Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167882.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_15, 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: 22478863
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 61000 characters in sequence are not A, C, G, or T
File 12 of 106
Found at i:1914253 original size:66 final size:66
Alignment explanation
Indices: 1914169--1914299 Score: 235
Period size: 66 Copynumber: 2.0 Consensus size: 66
1914159 GATGTTTCTT
1914169 ATATTTATTGCATGATGTCTTGGCATGATTTTTTATAGAATTTTTATTGGCATGATATTTGTTAT
1 ATATTTATTGCATGATGTCTTGGCATGATTTTTTATAGAATTTTTATTGGCATGATATTTGTTAT
1914234 G
66 G
* * *
1914235 ATATTTATTGTATGATGTCTTGGCATGATTTTTTATAGAATTTTTATTGGTATGATATTTTTTAT
1 ATATTTATTGCATGATGTCTTGGCATGATTTTTTATAGAATTTTTATTGGCATGATATTTGTTAT
1914300 ATTTGCATGA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.24, C:0.05, G:0.17, T:0.54
Consensus pattern (66 bp):
ATATTTATTGCATGATGTCTTGGCATGATTTTTTATAGAATTTTTATTGGCATGATATTTGTTAT
G
Found at i:1914258 original size:39 final size:40
Alignment explanation
Indices: 1914215--1914290 Score: 104
Period size: 39 Copynumber: 1.9 Consensus size: 40
1914205 AGAATTTTTA
1914215 TTGGCATGATATTTGTTAT-G-ATATTTATT-GTATGATGTC
1 TTGGCATGAT-TTT-TTATAGAATATTTATTGGTATGATGTC
*
1914254 TTGGCATGATTTTTTATAGAATTTTTATTGGTATGAT
1 TTGGCATGATTTTTTATAGAATATTTATTGGTATGAT
1914291 ATTTTTTATA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
37 4 0.12
38 4 0.12
39 18 0.55
40 7 0.21
ACGTcount: A:0.24, C:0.04, G:0.20, T:0.53
Consensus pattern (40 bp):
TTGGCATGATTTTTTATAGAATATTTATTGGTATGATGTC
Found at i:1915780 original size:133 final size:135
Alignment explanation
Indices: 1915540--1915781 Score: 355
Period size: 133 Copynumber: 1.8 Consensus size: 135
1915530 TGTTATTATT
* * * *
1915540 ATGTATTGCATACATGTATTTGCATATATATATTTGTATCCGTGTAAACATCTTTGTATGTGCAT
1 ATGTATTACATACATGTATTTACATATATATATTTGTATCCATGTAAACATCTTTGTATGTACAT
* * *
1915605 TCTTTCATTTGTTTGGGGGCAATCTTTGTATTTTCTATTTTGTATGTAGCTTTAAATAAATTTTT
66 TATTTCATTTGTTTGGGAGCAATCTTTGCATTTTCTATTTTGTATGTAGCTTTAAATAAATTTTT
1915670 TTACC
131 TTACC
* *
1915675 ATGTATTACATACATGTATTTACATATATAT-TTT-TATTCATGTAAACATCTTTGTATGTATAT
1 ATGTATTACATACATGTATTTACATATATATATTTGTATCCATGTAAACATCTTTGTATGTACAT
* *
1915738 TATTTCATTTGTTTGGGAG-AATCTTTGCCTTTTTTAGTTTTGTA
66 TATTTCATTTGTTTGGGAGCAATCTTTGCATTTTCTA-TTTTGTA
1915782 CATAGTTTTG
Statistics
Matches: 95, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
132 14 0.15
133 49 0.52
134 3 0.03
135 29 0.31
ACGTcount: A:0.25, C:0.11, G:0.14, T:0.51
Consensus pattern (135 bp):
ATGTATTACATACATGTATTTACATATATATATTTGTATCCATGTAAACATCTTTGTATGTACAT
TATTTCATTTGTTTGGGAGCAATCTTTGCATTTTCTATTTTGTATGTAGCTTTAAATAAATTTTT
TTACC
Found at i:1917990 original size:7 final size:7
Alignment explanation
Indices: 1917978--1918023 Score: 65
Period size: 7 Copynumber: 6.6 Consensus size: 7
1917968 TTGAGATCTA
1917978 GTTTAAG
1 GTTTAAG
1917985 GTTTAAG
1 GTTTAAG
1917992 GTTTAAG
1 GTTTAAG
*
1917999 GTTTAGG
1 GTTTAAG
*
1918006 GTTTAGG
1 GTTTAAG
*
1918013 GTTTAGG
1 GTTTAAG
1918020 GTTT
1 GTTT
1918024 CAAACTTGGG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.20, C:0.00, G:0.35, T:0.46
Consensus pattern (7 bp):
GTTTAAG
Found at i:1917997 original size:14 final size:14
Alignment explanation
Indices: 1917978--1918023 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
1917968 TTGAGATCTA
*
1917978 GTTTAAGGTTTAAG
1 GTTTAAGGTTTAGG
1917992 GTTTAAGGTTTAGG
1 GTTTAAGGTTTAGG
*
1918006 GTTTAGGGTTTAGG
1 GTTTAAGGTTTAGG
1918020 GTTT
1 GTTT
1918024 CAAACTTGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.20, C:0.00, G:0.35, T:0.46
Consensus pattern (14 bp):
GTTTAAGGTTTAGG
Found at i:1920485 original size:10 final size:10
Alignment explanation
Indices: 1920472--1920538 Score: 54
Period size: 10 Copynumber: 6.7 Consensus size: 10
1920462 TCATTTTAGT
1920472 TTTTTTTCTC
1 TTTTTTTCTC
1920482 TTTTCCTTT-TC
1 TTTT--TTTCTC
1920493 TTTCTTTTCT-
1 TTT-TTTTCTC
1920503 TTTCTTATTC-C
1 TTT-TT-TTCTC
1920514 -TTTTTTCTC
1 TTTTTTTCTC
1920523 TTTTTTT-TC
1 TTTTTTTCTC
1920532 TTTTTTT
1 TTTTTTT
1920539 TTTCACTTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 17
0.74 0.00 0.26
Matches are distributed among these distances:
8 3 0.06
9 12 0.24
10 21 0.43
11 9 0.18
12 4 0.08
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTTTCTC
Found at i:1920500 original size:22 final size:21
Alignment explanation
Indices: 1920475--1920580 Score: 69
Period size: 22 Copynumber: 5.0 Consensus size: 21
1920465 TTTTAGTTTT
1920475 TTTTCTCTTTTCCTTTTCTTTC
1 TTTTCTCTTTT-CTTTTCTTTC
*
1920497 -TTT-TCTTTTCTTATTCCTT-
1 TTTTCTCTTTTCTT-TTCTTTC
*
1920516 TTTTCTCTTTT-TTTTCTTTTTT
1 TTTTCTCTTTTCTTTTC--TTTC
*
1920538 TTTTCACTTTTACTTTT-TTTC
1 TTTTCTCTTTT-CTTTTCTTTC
* *
1920559 TTTTTTTACTTTCCTTTTCTTT
1 -TTTTCT-CTTTTCTTTTCTTT
1920581 GAGTGGATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 21
0.70 0.07 0.22
Matches are distributed among these distances:
19 6 0.09
20 16 0.24
21 14 0.21
22 19 0.29
23 7 0.11
24 4 0.06
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTCTCTTTTCTTTTCTTTC
Found at i:1920526 original size:35 final size:33
Alignment explanation
Indices: 1920482--1920580 Score: 94
Period size: 35 Copynumber: 2.8 Consensus size: 33
1920472 TTTTTTTCTC
*
1920482 TTTTC-CTTTTCTTTCTTTTCTTTTCTTATTCCTT
1 TTTTCTCTTTT-TTTCTTTTCTTTTCTT-TTACTT
*
1920516 TTTTCTCTTTTTTTTCTTTTTTTTTTCACTTTTACTT
1 TTTTCTC-TTTTTTTC-TTTTCTTTT--CTTTTACTT
*
1920553 TTTT-TCTTTTTTTACTTTCCTTTTCTTT
1 TTTTCTCTTTTTTT-CTTTTCTTTTCTTT
1920581 GAGTGGATTT
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
33 4 0.07
34 5 0.09
35 19 0.35
36 15 0.27
37 9 0.16
38 3 0.05
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (33 bp):
TTTTCTCTTTTTTTCTTTTCTTTTCTTTTACTT
Found at i:1920557 original size:30 final size:29
Alignment explanation
Indices: 1920482--1920580 Score: 73
Period size: 30 Copynumber: 3.5 Consensus size: 29
1920472 TTTTTTTCTC
* *
1920482 TTTTCCTTTT-C--TTTCTTTTCTTTTCT
1 TTTTCCTTTTACTTTTTTTTTTCTTTTTT
* * *
1920508 TATTCCTTTTTTCTCTTTTTTTTCTTTTTT
1 TTTTCC-TTTTACTTTTTTTTTTCTTTTTT
* *
1920538 TTTTCACTTTTACTTTTTTTCTT-TTTTTA
1 TTTTC-CTTTTACTTTTTTTTTTCTTTTTT
*
1920567 CTTTCCTTTT-CTTT
1 TTTTCCTTTTACTTT
1920581 GAGTGGATTT
Statistics
Matches: 59, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
26 5 0.08
27 8 0.14
28 6 0.10
29 9 0.15
30 30 0.51
31 1 0.02
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (29 bp):
TTTTCCTTTTACTTTTTTTTTTCTTTTTT
Found at i:1921760 original size:7 final size:8
Alignment explanation
Indices: 1921739--1921769 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
1921729 TTTTTTTTCA
1921739 AATTTTTT
1 AATTTTTT
1921747 AATTTTTT
1 AATTTTTT
1921755 AATTTTTT
1 AATTTTTT
*
1921763 GATTTTT
1 AATTTTT
1921770 CCTTCTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (8 bp):
AATTTTTT
Found at i:1921789 original size:11 final size:11
Alignment explanation
Indices: 1921765--1921799 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1921755 AATTTTTTGA
1921765 TTTTTCCTTCTT
1 TTTTTCCTT-TT
*
1921777 TTTTTTCTTTT
1 TTTTTCCTTTT
1921788 TTTTTCCTTTT
1 TTTTTCCTTTT
1921799 T
1 T
1921800 ATGGTTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 13 0.62
12 8 0.38
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTCCTTTT
Found at i:1922126 original size:138 final size:138
Alignment explanation
Indices: 1921890--1922155 Score: 424
Period size: 138 Copynumber: 1.9 Consensus size: 138
1921880 AAAAATATGT
* **
1921890 ACTAACAAGAAATTAAAATGCTTCAAATGACAATATTTACAAGTGAAATATGTAATGATTGAAAC
1 ACTAACAAGAAATTAAAATGCTTCAAATGACAATATTGACAAACGAAATATGTAATGATTGAAAC
* *
1921955 TTAAAGTTCTTTCACTCAATGCAAATATCCCACCCAATCTAACATCCTAAAAAATGATAAAATAA
66 TTAAAGTTCTTTCACTCAATGCAAATATCCCACCCAATCCAACATCCTAAAAAATAATAAAATAA
1922020 ACTATGAA
131 ACTATGAA
* *
1922028 ACTAACAAGAAATTAAAATGCTTCAAATGACAATATTGACAAACGAACTGTGTAATGATTGAAAC
1 ACTAACAAGAAATTAAAATGCTTCAAATGACAATATTGACAAACGAAATATGTAATGATTGAAAC
** * * *
1922093 TTAAAGTTCTTTCACTCGGTGTAAATATTCCACCCAATCCAACATCTTAAAAAATAATAAAAT
66 TTAAAGTTCTTTCACTCAATGCAAATATCCCACCCAATCCAACATCCTAAAAAATAATAAAAT
1922156 TCATAAACTC
Statistics
Matches: 116, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
138 116 1.00
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.28
Consensus pattern (138 bp):
ACTAACAAGAAATTAAAATGCTTCAAATGACAATATTGACAAACGAAATATGTAATGATTGAAAC
TTAAAGTTCTTTCACTCAATGCAAATATCCCACCCAATCCAACATCCTAAAAAATAATAAAATAA
ACTATGAA
Found at i:1925135 original size:26 final size:25
Alignment explanation
Indices: 1925097--1925174 Score: 70
Period size: 26 Copynumber: 3.2 Consensus size: 25
1925087 GAGTTAAGGA
* *
1925097 TTTAGGTTTAGGGTTTGATTTAGGG
1 TTTAGGCTTAGGGTATGATTTAGGG
* * *
1925122 TTTAGGGCTTAGGGCAAGATTTAAGG
1 TTTA-GGCTTAGGGTATGATTTAGGG
* *
1925148 TTTAGGC-TA-GGTGTGATTTAGGA
1 TTTAGGCTTAGGGTATGATTTAGGG
1925171 TTTA
1 TTTA
1925175 AGGTAAGTTT
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
23 13 0.31
24 2 0.05
25 7 0.17
26 20 0.48
ACGTcount: A:0.22, C:0.04, G:0.33, T:0.41
Consensus pattern (25 bp):
TTTAGGCTTAGGGTATGATTTAGGG
Found at i:1925283 original size:18 final size:18
Alignment explanation
Indices: 1925255--1925300 Score: 74
Period size: 18 Copynumber: 2.5 Consensus size: 18
1925245 AGTTTCAATT
1925255 TTAAGGTTTATGGTTTAGA
1 TTAA-GTTTATGGTTTAGA
1925274 TTAAGTTTATGGTTTAGA
1 TTAAGTTTATGGTTTAGA
*
1925292 GTAAGTTTA
1 TTAAGTTTA
1925301 AGATTTCATC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 22 0.85
19 4 0.15
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (18 bp):
TTAAGTTTATGGTTTAGA
Found at i:1926459 original size:19 final size:20
Alignment explanation
Indices: 1926435--1926476 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1926425 TAGTCAATCA
1926435 CAAA-TTGACCAAGTTTGAT
1 CAAATTTGACCAAGTTTGAT
1926454 CAAATTTGACCAAGTTTGAT
1 CAAATTTGACCAAGTTTGAT
1926474 CAA
1 CAA
1926477 GGGGCATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (20 bp):
CAAATTTGACCAAGTTTGAT
Found at i:1926477 original size:10 final size:10
Alignment explanation
Indices: 1926439--1926477 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1926429 CAATCACAAA
1926439 TTGACCAAGT
1 TTGACCAAGT
* *
1926449 TTGATCAAAT
1 TTGACCAAGT
1926459 TTGACCAAGT
1 TTGACCAAGT
*
1926469 TTGATCAAG
1 TTGACCAAG
1926478 GGGCATTTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (10 bp):
TTGACCAAGT
Found at i:1935808 original size:306 final size:306
Alignment explanation
