Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011932.1 Kokia drynarioides strain JFW-HI SEQ_126930, 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: 60090
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:54 original size:2 final size:2
Alignment explanation
Indices: 47--82 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
37 TTTGGCTTTA
47 AT AT AT 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 AT AT AT
83 TTAATTAATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10246 original size:33 final size:33
Alignment explanation
Indices: 10204--10276 Score: 146
Period size: 33 Copynumber: 2.2 Consensus size: 33
10194 CACATATGGA
10204 GGATCGAATCGGATCATACTTATGTAATCCCTT
1 GGATCGAATCGGATCATACTTATGTAATCCCTT
10237 GGATCGAATCGGATCATACTTATGTAATCCCTT
1 GGATCGAATCGGATCATACTTATGTAATCCCTT
10270 GGATCGA
1 GGATCGA
10277 GGAAGTTGGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (33 bp):
GGATCGAATCGGATCATACTTATGTAATCCCTT
Found at i:11048 original size:6 final size:6
Alignment explanation
Indices: 11024--11057 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
11014 TTTTAAAGTG
*
11024 AATTAA AAGTAA AATTTAA AATTAA AATTAA AAT
1 AATTAA AATTAA AA-TTAA AATTAA AATTAA AAT
11058 AATTTAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (6 bp):
AATTAA
Found at i:16852 original size:11 final size:12
Alignment explanation
Indices: 16823--16851 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
16813 ATTCTATATC
16823 ATTTTTGTAATT
1 ATTTTTGTAATT
16835 ATTTTTGTAATT
1 ATTTTTGTAATT
16847 ATTTT
1 ATTTT
16852 GAAAAAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (12 bp):
ATTTTTGTAATT
Found at i:19224 original size:280 final size:279
Alignment explanation
Indices: 18703--19273 Score: 1079
Period size: 280 Copynumber: 2.0 Consensus size: 279
18693 GGGGTCTTCT
18703 TCTTCACATGTTTCATGCTTATCTCTTTATTTATTTTGGTTTCTTTCGTTTTGAAAACTTTAATA
1 TCTTCACATGTTTCATGCTTATCTCTTTATTTATTTTGGTTTCTTTCGTTTTGAAAACTTTAATA
*
18768 AGATGAAGTGTGTTAGGTGAATTTTCTTTACCAAAATTCTTTTTACATTCATTATACAAAAGAAT
66 AGATGAAGTATGTTAGGTGAATTTTCTTTACCAAAATTCTTTTTACATTCATTATACAAAAGAAT
18833 CTTCAACGTGATATCTTATTTGATAAATAGTCAAGAAAATAGTAGTGGGGAGAGAGACCTTAAAC
131 CTTCAACGTGATATCTTATTTGATAAATAGTCAAGAAAATAGTAGTGGGGAGAGAGACCTTAAAC
*
18898 CTAGTTTGAGAGTAATGTTATAGTCATTGAAACCAGCTGTAGAAAATAGCATAGCCCATTCATCT
196 CTAGTATGAGAGTAATGTTATAGTCATTGAAACCAGCTGTAGAAAATAGCATAGCCCATTCATCT
18963 TTTCCATTGATCCCCATCA
261 TTTCCATTGATCCCCATCA
18982 TCTTCACATGTTTCATGCTTCATCTCTTTATTTATTTTGGTTTCTTTCGTTTTGAAAACTTTAAT
1 TCTTCACATGTTTCATGCTT-ATCTCTTTATTTATTTTGGTTTCTTTCGTTTTGAAAACTTTAAT
*
19047 AAGATGAAGTATGTTAGGTGAATTTTCTTTACCAAAATTCTTTTTACATTCATTGTACAAAAGAA
65 AAGATGAAGTATGTTAGGTGAATTTTCTTTACCAAAATTCTTTTTACATTCATTATACAAAAGAA
19112 TCTTCAACGTGATATCTTATTTGATAAATAGTCAAGAAAATAGTAGTGGGGAGAGAGACCTTAAA
130 TCTTCAACGTGATATCTTATTTGATAAATAGTCAAGAAAATAGTAGTGGGGAGAGAGACCTTAAA
*
19177 CCTAGTATGAGAGTAATGTTATAGTCATTGAAACCAGCTGTAGAAAATAGCATAGCCCGTTCATC
195 CCTAGTATGAGAGTAATGTTATAGTCATTGAAACCAGCTGTAGAAAATAGCATAGCCCATTCATC
19242 TTTTCCATTGATCCCCATCA
260 TTTTCCATTGATCCCCATCA
*
19262 TCATCAGCATGT
1 TCTTCA-CATGT
19274 CAAAGAAGAG
Statistics
Matches: 285, Mismatches: 5, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
279 20 0.07
280 260 0.91
281 5 0.02
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (279 bp):
