Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012752.1 Kokia drynarioides strain JFW-HI SEQ_127763, 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: 2492
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Found at i:24 original size:17 final size:17
Alignment explanation
Indices: 2--68 Score: 98
Period size: 17 Copynumber: 3.9 Consensus size: 17
1 A
*
2 TTTAAATTTAAGTTTAT
1 TTTAAATTTAAATTTAT
19 TTTAAATTTAAATTTAT
1 TTTAAATTTAAATTTAT
*
36 TTGAAATTTAAATTTAT
1 TTTAAATTTAAATTTAT
* *
53 TATAAAATTAAATTTA
1 TTTAAATTTAAATTTA
69 GAAAGTCCAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 45 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
TTTAAATTTAAATTTAT
Found at i:44 original size:7 final size:6
Alignment explanation
Indices: 1--68 Score: 56
Period size: 6 Copynumber: 11.8 Consensus size: 6
* *
1 ATTTAA ATTTAA GTTT-A TTTTAA ATTTAA ATTT-- ATTTGAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA ATTTAA
*
47 ATTT-- ATTATAA AATTAA ATTTA
1 ATTTAA ATT-TAA ATTTAA ATTTA
69 GAAAGTCCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
4 7 0.14
5 5 0.10
6 32 0.64
7 6 0.12
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (6 bp):
ATTTAA
Found at i:87 original size:12 final size:13
Alignment explanation
Indices: 70--109 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
60 TTAAATTTAG
70 AAAGTCCAATTA-
1 AAAGTCCAATTAC
*
82 AAAGTCCAA-AAC
1 AAAGTCCAATTAC
94 AAAGTCCAATTAC
1 AAAGTCCAATTAC
107 AAA
1 AAA
110 TGATCCAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 1 0.04
12 18 0.75
13 5 0.21
ACGTcount: A:0.55, C:0.20, G:0.07, T:0.17
Consensus pattern (13 bp):
AAAGTCCAATTAC
Found at i:798 original size:14 final size:14
Alignment explanation
Indices: 781--822 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
771 ATAATGTTAT
781 TATTATTAATATAA
1 TATTATTAATATAA
* *
795 TATTAATAATA-AT
1 TATTATTAATATAA
808 TATTATTAA-ATAA
1 TATTATTAATATAA
821 TA
1 TA
823 AAAAGGGAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
12 1 0.04
13 12 0.52
14 10 0.43
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TATTATTAATATAA
Found at i:1992 original size:59 final size:59
Alignment explanation
Indices: 1882--2262 Score: 545
Period size: 59 Copynumber: 6.5 Consensus size: 59
1872 AAAGTCCCTA
*
1882 AACCTTCTAAAAATTACCATTTTA-CCCCAAACTTCCAAAAATCTCATTTTTGACCCCG
1 AACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCCCG
*
1940 AACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCCCG
1 AACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCCCG
* * * * *
1999 AACCTTCTAAAAATTATCATTTTGCCTCCGAACTTCCAAAAAT-TCTTTTTTGACCTCG
1 AACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCCCG
* *
2057 AACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATC-CTATTTTTGACTCCA
1 AACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTC-ATTTTTGACCCCG
* * *
2116 AACCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCT
1 AACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCCCG
* * * * *
2175 AACCTTCTAAAAATTACCATTTTACCCTCGAACTTTCAAAAATCCCATTTTTGACTCTG
1 AACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCCCG
* * *
2234 AACCCTCT-AAAACTACCATTTTGCCCCCG
1 AACCTTCTAAAAATTACCATTTTACCCCCG
2263 TGCATCCGAA
Statistics
Matches: 295, Mismatches: 24, Indels: 8
0.90 0.07 0.02
Matches are distributed among these distances:
58 96 0.33
59 198 0.67
60 1 0.00
ACGTcount: A:0.32, C:0.31, G:0.04, T:0.33
Consensus pattern (59 bp):
AACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCCCG
Found at i:2091 original size:117 final size:116
Alignment explanation
Indices: 1882--2260 Score: 555
Period size: 117 Copynumber: 3.2 Consensus size: 116
1872 AAAGTCCCTA
*
1882 AACCTTCTAAAAATTACCATTTTACCCCAAACTTCCAAAAATCTCATTTTTGACCCCGAACCTTC
1 AACCTTCTAAAAATTACCATTTTACCCCGAACTTCCAAAAATCTCATTTTTGACCCCGAACCTTC
* *
1947 TAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCCCG
66 TAAAAATTACCATTTTACCCCCGAACTTCCAAAAATC-CATTTTTGACTCCG
