Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013436.1 Kokia drynarioides strain JFW-HI SEQ_128462, 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: 34200
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:2339 original size:56 final size:56
Alignment explanation
Indices: 2253--2447 Score: 218
Period size: 56 Copynumber: 3.6 Consensus size: 56
2243 CTGAACCAAA
* **
2253 ATAGCTTTACGCTCTAACCGAGACATAAGCAACCCAAAGCTATACCTGAGCTATAC
1 ATAGCATTACGCTCTAACCGAGACATAAGCATTCCAAAGCTATACCTGAGCTATAC
* ** * * *
2309 ATAGCATTACGCTTTAACCGAGATGTAAGCATTCCAAAGCTTTACTTTAGCTATAC
1 ATAGCATTACGCTCTAACCGAGACATAAGCATTCCAAAGCTATACCTGAGCTATAC
* * * * *
2365 ATAG-A-T--GCTCCAACCGAGACATAATCGTTCCAAAGCTCTACCCGAGCTATAC
1 ATAGCATTACGCTCTAACCGAGACATAAGCATTCCAAAGCTATACCTGAGCTATAC
* *
2417 ATGGCATTACGCTCTAACCGAGACGTAAGCA
1 ATAGCATTACGCTCTAACCGAGACATAAGCA
2448 GATCAGAGCT
Statistics
Matches: 111, Mismatches: 24, Indels: 8
0.78 0.17 0.06
Matches are distributed among these distances:
52 39 0.35
53 1 0.01
54 2 0.02
55 1 0.01
56 68 0.61
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (56 bp):
ATAGCATTACGCTCTAACCGAGACATAAGCATTCCAAAGCTATACCTGAGCTATAC
Found at i:2458 original size:56 final size:56
Alignment explanation
Indices: 2253--2470 Score: 212
Period size: 56 Copynumber: 4.0 Consensus size: 56
2243 CTGAACCAAA
* * * *
2253 ATAGCTTTACGCTCTAACCGAGACATAAGCAACCCAAAGCTATACCTGAGCTATAC
1 ATAGCATTACGCTCTAACCGAGACATAAGCAATCCAAAGCTCTACCCGAGCTATAC
* ** * * ***
2309 ATAGCATTACGCTTTAACCGAGATGTAAGCATTCCAAAGCTTTACTTTAGCTATAC
1 ATAGCATTACGCTCTAACCGAGACATAAGCAATCCAAAGCTCTACCCGAGCTATAC
* * **
2365 ATAG-A-T--GCTCCAACCGAGACATAATCGTTCCAAAGCTCTACCCGAGCTATAC
1 ATAGCATTACGCTCTAACCGAGACATAAGCAATCCAAAGCTCTACCCGAGCTATAC
* * * *
2417 ATGGCATTACGCTCTAACCGAGACGTAAGCAGAT-CAGAGCTCTAACCGAGCTAT
1 ATAGCATTACGCTCTAACCGAGACATAAGCA-ATCCAAAGCTCTACCCGAGCTAT
2471 CCTTCGACAA
Statistics
Matches: 130, Mismatches: 27, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
52 39 0.30
53 1 0.01
54 2 0.02
55 1 0.01
56 86 0.66
57 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.24
Consensus pattern (56 bp):
ATAGCATTACGCTCTAACCGAGACATAAGCAATCCAAAGCTCTACCCGAGCTATAC
Found at i:2469 original size:108 final size:108
Alignment explanation
Indices: 2263--2470 Score: 249
Period size: 108 Copynumber: 1.9 Consensus size: 108
2253 ATAGCTTTAC
* * *
2263 GCTCTAACCGAGACATAAGCAACCCAAAGCTATACCTGAGCTATACATAGCATTACGCTTTAACC
1 GCTCCAACCGAGACATAAGCAACCCAAAGCTATACCCGAGCTATACATAGCATTACGCTCTAACC
* * * **
2328 GAGATGTAAGCATTCCAAAGCTTTACTTTAGCTATACATAGAT
66 GAGACGTAAGCAATCCAAAGCTTAACTCGAGCTATACATAGAT
* *** * *
2371 GCTCCAACCGAGACATAATCGTTCCAAAGCTCTACCCGAGCTATACATGGCATTACGCTCTAACC
