Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 193 of 210
Found at i:56737124 original size:22 final size:22
Alignment explanation
Indices: 56737097--56737248 Score: 223
Period size: 22 Copynumber: 6.9 Consensus size: 22
56737087 TGTTGATAGT
*
56737097 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
56737119 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
56737141 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
* * * **
56737163 ACGAACTAAACCCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
**
56737185 ACGTACTAAGCTCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
*
56737207 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
56737229 ACGTACTAAGCTCTCATGTT
1 ACGTACTAAGCTCTCATGTT
56737249 AATAACATAT
Statistics
Matches: 118, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 118 1.00
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.32
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTA
Found at i:56739660 original size:24 final size:24
Alignment explanation
Indices: 56739633--56739681 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 24
56739623 CCATTTTAAT
56739633 TTATATAATATACATAAAT-CATAC
1 TTATATAATATACAT-AATCCATAC
56739657 TTATATAATATACATAATCCATAC
1 TTATATAATATACATAATCCATAC
56739681 T
1 T
56739682 AACAATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (24 bp):
TTATATAATATACATAATCCATAC
Found at i:56740373 original size:12 final size:13
Alignment explanation
Indices: 56740339--56740373 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
56740329 GTTCTTCTTG
56740339 CTTTTGAGAAGTA
1 CTTTTGAGAAGTA
56740352 CTTTTGAGAAGTA
1 CTTTTGAGAAGTA
*
56740365 -TTTTCAGAA
1 CTTTTGAGAA
56740374 ATTTGAGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 8 0.38
13 13 0.62
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (13 bp):
CTTTTGAGAAGTA
Found at i:56740986 original size:22 final size:21
Alignment explanation
Indices: 56740961--56741004 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
56740951 AAGCATATGA
*
56740961 AAATGATTTGGTTATATTCAAT
1 AAATGATTTGGTTA-ATACAAT
56740983 AAATGATTTGGTTAATACAAT
1 AAATGATTTGGTTAATACAAT
56741004 A
1 A
56741005 CTTATATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (21 bp):
AAATGATTTGGTTAATACAAT
Found at i:56741031 original size:44 final size:44
Alignment explanation
Indices: 56740983--56741120 Score: 258
Period size: 44 Copynumber: 3.1 Consensus size: 44
56740973 TATATTCAAT
56740983 AAATGATTTGGTTAATACAATACTTATATTTGATAAGCATATGA
1 AAATGATTTGGTTAATACAATACTTATATTTGATAAGCATATGA
*
56741027 AAATGATTTGGTTAATACAATATTTATATTTGATAAGCATATGA
1 AAATGATTTGGTTAATACAATACTTATATTTGATAAGCATATGA
*
56741071 AAATGATTTGGTTAATACAATACTTGTATTTGATAAGCATATGA
1 AAATGATTTGGTTAATACAATACTTATATTTGATAAGCATATGA
56741115 AAATGA
1 AAATGA
56741121 AAGTCAAGAC
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 91 1.00
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.38
Consensus pattern (44 bp):
AAATGATTTGGTTAATACAATACTTATATTTGATAAGCATATGA
Found at i:56749016 original size:20 final size:20
Alignment explanation
Indices: 56748993--56749031 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
56748983 TTTTTTGTTT
* *
56748993 AATTACATTTTATTTTAATA
1 AATTACACTTTAATTTAATA
*
56749013 AATTATACTTTAATTTAAT
1 AATTACACTTTAATTTAAT
56749032 TATTTCCCTC
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:0.05, G:0.00, T:0.54
Consensus pattern (20 bp):
AATTACACTTTAATTTAATA
Found at i:56750717 original size:50 final size:50
Alignment explanation
Indices: 56750591--56750796 Score: 349
Period size: 50 Copynumber: 4.1 Consensus size: 50
56750581 TTACGGGGGG
** *
56750591 CCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACGGGGGGG
1 CCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTAC-ATGGGA
56750642 CCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA
1 CCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA
* *
56750692 CCTCTCATCTCGGTGCCAATGCCATGTCCCAGACATGATCTTACATGGGA
1 CCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA
*
56750742 CCTCTCATCTCGGTGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 CCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA
56750792 CCTCT
1 CCTCT
56750797 TTACCCAAAT
Statistics
Matches: 149, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
50 105 0.70
51 44 0.30
ACGTcount: A:0.19, C:0.33, G:0.23, T:0.25
Consensus pattern (50 bp):
CCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA
Found at i:56750912 original size:13 final size:13
Alignment explanation
Indices: 56750891--56750921 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
56750881 GCGTAGATCA
*
56750891 TCATCAAATAAAT
1 TCATAAAATAAAT
56750904 TCATAAAATAAAT
1 TCATAAAATAAAT
56750917 TCATA
1 TCATA
56750922 GTTGCTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:56751169 original size:30 final size:30
Alignment explanation
Indices: 56751134--56751191 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
56751124 CCTCGACTCT
* *
56751134 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTACCCCTA
* *
56751164 AACTTTTACATAATTACATTTTTACCCC
1 AACTTTTACAAAATTACAATTTTACCCC
56751192 AAGGCTCAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.33, C:0.24, G:0.02, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTACCCCTA
Found at i:56765819 original size:18 final size:17
Alignment explanation
Indices: 56765791--56765825 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
56765781 ATTATTAAGA
*
56765791 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
56765808 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
56765826 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:56772537 original size:19 final size:20
Alignment explanation
Indices: 56772513--56772550 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
56772503 GACAAACCAG
56772513 AAACTTATGTC-CTAATCAC
1 AAACTTATGTCTCTAATCAC
*
56772532 AAACTTATTTCTCTAATCA
1 AAACTTATGTCTCTAATCA
56772551 TATAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.37
Consensus pattern (20 bp):
AAACTTATGTCTCTAATCAC
Found at i:56776841 original size:8 final size:8
Alignment explanation
Indices: 56776828--56776856 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
56776818 TGAGATAGAA
