Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009346.1 Kokia drynarioides strain JFW-HI SEQ_124053, 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: 23019
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:1954 original size:21 final size:21
Alignment explanation
Indices: 1930--1979 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1920 GAATTTCAGT
*
1930 AGCAATCTATAGATTTTCAAA
1 AGCAAACTATAGATTTTCAAA
* *
1951 AGCAAACTGTGGATTTTCAAA
1 AGCAAACTATAGATTTTCAAA
*
1972 AGAAAACT
1 AGCAAACT
1980 GAGGCATCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (21 bp):
AGCAAACTATAGATTTTCAAA
Found at i:1980 original size:21 final size:21
Alignment explanation
Indices: 1941--1980 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1931 GCAATCTATA
*
1941 GATTTTCAAAAGCAAACTGTG
1 GATTTTCAAAAGAAAACTGTG
1962 GATTTTCAAAAGAAAACTG
1 GATTTTCAAAAGAAAACTG
1981 AGGCATCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.28
Consensus pattern (21 bp):
GATTTTCAAAAGAAAACTGTG
Found at i:4766 original size:19 final size:19
Alignment explanation
Indices: 4744--4788 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
4734 TTATATTAGG
4744 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
4763 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
4782 ATTTAAT
1 ATTTAAT
4789 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:6353 original size:23 final size:23
Alignment explanation
Indices: 6327--6429 Score: 120
Period size: 23 Copynumber: 4.5 Consensus size: 23
6317 TGCTGGGAAA
* * *
6327 CAGTAAGCACACACAGTGC-AAT
1 CAGTAGGCACACATAGCGCAAAT
*
6349 CCAGTAGGCACACATAGTGC-AAT
1 -CAGTAGGCACACATAGCGCAAAT
*
6372 CAGTAGGCGCACATAGCGCAAAT
1 CAGTAGGCACACATAGCGCAAAT
*
6395 CAGTAGGCGCACATAGCGCAAAT
1 CAGTAGGCACACATAGCGCAAAT
*
6418 CAGTAAGCACAC
1 CAGTAGGCACAC
6430 GAAGTGCGAA
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
22 17 0.23
23 56 0.77
ACGTcount: A:0.37, C:0.27, G:0.22, T:0.14
Consensus pattern (23 bp):
CAGTAGGCACACATAGCGCAAAT
Found at i:6444 original size:23 final size:22
Alignment explanation
Indices: 6300--6448 Score: 113
Period size: 23 Copynumber: 6.5 Consensus size: 22
6290 CGAAGTACTT
6300 AACAGTAAGCACACA-AGTGCTGGGA
1 AACAGTAAGCACACATAGTGC----A
*
6325 AACAGTAAGCACACACAGTGCA
1 AACAGTAAGCACACATAGTGCA
* *
6347 ATCCAGTAGGCACACATAGTGCA
1 A-ACAGTAAGCACACATAGTGCA
* * * *
6370 ATCAGTAGGCGCACATAGCGCA
1 AACAGTAAGCACACATAGTGCA
* * *
6392 AATCAGTAGGCGCACATAGCGCA
1 AA-CAGTAAGCACACATAGTGCA
6415 AATCAGTAAGCACACGA-AGTGCGA
1 AA-CAGTAAGCACAC-ATAGTGC-A
6439 AACAGTAAGC
1 AACAGTAAGC
6449 GCATTAGCGT
Statistics
Matches: 109, Mismatches: 10, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
22 21 0.19
23 64 0.59
24 4 0.04
25 15 0.14
26 5 0.05
ACGTcount: A:0.39, C:0.24, G:0.24, T:0.13
