Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 6 of 335
Found at i:1824523 original size:42 final size:42
Alignment explanation
Indices: 1824468--1824560 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 42
1824458 TTACACATCT
*
1824468 TCACATAAT-GATGCCATAGCCCAGCTATAGTCTTACAAGTAT
1 TCACAT-ATCGATGCCATAGCCCAGCTATAGTCTTACAAGTAA
* * * * *
1824510 TCATATATCGATGCCATGGTCCAGCTATGGTCTTACATGTAA
1 TCACATATCGATGCCATAGCCCAGCTATAGTCTTACAAGTAA
1824552 TCACATATC
1 TCACATATC
1824561 ACATATCACA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 2 0.05
42 41 0.95
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (42 bp):
TCACATATCGATGCCATAGCCCAGCTATAGTCTTACAAGTAA
Found at i:1824764 original size:31 final size:31
Alignment explanation
Indices: 1824726--1824793 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
1824716 TAGCCGAATA
*
1824726 TTCACTGATCAGGTAACCGAAGCTACCATTT
1 TTCACTGATCAGGTAACCGAAGCTACCACTT
*
1824757 TTCACTGATCAGGTAGCCGAAGCTACCACTT
1 TTCACTGATCAGGTAACCGAAGCTACCACTT
1824788 TTCACT
1 TTCACT
1824794 TTCACTTGTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.29
Consensus pattern (31 bp):
TTCACTGATCAGGTAACCGAAGCTACCACTT
Found at i:1827539 original size:13 final size:13
Alignment explanation
Indices: 1827521--1827571 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
1827511 TATGAGAAGA
1827521 GAGAAAAATAAAG
1 GAGAAAAATAAAG
1827534 GAGAAAAATAAGAG
1 GAGAAAAATAA-AG
*
1827548 AATG-AAAATAAA-
1 GA-GAAAAATAAAG
*
1827560 GAAAAAAATAAA
1 GAGAAAAATAAA
1827572 AAAAGTACAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
12 9 0.28
13 12 0.38
14 10 0.31
15 1 0.03
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.10
Consensus pattern (13 bp):
GAGAAAAATAAAG
Found at i:1827546 original size:26 final size:25
Alignment explanation
Indices: 1827517--1827570 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
1827507 AGAATATGAG
*
1827517 AAGAG-AGAAAAATAAAGGAGAAAAAT
1 AAGAGAAG-AAAATAAA-GAAAAAAAT
1827543 AAGAGAATGAAAATAAAGAAAAAAAT
1 AAGAGAA-GAAAATAAAGAAAAAAAT
1827569 AA
1 AA
1827571 AAAAAGTACA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 15 0.60
27 9 0.36
28 1 0.04
ACGTcount: A:0.72, C:0.00, G:0.19, T:0.09
Consensus pattern (25 bp):
AAGAGAAGAAAATAAAGAAAAAAAT
Found at i:1851236 original size:39 final size:39
Alignment explanation
Indices: 1851193--1851268 Score: 152
Period size: 39 Copynumber: 1.9 Consensus size: 39
1851183 ATTTATCATT
1851193 GCAACCAATAATCATTAGTGCTAATATGGCTTAATTATC
1 GCAACCAATAATCATTAGTGCTAATATGGCTTAATTATC
1851232 GCAACCAATAATCATTAGTGCTAATATGGCTTAATTA
1 GCAACCAATAATCATTAGTGCTAATATGGCTTAATTA
1851269 ATTAATGAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (39 bp):
GCAACCAATAATCATTAGTGCTAATATGGCTTAATTATC
Found at i:1853688 original size:27 final size:24
Alignment explanation
Indices: 1853646--1853703 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
1853636 TTTACGTAAA
1853646 AAAATTTCATCAATTTTACTATTTATT
1 AAAATTTCATCAA-TTT-CT-TTTATT
* * *
1853673 AAAATTTCTTCTATTTCTTTTGTT
1 AAAATTTCATCAATTTCTTTTATT
1853697 AAAATTT
1 AAAATTT
1853704 TCATTCATCC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 12 0.43
25 2 0.07
26 3 0.11
27 11 0.39
ACGTcount: A:0.33, C:0.10, G:0.02, T:0.55
Consensus pattern (24 bp):
AAAATTTCATCAATTTCTTTTATT
Found at i:1862981 original size:35 final size:35
Alignment explanation
Indices: 1862937--1863103 Score: 192
Period size: 35 Copynumber: 4.6 Consensus size: 35
1862927 TCCTCATTGA
** *
1862937 AATACCATACCTACATTTTTCAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* ** *
1862972 AATGCCATACCTACATTTCTTAACTCAGTAAGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGT----A-TGGAT
*
1863012 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
1863047 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
1863082 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
1863104 CTTTGCCATG
Statistics
Matches: 114, Mismatches: 12, Indels: 12
0.83 0.09 0.09
Matches are distributed among these distances:
35 84 0.74
36 1 0.01
39 3 0.03
40 26 0.23
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.31
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:1863021 original size:75 final size:73
Alignment explanation
Indices: 1862932--1863103 Score: 217
Period size: 75 Copynumber: 2.4 Consensus size: 73
1862922 GGTTTTCCTC
** * * **
1862932 ATTGAAATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC
1862996 TCAGTAAGG
65 TCAGTAAGG
*
1863005 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
*
1863070 CTCAGTATGG
64 CTCAGTAAGG
1863080 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
1863104 CTTTGCCATG
Statistics
Matches: 88, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
70 21 0.24
73 3 0.03
74 7 0.08
75 57 0.65
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
CAGTAAGG
Found at i:1865287 original size:21 final size:21
Alignment explanation
Indices: 1865261--1865301 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1865251 ATCTGCTCAA
* *
1865261 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
1865282 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
1865302 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:1873384 original size:2 final size:2
Alignment explanation
Indices: 1873377--1873410 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1873367 ATTCAACCTA
1873377 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1873411 GTAAAAGGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1878851 original size:32 final size:33
Alignment explanation
Indices: 1878783--1878851 Score: 95
Period size: 32 Copynumber: 2.1 Consensus size: 33
1878773 TTTTTATTCT
* *
1878783 TTTTGACAAAATACTTAAAACTATTAATAGCTTC
1 TTTTGACAAAATA-TTAAAACTATTAATAACCTC
*
1878817 TTTTGTCAAAAT-TTAAAACTATTAATAACCTC
1 TTTTGACAAAATATTAAAACTATTAATAACCTC
1878849 TTT
1 TTT
1878852 CAACTCGTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 21 0.66
34 11 0.34
ACGTcount: A:0.39, C:0.14, G:0.04, T:0.42
Consensus pattern (33 bp):
TTTTGACAAAATATTAAAACTATTAATAACCTC
Found at i:1885971 original size:10 final size:10
Alignment explanation
Indices: 1885958--1885989 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
1885948 AAAAAACTTA
*
1885958 AAAAATATAT
1 AAAAATACAT
1885968 AAAAATACAT
1 AAAAATACAT
1885978 AAAAATACAT
1 AAAAATACAT
1885988 AA
1 AA
1885990 CTATTTTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (10 bp):
AAAAATACAT
Found at i:1886035 original size:6 final size:6
Alignment explanation
Indices: 1886026--1886050 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1886016 TTTAAATTTT
1886026 ATATTA ATATTA ATATTA ATATTA A
1 ATATTA ATATTA ATATTA ATATTA A
1886051 ATAAAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATATTA
Found at i:1900325 original size:2 final size:2
Alignment explanation
Indices: 1900320--1900345 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1900310 TAGCTATAGA
1900320 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
1900346 TAGATTAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1905785 original size:13 final size:14
Alignment explanation
Indices: 1905769--1905804 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
1905759 CAATCTCATA
1905769 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
1905782 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
1905795 TCTC-ATTTCA
1 TCTCAATTTCA
1905805 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:1905794 original size:18 final size:19
Alignment explanation
Indices: 1905756--1905796 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
1905746 TGGTTCATGT
1905756 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
1905775 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
1905793 TTTC
1 TTTC
1905797 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:1905927 original size:23 final size:23
Alignment explanation
Indices: 1905901--1905958 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
1905891 GCAGATTCCT
*
