Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006311.1 Kokia drynarioides strain JFW-HI SEQ_120886, 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: 13845
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Warning! 46 characters in sequence are not A, C, G, or T
Found at i:62 original size:41 final size:41
Alignment explanation
Indices: 1--148 Score: 197
Period size: 41 Copynumber: 3.6 Consensus size: 41
* * **
1 TTAGCGGCGTTTTCTAATAAACGCTTCTAATGCTCTGACAT
1 TTAGCGACGTTTTCTCATAAACGCCACTAATGCTCTGACAT
* *
42 TTAGCGGCGTTTTCTCATAAACGCCACTAATGCTCTGACTT
1 TTAGCGACGTTTTCTCATAAACGCCACTAATGCTCTGACAT
* * *
83 TTAACGACGTTTTCTCATAAACGCCACTAATGCTTTGATAT
1 TTAGCGACGTTTTCTCATAAACGCCACTAATGCTCTGACAT
*
124 TTAGCGACGTTTTTCTTATAAACGC
1 TTAGCGACG-TTTTCTCATAAACGC
149 TGATATTGTT
Statistics
Matches: 95, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
41 81 0.85
42 14 0.15
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (41 bp):
TTAGCGACGTTTTCTCATAAACGCCACTAATGCTCTGACAT
Found at i:4890 original size:19 final size:20
Alignment explanation
Indices: 4866--4905 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
4856 TGTTTGAGTG
4866 TTTATTGTAA-TTAGTG-AAT
1 TTTATTG-AATTTAGTGTAAT
4885 TTTATTGAATTTAGTGTAAT
1 TTTATTGAATTTAGTGTAAT
4905 T
1 T
4906 GAAATATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.11
19 13 0.68
20 4 0.21
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (20 bp):
TTTATTGAATTTAGTGTAAT
Found at i:6763 original size:20 final size:20
Alignment explanation
Indices: 6740--6791 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 20
6730 TTATTAAATT
**
6740 ATATATTTTTTAATTTTTGG
1 ATATATTTTTTAATTTTTAA
* *
6760 ATAT-TTTTATAAATTTTAA
1 ATATATTTTTTAATTTTTAA
6779 AT-TATTTTTTAAT
1 ATATATTTTTTAAT
6792 GTGACATATA
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
18 1 0.04
19 20 0.80
20 4 0.16
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (20 bp):
ATATATTTTTTAATTTTTAA
Found at i:8212 original size:19 final size:18
Alignment explanation
Indices: 8167--8295 Score: 66
Period size: 19 Copynumber: 6.8 Consensus size: 18
8157 TAGTACGATA
8167 ATTTTTATATTTTTTACG
1 ATTTTTATATTTTTTACG
*
8185 AATTTTATATTTCTTTAC-
1 ATTTTTATATTT-TTTACG
8203 ATTTTCTATAATTTTCTTAC-
1 ATTTT-TAT-ATTTT-TTACG
* ** **
8223 AGTTTTATAAAATTTTATA
1 ATTTTTAT-ATTTTTTACG
* * *
8242 ATTTTTTCTATATTTCTA-T
1 A-TTTTTATAT-TTTTTACG
*
8261 ATATTTTATAATTTTTACG
1 AT-TTTTATATTTTTTACG
8280 ATTTTTATAATTTTTT
1 ATTTTTAT-ATTTTTT
8296 CTAATTTGTA
Statistics
Matches: 84, Mismatches: 17, Indels: 19
0.70 0.14 0.16
Matches are distributed among these distances:
18 30 0.36
19 33 0.39
20 21 0.25
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (18 bp):
ATTTTTATATTTTTTACG
Found at i:8216 original size:10 final size:9
Alignment explanation
Indices: 8164--8374 Score: 72
Period size: 9 Copynumber: 22.0 Consensus size: 9
8154 TTTTAGTACG
8164 ATAATTTTT
1 ATAATTTTT
*
8173 ATATTTTTT
1 ATAATTTTT
*
8182 ACGAA-TTTT
1 A-TAATTTTT
8191 AT-ATTTCTT
1 ATAATTT-TT
8200 -TACATTTTCT
1 ATA-ATTTT-T
8210 ATAATTTTCT
1 ATAATTTT-T
*
8220 -TACAGTTTT
1 ATA-ATTTTT
*
8229 ATAAAATTTT
1 AT-AATTTTT
8239 ATAATTTTTT
1 ATAA-TTTTT
* *
8249 CTATATTTCT
1 ATA-ATTTTT
8259 AT-ATATTTT
1 ATAAT-TTTT
8268 ATAATTTTT
1 ATAATTTTT
**
8277 ACGATTTTT
1 ATAATTTTT
8286 ATAATTTTTT
1 ATAA-TTTTT
*
8296 CTAATTTGTAAT
1 ATAATTT-T--T
* **
8308 AAAATTTAA
1 ATAATTTTT
*
8317 ATATTTTTTT
1 ATA-ATTTTT
8327 ATAATTTTTT
1 ATAA-TTTTT
* *
8337 ATTAAAATTTA
1 A-T-AATTTTT
*
8348 ATATTTTTT
1 ATAATTTTT
*
8357 ATAACTTTT
1 ATAATTTTT
8366 ATAATTTTT
1 ATAATTTTT
8375 TGTCACATGT
Statistics
Matches: 147, Mismatches: 33, Indels: 44
0.66 0.15 0.20
Matches are distributed among these distances:
7 1 0.01
8 5 0.03
9 64 0.44
10 60 0.41
11 9 0.06
12 8 0.05
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (9 bp):
ATAATTTTT
