Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold475
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: 1773841
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 9 of 12
Found at i:1295097 original size:18 final size:18
Alignment explanation
Indices: 1295034--1295097 Score: 62
Period size: 18 Copynumber: 3.7 Consensus size: 18
1295024 GATGAAGATA
* *
1295034 ATGATAATGATAATAATA
1 ATGATAATGATGATAATG
1295052 ATGAT-A--ATGATAATG
1 ATGATAATGATGATAATG
* * *
1295067 ATAATGATAATGATAATG
1 ATGATAATGATGATAATG
1295085 ATGATAATGATGA
1 ATGATAATGATGA
1295098 AGTTGACTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
15 11 0.30
16 1 0.03
17 1 0.03
18 24 0.65
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (18 bp):
ATGATAATGATGATAATG
Found at i:1297780 original size:14 final size:15
Alignment explanation
Indices: 1297751--1297793 Score: 68
Period size: 15 Copynumber: 2.8 Consensus size: 15
1297741 GTAAAAAGAT
1297751 ATTTTTAATAGAAAA
1 ATTTTTAATAGAAAA
1297766 ATTTTTAATAGAAAA
1 ATTTTTAATAGAAAA
*
1297781 AGGTTTTAATAGA
1 A-TTTTTAATAGA
1297794 GGAAATATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.62
16 10 0.38
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.40
Consensus pattern (15 bp):
ATTTTTAATAGAAAA
Found at i:1297781 original size:16 final size:16
Alignment explanation
Indices: 1297751--1297793 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
1297741 GTAAAAAGAT
1297751 ATTTTTAATAG-AAAA
1 ATTTTTAATAGAAAAA
1297766 ATTTTTAATAGAAAAA
1 ATTTTTAATAGAAAAA
**
1297782 GGTTTTAATAGA
1 ATTTTTAATAGA
1297794 GGAAATATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.40
Consensus pattern (16 bp):
ATTTTTAATAGAAAAA
Found at i:1301880 original size:13 final size:13
Alignment explanation
Indices: 1301862--1301886 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1301852 CATGGCACAC
1301862 TGTATCGATACAA
1 TGTATCGATACAA
1301875 TGTATCGATACA
1 TGTATCGATACA
1301887 TAACAAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1304014 original size:15 final size:15
Alignment explanation
Indices: 1303994--1304041 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
1303984 ATTCCACCAA
1303994 ATCCACCACAAAATC
1 ATCCACCACAAAATC
** *
1304009 ATCCACCACCTAATT
1 ATCCACCACAAAATC
*
1304024 ACCCACCACAAAATC
1 ATCCACCACAAAATC
1304039 ATC
1 ATC
1304042 GATACACTGC
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.17
Consensus pattern (15 bp):
ATCCACCACAAAATC
Found at i:1311330 original size:28 final size:27
Alignment explanation
Indices: 1311290--1311488 Score: 146
Period size: 28 Copynumber: 7.1 Consensus size: 27
1311280 GTTAATACGA
1311290 CACCTTTTCAAAGCCCACAAATCAATGG
1 CACCTTTTCAAAGCCCAC-AATCAATGG
* * *
1311318 CACCTTCTCAAAGCCCACAATTAGTGG
1 CACCTTTTCAAAGCCCACAATCAATGG
* *
1311345 CACCTTTTCAAAGCCCATCAGTCAGTGG
1 CACCTTTTCAAAGCCCA-CAATCAATGG
* * * * *
1311373 CATCTTTTCAGAGCCCATAAGTTAGTGG
1 CACCTTTTCAAAGCCCACAA-TCAATGG
** ** *
1311401 CTTCTTTTCAAAGCCCACAAGTCGGTGT
1 CACCTTTTCAAAGCCCACAA-TCAATGG
* * * *
1311429 CACCCTTTCAAAGCCCACGAGTTAGTGG
1 CACCTTTTCAAAGCCCAC-AATCAATGG
*
1311457 CATGCCTTTTCAAAGCCCACAAGTCAGTGG
1 CA--CCTTTTCAAAGCCCACAA-TCAATGG
1311487 CA
1 CA
1311489 TCCCTTTTTG
Statistics
Matches: 138, Mismatches: 27, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
27 24 0.17
28 89 0.64
29 2 0.01
30 23 0.17
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (27 bp):
CACCTTTTCAAAGCCCACAATCAATGG
Found at i:1311416 original size:56 final size:56
Alignment explanation
Indices: 1311292--1311488 Score: 245
Period size: 56 Copynumber: 3.5 Consensus size: 56
1311282 TAATACGACA
* * * *
1311292 CCTTTTCAAAGCCCACAAATCAATGGCACCTTCTCAAAGCCCACAA-TTAGTGGCA
1 CCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTTAGTGGCT
* * *
1311347 CCTTTTCAAAGCCCATC-AGTCAGTGGCATCTTTTCAGAGCCCATAAGTTAGTGGCT
1 CCTTTTCAAAGCCCA-CAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTTAGTGGCT
* * * * *
1311403 TCTTTTCAAAGCCCACAAGTCGGTGTCACCCTTTCAAAGCCCACGAGTTAGTGGCAT
1 CCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTTAGTGGC-T
1311460 GCCTTTTCAAAGCCCACAAGTCAGTGGCA
1 -CCTTTTCAAAGCCCACAAGTCAGTGGCA
1311489 TCCCTTTTTG
Statistics
Matches: 119, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
55 39 0.33
56 54 0.45
57 1 0.01
58 25 0.21
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (56 bp):
CCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTTAGTGGCT
Found at i:1311828 original size:19 final size:19
Alignment explanation
Indices: 1311785--1311857 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
1311775 CACACCTAGA
*
1311785 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGT-T-CAT
1311805 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTTCAT
**
1311824 TGTATCGATACATGGACACT
1 TGTATCGATACATGTTCA-T
1311844 TGTATCGATACATG
1 TGTATCGATACATG
1311858 AAACTGGCAA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
19 18 0.38
20 29 0.60
21 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:1311928 original size:33 final size:33
Alignment explanation
Indices: 1311886--1311954 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
1311876 CTACCATTGT
* *
1311886 TTGTATCGATACATGGT-ACATTGTATCGATATA
1 TTGTATCGATACATGATGA-ATTGTATCGATACA
*
1311919 TTGTGTCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGATGAATTGTATCGATACA
1311952 TTG
1 TTG
1311955 CTTGTAACCG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (33 bp):
TTGTATCGATACATGATGAATTGTATCGATACA
Found at i:1312740 original size:28 final size:28
Alignment explanation
Indices: 1312695--1312823 Score: 204
Period size: 28 Copynumber: 4.5 Consensus size: 28
1312685 AGCTTTCACT
1312695 TTTCAAAGCCCACAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
1312723 GTTCAAAGCCCACGAGTCAATGGCATCAC
1 TTTCAAAGCCCACAAGTCAGTGGCATC-C
*
1312752 TTTTCAAAGCCCACAAGTTAGTGGCATCC
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
1312781 TTTCAAAGCCCACAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
1312809 TTTCAAAGCCCACAA
1 TTTCAAAGCCCACAA
1312824 AAGTCGGTGG
Statistics
Matches: 91, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
28 66 0.73
29 2 0.02
30 23 0.25
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.22
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTCAGTGGCATCC
Found at i:1312760 original size:58 final size:58
Alignment explanation
Indices: 1312690--1312823 Score: 218
Period size: 58 Copynumber: 2.3 Consensus size: 58
1312680 CCTTGAGCTT
*
1312690 TCACTTTTCAAAGCCCACAAGTCAGTGGCATCCGTTCAAAGCCCACGAGTCAATGGCA
1 TCACTTTTCAAAGCCCACAAGTCAGTGGCATCCGTTCAAAGCCCACAAGTCAATGGCA
* * *
1312748 TCACTTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCA
1 TCACTTTTCAAAGCCCACAAGTCAGTGGCATCCGTTCAAAGCCCACAAGTCAATGGCA
1312806 TC-C-TTTCAAAGCCCACAA
1 TCACTTTTCAAAGCCCACAA
1312824 AAGTCGGTGG
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
56 15 0.21
57 1 0.01
58 56 0.78
ACGTcount: A:0.30, C:0.31, G:0.16, T:0.22
Consensus pattern (58 bp):
TCACTTTTCAAAGCCCACAAGTCAGTGGCATCCGTTCAAAGCCCACAAGTCAATGGCA
Found at i:1312840 original size:86 final size:89
Alignment explanation
Indices: 1312695--1312867 Score: 221
Period size: 86 Copynumber: 2.0 Consensus size: 89
1312685 AGCTTTCACT
* *
1312695 TTTCAAAGCCCACAAGTCAGTGGCATCCGTTCAAAGCCCACGAGTCAATGGCATCACTTT-TC-A
1 TTTCAAAGCCCACAAGTCAGTGGCATCCGTTCAAAGCCCACAAGTCAATGG-ATAACTTTATCTA
1312758 AA-GCC-CACAAGTTAGTGGCATCC
65 AAGGCCACACAAGTTAGTGGCATCC
* **
1312781 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAAAGTCGGTGG-TAACTTTATCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCCGTTCAAAGCCCAC--AAGTCAATGGATAACTTTATCT
* *
1312845 AAAGGCCATACAAGTTGGTGGCA
64 AAAGGCCACACAAGTTAGTGGCA
1312868 ACCCTTCTAA
Statistics
Matches: 74, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
86 46 0.62
87 2 0.03
88 10 0.14
89 3 0.04
90 13 0.18
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (89 bp):
TTTCAAAGCCCACAAGTCAGTGGCATCCGTTCAAAGCCCACAAGTCAATGGATAACTTTATCTAA
AGGCCACACAAGTTAGTGGCATCC
Found at i:1313942 original size:30 final size:30
Alignment explanation
Indices: 1313902--1313976 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
1313892 TGAACAGTAT
*
1313902 ATGTAACGATACATTCTGATTTT-TTCCCAG
1 ATGTAACGATACATTCT-ATTTTGTTACCAG
*
1313932 ATGTACCGATACATTCTATTTTGTTACCAG
1 ATGTAACGATACATTCTATTTTGTTACCAG
* *
1313962 ATGTATCTATACATT
1 ATGTAACGATACATT
1313977 ATTCAGTGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 5 0.12
30 35 0.88
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (30 bp):
ATGTAACGATACATTCTATTTTGTTACCAG
Found at i:1315206 original size:18 final size:19
Alignment explanation
Indices: 1315167--1315208 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
1315157 AATCAAAAAG
**
1315167 AAAAAATTCAAATTTCTAA
1 AAAAAATTCAAATTAATAA
1315186 AAAAAATTCAAATTAATAA
1 AAAAAATTCAAATTAATAA
1315205 AAAA
1 AAAA
1315209 TAAAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (19 bp):
AAAAAATTCAAATTAATAA
Found at i:1322009 original size:14 final size:14
Alignment explanation
Indices: 1321974--1322020 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
1321964 TATTCTTTTT
1321974 AGCAAAAAAAAA-A
1 AGCAAAAAAAAAGA
* *
1321987 AAC-ACAAAAAAGA
1 AGCAAAAAAAAAGA
1322000 AGCAAAAAAAAAGA
1 AGCAAAAAAAAAGA
1322014 AG-AAAAA
1 AGCAAAAA
1322021 TCTTTTTCAC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 7 0.25
13 10 0.36
14 11 0.39
ACGTcount: A:0.81, C:0.09, G:0.11, T:0.00
Consensus pattern (14 bp):
AGCAAAAAAAAAGA
Found at i:1323134 original size:62 final size:62
Alignment explanation
Indices: 1322945--1324255 Score: 1388
Period size: 62 Copynumber: 21.1 Consensus size: 62
1322935 ACATCTTCAT
* ** * * * **
1322945 CCTTT-AGTCCTCCAAGAGCAGGACACATTTTTCTTTTCAAAGCCCACATGAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * * **
1323006 CATTTTTTAGTCCTAAAAGAGTAGGATGCCTTATT-CTTTTCAAAGCCCACATGAGTTGGTGGCA
1 C--CTTTCAGTCCTCAAAGAGCAGGATGCCTT-TTCCTTTTTAAAGCCCACACAAGTTGGTGGCA
* * ** ** * * *
1323070 CCCTTTTAGCCCTCAAAGAGCAAAACACCTTTTTC-TTTTAAAGCCCATACGAGTTGGTGGCA
1 -CCTTTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * *
1323132 CCCTTTCAATCCTTAAAAAGCAGGATGCCTTTTTCTTTTTAAAGCCCA-ACCAAGTTGTTGGCA
1 -CCTTTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTTAAAGCCCACA-CAAGTTGGTGGCA
* * * *
1323195 CCTTTCAGTCCTCAAAGAGTAGGATGCCTTTTCCTTTTTAAAGCCTATACGAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * *
1323257 CCTGTCAGTCTTCAAAGAGTAGGATGCCTTTTCCTTTTTAAAGTCCACACAAGTTGTTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCA
* *
1323319 CCTTTCAGTCCTCAAAGAGCAGGCA--CTTTTTCCTTTTTAAAGCCCACACAAGTTTGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGG-ATGCCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCA
* * ** *
1323380 CCTTTCAGTCTTCAAAGAGTAGGACACCTTTTCCTTTTTAAAGCCCACACAAGTTGTTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCA
* *
1323442 CCTTTCAGTCCTTAAAGAGCCGGATGCCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
1323504 CCTGTT-AGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTTAAAGCCCAGACAAGTTGTTAGCA
1 CCT-TTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
1323566 CCTTTCAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTTGAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * **
1323628 -CTTGACAGTCCTCAAAGAGCACGATGCCTTTTCCTTTTTAAAGTCGACACAAGTTATTGGCA
1 CCTT-TCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCA
* *** *
1323690 CCTTTCAGTCCTCAAAGAGTAGGGCACCTTTTCCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * *
1323752 CC-TGCTAGTCCTCAAAGAGTAAGATGCCTTTTCCTTTTTAAAGCCCACACAAGTTGTTAGCA
1 CCTTTC-AGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * *
1323814 CCTTTCAGTCCTTAAAGAGCTGGATGCCTTTTCCTTTTCAAAGCCCACACAAGTTGTTAGCA
1 CCTTTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCA
*** * *
1323876 CCTTTCAGTCCTCAAAGAGCAGGGCACCTTTTCCTTTTTAAAGCCCACACAAGTTGCTGACA
1 CCTTTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCA
* *
1323938 CCTTTCAGTCCTTAAAGAGTAGGATGCCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCA
* * * **
1324000 CCTTTCAGTCTTCAAAGAGCATGATG-CTTTTTCTTTTTAAAGCCCACATGAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * * * * *
1324061 CCTCTTTAGTCCTCAAAAAGCAAGATGCTTTTTTCTTTTCAAAGCTCACACGAGTTGGTGGCA
1 CCT-TTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * * * ***
1324124 CCCTTT-AGTCCTTAAAGAGTAAGATGCCTTTTTTTCTTTTCAAAGCCTACATGTGTTGGTGGCA
1 -CCTTTCAGTCCTCAAAGAGCAGGATGCC--TTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * * *
1324188 CCACTTT-AGTCCTCAAAGAGAAGGATGTCTTTTTCTTTTCAAAG-CTACATAAGTTGGTGGCAA
1 -C-CTTTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGC-A
1324251 CCTTT
1 CCTTT
1324256 TCTAAAGCCC
Statistics
Matches: 1070, Mismatches: 155, Indels: 50
0.84 0.12 0.04
Matches are distributed among these distances:
60 1 0.00
61 100 0.09
62 756 0.71
63 106 0.10
64 82 0.08
65 25 0.02
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (62 bp):
CCTTTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:1324280 original size:32 final size:30
Alignment explanation
Indices: 1324222--1324291 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 30
1324212 ATGTCTTTTT
* * *
1324222 CTTTTC-AAAGCTACATAAGTTGGTGGCAA
1 CTTTTCTAAAGCCACACAAGTTAGTGGCAA
1324251 CCTTTTCTAAAGCCCACACAAGTTAGTGGCAA
1 -CTTTTCTAAAG-CCACACAAGTTAGTGGCAA
*
1324283 CTCTTCTAA
