Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010960.1 Kokia drynarioides strain JFW-HI SEQ_125928, 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: 192528
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 127 characters in sequence are not A, C, G, or T
Found at i:3948 original size:41 final size:41
Alignment explanation
Indices: 3889--4203 Score: 278
Period size: 41 Copynumber: 7.7 Consensus size: 41
3879 CTATTGGTTA
* * *
3889 ACCTTTAGCGACGTTTTTCCCATAAACGTCGCTAATGCTCTT
1 ACCTTTTGCGGCG-TTTTCTCATAAACGTCGCTAATGCTCTT
* * *
3931 ACCTTTTGCGGTGTTTTCTCATAAACGTCGTTAATGCTCAT
1 ACCTTTTGCGGCGTTTTCTCATAAACGTCGCTAATGCTCTT
** *
3972 ACCTTTTGCGGCGTTTATGACA-AAATGTCGCTAATGCTCTT
1 ACCTTTTGCGGCGTTT-TCTCATAAACGTCGCTAATGCTCTT
* * * * *
4013 ATCTTTTGAGGCGTTTTGTCATAAACGTCACTAATTCTCTT
1 ACCTTTTGCGGCGTTTTCTCATAAACGTCGCTAATGCTCTT
* * * *
4054 ACCTTTTGCGACGTTTTGTCATAAACGCCACTAATGCTCTT
1 ACCTTTTGCGGCGTTTTCTCATAAACGTCGCTAATGCTCTT
** * *
4095 ACCTTTTGCGGTTTTTTTTCTCATAAACGCCGCTATTGCT-TT
1 ACCTTTTGCGG--CGTTTTCTCATAAACGTCGCTAATGCTCTT
* * * * * * * *
4137 ACCTTTTGCGACG-TTTATGAGAAAATGCCACTATTGCT-TT
1 ACCTTTTGCGGCGTTTTCTCA-TAAACGTCGCTAATGCTCTT
*
4177 ACCTTTTGCGGCGTTTTTTCATAAACG
1 ACCTTTTGCGGCGTTTTCTCATAAACG
4204 CGGTTATTGC
Statistics
Matches: 225, Mismatches: 42, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
39 5 0.02
40 36 0.16
41 137 0.61
42 25 0.11
43 22 0.10
ACGTcount: A:0.21, C:0.23, G:0.16, T:0.40
Consensus pattern (41 bp):
ACCTTTTGCGGCGTTTTCTCATAAACGTCGCTAATGCTCTT
Found at i:4029 original size:82 final size:82
Alignment explanation
Indices: 3920--4203 Score: 340
Period size: 82 Copynumber: 3.5 Consensus size: 82
3910 ATAAACGTCG
* * * *
3920 CTAATGCTCTTACCTTTTGCGGTGTTTTCTCATAAACGTCGTTAATGCTCATACCTTTTGCGGCG
1 CTAATGCTCTTACCTTTTGCGGCGTTTTCTCATAAACGTCGCTAATGCTCTTACCTTTTGCGACG
* *
3985 TTTATGACAAAATGTCG
66 TTTATGACAAAATGCCA
* * * * *
4002 CTAATGCTCTTATCTTTTGAGGCGTTTTGTCATAAACGTCACTAATTCTCTTACCTTTTGCGACG
1 CTAATGCTCTTACCTTTTGCGGCGTTTTCTCATAAACGTCGCTAATGCTCTTACCTTTTGCGACG
* *
4067 TTT-TGTCATAAACGCCA
66 TTTATGACA-AAATGCCA
** * *
4084 CTAATGCTCTTACCTTTTGCGGTTTTTTTTCTCATAAACGCCGCTATTGCT-TTACCTTTTGCGA
1 CTAATGCTCTTACCTTTTGCGG--CGTTTTCTCATAAACGTCGCTAATGCTCTTACCTTTTGCGA
*
4148 CGTTTATGAGAAAATGCCA
64 CGTTTATGACAAAATGCCA
* *
4167 CTATTGCT-TTACCTTTTGCGGCGTTTTTTCATAAACG
1 CTAATGCTCTTACCTTTTGCGGCGTTTTCTCATAAACG
4204 CGGTTATTGC
Statistics
Matches: 169, Mismatches: 29, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
80 13 0.08
81 4 0.02
82 97 0.57
83 32 0.19
84 23 0.14
ACGTcount: A:0.20, C:0.23, G:0.16, T:0.41
Consensus pattern (82 bp):
CTAATGCTCTTACCTTTTGCGGCGTTTTCTCATAAACGTCGCTAATGCTCTTACCTTTTGCGACG
TTTATGACAAAATGCCA
Found at i:10356 original size:29 final size:29
Alignment explanation
Indices: 10314--10388 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 29
10304 TAAAAATATA
* * *
10314 AAAAATAAAAAAACTAAATTTTTAAA-AAT
1 AAAAATATAGAAACTAAA-TTCTAAATAAT
*
10343 AAAAATATAGAAACTAAATTCTAAATTTAT
1 AAAAATATAGAAACTAAATTCTAAA-TAAT
10373 AAAAATTATAGAAACT
1 AAAAA-TATAGAAACT
10389 TATGGTATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 6 0.15
29 16 0.41
30 7 0.18
31 10 0.26
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (29 bp):
AAAAATATAGAAACTAAATTCTAAATAAT
Found at i:11591 original size:16 final size:16
Alignment explanation
Indices: 11572--11628 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
11562 AACAAAATTT
*
11572 AACTTGAAATAACTCA
1 AACTCGAAATAACTCA
*
11588 AACTCGAAATGACTCA
1 AACTCGAAATAACTCA
*
11604 AA-TCCGAAACTAA-TCC
1 AACT-CGAAA-TAACTCA
11620 AACTCGAAA
1 AACTCGAAA
11629 AAATAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 1 0.03
16 30 0.88
17 3 0.09
ACGTcount: A:0.47, C:0.25, G:0.09, T:0.19
Consensus pattern (16 bp):
AACTCGAAATAACTCA
Found at i:33560 original size:21 final size:21
Alignment explanation
Indices: 33534--33573 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
33524 GGTAGGTTTT
33534 TTTCCTTCTTTC-TCTTCTTCC
1 TTTCCTT-TTTCTTCTTCTTCC
33555 TTTCCTTTTTCTTCTTCTT
1 TTTCCTTTTTCTTCTTCTT
33574 ATTGATCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTCCTTTTTCTTCTTCTTCC
Found at i:52411 original size:118 final size:118
Alignment explanation
