Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013939.1 Kokia drynarioides strain JFW-HI SEQ_128969, 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: 28205
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:784 original size:26 final size:22
Alignment explanation
Indices: 755--801 Score: 58
Period size: 26 Copynumber: 2.0 Consensus size: 22
745 TCCTTTACTT
755 TTTTAACGATAAAAATAAATAAAAAC
1 TTTTAAC-A-AAAAA-AAA-AAAAAC
781 TTTTAACAAAAAAAAAAAAAA
1 TTTTAACAAAAAAAAAAAAAA
802 TTTATTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 5 0.24
23 3 0.14
24 5 0.24
25 1 0.05
26 7 0.33
ACGTcount: A:0.68, C:0.06, G:0.02, T:0.23
Consensus pattern (22 bp):
TTTTAACAAAAAAAAAAAAAAC
Found at i:807 original size:92 final size:92
Alignment explanation
Indices: 665--850 Score: 363
Period size: 92 Copynumber: 2.0 Consensus size: 92
655 AAATCAATTC
665 TTAACGATAAAAATAAATAAAAACTTTTAACAAAAAAAAAAAAAAATTATTCTTTGATCTAACGT
1 TTAACGATAAAAATAAATAAAAACTTTTAACAAAAAAAAAAAAAAATTATTCTTTGATCTAACGT
730 ATAGAGATTAAAAACTCCTTTACTTTT
66 ATAGAGATTAAAAACTCCTTTACTTTT
*
757 TTAACGATAAAAATAAATAAAAACTTTTAACAAAAAAAAAAAAAATTTATTCTTTGATCTAACGT
1 TTAACGATAAAAATAAATAAAAACTTTTAACAAAAAAAAAAAAAAATTATTCTTTGATCTAACGT
822 ATAGAGATTAAAAACTCCTTTACTTTT
66 ATAGAGATTAAAAACTCCTTTACTTTT
849 TT
1 TT
851 TTTATAAATA
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 93 1.00
ACGTcount: A:0.50, C:0.11, G:0.05, T:0.34
Consensus pattern (92 bp):
TTAACGATAAAAATAAATAAAAACTTTTAACAAAAAAAAAAAAAAATTATTCTTTGATCTAACGT
ATAGAGATTAAAAACTCCTTTACTTTT
Found at i:7809 original size:54 final size:53
Alignment explanation
Indices: 7751--7857 Score: 196
Period size: 54 Copynumber: 2.0 Consensus size: 53
7741 ATTTTGATCC
*
7751 AAAAAAAAAGAAAAAAAGAAATCAAACAAAATTCGAGACGAGAAAGAGTGAGA
1 AAAAAAAAAAAAAAAAAGAAATCAAACAAAATTCGAGACGAGAAAGAGTGAGA
7804 NAAAAAAAAAAAAAAAAAGAAATCAAACAAAATTCGAGACGAGAAAGAGTGAGA
1 -AAAAAAAAAAAAAAAAAGAAATCAAACAAAATTCGAGACGAGAAAGAGTGAGA
7858 GTTGAAGTAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.66, C:0.07, G:0.18, T:0.07
Consensus pattern (53 bp):
AAAAAAAAAAAAAAAAAGAAATCAAACAAAATTCGAGACGAGAAAGAGTGAGA
Found at i:9494 original size:31 final size:32
Alignment explanation
Indices: 9458--9562 Score: 185
Period size: 32 Copynumber: 3.3 Consensus size: 32
9448 TTTCATTTCA
9458 CAACAAGTCAC-AGAAAAACCATATTTCGTCG
1 CAACAAGTCACAAGAAAAACCATATTTCGTCG
9489 CAACAAGTCACAAGAAAAACCATATTTCGTCG
1 CAACAAGTCACAAGAAAAACCATATTTCGTCG
* *
9521 CAACAAGTCACGAGAAAAACCGTATTTCGTCG
1 CAACAAGTCACAAGAAAAACCATATTTCGTCG
9553 CAACAAGTCA
1 CAACAAGTCA
9563 AAAGCCAACA
Statistics
Matches: 71, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
31 11 0.15
32 60 0.85
ACGTcount: A:0.42, C:0.26, G:0.14, T:0.18
Consensus pattern (32 bp):
CAACAAGTCACAAGAAAAACCATATTTCGTCG
Found at i:11021 original size:30 final size:30
Alignment explanation
Indices: 10985--11043 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
10975 TGACAAAATC
10985 ATTTAGTCACTATATAAATTCATTGGAACG
1 ATTTAGTCACTATATAAATTCATTGGAACG
11015 ATTTAGTCACTATATAAATTCATTGGAAC
1 ATTTAGTCACTATATAAATTCATTGGAAC
11044 TACGTTTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (30 bp):
ATTTAGTCACTATATAAATTCATTGGAACG
