Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008105.1 Hibiscus syriacus cultivar Beakdansim tig00110637_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: 5962497
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 30
Found at i:1863731 original size:12 final size:12
Alignment explanation
Indices: 1863716--1863746 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1863706 TATATTATAA
*
1863716 AATTAAATAATG
1 AATTAAATAACG
1863728 AATTAAATAACG
1 AATTAAATAACG
1863740 AATTAAA
1 AATTAAA
1863747 GATATTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.29
Consensus pattern (12 bp):
AATTAAATAACG
Found at i:1865451 original size:16 final size:16
Alignment explanation
Indices: 1865432--1865484 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
1865422 CCATAACCCC
1865432 TATCACACATATATCA
1 TATCACACATATATCA
** * *
1865448 TATCATGCACACATCA
1 TATCACACATATATCA
1865464 TATCACACATCATATACA
1 TATCACACAT-ATAT-CA
1865482 TAT
1 TAT
1865485 ATCACATACA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
16 19 0.70
17 3 0.11
18 5 0.19
ACGTcount: A:0.42, C:0.26, G:0.02, T:0.30
Consensus pattern (16 bp):
TATCACACATATATCA
Found at i:1865683 original size:23 final size:23
Alignment explanation
Indices: 1865657--1865725 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
1865647 CACCACAACT
*
1865657 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
1865680 CGTAGAATTGCACC-AGAGTGCCG
1 CGTAGAATTGCACCGA-AGTGCCA
*
1865703 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
1865726 TATAATAATG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
22 1 0.03
23 39 0.98
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:1865912 original size:103 final size:103
Alignment explanation
Indices: 1865741--1865953 Score: 372
Period size: 103 Copynumber: 2.1 Consensus size: 103
1865731 TAATGTCCAT
* **
1865741 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAAGATCAAGTATGTGTCTCACCA
1865806 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
1865844 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGTCTCACTA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAAGATCAAGTATGTGTCTCACCA
*
1865909 GACTTCACACATGTTCCAAAGAATACATATATGTTCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1865947 AAGGACC
1 AAGGACC
1865954 GTATAGACCC
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAAGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1870903 original size:23 final size:23
Alignment explanation
Indices: 1870877--1870940 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
1870867 CAGCTCGTAT
1870877 AATTGCACCGAAGTGCCACATAG
1 AATTGCACCGAAGTGCCACATAG
* * *
1870900 AATTGCACCGGAGTGCCGCTTAG
1 AATTGCACCGAAGTGCCACATAG
* *
1870923 AATTGTACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
1870941 TATAATAATG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.22
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACATAG
Found at i:1871127 original size:103 final size:103
Alignment explanation
Indices: 1870956--1871168 Score: 381
Period size: 103 Copynumber: 2.1 Consensus size: 103
1870946 TAATGTCCAT
* * *
1870956 AAGGACCACATATCATTCTTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1871021 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
1871059 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATTAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1871124 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1871162 AAGGACC
1 AAGGACC
1871169 GCGTAGACCC
Statistics
Matches: 105, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1877035 original size:13 final size:13
Alignment explanation
Indices: 1877017--1877043 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1877007 TTACAGACGC
1877017 GCATATGAAGACT
1 GCATATGAAGACT
1877030 GCATATGAAGACT
1 GCATATGAAGACT
1877043 G
1 G
1877044 TTAATCTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:1883577 original size:45 final size:46
Alignment explanation
Indices: 1883496--1883582 Score: 140
Period size: 45 Copynumber: 1.9 Consensus size: 46
1883486 GGTAGAACGT
**
1883496 TACCTAAAATGTTATTTTTTCTATTGGAAATATTAATATTGGGCGC
1 TACCTAAAATGTTATTTTTTCTACCGGAAATATTAATATTGGGCGC
*
1883542 TACCTAAAATGTTA-TTTTTCTACCGGAAATGTTAATATTGG
1 TACCTAAAATGTTATTTTTTCTACCGGAAATATTAATATTGG
1883583 AAATATTCAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
45 24 0.63
46 14 0.37
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.43
Consensus pattern (46 bp):
TACCTAAAATGTTATTTTTTCTACCGGAAATATTAATATTGGGCGC
Found at i:1883615 original size:21 final size:21
Alignment explanation
Indices: 1883591--1883642 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
1883581 GGAAATATTC
*
1883591 ATTTTAGGTAGCAAAATTAAT
1 ATTTTAGGTAGCAAAAATAAT
*
1883612 ATTTTCGGTA--AAAAATAAT
1 ATTTTAGGTAGCAAAAATAAT
1883631 ATTTTAGGTAGC
1 ATTTTAGGTAGC
1883643 GTTCTATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 17 0.65
21 9 0.35
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.38
Consensus pattern (21 bp):
ATTTTAGGTAGCAAAAATAAT
Found at i:1884446 original size:15 final size:14
Alignment explanation
Indices: 1884419--1884459 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1884409 ACATGGCCAA
1884419 CTGAGTCAACTCGCG
1 CTGAGTCAACTCG-G
* *
1884434 CTTAGTTAACTCGG
1 CTGAGTCAACTCGG
1884448 CTGAGTCAACTC
1 CTGAGTCAACTC
1884460 ACTGGGTCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (14 bp):
CTGAGTCAACTCGG
Found at i:1886813 original size:24 final size:24
Alignment explanation
Indices: 1886786--1886868 Score: 89
Period size: 24 Copynumber: 3.5 Consensus size: 24
1886776 ATTTTCAATT
*
1886786 TGAATTCTGTTATGATATCTGATC
1 TGAATTCTGTTCTGATATCTGATC
* *
1886810 TGAAATGTGTTCTGAT-TCTTGA-C
1 TGAATTCTGTTCTGATATC-TGATC
*
1886833 ATGGATTCTGTTCTGATATCTGATC
1 -TGAATTCTGTTCTGATATCTGATC
*
1886858 TGAATTATGTT
1 TGAATTCTGTT
1886869 TTGTTTTCTG
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
23 3 0.06
24 41 0.87
25 3 0.06
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTGATC
Found at i:1888973 original size:13 final size:13
Alignment explanation
Indices: 1888947--1888989 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
1888937 GGTCAACCCG
*
1888947 TTGATCGTTGACT
1 TTGATAGTTGACT
* *
1888960 TTGATTGTTTACT
1 TTGATAGTTGACT
1888973 TTGATAGTTGACT
1 TTGATAGTTGACT
1888986 TTGA
1 TTGA
1888990 CCAAAAAGTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.19, C:0.09, G:0.21, T:0.51
Consensus pattern (13 bp):
TTGATAGTTGACT
Found at i:1889532 original size:13 final size:13
Alignment explanation
Indices: 1889514--1889539 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1889504 TACTTCGATT
1889514 AGGTAAATTACGA
1 AGGTAAATTACGA
1889527 AGGTAAATTACGA
1 AGGTAAATTACGA
1889540 GAATACTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.23, T:0.23
Consensus pattern (13 bp):
AGGTAAATTACGA
Found at i:1892704 original size:2 final size:2
Alignment explanation
Indices: 1892697--1892728 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1892687 TCTATTTGTA
1892697 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1892729 AGCTGCAAAG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1898313 original size:36 final size:35
Alignment explanation
Indices: 1898250--1898349 Score: 94
Period size: 36 Copynumber: 2.8 Consensus size: 35
1898240 CACTCAATCA
* * * *
1898250 TTAATTA-TATCATGTGGTCAGAGCTACTAGATGGG
1 TTAATTACTAACACGTGGTCATATCTACTA-ATGGG
* * * * *
1898285 TTGATTACTATCACGTGTTCATATCTACTTAATTGT
1 TTAATTACTAACACGTGGTCATATCTAC-TAATGGG
1898321 TTAATTACTAACACGTGGTCATATCTACT
1 TTAATTACTAACACGTGGTCATATCTACT
1898350 TAATCCGTCA
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
35 7 0.13
36 44 0.83
37 2 0.04
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (35 bp):
TTAATTACTAACACGTGGTCATATCTACTAATGGG
Found at i:1898367 original size:36 final size:36
Alignment explanation
Indices: 1898291--1898369 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 36
1898281 TGGGTTGATT
* * * * *
1898291 ACTATCACGTGTTCATATCTACTTAATTGTTTAATT
1 ACTAACACGTGGTCATATCTACTTAATCGTTCAATA
1898327 ACTAACACGTGGTCATATCTACTTAATCCG-TCAATA
1 ACTAACACGTGGTCATATCTACTTAAT-CGTTCAATA
1898363 ACTAACA
1 ACTAACA
1898370 AATCTCGTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 36 0.97
37 1 0.03
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.37
Consensus pattern (36 bp):
ACTAACACGTGGTCATATCTACTTAATCGTTCAATA
Found at i:1900611 original size:7 final size:7
Alignment explanation
Indices: 1900599--1900626 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
1900589 TTTTATGCTG
1900599 AGGAAGA
1 AGGAAGA
1900606 AGGAAGA
1 AGGAAGA
1900613 AGGAAGA
1 AGGAAGA
1900620 AGGAAGA
1 AGGAAGA
1900627 GCAGTTATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (7 bp):
AGGAAGA
Found at i:1901208 original size:22 final size:22
Alignment explanation
Indices: 1901180--1901221 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1901170 GGAAGATATG
*
