Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold258
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: 5730937
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 25
Found at i:1805406 original size:4 final size:4
Alignment explanation
Indices: 1805397--1805423 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1805387 TTCTTCTTCT
1805397 GAAA GAAA GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAA
1805424 TTTTTCACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:1810961 original size:18 final size:18
Alignment explanation
Indices: 1810903--1810962 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
1810893 AGTAAATTTG
* *
1810903 ATTTATAATATTTTTATAT
1 ATTTAT-ATATTTATATAA
*
1810922 A-TTATA-ATTATATTTAAA
1 ATTTATATATT-TATAT-AA
1810940 ATTTATATATTTATATAA
1 ATTTATATATTTATATAA
1810958 ATTTA
1 ATTTA
1810963 ATACGTTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
16 3 0.09
17 4 0.12
18 13 0.39
19 10 0.30
20 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTATATATTTATATAA
Found at i:1811020 original size:11 final size:11
Alignment explanation
Indices: 1810978--1811051 Score: 50
Period size: 11 Copynumber: 6.8 Consensus size: 11
1810968 TTAATATTTT
1810978 ATTTTAT-TTAA
1 ATTTTATATT-A
* *
1810989 ATTTTAAAAT-
1 ATTTTATATTA
1810999 ATTTATATATTA
1 ATTT-TATATTA
1811011 ATTTTATATTA
1 ATTTTATATTA
1811022 ATATTT-T-TTA
1 AT-TTTATATTA
1811032 TATTTTAT-TTA
1 -ATTTTATATTA
*
1811043 TTTTTATAT
1 ATTTTATAT
1811052 CGTAAAATTT
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
10 16 0.31
11 27 0.53
12 8 0.16
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTTTATATTA
Found at i:1811068 original size:35 final size:35
Alignment explanation
Indices: 1810978--1811080 Score: 101
Period size: 34 Copynumber: 3.1 Consensus size: 35
1810968 TTAATATTTT
**
1810978 ATTTTAT-TT-AAATTTTAAAATATTTATATATTA
1 ATTTTATATTAAAATTTTATTATATTTATATATTA
*
1811011 ATTTTATATTAATATTTT-TTATATTT-TAT-TTA
1 ATTTTATATTAAAATTTTATTATATTTATATATTA
* *
1811043 TTTTTATATCGTAAAATTTTATTATATTTA-AAATTA
1 ATTTTATAT--TAAAATTTTATTATATTTATATATTA
1811079 AT
1 AT
1811081 AGATTTATTG
Statistics
Matches: 56, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
32 11 0.20
33 10 0.18
34 16 0.29
35 15 0.27
36 4 0.07
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (35 bp):
ATTTTATATTAAAATTTTATTATATTTATATATTA
Found at i:1811076 original size:17 final size:17
Alignment explanation
Indices: 1810928--1811077 Score: 57
Period size: 17 Copynumber: 8.9 Consensus size: 17
1810918 ATATATTATA
1810928 ATTATATTTAAAA-TTT
1 ATTATATTTAAAATTTT
*
1810944 A-TATATTTATATAAATTT
1 ATTATATTTA-A-AATTTT
* *
1810962 A--ATACGTTAATATTTT
1 ATTATA-TTTAAAATTTT
*
1810978 ATTTTATTT-AAATTTT
1 ATTATATTTAAAATTTT
** *
1810994 AAAATATTTATATATTAATT
1 ATTATATTTA-AAATT--TT
*
1811014 -TTATA-TTAATATTTT
1 ATTATATTTAAAATTTT
* *
1811029 -TTATATTT-TATTTATT
1 ATTATATTTAAAATT-TT
* *
1811045 TTTATATCGTAAAATTTT
1 ATTATAT-TTAAAATTTT
1811063 ATTATATTTAAAATT
1 ATTATATTTAAAATT
1811078 AATAGATTTA
Statistics
Matches: 99, Mismatches: 20, Indels: 29
0.67 0.14 0.20
Matches are distributed among these distances:
15 17 0.17
16 23 0.23
17 26 0.26
18 25 0.25
19 6 0.06
20 2 0.02
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (17 bp):
ATTATATTTAAAATTTT
Found at i:1811336 original size:29 final size:29
Alignment explanation
Indices: 1811304--1811367 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
1811294 AGTTATGTTC
1811304 TATTATTTTTTAATAT-TAT-TTTTATTTAT
1 TATTATTTTTTAA-ATCTATATTTTA-TTAT
*
1811333 TATT-TATTTTAAATCTATATTTTATTAT
1 TATTATTTTTTAAATCTATATTTTATTAT
1811361 T-TTATTT
1 TATTATTT
1811368 ATATATAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
27 4 0.13
28 17 0.57
29 9 0.30
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (29 bp):
TATTATTTTTTAAATCTATATTTTATTAT
Found at i:1811595 original size:57 final size:56
Alignment explanation
Indices: 1811507--1811617 Score: 186
Period size: 57 Copynumber: 2.0 Consensus size: 56
1811497 GCCACCGGTT
* *
1811507 CAGCACCTAGTTGTCATGTAGGATATGTTTTTCCTAGGTTTTTGCCTATTTGCTGTA
1 CAGCACCTAGTTGTCATGTAGGACATGTTTTTCCTAGG-TTTTACCTATTTGCTGTA
*
1811564 CAGCACCTAGTTGTCTTGTAGGACATGTTTTTCCTAGGTTTTACCTATTTGCTG
1 CAGCACCTAGTTGTCATGTAGGACATGTTTTTCCTAGGTTTTACCTATTTGCTG
1811618 CGGTGTCTGA
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
56 15 0.29
57 36 0.71
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.43
Consensus pattern (56 bp):
CAGCACCTAGTTGTCATGTAGGACATGTTTTTCCTAGGTTTTACCTATTTGCTGTA
Found at i:1814009 original size:3 final size:3
Alignment explanation
Indices: 1814001--1814030 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1813991 ATGAATGTTT
*
1814001 TGA TGA TGA TGA TGA TGA TGA TGA AGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1814031 AGAATTCAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.33, T:0.30
Consensus pattern (3 bp):
TGA
Found at i:1815597 original size:8 final size:8
Alignment explanation
Indices: 1815584--1815611 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
1815574 TGTACGAATT
1815584 AGATAAAA
1 AGATAAAA
1815592 AGATAAAA
1 AGATAAAA
1815600 AGATAAAA
1 AGATAAAA
1815608 AGAT
1 AGAT
1815612 GTAGGCACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (8 bp):
AGATAAAA
Found at i:1824347 original size:2 final size:2
Alignment explanation
Indices: 1824340--1824390 Score: 66
Period size: 2 Copynumber: 23.5 Consensus size: 2
1824330 ATGAAGGATT
1824340 TA TA TA TA TA TCA TGA GTCA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA T-A T-A -T-A TA TA TA TA TA TA TA TA TA TA TA TA
1824384 TA TA TA T
1 TA TA TA T
1824391 CAGGAGTTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 39 0.87
3 4 0.09
4 2 0.04
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1828140 original size:2 final size:2
Alignment explanation
Indices: 1828133--1828164 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1828123 ACTGCTATTA
1828133 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
1828165 TCTCGCTCAA
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:1828922 original size:2 final size:2
Alignment explanation
Indices: 1828915--1828952 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1828905 GACTTATGTT
*
1828915 CA CA CA CA CA CA CA CA CA CA CG CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1828953 TATCTATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.50, G:0.03, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1829916 original size:2 final size:2
Alignment explanation
Indices: 1829909--1829933 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1829899 TCATTTTAGA
1829909 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1829934 AAGAGAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1831454 original size:10 final size:10
Alignment explanation
Indices: 1831439--1831467 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1831429 TAAATTTTAA
1831439 ATTTATAAAT
1 ATTTATAAAT
1831449 ATTTATAAAT
1 ATTTATAAAT
1831459 ATTT-TAAAT
1 ATTTATAAAT
1831468 TAATTATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.26
10 14 0.74
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
ATTTATAAAT
Found at i:1831831 original size:16 final size:17
Alignment explanation
Indices: 1831812--1831844 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1831802 TTTATTTTTT
1831812 AATTAAA-ATTTATAAA
1 AATTAAATATTTATAAA
*
1831828 AATTAAATATTTTTAAA
1 AATTAAATATTTATAAA
