Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008206.1 Hibiscus syriacus cultivar Beakdansim tig00110828_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: 1504526
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 9
Found at i:1363024 original size:63 final size:63
Alignment explanation
Indices: 1362946--1363111 Score: 289
Period size: 63 Copynumber: 2.7 Consensus size: 63
1362936 AGAGTCGAGG
*
1362946 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGTACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
*
1363009 GTATACCTATGTTCTACGGAACATATGGAAAGAATTACCTATGTCTTTCGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
* *
1363072 GTATACCTATGTTCTAAGGAACATATGGACAG-TTTACCTA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTA
1363112 GGTTCTTAGG
Statistics
Matches: 98, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
62 7 0.07
63 91 0.93
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (63 bp):
GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
Found at i:1363096 original size:31 final size:31
Alignment explanation
Indices: 1362946--1363139 Score: 187
Period size: 31 Copynumber: 6.2 Consensus size: 31
1362936 AGAGTCGAGG
*
1362946 GTATACCTATGTTCTACGGAACATATGGACA
1 GTATACCTATGTTCTAAGGAACATATGGACA
* *** *
1362977 GAATTACCTATG-TCTTTCGAGACATATGTACA
1 GTA-TACCTATGTTCTAAGGA-ACATATGGACA
* *
1363009 GTATACCTATGTTCTACGGAACATATGGAAA
1 GTATACCTATGTTCTAAGGAACATATGGACA
* ***
1363040 GAATTACCTATG-TCTTTCGAGACATATGGACA
1 GTA-TACCTATGTTCTAAGGA-ACATATGGACA
1363072 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTATACCTATGTTCTAAGGAACATATGGACA
* * * *
1363103 GTTTACCTAGGTTCTTAGGAACCTATGGACA
1 GTATACCTATGTTCTAAGGAACATATGGACA
1363134 GT-TACC
1 GTATACC
1363140 GAGGATCTTT
Statistics
Matches: 133, Mismatches: 24, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
30 4 0.03
31 79 0.59
32 50 0.38
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (31 bp):
GTATACCTATGTTCTAAGGAACATATGGACA
Found at i:1371597 original size:16 final size:17
Alignment explanation
Indices: 1371547--1371601 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
1371537 TAAAAAAAAT
*
1371547 TATTTATCTAATAACAAA
1 TATTT-TCTAATAACTAA
*
1371565 TATTTTCTAATGA-TAA
1 TATTTTCTAATAACTAA
*
1371581 TA-TTTGTAATAACTAA
1 TATTTTCTAATAACTAA
1371597 T-TTTT
1 TATTTT
1371602 TAAATTGTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
15 8 0.26
16 11 0.35
17 7 0.23
18 5 0.16
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (17 bp):
TATTTTCTAATAACTAA
Found at i:1371903 original size:7 final size:7
Alignment explanation
Indices: 1371885--1371964 Score: 56
Period size: 7 Copynumber: 11.6 Consensus size: 7
1371875 GTGCTATGGT
*
1371885 TTTAAGG
1 TTTAGGG
1371892 TTTAGGG
1 TTTAGGG
*
1371899 TTTAGAG
1 TTTAGGG
*
1371906 TTTAGGA
1 TTTAGGG
*
1371913 TTTAGAG
1 TTTAGGG
*
1371920 TTTA-TG
1 TTTAGGG
* *
1371926 TGATAGGA
1 T-TTAGGG
*
1371934 TTTAAGG
1 TTTAGGG
*
1371941 TTTAGAG
1 TTTAGGG
1371948 TTTAGGG
1 TTTAGGG
1371955 TTTA-GG
1 TTTAGGG
1371961 TTTA
1 TTTA
1371965 TATGTTAGGG
Statistics
Matches: 55, Mismatches: 16, Indels: 5
0.72 0.21 0.07
Matches are distributed among these distances:
6 8 0.15
7 46 0.84
8 1 0.02
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.45
Consensus pattern (7 bp):
TTTAGGG
Found at i:1371908 original size:14 final size:14
Alignment explanation
Indices: 1371891--1371964 Score: 73
Period size: 14 Copynumber: 5.4 Consensus size: 14
1371881 TGGTTTTAAG
1371891 GTTTAGGGTTTAGA
1 GTTTAGGGTTTAGA
*
1371905 GTTTAGGATTTAGA
1 GTTTAGGGTTTAGA
* *
1371919 GTTTA-TGTGATAG-
1 GTTTAGGGT-TTAGA
*
1371932 GATTTAAGGTTTAGA
1 G-TTTAGGGTTTAGA
1371947 GTTTAGGGTTTAG-
1 GTTTAGGGTTTAGA
1371960 GTTTA
1 GTTTA
1371965 TATGTTAGGG
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
13 7 0.14
14 39 0.80
15 3 0.06
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.45
Consensus pattern (14 bp):
GTTTAGGGTTTAGA
Found at i:1371916 original size:21 final size:21
Alignment explanation
Indices: 1371885--1372000 Score: 96
Period size: 21 Copynumber: 5.6 Consensus size: 21
1371875 GTGCTATGGT
* *
1371885 TTTAAGGTTTAGGGTTTAGAG
1 TTTAGGGTTTAAGGTTTAGAG
* *
1371906 TTTAGGATTT-AGAGTTTA-TG
1 TTTAGGGTTTAAG-GTTTAGAG
* *
1371926 TGATAGGATTTAAGGTTTAGAG
1 T-TTAGGGTTTAAGGTTTAGAG
*
1371948 TTTAGGGTTT-AGGTTTATA-
1 TTTAGGGTTTAAGGTTTAGAG
* *
1371967 TGTTAGGGGTTAAGGTTTAAAG
1 T-TTAGGGTTTAAGGTTTAGAG
1371989 TTTAGGGTTTAA
1 TTTAGGGTTTAA
1372001 ATGTACAAAA
Statistics
Matches: 76, Mismatches: 12, Indels: 14
0.75 0.12 0.14
Matches are distributed among these distances:
19 1 0.01
20 19 0.25
21 51 0.67
22 5 0.07
ACGTcount: A:0.26, C:0.00, G:0.30, T:0.44
Consensus pattern (21 bp):
TTTAGGGTTTAAGGTTTAGAG
Found at i:1373586 original size:12 final size:12
Alignment explanation
Indices: 1373571--1373628 Score: 55
Period size: 12 Copynumber: 4.9 Consensus size: 12
1373561 TAGGTTTAAA
1373571 TTCGAGTTTGAG
1 TTCGAGTTTGAG
*
1373583 TTCGAGCTTGA-
1 TTCGAGTTTGAG
* ** *
1373594 ATCGAGTTCAAA
1 TTCGAGTTTGAG
1373606 TTCGAGTTTGAG
1 TTCGAGTTTGAG
*
1373618 TTCGAGCTTGA
1 TTCGAGTTTGA
1373629 ATCGAGCTCA
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
11 7 0.20
12 28 0.80
ACGTcount: A:0.22, C:0.14, G:0.28, T:0.36
Consensus pattern (12 bp):
TTCGAGTTTGAG
Found at i:1373614 original size:35 final size:35
Alignment explanation
Indices: 1373568--1373646 Score: 140
Period size: 35 Copynumber: 2.3 Consensus size: 35
1373558 TTGTAGGTTT
*
1373568 AAATTCGAGTTTGAGTTCGAGCTTGAATCGAGTTC
1 AAATTCGAGTTTGAGTTCGAGCTTGAATCGAGCTC
1373603 AAATTCGAGTTTGAGTTCGAGCTTGAATCGAGCTC
1 AAATTCGAGTTTGAGTTCGAGCTTGAATCGAGCTC
*
1373638 AAAATCGAG
1 AAATTCGAG
1373647 CTTCAATCGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.30
Consensus pattern (35 bp):
AAATTCGAGTTTGAGTTCGAGCTTGAATCGAGCTC
Found at i:1376984 original size:24 final size:24
Alignment explanation
Indices: 1376951--1377012 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
1376941 AATAGACTAT
*
1376951 AGTAAATAATTGTACTCGATGAATG
1 AGTAAATAATTGTACTCAATGAA-G
*
1376976 -GTAAATAATTGTAGTCAATGAAG
1 AGTAAATAATTGTACTCAATGAAG
1376999 AGTAAATAATTGTA
1 AGTAAATAATTGTA
1377013 TAAAAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
23 1 0.03
24 33 0.97
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.32
Consensus pattern (24 bp):
AGTAAATAATTGTACTCAATGAAG
Found at i:1377737 original size:17 final size:17
Alignment explanation
Indices: 1377715--1377750 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1377705 CTAAATTCAC
*
1377715 CTCTATTGACATAACAT
1 CTCTATTGACATAAAAT
*
1377732 CTCTATTGATATAAAAT
1 CTCTATTGACATAAAAT
1377749 CT
1 CT
1377751 TACTTTTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.36, C:0.19, G:0.06, T:0.39
Consensus pattern (17 bp):
CTCTATTGACATAAAAT
Found at i:1380364 original size:16 final size:16
Alignment explanation
Indices: 1380340--1380370 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1380330 AATTGAAAAC
1380340 TGATACTAAAATAAAT
1 TGATACTAAAATAAAT
*
1380356 TGATGCTAAAATAAA
1 TGATACTAAAATAAA
1380371 ATAAAAACTA
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:0.55, C:0.06, G:0.10, T:0.29
Consensus pattern (16 bp):
TGATACTAAAATAAAT
Found at i:1380457 original size:45 final size:44