1901180 ATCATATCTCGAGATATTTTTT
1 ATCATATCTCGAGACATTTTTT
1901202 ATCATATCTCGAGACATTTT
1 ATCATATCTCGAGACATTTT
1901222 GCCTATACGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.45
Consensus pattern (22 bp):
ATCATATCTCGAGACATTTTTT
Found at i:1907828 original size:16 final size:15
Alignment explanation
Indices: 1907807--1907855 Score: 62
Period size: 17 Copynumber: 3.1 Consensus size: 15
1907797 TATTTTAAAT
1907807 TTTAAATATAAAATAA
1 TTTAAATATAAAA-AA
1907823 TTTAAATATTCAAAAAA
1 TTTAAATA-T-AAAAAA
*
1907840 ATTAAATATAAAAAA
1 TTTAAATATAAAAAA
1907855 T
1 T
1907856 AAAAATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 6 0.21
16 9 0.31
17 10 0.34
18 4 0.14
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (15 bp):
TTTAAATATAAAAAA
Found at i:1907861 original size:20 final size:20
Alignment explanation
Indices: 1907836--1907906 Score: 72
Period size: 20 Copynumber: 3.4 Consensus size: 20
1907826 AAATATTCAA
1907836 AAAAATTAAATATAAAAAAT
1 AAAAATTAAATATAAAAAAT
1907856 AAAAATTAAATTATTAAAAAATT
1 AAAAATTAAA-TA-TAAAAAA-T
* * *
1907879 AAATATT-CATATTAAAAAT
1 AAAAATTAAATATAAAAAAT
1907898 ACAAAATTA
1 A-AAAATTA
1907907 CCATAATTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
19 2 0.05
20 21 0.50
21 4 0.10
22 8 0.19
23 7 0.17
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAAATTAAATATAAAAAAT
Found at i:1910597 original size:17 final size:17
Alignment explanation
Indices: 1910556--1910599 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
1910546 TAAATACATG
*
1910556 TATCCCAAAAACCGGTA
1 TATCCCAAAAACCGATA
* * *
1910573 GATGCCAAAAACTGATA
1 TATCCCAAAAACCGATA
1910590 TATCCCAAAA
1 TATCCCAAAA
1910600 CACTCTTCCA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.45, C:0.25, G:0.11, T:0.18
Consensus pattern (17 bp):
TATCCCAAAAACCGATA
Found at i:1913631 original size:21 final size:22
Alignment explanation
Indices: 1913591--1913635 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1913581 ACATTGTAGA
1913591 TAGACTAAATTGATTTTTTTGT
1 TAGACTAAATTGATTTTTTTGT
1913613 TAGACTAAATTGATTTTTTTGT
1 TAGACTAAATTGATTTTTTTGT
1913635 T
1 T
1913636 CGAAGGTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.04, G:0.13, T:0.56
Consensus pattern (22 bp):
TAGACTAAATTGATTTTTTTGT
Found at i:1913647 original size:25 final size:24
Alignment explanation
Indices: 1913595--1913666 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 24
1913585 TGTAGATAGA
*
1913595 CTAAATTGATTTTTTTGTTAG-A-
1 CTAAATTGATTTTTTTGTTCGAAG
1913617 CTAAATTGATTTTTTTGTTCGAAG
1 CTAAATTGATTTTTTTGTTCGAAG
* *
1913641 GTCAAATT-AGTTTTTTTAATTCGAAG
1 CT-AAATTGA-TTTTTTT-GTTCGAAG
1913667 TCTTATTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
22 20 0.48
23 1 0.02
24 2 0.05
25 12 0.29
26 7 0.17
ACGTcount: A:0.28, C:0.07, G:0.15, T:0.50
Consensus pattern (24 bp):
CTAAATTGATTTTTTTGTTCGAAG
Found at i:1913766 original size:28 final size:28
Alignment explanation
Indices: 1913701--1913766 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 28
1913691 TAAAGTTATT
* *
1913701 TTAAATATAAAATTATTCAAATATTCAAAA
1 TTAAATATAAAATAATACAAATA-T-AAAA
1913731 TTAAATATAAAAATAATACAAATA-AAAA
1 TTAAATAT-AAAATAATACAAATATAAAA
1913759 TTAAATAT
1 TTAAATAT
1913767 TTATATTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 12 0.36
30 8 0.24
31 13 0.39
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (28 bp):
TTAAATATAAAATAATACAAATATAAAA
Found at i:1913999 original size:25 final size:25
Alignment explanation
Indices: 1913943--1914002 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
1913933 GGTTTTTTAC
*
1913943 TGGATTAATCGAGACATACAAAATT
1 TGGATTAGTCGAGACATACAAAATT
** * * *
1913968 TAAATTAGTCGAGTCTTACAAATTT
1 TGGATTAGTCGAGACATACAAAATT
1913993 TGGATTAGTC
1 TGGATTAGTC
1914003 AAAATTTATT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.35
Consensus pattern (25 bp):
TGGATTAGTCGAGACATACAAAATT
Found at i:1914353 original size:15 final size:16
Alignment explanation
Indices: 1914335--1914367 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1914325 AGTTGTTTTA
1914335 TTTTA-TTTTTAATAT
1 TTTTATTTTTTAATAT
1914350 TTTTATTTTTTAATAT
1 TTTTATTTTTTAATAT
1914366 TT
1 TT
1914368 GGATAGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTATTTTTTAATAT
Found at i:1914540 original size:21 final size:22
Alignment explanation
Indices: 1914497--1914544 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
1914487 TATACCACGT
* *
1914497 CATCAACTATAGTAGACTGCCA
1 CATCAACTATAGTAGAATACCA
*
1914519 CATCAAC-ATCGTAGAATACCA
1 CATCAACTATAGTAGAATACCA
1914540 CATCA
1 CATCA
1914545 CCACCGTAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.40, C:0.29, G:0.10, T:0.21
Consensus pattern (22 bp):
CATCAACTATAGTAGAATACCA
Found at i:1914712 original size:20 final size:20
Alignment explanation
Indices: 1914689--1914740 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1914679 AACGCGATCC
1914689 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
1914709 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
1914729 CCAAAATCGCAA
1 CCAGAATCGCAA
1914741 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:1914757 original size:21 final size:20
Alignment explanation
Indices: 1914730--1914828 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
1914720 AATCAGTTTC
1914730 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
1914751 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1914772 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1914792 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1914813 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1914829 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1914857 original size:20 final size:20
Alignment explanation
Indices: 1914795--1914988 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
1914785 CGATTTTCCA
* ** *
1914795 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1914815 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1914835 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1914855 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
1914875 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
1914895 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1914915 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
1914935 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
1914955 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
1914976 AAATCGCAACGCG
1 AAATCGCAACGCG
1914989 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1914879 original size:60 final size:60
Alignment explanation
Indices: 1914795--1914988 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
1914785 CGATTTTCCA
* ** * *
1914795 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
1914855 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
1914915 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
1914976 AAATCGCAACGCG
1 AAATCGCAACGCG
1914989 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:1915408 original size:33 final size:33
Alignment explanation
Indices: 1915369--1915476 Score: 171
Period size: 33 Copynumber: 3.3 Consensus size: 33
1915359 TTCACTTAGA
* *
1915369 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTGCGATTCTCTCGTTGCGAT
*
1915402 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTGCGATTCTCTCGTTGCGAT
* *
1915435 TGTCATCTCGCGTTGCGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTGCGATTCTCTCGTTGCGAT
1915468 TTTCATTTC
1 TTTCATTTC
1915477 AACCAAAAGA
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 67 1.00
ACGTcount: A:0.10, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
TTTCATTTCGCGTTGCGATTCTCTCGTTGCGAT
Found at i:1915417 original size:19 final size:18
Alignment explanation
Indices: 1915393--1915474 Score: 54
Period size: 14 Copynumber: 4.9 Consensus size: 18
1915383 ACGATTCTGT
1915393 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCA-TTCG
* *
1915412 CGTTGC--TATTC--TCT
1 CGTTGCGATTTTCATTCG
*
1915426 CGTTGCGATTGTCATCTCG
1 CGTTGCGATTTTCAT-TCG
*
1915445 CGTTGCGA--TTC--TCT
1 CGTTGCGATTTTCATTCG
1915459 CGTTGCGATTTTCATT
1 CGTTGCGATTTTCATT
1915475 TCAACCAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 19
0.64 0.10 0.26
Matches are distributed among these distances:
14 18 0.38
16 6 0.13
17 6 0.13
18 1 0.02
19 16 0.34
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (18 bp):
CGTTGCGATTTTCATTCG
Found at i:1915431 original size:14 final size:14
Alignment explanation
Indices: 1915412--1915468 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1915402 TTTCATTTCG
*
1915412 CGTTGCTATTCTCT
1 CGTTGCGATTCTCT
1915426 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
1915443 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
1915459 CGTTGCGATT
1 CGTTGCGATT
1915469 TTCATTTCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 17 0.46
15 1 0.03
16 5 0.14
17 5 0.14
18 1 0.03
19 8 0.22
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1917402 original size:185 final size:186
Alignment explanation
