Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009590.1 Hibiscus syriacus cultivar Beakdansim tig00116969_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: 297105
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
File 1 of 2
Found at i:1570 original size:21 final size:21
Alignment explanation
Indices: 1546--1587 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1536 TATGAGAAAT
*
1546 TGTTTTAAAATAT-AAAAATGA
1 TGTTTCAAAAT-TGAAAAATGA
1567 TGTTTCAAAATTGAAAAATGA
1 TGTTTCAAAATTGAAAAATGA
1588 AAACAAACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.36
Consensus pattern (21 bp):
TGTTTCAAAATTGAAAAATGA
Found at i:5361 original size:20 final size:21
Alignment explanation
Indices: 5332--5387 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
5322 TTTGTGCTTC
*
5332 ATGCACCGATGCAT-TT-AACA
1 ATGCATCGATGCATCTTGAA-A
*
5352 ATGCATCGATGCATCCTTGAAT
1 ATGCATCGATGCAT-CTTGAAA
5374 ATGCATCGATGCAT
1 ATGCATCGATGCAT
5388 AAGACCATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.42
22 16 0.52
23 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGCATCGATGCATCTTGAAA
Found at i:6946 original size:21 final size:21
Alignment explanation
Indices: 6904--6947 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
6894 ACCCCGGGAG
*
6904 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
6925 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
6946 CT
1 CT
6948 CCTCCTCCCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:7776 original size:19 final size:19
Alignment explanation
Indices: 7752--7788 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
7742 GAATGCATTC
7752 CATGCACCGATGCACTCTT
1 CATGCACCGATGCACTCTT
*
7771 CATGCATCGATGCACTCT
1 CATGCACCGATGCACTCT
7789 GAATATTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.35, G:0.16, T:0.27
Consensus pattern (19 bp):
CATGCACCGATGCACTCTT
Found at i:7784 original size:64 final size:64
Alignment explanation
Indices: 7687--7916 Score: 234
Period size: 64 Copynumber: 3.6 Consensus size: 64
7677 TATTCAAAGG
* *
7687 CATGCACCGATGCATCAGTCCATGCATCGATGCATCGATGAATTAATT-AAACATCGAATGCATT
1 CATGCACCGATGCA-CACTCCATGCATCGATGCATC-ATGAATTATTTCAAACATCGAATGCATT
*
7751 C
64 T
* *
7752 CATGCACCGATGCACTCTTCATGCATCGATGCACTC-TGAA-TATTTTCAAAACATCGAATGCAT
1 CATGCACCGATGCACACTCCATGCATCGATGCA-TCATGAATTA-TTTC-AAACATCGAATGCAT
7815 TT
63 TT
* * ** * *
7817 GATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATT-TTTCAAACATCGAATGCATTT
1 CATGCACCGATGCACACTCCATGCATCGATGCATCATG-AATTATTTCAAACATCGAATGCATTT
* *** *
7881 CATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 CATGCACCGATGCACACTCCATGCATCGATGCATCA
7917 AGTGTTCCAA
Statistics
Matches: 138, Mismatches: 20, Indels: 15
0.80 0.12 0.09
Matches are distributed among these distances:
62 2 0.01
63 6 0.04
64 64 0.46
65 64 0.46
66 1 0.01
67 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (64 bp):
CATGCACCGATGCACACTCCATGCATCGATGCATCATGAATTATTTCAAACATCGAATGCATTT
Found at i:11102 original size:24 final size:24
Alignment explanation
Indices: 11005--11092 Score: 133
Period size: 24 Copynumber: 3.7 Consensus size: 24
10995 TTCTATTATA
* *
11005 ATACCTGACCTGGATTCTGATCAG
1 ATACTTGACCTGGATTCTGATCTG
11029 ATACTTGACCTGGATTCTGAT-TG
1 ATACTTGACCTGGATTCTGATCTG
*
11052 AATACTTGACCTGGATTTTGATCTG
1 -ATACTTGACCTGGATTCTGATCTG
11077 ATACTTGACCTGGATT
1 ATACTTGACCTGGATT
11093 ATGTTTTGAT
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
23 1 0.02
24 56 0.95
25 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.36
Consensus pattern (24 bp):
ATACTTGACCTGGATTCTGATCTG
Found at i:15770 original size:24 final size:24
Alignment explanation
Indices: 15743--15830 Score: 140
Period size: 24 Copynumber: 3.7 Consensus size: 24
15733 TTCTATTATA
*
15743 ATACCTGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATCGG
*
15767 ATACTTGACCTGGATTCTGATCGA
1 ATACTTGACCTGGATTCTGATCGG
* *
15791 ATACTTGACCTGGATTTTGATCTG
1 ATACTTGACCTGGATTCTGATCGG
15815 ATACTTGACCTGGATT
1 ATACTTGACCTGGATT
15831 ATGTTTTGAT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (24 bp):
ATACTTGACCTGGATTCTGATCGG
Found at i:15951 original size:35 final size:35
Alignment explanation
Indices: 15911--16008 Score: 178
Period size: 35 Copynumber: 2.8 Consensus size: 35
15901 TATACTTGGA
15911 AGCTCCTCGGCTGTGTGCTCAGGGCCTTACTTACC
1 AGCTCCTCGGCTGTGTGCTCAGGGCCTTACTTACC
*
15946 GGCTCCTCGGCTGTGTGCTCAGGGCCTTACTTACC
1 AGCTCCTCGGCTGTGTGCTCAGGGCCTTACTTACC
*
15981 AACTCCTCGGCTGTGTGCTCAGGGCCTT
1 AGCTCCTCGGCTGTGTGCTCAGGGCCTT
16009 TCTGGACTTG
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 60 1.00
ACGTcount: A:0.10, C:0.34, G:0.28, T:0.29
Consensus pattern (35 bp):
AGCTCCTCGGCTGTGTGCTCAGGGCCTTACTTACC
Found at i:19809 original size:22 final size:25
Alignment explanation
Indices: 19784--19843 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 25
19774 ATTCAAGAAG
19784 TTCTCTTCTCTT-GAAAA-A-TATT
1 TTCTCTTCTCTTAGAAAATATTATT
*
19806 TTCTCTCCTTCTTAGAAAATATTATT
1 TTCTCTTC-TCTTAGAAAATATTATT
19832 TTC-C-TCTCTTAG
1 TTCTCTTCTCTTAG
19844 TTTTTCCGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 7 0.22
23 10 0.31
24 6 0.19
25 2 0.06
26 7 0.22
ACGTcount: A:0.23, C:0.22, G:0.05, T:0.50
Consensus pattern (25 bp):
TTCTCTTCTCTTAGAAAATATTATT
Found at i:21190 original size:21 final size:21
Alignment explanation
Indices: 21164--21208 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
21154 ATTCTGACTA
21164 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
*
21185 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
21206 TCG
1 TCG
21209 AAATGCAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:21277 original size:20 final size:20
Alignment explanation
Indices: 21216--21359 Score: 180
Period size: 20 Copynumber: 7.2 Consensus size: 20
21206 TCGAAATGCA
*
21216 AATACGTAAATGGCAACGCG
1 AATACGTAAATCGCAACGCG
** * * *
21236 AATTTGGAAAATCGTAATGCG
1 AA-TACGTAAATCGCAACGCG
* *
21257 ATTACGTAAATTGCAACGCG
1 AATACGTAAATCGCAACGCG
21277 AATACGTAAATCGCAACGCG
1 AATACGTAAATCGCAACGCG
*
21297 AATACGTAAATCGCAACGTG
1 AATACGTAAATCGCAACGCG
* *
21317 AATACGTAAATCACAATGCG
1 AATACGTAAATCGCAACGCG
21337 AATACGTAAATCGCAACGCG
1 AATACGTAAATCGCAACGCG
21357 AAT
1 AAT
21360 CTGACTATCT
Statistics
Matches: 102, Mismatches: 21, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
20 89 0.87
21 13 0.13
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.20
Consensus pattern (20 bp):
AATACGTAAATCGCAACGCG
Found at i:21373 original size:20 final size:20
Alignment explanation
Indices: 21350--21388 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
21340 ACGTAAATCG
*
21350 CAACGCGAATCTGACTATCT
1 CAACGAGAATCTGACTATCT
* *
21370 CAACGAGATTTTGACTATC
1 CAACGAGAATCTGACTATC
21389 GCAATACTGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (20 bp):
CAACGAGAATCTGACTATCT
Found at i:22266 original size:24 final size:24
Alignment explanation
Indices: 22234--22287 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
22224 GTATTCGAAA
*
22234 TTTGATCTTGGTTAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
22258 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
22282 TTTGAT
1 TTTGAT
22288 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:24742 original size:20 final size:20
Alignment explanation
Indices: 24717--24805 Score: 144
Period size: 20 Copynumber: 4.5 Consensus size: 20
24707 CAATGCAGAA
24717 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
*
24737 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
*
24757 ATCGCAACGCGGAATTGACT
1 ATCGCAACGCGGAAATGACT
24777 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
24797 ATCGCAACG
1 ATCGCAACG
24806 AGAGAATCGC
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
20 61 0.95
21 3 0.05
ACGTcount: A:0.35, C:0.26, G:0.22, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:24816 original size:14 final size:14
Alignment explanation
Indices: 24797--24850 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
24787 GGAAATGACT
24797 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
24811 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
24830 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
24844 ATCGCAA
1 ATCGCAA
24851 TGCGAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:24865 original size:34 final size:33
Alignment explanation
Indices: 24777--24871 Score: 145
Period size: 33 Copynumber: 2.8 Consensus size: 33
24767 GGAATTGACT
* **
24777 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
24811 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
24844 ATCGCAATGCGAAAATGAAAATCGCAAC
1 ATCGCAATGCG-AAATGAAAATCGCAAC
24872 ACGAATTTAG
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 32 0.56
34 25 0.44
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:25005 original size:14 final size:14
Alignment explanation
Indices: 24986--25022 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
24976 CATCAATTAA
24986 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
25000 ACAAATCATCTTTT
1 ACAAATCAACATTT
25014 ACAAATCAA
1 ACAAATCAA
25023 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:26968 original size:20 final size:20
Alignment explanation
Indices: 26942--27010 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
26932 GAAACTTAAA
26942 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
26962 ATTGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
26982 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
27002 ATCGCAACG