Consensus pattern (22 bp):
AACAGTAAGCACACATAGTGCA
Found at i:10247 original size:24 final size:24
Alignment explanation
Indices: 10219--10281 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
10209 TAGACTAATA
* *
10219 AGAGTTTGATTCAAACAAATAAAC
1 AGAGTTTAATTAAAACAAATAAAC
* *
10243 AGAGTTTAATTAAAACAATTAAAT
1 AGAGTTTAATTAAAACAAATAAAC
*
10267 AGAGTTTAACTAAAA
1 AGAGTTTAATTAAAA
10282 GATTATTTCG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.29
Consensus pattern (24 bp):
AGAGTTTAATTAAAACAAATAAAC
Found at i:13901 original size:38 final size:38
Alignment explanation
Indices: 13850--13927 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
13840 TATATCATGC
13850 TTTGGAATGATCGGGCAAATAGGTGCTCAACCTTGTAT
1 TTTGGAATGATCGGGCAAATAGGTGCTCAACCTTGTAT
13888 TTTGGAATGATCGGGCAAATAGGTGCTCAACCTTGTAT
1 TTTGGAATGATCGGGCAAATAGGTGCTCAACCTTGTAT
13926 TT
1 TT
13928 GTGTAACAGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (38 bp):
TTTGGAATGATCGGGCAAATAGGTGCTCAACCTTGTAT
Found at i:14139 original size:24 final size:23
Alignment explanation
Indices: 14102--14153 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
14092 GTTCAGATTT
*
14102 CGAGCCCGAGGATGAGCCCAATGA
1 CGAGCCCGAGGATGA-CCCAAGGA
** *
14126 CGAGCCCGCTGATGACCCACGGA
1 CGAGCCCGAGGATGACCCAAGGA
14149 CGAGC
1 CGAGC
14154 TCGATTACGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.25, C:0.35, G:0.33, T:0.08
Consensus pattern (23 bp):
CGAGCCCGAGGATGACCCAAGGA
Found at i:15630 original size:39 final size:42
Alignment explanation
Indices: 15586--15671 Score: 117
Period size: 44 Copynumber: 2.1 Consensus size: 42
15576 CTGCTATGGC
15586 ATGGCCAACA-CAAAAAA-ATTG-AA-TTTTTTATCTGACAAA
1 ATGGCCAACACCAAAAAATATTGAAATTTTTTTATCTGA-AAA
*
15625 ATGGCCAACACCAAAAAATTTTGAAATTTTTTTTATCTGAAAA
1 ATGGCCAACACCAAAAAATATTGAAA-TTTTTTTATCTGAAAA
15668 ATGG
1 ATGG
15672 GTTGTCGGCC
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
39 10 0.24
40 7 0.17
41 3 0.07
42 2 0.05
43 7 0.17
44 12 0.29
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (42 bp):
ATGGCCAACACCAAAAAATATTGAAATTTTTTTATCTGAAAA
Found at i:15824 original size:61 final size:60
Alignment explanation
Indices: 15625--15827 Score: 237
Period size: 60 Copynumber: 3.3 Consensus size: 60
15615 ATCTGACAAA
* * * *
15625 ATGGCCAACACCAAAAAATTTTGAAATTTTTTTTATCTGAAAAATGGGTTGTCGGCCATTAC
1 ATGGCCAACACAAAAAAATTTTGAAA--ATTTTTATCTGAAAAAAGGGGTGTCGGCCATTAC
* * * * *
15687 ATGACCAACA-ACAAAAATTTTTAAAAATTTTTATCTGAAAAAAGAGGTGTCGGCTATTAC
1 ATGGCCAACACA-AAAAAATTTTGAAAATTTTTATCTGAAAAAAGGGGTGTCGGCCATTAC
** * * *
15747 ATGTTCAACACCAAAAAATTTTGAAAATTTTTAATCTGAAAAAGGGGGTGTCGGCCATTAT
1 ATGGCCAACACAAAAAAATTTTGAAAATTTTT-ATCTGAAAAAAGGGGTGTCGGCCATTAC
15808 ATGGCCAACACAAAAAAATT
1 ATGGCCAACACAAAAAAATT
