Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006687.1 Kokia drynarioides strain JFW-HI SEQ_121281, 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: 21677
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.31
Found at i:152 original size:24 final size:24
Alignment explanation
Indices: 125--170 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
115 ATTCTTAAGT
*
125 CAAATAAAATATGCTAATAAATGC
1 CAAATAAAATATACTAATAAATGC
* *
149 CAAATATATTATACTAATAAAT
1 CAAATAAAATATACTAATAAAT
171 ATTAAATCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.54, C:0.11, G:0.04, T:0.30
Consensus pattern (24 bp):
CAAATAAAATATACTAATAAATGC
Found at i:519 original size:14 final size:14
Alignment explanation
Indices: 496--541 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
486 ATGAAAAATT
*
496 ATAATTATTTATTA
1 ATAATAATTTATTA
* *
510 ATAATAATTTTTTG
1 ATAATAATTTATTA
524 ATAAT--TTTATTA
1 ATAATAATTTATTA
536 ATAATA
1 ATAATA
542 TTTTTATTGT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
12 10 0.38
14 16 0.62
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (14 bp):
ATAATAATTTATTA
Found at i:2360 original size:3 final size:3
Alignment explanation
Indices: 2352--2379 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2342 GTTGATCTGC
2352 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2380 ATGATAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3231 original size:30 final size:30
Alignment explanation
Indices: 3102--3405 Score: 230
Period size: 30 Copynumber: 10.2 Consensus size: 30
3092 GAACTTTCCA
* * *
3102 AAAATCACATTTTAATCCC-CAAACTTCAT-A
1 AAAATTACATTTTAA-CCCTAAAACTTC-TCT
* * * *
3132 AAAATTACATTTTGACCCTCAAACTTCACA
1 AAAATTACATTTTAACCCTAAAACTTCTCT
* * * *
3162 AAAAATACATTTTGACCCTTAAACTTCAC-
1 AAAATTACATTTTAACCCTAAAACTTCTCT
3191 AAAATTACATTTTAACCCTAAAACTTCTCT
1 AAAATTACATTTTAACCCTAAAACTTCTCT
* * *
3221 AAACTTACATTTTAACCTCT-AAACTTTTCC
1 AAAATTACATTTTAACC-CTAAAACTTCTCT
* * *
3251 AAAATTACATTTTAACCCTAAAAATTTTAT
1 AAAATTACATTTTAACCCTAAAACTTCTCT
* * *
3281 AAAATCA-AGTTTTAACTCTTAAACTT-TCCTT
1 AAAATTACA-TTTTAACCCTAAAACTTCT-C-T
* *
3312 AAAATCACATTTTAACCCT-AAACTTCTTT
1 AAAATTACATTTTAACCCTAAAACTTCTCT
** *
3341 AAAATTACATTTTAACCCTAAATTTTC-CC
1 AAAATTACATTTTAACCCTAAAACTTCTCT
* *
3370 AAAATTACATTTTTACCCCT-AAACTTTTTCT
1 AAAATTACA-TTTTAACCCTAAAAC-TTCTCT
3401 AAAAT
1 AAAAT
3406 CATGTTTTAA
Statistics
Matches: 227, Mismatches: 33, Indels: 27
0.79 0.11 0.09
Matches are distributed among these distances:
29 62 0.27
30 138 0.61
31 26 0.11
32 1 0.00
ACGTcount: A:0.39, C:0.23, G:0.01, T:0.37
Consensus pattern (30 bp):
AAAATTACATTTTAACCCTAAAACTTCTCT
Found at i:3393 original size:59 final size:59
Alignment explanation
Indices: 3132--3405 Score: 254
Period size: 59 Copynumber: 4.6 Consensus size: 59
