Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold36
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: 4808052
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 18886 characters in sequence are not A, C, G, or T
File 12 of 28
Found at i:1898655 original size:18 final size:18
Alignment explanation
Indices: 1898632--1898679 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
1898622 TTTTTTAAAA
1898632 AATTATTTATTAAAAATT
1 AATTATTTATTAAAAATT
*
1898650 AATTATTAACTTAAAAATT
1 AATTATTTA-TTAAAAATT
1898669 ATATT-TTTATT
1 A-ATTATTTATT
1898680 TATTTTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 10 0.38
19 13 0.50
20 3 0.12
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
AATTATTTATTAAAAATT
Found at i:1898721 original size:18 final size:17
Alignment explanation
Indices: 1898700--1898739 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 17
1898690 TTAATATATA
1898700 TTTTTAAAATATAATAATT
1 TTTTTAAAATAT--TAATT
1898719 TTTATTAAAATATTAATT
1 TTT-TTAAAATATTAATT
1898737 TTT
1 TTT
1898740 ACTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.40
19 3 0.15
20 9 0.45
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTTTAAAATATTAATT
Found at i:1898751 original size:21 final size:19
Alignment explanation
Indices: 1898703--1898740 Score: 60
Period size: 18 Copynumber: 2.0 Consensus size: 19
1898693 ATATATATTT
1898703 TTAAAATATAATAATTTTTA
1 TTAAAATAT-ATAATTTTTA
1898723 TTAAAATAT-TAATTTTTA
1 TTAAAATATATAATTTTTA
1898741 CTTATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
20 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTAAAATATATAATTTTTA
Found at i:1899180 original size:13 final size:14
Alignment explanation
Indices: 1899152--1899184 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1899142 ACTAATATAT
1899152 TTTTTAATTAAATA
1 TTTTTAATTAAATA
*
1899166 TTTTTAA-TAATTA
1 TTTTTAATTAAATA
1899179 TTTTTA
1 TTTTTA
1899185 TTTTCATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTTAATTAAATA
Found at i:1902387 original size:3 final size:3
Alignment explanation
Indices: 1902379--1902413 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
1902369 GCTTGTTTCT
*
1902379 TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1902414 TTACTGCTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1908125 original size:13 final size:13
Alignment explanation
Indices: 1908109--1908150 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
1908099 CTATAAAATT
1908109 ATATAAAAATTAA
1 ATATAAAAATTAA
* *
1908122 ATATATAAA-CAA
1 ATATAAAAATTAA
*
1908134 ATATAAAATTTAA
1 ATATAAAAATTAA
1908147 ATAT
1 ATAT
1908151 TTAAATTTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (13 bp):
ATATAAAAATTAA
Found at i:1908128 original size:25 final size:25
Alignment explanation
Indices: 1908100--1908160 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
1908090 AAAATAAAAC
1908100 TATAAAATTATATAAAAATTAAATA
1 TATAAAATTATATAAAAATTAAATA
* *
1908125 TATAAACA-AATATAAAATTTAAATA
1 TATAAA-ATTATATAAAAATTAAATA
* *
1908150 TTTAAATTTAT
1 TATAAAATTAT
1908161 TATTTATATA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
25 28 0.97
26 1 0.03
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (25 bp):
TATAAAATTATATAAAAATTAAATA
Found at i:1908223 original size:49 final size:46
Alignment explanation
Indices: 1908126--1908225 Score: 112
Period size: 49 Copynumber: 2.1 Consensus size: 46
1908116 AATTAAATAT
* * *
1908126 ATAAACAAATATAAAATTTAAATATTTAAATTTATTATTTATATAA
1 ATAAACAAATATAAAATTCAAATATTTAAATTTATTATTCATAAAA
* *
1908172 ATAAACCAAATTTAAATATTCAAATTATTTGAATTTGA-TATTCATAAAA
1 ATAAA-CAAATATAAA-ATTCAAA-TATTTAAATTT-ATTATTCATAAAA
1908221 ATAAA
1 ATAAA
1908226 GTGAATTTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
46 5 0.11
47 9 0.20
48 6 0.13
49 24 0.53
50 1 0.02
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (46 bp):
ATAAACAAATATAAAATTCAAATATTTAAATTTATTATTCATAAAA
Found at i:1908293 original size:40 final size:40
Alignment explanation
Indices: 1908249--1908325 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
1908239 AATATTTTGG
*
1908249 ATATCCAAAATTATTCATATAAAAATCAAAGTAGATTTAA
1 ATATCCAAAATTATTCATATAAAAATCAAAATAGATTTAA
* * *
1908289 ATATCGAATATTATTCATATAAAAATTAAAATAGATT
1 ATATCCAAAATTATTCATATAAAAATCAAAATAGATT
1908326 AAGATACAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.52, C:0.08, G:0.05, T:0.35
Consensus pattern (40 bp):
ATATCCAAAATTATTCATATAAAAATCAAAATAGATTTAA
Found at i:1908881 original size:20 final size:21
Alignment explanation
Indices: 1908843--1908884 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1908833 AAACTAGGGT
*
1908843 TAGGGTTTTACTTTATCTCTC
1 TAGGGTTTTACTATATCTCTC
1908864 TAGGGTTTTAC-ATATCTCTC
1 TAGGGTTTTACTATATCTCTC
1908884 T
1 T
1908885 TTCTTTGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.17, C:0.19, G:0.14, T:0.50
Consensus pattern (21 bp):
TAGGGTTTTACTATATCTCTC
Found at i:1913659 original size:2 final size:2
Alignment explanation
Indices: 1913652--1913677 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1913642 TCAAGGGAAA
1913652 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
1913678 CCATTTTAAC
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:1915490 original size:22 final size:22
Alignment explanation
Indices: 1915439--1915490 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
1915429 TTCAATTAAG
*
1915439 TAAAATATTAAAAATTAATCAAT
1 TAAAA-ATTAAAAATTAATCAAA
* *
1915462 TATAAATTAAATATTAAT-ATAA
1 TAAAAATTAAAAATTAATCA-AA
1915484 TAAAAAT
1 TAAAAAT
1915491 ATTTATATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 1 0.04
22 19 0.79
23 4 0.17
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAAAATTAAAAATTAATCAAA
Found at i:1916672 original size:22 final size:20
Alignment explanation
Indices: 1916647--1916696 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
1916637 TTTTTTATCT
*
1916647 ATTATTATTTAATATAAGTTTA
1 ATTATTATTT-AT-TAAGTATA
*
1916669 ATTATAATTTATTAAGTATA
1 ATTATTATTTATTAAGTATA
*
1916689 ATTTTTAT
1 ATTATTAT
1916697 AATTTATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 13 0.54
21 2 0.08
22 9 0.38
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (20 bp):
ATTATTATTTATTAAGTATA
Found at i:1916680 original size:26 final size:24
Alignment explanation
Indices: 1916651--1916703 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
1916641 TTATCTATTA
1916651 TTATTTAA-TATAAGTTTAATTATAAT
1 TTATTTAAGTATAA-TTT--TTATAAT
1916677 TTA-TTAAGTATAATTTTTATAAT
1 TTATTTAAGTATAATTTTTATAAT
1916700 TTAT
1 TTAT
1916704 AAATAAATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
23 10 0.40
25 7 0.28
26 8 0.32
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.57
Consensus pattern (24 bp):
TTATTTAAGTATAATTTTTATAAT
Found at i:1917167 original size:20 final size:20
Alignment explanation
Indices: 1917131--1917168 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1917121 ATATTAATTT
*
1917131 AATTAATAAAAATATAATAA
1 AATTAATAAAAAGATAATAA
1917151 AATTAA-AATAAAGATAAT
1 AATTAATAA-AAAGATAAT
1917169 TATTTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (20 bp):
AATTAATAAAAAGATAATAA
Found at i:1917201 original size:14 final size:14
Alignment explanation
Indices: 1917164--1917209 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
1917154 TAAAATAAAG
*
1917164 ATAAT-TATTTTTT
1 ATAATATATTTTAT
1917177 ATAA-A-ATTTTAT
1 ATAATATATTTTAT
1917189 ATAATATATTTTAT
1 ATAATATATTTTAT
*
1917203 AAAATAT
1 ATAATAT
1917210 TATCTATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
12 10 0.36
13 5 0.18
14 13 0.46
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
ATAATATATTTTAT
Found at i:1917221 original size:25 final size:24
Alignment explanation
Indices: 1917167--1917231 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
1917157 AATAAAGATA
* *
1917167 ATTATTTTTTATAAAATTTTATAT
1 ATTATATTTTATAAAATATTATAT
* *
1917191 AATATATTTTATAAAATATTATCT
1 ATTATATTTTATAAAATATTATAT
*
1917215 ATTTATATTTAATAAAA
1 A-TTATATTTTATAAAA
