Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013682.1 Kokia drynarioides strain JFW-HI SEQ_128710, 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: 104920
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 156 characters in sequence are not A, C, G, or T
Found at i:5828 original size:38 final size:38
Alignment explanation
Indices: 5775--5884 Score: 193
Period size: 38 Copynumber: 2.9 Consensus size: 38
5765 AGCATTCATG
* * *
5775 TAATTATATAATTTCAGAACGAATTCTGTCCAAAGAAA
1 TAATTAAATAGTTTCAGAACAAATTCTGTCCAAAGAAA
5813 TAATTAAATAGTTTCAGAACAAATTCTGTCCAAAGAAA
1 TAATTAAATAGTTTCAGAACAAATTCTGTCCAAAGAAA
5851 TAATTAAATAGTTTCAGAACAAATTCTGTCCAAA
1 TAATTAAATAGTTTCAGAACAAATTCTGTCCAAA
5885 ATTTCTTTGG
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 69 1.00
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (38 bp):
TAATTAAATAGTTTCAGAACAAATTCTGTCCAAAGAAA
Found at i:9994 original size:21 final size:21
Alignment explanation
Indices: 9959--10015 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 21
9949 CCCCTGCATT
9959 TTTATTTTGTTTTAATTTAAT-CC
1 TTTA-TTT-TTTTAATTT-ATGCC
9982 TTTATTTTTTTAATTTATGCC
1 TTTATTTTTTTAATTTATGCC
*
10003 TTTAATTTGTTTA
1 TTT-ATTTTTTTA
10016 CAATTTTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 2 0.06
21 14 0.45
22 11 0.35
23 4 0.13
ACGTcount: A:0.21, C:0.07, G:0.05, T:0.67
Consensus pattern (21 bp):
TTTATTTTTTTAATTTATGCC
Found at i:10243 original size:17 final size:15
Alignment explanation
Indices: 10217--10260 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
10207 AAATTATATC
10217 ATTT-TTATTTTCTT
1 ATTTATTATTTTCTT
*
10231 ATTTTAATTATTTTTTT
1 A-TTT-ATTATTTTCTT
10248 ATTTATTATTTTC
1 ATTTATTATTTTC
10261 AACTATGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
14 1 0.04
15 11 0.44
16 3 0.12
17 10 0.40
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (15 bp):
ATTTATTATTTTCTT
Found at i:13038 original size:11 final size:11
Alignment explanation
Indices: 13024--13048 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
13014 AAAAATATTA
13024 TTTTAATTTTT
1 TTTTAATTTTT
13035 TTTTAATTTTT
1 TTTTAATTTTT
13046 TTT
1 TTT
13049 AGTTTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTAATTTTT
Found at i:18136 original size:31 final size:31
Alignment explanation
Indices: 18101--18163 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
18091 AAGGAATGCT
18101 TCCATGGGAGAGGCATCAAAGCTCCCTTTAC
1 TCCATGGGAGAGGCATCAAAGCTCCCTTTAC
*
18132 TCCATGGGAGAGGCATCAAAGCTTCCTTTAC
1 TCCATGGGAGAGGCATCAAAGCTCCCTTTAC
18163 T
1 T
18164 TTTTTATGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (31 bp):
TCCATGGGAGAGGCATCAAAGCTCCCTTTAC
Found at i:31151 original size:6 final size:6
Alignment explanation
Indices: 31104--31154 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
31094 ACAATTCATA
* * * * *
31104 TCACTT TCAATT CCAATT TCACTT TTACTT TCACTC TCACTT TCACTT
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT
31152 TCA
1 TCA
31155 ATTTTGATCA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.22, C:0.31, G:0.00, T:0.47
Consensus pattern (6 bp):
TCACTT
Found at i:42746 original size:2 final size:2
Alignment explanation
Indices: 42739--42771 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
42729 AGTAAACTTT
