Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold242
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: 704627
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.32
Warning! 37713 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:241 original size:13 final size:13
Alignment explanation
Indices: 223--247 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
213 ATCAAATTTG
223 TATGTACTCTTTA
1 TATGTACTCTTTA
236 TATGTACTCTTT
1 TATGTACTCTTT
248 CACTAATAAA
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:0.20, C:0.16, G:0.08, T:0.56
Consensus pattern (13 bp):
TATGTACTCTTTA
Found at i:267 original size:51 final size:52
Alignment explanation
Indices: 212--317 Score: 151
Period size: 52 Copynumber: 2.1 Consensus size: 52
202 TATATATTAG
** * *
212 TATCAAATTTGTAT-GTACTCTTTATATGTACTCTTTCACTAATAAATTATA
1 TATCAAATTTGTATCAAAATCTTTATATGTACGCTTTCACTAATAAATTATA
* *
263 TATCAAATTTGTATCAAAATTTTTTTATGTACGCTTTCACTAATAAATTATA
1 TATCAAATTTGTATCAAAATCTTTATATGTACGCTTTCACTAATAAATTATA
315 TAT
1 TAT
318 TAGTAAAAAG
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
51 14 0.29
52 34 0.71
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (52 bp):
TATCAAATTTGTATCAAAATCTTTATATGTACGCTTTCACTAATAAATTATA
Found at i:17324 original size:32 final size:32
Alignment explanation
Indices: 17255--17324 Score: 92
Period size: 31 Copynumber: 2.2 Consensus size: 32
17245 ATGTTTGAAA
* *
17255 TGTT-ACATTTTAGTCACTTATGTTATTGTGT
1 TGTTAACATTTTAGTCACTGATGTTAATGTGT
17286 TG-TAACATTTTAGTCACTGAGTGTTAAT-TGT
1 TGTTAACATTTTAGTCACTGA-TGTTAATGTGT
17317 TGTTAACA
1 TGTTAACA
17325 GTGTAACGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 1 0.03
31 22 0.65
32 11 0.32
ACGTcount: A:0.24, C:0.10, G:0.17, T:0.49
Consensus pattern (32 bp):
TGTTAACATTTTAGTCACTGATGTTAATGTGT
Found at i:17473 original size:19 final size:19
Alignment explanation
Indices: 17438--17480 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
17428 CTTTTTTTTA
*
17438 TTTTTTTTTGTACTTTC-T
1 TTTTTTTTTCTACTTTCAT
*
17456 TTTTTTTTCTCTATTTTCAT
1 TTTTTTTT-TCTACTTTCAT
17476 TTTTT
1 TTTTT
17481 CTCTATGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 8 0.38
19 7 0.33
20 6 0.29
ACGTcount: A:0.07, C:0.12, G:0.02, T:0.79
Consensus pattern (19 bp):
TTTTTTTTTCTACTTTCAT
Found at i:27728 original size:21 final size:21
Alignment explanation
Indices: 27702--27773 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
27692 GCTCGTAAGC
27702 TGAACAGAAACTCTTAAGAGT
1 TGAACAGAAACTCTTAAGAGT
* * * *
27723 TGAACAGAAGCTCATAATAGC
1 TGAACAGAAACTCTTAAGAGT
27744 TGAACAGAAACTCTTAAGAGT
1 TGAACAGAAACTCTTAAGAGT
*
27765 TGAATAGAA
1 TGAACAGAA
27774 GCTCATAGCT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.44, C:0.14, G:0.19, T:0.22
Consensus pattern (21 bp):
TGAACAGAAACTCTTAAGAGT
Found at i:27751 original size:42 final size:41
Alignment explanation
Indices: 27685--27780 Score: 158
Period size: 42 Copynumber: 2.3 Consensus size: 41
27675 GTACATCGTT
*
27685 AACAGAAGCTCGT-AAGCTGAACAGAAACTCTTAAGAGTTG
1 AACAGAAGCTCATAAAGCTGAACAGAAACTCTTAAGAGTTG
27725 AACAGAAGCTCATAATAGCTGAACAGAAACTCTTAAGAGTTG
1 AACAGAAGCTCATAA-AGCTGAACAGAAACTCTTAAGAGTTG
*
27767 AATAGAAGCTCATA
1 AACAGAAGCTCATA
27781 GCTAAACGGA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
40 12 0.23
41 1 0.02
42 39 0.75
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.21
Consensus pattern (41 bp):
AACAGAAGCTCATAAAGCTGAACAGAAACTCTTAAGAGTTG
Found at i:27849 original size:21 final size:21
Alignment explanation
Indices: 27825--27907 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
27815 TGAACGAAAA
*
27825 CTCATAAGAGTTTAACAGAAG
1 CTCATAAGAGTTAAACAGAAG
* * *
27846 CTCA-ATAGAGTTGAACGGAAA
1 CTCATA-AGAGTTAAACAGAAG
**
27867 CTCATTTGAGTTAAACAGAAG
1 CTCATAAGAGTTAAACAGAAG
* *
27888 CTCGTAAGAGCTAAACAGAA
1 CTCATAAGAGTTAAACAGAA
27908 AGTAAAACAC
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
20 1 0.02
21 47 0.98
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.22
Consensus pattern (21 bp):
CTCATAAGAGTTAAACAGAAG
Found at i:27878 original size:42 final size:42
Alignment explanation
Indices: 27810--27890 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
27800 TAAACTCGTA
*
27810 AGAGCTGAACGAAAACTCATAAGAGTTTAACAGAAGCTCAAT
1 AGAGCTGAACGAAAACTCATAAGAGTTAAACAGAAGCTCAAT
* * **
27852 AGAGTTGAACGGAAACTCATTTGAGTTAAACAGAAGCTC
1 AGAGCTGAACGAAAACTCATAAGAGTTAAACAGAAGCTC
27891 GTAAGAGCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.21
Consensus pattern (42 bp):
AGAGCTGAACGAAAACTCATAAGAGTTAAACAGAAGCTCAAT
Found at i:30761 original size:17 final size:16
Alignment explanation
Indices: 30737--30772 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
30727 TTCAATATTA
*
30737 GTTTTAGTTTATTTTT
1 GTTTTAGTTCATTTTT
30753 GTTTCTAGTTCATTTTT
1 GTTT-TAGTTCATTTTT
30770 GTT
1 GTT
30773 AATTGTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.11, C:0.06, G:0.14, T:0.69
Consensus pattern (16 bp):
GTTTTAGTTCATTTTT
Found at i:31733 original size:33 final size:34
Alignment explanation
Indices: 31677--31742 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 34
31667 ATTTATGATC
31677 TCAGTGATAAAAATTTATTTATTGCCTTCTTTCT
1 TCAGTGATAAAAATTTATTTATTGCCTTCTTTCT
31711 TCAGTGATAAAAA-TTATTTATTGCCTTCTTTC
1 TCAGTGATAAAAATTTATTTATTGCCTTCTTTC
31743 ACTGACTTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 19 0.59
34 13 0.41
ACGTcount: A:0.27, C:0.15, G:0.09, T:0.48
Consensus pattern (34 bp):
TCAGTGATAAAAATTTATTTATTGCCTTCTTTCT
Found at i:33370 original size:2 final size:2
Alignment explanation
Indices: 33359--33391 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
33349 ACACATGCAC
33359 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33392 TATTCCTCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:33493 original size:9 final size:9
Alignment explanation
Indices: 33479--33507 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
33469 AATTTACTTG
33479 TTCAGAATT
1 TTCAGAATT
33488 TTCAGAATT
1 TTCAGAATT
33497 TTCAGAATT
1 TTCAGAATT
33506 TT
1 TT
33508 TGGTTCAGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.48
Consensus pattern (9 bp):
TTCAGAATT
Found at i:45552 original size:73 final size:71
Alignment explanation
Indices: 45461--45596 Score: 236
Period size: 73 Copynumber: 1.9 Consensus size: 71
45451 ACCAAAAACT
* *
45461 AAAGACAACATTTTAAGTCAAAAGAAAGGTTTGGCTTAGAGATCAAAAATCAAAATAAATATAAC
1 AAAGAAAACATTTTAAGTCAAAA-AAAGGTTTGACTTAGAGAT-AAAAATCAAAATAAATATAAC
45526 TGCCAAAA
64 TGCCAAAA
45534 AAAGAAAACATTTTAAGTCAAAAAAAGGTTTGACTTAGAGATAAAAATCAAAATAAATATAAC
1 AAAGAAAACATTTTAAGTCAAAAAAAGGTTTGACTTAGAGATAAAAATCAAAATAAATATAAC
45597 ACTGAAGATA
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
71 21 0.34
72 18 0.30
73 22 0.36
ACGTcount: A:0.54, C:0.10, G:0.12, T:0.23
Consensus pattern (71 bp):
AAAGAAAACATTTTAAGTCAAAAAAAGGTTTGACTTAGAGATAAAAATCAAAATAAATATAACTG
CCAAAA
Found at i:47634 original size:27 final size:27
Alignment explanation
Indices: 47604--47663 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
47594 AAAATATATA
*
47604 TTTATA-ATATTTTA-ATGTTTAATAATT
1 TTTATACAT-TTTTATATGTTGAA-AATT
*
47631 TTTATACATTTTTATTTGTTGAAAATT
1 TTTATACATTTTTATATGTTGAAAATT
47658 TTTATA
1 TTTATA
47664 TAATCATCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 21 0.72
28 8 0.28
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (27 bp):
TTTATACATTTTTATATGTTGAAAATT
Found at i:52036 original size:1 final size:1
Alignment explanation
Indices: 52030--52055 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
52020 GGTAAACCTT
52030 CCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCC
52056 AAAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:75593 original size:17 final size:18
Alignment explanation
Indices: 75565--75600 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
75555 TTACCAATTG
75565 CTTTCATCCCCCCCCCCC
1 CTTTCATCCCCCCCCCCC
75583 CTTTC-TCCCCCCCCCCC
1 CTTTCATCCCCCCCCCCC
75600 C
1 C
75601 CCTCTCTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.03, C:0.75, G:0.00, T:0.22
Consensus pattern (18 bp):
CTTTCATCCCCCCCCCCC
Found at i:75606 original size:17 final size:17
Alignment explanation
Indices: 75571--75606 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