Found at i:8220 original size:21 final size:21
Alignment explanation
Indices: 8194--8238 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
8184 GAATTTTATA
* *
8194 TTTCTTTACA-TTTTCTATAAT
1 TTTC-TTACAGTTTTATAAAAT
8215 TTTCTTACAGTTTTATAAAAT
1 TTTCTTACAGTTTTATAAAAT
8236 TTT
1 TTT
8239 ATAATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.27, C:0.11, G:0.02, T:0.60
Consensus pattern (21 bp):
TTTCTTACAGTTTTATAAAAT
Found at i:8332 original size:31 final size:30
Alignment explanation
Indices: 8289--8370 Score: 94
Period size: 31 Copynumber: 2.7 Consensus size: 30
8279 GATTTTTATA
*
8289 ATTTTTTCTAA-TTTGTAATAAAATTTAAAT
1 ATTTTTTATAATTTTGTAATAAAATTT-AAT
* *
8319 ATTTTTTTATAATTTTTTATTAAAATTTAAT
1 A-TTTTTTATAATTTTGTAATAAAATTTAAT
*
8350 ATTTTTTATAACTTTTATAAT
1 ATTTTTTATAA-TTTTGTAAT
8371 TTTTTGTCAC
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
30 11 0.25
31 20 0.45
32 13 0.30
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (30 bp):
ATTTTTTATAATTTTGTAATAAAATTTAAT
Found at i:8366 original size:19 final size:20
Alignment explanation
Indices: 8324--8375 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
8314 TAAATATTTT
8324 TTTATAATTTTTTATTAAAA
1 TTTATAATTTTTTATTAAAA
**
8344 TTTA-ATATTTTTTA-TAACT
1 TTTATA-ATTTTTTATTAAAA
8363 TTTATAATTTTTT
1 TTTATAATTTTTT
8376 GTCACATGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTATAATTTTTTATTAAAA
Found at i:8375 original size:10 final size:10
Alignment explanation
Indices: 8225--8375 Score: 71
Period size: 10 Copynumber: 15.4 Consensus size: 10
8215 TTTCTTACAG
**
8225 TTTTATAAAA
1 TTTTATAATT
8235 TTTTATAATT
1 TTTTATAATT
*
8245 TTTTCT-ATAT
1 TTTTATAAT-T
* *
8255 TTCTAT-ATA
1 TTTTATAATT
8264 TTTTATAA-T
1 TTTTATAATT
**
8273 TTTTACGA-T
1 TTTTATAATT
8282 TTTTATAATT
1 TTTTATAATT
*
8292 TTTTCTAATT
1 TTTTATAATT
* * *
8302 TGTAATAAAAT
1 TTTTAT-AATT
** *
8313 TTAAATATTT
1 TTTTATAATT
8323 TTTTATAATT
1 TTTTATAATT
**
8333 TTTTATTAAAA
1 TTTTA-TAATT
*
8344 TTTAAT-ATT
1 TTTTATAATT
*
8353 TTTTATAA-C
1 TTTTATAATT
8362 TTTTATAATT
1 TTTTATAATT
8372 TTTT
1 TTTT
8376 GTCACATGTA
Statistics
Matches: 102, Mismatches: 32, Indels: 14
0.69 0.22 0.09
Matches are distributed among these distances:
9 34 0.33
10 54 0.53
11 14 0.14
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.62
Consensus pattern (10 bp):
TTTTATAATT
Found at i:8623 original size:88 final size:91
Alignment explanation
Indices: 8435--8667 Score: 260
Period size: 88 Copynumber: 2.6 Consensus size: 91
8425 AATAGGGGTG
* * *
8435 GTTCATGTACCCAATTGAGTGCAAAAAAGAAATCAATGGCTTAATTGATTTTTTTGAAAAAAATT
1 GTTCAAGTATCCAATTGAGTGCAAAAAA-AAATCAAGGGCTTAATTGATTTTTTTGAAAAAAATT
* *
8500 AAGAGCCTTTTTTTATGCATTTTGATA
65 AAGAGCCTTTTCTGATGCATTTTGATA
* * * * * * *
8527 GTTCAAGTATTCAATTGAGTGCAAAAAAAATTTAGGGGCTTAGTTGA-TTTTTTGAAAAAGATTG
1 GTTCAAGTATCCAATTGAGTGCAAAAAAAAATCAAGGGCTTAATTGATTTTTTTGAAAAAAATTA
* *
8591 AG-GTC-TTTCTGATGCATTTTTATA
66 AGAGCCTTTTCTGATGCATTTTGATA
* * *
8615 GTTCAAGTATCCAATTGAGTGGAAAAAAAAAT--AGAGACTTAATTGCTTTTTTT
1 GTTCAAGTATCCAATTGAGTGCAAAAAAAAATCAAG-GGCTTAATTGATTTTTTT
8668 TTTTGTAAGT
Statistics
Matches: 118, Mismatches: 21, Indels: 8
0.80 0.14 0.05
Matches are distributed among these distances:
86 1 0.01
87 8 0.07
88 51 0.43
89 2 0.02
90 17 0.14
91 14 0.12
92 25 0.21
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (91 bp):
GTTCAAGTATCCAATTGAGTGCAAAAAAAAATCAAGGGCTTAATTGATTTTTTTGAAAAAAATTA
AGAGCCTTTTCTGATGCATTTTGATA
Found at i:8864 original size:27 final size:27
Alignment explanation
Indices: 8812--8864 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
8802 TTTTTTTAAT
* * *
8812 TTTAAAATATTAGTAATAATTTTAAAA
1 TTTAAAAAATTAGTAATAAATATAAAA
8839 TTTAAAAAATTA-TAATGAAATATAAA
1 TTTAAAAAATTAGTAAT-AAATATAAA
8865 TATGGATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.40
Consensus pattern (27 bp):
TTTAAAAAATTAGTAATAAATATAAAA
Done.