Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008531.1 Hibiscus syriacus cultivar Beakdansim tig00111409_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3817888
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 19
Found at i:1961095 original size:20 final size:20
Alignment explanation
Indices: 1961038--1961098 Score: 61
Period size: 22 Copynumber: 3.0 Consensus size: 20
1961028 TAAGAAGGCC
1961038 ATCAGTAAGTCTTTCGAGCT
1 ATCAGTAAGTCTTTCGAGCT
* * *
1961058 -TGATGATGAAGTCCTTCGGGCT
1 ATCA-G-T-AAGTCTTTCGAGCT
1961080 ATCAGTAAGTCTTTCGAGC
1 ATCAGTAAGTCTTTCGAGC
1961099 ATGATGATTA
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
19 2 0.06
20 12 0.39
21 2 0.06
22 13 0.42
23 2 0.06
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.33
Consensus pattern (20 bp):
ATCAGTAAGTCTTTCGAGCT
Found at i:1961279 original size:135 final size:135
Alignment explanation
Indices: 1961035--1961334 Score: 429
Period size: 135 Copynumber: 2.2 Consensus size: 135
1961025 AAGTAAGAAG
** * * *
1961035 GCCATCAGTAAGTCTTTCGAGCTTGATGATGAAGTCCTTCGGGCTATCAGTAAGTCTTTCGAGCA
1 GCCATCAAAAAGTCTTTCGAGCATGATGATGAAGTCCTTCGAGCCATCAGTAAGTCTTTCGAGCA
* * * *
1961100 TGATGATTAAATCCTTCGGGTAACTTGTAAGCCTTCATCGAAGAGTAGTGAAGCAAATCCATCAG
66 TGATGATTAAATCCTCCGGGTAACTTGCAAGCCTTCACCAAAGAGTAGTGAAGCAAATCCATCAG
1961165 TAAGT
131 TAAGT
* * * *
1961170 GTCATCAAAAAGTCTTTCAAGCATGATGATGAAGTCCTTTGAGCCATCAGTAAGTCTTTTGAGCA
1 GCCATCAAAAAGTCTTTCGAGCATGATGATGAAGTCCTTCGAGCCATCAGTAAGTCTTTCGAGCA
* * *
1961235 TGATGATTAAATCCTCCGGGTAATTTGCAAGCCTTCACCAAAGAGTAGTGAATCAAATCTATCAG
66 TGATGATTAAATCCTCCGGGTAACTTGCAAGCCTTCACCAAAGAGTAGTGAAGCAAATCCATCAG
1961300 TAAGT
131 TAAGT
** *
1961305 GCCATCAGTAAGTCTTTTGAGCATGATGAT
1 GCCATCAAAAAGTCTTTCGAGCATGATGAT
1961335 TAAATCTTTC
Statistics
Matches: 144, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
135 144 1.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (135 bp):
GCCATCAAAAAGTCTTTCGAGCATGATGATGAAGTCCTTCGAGCCATCAGTAAGTCTTTCGAGCA
TGATGATTAAATCCTCCGGGTAACTTGCAAGCCTTCACCAAAGAGTAGTGAAGCAAATCCATCAG
TAAGT
Found at i:1968597 original size:13 final size:13
Alignment explanation
Indices: 1968581--1968611 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1968571 TAAATATGTT
*
1968581 TCATAAATGCGTG
1 TCATAAATGCGCG
1968594 TCATAAATGCGCG
1 TCATAAATGCGCG
1968607 TCATA
1 TCATA
1968612 GATTTATGAC
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:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (13 bp):
TCATAAATGCGCG
Found at i:1973840 original size:27 final size:27
Alignment explanation
Indices: 1973804--1973867 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
1973794 TGGATAATTA
*
1973804 TTGTATTTTTACAACATAAGGGCATTT
1 TTGTAATTTTACAACATAAGGGCATTT
** *
1973831 TTGTAATTTTACCCCATAAGGGTATTT
1 TTGTAATTTTACAACATAAGGGCATTT
*
1973858 TCGATAATTT
1 TTG-TAATTT
1973868 CTTATCCAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
27 25 0.81
28 6 0.19
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.45
Consensus pattern (27 bp):
TTGTAATTTTACAACATAAGGGCATTT
Found at i:1974534 original size:15 final size:15
Alignment explanation
Indices: 1974514--1974553 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
1974504 TAACTTTAAC
1974514 GAGTTGACTCAATCT
1 GAGTTGACTCAATCT
1974529 GAGTTGACTCAATCT
1 GAGTTGACTCAATCT
*
1974544 GGGTTGACTC
1 GAGTTGACTC
1974554 GGTTGGGTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.33
Consensus pattern (15 bp):
GAGTTGACTCAATCT
Found at i:1980460 original size:15 final size:15
Alignment explanation
Indices: 1980440--1980473 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1980430 GAACGAGTTT
*
1980440 ACTCTGTCTGGGTTG
1 ACTCTGTCCGGGTTG
1980455 ACTCTGTCCGGGTTG
1 ACTCTGTCCGGGTTG
1980470 ACTC
1 ACTC
1980474 GGTCAGGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.09, C:0.26, G:0.29, T:0.35
Consensus pattern (15 bp):
ACTCTGTCCGGGTTG
Found at i:1983094 original size:25 final size:26
Alignment explanation
Indices: 1983052--1983101 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
1983042 TATTTAATGT
*
1983052 AATTATTAAAAATTATAAAT-TTAAA
1 AATTATTAAAAATAATAAATATTAAA
1983077 AATTATTGAAAAA-AATAAATATTAA
1 AATTATT-AAAAATAATAAATATTAA
1983102 GATAAGTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (26 bp):
AATTATTAAAAATAATAAATATTAAA
Found at i:1983713 original size:34 final size:36
Alignment explanation
Indices: 1983669--1983769 Score: 129
Period size: 34 Copynumber: 2.8 Consensus size: 36
1983659 TTTCGTCCTA
1983669 CTAGGATTCAAACTCCTAAAAATATGATAGA-A-TAT
1 CTAGGATTCAAACTCCTAAAAATA-GATAGACATTAT
* *
1983704 -TAGGATTCAAACTCCTAAAAATAGGTA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGATAGACATTAT
1983738 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATA-GATAGA
1983770 GTTCTACTAA
Statistics
Matches: 57, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
32 1 0.02
33 4 0.07
34 25 0.44
36 23 0.40
37 3 0.05
38 1 0.02
ACGTcount: A:0.44, C:0.15, G:0.14, T:0.28
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGATAGACATTAT
Found at i:1984184 original size:18 final size:17
Alignment explanation
Indices: 1984145--1984187 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1984135 ATTATATGGA
1984145 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
1984161 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
1984179 TATTATTAT
1 TATTATTAT
1984188 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:1987313 original size:8 final size:8
Alignment explanation
Indices: 1987300--1987338 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
1987290 GAACATTTCA
*
1987300 TGCATTCT
1 TGCATTTT
1987308 TGCA-TTT
1 TGCATTTT
1987315 TGCATTTT
1 TGCATTTT
*
1987323 TGCCTTTT
1 TGCATTTT
1987331 TGCATTTT
1 TGCATTTT
1987339 CATCTACAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.10, C:0.18, G:0.13, T:0.59
Consensus pattern (8 bp):
TGCATTTT
Found at i:1988535 original size:18 final size:17
Alignment explanation
Indices: 1988533--1988579 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
1988523 AAAAAGAAAA
1988533 AAAAAGCAAAAAAAAAGC
1 AAAAAG-AAAAAAAAAGC
*
1988551 AAAAA-AAGAATAAAAAGA
1 AAAAAGAA-AA-AAAAAGC
1988569 AAAAAGAAAAA
1 AAAAAGAAAAA
1988580 GGGACAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 2 0.08
17 3 0.12
18 18 0.72
19 2 0.08
ACGTcount: A:0.83, C:0.04, G:0.11, T:0.02
Consensus pattern (17 bp):
AAAAAGAAAAAAAAAGC
Found at i:1988543 original size:11 final size:11
Alignment explanation
Indices: 1988523--1988557 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
1988513 TAAAAAGGGC
1988523 AAAAAG-AAAA
1 AAAAAGCAAAA
1988533 AAAAAGCAAAA
1 AAAAAGCAAAA
1988544 AAAAAGCAAAA
1 AAAAAGCAAAA
1988555 AAA
1 AAA
1988558 GAATAAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 6 0.25
11 18 0.75
ACGTcount: A:0.86, C:0.06, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAGCAAAA
Found at i:1988565 original size:11 final size:10
Alignment explanation
Indices: 1988523--1988573 Score: 61
Period size: 9 Copynumber: 5.2 Consensus size: 10
1988513 TAAAAAGGGC
1988523 AAAAAGAAAA
1 AAAAAGAAAA
1988533 AAAAAGCAAAA
1 AAAAAG-AAAA
*
1988544 AAAAAG-CAA
1 AAAAAGAAAA
*
1988553 AAAAAG-AAT
1 AAAAAGAAAA
1988562 AAAAAGAAAA
1 AAAAAGAAAA
1988572 AA
1 AA
1988574 GAAAAAGGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
9 15 0.43
10 10 0.29
11 10 0.29
ACGTcount: A:0.84, C:0.04, G:0.10, T:0.02
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:1989206 original size:22 final size:22
Alignment explanation
Indices: 1989178--1989221 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1989168 AGCTACCCCA
1989178 TCAAACC-TTTGAGCATCAAATG
1 TCAAACCATTT-AGCATCAAATG
1989200 TCAAACCATTTAGCATCAAATG
1 TCAAACCATTTAGCATCAAATG
1989222 AACAAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (22 bp):
TCAAACCATTTAGCATCAAATG
Found at i:1990293 original size:36 final size:36
Alignment explanation
Indices: 1990186--1990309 Score: 153
Period size: 36 Copynumber: 3.4 Consensus size: 36
1990176 ATTGAAAACA
* * *
1990186 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAATTTTCGTCTCTCTTGAGACAG
*
1990222 TTTCCCTTTG-AACTAAGTTTT-GTCTCTCTTAAGACAG
1 TTTCCC-TTGAAAC-AA-TTTTCGTCTCTCTTGAGACAG
* *
1990259 TTTCTCTTGAAACAATTTTCGTCTATCTTGAGACAG
1 TTTCCCTTGAAACAATTTTCGTCTCTCTTGAGACAG
1990295 TTTCCCTTGAAACAA
1 TTTCCCTTGAAACAA
1990310 AACCTTTGAA
Statistics
Matches: 75, Mismatches: 8, Indels: 10
0.81 0.09 0.11
Matches are distributed among these distances:
35 4 0.05
36 41 0.55
37 27 0.36
38 3 0.04
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACAATTTTCGTCTCTCTTGAGACAG
Found at i:1990403 original size:67 final size:68
Alignment explanation
Indices: 1990285--1990441 Score: 205
Period size: 68 Copynumber: 2.4 Consensus size: 68
1990275 TTTCGTCTAT
* **
1990285 CTTGAGACAGTTTCCCTTG-AA-ACAAAACCTTTGAATTTATTTCCCCTAAAACA-AATTTT-TT
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTT
1990346 CTCC
66 -TCC
* * *
1990350 CTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCTTAAAACATAATTTTGTT
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTT
1990415 TCC
66 TCC
* *
1990418 CTTGAGACCGTTTCTCATGAAACA
1 CTTGAGACAGTTTCTCTTGAAACA
1990442 ACAGATATCT
Statistics
Matches: 79, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
65 17 0.22
66 2 0.03
67 28 0.35
68 30 0.38
69 2 0.03
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (68 bp):
CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTT
TCC
Found at i:1991268 original size:105 final size:105
Alignment explanation
Indices: 1991085--1991811 Score: 1106
Period size: 105 Copynumber: 7.0 Consensus size: 105
1991075 GCACTCGAGG
* * ** *
1991085 CAACACAAGTTCAACTTCACAACGAAGGGACAACTGGTTGTCAACAAACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
1991150 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
1991191 CAACGCAAGTTCAACTTCACGACGAAGGGATCGCTGCCTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
1991256 GCCAATTTCAACTTCACAACGAATGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
1991296 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
1991361 GCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * *
1991401 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAATAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
1991466 GCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * *
1991506 CAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
1991571 GCCAATTTCAACTTCACAACGAAGGATATTGGACTACAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
1991611 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
** * *
1991671 TTCAATTTCAACTTCATAACGAAGGATATTGGACTCGAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * * * * ** *
1991711 CAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
*
1991776 AGCCAATTTCAACTTCACGACGGAA-GATATTGGACT
65 AGCCAATTTCAACTTCACAAC-GAAGGATATTGGACT
1991812 TGGAAAAATG
Statistics
Matches: 574, Mismatches: 40, Indels: 14
0.91 0.06 0.02
Matches are distributed among these distances:
100 81 0.14
101 3 0.01
102 3 0.01
103 4 0.01
104 3 0.01
105 407 0.71
106 70 0.12
107 3 0.01
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.22
Consensus pattern (105 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
Found at i:1992402 original size:34 final size:37
Alignment explanation
