Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001728.1 Kokia drynarioides strain JFW-HI SEQ_113430, 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: 45969
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:1058 original size:13 final size:14
Alignment explanation
Indices: 1036--1069 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
1026 TCAGTCACTT
1036 GAAAAAAAAAAG-A
1 GAAAAAAAAAAGAA
*
1049 GAAAATAAAAAGAA
1 GAAAAAAAAAAGAA
1063 GAAAAAA
1 GAAAAAA
1070 TTATATTTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (14 bp):
GAAAAAAAAAAGAA
Found at i:11997 original size:22 final size:22
Alignment explanation
Indices: 11969--12014 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
11959 CAAATAACAA
* *
11969 AAGAAAA-AAATAGCTAAAGCCT
1 AAGAAAAGAAACAACTAAA-CCT
11991 AAGAAAAGAAACAACTAAACCT
1 AAGAAAAGAAACAACTAAACCT
12013 AA
1 AA
12015 ATTACAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.63, C:0.15, G:0.11, T:0.11
Consensus pattern (22 bp):
AAGAAAAGAAACAACTAAACCT
Found at i:13890 original size:29 final size:29
Alignment explanation
Indices: 13831--13889 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
13821 TTTGGTCTAA
* *
13831 TGTGTAATTTTATACATGAATTTTAATTT
1 TGTGCAATTTTATACATGAAGTTTAATTT
*
13860 TGTGCAATTTTATACATGAAAGTTTGATTT
1 TGTGCAATTTTATACATG-AAGTTTAATTT
13890 GATTCAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.31, C:0.05, G:0.14, T:0.51
Consensus pattern (29 bp):
TGTGCAATTTTATACATGAAGTTTAATTT
Found at i:17127 original size:17 final size:17
Alignment explanation
Indices: 17105--17190 Score: 66
Period size: 17 Copynumber: 4.9 Consensus size: 17
17095 AGTCATTTTG
*
17105 AGTTTAAATTTGATTTA
1 AGTTTAAATTTAATTTA
**
17122 AGTTTAAACTTTTCTTTTAA
1 AGTTTAAA--TTTAATTT-A
* *
17142 AGCTTAAATTTAAATTA
1 AGTTTAAATTTAATTTA
*
17159 AGTTTAAATTTAAATTGA
1 AGTTTAAATTT-AATTTA
*
17177 A-TTTAAATTGAATT
1 AGTTTAAATTTAATT
17191 AAAGAAGTCC
Statistics
Matches: 55, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
16 4 0.07
17 27 0.49
18 10 0.18
19 6 0.11
20 8 0.15
ACGTcount: A:0.40, C:0.03, G:0.08, T:0.49
Consensus pattern (17 bp):
AGTTTAAATTTAATTTA
Found at i:17156 original size:6 final size:6
Alignment explanation
Indices: 17145--17185 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
17135 CTTTTAAAGC
* *
17145 TTAAAT TTAAA- TTAAGT TTAAAT TTAAA- TTGAAT TTAAAT T
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT T
17186 GAATTAAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
5 8 0.28
6 21 0.72
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (6 bp):
TTAAAT
Found at i:17186 original size:11 final size:11
Alignment explanation
Indices: 17165--17190 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
17155 ATTAAGTTTA