* * * *
1999 AACCTTCTAAAAATTATCATTTTGCCTCCGAACTTCCAAAAAT-TCTTTTTTGACCTCGAACCTT
1 AACCTTCTAAAAATTACCATTTTACC-CCGAACTTCCAAAAATCTCATTTTTGACCCCGAACCTT
*
2063 CTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCTATTTTTGACTCCA
65 CTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCC-ATTTTTGACTCCG
* *
2116 AACCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCTAACCTT
1 AACCTTCTAAAAATTACCATTTTACCC-CGAACTTCCAAAAATCTCATTTTTGACCCCGAACCTT
* * *
2181 CTAAAAATTACCATTTTACCCTCGAACTTTCAAAAATCCCATTTTTGACTCTG
65 CTAAAAATTACCATTTTACCCCCGAACTTCCAAAAAT-CCATTTTTGACTCCG
* * *
2234 AACCCTCT-AAAACTACCATTTTGCCCC
1 AACCTTCTAAAAATTACCATTTTACCCC
2261 CGTGCATCCG
Statistics
Matches: 236, Mismatches: 21, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
116 3 0.01
117 146 0.62
118 85 0.36
119 2 0.01
ACGTcount: A:0.32, C:0.31, G:0.04, T:0.33
Consensus pattern (116 bp):
AACCTTCTAAAAATTACCATTTTACCCCGAACTTCCAAAAATCTCATTTTTGACCCCGAACCTTC
TAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCATTTTTGACTCCG
Found at i:2181 original size:176 final size:177
Alignment explanation
Indices: 1882--2262 Score: 558
Period size: 176 Copynumber: 2.2 Consensus size: 177
1872 AAAGTCCCTA
* *
1882 AACCTTCTAAAAATTACCATTTTA-CCCCAAACTTCCAAAAATCTCATTTTTGACCCCGAACCTT
1 AACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCCCAAACCTT
*
1946 CTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCCCGAACCTTCTAAAA
66 CTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAA
* * * *
2011 ATTATCATTTT-GCCTCCGAACTTCCAAAAAT-TCTTTTTTGAC-CTCG
131 ATTACCATTTTACCCT-CGAACTTCCAAAAATCCCATTTTTGACTCT-G
*
2057 AACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATC-CTATTTTTGACTCCAAACCT
1 AACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTC-ATTTTTGACCCCAAACCT
* * *
2121 TCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCTAACCTTCTAAA
65 TCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAA
*
2186 AATTACCATTTTACCCTCGAACTTTCAAAAATCCCATTTTTGACTCTG
130 AATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACTCTG
* * *
2234 AACCCTCT-AAAACTACCATTTTGCCCCCG
1 AACCTTCTAAAAATTACCATTTTACCCCCG
2263 TGCATCCGAA
Statistics
Matches: 186, Mismatches: 15, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
175 25 0.13
176 139 0.75
177 20 0.11
178 2 0.01
ACGTcount: A:0.32, C:0.31, G:0.04, T:0.33
Consensus pattern (177 bp):
AACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCCCAAACCTT
CTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAA
ATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACTCTG
Found at i:2236 original size:29 final size:29
Alignment explanation
Indices: 1911--2236 Score: 131
Period size: 30 Copynumber: 11.1 Consensus size: 29
1901 TTTTACCCCA
* * *
1911 AACTTCCAAAAATCTCATTTTTGACCCCG
1 AACTTTCAAAAATCCCATTTTTGACCCTG
* * **
1940 AACCTTCTAAAAATTACCA-TTTT-ACCCCCA
1 AACTTTC-AAAAA-TCCCATTTTTGA-CCCTG
* * *
1970 AACTTCCAAAAATCTCATTTTTGACCCCG
1 AACTTTCAAAAATCCCATTTTTGACCCTG
* ** *
1999 AACCTTCTAAAAATTATCA-TTTTG-CCTCCG
1 AACTTTC-AAAAA-TCCCATTTTTGACC-CTG
* * *
2029 AACTTCCAAAAAT-TCTTTTTTGA-CCTCG
1 AACTTTCAAAAATCCCATTTTTGACCCT-G
* * *
2057 AACCTTCTAAAAATTACCA-TTTT-ACCCCCG
1 AACTTTC-AAAAA-TCCCATTTTTGA-CCCTG
* * *
2087 AACTTCCAAAAATCCTATTTTTGACTCC-A
1 AACTTTCAAAAATCCCATTTTTGAC-CCTG
* *
2116 AACCTTCTAAAAATTACCA-TTTT-ACCCTCG
1 AACTTTC-AAAAA-TCCCATTTTTGACCCT-G
*
2146 AACTTCCAAAAATCCCATTTTTGACCCCT-
1 AACTTTCAAAAATCCCATTTTTGA-CCCTG
* *
2175 AACCTTCTAAAAATTACCA-TTTT-ACCCTCG
1 AACTTTC-AAAAA-TCCCATTTTTGACCCT-G
*
2205 AACTTTCAAAAATCCCATTTTTGACTCTG
1 AACTTTCAAAAATCCCATTTTTGACCCTG
2234 AAC
1 AAC
2237 CCTCTAAAAC
Statistics
Matches: 224, Mismatches: 41, Indels: 64
0.68 0.12 0.19
Matches are distributed among these distances:
27 3 0.01
28 33 0.15
29 82 0.37
30 85 0.38
31 21 0.09
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.33
Consensus pattern (29 bp):
AACTTTCAAAAATCCCATTTTTGACCCTG
Done.