1905901 CCCAAGCACACCAGAATATCCAA
1 CCCAAACACACCAGAATATCCAA
1905924 CCCAAACACACCAGAATATCCAA
1 CCCAAACACACCAGAATATCCAA
1905947 CCCAAACACACC
1 CCCAAACACACC
1905959 CGGAATATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.45, C:0.43, G:0.05, T:0.07
Consensus pattern (23 bp):
CCCAAACACACCAGAATATCCAA
Found at i:1906349 original size:15 final size:15
Alignment explanation
Indices: 1906329--1906360 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1906319 TATTATATAT
1906329 TTCAATCAATATAAA
1 TTCAATCAATATAAA
1906344 TTCAATCAATATAAA
1 TTCAATCAATATAAA
1906359 TT
1 TT
1906361 TGATAAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (15 bp):
TTCAATCAATATAAA
Found at i:1907317 original size:32 final size:30
Alignment explanation
Indices: 1907281--1907354 Score: 82
Period size: 32 Copynumber: 2.5 Consensus size: 30
1907271 CATACATTTG
1907281 TCATAATTTAATATATTT-ATTACATAAAAATA
1 TCATAATTTAATATATTTAATTA-AT--AAATA
*
1907313 TCATAATATAAT-TATTTAATTAATAAATA
1 TCATAATTTAATATATTTAATTAATAAATA
*
1907342 TC-TTATTTAATAT
1 TCATAATTTAATAT
1907355 TAAATACTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
28 7 0.19
29 8 0.22
31 7 0.19
32 15 0.41
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (30 bp):
TCATAATTTAATATATTTAATTAATAAATA
Found at i:1907875 original size:13 final size:14
Alignment explanation
Indices: 1907857--1907885 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1907847 GATTAACTTC
1907857 ATAAATATTTT-TA
1 ATAAATATTTTCTA
1907870 ATAAATATTTTCTA
1 ATAAATATTTTCTA
1907884 AT
1 AT
1907886 CTATTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAAATATTTTCTA
Found at i:1909211 original size:30 final size:31
Alignment explanation
Indices: 1909150--1909211 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
1909140 ATAAAAATTA
* * *
1909150 TATATAAGTTTTGATTTAATGTGATATTTTAT
1 TATATAAATTTTGATTT-ATGTAAAATTTTAT
1909182 TATATAAATTTTGATTT-TGTAAAATTTTAT
1 TATATAAATTTTGATTTATGTAAAATTTTAT
1909212 ACATAATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 11 0.41
32 16 0.59
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (31 bp):
TATATAAATTTTGATTTATGTAAAATTTTAT
Found at i:1913390 original size:26 final size:26
Alignment explanation
Indices: 1913351--1913403 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
1913341 GGTGCTTTCC
1913351 TGCTGGTCTCCCAGCCGAAATCTGTT
1 TGCTGGTCTCCCAGCCGAAATCTGTT
*
1913377 TGCTGGTCTGCCAGCCGAAATCTGTT
1 TGCTGGTCTCCCAGCCGAAATCTGTT
1913403 T
1 T
1913404 TATGGGAGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.15, C:0.28, G:0.25, T:0.32
Consensus pattern (26 bp):
TGCTGGTCTCCCAGCCGAAATCTGTT
Found at i:1913473 original size:15 final size:15
Alignment explanation
Indices: 1913453--1913482 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1913443 GATTTTATAG
1913453 GATGACCAAATGCAT
1 GATGACCAAATGCAT
*
1913468 GATGACCAATTGCAT
1 GATGACCAAATGCAT
1913483 TTACTTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (15 bp):
GATGACCAAATGCAT
Found at i:1920524 original size:22 final size:23
Alignment explanation
Indices: 1920494--1920538 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1920484 AATAAGCTTC
*
1920494 TTATATATAT-TTTTTGAATTTT
1 TTATATATATCTTTTTCAATTTT
*
1920516 TTATTTATATCTTTTTCAATTTT
1 TTATATATATCTTTTTCAATTTT
1920539 AAATTATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.69
Consensus pattern (23 bp):
TTATATATATCTTTTTCAATTTT
Found at i:1920715 original size:2 final size:2
Alignment explanation
Indices: 1920708--1920744 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1920698 AAATTAACAA
1920708 AT AT AT AT AT AT 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 AT AT AT AT AT AT A
1920745 AACGTTGAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1921281 original size:19 final size:20
Alignment explanation
Indices: 1921239--1921288 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
1921229 AGATATGATC
1921239 AAAATCTAATTATTAAAAAAT
1 AAAAT-TAATTATTAAAAAAT
*
1921260 AAAA-TAATT-TTAAGAAAGT
1 AAAATTAATTATTAA-AAAAT
1921279 AAAATTAATT
1 AAAATTAATT
1921289 CAATTACTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 4 0.15
19 13 0.50
20 5 0.19
21 4 0.15
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (20 bp):
AAAATTAATTATTAAAAAAT
Found at i:1923238 original size:4 final size:4
Alignment explanation
Indices: 1923229--1923257 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
1923219 AAAATAGGAA
1923229 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1923258 TATACAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:1929547 original size:23 final size:22
Alignment explanation
Indices: 1929502--1929547 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
1929492 TTTGAAAATA
1929502 AATTTAAATTTCAAGTTAATTG
1 AATTTAAATTTCAAGTTAATTG
*
1929524 AATTTAATTATTT-AAGTTATTTG
1 AATTTAA--ATTTCAAGTTAATTG
1929547 A
1 A
1929548 TTTTTTTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 7 0.33
23 10 0.48
24 4 0.19
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50
Consensus pattern (22 bp):
AATTTAAATTTCAAGTTAATTG
Found at i:1931605 original size:22 final size:22
Alignment explanation
Indices: 1931561--1931615 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
1931551 TTAAACATAA
* *
1931561 AATATATAAATTTTTTATATTTT
1 AATA-ATATATTTTTAATATTTT
* * *
1931584 ATTATTATATTTTTAATTTTTT
1 AATAATATATTTTTAATATTTT
1931606 AATAATATAT
1 AATAATATAT
1931616 ATATAAATAA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 22 0.88
23 3 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
AATAATATATTTTTAATATTTT
Found at i:1931613 original size:20 final size:21
Alignment explanation
Indices: 1931572--1931613 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
1931562 ATATATAAAT
*
1931572 TTTTTATATTTTATTATTATA
1 TTTTTATATTTTATTATAATA
1931593 TTTTTA-ATTTT-TTAATAATA
1 TTTTTATATTTTATT-ATAATA
1931613 T
1 T
1931614 ATATATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 2 0.11
20 11 0.58
21 6 0.32
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTTTATATTTTATTATAATA
Found at i:1941482 original size:17 final size:16
Alignment explanation
Indices: 1941460--1941507 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
1941450 TTTTTGTAAA
1941460 ATTATATTTTAAATAT
1 ATTATATTTTAAATAT
* *
1941476 GATTATATGTAAAATAT
1 -ATTATATTTTAAATAT
1941493 ATTTAATATTTTAAA
1 A-TT-ATATTTTAAA
1941508 CATAAGTCCA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
16 1 0.04
17 16 0.64
18 8 0.32
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (16 bp):
ATTATATTTTAAATAT
Found at i:1942502 original size:21 final size:22
Alignment explanation
Indices: 1942476--1942516 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1942466 TTCTTTTAAA
1942476 AATTAAAATAATA-ATAAAAAT
1 AATTAAAATAATACATAAAAAT
*
1942497 AATTAAACTAATACATAAAA
1 AATTAAAATAATACATAAAA
1942517 TTAAACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (22 bp):
AATTAAAATAATACATAAAAAT
Found at i:1945623 original size:17 final size:17
Alignment explanation
Indices: 1945569--1945630 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 17
1945559 TGAAAGGTGA
1945569 GAAGTAAAAGTTTAGGG
1 GAAGTAAAAGTTTAGGG
* *
1945586 AGAAAATAAAAAGTTTTGGG
1 -G-AAGT-AAAAGTTTAGGG
1945606 GAA-TAAAAGTTTGAGGG
1 GAAGTAAAAGTTT-AGGG
1945623 GAAGTAAA
1 GAAGTAAA
1945631 TAGGGGGAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
16 8 0.22
17 7 0.19
18 7 0.19
19 4 0.11
20 11 0.30
ACGTcount: A:0.47, C:0.00, G:0.31, T:0.23
Consensus pattern (17 bp):
GAAGTAAAAGTTTAGGG
Found at i:1945750 original size:29 final size:30
Alignment explanation
Indices: 1945706--1945763 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 30
1945696 GGAGGTGGGA
1945706 TGGGAAGGAAGTAAAAATTTTAGGGGAAAG
1 TGGGAAGGAAGTAAAAATTTTAGGGGAAAG
*
1945736 TGGGAGGGAA-TAAAAATTTTAGGGGAAA
1 TGGGAAGGAAGTAAAAATTTTAGGGGAAA
1945764 ATAAAAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.43, C:0.00, G:0.36, T:0.21
Consensus pattern (30 bp):
TGGGAAGGAAGTAAAAATTTTAGGGGAAAG