Indices: 1992358--1992459 Score: 167
Period size: 34 Copynumber: 2.8 Consensus size: 37
1992348 TTTTGTCCTA
1992358 CTAGGATTCAAACTCCTAAAAATAGGATAGA-A-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
1992393 -TAGGATTCAAACTCCTAAAAATAGGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
1992428 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
1992460 GTTCTACTAA
Statistics
Matches: 62, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
33 1 0.02
34 29 0.47
35 3 0.05
37 28 0.45
38 1 0.02
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (37 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
Found at i:1992443 original size:37 final size:35
Alignment explanation
Indices: 1992358--1992493 Score: 168
Period size: 37 Copynumber: 3.8 Consensus size: 35
1992348 TTTTGTCCTA
1992358 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1992393 -TAGGATTCAAACTCCTAAAAATAGGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGA-A-TTT
*
1992428 GCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTCT
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGAATT-T
* * * *
1992465 ACTAAGATTTAAATTCCTAAAGATAGGAT
1 -CTAGGATTCAAACTCCTAAAAATAGGAT
1992494 CCACAAGCAC
Statistics
Matches: 89, Mismatches: 6, Indels: 10
0.85 0.06 0.10
Matches are distributed among these distances:
33 1 0.01
34 29 0.33
35 3 0.03
36 2 0.02
37 53 0.60
38 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (35 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:1992865 original size:13 final size:12
Alignment explanation
Indices: 1992849--1992940 Score: 62
Period size: 13 Copynumber: 6.9 Consensus size: 12
1992839 ATTATATGGA
1992849 TATTTTATTCATT
1 TATTTTATT-ATT
1992862 TATTTTTATTATT
1 TA-TTTTATTATT
1992875 TATTATTATTATAT
1 TATT-TTATTAT-T
1992889 GTATATATATATTA-T
1 -TAT-T-T-TATTATT
*
1992904 TATTTGATT-TT
1 TATTTTATTATT
1992915 TATTTTTATATATT
1 TA-TTTTAT-TATT
1992929 TATTATTATTAT
1 TATT-TTATTAT
1992941 ATATATATTT
Statistics
Matches: 66, Mismatches: 2, Indels: 22
0.73 0.02 0.24
Matches are distributed among these distances:
11 6 0.09
12 8 0.12
13 21 0.32
14 19 0.29
15 4 0.06
16 3 0.05
17 5 0.08
ACGTcount: A:0.29, C:0.01, G:0.02, T:0.67
Consensus pattern (12 bp):
TATTTTATTATT
Found at i:1992880 original size:3 final size:3
Alignment explanation
Indices: 1992861--1992940 Score: 56
Period size: 3 Copynumber: 25.3 Consensus size: 3
1992851 TTTTATTCAT
*
1992861 TTA TTT TTA TTA TTTA TTA TTA TTA -TA TGTA TATA TATA TTA TTA TT-
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA T-TA T-TA T-TA TTA TTA TTA
* * *
1992908 TGA TTT TTA TTT TTA TATA TTTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA T-TA -TTA TTA TTA TTA T
1992941 ATATATATTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
2 3 0.05
3 41 0.66
4 17 0.27
5 1 0.02
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1992918 original size:17 final size:17
Alignment explanation
Indices: 1992861--1992949 Score: 83
Period size: 17 Copynumber: 5.1 Consensus size: 17
1992851 TTTTATTCAT
*
1992861 TTATTTTTAT-TATTTA
1 TTATTATTATATATTTA
*
1992877 TTATTATTATATGTATATA
1 TTATTATTATA--TATTTA
*
1992896 TATATTATTATTTGATTT-
1 T-TATTATTATAT-ATTTA
*
1992914 TTATTTTTATATATTTA
1 TTATTATTATATATTTA
*
1992931 TTATTATTATATATATA
1 TTATTATTATATATTTA
1992948 TT
1 TT
1992950 TCTTTAATAT
Statistics
Matches: 59, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
16 13 0.22
17 26 0.44
18 2 0.03
19 9 0.15
20 9 0.15
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.66
Consensus pattern (17 bp):
TTATTATTATATATTTA
Found at i:1994214 original size:2 final size:2
Alignment explanation
Indices: 1994207--1994232 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1994197 AACCTGAATC
1994207 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
1994233 GTTAAATGAA
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:2004440 original size:13 final size:13
Alignment explanation
Indices: 2004418--2004493 Score: 66
Period size: 13 Copynumber: 5.8 Consensus size: 13
2004408 AATGATAAAT
2004418 AATAAAAAAATTAC
1 AATAAAAAAA-TAC
*
2004432 AATAAAAAAATCC
1 AATAAAAAAATAC
* *
2004445 AATAAACAACTAC
1 AATAAAAAAATAC
*
2004458 AATAAAAAAGTAC
1 AATAAAAAAATAC
*
2004471 --TAAATACAAATAT
1 AATAAA-A-AAATAC
2004484 AATAAAAAAA
1 AATAAAAAAA
2004494 CAAAATCTAT
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
11 4 0.08
12 1 0.02
13 30 0.60
14 11 0.22
15 4 0.08
ACGTcount: A:0.70, C:0.11, G:0.01, T:0.18
Consensus pattern (13 bp):
AATAAAAAAATAC
Found at i:2004624 original size:6 final size:6
Alignment explanation
Indices: 2004615--2004663 Score: 62
Period size: 6 Copynumber: 8.2 Consensus size: 6
2004605 GCCATCATCA
* * * *
2004615 TCGTCC TCGTCC TCGTCC TCGTCG TCCTCC TCCTCA TCGTCC TCGTCC
1 TCGTCC TCGTCC TCGTCC TCGTCC TCGTCC TCGTCC TCGTCC TCGTCC
2004663 T
1 T
2004664 GAGCAGCTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.02, C:0.49, G:0.14, T:0.35
Consensus pattern (6 bp):
TCGTCC
Found at i:2004641 original size:15 final size:15
Alignment explanation
Indices: 2004621--2004663 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
2004611 ATCATCGTCC
*
2004621 TCGTCCTCGTCCTCG
1 TCGTCCTCGTCCTCA
*
2004636 TCGTCCTCCTCCTCA
1 TCGTCCTCGTCCTCA
2004651 TCGTCCTCGTCCT
1 TCGTCCTCGTCCT
2004664 GAGCAGCTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.02, C:0.49, G:0.14, T:0.35
Consensus pattern (15 bp):
TCGTCCTCGTCCTCA
Found at i:2006757 original size:17 final size:18
Alignment explanation
Indices: 2006737--2006774 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
2006727 ATTATATAAG
2006737 TAAAATA-TGAAATAAAT
1 TAAAATACTGAAATAAAT
*
2006754 T-AAATACTTAAATAAAT
1 TAAAATACTGAAATAAAT
2006771 TAAA
1 TAAA
2006775 TACAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
16 5 0.28
17 11 0.61
18 2 0.11
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (18 bp):
TAAAATACTGAAATAAAT
Found at i:2006836 original size:10 final size:10
Alignment explanation
Indices: 2006813--2006862 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
2006803 TACCTTAAAC
* *
2006813 AGAGAATATA
1 AGAGAATTTG
*
2006823 AGAGTATTTG
1 AGAGAATTTG
*
2006833 AGAGAAGTTG
1 AGAGAATTTG
*
2006843 AGAGAAATTG
1 AGAGAATTTG
2006853 AGAGAATTTG
1 AGAGAATTTG
2006863 GTGTGATGAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.44, C:0.00, G:0.30, T:0.26
Consensus pattern (10 bp):
AGAGAATTTG
Found at i:2012457 original size:2 final size:2
Alignment explanation
Indices: 2012450--2012505 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
2012440 ACCATATAAG
2012450 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
2012492 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
2012506 TTATTCATAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2015719 original size:65 final size:65
Alignment explanation
Indices: 2015642--2015814 Score: 181
Period size: 65 Copynumber: 2.7 Consensus size: 65
2015632 AGTACCCAAG
* ** * *
2015642 ATGCCTCCAGGGTCACTTAAAATTGGAGCCTACGTCCCACTAGTATACTCCTT-GAAGTACTTGG
1 ATGCCTTCAGGGTCACTTAGCATCGGAGCCTACGTCCAACTAGTATACT-CTTCGAAGTACTTGG
2015706 A
65 A
* ** * ** *
2015707 ATGCCTTCAGGGTCATTTAGCATCAAAGTCTACGTCCTTCTAGTCTACTCTTCGAAGTACTTGGA
1 ATGCCTTCAGGGTCACTTAGCATCGGAGCCTACGTCCAACTAGTATACTCTTCGAAGTACTTGGA
*
2015772 A--CATTTCCAGGGTCACTTAGCATCGGAGCCTACGTCCAACTAG
1 ATGC-CTT-CAGGGTCACTTAGCATCGGAGCCTACGTCCAACTAG
2015815 CGTTTTAAGT
Statistics
Matches: 87, Mismatches: 18, Indels: 6
0.78 0.16 0.05
Matches are distributed among these distances:
63 1 0.01
64 5 0.06
65 81 0.93
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.29
Consensus pattern (65 bp):
ATGCCTTCAGGGTCACTTAGCATCGGAGCCTACGTCCAACTAGTATACTCTTCGAAGTACTTGGA
Found at i:2017392 original size:24 final size:24
Alignment explanation
Indices: 2017356--2017427 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 24
2017346 GTAACCGGAG
*
2017356 ATATCAGAAATCAAAACTGAATTC
1 ATATCAGAAATCAAAACAGAATTC
* * * *
2017380 ATATCATATATCAGAACAGAATCC
1 ATATCAGAAATCAAAACAGAATTC
** *
2017404 AGGTCAG-AATCAGAACAGAATTC
1 ATATCAGAAATCAAAACAGAATTC
2017427 A
1 A
2017428 GGTAACGTAT
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
23 15 0.39
24 23 0.61
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (24 bp):
ATATCAGAAATCAAAACAGAATTC
Found at i:2017444 original size:24 final size:23
Alignment explanation
Indices: 2017388--2017451 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
2017378 TCATATCATA
* *
2017388 TATCAGAACAGAATCCAGGTCAG
1 TATCAGAACAGAATTCAGGTAAG
*
2017411 AATCAGAACAGAATTCAGGTAACG
1 TATCAGAACAGAATTCAGGTAA-G
*
2017435 TATCATAACAGAATTCA
1 TATCAGAACAGAATTCA
2017452 ATTCGGAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
23 19 0.54
24 16 0.46
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.20
Consensus pattern (23 bp):
TATCAGAACAGAATTCAGGTAAG
Found at i:2019906 original size:8 final size:8
Alignment explanation
Indices: 2019866--2019933 Score: 63
Period size: 8 Copynumber: 8.5 Consensus size: 8
2019856 TCAAAGTTTT
2019866 GGTCAACAG
1 GGTCAAC-G
2019875 TGGTCAACG
1 -GGTCAACG
2019884 TCGGTCAAC-
1 --GGTCAACG
2019893 GGTCAACG
1 GGTCAACG
2019901 GGTCAACG
1 GGTCAACG
*
2019909 GTTCAACG
1 GGTCAACG
2019917 GGT---CG
1 GGTCAACG
2019922 GGTCAACG
1 GGTCAACG
2019930 GGTC
1 GGTC
2019934 GGGTTGGGTT
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
5 5 0.10
7 7 0.14
8 23 0.46
9 1 0.02
10 14 0.28
ACGTcount: A:0.22, C:0.25, G:0.35, T:0.18
Consensus pattern (8 bp):
GGTCAACG
Found at i:2019929 original size:13 final size:13
Alignment explanation
Indices: 2019911--2019937 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2019901 GGTCAACGGT
2019911 TCAACGGGTCGGG
1 TCAACGGGTCGGG
2019924 TCAACGGGTCGGG
1 TCAACGGGTCGGG
2019937 T
1 T
2019938 TGGGTTAACG
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:0.15, C:0.22, G:0.44, T:0.19
Consensus pattern (13 bp):
TCAACGGGTCGGG
Found at i:2019942 original size:18 final size:18
Alignment explanation
Indices: 2019915--2019959 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
2019905 AACGGTTCAA
2019915 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
* *
2019933 CGGGTTGGGTTAACGGGT
1 CGGGTCGGGTCAACGGGT
2019951 C-GGTCGGGT
1 CGGGTCGGGT
2019960 TATGACCGTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 7 0.29
18 17 0.71
ACGTcount: A:0.09, C:0.18, G:0.51, T:0.22
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:2022139 original size:16 final size:16
Alignment explanation
Indices: 2022114--2022144 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2022104 AGTCTCAATA
2022114 GAGAAGATGAAGAAAG
1 GAGAAGATGAAGAAAG
*
2022130 GAGAATATGAAGAAA
1 GAGAAGATGAAGAAA
2022145 ACAAATGTGG
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:0.58, C:0.00, G:0.32, T:0.10
Consensus pattern (16 bp):
GAGAAGATGAAGAAAG
Found at i:2025660 original size:21 final size:20
Alignment explanation
Indices: 2025613--2025661 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
2025603 TTTTTAGTCG
*
2025613 TTTGTAACTCTTGTAATTAC
1 TTTGTAACTCTTGTAATTAA
2025633 TTCTGTAACTCTTGTAATTAA
1 TT-TGTAACTCTTGTAATTAA
2025654 TCTTGTAA
1 T-TTGTAA
2025662 TTGGCATAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 2 0.08
21 23 0.88
22 1 0.04
ACGTcount: A:0.27, C:0.14, G:0.10, T:0.49
Consensus pattern (20 bp):
TTTGTAACTCTTGTAATTAA