15828 GTATTTTTTA
Statistics
Matches: 117, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
60 55 0.47
61 41 0.35
62 21 0.18
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (60 bp):
ATGGCCAACACAAAAAAATTTTGAAAATTTTTATCTGAAAAAAGGGGTGTCGGCCATTAC
Found at i:15850 original size:121 final size:119
Alignment explanation
Indices: 15630--15856 Score: 289
Period size: 121 Copynumber: 1.9 Consensus size: 119
15620 ACAAAATGGC
* * * *
15630 CAACACCAAAAAATTTTGAAATTTTTTTTATCTGAAAAATGGGTTGTCGGCCATTACATGACCAA
1 CAACACCAAAAAATTTTGAAATATTTTTAATCTGAAAAAGGGGGTGTCGGCCATTACATGACCAA
* *
15695 CAACAAAAATTTTTAAAAATTTTTATCTGAAAAAAGAGGTGTCGGCTATTACATGTT
66 CAACAAAAAATTGT--AAATTTTTATCTGAAAAAAG-GGTGTCGGCTATTACATGTT
* *
15752 CAACACCAAAAAATTTTGAAA-ATTTTTAATCTGAAAAAGGGGGTGTCGGCCATTATATGGCCAA
1 CAACACCAAAAAATTTTGAAATATTTTTAATCTGAAAAAGGGGGTGTCGGCCATTACATGACCAA
*
15816 C-ACAAAAAAATTGT-ATTTTTTATCTGACAGAAAAAGGGTGT
66 CAAC-AAAAAATTGTAAATTTTTATCTG--A-AAAAAGGGTGT
15857 TGATCATGCA
Statistics
Matches: 92, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
118 11 0.12
120 8 0.09
121 52 0.57
122 21 0.23
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (119 bp):
CAACACCAAAAAATTTTGAAATATTTTTAATCTGAAAAAGGGGGTGTCGGCCATTACATGACCAA
CAACAAAAAATTGTAAATTTTTATCTGAAAAAAGGGTGTCGGCTATTACATGTT
Found at i:18487 original size:17 final size:17
Alignment explanation
Indices: 18464--18537 Score: 96
Period size: 17 Copynumber: 4.4 Consensus size: 17
18454 CCAGGTCCCT
18464 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
*
18482 -TTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
*
18498 TTTAGATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
18515 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
18532 TTTAAA
1 TTTAAA
18538 ATAAATAATG
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
16 1 0.02
17 48 0.98
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:19244 original size:26 final size:22
Alignment explanation
Indices: 19215--19281 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 22
19205 TGATGATATC
19215 AATAAGCATTAATAATGATAATTAAT
1 AATAA-CATTAATAAT--TAA-TAAT
*
19241 AATAACTATTAGTAATTAATAAT
1 AATAAC-ATTAATAATTAATAAT
*
19264 AATAATATTAATAATTAA
1 AATAACATTAATAATTAA
19282 AAAAGAGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
22 11 0.30
23 9 0.24
24 3 0.08
25 1 0.03
26 13 0.35
ACGTcount: A:0.55, C:0.03, G:0.04, T:0.37
Consensus pattern (22 bp):
AATAACATTAATAATTAATAAT
Found at i:19251 original size:13 final size:12
Alignment explanation
Indices: 19222--19278 Score: 55
Period size: 13 Copynumber: 4.8 Consensus size: 12
19212 ATCAATAAGC
*
19222 ATTAATAATGAT
1 ATTAATAATAAT
19234 AATTAATAATAACT
1 -ATTAATAATAA-T
*
19248 ATTAGTAAT--T
1 ATTAATAATAAT
*