17165 AATTTAAATTG
1 AATTTAAATTG
17176 AATTTAAATTG
1 AATTTAAATTG
17187 AATT
1 AATT
17191 AAAGAAGTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (11 bp):
AATTTAAATTG
Found at i:17952 original size:3 final size:3
Alignment explanation
Indices: 17932--17996 Score: 78
Period size: 3 Copynumber: 21.3 Consensus size: 3
17922 AATGGCAAAT
* *
17932 ATA ATTA ATA TTA TTA ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
17977 ATA ATA ATAA ATA GTA ATA A
1 ATA ATA AT-A ATA ATA ATA A
17997 AAAAGAAAGC
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
2 2 0.04
3 47 0.85
4 6 0.11
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:19120 original size:28 final size:29
Alignment explanation
Indices: 19008--19171 Score: 134
Period size: 30 Copynumber: 5.5 Consensus size: 29
18998 AAACTATCCA
* * * *
19008 AAAATAACATTTTGACCCCTAAATTTCTCC
1 AAAATTACATTTTTACCCTTAAATTT-TCT
* * * *
19038 AAAATTATATTTTAACCCTCAAACTTTTTT
1 AAAATTACATTTTTACCCTTAAA-TTTTCT
19068 AAAATTACATTTTTACCCTTAAATTTTCT
1 AAAATTACATTTTTACCCTTAAATTTTCT
* *
19097 AAAATTCCATTTTTTA-CCTT-AATTTTCCCA
1 AAAATTACA-TTTTTACCCTTAAATTTT--CT
* * * *
19127 AAAATTATATTTTTACCCCTAAACTTTCCA
1 AAAATTACATTTTTACCCTTAAA-TTTTCT
19157 AAAATTACATTTTTA
1 AAAATTACATTTTTA
19172 GCCCCGATTT
Statistics
Matches: 109, Mismatches: 18, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
28 6 0.06
29 23 0.21
30 72 0.66
31 5 0.05
32 3 0.03
ACGTcount: A:0.36, C:0.20, G:0.01, T:0.43
Consensus pattern (29 bp):
AAAATTACATTTTTACCCTTAAATTTTCT
Found at i:19217 original size:89 final size:85
Alignment explanation
Indices: 19015--19286 Score: 207
Period size: 89 Copynumber: 3.1 Consensus size: 85
19005 CCAAAAATAA
* ***
19015 CATTTTGACCCCTAAATTTCTCCAAAATTATA-TTTTAACCCTCAAACTTTTTTAAAATTACATT
1 CATTTT-ACCCCTAAA-TT-TCCAAAATTATATTTTTACCCCT-AAACTTTCCAAAAATTACATT
19079 TTTACCCTTAAATTTTCTAAAATTC
62 TTTACCC-TAAATTTTCTAAAATTC
* *
19104 CATTTTTTA-CCTTAATTTTCCCAAAAATTATATTTTTACCCCTAAACTTTCCAAAAATTACATT
1 CA--TTTTACCCCTAAATTT-CC-AAAATTATATTTTTACCCCTAAACTTTCCAAAAATTACATT
**
19168 TTTAGCCC-CGATTTTACTAAAATTCC
62 TTTA-CCCTAAATTTT-CTAAAATT-C
* *
19194 CATTTTACCCCCAAACTTTCCAAAATTCTATTTTTGACCCC--AA-TTTCACCAAAAATTACCA-
1 CATTTTACCCCTAAA-TTTCCAAAATTATATTTTT-ACCCCTAAACTTT--CCAAAAATTA-CAT
* * * *
19255 TTTTACCCTCGAACTTCCTAAAATTT
61 TTTTACCCT-AAATTTTCTAAAATTC
19281 CATTTT
1 CATTTT
19287 TGACCACAAT
Statistics
Matches: 150, Mismatches: 17, Indels: 34
0.75 0.08 0.17
Matches are distributed among these distances:
86 3 0.02
87 12 0.08
88 50 0.33
89 62 0.41
90 19 0.13
91 4 0.03
ACGTcount: A:0.32, C:0.25, G:0.02, T:0.41
Consensus pattern (85 bp):
CATTTTACCCCTAAATTTCCAAAATTATATTTTTACCCCTAAACTTTCCAAAAATTACATTTTTA
CCCTAAATTTTCTAAAATTC
Found at i:19249 original size:59 final size:59
