Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010327.1 Kokia drynarioides strain JFW-HI SEQ_125192, 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: 27038
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1755 original size:13 final size:13
Alignment explanation
Indices: 1737--1762 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1727 TTCATTATAT
1737 AAGAAAAGAAAAA
1 AAGAAAAGAAAAA
1750 AAGAAAAGAAAAA
1 AAGAAAAGAAAAA
1763 GATTTGGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAGAAAAGAAAAA
Found at i:5140 original size:6 final size:6
Alignment explanation
Indices: 5129--5203 Score: 77
Period size: 6 Copynumber: 13.2 Consensus size: 6
5119 ATTTGAGTAG
* * *
5129 AAATTT AAATTT ATA-TT AAATTT ATA-TT AAATTT AAATTT -ATTTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* *
5174 GAATTT AAATTT -AATTT AAGTTT AAATTT A
1 AAATTT AAATTT AAATTT AAATTT AAATTT A
5204 TTTTCCAAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
5 17 0.30
6 39 0.70
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (6 bp):
AAATTT
Found at i:5149 original size:11 final size:11
Alignment explanation
Indices: 5133--5163 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
5123 GAGTAGAAAT
5133 TTAAATTTATA
1 TTAAATTTATA
5144 TTAAATTTATA
1 TTAAATTTATA
5155 TTAAATTTA
1 TTAAATTTA
5164 AATTTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TTAAATTTATA
Found at i:5151 original size:17 final size:17
Alignment explanation
Indices: 5144--5235 Score: 82
Period size: 17 Copynumber: 5.3 Consensus size: 17
5134 TAAATTTATA
5144 TTAAATTTATATTAAAT
1 TTAAATTTATATTAAAT
* *
5161 TTAAATTTATTTTGAAT
1 TTAAATTTATATTAAAT
*
5178 TTAAATTTA-ATTTAAGT
1 TTAAATTTATA-TTAAAT
*
5195 TTAAATTTATTTTCCAAAT
1 TTAAATTTATATT--AAAT
5214 TTAAGA-TTAT-TATAAAT
1 TTAA-ATTTATAT-TAAAT
5231 TTAAA
1 TTAAA
5236 ATAAATAAGG
Statistics
Matches: 62, Mismatches: 7, Indels: 13
0.76 0.09 0.16
Matches are distributed among these distances:
16 1 0.02
17 47 0.76
18 1 0.02
19 12 0.19
20 1 0.02
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.52
Consensus pattern (17 bp):
TTAAATTTATATTAAAT
Found at i:5164 original size:28 final size:28
Alignment explanation
Indices: 5129--5197 Score: 93
Period size: 28 Copynumber: 2.5 Consensus size: 28
5119 ATTTGAGTAG
*
5129 AAATTTAAATTTATATTAAATTTATATT
1 AAATTTAAATTTATATTAAATTTAAATT
* *
5157 AAATTTAAATTTATTTTGAATTTAAATT
1 AAATTTAAATTTATATTAAATTTAAATT
* *
5185 TAATTTAAGTTTA
1 AAATTTAAATTTA
5198 AATTTATTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (28 bp):
AAATTTAAATTTATATTAAATTTAAATT
Found at i:6007 original size:18 final size:17
Alignment explanation
Indices: 5972--6011 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
5962 TGGGCGGTTT
5972 TAAT-AATATTTATTAA
1 TAATAAATATTTATTAA
*
5988 TAATAAATATTTTCTTAA
1 TAATAAATA-TTTATTAA
6006 TAATAA
1 TAATAA
6012 TAATAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.19
17 4 0.19
18 13 0.62
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATAAATATTTATTAA
Found at i:7185 original size:29 final size:29
Alignment explanation
Indices: 7130--7394 Score: 266
Period size: 30 Copynumber: 8.9 Consensus size: 29
7120 CCCCGAAGGT
* *
7130 CCCTAAACTGTCCAAAAATTCTATTTTTAC
1 CCCTAAACT-TCCAAAAATCCCATTTTTAC