Found at i:2034601 original size:111 final size:111
Alignment explanation
Indices: 2034379--2035029 Score: 1018
Period size: 111 Copynumber: 5.9 Consensus size: 111
2034369 CTCAGGGAAG
*
2034379 ATTGAATC-GTGGTAGACTTGTTCCGCTGTTACTCAGGGAATATCAAATCTTGAAAGAG-GGGAT
1 ATTGAATCAG-GGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGAT
* *
2034442 CTGTTCCGCTTTCTCTGAGGGAATATCAGATTTGGGAAAGTTGATTC
65 CTGTTCCGCTTCCTCTGAGGGAATATCAGATATGGGAAAGTTGATTC
* *
2034489 ATTGAATCAGGGTAGACTTGTTCCGTTGTCACTCAGGGAATATCAAATCATGAAAGAGAGGGATC
1 ATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATC
*
2034554 TGTTCCGCTTCCTCTGAGGGAATATCAGATATAGGAAAGTTGATTC
66 TGTTCCGCTTCCTCTGAGGGAATATCAGATATGGGAAAGTTGATTC
* *
2034600 ATTGAATTAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGAGATC
1 ATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATC
*
2034665 TGTTCCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTC
66 TGTTCCGCTTCCTCTGAGGGAATATCAGATATGGGAAAGTTGATTC
*
2034711 ATTGAATCAGGGTAGACTTGTTTCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATC
1 ATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATC
* * * *
2034776 TGTTTCGCTTCCTCTAAGGGATTATTAGATATGGGAAAGTTGATTC
66 TGTTCCGCTTCCTCTGAGGGAATATCAGATATGGGAAAGTTGATTC
* *
2034822 ATTGAATCATGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAATAGAGGGATC
1 ATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATC
* * *
2034887 TGTTCCGCTTTCTCTGAGGGAATATCAGATCTGGGAAAGCTGATTC
66 TGTTCCGCTTCCTCTGAGGGAATATCAGATATGGGAAAGTTGATTC
* * * ** *
2034933 ATTGAATCAGGGTAGACTTGTTCTGCTATCACTCAGGGAATATCAAATCTTGAAAAAGATAGATA
1 ATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATC
* * *
2034998 TGTTTCACTTCTTCTGAAGGGAATATCAGATA
66 TGTTCCGCTTCCTCTG-AGGGAATATCAGATA
2035030 GATGGATTTG
Statistics
Matches: 496, Mismatches: 42, Indels: 4
0.92 0.08 0.01
Matches are distributed among these distances:
110 53 0.11
111 429 0.86
112 14 0.03
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (111 bp):
ATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATC
TGTTCCGCTTCCTCTGAGGGAATATCAGATATGGGAAAGTTGATTC
Found at i:2035172 original size:79 final size:79
Alignment explanation
Indices: 2035029--2035197 Score: 230
Period size: 79 Copynumber: 2.1 Consensus size: 79
2035019 AATATCAGAT
* * ** * *
2035029 AGATGGATTTGTTTCACTATTCTTCCGTGAAGGCTTAAAATGGCCCGGAGGACTTAATCGTCATG
1 AGATGGATTTGCTTCACTATACTTCCGTGAAGGCTTAAAATGGCCCAAAGGACTTAAGCATCATG
* *
2035094 CTCGGAAGGCTTAC
66 CTCGAAAGACTTAC
* * * *
2035108 TGATGGATTTGCTTCACTATACTTCGGTGAAGGCTTAAGATGGCCCAAAGGATTTAAGCATCATG
1 AGATGGATTTGCTTCACTATACTTCCGTGAAGGCTTAAAATGGCCCAAAGGACTTAAGCATCATG
2035173 CTCGAAAGACTTAC
66 CTCGAAAGACTTAC
2035187 AGATGGATTTG
1 AGATGGATTTG
2035198 ATCATCATGC
Statistics
Matches: 77, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
79 77 1.00
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (79 bp):
AGATGGATTTGCTTCACTATACTTCCGTGAAGGCTTAAAATGGCCCAAAGGACTTAAGCATCATG
CTCGAAAGACTTAC
Found at i:2035258 original size:34 final size:34
Alignment explanation
Indices: 2035157--2035259 Score: 161
Period size: 34 Copynumber: 3.0 Consensus size: 34
2035147 ATGGCCCAAA
* * * *
2035157 GGATTTAAGCATCATGCTCGAAAGACTTACAGAT
1 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
2035191 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
1 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
*
2035225 GGATTTGATCATCATGCTCGGAAGACTTCCTGAT
1 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
2035259 G
1 G
2035260 ACCCGAATGA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 64 1.00
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.30
Consensus pattern (34 bp):
GGATTTGATCATCATGCTCGGAAGACTTACTGAT
Found at i:2043482 original size:2 final size:2
Alignment explanation
Indices: 2043475--2043514 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2043465 AACATTTTTA
2043475 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
2043515 GGGAAACATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2045048 original size:3 final size:3
Alignment explanation
Indices: 2045040--2045074 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
2045030 GCATATAAAT
2045040 TAA TAA TAA TAA TTAA TAA TAA TAA TAA TAA -AA TA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TA
2045075 TTAAAAGACA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.83
4 3 0.10
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2045053 original size:13 final size:13
Alignment explanation
Indices: 2045037--2045078 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
2045027 CCTGCATATA
2045037 AATTAATAATAAT
1 AATTAATAATAAT
2045050 AATTAATAATAAT
1 AATTAATAATAAT
2045063 AA-TAATAA-AAT
1 AATTAATAATAAT
2045074 -ATTAA
1 AATTAA
2045079 AAGACATGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.04
11 6 0.21
12 6 0.21
13 15 0.54
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AATTAATAATAAT
Found at i:2046048 original size:3 final size:3
Alignment explanation
Indices: 2046035--2046089 Score: 69
Period size: 3 Copynumber: 18.7 Consensus size: 3
2046025 GGACCCGTCT
* *
2046035 TTA TT- TTA TTA TTA TTA ATA TTA TTA TTA TT- TTT TTAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA
2046079 TTA TTA TTA TT
1 TTA TTA TTA TT
2046090 TTCTTGCAAG
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.09
3 40 0.87
4 2 0.04
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2047424 original size:27 final size:28
Alignment explanation
Indices: 2047392--2047447 Score: 96
Period size: 27 Copynumber: 2.0 Consensus size: 28
2047382 CAATAATTCT
*
2047392 TGTCATTTTGTACTAACGTG-TTTTATG
1 TGTCATTTTATACTAACGTGTTTTTATG
2047419 TGTCATTTTATACTAACGTGTTTTTATG
1 TGTCATTTTATACTAACGTGTTTTTATG
2047447 T
1 T
2047448 TTTCGCTTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 19 0.70
28 8 0.30
ACGTcount: A:0.20, C:0.11, G:0.16, T:0.54
Consensus pattern (28 bp):
TGTCATTTTATACTAACGTGTTTTTATG
Found at i:2049621 original size:32 final size:32
Alignment explanation
Indices: 2049561--2049628 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
2049551 AATTTAGGCA
* * *
2049561 TTACGTTTATTTGAGACTCCGAAGTCATACCT
1 TTACCTTTATTTGAGACACCAAAGTCATACCT
* * *
2049593 TTACCTTTTTTTGAGACACCAAATTCATACTT
1 TTACCTTTATTTGAGACACCAAAGTCATACCT
2049625 TTAC
1 TTAC
2049629 ATTCTCGGGT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.41
Consensus pattern (32 bp):
TTACCTTTATTTGAGACACCAAAGTCATACCT
Found at i:2050392 original size:2 final size:2
Alignment explanation
Indices: 2050387--2050413 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2050377 ATATATATAA
2050387 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
2050414 AAATATAGAA
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2050443 original size:30 final size:29
Alignment explanation
Indices: 2050409--2050486 Score: 124
Period size: 30 Copynumber: 2.7 Consensus size: 29
2050399 AGAGAGAGAG
*
2050409 AGAGAAAATATAGAAAAGGAAGAAGAGAAA
1 AGAGAAAATATAGAAAAGAAAGAAGA-AAA
2050439 AGAGAAAATATAGAAAAGAAAGAAGAAAA
1 AGAGAAAATATAGAAAAGAAAGAAGAAAA
2050468 AGAGAAAA-ATA-AAAAGAAA
1 AGAGAAAATATAGAAAAGAAA
2050487 AAAAAGGAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
27 8 0.17
28 3 0.06
29 11 0.23
30 25 0.53
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (29 bp):
AGAGAAAATATAGAAAAGAAAGAAGAAAA
Found at i:2050473 original size:20 final size:19
Alignment explanation
Indices: 2050436--2050488 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
2050426 GGAAGAAGAG
*
2050436 AAAAG-AGAAAATATAGAAA
1 AAAAGAAGAAAA-AGAGAAA
2050455 AGAAAGAAGAAAAAGAGAAA
1 A-AAAGAAGAAAAAGAGAAA
*
2050475 AATAAAAAGAAAAA
1 AA-AAGAAGAAAAA
2050489 AAAGGAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 2 0.07
20 21 0.72
21 6 0.21
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (19 bp):
AAAAGAAGAAAAAGAGAAA
Found at i:2050499 original size:24 final size:23
Alignment explanation
Indices: 2050457--2050511 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
2050447 TATAGAAAAG
* *
2050457 AAAGAAGAAAAAGAGAAAAATAA
1 AAAGAAAAAAAAGAAAAAAATAA
*
2050480 AAAGAAAAAAAAGGAAAAAAATAG
1 AAAGAAAAAAAA-GAAAAAAATAA
*
2050504 AGAGAAAA
1 AAAGAAAA
2050512 TAAATCAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 11 0.41
24 16 0.59
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (23 bp):
AAAGAAAAAAAAGAAAAAAATAA
Found at i:2050511 original size:23 final size:24
Alignment explanation
Indices: 2050409--2050511 Score: 68
Period size: 30 Copynumber: 3.9 Consensus size: 24
2050399 AGAGAGAGAG
2050409 AGAGAAAATATAGAAAAGGAAGAAGAGAAA
1 AGAGAAAA-ATA-AAAA-G-AGAA-A-AAA
2050439 AGAGAAAATATAGAAAAGAAAGAAGAAAA
1 AGAGAAAA-ATA-AAAAG--AGAA-AAAA
2050468 AGAGAAAAATAAAAAGA-AAAAAA
1 AGAGAAAAATAAAAAGAGAAAAAA
*
2050491 AG-GAAAAA-AATAGAGAGAAAA
1 AGAGAAAAATAA-AAAGAGAAAA
2050512 TAAATCAAGT
Statistics
Matches: 69, Mismatches: 1, Indels: 13
0.83 0.01 0.16
Matches are distributed among these distances:
21 2 0.03
22 10 0.14
23 10 0.14
24 2 0.03
25 1 0.01
27 5 0.07
28 3 0.04
29 12 0.17
30 24 0.35
ACGTcount: A:0.73, C:0.00, G:0.21, T:0.06
Consensus pattern (24 bp):
AGAGAAAAATAAAAAGAGAAAAAA
Found at i:2051555 original size:134 final size:134
Alignment explanation
Indices: 2051309--2051698 Score: 534
Period size: 134 Copynumber: 2.9 Consensus size: 134
2051299 TTAATTTCGA
* *
2051309 GATCAAAATTTTCTTGAGTCTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAGA
1 GATCAAAATTTTCTCGAGTATGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAGA
* *
2051374 TTTGGTCTTCCTAAAGAGCAGCGAAGCAAATCAAGTTTGGTTCAATCTTCCCTAAAGTGCAACAA
66 TTTGGTCTTCCTAAAGAGCAGCGAAGCAAATCAAGTTTGATTCAATCTTCCCTAAAGAGCAACAA
2051439 AGTG
131 AGTG
* *
2051443 GATCAAAATTTTCTCGAGTATGATATCCCCTAAAGAGTAGTGGAGCAGATTATTCTTCTTTCAGA
1 GATCAAAATTTTCTCGAGTATGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAGA
* * * * * ***
2051508 TTTGGTCTTCCTGAAGAGCAGCGAATCAAATCAAGTTTGATTTAATCTTCCCTGAAGAGTAGTGA
66 TTTGGTCTTCCTAAAGAGCAGCGAAGCAAATCAAGTTTGATTCAATCTTCCCTAAAGAGCAACAA
2051573 AGTG
131 AGTG
* * *
2051577 GATTAAAATTTTCTCAAGTCAGGA-CTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAG
1 GATCAAAATTTTCTCGAGT-ATGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAG
* * * ** *
2051641 ATTT-GTCTTCCTTAAGAGTAGTGAAGCAAATGGA-TTTCGATTCAATCTTCCCTGAAGA
65 ATTTGGTCTTCCTAAAGAGCAGCGAAGCAAATCAAGTTT-GATTCAATCTTCCCTAAAGA
2051699 ATAATAAAAT
Statistics
Matches: 228, Mismatches: 26, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
132 3 0.01
133 43 0.19
134 179 0.79
135 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (134 bp):
GATCAAAATTTTCTCGAGTATGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAGA
TTTGGTCTTCCTAAAGAGCAGCGAAGCAAATCAAGTTTGATTCAATCTTCCCTAAAGAGCAACAA
AGTG
Found at i:2051905 original size:3 final size:3
Alignment explanation
Indices: 2051892--2051942 Score: 61
Period size: 3 Copynumber: 17.7 Consensus size: 3
2051882 GGACCCGTCT
* * *
2051892 TTA TT- TTA TTA TTA TTA ATA TTA TTA TTA TTC TT- TAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2051938 TTA TT
1 TTA TT
2051943 TTCTTACAGG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
2 3 0.07
3 38 0.93
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2053301 original size:14 final size:14
Alignment explanation
Indices: 2053282--2053308 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2053272 TTCGTGAACG