Indices: 1917172--1917553 Score: 748
Period size: 185 Copynumber: 2.1 Consensus size: 186
1917162 TAGATTGCTT
1917172 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1917237 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1917302 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
1917357 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1917422 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1917487 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1917543 AGTAAATTTAT
1 AGTAAATTTAT
1917554 CCATTCAAGT
Statistics
Matches: 194, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
185 154 0.79
186 40 0.21
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1917486 original size:93 final size:93
Alignment explanation
Indices: 1917172--1917551 Score: 744
Period size: 93 Copynumber: 4.1 Consensus size: 93
1917162 TAGATTGCTT
*
1917172 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1917237 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1917265 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1917329 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1917357 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1917422 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1917450 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1917515 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1917543 AGTAAATTT
1 AGTAAATTT
1917552 ATCCATTCAA
Statistics
Matches: 285, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.32
93 193 0.68
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1917635 original size:19 final size:19
Alignment explanation
Indices: 1917595--1917723 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1917585 TAGTTTACTT
* *
1917595 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1917615 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1917634 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1917653 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
1917667 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
1917686 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1917700 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1917719 TCGCA
1 TCGCA
1917724 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1917674 original size:33 final size:32
Alignment explanation
Indices: 1917631--1917723 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
1917621 CGCGAAACCA
**
1917631 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1917663 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
1917696 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
1917724 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:1917721 original size:52 final size:52
Alignment explanation
Indices: 1917595--1917723 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
1917585 TAGTTTACTT
**
1917595 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
1917647 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
1917700 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
1917724 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:1917741 original size:19 final size:19
Alignment explanation
Indices: 1917719--1917853 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
1917709 GAAACCAAAA
*
1917719 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1917738 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
1917754 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1917771 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1917787 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1917804 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
1917823 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1917843 TCGTGTTGCGA
1 TCGCGTTGCGA
1917854 AAGTAAACTA
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1917760 original size:14 final size:14
Alignment explanation
Indices: 1917741--1917797 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1917731 TTTCATTTCG
1917741 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1917755 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
1917772 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
1917788 CGTTGCGATT
1 CGTTGCGATT
1917798 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.09, C:0.21, G:0.25, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1917766 original size:33 final size:33
Alignment explanation
Indices: 1917724--1917816 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
1917714 CAAAATCGCA
*
1917724 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1917757 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1917790 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1917817 TTGGTTTCGC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:1919713 original size:38 final size:38
Alignment explanation
Indices: 1919670--1919742 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
1919660 AATTGATTGT
*
1919670 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
1919708 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1919743 TGTAAAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.53
Consensus pattern (38 bp):
TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
Found at i:1919729 original size:19 final size:19
Alignment explanation
Indices: 1919665--1919729 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
1919655 AGTTTAATTG
*
1919665 ATTGTTTTTTGATTGTTTA
1 ATTGATTTTTGATTGTTTA
* * ** *
1919684 ATTGATTTGTAAAAG-TTG
1 ATTGATTTTTGATTGTTTA
*
1919702 ATTCAATTTTTGATTGTTTA
1 ATT-GATTTTTGATTGTTTA
1919722 ATTGATTT
1 ATTGATTT
1919730 GTAAAAGATG
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
18 5 0.16
19 21 0.68
20 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (19 bp):
ATTGATTTTTGATTGTTTA
Found at i:1919743 original size:14 final size:14
Alignment explanation
Indices: 1919724--1919759 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1919714 ATTGTTTAAT
1919724 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1919738 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1919752 TGATTTGT
1 TGATTTGT
1919760 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1919882 original size:19 final size:19
Alignment explanation
Indices: 1919866--1919967 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
1919856 AAAAATGACT
1919866 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1919885 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1919904 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1919918 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1919937 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1919957 ATCGCAATGCG
1 ATCGCAATGCG
1919968 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1920020 original size:19 final size:19
Alignment explanation
Indices: 1919996--1920321 Score: 405
Period size: 19 Copynumber: 18.4 Consensus size: 19
1919986 GATTATCTCG
1919996 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1920015 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1920034 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
1920048 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1920067 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1920086 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
1920105 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
1920124 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1920143 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1920157 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1920176 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1920195 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1920209 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1920228 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1920247 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1920261 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1920281 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
1920295 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
1920314 TTGCGATT
1 TTGCGATT
1920322 GTATTTTCCG
Statistics
Matches: 269, Mismatches: 12, Indels: 52
0.81 0.04 0.16
Matches are distributed among these distances:
14 35 0.13
16 31 0.12
17 28 0.10
18 3 0.01
19 160 0.59
20 12 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1920036 original size:52 final size:52
Alignment explanation
Indices: 1919974--1920293 Score: 550
Period size: 52 Copynumber: 6.0 Consensus size: 52
1919964 TGCGTTTATA
*
1919974 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
1920026 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
1920078 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1920135 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1920187 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1920239 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
1920292 AT
1 AT
1920294 GTTGGGATTT
Statistics
