Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012153.1 Kokia drynarioides strain JFW-HI SEQ_127153, 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: 12276
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:191 original size:60 final size:61
Alignment explanation
Indices: 116--254 Score: 142
Period size: 62 Copynumber: 2.3 Consensus size: 61
106 GATATCTAAA
* * * *
116 TTTTTTTTATCCAATTTAAT-CTTTGAAGTTGATA-TTTTTTT-TTACTTTGATA-TCTTAGC
1 TTTTTTTGATCCAATTTAATAC-TTGAACTTGACATTTTTTTTCTTAATTTGATACT-TTAGC
** *
175 TTTTTTTGGATCCAATTTGGTACTTGAACTTGACATTTTTTTTCTTAATTTGCTACTTTAGC
1 TTTTTTT-GATCCAATTTAATACTTGAACTTGACATTTTTTTTCTTAATTTGATACTTTAGC
*
237 TTTTTTTAGATTCAATTT
1 TTTTTTT-GATCCAATTT
255 GGTACCTAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
59 7 0.11
60 20 0.30
61 8 0.12
62 30 0.45
63 1 0.02
ACGTcount: A:0.21, C:0.12, G:0.10, T:0.58
Consensus pattern (61 bp):
TTTTTTTGATCCAATTTAATACTTGAACTTGACATTTTTTTTCTTAATTTGATACTTTAGC
Found at i:465 original size:62 final size:58
Alignment explanation
Indices: 399--512 Score: 129
Period size: 62 Copynumber: 1.9 Consensus size: 58
389 GAATTAATAT
*
399 TAAAAAAATTAGGTACCAAATTAGGAAAAAAAAAGGCGAAGTTCAAGTACCAAATTGGACCC
1 TAAAAAAATTAAGTACCAAATT---AAAAAAAAAGGC-AAGTTCAAGTACCAAATTGGACCC
** * * * *
461 TAAAAAGTTTAAGTACCAACTTAAAAAAAATGTCAAGTTTAAGTACCAAATT
1 TAAAAAAATTAAGTACCAAATTAAAAAAAAAGGCAAGTTCAAGTACCAAATT
513 AAGAAAAAGT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
58 17 0.38
59 10 0.22
62 18 0.40
ACGTcount: A:0.50, C:0.13, G:0.14, T:0.23
Consensus pattern (58 bp):
TAAAAAAATTAAGTACCAAATTAAAAAAAAAGGCAAGTTCAAGTACCAAATTGGACCC
Found at i:501 original size:30 final size:31
Alignment explanation
Indices: 465--543 Score: 115
Period size: 31 Copynumber: 2.6 Consensus size: 31
455 GGACCCTAAA
*
465 AAGTTTAAGTACCAACTTAA-AAAAAATGTC
1 AAGTTTAAGTACCAACTTAAGAAAAAATATC
* *
495 AAGTTTAAGTACCAAATTAAGAAAAAGTATC
1 AAGTTTAAGTACCAACTTAAGAAAAAATATC
*
526 AAGTTTGAGTACCAACTT
1 AAGTTTAAGTACCAACTT
544 GGACCAAAGA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 19 0.44
31 24 0.56
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.28
Consensus pattern (31 bp):
AAGTTTAAGTACCAACTTAAGAAAAAATATC
Found at i:512 original size:92 final size:90
Alignment explanation
Indices: 411--603 Score: 210
Period size: 92 Copynumber: 2.1 Consensus size: 90
401 AAAAAATTAG
* ** *
411 GTACCAAATTAGGAAAAAAAAAGGCGAAGTTCAAGTACCAAATTGGACCCTA-AAAAGTTTAAGT
1 GTACCAAATTAAG-AAAAAAAA-GC-AAGTTCAAGTACCAAATTGGACCAAAGAAAAATTTAAGT
475 ACCAACTT-AAAAAAAATGTCAAGTTTAA
63 ACCAACTTAAAAAAAAATGTCAAGTTT-A
** * ** * *
503 GTACCAAATTAAGAAAAAGTATCAAGTTTGAGTACCAACTTGGACCAAAGAAAAATTTAGGTACC
1 GTACCAAATTAAGAAAAAAAAGCAAGTTCAAGTACCAAATTGGACCAAAGAAAAATTTAAGTACC
*
568 AATTTAAAAAAAAAATGTCAAGTTTA
66 AACTT-AAAAAAAAATGTCAAGTTTA
594 GTTACCAAAT
1 G-TACCAAAT
604 ATTATATTAA
Statistics
Matches: 85, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
89 21 0.25
90 18 0.21
91 8 0.09
92 38 0.45
ACGTcount: A:0.48, C:0.13, G:0.15, T:0.24
Consensus pattern (90 bp):
GTACCAAATTAAGAAAAAAAAGCAAGTTCAAGTACCAAATTGGACCAAAGAAAAATTTAAGTACC
AACTTAAAAAAAAATGTCAAGTTTA
Found at i:2029 original size:20 final size:20
Alignment explanation
Indices: 1993--2030 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1983 ATTTATAATT
*
1993 CCTTATTTCTATCTCATTAG
1 CCTTATTTCAATCTCATTAG
*
2013 CCTTATTTCAATTTCATT
1 CCTTATTTCAATCTCATT
2031 TCGTATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.24, G:0.03, T:0.53
Consensus pattern (20 bp):
CCTTATTTCAATCTCATTAG
Found at i:2281 original size:12 final size:13
Alignment explanation
Indices: 2265--2312 Score: 62
Period size: 14 Copynumber: 3.6 Consensus size: 13
2255 ATTATATATT
2265 TATATATTCTATTA
1 TATATATTCTA-TA
*
2279 TATATATATATATA
1 TATATAT-TCTATA
2293 TATATATTCTA-A
1 TATATATTCTATA
2305 TATATATT
1 TATATATT
2313 AGAATTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 9 0.29
