Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010242.1 Kokia drynarioides strain JFW-HI SEQ_125074, 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: 31801
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3514 original size:39 final size:40
Alignment explanation
Indices: 3460--3539 Score: 117
Period size: 39 Copynumber: 2.0 Consensus size: 40
3450 TATGCACTCA
* *
3460 ATGGACACCTTTTGAAGAGTTACAA-CCCTTTCAAATTGG
1 ATGGACACCTATTGAAGAGTCACAATCCCTTTCAAATTGG
* *
3499 ATGGACACCTATTGAAGAGTCACAATCCTTTTCATATTGG
1 ATGGACACCTATTGAAGAGTCACAATCCCTTTCAAATTGG
3539 A
1 A
3540 CATACCTCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 23 0.64
40 13 0.36
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Consensus pattern (40 bp):
ATGGACACCTATTGAAGAGTCACAATCCCTTTCAAATTGG
Found at i:3957 original size:32 final size:32
Alignment explanation
Indices: 3919--3985 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
3909 TGTTTATCAT
* *
3919 AAAAATTACAATTTAATTTCGACCTCC-CTTAA
1 AAAAATTACAATTTAACTTCAACCTCCAC-TAA
*
3951 AAAAATTATAATTTAACTTCAACCTCCACTAA
1 AAAAATTACAATTTAACTTCAACCTCCACTAA
3983 AAA
1 AAA
3986 CATTTTCTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 30 0.97
33 1 0.03
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.31
Consensus pattern (32 bp):
AAAAATTACAATTTAACTTCAACCTCCACTAA
Found at i:6086 original size:18 final size:18
Alignment explanation
Indices: 6060--6098 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
6050 AAATAGATTT
* *
6060 TTAATTAAATTAAATTAA
1 TTAAATAAATAAAATTAA
*
6078 TTAAATAAATAAAATTTA
1 TTAAATAAATAAAATTAA
6096 TTA
1 TTA
6099 TACTGGAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAAATAAATAAAATTAA
Found at i:6539 original size:43 final size:43
Alignment explanation
Indices: 6478--6564 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
6468 ATATGTGCTA
6478 GTGCAGCTGGTTTTTGAACTGCAACATACCTAGTGGAAGCAGT
1 GTGCAGCTGGTTTTTGAACTGCAACATACCTAGTGGAAGCAGT
6521 GTGCAGCTGGTTTTTGAACTGCAACATACCTAGTGGAAGCAGT
1 GTGCAGCTGGTTTTTGAACTGCAACATACCTAGTGGAAGCAGT
6564 G
1 G
6565 GGCATAATCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (43 bp):
GTGCAGCTGGTTTTTGAACTGCAACATACCTAGTGGAAGCAGT
Found at i:9323 original size:29 final size:28
Alignment explanation
Indices: 9283--9369 Score: 94
Period size: 29 Copynumber: 3.2 Consensus size: 28
9273 AGTTTAAGTG
9283 ATATTATTGTGATTTGTATGCTTTTGTAT
1 ATATTATTGTGATTTGTAT-CTTTTGTAT
*
9312 ATATTATTGTGATAT-TA--TTTT-TAT
1 ATATTATTGTGATTTGTATCTTTTGTAT
*
9336 -TATTATTGTGATTTGCATACTTTTGTATT
1 ATATTATTGTGATTTGTAT-CTTTTGTA-T
9365 ATATT
1 ATATT
9370 TATGTGTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
23 13 0.27
24 4 0.08
25 4 0.08
27 4 0.08
28 4 0.08
29 15 0.31
30 4 0.08
ACGTcount: A:0.24, C:0.03, G:0.13, T:0.60
Consensus pattern (28 bp):
ATATTATTGTGATTTGTATCTTTTGTAT
Found at i:16005 original size:34 final size:34
Alignment explanation
Indices: 15962--16031 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
