Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold294
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: 684262
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.33
Warning! 27869 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:90 original size:30 final size:29
Alignment explanation
Indices: 35--150 Score: 101
Period size: 29 Copynumber: 3.9 Consensus size: 29
25 CAAACACAGC
* * *
35 AAAACTTATGGGGTTAAAGTGTAATTTTGAGA
1 AAAATTTA-GGGGTCAAAATGTAATTTT-A-A
67 AAAATTTA-GGGTCAAAATGTAATTTTAA
1 AAAATTTAGGGGTCAAAATGTAATTTTAA
* * * * *
95 AAAGTTGAGGGGTTAAAGTG-AAGTTTCAA
1 AAAATTTAGGGGTCAAAATGTAA-TTTTAA
*
124 AAATTTTAGGGGTCAAAATGTAATTTT
1 AAAATTTAGGGGTCAAAATGTAATTTT
151 TTTATTTTTG
Statistics
Matches: 68, Mismatches: 13, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
28 9 0.13
29 34 0.50
30 18 0.26
32 7 0.10
ACGTcount: A:0.40, C:0.03, G:0.22, T:0.34
Consensus pattern (29 bp):
AAAATTTAGGGGTCAAAATGTAATTTTAA
Found at i:4534 original size:20 final size:21
Alignment explanation
Indices: 4494--4534 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
4484 GACTAAACCT
*
4494 TAAACCTCAATCTCCAAGCCC
1 TAAACCTCAAACTCCAAGCCC
*
4515 TAAACCT-AAACTCTAAGCCC
1 TAAACCTCAAACTCCAAGCCC
4535 AGATCACAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.37, C:0.39, G:0.05, T:0.20
Consensus pattern (21 bp):
TAAACCTCAAACTCCAAGCCC
Found at i:5222 original size:133 final size:133
Alignment explanation
Indices: 4879--5273 Score: 395
Period size: 133 Copynumber: 2.9 Consensus size: 133
4869 ATCCAAACCG
* * * * * *
4879 TTTCCGGCGTTTTTTAACATTTCACCACTAAAG-CATAAAAAGGAAACAACAAAATGGTACCGTT
1 TTTCCGGCGTTTTTTAA-AATGCGCCACTAAAGAAAT-AAAATGAAACAACAAAACGGTACCGTT
** * *
4943 TTGCTCAAAAATTTTCCTCAAATTAGATATCTTTATCGGCGTTTCTCC-AATAACGCCACTATAT
64 TTGCTCAAATTTTTTCCTCAAATTAGATATCTTTACCGGCGTTTC-CCGAA-AACGCCGCTATAT
5007 CCCAATA
127 CCCAATA
* * * * * * * * *
5014 TTTGCGGCGTATTTTACAGTGCGCCACTAAGGAAATAAAATGAAGCAATAAAACTGTAGCGTTTT
1 TTTCCGGCGTTTTTTAAAATGCGCCACTAAAGAAATAAAATGAAACAACAAAACGGTACCGTTTT
*
5079 G-TCCAAATTTTTTCCTCAAATTAGATATCTTTACCGGCGTTTCCCTGAAAACGCCGCTA-AT-G
66 GCT-CAAATTTTTTCCTCAAATTAGATATCTTTACCGGCGTTTCCC-GAAAACGCCGCTATATCC
* *
5141 CATTCT
129 CAAT-A
* **
5147 TTTCCAGCGTTTTTTAAAATGCGCCACTAAAGAAATAAAATGAAACAACAAAACGGTATTGTTTT
1 TTTCCGGCGTTTTTTAAAATGCGCCACTAAAGAAATAAAATGAAACAACAAAACGGTACCGTTTT
* * * * * * *
5212 GCTCAGATTTTTTCCTCAAATTCGTTATCATTACCGGCATTTCTCAGAAAATGCCGCTATAT
66 GCTCAAATTTTTTCCTCAAATTAGATATCTTTACCGGCGTTTC-CCGAAAACGCCGCTATAT
5274 TCTAATTTTT
Statistics
Matches: 213, Mismatches: 39, Indels: 17
0.79 0.14 0.06
Matches are distributed among these distances:
132 3 0.01
133 107 0.50
134 85 0.40
135 18 0.08
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (133 bp):
TTTCCGGCGTTTTTTAAAATGCGCCACTAAAGAAATAAAATGAAACAACAAAACGGTACCGTTTT
GCTCAAATTTTTTCCTCAAATTAGATATCTTTACCGGCGTTTCCCGAAAACGCCGCTATATCCCA
ATA
Found at i:6197 original size:6 final size:6
Alignment explanation
Indices: 6186--6215 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
6176 ATCACGCTCG
*
6186 ACTATT ACTATT ACTATT ACTATT ATTATT
1 ACTATT ACTATT ACTATT ACTATT ACTATT
6216 TGTTGCGGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.53
Consensus pattern (6 bp):
ACTATT
Found at i:8484 original size:14 final size:16
Alignment explanation
Indices: 8459--8492 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
8449 TGAAAGCCTT
8459 AAAAATAAAAAAAGCC
1 AAAAATAAAAAAAGCC
8475 AAAAA-AAAAAAAGCC
1 AAAAATAAAAAAAGCC
8490 AAA
1 AAA
8493 GATACGCCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.79, C:0.12, G:0.06, T:0.03
Consensus pattern (16 bp):
AAAAATAAAAAAAGCC
Found at i:9114 original size:3 final size:3
Alignment explanation
Indices: 9106--9154 Score: 62
Period size: 3 Copynumber: 16.3 Consensus size: 3
9096 TATGCTCGAC
* * * *
9106 TCT TCT TCT TCT TCT CCT TCT CCT TCT CCT TCT TCT CCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
9154 T
1 T
9155 TATTAATCTT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (3 bp):
TCT
Found at i:10291 original size:14 final size:14
Alignment explanation
Indices: 10272--10302 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
10262 TTAGATGTTA
10272 TATAAATTATAGAT
1 TATAAATTATAGAT
*
10286 TATAAATTATAGTT
1 TATAAATTATAGAT
10300 TAT
1 TAT
10303 TTTCAGAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (14 bp):
TATAAATTATAGAT
Found at i:13139 original size:108 final size:108
Alignment explanation
Indices: 12920--13138 Score: 323
Period size: 108 Copynumber: 2.0 Consensus size: 108
12910 GACATGGATT
* ** *
12920 AAAATTCAAGAGGATATTTCGCTATTTAGTTAAACGAGAAAAATCGACACCCAGCACCTTAGGGC
1 AAAATTCAAAAGGATATTAAGCCATTTAGTTAAACGAGAAAAATCGACACCCAGCACCTTAGGGC
* *
12985 ATGTTTTCTCGAATTTCCAAACACAAAACATTGCCTCATTTTA
66 ACGTTTTCTCGAATTACCAAACACAAAACATTGCCTCATTTTA
* * *
13028 AAAATTTAAAAGGATATTAAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGC
1 AAAATTCAAAAGGATATTAAGCCATTTAGTTAAACGAGAAAAATCGACACCCAGCACCTTAGGGC
** *
13093 ACG-TTTCTCGAATTACCAAATGCAAAACATTGCCTTATTTTA
66 ACGTTTTCTCGAATTACCAAACACAAAACATTGCCTCATTTTA
13135 AAAA
1 AAAA
13139 AATTTCCTTT
Statistics
Matches: 99, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
107 39 0.39
108 60 0.61
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (108 bp):
AAAATTCAAAAGGATATTAAGCCATTTAGTTAAACGAGAAAAATCGACACCCAGCACCTTAGGGC
ACGTTTTCTCGAATTACCAAACACAAAACATTGCCTCATTTTA
Found at i:17897 original size:24 final size:24
Alignment explanation
Indices: 17870--17921 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
17860 TTAGTAAGTC
*
17870 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
17894 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
17918 AAAT
1 AAAT
17922 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:23277 original size:29 final size:29
Alignment explanation
Indices: 23206--23277 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
23196 TTACACGACA
* * *
23206 CCACACGGTCGTATGCTCTGCTGTGTGAG
1 CCACACGGGCGTGTGCTCTACTGTGTGAG
* *
23235 CCACAC-AGCTGTGTGCTCTATTGTGTGAG
1 CCACACGGGC-GTGTGCTCTACTGTGTGAG
23264 CCACACGGGCGTGT
1 CCACACGGGCGTGT
23278 AAGTCACATA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
28 1 0.03
29 32 0.91
30 2 0.06
ACGTcount: A:0.15, C:0.28, G:0.31, T:0.26
Consensus pattern (29 bp):
CCACACGGGCGTGTGCTCTACTGTGTGAG
Found at i:27625 original size:22 final size:23
Alignment explanation
Indices: 27580--27626 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
27570 AAGAATTTAC
27580 TTTTACAAAAAAACAAGTCGAAA
1 TTTTACAAAAAAACAAGTCGAAA
* * *
27603 TTTTAGAAAATAACAA-TCTAAA
1 TTTTACAAAAAAACAAGTCGAAA
27625 TT
1 TT
27627 CTCAAGAAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.53, C:0.11, G:0.06, T:0.30
Consensus pattern (23 bp):
TTTTACAAAAAAACAAGTCGAAA
Found at i:29999 original size:17 final size:17
Alignment explanation
Indices: 29973--30008 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
29963 AATAAGATCA
*
29973 TGAAAGAAAAAATAAGG
1 TGAAAAAAAAAATAAGG
29990 TGAAAAAAAAAATAAGG
1 TGAAAAAAAAAATAAGG
30007 TG
1 TG
30009 TGCACTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.22, T:0.14
Consensus pattern (17 bp):
TGAAAAAAAAAATAAGG
Found at i:38806 original size:21 final size:21
Alignment explanation
Indices: 38780--38826 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
38770 AATATATTTA
*
38780 TTTTTTAAATTTTAAAATACT
1 TTTTTTAAATTTTAAAATAAT
*
38801 TTTTTTAATTTTTAAAATAAT
1 TTTTTTAAATTTTAAAATAAT
38822 TTTTT
1 TTTTT
38827 GGTATTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTTTAAATTTTAAAATAAT
Found at i:38971 original size:16 final size:15
Alignment explanation
Indices: 38950--38980 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
38940 AATTTTTTAT
38950 GGCCCGGCCCGAACCC
1 GGCCCGGCCC-AACCC
38966 GGCCCGGCCCAACCC
1 GGCCCGGCCCAACCC
38981 ATGAGCACCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.13, C:0.58, G:0.29, T:0.00
Consensus pattern (15 bp):
GGCCCGGCCCAACCC
Found at i:40488 original size:13 final size:13
Alignment explanation
Indices: 40470--40504 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
40460 TATAAAAAAA
40470 ATATCATTTAATC
1 ATATCATTTAATC
40483 ATATCATTTAATC
1 ATATCATTTAATC
40496 ATATCATTT
1 ATATCATTT
40505 CTATATCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (13 bp):
ATATCATTTAATC
Found at i:45636 original size:31 final size:31