Matches: 257, Mismatches: 5, Indels: 11
0.94 0.02 0.04
Matches are distributed among these distances:
52 182 0.71
53 17 0.07
54 7 0.03
55 8 0.03
57 43 0.17
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:1920071 original size:71 final size:72
Alignment explanation
Indices: 1919996--1920321 Score: 389
Period size: 71 Copynumber: 4.6 Consensus size: 72
1919986 GATTATCTCG
1919996 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCG-TTGCGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
1920060 TTTCGCA
66 TTTCGCA
* *
1920067 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG-ATTGCGATT
1920132 TTCATTTCGCA
62 TTCATTTCGCA
*
1920143 TTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG-ATTGCGATT
*
1920201 TTC-TCTCG--
62 TTCATTTCGCA
*
1920209 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG-TTGCGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
1920273 TTTCCGCA
66 TTT-CGCA
* *
1920281 TTGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
1920322 GTATTTTCCG
Statistics
Matches: 227, Mismatches: 11, Indels: 38
0.82 0.04 0.14
Matches are distributed among these distances:
66 12 0.05
67 25 0.11
68 14 0.06
69 13 0.06
70 3 0.01
71 109 0.48
72 12 0.05
73 6 0.03
74 8 0.04
76 25 0.11
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (72 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
TTTCGCA
Found at i:1920239 original size:161 final size:157
Alignment explanation
Indices: 1919974--1920293 Score: 552
Period size: 161 Copynumber: 2.0 Consensus size: 157
1919964 TGCGTTTATA
1919974 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
* *
1920039 ATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGT
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG-
1920104 ATTGCGATTTTAATTT-CGCATTGCGATTTTC
127 -TTGCGATTTTAATTTCCGCATTGCGATTTTC
*
1920135 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1920200 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
*
1920265 GATTTTCATTTCCGCATTGCGATTTTC
131 GATTTTAATTTCCGCATTGCGATTTTC
1920292 AT
1 AT
1920294 GTTGGGATTT
Statistics
Matches: 154, Mismatches: 4, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
156 14 0.09
157 17 0.11
158 4 0.03
159 3 0.02
161 116 0.75
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (157 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
GATTTTAATTTCCGCATTGCGATTTTC
Found at i:1920265 original size:33 final size:33
Alignment explanation
Indices: 1920015--1920321 Score: 280
Period size: 33 Copynumber: 8.8 Consensus size: 33
1920005 TCATTTCGCA
*
1920015 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1920048 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * *
1920084 CATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCG
1 --TTGCGATTTTCATTTCGCATTGCGA--TT-CTCTCG
1920122 CATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1920157 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
1920193 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
1920228 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1920261 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
* *
1920295 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
1920322 GTATTTTCCG
Statistics
Matches: 235, Mismatches: 20, Indels: 38
0.80 0.07 0.13
Matches are distributed among these distances:
31 9 0.04
32 5 0.02
33 87 0.37
34 29 0.12
35 13 0.06
36 11 0.05
37 2 0.01
38 67 0.29
39 3 0.01
40 9 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:1922645 original size:12 final size:12
Alignment explanation
Indices: 1922628--1922652 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1922618 TCTTCGGGGA
1922628 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1922640 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1922652 C
1 C
1922653 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1922861 original size:24 final size:24
Alignment explanation
Indices: 1922827--1922873 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1922817 CTGAAACATC
1922827 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1922851 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1922874 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1923575 original size:20 final size:20
Alignment explanation
Indices: 1923547--1923915 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
1923537 AAATTTCAGT
* * * *
1923547 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1923567 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
1923587 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1923607 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1923627 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1923647 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1923667 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
1923687 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1923707 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1923727 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
1923747 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
1923767 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1923787 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
1923807 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
1923827 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
1923847 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
1923867 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
1923887 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
1923907 GTTGCGATT
1 GTTGCGATT
1923916 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:1925715 original size:28 final size:27
Alignment explanation
Indices: 1925668--1925736 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 27
1925658 AATTAAAGAA
* * * *
1925668 AAAAATAAGGGCCTTAATTATAAATAT
1 AAAAATTAGGGCATCAATTATAAAAAT
* *
1925695 AGATATTAGAGGCATCAATTATAAAAAT
1 AAAAATTAG-GGCATCAATTATAAAAAT
1925723 AAAAATTAGGGCAT
1 AAAAATTAGGGCAT
1925737 GAGCAATAGC
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
27 11 0.33
28 22 0.67
ACGTcount: A:0.51, C:0.07, G:0.14, T:0.28
Consensus pattern (27 bp):
AAAAATTAGGGCATCAATTATAAAAAT
Found at i:1926091 original size:17 final size:17
Alignment explanation
Indices: 1926069--1926107 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
1926059 TGAATCAAAT
1926069 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
1926086 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
1926103 -AATTA
1 TAATTA
1926108 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:1927592 original size:10 final size:10
Alignment explanation
Indices: 1927565--1927606 Score: 57
Period size: 10 Copynumber: 4.0 Consensus size: 10
1927555 AAAATATGGT
1927565 ATGAACAATA
1 ATGAACAATA
1927575 CTATGAACAATA
1 --ATGAACAATA
*
1927587 ATGAACAGTA
1 ATGAACAATA
1927597 ATGAACAATA
1 ATGAACAATA
1927607 CCATGAATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 18 0.64
12 10 0.36
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.21
Consensus pattern (10 bp):
ATGAACAATA
Found at i:1927734 original size:6 final size:6
Alignment explanation
Indices: 1927698--1927725 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1927688 TTCATTACTA
1927698 TACATT TACATT TACATT TACATT TACA
1 TACATT TACATT TACATT TACATT TACA
1927726 CATATACATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.00, T:0.46
Consensus pattern (6 bp):
TACATT
Found at i:1928635 original size:23 final size:21
Alignment explanation
Indices: 1928605--1928651 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 21
1928595 ATCATGTCTC
1928605 ATAGCATGTATCA-CATATGCAT
1 ATAGCATGTAT-ATCATAT-CAT
1928627 ATAGTCATGTATATCATATCAT
1 ATAG-CATGTATATCATATCAT
1928649 ATA
1 ATA
1928652 TCTTATGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (21 bp):
ATAGCATGTATATCATATCAT
Found at i:1931566 original size:20 final size:21
Alignment explanation
Indices: 1931529--1931568 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1931519 AAATTAAGTT
1931529 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
1931550 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
1931569 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:1932373 original size:21 final size:21
Alignment explanation
Indices: 1932349--1932392 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1932339 CTGAAGGAGG
*
1932349 AGGAGGAGAACGAGAAGAACT
1 AGGAGCAGAACGAGAAGAACT
**
1932370 AGGAGCAGCTCGAGAAGAACT
1 AGGAGCAGAACGAGAAGAACT
1932391 AG
1 AG
1932393 CTCCCGGAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.14, G:0.36, T:0.07
Consensus pattern (21 bp):
AGGAGCAGAACGAGAAGAACT
Found at i:1937867 original size:22 final size:21
Alignment explanation
Indices: 1937825--1937864 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1937815 GAGTTTGTTT
*
1937825 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1937846 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1937865 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1938815 original size:20 final size:21
