Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008025.1 Hibiscus syriacus cultivar Beakdansim tig00110500_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: 2744542
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 12
Found at i:1881846 original size:23 final size:23
Alignment explanation
Indices: 1881814--1881875 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
1881804 ATCTTATATT
1881814 GCACTACGGTGCATTTCTACACG
1 GCACTACGGTGCATTTCTACACG
* * **
1881837 GCACTTCGGTGCAATTCTACGTG
1 GCACTACGGTGCATTTCTACACG
* *
1881860 GCACTCCAGTGCATTT
1 GCACTACGGTGCATTT
1881876 ATACGAGCTG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.19, C:0.29, G:0.23, T:0.29
Consensus pattern (23 bp):
GCACTACGGTGCATTTCTACACG
Found at i:1882178 original size:6 final size:6
Alignment explanation
Indices: 1882163--1882194 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
1882153 TATAATTTGG
1882163 TATG-A TATGTA TATGTA TATGTA TATGTA TAT
1 TATGTA TATGTA TATGTA TATGTA TATGTA TAT
1882195 ATTTATGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (6 bp):
TATGTA
Found at i:1882201 original size:18 final size:18
Alignment explanation
Indices: 1882163--1882202 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1882153 TATAATTTGG
*
1882163 TATG-ATATGTATATGTA
1 TATGTATATGTATATATA
*
1882180 TATGTATATGTATATATT
1 TATGTATATGTATATATA
1882198 TATGT
1 TATGT
1882203 TTTGCAGGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.53
Consensus pattern (18 bp):
TATGTATATGTATATATA
Found at i:1885131 original size:22 final size:21
Alignment explanation
Indices: 1885106--1885148 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1885096 ATATTCTTTA
1885106 TCATACTTT-ACATTATTTTATT
1 TCAT-CTTTGACATT-TTTTATT
*
1885128 TCATTTTTGACATTTTTTATT
1 TCATCTTTGACATTTTTTATT
1885149 ATTTTATTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.23, C:0.12, G:0.02, T:0.63
Consensus pattern (21 bp):
TCATCTTTGACATTTTTTATT
Found at i:1886663 original size:20 final size:20
Alignment explanation
Indices: 1886639--1886676 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1886629 AAAGACTTAA
1886639 AAAAAATA-AGAAAAAGAAG
1 AAAAAATATAGAAAAAGAAG
1886658 AAAAAATATAGAAAAAGAA
1 AAAAAATATAGAAAAAGAA
1886677 AAAGGAAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (20 bp):
AAAAAATATAGAAAAAGAAG
Found at i:1886713 original size:5 final size:5
Alignment explanation
Indices: 1886670--1886755 Score: 52
Period size: 5 Copynumber: 16.8 Consensus size: 5
1886660 AAAATATAGA
* * * * *
1886670 AAAAG AAAAAG GAAAG GAAAG GAAAG GAAAG AAAA- AAAAG AAAAA AAAAG
1 AAAAG -AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
*
1886720 AGAGAAG AGAAAG -AAAG -AAAG AAATAA AAAAG AAAA
1 A-A-AAG A-AAAG AAAAG AAAAG AAA-AG AAAAG AAAA
1886756 TTGAAAAGAG
Statistics
Matches: 69, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
4 12 0.17
5 38 0.55
6 13 0.19
7 6 0.09
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.01
Consensus pattern (5 bp):
AAAAG
Found at i:1886734 original size:4 final size:4
Alignment explanation
Indices: 1886671--1886754 Score: 59
Period size: 4 Copynumber: 20.8 Consensus size: 4
1886661 AAATATAGAA
* *
1886671 AAAG AAA- AAGG AAAGG AAAGG AAAGG AAAG AAAAA AAAG AAA- AAA-
1 AAAG AAAG AAAG AAA-G AAA-G AAA-G AAAG -AAAG AAAG AAAG AAAG
* *
1886716 AAAG AGAG AAGAG AAAG AAAG AAAG AAAT AAA- AAAG AAA
1 AAAG AAAG AA-AG AAAG AAAG AAAG AAAG AAAG AAAG AAA
1886755 ATTGAAAAGA
Statistics
Matches: 67, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
3 11 0.16
4 35 0.52
5 21 0.31
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.01
Consensus pattern (4 bp):
AAAG
Found at i:1886736 original size:41 final size:40
Alignment explanation
Indices: 1886651--1886755 Score: 110
Period size: 41 Copynumber: 2.5 Consensus size: 40
1886641 AAAATAAGAA
1886651 AAAG-AAGAAAAAATATAGAAAAAGAAAAAGGAAAGGAAAGG
1 AAAGAAAGAAAAAA-A-AGAAAAAGAAAAAGGAAAGGAAAGG
1886692 AAAGGAAAGAAAAAAAAG-AAAA-AAAAAGAGAGAAGAGAAA-G
1 AAA-GAAAGAAAAAAAAGAAAAAGAAAAAG-GA-AAG-GAAAGG
1886733 AAAGAAAGAAATAAAAAAGAAAA
1 AAAGAAAG-AA-AAAAAAGAAAA
1886756 TTGAAAAGAG
Statistics
Matches: 56, Mismatches: 0, Indels: 14
0.80 0.00 0.20
Matches are distributed among these distances:
39 6 0.11
40 11 0.20
41 14 0.25
42 13 0.23
43 12 0.21
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (40 bp):
AAAGAAAGAAAAAAAAGAAAAAGAAAAAGGAAAGGAAAGG
Found at i:1889815 original size:17 final size:17
Alignment explanation
Indices: 1889783--1889816 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1889773 AGCATGTTTA
* *
1889783 AAAATAAAACTTAAAAT
1 AAAATAAAAATGAAAAT
1889800 AAAATAAAAATGAAAAT
1 AAAATAAAAATGAAAAT
1889817 TTGAAAAGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (17 bp):
AAAATAAAAATGAAAAT
Found at i:1890981 original size:9 final size:10
Alignment explanation
Indices: 1890949--1890975 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1890939 AACAATGTAC
1890949 TTTTTTTGAA
1 TTTTTTTGAA
1890959 TTTTTTTGAA
1 TTTTTTTGAA
1890969 TTTTTTT
1 TTTTTTT
1890976 CATTTTCCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:1891745 original size:12 final size:12
Alignment explanation
Indices: 1891728--1891752 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1891718 TGAAGGTGGC
1891728 GCAAGGCTAAAA
1 GCAAGGCTAAAA
1891740 GCAAGGCTAAAA
1 GCAAGGCTAAAA
1891752 G
1 G
1891753 AAAAAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.16, G:0.28, T:0.08
Consensus pattern (12 bp):
GCAAGGCTAAAA
Found at i:1900140 original size:23 final size:23
Alignment explanation
Indices: 1900114--1900164 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
1900104 ACTACATTTG
1900114 TAACCACTAACTTTTCTAACTA-C
1 TAACCACTAACTTTTCTAAC-AGC
*
1900137 TAACCGCTAACTTTTCTAACAGC
1 TAACCACTAACTTTTCTAACAGC
1900160 TAACC
1 TAACC
1900165 TTTCTAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 1 0.04
23 25 0.96
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.31
Consensus pattern (23 bp):
TAACCACTAACTTTTCTAACAGC
Found at i:1900155 original size:16 final size:16
Alignment explanation
Indices: 1900136--1900178 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
1900126 TTTCTAACTA
* *
1900136 CTAACCGCTAACTTTT
1 CTAACAGCTAACCTTT
1900152 CTAACAGCTAACCTTT
1 CTAACAGCTAACCTTT
*
1900168 CTAATAGCTAA
1 CTAACAGCTAA
1900179 TTACTAAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.33, C:0.28, G:0.07, T:0.33
Consensus pattern (16 bp):
CTAACAGCTAACCTTT
Found at i:1901039 original size:10 final size:10
Alignment explanation
Indices: 1901024--1901053 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1901014 TGGTGAATCC
1901024 AATTCAAAAT
1 AATTCAAAAT
*
1901034 AATTCAAACT
1 AATTCAAAAT
1901044 AATTCAAAAT
1 AATTCAAAAT
1901054 CCCAATTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (10 bp):
AATTCAAAAT
Found at i:1905680 original size:44 final size:44
Alignment explanation
Indices: 1905630--1905772 Score: 214
Period size: 44 Copynumber: 3.2 Consensus size: 44
1905620 TCACAATTTG
* *
1905630 CTCGATTCCATTGCATATGGAGTTAGATCAACATCAACATTTCA
1 CTCGATTCCATCGCATATGGAGTTGGATCAACATCAACATTTCA
* * * **
1905674 CTCGATTCCATCGCATAAGGAGTTGGAGCAACATCAATATTTTG
1 CTCGATTCCATCGCATATGGAGTTGGATCAACATCAACATTTCA
*
1905718 CTCGATTCCATCACATATGGAGTTGGATCAACATCAACATTTCA
1 CTCGATTCCATCGCATATGGAGTTGGATCAACATCAACATTTCA
1905762 CTCGATTCCAT
1 CTCGATTCCAT
1905773 AACAAAAGGA
Statistics
Matches: 86, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 86 1.00
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (44 bp):
CTCGATTCCATCGCATATGGAGTTGGATCAACATCAACATTTCA
Found at i:1905793 original size:44 final size:44
Alignment explanation
Indices: 1905630--1905793 Score: 179
Period size: 44 Copynumber: 3.7 Consensus size: 44
1905620 TCACAATTTG
** *
1905630 CTCGATTCCATTGCATATGGAGTTA-GATCAACATCAACATTTCA
1 CTCGATTCCATCACATAAGGAG-TAGGATCAACATCAACATTTCA
* * * * **
1905674 CTCGATTCCATCGCATAAGGAGTTGGAGCAACATCAATATTTTG
1 CTCGATTCCATCACATAAGGAGTAGGATCAACATCAACATTTCA
* *
1905718 CTCGATTCCATCACATATGGAGTTGGATCAACATCAACATTTCA
1 CTCGATTCCATCACATAAGGAGTAGGATCAACATCAACATTTCA
* *
1905762 CTCGATTCCATAACAAAAGGAGTCAGG-TCAAC
1 CTCGATTCCATCACATAAGGAGT-AGGATCAAC
1905794 TTTACCTTTC
Statistics
Matches: 101, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
43 1 0.01
44 98 0.97
45 2 0.02
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.28
Consensus pattern (44 bp):
CTCGATTCCATCACATAAGGAGTAGGATCAACATCAACATTTCA
Found at i:1905954 original size:44 final size:44
Alignment explanation
Indices: 1905906--1906004 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 44
1905896 CTCATCTATG
* * * * *
1905906 GCATAAGGAGTCAGATCAGCTTTACCTTTCTTGTCCCATCCGTC
1 GCATAAGGAGTCAGATCAGCCTCACATTTCTTATCCCATCCATC
* * *
1905950 GCATATGGAGTCAGATCATCCTCACATTTCTTATCTCATCCATC
1 GCATAAGGAGTCAGATCAGCCTCACATTTCTTATCCCATCCATC
1905994 GCATAAGGAGT
1 GCATAAGGAGT
1906005 TGGATTAGTG
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.24, C:0.27, G:0.17, T:0.31
Consensus pattern (44 bp):
GCATAAGGAGTCAGATCAGCCTCACATTTCTTATCCCATCCATC
Found at i:1906043 original size:132 final size:127
Alignment explanation
Indices: 1905767--1906048 Score: 312
Period size: 132 Copynumber: 2.1 Consensus size: 127
1905757 TTTCACTCGA
* * * ** **
1905767 TTCCATAACAAAAGGAGTCAGGTCAACTTTACCTTTCTTGGCCCATTTGTCGCATATGGAGTTGG
1 TTCCATCACATAAGGAGTCAGATCAACTTTACCTTTCTTGGCCCATCCGTCGCATATGGAGTCAG
* * * * *
1905832 ATCAGCCTCATATTTTTTAGCTCGTCCATCGCATATGGAGTTAGATCATCACCATTTTCCCT
66 ATCAGCCTCACATTTCTTAGCTCATCCATCGCATAAGGAGTTAGATCATCACCATTTTCCAT
* *
1905894 TTCTCATCTATGGCATAAGGAGTCAGATCAGCTTTACCTTTCTTGTCCCATCCGTCGCATATGGA
1 TTC-CATC-A---CATAAGGAGTCAGATCAACTTTACCTTTCTTGGCCCATCCGTCGCATATGGA
* * * *
1905959 GTCAGATCATCCTCACATTTCTTATCTCATCCATCGCATAAGGAGTTGGATTAGTGTCACCATTT
61 GTCAGATCAGCCTCACATTTCTTAGCTCATCCATCGCATAAGGAGTTAGATCA---TCACCATTT
1906024 TGCTCAT
123 T-C-CAT
1906031 TTCCATCACATAAGGAGT
1 TTCCATCACATAAGGAGT
1906049 TGGAACATCA
Statistics
Matches: 127, Mismatches: 18, Indels: 15
0.79 0.11 0.09
Matches are distributed among these distances:
127 3 0.02
128 3 0.02
129 1 0.01
132 99 0.78
135 11 0.09
136 5 0.04
137 5 0.04
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (127 bp):
TTCCATCACATAAGGAGTCAGATCAACTTTACCTTTCTTGGCCCATCCGTCGCATATGGAGTCAG
ATCAGCCTCACATTTCTTAGCTCATCCATCGCATAAGGAGTTAGATCATCACCATTTTCCAT
Found at i:1911233 original size:64 final size:64
Alignment explanation
Indices: 1911132--1911255 Score: 221
Period size: 64 Copynumber: 1.9 Consensus size: 64
1911122 GGGCTGTAAA
* *
1911132 CGAGTTGAGTTCGATTCGAAAATTTTAAAATAAAGTTTGACCCAGTCCAACTCAAATCAATTTT
1 CGAGTTGAGTTCGATTCAAAAATTTTAAAATAAAGTTTGACCCAGCCCAACTCAAATCAATTTT
*
1911196 CGAGTTGAGTTCGATTCAAAAATTTTAAAATGAAGTTTGACCCAGCCCAACTCAAATCAA
1 CGAGTTGAGTTCGATTCAAAAATTTTAAAATAAAGTTTGACCCAGCCCAACTCAAATCAA
1911256 AATCATAAAT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.30
Consensus pattern (64 bp):
CGAGTTGAGTTCGATTCAAAAATTTTAAAATAAAGTTTGACCCAGCCCAACTCAAATCAATTTT
Found at i:1917713 original size:29 final size:29
Alignment explanation
Indices: 1917671--1917756 Score: 154
Period size: 29 Copynumber: 3.0 Consensus size: 29
1917661 AAGCAAGACT
1917671 AAGCACCAACAGGTACAGACATCCATATA
1 AAGCACCAACAGGTACAGACATCCATATA
*
1917700 AAGCACCAACAGGTACAAACATCCATATA
1 AAGCACCAACAGGTACAGACATCCATATA
*
1917729 AAGCCCCAACAGGTACAGACATCCATAT