1831845 GAAAATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTAAATATTTATAAA
Found at i:1834913 original size:23 final size:21
Alignment explanation
Indices: 1834880--1834925 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 21
1834870 AAAAACATTA
*
1834880 AATATTAAATAAGTATTTAAT
1 AATATTAAATAAATATTTAAT
1834901 AATATATATAATAAATATTTAAT
1 AATAT-TA-AATAAATATTTAAT
1834924 AA
1 AA
1834926 AAATATATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.23
22 2 0.09
23 15 0.68
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
AATATTAAATAAATATTTAAT
Found at i:1834926 original size:11 final size:11
Alignment explanation
Indices: 1834878--1834926 Score: 62
Period size: 11 Copynumber: 4.4 Consensus size: 11
1834868 TTAAAAACAT
*
1834878 TAAATATTAAA
1 TAAATATTTAA
*
1834889 TAAGTATTTAA
1 TAAATATTTAA
*
1834900 TAATATATATAA
1 TAA-ATATTTAA
1834912 TAAATATTTAA
1 TAAATATTTAA
1834923 TAAA
1 TAAA
1834927 AATATATCTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
11 23 0.72
12 9 0.28
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (11 bp):
TAAATATTTAA
Found at i:1835704 original size:23 final size:23
Alignment explanation
Indices: 1835678--1835726 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
1835668 ATTAATATAT
1835678 TAAATTTAATGTTTTTATAATAA
1 TAAATTTAATGTTTTTATAATAA
* *
1835701 TAAATTTTATTTTTTTATAATAA
1 TAAATTTAATGTTTTTATAATAA
1835724 TAA
1 TAA
1835727 GTTCATGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
TAAATTTAATGTTTTTATAATAA
Found at i:1836623 original size:17 final size:18
Alignment explanation
Indices: 1836601--1836641 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1836591 TTTGTCCATT
1836601 TATATATGTT-TTTAA-AA
1 TATATAT-TTGTTTAAGAA
1836618 TATATATTTGTTTAAGAA
1 TATATATTTGTTTAAGAA
1836636 TA-ATAT
1 TATATAT
1836642 AAAAATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 2 0.09
17 16 0.73
18 4 0.18
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (18 bp):
TATATATTTGTTTAAGAA
Found at i:1836658 original size:17 final size:17
Alignment explanation
Indices: 1836638--1836673 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1836628 TTTAAGAATA
1836638 ATATAAAAATAAAATTT
1 ATATAAAAATAAAATTT
**
1836655 ATATTTAAATAAAATTT
1 ATATAAAAATAAAATTT
1836672 AT
1 AT
1836674 CAAATTATAT
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:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATAAAAATAAAATTT
Found at i:1836734 original size:21 final size:19
Alignment explanation
Indices: 1836705--1836743 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
1836695 ATGAATAAAA
1836705 AATAAATAAGATAATATATTC
1 AATAAATAA-A-AATATATTC
*
1836726 AATATATAAAAATATATT
1 AATAAATAAAAATATATT
1836744 ACTTATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 1 0.06
21 8 0.47
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (19 bp):
AATAAATAAAAATATATTC
Found at i:1836769 original size:12 final size:14
Alignment explanation
Indices: 1836751--1836782 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
1836741 ATTACTTATA
1836751 AATTTTAAAA-AAT
1 AATTTTAAAATAAT
1836764 -ATTTTAAAATAAT
1 AATTTTAAAATAAT
1836777 AATTTT
1 AATTTT
1836783 GATTTATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 9 0.53
13 3 0.18
14 5 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AATTTTAAAATAAT
Found at i:1842233 original size:17 final size:17
Alignment explanation
Indices: 1842213--1842250 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1842203 TTATTTAGCA
1842213 TATTATTT-TTATTAAAT
1 TATTATTTATTATT-AAT
*
1842230 TATTTTTTATTATTAAT
1 TATTATTTATTATTAAT
1842247 TATT
1 TATT
1842251 GTTGAACTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TATTATTTATTATTAAT
Found at i:1842335 original size:18 final size:18
Alignment explanation
Indices: 1842312--1842348 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1842302 ATGAAATGAA
1842312 ATAATAAAGAAGTATTAT
1 ATAATAAAGAAGTATTAT
1842330 ATAATAAAGAAGTATTAT
1 ATAATAAAGAAGTATTAT
1842348 A
1 A
1842349 AAACATTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (18 bp):
ATAATAAAGAAGTATTAT
Found at i:1846535 original size:14 final size:13
Alignment explanation
Indices: 1846516--1846543 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1846506 AATCCACGGC
1846516 AAAAAAAAAAAGG
1 AAAAAAAAAAAGG
1846529 AAAAAAAAAAAGG
1 AAAAAAAAAAAGG
1846542 AA
1 AA
1846544 GATTGGTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAGG
Found at i:1847362 original size:21 final size:21
Alignment explanation
Indices: 1847308--1847363 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 21
1847298 ACTTGGCGTA
*
1847308 AGTTAAATTTAAATATTTAATT
1 AGTT-AATTTAATTATTTAATT
1847330 AGTTAATTTAATTAATTTAAATT
1 AGTTAATTTAATT-ATTT-AATT
1847353 A-TT-ATTTAATT
1 AGTTAATTTAATT
1847364 TATAAAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
21 16 0.52
22 10 0.32
23 5 0.16
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (21 bp):
AGTTAATTTAATTATTTAATT
Found at i:1847397 original size:14 final size:15
Alignment explanation
Indices: 1847355--1847403 Score: 57
Period size: 14 Copynumber: 3.3 Consensus size: 15
1847345 TTTAAATTAT
1847355 TATTTAATTTATAAAA
1 TATTTAA-TTATAAAA
*
1847371 TATTT-TTTATAAAA
1 TATTTAATTATAAAA
1847385 TATTTAATT-TAAAA
1 TATTTAATTATAAAA
*
1847399 AATTT
1 TATTT
1847404 TCAATAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 22 0.76
15 2 0.07
16 5 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTTAATTATAAAA
Found at i:1847417 original size:26 final size:27
Alignment explanation
Indices: 1847325--1847415 Score: 76
Period size: 26 Copynumber: 3.3 Consensus size: 27
1847315 TTTAAATATT
* **
1847325 TAATTAGTTAATTTAATTAA-TTTAAA
1 TAATTATTTAATTTAAAAAATTTTAAA
* **
1847351 TTATTATTTAATTTATAAAATATTTTTTA
1 TAATTATTTAATTTA-AAAA-ATTTTAAA
* *
1847380 TAAAATATTTAATTTAAAAAATTTTCAA
1 T-AATTATTTAATTTAAAAAATTTTAAA
1847408 TAATTATT
1 TAATTATT
1847416 AAAATATACA
Statistics
Matches: 50, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
26 13 0.26
27 8 0.16
28 8 0.16
29 9 0.18
30 12 0.24
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (27 bp):
TAATTATTTAATTTAAAAAATTTTAAA
Found at i:1847559 original size:2 final size:2
Alignment explanation
Indices: 1847552--1847604 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
1847542 GCTTTTTGTC
* *
1847552 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1847594 TA TA TA TA TA T
1 TA TA TA TA TA T
1847605 CAAAAAACCA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1848110 original size:14 final size:14
Alignment explanation
Indices: 1848083--1848138 Score: 55
Period size: 13 Copynumber: 4.2 Consensus size: 14
1848073 TAATAAAAAT
*
1848083 ATATT-TTATTTAA
1 ATATTATTATATAA
*
1848096 ATTTTATTATATAA
1 ATATTATTATATAA
*
1848110 ATATTAATATA-AA
1 ATATTATTATATAA
*
1848123 ATATTA-TATTTAA
1 ATATTATTATATAA
1848136 ATA
1 ATA
1848139 ATAATTTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
12 3 0.08
13 17 0.47
14 16 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATATTATTATATAA
Found at i:1848660 original size:15 final size:14
Alignment explanation
Indices: 1848627--1848679 Score: 54
Period size: 15 Copynumber: 3.8 Consensus size: 14
1848617 TAATGAAAGG
*
1848627 AATATTTTAATTTT
1 AATATTTTAAATTT
*
1848641 TATATTATTAAATTT
1 AATATT-TTAAATTT
*
1848656 AATATTTT-ATTTT
1 AATATTTTAAATTT
*
1848669 TATATTTTAAA
1 AATATTTTAAA
1848680 ATATAGTAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
13 11 0.35
14 8 0.26
15 12 0.39
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