Alignment explanation
Indices: 1938778--1938817 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1938768 AAATTAAGTT
1938778 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
1938799 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
1938818 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:1939009 original size:12 final size:12
Alignment explanation
Indices: 1938994--1939032 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1938984 GCATGCACCG
1938994 ATGCATCAGTTC
1 ATGCATCAGTTC
1939006 ATGCATC-G---
1 ATGCATCAGTTC
1939014 ATGCATCAGTTC
1 ATGCATCAGTTC
1939026 ATGCATC
1 ATGCATC
1939033 GATGAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
8 7 0.30
9 1 0.04
11 1 0.04
12 14 0.61
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.31
Consensus pattern (12 bp):
ATGCATCAGTTC
Found at i:1939010 original size:20 final size:20
Alignment explanation
Indices: 1938985--1939036 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1938975 TATTTAAAGG
*
1938985 CATGCACCGATGCATCAGTT
1 CATGCATCGATGCATCAGTT
1939005 CATGCATCGATGCATCAGTT
1 CATGCATCGATGCATCAGTT
1939025 CATGCATCGATG
1 CATGCATCGATG
1939037 AATTAATTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (20 bp):
CATGCATCGATGCATCAGTT
Found at i:1939199 original size:64 final size:64
Alignment explanation
Indices: 1939046--1939206 Score: 191
Period size: 65 Copynumber: 2.5 Consensus size: 64
1939036 GAATTAATTG
* * * ** **
1939046 AACATCGAATGCATTCCACGCACCGATGCACTCTGCATGCATCGATGCACTCTTAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCAC-AAGCATGCATCGATGCACTCAGAATATTTTCAA
* **
1939111 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAG-CATGCATCGATGCACTCAGAATA-TTTTCA
1939174 A
64 A
1939175 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
1939207 CTTGGTGCAC
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 36 0.43
65 47 0.57
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:1941977 original size:29 final size:29
Alignment explanation
Indices: 1941943--1942059 Score: 103
Period size: 29 Copynumber: 3.8 Consensus size: 29
1941933 TATATATAAA
1941943 ATAATATTATATTATTATATATTTAAT-TAT
1 ATAATATTATATTATTATATA--TAATATAT
*
1941973 -TAATAATATATTATTATATATAATATAT
1 ATAATATTATATTATTATATATAATATAT
*
1942001 ATAATATTATTAATAATATTATATTATTATATAT
1 ATAATATTA-T-AT--TATTATA-TATAATATAT
* *
1942035 TTAATTATTAATAATATTATATATA
1 ATAA-TATT-ATATTATTATATATA
1942060 CATTTAAATT
Statistics
Matches: 72, Mismatches: 6, Indels: 17
0.76 0.06 0.18
Matches are distributed among these distances:
27 4 0.06
28 3 0.04
29 26 0.36
30 1 0.01
31 5 0.07
32 7 0.10
33 7 0.10
34 13 0.18
35 5 0.07
36 1 0.01
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
ATAATATTATATTATTATATATAATATAT
Found at i:1942047 original size:41 final size:39
Alignment explanation
Indices: 1941953--1942053 Score: 112
Period size: 41 Copynumber: 2.4 Consensus size: 39
1941943 ATAATATTAT
*
1941953 ATTATTATATATTTAATTATTAATAATATATTATTATATATA
1 ATTATTA-ATA-TT-ATTAATAATAATATATTATTATATATA
*
1941995 ATATATATAATATTATTAATAATATTATATTATTATATATTTA
1 AT-TAT-TAATATTATTAATAATAATATATTATTATATA--TA
*
1942038 ATTATTAATAATATTA
1 ATTATTAATATTATTA
1942054 TATATACATT
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
41 33 0.63
42 7 0.13
43 10 0.19
44 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (39 bp):
ATTATTAATATTATTAATAATAATATATTATTATATATA
Found at i:1942056 original size:32 final size:33
Alignment explanation
Indices: 1941942--1942054 Score: 151
Period size: 32 Copynumber: 3.3 Consensus size: 33
1941932 TTATATATAA
1941942 AATAATATTA-TATTATTATATATTTAATTATT
1 AATAATATTATTATTATTATATATTTAATTATT
1941974 AATAATA-TATTATTATATATAATATATATAATATTATT
1 AATAATATTATTATTAT-TAT-ATAT-T-T-A-ATTATT
1942012 AATAATATTA-TATTATTATATATTTAATTATT
1 AATAATATTATTATTATTATATATTTAATTATT
1942044 AATAATATTAT
1 AATAATATTAT
1942055 ATATACATTT
Statistics
Matches: 72, Mismatches: 0, Indels: 17
0.81 0.00 0.19
Matches are distributed among these distances:
31 2 0.03
32 29 0.40
33 4 0.06
34 5 0.07
35 2 0.03
36 5 0.07
37 4 0.06
38 19 0.26
39 2 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (33 bp):
AATAATATTATTATTATTATATATTTAATTATT
Found at i:1942488 original size:23 final size:24
Alignment explanation
Indices: 1942462--1942516 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 24
1942452 ACTTAAATAA
1942462 TATTTTAA-AATCAAAT-ATATTTT
1 TATTTTAATAAT-AAATGATATTTT
*
1942485 TA-TTTAATAATTAATGATATTTT
1 TATTTTAATAATAAATGATATTTT
1942508 TATATTTAA
1 TAT-TTTAA
1942517 CTTTTTATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 8 0.30
23 14 0.52
25 5 0.19
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (24 bp):
TATTTTAATAATAAATGATATTTT
Found at i:1951462 original size:12 final size:12
Alignment explanation
Indices: 1951430--1951463 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1951420 AATATGTTTA
*
1951430 AATTATTACTTT
1 AATTATTATTTT
1951442 AATTATTATTTT
1 AATTATTATTTT
*
1951454 TATTATTATT
1 AATTATTATT
1951464 ATATAGTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (12 bp):
AATTATTATTTT
Found at i:1951721 original size:123 final size:122
Alignment explanation
Indices: 1951578--1951800 Score: 349
Period size: 123 Copynumber: 1.8 Consensus size: 122
1951568 AAAATAATCA
* *
1951578 TATTTTAATATTTATTTATTTTTTAATATTAAGAAATGAGCTGTCTTAAAGCACCTAGAAGTCCT
1 TATTTTAATAATTATTTATTTTTTAATATTAAGAAATGAGCTGTCTTAAAGCACCTAGAAGTCAT
*
1951643 TTTCTGATA-TTCTTAAATAAATAGATATCCTATTTTTATGAATTATATATATTATTT
66 TTTCTGATATTTC-TAAATAAATAAATATCCTATTTTTATGAATTATATATATTATTT
* * *
1951700 TATTTTAATTAATTATTTATTTTTTAATATTAAGAGATGGGTTGTCTTAAAGCACCTAGAAGTCA
1 TATTTTAA-TAATTATTTATTTTTTAATATTAAGAAATGAGCTGTCTTAAAGCACCTAGAAGTCA
* *
1951765 TTTTCTGATATTTCTAAGTAAATAAATATCGTATTT
65 TTTTCTGATATTTCTAAATAAATAAATATCCTATTT
1951801 ATAAAAATAA
Statistics
Matches: 91, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
122 8 0.09
123 80 0.88
124 3 0.03
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.48
Consensus pattern (122 bp):
TATTTTAATAATTATTTATTTTTTAATATTAAGAAATGAGCTGTCTTAAAGCACCTAGAAGTCAT
TTTCTGATATTTCTAAATAAATAAATATCCTATTTTTATGAATTATATATATTATTT
Found at i:1956567 original size:54 final size:54
Alignment explanation
Indices: 1956462--1956567 Score: 169
Period size: 54 Copynumber: 2.0 Consensus size: 54
1956452 CCTTGACCAG
*
1956462 ACCTCTGGACAGAAGCCACAAGAAAAGATGAATGTGTTGTCAAATATTTTACGA
1 ACCTCTGGACAGAAGCCACAAGAAAAGATGAATGTGTTGTCAAATACTTTACGA
* *
1956516 ACCTCTGGGCAGAAGCCAC-AGTAAAAGATGAATGTGTTGTCAAATGCTTTAC
1 ACCTCTGGACAGAAGCCACAAG-AAAAGATGAATGTGTTGTCAAATACTTTAC
1956568 AAACATCTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
53 2 0.04
54 46 0.96
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.25
Consensus pattern (54 bp):
ACCTCTGGACAGAAGCCACAAGAAAAGATGAATGTGTTGTCAAATACTTTACGA
Found at i:1956589 original size:54 final size:54
Alignment explanation
Indices: 1956471--1956615 Score: 148
Period size: 54 Copynumber: 2.7 Consensus size: 54
1956461 GACCTCTGGA
* * ** * * **
1956471 CAGAAGCCACAAGAAAAGATGAATGTGTTGTCAAATATTTTACGAACCTCTGGG
1 CAGAAACCACATGAAAAGATGAATGTGTTGTCAAATGCTTTACAAACATCTAAG
*
1956525 CAGAAGCCACA-GTAAAAGATGAATGTGTTGTCAAATGCTTTACAAACATCTAAG
1 CAGAAACCACATG-AAAAGATGAATGTGTTGTCAAATGCTTTACAAACATCTAAG
* * * * *
1956579 TAGAAACCACATGAGATGATGAATGTATTATCAAATG
1 CAGAAACCACATGAAAAGATGAATGTGTTGTCAAATG
1956616 TTATACGAAC
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
53 1 0.01
54 75 0.97
55 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (54 bp):
CAGAAACCACATGAAAAGATGAATGTGTTGTCAAATGCTTTACAAACATCTAAG
Found at i:1957020 original size:22 final size:22
Alignment explanation
Indices: 1956992--1957090 Score: 126
Period size: 22 Copynumber: 4.5 Consensus size: 22
1956982 ATCTACACTA
*
1956992 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTC
* *
1957014 TTCAAAGATGATATATTTTCTC
1 TTCAAAGATGATAGATTCTCTC
* * *
1957036 TTAAAAGATGATAGCTTTTCTC
1 TTCAAAGATGATAGATTCTCTC
* *
1957058 TTCAAAGATGATATATTCTCTT
1 TTCAAAGATGATAGATTCTCTC
1957080 TTCAAAGATGA
1 TTCAAAGATGA
1957091 AAGCTTTATT
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 66 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTC
Found at i:1957096 original size:44 final size:44
Alignment explanation
Indices: 1956992--1957097 Score: 149
Period size: 44 Copynumber: 2.4 Consensus size: 44
1956982 ATCTACACTA
* * * *
1956992 TTCAAAGATGATAGATTCTCTTTTCAAAGATGATATATTTTCTC
1 TTCAAAGATGATAGCTTTTCTCTTCAAAGATGATATATTCTCTC
* *
1957036 TTAAAAGATGATAGCTTTTCTCTTCAAAGATGATATATTCTCTT
1 TTCAAAGATGATAGCTTTTCTCTTCAAAGATGATATATTCTCTC
*
1957080 TTCAAAGATGAAAGCTTT
1 TTCAAAGATGATAGCTTT
1957098 ATTGGATTTC
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 54 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (44 bp):
TTCAAAGATGATAGCTTTTCTCTTCAAAGATGATATATTCTCTC
Found at i:1957807 original size:45 final size:45
Alignment explanation
Indices: 1957743--1957869 Score: 209
