Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007630.1 Kokia drynarioides strain JFW-HI SEQ_122261, 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: 19094
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Found at i:182 original size:8 final size:8
Alignment explanation
Indices: 169--254 Score: 57
Period size: 8 Copynumber: 10.1 Consensus size: 8
159 ATTAGTTTAA
169 AAATATAT
1 AAATATAT
177 AAATATA-
1 AAATATAT
*
184 AATTTATAT
1 AA-ATATAT
193 AAATATAT
1 AAATATAT
201 AAAATATAT
1 -AAATATAT
210 ATCAATATAT
1 A--AATATAT
*
220 AAAAGTGTAT
1 -AAA-TATAT
*
230 AAATTTAT
1 AAATATAT
* *
238 AAAAATTT
1 AAATATAT
*
246 AAAAATAT
1 AAATATAT
254 A
1 A
255 TACAATTAAC
Statistics
Matches: 63, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
7 2 0.03
8 34 0.54
9 15 0.24
10 11 0.17
11 1 0.02
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.37
Consensus pattern (8 bp):
AAATATAT
Found at i:306 original size:10 final size:10
Alignment explanation
Indices: 183--306 Score: 52
Period size: 10 Copynumber: 13.3 Consensus size: 10
173 ATATAAATAT
* *
183 AAATTTATAT
1 AAATATATAA
193 AAATATAT-A
1 AAATATATAA
*
202 AAATATATAT
1 AAATATATAA
*
212 CAATATATAA
1 AAATATATAA
* *
222 AAGTGTAT--
1 AAATATATAA
*
230 AAATTTATAA
1 AAATATATAA
240 AAAT-T-TAA
1 AAATATATAA
248 AAATATAT--
1 AAATATATAA
*
256 ACA-AT-TAA
1 AAATATATAA
*
264 CAATATATAA
1 AAATATATAA
*
274 AAAGCATAT-A
1 AAA-TATATAA
* * *
284 ATATTTTTAA
1 AAATATATAA
294 AAATATATAA
1 AAATATATAA
304 AAA
1 AAA
307 AGTTACAATA
Statistics
Matches: 81, Mismatches: 22, Indels: 22
0.65 0.18 0.18
Matches are distributed among these distances:
6 1 0.01
7 2 0.02
8 16 0.20
9 14 0.17
10 44 0.54
11 4 0.05
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.35
Consensus pattern (10 bp):
AAATATATAA
Found at i:466 original size:19 final size:18
Alignment explanation
Indices: 442--483 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
432 TCGTTCTTAA
*
442 TAATT-ATTGTATATTTTAT
1 TAATTAATT-TATATATT-T
461 TAATTAATTTATATATTT
1 TAATTAATTTATATATTT
479 TAATT
1 TAATT
484 TAGGCTCAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 6 0.29
19 12 0.57
20 3 0.14
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
TAATTAATTTATATATTT
Found at i:1221 original size:23 final size:23
Alignment explanation
Indices: 1191--1431 Score: 254
Period size: 23 Copynumber: 10.5 Consensus size: 23
1181 CTATCTACAA
1191 ATAAATCACATTAATATTTAAGC
1 ATAAATCACATTAATATTTAAGC
*
1214 ATACATCACATTAATATTTAAGC
1 ATAAATCACATTAATATTTAAGC
* *
1237 ATAAATCATATTAACATTTAAGC
1 ATAAATCACATTAATATTTAAGC
* *
1260 ACAAATCACATTAATCTTTAA-C
1 ATAAATCACATTAATATTTAAGC
1282 TATAAATCACATTAACT-TTTAAGC
1 -ATAAATCACATTAA-TATTTAAGC
** *
1306 ATAAATCGTACTAATATTTAAGC
1 ATAAATCACATTAATATTTAAGC
* *
1329 ACAAATTACATTAATATTTAAGC
1 ATAAATCACATTAATATTTAAGC
* * *
1352 ATAAATCACTTTTATATTTCAGC
1 ATAAATCACATTAATATTTAAGC
** **
1375 CCAAATCATGTTAATATTTAAGC
1 ATAAATCACATTAATATTTAAGC
** *
1398 CCAAATCACATTAATGTTTAAGC
1 ATAAATCACATTAATATTTAAGC
1421 ATATAA-CACAT
1 ATA-AATCACAT
1432 GAATCATAAC
Statistics
Matches: 180, Mismatches: 33, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
22 2 0.01