AATATTTTAAATTT
Found at i:1848730 original size:20 final size:21
Alignment explanation
Indices: 1848690--1848730 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1848680 ATATAGTAAG
*
1848690 TAAAAAAATAATTTATGATAT
1 TAAAAAAATAATTTATAATAT
*
1848711 TAAAAAAATTATTTA-AATAT
1 TAAAAAAATAATTTATAATAT
1848731 CGATAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
TAAAAAAATAATTTATAATAT
Found at i:1848974 original size:21 final size:21
Alignment explanation
Indices: 1848930--1848974 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1848920 ACTATTTTCA
*
1848930 AAATATAAGAATTAAAATATT
1 AAATATAAGAATTAAAATACT
*
1848951 AAATTTAAGAATATAAAA-ACT
1 AAATATAAGAAT-TAAAATACT
1848972 AAA
1 AAA
1848975 ATGTTTCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.29
Consensus pattern (21 bp):
AAATATAAGAATTAAAATACT
Found at i:1849684 original size:21 final size:21
Alignment explanation
Indices: 1849645--1849685 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1849635 AATTTAAAAA
*
1849645 TTATTTTATTTTAATATTTAT
1 TTATTTTATATTAATATTTAT
1849666 TTATTTTATAATTAA-ATTTA
1 TTATTTTAT-ATTAATATTTA
1849686 AATAAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TTATTTTATATTAATATTTAT
Found at i:1849708 original size:38 final size:37
Alignment explanation
Indices: 1849655--1849733 Score: 88
Period size: 38 Copynumber: 2.1 Consensus size: 37
1849645 TTATTTTATT
* **
1849655 TTAATATTTATTTATTTTATAATTAAATTTAAA-TAAAA
1 TTAATATTTAATTATTAAATAA-T-AATTTAAATTAAAA
* *
1849693 TTAATTTTTAATTATTAAATAATAATTTAAATTAAAC
1 TTAATATTTAATTATTAAATAATAATTTAAATTAAAA
1849730 TTAA
1 TTAA
1849734 ATAATTCGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
36 8 0.23
37 9 0.26
38 18 0.51
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (37 bp):
TTAATATTTAATTATTAAATAATAATTTAAATTAAAA
Found at i:1851513 original size:38 final size:39
Alignment explanation
Indices: 1851464--1851561 Score: 101
Period size: 38 Copynumber: 2.5 Consensus size: 39
1851454 AAAAAATTAT
*
1851464 TAAATTTTATAAAATTTTATATTTTTATTAA-ATTTAAAA
1 TAAATTTTATAAAATTTTA-ATTTGTATTAATATTTAAAA
** **
1851503 TAAA-TTTATAATCTTTTAATTTGTATTAATATTTAATT
1 TAAATTTTATAAAATTTTAATTTGTATTAATATTTAAAA
* *
1851541 TATATTTAAATAAAATTTTAA
1 TAAATTT-TATAAAATTTTAA
1851562 CATAAATTAA
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
37 10 0.21
38 21 0.45
39 6 0.13
40 10 0.21
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (39 bp):
TAAATTTTATAAAATTTTAATTTGTATTAATATTTAAAA
Found at i:1855018 original size:32 final size:32
Alignment explanation
Indices: 1854976--1855075 Score: 89
Period size: 32 Copynumber: 3.1 Consensus size: 32
1854966 ATTGTATAAA
*
1854976 AAATAATTTAAATATAATATAATATAAATATAT
1 AAAT-ATTTAAATATTATATAATATAAATATAT
*
1855009 AAATATTTAAA-ATTTATATAAAATAAACTAT-T
1 AAATATTTAAATA-TTATATAATATAAA-TATAT
* * *
1855041 AACTTATTTAAAT-TTATTTAAATATATATATAT
1 AA-ATATTTAAATATTATAT-AATATAAATATAT
1855074 AA
1 AA
1855076 TATAATACAT
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
31 1 0.02
32 30 0.55
33 24 0.44
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (32 bp):
AAATATTTAAATATTATATAATATAAATATAT
Found at i:1855019 original size:16 final size:17
Alignment explanation
Indices: 1854970--1855019 Score: 52
Period size: 16 Copynumber: 3.0 Consensus size: 17
1854960 CGGTACATTG
*
1854970 TATAAAAAATAATTTAAA
1 TATAATAAAT-ATTTAAA
1854988 TATAATATAATA--TAAA
1 TATAATA-AATATTTAAA
1855004 TAT-ATAAATATTTAAA
1 TATAATAAATATTTAAA
1855020 ATTTATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
14 4 0.14
15 3 0.11
16 11 0.39
18 7 0.25
19 3 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TATAATAAATATTTAAA
Found at i:1856932 original size:2 final size:2
Alignment explanation
Indices: 1856925--1856955 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1856915 TTCTAACATC
1856925 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1856956 CACTGTCATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1860254 original size:2 final size:2
Alignment explanation
Indices: 1860247--1860295 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1860237 ATGCATATGA
1860247 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1860289 AG AG AG A
1 AG AG AG A
1860296 ATAATAAATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1860866 original size:2 final size:2
Alignment explanation
Indices: 1860861--1860893 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1860851 TAATCTTTAG
1860861 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1860894 TATATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1863524 original size:20 final size:20
Alignment explanation
Indices: 1863499--1863541 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1863489 TAAATATAAA
*
1863499 ATTTTTATTAATTATTTATT
1 ATTTTTAATAATTATTTATT
*
1863519 ATTTTTAATATTTATTTATT
1 ATTTTTAATAATTATTTATT
1863539 ATT
1 ATT
1863542 AAAATTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
ATTTTTAATAATTATTTATT
Found at i:1863537 original size:17 final size:17
Alignment explanation
Indices: 1863503--1863543 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
1863493 TATAAAATTT
1863503 TTATTAATTATTTATTA
1 TTATTAATTATTTATTA
*
1863520 TTTTTAA-TATTTATTTA
1 TTATTAATTATTTA-TTA
1863537 TTATTAA
1 TTATTAA
1863544 AATTATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTATTAATTATTTATTA
Found at i:1863550 original size:20 final size:21
Alignment explanation
Indices: 1863505--1863551 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
1863495 TAAAATTTTT
* **
1863505 ATTAATTATTTATTATTTTTA
1 ATTATTTATTTATTATTTAAA
1863526 A-TATTTATTTATTA-TTAAA
1 ATTATTTATTTATTATTTAAA
1863545 ATTATTT
1 ATTATTT
1863552 TTCAAGCACT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 4 0.18
20 17 0.77
21 1 0.05
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTATTTATTTATTATTTAAA
Found at i:1868565 original size:12 final size:13
Alignment explanation
Indices: 1868545--1868577 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1868535 AGGTAAGCTC
1868545 TTTTCTTTTTCT-
1 TTTTCTTTTTCTA
*
1868557 TTTTTTTTTTCTA
1 TTTTCTTTTTCTA
1868570 TTTTCTTT
1 TTTTCTTT
1868578 CGATTATTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTCTTTTTCTA
Found at i:1868628 original size:1 final size:1
Alignment explanation
Indices: 1868624--1868651 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
1868614 AAGGAGAGAA
1868624 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
1868652 CTTCCCGCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:1869066 original size:16 final size:19
Alignment explanation
Indices: 1869045--1869081 Score: 53
Period size: 16 Copynumber: 2.1 Consensus size: 19
1869035 AAAATTAAAA
1869045 TATTTT-TA-AAAAT-ATT
1 TATTTTATATAAAATAATT
1869061 TATTTTATATAAAATAATT
1 TATTTTATATAAAATAATT
1869080 TA
1 TA
1869082 AAATTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.33
17 2 0.11
18 5 0.28
19 5 0.28
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTTTATATAAAATAATT
Found at i:1869177 original size:16 final size:16
Alignment explanation
Indices: 1869158--1869188 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1869148 AATACGAATA
*
1869158 TTAATTTTTTAAAAAT
1 TTAATTTTGTAAAAAT
1869174 TTAATTTTGTAAAAA
1 TTAATTTTGTAAAAA
1869189 AAAACTAATT
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:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (16 bp):
TTAATTTTGTAAAAAT
Found at i:1869358 original size:20 final size:20
Alignment explanation