Period size: 45 Copynumber: 2.8 Consensus size: 45
1957733 ACTATTTCCC
* *
1957743 ACATCTGTAAGCCCTTCAGTGTATGATGTTTTCAAAACCTTTGGG
1 ACATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
*
1957788 ACATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGG
1 ACATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
* *
1957833 TCATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAA
1 ACATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAA
1957870 AGTCTTCGGG
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 76 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.33
Consensus pattern (45 bp):
ACATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
Found at i:1957956 original size:45 final size:45
Alignment explanation
Indices: 1957892--1958173 Score: 510
Period size: 45 Copynumber: 6.3 Consensus size: 45
1957882 CTTTTCGATA
1957892 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATG
1 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATG
1957937 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATG
1 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATG
*
1957982 TTTTCAAAACCTTCGGTTCATCTGTAAGCCCTTCAGTGCATGATG
1 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATG
* * *
1958027 TTTTTAAAACCTTCGGTTCATTTGTAAGCCCTTCAGTGCATGATG
1 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATG
1958072 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATG
1 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATG
*
1958117 TTTTCAAAACCTTTGGGTCATCTGTAAGCCCTTCAGTGCATGATG
1 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATG
*
1958162 TTTTCAAGACCT
1 TTTTCAAAACCT
1958174 CTGGACAGAA
Statistics
Matches: 229, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 229 1.00
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.35
Consensus pattern (45 bp):
TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATG
Found at i:1958308 original size:3 final size:3
Alignment explanation
Indices: 1958300--1958330 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
1958290 TTCAGTTTAC
1958300 TTA TTA TTA TTA TTA TATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
1958331 AATAAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1959594 original size:31 final size:30
Alignment explanation
Indices: 1959545--1959611 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 30
1959535 TTTAGTCACT
* **
1959545 ATTTAATTGCAATTTATTTTTATTATTATC
1 ATTTAATTGCAATATATTTAAATTATTATC
*
1959575 ATTTCAATTTCAATATATTTAAATTATTA-C
1 ATTT-AATTGCAATATATTTAAATTATTATC
1959605 -TTTAATT
1 ATTTAATT
1959612 ATTATTATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 4 0.12
29 3 0.09
30 5 0.16
31 20 0.62
ACGTcount: A:0.34, C:0.07, G:0.01, T:0.57
Consensus pattern (30 bp):
ATTTAATTGCAATATATTTAAATTATTATC
Found at i:1959981 original size:123 final size:120
Alignment explanation
Indices: 1959744--1959973 Score: 290
Period size: 123 Copynumber: 1.9 Consensus size: 120
1959734 AAAATAATCA
* * *
1959744 TATTTTAATATTTATTTATTTTTTAATATTAAGAAATTGGCTGTCTTAAAGCACCTAGAAGTCAT
1 TATTTTAATAATTATTTATTTTTTAATATTAAGAAATTGGATGTCTTAAAGAACCT--AAGTCAT
* ** *
1959809 TTTCTGATATTCTTAAATAAATAAATATTCTATTTTTATAAATTATATATGTTATTT
64 TTTCTAATATTCTTAAATAAATAAATATTCTATTTACAAAAATTATATATGTTATTT
1959866 TATTTTAATTAATTATTTATTTTTTAATATTAAGAAA-TGGAATGTCTTAAAGAACCT-AGTCCA
1 TATTTTAA-TAATTATTTATTTTTTAATATTAAGAAATTGG-ATGTCTTAAAGAACCTAAGT-CA
*
1959929 -TTTCTAATATT-TCTAAGTAAATAAATA-TCGTATTTACAAAAATTA
63 TTTTCTAATATTCT-TAAATAAATAAATATTC-TATTTACAAAAATTA
1959974 AAATATATTA
Statistics
Matches: 95, Mismatches: 8, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
119 3 0.03
120 38 0.40
121 2 0.02
122 11 0.12
123 41 0.43
ACGTcount: A:0.38, C:0.08, G:0.07, T:0.47
Consensus pattern (120 bp):
TATTTTAATAATTATTTATTTTTTAATATTAAGAAATTGGATGTCTTAAAGAACCTAAGTCATTT
TCTAATATTCTTAAATAAATAAATATTCTATTTACAAAAATTATATATGTTATTT
Found at i:1960821 original size:15 final size:16
Alignment explanation
Indices: 1960801--1960835 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
1960791 TTTTCCTTCA
1960801 TTTTTTCTTCTT-TTC
1 TTTTTTCTTCTTATTC
1960816 TTTTTTCTTCTTATTC
1 TTTTTTCTTCTTATTC
1960832 TTTT
1 TTTT
1960836 CTTTTAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTTCTTCTTATTC
Found at i:1964363 original size:23 final size:23
Alignment explanation
Indices: 1964336--1964388 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
1964326 ATAAGAGTCA
1964336 CTCAGGAAACTTAAGTCTATATT
1 CTCAGGAAACTTAAGTCTATATT
*
1964359 CTCAGGAAACTTACGTCTATATT
1 CTCAGGAAACTTAAGTCTATATT
1964382 CTCAGGA
1 CTCAGGA
1964389 TGATCCTACT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (23 bp):
CTCAGGAAACTTAAGTCTATATT
Found at i:1967052 original size:21 final size:21
Alignment explanation
Indices: 1967026--1967066 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1967016 TTGTACATTC
*
1967026 CGCAGTCATTTCAGATGGCAT
1 CGCAGTCATATCAGATGGCAT
1967047 CGCAGTCATATCAGATGGCA
1 CGCAGTCATATCAGATGGCA
1967067 CCACAACCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (21 bp):
CGCAGTCATATCAGATGGCAT
Found at i:1970036 original size:60 final size:60
Alignment explanation
Indices: 1969921--1970038 Score: 148
Period size: 60 Copynumber: 2.0 Consensus size: 60
1969911 CCACGATGTC
* * * * * *
1969921 GACATTTAGGTCGAACAAGCTAGTAGTTGTATGTCTTCCCCTTGAACTTGTAGGCATCTT
1 GACATTAAGGTCGAAAAAGCTAGCAGTTGAATGTCCTCCCCTTGAACTTGAAGGCATCTT
* *
1969981 GACATTAAGGTCGAAAAAGCTCGCAGTTGAATG-CCTCCCCTTGGAGCTTGAAGGCATC
1 GACATTAAGGTCGAAAAAGCTAGCAGTTGAATGTCCTCCCCTT-GAACTTGAAGGCATC
1970039 GTGTCAAATG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 8 0.16
60 41 0.84
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (60 bp):
GACATTAAGGTCGAAAAAGCTAGCAGTTGAATGTCCTCCCCTTGAACTTGAAGGCATCTT
Found at i:1970198 original size:3 final size:3
Alignment explanation
Indices: 1970180--1970287 Score: 116
Period size: 3 Copynumber: 36.0 Consensus size: 3
1970170 TTTTATTTAT
* * * *
1970180 TTA TTT TTA ATA TTA TTA TTA TTA TT- TTA TT- TATA CTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
1970224 TTA TTA TT- TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
1970268 CTTA TTA TTA TTA TATA TTA
1 -TTA TTA TTA TTA T-TA TTA
1970288 CAGACCCAAA
Statistics
Matches: 91, Mismatches: 6, Indels: 16
0.81 0.05 0.14
Matches are distributed among these distances:
2 7 0.08
3 77 0.85
4 5 0.05
5 2 0.02
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1970210 original size:17 final size:17
Alignment explanation
Indices: 1970179--1970281 Score: 102
Period size: 17 Copynumber: 6.0 Consensus size: 17
1970169 TTTTTATTTA
* *
1970179 TTTATTTTTAATATTAT
1 TTTATTATTATTATTAT
1970196 TATTATTATT-TTATTTAT
1 T-TTATTATTATTA-TTAT
** *
1970214 ACTACTATTATTATTAT
1 TTTATTATTATTATTAT
1970231 TTTATTATTATTATTAT
1 TTTATTATTATTATTAT
*
1970248 TATATTATTATTATTA-
1 TTTATTATTATTATTAT
*
1970264 TTAACTTATTATTATTAT
1 TTTA-TTATTATTATTAT
1970282 ATATTACAGA
Statistics
Matches: 70, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
16 2 0.03
17 54 0.77
18 14 0.20
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTATTATTATTATTAT
Found at i:1970273 original size:20 final size:20
Alignment explanation
Indices: 1970180--1970287 Score: 109
Period size: 20 Copynumber: 5.5 Consensus size: 20
1970170 TTTTATTTAT
*
1970180 TTATTTTTAATATTATTATTA
1 TTATTATTAAT-TTATTATTA
*
1970201 TTATT-TT-ATTTATACTACTA
1 TTATTATTAATTTAT--TATTA
*
1970221 TTATTATTATTTTATTATTA
1 TTATTATTAATTTATTATTA
1970241 TTATTATT-A--TATTATTA
1 TTATTATTAATTTATTATTA
*
1970258 TTATTATTAACTTATTATTA
1 TTATTATTAATTTATTATTA
1970278 TTATATATTA
1 TTAT-TATTA
1970288 CAGACCCAAA
Statistics
Matches: 75, Mismatches: 4, Indels: 16
0.79 0.04 0.17
Matches are distributed among these distances:
17 16 0.21
18 5 0.07
19 2 0.03
20 35 0.47
21 12 0.16
22 5 0.07
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (20 bp):
TTATTATTAATTTATTATTA
Found at i:1971658 original size:12 final size:12
Alignment explanation
Indices: 1971641--1971674 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1971631 GATATGTTTA
*
1971641 AATTATTATTTT
1 AATTATTATGTT
1971653 AATTATTATGTT
1 AATTATTATGTT
1971665 -ATTATTATGT
1 AATTATTATGT
1971675 AGCCATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (12 bp):
AATTATTATGTT
Found at i:1977229 original size:20 final size:19
Alignment explanation
Indices: 1977186--1977230 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
1977176 CTCATCCATC
1977186 AAAAAAAAGAGGAAAAAAG
1 AAAAAAAAGAGGAAAAAAG
*
1977205 TAAAACAAA-AGGAAAAAATG
1 -AAAAAAAAGAGGAAAAAA-G
1977225 AAAAAA
1 AAAAAA
1977231 TTGAATCAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04
Consensus pattern (19 bp):
AAAAAAAAGAGGAAAAAAG
Found at i:1981802 original size:22 final size:22
Alignment explanation
Indices: 1981773--1981826 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
1981763 ATCTATACCC
1981773 TTCAAAGATGATAAATTCT-TT
1 TTCAAAGATGATAAATTCTCTT
*