56776828 TTTTAAAT
1 TTTTAAAT
56776836 TTTTAAAT
1 TTTTAAAT
56776844 TTTTAAAT
1 TTTTAAAT
56776852 TTTTA
1 TTTTA
56776857 TATTAAAAAT
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
TTTTAAAT
Found at i:56777884 original size:29 final size:28
Alignment explanation
Indices: 56777834--56777897 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 28
56777824 ATTTCTGAAC
*
56777834 TATTTGTATATTTAGAATTTAGTTATTA
1 TATTTTTATATTTAGAATTTAGTTATTA
* * *
56777862 TATTTTTATTTTTAAGAATTTAGTTTTTT
1 TATTTTTATATTT-AGAATTTAGTTATTA
56777891 TATTTTT
1 TATTTTT
56777898 CAAATTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 11 0.35
29 20 0.65
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.66
Consensus pattern (28 bp):
TATTTTTATATTTAGAATTTAGTTATTA
Found at i:56778950 original size:10 final size:10
Alignment explanation
Indices: 56778935--56778960 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
56778925 GTGATTAACT
56778935 ATATATATAC
1 ATATATATAC
56778945 ATATATATAC
1 ATATATATAC
56778955 ATATAT
1 ATATAT
56778961 CTTAATTGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (10 bp):
ATATATATAC
Found at i:56781914 original size:20 final size:21
Alignment explanation
Indices: 56781875--56781915 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
56781865 ATAGTATAAA
*
56781875 AATAAAATTGACTCATTTAAT
1 AATAAAATTGACTAATTTAAT
*
56781896 AATAAAA-TGATTAATTTAAT
1 AATAAAATTGACTAATTTAAT
56781916 CCGGTTATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (21 bp):
AATAAAATTGACTAATTTAAT
Found at i:56784580 original size:41 final size:39
Alignment explanation
Indices: 56784535--56784666 Score: 122
Period size: 40 Copynumber: 3.3 Consensus size: 39
56784525 TAGCGGCATT
* *
56784535 TTAGCGGCGTTTGGACAAAAAACGCCACTAAAAATCGAGCA
1 TTAGCGGCGTTT-AACAAAAAACGCCGCTAAAAAT-GAGCA
* * ** *
56784576 TTAGCGGCGCTTTTA-TAAAAACGCCGCTAAAGGTAGAGAA
1 TTAGCGGCG-TTTAACAAAAAACGCCGCTAAAAAT-GAGCA
** * *
56784616 TTAGCGGCACTTAACAGAAAACGCCGCTAAAAATTAGCA
1 TTAGCGGCGTTTAACAAAAAACGCCGCTAAAAATGAGCA
56784655 TTAGCGGCGTTT
1 TTAGCGGCGTTT
56784667 TTTGAAAATC
Statistics
Matches: 71, Mismatches: 18, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
39 16 0.23
40 42 0.59
41 10 0.14
42 3 0.04
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (39 bp):
TTAGCGGCGTTTAACAAAAAACGCCGCTAAAAATGAGCA
Found at i:56784596 original size:40 final size:39
Alignment explanation
Indices: 56784535--56784686 Score: 121
Period size: 40 Copynumber: 3.8 Consensus size: 39
56784525 TAGCGGCATT
* *
56784535 TTAGCGGCG-TTTGGACAAAAAACGCCACTAAAAATCGAGCA
1 TTAGCGGCGCTTT-TAC-AAAAACGCCGCTAAAAAT-GAGCA
* ** *
56784576 TTAGCGGCGCTTTTATAAAAACGCCGCTAAAGGTAGAGAA
1 TTAGCGGCGCTTTTACAAAAACGCCGCTAAAAAT-GAGCA
* * *
56784616 TTAGCGGCAC-TTAACAGAAAACGCCGCTAAAAATTAGCA
1 TTAGCGGCGCTTTTACA-AAAACGCCGCTAAAAATGAGCA
* ** *
56784655 TTAGCGGCGTTTTTTGAAAATCGCCGC-AAAAA
1 TTAGCGGCGCTTTTACAAAAACGCCGCTAAAAA
56784687 GCCTAAGCCA
Statistics
Matches: 88, Mismatches: 20, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
38 5 0.06
39 24 0.27
40 46 0.52
41 10 0.11
42 3 0.03
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.21
Consensus pattern (39 bp):
TTAGCGGCGCTTTTACAAAAACGCCGCTAAAAATGAGCA
Found at i:56784791 original size:41 final size:40
Alignment explanation
Indices: 56784723--56784963 Score: 180
Period size: 41 Copynumber: 5.9 Consensus size: 40
56784713 GAGTTTTTGG
* *
56784723 GGCCCTTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCTCT
1 GGCCTTTAGCGGCG-TTTTTGAGAAGCGCCGCTAATGCTCT
* *
56784764 GGCCTTTAGCGGCGTTTTTGAGTAAGCGCCGCTAAAAGC-CA
1 GGCCTTTAGCGGCGTTTTTGAG-AAGCGCCGCT-AATGCTCT
* * * * * *
56784805 GAG-CATTAGCGGTGCTTCTTAAAAAACGCCGCTAATGCTCT
1 G-GCCTTTAGCGGCG-TTTTTGAGAAGCGCCGCTAATGCTCT
** * *
56784846 ATCCTTTAGCGACGTTTTTGAAGAAGCGCCGGTAATGCTCT
1 GGCCTTTAGCGGCGTTTTTG-AGAAGCGCCGCTAATGCTCT
* * * * **
56784887 GGCCTTTAGCAGCATTTTTGAAGAAGTGTCGCTAATGCTAA
1 GGCCTTTAGCGGCGTTTTTG-AGAAGCGCCGCTAATGCTCT
** * *
56784928 GATCTTTAGCGGCATTTTTGAAAAAGCGCCGCTAAT
1 GGCCTTTAGCGGCGTTTTTG-AGAAGCGCCGCTAAT
56784964 ATATTTTTTA
Statistics
Matches: 155, Mismatches: 38, Indels: 14
0.75 0.18 0.07
Matches are distributed among these distances:
40 15 0.10
41 130 0.84
42 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (40 bp):
GGCCTTTAGCGGCGTTTTTGAGAAGCGCCGCTAATGCTCT
Found at i:56788328 original size:23 final size:24
Alignment explanation
Indices: 56788298--56788361 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 24
56788288 ACTTACATTA
* *
56788298 AATA-ATATTTTTATAATTT-TTT
1 AATATATATTTTTAAAATTTATAT
*
56788320 AATATATATATTTAAAATTTATAT
1 AATATATATTTTTAAAATTTATAT
*
56788344 -ATATATATATTTAAAATT
1 AATATATATTTTTAAAATT
56788362 CGAATAACAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
22 4 0.11
23 31 0.84
24 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
AATATATATTTTTAAAATTTATAT
Found at i:56788966 original size:14 final size:14
Alignment explanation
Indices: 56788947--56788976 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
56788937 AATTTGAATT
56788947 TCGAGTTAAACGAA
1 TCGAGTTAAACGAA
*
56788961 TCGAGTTAATCGAA
1 TCGAGTTAAACGAA
56788975 TC
1 TC
56788977 AATTCGAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27
Consensus pattern (14 bp):
TCGAGTTAAACGAA
Found at i:56789176 original size:14 final size:14
Alignment explanation
Indices: 56789157--56789194 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
56789147 TTTTTTCCCA
56789157 ATCCACCTCCACCG
1 ATCCACCTCCACCG
56789171 ATCCACCTCCACCG
1 ATCCACCTCCACCG
56789185 ATCCACCTCC
1 ATCCACCTCC
56789195 GGTCCTCCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.21, C:0.58, G:0.05, T:0.16
Consensus pattern (14 bp):
ATCCACCTCCACCG
Found at i:56791965 original size:5 final size:5
Alignment explanation
Indices: 56791957--56792004 Score: 53
Period size: 5 Copynumber: 9.4 Consensus size: 5
56791947 CGAACAAATA
* *
56791957 ATTCG ATTCG ATTCG ATTCG ATTTCT ATCTC- ACTCG ATTCG ATTCG AT
1 ATTCG ATTCG ATTCG ATTCG A-TTCG AT-TCG ATTCG ATTCG ATTCG AT
56792005 AAAATTTCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
4 2 0.05
5 29 0.78
6 6 0.16
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.42
Consensus pattern (5 bp):
ATTCG
Found at i:56792277 original size:12 final size:12