2053282 TTCGGTTATGTTCC
1 TTCGGTTATGTTCC
2053296 TTCGGTTATGTTC
1 TTCGGTTATGTTC
2053309 GTTTATGTTC
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:0.07, C:0.19, G:0.22, T:0.52
Consensus pattern (14 bp):
TTCGGTTATGTTCC
Found at i:2053334 original size:24 final size:24
Alignment explanation
Indices: 2053281--2053335 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
2053271 GTTCGTGAAC
* *
2053281 GTTCGGTTATGTTCCTTCGGTTAT
1 GTTCGTTTATGTTCCTTCGATTAT
* *
2053305 GTTCGTTTATGTTCGTTTGATTAT
1 GTTCGTTTATGTTCCTTCGATTAT
2053329 GTTCGTT
1 GTTCGTT
2053336 CATTTATGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.09, C:0.13, G:0.24, T:0.55
Consensus pattern (24 bp):
GTTCGTTTATGTTCCTTCGATTAT
Found at i:2054131 original size:16 final size:16
Alignment explanation
Indices: 2054110--2054168 Score: 91
Period size: 16 Copynumber: 3.7 Consensus size: 16
2054100 GTCTCTAACG
2054110 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
* *
2054126 TTTATGTTCATGTTCG
1 TTTATGTTCGTGTTCA
2054142 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
2054158 TTTATTTTCGT
1 TTTATGTTCGT
2054169 TTTTTTATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.12, C:0.12, G:0.17, T:0.59
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:2055060 original size:22 final size:23
Alignment explanation
Indices: 2055030--2055077 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
2055020 GTTTTTCTGC
*
2055030 TTTCGAATA-GAAAAGTAATAG-T
1 TTTCAAATAGGAAAA-TAATAGCT
2055052 TTTCAAATAGGAAAATAATAGCT
1 TTTCAAATAGGAAAATAATAGCT
2055075 TTT
1 TTT
2055078 GAAAACTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (23 bp):
TTTCAAATAGGAAAATAATAGCT
Found at i:2056159 original size:41 final size:40
Alignment explanation
Indices: 2056100--2056244 Score: 125
Period size: 41 Copynumber: 3.5 Consensus size: 40
2056090 TCACCTCTTT
2056100 TGGCGTTTACA-ACAAACGCCGATATAGATTAGTACTTTAG
1 TGGCGTTTACATACAAACGCCGATATAGATTAGTA-TTTAG
* * *
2056140 TGGCGTTTTCATACAAACGCCGCA-ATAGATATAATATATAG
1 TGGCGTTTACATACAAACGCCG-ATATAGAT-TAGTATTTAG
* *** *
2056181 TGGTGTTTTTTTAACAAACGCC-ACTATAGATTTGTATATTAG
1 TGGCGTTTACAT-ACAAACGCCGA-TATAGATTAGTAT-TTAG
* *
2056223 TGGCGTTTAAAAACAAACGCCG
1 TGGCGTTTACATACAAACGCCG
2056245 GAAAAGCTAA
Statistics
Matches: 83, Mismatches: 14, Indels: 14
0.75 0.13 0.13
Matches are distributed among these distances:
40 11 0.13
41 42 0.51
42 30 0.36
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32
Consensus pattern (40 bp):
TGGCGTTTACATACAAACGCCGATATAGATTAGTATTTAG
Found at i:2056259 original size:83 final size:83
Alignment explanation
Indices: 2056110--2056266 Score: 201
Period size: 83 Copynumber: 1.9 Consensus size: 83
2056100 TGGCGTTTAC
** * * *
2056110 AACAAACGCCGATATAGATTAGTACTTTAGTGGCGTTTTCATACAAACGCCGCAATAGATATAAT
1 AACAAACGCCGATATAGATTAGTACTTTAGTGGCGTTTAAAAACAAACGCCGCAAAAGATAAAAT
2056175 ATATAGTGGTGTTTTTTT
66 ATATAGTGGTGTTTTTTT
* * *
2056193 AACAAACGCC-ACTATAGATTTGTA-TATTAGTGGCGTTTAAAAACAAACGCCGGAAAAGCTAAA
1 AACAAACGCCGA-TATAGATTAGTACT-TTAGTGGCGTTTAAAAACAAACGCCGCAAAAGATAAA
*
2056256 ATATTTAGTGG
64 ATATATAGTGG
2056267 CAATTTTTTG
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
82 2 0.03
83 61 0.97
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (83 bp):
AACAAACGCCGATATAGATTAGTACTTTAGTGGCGTTTAAAAACAAACGCCGCAAAAGATAAAAT
ATATAGTGGTGTTTTTTT
Found at i:2060576 original size:283 final size:283
Alignment explanation
Indices: 2060069--2060929 Score: 1661
Period size: 283 Copynumber: 3.0 Consensus size: 283
2060059 GCTTTTGTCT
*
2060069 TTTGTCAAATGATAAAATACTGTTATTTTTATAAATGATCTTTTGAAGGATATTATGGTCATAAA
1 TTTGTCAAATGATAAAATACTGTTATTTTTATAAATGATCTTTTGAAGGATATTATGGTCCTAAA
*
2060134 TAAACAAATGATACATTTGAATAATAAATTCGTTAAATATTATAGGATGTTGTATAACAAACGCC
66 CAAACAAATGATACATTTGAATAATAAATTCGTTAAATATTATAGGATGTTGTATAACAAACGCC
2060199 ACCGTCAAAGAAATGCAAATACTACATGCATATAAAAACCAATGCCACCGTCCTATAAAATGTAT
131 ACCGTCAAAGAAATGCAAATACTACATGCATATAAAAACCAATGCCACCGTCCTATAAAATGTAT
2060264 AAGATTACTCATTACTAGTCCAACAGAAGACTACAAATTCCCCATGAAAAACAACCTTTGCACCC
196 AAGATTACTCATTACTAGTCCAACAGAAGACTACAAATTCCCCATGAAAAACAACCTTTGCACCC
2060329 GTTGAACGTGAAAGATCTTCGAA
261 GTTGAACGTGAAAGATCTTCGAA
2060352 TTTGTCAAATGATAAAATACTGTTATTTTTATAAATGATCTTTTGAAGGATATTATGGTCCTAAA
1 TTTGTCAAATGATAAAATACTGTTATTTTTATAAATGATCTTTTGAAGGATATTATGGTCCTAAA
2060417 CAAACAAATGATACATTTGAATAATAAATTCGTTAAATATTATAGGATGTTGTATAACAAACGCC
66 CAAACAAATGATACATTTGAATAATAAATTCGTTAAATATTATAGGATGTTGTATAACAAACGCC
2060482 ACCGTCAAAGAAATGCAAATACTACATGCATATAAAAACCAATGCCACCGTCCTATAAAATGTAT
131 ACCGTCAAAGAAATGCAAATACTACATGCATATAAAAACCAATGCCACCGTCCTATAAAATGTAT
*
2060547 AAGATTACTCATTACTAGTCCAACAGAAGACTACAAATTCCCCATGAAAAACAACCTTTCCACCC
196 AAGATTACTCATTACTAGTCCAACAGAAGACTACAAATTCCCCATGAAAAACAACCTTTGCACCC
2060612 GTTGAACGTGAAAGATCTTCGAA
261 GTTGAACGTGAAAGATCTTCGAA
2060635 TTTGTCAAATGATAAAATACTGTTATTTTTATAAATGATCTTTTGAAGGATATTATGGTCAC-AA
1 TTTGTCAAATGATAAAATACTGTTATTTTTATAAATGATCTTTTGAAGGATATTATGGTC-CTAA
2060699 ACAAACAAATGATACATTTGAATAATAAATTCGTTAAATATTATAGGATGTTGTATAACAAACGC
65 ACAAACAAATGATACATTTGAATAATAAATTCGTTAAATATTATAGGATGTTGTATAACAAACGC
*
2060764 CACCGTCAAAGAAATGCAAATACTACATGCATATAAAAACCAATGCCACCGTCCTACAAAATGTA
130 CACCGTCAAAGAAATGCAAATACTACATGCATATAAAAACCAATGCCACCGTCCTATAAAATGTA
*
2060829 TAAGATTACTCATTACTAGTCCAACAGCAGACTACAAATTCCCCATGAAAAACAACCTTTGCACC
195 TAAGATTACTCATTACTAGTCCAACAGAAGACTACAAATTCCCCATGAAAAACAACCTTTGCACC
2060894 CGTTGAACGTGAAAGATCTTCGAA
260 CGTTGAACGTGAAAGATCTTCGAA
2060918 TTTGTCAAATGA
1 TTTGTCAAATGA
2060930 ATCCGCAAAC
Statistics
Matches: 571, Mismatches: 6, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
283 570 1.00
284 1 0.00
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.29
Consensus pattern (283 bp):
TTTGTCAAATGATAAAATACTGTTATTTTTATAAATGATCTTTTGAAGGATATTATGGTCCTAAA
CAAACAAATGATACATTTGAATAATAAATTCGTTAAATATTATAGGATGTTGTATAACAAACGCC
ACCGTCAAAGAAATGCAAATACTACATGCATATAAAAACCAATGCCACCGTCCTATAAAATGTAT
AAGATTACTCATTACTAGTCCAACAGAAGACTACAAATTCCCCATGAAAAACAACCTTTGCACCC
GTTGAACGTGAAAGATCTTCGAA
Found at i:2064135 original size:3 final size:3
Alignment explanation
Indices: 2064127--2064177 Score: 75
Period size: 3 Copynumber: 16.7 Consensus size: 3
2064117 GTATCAACAT
* *
2064127 TAA TAA TAA TAT TAG TAA TAA TAA TAA TAA TAA TAA TAA GTAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA
2064173 TAA TA
1 TAA TA
2064178 TAAAAGCGGG
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2064535 original size:134 final size:135
Alignment explanation
Indices: 2064373--2064717 Score: 383
Period size: 134 Copynumber: 2.6 Consensus size: 135
2064363 GAATCAAAGT
* * * * * * *
2064373 AGACTTGTTCCACTGTTACTTAGAGAATATCAAATCTTGGAAATA-AGGGATTTGTTCTGCTTTT
1 AGACTTGTTCCACTGTTACTAAGGGAATATCAAATCTTGGAAAGAGAAGGATATGTTCCGCTTCT
* * * * * *
2064437 TCTTGAGGGAAAATCATATTTAGGGACGTTGATTAATTCCACCATTA-TTAAAGGAAGATTGAAT
66 TCTTGAGAGAAAATCAGATATAGGGACGGTGATTAATTCCACCATCACTT-AAGGAAGATTAAAT
*
2064501 TGAGGC
130 TGAGGA
*
2064507 GGACTTGTTCCACTGTTACTAAGGGAATATCAAATCTT-GAAAGAGAAGGATATGTTCCGCTTCT
1 AGACTTGTTCCACTGTTACTAAGGGAATATCAAATCTTGGAAAGAGAAGGATATGTTCCGCTTCT
* * * ** *
2064571 TCTTGAGAGAAAATCAGATATGGGGATGGTGATTCATTCCACTGTCACTTAGGGAAGATTAAATT
66 TCTTGAGAGAAAATCAGATATAGGGACGGTGATTAATTCCACCATCACTTAAGGAAGATTAAATT
2064636 GAGGA
131 GAGGA
* * * * * * *
2064641 AAACTTGTTCCACTATTACTCATGGAATATCAAATCTT-GAAAGAGATGGGTATGTTTCGCTTCT
1 AGACTTGTTCCACTGTTACTAAGGGAATATCAAATCTTGGAAAGAGAAGGATATGTTCCGCTTCT
* *
2064705 TCCTGAGGGAAAA
66 TCTTGAGAGAAAA
2064718 ATCAAATCTG
Statistics
Matches: 178, Mismatches: 31, Indels: 4
0.84 0.15 0.02
Matches are distributed among these distances:
133 5 0.03
134 171 0.96
135 2 0.01
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.32
Consensus pattern (135 bp):
AGACTTGTTCCACTGTTACTAAGGGAATATCAAATCTTGGAAAGAGAAGGATATGTTCCGCTTCT
TCTTGAGAGAAAATCAGATATAGGGACGGTGATTAATTCCACCATCACTTAAGGAAGATTAAATT
GAGGA
Found at i:2065031 original size:17 final size:17
Alignment explanation
Indices: 2065004--2065037 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
2064994 AATCGGTTAC
2065004 TTTTTCAAAAAT-TTTA
1 TTTTTCAAAAATATTTA
2065020 TTTTTCAGAAAATATTTA
1 TTTTTCA-AAAATATTTA
2065038 AATGAGAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 5 0.31
18 4 0.25
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTTTCAAAAATATTTA
Found at i:2065447 original size:237 final size:233
Alignment explanation
Indices: 2065128--2065594 Score: 607
Period size: 237 Copynumber: 2.0 Consensus size: 233
2065118 CTCAAGAGGC
* * * *
2065128 TTATGGATGACTCTAAGGATTTAAGCATCATGTTCAAAAGATATACTGATGGCCTGAAGGATTTA
1 TTATAGATGACTCTAAGGATTTAAGCATCATGCTCAAAAGATATACTGATGGCCCGAAGGACTTA
* *
2065193 CAAAATTTGAGAATAGTTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAGAAATTCAATTTTT
66 CAAAATTTGAGAATAGTTTACTAGGTAAGAAACTTTCCTTACTTTTC-AAA-AAATTCAATTTTC
* * *
2065258 AGATTTAAATGAGAAACTTTTCTCATTTTTTTTGAAAAACATGCGAAAACATTCTGTCCAAAGGT
129 AGATTTAAATGAAAAACTTTTCTCA--TTTTTTGAAAAACATGCGAAAACATCCTGCCCAAAGGT
* * *
2065323 CTTGTGGATGGCCCAAAGAACTTATCAACTTTCTCGAAATAT
192 CTTGAGGATGGACCAAAGAACTTATCAACTTACTCGAAATAT
* * *
2065365 TTATAGATGAC-CTAAAGGATTTAAGCATCATGCTCGAAAGACT-TACTGATTGCCCGAGGGACT
1 TTATAGATGACTCT-AAGGATTTAAGCATCATGCTCAAAAGA-TATACTGATGGCCCGAAGGACT
* * * *
2065428 TACTAATTTTG-GAAATAGTTTACTAGGTACGAAACTTTCCTTACTTTTCAAAAATTTCAATTTT
64 TACAAAATTTGAG-AATAGTTTACTAGGTAAGAAACTTTCCTTACTTTTCAAAAAATTCAATTTT
* * * * *
2065492 CAGTTTTGAATGAAAAACTTTTCTCATTTTTTGAGAGACATGTGAAAACATCCTGCCCAAAGGTC
128 CAGATTTAAATGAAAAACTTTTCTCATTTTTTGAAAAACATGCGAAAACATCCTGCCCAAAGGTC
** *
2065557 TTGAGGATGGACTGAAGAACTTATCATCTTACTCGAAA
193 TTGAGGATGGACCAAAGAACTTATCAACTTACTCGAAA
2065595 GAATTACTAA
Statistics
Matches: 200, Mismatches: 27, Indels: 10
0.84 0.11 0.04
Matches are distributed among these distances:
233 66 0.33
235 33 0.17
236 6 0.03
237 94 0.47
238 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Consensus pattern (233 bp):
TTATAGATGACTCTAAGGATTTAAGCATCATGCTCAAAAGATATACTGATGGCCCGAAGGACTTA
CAAAATTTGAGAATAGTTTACTAGGTAAGAAACTTTCCTTACTTTTCAAAAAATTCAATTTTCAG
ATTTAAATGAAAAACTTTTCTCATTTTTTGAAAAACATGCGAAAACATCCTGCCCAAAGGTCTTG
AGGATGGACCAAAGAACTTATCAACTTACTCGAAATAT
Found at i:2065806 original size:191 final size:190
Alignment explanation
Indices: 2065397--2065807 Score: 542
Period size: 191 Copynumber: 2.1 Consensus size: 190
2065387 AAGCATCATG
* * *
2065397 CTCGAAAGACTTACTGATTGCCCGAGGGACTTACTAATTTTGGAAATAGTTTACTAGGTACGAAA
1 CTCGAAAGACTTACAGA-TGCCCGAAGGACTTACTAATTTTGGAAATAGTTTACTAGGTAAGAAA
* * * *
2065462 CTTTCCTTACTTTTCAAAAATTTCAATTTTCAGTTTTGAATGAAAAACTTTTCTCATTTTTTGAG
65 CCTTCCTGAATTTTCAAAAATTTCAATTTTCAATTTTGAATGAAAAACTTTTCTCATTTTTTGAG
* *
2065527 AGACATGTGAAAACATCCTGCCCAAAGGTCTTGAGGATGGACTGAAGAACTTATCATCTTA
130 AGACATGTGAAAACATCCTGCCCAAAGATCTTGAGGATGGACCGAAGAACTTATCATCTTA
* *
2065588 CTCGAAAGAATTACTA-ATGGCCCGAAGGACTTACTAATTTTGGAAATGGTTTACTAGGTAAGAA
1 CTCGAAAGACTTAC-AGAT-GCCCGAAGGACTTACTAATTTTGGAAATAGTTTACTAGGTAAGAA
* * *
2065652 ACCTTCCTGAATTTTCAAAATTTTCAATTTTCATATTTTGAATGAGAAATTTTTCTC-TTTTTTC
64 ACCTTCCTGAATTTTCAAAAATTTCAATTTTCA-ATTTTGAATGAAAAACTTTTCTCATTTTTT-
* * * * *
2065716 GAGAGACATGTGAAAACATCC-GACCC-AAGATCTTGTGGATGGCCCGAAGGACTTATTATTTTA