Indices: 52203--52439 Score: 465
Period size: 118 Copynumber: 2.0 Consensus size: 118
52193 TAGAGCAGAA
52203 TAAGAAGTCTATGTTTGATGACGAATGTCTAGACGCATTTTTCAAAATAAAGGAGAAATTAGTAC
1 TAAGAAGTCTATGTTTGATGACGAATGTCTAGACGCATTTTTCAAAATAAAGGAGAAATTAGTAC
52268 AAGCTCCAATTATCGTCGCACCGGATTAGACGCAATCATTTGAATTAATATGT
66 AAGCTCCAATTATCGTCGCACCGGATTAGACGCAATCATTTGAATTAATATGT
*
52321 TAAGAAGTCTATGTTTGATGACGAGTGTCTAGACGCATTTTTCAAAATAAAGGAGAAATTAGTAC
1 TAAGAAGTCTATGTTTGATGACGAATGTCTAGACGCATTTTTCAAAATAAAGGAGAAATTAGTAC
52386 AAGCTCCAATTATCGTCGCACCGGATTAGACGCAATCATTTGAATTAATATGT
66 AAGCTCCAATTATCGTCGCACCGGATTAGACGCAATCATTTGAATTAATATGT
52439 T
1 T
52440 CGCAAGCAAC
Statistics
Matches: 118, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
118 118 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (118 bp):
TAAGAAGTCTATGTTTGATGACGAATGTCTAGACGCATTTTTCAAAATAAAGGAGAAATTAGTAC
AAGCTCCAATTATCGTCGCACCGGATTAGACGCAATCATTTGAATTAATATGT
Found at i:58467 original size:16 final size:16
Alignment explanation
Indices: 58446--58477 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
58436 ATAGGGGGAG
58446 GTTAAATTCAAAATGT
1 GTTAAATTCAAAATGT
58462 GTTAAATTCAAAATGT
1 GTTAAATTCAAAATGT
58478 CTTTTATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (16 bp):
GTTAAATTCAAAATGT
Found at i:58870 original size:22 final size:22
Alignment explanation
Indices: 58834--58897 Score: 87
Period size: 21 Copynumber: 3.0 Consensus size: 22
58824 CAAATAGTGA
*
58834 CAAAAAA-TATGGATACCTTTT
1 CAAAAAAGTATAGATACCTTTT
*
58855 CAAAAAAGTATAGATACCGTTT
1 CAAAAAAGTATAGATACCTTTT
*
58877 C-AAAAAGTATAAATACCTTTT
1 CAAAAAAGTATAGATACCTTTT
58898 ATCAAGTATC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
21 25 0.66
22 13 0.34
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.31
Consensus pattern (22 bp):
CAAAAAAGTATAGATACCTTTT
Found at i:63049 original size:52 final size:52
Alignment explanation
Indices: 62973--63076 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
62963 TCTGAAGGCA
62973 AAAGAACACTGTAAGGCTATCACTCTTAGGAGTGGCAAACAAACTGGTGAGC
1 AAAGAACACTGTAAGGCTATCACTCTTAGGAGTGGCAAACAAACTGGTGAGC
*
63025 AAAGAACACTGTAAGGTTATCACTCTTAGGAGTGGCAAACAAACTGGTGAGC
1 AAAGAACACTGTAAGGCTATCACTCTTAGGAGTGGCAAACAAACTGGTGAGC
63077 CGACTATAGG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20
Consensus pattern (52 bp):
AAAGAACACTGTAAGGCTATCACTCTTAGGAGTGGCAAACAAACTGGTGAGC
Found at i:73475 original size:29 final size:29
Alignment explanation
Indices: 73432--73489 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
73422 CCCGAGGAAG
* *
73432 TATGTAATTGAACCGACACATACTCTTGC
1 TATGTAATTGAACCGACAAACACTCTTGC
*
73461 TATGTAATTGCACCGACAAACACTCTTGC
1 TATGTAATTGAACCGACAAACACTCTTGC
73490 AGTGATAGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (29 bp):
TATGTAATTGAACCGACAAACACTCTTGC
Found at i:87750 original size:14 final size:14
Alignment explanation
Indices: 87731--87780 Score: 66
Period size: 16 Copynumber: 3.5 Consensus size: 14
87721 TTTAAAATAA
87731 TTAAAATTATTTTT
1 TTAAAATTATTTTT
87745 TTAAAATATATATTTT
1 TTAAAAT-TAT-TTTT
*
87761 TTAAAATTA-ATTT
1 TTAAAATTATTTTT
87774 TTAAAAT
1 TTAAAAT
87781 ATAAAATTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
13 10 0.30
14 7 0.21
15 5 0.15
16 11 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTAAAATTATTTTT
Found at i:87793 original size:29 final size:30
Alignment explanation
Indices: 87723--87796 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
87713 CAGATAATTT
* *
87723 TAAAATAATTAAAATTATTTTTTTAAAATA
1 TAAAATTATTAAAATTATATTTTTAAAATA
* * *
87753 TATATTTTTTAAAATTA-ATTTTTAAAATA
1 TAAAATTATTAAAATTATATTTTTAAAATA
87782 TAAAATTATTAAAAT
1 TAAAATTATTAAAAT
87797 CATCATTTCC
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
29 23 0.64
30 13 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
TAAAATTATTAAAATTATATTTTTAAAATA
Found at i:88565 original size:21 final size:21
Alignment explanation
Indices: 88541--88581 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
88531 TTTGTTTTTT
*
88541 CCTTCACTTTCTTCCAAATTC
1 CCTTCACTTTCCTCCAAATTC
* *
88562 CCTTCATTTTCCTCGAAATT
1 CCTTCACTTTCCTCCAAATT
88582 TGTTTTCTCG
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:0.20, C:0.34, G:0.02, T:0.44
Consensus pattern (21 bp):
