Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001157.1 Hibiscus syriacus cultivar Beakdansim tig00002307_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: 66716
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1686 original size:33 final size:33
Alignment explanation
Indices: 1557--1667 Score: 181
Period size: 33 Copynumber: 3.4 Consensus size: 33
1547 CACAACCCGG
* *
1557 TGCTAATCCCTATGGCCAA-CT-CACAGCCAAA
1 TGCTAATCCATATGGTCAACCTGCACAGCCAAA
1588 TGCTAATCCATATGGTCAACCTGCACAGCCAAA
1 TGCTAATCCATATGGTCAACCTGCACAGCCAAA
1621 TGCTAATCCATATGGTCAACCTGCACAGCCAAA
1 TGCTAATCCATATGGTCAACCTGCACAGCCAAA
*
1654 CGCTAATCCATATG
1 TGCTAATCCATATG
1668 CCCAAACCAT
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
31 17 0.23
32 2 0.03
33 56 0.75
ACGTcount: A:0.32, C:0.32, G:0.14, T:0.22
Consensus pattern (33 bp):
TGCTAATCCATATGGTCAACCTGCACAGCCAAA
Found at i:2433 original size:33 final size:33
Alignment explanation
Indices: 2395--2475 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
2385 CTATGGGCAT
2395 GGGAATGGGGATGAACAACATGGGCATGAATCC
1 GGGAATGGGGATGAACAACATGGGCATGAATCC
* *
2428 TGGAATGGGGATGAACAACGTGGGCATGAATCC
1 GGGAATGGGGATGAACAACATGGGCATGAATCC
*
2461 GGGAATGAGGATGAA
1 GGGAATGGGGATGAA
2476 TATGGGAATG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.33, C:0.12, G:0.38, T:0.16
Consensus pattern (33 bp):
GGGAATGGGGATGAACAACATGGGCATGAATCC
Found at i:5601 original size:15 final size:15
Alignment explanation
Indices: 5581--5613 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
5571 TATGTTGTGA
5581 GTTCTAGAATAGTTT
1 GTTCTAGAATAGTTT
5596 GTTCTAGAATAGTTT
1 GTTCTAGAATAGTTT
5611 GTT
1 GTT
5614 AGCTTGTAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.06, G:0.21, T:0.48
Consensus pattern (15 bp):
GTTCTAGAATAGTTT
Found at i:8741 original size:31 final size:31
Alignment explanation
Indices: 8703--8856 Score: 226
Period size: 31 Copynumber: 5.0 Consensus size: 31
8693 CCCGAAGGAC
*
8703 CAGTCCATAGATCCCGAAGAACCTAGGTAAA
1 CAGTCCATAGATCCCGAAGAACATAGGTAAA
* *
8734 CAGTCCATATATCCCGAAGAACATAGTTAAA
1 CAGTCCATAGATCCCGAAGAACATAGGTAAA
8765 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
1 CAGTCCATA-GATCCCGAAGAACATAGGTAAA
8796 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
1 CAGTCCATA-GATCCCGAAGAACATAGGTAAA
*
8827 CAGTCCATATATCCCGAAGAAC--AGGTAAA
1 CAGTCCATAGATCCCGAAGAACATAGGTAAA
8856 C
1 C
8857 CCTCGACCCT
Statistics
Matches: 115, Mismatches: 6, Indels: 6
0.91 0.05 0.05
Matches are distributed among these distances:
29 8 0.07
31 107 0.93
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.19
Consensus pattern (31 bp):
CAGTCCATAGATCCCGAAGAACATAGGTAAA
Found at i:9576 original size:61 final size:61
Alignment explanation
Indices: 9502--9619 Score: 164
Period size: 61 Copynumber: 1.9 Consensus size: 61
9492 TTCAATGAAA
* * *
9502 GTATGCATCGATGCACTACTGATGCATCGGTGCACAAAATGCATTCGTTGTATTATTACTG
1 GTATGCATCGATGCACTAATGATGCATCGATGCACAAAATGCATTCGATGTATTATTACTG
* ** * *
9563 GTATGCATCGATGCACTAATTATGCATCGATGCATGAATTGCATTCGATGTTTTATT
1 GTATGCATCGATGCACTAATGATGCATCGATGCACAAAATGCATTCGATGTATTATT
9620 TTAAAAGAGT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (61 bp):
GTATGCATCGATGCACTAATGATGCATCGATGCACAAAATGCATTCGATGTATTATTACTG
Found at i:10182 original size:3 final size:3
Alignment explanation
Indices: 10174--10202 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
10164 TCTCGTACAT
10174 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
10203 GATGAAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:12818 original size:23 final size:23
Alignment explanation
Indices: 12790--12833 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
12780 AACATAATGC
12790 ATACTTATACA-TATATCATTAAT
1 ATACTTAT-CAGTATATCATTAAT
12813 ATACTTATCAGTATATCATTA
1 ATACTTATCAGTATATCATTA
12834 TTACTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.43
Consensus pattern (23 bp):
ATACTTATCAGTATATCATTAAT
Found at i:18818 original size:20 final size:19
Alignment explanation
Indices: 18793--18846 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
18783 GCGAAATAAA
18793 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
18813 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
18833 AATCGCAACGCGAT
1 AATCGCAACGCGAT
18847 TATGAAGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:18857 original size:21 final size:20
Alignment explanation
Indices: 18833--18950 Score: 62
Period size: 20 Copynumber: 5.8 Consensus size: 20
18823 CAGTTCCCAG
18833 AATCGCAACGCGATTATGAA
1 AATCGCAACGCGATTATGAA
* *
18853 GAATCGTAATGCGA-TA-GTACA
1 -AATCGCAACGCGATTATG-A-A
** * * *
18874 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTAT-GAA
* *
18896 AATCGCAAGGCGAATATGAA
1 AATCGCAACGCGATTATGAA
**
18916 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGCGATTATGA-A
18936 AATCGCAACGCGATT
1 AATCGCAACGCGATT
18951 CTAACTATCG
Statistics
Matches: 73, Mismatches: 17, Indels: 15
0.70 0.16 0.14
Matches are distributed among these distances:
19 2 0.03
20 35 0.48
21 32 0.44
22 3 0.04
23 1 0.01
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.22
Consensus pattern (20 bp):
AATCGCAACGCGATTATGAA
Found at i:18921 original size:20 final size:20
Alignment explanation
Indices: 18896--18948 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
18886 GATTTTCCAG
* *
18896 AATCGCAAGGCGAATATGA-A
1 AATCGCAACGCGAACAT-ATA
18916 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAACATATA
18936 AATCGCAACGCGA
1 AATCGCAACGCGA