127 GAGAGACATGTGAAAACATCCTG-CCCAAAGATCTTGAGGATGGACCGAAGAACTTATCATCTTA
* *
2065779 CTCTAAAGACTTACAGATGAACCGAAGGA
1 CTCGAAAGACTTACAGATG-CCCGAAGGA
2065808 TTTAAGCATC
Statistics
Matches: 191, Mismatches: 22, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
190 3 0.02
191 144 0.75
192 44 0.23
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (190 bp):
CTCGAAAGACTTACAGATGCCCGAAGGACTTACTAATTTTGGAAATAGTTTACTAGGTAAGAAAC
CTTCCTGAATTTTCAAAAATTTCAATTTTCAATTTTGAATGAAAAACTTTTCTCATTTTTTGAGA
GACATGTGAAAACATCCTGCCCAAAGATCTTGAGGATGGACCGAAGAACTTATCATCTTA
Found at i:2066518 original size:232 final size:232
Alignment explanation
Indices: 2065592--2066644 Score: 1348
Period size: 233 Copynumber: 4.5 Consensus size: 232
2065582 ATCTTACTCG
* * * * *
2065592 AAAGAATTACTAATGGCCCGAAGGACTTACTAATTTTGGAAATGGTTTACTAGGTAAGAAACCTT
1 AAAGACTTACTGATGGCCTGAAGGACTTACTACTTTTGGAAATAGTTTACTAGGTAAGAAACCTT
* * * * *
2065657 CCTGAATTTTCAAAATTTTCAATTTTCATATTTTGAATGAGAAATTTTTCTCTTTTTTCGAGAGA
66 TCTTACTTTTCAAAAATTTCAATTTTCATA-TTTGAATGAGAAA-TTTTCTCATTTTTCGAGAGA
* * * * *
2065722 CATGTGAAAACATCCGACCC-AAGATCTTGTGGATGGCCCGAAGGACTTATTATTTTACTCTAAA
129 CATGTGAAAACATCCTACCCAAAGGTCTTGTGGATGGCCCGAAGGACTTATCATCTTACTCGAAA
*
2065786 GACTTACAGATGAACCGAAGGATTTAAGCATCATGCTCA
194 GACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCA
* * *
2065825 AAAGACTTACTGATGGCCTGAAGGACTTACCAAC-TTTGGAAGTAGTTTACTAGGTAAGAAACTT
1 AAAGACTTACTGATGGCCTGAAGGACTTA-CTACTTTTGGAAATAGTTTACTAGGTAAGAAACCT
* *
2065889 TTCTTATTTTTCAAAAATTTCAATTTTCATATTTGAATGAGAAACTTTTCTTATTTTTCGAGAGA
65 TTCTTACTTTTCAAAAATTTCAATTTTCATATTTGAATGAGAAA-TTTTCTCATTTTTCGAGAGA
* * * * * * * * * * * *
2065954 CACGTCAAATCATCTTGCCCAAAGGTCTTTTGTAT-GTCCTAGAGAACTTATAATCTTGCTCGAA
129 CATGTGAAAACATCCTACCCAAAGGTCTTGTGGATGGCCCGA-AGGACTTATCATCTTACTCGAA
* * *
2066018 AGACTTACAGATGACCCGAAGGATTTAAACTTCATGCTCG
193 AGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCA
* *
2066058 AAAGACTTACTGATGGTCC--AAGGGACTTACTAATTTTAGAAATAGTTTACTAGGTAAGAAA-C
1 AAAGACTTACTGATGG-CCTGAA-GGACTTACTACTTTTGGAAATAGTTTACTAGGTAAGAAACC
* * *
2066120 TTTCCTTACTTTTCAAAAATTTCAGTTTTCATATTTAAATGAGATAATTTTCTCATTTTTAGAGA
64 TTT-CTTACTTTTCAAAAATTTCAATTTTCATATTTGAATGAGA-AATTTTCTCATTTTTCGAGA
* * * * * *
2066185 GCCATGTGAAAACATCTTGCCCAAGGGTCTTGTGGATAGCCCGAAGGACTTATCATCTTGCTCGA
127 GACATGTGAAAACATCCTACCCAAAGGTCTTGTGGATGGCCCGAAGGACTTATCATCTTACTCGA
* *
2066250 AAGACTTATAAATGACCCGAAGGATTT-AGACATCATGCTCA
192 AAGACTTACAGATGACCCGAAGGATTTAAG-CATCATGCTCA
* * *
2066291 AAAGATTTACTGATGGCCTGAGGGACTTACTACTTTTGGAAATAGTTTACTAGGTAAGAATCCTT
1 AAAGACTTACTGATGGCCTGAAGGACTTACTACTTTTGGAAATAGTTTACTAGGTAAGAAACCTT
*
2066356 TCTTACTTTTCAAAAATTTCAATTTTCAGATTTGAATGAGAAATTTTCTCATTTTTCGAGAGACA
66 TCTTACTTTTCAAAAATTTCAATTTTCATATTTGAATGAGAAATTTTCTCATTTTTCGAGAGACA
* * *
2066421 TGTGAAAACATCCTACCCAAAGGTCTTGTGGATGGCCCGAATGACTTATCATCATACTTGAAAGA
131 TGTGAAAACATCCTACCCAAAGGTCTTGTGGATGGCCCGAAGGACTTATCATCTTACTCGAAAGA
* *
2066486 CTTACAGATTACCCGAAGGATTTAAGCATCATGCTCG
196 CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCA
* * *
2066523 AAAGACTTACTGATGGCCTGAAGAACTTACCAAC-TTTGGAAATAGTTTACTAGGTAAGAAACGT
1 AAAGACTTACTGATGGCCTGAAGGACTTA-CTACTTTTGGAAATAGTTTACTAGGTAAGAAACCT
** * * *
2066587 TTCTTACTTTTCAAAAATTTCAATTTTCAGCTTTAAATGACAAAATTTTCTCCTTTTT
65 TTCTTACTTTTCAAAAATTTCAATTTTCATATTTGAATGA-GAAATTTTCTCATTTTT
2066645 TAACTTATAA
Statistics
Matches: 711, Mismatches: 93, Indels: 32
0.85 0.11 0.04
Matches are distributed among these distances:
232 260 0.37
233 436 0.61
234 15 0.02
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (232 bp):
AAAGACTTACTGATGGCCTGAAGGACTTACTACTTTTGGAAATAGTTTACTAGGTAAGAAACCTT
TCTTACTTTTCAAAAATTTCAATTTTCATATTTGAATGAGAAATTTTCTCATTTTTCGAGAGACA
TGTGAAAACATCCTACCCAAAGGTCTTGTGGATGGCCCGAAGGACTTATCATCTTACTCGAAAGA
CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCA
Found at i:2070183 original size:137 final size:136
Alignment explanation
Indices: 2069950--2070201 Score: 359
Period size: 137 Copynumber: 1.8 Consensus size: 136
2069940 GTATGTAATG
* *
2069950 GTTATCGATCGATTTTGTTTAATGCATATGTTGCATTTTCGTATCAGTACTATGTGTACTTTCGG
1 GTTATCGATCGATTTTGTTTAATGCATATGTTGCATTTTCGTATCAGTACTATATGTACTTTCGA
* *
2070015 AACTAGATGTGAAACCATGGTATTCATAATGAGCGTTTG-AATTACCATTTTGACATACAATTGT
66 AACTAGATGTGAAACCATGGAATTCAAAATGA--GTTTGTAATTACCATTTTGACATACAATTGT
2070079 GTATAAAA
129 GTATAAAA
*
2070087 GTTATC-ATTCGATTTTGTTTAATGCATATGTTGCATTTTTGTATCAGTACTATATGTACTTTC-
1 GTTATCGA-TCGATTTTGTTTAATGCATATGTTGCATTTTCGTATCAGTACTATATGTACTTTCG
* *
2070150 AACACTATG-TGTGCATCCATGGAATTCAAAATGAGTTTGTTAATTACCATTT
65 AA-ACTA-GATGTGAAACCATGGAATTCAAAATGAGTTTG-TAATTACCATTT
2070202 CAGTACTTAG
Statistics
Matches: 103, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
135 5 0.05
136 2 0.02
137 95 0.92
138 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (136 bp):
GTTATCGATCGATTTTGTTTAATGCATATGTTGCATTTTCGTATCAGTACTATATGTACTTTCGA
AACTAGATGTGAAACCATGGAATTCAAAATGAGTTTGTAATTACCATTTTGACATACAATTGTGT
ATAAAA
Found at i:2081706 original size:16 final size:16
Alignment explanation
Indices: 2081685--2081716 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2081675 AAAGCATGAC
2081685 TGGGTAGATACCATGT
1 TGGGTAGATACCATGT
*
2081701 TGGGTAGATATCATGT
1 TGGGTAGATACCATGT
2081717 GAATAAGGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.09, G:0.31, T:0.34
Consensus pattern (16 bp):
TGGGTAGATACCATGT
Found at i:2091757 original size:17 final size:17
Alignment explanation
Indices: 2091694--2091758 Score: 55
Period size: 17 Copynumber: 3.8 Consensus size: 17
2091684 GAAAAAAAGA
*
2091694 AAAAGAAA-AAATGAATG
1 AAAAGAAATAAA-AAATG
2091711 AAAA-AAATATAAAAAT-
1 AAAAGAAATA-AAAAATG
*
2091727 ATAAAAAAATAAAAAATG
1 A-AAAGAAATAAAAAATG
*
2091745 AAAAGAAACAAAAA
1 AAAAGAAATAAAAA
2091759 GAAACAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
16 4 0.10
17 28 0.70
18 8 0.20
ACGTcount: A:0.78, C:0.02, G:0.08, T:0.12
Consensus pattern (17 bp):
AAAAGAAATAAAAAATG
Found at i:2092828 original size:55 final size:55
Alignment explanation
Indices: 2092760--2093139 Score: 489
Period size: 55 Copynumber: 6.9 Consensus size: 55
2092750 GGTTCCCTAG
* * * *
2092760 CGATTGTTGAAGATTGTTCGAGTATTATACTCTCCGAAGAAATAGAGAGCATACA
1 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACA
* * * *
2092815 TGATTGTTGAAGATTGTTCGAGTCTTATAATCTCTGAAGAAATAGAGAGCAAACA
1 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACA
*
2092870 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGATA
1 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACA
*
2092925 CAATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACA
1 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACA
*
2092980 CGAGTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACA
1 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACA
* * * * * *
2093035 CGATTATTGATGATTGTTCGAGT-TCTATACTCCCTGAAGGAAGAGGGA--ATGAACC
1 CGATTGTTGAAGATTGTTCGAGTCT-TATACTCTCTGAAGAAATAGGGAGCA-G-ACA
* * * * * *
2093090 CGATTGATGAATATTGTCCGAGT-TCTATACTCCCTAAAGAAAGAGGGAGC
1 CGATTGTTGAAGATTGTTCGAGTCT-TATACTCTCTGAAGAAATAGGGAGC
2093140 GAACCCGTTG
Statistics
Matches: 292, Mismatches: 28, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
53 1 0.00
54 2 0.01
55 289 0.99
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.29
Consensus pattern (55 bp):
CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACA
Found at i:2101413 original size:137 final size:137
Alignment explanation
Indices: 2101167--2101418 Score: 380
Period size: 137 Copynumber: 1.8 Consensus size: 137
2101157 GTATGTAATG
* * * * *
2101167 GTTATAGATCGATTTTGTTTAATGCATATGTTGCATTTTTGTATCAATACTATGTGTACTTTCGG
1 GTTATAGATCAATTTTGCTTAATGCATATGTTGCATTTTCGTATCAATACTATATGTACTTTCGA
** *
2101232 CACTAGATGTGCAACCATATTATTCATAATGAGTTTGTGAATTACCATTTTGACATACAATTGTG
66 CACTAGATGTGCAACCATAGAATTCATAATGAGTTTGTAAATTACCATTTTGACATACAATTGTG
2101297 TATAAAA
131 TATAAAA
* *
2101304 GTTATTGATCAATTTTGCTTAATGCATATGTTGCATTTTCGTATCAGTACTATATGTACTTTCGA
1 GTTATAGATCAATTTTGCTTAATGCATATGTTGCATTTTCGTATCAATACTATATGTACTTTCGA
* *
2101369 CACTATG-TGTGCATCCATGGAATTCATAATGAGTTTGTAAATTACCATTT
66 CACTA-GATGTGCAACCATAGAATTCATAATGAGTTTGTAAATTACCATTT
2101419 CGGCACTTAG
Statistics
Matches: 102, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
137 101 0.99
138 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (137 bp):
GTTATAGATCAATTTTGCTTAATGCATATGTTGCATTTTCGTATCAATACTATATGTACTTTCGA
CACTAGATGTGCAACCATAGAATTCATAATGAGTTTGTAAATTACCATTTTGACATACAATTGTG
TATAAAA
Found at i:2102177 original size:1 final size:1
Alignment explanation
Indices: 2102171--2102313 Score: 61
Period size: 1 Copynumber: 143.0 Consensus size: 1
2102161 CTTATCTATA
* * * * * *** * * *
2102171 TTTTTTTTCTTTTTTTTTCTTTTTTTTTCTTTCTTTTTTTCTTTTTTTTCAATCTCTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * ** * * * * * *
2102236 TTCTTCTTTTTTCTTCTTTCCTTTATTTTTTTCTTTCTTTTTCTTTTTTCTTTTTTTTTTTCTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
2102301 CTTTGTTTTTTTT
1 TTTTTTTTTTTTT
2102314 AGTGTGGTAT
Statistics
Matches: 97, Mismatches: 45, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
1 97 1.00
ACGTcount: A:0.02, C:0.15, G:0.01, T:0.83
Consensus pattern (1 bp):
T
Found at i:2102188 original size:12 final size:12
Alignment explanation
Indices: 2102171--2102310 Score: 103
Period size: 12 Copynumber: 11.7 Consensus size: 12
2102161 CTTATCTATA
2102171 TTTTTTTTC--T
1 TTTTTTTTCTTT
2102181 TTTTTTTTC--T
1 TTTTTTTTCTTT
2102191 TTTTTTTTCTTT
1 TTTTTTTTCTTT
*
2102203 CTTTTTTTCTTT
1 TTTTTTTTCTTT
* *
2102215 TTTTTCAATCTCTTC
1 TTTTT---TTTCTTT
2102230 TTTTTTTTC--T
1 TTTTTTTTCTTT
* *
2102240 TCTTTTTTCTTC
1 TTTTTTTTCTTT
** *
2102252 TTTCCTTTATTT
1 TTTTTTTTCTTT
*
2102264 TTTTCTTTCTTT
1 TTTTTTTTCTTT
2102276 TTCTTTTTTCTTT
1 TT-TTTTTTCTTT
2102289 TTTTTTTTCTTT
1 TTTTTTTTCTTT
2102301 CTTTGTTTTT
1 -TTT-TTTTT
2102311 TTTAGTGTGG
Statistics
Matches: 104, Mismatches: 16, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
10 27 0.26
12 48 0.46
13 14 0.13
14 5 0.05
15 10 0.10
ACGTcount: A:0.02, C:0.15, G:0.01, T:0.82
Consensus pattern (12 bp):
TTTTTTTTCTTT
Found at i:2102216 original size:30 final size:30
Alignment explanation
Indices: 2102170--2102313 Score: 86
Period size: 29 Copynumber: 4.6 Consensus size: 30
2102160 TCTTATCTAT
2102170 ATTT-TTTTTCTTTTTTTTTCTTTTTTTTTC
1 ATTTCTTTTT-TTTTTTTTTCTTTTTTTTTC
2102200 -TTTCTTTTTTTCTTTTTTTTCAATCTCTTCTTTTT-
1 ATTTC-TTTTTT-TTTTTTTTC--T-T-TT-TTTTTC
*
2102235 -TTTCTTCTTTTTTCTTCTTTCCTTTATTTTTTTC
1 ATTTCTT-TTTTTT-TT-TTTTC-TT-TTTTTTTC
*
2102269 -TTTCTTTTTCTTTTTTCTT-TTTTTTTTTC
1 ATTTCTTTTT-TTTTTTTTTCTTTTTTTTTC
*
2102298 -TTTCTTTGTTTTTTTT
1 ATTTCTTTTTTTTTTTT
2102314 AGTGTGGTAT
Statistics
Matches: 94, Mismatches: 7, Indels: 28
0.73 0.05 0.22
Matches are distributed among these distances:
28 6 0.06
29 19 0.20
30 3 0.03
31 14 0.15
32 2 0.02
33 11 0.12
34 17 0.18
35 13 0.14
36 9 0.10
ACGTcount: A:0.03, C:0.15, G:0.01, T:0.82
Consensus pattern (30 bp):
ATTTCTTTTTTTTTTTTTTCTTTTTTTTTC
Found at i:2102265 original size:49 final size:45
Alignment explanation
Indices: 2102181--2102313 Score: 142
Period size: 46 Copynumber: 2.8 Consensus size: 45
2102171 TTTTTTTTCT
* *
2102181 TTTTTTTTCTTTTTTTTTCTTTCTTTTTTTCTTTTTTTTCAATCTCTTC
1 TTTTTTTTC-TTTTTTTTC-TTCTTTCTTTATTTTTTTTC--TCTCTTC
* *