Indices: 1935255--1935839 Score: 976
Period size: 306 Copynumber: 1.9 Consensus size: 306
1935245 TCCTAGGTAG
* * * *
1935255 AACCATGCCATTATTTCATAGAAATTACTCGAATTAGGGCATGAGAGAAACATCCCACTACAATC
1 AACCATGCCACTATTTCATAGAAATTACTCGAATTAGAGCACGAGAGAAACATCCCAATACAATC
* ** *
1935320 TTTATTTAGGTGTAGAATAGTGCAAATAAAACTAAAATTTTGAAAAAAAAAGAGGGAAAAATGAG
66 TTTATTTAGGTGCAGAATAGTGCAAATAAAACTAAAATTTTGAAAAAAAAAGAAAGAAAAAGGAG
* *
1935385 AAATAAAAGAGGAACAATCTTTTAATAAAATTTCTTTTTAACATATGGTTTGACTGATCTAGTAC
131 AAATAAAAGAGGAACAATCTTTTAATAAAATTTCTTTTTAACAAATGGTTTGACTCATCTAGTAC
*
1935450 TTGTCCAAAATTTGTACTTTCAAAAAATATTTCTAAAAAAGAAGGAAGATTTTTTTTAGCAAACA
196 TTGTCCAAAATTTATACTTTCAAAAAATATTTCTAAAAAAGAAGGAAGATTTTTTTTAGCAAACA
1935515 AACAAACACAAATGAAATTAAAAAAAAAAAGCTTTTTTATTAACCA
261 AACAAACACAAATGAAATTAAAAAAAAAAAGCTTTTTTATTAACCA
* *
1935561 AACCATGCCACTATTTCATAGAAATTACTCGGATTAGAGCACGAGAGAAACATCCTAATACAATC
1 AACCATGCCACTATTTCATAGAAATTACTCGAATTAGAGCACGAGAGAAACATCCCAATACAATC
1935626 TTTATTTAGGTGCAGAATAGTGCAAATAAAACTAAAATTTTGAAAAAAAAA-AAAGAAAAAGGGA
66 TTTATTTAGGTGCAGAATAGTGCAAATAAAACTAAAATTTTGAAAAAAAAAGAAAGAAAAA-GGA
* *
1935690 GAAATAAAAGAGGAACAATCTTTTAATAAAATTTCTTTTTGACAAATGGTTTGATTCATCTAGTA
130 GAAATAAAAGAGGAACAATCTTTTAATAAAATTTCTTTTTAACAAATGGTTTGACTCATCTAGTA
* *
1935755 CTTGTCCAAATTTTATATTTTCAAAAAATATTTTCT-AAAAAGAAGGAAGATTTTTTTTAGCAAA
195 CTTGTCCAAAATTTATACTTTCAAAAAATA-TTTCTAAAAAAGAAGGAAGATTTTTTTTAGCAAA
*
1935819 CAAACAAACATAAATGAAATT
259 CAAACAAACACAAATGAAATT
1935840 TTTTGAAACA
Statistics
Matches: 259, Mismatches: 18, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
305 7 0.03
306 247 0.95
307 5 0.02
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.30
Consensus pattern (306 bp):
AACCATGCCACTATTTCATAGAAATTACTCGAATTAGAGCACGAGAGAAACATCCCAATACAATC
TTTATTTAGGTGCAGAATAGTGCAAATAAAACTAAAATTTTGAAAAAAAAAGAAAGAAAAAGGAG
AAATAAAAGAGGAACAATCTTTTAATAAAATTTCTTTTTAACAAATGGTTTGACTCATCTAGTAC
TTGTCCAAAATTTATACTTTCAAAAAATATTTCTAAAAAAGAAGGAAGATTTTTTTTAGCAAACA
AACAAACACAAATGAAATTAAAAAAAAAAAGCTTTTTTATTAACCA
Found at i:1940690 original size:26 final size:27
Alignment explanation
Indices: 1940637--1940690 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
1940627 AAAAAAGTCA
* *
1940637 CTTGTATTTGCATCAAGCATTCACATT
1 CTTGCATTTGCATCAAACATTCACATT
1940664 CTTGCATTTGCAT-AAACATTCACATT
1 CTTGCATTTGCATCAAACATTCACATT
1940690 C
1 C
1940691 ATAACTTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 13 0.52
27 12 0.48
ACGTcount: A:0.28, C:0.24, G:0.09, T:0.39
Consensus pattern (27 bp):
CTTGCATTTGCATCAAACATTCACATT
Found at i:1940700 original size:27 final size:27
Alignment explanation
Indices: 1940642--1940700 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
1940632 AGTCACTTGT
* **
1940642 ATTTGCATCAAGCATTCACATTCTTGC
1 ATTTGCATCAAACATTCACATTCTAAC
1940669 ATTTGCAT-AAACATTCACATTCATAAC
1 ATTTGCATCAAACATTCACATTC-TAAC
*
1940696 TTTTG
1 ATTTG
1940701 ATAGAAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 13 0.48
27 14 0.52
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (27 bp):
ATTTGCATCAAACATTCACATTCTAAC
Found at i:1941040 original size:20 final size:18
Alignment explanation
Indices: 1941017--1941057 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
1941007 TGAAAAGTCG
1941017 AAAAACATTATTTGCAAAAA
1 AAAAACATTA-TTG-AAAAA
*
1941037 AAAAAGATTATTGAAAAA
1 AAAAACATTATTGAAAAA
1941055 AAA
1 AAA
1941058 TGAGCTTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 3 0.15
20 9 0.45
ACGTcount: A:0.66, C:0.05, G:0.07, T:0.22
Consensus pattern (18 bp):
AAAAACATTATTGAAAAA
Found at i:1941477 original size:105 final size:105
Alignment explanation
Indices: 1941272--1941909 Score: 611
Period size: 105 Copynumber: 6.0 Consensus size: 105
1941262 AAACCTACAG
* * ** * *
1941272 GGTAAAATATTTTAAAATTTCAAAGTTTTGATGCCTTTGATTGGGAGGAA-CATTAAAAAATGTT
1 GGTAAAACATTTTAAATTTTCAAAGTTTCAATGCCTTTGATTAGGA-GAAGCATTAAAAAATGTC
* ** *
1941336 GAG-TTTGTAAGACCTTTGGGCATAATCTCCAAGACCTCT-
65 AAGATTTGTAAGACCTTCAGGCATAATCTTCAAGACCTCTA
* * * * *
1941375 GGATAAAACATTTTAAAATTTCAAAGATTCAATGCTTTTGATTAGGAGAAGCATTCAAAGATGTC
1 GG-TAAAACATTTTAAATTTTCAAAGTTTCAATGCCTTTGATTAGGAGAAGCATTAAAAAATGTC
*
1941440 AAGATATGTAAGACCTTCAGGCATAATCTTCAAGACCTCTA
65 AAGATTTGTAAGACCTTCAGGCATAATCTTCAAGACCTCTA
* * *
1941481 GGTAAGACATTTTAAATTTTCAAAGTTTCAATGCCTTTGATT-GAGAGGAA-CATTCAAAGATGT
1 GGTAAAACATTTTAAATTTTCAAAGTTTCAATGCCTTTGATTAG-GA-GAAGCATTAAAAAATGT
* * * *
1941544 CAAAATTTGTAAGACC-TCTGAGCATAATCTCCAAGACTTCTA
64 CAAGATTTGTAAGACCTTCAG-GCATAATCTTCAAGACCTCTA
* * *
1941586 GGTAAAACATTTTAAATTTTCAAAGTTTCAATGCCTCTGCCTCTAATTAGGA-AAGCATTCAAAG
1 GGTAAAACATTTTAAATTTTCAAAGTTTCAATG-C-CT---T-TGATTAGGAGAAGCATTAAAAA
* * * * *
1941650 ATGTTAAGATTTGTAAAACCTTCGGGCATAA-CCTCTAAGACCT-TT
60 ATGTCAAGATTTGTAAGACCTTCAGGCATAATCTTC-AAGACCTCTA
* * * * *
1941695 GAGTAAAACATTTTAAATTTTTAAAGTTTTAATGCCTCTGATTA-AAAAGAGCATTAAAAAATGT
1 G-GTAAAACATTTTAAATTTTCAAAGTTTCAATGCCTTTGATTAGGAGA-AGCATTAAAAAATGT
* *
1941759 CAAGATTTGTAAAACCTTC-GGATATAATC-TCTAAGACCT-TAA
64 CAAGATTTGTAAGACCTTCAGG-CATAATCTTC-AAGACCTCT-A
* * *
1941801 GGTAAAACAATTTAAATTTTCAAAGTTTTAATG-CTTCTGATTGGGAGAAGCATTAAAAAATGTC
1 GGTAAAACATTTTAAATTTTCAAAGTTTCAATGCCTT-TGATTAGGAGAAGCATTAAAAAATGTC
* * * *
1941865 AAGATTTGTAAGACCTCCAAGCATAATCTTTAAGACTTCTA
65 AAGATTTGTAAGACCTTCAGGCATAATCTTCAAGACCTCTA
1941906 GGTA
1 GGTA
1941910 TAGTTGGTAA
Statistics
Matches: 452, Mismatches: 55, Indels: 54
0.81 0.10 0.10
Matches are distributed among these distances:
103 6 0.01
104 65 0.14
105 278 0.62
106 13 0.03
107 2 0.00
108 2 0.00
109 7 0.02
110 69 0.15
111 9 0.02
112 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.33
Consensus pattern (105 bp):
GGTAAAACATTTTAAATTTTCAAAGTTTCAATGCCTTTGATTAGGAGAAGCATTAAAAAATGTCA
AGATTTGTAAGACCTTCAGGCATAATCTTCAAGACCTCTA
Found at i:1941731 original size:215 final size:213
Alignment explanation
Indices: 1941272--1941909 Score: 681
Period size: 215 Copynumber: 3.0 Consensus size: 213
1941262 AAACCTACAG
* * * * *
1941272 GGTAAAATATTTTAAAATTTCAAAGTTTTGATGCCTTTGATTGGGAGGAACATTAAAAAATGT-T
1 GGTAAAACATTTTAAATTTTCAAAGTTTTAATGCCTTTGATTGAGAGGAACATTAAAAAATGTCA
* * * * * *
1941336 GAGTTTGTAAGACCTTTGGGCATAATCTCCAAGACCTCT-GGATAAAACATTTTAAAATTTCAAA
66 AAATTTGTAAGACCTCTGAGCATAATCTCCAAGACTTCTAGG-TAAAACATTTTAAATTTTCAAA
* * *
1941400 GATTCAATG-CT-T-TTGATTAGGAGAAGCATTCAAAGATGTCAAGATATGTAAGACCTTCAGGC
130 GTTTCAATGCCTCTGTTAATTAGGAGAAGCATTCAAAGATGTCAAGATATGTAAAACCTTCAGGC
*
1941462 ATAATCTTCAAGACCTCTA
195 ATAACCTTCAAGACCTCTA
* * * *
1941481 GGTAAGACATTTTAAATTTTCAAAGTTTCAATGCCTTTGATTGAGAGGAACATTCAAAGATGTCA
1 GGTAAAACATTTTAAATTTTCAAAGTTTTAATGCCTTTGATTGAGAGGAACATTAAAAAATGTCA
1941546 AAATTTGTAAGACCTCTGAGCATAATCTCCAAGACTTCTAGGTAAAACATTTTAAATTTTCAAAG
66 AAATTTGTAAGACCTCTGAGCATAATCTCCAAGACTTCTAGGTAAAACATTTTAAATTTTCAAAG
* * *
1941611 TTTCAATGCCTCTGCCTCTAATTAGGA-AAGCATTCAAAGATGTTAAGATTTGTAAAACCTTCGG
131 TTTCAATGCCTCTG--T-TAATTAGGAGAAGCATTCAAAGATGTCAAGATATGTAAAACCTTCAG
*
1941675 GCATAACC-TCTAAGACCT-TT
193 GCATAACCTTC-AAGACCTCTA
* * * * * *
1941695 GAGTAAAACATTTTAAATTTTTAAAGTTTTAATGCCTCTGATTAAAAAGAGCATTAAAAAATGTC
1 G-GTAAAACATTTTAAATTTTCAAAGTTTTAATGCCTTTGATTGAGAGGAACATTAAAAAATGTC
* * * * * * *
1941760 AAGATTTGTAAAACCTTCGGA-TATAATCTCTAAGACCTT-AAGGTAAAACAATTTAAATTTTCA
65 AAAATTTGTAAGACC-TCTGAGCATAATCTCCAAGA-CTTCTAGGTAAAACATTTTAAATTTTCA
* * * * * * * * *
1941823 AAGTTTTAATGCTTCTG---ATTGGGAGAAGCATTAAAAAATGTCAAGATTTGTAAGACCTCCAA
128 AAGTTTCAATGCCTCTGTTAATTAGGAGAAGCATTCAAAGATGTCAAGATATGTAAAACCTTCAG
* * *
1941885 GCATAATCTTTAAGACTTCTA
193 GCATAACCTTCAAGACCTCTA
1941906 GGTA
1 GGTA
1941910 TAGTTGGTAA
Statistics
Matches: 360, Mismatches: 54, Indels: 29
0.81 0.12 0.07
Matches are distributed among these distances:
209 61 0.17
210 109 0.30
211 7 0.02
212 1 0.00
214 4 0.01
215 163 0.45
216 15 0.04
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.33
Consensus pattern (213 bp):
GGTAAAACATTTTAAATTTTCAAAGTTTTAATGCCTTTGATTGAGAGGAACATTAAAAAATGTCA
AAATTTGTAAGACCTCTGAGCATAATCTCCAAGACTTCTAGGTAAAACATTTTAAATTTTCAAAG
TTTCAATGCCTCTGTTAATTAGGAGAAGCATTCAAAGATGTCAAGATATGTAAAACCTTCAGGCA
TAACCTTCAAGACCTCTA
Found at i:1942046 original size:126 final size:127
Alignment explanation
Indices: 1941811--1942053 Score: 283
Period size: 126 Copynumber: 1.9 Consensus size: 127
1941801 GGTAAAACAA
* * **
1941811 TTTAAATTTTCAAAGTTTTAATGCTTCTGATTGGGAGAAGCATTAAAAAATGTCAAGATTTGTAA
1 TTTAAATTTTCAAAGTTTCAATGCTTATGATTGAAAGAAGCATTAAAAAATGTCAAGATTTGTAA
* * * **
1941876 GACCTCCAAGCATAATCTTTAAGACTTCTAGGTATAGTTGGTAAGACTTTCAGGCAAAAAAT
66 GACCTCCAAGCATAATCTCTAAGACCTCCAAATATAGTTGGTAAGACTTTCAGGCAAAAAAT
* * * * *
1941938 TTTAAATTTTTAAAGTTTCAATGCTTATTATT-AAAGAAGCATTCAAAGATGTCGAGATTTGTAA
1 TTTAAATTTTCAAAGTTTCAATGCTTATGATTGAAAGAAGCATTAAAAAATGTCAAGATTTGTAA
*** * * *
1942002 GACCTCTGGGCATAATCTCTAAGTCCTCCAAATA-AGGTTTGTAAGTCTTTCA
66 GACCTCCAAGCATAATCTCTAAGACCTCCAAATATA-GTTGGTAAGACTTTCA
1942054 AGCTAAATCT
Statistics
Matches: 95, Mismatches: 20, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
125 1 0.01
126 66 0.69
127 28 0.29
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (127 bp):
TTTAAATTTTCAAAGTTTCAATGCTTATGATTGAAAGAAGCATTAAAAAATGTCAAGATTTGTAA
GACCTCCAAGCATAATCTCTAAGACCTCCAAATATAGTTGGTAAGACTTTCAGGCAAAAAAT
Found at i:1942227 original size:16 final size:15
Alignment explanation
Indices: 1942218--1942261 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1942208 AAAAACCCAA
1942218 AAAAAAAAAAAAACC
1 AAAAAAAAAAAAACC
* * *
1942233 AAAACAAAACAAAGC
1 AAAAAAAAAAAAACC
1942248 AAAAACAAAAAAAA
1 AAAAA-AAAAAAAA
1942262 AAACTCTTGA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.84, C:0.14, G:0.02, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAACC
Found at i:1949906 original size:106 final size:110
Alignment explanation
Indices: 1949721--1949936 Score: 307
Period size: 106 Copynumber: 2.0 Consensus size: 110
1949711 ATTTTTAGGG
*
1949721 ATACTTACAAAAAAAATTTCAAAAATAGTTTTGCACAAAAGATTTCTTCCCCCCTCTAAACACTT
1 ATACTTACAAAAAAAATTTCAAAAATAGTTTTACACAAAAGATTTCTT--CCCCTCT-AACACTT
1949786 GGTTTGCATAATATTTCACATAAAACATTAAAGGATTAGGGAAAAGGA
63 GGTTTGCATAATATTTCACATAAAACATTAAAGGATTAGGGAAAAGGA
* * *
1949834 ATACTTA-AAAAAAAATTT-GAAAATAGTTTTACATAAAAGATTTCCTT-CCC-CT-ACGCTTGG
1 ATACTTACAAAAAAAATTTCAAAAATAGTTTTACACAAAAGATTT-CTTCCCCTCTAACACTTGG
* *
1949894 TTTGCATTATATTTCACATGAAACATTAAAGGATTAGGGAAAA
65 TTTGCATAATATTTCACATAAAACATTAAAGGATTAGGGAAAA
1949937 AATTCCCCTA
Statistics
Matches: 96, Mismatches: 6, Indels: 9
0.86 0.05 0.08
Matches are distributed among these distances:
