Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008754.1 Kokia drynarioides strain JFW-HI SEQ_123437, 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: 40207
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Found at i:2169 original size:23 final size:23
Alignment explanation
Indices: 2143--2191 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
2133 AGACAAAAGT
* * *
2143 GTGCCACAAGTTAGAGGAAAAAC
1 GTGCCACAAGGTAAAAGAAAAAC
2166 GTGCCACAAGGTAAAAGAAAAAC
1 GTGCCACAAGGTAAAAGAAAAAC
2189 GTG
1 GTG
2192 TCACGAAAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.16, G:0.27, T:0.12
Consensus pattern (23 bp):
GTGCCACAAGGTAAAAGAAAAAC
Found at i:2635 original size:18 final size:18
Alignment explanation
Indices: 2606--2659 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
2596 TTTAAGATGC
*
2606 CATAATTATATTTTACTAAA
1 CATAA-TATATTATA-TAAA
2626 -ATAATATATTATATAAA
1 CATAATATATTATATAAA
*
2643 CTTAATATATTAATATA
1 CATAATATATT-ATATA
2660 TCATATTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 4 0.13
18 17 0.57
19 9 0.30
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (18 bp):
CATAATATATTATATAAA
Found at i:2833 original size:22 final size:23
Alignment explanation
Indices: 2811--2852 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2801 TTAAATTTTA
2811 AAATT-TT-AAAATAAAAATATT
1 AAATTCTTAAAAATAAAAATATT
2832 AAATTCTTAAAAATAAAAATA
1 AAATTCTTAAAAATAAAAATA
2853 AAATGAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 5 0.26
22 2 0.11
23 12 0.63
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
AAATTCTTAAAAATAAAAATATT
Found at i:2833 original size:29 final size:29
Alignment explanation
Indices: 2799--2880 Score: 89
Period size: 29 Copynumber: 2.8 Consensus size: 29
2789 TAACAGTTGA
2799 AATTAAATTTTAAAATTTTAAAATAAAA-
1 AATTAAATTTTAAAATTTTAAAATAAAAT
* *
2827 ATATTAAATTCTTAAAA-ATAAAAATAAAAT
1 A-ATTAAATT-TTAAAATTTTAAAATAAAAT
2857 GAATTAAATTTT-AAATTTATAAAA
1 -AATTAAATTTTAAAATTT-TAAAA
2881 AGTAGAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
28 4 0.09
29 21 0.48
30 18 0.41
31 1 0.02
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (29 bp):
AATTAAATTTTAAAATTTTAAAATAAAAT
Found at i:8018 original size:3 final size:3
Alignment explanation
Indices: 8010--8037 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
8000 TTGTAGTTTC
8010 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
8038 AAGTGAAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:12606 original size:124 final size:124
Alignment explanation
Indices: 12477--12727 Score: 450
Period size: 124 Copynumber: 2.0 Consensus size: 124
12467 GCTAGTGTGT
*
12477 TAGGTAAATCTATGGATTTCTGATTAGTTGT-TCCTTTTCTCATGATCTATTTTTATGTTTCTTA
1 TAGGTAAATCTATGGATTTCTGATTAGTTGTCCCCTTTT-TCATGATCTATTTTTATGTTTCTTA
*
12541 TTAATTATATTATATGTTACATACAAAACCTTTTTTTTTAAATATCATAGATTTGGATCA
65 TTAATTATATTATATGTTACATACAAAACATTTTTTTTTAAATATCATAGATTTGGATCA
*
12601 TAGGTAAATCTATGGATTTCTGATTAGTTGTCCCCTTTTTCATGATCTATTTTTATGTTTCTTGT
1 TAGGTAAATCTATGGATTTCTGATTAGTTGTCCCCTTTTTCATGATCTATTTTTATGTTTCTTAT
*
12666 TAATTATATTATATGTTATATACAAAACATTTTTTTTTAAATATCATAGATTTGGATCA
66 TAATTATATTATATGTTACATACAAAACATTTTTTTTTAAATATCATAGATTTGGATCA
12725 TAG
1 TAG
12728 TTTTTCTTCA
Statistics
Matches: 122, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
124 116 0.95
125 6 0.05
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.50
Consensus pattern (124 bp):
TAGGTAAATCTATGGATTTCTGATTAGTTGTCCCCTTTTTCATGATCTATTTTTATGTTTCTTAT
TAATTATATTATATGTTACATACAAAACATTTTTTTTTAAATATCATAGATTTGGATCA
Found at i:15610 original size:2 final size:2
Alignment explanation
Indices: 15603--15637 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
15593 TACCCCCTGA
15603 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
15638 GGGATACAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:20487 original size:138 final size:137
Alignment explanation
Indices: 20109--20513 Score: 410
Period size: 138 Copynumber: 3.0 Consensus size: 137
20099 TGATCTTTCA
* * * * *
20109 AAGC-AATCGAGACATCTTAGCAATGCATACATAGATGCATTTAAAACTTGTATCAGTTCC-AAA
