Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009036.1 Kokia drynarioides strain JFW-HI SEQ_123734, 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: 109072
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Warning! 95 characters in sequence are not A, C, G, or T
Found at i:4243 original size:21 final size:21
Alignment explanation
Indices: 4217--4263 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
4207 TGAAGGTTGA
4217 AATTAATAAATCACTTATTGT
1 AATTAATAAATCACTTATTGT
4238 AATTAATAAATCACTTATTGT
1 AATTAATAAATCACTTATTGT
4259 -ATTAA
1 AATTAA
4264 CACCAAATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 5 0.19
21 21 0.81
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.43
Consensus pattern (21 bp):
AATTAATAAATCACTTATTGT
Found at i:5688 original size:14 final size:14
Alignment explanation
Indices: 5669--5699 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5659 TGCTATCATT
5669 TTACTATTATGTTA
1 TTACTATTATGTTA
*
5683 TTACTATTTTGTTA
1 TTACTATTATGTTA
5697 TTA
1 TTA
5700 ATGATTGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.61
Consensus pattern (14 bp):
TTACTATTATGTTA
Found at i:10209 original size:153 final size:152
Alignment explanation
Indices: 9927--10209 Score: 381
Period size: 153 Copynumber: 1.9 Consensus size: 152
9917 ATCAACTAAT
* * *
9927 TTACTGGCCACGTCACTTGTCTCGTTAGGCCTATAGCGAAAAATATAAATGAGTGATTGATTTGC
1 TTACTGGCCACGTCACTTGTCCCGTAAGGCCTATAACGAAAAATATAAATGAGTGATTGATTTGC
* * * *
9992 CACTTTTCCATAACGTTAGTGACTGATTTGTTATTTTTTGAAAGTTGAGTGACTGAATTGAAACT
66 CACTTTTCCATAACGTTAGTGACTGATTTGTTATTTTTCGAAAATTGAATGACTAAATTGAAACT
10057 TTATCTCATCCAACGTGGGAAG
131 TTATCTCATCCAACGTGGGAAG
* * * * *
10079 TTACTTGGCCACGTCACCTT-TCCCGTAAGGTCTATAACGGAAAATGTTAATG-GATGATTGGTT
1 TTAC-TGGCCACGTCA-CTTGTCCCGTAAGGCCTATAACGAAAAATATAAATGAG-TGATTGATT
* * * *
10142 TGTCACTTTTCGATAATGTTAGTGACTGTTTTGTTATTTTTCGAAAATTGAATGACTAAATTGAA
63 TGCCACTTTTCCATAACGTTAGTGACTGATTTGTTATTTTTCGAAAATTGAATGACTAAATTGAA
10207 ACT
128 ACT
10210 AGAGTGTTGA
Statistics
Matches: 112, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
152 5 0.04
153 104 0.93
154 3 0.03
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.37
Consensus pattern (152 bp):
TTACTGGCCACGTCACTTGTCCCGTAAGGCCTATAACGAAAAATATAAATGAGTGATTGATTTGC
CACTTTTCCATAACGTTAGTGACTGATTTGTTATTTTTCGAAAATTGAATGACTAAATTGAAACT
TTATCTCATCCAACGTGGGAAG
Found at i:34710 original size:5 final size:5
Alignment explanation
Indices: 34700--34730 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
34690 GATGAGGAGA
34700 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG A
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG A
34731 GGACGTATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:35788 original size:15 final size:15
Alignment explanation
Indices: 35765--35807 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
35755 TATTTAGTAT
* *
35765 TTAAATTTTTAATAC
1 TTAATTTTTTAATAA
*
35780 TTATTTTTTTAATAA
1 TTAATTTTTTAATAA
*
35795 TTAATATTTTAAT
1 TTAATTTTTTAAT
35808 TTATTAAACT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (15 bp):
TTAATTTTTTAATAA
Found at i:50383 original size:31 final size:31
Alignment explanation
Indices: 50346--50417 Score: 126
Period size: 31 Copynumber: 2.3 Consensus size: 31
50336 AAAATAGTAG
50346 ATGAAAGTGGAGAAAATGAGAAGAAAAAGGA
1 ATGAAAGTGGAGAAAATGAGAAGAAAAAGGA
*
50377 ATGAAAGTGGAGAAAATGAGAAGAAAAATGA