106 48 0.50
108 2 0.02
109 3 0.03
111 22 0.23
112 14 0.15
113 7 0.07
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (110 bp):
ATACTTACAAAAAAAATTTCAAAAATAGTTTTACACAAAAGATTTCTTCCCCTCTAACACTTGGT
TTGCATAATATTTCACATAAAACATTAAAGGATTAGGGAAAAGGA
Found at i:1954219 original size:19 final size:22
Alignment explanation
Indices: 1954172--1954275 Score: 99
Period size: 22 Copynumber: 4.7 Consensus size: 22
1954162 AATTTGATAG
1954172 ATTAGTAGTAAATCACTAATAAT
1 ATTA-TAGTAAATCACTAATAAT
1954195 ATTATAGTAAATCACTAATAAT
1 ATTATAGTAAATCACTAATAAT
*
1954217 A-TAGTAATAAATCACTAA-AA-
1 ATTA-TAGTAAATCACTAATAAT
* * *
1954237 ACT-TAGTTAATGATCATTAATAAC
1 ATTATAG-TAA--ATCACTAATAAT
1954261 ATTATAGTAAATCAC
1 ATTATAGTAAATCAC
1954276 CGTTAAATTA
Statistics
Matches: 68, Mismatches: 5, Indels: 17
0.76 0.06 0.19
Matches are distributed among these distances:
19 2 0.03
20 4 0.06
21 5 0.07
22 43 0.63
23 6 0.09
24 5 0.07
25 3 0.04
ACGTcount: A:0.49, C:0.11, G:0.07, T:0.34
Consensus pattern (22 bp):
ATTATAGTAAATCACTAATAAT
Found at i:1958915 original size:22 final size:22
Alignment explanation
Indices: 1958867--1958918 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
1958857 AACAAAAGTA
* *
1958867 ATAACTTAGTAGTTAATCATTT
1 ATAACTTAGTAGTTAATCAATG
*
1958889 TTAACTTAGTA-TTAAATCAATG
1 ATAACTTAGTAGTT-AATCAATG
1958911 ATAACTTA
1 ATAACTTA
1958919 ATAATAAGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 2 0.08
22 23 0.92
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (22 bp):
ATAACTTAGTAGTTAATCAATG
Found at i:1959385 original size:22 final size:22
Alignment explanation
Indices: 1959360--1959453 Score: 107
Period size: 22 Copynumber: 4.3 Consensus size: 22
1959350 TAACTTAATG
* *
1959360 GTAAATCATTTATAAATTAGTA
1 GTAAATCATTAATAATTTAGTA
*
1959382 GTAAATCAATAATAATTTAGTA
1 GTAAATCATTAATAATTTAGTA
* * *
1959404 TTAAACCATTGATAATTTAGTA
1 GTAAATCATTAATAATTTAGTA
* * *
1959426 ATAAATCATTAATAGTTTAATA
1 GTAAATCATTAATAATTTAGTA
1959448 GTAAAT
1 GTAAAT
1959454 AACTGATATT
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 59 1.00
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.39
Consensus pattern (22 bp):
GTAAATCATTAATAATTTAGTA
Found at i:1959461 original size:44 final size:44
Alignment explanation
Indices: 1959349--1959509 Score: 144
Period size: 44 Copynumber: 3.7 Consensus size: 44
1959339 TTAATTATTC
* * * * * *
1959349 ATAACTTAATGGTAAATCATTTATAAATTAGTAGTAAATCAATA
1 ATAATTTAATAGTAAATAATTGATAATTTAGTAATAAATCAATA
* * ** *
1959393 ATAATTTAGTATTAAACCATTGATAATTTAGTAATAAATCATTA
1 ATAATTTAATAGTAAATAATTGATAATTTAGTAATAAATCAATA
* * * *
1959437 ATAGTTTAATAGTAAATAACTGAT-ATTATAGAAATAAATCAATG
1 ATAATTTAATAGTAAATAATTGATAATT-TAGTAATAAATCAATA
* * *
1959481 ATAAATTAATTGTCAATAATTGATAATTT
1 ATAATTTAATAGTAAATAATTGATAATTT
1959510 TTTATACTTA
Statistics
Matches: 92, Mismatches: 23, Indels: 4
0.77 0.19 0.03
Matches are distributed among these distances:
43 3 0.03
44 86 0.93
45 3 0.03
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.39
Consensus pattern (44 bp):
ATAATTTAATAGTAAATAATTGATAATTTAGTAATAAATCAATA
Found at i:1961776 original size:20 final size:20
Alignment explanation
Indices: 1961753--1961818 Score: 63
Period size: 20 Copynumber: 3.6 Consensus size: 20
1961743 ACATATAGGG
*
1961753 TTTAGGGTTTCATTTTATGA
1 TTTAGGGTTTCATTTTAAGA
*
1961773 TTTA-GG----A-TTTAGGA
1 TTTAGGGTTTCATTTTAAGA
*
1961787 TTTAGGGTTTCATTTTAAGG
1 TTTAGGGTTTCATTTTAAGA
1961807 TTTAGGGTTTCA
1 TTTAGGGTTTCA
1961819 ATTAGAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
14 10 0.27
15 3 0.08
19 3 0.08
20 21 0.57
ACGTcount: A:0.21, C:0.05, G:0.24, T:0.50
Consensus pattern (20 bp):
TTTAGGGTTTCATTTTAAGA
Found at i:1961791 original size:34 final size:34
Alignment explanation
Indices: 1961748--1961812 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
1961738 GGTTTACATA
* *
1961748 TAGGGTTTAGGGTTTCATTTTATGATTTAGGATT
1 TAGGATTTAGGGTTTCATTTTAAGATTTAGGATT
*
1961782 TAGGATTTAGGGTTTCATTTTAAGGTTTAGG
1 TAGGATTTAGGGTTTCATTTTAAGATTTAGG
1961813 GTTTCAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.22, C:0.03, G:0.28, T:0.48
Consensus pattern (34 bp):
TAGGATTTAGGGTTTCATTTTAAGATTTAGGATT
Found at i:1961891 original size:14 final size:13
Alignment explanation
Indices: 1961847--1961898 Score: 68
Period size: 13 Copynumber: 3.9 Consensus size: 13
1961837 GGACATAAGG
1961847 TTTAAGGTTTCAT
1 TTTAAGGTTTCAT
*
1961860 TTTAAGGTTTTAT
1 TTTAAGGTTTCAT
*
1961873 TTTAGGGTTTCACT
1 TTTAAGGTTTCA-T
*
1961887 TTTAGGGTTTCA
1 TTTAAGGTTTCA
1961899 AAGAACCTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
13 22 0.63
14 13 0.37
ACGTcount: A:0.19, C:0.08, G:0.19, T:0.54
Consensus pattern (13 bp):
TTTAAGGTTTCAT
Found at i:1961984 original size:3 final size:3
Alignment explanation
Indices: 1961971--1962007 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
1961961 GATTGTAAAA
*
1961971 TAT TAAT TAT TAT TAT TAT TAT TAT GAT TAT TAT TAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1962008 ACTTTTCTCC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1962866 original size:7 final size:7
Alignment explanation
Indices: 1962854--1962909 Score: 66
Period size: 7 Copynumber: 8.6 Consensus size: 7
1962844 CTCTTGTTTT
1962854 TTTATTA
1 TTTATTA
1962861 TTTATTA
1 TTTATTA
1962868 TTTATT-
1 TTTATTA
* *
1962874 TCT-TTG
1 TTTATTA
1962880 TTT-TTA
1 TTTATTA
1962886 TTTATTA
1 TTTATTA
1962893 TTTATTA
1 TTTATTA
1962900 TTTATT-
1 TTTATTA
1962906 TTTA
1 TTTA
1962910 ATAGCCAAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
5 2 0.05
6 13 0.30
7 29 0.66
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (7 bp):
TTTATTA
Found at i:1962895 original size:32 final size:31
Alignment explanation
Indices: 1962842--1962906 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 31
1962832 AACTAAATTG
1962842 TTCTCTTGTTTTTTTATTATTTATTATTTAT
1 TTCTCTTGTTTTTTTATTATTTATTATTTAT
1962873 TTCT-TTGTTTTTATTTATTATTTATTATTTAT
1 TTCTCTTG-TTTT-TTTATTATTTATTATTTAT
1962905 TT
1 TT
1962907 TTAATAGCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
30 3 0.09
31 8 0.25
32 21 0.66
ACGTcount: A:0.17, C:0.05, G:0.03, T:0.75
Consensus pattern (31 bp):
TTCTCTTGTTTTTTTATTATTTATTATTTAT
Found at i:1966580 original size:34 final size:34
Alignment explanation
Indices: 1966537--1966607 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
1966527 CTGGATCATC
1966537 AAAATTAAGCTTGTTAATCTATGGTATTAAGATG
1 AAAATTAAGCTTGTTAATCTATGGTATTAAGATG
1966571 AAAATTAAGCTTGTTAATCTATGGTATTAAGATG
1 AAAATTAAGCTTGTTAATCTATGGTATTAAGATG
1966605 AAA
1 AAA
1966608 TGCATGCTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.41, C:0.06, G:0.17, T:0.37
Consensus pattern (34 bp):
AAAATTAAGCTTGTTAATCTATGGTATTAAGATG
Found at i:1970273 original size:75 final size:75
Alignment explanation
Indices: 1970184--1970334 Score: 257
Period size: 75 Copynumber: 2.0 Consensus size: 75
1970174 CAGAATTTTA
*
1970184 CTTAACCAGATTGCTTGATTAACAGCAACCGCAGCAGCTACGTACTGTGCTTCTGCCGTTGATTG
1 CTTAACCAGATTGCTTGATTAACAGCAACCGCAGCAGCTACGTACTCTGCTTCTGCCGTTGATTG
1970249 AGCCATTGTT
66 AGCCATTGTT
* * * *
1970259 CTTAACCAGATTGCTTGATTAACAGCAGCTGCAGCAGCTATGTACTCTGCTTCTGCTGTTGATTG
1 CTTAACCAGATTGCTTGATTAACAGCAACCGCAGCAGCTACGTACTCTGCTTCTGCCGTTGATTG
1970324 AGCCATTGTT
66 AGCCATTGTT
1970334 C
1 C
1970335 CTTATTTCTT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 71 1.00
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (75 bp):
CTTAACCAGATTGCTTGATTAACAGCAACCGCAGCAGCTACGTACTCTGCTTCTGCCGTTGATTG
AGCCATTGTT
Found at i:1970406 original size:23 final size:23
Alignment explanation
Indices: 1970380--1970426 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1970370 CCAATGAAGA
1970380 ACACATAGCCTGAGGTTCTCTTC
1 ACACATAGCCTGAGGTTCTCTTC
1970403 ACACATAGCCTGAGGTTCTCTTC
1 ACACATAGCCTGAGGTTCTCTTC
1970426 A
1 A
1970427 TGTATTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.30
Consensus pattern (23 bp):
ACACATAGCCTGAGGTTCTCTTC
Found at i:1972270 original size:17 final size:19
Alignment explanation
Indices: 1972230--1972270 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
1972220 TTTAAAATAT
*
1972230 TTAAAATAATATTACTATTC
1 TTAAAATAATATTA-TATTA
1972250 TTAAAATAATATT-T-TTA
1 TTAAAATAATATTATATTA
1972267 TTAA
1 TTAA
1972271 TACAATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 6 0.30
18 1 0.05
20 13 0.65
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (19 bp):
TTAAAATAATATTATATTA
Found at i:1972410 original size:34 final size:30
Alignment explanation
Indices: 1972372--1972433 Score: 88
Period size: 34 Copynumber: 1.9 Consensus size: 30
1972362 ATATTTATTA
1972372 TTAAAATAATAATATAAGTATATTAATAAATAAT
1 TTAAAATAATAATA-AA-T-TATTAA-AAATAAT
1972406 TTAAAATAATAATAAATTATTAAAAATA
1 TTAAAATAATAATAAATTATTAAAAATA
1972434 TTCATTTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
30 5 0.18
31 6 0.21
32 1 0.04
33 2 0.07
34 14 0.50
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (30 bp):
TTAAAATAATAATAAATTATTAAAAATAAT
Found at i:1972415 original size:17 final size:17
Alignment explanation
Indices: 1972371--1972424 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
1972361 TATATTTATT
1972371 ATTAAAATAATAATATA
1 ATTAAAATAATAATATA
* * *
1972388 AGTATATTAATAA-ATA
1 ATTAAAATAATAATATA
1972404 ATTTAAAATAATAATA-A
1 A-TTAAAATAATAATATA
1972421 ATTA
1 ATTA
1972425 TTAAAAATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
16 7 0.24
17 21 0.72
18 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (17 bp):
ATTAAAATAATAATATA
Found at i:1972418 original size:20 final size:20
Alignment explanation
Indices: 1972395--1972433 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1972385 ATAAGTATAT
*
1972395 TAATAAATAATTTAAAATAA
1 TAATAAATAATTAAAAATAA
*
1972415 TAATAAATTATTAAAAATA
1 TAATAAATAATTAAAAATA
1972434 TTCATTTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TAATAAATAATTAAAAATAA
Found at i:1972556 original size:28 final size:26
Alignment explanation
Indices: 1972513--1972586 Score: 80
Period size: 28 Copynumber: 2.8 Consensus size: 26
1972503 TTTAATATTT
* *
1972513 AATATTCATTATTAAATAATATTATAA
1 AATATTTATTGTTAAATAATATTA-AA
*
1972540 TATTATTTATTGTTAAA-AATATTAAA
1 -AATATTTATTGTTAAATAATATTAAA
*
1972566 AATATTTA-TGTTTAATAATAT
1 AATATTTATTGTTAAATAATAT
1972587 ACCAAATAGA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
24 6 0.15
25 12 0.30
26 2 0.05
27 7 0.17
28 13 0.32
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (26 bp):
AATATTTATTGTTAAATAATATTAAA