1 ATCGCAACG
27011 AGAGAATCGC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:27080 original size:20 final size:20
Alignment explanation
Indices: 27055--27231 Score: 157
Period size: 20 Copynumber: 9.5 Consensus size: 20
27045 GATTCTTTCG
**
27055 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
27075 TTGCGATGGTCATTTTCGAA
1 TTGCGATAGTCATTTTCGCA
27095 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
27115 TTGCGATAGTCATTTTTGCG
1 TTGCGATAGTCATTTTCGCA
27135 TTGCGAT--T--TTGTT-G--
1 TTGCGATAGTCATT-TTCGCA
**
27149 TTGCGATTTTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
27168 TTGC-A-ATTC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
27182 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
27202 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
27222 TTGCGATAGT
1 TTGCGATAGT
27232 AAACTATTCT
Statistics
Matches: 131, Mismatches: 12, Indels: 28
0.77 0.07 0.16
Matches are distributed among these distances:
14 11 0.08
15 1 0.01
16 13 0.10
17 7 0.05
18 6 0.05
19 4 0.03
20 89 0.68
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.42
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:27139 original size:40 final size:40
Alignment explanation
Indices: 27017--27231 Score: 157
Period size: 40 Copynumber: 5.9 Consensus size: 40
27007 AACGAGAGAA
* **
27017 TCGCAATGCGATTTTCA-TTTCGCATTGCGAT--TC--TT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
** *
27052 TCG--TTGCGATAGTCAAATTCGCATTGCGATGGTCATTT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
*
27090 TCGAATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
* * **
27130 TTGCGTTGCGAT--T--TTGTT-G--TTGCGATTTTCA-TT
1 TCGCATTGCGATAGTCATT-TTCGCATTGCGATAGTCATTT
* *
27163 TCGCATTGC-A-ATTC--TCTCG--TTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
27197 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGT
27232 AAACTATTCT
Statistics
Matches: 142, Mismatches: 19, Indels: 33
0.73 0.10 0.17
Matches are distributed among these distances:
32 2 0.01
33 31 0.22
34 34 0.24
35 4 0.03
36 8 0.06
37 2 0.01
38 10 0.07
40 51 0.36
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.42
Consensus pattern (40 bp):
TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
Found at i:27153 original size:34 final size:34
Alignment explanation
Indices: 27115--27208 Score: 109
Period size: 33 Copynumber: 2.8 Consensus size: 34
27105 CATTTTCGCA
* * * * *
27115 TTGCGATAGTCATTTTTGCGTTGCGATTTTGTTG
1 TTGCGATAGTCATTTTCGCATTGCGATTCTCTCG
** *
27149 TTGCGATTTTCA-TTTCGCATTGCAATTCTCTCG
1 TTGCGATAGTCATTTTCGCATTGCGATTCTCTCG
27182 TTGCGATAGTCATTTTCGCATTGCGAT
1 TTGCGATAGTCATTTTCGCATTGCGAT
27209 AGTCATTTTC
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
33 25 0.52
34 23 0.48
ACGTcount: A:0.15, C:0.18, G:0.21, T:0.46
Consensus pattern (34 bp):
TTGCGATAGTCATTTTCGCATTGCGATTCTCTCG
Found at i:29174 original size:20 final size:20
Alignment explanation
Indices: 29116--29185 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
29106 GAAACTTTAA
* **
29116 ATCGCAACACGAAAATGAAA
1 ATCGCAACGCGAAAATGACT
*
29136 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
29156 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
29176 ATCGCAACGC
1 ATCGCAACGC
29186 AAGAATCGCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.41, C:0.26, G:0.17, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:29224 original size:33 final size:33
Alignment explanation
Indices: 29115--29228 Score: 95
Period size: 33 Copynumber: 3.2 Consensus size: 33
29105 TGAAACTTTA
* *
29115 AATCGCAACACGAAAATGAAAATCGCAACACGAAAATG
1 AATCGCAACGCG-AAATGAAAATCGC-A-ACG-ACA-G
* **
29153 ACTATCGCAACGCGAATTTGACTATCGCAACG-CAAG
1 A--ATCGCAACGCGAA-ATGAAAATCGCAACGAC-AG
29189 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
29222 AATCGCA
1 AATCGCA
29229 TTGCGATAGT
Statistics
Matches: 63, Mismatches: 8, Indels: 15
0.73 0.09 0.17
Matches are distributed among these distances:
33 21 0.33
34 14 0.22
36 2 0.03
37 1 0.02
38 4 0.06
39 3 0.05
40 18 0.29
ACGTcount: A:0.44, C:0.25, G:0.18, T:0.13
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:29609 original size:22 final size:22
Alignment explanation
Indices: 29545--29610 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
29535 TGACCGTGAA
* *
29545 TGATTTCGTCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAT
* *
29567 TGATATCGTCGGAGATTGGGAT
1 TGATTTCGTCGGAGATGGGGAT
*
29589 TGATTTCATCGGAGATGGGGAT
1 TGATTTCGTCGGAGATGGGGAT
29611 GGATGTCACC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.23, C:0.11, G:0.36, T:0.30
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAT
Found at i:29822 original size:20 final size:20
Alignment explanation
Indices: 29794--29843 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
29784 TATGTAAATC
29794 GCATTGCGATAGTCAGATTA
1 GCATTGCGATAGTCAGATTA
* *
29814 GCGTTGCGATAGTCAGATTC
1 GCATTGCGATAGTCAGATTA
29834 GCATTGCGAT
1 GCATTGCGAT
29844 TTACGTATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (20 bp):
GCATTGCGATAGTCAGATTA
Found at i:29853 original size:20 final size:20
Alignment explanation
Indices: 29830--29963 Score: 196
Period size: 20 Copynumber: 6.7 Consensus size: 20
29820 CGATAGTCAG
29830 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
29850 ATTCGCATTGCAATTTACGT
1 ATTCGCATTGCGATTTACGT
29870 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
29890 ATTCGCATAGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * **
29910 AATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
*
29931 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
29951 ATTCGCATTGCGA
1 ATTCGCATTGCGA
29964 ATTAGGAAAA
Statistics
Matches: 99, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
20 84 0.85
21 15 0.15
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.37
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:29984 original size:21 final size:21
Alignment explanation
Indices: 29960--30000 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
29950 TATTCGCATT
29960 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
*
29981 GCGAATTTGGAAAATCGCAA
1 GCGAATTAGGAAAATCGCAA
30001 TGTGATAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:33983 original size:17 final size:17
Alignment explanation
Indices: 33961--33994 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
33951 TCCATTAAAA
*
33961 CCTTTAACTTTTTACCC
1 CCTTTAACTCTTTACCC
33978 CCTTTAACTCTTTACCC
1 CCTTTAACTCTTTACCC
33995 GTTAACCCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.38, G:0.00, T:0.44
Consensus pattern (17 bp):
CCTTTAACTCTTTACCC
Found at i:36805 original size:9 final size:10
Alignment explanation
Indices: 36776--36809 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
36766 TATGTCTTTT
*
36776 ATTTTTCTTT
1 ATTTTTCTTA
36786 ATTTTTCTTA
1 ATTTTTCTTA
36796 ATTTTT-TTA
1 ATTTTTCTTA
36805 ATTTT
1 ATTTT
36810 AAATAAGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (10 bp):
ATTTTTCTTA
Found at i:43123 original size:191 final size:193
Alignment explanation
Indices: 42799--43186 Score: 746
Period size: 191 Copynumber: 2.0 Consensus size: 193
42789 ACTGTTTAGG
42799 TTGTCCAAGTATTGTTTTGTTAGAAAATGAAAAAGGAAAGTGACCAATCAACAACAACCAAGGGA
1 TTGTCCAAGTATTGTTTTGTTAGAAAATGAAAAAGGAAAGTGACCAATCAACAACAACCAAGGGA
42864 AAAAAAGGAAGACAATTCTCTCTGGGGGTGCTTATGGAGCGTCGATCACGAGTTGATAGTATTTG
66 AAAAAAGGAAGACAATTCTCTCTGGGGGTGCTTATGGAGCGTCGATCACGAGTTGATAGTATTTG
42929 ATTTGTGTTCGTT-AAAAAATTTATTATTTGATTTGACTCGTTGCTCG-TAAATTCATTAAAA
131 ATTTGTGTTCGTTAAAAAAATTTATTATTTGATTTGACTCGTTGCTCGTTAAATTCATTAAAA
42990 TTGTCCAAGTATTGTTTTGTTAGAAAATGAAAAAGGAAAGTGACCAATCAACAACAACCAAGGGA
1 TTGTCCAAGTATTGTTTTGTTAGAAAATGAAAAAGGAAAGTGACCAATCAACAACAACCAAGGGA
43055 AAAAAAGGAAGACAATTCTCTCTGGGGGTGCTTATGGAGAC-TCGATCACGAGTTGATAGTATTT
66 AAAAAAGGAAGACAATTCTCTCTGGGGGTGCTTATGGAG-CGTCGATCACGAGTTGATAGTATTT
43119 GATTTGTGTTCGTTAAAAAAATTTATTATTTGATTTGACTCGTTGCTCGTTAAATTCATTAAAA
130 GATTTGTGTTCGTTAAAAAAATTTATTATTTGATTTGACTCGTTGCTCGTTAAATTCATTAAAA
43183 TTGT
1 TTGT
43187 GTTCGACTCG
Statistics
Matches: 194, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
191 141 0.73
192 35 0.18
193 18 0.09
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (193 bp):
TTGTCCAAGTATTGTTTTGTTAGAAAATGAAAAAGGAAAGTGACCAATCAACAACAACCAAGGGA
AAAAAAGGAAGACAATTCTCTCTGGGGGTGCTTATGGAGCGTCGATCACGAGTTGATAGTATTTG
ATTTGTGTTCGTTAAAAAAATTTATTATTTGATTTGACTCGTTGCTCGTTAAATTCATTAAAA
Found at i:43543 original size:20 final size:21
Alignment explanation
Indices: 43518--43610 Score: 91
Period size: 21 Copynumber: 4.5 Consensus size: 21
43508 TTTTCCCAAT
*
43518 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
43538 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
43559 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* * **
43579 TTGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
43600 TCGCAATGCGA
1 TCGCAATGCGA
43611 TACTTACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.46
21 30 0.54
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:43563 original size:41 final size:41
Alignment explanation
Indices: 43518--43610 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
43508 TTTTCCCAAT
43518 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
*
43559 TCGCAATGCGAATAAGTAAATTGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
43600 TCGCAATGCGA
1 TCGCAATGCGA
43611 TACTTACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:43624 original size:20 final size:20
Alignment explanation