Indices: 1869324--1869376 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
1869314 CGAACATTTC
1869324 CTTTCCTTTTCTTTTCTTTT
1 CTTTCCTTTTCTTTTCTTTT
*
1869344 CTTTCACTTTT-TTTTTTTTT
1 CTTTC-CTTTTCTTTTCTTTT
1869364 CTTT-C-TTTCTTTT
1 CTTTCCTTTTCTTTT
1869377 TATTTAGCAC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
17 3 0.10
18 5 0.17
20 17 0.57
21 5 0.17
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (20 bp):
CTTTCCTTTTCTTTTCTTTT
Found at i:1869531 original size:21 final size:21
Alignment explanation
Indices: 1869507--1869546 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1869497 TATAAAATTT
1869507 AAAAT-TTATATTAAATTTATC
1 AAAATATTATA-TAAATTTATC
1869528 AAAATATTATATAAATTTA
1 AAAATATTATATAAATTTA
1869547 CATTTATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (21 bp):
AAAATATTATATAAATTTATC
Found at i:1870028 original size:12 final size:12
Alignment explanation
Indices: 1869991--1870028 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
1869981 GTTTATTAAG
1869991 TTTTCTTACATAA
1 TTTTCTTACAT-A
1870004 TTTTC-TA-ATA
1 TTTTCTTACATA
1870014 TTTTCTTACATA
1 TTTTCTTACATA
1870026 TTT
1 TTT
1870029 CTTTAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
10 6 0.26
11 4 0.17
12 8 0.35
13 5 0.22
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.61
Consensus pattern (12 bp):
TTTTCTTACATA
Found at i:1870396 original size:13 final size:13
Alignment explanation
Indices: 1870364--1870397 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1870354 TAAATTTAAA
1870364 ATTTAATATAATT
1 ATTTAATATAATT
**
1870377 AAATAATATAATT
1 ATTTAATATAATT
1870390 ATTTAATA
1 ATTTAATA
1870398 AAAAATTATT
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTTAATATAATT
Found at i:1871047 original size:17 final size:19
Alignment explanation
Indices: 1871013--1871050 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
1871003 TTTAGAAAAT
1871013 ATTTTAATTATATTTTAAA
1 ATTTTAATTATATTTTAAA
1871032 ATTTT-ATTAT-TTTTAAA
1 ATTTTAATTATATTTTAAA
1871049 AT
1 AT
1871051 AAAATATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.47
18 5 0.26
19 5 0.26
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTAATTATATTTTAAA
Found at i:1872684 original size:22 final size:23
Alignment explanation
Indices: 1872658--1872700 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1872648 TATATTAATA
1872658 AAATATAA-TTATTTAAATATTT
1 AAATATAATTTATTTAAATATTT
*
1872680 AAATATAATTTTTTTAAATAT
1 AAATATAATTTATTTAAATAT
1872701 CAAAATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
AAATATAATTTATTTAAATATTT
Found at i:1872706 original size:23 final size:22
Alignment explanation
Indices: 1872657--1872711 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
1872647 ATATATTAAT
*
1872657 AAAATATAATTATTTAAATATT
1 AAAATATAATTATTTAAATATC
* *
1872679 TAAATATAATTTTTTTAAATATC
1 AAAATATAA-TTATTTAAATATC
1872702 AAAATTATAA
1 AAAA-TATAA
1872712 ATTAAATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 8 0.30
23 14 0.52
24 5 0.19
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
AAAATATAATTATTTAAATATC
Found at i:1872720 original size:12 final size:13
Alignment explanation
Indices: 1872696--1872737 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
1872686 AATTTTTTTA
1872696 AATATCAAAATTAT
1 AATAT-AAAATTAT
*
1872710 AA-ATTAAATTAT
1 AATATAAAATTAT
1872722 AATATAAAATTA-
1 AATATAAAATTAT
1872734 AATA
1 AATA
1872738 ATACATTACC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 13 0.52
13 10 0.40
14 2 0.08
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (13 bp):
AATATAAAATTAT
Found at i:1875381 original size:16 final size:16
Alignment explanation
Indices: 1875360--1875391 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1875350 CATAAGATCA
*
1875360 TAATAAATTTATAATT
1 TAATAAATTTAAAATT
1875376 TAATAAATTTAAAATT
1 TAATAAATTTAAAATT
1875392 ATTTTAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TAATAAATTTAAAATT
Found at i:1877060 original size:34 final size:34
Alignment explanation
Indices: 1877014--1877198 Score: 257
Period size: 34 Copynumber: 5.5 Consensus size: 34
1877004 GTAAAAACCA
*
1877014 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1877048 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
1877082 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1877116 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
1877150 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
1877183 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
1877199 TCTCCCACTT
Statistics
Matches: 135, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 18 0.13
34 113 0.84
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:1881291 original size:19 final size:19
Alignment explanation
Indices: 1881264--1881326 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
1881254 TCACGTGTAC
* *
1881264 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
1881283 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
1881302 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
1881321 AGTACC
1 AGTACC
1881327 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:1881674 original size:34 final size:34
Alignment explanation
Indices: 1881628--1881810 Score: 244
Period size: 34 Copynumber: 5.4 Consensus size: 34
1881618 GTAAAAACCA
**
1881628 CCATTTAATCAACAATGACAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1881662 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
1881696 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1881730 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
1881764 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
1881797 CCATTTAATCAACA
1 CCATTTAATCAACA
1881811 TCATGAACGA
Statistics
Matches: 132, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
33 16 0.12
34 112 0.85
35 4 0.03
ACGTcount: A:0.40, C:0.27, G:0.07, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:1882372 original size:3 final size:3
Alignment explanation
Indices: 1882364--1882398 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1882354 CCCTTTTCAT
1882364 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1882399 TAAAAAAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1883515 original size:23 final size:23
Alignment explanation
Indices: 1883482--1883530 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
1883472 AAAGGCAAAT
*
1883482 ATTTATATTTATATTTTATTATAA
1 ATTTATATTTATATTTTA-AATAA
*
1883506 ATTTA-ATTTATTTTTTAAATAA
1 ATTTATATTTATATTTTAAATAA
1883528 ATT
1 ATT
1883531 ATCAATTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 7 0.30
23 11 0.48
24 5 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
ATTTATATTTATATTTTAAATAA
Found at i:1884708 original size:2 final size:2
Alignment explanation
Indices: 1884701--1884728 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1884691 ACTTCAATAA
1884701 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
1884729 CATTCTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1888477 original size:14 final size:14
Alignment explanation
Indices: 1888458--1888496 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
1888448 ATGATATTCA
1888458 AGAAAAAAAGAAAG
1 AGAAAAAAAGAAAG
1888472 AGAAAAAAA-AAAG
1 AGAAAAAAAGAAAG
1888485 AGAAAAGAAAGA
1 AGAAAA-AAAGA
1888497 GCCACCGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 10 0.43
14 12 0.52
15 1 0.04
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AGAAAAAAAGAAAG
Found at i:1888479 original size:13 final size:13