1 AAGCACCAACAGGTACAGACATCCATAT
1917757 GCATAAGAGT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.44, C:0.29, G:0.13, T:0.14
Consensus pattern (29 bp):
AAGCACCAACAGGTACAGACATCCATATA
Found at i:1921445 original size:21 final size:20
Alignment explanation
Indices: 1921378--1921454 Score: 70
Period size: 21 Copynumber: 3.9 Consensus size: 20
1921368 GGCATGTGAA
*
1921378 ATCTGTGTCCCGAAGGACCT
1 ATCTATGTCCCGAAGGACCT
**
1921398 ATC-AT-T-CCGAAGGATGT
1 ATCTATGTCCCGAAGGACCT
*
1921415 CATCTGTGTCCCGAAGGACCT
1 -ATCTATGTCCCGAAGGACCT
*
1921436 ATCATATGTCTCGAAGGAC
1 ATC-TATGTCCCGAAGGAC
1921455 ATATGTAACC
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
17 9 0.20
18 4 0.09
19 2 0.05
20 7 0.16
21 22 0.50
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (20 bp):
ATCTATGTCCCGAAGGACCT
Found at i:1923595 original size:30 final size:29
Alignment explanation
Indices: 1923561--1923635 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 29
1923551 AAATTACCAT
* * *
1923561 TTTGGTCCCTAAACTTTTCAAAGT-TTATAC
1 TTTGGTACC-AAACTTTT-AAAATCTTATAA
1923591 TTTGGTTACCAAACTTTTAAAATCTTATAA
1 TTTGG-TACCAAACTTTTAAAATCTTATAA
1923621 TTTGGTTACCAAACT
1 TTTGG-TACCAAACT
1923636 AAATCAATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
29 4 0.10
30 33 0.82
31 3 0.08
ACGTcount: A:0.31, C:0.17, G:0.09, T:0.43
Consensus pattern (29 bp):
TTTGGTACCAAACTTTTAAAATCTTATAA
Found at i:1924473 original size:11 final size:11
Alignment explanation
Indices: 1924457--1924531 Score: 55
Period size: 11 Copynumber: 6.7 Consensus size: 11
1924447 GCATCTCCCA
1924457 TTTTTTTTTC-
1 TTTTTTTTTCT
*
1924467 -TTTTTTTTCA
1 TTTTTTTTTCT
*
1924477 TTTTGTTTTCT
1 TTTTTTTTTCT
* *
1924488 GTTTTTCTTCT
1 TTTTTTTTTCT
* *
1924499 TTTTTTCTTAT
1 TTTTTTTTTCT
1924510 TTTTCTTCTTTCT
1 TTTT-TT-TTTCT
1924523 TCTTTTTTT
1 T-TTTTTTT
1924532 AGCTCTTATG
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
9 9 0.18
11 29 0.57
12 4 0.08
13 6 0.12
14 3 0.06
ACGTcount: A:0.03, C:0.13, G:0.03, T:0.81
Consensus pattern (11 bp):
TTTTTTTTTCT
Found at i:1924478 original size:20 final size:19
Alignment explanation
Indices: 1924457--1924531 Score: 80
Period size: 19 Copynumber: 3.9 Consensus size: 19
1924447 GCATCTCCCA
1924457 TTTTTTTTTCTTTTTTTTC
1 TTTTTTTTTCTTTTTTTTC
* *
1924476 ATTTTGTTTTC-TGTTTTTC
1 -TTTTTTTTTCTTTTTTTTC
*
1924495 TTCTTTTTTTCTTATTTTTC
1 TT-TTTTTTTCTTTTTTTTC
* *
1924515 TTCTTTCTTCTTTTTTT
1 TTTTTTTTTCTTTTTTT
1924532 AGCTCTTATG
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
18 2 0.04
19 26 0.57
20 18 0.39
ACGTcount: A:0.03, C:0.13, G:0.03, T:0.81
Consensus pattern (19 bp):
TTTTTTTTTCTTTTTTTTC
Found at i:1927504 original size:38 final size:38
Alignment explanation
Indices: 1927391--1927506 Score: 164
Period size: 38 Copynumber: 3.1 Consensus size: 38
1927381 GGCATGTGAA
*
1927391 ATCTGTGTCCCGAATGACCTATCATCCCGAAGGACT-TA
1 ATCTGTGTCCCGAATGACCTATCATCCCGAAGGA-TGTC
* *
1927429 AT-TCGTGTCCCGAATGACCTATCGTCTCGAAGGATGTC
1 ATCT-GTGTCCCGAATGACCTATCATCCCGAAGGATGTC
*
1927467 ATCTGTGTCCCGAAGGACCTATCATCCCGAAGGATGTC
1 ATCTGTGTCCCGAATGACCTATCATCCCGAAGGATGTC
1927505 AT
1 AT
1927507 ATGTAACCCT
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
37 2 0.03
38 66 0.96
39 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.27
Consensus pattern (38 bp):
ATCTGTGTCCCGAATGACCTATCATCCCGAAGGATGTC
Found at i:1927689 original size:33 final size:33
Alignment explanation
Indices: 1927642--1927706 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
1927632 ATCATGTAGC
1927642 TTGTATAACATTCTTGTATGATCTCATAGATCA
1 TTGTATAACATTCTTGTATGATCTCATAGATCA
*
1927675 TTGTGTAACATTCTTGTATGATCTCATAGATC
1 TTGTATAACATTCTTGTATGATCTCATAGATC
1927707 CCTTTTCATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (33 bp):
TTGTATAACATTCTTGTATGATCTCATAGATCA
Found at i:1928845 original size:31 final size:28
Alignment explanation
Indices: 1928804--1928867 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 28
1928794 ATTCACAACT
* *
1928804 TTTTCCAAAATTACCAAATTGGTCCCCTAA
1 TTTTCAAAAATTA-CAAAATGGTCCCC-AA
1928834 CTTTTCAAAAATTACAAAATGGTCCCCAA
1 -TTTTCAAAAATTACAAAATGGTCCCCAA
1928863 TTTTC
1 TTTTC
1928868 TAACTCTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 5 0.16
29 2 0.06
30 12 0.39
31 12 0.39
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.34
Consensus pattern (28 bp):
TTTTCAAAAATTACAAAATGGTCCCCAA
Found at i:1929339 original size:175 final size:175
Alignment explanation
Indices: 1929048--1929400 Score: 688
Period size: 175 Copynumber: 2.0 Consensus size: 175
1929038 TTTAACATCT
*
1929048 CCACAATAAAATCCCTAATTAACTCTCATCATAACAAAAAGTTCTACAATTTCCTCTTTTGGCCG
1 CCACAATAAAATCCCTAATCAACTCTCATCATAACAAAAAGTTCTACAATTTCCTCTTTTGGCCG
1929113 AATTTAAAGAATAATTTCTAGAAAGATTGAACATGTTTTAACCATAAATCAAGCTTGAAAATGAA
66 AATTTAAAGAATAATTTCTAGAAAGATTGAACATGTTTTAACCATAAATCAAGCTTGAAAATGAA
1929178 TCTACAACCTCTAAATCATCAAGATTCATCATCAATTTCATGAAC
131 TCTACAACCTCTAAATCATCAAGATTCATCATCAATTTCATGAAC
*
1929223 CCACAATAAAATCCCTAATCAACTCTCATCATAACAAAAAGTTCTACAATTTCCTCTTTTGGTCG
1 CCACAATAAAATCCCTAATCAACTCTCATCATAACAAAAAGTTCTACAATTTCCTCTTTTGGCCG
1929288 AATTTAAAGAATAATTTCTAGAAAGATTGAACATGTTTTAACCATAAATCAAGCTTGAAAATGAA
66 AATTTAAAGAATAATTTCTAGAAAGATTGAACATGTTTTAACCATAAATCAAGCTTGAAAATGAA
1929353 TCTACAACCTCTAAATCATCAAGATTCATCATCAATTTCATGAAC
131 TCTACAACCTCTAAATCATCAAGATTCATCATCAATTTCATGAAC
1929398 CCA
1 CCA
1929401 ATCATGAACA
Statistics
Matches: 176, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
175 176 1.00
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.31
Consensus pattern (175 bp):
CCACAATAAAATCCCTAATCAACTCTCATCATAACAAAAAGTTCTACAATTTCCTCTTTTGGCCG
AATTTAAAGAATAATTTCTAGAAAGATTGAACATGTTTTAACCATAAATCAAGCTTGAAAATGAA
TCTACAACCTCTAAATCATCAAGATTCATCATCAATTTCATGAAC
Found at i:1930027 original size:30 final size:31
Alignment explanation
Indices: 1929993--1930057 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 31
1929983 TTTGGTCCAT
* **
1929993 AAACTTTTCAAAGT-TTATTCTTTGGTCACC
1 AAACTTTTCAAAATCTTATAATTTGGTCACC
1930023 AAAC-TTTCAAAATCTTATAATTTGGTCACC
1 AAACTTTTCAAAATCTTATAATTTGGTCACC
1930053 AAACT
1 AAACT
1930058 AAATCCATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 8 0.27
30 22 0.73
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.38
Consensus pattern (31 bp):
AAACTTTTCAAAATCTTATAATTTGGTCACC
Found at i:1934680 original size:20 final size:20
Alignment explanation
Indices: 1934655--1934733 Score: 131
Period size: 20 Copynumber: 4.0 Consensus size: 20
1934645 TTTTCAAAGG
1934655 CATGCACCGATGCACCAATC
1 CATGCACCGATGCACCAATC
*
1934675 CATGCACCAATGCACCAATC
1 CATGCACCGATGCACCAATC
1934695 CATGCACCGATGCACCAATC
1 CATGCACCGATGCACCAATC
* *
1934715 CATGCATCGATGCATCAAT
1 CATGCACCGATGCACCAAT
1934734 TAATTTCTTA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.32, C:0.37, G:0.14, T:0.18
Consensus pattern (20 bp):
CATGCACCGATGCACCAATC
Found at i:1934720 original size:12 final size:12
Alignment explanation
Indices: 1934664--1934702 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1934654 GCATGCACCG
1934664 ATGCACCAATCC
1 ATGCACCAATCC
1934676 ATGCACC-A---
1 ATGCACCAATCC
1934684 ATGCACCAATCC
1 ATGCACCAATCC
1934696 ATGCACC
1 ATGCACC
1934703 GATGCACCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
8 7 0.30
9 1 0.04
11 1 0.04
12 14 0.61
ACGTcount: A:0.33, C:0.41, G:0.10, T:0.15
Consensus pattern (12 bp):
ATGCACCAATCC
Found at i:1934802 original size:45 final size:46
Alignment explanation
Indices: 1934753--1934842 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 46
1934743 AAACATCGAA
* *
1934753 TGCATTTTATGCATCGATGCAC-ATACCATGCATCAATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCAATGCACTCAG
*
1934798 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCA
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCAATGCACTCA
1934843 AGCTTTTTCA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 21 0.51
46 20 0.49
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.27
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCAATGCACTCAG
Found at i:1940560 original size:24 final size:24
Alignment explanation
Indices: 1940532--1940635 Score: 112
Period size: 24 Copynumber: 4.5 Consensus size: 24
1940522 CACTTAACAA
1940532 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGATGCATCCCTTTGAATG
*
1940556 TGCATCGATGCATCCCTTTGAATA
1 TGCATCGATGCATCCCTTTGAATG
* *
1940580 TGCATCGATTCAT-CATGTTG-A--
1 TGCATCGATGCATCCCT-TTGAATG
*
1940601 TGCACCGATGCA-CGCC-TTGAATG
1 TGCATCGATGCATC-CCTTTGAATG
1940624 TGCATCGATGCA
1 TGCATCGATGCA
1940636 CAGGGTCATG
Statistics
Matches: 67, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
20 3 0.04
21 11 0.16
22 1 0.01
23 14 0.21
24 38 0.57
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (24 bp):
TGCATCGATGCATCCCTTTGAATG
Found at i:1943352 original size:20 final size:20
Alignment explanation
Indices: 1943327--1943365 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1943317 TTTTCAAAGG
1943327 CATGCACCGATGCAGCAATC
1 CATGCACCGATGCAGCAATC
* *
1943347 CATGCATCGATGCATCAAT
1 CATGCACCGATGCAGCAAT
1943366 TAATTTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.21
Consensus pattern (20 bp):
CATGCACCGATGCAGCAATC
Found at i:1944824 original size:3 final size:3
Alignment explanation
Indices: 1944816--1944855 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
1944806 TTATATTATG
*
1944816 TTA TTA TTA TTA TTA TTAA TTA TT- TTA TTA TTA TTT TTA T
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA T
1944856 AGGATTTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:1944838 original size:24 final size:25
Alignment explanation
Indices: 1944805--1944855 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
1944795 CTACAAAAAC
1944805 ATTATATTATGTTATTATTATTATT
1 ATTATATTATGTTATTATTATTATT
* *
1944830 ATTA-ATTATTTTATTATTATTTTT
1 ATTATATTATGTTATTATTATTATT
1944854 AT
1 AT
1944856 AGGATTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (25 bp):
ATTATATTATGTTATTATTATTATT
Found at i:1945668 original size:3 final size:3
Alignment explanation
Indices: 1945656--1945703 Score: 51
Period size: 3 Copynumber: 14.3 Consensus size: 3
1945646 AATGATAATA
1945656 TAT TATT TAT TAT TATT TATT TATT TATT TAT TAT TAT TAT TAT TAT
1 TAT TA-T TAT TAT TA-T TA-T TA-T TA-T TAT TAT TAT TAT TAT TAT
1945703 T
1 T
1945704 TATTCATTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 25 0.58
4 18 0.42
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:1945675 original size:4 final size:4
Alignment explanation
Indices: 1945658--1945712 Score: 52
Period size: 4 Copynumber: 15.5 Consensus size: 4
1945648 TGATAATATA
1945658 TTAT TTA- TTA- TTAT TTAT TTAT TTAT TTA- TTA- TTA- TTA- TTA-
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
*
1945699 TTAT TTAT TCAT TT
1 TTAT TTAT TTAT TT
1945713 TTTTCTTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
3 21 0.45
4 26 0.55
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:1945839 original size:13 final size:13
Alignment explanation
Indices: 1945823--1945852 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1945813 TGAATCGGGT
1945823 TTTTAAATTTTAA
1 TTTTAAATTTTAA
*
1945836 TTTTAATTTTTAA
1 TTTTAAATTTTAA
1945849 TTTT
1 TTTT
1945853 TGCAATTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:1946710 original size:21 final size:20
