Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011443.1 Kokia drynarioides strain JFW-HI SEQ_126427, 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: 9593
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Found at i:2384 original size:15 final size:15
Alignment explanation
Indices: 2336--2385 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
2326 GCTCCAATGT
2336 TCGCAACATGAGTGC
1 TCGCAACATGAGTGC
* ** * *
2351 TCGTAACACCAATGT
1 TCGCAACATGAGTGC
2366 TCGCAACATGAGTGC
1 TCGCAACATGAGTGC
2381 TCGCA
1 TCGCA
2386 TCTTCCAAGC
Statistics
Matches: 25, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (15 bp):
TCGCAACATGAGTGC
Found at i:6465 original size:24 final size:24
Alignment explanation
Indices: 6436--6573 Score: 150
Period size: 24 Copynumber: 5.8 Consensus size: 24
6426 CTTGTCAAAT
* *
6436 ACTTTAGGTTTATGCTTGTCAGCC
1 ACTTTACGTTTATGCTCGTCAGCC
* * * *
6460 ATTTTACATTTATGCTTGTCAGAC
1 ACTTTACGTTTATGCTCGTCAGCC
* *
6484 ACTTTACGTTTACGCACGTCAGCC
1 ACTTTACGTTTATGCTCGTCAGCC
* *
6508 ATTTTACGTTTTTGCTCGTCAGCC
1 ACTTTACGTTTATGCTCGTCAGCC
*
6532 ACTTTACGTTTATGCTCATCAGCC
1 ACTTTACGTTTATGCTCGTCAGCC
* * *
6556 ACCTTACATTTGTGCTCG
1 ACTTTACGTTTATGCTCG
6574 AAGGAATGGA
Statistics
Matches: 93, Mismatches: 21, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 93 1.00
ACGTcount: A:0.19, C:0.25, G:0.16, T:0.40
Consensus pattern (24 bp):
ACTTTACGTTTATGCTCGTCAGCC
Found at i:6488 original size:48 final size:48
Alignment explanation
Indices: 6415--6571 Score: 167
Period size: 48 Copynumber: 3.3 Consensus size: 48
6405 GCAAATCTTA
* * * *
6415 ATTTTAC-TTTA--CTTGTCAAATACTTTAGGTTTATGCTTGTCAGCC
1 ATTTTACATTTATGCTTGTCAGACACTTTACGTTTATGCTCGTCAGCC
* *
6460 ATTTTACATTTATGCTTGTCAGACACTTTACGTTTACGCACGTCAGCC
1 ATTTTACATTTATGCTTGTCAGACACTTTACGTTTATGCTCGTCAGCC
* * * * *
6508 ATTTTACGTTTTTGCTCGTCAGCCACTTTACGTTTATGCTCATCAGCC
1 ATTTTACATTTATGCTTGTCAGACACTTTACGTTTATGCTCGTCAGCC
** *
6556 ACCTTACATTTGTGCT
1 ATTTTACATTTATGCT
6572 CGAAGGAATG
Statistics
Matches: 92, Mismatches: 17, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
45 7 0.08
46 4 0.04
48 81 0.88
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.42
Consensus pattern (48 bp):
ATTTTACATTTATGCTTGTCAGACACTTTACGTTTATGCTCGTCAGCC
Found at i:6572 original size:48 final size:48
Alignment explanation
Indices: 6436--6573 Score: 168
Period size: 48 Copynumber: 2.9 Consensus size: 48
6426 CTTGTCAAAT
* * *
6436 ACTTTAGGTTTATGCTTGTCAGCCATTTTACATTTATGCTTGTCAGAC
1 ACTTTACGTTTATGCTCGTCAGCCATTTTACATTTATGCTCGTCAGAC
* * * * *
6484 ACTTTACGTTTACGCACGTCAGCCATTTTACGTTTTTGCTCGTCAGCC
1 ACTTTACGTTTATGCTCGTCAGCCATTTTACATTTATGCTCGTCAGAC
* ** *
6532 ACTTTACGTTTATGCTCATCAGCCACCTTACATTTGTGCTCG
1 ACTTTACGTTTATGCTCGTCAGCCATTTTACATTTATGCTCG
6574 AAGGAATGGA
Statistics
Matches: 75, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 75 1.00
ACGTcount: A:0.19, C:0.25, G:0.16, T:0.40
Consensus pattern (48 bp):
ACTTTACGTTTATGCTCGTCAGCCATTTTACATTTATGCTCGTCAGAC
Found at i:6935 original size:213 final size:214
Alignment explanation
Indices: 6660--7101 Score: 536
Period size: 216 Copynumber: 2.1 Consensus size: 214
6650 TTCAGCCAAG
** * * *
6660 AACCAAGAGAGAAATAATTTTCACGTAAATAAGTTTTTAATTCAAAGACTAAAAGGTGTTTACGA
1 AACCAAGAGAG-AATAATTTTCACAAAAATAAGTTTTTAATTCAAACACCAAAAGGTGTTTACAA
* * * *
6725 AACGACAAACTATTTAGACCAAATGA-C-ATATCCCAAGCATGGAATG-TTCGAAAAATTGCTCG
