Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008652.1 Kokia drynarioides strain JFW-HI SEQ_123333, 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: 10911
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:1264 original size:33 final size:33
Alignment explanation
Indices: 1227--1305 Score: 158
Period size: 33 Copynumber: 2.4 Consensus size: 33
1217 AACACCTGAC
1227 GCCTTTCGCAAGCTCTCGCAAGCGCCCGACGCA
1 GCCTTTCGCAAGCTCTCGCAAGCGCCCGACGCA
1260 GCCTTTCGCAAGCTCTCGCAAGCGCCCGACGCA
1 GCCTTTCGCAAGCTCTCGCAAGCGCCCGACGCA
1293 GCCTTTCGCAAGC
1 GCCTTTCGCAAGC
1306 GCCCGACGCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.18, C:0.42, G:0.24, T:0.16
Consensus pattern (33 bp):
GCCTTTCGCAAGCTCTCGCAAGCGCCCGACGCA
Found at i:1363 original size:23 final size:23
Alignment explanation
Indices: 1275--1359 Score: 134
Period size: 23 Copynumber: 3.7 Consensus size: 23
1265 TCGCAAGCTC
*
1275 TCGCAAGCGCCCGACGCAGCCTT
1 TCGCAAGCACCCGACGCAGCCTT
*
1298 TCGCAAGCGCCCGACGCAGCCTT
1 TCGCAAGCACCCGACGCAGCCTT
**
1321 TCGCAAGCACCCGACATAGCCTT
1 TCGCAAGCACCCGACGCAGCCTT
1344 TCGCAAGCACCCGACG
1 TCGCAAGCACCCGACG
1360 TAGCTTCGGC
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 58 1.00
ACGTcount: A:0.21, C:0.42, G:0.24, T:0.13
Consensus pattern (23 bp):
TCGCAAGCACCCGACGCAGCCTT
Found at i:6367 original size:85 final size:82
Alignment explanation
Indices: 6136--6385 Score: 229
Period size: 83 Copynumber: 3.0 Consensus size: 82
6126 TTGTTAATTG
* * * *
6136 GCGAGAATAAATCCTGAAACAGATTTAGTCAACTTATTCTTGTTTTGAAAATAAAATCAAACTGT
1 GCGAGAATAAATCCTGAAACAGATTTATTCAACTTATTC-TGTTTTGGAAATAAAATCAAAATAT
*
6201 AATAAAATCTTTTAAACA
65 AATAAAATCTGTTAAACA
* * *
6219 GCGAGAATAAATCCCGAAACAGATTTATT-TACTTAATTAT-TATTTGGAACCA-AAAATCTAAA
1 GCGAGAATAAATCCTGAAACAGATTTATTCAACTT-ATTCTGT-TTTGGAA--ATAAAATC-AAA
* * **
6281 TATAGAATCAAAA-CTGTTGAATG
61 -ATATAAT-AAAATCTGTTAAACA
* * * * *
6304 GGGAGAATAAATCTTGAAACAAATTTATTCAACTTATTCTCGTTTTGGAAATAAATTCAAAATAG
1 GCGAGAATAAATCCTGAAACAGATTTATTCAACTTATTCT-GTTTTGGAAATAAAATCAAAATAT
*
6369 AATAAAATTTGTTAAAC
65 AATAAAATCTGTTAAAC
6386 GTCAGGAAAT
Statistics
Matches: 133, Mismatches: 22, Indels: 24
0.74 0.12 0.13
Matches are distributed among these distances:
81 1 0.01
82 15 0.11
83 49 0.37
84 8 0.06
85 44 0.33
86 15 0.11
87 1 0.01
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (82 bp):
GCGAGAATAAATCCTGAAACAGATTTATTCAACTTATTCTGTTTTGGAAATAAAATCAAAATATA
ATAAAATCTGTTAAACA
Found at i:6375 original size:168 final size:168
Alignment explanation
Indices: 6103--6416 Score: 408
Period size: 168 Copynumber: 1.9 Consensus size: 168