18949 TTCTAACTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.43, C:0.23, G:0.21, T:0.13
Consensus pattern (20 bp):
AATCGCAACGCGAACATATA
Found at i:18984 original size:41 final size:41
Alignment explanation
Indices: 18935--19169 Score: 302
Period size: 41 Copynumber: 5.8 Consensus size: 41
18925 GCGAACATAT
* *
18935 AAATCGCAACGCG-ATTC-TAACTATCGCAACGAGTATCCGTA
1 AAATCGCAACGCGTATTCGTAA--ATCGCAACGAGAATACGTA
* *
18976 AAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTA
1 AAATCGCAACGCGTATTCGTAAATCGCAACGAGAATACGTA
*
19017 AAATCGCAACGCGTATTCGTAAATCGCAACGAGAATACAT-
1 AAATCGCAACGCGTATTCGTAAATCGCAACGAGAATACGTA
19057 AAATCGCAACGCGTA-TCTGTAAATCGCAACGAGAATACGT-
1 AAATCGCAACGCGTATTC-GTAAATCGCAACGAGAATACGTA
* * *
19097 AAATCGCAATGCGTATCCGTAAATTTGCAACGACG-ATACGTA
1 AAATCGCAACGCGTATTCGTAAA-TCGCAACGA-GAATACGTA
*
19139 AAATCGCAACGCGTATCCGTAAATCGCAACG
1 AAATCGCAACGCGTATTCGTAAATCGCAACG
19170 CGATTTTTAA
Statistics
Matches: 174, Mismatches: 13, Indels: 14
0.87 0.06 0.07
Matches are distributed among these distances:
39 2 0.01
40 55 0.32
41 88 0.51
42 26 0.15
43 3 0.02
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (41 bp):
AAATCGCAACGCGTATTCGTAAATCGCAACGAGAATACGTA
Found at i:19001 original size:20 final size:20
Alignment explanation
Indices: 18934--19171 Score: 232
Period size: 20 Copynumber: 11.7 Consensus size: 20
18924 CGCGAACATA
*
18934 TAAATCGCAACGCG-ATTC-
1 TAAATCGCAACGCGTATCCG
*
18952 TAACTATCGCAACGAGTATCCG
1 TAA--ATCGCAACGCGTATCCG
18974 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACGCGTATCCG
* *
18995 TAAATCGCAACGAC-AATACG
1 TAAATCGCAACG-CGTATCCG
*
19015 TAAAATCGCAACGCGTATTCG
1 T-AAATCGCAACGCGTATCCG
* * * *
19036 TAAATCGCAACGAGAATACA
1 TAAATCGCAACGCGTATCCG
*
19056 TAAATCGCAACGCGTATCTG
1 TAAATCGCAACGCGTATCCG
* * *
19076 TAAATCGCAACGAGAATACG
1 TAAATCGCAACGCGTATCCG
*
19096 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCGTATCCG
* *
19116 TAAATTTGCAACGACG-ATACG
1 TAAA-TCGCAACG-CGTATCCG
19137 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACGCGTATCCG
19158 TAAATCGCAACGCG
1 TAAATCGCAACGCG
19172 ATTTTTAAAG
Statistics
Matches: 179, Mismatches: 29, Indels: 22
0.78 0.13 0.10
Matches are distributed among these distances:
18 3 0.02
20 108 0.60
21 60 0.34
22 6 0.03
23 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
TAAATCGCAACGCGTATCCG
Found at i:19059 original size:122 final size:122
Alignment explanation
Indices: 18915--19169 Score: 372
Period size: 122 Copynumber: 2.1 Consensus size: 122
18905 GCGAATATGA
* * * *
18915 AAATCGCAACGCGAACATATAAATCGCAACGCG-AT-TCTAACTATCGCAACGAGTATCCGTAAA
1 AAATCGCAACGAGAACACATAAATCGCAACGCGTATCTCTAA--ATCGCAACGAGAATACGT-AA
*
18978 ATCGCAACGCGTATCCGTAAA-TCGCAACGACAATACGTAAAATCGCAACGCGTATTCGT
63 ATCGCAACGCGTATCCGTAAATTCGCAACGACAATACGTAAAATCGCAACGCGTATCCGT
* *
19037 AAATCGCAACGAGAATACATAAATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAAATC
1 AAATCGCAACGAGAACACATAAATCGCAACGCGTATCTCTAAATCGCAACGAGAATACGTAAATC
* * *
19102 GCAATGCGTATCCGTAAATTTGCAACGACGATACGTAAAATCGCAACGCGTATCCGT
66 GCAACGCGTATCCGTAAATTCGCAACGACAATACGTAAAATCGCAACGCGTATCCGT
19159 AAATCGCAACG
1 AAATCGCAACG
19170 CGATTTTTAA
Statistics
Matches: 120, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
121 22 0.18
122 92 0.77
123 2 0.02
124 4 0.03
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (122 bp):
AAATCGCAACGAGAACACATAAATCGCAACGCGTATCTCTAAATCGCAACGAGAATACGTAAATC
GCAACGCGTATCCGTAAATTCGCAACGACAATACGTAAAATCGCAACGCGTATCCGT
Found at i:19443 original size:27 final size:26
Alignment explanation
Indices: 19387--19437 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
19377 ATCTCCGGCA
*
19387 AAATCCCTCACAACCATTCACGGTAAG
1 AAATCCCTCACAACCATTCAC-GAAAG
*
19414 AAATCCCTCACAATCATTCA-GAAA
1 AAATCCCTCACAACCATTCACGAAA
19438 TGGAAAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
27 19 0.86
ACGTcount: A:0.41, C:0.31, G:0.08, T:0.20
Consensus pattern (26 bp):
AAATCCCTCACAACCATTCACGAAAG
Found at i:19755 original size:20 final size:19
Alignment explanation
Indices: 19730--19801 Score: 90
Period size: 20 Copynumber: 3.6 Consensus size: 19
19720 TTCTAAACTT
19730 AAAATCGCAACATGAAAATG
1 AAAATCGCAACA-GAAAATG
19750 AAAATCGCAACACGAAAATG
1 AAAATCGCAACA-GAAAATG
**
19770 ATTATCGCAACGAGAGAAATG
1 AAAATCGCAAC-AGA-AAATG
19791 AAAATCGCAAC
1 AAAATCGCAAC
19802 GCAAAACCAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
20 30 0.67
21 15 0.33
ACGTcount: A:0.51, C:0.18, G:0.17, T:0.14
Consensus pattern (19 bp):
AAAATCGCAACAGAAAATG
Found at i:19791 original size:21 final size:21
Alignment explanation
Indices: 19730--19818 Score: 89
Period size: 20 Copynumber: 4.4 Consensus size: 21
19720 TTCTAAACTT
*
19730 AAAATCGCAAC-ATGAAAATG
1 AAAATCGCAACGACGAAAATG
19750 AAAATCGCAAC-ACGAAAATG
1 AAAATCGCAACGACGAAAATG
**
19770 ATTATCGCAACGA-GAGAAATG
1 AAAATCGCAACGACGA-AAATG
**
19791 AAAATCGCAACG-C-AAAACC
1 AAAATCGCAACGACGAAAATG
19810 AAAATCGCA
1 AAAATCGCA
19819 TTACGATTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
19 12 0.20
20 31 0.53
21 16 0.27
ACGTcount: A:0.52, C:0.20, G:0.16, T:0.12
Consensus pattern (21 bp):
AAAATCGCAACGACGAAAATG
Found at i:19817 original size:40 final size:40
Alignment explanation
Indices: 19730--19818 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 40
19720 TTCTAAACTT
**
19730 AAAATCGCAACATGAAAATGAAAATCGCAACACGAAAATG
1 AAAATCGCAACATGAAAATGAAAATCGCAACACGAAAACC
** *
19770 ATTATCGCAACGA-GAGAAATGAAAATCGCAACGC-AAAACC
1 AAAATCGCAAC-ATGA-AAATGAAAATCGCAACACGAAAACC
19810 AAAATCGCA
1 AAAATCGCA