Indices: 43599--43692 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
43589 AATTGGGAAA
*
43599 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * *
43619 ATCGCAATGCGATA-ATACAAA
1 ATCGCAACGCGATACTTAC--T
*
43640 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
43660 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
43680 TTCGCAACGCGAT
1 ATCGCAACGCGAT
43693 TTACATAATC
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 44 0.71
21 12 0.19
22 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:43641 original size:41 final size:41
Alignment explanation
Indices: 43596--43673 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
43586 GCGAATTGGG
* * *
43596 AAAATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTTACTATCGCAACGCGATAATAC
*
43637 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTTACTATCGCAACGCGATA
43674 CTGACTTTCG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTTACTATCGCAACGCGATAATAC
Found at i:43906 original size:21 final size:21
Alignment explanation
Indices: 43880--43921 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
43870 CACTCTCTCA
43880 CCATCTCCGACGAAATCCGTC
1 CCATCTCCGACGAAATCCGTC
*
43901 CCATCTCCGGCGAAATCCGTC
1 CCATCTCCGACGAAATCCGTC
43922 TATCTAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.43, G:0.17, T:0.19
Consensus pattern (21 bp):
CCATCTCCGACGAAATCCGTC
Found at i:44191 original size:20 final size:20
Alignment explanation
Indices: 44162--44205 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
44152 CGCGATTTAG
44162 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
44182 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
44202 TTTC
1 TTTC
44206 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.18, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:45526 original size:18 final size:18
Alignment explanation
Indices: 45500--45544 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
45490 CTCACTTCGG
* *
45500 GAGCCATCACCTCGCCCA
1 GAGCCATCACCCCACCCA
*
45518 GAGCTATCACCCCACCCA
1 GAGCCATCACCCCACCCA
45536 GAGCCATCA
1 GAGCCATCA
45545 TCTGATCGGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.47, G:0.16, T:0.11
Consensus pattern (18 bp):
GAGCCATCACCCCACCCA
Found at i:46039 original size:20 final size:19
Alignment explanation
Indices: 46005--46070 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
45995 ATAGTTACTT
*
46005 TCGCAACACGAAATGACTA
1 TCGCAACGCGAAATGACTA
*
46024 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGACTA
* **
46044 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGACTA
46063 TCGCAACG
1 TCGCAACG
46071 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 22 0.56
20 17 0.44
ACGTcount: A:0.38, C:0.24, G:0.23, T:0.15
Consensus pattern (19 bp):
TCGCAACGCGAAATGACTA
Found at i:46116 original size:14 final size:14
Alignment explanation
Indices: 46059--46114 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
46049 ATGCGAAATG
46059 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
46073 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
*
46089 ATGAAATCGCAATGAC
1 A--AAATCGCAACGAC
46105 AAAATCGCAA
1 AAAATCGCAA
46115 TGCGAAATGA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
14 19 0.54
16 7 0.20
18 9 0.26
ACGTcount: A:0.50, C:0.23, G:0.16, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:46134 original size:33 final size:33
Alignment explanation
Indices: 46043--46135 Score: 161
Period size: 32 Copynumber: 2.8 Consensus size: 33
46033 GGAAATGGCT
*
46043 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
*
46076 ATCGCAACGCGAAATG-AAATCGCAATGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
46108 ATCGCAATGCGAAATGAAAATCGCAATG
1 ATCGCAATGCGAAATGAAAATCGCAATG
46136 CGATTTGTGT
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.54
33 26 0.46
ACGTcount: A:0.46, C:0.20, G:0.19, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAATGACAAA
Found at i:46179 original size:19 final size:19
Alignment explanation
Indices: 46164--46267 Score: 111
Period size: 19 Copynumber: 5.4 Consensus size: 19
46154 GCGATTTTGT
46164 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
46182 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
46201 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
46221 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
46240 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
46260 TGTTGCGA
1 CGTTGCGA
46268 AAGTAAACTA
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
18 8 0.11
19 36 0.49
20 29 0.40
ACGTcount: A:0.14, C:0.21, G:0.24, T:0.40
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:46225 original size:39 final size:38
Alignment explanation
Indices: 46175--46248 Score: 112
Period size: 39 Copynumber: 1.9 Consensus size: 38
46165 GTTGCGATTT
**
46175 CATTTCGCGTTGCGATTTTCATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGTCATTTCGCATTGCGATAGC
*
46213 CATTTCCGCGTTGCGATAGTCATTTCGCGTTGCGAT
1 CATTT-CGCGTTGCGATAGTCATTTCGCATTGCGAT
46249 TTTAAGTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 5 0.16
39 27 0.84
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.38
Consensus pattern (38 bp):
CATTTCGCGTTGCGATAGTCATTTCGCATTGCGATAGC
Found at i:48246 original size:18 final size:18
Alignment explanation
Indices: 48207--48269 Score: 99
Period size: 19 Copynumber: 3.4 Consensus size: 18
48197 AAAACAGACT
*
48207 ATCGCAACGCGAAATGGAA
1 ATCGCAATGCGAAAT-GAA
48226 ATCGCAATGCGAAATGAA
1 ATCGCAATGCGAAATGAA
48244 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
48263 ATCGCAA
1 ATCGCAA
48270 CGAGAAAATC
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
18 19 0.45
19 23 0.55
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.14
Consensus pattern (18 bp):
ATCGCAATGCGAAATGAA
Found at i:48332 original size:20 final size:20
Alignment explanation
Indices: 48307--48363 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
48297 TCGCATTGCG
*
48307 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAACC
*
48327 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAACC
*
48347 ATTTTCGCATTGCGATA
1 ATTTTCGCGTTGCGATA
48364 GTCAAATGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAACC
Found at i:49428 original size:24 final size:24
Alignment explanation
Indices: 49401--49454 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
49391 GTATTCGAAA
* *
49401 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
49425 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
49449 TTTGAT
1 TTTGAT
49455 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:49646 original size:12 final size:12
Alignment explanation
Indices: 49629--49653 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49619 ATATAATCCT
49629 GAAGAAGAAAAA
1 GAAGAAGAAAAA
49641 GAAGAAGAAAAA
1 GAAGAAGAAAAA
49653 G
1 G
49654 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:51954 original size:39 final size:36
Alignment explanation
Indices: 51911--52058 Score: 145
Period size: 33 Copynumber: 4.3 Consensus size: 36
51901 CTTAATGTCC
*
51911 ATCGCAACGCGGAAATTACTATCGCAATGCGAAATGAAA
1 ATCGCAACGCGGAAA-GA--ATCGCAATGCGAAATGAAA
*
51950 ATCGCAA--C-GAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGCGGAAAGAATCGCAATGCGAAATGAAA
* **
51983 ATCGCAACGC--TAA-TTTCGCAATGCGAAATGAAA
1 ATCGCAACGCGGAAAGAATCGCAATGCGAAATGAAA
*
52016 ATCGCAACGAGG---GAATCGCAATGCGAAATG-AA
1 ATCGCAACGCGGAAAGAATCGCAATGCGAAATGAAA
52048 ATCGCAACGCG
1 ATCGCAACGCG
52059 AATTTAATTT
Statistics
Matches: 94, Mismatches: 10, Indels: 17
0.78 0.08 0.14
Matches are distributed among these distances:
32 12 0.13
33 68 0.72
34 1 0.01
35 2 0.02
36 3 0.03
37 1 0.01
39 7 0.07
ACGTcount: A:0.41, C:0.21, G:0.23, T:0.16
Consensus pattern (36 bp):
ATCGCAACGCGGAAAGAATCGCAATGCGAAATGAAA
Found at i:51973 original size:33 final size:33
Alignment explanation
Indices: 51931--52056 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
51921 GGAAATTACT
51931 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
51964 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
51996 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
52030 ATCGCAATGCGAAATG-AAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
52057 CGAATTTAAT
Statistics
Matches: 84, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
32 12 0.14
33 71 0.85
34 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:52038 original size:66 final size:65
Alignment explanation
Indices: 51932--52063 Score: 237
Period size: 66 Copynumber: 2.0 Consensus size: 65
51922 GAAATTACTA
*
51932 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATG-AAATCGCAACGCGAAT
51997 T
65 T
*
51998 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAATCGCAACGCGAATT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAATCGCAACGCGAATT
52063 T
1 T
52064 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
65 17 0.27
66 47 0.73
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (65 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAATCGCAACGCGAATT
Found at i:52078 original size:19 final size:20
Alignment explanation
Indices: 52056--52098 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
52046 AAATCGCAAC
52056 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
52075 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
52095 GCGA
1 GCGA
52099 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:52083 original size:14 final size:14
Alignment explanation
Indices: 52084--52117 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