Alignment explanation
Indices: 56792262--56792295 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
56792252 TAACCTACAT
56792262 AACTTACATAGA
1 AACTTACATAGA
*
56792274 AACTTATATAGA
1 AACTTACATAGA
*
56792286 AACTTGCATA
1 AACTTACATA
56792296 ACTTACATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.47, C:0.15, G:0.09, T:0.29
Consensus pattern (12 bp):
AACTTACATAGA
Found at i:56792354 original size:16 final size:16
Alignment explanation
Indices: 56792335--56792446 Score: 74
Period size: 16 Copynumber: 7.2 Consensus size: 16
56792325 ATACATAGCG
56792335 TACATAACTTACATAA
1 TACATAACTTACATAA
**
56792351 TACACCACTTACAT-A
1 TACATAACTTACATAA
*
56792366 -A-ATAACTTGCATAA
1 TACATAACTTACATAA
**
56792380 TACACCACTTACAT-A
1 TACATAACTTACATAA
*
56792395 -A-ATAACTTGCATAA
1 TACATAACTTACATAA
* * *
56792409 TACATAGCCTACGTAA
1 TACATAACTTACATAA
*
56792425 CTTACTTAACTTACATAA
1 --TACATAACTTACATAA
56792443 TACA
1 TACA
56792447 CCACTTACGT
Statistics
Matches: 68, Mismatches: 20, Indels: 16
0.65 0.19 0.15
Matches are distributed among these distances:
13 16 0.24
14 4 0.06
15 4 0.06
16 32 0.47
18 12 0.18
ACGTcount: A:0.44, C:0.23, G:0.04, T:0.29
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:56792380 original size:29 final size:29
Alignment explanation
Indices: 56792338--56792412 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
56792328 CATAGCGTAC
*
56792338 ATAACTTACATAATACACCACTTACATAA
1 ATAACTTGCATAATACACCACTTACATAA
56792367 ATAACTTGCATAATACACCACTTACATAA
1 ATAACTTGCATAATACACCACTTACATAA
56792396 ATAACTTGCATAATACA
1 ATAACTTGCATAATACA
56792413 TAGCCTACGT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.47, C:0.23, G:0.03, T:0.28
Consensus pattern (29 bp):
ATAACTTGCATAATACACCACTTACATAA
Found at i:56799059 original size:43 final size:43
Alignment explanation
Indices: 56798989--56799259 Score: 181
Period size: 43 Copynumber: 6.3 Consensus size: 43
56798979 NNNNNNNNNN
*
56798989 CGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAAAAAG
1 CGCCGCTAAAGATAAGGGTCTTCAGCGGCGTTTGTGGAAAAAG
* * * * **
56799032 CGCCACTAAAGATCATGGTCTTCAGCGGCGTTTTTGGGGAAAG
1 CGCCGCTAAAGATAAGGGTCTTCAGCGGCGTTTGTGGAAAAAG
* * * * *** *
56799075 CGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTTGTGGTCGAAC
1 CGCCGCTAAAGATAAGGGTCTTCAGCGGCG-TTTGTGGAAAAAG
* * * * **
56799119 CGCCGCTATAGATCAGGGTCTAT-TGCGGCATTT-TAGGGGAAAG
1 CGCCGCTAAAGATAAGGGTCT-TCAGCGGCGTTTGT-GGAAAAAG
* * * * **
56799162 CGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCAAAG
1 CGCCGCTAAAGATAAGGGTCTTCAGCGGCGTTTGTGGAAAAAG
* * * * *
56799205 CGCCGCTATAGATCAGGGTCTATTC--CGGCGTTTGAGAAAAAAA
1 CGCCGCTAAAGATAAGGGTC--TTCAGCGGCGTTTGTGGAAAAAG
56799248 CGCCGCTAAAGA
1 CGCCGCTAAAGA
56799260 CCCTGATCTA
Statistics
Matches: 174, Mismatches: 47, Indels: 14
0.74 0.20 0.06
Matches are distributed among these distances:
42 2 0.01
43 138 0.79
44 31 0.18
45 3 0.02
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (43 bp):
CGCCGCTAAAGATAAGGGTCTTCAGCGGCGTTTGTGGAAAAAG
Found at i:56799235 original size:130 final size:130
Alignment explanation
Indices: 56798989--56799237 Score: 281
Period size: 130 Copynumber: 1.9 Consensus size: 130
56798979 NNNNNNNNNN
*
56798989 CGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCATGGTCTT
1 CGCCGCTAAAGATAAGGGTCTTTAGCGGCATTTGTGGAAAAAGCGCCACTAAAGATCATGGTCTT
* * * * **
56799054 CAGCGGCGTTTTTGGGGAAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTTGTGGTCGAAC
66 CAGCGGCGTTTGTGGGCAAAGCGCCGCTAAAGATCAGGGTCTTTACCGGCGTTTTGTGGTCGAAC
* * ** * *
56799119 CGCCGCTATAGATCAGGGTCTATT-GCGGCATTT-TAGGGGAAAGCGCCGCTAAAGATTA-GGTT
1 CGCCGCTAAAGATAAGGGTCT-TTAGCGGCATTTGT-GGAAAAAGCGCCACTAAAGATCATGG-T
* * * *
56799181 CTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGGTCTATT-CCGGCGTTT
63 CTTCAGCGGCGTTTGTGGGCAAAGCGCCGCTAAAGATCAGGGTCT-TTACCGGCGTTT
56799238 GAGAAAAAAA
Statistics
Matches: 98, Mismatches: 17, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
129 3 0.03
130 91 0.93
131 4 0.04
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.29
Consensus pattern (130 bp):
CGCCGCTAAAGATAAGGGTCTTTAGCGGCATTTGTGGAAAAAGCGCCACTAAAGATCATGGTCTT
CAGCGGCGTTTGTGGGCAAAGCGCCGCTAAAGATCAGGGTCTTTACCGGCGTTTTGTGGTCGAAC
Found at i:56799259 original size:86 final size:86
Alignment explanation
Indices: 56798989--56799237 Score: 340
Period size: 87 Copynumber: 2.9 Consensus size: 86
56798979 NNNNNNNNNN
* * * ** * * *
56798989 CGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCATGGTC--
1 CGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGGTCTA
*
56799052 TTCAGCGGCGTTTTTGGGGAAAG
66 TTC--CGGCGTTTTAGGGGAAAG
* *
56799075 CGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTTGTGGTCGAACCGCCGCTATAGATCAGGGTCT
1 CGCCGCTAAAGATTAGGTTCTTTAGTGGCG-TTTGTGGTCAAAGCGCCGCTATAGATCAGGGTCT
* *
56799140 ATTGCGGCATTTTAGGGGAAAG
65 ATTCCGGCGTTTTAGGGGAAAG
56799162 CGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGGTCTA
1 CGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGGTCTA
56799227 TTCCGGCGTTT
66 TTCCGGCGTTT
56799238 GAGAAAAAAA
Statistics
Matches: 143, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
86 69 0.48
87 72 0.50
89 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.29
Consensus pattern (86 bp):
CGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGGTCTA
TTCCGGCGTTTTAGGGGAAAG
Found at i:56800322 original size:17 final size:18
Alignment explanation
Indices: 56800284--56800350 Score: 68
Period size: 17 Copynumber: 3.8 Consensus size: 18
56800274 AAAAATATTT
* * *
56800284 TTTTTTGAAAATATAAGC
1 TTTTTTAAAAATAAAATC
56800302 -TTTTTAAAAA-AAATAT-
1 TTTTTTAAAAATAAA-ATC
56800318 TTTTTTAAAAATAAAATC
1 TTTTTTAAAAATAAAATC
56800336 TTATTTTAAAAATAA
1 TT-TTTTAAAAATAA
56800351 TTAAAATTTG
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
16 2 0.05
17 22 0.54
18 5 0.12
19 12 0.29
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (18 bp):
TTTTTTAAAAATAAAATC
Found at i:56800323 original size:18 final size:18
Alignment explanation
Indices: 56800274--56800347 Score: 53
Period size: 18 Copynumber: 4.1 Consensus size: 18
56800264 CCACATCAAC
**
56800274 AAAAATATTTTTTTTTGA
1 AAAAATATTTTTTTTAAA
* ***
56800292 AAATATAAGCTTTTTAAA
1 AAAAATATTTTTTTTAAA
56800310 AAAAATA-TTTTTTTAAA