42739 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42772 TCCATTTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:51293 original size:14 final size:14
Alignment explanation
Indices: 51274--51300 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
51264 ATAACTATAA
51274 AAAAAGAAAAAAAG
1 AAAAAGAAAAAAAG
51288 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
51301 AGGCAACATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAAG
Found at i:57150 original size:120 final size:120
Alignment explanation
Indices: 56937--57177 Score: 439
Period size: 120 Copynumber: 2.0 Consensus size: 120
56927 AACACGGCCA
56937 TACATTGCATTTTATGTTAACAAGTTGAGTCAATACATGAACTCACCATGTGAAGTACATTGGAA
1 TACATTGCATTTTATGTTAACAAGTTGAGTCAATACATGAACTCACCATGTGAAGTACATTGGAA
* *
57002 GGCTGTAAAAAGGGTTTTAATATACTTGAGTGGCACTGTTAATTATGGACTGTAG
66 GGATGTAAAAAGGGTTTTAAGATACTTGAGTGGCACTGTTAATTATGGACTGTAG
*
57057 TACATTGCATTTTGTGTTAACAAGTTGAGTCAATACATGAACTCACCATGTGAAGTACACTT-GA
1 TACATTGCATTTTATGTTAACAAGTTGAGTCAATACATGAACTCACCATGTGAAGTACA-TTGGA
57121 AGGATGTAAAAAGGGTTTTAAGATACTTGAGTGGCACTGTTAATTATGGACTGTAG
65 AGGATGTAAAAAGGGTTTTAAGATACTTGAGTGGCACTGTTAATTATGGACTGTAG
57177 T
1 T
57178 TCAAAAAAGG
Statistics
Matches: 117, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
120 115 0.98
121 2 0.02
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.33
Consensus pattern (120 bp):
TACATTGCATTTTATGTTAACAAGTTGAGTCAATACATGAACTCACCATGTGAAGTACATTGGAA
GGATGTAAAAAGGGTTTTAAGATACTTGAGTGGCACTGTTAATTATGGACTGTAG
Found at i:58159 original size:20 final size:21
Alignment explanation
Indices: 58126--58168 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
58116 TAAAAGATAA
*
58126 AAAAATGTAAATAAATAATTT
1 AAAAATGTAAATAAAAAATTT
*
58147 AAAAA-GTATATAAAAAATTT
1 AAAAATGTAAATAAAAAATTT
58167 AA
1 AA
58169 GTAATATCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (21 bp):
AAAAATGTAAATAAAAAATTT
Found at i:67955 original size:22 final size:24
Alignment explanation
Indices: 67930--67980 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 24
67920 NNNNNNNAAA
67930 AAAAAAAAAACC-TAAAATT-TCT
1 AAAAAAAAAACCATAAAATTCTCT
* * *
67952 AAAAAGAATACCATAAAATTCTTT
1 AAAAAAAAAACCATAAAATTCTCT
67976 AAAAA
1 AAAAA
67981 TTTCATAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 10 0.42
23 7 0.29
24 7 0.29
ACGTcount: A:0.63, C:0.12, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAAAAAAAACCATAAAATTCTCT
Found at i:68199 original size:3 final size:3
Alignment explanation
Indices: 68191--68223 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
68181 ACTAACAAAA
68191 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
68224 TTAGGTATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:78005 original size:12 final size:12
Alignment explanation
Indices: 77984--78018 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
77974 ATAAATTTAA
77984 AAACATTAAAAT
1 AAACATTAAAAT
*
77996 AAATATTAAAAT
1 AAACATTAAAAT
*
78008 GAACATTAAAA
1 AAACATTAAAA
78019 AATTAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.66, C:0.06, G:0.03, T:0.26
Consensus pattern (12 bp):
AAACATTAAAAT
Found at i:78148 original size:32 final size:32
Alignment explanation
Indices: 78112--78180 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
78102 AAAAACACAT
* * *
78112 AAAAATAAC-GTCCAAACAACTAAAATAGCAAC
1 AAAAATAACAGT-AAAACAACAAAAATAACAAC