Found at i:15416 original size:11 final size:10
Alignment explanation
Indices: 15400--15464 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 10
15390 TCGTTAGTTT
15400 TATTTTGTATG
1 TATTTT-TATG
15411 TATTTTTATG
1 TATTTTTATG
15421 ATATTATTATTAT-
1 -TA-T-TT-TTATG
15434 TATTTTGTATG
1 TATTTT-TATG
15445 TATTTTTATG
1 TATTTTTATG
*
15455 ATATTATTAT
1 -TATTTTTAT
15465 CATTTGTCAT
Statistics
Matches: 46, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
9 1 0.02
10 13 0.28
11 23 0.50
12 3 0.07
13 2 0.04
14 4 0.09
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (10 bp):
TATTTTTATG
Found at i:15419 original size:17 final size:17
Alignment explanation
Indices: 15397--15453 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
15387 TACTCGTTAG
15397 TTTTATTTTGTATGTAT
1 TTTTATTTTGTATGTAT
*
15414 TTTTATGATAT-TAT-TAT
1 TTTTAT--TTTGTATGTAT
*
15431 TATTATTTTGTATGTAT
1 TTTTATTTTGTATGTAT
15448 TTTTAT
1 TTTTAT
15454 GATATTATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
15 2 0.06
16 3 0.09
17 22 0.69
18 3 0.09
19 2 0.06
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.68
Consensus pattern (17 bp):
TTTTATTTTGTATGTAT
Found at i:15439 original size:34 final size:34
Alignment explanation
Indices: 15399--15464 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
15389 CTCGTTAGTT
15399 TTATTTTGTATGTATTTTTATGATATTATTATTA
1 TTATTTTGTATGTATTTTTATGATATTATTATTA
15433 TTATTTTGTATGTATTTTTATGATATTATTAT
1 TTATTTTGTATGTATTTTTATGATATTATTAT
15465 CATTTGTCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (34 bp):
TTATTTTGTATGTATTTTTATGATATTATTATTA
Found at i:18210 original size:16 final size:17
Alignment explanation
Indices: 18178--18210 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
18168 CAAAAATGAC
*
18178 TTCAAACTTTGAAATAA
1 TTCAAACTTTAAAATAA
18195 TTCAAAC-TTAAAATAA
1 TTCAAACTTTAAAATAA
18211 ATGTTTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.52, C:0.12, G:0.03, T:0.33
Consensus pattern (17 bp):
TTCAAACTTTAAAATAA
Found at i:19492 original size:61 final size:58
Alignment explanation
Indices: 19387--19519 Score: 185
Period size: 61 Copynumber: 2.2 Consensus size: 58
19377 TACACTAGTA
* *
19387 GTCACCCAACTATTAGTGAATTCTTTTTTGGTCACCCAATTATGAAAAGTTAAAAAATG
1 GTCA-CCAACTATTAGTAAATTCTTTTTTGGTCACCCAACTATGAAAAGTTAAAAAATG
* * *
19446 GTCACCTAACTATTAGTAAATTTATTTTTTTGGTCACCCAACTATGAAAAGTTACAAAATT
1 GTCACC-AACTATTAGTAAA-TT-CTTTTTTGGTCACCCAACTATGAAAAGTTAAAAAATG
19507 GTCACCAACTATT
1 GTCACCAACTATT
19520 CAATTTTGTC
Statistics
Matches: 66, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
58 2 0.03
59 16 0.24
60 9 0.14
61 39 0.59
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.35
Consensus pattern (58 bp):
GTCACCAACTATTAGTAAATTCTTTTTTGGTCACCCAACTATGAAAAGTTAAAAAATG
Found at i:26922 original size:17 final size:17
Alignment explanation
Indices: 26900--26938 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
26890 CTCCACCTTG
* *
26900 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCGACGA
26917 ACAAGAACTCTCGACGA
1 ACAAGAACTCTCGACGA
26934 ACAAG
1 ACAAG
26939 TTCTCCACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.44, C:0.26, G:0.15, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCGACGA
Done.