Alignment explanation
Indices: 1380403--1380496 Score: 125
Period size: 45 Copynumber: 2.1 Consensus size: 44
1380393 AATTGATACT
*
1380403 AAAATAAAATAAAAACTTTTAATGACAGATATCAAAATGAAACA
1 AAAATAAAATAAAAACTTTTAACGACAGATATCAAAATGAAACA
** * * *
1380447 AAAATAAAAATAAAATTTTTTTACGATAGATATTAAAATGAAACA
1 AAAAT-AAAATAAAAACTTTTAACGACAGATATCAAAATGAAACA
1380492 AAAAT
1 AAAAT
1380497 TAAACTTTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 5 0.12
45 38 0.88
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.27
Consensus pattern (44 bp):
AAAATAAAATAAAAACTTTTAACGACAGATATCAAAATGAAACA
Found at i:1383468 original size:15 final size:15
Alignment explanation
Indices: 1383448--1383507 Score: 86
Period size: 15 Copynumber: 4.0 Consensus size: 15
1383438 TAATAATGTT
*
1383448 ATTTATTTTAAAATA
1 ATTTATTATAAAATA
1383463 ATTTATTATAAAATA
1 ATTTATTATAAAATA
1383478 ATTTACTT-TAAAATA
1 ATTTA-TTATAAAATA
*
1383493 AATTATTATAAAATA
1 ATTTATTATAAAATA
1383508 TGGATTGATT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
14 2 0.05
15 37 0.90
16 2 0.05
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTTATTATAAAATA
Found at i:1383488 original size:30 final size:30
Alignment explanation
Indices: 1383448--1383507 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
1383438 TAATAATGTT
* *
1383448 ATTTATTTTAAAATAATTTATTATAAAATA
1 ATTTACTTTAAAATAAATTATTATAAAATA
1383478 ATTTACTTTAAAATAAATTATTATAAAATA
1 ATTTACTTTAAAATAAATTATTATAAAATA
1383508 TGGATTGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (30 bp):
ATTTACTTTAAAATAAATTATTATAAAATA
Found at i:1383528 original size:37 final size:34
Alignment explanation
Indices: 1383448--1383562 Score: 105
Period size: 33 Copynumber: 3.4 Consensus size: 34
1383438 TAATAATGTT
* * *
1383448 ATTTATTTTAAAAT-AATTTAT---TATAAAATA
1 ATTTATTTTAAAATAAATTTATAAATATGAATTG
* *
1383478 ATTTACTTTAAAATAAATTATTATAAAATATGGATTG
1 ATTTATTTTAAAATAAA-T-TTAT-AAATATGAATTG
* *
1383515 ATTTATTTTAAAAT-AATTTATTAGTATGAATTG
1 ATTTATTTTAAAATAAATTTATAAATATGAATTG
1383548 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
1383563 TAGATTGATT
Statistics
Matches: 68, Mismatches: 9, Indels: 12
0.76 0.10 0.13
Matches are distributed among these distances:
30 13 0.19
31 2 0.03
32 1 0.01
33 27 0.40
34 4 0.06
35 1 0.01
36 2 0.03
37 18 0.26
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.49
Consensus pattern (34 bp):
ATTTATTTTAAAATAAATTTATAAATATGAATTG
Found at i:1383611 original size:54 final size:54
Alignment explanation
Indices: 1383495--1384133 Score: 400
Period size: 54 Copynumber: 11.8 Consensus size: 54
1383485 TTAAAATAAA
* * *
1383495 TTATTATAAAATATGGATTGATTTATTTTAAAATAATTTATTAGTATGAATTGAT
1 TTATTTTAAAATATAGATTGATTTATTTT-AAATAATTTATTAGTATGGATTGAT
1383550 TTATTTTAAAATATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
1 TTATTTTAAAATATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
* * *
1383604 TT-TTTTTAAATATGGATTGATTTA--TT--AT--TGTAGTT-GTATGGATTGAT
1 TTATTTTAAAATATAGATTGATTTATTTTAAATAATTTA-TTAGTATGGATTGAT
* * * *
1383651 TTATTTTAAATAATTTATTAGTATGGATTGA-TTT--AT--TTTA-AAATATGGATTGAT
1 TTATTTT-AA-AA--TA-TAG-ATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
*
1383705 TTATTTTAAATAATTTATTCGTATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGAT
1 TTATTTT-AA-AA--TA----TA--GATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
* * *
1383769 TTATTTTAAAACATAGATTGATTTA--TT--AT--TGTAGTT-GTATAGATTGAT
1 TTATTTTAAAATATAGATTGATTTATTTTAAATAATTTA-TTAGTATGGATTGAT
1383817 TTATTTTAAAATAT-GAATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
1 TTATTTTAAAATATAG-ATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
** ** * *
1383871 TTATTTTAAAATAT-GAATTGATTTATTTTAAA-ATATGGATT-G-ATTTATTTTAA
1 TTATTTTAAAATATAG-ATTGATTTATTTTAAATA-ATTTATTAGTATGGA-TTGAT
* * * * * *
1383924 ATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGAT
1 TTATTTTA-AAATATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
** * * ** * * * *
1383979 TTATTTT-AAATAATTTATTAGTATGTA-TTGATTTATTTTA-CAATATAGATTGAT
1 TTATTTTAAAAT-ATAGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTGAT
*** * * *
1384033 TTATTATTGTAGTTGTGTGGATTAATTTATTTTTAAATAATTTATTAGTATGGATTGAT
1 TTA-T-TT-TA-AAATATAGATTGATTTA-TTTTAAATAATTTATTAGTATGGATTGAT
*
1384092 TTATTTTAAAATATTGATTGATTTATTTTAAATAATTTATTA
1 TTATTTTAAAATATAGATTGATTTATTTTAAATAATTTATTA
1384134 TTGTAGTTGT
Statistics
Matches: 459, Mismatches: 77, Indels: 97
0.73 0.12 0.15
Matches are distributed among these distances:
47 18 0.04
48 42 0.09
49 5 0.01
50 6 0.01
51 2 0.00
52 9 0.02
53 37 0.08
54 182 0.40
55 67 0.15
56 17 0.04
57 5 0.01
58 21 0.05
59 19 0.04
60 1 0.00
61 2 0.00
62 2 0.00
63 6 0.01
64 18 0.04
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (54 bp):
TTATTTTAAAATATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
Found at i:1383680 original size:32 final size:32
Alignment explanation
Indices: 1383639--1384023 Score: 316
Period size: 32 Copynumber: 12.8 Consensus size: 32
1383629 TATTGTAGTT
1383639 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
1383671 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
1383694 -TATGGATTGATTTATTTTAAATAATTTATTC
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
1383725 GTATGGATTGATTTATTTTAAATAATTTATTT
1 GTATGGATTGATTTATTTTAAATAATTTATTA
**
1383757 GTATGGATTGATTTATTTTAAA-ACATAGATT-
1 GTATGGATTGATTTATTTTAAATA-ATTTATTA
** * *
1383788 G-ATTTATT-ATTGTAGTTGTATAGATTGATTTATTTTAAA
1 GTATGGATTGATT-TA-TT-T-TA-AATAATTTA--TT--A
* *
1383827 ATATGAATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
1383859 GTATGGATTGATTTATTTT-AA-AA--TA-T-
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
1383885 G-A---ATTGATTTATTTTAAAA---------
1 GTATGGATTGATTTATTTTAAATAATTTATTA
1383904 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
1383935 GTATGGATTGATTTATTTTAAATAATTTATTT
1 GTATGGATTGATTTATTTTAAATAATTTATTA
1383967 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
1383999 GTATGTATTGATTTATTTTACAATA
1 GTATGGATTGATTTATTTTA-AATA
1384024 TAGATTGATT
Statistics
Matches: 291, Mismatches: 21, Indels: 81
0.74 0.05 0.21
Matches are distributed among these distances:
19 1 0.00
22 43 0.15
23 6 0.02
25 2 0.01
26 4 0.01
27 1 0.00
28 5 0.02
29 4 0.01
30 9 0.03
31 9 0.03
32 171 0.59
33 6 0.02
34 6 0.02
36 9 0.03
37 2 0.01
38 1 0.00
39 2 0.01
40 7 0.02
41 3 0.01
ACGTcount: A:0.34, C:0.01, G:0.12, T:0.52
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:1383697 original size:22 final size:22
Alignment explanation
Indices: 1383672--1383714 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1383662 AATTTATTAG
1383672 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
1383694 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1383715 TAATTTATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1383787 original size:22 final size:22
Alignment explanation
Indices: 1383762--1383924 Score: 114
Period size: 22 Copynumber: 6.8 Consensus size: 22
1383752 TATTTGTATG
*
1383762 GATTGATTTATTTTAAAACATA
1 GATTGATTTATTTTAAAATATA
***
1383784 GATTGATTTATTATTGTAGTTGTATA
1 GATTGATTTA-T-TT-TA-AAATATA
1383810 GATTGATTTATTTTAAAATAT-
1 GATTGATTTATTTTAAAATATA
1383831 GAATTGATTTATTTTAAATAATTTATTA
1 G-ATTGATTTATTTT-AA-AA--TA-TA
*
1383859 GTATGGATTGATTTATTTTAAAATAT-