Alignment explanation
Indices: 1946682--1946721 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1946672 TCTCACTAAC
*
1946682 TTTTTTTCCTTTCATTTTTG
1 TTTTTTTCATTTCATTTTTG
*
1946702 TTTTCTTTCATTTTATTTTT
1 TTTT-TTTCATTTCATTTTT
1946722 TATTATTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.07, C:0.12, G:0.03, T:0.78
Consensus pattern (20 bp):
TTTTTTTCATTTCATTTTTG
Found at i:1946721 original size:16 final size:16
Alignment explanation
Indices: 1946682--1946721 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 16
1946672 TCTCACTAAC
1946682 TTTTTTTCCTTTCATT
1 TTTTTTTCCTTTCATT
1946698 TTTGTTTT-CTTTCATT
1 TTT-TTTTCCTTTCATT
1946714 TTATTTTT
1 TT-TTTTT
1946722 TATTATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.07, C:0.12, G:0.03, T:0.78
Consensus pattern (16 bp):
TTTTTTTCCTTTCATT
Found at i:1948180 original size:103 final size:103
Alignment explanation
Indices: 1948001--1948226 Score: 391
Period size: 103 Copynumber: 2.2 Consensus size: 103
1947991 CCATATAATA
* *
1948001 ATGT-CCATAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGT
1 ATGTCCCA-AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGT
*
1948065 GTCTCACCAGACTTCACACATGTTCTAAAGAATACATAT
65 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
*
1948104 ATGTCCCAAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTG
1 ATGTCCCAAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTG
1948169 TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
66 TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
*
1948207 ATGTCCCGAAGGACCACATA
1 ATGTCCCAAAGGACCACATA
1948227 GACCCTCGAC
Statistics
Matches: 117, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
103 114 0.97
104 3 0.03
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
ATGTCCCAAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTG
TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
Found at i:1952999 original size:23 final size:22
Alignment explanation
Indices: 1952968--1953046 Score: 77
Period size: 23 Copynumber: 3.4 Consensus size: 22
1952958 CACCACAGCT
1952968 CATATAAATGCACCGAAGTGCCA
1 CATA-AAATGCACCGAAGTGCCA
* *
1952991 CATAGAAATGCACCGTAGTGCCG
1 CATA-AAATGCACCGAAGTGCCA
* *
1953014 CATAAAATTGCACCGTAGTTCCA
1 CATAAAA-TGCACCGAAGTGCCA
*
1953037 TATAATAATG
1 CATAA-AATG
1953047 TCCATAAGGA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
22 3 0.06
23 43 0.90
24 2 0.04
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.23
Consensus pattern (22 bp):
CATAAAATGCACCGAAGTGCCA
Found at i:1953223 original size:103 final size:103
Alignment explanation
Indices: 1953052--1953269 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
1953042 TAATGTCCAT
* * *
1953052 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCGTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1953117 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
1953155 AAGGACCACATATCATTCCGTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCGTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1953220 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1953258 AAGGACCACATA
1 AAGGACCACATA
1953270 GACCCTCGAC
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.25
Consensus pattern (103 bp):
AAGGACCACATATCATTCCGTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1954288 original size:2 final size:2
Alignment explanation
Indices: 1954281--1954334 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1954271 ATATTTCATT
1954281 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1954323 TA TA TA TA TA TA
1 TA TA TA TA TA TA
1954335 ACTTATCTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1954771 original size:23 final size:22
Alignment explanation
Indices: 1954746--1954788 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1954736 TTTCCTTTAG
1954746 GGGGGAATCGGTTCCCACTTGT
1 GGGGGAATCGGTTCCCACTTGT
* *
1954768 GGGGGTATCGGTTCCCCCTTG
1 GGGGGAATCGGTTCCCACTTG
1954789 ACATTCTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.26, G:0.37, T:0.28
Consensus pattern (22 bp):
GGGGGAATCGGTTCCCACTTGT
Found at i:1958527 original size:122 final size:122
Alignment explanation
Indices: 1958176--1958558 Score: 545
Period size: 124 Copynumber: 3.1 Consensus size: 122
1958166 TTCAGAACCA
**
1958176 ATTTTAACTTCACGGCAAAGGATATTCAAGTTAAGGCTCAACTTCACAACGAAGGGGCCATCCAC
1 ATTTTAACTTCACGATAAA-GATATTCAAGTTAAGGCTCAACTTCACAACGAAGGGGCCATCCAC
* **
1958241 GGTTTCAACTTCACGACGAAGGGAATCATGCTCACTAATAACATTCATCTTTAGCTTGG
65 GGTTTCAACTTCACGACGAAGGGAATCGTGCTCACTAGCAACATTCATCTTTAG-TTGG
* * *
1958300 ATTTTAACTTCACGATGAATGATATTCAAGTTAAGGTTCAACTTCACAACGAATGGGCCATCCAC
1 ATTTTAACTTCACGAT-AAAGATATTCAAGTTAAGGCTCAACTTCACAACGAAGGGGCCATCCAC
* *
1958365 GGTTTCAACTTCACGATGAAGGGAATCGTGCTCACCAGCAACATTCATCTTTAGATTGG
65 GGTTTCAACTTCACGACGAAGGGAATCGTGCTCACTAGCAACATTCATCTTTAG-TTGG
* * *
1958424 ATTTCAACTTCACGATAAAGATATCCAA-TTCAAGGCTCAACTTCACAACGAA-GGGCCATCCAT
1 ATTTTAACTTCACGATAAAGATATTCAAGTT-AAGGCTCAACTTCACAACGAAGGGGCCATCCAC
* * * *
1958487 GGTTTCAACTTCACGACGAAGGGAATCGTACCCACTAGCAACATTCATATTCAGTGTGG
65 GGTTTCAACTTCACGACGAAGGGAATCGTGCTCACTAGCAACATTCATCTTTAGT-TGG
1958546 ATTTTAACTTCAC
1 ATTTTAACTTCAC
1958559 AACGAATAAC
Statistics
Matches: 233, Mismatches: 23, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
121 1 0.00
122 75 0.32
123 30 0.13
124 125 0.54
125 2 0.01
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.27
Consensus pattern (122 bp):
ATTTTAACTTCACGATAAAGATATTCAAGTTAAGGCTCAACTTCACAACGAAGGGGCCATCCACG
GTTTCAACTTCACGACGAAGGGAATCGTGCTCACTAGCAACATTCATCTTTAGTTGG
Found at i:1958874 original size:36 final size:36
Alignment explanation
Indices: 1958821--1959224 Score: 398
Period size: 36 Copynumber: 11.2 Consensus size: 36
1958811 AATTTACTCA
* *
1958821 AAACAAAGTTTTGTCTCTCTTCAGACAGTTTCTCTTA
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTTG
*
1958858 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
*
1958894 AAACAAATTTTGTCTCTCTTGAGATC-GTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGA-CAGTTTCTCTTG
* * *
1958930 AAACAAATTCTGTATCTCTTGAGACAGTTTCGCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* *
1958966 AAACAAATTTTGTCTCTCTTGAGATAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* *
1959002 AAACAAA------ATCT-TTGA-ATATGTTT-TACATT-
1 AAACAAATTTTGTCTCTCTTGAGACA-GTTTCT-C-TTG
* * * *
1959031 AAACAAATTTCGTCTCCCTTGAGATAGTTTCTTTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* * * * *
1959067 GAACTAAGTTTTGTATCTCTTGAGACAGTTTCTATCG
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
*
1959104 AAACAAATTTTGTCTTTATCTCTTTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTC----TCTC--TTGAGACAGTTTCTCTTG
* *
1959146 AAACAAATTTTGTTTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* *
1959182 AAACAAATTTTGTCTCTCTTGGGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
1959218 AAACAAA
1 AAACAAA
1959225 ATCTTTGAAT
Statistics
Matches: 313, Mismatches: 32, Indels: 45
0.80 0.08 0.12
Matches are distributed among these distances:
28 3 0.01
29 16 0.05
30 5 0.02
35 5 0.02
36 208 0.66
37 40 0.13
38 4 0.01
40 4 0.01
42 28 0.09
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
Found at i:1958934 original size:72 final size:72
Alignment explanation
Indices: 1958821--1959224 Score: 441
Period size: 72 Copynumber: 5.6 Consensus size: 72
1958811 AATTTACTCA
* * * *
1958821 AAACAAAGTTTTGTCTCTCTTCAGACAGTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAGT
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTATCTCTTGAGACAGT
1958886 TTCCCTTG
65 TTCCCTTG
*
1958894 AAACAAATTTTGTCTCTCTTGAGATC-GTTTCCCTTGAAACAAATTCTGTATCTCTTGAGACAGT
1 AAACAAATTTTGTCTCTCTTGAGA-CAGTTTCCCTTGAAACAAATTTTGTATCTCTTGAGACAGT
*
1958958 TTCGCTTG
65 TTCCCTTG
* *
1958966 AAACAAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAA------ATCT-TTGA-ATATGT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTATCTCTTGAGACA-G-
* *
1959023 TTTACATT-
64 TTTCCCTTG
* * * ** * *
1959031 AAACAAATTTCGTCTCCCTTGAGATAGTTTCTTTTGGAACTAAGTTTTGTATCTCTTGAGACAGT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTATCTCTTGAGACAGT
** *
1959096 TTCTATCG
65 TTCCCTTG
*
1959104 AAACAAATTTTGTCTTTATCTCTTTTGAGACAGTTTCCCTTGAAACAAATTTTGTTTCTCTTGAG
1 AAACAAATTTTGTC----TCTC--TTGAGACAGTTTCCCTTGAAACAAATTTTGTATCTCTTGAG
1959169 ACAGTTTCCCTTG
60 ACAGTTTCCCTTG
*
1959182 AAACAAATTTTGTCTCTCTTGGGACAGTTTCCCTTGAAACAAA
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1959225 ATCTTTGAAT
Statistics
Matches: 278, Mismatches: 33, Indels: 41
0.79 0.09 0.12
Matches are distributed among these distances:
64 2 0.01
65 40 0.14
66 11 0.04
72 131 0.47
73 26 0.09
74 6 0.02
77 3 0.01
78 41 0.15
79 18 0.06
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (72 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTATCTCTTGAGACAGTT
TCCCTTG
Found at i:1959109 original size:138 final size:139
Alignment explanation
Indices: 1958894--1959152 Score: 351
Period size: 138 Copynumber: 1.8 Consensus size: 139
1958884 GTTTCCCTTG
* * *
1958894 AAACAAATTTTGTCTCTCTTGAGATCGTTTCCCTTGAAACAAATTCTGTATCTCTTGAGACAGTT
1 AAACAAATTTCGTCTCCCTTGAGATAGTTTCCCTTGAAACAAATTCTGTATCTCTTGAGACAGTT
* * *
1958959 TCGCTTGAAACAAATTTTGTC-TCTC-TTGAGATAGTTTCCCTTGAAACAAAATCTTTGAATATG
66 TCGATCGAAACAAATTTTGTCTTCTCTTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATG
1959022 TTTTACATT
131 TTTTACATT
** * * *
1959031 AAACAAATTTCGTCTCCCTTGAGATAGTTTCTTTTGGAACTAAGTTTTGTATCTCTTGAGACAGT
1 AAACAAATTTCGTCTCCCTTGAGATAGTTTCCCTTGAAAC-AAATTCTGTATCTCTTGAGACAGT
*
1959096 TTCTATCGAAACAAATTTTGTCTTTATCTCTTTTGAGACAGTTTCCCTTGAAACAAA
65 TTCGATCGAAACAAATTTTGTC--T-TCTC-TTTGAGACAGTTTCCCTTGAAACAAA
1959153 TTTTGTTTCT
Statistics
Matches: 103, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
137 34 0.33
138 41 0.40
142 4 0.04
144 24 0.23
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (139 bp):
AAACAAATTTCGTCTCCCTTGAGATAGTTTCCCTTGAAACAAATTCTGTATCTCTTGAGACAGTT
TCGATCGAAACAAATTTTGTCTTCTCTTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATG
TTTTACATT
Found at i:1959166 original size:21 final size:21
Alignment explanation
Indices: 1959136--1959194 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 21
1959126 TTTTGAGACA
1959136 GTTTCCCTTGAAACAAATTTT
1 GTTTCCCTTGAAACAAATTTT
* *
1959157 GTTTCTCTTGAGAC--A----
1 GTTTCCCTTGAAACAAATTTT
1959172 GTTTCCCTTGAAACAAATTTT
1 GTTTCCCTTGAAACAAATTTT
1959193 GT
1 GT
1959195 CTCTCTTGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 12
0.64 0.09 0.27
Matches are distributed among these distances:
15 12 0.43
17 1 0.04
19 1 0.04
21 14 0.50
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (21 bp):
GTTTCCCTTGAAACAAATTTT
Found at i:1959306 original size:252 final size:241
Alignment explanation
Indices: 1958794--1959395 Score: 625
Period size: 252 Copynumber: 2.4 Consensus size: 241
1958784 AAACAAAGGG
* * *
1958794 TCGTCTCCCTTGAGACTAATTTACTC--AAAACAAAGTTTTGTCTCTCTTCAGACAGTTTCTCTT
1 TCGTCTCCCTTGAGAC-AGTTT-CTCTTGAAAC-AAGTTTTGTCTCTCTTGAGACAGTTTCTCTT
*
1958857 AAAACAAATTTTGTC-TCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATCG
63 GAAACAAATTTTGTCTTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATCG
* *
1958921 TTTCCCTTGAAACAAATTCTGTATCTCTTGAGACAGTTTCGCTTGAAACAAATTTTGTCTCTCTT
128 TTTCCCTTGAAACAAATTCTGTATCTCTTGAGACAGTTTCCCTTGAAACAAA-----TATCTCTT
*
