Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold102
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: 331322
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.28
Warning! 50393 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:3629 original size:52 final size:52
Alignment explanation
Indices: 3551--3657 Score: 178
Period size: 52 Copynumber: 2.1 Consensus size: 52
3541 CGAAATATGA
*
3551 AAATTTACCTACATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTACCTACATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
* * *
3603 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTACCTACATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
3655 AAA
1 AAA
3658 AAAAAATGTA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.35
Consensus pattern (52 bp):
AAATTTACCTACATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
Found at i:3702 original size:13 final size:13
Alignment explanation
Indices: 3684--3708 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3674 CAAAGATCAG
3684 TGTATCGATACAA
1 TGTATCGATACAA
3697 TGTATCGATACA
1 TGTATCGATACA
3709 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:3791 original size:13 final size:13
Alignment explanation
Indices: 3773--3797 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3763 ACAAAAAATA
3773 TGTATCGATACAT
1 TGTATCGATACAT
3786 TGTATCGATACA
1 TGTATCGATACA
3798 ACACTTTATG
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:3793 original size:32 final size:33
Alignment explanation
Indices: 3752--3817 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
3742 AGTAGCTTAA
3752 ATTGTATCGATACAA-AAAATATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
***
3784 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
3817 A
1 A
3818 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAACAAAATATGTATCGATAC
Found at i:8907 original size:17 final size:17
Alignment explanation
Indices: 8885--8918 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
8875 GATAAAGTGT
8885 TTGAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAA
8902 TTGAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAA
8919 AAAAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (17 bp):
TTGAAAAAAAAAAAAAA
Found at i:8952 original size:21 final size:21
Alignment explanation
Indices: 8928--8984 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
8918 AAAAAATTTA
8928 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
8949 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
8970 AATGTATCGATACAT
1 AATGTATCGATACAT
8985 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:9064 original size:19 final size:19
Alignment explanation
Indices: 9040--9107 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
9030 AATTCAACAA
9040 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
9059 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
9074 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
9091 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
9108 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:9079 original size:13 final size:13
Alignment explanation
Indices: 9061--9085 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9051 ACATAAGTTT
9061 TGTATCGATACAA
1 TGTATCGATACAA
9074 TGTATCGATACA
1 TGTATCGATACA
9086 TAAGTATTGT
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:9083 original size:32 final size:32
Alignment explanation
Indices: 9042--9104 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
9032 TTCAACAATT
*
9042 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
9074 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
9105 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:9165 original size:13 final size:13
Alignment explanation
Indices: 9147--9172 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9137 CATTTTTCTG
9147 TGTATCGATACAT
1 TGTATCGATACAT
9160 TGTATCGATACAT
1 TGTATCGATACAT
9173 GGATCTTTGT
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:9169 original size:33 final size:33
Alignment explanation
Indices: 9127--9193 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
9117 GCCAAGGAAA
***
9127 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
9160 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
9193 T
1 T
9194 TGGAAATTTT
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:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:11795 original size:102 final size:102
Alignment explanation
Indices: 11535--11816 Score: 365
Period size: 102 Copynumber: 2.8 Consensus size: 102
11525 CAAGTTTTCT
* * * * *
11535 CAATTTTGCATAATCGGGGATACTCCAACCCCGGTTTTACTTCTAAAACATTAATTTTCCACAAT
1 CAATTTTCCATCATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATTAATTTTCTATAAT
* * *
11600 CGGGGACACTCCAACTCCGATTTTATTCTCAGAACAC
66 CGGGGATACTCCAACTCCGATTGTATTCTCAAAACAC
**
11637 CAATTTTCCA-CAATCGGGGATACTCCAACCCCGGTTTTATTT-TCAAAACACCAATTTTCTATA
1 CAATTTTCCATC-ATCGGGGATACTCCAACCCCGGTTTTATTTCT-AAAACATTAATTTTCTATA
*
11700 ATCGGGGATACTCCAACTCCGATTGTATT-TCCAAAATAC
64 ATCGGGGATACTCCAACTCCGATTGTATTCT-CAAAACAC
* * * *
11739 TAATTTTTCATCATCGGGGATACTCCAACCCCGTTTTTATTTCTAAAATATTAA-TTTCTCATAA
1 CAATTTTCCATCATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATTAATTTTCT-ATAA
11803 TCGGGGATACTCCA
65 TCGGGGATACTCCA
11817 TCCCCGTTAT
Statistics
Matches: 157, Mismatches: 17, Indels: 12
0.84 0.09 0.06
Matches are distributed among these distances:
101 7 0.04
102 148 0.94
103 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (102 bp):
CAATTTTCCATCATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATTAATTTTCTATAAT
CGGGGATACTCCAACTCCGATTGTATTCTCAAAACAC
Found at i:11813 original size:153 final size:153
Alignment explanation
Indices: 11535--11822 Score: 359
Period size: 153 Copynumber: 1.9 Consensus size: 153
11525 CAAGTTTTCT
* * * *
11535 CAATTTTGCATAATCGGGGATACTCCAACCCCGGTTTTACTTCTAAAACATTAATTTTCCACAAT
1 CAATTTTGCATAATCGGGGATACTCCAACCCCGATTGTACTTCCAAAACACTAATTTTCCACAAT
* *
11600 CGGGGACACTCCAACTCCGATTTTATTCTCAGAACACCAATTTTCCACAATCGGGGATACTCCAA
66 CGGGGACACTCCAACCCCGATTTTATTCTCAAAACACCAATTTTCCACAATCGGGGATACTCCAA
11665 CCCCGGTTTTATTTTCAAAACAC
131 CCCCGGTTTTATTTTCAAAACAC
* * * *
11688 CAATTTT-CTATAATCGGGGATACTCCAACTCCGATTGTATTTCCAAAATACTAATTTTTCATC-
1 CAATTTTGC-ATAATCGGGGATACTCCAACCCCGATTGTACTTCCAAAACACTAATTTTCCA-CA
* * * ** *
11751 ATCGGGGATACTCCAACCCCGTTTTTATT-TCTAAAATATTAA-TTTCTCATAATCGGGGATACT
64 ATCGGGGACACTCCAACCCCGATTTTATTCTC-AAAACACCAATTTTC-CACAATCGGGGATACT
*
11814 CCATCCCCG
127 CCAACCCCG
11823 TTATTTTCGA
Statistics
Matches: 114, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
152 7 0.06
153 106 0.93
154 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (153 bp):
CAATTTTGCATAATCGGGGATACTCCAACCCCGATTGTACTTCCAAAACACTAATTTTCCACAAT
CGGGGACACTCCAACCCCGATTTTATTCTCAAAACACCAATTTTCCACAATCGGGGATACTCCAA
CCCCGGTTTTATTTTCAAAACAC
Found at i:11824 original size:51 final size:50
Alignment explanation
Indices: 11536--11822 Score: 308
Period size: 51 Copynumber: 5.6 Consensus size: 50
11526 AAGTTTTCTC
* * *
11536 AATTTTGCATAATCGGGGATACTCCAACCCCGGTTTTACTTCTAAAACATT
1 AATTTT-CATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACT
* * * * *
11587 AATTTTCCACAATCGGGGACACTCCAACTCCGATTTTA-TTCTCAGAACACC
1 AATTTT-CATAATCGGGGATACTCCAACCCCGATTTTATTTCT-AAAACACT
* * *
11638 AATTTTCCACAATCGGGGATACTCCAACCCCGGTTTTATTT-TCAAAACACC
1 AATTTT-CATAATCGGGGATACTCCAACCCCGATTTTATTTCT-AAAACACT
* * * *
11689 AATTTTCTATAATCGGGGATACTCCAACTCCGATTGTATTTCCAAAATACT
1 AATTTTC-ATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACT
* * * *
11740 AATTTTTCATCATCGGGGATACTCCAACCCCGTTTTTATTTCTAAAATATT
1 AA-TTTTCATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACT
*
11791 AATTTCTCATAATCGGGGATACTCCATCCCCG
1 AATTT-TCATAATCGGGGATACTCCAACCCCG
11823 TTATTTTCGA
Statistics
Matches: 203, Mismatches: 27, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
50 8 0.04
51 188 0.93
52 7 0.03
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (50 bp):
AATTTTCATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACT
Found at i:24419 original size:8 final size:8
Alignment explanation
Indices: 24403--24471 Score: 54
Period size: 8 Copynumber: 8.8 Consensus size: 8
24393 CCTTCTCTTC
24403 AAAAAAA-
1 AAAAAAAG
24410 AAAAAGAA-
1 AAAAA-AAG
*
24418 AAAAAAAA
1 AAAAAAAG
*
24426 AAAAAAAC
1 AAAAAAAG
*
24434 AAAAAAAC
1 AAAAAAAG
24442 AAAACAAAG
1 AAAA-AAAG
*
24451 AAAAAGAG
1 AAAAAAAG
*
24459 -AGAAAAG
1 AAAAAAAG
24466 AAAAAA
1 AAAAAA
24472 CCTACTTAAG
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
7 12 0.23
8 33 0.63
9 7 0.13
ACGTcount: A:0.87, C:0.04, G:0.09, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:24423 original size:15 final size:16
Alignment explanation
Indices: 24403--24471 Score: 63
Period size: 15 Copynumber: 4.2 Consensus size: 16
24393 CCTTCTCTTC
24403 AAAAAAAA-AAAAGAA
1 AAAAAAAACAAAAGAA
24418 AAAAAAAA-AAAA-AA
1 AAAAAAAACAAAAGAA
*
24432 ACAAAAAAACAAAACAA
1 A-AAAAAAACAAAAGAA
*
24449 AGAAAAAGAGAGAAAAGAA
1 A-AAAAA-A-ACAAAAGAA
24468 AAAA
1 AAAA
24472 CCTACTTAAG
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
14 3 0.07
15 19 0.41
16 4 0.09
17 8 0.17
18 4 0.09
19 8 0.17
ACGTcount: A:0.87, C:0.04, G:0.09, T:0.00
Consensus pattern (16 bp):
AAAAAAAACAAAAGAA
Found at i:24425 original size:17 final size:17
Alignment explanation
Indices: 24403--24455 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
24393 CCTTCTCTTC
24403 AAAAAAAAAAAAGAAAA
1 AAAAAAAAAAAAGAAAA
24420 AAAAAAAAAAAA-ACAAA
1 AAAAAAAAAAAAGA-AAA
*
24437 AAAACAAAACAAAGAAAA
1 AAAA-AAAAAAAAGAAAA
24455 A
1 A
24456 GAGAGAAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
16 1 0.03
17 19 0.59
18 11 0.34
19 1 0.03
ACGTcount: A:0.91, C:0.06, G:0.04, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAGAAAA
Found at i:24426 original size:18 final size:18
Alignment explanation
Indices: 24403--24455 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
24393 CCTTCTCTTC
24403 AAAAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAGAAAAA
*
24421 AAAAAAAAAAAA-CAAAA
1 AAAAAAAAAAAAGAAAAA
* *
24438 AAACAAAACAAAGAAAAA
1 AAAAAAAAAAAAGAAAAA
24456 GAGAGAAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 14 0.47
18 16 0.53
ACGTcount: A:0.91, C:0.06, G:0.04, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAAGAAAAA
Found at i:24471 original size:1 final size:1
Alignment explanation
Indices: 24403--24455 Score: 61
Period size: 1 Copynumber: 53.0 Consensus size: 1
24393 CCTTCTCTTC
* * * * *
24403 AAAAAAAAAAAAGAAAAAAAAAAAAAAAAACAAAAAAACAAAACAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
24456 GAGAGAAAAG
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.91, C:0.06, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:25522 original size:55 final size:55
Alignment explanation
Indices: 25437--26168 Score: 1083
Period size: 55 Copynumber: 13.3 Consensus size: 55
25427 TCCGCTTTTT
*
25437 AGTCCCCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
25492 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-C
* *
25547 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-C
* *