1 CTTTTCTAA
1324292 GTTCGATGTC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 6 0.18
31 12 0.35
32 16 0.47
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (30 bp):
CTTTTCTAAAGCCACACAAGTTAGTGGCAA
Found at i:1324443 original size:62 final size:61
Alignment explanation
Indices: 1324363--1324501 Score: 156
Period size: 61 Copynumber: 2.3 Consensus size: 61
1324353 TTGATATTAT
* * * *
1324363 TGGCCGTGAATCAGCATATCGGCACCTTTATCTTTTCTT-TGCATCTTTAA-GTCTAATATCGC
1 TGGCCTTGAATCAACATATCGGCACCTTTATC-ATTCTTCT-CAT-TTAAATGTCTAATATCGC
* * * *
1324425 TGGCCTTGAATCAACATATTGGCACTTTTATCATTCTTCTCATTTAAATGTCTAATGTCGT
1 TGGCCTTGAATCAACATATCGGCACCTTTATCATTCTTCTCATTTAAATGTCTAATATCGC
*
1324486 TAGCCTTGAATCAACA
1 TGGCCTTGAATCAACA
1324502 CATCAGCATT
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
60 4 0.06
61 33 0.50
62 29 0.44
ACGTcount: A:0.24, C:0.22, G:0.14, T:0.39
Consensus pattern (61 bp):
TGGCCTTGAATCAACATATCGGCACCTTTATCATTCTTCTCATTTAAATGTCTAATATCGC
Found at i:1324577 original size:52 final size:52
Alignment explanation
Indices: 1324476--1324578 Score: 118
Period size: 52 Copynumber: 2.0 Consensus size: 52
1324466 ATTTAAATGT
* * * *
1324476 CTAATGTCGTTAGCCTTGAATCAACACATCAGCATTTTTTTCATTTTTAAGC
1 CTAATGTCGTTAGCCTAGAATCAACACATCAGCATCTTCTTCATCTTTAAGC
* * **
1324528 CTAATGTCGTTAGCCTAGAATTAGCACATTGGCACTCTTCTT-ATCTTTAAG
1 CTAATGTCGTTAGCCTAGAATCAACACATCAGCA-TCTTCTTCATCTTTAAG
1324579 TCTAGGCCTC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
52 37 0.88
53 5 0.12
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (52 bp):
CTAATGTCGTTAGCCTAGAATCAACACATCAGCATCTTCTTCATCTTTAAGC
Found at i:1325444 original size:19 final size:19
Alignment explanation
Indices: 1325411--1325455 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
1325401 AATCAAAAAC
* **
1325411 AAAAAAAATTAAAATTTCT
1 AAAAAAAATGAAAATTAAT
*
1325430 AAAAAAAATGCAAATTAAT
1 AAAAAAAATGAAAATTAAT
1325449 AAAAAAA
1 AAAAAAA
1325456 TGCTTGAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.22
Consensus pattern (19 bp):
AAAAAAAATGAAAATTAAT
Found at i:1328050 original size:20 final size:22
Alignment explanation
Indices: 1328010--1328050 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1328000 TAGCCTTTGA
*
1328010 CCATGCATATTTTTACTATGTT
1 CCATGCATATTTTAACTATGTT
1328032 CCATGCAT-TTTTAAC-ATGT
1 CCATGCATATTTTAACTATGT
1328051 ACAACATCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 6 0.33
22 8 0.44
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (22 bp):
CCATGCATATTTTAACTATGTT
Found at i:1330171 original size:67 final size:67
Alignment explanation
Indices: 1330063--1330196 Score: 268
Period size: 67 Copynumber: 2.0 Consensus size: 67
1330053 TTATAGAAGT
1330063 TCGGTCCAAACACGGCAGCTACGTCCTCTCTCCTTGGCACTTCCTTACCAAGTGGTTTCCACAAT
1 TCGGTCCAAACACGGCAGCTACGTCCTCTCTCCTTGGCACTTCCTTACCAAGTGGTTTCCACAAT
1330128 TC
66 TC
1330130 TCGGTCCAAACACGGCAGCTACGTCCTCTCTCCTTGGCACTTCCTTACCAAGTGGTTTCCACAAT
1 TCGGTCCAAACACGGCAGCTACGTCCTCTCTCCTTGGCACTTCCTTACCAAGTGGTTTCCACAAT
1330195 TC
66 TC
1330197 ACTACTCGAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.19, C:0.36, G:0.16, T:0.28
Consensus pattern (67 bp):
TCGGTCCAAACACGGCAGCTACGTCCTCTCTCCTTGGCACTTCCTTACCAAGTGGTTTCCACAAT
TC
Found at i:1333381 original size:52 final size:52
Alignment explanation
Indices: 1333303--1333430 Score: 224
Period size: 52 Copynumber: 2.5 Consensus size: 52
1333293 CGAAATATGA
*
1333303 AAATTTGCCTGCATGTATCGATACA-TTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGGGC
1333355 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
1333407 AAA-TTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1333431 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
51 21 0.28
52 48 0.65
53 5 0.07
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
Found at i:1333457 original size:13 final size:13
Alignment explanation
Indices: 1333439--1333463 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1333429 CAAAGATCAG
1333439 TGTATCGATACAA
1 TGTATCGATACAA
1333452 TGTATCGATACA
1 TGTATCGATACA
1333464 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1333541 original size:33 final size:33
Alignment explanation
Indices: 1333504--1333570 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1333494 AGTAGCTTAA
1333504 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1333537 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1333570 A
1 A
1333571 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1333544 original size:13 final size:13
Alignment explanation
Indices: 1333526--1333550 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1333516 CAAAAAAATA
1333526 TGTATCGATACAT
1 TGTATCGATACAT
1333539 TGTATCGATACA
1 TGTATCGATACA
1333551 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1334512 original size:10 final size:10
Alignment explanation
Indices: 1334484--1334513 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1334474 ATACTATACT
*
1334484 TGAACAGTAA
1 TGAACAGTGA
1334494 TGAACAGTGA
1 TGAACAGTGA
1334504 TGAACAGTGA
1 TGAACAGTGA
1334514 AAATGAGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.43, C:0.10, G:0.27, T:0.20
Consensus pattern (10 bp):
TGAACAGTGA
Found at i:1337030 original size:23 final size:24
Alignment explanation
Indices: 1336985--1337030 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
1336975 CAAAGGATTG
*
1336985 AACACAAATTCAATTAAGCACAAA
1 AACACAAATTCAATTAAGAACAAA
1337009 AACACAAA-TCAATTGAA-AACAA
1 AACACAAATTCAATT-AAGAACAA
1337031 CTTTTCAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.61, C:0.20, G:0.04, T:0.15
Consensus pattern (24 bp):
AACACAAATTCAATTAAGAACAAA
Found at i:1337956 original size:21 final size:21
Alignment explanation
Indices: 1337931--1337975 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1337921 CACTTGCAAC
*
1337931 TCATTTCTTTTATCTTCTAAT
1 TCATTTATTTTATCTTCTAAT
* *
1337952 TCATTTATTTTCTTTTCTAAT
1 TCATTTATTTTATCTTCTAAT
1337973 TCA
1 TCA
1337976 CTTAATTTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.18, G:0.00, T:0.62
Consensus pattern (21 bp):
TCATTTATTTTATCTTCTAAT
Found at i:1337984 original size:21 final size:21
Alignment explanation
Indices: 1337945--1337989 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1337935 TTCTTTTATC
* *
1337945 TTCTAATTCATTTATTTTCTT
1 TTCTAATTCACTTAATTTCTT
1337966 TTCTAATTCACTTAATTTCTT
1 TTCTAATTCACTTAATTTCTT
1337987 TTC
1 TTC
1337990 AAGAATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.20, C:0.18, G:0.00, T:0.62
Consensus pattern (21 bp):
TTCTAATTCACTTAATTTCTT
Found at i:1340130 original size:24 final size:24
Alignment explanation
Indices: 1340077--1340126 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1340067 ATGTATAGAT
* *
1340077 ACATGAACAGTAATGAATAGTGAT
1 ACATGAACAGTAATGAACAGTGAA
*
1340101 ACATGAACAGTTATGAACAGT-AA
1 ACATGAACAGTAATGAACAGTGAA
1340124 ACA
1 ACA
1340127 ATGATGAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.22
Consensus pattern (24 bp):
ACATGAACAGTAATGAACAGTGAA
Found at i:1340274 original size:53 final size:53
Alignment explanation
Indices: 1340212--1340378 Score: 161
Period size: 53 Copynumber: 3.2 Consensus size: 53
1340202 CCAATTTATT
1340212 TATCGATACAATGTATCAATACTAAGCAAAATGTATCGATACATTTGGGTATG
1 TATCGATACAATGTATCAATACTAAGCAAAATGTATCGATACATTTGGGTATG
* * * * * * * * *
1340265 TATCGATAC-ATG-AACAGTGA-AAATG--AAATTTAGCTACAGCCAATT---TATT
1 TATCGATACAATGTATCAAT-ACTAA-GCAAAATGTATCGATA--CATTTGGGTATG
1340314 TATCGATACAATGTATCAATACTAAGCAAAATGTATCGATACATTTGGGTATG
1 TATCGATACAATGTATCAATACTAAGCAAAATGTATCGATACATTTGGGTATG
1340367 TATCGATACAAT
1 TATCGATACAAT
1340379 TAAGGGTTTT
Statistics
Matches: 84, Mismatches: 18, Indels: 24
0.67 0.14 0.19
Matches are distributed among these distances:
49 12 0.14
50 18 0.21
51 12 0.14
52 18 0.21
53 24 0.29
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (53 bp):
TATCGATACAATGTATCAATACTAAGCAAAATGTATCGATACATTTGGGTATG
Found at i:1340316 original size:102 final size:102
Alignment explanation
Indices: 1340160--1340376 Score: 434
Period size: 102 Copynumber: 2.1 Consensus size: 102
1340150 ACTATTTACA
1340160 ATGTATCGATACATGAACAGTGAAAATGAAATTTAGCTACAGCCAATTTATTTATCGATACAATG
1 ATGTATCGATACATGAACAGTGAAAATGAAATTTAGCTACAGCCAATTTATTTATCGATACAATG
1340225 TATCAATACTAAGCAAAATGTATCGATACATTTGGGT
66 TATCAATACTAAGCAAAATGTATCGATACATTTGGGT
1340262 ATGTATCGATACATGAACAGTGAAAATGAAATTTAGCTACAGCCAATTTATTTATCGATACAATG
1 ATGTATCGATACATGAACAGTGAAAATGAAATTTAGCTACAGCCAATTTATTTATCGATACAATG
1340327 TATCAATACTAAGCAAAATGTATCGATACATTTGGGT
66 TATCAATACTAAGCAAAATGTATCGATACATTTGGGT
1340364 ATGTATCGATACA
1 ATGTATCGATACA
1340377 ATTAAGGGTT
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 115 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (102 bp):
ATGTATCGATACATGAACAGTGAAAATGAAATTTAGCTACAGCCAATTTATTTATCGATACAATG
TATCAATACTAAGCAAAATGTATCGATACATTTGGGT
Found at i:1340323 original size:49 final size:49
Alignment explanation
Indices: 1340163--1340323 Score: 141
Period size: 49 Copynumber: 3.2 Consensus size: 49
1340153 ATTTACAATG
1340163 TATCGATACATGAACAGTGAAAATGAAATTTAGCTACAGCCAATTTATT
1 TATCGATACATGAACAGTGAAAATGAAATTTAGCTACAGCCAATTTATT
* * * * * * * * *
1340212 TATCGATACAATGTATCAAT-ACTAA-GCAAAATGTATCGATA--CATTTGGGTATG
1 TATCGATAC-ATG-AACAGTGA-AAATG--AAATTTAGCTACAGCCAATT---TATT
1340265 TATCGATACATGAACAGTGAAAATGAAATTTAGCTACAGCCAATTTATT
1 TATCGATACATGAACAGTGAAAATGAAATTTAGCTACAGCCAATTTATT
1340314 TATCGATACA
1 TATCGATACA
1340324 ATGTATCAAT
Statistics
Matches: 82, Mismatches: 18, Indels: 24
0.66 0.15 0.19
Matches are distributed among these distances:
49 22 0.27
50 18 0.22
51 12 0.15
52 18 0.22
53 12 0.15
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (49 bp):
TATCGATACATGAACAGTGAAAATGAAATTTAGCTACAGCCAATTTATT
Found at i:1342364 original size:272 final size:271
Alignment explanation
Indices: 1341879--1342414 Score: 901
Period size: 272 Copynumber: 2.0 Consensus size: 271
1341869 AGAAAGGGAG
*
1341879 GCCAATGCCATAAGTTATGCCAACCCGCCATAGCTAAGACAACATCGAGCACCCGGTCCTTACTA
1 GCCAATGCCATAAGTTATGCCAACCCACCATAGCTAAGACAACATCGAGCACCCGGTCCTTACTA
* * * * * *
1341944 CCATGTGCACTTTACCTAGGCCTATTCATGATACCTTCCCAACCAGTGTATGCCGCAACTTATAG
66 CCACGTGCACCTTACCCAAGCCTAGTCATGATACCTACCCAACCAGTGTATGCCGCAACTTATAG
*
1342009 CCCATCCCTTGCTATCCCACCATGGCCACCATGAAATAACCATCCCCAAGCTAACCAAAATGCCA
131 CCCATCCCTTGCTATCCCACCATGGCCACCACGAAATAACCATCCCCAAGCTAACCAAAATGCCA
* *
1342074 ACCCTAATGCCAATGATGCACTAAACAATCAGGGTGTGAACCAGCGAAGGCAGCATTTCGACCCT
196 ACCCTAATGCCAATGATGCACTAAACAATCAGGGTGCGAACCAGCGAAGGCACCATTTCGACCCT
1342139 ATCCAAGTTAT
261 ATCCAAGTTAT
* *
1342150 GCCAATGCCATAAGTTATGCCAACCCACCATAGCTGAGACAACATCGAGCACCCGGTCCTTTCTA
1 GCCAATGCCATAAGTTATGCCAACCCACCATAGCTAAGACAACATCGAGCACCCGGTCCTTACTA
*
1342215 CCCACGTGCACCTTACCCAAGCCTAGTCATGATACCTACCCATCCAGTGTATGCCGCAACTTATA
66 -CCACGTGCACCTTACCCAAGCCTAGTCATGATACCTACCCAACCAGTGTATGCCGCAACTTATA
* *
1342280 GCCCATCCCTTGCTATCCCACCATGGCCACCACGAAATAACCGTCCCTAAGCTAACCAAAATGCC
130 GCCCATCCCTTGCTATCCCACCATGGCCACCACGAAATAACCATCCCCAAGCTAACCAAAATGCC
* * *
1342345 AACCCTAATGCCAATGATGCACTAAATAATCCGGGTGCGAACCAGCGAAGGCACCATTTTGACCC
195 AACCCTAATGCCAATGATGCACTAAACAATCAGGGTGCGAACCAGCGAAGGCACCATTTCGACCC
1342410 TATCC
260 TATCC
1342415 CGATGACATA
Statistics
Matches: 246, Mismatches: 18, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
271 62 0.25
272 184 0.75
ACGTcount: A:0.30, C:0.34, G:0.15, T:0.21
Consensus pattern (271 bp):
GCCAATGCCATAAGTTATGCCAACCCACCATAGCTAAGACAACATCGAGCACCCGGTCCTTACTA
CCACGTGCACCTTACCCAAGCCTAGTCATGATACCTACCCAACCAGTGTATGCCGCAACTTATAG
CCCATCCCTTGCTATCCCACCATGGCCACCACGAAATAACCATCCCCAAGCTAACCAAAATGCCA
ACCCTAATGCCAATGATGCACTAAACAATCAGGGTGCGAACCAGCGAAGGCACCATTTCGACCCT
ATCCAAGTTAT
Found at i:1344786 original size:34 final size:33
Alignment explanation
Indices: 1344726--1345222 Score: 182
Period size: 34 Copynumber: 15.3 Consensus size: 33
1344716 TTCTCCAAAT
* *
1344726 CTTTTTCCTTCTTCAAAGTACATGACTCCGTGGCACC
1 CTTTTT-CTT-TTC-AAGTCCATGACTCAGTGGCA-C
* *
1344763 CTTTTTCTTTTCAAGTCCATGACTTAGTGGCAT
1 CTTTTTCTTTTCAAGTCCATGACTCAGTGGCAC
*
1344796 CTTTTATC----AAAGTCCATGACTTC-GTGGCACC
1 CTTTT-TCTTTTCAAGTCCATGAC-TCAGTGGCA-C
* *
1344827 CTTTTTCTTTTTAAGACCATGACTCAGTGGCA-
1 CTTTTTCTTTTCAAGTCCATGACTCAGTGGCAC
* * * * *
1344859 ---TCTCTTCTCAAAGTCCACGACTCTGTGGTAC
1 CTTTTTCTTTTC-AAGTCCATGACTCAGTGGCAC
*
1344890 CTTTTCTCTTTTTAAGTCCATGACTCAGTGGCA-
1 CTTTT-TCTTTTCAAGTCCATGACTCAGTGGCAC
* * * *
1344923 ---TCTCTTCTCAAAGTCCACGACTCTGTGGCAC
1 CTTTTTCTTTTC-AAGTCCATGACTCAGTGGCAC
* * *
1344954 CCTTTTATTTTCAAGTCTATGACTCAGTGG---
1 CTTTTTCTTTTCAAGTCCATGACTCAGTGGCAC
* * * *
1344984 -TATTTCTTTTAAAGTCCACGACTCTGTGGCACC
1 CTTTTTCTTTTCAAGTCCATGACTCAGTGGCA-C
* *
1345017 CTTTTTATTTTCAAGTCCACT-ACTCAATGG---
1 CTTTTTCTTTTCAAGTCCA-TGACTCAGTGGCAC
* * ** **
1345047 -TATTTCTTTTAAAGTCCACAACTTTGTGGCAC
1 CTTTTTCTTTTCAAGTCCATGACTCAGTGGCAC
* ** * *
1345079 ATTTTTC--TTCAAAGTCCACAACTCCGTGGTAC
1 CTTTTTCTTTTC-AAGTCCATGACTCAGTGGCAC
* ** **
1345111 CATTTTTCTTTTTAAGTCCACAACTTTGTGGCAC
1 C-TTTTTCTTTTCAAGTCCATGACTCAGTGGCAC
* * *
1345145 C-TTTT-TTCTCTAAATCCATGACTTAGTGGCATC
1 CTTTTTCTTTTC-AAGTCCATGACTCAGTGGCA-C
* * * * ** *
1345178 ATTTTCCTTTTAAAGTCTACAACTCCGTGGCACC
1 CTTTTTCTTTTCAAGTCCATGACTCAGTGGCA-C
*
1345212 CTTTTCCTTTT
1 CTTTTTCTTTT
1345223 AAGCTCACAC