1958986 GAGATAGTTTCCCTTGAAACAAAATCTTTGAATATGTTTTACATTAAACAAATT
188 GAGATAGTTTCCCTTGAAACAAAATCTTTGAACATGTTTTACATTAAACAAATT
* * * * * *
1959040 TCGTCTCCCTTGAGATAGTTTCTTTTGGAACTAAGTTTTGTATCTCTTGAGACAGTTTCTATCGA
1 TCGTCTCCCTTGAGACAGTTTCTCTTGAAAC-AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGA
*
1959105 AACAAATTTTGTCTTTATCTCTTTTGAGACAGTTTCCCTTGAAACAAATTTTGTTTCTCTTGAGA
65 AACAAATTTTGTC--T-TCTC--TTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGA
* * *
1959170 -CAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGGGACAGTTTCCCTTGAAACAAA-ATCT-TTG
125 TC-GTTTCCCTTGAAACAAATTCTGTATCTCTTGAGACAGTTTCCCTTGAAACAAATATCTCTTG
* * * *
1959232 A-ATATGTTTTCCTTGAAACAAATTCGTCTCCCTTGAGACA-G-TTTA-TTTCGAAACTAAGTT
189 AGATA-GTTTCCCTTGAAACAAA---ATCT---TTGA-ACATGTTTTACATT--AAAC-AAATT
* * * * *
1959292 TTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTATCTCTCTTGAGA-AGTTTCCCTTGAA
1 TCGTCTCCCTTGAGACAGTTTCTCTTGAAACAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAA
**
1959356 ACAAAATTTTGTC-TCTCTTGAGACAGTTTCTTTTGAAACA
66 AC-AAATTTTGTCTTCTCTTGAGACAGTTTCCCTTGAAACA
1959396 CCAATCTTTG
Statistics
Matches: 300, Mismatches: 35, Indels: 43
0.79 0.09 0.11
Matches are distributed among these distances:
244 5 0.02
245 45 0.15
246 62 0.21
247 4 0.01
248 3 0.01
249 2 0.01
250 20 0.07
251 37 0.12
252 122 0.41
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (241 bp):
TCGTCTCCCTTGAGACAGTTTCTCTTGAAACAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAA
ACAAATTTTGTCTTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATCGTTT
CCCTTGAAACAAATTCTGTATCTCTTGAGACAGTTTCCCTTGAAACAAATATCTCTTGAGATAGT
TTCCCTTGAAACAAAATCTTTGAACATGTTTTACATTAAACAAATT
Found at i:1959339 original size:173 final size:176
Alignment explanation
Indices: 1959122--1959460 Score: 535
Period size: 173 Copynumber: 1.9 Consensus size: 176
1959112 TTTGTCTTTA
* * *
1959122 TCTCTTTTGAGACAGTTTCCCTTGAAACAAATTTTGTTTCTCTTGAGACAGTTTCCCTTGAAAC-
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTATCTCTCTTGAGA-AGTTTCCCTTGAAACA
*
1959186 AAATTTTGTCTCTCTTGGGACAGTTTCCCTTGAAACA-AAATCTTTGAATATGTTTTC-CTTGAA
65 AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACACAAATCTTTGAATAT-TTTTCTCTTGAA
1959249 AC-AAA-TTCGTCTCCCTTGAGACAGTTTATTTCGAAACTAAGTTTTG
129 ACAAAATTTCGTCTCCCTTGAGACAGTTTATTTCGAAACTAAGTTTTG
*
1959295 TCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTATCTCTCTTGAGAAGTTTCCCTTGAAACAA
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTATCTCTCTTGAGAAGTTTCCCTTGAAACAA
** *
1959360 AATTTTGTCTCTCTTGAGACAGTTTCTTTTGAAACACCAATCTTTGAATATTTTTCTCTTGAAAC
66 AATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACACAAATCTTTGAATATTTTTCTCTTGAAAC
* *
1959425 AAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGAAA
131 AAAATTTCGTCTCCCTTGAGACAGTTTATTTCGAAA
1959461 AAAAACCTTT
Statistics
Matches: 151, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
172 15 0.10
173 83 0.55
174 21 0.14
175 3 0.02
176 29 0.19
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (176 bp):
TCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTATCTCTCTTGAGAAGTTTCCCTTGAAACAA
AATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACACAAATCTTTGAATATTTTTCTCTTGAAAC
AAAATTTCGTCTCCCTTGAGACAGTTTATTTCGAAACTAAGTTTTG
Found at i:1959342 original size:36 final size:36
Alignment explanation
Indices: 1959239--1959395 Score: 196
Period size: 36 Copynumber: 4.4 Consensus size: 36
1959229 TTGAATATGT
* *
1959239 TTTC-CTTGAAACAAA-TTCGTCTCCCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* *
1959273 TTTAT-TTCGAAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTT-GAAAC-AAATTTTGTCTCTCTTGAGACAG
*
1959310 TTTCTCTTGAAACAAATTTTATCTCTCTTGAGA-AG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
*
1959345 TTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
*
1959382 TTTCTTTTGAAACA
1 TTTCTCTTGAAACA
1959396 CCAATCTTTG
Statistics
Matches: 105, Mismatches: 11, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
34 5 0.05
35 19 0.18
36 40 0.38
37 39 0.37
38 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:1959451 original size:67 final size:66
Alignment explanation
Indices: 1959344--1959491 Score: 215
Period size: 67 Copynumber: 2.2 Consensus size: 66
1959334 CTCTTGAGAA
* * * ** * *
1959344 GTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTTTTGAAACACCAATCTTTGAAT
1 GTTTCTCTTGAAACAAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGAAA-AAAAACCTTTGAAA
1959409 AT
65 AT
*
1959411 TTTTCTCTTGAAACAAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGAAAAAAAACCTTTGAAAA
1 GTTTCTCTTGAAACAAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGAAAAAAAACCTTTGAAAA
1959476 T
66 T
1959477 GTTTCTCTTGAAACA
1 GTTTCTCTTGAAACA
1959492 CCAAACCTTC
Statistics
Matches: 72, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
66 26 0.36
67 46 0.64
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.39
Consensus pattern (66 bp):
GTTTCTCTTGAAACAAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGAAAAAAAACCTTTGAAAA
T
Found at i:1959637 original size:83 final size:82
Alignment explanation
Indices: 1959491--1959745 Score: 330
Period size: 83 Copynumber: 3.1 Consensus size: 82
1959481 CTCTTGAAAC
* *
1959491 ACCAAACCTTCGAGTTCGGTTACACTCAGCTCAAAGGCATATCATTTGCAGCATAACTTAAGGCA
1 ACCAAACCTTCGAGTTCGATTACACTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGGCA
1959556 AGAAGGGCTATCTGCCA
66 AGAAGGGCTATCTGCCA
* * *
1959573 ACCAAGACCTTCGAGTTCGATTACACTCAGCTCCAAGGCATATCGTTTGCAACATAACTCAAGGC
1 ACCAA-ACCTTCGAGTTCGATTACACTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGGC
* * *
1959638 AATAAGGGCTATTTACCA
65 AAGAAGGGCTATCTGCCA
* ** * * * * *
1959656 ACCAAATACCTTTGAGTTTAACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGT
1 ACC-AA-ACCTTCGAGTTCGATTACACTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGG
*
1959721 CGAGAAGGGCTATCTGCCA
64 CAAGAAGGGCTATCTGCCA
1959740 ACCAAA
1 ACCAAA
1959746 GATCTGACAA
Statistics
Matches: 147, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
82 6 0.04
83 74 0.50
84 67 0.46
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (82 bp):
ACCAAACCTTCGAGTTCGATTACACTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGGCA
AGAAGGGCTATCTGCCA
Found at i:1960010 original size:3 final size:3
Alignment explanation
Indices: 1960002--1960038 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
1959992 TTATATTATG
*
1960002 TTA TTA TTA TTA TTA AT- TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1960039 GCAGGATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 1 0.03
3 30 0.97
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1960867 original size:20 final size:20
Alignment explanation
Indices: 1960842--1960879 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1960832 AATTATAATA
*
1960842 TATTATTTATTTATTTTTAT
1 TATTATTTATTCATTTTTAT
1960862 TATTATTTATTCATTTTT
1 TATTATTTATTCATTTTT
1960880 TTCTTTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (20 bp):
TATTATTTATTCATTTTTAT
Found at i:1960872 original size:27 final size:28
Alignment explanation
Indices: 1960833--1960887 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
1960823 GAATTATGAA
1960833 ATTATAATATATT-ATTTATTTATTTTT
1 ATTATAATATATTCATTTATTTATTTTT
* * * *
1960860 ATTATTATTTATTCATTTTTTTCTTTTT
1 ATTATAATATATTCATTTATTTATTTTT
1960888 GTTTAGCATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (28 bp):
ATTATAATATATTCATTTATTTATTTTT
Found at i:1964275 original size:19 final size:19
Alignment explanation
Indices: 1964251--1964295 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
1964241 CTCGAAAAAG
1964251 GAATAAATAGAATGGCTGA
1 GAATAAATAGAATGGCTGA
*
1964270 GAATAAATATAATGGCTGA
1 GAATAAATAGAATGGCTGA
1964289 GAATAAA
1 GAATAAA
1964296 CCTCAGTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.51, C:0.04, G:0.22, T:0.22
Consensus pattern (19 bp):
GAATAAATAGAATGGCTGA
Found at i:1965768 original size:66 final size:66
Alignment explanation
Indices: 1965652--1965775 Score: 178
Period size: 66 Copynumber: 1.9 Consensus size: 66
1965642 ATGAGAACTT
* * * *
1965652 TGGCAGGTTCAGTTGTTGCTGGTAATTCATTGTATAGGTTTTGCATCGACTGGTAATTTCTATCT
1 TGGCAGGTTCAGTCGTTGCTGGTAATTCATTGTATAGGTTATGCACCGACTGATAATTTCTATCT
1965717 C
66 C
* *
1965718 TGGCAGGTTCAGTCGTTGCTGGTAATTCCTTTTATAGGTTCAT-CACCGACTGATAATT
1 TGGCAGGTTCAGTCGTTGCTGGTAATTCATTGTATAGGTT-ATGCACCGACTGATAATT
1965776 CCTTGTGGAC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
66 50 0.98
67 1 0.02
ACGTcount: A:0.19, C:0.17, G:0.23, T:0.40
Consensus pattern (66 bp):
TGGCAGGTTCAGTCGTTGCTGGTAATTCATTGTATAGGTTATGCACCGACTGATAATTTCTATCT
C
Found at i:1967577 original size:18 final size:18
Alignment explanation
Indices: 1967550--1967586 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1967540 GTGTTTAACC
* *
1967550 TAGAATGTTTACACGGTA
1 TAGAAGGTTTACAAGGTA
1967568 TAGAAGGTTTACAAGGTA
1 TAGAAGGTTTACAAGGTA
1967586 T
1 T
1967587 TTATAGGGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.35, C:0.08, G:0.24, T:0.32
Consensus pattern (18 bp):
TAGAAGGTTTACAAGGTA
Found at i:1970977 original size:22 final size:24
Alignment explanation
Indices: 1970932--1970977 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1970922 TCTTGAAATG
*
1970932 TAGTGTTTTTCTTTGCAATTGTTT
1 TAGTGTTTTACTTTGCAATTGTTT
1970956 TAGTGTTTTAC-TTGC-ATTGTTT
1 TAGTGTTTTACTTTGCAATTGTTT
1970978 CAAATTTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.33
23 4 0.19
24 10 0.48
ACGTcount: A:0.13, C:0.09, G:0.17, T:0.61
Consensus pattern (24 bp):
TAGTGTTTTACTTTGCAATTGTTT
Found at i:1976966 original size:49 final size:48
Alignment explanation
Indices: 1976893--1976986 Score: 170
Period size: 49 Copynumber: 1.9 Consensus size: 48
1976883 GAGATTGTTG
1976893 GTCAAACTTGCAGTGCAATAAATGGCAATAGGAGAAATTGGTTGCCAA
1 GTCAAACTTGCAGTGCAATAAATGGCAATAGGAGAAATTGGTTGCCAA
*
1976941 GTCAAACTTGCAGGTGCAATAAATGGCAATATGAGAAATTGGTTGC
1 GTCAAACTTGCA-GTGCAATAAATGGCAATAGGAGAAATTGGTTGC
1976987 TAACCCAACA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 12 0.27
49 32 0.73
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24
Consensus pattern (48 bp):
GTCAAACTTGCAGTGCAATAAATGGCAATAGGAGAAATTGGTTGCCAA
Found at i:1991741 original size:134 final size:134
Alignment explanation
Indices: 1991498--1992776 Score: 1405
Period size: 134 Copynumber: 9.5 Consensus size: 134
1991488 ATCCATTTTG
* * * * * *
1991498 CTGTCACTCATGGAATATCAAATCTTGAAAGAAATGGATCTGTT-TAACTTCTTTTGAAGGGAAT
1 CTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATTTGTTCT-GCTTCTTCTGAAGGGAAT
* * * *
1991562 ATCAGATCT-ACGAGAGTTGATCCATTTCGCTGTAACTTAGGGAAGATTGAATCGGGGCAGACTT
65 ATCAGATCTGA-GGGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGGCAGACTT
*
1991626 GTTCCG
129 GTTCCA
* * * * *
1991632 CTGTCACTCAAGGAATATCAAATCTTGAAAGAAATGGATATATTCTGCTTCTTCTGAAGGGAATA
1 CTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATTTGTTCTGCTTCTTCTGAAGGGAATA
* ** * *
1991697 TCAGATCTGAAGGAGTTGATCCATTCCGCTGTCACTCAAAGAAGATTAAATCGGGGTAGACTTGT
66 TCAGATCTGAGGGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGGCAGACTTGT
*
1991762 TACA
131 TCCA
* * * * * * ** *
1991766 TTCTCATTTAGGGAATATTAAATCTTGAAAGAGAGGAATTTGTTCCACTTCTTCTGAAGGAAATA
1 CTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATTTGTTCTGCTTCTTCTGAAGGGAATA
* * * * * * *
1991831 TCATATATGGGGGAGTTGATCCATTTCGCTGTCACTAAGGGAA-ATTTGAATTGGGGCAAACTTG
