Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011856.1 Kokia drynarioides strain JFW-HI SEQ_126853, 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: 19666
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Found at i:7951 original size:2 final size:2
Alignment explanation
Indices: 7944--7976 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
7934 GCAAAATAGA
7944 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7977 ATAAATTCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8441 original size:6 final size:6
Alignment explanation
Indices: 8417--8491 Score: 77
Period size: 6 Copynumber: 13.0 Consensus size: 6
8407 TTTTAGACTT
* * *
8417 TTTAAT TTTGAA TTTAAA TTCAAA -TTAAA TTTAAA TTTAAGA -TTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA
*
8464 -TTAAA TTTAAA TTT-AA GTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
8492 ATAAATTAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
5 14 0.24
6 43 0.74
7 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:8446 original size:11 final size:11
Alignment explanation
Indices: 8427--8498 Score: 76
Period size: 11 Copynumber: 6.4 Consensus size: 11
8417 TTTAATTTTG
8427 AATTTAAATTCA
1 AATTTAAATT-A
8439 AA-TTAAATTTA
1 AATTTAAA-TTA
8450 AATTTAAGATTA
1 AATTTAA-ATTA
8462 AA-TTAAATTTA
1 AATTTAAA-TTA
*
8473 AATTTAAGTTA
1 AATTTAAATTA
*
8484 AATTTAAAATA
1 AATTTAAATTA
8495 AATT
1 AATT
8499 AAAGAAAGGG
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
10 1 0.02
11 33 0.63
12 17 0.33
13 1 0.02
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (11 bp):
AATTTAAATTA
Found at i:8449 original size:17 final size:17
Alignment explanation
Indices: 8427--8498 Score: 92
Period size: 17 Copynumber: 4.2 Consensus size: 17
8417 TTTAATTTTG
*
8427 AATTTAAATTCAAATTA
1 AATTTAAATTTAAATTA
8444 AATTTAAATTTAAGATTA
1 AATTTAAATTTAA-ATTA
*
8462 AA-TTAAATTTAAATTT
1 AATTTAAATTTAAATTA
* *
8478 AAGTTAAATTTAAAATA
1 AATTTAAATTTAAATTA
8495 AATT
1 AATT
8499 AAAGAAAGGG
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
16 5 0.10
17 37 0.77
18 6 0.12
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (17 bp):
AATTTAAATTTAAATTA
Found at i:8491 original size:23 final size:22
Alignment explanation
Indices: 8418--8487 Score: 95
Period size: 23 Copynumber: 3.1 Consensus size: 22
8408 TTTAGACTTT
* * *
8418 TTAATTTTGAATTTAAATTCAAA
1 TTAAATTTAAATTTAAGTT-AAA
8441 TTAAATTTAAATTTAAGATTAAA
1 TTAAATTTAAATTTAAG-TTAAA
8464 TTAAATTTAAATTTAAGTTAAA
1 TTAAATTTAAATTTAAGTTAAA
8486 TT
1 TT
8488 TAAAATAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
22 7 0.16
23 34 0.79
24 2 0.05
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (22 bp):
TTAAATTTAAATTTAAGTTAAA
Found at i:14295 original size:91 final size:90
Alignment explanation
Indices: 14156--14425 Score: 343
Period size: 91 Copynumber: 3.0 Consensus size: 90
14146 TTTTTTATCC
* * * *
14156 TAGTTAATCTCTATTAT-TTCTCTGGCTCAGTTAAACTCTGATTTATTTAGGAATATTTTCGTCA
1 TAGTTAA-CTCTATTATCTTTTCTGGCCCAATTAAACTCTGATTTATTTAGGAATATTTTAGTCA
14220 TATTAAGACTTTAATATTAGTCTATT
65 TATTAAGACTTTAATATTAGTCTATT
* * *
14246 TAGTTCAACTCTATTATCTTTTCTGACCCAATTAAATTCTTATTTATTTAGGAATATTTTAGTCA
1 TAGTT-AACTCTATTATCTTTTCTGGCCCAATTAAACTCTGATTTATTTAGGAATATTTTAGTCA
*
14311 TATTAAGACTTTAATATTAGCCTATT
65 TATTAAGACTTTAATATTAGTCTATT
* * * *
14337 TAGTT---TATGTTATCTTTTCCGGCCCAATTAAACTCTGATTTATTTAGGAATATTTTTGTCAT
1 TAGTTAACTCTATTATCTTTTCTGGCCCAATTAAACTCTGATTTATTTAGGAATATTTTAGTCAT
* * *
14399 ACTGAGA-TTCTAATATTAGTTTATT
66 ATTAAGACTT-TAATATTAGTCTATT
14424 TA
1 TA
