Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008640.1 Hibiscus syriacus cultivar Beakdansim tig00111616_pilon, 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: 250914
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:168357 original size:16 final size:16
Alignment explanation
Indices: 168333--168562 Score: 62
Period size: 16 Copynumber: 14.8 Consensus size: 16
168323 TAACATGTAC
* *
168333 ATATGTACATGCATGT
1 ATATATACATACATGT
*
168349 ATATATACATACATGC
1 ATATATACATACATGT
*
168365 ATGTAT--AT--ATGT
1 ATATATACATACATGT
*
168377 -TATATA-AGACATGT
1 ATATATACATACATGT
* * *
168391 ATGTAT--GTATATGT
1 ATATATACATACATGT
* * **
168405 ATATAGATATGTATGT
1 ATATATACATACATGT
* **
168421 ATGTATATCATACATAC
1 ATATATA-CATACATGT
* **
168438 ATACATACATACATAC
1 ATATATACATACATGT
* **
168454 ATACATACATACATAC
1 ATATATACATACATGT
* **
168470 ATACATACATACATAC
1 ATATATACATACATGT
* **
168486 ATACATACATACATAC
1 ATATATACATACATGT
* **
168502 ATACATACATACATAC
1 ATATATACATACATGT
* **
168518 ATACATACATACATAC
1 ATATATACATACATGT
* **
168534 ATACATACATACATAC
1 ATATATACATACATGT
*
168550 ATACATACATACA
1 ATATATACATACA
168563 CACATACACA
Statistics
Matches: 183, Mismatches: 24, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
11 4 0.02
12 4 0.02
14 15 0.08
15 4 0.02
16 147 0.80
17 9 0.05
ACGTcount: A:0.44, C:0.17, G:0.07, T:0.32
Consensus pattern (16 bp):
ATATATACATACATGT
Found at i:168423 original size:26 final size:28
Alignment explanation
Indices: 168345--168428 Score: 95
Period size: 26 Copynumber: 3.1 Consensus size: 28
168335 ATGTACATGC
* *
168345 ATGTATATATACATACATGCATGTA--TAT
1 ATGT-TATATA-AGACATGTATGTATGTAT
168373 ATGTTATATAAGACATGTATGTATGTAT
1 ATGTTATATAAGACATGTATGTATGTAT
*
168401 ATG-TATAT-AGATATGTATGTATGTAT
1 ATGTTATATAAGACATGTATGTATGTAT
168427 AT
1 AT
168429 CATACATACA
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
26 30 0.59
27 11 0.22
28 10 0.20
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.43
Consensus pattern (28 bp):
ATGTTATATAAGACATGTATGTATGTAT
Found at i:168436 original size:4 final size:4
Alignment explanation
Indices: 168429--168570 Score: 275
Period size: 4 Copynumber: 35.5 Consensus size: 4
168419 GTATGTATAT
168429 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
168477 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
168525 CATA CATA CATA CATA CATA CATA CATA CATA CATA CACA CATA CA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CA
168571 CACACGCACA
Statistics
Matches: 136, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
4 136 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:168575 original size:12 final size:12
Alignment explanation
Indices: 168432--168817 Score: 113
Period size: 12 Copynumber: 32.5 Consensus size: 12
168422 TGTATATCAT
* *
168432 ACATACATACAT
1 ACATACACACAC
* *
168444 ACATACATACAT
1 ACATACACACAC
* *
168456 ACATACATACAT
1 ACATACACACAC
* *
168468 ACATACATACAT
1 ACATACACACAC
* *
168480 ACATACATACAT
1 ACATACACACAC
* *
168492 ACATACATACAT
1 ACATACACACAC
* *
168504 ACATACATACAT
1 ACATACACACAC
* *
168516 ACATACATACAT
1 ACATACACACAC
* *
168528 ACATACATACAT
1 ACATACACACAC
* *
168540 ACATACATACAT
1 ACATACACACAC
*
168552 ACATACATACAC
1 ACATACACACAC
168564 ACATACACACAC
1 ACATACACACAC
* *
168576 GC--ACACGCAC
1 ACATACACACAC
* * *
168586 AC--GCGCACGC
1 ACATACACACAC
* * *
168596 GC--ACGCGCAC
1 ACATACACACAC
* *** *
168606 GCGCGCACACGC
1 ACATACACACAC
** *
168618 ACACGCACACGC
1 ACATACACACAC
* *
168630 ACACACGCACAC
1 ACATACACACAC
* *
168642 GCATACACGCAC
1 ACATACACACAC
*** *
168654 ACGCGCACACGC
1 ACATACACACAC
** *
168666 ACACGCACACGC
1 ACATACACACAC
* *
168678 ACACACTCACAC
1 ACATACACACAC
* *
168690 TCACACACACAC
1 ACATACACACAC
* *
168702 TCACACACACAC
1 ACATACACACAC
168714 ACATACACACACAC
1 ACAT--ACACACAC
*
168728 ACATACATACAC
1 ACATACACACAC
168740 ACAT--ACACAC
1 ACATACACACAC
*
168750 ACATACACACAT
1 ACATACACACAC
* *
168762 ACATACATATATAC
1 ACATAC--ACACAC
*
168776 ACATACACATAC
1 ACATACACACAC
*
168788 ACATACAGACAC
1 ACATACACACAC
* * *
168800 ATACAAACACAC
1 ACATACACACAC
168812 ACATAC
1 ACATAC
168818 TTTTAAAATG