75561 ATTGCTTTCA
**
75571 TCCCCCCCCCCCCTTTC
1 TCCCCCCCCCCCCCCTC
75588 TCCCCCCCCCCCCCCTC
1 TCCCCCCCCCCCCCCTC
75605 TC
1 TC
75607 TCTCTCTCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.81, G:0.00, T:0.19
Consensus pattern (17 bp):
TCCCCCCCCCCCCCCTC
Found at i:75610 original size:21 final size:19
Alignment explanation
Indices: 75572--75608 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
75562 TTGCTTTCAT
75572 CCCCCCCCCCCCTTTCTCC
1 CCCCCCCCCCCCTTTCTCC
*
75591 CCCCCCCCCCCCTCTCTC
1 CCCCCCCCCCCCTTTCTC
75609 TCTCTCTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.00, C:0.81, G:0.00, T:0.19
Consensus pattern (19 bp):
CCCCCCCCCCCCTTTCTCC
Found at i:79211 original size:51 final size:51
Alignment explanation
Indices: 79155--79262 Score: 139
Period size: 51 Copynumber: 2.1 Consensus size: 51
79145 TCATTTTCAA
* *
79155 TTTCATTTTGGAGAAAACC-ATATTCATTTTCAAATAATT-CCATTTCTCCAT
1 TTTCATTTTGGAG-AAACCGATAATCATTTCCAAAT-ATTACCATTTCTCCAT
* *
79206 TTTCATTTTGGAGAAACCGATAATCATTTCCAAATGTTACCCATTTCTTCAT
1 TTTCATTTTGGAGAAACCGATAATCATTTCCAAATATTA-CCATTTCTCCAT
79258 TTTCA
1 TTTCA
79263 CCATTTCTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
50 7 0.14
51 27 0.54
52 16 0.32
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (51 bp):
TTTCATTTTGGAGAAACCGATAATCATTTCCAAATATTACCATTTCTCCAT
Found at i:82243 original size:20 final size:21
Alignment explanation
Indices: 82218--82256 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
82208 CTGACTTCTA
*
82218 CTTT-AAAAATTAATTTGGCT
1 CTTTAAAAAAATAATTTGGCT
82238 CTTTAAAAAAATAATTTGG
1 CTTTAAAAAAATAATTTGG
82257 ATTTTTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (21 bp):
CTTTAAAAAAATAATTTGGCT
Found at i:82263 original size:21 final size:21
Alignment explanation
Indices: 82218--82264 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
82208 CTGACTTCTA
* *
82218 CTTT-AAAAATTAATTTGGCT
1 CTTTAAAAAAATAATTTGGAT
82238 CTTTAAAAAAATAATTTGGAT
1 CTTTAAAAAAATAATTTGGAT
*
82259 TTTTAA
1 CTTTAA
82265 TTTATCAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (21 bp):
CTTTAAAAAAATAATTTGGAT
Found at i:94148 original size:16 final size:15
Alignment explanation
Indices: 94099--94150 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
94089 GAAAATTTAT
*
94099 ATTTTCCATCTTTCT
1 ATTTTCCATCTTTCA
* *
94114 ATATTTCTATCCCTTCA
1 AT-TTTCCAT-CTTTCA
94131 ATTTTCCATCTTTCCA
1 ATTTTCCATCTTT-CA
94147 ATTT
1 ATTT
94151 CCTTTCCACC
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
15 5 0.17
16 18 0.62
17 6 0.21
ACGTcount: A:0.19, C:0.27, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTTTCCATCTTTCA
Found at i:109126 original size:41 final size:40
Alignment explanation
Indices: 109025--109129 Score: 101
Period size: 41 Copynumber: 2.6 Consensus size: 40
109015 AGTTCGAAGC
*
109025 AATAGTTGACACCCAGTGTCTCATCG-ACAAAGCCGAAGAA
1 AATAG-TGACACCCAGTGTCTCATCGAACAAACCCGAAGAA
** ** *
109065 AAT--TGGTACCCAGTACCTCATCGAATC-TACCCGAAGAA
1 AATAGTGACACCCAGTGTCTCATCGAA-CAAACCCGAAGAA
109103 ATATAGTGACACCCAGTGTCTCATCGA
1 A-ATAGTGACACCCAGTGTCTCATCGA
109130 CTCGAGGTCG
Statistics
Matches: 50, Mismatches: 10, Indels: 9
0.72 0.14 0.13
Matches are distributed among these distances:
37 16 0.32
38 11 0.22
39 3 0.06
40 3 0.06
41 17 0.34
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (40 bp):
AATAGTGACACCCAGTGTCTCATCGAACAAACCCGAAGAA
Found at i:110748 original size:142 final size:142
Alignment explanation
Indices: 110492--110775 Score: 568
Period size: 142 Copynumber: 2.0 Consensus size: 142
110482 GTCATTACAT
110492 AGGGACTAAATCGAAGACTTAAAAAATTTTTCGAAAAATATTTAAAATTTTCAACACTGCAGGGG
1 AGGGACTAAATCGAAGACTTAAAAAATTTTTCGAAAAATATTTAAAATTTTCAACACTGCAGGGG
110557 TCACATGGCCATGTCTCAGCCAGTGTCCATGCCCGTATAAGTATACTGACTTGGGTTACATGGCC
66 TCACATGGCCATGTCTCAGCCAGTGTCCATGCCCGTATAAGTATACTGACTTGGGTTACATGGCC
110622 AAGTCACACACC
131 AAGTCACACACC
110634 AGGGACTAAATCGAAGACTTAAAAAATTTTTCGAAAAATATTTAAAATTTTCAACACTGCAGGGG
1 AGGGACTAAATCGAAGACTTAAAAAATTTTTCGAAAAATATTTAAAATTTTCAACACTGCAGGGG
110699 TCACATGGCCATGTCTCAGCCAGTGTCCATGCCCGTATAAGTATACTGACTTGGGTTACATGGCC
66 TCACATGGCCATGTCTCAGCCAGTGTCCATGCCCGTATAAGTATACTGACTTGGGTTACATGGCC
110764 AAGTCACACACC
131 AAGTCACACACC
110776 CCTATGTTAG
Statistics
Matches: 142, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
142 142 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (142 bp):
AGGGACTAAATCGAAGACTTAAAAAATTTTTCGAAAAATATTTAAAATTTTCAACACTGCAGGGG
TCACATGGCCATGTCTCAGCCAGTGTCCATGCCCGTATAAGTATACTGACTTGGGTTACATGGCC
AAGTCACACACC
Found at i:112110 original size:33 final size:33
Alignment explanation
Indices: 112073--112215 Score: 117
Period size: 33 Copynumber: 4.3 Consensus size: 33
112063 TGGTCCAACC
*
112073 ATGGTCTTACGTTCATAGTGCCATAACCCAGTT
1 ATGGTCTTACGTTCATAGTGCCATAACCCAGCT
** * *
112106 ATGGTCTTATC-ACCAGAATGCCATAACCCAGCT
1 ATGGTCTTA-CGTTCATAGTGCCATAACCCAGCT
* * * * *** * *
112139 ATGGTCTTACATATAAACACTGCCATGGTCCAACC
1 ATGGTCTTACGT-T-CATAGTGCCATAACCCAGCT
*
112174 ATGGTCTTACGTTCATAGTGCCATAACCCAGTT
1 ATGGTCTTACGTTCATAGTGCCATAACCCAGCT
112207 ATGGTCTTA
1 ATGGTCTTA
112216 TCCGTCAATT
Statistics
Matches: 81, Mismatches: 25, Indels: 8
0.71 0.22 0.07
Matches are distributed among these distances:
32 1 0.01
33 55 0.68
34 2 0.02
35 23 0.28
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (33 bp):
ATGGTCTTACGTTCATAGTGCCATAACCCAGCT
Found at i:112162 original size:101 final size:101
Alignment explanation
Indices: 111978--112217 Score: 401
Period size: 101 Copynumber: 2.4 Consensus size: 101
111968 AATTCATCCT
* * * *
111978 TTACATTCGTAGTGCCATAACCCAGTTATGGTCTTTTCATCAGAATGCCATAGACCAACTATGAT
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCACCAGAATGCCATAGACCAACTATGAT
*
112043 CTTACATATAACCACTGCCATGGTCCAACCATGGTC
66 CTTACATATAAACACTGCCATGGTCCAACCATGGTC
* *
112079 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCACCAGAATGCCATA-ACCCAGCTATGG
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCACCAGAATGCCATAGA-CCAACTATGA
112143 TCTTACATATAAACACTGCCATGGTCCAACCATGGTC
65 TCTTACATATAAACACTGCCATGGTCCAACCATGGTC
112180 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATC
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATC
112218 CGTCAATTCA
Statistics
Matches: 131, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
100 1 0.01
101 130 0.99
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (101 bp):
TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCACCAGAATGCCATAGACCAACTATGAT
CTTACATATAAACACTGCCATGGTCCAACCATGGTC
Found at i:114456 original size:22 final size:22
Alignment explanation
Indices: 114411--114456 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
114401 TAATATAGAC
* *
114411 TTAATAGATGCAGGAAAATATT
1 TTAATAGATGAAAGAAAATATT
114433 TTAATAGATGAAAAGAAAAT-TT
1 TTAATAGATG-AAAGAAAATATT
114455 TT
1 TT
114457 GAACTACTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.48, C:0.02, G:0.15, T:0.35
Consensus pattern (22 bp):
TTAATAGATGAAAGAAAATATT
Found at i:120737 original size:21 final size:22
Alignment explanation
Indices: 120713--120768 Score: 73
Period size: 21 Copynumber: 2.6 Consensus size: 22
120703 AATATTTTTC
*
120713 TCATAAAATTTATTTAAAAA-A
1 TCATAAAAATTATTTAAAAATA
120734 TCATAAAAAATTA-TTAAAAATA
1 TCAT-AAAAATTATTTAAAAATA
120756 T-ATAAAAATTATT
1 TCATAAAAATTATT
120769 AAATATTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 8 0.26
21 14 0.45
22 9 0.29
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.38
Consensus pattern (22 bp):
TCATAAAAATTATTTAAAAATA
Found at i:120754 original size:20 final size:20
Alignment explanation
Indices: 120715--120771 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
120705 TATTTTTCTC
*
120715 ATAAAATTTATTTAAAAA-AT
1 ATAAAAATTA-TTAAAAATAT
120735 CATAAAAAATTATTAAAAATAT
1 -AT-AAAAATTATTAAAAATAT
120757 ATAAAAATTATTAAA
1 ATAAAAATTATTAAA
120772 TATTTTAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
20 13 0.39
21 11 0.33
22 9 0.27
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
ATAAAAATTATTAAAAATAT
Found at i:120771 original size:10 final size:10
Alignment explanation
Indices: 120729--120781 Score: 56
Period size: 10 Copynumber: 5.4 Consensus size: 10
120719 AATTTATTTA
* *
120729 AAAAATCATA
1 AAAAATTATT
120739 AAAAATTATT
1 AAAAATTATT