52074 TGCGATTTTC
52084 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
52098 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
52112 ATTTTC
1 ATTTTC
52118 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:52259 original size:14 final size:14
Alignment explanation
Indices: 52240--52276 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
52230 CATCAATTAA
52240 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
52254 ACAAATCACCTTTT
1 ACAAATCAACTTTT
52268 ACAAATCAA
1 ACAAATCAA
52277 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:53674 original size:21 final size:21
Alignment explanation
Indices: 53645--53725 Score: 65
Period size: 21 Copynumber: 3.9 Consensus size: 21
53635 GAATGGTGGG
*
53645 AGGGACCTCTTCAACGATGAT
1 AGGGGCCTCTTCAACGATGAT
* * * **
53666 AGTGGCCTCTTGAACGGTGGG
1 AGGGGCCTCTTCAACGATGAT
* * *
53687 AGGGGACTC-TCGAGGAATGAT
1 AGGGGCCTCTTCAACG-ATGAT
53708 AGGGGCCTCTTCAACGAT
1 AGGGGCCTCTTCAACGAT
53726 ATGAGTGGAC
Statistics
Matches: 41, Mismatches: 17, Indels: 4
0.66 0.27 0.06
Matches are distributed among these distances:
20 3 0.07
21 34 0.83
22 4 0.10
ACGTcount: A:0.23, C:0.21, G:0.33, T:0.22
Consensus pattern (21 bp):
AGGGGCCTCTTCAACGATGAT
Found at i:53707 original size:42 final size:41
Alignment explanation
Indices: 53630--53752 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
53620 GTGAATCGGG
* * * *
53630 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGATAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
53672 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * ** * *
53714 CTCTTCAACGATATGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
53753 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.17, G:0.36, T:0.24
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:55779 original size:20 final size:19
Alignment explanation
Indices: 55748--55891 Score: 74
Period size: 20 Copynumber: 7.9 Consensus size: 19
55738 TCTTTTGGTT
55748 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
55767 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
55788 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
55807 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
**
55821 GAAATGACTATCG---CGA
1 GAAATGAAAATCGCAACGA
** * *
55837 -CCA-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
55854 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGA
*
55874 GAAATAAAAATCGCAACG
1 GAAATGAAAATCGCAACG
55892 CGATTTTGGT
Statistics
Matches: 95, Mismatches: 17, Indels: 26
0.69 0.12 0.19
Matches are distributed among these distances:
14 17 0.18
15 1 0.01
16 4 0.04
17 4 0.04
18 1 0.01
19 19 0.20
20 47 0.49
21 2 0.02
ACGTcount: A:0.43, C:0.23, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:55830 original size:33 final size:33
Alignment explanation
Indices: 55773--55871 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
55763 ACGAGATAAT
*
55773 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
55807 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
55840 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
55872 GCGAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:55913 original size:19 final size:19
Alignment explanation
Indices: 55891--55934 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
55881 AAATCGCAAC
*
55891 GCGATTTTGGTTTCGCGTT
1 GCGATTTTGATTTCGCGTT
*
55910 GCGATTTTTATTTCGCGTT
1 GCGATTTTGATTTCGCGTT
55929 GCGATT
1 GCGATT
55935 ATCTCGTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.48
Consensus pattern (19 bp):
GCGATTTTGATTTCGCGTT
Found at i:56597 original size:20 final size:20
Alignment explanation
Indices: 56572--56645 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
56562 GATTTTCCCA
*
56572 ATTCGCGTTGTGATTTACTT
1 ATTCGCGTTGCGATTTACTT
* * **
56592 ATTCGCATTGCGATTTTCCCA
1 ATTCGCGTTGCGA-TTTACTT
56613 ATTCGCGTTGCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
*
56633 ATTCGCATTGCGA
1 ATTCGCGTTGCGA
56646 ATTGGGAAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.63
21 16 0.37
ACGTcount: A:0.18, C:0.22, G:0.19, T:0.42
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTACTT
Found at i:56606 original size:41 final size:41
Alignment explanation
Indices: 56556--56645 Score: 171
Period size: 41 Copynumber: 2.2 Consensus size: 41
56546 AAGTATATCA
*
56556 CATTGCGATTTTCCCAATTCGCGTTGTGATTTACTTATTCG
1 CATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCG
56597 CATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCG
1 CATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCG
56638 CATTGCGA
1 CATTGCGA
56646 ATTGGGAAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.41
Consensus pattern (41 bp):
CATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCG
Found at i:56617 original size:21 final size:20
Alignment explanation
Indices: 56556--56645 Score: 81
Period size: 20 Copynumber: 4.4 Consensus size: 20
56546 AAGTATATCA
*
56556 CATTGCGATTTTCCCAATTCG
1 CATTGCGA-TTTACCAATTCG
* * **
56577 CGTTGTGATTTACTTATTCG
1 CATTGCGATTTACCAATTCG
*
56597 CATTGCGATTTTCCCAATTCG
1 CATTGCGA-TTTACCAATTCG
* **
56618 CGTTGCGATTTACTTATTCG
1 CATTGCGATTTACCAATTCG
56638 CATTGCGA
1 CATTGCGA
56646 ATTGGGAAAA
Statistics
Matches: 53, Mismatches: 15, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
20 31 0.58
21 22 0.42
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.41
Consensus pattern (20 bp):
CATTGCGATTTACCAATTCG
Found at i:64466 original size:12 final size:12
Alignment explanation
Indices: 64449--64477 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
64439 GGAGAAGAGG
64449 TTTTAGATAAAC
1 TTTTAGATAAAC
64461 TTTTAGATAAAC
1 TTTTAGATAAAC
64473 TTTTA
1 TTTTA
64478 TCTATGAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (12 bp):
TTTTAGATAAAC
Found at i:65973 original size:6 final size:6
Alignment explanation
Indices: 65962--66000 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
65952 TGAGCAAAAG
* * *
65962 TTGCTT TTGCTT TTGCTT TTGTTT TTACTT TTACTT TTG
1 TTGCTT TTGCTT TTGCTT TTGCTT TTGCTT TTGCTT TTG
66001 TTCTAATCCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.05, C:0.13, G:0.13, T:0.69
Consensus pattern (6 bp):
TTGCTT
Found at i:66961 original size:18 final size:18
Alignment explanation
Indices: 66919--66962 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
66909 ATAAAATTTT
66919 AAAAATAATTATTTTATAC
1 AAAAAT-ATTATTTTATAC
*
66938 ATAAATATTATTTTATTA-
1 AAAAATATTATTTTA-TAC
66956 AAAAATA
1 AAAAATA
66963 AAATTTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
AAAAATATTATTTTATAC
Found at i:68562 original size:13 final size:13
Alignment explanation
Indices: 68544--68573 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
68534 TTTGAAAAAC
*
68544 AAAATATTTTTTT
1 AAAATAATTTTTT
68557 AAAATAATTTTTT
1 AAAATAATTTTTT
68570 AAAA
1 AAAA
68574 AATATATGAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AAAATAATTTTTT
Found at i:69412 original size:20 final size:21
Alignment explanation
Indices: 69383--69431 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
69373 TTATTGTGTA
69383 AGTTACAGAG-TAATTACAAG
1 AGTTACAGAGTTAATTACAAG
* *
69403 AGTTATAGAGTTAATTACATGG
1 AGTTACAGAGTTAATTACA-AG
69425 AGTTACA
1 AGTTACA
69432 AGCGACTGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 9 0.38
21 8 0.33
22 7 0.29
ACGTcount: A:0.41, C:0.08, G:0.20, T:0.31
Consensus pattern (21 bp):
AGTTACAGAGTTAATTACAAG
Found at i:70006 original size:25 final size:28
Alignment explanation
Indices: 69974--70036 Score: 89
Period size: 25 Copynumber: 2.4 Consensus size: 28
69964 TATTAACATG
69974 AAAAATATTTTTA-TATTAATTT-AT-T
1 AAAAATATTTTTATTATTAATTTAATAT
*
69999 AAATATA-TTTTATTATTAATTTAATAT
1 AAAAATATTTTTATTATTAATTTAATAT
70026 AAAAATATTTT
1 AAAAATATTTT
70037 ATTTTTATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 5 0.16
25 15 0.47
26 2 0.06
27 7 0.22
28 3 0.09
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
AAAAATATTTTTATTATTAATTTAATAT
Found at i:74472 original size:14 final size:14
Alignment explanation
Indices: 74429--74472 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
74419 TAACAAAAAA
74429 TAATAATTTTATAC
1 TAATAATTTTATAC
* *
74443 TAAT--TTTTTTAG
1 TAATAATTTTATAC
74455 TAATAATTTTATAC
1 TAATAATTTTATAC
74469 TAAT
1 TAAT
74473 TGAATGAGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
12 10 0.42
14 14 0.58
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.55
Consensus pattern (14 bp):
TAATAATTTTATAC
Found at i:75228 original size:2 final size:2
Alignment explanation
Indices: 75223--75290 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
75213 TAACTTTTTA
75223 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
75265 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
75291 TGTTTCTCTC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:82102 original size:27 final size:30
Alignment explanation
Indices: 82072--82132 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
82062 TTCGAACTAA
82072 TTCGGTTAA-CCGATC-G-AACCGAATTAG
1 TTCGGTTAATCCGATCGGCAACCGAATTAG
* *
82099 TTCGGTTAATTCGATCGGCCACCGAATTAG
1 TTCGGTTAATCCGATCGGCAACCGAATTAG
82129 TTCG
1 TTCG
82133 ATCGGTTAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 9 0.31
28 5 0.17
29 1 0.03
30 14 0.48
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (30 bp):
TTCGGTTAATCCGATCGGCAACCGAATTAG
Found at i:91597 original size:22 final size:22
Alignment explanation
Indices: 91569--91612 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