1917232 ATTCACACTT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
24 21 0.62
25 13 0.38
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
ATTATATTTTATAAAATATTATAT
Found at i:1919679 original size:50 final size:49
Alignment explanation
Indices: 1919543--1919727 Score: 192
Period size: 50 Copynumber: 3.7 Consensus size: 49
1919533 AGTTGTTTAG
* * * * * *
1919543 AGTCAACAATTACGGTCATCTCTCTCAATTATCAAATGTTAGTAAAAAAT
1 AGTCAACAATTACGATCACCTCTCTCGATTGTCAAAAGTTGGT-AAAAAT
* * *
1919593 CGTCAACAATTATGATCA-CTTTCTCGATTGTCAAAAGTTGGTAAAGAAT
1 AGTCAACAATTACGATCACCTCTCTCGATTGTCAAAAGTTGGTAAA-AAT
* * *
1919642 AGTCAACAATTACAACCACCTCTCTCGATTGTCAAAAGTTGATGAAAAAT
1 AGTCAACAATTACGATCACCTCTCTCGATTGTCAAAAGTTGGT-AAAAAT
* * * *
1919692 AATTAATAATTACGATTACCTCTCTCGATTGTCAAA
1 AGTCAACAATTACGATCACCTCTCTCGATTGTCAAA
1919728 GATTGATAAA
Statistics
Matches: 112, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
48 3 0.03
49 36 0.32
50 70 0.62
51 3 0.03
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (49 bp):
AGTCAACAATTACGATCACCTCTCTCGATTGTCAAAAGTTGGTAAAAAT
Found at i:1920584 original size:16 final size:16
Alignment explanation
Indices: 1920563--1920599 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
1920553 CCTAATTTTA
1920563 AAATTTATTTCAAAAT
1 AAATTTATTTCAAAAT
*
1920579 AAATTTATTTTAAAAT
1 AAATTTATTTCAAAAT
1920595 AAATT
1 AAATT
1920600 ATCGAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (16 bp):
AAATTTATTTCAAAAT
Found at i:1920747 original size:30 final size:27
Alignment explanation
Indices: 1920713--1920793 Score: 83
Period size: 28 Copynumber: 2.9 Consensus size: 27
1920703 TCACCTTAGG
*
1920713 TATTTTGAATGTTTTTCTAATTATTATGTA
1 TATTTTGAA--TTTTT-GAATTATTATGTA
*
1920743 TATTTAGAATTTTTGAATTATTATGTA
1 TATTTTGAATTTTTGAATTATTATGTA
*
1920770 T-TTTTGTATACTTTTGAATTATTA
1 TATTTTG-A-ATTTTTGAATTATTA
1920794 GCCTTTTTCT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
26 4 0.09
27 14 0.31
28 19 0.42
30 8 0.18
ACGTcount: A:0.28, C:0.02, G:0.10, T:0.59
Consensus pattern (27 bp):
TATTTTGAATTTTTGAATTATTATGTA
Found at i:1920762 original size:27 final size:28
Alignment explanation
Indices: 1920731--1920793 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 28
1920721 ATGTTTTTCT
*
1920731 AATTATTATGTATATTTAG-A-ATTTTTG
1 AATTATTATGTAT-TTTAGTATACTTTTG
*
1920758 AATTATTATGTATTTTTGTATACTTTTG
1 AATTATTATGTATTTTAGTATACTTTTG
1920786 AATTATTA
1 AATTATTA
1920794 GCCTTTTTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
26 4 0.12
27 14 0.44
28 14 0.44
ACGTcount: A:0.32, C:0.02, G:0.10, T:0.57
Consensus pattern (28 bp):
AATTATTATGTATTTTAGTATACTTTTG
Found at i:1924100 original size:23 final size:22
Alignment explanation
Indices: 1924056--1924113 Score: 75
Period size: 23 Copynumber: 2.7 Consensus size: 22
1924046 ATATTAATAT
* *
1924056 ATAATAT-AAATATGATATAAA
1 ATAATATAAAATATAATAAAAA
1924077 ATAATATAATAATATAATAAAAA
1 ATAATATAA-AATATAATAAAAA
1924100 ATAAT-TAAAATATA
1 ATAATATAAAATATA
1924114 TTATATAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.39
22 4 0.12
23 16 0.48
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
ATAATATAAAATATAATAAAAA
Found at i:1926159 original size:17 final size:19
Alignment explanation
Indices: 1926128--1926164 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1926118 TGTCTTCGAG
*
1926128 TCATGATCATGTTAT-TTT
1 TCATGATCATCTTATATTT
1926146 TCATG-TCATCTTATATTT
1 TCATGATCATCTTATATTT
1926164 T
1 T
1926165 AATTATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.22, C:0.14, G:0.08, T:0.57
Consensus pattern (19 bp):
TCATGATCATCTTATATTT
Found at i:1926247 original size:84 final size:84
Alignment explanation
Indices: 1926153--1926322 Score: 295
Period size: 84 Copynumber: 2.0 Consensus size: 84
1926143 TTTTCATGTC
* * *
1926153 ATCTTATATTTTAATTATTTTTTTCATATTATATTTATATTATATCTCAATTCATTTACTTGAGA
1 ATCTTATATTTTAATTATTTATTTCATATTATATTTATATTATATCTCAATTCATTTACTTAAAA
1926218 ATAGATCATAACATCTAAT
66 ATAGATCATAACATCTAAT
1926237 ATCTTATATTTTAATTATTTATTTCATATTATATTTATATTATATCTCAATTCATTTACTTAAAA
1 ATCTTATATTTTAATTATTTATTTCATATTATATTTATATTATATCTCAATTCATTTACTTAAAA
* *
1926302 ATCGATCATTACATCTAAT
66 ATAGATCATAACATCTAAT
1926321 AT
1 AT
1926323 ATATATATAT
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
84 81 1.00
ACGTcount: A:0.35, C:0.11, G:0.02, T:0.51
Consensus pattern (84 bp):
ATCTTATATTTTAATTATTTATTTCATATTATATTTATATTATATCTCAATTCATTTACTTAAAA
ATAGATCATAACATCTAAT
Found at i:1928488 original size:19 final size:20
Alignment explanation
Indices: 1928464--1928501 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1928454 ATATCATATT
1928464 TATATTT-AAAATTTTTATA
1 TATATTTGAAAATTTTTATA
*
1928483 TATATTTGATAATTTTTAT
1 TATATTTGAAAATTTTTAT
1928502 TGTGTATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (20 bp):
TATATTTGAAAATTTTTATA
Found at i:1929170 original size:17 final size:17
Alignment explanation
Indices: 1929145--1929178 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1929135 TAAATACTTT
* *
1929145 ATTTTAAATTTAATTTA
1 ATTTAAAATTAAATTTA
1929162 ATTTAAAATTAAATTTA
1 ATTTAAAATTAAATTTA
1929179 TTGAATCTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTAAAATTAAATTTA
Found at i:1930507 original size:2 final size:2
Alignment explanation
Indices: 1930502--1930536 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1930492 TATATGTGTG
1930502 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
1930537 GCCTAGCAAA
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:1932607 original size:3 final size:3
Alignment explanation
Indices: 1932566--1932591 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1932556 GTTCCTTTCT
1932566 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1932592 CGATATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1932775 original size:2 final size:2
Alignment explanation
Indices: 1932768--1932815 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1932758 GTGAAAAATG
1932768 TA 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 TA
1932810 TA TA TA
1 TA TA TA
1932816 ATAGAGCTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1935984 original size:2 final size:2
Alignment explanation
Indices: 1935977--1936003 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1935967 TGGATGGTAT
1935977 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 T
1936004 TTAGAACCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1936110 original size:2 final size:2
Alignment explanation
Indices: 1936097--1936137 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1936087 TCTAAAACAC
*
1936097 TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1936138 TAATTTGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1937321 original size:8 final size:8
Alignment explanation
Indices: 1937310--1937339 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1937300 TCATATAAAC
1937310 ATATATAA
1 ATATATAA
1937318 ATATATAA
1 ATATATAA
*
1937326 ATAAATAA
1 ATATATAA
1937334 ATATAT
1 ATATAT
1937340 CAAAATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
ATATATAA
Found at i:1937416 original size:30 final size:32
Alignment explanation
Indices: 1937380--1937450 Score: 85
Period size: 35 Copynumber: 2.2 Consensus size: 32
1937370 TTTAAACGTG
1937380 TTATTTTA-AT-TA-TATTTTTTAAAACATATT
1 TTATTTTATATATACTATTTTTT-AAACATATT
1937410 TTATTTTATTTATCATACTATTTTTTAAACATATT
1 TTATTTTA--TAT-ATACTATTTTTTAAACATATT
1937445 TTATTT
1 TTATTT
1937451 ATTATGTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
30 8 0.23
33 2 0.06
35 17 0.49
36 8 0.23
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (32 bp):
TTATTTTATATATACTATTTTTTAAACATATT
Found at i:1937765 original size:2 final size:2
Alignment explanation
Indices: 1937760--1937802 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1937750 GGGCCATAGT
*
1937760 TC TC TC TC TC TC TC AC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1937802 T
1 T
1937803 ATATATATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.02, C:0.49, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:1937807 original size:2 final size:2