120749 AAAAA-TATAT
1 AAAAATTAT-T
120759 AAAAATTATT
1 AAAAATTATT
*
120769 AAATATT-TT
1 AAAAATTATT
120778 AAAA
1 AAAA
120782 TATGAAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
9 8 0.22
10 26 0.70
11 3 0.08
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (10 bp):
AAAAATTATT
Found at i:120910 original size:20 final size:20
Alignment explanation
Indices: 120885--120959 Score: 62
Period size: 20 Copynumber: 3.7 Consensus size: 20
120875 ACATGTCTAT
120885 AAAAATCATAAAAATTATAA
1 AAAAATCATAAAAATTATAA
* * *
120905 AAAAATTATTAAAATTGGT-A
1 AAAAATCATAAAAATT-ATAA
* * * *
120925 TAAACTTATACAAATTATAAA
1 AAAAATCATAAAAATTAT-AA
120946 AAAAATCATAAAAA
1 AAAAATCATAAAAA
120960 CTTGAAGTGG
Statistics
Matches: 40, Mismatches: 12, Indels: 5
0.70 0.21 0.09
Matches are distributed among these distances:
19 1 0.03
20 27 0.68
21 12 0.30
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (20 bp):
AAAAATCATAAAAATTATAA
Found at i:121087 original size:8 final size:8
Alignment explanation
Indices: 121074--121116 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
121064 TGAACCAATT
121074 TTTTTTAA
1 TTTTTTAA
121082 TTTTTTAA
1 TTTTTTAA
121090 TTTTTTAA
1 TTTTTTAA
*
121098 TATTTTAA
1 TTTTTTAA
* *
121106 TATTTTGA
1 TTTTTTAA
121114 TTT
1 TTT
121117 ATTATGTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (8 bp):
TTTTTTAA
Found at i:121483 original size:19 final size:18
Alignment explanation
Indices: 121418--121483 Score: 55
Period size: 17 Copynumber: 3.6 Consensus size: 18
121408 AGTTTATATC
*
121418 AATTTAAATATTTTTAT-
1 AATTTAAATATTTTTTTA
*
121435 AATGTTACAT-TTTTTTTA
1 AAT-TTAAATATTTTTTTA
*
121453 AGAATTACAATATGTTTTTTA
1 A-ATTTA-AATAT-TTTTTTA
121474 AATTTAAATA
1 AATTTAAATA
121484 AGTTTTATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
17 9 0.24
18 9 0.24
19 7 0.18
20 5 0.13
21 8 0.21
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (18 bp):
AATTTAAATATTTTTTTA
Found at i:121488 original size:19 final size:21
Alignment explanation
Indices: 121446--121494 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
121436 ATGTTACATT
*
121446 TTTTTTAAGAATTACAATATG
1 TTTTTTAAGAATTACAATAAG
*
121467 TTTTTTAA-ATTTA-AATAAG
1 TTTTTTAAGAATTACAATAAG
121486 TTTTATTAA
1 TTTT-TTAA
121495 TNNNNNNNNN
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 9 0.36
20 8 0.32
21 8 0.32
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (21 bp):
TTTTTTAAGAATTACAATAAG
Found at i:121679 original size:9 final size:9
Alignment explanation
Indices: 121667--121697 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
121657 AATTTTATTT
121667 TTTTAAATA
1 TTTTAAATA
121676 TTTTAAATA
1 TTTTAAATA
121685 TTTTAAATA
1 TTTTAAATA
121694 TTTT
1 TTTT
121698 TGATGATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
TTTTAAATA
Found at i:121689 original size:34 final size:36
Alignment explanation
Indices: 121630--121697 Score: 90
Period size: 35 Copynumber: 1.9 Consensus size: 36
121620 NNNNNNNNTA
121630 TTTTTTATAATTTATTAGAATTTTTAAA-ATTTTAT
1 TTTTTTATAATTTATTAGAATTTTTAAATATTTTAT
121665 TTTTTTA-AATATT-TTA-AATATTTTAAATATTTT
1 TTTTTTATAAT-TTATTAGAAT-TTTTAAATATTTT
121698 TGATGATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
33 3 0.10
34 13 0.43
35 14 0.47
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.63
Consensus pattern (36 bp):
TTTTTTATAATTTATTAGAATTTTTAAATATTTTAT
Found at i:139595 original size:55 final size:55
Alignment explanation
Indices: 139511--139621 Score: 186
Period size: 55 Copynumber: 2.0 Consensus size: 55
139501 CGTTTAACCC
* * *
139511 TAATGGGTTTTAGTTCAACTCTTTTGAGCTTCGGTTTAACCCTTATGGGTTTCCG
1 TAATGAGTTTCAGTTCAACTCTTTTGAGCTTCAGTTTAACCCTTATGGGTTTCCG
*
139566 TAATGAGTTTCAGTTCAGCTCTTTTGAGCTTCAGTTTAACCCTTATGGGTTTCCG
1 TAATGAGTTTCAGTTCAACTCTTTTGAGCTTCAGTTTAACCCTTATGGGTTTCCG
139621 T
1 T
139622 TCAGCTCTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.43
Consensus pattern (55 bp):
TAATGAGTTTCAGTTCAACTCTTTTGAGCTTCAGTTTAACCCTTATGGGTTTCCG
Found at i:139598 original size:21 final size:21
Alignment explanation
Indices: 139568--139654 Score: 75
Period size: 21 Copynumber: 4.1 Consensus size: 21
139558 GGTTTCCGTA
*
139568 ATGAGTTTCAGTTCAGCTCTT
1 ATGAGCTTCAGTTCAGCTCTT
* * * *
139589 TTGAGCTTCAGTTTAACCCTT
1 ATGAGCTTCAGTTCAGCTCTT
* * *
139610 ATGGGTTTCCGTTCAGCTCTT
1 ATGAGCTTCAGTTCAGCTCTT
* * *
139631 ATGAGCTTCTGTTCAACCCTT
1 ATGAGCTTCAGTTCAGCTCTT
139652 ATG
1 ATG
139655 GGTTTCCGTT
Statistics
Matches: 49, Mismatches: 17, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.41
Consensus pattern (21 bp):
ATGAGCTTCAGTTCAGCTCTT
Found at i:139636 original size:42 final size:42
Alignment explanation
Indices: 139572--139664 Score: 150
Period size: 42 Copynumber: 2.2 Consensus size: 42
139562 TCCGTAATGA
* * *
139572 GTTTCAGTTCAGCTCTTTTGAGCTTCAGTTTAACCCTTATGG
1 GTTTCCGTTCAGCTCTTATGAGCTTCAGTTCAACCCTTATGG
*
139614 GTTTCCGTTCAGCTCTTATGAGCTTCTGTTCAACCCTTATGG
1 GTTTCCGTTCAGCTCTTATGAGCTTCAGTTCAACCCTTATGG
139656 GTTTCCGTT
1 GTTTCCGTT
139665 TAGCACTTGT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (42 bp):
GTTTCCGTTCAGCTCTTATGAGCTTCAGTTCAACCCTTATGG
Found at i:139681 original size:42 final size:42
Alignment explanation
Indices: 139572--139684 Score: 145
Period size: 42 Copynumber: 2.7 Consensus size: 42
139562 TCCGTAATGA
* * * * *
139572 GTTTCAGTTCAGCTCTTTTGAGCTTCAGTTTAACCCTTATGG
1 GTTTCCGTTCAGCACTTATGAGCTTCTGTTCAACCCTTATGG
*
139614 GTTTCCGTTCAGCTCTTATGAGCTTCTGTTCAACCCTTATGG
1 GTTTCCGTTCAGCACTTATGAGCTTCTGTTCAACCCTTATGG
* * *
139656 GTTTCCGTTTAGCACTTGTGTGCTTCTGT
1 GTTTCCGTTCAGCACTTATGAGCTTCTGT
139685 GTAGCCTTCG
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.43
Consensus pattern (42 bp):
GTTTCCGTTCAGCACTTATGAGCTTCTGTTCAACCCTTATGG
Found at i:141146 original size:32 final size:32
Alignment explanation
Indices: 141100--141165 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
141090 ATGGTAGAGT
141100 ATGAAGCTTAAAATTATGTTAAACAACTTTTG
1 ATGAAGCTTAAAATTATGTTAAACAACTTTTG
*
141132 ATGAAGCTTGAAATTATGTTAAACAACTTTTG
1 ATGAAGCTTAAAATTATGTTAAACAACTTTTG
141164 AT
1 AT
141166 TTTTATGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (32 bp):
ATGAAGCTTAAAATTATGTTAAACAACTTTTG
Found at i:142891 original size:111 final size:111
Alignment explanation
Indices: 142725--142946 Score: 444
Period size: 111 Copynumber: 2.0 Consensus size: 111
142715 ATTATAAAAA
142725 TTTTATGGAAAGTATATATATGAGTCTAGTTTCAGGTAAAATTTATGGAGTTAAATTTCGAGTTC
1 TTTTATGGAAAGTATATATATGAGTCTAGTTTCAGGTAAAATTTATGGAGTTAAATTTCGAGTTC
142790 CGTAGATCGAGTTATAATTAATTTAGTAACTGCTGCGCGATTGGAC
66 CGTAGATCGAGTTATAATTAATTTAGTAACTGCTGCGCGATTGGAC
142836 TTTTATGGAAAGTATATATATGAGTCTAGTTTCAGGTAAAATTTATGGAGTTAAATTTCGAGTTC
1 TTTTATGGAAAGTATATATATGAGTCTAGTTTCAGGTAAAATTTATGGAGTTAAATTTCGAGTTC
142901 CGTAGATCGAGTTATAATTAATTTAGTAACTGCTGCGCGATTGGAC
66 CGTAGATCGAGTTATAATTAATTTAGTAACTGCTGCGCGATTGGAC
142947 AGCTTTGCTG
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 111 1.00
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.38
Consensus pattern (111 bp):
TTTTATGGAAAGTATATATATGAGTCTAGTTTCAGGTAAAATTTATGGAGTTAAATTTCGAGTTC
CGTAGATCGAGTTATAATTAATTTAGTAACTGCTGCGCGATTGGAC
Found at i:146343 original size:21 final size:22
Alignment explanation
Indices: 146310--146351 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
146300 TATTTTTGAA
* *
146310 ATTTTTATATTTTTTAATTTTG
1 ATTTTGATATTTTATAATTTTG
146332 ATTTTGAT-TTTTATAATTTT
1 ATTTTGATATTTTATAATTTT
146352 TGAATTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (22 bp):
ATTTTGATATTTTATAATTTTG
Found at i:146366 original size:28 final size:27
Alignment explanation
Indices: 146310--146366 Score: 62
Period size: 28 Copynumber: 2.0 Consensus size: 27
146300 TATTTTTGAA
* *
146310 ATTTTTATATTTTTTAATTTTGATTTTG
1 ATTTTTATATTTTTGAATTTT-ATATTG
146338 ATTTTTATAATTTTTGAATTATT-TATTG
1 ATTTTTAT-ATTTTTGAATT-TTATATTG
146366 A
1 A
146367 CGTGACAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
28 13 0.52
29 10 0.40
30 2 0.08
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (27 bp):
ATTTTTATATTTTTGAATTTTATATTG
Found at i:149335 original size:5 final size:5
Alignment explanation
Indices: 149327--149352 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
149317 AAGATGAAAT