3122 AAACTTCATA
* * *** * * * *
3132 AAAATTACATTTTGACCCTCAAACTTCACAAAAAATACATTTTGACCCTTAAA-CTTCAC
1 AAAATTACATTTTAACCCTAAAACTTCTTTAAAATTACATTTTAACCC-TAAATTTTCCC
* *
3191 AAAATTACATTTTAACCCTAAAACTTCTCTAAACTTACATTTTAACCTCTAAACTTTT-CC
1 AAAATTACATTTTAACCCTAAAACTTCTTTAAAATTACATTTTAACC-CTAAA-TTTTCCC
* * * * *
3251 AAAATTACATTTTAACCCTAAAAATT-TTATAAAATCA-AGTTTTAACTCTTAAACTTTCCTT
1 AAAATTACATTTTAACCCTAAAACTTCTT-TAAAATTACA-TTTTAAC-CCTAAATTTTCC-C
*
3312 AAAATCACATTTTAACCCT-AAACTTCTTTAAAATTACATTTTAACCCTAAATTTTCCC
1 AAAATTACATTTTAACCCTAAAACTTCTTTAAAATTACATTTTAACCCTAAATTTTCCC
* *
3370 AAAATTACATTTTTACCCCT-AAACTTTTTCTAAAAT
1 AAAATTACA-TTTTAACCCTAAAACTTCTT-TAAAAT
3406 CATGTTTTAA
Statistics
Matches: 178, Mismatches: 25, Indels: 23
0.79 0.11 0.10
Matches are distributed among these distances:
58 8 0.04
59 76 0.43
60 70 0.39
61 24 0.13
ACGTcount: A:0.39, C:0.22, G:0.01, T:0.38
Consensus pattern (59 bp):
AAAATTACATTTTAACCCTAAAACTTCTTTAAAATTACATTTTAACCCTAAATTTTCCC
Found at i:3414 original size:30 final size:30
Alignment explanation
Indices: 3063--3417 Score: 194
Period size: 30 Copynumber: 11.8 Consensus size: 30
3053 AAAGCCTTTG
* *
3063 TTTTGTCTAAAAATCACATTTTGACCCTCGAAC
1 TTTT-TCT-AAAATCACATTTTAACCCT-AAAC
* * *
3096 -TTTCCAAAAATCACATTTTAATCCCCAAAC
1 TTTTTCTAAAATCACATTTTAA-CCCTAAAC
** * * *
3126 TTCAT-AAAAATTACATTTTGACCCTCAAAC
1 TTTTTCTAAAATCACATTTTAACCCT-AAAC
** * *
3156 -TTCACAAAAAAT-ACATTTTGACCCTTAAAC
1 TTTTTC-TAAAATCACATTTTAACCC-TAAAC
** *
3186 -TTCAC-AAAATTACATTTTAACCCTAAAAC
1 TTTTTCTAAAATCACATTTTAACCCT-AAAC
* * *
3215 -TTCTCTAAACTTACATTTTAACCTCTAAAC
1 TTTTTCTAAAATCACATTTTAACC-CTAAAC
* * *
3245 -TTTTCCAAAATTACATTTTAACCCTAAAA
1 TTTTTCTAAAATCACATTTTAACCCTAAAC
* * *
3274 ATTTTATAAAATCA-AGTTTTAACTCTTAAAC
1 TTTTTCTAAAATCACA-TTTTAAC-CCTAAAC
*
3305 -TTTCCTTAAAATCACATTTTAACCCTAAAC
1 TTTTTC-TAAAATCACATTTTAACCCTAAAC
* *
3335 TTCTT-TAAAATTACATTTTAACCCTAAA-
1 TTTTTCTAAAATCACATTTTAACCCTAAAC
* * * *
3363 TTTTCCCAAAATTACATTTTTACCCCTAAAC
1 TTTTTCTAAAATCACA-TTTTAACCCTAAAC
**
3394 TTTTTCTAAAATCATGTTTTAACC
1 TTTTTCTAAAATCACATTTTAACC
3418 TCATATTCTT
Statistics
Matches: 261, Mismatches: 42, Indels: 41
0.76 0.12 0.12
Matches are distributed among these distances:
28 9 0.03
29 60 0.23
30 141 0.54
31 47 0.18
32 4 0.02
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.37
Consensus pattern (30 bp):
TTTTTCTAAAATCACATTTTAACCCTAAAC
Found at i:15876 original size:36 final size:36
Alignment explanation
Indices: 15751--15936 Score: 183
Period size: 36 Copynumber: 5.1 Consensus size: 36
15741 GGTTAAAGAT
* ** *
15751 TCCGATCTCTCACCCCGAGCCAAGGACAGATCACGATCA
1 TCCGATCTCTTACCCCGAGCCTGGGGCAGATCAC---CA
* *
15790 ACCAATCTCTTACCCCGAGCCTGGGGCAGATCAGCCA
1 TCCGATCTCTTACCCCGAGCCTGGGGCAGATCA-CCA
* **