Statistics
Matches: 310, Mismatches: 56, Indels: 16
0.81 0.15 0.04
Matches are distributed among these distances:
10 29 0.09
12 260 0.84
14 21 0.07
ACGTcount: A:0.44, C:0.37, G:0.06, T:0.13
Consensus pattern (12 bp):
ACATACACACAC
Found at i:168580 original size:6 final size:6
Alignment explanation
Indices: 168571--168713 Score: 119
Period size: 6 Copynumber: 22.8 Consensus size: 6
168561 CACACATACA
* * * *
168571 CACACG CACACG CACACG CGCACG CGCACG CGCACG --CGCG CACACG
1 CACACG CACACG CACACG CACACG CACACG CACACG CACACG CACACG
168617 CACACG CACACG CACACACG CACACG CATACACG CACACGCG CACACG
1 CACACG CACACG --CACACG CACACG C--ACACG CACA--CG CACACG
* * * * *
168665 CACACG CACACG CACACACT CACACT CACACA CACACT CACACA CACAC
1 CACACG CACACG --CACACG CACACG CACACG CACACG CACACG CACAC
168714 ACATACACAC
Statistics
Matches: 120, Mismatches: 7, Indels: 20
0.82 0.05 0.14
Matches are distributed among these distances:
4 3 0.03
6 94 0.78
8 23 0.19
ACGTcount: A:0.32, C:0.50, G:0.15, T:0.03
Consensus pattern (6 bp):
CACACG
Found at i:168586 original size:14 final size:14
Alignment explanation
Indices: 168577--168729 Score: 129
Period size: 14 Copynumber: 11.4 Consensus size: 14
168567 TACACACACG
*
168577 CACACGCACACGCG
1 CACACGCACACGCA
* *
168591 CACGCGCACGCGCA
1 CACACGCACACGCA
* *
168605 CGCGCGCACACG--
1 CACACGCACACGCA
168617 CACACGCACACGCA
1 CACACGCACACGCA
168631 CACACGCACACGCA
1 CACACGCACACGCA
* *
168645 TACACGCACACGCG
1 CACACGCACACGCA
168659 CACACGCACACG--
1 CACACGCACACGCA
* *
168671 CACACGCACACACT
1 CACACGCACACGCA
*
168685 CACACTCACA--CA
1 CACACGCACACGCA
* *
168697 CACACTCACACACA
1 CACACGCACACGCA
** *
168711 CACACATACACACA
1 CACACGCACACGCA
168725 CACAC
1 CACAC
168730 ATACATACAC
Statistics
Matches: 118, Mismatches: 15, Indels: 12
0.81 0.10 0.08
Matches are distributed among these distances:
12 32 0.27
14 86 0.73
ACGTcount: A:0.34, C:0.49, G:0.14, T:0.03
Consensus pattern (14 bp):
CACACGCACACGCA
Found at i:168586 original size:20 final size:20
Alignment explanation
Indices: 168560--168729 Score: 133
Period size: 20 Copynumber: 8.5 Consensus size: 20
168550 ATACATACAT
* *
168560 ACACACATACACACACGCAC
1 ACACACACACGCACACGCAC
* * *
168580 ACGCACACGCGCACGCGCAC
1 ACACACACACGCACACGCAC
* * * *
168600 GCGCACGCGCGCACACGCAC
1 ACACACACACGCACACGCAC
* * *
168620 ACGCACACGCACACACGCAC
1 ACACACACACGCACACGCAC
* * *
168640 ACGCATACACGCACACGCGC
1 ACACACACACGCACACGCAC
*
168660 ACACGCACACGCACACGCAC
1 ACACACACACGCACACGCAC
* * *
168680 ACACTCACACTCACACACAC
1 ACACACACACGCACACGCAC
* * **
168700 ACTCACACACACACACATAC
1 ACACACACACGCACACGCAC
168720 ACACACACAC
1 ACACACACAC
168730 ATACATACAC
Statistics
Matches: 123, Mismatches: 27, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 123 1.00
ACGTcount: A:0.35, C:0.48, G:0.13, T:0.04
Consensus pattern (20 bp):
ACACACACACGCACACGCAC
Found at i:168714 original size:6 final size:6
Alignment explanation
Indices: 168611--168814 Score: 129
Period size: 6 Copynumber: 34.0 Consensus size: 6
168601 CGCACGCGCG
* * * * * * * * *
168611 CACACG CACACG CACACG CACACA CGCACA CGCATA CACGCA CACGCG
1 CACACA CACACA CACACA CACACA CACACA CACACA CACACA CACACA
* * * * * *
168659 CACACG CACACG CACACG CACACA CTCACA CTCACA CACACA CTCACA
1 CACACA CACACA CACACA CACACA CACACA CACACA CACACA CACACA
* * * * *
168707 CACACA CACATA CACACA CACACA TACATA CACACA TACACA CACATA
1 CACACA CACACA CACACA CACACA CACACA CACACA CACACA CACACA
* * * * * * * * * *
168755 CACACA TACATA CATATA TACACA TACACA TACACA TACAGA CACATA
1 CACACA CACACA CACACA CACACA CACACA CACACA CACACA CACACA
*
168803 CAAACA CACACA
1 CACACA CACACA
168815 TACTTTTAAA
Statistics
Matches: 162, Mismatches: 36, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 162 1.00
ACGTcount: A:0.44, C:0.42, G:0.06, T:0.09
Consensus pattern (6 bp):
CACACA
Found at i:168721 original size:26 final size:25
Alignment explanation
Indices: 168677--168817 Score: 114
Period size: 26 Copynumber: 5.7 Consensus size: 25
168667 CACGCACACG
*
168677 CACACACTCACAC-TCACACACACACT
1 CACACACACACACAT-ACACACACA-T
168703 CACACACACACACATACACACACA-