19819 TTACGATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
40 22 0.55
41 18 0.45
ACGTcount: A:0.52, C:0.20, G:0.16, T:0.12
Consensus pattern (40 bp):
AAAATCGCAACATGAAAATGAAAATCGCAACACGAAAACC
Found at i:19889 original size:14 final size:14
Alignment explanation
Indices: 19870--19925 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
19860 TTAAATTTCG
19870 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
19884 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
19903 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
19917 CGTTGCGAT
1 CGTTGCGAT
19926 AGTCATTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:19906 original size:33 final size:33
Alignment explanation
Indices: 19822--19945 Score: 194
Period size: 34 Copynumber: 3.7 Consensus size: 33
19812 AATCGCATTA
19822 CGATTTTCATTTCGCGTTGCGATTCTCTCGTTG
1 CGATTTTCATTTCGCGTTGCGATTCTCTCGTTG
* *
19855 TGATTTTAAATTTCGCGTTGCGATTCTCTCGTTG
1 CGATTTT-CATTTCGCGTTGCGATTCTCTCGTTG
19889 CGATTTTCATTTCGCGTTGCGATTCTCTCGTTG
1 CGATTTTCATTTCGCGTTGCGATTCTCTCGTTG
**
19922 CGATAGTCATTTCCGCGTTGCGAT
1 CGATTTTCATTT-CGCGTTGCGAT
19946 AGTCATTCTC
Statistics
Matches: 83, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
33 41 0.49
34 42 0.51
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.44
Consensus pattern (33 bp):
CGATTTTCATTTCGCGTTGCGATTCTCTCGTTG
Found at i:19960 original size:20 final size:20
Alignment explanation
Indices: 19910--19962 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
19900 TCGCGTTGCG
19910 ATTCTCTCGTTGCGATAGTC
1 ATTCTCTCGTTGCGATAGTC
*
19930 ATT-TCCGCGTTGCGATAGTC
1 ATTCT-CTCGTTGCGATAGTC
19950 ATTCTCTCGTTGC
1 ATTCTCTCGTTGC
19963 AATTTTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 1 0.03
20 27 0.93
21 1 0.03
ACGTcount: A:0.13, C:0.26, G:0.21, T:0.40
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATAGTC
Found at i:22064 original size:94 final size:94
Alignment explanation
Indices: 21662--22041 Score: 638
Period size: 94 Copynumber: 4.1 Consensus size: 94
21652 TAGATTGCTT
* * * *
21662 AGTAAATTTATTCGGTTTCTGCCAATACTGCTAAACTGTTTATTCTTTAACAATGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
21727 ATTTGTCTTTTGTTTTATCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
21756 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
21821 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * *
21850 AGTAAATTTGTTCGGTTGCTTCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAAT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
21915 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * *
21944 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
22009 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
22037 AGTAA
1 AGTAA
22042 TGTAATCCAT
Statistics
Matches: 273, Mismatches: 12, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
93 25 0.09
94 248 0.91
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.48
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:22145 original size:19 final size:17
Alignment explanation
Indices: 22129--22207 Score: 76
Period size: 19 Copynumber: 4.6 Consensus size: 17
22119 AAAAATGACT
*
22129 ATCGCAACGCGAAATGA
1 ATCGCAACGAGAAATGA
22146 ATCGCAACGAGAAATGAAA
1 ATCGCAACGAGAAATG--A
22165 ATCGCAACGAG--A-GA
1 ATCGCAACGAGAAATGA
22179 ATCGCAACGCA-AAATGAAA
1 ATCGCAACG-AGAAATG--A
22198 ATCGCAACGA
1 ATCGCAACGA
22208 CAAAATCGCA
Statistics
Matches: 53, Mismatches: 1, Indels: 15
0.77 0.01 0.22
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
17 17 0.32
18 1 0.02
19 22 0.42
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.10
Consensus pattern (17 bp):
ATCGCAACGAGAAATGA
Found at i:22235 original size:33 final size:33
Alignment explanation
Indices: 22145--22225 Score: 126
Period size: 33 Copynumber: 2.5 Consensus size: 33
22135 ACGCGAAATG
* * *
22145 AATCGCAACGAGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAA
*
22178 AATCGCAACGCAAAATGAAAATCGCAACGACAA
1 AATCGCAACGCGAAATGAAAATCGCAACGACAA
22211 AATCGCAACGCGAAA
1 AATCGCAACGCGAAA
22226 CTATAATCGC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.49, C:0.22, G:0.20, T:0.09
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAA
Found at i:22295 original size:20 final size:20
Alignment explanation
Indices: 22270--22336 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
22260 GATTCTCTCG
**
22270 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
22290 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
22310 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
22330 TTGCGAT
1 TTGCGAT
22337 TTTAAGTTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:22909 original size:21 final size:20
Alignment explanation
Indices: 22820--22922 Score: 66
Period size: 21 Copynumber: 5.0 Consensus size: 20
22810 GACTCACCTG
22820 TCATCGTTCAAGAGG-CCTCC
1 TCATCGTTCAAGAGGCCCT-C
* *
22840 CCTATCGTTCAAGA-GCCCTA
1 TC-ATCGTTCAAGAGGCCCTC
** *
22860 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAG-GCCCTC
* * *
22881 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCC-CTC
*
22902 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGG-CCCTC
22923 CCAACATTCT
Statistics
Matches: 60, Mismatches: 17, Indels: 11
0.68 0.19 0.12
Matches are distributed among these distances:
19 9 0.15
20 5 0.08
21 44 0.73
22 2 0.03
ACGTcount: A:0.21, C:0.37, G:0.18, T:0.23
Consensus pattern (20 bp):
TCATCGTTCAAGAGGCCCTC
Found at i:24300 original size:14 final size:14
Alignment explanation
Indices: 24281--24316 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
24271 ATTGTTTAAT