CCTTCACTTTCCTCCAAATTC
Found at i:88917 original size:20 final size:20
Alignment explanation
Indices: 88892--88935 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
88882 TAATTTTATA
88892 TTTAAAA-AATTTAAAATAAT
1 TTTAAAATAATTTAAAA-AAT
88912 TTTAAAATAATTTAAAAAAT
1 TTTAAAATAATTTAAAAAAT
88932 TTTA
1 TTTA
88936 TATTTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TTTAAAATAATTTAAAAAAT
Found at i:88935 original size:10 final size:10
Alignment explanation
Indices: 88891--88933 Score: 63
Period size: 9 Copynumber: 4.4 Consensus size: 10
88881 ATAATTTTAT
88891 ATTTAAAA-A
1 ATTTAAAATA
88900 ATTTAAAATA
1 ATTTAAAATA
88910 ATTTTAAAATA
1 A-TTTAAAATA
88921 ATTTAAAA-A
1 ATTTAAAATA
88930 ATTT
1 ATTT
88934 TATATTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
9 13 0.41
10 9 0.28
11 10 0.31
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
ATTTAAAATA
Found at i:88952 original size:20 final size:21
Alignment explanation
Indices: 88925--88967 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
88915 AAAATAATTT
88925 AAAAAATTTT-AT-ATTTTAA
1 AAAAAATTTTAATAATTTTAA
88944 AAAATAATTTTAATAATTTTAA
1 AAAA-AATTTTAATAATTTTAA
88966 AA
1 AA
88968 TCATTTGCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 6 0.29
21 2 0.10
22 9 0.43
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AAAAAATTTTAATAATTTTAA
Found at i:88968 original size:20 final size:20
Alignment explanation
Indices: 88901--88973 Score: 73
Period size: 20 Copynumber: 3.6 Consensus size: 20
88891 ATTTAAAAAA
88901 TTTAAAATAATTTTAA-AAT
1 TTTAAAATAATTTTAATAAT
88920 AATTTAAAA-AATTTT-AT-AT
1 --TTTAAAATAATTTTAATAAT
88939 TTTAAAAAATAATTTTAATAAT
1 TTT--AAAATAATTTTAATAAT
*
88961 TTTAAAATCATTT
1 TTTAAAATAATTT
88974 GCTGACGTAG
Statistics
Matches: 45, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
17 3 0.07
19 7 0.16
20 21 0.47
21 9 0.20
22 5 0.11
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (20 bp):
TTTAAAATAATTTTAATAAT
Found at i:90521 original size:21 final size:21
Alignment explanation
Indices: 90488--90541 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
90478 AGAGTTTTTA
*
90488 GTATAGGTAGAAG-CATGACTT
1 GTATCGGTAGAAGTCAT-ACTT
* *
90509 GTTTCGTTAGAAGTCATACTT
1 GTATCGGTAGAAGTCATACTT
90530 GTATCGGTAGAA
1 GTATCGGTAGAA
90542 CTATCACAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.33
Consensus pattern (21 bp):
GTATCGGTAGAAGTCATACTT
Found at i:105507 original size:7 final size:7
Alignment explanation
Indices: 105497--105597 Score: 54
Period size: 7 Copynumber: 15.0 Consensus size: 7
105487 TTGACCGATC
105497 GTTGACT
1 GTTGACT
105504 GTTGACT
1 GTTGACT
105511 -TTGA-T
1 GTTGACT
105516 AGTTGA-T
1 -GTTGACT
105523 CGTTGACT
1 -GTTGACT
*
105531 -TTGACC
1 GTTGACT
105537 GTTGA-T
1 GTTGACT
*
105543 CGTTGATT
1 -GTTGACT
*
105551 GTTCACT
1 GTTGACT
105558 GTTGACT
1 GTTGACT
105565 -TTGACT
1 GTTGACT
** *
105571 ACTGACC
1 GTTGACT
*
105578 ATTGACT
1 GTTGACT
*
105585 G-TGACC
1 GTTGACT
105591 GTTGACT
1 GTTGACT
105598 TTTTCCAAGA
Statistics
Matches: 73, Mismatches: 13, Indels: 16
0.72 0.13 0.16
Matches are distributed among these distances:
5 1 0.01
6 20 0.27
7 50 0.68
8 2 0.03
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.41
Consensus pattern (7 bp):
GTTGACT
Found at i:105523 original size:27 final size:27
Alignment explanation
Indices: 105493--105568 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 27
105483 ACCGTTGACC
105493 GATCGTTGACTGTTGACTTTGATAGTT
1 GATCGTTGACTGTTGACTTTGATAGTT
* *
105520 GATCGTTGACT-TTGACCGTTGATCGTT
1 GATCGTTGACTGTTGA-CTTTGATAGTT
* *
105547 GATTGTTCACTGTTGACTTTGA
1 GATCGTTGACTGTTGACTTTGA
105569 CTACTGACCA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 4 0.10
27 34 0.81
28 4 0.10
ACGTcount: A:0.17, C:0.14, G:0.25, T:0.43
Consensus pattern (27 bp):
GATCGTTGACTGTTGACTTTGATAGTT
Found at i:105527 original size:20 final size:20
Alignment explanation
Indices: 105504--105548 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
105494 ATCGTTGACT
*
105504 GTTGACTTTGATAGTTGATC
1 GTTGACTTTGACAGTTGATC
*
105524 GTTGACTTTGACCGTTGATC
1 GTTGACTTTGACAGTTGATC
105544 GTTGA
1 GTTGA
105549 TTGTTCACTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.18, C:0.13, G:0.27, T:0.42