1 AAAAATATTTTTTTTAAA
*
56800327 AATAAA-ATCTTATTTTAAA
1 AA-AAATAT-TTTTTTTAAA
56800346 AA
1 AA
56800348 TAATTAAAAT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
17 11 0.26
18 21 0.49
19 11 0.26
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (18 bp):
AAAAATATTTTTTTTAAA
Found at i:56800347 original size:34 final size:35
Alignment explanation
Indices: 56800274--56800347 Score: 87
Period size: 34 Copynumber: 2.1 Consensus size: 35
56800264 CCACATCAAC
* * *
56800274 AAAAATATTTTTTTTTGAAAATATAAGCTTTTTAA
1 AAAAATATATTTTTTTAAAAATAAAAGCTTTTTAA
* *
56800309 AAAAA-ATATTTTTTTAAAAATAAAATCTTATTTTA
1 AAAAATATATTTTTTTAAAAATAAAAGCTT-TTTAA
56800344 AAAA
1 AAAA
56800348 TAATTAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
34 20 0.61
35 13 0.39
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (35 bp):
AAAAATATATTTTTTTAAAAATAAAAGCTTTTTAA
Found at i:56801423 original size:21 final size:21
Alignment explanation
Indices: 56801390--56801445 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
56801380 CACGGTCTAC
**
56801390 CCACACGCCCGTGT-CCTTCAG
1 CCACACGGTCGTGTCCCTT-AG
*
56801411 CCACATGGTCGTGTCCCTTAG
1 CCACACGGTCGTGTCCCTTAG
*
56801432 CCACACGGTTGTGT
1 CCACACGGTCGTGT
56801446 ATTCCTGCCA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 25 0.86
22 4 0.14
ACGTcount: A:0.14, C:0.38, G:0.23, T:0.25
Consensus pattern (21 bp):
CCACACGGTCGTGTCCCTTAG
Found at i:56801455 original size:21 final size:21
Alignment explanation
Indices: 56801431--56801479 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
56801421 GTGTCCCTTA
56801431 GCCACACGGTTGTGTATTCCT
1 GCCACACGGTTGTGTATTCCT
* *
56801452 GCCACATGGTTGTGTATTCTT
1 GCCACACGGTTGTGTATTCCT
*
56801473 GTCACAC
1 GCCACAC
56801480 AGTCTGAATC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.16, C:0.27, G:0.22, T:0.35
Consensus pattern (21 bp):
GCCACACGGTTGTGTATTCCT
Found at i:56801542 original size:21 final size:21
Alignment explanation
Indices: 56801516--56801561 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
56801506 CCATACGGTC
*
56801516 GTGTCCCTCAGCTACATGGTT
1 GTGTCCCTCAGCCACATGGTT
*
56801537 GTGTCCCTTAGCCACATGGTT
1 GTGTCCCTCAGCCACATGGTT
56801558 GTGT
1 GTGT
56801562 ATTCCTGTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.13, C:0.26, G:0.26, T:0.35
Consensus pattern (21 bp):
GTGTCCCTCAGCCACATGGTT
Found at i:56801580 original size:95 final size:95
Alignment explanation
Indices: 56801411--56801689 Score: 285
Period size: 95 Copynumber: 2.9 Consensus size: 95
56801401 TGTCCTTCAG
* * * * * *
56801411 CCACATGGTCGTGTCCCTTAGCCACACGGTTGTGTATTCC-T-GCCACATGGTTGTGTATTCTTG
1 CCACACGGTCGTGTCCCTCAGCTACATGGTTGTG--TCCCTTAGCCACATGGTTGTGTATTCCTG
*
56801474 TCACACAGTCTGAATCCTCCCACACGATCTGC
64 TCACACAGTCTGAACCCTCCCACACGATCTGC
*
56801506 CCATACGGTCGTGTCCCTCAGCTACATGGTTGTGTCCCTTAGCCACATGGTTGTGTATTCCTGTC
1 CCACACGGTCGTGTCCCTCAGCTACATGGTTGTGTCCCTTAGCCACATGGTTGTGTATTCCTGTC
* * * *
56801571 ACACGGTCTGAACCCTCCTATACGGTCTGC
66 ACACAGTCTGAACCCTCCCACACGATCTGC
* ** * * * * * * * * *
56801601 CCACATGACCATATCCCTCAGTTACATAGTCGTGTCTCTCAGCCACATGGTTGTTTATTCCTATC
1 CCACACGGTCGTGTCCCTCAGCTACATGGTTGTGTCCCTTAGCCACATGGTTGTGTATTCCTGTC
*
56801666 ACACAGTTTGAACCC-CCTCACACG
66 ACACAGTCTGAACCCTCC-CACACG
56801690 GCCGTGTGGT
Statistics
Matches: 152, Mismatches: 29, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
93 3 0.02
94 3 0.02
95 146 0.96
ACGTcount: A:0.19, C:0.32, G:0.19, T:0.30
Consensus pattern (95 bp):
CCACACGGTCGTGTCCCTCAGCTACATGGTTGTGTCCCTTAGCCACATGGTTGTGTATTCCTGTC
ACACAGTCTGAACCCTCCCACACGATCTGC
Found at i:56804987 original size:17 final size:17
Alignment explanation
Indices: 56804965--56805007 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
56804955 GAAATTCTTT
*
56804965 AATAAAATCAGAATAAA
1 AATAAAATCAAAATAAA
*
56804982 AATAAAATTAAAATAAA
1 AATAAAATCAAAATAAA
56804999 AGATAAAAT
1 A-ATAAAAT
56805008 TTAAGAAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (17 bp):
AATAAAATCAAAATAAA
Found at i:56805240 original size:11 final size:11
Alignment explanation
Indices: 56805221--56805251 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
56805211 GTGTTGTAGT
*
56805221 TTTTTTTCTCC
1 TTTTCTTCTCC
56805232 TTTTCTTCTCC
1 TTTTCTTCTCC
56805243 TTTTCTTCT
1 TTTTCTTCT
56805252 ACAATTCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTTCTTCTCC
Found at i:56808871 original size:2 final size:2
Alignment explanation
Indices: 56808859--56808908 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
56808849 CATATTTATG
*
56808859 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
56808901 TA TA TA TA
1 TA TA TA TA
56808909 ACATACCCAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:56809055 original size:5 final size:5
Alignment explanation
Indices: 56809041--56809078 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
56809031 AAATAGCCTA
56809041 CATA- CATAC CATAC CATAC CATAC CATAC CATAC CATA
1 CATAC CATAC CATAC CATAC CATAC CATAC CATAC CATA
56809079 TATACATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.12
5 29 0.88
ACGTcount: A:0.42, C:0.37, G:0.00, T:0.21
Consensus pattern (5 bp):
CATAC
Found at i:56811741 original size:20 final size:20
Alignment explanation
Indices: 56811716--56811760 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
56811706 GATATTCTTA
*
56811716 TCTCTTTGGGATAAATTTGC
1 TCTCTTTGGGATAAATCTGC
56811736 TCTCTTTGGGATAAATCTGC
1 TCTCTTTGGGATAAATCTGC
56811756 TCTCT
1 TCTCT
56811761 CAATATGATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.44
Consensus pattern (20 bp):
TCTCTTTGGGATAAATCTGC
Found at i:56816627 original size:6 final size:6
Alignment explanation
Indices: 56816616--56816641 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
56816606 CTGTGTGTTC
56816616 TTTATT TTTATT TTTATT TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TT
56816642 CTTTGCAATA
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:56822954 original size:15 final size:16
Alignment explanation
Indices: 56822934--56822966 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
56822924 GTTGTAATAT
*
56822934 AATGAA-AAATAAAAA
1 AATGAACAAAGAAAAA
56822949 AATGAACAAAGAAAAA
1 AATGAACAAAGAAAAA
56822965 AA
1 AA
56822967 ATATCAGCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.79, C:0.03, G:0.09, T:0.09