Found at i:1945992 original size:9 final size:9
Alignment explanation
Indices: 1945978--1946023 Score: 74
Period size: 9 Copynumber: 5.1 Consensus size: 9
1945968 TATAGTTTGA
1945978 TATTCGAAT
1 TATTCGAAT
1945987 TATTCGAAT
1 TATTCGAAT
*
1945996 TATTCGAGT
1 TATTCGAAT
*
1946005 TATTCGAGT
1 TATTCGAAT
1946014 TATTCGAAT
1 TATTCGAAT
1946023 T
1 T
1946024 TGAAAACTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:1946089 original size:9 final size:9
Alignment explanation
Indices: 1946075--1946107 Score: 66
Period size: 9 Copynumber: 3.7 Consensus size: 9
1946065 ATTCGAGTTG
1946075 ACTCGAATA
1 ACTCGAATA
1946084 ACTCGAATA
1 ACTCGAATA
1946093 ACTCGAATA
1 ACTCGAATA
1946102 ACTCGA
1 ACTCGA
1946108 TTCGTTTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.42, C:0.24, G:0.12, T:0.21
Consensus pattern (9 bp):
ACTCGAATA
Found at i:1946559 original size:30 final size:26
Alignment explanation
Indices: 1946534--1946585 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
1946524 TTTTATTCAC
1946534 TTCA-CTAATAAAGTATATAGATTTA
1 TTCATCTAATAAAGTATATAGATTTA
*
1946559 TTGATCTAATAAAGTATATAGATTTA
1 TTCATCTAATAAAGTATATAGATTTA
1946585 T
1 T
1946586 CTGGTATCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 3 0.12
26 22 0.88
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (26 bp):
TTCATCTAATAAAGTATATAGATTTA
Found at i:1954740 original size:2 final size:2
Alignment explanation
Indices: 1954733--1954764 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1954723 AACACTGAAC
*
1954733 CA CA CA CA GA CA CA CA 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
1954765 AAAAAAAAAA
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:0.50, C:0.47, G:0.03, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1961081 original size:46 final size:44
Alignment explanation
Indices: 1960977--1961084 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
1960967 TGTCTTTGAC
** * * *
1960977 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
1961021 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
1961067 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
1961085 TTTCGTTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:1974889 original size:14 final size:14
Alignment explanation
Indices: 1974867--1974906 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1974857 TAACCATAAA
* *
1974867 AAATACAAAACTTT
1 AAATCCAAAACCTT
1974881 AAATCCAAAACCTT
1 AAATCCAAAACCTT
*
1974895 AAATCTAAAACC
1 AAATCCAAAACC
1974907 AAAAACCCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.55, C:0.23, G:0.00, T:0.23
Consensus pattern (14 bp):
AAATCCAAAACCTT
Found at i:1995693 original size:24 final size:25
Alignment explanation
Indices: 1995666--1995712 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
1995656 TAATTAAATT
*
1995666 TTATAAATAATTAATATT-TATTAG
1 TTATAAATAATTAAAATTATATTAG
*
1995690 TTATAAATATTTAAAATTATATT
1 TTATAAATAATTAAAATTATATT
1995713 TCATATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
TTATAAATAATTAAAATTATATTAG
Found at i:1995803 original size:20 final size:20
Alignment explanation
Indices: 1995750--1995803 Score: 51
Period size: 19 Copynumber: 2.8 Consensus size: 20
1995740 TATAATAATT
1995750 TTTAAATATT-TTT-ACTAA
1 TTTAAATATTATTTAACTAA
** *
1995768 AATATAATAATA-TTAACTAA
1 TTTA-AATATTATTTAACTAA
1995788 TTTAAATATTATTTAA
1 TTTAAATATTATTTAA
1995804 ATGCATATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
18 2 0.08
19 13 0.50
20 11 0.42
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (20 bp):
TTTAAATATTATTTAACTAA
Found at i:2003655 original size:89 final size:89
Alignment explanation
Indices: 2003518--2003697 Score: 351
Period size: 89 Copynumber: 2.0 Consensus size: 89
2003508 TTCTATAATC
*
2003518 TCTCTACAGCTCATATTTATAACATTTTCACAAAAAAATTTATATAATATTATTATTTTAACCAT
1 TCTCTACAGCTCATATTTATAACATTTTCACAAAAAAAATTATATAATATTATTATTTTAACCAT
2003583 TTAATCCTTAAATTTAAAAATTAA
66 TTAATCCTTAAATTTAAAAATTAA
2003607 TCTCTACAGCTCATATTTATAACATTTTCACAAAAAAAATTATATAATATTATTATTTTAACCAT
1 TCTCTACAGCTCATATTTATAACATTTTCACAAAAAAAATTATATAATATTATTATTTTAACCAT
2003672 TTAATCCTTAAATTTAAAAATTAA
66 TTAATCCTTAAATTTAAAAATTAA
2003696 TC
1 TC
2003698 AAAGTTACTT
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 90 1.00
ACGTcount: A:0.43, C:0.14, G:0.01, T:0.42
Consensus pattern (89 bp):
TCTCTACAGCTCATATTTATAACATTTTCACAAAAAAAATTATATAATATTATTATTTTAACCAT
TTAATCCTTAAATTTAAAAATTAA
Found at i:2004996 original size:20 final size:19
Alignment explanation
Indices: 2004946--2004998 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
2004936 CTCTTTCAAC
2004946 AAAAATTACAAAATAATTTT
1 AAAAATT-CAAAATAATTTT
*
2004966 TAAAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
2004985 AAAAACTTCAAAAT
1 AAAAA-TTCAAAAT
2004999 TTGTGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 4 0.14
19 11 0.38
20 14 0.48
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:2005184 original size:16 final size:16
Alignment explanation
Indices: 2005165--2005195 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2005155 TTGAAAAAGT
2005165 TTTCAAATATATATGG
1 TTTCAAATATATATGG
*
2005181 TTTCAAATTTATATG
1 TTTCAAATATATATG
2005196 CTAATTATAT
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:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGG
Found at i:2005477 original size:15 final size:15
Alignment explanation
Indices: 2005457--2005485 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2005447 AAATCGATAA
2005457 TAATAATATTAATAT
1 TAATAATATTAATAT
2005472 TAATAATATTAATA
1 TAATAATATTAATA
2005486 AAACCAACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TAATAATATTAATAT
Found at i:2010663 original size:14 final size:14
Alignment explanation
Indices: 2010644--2010688 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
2010634 CCTGCAAGCC
*
2010644 ATATATGTCAATAT
1 ATATATGTCTATAT
2010658 ATATATGTCTATAT
1 ATATATGTCTATAT
*
2010672 ATATGTGTCTATAT
1 ATATATGTCTATAT
2010686 ATA
1 ATA
2010689 ATTTTAAGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.47
Consensus pattern (14 bp):
ATATATGTCTATAT
Found at i:2029382 original size:2 final size:2
Alignment explanation
Indices: 2029375--2029399 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2029365 TTATACATGT
2029375 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 A
2029400 TTAAGGGTGA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2054001 original size:36 final size:36
Alignment explanation
Indices: 2053955--2054056 Score: 108
Period size: 36 Copynumber: 2.9 Consensus size: 36
2053945 GGGGGTGACA
*
2053955 GTGGTGGTGGTGGAGGTGAATGGTAAATAACTGAAG
1 GTGGTGGTGGTGGAGGTGAATGGTAAATAACTGAAC
* *
2053991 GTGGTGGTGGTGGTGGTG-A-GG-AATATGTTAC--AAC
1 GTGGTGGTGGTGGAGGTGAATGGTAA-A--TAACTGAAC
2054025 G-GGTGGTGGTGGAGGTGAATGGTAAATAACTG
1 GTGGTGGTGGTGGAGGTGAATGGTAAATAACTG
2054057 GAGGCGGCGG
Statistics
Matches: 53, Mismatches: 5, Indels: 17
0.71 0.07 0.23
Matches are distributed among these distances:
33 20 0.38
34 7 0.13
35 4 0.08
36 22 0.42
ACGTcount: A:0.25, C:0.04, G:0.45, T:0.26
Consensus pattern (36 bp):
GTGGTGGTGGTGGAGGTGAATGGTAAATAACTGAAC
Found at i:2054072 original size:69 final size:70
Alignment explanation
Indices: 2053957--2054111 Score: 213
Period size: 69 Copynumber: 2.2 Consensus size: 70
2053947 GGGTGACAGT
* * *
2053957 GGTGGTGGTGGAGGTGAATGGTAAATAACTGAAGGTGGTGG-TGGTGGTGGTGAGGAATATGTTA
1 GGTGGTGGTGGAGGTGAATGGTAAATAACTGAAGGCGGCGGCGGGTGGTGGTGAGGAATATGTTA
2054021 CAACG
66 CAACG
*
2054026 GGTGGTGGTGGAGGTGAATGGTAAATAACTGGAGGCGGCGGCGGTGGTGGTGGTGGTGAGGAATA
1 GGTGGTGGTGGAGGTGAATGGTAAATAACTGAAGGCGGCGGC----G-GGTGGTGGTGAGGAATA
2054091 TGTTACAACG
61 TGTTACAACG
*
2054101 GGTGGCGGTGG
1 GGTGGTGGTGG
2054112 TGAAGGTGAT
Statistics
Matches: 75, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
69 38 0.51
75 37 0.49
ACGTcount: A:0.21, C:0.06, G:0.48, T:0.24
Consensus pattern (70 bp):
GGTGGTGGTGGAGGTGAATGGTAAATAACTGAAGGCGGCGGCGGGTGGTGGTGAGGAATATGTTA
CAACG
Found at i:2054086 original size:75 final size:69
