Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005750.1 Kokia drynarioides strain JFW-HI SEQ_119998, 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: 72629
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 210 characters in sequence are not A, C, G, or T
Found at i:984 original size:9 final size:9
Alignment explanation
Indices: 963--996 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
953 ATATATTTTT
963 AAAATAAATA
1 AAAAT-AATA
973 AAAAT-ATA
1 AAAATAATA
981 AAAATAATA
1 AAAATAATA
990 AAAATAA
1 AAAATAA
997 ATTTTTTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.35
9 10 0.43
10 5 0.22
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAAATAATA
Found at i:4203 original size:22 final size:22
Alignment explanation
Indices: 4178--4220 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
4168 CCAATTTTAG
* *
4178 GTGTTATGTCATATAATTTCAA
1 GTGTTATATAATATAATTTCAA
4200 GTGTTATATAATATAATTTCA
1 GTGTTATATAATATAATTTCA
4221 CTAAATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.47
Consensus pattern (22 bp):
GTGTTATATAATATAATTTCAA
Found at i:7615 original size:20 final size:18
Alignment explanation
Indices: 7576--7611 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
7566 CCACCAAAAA
7576 TAAAATATATATTTAAAT
1 TAAAATATATATTTAAAT
*
7594 TAAACTATATATTTAAAT
1 TAAAATATATATTTAAAT
7612 ATTATATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAAATATATATTTAAAT
Found at i:7729 original size:25 final size:25
Alignment explanation
Indices: 7691--7738 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
7681 CACCACCAAA
* * *
7691 AAATTAAAATTTATTTTAAAAATAT
1 AAATAAAAAATTATTTAAAAAATAT
7716 AAATAAAAAATTATTTAAAAAAT
1 AAATAAAAAATTATTTAAAAAAT
7739 TTATTTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
AAATAAAAAATTATTTAAAAAATAT
Found at i:7857 original size:92 final size:91
Alignment explanation
Indices: 7620--7918 Score: 401
Period size: 93 Copynumber: 3.3 Consensus size: 91
7610 ATATTATATA
*
7620 ATAAATAAAAAATAATTTTAAAAAAATTATTTAATTAAAGTGGTGGCGCCATCTAATATGACACC
1 ATAAATAAAAAATAA--TT-AAAAAATTATTTAATTAAAGTGGTGGCGCCATTTAATATGACACC
7685 ACCAAAAAA-TTAAAATTTATTTTAAAAAT
63 ACCAAAAAATTTAAAA-TTATTTTAAAAAT
* * *
7714 ATAAATAAAAAATTATTTAAAAAATTTATTTAATTAAAGGGGTGGCGCCATTTAATATGGCACCA
1 ATAAATAAAAAA-TAATTAAAAAA-TTATTTAATTAAAGTGGTGGCGCCATTTAATATGACACCA
7779 CCAAAAAAATTTAAAATTATTTTAAAAAT
64 CC-AAAAAATTTAAAATTATTTTAAAAAT
*
7808 ATAAATAAAAAATAATTAAAAAATTATTTAATTAAAATGGTGGCGCCATTTAATATGACACCACT
1 ATAAATAAAAAATAATTAAAAAATTATTTAATTAAAGTGGTGGCGCCATTTAATATGACACCAC-
* *
7873 C-AAAAATTT-AAA-T-TTTCAAAAAA
65 CAAAAAATTTAAAATTATTTTAAAAAT
** *
7896 ATAAATATTAAATAATGAAAAAA
1 ATAAATAAAAAATAATTAAAAAA
7919 ATAAACTGAC
Statistics
Matches: 187, Mismatches: 13, Indels: 16
0.87 0.06 0.07
Matches are distributed among these distances:
88 28 0.15
89 1 0.01
90 3 0.02
91 8 0.04
92 44 0.24
93 52 0.28
94 43 0.23
95 8 0.04
ACGTcount: A:0.52, C:0.09, G:0.08, T:0.31
Consensus pattern (91 bp):
ATAAATAAAAAATAATTAAAAAATTATTTAATTAAAGTGGTGGCGCCATTTAATATGACACCACC