Statistics
Matches: 341, Mismatches: 81, Indels: 79
0.68 0.16 0.16
Matches are distributed among these distances:
29 54 0.16
30 54 0.16
31 11 0.03
32 38 0.11
33 34 0.10
34 128 0.38
35 13 0.04
36 3 0.01
37 6 0.02
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.39
Consensus pattern (33 bp):
CTTTTTCTTTTCAAGTCCATGACTCAGTGGCAC
Found at i:1344810 original size:30 final size:30
Alignment explanation
Indices: 1344775--1344959 Score: 113
Period size: 30 Copynumber: 5.9 Consensus size: 30
1344765 TTTTCTTTTC
* *
1344775 AAGTCCATGACTTAGTGGCATCTTTTATCA
1 AAGTCCATGACTTAGTGGCACCTTTTCTCA
* **
1344805 AAGTCCATGACTTCGTGGCACCCTTTTTCTTTTT
1 AAGTCCATGACTTAGTGGCA-CC-TTTTC--TCA
* * * *
1344839 AAGACCATGACTCAGTGGCATCTCTTCTCA
1 AAGTCCATGACTTAGTGGCACCTTTTCTCA
* * *
1344869 AAGTCCACGACTCT-GTGGTACCTTTTCTCTTTTT
1 AAGTCCATGACT-TAGTGGCACCTTTTCTC----A
* * *
1344903 AAGTCCATGACTCAGTGGCATCTCTTCTCA
1 AAGTCCATGACTTAGTGGCACCTTTTCTCA
*
1344933 AAGTCCACGACTCT-GTGGCACCCTTTT
1 AAGTCCATGACT-TAGTGGCA-CCTTTT
1344960 ATTTTCAAGT
Statistics
Matches: 114, Mismatches: 29, Indels: 23
0.69 0.17 0.14
Matches are distributed among these distances:
30 59 0.52
31 5 0.04
32 8 0.07
33 1 0.01
34 41 0.36
ACGTcount: A:0.21, C:0.28, G:0.16, T:0.36
Consensus pattern (30 bp):
AAGTCCATGACTTAGTGGCACCTTTTCTCA
Found at i:1344847 original size:64 final size:64
Alignment explanation
Indices: 1344733--1345087 Score: 409
Period size: 64 Copynumber: 5.6 Consensus size: 64
1344723 AATCTTTTTC
* * * *
1344733 CTTCTTCAAAGTACATGACTCCGTGGCACCCTTTTTCTTTTCAAGTCCATGACTTAGTGGCATCT
1 CTTC-TCAAAGTCCACGACTCTGTGGCACCCTTTTTCTTTTCAAGTCCATGACTCAGTGGCATCT
* * * * *
1344798 TTTATCAAAGTCCATGACT-TCGTGGCACCCTTTTTCTTTTTAAGACCATGACTCAGTGGCATCT
1 CTTCTCAAAGTCCACGACTCT-GTGGCACCCTTTTTCTTTTCAAGTCCATGACTCAGTGGCATCT
* *
1344862 CTTCTCAAAGTCCACGACTCTGTGGTA-CCTTTTCTCTTTTTAAGTCCATGACTCAGTGGCATCT
1 CTTCTCAAAGTCCACGACTCTGTGGCACCCTTTT-TCTTTTCAAGTCCATGACTCAGTGGCATCT
* * * *
1344926 CTTCTCAAAGTCCACGACTCTGTGGCACCC-TTTTATTTTCAAGTCTATGACTCAGTGGTATTT
1 CTTCTCAAAGTCCACGACTCTGTGGCACCCTTTTTCTTTTCAAGTCCATGACTCAGTGGCATCT
* * * * *
1344989 CTT-TTAAAGTCCACGACTCTGTGGCACCCTTTTTATTTTCAAGTCCACT-ACTCAATGGTATTT
1 CTTCTCAAAGTCCACGACTCTGTGGCACCCTTTTTCTTTTCAAGTCCA-TGACTCAGTGGCATCT
* * * *
1345052 CTT-TTAAAGTCCACAACTTTGTGGCA-CATTTTTCTT
1 CTTCTCAAAGTCCACGACTCTGTGGCACCCTTTTTCTT
1345088 CAAAGTCCAC
Statistics
Matches: 259, Mismatches: 25, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
62 33 0.13
63 87 0.34
64 134 0.52
65 5 0.02
ACGTcount: A:0.21, C:0.26, G:0.15, T:0.39
Consensus pattern (64 bp):
CTTCTCAAAGTCCACGACTCTGTGGCACCCTTTTTCTTTTCAAGTCCATGACTCAGTGGCATCT
Found at i:1345094 original size:32 final size:33
Alignment explanation
Indices: 1345049--1345210 Score: 132
Period size: 32 Copynumber: 4.9 Consensus size: 33
1345039 CTCAATGGTA
*
1345049 TTTCTTTTAAAGTCCACAACTTTGTGGCACATT
1 TTTCTTTCAAAGTCCACAACTTTGTGGCACATT
** *
1345082 TTTC-TTCAAAGTCCACAACTCCGTGGTACCATT
1 TTTCTTTCAAAGTCCACAACTTTGTGGCA-CATT
** *
1345115 TTTCTTTTTAAGTCCACAACTTTGTGGCACCTT
1 TTTCTTTCAAAGTCCACAACTTTGTGGCACATT
* ** *
1345148 TTT-TCTCTAAA-TCCATGACTTAGTGGCATCATT
1 TTTCTTTC-AAAGTCCACAACTTTGTGGCA-CATT
* * * **
1345181 TTCCTTTTAAAGTCTACAACTCCGTGGCAC
1 TTTCTTTCAAAGTCCACAACTTTGTGGCAC
1345211 CCTTTTCCTT
Statistics
Matches: 98, Mismatches: 25, Indels: 12
0.73 0.19 0.09
Matches are distributed among these distances:
32 36 0.37
33 29 0.30
34 33 0.34
ACGTcount: A:0.23, C:0.25, G:0.12, T:0.40
Consensus pattern (33 bp):
TTTCTTTCAAAGTCCACAACTTTGTGGCACATT
Found at i:1345181 original size:66 final size:67
Alignment explanation
Indices: 1344986--1345216 Score: 192
Period size: 66 Copynumber: 3.5 Consensus size: 67
1344976 CTCAGTGGTA
* * * * * *
1344986 TTTCTTTTAAAGTCCACGACTCTGTGGCACCCTTTTTATTTTC-AAGTCCACTACTCAATGG---
1 TTTCTTTTAAAGTCCACAACTTTGTGGCA-CCATTTT-TCTTCAAAGTCCACAACTCAGTGGCAC
*
1345047 --TA
64 CATT
* *
1345049 TTTCTTTTAAAGTCCACAACTTTGTGGCA-CATTTTTCTTCAAAGTCCACAACTCCGTGGTACCA
1 TTTCTTTTAAAGTCCACAACTTTGTGGCACCATTTTTCTTCAAAGTCCACAACTCAGTGGCACCA
1345113 TT
66 TT
* * ** * *
1345115 TTTCTTTTTAAGTCCACAACTTTGTGGCACCTTTTTTC-TCTAAA-TCCATGACTTAGTGGCATC
1 TTTCTTTTAAAGTCCACAACTTTGTGGCACCATTTTTCTTC-AAAGTCCACAACTCAGTGGCACC
1345178 ATT
65 ATT
* * ** *
1345181 TTCCTTTTAAAGTCTACAACTCCGTGGCACCCTTTT
1 TTTCTTTTAAAGTCCACAACTTTGTGGCACCATTTT
1345217 CCTTTTAAGC
Statistics
Matches: 138, Mismatches: 22, Indels: 13
0.80 0.13 0.08
Matches are distributed among these distances:
60 4 0.03
61 20 0.14
63 27 0.20
66 77 0.56
67 10 0.07
ACGTcount: A:0.22, C:0.26, G:0.12, T:0.40
Consensus pattern (67 bp):
TTTCTTTTAAAGTCCACAACTTTGTGGCACCATTTTTCTTCAAAGTCCACAACTCAGTGGCACCA
TT
Found at i:1345402 original size:33 final size:33
Alignment explanation
Indices: 1345223--1346322 Score: 879
Period size: 33 Copynumber: 33.9 Consensus size: 33
1345213 TTTTCCTTTT
* * *
1345223 AAGCTCACACAAGTTGGTGGCAACCCATCTCTA
1 AAGCCCACACAAGTCGGTGGCAACCCTTCTCTA
*
1345256 AAG-CC-CACAAGTCGGTCGCAACCCCTT-TCTA
1 AAGCCCACACAAGTCGGTGGCAA-CCCTTCTCTA
** *
1345287 AAGCCCACACAAGTTAGTGGC-ACCCCT-TCTA
1 AAGCCCACACAAGTCGGTGGCAACCCTTCTCTA
*
1345318 AAGCCCACACAAGTCGATGGCAA-CC--CTCTA
1 AAGCCCACACAAGTCGGTGGCAACCCTTCTCTA
* * **
1345348 AAGCCCATACAAATTAGTGGCAACCCTTCTCTA
1 AAGCCCACACAAGTCGGTGGCAACCCTTCTCTA
** **
1345381 AAGCTTACACAAGTCAATGGCAACCCCTT-TCTA
1 AAGCCCACACAAGTCGGTGGCAA-CCCTTCTCTA
* *
1345414 AAGCCCACACAAGTTGCTGGCAACCCCTT-TCTA
1 AAGCCCACACAAGTCGGTGGCAA-CCCTTCTCTA
* * * *
1345447 AAGCCCACATAAGTTGGTGGCAACCCTCCTTTA
1 AAGCCCACACAAGTCGGTGGCAACCCTTCTCTA
* * *
1345480 AAGCCCACAAAAATCGGTGAC-ACCC--CTCTA
1 AAGCCCACACAAGTCGGTGGCAACCCTTCTCTA
* *
1345510 AAGCCCACATAAGTCAGTGGCAACCTCTT-TCTA
1 AAGCCCACACAAGTCGGTGGCAACC-CTTCTCTA
* * * *
1345543 AAGCCCACATAAGTAGGTGGCAACCC-CCTTCAA
1 AAGCCCACACAAGTCGGTGGCAACCCTTC-TCTA
* * * *
1345576 AAGTCCACACAAGTCGATGGCAACCC-CCTTTA
1 AAGCCCACACAAGTCGGTGGCAACCCTTCTCTA
* * *
1345608 AAGCCCATACAAGTTGCTGGCAACCCTTCTCTA
1 AAGCCCACACAAGTCGGTGGCAACCCTTCTCTA
* **
1345641 AAACCCACACAAGTTAGTGGCAACCCCTT-TCTA
1 AAGCCCACACAAGTCGGTGGCAA-CCCTTCTCTA
* *
1345674 AAGCCCACACAAGTTGGTGGCAACCC-CCTTCTA
1 AAGCCCACACAAGTCGGTGGCAACCCTTC-TCTA
* * * *
1345707 AAGCCCGCACAAGTTGCTGGCAACCCTCCTCTA
1 AAGCCCACACAAGTCGGTGGCAACCCTTCTCTA
* * *
1345740 AAGCCCACACAAGTCGATAGCAACCC-CCTCTA
1 AAGCCCACACAAGTCGGTGGCAACCCTTCTCTA
* * *
1345772 AAGCCCACATAAGTTGGTGACAACCCTTCTCTA
1 AAGCCCACACAAGTCGGTGGCAACCCTTCTCTA
* * * **
1345805 AAACCCACATAAGCCAATGGCAACCCCTT-TCTA
1 AAGCCCACACAAGTCGGTGGCAA-CCCTTCTCTA
* *
1345838 AAGCCCACATAAGTTGGTGGCAACCCCTT-TCTA
1 AAGCCCACACAAGTCGGTGGCAA-CCCTTCTCTA
* *
1345871 AAGCCCACATAAGTCGGTGGCAACCCTCCTCTA
1 AAGCCCACACAAGTCGGTGGCAACCCTTCTCTA
*
1345904 AAGCCCACACAAGTCGGTGGC-A-CC-TATCTA
1 AAGCCCACACAAGTCGGTGGCAACCCTTCTCTA
* * * *
1345934 AAACCCACACAAGTCAGTGGCAACCC-CCTTCAA
1 AAGCCCACACAAGTCGGTGGCAACCCTTC-TCTA
* ***
1345967 AAGTCCACACAAGTAAATGGCAA-CC-TCTTCTA
1 AAGCCCACACAAGTCGGTGGCAACCCTTC-TCTA
* * * *
1345999 AAGCCCATACAAGTTGGCGACAACCCTTCTCTA
1 AAGCCCACACAAGTCGGTGGCAACCCTTCTCTA
* *
1346032 AAGCCCACACAAATCGATGGCAAACCCTT-TCTA
1 AAGCCCACACAAGTCGGTGGC-AACCCTTCTCTA
* ** * *
1346065 AAGCTCACACAAGTTAGTAGCAACACTTCTCTA
1 AAGCCCACACAAGTCGGTGGCAACCCTTCTCTA
* *
1346098 AAGCCCACACAAGTCGGTGGTAACCCCTT-TTTA
1 AAGCCCACACAAGTCGGTGGCAA-CCCTTCTCTA
* * *
1346131 AAGCCCACACAAGTTGGTGGCAA-CATTCCTTTA
1 AAGCCCACACAAGTCGGTGGCAACCCTT-CTCTA
* *
1346164 AAGCCTACACAAGTCAGTGGC-ACCC--CTCTA
1 AAGCCCACACAAGTCGGTGGCAACCCTTCTCTA
* ** *
1346194 AAGCCCACATAAGTCAATGGAAACCCCTT-TCTA
1 AAGCCCACACAAGTCGGTGGCAA-CCCTTCTCTA
* *
1346227 AAGCCCACACAAGTCGTTGGCAA-CC-TCATTTA
1 AAGCCCACACAAGTCGGTGGCAACCCTTC-TCTA
* * *
1346259 CAAGTCTACACAAGTCGGTGGCAACCC-TCTCAA
1 -AAGCCCACACAAGTCGGTGGCAACCCTTCTCTA
* *
1346292 AAGCCCACACAAGTCGATGGCATCTCCTTCT
1 AAGCCCACACAAGTCGGTGGCAAC-CCTTCT
1346323 AAACCCAATG
Statistics
Matches: 867, Mismatches: 155, Indels: 89
0.78 0.14 0.08
Matches are distributed among these distances:
30 88 0.10
31 63 0.07
32 136 0.16
33 543 0.63
34 37 0.04
ACGTcount: A:0.31, C:0.33, G:0.15, T:0.20
Consensus pattern (33 bp):
AAGCCCACACAAGTCGGTGGCAACCCTTCTCTA
Found at i:1345447 original size:66 final size:66
Alignment explanation
Indices: 1345223--1346329 Score: 975
Period size: 66 Copynumber: 17.1 Consensus size: 66
1345213 TTTTCCTTTT
* * * *
1345223 AAGCTCACACAAGTTGGTGGCAACCCATCTCTAAAG-CC-CACAAGTCGGTCGCAACCCCTTTCT
1 AAGCCCACACAAGTTGGTGGCAACCCCTTTCTAAAGCCCACACAAGTCGGTGGCAACCCCTTTCT
1345286 A
66 A
* *
1345287 AAGCCCACACAAGTTAGTGGC-ACCCC-TTCTAAAGCCCACACAAGTCGATGGCAA-CCC--TCT
1 AAGCCCACACAAGTTGGTGGCAACCCCTTTCTAAAGCCCACACAAGTCGGTGGCAACCCCTTTCT
1345347 A
66 A
* * * ** **
1345348 AAGCCCATACAAATTAGTGGCAA-CCCTTCTCTAAAGCTTACACAAGTCAATGGCAACCCCTTTC
1 AAGCCCACACAAGTTGGTGGCAACCCCTT-TCTAAAGCCCACACAAGTCGGTGGCAACCCCTTTC
1345412 TA
65 TA
* * * *
1345414 AAGCCCACACAAGTTGCTGGCAACCCCTTTCTAAAGCCCACATAAGTTGGTGGCAACCCTCCTT-
1 AAGCCCACACAAGTTGGTGGCAACCCCTTTCTAAAGCCCACACAAGTCGGTGGCAACCC-CTTTC
1345478 TA
65 TA
* * * * * * *
1345480 AAGCCCACAAAAATCGGTGAC-ACCCC--TCTAAAGCCCACATAAGTCAGTGGCAACCTCTTTCT
1 AAGCCCACACAAGTTGGTGGCAACCCCTTTCTAAAGCCCACACAAGTCGGTGGCAACCCCTTTCT
1345542 A
66 A
* * * * * * *
1345543 AAGCCCACATAAGTAGGTGGCAACCCCCTTCAAAAGTCCACACAAGTCGATGGCAACCCCCTT-T
1 AAGCCCACACAAGTTGGTGGCAACCCCTTTCTAAAGCCCACACAAGTCGGTGGCAACCCCTTTCT
1345607 A
66 A
* * * **
1345608 AAGCCCATACAAGTTGCTGGCAA-CCCTTCTCTAAAACCCACACAAGTTAGTGGCAACCCCTTTC
1 AAGCCCACACAAGTTGGTGGCAACCCCTT-TCTAAAGCCCACACAAGTCGGTGGCAACCCCTTTC
1345672 TA
65 TA
* * * * *
1345674 AAGCCCACACAAGTTGGTGGCAACCCCCTTCTAAAGCCCGCACAAGTTGCTGGCAA-CCCTCCTC
1 AAGCCCACACAAGTTGGTGGCAACCCCTTTCTAAAGCCCACACAAGTCGGTGGCAACCCCT-TTC
1345738 TA
65 TA
* * * * * * *
1345740 AAGCCCACACAAGTCGATAGCAACCCC-CTCTAAAGCCCACATAAGTTGGTGACAA-CCCTTCTC
1 AAGCCCACACAAGTTGGTGGCAACCCCTTTCTAAAGCCCACACAAGTCGGTGGCAACCCCTT-TC
1345803 TA
65 TA
* * **** * *
1345805 AAACCCACATAAGCCAATGGCAACCCCTTTCTAAAGCCCACATAAGTTGGTGGCAACCCCTTTCT
1 AAGCCCACACAAGTTGGTGGCAACCCCTTTCTAAAGCCCACACAAGTCGGTGGCAACCCCTTTCT
1345870 A
66 A
* * * *
1345871 AAGCCCACATAAGTCGGTGGCAA-CCCTCCTCTAAAGCCCACACAAGTCGGTGGC-A--CCTATC
1 AAGCCCACACAAGTTGGTGGCAACCCCT-TTCTAAAGCCCACACAAGTCGGTGGCAACCCCTTTC
1345932 TA
65 TA
* ** * * * *** *
1345934 AAACCCACACAAGTCAGTGGCAACCCCCTTCAAAAGTCCACACAAGTAAATGGCAACCTC-TTCT
1 AAGCCCACACAAGTTGGTGGCAACCCCTTTCTAAAGCCCACACAAGTCGGTGGCAACCCCTTTCT
1345998 A
66 A
* * * * * *
1345999 AAGCCCATACAAGTTGGCGACAA-CCCTTCTCTAAAGCCCACACAAATCGATGGCAAACCCTTTC
1 AAGCCCACACAAGTTGGTGGCAACCCCTT-TCTAAAGCCCACACAAGTCGGTGGCAACCCCTTTC
1346063 TA
65 TA
* * * * * *
1346065 AAGCTCACACAAGTTAGTAGCAA-CACTTCTCTAAAGCCCACACAAGTCGGTGGTAACCCCTTTT
1 AAGCCCACACAAGTTGGTGGCAACCCCTT-TCTAAAGCCCACACAAGTCGGTGGCAACCCCTTTC
1346129 TA
65 TA
* * *
1346131 AAGCCCACACAAGTTGGTGGCAACATTCC-TT-TAAAGCCTACACAAGTCAGTGGC-ACCCC--T
1 AAGCCCACACAAGTTGGTGGCAAC--CCCTTTCTAAAGCCCACACAAGTCGGTGGCAACCCCTTT
1346191 CTA
64 CTA
* *** * * * *
1346194 AAGCCCACATAAGTCAATGGAAACCCCTTTCTAAAGCCCACACAAGTCGTTGGCAACCTCATT-T
1 AAGCCCACACAAGTTGGTGGCAACCCCTTTCTAAAGCCCACACAAGTCGGTGGCAACCCCTTTCT
1346258 A
66 A
* * * * * * * *
1346259 CAAGTCTACACAAGTCGGTGGCAA-CCCTCTCAAAAGCCCACACAAGTCGATGGCATCTCC-TTC
1 -AAGCCCACACAAGTTGGTGGCAACCCCTTTCTAAAGCCCACACAAGTCGGTGGCAACCCCTTTC
1346322 TA
65 TA
1346324 AA-CCCA
1 AAGCCCA
1346330 ATGTCGTTGG
Statistics
Matches: 848, Mismatches: 157, Indels: 77
0.78 0.15 0.07
Matches are distributed among these distances:
61 28 0.03
62 14 0.02
63 170 0.20
64 61 0.07
65 199 0.23
66 356 0.42
67 18 0.02
68 1 0.00
69 1 0.00
ACGTcount: A:0.31, C:0.34, G:0.15, T:0.20
Consensus pattern (66 bp):
AAGCCCACACAAGTTGGTGGCAACCCCTTTCTAAAGCCCACACAAGTCGGTGGCAACCCCTTTCT
A
Found at i:1345943 original size:260 final size:260
Alignment explanation
Indices: 1345223--1346329 Score: 1154
Period size: 260 Copynumber: 4.3 Consensus size: 260
1345213 TTTTCCTTTT
* * *
1345223 AAGCTCACACAAGTTGGTGGCAACCCATCTCTAAAG-CC-CACAAGTCGGTCGCAACCCCTTTCT
1 AAGCCCACACAAGTCGGTGGCAACCC-TCTCTAAAGCCCACACAAGTCGGTGGCAA-CCCTTTCT
1345286 AAAGCCCACACAAGTTAGTGGC-ACCCC-TTCTAAAGCCCACACAAGTCGATGGCAA-CCC--TC
64 AAAGCCCACACAAGTTAGTGGCAACCCCTTTCTAAAGCCCACACAAGTCGATGGCAACCCCTTTC
* * * * ** *
1345346 TAAAGCCCATACAAATTAGTGGCAACCCTTCTCTAAAGCTTACACAAGTCAATGGCAACCCCTTT
129 TAAAGCCCACACAAGTTGGTGGCAACCCTCCTCTAAAGCCCACACAAGTCAGTGGCAA-CCCTTT
* * * *
1345411 CTAAAGCCCACACAAGT-TGCTGGCAACCCCTTTCTAAAGCCCACATAAGTTGGTGGCAACCCTC
193 CTAAAGCCCACACAAGTCAG-TGGCAACCCCCTTCTAAAGCCCACACAAGTTGATGGCAA-CCTC
*
1345475 CTTTA
256 CTCTA
* * * * *
1345480 AAGCCCACAAAAATCGGTGAC-ACCC-CTCTAAAGCCCACATAAGTCAGTGGCAACCTCTTTCTA
1 AAGCCCACACAAGTCGGTGGCAACCCTCTCTAAAGCCCACACAAGTCGGTGGCAACC-CTTTCTA
* * * * *
1345543 AAGCCCACATAAG-TAGGTGGCAACCCCCTTCAAAAGTCCACACAAGTCGATGGCAACCCCCTT-
65 AAGCCCACACAAGTTA-GTGGCAACCCCTTTCTAAAGCCCACACAAGTCGATGGCAACCCCTTTC
* * * * *
1345606 TAAAGCCCATACAAGTTGCTGGCAACCCTTCTCTAAAACCCACACAAGTTAGTGGCAACCCCTTT
129 TAAAGCCCACACAAGTTGGTGGCAACCCTCCTCTAAAGCCCACACAAGTCAGTGGCAA-CCCTTT
** * *
1345671 CTAAAGCCCACACAAGTTGGTGGCAACCCCCTTCTAAAGCCCGCACAAGTTGCTGGCAACCCTCC
193 CTAAAGCCCACACAAGTCAGTGGCAACCCCCTTCTAAAGCCCACACAAGTTGATGGCAA-CCTCC
1345736 TCTA
257 TCTA
* * * * * *
1345740 AAGCCCACACAAGTCGATAGCAACCCCCTCTAAAGCCCACATAAGTTGGTGACAACCCTTCTCTA
1 AAGCCCACACAAGTCGGTGGCAACCCTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTT-TCTA
