Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005595.1 Kokia drynarioides strain JFW-HI SEQ_119723, 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: 10269
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Found at i:370 original size:20 final size:20
Alignment explanation
Indices: 345--386 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
335 TTAAAGAAAC
345 ATTCAATATATATCAAGAAG
1 ATTCAATATATATCAAGAAG
365 ATTCAATATATATCAAGAAG
1 ATTCAATATATATCAAGAAG
385 AT
1 AT
387 ATTAGCAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.31
Consensus pattern (20 bp):
ATTCAATATATATCAAGAAG
Found at i:2434 original size:33 final size:33
Alignment explanation
Indices: 2397--2466 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
2387 ATCCGTACCA
*
2397 ATGTTTTCGTGAAGTTTTCACTTCCGTGCAAAT
1 ATGTTTTCGTGAAGTTTTCACTTCCGTGCAAAC
2430 ATGTTTTCGTGAAGTTTTCACTTCCGTGCAAAC
1 ATGTTTTCGTGAAGTTTTCACTTCCGTGCAAAC
2463 ATGT
1 ATGT
2467 GGGAAATGTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (33 bp):
ATGTTTTCGTGAAGTTTTCACTTCCGTGCAAAC
Found at i:8026 original size:51 final size:51
Alignment explanation
Indices: 7958--8296 Score: 241
Period size: 51 Copynumber: 6.7 Consensus size: 51
7948 TCAGTACCAT
* *
7958 GAAGACATGAAGGGAAAGGTCTAAGTCGCAACGGCAAGACCGTGTACCTCA
1 GAAGACACGAAGGGAAAGATCTAAGTCGCAACGGCAAGACCGTGTACCTCA
* * * * ** *
8009 GAAGAAACGAAGGGAAAGATTTAAGCCGCAACGGTGAA-TTC-AGTACCAT-A
1 GAAGACACGAAGGGAAAGATCTAAGTCGCAACGG-CAAGACCGTGTACC-TCA
* * * * *
8059 -AAGATACAAAAGGGAAAGGTCTAAGTTGCAACGGCAGGACCGTGTACCTCA
1 GAAGACAC-GAAGGGAAAGATCTAAGTCGCAACGGCAAGACCGTGTACCTCA
* * * * **
8110 GAAGACACGAAGGGAAAGATTTAAGTCGCAACGGTGAA-TCC-AGTACGACA
1 GAAGACACGAAGGGAAAGATCTAAGTCGCAACGG-CAAGACCGTGTACCTCA
* * * *
8160 -AAGATACAAAAGGGAAAGGTCTAAGTCGCAACAGCAAGACCGTGTACCTCA
1 GAAGACAC-GAAGGGAAAGATCTAAGTCGCAACGGCAAGACCGTGTACCTCA
* * * ** *
8211 GAAGACACGAAGGGGAAGATTTAAGCCGCAACGGTGA-ATC-TAGTA-C-CA
1 GAAGACACGAAGGGAAAGATCTAAGTCGCAACGGCAAGACCGT-GTACCTCA
* *
8259 TGAAGACATGAAGGGAAAGATCTAAGACCGCAACGGCA
1 -GAAGACACGAAGGGAAAGATCTAAG-TCGCAACGGCA
8297 GATCCAGTAC
Statistics
Matches: 217, Mismatches: 56, Indels: 31
0.71 0.18 0.10
Matches are distributed among these distances:
48 2 0.01
49 39 0.18
50 73 0.34
51 88 0.41
52 15 0.07
ACGTcount: A:0.39, C:0.19, G:0.27, T:0.14
Consensus pattern (51 bp):
GAAGACACGAAGGGAAAGATCTAAGTCGCAACGGCAAGACCGTGTACCTCA
Found at i:8142 original size:101 final size:101
Alignment explanation
Indices: 7967--8358 Score: 499
Period size: 101 Copynumber: 3.9 Consensus size: 101
7957 TGAAGACATG
*
7967 AAGGGAAAGGTCTAAGTCGCAACGGCAAGACCGTGTACCTCAGAAGAAACGAAGGGAAAGATTTA
1 AAGGGAAAGGTCTAAGTCGCAACGGCAAGACCGTGTACCTCAGAAGACACGAAGGGAAAGATTTA
8032 AGCCGCAACGGTGAATTCAGTACCATAAAGATACAA
66 AGCCGCAACGGTGAATTCAGTACCATAAAGATACAA
* *