15827 TCCGATCTTTTACCTTGAGCCTGGGGCAGATCACCA
1 TCCGATCTCTTACCCCGAGCCTGGGGCAGATCACCA
* * *
15863 TCCGATCTCTTACCCCAAGCTTGAGGCAGATCACCA
1 TCCGATCTCTTACCCCGAGCCTGGGGCAGATCACCA
* ** * *
15899 TCCGATCTCTTACCCTGAGTTTAGAGCAGATCACCA
1 TCCGATCTCTTACCCCGAGCCTGGGGCAGATCACCA
15935 TC
1 TC
15937 AGCATAATGG
Statistics
Matches: 123, Mismatches: 23, Indels: 5
0.81 0.15 0.03
Matches are distributed among these distances:
36 65 0.53
37 30 0.24
39 27 0.22
40 1 0.01
ACGTcount: A:0.24, C:0.35, G:0.19, T:0.22
Consensus pattern (36 bp):
TCCGATCTCTTACCCCGAGCCTGGGGCAGATCACCA
Found at i:16462 original size:3 final size:3
Alignment explanation
Indices: 16454--16503 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
16444 TGATTTGCAA
16454 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16502 AA
1 AA
16504 ATGACAAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:17278 original size:30 final size:30
Alignment explanation
Indices: 17255--17452 Score: 179
Period size: 30 Copynumber: 6.6 Consensus size: 30
17245 AAACTTCGTA
*
17255 AAAATTACATTTTAACCCCCAAACTTCTCT
1 AAAATTACATTTTAACCCCCAAACTTCTCC
** *
17285 AAAATTACATTTTAACCATCAAACTTTTCC
1 AAAATTACATTTTAACCCCCAAACTTCTCC
** *
17315 AAAATTACATTTTAACCCTAAAACTTTTCC
1 AAAATTACATTTTAACCCCCAAACTTCTCC
* *
17345 AAAATCA-AGTTTTAACCCCTAAACTTC-CTC
1 AAAATTACA-TTTTAACCCCCAAACTTCTC-C
* * *
17375 AAAATCACATTTTGA-CCCCAAACTTCTCT
1 AAAATTACATTTTAACCCCCAAACTTCTCC
* * * *
17404 AAAATTATATTTT-ACCCCTAAACTTTTTCT
1 AAAATTACATTTTAACCCCCAAAC-TTCTCC
**
17434 AAAATTATGTTTTAACCCC
1 AAAATTACATTTTAACCCC
17453 GTATTCTTTG
Statistics
Matches: 143, Mismatches: 18, Indels: 13
0.82 0.10 0.07
Matches are distributed among these distances:
28 1 0.01
29 30 0.21
30 106 0.74
31 6 0.04
ACGTcount: A:0.37, C:0.26, G:0.02, T:0.36
Consensus pattern (30 bp):
AAAATTACATTTTAACCCCCAAACTTCTCC
Found at i:17438 original size:89 final size:90
Alignment explanation
Indices: 17264--17452 Score: 240
Period size: 89 Copynumber: 2.1 Consensus size: 90
17254 AAAAATTACA
* * *
17264 TTTTAACCCCCAAACTTCTCTAAAATTACATTTTAACCATCAAACTTTTCCAAAATTACATTTTA
1 TTTTAACCCCCAAACTTCTCTAAAATCACATTTTAACCACCAAACTTCTCCAAAATTACATTTTA
17329 ACCCTAAAACTTTTCCAAAATCAAG
66 ACCCTAAAACTTTTCCAAAATCAAG
* * * *
17354 TTTTAACCCCTAAACTTC-CTCAAAATCACATTTTGACC-CCAAACTTCTCTAAAATTATATTTT
1 TTTTAACCCCCAAACTTCTCT-AAAATCACATTTTAACCACCAAACTTCTCCAAAATTACATTTT
* * * *
17417 ACCCCT-AAACTTTTTCTAAAATTATG
65 AACCCTAAAAC-TTTTCCAAAATCAAG
17443 TTTTAACCCC
1 TTTTAACCCC
17453 GTATTCTTTG
Statistics
Matches: 86, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
88 4 0.05
89 50 0.58
90 32 0.37
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.37
Consensus pattern (90 bp):
TTTTAACCCCCAAACTTCTCTAAAATCACATTTTAACCACCAAACTTCTCCAAAATTACATTTTA
ACCCTAAAACTTTTCCAAAATCAAG
Done.