Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005806.1 Kokia drynarioides strain JFW-HI SEQ_120088, 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: 61049
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 108 characters in sequence are not A, C, G, or T
Found at i:5916 original size:20 final size:20
Alignment explanation
Indices: 5891--5939 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
5881 CTCAAATCCG
5891 ACCCCAAACCCTAAACATGA
1 ACCCCAAACCCTAAACATGA
5911 ACCCCAAACCCTAAACATGA
1 ACCCCAAACCCTAAACATGA
5931 ACCCCAAAC
1 ACCCCAAAC
5940 ATAAACTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.43, G:0.04, T:0.08
Consensus pattern (20 bp):
ACCCCAAACCCTAAACATGA
Found at i:5954 original size:20 final size:20
Alignment explanation
Indices: 5891--5945 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
5881 CTCAAATCCG
*
5891 ACCCCAAACCCTAAACATGA
1 ACCCCAAACCATAAACATGA
*
5911 ACCCCAAACCCTAAACATGA
1 ACCCCAAACCATAAACATGA
5931 ACCCCAAA-CATAAAC
1 ACCCCAAACCATAAAC
5946 TTTGAACCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 6 0.18
20 28 0.82
ACGTcount: A:0.47, C:0.40, G:0.04, T:0.09
Consensus pattern (20 bp):
ACCCCAAACCATAAACATGA
Found at i:6096 original size:20 final size:19
Alignment explanation
Indices: 6056--6101 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
6046 AGGTTTGAGT
*
6056 TTTG-GTTTGGGTTCGATG
1 TTTGTGTTTGGGTTCGAAG
6074 TTTGGTGTTTAGGGTTC-AAG
1 TTT-GTGTTT-GGGTTCGAAG
6094 TTTGTGTT
1 TTTGTGTT
6102 CAGTGTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 3 0.12
19 6 0.25
20 9 0.38
21 6 0.25
ACGTcount: A:0.09, C:0.04, G:0.35, T:0.52
Consensus pattern (19 bp):
TTTGTGTTTGGGTTCGAAG
Found at i:7027 original size:34 final size:34
Alignment explanation
Indices: 6984--7054 Score: 115
Period size: 34 Copynumber: 2.1 Consensus size: 34
6974 AGCGGCAAGC
*
6984 GTTCGATCGAATTAAATAAAAAAATTTTATGTTA
1 GTTCAATCGAATTAAATAAAAAAATTTTATGTTA
* *
7018 GTTCAATCGAATTAAATGAAAAAATTTTGTGTTA
1 GTTCAATCGAATTAAATAAAAAAATTTTATGTTA
7052 GTT
1 GTT
7055 AAATTGACGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.39
Consensus pattern (34 bp):
GTTCAATCGAATTAAATAAAAAAATTTTATGTTA
Found at i:7136 original size:26 final size:26
Alignment explanation
Indices: 7101--7155 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
7091 TTGAAATTTT
* *
7101 TTCGAATCGAGTCGAGTGAAATGAAA
1 TTCGAATCGAGCCGAATGAAATGAAA
* * *
7127 TTCGAGTCGAGCCGAATTAAGTGAAA
1 TTCGAATCGAGCCGAATGAAATGAAA
7153 TTC
1 TTC
7156 TTAGAGTTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (26 bp):
TTCGAATCGAGCCGAATGAAATGAAA
Found at i:9397 original size:27 final size:27
Alignment explanation
Indices: 9350--9408 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
9340 TCTTCCATCA
*
9350 TTTTCATTATTTATTTCAAA-GTGTCT
1 TTTTCATTATTTATTTAAAAGGTGTCT
*
9376 TTTTCATATATTT-TTTGAAAAGGTGTTT
1 TTTTCAT-TATTTATTT-AAAAGGTGTCT
9404 TTTTC
1 TTTTC
9409 CCTTGGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 10 0.36
27 8 0.29
28 10 0.36
ACGTcount: A:0.22, C:0.08, G:0.10, T:0.59
Consensus pattern (27 bp):
TTTTCATTATTTATTTAAAAGGTGTCT
Found at i:13249 original size:27 final size:26
Alignment explanation
Indices: 13198--13249 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
13188 ATTTGGATAG
*
13198 TTTTTTTAATTTGGTATTTATATTTT
1 TTTTTTTAATTTGGTATTGATATTTT
13224 TTTTGTTTAATTTGGTATCTGA-ATTT