149327 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
149353 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:149958 original size:30 final size:31
Alignment explanation
Indices: 149917--149977 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
149907 NNNNNNGGAG
* *
149917 GGGAGAGGAGTAAAAGTTTTGGGGGGAAAGT
1 GGGAGAGGAGTAAAAGTTTTGAGGGAAAAGT
149948 GGGA-AGGAGTAAAAGTTTTGAGGGAAAAGT
1 GGGAGAGGAGTAAAAGTTTTGAGGGAAAAGT
149978 AAAAAGGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.36, C:0.00, G:0.44, T:0.20
Consensus pattern (31 bp):
GGGAGAGGAGTAAAAGTTTTGAGGGAAAAGT
Found at i:150585 original size:14 final size:15
Alignment explanation
Indices: 150527--150587 Score: 54
Period size: 15 Copynumber: 4.1 Consensus size: 15
150517 ATAACTTAAG
*
150527 TTCATCATTTAATTT
1 TTCAACATTTAATTT
** *
150542 TTCAGTATTTATTTT
1 TTCAACATTTAATTT
*
150557 TTCAGACACTT-ATTT
1 TTCA-ACATTTAATTT
150572 TT-AACATTTAATTT
1 TTCAACATTTAATTT
150586 TT
1 TT
150588 TACTTATTCA
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
13 5 0.14
14 7 0.19
15 21 0.58
16 3 0.08
ACGTcount: A:0.26, C:0.11, G:0.03, T:0.59
Consensus pattern (15 bp):
TTCAACATTTAATTT
Found at i:154599 original size:23 final size:24
Alignment explanation
Indices: 154555--154600 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
154545 TAACTAAGCT
*
154555 TACTTACTTTTTTAGCTTATTTCA
1 TACTTACTTTTCTAGCTTATTTCA
154579 TACTT-CTTTTCTA-CTTAATTTC
1 TACTTACTTTTCTAGCTT-ATTTC
154601 TTACCATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 12 0.60
24 5 0.25
ACGTcount: A:0.20, C:0.20, G:0.02, T:0.59
Consensus pattern (24 bp):
TACTTACTTTTCTAGCTTATTTCA
Found at i:155009 original size:13 final size:13
Alignment explanation
Indices: 154991--155023 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
154981 CTTTCTCTGT
154991 TTCTTTTATGTTC
1 TTCTTTTATGTTC
155004 TTCTTTTATGTTC
1 TTCTTTTATGTTC
155017 TTCTTTT
1 TTCTTTT
155024 GTTTCTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.06, C:0.15, G:0.06, T:0.73
Consensus pattern (13 bp):
TTCTTTTATGTTC
Found at i:156716 original size:20 final size:20
Alignment explanation
Indices: 156691--156757 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
156681 CTGTTTAACC
156691 CTTATGGTTTCCGTTCAGCT
1 CTTATGGTTTCCGTTCAGCT
*
156711 CTTATGAGCTTCCGTTCA-CT
1 CTTATG-GTTTCCGTTCAGCT
* * *
156731 CTTATAGGTTTCTGTTTAGCA
1 CTTAT-GGTTTCCGTTCAGCT
156752 CTTATG
1 CTTATG
156758 TGCTTCTATT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 22 0.56
21 17 0.44
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (20 bp):
CTTATGGTTTCCGTTCAGCT
Found at i:156725 original size:21 final size:21
Alignment explanation
Indices: 156661--156735 Score: 73
Period size: 20 Copynumber: 3.7 Consensus size: 21
156651 AATGGGTTTT
* *
156661 CGTTGAGCTCTTTTGAGCTTC
1 CGTTCAGCTCTTATGAGCTTC
* * * * *
156682 TGTTTAACCCTTATG-GTTTC
1 CGTTCAGCTCTTATGAGCTTC
156702 CGTTCAGCTCTTATGAGCTTC
1 CGTTCAGCTCTTATGAGCTTC
156723 CGTTCA-CTCTTAT
1 CGTTCAGCTCTTAT
156736 AGGTTTCTGT
Statistics
Matches: 42, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
20 22 0.52
21 20 0.48
ACGTcount: A:0.13, C:0.25, G:0.17, T:0.44
Consensus pattern (21 bp):
CGTTCAGCTCTTATGAGCTTC
Found at i:156741 original size:41 final size:41
Alignment explanation
Indices: 156655--156763 Score: 112
Period size: 41 Copynumber: 2.7 Consensus size: 41
156645 AAACCTAATG
* * * *
156655 GGTTTTCGTTGAGCTCTTTTGAGCTTCTGTTTAACCCTTAT
1 GGTTTCCGTTCAGCTCTTATGAGCTTCCGTTTAACCCTTAT
* *
156696 GGTTTCCGTTCAGCTCTTATGAGCTTCCG-TTCACTCTTAT
1 GGTTTCCGTTCAGCTCTTATGAGCTTCCGTTTAACCCTTAT
* * * *
156736 AGGTTTCTGTTTAGCACTTATGTGCTTC
1 -GGTTTCCGTTCAGCTCTTATGAGCTTC
156764 TATTCAGCCT
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
40 9 0.16
41 48 0.84
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (41 bp):
GGTTTCCGTTCAGCTCTTATGAGCTTCCGTTTAACCCTTAT
Found at i:159509 original size:38 final size:38
Alignment explanation
Indices: 159409--159539 Score: 131
Period size: 38 Copynumber: 3.4 Consensus size: 38
159399 CCTTGAGTCA
* * *
159409 ATGAGACACTGGGTGTCACTATTTTACTTCGGATAGATTCG
1 ATGAGACACTGGGTGTCA--ACTTTACTTCGGCTAG-TCCG
* * *
159450 ATGAGATACTGGGTATC-ACTTTACTTCGGCTAGGCCG
1 ATGAGACACTGGGTGTCAACTTTACTTCGGCTAGTCCG
* *
159487 ATGAGACACTGGGTGTCAACTTTGCTTCGAACTA-TCCG
1 ATGAGACACTGGGTGTCAACTTTACTTCG-GCTAGTCCG
*
159525 ATGAGGCACTGGGTG
1 ATGAGACACTGGGTG
159540 CCAATCTGGT
Statistics
Matches: 76, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
37 17 0.22
38 41 0.54
39 3 0.04
41 15 0.20
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (38 bp):
ATGAGACACTGGGTGTCAACTTTACTTCGGCTAGTCCG
Found at i:162111 original size:16 final size:16
Alignment explanation
Indices: 162074--162113 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
162064 TTAATAAAAT
* *
162074 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
162090 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
162106 TAAAATTA
1 TAAAATTA
162114 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:162113 original size:22 final size:22
Alignment explanation
Indices: 162046--162098 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
162036 TAATTAAAAT
* * *
162046 TAAAATTAAAATTATTTTTTAA
1 TAAAATTAAAACTAATTGTTAA
*
162068 TAAAATTAAAACTAATTGTTAT
1 TAAAATTAAAACTAATTGTTAA
162090 TAAAATTAA
1 TAAAATTAA
162099 TTGTTAGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
TAAAATTAAAACTAATTGTTAA
Found at i:165947 original size:9 final size:9
Alignment explanation
Indices: 165933--165969 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
165923 TATAGTTTGA
165933 TATTCGAAT
1 TATTCGAAT
165942 TATTCGAAT
1 TATTCGAAT
*
165951 TATTCGAGT
1 TATTCGAAT
*
165960 TATTAGAAT
1 TATTCGAAT
165969 T
1 T
165970 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:177106 original size:18 final size:18
Alignment explanation
Indices: 177083--177149 Score: 98
Period size: 18 Copynumber: 3.7 Consensus size: 18
177073 TTTGGTTAAA
* *
177083 AATTAACCGAATTATCTG
1 AATTAACCGAATTACCCG
*
177101 AATTAACCGGATTACCCG
1 AATTAACCGAATTACCCG
*
177119 AATTAACTGAATTACCCG
1 AATTAACCGAATTACCCG
177137 AATTAACCGAATT
1 AATTAACCGAATT
177150 GAATCACTAC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.28
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:177114 original size:9 final size:9
Alignment explanation
Indices: 177083--177149 Score: 80
Period size: 9 Copynumber: 7.4 Consensus size: 9
177073 TTTGGTTAAA
177083 AATTAACCG
1 AATTAACCG
* *
177092 AATTATCTG
1 AATTAACCG
177101 AATTAACCG
1 AATTAACCG
* *
177110 GATTACCCG
1 AATTAACCG
*
177119 AATTAACTG
1 AATTAACCG
*
177128 AATTACCCG
1 AATTAACCG
177137 AATTAACCG
1 AATTAACCG
177146 AATT
1 AATT
177150 GAATCACTAC
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 46 1.00
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:177119 original size:27 final size:27
Alignment explanation
Indices: 177083--177149 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
177073 TTTGGTTAAA
*
177083 AATTAACCGAATTATCTGAATTAACCG
1 AATTAACCGAATTAACTGAATTAACCG
* * *
177110 GATTACCCGAATTAACTGAATTACCCG
1 AATTAACCGAATTAACTGAATTAACCG
177137 AATTAACCGAATT
1 AATTAACCGAATT
177150 GAATCACTAC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.28
Consensus pattern (27 bp):
AATTAACCGAATTAACTGAATTAACCG
Found at i:196346 original size:20 final size:19
Alignment explanation
Indices: 196294--196345 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
196284 TTTTAGAAAA
196294 TTTTA-AAATTTTTAACTT
1 TTTTATAAATTTTTAACTT
*
196312 TCTTTATATATTTTTAGA-TT
1 T-TTTATAAATTTTTA-ACTT
196332 TTTTATAAATTTTT
1 TTTTATAAATTTTT
196346 TTACAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 1 0.03
19 16 0.55
20 11 0.38
21 1 0.03
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (19 bp):
TTTTATAAATTTTTAACTT
Found at i:196382 original size:19 final size:19
Alignment explanation
Indices: 196358--196407 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
196348 ACAAATAAAT
196358 TTTTGAAATTTAAAAATTA
1 TTTTGAAATTTAAAAATTA
* * *
196377 TTTTGAATTTTTTAAAATTT
1 TTTTGAA-ATTTAAAAATTA
*
196397 TTTTAAAATTT
1 TTTTGAAATTT
196408 TTTTGTAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
TTTTGAAATTTAAAAATTA
Found at i:196420 original size:11 final size:11
