Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 187 of 196
Found at i:55139428 original size:48 final size:48
Alignment explanation
Indices: 55139323--55139431 Score: 134
Period size: 48 Copynumber: 2.3 Consensus size: 48
55139313 CGGCCCGAAG
* * *
55139323 AAGAGGAAGAAAAAGAAAGGAAAAAAGAGAAGAAAAAGAGAGAAGAAA
1 AAGAGAAAGAAAAAGAAAGAAAAAAAGAGAAGAAAAAAAGAGAAGAAA
*
55139371 AAGAGAAAGAAAAAGAAAGAAAAAAAG-GAGAGAAAAAAATAGAA-AAGGA
1 AAGAGAAAGAAAAAGAAAGAAAAAAAGAGA-AGAAAAAAAGAGAAGAA--A
55139420 AAGA-AAAGAAAA
1 AAGAGAAAGAAAA
55139432 TAAAAAAATA
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
47 4 0.07
48 45 0.83
49 5 0.09
ACGTcount: A:0.73, C:0.00, G:0.26, T:0.01
Consensus pattern (48 bp):
AAGAGAAAGAAAAAGAAAGAAAAAAAGAGAAGAAAAAAAGAGAAGAAA
Found at i:55139431 original size:22 final size:22
Alignment explanation
Indices: 55139368--55139438 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 22
55139358 AAGAGAGAAG
55139368 AAAAAGAGAAAGAAAAAGAAAGA-A
1 AAAAAG-GAAAG-AAAAGAAA-ATA
*
55139392 AAAAAGGAGAG-AAA-AAAATA
1 AAAAAGGAAAGAAAAGAAAATA
*
55139412 GAAAAGGAAAGAAAAGAAAATA
1 AAAAAGGAAAGAAAAGAAAATA
55139434 AAAAA
1 AAAAA
55139439 ATAAAAAGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
19 1 0.03
20 13 0.32
21 6 0.15
22 10 0.25
23 4 0.10
24 6 0.15
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (22 bp):
AAAAAGGAAAGAAAAGAAAATA
Found at i:55139558 original size:13 final size:13
Alignment explanation
Indices: 55139539--55139578 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
55139529 GGCCAGCCCA
*
55139539 AAAAAAAACAAAGC
1 AAAAAAAA-GAAGC
55139553 AAAAAAAAGAAGC
1 AAAAAAAAGAAGC
55139566 AGAAAAAAAGAAG
1 A-AAAAAAAGAAG
55139579 AAGAAAGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 5 0.21
14 19 0.79
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGAAGC
Found at i:55139575 original size:14 final size:14
Alignment explanation
Indices: 55139549--55139584 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
55139539 AAAAAAAACA
55139549 AAGCA-AAAAAAAG
1 AAGCAGAAAAAAAG
55139562 AAGCAGAAAAAAAG
1 AAGCAGAAAAAAAG
*
55139576 AAGAAGAAA
1 AAGCAGAAA
55139585 GAAGCAGCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 5 0.24
14 16 0.76
ACGTcount: A:0.75, C:0.06, G:0.19, T:0.00
Consensus pattern (14 bp):
AAGCAGAAAAAAAG
Found at i:55139748 original size:15 final size:15
Alignment explanation
Indices: 55139728--55139762 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
55139718 AACATCCAGC
55139728 AAAAAAAAAA-GAAA
1 AAAAAAAAAAGGAAA
55139742 GAAAAAAAAAAGGAAA
1 -AAAAAAAAAAGGAAA
55139758 AAAAA
1 AAAAA
55139763 GGCCCATAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAGGAAA
Found at i:55140367 original size:16 final size:16
Alignment explanation
Indices: 55140319--55140367 Score: 64
Period size: 16 Copynumber: 3.0 Consensus size: 16
55140309 TTTCTTTCTA
*
55140319 AAAAAATCGTGTTTTC
1 AAAAATTCGTGTTTTC
55140335 AAAAATTTCCGTG-TTTC
1 AAAAA-TT-CGTGTTTTC
55140352 AAAAATTCGTGTTTTC
1 AAAAATTCGTGTTTTC
55140368 GTGTTTTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
15 4 0.14
16 11 0.38
17 10 0.34
18 4 0.14
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (16 bp):
AAAAATTCGTGTTTTC
Found at i:55140396 original size:19 final size:20
Alignment explanation
Indices: 55140366--55140403 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
55140356 ATTCGTGTTT
55140366 TCGTGTTTTCAAAAAAAATC
1 TCGTGTTTTCAAAAAAAATC
55140386 TCGTG-TTTCAAAAAAAAT
1 TCGTGTTTTCAAAAAAAAT
55140404 AAAAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (20 bp):
TCGTGTTTTCAAAAAAAATC
Found at i:55140399 original size:1 final size:1
Alignment explanation
Indices: 55140395--55140448 Score: 63
Period size: 1 Copynumber: 54.0 Consensus size: 1
55140385 CTCGTGTTTC
* * * * *
55140395 AAAAAAAATAAAAAATAAAAAAAATAAAAAAAATAAAAAAAAATAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
55140449 TTCTCGTGAA
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (1 bp):
A
Found at i:55140409 original size:9 final size:9
Alignment explanation
Indices: 55140395--55140446 Score: 81
Period size: 9 Copynumber: 5.9 Consensus size: 9
55140385 CTCGTGTTTC
55140395 AAAAAAAAT
1 AAAAAAAAT
55140404 --AAAAAAT
1 AAAAAAAAT
55140411 AAAAAAAAT
1 AAAAAAAAT
55140420 AAAAAAAAT
1 AAAAAAAAT
55140429 AAAAAAAAAT
1 -AAAAAAAAT
55140439 AAAAAAAA
1 AAAAAAAA
55140447 AATTCTCGTG
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
7 7 0.17
9 24 0.60
10 9 0.22
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:55140534 original size:18 final size:18
Alignment explanation
Indices: 55140513--55140947 Score: 204
Period size: 18 Copynumber: 25.0 Consensus size: 18
55140503 AAATTTTGTG
55140513 TTTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
55140531 TTTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
55140549 TCTTT-GTGTTTTCAGAAA
1 T-TTTCGTGTTTTCAAAAA
* * *
55140567 TTCTGGCG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
**
55140584 TTTTCGTGTTTAAAAAAAAA
1 TTTTCGTGTTT--TCAAAAA
* *
55140604 TTTACGTGTTTTCACAAA
1 TTTTCGTGTTTTCAAAAA
*
55140622 TTTTCGTG-TTTCACAAA
1 TTTTCGTGTTTTCAAAAA
*
55140639 TTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* * *
55140657 -CTCCAGTG-TTTC-AAAG
1 TTTTC-GTGTTTTCAAAAA
* *
55140673 TTTCCATGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* * **
55140691 TTCTCGCGTTTAAAAAAAA
1 TTTTCGTGTTT-TCAAAAA
**
55140710 AATTCGTG-TTTCAAAATA
1 TTTTCGTGTTTTCAAAA-A
* **
55140728 TTCTCG-CATTTC---AA
1 TTTTCGTGTTTTCAAAAA
**
55140742 TTTT--TGTTTT-TTAAA
1 TTTTCGTGTTTTCAAAAA
55140757 ---TCGTG-TTTCAAAAAA
1 TTTTCGTGTTTTC-AAAAA
* *
55140772 ATATCGTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
*
55140789 TTTTCGTG-TTTCTAAAA
1 TTTTCGTGTTTTCAAAAA
* *
55140806 TTTCCCTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
**
55140823 TTCCCGTG-TTTCAAAAAAAA
1 TTTTCGTGTTTTC---AAAAA
* *
55140843 ATGTCGTGTTTT-AAGAAA
1 TTTTCGTGTTTTCAA-AAA
* *
55140861 ATTTCGTTTTTTCTAAAAA
1 TTTTCGTGTTTTC-AAAAA
*
55140880 TTTTCGTG-TTTCTAAAA
1 TTTTCGTGTTTTCAAAAA
*
55140897 TTTTCGTG-TTT-ACAAA
1 TTTTCGTGTTTTCAAAAA
*
55140913 TTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
55140931 TTCTCGTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
55140948 AAAAAACTTT
Statistics
Matches: 316, Mismatches: 64, Indels: 75
0.69 0.14 0.16
Matches are distributed among these distances:
12 1 0.00
13 6 0.02
14 6 0.02
15 6 0.02
16 21 0.07
17 103 0.33
18 119 0.38
19 24 0.08
20 27 0.09
21 3 0.01
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (18 bp):
TTTTCGTGTTTTCAAAAA
Found at i:55140594 original size:17 final size:17
Alignment explanation
Indices: 55140513--55140947 Score: 192
Period size: 17 Copynumber: 25.0 Consensus size: 17
55140503 AAATTTTGTG
55140513 TTTTCGTGTTTTCAAAAA
1 TTTTCGTG-TTTCAAAAA
55140531 TTTTCGTGTTTTCAAAAA
1 TTTTCGTG-TTTCAAAAA
*
55140549 TCTTT-GTGTTTTCAGAAA
1 T-TTTCGTG-TTTCAAAAA
* * *
55140567 TTCTGGCGTTTCAAAAA
1 TTTTCGTGTTTCAAAAA
*
55140584 TTTTCGTGTTTAAAAAAAAA
1 TTTTCGTGTTT---CAAAAA
* *
55140604 TTTACGTGTTTTCACAAA
1 TTTTCGTG-TTTCAAAAA
*
55140622 TTTTCGTGTTTCACAAA
1 TTTTCGTGTTTCAAAAA
*
55140639 TTCTCGTGTTTTCAAAAA
1 TTTTCGTG-TTTCAAAAA
* * *
55140657 -CTCCAGTGTTTC-AAAG
1 TTTTC-GTGTTTCAAAAA
* *
55140673 TTTCCATGTTTTCAAAAA
1 TTTTCGTG-TTTCAAAAA
* * *
55140691 TTCTCGCGTTTAAAAAAAA
1 TTTTCGTGTTT--CAAAAA
**
55140710 AATTCGTGTTTCAAAATA
1 TTTTCGTGTTTCAAAA-A
* **
55140728 TTCTCGCATTTC---AA
1 TTTTCGTGTTTCAAAAA
***
55140742 TTTT--TGTTTTTTAAA
1 TTTTCGTGTTTCAAAAA
55140757 ---TCGTGTTTCAAAAAA
1 TTTTCGTGTTTC-AAAAA
* * *
55140772 ATATCGTGTTTTAAAAA
1 TTTTCGTGTTTCAAAAA
*
55140789 TTTTCGTGTTTCTAAAA
1 TTTTCGTGTTTCAAAAA
* * *
55140806 TTTCCCTGTTTTAAAAA
1 TTTTCGTGTTTCAAAAA
**
55140823 TTCCCGTGTTTCAAAAAAAA
1 TTTTCGTGTTTC---AAAAA
* * *
55140843 ATGTCGTGTTTTAAGAAA
1 TTTTCGTGTTTCAA-AAA
* *
55140861 ATTTCGTTTTTTCTAAAAA
1 TTTTCG-TGTTTC-AAAAA
*
55140880 TTTTCGTGTTTCTAAAA
1 TTTTCGTGTTTCAAAAA
*
55140897 TTTTCGTGTTT-ACAAA
1 TTTTCGTGTTTCAAAAA
*
55140913 TTCTCGTGTTTTCAAAAA
1 TTTTCGTG-TTTCAAAAA
* *
55140931 TTCTCGTGTTTTAAAAA
1 TTTTCGTGTTTCAAAAA
55140948 AAAAAACTTT
Statistics
Matches: 316, Mismatches: 70, Indels: 63
0.70 0.16 0.14
Matches are distributed among these distances:
12 4 0.01
14 9 0.03
15 6 0.02
16 15 0.05
17 121 0.38
18 104 0.33
19 27 0.09
20 27 0.09
21 3 0.01
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (17 bp):
TTTTCGTGTTTCAAAAA
Found at i:55140656 original size:55 final size:53
Alignment explanation
Indices: 55140513--55140656 Score: 171
Period size: 55 Copynumber: 2.7 Consensus size: 53
55140503 AAATTTTGTG
** *
55140513 TTTTCGTGTTTTCAAAAATTTTCGTGTTTTCAAAAATCTTTGTGTTTTCAGAAA
1 TTTTCGTG-TTTCAAAAATTTTCGTGTTTTCAAAAAAATTTGTGTTTTCACAAA
* * * **
55140567 TTCTGGCGTTTCAAAAATTTTCGTGTTTAAAAAAAAATTTACGTGTTTTCACAAA
1 TTTTCGTGTTTCAAAAATTTTCGTGTTTTCAAAAAAATTT--GTGTTTTCACAAA
* *
55140622 TTTTCGTGTTTCACAAATTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTCAAAAATTTTCGTGTTTTCAAAAA
55140657 CTCCAGTGTT
Statistics
Matches: 73, Mismatches: 15, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
53 28 0.38
54 5 0.07
55 40 0.55
ACGTcount: A:0.29, C:0.13, G:0.12, T:0.45
Consensus pattern (53 bp):
TTTTCGTGTTTCAAAAATTTTCGTGTTTTCAAAAAAATTTGTGTTTTCACAAA
Found at i:55140666 original size:73 final size:73
Alignment explanation
Indices: 55140526--55140667 Score: 173
Period size: 73 Copynumber: 1.9 Consensus size: 73
55140516 TCGTGTTTTC
* * * * *
55140526 AAAAATTTTCGTGTTTTCAAAAATCTTTGTGTTTTCAGAAATTCTGGCGTTTCAAAAATTTTCGT
1 AAAAATTTACGTGTTTTCAAAAATCTTTGTGTTTTCACAAATTCTCGCGTTTCAAAAATCTCCGT
55140591 GTTTAAAA
66 GTTTAAAA
* *
55140599 AAAAATTTACGTGTTTTCACAAAT-TTTCGTG-TTTCACAAATTCTCGTGTTTTCAAAAA-CTCC
1 AAAAATTTACGTGTTTTCAAAAATCTTT-GTGTTTTCACAAATTCTCGCG-TTTCAAAAATCTCC
55140661 AGTGTTT
64 -GTGTTT
55140668 CAAAGTTTCC
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
72 19 0.32
73 40 0.68
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (73 bp):
AAAAATTTACGTGTTTTCAAAAATCTTTGTGTTTTCACAAATTCTCGCGTTTCAAAAATCTCCGT
GTTTAAAA
Found at i:55140886 original size:91 final size:89
Alignment explanation
Indices: 55140757--55140930 Score: 242
Period size: 91 Copynumber: 1.9 Consensus size: 89
55140747 GTTTTTTAAA
55140757 TCGTGTTTCAAAAAAATATCGTGTTTTAAAAATTTTCGTGTTTCTAAAATTTCCCTGTTTTAAAA
1 TCGTGTTTCAAAAAAATATCGTGTTTTAAAAATTTTCGTGTTTCTAAAATTTCCCTG-TTTAAAA
55140822 ATTCCCGTG-TTTCAAAAAAAAATG
65 ATTCCCGTGTTTTCAAAAAAAAATG
* * * * * * *
55140846 TCGTGTTTTAAGAAAATTTCGTTTTTTCTAAAAATTTTCGTGTTTCTAAAATTTTCGTGTTTACA
1 TCGTGTTTCAAAAAAATATCG-TGTTT-TAAAAATTTTCGTGTTTCTAAAATTTCCCTGTTTAAA
*
55140911 AATTCTCGTGTTTTCAAAAA
64 AATTCCCGTGTTTTCAAAAA
55140931 TTCTCGTGTT
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
89 18 0.24
90 18 0.24
91 38 0.51
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44
Consensus pattern (89 bp):
TCGTGTTTCAAAAAAATATCGTGTTTTAAAAATTTTCGTGTTTCTAAAATTTCCCTGTTTAAAAA
TTCCCGTGTTTTCAAAAAAAAATG
Found at i:55152980 original size:125 final size:121
Alignment explanation
Indices: 55152697--55153213 Score: 655