* * ** * * * *
1345805 AAACCCACATAAGCCAATGGCAACCCCTTTCTAAAGCCCACATAAGTTGGTGGCAACCCCTTTCT
65 AAGCCCACACAAGTTAGTGGCAACCCCTTTCTAAAGCCCACACAAGTCGATGGCAACCCCTTTCT
* * * *
1345870 AAAGCCCACATAAGTCGGTGGCAACCCTCCTCTAAAGCCCACACAAGTCGGTGGC-A-CCTATCT
130 AAAGCCCACACAAGTTGGTGGCAACCCTCCTCTAAAGCCCACACAAGTCAGTGGCAACCCTTTCT
* * * ** *
1345933 AAAACCCACACAAGTCAGTGGCAACCCCCTTCAAAAGTCCACACAAGTAAATGGCAACCTCTTCT
195 AAAGCCCACACAAGTCAGTGGCAACCCCCTTCTAAAGCCCACACAAGTTGATGGCAACCTCCTCT
1345998 A
260 A
* * * * * *
1345999 AAGCCCATACAAGTTGGCGACAACCCTTCTCTAAAGCCCACACAAATCGATGGCAAACCCTTTCT
1 AAGCCCACACAAGTCGGTGGCAACCC-TCTCTAAAGCCCACACAAGTCGGTGGC-AACCCTTTCT
* * * * *
1346064 AAAGCTCACACAAGTTAGTAGCAA-CACTTCTCTAAAGCCCACACAAGTCGGTGGTAACCCCTTT
64 AAAGCCCACACAAGTTAGTGGCAACCCCTT-TCTAAAGCCCACACAAGTCGATGGCAACCCCTTT
* ** * * *
1346128 TTAAAGCCCACACAAGTTGGTGGCAACATTCCTTTAAAGCCTACACAAGTCAGTGGC-ACCC-CT
128 CTAAAGCCCACACAAGTTGGTGGCAACCCTCCTCTAAAGCCCACACAAGTCAGTGGCAACCCTTT
* * * * * * *
1346191 CTAAAGCCCACATAAGTCAATGGAAACCCCTTTCTAAAGCCCACACAAGTCGTTGGCAACCTCAT
193 CTAAAGCCCACACAAGTCAGTGGCAACCCCCTTCTAAAGCCCACACAAGTTGATGGCAACCTCCT
*
1346256 TTA
258 CTA
* * * * *
1346259 CAAGTCTACACAAGTCGGTGGCAACCCTCTCAAAAGCCCACACAAGTCGATGGCATCTCC-TTCT
1 -AAGCCCACACAAGTCGGTGGCAACCCTCTCTAAAGCCCACACAAGTCGGTGGCAAC-CCTTTCT
1346323 AAA-CCCA
64 AAAGCCCA
1346330 ATGTCGTTGG
Statistics
Matches: 713, Mismatches: 116, Indels: 41
0.82 0.13 0.05
Matches are distributed among these distances:
254 8 0.01
255 6 0.01
256 41 0.06
257 21 0.03
258 29 0.04
259 44 0.06
260 394 0.55
261 38 0.05
262 83 0.12
263 49 0.07
ACGTcount: A:0.31, C:0.34, G:0.15, T:0.20
Consensus pattern (260 bp):
AAGCCCACACAAGTCGGTGGCAACCCTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTTCTAA
AGCCCACACAAGTTAGTGGCAACCCCTTTCTAAAGCCCACACAAGTCGATGGCAACCCCTTTCTA
AAGCCCACACAAGTTGGTGGCAACCCTCCTCTAAAGCCCACACAAGTCAGTGGCAACCCTTTCTA
AAGCCCACACAAGTCAGTGGCAACCCCCTTCTAAAGCCCACACAAGTTGATGGCAACCTCCTCTA
Found at i:1346452 original size:52 final size:51
Alignment explanation
Indices: 1346381--1346681 Score: 370
Period size: 52 Copynumber: 5.8 Consensus size: 51
1346371 CATTTCTTTC
* * * * *
1346381 TAAGTCCAATGTCGCTGGCCTTGAATTAGCACATTGGCACCTTTTTCTTTCT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTC-ATCT
* *
1346433 TAAGTCCAATATCGTTGGCCTTGAATCAACATATTGGCACCTTTGTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATC-T
* * * *
1346485 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTTTCTTTCT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTC-ATCT
* * ** *
1346537 TACGTCCAATATCGTTGGCCTTGAATCAGCATATTGGTGCCTTTGTCACCT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCT
*
1346588 TCAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTT
1 T-AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATC-T
* * *
1346641 TAAGTCCAATGTCGCTGGCCTTG-ATTAGCATATCGGCACCT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCT
1346682 GTATTGTTCT
Statistics
Matches: 215, Mismatches: 30, Indels: 9
0.85 0.12 0.04
Matches are distributed among these distances:
51 21 0.10
52 190 0.88
53 4 0.02
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (51 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCT
Found at i:1346509 original size:104 final size:104
Alignment explanation
Indices: 1346381--1346681 Score: 435
Period size: 104 Copynumber: 2.9 Consensus size: 104
1346371 CATTTCTTTC
*
1346381 TAAGTCCAATGTCGCTGGCCTTGAATTAGCACATTGGCACCTTTTTCTTTCTTAAGTCCAATATC
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTTTCTTTCTTAAGTCCAATATC
* *
1346446 GTTGGCCTTGAATCAACATATTGGCACCTTTGTCATCTT
66 GTTGGCCTTGAATCAGCATATTGGCACCTTTGTCACCTT
*
1346485 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTTTCTTTCTTACGTCCAATATC
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTTTCTTTCTTAAGTCCAATATC
**
1346550 GTTGGCCTTGAATCAGCATATTGGTGCCTTTGTCACCTT
66 GTTGGCCTTGAATCAGCATATTGGCACCTTTGTCACCTT
* * * * * * *
1346589 CAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTGTC-ATCTTTAAGTCCAATGT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTTTCTTTC-TTAAGTCCAATAT
* * *
1346653 CGCTGGCCTTG-ATTAGCATATCGGCACCT
65 CGTTGGCCTTGAATCAGCATATTGGCACCT
1346682 GTATTGTTCT
Statistics
Matches: 177, Mismatches: 19, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
103 16 0.09
104 161 0.91
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (104 bp):
TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTTTCTTTCTTAAGTCCAATATC
GTTGGCCTTGAATCAGCATATTGGCACCTTTGTCACCTT
Found at i:1346622 original size:156 final size:154
Alignment explanation
Indices: 1346373--1346681 Score: 458
Period size: 156 Copynumber: 2.0 Consensus size: 154
1346363 TGTCAAGCCA
* * * **
1346373 TTTCTTTCTAAGTCCAATGTCGCTGGCCTTGAATTAGCACATTGGCACCTTTTTCTTTCTTAAGT
1 TTTCTTTCTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTGTCTACCTTAAGT
1346438 CCAATATCGTTGGCCTTGAATCAACATATTGGCACCTTTGTCATCTTTAAGTCCAATGTCGCTGG
66 CCAATATCGTTGGCCTTGAATCAACATATTGGCACCTTTGTCATCTTTAAGTCCAATGTCGCTGG
*
1346503 CCTTGAATCAGCACATTGGCACCTT
131 CCTTG-ATCAGCACATCGGCACCTT
* * * **
1346528 TTTCTTTCTTACGTCCAATATCGTTGGCCTTGAATCAGCATATTGGTGCCTTTGTC-ACCTTCAA
1 TTTCTTTC-TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTGTCTACCTT-AA
*
1346592 GTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAATGTCGCT
64 GTCCAATATCGTTGGCCTTGAATCAACATATTGGCACCTTTGTCATCTTTAAGTCCAATGTCGCT
* *
1346657 GGCCTTGATTAGCATATCGGCACCT
129 GGCCTTGATCAGCACATCGGCACCT
1346682 GTATTGTTCT
Statistics
Matches: 138, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
155 26 0.19
156 112 0.81
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.37
Consensus pattern (154 bp):
TTTCTTTCTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTGTCTACCTTAAGT
CCAATATCGTTGGCCTTGAATCAACATATTGGCACCTTTGTCATCTTTAAGTCCAATGTCGCTGG
CCTTGATCAGCACATCGGCACCTT
Found at i:1346758 original size:61 final size:61
Alignment explanation
Indices: 1346667--1346831 Score: 165
Period size: 61 Copynumber: 2.7 Consensus size: 61
1346657 GGCCTTGATT
* * ** * *
1346667 AGCATATCGGCACCTGTATTGTTCTTCTCATCTTCAAGTCCAATGTCTTTAGCCT-CGAATC
1 AGCATATTGGCACCTTTATCATTCTTCTCATCTTCAAGTCCAATATCGTT-GCCTGCGAATC
* * * * * *
1346728 AGCATTTTGGCACCTTTATCATTTTTCTCATCTCCAAG-CCTGATATCGTTGGCTGGGAATC
1 AGCATATTGGCACCTTTATCATTCTTCTCATCTTCAAGTCC-AATATCGTTGCCTGCGAATC
*
1346789 AGCATATTGGCACCTTTATCATTCTTCGCATCCTT-AAGTCCAA
1 AGCATATTGGCACCTTTATCATTCTTCTCAT-CTTCAAGTCCAA
1346832 CGTCACTGAC
Statistics
Matches: 83, Mismatches: 17, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
60 5 0.06
61 74 0.89
62 4 0.05
ACGTcount: A:0.22, C:0.27, G:0.15, T:0.36
Consensus pattern (61 bp):
AGCATATTGGCACCTTTATCATTCTTCTCATCTTCAAGTCCAATATCGTTGCCTGCGAATC
Found at i:1347645 original size:41 final size:40
Alignment explanation
Indices: 1347593--1347671 Score: 122
Period size: 40 Copynumber: 1.9 Consensus size: 40
1347583 ATTTTCGGAG
*
1347593 GAAATTGTATCGATACATTTTTTAAATGTATCGATACATAA
1 GAAATTGTATCGATACA-TTTCTAAATGTATCGATACATAA
* *
1347634 GAAATTGTATCGATACATTTCTCATTGTATCGATACAT
1 GAAATTGTATCGATACATTTCTAAATGTATCGATACAT
1347672 TCTAGGTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
40 18 0.51
41 17 0.49
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (40 bp):
GAAATTGTATCGATACATTTCTAAATGTATCGATACATAA
Found at i:1347660 original size:20 final size:20
Alignment explanation
Indices: 1347595--1347672 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 20
1347585 TTTCGGAGGA
*
1347595 AATTGTATCGATACATTTTTT
1 AATTGTATCGATACA-TTTCT
* ****
1347616 AAATGTATCGATACATAAGA
1 AATTGTATCGATACATTTCT
1347636 AATTGTATCGATACATTTCT
1 AATTGTATCGATACATTTCT
*
1347656 CATTGTATCGATACATT
1 AATTGTATCGATACATT
1347673 CTAGGTTTTG
Statistics
Matches: 46, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
20 32 0.70
21 14 0.30
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.41
Consensus pattern (20 bp):
AATTGTATCGATACATTTCT
Found at i:1352025 original size:20 final size:20
Alignment explanation
Indices: 1352000--1352038 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1351990 GCTTACAATA
* *
1352000 TATCGATATATTCACTTATG
1 TATCGATACATTAACTTATG
1352020 TATCGATACATTAACTTAT
1 TATCGATACATTAACTTAT
1352039 TATATTAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (20 bp):
TATCGATACATTAACTTATG
Found at i:1355245 original size:13 final size:13
Alignment explanation
Indices: 1355227--1355252 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1355217 TACACAAAGT
1355227 ATGTATCGATACA
1 ATGTATCGATACA
1355240 ATGTATCGATACA
1 ATGTATCGATACA
1355253 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1355250 original size:32 final size:33
Alignment explanation
Indices: 1355209--1355272 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1355199 TAGCCAAACT
**
1355209 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1355241 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1355273 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1357506 original size:21 final size:21
Alignment explanation
Indices: 1357473--1357522 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
1357463 TTGCAAGTTG
*
1357473 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1357495 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
1357516 AAATAAA
1 AAATAAA
1357523 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1359334 original size:15 final size:15
Alignment explanation
Indices: 1359314--1359344 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1359304 GCAAGATGTC
*
1359314 CAAAATGAGGAAGCT
1 CAAAATGACGAAGCT
1359329 CAAAATGACGAAGCT
1 CAAAATGACGAAGCT
1359344 C
1 C
1359345 CATACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGACGAAGCT
Found at i:1361394 original size:13 final size:13
Alignment explanation
Indices: 1361376--1361414 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1361366 CATTTATTCT
1361376 TTGTATCGATACA
1 TTGTATCGATACA
*
1361389 TTGTATTGATACA
1 TTGTATCGATACA
1361402 TTGTATCGATACA
1 TTGTATCGATACA
1361415 GGGTGATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1363981 original size:13 final size:13
Alignment explanation
Indices: 1363963--1363988 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1363953 TACACCAAGT
1363963 ATGTATCGATACA
1 ATGTATCGATACA
1363976 ATGTATCGATACA
1 ATGTATCGATACA
1363989 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1363986 original size:32 final size:33
Alignment explanation
Indices: 1363945--1364008 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1363935 TAGCCAAACT
* **
1363945 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1363977 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1364009 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1366312 original size:4 final size:4
Alignment explanation
Indices: 1366303--1366339 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
1366293 CATATATTAT
1366303 ATAC ATAC ATAC ATAC ATAC ATAC ATAC -T-C ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1366340 ACTATTAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 1 0.03
3 2 0.06
4 28 0.90
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:1370201 original size:24 final size:24
Alignment explanation
Indices: 1370181--1370225 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 24
1370171 GTTTTTTCTT
1370181 TTTCT-TATTTCCTCTCCTTTTTC
1 TTTCTATATTTCCTCTCCTTTTTC
1370204 TTTCTATATTT--TCT-CTTTTTC
1 TTTCTATATTTCCTCTCCTTTTTC
1370225 T
1 T
1370226 CCAAGTTTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 8 0.38
22 3 0.14
23 5 0.24
24 5 0.24
ACGTcount: A:0.07, C:0.24, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTCTATATTTCCTCTCCTTTTTC
Found at i:1373885 original size:13 final size:13
Alignment explanation
Indices: 1373867--1373891 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1373857 CATTTTATGG
1373867 TGTATCGATACAA
1 TGTATCGATACAA
1373880 TGTATCGATACA
1 TGTATCGATACA
1373892 TACTGTGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1373907 original size:32 final size:33
Alignment explanation
Indices: 1373844--1373911 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
1373834 CGTTACAAGC
**
1373844 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
*
1373877 CAATGTATCGATACATACTGT-GTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
1373909 CAA
1 CAA
1373912 GTTTAGCTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATACTATGGTGTATCGATA
Found at i:1373969 original size:20 final size:20
Alignment explanation
Indices: 1373944--1373996 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1373934 CCAATGACTT
**
1373944 GTATCGATACATTTTTTCAA
1 GTATCGATACATTTAGTCAA
*
1373964 GTATCGATACATTTAGTCAT
1 GTATCGATACATTTAGTCAA
1373984 GTATCGATACATT
1 GTATCGATACATT
1373997 GTATCGATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (20 bp):
GTATCGATACATTTAGTCAA
Found at i:1374603 original size:21 final size:20
Alignment explanation
Indices: 1374560--1374603 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
1374550 ATTTTTCTTT
* *
1374560 TTTCTCCCCTTAATCAAACA
1 TTTCTCCCCTTAATAAAAAA
*
1374580 TTTCTCCCCCTTAGTAAAAAA
1 TTTCT-CCCCTTAATAAAAAA
1374601 TTT
1 TTT
1374604 AACACTTTCG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.30, C:0.30, G:0.02, T:0.39
Consensus pattern (20 bp):