Alignment explanation
Indices: 2053957--2054111 Score: 229
Period size: 75 Copynumber: 2.2 Consensus size: 69
2053947 GGGTGACAGT
*
2053957 GGTGGTGGTGGAGGTGAATGGTAAATAACTGAAGGTGGTGGTGGTGGTGGTGAGGAATATGTTAC
1 GGTGGTGGTGGAGGTGAATGGTAAATAACTGAAGGCGGTGGTGGTGGTGGTGAGGAATATGTTAC
2054022 AACG
66 AACG
*
2054026 GGTGGTGGTGGAGGTGAATGGTAAATAACTGGAGGCGGCGGCGGTGGTGGTGGTGGTGAGGAATA
1 GGTGGTGGTGGAGGTGAATGGTAAATAACT-GA-----AGGCGGTGGTGGTGGTGGTGAGGAATA
2054091 TGTTACAACG
60 TGTTACAACG
*
2054101 GGTGGCGGTGG
1 GGTGGTGGTGG
2054112 TGAAGGTGAT
Statistics
Matches: 77, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
69 30 0.39
70 2 0.03
75 45 0.58
ACGTcount: A:0.21, C:0.06, G:0.48, T:0.24
Consensus pattern (69 bp):
GGTGGTGGTGGAGGTGAATGGTAAATAACTGAAGGCGGTGGTGGTGGTGGTGAGGAATATGTTAC
AACG
Found at i:2054536 original size:39 final size:39
Alignment explanation
Indices: 2054493--2054598 Score: 122
Period size: 39 Copynumber: 2.7 Consensus size: 39
2054483 ATATTGGCGC
* * *
2054493 AGGTGGTGAGGGTGAAGGGGGCGGTGGTAACGGATAAGT
1 AGGTGGTGGGGGTGAAGGAGGTGGTGGTAACGGATAAGT
* * * * * *
2054532 AGGTGGCGGGGGTGAAGGCGGTGGAGGTGATGGATATGT
1 AGGTGGTGGGGGTGAAGGAGGTGGTGGTAACGGATAAGT
*
2054571 AGGGGGTGGGGGTGAAGGAGGTGGTGGT
1 AGGTGGTGGGGGTGAAGGAGGTGGTGGT
2054599 GAGGGCGGTG
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.19, C:0.04, G:0.58, T:0.19
Consensus pattern (39 bp):
AGGTGGTGGGGGTGAAGGAGGTGGTGGTAACGGATAAGT
Found at i:2054599 original size:15 final size:15
Alignment explanation
Indices: 2054575--2054627 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
2054565 ATATGTAGGG
*
2054575 GGTGGGGGTGAAGGA
1 GGTGGAGGTGAAGGA
* * *
2054590 GGTGGTGGTGAGGGC
1 GGTGGAGGTGAAGGA
* *
2054605 GGTGGAGGTGATGGT
1 GGTGGAGGTGAAGGA
2054620 GGTGGAGG
1 GGTGGAGG
2054628 AGGTGGAGAG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.13, C:0.02, G:0.66, T:0.19
Consensus pattern (15 bp):
GGTGGAGGTGAAGGA
Found at i:2054651 original size:54 final size:54
Alignment explanation
Indices: 2054536--2054653 Score: 123
Period size: 54 Copynumber: 2.2 Consensus size: 54
2054526 ATAAGTAGGT
* * * * *
2054536 GGCGGGGGTGAAGGCGGTGGAGGTGATGGATATGTAGGGGGTGGGGGTGAAGGA
1 GGCGGTGGTGAAGGCGGTGGAGGTGATGGATATGGAGGAGGTGGGAGTGAAAGA
* * * *
2054590 GGTGGTGGTGAGGGCGGTGGAGGTGATGG-TGGTGGAGGAGGTGGAGAGT-AAATA
1 GGCGGTGGTGAAGGCGGTGGAGGTGATGGAT-ATGGAGGAGGTGG-GAGTGAAAGA
2054644 GGCGGTGGTG
1 GGCGGTGGTG
2054654 GTGGCGGAGG
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
53 1 0.02
54 48 0.92
55 3 0.06
ACGTcount: A:0.18, C:0.03, G:0.60, T:0.19
Consensus pattern (54 bp):
GGCGGTGGTGAAGGCGGTGGAGGTGATGGATATGGAGGAGGTGGGAGTGAAAGA
Found at i:2056387 original size:102 final size:102
Alignment explanation
Indices: 2056255--2056459 Score: 365
Period size: 102 Copynumber: 2.0 Consensus size: 102
2056245 GTTTGAGGAG
* * *
2056255 AGAGACAAGGGGATGAAAGGGTGTTTTTCTAGTAGGAATTGTAGGGCATGTGCTTGTGTGAGAGA
1 AGAGACAAAGGGATGAAAGGGTGTTTTTCTAGTAGGAATCGTAGGGCATGTGCTTGTGTAAGAGA
* *
2056320 AATGAAAATAACAATAATAAAAAGAAGGAGAAGAAAA
66 AAGGAAAAAAACAATAATAAAAAGAAGGAGAAGAAAA
2056357 AGAGACAAAGGGATGAAAGGGTGTTTTTCTAGTAGGAATCGTAGGGCATGTGCTTGTGTAAGAGA
1 AGAGACAAAGGGATGAAAGGGTGTTTTTCTAGTAGGAATCGTAGGGCATGTGCTTGTGTAAGAGA
2056422 AAGGAAAAAAACAATAATAAAAAGAAGGAGAAGAAAA
66 AAGGAAAAAAACAATAATAAAAAGAAGGAGAAGAAAA
2056459 A
1 A
2056460 AAGAAATAAT
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 98 1.00
ACGTcount: A:0.45, C:0.05, G:0.30, T:0.20
Consensus pattern (102 bp):
AGAGACAAAGGGATGAAAGGGTGTTTTTCTAGTAGGAATCGTAGGGCATGTGCTTGTGTAAGAGA
AAGGAAAAAAACAATAATAAAAAGAAGGAGAAGAAAA
Found at i:2060903 original size:19 final size:20
Alignment explanation
Indices: 2060865--2060903 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
2060855 AAATATTTAC
*
2060865 AAATATCAAATAATAAAATT
1 AAATATCAAAAAATAAAATT
*
2060885 AAATAT-AAAAAATATAATT
1 AAATATCAAAAAATAAAATT
2060904 TTGGTTAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (20 bp):
AAATATCAAAAAATAAAATT
Found at i:2068903 original size:15 final size:15
Alignment explanation
Indices: 2068883--2068911 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2068873 TCTATTTCCA
2068883 AAAATATATTATTAC
1 AAAATATATTATTAC
2068898 AAAATATATTATTA
1 AAAATATATTATTA
2068912 ATACTATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAATATATTATTAC
Found at i:2082661 original size:20 final size:20
Alignment explanation
Indices: 2082609--2082651 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
2082599 ATTAGTATTC
2082609 TTATCCTGAATTTTAGAATT
1 TTATCCTGAATTTTAGAATT
*
2082629 TTATCCTGAATTTTAGTATT
1 TTATCCTGAATTTTAGAATT
2082649 TTA
1 TTA
2082652 ATTTGAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.53
Consensus pattern (20 bp):
TTATCCTGAATTTTAGAATT
Found at i:2087783 original size:19 final size:19
Alignment explanation
Indices: 2087759--2087797 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2087749 GACCTTCATT
*
2087759 TTTTATTATTA-TTTATAAA
1 TTTTA-TATTAGTTGATAAA
2087778 TTTTATATTAGTTGATAAA
1 TTTTATATTAGTTGATAAA
2087797 T
1 T
2087798 AATGTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
TTTTATATTAGTTGATAAA
Found at i:2091842 original size:23 final size:23
Alignment explanation
Indices: 2091816--2091859 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2091806 TCTAGTAGTG
*
2091816 ATTTAATTAACATGCATGAATAT
1 ATTTAATTAAAATGCATGAATAT
* *
2091839 ATTTATTTAAAATGCGTGAAT
1 ATTTAATTAAAATGCATGAAT
2091860 GTAATAGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (23 bp):
ATTTAATTAAAATGCATGAATAT
Found at i:2092016 original size:22 final size:22
Alignment explanation
Indices: 2091970--2092016 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2091960 GCTTCCAACA
* * * *
2091970 ATATATTTTGATTTTTTTATTC
1 ATATATTTTGAATCTTTGATGC
2091992 ATATATTTTGAATCTTTGATGC
1 ATATATTTTGAATCTTTGATGC
2092014 ATA
1 ATA
2092017 CATAATTACC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.28, C:0.06, G:0.09, T:0.57
Consensus pattern (22 bp):
ATATATTTTGAATCTTTGATGC
Found at i:2092378 original size:33 final size:33
Alignment explanation
Indices: 2092336--2092406 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
2092326 GTTGAAATAC
* *
2092336 TAATCTTAAATATACCCTCTAATTAAATGCCTA
1 TAATTTTAAATATACCCTCGAATTAAATGCCTA
2092369 TAATTTTAAATATACCCTCGAATTAAATGCCTA
1 TAATTTTAAATATACCCTCGAATTAAATGCCTA
2092402 TAATT
1 TAATT
2092407 AGGGTTGGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.39, C:0.18, G:0.04, T:0.38
Consensus pattern (33 bp):
TAATTTTAAATATACCCTCGAATTAAATGCCTA
Found at i:2096908 original size:30 final size:31
Alignment explanation
Indices: 2096872--2096933 Score: 99
Period size: 30 Copynumber: 2.0 Consensus size: 31
2096862 AAATAGAAGC
2096872 CTGGAATCATCGAGGT-ATTACTAATATCGG
1 CTGGAATCATCGAGGTAATTACTAATATCGG
2096902 CTGGAATCATCGAGGTGAAATTACTAATATCG
1 CTGGAATCATCGAGGT--AATTACTAATATCG
2096934 TCAATAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
30 16 0.55
33 13 0.45
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (31 bp):
CTGGAATCATCGAGGTAATTACTAATATCGG
Found at i:2100042 original size:1 final size:1
Alignment explanation
Indices: 2100036--2100063 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
2100026 CTTCTTCATC
2100036 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
2100064 AACTGGAGGT
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:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:2103418 original size:30 final size:30
Alignment explanation
Indices: 2103361--2103418 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
2103351 AAGAACATAC
* * *
2103361 AGAAAACAGTTTAAAACTTTCCCAATTTAA
1 AGAAAACAGTTAAAAACTTTACAAATTTAA
2103391 AGAAAA-AGTTAAAAACTTTAACAAATTT
1 AGAAAACAGTTAAAAACTTT-ACAAATTT
2103419 CAGCATCCGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.52, C:0.12, G:0.07, T:0.29
Consensus pattern (30 bp):
AGAAAACAGTTAAAAACTTTACAAATTTAA
Found at i:2103725 original size:2 final size:2
Alignment explanation
Indices: 2103715--2103746 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
