Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013954.1 Kokia drynarioides strain JFW-HI SEQ_128984, 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: 16437
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Found at i:3282 original size:4 final size:4
Alignment explanation
Indices: 3273--3300 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
3263 CCATCAACAT
3273 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
3301 ACTACACACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:5482 original size:245 final size:250
Alignment explanation
Indices: 5045--5492 Score: 567
Period size: 242 Copynumber: 1.8 Consensus size: 250
5035 ATATTACATA
*
5045 ATATTATAATGTTTAATCAATGATGCATATGTATAAACTATTACCATATTATATACTATATAATA
1 ATATTATAATGTTCAATCAATGATGCATA-GTATAAACTATTA-CATATTATATACTATATAATA
*
5110 TGATATTGCATTATATAATATAGTAGGAGAGTTAACATTCAAATGTACCAAAAATATAAGAACTT
64 TGATATTGCATTATATAATATAGTAGGAGAGCTAACATTCAAATGTACCAAAAATATAAGAACTT
* *
5175 AGAATATATTTCAACCAGAATAATAACAAACAATAATAATTAATAATTAATATATAATGTACTAC
129 AGAACATATTTCAACCAGAATAATAACAAACAATAATAATTAATAATTAACATATAATGTACTAC
5240 TATTATATATAACTATTATTTTATTATAGATTATAATTAAAGATATAGTATTAAGTG
194 TATTATATATAACTATTATTTTATTATAGATTATAATTAAAGATATAGTATTAAGTG
* * *
5297 ATATTATAATGTTCAATCATTGATTCATA-TATATACTATTA-ATA-TAT-TA-TATAGT-ATAT
1 ATATTATAATGTTCAATCAATGATGCATAGTATAAACTATTACATATTATATACTATA-TAATAT
* * * * * *
5356 GATA-TG-ATGTA-ATACTATAGTAGGAG-GACTAACTTTCATATGTA-CGAAAGTATAGGAACT
65 GATATTGCAT-TATATAATATAGTAGGAGAG-CTAACATTCAAATGTACCAAAAATATAAGAACT
* * ** * * *
5416 TAGAGCATATTTTAATTAGTATAATAATAAATAATAATATATGATAATAATTAACATATAATGTA
128 TAGAACATATTTCAACCAGAATAATAACAAACAATAATA-AT--TAATAATTAACATATAATGTA
5481 CTACTATTATAT
190 CTACTATTATAT
5493 TTATAGAATA
Statistics
Matches: 170, Mismatches: 20, Indels: 19
0.81 0.10 0.09
Matches are distributed among these distances:
242 45 0.26
243 31 0.18
244 4 0.02
245 44 0.26
246 3 0.02
247 3 0.02
248 3 0.02
250 11 0.06
252 26 0.15
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.38
Consensus pattern (250 bp):
ATATTATAATGTTCAATCAATGATGCATAGTATAAACTATTACATATTATATACTATATAATATG
ATATTGCATTATATAATATAGTAGGAGAGCTAACATTCAAATGTACCAAAAATATAAGAACTTAG
AACATATTTCAACCAGAATAATAACAAACAATAATAATTAATAATTAACATATAATGTACTACTA
TTATATATAACTATTATTTTATTATAGATTATAATTAAAGATATAGTATTAAGTG
Found at i:6280 original size:23 final size:25
Alignment explanation
Indices: 6252--6297 Score: 78
Period size: 23 Copynumber: 1.9 Consensus size: 25
6242 AGACCCGTCC
6252 ATATTAATTTTA-AT-TTTTTTAAA
1 ATATTAATTTTATATATTTTTTAAA
6275 ATATTAATTTTATATATTTTTTA
1 ATATTAATTTTATATATTTTTTA
6298 TTTATTGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 12 0.57
24 2 0.10
25 7 0.33
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
ATATTAATTTTATATATTTTTTAAA
