Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010724.1 Kokia drynarioides strain JFW-HI SEQ_125676, 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: 26067
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Warning! 31 characters in sequence are not A, C, G, or T
Found at i:121 original size:4 final size:4
Alignment explanation
Indices: 114--153 Score: 55
Period size: 4 Copynumber: 10.0 Consensus size: 4
104 TTCCTTCTTA
*
114 TTTC TTTC TTTC TTTC TTTC TCTTT TTTC TTTC TTT- TTTC
1 TTTC TTTC TTTC TTTC TTTC T-TTC TTTC TTTC TTTC TTTC
154 CTTCATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 3 0.09
4 26 0.81
5 3 0.09
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:122 original size:25 final size:24
Alignment explanation
Indices: 94--148 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
84 CATCTTCTCC
94 TTCTTCCTTCTTCCTTCTTATTTCT
1 TTCTTCCTTCTTCC-TCTTATTTCT
* * *
119 TTCTTTCTTTCTTTCTCTTTTTTCT
1 TTC-TTCCTTCTTCCTCTTATTTCT
144 TTCTT
1 TTCTT
149 TTTTCCTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 2 0.08
25 15 0.58
26 9 0.35
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (24 bp):
TTCTTCCTTCTTCCTCTTATTTCT
Found at i:162 original size:12 final size:11
Alignment explanation
Indices: 104--164 Score: 50
Period size: 11 Copynumber: 5.3 Consensus size: 11
94 TTCTTCCTTC
*
104 TTCCTTCTTAT
1 TTCCTTCTTTT
*
115 TTCTTTCTTTCT
1 TTCCTTCTTT-T
*
127 TTCTTTCTCTTTT
1 TTC-CT-TCTTTT
*
140 TTCTTTCTTTT
1 TTCCTTCTTTT
*
151 TTCCTTCATTT
1 TTCCTTCTTTT
162 TTC
1 TTC
165 GTTGGTCCTC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
11 26 0.60
12 6 0.14
13 6 0.14
14 5 0.12
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.72
Consensus pattern (11 bp):
TTCCTTCTTTT
Found at i:2694 original size:23 final size:23
Alignment explanation
Indices: 2659--2702 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
2649 AATTTGTATA
2659 TTTAAAATCTAATCTAT-TTACTT
1 TTTAAAATCTAAT-TATGTTACTT
* *
2682 TTTAAAGTTTAATTATGTTAC
1 TTTAAAATCTAATTATGTTAC
2703 ATTCAAGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.17
23 15 0.83
ACGTcount: A:0.34, C:0.09, G:0.05, T:0.52
Consensus pattern (23 bp):
TTTAAAATCTAATTATGTTACTT
Found at i:3100 original size:3 final size:3
Alignment explanation
Indices: 3092--3120 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3082 TAAAAACAGT
3092 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3121 TTCTCATCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:4592 original size:3 final size:3
Alignment explanation
Indices: 4584--4618 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
4574 GGATCAACCC
4584 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
4619 ACAACAACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:8136 original size:30 final size:30
Alignment explanation
Indices: 8097--8293 Score: 133
Period size: 29 Copynumber: 6.6 Consensus size: 30
8087 GAGAGTTTTT
8097 GGGTCAAAAATAG-AATTTTTTGGAAGTTCGA
1 GGGT-AAAAAT-GTAATTTTTTGGAAGTTCGA
* * *
8128 GGCTAAAAATGTAA-TTTTTGAAAGTTTTG-
1 GGGTAAAAATGTAATTTTTTGGAAG-TTCGA
* * * * *
8157 GGTTTAAAAATGGATTTTTTTGGATA-TTTGG
1 GG-GTAAAAATGTAATTTTTTGGA-AGTTCGA
8188 GGGT-AAAATGTAA-TTTTTGGAAGTTTC-A
1 GGGTAAAAATGTAATTTTTTGGAAG-TTCGA
* * *
8216 AGGTCAAAATG-AATTTTTTGGAAGTTCGG
1 GGGTAAAAATGTAATTTTTTGGAAGTTCGA
* **
8245 GGGTAAAAATGTATTTTTTTGGAAGTTTTA
1 GGGTAAAAATGTAATTTTTTGGAAGTTCGA
8275 GGGTTAAAAAT-TGAATTTT
1 GGG-TAAAAATGT-AATTTT
8294 GGAGAAGTTT
Statistics