91559 GAAATGTTAA
91569 AAGTCATAAAAAGGGGATGCAC
1 AAGTCATAAAAAGGGGATGCAC
* *
91591 AAGTCATAGAAAGGGGCTGCAC
1 AAGTCATAAAAAGGGGATGCAC
91613 CGAAAGTACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.41, C:0.16, G:0.30, T:0.14
Consensus pattern (22 bp):
AAGTCATAAAAAGGGGATGCAC
Found at i:94333 original size:15 final size:15
Alignment explanation
Indices: 94313--94341 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
94303 GAGAGATTAG
94313 AATTAAGATGGGATA
1 AATTAAGATGGGATA
94328 AATTAAGATGGGAT
1 AATTAAGATGGGAT
94342 TTAAGTATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.28, T:0.28
Consensus pattern (15 bp):
AATTAAGATGGGATA
Found at i:94469 original size:21 final size:21
Alignment explanation
Indices: 94443--94486 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
94433 ATTTTGGGCT
*
94443 AGGGGAATCGATACACATTCA
1 AGGGGAACCGATACACATTCA
* *
94464 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACACATTCA
94485 AG
1 AG
94487 CGAATAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.25, G:0.25, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACACATTCA
Found at i:94556 original size:22 final size:22
Alignment explanation
Indices: 94513--94556 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
94503 AATGTCATGG
*
94513 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
94535 GGGAACCGAT-CCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
94557 AAATTGTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.32, C:0.34, G:0.27, T:0.07
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:96082 original size:91 final size:95
Alignment explanation
Indices: 95879--96090 Score: 278
Period size: 91 Copynumber: 2.2 Consensus size: 95
95869 GAGTCGAGGG
*
95879 TGATATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACA
1 TGATATGTGGTCCTTC-GGAC--ATATGTA-T-TTTGGAACATGTATGAAGTCTGGTGAGACACA
95944 TACTTGATCCCTAGTATATGTATATGATTCTTAAAA
61 TACTTGATCCCTAGTATATG-ATATGATTCTTAAAA
95980 TGATA-GT-GTCCTTCGGACATAT-TA-TTTGGAACATGTATGAAGTCTGGTGAGA-ACATACTT
1 TGATATGTGGTCCTTCGGACATATGTATTTTGGAACATGTATGAAGTCTGGTGAGACACATACTT
96040 GATCCCTAGTATATG-TAT-A-TCTTAAGGAA
66 GATCCCTAGTATATGATATGATTCTTAA--AA
*
96069 TGATATGTGGTCCTTAGGACAT
1 TGATATGTGGTCCTTCGGACAT
96091 TATATATGGC
Statistics
Matches: 105, Mismatches: 2, Indels: 18
0.84 0.02 0.14
Matches are distributed among these distances:
87 6 0.06
88 1 0.01
89 10 0.10
90 2 0.02
91 35 0.33
92 27 0.26
95 2 0.02
96 4 0.04
98 4 0.04
99 7 0.07
100 2 0.02
101 5 0.05
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (95 bp):
TGATATGTGGTCCTTCGGACATATGTATTTTGGAACATGTATGAAGTCTGGTGAGACACATACTT
GATCCCTAGTATATGATATGATTCTTAAAA
Found at i:96128 original size:23 final size:23
Alignment explanation
Indices: 96098--96202 Score: 124
Period size: 23 Copynumber: 4.6 Consensus size: 23
96088 CATTATATAT
96098 GGCACTACGGTGCAACTCTACGC
1 GGCACTACGGTGCAACTCTACGC
* *
96121 GGCACTACGGTGCAATTCTA--T
1 GGCACTACGGTGCAACTCTACGC
96142 GGCACTACGGTGCAACTCTACGC
1 GGCACTACGGTGCAACTCTACGC
* * * *
96165 GGGCACTATGGTGCAATTCTATGT
1 -GGCACTACGGTGCAACTCTACGC
*
96189 GGCACTTCGGTGCA
1 GGCACTACGGTGCA
96203 TTATATGAGC
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
21 19 0.28
23 31 0.45
24 19 0.28
ACGTcount: A:0.21, C:0.28, G:0.28, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAACTCTACGC
Found at i:96158 original size:44 final size:45
Alignment explanation
Indices: 96095--96202 Score: 173
Period size: 44 Copynumber: 2.4 Consensus size: 45
96085 GGACATTATA
96095 TATGGCACTACGGTGCAACTCTACGC-GGCACTACGGTGCAATTC
1 TATGGCACTACGGTGCAACTCTACGCGGGCACTACGGTGCAATTC
*
96139 TATGGCACTACGGTGCAACTCTACGCGGGCACTATGGTGCAATTC
1 TATGGCACTACGGTGCAACTCTACGCGGGCACTACGGTGCAATTC
*
96184 TATGTGGCACTTCGGTGCA
1 TA--TGGCACTACGGTGCA
96203 TTATATGAGC
Statistics
Matches: 59, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
44 26 0.44
45 19 0.32
47 14 0.24
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (45 bp):
TATGGCACTACGGTGCAACTCTACGCGGGCACTACGGTGCAATTC
Found at i:106986 original size:18 final size:20
Alignment explanation
Indices: 106944--106984 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
106934 TTAGTTTATA
* *
106944 AAATATAAGATTATCAGTGG
1 AAATAAAAGATTATCAGTAG
106964 AAATAAAAGATTATCAG-AG
1 AAATAAAAGATTATCAGTAG
106983 AA
1 AA
106985 TAGAATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.54, C:0.05, G:0.17, T:0.24
Consensus pattern (20 bp):
AAATAAAAGATTATCAGTAG
Found at i:107166 original size:36 final size:38
Alignment explanation
Indices: 107121--107209 Score: 98
Period size: 36 Copynumber: 2.4 Consensus size: 38
107111 TTTGTATATT
*
107121 ATTACAAATTATAAAATATTTATAT-ATTTTCTTTA-AAA
1 ATTA-AAATTATAAAATATTTATATAAATTT-TTTACAAA
107159 ATT-AAATTCAT--AATATTTATATAAATTTTTTACAAA
1 ATTAAAATT-ATAAAATATTTATATAAATTTTTTACAAA
*
107195 ATTAAAAATATAAAA
1 ATTAAAATTATAAAA
107210 AAAGTTTAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
35 15 0.35
36 17 0.40
37 6 0.14
38 5 0.12
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (38 bp):
ATTAAAATTATAAAATATTTATATAAATTTTTTACAAA
Found at i:107205 original size:31 final size:31
Alignment explanation
Indices: 107122--107205 Score: 75
Period size: 35 Copynumber: 2.6 Consensus size: 31
107112 TTGTATATTA
*
107122 TTAC-AAATTATAAAATATTTATATATTTTCT
1 TTACAAAATTA-AAAATATTTATATAATTTCT
107153 TTA-AAAATTAAATTCATAATATTTATATAAATTT-T
1 TTACAAAATT-AA---A-AATATTTATAT-AATTTCT
107188 TTACAAAATTAAAAATAT
1 TTACAAAATTAAAAATAT
107206 AAAAAAAGTT
Statistics
Matches: 44, Mismatches: 1, Indels: 16
0.72 0.02 0.26
Matches are distributed among these distances:
31 14 0.32
32 2 0.05
34 1 0.02
35 17 0.39
36 10 0.23
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (31 bp):
TTACAAAATTAAAAATATTTATATAATTTCT
Found at i:110936 original size:22 final size:22
Alignment explanation
Indices: 110911--110961 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
110901 TGATGGGAAT
*
110911 CACGGGTTCTGCAAGGAGAGAG
1 CACGGGTTCTGCAAGGAGAAAG
*
110933 CACGGGTTCTGCAAGGAGAAAT
1 CACGGGTTCTGCAAGGAGAAAG
110955 CACGGGT
1 CACGGGT
110962 CCTGGGTCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.27, C:0.20, G:0.37, T:0.16
Consensus pattern (22 bp):
CACGGGTTCTGCAAGGAGAAAG
Found at i:111004 original size:23 final size:23
Alignment explanation
Indices: 110978--111021 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
110968 TCCTGCAAGG
110978 CTGCACGTCTGCATGTGGGGGTC
1 CTGCACGTCTGCATGTGGGGGTC
111001 CTGCACGTCTGCATGTGGGGG
1 CTGCACGTCTGCATGTGGGGG
111022 GCATGCAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.09, C:0.25, G:0.41, T:0.25
Consensus pattern (23 bp):
CTGCACGTCTGCATGTGGGGGTC
Found at i:111028 original size:23 final size:23
Alignment explanation
Indices: 110979--111028 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
110969 CCTGCAAGGC
* *
110979 TGCACGTCTGCATGTGGGGGTCC
1 TGCACGTCTGCATGTGGGGGGCA
111002 TGCACGTCTGCATGTGGGGGGCA
1 TGCACGTCTGCATGTGGGGGGCA
111025 TGCA
1 TGCA
111029 ACTGTTGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.12, C:0.24, G:0.40, T:0.24
Consensus pattern (23 bp):
TGCACGTCTGCATGTGGGGGGCA
Found at i:111761 original size:172 final size:173
Alignment explanation
Indices: 111474--111832 Score: 560
Period size: 172 Copynumber: 2.1 Consensus size: 173
111464 TTGTAAAGTT
* * * *
111474 TTAGGGACCATTTTGTAAAATTTAAGGAATTTAAGGAATAAGAGTAAATTATTAAAAGTTGCTAT
1 TTAGGGATCATTTTGCAAAATTTAAGGAATTTAAGAAATAAGAGTAAATTATAAAAAGTTGCTAT
*
111539 ACTATGCTGGAATTTAGTATTAGTATGCTTAATTGGTTAAATTAGAAAGAATTTA-AAATTTA-T
66 ACTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTAGT
*
111602 GGATTAAATTGCTAACTTTGAAAATGTTGAGAACCAAATAGTAA
131 -GATTAAATTGCAAACTTTGAAAATGTTGAGAACCAAATAGTAA
* * * *
111646 TTAGGGATCGTTTTGCAAAATTTGAGGAATTTAAGAAATTAGAGTAAATTATAAAAAGTTGGTAT
1 TTAGGGATCATTTTGCAAAATTTAAGGAATTTAAGAAATAAGAGTAAATTATAAAAAGTTGCTAT
* *
111711 ACTATGCTTGAATTTAGTATTAATATGCTTAATTGGTTAAATTTGAAAGAATTTATAAATTTAGT
66 ACTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTAGT
* *
111776 GATTAAATTGCAAAGTTTGAAAATGTTGAGAAGCAAATAGTAA
131 GATTAAATTGCAAACTTTGAAAATGTTGAGAACCAAATAGTAA
*
111819 TTAGGAATCATTTT
1 TTAGGGATCATTTT
111833 ATATTTGATG
Statistics
Matches: 169, Mismatches: 16, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
172 109 0.64
173 59 0.35
174 1 0.01
ACGTcount: A:0.40, C:0.05, G:0.18, T:0.37
Consensus pattern (173 bp):
TTAGGGATCATTTTGCAAAATTTAAGGAATTTAAGAAATAAGAGTAAATTATAAAAAGTTGCTAT
ACTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTAGT
GATTAAATTGCAAACTTTGAAAATGTTGAGAACCAAATAGTAA
Found at i:113586 original size:6 final size:6
Alignment explanation
Indices: 113575--113599 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
113565 CAAGAAGGAC
113575 TGGGAG TGGGAG TGGGAG TGGGAG T
1 TGGGAG TGGGAG TGGGAG TGGGAG T
113600 TCTTCTCACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.64, T:0.20
Consensus pattern (6 bp):
TGGGAG
Found at i:114112 original size:8 final size:8
Alignment explanation
Indices: 114099--114576 Score: 344
Period size: 8 Copynumber: 62.9 Consensus size: 8
114089 AGTAATTATT
114099 ATTAAATC
1 ATTAAATC
114107 ATTAAA--
1 ATTAAATC
114113 ATTAAATC
1 ATTAAATC
114121 ATTAAA--
1 ATTAAATC
* *
114127 ATTAAGTA
1 ATTAAATC
*
114135 ATT--ATT
1 ATTAAATC
*
114141 ATTAAATT
1 ATTAAATC
114149 ATTAAA--
1 ATTAAATC
114155 ATTAAATC
1 ATTAAATC
*
114163 ATTAAAGTA
1 ATTAAA-TC
*
114172 ATT--ATT
1 ATTAAATC
114178 ATTAAATC
1 ATTAAATC
114186 ATTAAATC
1 ATTAAATC