1 G-ATTGA-T---TTATTTTAAAATATA
*
1383885 GAATTGATTTATTTTAAAATATG
1 G-ATTGATTTATTTTAAAATATA
1383908 GATTGATTTATTTTAAA
1 GATTGATTTATTTTAAA
1383925 TAATTTATTA
Statistics
Matches: 114, Mismatches: 11, Indels: 32
0.73 0.07 0.20
Matches are distributed among these distances:
21 1 0.01
22 56 0.49
23 6 0.05
24 6 0.05
25 4 0.04
26 20 0.18
27 2 0.02
28 7 0.06
29 1 0.01
30 2 0.02
31 2 0.02
32 7 0.06
ACGTcount: A:0.36, C:0.01, G:0.12, T:0.51
Consensus pattern (22 bp):
GATTGATTTATTTTAAAATATA
Found at i:1383906 original size:76 final size:76
Alignment explanation
Indices: 1383811--1383956 Score: 283
Period size: 76 Copynumber: 1.9 Consensus size: 76
1383801 AGTTGTATAG
1383811 ATTGATTTATTTTAAAATATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATT
1 ATTGATTTATTTTAAAATATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATT
1383876 TTAAAATATGA
66 TTAAAATATGA
*
1383887 ATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATT
1 ATTGATTTATTTTAAAATATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATT
1383952 TTAAA
66 TTAAA
1383957 TAATTTATTT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 69 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (76 bp):
ATTGATTTATTTTAAAATATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATT
TTAAAATATGA
Found at i:1383980 original size:18 final size:18
Alignment explanation
Indices: 1383927--1383984 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
1383917 ATTTTAAATA
*
1383927 ATTTATTAGTATGGATTG
1 ATTTATTTGTATGGATTG
* *
1383945 ATTTATTT-TA---AATA
1 ATTTATTTGTATGGATTG
1383959 ATTTATTTGTATGGATTG
1 ATTTATTTGTATGGATTG
1383977 ATTTATTT
1 ATTTATTT
1383985 TAAATAATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
14 10 0.32
15 2 0.06
17 2 0.06
18 17 0.55
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (18 bp):
ATTTATTTGTATGGATTG
Found at i:1383993 original size:140 final size:145
Alignment explanation
Indices: 1383828--1384101 Score: 425
Period size: 140 Copynumber: 1.9 Consensus size: 145
1383818 TATTTTAAAA
1383828 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATAT-GAATTGA
1 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAG-ATTGA
*
1383892 TTTA-T-TT-TA-AAATATGGATTGATTTA-TTTTAAATAATTTATTAGTATGGATTGATTTATT
65 TTTATTATTGTAGAAATATGGATTAATTTATTTTTAAATAATTTATTAGTATGGATTGATTTATT
1383952 TTAAATAATTTATTTG
130 TTAAATAATTTATTTG
* * *
1383968 TATGGATTGATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTACAATATAGATTGAT
1 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGAT
*** *
1384033 TTATTATTGTAGTTGTGTGGATTAATTTATTTTTAAATAATTTATTAGTATGGATTGATTTATTT
66 TTATTATTGTAGAAATATGGATTAATTTATTTTTAAATAATTTATTAGTATGGATTGATTTATTT
1384098 TAAA
131 TAAA
1384102 ATATTGATTG
Statistics
Matches: 120, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
140 63 0.52
141 2 0.02
142 2 0.02
143 2 0.02
144 12 0.10
145 39 0.32
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (145 bp):
TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGAT
TTATTATTGTAGAAATATGGATTAATTTATTTTTAAATAATTTATTAGTATGGATTGATTTATTT
TAAATAATTTATTTG
Found at i:1384097 original size:22 final size:22
Alignment explanation
Indices: 1384081--1384123 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1384071 AATTTATTAG
1384081 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
*
1384103 TATTGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1384124 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1384182 original size:31 final size:31
Alignment explanation
Indices: 1384147--1384206 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
1384137 TAGTTGTATG
* *
1384147 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTGCAAAACTAA
1384178 AATTATTTAAATCTCAGTATTGCAAAACT
1 AATTATTTAAATCTCAGTATTGCAAAACT
1384207 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGCAAAACTAA
Found at i:1400219 original size:60 final size:60
Alignment explanation
Indices: 1400110--1400239 Score: 147
Period size: 60 Copynumber: 2.1 Consensus size: 60
1400100 GTCGTGTGAC
* ** * *
1400110 CATTTTATAACTTTTAATAGTTGAGGGACTCAACAAAGTAACTCTCTATAG-TCAAGGGAT
1 CATTTTATAACATTTAATAGTCAAGAGACTCAACAAAGTAAATCTCTATAGTTCAA-GGAT
* * *
1400170 CATTTTGTAACATTTAATAGTCAAGAGACTCAATAAAGTAATATC-CTATAGTTGAAGGAT
1 CATTTTATAACATTTAATAGTCAAGAGACTCAACAAAGTAA-ATCTCTATAGTTCAAGGAT
1400230 CATTTGTATA
1 CATTT-TATA
1400240 TTTTACCCTA
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
60 50 0.86
61 8 0.14
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (60 bp):
CATTTTATAACATTTAATAGTCAAGAGACTCAACAAAGTAAATCTCTATAGTTCAAGGAT
Found at i:1402840 original size:48 final size:48
Alignment explanation
Indices: 1402788--1402883 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
1402778 ATGTCCCATG
* *
1402788 GTTAGTTTAAAAACCGATAGTTGACTAATGATCAATGTTTATAGTTGA
1 GTTAGTTTAAAAACCAATAGTTGACTAATCATCAATGTTTATAGTTGA
1402836 GTTAGTTTAAAAACCAATAGTTGACTAATCATCAATGTTTATAGTTGA
1 GTTAGTTTAAAAACCAATAGTTGACTAATCATCAATGTTTATAGTTGA
1402884 CGTGACAAGT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (48 bp):
GTTAGTTTAAAAACCAATAGTTGACTAATCATCAATGTTTATAGTTGA
Found at i:1402979 original size:32 final size:32
Alignment explanation
Indices: 1402937--1402999 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
1402927 CACATATGTG
*
1402937 ATGACATGACATATGTCACGTGTACACAAATA
1 ATGACATGACATATATCACGTGTACACAAATA
* * *
1402969 ATGATATGACATATATCATGTGTACATAAAT
1 ATGACATGACATATATCACGTGTACACAAAT
1403000 GACGTGCACA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (32 bp):
ATGACATGACATATATCACGTGTACACAAATA
Found at i:1404144 original size:26 final size:26
Alignment explanation
Indices: 1404096--1404150 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 26
1404086 ACACTTTTAA
* *
1404096 AAAATACTTTTAAAAATTCATTTC-T
1 AAAACACTTTTAAAAATTAATTTCGT
1404121 AAAACACTTTTAAAAATTAAATTTCGT
1 AAAACACTTTTAAAAATT-AATTTCGT
1404148 AAA
1 AAA
1404151 CAATATCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 17 0.65
26 5 0.19
27 4 0.15
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (26 bp):
AAAACACTTTTAAAAATTAATTTCGT
Found at i:1416792 original size:17 final size:18
Alignment explanation
Indices: 1416751--1416799 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
1416741 TGTTTCTGAG
1416751 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGTGAA
* * *
1416769 AGAATTGAAATCTGT-CA
1 GGAATTGGAATCTGTGAA
1416786 GGAATTGGAATCTG
1 GGAATTGGAATCTG
1416800 AATTTGAAAC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.35, C:0.08, G:0.29, T:0.29
Consensus pattern (18 bp):
GGAATTGGAATCTGTGAA
Found at i:1417355 original size:27 final size:25
Alignment explanation
Indices: 1417276--1417338 Score: 85
Period size: 25 Copynumber: 2.5 Consensus size: 25
1417266 CTTAAAAAAT
1417276 CCTAAACCCGACCTGA-ACCT-TAAAC
1 CCTAAACCCGACCT-ATA-CTATAAAC
*
1417301 CCTAAACTCGACCTATACTATAAAC
1 CCTAAACCCGACCTATACTATAAAC
1417326 CCTAAACCCGACC
1 CCTAAACCCGACC
1417339 CTTATACTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 3 0.09
25 31 0.91
ACGTcount: A:0.37, C:0.40, G:0.06, T:0.17
Consensus pattern (25 bp):
CCTAAACCCGACCTATACTATAAAC
Found at i:1419137 original size:24 final size:22
Alignment explanation
Indices: 1419109--1419152 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