Alignment explanation
Indices: 1937802--1937829 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1937792 TCTCTCTCTC
1937802 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
1937830 AGGGCTGCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1938241 original size:16 final size:16
Alignment explanation
Indices: 1938219--1938266 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
1938209 ATTAAAAATT
*
1938219 AATAAAATATAACATA
1 AATAAAAAATAACATA
* *
1938235 TATAAAAAATAATATA
1 AATAAAAAATAACATA
1938251 AATAAAAAATAA-ATA
1 AATAAAAAATAACATA
1938266 A
1 A
1938267 TGAATATATC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
15 4 0.14
16 24 0.86
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (16 bp):
AATAAAAAATAACATA
Found at i:1938255 original size:25 final size:25
Alignment explanation
Indices: 1938203--1938254 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
1938193 ATTTTAAACC
*
1938203 TAACATATTAAAAATTAATAAAATA
1 TAACATATTAAAAAATAATAAAATA
1938228 TAACATATATAAAAAATAATATAAATA
1 TAACATAT-TAAAAAATAATA-AAATA
1938255 AAAAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 8 0.33
26 11 0.46
27 5 0.21
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (25 bp):
TAACATATTAAAAAATAATAAAATA
Found at i:1938266 original size:27 final size:26
Alignment explanation
Indices: 1938211--1938266 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
1938201 CCTAACATAT
* * * *
1938211 TAAAAATTAATAAAATATAACATATA
1 TAAAAAATAATAAAATAAAAAATAAA
1938237 TAAAAAATAATATAAATAAAAAATAAA
1 TAAAAAATAATA-AAATAAAAAATAAA
1938264 TAA
1 TAA
1938267 TGAATATATC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (26 bp):
TAAAAAATAATAAAATAAAAAATAAA
Found at i:1938305 original size:32 final size:32
Alignment explanation
Indices: 1938259--1938320 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
1938249 TAAATAAAAA
1938259 ATAAATAATGAATATATCAAAATTTATATAAT
1 ATAAATAATGAATATATCAAAATTTATATAAT
* * * *
1938291 ATAAATTATTAATATATTAAATTTTATATA
1 ATAAATAATGAATATATCAAAATTTATATA
1938321 TATTATTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (32 bp):
ATAAATAATGAATATATCAAAATTTATATAAT
Found at i:1938313 original size:16 final size:16
Alignment explanation
Indices: 1938270--1938325 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 16
1938260 TAAATAATGA
* *
1938270 ATATATCAAAATTTAT
1 ATATATTAAATTTTAT
1938286 ATA-ATATAAATTATTA-
1 ATATAT-TAAATT-TTAT
1938302 ATATATTAAATTTTAT
1 ATATATTAAATTTTAT
1938318 ATATATTA
1 ATATATTA
1938326 TTTAAACATG
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
15 5 0.15
16 24 0.71
17 5 0.15
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATATTAAATTTTAT
Found at i:1939646 original size:2 final size:2
Alignment explanation
Indices: 1939641--1939678 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1939631 GCAAGTGTAC
1939641 AT AT 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 AT AT
1939679 GGATTTGATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1940216 original size:227 final size:227
Alignment explanation
Indices: 1939821--1940277 Score: 878
Period size: 227 Copynumber: 2.0 Consensus size: 227
1939811 AAAATCTCAC
1939821 ATTGAACAGTAGCTAATCATGTAACATCAATTCATCACATGTAAAAGTAATTAAACACTATAAAT
1 ATTGAACAGTAGCTAATCATGTAACATCAATTCATCACATGTAAAAGTAATTAAACACTATAAAT
1939886 CTAAGCAAAATCTTAATCTCAAGATTGCTTTCTACCCCAGCAAAAGGAAATGGAATTGGAATTTA
66 CTAAGCAAAATCTTAATCTCAAGATTGCTTTCTACCCCAGCAAAAGGAAATGGAATTGGAATTTA
* *
1939951 AGGTTACTGGGGGCAAATTTAACCTTCTCAGTGTAGTATCTTAAACTCGGATTAGAAACATGGGA
131 AGGTTACTGGAGGCAAATTTAACCTTCTCAGTGTAGTATCTTAAACTCAGATTAGAAACATGGGA
1940016 AATTTAGCAAACTAATGTTATAGCATTGTAAT
196 AATTTAGCAAACTAATGTTATAGCATTGTAAT
1940048 ATTGAACAGTAGCTAATCATGTAACATCAATTCATCACATGTAAAAGTAATTAAACACTATAAAT
1 ATTGAACAGTAGCTAATCATGTAACATCAATTCATCACATGTAAAAGTAATTAAACACTATAAAT
*
1940113 CTAAGCAAAATCTTAATCTCAAGATTGCTTTCTACCCCAGCAAAAGGAAATGGAATTGGAATTTG
66 CTAAGCAAAATCTTAATCTCAAGATTGCTTTCTACCCCAGCAAAAGGAAATGGAATTGGAATTTA
*
1940178 AGGTTACTGGAGGCAAATTTAACCTTCTCAGTGTAGTATCTTAAGCTCAGATTAGAAACATGGGA
131 AGGTTACTGGAGGCAAATTTAACCTTCTCAGTGTAGTATCTTAAACTCAGATTAGAAACATGGGA
1940243 AATTTAGCAAACTAATGTTATAGCATTGTAAT
196 AATTTAGCAAACTAATGTTATAGCATTGTAAT
1940275 ATT
1 ATT
1940278 ATCAGCATAC
Statistics
Matches: 226, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
227 226 1.00
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (227 bp):
ATTGAACAGTAGCTAATCATGTAACATCAATTCATCACATGTAAAAGTAATTAAACACTATAAAT
CTAAGCAAAATCTTAATCTCAAGATTGCTTTCTACCCCAGCAAAAGGAAATGGAATTGGAATTTA
AGGTTACTGGAGGCAAATTTAACCTTCTCAGTGTAGTATCTTAAACTCAGATTAGAAACATGGGA
AATTTAGCAAACTAATGTTATAGCATTGTAAT
Found at i:1941723 original size:214 final size:214
Alignment explanation
Indices: 1941354--1941776 Score: 837
Period size: 214 Copynumber: 2.0 Consensus size: 214
1941344 AACAAACATG
1941354 TTACTGAAGTGGAAACCAAAAGATGAAAAACAAGCTATATTTTGAGATTCAAGAAAAAAAAATTG
1 TTACTGAAGTGGAAACCAAAAGATGAAAAACAAGCTATATTTTGAGATTCAAGAAAAAAAAATTG
*
1941419 TTGAAAATTACTTTTTTATGTTTGTCACCTACTGATGTCCTCAAACAACTGTACTGAAGAGTTGA
66 TTGAAAATTACTTTTTTATGTTTGCCACCTACTGATGTCCTCAAACAACTGTACTGAAGAGTTGA
1941484 CCAAATGTTGGCTGAATTATAGGTGAAATCTTTGAAGATTTCCTAGCTAAAAATACTGATGTAAT
131 CCAAATGTTGGCTGAATTATAGGTGAAATCTTTGAAGATTTCCTAGCTAAAAATACTGATGTAAT
1941549 TGCTGTAAATATAGCTTGT
196 TGCTGTAAATATAGCTTGT
1941568 TTACTGAAGTGGAAACCAAAAGATGAAAAACAAGCTATATTTTGAGATTCAAGAAAAAAAAATTG
1 TTACTGAAGTGGAAACCAAAAGATGAAAAACAAGCTATATTTTGAGATTCAAGAAAAAAAAATTG
1941633 TTGAAAATTACTTTTTTATGTTTGCCACCTACTGATGTCCTCAAACAACTGTACTGAAGAGTTGA
66 TTGAAAATTACTTTTTTATGTTTGCCACCTACTGATGTCCTCAAACAACTGTACTGAAGAGTTGA
1941698 CCAAATGTTGGCTGAATTATAGGTGAAATCTTTGAAGATTTCCTAGCTAAAAATACTGATGTAAT
131 CCAAATGTTGGCTGAATTATAGGTGAAATCTTTGAAGATTTCCTAGCTAAAAATACTGATGTAAT
1941763 TGCTGTAAATATAG
196 TGCTGTAAATATAG
1941777 TCAGACCTAT
Statistics
Matches: 208, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
214 208 1.00
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (214 bp):
TTACTGAAGTGGAAACCAAAAGATGAAAAACAAGCTATATTTTGAGATTCAAGAAAAAAAAATTG
TTGAAAATTACTTTTTTATGTTTGCCACCTACTGATGTCCTCAAACAACTGTACTGAAGAGTTGA
CCAAATGTTGGCTGAATTATAGGTGAAATCTTTGAAGATTTCCTAGCTAAAAATACTGATGTAAT
TGCTGTAAATATAGCTTGT
Found at i:1946769 original size:8 final size:8
Alignment explanation
Indices: 1946756--1946781 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1946746 TGTAAACTTA
1946756 TTAATATT
1 TTAATATT
1946764 TTAATATT
1 TTAATATT
1946772 TTAATATT
1 TTAATATT
1946780 TT
1 TT
1946782 GCTTGAATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
TTAATATT
Found at i:1946875 original size:20 final size:20
Alignment explanation
Indices: 1946852--1946897 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1946842 TTGATTTGTA
*
1946852 TTAAAAAT-TTTAATTTAAAT
1 TTAAAAATATATAA-TTAAAT
*
1946872 TTAAATATATATAATTAAAT
1 TTAAAAATATATAATTAAAT
1946892 TTAAAA
1 TTAAAA
1946898 TTAAGTATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTAAAAATATATAATTAAAT
Found at i:1952336 original size:12 final size:12
Alignment explanation
Indices: 1952319--1952384 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
1952309 TAATTGAATC
1952319 TTTTTTAATTAA
1 TTTTTTAATTAA
* *
1952331 TTTTTTTATCAA
1 TTTTTTAATTAA
*
1952343 ---TTAAATTAA
1 TTTTTTAATTAA
1952352 TTTTTTAATTAA
1 TTTTTTAATTAA
*
1952364 TTTAATT-ATTAA
1 TTT-TTTAATTAA
1952376 -TTTTTAATT
1 TTTTTTAATT
1952385 CAATAGTCAA
Statistics
Matches: 41, Mismatches: 8, Indels: 11
0.68 0.13 0.18
Matches are distributed among these distances:
9 6 0.15
10 2 0.05
11 5 0.12
12 26 0.63
13 2 0.05
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTTTTAATTAA
Found at i:1952351 original size:21 final size:22
Alignment explanation
Indices: 1952325--1952388 Score: 69
Period size: 21 Copynumber: 2.9 Consensus size: 22
1952315 AATCTTTTTT
*
1952325 AATTAATTTTTTTATCAA-TTA
1 AATTAATTTTTTAATCAATTTA
*
1952346 AATTAATTTTTTAATTAATTTA
1 AATTAATTTTTTAATCAATTTA