25602 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACCCAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-C
25657 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTC
*
25712 AGTCCTCAAAGAGCAGGACATCTCTT-AAAGCCCACACAAGTTGGTGGCA-CTTGTC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTT-TC
*
25767 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
25822 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTC
*
25877 AGTCC-CAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-C
* *
25931 AGTCCTCAAAGAACAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-C
25986 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * *
26041 ATTCCCCAAAGAGCAGGACACTTTTCAAAGCCCACACAAGTGGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * *
26096 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
26151 ACTCCTCAATGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
26169 TACAACTTAT
Statistics
Matches: 634, Mismatches: 29, Indels: 28
0.92 0.04 0.04
Matches are distributed among these distances:
53 5 0.01
54 58 0.09
55 556 0.88
56 15 0.02
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
Found at i:26770 original size:1 final size:1
Alignment explanation
Indices: 26764--26796 Score: 57
Period size: 1 Copynumber: 33.0 Consensus size: 1
26754 AAAGTGTTTG
*
26764 AAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
26797 TTTAAATGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.97, C:0.00, G:0.00, T:0.03
Consensus pattern (1 bp):
A
Found at i:26802 original size:19 final size:17
Alignment explanation
Indices: 26764--26797 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
26754 AAAGTGTTTG
26764 AAAAAAAAAAAAAAAAT
1 AAAAAAAAAAAAAAAAT
26781 AAAAAAAAAAAAAAAAT
1 AAAAAAAAAAAAAAAAT
26798 TTAAATGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.94, C:0.00, G:0.00, T:0.06
Consensus pattern (17 bp):
AAAAAAAAAAAAAAAAT
Found at i:26825 original size:21 final size:21
Alignment explanation
Indices: 26801--26857 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
26791 AAAAAATTTA
26801 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
26822 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
26843 AATGTATCGATACAT
1 AATGTATCGATACAT
26858 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:26937 original size:19 final size:19
Alignment explanation
Indices: 26913--26980 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
26903 AATTCAACAA
26913 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
26932 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
26947 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
26964 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
26981 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:26952 original size:13 final size:13
Alignment explanation
Indices: 26934--26958 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26924 ACATAAGTTT
26934 TGTATCGATACAA
1 TGTATCGATACAA
26947 TGTATCGATACA
1 TGTATCGATACA
26959 TAAGTATTGT
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:26956 original size:32 final size:32
Alignment explanation
Indices: 26915--26977 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
26905 TTCAACAATT
*
26915 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
26947 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
26978 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:27038 original size:13 final size:13
Alignment explanation
Indices: 27020--27045 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27010 CATTTTTCTG
27020 TGTATCGATACAT
1 TGTATCGATACAT
27033 TGTATCGATACAT
1 TGTATCGATACAT
27046 GGATCTTTGT
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:27042 original size:33 final size:33
Alignment explanation
Indices: 27000--27066 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
26990 GCCAAGGAAA
***
27000 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
27033 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
27066 T
1 T
27067 TGGAAATTTT
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:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:29668 original size:102 final size:102
Alignment explanation
Indices: 29408--29689 Score: 365
Period size: 102 Copynumber: 2.8 Consensus size: 102
29398 CAAGTTTTCT
* * * * *
29408 CAATTTTGCATAATCGGGGATACTCCAACCCCGGTTTTACTTCTAAAACATTAATTTTCCACAAT
1 CAATTTTCCATCATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATTAATTTTCTATAAT
* * *
29473 CGGGGACACTCCAACTCCGATTTTATTCTCAGAACAC
66 CGGGGATACTCCAACTCCGATTGTATTCTCAAAACAC
**
29510 CAATTTTCCA-CAATCGGGGATACTCCAACCCCGGTTTTATTT-TCAAAACACCAATTTTCTATA
1 CAATTTTCCATC-ATCGGGGATACTCCAACCCCGGTTTTATTTCT-AAAACATTAATTTTCTATA
*
29573 ATCGGGGATACTCCAACTCCGATTGTATT-TCCAAAATAC
64 ATCGGGGATACTCCAACTCCGATTGTATTCT-CAAAACAC
* * * *
29612 TAATTTTTCATCATCGGGGATACTCCAACCCCGTTTTTATTTCTAAAATATTAA-TTTCTCATAA
1 CAATTTTCCATCATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATTAATTTTCT-ATAA
29676 TCGGGGATACTCCA
65 TCGGGGATACTCCA
29690 TCCCCGTTAT
Statistics
Matches: 157, Mismatches: 17, Indels: 12
0.84 0.09 0.06
Matches are distributed among these distances:
101 7 0.04
102 148 0.94
103 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (102 bp):
CAATTTTCCATCATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATTAATTTTCTATAAT
CGGGGATACTCCAACTCCGATTGTATTCTCAAAACAC
Found at i:29686 original size:153 final size:153
Alignment explanation
Indices: 29408--29695 Score: 359
Period size: 153 Copynumber: 1.9 Consensus size: 153
29398 CAAGTTTTCT
* * * *
29408 CAATTTTGCATAATCGGGGATACTCCAACCCCGGTTTTACTTCTAAAACATTAATTTTCCACAAT
1 CAATTTTGCATAATCGGGGATACTCCAACCCCGATTGTACTTCCAAAACACTAATTTTCCACAAT
* *
29473 CGGGGACACTCCAACTCCGATTTTATTCTCAGAACACCAATTTTCCACAATCGGGGATACTCCAA
66 CGGGGACACTCCAACCCCGATTTTATTCTCAAAACACCAATTTTCCACAATCGGGGATACTCCAA
29538 CCCCGGTTTTATTTTCAAAACAC
131 CCCCGGTTTTATTTTCAAAACAC
* * * *
29561 CAATTTT-CTATAATCGGGGATACTCCAACTCCGATTGTATTTCCAAAATACTAATTTTTCATC-
1 CAATTTTGC-ATAATCGGGGATACTCCAACCCCGATTGTACTTCCAAAACACTAATTTTCCA-CA
* * * ** *
29624 ATCGGGGATACTCCAACCCCGTTTTTATT-TCTAAAATATTAA-TTTCTCATAATCGGGGATACT
64 ATCGGGGACACTCCAACCCCGATTTTATTCTC-AAAACACCAATTTTC-CACAATCGGGGATACT
*
29687 CCATCCCCG
127 CCAACCCCG
29696 TTATTTTCGA
Statistics
Matches: 114, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
152 7 0.06
153 106 0.93
154 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (153 bp):
CAATTTTGCATAATCGGGGATACTCCAACCCCGATTGTACTTCCAAAACACTAATTTTCCACAAT
CGGGGACACTCCAACCCCGATTTTATTCTCAAAACACCAATTTTCCACAATCGGGGATACTCCAA
CCCCGGTTTTATTTTCAAAACAC
Found at i:29697 original size:51 final size:50
Alignment explanation
Indices: 29409--29695 Score: 308
Period size: 51 Copynumber: 5.6 Consensus size: 50
29399 AAGTTTTCTC
* * *
29409 AATTTTGCATAATCGGGGATACTCCAACCCCGGTTTTACTTCTAAAACATT
1 AATTTT-CATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACT
* * * * *
29460 AATTTTCCACAATCGGGGACACTCCAACTCCGATTTTA-TTCTCAGAACACC
1 AATTTT-CATAATCGGGGATACTCCAACCCCGATTTTATTTCT-AAAACACT
* * *
29511 AATTTTCCACAATCGGGGATACTCCAACCCCGGTTTTATTT-TCAAAACACC
1 AATTTT-CATAATCGGGGATACTCCAACCCCGATTTTATTTCT-AAAACACT
* * * *
29562 AATTTTCTATAATCGGGGATACTCCAACTCCGATTGTATTTCCAAAATACT
1 AATTTTC-ATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACT
* * * *
29613 AATTTTTCATCATCGGGGATACTCCAACCCCGTTTTTATTTCTAAAATATT
1 AA-TTTTCATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACT
*
29664 AATTTCTCATAATCGGGGATACTCCATCCCCG
1 AATTT-TCATAATCGGGGATACTCCAACCCCG
29696 TTATTTTCGA
Statistics
Matches: 203, Mismatches: 27, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
50 8 0.04
51 188 0.93
52 7 0.03
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (50 bp):
AATTTTCATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACT
Found at i:31297 original size:164 final size:165
Alignment explanation
Indices: 30994--31304 Score: 452
Period size: 164 Copynumber: 1.9 Consensus size: 165
30984 ATTCCTTTTA
* * * *
30994 TTTTCAAATTACGGGATTTTCTTCTCTATAAATTTTTTTGGGGAGATTTTTTCTTCGTTTTTAAT
1 TTTTCAAAATACGGGATTTTCTACTCTATAAATTTTTTCGGGGAGATTTTTTCTTAGTTTTTAAT
31059 TTTAAAATTCATCAAATATTATTATTTATTTCACATTAATTCAATTTTCAAAAATTCATTCTTTT
66 TTTAAAATTCATCAAATATTATTATTTATTTCACATTAATTCAATTTTCAAAAATTCATTCTTTT
*
31124 CCATAAATTTTGAATTTTTTCTTGAAATTTTCCTT
131 CCATAAATTTTAAATTTTTTCTTGAAATTTTCCTT
* *
31159 TTTTCAAAATAC-GGAGTTTTCTACTTTGTAAATTTTTTC-GGGAGGA-TTTTTCTTAGTTTTTG
1 TTTTCAAAATACGGGA-TTTTCTACTCTATAAATTTTTTCGGGGA-GATTTTTTCTTAGTTTTT-
* * * *
31221 ATTTTTAAAATTCATCAAATATTA-TATTTATTTCACATTAATTGAGTTTTCAAAAATTTATTCA
63 AATTTTAAAATTCATCAAATATTATTATTTATTTCACATTAATTCAATTTTCAAAAATTCATTC-
31285 TTTT-CATAAATTTTAAATTT
127 TTTTCCATAAATTTTAAATTT
31305 CCTTGAAATT
Statistics
Matches: 131, Mismatches: 11, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
164 72 0.55
165 59 0.45
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.52
Consensus pattern (165 bp):
TTTTCAAAATACGGGATTTTCTACTCTATAAATTTTTTCGGGGAGATTTTTTCTTAGTTTTTAAT
TTTAAAATTCATCAAATATTATTATTTATTTCACATTAATTCAATTTTCAAAAATTCATTCTTTT
CCATAAATTTTAAATTTTTTCTTGAAATTTTCCTT
Found at i:31389 original size:162 final size:164
Alignment explanation
Indices: 31058--31392 Score: 409
Period size: 162 Copynumber: 2.0 Consensus size: 164
31048 TCGTTTTTAA
31058 TTTTAAAATTCATCAAATATTATTATTTATTTCACATTAATTCAATTTTCAAAAATTCATTCTTT
1 TTTTAAAATTCATCAAATATTATTATTTATTTCACATTAATTCAATTTTCAAAAATTCATTCTTT
* * * **
31123 TCCATAAATTTTGAATTTTTTCTTGAAATTTTCCTTTTTTCAAAATACGGAGTTTTCTACTTTGT
66 TCCATAAATTTTGAATATTTCCTTGAAA-TTTCCTTTTTCCAAAATACGGAGTTTTCTACTTCAT
* * ***
31188 AAATTTTTTCGGGAGGATTTTTCTTAGTTTTTGAT
130 AAATATTTTCGGGAGGATTTTTCTTAGTCTAAAAT
* * *
31223 TTTTAAAATTCATCAAATATTA-TATTTATTTCACATTAATTGAGTTTTCAAAAATTTATTCATT
1 TTTTAAAATTCATCAAATATTATTATTTATTTCACATTAATTCAATTTTCAAAAATTCATTC-TT
31287 TT-CATAAATTTT-AA-ATTTCCTTGAAA-TTCCTCTTTCTCCGAAAA-ATC-GAGTTTTCTA-T
65 TTCCATAAATTTTGAATATTTCCTTGAAATTTCCT-TTT-TCC-AAAATA-CGGAGTTTTCTACT
*
31345 TCCATAAATATTTTCGGGGGGA-TTTTCTTCAGTCTAAAAT
126 T-CATAAATATTTTCGGGAGGATTTTTCTT-AGTCTAAAAT
31385 TTTTAAAA
1 TTTTAAAA
31393 AGTATATAAT
Statistics
Matches: 149, Mismatches: 14, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
160 5 0.03
161 12 0.08
162 53 0.36
163 7 0.05
164 46 0.31
165 26 0.17
ACGTcount: A:0.31, C:0.13, G:0.08, T:0.49
Consensus pattern (164 bp):
TTTTAAAATTCATCAAATATTATTATTTATTTCACATTAATTCAATTTTCAAAAATTCATTCTTT
TCCATAAATTTTGAATATTTCCTTGAAATTTCCTTTTTCCAAAATACGGAGTTTTCTACTTCATA
AATATTTTCGGGAGGATTTTTCTTAGTCTAAAAT
Found at i:33791 original size:3 final size:3
Alignment explanation
Indices: 33785--33822 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
33775 TAATGAAGAA
33785 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
33823 AGTTAACTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:33792 original size:12 final size:12
Alignment explanation
Indices: 33771--33819 Score: 62
Period size: 12 Copynumber: 4.1 Consensus size: 12
33761 TCAACCAACA
* *
33771 AAGATAATGAAG
1 AAGATGATGATG
33783 AAGATGATGATG
1 AAGATGATGATG
*
33795 ATGATGATGATG
1 AAGATGATGATG
*
33807 ATGATGATGATG
1 AAGATGATGATG
33819 A
1 A
33820 TGAAGTTAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.43, C:0.00, G:0.31, T:0.27
Consensus pattern (12 bp):