1419099 AGTCAATATG
*
1419109 CTTTAATTTGATATAATTTTATCA
1 CTTTAA-TTG-TATAATGTTATCA
1419133 CTTTAATTGTATAATGTTAT
1 CTTTAATTGTATAATGTTAT
1419153 TAATTAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 3 0.16
24 6 0.32
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.55
Consensus pattern (22 bp):
CTTTAATTGTATAATGTTATCA
Found at i:1419260 original size:3 final size:3
Alignment explanation
Indices: 1419252--1419277 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1419242 ATAAGATACT
1419252 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
1419278 GTCAATCGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1421350 original size:31 final size:31
Alignment explanation
Indices: 1421305--1421379 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
1421295 TAACCCATGA
* *
1421305 TGACCACGTCTTAATTAAATAAAAACGAAAG
1 TGACCACATCTTAATTAAACAAAAACGAAAG
* *
1421336 TGACCACATTTTAATTAAACAAAAATGAAAG
1 TGACCACATCTTAATTAAACAAAAACGAAAG
* *
1421367 TGATCATATCTTA
1 TGACCACATCTTA
1421380 TGTTTTTTAA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.28
Consensus pattern (31 bp):
TGACCACATCTTAATTAAACAAAAACGAAAG
Found at i:1424091 original size:23 final size:20
Alignment explanation
Indices: 1424048--1424105 Score: 55
Period size: 22 Copynumber: 2.8 Consensus size: 20
1424038 ATCATTATAT
1424048 ATATTATTTTT-TTAATCAAA
1 ATATTATTTTTATTAAT-AAA
*
1424068 TTATTATTTTTATTGAATAAAA
1 ATATTATTTTTATT-AAT-AAA
*
1424090 ATAATATCTTTTATTA
1 ATATTAT-TTTTATTA
1424106 TTTCGAGTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 10 0.32
21 2 0.06
22 12 0.39
23 7 0.23
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (20 bp):
ATATTATTTTTATTAATAAA
Found at i:1435415 original size:22 final size:23
Alignment explanation
Indices: 1435385--1435436 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
1435375 CATATTAGTC
*
1435385 ATATAAATATATATTT-GTTTAA
1 ATATTAATATATATTTAGTTTAA
* * *
1435407 ATATTAATATTTATTTATTTTTA
1 ATATTAATATATATTTAGTTTAA
1435430 ATATTAA
1 ATATTAA
1435437 GAAATGGGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
ATATTAATATATATTTAGTTTAA
Found at i:1440782 original size:2 final size:2
Alignment explanation
Indices: 1440775--1440806 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1440765 TTATCCTTTA
1440775 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
1440807 CCTTTGTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1441126 original size:16 final size:17
Alignment explanation
Indices: 1441100--1441131 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1441090 CTCTTCCAAC
1441100 AAAGAAAGAAGAAAAAA
1 AAAGAAAGAAGAAAAAA
1441117 AAAG-AAGAAGAAAAA
1 AAAGAAAGAAGAAAAA
1441132 GGAAAATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (17 bp):
AAAGAAAGAAGAAAAAA
Found at i:1443600 original size:114 final size:114
Alignment explanation
Indices: 1443400--1443739 Score: 590
Period size: 114 Copynumber: 3.0 Consensus size: 114
1443390 AAGTGCCATG
*
1443400 TGCTCATAGTAGAAATAAGAAGATCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
*
1443465 TGATTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATT
66 TGATTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATT
1443514 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
*
1443579 TGATTTGGTATGAACCCCAAAACCAATCATTAGATTTAAAAGATGAATT
66 TGATTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATT
* *
1443628 TGCTCATAGTAGAAATAAGGAGACCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * * * *
1443693 TGGTTCGGTAGGAACCCCAGAACCAATCATTGGAATTAAAAGATGAA
66 TGATTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAA
1443740 CTGCATGATC
Statistics
Matches: 215, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 215 1.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.31
Consensus pattern (114 bp):
TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGATTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATT
Found at i:1445885 original size:54 final size:54
Alignment explanation
Indices: 1445803--1445968 Score: 278
Period size: 54 Copynumber: 3.1 Consensus size: 54
1445793 CAATGATTGA
1445803 GAACATCTGAGCAGAAACCACAGGAAATGATGAATGTGTTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAACCACAGGAAATGATGAATGTGTTGTCAAATGTTTTAC
* *
1445857 GAACATCTGAGAAGAAACTACAGGAAATGATGAATGTGTTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAACCACAGGAAATGATGAATGTGTTGTCAAATGTTTTAC
* * **
1445911 GAACATCTGAGCAGAAGCCACAGGAAAGGATGAATGTGCCGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAACCACAGGAAATGATGAATGTGTTGTCAAATGTTTTAC
1445965 GAAC
1 GAAC
1445969 CTGCTATTCT
Statistics
Matches: 104, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 104 1.00
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.24
Consensus pattern (54 bp):
GAACATCTGAGCAGAAACCACAGGAAATGATGAATGTGTTGTCAAATGTTTTAC
Found at i:1446352 original size:22 final size:22
Alignment explanation
Indices: 1446326--1446404 Score: 113
Period size: 22 Copynumber: 3.6 Consensus size: 22
1446316 ACATCTACAT
1446326 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
1446348 TCTTCAAAGATGATAGATTCCC
1 TCTTCAAAGATGATAGATTCTC
* * *
1446370 TTTTTAAAGATGACAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
1446392 TTTTCAAAGATGA
1 TCTTCAAAGATGA
1446405 AAGCTTTATC
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:1447010 original size:113 final size:113
Alignment explanation
Indices: 1446812--1447128 Score: 528
Period size: 113 Copynumber: 2.8 Consensus size: 113
1446802 GATTTAAATC
* *
1446812 CATCATTCAATGGATCAGCATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCGATGGATCAACATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1446877 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
* * *
1446925 CATCATTCGATGAATCATCATTGCCAGGTCGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCGATGGATCAACATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1446990 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
* * ** *
1447038 CATCATTCGATGGATCAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATTTGAAGAAGG
1 CATCATTCGATGGATCAACATTGCCAG-GTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1447102 AAGAAGAAGTTCATAATGAGAAGAACT
65 AAGAAGAAGTTCATAATGAGAAGAACT
1447129 CATCTGAAGA
Statistics
Matches: 191, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
113 190 0.99
114 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.27
Consensus pattern (113 bp):
CATCATTCGATGGATCAACATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
Found at i:1447123 original size:40 final size:40
Alignment explanation
Indices: 1447068--1447165 Score: 187
Period size: 40 Copynumber: 2.5 Consensus size: 40
1447058 TTTCCAGAGA
*
1447068 AAGTTCATAATGAGAAGAACTCATTTGAAGAAGGAAGAAG
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1447108 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1447148 AAGTTCATAATGAGAAGA
1 AAGTTCATAATGAGAAGA
1447166 GCTTGTTCAA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 57 1.00
ACGTcount: A:0.48, C:0.08, G:0.24, T:0.19
Consensus pattern (40 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
Found at i:1447130 original size:153 final size:156
Alignment explanation
Indices: 1446956--1447431 Score: 620