Alignment explanation
Indices: 1888458--1888490 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1888448 ATGATATTCA
1888458 AGAAAAAAAGAAAG
1 AGAAAAAAA-AAAG
1888472 AGAAAAAAAAAAG
1 AGAAAAAAAAAAG
1888485 AGAAAA
1 AGAAAA
1888491 GAAAGAGCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAAAAG
Found at i:1888483 original size:18 final size:18
Alignment explanation
Indices: 1888460--1888494 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1888450 GATATTCAAG
*
1888460 AAAAAAAGA-AAGAGAAA
1 AAAAAAAGAGAAAAGAAA
1888477 AAAAAAAGAGAAAAGAAA
1 AAAAAAAGAGAAAAGAAA
1888495 GAGCCACCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAAAAGAGAAAAGAAA
Found at i:1892745 original size:165 final size:165
Alignment explanation
Indices: 1892466--1892787 Score: 495
Period size: 165 Copynumber: 2.0 Consensus size: 165
1892456 AAGAGGTCAT
* * *
1892466 ATGCTAAGAACTTTTGAAAATATTGAATTTAAGTTGGTAGAAAGCAAGGTGAAGAGACTGTTATT
1 ATGCTAAGAACTTTTGAAAATATTGAACTTAAATTGGTAGAAAGCAAGGTGAAGAGACTGTTATC
* *
1892531 GGAAGGAAGAAAGTTGATAGTAAACAATTAAAATCTTAGTTTTGTTTACTT-TGGTACAGTTTTG
66 GGAAGGAAGAAAGTTGATAGTAAACAATTAAAATCTTAGTTTGGTTTACTTCT-GCACAGTTTTG
* * *
1892595 GCACTTACTGGAAGCTTATATGATTAAGAGAGTTAC
130 GCACTTACTGAAAACTGATATGATTAAGAGAGTTAC
* *
1892631 ATGCTAAGAACTTTTGAAAATATTGAACTTAAATTGGTAGAAAGCAAGTTGAAGAGATTGTTATC
1 ATGCTAAGAACTTTTGAAAATATTGAACTTAAATTGGTAGAAAGCAAGGTGAAGAGACTGTTATC
* * *
1892696 GGAAGGAAGAAAGGTT-ATATTGAACAATTAGAATCTTAGTTTGGTTTACTTCTGCACAGTTTTG
66 GGAAGGAAGAAA-GTTGATAGTAAACAATTAAAATCTTAGTTTGGTTTACTTCTGCACAGTTTTG
1892760 GCACTTACTGAAAACTGATATGATTAAG
130 GCACTTACTGAAAACTGATATGATTAAG
1892788 CATGTCATGA
Statistics
Matches: 142, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
165 138 0.97
166 4 0.03
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.34
Consensus pattern (165 bp):
ATGCTAAGAACTTTTGAAAATATTGAACTTAAATTGGTAGAAAGCAAGGTGAAGAGACTGTTATC
GGAAGGAAGAAAGTTGATAGTAAACAATTAAAATCTTAGTTTGGTTTACTTCTGCACAGTTTTGG
CACTTACTGAAAACTGATATGATTAAGAGAGTTAC
Found at i:1903770 original size:253 final size:252
Alignment explanation
Indices: 1903323--1903831 Score: 1009
Period size: 253 Copynumber: 2.0 Consensus size: 252
1903313 TGTCGGCTTT
1903323 CCAAAATGACAGAAGAACCGTGAGTTTACGTTTTCAAGGGTTTAAACTTTTGAACGAAACGGTGA
1 CCAAAATGACAGAAGAACCGTGAGTTTACGTTTTCAAGGGTTTAAACTTTTGAACGAAACGGTGA
1903388 TAAGGTTTTAGCCTTTTGAAAATTTAAGAAAGAGTGCTTTAGACGACGTCGTTTAGCAACAAATG
66 TAAGGTTTTAGCCTTTTGAAAATTTAAGAAAGAGTGCTTTAGACGACGTCGTTTAGCAACAAATG
1903453 ATATTATACGAAGACTGAACCTGGTCCATGGATCAGAAATCTGACTGCTCTGGGCTGAAATGAAA
131 ATATTATACGAAGACTGAACCTGGTCCATGGATCAGAAATCTGACTGCTCTGGGCTGAAATGAAA
1903518 TAATTGAACTATAAAGTTTTCTCCATTGTAAAATTGGTTAAAAATGGGTCCGGCGGC
196 TAATTGAACTATAAAGTTTTCTCCATTGTAAAATTGGTTAAAAATGGGTCCGGCGGC
1903575 CCAAAATGACAGAAGAACCGTGAGTTTACGTTTTCAAGGGTTTAAACTTTTGAACGAAACGGTGA
1 CCAAAATGACAGAAGAACCGTGAGTTTACGTTTTCAAGGGTTTAAACTTTTGAACGAAACGGTGA
1903640 TAAGGTTTTAGCCTTTTGAAAATTTAAGAAAAGAGTGCTTTAGACGACGTCGTTTAGCAACAAAT
66 TAAGGTTTTAGCCTTTTGAAAATTTAAG-AAAGAGTGCTTTAGACGACGTCGTTTAGCAACAAAT
1903705 GATATTATACGAAGACTGAACCTGGTCCATGGATCAGAAATCTGACTGCTCTGGGCTGAAATGAA
130 GATATTATACGAAGACTGAACCTGGTCCATGGATCAGAAATCTGACTGCTCTGGGCTGAAATGAA
1903770 ATAATTGAACTATAAAGTTTTCTCCATTGTAAAATTGGTTAAAAATGGGTCCGGCGGC
195 ATAATTGAACTATAAAGTTTTCTCCATTGTAAAATTGGTTAAAAATGGGTCCGGCGGC
1903828 CCAA
1 CCAA
1903832 CATATCACCC
Statistics
Matches: 256, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
252 93 0.36
253 163 0.64
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (252 bp):
CCAAAATGACAGAAGAACCGTGAGTTTACGTTTTCAAGGGTTTAAACTTTTGAACGAAACGGTGA
TAAGGTTTTAGCCTTTTGAAAATTTAAGAAAGAGTGCTTTAGACGACGTCGTTTAGCAACAAATG
ATATTATACGAAGACTGAACCTGGTCCATGGATCAGAAATCTGACTGCTCTGGGCTGAAATGAAA
TAATTGAACTATAAAGTTTTCTCCATTGTAAAATTGGTTAAAAATGGGTCCGGCGGC
Found at i:1904025 original size:17 final size:17
Alignment explanation
Indices: 1904000--1904035 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1903990 CAACAAAATT
*
1904000 ATAATTTAAAAATAAAA
1 ATAAATTAAAAATAAAA
*
1904017 ATAAATTAAAAATATAA
1 ATAAATTAAAAATAAAA
1904034 AT
1 AT
1904036 TTTAAAATTT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
ATAAATTAAAAATAAAA
Found at i:1904240 original size:10 final size:10
Alignment explanation
Indices: 1904225--1904259 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
1904215 TGTCTTTCTC
1904225 CTTTTTTTTT
1 CTTTTTTTTT
1904235 CTTTTTTTTT
1 CTTTTTTTTT
*
1904245 -TTTTTCTTT
1 CTTTTTTTTT
1904254 CTTTTT
1 CTTTTT
1904260 CAAGGAGTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:1904246 original size:15 final size:16
Alignment explanation
Indices: 1904226--1904259 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
1904216 GTCTTTCTCC
1904226 TTTTTTTTTCTTT-TT
1 TTTTTTTTTCTTTCTT
1904241 TTTTTTTTTCTTTCTT
1 TTTTTTTTTCTTTCTT
1904257 TTT
1 TTT
1904260 CAAGGAGTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (16 bp):
TTTTTTTTTCTTTCTT
Found at i:1904460 original size:46 final size:44
Alignment explanation
Indices: 1904349--1904483 Score: 243
Period size: 44 Copynumber: 3.0 Consensus size: 44
1904339 CCATAAACCA
1904349 AAAGTGCTGGCCTCGCCCTCTCTCTCTCATGCATGTTTTCTTTG
1 AAAGTGCTGGCCTCGCCCTCTCTCTCTCATGCATGTTTTCTTTG
1904393 AAAGTGCTGGCCTCGCCCTCTCTCTCTCATGCATGTTTTCTTTG
1 AAAGTGCTGGCCTCGCCCTCTCTCTCTCATGCATGTTTTCTTTG
*
1904437 AAAGTGCTGGCCTCGCCCTCTCTCTCTCTCATACATGTTTTCTTTG
1 AAAGTGCTGGCCTCG-CC-CTCTCTCTCTCATGCATGTTTTCTTTG
1904483 A
1 A
1904484 TCATTCTTTT
Statistics
Matches: 88, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
44 59 0.67
45 2 0.02
46 27 0.31
ACGTcount: A:0.13, C:0.32, G:0.17, T:0.39
Consensus pattern (44 bp):
AAAGTGCTGGCCTCGCCCTCTCTCTCTCATGCATGTTTTCTTTG
Found at i:1906736 original size:29 final size:29
Alignment explanation
Indices: 1906695--1906753 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
1906685 ATAAAAATAT
* * *
1906695 ATAATAATAAAATTTTAATATTTT-ATAA
1 ATAATAAAAAAATATTAAAATTTTGATAA
1906723 ATAATAAAACAAATATTAAAATTTTGATAA
1 ATAATAAAA-AAATATTAAAATTTTGATAA
1906753 A
1 A
1906754 AAATTTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 8 0.31
29 13 0.50
30 5 0.19
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (29 bp):
ATAATAAAAAAATATTAAAATTTTGATAA
Found at i:1907424 original size:29 final size:29
Alignment explanation
Indices: 1907354--1907448 Score: 77
Period size: 29 Copynumber: 3.3 Consensus size: 29
1907344 ATTATTATTA
*
1907354 AAATAATTTTTA-AAATTAAAA-ATTACAT
1 AAATAATTTTTATAAA-TAAAATATTAAAT
** *
1907382 TTATATTTTATTATAAATAAAATATTAAAT
1 AAATAATTT-TTATAAATAAAATATTAAAT
* * * *
1907412 AAATAATTTTTATGATTAAAATAATAATT
1 AAATAATTTTTATAAATAAAATATTAAAT
*
1907441 TAATAATT
1 AAATAATT
1907449 CAAATAAAAA
Statistics
Matches: 52, Mismatches: 12, Indels: 5
0.75 0.17 0.07
Matches are distributed among these distances:
28 6 0.12
29 31 0.60
30 15 0.29
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (29 bp):
AAATAATTTTTATAAATAAAATATTAAAT
Found at i:1907805 original size:20 final size:20
Alignment explanation
Indices: 1907754--1907805 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
1907744 GATTTTTTTT
*
1907754 ATTAGAATATATAATTTAAGA
1 ATTA-AATATATAAATTAAGA
* **
1907775 ATAAAAT-TATAAATTATTA
1 ATTAAATATATAAATTAAGA
1907794 ATTAAATATATA
1 ATTAAATATATA
1907806 TTTATAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 15 0.60
20 7 0.28
21 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (20 bp):
ATTAAATATATAAATTAAGA
Found at i:1907900 original size:15 final size:15
