Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003674.1 Kokia drynarioides strain JFW-HI SEQ_116596, 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: 48667
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Found at i:2437 original size:80 final size:80
Alignment explanation
Indices: 2235--2522 Score: 281
Period size: 80 Copynumber: 3.5 Consensus size: 80
2225 AGTTTAACTG
* * * * * * *
2235 ACTAGAGCTGGACTCATTTTTGCGGTTTATCCGCTAGGCACTAGGTGCTAGGATTTGACGGATAT
1 ACTAGAGCTGGGCTCACTTTTGCGGTTTATCCACTAGGCACTGGGTGCTAAGATTTGACGAACAT
* *
2300 TTGTTGGTTAATTCA
66 TTGTTAGTTAATCCA
* *
2315 ACTAGAGCTGAGCTCACTTTTACGGTTTATCCACTAGGCACTGGGTGCTAAGATTTGACGAACAT
1 ACTAGAGCTGGGCTCACTTTTGCGGTTTATCCACTAGGCACTGGGTGCTAAGATTTGACGAACAT
2380 TTGTTAGTTAATCCA
66 TTGTTAGTTAATCCA
* * * * *
2395 ACTAGAGTTGGGCTCACTTTTGCGATTTATTCATTAGGCACTGTGTGCGCACTGGGTGCCAGGAT
1 ACTAGAGCTGGGCTCACTTTTGCGGTTTA-TC------CAC--T-AG-GCACTGGGTGCTAAGAT
* * * *
2460 TTTACGGATATTTGCTAGTTAA-CCA
55 TTGACGAACATTTGTTAGTTAATCCA
*
2485 ACTAGAGCTGGGCTCACTTTTGCGGTTTATCCGCTAGG
1 ACTAGAGCTGGGCTCACTTTTGCGGTTTATCCACTAGG
2523 GTGTCAGGAT
Statistics
Matches: 171, Mismatches: 26, Indels: 23
0.78 0.12 0.10
Matches are distributed among these distances:
79 1 0.01
80 95 0.56
81 3 0.02
83 2 0.01
87 3 0.02
89 3 0.02
90 31 0.18
91 33 0.19
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (80 bp):
ACTAGAGCTGGGCTCACTTTTGCGGTTTATCCACTAGGCACTGGGTGCTAAGATTTGACGAACAT
TTGTTAGTTAATCCA
Found at i:6231 original size:31 final size:31
Alignment explanation
Indices: 6188--6250 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
6178 AAGGGGGTTT
6188 AGCCCTTCAAAAATTTGAAAAATTATAATTA
1 AGCCCTTCAAAAATTTGAAAAATTATAATTA
* * *
6219 AGCCTTTCAAAAATTTTAAAAATTTTAATTA
1 AGCCCTTCAAAAATTTGAAAAATTATAATTA
6250 A
1 A
6251 ACCTCCAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.37
Consensus pattern (31 bp):
AGCCCTTCAAAAATTTGAAAAATTATAATTA
Found at i:7504 original size:104 final size:104
Alignment explanation
Indices: 7324--7532 Score: 373
Period size: 104 Copynumber: 2.0 Consensus size: 104
7314 AAAAGGGACT
*
7324 GGATTTGCATAGCTTTAAATCCAAATGTCGGATGTGCAATCACCACCTGGATATCTCATCTCATG
1 GGATTTGCATAGCTTTAAATCCAAATGTCGGAAGTGCAATCACCACCTGGATATCTCATCTCATG
*
7389 TGCGACGGAGGGACCATCTGGTTCTGCTCCGAAGTCCAC
66 TGCGACGGAGGGACCATCTGGTTCTGCTCCAAAGTCCAC
* *
7428 GGATTTGCATTGCTTTAAATCCAAATGTCTGAAGTGCAATCACCACCTGGATATCTCATCTCATG
1 GGATTTGCATAGCTTTAAATCCAAATGTCGGAAGTGCAATCACCACCTGGATATCTCATCTCATG
*
7493 TGCGAGGGAGGGACCATCTGGTTCTGCTCCAAAGTCCAC
66 TGCGACGGAGGGACCATCTGGTTCTGCTCCAAAGTCCAC
7532 G
1 G
7533 AAAAAGTTGG
Statistics
Matches: 100, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
104 100 1.00
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.27
Consensus pattern (104 bp):
GGATTTGCATAGCTTTAAATCCAAATGTCGGAAGTGCAATCACCACCTGGATATCTCATCTCATG
TGCGACGGAGGGACCATCTGGTTCTGCTCCAAAGTCCAC
Found at i:14702 original size:18 final size:18
Alignment explanation