Alignment explanation
Indices: 45601--45660 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
45591 AAAAACTCAG
* **
45601 GTACCGAATTGAATGTTGAAGCCAAACTTGA
1 GTACCAAATTGAACATTGAAGCCAAACTTGA
*
45632 GTACCAAATTGAACATTGAAGCTAAACTT
1 GTACCAAATTGAACATTGAAGCCAAACTT
45661 AGATACTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (31 bp):
GTACCAAATTGAACATTGAAGCCAAACTTGA
Found at i:61766 original size:3 final size:3
Alignment explanation
Indices: 61758--61820 Score: 119
Period size: 3 Copynumber: 21.3 Consensus size: 3
61748 TTTATTTCTG
61758 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
61805 TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT T
61821 TTCTGATGGC
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 57 0.97
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:64606 original size:188 final size:188
Alignment explanation
Indices: 64289--64664 Score: 718
Period size: 188 Copynumber: 2.0 Consensus size: 188
64279 TCGACATATT
64289 CTATTCACTTAAGTGGTTTCCACTACATCTAGTGGCATGCATGAAGCAACCTTGGCCAAATATTT
1 CTATTCACTTAAGTGGTTTCCACTACATCTAGTGGCATGCATGAAGCAACCTTGGCCAAATATTT
64354 TCCTCATTTAAAGGGGAGAAAAAAAGTGTTTGTGTCACATGCTTTAATAAATCTTTTCTAAATTT
66 TCCTCATTTAAAGGGGAGAAAAAAAGTGTTTGTGTCACATGCTTTAATAAATCTTTTCTAAATTT
*
64419 TAATATTTGTGATTAATTAAATCTTTGTAGACCTTAAATTGGAATC-TTAAACTCTACA
131 TAATATTTGTGATTAATTAAATCTTTGCAGACCTTAAATTGGAATCTTTAAA-TCTACA
64477 CTATTCACTTAAGTGGTTTCCACTACATCTAGTGGCATGCATGAAGCAACCTTGGCCAAATATTT
1 CTATTCACTTAAGTGGTTTCCACTACATCTAGTGGCATGCATGAAGCAACCTTGGCCAAATATTT
64542 TCCTCATTTAAAGGGGAGAAAAAAAGTGTTTGTGTCACATGCTTTAATAAATCTTTTCTAAATTT
66 TCCTCATTTAAAGGGGAGAAAAAAAGTGTTTGTGTCACATGCTTTAATAAATCTTTTCTAAATTT
*
64607 TAATATTTGTGATTAATTAAATCTTTGCAGACCTTGAATTGGAATCTTTAAATCTACA
131 TAATATTTGTGATTAATTAAATCTTTGCAGACCTTAAATTGGAATCTTTAAATCTACA
64665 TTCAGATCCT
Statistics
Matches: 185, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
188 180 0.97
189 5 0.03
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (188 bp):
CTATTCACTTAAGTGGTTTCCACTACATCTAGTGGCATGCATGAAGCAACCTTGGCCAAATATTT
TCCTCATTTAAAGGGGAGAAAAAAAGTGTTTGTGTCACATGCTTTAATAAATCTTTTCTAAATTT
TAATATTTGTGATTAATTAAATCTTTGCAGACCTTAAATTGGAATCTTTAAATCTACA
Found at i:73333 original size:4 final size:4
Alignment explanation
Indices: 73324--73360 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
73314 ACATTAAAAA
* *
73324 ACAT ACAT ACAT AAAT ACAT ACAT ACAT ACAC ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
73361 TGCATACCAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.54, C:0.24, G:0.00, T:0.22
Consensus pattern (4 bp):
ACAT
Found at i:73961 original size:2 final size:2
Alignment explanation
Indices: 73954--73978 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
73944 CCTATAGTTT
73954 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
73979 TGAAAGATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:78919 original size:11 final size:11
Alignment explanation
Indices: 78889--78931 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
78879 AATCATTTAA
*
78889 TAATAAAATAT
1 TAATAAAATCT
*
78900 TACTAAAAATCT
1 TAAT-AAAATCT
78912 TAATAAAATCT
1 TAATAAAATCT
*
78923 TAATTAAAT
1 TAATAAAAT
78932 AACATTTATC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (11 bp):
TAATAAAATCT
Found at i:82952 original size:84 final size:83
Alignment explanation
Indices: 82719--83011 Score: 300
Period size: 79 Copynumber: 3.6 Consensus size: 83
82709 GAATTGTTAG
* *
82719 GGAAATT-AGGGGTTTGTATGAAAAAGTTT-AACCTTTTGGCCTTGATTGAAACAAAGTCCTGAT
1 GGAAATTGA-GGGTTTGTATGAAAAAGTTTAAACCTTTTGGCCTTGATTGAAACCAAGTTCTGAT
*
82782 TGTTTATTTGAATCGTGAA
65 TGTTTATTTGGATCGTGAA
* * * * * * *
82801 GGAAATTGTGGG-TTGTAT-TAGAAGTTCAAA-C-TTTGGCTTTGATTGAAACCAAATTTTGATT
1 GGAAATTGAGGGTTTGTATGAAAAAGTTTAAACCTTTTGGCCTTGATTGAAACCAAGTTCTGATT
82862 GTTTATTTGGATCGTGAA
66 GTTTATTTGGATCGTGAA
* *
82880 GGAAATTGAGGGTTTGTATGAAAAAATTTTAAACCTTTTGGCCTTGATTGAGACCAAGTTCTGAT
1 GGAAATTGAGGGTTTGTATG-AAAAAGTTTAAACCTTTTGGCCTTGATTGAAACCAAGTTCTGAT
* * *
82945 T-TGTTA-TTGGAATTGTTAG
65 TGT-TTATTTGG-ATCGTGAA
* * * *
82964 GGAAATTGGGGGGTTTGTATG-AAATGTTT-AACCTTTTGGTCTTAATTG
1 GGAAATT-GAGGGTTTGTATGAAAAAGTTTAAACCTTTTGGCCTTGATTG
83012 TTAGGGAAAT
Statistics
Matches: 174, Mismatches: 27, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
79 53 0.30
80 13 0.07
81 8 0.05
82 35 0.20
83 12 0.07
84 41 0.24
85 12 0.07
ACGTcount: A:0.28, C:0.08, G:0.25, T:0.39
Consensus pattern (83 bp):
GGAAATTGAGGGTTTGTATGAAAAAGTTTAAACCTTTTGGCCTTGATTGAAACCAAGTTCTGATT
GTTTATTTGGATCGTGAA
Found at i:83263 original size:299 final size:300
Alignment explanation
Indices: 82710--83305 Score: 696
Period size: 299 Copynumber: 2.0 Consensus size: 300
82700 GGTTCATTTG
* * *
82710 AATTGTTAGGGAAATTAGGGGTTTGTATGAAAAAGTTTAACCTTTTGGCCTTGATTGAAACAAAG
1 AATTGTTAGGGAAATTAGGGGTTTGTATGAAAAAGTTTAAACTTTTGGCCTTGAATAAAACAAAG
* * * * * *
82775 TCCTGATTGTTTATTTGAATCGTGAAGGAAATTGTGGGTTGTATTAGAAGTTCAAACTTTGGCTT
66 TCCTGATTGTTTATTCGAATCGTGAAGGAAATTGTGGGTTGAATAACAAGTTCAAACTTTAGCCT
* *
82840 TGATTGAAACCAAATTTTGATTGTTTATTTGGATCGTGAAGGAAATTGAGGGTTTGTATGAAAAA
131 TGATTGAAACCAAATTCTGATTGTTTATTTGAATCGTGAAGGAAATTGAGGGTTTGTATG-AAAA
* * *
82905 ATTTTAAACCTTTTGGCCTTGATTGAGACCAAGTTCTGATTTGTTATTGGAATTGTTAGGGAAAT
195 AGTTTAAACCTTTGGGCCTTGATTAAGACCAAGTTCTGATTTGTTATTGGAATTGTTAGGGAAAT
*
82970 TGGG-GGGTTTGTATG-A-AATGTTT-AACCTTTTGGTCTT
260 TGGGAGGGTTTGTATGAATAAAGTTTAAACCTTTTGGTCTT
* * *
83007 AATTGTTAGGGAAATTGTGGGGTTTGTATGAAAAAAGTTTAAAC-TTTGGCTTTGAATAAAACCA
1 AATTGTTAGGGAAATT-AGGGGTTTGTATG-AAAAAGTTTAAACTTTTGGCCTTGAATAAAACAA
** * * * *
83071 AGTTTTGATTGTTTATTCGAATTGTTATGGAAATTGTGGGTTTGAATGAACAA-TGT-AAGCTTT
64 AGTCCTGATTGTTTATTCGAATCGTGAAGGAAATTGTGGG-TTGAAT-AACAAGT-TCAAAC--T
* * *
83134 TTAGCCTTGATT-AAGACCAAAGTTCTGATT-TGTTATTTGAATTGTTAGGGAAATTTG-GGGTT
124 TTAGCCTTGATTGAA-ACCAAA-TTCTGATTGT-TTATTTGAATCGTGAAGGAAA-TTGAGGGTT
* * * * *
83196 TGTATG-AAAAGTTT-AACCTTTGGGTCTTGATTAAGATCAAGTTTTTATTTGTTATT-TAATTT
185 TGTATGAAAAAGTTTAAACCTTTGGGCCTTGATTAAGACCAAGTTCTGATTTGTTATTGGAA-TT
83258 GTTAGGGAAATTGGGAGGGTTTGTATGAATAAAGTTTAAACCTTTTGG
249 GTTAGGGAAATTGGGAGGGTTTGTATGAATAAAGTTTAAACCTTTTGG
83306 CCTTGAATCA
Statistics
Matches: 251, Mismatches: 32, Indels: 26
0.81 0.10 0.08
Matches are distributed among these distances:
297 16 0.06
298 64 0.25
299 74 0.29
300 24 0.10
301 19 0.08
302 41 0.16
303 13 0.05
ACGTcount: A:0.29, C:0.07, G:0.24, T:0.40
Consensus pattern (300 bp):
AATTGTTAGGGAAATTAGGGGTTTGTATGAAAAAGTTTAAACTTTTGGCCTTGAATAAAACAAAG
TCCTGATTGTTTATTCGAATCGTGAAGGAAATTGTGGGTTGAATAACAAGTTCAAACTTTAGCCT
TGATTGAAACCAAATTCTGATTGTTTATTTGAATCGTGAAGGAAATTGAGGGTTTGTATGAAAAA
GTTTAAACCTTTGGGCCTTGATTAAGACCAAGTTCTGATTTGTTATTGGAATTGTTAGGGAAATT
GGGAGGGTTTGTATGAATAAAGTTTAAACCTTTTGGTCTT
Found at i:88754 original size:27 final size:26
Alignment explanation
Indices: 88682--88766 Score: 91
Period size: 27 Copynumber: 3.2 Consensus size: 26
88672 ACCTAATCAG
*
88682 GCCAATTAAATTGGCGGCACCAAAGGT
1 GCCAA-TAAATTGGCGGCACCAATGGT
* *
88709 GCCAAATAAATCGGTGGCACCAATGGT
1 GCC-AATAAATTGGCGGCACCAATGGT
**
88736 GCCAATGTGATTGGCGGCACC-ATGGT
1 GCCAAT-AAATTGGCGGCACCAATGGT
88762 GCCAA
1 GCCAA
88767 AGGAAAAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
26 13 0.27
27 34 0.69
28 2 0.04
ACGTcount: A:0.29, C:0.24, G:0.28, T:0.19
Consensus pattern (26 bp):
GCCAATAAATTGGCGGCACCAATGGT
Found at i:88879 original size:18 final size:19
Alignment explanation
Indices: 88842--88908 Score: 91
Period size: 19 Copynumber: 3.6 Consensus size: 19
88832 TCAACTCATT
*
88842 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
*
88861 TTTTAATTTAATAA-ACTA
1 TTTTAATTTAATAACTCTA
* *
88879 TTCTCATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
88898 TTTTAATTTAA
1 TTTTAATTTAA
88909 GGAGGGCTTA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
18 15 0.38
19 25 0.62
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTTAATTTAATAACTCTA
Found at i:89248 original size:27 final size:27
Alignment explanation
Indices: 89191--89275 Score: 86
Period size: 27 Copynumber: 3.1 Consensus size: 27
89181 CACATTTTTT
* *
89191 TTTGGCACCA-TGGTGCCGCCAA-TCA
1 TTTGGCACCATTGGTGCCACCAATTTA
*
89216 CATTGGCACCATTGGTGCCACCAATTTA
1 -TTTGGCACCATTGGTGCCACCAATTTA
*
89244 TTTGGCACCTTTGGTG-CAGCCAATTTAA
1 TTTGGCACCATTGGTGCCA-CCAATTT-A
89272 TTTG
1 TTTG
89276 CCTGATCAGA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