14426 AAGGGTCCTT
Statistics
Matches: 158, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
86 2 0.01
87 70 0.44
90 14 0.09
91 72 0.46
ACGTcount: A:0.29, C:0.13, G:0.10, T:0.48
Consensus pattern (90 bp):
TAGTTAACTCTATTATCTTTTCTGGCCCAATTAAACTCTGATTTATTTAGGAATATTTTAGTCAT
ATTAAGACTTTAATATTAGTCTATT
Found at i:14424 original size:87 final size:88
Alignment explanation
Indices: 14186--14425 Score: 322
Period size: 87 Copynumber: 2.7 Consensus size: 88
14176 TCTGGCTCAG
*
14186 TTAAACTCTGATTTATTTAGGAATATTTTCGTCATATTAAGACTTTAATATTAGTCTATTTAGTT
1 TTAAACTCTGATTTATTTAGGAATATTTTAGTCATATTAAGACTTTAATATTAGTCTATTTAGTT
* *
14251 CAACTCTATTATCTTTTCTGACCCAA
66 --A-TATATTATCTTTTCCGACCCAA
* * *
14277 TTAAATTCTTATTTATTTAGGAATATTTTAGTCATATTAAGACTTTAATATTAGCCTATTTAGTT
1 TTAAACTCTGATTTATTTAGGAATATTTTAGTCATATTAAGACTTTAATATTAGTCTATTTAGTT
* *
14342 -TATGTTATCTTTTCCGGCCCAA
66 ATATATTATCTTTTCCGACCCAA
* * * *
14364 TTAAACTCTGATTTATTTAGGAATATTTTTGTCATACTGAGA-TTCTAATATTAGTTTATTTA
1 TTAAACTCTGATTTATTTAGGAATATTTTAGTCATATTAAGACTT-TAATATTAGTCTATTTA
14426 AAGGGTCCTT
Statistics
Matches: 133, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
86 2 0.02
87 70 0.53
91 61 0.46
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.48
Consensus pattern (88 bp):
TTAAACTCTGATTTATTTAGGAATATTTTAGTCATATTAAGACTTTAATATTAGTCTATTTAGTT
ATATATTATCTTTTCCGACCCAA
Found at i:15839 original size:60 final size:60
Alignment explanation
Indices: 15775--15889 Score: 133
Period size: 60 Copynumber: 1.9 Consensus size: 60
15765 TTTTTGAAGT
* * * * * * *
15775 TTTAGAGTTAAGATTAAATTAATATATTGTGTAAACATTGA-GGACTAAATTTGTTTCCTG
1 TTTAGAATTAAGATCAAATTAACAAAATGTATAAACATTAATGGA-TAAATTTGTTTCCTG
* *
15835 TTTAGAATTATGATCAATTTAACAAAATGTATAAACATTAATGGATAAATTTGTT
1 TTTAGAATTAAGATCAAATTAACAAAATGTATAAACATTAATGGATAAATTTGTT
15890 ATTATATCAA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
60 42 0.93
61 3 0.07
ACGTcount: A:0.39, C:0.06, G:0.14, T:0.41
Consensus pattern (60 bp):
TTTAGAATTAAGATCAAATTAACAAAATGTATAAACATTAATGGATAAATTTGTTTCCTG
Found at i:16251 original size:15 final size:15
Alignment explanation
Indices: 16201--16251 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
16191 AGAGGTGGAG
16201 AATTTGTTCGTTGAA
1 AATTTGTTCGTTGAA
* *
16216 AGTTTG-T-GGTGAAA
1 AATTTGTTCGTTG-AA
*
16230 AACTTGTTCGTTGAA
1 AATTTGTTCGTTGAA
16245 AATTTGT
1 AATTTGT
16252 GTTAAGGTGG
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
13 3 0.11
14 7 0.26
15 14 0.52
16 3 0.11
ACGTcount: A:0.27, C:0.06, G:0.24, T:0.43
Consensus pattern (15 bp):
AATTTGTTCGTTGAA
Found at i:16369 original size:24 final size:24
Alignment explanation
Indices: 16342--16388 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
16332 ATTTCTAGAA
16342 GATTTGATT-GTATAATATATTTTG
1 GATTT-ATTAGTATAATATATTTTG
16366 GATTTATTAGTATAATATATTTT
1 GATTTATTAGTATAATATATTTT
16389 ACATTGATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 3 0.14
24 19 0.86
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (24 bp):
GATTTATTAGTATAATATATTTTG
Found at i:16398 original size:24 final size:24
Alignment explanation
Indices: 16345--16399 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
16335 TCTAGAAGAT
**
16345 TTGATT-GTATAATATATTTTGGA
1 TTGATTAGTATAATATATTTTACA
*
16368 TTTATTAGTATAATATATTTTACA
1 TTGATTAGTATAATATATTTTACA
16392 TTGATTAG
1 TTGATTAG
16400 AATTAAGCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 5 0.19
24 22 0.81
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.53
Consensus pattern (24 bp):
TTGATTAGTATAATATATTTTACA
Done.