TTTCTCCCCTTAATAAAAAA
Found at i:1374653 original size:19 final size:19
Alignment explanation
Indices: 1374629--1374666 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1374619 TAACCATTTC
1374629 TTTCTCCCCCTTAATCATA
1 TTTCTCCCCCTTAATCATA
1374648 TTTCTCCCCCTTAATCATA
1 TTTCTCCCCCTTAATCATA
1374667 AAAAATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.37, G:0.00, T:0.42
Consensus pattern (19 bp):
TTTCTCCCCCTTAATCATA
Found at i:1376015 original size:20 final size:21
Alignment explanation
Indices: 1375987--1376027 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
1375977 AGGGGCTGCT
*
1375987 CGGTTGCGACCTGG-GGGTGC
1 CGGTCGCGACCTGGTGGGTGC
1376007 CGGTCGCGACCTGGTGGGTGC
1 CGGTCGCGACCTGGTGGGTGC
1376028 TGCCTAGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.05, C:0.27, G:0.49, T:0.20
Consensus pattern (21 bp):
CGGTCGCGACCTGGTGGGTGC
Found at i:1376312 original size:22 final size:22
Alignment explanation
Indices: 1376289--1376330 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1376279 GTTGTTTTTG
1376289 ATGATG-ATTTTG-A-TGAAAA
1 ATGATGTATTTTGAAGTGAAAA
1376308 ATGATGTATTTTGAAGTGAAAA
1 ATGATGTATTTTGAAGTGAAAA
1376330 A
1 A
1376331 CAAGAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 6 0.30
21 1 0.05
22 7 0.35
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.36
Consensus pattern (22 bp):
ATGATGTATTTTGAAGTGAAAA
Found at i:1376471 original size:13 final size:13
Alignment explanation
Indices: 1376453--1376491 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1376443 ATAATCCCCT
*
1376453 TGTATCGATACAG
1 TGTATCGATACAA
1376466 TGTATCGATACAA
1 TGTATCGATACAA
*
1376479 TGTATCAATACAA
1 TGTATCGATACAA
1376492 AGAATGCTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1382670 original size:13 final size:13
Alignment explanation
Indices: 1382652--1382676 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1382642 CATTTTATGG
1382652 TGTATCGATACAA
1 TGTATCGATACAA
1382665 TGTATCGATACA
1 TGTATCGATACA
1382677 TACTGTGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1382692 original size:32 final size:33
Alignment explanation
Indices: 1382629--1382696 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
1382619 TGTTACAAGC
**
1382629 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
*
1382662 CAATGTATCGATACATACTGT-GTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
1382694 CAA
1 CAA
1382697 GTTTAGCTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATACTATGGTGTATCGATA
Found at i:1382754 original size:20 final size:20
Alignment explanation
Indices: 1382729--1382781 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1382719 CCAATGACTT
**
1382729 GTATCGATACATTTTTTCAA
1 GTATCGATACATTTAGTCAA
* *
1382749 GTATCGATAGATTTAGTCAT
1 GTATCGATACATTTAGTCAA
1382769 GTATCGATACATT
1 GTATCGATACATT
1382782 GTATCGATAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (20 bp):
GTATCGATACATTTAGTCAA
Found at i:1383749 original size:81 final size:78
Alignment explanation
Indices: 1383632--1384107 Score: 405
Period size: 81 Copynumber: 5.9 Consensus size: 78
1383622 TACCCTTAAT
* * *
1383632 GATGAAAATTTGATA-TTTT-AGAAATAAAAATGGGGTTAGAGTATTCCTTTGAAAGTGGTAGGG
1 GATGAAAATTTGATATTTTTAAG-AGTAAAAACGGGGTTAGAGTATCCCTTTGAAA-TGGT-GGG
1383695 TTGGAGTATCCCCGAA
63 TTGGAGTATCCCCGAA
* * *
1383711 GATAGAAAATTTGATATTTTTAAGAGTAAAAATGGGGTTGGAGTATCCCTTTGGAAACGGTGGGG
1 GAT-GAAAATTTGATATTTTTAAGAGTAAAAACGGGGTTAGAGTATCCCTTT-GAAATGGT-GGG
1383776 TTGGAGTATCCCC-AA
63 TTGGAGTATCCCCGAA
* ** * ** *
1383791 TGGTGAAAATTTTGATATTTTGGA-AGTAAAAATGGGGTTCA-AGTATCCCTTCAAAAATGTTGG
1 -GATGAAAA-TTTGATATTTTTAAGAGTAAAAACGGGGTT-AGAGTATCCCTT-TGAAATGGTGG
* *
1383854 GTTAGAGTATCCTCGATA
62 GTTGGAGTATCCCCGA-A
* * * ** ** *
1383872 G-TGAAAAATCGATATTTTTGAA-A-TAACAACAAGGTTAGAGTATCCCCTCAGAAGTGGTGGGA
1 GATGAAAATTTGATATTTTT-AAGAGTAAAAACGGGGTTAGAGTAT-CCCTTTGAAATGGTGGG-
1383934 TTGGAGTATCCCCGAA
63 TTGGAGTATCCCCGAA
* *
1383950 GATGGAAAATTTGATATTTTTAAAAGTAAAAACGGGGTTGGAGTAT-CCTTTCAGAAATGGTAGG
1 GAT-GAAAATTTGATATTTTTAAGAGTAAAAACGGGGTTAGAGTATCCCTTT--GAAATGGT-GG
* *
1384014 GTTGGAGTATCCTCGTA
62 GTTGGAGTATCCCCGAA
* ** *
1384031 GATGGAAAATTTGATATTTTT-AGAAGTAAAAACGGCGTCGGAGTATCCCCTTGAAAATGGTGAG
1 GAT-GAAAATTTGATATTTTTAAG-AGTAAAAACGGGGTTAGAGTATCCCTTTG-AAATGGTG-G
1384095 GTTGGAGTATCCC
62 GTTGGAGTATCCC
1384108 TAATGGTGAA
Statistics
Matches: 327, Mismatches: 45, Indels: 48
0.78 0.11 0.11
Matches are distributed among these distances:
77 1 0.00
78 34 0.10
79 48 0.15
80 70 0.21
81 161 0.49
82 13 0.04
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (78 bp):
GATGAAAATTTGATATTTTTAAGAGTAAAAACGGGGTTAGAGTATCCCTTTGAAATGGTGGGTTG
GAGTATCCCCGAA
Found at i:1384121 original size:81 final size:81
Alignment explanation
Indices: 1383585--1384122 Score: 364
Period size: 81 Copynumber: 6.7 Consensus size: 81
1383575 GTGAAAATCA
* * * * * *
1383585 GGGTTGGAGTATCCTCTCGAAAAAGAT-AGGGTTAGAGTA-CCCTTAATGATG-AAAATTTGATA
1 GGGTTGGAGTATCCCCTTGAAAATGGTGA-GGTTGGAGTATCCC-TAATGGTGAAAAATTTGATA
* *
1383647 -TTTTAGAAATAAAAATG
64 TTTTTAGAAGTAAAAACG
* * * * * *
1383664 GGGTTAGAGTATTCCTTTGAAAGTGGT-AGGGTTGGAGTATCCCCGAA-GAT-AGAAAATTTGAT
1 GGGTTGGAGTATCCCCTTGAAAATGGTGA-GGTTGGAGTAT-CCCTAATGGTGA-AAAATTTGAT
*
1383726 ATTTTTA-AGAGTAAAAATG
63 ATTTTTAGA-AGTAAAAACG
* * * * * *
1383745 GGGTTGGAGTATCCCTTTGGAAACGGTGGGGTTGGAGTATCCCCAATGGTGAAAATTTTGATA-T
1 GGGTTGGAGTATCCCCTTGAAAATGGTGAGGTTGGAGTATCCCTAATGGTGAAAAATTTGATATT
* *
1383809 TTTGGAAGTAAAAATG
66 TTTAGAAGTAAAAACG
** * * * * * *
1383825 GGGTTCAAGTAT-CCCTTCAAAAATGTTG-GGTTAGAGTAT-CCTCGATAGTGAAAAA-TCGATA
1 GGGTTGGAGTATCCCCTT-GAAAATGGTGAGGTTGGAGTATCCCT-AATGGTGAAAAATTTGATA
* * *
1383886 TTTTT-GAAATAACAACA
64 TTTTTAGAAGTAAAAACG
* * * * * * *
1383903 AGGTTAGAGTATCCCC-TCAGAAGTGGTG-GGATTGGAGTATCCCCGAA-GATGGAAAATTTGAT
1 GGGTTGGAGTATCCCCTTGA-AAATGGTGAGG-TTGGAGTAT-CCCTAATGGTGAAAAATTTGAT
*
1383965 ATTTTTAAAAGTAAAAACG
63 ATTTTTAGAAGTAAAAACG
* *
1383984 GGGTTGGAGTAT-CCTTTCAGAAATGGT-AGGGTTGGAGTATCCTCGTAGAT-G-G-AAAATTTG
1 GGGTTGGAGTATCCCCTTGA-AAATGGTGA-GGTTGGAGTATCC-C-TA-ATGGTGAAAAATTTG
1384044 ATATTTTTAGAAGTAAAAACG
61 ATATTTTTAGAAGTAAAAACG
* *
1384065 GCGTCGGAGTATCCCCTTGAAAATGGTGAGGTTGGAGTATCCCTAATGGTGAAAAATT
1 GGGTTGGAGTATCCCCTTGAAAATGGTGAGGTTGGAGTATCCCTAATGGTGAAAAATT
1384123 AGATGCTTTT
Statistics
Matches: 361, Mismatches: 66, Indels: 62
0.74 0.13 0.13
Matches are distributed among these distances:
77 1 0.00
78 35 0.10
79 80 0.22
80 66 0.18
81 167 0.46
82 11 0.03
83 1 0.00
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (81 bp):
GGGTTGGAGTATCCCCTTGAAAATGGTGAGGTTGGAGTATCCCTAATGGTGAAAAATTTGATATT
TTTAGAAGTAAAAACG
Found at i:1386597 original size:20 final size:21
Alignment explanation
Indices: 1386572--1386626 Score: 85
Period size: 20 Copynumber: 2.7 Consensus size: 21
1386562 TCATTTTAGA
1386572 CATGTATCGATACATTCAC-T
1 CATGTATCGATACATTCACTT
1386592 CATGTATCGATACATTCACTT
1 CATGTATCGATACATTCACTT
**
1386613 TTTGTATCGATACA
1 CATGTATCGATACA
1386627 AATTGCGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 19 0.59
21 13 0.41
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38
Consensus pattern (21 bp):
CATGTATCGATACATTCACTT
Found at i:1386703 original size:21 final size:21
Alignment explanation
Indices: 1386662--1386703 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1386652 CTATTGTGAC
* *
1386662 CATGTATCGATACATGGAAGA
1 CATGCATCGATACATCGAAGA
*
1386683 CATGCATCGATACATCTAAGA
1 CATGCATCGATACATCGAAGA
1386704 AAAAATATGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (21 bp):
CATGCATCGATACATCGAAGA
Found at i:1388691 original size:16 final size:15
Alignment explanation
Indices: 1388670--1388718 Score: 53
Period size: 17 Copynumber: 3.1 Consensus size: 15
1388660 TTGAGGGCTC
1388670 AGCAAAAGAGAAAAAA
1 AGCAAAA-AGAAAAAA
*
1388686 AGCAAAAAAAAAAAA
1 AGCAAAAAGAAAAAA
*
1388701 AGAAGAAAAAGAAAAAA
1 AG--CAAAAAGAAAAAA
1388718 A
1 A
1388719 AAGAGGAGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 9 0.32
16 7 0.25
17 12 0.43
ACGTcount: A:0.82, C:0.04, G:0.14, T:0.00
Consensus pattern (15 bp):
AGCAAAAAGAAAAAA
Found at i:1388692 original size:9 final size:8
Alignment explanation
Indices: 1388673--1388718 Score: 58
Period size: 8 Copynumber: 5.8 Consensus size: 8
1388663 AGGGCTCAGC
*
1388673 AAAAGAGA
1 AAAAAAGA
*
1388681 AAAAAAGC
1 AAAAAAGA
1388689 AAAAAA-A
1 AAAAAAGA
1388696 AAAAAAGA
1 AAAAAAGA
1388704 AGAAAAAGA
1 A-AAAAAGA
1388713 AAAAAA
1 AAAAAA
1388719 AAGAGGAGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
7 6 0.18
8 19 0.58
9 8 0.24
ACGTcount: A:0.85, C:0.02, G:0.13, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:1388704 original size:23 final size:23
Alignment explanation
Indices: 1388673--1388720 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
1388663 AGGGCTCAGC
*
1388673 AAAAGAGAA-AAAAAGCAAAAAAA
1 AAAAAAGAAGAAAAAG-AAAAAAA
1388696 AAAAAAGAAGAAAAAGAAAAAAA
1 AAAAAAGAAGAAAAAGAAAAAAA
1388719 AA
1 AA
1388721 GAGGAGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.85, C:0.02, G:0.12, T:0.00
Consensus pattern (23 bp):
AAAAAAGAAGAAAAAGAAAAAAA
Found at i:1391043 original size:79 final size:79
Alignment explanation
Indices: 1390928--1391136 Score: 242
Period size: 80 Copynumber: 2.6 Consensus size: 79
1390918 GTGAAAATTA
* ** *
1390928 GGGTTGGAGTATCCCCATAGACATAAAATTTAGTGTTT-TGAAGTAAAAATGGGGTTAGAGTATC
1 GGGTTGGAGTAT-CCCATAGACATAAAATTTAGTGTTTGAGAAGTAAAAACAGGGTTAGACTATC
*
1390992 CCCTCGGAAATGGTG
65 CCCTCGAAAATGGTG
* *
1391007 GGGTTAGAGTATCCCAT-GAGATGAAAATTTAGGTGTTTGAGAAGTAAAAACAGGGTTAGACTAT
1 GGGTTGGAGTATCCCATAGACAT-AAAATTTA-GTGTTTGAGAAGTAAAAACAGGGTTAGACTAT
1391071 CCCCTCGAAAATGGTG
64 CCCCTCGAAAATGGTG
* * * * * *
1391087 GGGTTGGAGTATCTCCAAAGATAAAGAAATTCAATGTTTTAGAAGTAAAA
1 GGGTTGGAGTATC-CCATAGACATA-AAATTTAGTGTTTGAGAAGTAAAA
1391137 GCGGTATTGA
Statistics
Matches: 110, Mismatches: 14, Indels: 10
0.82 0.10 0.07
Matches are distributed among these distances:
77 4 0.04
78 13 0.12
79 17 0.15
80 48 0.44
81 19 0.17
82 9 0.08
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.28
Consensus pattern (79 bp):
GGGTTGGAGTATCCCATAGACATAAAATTTAGTGTTTGAGAAGTAAAAACAGGGTTAGACTATCC
CCTCGAAAATGGTG
Found at i:1391232 original size:79 final size:79
Alignment explanation
Indices: 1390928--1391548 Score: 522
Period size: 79 Copynumber: 7.8 Consensus size: 79
1390918 GTGAAAATTA
* * * * * * *
1390928 GGGTTGGAGTATCCCCATAGA-CATAAAATTTAGTGTTTT-GAAGTAAAAATGGGGTTAGAGTAT
1 GGGTTGGAGTATCCCC-GAGATGA-AAAATTCAATATTTTGGAAGTAAAAACGGGGTTGGAGTAT
* *
1390991 CCCCTCGGAAATGGTG
64 CCCCTCGAAAATGATG
* * * * * * * *
1391007 GGGTTAGAGTATCCCATGAGATG-AAAATTTAGGT-GTTTGAGAAGTAAAAACAGGGTTAGACTA
1 GGGTTGGAGTATCCC-CGAGATGAAAAATTCA-ATATTTTG-GAAGTAAAAACGGGGTTGGAGTA
*
1391070 TCCCCTCGAAAATGGTG
63 TCCCCTCGAAAATGATG
** * * * * ** * *
1391087 GGGTTGGAGTATCTCCAAAGATAAAGAAATTCAATGTTTTAGAAGTAAAAGCGGTATTGAAATAT
1 GGGTTGGAGTATC-CCCGAGATGAA-AAATTCAATATTTTGGAAGTAAAAACGGGGTTGGAGTAT
*
1391152 CCCCTCGAAAATAATG
64 CCCCTCGAAAATGATG
* ** * **
1391168 GTGTTCCAGTATCCCCGAGATGAAAAATTCAATTTTTTGGAAGTAAAAATAGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCGAGATGAAAAATTCAATATTTTGGAAGTAAAAACGGGGTTGGAGTATCC
* * *
1391233 TCT-TAGAAATTATG
66 CCTCGA-AAATGATG
* * * *
1391247 GAGTTGGAGTATCCCCAAGATGAAAAATTCAATGA-TTTGGAAGTGAAAACGAGGTTGGAGTATC
1 GGGTTGGAGTATCCCCGAGATGAAAAATTCAAT-ATTTTGGAAGTAAAAACGGGGTTGGAGTATC
* *
1391311 CCCTTGAAAATGGTG
65 CCCTCGAAAATGATG
** ** * **
1391326 GGGTTAAAGTATCCTTAGAGATGAAAAATTGTAATATTTTAAAAGTAAAAACGGGGTTGGAGTAT
1 GGGTTGGAGTATCC-CCGAGATGAAAAATT-CAATATTTTGGAAGTAAAAACGGGGTTGGAGTAT
* **
1391391 CCCTTTAAAAATGAT-
64 CCCCTCGAAAATGATG
*
1391406 GGGTTGGAATATCCCCGAGAT-AAAAATTCAATATTTTGGAAGTAAAAACGGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCGAGATGAAAAATTCAATATTTTGGAAGTAAAAACGGGGTTGGAGTATCC
* **
1391470 CTTTAAAAATGAT-
66 CCTCGAAAATGATG
* * * *
1391483 GGGTTGGAATATCCCCAAGATAAAAAATTCAATATTTTAGAAGTAAAAACGGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCGAGATGAAAAATTCAATATTTTGGAAGTAAAAACGGGGTTGGAGTATCC
1391548 C
66 C
1391549 TTCTTGATAT
Statistics
Matches: 445, Mismatches: 81, Indels: 33
0.80 0.14 0.06
Matches are distributed among these distances:
77 66 0.15
78 62 0.14
79 139 0.31
80 85 0.19
81 84 0.19
82 9 0.02
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (79 bp):
GGGTTGGAGTATCCCCGAGATGAAAAATTCAATATTTTGGAAGTAAAAACGGGGTTGGAGTATCC
CCTCGAAAATGATG
Found at i:1391399 original size:25 final size:26
Alignment explanation
Indices: 1391371--1391420 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
1391361 ATTTTAAAAG
*
1391371 TAAAAACG-GGGTTGGAGTATCCCTT
1 TAAAAACGAGGGTTGGAATATCCCTT
*
1391396 TAAAAATGATGGGTTGGAATATCCC
1 TAAAAACGA-GGGTTGGAATATCCC
1391421 CGAGATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
27 14 0.67
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (26 bp):
TAAAAACGAGGGTTGGAATATCCCTT
Found at i:1393973 original size:20 final size:20
Alignment explanation
Indices: 1393909--1393981 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 20
1393899 AAAACCCAAC
*
1393909 ATGTATCGATACAATG-AGAA
1 ATGTATCGATACATTGAAG-A
* * ** *
1393929 ATGTATTGTTATTTTAGAAGC
1 ATGTATCGATACATT-GAAGA
1393950 ATGTATCGATACATTGAAGA
1 ATGTATCGATACATTGAAGA
*
1393970 ATGTATTGATAC
1 ATGTATCGATAC
1393982 CTTTGGGTTA
Statistics