*
78144 AAAAATAACAGTAAAACAACAAAAATAACAAT
1 AAAAATAACAGTAAAACAACAAAAATAACAAC
78176 AAAAA
1 AAAAA
78181 CAATAACAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 30 0.94
33 2 0.06
ACGTcount: A:0.68, C:0.16, G:0.04, T:0.12
Consensus pattern (32 bp):
AAAAATAACAGTAAAACAACAAAAATAACAAC
Found at i:78165 original size:20 final size:20
Alignment explanation
Indices: 78140--78179 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
78130 ACTAAAATAG
*
78140 CAACAAAAATAACAGTAAAA
1 CAACAAAAATAACAATAAAA
78160 CAACAAAAATAACAATAAAA
1 CAACAAAAATAACAATAAAA
78180 ACAATAACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.72, C:0.15, G:0.03, T:0.10
Consensus pattern (20 bp):
CAACAAAAATAACAATAAAA
Found at i:78173 original size:12 final size:12
Alignment explanation
Indices: 78158--78197 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
78148 ATAACAGTAA
78158 AACAACAAAAAT
1 AACAACAAAAAT
* *
78170 AACAATAAAAAC
1 AACAACAAAAAT
*
78182 AATAACAAAAAT
1 AACAACAAAAAT
78194 AACA
1 AACA
78198 TCAATACAGT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.75, C:0.15, G:0.00, T:0.10
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:78194 original size:9 final size:9
Alignment explanation
Indices: 78141--78197 Score: 50
Period size: 9 Copynumber: 6.4 Consensus size: 9
78131 CTAAAATAGC
78141 AACAAAAAT
1 AACAAAAAT
*
78150 AACAGTAAAAC
1 AACA--AAAAT
78161 AACAAAAAT
1 AACAAAAAT
78170 AAC---AAT
1 AACAAAAAT
78176 AA-AAACAAT
1 AACAAA-AAT
78185 AACAAAAAT
1 AACAAAAAT
78194 AACA
1 AACA
78198 TCAATACAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
6 5 0.13
9 23 0.59
10 3 0.08
11 8 0.21
ACGTcount: A:0.74, C:0.14, G:0.02, T:0.11
Consensus pattern (9 bp):
AACAAAAAT
Found at i:78212 original size:44 final size:40
Alignment explanation
Indices: 78141--78230 Score: 94
Period size: 44 Copynumber: 2.2 Consensus size: 40
78131 CTAAAATAGC
78141 AACAAAAATAACAGTAAAACAACAAAAATAACAATAAAAACAAT
1 AACAAAAATAACAGTAAAACAACAAAAA-AAC--T-AAAACAAT
* **
78185 AACAAAAATAACA-TCAATACAGTAAAAAAACTAAAACAAT
1 AACAAAAATAACAGT-AAAACAACAAAAAAACTAAAACAAT
78225 AA-AAAA
1 AACAAAA
78231 CAGCAATCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
39 4 0.10
40 10 0.24
41 1 0.02
43 4 0.10
44 23 0.55
ACGTcount: A:0.72, C:0.13, G:0.02, T:0.12
Consensus pattern (40 bp):
AACAAAAATAACAGTAAAACAACAAAAAAACTAAAACAAT
Found at i:83161 original size:23 final size:23
Alignment explanation
Indices: 83133--83259 Score: 139
Period size: 23 Copynumber: 5.4 Consensus size: 23
83123 AGTGCTGGGC
*
83133 AACAGAAAGCACACACAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
* * *
83156 AACAGAGAGTACACAAAGTACTA
1 AACAGAGAGCACACACAGTGCTA
* * *
83179 ATCAGAGAGCACACAAAATGCTA
1 AACAGAGAGCACACACAGTGCTA
*
83202 ATCAGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACACAGTGCT-A
*
83226 TAACAGAGAGCACGAGACA-TGCTA
1 -AACAGAGAGCAC-ACACAGTGCTA
83250 AACAGAGAGC
1 AACAGAGAGC
83260 GCGCTAGTGT
Statistics
Matches: 89, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
23 68 0.76
24 2 0.02
25 15 0.17
26 4 0.04
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.11
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Found at i:83213 original size:69 final size:67
Alignment explanation
Indices: 83086--83235 Score: 187
Period size: 69 Copynumber: 2.1 Consensus size: 67