AAGATGATGATG
Found at i:40828 original size:20 final size:19
Alignment explanation
Indices: 40805--40855 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
40795 CACATCCAAA
* *
40805 TGTATTGATACATTATGCTT
1 TGTATTGATACATGAT-CAT
* *
40825 TGTATCGATACATGCTCAT
1 TGTATTGATACATGATCAT
40844 TGTATTGATACA
1 TGTATTGATACA
40856 CACTCAATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (19 bp):
TGTATTGATACATGATCAT
Found at i:40861 original size:19 final size:19
Alignment explanation
Indices: 40824--40875 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
40814 ACATTATGCT
**
40824 TTGTATCGATACATGCTCA
1 TTGTATCGATACACACTCA
*
40843 TTGTATTGATACACACTCAA
1 TTGTATCGATACACACTC-A
* *
40863 TTATATCAATACA
1 TTGTATCGATACA
40876 TAAAACTGGC
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACACACTCA
Found at i:43253 original size:28 final size:28
Alignment explanation
Indices: 43221--43283 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
43211 AAGATATTCT
*
43221 AACCCTGTTATTTCTGA-TGTGATACTCC
1 AACCCTGTTATTTCTGAGGGT-ATACTCC
** *
43249 AACCCAATTATTTTTGAGGGTATACTCC
1 AACCCTGTTATTTCTGAGGGTATACTCC
43277 AACCCTG
1 AACCCTG
43284 ATTTTATTTC
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
28 26 0.93
29 2 0.07
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.35
Consensus pattern (28 bp):
AACCCTGTTATTTCTGAGGGTATACTCC
Found at i:43372 original size:79 final size:79
Alignment explanation
Indices: 43256--43511 Score: 340
Period size: 79 Copynumber: 3.2 Consensus size: 79
43246 TCCAACCCAA
43256 TTATTTTTG-AGGGTATACTCCAACCCTGATTTTATTTCTAAAACATCGATTTTCCACCATCGGG
1 TTATTTTTGAAGGG-ATACTCCAACCCTGATTTTATTTCTAAAACATCGATTTTCCACCATCGGG
43320 GATACTCTAACCTCG
65 GATACTCTAACCTCG
* ** *
43335 TTATTTCTGAAGGGATACTCCAA-CCTCGGCTTTATTTCTAAAACATCGATGTTCCACCATC-GG
1 TTATTTTTGAAGGGATACTCCAACCCT-GATTTTATTTCTAAAACATCGATTTTCCACCATCGGG
* *
43398 GAGTACTCCAACC-CTA
65 GA-TACTCTAACCTC-G
* * *
43414 TTATTTTTGAAGGGATACTCCAACCCTGATTTTATTTCTAAAACATCAATTTTTCACCATCGGAG
1 TTATTTTTGAAGGGATACTCCAACCCTGATTTTATTTCTAAAACATCGATTTTCCACCATCGGGG
*
43479 ATACTCTATCCTCG
66 ATACTCTAACCTCG
* *
43493 TTATTTTCGAGGGGATACT
1 TTATTTTTGAAGGGATACT
43512 TTTACCTCGT
Statistics
Matches: 152, Mismatches: 18, Indels: 14
0.83 0.10 0.08
Matches are distributed among these distances:
78 8 0.05
79 133 0.88
80 11 0.07
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (79 bp):
TTATTTTTGAAGGGATACTCCAACCCTGATTTTATTTCTAAAACATCGATTTTCCACCATCGGGG
ATACTCTAACCTCG
Found at i:43523 original size:186 final size:186
Alignment explanation
Indices: 43317--43667 Score: 474
Period size: 186 Copynumber: 1.9 Consensus size: 186
43307 TTCCACCATC
* *
43317 GGGGATACTCTAACCTCGTTATTTCTGAAGGGATACTCCAACCTCGGCTTTATTTCTAAAACATC
1 GGGGATACTCTAACCTCGTTATTTCTGAAGGGATACTCCAACCCCGACTTTATTTCTAAAACATC
* *
43382 GATGTTCCACCATC-GGGAGTACTCCAACCCTATTATTTTTGAA-GGGATACTCCAACCCTGA-T
66 GATGTTCCACCATCAAGGA-TACTCCAACCCTATTA-TTTTCAAGGGGATACTCCAACCCT-ATT
*
43444 TTTATTTCTAAAACATCAATTTTTCACCATCGGAGATACTCTATCCTCGTTATTTTCGA
128 TTTATTTCTAAAACATCAACTTTTCACCATCGGAGATACTCTATCCTCGTTATTTTCGA
* * * * * * *
43503 GGGGATACTTTTACCTCGTTATTTTTGAAGGGATACTCTAACCCCGATTTTGTTTCTAAAATATC
1 GGGGATACTCTAACCTCGTTATTTCTGAAGGGATACTCCAACCCCGACTTTATTTCTAAAACATC
* * * * *
43568 GATTTTCCACCATCAAGGATACTCCAATCTTGTTATTTTCAAGGGGATACTCTAACCCTATTTTT
66 GATGTTCCACCATCAAGGATACTCCAACCCTATTATTTTCAAGGGGATACTCCAACCCTATTTTT
* * *
43633 ATTTCTAAAATATCAACTTTTCACTATCGGGGATA
131 ATTTCTAAAACATCAACTTTTCACCATCGGAGATA
43668 TTCCAACCCC
Statistics
Matches: 142, Mismatches: 20, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
185 7 0.05
186 132 0.93
187 3 0.02
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (186 bp):
GGGGATACTCTAACCTCGTTATTTCTGAAGGGATACTCCAACCCCGACTTTATTTCTAAAACATC
GATGTTCCACCATCAAGGATACTCCAACCCTATTATTTTCAAGGGGATACTCCAACCCTATTTTT
ATTTCTAAAACATCAACTTTTCACCATCGGAGATACTCTATCCTCGTTATTTTCGA
Found at i:43603 original size:107 final size:107
Alignment explanation
Indices: 43414--43618 Score: 288
Period size: 107 Copynumber: 1.9 Consensus size: 107
43404 TCCAACCCTA
* * *
43414 TTATTTTTGAAGGGATACTCCAACCCTGATTTTATTTCTAAAACATCAATTTTTCACCATCGGAG
1 TTATTTTTGAAGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTCCACCATCAGAG
* *
43479 ATACTCTATCCTCGTTATTTTCGAGGGGATACTTTTACCTCG
66 ATACTCAATCCTCGTTATTTTCAAGGGGATACTTTTACCTCG
* * * *
43521 TTATTTTTGAAGGGATACTCTAACCCCGATTTTGTTTCTAAAATATCGATTTTCCACCATCA-AG
1 TTATTTTTGAAGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTCCACCATCAGA-
*
43585 GATACTCCAAT-CTTGTTATTTTCAAGGGGATACT
65 GATACT-CAATCCTCGTTATTTTCAAGGGGATACT
43619 CTAACCCTAT
Statistics
Matches: 86, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
106 1 0.01
107 82 0.95
108 3 0.03
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.39
Consensus pattern (107 bp):
TTATTTTTGAAGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTCCACCATCAGAG
ATACTCAATCCTCGTTATTTTCAAGGGGATACTTTTACCTCG
Found at i:43676 original size:51 final size:51
Alignment explanation
Indices: 43610--43721 Score: 161
Period size: 51 Copynumber: 2.2 Consensus size: 51
43600 TTATTTTCAA
* * * * *
43610 GGGGATACTCTAACCCTATTTTTATTTCTAAAATATCAACTTTTCACTATC
1 GGGGATACTCCAACCCCATTTTTATTTCCAAAAGATCAACTTTTCACCATC
* *
43661 GGGGATATTCCAACCCCATTTTTATTTCCAAAAGATCAATTTTTCACCATC
1 GGGGATACTCCAACCCCATTTTTATTTCCAAAAGATCAACTTTTCACCATC
43712 GGGGATACTC
1 GGGGATACTC
43722 TAATCCTGCT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.37
Consensus pattern (51 bp):
GGGGATACTCCAACCCCATTTTTATTTCCAAAAGATCAACTTTTCACCATC
Found at i:43773 original size:130 final size:130
Alignment explanation
Indices: 43532--43775 Score: 296
Period size: 130 Copynumber: 1.9 Consensus size: 130
43522 TATTTTTGAA
* * * * *
43532 GGGATACTCTAACCCCGATTTTGTTTCTAAAATATCGATTTTCCACCATCAAGGATACTCCAATC
1 GGGATACTCCAACCCCGATTTTATTTCCAAAAGATCAATTTTCCACCATCAAGGATACTCCAATC
* * * * *
43597 TTGTTATTTTCAAGGGGATACTCTAACCCTATTTTTATTTCTAAAATATCAACTTTTCACTATCG
66 CTGCTATTTTCAAGGAGATACTCTAACCCTATTTTTATCTCCAAAATATCAACTTTTCACTATCG
* * ** *
43662 GGGATATTCCAACCCC-ATTTTTATTTCCAAAAGATCAATTTTTCACCATCGGGGATACTCTAAT
1 GGGATACTCCAACCCCGA-TTTTATTTCCAAAAGATCAATTTTCCACCATCAAGGATACTCCAAT
*
43726 CCTGCTATTTTCGAA-GAGATA-TTTCAACCCTATTTTTATCTCCAAAATAT
65 CCTGCTATTTTC-AAGGAGATACTCT-AACCCTATTTTTATCTCCAAAATAT
43776 TAAATTTCTC
Statistics
Matches: 95, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
129 3 0.03
130 90 0.95
131 2 0.02
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.38
Consensus pattern (130 bp):
GGGATACTCCAACCCCGATTTTATTTCCAAAAGATCAATTTTCCACCATCAAGGATACTCCAATC
CTGCTATTTTCAAGGAGATACTCTAACCCTATTTTTATCTCCAAAATATCAACTTTTCACTATCG
Found at i:45547 original size:19 final size:20
Alignment explanation
Indices: 45523--45582 Score: 70
Period size: 19 Copynumber: 3.0 Consensus size: 20
45513 TTTGAATTTC
45523 AACAGT-TTGTATCGATACA
1 AACAGTATTGTATCGATACA
*
45542 AACAGTAAATGTATCGATACA
1 AACAGT-ATTGTATCGATACA
* *
45563 TA-AGTGTTGTATCGATACA
1 AACAGTATTGTATCGATACA
45582 A
1 A
45583 TATATCGCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
19 18 0.53
20 3 0.09
21 13 0.38
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (20 bp):
AACAGTATTGTATCGATACA
Found at i:53262 original size:31 final size:30
Alignment explanation
Indices: 53211--53295 Score: 118
Period size: 31 Copynumber: 2.8 Consensus size: 30
53201 TCCCCAATAA
*
53211 AGTGGCATCTCTTTTCAAAGTCCACAACTT
1 AGTGGCATCTCTTTTCAAAGTCCACAACAT
*
53241 AGTGGCATC-CTTTCTTCAAAGTCCACGACAT
1 AGTGGCATCTC-TT-TTCAAAGTCCACAACAT
*
53272 GGTGGCATCTCTTTTCAAAGTCCA
1 AGTGGCATCTCTTTTCAAAGTCCA
53296 TGACTCTGTG
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
29 1 0.02
30 22 0.45
31 25 0.51
32 1 0.02
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.32
Consensus pattern (30 bp):
AGTGGCATCTCTTTTCAAAGTCCACAACAT
Found at i:53307 original size:30 final size:29
Alignment explanation
Indices: 53212--53316 Score: 122
Period size: 30 Copynumber: 3.5 Consensus size: 29
53202 CCCCAATAAA
*
53212 GTGGCATCTCTTTTCAAAGTCCACAACTT
1 GTGGCATCTCTTTTCAAAGTCCACGACTT
*
53241 AGTGGCATC-CTTTCTTCAAAGTCCACGACATG
1 -GTGGCATCTC-TT-TTCAAAGTCCACGAC-TT
*
53273 GTGGCATCTCTTTTCAAAGTCCATGACTCT
1 GTGGCATCTCTTTTCAAAGTCCACGACT-T
*
53303 GTGGCACCTCTTTT
1 GTGGCATCTCTTTT
53317 ATCCTTTTTA
Statistics
Matches: 65, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
29 2 0.03
30 37 0.57
31 24 0.37
32 2 0.03
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (29 bp):
GTGGCATCTCTTTTCAAAGTCCACGACTT
Found at i:53399 original size:62 final size:62
Alignment explanation
Indices: 53348--53711 Score: 498
Period size: 62 Copynumber: 5.9 Consensus size: 62
53338 GCAAGACACT
* * *
53348 TTTTTCTTTTTATAGCCCATACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATGCC
1 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATGCC
* * * *
53410 -TTTTCTTTTCAAAGCCTACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGTAGGATGCG
1 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATGCC
* * *
53471 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCTTCAAAGAGTAGGATGCC
1 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATGCC
* * * * * *
53533 TTTTCCTTTTCAAAGACCACATGAGTTAGAGGCA-CTTTTAGTCCTCAAAGAGCAAGATGCC
1 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATGCC
* * * * *
53594 TTTTCCTTTTCAAAGCCCACACGAGTTGCTGGCATCTTTTAGTCCTCAAAGAGTAGGACGCCC
1 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATG-CC
* *
53657 TTTTTCTTTTCAAAGCCTACACGAGTTGGTGGCACCTTTTAGTCCTCAAGGAGCA
1 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCA
53712 TTTCCCTCTT
Statistics
Matches: 266, Mismatches: 33, Indels: 5
0.88 0.11 0.02
Matches are distributed among these distances:
61 106 0.40
62 109 0.41
63 51 0.19
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.33
Consensus pattern (62 bp):
TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATGCC
Found at i:53433 original size:61 final size:61
Alignment explanation
Indices: 53349--53711 Score: 485
Period size: 61 Copynumber: 5.9 Consensus size: 61
53339 CAAGACACTT
* * *
53349 TTTTCTTTTTATAGCCCATACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATGCC
1 TTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATGCC
* * * *
53410 TTTTCTTTTCAAAGCCTACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGTAGGATGCGT
1 TTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATGC-C
* * *
53472 TTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCTTCAAAGAGTAGGATGCC
1 TTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATGCC
* * * * *
53533 TTTTCCTTTTCAAAGACCACATGAGTTAGAGGCA-CTTTTAGTCCTCAAAGAGCAAGATGCC
1 TTTT-CTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATGCC
* * * *
53594 TTTTCCTTTTCAAAGCCCACACGAGTTGCTGGCATCTTTTAGTCCTCAAAGAGTAGGACGCCC
1 TTTT-CTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATG-CC
* *
53657 TTTTTCTTTTCAAAGCCTACACGAGTTGGTGGCACCTTTTAGTCCTCAAGGAGCA
1 -TTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCA
53712 TTTCCCTCTT
Statistics
Matches: 266, Mismatches: 31, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
61 110 0.41
62 105 0.39
63 47 0.18
64 4 0.02
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.33