Matches: 39, Mismatches: 12, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
20 25 0.64
21 12 0.31
22 2 0.05
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGAAGA
Found at i:1394125 original size:21 final size:20
Alignment explanation
Indices: 1394055--1394125 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
1394045 CATAGTCTAA
* *
1394055 TATCAATACATTTACTTATG
1 TATCGATACATTCACTTATG
*
1394075 TATCGATACATTCACTTATA
1 TATCGATACATTCACTTATG
* *
1394095 TATTGATACA-TCAACTTGTTG
1 TATCGATACATTC-ACTT-ATG
1394116 TATCGATACA
1 TATCGATACA
1394126 AATTGTAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.05
20 30 0.71
21 10 0.24
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.41
Consensus pattern (20 bp):
TATCGATACATTCACTTATG
Found at i:1394800 original size:71 final size:72
Alignment explanation
Indices: 1394628--1395230 Score: 647
Period size: 70 Copynumber: 8.4 Consensus size: 72
1394618 GCGAGCTTTG
* *
1394628 AAAGGTGCCACCAGCTTGT-TAGGCTTTAAAAA-AAAAAA-ACGTGACTTACTCTTTGAGGACTA
1 AAAGGTGCCACCAGCTTGTGTAGGCTTTAAAAAGAAAAAAGACAT--CCTACTCTTTGAGGACTA
1394690 AGAAAGGGTAAAA
64 A-AAAGGGT---A
* * ** *
1394703 AAAGGTGCCACCAGCTTCTGTGGGCTTTAAAAAGAAAAAAGACATCCTACTCTTCAAGGACTAGA
1 AAAGGTGCCACCAGCTTGTGTAGGCTTTAAAAAGAAAAAAGACATCCTACTCTTTGAGGACTAAA
1394768 AA-GGTA
66 AAGGGTA
* *
1394774 AAAGGTGCCACCAGCTTGTGTAGGCTTT-AAAAG-GAAAAGACATCTTACTCTTTGAGGACTAAA
1 AAAGGTGCCACCAGCTTGTGTAGGCTTTAAAAAGAAAAAAGACATCCTACTCTTTGAGGACTAAA
1394837 AA-GGTA
66 AAGGGTA
* * * * * * ** *
1394843 AAAGGTACTATCAACTTGTGTAGCCTTTAAAAGGAAAAAA-ACGCCCTACTCTTTGAAGACTAAA
1 AAAGGTGCCACCAGCTTGTGTAGGCTTTAAAAAGAAAAAAGACATCCTACTCTTTGAGGACTAAA
1394907 AA-GGTA
66 AAGGGTA
* * * * * * *
1394913 AAAGGTTCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGGACATCTTGCACTTTGAGGACT-AA
1 AAAGGTGCCACCAGCTTGTGTAGGCTTTAAAAAGAAAAAAGACATCCTACTCTTTGAGGACTAAA
1394977 AAGGGTA
66 AAGGGTA
* *
1394984 GAAGGTGCCACCAGCTTTTGTAGGCTTT-AAAAG-AAAAAGACATCCTACTCTTTGAGGACTAAA
1 AAAGGTGCCACCAGCTTGTGTAGGCTTTAAAAAGAAAAAAGACATCCTACTCTTTGAGGACTAAA
1395047 AAGGAGTAA
66 AAGG-GT-A
* * * *
1395056 AAAAGTGCCACCAGCTTGTGTAGGCTTTAAAAAGAAAAAAGACGTCCTGCTGC-TTGAGGATTAA
1 AAAGGTGCCACCAGCTTGTGTAGGCTTTAAAAAGAAAAAAGACATCCTACT-CTTTGAGGACTAA
* *
1395120 AAAAGGTT
65 AAAGGGTA
* * * ** *
1395128 AAAGGTACCACCAGCTTGTGTGGGCTTTAAAAAGGAAAAAAAATGTCTTACTCTTTGAGGACTAA
1 AAAGGTGCCACCAGCTTGTGTAGGCTTTAAAAA-GAAAAAAGACATCCTACTCTTTGAGGACT-A
1395193 AAAAGGGTA
64 AAAAGGGTA
*
1395202 AGAAGGTGCCACCAGCTTGTGTGGGCTTT
1 A-AAGGTGCCACCAGCTTGTGTAGGCTTT
1395231 TTTTTCGTAT
Statistics
Matches: 445, Mismatches: 66, Indels: 34
0.82 0.12 0.06
Matches are distributed among these distances:
69 77 0.17
70 83 0.19
71 75 0.17
72 57 0.13
73 29 0.07
74 40 0.09
75 48 0.11
76 27 0.06
77 6 0.01
78 3 0.01
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.24
Consensus pattern (72 bp):
AAAGGTGCCACCAGCTTGTGTAGGCTTTAAAAAGAAAAAAGACATCCTACTCTTTGAGGACTAAA
AAGGGTA
Found at i:1397038 original size:21 final size:21
Alignment explanation
Indices: 1397012--1397067 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
1397002 TTTTTATCCA
1397012 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
1397033 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
1397054 AATGTATCGATACA
1 AATGTATCGATACA
1397068 CGGTCCCAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.36
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:1397152 original size:19 final size:18
Alignment explanation
Indices: 1397101--1397190 Score: 66
Period size: 19 Copynumber: 5.1 Consensus size: 18
1397091 TTGAATTCCA
1397101 ATAA-TTTGTATCGATAC
1 ATAAGTTTGTATCGATAC
* *
1397118 ATTCAGTAAATGTATCGATAC
1 A-TAAGT--TTGTATCGATAC
1397139 ATAAGTGTTGTATCGATAC
1 ATAAGT-TTGTATCGATAC
*
1397158 --AA---TGTATCAATAC
1 ATAAGTTTGTATCGATAC
1397171 ATAAGTTTTGTATCGATAC
1 ATAAG-TTTGTATCGATAC
1397190 A
1 A
1397191 ATGTATCGCT
Statistics
Matches: 56, Mismatches: 7, Indels: 18
0.69 0.09 0.22
Matches are distributed among these distances:
13 10 0.18
15 2 0.04
17 3 0.05
18 2 0.04
19 23 0.41
20 4 0.07
21 12 0.21
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (18 bp):
ATAAGTTTGTATCGATAC
Found at i:1397171 original size:32 final size:32
Alignment explanation
Indices: 1397126--1397197 Score: 126
Period size: 32 Copynumber: 2.2 Consensus size: 32
1397116 ACATTCAGTA
*
1397126 AATGTATCGATACATAAGTGTTGTATCGATAC
1 AATGTATCAATACATAAGTGTTGTATCGATAC
*
1397158 AATGTATCAATACATAAGTTTTGTATCGATAC
1 AATGTATCAATACATAAGTGTTGTATCGATAC
1397190 AATGTATC
1 AATGTATC
1397198 GCTAGGAAGC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (32 bp):
AATGTATCAATACATAAGTGTTGTATCGATAC
Found at i:1397247 original size:20 final size:20
Alignment explanation
Indices: 1397221--1397274 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1397211 TGCCAAGGAA
1397221 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
1397241 GTGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
1397261 ATGTATCGATACAT
1 ATGTATCGATACAT
1397275 CGTATCGATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:1397281 original size:13 final size:13
Alignment explanation
Indices: 1397263--1397288 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1397253 ATTTTTCTAT
1397263 GTATCGATACATC
1 GTATCGATACATC
1397276 GTATCGATACATC
1 GTATCGATACATC
1397289 TATTCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
GTATCGATACATC
Found at i:1397305 original size:34 final size:33
Alignment explanation
Indices: 1397243--1397309 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 33
1397233 ATTTTTCTGT
*
1397243 GTATCGATACATTTTTCTATGTATCGATACATC
1 GTATCGATACATTATTCTATGTATCGATACATC
*
1397276 GTATCGATACATCTATTCTTTGTATCGATACATC
1 GTATCGATACAT-TATTCTATGTATCGATACATC
1397310 TAGGAAGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 12 0.39
34 19 0.61
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (33 bp):
GTATCGATACATTATTCTATGTATCGATACATC
Found at i:1399755 original size:52 final size:52
Alignment explanation
Indices: 1399634--1399769 Score: 168
Period size: 52 Copynumber: 2.6 Consensus size: 52
1399624 TGTTAAGTTT
* * *
1399634 CTCAATTGTTCATAATCGGGGATACTCTAACCCCGATTTTATTTTCAAAACA
1 CTCAATTTTTCATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACA
** *
1399686 C-CAATTTTCTTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAA-A
1 CTCAATTTT-TCATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACA
* *
1399737 CCTCAATTTTTCACAATCGAGGATACTCCAACC
1 -CTCAATTTTTCATAATCGGGGATACTCCAACC
1399770 TCGTTATTTC
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
51 7 0.10
52 56 0.80
53 7 0.10
ACGTcount: A:0.30, C:0.26, G:0.10, T:0.34
Consensus pattern (52 bp):
CTCAATTTTTCATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACA
Found at i:1399780 original size:31 final size:28
Alignment explanation
Indices: 1399752--1399828 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
1399742 ATTTTTCACA
*
1399752 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGAGGATACTCCAACCCCGTTATTTC
* **
1399780 ATCGGGGATACTCCAACCCCGTTACCTC
1 ATCGAGGATACTCCAACCCCGTTATTTC
1399808 --CGAGGGGATACTCCAACCCCG
1 ATCGA--GGATACTCCAACCCCG
1399829 GCTTTATTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 2 0.05
28 40 0.95
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.22
Consensus pattern (28 bp):
ATCGAGGATACTCCAACCCCGTTATTTC
Found at i:1399892 original size:79 final size:80
Alignment explanation
Indices: 1399782--1400003 Score: 238
Period size: 79 Copynumber: 2.8 Consensus size: 80
1399772 GTTATTTCAT
** * *
1399782 CGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTTCCAAAATAC
1 CGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCC-GATTTATTTCCAAAATAC
* **
1399847 -T-GATTTCTCATAGT
65 ATCGATTTCTCACAAC
* * * * *
1399861 TGGGGATACTCCAACCCCATTATTTCTGAGGGGATACTCCAATCCCGATTCTATTTTC-TAAT-C
1 CGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGATT-TATTTCCAAAATAC
*
1399924 ATCGATTTTTCACAAC
65 ATCGATTTCTCACAAC
* *
1399940 CGGGGATACTCCAACCCCGTTATTT-TCGAGGGGATACTCCAACCCCGTTATTATCTCCAAAATA
1 CGGGGATACTCCAACCCCGTTATTTCT-GAGGGGATACTCCAACCCCGAT-TTATTTCCAAAATA
1400004 TTAAATTTCT
Statistics
Matches: 116, Mismatches: 20, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
77 1 0.01
78 8 0.07
79 103 0.89
80 4 0.03
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (80 bp):
CGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGATTTATTTCCAAAATACA
TCGATTTCTCACAAC
Found at i:1399896 original size:107 final size:108
Alignment explanation
Indices: 1399703--1399907 Score: 254
Period size: 107 Copynumber: 1.9 Consensus size: 108
1399693 TCTTTTAATC
* * *
1399703 GGGGATACTCCAACTCCGATTTTATTTCCAAAAACCTCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAACCTCAATTTCTCACAATCGAGGATACTCCAA
* * *
1399768 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACCTCCGA
66 CCCCATTATTTCATAGGGGATACTCCAACCCCGTTACCTCCGA
* * * * * *
1399811 GGGGATACTCCAACCCCGGCTTTATTTCCAAAATA-CT-GATTTCTCATAGTTGGGGATACTCCA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAA-ACCTCAATTTCTCACAATCGAGGATACTCCA
*
1399874 ACCCCATTATTTC-TGAGGGGATACTCCAATCCCG
65 ACCCCATTATTTCAT-AGGGGATACTCCAACCCCG
1399908 ATTCTATTTT
Statistics
Matches: 82, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
106 1 0.01
107 48 0.59
108 32 0.39
109 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (108 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAAACCTCAATTTCTCACAATCGAGGATACTCCAA
CCCCATTATTTCATAGGGGATACTCCAACCCCGTTACCTCCGA
Found at i:1407473 original size:29 final size:29
Alignment explanation
Indices: 1407440--1407502 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 29
1407430 AGTAATCTTT
*
1407440 TTTATAAAACAATCTTTCCCTTTTTCAAA
1 TTTATAAAACAATCTCTCCCTTTTTCAAA
*
1407469 TTTATAAAACAATCTCTCCTTTTTTCAAA
1 TTTATAAAACAATCTCTCCCTTTTTCAAA
1407498 TTTAT
1 TTTAT
1407503 TTTCAAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.48
Consensus pattern (29 bp):
TTTATAAAACAATCTCTCCCTTTTTCAAA
Found at i:1418486 original size:69 final size:69
Alignment explanation
Indices: 1418303--1418823 Score: 357
Period size: 69 Copynumber: 7.6 Consensus size: 69
1418293 CGACGCCCTT
* *** *
1418303 ACTTAAAGCCAACACAAGCTTGTGGCACCATCTATCTACCTTAGTCCTCAAGGGGCAGGACACTT
1 ACTTAAAGCCTACACAAGCTTGTGGCACCATCTATCTACCTTAGTCCTCAAAAAGCAGGACGCTT
* *
1418368 ATCT
66 ACCC
* * * * *
1418372 ACCTTAAAACCTGCACAAGCTTATGGCACCATCTATCTACTTTAGTCCTCAAAAAGTAGGACGCT
1 A-CTTAAAGCCTACACAAGCTTGTGGCACCATCTATCTACCTTAGTCCTCAAAAAGCAGGACGCT
1418437 TACCC
65 TACCC
* * * * * *
1418442 ACTTAAAGCTTACATAAGCTTGTGGCACTATTTATCTACCTTAGTTCTCAAAAAGCAGGATGCTT
1 ACTTAAAGCCTACACAAGCTTGTGGCACCATCTATCTACCTTAGTCCTCAAAAAGCAGGACGCTT
*
1418507 ACTC
66 ACCC
* * * * * * *
1418511 ACTCAAAGCCCATACAAGCTGGT-G-A-C--CTATCCACCTTAGTCCAT-GAAAAGCTA-GATGC
1 ACTTAAAGCCTACACAAGCTTGTGGCACCATCTATCTACCTTAGTCC-TCAAAAAGC-AGGACGC
* **
1418569 CTACTT
64 TTACCC
* * * * * * * *
1418575 ACCTTAAAGCCTACACAAGCTTGTGGCACCATCTATTTACCTTAATCTTTAAAGAGCAAGATGTT
1 A-CTTAAAGCCTACACAAGCTTGTGGCACCATCTATCTACCTTAGTCCTCAAAAAGCAGGACGCT
*
1418640 TACCT
65 TACCC
* * * * * * * * *
1418645 ACCTCAAAGCCCACAAAAGATGGTGGCA-C-T-TATCCACCTCAGTCCAT-GAAAAGCTA-GATG
1 A-CTTAAAGCCTACACAAGCTTGTGGCACCATCTATCTACCTTAGTCC-TCAAAAAGC-AGGACG
* *
1418705 CCTACCT
63 CTTACCC
* * * * ** * *
1418712 ACCTAAAGCCTACACAAGCTCGTGGCACCATCTATCAACCTTACTTGTCAAAAAGTAGGACGTTT
1 ACTTAAAGCCTACACAAGCTTGTGGCACCATCTATCTACCTTAGTCCTCAAAAAGCAGGACGCTT
1418777 ACCC
66 ACCC
*
1418781 ACTTAAAG-CTCACACAAGTTTGTGGCACCATCTATCTACCTTA
1 ACTTAAAGCCT-ACACAAGCTTGTGGCACCATCTATCTACCTTA
1418824 ATGGCACTAT
Statistics
Matches: 348, Mismatches: 85, Indels: 38
0.74 0.18 0.08
Matches are distributed among these distances:
64 29 0.08
65 20 0.06
66 21 0.06
67 28 0.08
68 10 0.03
69 135 0.39
70 105 0.30
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (69 bp):
ACTTAAAGCCTACACAAGCTTGTGGCACCATCTATCTACCTTAGTCCTCAAAAAGCAGGACGCTT
ACCC
Found at i:1418616 original size:134 final size:134
Alignment explanation
Indices: 1418443--1418809 Score: 425
Period size: 134 Copynumber: 2.7 Consensus size: 134
1418433 CGCTTACCCA
* * * * *
1418443 CTTAAAGCTTACATAAGCTTGTGGCACTATTTATCTACCTTAGTTCTCAAAAAGCAGGATGCTTA
1 CTTAAAGCCTACACAAGCTTGTGGCACCATCTATCTACCTTA-TTCTCAAAAAGCAGGATGTTTA
* * *
1418508 CTCACTCAAAGCCCATACAAGCTGGT-G-ACCTATCCACCTTAGTCCATGAAAAGCTAGATGCCT
65 C-CACTCAAAGCCCACACAAGATGGTGGCACCTATCCACCTCAGTCCATGAAAAGCTAGATGCCT
*
1418571 ACTTAC
129 ACCTAC
* * * * *
1418577 CTTAAAGCCTACACAAGCTTGTGGCACCATCTATTTACCTTAATCTTTAAAGAGCAAGATGTTTA
1 CTTAAAGCCTACACAAGCTTGTGGCACCATCTATCTACCTTATTC-TCAAAAAGCAGGATGTTTA
* *
1418642 CCTACCTCAAAGCCCACAAAAGATGGTGGCACTTATCCACCTCAGTCCATGAAAAGCTAGATGCC
65 CC-A-CTCAAAGCCCACACAAGATGGTGGCACCTATCCACCTCAGTCCATGAAAAGCTAGATGCC
1418707 TACCTAC
128 TACCTAC
* * * * *
1418714 C-TAAAGCCTACACAAGCTCGTGGCACCATCTATCAACCTTACTTGTCAAAAAGTAGGACGTTTA
1 CTTAAAGCCTACACAAGCTTGTGGCACCATCTATCTACCTTA-TTCTCAAAAAGCAGGATGTTTA
* * * *
1418778 CCCACTTAAAGCTCACACAAGTTTGTGGCACC
65 -CCACTCAAAGCCCACACAAGATGGTGGCACC
1418810 ATCTATCTAC
Statistics
Matches: 194, Mismatches: 32, Indels: 13
0.81 0.13 0.05
Matches are distributed among these distances:
133 3 0.02
134 54 0.28
135 41 0.21
136 53 0.27
137 43 0.22
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (134 bp):
CTTAAAGCCTACACAAGCTTGTGGCACCATCTATCTACCTTATTCTCAAAAAGCAGGATGTTTAC