26 11 0.22
27 32 0.64
28 7 0.14
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (27 bp):
TTTGGCACCATTGGTGCCACCAATTTA
Found at i:93325 original size:17 final size:18
Alignment explanation
Indices: 93303--93336 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
93293 GCGAACCTAA
93303 TTTTAT-AATTTTTTTAT
1 TTTTATGAATTTTTTTAT
93320 TTTTATGAATTTTTTTA
1 TTTTATGAATTTTTTTA
93337 ATAATTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (18 bp):
TTTTATGAATTTTTTTAT
Found at i:102516 original size:15 final size:14
Alignment explanation
Indices: 102496--102550 Score: 58
Period size: 15 Copynumber: 3.9 Consensus size: 14
102486 TATTTAAATT
102496 TTAAAATTTACAAAA
1 TTAAAATTTA-AAAA
102511 TTAAAATTTTAAAAA
1 TTAAAA-TTTAAAAA
* *
102526 TAAAAATAT-AAAA
1 TTAAAATTTAAAAA
*
102539 TTAAATTTTAAA
1 TTAAAATTTAAA
102551 TTTTCAAAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
13 10 0.30
14 4 0.12
15 15 0.45
16 4 0.12
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (14 bp):
TTAAAATTTAAAAA
Found at i:102540 original size:22 final size:23
Alignment explanation
Indices: 102491--102540 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
102481 AATTGTATTT
*
102491 AAATTTTAAAATTTACAAAATTA
1 AAATTTTAAAATATACAAAATTA
102514 AAATTTTAAAA-ATA-AAAATATA
1 AAATTTTAAAATATACAAAAT-TA
102536 AAATT
1 AAATT
102541 AAATTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 5 0.20
22 9 0.36
23 11 0.44
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (23 bp):
AAATTTTAAAATATACAAAATTA
Found at i:104272 original size:51 final size:51
Alignment explanation
Indices: 104196--104308 Score: 138
Period size: 51 Copynumber: 2.2 Consensus size: 51
104186 TGTTGTGAGA
* * * *
104196 TAAATTTGTTAAATCAAGACTAAATTGACAGAATATATAAATATT-ACGGGC
1 TAAATTTATTAAATCAAGACCAAATTGACAAAATATATAAATATTGA-AGGC
* * * *
104247 TAAATTTATTAAATCATGACCAAATTGACAAAATGTGTAAATTTTGAAGGC
1 TAAATTTATTAAATCAAGACCAAATTGACAAAATATATAAATATTGAAGGC
104298 TAAATTTATTA
1 TAAATTTATTA
104309 TTATACCAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
51 52 0.98
52 1 0.02
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (51 bp):
TAAATTTATTAAATCAAGACCAAATTGACAAAATATATAAATATTGAAGGC
Found at i:109431 original size:21 final size:20
Alignment explanation
Indices: 109401--109439 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
109391 GAAAAAATAA
* *
109401 ATTATTAAAAGTTTTAAAAAT
1 ATTA-TAAAAATTATAAAAAT
109422 ATTATAAAAATTATAAAA
1 ATTATAAAAATTATAAAA
109440 TGGTTAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
ATTATAAAAATTATAAAAAT
Found at i:114740 original size:17 final size:17
Alignment explanation
Indices: 114718--114750 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
114708 TATATATTTA
114718 TTTTTAATCAAATATAC
1 TTTTTAATCAAATATAC
114735 TTTTTAATCAAATATA
1 TTTTTAATCAAATATA
114751 TATATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTTAATCAAATATAC
Found at i:116034 original size:50 final size:47
Alignment explanation
Indices: 115957--116074 Score: 137
Period size: 50 Copynumber: 2.4 Consensus size: 47
115947 TTAAGCATCG
115957 ATTTAATTGTTTTTCAGATATGATGTTTTAAAAAAATATAAATATTT
1 ATTTAATTGTTTTTCAGATATGATGTTTTAAAAAAATATAAATATTT
* * * *
116004 ATTTAATTTGTTTTGTTTAGATATGGTGTTTTACATAAATATAAATATTT
1 ATTTAA-TTG-TTT-TTCAGATATGATGTTTTAAAAAAATATAAATATTT
* *
116054 GTTTATATTATTTGTTCAGAT
1 ATTTA-ATTGTTT-TTCAGAT
116075 CTTGTATTTA
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
47 6 0.10
48 3 0.05
49 13 0.22
50 37 0.62
51 1 0.02
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.53
Consensus pattern (47 bp):
ATTTAATTGTTTTTCAGATATGATGTTTTAAAAAAATATAAATATTT
Found at i:116283 original size:23 final size:24
Alignment explanation
Indices: 116234--116283 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
116224 ATAAAAATAT
* * * *
116234 AGTAAATGTATTTATGTGATTCGA
1 AGTAAATGAATTTATATGATACAA
116258 AGTAAAT-AATTTATATGATACAA
1 AGTAAATGAATTTATATGATACAA
116281 AGT
1 AGT
116284 GATATATGTG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.42, C:0.04, G:0.16, T:0.38
Consensus pattern (24 bp):
AGTAAATGAATTTATATGATACAA
Found at i:118045 original size:16 final size:16
Alignment explanation
Indices: 118024--118057 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
118014 AATTGGAATC
* *
118024 AAAATGTTTCTTCAAA
1 AAAATGTGTCCTCAAA
118040 AAAATGTGTCCTCAAA
1 AAAATGTGTCCTCAAA
118056 AA
1 AA
118058 TTAAAGTGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.15, G:0.09, T:0.29
Consensus pattern (16 bp):
AAAATGTGTCCTCAAA
Found at i:124082 original size:16 final size:17
Alignment explanation
Indices: 124063--124094 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
124053 AGTTCGAGTT
124063 GTTTTT-GGTTTGAATC
1 GTTTTTAGGTTTGAATC
124079 GTTTTTAGGTTTGAAT
1 GTTTTTAGGTTTGAAT
124095 TGAGCAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.16, C:0.03, G:0.25, T:0.56
Consensus pattern (17 bp):
GTTTTTAGGTTTGAATC
Found at i:129690 original size:15 final size:15
Alignment explanation
Indices: 129670--129699 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
129660 TATATTTTGG
129670 TTATTAAATTTTAAT
1 TTATTAAATTTTAAT
*
129685 TTATTATATTTTAAT
1 TTATTAAATTTTAAT
129700 CATTAATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTATTAAATTTTAAT
Found at i:134198 original size:11 final size:10
Alignment explanation
Indices: 134184--134228 Score: 56
Period size: 11 Copynumber: 4.4 Consensus size: 10
134174 GAATATATAA
134184 TAAATATATTT
1 TAAATAT-TTT
134195 TAAAT-TTTT
1 TAAATATTTT
*
134204 AAAATATTTT
1 TAAATATTTT
134214 TAAAATATTTT
1 T-AAATATTTT
134225 TAAA
1 TAAA
134229 ATACTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
9 7 0.23
10 8 0.27
11 15 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
TAAATATTTT
Found at i:134210 original size:20 final size:19
Alignment explanation
Indices: 134185--134245 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 19
134175 AATATATAAT
134185 AAATATATTTTAAATTTTTA
1 AAATAT-TTTTAAATTTTTA
134205 AAATATTTTTAAAATATTTTTA
1 AAATATTTTT--AA-ATTTTTA
*
134227 AAATACTTTTTTAATTTTT
1 AAATA-TTTTTAAATTTTT
134246 GGTGTTTATT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
19 4 0.11
20 12 0.33
21 3 0.08
22 12 0.33
23 5 0.14
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
AAATATTTTTAAATTTTTA
Found at i:134229 original size:11 final size:11
Alignment explanation
Indices: 134198--134237 Score: 71
Period size: 11 Copynumber: 3.5 Consensus size: 11
134188 TATATTTTAA
134198 ATTTTTAAAAT
1 ATTTTTAAAAT
134209 ATTTTTAAAAT
1 ATTTTTAAAAT
134220 ATTTTTAAAAT
1 ATTTTTAAAAT
134231 ACTTTTT
1 A-TTTTT
134238 TAATTTTTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 23 0.82
12 5 0.18
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (11 bp):
ATTTTTAAAAT
Found at i:138684 original size:16 final size:16
Alignment explanation
Indices: 138640--138689 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
138630 ACTAAAATGG
138640 TAAAATTTT-AATTTA
1 TAAAATTTTAAATTTA
* *
138655 -GATATTTTATAATTTA
1 TAAAATTTTA-AATTTA
*
138671 TAAAATTTTAAATTAA
1 TAAAATTTTAAATTTA
138687 TAA
1 TAA
138690 TGGTAAAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
14 6 0.22
16 14 0.52
17 7 0.26
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
TAAAATTTTAAATTTA
Found at i:141502 original size:18 final size:22
Alignment explanation
Indices: 141479--141524 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
141469 TTCAAACTTG
141479 ACTTGA-C-CAAAAA-AT-CGA
1 ACTTGAGCTCAAAAAGATCCGA
141497 ACTTGAGCTCAAAAAGATCCGA
1 ACTTGAGCTCAAAAAGATCCGA
141519 ACTTGA
1 ACTTGA
141525 AAAAAGCAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.25
19 1 0.04
20 6 0.25
21 2 0.08
22 9 0.38
ACGTcount: A:0.43, C:0.22, G:0.15, T:0.20
Consensus pattern (22 bp):
ACTTGAGCTCAAAAAGATCCGA
Found at i:144259 original size:3 final size:3
Alignment explanation
Indices: 144245--144277 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
144235 AAAGAGACAG
*
144245 ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
144278 GAAGAGTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:145895 original size:16 final size:16
Alignment explanation
Indices: 145841--145895 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
145831 AAAAATTACG
*
145841 ATTTAAATTTAAATTG
1 ATTTAAATTTAAATTA
* * *
145857 ATTAAAAATTATATTA
1 ATTTAAATTTAAATTA
