Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003887.1 Kokia drynarioides strain JFW-HI SEQ_116935, 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: 3025
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Found at i:329 original size:9 final size:9
Alignment explanation
Indices: 315--402 Score: 50
Period size: 9 Copynumber: 10.1 Consensus size: 9
305 ACAAATGATT
315 TTAAAATTA
1 TTAAAATTA
324 TTAAAATTAA
1 TTAAAATT-A
*
334 TTTTTTAAA-TA
1 ---TTAAAATTA
345 -TAAAATTA
1 TTAAAATTA
353 TTAAAATTA
1 TTAAAATTA
362 TT----TT-
1 TTAAAATTA
366 TTAAAA-TA
1 TTAAAATTA
374 -TAAAATTA
1 TTAAAATTA
382 TTAAAATTA
1 TTAAAATTA
391 TTTTAAAATTA
1 --TTAAAATTA
402 T
1 T
403 AATCATCATC
Statistics
Matches: 62, Mismatches: 2, Indels: 30
0.66 0.02 0.32
Matches are distributed among these distances:
4 2 0.03
5 2 0.03
7 10 0.16
8 4 0.06
9 27 0.44
10 1 0.02
11 10 0.16
12 1 0.02
13 5 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
TTAAAATTA
Found at i:358 original size:29 final size:29
Alignment explanation
Indices: 316--394 Score: 142
Period size: 29 Copynumber: 2.7 Consensus size: 29
306 CAAATGATTT
316 TAAAATTATTAAAATTAATTTTTT-AAATA
1 TAAAATTATTAAAATT-ATTTTTTAAAATA
345 TAAAATTATTAAAATTATTTTTTAAAATA
1 TAAAATTATTAAAATTATTTTTTAAAATA
374 TAAAATTATTAAAATTATTTT
1 TAAAATTATTAAAATTATTTT
395 AAAATTATAA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
28 7 0.14
29 42 0.86
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
TAAAATTATTAAAATTATTTTTTAAAATA
Found at i:394 original size:28 final size:28
Alignment explanation
Indices: 316--404 Score: 135
Period size: 29 Copynumber: 3.1 Consensus size: 28
306 CAAATGATTT
*
316 TAAAATTATTAAAATTAATTTTTTAAATA
1 TAAAATTATTAAAATT-ATTTTTAAAATA
345 TAAAATTATTAAAATTATTTTTTAAAATA
1 TAAAATTATTAAAATTA-TTTTTAAAATA
374 TAAAATTATTAAAATTA-TTTTAAAATTA
1 TAAAATTATTAAAATTATTTTTAAAA-TA
402 TAA
1 TAA
405 TCATCATCAT
Statistics
Matches: 57, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
27 8 0.14
28 6 0.11
29 43 0.75
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
TAAAATTATTAAAATTATTTTTAAAATA
Found at i:397 original size:20 final size:20
Alignment explanation
Indices: 307--402 Score: 64
Period size: 20 Copynumber: 4.9 Consensus size: 20
297 CCATGTCAAC
*
307 AAATGATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
*
327 AAATTAATTTTTTAAA-TA-TA
1 AAATT-A-TTTTAAAATTATTA
347 AAATTA--TTAAAATTATTTTTTA
1 AAATTATTTTAAAATTA----TTA
369 AAA-TA---TAAAATTATTA
1 AAATTATTTTAAAATTATTA
385 AAATTATTTTAAAATTAT
1 AAATTATTTTAAAATTAT
403 AATCATCATC
Statistics
Matches: 61, Mismatches: 3, Indels: 24
0.69 0.03 0.27
Matches are distributed among these distances:
16 11 0.18
17 4 0.07
19 1 0.02
20 28 0.46
21 5 0.08
22 12 0.20
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:1197 original size:24 final size:27
Alignment explanation
Indices: 1170--1227 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
1160 CCAAACAACC
*
1170 AAAATAACA-AAAAAA-A-CAACAGTA
1 AAAATAACAGAAAAAATAGCAACAATA
*
1194 AAAATAATAGAAAAAATAGCAACAATA
1 AAAATAACAGAAAAAATAGCAACAATA
*
1221 ATAATAA
1 AAAATAA
1228 TAATAACTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 8 0.29
25 6 0.21
26 1 0.04
27 13 0.46
ACGTcount: A:0.72, C:0.09, G:0.05, T:0.14
Consensus pattern (27 bp):
AAAATAACAGAAAAAATAGCAACAATA
Found at i:1262 original size:19 final size:19
Alignment explanation
Indices: 1238--1274 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1228 TAATAACTGA
*
1238 ACCAAAATAGTAAAAAAAC
1 ACCAAAATAGCAAAAAAAC
1257 ACCAAAATAGCAAAAAAA
1 ACCAAAATAGCAAAAAAA
1275 ATGATAACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.70, C:0.16, G:0.05, T:0.08
Consensus pattern (19 bp):
ACCAAAATAGCAAAAAAAC
Found at i:1310 original size:26 final size:24
Alignment explanation
Indices: 1249--1315 Score: 73
Period size: 24 Copynumber: 2.7 Consensus size: 24
1239 CCAAAATAGT
*
1249 AAAAAAACACCAAAATAGCAAAAA
1 AAAAAAACACCAAAACAGCAAAAA
* *
1273 AAATGATA-ACCAAAACAGCAAAAA
1 AAA-AAAACACCAAAACAGCAAAAA
1297 AAAAAACAGCACCAAAACA
1 AAAAAA-A-CACCAAAACA
1316 ACAATAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
23 1 0.03
24 22 0.65
25 2 0.06
26 9 0.26
ACGTcount: A:0.70, C:0.19, G:0.06, T:0.04
Consensus pattern (24 bp):
AAAAAAACACCAAAACAGCAAAAA
Found at i:1837 original size:30 final size:30
Alignment explanation
Indices: 1776--1861 Score: 88
Period size: 30 Copynumber: 3.0 Consensus size: 30
1766 ACCCTAAATA
* **
1776 AAAATCCCCAAA-TCAA-AACTCTTAA-CC
1 AAAATCCCCAAATTCAACAACCCAAAATCC
* * *
1803 AAAATCCCTAAATTCGACCACCCAAAATCC
1 AAAATCCCCAAATTCAACAACCCAAAATCC
*
1833 AAAATCCCCAAATTCAACAACCTAAAATC
1 AAAATCCCCAAATTCAACAACCCAAAATC
1862 TCCAAATTCA
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
27 11 0.24
28 3 0.07
29 5 0.11
30 27 0.59
ACGTcount: A:0.48, C:0.34, G:0.01, T:0.17
Consensus pattern (30 bp):
AAAATCCCCAAATTCAACAACCCAAAATCC
Found at i:1866 original size:23 final size:23
Alignment explanation
Indices: 1833--1881 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
1823 CCCAAAATCC
1833 AAAATCCCCAAATTCAACAACC-T
1 AAAATCCCCAAATTCAA-AACCAT
*
1856 AAAATCTCCAAATTCAAAACCAT
1 AAAATCCCCAAATTCAAAACCAT
1879 AAA
1 AAA
1882 CAATTCATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.53, C:0.29, G:0.00, T:0.18
Consensus pattern (23 bp):
AAAATCCCCAAATTCAAAACCAT
Done.