114194 ATTAAATC
1 ATTAAATC
*
114202 ATTAAAATA
1 ATT-AAATC
*
114211 ATT--ATT
1 ATTAAATC
114217 ATTAAATC
1 ATTAAATC
114225 ATTAAATC
1 ATTAAATC
114233 ATTAAATC
1 ATTAAATC
*
114241 ATTAAAGTA
1 ATTAAA-TC
*
114250 ATT--ATT
1 ATTAAATC
114256 ATTAAATC
1 ATTAAATC
114264 ATTAAA--
1 ATTAAATC
*
114270 GTTAAATC
1 ATTAAATC
*
114278 ATTAAAGTA
1 ATTAAA-TC
*
114287 ATT--ATT
1 ATTAAATC
114293 ATTAAATC
1 ATTAAATC
114301 ATTAAATC
1 ATTAAATC
114309 ATTAAATC
1 ATTAAATC
114317 ATTAAATC
1 ATTAAATC
114325 ATTAAATC
1 ATTAAATC
*
114333 ATTAAAGTA
1 ATTAAA-TC
*
114342 ATT--ATT
1 ATTAAATC
114348 ATTAAATC
1 ATTAAATC
114356 ATTAAATC
1 ATTAAATC
114364 ATTAAATC
1 ATTAAATC
*
114372 ATTAAAGTA
1 ATTAAA-TC
*
114381 ATT--ATT
1 ATTAAATC
114387 ATTAAATC
1 ATTAAATC
114395 ATTAAATC
1 ATTAAATC
114403 ATTAAATC
1 ATTAAATC
*
114411 ATTAAAATA
1 ATT-AAATC
*
114420 ATT--ATT
1 ATTAAATC
114426 ATTAAATC
1 ATTAAATC
114434 ATTAAATC
1 ATTAAATC
114442 ATTAAATC
1 ATTAAATC
*
114450 ATTAAAGTA
1 ATTAAA-TC
*
114459 ATT--ATT
1 ATTAAATC
114465 ATTAAATC
1 ATTAAATC
114473 ATTAAA--
1 ATTAAATC
*
114479 GTTAAATC
1 ATTAAATC
*
114487 ATTAAAGTA
1 ATTAAA-TC
*
114496 ATT--ATT
1 ATTAAATC
114502 ATTAAATC
1 ATTAAATC
114510 ATTAAA--
1 ATTAAATC
*
114516 GTTAAATC
1 ATTAAATC
*
114524 ATTAAAGTA
1 ATTAAA-TC
*
114533 ATT--ATT
1 ATTAAATC
114539 ATTAAATC
1 ATTAAATC
114547 ATTAAA--
1 ATTAAATC
*
114553 GTTAAATC
1 ATTAAATC
*
114561 ATTAAAGTA
1 ATTAAA-TC
114570 ATTAAAT
1 ATTAAAT
114577 TTAAATAATT
Statistics
Matches: 381, Mismatches: 42, Indels: 94
0.74 0.08 0.18
Matches are distributed among these distances:
6 83 0.22
7 8 0.02
8 237 0.62
9 53 0.14
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (8 bp):
ATTAAATC
Found at i:114213 original size:39 final size:39
Alignment explanation
Indices: 114113--114573 Score: 520
Period size: 37 Copynumber: 11.7 Consensus size: 39
114103 AATCATTAAA
*
114113 ATTAAATCATTAAA--ATT-AAGTAATTATTATTAAATT
1 ATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
114149 ATTAAA--ATTAAATCATTAAAGTAATTATTATTAAATC
1 ATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
*
114186 ATTAAATCATTAAATCATTAAAATAATTATTATTAAATC
1 ATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
114225 ATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
1 ATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
*
114264 ATTAAA--GTTAAATCATTAAAGTAATTATTATTAAATC
1 ATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
* * * *
114301 ATTAAATCATTAAATCATTAAATCATTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAATCATT-AA--AGT-AATTATT--ATTAA--ATC
* * * *
114348 ATTAAATCATTAAATCATTAAA-TCATTA-AAGTAATTATT
1 ATTAAATCATTAAATCATTAAAGTAATTATTATTAA--ATC
*
114387 ATTAAATCATTAAATCATTAAATCATTAAAATAATTATTATTAAATC
1 ATTAAATCATT-AA--A-T----CATTAAAGTAATTATTATTAAATC
114434 ATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
1 ATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
*
114473 ATTAAA--GTTAAATCATTAAAGTAATTATTATTAAATC
1 ATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
*
114510 ATTAAA--GTTAAATCATTAAAGTAATTATTATTAAATC
1 ATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
*
114547 ATTAAA--GTTAAATCATTAAAGTAATTA
1 ATTAAATCATTAAATCATTAAAGTAATTA
114574 AATTTAAATA
Statistics
Matches: 382, Mismatches: 18, Indels: 49
0.85 0.04 0.11
Matches are distributed among these distances:
34 6 0.02
36 9 0.02
37 154 0.40
39 134 0.35
40 4 0.01
42 6 0.02
43 9 0.02
44 2 0.01
45 4 0.01
46 4 0.01
47 41 0.11
48 5 0.01
49 4 0.01
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.41
Consensus pattern (39 bp):
ATTAAATCATTAAATCATTAAAGTAATTATTATTAAATC
Found at i:114355 original size:23 final size:23
Alignment explanation
Indices: 114271--114575 Score: 96
Period size: 23 Copynumber: 13.6 Consensus size: 23
114261 ATCATTAAAG
*
114271 TTAAATCATTAAAGTAATTATTA
1 TTAAATCATTAAAGTAATTATCA
*
114294 TTAAATCATTAAA-TCATTAAATCA
1 TTAAATCATTAAAGTAATT--ATCA
* *
114318 TTAAATCATTAAA-TCATTA-AA
1 TTAAATCATTAAAGTAATTATCA
* * *
114339 GT-AATTATT--ATTAA--ATCA
1 TTAAATCATTAAAGTAATTATCA
* *
114357 TTAAATCATTAAA-TCATTA-AA
1 TTAAATCATTAAAGTAATTATCA
* * *
114378 GT-AATTATT--ATTAA--ATCA
1 TTAAATCATTAAAGTAATTATCA
* *
114396 TTAAATCATTAAA-TCATTA-AA
1 TTAAATCATTAAAGTAATTATCA
* * *
114417 ATAATTATTATTAAA-TCATTAAATCA
1 TTAA--ATCATTAAAGTAATT--ATCA
*
114443 TTAAATCATTAAAGTAATTATTA
1 TTAAATCATTAAAGTAATTATCA
114466 TTAAATCATTAAAGTTAA--ATCA
1 TTAAATCATTAAAG-TAATTATCA
* * * * *
114488 TTAAAGTAATTATTATTAAATCATTAAA
1 TTAAA-TCATTA-AAGT-AATTA-T-CA
*
114516 GTTAAATCATTAAAGTAATTATTA
1 -TTAAATCATTAAAGTAATTATCA
114540 TTAAATCATTAAAGTTAA--ATCA
1 TTAAATCATTAAAG-TAATTATCA
*
114562 TTAAAGTAATTAAA
1 TTAAA-TCATTAAA
114576 TTTAAATAAT
Statistics
Matches: 211, Mismatches: 38, Indels: 66
0.67 0.12 0.21
Matches are distributed among these distances:
17 2 0.01
18 6 0.03
19 16 0.08
20 16 0.08
21 10 0.05
22 23 0.11
23 70 0.33
24 39 0.18
25 6 0.03
26 9 0.04
27 3 0.01
28 6 0.03
29 5 0.02
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (23 bp):
TTAAATCATTAAAGTAATTATCA
Found at i:114394 original size:209 final size:207
Alignment explanation
Indices: 114053--114596 Score: 800
Period size: 209 Copynumber: 2.7 Consensus size: 207
114043 ATATATTTAC
* * * *
114053 TATTATTATATCAGTAAA-TATAAATCATTAAAGTCAAGTA--ATT--ATTATTAAATCATTAAA
1 TATTATTAAATCATTAAAGT-TAAATCATTAAAGT-AATTATTATTAAATCATTAAATCATTAAA
*
114113 --ATTAAATCATTAAA-ATT-AAGTAATTATTATTAAATTATTAAA-ATTAAATCATTAAAGTAA
64 TCATTAAATCATTAAATATTAAAGTAATTATTATTAAATCATTAAATATTAAATCATTAAAGTAA
114173 TTATTATTAAATCATTAAATCATTAAATCATTAAAATAATTATTATTAAATCATTAAATCATTAA
129 TTATTATTAAATCATTAAATCATTAAATCATTAAAATAATTATTATTAAATCATTAAATCATTAA
114238 ATCATTAAAGTAAT
194 ATCATTAAAGTAAT
114252 TATTATTAAATCATTAAAGTTAAATCATTAAAGTAATTATTATTAAATCATTAAATCATTAAATC
1 TATTATTAAATCATTAAAGTTAAATCATTAAAGTAATTATTATTAAATCATTAAATCATTAAATC
114317 ATTAAATCATTAAATCATTAAAGTAATTATTATTAAATCATTAAATCATTAAATCATTAAAGTAA
66 ATTAAATCATTAAAT-ATTAAAGTAATTATTATTAAATCATTAAAT-ATTAAATCATTAAAGTAA
114382 TTATTATTAAATCATTAAATCATTAAATCATTAAAATAATTATTATTAAATCATTAAATCATTAA
129 TTATTATTAAATCATTAAATCATTAAATCATTAAAATAATTATTATTAAATCATTAAATCATTAA
114447 ATCATTAAAGTAAT
194 ATCATTAAAGTAAT
*
114461 TATTATTAAATCATTAAAGTTAAATCATTAAAGTAATTATTATTAAATCATTAAA--GTTAAATC
1 TATTATTAAATCATTAAAGTTAAATCATTAAAGTAATTATTATTAAATCATTAAATCATTAAATC
* * * *
114524 ATTAAAGTAATT-ATTATTAAA-TCATTA-AAGTTAAATCATTAAAGTAATTAAAT--TTAAA-T
66 ATTAAA-TCATTAAATATTAAAGTAATTATTA-TTAAATCATTAAA-T-ATTAAATCATTAAAGT
114583 AATTATTATTAAAT
127 AATTATTATTAAAT
114597 ATGTACTCGA
Statistics
Matches: 319, Mismatches: 11, Indels: 26
0.90 0.03 0.07
Matches are distributed among these distances:
198 4 0.01
199 30 0.09
200 4 0.01
202 16 0.05
203 15 0.05
204 20 0.06
205 18 0.06
206 17 0.05
207 39 0.12
208 4 0.01
209 152 0.48
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (207 bp):
TATTATTAAATCATTAAAGTTAAATCATTAAAGTAATTATTATTAAATCATTAAATCATTAAATC
ATTAAATCATTAAATATTAAAGTAATTATTATTAAATCATTAAATATTAAATCATTAAAGTAATT
ATTATTAAATCATTAAATCATTAAATCATTAAAATAATTATTATTAAATCATTAAATCATTAAAT
CATTAAAGTAAT
Found at i:114469 original size:31 final size:30
Alignment explanation
Indices: 114091--114552 Score: 205
Period size: 31 Copynumber: 14.7 Consensus size: 30
114081 TAAAGTCAAG
114091 TAATTATTATTAAATCATTAAA--ATTAAA
1 TAATTATTATTAAATCATTAAATCATTAAA
* ** * * *
114119 TCATTAAAATTAAGTAATT--ATTATTAAA
1 TAATTATTATTAAATCATTAAATCATTAAA
* ** *
114147 TTATTAAAATTAAATCATTAAAGTAATT--A
1 TAATTATTATTAAATCATTAAA-TCATTAAA
* *
114176 TTATTAAATCATTAAATCATTAAATCATTAAAA
1 TAATT--ATTATTAAATCATTAAATCATT-AAA
114209 TAATTATTATTAAATCATTAAATCATTAAA
1 TAATTATTATTAAATCATTAAATCATTAAA
* * * *
114239 TCATTA-AAGTAATTATTATTAAATCATTAAA
1 TAATTATTATTAA--ATCATTAAATCATTAAA
* * *
114270 GTTAAATCATTAAAGTAATTATTATTAAATCATTAAA
1 --T-AATTATT--ATTAA--ATCATTAAATCATTAAA
* *
114307 TCATTAAATCATTAAATCATTAAATCATTAAA
1 TAATT--ATTATTAAATCATTAAATCATTAAA
114339 GTAATTATTATTAAATCATTAAATCATTAAA
1 -TAATTATTATTAAATCATTAAATCATTAAA
* * * *
114370 TCATTA-AAGTAATTATTATTAAATCATTAAA
1 TAATTATTATTAA--ATCATTAAATCATTAAA
* * * *
114401 TCATTAAATCATTAAAATAATT--ATTATTAAA
1 TAATT--ATTATT-AAATCATTAAATCATTAAA
* * *
114432 TCATTAAATCATTAAATCATTAAAGTAATT--A
1 TAATT--ATTATTAAATCATTAAA-TCATTAAA
* * *
114463 TTATTAAATCATTAAA--GTTAAATCATTAAA
1 TAATT--ATTATTAAATCATTAAATCATTAAA
114493 GTAATTATTATTAAATCATTAAAGTTAAATCATTAAA
1 -TAATTATTATTAAATC-----A-TTAAATCATTAAA
114530 GTAATTATTATTAAATCATTAAA
1 -TAATTATTATTAAATCATTAAA
114553 GTTAAATCAT
Statistics
Matches: 349, Mismatches: 44, Indels: 79
0.74 0.09 0.17
Matches are distributed among these distances:
26 1 0.00
28 40 0.11
29 27 0.08
30 26 0.07
31 147 0.42
32 18 0.05
33 20 0.06
34 11 0.03
35 3 0.01
36 2 0.01
37 54 0.15
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (30 bp):
TAATTATTATTAAATCATTAAATCATTAAA
Found at i:114595 original size:37 final size:37
Alignment explanation
Indices: 114309--114596 Score: 368
Period size: 39 Copynumber: 7.6 Consensus size: 37
114299 TCATTAAATC
*
114309 ATTAAATCATTAAATCATTAAATCATTAAAGTAATTATT
1 ATTAAATCATT--ATAATTAAATCATTAAAGTAATTATT
*
114348 ATTAAATCATTAAATCATTAAATCATTAAAGTAATTATT
1 ATTAAATCATT--ATAATTAAATCATTAAAGTAATTATT
* *
114387 ATTAAATCATTAAATCATTAAATCATTAAAATAATTATT
1 ATTAAATCATT--ATAATTAAATCATTAAAGTAATTATT
*
114426 ATTAAATCATTAAATCATTAAATCATTAAAGTAATTATT
1 ATTAAATCATT--ATAATTAAATCATTAAAGTAATTATT
114465 ATTAAATCATTA-AAGTTAAATCATTAAAGTAATTATT
1 ATTAAATCATTATAA-TTAAATCATTAAAGTAATTATT