66 TCAGATCTGAGGGAGTTGATCCATTCCGCTGTCACTCAGGGAAGA-TTGAATCGGGGCAGACTTG
1991895 TTCCA
130 TTCCA
* * * *
1991900 CAGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTCCGCTTCTTTTGAAGGGAATA
1 CTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATTTGTTCTGCTTCTTCTGAAGGGAATA
* * * * * *
1991965 TTAGACCTCG-GGGAGTTGATCCATTCCACTGTCAATCAGGGAAGATTGAATTGGGACAGACTTG
66 TCAGATCT-GAGGGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGGCAGACTTG
**
1992029 TTCTG
130 TTCCA
* * * * * * *
1992034 CTATTACTCAGGGAATATCAAATCATGAAAGAGAGGGGTTTGTTCTGCTTTTTTTGGAGGGAATA
1 CTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATTTGTTCTGCTTCTTCTGAAGGGAATA
* * * * *
1992099 TCAGATCTGAGGGAGTTGATTCATTCTGTTATCACTCAGGGAAGATTGAATCGGGGTAGACTTGT
66 TCAGATCTGAGGGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGGCAGACTTGT
1992164 TCCA
131 TCCA
*
1992168 CTATCACTCAGGGAATATCAAATCTT-ATAAGAGAGGGATTTGTTCTGCTTCTTCTTG-AGGGAA
1 CTGTCACTCAGGGAATATCAAATCTTGA-AAGAGAGGGATTTGTTCTGCTTCTTC-TGAAGGGAA
* * * *
1992231 TATCATATCTGGGGGAGTTGATACATTCTGCTGTCACTCAGGGAAGATTGAATCGGGGCAGACTT
64 TATCAGATCTGAGGGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGGCAGACTT
*
1992296 GTTCCG
129 GTTCCA
* *
1992302 CTGTCACTCAGGGAATATCAAATCTT-AGAAGAGAGGGATTTGTT-TCGTTTCTTATGAAGGGAA
1 CTGTCACTCAGGGAATATCAAATCTTGA-AAGAGAGGGATTTGTTCT-GCTTCTTCTGAAGGGAA
* * * *
1992365 TATCAGATCTGGGGGAGTTGATCCATTTCGCTATCATTCAGGGAAGATTGAATCGGGGCAGACTT
64 TATCAGATCTGAGGGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGGCAGACTT
*
1992430 ATTCCA
129 GTTCCA
* * * * * *
1992436 CTATCACTCAAGGAATATCAAATCTTGGAAGAGAGGGATATGTTATACTTCTTCTGAAGGGAATA
1 CTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATTTGTTCTGCTTCTTCTGAAGGGAATA
* * * * * **
1992501 TCAGATC-CAGGGGAGTCGATCCATTCTGCTGTCACTCAAGGAAGATTGAATCGAGATAGACTTG
66 TCAGATCTGA-GGGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGGCAGACTTG
**
1992565 TTCTG
130 TTCCA
* * * * * *
1992570 CTATCACTCAGGGAATATTAAATCTTGGAAGAGTA-GGATATGTTCCT-CTTCATCTGAAAGGAA
1 CTGTCACTCAGGGAATATCAAATCTTGAAAGAG-AGGGATTTGTT-CTGCTTCTTCTGAAGGGAA
* * * * * ** *
1992633 TATCAAATATGGGGGAGTTGATCTATTCCGCTGTCACTTAGGGAAGATTGAATCAAGGAAGACTT
64 TATCAGATCTGAGGGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGGCAGACTT
1992698 GTTCCA
129 GTTCCA
*
1992704 CTGTCACTCAGGGAATATCAAATCTT-AGAAGAGGGGGATTTGTT-TCGCTTCTTCTGAAGGGAA
1 CTGTCACTCAGGGAATATCAAATCTTGA-AAGAGAGGGATTTGTTCT-GCTTCTTCTGAAGGGAA
1992767 TATCAGATCT
64 TATCAGATCT
1992777 AAAAATTAAA
Statistics
Matches: 964, Mismatches: 161, Indels: 40
0.83 0.14 0.03
Matches are distributed among these distances:
132 1 0.00
133 6 0.01
134 948 0.98
135 9 0.01
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (134 bp):
CTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATTTGTTCTGCTTCTTCTGAAGGGAATA
TCAGATCTGAGGGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGGCAGACTTGT
TCCA
Found at i:1992246 original size:402 final size:400
Alignment explanation
Indices: 1991498--1992776 Score: 1615
Period size: 402 Copynumber: 3.2 Consensus size: 400
1991488 ATCCATTTTG
* * * * **
1991498 CTGTCACTCATGGAATATCAAATCTT-GAAAGAAATGGATCTGTTTAACTTCTTTTGAAGGGAAT
1 CTGTCACTCAGGGAATATCAAATCTTAG-AAGAGAGGGATTTGTTTCGCTTCTTTTGAAGGGAAT
* *
1991562 ATCAGATCTAC-GAGAGTTGATCCATTTCGCTGT-AACTTAGGGAAGATTGAATCGGGGCAGACT
65 ATCAGATCT-CGGGGAGTTGATCCATTTCGCTGTCAA-TCAGGGAAGATTGAATCGGGGCAGACT
* * * *
1991625 TGTTCCGCTGTCACTCAAGGAATATCAAATCTTGAAAGAAATGGATATATTCTGCTTCTTCTGAA
128 TGTTCCGCTATCACTCAAGGAATATCAAATCTTGAAAGAGAGGGATATGTTCTGCTTCTTCTGAA
* * * *
1991690 GGGAATATCAGATCTGAAGGAGTTGATCCATTCCGCTGTCACTCAAAGAAGATTAAATCGGGGTA
193 GGGAATATCAGATCTGAGGGAGTTGATCCATTCTGCTGTCACTCAAGGAAGATTGAATCGGGGTA
* * * * * * *
1991755 GACTTGTTACATTCTCATTTAGGGAATATTAAATCTTGAAAGAGAGGAATTTGTTCCACTTCTTC
258 GACTTGTTCCACTATCACTCAGGGAATATTAAATCTT-AAAGAGAGGGATTTGTT-CTCTTCTTC
* *
1991820 TGAAGGAAATATCATATATGGGGGAGTTGATCCATTTCGCTGTCACTAAGGGAA-ATTTGAATTG
321 TGAAGGGAATATCATATATGGGGGAGTTGATCCATTTCGCTGTCACTAAGGGAAGA-TTGAATCG
1991884 GGGCAAACTTGTTCCA
385 GGGCAAACTTGTTCCA
* * *
1991900 CAGTCACTCAGGGAATATCAAATCTT-GAAAGAGAGGGATATGTTCCGCTTCTTTTGAAGGGAAT
1 CTGTCACTCAGGGAATATCAAATCTTAG-AAGAGAGGGATTTGTTTCGCTTCTTTTGAAGGGAAT
* * * * * *
1991964 ATTAGACCTCGGGGAGTTGATCCATTCCACTGTCAATCAGGGAAGATTGAATTGGGACAGACTTG
65 ATCAGATCTCGGGGAGTTGATCCATTTCGCTGTCAATCAGGGAAGATTGAATCGGGGCAGACTTG
* * * * * * * * *
1992029 TTCTGCTATTACTCAGGGAATATCAAATCATGAAAGAGAGGGGTTTGTTCTGCTTTTTTTGGAGG
130 TTCCGCTATCACTCAAGGAATATCAAATCTTGAAAGAGAGGGATATGTTCTGCTTCTTCTGAAGG
* * * *
1992094 GAATATCAGATCTGAGGGAGTTGATTCATTCTGTTATCACTCAGGGAAGATTGAATCGGGGTAGA
195 GAATATCAGATCTGAGGGAGTTGATCCATTCTGCTGTCACTCAAGGAAGATTGAATCGGGGTAGA
*
1992159 CTTGTTCCACTATCACTCAGGGAATATCAAATCTTATAAGAGAGGGATTTGTTCTGCTTCTTCTT
260 CTTGTTCCACTATCACTCAGGGAATATTAAATCTTA-AAGAGAGGGATTTGTTCT-CTTCTTC-T
* * *
1992224 G-AGGGAATATCATATCTGGGGGAGTTGATACA-TTCTGCTGTCACTCAGGGAAGATTGAATCGG
322 GAAGGGAATATCATATATGGGGGAGTTGATCCATTTC-GCTGTCACTAAGGGAAGATTGAATCGG
* *
1992287 GGCAGACTTGTTCCG
386 GGCAAACTTGTTCCA
* *
1992302 CTGTCACTCAGGGAATATCAAATCTTAGAAGAGAGGGATTTGTTTCGTTTCTTATGAAGGGAATA
1 CTGTCACTCAGGGAATATCAAATCTTAGAAGAGAGGGATTTGTTTCGCTTCTTTTGAAGGGAATA
* * * *
1992367 TCAGATCTGGGGGAGTTGATCCATTTCGCTATCATTCAGGGAAGATTGAATCGGGGCAGACTTAT
66 TCAGATCTCGGGGAGTTGATCCATTTCGCTGTCAATCAGGGAAGATTGAATCGGGGCAGACTTGT
* * * *
1992432 TCCACTATCACTCAAGGAATATCAAATCTTGGAAGAGAGGGATATGTTATACTTCTTCTGAAGGG
131 TCCGCTATCACTCAAGGAATATCAAATCTTGAAAGAGAGGGATATGTTCTGCTTCTTCTGAAGGG
* * * *
1992497 AATATCAGATC-CAGGGGAGTCGATCCATTCTGCTGTCACTCAAGGAAGATTGAATCGAGATAGA
196 AATATCAGATCTGA-GGGAGTTGATCCATTCTGCTGTCACTCAAGGAAGATTGAATCGGGGTAGA
** * * *
1992561 CTTGTTCTGCTATCACTCAGGGAATATTAAATCTTGGAAGAGTA-GGATATGTTCCTCTTCATCT
260 CTTGTTCCACTATCACTCAGGGAATATTAAATCTT-AAAGAG-AGGGATTTGTT-CTCTTCTTCT
* * * * * **
1992625 GAAAGGAATATCAAATATGGGGGAGTTGATCTATTCCGCTGTCACTTAGGGAAGATTGAATCAAG
322 GAAGGGAATATCATATATGGGGGAGTTGATCCATTTCGCTGTCACTAAGGGAAGATTGAATCGGG
1992690 G-AAGACTTGTTCCA
387 GCAA-ACTTGTTCCA
* *
1992704 CTGTCACTCAGGGAATATCAAATCTTAGAAGAGGGGGATTTGTTTCGCTTCTTCTGAAGGGAATA
1 CTGTCACTCAGGGAATATCAAATCTTAGAAGAGAGGGATTTGTTTCGCTTCTTTTGAAGGGAATA
1992769 TCAGATCT
66 TCAGATCT
1992777 AAAAATTAAA
Statistics
Matches: 754, Mismatches: 108, Indels: 30
0.85 0.12 0.03
Matches are distributed among these distances:
401 10 0.01
402 733 0.97
403 11 0.01
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (400 bp):
CTGTCACTCAGGGAATATCAAATCTTAGAAGAGAGGGATTTGTTTCGCTTCTTTTGAAGGGAATA
TCAGATCTCGGGGAGTTGATCCATTTCGCTGTCAATCAGGGAAGATTGAATCGGGGCAGACTTGT
TCCGCTATCACTCAAGGAATATCAAATCTTGAAAGAGAGGGATATGTTCTGCTTCTTCTGAAGGG
AATATCAGATCTGAGGGAGTTGATCCATTCTGCTGTCACTCAAGGAAGATTGAATCGGGGTAGAC
TTGTTCCACTATCACTCAGGGAATATTAAATCTTAAAGAGAGGGATTTGTTCTCTTCTTCTGAAG
GGAATATCATATATGGGGGAGTTGATCCATTTCGCTGTCACTAAGGGAAGATTGAATCGGGGCAA
ACTTGTTCCA
Found at i:2000041 original size:2 final size:2
Alignment explanation
Indices: 2000034--2000059 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2000024 AGTAGTTTTA
2000034 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
2000060 TATGTTCATT
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:2000233 original size:2 final size:2
Alignment explanation
Indices: 2000226--2000280 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
2000216 GAAATAAAAT
2000226 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2000268 TA TA TG TA TA TA T
1 TA TA TA TA TA TA T
2000281 CCTTAAAATT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2007464 original size:20 final size:20
Alignment explanation
Indices: 2007439--2007499 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
2007429 TTTTGGTGCA
*
2007439 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
* *
2007459 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATACCCCC-AT
*
2007480 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATACCCCC
2007500 CACATGGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 16 0.46
21 2 0.06
22 1 0.03
23 16 0.46
ACGTcount: A:0.25, C:0.33, G:0.26, T:0.16
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:2009532 original size:17 final size:17
Alignment explanation
Indices: 2009499--2009532 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2009489 TTGAATATTT
* *
2009499 TGGATTGTTTGATTTTG
1 TGGATTGTTAGACTTTG
2009516 TGGATTGTTAGACTTTG
1 TGGATTGTTAGACTTTG
2009533 GATTTGTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.03, G:0.29, T:0.53
Consensus pattern (17 bp):
TGGATTGTTAGACTTTG
Found at i:2016172 original size:27 final size:27
Alignment explanation
Indices: 2016134--2016186 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
2016124 TTCCTTAAGA
* *
2016134 TATTCAGTGATGATTCTGAAGATGATT
1 TATTCAGTGATGAGTCCGAAGATGATT
*
2016161 TATTCATTGATGAGTCCGAAGATGAT
1 TATTCAGTGATGAGTCCGAAGATGAT
2016187 CTATGGATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.38
Consensus pattern (27 bp):
TATTCAGTGATGAGTCCGAAGATGATT
Found at i:2016594 original size:24 final size:24
Alignment explanation
Indices: 2016567--2016613 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
2016557 TTCGATCTGA
*
2016567 ATTCTATTCTGATACCTGACCTGG
1 ATTCTATTATGATACCTGACCTGG
* **
2016591 ATTCTGTTATGATATTTGACCTG
1 ATTCTATTATGATACCTGACCTG
2016614 AATTATTTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.43
Consensus pattern (24 bp):
ATTCTATTATGATACCTGACCTGG
Found at i:2020164 original size:27 final size:27
Alignment explanation
Indices: 2020131--2020191 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
2020121 GTTTCCTTAA
*
2020131 GATCTATTCAGTGATGATTCTGAAGAT
1 GATCTATTCAGTGATGAGTCTGAAGAT
2020158 GATCTATTCAGTGATGAGTCTGAAGAT
1 GATCTATTCAGTGATGAGTCTGAAGAT
2020185 GATCTAT
1 GATCTAT
2020192 GGATAAGAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.36
Consensus pattern (27 bp):
GATCTATTCAGTGATGAGTCTGAAGAT
Found at i:2020554 original size:12 final size:12
Alignment explanation
Indices: 2020537--2020578 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
2020527 GAATGTTTTA
2020537 TCTGATTTCTGT
1 TCTGATTTCTGT
*
2020549 TCTGATTTCTGA
1 TCTGATTTCTGT
* *
2020561 TCTGAATTCTAT
1 TCTGATTTCTGT
2020573 TCTGAT
1 TCTGAT
2020579 ACCTGACCTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.17, C:0.17, G:0.14, T:0.52
Consensus pattern (12 bp):
TCTGATTTCTGT
Found at i:2020570 original size:24 final size:24
Alignment explanation
Indices: 2020536--2020633 Score: 92
Period size: 24 Copynumber: 4.1 Consensus size: 24
2020526 TGAATGTTTT
*
2020536 ATCTGATTTCTGTTCTGATTTCTG
1 ATCTGAATTCTGTTCTGATTTCTG
* **
2020560 ATCTGAATTCTATTCTGATACCTG
1 ATCTGAATTCTGTTCTGATTTCTG
*
2020584 ACCTTG-ATTCTGTTCTGATATT-TG
1 ATC-TGAATTCTGTTCTGAT-TTCTG
* * *
2020608 ACCTGAATTATGTTTTGATTTCTG
1 ATCTGAATTCTGTTCTGATTTCTG
2020632 AT
1 AT
2020634 ATCTCCGTTT
Statistics
Matches: 59, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
23 4 0.07
24 53 0.90
25 2 0.03
ACGTcount: A:0.19, C:0.16, G:0.15, T:0.49
Consensus pattern (24 bp):
ATCTGAATTCTGTTCTGATTTCTG
Found at i:2026282 original size:9 final size:9
Alignment explanation
Indices: 2026270--2026335 Score: 57
Period size: 9 Copynumber: 7.2 Consensus size: 9
2026260 ATCATTATTA
2026270 TTTATATAT
1 TTTATATAT
2026279 TTTATTACTAT
1 TTTA-TA-TAT
*
2026290 TATTATATGT
1 T-TTATATAT
*
2026300 TTTATATAGA
1 TTTATATA-T