1 CACACACACACACATACACACACAT
*
168727 CACATACATACACACATACACACACAT
1 CAC--ACACACACACATACACACACAT
* * * *
168754 ACACACATACATACATATATACACAT
1 -CACACACACACACATACACACACAT
* *
168780 ---ACACATACACATACAGACACAT
1 CACACACACACACATACACACACAT
*
168802 -ACAAACACACACATAC
1 CACACACACACACATAC
168818 TTTTAAAATG
Statistics
Matches: 96, Mismatches: 12, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
22 17 0.18
24 15 0.16
26 60 0.62
27 1 0.01
28 3 0.03
ACGTcount: A:0.48, C:0.38, G:0.01, T:0.13
Consensus pattern (25 bp):
CACACACACACACATACACACACAT
Found at i:168730 original size:20 final size:20
Alignment explanation
Indices: 168444--168814 Score: 122
Period size: 20 Copynumber: 18.6 Consensus size: 20
168434 ATACATACAT
* * * *
168444 ACATACATACATACATACAT
1 ACATACACACACACACACAC
* * * *
168464 ACATACATACATACATACAT
1 ACATACACACACACACACAC
* * * *
168484 ACATACATACATACATACAT
1 ACATACACACACACACACAC
* * * *
168504 ACATACATACATACATACAT
1 ACATACACACACACACACAC
* * * *
168524 ACATACATACATACATACAT
1 ACATACACACACACACACAC
* * *
168544 ACATACATACATACATACAC
1 ACATACACACACACACACAC
* *
168564 ACATACACACACGCACACGC
1 ACATACACACACACACACAC
* * * * *
168584 AC--ACGCGCACGCGCACGC
1 ACATACACACACACACACAC
* ** * * *
168602 GCACGCGCGCACACGCACAC
1 ACATACACACACACACACAC
* * * *
168622 GCACACGCACACACGCACAC
1 ACATACACACACACACACAC
* * * *
168642 GCATACACGCACACGCGCAC
1 ACATACACACACACACACAC
** * *
168662 ACGCACACGCACACGCACAC
1 ACATACACACACACACACAC
*
168682 AC-T-CACACTCACACACAC
1 ACATACACACACACACACAC
*
168700 AC-TCACACACACACACATAC
1 ACAT-ACACACACACACACAC
* * *
168720 ACACACACACATACATACAC
1 ACATACACACACACACACAC
*
168740 ACATACACACACATACACACAT
1 ACATACACACAC--ACACACAC
* * * *
168762 ACATACATATATACACATAC
1 ACATACACACACACACACAC
* * *
168782 ACATACACATACAGACACAT
1 ACATACACACACACACACAC
*
168802 ACAAACACACACA
1 ACATACACACACA
168815 TACTTTTAAA
Statistics
Matches: 295, Mismatches: 49, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
18 29 0.10
20 251 0.85
22 15 0.05
ACGTcount: A:0.44, C:0.37, G:0.06, T:0.13
Consensus pattern (20 bp):
ACATACACACACACACACAC
Found at i:168946 original size:62 final size:61
Alignment explanation
Indices: 168818--169008 Score: 152
Period size: 62 Copynumber: 3.1 Consensus size: 61
168808 ACACACATAC
* * * * * * * * * * * *
168818 TTTTAAAATGGAAACATTTCTTCTTCTCTCTACACT-CATACTTTTAAAAATTTTAATGAA
1 TTTTAAAATGAAAACCTTTCATATTATCTCTTCCCTCCATAATTTTCAAAACTTTAGTAAA
* * * * *
168878 TATTTAAAATGAAAACTTTTCCTCTTATTTCTTCCCTCTATAATTTTCAAAA-TTGTAGTAAAA
1 T-TTTAAAATGAAAACCTTTCATATTATCTCTTCCCTCCATAATTTTCAAAACTT-TAGT-AAA
* * * *
168941 TTTTAAAATGAAAACCTTTCATATTCTCTCTTTCCTCCATAATTTTTAAAACTTTAGTGAA
1 TTTTAAAATGAAAACCTTTCATATTATCTCTTCCCTCCATAATTTTCAAAACTTTAGTAAA
169002 TTTTAAA
1 TTTTAAA
169009 TGGATTTTTT
Statistics
Matches: 105, Mismatches: 21, Indels: 9
0.78 0.16 0.07
Matches are distributed among these distances:
60 1 0.01
61 39 0.37
62 60 0.57
63 5 0.05
ACGTcount: A:0.35, C:0.16, G:0.05, T:0.45
Consensus pattern (61 bp):
TTTTAAAATGAAAACCTTTCATATTATCTCTTCCCTCCATAATTTTCAAAACTTTAGTAAA
Found at i:173686 original size:32 final size:32
Alignment explanation
Indices: 173592--173689 Score: 128
Period size: 32 Copynumber: 3.1 Consensus size: 32
173582 GCGTTATTGG
* * *
173592 CTCTGCTGTGCAATATCTGAATGCT-ATACTAA
1 CTCTACTGTGCATTATCTGAATG-TAATACTGA
*
173624 CTCTGA-TGTGCATTATTTGAATGTAATACTGA
1 CTCT-ACTGTGCATTATCTGAATGTAATACTGA
173656 CTCTACTGTGCATTATCTGAATGTAATACTGA
1 CTCTACTGTGCATTATCTGAATGTAATACTGA
173688 CT
1 CT
173690 ATGTTGTGAC
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
31 2 0.03
32 56 0.97
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (32 bp):
CTCTACTGTGCATTATCTGAATGTAATACTGA
Found at i:182182 original size:40 final size:40
Alignment explanation
Indices: 182138--182217 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
182128 CATTTTTTAA
*
182138 CAATAATCAGTACATATAGCTCAATTAGGA-ATTAGACATC
1 CAATAATCAATACATATAGCTCAATT-GGAGATTAGACATC
* *
182178 CAATAATCAATACATATGGCTCAATTGGAGATTATACATC
1 CAATAATCAATACATATAGCTCAATTGGAGATTAGACATC