2103705 AACGTTGGGA
2103715 AT AT GAT 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 AT AT AT A
2103747 CCTTTTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2104510 original size:48 final size:48
Alignment explanation
Indices: 2104415--2104511 Score: 113
Period size: 48 Copynumber: 2.0 Consensus size: 48
2104405 ATATTGTTAT
* * * ** * *
2104415 TTTTATTTTTATTTAAAAATTAATATATTTTAATTCCCAATCTAATCA
1 TTTTATTTTGATTTAAAAAATAAAATATTTTAATGACCAACCCAATCA
* *
2104463 TTTTATTTTGATTTAAAAAATAAAATATTTTAGTGATCAACCCAATCA
1 TTTTATTTTGATTTAAAAAATAAAATATTTTAATGACCAACCCAATCA
2104511 T
1 T
2104512 GCTTTATATA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.39, C:0.10, G:0.03, T:0.47
Consensus pattern (48 bp):
TTTTATTTTGATTTAAAAAATAAAATATTTTAATGACCAACCCAATCA
Found at i:2104523 original size:2 final size:2
Alignment explanation
Indices: 2104516--2104550 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2104506 AATCATGCTT
2104516 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 T
2104551 TTCAAATAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2118550 original size:22 final size:22
Alignment explanation
Indices: 2118525--2118609 Score: 79
Period size: 22 Copynumber: 3.9 Consensus size: 22
2118515 GGTATAACTC
2118525 TAAAAGTAAAAATATATTT-TAA
1 TAAAA-TAAAAATATATTTATAA
*
2118547 TAAAA-ACAAAATATTTTTTATAA
1 TAAAATA-AAAATA-TATTTATAA
*
2118570 TAAAAT-AAAATCTATTTAATAA
1 TAAAATAAAAATATATTT-ATAA
*
2118592 TAAAAT-AAAATCTATTTA
1 TAAAATAAAAATATATTTA
2118610 ATCTTTAGAA
Statistics
Matches: 55, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
20 1 0.02
21 11 0.20
22 35 0.64
23 8 0.15
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.38
Consensus pattern (22 bp):
TAAAATAAAAATATATTTATAA
Found at i:2118610 original size:22 final size:22
Alignment explanation
Indices: 2118566--2118611 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
2118556 AATATTTTTT
2118566 ATAATAAAATAAAATCTATTTA
1 ATAATAAAATAAAATCTATTTA
2118588 ATAATAAAATAAAATCTATTTA
1 ATAATAAAATAAAATCTATTTA
2118610 AT
1 AT
2118612 CTTTAGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (22 bp):
ATAATAAAATAAAATCTATTTA
Found at i:2123000 original size:39 final size:39
Alignment explanation
Indices: 2122953--2123028 Score: 152
Period size: 39 Copynumber: 1.9 Consensus size: 39
2122943 TATTATGTTC
2122953 ATTAAACTCCTATATGCTATAGGACATGGGCTTCAATAT
1 ATTAAACTCCTATATGCTATAGGACATGGGCTTCAATAT
2122992 ATTAAACTCCTATATGCTATAGGACATGGGCTTCAAT
1 ATTAAACTCCTATATGCTATAGGACATGGGCTTCAAT
2123029 TCCCACCAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (39 bp):
ATTAAACTCCTATATGCTATAGGACATGGGCTTCAATAT
Found at i:2123795 original size:20 final size:19
Alignment explanation
Indices: 2123772--2123813 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
2123762 ATGAAAATAA
2123772 AAATATATTT-TAATAAAAAT
1 AAAT-TATTTATAAT-AAAAT
*
2123792 AAATTTTTTATAATAAAAT
1 AAATTATTTATAATAAAAT
2123811 AAA
1 AAA
2123814 ATCTATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AAATTATTTATAATAAAAT
Found at i:2123804 original size:17 final size:16
Alignment explanation
Indices: 2123767--2123798 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2123757 TAACTATGAA
*
2123767 AATAAAAATATATTTT
1 AATAAAAATAAATTTT
2123783 AATAAAAATAAATTTT
1 AATAAAAATAAATTTT
2123799 TTATAATAAA
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATAAAAATAAATTTT
Found at i:2123824 original size:19 final size:19
Alignment explanation
Indices: 2123765--2123825 Score: 52
Period size: 20 Copynumber: 3.1 Consensus size: 19
2123755 TATAACTATG
2123765 AAAATAAAAATATATTTTAAT
1 AAAAT-AAAATATA-TTTAAT
* *
2123786 AAAA-ATAAATTTTTTATAAT
1 AAAATA-AAATATATT-TAAT
*
2123806 AAAATAAAATCTATTTAAT
1 AAAATAAAATATATTTAAT
2123825 A
1 A
2123826 TTTAGAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
19 8 0.24
20 20 0.61
21 5 0.15
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATAAAATATATTTAAT
Found at i:2132311 original size:21 final size:21
Alignment explanation
Indices: 2132259--2132313 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
2132249 TTCAAAACAG
2132259 AATTAACTTA-TT-AATTATT
1 AATTAACTTATTTAAATTATT
*
2132278 AATTAA-TAAATTTAAATTATT
1 AATTAACT-TATTTAAATTATT
2132299 AATTAACTTATTTAA
1 AATTAACTTATTTAA
2132314 GTATGAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 1 0.03
19 7 0.23
20 2 0.07
21 19 0.63
22 1 0.03
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (21 bp):
AATTAACTTATTTAAATTATT
Found at i:2134594 original size:7 final size:7
Alignment explanation
Indices: 2134582--2134624 Score: 86
Period size: 7 Copynumber: 6.1 Consensus size: 7
2134572 TTCTTCTGCT
2134582 TTTTAAA
1 TTTTAAA
2134589 TTTTAAA
1 TTTTAAA
2134596 TTTTAAA
1 TTTTAAA
2134603 TTTTAAA
1 TTTTAAA
2134610 TTTTAAA
1 TTTTAAA
2134617 TTTTAAA
1 TTTTAAA
2134624 T
1 T
2134625 ATAATTATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TTTTAAA
Found at i:2149584 original size:17 final size:17
Alignment explanation
Indices: 2149562--2149596 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2149552 CTTAAGATAG
2149562 TTTATTACTAATTAATT
1 TTTATTACTAATTAATT
2149579 TTTATTACTAATTAATT
1 TTTATTACTAATTAATT
2149596 T
1 T
2149597 GCTGCTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTATTACTAATTAATT
Found at i:2149718 original size:69 final size:70
Alignment explanation
Indices: 2149586--2149718 Score: 205
Period size: 69 Copynumber: 1.9 Consensus size: 70
2149576 ATTTTTATTA
* * * *
2149586 CTAATTAATTTGCTGCTATAATGCTGTAAATTATTGGCTGTCCAAATTAGCACAAATTTATGGTA
1 CTAATTAATATGCTGCTATAATACTGTAAATTATTGGCTGTCCAAATTAGCACAAAATCATGGTA
2149651 CTTAG
66 CTTAG
* *
2149656 CTAATTAATATGCTGCTGTAATACT-TAAATTATTGGCTGTCCAAATTAGGACAAAATCATGGT
1 CTAATTAATATGCTGCTATAATACTGTAAATTATTGGCTGTCCAAATTAGCACAAAATCATGGT
2149719 GTTATGTGCT
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
69 35 0.61
70 22 0.39
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (70 bp):
CTAATTAATATGCTGCTATAATACTGTAAATTATTGGCTGTCCAAATTAGCACAAAATCATGGTA
CTTAG
Found at i:2150547 original size:40 final size:40
Alignment explanation
Indices: 2150499--2150731 Score: 301
Period size: 40 Copynumber: 5.9 Consensus size: 40
2150489 GTCCGCAAGT
2150499 TTCGTGCTGGAATTGTATCCGGGCTTAAAGACCCGCAGGC
1 TTCGTGCTGGAATTGTATCCGGGCTTAAAGACCCGCAGGC
* *
2150539 TGT-ATGCTGGAATTATATCCGGGCTTAAAGACCCGCAGGC
1 T-TCGTGCTGGAATTGTATCCGGGCTTAAAGACCCGCAGGC
* * **
2150579 TTTGTGCTGGAATTGTATCCGGACTT-AAGGTCCGCAGGC
1 TTCGTGCTGGAATTGTATCCGGGCTTAAAGACCCGCAGGC
* *
2150618 TTCGTGCTGGAATTGTATCTGGGCTTAAAGACCCACAGGC
1 TTCGTGCTGGAATTGTATCCGGGCTTAAAGACCCGCAGGC
* * * *
2150658 TTCGTGATGAAATTGTATCTGAGCTTAAAGACCCGCAGGC
1 TTCGTGCTGGAATTGTATCCGGGCTTAAAGACCCGCAGGC
* * *
2150698 TTCATGCTGGAATTGTATTCGGACTT-AAGACCCG
1 TTCGTGCTGGAATTGTATCCGGGCTTAAAGACCCG
2150732 TAAGCTTTGT
Statistics
Matches: 166, Mismatches: 24, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
39 43 0.26
40 122 0.73
41 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (40 bp):
TTCGTGCTGGAATTGTATCCGGGCTTAAAGACCCGCAGGC
Found at i:2150628 original size:79 final size:80
Alignment explanation
Indices: 2150502--2150742 Score: 301
Period size: 79 Copynumber: 3.0 Consensus size: 80
2150492 CGCAAGTTTC
* *
2150502 GTGCTGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTGT-ATGCTGGAATTATATCCGGGCTTA
1 GTGCTGGAATTGTATCCGGACTTAAAGACCCGCAGGCT-TCATGCTGGAATTGTATCCGGGCTTA
2150566 AAGACCCGCAGGCTTT
65 AAGACCCGCAGGCTTT
** * *
2150582 GTGCTGGAATTGTATCCGGACTT-AAGGTCCGCAGGCTTCGTGCTGGAATTGTATCTGGGCTTAA
1 GTGCTGGAATTGTATCCGGACTTAAAGACCCGCAGGCTTCATGCTGGAATTGTATCCGGGCTTAA
* *
2150646 AGACCCACAGGCTTC
66 AGACCCGCAGGCTTT
* * * * *
2150661 GTGATGAAATTGTAT-CTGAGCTTAAAGACCCGCAGGCTTCATGCTGGAATTGTATTCGGACTT-
1 GTGCTGGAATTGTATCCGGA-CTTAAAGACCCGCAGGCTTCATGCTGGAATTGTATCCGGGCTTA
* *
2150724 AAGACCCGTAAGCTTT
65 AAGACCCGCAGGCTTT
2150740 GTG
1 GTG
2150743 TTGGTGATTG
Statistics
Matches: 137, Mismatches: 21, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