Consensus pattern (20 bp):
GTTGACTTTGACAGTTGATC
Found at i:107351 original size:15 final size:16
Alignment explanation
Indices: 107312--107354 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
107302 GGTCAGCCAG
107312 TTGTTGGAGGAGACTTAA
1 TTGTT-GAGGAGACTT-A
*
107330 CTGTTGAGGAGACTT-
1 TTGTTGAGGAGACTTA
107345 TTGTTGAGGA
1 TTGTTGAGGA
107355 TGTACCCGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 9 0.39
17 10 0.43
18 4 0.17
ACGTcount: A:0.23, C:0.07, G:0.35, T:0.35
Consensus pattern (16 bp):
TTGTTGAGGAGACTTA
Found at i:112846 original size:7 final size:7
Alignment explanation
Indices: 112834--112883 Score: 57
Period size: 7 Copynumber: 7.3 Consensus size: 7
112824 TCGTTGACCA
112834 ACCGTTG
1 ACCGTTG
112841 ACCGTTG
1 ACCGTTG
*
112848 ACTGTTG
1 ACCGTTG
*
112855 ACTGTTG
1 ACCGTTG
112862 ACCGTTG
1 ACCGTTG
*
112869 A-CTTTG
1 ACCGTTG
*
112875 ATCGTTG
1 ACCGTTG
112882 AC
1 AC
112884 TTTTTCCAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
6 5 0.14
7 32 0.86
ACGTcount: A:0.16, C:0.22, G:0.26, T:0.36
Consensus pattern (7 bp):
ACCGTTG
Found at i:112856 original size:14 final size:14
Alignment explanation
Indices: 112834--112884 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 14
112824 TCGTTGACCA
*
112834 ACCGTTGACCGTTG
1 ACCGTTGACTGTTG
*
112848 ACTGTTGACTGTTG
1 ACCGTTGACTGTTG
112862 ACCGTTGACT-TTG
1 ACCGTTGACTGTTG
*
112875 ATCGTTGACT
1 ACCGTTGACT
112885 TTTTCCAAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
13 12 0.36
14 21 0.64
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.37
Consensus pattern (14 bp):
ACCGTTGACTGTTG
Found at i:112863 original size:21 final size:20
Alignment explanation
Indices: 112836--112883 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
112826 GTTGACCAAC
112836 CGTTGACCGTTGACTGTTGA-
1 CGTTGACCGTTGACT-TTGAT
112856 CTGTTGACCGTTGACTTTGAT
1 C-GTTGACCGTTGACTTTGAT
112877 CGTTGAC
1 CGTTGAC
112884 TTTTTCCAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.15, C:0.21, G:0.27, T:0.38
Consensus pattern (20 bp):
CGTTGACCGTTGACTTTGAT
Found at i:122136 original size:59 final size:57
Alignment explanation
Indices: 122069--122267 Score: 175
Period size: 59 Copynumber: 3.4 Consensus size: 57
122059 ACGAAAAAAA
* *
122069 AGGGGTCAAAAATGAAGTTTTTAAGAATTTCGGGGTAAAATGTAATTTTGGGAAAGTTT
1 AGGGGTCAAAAAT-AA-TTTTTAAGAATTTAGGGGTAAAATGTAATTTTAGGAAAGTTT
* * *
122128 AGGGGTCAAAATATAATTTTGGAA-ATATTTATGGGTTAAAATGTAATTTTAAGAAAGTTT
1 AGGGGTCAAAA-ATAATTTT-TAAGA-ATTTA-GGGGTAAAATGTAATTTTAGGAAAGTTT
* * * * ** * *
122188 AAGGGTAAAAAATATAATTTTAGGTGTTTAGGGGTTAAAATGTAGTTTTAGAAAAGTTT
1 AGGGGTCAAAAATA-ATTTTTAAGAATTTAGGGG-TAAAATGTAATTTTAGGAAAGTTT
* *
122247 AGAGGTCAAAATGTAATTTTT
1 AGGGGTCAAAA-ATAATTTTT
122268 GGAAAAGTTT
Statistics
Matches: 111, Mismatches: 21, Indels: 16
0.75 0.14 0.11
Matches are distributed among these distances:
58 8 0.07
59 61 0.55
60 42 0.38
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (57 bp):
AGGGGTCAAAAATAATTTTTAAGAATTTAGGGGTAAAATGTAATTTTAGGAAAGTTT
Found at i:122139 original size:30 final size:30
Alignment explanation
Indices: 122100--122296 Score: 179
Period size: 30 Copynumber: 6.6 Consensus size: 30
122090 TAAGAATTTC
*
122100 GGGG-TAAAATGTAATTTTGGGAAAGTTTA
1 GGGGTTAAAATGTAATTTTAGGAAAGTTTA
* * *
122129 GGGGTCAAAATATAATTTT-GGAAATATTTA
1 GGGGTTAAAATGTAATTTTAGGAAA-GTTTA
* *
122159 TGGGTTAAAATGTAATTTTAAGAAAGTTTA
1 GGGGTTAAAATGTAATTTTAGGAAAGTTTA
* * * *
122189 AGGGTAAAAAATATAATTTTAGG--TGTTTA
1 GGGGT-TAAAATGTAATTTTAGGAAAGTTTA
* *
122218 GGGGTTAAAATGTAGTTTTAGAAAAGTTTA
1 GGGGTTAAAATGTAATTTTAGGAAAGTTTA
* * *
122248 GAGGTCAAAATGTAATTTTTGGAAAAGTTT-
1 GGGGTTAAAATGTAATTTTAGG-AAAGTTTA
* *
122278 GAGGTTAAAATGCAATTTT
1 GGGGTTAAAATGTAATTTT
122297 GAAAGAGTTC
Statistics
Matches: 135, Mismatches: 26, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
28 13 0.10
29 18 0.13
30 79 0.59
31 25 0.19
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (30 bp):
GGGGTTAAAATGTAATTTTAGGAAAGTTTA
Found at i:122174 original size:60 final size:60
Alignment explanation
Indices: 122104--122296 Score: 207
Period size: 60 Copynumber: 3.2 Consensus size: 60
122094 AATTTCGGGG
*
122104 TAAAATGTAATTTTGGGAAAGTTTAGGGGTCAAAATATAATTTTGGAAATATTTATGGGT