TCTTCACATGTTTCATGCTTATCTCTTTATTTATTTTGGTTTCTTTCGTTTTGAAAACTTTAATA
AGATGAAGTATGTTAGGTGAATTTTCTTTACCAAAATTCTTTTTACATTCATTATACAAAAGAAT
CTTCAACGTGATATCTTATTTGATAAATAGTCAAGAAAATAGTAGTGGGGAGAGAGACCTTAAAC
CTAGTATGAGAGTAATGTTATAGTCATTGAAACCAGCTGTAGAAAATAGCATAGCCCATTCATCT
TTTCCATTGATCCCCATCA
Found at i:20991 original size:21 final size:20
Alignment explanation
Indices: 20946--20993 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
20936 ATTACTGTTA
20946 ATTAAATTCACCACTCCACC
1 ATTAAATTCACCACTCCACC
* * *
20966 CTTAAATTCACCCCTTTCACC
1 ATTAAATTCACCAC-TCCACC
20987 ATTAAAT
1 ATTAAAT
20994 CCTTTATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.33, C:0.35, G:0.00, T:0.31
Consensus pattern (20 bp):
ATTAAATTCACCACTCCACC
Found at i:21459 original size:3 final size:3
Alignment explanation
Indices: 21451--21485 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
21441 AATGTAAATA
21451 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
21486 CATGTGAATA
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:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:21597 original size:41 final size:40
Alignment explanation
Indices: 21543--21619 Score: 136
Period size: 41 Copynumber: 1.9 Consensus size: 40
21533 ATATTTCGTA
*
21543 TATTTTTTTAAATAATAATTAATATTATTATGATATCTAT
1 TATTTTTTTAAATAATAATTAATATTAATATGATATCTAT
21583 TATTTCTTTTAAATAATAATTAATATTAATATGATAT
1 TATTT-TTTTAAATAATAATTAATATTAATATGATAT
21620 GGATATATGG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 5 0.14
41 30 0.86
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (40 bp):
TATTTTTTTAAATAATAATTAATATTAATATGATATCTAT
Found at i:22065 original size:29 final size:28
Alignment explanation
Indices: 22001--22076 Score: 73
Period size: 30 Copynumber: 2.6 Consensus size: 28
21991 ATTTTATATG
**
22001 TATAATTAT-AATAAATTAAAATTCATA
1 TATAATTATAAATTTATTAAAATTCATA
*
22028 TCTCAAATTATAAATTTATTCAAAATTCATA
1 TAT--AATTATAAATTTATT-AAAATTCATA
*
22059 TATAATTTTAAAATTTAT
1 TATAATTAT-AAATTTAT
22077 CCTAACAGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
27 2 0.05
29 11 0.28
30 14 0.36
31 12 0.31
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.45
Consensus pattern (28 bp):
TATAATTATAAATTTATTAAAATTCATA
Found at i:23803 original size:26 final size:26
Alignment explanation
Indices: 23760--23811 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
23750 TATAGAAATT
*
23760 TATATAAAATTATTTAAAAATTCAAA
1 TATATAAAATTATCTAAAAATTCAAA
*
23786 TATATATAAATTA-CTAAAATTTCAAA
1 TATATA-AAATTATCTAAAAATTCAAA
23812 AAGAATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 17 0.74
27 6 0.26
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (26 bp):
TATATAAAATTATCTAAAAATTCAAA
Found at i:29479 original size:5 final size:5
Alignment explanation
Indices: 29469--29493 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
29459 TCTGTGTGTA
29469 TGGTT TGGTT TGGTT TGGTT TGGTT
1 TGGTT TGGTT TGGTT TGGTT TGGTT
29494 ATCAAGAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.40, T:0.60
Consensus pattern (5 bp):
TGGTT
Found at i:30183 original size:39 final size:40
Alignment explanation
Indices: 30111--30189 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
30101 CCCTTTGAAG
30111 AGTCACAACCCTTTCATATTGGATGGACAAC-TTTTGGAA
1 AGTCACAACCCTTTCATATTGGATGGACAACTTTTTGGAA
*
30150 AGTCACAACCTTTTTCATATTGGATGGAC-ACTTTTTGGAA