Consensus pattern (61 bp):
TTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATGCC
Found at i:53488 original size:123 final size:122
Alignment explanation
Indices: 53322--53711 Score: 521
Period size: 123 Copynumber: 3.2 Consensus size: 122
53312 CTTTTATCCT
* * ** * * * *
53322 TTTTACTCCTTAAAGAGCAAGACACTTTTTTCTTTTTATAGCCCATACGAGTTGGTGGCACCTTT
1 TTTTAGTCCTCAAAGAGCAAGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTT
*
53387 TAGTCCTCAAAGAGCAGGATGCCTTTTCTTTTCAAAGCCTACACGAGTTGGTGGCAC
66 TAGTCCTCAAAGAGTAGGATGCCTTTTCTTTTCAAAGCCTACACGAGTTGGTGGCAC
* * * *
53444 TTTTTAGTCCTCAAAGAGTAGGATGCGTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACTTT
1 -TTTTAGTCCTCAAAGAGCAAGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTT
* * * *
53509 TTAGTCTTCAAAGAGTAGGATGCCTTTTCCTTTTCAAAGACC-ACATGAGTTAGAGGCAC
65 TTAGTCCTCAAAGAGTAGGATGCCTTTT-CTTTTCAAAG-CCTACACGAGTTGGTGGCAC
* * *
53568 TTTTAGTCCTCAAAGAGCAAGATGCCTTTTCCTTTTCAAAGCCCACACGAGTTGCTGGCATCTTT
1 TTTTAGTCCTCAAAGAGCAAGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTT
*
53633 TAGTCCTCAAAGAGTAGGACGCCCTTTTTCTTTTCAAAGCCTACACGAGTTGGTGGCACC
66 TAGTCCTCAAAGAGTAGGATG-CC-TTTTCTTTTCAAAGCCTACACGAGTTGGTGGCA-C
*
53693 TTTTAGTCCTCAAGGAGCA
1 TTTTAGTCCTCAAAGAGCA
53712 TTTCCCTCTT
Statistics
Matches: 232, Mismatches: 29, Indels: 10
0.86 0.11 0.04
Matches are distributed among these distances:
123 158 0.68
124 49 0.21
125 25 0.11
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (122 bp):
TTTTAGTCCTCAAAGAGCAAGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTT
TAGTCCTCAAAGAGTAGGATGCCTTTTCTTTTCAAAGCCTACACGAGTTGGTGGCAC
Found at i:53778 original size:42 final size:42
Alignment explanation
Indices: 53719--53938 Score: 145
Period size: 42 Copynumber: 5.4 Consensus size: 42
53709 GCATTTCCCT
* * *
53719 CTTTTC-CCTTTATCCTCAAATAGCAGAATGCACTTTATTTC
1 CTTTTCTCCTTTGTCCTCAAAAAGCAGAACGCACTTTATTTC
* * *
53760 CTTTTCTTCTTTGTCCTCAAAAAGCAGGACGCCCTTTATTTC
1 CTTTTCTCCTTTGTCCTCAAAAAGCAGAACGCACTTTATTTC
* * *
53802 TTTTTCTCCTTTGTCCT---TAA--AG-ACGCACTTTATTTT
1 CTTTTCTCCTTTGTCCTCAAAAAGCAGAACGCACTTTATTTC
* * * * *
53838 CTTTTCT-CTATTGTCTTCAAAGAGCAGGACGCGCTTCATTTC
1 CTTTTCTCCT-TTGTCCTCAAAAAGCAGAACGCACTTTATTTC
* * * * * * *
53880 CTTCTTTTCCCTTCGTTCTCAAAGAGCAGGATGCAC-TCATTTC
1 CTT-TTCT-CCTTTGTCCTCAAAAAGCAGAACGCACTTTATTTC
53923 CTTTT-TCTCTTTGTCC
1 CTTTTCTC-CTTTGTCC
53939 CCGAAAAATA
Statistics
Matches: 141, Mismatches: 26, Indels: 24
0.74 0.14 0.13
Matches are distributed among these distances:
35 2 0.01
36 24 0.17
37 2 0.01
39 3 0.02
40 1 0.01
41 15 0.11
42 60 0.43
43 13 0.09
44 19 0.13
45 2 0.01
ACGTcount: A:0.18, C:0.27, G:0.11, T:0.43
Consensus pattern (42 bp):
CTTTTCTCCTTTGTCCTCAAAAAGCAGAACGCACTTTATTTC
Found at i:53852 original size:36 final size:36
Alignment explanation
Indices: 53787--53860 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
53777 CAAAAAGCAG
*
53787 GACGCCCTTTATTTCTTTTTCTCCTTTGTCCTT-AAA
1 GACGCACTTTATTTCTTTTTCTCCTTTGT-CTTCAAA
53823 GACGCACTTTATTT-TCTTTTCT-CTATTGTCTTCAAA
1 GACGCACTTTATTTCT-TTTTCTCCT-TTGTCTTCAAA
53859 GA
1 GA
53861 GCAGGACGCG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
35 6 0.18
36 28 0.82
ACGTcount: A:0.18, C:0.24, G:0.09, T:0.49
Consensus pattern (36 bp):
GACGCACTTTATTTCTTTTTCTCCTTTGTCTTCAAA
Found at i:55031 original size:13 final size:13
Alignment explanation
Indices: 55013--55039 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
55003 ACATTTTGGG
55013 ATGTATCGATACA
1 ATGTATCGATACA
55026 ATGTATCGATACA
1 ATGTATCGATACA
55039 A
1 A
55040 ATTTGGCTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:55119 original size:20 final size:22
Alignment explanation
Indices: 55072--55124 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
55062 GCCAATGACC
**
55072 TGTATCGATACATTCTTTTCGA
1 TGTATCGATACATTCTGGTCGA
55094 -GTATCGATACATT-TGGTC-A
1 TGTATCGATACATTCTGGTCGA
55113 TGTATCGATACA
1 TGTATCGATACA
55125 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 1 0.04
20 14 0.50
21 13 0.46
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (22 bp):
TGTATCGATACATTCTGGTCGA
Found at i:55130 original size:13 final size:13
Alignment explanation
Indices: 55112--55136 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55102 ACATTTGGTC
55112 ATGTATCGATACA
1 ATGTATCGATACA
55125 ATGTATCGATAC
1 ATGTATCGATAC
55137 TGTGCAATTT
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):
ATGTATCGATACA
Found at i:55800 original size:24 final size:24
Alignment explanation
Indices: 55769--55815 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
55759 TTCTTTCTCC
55769 CCCTTAATCATAAAATTTATTTAT
1 CCCTTAATCATAAAATTTATTTAT
55793 CCCTTAATCATAAAATTTATTTA
1 CCCTTAATCATAAAATTTATTTA
55816 CAAAGATTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.45
Consensus pattern (24 bp):
CCCTTAATCATAAAATTTATTTAT
Found at i:57472 original size:20 final size:21
Alignment explanation
Indices: 57443--57483 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
57433 TGTTTTTGTT
57443 GATGATTTTG-A-TGAAAAAC
1 GATGATTTTGAAGTGAAAAAC
57462 GATGTATTTTGAAGTGAAAAAC
1 GATG-ATTTTGAAGTGAAAAAC
57484 AAGAAATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
21 1 0.05
22 8 0.42
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (21 bp):
GATGATTTTGAAGTGAAAAAC
Found at i:57633 original size:13 final size:13
Alignment explanation
Indices: 57615--57654 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
57605 ATAAACCCTT
57615 TGTATCGATACAC
1 TGTATCGATACAC
*
57628 TGTATCGATACAA
1 TGTATCGATACAC
57641 TGTATCGATACAC
1 TGTATCGATACAC
57654 T
1 T
57655 TGAACATGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:57821 original size:8 final size:8
Alignment explanation
Indices: 57808--57837 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
57798 AACATCATTC
57808 ATCACAAA
1 ATCACAAA
57816 ATCACAAA
1 ATCACAAA
57824 ATCACAAA
1 ATCACAAA
57832 ATCACA
1 ATCACA
57838 CAATTTAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.60, C:0.27, G:0.00, T:0.13
Consensus pattern (8 bp):
ATCACAAA
Found at i:63793 original size:13 final size:13
Alignment explanation
Indices: 63775--63800 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
63765 GCATTTTGGG
63775 ATGTATCGATACA
1 ATGTATCGATACA
63788 ATGTATCGATACA
1 ATGTATCGATACA
63801 TATTGTGTGT
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:63795 original size:33 final size:32
Alignment explanation
Indices: 63753--63816 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
63743 AGTTACAAGC
* *
63753 CAATGTATCGATGCATTTTGGGATGTATCGATA
1 CAATGTATCGATACATATTGGG-TGTATCGATA
*
63786 CAATGTATCGATACATATTGTGTGTATCGAT
1 CAATGTATCGATACATATTGGGTGTATCGAT
63817 GCAAATTTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 9 0.32
33 19 0.68
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (32 bp):
CAATGTATCGATACATATTGGGTGTATCGATA
Found at i:64712 original size:25 final size:20
Alignment explanation
Indices: 64644--64698 Score: 92
Period size: 20 Copynumber: 2.7 Consensus size: 20
64634 GACAATTTGC
*
64644 ATCGATACAAATAGTAAATGT
1 ATCGATACATA-AGTAAATGT
64665 ATCGATACATAAGTAAATGT
1 ATCGATACATAAGTAAATGT
64685 ATCGATACATAAGT
1 ATCGATACATAAGT
64699 GCCTTAAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 23 0.70
21 10 0.30
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.29
Consensus pattern (20 bp):
ATCGATACATAAGTAAATGT
Found at i:66726 original size:77 final size:78
Alignment explanation
Indices: 66389--66766 Score: 376
Period size: 79 Copynumber: 4.9 Consensus size: 78
66379 TCATTGATGT
* * * *
66389 TTTTATTTCTAAAATATCGATTTTCCACC-TCGAGGATACTCCAACCCCATTATTTCTGAGGGGA
1 TTTTATTTCTAAAACATCGATTTTCCACCATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGA
* *
66453 TACTCCAACC-CCA
66 TACT-CTACCTCGA
* * * * *
66466 GTTTTATTTCTAAAACA-CTGATTTTTCACCATCAGGGATACTCCAACTCCGTTATTTCTGAGAG
1 -TTTTATTTCTAAAACATC-GATTTTCCACCATCGGGGATACTCCAACCCCGTTATTTTTGAGGG
* * *
66530 GATTCTCCAGCCTTGA
64 GATACTCTA-CCTCGA
* * * * * *
66546 TTTTATTTTTAAAACACCGATTTTCCACCATTGGGGATACTCAAACCCTGTTATTTTTGAGGAGA
1 TTTTATTTCTAAAACATCGATTTTCCACCATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGA
*
66611 TA--CT-CCT-GG
66 TACTCTACCTCGA
* *
66620 TTTTATTTCTAAAACATCAATTTTCCACCATCGGGGATACTCCAACCTCGTTATTTTTGAGGGGA
1 TTTTATTTCTAAAACATCGATTTTCCACCATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGA
*
66685 TAGTCTACCTCGA
66 TACTCTACCTCGA
* * ** * ** *
66698 TTTT-TTTCTAAAACATCGATTTTTCACCATAGGAAACACTCCAACCCCGTTGCTTTCGAGGGGA
1 TTTTATTTCTAAAACATCGATTTTCCACCATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGA
66762 TACTC
66 TACTC
66767 CAACCCCATT
Statistics
Matches: 247, Mismatches: 44, Indels: 19
0.80 0.14 0.06
Matches are distributed among these distances:
74 60 0.24
75 3 0.01
76 2 0.01
77 59 0.24
78 32 0.13
79 89 0.36
80 2 0.01
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (78 bp):
TTTTATTTCTAAAACATCGATTTTCCACCATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGA
TACTCTACCTCGA
Found at i:66769 original size:105 final size:105
Alignment explanation
Indices: 66652--66882 Score: 295
Period size: 106 Copynumber: 2.2 Consensus size: 105
66642 TTCCACCATC
* * * * *
66652 GGGGATACTCCAACCTCGTTATTTTTGAGGGGATAGT-CTACCTCGATTTTTTTCTAAAACATCG
1 GGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCTACCTCGATTTATTTCTAAAACATCG
* *
66716 ATTTTTCACCAT-AGGAAACACTCCAACCCCGTTGCTTTCGA
66 ATTTTCCACCATCAGG--ACACTCCAACCCCGTTACTTTCGA
* *
66757 GGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCTACCTCGGTTTATTTCTAAAACATTG
1 GGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCTACCTCGATTTATTTCTAAAACATCG
* * * * *
66822 ATTTTCCACCATCGAGGATACTCCAATCCCTTTATTTTTGA
66 ATTTTCCACCATC-AGGACACTCCAACCCCGTTACTTTCGA
66863 GGGGATACTCCAACCCCATT
1 GGGGATACTCCAACCCCATT
66883 TTTATTTCCA
Statistics
Matches: 109, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
105 33 0.30
106 73 0.67
108 3 0.03
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.33
Consensus pattern (105 bp):
GGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCTACCTCGATTTATTTCTAAAACATCG
ATTTTCCACCATCAGGACACTCCAACCCCGTTACTTTCGA
Found at i:66779 original size:153 final size:154
Alignment explanation
Indices: 66389--66780 Score: 361
Period size: 153 Copynumber: 2.5 Consensus size: 154
66379 TCATTGATGT
* * * *
66389 TTTTATTTCTAAAATATCGATTTTCCACC-TCGAGG--ATACTCCAACCCCATTATTTCTGAGGG
1 TTTTATTTCTAAAACACCGATTTTCCACCAT--AGGAAACACTCCAACCCCGTTATTTC-GAGGG
* *
66451 GATACTCCAACCCCAGTTTTATTTCTAAAACACTGATTTTTCACCATCAGGGATACTCCAACTCC
63 GATACTCCAACCCCA---TTATTTCTAAAACACTAATTTTCCACCATCAGGGATACTCCAACTCC
* *
66516 GTTATTTCTGAGAGGATTCTCCAGCCTTGA
125 GTTATTTCTGAGAGGATACTCCAGCCTCGA
* * ** * * * * *
66546 TTTTATTTTTAAAACACCGATTTTCCACCATTGGGGATACTCAAACCCTGTTATTTTTGAGGAGA
1 TTTTATTTCTAAAACACCGATTTTCCACCATAGGAAACACTCCAACCCCGTTA-TTTCGAGGGGA
***** *
66611 TACTCC--TGGTTTTATTTCTAAAACA-TCAATTTTCCACCATCGGGGATACTCCAAC-CTCGTT
65 TACTCCAACCCCATTATTTCTAAAACACT-AATTTTCCACCATCAGGGATACTCCAACTC-CGTT
* * * *
66672 ATTTTTGAGGGGATAGTCTA-CCTCGA
128 ATTTCTGAGAGGATACTCCAGCCTCGA
* * *
66698 TTTT-TTTCTAAAACATCGATTTTTCACCATAGGAAACACTCCAACCCCGTTGCTTTCGAGGGGA
1 TTTTATTTCTAAAACACCGATTTTCCACCATAGGAAACACTCCAACCCCGTT-ATTTCGAGGGGA