1 GCTCCAACCGAGACATAAGCAACCCAAAGCTATACCCGAGCTATACATAGCATTACGCTCTAACC
*
2436 GAGACGTAAGCAGAT-CAGAGCTCTAAC-CGAGCTAT
66 GAGACGTAAGCA-ATCCAAAGCT-TAACTCGAGCTAT
2471 CCTTCGACAA
Statistics
Matches: 83, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
108 79 0.95
109 4 0.05
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (108 bp):
GCTCCAACCGAGACATAAGCAACCCAAAGCTATACCCGAGCTATACATAGCATTACGCTCTAACC
GAGACGTAAGCAATCCAAAGCTTAACTCGAGCTATACATAGAT
Found at i:14977 original size:12 final size:12
Alignment explanation
Indices: 14960--14985 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
14950 TGTTATCATG
14960 ATGAATGTTATT
1 ATGAATGTTATT
14972 ATGAATGTTATT
1 ATGAATGTTATT
14984 AT
1 AT
14986 TTCTTTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (12 bp):
ATGAATGTTATT
Found at i:15646 original size:74 final size:74
Alignment explanation
Indices: 15525--15673 Score: 289
Period size: 74 Copynumber: 2.0 Consensus size: 74
15515 AGTGATGTTG
15525 TTCATAAGTTAGCAAGATACCGGGTTGTCGTGAATATTAGTTCGTAACAAGCGTGAACATAATTT
1 TTCATAAGTTAGCAAGATACCGGGTTGTCGTGAATATTAGTTCGTAACAAGCGTGAACATAATTT
15590 ATATTTAAT
66 ATATTTAAT
*
15599 TTCATAAGTTAGCAAGATACCGGGTTGTTGTGAATATTAGTTCGTAACAAGCGTGAACATAATTT
1 TTCATAAGTTAGCAAGATACCGGGTTGTCGTGAATATTAGTTCGTAACAAGCGTGAACATAATTT
15664 ATATTTAAT
66 ATATTTAAT
15673 T
1 T
15674 AAGTAATTAG
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (74 bp):
TTCATAAGTTAGCAAGATACCGGGTTGTCGTGAATATTAGTTCGTAACAAGCGTGAACATAATTT
ATATTTAAT
Found at i:16145 original size:74 final size:74
Alignment explanation
Indices: 16024--16172 Score: 289
Period size: 74 Copynumber: 2.0 Consensus size: 74
16014 NGTGATGTTG
16024 TTCATAAGTTAGCAAGATACCGGGTTGTCGTGAATATTAGTTCGTAACAAGCGTGAACATAATTT
1 TTCATAAGTTAGCAAGATACCGGGTTGTCGTGAATATTAGTTCGTAACAAGCGTGAACATAATTT
16089 ATATTTAAT
66 ATATTTAAT
*
16098 TTCATAAGTTAGCAAGATACCGGGTTGTTGTGAATATTAGTTCGTAACAAGCGTGAACATAATTT
1 TTCATAAGTTAGCAAGATACCGGGTTGTCGTGAATATTAGTTCGTAACAAGCGTGAACATAATTT
16163 ATATTTAAT
66 ATATTTAAT
16172 T
1 T
16173 AAGTAATTAG
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (74 bp):
TTCATAAGTTAGCAAGATACCGGGTTGTCGTGAATATTAGTTCGTAACAAGCGTGAACATAATTT
ATATTTAAT
Found at i:20434 original size:21 final size:21
Alignment explanation
Indices: 20410--20453 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
20400 TGTTAAAACT
20410 CCAACATT-ACCAGAACTAGAA
1 CCAA-ATTCACCAGAACTAGAA
* *
20431 CCAATTTCACTAGAACTAGAA
1 CCAAATTCACCAGAACTAGAA
20452 CC
1 CC
20454 GATCAAGCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.43, C:0.30, G:0.09, T:0.18
Consensus pattern (21 bp):
CCAAATTCACCAGAACTAGAA
Done.