Period size: 125 Copynumber: 4.3 Consensus size: 121
55152687 CTTTCCAAGG
* *
55152697 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTTATAA-TTTT-TTTTTCAAAAATCAACTC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTTTGTTTTTC-AAAATCAACTC
* * * *
55152760 ATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCAGGTATTTTTAGTTTATGTTTT-
65 ATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGCAGGTA-TTTTAATTTCTGTTTTA
** *
55152817 -AAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACTCA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTTTGTTTTTCAAAATCAACTCA
* * *
55152881 TATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTGTTA
66 TATTGCGAGAAGTGAGTTGAGCCTCAGGACACGC--AGGT-ATTTTAATTTCTGTT-TTA
*
55152941 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTTCAAAATCAACTCA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTTTGTTTTTCAAAATCAACTCA
*
55153006 TATTGCGAGAAGTGAGTTGAGCC-CA-G-CACGCAGGTATTTT--TTTTTG-TTT-
66 TATTGCGAGAAGTGAGTTGAGCCTCAGGACACGCAGGTATTTTAATTTCTGTTTTA
** * *
55153055 AAAATTGACTCATATTGCGAGAGGTGAGTTAAG-C-TTTAATTTATGTTTTTCAAAATCAACTCA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTTTGTTTTTCAAAATCAACTCA
* *
55153118 TATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTAATTTCTGTTTAAAA
66 TATTGCGAGAAGTGAGTTGAGCCTCAGGACACGC--AGGTATTTTAATTTCTGTTT--TA
**
55153178 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
55153214 CAGGACACGC
Statistics
Matches: 344, Mismatches: 32, Indels: 37
0.83 0.08 0.09
Matches are distributed among these distances:
112 50 0.15
113 3 0.01
114 31 0.09
115 7 0.02
116 1 0.00
117 14 0.04
119 44 0.13
120 52 0.15
121 6 0.02
122 20 0.06
123 32 0.09
124 3 0.01
125 81 0.24
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (121 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTTTGTTTTTCAAAATCAACTCA
TATTGCGAGAAGTGAGTTGAGCCTCAGGACACGCAGGTATTTTAATTTCTGTTTTA
Found at i:55153007 original size:53 final size:53
Alignment explanation
Indices: 55152927--55153141 Score: 218
Period size: 53 Copynumber: 3.9 Consensus size: 53
55152917 AGGTAATTTC
* *
55152927 AATTTCTGTTGTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT
1 AATTTCTGTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT
* ****
55152980 AATTTCTGTTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCCAGCACGC
1 AATTTCTGTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAG--C--CTTTT
* * * ** *
55153037 AGGTATTTTTTTTTGTTTAAAATTGACTCATATTGCGAGAGGTGAGTTAAG-C-TTT
1 A---ATTTCTGTTT-TTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT
*
55153092 AATTTATGTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 AATTTCTGTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
55153142 CAGGACACGC
Statistics
Matches: 129, Mismatches: 23, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
51 32 0.25
52 9 0.07
53 44 0.34
55 2 0.02
56 1 0.01
57 2 0.02
60 8 0.06
61 31 0.24
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.37
Consensus pattern (53 bp):
AATTTCTGTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT
Found at i:55153131 original size:237 final size:241
Alignment explanation
Indices: 55152697--55153213 Score: 834
Period size: 237 Copynumber: 2.1 Consensus size: 241
55152687 CTTTCCAAGG
55152697 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTTATAATTTTTTTTTCAAAAATCAACTCAT
1 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTTATAATTTTTTTTTCAAAAATCAACTCAT
* *
55152762 ATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCAGGTATTTTTAGTTTATGTTTTAAATTGACTC
66 ATTGCGAGAAGTGAGTTGAGCCTC-GAGCACGCAGGTATTTTTA-TTTATGTTTAAAATTGACTC
* *
55152827 ATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAG
129 ATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTATGTTTTTCAAAATCAACTCATATTGCGAGAG
*
55152892 GTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTGT-TA
194 GTGAGTTGAGCCTCAGGACACGCTGAGGT-ATTTCAATTTCTGTT-TAAA
* *
55152941 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTTC-AAAATCAACTC
1 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTTATAATTT-T-TTTTTCAAAAATCAACTC
55153005 ATATTGCGAGAAGTGAGTTGAGCC-C-AGCACGCAGGTATTTTT-TTT-TGTTTAAAATTGACTC
64 ATATTGCGAGAAGTGAGTTGAGCCTCGAGCACGCAGGTATTTTTATTTATGTTTAAAATTGACTC
55153066 ATATTGCGAGAGGTGAGTTAAG-C-TTTAATTTATGTTTTTCAAAATCAACTCATATTGCGAGAG
129 ATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTATGTTTTTCAAAATCAACTCATATTGCGAGAG
*
55153129 GTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTAATTTCTGTTTAAAA
194 GTGAGTTGAGCCTCAGGACACGCTGAGGTATTTCAATTTCTGTTT-AAA
*
55153178 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCT
1 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCT
55153214 CAGGACACGC
Statistics
Matches: 259, Mismatches: 10, Indels: 15
0.91 0.04 0.05
Matches are distributed among these distances:
235 1 0.00
236 14 0.05
237 102 0.39
238 1 0.00
239 37 0.14
240 3 0.01
242 16 0.06
244 43 0.17
245 36 0.14
246 6 0.02
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (241 bp):
AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTTATAATTTTTTTTTCAAAAATCAACTCAT
ATTGCGAGAAGTGAGTTGAGCCTCGAGCACGCAGGTATTTTTATTTATGTTTAAAATTGACTCAT
ATTGCGAGAGGTGAGTTAAGCCTTTTAATTTATGTTTTTCAAAATCAACTCATATTGCGAGAGGT
GAGTTGAGCCTCAGGACACGCTGAGGTATTTCAATTTCTGTTTAAA
Found at i:55153598 original size:67 final size:69
Alignment explanation
Indices: 55153092--55153689 Score: 708
Period size: 70 Copynumber: 8.7 Consensus size: 69
55153082 GTTAAGCTTT
* *
55153092 AATTTATGTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGG
1 AATTTCTG-TTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA-GACACGTTGAGG
*
55153157 TATTTT
64 TATTTC
** ** *
55153163 AATTTCTGTTTAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAG
1 AATTTCTGTTT--TCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA-GACACGTTGAG
55153228 GTAATTTC
63 GT-ATTTC
*
55153236 AATTTCTGTTTTCAAAATTCAACT--TATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGG
1 AATTTCTGTTTTCAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA-GACACGTTGAGG
55153299 TATTTC
64 TATTTC
55153305 AATTTCTG-TTTCAAAATCAACTCATATTGCGAGA--TGAGTTGAGCCTCA-ACACGTTGAGGTA
1 AATTTCTGTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACACGTTGAGGT-
55153366 ATTTC
65 ATTTC
55153371 AATTT-TG---TCAAAATCAACTCATATT--GAGA--TGAGTTGAGCCTCAAGACA-G-TGAGGT
1 AATTTCTGTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGACACGTTGAGGT
55153426 ATTTTC
65 A-TTTC
55153432 AATTT-TGCTTTTC-AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACACGTTGAGGT
1 AATTTCTG-TTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACACGTTGAGGT
55153495 ATTTC
65 ATTTC
* *
55153500 AATTTATGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA-A-ACATTGAGGT
1 AATTTCTGTTTTC-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACACGTTGAGGT
55153563 ATTTTC
65 A-TTTC
55153569 AATTT-TGTTTTTC-AAATCAACTCATATTGCGAGA--TGAGTTGAGCCTCAAGACATAC-TT-A
1 AATTTCTG-TTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGAC--ACGTTGA
55153628 GGTATTTC
62 GGTATTTC
*
55153636 AATTTTTTTGTTGTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
1 AA--TTTCTGTT-TTC-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
55153690 CCTCCAAGGA
Statistics
Matches: 477, Mismatches: 12, Indels: 73
0.85 0.02 0.13
Matches are distributed among these distances:
60 1 0.00
61 34 0.07
62 2 0.00
63 21 0.04
64 15 0.03
65 28 0.06
66 15 0.03
67 53 0.11
68 53 0.11
69 54 0.11
70 85 0.18
71 11 0.02
72 77 0.16
73 15 0.03
74 13 0.03
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (69 bp):
AATTTCTGTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACACGTTGAGGTA
TTTC
Found at i:55153825 original size:84 final size:87
Alignment explanation
Indices: 55153644--55153865 Score: 238
Period size: 85 Copynumber: 2.5 Consensus size: 87
55153634 TCAATTTTTT
* * * * **
55153644 TGTTGTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCCCTCCAAGG-ACATTTGAG
1 TGTTTTTCAAAAATCAACTCATATTGCAAGAGGTGAGCTGAG----CCT-CAGGGCAC-GCTGAG
**
55153708 GTATTTTCATTTCTGTTTTTCAATTTAA
60 GTATTTTCATTTCTACTTTTCAATTTAA
*
55153736 TG-TTTTCAAAAATC-ATTCATATTGCAAGAGGTGAG-TGAGCCTCAGGGCACGCTGAGGTATTT
1 TGTTTTTCAAAAATCAACTCATATTGCAAGAGGTGAGCTGAGCCTCAGGGCACGCTGAGGTATTT
*
55153798 TCAATTTCTACTTTTCAATTT-C
66 TC-ATTTCTACTTTTCAATTTAA
*
55153820 TGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGCTGAGCCT
1 TG-TTTTTCAAAAATCAACTCATATTGCAAGAGGTGAGCTGAGCCT
55153866 TTTAATTTTT
Statistics
Matches: 113, Mismatches: 11, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
84 18 0.16
85 21 0.19
86 12 0.11
87 19 0.17
88 7 0.06
89 4 0.04
90 19 0.17
91 11 0.10
92 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (87 bp):
TGTTTTTCAAAAATCAACTCATATTGCAAGAGGTGAGCTGAGCCTCAGGGCACGCTGAGGTATTT
TCATTTCTACTTTTCAATTTAA
Found at i:55153919 original size:55 final size:54
Alignment explanation
Indices: 55153808--55154033 Score: 249
Period size: 54 Copynumber: 4.1 Consensus size: 54
55153798 TCAATTTCTA
* *
55153808 CTTTTCAATTTCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGCTGAGC
1 CTTTTCAATTT-T-TGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
*
55153864 CTTTT-AATTTTTGTTTTCAAAAAACCAACTCATATTGCGAGAGGTGAGTTTGAGC
1 CTTTTCAATTTTTGTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAG-TTGAGC
* ******
55153919 CTTTTTCTATTTTTCAAAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 C-TTTTCAATTTTT--GTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* *
55153976 CTTTTGCAA-TTCTGTTTTCAAAAATCAACTCAATATTGCGAGAAGTGAGTTGAGC
1 CTTTT-CAATTTTTGTTTTCAAAAATCAACTC-ATATTGCGAGAGGTGAGTTGAGC
55154031 CTT
1 CTT
55154034 GGCTCATCAC
Statistics
Matches: 142, Mismatches: 20, Indels: 17
0.79 0.11 0.09
Matches are distributed among these distances:
53 6 0.04
54 41 0.29
55 36 0.25
56 16 0.11
57 15 0.11
58 28 0.20
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (54 bp):
CTTTTCAATTTTTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
Found at i:55153965 original size:58 final size:55
Alignment explanation
Indices: 55153829--55153980 Score: 189
Period size: 58 Copynumber: 2.7 Consensus size: 55
55153819 CTGTTTTTTC
* ******
55153829 AAAAATCAACTCATATTGCGAGAGGTGAGCTGAGCC-TTTTAATTTTTGTTTTCA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTTAATTTTTAAAAAAA
* *
55153883 AAAAACCAACTCATATTGCGAGAGGTGAGTTTGAGCCTTTTTCTATTTTTCAAAAAAA
1 AAAAATCAACTCATATTGCGAGAGGTGAG-TTGAGCCTTTTT-AATTTTT-AAAAAAA
55153941 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT
55153981 GCAATTCTGT
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
54 28 0.33
55 6 0.07
56 4 0.05
57 17 0.20
58 29 0.35
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (55 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTTAATTTTTAAAAAAA
Found at i:55154006 original size:112 final size:112
Alignment explanation
Indices: 55153829--55154033 Score: 326
Period size: 112 Copynumber: 1.8 Consensus size: 112
55153819 CTGTTTTTTC
*
55153829 AAAAATCAACTCATATTGCGAGAGGTGAGCTGAGCCTTTTAATTTTTGTTTTCAAAAAACCAACT
1 AAAAATCAACTCATATTGCGAGAGGTGAGCTGAGCCTTTTAATTTCTGTTTTCAAAAAACCAACT