15952 CATGTATAAA
15962 TGTTAAAATTGTACAGTGTCCAACTACACCGCTT
1 TGTTAAAATTGTACAGTGTCCAACTACACCGCTT
*
15996 TGTTAAAATTGTATAGTGTCCAACTACACCGCTT
1 TGTTAAAATTGTACAGTGTCCAACTACACCGCTT
16030 TG
1 TG
16032 ACACCATATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (34 bp):
TGTTAAAATTGTACAGTGTCCAACTACACCGCTT
Found at i:18887 original size:37 final size:37
Alignment explanation
Indices: 18837--18950 Score: 201
Period size: 37 Copynumber: 3.1 Consensus size: 37
18827 AAAGAATGTG
*
18837 ATAGAAGTAAGAAGCTTTCTCGGTTTGGTCGATTATT
1 ATAGAAGTAAGAAGCTTTCTCGATTTGGTCGATTATT
*
18874 ATAGAAGTAAGAAGCTTTCTCGATTTGGTCGATTGTT
1 ATAGAAGTAAGAAGCTTTCTCGATTTGGTCGATTATT
*
18911 ATAGAAGTAAGAAGCTTTCTCGATTTGGCCGATTATT
1 ATAGAAGTAAGAAGCTTTCTCGATTTGGTCGATTATT
18948 ATA
1 ATA
18951 AACCTTTGAC
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 73 1.00
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.37
Consensus pattern (37 bp):
ATAGAAGTAAGAAGCTTTCTCGATTTGGTCGATTATT
Found at i:26391 original size:19 final size:20
Alignment explanation
Indices: 26369--26416 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
26359 CAAACTCTTG
26369 ATAATAATTAATATA-AATT
1 ATAATAATTAATATATAATT
*
26388 ATAA-AATTTAATTTATAATT
1 ATAATAA-TTAATATATAATT
26408 -TAAT-ATTAA
1 ATAATAATTAA
26417 GTATTATCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 6 0.24
19 15 0.60
20 4 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATAATAATTAATATATAATT
Found at i:26547 original size:28 final size:30
Alignment explanation
Indices: 26498--26556 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
26488 TGTTTTAAAA
*
26498 AATATTTACAGAAATGAACAA-CTAATTTT
1 AATATTTACAGAAATGAACAACCAAATTTT
*
26527 AATATTTACA-AAATTAACAACCAAATTTT
1 AATATTTACAGAAATGAACAACCAAATTTT
26556 A
1 A
26557 CGAAAACTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 9 0.33
29 18 0.67
ACGTcount: A:0.51, C:0.12, G:0.03, T:0.34
Consensus pattern (30 bp):
AATATTTACAGAAATGAACAACCAAATTTT
Found at i:30226 original size:10 final size:10
Alignment explanation
Indices: 30207--30264 Score: 52
Period size: 10 Copynumber: 6.1 Consensus size: 10
30197 TAATGATTTA
*
30207 AATTATTATT
1 AATTAATATT
30217 AATTAATATT
1 AATTAATATT
30227 -A-TAATA-T
1 AATTAATATT
*
30234 AA-TAATATA
1 AATTAATATT
*
30243 AATTATTATTT
1 AATTAATA-TT
30254 AATTAATATT
1 AATTAATATT
30264 A
1 A
30265 TTTTATTATA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
7 1 0.03
8 11 0.28
9 3 0.08
10 16 0.41
11 8 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
AATTAATATT
Found at i:30481 original size:19 final size:20
Alignment explanation
Indices: 30445--30487 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
30435 TATGTGATAT
30445 AAAAGAATAAAGAAAAGAA-
1 AAAAGAATAAAGAAAAGAAC
*
30464 AAAAGAAATAAA-AGAAGAAC
1 AAAAG-AATAAAGAAAAGAAC
30484 AAAA
1 AAAA
30488 TAGAAGCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.79, C:0.02, G:0.14, T:0.05
Consensus pattern (20 bp):
AAAAGAATAAAGAAAAGAAC
Done.