Matches: 131, Mismatches: 21, Indels: 28
0.73 0.12 0.16
Matches are distributed among these distances:
27 1 0.01
28 16 0.12
29 46 0.35
30 43 0.33
31 24 0.18
32 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.24, T:0.41
Consensus pattern (30 bp):
GGGTAAAAATGTAATTTTTTGGAAGTTCGA
Found at i:8156 original size:59 final size:58
Alignment explanation
Indices: 8078--8293 Score: 222
Period size: 59 Copynumber: 3.6 Consensus size: 58
8068 GGGTAAGAGG
* * *
8078 GTAATTTTTGAGAGTTTTTGGGTCAAAAATAGAATTTTTTGGAAGTTCGAGGCTAAAAAT
1 GTAATTTTTGAAAG-TTTTGGGTCAAAAAT-GAATTTTTTGGAAGTTCGGGGGTAAAAAT
* * *
8138 GTAATTTTTGAAAGTTTTGGGTTTAAAAATGGATTTTTTTGGATA-TTTGGGGGT-AAAAT
1 GTAATTTTTGAAAGTTTTGGG-TCAAAAAT-GAATTTTTTGGA-AGTTCGGGGGTAAAAAT
* **
8197 GTAATTTTTGGAAGTTTCAAGGTC-AAAATGAATTTTTTGGAAGTTCGGGGGTAAAAAT
1 GTAATTTTTGAAAGTTT-TGGGTCAAAAATGAATTTTTTGGAAGTTCGGGGGTAAAAAT
* * *
8255 GTATTTTTTTGGAAGTTTTAGGGTTAAAAATTGAATTTT
1 GTA-ATTTTTGAAAGTTTT-GGGTCAAAAA-TGAATTTT
8294 GGAGAAGTTT
Statistics
Matches: 130, Mismatches: 17, Indels: 17
0.79 0.10 0.10
Matches are distributed among these distances:
56 1 0.01
57 19 0.15
58 13 0.10
59 45 0.35
60 43 0.33
61 9 0.07
ACGTcount: A:0.31, C:0.03, G:0.24, T:0.42
Consensus pattern (58 bp):
GTAATTTTTGAAAGTTTTGGGTCAAAAATGAATTTTTTGGAAGTTCGGGGGTAAAAAT
Found at i:8294 original size:59 final size:59
Alignment explanation
Indices: 8050--8321 Score: 218
Period size: 60 Copynumber: 4.6 Consensus size: 59
8040 ATCAAAAACG
* * ** * * *
8050 GAATTTTTGGACA-TCCGGGGGTAAGAGGGTAATTTTT-GAGAGTTTTTGGGTCAAAAATA
1 GAATTTTTGGA-AGTTCGGGGGTAAAAATGTAATTTTTGGA-AGTTTTAGGGTTAAAAATT
* * * *
8109 GAATTTTTTGGAAGTTCGAGGCTAAAAATGTAATTTTTGAAAGTTTT-GGGTTTAAAAATG
1 GAA-TTTTTGGAAGTTCGGGGGTAAAAATGTAATTTTTGGAAGTTTTAGGG-TTAAAAATT
* * * * *
8169 GATTTTTTTGGATA-TTTGGGGGT-AAAATGTAATTTTTGGAAGTTTCAAGG-TCAAAA-T
1 GA-ATTTTTGGA-AGTTCGGGGGTAAAAATGTAATTTTTGGAAGTTTTAGGGTTAAAAATT
*
8226 GAATTTTTTGGAAGTTCGGGGGTAAAAATGTATTTTTTTGGAAGTTTTAGGGTTAAAAATT
1 GAA-TTTTTGGAAGTTCGGGGGTAAAAATGTA-ATTTTTGGAAGTTTTAGGGTTAAAAATT
* * * *
8287 GAATTTTGGAGAAGTT-TGGGGTCAAAATATAATTT
1 GAATTTTTG-GAAGTTCGGGGGTAAAAATGTAATTT
8322 CTAGATAGTT
Statistics
Matches: 170, Mismatches: 29, Indels: 28
0.75 0.13 0.12
Matches are distributed among these distances:
56 1 0.01
57 18 0.11
58 13 0.08
59 47 0.28
60 79 0.46
61 12 0.07
ACGTcount: A:0.31, C:0.04, G:0.26, T:0.39
Consensus pattern (59 bp):
GAATTTTTGGAAGTTCGGGGGTAAAAATGTAATTTTTGGAAGTTTTAGGGTTAAAAATT
Found at i:9434 original size:3 final size:3
Alignment explanation
Indices: 9423--9454 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
9413 TTAAAGCTAC
9423 ATT ATTT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT A
9455 ATGATACTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:9783 original size:6 final size:6
Alignment explanation
Indices: 9768--9857 Score: 82
Period size: 6 Copynumber: 15.7 Consensus size: 6
9758 TGTAATTGAT
* * *
9768 TTTAAA TTTAAG TTTAAA ATT--A TTTCAAA TTTAAA -CTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
* * *
9814 TTTAAA -ATAAA TTTAAA TTTAAA TTTAAA -GTAAA TTTAAT TTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA
9858 GAAATAAATC
Statistics
Matches: 67, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
4 3 0.04
5 12 0.18
6 48 0.72
7 4 0.06
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:9810 original size:11 final size:11
Alignment explanation
Indices: 9810--9852 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