Found at i:1972571 original size:25 final size:28
Alignment explanation
Indices: 1972512--1972586 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 28
1972502 ATTTAATATT
*
1972512 TAATATTCATTATTAAATAATATTATAA
1 TAATATTTATTATTAAATAATATTATAA
* *
1972540 TATTATTTATTGTTAAA-AATATTA-AA
1 TAATATTTATTATTAAATAATATTATAA
1972566 -AATATTTATGT-TT-AATAATAT
1 TAATATTTAT-TATTAAATAATAT
1972587 ACCAAATAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
24 2 0.05
25 15 0.37
26 3 0.07
27 7 0.17
28 14 0.34
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (28 bp):
TAATATTTATTATTAAATAATATTATAA
Found at i:1972816 original size:19 final size:19
Alignment explanation
Indices: 1972794--1972831 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1972784 TTTACAAAAA
1972794 ATTAA-ATAAAAATAATTTT
1 ATTAATATAAAAAT-ATTTT
*
1972813 ATTAATATAATAATATTTT
1 ATTAATATAAAAATATTTT
1972832 GAGTCAAGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTAATATAAAAATATTTT
Found at i:1973924 original size:16 final size:16
Alignment explanation
Indices: 1973903--1973933 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1973893 ATTAAAAATT
1973903 TTTTAAAAAAATTTTA
1 TTTTAAAAAAATTTTA
*
1973919 TTTTAAAAATATTTT
1 TTTTAAAAAAATTTT
1973934 TTTATTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTTAAAAAAATTTTA
Found at i:1973926 original size:14 final size:13
Alignment explanation
Indices: 1973894--1973937 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
1973884 CATTTAAAAA
1973894 TTAAAAATTTTTT
1 TTAAAAATTTTTT
**
1973907 AAAAAAATTTTATT
1 TTAAAAATTTT-TT
1973921 TTAAAAATATTTTT
1 TTAAAAAT-TTTTT
1973935 TTA
1 TTA
1973938 TTTTTTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
13 9 0.36
14 13 0.52
15 3 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TTAAAAATTTTTT
Found at i:1974172 original size:7 final size:7
Alignment explanation
Indices: 1974160--1974189 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1974150 TATTTTATAC
1974160 ATATTAA
1 ATATTAA
1974167 ATATTAA
1 ATATTAA
*
1974174 ATAATAA
1 ATATTAA
1974181 ATATTAA
1 ATATTAA
1974188 AT
1 AT
1974190 TATCAAATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
ATATTAA
Found at i:1976194 original size:2 final size:2
Alignment explanation
Indices: 1976187--1976221 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1976177 TAAGTGTAAC
1976187 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 A
1976222 ACATTAAATG
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1988377 original size:15 final size:14
Alignment explanation
Indices: 1988350--1988387 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
1988340 GTAAAGGTTC
1988350 GAATATTATTTTTT
1 GAATATTATTTTTT
1988364 GAATATTAATTTTTT
1 GAATATT-ATTTTTT
1988379 -AA-ATTATTT
1 GAATATTATTT
1988388 ACCATTATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.17
13 3 0.13
14 9 0.39
15 7 0.30
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (14 bp):
GAATATTATTTTTT
Found at i:1995284 original size:21 final size:21
Alignment explanation
Indices: 1995227--1995284 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
1995217 ATTATGGAAA
*
1995227 TAATTATT-ATTAATGATATC
1 TAATTATTAATTAATAATATC
* *
1995247 TAATTA-TAAATATATAATATG
1 TAATTATTAATTA-ATAATATC
*
1995268 TATTTATTAATTAATAA
1 TAATTATTAATTAATAA
1995285 CTTTCAAAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
19 1 0.03
20 9 0.30
21 15 0.50
22 5 0.17
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (21 bp):
TAATTATTAATTAATAATATC
Found at i:1995872 original size:21 final size:20
Alignment explanation
Indices: 1995834--1995872 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1995824 TATATTAAAA
*
1995834 TTAAATTATATTTTAAACTC
1 TTAAATTATATTTAAAACTC
*
1995854 TTAAATTTTTATTTAAAAC
1 TTAAA-TTATATTTAAAAC
1995873 AAATTAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (20 bp):
TTAAATTATATTTAAAACTC
Found at i:1995975 original size:16 final size:17
Alignment explanation
Indices: 1995954--1995995 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1995944 TCATATATTT
1995954 TTAATTAAAATTTT-AA
1 TTAATTAAAATTTTAAA
* *
1995970 TTAATTTAATTTTTAAA
1 TTAATTAAAATTTTAAA
1995987 TCTAATTAA
1 T-TAATTAA
1995996 TAAAATATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 12 0.57
17 3 0.14
18 6 0.29
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAATTAAAATTTTAAA
Found at i:2000069 original size:15 final size:15
Alignment explanation
Indices: 2000046--2000076 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2000036 GCTGAAGCGG
*
2000046 TAATTTTTTCAATTA
1 TAATGTTTTCAATTA
2000061 TAATGTTTTCAATTA
1 TAATGTTTTCAATTA
2000076 T
1 T
2000077 GCTTTCTTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.58
Consensus pattern (15 bp):
TAATGTTTTCAATTA
Found at i:2003252 original size:15 final size:15
Alignment explanation
Indices: 2003226--2003335 Score: 73
Period size: 15 Copynumber: 7.1 Consensus size: 15
2003216 ATAATATTTT
2003226 TATTATATAAATATTA
1 TATTA-ATAAATATTA
*
2003242 TATTAATAAATAATA
1 TATTAATAAATATTA
**
2003257 TATT-ATTTAT-TTA
1 TATTAATAAATATTA
2003270 CTTATTAATATACTATATTA
1 --TATTAATA-A--ATATTA
* *
2003290 T-TTATTAATATAATA
1 TATTAATAA-ATATTA
* *
2003305 TATTAACAAATAATA
1 TATTAATAAATATTA
2003320 TATTAATAAATATTA
1 TATTAATAAATATTA
2003335 T
1 T
2003336 TATATTATTA
Statistics
Matches: 74, Mismatches: 12, Indels: 17
0.72 0.12 0.17
Matches are distributed among these distances:
13 2 0.03
14 4 0.05
15 44 0.59
16 13 0.18
17 5 0.07
18 1 0.01
19 2 0.03
20 3 0.04
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (15 bp):
TATTAATAAATATTA
Found at i:2003261 original size:20 final size:20
Alignment explanation
Indices: 2003201--2003354 Score: 88
Period size: 20 Copynumber: 7.8 Consensus size: 20
2003191 ACGTTACAAT
2003201 TATTATATTAATAAAATAATA
1 TATTATATTAAT-AAATAATA
*
2003222 T-TTTTATT-AT--ATAA-A
1 TATTATATTAATAAATAATA
2003237 TATTATATTAATAAATAATA
1 TATTATATTAATAAATAATA
* * *
2003257 TATTATTTATTTACTTATTAATA
1 TATTA--TA-TTAATAAATAATA
* * * *
2003280 TACTATATTATTTATTAATA
1 TATTATATTAATAAATAATA
* *
2003300 TAATATATTAACAAATAATA
1 TATTATATTAATAAATAATA
* * *
2003320 TATTA-ATAAAT-ATTATTA
1 TATTATATTAATAAATAATA
*
2003338 TATTATTAATAATAAAT
1 TATTA-TATTAATAAAT
2003355 GGAGTCTAAA
Statistics
Matches: 102, Mismatches: 20, Indels: 22
0.71 0.14 0.15
Matches are distributed among these distances:
15 2 0.02
16 10 0.10
17 2 0.02
18 10 0.10
19 10 0.10
20 47 0.46
21 5 0.05
22 2 0.02
23 14 0.14
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTATATTAATAAATAATA
Found at i:2003278 original size:23 final size:25
Alignment explanation
Indices: 2003258--2003344 Score: 65
Period size: 28 Copynumber: 3.4 Consensus size: 25
2003248 TAAATAATAT
2003258 ATTAT-TTATTTACTT-AT-TAATAT
1 ATTATATTATTTA-TTAATATAATAT
*
2003281 ACTATATTATTTATTAATATAATAT
1 ATTATATTATTTATTAATATAATAT
* * *
2003306 ATTAACAAATAATATATTAATA-AATATT
1 ATT---ATATTATTTATTAATATAATA-T
2003334 ATTATATTATT
1 ATTATATTATT
2003345 AATAATAAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
23 6 0.12
24 9 0.18
25 13 0.27
27 4 0.08
28 17 0.35
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (25 bp):
ATTATATTATTTATTAATATAATAT
Found at i:2007135 original size:17 final size:18
Alignment explanation
Indices: 2007099--2007146 Score: 66
Period size: 16 Copynumber: 2.8 Consensus size: 18
2007089 AAAACGCATT
2007099 ATCC-TTTAAATATTCGA
1 ATCCATTTAAATATTCGA
2007116 ATCCATTTAAATATTC-A
1 ATCCATTTAAATATTCGA
*
2007133 AT-CACTTAAATATT
1 ATCCATTTAAATATT
2007147 TTTGTGAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 11 0.38
17 7 0.24
18 11 0.38
ACGTcount: A:0.40, C:0.17, G:0.02, T:0.42
Consensus pattern (18 bp):
ATCCATTTAAATATTCGA
Found at i:2007713 original size:29 final size:29
Alignment explanation
Indices: 2007680--2007737 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
2007670 CCTTATATAA
*
2007680 TAAAATAGT-AAATTCTATAATTAGAAATT
1 TAAAATAGTAAAATT-TATAATTAAAAATT
*
2007709 TAAAATAGTAAAATTTATGATTAAAAATT
1 TAAAATAGTAAAATTTATAATTAAAAATT
2007738 AAGGTTCATG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (29 bp):
TAAAATAGTAAAATTTATAATTAAAAATT
Found at i:2012775 original size:24 final size:25
Alignment explanation
Indices: 2012730--2012778 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
2012720 TTAAAAAATT
*
2012730 ATTATTAAAAAAATCATAAATTTTAA
1 ATTAATAAAAAAA-CATAAATTTTAA
*
2012756 ATTAATAAAAAAA-ATTAATTTTA
1 ATTAATAAAAAAACATAAATTTTA
2012779 CCATTTTGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 9 0.43
26 12 0.57
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (25 bp):
ATTAATAAAAAAACATAAATTTTAA
Found at i:2016525 original size:141 final size:143
Alignment explanation
Indices: 2016366--2016641 Score: 316
Period size: 141 Copynumber: 1.9 Consensus size: 143
2016356 TCGAAGTTAA
* *
2016366 ATTTTTGTGAAAACTTTCAAAGCATAATTGAAT-ATATTTAATGATTTTTTA-TGCATTGAAAAC
1 ATTTTTGTGAAAACTTTCAAAGCATAATTGAATAATATTTAATGA-TTTTTAGTGCA-TCAAAAA
* *
2016429 CTA-GATCA-TACCCT-GAGAGATGTGAAATTACC-AAATGCCCCAT-AGAGATAATTTCGTAAT
64 CTACGAT-AGTACCCTGGAAAG-TGTGAAATTACCAAAATACCCCATAAG-GATAATTTCGTAAT
2016489 TTGACCTTTTTAAGGTCG
126 TTGACCTTTTTAAGGTCG
* * ** *
2016507 ATTTTTGTG-AAACTTTTCAAATCATGATTTTATAATATTTTATGATTTTTAGTGCATCAAAAAC
1 ATTTTTGTGAAAAC-TTTCAAAGCATAATTGAATAATATTTAATGATTTTTAGTGCATCAAAAAC
** * * *
2016571 TACGATAGTACTTTGGAAAGTGTGAAATTACCAAAATACCTCTTAAGGGTAATTTCGTAATTTGA
65 TACGATAGTACCCTGGAAAGTGTGAAATTACCAAAATACCCCATAAGGATAATTTCGTAATTTGA
2016636 CCTTTT
130 CCTTTT
2016642 CGAGGTTAGA
Statistics
Matches: 113, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
140 4 0.04
141 39 0.35
142 33 0.29
143 35 0.31
144 2 0.02
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (143 bp):
ATTTTTGTGAAAACTTTCAAAGCATAATTGAATAATATTTAATGATTTTTAGTGCATCAAAAACT
ACGATAGTACCCTGGAAAGTGTGAAATTACCAAAATACCCCATAAGGATAATTTCGTAATTTGAC
CTTTTTAAGGTCG
Found at i:2018195 original size:27 final size:27
Alignment explanation
Indices: 2018165--2018216 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
2018155 CAAAACACTA
2018165 AACCATAAAC-CTTAAACCCTAAATCCT
1 AACCATAAACGC-TAAACCCTAAATCCT
* *
2018192 AACCTTAAACGCTAAATCCTAAATC
1 AACCATAAACGCTAAACCCTAAATC
2018217 AAACCCTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.44, C:0.31, G:0.02, T:0.23
Consensus pattern (27 bp):
AACCATAAACGCTAAACCCTAAATCCT
Found at i:2018197 original size:20 final size:20
Alignment explanation
Indices: 2018172--2018226 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
2018162 CTAAACCATA
2018172 AACCTTAAACCCTAAATCCT
