Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011716.1 Kokia drynarioides strain JFW-HI SEQ_126710, 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: 104126
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 16 characters in sequence are not A, C, G, or T
Found at i:197 original size:10 final size:10
Alignment explanation
Indices: 182--212 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
172 GGAGCATCAT
182 AAAAACAAAA
1 AAAAACAAAA
192 AAAAACAAAA
1 AAAAACAAAA
202 AAAACACAAAA
1 AAAA-ACAAAA
213 TGGTTGAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 14 0.70
11 6 0.30
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAACAAAA
Found at i:8890 original size:31 final size:31
Alignment explanation
Indices: 8839--8930 Score: 89
Period size: 31 Copynumber: 3.0 Consensus size: 31
8829 TCTAAAATTA
* *
8839 ATAATACATAAAATAT-TTTAAA-ATTTTAAAT
1 ATAATA-ATAAATTATATTTAAATAATTT-AAT
8870 ATAATAATAAATTATATTTAAATAATTTAAT
1 ATAATAATAAATTATATTTAAATAATTTAAT
* ** * *
8901 ATAGTGGTAAATAATATTTAAATGATTTAA
1 ATAATAATAAATTATATTTAAATAATTTAA
8931 AATAGTGCTG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
30 8 0.15
31 40 0.77
32 4 0.08
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.42
Consensus pattern (31 bp):
ATAATAATAAATTATATTTAAATAATTTAAT
Found at i:8936 original size:31 final size:31
Alignment explanation
Indices: 8877--8937 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
8867 AATATAATAA
* *
8877 TAAATTATATTTAAATAATTTAATATAGTGG
1 TAAATAATATTTAAATAATTTAAAATAGTGG
*
8908 TAAATAATATTTAAATGATTTAAAATAGTG
1 TAAATAATATTTAAATAATTTAAAATAGTG
8938 CTGCATAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.43
Consensus pattern (31 bp):
TAAATAATATTTAAATAATTTAAAATAGTGG
Found at i:11967 original size:104 final size:104
Alignment explanation
Indices: 11779--12091 Score: 590
Period size: 104 Copynumber: 3.0 Consensus size: 104
11769 GGGTACTGAA
11779 AATAGCCTTAAAATTCTAAGTTGTGGGCATTTTATGTTTATTGGTTATCCATTTGTGAAAGTGAG
1 AATAGCCTTAAAATTCTAAGTTGTGGGCATTTTATGTTTATTGGTTATCCATTTGTGAAAGTGAG
*
11844 AAGCTCAGGTTGATTGTGTCAATAGGAAGCAATTTCAGT
66 AAGTTCAGGTTGATTGTGTCAATAGGAAGCAATTTCAGT
* *
11883 AATAACCTTAAAATTCTAAGTTGTGGGCATTTTATGTTTATTGGTTGTCCATTTGTGAAAGTGAG
1 AATAGCCTTAAAATTCTAAGTTGTGGGCATTTTATGTTTATTGGTTATCCATTTGTGAAAGTGAG
*
11948 AAGTTCAGGTTGATCGTGTCAATAGGAAGCAATTTCAGT
66 AAGTTCAGGTTGATTGTGTCAATAGGAAGCAATTTCAGT
11987 AATAGCCTTAAAATTCTAAGTTGTGGGCATTTTATGTTTATTGGTTATCCATTTGTGAAAGTGAG
1 AATAGCCTTAAAATTCTAAGTTGTGGGCATTTTATGTTTATTGGTTATCCATTTGTGAAAGTGAG
12052 AAGTTCAGGTTGATTGTGTCAATAGGAAGCAATTTCAGT
66 AAGTTCAGGTTGATTGTGTCAATAGGAAGCAATTTCAGT
12091 A
1 A
12092 GTAGTATTAG
Statistics
Matches: 202, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
104 202 1.00
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.38
Consensus pattern (104 bp):
AATAGCCTTAAAATTCTAAGTTGTGGGCATTTTATGTTTATTGGTTATCCATTTGTGAAAGTGAG
AAGTTCAGGTTGATTGTGTCAATAGGAAGCAATTTCAGT
Found at i:18901 original size:5 final size:5
Alignment explanation
Indices: 18891--18916 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
18881 AGTTGCTAAC
18891 TGTGT TGTGT TGTGT TGTGT TGTGT T
1 TGTGT TGTGT TGTGT TGTGT TGTGT T
18917 TAGGTCTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.38, T:0.62
Consensus pattern (5 bp):
TGTGT
Found at i:20089 original size:9 final size:9
Alignment explanation
Indices: 20051--20216 Score: 56
Period size: 10 Copynumber: 17.9 Consensus size: 9
20041 GACATGTGAA
20051 AAAAATTAT