13 3 0.10
14 16 0.52
15 3 0.10
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATATTCTATA
Found at i:2291 original size:28 final size:30
Alignment explanation
Indices: 2257--2336 Score: 101
Period size: 28 Copynumber: 2.7 Consensus size: 30
2247 TTAATTCTAT
2257 TATATATTTATATATTCTATTATATA-TA-
1 TATATATTTATATATTCTATTATATATTAG
* *
2285 TATATATATATATATTCTAATATATATTAG
1 TATATATTTATATATTCTATTATATATTAG
* * *
2315 AATTTATTTATATATTTTATTA
1 TATATATTTATATATTCTATTA
2337 AAATTTTTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 24 0.56
29 2 0.05
30 17 0.40
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (30 bp):
TATATATTTATATATTCTATTATATATTAG
Found at i:2311 original size:20 final size:20
Alignment explanation
Indices: 2250--2291 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
2240 TAGAATATTA
*
2250 ATTCTATTATATATTTATAT
1 ATTCTATTATATATATATAT
2270 ATTCTATTATATATATATAT
1 ATTCTATTATATATATATAT
2290 AT
1 AT
2292 ATATATATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTCTATTATATATATATAT
Found at i:2329 original size:2 final size:2
Alignment explanation
Indices: 2257--2311 Score: 55
Period size: 2 Copynumber: 29.5 Consensus size: 2
2247 TTAATTCTAT
* *
2257 TA TA TA TT TA TA TA T- TC TA T- TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2297 TA T- TC TA -A TA TA TA T
1 TA TA TA TA TA TA TA TA T
2312 TAGAATTTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
1 4 0.09
2 41 0.91
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:2331 original size:12 final size:12
Alignment explanation
Indices: 2261--2360 Score: 54
Period size: 12 Copynumber: 8.7 Consensus size: 12
2251 TTCTATTATA
2261 TATTTATATATT
1 TATTTATATATT
*
2273 CTA-TTATATATA
1 -TATTTATATATT
* *
2285 TATATATATATA
1 TATTTATATATT
*
2297 TATTCTA-ATATA
1 TATT-TATATATT
*
2309 TA-TTAGA-ATT
1 TATTTATATATT
2319 TATTTATATATT
1 TATTTATATATT
*
2331 T-TATTA-A-AAT
1 TAT-TTATATATT
2341 T-TTTATATATTT
1 TATTTATATA-TT
2353 TATTTATA
1 TATTTATA
2361 ATATATTAGA
Statistics
Matches: 70, Mismatches: 7, Indels: 20
0.72 0.07 0.21
Matches are distributed among these distances:
9 3 0.04
10 11 0.16
11 11 0.16
12 35 0.50
13 10 0.14
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (12 bp):
TATTTATATATT
Found at i:2438 original size:20 final size:19
Alignment explanation
Indices: 2256--2446 Score: 74
Period size: 20 Copynumber: 10.0 Consensus size: 19
2246 ATTAATTCTA
2256 TTATA-TATTTATATATTCT
1 TTATATTATTTATATATT-T
* *
2275 ATTATA-TATATATATATAT
1 -TTATATTATTTATATATTT
* * * *
2294 ATATATTCTAATATATATTA
1 TTATATTAT-TTATATATTT
**
2314 GAAT-TTATTTATATATTTT
1 TTATATTATTTATATA-TTT
*
2333 ATTAAAATT-TTTATATA-TT
1 -TT-ATATTATTTATATATTT
* *
2352 TTAT-TTA-TAATATATTA
1 TTATATTATTTATATATTT
**
2369 GAATATTATATTA-ATATTTT
1 TTATATTAT-TTATATA-TTT
*
2389 TTATATTATTGATATATTT
1 TTATATTATTTATATATTT
* * * *
2408 CTATTTTATTTATTTCCTTT
1 TTATATTATTTATAT-ATTT
*
2428 TTATATTATTTATCTATTT
1 TTATATTATTTATATATTT
2447 CTATTTCATT
Statistics
Matches: 124, Mismatches: 33, Indels: 29
0.67 0.18 0.16
Matches are distributed among these distances:
16 8 0.06
17 4 0.03
18 15 0.12
19 32 0.26
20 54 0.44
21 9 0.07
22 2 0.02
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (19 bp):
TTATATTATTTATATATTT
Found at i:4272 original size:23 final size:25
Alignment explanation
Indices: 4246--4291 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
4236 CCAATTAGGG
4246 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
4269 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
4292 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:5356 original size:3 final size:3
Alignment explanation
Indices: 5348--5385 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
5338 TTTAGTCATT
*
5348 TTA TTA TTA TAA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5386 TGCATTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Done.