1 AAGCTAATCGAGACATTTTA-CAAAGCATACATAGATGCA-TTGAAACTCGTATCAATTCCTAAA
* * * * *
20172 -ACTC-AAAAGAAAG-AGAAAATCAAATGATACACAAGTATACTCACTAATAAAAATAAATTCAC
64 CACACGAAAA-AAAGCA-AAAATCAAAAGACACACAAGTATACTTATTAATAAAAATAAATTCAC
*
20234 AACACAAAGAG
127 AAAACAAAGAG
* * * * * * * *
20245 AGGCTAATTGAGACACCTTAACAAAG--TACACAGATGCATTAGAAACTCATATCCACTCCTAAA
1 AAGCTAATCGAGACA-TTTTACAAAGCATACATAGATGCATT-GAAACTCGTATCAATTCCTAAA
** * **
20308 CTTACGAAAGAAAGCGGAAATCAAAAGACACACAAGTATACTTATTAATAAAAATAAATTCACAA
64 CACACGAAAAAAAGCAAAAATCAAAAGACACACAAGTATACTTATTAATAAAAATAAATTCACAA
*
20373 AAGAAAGAG
129 AACAAAGAG
* * *
20382 AAGCTAATCAAGACATTTTACAAAGCATGCATAGATGTATTGAAAGCTCGTATCAATTCCTAAAC
1 AAGCTAATCGAGACATTTTACAAAGCATACATAGATGCATTGAAA-CTCGTATCAATTCCTAAAC
* * * *
20447 ACACGAAAAAAAGCAAAAATCAAAGGGCACACAAGCATACTTATTAATAAAAATAAATTCATAAA
65 ACACGAAAAAAAGCAAAAATCAAAAGACACACAAGTATACTTATTAATAAAAATAAATTCACAAA
20512 AC
130 AC
20514 CTCTCTATCT
Statistics
Matches: 213, Mismatches: 46, Indels: 18
0.77 0.17 0.06
Matches are distributed among these distances:
134 2 0.01
135 23 0.11
136 14 0.07
137 85 0.40
138 89 0.42
ACGTcount: A:0.49, C:0.18, G:0.12, T:0.21
Consensus pattern (137 bp):
AAGCTAATCGAGACATTTTACAAAGCATACATAGATGCATTGAAACTCGTATCAATTCCTAAACA
CACGAAAAAAAGCAAAAATCAAAAGACACACAAGTATACTTATTAATAAAAATAAATTCACAAAA
CAAAGAG
Found at i:21708 original size:22 final size:22
Alignment explanation
Indices: 21661--21711 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
21651 TATAATATTT
*
21661 AAATAATATTAAAAAAGATAGCA
1 AAATAATAATAAAAAAGATA-CA
*
21684 AAATAATAATAAAAATGCATA-A
1 AAATAATAATAAAAAAG-ATACA
21706 AAATAA
1 AAATAA
21712 CATTCAAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 7 0.28
23 15 0.60
24 3 0.12
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.22
Consensus pattern (22 bp):
AAATAATAATAAAAAAGATACA
Found at i:21775 original size:12 final size:12
Alignment explanation
Indices: 21747--21793 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
21737 AAAACAATAG
*
21747 TAAAAATAATAGA
1 TAAAAATAACA-A
*
21760 -AAAAATAGCAA
1 TAAAAATAACAA
21771 TAAAAATAACAA
1 TAAAAATAACAA
*
21783 TAAAAACAACA
1 TAAAAATAACA
21794 CCAAAATGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 1 0.03
12 28 0.97
ACGTcount: A:0.72, C:0.09, G:0.04, T:0.15
Consensus pattern (12 bp):
TAAAAATAACAA
Found at i:21778 original size:21 final size:22
Alignment explanation
Indices: 21737--21778 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
21727 AATAACAACC
*
21737 AAAACAATAGTAAAAATAATAG
1 AAAACAATAGCAAAAATAATAG
21759 AAAA-AATAGCAATAAA-AATA
1 AAAACAATAGCAA-AAATAATA
21779 ACAATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.71, C:0.05, G:0.07, T:0.17
Consensus pattern (22 bp):
AAAACAATAGCAAAAATAATAG
Found at i:21864 original size:22 final size:22
Alignment explanation
Indices: 21839--21880 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
21829 CCAAAACTAT
21839 AAAAACACAAC-ATCAAAACAGC
1 AAAAA-ACAACAATCAAAACAGC
*
21861 AAAAAATAACAATCAAAACA
1 AAAAAACAACAATCAAAACA
21881 ATAACAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.69, C:0.21, G:0.02, T:0.07
Consensus pattern (22 bp):
AAAAAACAACAATCAAAACAGC
Found at i:24241 original size:13 final size:13
Alignment explanation
Indices: 24223--24249 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
24213 CAGCTTCAAT
24223 ATTCTAAAATTTC
1 ATTCTAAAATTTC
24236 ATTCTAAAATTTC
1 ATTCTAAAATTTC
24249 A
1 A
24250 CCGTGGTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTCTAAAATTTC
Found at i:24925 original size:21 final size:19
Alignment explanation
Indices: 24899--24946 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 19
24889 ATTAGACCCA
24899 TCATCATCCATTAAATCATCT
1 TCATCATCCATT--ATCATCT
*
24920 TCATCAAATTCATTATCATCT
1 TCATC--ATCCATTATCATCT
24941 TCATCA
1 TCATCA
24947 CTGTCTGATC
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
19 1 0.04
21 17 0.71
23 6 0.25
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.40
Consensus pattern (19 bp):
TCATCATCCATTATCATCT
Done.