1 AAAAATTAT
*
20060 GAAAA--AT
1 AAAAATTAT
*
20067 AAAATTTAAT
1 AAAAATT-AT
*
20077 AAAAGTTAT
1 AAAAATTAT
20086 AAAAATTATT
1 AAAAATTA-T
**
20096 AAATTTTAAT
1 AAAAATT-AT
20106 AAAAA-TAT
1 AAAAATTAT
*
20114 AAAAATATTT
1 AAAAAT-TAT
*
20124 AAAATTTATT
1 AAAAATTA-T
* *
20134 ATAAAATAGAA
1 A-AAAAT-TAT
20145 AAAAATATAT
1 AAAAAT-TAT
* *
20155 AAATAGTA-
1 AAAAATTAT
*
20163 AAAAATATAA
1 AAAAAT-TAT
*
20173 AAAAATTGT
1 AAAAATTAT
*
20182 AAAATTTTAT
1 AAAA-ATTAT
*
20192 AAAAATCAT
1 AAAAATTAT
20201 -AAAA-TAT
1 AAAAATTAT
20208 AAAATATTA
1 AAAA-ATTA
20217 AAATTTTATA
Statistics
Matches: 113, Mismatches: 28, Indels: 31
0.66 0.16 0.18
Matches are distributed among these distances:
7 7 0.06
8 18 0.16
9 28 0.25
10 53 0.47
11 6 0.05
12 1 0.01
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:20125 original size:28 final size:27
Alignment explanation
Indices: 20068--20204 Score: 98
Period size: 28 Copynumber: 4.8 Consensus size: 27
20058 ATGAAAAATA
* *
20068 AAATTTAATAAAAGTTATAAAAAT-TATT
1 AAATTTTATAAAA-ATATAAAAATAT-TT
20096 AAATTTTAATAAAAATATAAAAATATTT
1 AAATTTT-ATAAAAATATAAAAATATTT
* * *
20124 AAAATTTATTATAAAATAGAAAAAAATATAT
1 -AAA-TT-TTATAAAA-ATATAAAAATATTT
** *
20155 AAATAGTA-AAAAATATAAAAAAATTGT
1 AAATTTTATAAAAATATAAAAATATT-T
20182 AAAATTTTATAAAAATCATAAAA
1 -AAATTTTATAAAAAT-ATAAAA
20205 TATAAAATAT
Statistics
Matches: 86, Mismatches: 13, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
26 9 0.10
27 5 0.06
28 25 0.29
29 17 0.20
30 17 0.20
31 13 0.15
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.34
Consensus pattern (27 bp):
AAATTTTATAAAAATATAAAAATATTT
Found at i:20466 original size:10 final size:9
Alignment explanation
Indices: 20451--20529 Score: 54
Period size: 10 Copynumber: 8.6 Consensus size: 9
20441 TAAAGAACAT
20451 TTTTTATGCA
1 TTTTTATG-A
*
20461 TTTTTATAA
1 TTTTTATGA
20470 TTTTTAATGA
1 TTTTT-ATGA
*
20480 TTTTTATAAA
1 TTTTTAT-GA
* **
20490 ATTTTACAA
1 TTTTTATGA
20499 TTTTTTAT-A
1 -TTTTTATGA
20508 TTTTTATGA
1 TTTTTATGA
*
20517 -TTTTATAA
1 TTTTTATGA
20525 TTTTT
1 TTTTT
20530 TTTCTAATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 11
0.75 0.11 0.15
Matches are distributed among these distances:
8 14 0.25
9 16 0.29
10 26 0.46
ACGTcount: A:0.29, C:0.03, G:0.04, T:0.65
Consensus pattern (9 bp):
TTTTTATGA
Found at i:20475 original size:19 final size:18
Alignment explanation
Indices: 20451--20529 Score: 81
Period size: 19 Copynumber: 4.3 Consensus size: 18
20441 TAAAGAACAT
20451 TTTTTATGCATTTTTATAA
1 TTTTTATG-ATTTTTATAA
20470 TTTTTAATGATTTTTATAAA
1 TTTTT-ATGATTTTTAT-AA
* **
20490 ATTTTACAATTTTT-TATA
1 TTTTTATGATTTTTATA-A
20508 TTTTTATGA-TTTTATAA
1 TTTTTATGATTTTTATAA
20525 TTTTT
1 TTTTT
20530 TTTCTAATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
17 11 0.22
18 10 0.20
19 20 0.40
20 9 0.18
ACGTcount: A:0.29, C:0.03, G:0.04, T:0.65
Consensus pattern (18 bp):
TTTTTATGATTTTTATAA
Found at i:20530 original size:10 final size:9
Alignment explanation
Indices: 20460--20529 Score: 63
Period size: 9 Copynumber: 7.7 Consensus size: 9
20450 TTTTTTATGC
20460 ATTTTTATA
1 ATTTTTATA
*
20469 ATTTTTAATG
1 ATTTTT-ATA
20479 ATTTTTATAA
1 ATTTTTAT-A
* *
20489 AATTTTACA
1 ATTTTTATA
20498 ATTTTT-TA
1 ATTTTTATA
*
20506 TATTTTTATG
1 -ATTTTTATA
20516 A-TTTTATA
1 ATTTTTATA
20524 ATTTTT
1 ATTTTT
20530 TTTCTAATTT
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
8 8 0.17
9 25 0.52
10 15 0.31
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.64
Consensus pattern (9 bp):