9800 AAACTAAATT
9810 TAAATTTAAAA
1 TAAATTTAAAA
*
9821 TAAATTTAAATT
1 TAAATTTAAA-A
*
9833 TAAATTTAAAG
1 TAAATTTAAAA
9844 TAAATTTAA
1 TAAATTTAA
9853 TTTTAGAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:9834 original size:23 final size:23
Alignment explanation
Indices: 9804--9857 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
9794 AAATTTAAAC
9804 TAAATTTAAATTTAAAATAAATT
1 TAAATTTAAATTTAAAATAAATT
*
9827 TAAATTTAAATTTAAAGTAAATT
1 TAAATTTAAATTTAAAATAAATT
*
9850 TAATTTTA
1 TAAATTTA
9858 GAAATAAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
TAAATTTAAATTTAAAATAAATT
Found at i:9852 original size:17 final size:17
Alignment explanation
Indices: 9770--9836 Score: 91
Period size: 17 Copynumber: 3.9 Consensus size: 17
9760 TAATTGATTT
*
9770 TAAATTTAAGTTTAAAA
1 TAAATTTAAATTTAAAA
* *
9787 T-TATTTCAAATTTAAAC
1 TAAATTT-AAATTTAAAA
9804 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
9821 TAAATTTAAATTTAAA
1 TAAATTTAAATTTAAA
9837 TTTAAAGTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
16 4 0.09
17 35 0.81
18 4 0.09
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:9865 original size:23 final size:23
Alignment explanation
Indices: 9804--9865 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
9794 AAATTTAAAC
*
9804 TAAATTTAAATTTAAAATAAATT
1 TAAATTTAAATATAAAATAAATT
* *
9827 TAAATTTAAATTTAAAGTAAATT
1 TAAATTTAAATATAAAATAAATT
*
9850 TAATTTTAGAA-ATAAA
1 TAAATTTA-AATATAAA
9866 TCTAAAACCC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
23 33 0.94
24 2 0.06
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (23 bp):
TAAATTTAAATATAAAATAAATT
Found at i:12007 original size:20 final size:18
Alignment explanation
Indices: 11979--12026 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 18
11969 TCACGTTAAC
*
11979 AAATAATTTTAAAATTATAA
1 AAATTATTTTAAAA-TAT-A
11999 AAATTATTTTTTAAAATATA
1 AAATTA--TTTTAAAATATA
12019 AAATTATT
1 AAATTATT
12027 AAAAAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 2 0.08
20 12 0.48
21 3 0.12
22 8 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AAATTATTTTAAAATATA
Found at i:12018 original size:21 final size:21
Alignment explanation
Indices: 11985--12026 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
11975 TAACAAATAA
11985 TTTTAAAATTATAAAAATTATT
1 TTTTAAAATTAT-AAAATTATT
12007 TTTTAAAA-TATAAAATTATT
1 TTTTAAAATTATAAAATTATT
12027 AAAAAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 3 0.15
22 8 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTTAAAATTATAAAATTATT
Found at i:12879 original size:19 final size:20
Alignment explanation
Indices: 12836--12881 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
12826 TCTAGGTGGA
*
12836 AAAAAATTACCACATTGACC
1 AAAAAATGACCACATTGACC
12856 AAAAAATGACCA-ATTTGACC
1 AAAAAATGACCACA-TTGACC
12876 AAAAAA
1 AAAAAA
12882 ACAAAGATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.57, C:0.20, G:0.07, T:0.17
Consensus pattern (20 bp):
AAAAAATGACCACATTGACC
Found at i:15022 original size:20 final size:21
Alignment explanation
Indices: 14971--15022 Score: 54
Period size: 24 Copynumber: 2.4 Consensus size: 21
14961 CTAAAATTCT
14971 AAATT-TTTTAAATAAAATTAA
1 AAATTATTTTAAATAAAA-TAA
*
14992 AATATTGATTTTAATTAAAA-AA
1 AA-ATT-ATTTTAAATAAAATAA
15014 AAATTATTT
1 AAATTATTT
15023 ATACAAACTG
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
20 4 0.15
21 5 0.19
22 7 0.26
24 11 0.41
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
AAATTATTTTAAATAAAATAA
Done.