83076 TAAACGGAAC
* *
83086 AAACAGAGAGTACCAAAGTACTAATAGAGAGCACATAAGTGCTGGGCAACAGAAAGCACACACAG
1 AAACAGAGAGTACCAAAGTACTAATAGAGAGCACAAAAATGCT--G-AACAGAAAGCACACACAG
83151 TGCT-
63 TGCTA
*
83155 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAATGCT-AATCAGAGAGCACACACA
1 AAACAGAGAGTAC-CAAAGTACTAAT-AGAGAGCACA-AAAATGCTGAA-CAGAAAGCACACACA
83219 GTGCTA
62 GTGCTA
83225 ATAACAGAGAG
1 A-AACAGAGAG
83236 CACGAGACAT
Statistics
Matches: 72, Mismatches: 3, Indels: 10
0.85 0.04 0.12
Matches are distributed among these distances:
68 2 0.03
69 32 0.44
70 13 0.18
71 19 0.26
72 6 0.08
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.13
Consensus pattern (67 bp):
AAACAGAGAGTACCAAAGTACTAATAGAGAGCACAAAAATGCTGAACAGAAAGCACACACAGTGC
TA
Found at i:90526 original size:22 final size:22
Alignment explanation
Indices: 90489--90530 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
90479 ATTACATGAG
90489 TTTATTTTTTAAAAATGTATATT
1 TTTATTTTTTAAAAAT-TATATT
*
90512 TTTATTTTTT-GAAATTATA
1 TTTATTTTTTAAAAATTATA
90531 AAGAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 4 0.22
23 10 0.56
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (22 bp):
TTTATTTTTTAAAAATTATATT
Found at i:91026 original size:16 final size:17
Alignment explanation
Indices: 90994--91037 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
90984 ATATATTGTT
* *
90994 TAAATTTTTAAAAAAATT
1 TAAA-TTTTAAAAATATA
91012 TATAATTTTAAAAATATA
1 TA-AATTTTAAAAATATA
91030 TAAATTTT
1 TAAATTTT
91038 GGAATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 6 0.26
18 15 0.65
19 2 0.09
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TAAATTTTAAAAATATA
Found at i:91355 original size:2 final size:2
Alignment explanation
Indices: 91348--91374 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
91338 GTTAAGTATC
91348 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
91375 TAACCAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:95690 original size:20 final size:22
Alignment explanation
Indices: 95665--95709 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
95655 CTCCATGATT
95665 ATTTTTATGAAT-TTTTT-TAA
1 ATTTTTATGAATATTTTTATAA
*
95685 ATTTTTTTGAATATTTTTATAA
1 ATTTTTATGAATATTTTTATAA
95707 ATT
1 ATT
95710 ATAAATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.50
21 5 0.23
22 6 0.27
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (22 bp):
ATTTTTATGAATATTTTTATAA
Found at i:97203 original size:16 final size:16
Alignment explanation
Indices: 97184--97218 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
97174 TATAAGGATT
* *
97184 AAAATTTAAAATTTAA
1 AAAATATAAAAATTAA
97200 AAAATATAAAAATTAA
1 AAAATATAAAAATTAA
97216 AAA
1 AAA
97219 TGATCAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATATAAAAATTAA
Found at i:103063 original size:23 final size:23
Alignment explanation
Indices: 103033--103093 Score: 79
Period size: 23 Copynumber: 2.6 Consensus size: 23
103023 TAATAGGGAT
103033 TTTCAATTTACAATTCA-TATCAC
1 TTTCAATTT-CAATTCACTATCAC
*
103056 TTTCAATTTCAAATTCACTTTCAC
1 TTTCAATTTC-AATTCACTATCAC
*
103080 TTTCACTTTCAATT
1 TTTCAATTTCAATT
103094 TTGATCAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 1 0.03
23 19 0.56
24 14 0.41
ACGTcount: A:0.30, C:0.23, G:0.00, T:0.48
Consensus pattern (23 bp):
TTTCAATTTCAATTCACTATCAC
Done.