19258 AATAATAATAAT
1 ATTAATAATAAT
19270 ATTAATAAT
1 ATTAATAAT
19279 TAAAAAAGAG
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
10 8 0.22
12 9 0.25
13 18 0.50
14 1 0.03
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (12 bp):
ATTAATAATAAT
Found at i:20154 original size:29 final size:30
Alignment explanation
Indices: 20104--20421 Score: 204
Period size: 29 Copynumber: 10.8 Consensus size: 30
20094 AAAAATCCCT
** *
20104 AAACTATCCAAAAATTTTATTTTTAATCTCG
1 AAACT-TCCAAAAATTACATTTTTAACCTCG
* * * *
20135 AAA-TTTCAAAAATTATATTTTTATCGTCG
1 AAACTTCCAAAAATTACATTTTTAACCTCG
* *
20164 -AACTTCCAAAAATTCCATTTTTGACCTCG
1 AAACTTCCAAAAATTACATTTTTAACCTCG
* * *
20193 AAACTTACAAAAATCACATTTTTACCCTC-
1 AAACTTCCAAAAATTACATTTTTAACCTCG
* * * *
20222 AAACTTCCAAAAATTCCATTTTTGACCCCA
1 AAACTTCCAAAAATTACATTTTTAACCTCG
* * *
20252 AAACTTTCAAAAATTACATTTTTACCCTTG
1 AAACTTCCAAAAATTACATTTTTAACCTCG
* * * * *
20282 -AGCCTCCAAAAATTCCATTTTTGACCCCG
1 AAACTTCCAAAAATTACATTTTTAACCTCG
* * *
20311 AAACTTCAAAAAATTACATTTTT-ACCCCC
1 AAACTTCCAAAAATTACATTTTTAACCTCG
* ** *
20340 AAA-TGTCCAAAAAAT-CAAAATTTAACCCCG
1 AAACT-TCCAAAAATTAC-ATTTTTAACCTCG
* ** * *
20370 AAACTTTCAAAAATTACCCTTTTACCCTTG
1 AAACTTCCAAAAATTACATTTTTAACCTCG
*
20400 --ACTATCCAAAAATTCCATTTTT
1 AAACT-TCCAAAAATTACATTTTT
20422 TATCCTGATT
Statistics
Matches: 218, Mismatches: 59, Indels: 22
0.73 0.20 0.07
Matches are distributed among these distances:
28 7 0.03
29 118 0.54
30 88 0.40
31 5 0.02
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.34
Consensus pattern (30 bp):
AAACTTCCAAAAATTACATTTTTAACCTCG
Found at i:20231 original size:59 final size:60
Alignment explanation
Indices: 20100--20421 Score: 327
Period size: 59 Copynumber: 5.5 Consensus size: 60
20090 CCCTAAAAAT
** * * * *
20100 CCCT-AAACTATCCAAAAATTTTATTTTTAATCTCGAAA-TTTCAAAAATTATATTTTTA
1 CCCTCAAACTATCCAAAAATTCCATTTTTGACCCCGAAACTTTCAAAAATTACATTTTTA
* * * * * *
20158 TCGTCGAACT-TCCAAAAATTCCATTTTTGACCTCGAAACTTACAAAAATCACATTTTTA
1 CCCTCAAACTATCCAAAAATTCCATTTTTGACCCCGAAACTTTCAAAAATTACATTTTTA
*
20217 CCCTCAAACT-TCCAAAAATTCCATTTTTGACCCCAAAACTTTCAAAAATTACATTTTTA
1 CCCTCAAACTATCCAAAAATTCCATTTTTGACCCCGAAACTTTCAAAAATTACATTTTTA
** * *
20276 CCCTTGAGC-CTCCAAAAATTCCATTTTTGACCCCGAAAC-TTCAAAAAATTACATTTTTA
1 CCCTCAAACTATCCAAAAATTCCATTTTTGACCCCGAAACTTTC-AAAAATTACATTTTTA
* * * * ** * **
20335 CCCCCAAA-TGTCCAAAAAATCAAAATTTAACCCCGAAACTTTCAAAAATTACCCTTTTA
1 CCCTCAAACTATCCAAAAATTCCATTTTTGACCCCGAAACTTTCAAAAATTACATTTTTA
**
20394 CCCT-TGACTATCCAAAAATTCCATTTTT
1 CCCTCAAACTATCCAAAAATTCCATTTTT
20422 TATCCTGATT
Statistics
Matches: 216, Mismatches: 41, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
58 30 0.14
59 183 0.85
60 3 0.01
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.34