66762 TACTCCAACCCCATTATTT
65 TACTCCAACCCCATTATTT
66781 TCGAGGGGAT
Statistics
Matches: 186, Mismatches: 40, Indels: 22
0.75 0.16 0.09
Matches are distributed among these distances:
151 53 0.28
152 11 0.06
153 64 0.34
156 2 0.01
157 26 0.14
158 27 0.15
159 3 0.02
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (154 bp):
TTTTATTTCTAAAACACCGATTTTCCACCATAGGAAACACTCCAACCCCGTTATTTCGAGGGGAT
ACTCCAACCCCATTATTTCTAAAACACTAATTTTCCACCATCAGGGATACTCCAACTCCGTTATT
TCTGAGAGGATACTCCAGCCTCGA
Found at i:66782 original size:28 final size:28
Alignment explanation
Indices: 66735--66795 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
66725 CATAGGAAAC
* *
66735 ACTCCAACCCCGTTGCTTTCGAGGGGAT
1 ACTCCAACCCCATTACTTTCGAGGGGAT
*
66763 ACTCCAACCCCATTATTTTCGAGGGGAT
1 ACTCCAACCCCATTACTTTCGAGGGGAT
66791 ACTCC
1 ACTCC
66796 TACCTCGGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.21, C:0.33, G:0.20, T:0.26
Consensus pattern (28 bp):
ACTCCAACCCCATTACTTTCGAGGGGAT
Found at i:66847 original size:78 final size:78
Alignment explanation
Indices: 66759--66933 Score: 210
Period size: 78 Copynumber: 2.2 Consensus size: 78
66749 GCTTTCGAGG
* * * *
66759 GGATACTCCAACCCCATTATTTTCGAGGGGATACTCCTACCTC-GGTTTATTTCTAAAACATTGA
1 GGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCAGGTTTATTTCCAAAACATTAA
66823 -TTTTCCACCATCGA
66 CTTTT-CACCATC-A
* * * ** *
66837 GGATACTCCAATCCCTTTATTTTTGAGGGGATACTCCAACCCCATTTTTATTTCCAAAATATTAA
1 GGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCAGGTTTATTTCCAAAACATTAA
66902 CTTTTCACCATCA
66 CTTTTCACCATCA
*
66915 GAGATACTCTAACCCCATT
1 G-GATACTCCAACCCCATT
66934 TTTATTTTCG
Statistics
Matches: 81, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
78 40 0.49
79 37 0.46
80 4 0.05
ACGTcount: A:0.27, C:0.27, G:0.11, T:0.34
Consensus pattern (78 bp):
GGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCAGGTTTATTTCCAAAACATTAA
CTTTTCACCATCA
Found at i:66929 original size:51 final size:51
Alignment explanation
Indices: 66866--66979 Score: 156
Period size: 51 Copynumber: 2.2 Consensus size: 51
66856 TTTTTGAGGG
* *
66866 GATACTCCAACCCCATTTTTATTTCCAAAATATTAACTTTTCACCATCAGA
1 GATACTCCAACCCCATTTTTATTTCCAAAATATCAAATTTTCACCATCAGA
* * * * *
66917 GATACTCTAACCCCATTTTTATTTTCGAAATATCAAATTTTCACCATCGGG
1 GATACTCCAACCCCATTTTTATTTCCAAAATATCAAATTTTCACCATCAGA
*
66968 GATATTCCAACC
1 GATACTCCAACC
66980 TATTGTTTTC
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.32, C:0.26, G:0.07, T:0.35
Consensus pattern (51 bp):
GATACTCCAACCCCATTTTTATTTCCAAAATATCAAATTTTCACCATCAGA
Found at i:68019 original size:32 final size:33
Alignment explanation
Indices: 67983--68134 Score: 220
Period size: 32 Copynumber: 4.7 Consensus size: 33
67973 TGAAAGGGGA
67983 TGCCACCAACTTGTGTGGGCTTTTGA-GAAGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAGGAAGGT
68015 TGCCACCAACTTGTGTGGGC-TTTGAGGAAGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAGGAAGGT
*
68047 TCCCACCAACTTGTGTGGGC-TTTGAGGAAGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAGGAAGGT
* * * ** *
68079 TGCCACCAGCTTGTGTGAGCTTTGGAAAAAGGG
1 TGCCACCAACTTGTGTGGGCTTTTGAGGAAGGT
68112 TGCCACCAACTTGTGTGGGCTTT
1 TGCCACCAACTTGTGTGGGCTTT
68135 GCTGGCTAGC
Statistics
Matches: 108, Mismatches: 10, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
31 5 0.05
32 74 0.69
33 29 0.27
ACGTcount: A:0.19, C:0.20, G:0.32, T:0.29
Consensus pattern (33 bp):
TGCCACCAACTTGTGTGGGCTTTTGAGGAAGGT
Found at i:68358 original size:65 final size:64
Alignment explanation
Indices: 68289--68529 Score: 187
Period size: 65 Copynumber: 3.7 Consensus size: 64
68279 GCTATGGAGT
*
68289 TGTGGACTTTAAAAGGAAGGTGCCACAGAGTTATGGGCTTTGAAAGAAAGGATGCGATCAACTTG
1 TGTGGACTTTAAAAGGAAGGTGCCACAGAGTTATGGGCTTTGAAAGAAA-GATGCCATCAACTTG
* * * **
68354 TGTGGGCTTTTGAGAAA--AA-ATGCCACCA-ACTTATGTGGGCTTAAAAAGATGAAG-TGCCA-
1 TGTGGAC-TTT-A-AAAGGAAGGTGCCA-CAGAGTTA--TGGGCTTTGAAAGA--AAGATGCCAT
68413 CGGAA--T-
58 C--AACTTG
*
68419 TGTGGACTTTAAAAGGAAGGTGCCACAGAGTTGTGGGCTTTGAAAGAAAAGATGCCATCAACTTG
1 TGTGGACTTTAAAAGGAAGGTGCCACAGAGTTATGGGCTTTGAAAG-AAAGATGCCATCAACTTG
* * * *
68484 TGTGGGC-TTAAAAGGATAAGGTGCAACAGAGTCATGGACTTTGAAA
1 TGTGGACTTTAAAAGG--AAGGTGCCACAGAGTTATGGGCTTTGAAA
68530 ACGTTACTCT
Statistics
Matches: 137, Mismatches: 17, Indels: 43
0.70 0.09 0.22
Matches are distributed among these distances:
62 8 0.06
63 17 0.12
64 18 0.13
65 35 0.26
66 34 0.25
67 17 0.12
68 6 0.04
69 2 0.01
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.24
Consensus pattern (64 bp):
TGTGGACTTTAAAAGGAAGGTGCCACAGAGTTATGGGCTTTGAAAGAAAGATGCCATCAACTTG
Found at i:68377 original size:130 final size:130
Alignment explanation
Indices: 68219--68492 Score: 431
Period size: 130 Copynumber: 2.1 Consensus size: 130
68209 GGTGCCACCG
* ** * * * * *
68219 ACTTGTGTGGACTTTTAAGAAAGGATGCCACTAACTTGTGTGGGCTTAAAAGGATGAAGTGCTAT
1 ACTTGTGTGGGCTTTTAAGAAAAAATGCCACCAACTTATGTGGGCTTAAAAAGATGAAGTGCCAC
* * *
68284 GGAGTTGTGGACTTTAAAAGGAAGGTGCCACAGAGTTATGGGCTTTGAAAGAAAGGATGCGATCA
66 GGAATTGTGGACTTTAAAAGGAAGGTGCCACAGAGTTATGGGCTTTGAAAGAAAAGATGCCATCA
*
68349 ACTTGTGTGGGCTTTTGAGAAAAAATGCCACCAACTTATGTGGGCTTAAAAAGATGAAGTGCCAC
1 ACTTGTGTGGGCTTTTAAGAAAAAATGCCACCAACTTATGTGGGCTTAAAAAGATGAAGTGCCAC
*
68414 GGAATTGTGGACTTTAAAAGGAAGGTGCCACAGAGTTGTGGGCTTTGAAAGAAAAGATGCCATCA
66 GGAATTGTGGACTTTAAAAGGAAGGTGCCACAGAGTTATGGGCTTTGAAAGAAAAGATGCCATCA
68479 ACTTGTGTGGGCTT
1 ACTTGTGTGGGCTT
68493 AAAAGGATAA
Statistics
Matches: 131, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
130 131 1.00
ACGTcount: A:0.31, C:0.13, G:0.30, T:0.27
Consensus pattern (130 bp):
ACTTGTGTGGGCTTTTAAGAAAAAATGCCACCAACTTATGTGGGCTTAAAAAGATGAAGTGCCAC
GGAATTGTGGACTTTAAAAGGAAGGTGCCACAGAGTTATGGGCTTTGAAAGAAAAGATGCCATCA
Found at i:68398 original size:97 final size:94
Alignment explanation
Indices: 68297--68529 Score: 229
Period size: 97 Copynumber: 2.4 Consensus size: 94
68287 GTTGTGGACT
* * *
68297 TTAAAAGGAAGGTGCCACAGAGTTATGGGCTTTGAAAGAAAGGATGCGATCA-ACTTGTGTGGGC
1 TTAAAAGGAAGGTGCCACAGAGTTATGGACTTTGAAAGAAAGG-TGCCA-CAGA-GT-TGTGGGC
68361 TTTTG-AGAAAAAATGCCACCAACTTATGTGGGC
62 -TTTGAAGAAAAAATGCCACCAACTTATGTGGGC
* * * * *
68394 TTAAAAAGATGAA-GTGCCACGGAATTGTGGACTTTAAAAGGAAGGTGCCACAGAGTTGTGGGCT
1 TT-AAAAG--GAAGGTGCCACAGAGTTATGGACTTTGAAAGAAAGGTGCCACAGAGTTGTGGGCT
* * *
68458 TTGAAAGAAAAGATGCCATCAACTTGTGTGGGC
63 TTG-AAGAAAAAATGCCACCAACTTATGTGGGC
* *
68491 TTAAAAGGATAAGGTGCAACAGAGTCATGGACTTTGAAA
1 TTAAAAGG--AAGGTGCCACAGAGTTATGGACTTTGAAA
68530 ACGTTACTCT
Statistics
Matches: 110, Mismatches: 17, Indels: 18
0.76 0.12 0.12
Matches are distributed among these distances:
94 1 0.01
95 4 0.04
96 14 0.13
97 52 0.47
98 10 0.09
99 26 0.24
100 3 0.03
ACGTcount: A:0.34, C:0.13, G:0.29, T:0.24
Consensus pattern (94 bp):
TTAAAAGGAAGGTGCCACAGAGTTATGGACTTTGAAAGAAAGGTGCCACAGAGTTGTGGGCTTTG
AAGAAAAAATGCCACCAACTTATGTGGGC
Found at i:68433 original size:32 final size:32
Alignment explanation
Indices: 68387--68475 Score: 92
Period size: 31 Copynumber: 2.8 Consensus size: 32
68377 CACCAACTTA
* *
68387 TGTGGGCTTAAAAAGATGAA-GTGCCACGGAAT
1 TGTGGGCTTTAAAAGA-GAAGGTGCCACAGAAT
* *
68419 TGTGGACTTTAAAAG-GAAGGTGCCACAGAGT
1 TGTGGGCTTTAAAAGAGAAGGTGCCACAGAAT
* * *
68450 TGTGGGCTTTGAAAGAAAAGATGCCA
1 TGTGGGCTTTAAAAGAGAAGGTGCCA
68476 TCAACTTGTG
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
30 3 0.06
31 23 0.49
32 21 0.45
ACGTcount: A:0.34, C:0.12, G:0.31, T:0.22
Consensus pattern (32 bp):
TGTGGGCTTTAAAAGAGAAGGTGCCACAGAAT
Found at i:68794 original size:52 final size:52
Alignment explanation
Indices: 68733--68834 Score: 134
Period size: 52 Copynumber: 2.0 Consensus size: 52
68723 CAAATTAAAT
* * * *
68733 TTAAAGATGATGAAGGTACCAACGTGATGATTCAAGG-CTAGCAACATTGGTC
1 TTAAAGATGATAAAAGTACCAACGTGATAATCCAAGGTC-AGCAACATTGGTC
* *
68785 TTAAAGATGATAAAAGTGCCAACGTGCTAATCCAAGGTCAGCAACATTGG
1 TTAAAGATGATAAAAGTACCAACGTGATAATCCAAGGTCAGCAACATTGG
68835 AATGAAAGAA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
52 42 0.98
53 1 0.02
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.24
Consensus pattern (52 bp):
TTAAAGATGATAAAAGTACCAACGTGATAATCCAAGGTCAGCAACATTGGTC
Found at i:89513 original size:21 final size:21
Alignment explanation
Indices: 89487--89542 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
89477 AGGGTGGTTC
89487 TGTATCGATACATTTCAGC-CA
1 TGTATCGATACATTTCA-CTCA
*
89508 TGTATCGATACA-TTCACTTA
1 TGTATCGATACATTTCACTCA
*
89528 TGCATCGATACATTT
1 TGTATCGATACATTT
89543 ATTGTTTGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.03
20 16 0.52
21 14 0.45
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTTCACTCA
Found at i:90437 original size:20 final size:21
Alignment explanation
Indices: 90412--90465 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
90402 GTTATAAGCA
*
90412 ATGTATTGATACAATT-CACC
1 ATGTATCGATACAATTGCACC
*
90432 ATGTATCGATAC-ATTGTACC
1 ATGTATCGATACAATTGCACC
90452 ATGTATCGATACAA
1 ATGTATCGATACAA
90466 ATAGTGGTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 3 0.10
20 26 0.87
21 1 0.03
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACAATTGCACC
Found at i:154609 original size:28 final size:28
Alignment explanation
Indices: 154569--154640 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
154559 GGAATAAAGC
** *
154569 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
154597 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
154625 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
154641 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:154693 original size:108 final size:108
Alignment explanation
Indices: 154554--154906 Score: 336
Period size: 108 Copynumber: 3.3 Consensus size: 108
154544 AGAATCAATA
* * * *
154554 TTTTGGGAATAAAGCCGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATG
1 TTTTGGAAATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG
*
154619 AAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTAT
66 AAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATTGGTAT
* * * ** * **
154662 TTTTGGAAATAAAATCGGAGTTGGAGTAT-CCC-C-G-ATTAAAGGAAAATTGGCGT-T--TTGA
1 TTTTGGAAATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAACGG--GGTTGGAGTATCCCCGA
* * *
154720 --AAATAAAACCAGGATTGGAGTATCCCCGATTGTGGAAAAATTAGTGT
64 TGAAAT--AACGAGG-TTGGAGTATCCCCGATTGT-GAAAAATTGGTAT
*
154767 TTTAGCG--ATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAAC-GGGTTGGAGTATCCCCGAT
1 TTTTG-GAAATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGAT
* * *
154829 G-ATTAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTT
65 GAAATAACGAGGTTGGAGTATCCCCGATTGTGAA-AAATTGGT-AT
* *
154874 TTTTGGAAATAAAATCGGAGTTAGAGTATCCCC
1 TTTTGGAAATAAAACCGGAGTTGGAGTATCCCC
154907 GATTATAGAA
Statistics
Matches: 193, Mismatches: 32, Indels: 40
0.73 0.12 0.15
Matches are distributed among these distances:
101 4 0.02
103 8 0.04
104 44 0.23
105 29 0.15
106 37 0.19
107 15 0.08
108 54 0.28
109 2 0.01
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (108 bp):
TTTTGGAAATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG
AAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATTGGTAT
Found at i:154698 original size:52 final size:52
Alignment explanation
Indices: 154629--154964 Score: 201
