Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010340.1 Kokia drynarioides strain JFW-HI SEQ_125207, 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: 16277
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Found at i:2983 original size:21 final size:21
Alignment explanation
Indices: 2942--2983 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2932 ATAAATTTAC
* *
2942 ATATATATTTTTTGAGTTTTT
1 ATATATATTTTTTCAGATTTT
2963 ATATATATTTTTTTCA-ATTTT
1 ATATATA-TTTTTTCAGATTTT
2984 TGTTTCATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (21 bp):
ATATATATTTTTTCAGATTTT
Found at i:3091 original size:20 final size:20
Alignment explanation
Indices: 3054--3092 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3044 AATCTTTATG
*
3054 TACATATATATTGGAATTTA
1 TACATATATATTGAAATTTA
* *
3074 TACATATTTTTTGAAATTT
1 TACATATATATTGAAATTT
3093 TTATATTTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.51
Consensus pattern (20 bp):
TACATATATATTGAAATTTA
Found at i:3110 original size:28 final size:26
Alignment explanation
Indices: 3070--3136 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 26
3060 TATATTGGAA
*
3070 TTTATACATATTTTTTGA-AATTTTTATAT
1 TTTATATA-ATTTTTTGATAA--TTT-TAT
*
3099 TTTATATAATTTTTTTATAATTTTAT
1 TTTATATAATTTTTTGATAATTTTAT
3125 TTTATATAATTT
1 TTTATATAATTT
3137 ATCTGTTATG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 15 0.43
27 3 0.09
28 8 0.23
29 9 0.26
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (26 bp):
TTTATATAATTTTTTGATAATTTTAT
Found at i:3116 original size:13 final size:14
Alignment explanation
Indices: 3096--3138 Score: 63
Period size: 13 Copynumber: 3.2 Consensus size: 14
3086 GAAATTTTTA
3096 TATTTTATATAATT
1 TATTTTATATAATT
*
3110 T-TTTTATA-ATTT
1 TATTTTATATAATT
3122 TATTTTATATAATT
1 TATTTTATATAATT
3136 TAT
1 TAT
3139 CTGTTATGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 4 0.16
13 14 0.56
14 7 0.28
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTTTATATAATT
Found at i:4352 original size:34 final size:34
Alignment explanation
Indices: 4277--4355 Score: 104
Period size: 34 Copynumber: 2.3 Consensus size: 34
4267 TAAGCATATA
* *
4277 AACAATCGATTCAAAAGAAGAAATATTTCACCAT
1 AACAATCGATTCAAAAGAAGAAATATTCCAACAT
* * *
4311 AATAATCGATTCAAAAGAAGCAGTATTCCAACAT
1 AACAATCGATTCAAAAGAAGAAATATTCCAACAT
*
4345 TACAATCGATT
1 AACAATCGATT
4356 TAAACATATA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.47, C:0.18, G:0.10, T:0.25
Consensus pattern (34 bp):
AACAATCGATTCAAAAGAAGAAATATTCCAACAT
Found at i:6125 original size:19 final size:19
Alignment explanation
Indices: 6097--6137 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
6087 AAGTTTATTT
6097 AAAATAAATAAATAATAAG
1 AAAATAAATAAATAATAAG
* * *
6116 AAAATTAATAATTATTAAG
1 AAAATAAATAAATAATAAG
6135 AAA
1 AAA
6138 TTTCCCTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (19 bp):
AAAATAAATAAATAATAAG
Found at i:9350 original size:31 final size:30
Alignment explanation
Indices: 9280--9377 Score: 92
Period size: 31 Copynumber: 3.3 Consensus size: 30
9270 CATTTTGAAA
* * *
9280 ACCCTTATTTGAGCACTTTTAAAAATATTTG
1 ACCCTTATTTGACCAC-TTTGAAAAGATTTG
*** *
9311 ATATTTATTTGATCACTTTCGAAAAGATTTG
1 ACCCTTATTTGACCACTTT-GAAAAGATTTG
*
9342 ACCCTTATTTGACCAATTTG-AAAGATTTG
1 ACCCTTATTTGACCACTTTGAAAAGATTTG
9371 A-CCTTAT
1 ACCCTTAT
9378 GTGAGCATTT
Statistics
Matches: 55, Mismatches: 11, Indels: 5
0.77 0.15 0.07
Matches are distributed among these distances:
28 6 0.11
29 10 0.18
30 4 0.07
31 35 0.64
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (30 bp):
ACCCTTATTTGACCACTTTGAAAAGATTTG
Found at i:13777 original size:30 final size:30
Alignment explanation
Indices: 13742--13806 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
13732 ACATATGTAT
* *
13742 GTTTTGGTGCCTAATTAAAATATTTAAAAA
1 GTTTTGGAGACTAATTAAAATATTTAAAAA
* *
13772 GTTTTGGAGATTAATTAAAATTTTTAAAAA
1 GTTTTGGAGACTAATTAAAATATTTAAAAA
13802 -TTTTG
1 GTTTTG
13807 AAAGGTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 5 0.16
30 26 0.84
ACGTcount: A:0.38, C:0.03, G:0.14, T:0.45
Consensus pattern (30 bp):
GTTTTGGAGACTAATTAAAATATTTAAAAA
Found at i:15496 original size:39 final size:40
Alignment explanation
Indices: 15451--15538 Score: 142
Period size: 39 Copynumber: 2.2 Consensus size: 40
15441 AAAAATTATA
* *
15451 TTTAATATAATAAAATATTTATTATATTTAT-TTGTGTTT
1 TTTAATATAATAAAACATTTATTATATTTATATAGTGTTT
15490 TTTAATATAATAAAACATTTATTATATTTATGATAGTGTTT
1 TTTAATATAATAAAACATTTATTATATTTAT-ATAGTGTTT
15531 TTTAATAT
1 TTTAATAT
15539 TAATGTATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
39 30 0.67
41 15 0.33
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.56
Consensus pattern (40 bp):
TTTAATATAATAAAACATTTATTATATTTATATAGTGTTT
Found at i:15760 original size:18 final size:18
Alignment explanation
Indices: 15737--15772 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
15727 AAATTCGGAA
15737 TGGATAAAAGAATTGATT
1 TGGATAAAAGAATTGATT
15755 TGGATAAAAGAATTGATT
1 TGGATAAAAGAATTGATT
15773 ATGTTTACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (18 bp):
TGGATAAAAGAATTGATT
Found at i:15972 original size:43 final size:43
Alignment explanation
Indices: 15913--16097 Score: 226
Period size: 43 Copynumber: 4.3 Consensus size: 43
15903 TTATTAGGAA
* * *
15913 AAACGCCGTTAAAGAACATGGTCTTTAGCAACGCTTTCCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGACGCTTTCTCCAC
* * * *
15956 AAATGCCGCTGAAGAACATGGTCTTCAGCGGCGCTTTCTCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGACGCTTTCTCCAC
* * *
15999 AAACGCCGCTAAAGATCATGGCCTTTAGCGACGCTTTCTCCAT
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGACGCTTTCTCCAC
** * *
16042 AAACGCCGCTAAAGAACATGACCTTTAGTGGCGCTTTCTCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGACGCTTTCTCCAC
* *
16085 AAACACCACTAAA
1 AAACGCCGCTAAA
16098 ATTCACAGAT
Statistics
Matches: 121, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 121 1.00
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGGTCTTTAGCGACGCTTTCTCCAC
Done.