1952368 ATTATTAA-TTTTTAATTCAAT
1 A--ATTAATTTTTTAA-TCAAT
1952389 AGTCAATCTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 16 0.44
22 4 0.11
23 7 0.19
24 9 0.25
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (22 bp):
AATTAATTTTTTAATCAATTTA
Found at i:1952827 original size:31 final size:31
Alignment explanation
Indices: 1952786--1952845 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
1952776 AAATTATTTT
*
1952786 AATTTGATTTAAATTATAATT-TAATAATAAA
1 AATTTGATTTAAATT-TAATTATAAAAATAAA
*
1952817 AATTTTATTTAAATTTAATTATAAAAATA
1 AATTTGATTTAAATTTAATTATAAAAATA
1952846 TTTTTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (31 bp):
AATTTGATTTAAATTTAATTATAAAAATAAA
Found at i:1952831 original size:25 final size:24
Alignment explanation
Indices: 1952803--1952873 Score: 81
Period size: 25 Copynumber: 2.9 Consensus size: 24
1952793 TTTAAATTAT
*
1952803 AATTTAATAATAAAAATTTTATTTA
1 AATTTAATAATAAAAATATT-TTTA
*
1952828 AATTTAATTATAAAAATATTTTTA
1 AATTTAATAATAAAAATATTTTTA
*
1952852 AA-TTAATATTTAAATAATATTT
1 AATTTAATA-ATAAA-AATATTT
1952874 AAATAATAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.12
24 10 0.25
25 25 0.62
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
AATTTAATAATAAAAATATTTTTA
Found at i:1952866 original size:22 final size:21
Alignment explanation
Indices: 1952841--1952932 Score: 64
Period size: 22 Copynumber: 4.2 Consensus size: 21
1952831 TTAATTATAA
1952841 AAATATTTTTAAATTAATATTT
1 AAATATTTTTAAATT-ATATTT
* * *
1952863 AAATAATATTTAAATAATAAAATT
1 AAAT-ATTTTTAAAT--TATATTT
*
1952887 -ATTATTTTTAAATTA-ATTT
1 AAATATTTTTAAATTATATTT
*
1952906 AAAT-TTAACTTAAATTATATTT
1 AAATATT--TTTAAATTATATTT
1952928 AAATA
1 AAATA
1952933 AAAATTTTAA
Statistics
Matches: 54, Mismatches: 8, Indels: 15
0.70 0.10 0.19
Matches are distributed among these distances:
19 5 0.09
20 4 0.07
21 8 0.15
22 21 0.39
23 11 0.20
24 4 0.07
25 1 0.02
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (21 bp):
AAATATTTTTAAATTATATTT
Found at i:1952874 original size:23 final size:22
Alignment explanation
Indices: 1952822--1952881 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 22
1952812 ATAAAAATTT
1952822 TATTTAAATTTAAT-TATAAAAA
1 TATTTAAA-TTAATATATAAAAA
*
1952844 TATTTTTAAATTAATATTTAAATAA
1 TA--TTTAAATTAATATATAAA-AA
1952869 TATTTAAA-TAATA
1 TATTTAAATTAATA
1952882 AAATTATTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 7 0.21
23 11 0.33
24 11 0.33
25 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TATTTAAATTAATATATAAAAA
Found at i:1952878 original size:11 final size:11
Alignment explanation
Indices: 1952848--1952881 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
1952838 TAAAAATATT
1952848 TTTAAATTAATA
1 TTTAAA-TAATA
1952860 TTTAAATAATA
1 TTTAAATAATA
1952871 TTTAAATAATA
1 TTTAAATAATA
1952882 AAATTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 16 0.73
12 6 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TTTAAATAATA
Found at i:1952913 original size:11 final size:10
Alignment explanation
Indices: 1952893--1952931 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
1952883 AATTATTATT
1952893 TTTAAATTAA
1 TTTAAATTAA
1952903 TTTAAATTTAA
1 TTTAAA-TTAA
*
1952914 CTTAAATTATA
1 TTTAAATTA-A
1952925 TTTAAAT
1 TTTAAAT
1952932 AAAAATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (10 bp):
TTTAAATTAA
Found at i:1952918 original size:16 final size:16
Alignment explanation
Indices: 1952893--1952931 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1952883 AATTATTATT
*
1952893 TTTAAATTAATTTAAA
1 TTTAAATTAAATTAAA
* *
1952909 TTTAACTTAAATTATA
1 TTTAAATTAAATTAAA
1952925 TTTAAAT
1 TTTAAAT
1952932 AAAAATTTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (16 bp):
TTTAAATTAAATTAAA
Found at i:1953156 original size:13 final size:13
Alignment explanation
Indices: 1953138--1953168 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
1953128 TTTATTTATT
1953138 AAGAAAAAGAAAA
1 AAGAAAAAGAAAA
1953151 AAGAAAAAGAAAA
1 AAGAAAAAGAAAA
1953164 AAGAA
1 AAGAA
1953169 GCTTTGCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAGAAAAAGAAAA
Found at i:1953394 original size:3 final size:3
Alignment explanation
Indices: 1953386--1953414 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1953376 TTCTTTATAT
1953386 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1953415 TCATCTATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:1953456 original size:24 final size:24
Alignment explanation
Indices: 1953429--1953474 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
1953419 CTATCACTCT
1953429 AACCACTAACCCTTCAAAGTCTGA
1 AACCACTAACCCTTCAAAGTCTGA
1953453 AACCACTAACCCTTCAAAGTCT
1 AACCACTAACCCTTCAAAGTCT
1953475 TCAAACTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.37, C:0.35, G:0.07, T:0.22
Consensus pattern (24 bp):
AACCACTAACCCTTCAAAGTCTGA
Found at i:1954692 original size:21 final size:22
Alignment explanation
Indices: 1954647--1954693 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 22
1954637 TATCTCTTCT
1954647 TCTTGGAGCTTACTGATAAAAACTA
1 TCTTGGAGCTTACTG---AAAACTA
1954672 TCTTGGAGCTTACTG-AAACTA
1 TCTTGGAGCTTACTGAAAACTA
1954693 T
1 T
1954694 GTGATGTCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 7 0.32
25 15 0.68
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (22 bp):
TCTTGGAGCTTACTGAAAACTA
Found at i:1961075 original size:14 final size:15
Alignment explanation
Indices: 1961056--1961084 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1961046 ATTAAAATAT
1961056 TATTTTTAT-ATTAA
1 TATTTTTATAATTAA
1961070 TATTTTTATAATTAA
1 TATTTTTATAATTAA
1961085 AATTAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTTTTATAATTAA
Found at i:1961562 original size:29 final size:28
Alignment explanation
Indices: 1961508--1961566 Score: 66
Period size: 30 Copynumber: 2.0 Consensus size: 28
1961498 TTTTTATAAA
1961508 TTTTAATATAATTTTATATTCATATTATTT
1 TTTTAATATAATTTTATATT-ATATT-TTT
* *
1961538 TTTTATTATATTTATTATATT-TATTTTT
1 TTTTAATATAATT-TTATATTATATTTTT
1961566 T
1 T
1961567 ATTTTCAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 4 0.15
29 4 0.15
30 11 0.42
31 7 0.27
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (28 bp):
TTTTAATATAATTTTATATTATATTTTT
Found at i:1962567 original size:4 final size:4
Alignment explanation
Indices: 1962554--1962583 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
1962544 AAGTCGAAAC
1962554 TTTA -TTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1962584 TTTGTGATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:1965561 original size:8 final size:8
Alignment explanation
Indices: 1965548--1965574 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
1965538 TGGGAGCTAA
1965548 AAAAAAAT
1 AAAAAAAT
1965556 AAAAAAAT
1 AAAAAAAT
1965564 AAAAAAAT
1 AAAAAAAT
1965572 AAA
1 AAA
1965575 TGGCAGGGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAAAAAT
Found at i:1967520 original size:35 final size:36
Alignment explanation
Indices: 1967481--1967559 Score: 88
Period size: 35 Copynumber: 2.2 Consensus size: 36
1967471 TTTCTAAATT
* **
1967481 AATTTTAAATAAAAATATGAAATT-ATAAAAAAAAA
1 AATTTAAAATAAAAATAAAAAATTCATAAAAAAAAA
* * *
1967516 AATTTAAAATTAAATTAAAAAATTCATAAAAAATAA
1 AATTTAAAATAAAAATAAAAAATTCATAAAAAAAAA
*
1967552 AATGTAAA
1 AATTTAAA
1967560 GTCATTTTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
35 19 0.53
36 17 0.47
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (36 bp):
AATTTAAAATAAAAATAAAAAATTCATAAAAAAAAA
Found at i:1967990 original size:23 final size:22
Alignment explanation
Indices: 1967953--1967995 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
1967943 TAAAAACTAA
1967953 AAATATAAAATTAAATAATTACT
1 AAATATAAAATTAAA-AATTACT
1967976 AAATATGAAAA-TAAAAATTA
1 AAATAT-AAAATTAAAAATTA
1967996 AATAGTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 10 0.53
24 4 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (22 bp):
AAATATAAAATTAAAAATTACT
Found at i:1968501 original size:23 final size:24
Alignment explanation