AAAAAATTTAAAATTATTTTAAAAAT
Found at i:7906 original size:23 final size:22
Alignment explanation
Indices: 7876--7923 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
7866 CACCACTCAA
**
7876 AAATTTAAATTTTCAAAAAAAT
1 AAATTTAAATAATCAAAAAAAT
*
7898 AAATATTAAATAATGAAAAAAAT
1 AAAT-TTAAATAATCAAAAAAAT
7921 AAA
1 AAA
7924 CTGACAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (22 bp):
AAATTTAAATAATCAAAAAAAT
Found at i:8473 original size:6 final size:6
Alignment explanation
Indices: 8462--8493 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
8452 CTTATCCGAC
*
8462 CAGCCT CAGCCT CAGCCT CAACCT CAGCCT CA
1 CAGCCT CAGCCT CAGCCT CAGCCT CAGCCT CA
8494 CTTCGTGTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.22, C:0.50, G:0.12, T:0.16
Consensus pattern (6 bp):
CAGCCT
Found at i:13093 original size:15 final size:16
Alignment explanation
Indices: 13075--13125 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
13065 GTATTTAATA
13075 ATTTAAT-AATTTTTT
1 ATTTAATAAATTTTTT
*
13090 ATTTATTAAATTTTTTT
1 ATTTAATAAA-TTTTTT
*
13107 ATATAATTAACATTTTTT
1 ATTTAA-TAA-ATTTTTT
13125 A
1 A
13126 ATGTTTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 6 0.21
16 2 0.07
17 10 0.34
18 10 0.34
19 1 0.03
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (16 bp):
ATTTAATAAATTTTTT
Found at i:13106 original size:19 final size:19
Alignment explanation
Indices: 13084--13124 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
13074 AATTTAATAA
*
13084 TTTTTTAT-TTATTAA-AT
1 TTTTTTATATAATTAACAT
13101 TTTTTTATATAATTAACAT
1 TTTTTTATATAATTAACAT
13120 TTTTT
1 TTTTT
13125 AATGTTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.38
18 6 0.29
19 7 0.33
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTTTATATAATTAACAT
Found at i:13125 original size:18 final size:16
Alignment explanation
Indices: 13082--13125 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
13072 ATAATTTAAT
*
13082 AATTTTTTATTTATTA
1 AATTTTTTATTAATTA
13098 AATTTTTTTATATAATTA
1 AA-TTTTTTAT-TAATTA
13116 ACATTTTTTA
1 A-ATTTTTTA
13126 ATGTTTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 2 0.08
17 8 0.33
18 13 0.54
19 1 0.04
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (16 bp):
AATTTTTTATTAATTA
Found at i:20514 original size:27 final size:26
Alignment explanation
Indices: 20457--20514 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
20447 GTTAGGGGTT
**
20457 TTAAGTCTATTTAAAATTAAATTTATT
1 TTAAGTCTATTTAAAA-TAAATTTAGA
20484 TTAAGTCTATTTAAAA-AAATTTCACGA
1 TTAAGTCTATTTAAAATAAATTT-A-GA
20511 TTAA
1 TTAA
20515 ATCAATCTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 6 0.22
26 1 0.04
27 20 0.74
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (26 bp):
TTAAGTCTATTTAAAATAAATTTAGA
Found at i:24180 original size:17 final size:17
Alignment explanation
Indices: 24158--24235 Score: 86
Period size: 17 Copynumber: 4.5 Consensus size: 17
24148 CTAACAGGAT
24158 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
**
24175 TTAAATTTATTTTAAGT