2026310 TTTAT-TA-
1 TTTATATAT
2026317 -TTATATAT
1 TTTATATAT
2026325 TTTATATAT
1 TTTATATAT
2026334 TT
1 TT
2026336 CATTTTATCT
Statistics
Matches: 47, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
6 4 0.09
7 2 0.04
9 22 0.47
10 10 0.21
11 6 0.13
12 3 0.06
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.64
Consensus pattern (9 bp):
TTTATATAT
Found at i:2026330 original size:25 final size:23
Alignment explanation
Indices: 2026254--2026332 Score: 81
Period size: 25 Copynumber: 3.3 Consensus size: 23
2026244 TTCTTTTGAC
*
2026254 TTTATTATCATTATTATTTATATAT
1 TTTA-TATAATTATTA-TTATATAT
* *
2026279 TTTAT-T-ACTATTATTATATGT
1 TTTATATAATTATTATTATATAT
2026300 TTTATATAGATTTATTATTATATAT
1 TTTATATA-A-TTATTATTATATAT
2026325 TTTATATA
1 TTTATATA
2026333 TTTCATTTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
21 12 0.26
22 7 0.15
23 1 0.02
24 2 0.04
25 24 0.52
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (23 bp):
TTTATATAATTATTATTATATAT
Found at i:2030633 original size:95 final size:94
Alignment explanation
Indices: 2030455--2030634 Score: 256
Period size: 95 Copynumber: 1.9 Consensus size: 94
2030445 TATAATATTA
*
2030455 TATATATACAATAAAGCTTGAGTTATCCCTCTAGAGCAATTGGTTAAACGCACCGACTTTATGGA
1 TATATATACAATAAAGCTTGAGCTATCCCTCTAGAGCAATTGGTTAAACGCACCGACTTTATGGA
* *
2030520 TAATATTTAGCTAGCCTGATAAAGGTGAT
66 TAATATTCAGCTAACCTGATAAAGGTGAT
* * *
2030549 TATACTATACAATAAAGCTTGAGCTGTCCCTCTA-AGGCAATTGGTTAAACGCTCCGGCTTTATG
1 TATA-TATACAATAAAGCTTGAGCTATCCCTCTAGA-GCAATTGGTTAAACGCACCGACTTTATG
*
2030613 GATAAGT-TTCATCTAACCTGAT
64 GATAA-TATTCAGCTAACCTGAT
2030635 TAAGCTATTT
Statistics
Matches: 76, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
94 5 0.07
95 70 0.92
96 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (94 bp):
TATATATACAATAAAGCTTGAGCTATCCCTCTAGAGCAATTGGTTAAACGCACCGACTTTATGGA
TAATATTCAGCTAACCTGATAAAGGTGAT
Found at i:2032047 original size:36 final size:36
Alignment explanation
Indices: 2031987--2032345 Score: 326
Period size: 36 Copynumber: 10.1 Consensus size: 36
2031977 CTGTGAATTC
* *
2031987 GTTTTCCTTGAAACAAAGTGTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACA
* * *
2032024 GTTTCTCTTAAAACATATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
*
2032060 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * *
2032096 GTTTCCCTTTAATCAAATTTGGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * * *
2032132 GTTTCCCTTTAATCAAATTTGGTCTCTCTTGAGTCA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * *
2032168 GTTTCCCTTGAAACAAA------ATC-ATTGA-ATA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
** * * *
2032196 TGTTTTTCTTTAAACAAATTTCGCCTCTC-T--GACA
1 -GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
** * * *
2032230 GTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATA
1 GTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACA
* *
2032267 ATTTCCCTTAAAACAAAGTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACA
* *
2032304 ATTTCCCTTAAAACAAAGTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACA
2032341 GTTTC
1 GTTTC
2032346 TCTTAAAGCA
Statistics
Matches: 268, Mismatches: 40, Indels: 28
0.80 0.12 0.08
Matches are distributed among these distances:
28 1 0.00
29 18 0.07
30 2 0.01
33 10 0.04
34 13 0.05
35 4 0.01
36 136 0.51
37 84 0.31
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.42
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:2032287 original size:37 final size:37
Alignment explanation
Indices: 2032245--2032352 Score: 189
Period size: 37 Copynumber: 2.9 Consensus size: 37
2032235 TTTTGGAACT
*
2032245 AAGTTTTGTCTCTCTTGAGATAATTTCCCTTAAAACA
1 AAGTTTTGTCTCTCTTGAGACAATTTCCCTTAAAACA
2032282 AAGTTTTGTCTCTCTTGAGACAATTTCCCTTAAAACA
1 AAGTTTTGTCTCTCTTGAGACAATTTCCCTTAAAACA
* *
2032319 AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTAAA
1 AAGTTTTGTCTCTCTTGAGACAATTTCCCTTAAA
2032353 GCACCAATCT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (37 bp):
AAGTTTTGTCTCTCTTGAGACAATTTCCCTTAAAACA
Found at i:2032375 original size:30 final size:29
Alignment explanation
Indices: 2032341--2032425 Score: 80
Period size: 31 Copynumber: 2.8 Consensus size: 29
2032331 TCTTGAGACA
* *
2032341 GTTTCTCTTAAAGCACCAATCTTTGAAATT
1 GTTTCTCTTAAA-CACCAACCTTTGAAAAT
* **
2032371 GTTTCTCATGAAACATAAAACCTTTGAAAAT
1 GTTTCTC-TTAAACA-CCAACCTTTGAAAAT
2032402 GTTTCTCTTAAAACACCAAACCTT
1 GTTTCTCTT-AAACACC-AACCTT
2032426 CGAGTTCAGT
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
30 10 0.23
31 33 0.77
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.35
Consensus pattern (29 bp):
GTTTCTCTTAAACACCAACCTTTGAAAAT
Found at i:2032416 original size:31 final size:31
Alignment explanation
Indices: 2032361--2032425 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
2032351 AAGCACCAAT
* * *
2032361 CTTTGAAATTGTTTCTCATGAAACATAAAAC
1 CTTTGAAAATGTTTCTCATAAAACACAAAAC
* *
2032392 CTTTGAAAATGTTTCTCTTAAAACACCAAAC
1 CTTTGAAAATGTTTCTCATAAAACACAAAAC
2032423 CTT
1 CTT
2032426 CGAGTTCAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.37, C:0.20, G:0.08, T:0.35
Consensus pattern (31 bp):
CTTTGAAAATGTTTCTCATAAAACACAAAAC
Found at i:2034126 original size:9 final size:9
Alignment explanation
Indices: 2034114--2034179 Score: 66
Period size: 9 Copynumber: 7.2 Consensus size: 9
2034104 ATCATTATTA
2034114 TTTATATAT
1 TTTATATAT
2034123 TTTATTACTAT
1 TTTA-TA-TAT
*
2034134 TATTATATGT
1 T-TTATATAT
2034144 TTTATATAT
1 TTTATATAT
2034153 ATTTAT-TA-
1 -TTTATATAT
2034161 -TTATATAT
1 TTTATATAT
2034169 TTTATATAT
1 TTTATATAT
2034178 TT
1 TT
2034180 CATTTTATCT
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
6 4 0.08
7 2 0.04
9 23 0.48
10 10 0.21
11 6 0.12
12 3 0.06
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTATATAT
Found at i:2034126 original size:25 final size:24
Alignment explanation
Indices: 2034098--2034173 Score: 88
Period size: 25 Copynumber: 3.2 Consensus size: 24
2034088 TTCTTTTGAC
2034098 TTTATTATCATTATTATTTATATAT
1 TTTATTATCATTATTA-TTATATAT
*
2034123 TTTATTA-C--TATTATTATATGT
1 TTTATTATCATTATTATTATATAT
2034144 TTTATATAT-ATTTATTATTATATAT
1 TTTAT-TATCA-TTATTATTATATAT
2034169 TTTAT
1 TTTAT
2034174 ATATTTCATT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
21 12 0.27
22 7 0.16
24 1 0.02
25 24 0.55
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (24 bp):
TTTATTATCATTATTATTATATAT
Found at i:2039917 original size:36 final size:36
Alignment explanation
Indices: 2039827--2039918 Score: 130
Period size: 36 Copynumber: 2.5 Consensus size: 36
2039817 TAATTTACTC
*
2039827 AAAACAATGTTTTGTCTCTCCTGAGACAGTTTCTCTT
1 AAAACAA-ATTTTGTCTCTCCTGAGACAGTTTCTCTT
* *
2039864 AAAACAAATTTGGTCTCTCCTGAGACATTTTCTCTT
1 AAAACAAATTTTGTCTCTCCTGAGACAGTTTCTCTT
* *
2039900 CAAACAAATTTTATCTCTC
1 AAAACAAATTTTGTCTCTC
2039919 TTGAAACAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
36 42 0.86
37 7 0.14
ACGTcount: A:0.28, C:0.23, G:0.10, T:0.39
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCTCCTGAGACAGTTTCTCTT
Found at i:2039942 original size:21 final size:21
Alignment explanation
Indices: 2039894--2039943 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
2039884 TGAGACATTT
*
2039894 TCTCTTCAAACAAATTTTATC
1 TCTCTTGAAACAAATTTTATC
*
2039915 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTATC
2039936 TCTCTTGA
1 TCTCTTGA
2039944 GACAGTTTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.28, C:0.22, G:0.06, T:0.44
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTTATC
Found at i:2039978 original size:57 final size:57
Alignment explanation
Indices: 2039858--2039979 Score: 163
Period size: 57 Copynumber: 2.1 Consensus size: 57
2039848 TGAGACAGTT
* * * *
2039858 TCTCTTAAAACAAATTTGGTCTCTCCTGAGACATTTTCTCTTCAAACAAATTTTATC
1 TCTCTTGAAACAAATTTGGTCTCTCCTGAGACAGTTTCCCTTCAAACAAATTTGATC
* * * * *
2039915 TCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTTAATCAAATTTGGTC
1 TCTCTTGAAACAAATTTGGTCTCTCCTGAGACAGTTTCCCTTCAAACAAATTTGATC
2039972 TCTCTTGA
1 TCTCTTGA
2039980 GACAGTTTCC
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.42
Consensus pattern (57 bp):
TCTCTTGAAACAAATTTGGTCTCTCCTGAGACAGTTTCCCTTCAAACAAATTTGATC
Found at i:2040097 original size:102 final size:99
Alignment explanation
Indices: 2039836--2040204 Score: 394
Period size: 102 Copynumber: 3.7 Consensus size: 99
2039826 CAAAACAATG
* * * * * * *
2039836 TTTTGTCTCTCCTGAGACAGTTTCTCTTAAAACAAATTTGGTCTCTCCTGAGACATTTTCTCTTC
1 TTTTGTCTCTCTTGAGACAGTTTCT-TTTAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* *
2039901 AAAC-AAATT-T-TA-TC--TCTC-TTGAAACAAA
65 AAACAAAATTGTGAATTCGTTTTCATTGAAACAAA
* * *
2039929 TTTTGTCTCTCTTGAGACAGTTTCCCTTTAATCAAATTTGGTCTCTCTTGAGACAGTTTCCCTTG
1 TTTTGTCTCTCTTGAGACAGTTT-CTTTTAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * *
2039994 AAACAAAATCTTTGAATGT-GTTTTTATTTAAACAAA
65 AAACAAAAT-TGTGAAT-TCGTTTTCATTGAAACAAA
** * *
2040030 TTTTGTCTCTCTCAAGACAGTTTCTTTTGGAACCAAATTTTGTCTCTCTTGAGACGGTTTCCCTT
1 TTTTGTCTCTCTTGAGACAGTTTCTTTT--AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTT
*
2040095 GAAACAAAAATTGTGAATTCGTTTTCCTTGAAACAAA
64 GAAAC-AAAATTGTGAATTCGTTTTCATTGAAACAAA
* * *
2040132 GTTTTGTCTCTCTTGAGACAGTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGATAGTTTCTCTT
1 -TTTTGTCTCTCTTGAGACAGTTTCT-TTTAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTT
2040197 GAAACAAA
64 GAAACAAA
2040205 TTTTGTCTCT
Statistics
Matches: 231, Mismatches: 29, Indels: 24
0.81 0.10 0.08
Matches are distributed among these distances:
93 59 0.26
94 5 0.02
95 1 0.00
96 1 0.00
97 1 0.00
99 1 0.00
100 6 0.03
101 34 0.15
102 93 0.40
103 28 0.12
104 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.41
Consensus pattern (99 bp):
TTTTGTCTCTCTTGAGACAGTTTCTTTTAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA
AACAAAATTGTGAATTCGTTTTCATTGAAACAAA
Found at i:2040196 original size:36 final size:36
Alignment explanation
Indices: 2040023--2040102 Score: 97
Period size: 37 Copynumber: 2.2 Consensus size: 36
2040013 GTTTTTATTT
** *
2040023 AAACAAATTTTGTCTCTCTCAAGACAGTTTCTTTTGG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT-G
* * *
2040060 AACCAAATTTTGTCTCTCTTGAGACGGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
2040096 AAACAAA
1 AAACAAA
2040103 AATTGTGAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
36 7 0.19
37 29 0.81
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
Found at i:2040241 original size:36 final size:36
Alignment explanation
Indices: 2040115--2040403 Score: 265
Period size: 36 Copynumber: 8.1 Consensus size: 36
2040105 TTGTGAATTC
* *
2040115 GTTTTCCTTGAAACAAAGTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTTAAACAAA-TTTTGTCTCTCTTGAGACA
* * *
2040152 GTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGATA
1 GTTTCCCTTTAAACAAATTTTGTCTCTCTTGAGACA
* *
2040188 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTTAAACAAATTTTGTCTCTCTTGAGACA
* *
2040224 GTTTCCCTTTAATCAAATTTGGTCTCTCTTGAGACA
1 GTTTCCCTTTAAACAAATTTTGTCTCTCTTGAGACA
* * **
2040260 GTTTCCCTTGAAACAAA------ATCT-TTGA-ATTT
1 GTTTCCCTTTAAACAAATTTTGTCTCTCTTGAGA-CA
** * *
2040289 GTTTTTCTTTAAACAAATTTCGTCTCTCTCT-AGAAA
1 GTTTCCCTTTAAACAAATTTTGTCTCTCT-TGAGACA
* * *
2040325 GTTT-CTTTTGGAACTAAGTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTT-AAAC-AAATTTTGTCTCTCTTGAGACA
*