114502 ATTAAATCATTA-AAGTTAAATCATTAAAGTAATTATT
1 ATTAAATCATTATAA-TTAAATCATTAAAGTAATTATT
*
114539 ATTAAATCATTA-AAGTTAAATCATTAAAGTAATTA-A
1 ATTAAATCATTATAA-TTAAATCATTAAAGTAATTATT
* *
114575 ATTTAAATAATTATTATTAAAT
1 A-TTAAATCATTATAATTAAAT
114597 ATGTACTCGA
Statistics
Matches: 240, Mismatches: 6, Indels: 8
0.94 0.02 0.03
Matches are distributed among these distances:
36 2 0.01
37 111 0.46
38 1 0.00
39 126 0.52
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (37 bp):
ATTAAATCATTATAATTAAATCATTAAAGTAATTATT
Found at i:118429 original size:110 final size:97
Alignment explanation
Indices: 118235--118441 Score: 288
Period size: 97 Copynumber: 2.0 Consensus size: 97
118225 GAGATTCCGC
118235 CAGACGACAGGTGAAGACGCCGAGAGATCCACCTTGGCATTCCTATGCAGAAGACGCCGAGAGAT
1 CAGACGACAGGTGAAGACGCCGAGAGATCCACCTTGGCATTCCTATGCAGAAGACGCCGAGAGAT
118300 CCCAATTGCTTGAAGACGCCGAGCATTCCCAT
66 CCCAATTGCTTGAAGACGCCGAGCATTCCCAT
118332 CAGACGACAGGTGAAGACGCCGAGAGATCCACCTTGGCATTCCTTGTAGCATGCAGAAGACGCCG
1 CAGACGACAGGTGAAGACGCCGAGAGATCCACCTTGGCATTCC---T---ATGCAGAAGACGCCG
*
118397 AGATATCCCACAGGCCAATTGCTTGAAGACGCCGAGCATTCCCAT
60 AGAGAT----C---CCAATTGCTTGAAGACGCCGAGCATTCCCAT
118442 AGTTTCATAA
Statistics
Matches: 96, Mismatches: 1, Indels: 13
0.87 0.01 0.12
Matches are distributed among these distances:
97 43 0.45
100 1 0.01
103 20 0.21
107 1 0.01
110 31 0.32
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.17
Consensus pattern (97 bp):
CAGACGACAGGTGAAGACGCCGAGAGATCCACCTTGGCATTCCTATGCAGAAGACGCCGAGAGAT
CCCAATTGCTTGAAGACGCCGAGCATTCCCAT
Found at i:120010 original size:21 final size:20
Alignment explanation
Indices: 119984--120040 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
119974 TCCATATTCG
119984 CAACGCGATAGTCTAAAATCA
1 CAACGCGATAGTC-AAAATCA
* * *
120005 CAACGCGATAATCAAATTTA
1 CAACGCGATAGTCAAAATCA
*
120025 CAACGCGAAAGTCAAA
1 CAACGCGATAGTCAAA
120041 TCCAAAATCG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 19 0.61
21 12 0.39
ACGTcount: A:0.46, C:0.23, G:0.14, T:0.18
Consensus pattern (20 bp):
CAACGCGATAGTCAAAATCA
Found at i:121095 original size:22 final size:22
Alignment explanation
Indices: 121067--121109 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
121057 TTGATTATTT
121067 TATTATAATATTAAAAATATAA
1 TATTATAATATTAAAAATATAA
* *
121089 TATTATATTATTAGAAATATA
1 TATTATAATATTAAAAATATA
121110 TTTTAAATAT
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:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
TATTATAATATTAAAAATATAA
Found at i:121117 original size:11 final size:11
Alignment explanation
Indices: 121103--121130 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
121093 ATATTATTAG
121103 AAATATATTTT
1 AAATATATTTT
121114 AAATATATTTT
1 AAATATATTTT
121125 AAATAT
1 AAATAT
121131 TTTAATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AAATATATTTT
Found at i:121122 original size:22 final size:23
Alignment explanation
Indices: 121074--121122 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
121064 TTTTATTATA
*
121074 ATATTAAAAATATAATATTATAT
1 ATATTAAAAATATAATATTAAAT
* *
121097 -TATTAGAAATAT-ATTTTAAAT
1 ATATTAAAAATATAATATTAAAT
121118 ATATT
1 ATATT
121123 TTAAATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
ATATTAAAAATATAATATTAAAT
Found at i:121130 original size:9 final size:10
Alignment explanation
Indices: 121104--121137 Score: 52
Period size: 11 Copynumber: 3.4 Consensus size: 10
121094 TATTATTAGA
121104 AATATATTTT
1 AATATATTTT
121114 AAATATATTTT
1 -AATATATTTT
121125 AA-ATATTTT
1 AATATATTTT
121134 AATA
1 AATA
121138 ATTAATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.41
10 3 0.14
11 10 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
AATATATTTT
Found at i:121130 original size:53 final size:53
Alignment explanation
Indices: 121009--121131 Score: 137
Period size: 55 Copynumber: 2.3 Consensus size: 53
120999 ATAATTTATT
* *
121009 ATATATTATTAAA-A-TAAAAATATAATATCTTATATTATTATAATATAATTGA
1 ATATATTATTAAATATTAAAAATATAATA-CTTATATTATTAAAATATAATTAA
* * *
121061 TTATTTTATTATAATATTAAAAATATAATA-TTATATTATTAGAAATATATTTTAA
1 ATATATTATTA-AATATTAAAAATATAATACTTATATTATTA-AAATATA-ATTAA
121116 ATATATT-TTAAATATT
1 ATATATTATTAAATATT
121132 TTAATAATTA
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
52 9 0.15
53 19 0.32
54 10 0.17
55 21 0.36
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.49
Consensus pattern (53 bp):
ATATATTATTAAATATTAAAAATATAATACTTATATTATTAAAATATAATTAA
Found at i:125824 original size:20 final size:20
Alignment explanation
Indices: 125801--125840 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
125791 ATACAAGGAC
125801 CTTTATCTGGGAACATTTAG
1 CTTTATCTGGGAACATTTAG
125821 CTTTATCTGGGAACATTTAG
1 CTTTATCTGGGAACATTTAG
125841 TAAGTTGTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (20 bp):
CTTTATCTGGGAACATTTAG
Found at i:129603 original size:24 final size:24
Alignment explanation
Indices: 129576--129629 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
129566 GTATTCGAAA
*
129576 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
129600 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
129624 TTTGAT
1 TTTGAT
129630 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:132166 original size:19 final size:20
Alignment explanation
Indices: 132085--132178 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
132075 GGCAATCATT
*
132085 TGACTATCGCAACACAGAAA
1 TGACTATCGCAACGCAGAAA
* **
132105 TGACGT-TCGCAA-TCATCTTAA
1 TGAC-TATCGCAACGCA--GAAA
*
132126 TGTCTATCGCAACGCAGAAA
1 TGACTATCGCAACGCAGAAA
*
132146 TGACTATCGCAATGC-GAAA
1 TGACTATCGCAACGCAGAAA
**
132165 TGAAAATCGCAACG
1 TGACTATCGCAACG
132179 AGAGAATCGC
Statistics
Matches: 57, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
19 17 0.30
20 26 0.46
21 12 0.21
22 2 0.04
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
TGACTATCGCAACGCAGAAA
Found at i:132193 original size:33 final size:33
Alignment explanation
Indices: 132151--132277 Score: 218
Period size: 33 Copynumber: 3.8 Consensus size: 33
132141 AGAAATGACT
132151 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
132184 ATCGCAATGCAAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
132217 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
132250 ATCACAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
132278 CGAATTTAGT
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 89 1.00
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:132280 original size:19 final size:18
Alignment explanation
Indices: 132131--132281 Score: 83
Period size: 19 Copynumber: 8.7 Consensus size: 18
132121 CTTAATGTCT
**
132131 ATCGCAACGCAGAAATGACT
1 ATCGCAA-GC-GAAATGAAA
132151 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
132170 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
*
132184 ATCGCAATGCAAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
132203 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
132217 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
**
132236 ATCGCAA-CG--A-GGGA
1 ATCGCAAGCGAAATGAAA
*
132250 ATCACAAAGCGAAATGAAA
1 ATCGC-AAGCGAAATGAAA
132269 ATCGCAACGCGAA
1 ATCGCAA-GCGAA
132282 TTTAGTTTCG
Statistics
Matches: 100, Mismatches: 15, Indels: 33
0.68 0.10 0.22
Matches are distributed among these distances:
14 26 0.26
15 5 0.05
16 5 0.05
17 5 0.05
18 5 0.05
19 45 0.45
20 9 0.09
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.12
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:132445 original size:14 final size:14
Alignment explanation
Indices: 132426--132476 Score: 84
Period size: 14 Copynumber: 3.6 Consensus size: 14
132416 CATCAATTAA
132426 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
132440 ACAAATCATCTTTT
1 ACAAATCAACTTTT
*
132454 ACAAATCATCTTTT
1 ACAAATCAACTTTT
132468 ACAAATCAA
1 ACAAATCAA
132477 TTTAACAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.43, C:0.22, G:0.00, T:0.35
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:133900 original size:42 final size:42
Alignment explanation
Indices: 133854--133933 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
133844 CGATGACAGT
* * *
133854 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
133896 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
133934 CAGGCGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:134456 original size:94 final size:94
Alignment explanation
Indices: 134295--134599 Score: 503
Period size: 94 Copynumber: 3.3 Consensus size: 94
134285 GAATAGTTTC
*
134295 AATTGGCAGCAAACGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
1 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
134360 ACAGTGTTAAAGAATACACAGTTTAGCAG
66 ACAGTGTTAAAGAATACACAGTTTAGCAG
*
134389 AATTGGCACCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
1 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
134454 ACAGTGTTAAAGAATACACAGTTTAGCAG
66 ACAGTGTTAAAGAATACACAGTTTAGCAG
* *
134483 AATTTGCAGCAACCGAATAAATTTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTT
1 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTT
*
134547 CACAGTGTT----AATAAACAGTTTAGCAG
65 CACAGTGTTAAAGAATACACAGTTTAGCAG
* *
134573 TATTGGCAGCAACCGAATAAATTTACT
1 AATTGGCAGCAACCGAACAAATTTACT
134600 AAGCAATCTA
Statistics
Matches: 201, Mismatches: 8, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
90 40 0.20
93 19 0.09
94 142 0.71
ACGTcount: A:0.47, C:0.20, G:0.12, T:0.22
Consensus pattern (94 bp):
AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