182218 TGATATTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 3 0.08
40 33 0.92
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.29
Consensus pattern (40 bp):
CAATAATCAATACATATAGCTCAATTGGAGATTAGACATC
Found at i:183078 original size:35 final size:35
Alignment explanation
Indices: 183039--183110 Score: 128
Period size: 35 Copynumber: 2.1 Consensus size: 35
183029 GTTGTTTAGG
183039 GAAAATATTATCATA-TCGAATACAGGTGTTGGCAT
1 GAAAATATTATCA-ACTCGAATACAGGTGTTGGCAT
183074 GAAAATATTATCAACTCGAATACAGGTGTTGGCAT
1 GAAAATATTATCAACTCGAATACAGGTGTTGGCAT
183109 GA
1 GA
183111 TTCTGCTTCG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
34 1 0.03
35 35 0.97
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (35 bp):
GAAAATATTATCAACTCGAATACAGGTGTTGGCAT
Found at i:186318 original size:13 final size:13
Alignment explanation
Indices: 186300--186329 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
186290 GACCGGTCAC
*
186300 GACCCGACCCGTT
1 GACCCGAACCGTT
186313 GACCCGAACCGTT
1 GACCCGAACCGTT
186326 GACC
1 GACC
186330 GTTGACCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.43, G:0.23, T:0.13
Consensus pattern (13 bp):
GACCCGAACCGTT
Found at i:188889 original size:24 final size:24
Alignment explanation
Indices: 188775--188886 Score: 145
Period size: 24 Copynumber: 4.7 Consensus size: 24
188765 ATTTGAATTA
188775 TGATCTGATACTTGACATGGATTC
1 TGATCTGATACTTGACATGGATTC
* *
188799 TGATATAATA-TCTGACATGGATTC
1 TGATCTGATACT-TGACATGGATTC
*
188823 TGATCTGATACTTGACTTGGATTC
1 TGATCTGATACTTGACATGGATTC
* * *
188847 TGATCTGTTACTTGACCTGGTTTC
1 TGATCTGATACTTGACATGGATTC
*
188871 TGATATGATACTTGAC
1 TGATCTGATACTTGAC
188887 CTGATTTATG
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
23 1 0.01
24 74 0.97
25 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (24 bp):
TGATCTGATACTTGACATGGATTC
Found at i:188903 original size:24 final size:24
Alignment explanation
Indices: 188772--188896 Score: 69
Period size: 24 Copynumber: 5.2 Consensus size: 24
188762 TTGATTTGAA
* *
188772 TTATGATCTGATACTTGACATGGA-
1 TTATGATATGATACTTGACCT-GAT
* * *
188796 TTCTGATATAATA-TCTGACATGGA-
1 TTATGATATGATACT-TGACCT-GAT
* * *
188820 TTCTGATCTGATACTTGACTTGGA-
1 TTATGATATGATACTTGACCT-GAT
* * * *
188844 TTCTGATCTGTTACTTGACCTGGT
1 TTATGATATGATACTTGACCTGAT
*
188868 TTCTGATATGATACTTGACCTGAT
1 TTATGATATGATACTTGACCTGAT
188892 TTATG
1 TTATG
188897 TTTTGATTTT
Statistics
Matches: 85, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
23 2 0.02
24 82 0.96
25 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (24 bp):
TTATGATATGATACTTGACCTGAT
Found at i:194945 original size:12 final size:13
Alignment explanation
Indices: 194918--194946 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
194908 CATGATTATC
194918 ATTTTATTTAAAT
1 ATTTTATTTAAAT
194931 ATTTTATTT-AAT
1 ATTTTATTTAAAT
194943 ATTT
1 ATTT
194947 CTAGTCAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
ATTTTATTTAAAT
Found at i:197024 original size:26 final size:26
Alignment explanation
Indices: 196995--197076 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
196985 GAATTGTGGT
*
196995 TTTTGAGTAGGGATCTAATATTGAGC
1 TTTTGAGTAGGGATCTAATATTGAGA
* * * * *
197021 TTTTGGGAATGG-TTTGAAT-TGTG-GT
1 TTTTGAGTAGGGATCT-AATAT-TGAGA
197046 TTTTGAGTAGGGATCTAATATTGAGA
1 TTTTGAGTAGGGATCTAATATTGAGA
197072 TTTTG
1 TTTTG
197077 GGAATTTGGG
Statistics
Matches: 41, Mismatches: 10, Indels: 10
0.67 0.16 0.16
Matches are distributed among these distances:
25 18 0.44
26 23 0.56
ACGTcount: A:0.23, C:0.04, G:0.29, T:0.44
Consensus pattern (26 bp):
TTTTGAGTAGGGATCTAATATTGAGA
Found at i:197035 original size:51 final size:51
Alignment explanation
Indices: 196969--197081 Score: 217
Period size: 51 Copynumber: 2.2 Consensus size: 51
196959 GAAAAGTTTA
196969 ATTTTGGGAATGGTTTGAATTGTGGTTTTTGAGTAGGGATCTAATATTGAG
1 ATTTTGGGAATGGTTTGAATTGTGGTTTTTGAGTAGGGATCTAATATTGAG
*
197020 CTTTTGGGAATGGTTTGAATTGTGGTTTTTGAGTAGGGATCTAATATTGAG
1 ATTTTGGGAATGGTTTGAATTGTGGTTTTTGAGTAGGGATCTAATATTGAG
197071 ATTTTGGGAAT
1 ATTTTGGGAAT
197082 TTGGGCGGAG
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.23, C:0.03, G:0.31, T:0.43