*
55153894 C-ATATTGCGAGAGGTGAGTTTGAGCCTTTTTCTATTTTTCAAAAAAA
66 CAATATTGCGAGAAGTGAG-TTGAGCCTTTTTCTATTTTTCAAAAAAA
* *
55153941 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTGCAA-TTCTGTTTTC-AAAAATCAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGCTGAGCCTTTT--AATTTCTGTTTTCAAAAAACCAA
55154004 CTCAATATTGCGAGAAGTGAGTTGAGCCTT
64 CTCAATATTGCGAGAAGTGAGTTGAGCCTT
55154034 GGCTCATCAC
Statistics
Matches: 86, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
112 59 0.69
113 25 0.29
114 2 0.02
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (112 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGCTGAGCCTTTTAATTTCTGTTTTCAAAAAACCAACT
CAATATTGCGAGAAGTGAGTTGAGCCTTTTTCTATTTTTCAAAAAAA
Found at i:55154307 original size:14 final size:15
Alignment explanation
Indices: 55154280--55154315 Score: 63
Period size: 15 Copynumber: 2.3 Consensus size: 15
55154270 TTTAATTTTC
55154280 AAAAATTTTAAAAAA
1 AAAAATTTTAAAAAA
55154295 AAAAATTTTAAAAAA
1 AAAAATTTTAAAAAA
55154310 ATAAAA
1 A-AAAA
55154316 ATTGGCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (15 bp):
AAAAATTTTAAAAAA
Found at i:55154357 original size:29 final size:30
Alignment explanation
Indices: 55154321--55154413 Score: 102
Period size: 29 Copynumber: 3.2 Consensus size: 30
55154311 TAAAAATTGG
*
55154321 CATTTTGACCCCTAAACTTTC-CTAAATTT
1 CATTTTGACCCCTAAACTTTCATTAAATTT
* *
55154350 CATTTTGACCCTTAAACTTTTCTTTAAA-TT
1 CATTTTGACCCCTAAAC-TTTCATTAAATTT
* * *
55154380 CACTTAGACCCCT-AACCTTCATTAAATTT
1 CATTTTGACCCCTAAACTTTCATTAAATTT
55154409 CATTT
1 CATTT
55154414 AATCCTAAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
28 8 0.15
29 25 0.47
30 16 0.30
31 4 0.08
ACGTcount: A:0.28, C:0.26, G:0.03, T:0.43
Consensus pattern (30 bp):
CATTTTGACCCCTAAACTTTCATTAAATTT
Found at i:55154962 original size:12 final size:12
Alignment explanation
Indices: 55154942--55155005 Score: 51
Period size: 13 Copynumber: 5.0 Consensus size: 12
55154932 CGAAGAAGAG
55154942 GGAAGAAAAGAAA
1 GGAA-AAAAGAAA
55154955 GGAAAAAAGAGAA
1 GGAAAAAAGA-AA
55154968 -GAAAAAGAGAGAA
1 GGAAAAA-AGA-AA
55154981 -GAAAAAGAGAAA
1 GGAAAAA-AGAAA
*
55154993 GAAAAAGAAGAAA
1 GGAAAA-AAGAAA
55155006 AAAGGAGAGA
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
12 14 0.30
13 31 0.67
14 1 0.02
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GGAAAAAAGAAA
Found at i:55154973 original size:13 final size:13
Alignment explanation
Indices: 55154947--55155038 Score: 72
Period size: 12 Copynumber: 7.5 Consensus size: 13
55154937 AAGAGGGAAG
*
55154947 AAAAGA-AAGGAA
1 AAAAGAGAAGAAA
55154959 AAAAGAGAAGAAA
1 AAAAGAGAAGAAA
*
55154972 AAGAGAGAAG--A
1 AAAAGAGAAGAAA
*
55154983 AAAAGAG-A-AAG
1 AAAAGAGAAGAAA
55154994 AAAA-AGAAGAAA
1 AAAAGAGAAGAAA
*
55155006 AAAGGAG-AGAAA
1 AAAAGAGAAGAAA
*
55155018 AAAATAGAAGGAAA
1 AAAAGAGAA-GAAA
55155032 GAAAAGA
1 -AAAAGA
55155039 AAAATAAAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
10 3 0.05
11 12 0.19
12 21 0.34
13 17 0.27
14 4 0.06
15 5 0.08
ACGTcount: A:0.73, C:0.00, G:0.26, T:0.01
Consensus pattern (13 bp):
AAAAGAGAAGAAA
Found at i:55154982 original size:35 final size:35
Alignment explanation
Indices: 55154937--55155042 Score: 110
Period size: 35 Copynumber: 3.0 Consensus size: 35
55154927 TTCGCCGAAG
*
55154937 AAGAGGGAAGAAAAGA-AAGGAAAAAAGAGAAGAAA
1 AAGAGAGAAGAAAAGAGAAGGAAAAAAGAGAA-AAA
*
55154972 AAGAGAGAAGAAAAAGAGAAAG-AAAAAGAAGAAAAA
1 AAGAGAGAAG-AAAAGAGAAGGAAAAAAG-AGAAAAA
* * *
55155008 AGGAGAGAAAAAAATAGAAGGAAAGAAA-AGAAAAA
1 AAGAGAGAAGAAAAGAGAAGGAAA-AAAGAGAAAAA
55155043 TAAAAAATAA
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
35 25 0.42
36 25 0.42
37 10 0.17
ACGTcount: A:0.72, C:0.00, G:0.27, T:0.01
Consensus pattern (35 bp):
AAGAGAGAAGAAAAGAGAAGGAAAAAAGAGAAAAA
Found at i:55154994 original size:25 final size:24
Alignment explanation
Indices: 55154958--55155042 Score: 83
Period size: 24 Copynumber: 3.7 Consensus size: 24
55154948 AAAGAAAGGA
55154958 AAAAAGAG-AAGAAAAAGAGAGAAG
1 AAAAAGAGAAAGAAAAAGA-AGAAG
55154982 AAAAAGAGAAAGAAAAAGAAGAA-
1 AAAAAGAGAAAGAAAAAGAAGAAG
* *
55155005 AAAAGGAGAGAA-AAAAA-TAGAAG
1 AAAAAGAGA-AAGAAAAAGAAGAAG
*
55155028 -GAAAGA-AAAGAAAAA
1 AAAAAGAGAAAGAAAAA
55155043 TAAAAAATAA
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
20 2 0.04
21 6 0.11
22 8 0.15
23 13 0.25
24 14 0.26
25 10 0.19
ACGTcount: A:0.74, C:0.00, G:0.25, T:0.01
Consensus pattern (24 bp):
AAAAAGAGAAAGAAAAAGAAGAAG
Found at i:55269940 original size:20 final size:20
Alignment explanation
Indices: 55269878--55269942 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 20
55269868 TAAGTTTATT
*
55269878 TTAAAAAAACTATTAAAATA
1 TTAAAAAAATTATTAAAATA
* * *
55269898 TTATAAAAATTATTGAAA-C
1 TTAAAAAAATTATTAAAATA
*
55269917 TTAAAAAAATTATAAAAATA
1 TTAAAAAAATTATTAAAATA
55269937 TTAAAA
1 TTAAAA
55269943 CTTTTAAATA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
19 15 0.42
20 21 0.58
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (20 bp):
TTAAAAAAATTATTAAAATA
Found at i:55269955 original size:28 final size:28
Alignment explanation
Indices: 55269883--55269956 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
55269873 TTATTTTAAA
*
55269883 AAAACTATTAAAATATTATAAAAATTATT
1 AAAACTTTTAAAA-ATTATAAAAATTATT
* **
55269912 GAAACTTAAAAAAATTATAAAAA-TATT
1 AAAACTTTTAAAAATTATAAAAATTATT
55269939 AAAACTTTTAAATAATTA
1 AAAACTTTTAAA-AATTA
55269957 CAATAAACTA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
27 13 0.35
28 15 0.41
29 9 0.24
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.35
Consensus pattern (28 bp):
AAAACTTTTAAAAATTATAAAAATTATT
Found at i:55271341 original size:24 final size:24
Alignment explanation
Indices: 55271301--55271355 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
55271291 ATAAATTTGA
*
55271301 AATTTAATCTTTGTATTTTTTTAG
1 AATTTAATCTTTCTATTTTTTTAG
*
55271325 AATTTAATTTTTCTATTTTTTTAG
1 AATTTAATCTTTCTATTTTTTTAG
*
55271349 ATTTTAA
1 AATTTAA
55271356 AATTAAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.27, C:0.04, G:0.05, T:0.64
Consensus pattern (24 bp):
AATTTAATCTTTCTATTTTTTTAG
Found at i:55271553 original size:7 final size:7
Alignment explanation
Indices: 55271541--55271575 Score: 61
Period size: 7 Copynumber: 4.9 Consensus size: 7
55271531 AAGTCAAGGT
55271541 TGGCAAA
1 TGGCAAA
55271548 TGGCAAA
1 TGGCAAA
55271555 TGGCAAA
1 TGGCAAA
55271562 TGGCAAA
1 TGGCAAA
55271569 CTGGCAA
1 -TGGCAA
55271576 TGATATATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 21 0.78
8 6 0.22
ACGTcount: A:0.40, C:0.17, G:0.29, T:0.14
Consensus pattern (7 bp):
TGGCAAA
Found at i:55272351 original size:3 final size:3
Alignment explanation
Indices: 55272343--55272367 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
55272333 ATCAATACCT
55272343 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
55272368 AGTCAACCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:55272717 original size:11 final size:12
Alignment explanation
Indices: 55272691--55272716 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
55272681 GATGACATGG
55272691 TTTGTTCTTTTT
1 TTTGTTCTTTTT
55272703 TTTGTTCTTTTT
1 TTTGTTCTTTTT
55272715 TT
1 TT
55272717 GGTTAACTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.85
Consensus pattern (12 bp):
TTTGTTCTTTTT
Found at i:55282005 original size:6 final size:6
Alignment explanation
Indices: 55281994--55282021 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
55281984 TCCCTTAAAT
55281994 ATATAG ATATAG ATATAG ATATAG ATAT
1 ATATAG ATATAG ATATAG ATATAG ATAT
55282022 CGATCCCATC
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:0.14, T:0.36
Consensus pattern (6 bp):
ATATAG
Found at i:55302530 original size:160 final size:157
Alignment explanation
Indices: 55302266--55302579 Score: 556
Period size: 160 Copynumber: 2.0 Consensus size: 157
55302256 AGTTCCCAGT
*
55302266 GATTGATGTTATCAGGACTCTAGCTTTGCAGCTTAGCAAAACATTTTTGAGAGGTTTAGGAAGAG
1 GATTGATGTTATCAAGACTCTAGCTTTGCAGCTTAGCAAAACATTTTTGAGAGGTTTAGGAAGAG
*
55302331 ATTTTGAAGCTATGCTGTGAACGCCGAAATAGTTATTTCATCTTATATCTGTTTATATCCTGTAT
66 ATTTTGAAGCTATGCTGTGAACGCCAAAATAGTTATTTCATCTTATATCTGTTTATATCCTGTAT
55302396 ACAAAACTTGAATATAAATAATCACTATCG
131 ACAAAACTT---TATAAATAATCACTATCG
*
55302426 GATTGATGTTATCAAGACTCTAGCTTTGCAGCTTAGCAAAATATTTTTGAGAGGTTTAGGAAGAG
1 GATTGATGTTATCAAGACTCTAGCTTTGCAGCTTAGCAAAACATTTTTGAGAGGTTTAGGAAGAG
* *
55302491 GTTTTGAAGCTATGCTGTGAATGCCAAAATAGTTATTTCATCTTATATCTGTTTATATCCTGTAT
66 ATTTTGAAGCTATGCTGTGAACGCCAAAATAGTTATTTCATCTTATATCTGTTTATATCCTGTAT
55302556 ACAAAACTTTATAAATAATCACTA
131 ACAAAACTTTATAAATAATCACTA
55302580 CGCCTCCAAA
Statistics
Matches: 149, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
157 15 0.10
160 134 0.90
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.37
Consensus pattern (157 bp):
GATTGATGTTATCAAGACTCTAGCTTTGCAGCTTAGCAAAACATTTTTGAGAGGTTTAGGAAGAG
ATTTTGAAGCTATGCTGTGAACGCCAAAATAGTTATTTCATCTTATATCTGTTTATATCCTGTAT
ACAAAACTTTATAAATAATCACTATCG
Found at i:55308653 original size:30 final size:30
Alignment explanation
Indices: 55308631--55308687 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
55308621 TTAATATTTT
*
55308631 TTTTATA-ATTCTTAATCATTTTAA-AATAA
1 TTTTATATATTCTTAA-AATTTTAATAATAA
55308660 TTTTATATATTCTTAAAATTTTAATAAT
1 TTTTATATATTCTTAAAATTTTAATAAT
55308688 TCTTTAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.54
Consensus pattern (30 bp):
TTTTATATATTCTTAAAATTTTAATAATAA
Found at i:55308659 original size:21 final size:21
Alignment explanation
Indices: 55308635--55308678 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
55308625 TATTTTTTTT
55308635 ATAATTCTTA-ATCATT-TTAAA
1 ATAATT-TTATAT-ATTCTTAAA
55308656 ATAATTTTATATATTCTTAAA
1 ATAATTTTATATATTCTTAAA
55308677 AT
1 AT
55308679 TTTAATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAATTTTATATATTCTTAAA
Found at i:55308681 original size:18 final size:19
Alignment explanation
Indices: 55308658--55308696 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
55308648 ATTTTAAAAT
55308658 AATTTT-ATATATTC-TTAA
1 AATTTTAATA-ATTCTTTAA
55308676 AATTTTAATAATTCTTTAA
1 AATTTTAATAATTCTTTAA
55308695 AA
1 AA
55308697 AATCGCATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (19 bp):
AATTTTAATAATTCTTTAA
Found at i:55308698 original size:21 final size:21
Alignment explanation
Indices: 55308650--55308699 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 21
55308640 TCTTAATCAT
55308650 TTTAAAATAATTTTATATATTC
1 TTTAAAA-AATTTTATATATTC
55308672 -TT--AAAATTTTA-ATAATTC
1 TTTAAAAAATTTTATAT-ATTC
55308690 TTTAAAAAAT
1 TTTAAAAAAT
55308700 CGCATTCAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 9
0.73 0.00 0.27
Matches are distributed among these distances:
17 2 0.08
18 11 0.46
19 4 0.17
21 7 0.29
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTAAAAAATTTTATATATTC
Found at i:55315768 original size:8 final size:8
Alignment explanation
Indices: 55315755--55315783 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
55315745 TTTTAAATAA
55315755 TATTTTAT
1 TATTTTAT
55315763 TATTTTAT