Alignment explanation
Indices: 196384--196411 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
196374 TTATTTTGAA
196384 TTTTTTAAAAT
1 TTTTTTAAAAT
196395 TTTTTTAAAAT
1 TTTTTTAAAAT
196406 TTTTTT
1 TTTTTT
196412 GTAATTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTTTTAAAAT
Found at i:197031 original size:31 final size:31
Alignment explanation
Indices: 196996--197054 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
196986 ATATGTACAA
* *
196996 TTGAATCAAAA-CTAAAGTTTCATGTATACGT
1 TTGAACCAAAATC-AAAGTTCCATGTATACGT
*
197027 TTGAACCACAATCAAAGTTCCATGTATA
1 TTGAACCAAAATCAAAGTTCCATGTATA
197055 TAATTGCACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 23 0.96
32 1 0.04
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (31 bp):
TTGAACCAAAATCAAAGTTCCATGTATACGT
Found at i:198738 original size:25 final size:25
Alignment explanation
Indices: 198686--198756 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 25
198676 TTTTGTTTAA
*
198686 TTTACTTTTTGTAT-ATTTTTATA-CT
1 TTTA-TTTTT-TATAATTTTAATATCT
*
198711 TTTATTTTTATATAATTTTAATATTT
1 TTTATTTTT-TATAATTTTAATATCT
*
198737 TTTAGTTTTTATAATTTTAA
1 TTTATTTTTTATAATTTTAA
198757 AAGAAAATCA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.20
25 23 0.57
26 9 0.22
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.68
Consensus pattern (25 bp):
TTTATTTTTTATAATTTTAATATCT
Found at i:203207 original size:50 final size:50
Alignment explanation
Indices: 203136--203286 Score: 293
Period size: 50 Copynumber: 3.0 Consensus size: 50
203126 AGAACCTTAA
203136 TTTTTTGCTTATTCTTCTCTTTAATCTTTTTCATGGTGCAAGATACTAAT
1 TTTTTTGCTTATTCTTCTCTTTAATCTTTTTCATGGTGCAAGATACTAAT
203186 TTTTTTGCTTATTCTTCTCTTTAATCTTTTTCATGGTGCAAGATACTAAT
1 TTTTTTGCTTATTCTTCTCTTTAATCTTTTTCATGGTGCAAGATACTAAT
*
203236 TTTTTTGCTTATTCTTCTCTTTAATCTTTTTCATGGTGCAAGATTCTAAT
1 TTTTTTGCTTATTCTTCTCTTTAATCTTTTTCATGGTGCAAGATACTAAT
203286 T
1 T
203287 GAAACTCACA
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 100 1.00
ACGTcount: A:0.19, C:0.16, G:0.10, T:0.55
Consensus pattern (50 bp):
TTTTTTGCTTATTCTTCTCTTTAATCTTTTTCATGGTGCAAGATACTAAT
Found at i:206398 original size:15 final size:15
Alignment explanation
Indices: 206373--206407 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
206363 AACTCTATTT
*
206373 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
206387 TAATTAATATTAAGA
1 TAATTAATATTAAGA
206402 TAATTA
1 TAATTA
206408 TGAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:207083 original size:55 final size:56
Alignment explanation
Indices: 206998--207109 Score: 217
Period size: 55 Copynumber: 2.0 Consensus size: 56
206988 TAGAGTCAGG
206998 CTCCACTAAATCGAAAGTCTAAATCCTTGGAGCTGGTGGTCGTAGGCGTTCTCTTC
1 CTCCACTAAATCGAAAGTCTAAATCCTTGGAGCTGGTGGTCGTAGGCGTTCTCTTC
207054 CTCCAC-AAATCGAAAGTCTAAATCCTTGGAGCTGGTGGTCGTAGGCGTTCTCTTC
1 CTCCACTAAATCGAAAGTCTAAATCCTTGGAGCTGGTGGTCGTAGGCGTTCTCTTC
207109 C
1 C
207110 ACTATAACTG
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 50 0.89
56 6 0.11
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.29
Consensus pattern (56 bp):
CTCCACTAAATCGAAAGTCTAAATCCTTGGAGCTGGTGGTCGTAGGCGTTCTCTTC
Found at i:207332 original size:17 final size:17
Alignment explanation
Indices: 207307--207342 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
207297 GATCCAAACC
207307 TTTAATTTTGTTATTTT
1 TTTAATTTTGTTATTTT
* *
207324 TTTATTTTTTTTATTTT
1 TTTAATTTTGTTATTTT
207341 TT
1 TT
207343 CAGGAACGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (17 bp):
TTTAATTTTGTTATTTT
Found at i:209879 original size:21 final size:21
Alignment explanation
Indices: 209833--209895 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
209823 CCCCGAACCA
*
209833 TGAACTCTAAATCTTGAATCT
1 TGAACTCTAAATATTGAATCT
*
209854 CGAACTTCTAAATATTGAA-CT
1 TGAAC-TCTAAATATTGAATCT
* * *
209875 TGAACCCTAAACACTGAATCT
1 TGAACTCTAAATATTGAATCT
209896 CAAACCCCAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
20 10 0.29
21 12 0.35
22 12 0.35
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.32
Consensus pattern (21 bp):
TGAACTCTAAATATTGAATCT
Found at i:218412 original size:23 final size:24
Alignment explanation
Indices: 218386--218444 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
218376 AAATTTTAAA
218386 AATATTTATATTATTT-TAAATTT
1 AATATTTATATTATTTATAAATTT
218409 AATATTTA-A-TATTTAATAAATTT
1 AATATTTATATTATTT-ATAAATTT
*
218432 ATATATTTTTATT
1 A-ATATTTATATT
218445 GATTAAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 5 0.17
22 1 0.03
23 16 0.53
24 6 0.20
25 1 0.03
26 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
AATATTTATATTATTTATAAATTT
Found at i:218422 original size:14 final size:15
Alignment explanation
Indices: 218386--218426 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
218376 AAATTTTAAA
218386 AATATTTATATTATTTT
1 AATATTTA-A-TATTTT
218403 AA-ATTTAATA-TTT
1 AATATTTAATATTTT
218416 AATATTTAATA
1 AATATTTAATA
218427 AATTTATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 5 0.22
14 10 0.43
15 1 0.04
16 5 0.22
17 2 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
AATATTTAATATTTT
Found at i:218451 original size:23 final size:23
Alignment explanation
Indices: 218401--218451 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
218391 TTATATTATT
*
218401 TTAAATTTAATATTTAATATTTA
1 TTAAATTTAATATTTAATATTGA
* *
218424 ATAAATTTATATATTT-TTATTGA
1 TTAAATTTA-ATATTTAATATTGA
218447 TTAAA
1 TTAAA
218452 ATTTTAAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
TTAAATTTAATATTTAATATTGA
Found at i:223099 original size:13 final size:13
Alignment explanation
Indices: 223083--223107 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
223073 TGGAAATTAA
223083 AAAAATAAAAAAT
1 AAAAATAAAAAAT
223096 AAAAATAAAAAA
1 AAAAATAAAAAA
223108 GGGAAACAAA
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:224763 original size:2 final size:2
Alignment explanation
Indices: 224751--224788 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
224741 AAAATAATTG
*
224751 GA GA CA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
224789 TAAAGTAGGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:227311 original size:15 final size:16
Alignment explanation
Indices: 227291--227320 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
227281 CATCATACAA
227291 TTATTC-TCTTCTTTC
1 TTATTCTTCTTCTTTC
227306 TTATTCTTCTTCTTT
1 TTATTCTTCTTCTTT
227321 GCAAATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.07, C:0.23, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTCTTCTTCTTTC
Found at i:231521 original size:21 final size:21
Alignment explanation
Indices: 231469--231515 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
231459 AAATATACAG
231469 TATATG-GCATTTAAACTATA
1 TATATGAGCATTTAAACTATA
**
231489 TATATGAGCATTTAATGTATA
1 TATATGAGCATTTAAACTATA
231510 TATATG
1 TATATG
231516 CTCATTAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.43
Consensus pattern (21 bp):
TATATGAGCATTTAAACTATA
Found at i:248072 original size:14 final size:14
Alignment explanation
Indices: 248053--248086 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
248043 TCAGAAATTT
248053 AAAAAAAAAAAAGA
1 AAAAAAAAAAAAGA
*
248067 AAAAAAAACAAAGA
1 AAAAAAAAAAAAGA
248081 ACAAAA
1 A-AAAA
248087 GAATAGGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.88, C:0.06, G:0.06, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAGA
Found at i:251077 original size:5 final size:5
Alignment explanation
Indices: 251069--251168 Score: 68
Period size: 5 Copynumber: 20.0 Consensus size: 5
251059 ATTTAAAATA
* *
251069 TATAT TATAT TATA- TATACG TA-AT TAATGAT TATGT T-T-T TATAT
1 TATAT TATAT TATAT TATA-T TATAT T-AT-AT TATAT TATAT TATAT
* *
251113 TGTAT TATTAT TA-A- TATAT TATAT TATAT TATAT TATAT TACAT ATATAT
1 TATAT TA-TAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT -TATAT
251163 ATATAT
1 -TATAT
251169 AACAGAAGAA
Statistics
Matches: 78, Mismatches: 6, Indels: 21
0.74 0.06 0.20
Matches are distributed among these distances:
3 4 0.05
4 9 0.12
5 43 0.55
6 19 0.24
7 3 0.04
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (5 bp):
TATAT
Found at i:251132 original size:19 final size:18
Alignment explanation
Indices: 251068--251153 Score: 57
