Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008189.1 Kokia drynarioides strain JFW-HI SEQ_122848, 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: 9384
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Found at i:112 original size:16 final size:14
Alignment explanation
Indices: 91--134 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
81 ATTTTTATGG
91 ATTAAAGAATAATTA
1 ATTAAA-AATAATTA
*
106 TATTAAAAATAAATA
1 -ATTAAAAATAATTA
121 ATATAAAAATAATT
1 AT-TAAAAATAATT
135 CAATATGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 2 0.08
15 17 0.68
16 6 0.24
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (14 bp):
ATTAAAAATAATTA
Found at i:1307 original size:16 final size:16
Alignment explanation
Indices: 1286--1316 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1276 ATAATGTGAA
1286 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
1302 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
1317 AGATCCATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:1405 original size:10 final size:10
Alignment explanation
Indices: 1390--1419 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
1380 TAATTTATCG
1390 GTGCAATGAA
1 GTGCAATGAA
1400 GTGCAATGAA
1 GTGCAATGAA
1410 GTGCAATGAA
1 GTGCAATGAA
1420 CATCTTACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.30, T:0.20
Consensus pattern (10 bp):
GTGCAATGAA
Found at i:2016 original size:54 final size:55
Alignment explanation
Indices: 1922--2031 Score: 204
Period size: 54 Copynumber: 2.0 Consensus size: 55
1912 AAAGCTAGGT
*
1922 TAAAGAAGATAATATTGCAAAAATGAGAGACTAAAGGAAGAGGGAGACACCTTTC
1 TAAAGAAGATAATATTGCAAAAATGAGAGACTAAAGGAAGAGAGAGACACCTTTC
1977 TAAAGAAGATAATATTGC-AAAATGAGAGACTAAAGGAAGAGAGAGACACCTTTC
1 TAAAGAAGATAATATTGCAAAAATGAGAGACTAAAGGAAGAGAGAGACACCTTTC
2031 T
1 T
2032 CTTTCCTTGT
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
54 36 0.67
55 18 0.33
ACGTcount: A:0.47, C:0.11, G:0.23, T:0.19
Consensus pattern (55 bp):
TAAAGAAGATAATATTGCAAAAATGAGAGACTAAAGGAAGAGAGAGACACCTTTC
Found at i:2223 original size:26 final size:26
Alignment explanation
Indices: 2180--2234 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
2170 AATTTTAGGC
*
2180 ACAATTCTGGACACGTTCATGCAGTG
1 ACAATTCTGGACACGTTCATGCAGCG
* *
2206 ACAATTCTGTACATGTTCATGCAGCG
1 ACAATTCTGGACACGTTCATGCAGCG
2232 ACA
1 ACA
2235 TTCCTAGGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (26 bp):
ACAATTCTGGACACGTTCATGCAGCG
Found at i:2265 original size:37 final size:38
Alignment explanation
Indices: 2224--2295 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 38
2214 GTACATGTTC
*
2224 ATGCAGCGACA-TTCCTAGGTGCAA-TTGAAGAATACTT
1 ATGCAGCGACAGTT-CTAGATGCAATTTGAAGAATACTT
* *
2261 ATGCAGTGATAGTTCTAGATGCAATTTGAAGAATA
1 ATGCAGCGACAGTTCTAGATGCAATTTGAAGAATA
2296 TTTTTGCAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
37 18 0.60
38 12 0.40
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (38 bp):
ATGCAGCGACAGTTCTAGATGCAATTTGAAGAATACTT
Found at i:2310 original size:38 final size:37
Alignment explanation
Indices: 2238--2311 Score: 94
Period size: 38 Copynumber: 2.0 Consensus size: 37
2228 AGCGACATTC
* **
2238 CTAGGTGCAATTGAAGAATACTTATGCAGTGATAGTT
1 CTAGATGCAATTGAAGAATACTTATGCAACGATAGTT
* *
2275 CTAGATGCAATTTGAAGAATATTTTTGCAACGATAGT
1 CTAGATGCAA-TTGAAGAATACTTATGCAACGATAGT
2312 CTTGGGTTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
37 9 0.29
38 22 0.71
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.34
Consensus pattern (37 bp):
CTAGATGCAATTGAAGAATACTTATGCAACGATAGTT
Found at i:2395 original size:36 final size:36
Alignment explanation
Indices: 2343--2411 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
2333 TTCTTGCAGC
* *
2343 GACATTTTTGGTGCAATCTAGAAGTGCTCATGCGGT
1 GACAGTTTTGGCGCAATCTAGAAGTGCTCATGCGGT
2379 GACAGTTTTGGCGCAATCTAGAAGTGCTCATGC
1 GACAGTTTTGGCGCAATCTAGAAGTGCTCATGC
2412 AACGACATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (36 bp):
GACAGTTTTGGCGCAATCTAGAAGTGCTCATGCGGT
Found at i:2425 original size:36 final size:36
Alignment explanation
Indices: 2337--2425 Score: 117
Period size: 36 Copynumber: 2.5 Consensus size: 36
2327 AAAATATTCT
* *
2337 TGCAGCGACATTTTTGGTGCAATCTAGAAGTGCTCA
1 TGCAGCGACATGTTTGGCGCAATCTAGAAGTGCTCA
* *
2373 TGCGGTGACA-GTTTTGGCGCAATCTAGAAGTGCTCA
1 TGCAGCGACATG-TTTGGCGCAATCTAGAAGTGCTCA
*
2409 TGCAACGACATGTTTGG
1 TGCAGCGACATGTTTGG
2426 GGGTAATTCT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
36 43 0.98
37 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (36 bp):
TGCAGCGACATGTTTGGCGCAATCTAGAAGTGCTCA
Found at i:3608 original size:17 final size:17
Alignment explanation
Indices: 3569--3617 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
3559 ATATATATGG
* **
3569 AAATGCAATGACAATGT
1 AAATGCAACGACAATAA
*
3586 AGATGCAACGACAATAA
1 AAATGCAACGACAATAA
*
3603 AAATGCAAGGACAAT
1 AAATGCAACGACAAT
3618 TATACTACAG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.51, C:0.14, G:0.18, T:0.16
Consensus pattern (17 bp):
AAATGCAACGACAATAA
Found at i:5892 original size:16 final size:16
Alignment explanation
Indices: 5871--5901 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5861 ATAATGTGAA
5871 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
5887 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
5902 GGATCCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Done.