1 TATTTTAT
55315771 TATTTTAT
1 TATTTTAT
55315779 TATTT
1 TATTT
55315784 AGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:55319668 original size:30 final size:30
Alignment explanation
Indices: 55319615--55319673 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
55319605 ACTTTCATAA
* * *
55319615 CAAATTTAAGATCACTATTCAATTTCAATTT
1 CAAATTCAAGATCAATATACAA-TTCAATTT
55319646 CAAATTCAA-ATCAATATACAATTCAATT
1 CAAATTCAAGATCAATATACAATTCAATT
55319674 ATACTTACAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 7 0.28
30 10 0.40
31 8 0.32
ACGTcount: A:0.44, C:0.17, G:0.02, T:0.37
Consensus pattern (30 bp):
CAAATTCAAGATCAATATACAATTCAATTT
Found at i:55320700 original size:25 final size:25
Alignment explanation
Indices: 55320670--55320741 Score: 85
Period size: 25 Copynumber: 3.0 Consensus size: 25
55320660 AGCACTCTCT
* *
55320670 CGAGCCATATAACAGGATGCTCATG
1 CGAGCCATATAACAGGAAGCTCATC
* * *
55320695 TGAGCCATGTAACAGGAAGCTTATC
1 CGAGCCATATAACAGGAAGCTCATC
55320720 CGAG-C-TATAACAGGAAGCTCAT
1 CGAGCCATATAACAGGAAGCTCAT
55320742 TAAGCTTAAC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
23 15 0.38
24 1 0.03
25 23 0.59
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (25 bp):
CGAGCCATATAACAGGAAGCTCATC
Found at i:55321027 original size:24 final size:25
Alignment explanation
Indices: 55320971--55321038 Score: 77
Period size: 24 Copynumber: 2.8 Consensus size: 25
55320961 ATACCGATTG
* *
55320971 GGATGCTCGCAAGAACTATATAACG
1 GGATGCTCGCAAGAGCTATATAACA
*
55320996 GGAAGCTCG-AGAGAGCT-TATAACA
1 GGATGCTCGCA-AGAGCTATATAACA
*
55321020 GGATGCTCGTAAGAGCTAT
1 GGATGCTCGCAAGAGCTAT
55321039 GGTGTGTCCG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
24 21 0.58
25 15 0.42
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.21
Consensus pattern (25 bp):
GGATGCTCGCAAGAGCTATATAACA
Found at i:55321267 original size:25 final size:25
Alignment explanation
Indices: 55321228--55321275 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
55321218 TATACACAAA
55321228 TATATCAGGAAGCTCACAAATAGTC
1 TATATCAGGAAGCTCACAAATAGTC
* * *
55321253 TATATCATGACGCTCATAAATAG
1 TATATCAGGAAGCTCACAAATAG
55321276 CTGCGGTATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.27
Consensus pattern (25 bp):
TATATCAGGAAGCTCACAAATAGTC
Found at i:55321584 original size:410 final size:410
Alignment explanation
Indices: 55320824--55321638 Score: 1382
Period size: 410 Copynumber: 2.0 Consensus size: 410
55320814 GAACCACATT
* *
55320824 AGGAAGCTCACAAGGAGCCTATATCATGACGCTCATAAATAGCTGTGGTATGTTCGCATTATATG
1 AGGAAGCTCACAAAGAGCCTATATCATGACGCTCATAAATAGCTGCGGTATGTTCGCATTATATG
* *
55320889 TAGGATCCATACTGATATTATAACATGACGCTCACAAAGAGCTGCGGTATGACTGCAACACATGC
66 TAGGATCCATACCGATATTATAACAGGACGCTCACAAAGAGCTGCGGTATGACTGCAACACATGC
* *
55320954 AGGGTCAATACCGATTGGGATGCTCGCAAGAACTATATAACGGGAAGCTCGAGAGAGCTTATAAC
131 AGGGTCAATACCGATTGGGATGCTCGCAAGAACCATATAACGGAAAGCTCGAGAGAGCTTATAAC
* * *
55321019 AGGATGCTCGTAAGAGCTATGGTGTGTCCGCAACATATGCAGAACCACAACCAATATGGGAAATC
196 AGGATGCTCGTAAGAGCTATGGTGTGTCCACAACATATGCAGAACCACAACCAATACGAGAAATC
* *
55321084 CTGTTCCCATCGAATTTCATTAATTCAAACAGGACATATTACTTATTAGGCATTATTGAACATGA
261 ATGTTCCCATCGAATTTCATTAATTCAAACAGGACATATTACTTATCAGGCATTATTGAACATGA
*
55321149 GATCAATTTCATATTTTCATAGCATTTATATAATTCACATATACACGACGTTCAATTCAAACATA
326 GATCAATTTCATATTTTCATAGCATTTATACAATTCACATATACACGACGTTCAATTCAAACATA
*
55321214 TAAATATACACAAATATATC
391 CAAATATACACAAATATATC
* *
55321234 AGGAAGCTCACAAATAGTCTATATCATGACGCTCATAAATAGCTGCGGTATG-TCTGCATTATAT
1 AGGAAGCTCACAAAGAGCCTATATCATGACGCTCATAAATAGCTGCGGTATGTTC-GCATTATAT
* *
55321298 GTAGGATCCATACCGATCA-TATAACAGGACGCTCACAAAGAGCTGTGGTATGACTGCAACATAT
65 GTAGGATCCATACCGAT-ATTATAACAGGACGCTCACAAAGAGCTGCGGTATGACTGCAACACAT
* *
55321362 GCAGGGTCAATACCGATTGGGATGCTTGCAATAACCATATAACGGAAAGCTCGAGAGAGCTTATA
129 GCAGGGTCAATACCGATTGGGATGCTCGCAAGAACCATATAACGGAAAGCTCGAGAGAGCTTATA
*
55321427 ACAGGATGCTCGTAAGAGCTATGGTGTGTTCACAACATATGCAGAACCACAACCAATACGAGAAA
194 ACAGGATGCTCGTAAGAGCTATGGTGTGTCCACAACATATGCAGAACCACAACCAATACGAGAAA
* * *
55321492 TCATGTTTCCATCGAATTTCATTAATTCAAACGGGACATATTACTTATCGGGCATTATTGAACAT
259 TCATGTTCCCATCGAATTTCATTAATTCAAACAGGACATATTACTTATCAGGCATTATTGAACAT
*
55321557 GTGATCAATTTCATATTTTCATAGCATTTATACAATTCACATATACACGACGTTCAATTCAAACA
324 GAGATCAATTTCATATTTTCATAGCATTTATACAATTCACATATACACGACGTTCAATTCAAACA
55321622 TACAAATATACACAAAT
389 TACAAATATACACAAAT
55321639 TAGTTACACA
Statistics
Matches: 379, Mismatches: 24, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
409 2 0.01
410 376 0.99
411 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (410 bp):
AGGAAGCTCACAAAGAGCCTATATCATGACGCTCATAAATAGCTGCGGTATGTTCGCATTATATG
TAGGATCCATACCGATATTATAACAGGACGCTCACAAAGAGCTGCGGTATGACTGCAACACATGC
AGGGTCAATACCGATTGGGATGCTCGCAAGAACCATATAACGGAAAGCTCGAGAGAGCTTATAAC
AGGATGCTCGTAAGAGCTATGGTGTGTCCACAACATATGCAGAACCACAACCAATACGAGAAATC
ATGTTCCCATCGAATTTCATTAATTCAAACAGGACATATTACTTATCAGGCATTATTGAACATGA
GATCAATTTCATATTTTCATAGCATTTATACAATTCACATATACACGACGTTCAATTCAAACATA
CAAATATACACAAATATATC
Found at i:55327203 original size:52 final size:52
Alignment explanation
Indices: 55327146--55327250 Score: 185
Period size: 52 Copynumber: 2.0 Consensus size: 52
55327136 AAAACTTTGT
55327146 TAGGTG-CTGGTAGATTGGATTGGGTTTTTAGATTATGGTTAGAATTGATTAG
1 TAGGTGTC-GGTAGATTGGATTGGGTTTTTAGATTATGGTTAGAATTGATTAG
*
55327198 TAGGTGTCGGTAGATTGGATTGGGTTTTTAGGTTATGGTTAGAATTGATTAG
1 TAGGTGTCGGTAGATTGGATTGGGTTTTTAGATTATGGTTAGAATTGATTAG
55327250 T
1 T
55327251 CTAATTCAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
52 50 0.98
53 1 0.02
ACGTcount: A:0.22, C:0.02, G:0.33, T:0.43
Consensus pattern (52 bp):
TAGGTGTCGGTAGATTGGATTGGGTTTTTAGATTATGGTTAGAATTGATTAG
Found at i:55345112 original size:23 final size:24
Alignment explanation
Indices: 55345056--55345113 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 24
55345046 TAGTGAAAAT
55345056 AATTA-CTCTCAATTTGGAATCTA
1 AATTAGCTCTCAATTTGGAATCTA
* *
55345079 AATTAG-T-TCAATTTTGAAT-TC
1 AATTAGCTCTCAATTTGGAATCTA
*
55345100 AATTGGCTCTCAAT
1 AATTAGCTCTCAAT
55345114 AATACTACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 6 0.21
22 12 0.41
23 11 0.38
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (24 bp):
AATTAGCTCTCAATTTGGAATCTA
Found at i:55346248 original size:23 final size:24
Alignment explanation
Indices: 55346200--55346248 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
55346190 AAAATCAGAT
*
55346200 AATTACTTAATTTTTTATTAATTA
1 AATTACTTAATTTTTTATTAAATA
*
55346224 AATTA-TTTATTTTTT-TCTAAATA
1 AATTACTTAATTTTTTAT-TAAATA
55346247 AA
1 AA
55346249 GTAAAATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 1 0.05
23 16 0.73
24 5 0.23
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (24 bp):
AATTACTTAATTTTTTATTAAATA
Found at i:55364485 original size:27 final size:27
Alignment explanation
Indices: 55364434--55364488 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
55364424 CATTCCTCTA
55364434 AAACCCTCGGTTTTCCATATATATTTT
1 AAACCCTCGGTTTTCCATATATATTTT
*
55364461 AAACCCT-GGATTGTTCCAT-TGTATTTT
1 AAACCCTCGG-TT-TTCCATATATATTTT
55364488 A
1 A
55364489 TACCATGCGG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 2 0.08
27 17 0.68
28 6 0.24
ACGTcount: A:0.25, C:0.20, G:0.11, T:0.44
Consensus pattern (27 bp):
AAACCCTCGGTTTTCCATATATATTTT
Found at i:55367091 original size:20 final size:19
Alignment explanation
Indices: 55367057--55367095 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
55367047 GAGTTTAGAG
*
55367057 TTTATGATTTTATTATTTA
1 TTTATAATTTTATTATTTA
55367076 TTTATAATTATTATTATTTA
1 TTTATAATT-TTATTATTTA
55367096 GTTGTGCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTATAATTTTATTATTTA
Found at i:55379500 original size:17 final size:16
Alignment explanation
Indices: 55379474--55379510 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
55379464 TAATCTAATT
55379474 TATTTAATATATTTAAA
1 TATTTAATATA-TTAAA
*
55379491 TATTTTATATATTAAA
1 TATTTAATATATTAAA
55379507 TATT
1 TATT
55379511 GATAAATTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTTAATATATTAAA
Found at i:55384760 original size:50 final size:50
Alignment explanation
Indices: 55384698--55385260 Score: 307
Period size: 50 Copynumber: 11.3 Consensus size: 50
55384688 GATCTGTAAT
* * * ** *
55384698 CTTCAATTTGTTCAACTGCAATGTTGGGGAAACTAGATCCACCGTCGTAG
1 CTTCAATCTGTTCAATTGCAATATCAGGGAAACTAGATCCGCCGTCGTAG
* * *** * * * *
55384748 CTTCAATCTGTTCCACTGCACCGTCAGGG-AAGTAAGATCTGCCGTTGTGG
1 CTTCAATCTGTTCAATTGCAATATCAGGGAAACT-AGATCCGCCGTCGTAG
* * * * *
55384798 CTTCAATCTTTTTAATTGCAATGTCAGGAAAACTAGATCCACCGTCGTAG
1 CTTCAATCTGTTCAATTGCAATATCAGGGAAACTAGATCCGCCGTCGTAG
* * * ** * * * * *
55384848 TTTCAATCTATTCCATTGCGCT-GCTAAGG-AAGTAAGATCCGCCGTTGTGG
1 CTTCAATCTGTTCAATTGCAATATC-AGGGAAACT-AGATCCGCCGTCGTAG
* * * * *
55384898 CTTCAATCTTTTTAATTACAATATCAGGGAAACCAGATCCACCGTCGTAG
1 CTTCAATCTGTTCAATTGCAATATCAGGGAAACTAGATCCGCCGTCGTAG
*** * * * * * *
55384948 CTTCAATCTGTTCCGCTGCACTA-CTAAGG-AAGTAAGATCTGCCGTTGTGG
1 CTTCAATCTGTTCAATTGCAATATC-AGGGAAACT-AGATCCGCCGTCGTAG
* * * *
55384998 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCTGCCGTCGTAG
1 CTTCAATCTGTTCAATTGCAATATCAGGGAAACTAGATCCGCCGTCGTAG
*** * * * * * * *
55385048 CTTCAATCTGTTCCGCTGTACTA-CTAAGG-AAGTAAGATCCGTCGTTGTGG
1 CTTCAATCTGTTCAATTGCAATATC-AGGGAAACT-AGATCCGCCGTCGTAG
* * * *
55385098 CTTCAATCTTTTTAATTGCAATATCAGGGAAACTAGATCCACCGTCATAG
1 CTTCAATCTGTTCAATTGCAATATCAGGGAAACTAGATCCGCCGTCGTAG
*** * * * * * *
55385148 CTTCAATCTGTTCCGCTGCACT-GCTAAGG-AAGTAAGATCCGCCGTTGTGG
1 CTTCAATCTGTTCAATTGCAATATC-AGGGAAACT-AGATCCGCCGTCGTAG
* * * *
55385198 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCTGCCGTCGTAG
1 CTTCAATCTGTTCAATTGCAATATCAGGGAAACTAGATCCGCCGTCGTAG
55385248 CTTCAATCTGTTC
1 CTTCAATCTGTTC
55385261 CGCTGCACTG
Statistics
Matches: 364, Mismatches: 131, Indels: 36
0.69 0.25 0.07
Matches are distributed among these distances:
49 17 0.05
50 331 0.91
51 16 0.04
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.31
Consensus pattern (50 bp):
CTTCAATCTGTTCAATTGCAATATCAGGGAAACTAGATCCGCCGTCGTAG
Found at i:55384831 original size:100 final size:100
Alignment explanation
Indices: 55384724--55385311 Score: 872
Period size: 100 Copynumber: 5.9 Consensus size: 100
55384714 TGCAATGTTG
* * * *
55384724 GGGAAACTAGATCCACCGTCGTAGCTTCAATCTGTTCCACTGCACCG-TCAGGGAAGTAAGATCT
1 GGGAAACCAGATCCACCGTCGTAGCTTCAATCTGTTCCGCTGCACCGCT-AAGGAAGTAAGATCC
*
55384788 GCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCA
65 GCCGTTGTGGCTTCAATCTTTTTAATTGCAATATCA
* * * * ** * *
55384824 GGAAAACTAGATCCACCGTCGTAGTTTCAATCTATTCCATTGCGCTGCTAAGGAAGTAAGATCCG
1 GGGAAACCAGATCCACCGTCGTAGCTTCAATCTGTTCCGCTGCACCGCTAAGGAAGTAAGATCCG
*
55384889 CCGTTGTGGCTTCAATCTTTTTAATTACAATATCA
66 CCGTTGTGGCTTCAATCTTTTTAATTGCAATATCA
** *
55384924 GGGAAACCAGATCCACCGTCGTAGCTTCAATCTGTTCCGCTGCACTACTAAGGAAGTAAGATCTG
1 GGGAAACCAGATCCACCGTCGTAGCTTCAATCTGTTCCGCTGCACCGCTAAGGAAGTAAGATCCG
55384989 CCGTTGTGGCTTCAATCTTTTTAATTGCAATATCA
66 CCGTTGTGGCTTCAATCTTTTTAATTGCAATATCA