1 TTAAATTTATTTTAAAA
*
24192 TTAAATTTA-CTTAAAA
1 TTAAATTTATTTTAAAA
* *
24208 TTTAAATTTATTATAAAT
1 -TTAAATTTATTTTAAAA
24226 TTAAAGTTTA
1 TTAAA-TTTA
24236 AATCTATTCA
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
16 4 0.08
17 38 0.76
18 8 0.16
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:24200 original size:34 final size:34
Alignment explanation
Indices: 24156--24235 Score: 108
Period size: 34 Copynumber: 2.3 Consensus size: 34
24146 GTCTAACAGG
* *
24156 ATTTAAATTTATTTTAAAA-TTAAATTTATTTTAA
1 ATTTAAATTTA-CTTAAAATTTAAATTTATTATAA
*
24190 GTTTAAATTTACTTAAAATTTAAATTTATTATAA
1 ATTTAAATTTACTTAAAATTTAAATTTATTATAA
24224 ATTTAAAGTTTA
1 ATTTAAA-TTTA
24236 AATCTATTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
33 6 0.15
34 30 0.75
35 4 0.10
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (34 bp):
ATTTAAATTTACTTAAAATTTAAATTTATTATAA
Found at i:24237 original size:7 final size:6
Alignment explanation
Indices: 24156--24238 Score: 59
Period size: 6 Copynumber: 14.3 Consensus size: 6
24146 GTCTAACAGG
* * * *
24156 ATTTAA ATTT-A TTTTAA AATTAA ATTT-A TTTTAA GTTTAA ATTT-A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* *
24201 CTTAAA ATTTAA ATTT-- ATTATAA ATTTAA AGTTTAA AT
1 ATTTAA ATTTAA ATTTAA ATT-TAA ATTTAA A-TTTAA AT
24239 CTATTCAAAT
Statistics
Matches: 59, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
4 3 0.05
5 12 0.20
6 35 0.59
7 9 0.15
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (6 bp):
ATTTAA
Found at i:24964 original size:3 final size:3
Alignment explanation
Indices: 24956--25047 Score: 157
Period size: 3 Copynumber: 30.0 Consensus size: 3
24946 TTAATAGCAT
24956 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
*
25005 TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
25048 CATTAATTAA
Statistics
Matches: 85, Mismatches: 2, Indels: 4
0.93 0.02 0.04
Matches are distributed among these distances:
3 79 0.93
4 6 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:25968 original size:22 final size:21
Alignment explanation
Indices: 25921--25988 Score: 57
Period size: 22 Copynumber: 3.2 Consensus size: 21
25911 TTGGTAATGC
* *
25921 TTTTTGCTGTTTTAATTACTAT
1 TTTTTGCTGTTTTGA-TGCTAT
*
25943 TTTTTGCTGTTTTGATGCTGT
1 TTTTTGCTGTTTTGATGCTAT
* * *
25964 GTTTTTACTATTTTGGTGCT-T
1 -TTTTTGCTGTTTTGATGCTAT
25985 TTTT
1 TTTT
25989 AACTATTTTG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
20 4 0.10
21 5 0.13
22 30 0.77
ACGTcount: A:0.10, C:0.09, G:0.16, T:0.65
Consensus pattern (21 bp):
TTTTTGCTGTTTTGATGCTAT
Found at i:26009 original size:21 final size:20
Alignment explanation
Indices: 25963--26009 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
25953 TTTGATGCTG
*
25963 TGTTTTTACTATTTTGGTGC
1 TGTTTTAACTATTTTGGTGC
*
25983 TTTTTTAACTATTTTGGTTGC
1 TGTTTTAACTATTTTGG-TGC
26004 TGTTTT
1 TGTTTT
26010 GTTGTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.11, C:0.09, G:0.17, T:0.64
Consensus pattern (20 bp):
TGTTTTAACTATTTTGGTGC
Found at i:26010 original size:32 final size:32
Alignment explanation