1 TTTT-TTTAATTTGGTAT-TGATATTT
13250 CATATTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 4 0.17
27 17 0.74
28 2 0.09
ACGTcount: A:0.19, C:0.02, G:0.12, T:0.67
Consensus pattern (26 bp):
TTTTTTTAATTTGGTATTGATATTTT
Found at i:16404 original size:2 final size:2
Alignment explanation
Indices: 16397--16426 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
16387 CATTAATACC
16397 AT AT 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 AT AT
16427 TTAAATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20387 original size:12 final size:12
Alignment explanation
Indices: 20370--20395 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20360 ATGAAGGAAG
20370 AAAAAAGAAAAA
1 AAAAAAGAAAAA
20382 AAAAAAGAAAAA
1 AAAAAAGAAAAA
20394 AA
1 AA
20396 GAGAACAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAA
Found at i:20972 original size:24 final size:24
Alignment explanation
Indices: 20941--20986 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
20931 AAAAAAAGAC
20941 TGTTGTTTTTTTATATTATTTTCT
1 TGTTGTTTTTTTATATTATTTTCT
* *
20965 TGTTGTTTTTTTTTATTGTTTT
1 TGTTGTTTTTTTATATTATTTT
20987 GTTACTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.09, C:0.02, G:0.11, T:0.78
Consensus pattern (24 bp):
TGTTGTTTTTTTATATTATTTTCT
Found at i:20980 original size:21 final size:24
Alignment explanation
Indices: 20941--20989 Score: 61
Period size: 21 Copynumber: 2.2 Consensus size: 24
20931 AAAAAAAGAC
20941 TGTTGTTTTTTTATATTATT-TTCT
1 TGTTGTTTTTTTATATTATTGTT-T
20965 TGTTG-TTTTTT-T-TTATTGTTT
1 TGTTGTTTTTTTATATTATTGTTT
20986 TGTT
1 TGTT
20990 ACTATTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 10 0.42
22 3 0.12
23 6 0.25
24 5 0.21
ACGTcount: A:0.08, C:0.02, G:0.12, T:0.78
Consensus pattern (24 bp):
TGTTGTTTTTTTATATTATTGTTT
Found at i:26132 original size:30 final size:30
Alignment explanation
Indices: 26089--26164 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 30
26079 TCTCGAGATT
*
26089 TAAAAATTTTGAAAATTTCAATCAAACCTTC
1 TAAAAACTTTGAAAATTTCAATC-AACCTTC
* * *
26120 TAAAAA-TTTGAAAAATTTCATTCAGCTTTC
1 TAAAAACTTTG-AAAATTTCAATCAACCTTC
26150 TAAAAACTTT-AAAAT
1 TAAAAACTTTGAAAAT
26165 ATTTTAATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
29 5 0.12
30 15 0.38
31 20 0.50
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.37
Consensus pattern (30 bp):
TAAAAACTTTGAAAATTTCAATCAACCTTC
Found at i:40876 original size:125 final size:125
Alignment explanation
Indices: 40654--40899 Score: 334
Period size: 125 Copynumber: 2.0 Consensus size: 125
40644 AGCTTTCCAA
* * * *
40654 TCTTGAATTTGAGGTTTCTTCCTTCTCCAAGAAATTTAACAACAAGATCTTCACCTAGTGTGTTA
1 TCTTGAATTTGAGGTTCCTTCCCTCTCCAAGAAATTGAACAACAAGATCCTCACCTAGTGTGTTA
* *
40719 AGTGTCCAAGTTTAATGTGAATTGTAAGTGTTGAGTTGCTTGTCAATTCTTGGTTACAGG
66 AGTGTCCAAGTTTAATGCGAATTGTAAGTGTTGAGTTGCTCGTCAATTCTTGGTTACAGG
* ** *
40779 TCTTGAATTTGAGGTTCCTTCCCTCTCTAATCAATTGAA-AAGCAAGATCCTCACTTAGTGTGTT
1 TCTTGAATTTGAGGTTCCTTCCCTCTCCAAGAAATTGAACAA-CAAGATCCTCACCTAGTGTGTT
* * * *
40843 AGGTGT-CTAGCTTTAATGCGAATTGTAAGTGTTGAGTTGCTCGTCAGTTGTTGGTTA
65 AAGTGTCCAAG-TTTAATGCGAATTGTAAGTGTTGAGTTGCTCGTCAATTCTTGGTTA
40900 ACTTCCAACT
Statistics
Matches: 105, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
124 5 0.05
125 100 0.95
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (125 bp):