* *
145873 ATCTAAATTTAAAATA
1 ATTTAAATTTAAATTA
145889 ATTTAAA
1 ATTTAAA
145896 CCTTTAATTA
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (16 bp):
ATTTAAATTTAAATTA
Found at i:146398 original size:14 final size:14
Alignment explanation
Indices: 146379--146408 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
146369 TTTTTGTAGA
146379 GATTAAAATTAAGT
1 GATTAAAATTAAGT
146393 GATTAAAATTAAGT
1 GATTAAAATTAAGT
146407 GA
1 GA
146409 ACGTTGGTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (14 bp):
GATTAAAATTAAGT
Found at i:152378 original size:31 final size:31
Alignment explanation
Indices: 152340--152408 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
152330 TTTTAGGACT
152340 TGAACTTGACAACTATACCCACATTGGGGCC
1 TGAACTTGACAACTATACCCACATTGGGGCC
* * * * * *
152371 TGAACTTGGCAATTGTTCCTATATTGGGGCC
1 TGAACTTGACAACTATACCCACATTGGGGCC
152402 TGAACTT
1 TGAACTT
152409 TTTTTTTCCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (31 bp):
TGAACTTGACAACTATACCCACATTGGGGCC
Found at i:152462 original size:31 final size:31
Alignment explanation
Indices: 152358--152468 Score: 90
Period size: 31 Copynumber: 3.7 Consensus size: 31
152348 ACAACTATAC
* **
152358 CCACATTGGGGCCTGAACTTGGCAATTG-TT
1 CCACATTGGGGCCTAAACTTTTCAATTGTTT
* *
152388 CCTATATTGGGGCCTGAACTTTT---TT-TTT
1 CC-ACATTGGGGCCTAAACTTTTCAATTGTTT
* *
152416 CCAAATT-AGGCCTTAAACTTTTCAATTGTTT
1 CCACATTGGGGCC-TAAACTTTTCAATTGTTT
*
152447 CCACATTGGGGCTTAAACTTTT
1 CCACATTGGGGCCTAAACTTTT
152469 TTTTGGCCAA
Statistics
Matches: 64, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
26 4 0.06
27 12 0.19
28 6 0.09
30 4 0.06
31 35 0.55
32 3 0.05
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.40
Consensus pattern (31 bp):
CCACATTGGGGCCTAAACTTTTCAATTGTTT
Found at i:156845 original size:366 final size:366
Alignment explanation
Indices: 156351--157078 Score: 1097
Period size: 366 Copynumber: 2.0 Consensus size: 366
156341 TTCTACACAT
* * *
156351 ACGAAGCTTATAAATTCTTCGATTCATTAACCGCGAAATAAATCCAATGAAAAAAACAAATTCCT
1 ACGAAGCTTATAAATTCTTCAATTCATTAACCGCAAAATAAATCCAACGAAAAAAACAAATTCCT
* * * *
156416 AGCACAATATCTTTAAATCACTGCCTGATCTTTTAGCTCGTTTTTCTTCTCCACTCATTTAAATC
66 AGCACAATATCTTCAAAACACTACCTGATCTTTTAGCTCATTTTTCTTCTCCACTCATTTAAATC
* *
156481 GAATAAT-AATCCTTCTAAATCCAGTTACTGTTCTTTCAAAATCTCTCACATAG-AAAAAAAAAA
131 GAATAATAAAT-CTTCTAAATCCAGTTACTGTTCTTTCAAAATCTATCACACAGAAAAAAAAAAA
* * *
156544 TCAAATAAAAACTAAAACTACTTAAACGACAAGACGAAAACAAACATATAT-ACAGAAATCAACA
195 TCAAATAAAAACTAAAACTACTTAAACAAAAAGACAAAAACAAACATATATAACAGAAATCAACA
*
156608 AATTTCACCAGTTTTTTTCAACCGTATATAAATCAACTCAACTGAAACTCAAACA-TTGAAGCAT
260 AATCTCACCAGTTTTTTTCAACCGTATATAAATCAACTCAACTGAAACTCAAACACTT-AAGCAT
* *
156672 CATTATCAATATCAACATCTCTATGCGGTATATTTCAACAAAA
324 CATTATAAATATCAACATCTCTATGCAGTATATTTCAACAAAA
*
156715 ACGAAGCTTATAAATTCTTCAATTCATTAACCGCAAAATTAATCCAACGAAAAAAAATCAAATTC
1 ACGAAGCTTATAAATTCTTCAATTCATTAACCGCAAAATAAATCCAACG-AAAAAAA-CAAATTC
** *
156780 CTAGCTTAGA-ATCTTCAAAACACTACCTGATCTTTTAGCTCATTTTTCTTCTCCACTCTTTTAA
64 CTAGCACA-ATATCTTCAAAACACTACCTGATCTTTTAGCTCATTTTTCTTCTCCACTCATTTAA
*
156844 ATTGAATAATAAATCTTCTAAATCCAGTTACTGTTCTTTCAAAATCTATCACACAGCAAAAAAAA
128 ATCGAATAATAAATCTTCTAAATCCAGTTACTGTTCTTTCAAAATCTATCACACAG-AAAAAAAA
*
156909 AAATCAAATAAAAACTAAAACTACTTAAACAAAAAGACAAAAACAAACATATATCCAGAAAATAG
192 AAATCAAATAAAAACTAAAACTACTTAAACAAAAAGACAAAAACAAACATATAT------AACAG
*
156974 AAATCAACAAATCTCACCAGTTTTTTTCTACCGTATATAAATCAACTCAACTGAAACTCAAACAC
251 AAATCAACAAATCTCACCAGTTTTTTTCAACCGTATATAAATCAACTCAACTGAAACTCAAACAC
* *
157039 TTAAGCATCATTGTAAATATCAATATCTCTATGCAGTATA
316 TTAAGCATCATTATAAATATCAACATCTCTATGCAGTATA
157079 CTCAACATAT
Statistics
Matches: 326, Mismatches: 24, Indels: 17
0.89 0.07 0.05
Matches are distributed among these distances:
364 45 0.14
365 7 0.02
366 111 0.34
367 4 0.01
368 58 0.18
375 99 0.30
376 2 0.01
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.29
Consensus pattern (366 bp):
ACGAAGCTTATAAATTCTTCAATTCATTAACCGCAAAATAAATCCAACGAAAAAAACAAATTCCT
AGCACAATATCTTCAAAACACTACCTGATCTTTTAGCTCATTTTTCTTCTCCACTCATTTAAATC
GAATAATAAATCTTCTAAATCCAGTTACTGTTCTTTCAAAATCTATCACACAGAAAAAAAAAAAT
CAAATAAAAACTAAAACTACTTAAACAAAAAGACAAAAACAAACATATATAACAGAAATCAACAA
ATCTCACCAGTTTTTTTCAACCGTATATAAATCAACTCAACTGAAACTCAAACACTTAAGCATCA
TTATAAATATCAACATCTCTATGCAGTATATTTCAACAAAA
Found at i:158013 original size:12 final size:13
Alignment explanation
Indices: 157998--158026 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
157988 TTTTTAACTT
157998 TTCTTTTTTTTC-
1 TTCTTTTTTTTCA
158010 TTCTTTTTTTTCA
1 TTCTTTTTTTTCA
158023 TTCT
1 TTCT
158027 CTTCTACTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.79
Consensus pattern (13 bp):
TTCTTTTTTTTCA
Found at i:158989 original size:22 final size:22
Alignment explanation
Indices: 158961--159005 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
158951 TTGGCAAAGG
158961 TTGAGGTTCCAAACTTTGAAGA
1 TTGAGGTTCCAAACTTTGAAGA
158983 TTGAGGTTCCAAACTTTGAAGA
1 TTGAGGTTCCAAACTTTGAAGA
159005 T
1 T
159006 CCAAATTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.33
Consensus pattern (22 bp):
TTGAGGTTCCAAACTTTGAAGA
Found at i:159750 original size:20 final size:20
Alignment explanation
Indices: 159699--159750 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 20
159689 AAATCATTGC
159699 AATATATGTAAAAATAATTT
1 AATATATGTAAAAATAATTT
* *
159719 AA-A-ATATAAAAAT-TTATT
1 AATATATGTAAAAATAAT-TT
159737 AATATATGTAAAAA
1 AATATATGTAAAAA
159751 CAACTTTTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
17 1 0.04
18 13 0.50
19 2 0.08
20 10 0.38
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (20 bp):
AATATATGTAAAAATAATTT
Found at i:159886 original size:34 final size:35
Alignment explanation
Indices: 159828--159894 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
159818 CAAATACCAG
159828 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
159863 AAAATATTTTTCAG-AAATCATTTTACGGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAA
159895 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.34
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:160514 original size:26 final size:28
Alignment explanation
Indices: 160453--160518 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 28
160443 TATGATTTAA
*
160453 AATAATATTATTAGTAAATAATAACTATG
1 AATAATATTATTAG-AAATAATAAATATG
*
160482 AAAAATATT-TTA-AAATAATAAAATAT-
1 AATAATATTATTAGAAATAAT-AAATATG
160508 AATAATATTAT
1 AATAATATTAT
160519 ATCTTAATCA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
26 15 0.47
27 6 0.19
28 3 0.09
29 8 0.25
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.38
Consensus pattern (28 bp):
AATAATATTATTAGAAATAATAAATATG
Found at i:160753 original size:3 final size:3
Alignment explanation
Indices: 160747--160772 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
160737 GAGATGATTG
160747 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
160773 AACACTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:166480 original size:27 final size:28
Alignment explanation
Indices: 166432--166494 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 28
166422 TATGATGTAA
* *
166432 TTTT-AATTAAAGTATTGAAATTTTCAT
1 TTTTAAATTAAAGTATTCAAATTATCAT
*
166459 TTTTAAATTAAA-TATTCTAATTATCAT
1 TTTTAAATTAAAGTATTCAAATTATCAT
*
166486 ATTTAAATT
1 TTTTAAATT
166495 TATATTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 24 0.77
28 7 0.23
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (28 bp):
TTTTAAATTAAAGTATTCAAATTATCAT
Found at i:167685 original size:12 final size:12
Alignment explanation
Indices: 167668--167694 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
167658 GTAACCTCCA
167668 ACATATATAAAT
1 ACATATATAAAT
167680 ACATATATAAAT
1 ACATATATAAAT
167692 ACA
1 ACA
167695 GCCCCTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (12 bp):
ACATATATAAAT
Found at i:169213 original size:21 final size:20
Alignment explanation
Indices: 169189--169247 Score: 55
Period size: 21 Copynumber: 2.9 Consensus size: 20
169179 CTTTTAATTT
169189 GATTCAACTGGTTTTTTAATC
1 GATTCAA-TGGTTTTTTAATC
* * * *
169210 GATTCGATTGATTTTTTTAGC
1 GATTC-AATGGTTTTTTAATC
*
169231 GATTCAATCGTTTTTTA
1 GATTCAATGGTTTTTTA
169248 GTTGTTTTAT
Statistics
Matches: 29, Mismatches: 8, Indels: 3
0.73 0.20 0.08
Matches are distributed among these distances:
20 8 0.28
21 20 0.69