24281 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
24295 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
24309 TGATTTGT
1 TGATTTGT
24317 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:24501 original size:20 final size:20
Alignment explanation
Indices: 24478--24564 Score: 131
Period size: 20 Copynumber: 4.3 Consensus size: 20
24468 GATTCTCTCA
24478 TTGCGATAGTCATTTCCGCG
1 TTGCGATAGTCATTTCCGCG
* *
24498 TTGCGATAGTCAATTCCGCA
1 TTGCGATAGTCATTTCCGCG
*
24518 TTGCGATAGTCATTTCCGTG
1 TTGCGATAGTCATTTCCGCG
24538 TTGCGATAGTCATATT-CGCG
1 TTGCGATAGTCAT-TTCCGCG
24558 TTGCGAT
1 TTGCGAT
24565 TTCCGCGTTG
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 58 0.97
21 2 0.03
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCGCG
Found at i:24702 original size:9 final size:9
Alignment explanation
Indices: 24688--24716 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
24678 CACACATAAT
24688 ATACACATA
1 ATACACATA
24697 ATACACATA
1 ATACACATA
24706 ATACAC-TA
1 ATACACATA
24714 ATA
1 ATA
24717 GTTGATTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 5 0.25
9 15 0.75
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.24
Consensus pattern (9 bp):
ATACACATA
Found at i:24853 original size:34 final size:33
Alignment explanation
Indices: 24776--24859 Score: 132
Period size: 33 Copynumber: 2.5 Consensus size: 33
24766 TTGCAACGCA
**
24776 GAAATGACTATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
*
24809 GAAATGAAAATCGCAACGAGTGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
24842 GAAAATGAAAATCGCAAC
1 G-AAATGAAAATCGCAAC
24860 ACGAAACTAA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 31 0.66
34 16 0.34
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAATGC
Found at i:24932 original size:33 final size:33
Alignment explanation
Indices: 24875--24959 Score: 116
Period size: 33 Copynumber: 2.5 Consensus size: 33
24865 ACTAATTTCA
*
24875 CGTTGCGATTTTCATTTTCGCATTGTGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
*
24909 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
* **
24942 CGTTACGATAGTCATTTC
1 CGTTGCGATTTTCATTTC
24960 CACGTTGCGA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 32 0.70
34 14 0.30
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:24970 original size:20 final size:20
Alignment explanation
Indices: 24942--25030 Score: 117
Period size: 20 Copynumber: 4.5 Consensus size: 20
24932 GCGATTCTCT
* *
24942 CGTTACGATAGTCATTTCCA
1 CGTTGCGATAGTCATTTCCG
*
24962 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
*
24982 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
25002 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
25022 CGTTGCGAT
1 CGTTGCGAT
25031 TTTCGCGTTG
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
20 58 0.97
21 2 0.03
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:25037 original size:14 final size:14
Alignment explanation
Indices: 25018--25044 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
25008 GATAGTCATA
25018 TTCGCGTTGCGATT
1 TTCGCGTTGCGATT
25032 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
25045 AGTCAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.22, G:0.30, T:0.41
Consensus pattern (14 bp):
TTCGCGTTGCGATT
Found at i:28067 original size:20 final size:21
Alignment explanation
Indices: 28005--28070 Score: 107
Period size: 21 Copynumber: 3.2 Consensus size: 21
27995 GTATATGATT
28005 CTTAAGGAATGATATGTGGTC
1 CTTAAGGAATGATATGTGGTC
* *
28026 CTTAAAGAATGATATGTAGTC
1 CTTAAGGAATGATATGTGGTC
28047 CTTAAGGAATG-TATGTGGTC
1 CTTAAGGAATGATATGTGGTC
28067 CTTA
1 CTTA
28071 TGGACATTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 12 0.29
21 29 0.71
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.35
Consensus pattern (21 bp):
CTTAAGGAATGATATGTGGTC
Found at i:30671 original size:24 final size:24
Alignment explanation
Indices: 30637--30690 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
30627 CTGAAAAATC
30637 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
30661 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
30685 ATCAAA
1 ATCAAA
30691 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:30704 original size:24 final size:24
Alignment explanation
Indices: 30637--30704 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
30627 CTGAAAAATC
* * *
30637 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
30661 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
30685 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
30705 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:31565 original size:20 final size:19
Alignment explanation
Indices: 31552--31657 Score: 58
Period size: 20 Copynumber: 5.3 Consensus size: 19
31542 CAGAATCTCG
31552 TTGCGATTTACAGATTCGTA
1 TTGCGATTTACAGATTCG-A
*
31572 TTGCGATTTAC-GTATTTGCA
1 TTGCGATTTACAG-ATTCG-A
* *
31592 TTACAATTTAC-GTATTCGCA
1 TTGCGATTTACAG-ATTCG-A
* *
31612 TTGCGATTTAC-GTAATCGCG
1 TTGCGATTTACAG-ATTCG-A
31632 TTGCGATTTAC-GTATTCGCA
1 TTGCGATTTACAG-ATTCG-A
31652 TTGCGA
1 TTGCGA
31658 ATTAGGAAAA
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
19 1 0.01
20 73 0.99
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.40
Consensus pattern (19 bp):
TTGCGATTTACAGATTCGA
Found at i:31641 original size:40 final size:39
Alignment explanation
Indices: 31544--31657 Score: 104
Period size: 40 Copynumber: 2.9 Consensus size: 39
31534 GCGATAGTCA
* **
31544 GAATCTCGTTGCGATTTACAG-ATTCGTATTGCGATTTAC
1 GAATCGCGTTGCGATTTAC-GTATTCGCGTTGCGATTTAC