Period size: 163 Copynumber: 3.0 Consensus size: 156
1446946 TGCCAGGTCG
* *
1446956 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
* * * * *
1447021 AACTTTTCGCTTGAATTC-AT-C-AT-TCGAT-GGATCAACTTTTCCAGAGAAAGTTCATAATGA
66 AACCTTT-GCTTG-ATTCTATACAATATAGATAGGATCAACATTTCCAGAAAAAGTTCATAATAA
1447081 GAAGAACTCATTTGAAGAAGGAAGAAGA
129 GAAGAACTCATTTGAAGAAGGAAGAAGA
1447109 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
* * * *
1447174 AACCTTTGTTTGATTCTATCACAGAATGAGATAGATCAGTATCAGCATTTCCATAAAAAGTTCAT
66 AACCTTTGCTTGATTCTAT-AC--AAT---ATAGAT-AGGATCAACATTTCCAGAAAAAGTTCAT
1447239 AATAAGAAGAACTCATTTGAAGAAGGAAGAAGA
124 AATAAGAAGAACTCATTTGAAGAAGGAAGAAGA
1447272 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
* * * * *
1447337 AACCTTTGTTTGATTTTATCACAGAATGAGATAGATCAGTATCAGCATTTCCATAAAAAGTTCAT
66 AACCTTTGCTTGATTCTAT-AC--AAT---ATAGAT-AGGATCAACATTTCCAGAAAAAGTTCAT
*
1447402 AATAAGAAGAACTCATCTGAAGAAGGAAGA
124 AATAAGAAGAACTCATTTGAAGAAGGAAGA
1447432 GAATTTGTTC
Statistics
Matches: 298, Mismatches: 13, Indels: 14
0.92 0.04 0.04
Matches are distributed among these distances:
151 4 0.01
152 6 0.02
153 69 0.23
154 1 0.00
157 2 0.01
161 4 0.01
163 212 0.71
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (156 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
AACCTTTGCTTGATTCTATACAATATAGATAGGATCAACATTTCCAGAAAAAGTTCATAATAAGA
AGAACTCATTTGAAGAAGGAAGAAGA
Found at i:1447249 original size:163 final size:163
Alignment explanation
Indices: 1447058--1447431 Score: 703
Period size: 163 Copynumber: 2.3 Consensus size: 163
1447048 TGGATCAACT
* * *
1447058 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATTTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCATAAAAAGTTCATAATAAGAAGAACTCATTTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1447123 AGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTGTTTGAT
66 AGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTGTTTGAT
1447188 TCTATCACAGAATGAGATAGATCAGTATCAGCA
131 TCTATCACAGAATGAGATAGATCAGTATCAGCA
1447221 TTTCCATAAAAAGTTCATAATAAGAAGAACTCATTTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCATAAAAAGTTCATAATAAGAAGAACTCATTTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1447286 AGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTGTTTGAT
66 AGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTGTTTGAT
*
1447351 TTTATCACAGAATGAGATAGATCAGTATCAGCA
131 TCTATCACAGAATGAGATAGATCAGTATCAGCA
*
1447384 TTTCCATAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGA
1 TTTCCATAAAAAGTTCATAATAAGAAGAACTCATTTGAAGAAGGAAGA
1447432 GAATTTGTTC
Statistics
Matches: 206, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
163 206 1.00
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (163 bp):
TTTCCATAAAAAGTTCATAATAAGAAGAACTCATTTGAAGAAGGAAGAAGAAGTTCATAATGAGA
AGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTGTTTGAT
TCTATCACAGAATGAGATAGATCAGTATCAGCA
Found at i:1447287 original size:40 final size:40
Alignment explanation
Indices: 1447231--1447328 Score: 178
Period size: 40 Copynumber: 2.5 Consensus size: 40
1447221 TTTCCATAAA
* *
1447231 AAGTTCATAATAAGAAGAACTCATTTGAAGAAGGAAGAAG
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1447271 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1447311 AAGTTCATAATGAGAAGA
1 AAGTTCATAATGAGAAGA
1447329 GCTTGTTCAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 56 1.00
ACGTcount: A:0.49, C:0.08, G:0.23, T:0.19
Consensus pattern (40 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
Found at i:1447630 original size:103 final size:101
Alignment explanation
Indices: 1447330--1447635 Score: 316
Period size: 102 Copynumber: 3.0 Consensus size: 101
1447320 ATGAGAAGAG
* * * * *
1447330 CTTGTTCAACC-TTTGTTTGATTTTATCACAGAATGAGATAGATCAGTATCAGCATTTCCATAAA
1 CTTGTTCAACCTTTTGCTTGATTCTATCACAGAA-G-G-TAGATCA-AATCAAC-TTTCCAGAAA
1447394 AAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAGAA
61 AAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAGAA
* * * * * *** **
1447435 TTTGTTCAACTTTTTGCTAGATTAC-ATTACAGAA-GAAGAT-AAATTGTCATCCCCAGCGAAAA
1 CTTGTTCAACCTTTTGCTTGATT-CTATCACAGAAGGTAGATCAAATCAAC-TTTCCA--GAAAA
*
1447497 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAGGAGAA
62 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAGAA
*
1447537 CTTGTTCAACCTTTTGCTTGATTCTATCACATAAGGTAGATCAACATCAACTTTGCCAGAAAAAG
1 CTTGTTCAACCTTTTGCTTGATTCTATCACAGAAGGTAGATCAA-ATCAACTTT-CCAGAAAAAG
*
1447602 TTCATAATGAGAAGAACTCATCTGAAGAA-GAAGA
64 TTCATAATAAGAAGAACTCATCTGAAGAAGGAAGA
1447636 AGTTCGTAAT
Statistics
Matches: 164, Mismatches: 28, Indels: 21
0.77 0.13 0.10
Matches are distributed among these distances:
100 8 0.05
101 2 0.01
102 78 0.48
103 41 0.25
104 3 0.02
105 15 0.09
106 17 0.10
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (101 bp):
CTTGTTCAACCTTTTGCTTGATTCTATCACAGAAGGTAGATCAAATCAACTTTCCAGAAAAAGTT
CATAATAAGAAGAACTCATCTGAAGAAGGAAGAGAA
Found at i:1449397 original size:22 final size:23
Alignment explanation
Indices: 1449367--1449418 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
1449357 CATATTAGTC
*
1449367 ATATAAATATATATTT-GTTTAA
1 ATATTAATATATATTTAGTTTAA
* * *
1449389 ATATTAATATTTATTTATTTTTA
1 ATATTAATATATATTTAGTTTAA
1449412 ATATTAA
1 ATATTAA
1449419 GAAATGGGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
ATATTAATATATATTTAGTTTAA
Found at i:1456577 original size:12 final size:12
Alignment explanation
Indices: 1456557--1456590 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
1456547 TTGAGTATGA
1456557 AATTTTATTTG-
1 AATTTTATTTGT
1456568 AATTTATATTTGT
1 AATTT-TATTTGT
1456581 AATTTTATTT
1 AATTTTATTT
1456591 TGGGATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 5 0.24
12 11 0.52
13 5 0.24
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (12 bp):
AATTTTATTTGT
Found at i:1458151 original size:317 final size:317
Alignment explanation
Indices: 1457576--1458209 Score: 1241
Period size: 317 Copynumber: 2.0 Consensus size: 317
1457566 TCAGGAAGGT
1457576 TGCTTTAGAGGTTCCAATTTTGTCGTTCACGTCAATGTTGTAGAAGATAGGGGAGATAGCTCTTC
1 TGCTTTAGAGGTTCCAATTTTGTCGTTCACGTCAATGTTGTAGAAGATAGGGGAGATAGCTCTTC
*
1457641 TATTATCCCCGGTTCTGCTCACAATAATATTTCTATCCCTAGGAAGGAGTTAACGTGGAGAGACT
66 TATTATCCCCGGTTCTGCTCACAAGAATATTTCTATCCCTAGGAAGGAGTTAACGTGGAGAGACT
1457706 CTTGTTTAGTTGGTAAAATCAAAAACAGGTTCAATGAAGATATTATTATTACAACTTTTAGAGCC
131 CTTGTTTAGTTGGTAAAATCAAAAACAGGTTCAATGAAGATATTATTATTACAACTTTTAGAGCC
1457771 GAAGGTCTGGATGTGAAGGTTAGTACCTGGCGTGATCTGTTGGTGATTATTAATTTTAGGAACGA
196 GAAGGTCTGGATGTGAAGGTTAGTACCTGGCGTGATCTGTTGGTGATTATTAATTTTAGGAACGA
1457836 ATCAGATCGTCAGGTAGTTTGGTCAAATAGAAAAGATTGGATAGGAGATTGGTTTGA
261 ATCAGATCGTCAGGTAGTTTGGTCAAATAGAAAAGATTGGATAGGAGATTGGTTTGA
*
1457893 TGCTTTAGAGGTTCCGATTTTGTCGTTCACGTCAATGTTGTAGAAGATAGGGGAGATAGCTCTTC
1 TGCTTTAGAGGTTCCAATTTTGTCGTTCACGTCAATGTTGTAGAAGATAGGGGAGATAGCTCTTC
1457958 TATTATCCCCGGTTCTGCTCACAAGAATATTTCTATCCCTAGGAAGGAGTTAACGTGGAGAGACT
66 TATTATCCCCGGTTCTGCTCACAAGAATATTTCTATCCCTAGGAAGGAGTTAACGTGGAGAGACT
*
1458023 CTTGTTTGGTTGGTAAAATCAAAAACAGGTTCAATGAAGATATTATTATTACAACTTTTAGAGCC
131 CTTGTTTAGTTGGTAAAATCAAAAACAGGTTCAATGAAGATATTATTATTACAACTTTTAGAGCC
1458088 GAAGGTCTGGATGTGAAGGTTAGTACCTGGCGTGATCTGTTGGTGATTATTAATTTTAGGAACGA
196 GAAGGTCTGGATGTGAAGGTTAGTACCTGGCGTGATCTGTTGGTGATTATTAATTTTAGGAACGA