6093 TAATTATTAT
** *
6103 AAAATCCAAATATAGAATATAATTTGTTAATTGGCGAGAATAAATCCTGAAACAGATTTAGTCAA
1 AAAATCCAAATATAGAATATAAACTGTTAATTGGCGAGAATAAATCCTGAAACAAATTTAGTCAA
* *
6168 CTTATTCTTGTTTTGAAAATAAAATCAAACTGTAATAAAATCTT-TTAAA---CAGCGAGAATAA
66 CTTATTCTCGTTTTGAAAATAAAATCAAAATGTAATAAAAT-TTGTTAAACGTCAG-GA-AATAA
*
6229 ATCCCGAAACAGATTTATTTACTTAATTATTATTTGGAACCA
128 ATCCCGAAACA-AATTATTTACTTAATTATTATTTGGAACCA
* * * *
6271 AAAATCTAAATATAGAATCA-AAACTGTTGAA-TGGGGAGAATAAATCTTGAAACAAATTTATTC
1 AAAATCCAAATATAGAAT-ATAAACTGTT-AATTGGCGAGAATAAATCCTGAAACAAATTTAGTC
* *
6334 AACTTATTCTCGTTTTGGAAATAAATTCAAAATAG-AATAAAATTTGTTAAACGTCAGGAAATAA
64 AACTTATTCTCGTTTTGAAAATAAAATCAAAAT-GTAATAAAATTTGTTAAACGTCAGGAAATAA
6398 ATCCCGAAACAAATTATTT
128 ATCCCGAAACAAATTATTT
6417 TCCAATTTTA
Statistics
Matches: 127, Mismatches: 12, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
167 2 0.02
168 100 0.79
169 20 0.16
170 2 0.02
171 3 0.02
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (168 bp):
AAAATCCAAATATAGAATATAAACTGTTAATTGGCGAGAATAAATCCTGAAACAAATTTAGTCAA
CTTATTCTCGTTTTGAAAATAAAATCAAAATGTAATAAAATTTGTTAAACGTCAGGAAATAAATC
CCGAAACAAATTATTTACTTAATTATTATTTGGAACCA
Found at i:6561 original size:6 final size:6
Alignment explanation
Indices: 6550--6577 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
6540 TAGCGAATAC
6550 ATATAA ATATAA ATATAA ATATAA ATAT
1 ATATAA ATATAA ATATAA ATATAA ATAT
6578 TTATATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
ATATAA
Found at i:6583 original size:18 final size:19
Alignment explanation
Indices: 6550--6589 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
6540 TAGCGAATAC
6550 ATATAAATATAAATA-TAA
1 ATATAAATATAAATATTAA
**
6568 ATATAAATATTTATATTAA
1 ATATAAATATAAATATTAA
6587 ATA
1 ATA
6590 CAATATCTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATATAAATATAAATATTAA
Found at i:6628 original size:50 final size:50
Alignment explanation
Indices: 6574--6692 Score: 129
Period size: 50 Copynumber: 2.4 Consensus size: 50
6564 ATAAATATAA
*
6574 ATATTTATATTAAATACA-ATATCTCAACAAAAT-AATATAAACAAATATTT
1 ATATTTATATTAAA-ACACATATCTAAAC-AAATCAATATAAACAAATATTT
* * * *
6624 ATATTTATA-TAAAACATCATATTTAAACAAATCACTTTAAATAAATATTT
1 ATATTTATATTAAAACA-CATATCTAAACAAATCAATATAAACAAATATTT
*
6674 ATATTTAT-TTAAAAAACAT
1 ATATTTATATTAAAACACAT
6693 TAGATCTAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
48 3 0.05
49 11 0.19
50 45 0.76
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (50 bp):
ATATTTATATTAAAACACATATCTAAACAAATCAATATAAACAAATATTT
Found at i:8466 original size:20 final size:20
Alignment explanation