1 AACCTTAAACCCTAAATCCT
*
2018192 AACCTTAAACGCTAAATCCT
1 AACCTTAAACCCTAAATCCT
* *
2018212 AA-ATCAAACCCTAAA
1 AACCTTAAACCCTAAA
2018227 CTAAACCCCA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 10 0.32
20 21 0.68
ACGTcount: A:0.45, C:0.31, G:0.02, T:0.22
Consensus pattern (20 bp):
AACCTTAAACCCTAAATCCT
Found at i:2018227 original size:7 final size:7
Alignment explanation
Indices: 2018157--2018240 Score: 52
Period size: 7 Copynumber: 12.7 Consensus size: 7
2018147 CCAAAAACCA
*
2018157 AAACACT
1 AAACCCT
*
2018164 AAACCAT
1 AAACCCT
*
2018171 AAACCTT
1 AAACCCT
2018178 AAACCCT
1 AAACCCT
*
2018185 AAATCCT
1 AAACCCT
*
2018192 -AACCTT
1 AAACCCT
*
2018198 AAACGCT
1 AAACCCT
*
2018205 AAATCCT
1 AAACCCT
*
2018212 AAA-TC-
1 AAACCCT
2018217 AAACCCT
1 AAACCCT
2018224 AAA--CT
1 AAACCCT
*
2018229 AAACCCC
1 AAACCCT
2018236 AAACC
1 AAACC
2018241 AAAACTCAAA
Statistics
Matches: 58, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
5 8 0.14
6 6 0.10
7 44 0.76
ACGTcount: A:0.48, C:0.33, G:0.01, T:0.18
Consensus pattern (7 bp):
AAACCCT
Found at i:2019274 original size:17 final size:18
Alignment explanation
Indices: 2019252--2019292 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
2019242 GGACATTTTG
2019252 AAAAAAAAAATTT-AAAT
1 AAAAAAAAAATTTAAAAT
**
2019269 AAAAAAAATTTTTAAAAT
1 AAAAAAAAAATTTAAAAT
2019287 AAAAAA
1 AAAAAA
2019293 GTGTCTTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAAAAAAAATTTAAAAT
Found at i:2019482 original size:25 final size:25
Alignment explanation
Indices: 2019418--2019472 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
2019408 GTGTGGTTTA
* * *
2019418 CATTTCATTCATAGTTTAATTATGT
1 CATTTTATGCATATTTTAATTATGT
*
2019443 CATTTTATGCATATTTTATTTATGT
1 CATTTTATGCATATTTTAATTATGT
2019468 CATTT
1 CATTT
2019473 ATTGTATATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.25, C:0.11, G:0.07, T:0.56
Consensus pattern (25 bp):
CATTTTATGCATATTTTAATTATGT
Found at i:2034947 original size:18 final size:17
Alignment explanation
Indices: 2034897--2034960 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
2034887 GTACTATGCT
*
2034897 TAAAAAAAGAGAAAAAAA
1 TAAAAAAA-AGAAAAATA
* *
2034915 TATAAAATAA-TAAAATGA
1 TA-AAAAAAAGAAAAAT-A
2034933 TAAAAAAAAGAAAAATA
1 TAAAAAAAAGAAAAATA
*
2034950 TGAAAAAAAGA
1 TAAAAAAAAGA
2034961 CTCAAGGCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
17 21 0.57
18 11 0.30
19 5 0.14
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (17 bp):
TAAAAAAAAGAAAAATA
Found at i:2036035 original size:44 final size:46
Alignment explanation
Indices: 2035968--2036102 Score: 144
Period size: 44 Copynumber: 3.1 Consensus size: 46
2035958 ATCAATGAGC
*
2035968 ATTTATTTTTCAAAAGTCATTGAGCCTCTGATTAGAGGAG-C-TTT
1 ATTTATTTTTCAAAAGTCATTGAGCCTCTAATTAGAGGAGCCATTT
*
2036012 ATTTATTTTTCCAAAA-TCGTTGAGCCTCTAATTAGAGGAGCC----
1 ATTTATTTTT-CAAAAGTCATTGAGCCTCTAATTAGAGGAGCCATTT
* * *
2036054 ATTTATTTTTGAAAAGTTCGTT--GCCTCTATTTAGAGGAGCCATTT
1 ATTTATTTTTCAAAAG-TCATTGAGCCTCTAATTAGAGGAGCCATTT
2036099 ATTT
1 ATTT
2036103 CTGGAAAGTT
Statistics
Matches: 79, Mismatches: 4, Indels: 15
0.81 0.04 0.15
Matches are distributed among these distances:
41 22 0.28
42 10 0.13
43 5 0.06
44 32 0.41
45 10 0.13
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.41
Consensus pattern (46 bp):
ATTTATTTTTCAAAAGTCATTGAGCCTCTAATTAGAGGAGCCATTT
Found at i:2036088 original size:41 final size:41
Alignment explanation
Indices: 2035967--2036294 Score: 316
Period size: 41 Copynumber: 8.0 Consensus size: 41
2035957 CATCAATGAG
* *
2035967 CATTTATTTTTCAAAAG-TCATTGAGCCTCTGA-TTAGAGGAGC
1 CATTTATTTTTGAAAAGTTCGTT--GCCTCT-ATTTAGAGGAGC
* * *
2036009 TTTATTTATTTTTCCAAAA--TCGTTGAGCCTCTAATTAGAGGAGC
1 --CATTTATTTTT-GAAAAGTTCGTT--GCCTCTATTTAGAGGAGC
2036053 CATTTATTTTTGAAAAGTTCGTTGCCTCTATTTAGAGGAGC
1 CATTTATTTTTGAAAAGTTCGTTGCCTCTATTTAGAGGAGC
* * *
2036094 CATTTATTTCTGGAAAGTTCGTTGCCTCTATTTAGAAGAGC
1 CATTTATTTTTGAAAAGTTCGTTGCCTCTATTTAGAGGAGC
* * *
2036135 CATTTATTTTT-ACAAAGTTTGTTGCCACTATTTAGAAGAGC
1 CATTTATTTTTGA-AAAGTTCGTTGCCTCTATTTAGAGGAGC
* *
2036176 CATTTATTTCCTG-AAAGTTCGTTGCCTCTATTCAGAGGAGC
1 CATTTATTT-TTGAAAAGTTCGTTGCCTCTATTTAGAGGAGC
* * * * *
2036217 CATTTATTTTT-CAAAGTCCGTTACCTCTATTCAGAGGAGT
1 CATTTATTTTTGAAAAGTTCGTTGCCTCTATTTAGAGGAGC
*
2036257 CATTTATTTTTG--AAG-TCTGTTGCTTCTATTTAGAGGAG
1 CATTTATTTTTGAAAAGTTC-GTTGCCTCTATTTAGAGGAG
2036295 TTTTGTTAAA
Statistics
Matches: 249, Mismatches: 25, Indels: 25
0.83 0.08 0.08
Matches are distributed among these distances:
38 1 0.00
39 20 0.08
40 37 0.15
41 137 0.55
42 11 0.04
43 6 0.02
44 32 0.13
45 5 0.02
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.40
Consensus pattern (41 bp):
CATTTATTTTTGAAAAGTTCGTTGCCTCTATTTAGAGGAGC
Found at i:2036534 original size:3 final size:3
Alignment explanation
Indices: 2036528--2036572 Score: 56
Period size: 3 Copynumber: 14.7 Consensus size: 3
2036518 TTTAATTTTT
*
2036528 TTA TTA TTA TTA TTA TTTA TTA TTTA TTT TTA TTA TT- TTA TTA TT
1 TTA TTA TTA TTA TTA -TTA TTA -TTA TTA TTA TTA TTA TTA TTA TT
2036573 TTCGCTATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 29 0.78
4 6 0.16
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (3 bp):
TTA
Found at i:2036545 original size:20 final size:20
Alignment explanation
Indices: 2036522--2036572 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
2036512 TTAATTTTTA
*
2036522 ATTTTTTTATTATTATTATT
1 ATTTTATTATTATTATTATT
*
2036542 A-TTTATTATTTATTTTTATT
1 ATTTTATTA-TTATTATTATT
2036562 ATTTTATTATT
1 ATTTTATTATT
2036573 TTCGCTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 6 0.22
20 14 0.52
21 7 0.26
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (20 bp):
ATTTTATTATTATTATTATT
Found at i:2036549 original size:13 final size:13
Alignment explanation
Indices: 2036528--2036572 Score: 56
Period size: 14 Copynumber: 3.4 Consensus size: 13
2036518 TTTAATTTTT
2036528 TTATTATTA-TTA
1 TTATTATTATTTA
2036540 TTATTTATTATTTA
1 TTA-TTATTATTTA
*
2036554 TTTTTATTATTTTA
1 TTATTATTA-TTTA
2036568 TTATT
1 TTATT
2036573 TTCGCTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 3 0.11
13 12 0.43
14 13 0.46
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
TTATTATTATTTA
Found at i:2036569 original size:37 final size:37
Alignment explanation
Indices: 2036503--2036605 Score: 120
Period size: 37 Copynumber: 2.7 Consensus size: 37
2036493 TTCTGGCCCA
* *
2036503 ATTTTAGTTTTAATTTTTAATTTTTTTATTATTATT-ATT
1 ATTTTA-TTTTTATTTTT-ATTTTTTTATTATT-TTCACT
* *
2036542 A-TTTATTATTTATTTTTATTATTTTATTATTTTCGCT
1 ATTTTATT-TTTATTTTTATTTTTTTATTATTTTCACT
2036579 ATTTTATTTTTATTTTTATTTTTTTAT
1 ATTTTATTTTTATTTTTATTTTTTTAT
2036606 CTGAAAAGTA
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
36 2 0.04
37 35 0.62
38 18 0.32
39 1 0.02
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (37 bp):
ATTTTATTTTTATTTTTATTTTTTTATTATTTTCACT
Found at i:2036591 original size:6 final size:6
Alignment explanation
Indices: 2036504--2036601 Score: 67
Period size: 6 Copynumber: 15.7 Consensus size: 6
2036494 TCTGGCCCAA
* * *
2036504 TTTTAGT TTTAAT TTTTAAT TTTT-T TATTAT TATTAT TATTTAT TATTTAT
1 TTTTA-T TTTTAT TTTT-AT TTTTAT TTTTAT TTTTAT T-TTTAT T-TTTAT
* *
2036555 TTTTAT TATT-T TATTAT TTTCGCTA- TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTT---TAT TTTTAT TTTTAT TTTTAT TTTT
2036602 TTATCTGAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 17
0.77 0.06 0.17
Matches are distributed among these distances:
5 11 0.14
6 39 0.51
7 22 0.29
8 3 0.04
9 2 0.03
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (6 bp):
TTTTAT
Found at i:2036600 original size:17 final size:17
Alignment explanation
Indices: 2036504--2036600 Score: 67
Period size: 17 Copynumber: 5.5 Consensus size: 17
2036494 TCTGGCCCAA
2036504 TTTTAGTTTTAATTTTTA-
1 TTTTA-TTTT-ATTTTTAT
* *
2036522 ATTT-TTTTATTATTAT
1 TTTTATTTTATTTTTAT
*
2036538 TATTA-TTTATTATTTAT
1 TTTTATTTTATT-TTTAT
*
2036555 TTTTATTATT-TTATTAT
1 TTTTATT-TTATTTTTAT
2036572 TTTCGCTATTTTATTTTTAT
1 TTT---TATTTTATTTTTAT
2036592 TTTTATTTT
1 TTTTATTTT
2036601 TTTATCTGAA
Statistics
Matches: 62, Mismatches: 8, Indels: 19
0.70 0.09 0.21
Matches are distributed among these distances:
15 6 0.10
16 12 0.19
17 21 0.34
18 6 0.10
19 4 0.06
20 13 0.21
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (17 bp):
TTTTATTTTATTTTTAT
Found at i:2037632 original size:7 final size:8
Alignment explanation
Indices: 2037613--2037643 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
2037603 TTCAAACAAA
2037613 AAAAATAT
1 AAAAATAT
2037621 AAAAATAT
1 AAAAATAT
2037629 AAAAAATAT
1 -AAAAATAT
2037638 AAAAAT
1 AAAAAT
2037644 TTTAGAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
AAAAATAT
Found at i:2037633 original size:9 final size:9
Alignment explanation
Indices: 2037612--2037642 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
2037602 TTTCAAACAA
2037612 AAAAAATAT
1 AAAAAATAT
2037621 -AAAAATAT
1 AAAAAATAT
2037629 AAAAAATAT
1 AAAAAATAT
2037638 AAAAA
1 AAAAA
2037643 TTTTAGAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAAAAATAT
Found at i:2040065 original size:3 final size:3
Alignment explanation
Indices: 2040059--2040085 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2040049 TAAATATTAA
2040059 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
2040086 TCTTCTACTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2041752 original size:6 final size:6
Alignment explanation
Indices: 2041741--2041765 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2041731 CTAAAAATCT
2041741 TTAAAA TTAAAA TTAAAA TTAAAA T
1 TTAAAA TTAAAA TTAAAA TTAAAA T
2041766 AATAAATAAT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
TTAAAA
Found at i:2042071 original size:15 final size:16
Alignment explanation
Indices: 2042053--2042088 Score: 58
Period size: 14 Copynumber: 2.4 Consensus size: 16
2042043 GAAAATGGAA
2042053 AAAAATAAA-AAGATT
1 AAAAATAAATAAGATT
2042068 -AAAATAAATAAGATT
1 AAAAATAAATAAGATT
2042083 AAAAAT
1 AAAAAT
2042089 TTAAGAGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 8 0.42
15 6 0.32
16 5 0.26
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (16 bp):
AAAAATAAATAAGATT
Found at i:2042094 original size:14 final size:15
Alignment explanation
Indices: 2042054--2042086 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
2042044 AAAATGGAAA
2042054 AAAATAAA-AAGATT
1 AAAATAAATAAGATT
2042068 AAAATAAATAAGATT
1 AAAATAAATAAGATT
2042083 AAAA
1 AAAA
2042087 ATTTAAGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (15 bp):