1 TAAAATGTAATTTTAGGAAAGTTTAGGGGTCAAAATATAATTTTGGAAATATTTATGGGT
* * * * *
122164 TAAAATGTAATTTTAAGAAAGTTTAAGGGTAAAAAATATAATTTTAGG---TGTTTAGGGGT
1 TAAAATGTAATTTTAGGAAAGTTTAGGGGT-CAAAATATAATTTT-GGAAATATTTATGGGT
* * * * *
122223 TAAAATGTAGTTTTAGAAAAGTTTAGAGGTCAAAATGTAATTTTTGGAAA-AGTT-TGAGGT
1 TAAAATGTAATTTTAGGAAAGTTTAGGGGTCAAAATATAA-TTTTGGAAATATTTATG-GGT
*
122283 TAAAATGCAATTTT
1 TAAAATGTAATTTT
122297 GAAAGAGTTC
Statistics
Matches: 108, Mismatches: 18, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
58 10 0.09
59 39 0.36
60 44 0.41
61 13 0.12
62 2 0.02
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.38
Consensus pattern (60 bp):
TAAAATGTAATTTTAGGAAAGTTTAGGGGTCAAAATATAATTTTGGAAATATTTATGGGT
Found at i:124233 original size:7 final size:7
Alignment explanation
Indices: 124219--124263 Score: 81
Period size: 7 Copynumber: 6.4 Consensus size: 7
124209 TGCCTCAGTG
124219 CCCTTTC
1 CCCTTTC
*
124226 CTCTTTC
1 CCCTTTC
124233 CCCTTTC
1 CCCTTTC
124240 CCCTTTC
1 CCCTTTC
124247 CCCTTTC
1 CCCTTTC
124254 CCCTTTC
1 CCCTTTC
124261 CCC
1 CCC
124264 ACCTCTTTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (7 bp):
CCCTTTC
Found at i:125624 original size:18 final size:20
Alignment explanation
Indices: 125586--125624 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
125576 CATTATTTAT
125586 TTTTTGAAATTATAAAATTA
1 TTTTTGAAATTATAAAATTA
*
125606 TTTTT-AAATT-TATAATTA
1 TTTTTGAAATTATAAAATTA
125624 T
1 T
125625 GTAAACAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 5 0.28
20 5 0.28
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
TTTTTGAAATTATAAAATTA
Found at i:129211 original size:29 final size:29
Alignment explanation
Indices: 129169--129225 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
129159 TGCTAGAAGG
129169 AGCTCGTAGGAGGAGACCGCGAGGCCTGA
1 AGCTCGTAGGAGGAGACCGCGAGGCCTGA
129198 AGCTCGTAGGAGGAGACCGCGAGGCCTG
1 AGCTCGTAGGAGGAGACCGCGAGGCCTG
129226 GCGAACGACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.23, C:0.25, G:0.42, T:0.11
Consensus pattern (29 bp):
AGCTCGTAGGAGGAGACCGCGAGGCCTGA
Found at i:132161 original size:24 final size:24
Alignment explanation
Indices: 132117--132162 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
132107 TCAAAAAATA
*
132117 TTTTATTTATGAAGTAAGTTATAT
1 TTTTATTTATGAAATAAGTTATAT
*
132141 TTTTATTATAT-AAATATGTTAT
1 TTTTATT-TATGAAATAAGTTAT
132163 TTCCATAGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.57
Consensus pattern (24 bp):
TTTTATTTATGAAATAAGTTATAT
Found at i:132975 original size:10 final size:10
Alignment explanation
Indices: 132960--132988 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
132950 CGCATTGCAT
132960 TGCCCCGCCC
1 TGCCCCGCCC
132970 TGCCCCGCCC
1 TGCCCCGCCC
132980 TGCCCCGCC
1 TGCCCCGCC
132989 TCTTTAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.69, G:0.21, T:0.10
Consensus pattern (10 bp):
TGCCCCGCCC
Found at i:138556 original size:12 final size:12
Alignment explanation
Indices: 138539--138563 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
138529 ATTAATTTTG
138539 TTTTGTATATTT
1 TTTTGTATATTT
138551 TTTTGTATATTT
1 TTTTGTATATTT
138563 T
1 T
138564 CTTGATAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (12 bp):
TTTTGTATATTT
Found at i:141716 original size:2 final size:2
Alignment explanation
Indices: 141709--141733 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
141699 ATCTCCAGAT
141709 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
141734 TTGAGGCCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:143215 original size:18 final size:18
Alignment explanation
Indices: 143166--143215 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
143156 CGACCCGATT
* *
143166 GAATTAATTCGATTAATC
1 GAATTAATTCGGTTAACC
*
143184 GAATTCGATT-GGTTAACC
1 GAATT-AATTCGGTTAACC
143202 GAATTAATTCGGTT
1 GAATTAATTCGGTT
143216 TTACCCAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 3 0.12
18 20 0.77
19 3 0.12
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (18 bp):
GAATTAATTCGGTTAACC
Found at i:143902 original size:26 final size:26
Alignment explanation
Indices: 143862--143914 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
143852 AAACCATAAG
*
143862 ATGGGTTAAGTAAATCCGAATGTGAA
1 ATGGGTTAAGCAAATCCGAATGTGAA