2102230 TTTTTTTTCTTCTTTTTTCTTCTTTCCTTTA-TTTTTTTCTTTCTTT
1 TTTTTTTTCTT-TTTTTTCTTCTTT-CTTTATTTTTTTTCTCTCTTC
* *
2102276 TTCTTTTTTCTTTTTTTTTTTCTTTCTTTGTTTTTTTT
1 TT-TTTTTTCTTTTTTTTCTTCTTTCTTTATTTTTTTT
2102314 AGTGTGGTAT
Statistics
Matches: 74, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
45 4 0.05
46 26 0.35
47 9 0.12
48 16 0.22
49 19 0.26
ACGTcount: A:0.02, C:0.15, G:0.01, T:0.82
Consensus pattern (45 bp):
TTTTTTTTCTTTTTTTTCTTCTTTCTTTATTTTTTTTCTCTCTTC
Found at i:2102309 original size:27 final size:26
Alignment explanation
Indices: 2102173--2102311 Score: 111
Period size: 27 Copynumber: 5.0 Consensus size: 26
2102163 TATCTATATT
*
2102173 TTTTTTCTTTTTTTTTCTTTTTTTTTC
1 TTTTTT-TTTTTCTTTCTTTTTTTTTC
*
2102200 TTTCTTTTTTTCTTT-TTTTTCAATCTCTTC
1 TTTTTTTTTTTCTTTCTTTTT---T-T-TTC
* *
2102230 TTTTTTTTCTTCTTT-TTTCTTCTTTCC
1 TTTTTTTTTTTCTTTCTTT-TT-TTTTC
*
2102257 TTTATTTTTTTCTTTCTTTTTCTTTTTTC
1 TTTTTTTTTTTCTTTC--TTT-TTTTTTC
2102286 TTTTTTTTTTTCTTTCTTTGTTTTTT
1 TTTTTTTTTTTCTTTCTTT-TTTTTT
2102312 TTAGTGTGGT
Statistics
Matches: 92, Mismatches: 11, Indels: 18
0.76 0.09 0.15
Matches are distributed among these distances:
25 5 0.05
26 8 0.09
27 29 0.32
28 2 0.02
29 21 0.23
30 25 0.27
31 2 0.02
ACGTcount: A:0.02, C:0.15, G:0.01, T:0.82
Consensus pattern (26 bp):
TTTTTTTTTTTCTTTCTTTTTTTTTC
Found at i:2127044 original size:3 final size:3
Alignment explanation
Indices: 2127036--2127089 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
2127026 AAAAATGTAG
* * *
2127036 TAA TAA TAA TAA TAA TAA CAA TAA TAA TAA TAA CAA TAT TAA GTAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
2127082 TAA TAA TA
1 TAA TAA TA
2127090 TAAAAGCGAG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:2129188 original size:23 final size:23
Alignment explanation
Indices: 2129162--2129255 Score: 58
Period size: 23 Copynumber: 4.3 Consensus size: 23
2129152 CGAACATGAT
2129162 TTTATATGAAATTAATTTAAATA
1 TTTATATGAAATTAATTTAAATA
**
2129185 TTTATA--AGCTTAATTT--AT-
1 TTTATATGAAATTAATTTAAATA
* *
2129203 TTT-TATGTAA-TAATTGATTAATAA
1 TTTATATGAAATTAATT--TAAAT-A
* *
2129227 TTTAAATAAAATTAATTTAAATA
1 TTTATATGAAATTAATTTAAATA
2129250 TTTATA
1 TTTATA
2129256 CGTTTAATCT
Statistics
Matches: 51, Mismatches: 10, Indels: 20
0.63 0.12 0.25
Matches are distributed among these distances:
17 2 0.04
18 8 0.16
19 2 0.04
20 1 0.02
21 8 0.16
22 2 0.04
23 12 0.24
24 7 0.14
25 4 0.08
26 5 0.10
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (23 bp):
TTTATATGAAATTAATTTAAATA
Found at i:2129990 original size:12 final size:12
Alignment explanation
Indices: 2129951--2129992 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
2129941 CTCTTATATT
*
2129951 TATATACTTACA
1 TATATACTTATA
2129963 T-TATACTTTATA
1 TATATAC-TTATA
*
2129975 TATATACTTGTA
1 TATATACTTATA
2129987 TATATA
1 TATATA
2129993 TACTCATACT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 5 0.19
12 16 0.62
13 5 0.19
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (12 bp):
TATATACTTATA
Found at i:2129990 original size:14 final size:13
Alignment explanation
Indices: 2129951--2129996 Score: 60
Period size: 14 Copynumber: 3.6 Consensus size: 13
2129941 CTCTTATATT
*
2129951 TATATAC-TTACA
1 TATATACTTTATA
2129963 T-TATACTTTATA
1 TATATACTTTATA
2129975 TATATACTTGTATA
1 TATATACTT-TATA
2129989 TATATACT
1 TATATACT
2129997 CATACTCTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
11 5 0.17
12 6 0.20
13 7 0.23
14 12 0.40
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (13 bp):
TATATACTTTATA
Found at i:2131150 original size:6 final size:6
Alignment explanation
Indices: 2131141--2131165 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2131131 CGCCGCCGTC
2131141 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
2131166 AATACGTGTC
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:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:2131276 original size:20 final size:20
Alignment explanation
Indices: 2131251--2131361 Score: 77
Period size: 20 Copynumber: 5.5 Consensus size: 20
2131241 TTTTAAAACT
2131251 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* **
2131271 ATCGCAA--CGACACTGTAGACT
1 ATCGCAACGCGA-AATG--GAAA
2131292 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* **
2131312 ATCGCAA--CGACACTGTAGACT
1 ATCGCAACGCGA-AATG--GAAA
*
2131333 ATCGCAATGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
2131353 ATCGCAACG
1 ATCGCAACG
2131362 ACACTGTAGA
Statistics
Matches: 68, Mismatches: 13, Indels: 20
0.67 0.13 0.20
Matches are distributed among these distances:
18 6 0.09
19 6 0.09
20 26 0.38
21 18 0.26
22 6 0.09
23 6 0.09
ACGTcount: A:0.40, C:0.23, G:0.23, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:2131459 original size:41 final size:41
Alignment explanation
Indices: 2131248--2131443 Score: 338
Period size: 41 Copynumber: 4.8 Consensus size: 41
2131238 CATTTTTAAA
2131248 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
2131289 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
*
2131330 ACTATCGCAATGCGAAATGGAAAATCGCAACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
* * * *
2131371 ACTATCGCAACACGAACTGGAAAATCACAACGACGCTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
*
2131412 ACTATCGCAACGCGAAATGGAAAACCGCAACG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACG
2131444 TGATTTTCAA
Statistics
Matches: 145, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 145 1.00
ACGTcount: A:0.39, C:0.25, G:0.21, T:0.14
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
Found at i:2131773 original size:14 final size:11
Alignment explanation
Indices: 2131740--2131770 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2131730 TTTAAATAAT
2131740 AAAATTATTGA
1 AAAATTATTGA
2131751 AAAATTATTGA
1 AAAATTATTGA
*
2131762 AACATTATT
1 AAAATTATT
2131771 ATTTCTGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (11 bp):
AAAATTATTGA
Found at i:2131846 original size:21 final size:21
Alignment explanation
Indices: 2131822--2131862 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2131812 TGATAAAGCA
*
2131822 CTATGTGTTTTGTTATTTTTT
1 CTATGGGTTTTGTTATTTTTT
2131843 CTATGGGTTTTGTTATTTTT
1 CTATGGGTTTTGTTATTTTT
2131863 AAACAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.05, G:0.17, T:0.68
Consensus pattern (21 bp):
CTATGGGTTTTGTTATTTTTT
Found at i:2142049 original size:75 final size:77
Alignment explanation
Indices: 2141959--2142149 Score: 221
Period size: 76 Copynumber: 2.5 Consensus size: 77
2141949 TCTCACTGGA
* ** * * * *
2141959 GATTGTTTTTCTT-AAAGAAGACTTTGTCTCACTTGAGA-TTGTTTTACTT-GATAGAATACATT
1 GATTGTTTTTCTTAAAACAAGA-TTTGTCTCACTTGAGACAAGTTTTA-TTCAAAACAAGACATT
*
2142021 TCATTTGACT-CAG
64 TCATTTCACTACAG
* *
2142034 GATTGTTTTTCTTAAAACAAGATTTGTCTCTCTTGGGACAAGTTTTATTCAAAACAAGACATTTC
1 GATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACAAGTTTTATTCAAAACAAGACATTTC
*
2142099 ATTTCACTACAT
66 ATTTCACTACAG
*
2142111 G-TTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACA
1 GATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACA
2142150 TTTTTTTCCT
Statistics
Matches: 99, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
75 29 0.29
76 67 0.68
77 3 0.03
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (77 bp):
GATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACAAGTTTTATTCAAAACAAGACATTTC
ATTTCACTACAG
Found at i:2142173 original size:40 final size:42
Alignment explanation
Indices: 2142128--2142307 Score: 198
Period size: 40 Copynumber: 4.5 Consensus size: 42
2142118 TTCTTAAAAC
* * *
2142128 AAGA-TTTGTCTCGCTTGAGACATT-TTTTTCCTTGAAACGG
1 AAGATTTTATCTCGCTTGAGAGATTATTTTTCCTTGAAACAG
* * * *
2142168 AAGATTTTATCTCAC-TCA-AGATTGTTTTTCCTTGAAACAA
1 AAGATTTTATCTCGCTTGAGAGATTATTTTTCCTTGAAACAG
* *
2142208 AAGATTTTATCTCGCTT--GAGA-TAGTTTCCCTTGAAACAG
1 AAGATTTTATCTCGCTTGAGAGATTATTTTTCCTTGAAACAG
*
2142247 AAGATTTTATCTCGC-TCA-AGATTATTTTTCCTTGAAACAG
1 AAGATTTTATCTCGCTTGAGAGATTATTTTTCCTTGAAACAG
*
2142287 AATATTTTATCTCGCTTGAGA
1 AAGATTTTATCTCGCTTGAGA
2142308 TAGTTTCCCT
Statistics
Matches: 116, Mismatches: 15, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
38 1 0.01
39 36 0.31
40 67 0.58
41 11 0.09
42 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.39
Consensus pattern (42 bp):
AAGATTTTATCTCGCTTGAGAGATTATTTTTCCTTGAAACAG
Found at i:2142250 original size:79 final size:79
Alignment explanation
Indices: 2142157--2142322 Score: 287
Period size: 79 Copynumber: 2.1 Consensus size: 79
2142147 ACATTTTTTT
* *
2142157 CCTTGAAACGGAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACAAAAGATTTTATCTCG
1 CCTTGAAACAGAAGATTTTATCTCACTCAAGATTATTTTTCCTTGAAACAAAAGATTTTATCTCG
2142222 CTTGAGATAGTTTC
66 CTTGAGATAGTTTC
* * *
2142236 CCTTGAAACAGAAGATTTTATCTCGCTCAAGATTATTTTTCCTTGAAACAGAATATTTTATCTCG
1 CCTTGAAACAGAAGATTTTATCTCACTCAAGATTATTTTTCCTTGAAACAAAAGATTTTATCTCG
2142301 CTTGAGATAGTTTC
66 CTTGAGATAGTTTC
2142315 CCTTGAAA
1 CCTTGAAA
2142323 AAAAAAATTG
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 82 1.00
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (79 bp):
CCTTGAAACAGAAGATTTTATCTCACTCAAGATTATTTTTCCTTGAAACAAAAGATTTTATCTCG
CTTGAGATAGTTTC
Found at i:2142251 original size:39 final size:39
Alignment explanation
Indices: 2142157--2142361 Score: 207
Period size: 40 Copynumber: 5.3 Consensus size: 39
2142147 ACATTTTTTT
* * ** * *
2142157 CCTTGAAACGGAAGATTTTATCTCACTCAAGATTGTTTTT
1 CCTTGAAACAGAAGATTTTATCTCGCTTGAGATAG-TTTC
*
2142197 CCTTGAAACAAAAGATTTTATCTCGCTTGAGATAGTTTC
1 CCTTGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTC
** * *
2142236 CCTTGAAACAGAAGATTTTATCTCGCTCAAGATTATTTTT
1 CCTTGAAACAGAAGATTTTATCTCGCTTGAGA-TAGTTTC
*
2142276 CCTTGAAACAGAATATTTTATCTCGCTTGAGATAGTTTC
1 CCTTGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTC
* ** * * *
2142315 CCTTGAAA-A-AAAAAATTGTCTCCCTTGAGACAGTTTC
1 CCTTGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTC
*
2142352 TCTTGAAACA
1 CCTTGAAACA
2142362 TAAACTTTGA
Statistics
Matches: 139, Mismatches: 24, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
37 29 0.21
38 2 0.01
39 45 0.32
40 63 0.45
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.37
Consensus pattern (39 bp):
CCTTGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTC
Found at i:2142385 original size:29 final size:28
Alignment explanation
Indices: 2142346--2142462 Score: 92
Period size: 29 Copynumber: 3.9 Consensus size: 28
2142336 CCCTTGAGAC
*
2142346 AGTTTCTCTTGAAACATAAACTTTGAAAA
1 AGTTTCCCTTGAAACA-AAACTTTGAAAA
* * *
2142375 AGTTTCCCTTGAAACAAATTTTGTCTCCATTGAGAC
1 AGTTTCCCTTGAAACAAA-----ACT---TTGAAAA
2142411 AGTTTCCCTTGAAACATAAACTTTGAAAA
1 AGTTTCCCTTGAAACA-AAACTTTGAAAA
*
2142440 TGTTTCCCTTGAAACAAAA-TTTG
1 AGTTTCCCTTGAAACAAAACTTTG
2142463 TCTCCCTTGA
Statistics
Matches: 71, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
27 4 0.06
28 5 0.07
29 35 0.49
32 2 0.03
33 2 0.03
36 21 0.30
37 2 0.03
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (28 bp):
AGTTTCCCTTGAAACAAAACTTTGAAAA
Found at i:2142414 original size:65 final size:65
Alignment explanation
Indices: 2142309--2142535 Score: 312
Period size: 65 Copynumber: 3.5 Consensus size: 65
2142299 CGCTTGAGAT
* *
2142309 AGTTTCCCTTGAAAAAAAAAATTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAA
