Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008800.1 Kokia drynarioides strain JFW-HI SEQ_123483, 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: 11656
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:2267 original size:5 final size:5
Alignment explanation
Indices: 2259--2402 Score: 59
Period size: 5 Copynumber: 28.6 Consensus size: 5
2249 TTATATTCAG
* * * *
2259 AAAAT AAAAAT AAAAAT AATATT AAAGT AAAAC AAAAT AAAAT AAAAGC
1 AAAAT -AAAAT -AAAAT AA-AAT AAAAT AAAAT AAAAT AAAAT AAAA-T
* * *
2308 AAAAT AAATGGT AAGAT -AAAT -AAAT AACAAT -AAAT -AAAT GCAAAT
1 AAAAT AAA--AT AAAAT AAAAT AAAAT AA-AAT AAAAT AAAAT -AAAAT
* ** * *
2353 ATAAT -AAAT GCAAT AAAA- ATAAT AAAAT AAAAT AAAAT AATAT -AAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
2400 AAA
1 AAA
2403 TATATGTATA
Statistics
Matches: 106, Mismatches: 21, Indels: 23
0.71 0.14 0.15
Matches are distributed among these distances:
4 23 0.22
5 54 0.51
6 26 0.25
7 3 0.03
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:2306 original size:21 final size:21
Alignment explanation
Indices: 2271--2311 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2261 AATAAAAATA
* * *
2271 AAAATAATATTAAAGTAAAAC
1 AAAATAAAATAAAAGCAAAAC
2292 AAAATAAAATAAAAGCAAAA
1 AAAATAAAATAAAAGCAAAA
2312 TAAATGGTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.17
Consensus pattern (21 bp):
AAAATAAAATAAAAGCAAAAC
Found at i:2312 original size:16 final size:15
Alignment explanation
Indices: 2259--2315 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 15
2249 TTATATTCAG
2259 AAAATAAAAATAAAA-
1 AAAAT-AAAATAAAAC
*
2274 ATAATATTAAAGTAAAAC
1 A-AA-A-TAAAATAAAAC
2292 AAAATAAAATAAAAGC
1 AAAATAAAATAAAA-C
2308 AAAATAAA
1 AAAATAAA
2316 TGGTAAGATA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
15 10 0.29
16 12 0.34
17 11 0.31
18 2 0.06
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.18
Consensus pattern (15 bp):
AAAATAAAATAAAAC
Found at i:2342 original size:14 final size:14
Alignment explanation
Indices: 2323--2404 Score: 55
Period size: 14 Copynumber: 5.8 Consensus size: 14
2313 AAATGGTAAG
2323 ATAAATAAATAACA
1 ATAAATAAATAACA
*
2337 ATAAATAAAT-GCAA
1 ATAAATAAATAAC-A
*
2351 ATATAATAAAT-GCA
1 ATA-AATAAATAACA
*
2365 ATAAAAATAATAA-A
1 ATAAATA-AATAACA
*
2379 ATAAAATAAAATAA-T
1 AT-AAAT-AAATAACA
2394 ATAAATAAATA
1 ATAAATAAATA
2405 TATGTATATA
Statistics
Matches: 57, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
13 9 0.16
14 28 0.49
15 19 0.33
16 1 0.02
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (14 bp):
ATAAATAAATAACA
Found at i:2346 original size:18 final size:18
Alignment explanation
Indices: 2323--2404 Score: 71
Period size: 19 Copynumber: 4.4 Consensus size: 18
2313 AAATGGTAAG
*
2323 ATAAATAAATAACAATAA
1 ATAAATAAATAATAATAA
2341 ATAAATGCAAAT-ATAATAA
1 ATAAAT--AAATAATAATAA
*
2360 ATGCAATAAA-AATAATAAA
1 AT-AAATAAATAATAAT-AA
2379 ATAAAATAAAATAAT-ATAA
1 AT-AAAT-AAATAATAATAA
2398 ATAAATA
1 ATAAATA
2405 TATGTATATA
Statistics
Matches: 53, Mismatches: 4, Indels: 15
0.74 0.06 0.21
Matches are distributed among these distances:
17 1 0.02
18 18 0.34
19 19 0.36
20 12 0.23
21 3 0.06
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (18 bp):
ATAAATAAATAATAATAA
Found at i:2360 original size:15 final size:14
Alignment explanation
Indices: 2309--2369 Score: 54
Period size: 14 Copynumber: 4.2 Consensus size: 14
2299 AATAAAAGCA
*
2309 AAATAAATGGTAAGAT
1 AAATAAAT-GCAA-AT
*
2325 AAATAAAT-AACAAT
1 AAATAAATGCA-AAT
2339 AAATAAATGCAAAT
1 AAATAAATGCAAAT
2353 ATAATAAATGC-AAT
1 A-AATAAATGCAAAT
2367 AAA
1 AAA
2370 AATAATAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
13 2 0.05
14 19 0.47
15 11 0.28
16 8 0.20
ACGTcount: A:0.64, C:0.05, G:0.08, T:0.23
Consensus pattern (14 bp):
AAATAAATGCAAAT
Found at i:2458 original size:9 final size:9
Alignment explanation
Indices: 2325--2464 Score: 56
Period size: 10 Copynumber: 14.9 Consensus size: 9
2315 ATGGTAAGAT
2325 AAATAAATA
1 AAATAAATA
2334 ACAATAAAT-
1 A-AATAAATA
2343 AAATGCAAATA
1 AAAT--AAATA
* *
2354 TAATAAATG
1 AAATAAATA
*
2363 CAATAAA-A
1 AAATAAATA
2371 ATAATAAAATA
1 A-AAT-AAATA
2382 AAATAAAATA
1 AAAT-AAATA
*
2392 ATATAAAT-
1 AAATAAATA
*
2400 AAATATAT-
1 AAATAAATA
** *
2408 GTATATACTA
1 AAATA-AATA
2418 CACAATAAACTA
1 -A-AATAAA-TA
*
2430 AAATAAACA
1 AAATAAATA
2439 ACAATAAATA
1 A-AATAAATA
*
2449 AAATAGATA
1 AAATAAATA
2458 AAA-AAAT
1 AAATAAAT
2465 TGAATCAAAA
Statistics
Matches: 99, Mismatches: 19, Indels: 27
0.68 0.13 0.19
Matches are distributed among these distances:
8 15 0.15
9 32 0.32
10 40 0.40
11 7 0.07
12 5 0.05
ACGTcount: A:0.67, C:0.06, G:0.03, T:0.24
Consensus pattern (9 bp):
AAATAAATA
Found at i:2523 original size:20 final size:18
Alignment explanation
Indices: 2486--2536 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 18
2476 GTAAAAATGC
* *
2486 TAAAAATAAACAACAAAA
1 TAAAAATAAAAAATAAAA
2504 TAAATAAGTAAAAAATAAAA
1 TAAA-AA-TAAAAAATAAAA
2524 TAAAAATAAAAAA
1 TAAAAATAAAAAA
2537 AGGTAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 11 0.38
19 4 0.14
20 14 0.48
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.16
Consensus pattern (18 bp):
TAAAAATAAAAAATAAAA
Found at i:11375 original size:13 final size:13
Alignment explanation
Indices: 11357--11381 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11347 TAAAGTTTTC
11357 TTTTAATTATTTA
1 TTTTAATTATTTA
11370 TTTTAATTATTT
1 TTTTAATTATTT
11382 TCGTTTCAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTAATTATTTA
Done.