Indices: 14679--14713 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
14669 ACGATGTGCC
14679 AAACTATTTTGGTACTTG
1 AAACTATTTTGGTACTTG
14697 AAACTATTTTGGTACTT
1 AAACTATTTTGGTACTT
14714 CCTGTTCTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (18 bp):
AAACTATTTTGGTACTTG
Found at i:19284 original size:20 final size:20
Alignment explanation
Indices: 19259--19299 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
19249 AAAGATTATT
19259 TAATAATTATAAGATGACAA
1 TAATAATTATAAGATGACAA
*
19279 TAATAATTATAGGATGACAA
1 TAATAATTATAAGATGACAA
19299 T
1 T
19300 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.51, C:0.05, G:0.12, T:0.32
Consensus pattern (20 bp):
TAATAATTATAAGATGACAA
Found at i:24905 original size:21 final size:21
Alignment explanation
Indices: 24865--24905 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
24855 GAAAGAAAAT
* * *
24865 TAGAAAGATAGAAGTTTAAAG
1 TAGAAAGACAGAAATATAAAG
24886 TAGAAAGACAGAAATATAAA
1 TAGAAAGACAGAAATATAAA
24906 TTTTCTTTTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.59, C:0.02, G:0.20, T:0.20
Consensus pattern (21 bp):
TAGAAAGACAGAAATATAAAG
Found at i:30499 original size:53 final size:53
Alignment explanation
Indices: 30419--30552 Score: 223
Period size: 53 Copynumber: 2.5 Consensus size: 53
30409 AGTATTTCAT
*
30419 TCTATTTACAGTAAGGACCATTTGACAGTTATATGAATATTGTTGAAGCAAAA
1 TCTATTTACAGTAAGGACCATTTGACAGTTATATGAATATTATTGAAGCAAAA
* *
30472 TCTATATACAGTAAGGACAATTTGACAGTTATATGAATATTATTGAAGCAAAA
1 TCTATTTACAGTAAGGACCATTTGACAGTTATATGAATATTATTGAAGCAAAA
* *
30525 TCTATTTGCAGTAAGAACCATTTGACAG
1 TCTATTTACAGTAAGGACCATTTGACAG
30553 GCTGACACTC
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 74 1.00
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (53 bp):
TCTATTTACAGTAAGGACCATTTGACAGTTATATGAATATTATTGAAGCAAAA
Found at i:31837 original size:13 final size:12
Alignment explanation
Indices: 31792--31845 Score: 53
Period size: 12 Copynumber: 4.7 Consensus size: 12
31782 AATTTATTAT
31792 TAAATATT--TA
1 TAAATATTAATA
31802 TAAAT-TATAATA
1 TAAATAT-TAATA
*
31814 TATAT-TTAATA
1 TAAATATTAATA
31825 TTAAATATTAATA
1 -TAAATATTAATA
31838 TAAATATT
1 TAAATATT
31846 TTCAATAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
9 1 0.03
10 6 0.16
11 5 0.14
12 19 0.51
13 6 0.16
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TAAATATTAATA
Found at i:31838 original size:20 final size:22
Alignment explanation
Indices: 31781--31838 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 22
31771 TATACTATAA
*
31781 AAATT-TATTATTAAATATTTAT
1 AAATTATAATATT-AATATTTAT
31803 AAATTATAATA-T-ATATTTA-
1 AAATTATAATATTAATATTTAT
*
31822 ATATTA-AATATTAATAT
1 AAATTATAATATTAATAT
31839 AAATATTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 4 0.13
19 6 0.19
20 11 0.35
22 6 0.19
23 4 0.13
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AAATTATAATATTAATATTTAT
Found at i:32589 original size:2 final size:2
Alignment explanation