22 1 0.03
ACGTcount: A:0.22, C:0.12, G:0.15, T:0.51
Consensus pattern (20 bp):
GATTCAATGGTTTTTTAATC
Found at i:170522 original size:30 final size:30
Alignment explanation
Indices: 170458--170524 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
170448 TCTAATATCT
*
170458 ATTTTCATACATAAATATTGATTTTGTGCG
1 ATTTTCATACATAAATATTGATTTTGTGCA
* *
170488 ATTTT-ATACATAAAATTTTGA-TTTGATTCA
1 ATTTTCATACAT-AAATATTGATTTTG-TGCA
170518 ATTTTCA
1 ATTTTCA
170525 CAAATCACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
29 10 0.32
30 20 0.65
31 1 0.03
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (30 bp):
ATTTTCATACATAAATATTGATTTTGTGCA
Found at i:174606 original size:22 final size:23
Alignment explanation
Indices: 174553--174608 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
174543 TTTAACTAAA
* * *
174553 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
174576 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
174598 ATTAAAATTAA
1 ATTAAAATTAA
174609 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:174621 original size:16 final size:16
Alignment explanation
Indices: 174584--174623 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
174574 TTAATAAAAT
* *
174584 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
174600 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
174616 TAAAATTA
1 TAAAATTA
174624 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:174729 original size:9 final size:9
Alignment explanation
Indices: 174696--174723 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
174686 TTTATCAAAT
174696 TATTAATTG
1 TATTAATTG
174705 TATTAATTG
1 TATTAATTG
174714 TATTAATTG
1 TATTAATTG
174723 T
1 T
174724 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:174733 original size:68 final size:68
Alignment explanation
Indices: 174612--174821 Score: 388
Period size: 68 Copynumber: 3.1 Consensus size: 68
174602 AAATTAATTG
*
174612 TTAGTAAAATTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
174675 TGA
66 TGA
174678 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
174743 TGA
66 TGA
*
174746 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
174811 TGA
66 TGA
174814 TTAGTAAA
1 TTAGTAAA
174822 ACAAACTTGA
Statistics
Matches: 140, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
66 26 0.19
68 114 0.81
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (68 bp):
TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
TGA
Found at i:174776 original size:9 final size:9
Alignment explanation
Indices: 174764--174791 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
174754 TTTATCAAAT
174764 TATTAATTG
1 TATTAATTG
174773 TATTAATTG
1 TATTAATTG
174782 TATTAATTG
1 TATTAATTG
174791 T
1 T
174792 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:174935 original size:23 final size:24
Alignment explanation
Indices: 174888--174933 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
174878 AAATAAACTT
174888 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
174912 AAAATAAAAAA-TATATATATTT
1 AAAATAAAAAACTAT-TATATTT
174934 AATATTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:184043 original size:23 final size:23
Alignment explanation
Indices: 183999--184043 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
183989 AGGATATTTT
* *
183999 ACAAATAAAATATTCAACTAATG
1 ACAAAAAAAATATTAAACTAATG
* *
184022 ACAAAAAAAATTTTAAAGTAAT
1 ACAAAAAAAATATTAAACTAAT
184044 TGCAAGGATC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.60, C:0.09, G:0.04, T:0.27
Consensus pattern (23 bp):
ACAAAAAAAATATTAAACTAATG
Found at i:187532 original size:30 final size:30
Alignment explanation
Indices: 187498--187560 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
187488 ATTTAACAAG
*
187498 CAAATGCC-TCTAAAATAATAGCAAAATTAA
1 CAAATGCCAT-TAAAATAATAACAAAATTAA
187528 CAAATGCCATTAAAATAATAACAAAATTAA
1 CAAATGCCATTAAAATAATAACAAAATTAA
187558 CAA
1 CAA
187561 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 30 0.97
31 1 0.03
ACGTcount: A:0.57, C:0.16, G:0.05, T:0.22
Consensus pattern (30 bp):
CAAATGCCATTAAAATAATAACAAAATTAA
Found at i:187645 original size:22 final size:22
Alignment explanation
Indices: 187597--187647 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
187587 ATAATAACAA
* * *
187597 TAAAATAGTAGCAACATGATAG
1 TAAAATAGTAGCAAAATAAGAG
187619 TAAAATAGTAGCAAAATAAGGAG
1 TAAAATAGTAGCAAAATAA-GAG
187642 -AAAATA
1 TAAAATA
187648 ACAAGAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 23 0.92
23 2 0.08
ACGTcount: A:0.57, C:0.06, G:0.18, T:0.20
Consensus pattern (22 bp):
TAAAATAGTAGCAAAATAAGAG
Found at i:189035 original size:3 final size:3
Alignment explanation
Indices: 189029--189064 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
189019 CTCTAATAAC
*
189029 AGA AGA AGA AGA AGA GGA A-A AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
189065 TAGACTGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:189213 original size:3 final size:3
Alignment explanation
Indices: 189207--189244 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
189197 TTCCCCAATA
189207 TTC TTC TTC TTC -TC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
189245 CCTTAGTTGC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:189884 original size:11 final size:10
Alignment explanation
Indices: 189866--189971 Score: 53
Period size: 11 Copynumber: 10.6 Consensus size: 10
189856 TTTATTTTTT
189866 TATTTTAAAA
1 TATTTTAAAA
189876 TACTTTTAAAA
1 TA-TTTTAAAA
189887 TATTTTTTAAAA
1 TA--TTTTAAAA
189899 T-TTTT-AAA
1 TATTTTAAAA
**
189907 -ATTTTAATT
1 TATTTTAAAA
*
189916 TTTTTTAAAA
1 TATTTTAAAA
**
189926 TACTTTTTTAA
1 TA-TTTTAAAA
**
189937 T-TTTT-TTA
1 TATTTTAAAA
189945 -ATTTTAAAA
1 TATTTTAAAA
189954 TATTTTTAAAA
1 TA-TTTTAAAA
189965 TACTTTT
1 TA-TTTT
189972 TTTAATTTTT
Statistics
Matches: 73, Mismatches: 13, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
8 13 0.18
9 10 0.14
10 10 0.14
11 31 0.42
12 9 0.12
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (10 bp):
TATTTTAAAA
Found at i:189892 original size:21 final size:20
Alignment explanation
Indices: 189868--189908 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
189858 TATTTTTTTA
189868 TTTTAAAATACTTTTAAAATATT
1 TTTTAAAAT--TTTTAAAATA-T
189891 TTTTAAAATTTTTAAAAT
1 TTTTAAAATTTTTAAAAT
189909 TTTAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 9 0.50
23 9 0.50
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTAAAATTTTTAAAATAT
Found at i:189922 original size:39 final size:39
Alignment explanation
Indices: 189867--189981 Score: 144
Period size: 39 Copynumber: 2.9 Consensus size: 39
189857 TTATTTTTTT
*
189867 ATTTTAAAATACTTTTAAAATA-TTTTTTAAAATTTTTAAA
1 ATTTTAAAATATTTTTAAAATACTTTTTT--AATTTTTAAA
* * **
189907 ATTTT-AATTTTTTTTAAAATACTTTTTTAATTTTTTTA
1 ATTTTAAAATATTTTTAAAATACTTTTTTAATTTTTAAA
189945 ATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTT
1 ATTTTAAAATATTTTTAAAATAC-TTTTTTAATTTTT
189982 GTTTTAATTT
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
38 13 0.20
39 28 0.43
40 24 0.37
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (39 bp):
ATTTTAAAATATTTTTAAAATACTTTTTTAATTTTTAAA
Found at i:194034 original size:24 final size:22
Alignment explanation
Indices: 193983--194034 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
193973 AATCTCATCG
*
193983 GTTTAAAAACTCATAAAGATGA
1 GTTTGAAAACTCATAAAGATGA
194005 -TGTTGAAAACTCATAAAGATATGA
1 GT-TTGAAAACTCATAAAG--ATGA
194029 GTTTGA
1 GTTTGA
194035 GTGAATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
21 1 0.04
22 15 0.60
24 8 0.32
25 1 0.04
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.31
Consensus pattern (22 bp):
GTTTGAAAACTCATAAAGATGA
Found at i:194502 original size:5 final size:5
Alignment explanation
Indices: 194492--194516 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
194482 TTGCCATTTG
194492 CCGTT CCGTT CCGTT CCGTT CCGTT
1 CCGTT CCGTT CCGTT CCGTT CCGTT
194517 GAAAGTCCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.40, G:0.20, T:0.40
Consensus pattern (5 bp):
CCGTT
Found at i:204107 original size:29 final size:29
Alignment explanation
Indices: 204071--204126 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
204061 TAACTATTTG
204071 AACTAATTAATAACATTATAAAAATATTA
1 AACTAATTAATAACATTATAAAAATATTA
*
204100 AACTAATTAATAACATTATAACAATAT
1 AACTAATTAATAACATTATAAAAATAT