Consensus pattern (16 bp):
AATGAACAAAGAAAAA
Found at i:56829080 original size:29 final size:32
Alignment explanation
Indices: 56829046--56829105 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 32
56829036 TTTTTAATAC
56829046 TTTTATA-ATTTCTAGAA-ATG-TAATAATTA
1 TTTTATATATTTCTAGAATATGTTAATAATTA
* *
56829075 TTTTATATATTTTTATAATATGTTAATAATT
1 TTTTATATATTTCTAGAATATGTTAATAATT
56829106 TATATAATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 7 0.27
30 8 0.31
31 3 0.12
32 8 0.31
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (32 bp):
TTTTATATATTTCTAGAATATGTTAATAATTA
Found at i:56829106 original size:29 final size:28
Alignment explanation
Indices: 56829039--56829111 Score: 69
Period size: 29 Copynumber: 2.6 Consensus size: 28
56829029 TTTAAACTTT
*
56829039 TTAATACTTTTATA-ATTTCTAGAAATG
1 TTAATAATTTTATATATTTCTAGAAATG
* * *
56829066 TAATAATTATTTTATATATTTTTATAATATG
1 T--TAATAATTTTATATATTTCTAGAA-ATG
56829097 TTAATAA-TTTATATA
1 TTAATAATTTTATATA
56829112 ATAGTTTGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
27 1 0.03
28 8 0.22
29 16 0.43
30 8 0.22
31 4 0.11
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (28 bp):
TTAATAATTTTATATATTTCTAGAAATG
Found at i:56834098 original size:3 final size:3
Alignment explanation
Indices: 56834090--56834123 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
56834080 TAAATAAAAT
56834090 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
56834124 GCAAGGCTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:56835711 original size:38 final size:39
Alignment explanation
Indices: 56835669--56835743 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 39
56835659 TTTGATCCTC
*
56835669 TAAAATAAGTAAAA-AATA-TTTAATCTCTTCAAAATTGA
1 TAAAATAA-TAAAATAATATTTTAATCTCTTAAAAATTGA
*
56835707 TAAAATAATAAAATTATATTTTAATCTCTTAAAAATT
1 TAAAATAATAAAATAATATTTTAATCTCTTAAAAATT
56835744 TATTCTTCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
37 5 0.15
38 11 0.33
39 17 0.52
ACGTcount: A:0.52, C:0.07, G:0.03, T:0.39
Consensus pattern (39 bp):
TAAAATAATAAAATAATATTTTAATCTCTTAAAAATTGA
Found at i:56836246 original size:15 final size:15
Alignment explanation
Indices: 56836222--56836255 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
56836212 TTTTATTTTT
*
56836222 ATTATTTATTTTGAA
1 ATTATATATTTTGAA
*
56836237 ATTATATATTTTGTA
1 ATTATATATTTTGAA
56836252 ATTA
1 ATTA
56836256 AGTAAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (15 bp):
ATTATATATTTTGAA
Found at i:56836711 original size:16 final size:17
Alignment explanation
Indices: 56836690--56836723 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
56836680 GTAAGGGTAT
56836690 AATAAA-ATATTTAAAA
1 AATAAATATATTTAAAA
*
56836706 AATAAATATTTTTAAAA
1 AATAAATATATTTAAAA
56836723 A
1 A
56836724 GAGACAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AATAAATATATTTAAAA
Found at i:56837371 original size:31 final size:31
Alignment explanation
Indices: 56837336--56837402 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
56837326 AAAAAACATT
56837336 AATAGCCCAATGACTTAAATAAAAACTTTTG
1 AATAGCCCAATGACTTAAATAAAAACTTTTG
** * *
56837367 AATAGTTCAGTGACTTAAATGAAAACTTTTG
1 AATAGCCCAATGACTTAAATAAAAACTTTTG
56837398 AATAG
1 AATAG
56837403 TTCACTGATC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.31
Consensus pattern (31 bp):
AATAGCCCAATGACTTAAATAAAAACTTTTG
Found at i:56837403 original size:31 final size:31
Alignment explanation
Indices: 56837346--56837406 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
56837336 AATAGCCCAA
56837346 TGACTTAAATAAAAACTTTTGAATAGTTCAG
1 TGACTTAAATAAAAACTTTTGAATAGTTCAG
*
56837377 TGACTTAAATGAAAACTTTTGAATAGTTCA
1 TGACTTAAATAAAAACTTTTGAATAGTTCA
56837407 CTGATCAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTTGAATAGTTCAG
Found at i:56837426 original size:30 final size:31
Alignment explanation
Indices: 56837346--56837416 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
56837336 AATAGCCCAA
* * *
56837346 TGACTTAAATAAAAACTTTTGAATAGTTCAG
1 TGACTCAAATGAAAACTTTTGAATAGTTCAC
*
56837377 TGACTTAAATGAAAACTTTTGAATAGTTCAC
1 TGACTCAAATGAAAACTTTTGAATAGTTCAC
56837408 TGA-TCAAAT
1 TGACTCAAAT
56837417 TGTAACTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
30 5 0.14
31 32 0.86
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (31 bp):
TGACTCAAATGAAAACTTTTGAATAGTTCAC
Found at i:56837922 original size:2 final size:2
Alignment explanation
Indices: 56837915--56837953 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
56837905 TAGGACCTTT
56837915 TA TA TA TA TA TA TA 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 TA TA T
56837954 GCAACTTGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:56840554 original size:3 final size:3
Alignment explanation
Indices: 56840546--56840575 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
56840536 TTACCAACAC
*
56840546 GTT GTT GTT GTT GTT GTT GTT GTT GAT GTT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT
56840576 TTCATCACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.03, C:0.00, G:0.33, T:0.63
Consensus pattern (3 bp):
GTT
Found at i:56855519 original size:14 final size:15
Alignment explanation
Indices: 56855497--56855573 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
56855487 TAATCAAACA
56855497 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
56855511 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
56855526 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
56855546 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
56855560 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
56855574 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:56855538 original size:20 final size:20
Alignment explanation
Indices: 56855513--56855552 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
56855503 AATATTTTCC
*
56855513 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
56855533 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
56855553 TCATTTTACG
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:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:56855558 original size:34 final size:35
Alignment explanation
Indices: 56855501--56855567 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