143888 ATGGGTTAAGCAAATCCGAATGTGAA
1 ATGGGTTAAGCAAATCCGAATGTGAA
143914 A
1 A
143915 GAAGAAATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.40, C:0.09, G:0.26, T:0.25
Consensus pattern (26 bp):
ATGGGTTAAGCAAATCCGAATGTGAA
Found at i:154098 original size:13 final size:12
Alignment explanation
Indices: 154080--154118 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 12
154070 CTTGACATAT
154080 AATAAAATAAATA
1 AATAAAATAAA-A
154093 AATAAAATAGAAA
1 AATAAAATA-AAA
154106 AATAAAAATAAAA
1 AAT-AAAATAAAA
154119 TTAATTGGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 16 0.67
14 8 0.33
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (12 bp):
AATAAAATAAAA
Found at i:155383 original size:21 final size:21
Alignment explanation
Indices: 155285--155376 Score: 139
Period size: 21 Copynumber: 4.4 Consensus size: 21
155275 TAGATGCCTC
* * *
155285 AGTTTTCTTTCGAAAATCTAC
1 AGTTTGCTTTTGAAAATCTAT
155306 AGTTTGCTTTTGAAAATCTAT
1 AGTTTGCTTTTGAAAATCTAT
*
155327 AGTTTGCTTTTGAAAATCTGT
1 AGTTTGCTTTTGAAAATCTAT
155348 AGTTTGCTTTTGAAAATCTAT
1 AGTTTGCTTTTGAAAATCTAT
*
155369 AGATTGCT
1 AGTTTGCT
155377 GCTGAAATTC
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 65 1.00
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (21 bp):
AGTTTGCTTTTGAAAATCTAT
Found at i:163156 original size:36 final size:36
Alignment explanation
Indices: 163106--163209 Score: 154
Period size: 36 Copynumber: 2.9 Consensus size: 36
163096 GGTAACAGGC
*
163106 ATGACCTTTGGGTCAACAGGGAGAAAAATGAGCATA
1 ATGACCTTTGGGTCAACAGGGAGTAAAATGAGCATA
* * * *
163142 ATGACCTTTAGGTCAATAAGGAGTAAAACGAGCATA
1 ATGACCTTTGGGTCAACAGGGAGTAAAATGAGCATA
163178 ATGACCTTTGGGATCAACAGGGAGTAAAATGA
1 ATGACCTTTGGG-TCAACAGGGAGTAAAATGA
163210 ATAATTATCA
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
36 42 0.72
37 16 0.28
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.21
Consensus pattern (36 bp):
ATGACCTTTGGGTCAACAGGGAGTAAAATGAGCATA
Found at i:166869 original size:15 final size:15
Alignment explanation
Indices: 166849--166886 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
166839 GTCATAAACC
166849 AAAAATAAAT-AAAT
1 AAAAATAAATAAAAT
166863 AAGAAAT-AATAAAAT
1 AA-AAATAAATAAAAT
166878 AAAAATAAA
1 AAAAATAAA
166887 AACCCGTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (15 bp):
AAAAATAAATAAAAT
Found at i:172513 original size:43 final size:43
Alignment explanation
Indices: 172452--172537 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
172442 TAACCATCTG
172452 TTTGCAGATGATATACAGTACTAAAGTTCAACCTAGTCCCTAA
1 TTTGCAGATGATATACAGTACTAAAGTTCAACCTAGTCCCTAA
*
172495 TTTGCAGATGATATACAGTACTAAAGTTCAACCTGGTCCCTAA
1 TTTGCAGATGATATACAGTACTAAAGTTCAACCTAGTCCCTAA
172538 AGCCTTATGT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (43 bp):
TTTGCAGATGATATACAGTACTAAAGTTCAACCTAGTCCCTAA
Found at i:179886 original size:37 final size:37
Alignment explanation
Indices: 179836--179906 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
179826 CATATCACTT
* *
179836 GTTTTGATCCAC-TTCTCTGTGTTTCATCAGGAAGATG
1 GTTTTGATCCACTTTCCCT-TATTTCATCAGGAAGATG
* *
179873 GTTTTGGTTCACTTTCCCTTATTTCATCAGGAAG
1 GTTTTGATCCACTTTCCCTTATTTCATCAGGAAG
179907 CTAACCATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 24 0.83
38 5 0.17
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.42
Consensus pattern (37 bp):
GTTTTGATCCACTTTCCCTTATTTCATCAGGAAGATG
Found at i:180148 original size:205 final size:202
Alignment explanation
Indices: 179896--180435 Score: 800
Period size: 204 Copynumber: 2.7 Consensus size: 202
179886 TTCCCTTATT
* * *
179896 TCATCAGGAAGCTAACCATTTATTGCTTTGACCTGCTTCTCAGTGTCTCATCAAGAAGCTAGGGT
1 TCATCAGGAAGCTAACCTTTTATTGCTTTGACCTGCTTCTCAGTGTCTCATCAGGAAGCTCGGGT
179961 TCGAAGATTTGCTCACGTCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAG
66 TCGAAGATTTG-TCAC-TCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAG
* * * * * * *
180026 ATGACTGCA-TCGTTGGTTTCAATTCGCTTCTCTGTATCTCGTTAGGAAGATGAATTTGGTCCCC
129 ATGA-T-CACGCGTTGGTTTCAATTCGCTTCTCTGTACCTCATCAGAAAGACGAATTTGGTCCAC
180090 TTCTCAGTATC
192 TTCTCAGTATC
* * *
180101 TCATCAAGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTAAGTGTCTCATCAGGAAGCTCGGGT
1 TCATCAGGAAGCTAACCTTTTATTGCTTTGACCTGCTTCTCAGTGTCTCATCAGGAAGCTCGGGT