Alignment explanation
Indices: 1907844--1907902 Score: 57
Period size: 15 Copynumber: 3.8 Consensus size: 15
1907834 TCACTTAAAT
1907844 TTTAATATTTAAAT-A
1 TTTAA-ATTTAAATAA
** *
1907859 TTTAAATTCTATTTAT
1 TTTAAATT-TAAATAA
1907875 TTTATAATTTAAATAA
1 TTTA-AATTTAAATAA
1907891 TTTAAATTTAAA
1 TTTAAATTTAAA
1907903 CTTCATAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
14 3 0.09
15 16 0.46
16 12 0.34
17 4 0.11
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTAAATTTAAATAA
Found at i:1909791 original size:17 final size:16
Alignment explanation
Indices: 1909766--1909807 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
1909756 AATACTATAA
1909766 AATTAATTAAAATTCTT
1 AATTAATTAAAATT-TT
*
1909783 AATTTATTAAAATTTT
1 AATTAATTAAAATTTT
*
1909799 AAGTAATTA
1 AATTAATTA
1909808 TCATTTTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (16 bp):
AATTAATTAAAATTTT
Found at i:1910152 original size:17 final size:17
Alignment explanation
Indices: 1910113--1910153 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1910103 TAATTGATCA
* *
1910113 AATTTTATTATATAATT
1 AATTTAATTATATAAAT
*
1910130 ATTTTAATTATATAAAT
1 AATTTAATTATATAAAT
1910147 AATTTAA
1 AATTTAA
1910154 GATATCATCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AATTTAATTATATAAAT
Found at i:1910591 original size:19 final size:18
Alignment explanation
Indices: 1910557--1910606 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
1910547 AGTGCAAATT
* *
1910557 TTAAAAAAATCTATTTAAC
1 TTAAAAAAAT-AATTTAAA
*
1910576 TCTAAAATAATAATTTAAA
1 T-TAAAAAAATAATTTAAA
1910595 TTAAAAAAATAA
1 TTAAAAAAATAA
1910607 AGACAGGTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 10 0.38
19 8 0.31
20 8 0.31
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (18 bp):
TTAAAAAAATAATTTAAA
Found at i:1910958 original size:3 final size:3
Alignment explanation
Indices: 1910950--1910991 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1910940 ATTTACAAGC
1910950 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1910992 GTCATGATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1916598 original size:19 final size:18
Alignment explanation
Indices: 1916566--1916613 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
1916556 TTTAATAATT
1916566 TATTTTAATATATATTTA
1 TATTTTAATATATATTTA
*
1916584 TATTTTTATATTATATTTA
1 TATTTTAATA-TATATTTA
* *
1916603 TGTTATAATAT
1 TATTTTAATAT
1916614 GTCTTATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
TATTTTAATATATATTTA
Found at i:1916625 original size:17 final size:16
Alignment explanation
Indices: 1916558--1916625 Score: 50
Period size: 17 Copynumber: 4.1 Consensus size: 16
1916548 TTTGATATTT
1916558 TAATA-ATTTATTTTA
1 TAATATATTTATTTTA
1916573 -ATATATATTTATATTTTTA
1 TA-ATATA-TT-TA-TTTTA
* *
1916592 TATTATATTTATGTTA
1 TAATATATTTATTTTA
*
1916608 TAATATGTCTTATTTTA
1 TAATATAT-TTATTTTA
1916625 T
1 T
1916626 TTATTTTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
14 1 0.02
15 3 0.07
16 11 0.27
17 12 0.29
18 4 0.10
19 9 0.22
20 1 0.02
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (16 bp):
TAATATATTTATTTTA
Found at i:1916973 original size:23 final size:21
Alignment explanation
Indices: 1916935--1916985 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 21
1916925 TTTTATAAGC
*
1916935 TTTAAT-AATTGTTTATAAATA
1 TTTAATAAATTGATTATAAA-A
*
1916956 TTTTAATAAATTGATTATTAAA
1 -TTTAATAAATTGATTATAAAA
1916978 TTTAATAA
1 TTTAATAA
1916986 TATAATTGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 8 0.31
22 7 0.27
23 11 0.42
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (21 bp):
TTTAATAAATTGATTATAAAA
Found at i:1921042 original size:33 final size:32
Alignment explanation
Indices: 1920988--1921050 Score: 74
Period size: 33 Copynumber: 1.9 Consensus size: 32
1920978 TAATATCAAT
1920988 TTAAAAATATAAAGATAATTTTATCAAAAAAAA
1 TTAAAAATATAAAGATAATTTT-TCAAAAAAAA
* * *
1921021 TTAAAGATAATAAA-ATTATTTTTCTAAAAA
1 TTAAAAAT-ATAAAGATAATTTTTCAAAAAA
1921051 TTAACATCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
32 7 0.27
33 14 0.54
34 5 0.19
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (32 bp):
TTAAAAATATAAAGATAATTTTTCAAAAAAAA
Found at i:1923371 original size:2 final size:2
Alignment explanation
Indices: 1923364--1923391 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1923354 TGTGTTTTCT
1923364 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1923392 ATGAACATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1925270 original size:21 final size:22
Alignment explanation
Indices: 1925227--1925273 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
1925217 TATTTTAATT
*
1925227 ATTT-TTTCATATTATATCTTA
1 ATTTATTTCATATTATATCATA
1925248 ATTTATTTCATATTATA-CATA
1 ATTTATTTCATATTATATCATA
1925269 ATTTA
1 ATTTA
1925274 CCATTGATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTATTTCATATTATATCATA
Found at i:1925622 original size:20 final size:20
Alignment explanation
Indices: 1925572--1925651 Score: 65
Period size: 22 Copynumber: 4.0 Consensus size: 20
1925562 AAAAATATAT
* * *
1925572 TATTAAAAATAA-AATAAAA
1 TATTAAAATTAATATTAATA
*
1925591 TA-TAAAAATAATATTAATA
1 TATTAAAATTAATATTAATA
*
1925610 TTTTAAAATTAATAATATAATA
1 TATTAAAATTAAT-AT-TAATA
* *
1925632 TATTAAAATTTATATAAATA
1 TATTAAAATTAATATTAATA
1925652 AAAATATTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
18 9 0.18
19 8 0.16
20 13 0.26
21 4 0.08
22 16 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TATTAAAATTAATATTAATA
Found at i:1925630 original size:22 final size:23
Alignment explanation
Indices: 1925597--1925641 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
1925587 AAAATATAAA
*
1925597 AATAATATTAATATTTTAAAATT
1 AATAATATTAATATATTAAAATT
1925620 AATAATA-TAATATATTAAAATT
1 AATAATATTAATATATTAAAATT
1925642 TATATAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
AATAATATTAATATATTAAAATT
Found at i:1927662 original size:2 final size:2
Alignment explanation
Indices: 1927655--1927685 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1927645 AGTGGACGAT
1927655 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1927686 TAATTATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1938199 original size:234 final size:234
Alignment explanation
Indices: 1937790--1938256 Score: 934
Period size: 234 Copynumber: 2.0 Consensus size: 234
1937780 AGCTTATACA
1937790 GATCAGCACACTATGAACCCCTCCCAAGGTTCAAAATTTGGAAGGAAACTAATCAAAACAGTTAC
1 GATCAGCACACTATGAACCCCTCCCAAGGTTCAAAATTTGGAAGGAAACTAATCAAAACAGTTAC
1937855 ATACAGGGTTAAGGCCATTCCTTCATCTACTAAAAGTTCAACTGAAATATCCAGAAATGGAGGTG
66 ATACAGGGTTAAGGCCATTCCTTCATCTACTAAAAGTTCAACTGAAATATCCAGAAATGGAGGTG
1937920 AAGTGTTTAATTCTTCAGGGGGAGCTGCTTCCACCGTTGCACCAAATGATCTCCATCCAACAAAA
131 AAGTGTTTAATTCTTCAGGGGGAGCTGCTTCCACCGTTGCACCAAATGATCTCCATCCAACAAAA
1937985 ATTTCTATAGTCAGTCTAGGGAAGTCTCCTTCTTACAAT
196 ATTTCTATAGTCAGTCTAGGGAAGTCTCCTTCTTACAAT
1938024 GATCAGCACACTATGAACCCCTCCCAAGGTTCAAAATTTGGAAGGAAACTAATCAAAACAGTTAC
1 GATCAGCACACTATGAACCCCTCCCAAGGTTCAAAATTTGGAAGGAAACTAATCAAAACAGTTAC
1938089 ATACAGGGTTAAGGCCATTCCTTCATCTACTAAAAGTTCAACTGAAATATCCAGAAATGGAGGTG
66 ATACAGGGTTAAGGCCATTCCTTCATCTACTAAAAGTTCAACTGAAATATCCAGAAATGGAGGTG
1938154 AAGTGTTTAATTCTTCAGGGGGAGCTGCTTCCACCGTTGCACCAAATGATCTCCATCCAACAAAA
131 AAGTGTTTAATTCTTCAGGGGGAGCTGCTTCCACCGTTGCACCAAATGATCTCCATCCAACAAAA
1938219 ATTTCTATAGTCAGTCTAGGGAAGTCTCCTTCTTACAA
196 ATTTCTATAGTCAGTCTAGGGAAGTCTCCTTCTTACAA
1938257 GGAAGTGGCT
Statistics