1458153 ATCAGATCGTCAGGTAGTTTGGTCAAATAGAAAAGATTGGATAGGAGATTGGTTTGA
261 ATCAGATCGTCAGGTAGTTTGGTCAAATAGAAAAGATTGGATAGGAGATTGGTTTGA
1458210 CGAGCTGGAA
Statistics
Matches: 314, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
317 314 1.00
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (317 bp):
TGCTTTAGAGGTTCCAATTTTGTCGTTCACGTCAATGTTGTAGAAGATAGGGGAGATAGCTCTTC
TATTATCCCCGGTTCTGCTCACAAGAATATTTCTATCCCTAGGAAGGAGTTAACGTGGAGAGACT
CTTGTTTAGTTGGTAAAATCAAAAACAGGTTCAATGAAGATATTATTATTACAACTTTTAGAGCC
GAAGGTCTGGATGTGAAGGTTAGTACCTGGCGTGATCTGTTGGTGATTATTAATTTTAGGAACGA
ATCAGATCGTCAGGTAGTTTGGTCAAATAGAAAAGATTGGATAGGAGATTGGTTTGA
Found at i:1466412 original size:49 final size:49
Alignment explanation
Indices: 1466317--1466413 Score: 113
Period size: 49 Copynumber: 2.0 Consensus size: 49
1466307 GTGTAATTAC
** * ** *
1466317 TATATTTTAATTAATCAGCTTTGCTAATATTATTATTCAGACGTTTGAA
1 TATATTTTAACCAATCAACTTTGAGAATATTATTATTCAAACGTTTGAA
* * *
1466366 TATATTTTAACCAATCAACTTTGAGATTATTATTATTTAAATGTTTGA
1 TATATTTTAACCAATCAACTTTGAGAATATTATTATTCAAACGTTTGA
1466414 GGGTAAAGGG
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
49 39 1.00
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.47
Consensus pattern (49 bp):
TATATTTTAACCAATCAACTTTGAGAATATTATTATTCAAACGTTTGAA
Found at i:1473234 original size:22 final size:22
Alignment explanation
Indices: 1473206--1473259 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
1473196 ACATCATTAT
1473206 TATGCATTATTATAATAAAACA
1 TATGCATTATTATAATAAAACA
*
1473228 TATGCATTATTATAATAAAACG
1 TATGCATTATTATAATAAAACA
1473250 TATGCATTAT
1 TATGCATTAT
1473260 GGAAATGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.39
Consensus pattern (22 bp):
TATGCATTATTATAATAAAACA
Found at i:1475485 original size:24 final size:22
Alignment explanation
Indices: 1475453--1475501 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
1475443 TTACTATTAT
* *
1475453 ATATATATTTATGAATATATAAAA
1 ATATATATTCAT-AA-AAATAAAA
*
1475477 ATATTTATTCATAAAAATAAAA
1 ATATATATTCATAAAAATAAAA
1475499 ATA
1 ATA
1475502 CTATTAAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 10 0.45
23 2 0.09
24 10 0.45
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
ATATATATTCATAAAAATAAAA
Found at i:1476415 original size:21 final size:21
Alignment explanation
Indices: 1476376--1476415 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1476366 GTTGGTATTA
**
1476376 GTTTGTTTTTTTCTTTTCTCT
1 GTTTGTTTTTTTCGGTTCTCT
*
1476397 GTTTTTTTTTTTCGGTTCT
1 GTTTGTTTTTTTCGGTTCT
1476416 GTCTCTGTCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.00, C:0.12, G:0.12, T:0.75
Consensus pattern (21 bp):
GTTTGTTTTTTTCGGTTCTCT
Found at i:1476990 original size:15 final size:15
Alignment explanation
Indices: 1476952--1477003 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
1476942 AATAATAATA
* **
1476952 ATAATAATAATATTA
1 ATAAAAATAATATGG
*
1476967 ATAATAATAATATGG
1 ATAAAAATAATATGG
1476982 ATAAAAATAATATGG
1 ATAAAAATAATATGG
1476997 ATAAAAA
1 ATAAAAA
1477004 ATAGTATCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (15 bp):
ATAAAAATAATATGG
Found at i:1476993 original size:3 final size:3
Alignment explanation
Indices: 1476902--1476978 Score: 145
Period size: 3 Copynumber: 25.7 Consensus size: 3
1476892 TAATATAAAT
1476902 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1476950 TAA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1476979 TGGATAAAAA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1477812 original size:113 final size:113
Alignment explanation
Indices: 1477282--1477812 Score: 794
Period size: 113 Copynumber: 4.7 Consensus size: 113
1477272 TCAGATAATA
*
1477282 TCAAAC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* * * *
1477346 TTTCATTCATGAACTTTCTCTGGCAATGTTGATCCATCAAATAATGAAT
66 TCTCATT-ATGAACTTTCTCTGGTAATGTTGATCCACCAAATGATGAAT
* * *
1477395 TTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* *
1477460 TCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAAT
66 TCTCATTATGAACTTTCTCTGGTAATGTTGATCCACCAAATGATGAAT
* * *
1477508 TTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* *
1477573 TCTCATTATGAACCTTCTCTGGTAATGTTGATCCACCAAATGATGGAT
66 TCTCATTATGAACTTTCTCTGGTAATGTTGATCCACCAAATGATGAAT
*** *
1477621 TCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* * * * *
1477686 TCTCATTATGAACTTTTTCTGGAAAAGATGATCCACCAAATGATGGAT
66 TCTCATTATGAACTTTCTCTGGTAATGTTGATCCACCAAATGATGAAT
*** *
1477734 TCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1477799 TCTCATTATGAACT
66 TCTCATTATGAACT
1477813 CTACCTTGCA
Statistics
Matches: 395, Mismatches: 22, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
113 334 0.85
114 61 0.15
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.38
Consensus pattern (113 bp):
TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
TCTCATTATGAACTTTCTCTGGTAATGTTGATCCACCAAATGATGAAT
Found at i:1478539 original size:47 final size:50
Alignment explanation
Indices: 1478469--1478574 Score: 139
Period size: 52 Copynumber: 2.1 Consensus size: 50
1478459 TCTAAATTCA
* *
1478469 ATGCT-TGATTCTGTCCAA--TCAGATAACTTAAAGAACACTTCCAGAAG
1 ATGCTATGATTCTGTCCAACCACAGATAACTCAAAGAACACTTCCAGAAG
1478516 ATGCTATG-TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGATTCTGTCCAACC--A-CAGATAACTCAAAGAACACTTCCAGAAG
1478568 ATGCTAT
1 ATGCTAT
1478575 TGGCATATTC
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
47 15 0.29
48 2 0.04
52 34 0.67
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (50 bp):
ATGCTATGATTCTGTCCAACCACAGATAACTCAAAGAACACTTCCAGAAG
Found at i:1479734 original size:6 final size:6
Alignment explanation
Indices: 1479723--1479819 Score: 62
Period size: 6 Copynumber: 16.5 Consensus size: 6
1479713 ACCTTGACCC
* * * *
1479723 TTTTCT TTTTCT ATTATT-T TTTT-T TCTTCT TCTTCT TTTTTT CTTTTCC
1 TTTTCT TTTTCT -TT-TTCT TTTTCT TTTTCT TTTTCT TTTTCT -TTTTCT
* *
1479772 CTTTCT TTTT-T TTTTC- -TTTCT TTTTCT TTTTC- TCTTCT TCTTTCT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT T-TTTCT
1479817 TTT
1 TTT
1479820 CTTCAAGCAT
Statistics
Matches: 72, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
4 4 0.06
5 15 0.21
6 39 0.54
7 12 0.17
8 2 0.03
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTCT
Found at i:1479747 original size:21 final size:20
Alignment explanation
Indices: 1479723--1479802 Score: 88
Period size: 21 Copynumber: 3.8 Consensus size: 20
1479713 ACCTTGACCC
*
1479723 TTTTCTTTTTCTATTATTTTT
1 TTTTCTTTTTCT-TTTTTTTT
*
1479744 TTTTCTTCTTCTTCTTTTTTT
1 TTTTCTTTTTCTT-TTTTTTT
**
1479765 CTTTTCCCTTTCTTTTTTTTT
1 -TTTTCTTTTTCTTTTTTTTT
1479786 TCTTTCTTTTTCTTTTT
1 T-TTTCTTTTTCTTTTT
1479803 CTCTTCTTCT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
20 2 0.04
21 37 0.76
22 10 0.20
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTCTTTTTCTTTTTTTTT
Found at i:1479758 original size:24 final size:22
Alignment explanation
Indices: 1479722--1479822 Score: 65
Period size: 21 Copynumber: 4.8 Consensus size: 22
1479712 CACCTTGACC
* *
1479722 CTTTTCTTTTTCTAT-TATTTTT
1 CTTTTCTTCTTCT-TCTTTTTTT
1479744 -TTTTCTTCTTCTTCTTTTTTT
1 CTTTTCTTCTTCTTCTTTTTTT
*
1479765 CTTTTC--CCT-TTC-TTTTTT
1 CTTTTCTTCTTCTTCTTTTTTT
* *
1479783 -TTTTCTTTCTTTTTCTTTTTCT
1 CTTTTC-TTCTTCTTCTTTTTTT