Consensus pattern (51 bp):
ATTTTGGGAATGGTTTGAATTGTGGTTTTTGAGTAGGGATCTAATATTGAG
Found at i:198536 original size:47 final size:49
Alignment explanation
Indices: 198485--198582 Score: 173
Period size: 49 Copynumber: 2.0 Consensus size: 49
198475 CGAAAAACAC
198485 AATATTAAACAAACAAAATAAAT-ATG-AGAGAACGTATCAAATTTACT
1 AATATTAAACAAACAAAATAAATAATGAAGAGAACGTATCAAATTTACT
*
198532 AATATTGAACAAACAAAATAAATAATGAAGAGAACGTATCAAATTTACT
1 AATATTAAACAAACAAAATAAATAATGAAGAGAACGTATCAAATTTACT
198581 AA
1 AA
198583 ATTCAACGAA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
47 22 0.46
48 3 0.06
49 23 0.48
ACGTcount: A:0.56, C:0.10, G:0.09, T:0.24
Consensus pattern (49 bp):
AATATTAAACAAACAAAATAAATAATGAAGAGAACGTATCAAATTTACT
Found at i:199333 original size:2 final size:2
Alignment explanation
Indices: 199326--199388 Score: 119
Period size: 2 Copynumber: 32.0 Consensus size: 2
199316 AAATAATTGG
199326 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
199368 AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
199389 GAGTTCTACC
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 59 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:200103 original size:3 final size:3
Alignment explanation
Indices: 200095--200138 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
200085 ATTAAACTTT
200095 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
200139 TGTTGTTGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:202758 original size:2 final size:2
Alignment explanation
Indices: 202751--202780 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
202741 TGCATAAATC
202751 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
202781 GAGTAAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:202983 original size:29 final size:29
Alignment explanation
Indices: 202919--202985 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
202909 ATATACTTAA
* ** *
202919 ATAATATATGTTTACAAAATATATTATAT
1 ATAATATATGTTTACAAAATAAAAGACAT
*
202948 ACT-ATATATGTTTACAAAGTAAAAGACAT
1 A-TAATATATGTTTACAAAATAAAAGACAT
202977 ATAATATAT
1 ATAATATAT
202986 TATGGGAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
28 1 0.03
29 29 0.94
30 1 0.03
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.39
Consensus pattern (29 bp):
ATAATATATGTTTACAAAATAAAAGACAT
Found at i:204710 original size:47 final size:47
Alignment explanation
Indices: 204650--204835 Score: 193
Period size: 48 Copynumber: 3.9 Consensus size: 47
204640 AAATATGATA
* *
204650 AGGGATATGTTCCGCTGTCACT-CAGGGAATATCAAATCTTGAATGAG
1 AGGGATATGTTCCGCT-TTACTGAAGGGAATATCAAATCTTGAATGAG
* * *
204697 AGGGATGTGTTCCGCTTTTGCTGAAGGGAATATCAAATATTGAATGAG
1 AGGGATATGTTCCGC-TTTACTGAAGGGAATATCAAATCTTGAATGAG
* * *
204745 AGGGATATGTTCCTCTTTTGTCTGAAGGGAATATCAAATCTTGGA-GA-
1 AGGGATATGTTCCGC-TTT-ACTGAAGGGAATATCAAATCTTGAATGAG
*
204792 AGAGACT-TGTTCCGC-TTACTCTGAAGGGAATATCAAATCTTGAA
1 AGGGA-TATGTTCCGCTTTA--CTGAAGGGAATATCAAATCTTGAA
204836 GAAGATAGAC
Statistics
Matches: 119, Mismatches: 14, Indels: 13
0.82 0.10 0.09
Matches are distributed among these distances:
45 2 0.02
46 23 0.19
47 28 0.24
48 44 0.37
49 22 0.18
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (47 bp):
AGGGATATGTTCCGCTTTACTGAAGGGAATATCAAATCTTGAATGAG
Found at i:204752 original size:95 final size:95
Alignment explanation
Indices: 204650--204835 Score: 227
Period size: 95 Copynumber: 2.0 Consensus size: 95
204640 AAATATGATA
* *
204650 AGGGATATGTTCCGC-TGTCACT-CAGGGAATATCAAATCTTGAATGAGAGGGA-TGTGTTCCGC
1 AGGGATATGTTCCGCTTGTCACTGAAGGGAATATCAAATCTTGAA-GA-AGAGACT-TGTTCCGC
*
204712 TT-TTGCTGAAGGGAATATCAAATATTGAATGAG
63 TTACT-CTGAAGGGAATATCAAATATTGAATGAG
* * ** *
204745 AGGGATATGTTCCTCTTTTGTCTGAAGGGAATATCAAATCTTGGAGAAGAGACTTGTTCCGCTTA
1 AGGGATATGTTCCGCTTGTCACTGAAGGGAATATCAAATCTTGAAGAAGAGACTTGTTCCGCTTA
*
204810 CTCTGAAGGGAATATCAAATCTTGAA
66 CTCTGAAGGGAATATCAAATATTGAA
204836 GAAGATAGAC
Statistics
Matches: 78, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
95 51 0.65
96 8 0.10
97 19 0.24
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (95 bp):