Period size: 19 Copynumber: 4.4 Consensus size: 18
251058 AATTTAAAAT
251068 ATATATTATATTATATATA
1 ATATATTATATTATAT-TA
* * *
251087 CGTA-ATTAATGATTATGTTT
1 -ATATATT-AT-ATTATATTA
* *
251107 TTATATTGTATTATTATTA
1 ATATATTATATTA-TATTA
251126 ATATATTATATTATATTA
1 ATATATTATATTATATTA
251144 TATTATATTA
1 -A-TATATTA
251154 CATATATATA
Statistics
Matches: 51, Mismatches: 9, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
18 9 0.18
19 21 0.41
20 15 0.29
21 6 0.12
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.56
Consensus pattern (18 bp):
ATATATTATATTATATTA
Found at i:251169 original size:29 final size:29
Alignment explanation
Indices: 251107--251166 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 29
251097 GATTATGTTT
*
251107 TTATATTGTATTATTATTAATATATTATA
1 TTATATTATATTATTATTAATATATTATA
251136 TTATATTATATTA-TATTACATATATATATA
1 TTATATTATATTATTATTA-ATATAT-TATA
251166 T
1 T
251167 ATAACAGAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 5 0.18
29 18 0.64
30 5 0.18
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (29 bp):
TTATATTATATTATTATTAATATATTATA
Found at i:251246 original size:35 final size:34
Alignment explanation
Indices: 251189--251255 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 34
251179 AGCATAGAAA
* *
251189 TGAGAAAGAAAGAAACAGAGAAGCAAAACGAAAAT
1 TGAGAAAGAAAGAAACAAAGAAG-AAAAAGAAAAT
*
251224 TGAGAAAGAAA-AAGAGAAAGAAGAAAAAGAAA
1 TGAGAAAGAAAGAA-ACAAAGAAGAAAAAGAAA
251256 GAGAGCCACG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 10 0.36
35 18 0.64
ACGTcount: A:0.67, C:0.04, G:0.24, T:0.04
Consensus pattern (34 bp):
TGAGAAAGAAAGAAACAAAGAAGAAAAAGAAAAT
Found at i:256162 original size:233 final size:235
Alignment explanation
Indices: 255745--256212 Score: 922
Period size: 233 Copynumber: 2.0 Consensus size: 235
255735 TTTTAAAATT
255745 TTTTAAAAATATTAAAATCATATAAAAGTTATAAAATGTTAACGTGTCACTTGCATGGTAATCCA
1 TTTTAAAAATATTAAAATCATATAAAAGTTATAAAATGTTAACGTGTCACTTGCATGGTAATCCA
255810 TGCGTATGCCATATCAATAAAGTTAATAATCGTTAATTTTTTATCCATTTTAGGGTGATTTGATA
66 TGCGTATGCCATATCAATAAAGTTAATAATCGTTAATTTTTTATCCATTTTAGGGTGATTTGATA
255875 AAAAAATACAAAATTAAGAACCGAAAGAGATGAAAAATTAAAGGAAGGGCTAAAATAATAAATTT
131 AAAAAATACAAAATTAAGAACCGAAAGAGATGAAAAATTAAAGGAAGGGCTAAAATAATAAATTT
255940 ATTTTGAAAAATTGGAGGGTAAAATTGGAAAAAGAAAAAA
196 ATTTTGAAAAATTGGAGGGTAAAATTGGAAAAAGAAAAAA
255980 TTTT-AAAA-ATTAAAATCATATAAAAGTTATAAAATGTTAACGTGTCACTTGCATGGTAATCCA
1 TTTTAAAAATATTAAAATCATATAAAAGTTATAAAATGTTAACGTGTCACTTGCATGGTAATCCA
256043 TGCGTATGCCATATCAATAAAGTTAATAATCGTTAATTTTTTATCCATTTTAGGGTGATTTGATA
66 TGCGTATGCCATATCAATAAAGTTAATAATCGTTAATTTTTTATCCATTTTAGGGTGATTTGATA
256108 AAAAAATACAAAATTAAGAACCGAAAGAGATGAAAAATTAAAGGAAGGGCTAAAATAATAAATTT
131 AAAAAATACAAAATTAAGAACCGAAAGAGATGAAAAATTAAAGGAAGGGCTAAAATAATAAATTT
256173 ATTTTGAAAAATTGGAGGGTAAAATTGGAAAAAGAAAAAA
196 ATTTTGAAAAATTGGAGGGTAAAATTGGAAAAAGAAAAAA
256213 AGGGAAAGGG
Statistics
Matches: 233, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
233 225 0.97
234 4 0.02
235 4 0.02
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (235 bp):
TTTTAAAAATATTAAAATCATATAAAAGTTATAAAATGTTAACGTGTCACTTGCATGGTAATCCA
TGCGTATGCCATATCAATAAAGTTAATAATCGTTAATTTTTTATCCATTTTAGGGTGATTTGATA
AAAAAATACAAAATTAAGAACCGAAAGAGATGAAAAATTAAAGGAAGGGCTAAAATAATAAATTT
ATTTTGAAAAATTGGAGGGTAAAATTGGAAAAAGAAAAAA
Found at i:266212 original size:6 final size:6
Alignment explanation
Indices: 266205--266243 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
266195 CTCTCTCGAA
*
266205 AAAAAA AAAAAG AAAAAG AAAAAG AAAAAG AAAAA- AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
266244 GATAAAAGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:270368 original size:15 final size:15
Alignment explanation
Indices: 270348--270383 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
270338 AGTGTTGAAC
*
270348 AAAAAACAAAAAC-A
1 AAAAAAAAAAAACGA
270362 AAAAAAAAAAAACGA
1 AAAAAAAAAAAACGA
270377 AAAAAAA
1 AAAAAAA
270384 GAAGAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.89, C:0.08, G:0.03, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAACGA
Found at i:270653 original size:15 final size:15
Alignment explanation
Indices: 270633--270668 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
270623 AGTGTTGAAC
*
270633 AAAAAACAAAAAC-A
1 AAAAAAAAAAAACGA
270647 AAAAAAAAAAAACGA
1 AAAAAAAAAAAACGA
270662 AAAAAAA
1 AAAAAAA
270669 GAAGAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.89, C:0.08, G:0.03, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAACGA
Found at i:270787 original size:285 final size:286
Alignment explanation
Indices: 270266--270836 Score: 1135
Period size: 285 Copynumber: 2.0 Consensus size: 286
270256 TATTATTAAT
270266 TAATCATACTGAAATTATTTATTATATAAATATATATTTTTTTGCAAATTGATCTTCTTTATTTG
1 TAATCATACTGAAATTATTTATTATATAAATATATATTTTTTTGCAAATTGATCTTCTTTATTTG
270331 AATCAGAAGTGTTGAACAAAAAACAAAAACAAAAAAAAAAAAACGAAAAAAAAGAAGAAAAAAAT
66 AATCAGAAGTGTTGAACAAAAAACAAAAACAAAAAAAAAAAAACGAAAAAAAAGAAGAAAAAAAT
270396 TGTAACCGAAGTCTGTAGGCAATGTCGAGGAGGCCAGTGAATCCCTCTAGACGTTACGGCGATGC
131 TGTAACCGAAGTCTGTAGGCAATGTCGAGGAGGCCAGTGAATCCCTCTAGACGTTACGGCGATGC
270461 CGGCGGCGGAGCTGCTCTCTTTTCGCTGTCTAAATCTCGTTCTCCGCCTTTGCTCTCCATTGTTC
196 CGGCGGCGGAGCTGCTCTCTTTTCGCTGTCTAAATCTCGTTCTCCGCCTTTGCTCTCCATTGTTC
270526 TCATTGTCCTGGTATTTTTTTAAGAA
261 TCATTGTCCTGGTATTTTTTTAAGAA
270552 TAATCATACT-AAATTATTTATTATATAAATATATATTTTTTTGCAAATTGATCTTCTTTATTTG
1 TAATCATACTGAAATTATTTATTATATAAATATATATTTTTTTGCAAATTGATCTTCTTTATTTG
270616 AATCAGAAGTGTTGAACAAAAAACAAAAACAAAAAAAAAAAAACGAAAAAAAAGAAGAAAAAAAT
66 AATCAGAAGTGTTGAACAAAAAACAAAAACAAAAAAAAAAAAACGAAAAAAAAGAAGAAAAAAAT
270681 TGTAACCGAAGTCTGTAGGCAATGTCGAGGAGGCCAGTGAATCCCTCTAGACGTTACGGCGATGC
131 TGTAACCGAAGTCTGTAGGCAATGTCGAGGAGGCCAGTGAATCCCTCTAGACGTTACGGCGATGC
270746 CGGCGGCGGAGCTGCTCTCTTTTCGCTGTCTAAATCTCGTTCTCCGCCTTTGCTCTCCATTGTTC
196 CGGCGGCGGAGCTGCTCTCTTTTCGCTGTCTAAATCTCGTTCTCCGCCTTTGCTCTCCATTGTTC
270811 TCATTGTCCTGGTATTTTTTTAAGAA
261 TCATTGTCCTGGTATTTTTTTAAGAA
270837 AACAAATCTT
Statistics
Matches: 285, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
285 275 0.96
286 10 0.04
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Consensus pattern (286 bp):
TAATCATACTGAAATTATTTATTATATAAATATATATTTTTTTGCAAATTGATCTTCTTTATTTG
AATCAGAAGTGTTGAACAAAAAACAAAAACAAAAAAAAAAAAACGAAAAAAAAGAAGAAAAAAAT
TGTAACCGAAGTCTGTAGGCAATGTCGAGGAGGCCAGTGAATCCCTCTAGACGTTACGGCGATGC
CGGCGGCGGAGCTGCTCTCTTTTCGCTGTCTAAATCTCGTTCTCCGCCTTTGCTCTCCATTGTTC
TCATTGTCCTGGTATTTTTTTAAGAA
Found at i:277976 original size:34 final size:34
Alignment explanation
Indices: 277928--277997 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
277918 GCCATGGTGG
*
277928 TAGCAGAGTCCCTAGTTGAGTCCCCCAAGAACCA
1 TAGCAGAGTCCCTAGTCGAGTCCCCCAAGAACCA
*
277962 TAGCGGAGTCCCTAGTCGAGTCCCCCAAGAACCA
1 TAGCAGAGTCCCTAGTCGAGTCCCCCAAGAACCA
277996 TA
1 TA
277998 TTAAGTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.29, C:0.33, G:0.21, T:0.17
Consensus pattern (34 bp):
TAGCAGAGTCCCTAGTCGAGTCCCCCAAGAACCA
Found at i:279125 original size:20 final size:20
Alignment explanation
Indices: 279100--279140 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
279090 CTCAAGGCAC
279100 CTCACTAACACATCATAAAT
1 CTCACTAACACATCATAAAT
279120 CTCACTAACACATCATAAAT
1 CTCACTAACACATCATAAAT
279140 C
1 C
279141 AAGTCTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.32, G:0.00, T:0.24
Consensus pattern (20 bp):
CTCACTAACACATCATAAAT
Found at i:282420 original size:7 final size:7
Alignment explanation
Indices: 282408--282442 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
282398 ACTAAGGCAT
282408 CTCATGG
1 CTCATGG
282415 CTCATGG
1 CTCATGG
282422 CTCATGG
1 CTCATGG
282429 CTCATGG
1 CTCATGG
282436 CTCATGG
1 CTCATGG
282443 TGGCACTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.14, C:0.29, G:0.29, T:0.29
Consensus pattern (7 bp):
CTCATGG
Found at i:287136 original size:3 final size:3
Alignment explanation
Indices: 287128--287216 Score: 169
Period size: 3 Copynumber: 29.7 Consensus size: 3
287118 ACCCCATAGC
287128 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
*
287176 AAG AAG AAG AAG AAG AAA AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
287217 ATGGACATAC