56855491 CAAACACCAG
*
56855501 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
56855536 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
56855568 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:56865260 original size:17 final size:18
Alignment explanation
Indices: 56865218--56865262 Score: 60
Period size: 16 Copynumber: 2.7 Consensus size: 18
56865208 TGTAAGAAAA
56865218 ATGAATTTTTTATTTTTC
1 ATGAATTTTTTATTTTTC
56865236 AT-AA-TTTTTATTTTT-
1 ATGAATTTTTTATTTTTC
*
56865251 TTGAATTTTTTA
1 ATGAATTTTTTA
56865263 AACAAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 1 0.04
16 13 0.54
17 8 0.33
18 2 0.08
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.69
Consensus pattern (18 bp):
ATGAATTTTTTATTTTTC
Found at i:56866776 original size:50 final size:50
Alignment explanation
Indices: 56866700--56866827 Score: 168
Period size: 50 Copynumber: 2.5 Consensus size: 50
56866690 GTGTACCAAT
* *
56866700 AAATTTAGCCCTCAA-AGTTTACACATTCTGTCAATTCCGTCTTGATTTAAC
1 AAATTTA-CCTTCAACA-TTTACACATTCTGTCAATTCAGTCTTGATTTAAC
* *
56866751 AAATTTACCTTCAACATTTACACATTTTGTCAATTTAGTCTTGATTTAAC
1 AAATTTACCTTCAACATTTACACATTCTGTCAATTCAGTCTTGATTTAAC
* *
56866801 AAATTTAGCTCACAACATTTACACATT
1 AAATTTACCT-TCAACATTTACACATT
56866828 ATACCAATCA
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
50 46 0.67
51 23 0.33
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (50 bp):
AAATTTACCTTCAACATTTACACATTCTGTCAATTCAGTCTTGATTTAAC
Found at i:56868966 original size:21 final size:20
Alignment explanation
Indices: 56868941--56868991 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
56868931 AATTAATTCG
56868941 TTAATATTTTAATAATTATTA
1 TTAATATTTTAA-AATTATTA
*
56868962 TTAATAGTTTTAAAATTTTTA
1 TTAATA-TTTTAAAATTATTA
*
56868983 ATAA-ATTTT
1 TTAATATTTT
56868992 TTTCATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 4 0.15
20 1 0.04
21 16 0.59
22 6 0.22
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
TTAATATTTTAAAATTATTA
Found at i:56869039 original size:23 final size:24
Alignment explanation
Indices: 56868999--56869045 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
56868989 TTTTTTCATT
*
56868999 TTTTATAAAATTTAAATAATTTTA
1 TTTTATAAAATTTAAATAAATTTA
* *
56869023 TTTT-TAAATTTTTAATAAATTTA
1 TTTTATAAAATTTAAATAAATTTA
56869046 AATCAAAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTTATAAAATTTAAATAAATTTA
Found at i:56870031 original size:20 final size:19
Alignment explanation
Indices: 56870003--56870067 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 19
56869993 TGATTTTTAA
*
56870003 TTAATTTTTAATAGTTTTT
1 TTAAATTTTAATAGTTTTT
*
56870022 TATAAATTTTAA-ATTTTTT
1 T-TAAATTTTAATAGTTTTT
*
56870041 TTATAATTTTAAT-GTCTTT
1 TTA-AATTTTAATAGTTTTT
56870060 TTAAATTT
1 TTAAATTT
56870068 ATTTTTATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
18 7 0.18
19 23 0.59
20 9 0.23
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.65
Consensus pattern (19 bp):
TTAAATTTTAATAGTTTTT
Found at i:56870667 original size:87 final size:87
Alignment explanation
Indices: 56870549--56870709 Score: 243
Period size: 87 Copynumber: 1.9 Consensus size: 87
56870539 CAATTTAAGT
*
56870549 AATTCACTCAAAAATCAATTCAAAATCGATTTATCTTATAATTCGAATTGATATAACAATCAATT
1 AATTCACTCAAAAATCAATTCAAAATCGATTTAACTTATAATTCGAATTGATATAACAATCAATT
56870614 CTCGACCCGGTTAGATTTGAGC
66 CTCGACCCGGTTAGATTTGAGC
* * * * *
56870636 AATTCACTCAAAAA-CTAATTCAAAATTGATTTAACTTTTTATTCGAATTGATATATCAATCAGT
1 AATTCACTCAAAAATC-AATTCAAAATCGATTTAACTTATAATTCGAATTGATATAACAATCAAT
*
56870700 TCTCGGCCCG
65 TCTCGACCCG
56870710 ACTCTAACCA
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
86 1 0.02
87 65 0.98
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.35
Consensus pattern (87 bp):
AATTCACTCAAAAATCAATTCAAAATCGATTTAACTTATAATTCGAATTGATATAACAATCAATT
CTCGACCCGGTTAGATTTGAGC
Found at i:56877610 original size:16 final size:16
Alignment explanation
Indices: 56877589--56877621 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
56877579 AAAGGCAAAG
56877589 TGTTTTTAAAAAACTA
1 TGTTTTTAAAAAACTA
56877605 TGTTTTTAAAAAACTA
1 TGTTTTTAAAAAACTA
56877621 T
1 T
56877622 CTTAAAAACA
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:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (16 bp):
TGTTTTTAAAAAACTA
Found at i:56886247 original size:22 final size:22
Alignment explanation
Indices: 56886221--56886262 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
56886211 AAATGTGTTG
56886221 TTTGATAAATTGAAAAGTTATA
1 TTTGATAAATTGAAAAGTTATA
*
56886243 TTTGATAAATTGAAAGGTTA
1 TTTGATAAATTGAAAAGTTA
56886263 AGTATTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (22 bp):
TTTGATAAATTGAAAAGTTATA
Found at i:56888223 original size:22 final size:19
Alignment explanation
Indices: 56888185--56888239 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 19
56888175 ATAAAATAAA
*
56888185 AATTTTATAAA-AT-AGTT
1 AATTTTTTAAATATAAGTT
56888202 AATTATTATTAAATTATAAGTT
1 AATT-TT-TTAAA-TATAAGTT
56888224 AATTTTTTAAATATAA
1 AATTTTTTAAATATAA
56888240 TCATATATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
17 4 0.12
18 2 0.06
19 9 0.28
20 5 0.16
21 4 0.12
22 8 0.25
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (19 bp):
AATTTTTTAAATATAAGTT
Found at i:56888267 original size:17 final size:18
Alignment explanation
Indices: 56888227--56888267 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
56888217 ATAAGTTAAT
*
56888227 TTTTTAAATATAATCATA
1 TTTTTAAACATAATCATA
*
56888245 -TATTAAACATAAT-ATA
1 TTTTTAAACATAATCATA
56888261 TTTTTAA
1 TTTTTAA
56888268 TTAATAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 3
0.76 0.12 0.12
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTTTAAACATAATCATA
Found at i:56893538 original size:10 final size:10
Alignment explanation
Indices: 56893523--56893563 Score: 55
Period size: 10 Copynumber: 3.8 Consensus size: 10
56893513 CTCTCCATAC
56893523 ATACATATAT
1 ATACATATAT
56893533 ATACATATAT
1 ATACATATAT
56893543 ATACATACATGAT
1 ATACAT--AT-AT
56893556 ATACATAT
1 ATACATAT
56893564 CATTATGCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 16 0.57
11 2 0.07
12 2 0.07
13 8 0.29
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37
Consensus pattern (10 bp):