2040362 GTTTCCCTTAAAACAAAGTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTTAAACAAA-TTTTGTCTCTCTTGAGACA
2040399 GTTTC
1 GTTTC
2040404 TCTTAAAGCA
Statistics
Matches: 206, Mismatches: 31, Indels: 30
0.77 0.12 0.11
Matches are distributed among these distances:
28 1 0.00
29 18 0.09
30 3 0.01
35 6 0.03
36 111 0.54
37 64 0.31
38 3 0.01
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.43
Consensus pattern (36 bp):
GTTTCCCTTTAAACAAATTTTGTCTCTCTTGAGACA
Found at i:2040255 original size:174 final size:175
Alignment explanation
Indices: 2040023--2040403 Score: 511
Period size: 174 Copynumber: 2.2 Consensus size: 175
2040013 GTTTTTATTT
** * * *
2040023 AAACAAATTTTGTCTCTCTCAAGACAGTTT-CTTTTGGAACCAAATTTTGTCTCTCTTGAGACGG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTT-GAACCAAATTTGGTCTCTCTTGAGACAG
*
2040087 TTTCCCTTGAAACAAAAAT-TGTGAATTCGTTTTCCTTGAAACAAAGTTTTGTCTCTCT-TGAGA
65 TTTCCCTTGAAAC-AAAATCTGTGAATTCGTTTTCCTTGAAACAAA-TTTCGTCTCTCTCT-AGA
* * * *
2040150 CAGTTTCTCTTAAAAC-AAATTTTGTCTCTCTTGAGATAGTTTCTCTTG
127 AAGTTTCTCTTAAAACTAAATTTTGTCTCTCTTGAGACAGTTTCCCTTA
*
2040198 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTT-AATCAAATTTGGTCTCTCTTGAGACAGT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTTGAACCAAATTTGGTCTCTCTTGAGACAGT
* * * *
2040262 TTCCCTTGAAACAAAATCTTTGAATTTGTTTTTCTTTAAACAAATTTCGTCTCTCTCTAGAAAGT
66 TTCCCTTGAAACAAAATCTGTGAATTCGTTTTCCTTGAAACAAATTTCGTCTCTCTCTAGAAAGT
* ** *
2040327 TTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTA
131 TTCTCTTAAAACTAAATTTTGTCTCTCTTGAGACAGTTTCCCTTA
2040372 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTC
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTC
2040404 TCTTAAAGCA
Statistics
Matches: 182, Mismatches: 19, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
173 31 0.17
174 95 0.52
175 52 0.29
176 4 0.02
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (175 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTTGAACCAAATTTGGTCTCTCTTGAGACAGT
TTCCCTTGAAACAAAATCTGTGAATTCGTTTTCCTTGAAACAAATTTCGTCTCTCTCTAGAAAGT
TTCTCTTAAAACTAAATTTTGTCTCTCTTGAGACAGTTTCCCTTA
Found at i:2040270 original size:72 final size:72
Alignment explanation
Indices: 2040115--2040403 Score: 299
Period size: 72 Copynumber: 4.1 Consensus size: 72
2040105 TTGTGAATTC
* *
2040115 GTTTTCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTAAAACAAATTTTGTCTCTC
1 GTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAATTTTGTCTCTC
*
2040180 TTGAGATA
65 TTGAGACA
* * * *
2040188 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTTAATCAAATTTGGTCTCTCT
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAATTTTGTCTCTCT
2040253 TGAGACA
66 TGAGACA
* ** ** * *
2040260 GTTTCCCTTGAAACAAA------ATCT-TTGA-ATTTGTTTTTCTTTAAACAAATTTCGTCTCTC
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGA-CAGTTTCCCTTAAAACAAATTTTGTCTCTC
*
2040317 TCT-AGAAA
65 T-TGAGACA
** * *
2040325 GTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAAGTTTTGTCTCT
1 GTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAA-TTTTGTCTCT
2040390 CTTGAGACA
64 CTTGAGACA
2040399 GTTTC
1 GTTTC
2040404 TCTTAAAGCA
Statistics
Matches: 175, Mismatches: 28, Indels: 25
0.77 0.12 0.11
Matches are distributed among these distances:
64 1 0.01
65 44 0.25
66 6 0.03
72 69 0.39
73 34 0.19
74 21 0.12
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.43
Consensus pattern (72 bp):
GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAATTTTGTCTCTCT
TGAGACA
Found at i:2040353 original size:37 final size:37
Alignment explanation
Indices: 2040289--2040410 Score: 140
Period size: 37 Copynumber: 3.3 Consensus size: 37
2040279 CTTTGAATTT
* * * *
2040289 GTTTTTCTTTAAACAAA-TTTCGTCTCTCTCT-AGAAA
1 GTTTCTCTTAAAACAAAGTTTTGTCTCTCT-TGAGACA
* ** *
2040325 GTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACA
1 GTTTCTCTTAAAACAAAGTTTTGTCTCTCTTGAGACA
*
2040362 GTTTCCCTTAAAACAAAGTTTTGTCTCTCTTGAGACA
1 GTTTCTCTTAAAACAAAGTTTTGTCTCTCTTGAGACA
2040399 GTTTCTCTTAAA
1 GTTTCTCTTAAA
2040411 GCACCAATCT
Statistics
Matches: 71, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
36 13 0.18
37 58 0.82
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.43
Consensus pattern (37 bp):
GTTTCTCTTAAAACAAAGTTTTGTCTCTCTTGAGACA
Found at i:2040457 original size:31 final size:31
Alignment explanation
Indices: 2040399--2040483 Score: 109
Period size: 31 Copynumber: 2.8 Consensus size: 31
2040389 TCTTGAGACA
* * * *
2040399 GTTTCTCTTAAAGCAC-CAATCTTTGAAATT
1 GTTTCTCTTAAAACACAAAACCTTTGAAAAT
*
2040429 GTTTCTCTTGAAACACAAAACCTTTGAAAAT
1 GTTTCTCTTAAAACACAAAACCTTTGAAAAT
*
2040460 GTTTCTCTTAAAACACCAAACCTT
1 GTTTCTCTTAAAACACAAAACCTT
2040484 CGAGTTTAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 14 0.30
31 33 0.70
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.35
Consensus pattern (31 bp):
GTTTCTCTTAAAACACAAAACCTTTGAAAAT
Found at i:2042062 original size:25 final size:23
Alignment explanation
Indices: 2042019--2042071 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 23
2042009 TACTTTTCTA
2042019 TTTTTATTTTTATTATACTATTAT
1 TTTTTATTTTTATTATACTA-TAT
*
2042043 TATTTTATTTCTT-TTTTACTATAT
1 T-TTTTATTT-TTATTATACTATAT
2042067 TTTTT
1 TTTTT
2042072 CATTATTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
23 4 0.15
24 5 0.19
25 15 0.58
26 2 0.08
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (23 bp):
TTTTTATTTTTATTATACTATAT
Found at i:2042115 original size:25 final size:24
Alignment explanation
Indices: 2042087--2042159 Score: 82
Period size: 25 Copynumber: 3.1 Consensus size: 24
2042077 TTCTTTTGAC
2042087 TTTATTATCATTATTATTTATATAT
1 TTTATTATCATTATTA-TTATATAT
*
2042112 TTTATTA-C--TATTATTATATGT
1 TTTATTATCATTATTATTATATAT
2042133 TTTATATAT-ATTTATTATTATATAT
1 TTTAT-TATCA-TTATTATTATATAT
2042158 TT
1 TT
2042160 CATTTTATCT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
21 12 0.29
22 7 0.17
24 1 0.02
25 21 0.51
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (24 bp):
TTTATTATCATTATTATTATATAT
Found at i:2042167 original size:14 final size:14
Alignment explanation
Indices: 2042091--2042159 Score: 51
Period size: 14 Copynumber: 5.1 Consensus size: 14
2042081 TTTGACTTTA
*
2042091 TTATCATTAT-TAT
1 TTATTATTATATAT
2042104 TTATATATT-T-TAT
1 TTAT-TATTATATAT
*
2042117 TACTATTATTATAT-G
1 T--TATTATTATATAT
2042132 TT-TTA-TATATAT
1 TTATTATTATATAT
2042144 TTATTATTATATAT
1 TTATTATTATATAT
2042158 TT
1 TT
2042160 CATTTTATCT
Statistics
Matches: 45, Mismatches: 3, Indels: 15
0.71 0.05 0.24
Matches are distributed among these distances:
11 5 0.11
12 5 0.11
13 13 0.29
14 16 0.36
15 5 0.11
16 1 0.02
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (14 bp):
TTATTATTATATAT
Found at i:2044077 original size:42 final size:37
Alignment explanation
Indices: 2044032--2044113 Score: 128
Period size: 37 Copynumber: 2.2 Consensus size: 37
2044022 TATTTTCTAG
* *
2044032 TCGAGTCGAATTTATGAAATTACAGCTCAAAATCAAT
1 TCGAGTCGAGTTTATGAAATTACAACTCAAAATCAAT
*
2044069 TCGAGTCGAGTTTATGAAATTACAACTCAAAGTCAAT
1 TCGAGTCGAGTTTATGAAATTACAACTCAAAATCAAT
*
2044106 TTGAGTCG
1 TCGAGTCG
2044114 TATTATTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (37 bp):
TCGAGTCGAGTTTATGAAATTACAACTCAAAATCAAT
Found at i:2045297 original size:15 final size:15
Alignment explanation
Indices: 2045277--2045318 Score: 84
Period size: 15 Copynumber: 2.8 Consensus size: 15
2045267 ACTTCTGTGT
2045277 TGAATCATTCAGCAC
1 TGAATCATTCAGCAC
2045292 TGAATCATTCAGCAC
1 TGAATCATTCAGCAC
2045307 TGAATCATTCAG
1 TGAATCATTCAG
2045319 AAGTGCGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (15 bp):
TGAATCATTCAGCAC
Found at i:2045400 original size:196 final size:196
Alignment explanation
Indices: 2044985--2045544 Score: 769
Period size: 196 Copynumber: 2.8 Consensus size: 196
2044975 TAAAGCGATG
* * * *
2044985 AATGATTCATAAGCTCTGTATGAATTAGCTCTGAATGTGACATGCTGTTTGATAATGGCTCTGAA
1 AATGATTCAGAGGCTCTGTATGAATTAGCTCTGAATGTGACATGCTGTTTGATAATGACTTTGAA
*
2045050 TCATTCAGAATGTACTTCTGTGTTGAATCATTCAGCACTATTTTGTTGAATCAGTCAGCACTTAA
66 TCATTCAGAATGTACTTCTGTGTTGAATCATTCAGCAC--------TGAATCAGTCAGCACTGAA
* * *
2045115 TCATTTAGAAGTGCGAAACAAACGCGCTGAATGTTGAACGGTTCAGCATTCAGCGCTGAATGGTT
123 TCATTCAGAAGTGCGAAACAAACGCGCTGAATGTTCAACGGTTCAACATTCAGCGCTGAATGGTT
2045180 CAAATGCTA
188 CAAATGCTA
* * * * *
2045189 AATGATTCGGAGGCTCTGTATGAATTAGCTATGAATGTGACATACTATTTGATAATGACTTTAAA
1 AATGATTCAGAGGCTCTGTATGAATTAGCTCTGAATGTGACATGCTGTTTGATAATGACTTTGAA
*
2045254 TCATTCAGAATGTACTTCTGTGTTGAATCATTCAGCACTGAATCATTCAGCACTGAATCATTCAG
66 TCATTCAGAATGTACTTCTGTGTTGAATCATTCAGCACTGAATCAGTCAGCACTGAATCATTCAG
*
2045319 AAGTGCGAAACAAACGCGCTGAATGTTCAATGGTTCAACATTCAGCGCTGAATGGTTCAAATGCT
131 AAGTGCGAAACAAACGCGCTGAATGTTCAACGGTTCAACATTCAGCGCTGAATGGTTCAAATGCT
*
2045384 T
196 A
*
2045385 AATGATTCAGAGGCTCTGTATGAATTAGCTCTGAATGTGACATGCTGTTTGATAATGTCTTTGAA
1 AATGATTCAGAGGCTCTGTATGAATTAGCTCTGAATGTGACATGCTGTTTGATAATGACTTTGAA
* * * *
2045450 TCATTCAGAATGTACTTCTGTGCTAAATCATTCAACACTGTTTTGCTGAATCAGTCAGCATTGAA
66 TCATTCAGAATGTACTTCTGTGTTGAATCATTCAGCA--------CTGAATCAGTCAGCACTGAA
* *
2045515 TAATTCAGAAGTGCGAAACAAACGCACTGA
123 TCATTCAGAAGTGCGAAACAAACGCGCTGA
2045545 TGGTTCCATT
Statistics
Matches: 319, Mismatches: 29, Indels: 16
0.88 0.08 0.04
Matches are distributed among these distances:
196 179 0.56
204 140 0.44
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (196 bp):
AATGATTCAGAGGCTCTGTATGAATTAGCTCTGAATGTGACATGCTGTTTGATAATGACTTTGAA
TCATTCAGAATGTACTTCTGTGTTGAATCATTCAGCACTGAATCAGTCAGCACTGAATCATTCAG
AAGTGCGAAACAAACGCGCTGAATGTTCAACGGTTCAACATTCAGCGCTGAATGGTTCAAATGCT
A
Found at i:2049527 original size:34 final size:34
Alignment explanation
Indices: 2049488--2049572 Score: 161
Period size: 34 Copynumber: 2.5 Consensus size: 34
2049478 ATTATATATA
2049488 TATATATATAATATTTTATATTTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
2049522 TATATATATAATATTTTATATTTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
*
2049556 TATATATAAAATATTTT
1 TATATATATAATATTTT
2049573 CGGGTTCGGG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (34 bp):
TATATATATAATATTTTATATTTTTTATATTAAT
Found at i:2049595 original size:20 final size:20
Alignment explanation
Indices: 2049565--2049602 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2049555 TTATATATAA
2049565 AATATTTTCGGGTTCGGGTAT
1 AATATTTTCGGGTT-GGGTAT
2049586 AATA-TTTCGGGTTGGGT
1 AATATTTTCGGGTTGGGT
2049603 TCGGGGACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 9 0.53
21 4 0.24
ACGTcount: A:0.18, C:0.08, G:0.32, T:0.42
Consensus pattern (20 bp):
AATATTTTCGGGTTGGGTAT
Found at i:2050719 original size:20 final size:20
Alignment explanation
Indices: 2050696--2050829 Score: 178
Period size: 20 Copynumber: 6.7 Consensus size: 20
2050686 GAATATGTAA
* * *
2050696 ATCGCAATGCGAGTATGACT
1 ATCGCAACGCGATTCTGACT
2050716 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* * *
2050736 GTCGTAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
2050756 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
2050776 GTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
2050796 GTCGCAACGCGATGCTGACT
1 ATCGCAACGCGATTCTGACT
*
2050816 ATCGCAATGCGATT
1 ATCGCAACGCGATT
2050830 TTCAAAGCGC
Statistics
Matches: 100, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 100 1.00
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:2050789 original size:60 final size:60