Period size: 52 Copynumber: 6.4 Consensus size: 52
154619 AAATAACGAG
*
154629 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
** * ** * *
154681 GTTGGAGTATCCCCGATTAAAGGAAAATTGG-CGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTATTTTTGGAAATAAAATC-GGA
* * * *
154734 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCG--ATAAAACCGGA
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTATTTTTG-GAAATAAAATCGGA
* **** * * *
154785 GTTGGAGTATCCCC--TCG-GAAATAACGGGTTGG-AGTATCCCCGATGAT-TAA-CGGG
1 GTTGGAGTATCCCCGATTGTGAAA-AA----TTGGTA-T-TTTTGGA-AATAAAATCGGA
*
154839 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGA
* * * * *
154893 GTTAGAGTATCCCCGATTAT-AGAAAATTAGT-GTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGA-AAAATTGGTATTTTTGGAAATAAAATCGGA
* *
154944 GTTGGAATATCCTCGATTGTG
1 GTTGGAGTATCCCCGATTGTG
154965 GAGAATTGAT
Statistics
Matches: 215, Mismatches: 43, Indels: 52
0.69 0.14 0.17
Matches are distributed among these distances:
48 4 0.02
49 2 0.01
50 2 0.01
51 37 0.17
52 79 0.37
53 38 0.18
54 41 0.19
55 2 0.01
56 4 0.02
57 5 0.02
58 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
Found at i:154823 original size:27 final size:27
Alignment explanation
Indices: 154785--154854 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
154775 TAAAACCGGA
**
154785 GTTGGAGTATCCCCTCGGAAATAAC-GG
1 GTTGGAGTATCCCCGAGG-AATAACGGG
* *
154812 GTTGGAGTATCCCCGATGATTAACGGG
1 GTTGGAGTATCCCCGAGGAATAACGGG
154839 GTTGGAGTATCCCCGA
1 GTTGGAGTATCCCCGA
154855 TTGTGAAGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
26 5 0.13
27 33 0.87
ACGTcount: A:0.23, C:0.21, G:0.31, T:0.24
Consensus pattern (27 bp):
GTTGGAGTATCCCCGAGGAATAACGGG
Found at i:154939 original size:51 final size:53
Alignment explanation
Indices: 154843--154961 Score: 145
Period size: 51 Copynumber: 2.3 Consensus size: 53
154833 AACGGGGTTG
* * *
154843 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGGAGTTA
*
154897 GAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
* *
154948 GAATATCCTCGATT
1 GAGTATCCCCGATT
154962 GTGGAGAATT
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
51 33 0.57
52 2 0.03
53 8 0.14
54 15 0.26
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.33
Consensus pattern (53 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
Found at i:157338 original size:13 final size:13
Alignment explanation
Indices: 157320--157345 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
157310 ACAAAGATCC
157320 ATGTATCGATACA
1 ATGTATCGATACA
157333 ATGTATCGATACA
1 ATGTATCGATACA
157346 CAGAAAAAGT
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:157423 original size:13 final size:13
Alignment explanation
Indices: 157405--157429 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
157395 ACAATACTTA
157405 TGTATCGATACAT
1 TGTATCGATACAT
157418 TGTATCGATACA
1 TGTATCGATACA
157430 AACTTATGTA
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:157423 original size:31 final size:31
Alignment explanation
Indices: 157387--157447 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
157377 TAGCTAATTA
157387 TGTATCG-TACAATACTTATGTATCGATACAT
1 TGTATCGATACAA-ACTTATGTATCGATACAT
157418 TGTATCGATACAAACTTATGTATCGATACA
1 TGTATCGATACAAACTTATGTATCGATACA
157448 AATCGTTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 24 0.83
32 5 0.17
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.36
Consensus pattern (31 bp):
TGTATCGATACAAACTTATGTATCGATACAT
Found at i:157449 original size:18 final size:18
Alignment explanation
Indices: 157384--157449 Score: 81
Period size: 18 Copynumber: 3.9 Consensus size: 18
157374 CAGTAGCTAA
157384 TTATGTATCG-TACAATAC
1 TTATGTATCGATACAA-AC
157402 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
157417 -T-TGTATCGATACAAAC
1 TTATGTATCGATACAAAC
157433 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
157450 TCGTTGAATT
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
15 1 0.02
16 1 0.02
17 1 0.02
18 24 0.57
19 3 0.07
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:158290 original size:56 final size:55
Alignment explanation
Indices: 158080--158871 Score: 1044
Period size: 54 Copynumber: 14.4 Consensus size: 55
158070 ATAAATTGTA
* * * *
158080 TCCTGCTCATTGAGGAGT-AAAAAGTGCCACCAACTCGTGTGGGCTTTGAA-AGGCG
1 TCCTGCTCTTTGAGGACTGAAAAA-TGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
** *
158135 T-CTGCTCTTTGAGGACTGAAAGGTGCCACC-ACTTGTGTGGGCTTTGAA-AAGTG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* * **
158188 TCCTGCTCTTTGGGGAATGAAAGGTGCCA-CAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
158242 T-CTGCTCTTTGAGGACTGAAAAAATGCCACCAACCTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTG-AAAAATGCCACCAA-CTTGTGTGGGCTTTAAGAGGTG
*
158298 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
** *
158353 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTTAAAGAGTTG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGC-TTT-AAGAGGTG
*
158410 TCCTGCTCTTTGAGGACTG-AAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
158464 TCCTGCTCTTTGAGGACTGAAAAAATGCCACCAACCTGCGTGTGGGCTTTAAAAGGTTG
1 TCCTGCTCTTTGAGGACTG-AAAAATGCCACCAA-CT-TGTGTGGGCTTTAAGAGG-TG
*
158523 TCCTGCTCTTTGAGGA-TGGAAAATGCCACCAAC-TGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* * **
158576 TCCTACTCTTTGGGGACTGGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
158632 TCCTGCTCTTTGAGGACTGGAAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
158688 TCCTGCTCTTTGAGGACTGGAAAATG-CACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* **
158742 TCCTGCTCTTTGAGGACTGGAAGCT-CCACC-ACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
**
158795 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGT-GGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
158849 TCCTGCTCTTTGAGGACT-AAAAA
1 TCCTGCTCTTTGAGGACTGAAAAA
158872 GCGGAAGGAG
Statistics
Matches: 667, Mismatches: 44, Indels: 54
0.87 0.06 0.07
Matches are distributed among these distances:
53 106 0.16
54 203 0.30
55 102 0.15
56 162 0.24
57 57 0.09
58 19 0.03
59 18 0.03
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
Found at i:158427 original size:112 final size:111
Alignment explanation
Indices: 158080--158866 Score: 1098
Period size: 112 Copynumber: 7.2 Consensus size: 111
158070 ATAAATTGTA
* * * * *
158080 TCCTGCTCATTGAGGAGT-AAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCGT-CTGCTCT
1 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCT
158143 TTGAGGACTGAAAGGTGCCACC-ACTTGTGTGGGCTTTGAAA-A-GTG
65 TTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAGAGGTG
* * *
158188 TCCTGCTCTTTGGGGAAT-GAAAGGTGCCA-CAACTTGTGTGGGCTTT-AAGAGGTGT-CTGCTC
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTC
**
158249 TTTGAGGACTGAAAAAATGCCACCAACCTTGTGTGGGCTTTAAA-AGGTG
64 TTTGAGGACTG-AAAGGTGCCACCAA-CTTGTGTGGGCTTTAAAGAGGTG
158298 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
*
158363 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTTAAAGAGTTG
66 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGC-TTTAAAGAGGTG
*
158410 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
** *
158474 TGAGGACTGAAAAAATGCCACCAACCTGCGTGTGGGCTTTAAA-AGGTTG
66 TGAGGACTG-AAAGGTGCCACCAA-CT-TGTGTGGGCTTTAAAGAGG-TG
*
158523 TCCTGCTCTTTGAGGA-TGGAAAATGCCACCAAC-TGTGTGGGCTTTGAAAGGTGTCCTACTCTT
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
*
158586 TGGGGACTGGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
66 TGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGAGGTG
158632 TCCTGCTCTTTGAGGACTGGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCT
1 TCCTGCTCTTTGAGGACTGG-AAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCT
*
158697 TTGAGGACTGGAAA-ATG-CACCAACTTGTGTGGGCTTT-AAGAGGTG
65 TTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGAGGTG
**
158742 TCCTGCTCTTTGAGGACTGGAAGCT-CCACC-ACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCT
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCT
158804 TTGAGGACTGAAAGGTGCCACCAACTTGTGT-GGCTTT-AAGAGGTG
65 TTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGAGGTG
158849 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
158867 AAAAAGCGGA
Statistics
Matches: 622, Mismatches: 32, Indels: 51
0.88 0.05 0.07
Matches are distributed among these distances:
106 8 0.01
107 110 0.18
108 51 0.08
109 28 0.05
110 114 0.18
111 117 0.19
112 144 0.23
113 42 0.07
114 8 0.01
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (111 bp):
TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGAGGTG
Found at i:158710 original size:27 final size:27
Alignment explanation
Indices: 158568--158710 Score: 65
Period size: 28 Copynumber: 5.1 Consensus size: 27
158558 TGTGGGCTTT
* *
158568 GAAAGGTGTCCTACTCTTTGGGGACTG
1 GAAAGGTGTCCTCCTCTTTGAGGACTG
* * * * *
158595 GAAAGGTG-CCACCAACTTGTGTGGGCTT
1 GAAAGGTGTCCTCC-TCTT-TGAGGACTG
* *
158623 TAAGAGGTGTCCTGCTCTTTGAGGACTG
1 GAA-AGGTGTCCTCCTCTTTGAGGACTG
** * * * * *
158651 GAAAAATG-CCACCAACTTGTGTGGGCTTT
1 GAAAGGTGTCCTCC-TCTT-TGAGGAC-TG
*
158680 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTCCTCTTTGAGGACTG
158707 GAAA
1 GAAA
158711 ATGCACCAAC
Statistics
Matches: 78, Mismatches: 30, Indels: 16
0.63 0.24 0.13
Matches are distributed among these distances:
26 6 0.08
27 22 0.28
28 26 0.33
29 18 0.23
30 6 0.08
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (27 bp):
GAAAGGTGTCCTCCTCTTTGAGGACTG
Found at i:159848 original size:1 final size:1
Alignment explanation
Indices: 159844--159897 Score: 54
Period size: 1 Copynumber: 54.0 Consensus size: 1
159834 CTTTTCTCTC
* * * * **
159844 TTTTTCTTTGTTTTGTTTTTTGTTTTTTTTTTTTTTTTTTTTGCTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
159898 GAAGAGAAGG
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.00, C:0.04, G:0.07, T:0.89
Consensus pattern (1 bp):
T
Found at i:159867 original size:12 final size:11
Alignment explanation
Indices: 159844--159898 Score: 76
Period size: 12 Copynumber: 4.9 Consensus size: 11
159834 CTTTTCTCTC
*
159844 TTTTTCTTTGT
1 TTTTTTTTTGT
159855 TTTGTTTTTTGT
1 TTT-TTTTTTGT
159867 TTTTTTTTT-T
1 TTTTTTTTTGT
159877 TTTTTTTTTGCT
1 TTTTTTTTTG-T
159889 TTTTTTTTTG
1 TTTTTTTTTG
159899 AAGAGAAGGT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
10 10 0.25
11 9 0.22
12 21 0.52
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.87
Consensus pattern (11 bp):
TTTTTTTTTGT
Found at i:159878 original size:21 final size:21
Alignment explanation
Indices: 159844--159897 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
159834 CTTTTCTCTC
*
159844 TTTTTCTTTGTTTTGTTTTTTG
1 TTTTT-TTTTTTTTGTTTTTTG
*
159866 TTTTTTTTTTTTTTTTTTTTG
1 TTTTTTTTTTTTTGTTTTTTG
*
159887 CTTTTTTTTTT
1 TTTTTTTTTTT
159898 GAAGAGAAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 24 0.83
22 5 0.17
ACGTcount: A:0.00, C:0.04, G:0.07, T:0.89
Consensus pattern (21 bp):
TTTTTTTTTTTTTGTTTTTTG
Found at i:165582 original size:17 final size:17
Alignment explanation
Indices: 165560--165593 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
165550 ACATCGATTC
*
165560 TTGACTGTGGCTTCCTT
1 TTGACTGTGCCTTCCTT
*
165577 TTGACTTTGCCTTCCTT
1 TTGACTGTGCCTTCCTT
165594 CTTACCTCTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.26, G:0.18, T:0.50