1 AGTCACAACC-CTTTCATATTGGATGGACAACTTTTTGGAA
30190 GAGACTTGTC
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
39 12 0.32
40 25 0.68
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (40 bp):
AGTCACAACCCTTTCATATTGGATGGACAACTTTTTGGAA
Found at i:35075 original size:39 final size:40
Alignment explanation
Indices: 35027--35121 Score: 156
Period size: 39 Copynumber: 2.4 Consensus size: 40
35017 ATGCACTCAT
* *
35027 TGGACACCTTTTGAAGAGTCACAACTCTT-TCATATTGGA
1 TGGACACCTTTTGAAAAGTCACAACCCTTCTCATATTGGA
35066 TGGACACCTTTTGAAAAGTCACAACCCTTCTCATATTGGA
1 TGGACACCTTTTGAAAAGTCACAACCCTTCTCATATTGGA
*
35106 TGGACACTTTTTGAAA
1 TGGACACCTTTTGAAA
35122 GAGACTTGTT
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 27 0.52
40 25 0.48
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (40 bp):
TGGACACCTTTTGAAAAGTCACAACCCTTCTCATATTGGA
Found at i:37332 original size:24 final size:24
Alignment explanation
Indices: 37297--37346 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
37287 TAAATAATTT
37297 AAGTTTAAAAAAA-TATTTCTATAC
1 AAGTTTAAAAAAATTATTT-TATAC
*
37321 AAGTTTATAAAAATTATTTTATAC
1 AAGTTTAAAAAAATTATTTTATAC
37345 AA
1 AA
37347 TAATAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (24 bp):
AAGTTTAAAAAAATTATTTTATAC
Found at i:48590 original size:30 final size:30
Alignment explanation
Indices: 48555--48611 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
48545 AATTGAAATA
*
48555 ATCTATCATCTGTCTGATCTGTTAAGATTG
1 ATCTATCATATGTCTGATCTGTTAAGATTG
*
48585 ATCTATCATATTTCTGATCTGTTAAGA
1 ATCTATCATATGTCTGATCTGTTAAGA
48612 CTGAATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44
Consensus pattern (30 bp):
ATCTATCATATGTCTGATCTGTTAAGATTG
Found at i:49194 original size:80 final size:79
Alignment explanation
Indices: 49057--49206 Score: 246
Period size: 80 Copynumber: 1.9 Consensus size: 79
49047 ATAATATTAC
* * *
49057 TATCATTGGTTACTATTGTACTAATTCAATGAATCTCTATTGTGCAAGTAAGTCCAAAAAAATGT
1 TATCATTGGTTACTATTATACTAATTCAATGAATCTCTATTGTGCAAGTAAGACC-AAAAAATGC
49122 AAAAGAGAACGTTGT
65 AAAAGAGAACGTTGT
* *
49137 TATCATTGGTTATTATTATACTAATTTAATGAATCTCTATTGTGCAAGTAAGACCAAAAAATGCA
1 TATCATTGGTTACTATTATACTAATTCAATGAATCTCTATTGTGCAAGTAAGACCAAAAAATGCA
49202 AAAGA
66 AAAGA
49207 TAATATTACC
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
79 14 0.22
80 51 0.78
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (79 bp):
TATCATTGGTTACTATTATACTAATTCAATGAATCTCTATTGTGCAAGTAAGACCAAAAAATGCA
AAAGAGAACGTTGT
Found at i:49276 original size:47 final size:47
Alignment explanation
Indices: 49192--49281 Score: 119
Period size: 47 Copynumber: 1.9 Consensus size: 47
49182 AAGTAAGACC
* *
49192 AAAAAATGCAAAAGATAATATTACCATCATTAGTTATTGTTGTCCAA
1 AAAAAATGCAAAAGACAATATTACCATCATTAGTTATTATTGTCCAA
* * *
49239 AAAAAATGTAAAAGACAATATTACTATTATTTA-TTATTATTGT
1 AAAAAATGCAAAAGACAATATTACCATCA-TTAGTTATTATTGT
49282 ACTAATTCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
47 34 0.92
48 3 0.08
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (47 bp):
AAAAAATGCAAAAGACAATATTACCATCATTAGTTATTATTGTCCAA
Found at i:49358 original size:80 final size:81
Alignment explanation
Indices: 49236--49405 Score: 252
Period size: 80 Copynumber: 2.1 Consensus size: 81
49226 TATTGTTGTC
* * * * * * **
49236 CAAAAAAAATGTAAAAGACAATATTACTATTATTTATTATTATTGTACTAATTCAATGAATTTTT