Indices: 25974--26041 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 32
25964 GTTTTTACTA
25974 TTTTGGTG-CTTTTTTAACTATTTTGGTTGCTG
1 TTTTGGTGTCTTTTTTAACTATTTTGG-TGCTG
* * * *
26006 TTTTGTTGTTTTTTTTTACTATTTTGGTGTTG
1 TTTTGGTGTCTTTTTTAACTATTTTGGTGCTG
26038 TTTT
1 TTTT
26042 TGTTGTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 15 0.48
33 16 0.52
ACGTcount: A:0.07, C:0.06, G:0.19, T:0.68
Consensus pattern (32 bp):
TTTTGGTGTCTTTTTTAACTATTTTGGTGCTG
Found at i:26027 original size:33 final size:34
Alignment explanation
Indices: 25983--26065 Score: 107
Period size: 33 Copynumber: 2.4 Consensus size: 34
25973 ATTTTGGTGC
*
25983 TTTTTTAACTATTTTGGTTGCTG-TTTTGTTGTT-
1 TTTTTTTACTATTTTGG-TGCTGTTTTTGTTGTTA
*
26016 TTTTTTTACTATTTTGGTGTTGTTTTTGTTGTTA
1 TTTTTTTACTATTTTGGTGCTGTTTTTGTTGTTA
*
26050 TTTTTGTTGCTATTTT
1 TTTTT-TTACTATTTT
26066 TTCTATTATT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
32 4 0.09
33 26 0.59
34 5 0.11
35 9 0.20
ACGTcount: A:0.08, C:0.05, G:0.17, T:0.70
Consensus pattern (34 bp):
TTTTTTTACTATTTTGGTGCTGTTTTTGTTGTTA
Found at i:26057 original size:21 final size:21
Alignment explanation
Indices: 26006--26132 Score: 69
Period size: 24 Copynumber: 5.6 Consensus size: 21
25996 TTGGTTGCTG
*
26006 TTTTGTTGTTTTT-TTTTACTAT
1 TTTTGTTGTTTTTGTTGT--TAT
26028 TTTGGTGTTGTTTTTGTTGTTAT
1 TTT--TGTTGTTTTTGTTGTTAT
* *
26051 TTTTGTTGCTATTTTTTCTATTAT
1 TTTTGTTG-T-TTTTGT-TGTTAT
*
26075 TTTTGCTACTGTTTTGGTTGTTAT
1 TTTTG-T--TGTTTTTGTTGTTAT
* * *
26099 TTTGGTTG-TTTGGATGTTAT
1 TTTTGTTGTTTTTGTTGTTAT
*
26119 TTTTATGTGTTTTT
1 TTTTGT-TGTTTTT
26133 ATTATTGTTT
Statistics
Matches: 83, Mismatches: 11, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
20 15 0.18
21 9 0.11
22 7 0.08
23 12 0.14
24 29 0.35
25 8 0.10
26 1 0.01
27 2 0.02
ACGTcount: A:0.09, C:0.04, G:0.18, T:0.69
Consensus pattern (21 bp):
TTTTGTTGTTTTTGTTGTTAT
Found at i:29469 original size:1 final size:1
Alignment explanation
Indices: 29463--29504 Score: 57
Period size: 1 Copynumber: 42.0 Consensus size: 1
29453 ATCCTGATTT
***
29463 AAAAAAAAAAAAAAAAAAAANTTAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
29505 GAGTAAAGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.93, C:0.00, G:0.00, T:0.05
Consensus pattern (1 bp):
A
Found at i:29491 original size:23 final size:22
Alignment explanation
Indices: 29461--29504 Score: 79
Period size: 23 Copynumber: 2.0 Consensus size: 22
29451 ACATCCTGAT
29461 TTAAAAAAAAAAAAAAAAAAAA
1 TTAAAAAAAAAAAAAAAAAAAA
29483 NTTAAAAAAAAAAAAAAAAAAA
1 -TTAAAAAAAAAAAAAAAAAAA
29505 GAGTAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.09
Consensus pattern (22 bp):
TTAAAAAAAAAAAAAAAAAAAA
Found at i:29511 original size:23 final size:23
Alignment explanation
Indices: 29462--29511 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
29452 CATCCTGATT
**
29462 TAAAAAAAAAAAAAAAAAAAANT
1 TAAAAAAAAAAAAAAAAAAAAAG
*
29485 TAAAAAAAAAAAAAAAAAAAGAG
1 TAAAAAAAAAAAAAAAAAAAAAG
29508 TAAA
1 TAAA