Found at i:7847 original size:33 final size:33
Alignment explanation
Indices: 7805--7873 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
7795 AGAGAAAATT
* * *
7805 TTTTTAAGCCCCTTAAAAGTTGATAAAACAAAA
1 TTTTTAAGCCCCTTAAAAGCTGAAAAAAAAAAA
**
7838 TTTTTAAGCCTTTTAAAAGCTGAAAAAAAAAAA
1 TTTTTAAGCCCCTTAAAAGCTGAAAAAAAAAAA
7871 TTT
1 TTT
7874 GAATCCCTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (33 bp):
TTTTTAAGCCCCTTAAAAGCTGAAAAAAAAAAA
Found at i:8026 original size:6 final size:6
Alignment explanation
Indices: 8004--8080 Score: 54
Period size: 6 Copynumber: 13.2 Consensus size: 6
7994 TAAACCCATT
* * * *
8004 TTTAAA TTTTAAG TTTAAA TTTAAA TTT-AT TTTGAA TTTAAA -TT-CA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
8050 TTCTAAA TTTAAA TTT-AT TTTTAA TTTAAA T
1 TT-TAAA TTTAAA TTTAAA TTTAAA TTTAAA T
8081 GTAATTAAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 11
0.72 0.13 0.14
Matches are distributed among these distances:
4 1 0.02
5 11 0.20
6 35 0.64
7 8 0.15
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:8043 original size:17 final size:17
Alignment explanation
Indices: 8017--8080 Score: 92
Period size: 17 Copynumber: 3.8 Consensus size: 17
8007 AAATTTTAAG
8017 TTTAAATTTAAATTTAT
1 TTTAAATTTAAATTTAT
* *
8034 TTTGAATTTAAATTCAT
1 TTTAAATTTAAATTTAT
*
8051 TCTAAATTTAAATTTAT
1 TTTAAATTTAAATTTAT
*
8068 TTTTAATTTAAAT
1 TTTAAATTTAAAT
8081 GTAATTAAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (17 bp):
TTTAAATTTAAATTTAT
Found at i:8722 original size:27 final size:27
Alignment explanation
Indices: 8691--8746 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
8681 TACTAAATGC
8691 TATTAAAT-GCATAATAAATAA-ATATAA
1 TATTAAATAG-ATAATAAATAATA-ATAA
8718 TATTAAATAGATAATAAATAATAATAA
1 TATTAAATAGATAATAAATAATAATAA
8745 TA
1 TA
8747 AAATTTGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 25 0.93
28 2 0.07
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.34
Consensus pattern (27 bp):
TATTAAATAGATAATAAATAATAATAA
Found at i:10152 original size:59 final size:57
Alignment explanation
Indices: 9863--10242 Score: 275
Period size: 59 Copynumber: 6.5 Consensus size: 57
9853 TTTTGTTTAA
* * *
9863 AAAATTATATTTTGACC-CTAAAC-TTCACAATAATTACATTTTAACCTCAAACTTTT-C
1 AAAATTACATTTTAACCTC-AAACTTTCA-AA-AATTACATTTTAACCTTAAACTTTTCC
* ** * *
9920 AAAATTACATTTTAACCCCTAAACTTTCCAAAAATTACATTTTAACCCTCGAAGTTTTCT
1 AAAATTACATTTTAACCTC-AAACTTT-CAAAAATTACATTTTAA-CCTTAAACTTTTCC
* * * * * *
9980 AAAATTACATTTTAACCCCAAAACATTTCCAAAATCATATTTTCACCTTAAACTTTCCC
1 AAAATTACATTTTAACCTC-AAAC-TTTCAAAAATTACATTTTAACCTTAAACTTTTCC
** * * * * **
10039 AAAATTACAATTTTTCCCTCGAA-TATCCAAAAATTACCATTTTGACCGTAAACTTTTTT
1 AAAATTAC-ATTTTAACCTCAAACT-TTCAAAAATTA-CATTTTAACCTTAAACTTTTCC
* * * * *