ATACATATAT
Found at i:56893538 original size:14 final size:14
Alignment explanation
Indices: 56893518--56893562 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
56893508 TTCATCTCTC
56893518 CATACATACATATA
1 CATACATACATATA
* *
56893532 TATACATATATATA
1 CATACATACATATA
*
56893546 CATACAT-GATATA
1 CATACATACATATA
56893559 CATA
1 CATA
56893563 TCATTATGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
13 9 0.33
14 18 0.67
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (14 bp):
CATACATACATATA
Found at i:56896427 original size:4 final size:4
Alignment explanation
Indices: 56896418--56896464 Score: 85
Period size: 4 Copynumber: 11.8 Consensus size: 4
56896408 AATCATTAGA
*
56896418 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACGT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
56896465 AGACAAGTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.49, C:0.26, G:0.02, T:0.23
Consensus pattern (4 bp):
ACAT
Found at i:56898995 original size:15 final size:16
Alignment explanation
Indices: 56898970--56899000 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
56898960 TAAAACCTAA
56898970 ATTTATTACAATATTT
1 ATTTATTACAATATTT
56898986 ATTT-TTACAATATTT
1 ATTTATTACAATATTT
56899001 GTTTCTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTATTACAATATTT
Found at i:56905068 original size:31 final size:31
Alignment explanation
Indices: 56905032--56905098 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
56905022 TTAACAGCTT
*
56905032 AGTGACTTAAATAAAA-ACTTTTGAATAGTTA
1 AGTGACTTAAATAAAACA-TTTCGAATAGTTA
* *
56905063 AGTGACTTAAATGAAACATTTCGAATAGTTT
1 AGTGACTTAAATAAAACATTTCGAATAGTTA
56905094 AGTGA
1 AGTGA
56905099 TCATTTTGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.34
Consensus pattern (31 bp):
AGTGACTTAAATAAAACATTTCGAATAGTTA
Found at i:56905669 original size:18 final size:19
Alignment explanation
Indices: 56905632--56905669 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
56905622 ACACCTCAAA
* *
56905632 CAATATATCTAAATACTAC
1 CAATAAATCTAAATAATAC
56905651 CAATAAATC-AAATAATAC
1 CAATAAATCTAAATAATAC
56905669 C
1 C
56905670 TCCAAATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (19 bp):
CAATAAATCTAAATAATAC
Found at i:56906819 original size:30 final size:30
Alignment explanation
Indices: 56906766--56906850 Score: 100
Period size: 30 Copynumber: 2.8 Consensus size: 30
56906756 TCTTCAATGT
* * *
56906766 CGTTTGTTCCCTTGTCATCTGTGTCCCTGC
1 CGTTAGTTTCCTTGTCATTTGTGTCCCTGC
* *
56906796 CGTTCAG-TTCCTTCTCATTTGTGTCCTTGC
1 CGTT-AGTTTCCTTGTCATTTGTGTCCCTGC
*
56906826 CGTTTGTTTCCTTGTCATTTGTGTC
1 CGTTAGTTTCCTTGTCATTTGTGTC
56906851 TTTCTGCGGG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
29 1 0.02
30 44 0.96
31 1 0.02
ACGTcount: A:0.05, C:0.28, G:0.19, T:0.48
Consensus pattern (30 bp):
CGTTAGTTTCCTTGTCATTTGTGTCCCTGC
Found at i:56906831 original size:15 final size:15
Alignment explanation
Indices: 56906811--56906850 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
56906801 AGTTCCTTCT
56906811 CATTTGTGTCCTTGC
1 CATTTGTGTCCTTGC
* * *
56906826 CGTTTGTTTCCTTGT
1 CATTTGTGTCCTTGC
56906841 CATTTGTGTC
1 CATTTGTGTC
56906851 TTTCTGCGGG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.05, C:0.23, G:0.20, T:0.53
Consensus pattern (15 bp):
CATTTGTGTCCTTGC
Found at i:56909499 original size:34 final size:36
Alignment explanation
Indices: 56909423--56909500 Score: 94
Period size: 34 Copynumber: 2.3 Consensus size: 36
56909413 TTTATTAAAA
* *
56909423 TAATAA-ATTATATTAATTATATATATTTGATTTAT
1 TAATAATATTATATTAAATATAAATATTTGATTTAT
*
56909458 T-AT-ATATTATTTTAAATATAAATATTT-ATTT-T
1 TAATAATATTATATTAAATATAAATATTTGATTTAT
56909490 TAATAATATTA
1 TAATAATATTA
56909501 AAAATAATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
32 2 0.05
33 7 0.19
34 27 0.73
35 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (36 bp):
TAATAATATTATATTAAATATAAATATTTGATTTAT
Found at i:56909501 original size:29 final size:32
Alignment explanation
Indices: 56909431--56909516 Score: 79
Period size: 34 Copynumber: 2.7 Consensus size: 32
56909421 AATAATAAAT
* *
56909431 TATATTAATTATATATATTTGATTTATTATATA
1 TATATTAAATATAAATATTT-ATTTATTATATA
*
56909464 TTATTTTAAATATAAATATTTATTT-TTA-ATA
1 -TATATTAAATATAAATATTTATTTATTATATA
*
56909495 -ATATTAAAAATAATTATATTTA
1 TATATTAAATATAA--ATATTTA
56909517 CAATCAATAT
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
29 11 0.24
31 10 0.22
32 3 0.07
33 4 0.09
34 17 0.38
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (32 bp):
TATATTAAATATAAATATTTATTTATTATATA
Found at i:56917685 original size:20 final size:20
Alignment explanation
Indices: 56917643--56917685 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
56917633 AACATTATAT
*
56917643 AAGTTATTTAAAATATTAAA
1 AAGTTATTTAAAAGATTAAA
*
56917663 AAGTTA-TTCAAAGATTAATA
1 AAGTTATTTAAAAGATTAA-A
56917683 AAG
1 AAG
56917686 ATATAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.35
Consensus pattern (20 bp):
AAGTTATTTAAAAGATTAAA
Found at i:56927063 original size:21 final size:22
Alignment explanation
Indices: 56927023--56927074 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
56927013 TTTTCTTTTT
* *
56927023 TTTCATTTTCTTCTGCTTCTCCC
1 TTTC-TTTTCCTCTGCTTCTCCA
*
56927046 TTTGTTTTCCTCT-CTTCTCCA
1 TTTCTTTTCCTCTGCTTCTCCA
56927067 TTTCTTTT
1 TTTCTTTT
56927075 AGCGTAGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 14 0.56
22 8 0.32
23 3 0.12
ACGTcount: A:0.04, C:0.31, G:0.04, T:0.62
Consensus pattern (22 bp):
TTTCTTTTCCTCTGCTTCTCCA
Found at i:56928339 original size:21 final size:22
Alignment explanation
Indices: 56928299--56928350 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
56928289 TTTTCTTTTT
* *
56928299 TTTCATTTTCTTCTGCTTCTCCC
1 TTTC-TTTTCCTCTGCTTCTCCA
*
56928322 TTTGTTTTCCTCT-CTTCTCCA
1 TTTCTTTTCCTCTGCTTCTCCA
56928343 TTTCTTTT
1 TTTCTTTT
56928351 AGCGTAGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 14 0.56
22 8 0.32
23 3 0.12
ACGTcount: A:0.04, C:0.31, G:0.04, T:0.62
Consensus pattern (22 bp):
TTTCTTTTCCTCTGCTTCTCCA
Found at i:56929592 original size:2 final size:2
Alignment explanation
Indices: 56929579--56929611 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
56929569 AACAAACGTC
*