Alignment explanation
Indices: 2050696--2050829 Score: 205
Period size: 60 Copynumber: 2.2 Consensus size: 60
2050686 GAATATGTAA
* * *
2050696 ATCGCAATGCGAGTATGACTATCGCAACGCGATTCTGACTGTCGTAACGAGATTCTGACT
1 ATCGCAATGCGATTATGACTATCGCAACGCGATTCTGACTGTCGCAACGAGATGCTGACT
* * * *
2050756 ATCGCAACGCGATTCTGACTGTCGCAACGCGATTCTGACTGTCGCAACGCGATGCTGACT
1 ATCGCAATGCGATTATGACTATCGCAACGCGATTCTGACTGTCGCAACGAGATGCTGACT
2050816 ATCGCAATGCGATT
1 ATCGCAATGCGATT
2050830 TTCAAAGCGC
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 66 1.00
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (60 bp):
ATCGCAATGCGATTATGACTATCGCAACGCGATTCTGACTGTCGCAACGAGATGCTGACT
Found at i:2051042 original size:22 final size:22
Alignment explanation
Indices: 2051003--2051045 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2050993 GGTGACATTC
*
2051003 GTCCCCATCTCTGACGAAATCA
1 GTCCCCATCTCAGACGAAATCA
2051025 GTCCCCATCTCCAG-CGAAATC
1 GTCCCCATCT-CAGACGAAATC
2051046 CGTCTATCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.26, C:0.40, G:0.14, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCAGACGAAATCA
Found at i:2051459 original size:19 final size:20
Alignment explanation
Indices: 2051435--2051545 Score: 109
Period size: 20 Copynumber: 5.7 Consensus size: 20
2051425 ATCACAATGT
2051435 GATTTT-AGTTTCGCGTTGC
1 GATTTTCAGTTTCGCGTTGC
2051454 GATTTTCA-TTTCGCGTTGC
1 GATTTTCAGTTTCGCGTTGC
** **
2051473 GATAGTCAAATTCGCGTTGC
1 GATTTTCAGTTTCGCGTTGC
** * *
2051493 GATAGTCATTTTCGTGTTGC
1 GATTTTCAGTTTCGCGTTGC
* *
2051513 GATTTTCATTTTCGTGTTGC
1 GATTTTCAGTTTCGCGTTGC
*
2051533 GATTTTAAGTTTC
1 GATTTTCAGTTTC
2051546 AGAAACTATT
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
19 23 0.29
20 57 0.71
ACGTcount: A:0.15, C:0.16, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTCAGTTTCGCGTTGC
Found at i:2051536 original size:20 final size:20
Alignment explanation
Indices: 2051443--2051538 Score: 113
Period size: 20 Copynumber: 4.8 Consensus size: 20
2051433 GTGATTTTAG
2051443 TTTCGCGTTGCGATTTTCA-
1 TTTCGCGTTGCGATTTTCAT
** *
2051462 TTTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATTTTCAT
* **
2051482 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATTTTCAT
*
2051502 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
*
2051522 TTTCGTGTTGCGATTTT
1 TTTCGCGTTGCGATTTT
2051539 AAGTTTCAGA
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
19 17 0.25
20 51 0.75
ACGTcount: A:0.14, C:0.18, G:0.23, T:0.46
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTCAT
Found at i:2053290 original size:18 final size:18
Alignment explanation
Indices: 2053267--2053316 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
2053257 TTTACTCGTA
2053267 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
2053285 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
2053303 ATTTCACTTAGATT
1 ATTTCACTTAGATT
2053317 GCTTAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:2053489 original size:20 final size:20
Alignment explanation
Indices: 2053464--2053511 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
2053454 TAGTTTACTT
2053464 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
**
2053484 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
2053504 TCGCAACG
1 TCGCAACG
2053512 AAAGAATCGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.33, C:0.27, G:0.21, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:2053583 original size:20 final size:20
Alignment explanation
Indices: 2053554--2053609 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
2053544 GCGATTCTCT
* *
2053554 CGTTGAGATAGTCATTTTTG
1 CGTTGCGATAGTCATTTTCG
2053574 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
2053594 CGTTGCGATAGTCATT
1 CGTTGCGATAGTCATT
2053610 CGTGTTACGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.18, C:0.16, G:0.25, T:0.41
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:2053620 original size:18 final size:19
Alignment explanation
Indices: 2053560--2053620 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 19
2053550 CTCTCGTTGA
* *
2053560 GATAGTCATTTTTGCGTTGC
1 GATAGTCA-TTTCGCGTTAC
*
2053580 GATAGTCATTTTCGCGTTGC
1 GATAGTCA-TTTCGCGTTAC
*
2053600 GATAGTCA-TTCGTGTTAC
1 GATAGTCATTTCGCGTTAC
2053618 GAT
1 GAT
2053621 TTTAAGTTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
18 11 0.29
20 27 0.71
ACGTcount: A:0.18, C:0.16, G:0.25, T:0.41
Consensus pattern (19 bp):
GATAGTCATTTCGCGTTAC
Found at i:2054151 original size:18 final size:19
Alignment explanation
Indices: 2054112--2054153 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
2054102 ATCACCTGTC
2054112 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
2054133 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
2054151 ATC
1 ATC
2054154 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:2054198 original size:42 final size:43
Alignment explanation
Indices: 2054135--2054216 Score: 103
Period size: 42 Copynumber: 1.9 Consensus size: 43
2054125 CCTCCCCTAT
* *
2054135 CGTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCTTCCCAC
1 CGTTCAAGAGGCCACTATCATCCCTAAAGAGGTCCCTTCCCAC
* * **
2054177 CGTTCAAGAGGTCACTGTCATCGTTAAAGAGGTCCCTTCC
1 CGTTCAAGAGGCCACTATCATCCCTAAAGAGGTCCCTTCC
2054217 AACATTCTAG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
42 24 0.73
43 9 0.27
ACGTcount: A:0.22, C:0.35, G:0.18, T:0.24
Consensus pattern (43 bp):
CGTTCAAGAGGCCACTATCATCCCTAAAGAGGTCCCTTCCCAC
Found at i:2055655 original size:14 final size:14
Alignment explanation
Indices: 2055621--2055682 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
2055611 TTGCTTGTTT
*
2055621 AATTGATTTATAAA
1 AATTGATTTGTAAA
*
2055635 AACTGATTTGTAAA
1 AATTGATTTGTAAA
* *
2055649 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
2055664 TATTGATGTGTAAA
1 AATTGATTTGTAAA
2055678 TAATT
1 -AATT
2055683 CTTATTTGTG
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
14 23 0.64
15 13 0.36
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.45
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:2055806 original size:20 final size:20
Alignment explanation
Indices: 2055781--2055833 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
2055771 AGGTACACTT
* *
2055781 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAACACAAAA
* *
2055801 TCGCAATGCGAAAGACAAAA
1 TCGCAACGCGAAACACAAAA
*
2055821 TCACAACGCGAAA
1 TCGCAACGCGAAA
2055834 GTCAATTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.47, C:0.26, G:0.15, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAACACAAAA
Found at i:2055922 original size:20 final size:20
Alignment explanation
Indices: 2055877--2056101 Score: 181
Period size: 20 Copynumber: 11.8 Consensus size: 20
2055867 GTGATTTTCT
* * *
2055877 CGTTGCGATAGTCAAATACC
1 CGTTGCGATAATCAAATTCG
* *
2055897 CATTGCGATAATTAAATTCG
1 CGTTGCGATAATCAAATTCG
* *
2055917 CGTTGCGATACTCAAATTCA
1 CGTTGCGATAATCAAATTCG
*
2055937 CGTTGCGAT--T----TTCT
1 CGTTGCGATAATCAAATTCG
* *
2055951 CGTTGCGATAGTCAAA-TAG
1 CGTTGCGATAATCAAATTCG
*
2055970 CCGTTGCGATAATCAAATTTG
1 -CGTTGCGATAATCAAATTCG
*
2055991 CATTGCGATAGA-CAAATTCG
1 CGTTGCGATA-ATCAAATTCG
*
2056011 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAATCAAATTCG
*
2056031 CGTTGCGAT--T----TTTG
1 CGTTGCGATAATCAAATTCG
*
2056045 AGTTGCGATAATCAAATTCG
1 CGTTGCGATAATCAAATTCG
*
2056065 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAATCAAATTCG
*
2056085 CGTTGCGATATTCAAAT
1 CGTTGCGATAATCAAAT
2056102 GAATGTGTAA
Statistics
Matches: 165, Mismatches: 24, Indels: 32
0.75 0.11 0.14
Matches are distributed among these distances:
14 23 0.14
16 2 0.01
18 2 0.01
19 1 0.01
20 134 0.81
21 3 0.02
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (20 bp):
CGTTGCGATAATCAAATTCG
Found at i:2055926 original size:74 final size:74
Alignment explanation
Indices: 2055837--2056019 Score: 240
Period size: 74 Copynumber: 2.5 Consensus size: 74
2055827 CGCGAAAGTC
* * * *
2055837 AATTCGCGTTGCGATAGTCTAATACGCTTTGTGATTTTCTCGTTGCGATAGTCAAATACCCATTG
1 AATTCGCGTTGCGATAGTCAAATACACGTTGCGATTTTCTCGTTGCGATAGTCAAATACCCATTG
*
2055902 CGATAATTA
66 CGATAATCA
* * * *
2055911 AATTCGCGTTGCGATACTCAAATTCACGTTGCGATTTTCTCGTTGCGATAGTCAAATAGCCGTTG
1 AATTCGCGTTGCGATAGTCAAATACACGTTGCGATTTTCTCGTTGCGATAGTCAAATACCCATTG
2055976 CGATAATCA
66 CGATAATCA
* * * * *
2055985 AATTTGCATTGCGATAGACAAATTCGCGTTGCGAT
1 AATTCGCGTTGCGATAGTCAAATACACGTTGCGAT
2056020 AGTCAAATTC
Statistics
Matches: 95, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
74 95 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (74 bp):
AATTCGCGTTGCGATAGTCAAATACACGTTGCGATTTTCTCGTTGCGATAGTCAAATACCCATTG
CGATAATCA
Found at i:2055975 original size:34 final size:34
Alignment explanation
Indices: 2055843--2055979 Score: 123
Period size: 34 Copynumber: 3.9 Consensus size: 34
2055833 AGTCAATTCG
* * * *
2055843 CGTTGCGATAGTCTAATACGCTTTGTGATTTTCT
1 CGTTGCGATAGTCAAATACACGTTGCGATTTTCT
* * *
2055877 CGTTGCGATAGTCAAATACCCATTGCGATAATTAAATTCG
1 CGTTGCGATAGTCAAATACACGTTGCG---ATT---TTCT
* *
2055917 CGTTGCGATACTCAAATTCACGTTGCGATTTTCT
1 CGTTGCGATAGTCAAATACACGTTGCGATTTTCT
2055951 CGTTGCGATAGTCAAATAGC-CGTTGCGAT
1 CGTTGCGATAGTCAAATA-CACGTTGCGAT
2055980 AATCAAATTT
Statistics
Matches: 84, Mismatches: 12, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
34 51 0.61
35 1 0.01
37 6 0.07
40 26 0.31
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.35
Consensus pattern (34 bp):
CGTTGCGATAGTCAAATACACGTTGCGATTTTCT
Found at i:2056101 original size:94 final size:94
Alignment explanation
Indices: 2055877--2056101 Score: 294
Period size: 94 Copynumber: 2.4 Consensus size: 94
2055867 GTGATTTTCT
* *
2055877 CGTTGCGATAGTCAAATACCCATTGCGATAATT-AAATTCGCGTTGCGATACTCAAATTCACGTT
1 CGTTGCGATAGTCAAATTCGCATTGCGAT-ATTCAAATTCGCGTTGCGATACTCAAATTCACGTT
* *
2055941 GCGATTTTCTCGTTGCGATAGTCAAATAGC
65 GCGATTTTCTAGTTGCGATAATCAAATAGC
* * ** * *
2055971 CGTTGCGATAATCAAATTTGCATTGCGATAGACAAATTCGCGTTGCGATAGTCAAATTCGCGTTG
1 CGTTGCGATAGTCAAATTCGCATTGCGATATTCAAATTCGCGTTGCGATACTCAAATTCACGTTG
*
2056036 CGATTTT-TGAGTTGCGATAATCAAAT-TC
66 CGATTTTCT-AGTTGCGATAATCAAATAGC
*
2056064 GCGTTGCGATAGTCAAATTCGCGTTGCGATATTCAAAT
1 -CGTTGCGATAGTCAAATTCGCATTGCGATATTCAAAT
2056102 GAATGTGTAA
Statistics
Matches: 112, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
93 3 0.03
94 109 0.97
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (94 bp):
CGTTGCGATAGTCAAATTCGCATTGCGATATTCAAATTCGCGTTGCGATACTCAAATTCACGTTG
CGATTTTCTAGTTGCGATAATCAAATAGC
Found at i:2056324 original size:140 final size:140
Alignment explanation
Indices: 2056072--2056341 Score: 504
Period size: 140 Copynumber: 1.9 Consensus size: 140
2056062 TCGCGTTGCG
*
2056072 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
* *
2056137 TAGCAATTTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTAAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
2056202 AATACACATA
131 AATACACATA
2056212 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
*
2056277 TAGCAATGTTCAAACTAAAGTTACTAATACATGCTTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTAAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
2056342 TACAACGTTT
Statistics
Matches: 126, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 126 1.00
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTAAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Done.