78 4 0.03
79 78 0.57
80 55 0.40
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (80 bp):
GTGCTGGAATTGTATCCGGACTTAAAGACCCGCAGGCTTCATGCTGGAATTGTATCCGGGCTTAA
AGACCCGCAGGCTTT
Found at i:2150686 original size:119 final size:119
Alignment explanation
Indices: 2150475--2150726 Score: 362
Period size: 119 Copynumber: 2.1 Consensus size: 119
2150465 ATTTGATGTA
* * *
2150475 TATCCAGACTTAAGGTCCGCAAGTTTCGTGCTGGAATTGTATCCGGGCTTAAAGACCCGCAGGCT
1 TATCCGGACTTAAGGTCCGCAAGCTTCGTGCTGGAATTGTATCCGGGCTTAAAGACCCACAGGCT
* * * **
2150540 GTATGCTGGAATTATATCCGGGCTTAAAGACCCGCAGGCTTTGTGCTGGAATTG
66 GTATGATGAAATTATATCCGAGCTTAAAGACCCGCAGGCTTCATGCTGGAATTG
* *
2150594 TATCCGGACTTAAGGTCCGCAGGCTTCGTGCTGGAATTGTATCTGGGCTTAAAGACCCACAGGCT
1 TATCCGGACTTAAGGTCCGCAAGCTTCGTGCTGGAATTGTATCCGGGCTTAAAGACCCACAGGCT
* * *
2150659 -TCGTGATGAAATTGTATCTGAGCTTAAAGACCCGCAGGCTTCATGCTGGAATTG
66 GT-ATGATGAAATTATATCCGAGCTTAAAGACCCGCAGGCTTCATGCTGGAATTG
*
2150713 TATTCGGACTTAAG
1 TATCCGGACTTAAG
2150727 ACCCGTAAGC
Statistics
Matches: 118, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
118 1 0.01
119 117 0.99
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.28
Consensus pattern (119 bp):
TATCCGGACTTAAGGTCCGCAAGCTTCGTGCTGGAATTGTATCCGGGCTTAAAGACCCACAGGCT
GTATGATGAAATTATATCCGAGCTTAAAGACCCGCAGGCTTCATGCTGGAATTG
Found at i:2152428 original size:55 final size:53
Alignment explanation
Indices: 2152346--2152499 Score: 195
Period size: 55 Copynumber: 2.9 Consensus size: 53
2152336 GGGGTGTTAC
** * *
2152346 AGTTC-TAAGGCAAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATA
1 AGTTCATAAGGCAAGGCTACCATGTAAGACCATGCCAAGACATGGCATTGATA
* * * *
2152398 AGTTACCATAAGGCAAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTG
1 AGTT--CATAAGGC-AAGGCTACCATGTAAGACCATGCCAAGACATGGCATTGATA
2152453 AGTTCATAAGGCAAGGCTACCATGTAAGACCATGCCAAGACATGGCA
1 AGTTCATAAGGCAAGGCTACCATGTAAGACCATGCCAAGACATGGCA
2152500 ATGGTAAGAA
Statistics
Matches: 88, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
52 8 0.09
53 36 0.41
54 1 0.01
55 39 0.44
56 4 0.05
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (53 bp):
AGTTCATAAGGCAAGGCTACCATGTAAGACCATGCCAAGACATGGCATTGATA
Found at i:2152484 original size:53 final size:52
Alignment explanation
Indices: 2152346--2152507 Score: 200
Period size: 53 Copynumber: 3.0 Consensus size: 52
2152336 GGGGTGTTAC
* * * *
2152346 AGTTC-TAAGGCAAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATA
1 AGTTCATAAGGCAAGG-TACCATGTAAGACCATGCCAAGACATGGCATTGGTA
* * *
2152398 AGTTACCATAAGGCAAAGGTCCCATGTAAGACCATGCCAAGGCATGGCATTGGTG
1 AGTT--CATAAGGC-AAGGTACCATGTAAGACCATGCCAAGACATGGCATTGGTA
*
2152453 AGTTCATAAGGCAAGGCTACCATGTAAGACCATGCCAAGACATGGCAATGGTA
1 AGTTCATAAGGCAAGG-TACCATGTAAGACCATGCCAAGACATGGCATTGGTA
2152506 AG
1 AG
2152508 AAAAAGGATA
Statistics
Matches: 94, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
52 8 0.09
53 42 0.45
54 1 0.01
55 39 0.41
56 4 0.04
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.20
Consensus pattern (52 bp):
AGTTCATAAGGCAAGGTACCATGTAAGACCATGCCAAGACATGGCATTGGTA
Found at i:2152543 original size:46 final size:46
Alignment explanation
Indices: 2152465--2152553 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
2152455 TTCATAAGGC
* * *
2152465 AAGGCTACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGAAA
1 AAGGATACCACGTAAGACCATGACAAGACATGGCAATGGTAAGAAA
*
2152511 AAGGATACCACGTAAGACCATGACAAGTCATGGCAATGGTAAG
1 AAGGATACCACGTAAGACCATGACAAGACATGGCAATGGTAAG
2152554 GTACCCGTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.40, C:0.19, G:0.25, T:0.16
Consensus pattern (46 bp):
AAGGATACCACGTAAGACCATGACAAGACATGGCAATGGTAAGAAA
Found at i:2162341 original size:50 final size:51
Alignment explanation
Indices: 2162264--2162384 Score: 183
Period size: 50 Copynumber: 2.4 Consensus size: 51
2162254 GACCATGGAA
*
2162264 ACAAGTGATAAGTGATAGCTTCGGCTACATTTATCTGATCAA-GGACAAATG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGG-CAAATG
2162315 A-AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGGCAAATG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGGCAAATG
* * *
2162365 ACAACTGAAAAGTGGTAGCT
1 ACAAGTGATAAGTGATAGCT
2162385 CCAGCTACCT
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
50 46 0.72
51 18 0.28
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (51 bp):
ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGGCAAATG
Found at i:2162454 original size:31 final size:31
Alignment explanation
Indices: 2162370--2162444 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
2162360 AAATGACAAC
* * *
2162370 TGAAAAGTGGTAGCTCCAGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCTGCTACCTAATCAG
2162401 TGAAAAGTGGTAGCTTCTGCTACCTAATCAG
1 TGAAAAGTGGTAGCTTCTGCTACCTAATCAG
*
2162432 TGAATAGTGGTAG
1 TGAAAAGTGGTAG
2162445 TTTTGGCTAC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (31 bp):
TGAAAAGTGGTAGCTTCTGCTACCTAATCAG
Found at i:2162608 original size:47 final size:47
Alignment explanation
Indices: 2162483--2162608 Score: 146
Period size: 47 Copynumber: 2.7 Consensus size: 47
2162473 CAAGTGATTT
* *
2162483 CTGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTA
1 CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGCTA
** * * *
2162530 CTGTATAAGACCATATCAAGGATATGACATCAGTGAGATATGTGATTA
1 CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATG-CTA
* * *
2162578 C-GTGTAAGACCATAGCTGGGCTATGGCATCA
1 CTGTATAAGACCATATCTGGGATATGGCATCA
2162609 TTATGTAAAG
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
47 62 0.95
48 3 0.05
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.29
Consensus pattern (47 bp):
CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGCTA
Found at i:2165641 original size:30 final size:30
Alignment explanation
Indices: 2165595--2165654 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
2165585 TTCCCGAGTC
* *
2165595 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGAAAAAATGTAATTATGCAAAAGTT
* *
2165625 TAGGGGAAAAAATGTAATTTTGCCAAAGTT
1 TAGGGGAAAAAATGTAATTATGCAAAAGTT
2165655 CGTATTAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.40, C:0.07, G:0.25, T:0.28
Consensus pattern (30 bp):
TAGGGGAAAAAATGTAATTATGCAAAAGTT
Found at i:2170458 original size:21 final size:21
Alignment explanation
Indices: 2170434--2170475 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2170424 TCATCAGATA
*
2170434 TACACCTTGAGGCATCGGGGG
1 TACACCTTGAGGAATCGGGGG
**
2170455 TACAGGTTGAGGAATCGGGGG
1 TACACCTTGAGGAATCGGGGG
2170476 AGGTGGGGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.17, G:0.43, T:0.19
Consensus pattern (21 bp):
TACACCTTGAGGAATCGGGGG
Found at i:2172735 original size:30 final size:30
Alignment explanation
Indices: 2172700--2172759 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
2172690 ATTTAATACG
2172700 AACTTTGGCAAAATTACAATTTTGCCCCTA
1 AACTTTGGCAAAATTACAATTTTGCCCCTA
* * * *
2172730 AACTTTTGCATAATTACACTTTTTCCCCTA
1 AACTTTGGCAAAATTACAATTTTGCCCCTA
2172760 GACTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.38
Consensus pattern (30 bp):
AACTTTGGCAAAATTACAATTTTGCCCCTA
Found at i:2175479 original size:22 final size:22
Alignment explanation
Indices: 2175454--2175495 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2175444 ATAGCTAAAG
2175454 TTAAAT-TTAAAATATAAAAAAA
1 TTAAATATT-AAATATAAAAAAA
*
2175476 TTAAATATTAAATATTAAAA
1 TTAAATATTAAATATAAAAA
2175496 TTATGAAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
TTAAATATTAAATATAAAAAAA
Found at i:2186221 original size:16 final size:16
Alignment explanation
Indices: 2186196--2186226 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2186186 TTAGGTTTTA
*
2186196 ATTTTGTTAAGTGATG
1 ATTTTATTAAGTGATG
2186212 ATTTTATTAAGTGAT
1 ATTTTATTAAGTGAT
2186227 TTCAATAGAA
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:0.29, C:0.00, G:0.19, T:0.52
Consensus pattern (16 bp):
ATTTTATTAAGTGATG
Found at i:2186879 original size:33 final size:34
Alignment explanation
Indices: 2186807--2186882 Score: 88