TCTTGAATTTGAGGTTCCTTCCCTCTCCAAGAAATTGAACAACAAGATCCTCACCTAGTGTGTTA
AGTGTCCAAGTTTAATGCGAATTGTAAGTGTTGAGTTGCTCGTCAATTCTTGGTTACAGG
Found at i:45767 original size:16 final size:18
Alignment explanation
Indices: 45746--45784 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
45736 TAGAAATATA
45746 ATTTTAT-TATTT-TAAT
1 ATTTTATATATTTATAAT
45762 ATTTTATATATTTATAAT
1 ATTTTATATATTTATAAT
45780 -TTTTA
1 ATTTTA
45785 AACAATTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.33
17 10 0.48
18 4 0.19
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTTATATATTTATAAT
Found at i:48429 original size:24 final size:25
Alignment explanation
Indices: 48402--48454 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
48392 TTTAATTTTT
48402 ATAATAATATTAAA-ATTAAATAAA
1 ATAATAATATTAAATATTAAATAAA
* * *
48426 ATAATTATATTAAATATTCAATGAA
1 ATAATAATATTAAATATTAAATAAA
48451 ATAA
1 ATAA
48455 AATTAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 13 0.52
25 12 0.48
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (25 bp):
ATAATAATATTAAATATTAAATAAA
Found at i:48434 original size:30 final size:30
Alignment explanation
Indices: 48400--48457 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
48390 AATTTAATTT
*
48400 TTATAAT-AATATTAAAATTAAATAAAATAA
1 TTATAATAAATATT-AAATGAAATAAAATAA
* *
48430 TTATATTAAATATTCAATGAAATAAAAT
1 TTATAATAAATATTAAATGAAATAAAAT
48458 TAAAAAAACC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 18 0.75
31 6 0.25
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (30 bp):
TTATAATAAATATTAAATGAAATAAAATAA
Found at i:48859 original size:22 final size:23
Alignment explanation
Indices: 48828--48872 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
48818 AGGAAGAGGC
*
48828 ATTTTTAAAATTT-TTAATATAT
1 ATTTTGAAAATTTATTAATATAT
*
48850 ATTTTGAAAATTTATTATTATAT
1 ATTTTGAAAATTTATTAATATAT
48873 TATTATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
ATTTTGAAAATTTATTAATATAT
Found at i:52030 original size:88 final size:88
Alignment explanation
Indices: 51879--52141 Score: 490
Period size: 88 Copynumber: 3.0 Consensus size: 88
51869 AATGCACTTA
*
51879 CCTCTGTCGAATTTTTAGTTAGTTGACGAATGCATTAGAAGGTGTCATTATTGACCTCAATTGAG
1 CCTCTGTCGAATTTTTAGTTAGTTGACGAATGCATTAGAAGGTGTCATTATTGACCTCGATTGAG
51944 GTTGTCTCCTGATTCTATAGAGG
66 GTTGTCTCCTGATTCTATAGAGG
* * *
51967 CCTCTGTCAAATTTTTAGTTAGTTGACGAATGCATTAGAAGGTGTCATTATTAACCTTGATTGAG
1 CCTCTGTCGAATTTTTAGTTAGTTGACGAATGCATTAGAAGGTGTCATTATTGACCTCGATTGAG
52032 GTTGTCTCCTGATTCTATAGAGG
66 GTTGTCTCCTGATTCTATAGAGG
52055 CCTCTGTCGAATTTTTAGTTAGTTGACGAATGCATTAGAAGGTGTCATTATTGACCTCGATTGAG
1 CCTCTGTCGAATTTTTAGTTAGTTGACGAATGCATTAGAAGGTGTCATTATTGACCTCGATTGAG
52120 GTTGTCTCCTGATTCTATAGAG
66 GTTGTCTCCTGATTCTATAGAG
52142 AGCCCGAGCA
Statistics
Matches: 168, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
88 168 1.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (88 bp):
CCTCTGTCGAATTTTTAGTTAGTTGACGAATGCATTAGAAGGTGTCATTATTGACCTCGATTGAG
GTTGTCTCCTGATTCTATAGAGG
Found at i:53274 original size:12 final size:12
Alignment explanation
Indices: 53257--53282 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
53247 GTTTTGGGTA
53257 GAAAACTTTAAG
1 GAAAACTTTAAG
53269 GAAAACTTTAAG
1 GAAAACTTTAAG
53281 GA
1 GA
53283 GAAGTAAGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.19, T:0.23
Consensus pattern (12 bp):
GAAAACTTTAAG