* **
7160 CCCTAAACTTCAAAAAAT-TTAGTTTTTAC
1 CCCTAAACTTCCAAAAATCCCA-TTTTTAC
7189 CCCTAAACTTCCAAAAATCCCATTTTTGAC
1 CCCTAAACTTCCAAAAATCCCATTTTT-AC
*
7219 CCCAAAACTTCCAAAAATCCCATTTTTAC
1 CCCTAAACTTCCAAAAATCCCATTTTTAC
* * *
7248 CCCTGAACTTCAAAAAATCCCATTTTTGAT
1 CCCTAAACTTCCAAAAATCCCATTTTT-AC
*****
7278 CCCTAAACTATCCAAAAATTTTGCTTTTA-
1 CCCTAAACT-TCCAAAAATCCCATTTTTAC
*
7307 CCCTCGAACTTCCAAAAATCCCATTTTTGA-
1 CCCT-AAACTTCCAAAAATCCCATTTTT-AC
*
7337 CCCTAAAACTTCCAAAAATCTCATTTTTACC
1 CCCT-AAACTTCCAAAAATCCCATTTTTA-C
* *
7368 CCCCAAACTTTCAAAAATCCCATTTTT
1 CCCTAAACTTCCAAAAATCCCATTTTT
7395 GACCTCAAAT
Statistics
Matches: 197, Mismatches: 29, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
28 2 0.01
29 81 0.41
30 99 0.50
31 15 0.08
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.33
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATCCCATTTTTAC
Found at i:7227 original size:59 final size:59
Alignment explanation
Indices: 7130--7403 Score: 311
Period size: 59 Copynumber: 4.6 Consensus size: 59
7120 CCCCGAAGGT
* * * * *
7130 CCCTAAACTGTCCAAAAATTCTATTTTT-ACCCCTAAACTTCAAAAAAT-TTAGTTTTTAC
1 CCCTAAACT-TCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATCTCA-TTTTTAC
*
7189 CCCTAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATCCCATTTTTAC
1 CCCTAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATCTCATTTTTAC
* * * * * ***
7248 CCCTGAACTTCAAAAAATCCCATTTTTGATCCCTAAACTATCCAAAAATTTTGCTTTTA-
1 CCCTAAACTTCCAAAAATCCCATTTTTGACCCCAAAACT-TCCAAAAATCTCATTTTTAC
* *
7307 CCCTCGAACTTCCAAAAATCCCATTTTTGACCCTAAAACTTCCAAAAATCTCATTTTTACC
1 CCCT-AAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATCTCATTTTTA-C
* * *
7368 CCCCAAACTTTCAAAAATCCCATTTTTGACCTCAAA
1 CCCTAAACTTCCAAAAATCCCATTTTTGACCCCAAA
7404 TTTTCCCAAA
Statistics
Matches: 181, Mismatches: 28, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
58 16 0.09
59 88 0.49
60 74 0.41
61 3 0.02
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32
Consensus pattern (59 bp):
CCCTAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATCTCATTTTTAC
Found at i:7415 original size:60 final size:59
Alignment explanation
Indices: 7134--7398 Score: 295
Period size: 60 Copynumber: 4.5 Consensus size: 59
7124 GAAGGTCCCT
* * * * *
7134 AAACTGTCCAAAAATTCTATTTTT-ACCCCT-AAACTTCAAAAAAT-TTAGTTTTTACCCCT
1 AAACT-TCCAAAAATCCCATTTTTGA-CCCTAAAACTTCCAAAAATCTCA-TTTTTACCCCC
* * *
7193 AAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATCCCATTTTTACCCCT
1 AAACTTCCAAAAATCCCATTTTTGACCCTAAAACTTCCAAAAATCTCATTTTTACCCCC
* * * *** *
7252 GAACTTCAAAAAATCCCATTTTTGATCCCT-AAACTATCCAAAAATTTTGCTTTTACCCTC
1 AAACTTCCAAAAATCCCATTTTTGA-CCCTAAAACT-TCCAAAAATCTCATTTTTACCCCC
*
7312 GAACTTCCAAAAATCCCATTTTTGACCCTAAAACTTCCAAAAATCTCATTTTTACCCCCC
1 AAACTTCCAAAAATCCCATTTTTGACCCTAAAACTTCCAAAAATCTCATTTTTA-CCCCC
*
7372 AAACTTTCAAAAATCCCATTTTTGACC
1 AAACTTCCAAAAATCCCATTTTTGACC
7399 TCAAATTTTC
Statistics
Matches: 175, Mismatches: 24, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
58 19 0.11
59 77 0.44
60 79 0.45
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (59 bp):
AAACTTCCAAAAATCCCATTTTTGACCCTAAAACTTCCAAAAATCTCATTTTTACCCCC
Found at i:7440 original size:119 final size:119
Alignment explanation