CACTCAAAGCCCACACAAGATGGTGGCACCTATCCACCTCAGTCCATGAAAAGCTAGATGCCTAC
CTAC
Found at i:1418777 original size:136 final size:134
Alignment explanation
Indices: 1418443--1418794 Score: 417
Period size: 136 Copynumber: 2.6 Consensus size: 134
1418433 CGCTTACCCA
* * * * * *
1418443 CTTAAAGCTTACATAAGCTTGTGGCACTATTTATCTACCTTAGTTCTCAAAAAGCAGGATGCTTA
1 CTTAAAGCCTACACAAGCTTGTGGCACCATCTATCTACCTTACTT-TCAAAAAGCAGGATGTTTA
* * * *
1418508 -CTCACTCAAAGCCCATACAAGCTGGTGACCTATCCACCTTAGTCCATGAAAAGCTAGATGCCTA
65 CCTCACTCAAAGCCCACAAAAGATGGTGACCTATCCACCTCAGTCCATGAAAAGCTAGATGCCTA
*
1418572 CTTAC
130 CCTAC
* * *
1418577 CTTAAAGCCTACACAAGCTTGTGGCACCATCTATTTACCTTAATCTTT-AAAGAGCAAGATGTTT
1 CTTAAAGCCTACACAAGCTTGTGGCACCATCTATCTACCTT-A-CTTTCAAAAAGCAGGATGTTT
*
1418641 ACCT-ACCTCAAAGCCCACAAAAGATGGTGGCACTTATCCACCTCAGTCCATGAAAAGCTAGATG
64 ACCTCA-CTCAAAGCCCACAAAAGATGGT-G-ACCTATCCACCTCAGTCCATGAAAAGCTAGATG
1418705 CCTACCTAC
126 CCTACCTAC
* * * *
1418714 C-TAAAGCCTACACAAGCTCGTGGCACCATCTATCAACCTTACTTGTCAAAAAGTAGGACGTTTA
1 CTTAAAGCCTACACAAGCTTGTGGCACCATCTATCTACCTTACTT-TCAAAAAGCAGGATGTTTA
* *
1418778 CC-CACTTAAAGCTCACA
65 CCTCACTCAAAGCCCACA
1418795 CAAGTTTGTG
Statistics
Matches: 185, Mismatches: 24, Indels: 17
0.82 0.11 0.08
Matches are distributed among these distances:
134 54 0.29
135 36 0.19
136 55 0.30
137 40 0.22
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (134 bp):
CTTAAAGCCTACACAAGCTTGTGGCACCATCTATCTACCTTACTTTCAAAAAGCAGGATGTTTAC
CTCACTCAAAGCCCACAAAAGATGGTGACCTATCCACCTCAGTCCATGAAAAGCTAGATGCCTAC
CTAC
Found at i:1418838 original size:22 final size:22
Alignment explanation
Indices: 1418803--1418845 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1418793 CACAAGTTTG
1418803 TGGCACCATCTATCTACCTTAA
1 TGGCACCATCTATCTACCTTAA
* *
1418825 TGGCACTATTTATCTACCTTA
1 TGGCACCATCTATCTACCTTA
1418846 GTCCTAAAAA
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:0.26, C:0.28, G:0.09, T:0.37
Consensus pattern (22 bp):
TGGCACCATCTATCTACCTTAA
Found at i:1422216 original size:21 final size:21
Alignment explanation
Indices: 1422192--1422233 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1422182 CTTAAGGTAA
*
1422192 TCTTTTTTCTTTCTCTTTTCT
1 TCTTTTTTCTCTCTCTTTTCT
*
1422213 TCTTTTTTCTCTCTTTTTTCT
1 TCTTTTTTCTCTCTCTTTTCT
1422234 CCCCCTTCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (21 bp):
TCTTTTTTCTCTCTCTTTTCT
Found at i:1422234 original size:11 final size:11
Alignment explanation
Indices: 1422192--1422234 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
1422182 CTTAAGGTAA
*
1422192 TCTTTTTTCTT
1 TCTTTTTTCTC
*
1422203 TCTCTTTTCT-
1 TCTTTTTTCTC
1422213 TCTTTTTTCTC
1 TCTTTTTTCTC
1422224 TCTTTTTTCTC
1 TCTTTTTTCTC
1422235 CCCCTTCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 9 0.31
11 20 0.69
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (11 bp):
TCTTTTTTCTC
Found at i:1423245 original size:168 final size:164
Alignment explanation
Indices: 1422856--1423269 Score: 480
Period size: 164 Copynumber: 2.5 Consensus size: 164
1422846 AAAATAGGAG
* * * *
1422856 AATTTCAAAGAAAAAATAAAAAATTTATGAAAATAAATGAATTTTTCAAAACTGATTTAAAAAGA
1 AATTTCAAAGAAAAAATGAAAAA-TTATGAAAATAAATGAATTTTTCAAAATTGATTTAATATGA
* * * * * * *
1422921 GTCT-AATGA-CACTGTTAGATAAATTTTAAAAACTTTAAATCGAGAAAAATCTCCTTGAAAACA
65 AT-TAAATGATGA-TATTTGATAAATTTTAAAAACTTTAAACCAAGAAAAATCTCCTCGAAAACA
* * *
1422984 TTGATGGGATAGAAAACTCGATTTTCAAAAATAGAAA
128 TTGAAGGGATAGAAAACTCGATTTTCAAAAACAAAAA
*
1423021 AATTTCAAAG-AAAAATGAAAAACTTATGAAAATAAATGAATTTTTCAAAATTGATTTACTATGA
1 AATTTCAAAGAAAAAATGAAAAA-TTATGAAAATAAATGAATTTTTCAAAATTGATTTAATATGA
* *
1423085 ATTAAATGATGATATTTGATAAATTTTTAAAAAGTTATAAACCAAGAAAAATTTCCTCGAAAACA
65 ATTAAATGATGATATTTGATAAA-TTTTAAAAACTT-TAAACCAAGAAAAATCTCCTCGAAAACA
* * *
1423150 TTTACAGTG-TAGAAAACTCCG-TATTTCGAAAACAAAAA
128 TTGA-AGGGATAGAAAACT-CGAT-TTTCAAAAACAAAAA
* *
1423188 AATTTCAAGAGAAAAAATGAAAAATTCATGAATA-AAAGGAATTTTTCAAAATTGATTTAATATG
1 AATTTCAA-AGAAAAAATGAAAAATT-ATGAAAATAAATGAATTTTTCAAAATTGATTTAATATG
*
1423252 AATTAAATAATGATATTT
64 AATTAAATGATGATATTT
1423270 AACGAATTTT
Statistics
Matches: 214, Mismatches: 25, Indels: 17
0.84 0.10 0.07
Matches are distributed among these distances:
163 1 0.00
164 63 0.29
165 22 0.10
166 37 0.17
167 24 0.11
168 49 0.23
169 18 0.08
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.31
Consensus pattern (164 bp):
AATTTCAAAGAAAAAATGAAAAATTATGAAAATAAATGAATTTTTCAAAATTGATTTAATATGAA
TTAAATGATGATATTTGATAAATTTTAAAAACTTTAAACCAAGAAAAATCTCCTCGAAAACATTG
AAGGGATAGAAAACTCGATTTTCAAAAACAAAAA
Found at i:1434776 original size:158 final size:157
Alignment explanation
Indices: 1434432--1434767 Score: 459
Period size: 158 Copynumber: 2.2 Consensus size: 157
1434422 ATCAATCTTG
* * * * * *
1434432 AAAATTCAGTTTATTTTCTAAGTTTTAGAATTTTTT-TATTATCAAAATAC--A--GAGTTTTCT
1 AAAATTAAATTTATTTTATGAGTTTTAAAATTTTTTCTATTATCGAAATACGGATGGAGTTTTCT
* * * *
1434492 TCTTCGTAAATTTTTTTGATAAGATTTTTTATGTTTATAATTTTCAAAATTCTTCAAATATTATT
66 TCTTCGTAAATTGTTTTGATAAGATTTTTTAAGTTTATAATTTTAAAAATTATTCAAATATTATT
* * *
1434557 GTTTAATTGATATTAAATTAGTTTTGA
131 GTTTAATTCATAGTAAATCAGTTTTGA
1434584 AAAATTAAATTTATTTTATGAGTTTTAAAATTTTTTCTATTATCGAAATACGGATGGAGTTTTCT
1 AAAATTAAATTTATTTTATGAGTTTTAAAATTTTTTCTATTATCGAAATACGGATGGAGTTTTCT
*
1434649 TCTTCGTAAATTGTTTTGGTAAGATTTTTCTAAGTTTATAATTTTAAAAATTATTCAAATATTAT
66 TCTTCGTAAATTGTTTTGATAAGATTTTT-TAAGTTTATAATTTTAAAAATTATTCAAATATTAT
1434714 TGTTTAATTCATAGTAAATCAGTTTTGA
130 TGTTTAATTCATAGTAAATCAGTTTTGA
* * *
1434742 AAACTT-CATTTATTTTCATGATTTTT
1 AAAATTAAATTTATTTT-ATGAGTTTT
1434768 TCATTTTTTC
Statistics
Matches: 160, Mismatches: 17, Indels: 8
0.86 0.09 0.04
Matches are distributed among these distances:
152 31 0.19
153 13 0.08
155 1 0.01
157 45 0.28
158 70 0.44
ACGTcount: A:0.32, C:0.07, G:0.10, T:0.51
Consensus pattern (157 bp):
AAAATTAAATTTATTTTATGAGTTTTAAAATTTTTTCTATTATCGAAATACGGATGGAGTTTTCT
TCTTCGTAAATTGTTTTGATAAGATTTTTTAAGTTTATAATTTTAAAAATTATTCAAATATTATT
GTTTAATTCATAGTAAATCAGTTTTGA
Found at i:1437112 original size:50 final size:51
Alignment explanation
Indices: 1437036--1437143 Score: 182
Period size: 50 Copynumber: 2.1 Consensus size: 51
1437026 TACATATATT
** *
1437036 GATACATTATGTTTTTTTACTTAGATGTATCGATATATTTTTCAATGTATC
1 GATACATTATGTTTTTTTACCAAGATGTATCGATACATTTTTCAATGTATC
1437087 GATACATT-TGTTTTTTTACCAAGATGTATCGATACATTTTTCAATGTATC
1 GATACATTATGTTTTTTTACCAAGATGTATCGATACATTTTTCAATGTATC
1437137 GATACAT
1 GATACAT
1437144 CTAGTTAATT
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
50 46 0.85
51 8 0.15
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (51 bp):
GATACATTATGTTTTTTTACCAAGATGTATCGATACATTTTTCAATGTATC
Found at i:1440312 original size:159 final size:158
Alignment explanation
Indices: 1440062--1440359 Score: 429
Period size: 159 Copynumber: 1.9 Consensus size: 158
1440052 ATAATCAAAA
* * * *
1440062 TAAAATCAATAAATATAACCTTTTAAAAATATAATTTCCATTTTCCCAACATTTCTATTGCTTTT
1 TAAAATCAATAAATATAACCTTTTAAAAATAAAATTTCCACTTTCCCAACATTTCTATTACTTCT
* * * **
1440127 ATGGGTTTCCGTAGGTATATAAAAATTTTCTAAAATTTTCGTATCTTCTT-AGTTTTTCGTTAGG
66 ATGGGTTTCCATAGGGATATAAAAATTTTCTAAAATTTTCATATCTT-TTCAG-TTTTCGAAAGG
1440191 TACGAAATGAATAAATATTTTCTAACCTTT
129 TACGAAATGAATAAATATTTTCTAACCTTT
*
1440221 TAAAATGAATAAATATAACCTTTTAAAAATAAAATTTCCAACTTT-CCAACATTTCTATTACTTC
1 TAAAATCAATAAATATAACCTTTTAAAAATAAAATTTCC-ACTTTCCCAACATTTCTATTACTTC
* * *
1440285 TATGGGTTTCTATAGGGGTATAGAAATTTTCTAAAATTTTCATATCTTTTCAGTTTTCGAAAGGT
65 TATGGGTTTCCATAGGGATATAAAAATTTTCTAAAATTTTCATATCTTTTCAGTTTTCGAAAGGT
*
1440350 ATGAAATGAA
130 ACGAAATGAA
1440360 ATTTTCAAAA
Statistics
Matches: 123, Mismatches: 14, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
158 21 0.17
159 98 0.80
160 4 0.03
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (158 bp):
TAAAATCAATAAATATAACCTTTTAAAAATAAAATTTCCACTTTCCCAACATTTCTATTACTTCT
ATGGGTTTCCATAGGGATATAAAAATTTTCTAAAATTTTCATATCTTTTCAGTTTTCGAAAGGTA
CGAAATGAATAAATATTTTCTAACCTTT
Found at i:1443507 original size:76 final size:75
Alignment explanation
Indices: 1443415--1443615 Score: 287
Period size: 76 Copynumber: 2.6 Consensus size: 75
1443405 AGAAACTACG
* * *
1443415 TATTCTACATCATGTTCCTTTCCTTTAGCCCTTTATTAGTTTGTTTTGTCTGTTGATAGAAATTT
1 TATTCTCCATCATGTTCCTTTCCTTTAGCCC-TTATTAGTTTGTTTTGGCTATTGATAGAAATTT
*
1443480 GGAAAACCTCA
65 GGAAAACCACA
* *
1443491 TATTCTCCATCATGTTCCTTTCTTTTAAGCCCTTATCAGTTTGTTTTGGCTATTGATAGAAATTT
1 TATTCTCCATCATGTTCCTTTCCTTT-AGCCCTTATTAGTTTGTTTTGGCTATTGATAGAAATTT
1443556 GGAAAACCACA
65 GGAAAACCACA
* *
1443567 TATTC-CCTATCATGTTCTTTTCCTTTAGTCCGTTATTAGTTTGTTTTGG
1 TATTCTCC-ATCATGTTCCTTTCCTTTAG-CCCTTATTAGTTTGTTTTGG
1443616 TTAGCCAAAT
Statistics
Matches: 112, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
75 4 0.04
76 103 0.92
77 5 0.04
ACGTcount: A:0.21, C:0.19, G:0.13, T:0.47
Consensus pattern (75 bp):
TATTCTCCATCATGTTCCTTTCCTTTAGCCCTTATTAGTTTGTTTTGGCTATTGATAGAAATTTG
GAAAACCACA
Found at i:1444338 original size:33 final size:33
Alignment explanation
Indices: 1444217--1444401 Score: 200
Period size: 33 Copynumber: 5.6 Consensus size: 33
1444207 TTTTTACTTA
1444217 GGTTTCACCTTGGTCACCTTTTTGTTGATGTGAT
1 GGTTTCACCTTGGTCACC-TTTTGTTGATGTGAT
*
1444251 GGTTTCACC-TAGTCACCCTTTTGTTGATGTGAT
1 GGTTTCACCTTGGTCA-CCTTTTGTTGATGTGAT
*
1444284 GGTTTCACC-TAGTCACCCTTTTGTTGATGTGAT
1 GGTTTCACCTTGGTCA-CCTTTTGTTGATGTGAT
* *
1444317 GGTTTCACCTTGGTCAACTTTTTTTCGACT-T-A-
1 GGTTTCACCTTGGTCACCTTTTGTT-GA-TGTGAT
* * * * *
1444349 GGTTTCGCCTTGGTCATCTTTTATCGACGTGAT
1 GGTTTCACCTTGGTCACCTTTTGTTGATGTGAT
*
1444382 GGTTTTACCTTGGTCACCTT
1 GGTTTCACCTTGGTCACCTT
1444402 CTTTTCATCT
Statistics
Matches: 132, Mismatches: 12, Indels: 15
0.83 0.08 0.09
Matches are distributed among these distances:
31 3 0.02
32 22 0.17
33 87 0.66
34 19 0.14
35 1 0.01
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.44
Consensus pattern (33 bp):
GGTTTCACCTTGGTCACCTTTTGTTGATGTGAT
Found at i:1444360 original size:32 final size:32
Alignment explanation
Indices: 1444317--1444548 Score: 150
Period size: 32 Copynumber: 7.2 Consensus size: 32
1444307 TTGATGTGAT
*
1444317 GGTTTCACCTTGGTCAACTTTTTTTCGACTTA
1 GGTTTCGCCTTGGTCAACTTTTTTTCGACTTA
* * *
1444349 GGTTTCGCCTTGGTCATC-TTTTATCGACGTGA
1 GGTTTCGCCTTGGTCAACTTTTTTTCGAC-TTA
** * *
1444381 TGGTTTTACCTTGGTCACCTTCTTTTC-ATCTTA
1 -GGTTTCGCCTTGGTCAACTTTTTTTCGA-CTTA
* * * * * * *
1444414 GGTTTTGCCTTAGTCATCATTTGTT-AACATAA
1 GGTTTCGCCTTGGTCAACTTTTTTTCGAC-TTA
* *
1444446 TGGTTTCGCCCTGGTCAACCTTTTTTCGACTTA
1 -GGTTTCGCCTTGGTCAACTTTTTTTCGACTTA
* * * * *
1444479 GG-TTCTGCCTTGGTCATCCTTTGTT-GAAATGA
1 GGTTTC-GCCTTGGTCAACTTTTTTTCG-ACTTA
*
1444511 TGGTTTTGCCTTGGTCAACTTTTTTTCGACTTA
1 -GGTTTCGCCTTGGTCAACTTTTTTTCGACTTA
1444544 GGTTT
1 GGTTT
1444549 TACCCTAGTC
Statistics
Matches: 151, Mismatches: 36, Indels: 26
0.71 0.17 0.12
Matches are distributed among these distances:
31 14 0.09
32 66 0.44
33 60 0.40
34 11 0.07
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.46
Consensus pattern (32 bp):
GGTTTCGCCTTGGTCAACTTTTTTTCGACTTA
Found at i:1444392 original size:65 final size:65
Alignment explanation
Indices: 1444303--1444875 Score: 476
Period size: 65 Copynumber: 8.8 Consensus size: 65
1444293 TAGTCACCCT
* * * * *
1444303 TTTGTTGATGTGATGGTTTCACCTTGGTCAACTTTTTTTCGACTTAGGTTTCGCCTTGGTCATCT
1 TTTGTTGACGTGATGGTTTCACCCTGGTCAACTTCTTTTCGACTTAGGTTTTGCCTTGGTCATCC
* * * * * *
1444368 TTTATCGACGTGATGGTTTTACCTTGGTCACCTTCTTTTC-ATCTTAGGTTTTGCCTTAGTCATC
1 TTTGTTGACGTGATGGTTTCACCCTGGTCAACTTCTTTTCGA-CTTAGGTTTTGCCTTGGTCATC
*
1444432 A
65 C
* * * * *
1444433 TTTGTTAACATAATGGTTTCGCCCTGGTCAACCTT-TTTTCGACTTAGGTTCTGCCTTGGTCATC
1 TTTGTTGACGTGATGGTTTCACCCTGGTCAA-CTTCTTTTCGACTTAGGTTTTGCCTTGGTCATC
1444497 C
65 C
** ** * * * * *
1444498 TTTGTTGAAATGATGGTTTTGCCTTGGTCAACTTTTTTTCGACTTAGGTTTTACCCTAGTCATCC
1 TTTGTTGACGTGATGGTTTCACCCTGGTCAACTTCTTTTCGACTTAGGTTTTGCCTTGGTCATCC
* * *
1444563 TTTGTTGACGTGATGGGTTT-GCCCTAGTCAACTTCTTTTCGAATTAGGTTTTGTCC-TGGTCAT
1 TTTGTTGACGTGAT-GGTTTCACCCTGGTCAACTTCTTTTCGACTTAGGTTTTG-CCTTGGTCAT
1444626 CC
64 CC
* * * * * * * *
1444628 TTTCTTGATGTGATAGTTTCACCCCGATCAACTTCTTTTCGAATTAGGTTTTGCTTTGGTCATCT
1 TTTGTTGACGTGATGGTTTCACCCTGGTCAACTTCTTTTCGACTTAGGTTTTGCCTTGGTCATCC
* * ** * * *** **
1444693 TTTGTTGACATGATGGTTTCGCCCTGGTCAACCACTTTTTGACCTAGGTTCCACCTTACTCATCC
1 TTTGTTGACGTGATGGTTTCACCCTGGTCAACTTCTTTTCGACTTAGGTTTTGCCTTGGTCATCC
* * * * * * * *
1444758 TTTGTTGACTTAATGGTTTCGCCCTAGTTAACCTCTTTTTGACTTAGGTTTCT-CAC-TAGTCA-
1 TTTGTTGACGTGATGGTTTCACCCTGGTCAACTTCTTTTCGACTTAGGTTT-TGC-CTTGGTCAT
1444820 CC
64 CC
* * * *
1444822 TTTTAAATTGACGTGATGGTTTCATCCTGGTCAACTTCTCTTAGACTTAGGTTT
1 -TTT--GTTGACGTGATGGTTTCACCCTGGTCAACTTCTTTTCGACTTAGGTTT
1444876 CACTCTGGTC
Statistics
Matches: 410, Mismatches: 85, Indels: 24
0.79 0.16 0.05
Matches are distributed among these distances:
64 11 0.03
65 349 0.85
66 12 0.03
67 38 0.09
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.44
Consensus pattern (65 bp):
TTTGTTGACGTGATGGTTTCACCCTGGTCAACTTCTTTTCGACTTAGGTTTTGCCTTGGTCATCC
Found at i:1444526 original size:33 final size:33
Alignment explanation
Indices: 1444414--1444527 Score: 99
Period size: 33 Copynumber: 3.5 Consensus size: 33
1444404 TTTCATCTTA
* *
1444414 GGTTTTGCCTTAGTCATCATTTGTT-AACATAAT
1 GGTTTTGCCTTGGTCATCCTTTGTTGAA-ATAAT
* * * * * *