* * * * * *
31583 GTATTTGCATTACAATTTACGTATTCGCATTGCGATTTAC
1 G-AATCGCGTTGCGATTTACGTATTCGCGTTGCGATTTAC
*
31623 GTAATCGCGTTGCGATTTACGTATTCGCATTGCGA
1 G-AATCGCGTTGCGATTTACGTATTCGCGTTGCGA
31658 ATTAGGAAAA
Statistics
Matches: 61, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
39 2 0.03
40 59 0.97
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (39 bp):
GAATCGCGTTGCGATTTACGTATTCGCGTTGCGATTTAC
Found at i:31678 original size:21 final size:21
Alignment explanation
Indices: 31654--31699 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
31644 TATTCGCATT
31654 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
31675 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
31696 GCGA
1 GCGA
31700 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:31794 original size:20 final size:20
Alignment explanation
Indices: 31750--31981 Score: 238
Period size: 20 Copynumber: 11.6 Consensus size: 20
31740 TACCGGAGAT
*
31750 CGCGTTGCGAATTATC-GAT-
1 CGCGTTGCGATTTA-CGGATA
31769 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
31789 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
31809 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
31830 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
31850 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
** * *
31870 CATGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
31890 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
31910 AGCGTTGCGATTTACGTAT-
1 CGCGTTGCGATTTACGGATA
*
31929 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
31950 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
31971 CTCGTTGCGAT
1 CGCGTTGCGAT
31982 AGTCAGAATC
Statistics
Matches: 176, Mismatches: 29, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
18 1 0.01
19 17 0.10
20 121 0.69
21 37 0.21
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:31855 original size:40 final size:40
Alignment explanation
Indices: 31750--32042 Score: 324
Period size: 40 Copynumber: 7.3 Consensus size: 40
31740 TACCGGAGAT
* *
31750 CGCGTTGCGAATTATCG-A-TCGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTA-CGTATTCTCGTTGCGATTTACGGATA
*
31789 CGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATA
1 CGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATA
* *
31830 CGCATTGCGATTTACGTATTCTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
**
31870 CATGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
* *
31910 AGCGTTGCGATTTACGTATTGTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
* * * *
31950 CGCGTTGCGATTTTACGGATACTCGTTGCGATAGT-CAGA-A
1 CGCGTTGCGA-TTTACGTATTCTCGTTGCGAT-TTACGGATA
** * * * ** *
31990 TCGCGTTGCGATTTATATGTTCGCGTTGCGATTTTCATATT
1 -CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
32031 CGCGTTGCGATT
1 CGCGTTGCGATT
32043 CTGGAAAATC
Statistics
Matches: 217, Mismatches: 29, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
39 13 0.06
40 144 0.66
41 59 0.27
42 1 0.00
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.37
Consensus pattern (40 bp):
CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
Found at i:32013 original size:20 final size:20
Alignment explanation
Indices: 31990--32042 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
31980 ATAGTCAGAA
*
31990 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
32010 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
32030 TCGCGTTGCGATT
1 TCGCGTTGCGATT
32043 CTGGAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:33659 original size:39 final size:39
Alignment explanation
Indices: 33602--33680 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
33592 TATTTTTGTA
**
33602 GCTTCTCCAGCATGATTCCTCTCCAAAACACGAGTGATG
1 GCTTCTCCAGCAACATTCCTCTCCAAAACACGAGTGATG
*
33641 GCTTCTTCAGCAACATTCCTCTCCAAAACACGAGTGATG
1 GCTTCTCCAGCAACATTCCTCTCCAAAACACGAGTGATG
33680 G
1 G
33681 AACCTTCATC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (39 bp):
GCTTCTCCAGCAACATTCCTCTCCAAAACACGAGTGATG
Found at i:35737 original size:34 final size:36
Alignment explanation
Indices: 35693--35794 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
35683 TTTCGTCCTA
*
35693 CTAGGATTCAAACTCCTAAAAATATGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
35728 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
35763 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
35795 GTTATACTAT
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
34 29 0.48
35 3 0.05
37 29 0.48
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:36225 original size:18 final size:17
Alignment explanation
Indices: 36186--36228 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
36176 ATTATATGGA
36186 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
36202 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
36220 TATTATTAT
1 TATTATTAT
36229 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:36294 original size:2 final size:2
Alignment explanation
Indices: 36287--36311 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
36277 ATTTTACTAT
36287 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
36312 TTCTTTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:36736 original size:2 final size:2
Alignment explanation
Indices: 36729--36799 Score: 135
Period size: 2 Copynumber: 36.0 Consensus size: 2
36719 TAATACTTTG
36729 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36771 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36800 TTTTCCTTTT