Alignment explanation
Indices: 19097--19298 Score: 173
Period size: 59 Copynumber: 3.4 Consensus size: 59
19087 TAAATTTTCT
* * ** * * *
19097 AAAATTCCATTTTTTACCTTAATTTTCCCAAAAATTA-TATTTTTACCCCTAAACTTTCCA
1 AAAATTCTATTTTTGACCCCAA-TTTCACAAAAATTACCA-TTTTACCCCCAAACTTTCCA
* * * *
19157 AAAATTAC-ATTTTT-AGCCCCGATTTTACTAAAATTCCCATTTTACCCCCAAACTTTCC-
1 AAAATT-CTATTTTTGA-CCCCAATTTCACAAAAATTACCATTTTACCCCCAAACTTTCCA
* * *
19215 AAAATTCTATTTTTGACCCCAATTTCACCAAAAATTACCATTTTACCCTCGAAC-TTCCT
1 AAAATTCTATTTTTGACCCCAATTTCA-CAAAAATTACCATTTTACCCCCAAACTTTCCA
*
19274 AAAATT-TCATTTTTGACCACAATTT
1 AAAATTCT-ATTTTTGACCCCAATTT
19299 TTTTCCAAAA
Statistics
Matches: 118, Mismatches: 16, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
57 1 0.01
58 26 0.22
59 74 0.63
60 16 0.14
61 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.02, T:0.39
Consensus pattern (59 bp):
AAAATTCTATTTTTGACCCCAATTTCACAAAAATTACCATTTTACCCCCAAACTTTCCA
Found at i:19262 original size:29 final size:30
Alignment explanation
Indices: 19124--19262 Score: 82
Period size: 30 Copynumber: 4.7 Consensus size: 30
19114 CTTAATTTTC
* *
19124 CCAAAAATTA-TATTTTTACCCCTAAACTTT-
1 CCAAAAATTACCATTTTTACCCC-CAA-TTTA
* *
19154 CCAAAAATTA-CATTTTTAGCCCCGATTTTA
1 CCAAAAATTACCATTTTTA-CCCCCAATTTA
* *
19184 -CTAAAATTCCCA-TTTTACCCCCAAACTTT-
1 CCAAAAATTACCATTTTTACCCCC-AA-TTTA
*
19213 CC-AAAATT-CTATTTTTGA-CCCCAATTTCA
1 CCAAAAATTACCATTTTT-ACCCCCAATTT-A
19242 CCAAAAATTACCA-TTTTACCC
1 CCAAAAATTACCATTTTTACCC
19263 TCGAACTTCC
Statistics
Matches: 87, Mismatches: 9, Indels: 26
0.71 0.07 0.21
Matches are distributed among these distances:
27 3 0.03
28 8 0.09
29 33 0.38
30 37 0.43
31 6 0.07
ACGTcount: A:0.34, C:0.28, G:0.02, T:0.36
Consensus pattern (30 bp):
CCAAAAATTACCATTTTTACCCCCAATTTA
Found at i:20377 original size:29 final size:29
Alignment explanation
Indices: 20343--20400 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
20333 TTTATTGATA
20343 AAATGAAATGATTTTAAGTTCATTAACTC
1 AAATGAAATGATTTTAAGTTCATTAACTC
20372 AAATGAAATGATTTTAAGTTCATTAACTC
1 AAATGAAATGATTTTAAGTTCATTAACTC
20401 CATGATTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.38
Consensus pattern (29 bp):
AAATGAAATGATTTTAAGTTCATTAACTC
Found at i:21281 original size:104 final size:104
Alignment explanation
Indices: 21156--21664 Score: 684
Period size: 104 Copynumber: 4.9 Consensus size: 104
21146 ATGCACAATC
* * *
21156 TTTGAGGTAAGGAAATCAAGTAATTGATAAATATATCATCTAAATGATAGGATTTCAAGAAACAT
1 TTTGAGATAAGGAAAACAAGTAATTGATAAATACATCATCTAAATGATAGGATTTCAAGAAACAT
* * * * *
21221 TTAAATTAGTACTTTTTGTTAAATTTTTTATATGTATCT
66 TTCAATTAGTACATTTTGTTAAAATTTTGATATGTACCT
* * * *
21260 TTTGAGATAAGGAAAACAAGTAATTGATAAATATATCAGCTAAATGATAAGACTTCAAGAAACAT