204127 AGAGATCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (29 bp):
AACTAATTAATAACATTATAAAAATATTA
Found at i:204270 original size:6 final size:6
Alignment explanation
Indices: 204259--204286 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
204249 TCGTTTGGAA
204259 TATAAT TATAAT TATAAT TATAAT TATA
1 TATAAT TATAAT TATAAT TATAAT TATA
204287 TTTAGGGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TATAAT
Found at i:204361 original size:29 final size:30
Alignment explanation
Indices: 204329--204387 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
204319 TATGGTTTAA
* *
204329 TGTGTAATTGAATACAT-GAATTTTGATTT
1 TGTGCAATTGAATACATAAAATTTTGATTT
**
204358 TGTGCAATTTTATACATAAAATTTTGATTT
1 TGTGCAATTGAATACATAAAATTTTGATTT
204388 GATCCAATTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.32, C:0.05, G:0.14, T:0.49
Consensus pattern (30 bp):
TGTGCAATTGAATACATAAAATTTTGATTT
Found at i:211350 original size:23 final size:23
Alignment explanation
Indices: 211318--211363 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
211308 CTTATCAAGC
*
211318 AAATACCTCTAAAATAATAGTAA
1 AAATAACTCTAAAATAATAGTAA
211341 AAATAACTCTAAAATAATAGTAA
1 AAATAACTCTAAAATAATAGTAA
211364 TAACAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.59, C:0.11, G:0.04, T:0.26
Consensus pattern (23 bp):
AAATAACTCTAAAATAATAGTAA
Found at i:211373 original size:20 final size:21
Alignment explanation
Indices: 211327--211374 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
211317 CAAATACCTC
**
211327 TAAAATAATAGTAAAAATAACTC
1 TAAAATAATAGT--AAATAACAA
211350 TAAAATAATAGT-AATAACAA
1 TAAAATAATAGTAAATAACAA
211370 TAAAA
1 TAAAA
211375 CAAGAGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 11 0.48
23 12 0.52
ACGTcount: A:0.65, C:0.06, G:0.04, T:0.25
Consensus pattern (21 bp):
TAAAATAATAGTAAATAACAA
Found at i:213037 original size:15 final size:15
Alignment explanation
Indices: 213017--213050 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
213007 TTTGTAACAA
213017 AATACGACTATTCAC
1 AATACGACTATTCAC
213032 AATACGACTATTCAC
1 AATACGACTATTCAC
213047 AATA
1 AATA
213051 GATTTTTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.24, G:0.06, T:0.26
Consensus pattern (15 bp):
AATACGACTATTCAC
Found at i:213883 original size:5 final size:5
Alignment explanation
Indices: 213873--213922 Score: 59
Period size: 5 Copynumber: 10.2 Consensus size: 5
213863 AACACTCTCG
* *
213873 TTTTC TTTTC TTTTC TTTGC -TTTC CTTT- TTTTC TTTTC TTTTCC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT-C TTTTC
213922 T
1 T
213923 CAATGCAGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
4 6 0.15
5 28 0.72
6 5 0.13
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (5 bp):
TTTTC
Found at i:213888 original size:10 final size:10
Alignment explanation
Indices: 213873--213922 Score: 59
Period size: 9 Copynumber: 5.1 Consensus size: 10
213863 AACACTCTCG
213873 TTTTCTTTTC
1 TTTTCTTTTC
*
213883 TTTTCTTTGC
1 TTTTCTTTTC
*
213893 -TTTCCTTT-
1 TTTTCTTTTC
213901 TTTTCTTTTC
1 TTTTCTTTTC
213911 TTTTCCTTTTC
1 TTTT-CTTTTC
213922 T
1 T
213923 CAATGCAGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
9 13 0.39
10 13 0.39
11 7 0.21
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (10 bp):
TTTTCTTTTC
Found at i:213906 original size:18 final size:19
Alignment explanation
Indices: 213873--213920 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
213863 AACACTCTCG
*
213873 TTTTCTTTTCTTTTCTTTGC
1 TTTTCCTTT-TTTTCTTTGC
*
213893 -TTTCCTTTTTTTCTTTTC
1 TTTTCCTTTTTTTCTTTGC
213911 TTTTCCTTTT
1 TTTTCCTTTT
213921 CTCAATGCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (19 bp):
TTTTCCTTTTTTTCTTTGC
Found at i:222468 original size:3 final size:3
Alignment explanation
Indices: 222460--222493 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
222450 TTAATGCTAT
222460 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
222494 CGAGACTCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:224032 original size:64 final size:65
Alignment explanation
Indices: 223931--224063 Score: 223
Period size: 64 Copynumber: 2.1 Consensus size: 65
223921 CATATGATTT
*
223931 TTCATGTATTTGGAGTCTTTGGAATCAGGATATACTACGGATACAAGTGTGAGACGC-AGAGGAC
1 TTCATGTATTTGGAGTCTTTGGAATCAGGATATACTACGGATACAAGTGTGAGACACAAGAGGAC
* * *
223995 TTCATGTATTTGGGGTCTTTGGGATCAGGATATACTACGGATACAAGTGTGAGACACAAGAGTAC
1 TTCATGTATTTGGAGTCTTTGGAATCAGGATATACTACGGATACAAGTGTGAGACACAAGAGGAC
224060 TTCA
1 TTCA
224064 AGAAACAAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
64 54 0.84
65 10 0.16
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.29
Consensus pattern (65 bp):
TTCATGTATTTGGAGTCTTTGGAATCAGGATATACTACGGATACAAGTGTGAGACACAAGAGGAC
Found at i:237390 original size:21 final size:21
Alignment explanation
Indices: 237365--237404 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
237355 AATTTCACTC
* *
237365 AATTTGATTTGACTCGACTTG
1 AATTTCATTTCACTCGACTTG
237386 AATTTCATTTCACTCGACT
1 AATTTCATTTCACTCGACT
237405 CGATTCGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.42
Consensus pattern (21 bp):
AATTTCATTTCACTCGACTTG
Found at i:239220 original size:21 final size:21
Alignment explanation
Indices: 239195--239234 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
239185 AATTTCACTC
* *
239195 AATTTGATTTGACTCGACTTG
1 AATTTCATTTCACTCGACTTG
239216 AATTTCATTTCACTCGACT
1 AATTTCATTTCACTCGACT
239235 CGATTCGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.42
Consensus pattern (21 bp):
AATTTCATTTCACTCGACTTG
Found at i:241496 original size:33 final size:33
Alignment explanation
Indices: 241456--241530 Score: 105
Period size: 33 Copynumber: 2.3 Consensus size: 33
241446 TTTGGTTTGA
* * *
241456 TTTTATATCGAATCAGACATAGGGTTATTTGGT
1 TTTTATATAGAATCAAACATAGGATTATTTGGT
* *
241489 TTTTATATAGATTTAAACATAGGATTATTTGGT
1 TTTTATATAGAATCAAACATAGGATTATTTGGT
241522 TTTTATATA
1 TTTTATATA
241531 AACTTTTAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.31, C:0.05, G:0.16, T:0.48
Consensus pattern (33 bp):
TTTTATATAGAATCAAACATAGGATTATTTGGT
Found at i:250916 original size:23 final size:23
Alignment explanation
Indices: 250870--250916 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
250860 TCTTGGACGG
**
250870 TTGGATTTTATTTTGGTACTTTC
1 TTGGATTTTATTTTGGTAAATTC
* *
250893 TTGGATTTTTTTTTGTTAAATTC
1 TTGGATTTTATTTTGGTAAATTC
250916 T
1 T
250917 ATTATTAGTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.15, C:0.06, G:0.15, T:0.64
Consensus pattern (23 bp):
TTGGATTTTATTTTGGTAAATTC
Found at i:256267 original size:14 final size:14
Alignment explanation
Indices: 256231--256264 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
256221 TCATCATTTG
*
256231 CCTATAACCAAAAC
1 CCTATAACTAAAAC
256245 CCTATAACTAAAAC
1 CCTATAACTAAAAC
256259 CC-ATAA
1 CCTATAA
256265 ACTCATACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (14 bp):
CCTATAACTAAAAC
Found at i:257179 original size:31 final size:31
Alignment explanation
Indices: 257115--257184 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
257105 AATAACTGCC
* * *
257115 TAATAACTTAAATAAAAATTTTCGAATAATT
1 TAATGACTTAAATAAAAAATTTCAAATAATT
*
257146 TAATGACTTAAATAAAAAAATTT-AAATATTT
1 TAATGACTTAAAT-AAAAAATTTCAAATAATT
257177 TAATGACT
1 TAATGACT
257185 ATTTTATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 26 0.76
32 8 0.24
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (31 bp):
TAATGACTTAAATAAAAAATTTCAAATAATT
Found at i:260595 original size:16 final size:18
Alignment explanation
Indices: 260572--260606 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
260562 TGACTTATTA
260572 ATTTTTTTAAT-ATTTAT
1 ATTTTTTTAATAATTTAT
260589 ATTTTTTTAATAATTTAT
1 ATTTTTTTAATAATTTAT
260607 TTAATTGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTTTTTTAATAATTTAT
Found at i:260607 original size:16 final size:17
Alignment explanation
Indices: 260568--260608 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
260558 TGGTTGACTT
260568 ATTA-ATTTTTTTAATA
1 ATTATATTTTTTTAATA
*
260584 TTTATATTTTTTTAATA
1 ATTATATTTTTTTAATA
260601 ATT-TATTT
1 ATTATATTT
260609 AATTGAACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTATATTTTTTTAATA
Found at i:262632 original size:92 final size:93
Alignment explanation
Indices: 262513--262698 Score: 365
Period size: 92 Copynumber: 2.0 Consensus size: 93
262503 TATAGGTATA