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 67 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:40571 original size:16 final size:16
Alignment explanation
Indices: 40545--40578 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
40535 AGATCCAATC
40545 AAGAACAAAAAAG-AA
1 AAGAACAAAAAAGCAA
40560 AAGAAGCAAAAAAGCAA
1 AAGAA-CAAAAAAGCAA
40577 AA
1 AA
40579 AAAACAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 8 0.47
17 4 0.24
ACGTcount: A:0.76, C:0.09, G:0.15, T:0.00
Consensus pattern (16 bp):
AAGAACAAAAAAGCAA
Found at i:40592 original size:22 final size:22
Alignment explanation
Indices: 40567--40645 Score: 76
Period size: 22 Copynumber: 3.6 Consensus size: 22
40557 GAAAAGAAGC
40567 AAAAA-AGCAAAAAAAACAAAG
1 AAAAAGAGCAAAAAAAACAAAG
*
40588 AAAAAGAG-AAACAAGAACAAA-
1 AAAAAGAGCAAA-AAAAACAAAG
*
40609 AAAAAGAGCAAAAATCAA-AAAG
1 AAAAAGAGCAAAAA-AAACAAAG
*
40631 AAAAAGGGACAAAAA
1 AAAAAGAG-CAAAAA
40646 GCACATGCAA
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
21 21 0.43
22 22 0.45
23 6 0.12
ACGTcount: A:0.76, C:0.09, G:0.14, T:0.01
Consensus pattern (22 bp):
AAAAAGAGCAAAAAAAACAAAG
Found at i:40627 original size:19 final size:19
Alignment explanation
Indices: 40567--40629 Score: 65
Period size: 21 Copynumber: 3.2 Consensus size: 19
40557 GAAAAGAAGC
40567 AAAAAAGCA-AAAAAAACAA
1 AAAAAAG-AGAAAAAAACAA
40586 AGAAAAAGAGAAACAAGAACAA
1 A-AAAAAGAGAAA-AA-AACAA
* *
40608 AAAAAAGAGCAAAAATCAA
1 AAAAAAGAGAAAAAAACAA
40627 AAA
1 AAA
40630 GAAAAAGGGA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
19 9 0.24
20 11 0.29
21 12 0.32
22 6 0.16
ACGTcount: A:0.78, C:0.10, G:0.11, T:0.02
Consensus pattern (19 bp):
AAAAAAGAGAAAAAAACAA
Found at i:41737 original size:18 final size:18
Alignment explanation
Indices: 41714--41749 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
41704 TCAACATCAA
* *
41714 ATATTGGGGCATTTTTGG
1 ATATTGAGGCATCTTTGG
41732 ATATTGAGGCATCTTTGG
1 ATATTGAGGCATCTTTGG
41750 GGATTCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.31, T:0.42
Consensus pattern (18 bp):
ATATTGAGGCATCTTTGG
Found at i:42272 original size:36 final size:36
Alignment explanation
Indices: 42229--42510 Score: 321
Period size: 36 Copynumber: 8.0 Consensus size: 36
42219 ACTAGAAGAG
42229 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
42265 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * *
42301 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
42337 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * * * *
42373 ------ATAT-TTGA-ATATGTTTTCTTTGAAACAAA
1 TTTTGTCTCTCTTGAGACA-GTTTCCCTTGAAACAAA
* * ** * *
42402 TTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAA
*
42439 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
42474 TTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTT-GTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
42511 ATCTTTGAAT
Statistics
Matches: 206, Mismatches: 28, Indels: 23
0.80 0.11 0.09
Matches are distributed among these distances:
28 2 0.01
29 19 0.09
30 2 0.01
35 6 0.03
36 142 0.69
37 35 0.17
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:42272 original size:71 final size:73
Alignment explanation
Indices: 42187--42510 Score: 248
Period size: 72 Copynumber: 4.6 Consensus size: 73
42177 GTTTTTCTTA
* * * * * *
42187 AAACAAGA-TTTGTCTCGCTTGAGACCGTTTTCACTAG-AA-GAGTTTTGTCTCTCTTGAGACAG
1 AAACAA-ATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAG
42249 TTTCCCTTG
65 TTTCCCTTG
* *
42258 AAACAAATTTTGTCTCTCTTGAGACAG-TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAGT
42322 TTCCCTTG
66 TTCCCTTG
* * * * *
42330 AAATAAATTTTGTCTCTCTTGAGACAG-TTTCCCTTGAAACAAA------ATAT-TTGA-ATATG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACA-G
* *
42386 TTTTCTTTG
65 TTTCCCTTG
* * ** * * * * *
42395 AAACAAATTTCGTCTCCCTTGAGACAG-TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAAC-AAATTTCGTCTATCTTGAGACAG
*
42459 TTTCTCTTG
65 TTTCCCTTG
* * *
42468 AAAC-AATTTTCGTCTATCTTGAGACAG-TTTCCCTTGAAACAAA
1 AAACAAATTTT-GTCTCTCTTGAGACAGTTTTCACTAGAAACAAA
42511 ATCTTTGAAT
Statistics
Matches: 205, Mismatches: 34, Indels: 27
0.77 0.13 0.10
Matches are distributed among these distances:
64 2 0.01
65 46 0.22
66 5 0.02
70 8 0.04
71 25 0.12
72 78 0.38
73 39 0.19
74 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (73 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAGT
TTCCCTTG
Found at i:42470 original size:102 final size:102
Alignment explanation
Indices: 42285--42473 Score: 299
Period size: 102 Copynumber: 1.9 Consensus size: 102
42275 CTTGAGACAG
*
42285 TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
1 TTTCTCTTGAAACAAATTTCGTCTACCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
42350 GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
66 GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
* ** * *
42387 TTTCT-TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTCGTCTACCTTGAGACAGTTTCCCTT-GAAATAAATTTTGTCTCTCT
*
42451 TGAGACAGTTTCTCTTGAAACAA
65 TGAGACAGTTTCCCTTGAAACAA
42474 TTTTCGTCTA
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 34 0.43
102 45 0.57
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.41
Consensus pattern (102 bp):
TTTCTCTTGAAACAAATTTCGTCTACCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
Found at i:42502 original size:138 final size:137
Alignment explanation
Indices: 42249--42573 Score: 454
Period size: 138 Copynumber: 2.4 Consensus size: 137
42239 CTTGAGACAG
*
42249 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
*
42314 GAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTT
66 GAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTT
*
42379 GAATATG
131 GAATATA
* * * * * * * *
42386 TTTTCTTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC-AAATTTCGTCTATCT
* * *
42451 TGAGACAGTTTCTCTTGAAA-CAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCT
65 TGAGACAGTTTCCCTTGAAATAAATTTT-GTCTATCTTGAGACAGTTTCCCTTGAAACAAAATAT
*
42515 TTGAATTTA
129 TTGAATATA
* * * *
42524 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAATTACTCTTGAAACA
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
42574 CAAAATCTTC
Statistics
Matches: 162, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
137 50 0.31
138 112 0.69
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.40
Consensus pattern (137 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
GAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATATTT
GAATATA
Found at i:42572 original size:65 final size:67
Alignment explanation
Indices: 42468--42625 Score: 196
Period size: 67 Copynumber: 2.4 Consensus size: 67
42458 GTTTCTCTTG
** * * **
42468 AAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAATTTATTTCCC
1 AAACAAATTTT-GTCTCCCTTGAGACAATTACCCTTGAAACACAAAATCTTCAAATTTATTTCCC
42530 CTA
65 CTA
* *
42533 AAACAAATTTTGTCTCCCTTGAGACAATTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAATTACCCTTGAAACACAAAATCTTCAAATTTATTTCCCC
42598 TA
66 TA
*
42600 AAACATAATTTTGTTTCCCTTGAGAC
1 AAACA-AATTTTGTCTCCCTTGAGAC
42626 CGTTTCTCAT
Statistics
Matches: 80, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
65 24 0.30
66 8 0.10
67 29 0.36
68 19 0.24
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (67 bp):
AAACAAATTTTGTCTCCCTTGAGACAATTACCCTTGAAACACAAAATCTTCAAATTTATTTCCCC
TA
Found at i:42602 original size:67 final size:65
Alignment explanation
Indices: 42459--42625 Score: 192
Period size: 65 Copynumber: 2.5 Consensus size: 65
42449 CTTGAGACAG
* * ** * * **
42459 TTTCTCTTGAAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTT
1 TTTCCCTTAAAACAAATTTT-GTCTCCCTTGAGACAATTACCCTTGAAACAAAATCTTCAAATTT
42523 A
65 A
* *
42524 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAATTACTCTTGAAACACAAAATCTTCAAATT
1 TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAATTACCCTTG-AA-ACAAAATCTTCAAATT
42589 TA
64 TA
*
42591 TTTCCCTTAAAACATAATTTTGTTTCCCTTGAGAC
1 TTTCCCTTAAAACA-AATTTTGTCTCCCTTGAGAC
42626 CGTTTCTCAT
Statistics
Matches: 86, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
65 30 0.35
66 8 0.09
67 29 0.34
68 19 0.22
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (65 bp):
TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAATTACCCTTGAAACAAAATCTTCAAATTTA
Found at i:43466 original size:105 final size:105
Alignment explanation
Indices: 43246--44011 Score: 1051
Period size: 105 Copynumber: 7.3 Consensus size: 105
43236 GCCATCTGCG
* * * * * *
43246 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
43311 TGGA-CGACTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACCG-CTGCTTGTCAAC-AACAACTTCTCAATTTCAGAGCCA
** * *
43355 ATTTCAACTTCACAACGAAAAATATTAGACTCCAGACAACGCAAGTTCAACTTCACGGCGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
43420 ACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
43460 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
43525 ACCGCTGCTTGTCAACAACAACTTCTTAATTTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* *
43565 ATTTCAACTTCACAACAAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
43630 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* *
43670 ATTTCAACTTCACAACGAAGGATATTGGACTCCATACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * *
43735 ACCGCTTCTTGTCAACAACAACTTCCCAATCTCAAAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* * *
43775 ATTTCAATTTCACAACGAAGGATATTAGATTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
**
43840 ACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGATTCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* * *
43875 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * ** *
43940 A-CGACTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCA
66 ACCG-CTGCTTGTCAAC-AACAACTTCTCAATTTCAGAGCCA
* * *
43981 ATTTCAACTTCACGACGGAGGATATTAGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
44012 TGGAACAATG
Statistics
Matches: 593, Mismatches: 56, Indels: 19
0.89 0.08 0.03
Matches are distributed among these distances:
99 2 0.00
100 77 0.13
101 3 0.01
102 3 0.01
103 4 0.01
104 3 0.01
105 399 0.67
106 78 0.13
107 4 0.01
109 20 0.03
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
Found at i:44590 original size:34 final size:36
Alignment explanation
Indices: 44546--44647 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
44536 TTTCGTCCTA
44546 CTAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
44581 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
44616 GCTATGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
44648 GTTATACTAT
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
34 30 0.49
35 3 0.05
37 28 0.46
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:44671 original size:37 final size:37
Alignment explanation
Indices: 44544--44681 Score: 149
Period size: 37 Copynumber: 3.8 Consensus size: 37
44534 TTTTTCGTCC
* *
44544 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATT-
1 TACTATGATTCAAACTCCTAAAAATAGGATAAAATTA
* *
44580 T--TAGGATTCAAACTCCTAAAAATAGGATAAAATTT
1 TACTATGATTCAAACTCCTAAAAATAGGATAAAATTA
* * *
44615 TGCTATGATTCAAACTCCTAAAAATAGGATAGAGTTA
1 TACTATGATTCAAACTCCTAAAAATAGGATAAAATTA
* * *