AGGGATATGTTCCGCTTGTCACTGAAGGGAATATCAAATCTTGAAGAAGAGACTTGTTCCGCTTA
CTCTGAAGGGAATATCAAATATTGAATGAG
Found at i:204851 original size:95 final size:96
Alignment explanation
Indices: 204673--204879 Score: 235
Period size: 95 Copynumber: 2.2 Consensus size: 96
204663 GCTGTCACTC
* *
204673 AGGGAATATCAAATCTTGAATGAGAGGGATGTGTTCCGCTTTTGCTGAAGGGAATATCAAATATT
1 AGGGAATATCAAATCTTGAATGAGAGAGATGTGTTCCGCTTCTGCTGAAGGGAATATCAAATATT
* * * **
204738 GAATGAGAGGGATATGTTCCTCTTTTGTCTGA
66 GAATGAGAGAGACATGTTCCAC-TTACTCTGA
* *
204770 AGGGAATATCAAATCTTGGA-GA-AGAGACT-TGTTCCGCTTACT-CTGAAGGGAATATCAAATC
1 AGGGAATATCAAATCTTGAATGAGAGAGA-TGTGTTCCGCTT-CTGCTGAAGGGAATATCAAATA
* *
204831 TTGAA-GAAGATAGACCTGTTCCACTTACTCTGA
64 TTGAATG-AGAGAGACATGTTCCACTTACTCTGA
*
204864 AGGGAATATCAGATCT
1 AGGGAATATCAAATCT
204880 GGGGAAGTTG
Statistics
Matches: 95, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
94 23 0.24
95 49 0.52
96 4 0.04
97 19 0.20
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.30
Consensus pattern (96 bp):
AGGGAATATCAAATCTTGAATGAGAGAGATGTGTTCCGCTTCTGCTGAAGGGAATATCAAATATT
GAATGAGAGAGACATGTTCCACTTACTCTGA
Found at i:204870 original size:48 final size:48
Alignment explanation
Indices: 204673--204879 Score: 215
Period size: 48 Copynumber: 4.3 Consensus size: 48
204663 GCTGTCACTC
* ** *
204673 AGGGAATATCAAATCTTGAATGAGAGGGATGTGTTCCGCTT-TTGCTGA
1 AGGGAATATCAAATCTTGAATGAGAGAGACATGTTCCGCTTACT-CTGA
* * * * **
204721 AGGGAATATCAAATATTGAATGAGAGGGATATGTTCCTCTTTTGTCTGA
1 AGGGAATATCAAATCTTGAATGAGAGAGACATGTTCCGC-TTACTCTGA
* *
204770 AGGGAATATCAAATCTTGGA-GA-AGAGACTTGTTCCGCTTACTCTGA
1 AGGGAATATCAAATCTTGAATGAGAGAGACATGTTCCGCTTACTCTGA
* * *
204816 AGGGAATATCAAATCTTGAA-GAAGATAGACCTGTTCCACTTACTCTGA
1 AGGGAATATCAAATCTTGAATG-AGAGAGACATGTTCCGCTTACTCTGA
*
204864 AGGGAATATCAGATCT
1 AGGGAATATCAAATCT
204880 GGGGAAGTTG
Statistics
Matches: 138, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
46 27 0.20
47 12 0.09
48 74 0.54
49 24 0.17
50 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.30
Consensus pattern (48 bp):
AGGGAATATCAAATCTTGAATGAGAGAGACATGTTCCGCTTACTCTGA
Found at i:204992 original size:113 final size:112
Alignment explanation
Indices: 204790--205011 Score: 381
Period size: 113 Copynumber: 2.0 Consensus size: 112
204780 AAATCTTGGA
* * *
204790 GAAGAGACTTGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGAAGAAGATAGACCTGTTCCAC
1 GAAGAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAAGAAGAGAGACCTGTTCCAA
204855 TTACTCTGAAGGGAATATCAGATCTGGGGAAGTTGATCCATTGACTC
66 TTACTCTGAAGGGAATATCAGATCTGGGGAAGTTGATCCATTGACTC
* *
204902 GAAGCAGACTTGTTCCACTTAGTCTGAAGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCA
1 GAAG-AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAAGAAGAGAGACCTGTTCCA
*
204967 ATTACTCTGAAGGGAATATCAGATCTGGGGGAGTTGATCCATTGA
65 ATTACTCTGAAGGGAATATCAGATCTGGGGAAGTTGATCCATTGA
205012 ATTGGGATCA
Statistics
Matches: 103, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
112 4 0.04
113 99 0.96
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.27
Consensus pattern (112 bp):
GAAGAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAAGAAGAGAGACCTGTTCCAA
TTACTCTGAAGGGAATATCAGATCTGGGGAAGTTGATCCATTGACTC
Found at i:206164 original size:17 final size:17
Alignment explanation
Indices: 206144--206183 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
206134 TTTTCTGTTC
206144 TTTTTTT-TATTTTTCA
1 TTTTTTTGTATTTTTCA
* *
206160 TTTTTTAGTCTTTTTCA
1 TTTTTTTGTATTTTTCA
206177 TTTTTTT
1 TTTTTTT
206184 AGGCGAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.10, C:0.07, G:0.03, T:0.80
Consensus pattern (17 bp):
TTTTTTTGTATTTTTCA
Found at i:214895 original size:29 final size:29
Alignment explanation
Indices: 214831--214897 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
214821 ATATACTTAA
* ** *
214831 ATAATATATGTTTACAAAATATATTATAT
1 ATAATATATGTTTACAAAATAAAAGACAT
*
214860 ACT-ATATATGTTTACAAAGTAAAAGACAT
1 A-TAATATATGTTTACAAAATAAAAGACAT
214889 ATAATATAT
1 ATAATATAT
214898 TATGGGAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
28 1 0.03
29 29 0.94
30 1 0.03