** * **
55385024 GGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCGCTGTACTACTAAGGAAGTAAGATCCG
1 GGGAAACCAGATCCACCGTCGTAGCTTCAATCTGTTCCGCTGCACCGCTAAGGAAGTAAGATCCG
*
55385089 TCGTTGTGGCTTCAATCTTTTTAATTGCAATATCA
66 CCGTTGTGGCTTCAATCTTTTTAATTGCAATATCA
* * *
55385124 GGGAAACTAGATCCACCGTCATAGCTTCAATCTGTTCCGCTGCACTGCTAAGGAAGTAAGATCCG
1 GGGAAACCAGATCCACCGTCGTAGCTTCAATCTGTTCCGCTGCACCGCTAAGGAAGTAAGATCCG
55385189 CCGTTGTGGCTTCAATCTTTTTAATTGCAATATCA
66 CCGTTGTGGCTTCAATCTTTTTAATTGCAATATCA
** * ** *
55385224 GGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCGCTGCACTGCTAATAAAGTAAGATGCG
1 GGGAAACCAGATCCACCGTCGTAGCTTCAATCTGTTCCGCTGCACCGCTAAGGAAGTAAGATCCG
55385289 CCGTTGTGGCTTCAATCTTTTTA
66 CCGTTGTGGCTTCAATCTTTTTA
55385312 CTTTTCAACT
Statistics
Matches: 448, Mismatches: 39, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
100 447 1.00
101 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (100 bp):
GGGAAACCAGATCCACCGTCGTAGCTTCAATCTGTTCCGCTGCACCGCTAAGGAAGTAAGATCCG
CCGTTGTGGCTTCAATCTTTTTAATTGCAATATCA
Found at i:55393409 original size:20 final size:20
Alignment explanation
Indices: 55393384--55393423 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
55393374 TAAAGGTCTT
55393384 TAATGCATATAATGCGATGC
1 TAATGCATATAATGCGATGC
* *
55393404 TAATGCATATGATTCGATGC
1 TAATGCATATAATGCGATGC
55393424 ATGAGGTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Consensus pattern (20 bp):
TAATGCATATAATGCGATGC
Found at i:55401076 original size:22 final size:22
Alignment explanation
Indices: 55401042--55401086 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
55401032 GGCTTCAAAA
55401042 TTCAATTTCATACCTAAGTTTT
1 TTCAATTTCATACCTAAGTTTT
* * * *
55401064 TTCATTTTGATACTTGAGTTTT
1 TTCAATTTCATACCTAAGTTTT
55401086 T
1 T
55401087 ATTTTTTCTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.56
Consensus pattern (22 bp):
TTCAATTTCATACCTAAGTTTT
Found at i:55407535 original size:40 final size:40
Alignment explanation
Indices: 55407472--55407558 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 40
55407462 AATTATGGAA
* * *
55407472 TACTGAATATTGTTTTGAGTACTG-AGTTGAATTGTGAAGT
1 TACTGAATATTGTTATGAGTACTGCA-TTGAACTGTGAAAT
*
55407512 TATTGAATATTGTTATGTA-TACTGCATTGAACTGTGAAAT
1 TACTGAATATTGTTATG-AGTACTGCATTGAACTGTGAAAT
55407552 TACTGAA
1 TACTGAA
55407559 GTAATGAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
40 38 0.95
41 2 0.05
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.41
Consensus pattern (40 bp):
TACTGAATATTGTTATGAGTACTGCATTGAACTGTGAAAT
Found at i:55407816 original size:33 final size:33
Alignment explanation
Indices: 55407764--55407840 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 33
55407754 CGACTACTGT
* *
55407764 TACTGTTACCGATTTGGCACTTTGTGTGTCGAA
1 TACTGTTACTGATTCGGCACTTTGTGTGTCGAA
*
55407797 TACTGTTACTGATTCGGCACTTTGTTTGTCGAA
1 TACTGTTACTGATTCGGCACTTTGTGTGTCGAA
*
55407830 TACTATTACTG
1 TACTGTTACTG
55407841 TTACTGTTAC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.42
Consensus pattern (33 bp):
TACTGTTACTGATTCGGCACTTTGTGTGTCGAA
Found at i:55407848 original size:45 final size:46
Alignment explanation
Indices: 55407797--55407986 Score: 228
Period size: 45 Copynumber: 4.2 Consensus size: 46
55407787 GTGTGTCGAA
* * *
55407797 TACTGTTACT-GATTCGGCACTTTGTTTGTCGAATACTATTACTGT
1 TACTGTTACTAGATTCGACACTTTGTGTGTCGAATACTATTACCGT
* * *
55407842 TACTGTTAC-CGATTCGACACTTTGTGTATCGAATACTGTTACCGT
1 TACTGTTACTAGATTCGACACTTTGTGTGTCGAATACTATTACCGT
* * * *
55407887 TACTGTTA-TCGGTTCGACACTTTGTGTGCCGAATACTGTTACCG-
1 TACTGTTACTAGATTCGACACTTTGTGTGTCGAATACTATTACCGT
* * *
55407931 TACTGTTA-TAGATTCGACACTTTGTGCGTTGAATACTATTACTGT
1 TACTGTTACTAGATTCGACACTTTGTGTGTCGAATACTATTACCGT
55407976 TACTGTTACTA
1 TACTGTTACTA
55407987 CTACCGTTAC
Statistics
Matches: 126, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
44 37 0.29
45 87 0.69
46 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Consensus pattern (46 bp):
TACTGTTACTAGATTCGACACTTTGTGTGTCGAATACTATTACCGT
Found at i:55407956 original size:89 final size:90
Alignment explanation
Indices: 55407809--55407983 Score: 235
Period size: 89 Copynumber: 2.0 Consensus size: 90
55407799 CTGTTACTGA
* * * * * *
55407809 TTCGGCACTTTGTTTGTCGAATACTATTACTGTTACTGTTACCGATTCGACACTTTGTGTATCGA
1 TTCGACACTTTGTGTGCCGAATACTATTACCGTTACTGTTACAGATTCGACACTTTGTGCATCGA
*
55407874 ATACTGTTACCGTTACTGTTATCGG
66 ATACTATTACCGTTACTGTTATCGG
* * * *
55407899 TTCGACACTTTGTGTGCCGAATACTGTTACCG-TACTGTTATAGATTCGACACTTTGTGCGTTGA
1 TTCGACACTTTGTGTGCCGAATACTATTACCGTTACTGTTACAGATTCGACACTTTGTGCATCGA
*
55407963 ATACTATTACTGTTACTGTTA
66 ATACTATTACCGTTACTGTTA
55407984 CTACTACCGT
Statistics
Matches: 73, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
89 46 0.63
90 27 0.37
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (90 bp):
TTCGACACTTTGTGTGCCGAATACTATTACCGTTACTGTTACAGATTCGACACTTTGTGCATCGA
ATACTATTACCGTTACTGTTATCGG
Found at i:55407995 original size:18 final size:19
Alignment explanation
Indices: 55407964--55408004 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
55407954 GTGCGTTGAA
* *
55407964 TACTATTACTGTTACTG-T
1 TACTACTACCGTTACTGAT
55407982 TACTACTACCGTTACTGAT
1 TACTACTACCGTTACTGAT
55408001 TACT
1 TACT
55408005 GTTTAGGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.44
Consensus pattern (19 bp):
TACTACTACCGTTACTGAT
Found at i:55409584 original size:20 final size:20
Alignment explanation
Indices: 55409559--55409601 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
55409549 AATCATTTAA
55409559 AAATTA-ATTTAGTAATATTT
1 AAATTATATTTA-TAATATTT
*
55409579 AAATTATATTTATAATTTTT
1 AAATTATATTTATAATATTT
55409599 AAA
1 AAA
55409602 AAATAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
AAATTATATTTATAATATTT
Found at i:55409611 original size:20 final size:20
Alignment explanation
Indices: 55409553--55409612 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
55409543 TTATGAAATC
*
55409553 ATTTAAAAATTAATTTAGTAAT
1 ATTTAAAAAATAA-TTA-TAAT
** *
55409575 ATTTAAATTATATTTATAAT
1 ATTTAAAAAATAATTATAAT
*
55409595 TTTTAAAAAATAATTATA
1 ATTTAAAAAATAATTATA
55409613 TAGATTTAAT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
20 18 0.60
21 3 0.10
22 9 0.30
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
ATTTAAAAAATAATTATAAT
Found at i:55417618 original size:17 final size:18
Alignment explanation
Indices: 55417591--55417624 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
55417581 GAAAAAACGT
55417591 ACAAATGTAAAAAAAAAA
1 ACAAATGTAAAAAAAAAA
55417609 ACAAAT-TAAAAAAAAA
1 ACAAATGTAAAAAAAAA
55417625 TCTTACTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.79, C:0.06, G:0.03, T:0.12
Consensus pattern (18 bp):
ACAAATGTAAAAAAAAAA
Found at i:55419069 original size:15 final size:14
Alignment explanation
Indices: 55419048--55419083 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
55419038 ATAATCCTTA
*
55419048 ATAATTATCTTAAT
1 ATAATTATCCTAAT
55419062 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
55419077 ATAATTA
1 ATAATTA
55419084 AAACAGAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:55422572 original size:13 final size:13
Alignment explanation
Indices: 55422556--55422582 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
55422546 CCATATTAGT
55422556 TTTTTATATATAA
1 TTTTTATATATAA
55422569 TTTTTATATATAA
1 TTTTTATATATAA
55422582 T
1 T
55422583 ACATCAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTTTATATATAA
Found at i:55427137 original size:25 final size:25
Alignment explanation
Indices: 55427101--55427168 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 25
55427091 AAACCCTAAT
*
55427101 TTTTCCTTTCTTTCTT-TCCCTTTTTC
1 TTTT-CTTTCTTT-TTCTCCCTGTTTC
55427127 TTTTCTTTCTTTTTCTCCCTGTTTC
1 TTTTCTTTCTTTTTCTCCCTGTTTC
* *
55427152 GTTTCTATTCTGTTTCT
1 TTTTCT-TTCTTTTTCT
55427169 TTTATTTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 2 0.05
25 22 0.59
26 13 0.35
ACGTcount: A:0.01, C:0.26, G:0.04, T:0.68
Consensus pattern (25 bp):
TTTTCTTTCTTTTTCTCCCTGTTTC
Found at i:55427241 original size:8 final size:8
Alignment explanation
Indices: 55427188--55427259 Score: 71
Period size: 8 Copynumber: 9.4 Consensus size: 8
55427178 TATATTTACT
55427188 TATTATAA
1 TATTATAA
55427196 TA-TATAA
1 TATTATAA
*
55427203 TATAATATA
1 TATTATA-A
*
55427212 TACT-TAA
1 TATTATAA
*
55427219 TAAT-TAA
1 TATTATAA
*
55427226 GA-TATAA
1 TATTATAA
55427233 TATTATAA
1 TATTATAA
55427241 TATTATAA
1 TATTATAA
55427249 TATTATAA
1 TATTATAA
55427257 TAT
1 TAT
55427260 ATATTTTTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
6 1 0.02
7 19 0.35
8 31 0.57
9 3 0.06
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (8 bp):
TATTATAA
Found at i:55427249 original size:16 final size:15
Alignment explanation
Indices: 55427188--55427262 Score: 82
Period size: 16 Copynumber: 4.9 Consensus size: 15
55427178 TATATTTACT
55427188 TATTATAATATATAA
1 TATTATAATATATAA
*
55427203 TATAAT-ATATACTTAA
1 TATTATAATATA--TAA
* *
55427219 TAAT-TAAGATATAA
1 TATTATAATATATAA
55427233 TATTATAATATTATAA
1 TATTATAATA-TATAA
55427249 TATTATAATATATA
1 TATTATAATATATA
55427263 TTTTTTAACT
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
14 11 0.22
15 14 0.29
16 24 0.49
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (15 bp):
TATTATAATATATAA
Found at i:55429991 original size:15 final size:15
Alignment explanation
Indices: 55429971--55430026 Score: 54
Period size: 14 Copynumber: 4.2 Consensus size: 15
55429961 ACATGAATTT
55429971 TTTAAAATAATATAA
1 TTTAAAATAATATAA
55429986 TTTAAAAT-ATAT-A
1 TTTAAAATAATATAA
*
55429999 -TT--ATTAATA-AA
1 TTTAAAATAATATAA
55430010 TTTAAAATAAT-TAA
1 TTTAAAATAATATAA
55430024 TTT
1 TTT
55430027 TATTATTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 13
0.69 0.04 0.27
Matches are distributed among these distances:
10 2 0.06
11 4 0.12
12 4 0.12
13 1 0.03
14 14 0.42
15 8 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TTTAAAATAATATAA
Found at i:55430107 original size:25 final size:26
Alignment explanation
Indices: 55430078--55430128 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
55430068 AAACTTATTA
*
55430078 TTTAAGTATAA-AATTAAAACCAAAT
1 TTTAAATATAATAATTAAAACCAAAT
*
55430103 TTTAAATATAATAATTAAAATCAAAT
1 TTTAAATATAATAATTAAAACCAAAT
55430129 CTTATTTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.35
Consensus pattern (26 bp):
TTTAAATATAATAATTAAAACCAAAT
Found at i:55443662 original size:46 final size:46
Alignment explanation
Indices: 55443598--55443691 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
55443588 CTTCACTCAT
55443598 CACACACAACAACCTTGATGCTCCTAAGAGGGACCCAGATTATTCA
1 CACACACAACAACCTTGATGCTCCTAAGAGGGACCCAGATTATTCA
*
55443644 CACACACAACAACCTTGATGCTGCTAAGAGGGACCCAGATTATTCA
1 CACACACAACAACCTTGATGCTCCTAAGAGGGACCCAGATTATTCA
55443690 CA
1 CA
55443692 TTCTTTTGAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.35, C:0.30, G:0.16, T:0.19
Consensus pattern (46 bp):
CACACACAACAACCTTGATGCTCCTAAGAGGGACCCAGATTATTCA
Found at i:55447052 original size:12 final size:12
Alignment explanation