ATTTTTATA
Found at i:20576 original size:27 final size:29
Alignment explanation
Indices: 20528--20583 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 29
20518 TTTATAATTT
* *
20528 TTTTTCTAATTTTTAATAAAATTTAAATA
1 TTTTTCTAATTTTCAATAAAATATAAATA
20557 TTTTT-TAATTTTCAA-AAAATATAAATA
1 TTTTTCTAATTTTCAATAAAATATAAATA
20584 CTTAAGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 11 0.44
28 9 0.36
29 5 0.20
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.52
Consensus pattern (29 bp):
TTTTTCTAATTTTCAATAAAATATAAATA
Found at i:21407 original size:23 final size:24
Alignment explanation
Indices: 21352--21411 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
21342 TCATTAACAT
* * *
21352 TGTTCGTGAATATGTTTAATTATA
1 TGTTAGTGAACATGTTCAATTATA
*
21376 TGTTAGTGAACATGTTCATTTA-A
1 TGTTAGTGAACATGTTCAATTATA
*
21399 TGTTTGTGAACAT
1 TGTTAGTGAACAT
21412 ATTTGATTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
23 13 0.42
24 18 0.58
ACGTcount: A:0.28, C:0.07, G:0.18, T:0.47
Consensus pattern (24 bp):
TGTTAGTGAACATGTTCAATTATA
Found at i:21470 original size:21 final size:21
Alignment explanation
Indices: 21446--21485 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
21436 TTCGTGAACA
21446 TTAAACAAACGAACATGAATT
1 TTAAACAAACGAACATGAATT
* *
21467 TTAAATAAACGAATATGAA
1 TTAAACAAACGAACATGAA
21486 CAAAAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.10, G:0.10, T:0.25
Consensus pattern (21 bp):
TTAAACAAACGAACATGAATT
Found at i:23588 original size:60 final size:60
Alignment explanation
Indices: 23437--23588 Score: 173
Period size: 60 Copynumber: 2.5 Consensus size: 60
23427 TCTAAAAAAA
* *
23437 AAAAAAAGCTTAGGTGCCAAATTAGAAAAAAAATGTCAAGTTCAGGTATCAAATTGTGTCC
1 AAAAAAAGCTTAGGTGCCAAATTA-AAAAAAAATGTCAAGTTCAAGTATCAAATTGTATCC
** * * * *
23498 AAAAAAAATTTAGGTGTCAAATCAAGAAAAAGTGTCAAGTTCAAGTATCAAATTAG-AT-C
1 AAAAAAAGCTTAGGTGCCAAATTAAAAAAAAATGTCAAGTTCAAGTATCAAATT-GTATCC
* * *
23557 AAAAAAGGCTTAAGTACCAAATTAAAAAAAAA
1 AAAAAAAGCTTAGGTGCCAAATTAAAAAAAAA
23589 AAAAATTCAA
Statistics
Matches: 73, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
59 24 0.33
60 28 0.38
61 21 0.29
ACGTcount: A:0.51, C:0.11, G:0.15, T:0.23
Consensus pattern (60 bp):
AAAAAAAGCTTAGGTGCCAAATTAAAAAAAAATGTCAAGTTCAAGTATCAAATTGTATCC
Found at i:32802 original size:16 final size:16
Alignment explanation
Indices: 32781--32811 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
32771 AGCAGCAGTG
32781 ACAATACCATATTGTA
1 ACAATACCATATTGTA
*
32797 ACAATACTATATTGT
1 ACAATACCATATTGT
32812 GAGATAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.35
Consensus pattern (16 bp):
ACAATACCATATTGTA
Found at i:35589 original size:21 final size:21
Alignment explanation
Indices: 35563--35604 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
35553 TTTTGATTTG
35563 ATATATAATCAAATACACTAT
1 ATATATAATCAAATACACTAT
35584 ATATATAATCAAATACACTAT
1 ATATATAATCAAATACACTAT
35605 CATTAGTGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.33
Consensus pattern (21 bp):
ATATATAATCAAATACACTAT
Found at i:51851 original size:15 final size:15
Alignment explanation
Indices: 51831--51861 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
51821 ATATTAAAAA
51831 ATAAAAAT-ATTTTT
1 ATAAAAATAATTTTT
51845 ATAAAAATAATTTTT
1 ATAAAAATAATTTTT
51860 AT
1 AT
51862 TTTTAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATAAAAATAATTTTT
Found at i:56588 original size:23 final size:23
Alignment explanation