Indices: 7198--7442 Score: 302
Period size: 119 Copynumber: 2.1 Consensus size: 119
7188 CCCCTAAACT
**
7198 TCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATCCCATTTTTACCCCTGAACTTCAAAA
1 TCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATCCCATTTTTACCCCCAAACTTCAAAA
** * * *
7263 AATCCCATTTTTGATCCCTAAACTATCCAAAAATTTTGCTTTTACCCTCGAACT
66 AATCCCATTTTTGATCCCTAAACTATCCAAAAATTCCGCTTTCACCCCCGAACA
* *
7317 TCCAAAAATCCCATTTTTGACCCTAAAACTTCCAAAAATCTCATTTTTACCCCCCAAACTTTC-A
1 TCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATCCCATTTTTA-CCCCCAAAC-TTCAA
* * *
7381 AAAATCCCATTTTTGA--CCTCAAATTTTCCCAAAATTACCG-TTTCACCCCCGAGA-A
64 AAAATCCCATTTTTGATCCCT-AAACTATCCAAAAATT-CCGCTTTCACCCCCGA-ACA
7436 TCCAAAA
1 TCCAAAA
7443 TTATCATTTT
Statistics
Matches: 109, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
118 3 0.03
119 77 0.71
120 26 0.24
121 3 0.03
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.31
Consensus pattern (119 bp):
TCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATCCCATTTTTACCCCCAAACTTCAAAA
AATCCCATTTTTGATCCCTAAACTATCCAAAAATTCCGCTTTCACCCCCGAACA
Found at i:7441 original size:28 final size:29
Alignment explanation
Indices: 7409--7472 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
7399 TCAAATTTTC
*
7409 CCAAAATTA-CCGTTTCACCCCCGAGAAT
1 CCAAAATTATCAGTTTCACCCCCGAGAAT
* **
7437 CCAAAATTATCATTTTTGCCCCCGAGAAT
1 CCAAAATTATCAGTTTCACCCCCGAGAAT
7466 CCGAAAA
1 CC-AAAA
7473 ATCTCATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 9 0.30
29 17 0.57
30 4 0.13
ACGTcount: A:0.34, C:0.31, G:0.11, T:0.23
Consensus pattern (29 bp):
CCAAAATTATCAGTTTCACCCCCGAGAAT
Found at i:7467 original size:29 final size:30
Alignment explanation
Indices: 7426--7482 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
7416 TACCGTTTCA
*
7426 CCCCCGAGAATCC-AAAATTATCATTTTTG
1 CCCCCGAGAATCCGAAAAATATCATTTTTG
*
7455 CCCCCGAGAATCCGAAAAATCTCATTTT
1 CCCCCGAGAATCCGAAAAATATCATTTT
7483 GAACTCCGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.32, C:0.30, G:0.11, T:0.28
Consensus pattern (30 bp):
CCCCCGAGAATCCGAAAAATATCATTTTTG
Found at i:11513 original size:60 final size:60
Alignment explanation
Indices: 11375--11500 Score: 191
Period size: 60 Copynumber: 2.1 Consensus size: 60
11365 CACGAAAATG
*
11375 AGTTGTTTATGAGTGTTATTTAGGAATAAAATTATATTTGGATTTAAAAATATTTAGGTTT
1 AGTT-TTTATGAGTGTTTTTTAGGAATAAAATTATATTTGGATTTAAAAATATTTAGGTTT
* * *
11436 AGTTTTTATGAGTGTTTTTTATGAATGAAATTATATTTGGGTTTAAAAATATTT-GAGTTT
1 AGTTTTTATGAGTGTTTTTTAGGAATAAAATTATATTTGGATTTAAAAATATTTAG-GTTT
11496 AGTTT
1 AGTTT
11501 GTTAATGGGT
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
59 1 0.02
60 55 0.92
61 4 0.07
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (60 bp):
AGTTTTTATGAGTGTTTTTTAGGAATAAAATTATATTTGGATTTAAAAATATTTAGGTTT
Found at i:16580 original size:24 final size:24
Alignment explanation
Indices: 16535--16580 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
16525 ATATAGTCAT
* *
16535 TTTAATATTATTTTAATGTTTACA
1 TTTAATAGTATTTTAATATTTACA
16559 TTTAAGTAGTATTTT-ATATTTA
1 TTTAA-TAGTATTTTAATATTTA
16581 GGATAAGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.59
Consensus pattern (24 bp):
TTTAATAGTATTTTAATATTTACA
Done.