AAAATAAATAAGATT
Found at i:2043423 original size:25 final size:26
Alignment explanation
Indices: 2043377--2043434 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 26
2043367 TTGGAATGAA
* **
2043377 AAAAAATCATAATCATGACAAAAAAT
1 AAAAAATAATAAAAATGACAAAAAAT
* *
2043403 AAAAAATAATAAAAATG-CAAATACT
1 AAAAAATAATAAAAATGACAAAAAAT
2043428 AAAAAAT
1 AAAAAAT
2043435 TACATCAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 13 0.48
26 14 0.52
ACGTcount: A:0.69, C:0.09, G:0.03, T:0.19
Consensus pattern (26 bp):
AAAAAATAATAAAAATGACAAAAAAT
Found at i:2053538 original size:17 final size:17
Alignment explanation
Indices: 2053516--2053558 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
2053506 TTTATATACA
2053516 TTTTAATTTATTTCAAT
1 TTTTAATTTATTTCAAT
*
2053533 TTTTAA-TT-TTTGAAT
1 TTTTAATTTATTTCAAT
2053548 TATTTAATTTA
1 T-TTTAATTTA
2053559 ATTATTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
15 7 0.32
16 7 0.32
17 8 0.36
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (17 bp):
TTTTAATTTATTTCAAT
Found at i:2053560 original size:21 final size:21
Alignment explanation
Indices: 2053534--2053574 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2053524 TATTTCAATT
2053534 TTTAATT-TTTGAATTATTTAA
1 TTTAATTATTT-AATTATTTAA
*
2053555 TTTAATTATTTAATTTTTTA
1 TTTAATTATTTAATTATTTA
2053575 TTAATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (21 bp):
TTTAATTATTTAATTATTTAA
Found at i:2053563 original size:13 final size:13
Alignment explanation
Indices: 2053545--2053570 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2053535 TTAATTTTTG
2053545 AATTATTTAATTT
1 AATTATTTAATTT
2053558 AATTATTTAATTT
1 AATTATTTAATTT
2053571 TTTATTAATA
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
AATTATTTAATTT
Found at i:2057944 original size:28 final size:29
Alignment explanation
Indices: 2057898--2057963 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
2057888 ACTCATTTAA
*
2057898 GATTTTTTTGTTCTTAATTTTATAATTAT
1 GATTTTTTTGTTCTAAATTTTATAATTAT
* *
2057927 -ATTTTGTTTGTT-TAAATTTTTTTATTAT
1 GATTTT-TTTGTTCTAAATTTTATAATTAT
2057955 GATTTTTTT
1 GATTTTTTT
2057964 ATTATTCATT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
28 21 0.66
29 11 0.34
ACGTcount: A:0.21, C:0.02, G:0.08, T:0.70
Consensus pattern (29 bp):
GATTTTTTTGTTCTAAATTTTATAATTAT
Found at i:2057961 original size:14 final size:14
Alignment explanation
Indices: 2057942--2057968 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2057932 GTTTGTTTAA
2057942 ATTTTTTTATTATG
1 ATTTTTTTATTATG
2057956 ATTTTTTTATTAT
1 ATTTTTTTATTAT
2057969 TCATTAACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (14 bp):
ATTTTTTTATTATG
Found at i:2059730 original size:10 final size:10
Alignment explanation
Indices: 2059715--2059745 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2059705 TTAGTCGAAC
2059715 CGAGTTGAAT
1 CGAGTTGAAT
2059725 CGAGTTGAAT
1 CGAGTTGAAT
*
2059735 CGACTTGAAT
1 CGAGTTGAAT
2059745 C
1 C
2059746 ATGTTCTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (10 bp):
CGAGTTGAAT
Found at i:2061839 original size:16 final size:15
Alignment explanation
Indices: 2061814--2061849 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
2061804 AATATTAAAC
2061814 AAATAAAATAAATAA
1 AAATAAAATAAATAA
*
2061829 AAATAATAATAATTAA
1 AAATAA-AATAAATAA
2061845 AAATA
1 AAATA
2061850 CTTAATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (15 bp):
AAATAAAATAAATAA
Found at i:2066176 original size:119 final size:120
Alignment explanation
Indices: 2065967--2066182 Score: 348
Period size: 119 Copynumber: 1.8 Consensus size: 120
2065957 TTGTGCAGGA
* *
2065967 AAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTTGAAACTTTTAATTTCAAGTAAAAT
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTTGAAACGTTTAATTTCAAGGAAAAT
*
2066032 TGATACTTTCAACTTTTCCTTAAAAATATTTTGTTTAGAAATCTTATTTTCAAGG
66 TGATACTTTCAACTTTTCCTCAAAAATATTTTGTTTAGAAATCTTATTTTCAAGG
* *
2066087 AAAATTGATACTTTCAACTTTT-TCTCAAAAATAT-TTTTTTAGAAA-GTTTATTTTCAAGGAAA
1 AAAATTGATACTTTCAACTTTTCCCT-AAAAATATATTTTTT-GAAACGTTTAATTTCAAGGAAA
2066149 ATTGATACTTTCAACTTTTCCTCAAAAATATTTT
64 ATTGATACTTTCAACTTTTCCTCAAAAATATTTT
2066183 TTCGAATTTT
Statistics
Matches: 89, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
119 55 0.62
120 34 0.38
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (120 bp):
AAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTTGAAACGTTTAATTTCAAGGAAAAT
TGATACTTTCAACTTTTCCTCAAAAATATTTTGTTTAGAAATCTTATTTTCAAGG
Found at i:2066209 original size:59 final size:59
Alignment explanation
Indices: 2065967--2066196 Score: 333
Period size: 60 Copynumber: 3.9 Consensus size: 59
2065957 TTGTGCAGGA
* *
2065967 AAAATTGATACTTTCAACTTTTCC-CTAAAAATATATTTTTT-GAAACTTTTAATTTCAAGT
1 AAAATTGATACTTTCAACTTTTCCTC-AAAAATAT-TTTTTTAGAAA-TTTTATTTTCAAGG
* *
2066027 AAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTGTTTAGAAATCTTATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTT-TTTAGAAATTTTATTTTCAAGG
* *
2066087 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTAGAAAGTTTATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTAGAAATTTTATTTTCAAGG
*
2066146 AAAATTGATACTTTCAACTTTTCCTCAAAAATA-TTTTTTCG-AATTTTATTT
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTAGAAATTTTATTT
2066197 AAAAAAATAA
Statistics
Matches: 156, Mismatches: 11, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
57 9 0.06
58 7 0.04
59 55 0.35
60 81 0.52
61 4 0.03
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.46
Consensus pattern (59 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTAGAAATTTTATTTTCAAGG
Found at i:2066214 original size:6 final size:6
Alignment explanation
Indices: 2066199--2066448 Score: 103
Period size: 6 Copynumber: 38.5 Consensus size: 6
2066189 TTTTATTTAA
* * *
2066199 AAAAAT AAAATAA AAAAAT GAAAAT AAAAAT AAAGAAA AGTAAAAT AAAAAAT
1 AAAAAT AAAA-AT AAAAAT AAAAAT AAAAAT AAA-AAT A--AAAAT -AAAAAT
* * *
2066252 AAAAAA AAGAATATT AAACAAT AATAAT AATAAT AAAAAAT AAATAAAT
1 AAAAAT AA-AA-A-T AAA-AAT AAAAAT AAAAAT -AAAAAT -AA-AAAT
* * *
2066301 AAATCAT AAAAAT AAATAAAT AAATAAT GAAAAAA ATAAAAT -AAAGT
1 AAA-AAT AAAAAT -AA-AAAT AAA-AAT -AAAAAT A-AAAAT AAAAAT
* * *
2066348 -AAAAT AAAAA- ATAAAT -TAAAT TAAAAT AAAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT -AAAAAT AAAAAT AAAAAT
* * * * * *
2066394 AAAAAT AAATGAAT ATTAAAC AACAAT AACAAT AATAAT AATAAT AATAAAT
1 AAAAAT AAA--AAT A-AAAAT AAAAAT AAAAAT AAAAAT AAAAAT AA-AAAT
2066446 AAA
1 AAA
2066449 TAAATAAATG
Statistics
Matches: 193, Mismatches: 26, Indels: 50
0.72 0.10 0.19
Matches are distributed among these distances:
5 17 0.09
6 90 0.47
7 59 0.31
8 20 0.10
9 7 0.04
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.21
Consensus pattern (6 bp):
AAAAAT
Found at i:2066260 original size:22 final size:22
Alignment explanation
Indices: 2066196--2066386 Score: 123
Period size: 22 Copynumber: 8.8 Consensus size: 22
2066186 GAATTTTATT
* *
2066196 TAAAAAAATAAAATAAAAAAATG
1 TAAAATAA-AAAATAAAAAAAAG
*
2066219 -AAAAT-AAAAATAAAGAAAAG
1 TAAAATAAAAAATAAAAAAAAG
2066239 TAAAATAAAAAATAAAAAAAAG
1 TAAAATAAAAAATAAAAAAAAG
* * * *
2066261 -AATATTAAACAATAATAATAA-
1 TAA-AATAAAAAATAAAAAAAAG
*
2066282 T--AATAAAAAAT-AAATAAA-
1 TAAAATAAAAAATAAAAAAAAG
*
2066300 T-AAATCATAAAAATAAATAAATAAA
1 TAAAAT-A-AAAAATAAA-AAA-AAG
* *
2066325 TAATGA-AAAAAATAAAATAAAG
1 TAA-AATAAAAAATAAAAAAAAG
** *
2066347 TAAAATAAAAAATAAATTAAAT
1 TAAAATAAAAAATAAAAAAAAG
2066369 TAAAATAAAAAATAAAAA
1 TAAAATAAAAAATAAAAA
2066387 TAAAAATAAA
Statistics
Matches: 132, Mismatches: 22, Indels: 29
0.72 0.12 0.16
Matches are distributed among these distances:
18 5 0.04
19 11 0.08
20 13 0.10
21 15 0.11
22 69 0.52
23 4 0.03
24 11 0.08
25 2 0.02
26 1 0.01
27 1 0.01
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.20
Consensus pattern (22 bp):
TAAAATAAAAAATAAAAAAAAG
Found at i:2066298 original size:4 final size:4
Alignment explanation
Indices: 2066283--2066457 Score: 81
Period size: 4 Copynumber: 43.8 Consensus size: 4
2066273 TAATAATAAT
2066283 AATA AA-A AATA AATA AATA AATCA TAA-A AATA AATA AATA AAT- AATGA
1 AATA AATA AATA AATA AATA AAT-A -AATA AATA AATA AATA AATA AAT-A
*
2066331 AAAA AATAA AATA AAGTAA AATA AA-A AATA AATTA AATTAA AATA AA-A
1 AATA AAT-A AATA AA-T-A AATA AATA AATA AA-TA AA-T-A AATA AATA
* * * *
2066379 AAT- AA-A AATA AA-A ATAAA AATA AATG AAT- ATTA AACAA CAATA ACA-A
1 AATA AATA AATA AATA A-ATA AATA AATA AATA AATA AA-TA -AATA A-ATA
2066426 TAAT- AAT- AAT- AAT- AATA AATA AATA AATA AAT
1 -AATA AATA AATA AATA AATA AATA AATA AATA AAT
2066458 GAAAAAAAAA
Statistics
Matches: 139, Mismatches: 8, Indels: 48
0.71 0.04 0.25
Matches are distributed among these distances:
3 34 0.24
4 73 0.53
5 22 0.16
6 10 0.07
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:2066341 original size:86 final size:86
Alignment explanation
Indices: 2066200--2066408 Score: 213
Period size: 86 Copynumber: 2.5 Consensus size: 86
2066190 TTTATTTAAA
* *
2066200 AAAATAAAATAA-AAAAATGAAAATAAAAATAAAGAAA-AGTAA-AAT--AAAAAATAAAAAAAA
1 AAAATAAAA-AATAAAAATAAAAATAAAAATAAATAAATA--AATAATGAAAAAAATAAAAAAAA
* *
2066260 G-AATATTAAACAAT-AA-T-AA-T
63 GTAA-AATAAAAAATAAATTAAATT
* *
2066280 AATAATAAAAAATAAATAAATAAATCATAAAAATAAATAAATAAATAATGAAAAAAATAAAATAA
1 AA-AATAAAAAAT-AA-AAATAAA-AATAAAAATAAATAAATAAATAATGAAAAAAATAAAAAAA
2066345 AGTAAAATAAAAAATAAATTAAATT
62 AGTAAAATAAAAAATAAATTAAATT
*
2066370 AAAATAAAAAATAAAAATAAAAATAAAAATAAATGAATA
1 AAAATAAAAAATAAAAATAAAAATAAAAATAAATAAATA
2066409 TTAAACAACA
Statistics
Matches: 107, Mismatches: 8, Indels: 22
0.78 0.06 0.16
Matches are distributed among these distances:
80 4 0.04
81 7 0.07
82 2 0.02
83 8 0.07
84 17 0.16
85 1 0.01
86 39 0.36
87 11 0.10
88 3 0.03
89 12 0.11
90 3 0.03
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.20
Consensus pattern (86 bp):
AAAATAAAAAATAAAAATAAAAATAAAAATAAATAAATAAATAATGAAAAAAATAAAAAAAAGTA
AAATAAAAAATAAATTAAATT
Found at i:2066352 original size:39 final size:39
Alignment explanation
Indices: 2066209--2066456 Score: 99
Period size: 40 Copynumber: 6.1 Consensus size: 39
2066199 AAAAATAAAA
*
2066209 TAAAAAAATGAAAATAAAAATAAAGA-AAAGTAAAATAAAAAAT
1 TAAAAAAAT-AAAAT-AAAATAAA-ATAAA-T-AAATAAATAAT
* * * *
2066252 AAAAAAAAGAATATTAAACAATAATAAT-AAT-AATAAA-AAA
1 TAAAAAAATAA-AAT-AA-AATAA-AATAAATAAATAAATAAT
*
2066292 TAAATAAATAAATCATAAAA-ATAAATAAATAAAT----AAT
1 TAAAAAAATAAA--ATAAAATA-AAATAAATAAATAAATAAT
* *
2066329 GAAAAAAATAAAATAAAGTAAAATAAA-AAATAAATTAAAT
1 TAAAAAAATAAAATAAAATAAAATAAATAAATAAA-T-AAT