44652 TACTATTATAT-AAATTCCTAAAGATAGGAT
1 TACTATGAT-TCAAACTCCTAAAAATAGGAT
44682 CCACAAGCAC
Statistics
Matches: 89, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
34 32 0.36
35 1 0.01
36 1 0.01
37 54 0.61
38 1 0.01
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.31
Consensus pattern (37 bp):
TACTATGATTCAAACTCCTAAAAATAGGATAAAATTA
Found at i:45078 original size:18 final size:17
Alignment explanation
Indices: 45043--45081 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
45033 TATGGATATT
*
45043 TTATTCATTTATTTTTA
1 TTATTCATTTATTCTTA
45060 TTATTCATGTTATTCTTA
1 TTATTCAT-TTATTCTTA
45078 TTAT
1 TTAT
45082 ATGTATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.23, C:0.08, G:0.03, T:0.67
Consensus pattern (17 bp):
TTATTCATTTATTCTTA
Found at i:45151 original size:2 final size:2
Alignment explanation
Indices: 45144--45184 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
45134 ATTTTACTAT
45144 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
45185 TTCTTTAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:45612 original size:2 final size:2
Alignment explanation
Indices: 45605--45652 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
45595 TAATACTTTG
45605 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
45647 TT AT AT
1 AT AT AT
45653 TTTTCCTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:51364 original size:22 final size:22
Alignment explanation
Indices: 51339--51380 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
51329 GTATAAAAAA
51339 AACACCAAATAAT-ATATATAGT
1 AACA-CAAATAATAATATATAGT
*
51361 AACACTAATAATAATATATA
1 AACACAAATAATAATATATA
51381 ATGTGGTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (22 bp):
AACACAAATAATAATATATAGT
Found at i:57862 original size:29 final size:29
Alignment explanation
Indices: 57830--57886 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
57820 ATCAAATAGT
*
57830 TAAGAATATTTTCGAAAATATATTATATA
1 TAAGAATATTTTCAAAAATATATTATATA
57859 TAAGAATATTTTCAAAAATATATTATAT
1 TAAGAATATTTTCAAAAATATATTATAT
57887 CGATAATCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (29 bp):
TAAGAATATTTTCAAAAATATATTATATA
Found at i:58673 original size:23 final size:20
Alignment explanation
Indices: 58627--58674 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 20
58617 TTTATATCTT
* *
58627 TTAAAAAAATTATAAATATT
1 TTAAAAAAATTATAAAAATG
58647 TTAAAAAAATTAATATTAAAATG
1 TTAAAAAAATT-ATA--AAAATG
58670 TTAAA
1 TTAAA
58675 TAACAACACA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 11 0.48
21 3 0.13
23 9 0.39
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
TTAAAAAAATTATAAAAATG
Found at i:61049 original size:71 final size:70
Alignment explanation
Indices: 60929--61072 Score: 261
Period size: 71 Copynumber: 2.0 Consensus size: 70
60919 GAAGTTTGGT
60929 GAAGATGACTTTAGTGATGGTAAAGTTGGTGAATGCAAGTTTGACGAAGGGAAAGGTGAAGAAAA
1 GAAGATGACTTTAGTGATGGTAAAGTTGGTGAATGCAAGTTTGACGAAGGGAAAGGTGAAG-AAA
60994 GAACAA
65 GAACAA
* *
61000 GAAGATGACTTTAGTGATGGTAAAGTTGGTGAATGCAAGTTTGATGAAGGTAAAGGTGAAGAAAG
1 GAAGATGACTTTAGTGATGGTAAAGTTGGTGAATGCAAGTTTGACGAAGGGAAAGGTGAAGAAAG
61065 AACAA
66 AACAA
61070 GAA
1 GAA
61073 TTTTCACCGG
Statistics
Matches: 71, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
70 12 0.17
71 59 0.83
ACGTcount: A:0.41, C:0.05, G:0.32, T:0.22
Consensus pattern (70 bp):
GAAGATGACTTTAGTGATGGTAAAGTTGGTGAATGCAAGTTTGACGAAGGGAAAGGTGAAGAAAG
AACAA
Found at i:62044 original size:297 final size:297
Alignment explanation
Indices: 61482--62077 Score: 1117
Period size: 297 Copynumber: 2.0 Consensus size: 297
61472 CTTGCTACTT
*
61482 TGAGAATATATTTATGCTTAGGTTTTGCAACCCATTTTGTTGAGGGGGTGGACACAACAACTTTG
1 TGAGAATATATTTATGCTTAAGTTTTGCAACCCATTTTGTTGAGGGGGTGGACACAACAACTTTG
*
61547 ATGAATAATCCCTAAAGATTGAAAAGAGAGAAACACATTTTGGTCCAAAAATACAGACCCATTAA
66 ATGAATAATCCCTAAAGATTGAAAAGAGAGAAACACATTTTGGTCCAAAAAAACAGACCCATTAA
61612 CACTTCTAAAAACTTTGACAGAGACAGATAACTGATTCTGAACAAGATGAAAGAAGGTTTAAGGA
131 CACTTCTAAAAACTTTGACAGAGACAGATAACTGATTCTGAACAAGATGAAAGAAGGTTTAAGGA
61677 AATAAATGTCGGCTGACTTTAGTCTCAACAGGTAAACCCGAGTCACTCTGCTAACATCATCTACT
196 AATAAATGTCGGCTGACTTTAGTCTCAACAGGTAAACCCGAGTCACTCTGCTAACATCATCTACT
61742 AAAGTAAGAAAGTACCTATGTCCACTATGGCTGGAAA
261 AAAGTAAGAAAGTACCTATGTCCACTATGGCTGGAAA
61779 TGAGAATATATTTATGCTTAAGTTTTGCAACCCATTTTGTTGAGGGGTGTGGACACAACAACTTT
1 TGAGAATATATTTATGCTTAAGTTTTGCAACCCATTTTGTTGAGGGG-GTGGACACAACAACTTT
61844 GATGAATAATCCCTAAAGATTG-AAAGAGAGAAACACA-TTTGGTCCAAAAAAAACAGACCCATT
65 GATGAATAATCCCTAAAGATTGAAAAGAGAGAAACACATTTTGGTCC-AAAAAAACAGACCCATT
*
61907 AACACTTCTGAAAACTTTGACAGAGACAGATAACTGATTCTGAACAAGATGAAAGAAGGCTTTAA
129 AACACTTCTAAAAACTTTGACAGAGACAGATAACTGATTCTGAACAAGATGAAAGAAGG-TTTAA
61972 GGAAATAAATGTCGGCTGACTTTAGTCTCAACAGGTAAACCCGAGTCACTCTGCTAACATCATCT
193 GGAAATAAATGTCGGCTGACTTTAGTCTCAACAGGTAAACCCGAGTCACTCTGCTAACATCATCT
62037 A-TAAAGTAAGAAAGTACCTATGTCCACTATGGCTGGAAA
258 ACTAAAGTAAGAAAGTACCTATGTCCACTATGGCTGGAAA
62076 TG
1 TG
62078 TGATAAGGGC
Statistics
Matches: 293, Mismatches: 3, Indels: 6
0.97 0.01 0.02
Matches are distributed among these distances:
296 8 0.03
297 175 0.60
298 110 0.38
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.26
Consensus pattern (297 bp):
TGAGAATATATTTATGCTTAAGTTTTGCAACCCATTTTGTTGAGGGGGTGGACACAACAACTTTG
ATGAATAATCCCTAAAGATTGAAAAGAGAGAAACACATTTTGGTCCAAAAAAACAGACCCATTAA
CACTTCTAAAAACTTTGACAGAGACAGATAACTGATTCTGAACAAGATGAAAGAAGGTTTAAGGA
AATAAATGTCGGCTGACTTTAGTCTCAACAGGTAAACCCGAGTCACTCTGCTAACATCATCTACT
AAAGTAAGAAAGTACCTATGTCCACTATGGCTGGAAA
Done.