65 AACAACAAAATATTTAGACCAAATGAGCGATATCCCAAGCATGCAACGCTT-GAAAAATTGCTCG
* * *
6787 AAAGAATGGATCGTATTAAATACTTTAAGGAA-CTACAGTTATAAAAGAACC-CGTAAAAGTTTG
129 AAAGAATGGATCATATTAAATACTTTAAGGAATC-AAAGTTATAAAA-AACCTCGTAAAAGTGTG
6850 ACAAGTTCAAAAGTTCGGTGAAA
192 ACAAGTTCAAAAGTTCGGTGAAA
* *
6873 AACCAAGAGAGAAT-ATTTTCACACAAAAATAAGTTTTTAATTCAAACACCAATAGTTGTTTACA
1 AACCAAGAGAGAATAATTTT--CACAAAAATAAGTTTTTAATTCAAACACCAAAAGGTGTTTACA
* * * **
6937 AAACAATAAAATGTTTAGACCAAATGATGCGATTTCCTGAGCATGCAACGCTTGAAAAATTGCTC
64 AAACAACAAAATATTTAGACCAAATGA-GCGATATCCCAAGCATGCAACGCTTGAAAAATTGCTC
* * *
7002 GAAGGAATGGATCATCTTGAATACTTTAAGGAATCAAAGTTATAAAAAACCTCGTAAAAGTGTGA
128 GAAAGAATGGATCATATTAAATACTTTAAGGAATCAAAGTTATAAAAAACCTCGTAAAAGTGTGA
** * *
7067 CAAGTTCAGGAGTTTGGTGAAG
193 CAAGTTCAAAAGTTCGGTGAAA
*
7089 AACCGAGAGAGAA
1 AACCAAGAGAGAA
7102 ACAATTCTCA
Statistics
Matches: 194, Mismatches: 27, Indels: 13
0.83 0.12 0.06
Matches are distributed among these distances:
211 5 0.03
212 3 0.02
213 70 0.36
215 5 0.03
216 108 0.56
217 3 0.02
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (214 bp):
AACCAAGAGAGAATAATTTTCACAAAAATAAGTTTTTAATTCAAACACCAAAAGGTGTTTACAAA
ACAACAAAATATTTAGACCAAATGAGCGATATCCCAAGCATGCAACGCTTGAAAAATTGCTCGAA
AGAATGGATCATATTAAATACTTTAAGGAATCAAAGTTATAAAAAACCTCGTAAAAGTGTGACAA
GTTCAAAAGTTCGGTGAAA
Found at i:7070 original size:216 final size:211
Alignment explanation
Indices: 6568--7101 Score: 565
Period size: 213 Copynumber: 2.5 Consensus size: 211
6558 CTTACATTTG
* * * * * * *
6568 TGCTCGAAGGAATGGAT-AGTCTTGAATGCTTTAAGGAGCCGAAGCTCTAAAAAAACTTGTAAAA
1 TGCTCGAAGGAATGGATCA-TCTTGAATACTTTAAGGA-ACAAAGTTATAAAAAACCTCGTAAAA
** * ** **
6632 GTTTGACAAGTTTGGAAA-TTCAGCCAAGAACCAAGAGAGAAATAATTTTCACGTAAATAAGTTT
64 GTTTGACAAG-TTCAAAAGTTCGGTGAAGAACCAAGAGAG-AATAATTTTCACAAAAATAAGTTT
* * * * *
6696 TTAATTCAAAGACTAAAAGGTGTTTACGAAACGACAAACTATTTAGACCAAATGACATATCCCAA
127 TTAATTCAAACACCAAAAGGTGTTTACAAAACAACAAAATATTTAGACCAAATGACATATCCCAA
* *
6761 GCATGGAATGTTCGAAAAAT
192 GCATGCAACGTTCGAAAAAT
* * * * *
6781 TGCTCGAAAGAATGGATCGTATTAAATACTTTAAGGAACTACAGTTATAAAAGAACC-CGTAAAA
1 TGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAAC-AAAGTTATAAAA-AACCTCGTAAAA
*
6845 GTTTGACAAGTTCAAAAGTTCGGTGAAAAACCAAGAGAGAAT-ATTTTCACACAAAAATAAGTTT
64 GTTTGACAAGTTCAAAAGTTCGGTGAAGAACCAAGAGAGAATAATTTT--CACAAAAATAAGTTT
* * * * *
6909 TTAATTCAAACACCAATAGTTGTTTACAAAACAATAAAATGTTTAGACCAAATGATGCGATTTCC
127 TTAATTCAAACACCAAAAGGTGTTTACAAAACAACAAAATATTTAGACCAAATGA--C-ATATCC
**
6974 TGAGCATGCAACGCTT-GAAAAAT
189 CAAGCATGCAACG-TTCGAAAAAT
6997 TGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAATCAAAGTTATAAAAAACCTCGTAAAAG
1 TGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAA-CAAAGTTATAAAAAACCTCGTAAAAG
* ** * *
7062 TGTGACAAGTTCAGGAGTTTGGTGAAGAACCGAGAGAGAA
65 TTTGACAAGTTCAAAAGTTCGGTGAAGAACCAAGAGAGAA
7102 ACAATTCTCA
Statistics
Matches: 264, Mismatches: 45, Indels: 21
0.80 0.14 0.06
Matches are distributed among these distances:
211 5 0.02
212 9 0.03
213 131 0.50
214 3 0.01
215 5 0.02
216 108 0.41
217 3 0.01
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (211 bp):
TGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAACAAAGTTATAAAAAACCTCGTAAAAGT
TTGACAAGTTCAAAAGTTCGGTGAAGAACCAAGAGAGAATAATTTTCACAAAAATAAGTTTTTAA
TTCAAACACCAAAAGGTGTTTACAAAACAACAAAATATTTAGACCAAATGACATATCCCAAGCAT
GCAACGTTCGAAAAAT
Done.