Consensus pattern (60 bp):
CCCTCAAACTATCCAAAAATTCCATTTTTGACCCCGAAACTTTCAAAAATTACATTTTTA
Found at i:20441 original size:118 final size:118
Alignment explanation
Indices: 20168--20470 Score: 355
Period size: 118 Copynumber: 2.6 Consensus size: 118
20158 TCGTCGAACT
* * *
20168 TCCAAAAATTCCATTTTTGACCTCGAAACTT-ACAAAAATCACATTTTTACCCTCAAACT-TCCA
1 TCCAAAAATTCCATTTTTGACCCCGAAACTTCA-AAAAATTACATTTTTACCCCCAAA-TGTCCA
* * ** * * *
20231 AAAATTCCATTTTTGACCCCAAAACTTTCAAAAATTACATTTTTACCCTTGAGCC
64 AAAAATCAAAATTTAACCCCAAAACTTTCAAAAATTACACTTTTACCCTTGAGCA
20286 TCCAAAAATTCCATTTTTGACCCCGAAACTTCAAAAAATTACATTTTTACCCCCAAATGTCCAAA
1 TCCAAAAATTCCATTTTTGACCCCGAAACTTCAAAAAATTACATTTTTACCCCCAAATGTCCAAA
* *
20351 AAATCAAAATTTAACCCCGAAACTTTCAAAAATTACCCTTTTACCCTTGA-CTA
66 AAATCAAAATTTAACCCCAAAACTTTCAAAAATTACACTTTTACCCTTGAGC-A
* * * ** * *
20404 TCCAAAAATTCCATTTTTTATCCTG-ATTTTCCTAAAAATTACCA-TTTTACCCCCAGATGTCCA
1 TCCAAAAATTCCATTTTTGACCCCGAAACTT-CAAAAAATTA-CATTTTTACCCCCAAATGTCCA
20467 AAAA
64 AAAA
20471 TTCCGTTTTT
Statistics
Matches: 161, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
117 5 0.03
118 153 0.95
119 3 0.02
ACGTcount: A:0.37, C:0.27, G:0.04, T:0.32
Consensus pattern (118 bp):
TCCAAAAATTCCATTTTTGACCCCGAAACTTCAAAAAATTACATTTTTACCCCCAAATGTCCAAA
AAATCAAAATTTAACCCCAAAACTTTCAAAAATTACACTTTTACCCTTGAGCA
Found at i:20452 original size:29 final size:29
Alignment explanation
Indices: 20377--20455 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 29
20367 CCGAAACTTT
*
20377 CAAAAATTACCCTTTTACCCTTGACTATC
1 CAAAAATTACCATTTTACCCTTGACTATC
* * *
20406 CAAAAATT-CCATTTTTTATCC-TGATTTTC
1 CAAAAATTACCA--TTTTACCCTTGACTATC
20435 CTAAAAATTACCATTTTACCC
1 C-AAAAATTACCATTTTACCC
20456 CCAGATGTCC
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
28 2 0.05
29 22 0.54
30 14 0.34
31 3 0.07
ACGTcount: A:0.32, C:0.27, G:0.03, T:0.39
Consensus pattern (29 bp):
CAAAAATTACCATTTTACCCTTGACTATC
Found at i:20467 original size:59 final size:58
Alignment explanation
Indices: 20378--20538 Score: 146
Period size: 59 Copynumber: 2.7 Consensus size: 58
20368 CGAAACTTTC
** * *
20378 AAAAATTACCCTTTTA-CCCTTGACTATCCAAAAATTCCATTTTTTATC-CTGATTTTCCT
1 AAAAATTA-CCTTTTACCCCCAGA-TGTCCAAAAATTCCATTTTTGATCTC-GATTTTCCT
* **
20437 AAAAATTACCATTTTACCCCCAGATGTCCAAAAATTCCGTTTTTGATCTCGATTTTTTT
1 AAAAATTACC-TTTTACCCCCAGATGTCCAAAAATTCCATTTTTGATCTCGATTTTCCT
* * * * * * *
20496 AAAAGTTATCGTTTACCCCCGGGTGTCTAAAAATTTCATTTTT
1 AAAAATTACCTTTTACCCCCAGATGTCCAAAAATTCCATTTTT
20539 AACCCCGAAC
Statistics
Matches: 84, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
58 29 0.35
59 49 0.58
60 6 0.07
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.41
Consensus pattern (58 bp):
AAAAATTACCTTTTACCCCCAGATGTCCAAAAATTCCATTTTTGATCTCGATTTTCCT
Done.