1479805 CTTCTTCTTTCTT-TTCTT
1 CTT-TTC-TTCTTCTTCTT
1479823 CAAGCATAAT
Statistics
Matches: 65, Mismatches: 5, Indels: 17
0.75 0.06 0.20
Matches are distributed among these distances:
17 5 0.08
18 6 0.09
19 3 0.05
20 5 0.08
21 20 0.31
22 10 0.15
23 7 0.11
24 9 0.14
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (22 bp):
CTTTTCTTCTTCTTCTTTTTTT
Found at i:1479761 original size:15 final size:15
Alignment explanation
Indices: 1479743--1479823 Score: 61
Period size: 14 Copynumber: 5.8 Consensus size: 15
1479733 CTATTATTTT
1479743 TTTTTCTTCTTCTTC
1 TTTTTCTTCTTCTTC
1479758 TTTTT-TTCTT-TTC
1 TTTTTCTTCTTCTTC
**
1479771 CCTTTC-T-TT-TT-
1 TTTTTCTTCTTCTTC
*
1479782 TTTTTCTTTCTTTTTC
1 TTTTTC-TTCTTCTTC
1479798 TTTTTC-TCTTCTTC
1 TTTTTCTTCTTCTTC
1479812 TTTCTT-TTCTTC
1 TTT-TTCTTCTTC
1479824 AAGCATAATA
Statistics
Matches: 53, Mismatches: 5, Indels: 16
0.72 0.07 0.22
Matches are distributed among these distances:
11 4 0.08
12 4 0.08
13 8 0.15
14 17 0.32
15 14 0.26
16 6 0.11
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTCTTCTTCTTC
Found at i:1479761 original size:17 final size:17
Alignment explanation
Indices: 1479741--1479823 Score: 80
Period size: 17 Copynumber: 4.6 Consensus size: 17
1479731 TTCTATTATT
1479741 TTTTTTTCTTCTTCTTC
1 TTTTTTTCTTCTTCTTC
1479758 TTTTTTTCTT-TTCCCTTTC
1 TTTTTTTCTTCTT--C-TTC
* *
1479777 TTTTTTTTTTCTTTCTTT
1 TTTTTTTCTTC-TTCTTC
1479795 TTCTTTTTC-TCTTCTTC
1 TT-TTTTTCTTCTTCTTC
1479812 TTTCTTTTCTTC
1 TTT-TTTTCTTC
1479824 AAGCATAATA
Statistics
Matches: 54, Mismatches: 4, Indels: 15
0.74 0.05 0.21
Matches are distributed among these distances:
16 3 0.06
17 22 0.41
18 9 0.17
19 18 0.33
21 2 0.04
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTTTTCTTCTTCTTC
Found at i:1479799 original size:40 final size:38
Alignment explanation
Indices: 1479739--1479819 Score: 110
Period size: 39 Copynumber: 2.1 Consensus size: 38
1479729 TTTTCTATTA
*
1479739 TTTTTTTTTCTTCTTCTTCTTTTTTTCTT-TTCCCTTTCT
1 TTTTTTTTTCTTCTTCTTCTTTTTCTCTTCTT--CTTTCT
*
1479778 TTTTTTTTTCTTTCTTTTTCTTTTTCTCTTCTTCTTTCT
1 TTTTTTTTTC-TTCTTCTTCTTTTTCTCTTCTTCTTTCT
1479817 TTT
1 TTT
1479820 CTTCAAGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
39 19 0.50
40 17 0.45
41 2 0.05
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (38 bp):
TTTTTTTTTCTTCTTCTTCTTTTTCTCTTCTTCTTTCT
Found at i:1479809 original size:21 final size:20
Alignment explanation
Indices: 1479746--1479814 Score: 68
Period size: 21 Copynumber: 3.5 Consensus size: 20
1479736 TTATTTTTTT
* *
1479746 TTCTTCTTCTTCTTTTTTTC
1 TTCTTCTTTTTCTTTTTCTC
** * *
1479766 TT-TTCCCTTTCTTTTTTTT
1 TTCTTCTTTTTCTTTTTCTC
1479785 TTCTTTCTTTTTCTTTTTCTC
1 TTC-TTCTTTTTCTTTTTCTC
1479806 TTCTTCTTT
1 TTCTTCTTT
1479815 CTTTTCTTCA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 15 0.38
20 8 0.21
21 16 0.41
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (20 bp):
TTCTTCTTTTTCTTTTTCTC
Found at i:1491164 original size:24 final size:22
Alignment explanation
Indices: 1491132--1491180 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
1491122 TTACTATTAT
* *
1491132 ATATATATTTATGAATATATAAAA
1 ATATATATTCAT-AA-AAATAAAA
*
1491156 ATATTTATTCATAAAAATAAAA
1 ATATATATTCATAAAAATAAAA
1491178 ATA
1 ATA
1491181 CTATTAAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 10 0.45
23 2 0.09
24 10 0.45
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
ATATATATTCATAAAAATAAAA
Found at i:1492094 original size:20 final size:21
Alignment explanation
Indices: 1492056--1492094 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1492046 GTTGGTATTA
**
1492056 GTTTGTTTTTTTCTTTTCTCT
1 GTTTGTTTTTTTCGGTTCTCT
1492077 GTTT-TTTTTTTCGGTTCT
1 GTTTGTTTTTTTCGGTTCT
1492095 ATCTCTGTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.00, C:0.13, G:0.13, T:0.74
Consensus pattern (21 bp):
GTTTGTTTTTTTCGGTTCTCT
Found at i:1492649 original size:15 final size:15
Alignment explanation
Indices: 1492626--1492662 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
1492616 AATAATAATA
*
1492626 ATAATAATAATATGG
1 ATAAAAATAATATGG
1492641 ATAAAAATAATATGG
1 ATAAAAATAATATGG
1492656 ATAAAAA
1 ATAAAAA
1492663 ATAGTATCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.11, T:0.27
Consensus pattern (15 bp):
ATAAAAATAATATGG
Found at i:1492652 original size:3 final size:3
Alignment explanation
Indices: 1492579--1492637 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
1492569 TAATATAAAT
1492579 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1492627 TAA TAA TAA TA
1 TAA TAA TAA TA
1492638 TGGATAAAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1498286 original size:20 final size:20
Alignment explanation
Indices: 1498261--1498310 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
1498251 AATCAAAATA
1498261 ATCGCAACGTGATTCTGACT
1 ATCGCAACGTGATTCTGACT
*
1498281 ATCGCAACGCGATTCTGACT
1 ATCGCAACGTGATTCTGACT
*
1498301 GTCGCAACGT
1 ATCGCAACGT
1498311 TGAATTTCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (20 bp):
ATCGCAACGTGATTCTGACT
Found at i:1499154 original size:24 final size:24
Alignment explanation
Indices: 1499127--1499180 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1499117 GTATTCGAAA
1499127 TTTGATATTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* * *
1499151 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
1499175 TTTGAT
1 TTTGAT
1499181 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:1501770 original size:136 final size:139
Alignment explanation
Indices: 1501504--1501777 Score: 500
Period size: 136 Copynumber: 2.0 Consensus size: 139
1501494 AACGTTGTAT
1501504 TGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAA
1 TGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCA-GTATTAGTAACTTGAGTTTGAA
1501569 CATTGCTATAATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAAT
65 CATTGCTATAATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAAT
1501634 TTGACTATTA
130 TTGACTATTA
1501644 TGTGTA-TTTATGTG-AAACTTTTAACATTTTCAGTTAGGCA-TATTAGTAACTTGAGTTTGAAC
1 TGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCAGTATTAGTAACTTGAGTTTGAAC
* *
1501706 ATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGGGAATT
66 ATTGCTATAATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATT
1501771 TGACTAT
131 TGACTAT
1501778 CGCAACTCAA
Statistics
Matches: 132, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
136 92 0.70
138 26 0.20
139 8 0.06
140 6 0.05
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (139 bp):
TGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCAGTATTAGTAACTTGAGTTTGAAC
ATTGCTATAATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATT
TGACTATTA
Found at i:1501773 original size:20 final size:20
Alignment explanation
Indices: 1501748--1501915 Score: 206
Period size: 20 Copynumber: 8.8 Consensus size: 20
1501738 TTACACATTC
* *
1501748 ATTTGAATATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
*
1501768 ATTTGACTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
*
1501787 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1501802 ATTTGACTATCACAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1501822 ATATGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