1 ATGAAAGTGGAGAAAATGAGAAGAAAAAGGA
*
50408 AGGAAAGTGG
1 ATGAAAGTGG
50418 TGAAGAAAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.56, C:0.00, G:0.33, T:0.11
Consensus pattern (31 bp):
ATGAAAGTGGAGAAAATGAGAAGAAAAAGGA
Found at i:50385 original size:170 final size:172
Alignment explanation
Indices: 50102--50448 Score: 536
Period size: 170 Copynumber: 2.0 Consensus size: 172
50092 AAATTTCCTT
** * *
50102 AGATATTAGAGAGAGAAGATGACTTAGAGATTCTAGAGAATATGTTCATCAATTTAGAAGCAAGA
1 AGATATTAGAGAGAGAAGATGAAGTAGAGATTCTAGAAAATATGTTCATAAATTTAGAAGCAAGA
* *
50167 AAATAGTAGATGAAAGTGGAGAAAATGAGAAGAAAAAGGAAGGAAAGTGGTG-A-AGAAGAGAAA
66 AAATAGTAGATGAAAGTGGAGAAAATGAGAAGAAAAAGGAAGGAAAGTGGAGAAGAGAAGAAAAA
* *
50230 TGCATGAAAATGAAGAAGAAAGGAAGAAATTCTTGACAAAGG
131 TGAAGGAAAATGAAGAAGAAAGGAAGAAATTCTTGACAAAGG
50272 AGATATTAGAGAGAGAAGATGAAGTAGAGATTCTAGAAAATATGTTCATAAATTTAGAAGCAAGA
1 AGATATTAGAGAGAGAAGATGAAGTAGAGATTCTAGAAAATATGTTCATAAATTTAGAAGCAAGA
*
50337 AAATAGTAGATGAAAGTGGAGAAAATGAGAAGAAAAAGGAATGAAAGTGGAGAAAATGAGAAGAA
66 AAATAGTAGATGAAAGTGGAGAAAATGAGAAGAAAAAGGAAGGAAAGTGGAG--AA-GAGAAGAA
* ** *
50402 AAATGAAGGAAAGTGGTGAAGAAAGGAAGAAATTCTTGATAAAGG
128 AAATGAAGGAAAATGAAGAAGAAAGGAAGAAATTCTTGACAAAGG
50447 AG
1 AG
50449 GTAAGTTTCA
Statistics
Matches: 159, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
170 111 0.70
173 1 0.01
175 47 0.30
ACGTcount: A:0.50, C:0.03, G:0.28, T:0.18
Consensus pattern (172 bp):
AGATATTAGAGAGAGAAGATGAAGTAGAGATTCTAGAAAATATGTTCATAAATTTAGAAGCAAGA
AAATAGTAGATGAAAGTGGAGAAAATGAGAAGAAAAAGGAAGGAAAGTGGAGAAGAGAAGAAAAA
TGAAGGAAAATGAAGAAGAAAGGAAGAAATTCTTGACAAAGG
Found at i:75310 original size:18 final size:18
Alignment explanation
Indices: 75287--75323 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
75277 CTAGTAGTAT
75287 TCATATATTATTAAA-AAA
1 TCATATA-TATTAAACAAA
75305 TCATATATATTAAACAAA
1 TCATATATATTAAACAAA
75323 T
1 T
75324 TAATGAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (18 bp):
TCATATATATTAAACAAA
Found at i:91277 original size:23 final size:24
Alignment explanation
Indices: 91251--91304 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
91241 ATAAAATAAT
91251 TATATTAAGAATTTTATT-AATTA
1 TATATTAAGAATTTTATTAAATTA
** *
91274 TATATTATTATTTTTATTAAATTA
1 TATATTAAGAATTTTATTAAATTA
91298 TAT-TTAA
1 TATATTAA
91305 TAATAATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 18 0.69
24 8 0.31
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
TATATTAAGAATTTTATTAAATTA
Found at i:91310 original size:61 final size:61
Alignment explanation
Indices: 91245--91368 Score: 187
Period size: 61 Copynumber: 2.0 Consensus size: 61
91235 TTTAATATAA
* * * *
91245 AATAATTATATTAAGAATTTTA-TTAATTATATATTATTATTTTTATTAAATTATATTTAAT
1 AATAATTATATTAA-AATATGACTAAATTATATATTATCATTTTTATTAAATTATATTTAAT
*
91306 AATAATTATATTAAAATATGACTAAATTATTTATTATCATTTTTATTAAATTATATTTAAT
1 AATAATTATATTAAAATATGACTAAATTATATATTATCATTTTTATTAAATTATATTTAAT
91367 AA
1 AA
91369 CAATAATAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
60 5 0.09
61 52 0.91
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (61 bp):
AATAATTATATTAAAATATGACTAAATTATATATTATCATTTTTATTAAATTATATTTAAT
Found at i:91550 original size:16 final size:16
Alignment explanation
Indices: 91526--91587 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 16
91516 TGAATTACTG
*
91526 ATTATAACTCTATTCT
1 ATTACAACTCTATTCT