Indices: 56547--56590 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
56537 AATATATATT
*
56547 TAATTTTAAAATGTTTAATAAAA
1 TAATTTTAAAATGTATAATAAAA
56570 TAATTTTAATAATG-ATAATAA
1 TAATTTTAA-AATGTATAATAA
56591 TTGAACTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (23 bp):
TAATTTTAAAATGTATAATAAAA
Found at i:57596 original size:21 final size:21
Alignment explanation
Indices: 57570--57616 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
57560 GTATGCTTCT
* *
57570 TTCTTTCACCTTCTTTAATAC
1 TTCTTTCACCTTCTTGAATAA
**
57591 TTCTTTCATTTTCTTGAATAA
1 TTCTTTCACCTTCTTGAATAA
57612 TTCTT
1 TTCTT
57617 CAATTACTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.21, G:0.02, T:0.57
Consensus pattern (21 bp):
TTCTTTCACCTTCTTGAATAA
Found at i:62787 original size:30 final size:31
Alignment explanation
Indices: 62753--62844 Score: 89
Period size: 31 Copynumber: 3.0 Consensus size: 31
62743 ATAATTTACA
* *
62753 AAAATAAGATCAAATCAAAATTT-TATATAT
1 AAAATAACATAAAATCAAAATTTATATATAT
* *
62783 AAAATTACATAAAATCAAAATTTATTTATAT
1 AAAATAACATAAAATCAAAATTTATATATAT
* * * *
62814 -AATTATACATTAAATCATAATTTATGTATAT
1 AAAATA-ACATAAAATCAAAATTTATATATAT
62845 TTTTTATATT
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
30 23 0.45
31 28 0.55
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (31 bp):
AAAATAACATAAAATCAAAATTTATATATAT
Found at i:62823 original size:31 final size:31
Alignment explanation
Indices: 62764--62844 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
62754 AAATAAGATC
62764 AAATCAAAATTT-TATATATAAAATTACATA
1 AAATCAAAATTTATATATATAAAATTACATA
* * *
62794 AAATCAAAATTTATTTATAT-AATTATACATT
1 AAATCAAAATTTATATATATAAAAT-TACATA
* *
62825 AAATCATAATTTATGTATAT
1 AAATCAAAATTTATATATAT
62845 TTTTTATATT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
30 15 0.34
31 29 0.66
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.42
Consensus pattern (31 bp):
AAATCAAAATTTATATATATAAAATTACATA
Found at i:70687 original size:16 final size:17
Alignment explanation
Indices: 70658--70690 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
70648 CAAATTTTTA
70658 AAAATATTCATTTAATAT
1 AAAATATT-ATTTAATAT
70676 AAAATATT-TTTAATA
1 AAAATATTATTTAATA
70691 CTATAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
AAAATATTATTTAATAT
Found at i:73715 original size:25 final size:24
Alignment explanation
Indices: 73687--73733 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
73677 AGTTAATAAT
73687 AATT-CTCTTTGAGTTTTTCTTCAAG
1 AATTGCTC-TTGAGTTTTT-TTCAAG
73712 AATTGCTCTTGAGTTTTTTTCA
1 AATTGCTCTTGAGTTTTTTTCA
73734 GAAGTTGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 4 0.19
25 14 0.67
26 3 0.14
ACGTcount: A:0.19, C:0.15, G:0.13, T:0.53
Consensus pattern (24 bp):
AATTGCTCTTGAGTTTTTTTCAAG
Found at i:78883 original size:13 final size:13
Alignment explanation
Indices: 78865--78889 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
78855 CTTCCATATC
78865 ACAGATTAGCAAA
1 ACAGATTAGCAAA
78878 ACAGATTAGCAA
1 ACAGATTAGCAA
78890 TAAAGAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (13 bp):
ACAGATTAGCAAA
Found at i:85611 original size:21 final size:21
Alignment explanation
Indices: 85587--85627 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
85577 AGGGTAAATT
*
85587 GAAAATTGAGGATTGAGAAAA
1 GAAAATTGAGGATGGAGAAAA
*
85608 GAAAATTTAGGATGGAGAAA
1 GAAAATTGAGGATGGAGAAA
85628 TAAATATTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.29, T:0.20
Consensus pattern (21 bp):
GAAAATTGAGGATGGAGAAAA
Done.