1444447 GGTTTCGCCCTGGTCAACCTTTTTTCG-ACTTA-
1 GGTTTTGCCTTGGTCATCCTTTGTT-GAAATAAT
* *
1444479 GGTTCTGCCTTGGTCATCCTTTGTTGAAATGAT
1 GGTTTTGCCTTGGTCATCCTTTGTTGAAATAAT
1444512 GGTTTTGCCTTGGTCA
1 GGTTTTGCCTTGGTCA
1444528 ACTTTTTTTC
Statistics
Matches: 61, Mismatches: 16, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
31 1 0.02
32 23 0.38
33 36 0.59
34 1 0.02
ACGTcount: A:0.16, C:0.20, G:0.21, T:0.43
Consensus pattern (33 bp):
GGTTTTGCCTTGGTCATCCTTTGTTGAAATAAT
Found at i:1448010 original size:165 final size:166
Alignment explanation
Indices: 1447575--1448167 Score: 781
Period size: 165 Copynumber: 3.6 Consensus size: 166
1447565 ATAAAAAAAT
* * * *
1447575 TATTATTCCTATGGGCTTT-CATAGGGGTTTAGAAATTCTCAAAACTTTTTGTA-CACTCTC-AG
1 TATTATTCCTAT-GGCTTTCCATAGGGGTTTAGAAATTTTTAAAACTTTTCGTATC-CTTTCGA-
* * *
1447637 TTTTTCATCAAGTATGAAATAGAATTTTCAAAAGTTTAGAGACTAAATAGCAAATCTAGTTTTTA
63 TTTTTCGTCAAGTATGAAATAAAATTTTCAAAAGTTTAGGGACTAAATAGCAAATCTAGTTTTTA
* *
1447702 GAAGAAAACTAATCATTTTAGTCATTTTCTTTAAATTTC
128 GAAGAAAAATAATCATCTTAGTCATTTTCTTTAAATTTC
* * * * *
1447741 T-TTATCCCTATGGCTTTCCATAAGGGTTTCGAAA-TTTTATAACTTTTCATAT-CTTCTCGATT
1 TATTATTCCTATGGCTTTCCATAGGGGTTTAGAAATTTTTAAAACTTTTCGTATCCTT-TCGATT
** *
1447803 TTTCGTCAAGTATGAAACGAAATTTTGAAAAGTTTAGGGACTAAATAGCAAATCTAGTTTTTAGA
65 TTTCGTCAAGTATGAAATAAAATTTTCAAAAGTTTAGGGACTAAATAGCAAATCTAGTTTTTAGA
* *
1447868 AGAAAAATAATAATCTTAGTCATTTTCTTTAAATTTA
130 AGAAAAATAATCATCTTAGTCATTTTCTTTAAATTTC
* *
1447905 TATTATTTCTATGGCTTTCCATAGGGGTTTAGAAATTTTTAAAACTTTTCGTATCCTTTCG-GTT
1 TATTATTCCTATGGCTTTCCATAGGGGTTTAGAAATTTTTAAAACTTTTCGTATCCTTTCGATTT
* * **
1447969 TTCGTTAGGTATGAAATGGAATTTTCAAAAGTTTAGGGACTAAATAGCAAATCTAGTTTTTAGAA
66 TTCGTCAAGTATGAAATAAAATTTTCAAAAGTTTAGGGACTAAATAGCAAATCTAGTTTTTAGAA
1448034 GAAAAATAATCATCTTAGTCATTTTCTTTAAATTTC
131 GAAAAATAATCATCTTAGTCATTTTCTTTAAATTTC
*** * *
1448070 TATTATTCCTATGGCTTTTTGTAGGGGTTTAGAAAATTTTAAAA-TATTTTGTATCCTCTT-GAT
1 TATTATTCCTATGGCTTTCCATAGGGGTTTAGAAATTTTTAAAACT-TTTCGTATCCT-TTCGAT
**
1448133 TTTTCGTCGGGTATGAAATAAAATTTTCAAAAGTT
64 TTTTCGTCAAGTATGAAATAAAATTTTCAAAAGTT
1448168 GTTACTGGGA
Statistics
Matches: 373, Mismatches: 44, Indels: 20
0.85 0.10 0.05
Matches are distributed among these distances:
163 2 0.01
164 116 0.31
165 199 0.53
166 53 0.14
167 3 0.01
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (166 bp):
TATTATTCCTATGGCTTTCCATAGGGGTTTAGAAATTTTTAAAACTTTTCGTATCCTTTCGATTT
TTCGTCAAGTATGAAATAAAATTTTCAAAAGTTTAGGGACTAAATAGCAAATCTAGTTTTTAGAA
GAAAAATAATCATCTTAGTCATTTTCTTTAAATTTC
Found at i:1451923 original size:7 final size:7
Alignment explanation
Indices: 1451911--1451951 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
1451901 TTACTCTTTC
1451911 AAAAAAT
1 AAAAAAT
1451918 AAAAAAT
1 AAAAAAT
*
1451925 AAAAACT
1 AAAAAAT
1451932 AAAAAAT
1 AAAAAAT
* *
1451939 AGAAAAC
1 AAAAAAT
1451946 AAAAAA
1 AAAAAA
1451952 ACAAAAAAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.83, C:0.05, G:0.02, T:0.10
Consensus pattern (7 bp):
AAAAAAT
Found at i:1451934 original size:14 final size:14
Alignment explanation
Indices: 1451911--1451958 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
1451901 TTACTCTTTC
*
1451911 AAAAAATAAAAAAT
1 AAAAACTAAAAAAT
1451925 AAAAACTAAAAAAT
1 AAAAACTAAAAAAT
* *
1451939 AGAAAACAAAAAAAC
1 A-AAAACTAAAAAAT
1451954 AAAAA
1 AAAAA
1451959 AGATTAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
14 18 0.60
15 12 0.40
ACGTcount: A:0.83, C:0.06, G:0.02, T:0.08
Consensus pattern (14 bp):
AAAAACTAAAAAAT
Found at i:1466509 original size:18 final size:18
Alignment explanation
Indices: 1466488--1466527 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1466478 AAAAAACCAT
*
1466488 TATTATATTTTTTTCCCA
1 TATTATATCTTTTTCCCA
*
1466506 TATTATATCTTTTTCCCT
1 TATTATATCTTTTTCCCA
1466524 TATT
1 TATT
1466528 GAAATAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTATATCTTTTTCCCA
Found at i:1467577 original size:65 final size:65
Alignment explanation
Indices: 1467501--1467688 Score: 223
Period size: 65 Copynumber: 2.9 Consensus size: 65
1467491 TCACCTAAAT
* * * * *
1467501 TTGGTTTGTATGGTTTTGTCTTAACTAGCTATTTTTTACTTACGTTTTGCCTTAGTCTCCCTTAG
1 TTGGTTCGTATGGTTTTATCTTAACTAACTATTTTTGACTTACGTTTTGCCTTAGTCTCCCGTAG
*
1467566 TTGGTTCGTATGGTTTTATCTTAGCTAACTATTTTTGACTTACGTTTTGCCTTAGTCTCCCGTAG
1 TTGGTTCGTATGGTTTTATCTTAACTAACTATTTTTGACTTACGTTTTGCCTTAGTCTCCCGTAG
** * ** * * * **
1467631 TTGGTTCAAATGGTTTCATCTTGGCTAACCTCTTTTTAACTTAGGTTTCACCTTAGTC
1 TTGGTTCGTATGGTTTTATCTTAACTAA-CTATTTTTGACTTACGTTTTGCCTTAGTC
1467689 ACCCAAAATT
Statistics
Matches: 107, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
65 83 0.78
66 24 0.22
ACGTcount: A:0.16, C:0.19, G:0.17, T:0.48
Consensus pattern (65 bp):
TTGGTTCGTATGGTTTTATCTTAACTAACTATTTTTGACTTACGTTTTGCCTTAGTCTCCCGTAG
Found at i:1467710 original size:66 final size:65
Alignment explanation
Indices: 1467564--1467954 Score: 255
Period size: 66 Copynumber: 5.9 Consensus size: 65
1467554 AGTCTCCCTT
* * * * ** * * *
1467564 AGTTGGTTCGTATGGTTTTATCTTAGCTAA-CTATTTTTGACTTACGTTTTGCCTTAGTCTCCCG
1 AGTTGGTTCATATGGTTTCATCTTAGCTAACCT-TTTTTAACTTAGGTTTCACCCTAGTCACCCA
*
1467628 T
65 A
* * *
1467629 AGTTGGTTCAAATGGTTTCATCTTGGCTAACCTCTTTTTAACTTAGGTTTCACCTTAGTCACCCA
1 AGTTGGTTCATATGGTTTCATCTTAGCTAACCT-TTTTTAACTTAGGTTTCACCCTAGTCACCCA
1467694 A
65 A
* * * * * * * *
1467695 AATTGATTCATATGGTTTCGTCCTAGCCAACCTTTTTTTGACTTAGGGTTCCACCCTAGTCACCT
1 AGTTGGTTCATATGGTTTCATCTTAGCTAACC-TTTTTTAACTTA-GGTTTCACCCTAGTCACCC
**
1467760 TT
64 AA
* * *** * * **
1467762 AGTTGGTTCGTATGGTTTCGTCCCGGCTAACCTTCTTTCAACTTAAGTTTTGCCCTAGTCACCCA
1 AGTTGGTTCATATGGTTTCATCTTAGCTAACCTT-TTTTAACTTAGGTTTCACCCTAGTCACCCA
1467827 A
65 A
* * * * * * *
1467828 AGTTGGTTCATATGGTTTCATCTTAGCCAACATTTTTTCGACTTAAG-TTCTGCCTTGGTCACCC
1 AGTTGGTTCATATGGTTTCATCTTAGCTAACCTTTTTT-AACTTAGGTTTC-ACCCTAGTCACCC
**
1467892 TT
64 AA
* ** * * * **
1467894 GGTTGGTTCATATGGTTTTGTCCTAGCCAACCTTTTTTCAAGTTAGGTTTTGCCCTAGTCA
1 AGTTGGTTCATATGGTTTCATCTTAGCTAACCTTTTTT-AACTTAGGTTTCACCCTAGTCA
1467955 ACTCTTTGAC
Statistics
Matches: 254, Mismatches: 65, Indels: 13
0.77 0.20 0.04
Matches are distributed among these distances:
65 31 0.12
66 170 0.67
67 53 0.21
ACGTcount: A:0.18, C:0.23, G:0.17, T:0.41
Consensus pattern (65 bp):
AGTTGGTTCATATGGTTTCATCTTAGCTAACCTTTTTTAACTTAGGTTTCACCCTAGTCACCCAA
Found at i:1467793 original size:133 final size:131
Alignment explanation
Indices: 1467618--1467954 Score: 359
Period size: 133 Copynumber: 2.5 Consensus size: 131
1467608 CGTTTTGCCT
* * * * *
1467618 TAGTCTCCCGTAGTTGGTTCAAATGGTTTCATCTTGGCTAACCTCTTTTTAACTTAGGTTTCACC
1 TAGTCACCCTTAGTTGGTTCATATGGTTTCGTCCTGGCTAACCT-TTTTTAACTTAGGTTTCACC
* * * * *
1467683 TTAGTCACCCAAAATTGATTCATATGGTTTCGTCCTAGCCAACCTTTTTTTGACTTAGGGTTCCA
65 CTAGTCACCCAAAATTGATTCATATGGTTTCATCCTAGCCAACATTTTTTCGACTTA-AGTTCCA
1467748 CCC
129 CCC
* * * * * **
1467751 TAGTCACCTTTAGTTGGTTCGTATGGTTTCGTCCCGGCTAACCTTCTTTCAACTTAAGTTTTGCC
1 TAGTCACCCTTAGTTGGTTCATATGGTTTCGTCCTGGCTAACCTT-TTTTAACTTAGGTTTCACC
* * * **
1467816 CTAGTCACCCAAAGTTGGTTCATATGGTTTCATCTTAGCCAACATTTTTTCGACTTAAGTTCTGC
65 CTAGTCACCCAAAATTGATTCATATGGTTTCATCCTAGCCAACATTTTTTCGACTTAAGTTCCAC
*
1467881 CT
130 CC
* * * * * * **
1467883 TGGTCACCCTTGGTTGGTTCATATGGTTTTGTCCTAGCCAACCTTTTTTCAAGTTAGGTTTTGCC
1 TAGTCACCCTTAGTTGGTTCATATGGTTTCGTCCTGGCTAACCTTTTTT-AACTTAGGTTTCACC
1467948 CTAGTCA
65 CTAGTCA
1467955 ACTCTTTGAC
Statistics
Matches: 168, Mismatches: 34, Indels: 5
0.81 0.16 0.02
Matches are distributed among these distances:
131 3 0.02
132 64 0.38
133 101 0.60
ACGTcount: A:0.19, C:0.24, G:0.17, T:0.40
Consensus pattern (131 bp):
TAGTCACCCTTAGTTGGTTCATATGGTTTCGTCCTGGCTAACCTTTTTTAACTTAGGTTTCACCC
TAGTCACCCAAAATTGATTCATATGGTTTCATCCTAGCCAACATTTTTTCGACTTAAGTTCCACC
C
Found at i:1468261 original size:123 final size:123
Alignment explanation
Indices: 1468129--1468352 Score: 272
Period size: 123 Copynumber: 1.8 Consensus size: 123
1468119 TTCATTTCGA
** * * * * * *
1468129 TCAACCTTTCTCATTTGTTGACTCAGATGGTTTCATCTCGGTTAACTATTTTCATTCGTTGA-CT
1 TCAACCTTTCTCATTCATTGACTCAGATGATTTAATCTCAGCTAACCATTCTCATTCGTTGACCT
** *
1468193 CGTAT-AGTTTTGTCCCAATCAATCCTTCTTATTCGTTGGCTCGTATCATTTTGTCCTGG
66 -GTATGA-TTTCATCCCAATCAATCCTTCTCATTCGTTGGCTCGTATCATTTTGTCCTGG
* * * *
1468252 TCAATCTTTCTTATTCATTGACTCATATGATTTAATCTTAGCTAACCATTCTCATTCGTTGACCT
1 TCAACCTTTCTCATTCATTGACTCAGATGATTTAATCTCAGCTAACCATTCTCATTCGTTGACCT
*
1468317 GTATGATTTCATCTCAATCAATCCTTCTCATTCGTT
66 GTATGATTTCATCCCAATCAATCCTTCTCATTCGTT
1468353 AACTCATATG
Statistics
Matches: 83, Mismatches: 16, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
123 80 0.96
124 3 0.04
ACGTcount: A:0.20, C:0.23, G:0.12, T:0.45
Consensus pattern (123 bp):
TCAACCTTTCTCATTCATTGACTCAGATGATTTAATCTCAGCTAACCATTCTCATTCGTTGACCT
GTATGATTTCATCCCAATCAATCCTTCTCATTCGTTGGCTCGTATCATTTTGTCCTGG
Found at i:1468345 original size:41 final size:41
Alignment explanation
Indices: 1468088--1468573 Score: 187
Period size: 41 Copynumber: 11.9 Consensus size: 41
1468078 TTCGTTCTAA
* * ** *
1468088 TCAACTCTTCTTATTCGTTGA-CTTGTATAATTTCATTTC-G
1 TCAAC-CTTCTCATTCGTTGACCTCGTATGGTTTCATCTCAG
* *
1468128 ATCAACCTTTCTCATTTGTTGA-CTCAG-ATGGTTTCATCTCGG
1 -TCAACC-TTCTCATTCGTTGACCTC-GTATGGTTTCATCTCAG
* * * * ** * *
1468170 TTAACTATTTTCATTCGTTGA-CTCGTATAGTTTTGTCCCAA
1 TCAAC-CTTCTCATTCGTTGACCTCGTATGGTTTCATCTCAG
* * ** ** *
1468211 TCAATCCTTCTTATTCGTTG-GCTCGTATCATTTTGTC-CTGG
1 TCAA-CCTTCTCATTCGTTGACCTCGTATGGTTTCATCTC-AG
* * * * * * *
1468252 TCAATCTTTCTTATTCATTGA-CTCATATGATTTAATCTTAG
1 TCAA-CCTTCTCATTCGTTGACCTCGTATGGTTTCATCTCAG
* *
1468293 -CTAACCATTCTCATTCGTTGACCT-GTATGATTTCATCTCAA
1 TC-AACC-TTCTCATTCGTTGACCTCGTATGGTTTCATCTCAG
* * *
1468334 TCAATCCTTCTCATTCGTT-AACTCATATGGTTTCATCCCAG
1 TCAA-CCTTCTCATTCGTTGACCTCGTATGGTTTCATCTCAG
* *** * * *
1468375 TCAACCTTTCTTATTTAATG-TCTCATATGGTTTCGTC-CTAG
1 TCAACC-TTCTCATTCGTTGACCTCGTATGGTTTCATCTC-AG
* * *
1468416 TCAAACCTTCTCATTCGTTGACAT-GTATGGTTTCGTCTTAG
1 TC-AACCTTCTCATTCGTTGACCTCGTATGGTTTCATCTCAG
* * *
1468457 TTAACCTTTCTCATTCGTTGA-CTCATATGGTTTCATCTCGG
1 TCAACC-TTCTCATTCGTTGACCTCGTATGGTTTCATCTCAG
* * * * * * *
1468498 TTAACCCTTTTCATTTGTT-AACTTGTATGATTTCATCTCAA
1 TCAA-CCTTCTCATTCGTTGACCTCGTATGGTTTCATCTCAG
* * *
1468539 TCAACCTTTTTCATTCGAT-AACTCGTATGGTTTCA
1 TCAACC-TTCTCATTCGTTGACCTCGTATGGTTTCA
1468574 GCCCAATCAA
Statistics
Matches: 342, Mismatches: 76, Indels: 54
0.72 0.16 0.11
Matches are distributed among these distances:
40 19 0.06
41 308 0.90
42 15 0.04
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.44
Consensus pattern (41 bp):
TCAACCTTCTCATTCGTTGACCTCGTATGGTTTCATCTCAG
Found at i:1468378 original size:123 final size:123
Alignment explanation
Indices: 1468251--1468493 Score: 310
Period size: 123 Copynumber: 2.0 Consensus size: 123
1468241 TTTTGTCCTG
* * * *
1468251 GTCAATCTTTCTTATTCATTGACTCATATGATTTAATCTTAG-CTAACCATTCTCATTCGTTGAC
1 GTCAACCTTTCTTATTCAATGACTCATATGATTTAATCCTAGTCAAACC-TTCTCATTCGTTGAC
*
1468315 CTGTATGATTTCATCTCAATCAATCC-TTCTCATTCGTTAACTCATATGGTTTCATCCCA
65 ATGTATGATTTCATCTCAATCAA-CCTTTCTCATTCGTTAACTCATATGGTTTCATCCCA
* * * **
1468374 GTCAACCTTTCTTATTTAATGTCTCATATGGTTTCGTCCTAGTCAAACCTTCTCATTCGTTGACA
1 GTCAACCTTTCTTATTCAATGACTCATATGATTTAATCCTAGTCAAACCTTCTCATTCGTTGACA
* * * * * *
1468439 TGTATGGTTTCGTCTTAGTTAACCTTTCTCATTCGTTGACTCATATGGTTTCATC
66 TGTATGATTTCATCTCAATCAACCTTTCTCATTCGTTAACTCATATGGTTTCATC
1468494 TCGGTTAACC
Statistics
Matches: 102, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
122 2 0.02
123 95 0.93
124 5 0.05
ACGTcount: A:0.22, C:0.23, G:0.12, T:0.43
Consensus pattern (123 bp):
GTCAACCTTTCTTATTCAATGACTCATATGATTTAATCCTAGTCAAACCTTCTCATTCGTTGACA
TGTATGATTTCATCTCAATCAACCTTTCTCATTCGTTAACTCATATGGTTTCATCCCA
Found at i:1468482 original size:82 final size:82
Alignment explanation
Indices: 1468277--1468677 Score: 261
Period size: 82 Copynumber: 4.9 Consensus size: 82
1468267 CATTGACTCA
* * * * * * * *
1468277 TATGATTTAATCTTAGCTAACCATTCTCATTCGTTGAC-CTGTATGATTTCAT-CTCAATCAATC
1 TATGGTTTCATCTTAGTTAACCTTTCTCATTCGTTGACTC-ATATGGTTTCATCCT-AGTCAAAC
*
1468340 CTTCTCATTCGTTAAC-TCA
64 CTTCTCATTCGTTAACAT-G
** * * *** * *
1468359 TATGGTTTCATCCCAGTCAACCTTTCTTATTTAATGTCTCATATGGTTTCGTCCTAGTCAAACCT
1 TATGGTTTCATCTTAGTTAACCTTTCTCATTCGTTGACTCATATGGTTTCATCCTAGTCAAACCT
*
1468424 TCTCATTCGTTGACATG
66 TCTCATTCGTTAACATG
* * * *
1468441 TATGGTTTCGTCTTAGTTAACCTTTCTCATTCGTTGACTCATATGGTTTCAT-CTCGGTTAACCC
1 TATGGTTTCATCTTAGTTAACCTTTCTCATTCGTTGACTCATATGGTTTCATCCT-AGTCAAACC
* * *
1468505 TTTTCATTTGTTAACTTG
65 TTCTCATTCGTTAACATG
* * * * * * * * * * * *
1468523 TATGATTTCATCTCAATCAACCTTTTTCATTCGATAACTCGTATGGTTTCAGCCCAATCAAATCT
1 TATGGTTTCATCTTAGTTAACCTTTCTCATTCGTTGACTCATATGGTTTCATCCTAGTCAAACCT
* * ***
1468588 TCTTATTCGTTAGCGCA
66 TCTCATTCGTTAACATG
* * * * * * ** *
1468605 CATGGTTTCATCTTGGTTAAACTTTCTCATTTGTTAACTCCTATGGTTTCATCCCGGTCAACCCT
1 TATGGTTTCATCTTAGTTAACCTTTCTCATTCGTTGACTCATATGGTTTCATCCTAGTCAAACCT
*
1468670 TTTCATTC
66 TCTCATTC
1468678 ACTGACTAGT
Statistics
Matches: 237, Mismatches: 77, Indels: 10
0.73 0.24 0.03
Matches are distributed among these distances:
81 2 0.01
82 230 0.97
83 5 0.02
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.43
Consensus pattern (82 bp):
TATGGTTTCATCTTAGTTAACCTTTCTCATTCGTTGACTCATATGGTTTCATCCTAGTCAAACCT
TCTCATTCGTTAACATG
Done.