Consensus pattern (17 bp):
TTGACTGTGCCTTCCTT
Found at i:172416 original size:78 final size:78
Alignment explanation
Indices: 172314--172505 Score: 226
Period size: 79 Copynumber: 2.5 Consensus size: 78
172304 GTTTGAGTGT
* * * *
172314 TCCCTT-GAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA-TTAGAAAAAAAA
1 TCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-ATTTAGAAAAAAAA
*
172377 TCGGGATTGGAGTA
65 CCGGGATTGGAGTA
* * * * *
172391 TCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAG
1 TCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATA-TTTAGAAAAAAAA
*
172456 CCGGGGTTGGAGTA
65 CCGGGATTGGAGTA
* * *
172470 TCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 TCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGAT
172506 GAAATAACGA
Statistics
Matches: 97, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
77 7 0.07
78 38 0.39
79 52 0.54
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.24
Consensus pattern (78 bp):
TCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGAAAAAAAAC
CGGGATTGGAGTA
Found at i:172497 original size:28 final size:28
Alignment explanation
Indices: 172457--172528 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
172447 GGAATAAAGC
** *
172457 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
172485 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
172513 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
172529 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:172586 original size:52 final size:52
Alignment explanation
Indices: 172517--172853 Score: 203
Period size: 52 Copynumber: 6.4 Consensus size: 52
172507 AAATAACGAG
*
172517 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
** * ** * *
172569 GTTGGAGTATCCCCGATTAAAGGAAAATTGG-CGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTATTTTTGGAAATAAAATC-GGA
* * *
172622 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCG--ATAAAATCGGA
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTATTTTTG-GAAATAAAATCGGA
* **** * * *
172673 GTTGGAGTATCCCC--TCG-GAAATAACGGAGTTGG-AGTATCCCCGATGAT-TAAT-GGG
1 GTTGGAGTATCCCCGATTGTG-AA-AA---A-TTGGTA-T-TTTTGGA-AATAAAATCGGA
*
172728 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGA
* * * * *
172782 GTTAGAGTATCCCCGATTAT-AGAAAATTAGT-GTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGA-AAAATTGGTATTTTTGGAAATAAAATCGGA
* *
172833 GTTGGAATATCCTCGATTGTG
1 GTTGGAGTATCCCCGATTGTG
172854 GAGAATTGAT
Statistics
Matches: 214, Mismatches: 45, Indels: 52
0.69 0.14 0.17
Matches are distributed among these distances:
48 1 0.00
49 2 0.01
50 4 0.02
51 37 0.17
52 78 0.36
53 35 0.16
54 28 0.13
55 17 0.08
56 3 0.01
57 8 0.04
58 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.31
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
Found at i:172756 original size:107 final size:106
Alignment explanation
Indices: 172403--172795 Score: 343
Period size: 107 Copynumber: 3.7 Consensus size: 106
172393 CCTTCGAAAA
* * * * * * ** *
172403 TAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAG
1 TAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTTGGAATAAAATCGGAGTTGGAG
* * *
172468 TATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAA
66 TATCCCCTCGGAAATAACGGAGTTGGAGTATCCCCGATG-AT
* * *
172510 TAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGA
1 TAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTTGG-AATAAAATCGGAGTTGGA
* * * * ** **
172575 GTAT-CCC-C-G-ATTAAAGGAAAATTGGCGT-T--TTGAAAAT
65 GTATCCCCTCGGAAATAACGG--AGTTGGAGTATCCCCGATGAT
* * * * *
172612 AAAACCAGGATTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCG-ATAAAATCGGAGTT
1 -TAA-CGGGGTTGGAGTATCCCCGATTGT-GAAAAATTAGTATTTTTG-GAATAAAATCGGAGTT
172676 GGAGTATCCCCTCGGAAATAACGGAGTTGGAGTATCCCCGATGAT
62 GGAGTATCCCCTCGGAAATAACGGAGTTGGAGTATCCCCGATGAT
* * * *
172721 TAATGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 TAACGGGGTTGGAGTATCCCCGATTGTGAA-AAATTAGT-ATTTTTGG-AATAAAATCGGAGTTG
172786 GAGTATCCCC
63 GAGTATCCCC
172796 GATTATAGAA
Statistics
Matches: 222, Mismatches: 46, Indels: 34
0.74 0.15 0.11
Matches are distributed among these distances:
102 1 0.00
103 4 0.02
104 47 0.21
105 20 0.09
106 19 0.09
107 71 0.32
108 32 0.14
109 28 0.13
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (106 bp):
TAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTTGGAATAAAATCGGAGTTGGAG
TATCCCCTCGGAAATAACGGAGTTGGAGTATCCCCGATGAT
Found at i:172809 original size:212 final size:212
Alignment explanation
Indices: 172461--172855 Score: 616
Period size: 212 Copynumber: 1.9 Consensus size: 212
172451 TAAAGCCGGG
* *
172461 GTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTA
1 GTTGGAGTATCCCCTCGGAAATAACGGAGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTA
* *
172526 TCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAG
66 TCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTAAAG
* *
172591 GAAAATTGGCGTTTTGAAAATAAAACCAGGA-TTGGAGTATCCCCGATTGTGGAAAAATTAGTGT
131 GAAAATTAGCGTTTTGAAAATAAAACC-GGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGT
172655 TTTAGCGATAAAATCGGA
195 TTTAGCGATAAAATCGGA
* * *
172673 GTTGGAGTATCCCCTCGGAAATAACGGAGTTGGAGTATCCCCGATG-ATTAATGGGGTTGGAGTA
1 GTTGGAGTATCCCCTCGGAAATAACGGAGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTA
* *
172737 TCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTAT
66 TCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTAA
* * *
172802 A-GAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCTCGATTGTGGA
129 AGGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGA
172856 GAATTGATAA
Statistics
Matches: 166, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
211 31 0.19
212 96 0.58
213 39 0.23
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (212 bp):
GTTGGAGTATCCCCTCGGAAATAACGGAGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTA
TCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTAAAG
GAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTT
TTAGCGATAAAATCGGA
Found at i:175224 original size:13 final size:13
Alignment explanation
Indices: 175206--175231 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
175196 ACAAAGATCC
175206 ATGTATCGATACA
1 ATGTATCGATACA
175219 ATGTATCGATACA
1 ATGTATCGATACA
175232 TAGAAAAATG
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:175227 original size:33 final size:33
Alignment explanation
Indices: 175185--175251 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
175175 AAAATTTCCA
***
175185 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
175218 AATGTATCGATACATAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
175251 A
1 A
175252 TTTCCTTGGC
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:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:175295 original size:19 final size:18
Alignment explanation
Indices: 175271--175338 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
175261 CAGTAGCTAA
175271 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
175290 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
175305 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
175322 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
175339 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:175311 original size:13 final size:13
Alignment explanation
Indices: 175293--175317 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
175283 ACAATACTTA
175293 TGTATCGATACAT
1 TGTATCGATACAT
175306 TGTATCGATACA
1 TGTATCGATACA
175318 AAACTTATGT
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:175315 original size:32 final size:32
Alignment explanation
Indices: 175274--175336 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
175264 TAGCTAATTA
*
175274 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
175306 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
175337 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:176011 original size:35 final size:35
Alignment explanation
Indices: 175826--176508 Score: 313
Period size: 34 Copynumber: 19.9 Consensus size: 35
175816 TGCCCTTAAA
*
175826 AGAGGCTTTTAAAAT-TGCTAAAAA-TATCCTTAAG
1 AGAGGCTTTTAAAATCT-CTAAAAACTATCCTCAAG
* * * * * *
175860 AAAGAG-TTTTAACATTTTTAAGAAGTATCCTCAAG
1 AGAG-GCTTTTAAAATCTCTAAAAACTATCCTCAAG
* * * * * * *
175895 AAAGGCTTGTGAAATCTCTTAGAAC-ATCATAAAG
1 AGAGGCTTTTAAAATCTCTAAAAACTATCCTCAAG
* * * *
175929 AGTGTCTTTTAAAAT-TGCTAAAAAC-ATTCTTAAG
1 AGAGGCTTTTAAAATCT-CTAAAAACTATCCTCAAG
175963 AGAGG-TTTATAAAATCTCTAAAAACTATCCTCAAG
1 AGAGGCTTT-TAAAATCTCTAAAAACTATCCTCAAG
* * * * *
175998 AGAGGTTTTTAAAAACGCTGAAAAGTATCACT-AAG
1 AGAGGCTTTTAAAATCTCTAAAAACTATC-CTCAAG
* ** * * ** *
176033 AGAGGCTTGTGTAATCTTTTAAAA-TATTTTCTAG
1 AGAGGCTTTTAAAATCTCTAAAAACTATCCTCAAG
* * *
176067 A-AGGACTTTTAAAATCGCTAAAAGC-ATCTTCAAG
1 AGAGG-CTTTTAAAATCTCTAAAAACTATCCTCAAG
* * * *
176101 AAAGGCTTATAAAATCTCTAAAAAATATCCTTAAG
1 AGAGGCTTTTAAAATCTCTAAAAACTATCCTCAAG
* * * *
176136 -GAGGCTCTCAATAATCTCGAAAAGC-ATCCTCAAG
1 AGAGGCTTTTAA-AATCTCTAAAAACTATCCTCAAG
* * * * * *
176170 AAAGGCTTGTGAAATATTTTAAAAC-ATCCTCAAG
1 AGAGGCTTTTAAAATCTCTAAAAACTATCCTCAAG
*
176204 AG-GGACTTTTAAAAT-TGCTAAAAAAC-ATTCTCAAG
1 AGAGG-CTTTTAAAATCT-CT-AAAAACTATCCTCAAG
* * * ** *
176239 AGAGGCCTATAAAATCTTTAAAAAAGATCCTAAAG
1 AGAGGCTTTTAAAATCTCTAAAAACTATCCTCAAG
** ** * ** *
176274 AGAGAATTTTATCATCTCCGAAAAGTTATCCTCAAA
1 AGAGGCTTTTAAAATCT-CTAAAAACTATCCTCAAG
* * * * * *
176310 ATAAG-TTTGTGAAATCTCTTAAAA-TATCCTTAAA
1 AGAGGCTTT-TAAAATCTCTAAAAACTATCCTCAAG
* * *
176344 AGAGGCTTTTAAAATCGCTAAAAA--ATTCTCAGG
1 AGAGGCTTTTAAAATCTCTAAAAACTATCCTCAAG
* *
176377 AAAGGCTTATAAAATCTCTGAAAAA-TATCCTCAAG
1 AGAGGCTTTTAAAATCTCT-AAAAACTATCCTCAAG
* *
176412 AAAGG-TTTTAACATCTCTAAAAAC-ATCCTCAAG
1 AGAGGCTTTTAAAATCTCTAAAAACTATCCTCAAG
* * * *
176445 AGTGG-TTTTAAAATCCCTAAAAA-TATCCTTAAA
1 AGAGGCTTTTAAAATCTCTAAAAACTATCCTCAAG
* * *
176478 AGAGGTTTTTGAATTCTCTAAAAAC-ATCCTC
1 AGAGGCTTTTAAAATCTCTAAAAACTATCCTC
176509 TAAAAAAGGC
Statistics
Matches: 479, Mismatches: 138, Indels: 64
0.70 0.20 0.09
Matches are distributed among these distances:
33 76 0.16
34 212 0.44
35 165 0.34
36 26 0.05
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (35 bp):
AGAGGCTTTTAAAATCTCTAAAAACTATCCTCAAG
Found at i:176049 original size:138 final size:137
Alignment explanation
Indices: 175882--176445 Score: 525
Period size: 138 Copynumber: 4.1 Consensus size: 137
175872 CATTTTTAAG
* * * *
175882 AAGTATCCTCAAGAAAGGCTTGTGAAATCTCTTAGAACATCATAAAGAGTGTCTTTTAAAATTGC
1 AAGTATCCTCAAGAAAGGCTTGTGAAATCTCTTAAAACATCTTAAAGAG-GACTTTTAAAATCGC
* * * *
175947 TAAAAACATTCTTAAGAGAGGTTTATAAAATCTCTAAAAACTATCCTCAAGAGAGGTTTTTAAAA
65 TAAAAACATTCTCAAGAAAGGCTTATAAAATCTCTAAAAAATATCCTCAAGAGAGGTTTTTAAAA
*
176012 ACGCTGAA
130 ACTCTGAA
* * * * * **
176020 AAGTATCACT-AAGAGAGGCTTGTGTAATCTTTTAAAATATTTTCTAGAAGGACTTTTAAAATCG
1 AAGTATC-CTCAAGAAAGGCTTGTGAAATCTCTTAAAACATCTTAAAG-AGGACTTTTAAAATCG
* * * * *
176084 CTAAAAGCA-TCTTCAAGAAAGGCTTATAAAATCTCTAAAAAATATCCTTAAG-GAGGCTCTCAA
64 CTAAAAACATTC-TCAAGAAAGGCTTATAAAATCTCTAAAAAATATCCTCAAGAGAGGTTTTTAA
*
176147 TAA-TCTCGAA
128 AAACTCT-GAA
* * * * * *
176157 AAGCATCCTCAAGAAAGGCTTGTGAAATATTTTAAAACATCCTCAAGAGGGACTTTTAAAATTGC