Indices: 55447005--55447052 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
55446995 AAGCTGCTCA
55447005 TATTAGTTGTTT
1 TATTAGTTGTTT
* *
55447017 TATTACTTATTCT
1 TATTAGTTGTT-T
* *
55447030 TGTTAGCTGTTT
1 TATTAGTTGTTT
55447042 TATTAGTTGTT
1 TATTAGTTGTT
55447053 AATGATGTAT
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
12 19 0.70
13 8 0.30
ACGTcount: A:0.17, C:0.06, G:0.15, T:0.62
Consensus pattern (12 bp):
TATTAGTTGTTT
Found at i:55452991 original size:6 final size:6
Alignment explanation
Indices: 55452980--55453004 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
55452970 AAGGTTGATC
55452980 GTTGAA GTTGAA GTTGAA GTTGAA G
1 GTTGAA GTTGAA GTTGAA GTTGAA G
55453005 AAGGAGAGTA
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:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (6 bp):
GTTGAA
Found at i:55455567 original size:13 final size:13
Alignment explanation
Indices: 55455549--55455573 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55455539 TTAAAAGAAC
55455549 TTATATATAATAT
1 TTATATATAATAT
55455562 TTATATATAATA
1 TTATATATAATA
55455574 AAATTTAAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTATATATAATAT
Found at i:55474594 original size:6 final size:6
Alignment explanation
Indices: 55474562--55474587 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
55474552 TTCCCTTTTA
55474562 TTTATT TTTATT TTTATT TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TT
55474588 CTTTTTCCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:55474811 original size:44 final size:44
Alignment explanation
Indices: 55474593--55474894 Score: 129
Period size: 44 Copynumber: 6.9 Consensus size: 44
55474583 ATTTTCTTTT
* * *
55474593 TCCCTCGGTTGCAGTGGAGCAGGTTGAAAATAGTAGATCTTGCC
1 TCCCTCGGTTGCAGTGGAACAGGTTGAAGATAGCAGATCTTGCC
* * * * * * * * * *
55474637 TTCCT-GCGTAGAAAG-CGAACCAGATCGAAGACACCA-ACCTCGCC
1 TCCCTCG-GTTG-CAGTGGAA-CAGGTTGAAGATAGCAGATCTTGCC
55474681 TCCCTCGGTTGCAGTGGAGA-AGGTTGAAGATAGCAGATCTTGCC
1 TCCCTCGGTTGCAGTGGA-ACAGGTTGAAGATAGCAGATCTTGCC
* * * * * ** * * *
55474725 TTCAT-GCGTAGACAG-CGAAGCAGATCAAAGACACCAG-CCTTGCC
1 TCCCTCG-GTTG-CAGTGGAA-CAGGTTGAAGATAGCAGATCTTGCC
*
55474769 TCCCTCGGTTGCAGTGGAACAGGTTGAAGATAGTAGATCTTGCC
1 TCCCTCGGTTGCAGTGGAACAGGTTGAAGATAGCAGATCTTGCC
* * * * * * * * *
55474813 TTCCT-GCGTAGACAG-CGAAGCAGATCGAAGACATCAG-CCTCGCC
1 TCCCTCG-GTTG-CAGTGGAA-CAGGTTGAAGATAGCAGATCTTGCC
* *
55474857 TCCCTCGATTGCAGTGGAGCAGGTTGAAGATAGCAGAT
1 TCCCTCGGTTGCAGTGGAACAGGTTGAAGATAGCAGAT
55474895 ATTGTCTTCC
Statistics
Matches: 174, Mismatches: 64, Indels: 40
0.63 0.23 0.14
Matches are distributed among these distances:
43 47 0.27
44 82 0.47
45 45 0.26
ACGTcount: A:0.26, C:0.25, G:0.27, T:0.21
Consensus pattern (44 bp):
TCCCTCGGTTGCAGTGGAACAGGTTGAAGATAGCAGATCTTGCC
Found at i:55474932 original size:88 final size:88
Alignment explanation
Indices: 55474593--55474906 Score: 493
Period size: 88 Copynumber: 3.6 Consensus size: 88
55474583 ATTTTCTTTT
* * * *
55474593 TCCCTCGGTTGCAGTGGAGCAGGTTGAAAATAGTAGATCTTGCCTTCCTGCGTAGAAAGCGAACC
1 TCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGC
*
55474658 AGATCGAAGACACCAACCTCGCC
66 AGATCGAAGACACCAGCCTCGCC
* *
55474681 TCCCTCGGTTGCAGTGGAGAAGGTTGAAGATAGCAGATCTTGCCTTCATGCGTAGACAGCGAAGC
1 TCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGC
* *
55474746 AGATCAAAGACACCAGCCTTGCC
66 AGATCGAAGACACCAGCCTCGCC
* *
55474769 TCCCTCGGTTGCAGTGGAACAGGTTGAAGATAGTAGATCTTGCCTTCCTGCGTAGACAGCGAAGC
1 TCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGC
*
55474834 AGATCGAAGACATCAGCCTCGCC
66 AGATCGAAGACACCAGCCTCGCC
* * *
55474857 TCCCTCGATTGCAGTGGAGCAGGTTGAAGATAGCAGATATTGTCTTCCTG
1 TCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTG
55474907 TACTGACGAC
Statistics
Matches: 205, Mismatches: 21, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 205 1.00
ACGTcount: A:0.26, C:0.25, G:0.27, T:0.22
Consensus pattern (88 bp):
TCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGC
AGATCGAAGACACCAGCCTCGCC
Found at i:55475085 original size:128 final size:128
Alignment explanation
Indices: 55474919--55475632 Score: 970
Period size: 128 Copynumber: 5.6 Consensus size: 128
55474909 CTGACGACAA
*
55474919 AGCAGATCGAAGACGGTGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCGCAAGTCCTA
1 AGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCGCAAGTCCTA
*
55474984 TATCCCTGGGCAGCAGTGGAATATGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGG
66 TATCCCTGGGCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGG
* * *
55475047 ATCAGATCGAAGATGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCGCAAGTACTA
1 AGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCGCAAGTCCTA
* *
55475112 TATCCCTGGGCAGTAGTGGAATATGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGG
66 TATCCCTGGGCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGG
55475175 AGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCGCAAGTCCTA
1 AGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCGCAAGTCCTA
* * *
55475240 TATCCCTGGGCAGCAATGAAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAATAGCGG
66 TATCCCTGGGCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGG
* * * * *
55475303 AGCAGATTGAAGACGGCAAATCTTATTTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAATCCTA
1 AGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCGCAAGTCCTA
* * * * *
55475368 TATCCCTAGGCAGCAGTGGAATAGGTTGAAAATTACAGATCTCGCCTCCCTAAGAAGTAGCGG
66 TATCCCTGGGCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGG
* *
55475431 AGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTT
1 AGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCGCAAGTCCTA
* ** ** ** * * * * *
55475496 TCTCCCTGAGGTTGCAGTGGAGCAGACT--AAGTAAGCAGGTCTTATCCCCCTGAAGTTGCAGT-
66 TATCCCTG-GGCAGCAGTGGAATAGGTTGGAAATTA-CAGATCTTGTCTCCCT-AA---GCAGTA
55475558 G-GG
125 GCGG
** * * * *
55475561 A-CAGATTAAAGACGGCAAATCTTATCTTCAAGTGTAAGGATGCAGATTTAAGCCACAAGTCCTT
1 AGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCGCAAGTCCTA
*
55475625 TCTCCCTG
66 TATCCCTG
55475633 AAGTTGCAGT
Statistics
Matches: 529, Mismatches: 51, Indels: 11
0.90 0.09 0.02
Matches are distributed among these distances:
127 4 0.01
128 435 0.82
129 82 0.16
130 3 0.01
131 1 0.00
132 4 0.01
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (128 bp):
AGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCGCAAGTCCTA
TATCCCTGGGCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGG
Found at i:55477533 original size:22 final size:22
Alignment explanation
Indices: 55477508--55477552 Score: 76
Period size: 20 Copynumber: 2.1 Consensus size: 22
55477498 AACCCTTTTT
55477508 TATATATATTA-TTATA-TAAA
1 TATATATATTATTTATATTAAA
55477528 TATATATATTATTTATATTAAA
1 TATATATATTATTTATATTAAA
55477550 TAT
1 TAT
55477553 TTCATTTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 11 0.48
21 5 0.22
22 7 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TATATATATTATTTATATTAAA
Found at i:55500821 original size:45 final size:45
Alignment explanation
Indices: 55500762--55500914 Score: 234
Period size: 45 Copynumber: 3.4 Consensus size: 45
55500752 CACCAGTATA
* ** *
55500762 CAGTAATCAGTAACAGTAACAGTATTCAACACACAAAGTGGTGAAC
1 CAGTAA-CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
* *
55500808 CTGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAGT
1 CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
*
55500853 CGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
1 CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
55500898 CAGTAACAGTAACAGTA
1 CAGTAACAGTAACAGTA
55500915 GTCGGCACAT
Statistics
Matches: 98, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
45 93 0.95
46 5 0.05
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.19
Consensus pattern (45 bp):
CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
Found at i:55500859 original size:39 final size:39
Alignment explanation
Indices: 55500768--55500941 Score: 154
Period size: 45 Copynumber: 4.2 Consensus size: 39
55500758 TATACAGTAA
* **
55500768 TCAGTAACAGTAACAGTATTCAACACACAAAGTGGTGAACCTG
1 TCAGTAACAGTAACAGTATTCGACACACAAAGTGCCG-A---G
55500811 TAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAGTCGG
1 T--CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGA----G
*
55500856 TAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAA
1 T--CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAG
* * *
55500897 TCAGTAACAGTAACAGTAGTCGGCACA-TAAGTGCCTGA-
1 TCAGTAACAGTAACAGTATTCGACACACAAAGTGCC-GAG
55500935 TCAGTAA
1 TCAGTAA
55500942 GCCGGCAAAT
Statistics
Matches: 118, Mismatches: 9, Indels: 13
0.84 0.06 0.09
Matches are distributed among these distances:
38 14 0.12
39 26 0.22
41 1 0.01
43 1 0.01
44 1 0.01
45 75 0.64
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.20
Consensus pattern (39 bp):
TCAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAG
Found at i:55501202 original size:39 final size:40
Alignment explanation
Indices: 55501116--55501203 Score: 110
Period size: 40 Copynumber: 2.2 Consensus size: 40
55501106 AATTCTTTAC
* *
55501116 TTCAGTAATTTCACAATTCAATGCATTATGCATAACAATA
1 TTCAGTATTTTCACAATTCAATGCATAATGCATAACAATA
*
55501156 TTCAGTATTTTCACAATTCACT-CAGTAAT-CA-AGACAATA
1 TTCAGTATTTTCACAATTCAATGCA-TAATGCATA-ACAATA
55501195 TTCAGTATT
1 TTCAGTATT
55501204 CCATAATTCG
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
38 1 0.02
39 19 0.44
40 23 0.53
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (40 bp):
TTCAGTATTTTCACAATTCAATGCATAATGCATAACAATA
Found at i:55501931 original size:11 final size:11
Alignment explanation
Indices: 55501915--55501940 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
55501905 CTTTTTCTTC
55501915 TTTCTCCCCTG
1 TTTCTCCCCTG
55501926 TTTCTCCCCTG
1 TTTCTCCCCTG
55501937 TTTC
1 TTTC
55501941 GTCTCTTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.42, G:0.08, T:0.50
Consensus pattern (11 bp):
TTTCTCCCCTG
Found at i:55514354 original size:20 final size:21
Alignment explanation
Indices: 55514326--55514380 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
55514316 ACAAAGATAG
55514326 GTATCGATACTTTTGTGAA-A
1 GTATCGATACTTTTGTGAATA
* *
55514346 GTATTGATAC-TTTGTTAATA
1 GTATCGATACTTTTGTGAATA
*
55514366 GTATCAATACTTTTG
1 GTATCGATACTTTTG
55514381 ATTTTTGCTC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 7 0.24
20 18 0.62
21 4 0.14
ACGTcount: A:0.29, C:0.09, G:0.16, T:0.45
Consensus pattern (21 bp):
GTATCGATACTTTTGTGAATA
Found at i:55517006 original size:2 final size:2
Alignment explanation
Indices: 55516989--55517023 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
55516979 CCCACCGAAT
* *
55516989 TA TA CA TA TT 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 TA TA TA TA TA T
55517024 TAATCACGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:55539041 original size:23 final size:23
Alignment explanation
Indices: 55539011--55539056 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
55539001 GTTTTAACTT
55539011 TTTTTTATTTACCAAAATATATA
1 TTTTTTATTTACCAAAATATATA
