Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012030.1 Kokia drynarioides strain JFW-HI SEQ_127028, 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: 28897
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.30
Warning! 117 characters in sequence are not A, C, G, or T
Found at i:10254 original size:44 final size:44
Alignment explanation
Indices: 10205--10290 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 44
10195 AATACTTCGA
* * * *
10205 CTAAAAACAAAAGGGGAGTTGA-GATGAAAACCCGCAAAGGGCGT
1 CTAAAAAAAAAAAGGG-GTTCAGGATGAAAACCAGCAAAGGGCGT
10249 CTAAAAAAAAAAAGGGGTTCAGGATGAAAACCAGCAAAGGGC
1 CTAAAAAAAAAAAGGGGTTCAGGATGAAAACCAGCAAAGGGC
10291 ATCCTGAAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
43 4 0.11
44 33 0.89
ACGTcount: A:0.47, C:0.15, G:0.28, T:0.10
Consensus pattern (44 bp):
CTAAAAAAAAAAAGGGGTTCAGGATGAAAACCAGCAAAGGGCGT
Found at i:10563 original size:27 final size:27
Alignment explanation
Indices: 10525--10584 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
10515 AATTTTCAAC
* *
10525 TAATGATTGTTTTCTTTGAACCTCTTTT
1 TAAT-ATTGTTTCCTCTGAACCTCTTTT
**
10553 TAATATTGTTTCCTCTGATTCTCTTTT
1 TAATATTGTTTCCTCTGAACCTCTTTT
10580 TAATA
1 TAATA
10585 GAATTTTTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 24 0.86
28 4 0.14
ACGTcount: A:0.20, C:0.15, G:0.08, T:0.57
Consensus pattern (27 bp):
TAATATTGTTTCCTCTGAACCTCTTTT
Found at i:11443 original size:204 final size:204
Alignment explanation
Indices: 11062--11828 Score: 1081
Period size: 204 Copynumber: 3.8 Consensus size: 204
11052 CGATATCCAA
* * * * * *
11062 AAACGACGCGGTCATCTTCTTGAAGAGATACTGAGAAGAAGACCAAATCAAAGCCACGCTCAAAG
1 AAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCGCGATG
** * *
11127 CAAGCAAAATCTTTGAACCCCAGCTTCCTGATGAGACA-TCGAGAAGCAGGTCGAAGCAAT-AAA
66 -AA-C-AAATCTTCAAACCCCAGCTTCCTGATGAGATACT-GAGAAGCAGGTCGAAGTAATAAAA
* * * * * *
11190 TGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTTGTCTTCCTAATGAGATATAGAGA
127 CGGATAGCTTCCTGATGAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGA
11255 AGCGGATTGAAAC
192 AGCGGATTGAAAC
* * *
11268 AAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCGCGACG
1 AAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCGCGATG
* * *
11333 AACAAATCTTCAAACCCCAGCTTCTTGATGAGATATTGAGAAGCAAGTCGAAGTAATAAAACGGA
66 AACAAATCTTCAAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAACGGA
*
11398 TAGCTTCCTGATGAGATACTGAGGAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGAAGCG
131 TAGCTTCCTGATGAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCG
11463 GATTGAAAC
196 GATTGAAAC
* * *
11472 AAACGACGCGATCATCTTCCTGATGAAATACTGAGAAGATGACCAAATCAAACCCACGCGCGATG
1 AAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCGCGATG
* * *
11537 AATAAATCTTCGAACCTCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAACGGA
66 AACAAATCTTCAAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAACGGA
* * * * *
11602 TAGCTTCCTGATGAGTTATTGAGGAGTGAGCCAAATTCGTCTTCTTGATGAGATGCAGAGAAGCG
131 TAGCTTCCTGATGAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCG
11667 GATTGAAAC
196 GATTGAAAC
* * * *
11676 AAACGACGCGGTCATCTTCTTGATGAGATATTAAGGAGAAGACCAAATCAAACCCACGCGCGATG
1 AAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCGCGATG
* * *
11741 AACGAATCTTCAAACCCCAGCTTCCGGATGAGATACTGAGAAGCAGGTCGAAGTAATAGAACGG-