Matches: 233, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
234 233 1.00
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (234 bp):
GATCAGCACACTATGAACCCCTCCCAAGGTTCAAAATTTGGAAGGAAACTAATCAAAACAGTTAC
ATACAGGGTTAAGGCCATTCCTTCATCTACTAAAAGTTCAACTGAAATATCCAGAAATGGAGGTG
AAGTGTTTAATTCTTCAGGGGGAGCTGCTTCCACCGTTGCACCAAATGATCTCCATCCAACAAAA
ATTTCTATAGTCAGTCTAGGGAAGTCTCCTTCTTACAAT
Found at i:1938922 original size:240 final size:240
Alignment explanation
Indices: 1938499--1938970 Score: 908
Period size: 240 Copynumber: 2.0 Consensus size: 240
1938489 CAAGAAACTA
1938499 GGTCAACTGCTGTGATGGAAGATAACTCTTCTTTGGCAGCATCTGAGAGGGTGGAAGGACAAGAA
1 GGTCAACTGCTGTGATGGAAGATAACTCTTCTTTGGCAGCATCTGAGAGGGTGGAAGGACAAGAA
1938564 CTTGGAGCTGGTGTTCATGAAGGTGTGCAGGATGGCATATTAAAAAATGACATGCCAAGTTCATT
66 CTTGGAGCTGGTGTTCATGAAGGTGTGCAGGATGGCATATTAAAAAATGACATGCCAAGTTCATT
1938629 TGATTCTCCTAAGAAGGAACTCTGTGAGAAGGATTTGTCTAGAGGTTTTGAACCCCACAGTATTT
131 TGATTCTCCTAAGAAGGAACTCTGTGAGAAGGATTTGTCTAGAGGTTTTGAACCCCACAGTATTT
*
1938694 CAAGCTCCACATTACAAAGGGTAGAAGAATTGAAGGATTTTTCTT
196 CAAACTCCACATTACAAAGGGTAGAAGAATTGAAGGATTTTTCTT
*
1938739 GGTCAACTGCTGTGATGGAAGATAACTCTTCTTTGGCAGTATCTGAGAGGGTGGAAGGACAAGAA
1 GGTCAACTGCTGTGATGGAAGATAACTCTTCTTTGGCAGCATCTGAGAGGGTGGAAGGACAAGAA
**
1938804 CTTGGAGCTGGTGTTCATGAATTTGTGCAGGATGGCATATTAAAAAATGACATGCCAAGTTCATT
66 CTTGGAGCTGGTGTTCATGAAGGTGTGCAGGATGGCATATTAAAAAATGACATGCCAAGTTCATT
1938869 TGATTCTCCTAAGAAGGAACTCTGTGAGAAGGATTTGTCTAGAGGTTTTGAACCCCACAGTATTT
131 TGATTCTCCTAAGAAGGAACTCTGTGAGAAGGATTTGTCTAGAGGTTTTGAACCCCACAGTATTT
1938934 CAAACTCCACATTACAAAGGGTAGAAGAATTGAAGGA
196 CAAACTCCACATTACAAAGGGTAGAAGAATTGAAGGA
1938971 CAAGCCCTTT
Statistics
Matches: 228, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
240 228 1.00
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (240 bp):
GGTCAACTGCTGTGATGGAAGATAACTCTTCTTTGGCAGCATCTGAGAGGGTGGAAGGACAAGAA
CTTGGAGCTGGTGTTCATGAAGGTGTGCAGGATGGCATATTAAAAAATGACATGCCAAGTTCATT
TGATTCTCCTAAGAAGGAACTCTGTGAGAAGGATTTGTCTAGAGGTTTTGAACCCCACAGTATTT
CAAACTCCACATTACAAAGGGTAGAAGAATTGAAGGATTTTTCTT
Found at i:1940972 original size:32 final size:32
Alignment explanation
Indices: 1940936--1941002 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
1940926 TATAATTGGA
1940936 TTTCATTCAACTGTATGACTTCAATTTTCACC
1 TTTCATTCAACTGTATGACTTCAATTTTCACC
* *
1940968 TTTCATTCAATTGTATGACTTCAATTTTCTCC
1 TTTCATTCAACTGTATGACTTCAATTTTCACC
1941000 TTT
1 TTT
1941003 TATGTTTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.49
Consensus pattern (32 bp):
TTTCATTCAACTGTATGACTTCAATTTTCACC
Found at i:1961134 original size:16 final size:15
Alignment explanation
Indices: 1961115--1961180 Score: 64
Period size: 16 Copynumber: 4.3 Consensus size: 15
1961105 GTGATGATTC
*
1961115 AAATTGAGATAATTT
1 AAATTGAAATAATTT
1961130 GAAATTGAAATAATTT
1 -AAATTGAAATAATTT
*
1961146 AAATTTAAAT--TTT
1 AAATTGAAATAATTT
*
1961159 AAATTAAAAAATAATTT
1 AAATT--GAAATAATTT
1961176 AAATT
1 AAATT
1961181 TAAAACGATT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
13 8 0.19
15 13 0.30
16 14 0.33
17 8 0.19
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (15 bp):
AAATTGAAATAATTT
Found at i:1967601 original size:2 final size:2
Alignment explanation
Indices: 1967596--1967624 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1967586 ATATATATAT
1967596 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1967625 CCAAATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1974445 original size:30 final size:28
Alignment explanation
Indices: 1974409--1974481 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 28
1974399 ATATTTATAT
*
1974409 TTTTATATGTTATAATTATATTTTAAAATA
1 TTTTATAT-TTATAA-TAAATTTTAAAATA
* *
1974439 TTTTATA-TAATATATAAATTTTAATATA
1 TTTTATATTTATA-ATAAATTTTAAAATA
1974467 TTTATATATTTATAA
1 TTT-TATATTTATAA
1974482 AGTATTTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
28 19 0.53
29 6 0.17
30 11 0.31
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (28 bp):
TTTTATATTTATAATAAATTTTAAAATA
Found at i:1974459 original size:28 final size:26
Alignment explanation
Indices: 1974428--1974501 Score: 76
Period size: 28 Copynumber: 2.7 Consensus size: 26
1974418 TTATAATTAT
1974428 ATTTTAAAATATTTTATATAATATATAA
1 ATTTTAAAATA-TTTATAT-ATATATAA
* *
1974456 ATTTTAATATATTTATATATTTATAA
1 ATTTTAAAATATTTATATATATATAA
* *
1974482 AGTATTTATATTATTTATAT
1 A-T-TTTAAAATATTTATAT
1974502 TTTTTTTTTC
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
26 8 0.21
27 8 0.21
28 23 0.59
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (26 bp):
ATTTTAAAATATTTATATATATATAA
Found at i:1976354 original size:6 final size:6
Alignment explanation
Indices: 1976339--1976374 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
1976329 TAATTATGGA
*
1976339 TTTTCC TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
1976375 GAATCCTTGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTCT
Found at i:1980840 original size:23 final size:23
Alignment explanation
Indices: 1980808--1980858 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 23
1980798 CCACTTGCAG
1980808 AAGTATAAAAACCATTTAATCAAGA
1 AAGTA-AAAAA-CATTTAATCAAGA
1980833 AAGTAAAAAACATTTAATCAAGA
1 AAGTAAAAAACATTTAATCAAGA
1980856 AAG
1 AAG
1980859 CTGAAACGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 16 0.62
24 5 0.19
25 5 0.19
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.22
Consensus pattern (23 bp):
AAGTAAAAAACATTTAATCAAGA
Found at i:1984238 original size:27 final size:26
Alignment explanation
Indices: 1984184--1984247 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 26
1984174 TAATTTTTTT
*
1984184 TATTAAATTAATATAAAAATAATTAA
1 TATTAATTTAATATAAAAATAATTAA
*
1984210 TATTAATTTAAT-TACATAAATTATTAA
1 TATTAATTTAATATA-A-AAATAATTAA
1984237 TA-TATATTTAA
1 TATTA-ATTTAA
1984248 AATATTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
25 2 0.06
26 14 0.42
27 17 0.52
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (26 bp):
TATTAATTTAATATAAAAATAATTAA
Found at i:1984269 original size:13 final size:13
Alignment explanation
Indices: 1984235--1984271 Score: 67
Period size: 12 Copynumber: 2.9 Consensus size: 13
1984225 ATAAATTATT
1984235 AATATATATTTAA
1 AATATATATTTAA
1984248 AATAT-TATTTAA
1 AATATATATTTAA
1984260 AATATATATTTA
1 AATATATATTTA
1984272 TATATAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
AATATATATTTAA
Found at i:1985707 original size:17 final size:17
Alignment explanation
Indices: 1985661--1985720 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 17
1985651 TTTTATATAA
* *
1985661 AAATATTATAA-TTTAA
1 AAATATTAAAATTTTAT
*
1985677 AAATA-AAAATATTTTAT
1 AAATATTAAA-ATTTTAT
*
1985694 AAATATTAAAATTTCAT
1 AAATATTAAAATTTTAT
*
1985711 AAATAATAAA
1 AAATATTAAA
1985721 CCTTGATAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
15 2 0.06
16 6 0.17
17 24 0.69
18 3 0.09
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATATTAAAATTTTAT
Found at i:1986867 original size:15 final size:15
Alignment explanation
Indices: 1986845--1986882 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
1986835 ATATCATATT
1986845 TAAA-AATATTTTTA
1 TAAATAATATTTTTA
1986859 TAAATAATATTTTTA
1 TAAATAATATTTTTA
*
1986874 TAATTAATA
1 TAAATAATA
1986883 ATATATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAAATAATATTTTTA
Found at i:1986884 original size:18 final size:17
Alignment explanation
Indices: 1986844--1986886 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
1986834 TATATCATAT
*