Indices: 1968475--1968519 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
1968465 TTATGGTTAT
*
1968475 TCCAATTTATTG-CTTATAATTGC
1 TCCAATTTATTGTCATATAATTGC
*
1968498 TCCATTTTATTGTCATATAATT
1 TCCAATTTATTGTCATATAATT
1968520 AATGTAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.27, C:0.16, G:0.07, T:0.51
Consensus pattern (24 bp):
TCCAATTTATTGTCATATAATTGC
Found at i:1969511 original size:158 final size:158
Alignment explanation
Indices: 1969036--1969511 Score: 889
Period size: 158 Copynumber: 3.0 Consensus size: 158
1969026 ATAATGTAAT
*
1969036 TTTTATTATTCCATTTTAGATATAAAACTATCAAGTTTTTTAATTAAAAAGCATATGCCATTATT
1 TTTTATTATTCCATTTTAGATATAAAACTATCAAGTTTTTTAATTAAAAAGCATATGCCACTATT
*
1969101 ACTTTAAAATATATAATTATATGTTACGTCTTTGTCACACTTGTATCTAAAAAGATATAAATGGA
66 ACCTTAAAATATATAATTATATGTTACGTCTTTGTCACACTTGTATCTAAAAAGATATAAATGGA
* *
1969166 GTAATAATCTTAAATGATTTTTTTATCA
131 GTGATAATCTTAAATGATCTTTTTATCA
*
1969194 ATTTATTATTCCATTTTAGATATAAAACTATCAAGTTTTTTAATTAAAAAAGCATATGCCACTAT
1 TTTTATTATTCCATTTTAGATATAAAACTATCAAGTTTTTTAATT-AAAAAGCATATGCCACTAT
1969259 TACCTTAAAATATATAATTATATGTTACGTCTTTGTCACACTTGTATCTAAAAAGATATAAATGG
65 TACCTTAAAATATATAATTATATGTTACGTCTTTGTCACACTTGTATCTAAAAAGATATAAATGG
1969324 AGTGATAATCTTAAATGATCTTTTTATCA
130 AGTGATAATCTTAAATGATCTTTTTATCA
1969353 TTTTATTATTCCATTTTAGATATAAAACTATCAAGTTTTTTAATTAAAAAGCATATGCCACTATT
1 TTTTATTATTCCATTTTAGATATAAAACTATCAAGTTTTTTAATTAAAAAGCATATGCCACTATT
*
1969418 ACCTTAAAATATATAATTATATGTTACGTCTTTGTCACACTTGTATCTAAAAAGATATAAATAGA
66 ACCTTAAAATATATAATTATATGTTACGTCTTTGTCACACTTGTATCTAAAAAGATATAAATGGA
1969483 GTGATAATCTTAAATGATCTTTTTATCA
131 GTGATAATCTTAAATGATCTTTTTATCA
1969511 T
1 T
1969512 AATTTATGAG
Statistics
Matches: 310, Mismatches: 7, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
158 157 0.51
159 153 0.49
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.42
Consensus pattern (158 bp):
TTTTATTATTCCATTTTAGATATAAAACTATCAAGTTTTTTAATTAAAAAGCATATGCCACTATT
ACCTTAAAATATATAATTATATGTTACGTCTTTGTCACACTTGTATCTAAAAAGATATAAATGGA
GTGATAATCTTAAATGATCTTTTTATCA
Found at i:1970095 original size:37 final size:34
Alignment explanation
Indices: 1970041--1970138 Score: 97
Period size: 37 Copynumber: 2.8 Consensus size: 34
1970031 TTATTAAGTG
* *
1970041 TGTTAGATAAACATATTAGGTGTGTTAAGTAGTA
1 TGTTAGGTAAATATATTAGGTGTGTTAAGTAGTA
* * ** * *
1970075 TGTTAGGTGAGTAATATATTAAGTGTATTCGGTGGTG
1 TGTTAGGT-A--AATATATTAGGTGTGTTAAGTAGTA
1970112 TGTTAGGTAAATATATTAGGTGTGTTA
1 TGTTAGGTAAATATATTAGGTGTGTTA
1970139 GGTGAACTTA
Statistics
Matches: 50, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
34 22 0.44
35 1 0.02
36 1 0.02
37 26 0.52
ACGTcount: A:0.30, C:0.02, G:0.28, T:0.41
Consensus pattern (34 bp):
TGTTAGGTAAATATATTAGGTGTGTTAAGTAGTA
Found at i:1976080 original size:52 final size:52
Alignment explanation
Indices: 1976002--1976203 Score: 284
Period size: 52 Copynumber: 3.9 Consensus size: 52
1975992 CGAAATATGA
1976002 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
** *
1976054 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATTGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
* * *
1976106 AAATTTGCCTGCATGTATCGATACATT-ATAAAATGTATCGATACATGC-AGGC
1 AAATTTGCCTGCATGTATCGATACATTGA-ATAGTGTATCGATACAT-CTGGGC
**
1976158 AAATTTGCCTGCATGTATCGATACAAAG-ATCAGTGTATCGATACAT
1 AAATTTGCCTGCATGTATCGATACATTGAAT-AGTGTATCGATACAT
1976204 TGTATCGATA
Statistics
Matches: 134, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
51 1 0.01
52 132 0.99
53 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
Found at i:1976209 original size:13 final size:13
Alignment explanation
Indices: 1976191--1976217 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1976181 CAAAGATCAG
1976191 TGTATCGATACAT
1 TGTATCGATACAT
1976204 TGTATCGATACAT
1 TGTATCGATACAT
1976217 T
1 T
1976218 TAAGTGATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1976296 original size:13 final size:13
Alignment explanation
Indices: 1976278--1976302 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1976268 CAAAAAAACA
1976278 TGTATCGATACAT
1 TGTATCGATACAT
1976291 TGTATCGATACA
1 TGTATCGATACA
1976303 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1976401 original size:21 final size:21
Alignment explanation
Indices: 1976360--1976401 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1976350 GTTGGGACCT
*
1976360 TGTATCGATACATTTTAACAA
1 TGTATCGATACATTTGAACAA
*
1976381 TGTATCGATACATTTGGACAA
1 TGTATCGATACATTTGAACAA
1976402 AAATGTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTGAACAA
Found at i:1978398 original size:12 final size:12
Alignment explanation
Indices: 1978381--1978405 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1978371 AAATATATTA
1978381 GGTATGTTAGGT
1 GGTATGTTAGGT
1978393 GGTATGTTAGGT
1 GGTATGTTAGGT
1978405 G
1 G
1978406 AGTAATATAT
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:0.44, T:0.40
Consensus pattern (12 bp):
GGTATGTTAGGT
Found at i:1978458 original size:22 final size:22
Alignment explanation
Indices: 1978430--1978471 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1978420 TGTTTTAGGT
*
1978430 GGTGTGTTAGGTAAACTTATTA
1 GGTGTGTCAGGTAAACTTATTA
*
1978452 GGTGTGTCAGGTGAACTTAT
1 GGTGTGTCAGGTAAACTTAT
1978472 CTTGTATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.24, C:0.07, G:0.31, T:0.38
Consensus pattern (22 bp):
GGTGTGTCAGGTAAACTTATTA
Found at i:1979549 original size:22 final size:22
Alignment explanation
Indices: 1979524--1979584 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
1979514 AGTGAAAAGT
*
1979524 TTTTTTTAAGTAAAAAGTG-GTA
1 TTTTTTTAAGTAAAAA-TGAATA
*
1979546 TTTTATTATAGTAAAAATGAATA
1 TTTTTTTA-AGTAAAAATGAATA
* *
1979569 GTTTTTCAAGTAAAAA
1 TTTTTTTAAGTAAAAA
1979585 ATAGATGTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
22 17 0.53
23 15 0.47
ACGTcount: A:0.43, C:0.02, G:0.13, T:0.43
Consensus pattern (22 bp):
TTTTTTTAAGTAAAAATGAATA
Found at i:1980121 original size:48 final size:49
Alignment explanation
Indices: 1980046--1980153 Score: 112
Period size: 48 Copynumber: 2.2 Consensus size: 49
1980036 TTAAATTTGA
* * * *
1980046 AAATGACCC-AAACTCGAAATAATTCGAATCCAAAATGACCCGAACTCG
1 AAATGACCCGAAACTCGAAATAACTCGAACCCAAAATAACCCGAACCCG
* * ** *
1980094 AAATGACCCGAATC-CGAAATGACTCGAACCCGGAATAACCTGAACCCG
1 AAATGACCCGAAACTCGAAATAACTCGAACCCAAAATAACCCGAACCCG
*
1980142 AAATGATCCGAA
1 AAATGACCCGAA
1980154 CATGATATGA
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
48 46 0.94
49 3 0.06
ACGTcount: A:0.42, C:0.28, G:0.16, T:0.15
Consensus pattern (49 bp):
AAATGACCCGAAACTCGAAATAACTCGAACCCAAAATAACCCGAACCCG
Found at i:1980122 original size:32 final size:32
Alignment explanation
Indices: 1980046--1980154 Score: 119
Period size: 32 Copynumber: 3.4 Consensus size: 32
1980036 TTAAATTTGA
* ** *
1980046 AAATGACCCAAACTCGAAATAATTCGAATCCA
1 AAATGACCCGAACTCGAAATAACCCGAATCCG
*
1980078 AAATGACCCGAACTCGAAATGACCCGAATCCG
1 AAATGACCCGAACTCGAAATAACCCGAATCCG
* * * * *
1980110 AAATGACTCGAACCCGGAATAACCTGAACCCG
1 AAATGACCCGAACTCGAAATAACCCGAATCCG
*
1980142 AAATGATCCGAAC
1 AAATGACCCGAAC
1980155 ATGATATGAT
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 64 1.00
ACGTcount: A:0.41, C:0.28, G:0.16, T:0.15
Consensus pattern (32 bp):
AAATGACCCGAACTCGAAATAACCCGAATCCG
Found at i:1980154 original size:16 final size:16
Alignment explanation
Indices: 1980046--1980154 Score: 92
Period size: 16 Copynumber: 6.8 Consensus size: 16
1980036 TTAAATTTGA
* *
1980046 AAATGACCCAAACTCG
1 AAATGACCCGAACCCG
* ** * *
1980062 AAATAATTCGAATCCA
1 AAATGACCCGAACCCG
*
1980078 AAATGACCCGAACTCG
1 AAATGACCCGAACCCG
*
1980094 AAATGACCCGAATCCG
1 AAATGACCCGAACCCG
*
1980110 AAATGACTCGAACCCG
1 AAATGACCCGAACCCG
* * *
1980126 GAATAACCTGAACCCG
1 AAATGACCCGAACCCG
*
1980142 AAATGATCCGAAC
1 AAATGACCCGAAC
1980155 ATGATATGAT
Statistics
Matches: 68, Mismatches: 25, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
16 68 1.00
ACGTcount: A:0.41, C:0.28, G:0.16, T:0.15
Consensus pattern (16 bp):