262513 AATATATTACAAATAAAAAATAATATTAAATAAATTTAAAAGAACCCGCACATGACGTTTATACA
1 AATATATTACAAATAAAAAATAATATTAAATAAATTTAAAAGAACCCGCACATGACGTTTATACA
262578 CGATAAAGTTCGAGTCTTTTTAGTCGTG
66 CGATAAAGTTCGAGTCTTTTTAGTCGTG
262606 AATATATTAC-AATAAAAAATAATATTAAATAAATTTAAAAGAACCCGCACATGACGTTTATACA
1 AATATATTACAAATAAAAAATAATATTAAATAAATTTAAAAGAACCCGCACATGACGTTTATACA
262670 CGATAAAGTTCGAGTCTTTTTAGTCGTG
66 CGATAAAGTTCGAGTCTTTTTAGTCGTG
262698 A
1 A
262699 CGGTAAAAAT
Statistics
Matches: 93, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
92 83 0.89
93 10 0.11
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.31
Consensus pattern (93 bp):
AATATATTACAAATAAAAAATAATATTAAATAAATTTAAAAGAACCCGCACATGACGTTTATACA
CGATAAAGTTCGAGTCTTTTTAGTCGTG
Found at i:266066 original size:12 final size:11
Alignment explanation
Indices: 266049--266088 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
266039 ATTTACGTTC
266049 AAAAAAATATAT
1 AAAAAAAT-TAT
*
266061 AAAAAAATTACC
1 AAAAAAATTA-T
266073 AAAAAAATTAT
1 AAAAAAATTAT
266084 AAAAA
1 AAAAA
266089 TAACGAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 7 0.28
12 18 0.72
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (11 bp):
AAAAAAATTAT
Found at i:268678 original size:21 final size:20
Alignment explanation
Indices: 268649--268690 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 20
268639 AAAGAAATAT
268649 TTTTATTTAATTATTATTATAA
1 TTTTATTTAA-TATT-TTATAA
268671 TTTT-TTTAATATTTTATAA
1 TTTTATTTAATATTTTATAA
268690 T
1 T
268691 GTATGAATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.35
20 4 0.20
21 5 0.25
22 4 0.20
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTATTTAATATTTTATAA
Found at i:288291 original size:43 final size:44
Alignment explanation
Indices: 288223--288309 Score: 133
Period size: 43 Copynumber: 2.0 Consensus size: 44
288213 TTTAAAGTAA
* *
288223 AAAAAATGGCGCGTTCACTAAAAAAAAATCCTTTT-GTAGCAAAT
1 AAAAAATGACACGTTCACTAAAAAAAAAT-CTTTTCGTAGCAAAT
288267 AAAAAATGACACGTTCACT-AAAAAAAATCTTTTCGTAGCAAAT
1 AAAAAATGACACGTTCACTAAAAAAAAATCTTTTCGTAGCAAAT
288310 CATTTATTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
42 5 0.12
43 18 0.45
44 17 0.43
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.25
Consensus pattern (44 bp):
AAAAAATGACACGTTCACTAAAAAAAAATCTTTTCGTAGCAAAT
Found at i:295513 original size:134 final size:134
Alignment explanation
Indices: 295273--295541 Score: 520
Period size: 134 Copynumber: 2.0 Consensus size: 134
295263 ATTCTAAAGT
295273 ATTTTAAAATGATTTTAAAGTCCTATAATTTATTTTATTTATTTTCCATAATTTTGTACAAATGT
1 ATTTTAAAATGATTTTAAAGTCCTATAATTTATTTTATTTATTTTCCATAATTTTGTACAAATGT
*
295338 TTTTAAATTTAATTTCTTAGTCCAATTAATGAACGAAAGACATTCGAGTTACTTTGGCAACATAA
66 TTTTAAATTTAATTTCTTAGTCCAATTAATGAACGAAAGACATTCGAGTTACTTCGGCAACATAA
295403 TGTG
131 TGTG
*
295407 ATTTTAAAATGATTTTAAAGTCCTATAGTTTATTTTATTTATTTTCCATAATTTTGTACAAATGT
1 ATTTTAAAATGATTTTAAAGTCCTATAATTTATTTTATTTATTTTCCATAATTTTGTACAAATGT
295472 TTTTAAATTTAATTTCTTAGTCCAATTAATGAACGAAAGACATTCGAGTTACTTCGGCAACATAA
66 TTTTAAATTTAATTTCTTAGTCCAATTAATGAACGAAAGACATTCGAGTTACTTCGGCAACATAA
295537 TGTG
131 TGTG
295541 A
1 A
295542 CATCTTGCAT
Statistics
Matches: 133, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
134 133 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44
Consensus pattern (134 bp):
ATTTTAAAATGATTTTAAAGTCCTATAATTTATTTTATTTATTTTCCATAATTTTGTACAAATGT
TTTTAAATTTAATTTCTTAGTCCAATTAATGAACGAAAGACATTCGAGTTACTTCGGCAACATAA
TGTG
Found at i:296185 original size:21 final size:21
Alignment explanation
Indices: 296161--296204 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
296151 GATATGAGAG
**
296161 TTTTAGCACTTAATTTGTTCA
1 TTTTAGCACTTAACCTGTTCA
296182 TTTTAGCACTTAACCTGTTCA
1 TTTTAGCACTTAACCTGTTCA
296203 TT
1 TT
296205 ATGTATTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.18, G:0.09, T:0.50
Consensus pattern (21 bp):
TTTTAGCACTTAACCTGTTCA
Found at i:297824 original size:6 final size:6
Alignment explanation
Indices: 297813--297845 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
297803 AGATTTCCAA
*
297813 AAATGG AAATGG AAATGG AAATGG AAATAG AAA
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAA
297846 CTTGCAATCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.58, C:0.00, G:0.27, T:0.15
Consensus pattern (6 bp):
AAATGG
Found at i:298022 original size:26 final size:26
Alignment explanation
Indices: 297988--298059 Score: 92
Period size: 26 Copynumber: 2.8 Consensus size: 26
297978 AATTTTCTCG
297988 AAATTTTATTGGGGGTAAAATCGTCA
1 AAATTTTATTGGGGGTAAAATCGTCA
* * * *
298014 AAATCTTATCGAGGGTAAAATTGTCA
1 AAATTTTATTGGGGGTAAAATCGTCA
*
298040 AAATTTTACT-GGGGTAAAAT
1 AAATTTTATTGGGGGTAAAAT
298060 TGGGGTGAGA
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
25 9 0.24
26 29 0.76
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.33
Consensus pattern (26 bp):
AAATTTTATTGGGGGTAAAATCGTCA
Found at i:299198 original size:104 final size:105
Alignment explanation
Indices: 299040--299249 Score: 413
Period size: 104 Copynumber: 2.0 Consensus size: 105
299030 AAGTCTAGAA
299040 AGAAGAATTAAAACCATAGAATATCAACTTATTACATTATATTATTTATTAAAATTAAAAAAAAA
1 AGAAGAATTAAAACCATAGAATATCAACTTATTACATTATATTATTTATTAAAATTAAAAAAAAA
299105 AAAAGATTAGAGAGAAAATACATGTGAAGACAGAAAAGTG
66 AAAAGATTAGAGAGAAAATACATGTGAAGACAGAAAAGTG
299145 AGAAGAATT-AAACCATAGAATATCAACTTATTACATTATATTATTTATTAAAATTAAAAAAAAA
1 AGAAGAATTAAAACCATAGAATATCAACTTATTACATTATATTATTTATTAAAATTAAAAAAAAA
299209 AAAAGATTAGAGAGAAAATACATGTGAAGACAGAAAAGTG
66 AAAAGATTAGAGAGAAAATACATGTGAAGACAGAAAAGTG
299249 A
1 A
299250 AAACAAGAGG
Statistics
Matches: 105, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
104 96 0.91
105 9 0.09
ACGTcount: A:0.55, C:0.07, G:0.12, T:0.26
Consensus pattern (105 bp):
AGAAGAATTAAAACCATAGAATATCAACTTATTACATTATATTATTTATTAAAATTAAAAAAAAA
AAAAGATTAGAGAGAAAATACATGTGAAGACAGAAAAGTG
Found at i:301588 original size:111 final size:111
Alignment explanation
Indices: 301432--301647 Score: 315
Period size: 111 Copynumber: 1.9 Consensus size: 111
301422 TTGTCTCCCA
* *
301432 TCTCGAGGTGTCACGTGTCGATTCGCTATTAGTAAACTAGGGATAAATGACAAGTGATCTGGTGT
1 TCTCGAGGTGTCACGTGTCGATTCACTATTAGTAAACTAGAGATAAATGACAAGTGATCTGGTGT
* *
301497 CATAGGCTTAAGTAGAATGGTGCTATGACGTGCCTTGAGTCTCTCG
66 CATAAGCTTAAGTAGAATAGTGCTATGACGTGCCTTGAGTCTCTCG
* * * * * *
301543 TCTCGAGGTGTCACGTGTTGATTTACTATTGGTAGATTAGAGATAAATGACAAGTGATTTGGTGT
1 TCTCGAGGTGTCACGTGTCGATTCACTATTAGTAAACTAGAGATAAATGACAAGTGATCTGGTGT
* * *
301608 CATAAGCTTAAGTAGAATAGTGTTATGATGTGTCTTGAGT
66 CATAAGCTTAAGTAGAATAGTGCTATGACGTGCCTTGAGT
301648 TATCTTAGAT
Statistics
Matches: 92, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
111 92 1.00
ACGTcount: A:0.26, C:0.13, G:0.27, T:0.34
Consensus pattern (111 bp):
TCTCGAGGTGTCACGTGTCGATTCACTATTAGTAAACTAGAGATAAATGACAAGTGATCTGGTGT
CATAAGCTTAAGTAGAATAGTGCTATGACGTGCCTTGAGTCTCTCG
Found at i:306258 original size:31 final size:31
Alignment explanation
Indices: 306211--306275 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
306201 TTTACTGTAA
* *
306211 GTACTAATTTGGACTAA-AAAGCCAAGTTCAG
1 GTACCAATTTGAACTAAGAAA-CCAAGTTCAG
306242 GTACCAATTTGAACTAAGAAACCAAGTTCAG
1 GTACCAATTTGAACTAAGAAACCAAGTTCAG
306273 GTA
1 GTA
306276 TCTAATTAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 28 0.90
32 3 0.10
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (31 bp):
GTACCAATTTGAACTAAGAAACCAAGTTCAG
Found at i:309858 original size:27 final size:27
Alignment explanation
Indices: 309828--309883 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
309818 CAAAATAATT
*
309828 TTCAAAA-ATTCAAAATAAATTTTAAAA
1 TTCAAAATATTCAAAA-AAATTCTAAAA
* *
309855 TTCAAAATATTTATAAAAATTCTAAAA
1 TTCAAAATATTCAAAAAAATTCTAAAA
309882 TT
1 TT
309884 TATAGTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (27 bp):
TTCAAAATATTCAAAAAAATTCTAAAA
Found at i:309875 original size:19 final size:19
Alignment explanation
Indices: 309811--309882 Score: 85
Period size: 19 Copynumber: 3.7 Consensus size: 19
309801 AAATTACAAA
*
309811 AAAAAATCAAAATAATTTT
1 AAAAATTCAAAATAATTTT
309830 CAAAAATTCAAAATAAATTTT
1 -AAAAATTCAAAAT-AATTTT
309851 -AAAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
309869 AAAAATTCTAAAAT
1 AAAAATTC-AAAAT
309883 TTATAGTTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
17 4 0.09
18 1 0.02
19 19 0.40
20 17 0.36
21 6 0.13