ACAGTGTTAAAGAATACACAGTTTAGCAG
Found at i:136319 original size:20 final size:20
Alignment explanation
Indices: 136294--136432 Score: 130
Period size: 20 Copynumber: 7.7 Consensus size: 20
136284 TTTTGGTTGA
*
136294 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGCGAG
136314 AATGAAAATCGCAACGCG-G
1 AATGAAAATCGCAACGCGAG
**
136333 AAATGACTATCGCAACGCGA-
1 -AATGAAAATCGCAACGCGAG
136353 AATGAAAATCGCAA--CGAG
1 AATGAAAATCGCAACGCGAG
136371 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGCGAG
136386 AATGAAAATCGCAA--CGAG
1 AATGAAAATCGCAACGCGAG
136404 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGCGAG
136419 AATGAAAATCGCAA
1 AATGAAAATCGCAA
136433 TGCAATTTTG
Statistics
Matches: 98, Mismatches: 5, Indels: 33
0.72 0.04 0.24
Matches are distributed among these distances:
14 16 0.16
16 10 0.10
17 10 0.10
19 29 0.30
20 33 0.34
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGCGAG
Found at i:136356 original size:19 final size:19
Alignment explanation
Indices: 136292--136432 Score: 149
Period size: 19 Copynumber: 7.8 Consensus size: 19
136282 TCTTTTGGTT
*
136292 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
136311 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
136331 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
136351 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
136368 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
136384 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
136401 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
136417 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
136433 TGCAATTTTG
Statistics
Matches: 101, Mismatches: 9, Indels: 24
0.75 0.07 0.18
Matches are distributed among these distances:
14 20 0.20
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 36 0.36
20 31 0.31
21 2 0.02
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:136378 original size:14 final size:14
Alignment explanation
Indices: 136359--136415 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
136349 GCGAAATGAA
136359 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
136373 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
136392 AATCGCAACGAGAG
1 AATCGCAACGAGAG
136406 AATCGCAACG
1 AATCGCAACG
136416 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:136383 original size:33 final size:33
Alignment explanation
Indices: 136300--136432 Score: 185
Period size: 33 Copynumber: 3.8 Consensus size: 33
136290 TTGAAATGAA
* *
136300 AATCGCAACGAGAGAATGAAAATCGCAACGCGGAAATG
1 AATCGCAACGCGA-AATGAAAATCGCAA--C-GAGA-G
136338 ACTATCGCAACGCGAAATGAAAATCGCAACGAGAG
1 A--ATCGCAACGCGAAATGAAAATCGCAACGAGAG
136373 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
136406 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
136433 TGCAATTTTG
Statistics
Matches: 91, Mismatches: 2, Indels: 9
0.89 0.02 0.09
Matches are distributed among these distances:
33 59 0.65
35 2 0.02
36 3 0.03
37 1 0.01
38 1 0.01
39 14 0.15
40 11 0.12
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:136466 original size:19 final size:19
Alignment explanation
Indices: 136433--136492 Score: 93
Period size: 19 Copynumber: 3.2 Consensus size: 19
136423 AAAATCGCAA
**
136433 TGCAATTTTGGTTTCGCGT
1 TGCAATTTTCATTTCGCGT
136452 TGCAATTTTCATTTCGCGT
1 TGCAATTTTCATTTCGCGT
*
136471 TGCGATTTTCATTTCGCGT
1 TGCAATTTTCATTTCGCGT
136490 TGC
1 TGC
136493 GATTATCTCG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.47
Consensus pattern (19 bp):
TGCAATTTTCATTTCGCGT
Found at i:136493 original size:19 final size:19
Alignment explanation
Indices: 136444--136565 Score: 111
Period size: 19 Copynumber: 6.9 Consensus size: 19
136434 GCAATTTTGG
*
136444 TTTCGCGTTGCAATTTTCA
1 TTTCGCGTTGCGATTTTCA
136463 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
136482 TTTCGCGTTGCGA--TT-A
1 TTTCGCGTTGCGATTTTCA
*
136498 --TCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
136515 TTTCGCATTGCGA--TTC-
1 TTTCGCGTTGCGATTTTCA
* **
136531 --TCTCGTTGCGATAGTCA
1 TTTCGCGTTGCGATTTTCA
136548 TTTCCGCGTTGCGATTTT
1 TTT-CGCGTTGCGATTTT
136566 TATTCTCGAA
Statistics
Matches: 82, Mismatches: 10, Indels: 21
0.73 0.09 0.19
Matches are distributed among these distances:
14 19 0.23
16 5 0.06
17 6 0.07
19 41 0.50
20 11 0.13
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.45
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:136510 original size:33 final size:33
Alignment explanation
Indices: 136468--136563 Score: 147
Period size: 33 Copynumber: 2.9 Consensus size: 33
136458 TTTCATTTCG
136468 CGTTGCGATTTTCATTTCGCGTTGCGATTATCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTATCT
* *
136501 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTATCT
**
136534 CGTTGCGATAGTCATTTCCGCGTTGCGATT
1 CGTTGCGATTTTCATTT-CGCGTTGCGATT
136564 TTTATTCTCG
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 46 0.81
34 11 0.19
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTATCT
Found at i:137159 original size:20 final size:20
Alignment explanation
Indices: 137113--137186 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
137103 CGATAGTCAG
* * *
137113 ATTCGCATTGCAATTTTCCT
1 ATTCGCATTGCGATTTACGT
137133 AATTCGCATTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGT
*
137154 ATTCGCATTGCGAATTACGT
1 ATTCGCATTGCGATTTACGT
137174 ATTCGCATTGCGA
1 ATTCGCATTGCGA
137187 ATTATGAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 32 0.65
21 17 0.35
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:137187 original size:20 final size:20
Alignment explanation
Indices: 137134--137312 Score: 112
Period size: 20 Copynumber: 8.8 Consensus size: 20
137124 AATTTTCCTA
*
137134 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGAATTACGT
137154 ATTCGCATTGCGAATTACGT
1 ATTCGCATTGCGAATTACGT
* *
137174 ATTCGCATTGCGAATTATGAA
1 ATTCGCATTGCGAATTACG-T
* **
137195 AATCGCAACGCGAA-TACGT
1 ATTCGCATTGCGAATTACGT
* * * *
137214 AAATCGCAATGCGAATTAGGAA
1 -ATTCGCATTGCGAATTACG-T
* * *
137236 AATGGCATTGCGATAGT-CAGT
1 ATTCGCATTGCGA-ATTAC-GT
* * **
137257 A-TCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-ATTACGT
* *
137277 ATTCGCATTGCGATTTACTT
1 ATTCGCATTGCGAATTACGT
137297 ATTCGCATTGCGAATT
1 ATTCGCATTGCGAATT
137313 GGGAAAATCG
Statistics
Matches: 126, Mismatches: 25, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
20 85 0.67
21 38 0.30
22 3 0.02
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (20 bp):
ATTCGCATTGCGAATTACGT
Found at i:137201 original size:41 final size:41
Alignment explanation
Indices: 137134--137324 Score: 156
Period size: 41 Copynumber: 4.7 Consensus size: 41
137124 AATTTTCCTA
* * * *
137134 ATTCGCATTGCGATTTACG-TATTCGCATTGCGAATTACGT
1 ATTCGCATTGCGAATTAGGAAAATCGCATTGCGAATTACGT
* **
137174 ATTCGCATTGCGAATTATGAAAATCGCAACGCGAA-TACGT
1 ATTCGCATTGCGAATTAGGAAAATCGCATTGCGAATTACGT
* * * *
137214 AAATCGCAATGCGAATTAGGAAAATGGCATTGCGATAGT-CAGT
1 -ATTCGCATTGCGAATTAGGAAAATCGCATTGCGA-ATTAC-GT
* *** * * *
137257 A-TCGCATTGCGATTTTCCAAATTCGCATTGCGATTTACTT
1 ATTCGCATTGCGAATTAGGAAAATCGCATTGCGAATTACGT
*
137297 ATTCGCATTGCGAATTGGGAAAATCGCA
1 ATTCGCATTGCGAATTAGGAAAATCGCA
137325 ACGCGAAATT
Statistics
Matches: 117, Mismatches: 27, Indels: 13
0.75 0.17 0.08
Matches are distributed among these distances:
40 25 0.21
41 86 0.74
42 3 0.03
43 3 0.03
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (41 bp):
ATTCGCATTGCGAATTAGGAAAATCGCATTGCGAATTACGT
Found at i:137351 original size:21 final size:22
Alignment explanation
Indices: 137299--137351 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
137289 ATTTACTTAT
137299 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
137320 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
137341 TCGCATTGCGA
1 TCGCATTGCGA
137352 TAGTAATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:144777 original size:2 final size:2
Alignment explanation
Indices: 144770--144798 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
144760 CCATAATGCA
144770 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
144799 ACAATTACCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:147879 original size:2 final size:2
Alignment explanation
Indices: 147872--147916 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
147862 GGTTGAGGAA
*
147872 AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT A- AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
147912 AT AT A
1 AT AT A
147917 GAGGGCGAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:149390 original size:14 final size:15
Alignment explanation
Indices: 149373--149402 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
149363 AAGAATTGGC
149373 ATAAAAACAAA-AGA
1 ATAAAAACAAACAGA
149387 ATAAAAACAAACAGA
1 ATAAAAACAAACAGA
149402 A
1 A
149403 GAGGGATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.77, C:0.10, G:0.07, T:0.07
Consensus pattern (15 bp):
ATAAAAACAAACAGA
Found at i:150062 original size:41 final size:43
Alignment explanation
Indices: 149989--150074 Score: 158
Period size: 42 Copynumber: 2.0 Consensus size: 43
149979 GGTCACTGAC
149989 ATGGTATTCTCGAAAAGAAGGTAAGGAACAATGAA-GGGAAGG
1 ATGGTATTCTCGAAAAGAAGGTAAGGAACAATGAATGGGAAGG
150031 ATGGTATTCTCGAAAA-AAGGTAAGGAACAATGAATGGGAAGG
1 ATGGTATTCTCGAAAAGAAGGTAAGGAACAATGAATGGGAAGG
150073 AT
1 AT
150075 TTCGGGCTGC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
41 18 0.42
42 25 0.58
ACGTcount: A:0.43, C:0.07, G:0.31, T:0.19
Consensus pattern (43 bp):
ATGGTATTCTCGAAAAGAAGGTAAGGAACAATGAATGGGAAGG
Done.