23 174 0.97
24 4 0.02
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.35
Consensus pattern (23 bp):
ATAAATCACATTAATATTTAAGC
Found at i:1269 original size:69 final size:69
Alignment explanation
Indices: 1193--1431 Score: 304
Period size: 69 Copynumber: 3.5 Consensus size: 69
1183 ATCTACAAAT
* *
1193 AAATCACATTAATATTTAAGCATACATCACATTAATATTTAAGCATAAATCATATTAACATTTAA
1 AAATCACATTAATATTTAAGCATAAATCACATTAATATTTAAGCATAAATCATATTAATATTTAA
1258 GCAC
66 GCAC
* * *
1262 AAATCACATTAATCTTTAA-CTATAAATCACATTAACT-TTTAAGCATAAATCGTACTAATATTT
1 AAATCACATTAATATTTAAGC-ATAAATCACATTAA-TATTTAAGCATAAATCATATTAATATTT
1325 AAGCAC
64 AAGCAC
* * * * ** *
1331 AAATTACATTAATATTTAAGCATAAATCACTTTTATATTTCAGCCCAAATCATGTTAATATTTAA
1 AAATCACATTAATATTTAAGCATAAATCACATTAATATTTAAGCATAAATCATATTAATATTTAA
*
1396 GCCC
66 GCAC
*
1400 AAATCACATTAATGTTTAAGCATATAA-CACAT
1 AAATCACATTAATATTTAAGCATA-AATCACAT
1432 GAATCATAAC
Statistics
Matches: 146, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
68 2 0.01
69 140 0.96
70 4 0.03
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.35
Consensus pattern (69 bp):
AAATCACATTAATATTTAAGCATAAATCACATTAATATTTAAGCATAAATCATATTAATATTTAA
GCAC
Found at i:4358 original size:20 final size:21
Alignment explanation
Indices: 4320--4358 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
4310 AATTTTGACT
* *
4320 TTTTGTATTTTTTTCATTAAA
1 TTTTGTATTTTTATAATTAAA
4341 TTTTGT-TTTTTATAATTA
1 TTTTGTATTTTTATAATTA
4359 TTAAAATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTTGTATTTTTATAATTAAA
Found at i:8881 original size:28 final size:27
Alignment explanation
Indices: 8841--8893 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
8831 TAACTTGATA
8841 TTTTTCCAAATTTGATACCTAAACTTT
1 TTTTTCCAAATTTGATACCTAAACTTT
* *
8868 TTTTTACCTAATTTGATACCTGAACT
1 TTTTT-CCAAATTTGATACCTAAACT
8894 AGACACTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (27 bp):
TTTTTCCAAATTTGATACCTAAACTTT
Found at i:8978 original size:60 final size:58
Alignment explanation
Indices: 8820--8981 Score: 164
Period size: 59 Copynumber: 2.7 Consensus size: 58
8810 TTAATATAAC
* * * * ** *
8820 ATTTGGTATCTTAACTTG-ATATTTTTCCAAATTTGATACCTAAACTTTTTTTTACCTA
1 ATTTGGTACCTGAACTTGCAT-TTTTTCCTAATTTGGTACCTAAACTTTTTTGGACCCA
* * * * **
8878 ATTTGATACCTGAACTAGACACTTATTCCTTGTTTGGTACCTAAACTTTTTTGGACCCA
1 ATTTGGTACCTGAACTTG-CATTTTTTCCTAATTTGGTACCTAAACTTTTTTGGACCCA
8937 ATTTGGTACCTGAACTTTGCATTTTCTTCCTAATTTGGTACCTAA
1 ATTTGGTACCTGAAC-TTGCATTTT-TTCCTAATTTGGTACCTAA
8982 GTTTTTTTTC
Statistics
Matches: 81, Mismatches: 19, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
58 14 0.17
59 47 0.58
60 20 0.25
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.44
Consensus pattern (58 bp):
ATTTGGTACCTGAACTTGCATTTTTTCCTAATTTGGTACCTAAACTTTTTTGGACCCA
Found at i:17605 original size:15 final size:14
Alignment explanation
Indices: 17579--17615 Score: 65
Period size: 15 Copynumber: 2.6 Consensus size: 14
17569 AAAATAAAAG
17579 TTTTATTTATTTAT
1 TTTTATTTATTTAT
17593 TTTTATGTTATTTAT
1 TTTTAT-TTATTTAT
17608 TTTTATTT
1 TTTTATTT
17616 TAAATTGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (14 bp):
TTTTATTTATTTAT
Done.