Found at i:53656 original size:20 final size:20
Alignment explanation
Indices: 53631--53679 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
53621 TATGATGGAT
*
53631 TACCAAAAATTATGAG-AGAG
1 TACCAAAAAATATGAGTA-AG
*
53651 TGCCAAAAAATATGAGTAAG
1 TACCAAAAAATATGAGTAAG
53671 TACCAAAAA
1 TACCAAAAA
53680 GTACCCAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.53, C:0.12, G:0.16, T:0.18
Consensus pattern (20 bp):
TACCAAAAAATATGAGTAAG
Found at i:54168 original size:25 final size:25
Alignment explanation
Indices: 54140--54194 Score: 60
Period size: 27 Copynumber: 2.2 Consensus size: 25
54130 AAAATAATTT
54140 TATT-AAT-ATTAAATAAATAAAAAA
1 TATTAAATAATTAAATAAA-AAAAAA
*
54164 GTATTTAAATAATTAAATTAAAAAAAA
1 -TA-TTAAATAATTAAATAAAAAAAAA
54191 TATT
1 TATT
54195 GATACGAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
25 4 0.15
26 4 0.15
27 9 0.35
28 9 0.35
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (25 bp):
TATTAAATAATTAAATAAAAAAAAA
Found at i:54648 original size:17 final size:17
Alignment explanation
Indices: 54626--54659 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
54616 GAAAAAAATC
*
54626 ATTTAAATGTTATTTAA
1 ATTTAAATATTATTTAA
54643 ATTTAAATATTATTTAA
1 ATTTAAATATTATTTAA
54660 TCACGTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTAAATATTATTTAA
Found at i:55193 original size:24 final size:25
Alignment explanation
Indices: 55157--55203 Score: 62
Period size: 23 Copynumber: 1.9 Consensus size: 25
55147 AAAATATGTT
*
55157 TATATTGTATTAAAATTTTAAAAAAA
1 TATATTGTATT-AAATATTAAAAAAA
55183 TATATT-T-TTAAATATTAAAAA
1 TATATTGTATTAAATATTAAAAA
55204 TTTTAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.55
24 2 0.10
25 1 0.05
26 6 0.30
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (25 bp):
TATATTGTATTAAATATTAAAAAAA
Found at i:55207 original size:16 final size:16
Alignment explanation
Indices: 55171--55226 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 16
55161 TTGTATTAAA
*
55171 ATTTTAAA-AAAATAT
1 ATTTTAAATAAAAAAT
*
55186 ATTTTTAAATATTAAAA-
1 A-TTTTAAATA-AAAAAT
55203 ATTTTAAATAAAAAAT
1 ATTTTAAATAAAAAAT
55219 ATTTTAAA
1 ATTTTAAA
55227 ATTTTTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
15 5 0.15
16 24 0.71
17 2 0.06
18 3 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATTTTAAATAAAAAAT
Found at i:55237 original size:33 final size:32
Alignment explanation
Indices: 55140--55237 Score: 99
Period size: 33 Copynumber: 2.9 Consensus size: 32
55130 TATATTTAAA
* *
55140 TAAATGAAAAATATGTTTATATTGTATTAAAATTT
1 TAAATAAAAAATAT-TTTAAATT-T-TTAAAATTT
* * *
55175 TAAA-AAAATATATTTTTAAATATTAAAAATTT
1 TAAATAAAAAATA-TTTTAAATTTTTAAAATTT
55207 TAAATAAAAAATATTTTAAAATTTTTAAAAT
1 TAAATAAAAAATATTTT-AAATTTTTAAAAT
55238 GACAAATTAA
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
32 16 0.31
33 19 0.37
34 12 0.23
35 5 0.10
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (32 bp):
TAAATAAAAAATATTTTAAATTTTTAAAATTT
Found at i:60810 original size:10 final size:10
Alignment explanation
Indices: 60795--60824 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
60785 TTCTTTTTTT
60795 AATATAAAAA
1 AATATAAAAA
60805 AATATAAAAA
1 AATATAAAAA
60815 AAT-TAAAAA
1 AATATAAAAA
60824 A
1 A
60825 TTATGTGCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 7 0.35
10 13 0.65
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (10 bp):
AATATAAAAA
Done.