* * * * *
180166 TCGAAGATTTATTCACATAGAGCGTGGGTTTGATTTGATTTTCTTCTCAGTATCTCATCAGAAAG
66 TCGAAGATTT-GTCAC-TCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAG
* *
180231 ATGATCACGCGTTTGTTTTAATTCGCTTCTCTGTACCTCATCAGAAAGACGAATTTGGTCCACTT
129 ATGATCACGCGTTGGTTTCAATTCGCTTCTCTGTACCTCATCAGAAAGACGAATTTGGTCCACTT
180296 CTCAGTATC
194 CTCAGTATC
*
180305 TCATCAGGAAGCTAACCTTTTATTGCTTTGACCTGCTTCTCAGTGTCTCATCAGGAAGTTCGGGT
1 TCATCAGGAAGCTAACCTTTTATTGCTTTGACCTGCTTCTCAGTGTCTCATCAGGAAGCTCGGGT
*
180370 TCGAAGATTTG---CTCGAGCATGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGAT
66 TCGAAGATTTGTCACTCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGAT
180432 GATC
131 GATC
180436 GCGTTGTTTG
Statistics
Matches: 302, Mismatches: 31, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
199 49 0.16
200 1 0.00
203 2 0.01
204 129 0.43
205 121 0.40
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (202 bp):
TCATCAGGAAGCTAACCTTTTATTGCTTTGACCTGCTTCTCAGTGTCTCATCAGGAAGCTCGGGT
TCGAAGATTTGTCACTCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGAT
GATCACGCGTTGGTTTCAATTCGCTTCTCTGTACCTCATCAGAAAGACGAATTTGGTCCACTTCT
CAGTATC
Found at i:191193 original size:96 final size:96
Alignment explanation
Indices: 191026--191210 Score: 234
Period size: 96 Copynumber: 1.9 Consensus size: 96
191016 GAAAAGGATG
* ** *
191026 TTCGATTATCTAGATTTGAGGAAAGGTTGCACTTAGTAAGTTAAGGCACAACATTTCAGAATCGA
1 TTCGATTATCTAGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAACATTTCAGAATCGA
*
191091 ACAT-AAAGAAACATTGCCTCGATTGAGAGTA
66 ACATAAAAG-AACATTACCTCGATTGAGAGTA
* *
191122 TTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAA-ATTTTC-GAAACT
1 TTCGATTATCTAGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAACA-TTTCAG-AA-T
*
191185 CGAA-ATAAAAGAATATTACCTCGATT
63 CGAACATAAAAGAACATTACCTCGATT
191211 TTAAAGTCTT
Statistics
Matches: 77, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
95 2 0.03
96 66 0.86
97 9 0.12
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.30
Consensus pattern (96 bp):
TTCGATTATCTAGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAACATTTCAGAATCGA
ACATAAAAGAACATTACCTCGATTGAGAGTA
Found at i:191542 original size:29 final size:29
Alignment explanation
Indices: 191488--191897 Score: 289
Period size: 29 Copynumber: 14.0 Consensus size: 29
191478 GTAATTTTGG
* *
191488 GGAAGTTCGAGGTTAAAAGATGGAATTTTT
1 GGAAGTTCGGGGGTAAAA-ATGGAATTTTT
*
191518 AGACA-TTCGGGGGTAAAAATGGAATTTTT
1 GGA-AGTTCGGGGGTAAAAATGGAATTTTT
* * * * *
191547 AGACA-TT-TGGGGTCGAAAATAGAGTTTTT
1 GGA-AGTTCGGGGGT-AAAAATGGAATTTTT
*
191576 GGACA--TCTGGGGG-CAAAATGGTAATTTTT
1 GGA-AGTTC-GGGGGTAAAAATGG-AATTTTT
* * * *
191605 GAAAGTTTCAGGGGTAAAAATAGAAATTTT
1 GGAAG-TTCGGGGGTAAAAATGGAATTTTT
* * *
191635 GGAGGTTCGAGGGTAAAAATGTAATTTTT
1 GGAAGTTCGGGGGTAAAAATGGAATTTTT
*
191664 GGAAGTTTCGGGGTTAAAAATGGAATTTTT
1 GGAAG-TTCGGGGGTAAAAATGGAATTTTT
* * *
191694 AGAAGATT-AGGGGTAAAAATTGAA-TTTT
1 GGAAG-TTCGGGGGTAAAAATGGAATTTTT
****
191722 GGAAGTTTTAAGGTCAAAAATGGAATTTTT
1 GGAAGTTCGGGGGT-AAAAATGGAATTTTT
* *** *
191752 AGAAGTTTAAGGGTAAAAATGAAATTTTT
1 GGAAGTTCGGGGGTAAAAATGGAATTTTT
* * *
191781 GGAGGTTTCGAGGTTAAAAATGGAATTTTT
1 GGAAG-TTCGGGGGTAAAAATGGAATTTTT
*
191811 -GAAGTTCGGGGGTCAAAATGGAATTTTT
1 GGAAGTTCGGGGGTAAAAATGGAATTTTT
* ** * *
191839 GGAAATTTTAGGGTTGAAAATGGAATTTTT
1 GG-AAGTTCGGGGGTAAAAATGGAATTTTT
*
191869 GGAAGTTCGAGGGTAAAAATGGAATTTTT
1 GGAAGTTCGGGGGTAAAAATGGAATTTTT
191898 AGAAATTTTA
Statistics
Matches: 301, Mismatches: 63, Indels: 33
0.76 0.16 0.08
Matches are distributed among these distances:
27 2 0.01
28 45 0.15
29 129 0.43
30 116 0.39
31 9 0.03
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (29 bp):
GGAAGTTCGGGGGTAAAAATGGAATTTTT
Found at i:191918 original size:117 final size:117
Alignment explanation
Indices: 191498--191969 Score: 395
Period size: 117 Copynumber: 4.0 Consensus size: 117
191488 GGAAGTTCGA
* * *
191498 GGTTAAAAGATGGAATTTTTAGACA-TTCGGGGGTAAAAATGGAATTTTTAGACA-TTTGGGGTC
1 GGTTAAAA-ATGGAATTTTTAGA-AGTTCGAGGGTAAAAATGGAATTTTTAGAAATTTTAGGGTC
* * * * * *
191561 GAAAATAGAGTTTTTGGACA--TCTGGGGGCAAAATGGTAATTTTT-GAAAGTTTCAG
64 AAAAATGGAATTTTTAGA-AGTTC-AGGGGCAAAATGG-AATTTTTGGAAA-TTTTAG
* * * * * * * * ** *