Period size: 33 Copynumber: 2.3 Consensus size: 34
2186797 ATGTTTAAAT
* *
2186807 GTAAGACCATACCTGGGTTATGGCATTTCAGTGAA
1 GTAAGACCATAACTGAGTTATGGCATTT-AGTGAA
2186842 --AAGACCATAACTGAGTTATGGCA-TT-GTGAA
1 GTAAGACCATAACTGAGTTATGGCATTTAGTGAA
2186872 CGTAAGACCAT
1 -GTAAGACCAT
2186883 GGTTGGACCA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
30 5 0.14
32 2 0.06
33 29 0.81
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (34 bp):
GTAAGACCATAACTGAGTTATGGCATTTAGTGAA
Found at i:2186950 original size:103 final size:97
Alignment explanation
Indices: 2186787--2187036 Score: 248
Period size: 103 Copynumber: 2.5 Consensus size: 97
2186777 ACCATGTTTA
* * * *
2186787 GACCATGGCAATGTTTAAATGTAAGACCATACCTGGGTTATGGCATTTCAGTGAAAAGACCATAA
1 GACCATGGCAAT-ATT-CATGTAAGACCATAGCTGGGCTATGGCA--TCAGTGAAAAGACCATAA
* ** **
2186852 CTGAGTTATGGCATTGTGAACGTAAGACCATGGTTG
62 CTGAGTTATGGCACTACGAACGTAAGACCATGGCAG
* *
2186888 GACCATGGCAATAAATATTCGTGTAAGACCATAGCTGGGCTATGGCATCATGATGATAAGACCAT
1 GACCATGGC----AATATTCATGTAAGACCATAGCTGGGCTATGGCATCA-G-TGAAAAGACCAT
* **
2186953 AACTGGGTTATGGCACTACGAGTGTAAGACCATGGCAG
60 AACTGAGTTATGGCACTACGAACGTAAGACCATGGCAG
* * * *
2186991 GGCCATGGCAATATTCATGTAAGACTATAGTTGGACTATGGCATCA
1 GACCATGGCAATATTCATGTAAGACCATAGCTGGGCTATGGCATCA
2187037 AGTAAACGAT
Statistics
Matches: 124, Mismatches: 19, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
99 33 0.27
101 12 0.10
102 1 0.01
103 73 0.59
104 2 0.02
105 3 0.02
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (97 bp):
GACCATGGCAATATTCATGTAAGACCATAGCTGGGCTATGGCATCAGTGAAAAGACCATAACTGA
GTTATGGCACTACGAACGTAAGACCATGGCAG
Found at i:2186953 original size:33 final size:32
Alignment explanation
Indices: 2186909--2187036 Score: 107
Period size: 33 Copynumber: 3.9 Consensus size: 32
2186899 TAAATATTCG
2186909 TGTAAGACCATAGCTGGGCTATGGCATCATGA
1 TGTAAGACCATAGCTGGGCTATGGCATCATGA
* * *
2186941 TGATAAGACCATAACTGGGTTATGGCA-CTACGA
1 TG-TAAGACCATAGCTGGGCTATGGCATC-ATGA
* * * *
2186974 GTGTAAGACCATGGCAGGGCCATGGCAAT-ATTCA
1 -TGTAAGACCATAGCTGGGCTATGGC-ATCA-TGA
* * *
2187008 TGTAAGACTATAGTTGGACTATGGCATCA
1 TGTAAGACCATAGCTGGGCTATGGCATCA
2187037 AGTAAACGAT
Statistics
Matches: 73, Mismatches: 16, Indels: 13
0.72 0.16 0.13
Matches are distributed among these distances:
32 5 0.07
33 64 0.88
34 4 0.05
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (32 bp):
TGTAAGACCATAGCTGGGCTATGGCATCATGA
Found at i:2210975 original size:23 final size:24
Alignment explanation
Indices: 2210928--2210976 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
2210918 TCTGTAAATA
* * *
2210928 TTAAGAGTTTAATTTTTTTTGGTG
1 TTAAGAGTTAAATATATTTTGGTG
2210952 TTAAGAGTTAAATATATTTT-GTG
1 TTAAGAGTTAAATATATTTTGGTG
2210975 TT
1 TT
2210977 GGTCGTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.27, C:0.00, G:0.18, T:0.55
Consensus pattern (24 bp):
TTAAGAGTTAAATATATTTTGGTG
Found at i:2211725 original size:24 final size:24
Alignment explanation
Indices: 2211698--2211756 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
2211688 CCCATCAGCT
*
2211698 CCTCCTCCTTCTACCA-CTCCATCC
1 CCTCCTCCTTCTACCACCT-CATCA
* *
2211722 CCTCCTCCTCCTTCCACCTCATCA
1 CCTCCTCCTTCTACCACCTCATCA
*
2211746 CCTCCGCCTTC
1 CCTCCTCCTTC
2211757 ATCCTCTGCC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
24 27 0.93
25 2 0.07
ACGTcount: A:0.10, C:0.59, G:0.02, T:0.29
Consensus pattern (24 bp):
CCTCCTCCTTCTACCACCTCATCA
Found at i:2211934 original size:36 final size:36
Alignment explanation
Indices: 2211845--2211936 Score: 103
Period size: 36 Copynumber: 2.6 Consensus size: 36
2211835 CTCATCAACA
* * * * *
2211845 CCATCTCCGCCGCCGCCACCGAGGAGTCCCGGTACT
1 CCATCTCCACCACCGCCTCCGAGGAATCCCGGGACT
* *
2211881 GCATCTCCACCACCGCCTCCGAGGAATTCCGGGACT
1 CCATCTCCACCACCGCCTCCGAGGAATCCCGGGACT
* *
2211917 CCATCTCCTCCTCCGCCTCC
1 CCATCTCCACCACCGCCTCC
2211937 TTCTGATTCC
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.14, C:0.49, G:0.20, T:0.17
Consensus pattern (36 bp):
CCATCTCCACCACCGCCTCCGAGGAATCCCGGGACT
Found at i:2254398 original size:3 final size:3
Alignment explanation
Indices: 2254390--2254430 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2254380 ATTTTTGCTT
2254390 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2254431 GTTCTCACAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2258541 original size:2 final size:2
Alignment explanation
Indices: 2258534--2258561 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2258524 AATCATAGCA
2258534 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
2258562 TACTTTACAA
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:2268832 original size:126 final size:126
Alignment explanation
Indices: 2268595--2268833 Score: 392
Period size: 126 Copynumber: 1.9 Consensus size: 126
2268585 TAGCTTTAAG
*
2268595 AGGATATTCGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATCCTTT
1 AGGATATTCGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATCATTT
* ***
2268660 GAATTCTTTAAATACCGAACATTGCCTTTATTTTGAAAATTTTTGAGAGTGAACCGGTAAA
66 GAATTCTTTAAATACCGAACATTGCCTTTATTTTAAAAACAATTGAGAGTGAACCGGTAAA
2268721 AGGATATTCTG-ATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATCATT
1 AGGATATTC-GAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATCATT
*
2268785 TGAATTCTTTAAATACCGAACATT-TCTATTATTTTAAAAACAATTGAGA
65 TGAATTCTTTAAATACCGAACATTGCCT-TTATTTTAAAAACAATTGAGA
2268834 ATAAATCTGT
Statistics
Matches: 105, Mismatches: 6, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
125 2 0.02
126 102 0.97
127 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (126 bp):
AGGATATTCGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATCATTT
GAATTCTTTAAATACCGAACATTGCCTTTATTTTAAAAACAATTGAGAGTGAACCGGTAAA
Found at i:2269268 original size:2 final size:2
Alignment explanation
Indices: 2269261--2269288 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2269251 CAATAATAAA
2269261 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
2269289 GAAACAATTA
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:2269495 original size:20 final size:21
Alignment explanation
Indices: 2269470--2269510 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2269460 ACGAACTATT
*
2269470 ATAATAGTAG-AATATAATAA
1 ATAATAGTAGTAATAAAATAA
*
2269490 ATAATATTAGTAATAAAATAA
1 ATAATAGTAGTAATAAAATAA
2269511 TATTAACTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (21 bp):
ATAATAGTAGTAATAAAATAA
Found at i:2269503 original size:16 final size:17
Alignment explanation
Indices: 2269484--2269515 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2269474 TAGTAGAATA
2269484 TAAT-AAATAATATTAG
1 TAATAAAATAATATTAG
2269500 TAATAAAATAATATTA
1 TAATAAAATAATATTA
2269516 ACTATTAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
TAATAAAATAATATTAG
Found at i:2269558 original size:15 final size:15
Alignment explanation
Indices: 2269533--2269575 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
2269523 ACAGTAAAGT
*
2269533 ATAAT-AAAATAGTA
1 ATAATAAAAATAATA
2269547 ATAATAAAAATAATA
1 ATAATAAAAATAATA
*
2269562 ATACTAAAAATAAT
1 ATAATAAAAATAAT
2269576 CAATTTTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 5 0.19
15 21 0.81
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (15 bp):
ATAATAAAAATAATA
Found at i:2270187 original size:10 final size:11
Alignment explanation
Indices: 2270167--2270191 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2270157 AAAAAGGTAA
2270167 TTTTTATTTTT
1 TTTTTATTTTT
2270178 TTTTTATTTTT
1 TTTTTATTTTT
2270189 TTT
1 TTT
2270192 AAAAAGTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTATTTTT
Found at i:2270642 original size:17 final size:15
Alignment explanation
Indices: 2270609--2270644 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 15
2270599 TAGGTTTAGG
2270609 TGGGTTTTGGGGTAT
1 TGGGTTTTGGGGTAT
2270624 TGGGTTATTGGGTGTAT
1 TGGGTT-TTGGG-GTAT
2270641 TGGG
1 TGGG
2270645 CTTAGAGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
16 5 0.26
17 8 0.42
ACGTcount: A:0.08, C:0.00, G:0.47, T:0.44