1986844 TTAAAAATATTTTTATA
1 TTAATAATATTTTTATA
1986861 --AATAATATTTTTATAA
1 TTAATAATATTTTTAT-A
1986877 TTAATAATAT
1 TTAATAATAT
1986887 ATTAAAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
15 13 0.59
16 1 0.05
18 8 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTAATAATATTTTTATA
Found at i:1987351 original size:2 final size:2
Alignment explanation
Indices: 1987346--1987377 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1987336 AGAGTTATTA
*
1987346 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1987378 TGCCGTCACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1988086 original size:18 final size:18
Alignment explanation
Indices: 1988063--1988108 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
1988053 GCCTTGTTCT
1988063 TATATATATATATGTATA
1 TATATATATATATGTATA
1988081 TATATATATATATGTATA
1 TATATATATATATGTATA
1988099 TATATATATA
1 TATATATATA
1988109 GTACAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (18 bp):
TATATATATATATGTATA
Found at i:1988127 original size:2 final size:2
Alignment explanation
Indices: 1988063--1988108 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
1988053 GCCTTGTTCT
* *
1988063 TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1988105 TA TA
1 TA TA
1988109 GTACAAATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1988727 original size:27 final size:28
Alignment explanation
Indices: 1988697--1988761 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 28
1988687 TTATAATTTT
*
1988697 ATTTAAAATATTTTAT-ATTTATATAAA
1 ATTTAAAATATTTAATAATTTATATAAA
* * *
1988724 ATTTAATATA-TTAATAATTTATATTAT
1 ATTTAAAATATTTAATAATTTATATAAA
*
1988751 ATTTTAAATAT
1 ATTTAAAATAT
1988762 ATATATATAT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
26 4 0.13
27 26 0.87
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
ATTTAAAATATTTAATAATTTATATAAA
Found at i:1988751 original size:18 final size:18
Alignment explanation
Indices: 1988703--1988753 Score: 56
Period size: 16 Copynumber: 3.0 Consensus size: 18
1988693 TTTTATTTAA
*
1988703 AATATTTTATATT-TATAT
1 AATAATTTATATTATAT-T
1988721 AA-AATTTA-A-TATATT
1 AATAATTTATATTATATT
1988736 AATAATTTATATTATATT
1 AATAATTTATATTATATT
1988754 TTAAATATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
15 4 0.14
16 10 0.36
17 6 0.21
18 8 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
AATAATTTATATTATATT
Found at i:1989353 original size:9 final size:9
Alignment explanation
Indices: 1989339--1989374 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
1989329 AATTAAGAAA
1989339 TAATTATTT
1 TAATTATTT
1989348 TAATTATTT
1 TAATTATTT
1989357 TATATTA-TT
1 TA-ATTATTT
1989366 TAATTATTT
1 TAATTATTT
1989375 ATTAACTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 4 0.16
9 17 0.68
10 4 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TAATTATTT
Found at i:1996983 original size:2 final size:2
Alignment explanation
Indices: 1996976--1997016 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1996966 GCTTTAGCAT
1996976 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1997017 GAATGTGCTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1997073 original size:15 final size:15
Alignment explanation
Indices: 1997053--1997086 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1997043 TTAAAGATTA
1997053 ATATATTTAT-TTTAG
1 ATATATTTATATTT-G
1997068 ATATATTTATATTTG
1 ATATATTTATATTTG
1997083 ATAT
1 ATAT
1997087 TTATTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 15 0.83
16 3 0.17
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (15 bp):
ATATATTTATATTTG
Found at i:1998321 original size:22 final size:21
Alignment explanation
Indices: 1998290--1998333 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
1998280 TAATTGTTTA
*
1998290 TTTAGTATTCATGAATATATT
1 TTTAGTATTCATAAATATATT
1998311 TTTAGATATTCATAAATATATT
1 TTTAG-TATTCATAAATATATT
1998333 T
1 T
1998334 GATTTATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (21 bp):
TTTAGTATTCATAAATATATT
Found at i:1998345 original size:25 final size:23
Alignment explanation
Indices: 1998286--1998388 Score: 93
Period size: 23 Copynumber: 4.4 Consensus size: 23
1998276 ACTTTAATTG
* *
1998286 TTTATTTAGTATTCATGAATATA
1 TTTATTTAATATTCATAAATATA
1998309 -TT-TTTAGATATTCATAAATATA
1 TTTATTTA-ATATTCATAAATATA
*
1998331 TTTGATTTATATATTCATAAATATG
1 TTT-ATTTA-ATATTCATAAATATA
* ** *
1998356 TTTATATAATATTCACGAATAAA
1 TTTATTTAATATTCATAAATATA
*
1998379 TTCATTTAAT
1 TTTATTTAAT
1998389 TTTAATGAAT
Statistics
Matches: 65, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
21 4 0.06
22 15 0.23
23 21 0.32
24 4 0.06
25 21 0.32
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (23 bp):
TTTATTTAATATTCATAAATATA
Found at i:2000602 original size:15 final size:17
Alignment explanation
Indices: 2000577--2000612 Score: 58
Period size: 15 Copynumber: 2.2 Consensus size: 17
2000567 AACCTGTTGC
2000577 ATTTCAATTGTTCCCA-
1 ATTTCAATTGTTCCCAG
2000593 ATTT-AATTGTTCCCAG
1 ATTTCAATTGTTCCCAG
2000609 ATTT
1 ATTT
2000613 GGTTAGGTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.25, C:0.19, G:0.08, T:0.47
Consensus pattern (17 bp):
ATTTCAATTGTTCCCAG
Found at i:2004089 original size:3 final size:3
Alignment explanation
Indices: 2004081--2004106 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2004071 TTTTAATAAG
2004081 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
2004107 GGTTGTAAAT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2004965 original size:6 final size:5
Alignment explanation
Indices: 2004933--2004985 Score: 54
Period size: 5 Copynumber: 10.6 Consensus size: 5
2004923 TCTCTCATTA
* * * *
2004933 TTTCT TTCCT TCTT-T TTTCT TTTCT TTTCC TTTGT TTTCT TTTCT TTTAT
1 TTTCT TTTCT T-TTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT
2004983 TTT
1 TTT
2004986 GTATATGTAC
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
4 2 0.05
5 36 0.92
6 1 0.03
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (5 bp):
TTTCT
Found at i:2004980 original size:20 final size:21
Alignment explanation
Indices: 2004933--2004980 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
2004923 TCTCTCATTA
*
2004933 TTTC-TTTCCTTCTTTTTTCT
1 TTTCTTTTCCTTCTGTTTTCT
2004953 TTTCTTTTCCTT-TGTTTTCT
1 TTTCTTTTCCTTCTGTTTTCT
2004973 TTTCTTTT
1 TTTCTTTT
2004981 ATTTTGTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (21 bp):
TTTCTTTTCCTTCTGTTTTCT
Found at i:2004986 original size:20 final size:20
Alignment explanation
Indices: 2004947--2004987 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2004937 TTTCCTTCTT
*
2004947 TTTTCTTTTCTTTTCCTTTG
1 TTTTCTTTTCTTTTACTTTG
*
2004967 TTTTCTTTTCTTTTATTTTG
1 TTTTCTTTTCTTTTACTTTG
2004987 T
1 T
2004988 ATATGTACAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.02, C:0.15, G:0.05, T:0.78
Consensus pattern (20 bp):
TTTTCTTTTCTTTTACTTTG
Found at i:2005659 original size:3 final size:3
Alignment explanation
Indices: 2005651--2005676 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2005641 ATTTTATACC
2005651 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
2005677 CAATCATTAA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2007467 original size:6 final size:6
Alignment explanation
Indices: 2007456--2007490 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
2007446 TCTTATACTC
2007456 TATACA TATACA TATACA TATACA TATACA TATAC
1 TATACA TATACA TATACA TATACA TATACA TATAC
2007491 TTTTATACTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (6 bp):
TATACA
Done.