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:310187 original size:184 final size:185
Alignment explanation
Indices: 309867--310235 Score: 731
Period size: 184 Copynumber: 2.0 Consensus size: 185
309857 CAAAATATTT
309867 ATAAAAATTCTAAAATTTATAGTTTTTAAAGAATTATAAAAATTAAAAAATCTAAAGAATATAGA
1 ATAAAAATTCTAAAATTTATAGTTTTTAAAGAATTATAAAAATTAAAAAATCTAAAGAATATAGA
309932 AAGGAAAAAAATTTTGGGGAATACTAAAATTTATGAAGTTGCCATGTAAGTTTGTTTTTGCTCAG
66 AAGGAAAAAAATTTTGGGGAATACTAAAATTTATGAAGTTGCCATGTAAGTTTGTTTTTGCTCAG
309997 GGGTGGATCTTGGGCCGGTACGACTAATAAAATGGAAAAAAAATTTCATTTAGAC
131 GGGTGGATCTTGGGCCGGTACGACTAATAAAATGGAAAAAAAATTTCATTTAGAC
310052 ATAAAAATTC-AAAATTTATAGTTTTTAAAGAATTATAAAAATTAAAAAATCTAAAGAATATAGA
1 ATAAAAATTCTAAAATTTATAGTTTTTAAAGAATTATAAAAATTAAAAAATCTAAAGAATATAGA
310116 AAGGAAAAAAATTTTGGGGAATACTAAAATTTATGAAGTTGCCATGTAAGTTTGTTTTTGCTCAG
66 AAGGAAAAAAATTTTGGGGAATACTAAAATTTATGAAGTTGCCATGTAAGTTTGTTTTTGCTCAG
310181 GGGTGGATCTTGGGCCGGTACGACTAATAAAATGGAAAAAAAATTTCATTTAGAC
131 GGGTGGATCTTGGGCCGGTACGACTAATAAAATGGAAAAAAAATTTCATTTAGAC
310236 TATTTATAAT
Statistics
Matches: 184, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
184 174 0.95
185 10 0.05
ACGTcount: A:0.43, C:0.08, G:0.17, T:0.32
Consensus pattern (185 bp):
ATAAAAATTCTAAAATTTATAGTTTTTAAAGAATTATAAAAATTAAAAAATCTAAAGAATATAGA
AAGGAAAAAAATTTTGGGGAATACTAAAATTTATGAAGTTGCCATGTAAGTTTGTTTTTGCTCAG
GGGTGGATCTTGGGCCGGTACGACTAATAAAATGGAAAAAAAATTTCATTTAGAC
Found at i:310858 original size:15 final size:15
Alignment explanation
Indices: 310820--310859 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
310810 TCATATCATT
*
310820 ATTACTTTATATTGA
1 ATTACTTTATATTAA
310835 ATTACTTTATATTTAA
1 ATTACTTTATA-TTAA
310851 ATTA-TTTAT
1 ATTACTTTAT
310860 TTTTCATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (15 bp):
ATTACTTTATATTAA
Found at i:313880 original size:15 final size:15
Alignment explanation
Indices: 313860--313889 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
313850 GACTACAATG
313860 GCCCCATCCTGAACC
1 GCCCCATCCTGAACC
313875 GCCCCATCCTGAACC
1 GCCCCATCCTGAACC
313890 ACAGGAGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.53, G:0.13, T:0.13
Consensus pattern (15 bp):
GCCCCATCCTGAACC
Found at i:324716 original size:21 final size:21
Alignment explanation
Indices: 324668--324717 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
324658 TACATTTTTG
* * *
324668 CTCACACGGCCGTGTGACCTA
1 CTCACACGGCCATGTAACCCA
324689 -TCTACACGGCCATGTAACCCA
1 CTC-ACACGGCCATGTAACCCA
324710 CTCACACG
1 CTCACACG
324718 TTCATATGGC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 2 0.08
21 20 0.83
22 2 0.08
ACGTcount: A:0.24, C:0.40, G:0.18, T:0.18
Consensus pattern (21 bp):
CTCACACGGCCATGTAACCCA
Found at i:330000 original size:5 final size:5
Alignment explanation
Indices: 329992--330017 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
329982 ATTAAAAATA
329992 TTAAT TTAAT TTAAT TTAAT TTAAT T
1 TTAAT TTAAT TTAAT TTAAT TTAAT T
330018 AGCATCAATA
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:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTAAT
Found at i:334847 original size:3 final size:3
Alignment explanation
Indices: 334839--334904 Score: 89
Period size: 3 Copynumber: 22.0 Consensus size: 3
334829 ATCCATTGTT
* *
334839 TCA TCA TCA TCA TCA TCA TCA TCA CCA TCA -GA CTCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA -TCA TCA TCA TCA
*
334884 TCA TCA TCA TCT TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA
334905 GACTCTTCTA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
2 1 0.02
3 53 0.96
4 1 0.02
ACGTcount: A:0.32, C:0.35, G:0.02, T:0.32
Consensus pattern (3 bp):
TCA
Found at i:338761 original size:31 final size:31
Alignment explanation
Indices: 338726--338790 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
338716 TATCAAATTT
338726 TTATTTTAAAAATT-AAAAAAGTATTTTAAAA
1 TTATTTT-AAAATTAAAAAAAGTATTTTAAAA
338757 TTATTTTAAAATTAAAAAAAGTATTTTAAAA
1 TTATTTTAAAATTAAAAAAAGTATTTTAAAA
338788 TTA
1 TTA
338791 AAAAAATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 6 0.18
31 27 0.82
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (31 bp):
TTATTTTAAAATTAAAAAAAGTATTTTAAAA
Found at i:338781 original size:20 final size:20
Alignment explanation
Indices: 338753--338796 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
338743 AAAGTATTTT
*
338753 AAAATTATTTTAAAATTAAA
1 AAAAGTATTTTAAAATTAAA
338773 AAAAGTATTTTAAAATTAAA
1 AAAAGTATTTTAAAATTAAA
338793 AAAA
1 AAAA
338797 TAATATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (20 bp):
AAAAGTATTTTAAAATTAAA
Found at i:339463 original size:10 final size:10
Alignment explanation
Indices: 339450--339478 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
339440 TTTCCTGAAT
339450 TTTTAATTTA
1 TTTTAATTTA
339460 TTTTAATTTA
1 TTTTAATTTA
339470 TTTT-ATTTA
1 TTTTAATTTA
339479 CTATGTAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.26
10 14 0.74
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTTAATTTA
Found at i:345277 original size:6 final size:6
Alignment explanation
Indices: 345266--345290 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
345256 GACGAAGGGA
345266 TTTCTT TTTCTT TTTCTT TTTCTT T
1 TTTCTT TTTCTT TTTCTT TTTCTT T
345291 GGCTTCCGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTCTT
Found at i:345354 original size:1 final size:1
Alignment explanation
Indices: 345348--345372 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
345338 TCCCGAGTGA
345348 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
345373 GCAGAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:345623 original size:46 final size:48
Alignment explanation
Indices: 345565--345655 Score: 143
Period size: 47 Copynumber: 1.9 Consensus size: 48
345555 TAAAAAATAT
*
345565 TTTATATAATTTTTTAGATT-TTAAAATTT-TCATTTAATTTTTATGTA
1 TTTATATAATTTTATAGATTATTAAAATTTCT-ATTTAATTTTTATGTA
345612 TTTATAT-ATTTTATAGATTATTAAAATTTCTATTTAATTTTTAT
1 TTTATATAATTTTATAGATTATTAAAATTTCTATTTAATTTTTAT
345656 AATTTTCTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
46 11 0.27
47 29 0.71
48 1 0.02
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (48 bp):
TTTATATAATTTTATAGATTATTAAAATTTCTATTTAATTTTTATGTA
Found at i:348311 original size:162 final size:162
Alignment explanation
Indices: 348112--348428 Score: 541
Period size: 162 Copynumber: 2.0 Consensus size: 162
348102 TAATTTCCTC
* * *
348112 AACAACATTTTCAATCTTTTAACCCTTTAGTCTACTATTACTTCATGTAGATTGTAGGAATCAAC
1 AACAACATTTTCAATCTTTTAACCCTTTAGCCTACTATTACTTCATGTAGATAGTAGGAACCAAC
348177 AAAGGGAGAAAGATGACAAGAAAGGTATCC-GTTTATTCTTG-GGCGATAGAGAGTCATCGGACT
66 AAAGGGAGAAAGATGACAAG-AAGGTA-CCGGTTTATTCTTGTGG-GATAGAGAGTCATCGGACT
348240 ATAATGGTGTAGATGGTTGTAGAGGTTAGTTGAGG
128 ATAATGGTGTAGATGGTTGTAGAGGTTAGTTGAGG
*
348275 AACAACATTTTCAATC-TTTAACCCTTTAGCCTACTATTACTTCATGTGGATAGTAGGAACCAAC
1 AACAACATTTTCAATCTTTTAACCCTTTAGCCTACTATTACTTCATGTAGATAGTAGGAACCAAC
348339 AAAGGGAGAAAGATGACAAGAAGGTACCGGTTTATTCTTGTGGGATAGAGAGTCATCGGACTATA
66 AAAGGGAGAAAGATGACAAGAAGGTACCGGTTTATTCTTGTGGGATAGAGAGTCATCGGACTATA
*
348404 GTGGTGTAGATGGTTGTAGAGGTTA
131 ATGGTGTAGATGGTTGTAGAGGTTA
348429 TAGAGAAGAA
Statistics
Matches: 147, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
160 2 0.01
161 63 0.43
162 66 0.45
163 16 0.11
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (162 bp):
AACAACATTTTCAATCTTTTAACCCTTTAGCCTACTATTACTTCATGTAGATAGTAGGAACCAAC
AAAGGGAGAAAGATGACAAGAAGGTACCGGTTTATTCTTGTGGGATAGAGAGTCATCGGACTATA
ATGGTGTAGATGGTTGTAGAGGTTAGTTGAGG
Found at i:365096 original size:97 final size:97
Alignment explanation
Indices: 364925--365105 Score: 272
Period size: 97 Copynumber: 1.9 Consensus size: 97
364915 TTCTTAATAA
* * * *
364925 CAACATTCGAGAATAAAATGAACCCTTGTAATTAGTCTAACGGCCGAATAATGTTCATTTGGACA
1 CAACATTCGAGAATAAAAAGAACCCTCGTAATTAGTCTAACGACCAAATAATGTTCATTTGGACA
*
364990 ACTCTCTTTAAACATAATATATGCATGTATAT
66 ACTCCCTTTAAACATAATATATGCATGTATAT
* * * *
365022 CAACATTCGAGAATAAAAAGAACCCTCGTAATTGGTCTGATGACCAAATGATGTTCATTTGGACA
1 CAACATTCGAGAATAAAAAGAACCCTCGTAATTAGTCTAACGACCAAATAATGTTCATTTGGACA
*
365087 ATTCCCTTTAAACATAATA
66 ACTCCCTTTAAACATAATA
365106 CGTCCACGTA
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
97 74 1.00
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (97 bp):
CAACATTCGAGAATAAAAAGAACCCTCGTAATTAGTCTAACGACCAAATAATGTTCATTTGGACA
ACTCCCTTTAAACATAATATATGCATGTATAT
Done.