AAATGACCCGAACCCG
Found at i:1983614 original size:18 final size:18
Alignment explanation
Indices: 1983591--1983626 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1983581 TATTTTTTCT
1983591 TCTCCCCATAAATTACAA
1 TCTCCCCATAAATTACAA
1983609 TCTCCCCATAAATTACAA
1 TCTCCCCATAAATTACAA
1983627 CATCGAGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.33, G:0.00, T:0.28
Consensus pattern (18 bp):
TCTCCCCATAAATTACAA
Found at i:1984661 original size:59 final size:59
Alignment explanation
Indices: 1984559--1984674 Score: 171
Period size: 59 Copynumber: 2.0 Consensus size: 59
1984549 GGGAATGTAG
* *
1984559 TGAAATGTGAATTGAAATTAAAAAAAGAAAACCCTAATCCACCCCGCCTTTATGTGTTA
1 TGAAATGTGAATTGAAATTAAAAAAAAAAAACCCTAATCCACCCCACCTTTATGTGTTA
* * *
1984618 TGAAATGTGAATTGAAATTAAAAAAAAAAAAGCTTAA-CTCACCCTACCTTTATGTGT
1 TGAAATGTGAATTGAAATTAAAAAAAAAAAACCCTAATC-CACCCCACCTTTATGTGT
1984675 AGTTGATATA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
58 1 0.02
59 50 0.98
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.28
Consensus pattern (59 bp):
TGAAATGTGAATTGAAATTAAAAAAAAAAAACCCTAATCCACCCCACCTTTATGTGTTA
Found at i:1984733 original size:26 final size:29
Alignment explanation
Indices: 1984704--1984768 Score: 68
Period size: 30 Copynumber: 2.3 Consensus size: 29
1984694 ACCAATTAAA
1984704 TTATAATAAA-TATTT-TTA-TAATTTAT
1 TTATAATAAATTATTTATTATTAATTTAT
*
1984730 TTATTAA-AAATTATTTAATTATTTATTTAT
1 TTA-TAATAAATTATTT-ATTATTAATTTAT
1984760 TTAT-ATAAA
1 TTATAATAAA
1984769 GAAAAAATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
26 6 0.19
27 8 0.25
28 1 0.03
29 7 0.22
30 10 0.31
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (29 bp):
TTATAATAAATTATTTATTATTAATTTAT
Found at i:1985834 original size:37 final size:37
Alignment explanation
Indices: 1985754--1985837 Score: 159
Period size: 37 Copynumber: 2.3 Consensus size: 37
1985744 GAATCTAGGA
*
1985754 TGACCCAAACTCGATTAACCCGAACGTTAAACCCGAT
1 TGACCCGAACTCGATTAACCCGAACGTTAAACCCGAT
1985791 TGACCCGAACTCGATTAACCCGAACGTTAAACCCGAT
1 TGACCCGAACTCGATTAACCCGAACGTTAAACCCGAT
1985828 TGACCCGAAC
1 TGACCCGAAC
1985838 CTGAAATGAC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.33, C:0.33, G:0.15, T:0.18
Consensus pattern (37 bp):
TGACCCGAACTCGATTAACCCGAACGTTAAACCCGAT
Found at i:1985884 original size:16 final size:16
Alignment explanation
Indices: 1985865--1985895 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1985855 CAAATCAATT
*
1985865 CGAACTCGAAATGACC
1 CGAACGCGAAATGACC
1985881 CGAACGCGAAATGAC
1 CGAACGCGAAATGAC
1985896 TTAAATCCGA
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:0.39, C:0.29, G:0.23, T:0.10
Consensus pattern (16 bp):
CGAACGCGAAATGACC
Found at i:1993258 original size:41 final size:41
Alignment explanation
Indices: 1993196--1993280 Score: 116
Period size: 41 Copynumber: 2.1 Consensus size: 41
1993186 AATACTTGGT
* * * * *
1993196 CTTGCAGTTTGGATACGAATTCACCAATATTCTTATCTGAA
1 CTTGCAGTCTAGATACAAATTCAACAATATTCTTACCTGAA
*
1993237 CTTGCAGTCTAGATACAAATTCAACAATGTTCTTACCTGAA
1 CTTGCAGTCTAGATACAAATTCAACAATATTCTTACCTGAA
1993278 CTT
1 CTT
1993281 CTACCATCTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (41 bp):
CTTGCAGTCTAGATACAAATTCAACAATATTCTTACCTGAA
Found at i:1993667 original size:152 final size:153
Alignment explanation
Indices: 1993355--1993792 Score: 682
Period size: 152 Copynumber: 2.9 Consensus size: 153
1993345 CCCATGTCAA
* * *
1993355 CTTTCATCTGGCCATTTATGCACAGCGGAGTTGCCTATCTTTTTTACGGCTTGTCAGGCTGAGCT
1 CTTTCATCTGTCCATTTATGCACAGCGGAGTTGCCTATCTTTTTCACGTCTTGTCAGGCTGAGCT
* *
1993420 TGTATTCTGTTTTCCTATATATCCTCTCTACATCCTTGGCGTTCGAGTATTGGTTGGTTCATTGT
66 TGTATTCTGTTTTCCCATATAT-C-CTCTACATACTTGGCGTTCGAGTATTGGTTGGTTCATTGT
1993485 GGCATCGCTACTTTTCCCATATCTC
129 GGCATCGCTACTTTTCCCATATCTC
* * * * *
1993510 CTTTCATCTGTCCATTTACGCACAGCGGACTTGCCCATCCTTTTCACGTCTTGTCAGGCTGATCT
1 CTTTCATCTGTCCATTTATGCACAGCGGAGTTGCCTATCTTTTTCACGTCTTGTCAGGCTGAGCT
* * *
1993575 TGTTTTCTG-TTTCCCATATATCCTCTGCATACTTAGCGTTCGAGTATTGGTTGGTTCATTGTGG
66 TGTATTCTGTTTTCCCATATATCCTCTACATACTTGGCGTTCGAGTATTGGTTGGTTCATTGTGG
1993639 CATCGCTACTTTTCCCATATCTC
131 CATCGCTACTTTTCCCATATCTC
* * *
1993662 CTTTCAGCTGTCCATTTATGCACAGCGGAGTTGCCTATCTTTTTCACTTCTTGTCACGCTGAGCT
1 CTTTCATCTGTCCATTTATGCACAGCGGAGTTGCCTATCTTTTTCACGTCTTGTCAGGCTGAGCT
* *
1993727 TGTATTCTGTTTTCCCATATA-CCTCCACGTACTTGGCGTTCGAGTATTGGTTGGTTCATTGTGG
66 TGTATTCTGTTTTCCCATATATCCTCTACATACTTGGCGTTCGAGTATTGGTTGGTTCATTGTGG
1993791 CA
131 CA
1993793 CTTACCTATC
Statistics
Matches: 256, Mismatches: 26, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
152 168 0.66
153 12 0.05
154 11 0.04
155 65 0.25
ACGTcount: A:0.15, C:0.26, G:0.19, T:0.40
Consensus pattern (153 bp):
CTTTCATCTGTCCATTTATGCACAGCGGAGTTGCCTATCTTTTTCACGTCTTGTCAGGCTGAGCT
TGTATTCTGTTTTCCCATATATCCTCTACATACTTGGCGTTCGAGTATTGGTTGGTTCATTGTGG
CATCGCTACTTTTCCCATATCTC
Found at i:1993879 original size:102 final size:100
Alignment explanation
Indices: 1993695--1993890 Score: 315
Period size: 98 Copynumber: 2.0 Consensus size: 100
1993685 AGCGGAGTTG
* *
1993695 CCTATCTTTTTCACTTCTTGTCACGCTGAGCTTGTATTCTGTTTTCCCATATACCTCCACGTACT
1 CCTATCTTTTTCACGTCTTGTCACGCTGAGCTTGTATTCTGTTTT--CATATACCTCCACATACT
1993760 TGGCGTTCGAGTATTGGTTGGTTCATTGTGGCACTTA
64 TGGCGTTCGAGTATTGGTTGGTTCATTGTGGCACTTA
* * *
1993797 CCTATCTTTTTCACGTCTTGTTAGGCTGAGCTTGTATTCTGTTTT-ATAT-CCTCTACATACTTG
1 CCTATCTTTTTCACGTCTTGTCACGCTGAGCTTGTATTCTGTTTTCATATACCTCCACATACTTG
1993860 GCGTTCGAGTATTGGTTGGTTCATTGTGGCA
66 GCGTTCGAGTATTGGTTGGTTCATTGTGGCA
1993891 TCGCTACCAT
Statistics
Matches: 89, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
98 43 0.48
99 4 0.04
102 42 0.47
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (100 bp):
CCTATCTTTTTCACGTCTTGTCACGCTGAGCTTGTATTCTGTTTTCATATACCTCCACATACTTG
GCGTTCGAGTATTGGTTGGTTCATTGTGGCACTTA
Found at i:1995145 original size:16 final size:14
Alignment explanation
Indices: 1995116--1995158 Score: 52
Period size: 16 Copynumber: 3.0 Consensus size: 14
1995106 AAAAATAATA
1995116 ATTAAATTTTAAAT
1 ATTAAATTTTAAAT
1995130 ATTAAATTTATTAAAT
1 ATTAAA-TT-TTAAAT
*
1995146 ATT-ATTTTTAAAT
1 ATTAAATTTTAAAT
1995159 TTATGAATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 6 0.23
14 8 0.31
15 3 0.12
16 9 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTAAATTTTAAAT
Found at i:1998182 original size:2 final size:2
Alignment explanation
Indices: 1998177--1998211 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1998167 ACACACACAC
1998177 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
1998212 CATTATTCAA
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:1999478 original size:24 final size:25
Alignment explanation
Indices: 1999451--1999509 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
1999441 TTAAAATTTT
* *
1999451 TTAAATATTTTTAAAATAT-TAATA
1 TTAAATAATATTAAAATATATAATA
1999475 TTAAATAAATATTAAAATATAATAATA
1 TTAAAT-AATATTAAAATAT-ATAATA
*
1999502 TTTAATAA
1 TTAAATAA
1999510 ATATATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 6 0.21
25 11 0.38
26 2 0.07
27 10 0.34
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
TTAAATAATATTAAAATATATAATA
Found at i:1999506 original size:17 final size:18
Alignment explanation
Indices: 1999465--1999535 Score: 62
Period size: 17 Copynumber: 4.0 Consensus size: 18
1999455 ATATTTTTAA
*
1999465 AATA-TTAATATTA-AAT
1 AATATTTAATAATATAAT
1999481 AA-ATATTAA-AATATAAT
1 AATAT-TTAATAATATAAT
1999498 AATATTTAATAA-ATATAT
1 AATATTTAATAATATA-AT
1999516 ATATGATTTAATAATATAAT
1 A-AT-ATTTAATAATATAAT
1999536 CTTTAATATA
Statistics
Matches: 45, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
15 1 0.02
16 5 0.11
17 16 0.36
18 7 0.16
19 2 0.04
20 11 0.24
21 3 0.07
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (18 bp):
AATATTTAATAATATAAT
Found at i:1999510 original size:20 final size:21
Alignment explanation
Indices: 1999487--1999529 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
1999477 AAATAAATAT
1999487 TAAAATATA-ATAAT-ATTTAA
1 TAAAATATATAT-ATGATTTAA