1501842 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1501862 A-TTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
* *
1501881 ATTTGATTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
1501901 ATTTGACTATCGCAA
1 ATTTGACTATCGCAA
1501916 TGAGAAAATC
Statistics
Matches: 127, Mismatches: 14, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
14 9 0.07
15 3 0.02
19 21 0.17
20 94 0.74
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:1501804 original size:34 final size:38
Alignment explanation
Indices: 1501756--1501902 Score: 176
Period size: 39 Copynumber: 3.9 Consensus size: 38
1501746 TCATTTGAAT
* *
1501756 ATCGCAACGGGAATTTGACTATCGCAACTC-AA-A-A-
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATAGAC
*
1501790 ATCGCAACGCGAATTTGACTATCACAACGCGAATATGAC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATA-GAC
*
1501829 TATCGCAACGCGAATTTGACTATCGCAACGCGAATTGAC
1 -ATCGCAACGCGAATTTGACTATCGCAACGCGAATAGAC
* * *
1501868 TATCGCAACGAGAATTTGATTATCGCAACGGGAAT
1 -ATCGCAACGCGAATTTGACTATCGCAACGCGAAT
1501903 TTGACTATCG
Statistics
Matches: 99, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
34 27 0.27
35 2 0.02
36 1 0.01
38 1 0.01
39 35 0.35
40 33 0.33
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (38 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATAGAC
Found at i:1501892 original size:59 final size:60
Alignment explanation
Indices: 1501790--1501915 Score: 200
Period size: 59 Copynumber: 2.1 Consensus size: 60
1501780 CAACTCAAAA
*
1501790 ATCGCAACGCGAATTTGACTATCACAACGCGAATATGACTATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACTATCACAACGAGAATATGACTATCGCAACGCGAATTTGACT
* * * *
1501850 ATCGCAACGCGAA-TTGACTATCGCAACGAGAATTTGATTATCGCAACGGGAATTTGACT
1 ATCGCAACGCGAATTTGACTATCACAACGAGAATATGACTATCGCAACGCGAATTTGACT
1501909 ATCGCAA
1 ATCGCAA
1501916 TGAGAAAATC
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
59 48 0.79
60 13 0.21
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (60 bp):
ATCGCAACGCGAATTTGACTATCACAACGAGAATATGACTATCGCAACGCGAATTTGACT
Found at i:1501958 original size:20 final size:20
Alignment explanation
Indices: 1501755--1501958 Score: 166
Period size: 20 Copynumber: 10.8 Consensus size: 20
1501745 TTCATTTGAA
* *
1501755 TATCGCAACGGGAATTTGAC
1 TATCGCAACGCGAATTAGAC
*
1501775 TATCGCAACTC-AA--A-A-
1 TATCGCAACGCGAATTAGAC
*
1501790 -ATCGCAACGCGAATTTGAC
1 TATCGCAACGCGAATTAGAC
*
1501809 TATCACAACGCGAA-TATGAC
1 TATCGCAACGCGAATTA-GAC
*
1501829 TATCGCAACGCGAATTTGAC
1 TATCGCAACGCGAATTAGAC
1501849 TATCGCAACGCGAATT-GAC
1 TATCGCAACGCGAATTAGAC
* * *
1501868 TATCGCAACGAGAATTTGAT
1 TATCGCAACGCGAATTAGAC
* *
1501888 TATCGCAACGGGAATTTGAC
1 TATCGCAACGCGAATTAGAC
* *
1501908 TATCGCAATGAG-A--A-A-
1 TATCGCAACGCGAATTAGAC
* *
1501923 -ATCGCAAAGCGTATTAGAC
1 TATCGCAACGCGAATTAGAC
1501942 TATCGCAACGCGAATTA
1 TATCGCAACGCGAATTA
1501959 ACTTTCGCGT
Statistics
Matches: 149, Mismatches: 20, Indels: 30
0.75 0.10 0.15
Matches are distributed among these distances:
14 18 0.12
15 3 0.02
16 2 0.01
17 1 0.01
18 2 0.01
19 22 0.15
20 100 0.67
21 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (20 bp):
TATCGCAACGCGAATTAGAC
Found at i:1502019 original size:20 final size:20
Alignment explanation
Indices: 1501959--1502033 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
1501949 ACGCGAATTA
*
1501959 ACTTTCGCGTTGCGATTTTG
1 ACTTTCGCATTGCGATTTTG
* *
1501979 GCTTTCGCATTGCAATTTTG
1 ACTTTCGCATTGCGATTTTG
1501999 ACTTTCGCATTGCGATTTTG
1 ACTTTCGCATTGCGATTTTG
* * *
1502019 AGTTTAGCGTTGCGA
1 ACTTTCGCATTGCGA
1502034 AAGTGTACCT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.15, C:0.19, G:0.24, T:0.43
Consensus pattern (20 bp):
ACTTTCGCATTGCGATTTTG
Found at i:1502165 original size:26 final size:23
Alignment explanation
Indices: 1502133--1502250 Score: 60
Period size: 26 Copynumber: 4.7 Consensus size: 23
1502123 ACAAATAAGA
1502133 ATTTTACACATCAATTAAACAAATC
1 ATTTTACA-ATCAATT-AACAAATC
*
1502158 ACTTTTACAAGTCAACTTTTACAAATC
1 A-TTTTACAA-TCAA--TTAACAAATC
* ** * * *
1502185 AATAAACAATCACAATAA-GAATT
1 ATTTTACAATCA-ATTAACAAATC
1502208 A-TTTACACATCAATTAACAAATC
1 ATTTTACA-ATCAATTAACAAATC
1502231 AACTTTTACAAATCAATTAA
1 -A-TTTTAC-AATCAATTAA
1502251 ACAAGCAAAA
Statistics
Matches: 69, Mismatches: 13, Indels: 21
0.67 0.13 0.20
Matches are distributed among these distances:
22 8 0.12
23 11 0.16
24 3 0.04
25 5 0.07
26 31 0.45
27 9 0.13
28 2 0.03
ACGTcount: A:0.48, C:0.19, G:0.02, T:0.31
Consensus pattern (23 bp):
ATTTTACAATCAATTAACAAATC
Found at i:1502177 original size:14 final size:14
Alignment explanation
Indices: 1502151--1502186 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1502141 CATCAATTAA
1502151 ACAAATC-ACTTTT
1 ACAAATCAACTTTT
*
1502164 ACAAGTCAACTTTT
1 ACAAATCAACTTTT
1502178 ACAAATCAA
1 ACAAATCAA
1502187 TAAACAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.44, C:0.22, G:0.03, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1502218 original size:74 final size:74
Alignment explanation
Indices: 1502086--1502246 Score: 211
Period size: 74 Copynumber: 2.1 Consensus size: 74
1502076 ATTGAAATCA
*
1502086 ACAAATCAACTTTTACATTTCAATCAATTAAATAAGCACAAATAAGAATTTTACACATCAATTAA
1 ACAAATCAACTTTTACA----AATCAATTAAACAAGCACAAATAAGAATTTTACACATCAATT-A
1502151 ACAAATC-ACTTTT
61 ACAAATCAACTTTT
* *
1502164 ACAAGTCAACTTTTACAAATCAA-TAAACAATCAC-AATAAGAATTATTTACACATCAATTAACA
1 ACAAATCAACTTTTACAAATCAATTAAACAAGCACAAATAAGAA-T-TTTACACATCAATTAACA
1502227 AATCAACTTTT
64 AATCAACTTTT
1502238 ACAAATCAA
1 ACAAATCAA
1502247 TTAAACAAGC
Statistics
Matches: 76, Mismatches: 4, Indels: 10
0.84 0.04 0.11
Matches are distributed among these distances:
72 8 0.11
73 18 0.24
74 34 0.45
78 16 0.21
ACGTcount: A:0.49, C:0.19, G:0.02, T:0.30
Consensus pattern (74 bp):
ACAAATCAACTTTTACAAATCAATTAAACAAGCACAAATAAGAATTTTACACATCAATTAACAAA
TCAACTTTT
Found at i:1503662 original size:21 final size:21
Alignment explanation
Indices: 1503638--1503730 Score: 66
Period size: 21 Copynumber: 4.5 Consensus size: 21
1503628 GGACCTTTTC
1503638 AACGATGACAGGGGCCTCTTG
1 AACGATGACAGGGGCCTCTTG
* *
1503659 AACGGTAGA-AGGGGACTCTTG
1 AACGAT-GACAGGGGCCTCTTG
** * *
1503680 AGGGATGATA-GGGCATCTTG
1 AACGATGACAGGGGCCTCTTG
* * *
1503700 AACGAT-AGGAGAGGCCTTTTG
1 AACGATGA-CAGGGGCCTCTTG
1503721 AACGATGACA
1 AACGATGACA
1503731 TGTGAGTCGG
Statistics
Matches: 53, Mismatches: 14, Indels: 10
0.69 0.18 0.13
Matches are distributed among these distances:
19 1 0.02
20 15 0.28
21 34 0.64
22 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.34, T:0.20
Consensus pattern (21 bp):
AACGATGACAGGGGCCTCTTG
Found at i:1503728 original size:41 final size:42
Alignment explanation
Indices: 1503631--1503730 Score: 103
Period size: 41 Copynumber: 2.4 Consensus size: 42
1503621 GTGGGAGGGA
* * * *
1503631 CCTTTTCAACGATGACAGGGGCCTCTTGAACGGTAGAAGGGG
1 CCTTTTGAACGATGACAGGGGCATCTTGAACGATAGAAGAGG
* * ** * *
1503673 ACTCTTGAGGGATGATA-GGGCATCTTGAACGATAGGAGAGG
1 CCTTTTGAACGATGACAGGGGCATCTTGAACGATAGAAGAGG
1503714 CCTTTTGAACGATGACA
1 CCTTTTGAACGATGACA
1503731 TGTGAGTCGG
Statistics
Matches: 43, Mismatches: 15, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
41 32 0.74
42 11 0.26
ACGTcount: A:0.27, C:0.18, G:0.32, T:0.23
Consensus pattern (42 bp):
CCTTTTGAACGATGACAGGGGCATCTTGAACGATAGAAGAGG
Done.