1 AAGTATCCTCAAGAAAGGCTTGTGAAATCTCTTAAAACATCTTAAAGA-GGACTTTTAAAATCGC
* * * * * ** **
176222 TAAAAAACATTCTCAAGAGAGGCCTATAAAATCTTTAAAAAAGATCCTAAAGAGAGAATTTTATC
65 T-AAAAACATTCTCAAGAAAGGCTTATAAAATCTCTAAAAAATATCCTCAAGAGAGGTTTTTAAA
* *
176287 ATCTCCGAA
129 AACTCTGAA
* * *
176296 AAGTTATCCTCAA-AATAAGTTTGTGAAATCTCTTAAAATATCCTTAAAAGAGG-CTTTTAAAAT
1 AAG-TATCCTCAAGAA-AGGCTTGTGAAATCTCTTAAAACAT-CTT-AAAGAGGACTTTTAAAAT
* * *
176359 CGCTAAAAA-ATTCTCAGGAAAGGCTTATAAAATCTCTGAAAAATATCCTCAAGAAAGG-TTTTA
62 CGCTAAAAACATTCTCAAGAAAGGCTTATAAAATCTCTAAAAAATATCCTCAAGAGAGGTTTTTA
* *
176422 ACATCTCT-AA
127 AAAACTCTGAA
**
176432 AAACATCCTCAAGA
1 AAGTATCCTCAAGA
176446 GTGGTTTTAA
Statistics
Matches: 344, Mismatches: 67, Indels: 32
0.78 0.15 0.07
Matches are distributed among these distances:
135 8 0.02
136 10 0.03
137 78 0.23
138 171 0.50
139 26 0.08
140 43 0.12
141 4 0.01
142 4 0.01
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (137 bp):
AAGTATCCTCAAGAAAGGCTTGTGAAATCTCTTAAAACATCTTAAAGAGGACTTTTAAAATCGCT
AAAAACATTCTCAAGAAAGGCTTATAAAATCTCTAAAAAATATCCTCAAGAGAGGTTTTTAAAAA
CTCTGAA
Found at i:176383 original size:33 final size:33
Alignment explanation
Indices: 176321--176517 Score: 157
Period size: 33 Copynumber: 5.8 Consensus size: 33
176311 TAAGTTTGTG
* * *
176321 AAATCTCTTAAAATATCCTTAA-AAGAGGCTTTTA
1 AAATCTCTAAAAACATCCTCAAGAA-AGG-TTTTA
* * * *
176355 AAATCGCTAAAAA-ATTCTCAGGAAAGGCTTATA
1 AAATCTCTAAAAACATCCTCAAGAAAGG-TTTTA
*
176388 AAATCTCTGAAAAATATCCTCAAGAAAGGTTTTA
1 AAATCTCT-AAAAACATCCTCAAGAAAGGTTTTA
* **
176422 ACATCTCTAAAAACATCCTCAAGAGTGGTTTTA
1 AAATCTCTAAAAACATCCTCAAGAAAGGTTTTA
* * * *
176455 AAATCCCTAAAAATATCCTTAA-AAGAGGTTTTTG
1 AAATCTCTAAAAACATCCTCAAGAA-AGG-TTTTA
* *
176489 AATTCTCTAAAAACATCCTCTAAAAAAGG
1 AAATCTCTAAAAACATCCTC-AAGAAAGG
176518 CTTAATGATT
Statistics
Matches: 131, Mismatches: 25, Indels: 13
0.78 0.15 0.08
Matches are distributed among these distances:
32 1 0.01
33 62 0.47
34 49 0.37
35 17 0.13
36 2 0.02
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (33 bp):
AAATCTCTAAAAACATCCTCAAGAAAGGTTTTA
Found at i:176421 original size:67 final size:66
Alignment explanation
Indices: 175935--176517 Score: 262
Period size: 69 Copynumber: 8.5 Consensus size: 66
175925 AAAGAGTGTC
* * * * * *
175935 TTTTAAAATTGCTAAAAACATTCTTAAGAGAGGTTTATAAAATCTCTAAAAACTATCCTCAAGAG
1 TTTTAAAATCGCTAAAAACATCCTCAAGAAAGG-TTATAAAATCTCTAAAAA-TATCCTTAAAAG
176000 AGG
64 AGG
* ** * * ** * * ** *
176003 TTTTTAAAAACGCTGAAAAGTATCACT-AAGAGAGGCTTGTGTAATCTTTTAAAATATTTTCTAG
1 -TTTTAAAATCGCT-AAAAACATC-CTCAAGAAAGG-TTATAAAATCTCTAAAAATATCCT-TAA
*
176067 AAG-GAC
61 AAGAG-G
* * *
176073 TTTTAAAATCGCTAAAAGCATCTTCAAGAAAGGCTTATAAAATCTCTAAAAAATATCCTT-AAGG
1 TTTTAAAATCGCTAAAAACATCCTCAAGAAAGG-TTATAAAATCTCT-AAAAATATCCTTAAAAG
176137 AGG
64 AGG
* * * * * * * * * * * * *
176140 CTCTCAATAATCTCGAAAAGCATCCTCAAGAAAGGCTTGTGAAATATTTTAAAACATCCTCAAGA
1 -TTTTAA-AATCGCTAAAAACATCCTCAAGAAAGG-TTATAAAATCTCTAAAAATATCCTTAAAA
176205 G-GG
63 GAGG
* * * * * *
176208 ACTTTTAAAATTGCTAAAAAACATTCTCAAGAGAGGCCTATAAAATCTTTAAAAAAGATCC-TAA
1 --TTTTAAAATCGCT-AAAAACATCCTCAAGAAAGG-TTATAAAATCTCT-AAAAATATCCTTAA
*
176272 AGAGAGAA
61 A-AGAG-G
** * * ** * * * * *
176280 TTTTATCATCTCCGAAAAGTTATCCTCAAAATAAGTTTGTGAAATCTCTTAAAATATCCTTAAAA
1 TTTTAAAATC-GCTAAAA-ACATCCTCAAGA-AAGGTTATAAAATCTCTAAAAATATCCTTAAAA
176345 GAGG
63 GAGG
* * *
176349 CTTTTAAAATCGCTAAAAA-ATTCTCAGGAAAGGCTTATAAAATCTCTGAAAAATATCCTCAAGA
1 -TTTTAAAATCGCTAAAAACATCCTCAAGAAAGG-TTATAAAATCTCT-AAAAATATCCTTAA-A
176413 A-AGG
62 AGAGG
* * ** * *
176417 TTTTAACATCTCTAAAAACATCCTCAAGAGTGGTTTTAAAATCCCTAAAAATATCCTTAAAAGAG
1 TTTTAAAATCGCTAAAAACATCCTCAAGAAAGGTTATAAAATCTCTAAAAATATCCTTAAAAGAG
176482 G
66 G
* * * *
176483 TTTTTGAATTCTCTAAAAACATCCTCTAAAAAAGG
1 -TTTTAAAATCGCTAAAAACATCCTC-AAGAAAGG
176518 CTTAATGATT
Statistics
Matches: 378, Mismatches: 108, Indels: 57
0.70 0.20 0.10
Matches are distributed among these distances:
65 2 0.01
66 19 0.05
67 70 0.19
68 76 0.20
69 113 0.30
70 71 0.19
71 25 0.07
72 2 0.01
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.30
Consensus pattern (66 bp):
TTTTAAAATCGCTAAAAACATCCTCAAGAAAGGTTATAAAATCTCTAAAAATATCCTTAAAAGAG
G
Found at i:178514 original size:16 final size:16
Alignment explanation
Indices: 178495--178534 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
178485 CAGTTTTCAT
*
178495 ATTTTTCTTTTTTTTA
1 ATTTTTCATTTTTTTA
*
178511 A-TTTTCATTTTTTTC
1 ATTTTTCATTTTTTTA
178526 ATTTTTCAT
1 ATTTTTCAT
178535 GTACAATTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (16 bp):
ATTTTTCATTTTTTTA
Found at i:189416 original size:20 final size:19
Alignment explanation
Indices: 189370--189423 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 19
189360 AAAACCCTGA
189370 AAAGTATCGATACACATTT
1 AAAGTATCGATACACATTT
*
189389 AAATGTATCGATACAGA-TT
1 AAA-GTATCGATACACATTT
189408 ACACAGTATCGATACA
1 A-A-AGTATCGATACA
189424 TTGTATCGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
19 6 0.19
20 24 0.77
21 1 0.03
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.28
Consensus pattern (19 bp):
AAAGTATCGATACACATTT
Found at i:189568 original size:33 final size:32
Alignment explanation
Indices: 189510--189577 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
189500 GTAGCCAACT
*
189510 TTGTATCGATACTCACAATATGTATCGATACA
1 TTGTATCGATACTCACAAAATGTATCGATACA
* *
189542 TTGTGTCGATACATCCCAAAATGTATCGATACA
1 TTGTATCGATAC-TCACAAAATGTATCGATACA
189575 TTG
1 TTG
189578 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 11 0.34
33 21 0.66
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (32 bp):
TTGTATCGATACTCACAAAATGTATCGATACA
Found at i:195732 original size:13 final size:13
Alignment explanation
Indices: 195714--195777 Score: 110
Period size: 13 Copynumber: 4.9 Consensus size: 13
195704 CAGCATTCTC
*
195714 TGTATCGATACAT
1 TGTATCGATACAG
195727 TGTATCGATACAG
1 TGTATCGATACAG
*
195740 TGTATCGATACAT
1 TGTATCGATACAG
195753 TGTATCGATACAG
1 TGTATCGATACAG
195766 TGTATCGATACA
1 TGTATCGATACA
195778 AAGGGTTTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 48 1.00
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:195750 original size:26 final size:26
Alignment explanation
Indices: 195714--195777 Score: 128
Period size: 26 Copynumber: 2.5 Consensus size: 26
195704 CAGCATTCTC
195714 TGTATCGATACATTGTATCGATACAG
1 TGTATCGATACATTGTATCGATACAG
195740 TGTATCGATACATTGTATCGATACAG
1 TGTATCGATACATTGTATCGATACAG
195766 TGTATCGATACA
1 TGTATCGATACA
195778 AAGGGTTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (26 bp):
TGTATCGATACATTGTATCGATACAG
Found at i:198235 original size:20 final size:21
Alignment explanation
Indices: 198186--198241 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
198176 GTCAAAACCC
198186 TAAA-AGTATCGATACACATT
1 TAAATAGTATCGATACACATT
*
198206 TAAATA-TATCGATACAGA-T
1 TAAATAGTATCGATACACATT
**
198225 TGCATAGTATCGATACA
1 TAAATAGTATCGATACA
198242 TTGTATCGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 5 0.16
20 25 0.81
21 1 0.03
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.30
Consensus pattern (21 bp):
TAAATAGTATCGATACACATT
Found at i:198249 original size:13 final size:13
Alignment explanation
Indices: 198231--198255 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
198221 AGATTGCATA
198231 GTATCGATACATT
1 GTATCGATACATT
198244 GTATCGATACAT
1 GTATCGATACAT
198256 GACCAAATGT
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):
GTATCGATACATT
Found at i:198268 original size:20 final size:22
Alignment explanation
Indices: 198243--198295 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
198233 ATCGATACAT
**
198243 TGTATCGATACAT-GACCA-AA
1 TGTATCGATACATCGAAAAGAA
198263 TGTATCGATAC-TCGAAAAGAA
1 TGTATCGATACATCGAAAAGAA
198284 TGTATCGATACA
1 TGTATCGATACA
198296 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 1 0.04
20 14 0.50
21 13 0.46
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (22 bp):
TGTATCGATACATCGAAAAGAA
Found at i:198353 original size:19 final size:20
Alignment explanation
Indices: 198329--198377 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
198319 TAGCCAAATT
*
198329 TGTATCGATACA-CACAATA
1 TGTATCGATACATCACAAAA
* *
198348 TGTATCAATACATCCCAAAA
1 TGTATCGATACATCACAAAA
198368 TGTATCGATA
1 TGTATCGATA
198378 TATTGGCTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (20 bp):
TGTATCGATACATCACAAAA
Found at i:198372 original size:20 final size:19
Alignment explanation
Indices: 198329--198373 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
198319 TAGCCAAATT
* *
198329 TGTATCGATACACACAATA
1 TGTATCAATACACACAAAA
*
198348 TGTATCAATACATCCCAAAA
1 TGTATCAATACA-CACAAAA
198368 TGTATC
1 TGTATC
198374 GATATATTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.29
Consensus pattern (19 bp):
TGTATCAATACACACAAAA
Found at i:205495 original size:25 final size:26
Alignment explanation
Indices: 205451--205503 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
205441 ATTTTTAGAT
205451 TTGACAAAGGGGGAGAAATGCTTTGA
1 TTGACAAAGGGGGAGAAATGCTTTGA
205477 TTGACAAAGGGGGAG-AATGCTTTGA
1 TTGACAAAGGGGGAGAAATGCTTTGA
205502 TT
1 TT
205504 AAAGGGGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 12 0.44
26 15 0.56
ACGTcount: A:0.32, C:0.08, G:0.34, T:0.26
Consensus pattern (26 bp):
TTGACAAAGGGGGAGAAATGCTTTGA
Found at i:205510 original size:21 final size:23
Alignment explanation
Indices: 205456--205514 Score: 77
Period size: 25 Copynumber: 2.5 Consensus size: 23
205446 TAGATTTGAC
205456 AAAGGGGGAGAAATGCTTTGATTGA
1 AAAGGGGGAG-AATGCTTTGATT-A
205481 CAAAGGGGGAGAATGCTTTGATT-
1 -AAAGGGGGAGAATGCTTTGATTA
205504 AAA-GGGGAGAA
1 AAAGGGGGAGAA
205515 ATTTTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
21 8 0.24
22 3 0.09
25 12 0.36
26 10 0.30
ACGTcount: A:0.37, C:0.05, G:0.37, T:0.20
Consensus pattern (23 bp):
AAAGGGGGAGAATGCTTTGATTA
Found at i:206246 original size:13 final size:13
Alignment explanation
Indices: 206225--206255 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
206215 CGATACATGG
*
206225 TACAATGTATCGA
1 TACATTGTATCGA
206238 TACATTGTATCGA
1 TACATTGTATCGA
206251 TACAT
1 TACAT
206256 GAGGAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:206251 original size:33 final size:33
Alignment explanation
Indices: 206209--206277 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
206199 CTACCACTGT
*
206209 TTGTATCGATACATG-GTACAATGTATCGATACA
1 TTGTATCGATACATGAGGA-AATGTATCGATACA
*
206242 TTGTATCGATACATGAGGAATTGTATCGATACA
1 TTGTATCGATACATGAGGAAATGTATCGATACA
206275 TTG
1 TTG
206278 CTTGTAACAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 31 0.94
34 2 0.06
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (33 bp):
TTGTATCGATACATGAGGAAATGTATCGATACA
Found at i:208257 original size:17 final size:17
Alignment explanation
Indices: 208216--208262 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 17
208206 AACTCCTTAT
208216 TTATCTCAATAAATAATA
1 TTATCT-AATAAATAATA
208234 TTAATCTAATAAA-AATAA
1 TT-ATCTAATAAATAAT-A
208252 TTATCTAATAA
1 TTATCTAATAA
208263 TTATAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 12 0.44
18 11 0.41
19 4 0.15
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (17 bp):
TTATCTAATAAATAATA
Done.