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.39
Consensus pattern (29 bp):
ATAATATATGTTTACAAAATAAAAGACAT
Found at i:216418 original size:3 final size:3
Alignment explanation
Indices: 216405--216443 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
216395 AAATATAAAT
216405 TAA TAA TTAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
216444 TATTTTTAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:223272 original size:21 final size:22
Alignment explanation
Indices: 223243--223290 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
223233 TATCATTGTA
* *
223243 ATTGTTGACAATTGCGCATGG-
1 ATTGCTGACAATTACGCATGGT
223264 ATTGCTGACAATTACGCATGGT
1 ATTGCTGACAATTACGCATGGT
223286 ATTGC
1 ATTGC
223291 AGGGATTCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (22 bp):
ATTGCTGACAATTACGCATGGT
Found at i:227830 original size:21 final size:21
Alignment explanation
Indices: 227804--227852 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
227794 TCAAGTGGGA
* *
227804 GATTGTTGACAAGTGCGCATG
1 GATTGTTAACAAGTACGCATG
*
227825 GATTGTTAACAATTACGCATG
1 GATTGTTAACAAGTACGCATG
227846 GTATTGT
1 G-ATTGT
227853 ATGGGATTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.35
Consensus pattern (21 bp):
GATTGTTAACAAGTACGCATG
Found at i:231873 original size:14 final size:14
Alignment explanation
Indices: 231854--231897 Score: 79
Period size: 14 Copynumber: 3.1 Consensus size: 14
231844 TCTTTCCAGA
*
231854 AGGGAGGAAGAGAG
1 AGGGAGGGAGAGAG
231868 AGGGAGGGAGAGAG
1 AGGGAGGGAGAGAG
231882 AGGGAGGGAGAGAG
1 AGGGAGGGAGAGAG
231896 AG
1 AG
231898 TACGTTTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (14 bp):
AGGGAGGGAGAGAG
Found at i:232494 original size:22 final size:23
Alignment explanation
Indices: 232453--232500 Score: 89
Period size: 22 Copynumber: 2.1 Consensus size: 23
232443 TTTAAAACTG
232453 TTAATTAGATTGAAAATTTTAAT
1 TTAATTAGATTGAAAATTTTAAT
232476 TTAATTAGATTG-AAATTTTAAT
1 TTAATTAGATTGAAAATTTTAAT
232498 TTA
1 TTA
232501 GTGATTATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 13 0.52
23 12 0.48
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (23 bp):
TTAATTAGATTGAAAATTTTAAT
Found at i:234603 original size:5 final size:5
Alignment explanation
Indices: 234274--234583 Score: 538
Period size: 5 Copynumber: 61.8 Consensus size: 5
234264 TAACCATTAA
234274 TATAT ATATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT -TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
234325 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
234375 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
234425 TATAT TATAT TATAT TATAT TATA- T-TAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
234473 TATAT TATAT TATAT TATAT TATA- TATATT TATAT TATAT TATAT TATA-
1 TATAT TATAT TATAT TATAT TATAT TATA-T TATAT TATAT TATAT TATAT
234522 TATAT TATAT TATAT TATAT TATAT ATATAT ATATATT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT -TATAT -TATA-T TATAT TATAT
*
234570 TATAT TATAA TATA
1 TATAT TATAT TATA
234584 ATGATAGAAT
Statistics
Matches: 296, Mismatches: 1, Indels: 15
0.95 0.00 0.05
Matches are distributed among these distances:
3 2 0.01
4 10 0.03
5 260 0.88
6 23 0.08
7 1 0.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:237447 original size:62 final size:62
Alignment explanation
Indices: 237376--237516 Score: 246
Period size: 62 Copynumber: 2.3 Consensus size: 62
237366 AGGGTCGAGG
*
237376 GTTTACCTATGTTCTTCGGGACATATGGACTATTTACCTATGTTCTTTGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTATTTACCTATGTTCTTTAGGACATATGGACT
*
237438 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTTAGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTATTTACCTATGTTCTTTAGGACATATGGACT
* *
237500 GATTACCTAGGTTCTTC
1 GTTTACCTATGTTCTTC
237517 TGAATCTATG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 75 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.40
Consensus pattern (62 bp):
GTTTACCTATGTTCTTCGGGACATATGGACTATTTACCTATGTTCTTTAGGACATATGGACT
Found at i:237527 original size:31 final size:31
Alignment explanation
Indices: 237376--237531 Score: 210