55539034 TTTTTTATTTACCAAAATATATA
1 TTTTTTATTTACCAAAATATATA
55539057 AAAAAACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTTTTATTTACCAAAATATATA
Found at i:55539159 original size:27 final size:29
Alignment explanation
Indices: 55539123--55539190 Score: 99
Period size: 27 Copynumber: 2.5 Consensus size: 29
55539113 TCACGCTAAA
*
55539123 GCCATTGGCGGCACCAATGGTGCCA-A-T
1 GCCATTGGCGGCACCAATAGTGCCATACT
55539150 GCCATTGGCGGCACCAATAGTGCCATACT
1 GCCATTGGCGGCACCAATAGTGCCATACT
55539179 G--ATTGGCGGCAC
1 GCCATTGGCGGCAC
55539191 TACTCGTATT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
27 35 0.92
28 1 0.03
29 2 0.05
ACGTcount: A:0.22, C:0.29, G:0.29, T:0.19
Consensus pattern (29 bp):
GCCATTGGCGGCACCAATAGTGCCATACT
Found at i:55539350 original size:19 final size:21
Alignment explanation
Indices: 55539312--55539350 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
55539302 AATAATTGAT
*
55539312 TATATTGTTGTTATTATTTTG
1 TATATTGTTGTTAATATTTTG
55539333 TATATT-TTG-TAATATTTT
1 TATATTGTTGTTAATATTTT
55539351 TTTGTTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (21 bp):
TATATTGTTGTTAATATTTTG
Found at i:55539446 original size:15 final size:15
Alignment explanation
Indices: 55539412--55539440 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
55539402 GTTAGTATTA
55539412 TTATTGTTGTTGTTG
1 TTATTGTTGTTGTTG
55539427 TTATTGTTGTTGTT
1 TTATTGTTGTTGTT
55539441 AGTATTAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.00, G:0.24, T:0.69
Consensus pattern (15 bp):
TTATTGTTGTTGTTG
Found at i:55544085 original size:28 final size:31
Alignment explanation
Indices: 55544035--55544101 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
55544025 TTACCTTCTT
55544035 TTTTCTTTTTTTTTCCTTCCTTC-CCTCTCC
1 TTTTCTTTTTTTTTCCTTCCTTCTCCTCTCC
*
55544065 TTCTTCTTTTTTTTT-C-T-CTTCTCCTTTCC
1 TT-TTCTTTTTTTTTCCTTCCTTCTCCTCTCC
55544094 TTTTCTTT
1 TTTTCTTT
55544102 CCTTCTTTCT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
28 10 0.29
29 9 0.26
30 3 0.09
31 12 0.35
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (31 bp):
TTTTCTTTTTTTTTCCTTCCTTCTCCTCTCC
Found at i:55544094 original size:39 final size:39
Alignment explanation
Indices: 55544029--55544227 Score: 155
Period size: 39 Copynumber: 5.2 Consensus size: 39
55544019 AAAAAATTAC
* * *
55544029 CTTCTTTTTTCTTT-TTTTTTCC-TTCCTTCCCTCTCCTT
1 CTTCTTTTTT-TTTCTCTTCTCCTTTCCTTTCCTCTCCTT
* *
55544067 CTTCTTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTT
1 CTTCTTTTTTTTTCTCTTCTCCTTTCCTTTCCTCTCCTT
* * *
55544106 CTTTCTTTCTTTTT-TCTTCTCCTTTCTTTTCTTCTCCTTT
1 C-TTCTTTTTTTTTCTCTTCTCCTTTCCTTTCCTCTCC-TT
* * * *
55544146 CTT-TCTTTTTTTCTCTTCTTCTTTCCTTTTCTTTCCTT
1 CTTCTTTTTTTTTCTCTTCTCCTTTCCTTTCCTCTCCTT
* *
55544184 CTT-TTTCTTTCTTTC-C-TCTCC-TTCC-TTCCTTTCTTT
1 CTTCTTT-TTT-TTTCTCTTCTCCTTTCCTTTCCTCTCCTT
55544220 CTTTCTTT
1 C-TTCTTT
55544228 CCCTCTCCTT
Statistics
Matches: 131, Mismatches: 21, Indels: 18
0.77 0.12 0.11
Matches are distributed among these distances:
36 10 0.08
37 9 0.07
38 37 0.28
39 57 0.44
40 18 0.14
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (39 bp):
CTTCTTTTTTTTTCTCTTCTCCTTTCCTTTCCTCTCCTT
Found at i:55544097 original size:21 final size:19
Alignment explanation
Indices: 55544073--55544198 Score: 100
Period size: 21 Copynumber: 6.4 Consensus size: 19
55544063 CCTTCTTCTT
55544073 TTTTTTTCTCTTCTCCTTTCC
1 TTTTTTTCTCTTCT-CTTT-C
55544094 TTTTCTTTC-C-T-TCTTTC
1 TTTT-TTTCTCTTCTCTTTC
*
55544111 TTTCTTTTTTCTTCTCCTTTC
1 TTT-TTTTCTCTTCT-CTTTC
*
55544132 TTTTCTTCTCCTT-TCTTTC
1 TTTTTTTCT-CTTCTCTTTC
55544151 TTTTTTTCTCTTCTTCTTTCC
1 TTTTTTTCTCTTC-TCTTT-C
*
55544172 TTTTCTTTC-CTTCTTTTTC
1 TTTT-TTTCTCTTCTCTTTC
*
55544191 TTTCTTTC
1 TTTTTTTC
55544199 CTCTCCTTCC
Statistics
Matches: 88, Mismatches: 6, Indels: 25
0.74 0.05 0.21
Matches are distributed among these distances:
17 7 0.08
18 13 0.15
19 19 0.22
20 16 0.18
21 25 0.28
22 8 0.09
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTTTTCTCTTCTCTTTC
Found at i:55544111 original size:4 final size:4
Alignment explanation
Indices: 55544095--55544228 Score: 96
Period size: 4 Copynumber: 32.0 Consensus size: 4
55544085 CTCCTTTCCT
*
55544095 TTTC TTTC CTTC TTTC TTTC TTT- TTTC TTCTCC TTTC TTTTC TTCTCC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-T-C TTTC -TTTC TT-T-C
* *
55544143 TTTC TTTC TTTT TTTC TCTTC -TTC TTTCC TTTTC TTTC CTTC -TT- TTTC
1 TTTC TTTC TTTC TTTC T-TTC TTTC TTT-C -TTTC TTTC TTTC TTTC TTTC
* * *
55544191 TTTC TTTCC TCTCC TTCC TTCC TTTC TTTC TTTC TTTC
1 TTTC TTT-C T-TTC TTTC TTTC TTTC TTTC TTTC TTTC
55544229 CCTCTCCTTC
Statistics
Matches: 109, Mismatches: 7, Indels: 28
0.76 0.05 0.19
Matches are distributed among these distances:
3 10 0.09
4 72 0.66
5 17 0.16
6 10 0.09
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (4 bp):
TTTC
Found at i:55544139 original size:54 final size:55
Alignment explanation
Indices: 55544076--55544237 Score: 153
Period size: 54 Copynumber: 3.0 Consensus size: 55
55544066 TCTTCTTTTT
55544076 TTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTCTTTCTTTTTTCTTCTCCTTTC
1 TTTT-TCTTCTCCTTTCCTTTTCTTTCCTTCTTTCTTTCTTTTTTCTTCTCCTTTC
*
55544132 -TTTTCTTCTCCTTTCTTTCTTTT-TTTCTCTTC-TTCTTTC-CTTTTCTT-TCC-TTC
1 TTTTTCTTCTCCTTTC---CTTTTCTTTC-CTTCTTTCTTTCTTTTTTCTTCTCCTTTC
* * *
55544185 TTTTTCTT-T-CTTTCC-TCTCCTTCCTTCCTTTCTTTCTTTCTTTCCCTCTCCTT
1 TTTTTCTTCTCCTTTCCTTTTCTTTCCTT-CTTTCTTTCTTT-TTT-CTTCTCCTT
55544238 CTGCCCCCCC
Statistics
Matches: 88, Mismatches: 5, Indels: 27
0.73 0.04 0.22
Matches are distributed among these distances:
48 5 0.06
49 5 0.06
50 7 0.08
51 1 0.01
52 8 0.09
53 6 0.07
54 25 0.28
55 11 0.12
56 11 0.12
57 9 0.10
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (55 bp):
TTTTTCTTCTCCTTTCCTTTTCTTTCCTTCTTTCTTTCTTTTTTCTTCTCCTTTC
Found at i:55544146 original size:44 final size:44
Alignment explanation
Indices: 55544030--55544198 Score: 138
Period size: 44 Copynumber: 4.0 Consensus size: 44
55544020 AAAAATTACC
* ** * *
55544030 TTCTTTTTTCTTTTTTTTTCCTTCCTTC-CCTCTCCTTC-TTCT
1 TTCTTTTTTCTTCTCCTTTCTTTCCTTCTCCTTTCCTTCTTTCT
* * *
55544072 TT-TTTTTTC-TCTTC-TCCTTTCCTT-TTCTTTCCTTCTTTCT
1 TTCTTTTTTCTTCTCCTTTCTTTCCTTCTCCTTTCCTTCTTTCT
* * *
55544112 TTCTTTTTTCTTCTCCTTTCTTTTCTTCTCCTTTCTTTCTTTTT
1 TTCTTTTTTCTTCTCCTTTCTTTCCTTCTCCTTTCCTTCTTTCT
* * *
55544156 TTCTCTTCTTCTT-TCCTTTTCTTTCCTTCT-TTTTCTTTCTTTC
1 TTCT-TTTTTCTTCTCC-TTTCTTTCCTTCTCCTTTCCTTCTTTC
55544199 CTCTCCTTCC
Statistics
Matches: 103, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
39 16 0.16
40 9 0.09
41 14 0.14
42 6 0.06
43 8 0.08
44 31 0.30
45 19 0.18
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (44 bp):
TTCTTTTTTCTTCTCCTTTCTTTCCTTCTCCTTTCCTTCTTTCT
Found at i:55544155 original size:78 final size:76
Alignment explanation
Indices: 55544028--55544227 Score: 268
Period size: 78 Copynumber: 2.7 Consensus size: 76
55544018 AAAAAAATTA
* *
55544028 CCTTCTTTTTTCTTTTTT-TT-TCCTTCCTTCCCTCTCC-TTCTTCTTTTTTTTTCTCTTCTCCT
1 CCTTCTTTTTTCTTTTTTCTTCTCCTTCCTTCCTTCTCCTTTCTT-TCTTTTTTTCTCTTCTCCT
55544090 TTCCTTTTCTTT
65 TTCCTTTTCTTT
* * *
55544102 CCTTCTTTCTTTCTTTTTTCTTCTCCTTTCTTTTCTTCTCCTTTCTTTCTTTTTTTCTCTTCTTC
1 CCTTCTTT-TTTCTTTTTTCTTCTCC-TTCCTTCCTTCTCCTTTCTTTCTTTTTTTCTCTTCTCC
55544167 TTTCCTTTTCTTT
64 TTTCCTTTTCTTT
*
55544180 CCTTC-TTTTTCTTTCTTTCCTCTCCTTCCTTCCTT-T-CTTTCTTTCTTT
1 CCTTCTTTTTTCTTT-TTTCTTCTCCTTCCTTCCTTCTCCTTTCTTTCTTT
55544228 CCCTCTCCTT
Statistics
Matches: 112, Mismatches: 8, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
74 20 0.18
75 11 0.10
76 17 0.15
77 14 0.12
78 45 0.40
79 5 0.04
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (76 bp):
CCTTCTTTTTTCTTTTTTCTTCTCCTTCCTTCCTTCTCCTTTCTTTCTTTTTTTCTCTTCTCCTT
TCCTTTTCTTT
Found at i:55544177 original size:18 final size:18
Alignment explanation
Indices: 55544064--55544187 Score: 83
Period size: 18 Copynumber: 6.6 Consensus size: 18
55544054 CTTCCCTCTC
**
55544064 CTTCTTCTTTTTTTTTCT
1 CTTCTTCTTTCCTTTTCT
*
55544082 CTTCTCCTTTCCTTTTCT
1 CTTCTTCTTTCCTTTTCT
*
55544100 -TTCCTTCTTTCTTTCTTTTTT
1 CTT-CTTCTTTC---CTTTTCT
*
55544121 CTTCTCCTTT-CTTTTCTT
1 CTTCTTCTTTCCTTTTC-T
* *
55544139 CTCCTTTCTTTCTTTTTTTCT
1 CTTC-TTCTTTC--CTTTTCT
55544160 CTTCTTCTTTCCTTTTCT
1 CTTCTTCTTTCCTTTTCT
55544178 -TTCCTTCTTT
1 CTT-CTTCTTT
55544188 TTCTTTCTTT
Statistics
Matches: 83, Mismatches: 12, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
17 9 0.11
18 39 0.47
19 5 0.06
20 7 0.08
21 16 0.19
22 7 0.08
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (18 bp):
CTTCTTCTTTCCTTTTCT
Found at i:55544187 original size:70 final size:66
Alignment explanation
Indices: 55544088--55544229 Score: 164
Period size: 70 Copynumber: 2.1 Consensus size: 66
55544078 TTCTCTTCTC
* * *
55544088 CTTTCCTTTTCTTTCCTTCTTTCTTTCTTTTTTCTTCTCCTTT-CTTTTCTT-C-TCCTTTCTTT
1 CTTTCCTTTTCTTTCCTTCTTTCCTTC-TTTTTCTT-T-CTTTCCTCTCCTTCCTTCCTTTCTTT
55544150 CTTT
63 CTTT
*
55544154 TTTTCTCTTCTTCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCTCCTTCCTTCCTTTCTT
1 CTTTC-CTT-TTCTTTCC--TTCTTTCCTTCTTTTTCTTTCTTTCCTCTCCTTCCTTCCTTTCTT
55544219 TCTTT
62 TCTTT
55544224 CTTTCC
1 CTTTCC
55544230 CTCTCCTTCT
Statistics
Matches: 64, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
66 4 0.06
67 7 0.11
68 15 0.23
69 10 0.16
70 28 0.44
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (66 bp):
CTTTCCTTTTCTTTCCTTCTTTCCTTCTTTTTCTTTCTTTCCTCTCCTTCCTTCCTTTCTTTCTT
T
Found at i:55544194 original size:18 final size:18
Alignment explanation
Indices: 55544095--55544200 Score: 83
Period size: 18 Copynumber: 5.6 Consensus size: 18
55544085 CTCCTTTCCT
55544095 TTTCTTTCCTTCTTTCTTTC
1 TTTCTTTCCTTC-TT-TTTC
*
55544115 TTT-TTT-CTTCTCCTTTC
1 TTTCTTTCCTTCT-TTTTC
*
55544132 TTTTCTTCTCCTT-TCTTTC
1 -TTTCTT-TCCTTCTTTTTC
*
55544151 TTTTTTTCTCTTCTTCTTTCC
1 TTTCTTTC-CTTCTT-TTT-C
55544172 TTTTCTTTCCTTCTTTTTC
1 -TTTCTTTCCTTCTTTTTC
55544191 TTTCTTTCCT
1 TTTCTTTCCT
55544201 CTCCTTCCTT
Statistics
Matches: 72, Mismatches: 4, Indels: 22
0.73 0.04 0.22
Matches are distributed among these distances:
17 7 0.10
18 25 0.35
19 12 0.17
20 11 0.15
21 10 0.14
22 7 0.10
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTCTTTCCTTCTTTTTC
Found at i:55544221 original size:44 final size:42
Alignment explanation
Indices: 55544086--55544228 Score: 108
Period size: 40 Copynumber: 3.5 Consensus size: 42
55544076 TTTTCTCTTC
*
55544086 TCCTTTCCTTTTCTTTCC-TTCTTTCTTTCTTT--T-TTCTT-C-
1 TCCTTT-C-TTTCTTTCCTTTCTTTCTTT-TTTCCTCTCCTTCCT
* * *
55544125 TCCTTTCTTTTCTTCTCCTTTCTTTCTTTTTTTCTCTTCTTCTT
1 TCCTTTC-TTTCTT-TCCTTTCTTTCTTTTTTCCTCTCCTTCCT
*
55544169 TCC--T-TTTCTTTCCTTCTTTTTCTTTCTTTCCTCTCCTTCCT
1 TCCTTTCTTTCTTTCCTT-TCTTTCTTT-TTTCCTCTCCTTCCT
55544210 TCCTTTCTTTCTTT-CTTTC
1 TCCTTTCTTTCTTTCCTTTC
55544229 CCTCTCCTTC
Statistics
Matches: 86, Mismatches: 6, Indels: 21
0.76 0.05 0.19
Matches are distributed among these distances:
38 8 0.09
39 17 0.20
40 24 0.28
41 16 0.19
42 7 0.08
43 4 0.05
44 10 0.12
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (42 bp):
TCCTTTCTTTCTTTCCTTTCTTTCTTTTTTCCTCTCCTTCCT