29512 GAAACAGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.86, C:0.00, G:0.04, T:0.08
Consensus pattern (23 bp):
TAAAAAAAAAAAAAAAAAAAAAG
Found at i:34726 original size:56 final size:53
Alignment explanation
Indices: 34658--34776 Score: 139
Period size: 53 Copynumber: 2.2 Consensus size: 53
34648 TGCCATACAC
* * *
34658 TCAAATAAATATTTTTAAATCTGAAAAAGGTGGTGTAAGTCATTGGGTGACAAACA
1 TCAAAAAAATATTTTTAAA--TG-AAAAGGTGGTATAAGCCATTGGGTGACAAACA
* * * *
34714 TCAAAAAAATATTTTTAAATGTAAGGGTGGTATAGGCCATTGGGTGGCAAACA
1 TCAAAAAAATATTTTTAAATGAAAAGGTGGTATAAGCCATTGGGTGACAAACA
34767 TCCAAAAAAA
1 T-CAAAAAAA
34777 AAAATTTTAT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
53 27 0.49
54 10 0.18
56 18 0.33
ACGTcount: A:0.42, C:0.10, G:0.20, T:0.28
Consensus pattern (53 bp):
TCAAAAAAATATTTTTAAATGAAAAGGTGGTATAAGCCATTGGGTGACAAACA
Found at i:47910 original size:3 final size:3
Alignment explanation
Indices: 47902--47929 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
47892 GGTGATCAAA
47902 ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG A
47930 AGGACAAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:54000 original size:20 final size:20
Alignment explanation
Indices: 53971--54008 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
53961 ATAATCATAA
* *
53971 AAAAATGACAAATGGAAGTT
1 AAAAACGACAAAAGGAAGTT
53991 AAAAACGACAAAAGGAAG
1 AAAAACGACAAAAGGAAG
54009 AGGTGAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.61, C:0.08, G:0.21, T:0.11
Consensus pattern (20 bp):
AAAAACGACAAAAGGAAGTT
Found at i:58160 original size:92 final size:92
Alignment explanation
Indices: 58001--58183 Score: 348
Period size: 92 Copynumber: 2.0 Consensus size: 92
57991 AGTTTTTACC
58001 CAAAGCTAATTACGTACACATTCATGCCGCTTCCATGTCGCCTTCTTTAATTCTTTTTAATCCGT
1 CAAAGCTAATTACGTACACATTCATGCCGCTTCCATGTCGCCTTCTTTAATTCTTTTTAATCCGT
58066 GATAACTGTGTTTTCTAGCAATGTTCT
66 GATAACTGTGTTTTCTAGCAATGTTCT
* *
58093 CAAAGCTAATTATGTACACATTCATGCCGCTTCCATGTCGCCTTCTTTAATTCTTTTTAATCGGT
1 CAAAGCTAATTACGTACACATTCATGCCGCTTCCATGTCGCCTTCTTTAATTCTTTTTAATCCGT
58158 GATAACTGTGTTTTCTAGCAATGTTC
66 GATAACTGTGTTTTCTAGCAATGTTC
58184 CTTCCCTTCT
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
92 89 1.00
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.40
Consensus pattern (92 bp):
CAAAGCTAATTACGTACACATTCATGCCGCTTCCATGTCGCCTTCTTTAATTCTTTTTAATCCGT
GATAACTGTGTTTTCTAGCAATGTTCT
Found at i:59567 original size:2 final size:2
Alignment explanation
Indices: 59562--59591 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
59552 ATATATATAA
*
59562 CT CT CT TT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
59592 GATGTGTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:71723 original size:23 final size:23
Alignment explanation
Indices: 71679--71724 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
71669 TATATGTTCG
* *
71679 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCGATGAAATTAAA
71702 TGAACATGTTC-ATGAACATTAAA
1 TGAACATGTTCGATGAA-ATTAAA
71725 CAAATGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Done.