Indices: 8425--8467 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
8415 ATATCCATTT
* *
8425 TTTATTTTTCTAACATAAAA
1 TTTATTTATCTAAAATAAAA
8445 TTTATTTAT-TAAAATAATAA
1 TTTATTTATCTAAAATAA-AA
8465 TTT
1 TTT
8468 TATAAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTATTTATCTAAAATAAAA
Found at i:8634 original size:76 final size:76
Alignment explanation
Indices: 8464--8636 Score: 239
Period size: 76 Copynumber: 2.3 Consensus size: 76
8454 TAAAATAATA
* * * * *
8464 ATTTTATAAAT-AT-TTT-TTTAAAACCCCGCAAACAAGAACTAAATCATATTTAAATTTTTCTT
1 ATTTTATAAATAATATTTATTTAAAAACCCACAAACAAGAACTAAACCATATTCAAACTTTTCTT
8526 TTTTTAGTTTT
66 TTTTTAGTTTT
8537 ATTTTATAAATAATGATTTATTTAAAAACCCACAAACAAG-ACTTAAACCATATTCAAACTTTTC
1 ATTTTATAAATAAT-ATTTATTTAAAAACCCACAAACAAGAAC-TAAACCATATTCAAACTTTTC
8601 -TTTTTTAGTTTT
64 TTTTTTTAGTTTT
8613 ATTTTATAAATAATAATTTATTTA
1 ATTTTATAAATAAT-ATTTATTTA
8637 TTATACATTT
Statistics
Matches: 89, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
73 11 0.12
74 2 0.02
76 40 0.45
77 36 0.40
ACGTcount: A:0.39, C:0.12, G:0.03, T:0.46
Consensus pattern (76 bp):
ATTTTATAAATAATATTTATTTAAAAACCCACAAACAAGAACTAAACCATATTCAAACTTTTCTT
TTTTTAGTTTT
Found at i:10307 original size:31 final size:30
Alignment explanation
Indices: 10264--10366 Score: 90
Period size: 31 Copynumber: 3.4 Consensus size: 30
10254 CAAAAAAAAA
*
10264 TTAAATACCAAATTAAGAAAAAATGTCAAG
1 TTAAGTACCAAATTAAGAAAAAATGTCAAG
*
10294 TTCAAGTACCAAATTTGAAAAAAAAATGTC---
1 TT-AAGTACCAAA-TT-AAGAAAAAATGTCAAG
*
10324 -TAAGTACCAAATT-AGAAAAAAGTGTTAAG
1 TTAAGTACCAAATTAAGAAAAAA-TGTCAAG
*
10353 TTTAGGTACCAAAT
1 -TTAAGTACCAAAT
10367 AAAATATTAA
Statistics
Matches: 59, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
25 7 0.12
26 3 0.05
27 2 0.03
28 10 0.17
29 1 0.02
30 2 0.03
31 20 0.34
32 2 0.03
33 12 0.20
ACGTcount: A:0.50, C:0.11, G:0.13, T:0.26
Consensus pattern (30 bp):
TTAAGTACCAAATTAAGAAAAAATGTCAAG
Found at i:10318 original size:59 final size:59
Alignment explanation
Indices: 10255--10366 Score: 147
Period size: 59 Copynumber: 1.9 Consensus size: 59
10245 AATTAGACCC
10255 AAAAAAAAAT-TAAATACCAAATTAAGAAAAAA-TGTCAAGTTCAAGTACCAAATTTGAA
1 AAAAAAAAATCTAAATACCAAATT-AGAAAAAAGTGTCAAGTTCAAGTACCAAATTTGAA
** * * * *
10313 AAAAAAATGTCTAAGTACCAAATTAGAAAAAAGTGTTAAGTTTAGGTACCAAAT
1 AAAAAAAAATCTAAATACCAAATTAGAAAAAAGTGTCAAGTTCAAGTACCAAAT
10367 AAAATATTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
58 16 0.35
59 30 0.65
ACGTcount: A:0.54, C:0.10, G:0.12, T:0.24
Consensus pattern (59 bp):
AAAAAAAAATCTAAATACCAAATTAGAAAAAAGTGTCAAGTTCAAGTACCAAATTTGAA
Done.