10098 AAAATTACATTTTAACCTCGAACTTTACAAAAATTATATTTTAACCCTTGAACTTCTCA
1 AAAATTACATTTTAACCTCAAACTTT-CAAAAATTACATTTTAA-CCTTAAACTTTTCC
* * * *
10157 AAAATCACATTTTAACCCTCAAAATTCTCTAAAATTACATTTTAACCCCTAAACTTTTCC
1 AAAATTACATTTTAA-CCTCAAACTT-TCAAAAATTACATTTTAA-CCTTAAACTTTTCC
* *
10217 AAAATCACATTTTCACC-CTAAACTTT
1 AAAATTACATTTTAACCTC-AAACTTT
10243 TTTAAAATTG
Statistics
Matches: 259, Mismatches: 49, Indels: 29
0.77 0.15 0.09
Matches are distributed among these distances:
57 16 0.06
58 48 0.19
59 97 0.37
60 94 0.36
61 4 0.02
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.37
Consensus pattern (57 bp):
AAAATTACATTTTAACCTCAAACTTTCAAAAATTACATTTTAACCTTAAACTTTTCC
Found at i:10231 original size:207 final size:206
Alignment explanation
Indices: 9894--10288 Score: 569
Period size: 207 Copynumber: 1.9 Consensus size: 206
9884 ACTTCACAAT
* *
9894 AATTACATTTTAACCTCAAACTTTTCAAAATTACATTTTAACCCCTAAACTTTCCAAAAATTACA
1 AATTACATTTTAACCTCAAACTTTACAAAATTACATTTTAACCCCTAAACTTTCCAAAAATCACA
* * * *
9959 TTTTAACCCTCGAAGTTTTCTAAAATTACATTTTAACCCCAAAACATTTCCAAAATCATATTTTC
66 TTTTAACCCTCAAAATTCTCTAAAATTACATTTTAACCCCAAAACATTTCCAAAATCACATTTTC
* *
10024 ACCTTAAACTTTCCCAAAATTACAATTTTT-CCCTCGAATATCCAAAAATTACCATTTTGACCGT
131 ACCCTAAACTTTCCCAAAATTAC-ATTTTTGCCCTCGAACATCCAAAAATTACCATTTTGACCGT
10088 AAACTTTTTTAA
195 AAACTTTTTTAA
* * * *
10100 AATTACATTTTAACCTCGAACTTTACAAAAATTATATTTTAACCCTTGAAC-TTCTCAAAAATCA
1 AATTACATTTTAACCTCAAACTTTAC-AAAATTACATTTTAACCCCTAAACTTTC-CAAAAATCA
* *
10164 CATTTTAACCCTCAAAATTCTCTAAAATTACATTTTAACCCCTAAACTTTTCCAAAATCACATTT
64 CATTTTAACCCTCAAAATTCTCTAAAATTACATTTTAACCCCAAAACATTTCCAAAATCACATTT
*** * * *
10229 TCACCCTAAACTTTTTTAAAATTGCATTTTTGCTCTTGAACATCCAAAAATTACCATTTT
129 TCACCCTAAACTTTCCCAAAATTACATTTTTGCCCTCGAACATCCAAAAATTACCATTTT
10289 ACCCTCAAAT
Statistics
Matches: 166, Mismatches: 20, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
206 33 0.20
207 133 0.80
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (206 bp):
AATTACATTTTAACCTCAAACTTTACAAAATTACATTTTAACCCCTAAACTTTCCAAAAATCACA
TTTTAACCCTCAAAATTCTCTAAAATTACATTTTAACCCCAAAACATTTCCAAAATCACATTTTC
ACCCTAAACTTTCCCAAAATTACATTTTTGCCCTCGAACATCCAAAAATTACCATTTTGACCGTA
AACTTTTTTAA
Found at i:10243 original size:29 final size:29
Alignment explanation
Indices: 9863--10258 Score: 279
Period size: 30 Copynumber: 13.4 Consensus size: 29
9853 TTTTGTTTAA
* *
9863 AAAATTATATTTTGACCCTAAAC--TTCAC
1 AAAATTACATTTTAACCCTAAACTTTTC-C
9891 AATAATTACATTTTAA-CCTCAAACTTTT-C
1 AA-AATTACATTTTAACCCT-AAACTTTTCC
9920 AAAATTACATTTTAACCCCTAAAC-TTTCC
1 AAAATTACATTTTAA-CCCTAAACTTTTCC
* * *
9949 AAAAATTACATTTTAACCCTCGAAGTTTTCT
1 -AAAATTACATTTTAACCCT-AAACTTTTCC
* *
9980 AAAATTACATTTTAACCCCAAAACATTTCC
1 AAAATTACATTTTAA-CCCTAAACTTTTCC
* * * * *
10010 AAAATCATATTTTCACCTTAAACTTTCCC
1 AAAATTACATTTTAACCCTAAACTTTTCC
