATAT
12274 -TTTTATTAAATAT
1 ATTTTA-TAAATAT
* *
12287 A-TATATTAATAT
1 ATTTTATAAATAT
12299 -TTTTAATAAATAT
1 ATTTT-ATAAATAT
12312 ATTTTAT-AATAT
1 ATTTTATAAATAT
12324 A
1 A
12325 AAATATTAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
10 4 0.08
11 2 0.04
12 18 0.35
13 23 0.45
14 4 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTTTATAAATAT
Found at i:19723 original size:26 final size:26
Alignment explanation
Indices: 19694--19743 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
19684 ATTATTCGAG
*
19694 TAATT-AATTTTTTCATATTATTTTAA
1 TAATTAAAATTTTT-ATATTATTTTAA
19720 TAATTAAAATTTTTATATTATTTT
1 TAATTAAAATTTTTATATTATTTT
19744 GGAGAAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (26 bp):
TAATTAAAATTTTTATATTATTTTAA
Found at i:23978 original size:23 final size:23
Alignment explanation
Indices: 23950--24003 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
23940 CGTCCATCCT
23950 TGCTGACTAGACCTTCTAGAAGC
1 TGCTGACTAGACCTTCTAGAAGC
* * *
23973 TGCTGACTGGATCTTGTAGAAGC
1 TGCTGACTAGACCTTCTAGAAGC
*
23996 TGTTGACT
1 TGCTGACT
24004 GGACACCACA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.31
Consensus pattern (23 bp):
TGCTGACTAGACCTTCTAGAAGC
Found at i:30898 original size:6 final size:6
Alignment explanation
Indices: 30887--30930 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
30877 TTGAAAACGA
* *
30887 GAAAGG GAAAGG AGTAAGGG GGAAGG GAAAGG GAAAGG GAAAGG
1 GAAAGG GAAAGG -G-AAAGG GAAAGG GAAAGG GAAAGG GAAAGG
30931 AGGAAGGGGG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
6 26 0.81
7 2 0.06
8 4 0.12
ACGTcount: A:0.45, C:0.00, G:0.52, T:0.02
Consensus pattern (6 bp):
GAAAGG
Found at i:30923 original size:26 final size:27
Alignment explanation
Indices: 30887--30953 Score: 84
Period size: 26 Copynumber: 2.5 Consensus size: 27
30877 TTGAAAACGA
* *
30887 GAAAGGGAAAGGAGTAAGGGGGAA-GG
1 GAAAGGGAAAGGAGAAAGGAGGAAGGG
30913 GAAAGGGAAAGG-GAAAGGAGGAAGGG
1 GAAAGGGAAAGGAGAAAGGAGGAAGGG
*
30939 GGAAGGGAAATGGAG
1 GAAAGGGAAA-GGAG
30954 GAGAGGCTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 9 0.26
26 23 0.66
27 2 0.06
28 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.54, T:0.03
Consensus pattern (27 bp):
GAAAGGGAAAGGAGAAAGGAGGAAGGG
Found at i:30928 original size:32 final size:32
Alignment explanation
Indices: 30887--30948 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
30877 TTGAAAACGA
*
30887 GAAAGGGAAAGGAGTAAGGGGGAAGGGAAAGG
1 GAAAGGGAAAGGAGGAAGGGGGAAGGGAAAGG
30919 GAAAGGGAAAGGAGGAAGGGGGAAGGGAAA
1 GAAAGGGAAAGGAGGAAGGGGGAAGGGAAA
30949 TGGAGGAGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.53, T:0.02
Consensus pattern (32 bp):
GAAAGGGAAAGGAGGAAGGGGGAAGGGAAAGG
Found at i:30935 original size:20 final size:21
Alignment explanation
Indices: 30912--30955 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
30902 AAGGGGGAAG
30912 GGAAAGGGAAAGGGAAA-GGA
1 GGAAAGGGAAAGGGAAATGGA
* *
30932 GGAAGGGGGAAGGGAAATGGA
1 GGAAAGGGAAAGGGAAATGGA
30953 GGA
1 GGA
30956 GAGGCTTCGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.43, C:0.00, G:0.55, T:0.02
Consensus pattern (21 bp):
GGAAAGGGAAAGGGAAATGGA
Done.