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 84 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:287763 original size:15 final size:17
Alignment explanation
Indices: 287739--287775 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
287729 TTTTGGATGC
*
287739 TTGTTATTTGGT-ATTT
1 TTGTTATTTGCTGATTT
287755 TTGTT-TTTGCTGATTT
1 TTGTTATTTGCTGATTT
287771 TTGTT
1 TTGTT
287776 GTTTTGTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.08, C:0.03, G:0.19, T:0.70
Consensus pattern (17 bp):
TTGTTATTTGCTGATTT
Found at i:289233 original size:2 final size:2
Alignment explanation
Indices: 289221--289250 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
289211 GTTCTTGGTG
*
289221 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
289251 ATTCTGAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:289408 original size:2 final size:2
Alignment explanation
Indices: 289396--289425 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
289386 CGGTTTGGTG
*
289396 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
289426 ATTCTGAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:289497 original size:175 final size:177
Alignment explanation
Indices: 289204--289555 Score: 690
Period size: 175 Copynumber: 2.0 Consensus size: 177
289194 AAATCCTATG
289204 CACATCGGTTCTTGGTGTATAAATATATATATATATATATATATATAATTCTGAAACATATACAT
1 CACATCGGTTCTTGGTGTATAAATATATATATATATATATATATATAATTCTGAAACATATACAT
289269 GGTCACTTCACTTGTATAGGAACTGGTGGAGTACATGGCAAAAATGAGAGGAAACAAGGTCAAGT
66 GGTCACTTCACTTGTATAGGAACTGGTGGAGTACATGGCAAAAATGAGAGGAAACAAGGTCAAGT
289334 TCGATCCCAACAACCTAGTGCTTGCCGCTGGTGCAACTTCAGCTAAC
131 TCGATCCCAACAACCTAGTGCTTGCCGCTGGTGCAACTTCAGCTAAC
289381 CACATCGG-T-TTGGTGTATAAATATATATATATATATATATATATAATTCTGAAACATATACAT
1 CACATCGGTTCTTGGTGTATAAATATATATATATATATATATATATAATTCTGAAACATATACAT
289444 GGTCACTTCACTTGTATAGGAACTGGTGGAGTACATGGCAAAAATGAGAGGAAACAAGGTCAAGT
66 GGTCACTTCACTTGTATAGGAACTGGTGGAGTACATGGCAAAAATGAGAGGAAACAAGGTCAAGT
289509 TCGATCCCAACAACCTAGTGCTTGCCGCTGGTGCAACTTCAGCTAAC
131 TCGATCCCAACAACCTAGTGCTTGCCGCTGGTGCAACTTCAGCTAAC
289556 GAGACTTTAA
Statistics
Matches: 175, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
175 166 0.95
176 1 0.01
177 8 0.05
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (177 bp):
CACATCGGTTCTTGGTGTATAAATATATATATATATATATATATATAATTCTGAAACATATACAT
GGTCACTTCACTTGTATAGGAACTGGTGGAGTACATGGCAAAAATGAGAGGAAACAAGGTCAAGT
TCGATCCCAACAACCTAGTGCTTGCCGCTGGTGCAACTTCAGCTAAC
Found at i:308681 original size:15 final size:13
Alignment explanation
Indices: 308646--308674 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
308636 TTTTAGACAA
308646 TTTATAA-TATTT
1 TTTATAATTATTT
308658 TTTATAATTATTT
1 TTTATAATTATTT
308671 TTTA
1 TTTA
308675 CTTAATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTATAATTATTT
Found at i:313619 original size:22 final size:21
Alignment explanation
Indices: 313583--313642 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
313573 GGCCCGGCTT
*
313583 ATTT-TTTTAATAAATACCAAAA
1 ATTTATTTTAA-AAATA-AAAAA
313605 ATTTATTTTAAAAATTAAAAAA
1 ATTTATTTTAAAAA-TAAAAAA
**
313627 AAGTATTTTAAAAATA
1 ATTTATTTTAAAAATA
313643 TTTTAAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
21 2 0.06
22 23 0.70
23 8 0.24
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (21 bp):
ATTTATTTTAAAAATAAAAAA
Found at i:313656 original size:17 final size:17
Alignment explanation
Indices: 313634--313680 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
313624 AAAAAGTATT
*
313634 TTAAAAATATTTTAAAA
1 TTAAAAATATTTAAAAA
*
313651 TTAAAAAAATTTAAAAA
1 TTAAAAATATTTAAAAA
* *
313668 ATAAATATATTTA
1 TTAAAAATATTTA
313681 TTATATCGGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAAAAATATTTAAAAA
Found at i:315570 original size:26 final size:27
Alignment explanation
Indices: 315527--315582 Score: 87
Period size: 26 Copynumber: 2.1 Consensus size: 27
315517 ATAACTAAAT
*
315527 TATTATAATTTTTTTTATTTACCAAAA
1 TATTATAATTTTTTTTATTTACAAAAA
*
315554 TATTAT-ATTTTTTTTATTTAGAAAAA
1 TATTATAATTTTTTTTATTTACAAAAA
315580 TAT
1 TAT
315583 ACTAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 21 0.78
27 6 0.22
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.57
Consensus pattern (27 bp):
TATTATAATTTTTTTTATTTACAAAAA
Found at i:316024 original size:19 final size:19
Alignment explanation
Indices: 316000--316065 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
315990 ATTAAAATAG
316000 TTTAATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
* *
316019 TTTAATGTAATAA-ACTAT
1 TTTAATTTAATAACTCTAT
* *
316037 TCTCATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
316056 TTTAATTTAA
1 TTTAATTTAA
316066 AAAAATTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
18 14 0.37
19 24 0.63
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.50
Consensus pattern (19 bp):
TTTAATTTAATAACTCTAT
Found at i:329729 original size:18 final size:19
Alignment explanation
Indices: 329706--329743 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
329696 AGAACTCAAC
*
329706 TAAAAA-TAATTTTAAATA
1 TAAAAACTAATTTAAAATA
329724 TAAAAACTAATTTAAAATA
1 TAAAAACTAATTTAAAATA
329743 T
1 T
329744 GAATTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAAAACTAATTTAAAATA
Found at i:335728 original size:4 final size:4
Alignment explanation
Indices: 335719--335743 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
335709 CATTCGCATG
335719 TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA T
335744 TCCACATGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (4 bp):
TACA
Found at i:340173 original size:20 final size:22
Alignment explanation
Indices: 340133--340174 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
340123 ATTAAGAATA
*
340133 TAATAAATATAATTTATTATTT
1 TAATAAATATAATTTAATATTT
340155 TAATAAAT-T-ATTTAATATTT
1 TAATAAATATAATTTAATATTT
340175 CAATTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 1 0.05
22 8 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TAATAAATATAATTTAATATTT
Found at i:340671 original size:14 final size:14
Alignment explanation
Indices: 340652--340688 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
340642 CTAGAAAAGT
340652 AAATTATTTTCCAA
1 AAATTATTTTCCAA
*
340666 AAATTATTTTCCGA
1 AAATTATTTTCCAA
*
340680 AAATCATTT
1 AAATTATTT
340689 CAGTGAAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.41, C:0.14, G:0.03, T:0.43
Consensus pattern (14 bp):
AAATTATTTTCCAA
Found at i:367941 original size:24 final size:22
Alignment explanation
Indices: 367897--367941 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
367887 ATCTTTTTAT
*
367897 TTTTATTTTAAAAATTTAGTCA
1 TTTTATTTTAAAAATTAAGTCA
*
367919 TTTTACTTTTCAAAATTCAAGTC
1 TTTTA-TTTTAAAAATT-AAGTC
367942 TAATTGTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 10 0.53
24 4 0.21
ACGTcount: A:0.33, C:0.11, G:0.04, T:0.51
Consensus pattern (22 bp):
TTTTATTTTAAAAATTAAGTCA
Found at i:370534 original size:24 final size:24
Alignment explanation
Indices: 370507--370556 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
370497 AGAACTATGC
370507 ACAATAAAACAAATAAAAGAACTT
1 ACAATAAAACAAATAAAAGAACTT
370531 ACAATAAAACAAATAAAAGAACTT
1 ACAATAAAACAAATAAAAGAACTT
370555 AC
1 AC
370557 TTGCCAATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.66, C:0.14, G:0.04, T:0.16
Consensus pattern (24 bp):
ACAATAAAACAAATAAAAGAACTT
Found at i:379537 original size:31 final size:31
Alignment explanation
Indices: 379499--379597 Score: 101
Period size: 39 Copynumber: 2.9 Consensus size: 31
379489 GACCCATTTT
379499 TATTTTAAAAATTTTAAAAAATTAAAAAAAG
1 TATTTTAAAAATTTTAAAAAATTAAAAAAAG
379530 TATTTTAAAAATATTTTAAAATTAAAAAATTAAAAAAAG
1 TATTTT-AAAA-A--TT----TTAAAAAATTAAAAAAAG
*
379569 TATTTTAAAAATATTT-TAAAATTAAAAAA
1 TATTTTAAAAAT-TTTAAAAAATTAAAAAA
379598 NNNNNNNNNN
Statistics
Matches: 58, Mismatches: 1, Indels: 18
0.75 0.01 0.23
Matches are distributed among these distances:
31 18 0.31
32 6 0.10
33 1 0.02
35 3 0.05
36 1 0.02
37 1 0.02
38 4 0.07
39 24 0.41
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (31 bp):
TATTTTAAAAATTTTAAAAAATTAAAAAAAG
Found at i:379539 original size:11 final size:11
Alignment explanation
Indices: 379499--379589 Score: 65
Period size: 10 Copynumber: 8.9 Consensus size: 11