Found at i:55544346 original size:27 final size:27
Alignment explanation
Indices: 55544269--55544347 Score: 113
Period size: 27 Copynumber: 2.9 Consensus size: 27
55544259 CCCTATTATA
*
55544269 CATTGGTGCCGCCAATGGTATTGGCAC
1 CATTGGTGCCGCCAATGGCATTGGCAC
*
55544296 CATTGGTGCCGCCAATGGCTTTGGCAC
1 CATTGGTGCCGCCAATGGCATTGGCAC
* * *
55544323 CTTTGGTGCCACCAATGCCATTGGC
1 CATTGGTGCCGCCAATGGCATTGGC
55544348 GTGACCAGTG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.16, C:0.29, G:0.28, T:0.27
Consensus pattern (27 bp):
CATTGGTGCCGCCAATGGCATTGGCAC
Found at i:55548287 original size:96 final size:97
Alignment explanation
Indices: 55548184--55548423 Score: 369
Period size: 96 Copynumber: 2.5 Consensus size: 97
55548174 AACAACTAGT
* **
55548184 TTTATTTGATTTTTCCTTAAAAACCCTAAATACTAAA-CCTCAATCTAATTTTTT-TTAAATTTA
1 TTTATTTGATTTTTCCTTAAAAACCCTAAACACTAAACCCT-AATCTAATTTTTTAAAAAATTTA
*
55548247 TAATTAATTTACTCAAGTAACTCTAAACCCTAA
65 TAATTAATTTACTCAAGTAACCCTAAACCCTAA
*
55548280 TTTATTTGATTTTTCCTTAAAAACCCTAAACACTAAACCCTAATAT-ATTTTTTAAAAAATTTAT
1 TTTATTTGATTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTAATTTTTTAAAAAATTTAT
*
55548344 AATTAATTTACTCAAGTAACCCTAAACCCTGA
66 AATTAATTTACTCAAGTAACCCTAAACCCTAA
* * *
55548376 TTTATTTAATTTTTTCTTAAAAACCATAAACACTAAACCCTAATCTAA
1 TTTATTTGATTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTAA
55548424 AAGTTATAAC
Statistics
Matches: 131, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
95 7 0.05
96 120 0.92
97 4 0.03
ACGTcount: A:0.39, C:0.18, G:0.02, T:0.40
Consensus pattern (97 bp):
TTTATTTGATTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTAATTTTTTAAAAAATTTAT
AATTAATTTACTCAAGTAACCCTAAACCCTAA
Found at i:55548645 original size:40 final size:41
Alignment explanation
Indices: 55548592--55548672 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 41
55548582 GTACTTTGTC
*
55548592 CACGTGGACACAAAGCGCTCCCTCAAGGAAGCGTTTTCTGTT
1 CACGTGGA-ACAAAGCGCTCCATCAAGGAAGCGTTTTCTGTT
* **
55548634 CACGTGG-ACAAAGCGCTTCATTGAGGAAGCGTTTTCTGT
1 CACGTGGAACAAAGCGCTCCATCAAGGAAGCGTTTTCTGT
55548673 CCAGCGCTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 28 0.80
42 7 0.20
ACGTcount: A:0.23, C:0.25, G:0.26, T:0.26
Consensus pattern (41 bp):
CACGTGGAACAAAGCGCTCCATCAAGGAAGCGTTTTCTGTT
Found at i:55548926 original size:18 final size:19
Alignment explanation
Indices: 55548890--55548948 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 19
55548880 TCAACAAAAA
*
55548890 TTATAAAAAATTATAAAATTT
1 TTAT-AAAAATTCT-AAATTT
* * *
55548911 TTTTAAAATTTC-AAATAT
1 TTATAAAAATTCTAAATTT
55548929 TTATAAAAATTCTAAATTT
1 TTATAAAAATTCTAAATTT
55548948 T
1 T
55548949 ATATTTAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
18 15 0.50
19 6 0.20
20 6 0.20
21 3 0.10
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.47
Consensus pattern (19 bp):
TTATAAAAATTCTAAATTT
Found at i:55548949 original size:18 final size:18
Alignment explanation
Indices: 55548886--55548951 Score: 55
Period size: 19 Copynumber: 3.6 Consensus size: 18
55548876 TTTCTCAACA
*
55548886 AAAATTATA-AAAAATTAT
1 AAAATTTTATAAAAATT-T
* *
55548904 AAAATTTTTTTAAAATTT
1 AAAATTTTATAAAAATTT
*
55548922 CAAATATTTATAAAAATTCT
1 AAAAT-TTTATAAAAATT-T
55548942 -AAATTTTATA
1 AAAATTTTATA
55548952 TTTAAAAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
18 18 0.46
19 20 0.51
20 1 0.03
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
AAAATTTTATAAAAATTT
Found at i:55549008 original size:27 final size:27
Alignment explanation
Indices: 55548970--55549022 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
55548960 ATAAATATTG
**
55548970 AAAATATTAAAATTTCTAAAAAAATAA
1 AAAATATTAAAAACTCTAAAAAAATAA
*
55548997 AAAAT-TTAAAAAACTCTAAAATAATA
1 AAAATATT-AAAAACTCTAAAAAAATA
55549023 TTTTTTGTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 2 0.09
27 20 0.91
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (27 bp):
AAAATATTAAAAACTCTAAAAAAATAA
Found at i:55551106 original size:26 final size:27
Alignment explanation
Indices: 55551074--55551136 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 27
55551064 AATAAAAATA
55551074 ACCAAAATATTATAA-CTTTTTTATTT
1 ACCAAAATATTATAATCTTTTTTATTT
* * *
55551100 ACTAAAATATTGTAATTTTTTTTATTT
1 ACCAAAATATTATAATCTTTTTTATTT
55551127 ACCAAAATAT
1 ACCAAAATAT
55551137 ACCCAAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 13 0.41
27 19 0.59
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.49
Consensus pattern (27 bp):
ACCAAAATATTATAATCTTTTTTATTT
Found at i:55551826 original size:18 final size:18
Alignment explanation
Indices: 55551805--55551912 Score: 92
Period size: 18 Copynumber: 5.8 Consensus size: 18
55551795 AGTAATAACT
55551805 CTATTTTAATTTAATAAA
1 CTATTTTAATTTAATAAA
* * *
55551823 CTATTCTCATTTAATAACT
1 CTATTTTAATTTAATAA-A
*
55551842 CTATTTTAATGTAATAAA
1 CTATTTTAATTTAATAAA
* * *
55551860 CTATTCTCATTTAATAACT
1 CTATTTTAATTTAATAA-A
*
55551879 CTATTTTAA-TTAAAAAA
1 CTATTTTAATTTAATAAA
*
55551896 TTATTACTTAATTTAAT
1 CTATT--TTAATTTAAT
55551913 TTAATTTTAA
Statistics
Matches: 68, Mismatches: 17, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
17 4 0.06
18 35 0.51
19 25 0.37
20 4 0.06
ACGTcount: A:0.40, C:0.11, G:0.01, T:0.48
Consensus pattern (18 bp):
CTATTTTAATTTAATAAA
Found at i:55551838 original size:37 final size:37
Alignment explanation
Indices: 55551797--55551889 Score: 177
Period size: 37 Copynumber: 2.5 Consensus size: 37
55551787 TCTAATTAAG
55551797 TAATAACTCTATTTTAATTTAATAAACTATTCTCATT
1 TAATAACTCTATTTTAATTTAATAAACTATTCTCATT
*
55551834 TAATAACTCTATTTTAATGTAATAAACTATTCTCATT
1 TAATAACTCTATTTTAATTTAATAAACTATTCTCATT
55551871 TAATAACTCTATTTTAATT
1 TAATAACTCTATTTTAATT
55551890 AAAAAATTAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.38, C:0.13, G:0.01, T:0.48
Consensus pattern (37 bp):
TAATAACTCTATTTTAATTTAATAAACTATTCTCATT
Found at i:55551922 original size:16 final size:16
Alignment explanation
Indices: 55551903--55551935 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
55551893 AAATTATTAC
55551903 TTAATTTAATTTAATT
1 TTAATTTAATTTAATT
55551919 TTAATTTAATTTAATT
1 TTAATTTAATTTAATT
55551935 T
1 T
55551936 AAAAAATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTAATTTAATTTAATT
Found at i:55551957 original size:5 final size:5
Alignment explanation
Indices: 55551903--55551937 Score: 61
Period size: 5 Copynumber: 6.8 Consensus size: 5
55551893 AAATTATTAC
55551903 TTAAT TTAAT TTAATT TTAAT TTAAT TTAAT TTAA
1 TTAAT TTAAT TTAA-T TTAAT TTAAT TTAAT TTAA
55551938 AAAATAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTAAT
Found at i:55552005 original size:20 final size:20
Alignment explanation
Indices: 55551968--55552006 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
55551958 TTTTAAAAAT
*
55551968 TAAAATAGAGTTATTTTAGG
1 TAAAATAGAGTTACTTTAGG
* *
55551988 TAAAATATATTTACTTTAG
1 TAAAATAGAGTTACTTTAG
55552007 AATGAAGAGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.13, T:0.44
Consensus pattern (20 bp):
TAAAATAGAGTTACTTTAGG
Found at i:55552851 original size:27 final size:27
Alignment explanation
Indices: 55552807--55552858 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
55552797 CCTTTTAGTC
*
55552807 CTTTGGCACCATTGGTGCCGCCAATCT
1 CTTTGGCACCATTAGTGCCGCCAATCT
*
55552834 CTTTGGCACCTTTAGTGCCGCCAAT
1 CTTTGGCACCATTAGTGCCGCCAAT
55552859 GAGATTGGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.15, C:0.33, G:0.21, T:0.31
Consensus pattern (27 bp):
CTTTGGCACCATTAGTGCCGCCAATCT
Found at i:55552866 original size:27 final size:27
Alignment explanation
Indices: 55552809--55552867 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
55552799 TTTTAGTCCT
* * *
55552809 TTGGCACCATTGGTGCCGCCAATCTCT
1 TTGGCACCATTAGTGCCGCCAATCACA
* * *
55552836 TTGGCACCTTTAGTGCCGCCAATGAGA
1 TTGGCACCATTAGTGCCGCCAATCACA
55552863 TTGGC
1 TTGGC
55552868 CTGATCAGGC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.17, C:0.29, G:0.25, T:0.29
Consensus pattern (27 bp):
TTGGCACCATTAGTGCCGCCAATCACA
Found at i:55552954 original size:27 final size:28
Alignment explanation
Indices: 55552920--55552981 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
55552910 TTTTTTTTGT
* *
55552920 ATATTTTGATAAAT-AAAAAAATTTATA
1 ATATTTTGAAAAATAAAAAAAAGTTATA
55552947 ATATTTTGAAAAATAAAAAAAAGTTATA
1 ATATTTTGAAAAATAAAAAAAAGTTATA
55552975 ATATTTT
1 ATATTTT
55552982 AGTTATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 13 0.41
28 19 0.59
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (28 bp):
ATATTTTGAAAAATAAAAAAAAGTTATA
Found at i:55574044 original size:83 final size:83
Alignment explanation
Indices: 55573881--55574060 Score: 181
Period size: 83 Copynumber: 2.2 Consensus size: 83
55573871 GTAAATCTTT
* ** *
55573881 TAAAAAATTAATTTAAAATCCTTTAAAATTTATAAAAATTTAAATTAGTAAAAGTAAAATTATAC
1 TAAAAATTTAATTT-AAATCCTTTAAAATTTATAAAAATAGAAATTAGTAAAAATAAAATTATAC
* *
55573946 TTTGACTTCCTTAAAACTAA
65 TTTGACTTCCATAAAAAT-A
* *
55573966 TAAAAATTTAATTT-AATCTTTTAAAATTTAT-AAAATAGAAA-TATTAAAATAATAAAATTATA
1 TAAAAATTTAATTTAAATCCTTTAAAATTTATAAAAATAGAAATTAGT-AAA-AATAAAATTATA
* *
55574028 TTTTTACTAT-CATAAAAATA
64 CTTTGACT-TCCATAAAAATA
*
55574048 T-AAAATCTAATTT
1 TAAAAATTTAATTT
55574061 CTAGCTCAAA
Statistics
Matches: 81, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
81 14 0.17
82 13 0.16
83 40 0.49
84 1 0.01
85 13 0.16
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (83 bp):
TAAAAATTTAATTTAAATCCTTTAAAATTTATAAAAATAGAAATTAGTAAAAATAAAATTATACT
TTGACTTCCATAAAAATA
Found at i:55574394 original size:13 final size:13
Alignment explanation
Indices: 55574359--55574399 Score: 57
Period size: 13 Copynumber: 3.1 Consensus size: 13
55574349 GAGATCTTTG
55574359 TAATTTG-AAATCT
1 TAATTTGAAAAT-T
55574372 TAAGTTTGAAAATT
1 TAA-TTTGAAAATT
55574386 TAATTTGAAAATT
1 TAATTTGAAAATT
55574399 T
1 T
55574400 GGAAACTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 14 0.54
14 8 0.31
15 4 0.15
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.46
Consensus pattern (13 bp):
TAATTTGAAAATT
Found at i:55576210 original size:13 final size:13
Alignment explanation
Indices: 55576192--55576221 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
55576182 AGCCCAAACT
*
55576192 CAATTACCTAACC
1 CAATTACCCAACC
55576205 CAATTACCCAACC
1 CAATTACCCAACC
55576218 CAAT
1 CAAT
55576222 AAAACTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (13 bp):
CAATTACCCAACC
Found at i:55576374 original size:9 final size:9
Alignment explanation
Indices: 55576362--55576429 Score: 93
Period size: 9 Copynumber: 7.4 Consensus size: 9
55576352 AAATAAAAAA
55576362 AATTCGGGT
1 AATTCGGGT
55576371 AATTCGGGT
1 AATTCGGGT
*
55576380 ATTTTTC-GGT
1 A--ATTCGGGT
*
55576390 AATTCGGTT
1 AATTCGGGT
55576399 AATTCGGGT
1 AATTCGGGT
55576408 AATTCGGGT
1 AATTCGGGT
55576417 AATTCGGGT
1 AATTCGGGT
55576426 AATT
1 AATT
55576430 TTTAACCAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
8 3 0.06
9 42 0.81
10 4 0.08
11 3 0.06
ACGTcount: A:0.22, C:0.10, G:0.28, T:0.40
Consensus pattern (9 bp):
AATTCGGGT
Done.