1 TTTGAGATAAGGAAAACAAGTAATTGATAAATACATCATCTAAATGATAGGATTTCAAGAAACAT
* * * *
21325 TTAAATTACTACTTTTTCTTAAAATTTTGATATGTACCT
66 TTCAATTAGTACATTTTGTTAAAATTTTGATATGTACCT
* * *
21364 TTTGA-AGTAAGGAAATCAAGTAGTTGATAAATACATCGTCTAAATGATAGGATTTCAAGAAACA
1 TTTGAGA-TAAGGAAAACAAGTAATTGATAAATACATCATCTAAATGATAGGATTTCAAGAAACA
* *
21428 TTTCAATTAGTGCATTTTGTTAAAATTTTGGTATGTACCT
65 TTTCAATTAGTACATTTTGTTAAAATTTTGATATGTACCT
* * * * *
21468 TTTGAGGTAAGGAAAGCAAGTAGCTT-ATAAATACATCGTCTAAATGATAAGATTTCAAGAAACA
1 TTTGAGATAAGGAAAACAAGTA-ATTGATAAATACATCATCTAAATGATAGGATTTCAAGAAACA
21532 TTTCAATTAGGT-CATTTTGTTAAAATTTTGATATGTACCT
65 TTTCAATTA-GTACATTTTGTTAAAATTTTGATATGTACCT
* **
21572 TTTGAGCTAAGGAAAACAAGTAGCTGATAAATACATCATCTAAATGATAGGACTTT-AAGAAACA
1 TTTGAGATAAGGAAAACAAGTAATTGATAAATACATCATCTAAATGATAGGA-TTTCAAGAAACA
*
21636 TTTCAATTAGTGCATTTTGTTAAAATTTT
65 TTTCAATTAGTACATTTTGTTAAAATTTT
21665 TACTTCTTGT
Statistics
Matches: 364, Mismatches: 34, Indels: 14
0.88 0.08 0.03
Matches are distributed among these distances:
103 4 0.01
104 353 0.97
105 7 0.02
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.37
Consensus pattern (104 bp):
TTTGAGATAAGGAAAACAAGTAATTGATAAATACATCATCTAAATGATAGGATTTCAAGAAACAT
TTCAATTAGTACATTTTGTTAAAATTTTGATATGTACCT
Found at i:30777 original size:27 final size:25
Alignment explanation
Indices: 30726--30781 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
30716 TAACTCCGAA
* *
30726 TTTTTATTTTTTTTGTTTTATATGT
1 TTTTTATTTTTTTTGTATTACATGT
30751 GTTTTTATTGTTTTTT-TCATTACATGT
1 -TTTTTATT-TTTTTTGT-ATTACATGT
30778 TTTT
1 TTTT
30782 GTTTGCATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 13 0.50
27 13 0.50
ACGTcount: A:0.12, C:0.04, G:0.09, T:0.75
Consensus pattern (25 bp):
TTTTTATTTTTTTTGTATTACATGT
Found at i:31359 original size:27 final size:28
Alignment explanation
Indices: 31321--31373 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
31311 GTATGAGTGC
* *
31321 TTAAAGAGAAAA-AAAAAGAAAAAAATG
1 TTAAAAAGAAAAGAAAAACAAAAAAATG
*
31348 TTAAAAAGAAAAGAAATACAAAAAAA
1 TTAAAAAGAAAAGAAAAACAAAAAAA
31374 GAATATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 11 0.50
28 11 0.50
ACGTcount: A:0.75, C:0.02, G:0.11, T:0.11
Consensus pattern (28 bp):
TTAAAAAGAAAAGAAAAACAAAAAAATG
Found at i:34589 original size:22 final size:23
Alignment explanation
Indices: 34539--34618 Score: 83
Period size: 24 Copynumber: 3.4 Consensus size: 23
34529 TACTTTAGTT
*
34539 GAATGCTCTAAGTGAGCAAGGGTC
1 GAATGCCCTAA-TGAGCAAGGGTC
* *
34563 AAATGCCCTAAT-AGTC-ATGGTC
1 GAATGCCCTAATGAG-CAAGGGTC
*
34585 GAATGCTCTAAATGAGCAAGGGTC
1 GAATGCCCT-AATGAGCAAGGGTC
34609 GAATGCCCTA
1 GAATGCCCTA
34619 GATTGGTTTG
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
22 14 0.31
23 7 0.16
24 24 0.53