1999507 T-AAATATATATATGATTTAA
1 TAAAATATATATATGATTTAA
1999527 TAA
1 TAA
1999530 TATAATCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
19 9 0.45
20 10 0.50
21 1 0.05
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
TAAAATATATATATGATTTAA
Found at i:1999511 original size:19 final size:21
Alignment explanation
Indices: 1999489--1999535 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 21
1999479 ATAAATATTA
1999489 AAATATAATA-AT-ATTTAAT
1 AAATATAATATATGATTTAAT
1999508 AAATAT-ATATATGATTTAAT
1 AAATATAATATATGATTTAAT
1999528 -AATATAAT
1 AAATATAAT
1999536 CTTTAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 3 0.12
19 13 0.52
20 9 0.36
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
AAATATAATATATGATTTAAT
Found at i:1999916 original size:31 final size:32
Alignment explanation
Indices: 1999875--1999939 Score: 82
Period size: 30 Copynumber: 2.1 Consensus size: 32
1999865 TTAACGTATC
*
1999875 AAAATTTATAATA-AATATGAAATATTTTAA-AT
1 AAAATTTATAACATAATA--AAATATTTTAATAT
1999907 AAAA-TTATAACATAATAAAATATTTTAATAT
1 AAAATTTATAACATAATAAAATATTTTAATAT
1999938 AA
1 AA
1999940 TAAAAATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 11 0.37
31 11 0.37
32 8 0.27
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (32 bp):
AAAATTTATAACATAATAAAATATTTTAATAT
Found at i:2001648 original size:38 final size:38
Alignment explanation
Indices: 2001551--2001679 Score: 150
Period size: 38 Copynumber: 3.4 Consensus size: 38
2001541 AGTTAACGGT
* ** * **
2001551 TAGAGAATTTAATTTGAAATTAACTGACGGCTAACGGT
1 TAGAGAATTCAATTTGAAATTGGCTGGCGGCTAACGAC
*
2001589 TAGAGAATTCAATTTGGAATTGGCTGGCGGCTAACGAC
1 TAGAGAATTCAATTTGAAATTGGCTGGCGGCTAACGAC
* * * *
2001627 TAGAGACTTCAATTTGAAATTGGCTGGTGGTTAGCGAC
1 TAGAGAATTCAATTTGAAATTGGCTGGCGGCTAACGAC
*
2001665 TAGAAAATTCAATTT
1 TAGAGAATTCAATTT
2001680 AGAATTGACT
Statistics
Matches: 77, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 77 1.00
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (38 bp):
TAGAGAATTCAATTTGAAATTGGCTGGCGGCTAACGAC
Found at i:2001686 original size:38 final size:37
Alignment explanation
Indices: 2001589--2001696 Score: 135
Period size: 38 Copynumber: 2.8 Consensus size: 37
2001579 GGCTAACGGT
* *
2001589 TAGAGAATTCAATTTGGAATTGGCTGGCGGCTAACGAC
1 TAGAGAATTCAATTT-GAATTGGCTGGTGGTTAACGAC
* *
2001627 TAGAGACTTCAATTTGAAATTGGCTGGTGGTTAGCGAC
1 TAGAGAATTCAATTTG-AATTGGCTGGTGGTTAACGAC
* *
2001665 TAGAAAATTCAATTTAGAATTGACTGGTGGTT
1 TAGAGAATTCAATTT-GAATTGGCTGGTGGTT
2001697 GGTGGCTAGA
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
37 1 0.02
38 59 0.97
39 1 0.02
ACGTcount: A:0.30, C:0.12, G:0.27, T:0.31
Consensus pattern (37 bp):
TAGAGAATTCAATTTGAATTGGCTGGTGGTTAACGAC
Found at i:2006285 original size:38 final size:38
Alignment explanation
Indices: 2006242--2006319 Score: 129
Period size: 38 Copynumber: 2.1 Consensus size: 38
2006232 GAATTAGCTA
* * *
2006242 ACGGTTAGAGAATTTAATTTGAAATTGGCTGGCGGTTG
1 ACGGTTAGAAAATTCAATTTGAAATTGGCTGGCGGCTG
2006280 ACGGTTAGAAAATTCAATTTGAAATTGGCTGGCGGCTG
1 ACGGTTAGAAAATTCAATTTGAAATTGGCTGGCGGCTG
2006318 AC
1 AC
2006320 TACTAAAGAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.28, C:0.12, G:0.29, T:0.31
Consensus pattern (38 bp):
ACGGTTAGAAAATTCAATTTGAAATTGGCTGGCGGCTG
Found at i:2006334 original size:38 final size:38
Alignment explanation
Indices: 2006247--2006392 Score: 111
Period size: 38 Copynumber: 3.8 Consensus size: 38
2006237 AGCTAACGGT
* * * **
2006247 TAGAGAATTTAATTTGAAATTGGCTGGCGGTTGACGGT
1 TAGAAAATTCAATTTGAAATTGGCTGGCGGCTGACGAC
*
2006285 TAGAAAATTCAATTTGAAATTGGCTGGCGGCTGACTAC
1 TAGAAAATTCAATTTGAAATTGGCTGGCGGCTGACGAC
* * * *
2006323 TA-AAGACTTCAATTTGGAATTTG-TCGGTGGCT-AGCGAC
1 TAGAA-AATTCAATTTGAAATTGGCT-GGCGGCTGA-CGAC
* * *
2006361 TAGAGAATTCAATTT-AGAATTGACTGGTGGCT
1 TAGAAAATTCAATTTGA-AATTGGCTGGCGGCT
2006393 AGAGAATTCT
Statistics
Matches: 86, Mismatches: 16, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
37 4 0.05
38 80 0.93
39 2 0.02
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.32
Consensus pattern (38 bp):
TAGAAAATTCAATTTGAAATTGGCTGGCGGCTGACGAC
Found at i:2007334 original size:16 final size:17
Alignment explanation
Indices: 2007293--2007345 Score: 67
Period size: 16 Copynumber: 3.2 Consensus size: 17
2007283 AATTTTGAAA
2007293 ATAAAATA-AAAATAAT
1 ATAAAATATAAAATAAT
*
2007309 -TAAAATATAATATAAT
1 ATAAAATATAAAATAAT
2007325 ATAAAA-ATAAAATACAT
1 ATAAAATATAAAATA-AT
2007342 ATAA
1 ATAA
2007346 TATGAATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 7 0.22
16 14 0.44
17 11 0.34
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (17 bp):
ATAAAATATAAAATAAT
Found at i:2008029 original size:16 final size:17
Alignment explanation
Indices: 2008010--2008044 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2008000 TTTAAAAAAT
2008010 AATTTTTCAAAA-ATAA
1 AATTTTTCAAAAGATAA
*
2008026 AATTTTTTAAAAGATAA
1 AATTTTTCAAAAGATAA
2008043 AA
1 AA
2008045 AATAATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (17 bp):
AATTTTTCAAAAGATAA
Found at i:2008393 original size:3 final size:3
Alignment explanation
Indices: 2008385--2008422 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
2008375 GATACATGGA
*
2008385 TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2008423 GTGACTCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2009563 original size:24 final size:23
Alignment explanation
Indices: 2009518--2009563 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
2009508 AGAATACATT
* *
2009518 TATTAAATATGTTATATTTATCG
1 TATTAAATATGTTAAATGTATCG
*
2009541 TATTAATTATAGTTAAATGTATC
1 TATTAAATAT-GTTAAATGTATC
2009564 ATCTTGTGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.50
Consensus pattern (23 bp):
TATTAAATATGTTAAATGTATCG
Found at i:2010442 original size:15 final size:16
Alignment explanation
Indices: 2010424--2010455 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
2010414 GTTTTTTATC
2010424 TCGTTTTG-TTTTGTT
1 TCGTTTTGTTTTTGTT
2010439 TCGTTTTGTTTTTGTT
1 TCGTTTTGTTTTTGTT
2010455 T
1 T
2010456 TTTTTTCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.00, C:0.06, G:0.19, T:0.75
Consensus pattern (16 bp):
TCGTTTTGTTTTTGTT
Found at i:2013177 original size:2 final size:2
Alignment explanation
Indices: 2013170--2013213 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2013160 GTTTAATCAA
2013170 AT AT AT AT 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 AT AT AT AT
2013212 AT
1 AT
2013214 GAATGTGAGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2015438 original size:23 final size:21
Alignment explanation
Indices: 2015400--2015457 Score: 82
Period size: 23 Copynumber: 2.7 Consensus size: 21
2015390 AGATCTTTTA
2015400 AAATTTAAATTATTTTAAATT
1 AAATTTAAATTATTTTAAATT
*
2015421 AAATTTATTAATTTTTTTAAATT
1 AAATTTA--AATTATTTTAAATT
2015444 AAA-TTAAATTATTT
1 AAATTTAAATTATTT
2015458 GATTAAATCG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
20 7 0.21
21 7 0.21
22 3 0.09
23 16 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
AAATTTAAATTATTTTAAATT
Found at i:2015463 original size:23 final size:23
Alignment explanation
Indices: 2015414--2015465 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
2015404 TTAAATTATT
* **
2015414 TTAAATTAAATTTATTAATTTTT
1 TTAAATTAAATTAATTAATTTGA
2015437 TTAAATTAAATTAAATT-ATTTGA
1 TTAAATTAAATT-AATTAATTTGA
2015460 TTAAAT
1 TTAAAT
2015466 CGTATTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 22 0.88
24 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
TTAAATTAAATTAATTAATTTGA
Found at i:2015818 original size:2 final size:2
Alignment explanation
Indices: 2015813--2015869 Score: 55
Period size: 2 Copynumber: 29.5 Consensus size: 2
2015803 ATAATCACAC
* * *
2015813 AT AT AT GT AT CT AT AT AT AT AT AT AT A- AT AT AA AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
2015853 AT AT AT AA AT AT TT AT A
1 AT AT AT AT AT AT AT AT A
2015870 CATTTATCTG
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2015849 original size:13 final size:13