379489 GACCCATTTT
379499 TATTTT-AAAA
1 TATTTTAAAAA
379509 -ATTTTAAAAA
1 TATTTTAAAAA
**
379519 -ATTAAAAAAA
1 TATTTTAAAAA
379529 GTATTTTAAAAA
1 -TATTTTAAAAA
379541 TATTTT--AAA
1 TATTTTAAAAA
379550 -A--TTAAAAA
1 TATTTTAAAAA
**
379558 -ATTAAAAAAA
1 TATTTTAAAAA
379568 GTATTTTAAAAA
1 -TATTTTAAAAA
379580 TATTTTAAAA
1 TATTTTAAAA
379590 TTAAAAAANN
Statistics
Matches: 64, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
6 2 0.03
8 5 0.08
9 8 0.12
10 17 0.27
11 16 0.25
12 16 0.25
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.38
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:379560 original size:39 final size:39
Alignment explanation
Indices: 379512--379597 Score: 172
Period size: 39 Copynumber: 2.2 Consensus size: 39
379502 TTTAAAAATT
379512 TTAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
1 TTAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
379551 TTAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
1 TTAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
379590 TTAAAAAA
1 TTAAAAAA
379598 NNNNNNNNNN
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (39 bp):
TTAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
Found at i:383334 original size:7 final size:6
Alignment explanation
Indices: 383317--383397 Score: 60
Period size: 6 Copynumber: 13.2 Consensus size: 6
383307 TCATTCTTTC
* *
383317 TTTCTT TTTCTCT TTTC-- TTTCTT TCATTCTT TGTT-TT GTTTCTT TCTCTC
1 TTTCTT TTTCT-T TTTCTT TTTCTT T--TTCTT T-TTCTT -TTTCTT TTTCTT
* *
383367 ATTCTT TTTCTA TTTCTT TTTCTT TTTCTT T
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT T
383398 ATCATCATAA
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
4 4 0.07
6 39 0.66
7 10 0.17
8 6 0.10
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.74
Consensus pattern (6 bp):
TTTCTT
Found at i:383334 original size:21 final size:20
Alignment explanation
Indices: 383310--383397 Score: 74
Period size: 21 Copynumber: 4.3 Consensus size: 20
383300 ATTTTTCTCA
383310 TTCTTTCTTTCTTTTTCTCTT
1 TTCTTTCTTTCTTTTTCT-TT
*
383331 TTCTTTCTTTCATTCTTT-GTT
1 TTCTTTCTTTC-TT-TTTCTTT
* *
383352 TTGTTTCTTTCTCTCATTCTTT
1 TTCTTTCTTTCT-T-TTTCTTT
*
383374 TTC--TATTTCTTTTTCTTT
1 TTCTTTCTTTCTTTTTCTTT
383392 TTCTTT
1 TTCTTT
383398 ATCATCATAA
Statistics
Matches: 54, Mismatches: 7, Indels: 13
0.73 0.09 0.18
Matches are distributed among these distances:
18 9 0.17
19 1 0.02
20 8 0.15
21 27 0.50
22 6 0.11
23 3 0.06
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.74
Consensus pattern (20 bp):
TTCTTTCTTTCTTTTTCTTT
Found at i:383340 original size:25 final size:24
Alignment explanation
Indices: 383329--383385 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
383319 TCTTTTTCTC
383329 TTTTCTTTCTTTCATTCTTTGTT-T
1 TTTTCTTTCTTTCATTCTTT-TTCT
*
383353 TGTTTCTTTCTCTCATTCTTTTTCT
1 T-TTTCTTTCTTTCATTCTTTTTCT
*
383378 ATTTCTTT
1 TTTTCTTT
383386 TTCTTTTTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 10 0.34
25 19 0.66
ACGTcount: A:0.05, C:0.19, G:0.04, T:0.72
Consensus pattern (24 bp):
TTTTCTTTCTTTCATTCTTTTTCT
Found at i:383470 original size:28 final size:29
Alignment explanation
Indices: 383406--383481 Score: 111
Period size: 28 Copynumber: 2.7 Consensus size: 29
383396 TTATCATCAT
*
383406 AATATAATAATATATATACTTAACTTTTA
1 AATATTATAATATATATACTTAACTTTTA
*
383435 AATATTATAATATATAT-TTTAAC-TTTA
1 AATATTATAATATATATACTTAACTTTTA
383462 AATATTTATAATATATATAC
1 AATA-TTATAATATATATAC
383482 ACTTATATCG
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
27 8 0.19
28 18 0.43
29 16 0.38
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (29 bp):
AATATTATAATATATATACTTAACTTTTA
Found at i:383806 original size:181 final size:181
Alignment explanation
Indices: 383500--383846 Score: 536
Period size: 181 Copynumber: 1.9 Consensus size: 181
383490 CGCCTTAATT
* *
383500 ATGACCATTGGCATAATTGCTCATTTGGTCCCGTTAATTATTCTTTAATCTATAATTCAACTTTC
1 ATGACCATTAGCATAATTGCTCATTTAGTCCCGTTAATTATTCTTTAATCTATAATTCAACTTTC
* *
383565 ACCCTTTATACAATTTAATCCTTTTGCCTAATTACTCTTAATTCATGCAATTTCACCTAACCAAA
66 ACCCTTTATACAATTTAATCCTTTTACCTAATTACTATTAATTCATGCAATTTCACCTAACCAAA
*
383630 ACCTAATTAACTACACAAATAACTTCGTAAATATTTTTAGTAAATATTTAC
131 ACCTAATTAACTACACAAATAACTTCGAAAATATTTTTAGTAAATATTTAC
* * *
383681 ATGACCATTAGCATAATTGCTCCTTTAG-CCTCTTTAATTTTTCTTTAATCTATAATTCAACTTT
1 ATGACCATTAGCATAATTGCTCATTTAGTCC-CGTTAATTATTCTTTAATCTATAATTCAACTTT
* * *
383745 CACCCTTTATACAAATTT-TTCCTTTTACCTAATTACTATTAATTCATGCTATTTTACCTAACCA
65 CACCCTTTATAC-AATTTAATCCTTTTACCTAATTACTATTAATTCATGCAATTTCACCTAACCA
* * *
383809 AAACCTAATTAACTATACAACTAACTTTGAAAATATTT
129 AAACCTAATTAACTACACAAATAACTTCGAAAATATTT
383847 ACGAGTTCGA
Statistics
Matches: 150, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
180 2 0.01
181 143 0.95
182 5 0.03
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.41
Consensus pattern (181 bp):
ATGACCATTAGCATAATTGCTCATTTAGTCCCGTTAATTATTCTTTAATCTATAATTCAACTTTC
ACCCTTTATACAATTTAATCCTTTTACCTAATTACTATTAATTCATGCAATTTCACCTAACCAAA
ACCTAATTAACTACACAAATAACTTCGAAAATATTTTTAGTAAATATTTAC
Found at i:385908 original size:24 final size:24
Alignment explanation
Indices: 385881--385932 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
385871 TTAGTAAGTC
* *
385881 AAATAAACTATCCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
385905 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
385929 AAAT
1 AAAT
385933 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:386922 original size:1 final size:1
Alignment explanation
Indices: 386916--386972 Score: 78
Period size: 1 Copynumber: 57.0 Consensus size: 1
386906 TAACAGAAAG
** **
386916 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGATCAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
386973 GACAGTCCGT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.93, C:0.02, G:0.04, T:0.02
Consensus pattern (1 bp):
A
Found at i:405715 original size:3 final size:3
Alignment explanation
Indices: 405707--405758 Score: 86
Period size: 3 Copynumber: 17.0 Consensus size: 3
405697 GTTATATTGC
*
405707 ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATT ATT ATT ATT GTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT
405753 ATT ATT
1 ATT ATT
405759 TCTATACATA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 43 0.93
4 3 0.07
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:405752 original size:25 final size:25
Alignment explanation
Indices: 405708--405759 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
405698 TTATATTGCA
405708 TTATTATTATTATTATTATTATTAT
1 TTATTATTATTATTATTATTATTAT
*
405733 TTATTATTATTATTGTTATTATTAT
1 TTATTATTATTATTATTATTATTAT
405758 TT
1 TT
405760 CTATACATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (25 bp):
TTATTATTATTATTATTATTATTAT
Found at i:406112 original size:6 final size:6
Alignment explanation
Indices: 406092--406123 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
406082 TATGTCATAC
406092 TTTTTA -TTTTA -TTTTA TTTTTA TTTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
406124 ATATATATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.40
6 15 0.60
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:406112 original size:11 final size:11
Alignment explanation
Indices: 406092--406125 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
406082 TATGTCATAC
406092 TTTTTATTTTA
1 TTTTTATTTTA
406103 -TTTTATTTTTA
1 TTTTTA-TTTTA
406114 TTTTTATTTTA
1 TTTTTATTTTA
406125 T
1 T
406126 ATATATACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
10 5 0.24
11 11 0.52
12 5 0.24
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:407279 original size:46 final size:46
Alignment explanation
Indices: 407212--407305 Score: 154
Period size: 46 Copynumber: 2.0 Consensus size: 46
407202 ACAATGCTAT
*
407212 AACTCAGTATGGTTTCTTTCACTAAAACACCATACCTACTTTTCAC
1 AACTCAATATGGTTTCTTTCACTAAAACACCATACCTACTTTTCAC
*
407258 AACTCAATATGGCTTTC-TTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAATATGG-TTTCTTTCACTAAAACACCATACCTACTTTTCAC
407304 AA
1 AA
407306 TTTTCCATGG
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
46 41 0.91
47 4 0.09
ACGTcount: A:0.32, C:0.29, G:0.06, T:0.33
Consensus pattern (46 bp):
AACTCAATATGGTTTCTTTCACTAAAACACCATACCTACTTTTCAC
Done.