Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013818.1 Kokia drynarioides strain JFW-HI SEQ_128846, 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: 14135
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:1481 original size:15 final size:16
Alignment explanation
Indices: 1463--1493 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1453 AACCGATTAA
1463 GCCATAA-CCCATAAG
1 GCCATAAGCCCATAAG
1478 GCCATAAGCCCATAAG
1 GCCATAAGCCCATAAG
1494 TCATTTACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.39, C:0.32, G:0.16, T:0.13
Consensus pattern (16 bp):
GCCATAAGCCCATAAG
Found at i:2558 original size:28 final size:28
Alignment explanation
Indices: 2526--2590 Score: 130
Period size: 28 Copynumber: 2.3 Consensus size: 28
2516 GGACACAAAG
2526 TGGCAGCACTAAGGGGTGTTTTGCCACT
1 TGGCAGCACTAAGGGGTGTTTTGCCACT
2554 TGGCAGCACTAAGGGGTGTTTTGCCACT
1 TGGCAGCACTAAGGGGTGTTTTGCCACT
2582 TGGCAGCAC
1 TGGCAGCAC
2591 CCCATTGTGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.18, C:0.23, G:0.32, T:0.26
Consensus pattern (28 bp):
TGGCAGCACTAAGGGGTGTTTTGCCACT
Found at i:2741 original size:12 final size:12
Alignment explanation
Indices: 2724--2748 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2714 GATTTGAAGG
2724 AAAAAAGAAAGA
1 AAAAAAGAAAGA
2736 AAAAAAGAAAGA
1 AAAAAAGAAAGA
2748 A
1 A
2749 GGAAGGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAGA
Found at i:2933 original size:18 final size:18
Alignment explanation
Indices: 2910--2944 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2900 GGAAGAAAGA
2910 TAAGTTTGATTAATTTTT
1 TAAGTTTGATTAATTTTT
*
2928 TAAGTTTGGTTAATTTT
1 TAAGTTTGATTAATTTT
2945 AAATTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (18 bp):
TAAGTTTGATTAATTTTT
Found at i:3157 original size:20 final size:21
Alignment explanation
Indices: 3116--3158 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
3106 TAATTTACTT
3116 TAATTTGATTTTGTTAGTTAG
1 TAATTTGATTTTGTTAGTTAG
*
3137 TAATTTTATTTTGTT-GTTAG
1 TAATTTGATTTTGTTAGTTAG
3157 TA
1 TA
3159 GTAGCAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.23, C:0.00, G:0.16, T:0.60
Consensus pattern (21 bp):
TAATTTGATTTTGTTAGTTAG
Found at i:3664 original size:23 final size:23
Alignment explanation
Indices: 3631--3683 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
3621 AGTATATTTA
3631 TAAAA-TAGTTATATAATACGGG
1 TAAAATTAGTTATATAATACGGG
3653 TAAAATTAGTTATATAATACGGG
1 TAAAATTAGTTATATAATACGGG
3676 TAAAATTA
1 TAAAATTA
3684 TAAAAAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 5 0.17
23 25 0.83
ACGTcount: A:0.47, C:0.04, G:0.15, T:0.34
Consensus pattern (23 bp):
TAAAATTAGTTATATAATACGGG
Found at i:3922 original size:16 final size:16
Alignment explanation
Indices: 3876--3924 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
3866 TAAACCTAGC
3876 TAATTAATTACCAAAA
1 TAATTAATTACCAAAA
3892 T-A-TAATATA--AAAA
1 TAATTAAT-TACCAAAA
3905 TAATTAATTACCAAAA
1 TAATTAATTACCAAAA
3921 TAAT
1 TAAT
3925 ATCCCCATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
13 5 0.18
14 7 0.25
15 7 0.25
16 9 0.32
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (16 bp):
TAATTAATTACCAAAA
Found at i:5280 original size:43 final size:43
Alignment explanation
Indices: 5198--5282 Score: 116
Period size: 43 Copynumber: 2.0 Consensus size: 43
5188 ATTAACATGT
* * *
5198 TAAATTATATTACTTGACTCGTGTTAATATGGTGGCATGTTAC
1 TAAATTATATTACTTGACTCGTATTAATATCGTGACATGTTAC
* * *
5241 TAAATTATATTACTTTACTCTTATTAATATCTTGACATGTTA
1 TAAATTATATTACTTGACTCGTATTAATATCGTGACATGTTA
5283 TTAATTGTGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.46
Consensus pattern (43 bp):
TAAATTATATTACTTGACTCGTATTAATATCGTGACATGTTAC
Found at i:5916 original size:45 final size:45
Alignment explanation
Indices: 5852--5940 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
5842 CTAGCTCATC
*
5852 AAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATACTT
1 AAGCCAAGGATATCAGCCTCAGTTTAACGAGCCACCGCAATACTT
*
5897 AAGCCAAGGATATCAGCCTCAGTTTAACGAGTCACCGCAATACT
1 AAGCCAAGGATATCAGCCTCAGTTTAACGAGCCACCGCAATACT
5941 CTACTCCTCC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.20
Consensus pattern (45 bp):
AAGCCAAGGATATCAGCCTCAGTTTAACGAGCCACCGCAATACTT
Found at i:6221 original size:21 final size:20
Alignment explanation
Indices: 6173--6223 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
6163 TAAATTTCAT
* *
6173 AACCTTAAACCCTAAAACTTA
1 AACCGTAAACTCT-AAACTTA
6194 AACCGTAAACTCTAAACTTGA
1 AACCGTAAACTCTAAACTT-A
*
6215 AATCGTAAA
1 AACCGTAAA
6224 TCCTAAACCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 6 0.23
21 20 0.77
ACGTcount: A:0.47, C:0.24, G:0.06, T:0.24
Consensus pattern (20 bp):
AACCGTAAACTCTAAACTTA
Found at i:6229 original size:21 final size:19
Alignment explanation
Indices: 6173--6231 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 19
6163 TAAATTTCAT
*
6173 AACCTTAAACCCTAAAACTTA
1 AACCGTAAA-CCT-AAACTTA
6194 AACCGTAAACTCTAAACTTGA
1 AACCGTAAAC-CTAAACTT-A
*
6215 AATCGTAAATCCTAAAC
1 AACCGTAAA-CCTAAAC
6232 CCTAGACTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 7 0.21
21 25 0.76
22 1 0.03
ACGTcount: A:0.46, C:0.25, G:0.05, T:0.24
Consensus pattern (19 bp):
AACCGTAAACCTAAACTTA
Found at i:9296 original size:20 final size:21
Alignment explanation
Indices: 9271--9313 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 21
9261 ACACATTACC
9271 TTTCTCTCCTTC-TTCTTTCT
1 TTTCTCTCCTTCTTTCTTTCT
9291 TTTCTCTCCTTCTTTCTTTCT
1 TTTCTCTCCTTCTTTCTTTCT
9312 TT
1 TT
9314 CTTTCCCGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTCTCTCCTTCTTTCTTTCT
Found at i:11275 original size:2 final size:2
Alignment explanation
Indices: 11268--11293 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11258 GCATCTATGA
11268 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
11294 TAAGAATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.