1 AGTTTCCCTTG-AAACAAAATTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAA
2142374 A
65 A
* * *
2142375 AGTTTCCCTTGAAACAAATTTTGTCTCCATTGAGACAGTTTCCCTTGAAACATAAACTTTGAAAA
1 AGTTTCCCTTGAAACAAAATTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAA
* *** * *
2142440 TGTTTCCCTTGAAACAAAATTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA-AGTTTTTGAGAC
1 AGTTTCCCTTGAAACAAAATTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAA
* *
2142504 AGTTTCTCTTGAAACAAAGTCTTGTCTCCCTT
1 AGTTTCCCTTGAAACAAAAT-TTGTCTCCCTT
2142536 AAAATGGTTT
Statistics
Matches: 143, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
64 24 0.17
65 108 0.76
66 11 0.08
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.35
Consensus pattern (65 bp):
AGTTTCCCTTGAAACAAAATTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAA
Found at i:2142611 original size:37 final size:36
Alignment explanation
Indices: 2142569--2142685 Score: 92
Period size: 37 Copynumber: 3.2 Consensus size: 36
2142559 CTTCGTATCG
2142569 CTTGAGACAGTATTCCCTTGAAACAAAATGTATCTCA
1 CTTGAGACAGT-TTCCCTTGAAACAAAATGTATCTCA
** ** * ** * * **
2142606 CTTGAGATGGTTTTTCTTAAAACCTACT-TCTTCTTG
1 CTTGAGACAGTTTCCCTTGAAACAAAATGT-ATCTCA
*
2142642 CTTTAGACAGTTTTCCCTTGAAACAAAATGTATCTCA
1 CTTGAGACAG-TTTCCCTTGAAACAAAATGTATCTCA
2142679 CTTGAGA
1 CTTGAGA
2142686 TGGTTTTTCT
Statistics
Matches: 53, Mismatches: 24, Indels: 6
0.64 0.29 0.07
Matches are distributed among these distances:
35 1 0.02
36 21 0.40
37 30 0.57
38 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.37
Consensus pattern (36 bp):
CTTGAGACAGTTTCCCTTGAAACAAAATGTATCTCA
Found at i:2142616 original size:73 final size:72
Alignment explanation
Indices: 2142497--2142701 Score: 266
Period size: 73 Copynumber: 2.8 Consensus size: 72
2142487 AAACAAGTTT
* * * * * * *
2142497 TTGAGACAGTTTCTCTTGAAACAAAGTCTTGTCTCCCTTAAAATGGTTTTTCTTAAAATCAACTT
1 TTGAGACAGTTTCCCTTGAAACAAAAT-GTATCTCACTTGAGATGGTTTTTCTTAAAATCAACTT
2142562 CGTATCGC
65 CGTATCGC
* *
2142570 TTGAGACAGTATTCCCTTGAAACAAAATGTATCTCACTTGAGATGGTTTTTCTTAAAACCTACTT
1 TTGAGACAGT-TTCCCTTGAAACAAAATGTATCTCACTTGAGATGGTTTTTCTTAAAATCAACTT
* * *
2142635 CTTCTTGC
65 CGTATCGC
*
2142643 TTTAGACAGTTTTCCCTTGAAACAAAATGTATCTCACTTGAGATGGTTTTTCTTAAAAT
1 TTGAGACAG-TTTCCCTTGAAACAAAATGTATCTCACTTGAGATGGTTTTTCTTAAAAT
2142702 ATATGTTGAG
Statistics
Matches: 116, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
73 100 0.86
74 16 0.14
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (72 bp):
TTGAGACAGTTTCCCTTGAAACAAAATGTATCTCACTTGAGATGGTTTTTCTTAAAATCAACTTC
GTATCGC
Found at i:2143226 original size:12 final size:12
Alignment explanation
Indices: 2143209--2143237 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
2143199 TTTTTGTGCT
2143209 TGCTCCTCGGGC
1 TGCTCCTCGGGC
2143221 TGCTCCTCGGGC
1 TGCTCCTCGGGC
2143233 TGCTC
1 TGCTC
2143238 AGGCTCATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.41, G:0.31, T:0.28
Consensus pattern (12 bp):
TGCTCCTCGGGC
Found at i:2144703 original size:20 final size:20
Alignment explanation
Indices: 2144666--2144704 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2144656 AGATTGAGTG
* * *
2144666 GATTTTGATGTTGTTTGCAT
1 GATTTTAATGATGATTGCAT
2144686 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
2144705 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.05, G:0.23, T:0.49
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAT
Found at i:2151183 original size:61 final size:61
Alignment explanation
Indices: 2151069--2151187 Score: 143
Period size: 61 Copynumber: 2.0 Consensus size: 61
2151059 TCGTCTTGCC
* * * *
2151069 TGAGACAGTTTTCCTTTGAAACAAAATGCATCTCCCTCGAGATGGTTTTTCTTAAAACCCT
1 TGAGACAATTTTCCTTTGAAACAAAATGCATCTCACTCGAGATGGCTTCTCTTAAAACCCT
** *
2151130 TGAGACAATTTT-CTTTCGAAACAAAATTTATCTCACTTGAGA-GAGCTTCTCTTAAAAC
1 TGAGACAATTTTCCTTT-GAAACAAAATGCATCTCACTCGAGATG-GCTTCTCTTAAAAC
2151188 AAGTTTCTTA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
60 5 0.10
61 44 0.90
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.34
Consensus pattern (61 bp):
TGAGACAATTTTCCTTTGAAACAAAATGCATCTCACTCGAGATGGCTTCTCTTAAAACCCT
Found at i:2155628 original size:12 final size:12
Alignment explanation
Indices: 2155611--2155693 Score: 58
Period size: 12 Copynumber: 6.6 Consensus size: 12
2155601 ATCGATACCT
2155611 TTTGCATTTACA
1 TTTGCATTTACA
*
2155623 TTTGCATTTTCA
1 TTTGCATTTACA
*
2155635 TCTTTGCATTTTTACG
1 --TTTGCA--TTTACA
* *
2155651 CTTGTATTTACA
1 TTTGCATTTACA
* ***
2155663 TTTTCATTTTTT
1 TTTGCATTTACA
2155675 TTTGCATTTACA
1 TTTGCATTTACA
2155687 TTTGCAT
1 TTTGCAT
2155694 CTTTGCATAA
Statistics
Matches: 51, Mismatches: 16, Indels: 8
0.68 0.21 0.11
Matches are distributed among these distances:
12 37 0.73
14 10 0.20
16 4 0.08
ACGTcount: A:0.18, C:0.16, G:0.08, T:0.58
Consensus pattern (12 bp):
TTTGCATTTACA
Found at i:2159175 original size:36 final size:38
Alignment explanation
Indices: 2159122--2159230 Score: 109
Period size: 36 Copynumber: 2.9 Consensus size: 38
2159112 AATACGGAGG
*
2159122 ATTT-ATCTCACTGGAGATTGTTTTTCTTAAAACATAC
1 ATTTCATCTCACTCGAGATTGTTTTTCTTAAAACATAC
* * *
2159159 -TTT-GTCTCACTTGAGATTGTTTTACTTGAAAGA-ATAC
1 ATTTCATCTCACTCGAGATTGTTTTTCTT-AAA-ACATAC
* * *
2159196 ATTTCATTTGACTCAAGATTGTTTTTCTTAAAACA
1 ATTTCATCTCACTCGAGATTGTTTTTCTTAAAACA
2159231 AGATTTGTCT
Statistics
Matches: 58, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
36 24 0.41
37 8 0.14
38 8 0.14
39 18 0.31
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (38 bp):
ATTTCATCTCACTCGAGATTGTTTTTCTTAAAACATAC
Found at i:2159224 original size:75 final size:77
Alignment explanation
Indices: 2159136--2159384 Score: 244
Period size: 76 Copynumber: 3.3 Consensus size: 77
2159126 ATCTCACTGG
* * * *
2159136 AGATTGTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGA-TTGTTTTACTT-GAAAGAATACAT
1 AGATTGTTTTTCTTAAAACA-AGATTTGTCTCACTTGAGACATGTTTTA-TTCAAAAGAAGACAT
*
2159198 TTCATTTGACT-CA
64 TTCATTTCACTACA
* * *
2159211 AGATTGTTTTTCTTAAAACAAGATTTGTCTCAATTGGGACATGTTTTATTCAAAATAAGACATTT
1 AGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACATGTTTTATTCAAAAGAAGACATTT
2159276 CATTTCACTACA
66 CATTTCACTACA
* * * * * *
2159288 TG-TTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACATTTTTTCCTTGAAGCAGAAG--AT
1 AGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACATGTTTT-ATTCAA-AAGAAGACAT
* *
2159350 TTTATCTCACT-CA
64 TTCATTTCACTACA
*
2159363 AGATTGTTTTTCCTTGAAACAA
1 AGATTGTTTTT-CTTAAAACAA
2159385 AAGGTTTTAT
Statistics
Matches: 145, Mismatches: 21, Indels: 14
0.81 0.12 0.08
Matches are distributed among these distances:
74 1 0.01
75 39 0.27
76 85 0.59
77 16 0.11
78 4 0.03
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (77 bp):
AGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACATGTTTTATTCAAAAGAAGACATTT
CATTTCACTACA
Found at i:2159375 original size:40 final size:40
Alignment explanation
Indices: 2159329--2159476 Score: 192
Period size: 40 Copynumber: 3.7 Consensus size: 40
2159319 CTTGAGACAT
*
2159329 TTTTTCCTTGAAGCAGAAGATTTTATCTCACTCAAGATTG
1 TTTTTCCTTGAAACAGAAGATTTTATCTCACTCAAGATTG
* * * ** *
2159369 TTTTTCCTTGAAACAAAAGGTTTTATCTCGCTTGAGATAG
1 TTTTTCCTTGAAACAGAAGATTTTATCTCACTCAAGATTG
* *
2159409 -TTTCCCTTGAAACAGAAGATTTTATCT-AGCTCAAGATTA
1 TTTTTCCTTGAAACAGAAGATTTTATCTCA-CTCAAGATTG
2159448 TTTTTCCTTGAAACAGAAGATTTTATCTC
1 TTTTTCCTTGAAACAGAAGATTTTATCTC
2159477 GCTTGAGATA
Statistics
Matches: 89, Mismatches: 16, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
39 30 0.34
40 59 0.66
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (40 bp):
TTTTTCCTTGAAACAGAAGATTTTATCTCACTCAAGATTG
Found at i:2159427 original size:79 final size:79
Alignment explanation
Indices: 2159306--2159501 Score: 288
Period size: 79 Copynumber: 2.5 Consensus size: 79
2159296 TTCTTAAAAC
* * * * * *
2159306 AAGA-TTTGTCTCGCTTGAGACATTTTTTCCTTGAAGCAGAAGATTTTATCTCA-CTCAAGATTG
1 AAGATTTTATCTCGCTTGAGATA-GTTTCCCTTGAAACAGAAGATTTTATCT-AGCTCAAGATTA
2159369 TTTTTCCTTGAAACAA
64 TTTTTCCTTGAAACAA
*
2159385 AAGGTTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAGAAGATTTTATCTAGCTCAAGATTATT
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAGAAGATTTTATCTAGCTCAAGATTATT
*
2159450 TTTCCTTGAAACAG
66 TTTCCTTGAAACAA
2159464 AAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACA
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACA
2159502 TAAACTTTGA
Statistics
Matches: 106, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
78 1 0.01
79 89 0.84
80 16 0.15
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (79 bp):
AAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAGAAGATTTTATCTAGCTCAAGATTATT
TTTCCTTGAAACAA
Found at i:2159521 original size:29 final size:29
Alignment explanation
Indices: 2159487--2159595 Score: 87
Period size: 29 Copynumber: 3.5 Consensus size: 29
2159477 GCTTGAGATA
2159487 GTTTCCCTTGAAACATAAACTTTGAAAAC
1 GTTTCCCTTGAAACATAAACTTTGAAAAC
* * *
2159516 GTTTCCCTTTAAACA-AATTTTGTCTCCCTTG-AGAC
1 GTTTCCCTTGAAACATAA-----ACT---TTGAAAAC
*
2159551 AGTTTCTCTTGAAACATAAACTTTGAAAAC
1 -GTTTCCCTTGAAACATAAACTTTGAAAAC
2159581 GTTTCCCTTGAAACA
1 GTTTCCCTTGAAACA
2159596 AATTCTGTCT
Statistics
Matches: 61, Mismatches: 8, Indels: 22
0.67 0.09 0.24
Matches are distributed among these distances:
28 2 0.03
29 31 0.51
30 3 0.05
32 2 0.03
33 2 0.03
35 3 0.05
36 16 0.26
37 2 0.03
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (29 bp):
GTTTCCCTTGAAACATAAACTTTGAAAAC
Found at i:2159571 original size:65 final size:65
Alignment explanation
Indices: 2159453--2159612 Score: 230
Period size: 65 Copynumber: 2.4 Consensus size: 65
2159443 GATTATTTTT
* * *
2159453 CCTTGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACATAAACTTTGAAAACGT
1 CCTTGAAAC--AA-ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACATAAACTTTGAAAACGT
2159518 TTC
63 TTC
* *
2159521 CCTTTAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAACGTTTC
1 CCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACATAAACTTTGAAAACGTTTC
* *
2159586 CCTTGAAACAAATTCTGTCTCTCTTGA
1 CCTTGAAACAAATTTTGTCTCCCTTGA
2159613 AACAAAATTT
Statistics
Matches: 84, Mismatches: 8, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
65 74 0.88
66 2 0.02
68 8 0.10
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (65 bp):
CCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACATAAACTTTGAAAACGTTTC
Found at i:2159633 original size:22 final size:21
Alignment explanation
Indices: 2159585--2159634 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
2159575 GAAAACGTTT
*
2159585 CCCTTGAAACAAATTCTGTCT
1 CCCTTGAAACAAATTCTGTCA
* *
2159606 CTCTTGAAACAAAATTTTGTCA
1 CCCTTGAAAC-AAATTCTGTCA
2159628 CCCTTGA
1 CCCTTGA
2159635 GACAGTTTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.30, C:0.26, G:0.10, T:0.34
Consensus pattern (21 bp):
CCCTTGAAACAAATTCTGTCA
Found at i:2159699 original size:87 final size:86
Alignment explanation
Indices: 2159519--2159699 Score: 299
Period size: 87 Copynumber: 2.1 Consensus size: 86
2159509 TGAAAACGTT
* *
2159519 TCCCTTTAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAACGTT
1 TCCCTTGAAACAAATTTTGTCACCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAACGTT
2159584 TCCCTTGAAACAAATTCTGTC
66 TCCCTTGAAACAAATTCTGTC
* *
2159605 TCTCTTGAAACAAAATTTTGTCACCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAATGT
1 TCCCTTGAAAC-AAATTTTGTCACCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAACGT
* *
2159670 TTCCCTTGAAACAAATTTTTTC
65 TTCCCTTGAAACAAATTCTGTC
2159692 TCCCTTGA
1 TCCCTTGA
2159700 GACAGTTTCT
Statistics
Matches: 87, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
86 9 0.10
87 78 0.90
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.37
Consensus pattern (86 bp):
TCCCTTGAAACAAATTTTGTCACCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAACGTT
TCCCTTGAAACAAATTCTGTC
Found at i:2159757 original size:152 final size:154
Alignment explanation
Indices: 2159454--2159758 Score: 438
Period size: 152 Copynumber: 2.0 Consensus size: 154
2159444 ATTATTTTTC
* * *
2159454 CTTGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACATAAACTTTGAAAACGTT
1 CTTGAAACAGAAGATTTTATCACCCTTGAGACAGTTTCCCTTGAAACATAAACTTTGAAAACGTT
*
2159519 TCCCTTTAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAACGTT
66 TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAACGTT
*
2159584 TCCCTTGAAACAAATTCTGTCTCT
131 TCCCTTGAAACAAAGTCTGTCTCT
* * *
2159608 CTTGAAACA-AA-ATTTTGTCACCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAATGTT
1 CTTGAAACAGAAGATTTTATCACCCTTGAGACAGTTTCCCTTGAAACATAAACTTTGAAAACGTT
* *** *
2159671 TCCCTTGAAACAAATTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACA-AGTTTTTG-AGACAGT
66 TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAAC-GT
*
2159734 TTCTCTTGAAACAAAGTCTTGTCTC
130 TTCCCTTGAAACAAAGTC-TGTCTC
2159759 CCTTAAAATG
Statistics
Matches: 135, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
150 3 0.02
151 23 0.17
152 98 0.73
153 2 0.01
154 9 0.07
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.36
Consensus pattern (154 bp):
CTTGAAACAGAAGATTTTATCACCCTTGAGACAGTTTCCCTTGAAACATAAACTTTGAAAACGTT
TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAACGTT
TCCCTTGAAACAAAGTCTGTCTCT
Found at i:2159759 original size:65 final size:65
Alignment explanation
Indices: 2159605--2159762 Score: 203
Period size: 65 Copynumber: 2.4 Consensus size: 65
2159595 AAATTCTGTC
*
2159605 TCTCTTGAAACAAAATTTTGTCACCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAATGT
1 TCTCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAATGT
2159670 T
65 T
* * *** *
2159671 TCCCTTGAAACAAATTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACA-AGTTTTTGAGACA-GT
1 TCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGA-AAATGT
2159734 T
65 T
*
2159735 TCTCTTGAAACAAAGTCTTGTCTCCCTT
1 TCTCTTGAAACAAA-TTTTGTCTCCCTT
2159763 AAAATGGTTT
Statistics
Matches: 80, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 22 0.28
65 48 0.60
66 10 0.12
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (65 bp):
TCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAATGTT
Found at i:2159809 original size:36 final size:35
Alignment explanation
Indices: 2159769--2159955 Score: 108
Period size: 36 Copynumber: 5.1 Consensus size: 35
2159759 CCTTAAAATG
2159769 GTTTTTCTTAAAATCAACTTCGTATCGCTTGAGACA
1 GTTTTTCTTAAAA-CAACTTCGTATCGCTTGAGACA
* ** * **
2159805 GTTTTTCCTTGAAACAAAAT-GTATCACACTTGAGATG
1 GTTTTT-CTTAAAACAACTTCGTAT--CGCTTGAGACA
* * * * *
2159842 GTTTTTCTTAAAACCTACTTCTTTTTGCTTAAGACA
1 GTTTTTCTTAAAA-CAACTTCGTATCGCTTGAGACA
* ** * *
2159878 GTTTTCCCTTAAAACAAAAT-GTATCTCACTTGAGATA
1 GTTTT-TCTTAAAACAACTTCGTA--TCGCTTGAGACA
* * *
2159915 GTTTTTCTTAAAATCTACTTCGTCTTGCTTGAGACA
1 GTTTTTCTTAAAA-CAACTTCGTATCGCTTGAGACA
2159951 GTTTT
1 GTTTT
2159956 CCTTTGAAAC
Statistics
Matches: 106, Mismatches: 35, Indels: 20
0.66 0.22 0.12
Matches are distributed among these distances:
35 5 0.05
36 51 0.48
37 46 0.43
38 4 0.04
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (35 bp):
GTTTTTCTTAAAACAACTTCGTATCGCTTGAGACA
Found at i:2159843 original size:73 final size:73
Alignment explanation
Indices: 2159724--2160000 Score: 351
Period size: 73 Copynumber: 3.8 Consensus size: 73
2159714 AAACAAGTTT
* * * * * * * *
2159724 TTGAGACAGTTTCT-CTTGAAACAAAGTCTTGTCTCCCTTAAAATGGTTTTTCTTAAAATCAACT
1 TTGAGACAGTTTTTCCTTGAAACAAAAT-GTATCTCACTTGAGATGGTTTTTCTTAAAATCTACT
*
2159788 TCGTATCGC
65 TCGTATTGC
* *
2159797 TTGAGACAGTTTTTCCTTGAAACAAAATGTATCACACTTGAGATGGTTTTTCTTAAAACCTACTT
1 TTGAGACAGTTTTTCCTTGAAACAAAATGTATCTCACTTGAGATGGTTTTTCTTAAAATCTACTT
* *
2159862 CTTTTTGC
66 CGTATTGC
* * * *
2159870 TTAAGACAGTTTTCCCTTAAAACAAAATGTATCTCACTTGAGATAGTTTTTCTTAAAATCTACTT
1 TTGAGACAGTTTTTCCTTGAAACAAAATGTATCTCACTTGAGATGGTTTTTCTTAAAATCTACTT
*
2159935 CGTCTTGC
66 CGTATTGC
*
2159943 TTGAGACAG-TTTTCCTTTGAAACAAAATGAATCTCACTTGAGATGGTTTTTCTTAAAA
1 TTGAGACAGTTTTTCC-TTGAAACAAAATGTATCTCACTTGAGATGGTTTTTCTTAAAA
2160001 CCCTTGAGAC
Statistics
Matches: 176, Mismatches: 26, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
72 5 0.03
73 159 0.90
74 12 0.07
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.39
Consensus pattern (73 bp):
TTGAGACAGTTTTTCCTTGAAACAAAATGTATCTCACTTGAGATGGTTTTTCTTAAAATCTACTT
CGTATTGC
Found at i:2159918 original size:37 final size:36
Alignment explanation
Indices: 2159796--2160001 Score: 112
Period size: 36 Copynumber: 5.6 Consensus size: 36
2159786 CTTCGTATCG
* *
2159796 CTTGAGACAGTTTTTCCTTGAAACAAAATGTATCACA
1 CTTGAGACAG-TTTTCCTTAAAACAAAATGTATCTCA
** * ** * * * **
2159833 CTTGAGATGGTTTTTCTTAAAACCTACT-TCTTTTTG
1 CTTGAGACAGTTTTCCTTAAAACAAAATGT-ATCTCA
*
2159869 CTTAAGACAGTTTTCCCTTAAAACAAAATGTATCTCA
1 CTTGAGACAGTTTT-CCTTAAAACAAAATGTATCTCA
* * * * * **
2159906 CTTGAGATAGTTTTTCTTAAAATC-TACT-TCGTCTTG
1 CTTGAGACAGTTTTCCTTAAAA-CAAAATGT-ATCTCA
* *
2159942 CTTGAGACAGTTTTCCTTTGAAACAAAATGAATCTCA
1 CTTGAGACAGTTTTCC-TTAAAACAAAATGTATCTCA
** *
2159979 CTTGAGATGGTTTTTCTTAAAAC
1 CTTGAGACAGTTTTCCTTAAAAC
2160002 CCTTGAGACA
Statistics
Matches: 117, Mismatches: 44, Indels: 17
0.66 0.25 0.10
Matches are distributed among these distances:
35 2 0.02
36 58 0.50
37 56 0.48
38 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (36 bp):
CTTGAGACAGTTTTCCTTAAAACAAAATGTATCTCA
Found at i:2160058 original size:61 final size:61
Alignment explanation
Indices: 2159942--2160062 Score: 147
Period size: 61 Copynumber: 2.0 Consensus size: 61
2159932 CTTCGTCTTG
* * * * *
2159942 CTTGAGACAGTTTTCCTTTGAAACAAAATGAATCTCACTTGAGATGGTTTTTCTTAAAACC
1 CTTGAGACAATTTTCCTTTGAAAAAAAATGAATCTCACTCGAGATGGCTTCTCTTAAAACC
**
2160003 CTTGAGACAATTTT-CTTTCGAAAAAAAATTTATCTCACTCGAGA-GAGCTTCTCTTAAAAC
1 CTTGAGACAATTTTCCTTT-GAAAAAAAATGAATCTCACTCGAGATG-GCTTCTCTTAAAAC
2160063 AAGTTTCTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
60 5 0.10
61 46 0.90
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (61 bp):
CTTGAGACAATTTTCCTTTGAAAAAAAATGAATCTCACTCGAGATGGCTTCTCTTAAAACC
Found at i:2161696 original size:30 final size:29
Alignment explanation
Indices: 2161594--2161697 Score: 86
Period size: 30 Copynumber: 3.5 Consensus size: 29
2161584 TGTTTTTGCC
* * *
2161594 ATTTTAGCCTTTTAAATTTCAGTTTGTAAT
1 ATTTTAGTCTTTTAAATTTCTGTTT-TATT
* * *
2161624 ATTTGA-TCTTTAAAATTTCTACTTTTATT
1 ATTTTAGTCTTTTAAATTTCT-GTTTTATT
* *
2161653 ATTCTAG-CTTTTTAAATTTCTGTTTATGTT
1 ATTTTAGTC-TTTTAAATTTCTGTTT-TATT
2161683 ATTTTAGTCTTTTAA
1 ATTTTAGTCTTTTAA
2161698 TTGTCCATTT
Statistics
Matches: 57, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
29 22 0.39
30 34 0.60
31 1 0.02
ACGTcount: A:0.25, C:0.10, G:0.08, T:0.58
Consensus pattern (29 bp):
ATTTTAGTCTTTTAAATTTCTGTTTTATT
Found at i:2162073 original size:17 final size:17
Alignment explanation
Indices: 2162046--2162093 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
2162036 ACAGACAAAT
2162046 TTTTGTCTTAAAAAATAA
1 TTTT-TCTTAAAAAATAA
* *
2162064 TTTTTCTTAAAAATTGA
1 TTTTTCTTAAAAAATAA
2162081 TTTTT-TTAAAAAA
1 TTTTTCTTAAAAAA
2162094 CGTTTTTAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 7 0.26
17 16 0.59
18 4 0.15
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (17 bp):
TTTTTCTTAAAAAATAA
Found at i:2164737 original size:2 final size:2
Alignment explanation
Indices: 2164732--2164756 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2164722 ATGTTGTATG
2164732 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2164757 AGAACATAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2165043 original size:22 final size:21
Alignment explanation
Indices: 2164915--2165051 Score: 125
Period size: 21 Copynumber: 6.5 Consensus size: 21
2164905 GGTTCTACGC
*
2164915 GGTCATTCGGGACATATATGT
1 GGTCCTTCGGGACATATATGT
* *
2164936 GATCCTT-GGGAACTTATATGT
1 GGTCCTTCGGG-ACATATATGT
* * * *
2164957 GATCCTTCGGGATATATGTTT
1 GGTCCTTCGGGACATATATGT
* * * *
2164978 GGACCTTTGGAACATACATGT
1 GGTCCTTCGGGACATATATGT
2164999 GGTCCTTCGGGACATATATGT
1 GGTCCTTCGGGACATATATGT
*
2165020 GGTCCTTCGGGACATTTTATGT
1 GGTCCTTCGGGACA-TATATGT
2165042 GG-CACTTCGG
1 GGTC-CTTCGG
2165052 TGCATATTCT
Statistics
Matches: 92, Mismatches: 20, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
20 3 0.03
21 72 0.78
22 17 0.18
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (21 bp):
GGTCCTTCGGGACATATATGT
Found at i:2165088 original size:24 final size:24
Alignment explanation
Indices: 2165042--2165088 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2165032 CATTTTATGT
*
2165042 GGCACTTCGGTGCATATTCTACGC
1 GGCACTTCGGTGCATATTATACGC
* *
2165066 GGCACTTTGGTGCATTTTATACG
1 GGCACTTCGGTGCATATTATACG
2165089 AGCTGTGGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.17, C:0.23, G:0.26, T:0.34
Consensus pattern (24 bp):
GGCACTTCGGTGCATATTATACGC
Found at i:2166437 original size:2 final size:2
Alignment explanation
Indices: 2166430--2166486 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
2166420 AATTATATTC
2166430 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
2166472 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
2166487 GCTATAATGA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2172957 original size:13 final size:13
Alignment explanation
Indices: 2172939--2172979 Score: 82
Period size: 13 Copynumber: 3.2 Consensus size: 13
2172929 TTAGTTGGAT
2172939 AAAGATTCTGAGC
1 AAAGATTCTGAGC
2172952 AAAGATTCTGAGC
1 AAAGATTCTGAGC
2172965 AAAGATTCTGAGC
1 AAAGATTCTGAGC
2172978 AA
1 AA
2172980 TATATATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.22
Consensus pattern (13 bp):
AAAGATTCTGAGC
Found at i:2176616 original size:55 final size:55
Alignment explanation
Indices: 2176532--2176641 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
2176522 AAGAAGACAG
2176532 AAGATGCACCAATAAAATGCTAGAGAATTGAGGGGTACTAAGAAGCCTAGTTGGT
1 AAGATGCACCAATAAAATGCTAGAGAATTGAGGGGTACTAAGAAGCCTAGTTGGT
2176587 AAGATGCACCAATAAAATGCTAGAGAATTGAGGGGTACTAAGAAGCCTAGTTGGT
1 AAGATGCACCAATAAAATGCTAGAGAATTGAGGGGTACTAAGAAGCCTAGTTGGT
2176642 TACTTAATAG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.38, C:0.13, G:0.27, T:0.22
Consensus pattern (55 bp):
AAGATGCACCAATAAAATGCTAGAGAATTGAGGGGTACTAAGAAGCCTAGTTGGT
Found at i:2179934 original size:30 final size:29
Alignment explanation
Indices: 2179878--2179935 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
2179868 GTTTTATATG
* **
2179878 AAAATGTTCTATTAAAAATATGCTATGTA
1 AAAATGTTCTAGTAAAAATACCCTATGTA
*
2179907 AAAATGTTCTACGTGAAAATACCCTATGT
1 AAAATGTTCTA-GTAAAAATACCCTATGT
2179936 GAATGTGCTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 11 0.46
30 13 0.54
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (29 bp):
AAAATGTTCTAGTAAAAATACCCTATGTA
Done.