1981794 TCTCAAAGATGATAGATTCTCTT
1 T-TCAAAGATGATAAATTCTCTT
1981817 TT-AAAGATGA
1 TTCAAAGATGA
1981827 AAGCTTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 9 0.30
22 18 0.60
23 3 0.10
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (22 bp):
TTCAAAGATGATAAATTCTCTT
Found at i:1982580 original size:37 final size:37
Alignment explanation
Indices: 1982472--1982581 Score: 96
Period size: 36 Copynumber: 3.0 Consensus size: 37
1982462 TTTCAAATAG
* *
1982472 TAATTTATCTCACTTGAGATCATTTTTATTAAAACAA
1 TAATTTATCTCACTTGAGATAATTTTTCTTAAAACAA
*** * * ** **
1982509 -AATGCGTCTCGCTTGAGACAATTTCACTCGAAACAA
1 TAATTTATCTCACTTGAGATAATTTTTCTTAAAACAA
**
1982545 TAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
1 TAATTTATCTCACTTGAGATAATTTTTCTTAAAACAA
1982582 GATTCGTCTC
Statistics
Matches: 50, Mismatches: 22, Indels: 2
0.68 0.30 0.03
Matches are distributed among these distances:
36 25 0.50
37 25 0.50
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (37 bp):
TAATTTATCTCACTTGAGATAATTTTTCTTAAAACAA
Found at i:1982591 original size:73 final size:73
Alignment explanation
Indices: 1982472--1982623 Score: 223
Period size: 73 Copynumber: 2.1 Consensus size: 73
1982462 TTTCAAATAG
1982472 TAATTTATCTCACTTGAGATCATTTTTATTAAAACAAAATGCGTCTCGCTTGAGACAATTTCACT
1 TAATTTATCTCACTTGAGATCATTTTTATTAAAACAAAATGCGTCTCGCTTGAGACAATTTCACT
*
1982537 CGAAACAA
66 AGAAACAA
** * * * *
1982545 TAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTCGTCTCGCTTGAGACAGTTTCACT
1 TAATTTATCTCACTTGAGATCATTTTTATTAAAACAAAATGCGTCTCGCTTGAGACAATTTCACT
*
1982610 ATAAACAA
66 AGAAACAA
*
1982618 AAATTT
1 TAATTT
1982624 CCATCACTCG
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
73 70 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (73 bp):
TAATTTATCTCACTTGAGATCATTTTTATTAAAACAAAATGCGTCTCGCTTGAGACAATTTCACT
AGAAACAA
Found at i:1982616 original size:36 final size:35
Alignment explanation
Indices: 1982503--1982619 Score: 99
Period size: 36 Copynumber: 3.2 Consensus size: 35
1982493 ATTTTTATTA
* * *
1982503 AAACAAAATGCGTCTCGCTTGAGACAATTTCACTCG
1 AAACAAAATTCGTCTCGCTTGAGACAGTTTCACT-T
** * ** **
1982539 AAACAATAATTTATCTCACTTGAGATTGTTTTTCTT
1 AAACAA-AATTCGTCTCGCTTGAGACAGTTTCACTT
*
1982575 AAAACAAGATTCGTCTCGCTTGAGACAGTTTCACTAT
1 -AAACAAAATTCGTCTCGCTTGAGACAGTTTCACT-T
1982612 AAACAAAA
1 AAACAAAA
1982620 ATTTCCATCA
Statistics
Matches: 59, Mismatches: 19, Indels: 6
0.70 0.23 0.07
Matches are distributed among these distances:
36 33 0.56
37 26 0.44
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.32
Consensus pattern (35 bp):
AAACAAAATTCGTCTCGCTTGAGACAGTTTCACTT
Found at i:1982909 original size:123 final size:123
Alignment explanation
Indices: 1982644--1983092 Score: 672
Period size: 123 Copynumber: 3.7 Consensus size: 123
1982634 ATGGATCAAT
* * *
1982644 ATTTCCAGAGAAAGTTTATAATAAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGA
1 ATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGA
*
1982709 AGAACTTGTTCAACC-TTTGCATGACTCTATCGCAGAAGGAGATAGATCATCACCAAC
66 AGAACTTGTTCAACCTTTTGCATGACTCTATCGCAGAAGGAGATAGATCAGCACCAAC
* *
1982766 ATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAATG-AGAAGAAGTTCATAATGAG
1 ATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGAG
*
1982830 AAGAACTTGTTCAACCTTTTGCATGACTCTATCGCAAAAGGAGATAGATCAGCACCAAC
65 AAGAACTTGTTCAACCTTTTGCATGACTCTATCGCAGAAGGAGATAGATCAGCACCAAC
1982889 ATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGA
1 ATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGA
* ** * * * * * *
1982954 AGAATTTGTTCAATTTTTTGCTTAATTCTATCACAGAATGAGATAGATCAGCATCAAC
66 AGAACTTGTTCAACCTTTTGCATGACTCTATCGCAGAAGGAGATAGATCAGCACCAAC
** *
1983012 ATTTCCAGA-AGTGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCATAATAAG
1 ATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGAG
*
1983075 AAGAATTTGTTCAACCTT
65 AAGAACTTGTTCAACCTT
1983093 GCCTTAATTC
Statistics
Matches: 301, Mismatches: 22, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
122 139 0.46
123 162 0.54
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.26
Consensus pattern (123 bp):
ATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGA
AGAACTTGTTCAACCTTTTGCATGACTCTATCGCAGAAGGAGATAGATCAGCACCAAC
Found at i:1983079 original size:245 final size:245
Alignment explanation
Indices: 1982644--1983092 Score: 711
Period size: 245 Copynumber: 1.8 Consensus size: 245
1982634 ATGGATCAAT
* *
1982644 ATTTCCAGAGAAAGTTTATAATAAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGA
1 ATTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGA
* * *
1982709 AGAACTTGTTCAACCTTTGCATGACTCTATCGCAGAAGGAGATAGATCATCACCAACATTTCCAG
66 AGAACTTGTTCAACCTTTGCATAACTCTATCACAGAAGGAGATAGATCAGCACCAACATTTCCAG
* * *
1982774 AGAAAGTTCATAATGAGAAGAACTTATCTGAAGAATGAGAAGAAGTTCATAATGAGAAGAACTTG
131 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATAAGAAGAACTTG
1982839 TTCAACCTTTTGCATGACTCTATCGCAAAAGGAGATAGATCAGCACCAAC
196 TTCAACCTTTTGCATGACTCTATCGCAAAAGGAGATAGATCAGCACCAAC
*
1982889 ATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGA
1 ATTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGA
* ** * * * *
1982954 AGAATTTGTTCAATTTTTTGCTTAATTCTATCACAGAATGAGATAGATCAGCATCAACATTTCCA
66 AGAACTTGTTCAA-CCTTTGCATAACTCTATCACAGAAGGAGATAGATCAGCACCAACATTTCCA
** *
1983019 GA-AGTGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATAAGAAGAATTT
130 GAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATAAGAAGAACTT
1983083 GTTCAACCTT
195 GTTCAACCTT
1983093 GCCTTAATTC
Statistics
Matches: 184, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
245 140 0.76
246 44 0.24
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.26
Consensus pattern (245 bp):
ATTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGA
AGAACTTGTTCAACCTTTGCATAACTCTATCACAGAAGGAGATAGATCAGCACCAACATTTCCAG
AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATAAGAAGAACTTG
TTCAACCTTTTGCATGACTCTATCGCAAAAGGAGATAGATCAGCACCAAC
Found at i:1983432 original size:4 final size:4
Alignment explanation
Indices: 1983423--1983450 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1983413 TTTTTTATCC
1983423 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1983451 TAATATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:1983472 original size:3 final size:3
Alignment explanation
Indices: 1983445--1983523 Score: 83
Period size: 3 Copynumber: 26.3 Consensus size: 3
1983435 ATTTATTTAT
* * *
1983445 TTA TT- TTA ATA TTA TTT TTA ATA TTA TTA TT- TTA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1983490 TTA TTA TTA TTAA CTTA TTA TTA TTA TATA TTA T
1 TTA TTA TTA TT-A -TTA TTA TTA TTA T-TA TTA T
1983524 AGACCCAAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
2 6 0.09
3 51 0.80
4 5 0.08
5 2 0.03
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1983483 original size:14 final size:14
Alignment explanation
Indices: 1983445--1983516 Score: 85
Period size: 14 Copynumber: 5.3 Consensus size: 14
1983435 ATTTATTTAT
*
1983445 TTATTTTAATATTA
1 TTATTTTATTATTA
*
1983459 -T-TTTTAATATTA
1 TTATTTTATTATTA
1983471 TTATTTTATTATTA
1 TTATTTTATTATTA
*
1983485 TTATATTATTATTA
1 TTATTTTATTATTA
**
1983499 TTAACTTATTATTA
1 TTATTTTATTATTA
1983513 TTAT
1 TTAT
1983517 ATATTATAGA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
12 11 0.22
13 2 0.04
14 38 0.75
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTTTATTATTA
Found at i:1985011 original size:2 final size:2
Alignment explanation
Indices: 1984998--1985066 Score: 56
Period size: 2 Copynumber: 36.0 Consensus size: 2
1984988 TTATGTAGCC
* * * * *
1984998 AT AT AA AT AT AT AT A- AT AA AT A- AT AT TT AT TT ACT -T AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
1985038 AT -T 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
1985067 TAAATAAAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
1 4 0.08
2 47 0.90
3 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1986612 original size:18 final size:20
Alignment explanation
Indices: 1986584--1986620 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1986574 ATTTTTTTTC
1986584 AAATAATCATAT-ATAAAAT
1 AAATAATCATATAATAAAAT
1986603 AAAT-ATCATATAATAAAA
1 AAATAATCATATAATAAAA
1986621 AATAATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (20 bp):
AAATAATCATATAATAAAAT
Found at i:1987182 original size:3 final size:3
Alignment explanation
Indices: 1987160--1987225 Score: 57
Period size: 3 Copynumber: 23.0 Consensus size: 3
1987150 TATCTCAGTT
* * * * * *
1987160 TTA TTA TT- TT- TTA TTT TTA TTA TTA TAA TAA CTA TAA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1987206 TT- TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
1987226 AATAATTTTA
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
2 6 0.12
3 45 0.88
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1988600 original size:20 final size:20
Alignment explanation
Indices: 1988575--1988614 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1988565 AATTTCTTTC