8068 AAGGGAAAGGTCTAAGTTGCAACGGCAGGACCGTGTACCTCAGAAGACACGAAGGGAAAGATTTA
1 AAGGGAAAGGTCTAAGTCGCAACGGCAAGACCGTGTACCTCAGAAGACACGAAGGGAAAGATTTA
* * * *
8133 AGTCGCAACGGTGAATCCAGTACGACAAAGATACAA
66 AGCCGCAACGGTGAATTCAGTACCATAAAGATACAA
* *
8169 AAGGGAAAGGTCTAAGTCGCAACAGCAAGACCGTGTACCTCAGAAGACACGAAGGGGAAGATTTA
1 AAGGGAAAGGTCTAAGTCGCAACGGCAAGACCGTGTACCTCAGAAGACACGAAGGGAAAGATTTA
* *
8234 AGCCGCAACGGTGAA-TCTAGTACCATGAAG--ACATG
66 AGCCGCAACGGTGAATTC-AGTACCATAAAGATACA-A
* * * * * * *
8269 AAGGGAAAGATCTAAGACCGCAACGGC-AGATCC-AGTACCACA-AAGATACAAAAGGGAAAGGT
1 AAGGGAAAGGTCTAAG-TCGCAACGGCAAGA-CCGTGTACCTCAGAAGACAC-GAAGGGAAAGAT
* ** *
8331 TTAAGCGGCAACGGCCAATCCAGTACCA
63 TTAAGCCGCAACGGTGAATTCAGTACCA
8359 CGAATTTTTG
Statistics
Matches: 255, Mismatches: 30, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
99 9 0.04
100 57 0.22
101 189 0.74
ACGTcount: A:0.39, C:0.20, G:0.27, T:0.14
Consensus pattern (101 bp):
AAGGGAAAGGTCTAAGTCGCAACGGCAAGACCGTGTACCTCAGAAGACACGAAGGGAAAGATTTA
AGCCGCAACGGTGAATTCAGTACCATAAAGATACAA
Found at i:8359 original size:50 final size:49
Alignment explanation
Indices: 8018--8359 Score: 235
Period size: 50 Copynumber: 6.8 Consensus size: 49
8008 AGAAGAAACG
* * *
8018 AAGGGAAAGATTTAAGCCGCAACGGTGAATTCAGTACCATAAAGATACAA
1 AAGGGAAAGATTTAAGCCGCAACGG-CAATCCAGTACCACAAAGATACAA
* * ** * * * *
8068 AAGGGAAAGGTCTAAGTTGCAACGGCAGGA-CCGTGTACCTCAGAAGACAC-G
1 AAGGGAAAGATTTAAGCCGCAACGGCA--ATCC-AGTACCACA-AAGATACAA
* * *
8119 AAGGGAAAGATTTAAGTCGCAACGGTGAATCCAGTACGACAAAGATACAA
1 AAGGGAAAGATTTAAGCCGCAACGG-CAATCCAGTACCACAAAGATACAA
* * * * * * * * *
8169 AAGGGAAAGGTCTAAGTCGCAACAGCAAGACCGTGTACCTCAGAAGACAC-G
1 AAGGGAAAGATTTAAGCCGCAACGGCAA-TCC-AGTACCACA-AAGATACAA
* * * ** *
8220 AAGGGGAAGATTTAAGCCGCAACGGTGAATCTAGTACCATGAAG--ACATG
1 AAGGGAAAGATTTAAGCCGCAACGG-CAATCCAGTACCACAAAGATACA-A
*
8269 AAGGGAAAGATCTAAGACCGCAACGGCAGATCCAGTACCACAAAGATACAA
1 AAGGGAAAGATTTAAG-CCGCAACGGCA-ATCCAGTACCACAAAGATACAA
* *
8320 AAGGGAAAGGTTTAAGCGGCAACGGCCAATCCAGTACCAC
1 AAGGGAAAGATTTAAGCCGCAACGG-CAATCCAGTACCAC
8360 GAATTTTTGA
Statistics
Matches: 222, Mismatches: 52, Indels: 36
0.72 0.17 0.12
Matches are distributed among these distances:
47 2 0.01
49 28 0.13
50 100 0.45
51 74 0.33
52 18 0.08
ACGTcount: A:0.39, C:0.20, G:0.26, T:0.14
Consensus pattern (49 bp):
AAGGGAAAGATTTAAGCCGCAACGGCAATCCAGTACCACAAAGATACAA
Found at i:8665 original size:101 final size:101
Alignment explanation
Indices: 8485--8670 Score: 282
Period size: 101 Copynumber: 1.8 Consensus size: 101
8475 AGATCAAAAC
* * * * *
8485 AACAATGGCAAGTCTTTATCTCTCTGAAGTTACAGTAATAGCAAGATGAAACTTTAACGTCAATT
1 AACAATAGCAAGTCTTTATCTCTCTGAAGTTACAGTAAGAGCAAGATGAAACTTCAACATCAAAT
*
8550 CCTATCCTCTTGAAGTTGCAATAAAGTTGGATTAAA
66 CCTATCCTCCTGAAGTTGCAATAAAGTTGGATTAAA
** *
8586 AACAATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAACATCAAAT
1 AACAATAGCAAGTCTTTATCTCTCTGAAGTTACAGTAAGAGCAAGATGAAACTTCAACATCAAAT
*
8651 CCTATCTTCCTGAAGTTGCA
66 CCTATCCTCCTGAAGTTGCA
8671 GCGAAGTTGG
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
101 75 1.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (101 bp):
AACAATAGCAAGTCTTTATCTCTCTGAAGTTACAGTAAGAGCAAGATGAAACTTCAACATCAAAT
CCTATCCTCCTGAAGTTGCAATAAAGTTGGATTAAA
Found at i:9622 original size:200 final size:194
Alignment explanation
Indices: 9185--9691 Score: 671
Period size: 200 Copynumber: 2.6 Consensus size: 194
9175 TTCGAACCCC
* *
9185 AGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGG
1 AGCTTCCTGATGAAATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGG
* ** * *
9250 ATTAAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGCGAA
66 ATTGAAACAAACGAGGCAGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAAGGCGAA
*
9315 CAAATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGGTGAAGCAATAAAAAGGTT
131 CAAATCTTCGAACCCTAGCTTCCTGATAAGATACTGAGAAGCAGGGTGAAGCAATAAAAAGGTT
* * **
9379 AGCTTCCTGATGAAACACTGAGAAGTGGACCAACTTCGTCTTCCTGATGAAATACAGAGAAGCGG
1 AGCTTCCTGATGAAATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGG
* * *
9444 ATTGAAACAAACGGGGCAGTTATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAGGGCTCG
66 ATTGAAACAAACGAGGCAGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAAGG--CG
*
9509 ATGTAGCAAATCTTCGAATCCC-AGCTTCCTGATAAGATA-TGGAGAAGTA-GGTCGAAGCAATA
129 A---A-CAAATCTTCGAA-CCCTAGCTTCCTGATAAGATACT-GAGAAGCAGGGT-GAAGCAATA
*
9571 AAATGGTT
187 AAAAGGTT
* * *
9579 AGCTTCTTGATGAAATACTGAGAAGTAGACCAAATTTGTCTTCCTGATGAGGTACAGAGAAGCGG
1 AGCTTCCTGATGAAATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGG
* * * * *
9644 ATTGAAACAAGCAATGCGGTCATCTTCCTGATAAGATACTA-AGAAGTA
66 ATTGAAACAAACGAGGCAGTCATCTTCCTGATGAGATAC-AGAGAAGTA
9692 GACTAAATCA
Statistics
Matches: 272, Mismatches: 31, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
194 112 0.41
196 3 0.01
199 5 0.02
200 148 0.54
201 4 0.01
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (194 bp):
AGCTTCCTGATGAAATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGG
ATTGAAACAAACGAGGCAGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAAGGCGAA
CAAATCTTCGAACCCTAGCTTCCTGATAAGATACTGAGAAGCAGGGTGAAGCAATAAAAAGGTT
Found at i:10089 original size:17 final size:17
Alignment explanation
Indices: 10034--10104 Score: 70
Period size: 17 Copynumber: 4.2 Consensus size: 17
10024 AATAAGTTTG
* *
10034 AATTTATTTTAAATTCA
1 AATTTACTTTAAATTTA
* * *
10051 AATTCACTTTGAGTTTA
1 AATTTACTTTAAATTTA
10068 AATTTACTTTAAATTTA
1 AATTTACTTTAAATTTA
** *
10085 AATTTTTTTTAAATTAA
1 AATTTACTTTAAATTTA
10102 AAT
1 AAT
10105 AAAATTAAAA
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 43 1.00
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (17 bp):
AATTTACTTTAAATTTA
Done.