* *
91542 ATTACAACTTTATTCC
1 ATTACAACTCTATTCT
*
91558 ATTACAA-TCCTATTGT
1 ATTACAACT-CTATTCT
*
91574 ATTACAATTCTATT
1 ATTACAACTCTATT
91588 TAATTTCAGT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
15 1 0.03
16 36 0.95
17 1 0.03
ACGTcount: A:0.32, C:0.19, G:0.02, T:0.47
Consensus pattern (16 bp):
ATTACAACTCTATTCT
Found at i:93996 original size:92 final size:90
Alignment explanation
Indices: 93748--94045 Score: 384
Period size: 89 Copynumber: 3.3 Consensus size: 90
93738 TATGTTTAAA
* * * * * *
93748 TTTGAATCGATTGTTACGTTGGAATACTGCTTT-TTTTGAATAAATTGTTTATATGTTTGAATCG
1 TTTGAATTGATTGTTATGGTGGAATACTGCTTTCTTTTGAATCAATTGTTTATATGTTTAAATCA
* *
93812 ATTGTCAAATTGGAATAGTGCTACT
66 ATTGTCAAATTGGAATACTGCTTCT
* *
93837 TTTGAATTGATTGTTATGGTAGAATACTAC-TTCTTTTGAATCAATTGTTTATATGTTTAAATCA
1 TTTGAATTGATTGTTATGGTGGAATACTGCTTTCTTTTGAATCAATTGTTTATATGTTTAAATCA
93901 ATTGTCAAATTGGAATACTGCTTCT
66 ATTGTCAAATTGGAATACTGCTTCT
* * *
93926 TTTGAGTTGATTGCTATTGTGGAATACTGCTTATTCTTTTGAATCAATTGTTTATATGTTTAAAT
1 TTTGAATTGATTGTTATGGTGGAATACTGC-T-TTCTTTTGAATCAATTGTTTATATGTTTAAAT
** * * *
93991 CAATTGTCATGTTGAAATATTACTTCT
64 CAATTGTCAAATTGGAATACTGCTTCT
* *
94018 TTTGAATAGGTTGTTATGGTGGAATACT
1 TTTGAATTGATTGTTATGGTGGAATACT
94046 ATTTATTATT
Statistics
Matches: 180, Mismatches: 25, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
88 2 0.01
89 101 0.56
92 77 0.43
ACGTcount: A:0.27, C:0.09, G:0.17, T:0.46
Consensus pattern (90 bp):
TTTGAATTGATTGTTATGGTGGAATACTGCTTTCTTTTGAATCAATTGTTTATATGTTTAAATCA
ATTGTCAAATTGGAATACTGCTTCT
Found at i:94032 original size:55 final size:55
Alignment explanation
Indices: 93959--94238 Score: 215
Period size: 55 Copynumber: 5.2 Consensus size: 55
93949 ATACTGCTTA
93959 TTCTTTTGAATCAATTGTTTATATGTTTAAATCAATTGTCATGTTGAAATATTAC
1 TTCTTTTGAATCAATTGTTTATATGTTTAAATCAATTGTCATGTTGAAATATTAC
* * ** * * * * * **
94014 TTCTTTTGAAT--A-GGTTGT-TATGGTGGAATACTATTTATTATTCTTTAAAT-CGA-
1 TTCTTTTGAATCAATTGTT-TATATGTTTAAAT-C-AATTGTCA-TGTTGAAATATTAC
* * * *
94067 TT-GTTT--ATTAATTGTTTATATGTTTAAATCAA-T-T-ATGGTGAAATACTGCTTC
1 TTCTTTTGAATCAATTGTTTATATGTTTAAATCAATTGTCATGTTGAAATA-T--TAC
* * * **
94119 TTCTTTTGAATCAATTGTTTATATGTTTAAATCGATTGTTATGTTGGAATACCAC
1 TTCTTTTGAATCAATTGTTTATATGTTTAAATCAATTGTCATGTTGAAATATTAC
* *
94174 TTCTTTTGAATCAATTGTTTATATGTTTAAATCAATTGTCATATTGAAATATTGC
1 TTCTTTTGAATCAATTGTTTATATGTTTAAATCAATTGTCATGTTGAAATATTAC
94229 TTCTTTTGAA
1 TTCTTTTGAA
94239 GAGATTGTTA
Statistics
Matches: 168, Mismatches: 38, Indels: 38
0.69 0.16 0.16
Matches are distributed among these distances:
47 6 0.04
48 1 0.01
49 1 0.01
50 3 0.02
51 1 0.01
52 19 0.11
53 19 0.11
54 6 0.04
55 101 0.60
56 1 0.01
57 1 0.01
58 9 0.05
ACGTcount: A:0.29, C:0.09, G:0.13, T:0.49
Consensus pattern (55 bp):
TTCTTTTGAATCAATTGTTTATATGTTTAAATCAATTGTCATGTTGAAATATTAC
Found at i:100633 original size:2 final size:2
Alignment explanation
Indices: 100628--100701 Score: 71
Period size: 2 Copynumber: 36.5 Consensus size: 2
100618 TATATATACT
* **
100628 GA GA GA GA GA GA GA GA GA GA GA GA GA CG- GA GA -A CGG GA GA TTT
1 GA GA GA GA GA GA GA GA GA GA GA GA GA -GA GA GA GA -GA GA GA -GA
*
100671 TA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
100702 GAAATGGAAG
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
1 2 0.03
2 58 0.95
3 1 0.02
ACGTcount: A:0.45, C:0.03, G:0.47, T:0.05
Consensus pattern (2 bp):
GA
Done.