1988575 ATTTTGATTAT-TATTATTTT
1 ATTTTG-TTATATATTATTTT
*
1988595 ATTTTGTTTTATATTATTTT
1 ATTTTGTTATATATTATTTT
1988615 CGATATATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (20 bp):
ATTTTGTTATATATTATTTT
Found at i:1989533 original size:2 final size:2
Alignment explanation
Indices: 1989526--1989567 Score: 61
Period size: 2 Copynumber: 21.5 Consensus size: 2
1989516 TTCAAAATTT
1989526 TA TA TA TA CT- TA T- 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 TA TA TA TA TA TA TA
1989567 T
1 T
1989568 TAATTGTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 2 0.05
2 34 0.92
3 1 0.03
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1994462 original size:32 final size:32
Alignment explanation
Indices: 1994426--1994487 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
1994416 TCTGGAAACA
*
1994426 AGAAGTATCTCTACAAGATGAGCATAACAACG
1 AGAAGTATCTCTACAAGATAAGCATAACAACG
*
1994458 AGAAGTATCTCTACCAGATAAGCATAACAA
1 AGAAGTATCTCTACAAGATAAGCATAACAA
1994488 TCATTTCTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.45, C:0.19, G:0.16, T:0.19
Consensus pattern (32 bp):
AGAAGTATCTCTACAAGATAAGCATAACAACG
Found at i:1998193 original size:22 final size:22
Alignment explanation
Indices: 1998165--1998221 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
1998155 ACATCTACAT
*
1998165 TCTTCAAAGATGATAGATTTTA
1 TCTTCAAAGATGATAGATTCTA
* *
1998187 TCTTCAAAGATGGTAGATTCTC
1 TCTTCAAAGATGATAGATTCTA
*
1998209 TTTTCAAAGATGA
1 TCTTCAAAGATGA
1998222 AATATTTATT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTA
Found at i:1999181 original size:37 final size:36
Alignment explanation
Indices: 1999074--1999200 Score: 110
Period size: 36 Copynumber: 3.5 Consensus size: 36
1999064 TTCAAATAGT
*
1999074 AATTTATCTCACTTAAGATTGTTTTTCTTAAAACAA
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
* ** * * ** * ***
1999110 ACTACATCTCGCTTTAGACAGTTTCTCCCGAAACAA
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
1999146 CAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
1 -AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
* * *
1999183 TATTTGTCTCGCTTGAGA
1 AATTTATCTCACTTGAGA
1999201 CAATTTCACT
Statistics
Matches: 65, Mismatches: 25, Indels: 2
0.71 0.27 0.02
Matches are distributed among these distances:
36 40 0.62
37 25 0.38
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (36 bp):
AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
Found at i:1999232 original size:73 final size:73
Alignment explanation
Indices: 1999074--1999217 Score: 191
Period size: 73 Copynumber: 2.0 Consensus size: 73
1999064 TTCAAATAGT
* * * *
1999074 AATTTATCTCACTTAAGATTGTTTTTCTTAAAACAAACTACATCTCGCTTTAGACAGTTTCTCCC
1 AATTTATCTCACTTAAGATTGTTTTTCTTAAAACAAACTACATCTCGCTTGAGACAATTTCACCA
1999139 GAAACAAC
66 GAAACAAC
* *** *
1999147 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAATA-TTTGTCTCGCTTGAGACAATTTCACT
1 AATTTATCTCACTTAAGATTGTTTTTCTTAAAACAA-ACTACATCTCGCTTGAGACAATTTCACC
1999211 AGAAACA
65 AGAAACA
1999218 GAAATTTTCA
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
73 60 0.98
74 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.38
Consensus pattern (73 bp):
AATTTATCTCACTTAAGATTGTTTTTCTTAAAACAAACTACATCTCGCTTGAGACAATTTCACCA
GAAACAAC
Found at i:1999527 original size:20 final size:21
Alignment explanation
Indices: 1999502--1999555 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
1999492 AGTTCATAAT
1999502 GAGAAGAAC-TTATCTGAAGA
1 GAGAAGAACTTTATCTGAAGA
*
1999522 GAGAAGAACTTTCTCTGAAGA
1 GAGAAGAACTTTATCTGAAGA
*
1999543 G-GAAGAAGTTTAT
1 GAGAAGAACTTTAT
1999556 AATAAGAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.41, C:0.09, G:0.26, T:0.24
Consensus pattern (21 bp):
GAGAAGAACTTTATCTGAAGA
Found at i:2000046 original size:3 final size:3
Alignment explanation
Indices: 2000038--2000084 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
2000028 TATCCCAGTT
* * *
2000038 TTA TTA TTA TAA TAA TTA TAA TTA TT- TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2000085 AATAATTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:2001378 original size:17 final size:17
Alignment explanation
Indices: 2001346--2001393 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 17
2001336 TAACAGTTTG
*
2001346 ATATTTTTCA-TTTAAT
1 ATATTTTGCATTTTAAT
2001362 ATATTTTGCATTTTAAT
1 ATATTTTGCATTTTAAT
*
2001379 AT-TATTGC-TTTTAAT
1 ATATTTTGCATTTTAAT
2001394 TTCTTTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 7 0.24
16 14 0.48
17 8 0.28
ACGTcount: A:0.29, C:0.06, G:0.04, T:0.60
Consensus pattern (17 bp):
ATATTTTGCATTTTAAT
Found at i:2001445 original size:22 final size:21
Alignment explanation
Indices: 2001409--2001463 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
2001399 TCATTTTGAT
* *
2001409 TATTATTATTTTATATTTTTA
1 TATTATTTTTTTATATGTTTA
2001430 TATTATTTTTTATATATGTTTA
1 TATTATTTTTT-TATATGTTTA
* *
2001452 AATTATTATTTT
1 TATTATTTTTTT
2001464 CATAATTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 11 0.38
22 18 0.62
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (21 bp):
TATTATTTTTTTATATGTTTA
Found at i:2003625 original size:25 final size:25
Alignment explanation
Indices: 2003597--2003645 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
2003587 TATTTTTTTT
*
2003597 CTATCGGAAATGTTAATATTGAGTC
1 CTATCGAAAATGTTAATATTGAGTC
*
2003622 CTATTGAAAATGTTAATATTGAGT
1 CTATCGAAAATGTTAATATTGAGT
2003646 TCTACATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (25 bp):
CTATCGAAAATGTTAATATTGAGTC
Found at i:2003657 original size:25 final size:24
Alignment explanation
Indices: 2003603--2003657 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
2003593 TTTTCTATCG
*
2003603 GAAATGTTAATATTGAGTCCTATT
1 GAAATGTTAATATTGAGTCCTAAT
*
2003627 GAAAATGTTAATATTGAGTTCTACAT
1 G-AAATGTTAATATTGAGTCCTA-AT
2003653 GAAAT
1 GAAAT
2003658 TAGTTAACGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 1 0.04
25 24 0.89
26 2 0.07
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.38
Consensus pattern (24 bp):
GAAATGTTAATATTGAGTCCTAAT
Found at i:2010694 original size:22 final size:21
Alignment explanation
Indices: 2010669--2010744 Score: 65
Period size: 22 Copynumber: 3.8 Consensus size: 21
2010659 TACTAAGAGA
*
2010669 TATCGATACCCCTATGAATGGG
1 TATCAATACCCCTATG-ATGGG
2010691 TATCAATA-CCC-----TGGG
1 TATCAATACCCCTATGATGGG
* *
2010706 TACCGATACCCCTATGACTGGG
1 TATCAATACCCCTATGA-TGGG
2010728 TATCAATACCCCTATGA
1 TATCAATACCCCTATGA
2010745 CTGCTCAAAC
Statistics
Matches: 42, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
15 10 0.24
16 3 0.07
21 3 0.07
22 26 0.62
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (21 bp):
TATCAATACCCCTATGATGGG
Found at i:2010745 original size:22 final size:22
Alignment explanation
Indices: 2010701--2010747 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
2010691 TATCAATACC
*
2010701 CTGGGTACCGATACCCCTATGA
1 CTGGGTACCAATACCCCTATGA
*
2010723 CTGGGTATCAATACCCCTATGA
1 CTGGGTACCAATACCCCTATGA
2010745 CTG
1 CTG
2010748 CTCAAACATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (22 bp):
CTGGGTACCAATACCCCTATGA
Found at i:2016662 original size:34 final size:34
Alignment explanation
Indices: 2016592--2016679 Score: 104
Period size: 34 Copynumber: 2.6 Consensus size: 34
2016582 TAATACTTAC
* *
2016592 TTTATTTTGTTAATTTGGTTGGATTTTTTAAAAA
1 TTTATTTTGTTAATTTTGTTGGACTTTTTAAAAA
* * ***
2016626 TTTGTTTTGTTTATTTTGTTGGACTTTTTGTTAA
1 TTTATTTTGTTAATTTTGTTGGACTTTTTAAAAA
*
2016660 TTTATTTTGATAATTTTGTT
1 TTTATTTTGTTAATTTTGTT
2016680 TATTACTATT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.19, C:0.01, G:0.15, T:0.65
Consensus pattern (34 bp):
TTTATTTTGTTAATTTTGTTGGACTTTTTAAAAA
Found at i:2020050 original size:21 final size:22
Alignment explanation
Indices: 2020024--2020069 Score: 85
Period size: 21 Copynumber: 2.1 Consensus size: 22
2020014 ACAATAAAAT
2020024 TTTTACACATAAACGT-AATAA
1 TTTTACACATAAACGTAAATAA
2020045 TTTTACACATAAACGTAAATAA
1 TTTTACACATAAACGTAAATAA
2020067 TTT
1 TTT
2020070 AAATAATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.37
Consensus pattern (22 bp):
TTTTACACATAAACGTAAATAA
Found at i:2020594 original size:17 final size:17
Alignment explanation
Indices: 2020569--2020602 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2020559 ACGCGCTGCA
2020569 GGGGCGTACCTTACCCC
1 GGGGCGTACCTTACCCC
*
2020586 GGGGTGTACCTTACCCC
1 GGGGCGTACCTTACCCC
2020603 ACGTGACGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.38, G:0.29, T:0.21
Consensus pattern (17 bp):
GGGGCGTACCTTACCCC
Found at i:2027317 original size:24 final size:25
Alignment explanation
Indices: 2027290--2027336 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
2027280 CTCTTATAAT
*
2027290 CACCATCATCATCATCAT-AACCAC
1 CACCATCACCATCATCATCAACCAC
2027314 CACCATCACCATCATCATCAACC
1 CACCATCACCATCATCATCAACC
2027337 TCATCTACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.36, C:0.45, G:0.00, T:0.19
Consensus pattern (25 bp):
CACCATCACCATCATCATCAACCAC
Done.