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (23 bp):
GAATGCCCTAATGAGCAAGGGTC
Found at i:36169 original size:12 final size:13
Alignment explanation
Indices: 36136--36170 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
36126 ACTTTGTTTT
36136 TATTTAGGATTAA
1 TATTTAGGATTAA
*
36149 TATTTAGGATTAT
1 TATTTAGGATTAA
36162 TA-TTAGGAT
1 TATTTAGGAT
36171 ATTGTTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 7 0.33
13 14 0.67
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (13 bp):
TATTTAGGATTAA
Found at i:36193 original size:13 final size:12
Alignment explanation
Indices: 36175--36208 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
36165 TAGGATATTG
36175 TTTATATTTAAAA
1 TTTATATTT-AAA
36188 TTTATATTT-AA
1 TTTATATTTAAA
36199 TTTATATTTA
1 TTTATATTTA
36209 TCTTTTAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 11 0.55
13 9 0.45
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTATATTTAAA
Found at i:36292 original size:60 final size:61
Alignment explanation
Indices: 36188--36301 Score: 169
Period size: 60 Copynumber: 1.9 Consensus size: 61
36178 ATATTTAAAA
* * *
36188 TTTATATTTAATTTATATTTATCTTTTAGAGTTTAATTTAGATTCAATTAGGGAATTAATG
1 TTTAGATTTAATTTATAATTATCTTTTAGAATTTAATTTAGATTCAATTAGGGAATTAATG
*
36249 TTTAGATTTAATTT-TAATTATCTTTTAGAATTTAGA-TTGGATTCAATTAGGGA
1 TTTAGATTTAATTTATAATTATCTTTTAGAATTTA-ATTTAGATTCAATTAGGGA
36302 TTTCTATGTA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
60 34 0.71
61 14 0.29
ACGTcount: A:0.32, C:0.04, G:0.13, T:0.51
Consensus pattern (61 bp):
TTTAGATTTAATTTATAATTATCTTTTAGAATTTAATTTAGATTCAATTAGGGAATTAATG
Found at i:41589 original size:17 final size:17
Alignment explanation
Indices: 41567--41613 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 17
41557 ATTCTCAAAA
41567 AAAATTAATATTTAAAT
1 AAAATTAATATTTAAAT
* * *
41584 AAAATTATTAATATAATT
1 AAAATTAAT-ATTTAAAT
41602 AAAATT-ATATTT
1 AAAATTAATATTT
41614 GTTTATAATA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
16 3 0.12
17 9 0.38
18 12 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAAATTAATATTTAAAT
Found at i:41951 original size:17 final size:17
Alignment explanation
Indices: 41926--41961 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
41916 TTCTAACGAG
*
41926 TTAATATTTAAAAAATT
1 TTAAAATTTAAAAAATT
*
41943 TTAAAATTTAAATAATT
1 TTAAAATTTAAAAAATT
41960 TT
1 TT
41962 TTATAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAAAATTTAAAAAATT
Found at i:45953 original size:14 final size:14
Alignment explanation
Indices: 45934--45961 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
45924 TATATTAGTA
45934 TTTTCTATTCTATT
1 TTTTCTATTCTATT
45948 TTTTCTATTCTATT
1 TTTTCTATTCTATT
45962 AGTATTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTCTATTCTATT
Done.