Alignment explanation
Indices: 2015827--2015857 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2015817 ATGTATCTAT
*
2015827 ATATATATATATA
1 ATATAAATATATA
2015840 ATATAAATATATA
1 ATATAAATATATA
2015853 ATATA
1 ATATA
2015858 TAAATATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATATAAATATATA
Found at i:2015849 original size:15 final size:16
Alignment explanation
Indices: 2015813--2015869 Score: 62
Period size: 15 Copynumber: 3.6 Consensus size: 16
2015803 ATAATCACAC
* * *
2015813 ATATATGTATCTATAT
1 ATATATATATATATAA
2015829 ATATATATATAATATAA
1 ATATATATAT-ATATAA
2015846 ATATATA-ATATATAA
1 ATATATATATATATAA
*
2015861 ATATTTATA
1 ATATATATA
2015870 CATTTATCTG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
15 12 0.34
16 12 0.34
17 11 0.31
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (16 bp):
ATATATATATATATAA
Found at i:2015864 original size:13 final size:13
Alignment explanation
Indices: 2015827--2015864 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
2015817 ATGTATCTAT
*
2015827 ATATATATATATA
1 ATATATAAATATA
2015840 ATATA-AATATATA
1 ATATATAA-ATATA
2015853 ATATATAAATAT
1 ATATATAAATAT
2015865 TTATACATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 1 0.05
13 19 0.86
14 2 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATATATAAATATA
Found at i:2017520 original size:17 final size:16
Alignment explanation
Indices: 2017498--2017578 Score: 65
Period size: 17 Copynumber: 4.9 Consensus size: 16
2017488 AATACATGTC
* *
2017498 ATATATTTATATTTAA
1 ATATATTTAAATATAA
2017514 TATATATTTAAATATAA
1 -ATATATTTAAATATAA
** *
2017531 ATATATAAAAAATTTTAA
1 ATATAT-TTAAA-TATAA
* *
2017549 ATATATTTAGATATGA
1 ATATATTTAAATATAA
2017565 ATAT-TTTAAATATA
1 ATATATTTAAATATA
2017579 TAAAAAATTT
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
15 8 0.16
16 13 0.26
17 19 0.38
18 10 0.20
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
ATATATTTAAATATAA
Found at i:2017549 original size:18 final size:18
Alignment explanation
Indices: 2017528--2017592 Score: 67
Period size: 18 Copynumber: 3.2 Consensus size: 18
2017518 TATTTAAATA
2017528 TAAATATATAAAAAATTT
1 TAAATATATAAAAAATTT
2017546 TAAATATATTTAGATATGAATATTT
1 TAAATATA--TA-A-A--AA-ATTT
2017571 TAAATATATAAAAAATTT
1 TAAATATATAAAAAATTT
2017589 TAAA
1 TAAA
2017593 AAATTAAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
18 16 0.40
19 2 0.05
20 2 0.05
21 2 0.05
22 2 0.05
23 2 0.05
24 2 0.05
25 12 0.30
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
TAAATATATAAAAAATTT
Found at i:2030000 original size:26 final size:26
Alignment explanation
Indices: 2029936--2030000 Score: 60
Period size: 26 Copynumber: 2.5 Consensus size: 26
2029926 TTAAAAAATT
2029936 TATTT-TATTTTTTAAAATATATTAA
1 TATTTATATTTTTTAAAATATATTAA
* * * * ***
2029961 AAATTAAATATTTTAGTTTATATTAA
1 TATTTATATTTTTTAAAATATATTAA
2029987 TATTTATATTTTTT
1 TATTTATATTTTTT
2030001 TAATAAATTT
Statistics
Matches: 28, Mismatches: 11, Indels: 1
0.70 0.28 0.03
Matches are distributed among these distances:
25 3 0.11
26 25 0.89
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (26 bp):
TATTTATATTTTTTAAAATATATTAA
Found at i:2031609 original size:2 final size:2
Alignment explanation
Indices: 2031602--2031638 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2031592 TTCAGAATTT
2031602 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2031639 TGTCCACCCT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2031688 original size:2 final size:2
Alignment explanation
Indices: 2031681--2031717 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2031671 AAATTCCTAT
*
2031681 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2031718 GAAAACTAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2032338 original size:20 final size:19
Alignment explanation
Indices: 2032294--2032341 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
2032284 TAACAATGTG
*
2032294 TTATATTTTTTTTAATAAT
1 TTATATTTATTTTAATAAT
* *
2032313 TTATATTTATTTTATTTAT
1 TTATATTTATTTTAATAAT
2032332 TTCATATTTA
1 TT-ATATTTA
2032342 AAAATTTTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (19 bp):
TTATATTTATTTTAATAAT
Found at i:2033798 original size:21 final size:18
Alignment explanation
Indices: 2033761--2033800 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
2033751 AGTGATTAAG
2033761 TTTTTAATTTTAAATTTA
1 TTTTTAATTTTAAATTTA
2033779 TTTTTATATATTTAATATTTA
1 TTTTTA-AT-TTTAA-ATTTA
2033800 T
1 T
2033801 ATATAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
19 2 0.11
20 5 0.26
21 6 0.32
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTTAATTTTAAATTTA
Found at i:2033880 original size:19 final size:18
Alignment explanation
Indices: 2033858--2033902 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
2033848 TATATAACTT
2033858 AATTAAATTTATCAAAATA
1 AATTAAA-TTATCAAAATA
*
2033877 AATTTAAATTATTAAAATA
1 AA-TTAAATTATCAAAATA
2033896 AATTAAA
1 AATTAAA
2033903 AATTAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 5 0.21
19 14 0.58
20 5 0.21
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTAAATTATCAAAATA
Found at i:2034233 original size:18 final size:18
Alignment explanation
Indices: 2034207--2034245 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2034197 ATTACTAGAT
2034207 ATATATATAA-TATTATTA
1 ATATATATAATTA-TATTA
*
2034225 ATATTTATAATTATATTA
1 ATATATATAATTATATTA
2034243 ATA
1 ATA
2034246 AATAAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATATATAATTATATTA
Found at i:2034513 original size:32 final size:31
Alignment explanation
Indices: 2034455--2034571 Score: 90
Period size: 30 Copynumber: 3.9 Consensus size: 31
2034445 ATCTTAAAAA
*
2034455 TAAATATATAAATATTTTAAAATATATAATT
1 TAAATATATAAATATATTAAAATATATAATT
* *
2034486 TAAAT-TATTAATATATTAAAAT-T-T-ATA
1 TAAATATATAAATATATTAAAATATATAATT
* *
2034513 TAAATATA-AAATAT-TTTAAATATTATTATAT
1 TAAATATATAAATATATTAAAATA-TATAAT-T
2034544 TAAA-ATA-AAATAT-TTAAATATAATATAA
1 TAAATATATAAATATATTAAA-AT-ATATAA
2034572 ATACTTGTAA
Statistics
Matches: 70, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
26 6 0.09
27 12 0.17
28 4 0.06
29 2 0.03
30 30 0.43
31 15 0.21
32 1 0.01
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
TAAATATATAAATATATTAAAATATATAATT
Found at i:2034561 original size:56 final size:58
Alignment explanation
Indices: 2034454--2034574 Score: 144
Period size: 56 Copynumber: 2.1 Consensus size: 58
2034444 AATCTTAAAA
* * *
2034454 ATAAATATATAAATATTTTAAAATATATAATTTAAATTATTAATATATTAAA-ATTTAT
1 ATAAATATATAAATATTTTAAAATATATAATTTAAAATATAAATATATTAAATA-TAAT
*
2034512 ATAAATATA-AAATATTTT-AAATATTATTATATTAAAATA-AAATAT-TTAAATATAAT
1 ATAAATATATAAATATTTTAAAATA-TATAAT-TTAAAATATAAATATATTAAATATAAT
2034568 ATAAATA
1 ATAAATA
2034575 CTTGTAAAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
56 20 0.36
57 20 0.36
58 16 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (58 bp):
ATAAATATATAAATATTTTAAAATATATAATTTAAAATATAAATATATTAAATATAAT
Found at i:2035365 original size:100 final size:101
Alignment explanation
Indices: 2035253--2035472 Score: 298
Period size: 100 Copynumber: 2.2 Consensus size: 101
2035243 GTAAAGTGAT
* * * *
2035253 TTGACTATTCTTCATCAACTTTGGATAATCGAGAGAGGTAGTCGTAATTATTGACTATTTTTCAC
1 TTGACTATTCTTCATCAACTTTGGACAATCGAGAGAAGTAGTCGAAATTATTGACTATTATTCAC
* *
2035318 CAAACTTTGACAATTAAGAGAAGTGAC-CGTAATTG
66 CAAACTTTGACAATCAAGAGAAGTGACTCGTAATTA
* * *
2035353 TTGACTATTCTTCACCAACTTTTGACAATCTAGAGAAGTAGTCGAAATTATTGACTATTATTCAC
1 TTGACTATTCTTCATCAACTTTGGACAATCGAGAGAAGTAGTCGAAATTATTGACTATTATTCAC
* * * * * *
2035418 CAATCTTTGACAATCGATAGAGGTGGCTTGTAATTA
66 CAAACTTTGACAATCAAGAGAAGTGACTCGTAATTA
2035454 TTGACTATTCTTCATCAAC
1 TTGACTATTCTTCATCAAC
2035473 CTTTAACAAT
Statistics
Matches: 103, Mismatches: 16, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
100 79 0.77
101 24 0.23
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (101 bp):
TTGACTATTCTTCATCAACTTTGGACAATCGAGAGAAGTAGTCGAAATTATTGACTATTATTCAC
CAAACTTTGACAATCAAGAGAAGTGACTCGTAATTA
Done.