* *
2066369 TAAAATAA-AAAATAAAAATAAAAATAAAAATAAATGAAT-AT
1 TAAAAAAATAAAAT-AAAAT-AAAAT--AAATAAATAAATAAT
*
2066410 TAAACAACAATAACAATAATAATAATAAT-AATAAATAAATAAA
1 TAAA-AA-AATAA-AATAA-AATAA-AATAAATAAATAAATAAT
2066453 TAAA
1 TAAA
2066457 TGAAAAAAAA
Statistics
Matches: 158, Mismatches: 19, Indels: 56
0.68 0.08 0.24
Matches are distributed among these distances:
34 4 0.03
35 12 0.08
36 1 0.01
37 12 0.08
38 4 0.03
39 12 0.08
40 28 0.18
41 18 0.11
42 13 0.08
43 24 0.15
44 20 0.13
45 10 0.06
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.21
Consensus pattern (39 bp):
TAAAAAAATAAAATAAAATAAAATAAATAAATAAATAAT
Found at i:2066383 original size:108 final size:108
Alignment explanation
Indices: 2066199--2066408 Score: 259
Period size: 108 Copynumber: 1.9 Consensus size: 108
2066189 TTTTATTTAA
2066199 AAAAATAAAATAAAAAAATGAAAATAAAAATAAAGAAAAGTAAAATAAAAAATAAAAAAAAGAAT
1 AAAAATAAAATAAAAAAATGAAAATAAAAATAAAGAAAAGTAAAATAAAAAATAAAAAAAAGAAT
* * * *
2066264 ATTAAACAATAATAATAATAATAAAAAATAAATAAATAAATCAT
66 AATAAAAAATAAAAATAAAAAT-AAAAATAAATAAATAAATCAT
* * *
2066308 AAAAAT-AAATAAATAAAT-AATGAA-AAAAATAAA-ATAAAGTAAAATAAAAAATAAATTAAAT
1 AAAAATAAAATAAAAAAATGAA--AATAAAAATAAAGA-AAAGTAAAATAAAAAATAAA-AAAAA
* *
2066369 TAA-AATAAAAAATAAAAATAAAAATAAAAATAAATGAATA
62 GAATAATAAAAAATAAAAATAAAAATAAAAATAAATAAATA
2066409 TTAAACAACA
Statistics
Matches: 88, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
107 17 0.19
108 58 0.66
109 13 0.15
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.20
Consensus pattern (108 bp):
AAAAATAAAATAAAAAAATGAAAATAAAAATAAAGAAAAGTAAAATAAAAAATAAAAAAAAGAAT
AATAAAAAATAAAAATAAAAATAAAAATAAATAAATAAATCAT
Found at i:2066431 original size:108 final size:107
Alignment explanation
Indices: 2066199--2066464 Score: 241
Period size: 108 Copynumber: 2.5 Consensus size: 107
2066189 TTTTATTTAA
*
2066199 AAAAATAAAATAAAAAAATGAA-AATAAAAATAAAGA-AAAGTAAAATAAAAAATAAAAAAAAGA
1 AAAAAT-AAAT-AAATAAT-AATAATAAAAATAAA-ATAAAGTAAAATAAAAAATAAAAAAAAGA
* * * *
2066262 ATATTAAACAATAATAATAATAATAAAAAATAAATAAATAAATCAT
62 ATAATAAAAAATAAAAATAAAAATAAAAAATAAATAAATAAATCAT
* **
2066308 AAAAATAAATAAATAAATAATGAA-AAAAATAAAATAAAGTAAAATAAAAAATAAATTAAATTAA
1 AAAAATAAATAAAT-AATAAT-AATAAAAATAAAATAAAGTAAAATAAAAAATAAA-AAAAAGAA
2066372 -AATAAAAAATAAAAATAAAAAT-AAAAATAAATGAATATTAAA-C--
63 TAATAAAAAATAAAAATAAAAATAAAAAATAAAT-AA-A-TAAATCAT
*
2066415 AACAATAACA-ATAATAATAATAATAATAAAT-AAATAAA-T-AAATGAAAAAA
1 AAAAATAA-ATA-AATAATAATAATAA-AAATAAAATAAAGTAAAAT-AAAAAA
2066465 AAACCTAAGA
Statistics
Matches: 135, Mismatches: 9, Indels: 29
0.78 0.05 0.17
Matches are distributed among these distances:
105 4 0.03
106 9 0.07
107 39 0.29
108 64 0.47
109 15 0.11
110 4 0.03
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.21
Consensus pattern (107 bp):
AAAAATAAATAAATAATAATAATAAAAATAAAATAAAGTAAAATAAAAAATAAAAAAAAGAATAA
TAAAAAATAAAAATAAAAATAAAAAATAAATAAATAAATCAT
Found at i:2066727 original size:22 final size:19
Alignment explanation
Indices: 2066701--2066749 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 19
2066691 TTTCTCAGAA
2066701 TCCCTTCTCTTCTTCTCTCTCT
1 TCCC-TCTCTT-TTC-CTCTCT
2066723 TCCCT-TCTTTTCCTCTCT
1 TCCCTCTCTTTTCCTCTCT
2066741 TCCCTCTCT
1 TCCCTCTCT
2066750 AACCTCGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 11 0.42
19 6 0.23
20 4 0.15
21 1 0.04
22 4 0.15
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (19 bp):
TCCCTCTCTTTTCCTCTCT
Found at i:2066740 original size:18 final size:17
Alignment explanation
Indices: 2066704--2066745 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
2066694 CTCAGAATCC
*
2066704 CTTCTCTTCTTCTCTCT
1 CTTCCCTTCTTCTCTCT
*
2066721 CTTCCCTTCTTTTCCTCT
1 CTTCCCTTCTTCT-CTCT
2066739 CTTCCCT
1 CTTCCCT
2066746 CTCTAACCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (17 bp):
CTTCCCTTCTTCTCTCT
Found at i:2067337 original size:23 final size:22
Alignment explanation
Indices: 2067311--2067417 Score: 76
Period size: 24 Copynumber: 4.7 Consensus size: 22
2067301 ATATTAATAG
*
2067311 ATAACAAAAAAATAATTAGATAA
1 ATAATAAAAAAATAA-TAGATAA
* *
2067334 AT-A-AAAGAAATAGATAAATATA
1 ATAATAAAAAAATA-ATAGATA-A
*
2067356 ATAATAAAAAATAAAAGTAGATAA
1 ATAATAAAAAA-ATAA-TAGATAA
*
2067380 ATAATAAAAATATTAATAGATAA
1 ATAATAAAAA-AATAATAGATAA
*
2067403 A-AATAATAATAATAA
1 ATAATAA-AAAAATAA
2067418 AAATAATATA
Statistics
Matches: 67, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
21 13 0.19
22 14 0.21
23 13 0.19
24 19 0.28
25 8 0.12
ACGTcount: A:0.69, C:0.01, G:0.06, T:0.24
Consensus pattern (22 bp):
ATAATAAAAAAATAATAGATAA
Found at i:2067353 original size:29 final size:28
Alignment explanation
Indices: 2067320--2067384 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 28
2067310 GATAACAAAA
2067320 AAATAATTAGATAAATAAA-AGAAA-TAGAT
1 AAATAATTA-ATAAA-AAATA-AAAGTAGAT
*
2067349 AAATATAATAATAAAAAATAAAAGTAGAT
1 AAATA-ATTAATAAAAAATAAAAGTAGAT
2067378 AAATAAT
1 AAATAAT
2067385 AAAAATATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
28 7 0.23
29 21 0.68
30 3 0.10
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.25
Consensus pattern (28 bp):
AAATAATTAATAAAAAATAAAAGTAGAT
Found at i:2067361 original size:3 final size:3
Alignment explanation
Indices: 2067353--2067456 Score: 54
Period size: 3 Copynumber: 33.3 Consensus size: 3
2067343 ATAGATAAAT
* *
2067353 ATA ATA ATA A-A A-A ATA A-A AGTA GATAA ATA ATA AAA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA A-TA -AT-A ATA ATA ATA ATA ATA ATA
* * *
2067398 GATA AAA ATA ATA ATA ATA AAA ATA ATA TATA TATA TTAA ATA ATGA
1 -ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA -ATA AT-A ATA AT-A
*
2067445 A-A ATA AAA ATA A
1 ATA ATA ATA ATA A
2067457 AAGCCCATTG
Statistics
Matches: 79, Mismatches: 12, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
2 8 0.10
3 51 0.65
4 18 0.23
5 2 0.03
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:2067366 original size:46 final size:50
Alignment explanation
Indices: 2067316--2067424 Score: 120
Period size: 52 Copynumber: 2.2 Consensus size: 50
2067306 AATAGATAAC
*
2067316 AAAAAAATAATTAGAT-A-AAT-AAAAGA-AATAGATAAATATAATAATA
1 AAAAAAATAATTAGATAATAATAAAAAGATAATAGATAAAAATAATAATA
* *
2067362 AAAAATAA-AAGTAGATAAATAATAAAAATATTAATAGATAAAAATAATAATA
1 AAAAA-AATAATTAGAT-AATAATAAAAAGA-TAATAGATAAAAATAATAATA
*
2067414 ATAAAAATAAT
1 AAAAAAATAAT
2067425 ATATATATAT
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
46 12 0.24
47 2 0.04
48 1 0.02
49 3 0.06
50 5 0.10
51 2 0.04
52 25 0.50
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.25
Consensus pattern (50 bp):
AAAAAAATAATTAGATAATAATAAAAAGATAATAGATAAAAATAATAATA
Found at i:2067385 original size:17 final size:16
Alignment explanation
Indices: 2067286--2067419 Score: 70
Period size: 17 Copynumber: 8.4 Consensus size: 16
2067276 AAGTAATCAA
2067286 AATAAAA-AGATAAAT
1 AATAAAATAGATAAAT
* *
2067301 -ATATTAATAGATAACAA
1 AATA-AAATAGATAA-AT
*
2067318 AAAAATAATTAGATAAAT
1 AATAA-AA-TAGATAAAT
*
2067336 AAAAGAAATAGATAAAT
1 AATA-AAATAGATAAAT
*
2067353 -AT--AATA-ATAAAA
1 AATAAAATAGATAAAT
2067365 AATAAAAGTAGATAAAT
1 AATAAAA-TAGATAAAT
* *
2067382 AATAAAA-ATATTAAT
1 AATAAAATAGATAAAT
2067397 AGATAAAAATA-AT-AAT
1 A-AT-AAAATAGATAAAT
2067413 AATAAAA
1 AATAAAA
2067420 ATAATATATA
Statistics
Matches: 94, Mismatches: 10, Indels: 31
0.70 0.07 0.23
Matches are distributed among these distances:
12 5 0.05
13 6 0.06
14 7 0.07
15 13 0.14
16 15 0.16
17 28 0.30
18 12 0.13
19 8 0.09
ACGTcount: A:0.69, C:0.01, G:0.06, T:0.25
Consensus pattern (16 bp):
AATAAAATAGATAAAT
Found at i:2067663 original size:9 final size:9
Alignment explanation
Indices: 2067649--2067678 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
2067639 AACTTGACAC
2067649 TTTTTTTGT
1 TTTTTTTGT
2067658 TTTTTTTGT
1 TTTTTTTGT
2067667 TTTGTTTTGT
1 TTT-TTTTGT
2067677 TT
1 TT
2067679 GTTAAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.60
10 8 0.40
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (9 bp):
TTTTTTTGT
Found at i:2067671 original size:14 final size:14
Alignment explanation
Indices: 2067652--2067681 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2067642 TTGACACTTT
*
2067652 TTTTGTTTTTTTTG
1 TTTTGTTTTGTTTG
2067666 TTTTGTTTTGTTTG
1 TTTTGTTTTGTTTG
2067680 TT
1 TT
2067682 AAATTTTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (14 bp):
TTTTGTTTTGTTTG
Found at i:2067794 original size:44 final size:44
Alignment explanation
Indices: 2067712--2067824 Score: 140
Period size: 44 Copynumber: 2.5 Consensus size: 44
2067702 ATAAGCAGAA
*
2067712 GCTTAATGAC-TTTGAGAAACATAAACAAAGCTCTTTTAATCAAAG
1 GCTTAATGACTTTTGA-AAA-ATAAACAAAGCTCATTTAATCAAAG
* *
2067757 GCTTAATGACTTTTGAAAAATAAACAAGGCTCATTTAATCAGAG
1 GCTTAATGACTTTTGAAAAATAAACAAAGCTCATTTAATCAAAG
* *
2067801 GCTCAACGA-TTTTGGAAAAATAAA
1 GCTTAATGACTTTT-GAAAAATAAA
2067825 TGGCTCCTCT
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
43 4 0.07
44 39 0.64
45 13 0.21
46 5 0.08
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.28
Consensus pattern (44 bp):
GCTTAATGACTTTTGAAAAATAAACAAAGCTCATTTAATCAAAG
Found at i:2067844 original size:42 final size:41
Alignment explanation
Indices: 2067792--2068125 Score: 295
Period size: 42 Copynumber: 8.1 Consensus size: 41
2067782 AAGGCTCATT
*
2067792 TAATCAGAGGCTCAACGATTTTGGAAAAATAAATGGCTCCTC
1 TAATCAGAGGCTCAACAATTTTGG-AAAATAAATGGCTCCTC
* * *
2067834 TAATTAGAGGCTCAACGACTTTGGAAAAATAAATGGCTCCTC
1 TAATCAGAGGCTCAACAATTTTGG-AAAATAAATGGCTCCTC
2067876 TAATCAGAGGCTCAACAATTTT-GAAAAGTAAATGGCTCCTC
1 TAATCAGAGGCTCAACAATTTTGGAAAA-TAAATGGCTCCTC
* * * *
2067917 TAATAAGAGACTCAACAACTTT-GAAAATAACTAAGGCTCCTC
1 TAATCAGAGGCTCAACAATTTTGGAAAATAA--ATGGCTCCTC
* * * *
2067959 TAATAAGAGGCTCAATGACTTTTGGAAAGTAAATGGCT-CTCC
1 TAATCAGAGGCTCAA-CAATTTTGGAAAATAAATGGCTCCT-C
* * *
2068001 TAATCAGAGGCTTAAC--TTTTGGAAAGTAAATTGCTCCTC
1 TAATCAGAGGCTCAACAATTTTGGAAAATAAATGGCTCCTC
* ** * *
2068040 TAAATAAAGACACCTCAAC--TTTTGGAAAGTAAATTGCTCCTC
1 T-AAT-CAGA-GGCTCAACAATTTTGGAAAATAAATGGCTCCTC
* * * * * *
2068082 TAAACAGAGGCACCACAACTTTGAAAAATAAATTGCTCCTC
1 TAATCAGAGGCTCAACAATTTTGGAAAATAAATGGCTCCTC
2068123 TAA
1 TAA
2068126 ACATAGGCAA
Statistics
Matches: 248, Mismatches: 32, Indels: 25
0.81 0.10 0.08
Matches are distributed among these distances:
39 24 0.10
40 15 0.06
41 68 0.27
42 130 0.52
43 4 0.02
44 7 0.03
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (41 bp):
TAATCAGAGGCTCAACAATTTTGGAAAATAAATGGCTCCTC
Found at i:2067931 original size:83 final size:82
Alignment explanation
Indices: 2067768--2068125 Score: 316