1 CAAAAAAAATGCAAAAAACAATATTACTATCATTGATAATTATTGTACTAACTCAATGAATCCTT
49301 ATTGTGCAAGT-AAGG
66 ATTGTGCAAGTAAAGG
*
49316 CAAAAAAAATGCAAAAAACAATATTACTATCATTGCTAATTATTGTACTAACTCAATGAATCCTT
1 CAAAAAAAATGCAAAAAACAATATTACTATCATTGATAATTATTGTACTAACTCAATGAATCCTT
49381 ATTGTGCAAGTAAAGG
66 ATTGTGCAAGTAAAGG
49397 CAAAAAAAA
1 CAAAAAAAA
49406 AAATATGATA
Statistics
Matches: 80, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
80 67 0.84
81 13 0.16
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (81 bp):
CAAAAAAAATGCAAAAAACAATATTACTATCATTGATAATTATTGTACTAACTCAATGAATCCTT
ATTGTGCAAGTAAAGG
Found at i:52733 original size:21 final size:22
Alignment explanation
Indices: 52693--52734 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
52683 TTTCAAATTA
*
52693 TTTATTTATTTACTAATAAAACT
1 TTTATTTATATAC-AATAAAACT
52716 TTTATTTATATA-AATAAAA
1 TTTATTTATATACAATAAAA
52735 TAATAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
23 11 0.61
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTATTTATATACAATAAAACT
Found at i:52977 original size:18 final size:18
Alignment explanation
Indices: 52954--53001 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
52944 AAATCAAATA
* *
52954 ATTATTTTTA-ACATCATT
1 ATTATTTTTATAAAT-ATC
52972 ATTATTTTTATAAATATC
1 ATTATTTTTATAAATATC
52990 ATTATTTTTATA
1 ATTATTTTTATA
53002 TTGAAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 24 0.89
19 3 0.11
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTATTTTTATAAATATC
Found at i:53717 original size:55 final size:54
Alignment explanation
Indices: 53636--53749 Score: 131
Period size: 55 Copynumber: 2.1 Consensus size: 54
53626 TTTGCACATA
* * *
53636 TGTCATGCGGACAGACCAAAAACGAGCAGACTTG-GGAGCAGGCAATGGTGCGAGC
1 TGTCATGCGGACAGACCAAAAACGAGCAGACTCGAGGA-CA-GAAAAGGTGCGAGC
**** *
53691 TGTCATGCGGACAGACCATGTGCGAGCTGACTCGAGGACAGAAAAGGTGCGAGC
1 TGTCATGCGGACAGACCAAAAACGAGCAGACTCGAGGACAGAAAAGGTGCGAGC
53745 TGTCA
1 TGTCA
53750 AGCAAAATTG
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
54 17 0.34
55 30 0.60
56 3 0.06
ACGTcount: A:0.29, C:0.22, G:0.34, T:0.15
Consensus pattern (54 bp):
TGTCATGCGGACAGACCAAAAACGAGCAGACTCGAGGACAGAAAAGGTGCGAGC
Found at i:54028 original size:24 final size:24
Alignment explanation
Indices: 53993--54040 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
53983 TAAAAACCTA
53993 AAACCATATATATATTCTAAAAGG
1 AAACCATATATATATTCTAAAAGG
*
54017 AAACCATTTATATATTCTAAAAGG
1 AAACCATATATATATTCTAAAAGG
54041 TTGAATAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.31
Consensus pattern (24 bp):
AAACCATATATATATTCTAAAAGG
Found at i:56017 original size:12 final size:13
Alignment explanation
Indices: 56000--56028 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
55990 AAAAAAGTTA
56000 ATATATATATA-C
1 ATATATATATACC
56012 ATATATATATACC
1 ATATATATATACC
56025 ATAT
1 ATAT
56029 CCGTAAAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.41
Consensus pattern (13 bp):
ATATATATATACC
Found at i:59882 original size:20 final size:19
Alignment explanation
Indices: 59831--59883 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
59821 ATTATTTGCC
*
59831 TTATAAAAAATATAAATTAT
1 TTATATAAAATA-AAATTAT
* **
59851 ATATATTTAATAAAATTATT
1 TTATATAAAATAAAATTA-T
59871 TTATATAAAATAA
1 TTATATAAAATAA
59884 TTAAAATGTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TTATATAAAATAAAATTAT
Done.