66 AACAAATCTTCAAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAACGGA
* *
11805 TCATCTTCCAGATGAGATACTGAG
131 T-AGCTTCCTGATGAGATACTGAG
11829 AAGAAGGCCA
Statistics
Matches: 502, Mismatches: 56, Indels: 8
0.89 0.10 0.01
Matches are distributed among these distances:
203 47 0.09
204 396 0.79
205 2 0.00
206 57 0.11
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (204 bp):
AAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCGCGATG
AACAAATCTTCAAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAACGGA
TAGCTTCCTGATGAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCG
GATTGAAAC
Found at i:12187 original size:17 final size:17
Alignment explanation
Indices: 12159--12238 Score: 88
Period size: 17 Copynumber: 4.7 Consensus size: 17
12149 GGCCTATTGG
*
12159 AAATTGAATTTATTTTA
1 AAATTAAATTTATTTTA
*
12176 AAATTAAGTTTATTTTA
1 AAATTAAATTTATTTTA
* *
12193 AATTTAAATTTATTTGA
1 AAATTAAATTTATTTTA
* * *
12210 AATTTAAATTTGTTATA
1 AAATTAAATTTATTTTA
*
12227 AATTTAAATTTA
1 AAATTAAATTTA
12239 AAATGTCCAA
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 54 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (17 bp):
AAATTAAATTTATTTTA
Found at i:12203 original size:34 final size:34
Alignment explanation
Indices: 12165--12238 Score: 103
Period size: 34 Copynumber: 2.2 Consensus size: 34
12155 TTGGAAATTG
* * *
12165 AATTTATTTTAAAATTAAGTTTATTTTAAATTTA
1 AATTTATTTGAAAATTAAATTTATTATAAATTTA
* *
12199 AATTTATTTGAAATTTAAATTTGTTATAAATTTA
1 AATTTATTTGAAAATTAAATTTATTATAAATTTA
12233 AATTTA
1 AATTTA
12239 AAATGTCCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (34 bp):
AATTTATTTGAAAATTAAATTTATTATAAATTTA
Found at i:12844 original size:3 final size:3
Alignment explanation
Indices: 12828--12874 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
12818 AAACGTTTTT
* *
12828 TAA TAA TCAT TAA TAA TAA TAA CT-G TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA
12874 T
1 T
12875 GAATGTGATA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
2 1 0.03
3 33 0.89
4 3 0.08
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:12885 original size:27 final size:27
Alignment explanation
Indices: 12828--12897 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
12818 AAACGTTTTT
*
12828 TAATAATCATTAATAATAATAACTGTAA
1 TAATAAT-AATAATAATAATAACTGTAA
*
12856 TAATAATAATAATAATAATGAA-TGTGA
1 TAATAATAATAATAATAAT-AACTGTAA
* *
12883 TAATATTAATTATAA
1 TAATAATAATAATAA
12898 CAGTAATGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 28 0.76
28 9 0.24
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.37
Consensus pattern (27 bp):
TAATAATAATAATAATAATAACTGTAA
Found at i:14162 original size:90 final size:88
Alignment explanation
Indices: 14022--14354 Score: 350
Period size: 90 Copynumber: 3.7 Consensus size: 88
14012 AAAAATTATA
*
14022 TTTTTACCCTTAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTA
1 TTTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTA
* *
14087 CCCTCGAATTTGCAAAAATTCTATT
66 CCCTCGAATTT-CAAAAATCCCA-T
** *
14112 TTTTTACCCCTAAACTTTTAAAAATCCCATTTTTGACCCTAAAACTTCCAAAAATTCCATTTTTA
1 TTTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTT-
*
14177 ACCC-CGAACTTCCAAAAATCCCAT
65 ACCCTCGAA-TTTCAAAAATCCCAT
* ** ** * **
14201 CTTCGA-CCCTGAAACTTCCAAAAATCTAATTTTTGACCCCGAAACTTCCAAAAATTATATTTTT