Period size: 83 Copynumber: 4.3 Consensus size: 82
2067758 CTTAATGACT
* * * * * *
2067768 TTTGAAAAATAAACAAGGCTCATTTAATCAGAGGCTCAACGATTTTGGAAAAATAAATGGCTCCT
1 TTTGAAAAAT-AA-ATGGCTCCTCTAATAAGAGGCTCAACAATTTT-GAAAAGTAAATGGCTCCT
* *
2067833 CTAATTAGAGGCTCAACGAC
63 CTAATAAGAGGCTCAACAAC
*
2067853 TTTGGAAAAATAAATGGCTCCTCTAATCAGAGGCTCAACAATTTTGAAAAGTAAATGGCTCCTCT
1 TTT-GAAAAATAAATGGCTCCTCTAATAAGAGGCTCAACAATTTTGAAAAGTAAATGGCTCCTCT
*
2067918 AATAAGAGACTCAACAAC
65 AATAAGAGGCTCAACAAC
* * * *
2067936 TTTG-AAAATAACTAAGGCTCCTCTAATAAGAGGCTCAATGACTTTTGGAAAGTAAATGGCT-CT
1 TTTGAAAAATAA--ATGGCTCCTCTAATAAGAGGCTCAA-CAATTTTGAAAAGTAAATGGCTCCT
* * *
2067999 CCTAATCAGAGGCTTAAC--T
63 -CTAATAAGAGGCTCAACAAC
* * * ** * *
2068018 TTTGGAAAGTAAATTGCTCCTCTAAATAAAGACACCTCAAC--TTTTGGAAAGTAAATTGCTCCT
1 TTTGAAAAATAAATGGCTCCTCT-AAT-AAGA-GGCTCAACAATTTTGAAAAGTAAATGGCTCCT
* *
2068081 CTAA-ACAGAGGCACCACAAC
63 CTAATA-AGAGGCTCAACAAC
*
2068101 TTTGAAAAATAAATTGCTCCTCTAA
1 TTTGAAAAATAAATGGCTCCTCTAA
2068126 ACATAGGCAA
Statistics
Matches: 229, Mismatches: 31, Indels: 29
0.79 0.11 0.10
Matches are distributed among these distances:
81 46 0.20
82 12 0.05
83 93 0.41
84 66 0.29
85 5 0.02
86 7 0.03
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (82 bp):
TTTGAAAAATAAATGGCTCCTCTAATAAGAGGCTCAACAATTTTGAAAAGTAAATGGCTCCTCTA
ATAAGAGGCTCAACAAC
Found at i:2067955 original size:125 final size:123
Alignment explanation
Indices: 2067810--2068125 Score: 349
Period size: 125 Copynumber: 2.6 Consensus size: 123
2067800 GGCTCAACGA
* *
2067810 TTTTGGAAAAATAAATGGCTCCTCTAATTAGAGGCTCAACGACTTTGGAAAAATAAATGGCTCCT
1 TTTTGG-AAAATAAAAGGCTCCTCTAATAAGAGGCTCAACGACTTTGGAAAAATAAATGGCTCCT
*
2067875 CTAATCAGAGGCTCAACAATTTTGAAAAGTAAATGGCTCCTCT-AATAAGAGACTCAACAAC
65 CTAATCAGAGGCTCAAC--TTTTGAAAAGTAAATGGCTCCTCTAAATAA-AGACACAACAAC
* *
2067936 -TTT-GAAAATAACTAAGGCTCCTCTAATAAGAGGCTCAATGACTTTTGG-AAAGTAAATGGCT-
1 TTTTGGAAAATAA--AAGGCTCCTCTAATAAGAGGCTCAACGAC-TTTGGAAAAATAAATGGCTC
* * * **
2067997 CTCCTAATCAGAGGCTTAACTTTTGGAAAGTAAATTGCTCCTCTAAATAAAGACACCTCAAC
63 CT-CTAATCAGAGGCTCAACTTTTGAAAAGTAAATGGCTCCTCTAAATAAAGACACAACAAC
* ** * * * *
2068059 TTTTGGAAAGTAAATTGCTCCTCTAA-ACAGAGGCACCACAACTTT-GAAAAATAAATTGCTCCT
1 TTTTGGAAAATAAAAGGCTCCTCTAATA-AGAGGCTCAACGACTTTGGAAAAATAAATGGCTCCT
2068122 CTAA
65 CTAA
2068126 ACATAGGCAA
Statistics
Matches: 161, Mismatches: 19, Indels: 24
0.79 0.09 0.12
Matches are distributed among these distances:
121 1 0.01
122 19 0.12
123 61 0.38
124 11 0.07
125 64 0.40
126 5 0.03
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.28
Consensus pattern (123 bp):
TTTTGGAAAATAAAAGGCTCCTCTAATAAGAGGCTCAACGACTTTGGAAAAATAAATGGCTCCTC
TAATCAGAGGCTCAACTTTTGAAAAGTAAATGGCTCCTCTAAATAAAGACACAACAAC
Found at i:2069915 original size:34 final size:33
Alignment explanation
Indices: 2069851--2069915 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 33
2069841 CATTTTTTCT
** **
2069851 TCTTTCTTTCTTTTTTTTCTTTTTTTTTCATCA
1 TCTTTCTTTCTTTTTTTAATTTTTCATTCATCA
*
2069884 TCTTTTTTTCTTTTTTCTAATTTTTCATTCAT
1 TCTTTCTTTCTTTTTT-TAATTTTTCATTCAT
2069916 TGTTAATATC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
33 15 0.58
34 11 0.42
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (33 bp):
TCTTTCTTTCTTTTTTTAATTTTTCATTCATCA
Found at i:2072257 original size:15 final size:15
Alignment explanation
Indices: 2072239--2072275 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
2072229 ACTGAGCTTA
2072239 AGGTGGACCAAAACC
1 AGGTGGACCAAAACC
2072254 AGGTGGACCAAAACC
1 AGGTGGACCAAAACC
2072269 AGGTGGA
1 AGGTGGA
2072276 TATAGGGGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.38, C:0.22, G:0.32, T:0.08
Consensus pattern (15 bp):
AGGTGGACCAAAACC
Found at i:2073943 original size:58 final size:59
Alignment explanation
Indices: 2073729--2073946 Score: 237
Period size: 58 Copynumber: 3.7 Consensus size: 59
2073719 TTGTGCAGGG
** * ** * *
2073729 AAATTGATACTTTCAACTTTTTTTCAAAAATATATTTTTTGAAATTTTTAATTTCGAA-AA
1 AAATTGATACTTTCAACTTTTCCTCAAAAATATAATTTTTGAAA-ACTT-ATTTCTAAGGA
* * *
2073789 AAATTGATACTTTCAACTTTTCCTCAAAAAT-TCACTTTTGAAAACTTGTTTCTAAGGA
1 AAATTGATACTTTCAACTTTTCCTCAAAAATATAATTTTTGAAAACTTATTTCTAAGGA
* * * ** *
2073847 AAATTGATACTTTGAGCTTTTTCTCAAAAAT-CCATTTTTGAAAACTTATTTTTAAGGA
1 AAATTGATACTTTCAACTTTTCCTCAAAAATATAATTTTTGAAAACTTATTTCTAAGGA
*
2073905 AAATTGATACTTTCAACTTTTCCTCAAAAATAT-TTTTTTGAA
1 AAATTGATACTTTCAACTTTTCCTCAAAAATATAATTTTTGAA
2073947 TTTTATTTAA
Statistics
Matches: 134, Mismatches: 22, Indels: 6
0.83 0.14 0.04
Matches are distributed among these distances:
57 6 0.04
58 90 0.67
59 9 0.07
60 29 0.22
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (59 bp):
AAATTGATACTTTCAACTTTTCCTCAAAAATATAATTTTTGAAAACTTATTTCTAAGGA
Found at i:2073967 original size:5 final size:5
Alignment explanation
Indices: 2073959--2074172 Score: 104
Period size: 5 Copynumber: 41.8 Consensus size: 5
2073949 TTATTTAAAG
*
2073959 AAAAT AAAAT --AAT AAAAT AAAAAT AAAAAT AAAGA- AAAGT AAAAT
1 AAAAT AAAAT AAAAT AAAAT -AAAAT -AAAAT AAA-AT AAAAT AAAAT
* * * * * **
2074004 AAAAAT AAAAT AAAAAT AAAAAT AAAAG AATAT TAAA- CAATT CTAAT
1 -AAAAT AAAAT -AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
* *
2074051 ATAAT AATAAT AATAAT AATAAT AAAAT AAAAT -AAA- AAAGT AAAAT
1 AAAAT AA-AAT AA-AAT AA-AAT AAAAT AAAAT AAAAT AAAAT AAAAT
* * * * *
2074097 AAAA- AATA- AAAAT AAAAT AAAAAT AAAAAT AAAAG AATAT TAAAC AATAAT
1 AAAAT AAAAT AAAAT AAAAT -AAAAT -AAAAT AAAAT AAAAT AAAAT AA-AAT
2074148 AATAAT AATAAT AAAAT AAAA- AAAA
1 AA-AAT AA-AAT AAAAT AAAAT AAAA
2074173 ACTTGGGAAC
Statistics
Matches: 170, Mismatches: 25, Indels: 29
0.76 0.11 0.13
Matches are distributed among these distances:
3 3 0.02
4 17 0.10
5 78 0.46
6 72 0.42
ACGTcount: A:0.75, C:0.01, G:0.02, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:2074059 original size:3 final size:3
Alignment explanation
Indices: 2074047--2074166 Score: 91
Period size: 3 Copynumber: 43.0 Consensus size: 3
2074037 TAAACAATTC
2074047 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA -AA TAA -AA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
2074090 GTAA -AA TAA -AA -AA TAA AAA TAA -AA TAA AAA TAA AAA TAA -AA
1 -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
2074131 GAA TAT TAAA CAA TAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2074167 AAAAAAACTT
Statistics
Matches: 95, Mismatches: 11, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
2 22 0.23
3 70 0.74
4 3 0.03
ACGTcount: A:0.73, C:0.01, G:0.02, T:0.24
Consensus pattern (3 bp):
TAA
Found at i:2074128 original size:100 final size:100
Alignment explanation
Indices: 2073959--2074168 Score: 320
Period size: 100 Copynumber: 2.1 Consensus size: 100
2073949 TTATTTAAAG
2073959 AAAATAAAATAATAAAATAAAAATAAAAATAAAGAAAAGTAAAATAAAAATAAAATAAAAATAAA
1 AAAATAAAATAATAAAATAAAAATAAAAATAAAGAAAAG-AAAATAAAAATAAAATAAAAATAAA
**
2074024 AATAAAAGAATATTAAACAATTCTAAT-ATAATAAT
65 AATAAAAGAATATTAAACAATAATAATAATAATAAT
*
2074059 AATAATAATAATAATAAAAT-AAAATAAAAAAGTAAA-ATAA-AAAATAAAAATAAAATAAAAAT
1 AA-AATAA-AATAATAAAATAAAAAT-AAAAA-TAAAGAAAAGAAAATAAAAATAAAATAAAAAT
2074121 AAAAATAAAAGAATATTAAACAATAATAATAATAATAAT
62 AAAAATAAAAGAATATTAAACAATAATAATAATAATAAT
2074160 AAAATAAAA
1 AAAATAAAA
2074169 AAAAACTTGG
Statistics
Matches: 102, Mismatches: 3, Indels: 11
0.88 0.03 0.09
Matches are distributed among these distances:
99 2 0.02
100 57 0.56
101 20 0.20
102 19 0.19
103 4 0.04
ACGTcount: A:0.74, C:0.01, G:0.02, T:0.22
Consensus pattern (100 bp):
AAAATAAAATAATAAAATAAAAATAAAAATAAAGAAAAGAAAATAAAAATAAAATAAAAATAAAA
ATAAAAGAATATTAAACAATAATAATAATAATAAT
Found at i:2074153 original size:6 final size:6
Alignment explanation
Indices: 2073961--2074166 Score: 95
Period size: 6 Copynumber: 36.3 Consensus size: 6
2073951 ATTTAAAGAA
* * * *
2073961 AATAA- AATAAT AA-AAT AAAAAT AAAAAT AA-AGAA AAGTAA- AATAAA
1 AATAAT AATAAT AATAAT AATAAT AATAAT AATA-AT AA-TAAT AATAAT
* * * * * **
2074007 AATAA- AATAAA AATAAA AATAA- AAGAAT ATTAAAC AATTCT AAT-AT
1 AATAAT AATAAT AATAAT AATAAT AATAAT AAT-AAT AATAAT AATAAT
2074053 AATAAT AATAAT AATAAT AATAA- AATAA- AATAA- AA-AAGT AA-AAT
1 AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT AATAA-T AATAAT
* * * * * *
2074097 AA-AA- AATAAA AATAA- AATAAA AATAAA AATAA- AAGAAT ATTAAAC
1 AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT AAT-AAT
2074142 AATAAT AATAAT AATAAT AA-AAT AA
1 AATAAT AATAAT AATAAT AATAAT AA
2074167 AAAAAAACTT
Statistics
Matches: 168, Mismatches: 16, Indels: 34
0.77 0.07 0.16
Matches are distributed among these distances:
4 4 0.02
5 60 0.36
6 94 0.56
7 9 0.05
8 1 0.01
ACGTcount: A:0.74, C:0.01, G:0.02, T:0.22
Consensus pattern (6 bp):
AATAAT
Found at i:2074169 original size:6 final size:6
Alignment explanation
Indices: 2073959--2074130 Score: 108
Period size: 6 Copynumber: 28.5 Consensus size: 6
2073949 TTATTTAAAG
*
2073959 AAAAT- AAAATAA TAAAATA AAAATA AAAATA AAGAAAA GTAAAATA AAAAT-
1 AAAATA AAAAT-A -AAAATA AAAATA AAAATA AA-AATA --AAAATA AAAATA
* * * * ** *
2074010 AAAATA AAAATA AAAAT- AAAAGA ATATTA AACAATT CTAAT- ATAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AA-AATA AAAATA AAAATA
* * *
2074057 ATAATA ATAATA ATAAT- AAAAT- AAAATA AAAA-A GTAAAATAA AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA --AAAAT-A AAAATA
2074105 AAAAT- AAAATA AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAA
2074131 GAATATTAAA
Statistics
Matches: 138, Mismatches: 13, Indels: 31
0.76 0.07 0.17
Matches are distributed among these distances:
5 33 0.24
6 79 0.57
7 15 0.11
8 8 0.06
9 3 0.02
ACGTcount: A:0.76, C:0.01, G:0.02, T:0.21
Consensus pattern (6 bp):
AAAATA
Found at i:2075078 original size:20 final size:20
Alignment explanation
Indices: 2075046--2075165 Score: 61
Period size: 20 Copynumber: 5.7 Consensus size: 20
2075036 AATATATTAA
2075046 TAGATAACA-AAAAAAATAAT
1 TAGATAA-ATAAAAAAATAAT
2075066 TAGATAAATAAAAGAAATAGAT
1 TAGATAAATAAAA-AAATA-AT
* *
2075088 AAATA-ATAATAATAAAAAATAAAAG
1 ---TAGAT-A-AATAAAAAA-ATAAT
*
2075113 CAGATAAATAATAAAAAT-AT
1 TAGATAAATAA-AAAAATAAT
*
2075133 TA-ATAGATAAAAATAATAAT
1 TAGATAAATAAAAA-AATAAT
*
2075153 AAGA-AAATAAAAA
1 TAGATAAATAAAAA
2075166 TAAAAAATAT
Statistics
Matches: 77, Mismatches: 9, Indels: 28
0.68 0.08 0.25
Matches are distributed among these distances:
18 3 0.04
19 11 0.14
20 24 0.31
21 12 0.16
22 8 0.10
23 2 0.03
24 2 0.03
25 6 0.08
26 9 0.12
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.22
Consensus pattern (20 bp):
TAGATAAATAAAAAAATAAT
Done.