Consensus pattern (15 bp):
TGGGTTTTGGGGTAT
Found at i:2283993 original size:2 final size:2
Alignment explanation
Indices: 2283986--2284018 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2283976 CTCATACGTA
2283986 AT AT AT AT 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 AT AT AT AT A
2284019 AATGGTGGGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2284216 original size:2 final size:2
Alignment explanation
Indices: 2284211--2284236 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2284201 CACAATATGA
2284211 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
2284237 TTGCTGAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2288248 original size:15 final size:12
Alignment explanation
Indices: 2288211--2288235 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2288201 CTCTTAACAC
2288211 TGTTAATTTTTT
1 TGTTAATTTTTT
2288223 TGTTAATTTTTT
1 TGTTAATTTTTT
2288235 T
1 T
2288236 AATGTTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (12 bp):
TGTTAATTTTTT
Found at i:2288750 original size:3 final size:3
Alignment explanation
Indices: 2288744--2288775 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2288734 TGGAAAGGAA
2288744 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2288776 GAACAAACTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2291981 original size:35 final size:35
Alignment explanation
Indices: 2291890--2292056 Score: 192
Period size: 35 Copynumber: 4.6 Consensus size: 35
2291880 CATGGCAAAG
*
2291890 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATTATCCATACTGAGT
*
2291925 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATTATCCATACTGAGT
2291960 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTA-T-T---ATCCATACTGAGT
*** * *
2292000 TAAAAAATGTAGGTATGGCATT-TCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATTAT-CCATACTGAGT
**
2292035 TGAAAAATGTAGGTATGGTATT
1 TGTGAAATGTAGGTATGGTATT
2292057 TCAATGAGGA
Statistics
Matches: 116, Mismatches: 10, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
34 1 0.01
35 83 0.72
36 1 0.01
37 1 0.01
38 1 0.01
39 1 0.01
40 28 0.24
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.34
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATTATCCATACTGAGT
Found at i:2292010 original size:75 final size:75
Alignment explanation
Indices: 2291890--2292060 Score: 212
Period size: 75 Copynumber: 2.4 Consensus size: 75
2291880 CATGGCAAAG
*** *
2291890 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAAAAATGTAGGTATGGCATT-TC
*
2291949 CCATACTGAGC
65 CCATACCGAGC
2291960 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAAAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAAAAATGTAGGTATGGCATTTCC
*
2292025 CATACCGAGT
66 CATACCGAGC
**
2292035 TGAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
2292061 TGAGGAAAAC
Statistics
Matches: 87, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
70 18 0.21
73 4 0.05
74 5 0.06
75 60 0.69
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAAAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:2299552 original size:2 final size:2
Alignment explanation
Indices: 2299547--2299586 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2299537 TTTTGTCTTC
2299547 TA TA TA TA TA TA 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
2299587 ATTATAAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2306576 original size:6 final size:6
Alignment explanation
Indices: 2306565--2306594 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
2306555 GATGAGTCCA
2306565 TGTAGG TGTAGG TGTAGG TGTAGG TGTAGG
1 TGTAGG TGTAGG TGTAGG TGTAGG TGTAGG
2306595 GTCTTCGACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.50, T:0.33
Consensus pattern (6 bp):
TGTAGG
Found at i:2313433 original size:59 final size:60
Alignment explanation
Indices: 2313341--2313512 Score: 170
Period size: 59 Copynumber: 2.9 Consensus size: 60
2313331 TTAATATAAC
* * * * * *
2313341 ATTTGCTACCTGAACTTCACACTTTTTCCTAATTTTGTACCTTAA-CTTTTTTTGGCCCA
1 ATTTGATACCTCAACTTGACACTTTTTCCTAATTTAGTACCTAAACCATTTTTTGGCCCA
* * * * *
2313400 ATTTGGTACCTCAACTTGACAGTTTTTCCTAATTTGGCACCTAAACCATTTTTTGGCCTA
1 ATTTGATACCTCAACTTGACACTTTTTCCTAATTTAGTACCTAAACCATTTTTTGGCCCA
* * * * *
2313460 ATTTTATATGC-CAACTTGCCATTTTTTCCTAATTTAGTACCT-AAGCATTTTTT
1 ATTTGATA-CCTCAACTTGACACTTTTTCCTAATTTAGTACCTAAACCATTTTTT
2313513 TTAGGTTCAT
Statistics
Matches: 94, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
59 48 0.51
60 45 0.48
61 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.45
Consensus pattern (60 bp):
ATTTGATACCTCAACTTGACACTTTTTCCTAATTTAGTACCTAAACCATTTTTTGGCCCA
Found at i:2313513 original size:60 final size:59
Alignment explanation
Indices: 2313341--2313513 Score: 163
Period size: 60 Copynumber: 2.9 Consensus size: 59
2313331 TTAATATAAC
* * * * *
2313341 ATTTGCTACCTGAACTTCACACTTTTTCCTAATTTTGTACCTTAAC-TTTTTTTGGCCCA
1 ATTTGATACCTCAACTTGACAGTTTTTCCTAATTTAGTACC-TAACATTTTTTTGGCCCA
* * * *
2313400 ATTTGGTACCTCAACTTGACAGTTTTTCCTAATTTGGCACCTAAACCA-TTTTTTGGCCTA
1 ATTTGATACCTCAACTTGACAGTTTTTCCTAATTTAGTACCT-AA-CATTTTTTTGGCCCA
* * * *
2313460 ATTTTATATGC-CAACTTGCCATTTTTTCCTAATTTAGTACCTAAGCATTTTTTT
1 ATTTGATA-CCTCAACTTGACAGTTTTTCCTAATTTAGTACCTAA-CATTTTTTT
2313514 TAGGTTCATT
Statistics
Matches: 94, Mismatches: 15, Indels: 9
0.80 0.13 0.08
Matches are distributed among these distances:
58 1 0.01
59 41 0.44
60 51 0.54
61 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.45
Consensus pattern (59 bp):
ATTTGATACCTCAACTTGACAGTTTTTCCTAATTTAGTACCTAACATTTTTTTGGCCCA
Found at i:2317294 original size:37 final size:38
Alignment explanation
Indices: 2317240--2317448 Score: 177
Period size: 46 Copynumber: 4.9 Consensus size: 38
2317230 GATATGAAAT
2317240 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGA
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGA
2317278 GTGTAAGA-CATGGTTGAAAGATACCATGGCAACCTGATATAAAA
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG-------A
2317322 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
1 -GTGTAAGACCATGGTTGAAAGATACCATGGCAACC-----TG--A
*
2317368 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATA
1 -GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG--A
*
2317409 TGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAAC
1 -G---TG--TAAGACCATGGTTGAAAGATACCATGGCAAC
2317449 ATGACAGAAA
Statistics
Matches: 149, Mismatches: 3, Indels: 30
0.82 0.02 0.16
Matches are distributed among these distances:
37 28 0.19
38 8 0.05
41 6 0.04
44 3 0.02
45 8 0.05
46 94 0.63
51 2 0.01
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (38 bp):
GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGA
Found at i:2317344 original size:46 final size:46
Alignment explanation
Indices: 2317278--2317492 Score: 306
Period size: 46 Copynumber: 4.7 Consensus size: 46
2317268 GGCAACCTGA
2317278 GTGTAAGA-CATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
*
2317323 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
* *
2317369 GTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
*** * * *
2317415 GAACAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
* * * *
2317461 GAGTAAGACCATAGTTGAAAGACACTATGGCA
1 GTGTAAGACCATGGTTGAAAGATACCATGGCA
2317493 TCATGTCAAA
Statistics
Matches: 155, Mismatches: 14, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
45 8 0.05
46 147 0.95
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (46 bp):
GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
Found at i:2318239 original size:31 final size:30
Alignment explanation
Indices: 2318204--2318261 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
2318194 TATTCTAAAT
*
2318204 TTTTGAAT-TTTTATGAACTTTTTAATTTTTA
1 TTTTGAATATTTTAT-AA-ATTTTAATTTTTA
2318235 TTTTGAATATTTTATAAATTTTAATTT
1 TTTTGAATATTTTATAAATTTTAATTT
2318262 ATTTGTTGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 9 0.36
31 10 0.40
32 6 0.24
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (30 bp):
TTTTGAATATTTTATAAATTTTAATTTTTA
Done.