Indices: 32582--32614 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
32572 CATCTTATGC
32582 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
32615 CTACATTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34880 original size:84 final size:84
Alignment explanation
Indices: 34739--34893 Score: 301
Period size: 84 Copynumber: 1.8 Consensus size: 84
34729 TTTATCTGCA
34739 AACCAGAATTCAATGAAGAGAAGACTAAAGGTTTCAATCATTCAATGGACGAATTTGATGGAGCA
1 AACCAGAATTCAATGAAGAGAAGACTAAAGGTTTCAATCATTCAATGGACGAATTTGATGGAGCA
34804 TTCAAGACGGAAGCTGGAC
66 TTCAAGACGGAAGCTGGAC
*
34823 AACCAGAATTCAATGAAGAGAAGACTAAAGGTTTCGATCATTCAATGGACGAATTTGATGGAGCA
1 AACCAGAATTCAATGAAGAGAAGACTAAAGGTTTCAATCATTCAATGGACGAATTTGATGGAGCA
34888 TTCAAG
66 TTCAAG
34894 TTGAACATAA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 70 1.00
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.23
Consensus pattern (84 bp):
AACCAGAATTCAATGAAGAGAAGACTAAAGGTTTCAATCATTCAATGGACGAATTTGATGGAGCA
TTCAAGACGGAAGCTGGAC
Found at i:35384 original size:23 final size:21
Alignment explanation
Indices: 35341--35385 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
35331 ATTTGATTGT
* *
35341 ACGTTCATGGATATTTGTTTA
1 ACGTTCATGAATATTTATTTA
35362 ACGTTCATGAATAAATTTATTTA
1 ACGTTCATGAAT--ATTTATTTA
35385 A
1 A
35386 TTTAAGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 11 0.55
23 9 0.45
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.44
Consensus pattern (21 bp):
ACGTTCATGAATATTTATTTA
Found at i:36544 original size:13 final size:13
Alignment explanation
Indices: 36518--36562 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
36508 TTTTAATAAA
* *
36518 CAATTAATAGAAT
1 CAATTGATAAAAT
*
36531 CAATTGATCAAAT
1 CAATTGATAAAAT
*
36544 CAATTAATAAAAT
1 CAATTGATAAAAT
36557 CAATTG
1 CAATTG
36563 GTGAAACCAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.31
Consensus pattern (13 bp):
CAATTGATAAAAT
Found at i:36573 original size:26 final size:26
Alignment explanation
Indices: 36518--36573 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
36508 TTTTAATAAA
* *
36518 CAATTAATAGAATCAATTGATCAAAT
1 CAATTAATAAAATCAATTGATCAAAC
* *
36544 CAATTAATAAAATCAATTGGTGAAAC
1 CAATTAATAAAATCAATTGATCAAAC
36570 CAAT
1 CAAT
36574 CACCGCAATC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.50, C:0.12, G:0.09, T:0.29
Consensus pattern (26 bp):
CAATTAATAAAATCAATTGATCAAAC
Found at i:37577 original size:30 final size:31
Alignment explanation
Indices: 37536--37606 Score: 101
Period size: 30 Copynumber: 2.3 Consensus size: 31
37526 TTTTTTGGAA
*
37536 TTTTTAAAAATGTTTTTAAAATTCT-T-GAT
1 TTTTTAAAAATGTTTATAAAATTCTATAGAT
*
37565 TTTTTGAAAAATGTTTATAAAATTTTATAGAT
1 TTTTT-AAAAATGTTTATAAAATTCTATAGAT
37597 TTTTTAAAAA
1 TTTTTAAAAA
37607 AATTATAACT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
29 5 0.14
30 18 0.49
31 6 0.16
32 8 0.22
ACGTcount: A:0.39, C:0.01, G:0.07, T:0.52
Consensus pattern (31 bp):
TTTTTAAAAATGTTTATAAAATTCTATAGAT
Done.