191616 GGGTAAAAATAGAAATTTTGGAGGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTTCGGGGTTAA
1 GGTTAAAAATGGAATTTTTAGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAATTTTAGGGTCAA
* * * *
191681 AAATGGAATTTTTAGAAGATT-AGGGGTAAAAATTGAA-TTTTGGAAGTTTTAA
66 AAATGGAATTTTTAGAAG-TTCAGGGG-CAAAATGGAATTTTTGGAAATTTTAG
* ** * * ** * *
191733 GGTCAAAAATGGAATTTTTAGAAGTTTAAGGGTAAAAATGAAATTTTT-GGAGGTTTCGAGGTTA
1 GGTTAAAAATGGAATTTTTAGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAATTTTAG-GGTCA
*
191797 AAAATGGAATTTTT-GAAGTTCGGGGGTCAAAATGGAATTTTTGGAAATTTTAG
65 AAAATGGAATTTTTAGAAGTTCAGGGG-CAAAATGGAATTTTTGGAAATTTTAG
* * * *
191850 GGTTGAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAATTTTAGGCTCGA
1 GGTTAAAAATGGAATTTTTAGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAATTTTAGGGTCAA
* * * * *
191915 AAATGGAATTTTTAAAAGTTCAAGGGCAAAAATGTAATTTTTGGATAGTTTAG
66 AAATGGAATTTTTAGAAGTTCAGGGGC-AAAATGGAATTTTTGGAAATTTTAG
191968 GG
1 GG
191970 ACCTCCAAGG
Statistics
Matches: 282, Mismatches: 59, Indels: 26
0.77 0.16 0.07
Matches are distributed among these distances:
115 2 0.01
116 23 0.08
117 174 0.62
118 76 0.27
119 6 0.02
120 1 0.00
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.34
Consensus pattern (117 bp):
GGTTAAAAATGGAATTTTTAGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAATTTTAGGGTCAA
AAATGGAATTTTTAGAAGTTCAGGGGCAAAATGGAATTTTTGGAAATTTTAG
Found at i:191947 original size:29 final size:29
Alignment explanation
Indices: 191590--191964 Score: 292
Period size: 30 Copynumber: 12.7 Consensus size: 29
191580 ATCTGGGGGC
* *
191590 AAAATGGTAATTTTTGAAAGTTTCAGGGGTA
1 AAAATGG-AATTTTTGGAAG-TTCAAGGGTA
* * * *
191621 AAAATAGAAATTTTGGAGGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTCAAGGGTA
* *
191650 AAAATGTAATTTTTGGAAGTTTC-GGGGTTA
1 AAAATGGAATTTTTGGAAG-TTCAAGGG-TA
* *
191680 AAAATGGAATTTTTAGAAGATT-AGGGGTA
1 AAAATGGAATTTTTGGAAG-TTCAAGGGTA
* *
191709 AAAATTGAA-TTTTGGAAGTTTTAA-GGTCA
1 AAAATGGAATTTTTGGAAG-TTCAAGGGT-A
* *
191738 AAAATGGAATTTTTAGAAGTTTAAGGGTA
1 AAAATGGAATTTTTGGAAGTTCAAGGGTA
* * * *
191767 AAAATGAAATTTTTGGAGGTTTCGAGGTTA
1 AAAATGGAATTTTTGGAAG-TTCAAGGGTA
** *
191797 AAAATGGAATTTTT-GAAGTTCGGGGGTC
1 AAAATGGAATTTTTGGAAGTTCAAGGGTA
* ** *
191825 AAAATGGAATTTTTGGAAATTTTAGGGTTG
1 AAAATGGAATTTTTGGAAGTTCAAGGG-TA
*
191855 AAAATGGAATTTTTGGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTCAAGGGTA
* * ** * *
191884 AAAATGGAATTTTTAGAAATTTTAGGCTCG
1 AAAATGGAATTTTTGGAAGTTCAAGGGT-A
** *
191914 AAAATGGAATTTTTAAAAGTTCAAGGGCA
1 AAAATGGAATTTTTGGAAGTTCAAGGGTA
*
191943 AAAATGTAATTTTTGGATAGTT
1 AAAATGGAATTTTTGGA-AGTT
191965 TAGGGACCTC
Statistics
Matches: 276, Mismatches: 56, Indels: 25
0.77 0.16 0.07
Matches are distributed among these distances:
28 34 0.12
29 117 0.42
30 119 0.43
31 6 0.02
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTCAAGGGTA
Found at i:191968 original size:59 final size:58
Alignment explanation
Indices: 191590--191965 Score: 355
Period size: 59 Copynumber: 6.4 Consensus size: 58
191580 ATCTGGGGGC
* * * * * * *
191590 AAAATGGTAATTTTTGAAAGTTTCAGGGGTAAAAATAGAAATTTTGGAGGTTCGAGGGTA
1 AAAAT-GTAATTTTTGGAAGTTTCA-GGTTAAAAATGGAATTTTTAGAAGTTCAAGGGTA
* *
191650 AAAATGTAATTTTTGGAAGTTTCGGGGTTAAAAATGGAATTTTTAGAAGATT-AGGGGTA
1 AAAATGTAATTTTTGGAAGTTTC-AGGTTAAAAATGGAATTTTTAGAAG-TTCAAGGGTA
* * *
191709 AAAAT-TGAA-TTTTGGAAGTTTTAAGGTCAAAAATGGAATTTTTAGAAGTTTAAGGGTA
1 AAAATGT-AATTTTTGGAAG-TTTCAGGTTAAAAATGGAATTTTTAGAAGTTCAAGGGTA
* * ** *
191767 AAAATGAAATTTTTGGAGGTTTCGAGGTTAAAAATGGAATTTTT-GAAGTTCGGGGGTC
1 AAAATGTAATTTTTGGAAGTTTC-AGGTTAAAAATGGAATTTTTAGAAGTTCAAGGGTA
* * * * * *
191825 AAAATGGAATTTTTGGAAATTTTAGGGTTGAAAATGGAATTTTTGGAAGTTCGAGGGTA
1 AAAATGTAATTTTTGGAAGTTTCA-GGTTAAAAATGGAATTTTTAGAAGTTCAAGGGTA
* * * * ** * *
191884 AAAATGGAATTTTTAGAAATTTTAGGCTCGAAAATGGAATTTTTAAAAGTTCAAGGGCA
1 AAAATGTAATTTTTGGAAGTTTCAGG-TTAAAAATGGAATTTTTAGAAGTTCAAGGGTA
191943 AAAATGTAATTTTTGGATAGTTT
1 AAAATGTAATTTTTGGA-AGTTT
191966 AGGGACCTCC
Statistics
Matches: 267, Mismatches: 37, Indels: 24
0.81 0.11 0.07
Matches are distributed among these distances:
57 3 0.01
58 98 0.37
59 155 0.58
60 11 0.04
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (58 bp):
AAAATGTAATTTTTGGAAGTTTCAGGTTAAAAATGGAATTTTTAGAAGTTCAAGGGTA
Done.