1 TTTTTACCCCT-AAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTT
*
14265 ACCCTCGAACTTTCAAAAAACGCCAT
65 ACCCTCGAA-TTTCAAAAATC-CCAT
* * * * * ** *
14291 TTTTTATCCCGAAATTTCCAAAAATTCCATTGTTG-CCCCCGAA-TGTCTAAAAATTCCATTTTT
1 TTTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCAAAACT-TCCAAAAATTCCATTTTT
14354 A
65 A
14355 AACCACAAAT
Statistics
Matches: 202, Mismatches: 34, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
88 9 0.04
89 85 0.42
90 99 0.49
91 9 0.04
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.35
Consensus pattern (88 bp):
TTTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTA
CCCTCGAATTTCAAAAATCCCAT
Found at i:14332 original size:30 final size:30
Alignment explanation
Indices: 14003--14353 Score: 279
Period size: 30 Copynumber: 11.8 Consensus size: 30
13993 GGAGGTCCCT
** **
14003 AAACTATCCAAAAATTATATTTTT-ACCCTT
1 AAACT-TCCAAAAATTCCATTTTTGACCCCG
* *
14033 AAACTTCCAAAAATCCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTGACCCCG
14063 AAACTTCCAAAAATTCCATTTTT-ACCCTCG
1 AAACTTCCAAAAATTCCATTTTTGACCC-CG
* * * * *
14093 -AATTTGCAAAAATTCTATTTTTTTACCCCT
1 AAACTTCCAAAAATTCCA-TTTTTGACCCCG
** * **
14123 AAACTTTTAAAAATCCCATTTTTGACCCTA
1 AAACTTCCAAAAATTCCATTTTTGACCCCG
*
14153 AAACTTCCAAAAATTCCATTTTTAACCCCG
1 AAACTTCCAAAAATTCCATTTTTGACCCCG
* * * *
14183 -AACTTCCAAAAATCCCATCTTCGACCCTG
1 AAACTTCCAAAAATTCCATTTTTGACCCCG
*
14212 AAACTTCCAAAAA-TCTAATTTTTGACCCCG
1 AAACTTCCAAAAATTC-CATTTTTGACCCCG
**
14242 AAACTTCCAAAAATTATATTTTT-ACCCTCG
1 AAACTTCCAAAAATTCCATTTTTGACCC-CG
* ** * *
14272 -AACTTTCAAAAAACGCCATTTTTTATCCCG
1 AAAC-TTCCAAAAATTCCATTTTTGACCCCG
* * *
14302 AAATTTCCAAAAATTCCATTGTTGCCCCCG
1 AAACTTCCAAAAATTCCATTTTTGACCCCG
*
14332 -AA-TGTCTAAAAATTCCATTTTT
1 AAACT-TCCAAAAATTCCATTTTT
14354 AAACCACAAA
Statistics
Matches: 255, Mismatches: 53, Indels: 27
0.76 0.16 0.08
Matches are distributed among these distances:
28 1 0.00
29 83 0.33
30 149 0.58
31 22 0.09
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.34
Consensus pattern (30 bp):
AAACTTCCAAAAATTCCATTTTTGACCCCG
Found at i:17256 original size:85 final size:85
Alignment explanation
Indices: 17156--17328 Score: 301
Period size: 85 Copynumber: 2.0 Consensus size: 85
17146 ATTATTAATT
17156 AAATTCAATAACTTAATTCAACAATTTATTTAATTTTTAAATATAATTATAAAAATAAATACGAT
1 AAATTCAATAACTTAATTCAACAATTTATTTAATTTTTAAATATAATTATAAAAATAAATACGAT
*
17221 TAAGATTAAAAATTGCTTTA
66 TAAGATTAAAAATTACTTTA
* * *
17241 AAATTCAATAACTTAATTCAACAATTTATTTGATTTTTAAATATAATTATAAAAATAGATATGAT
1 AAATTCAATAACTTAATTCAACAATTTATTTAATTTTTAAATATAATTATAAAAATAAATACGAT
*
17306 TATGATTAAAAATTACTTTA
66 TAAGATTAAAAATTACTTTA
17326 AAA
1 AAA
17329 CATCAAAATA
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 83 1.00
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.40
Consensus pattern (85 bp):
AAATTCAATAACTTAATTCAACAATTTATTTAATTTTTAAATATAATTATAAAAATAAATACGAT
TAAGATTAAAAATTACTTTA
Found at i:21452 original size:15 final size:15
Alignment explanation
Indices: 21429--21464 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
21419 AATTTTAAAG
*
21429 AAAAATGGATATTGT
1 AAAAATGGATATTCT
*
21444 AAAAGTGGATATTCT
1 AAAAATGGATATTCT
21459 AAAAAT
1 AAAAAT
21465 CTTGGTTTCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.50, C:0.03, G:0.17, T:0.31
Consensus pattern (15 bp):
AAAAATGGATATTCT
Done.