* * *
10039 AAAATTACAATTTT-TCCCTCGAA--TATCC
1 AAAATTAC-ATTTTAACCCT-AAACTTTTCC
* * **
10067 AAAAATTACCATTTTGACCGTAAACTTTTTT
1 -AAAATTA-CATTTTAACCCTAAACTTTTCC
* * *
10098 AAAATTACATTTTAA-CCTCGAACTTTACA
1 AAAATTACATTTTAACCCT-AAACTTTTCC
* * * *
10127 AAAATTATATTTTAACCCTTGAACTTCTCA
1 AAAATTACATTTTAACCC-TAAACTTTTCC
* * * *
10157 AAAATCACATTTTAACCCTCAAAATTCTCT
1 AAAATTACATTTTAACCCT-AAACTTTTCC
10187 AAAATTACATTTTAACCCCTAAACTTTTCC
1 AAAATTACATTTTAA-CCCTAAACTTTTCC
* * **
10217 AAAATCACATTTTCACCCTAAACTTTTTT
1 AAAATTACATTTTAACCCTAAACTTTTCC
*
10246 AAAATTGCATTTT
1 AAAATTACATTTT
10259 TGCTCTTGAA
Statistics
Matches: 291, Mismatches: 54, Indels: 45
0.75 0.14 0.12
Matches are distributed among these distances:
28 26 0.09
29 111 0.38
30 138 0.47
31 16 0.05
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.37
Consensus pattern (29 bp):
AAAATTACATTTTAACCCTAAACTTTTCC
Found at i:10348 original size:207 final size:206
Alignment explanation
Indices: 9862--10348 Score: 563
Period size: 207 Copynumber: 2.4 Consensus size: 206
9852 GTTTTGTTTA
* *** * *
9862 AAAAATTA-TATTTTGACCCTAAACTTCACAATAATTACATTTTAACCTCAAACTTTTC-AAAAT
1 AAAAATTACCATTTTGACCCTAAACTTTTTAA-AATCACATTTTAACCTCAAACTTTACAAAAAT
* * * * *
9925 TACATTTTAACCCCTAAACTTTCCAAAAATTACATTTTAACCCTCGAAGTTTTCTAAAATTACAT
65 TAGATTTTAACCCCTAAACTTTCCAAAAATCACATTTTAACCCTCAAAATTCTCTAAAATTACAT
* *
9990 TTTAACCCCAAAACATTTCCAAAATCATATTTTCACCTTAAACTTTCCCAAAATTACAATTTTTC
130 TTTAACCCCAAAACATTTCCAAAATCACATTTTCACCCTAAACTTTCCCAAAATTACAATTTTTC
*
10055 CCTCGAATATCC
195 CCTCGAACATCC
* * *
10067 AAAAATTACCATTTTGACCGTAAACTTTTTTAAAATTACATTTTAACCTCGAACTTTACAAAAAT
1 AAAAATTACCATTTTGACCCTAAAC-TTTTTAAAATCACATTTTAACCTCAAACTTTACAAAAAT
* * *
10132 TATATTTTAACCCTTGAAC-TTCTCAAAAATCACATTTTAACCCTCAAAATTCTCTAAAATTACA
65 TAGATTTTAACCCCTAAACTTTC-CAAAAATCACATTTTAACCCTCAAAATTCTCTAAAATTACA
* * *** *
10196 TTTTAACCCCTAAACTTTTCCAAAATCACATTTTCACCCTAAACTTTTTTAAAATTGC-ATTTTT
129 TTTTAACCCCAAAACATTTCCAAAATCACATTTTCACCCTAAACTTTCCCAAAATTACAATTTTT
* *
10260 GCTCTTGAACATCC
194 -CCCTCGAACATCC
* * * *
10274 AAAAATTACCATTTT-ACCCTCAAA-TTTTTAAAAGTCACATTTTCGACTTCAAATTTTCCAAAA
1 AAAAATTACCATTTTGACCCT-AAACTTTTTAAAA-TCACATTTT-AACCTCAAACTTTACAAAA
* *
10337 GTTCGATTTTAA
63 ATTAGATTTTAA
10349 TCCCAAATCT
Statistics
Matches: 239, Mismatches: 35, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
205 17 0.07
206 59 0.25
207 163 0.68
ACGTcount: A:0.37, C:0.22, G:0.03, T:0.37
Consensus pattern (206 bp):
AAAAATTACCATTTTGACCCTAAACTTTTTAAAATCACATTTTAACCTCAAACTTTACAAAAATT
AGATTTTAACCCCTAAACTTTCCAAAAATCACATTTTAACCCTCAAAATTCTCTAAAATTACATT
TTAACCCCAAAACATTTCCAAAATCACATTTTCACCCTAAACTTTCCCAAAATTACAATTTTTCC
CTCGAACATCC
Found at i:15276 original size:34 final size:36
Alignment explanation