Period size: 31 Copynumber: 5.0 Consensus size: 31
237366 AGGGTCGAGG
*
237376 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCTGGACATATGGACT
*
237407 ATTTACCTATGTTCTT-TGGGACATATGGACT
1 GTTTACCTATGTTCTTCT-GGACATATGGACT
*
237438 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCTGGACATATGGACT
237469 GTTTACCTATGTTCTT-TAGGACATATGGACT
1 GTTTACCTATGTTCTTCT-GGACATATGGACT
* * *
237500 GATTACCTAGGTTCTTCTGAATC-TATGGACT
1 GTTTACCTATGTTCTTCTGGA-CATATGGACT
237531 G
1 G
237532 GTCCTTCAGG
Statistics
Matches: 112, Mismatches: 8, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
31 110 0.98
32 2 0.02
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCTGGACATATGGACT
Found at i:238261 original size:11 final size:11
Alignment explanation
Indices: 238239--238272 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
238229 TTACGAAAGT
*
238239 TACTGTAGCAG
1 TACTGTATCAG
*
238250 TAGTGTATCAG
1 TACTGTATCAG
238261 TACTGTATCAG
1 TACTGTATCAG
238272 T
1 T
238273 GCATCGATGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (11 bp):
TACTGTATCAG
Found at i:238288 original size:21 final size:21
Alignment explanation
Indices: 238262--238301 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
238252 GTGTATCAGT
238262 ACTGTA-TCAGTGCATCGATGC
1 ACTGTAGT-AGTGCATCGATGC
238283 ACTGTAGTAGTGCATCGAT
1 ACTGTAGTAGTGCATCGAT
238302 ACACAATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (21 bp):
ACTGTAGTAGTGCATCGATGC
Found at i:241093 original size:20 final size:20
Alignment explanation
Indices: 241068--241116 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
241058 TGTTATCAGG
*
241068 GTATCTATACCATAGACAGA
1 GTATCTATACCATAAACAGA
*
241088 GTATCTATACCATAAACAGG
1 GTATCTATACCATAAACAGA
241108 GTATCTATA
1 GTATCTATA
241117 TCTCAGTTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (20 bp):
GTATCTATACCATAAACAGA
Found at i:241813 original size:62 final size:62
Alignment explanation
Indices: 241693--241816 Score: 187
Period size: 62 Copynumber: 2.0 Consensus size: 62
241683 AAGGTCGAGG
* * * *
241693 GTTTACCTATGTTCTTCGGGATATATGGACTGTTTACCTATGTTCTTCGGTACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAAGTTCTTCGGAACATATGGACT
*
241755 GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAAGTTCTTCTGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAAGTTCTTCGGAA-CATATGGACT
241817 TGTCCTTCGG
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
62 55 0.98
63 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (62 bp):
GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAAGTTCTTCGGAACATATGGACT
Found at i:241816 original size:31 final size:31
Alignment explanation
Indices: 241693--241802 Score: 184
Period size: 31 Copynumber: 3.5 Consensus size: 31
241683 AAGGTCGAGG
*
241693 GTTTACCTATGTTCTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
241724 GTTTACCTATGTTCTTCGGTACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
241755 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
241786 GATTACCTAAGTTCTTC
1 GTTTACCTATGTTCTTC
241803 TGAATCTATG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 74 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:246888 original size:21 final size:21
Alignment explanation
Indices: 246862--246901 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
246852 CAGAACCCCA
*
246862 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
246883 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
246902 TCAAAGGAGG
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:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:246934 original size:21 final size:21
Alignment explanation
Indices: 246883--246945 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 21
246873 ATTCCCCTGT
246883 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTT-CCC-TCAA
* *
246906 AGGAGGAATCGGTTCCCTCAA
1 GGGGGGAATCGGTTCCCTCAA
*
246927 GGGGGGAATCGATTCCCTC
1 GGGGGGAATCGGTTCCCTC
246946 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 20 0.57
22 3 0.09
23 12 0.34
ACGTcount: A:0.21, C:0.25, G:0.33, T:0.21
Consensus pattern (21 bp):
GGGGGGAATCGGTTCCCTCAA
Done.