Indices: 15227--15298 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 36
15217 CCATACTCCC
*
15227 TTTAAATTTATTTTAAAATTAAATTT-GTTTAAAAT
1 TTTAAAATTATTTTAAAATTAAATTTAGTTTAAAAT
* *
15262 TTTAAAATT-TTTTAAATTTAAATTTATTTTAAAAT
1 TTTAAAATTATTTTAAAATTAAATTTAGTTTAAAAT
15297 TT
1 TT
15299 AAATTTAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 15 0.45
35 18 0.55
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (36 bp):
TTTAAAATTATTTTAAAATTAAATTTAGTTTAAAAT
Found at i:15299 original size:18 final size:18
Alignment explanation
Indices: 15227--15341 Score: 114
Period size: 18 Copynumber: 6.6 Consensus size: 18
15217 CCATACTCCC
15227 TTTAAATTTATTTTAAAA
1 TTTAAATTTATTTTAAAA
*
15245 -TTAAATTT-GTTTAAAA
1 TTTAAATTTATTTTAAAA
*
15261 TTTTAAAATT-TTTT-AAA
1 -TTTAAATTTATTTTAAAA
15278 TTTAAATTTATTTTAAAA
1 TTTAAATTTATTTTAAAA
* * *
15296 TTTAAATTTAATTT-GAG
1 TTTAAATTTATTTTAAAA
* *
15313 TTTAAAATTATTTTCAAA
1 TTTAAATTTATTTTAAAA
15331 TTTAAAGTTTA
1 TTTAAA-TTTA
15342 AAATAAATAA
Statistics
Matches: 79, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
16 15 0.19
17 28 0.35
18 33 0.42
19 3 0.04
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (18 bp):
TTTAAATTTATTTTAAAA
Found at i:15299 original size:24 final size:24
Alignment explanation
Indices: 15231--15321 Score: 73
Period size: 24 Copynumber: 3.7 Consensus size: 24
15221 ACTCCCTTTA
15231 AATTT-ATTTTAAAA-TTAAATTT
1 AATTTAATTTTAAAATTTAAATTT
*
15253 -GTTTAAAATTTTAAAATTTTTTAAATTT
1 AATTT--AATTTTAAAA---TTTAAATTT
15281 AAATTT-ATTTTAAAATTTAAATTT
1 -AATTTAATTTTAAAATTTAAATTT
* *
15305 AATTTGAGTTTAAAATT
1 AATTTAATTTTAAAATT
15322 ATTTTCAAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
21 3 0.05
23 5 0.09
24 28 0.50
27 9 0.16
28 8 0.14
30 3 0.05
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (24 bp):
AATTTAATTTTAAAATTTAAATTT
Found at i:15308 original size:5 final size:6
Alignment explanation
Indices: 15272--15343 Score: 51
Period size: 6 Copynumber: 12.0 Consensus size: 6
15262 TTTAAAATTT
* * *
15272 TTTAAA TTTAAA TTT-AT TTTAAAA TTTAAA TTT-AA TTTGAG TTTAAA
1 TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
15319 ATT-AT TTTCAAA TTTAAA GTTTAAA
1 TTTAAA TTT-AAA TTTAAA -TTTAAA
15344 ATAAATAAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
5 12 0.24
6 25 0.49
7 14 0.27
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:16121 original size:7 final size:7
Alignment explanation
Indices: 16099--16130 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
16089 TCGATATTAA
16099 TAATAA-
1 TAATAAT
16105 TAAT-AT
1 TAATAAT
16111 TAATAAT
1 TAATAAT
16118 TAATAAT
1 TAATAAT
16125 TAATAA
1 TAATAA
16131 AAAAACACGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
5 1 0.04
6 8 0.33
7 15 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
TAATAAT
Done.