56929579 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
56929612 ATTCGAAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:56939303 original size:111 final size:111
Alignment explanation
Indices: 56939104--56939327 Score: 412
Period size: 111 Copynumber: 2.0 Consensus size: 111
56939094 CCGTGATTCA
* * *
56939104 TTGGCTATTGAAATGAAAATAACGTGTTTGACATTGTTTCAGAGTGACGTTGTCTGCATGCATAT
1 TTGGATATTGAAATGAAAATAACGTGTTTGACATTGTTTCAGAGTGAAGTGGTCTGCATGCATAT
56939169 CTTATTAAGTAGGCTTTCTTTAATTTGATATGAAATATTTCTCCTG
66 CTTATTAAGTAGGCTTTCTTTAATTTGATATGAAATATTTCTCCTG
*
56939215 TTGGATATTGAAATGAAAATAATGTGTTTGACATTGTTTCAGAGTGAAGTGGTCTGCATGCATAT
1 TTGGATATTGAAATGAAAATAACGTGTTTGACATTGTTTCAGAGTGAAGTGGTCTGCATGCATAT
56939280 CTTATTAAGTAGGCTTTCTTTAATTTGATATGAAATATTTCTCCTG
66 CTTATTAAGTAGGCTTTCTTTAATTTGATATGAAATATTTCTCCTG
56939326 TT
1 TT
56939328 ATCTTGTTAA
Statistics
Matches: 109, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 109 1.00
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (111 bp):
TTGGATATTGAAATGAAAATAACGTGTTTGACATTGTTTCAGAGTGAAGTGGTCTGCATGCATAT
CTTATTAAGTAGGCTTTCTTTAATTTGATATGAAATATTTCTCCTG
Found at i:56954670 original size:31 final size:31
Alignment explanation
Indices: 56954635--56954702 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
56954625 TAACAGCCCA
* *
56954635 AATGACTTAAATAAAAACTTTTGAATAGTTT
1 AATGACTTAAATAAAAACTTTCGAATAGTTC
*
56954666 AATGACTTAAATGAAAACTTTCGAATAGTTC
1 AATGACTTAAATAAAAACTTTCGAATAGTTC
56954697 AATGAC
1 AATGAC
56954703 CATTTTGTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (31 bp):
AATGACTTAAATAAAAACTTTCGAATAGTTC
Found at i:56971196 original size:25 final size:24
Alignment explanation
Indices: 56971168--56971247 Score: 106
Period size: 25 Copynumber: 3.2 Consensus size: 24
56971158 ATGCTCTCAT
*
56971168 GAGCTGTGAATTAAGAAGCTCATAC
1 GAGCTGTAAATT-AGAAGCTCATAC
*
56971193 GAGCTGCAAATTAGTAAGCTCATAC
1 GAGCTGTAAATTAG-AAGCTCATAC
*
56971218 GAGCTGTAAATCGAGAAGCTCATAC
1 GAGCTGTAAAT-TAGAAGCTCATAC
56971243 GAGCT
1 GAGCT
56971248 ATGGTGTGTC
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
24 2 0.04
25 45 0.92
26 2 0.04
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.23
Consensus pattern (24 bp):
GAGCTGTAAATTAGAAGCTCATAC
Found at i:56977059 original size:21 final size:21
Alignment explanation
Indices: 56977033--56977074 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
56977023 TTCATGCATG
56977033 GTGACGACTTGTTTGAGCTAA
1 GTGACGACTTGTTTGAGCTAA
56977054 GTGACGACTTGTTTGAGCTAA
1 GTGACGACTTGTTTGAGCTAA
56977075 CTGCTGATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.29, T:0.33
Consensus pattern (21 bp):
GTGACGACTTGTTTGAGCTAA
Found at i:56978118 original size:42 final size:42
Alignment explanation
Indices: 56978059--56978141 Score: 166
Period size: 42 Copynumber: 2.0 Consensus size: 42
56978049 CCTGAATAAG
56978059 AATGCATTTATATTCAGAAGCCTAGAGTGTCTTATATGGTTA
1 AATGCATTTATATTCAGAAGCCTAGAGTGTCTTATATGGTTA
56978101 AATGCATTTATATTCAGAAGCCTAGAGTGTCTTATATGGTT
1 AATGCATTTATATTCAGAAGCCTAGAGTGTCTTATATGGTT
56978142 CATCCAGATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (42 bp):
AATGCATTTATATTCAGAAGCCTAGAGTGTCTTATATGGTTA
Found at i:56986186 original size:19 final size:19
Alignment explanation
Indices: 56986162--56986201 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
56986152 ACAACAAAAT
*
56986162 AATAGTAACATAATAGTGA
1 AATAGTAACAAAATAGTGA
*
56986181 AATAGTAGCAAAATAGTGA
1 AATAGTAACAAAATAGTGA
56986200 AA
1 AA
56986202 AAACAAGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.55, C:0.05, G:0.17, T:0.23
Consensus pattern (19 bp):
AATAGTAACAAAATAGTGA
Found at i:56986575 original size:20 final size:21
Alignment explanation
Indices: 56986524--56986578 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
56986514 TTCCTCTCCT
*
56986524 TATTCTCTTTTAATTTTTTTATC
1 TATTCT-TTTT-ATTTTTCTATC
* *
56986547 TATTTTTTTTATTTTTCTATG
1 TATTCTTTTTATTTTTCTATC
56986568 T-TTCTTTTTAT
1 TATTCTTTTTAT
56986579 GATTTAATCT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 9 0.32
21 10 0.36
22 4 0.14
23 5 0.18
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.75
Consensus pattern (21 bp):
TATTCTTTTTATTTTTCTATC
Found at i:56991631 original size:45 final size:45
Alignment explanation
Indices: 56991581--56991693 Score: 181
Period size: 45 Copynumber: 2.5 Consensus size: 45
56991571 AGTAAACAGT
**
56991581 AATCGGTAACGGTAACAGTAACTGTATTCGACACACAAAGTGCCG
1 AATCGGTAACGGTAACAGTAACAATATTCGACACACAAAGTGCCG
*
56991626 AATCGGTAACGGTAACAGTAACAATATTCGACACACGAAGTGCCG
1 AATCGGTAACGGTAACAGTAACAATATTCGACACACAAAGTGCCG
* *
56991671 AACCGGTAACAGTAACAGTAACA
1 AATCGGTAACGGTAACAGTAACA
56991694 GTAACAGTAT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 63 1.00
ACGTcount: A:0.39, C:0.22, G:0.21, T:0.18
Consensus pattern (45 bp):
AATCGGTAACGGTAACAGTAACAATATTCGACACACAAAGTGCCG
Found at i:56991640 original size:51 final size:50
Alignment explanation
Indices: 56991579--56991729 Score: 161
Period size: 45 Copynumber: 3.1 Consensus size: 50
56991569 CCAGTAAACA
*
56991579 GTAATCGGTAACGGTAACAGTAACTGTATTCGACACACAAAGTGCCGAATCG
1 GTAA-CGGTAACAGTAACAGTAAC-GTATTCGACACACAAAGTGCCGAATCG
* *
56991631 GTAACGGTAACAGTAAC---AA--TATTCGACACACGAAGTGCCGAACCG
1 GTAACGGTAACAGTAACAGTAACGTATTCGACACACAAAGTGCCGAATCG
* * * * *
56991676 GTAACAGTAACAGTAACAGTAACAGTATTCGGCACA-TAAGTGCCTAATCA
1 GTAACGGTAACAGTAACAGTAAC-GTATTCGACACACAAAGTGCCGAATCG
56991726 GTAA
1 GTAA
56991730 GCCGACAAAT
Statistics
Matches: 84, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
45 40 0.48
48 4 0.05
50 14 0.17
51 22 0.26
52 4 0.05
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (50 bp):
GTAACGGTAACAGTAACAGTAACGTATTCGACACACAAAGTGCCGAATCG
Found at i:56991687 original size:6 final size:6
Alignment explanation
Indices: 56991676--56991702 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
56991666 TGCCGAACCG
56991676 GTAACA GTAACA GTAACA GTAACA GTA
1 GTAACA GTAACA GTAACA GTAACA GTA
56991703 TTCGGCACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.15, G:0.19, T:0.19
Consensus pattern (6 bp):
GTAACA
Found at i:56997772 original size:14 final size:14
Alignment explanation
Indices: 56997753--56997780 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
56997743 TAGCCTAGGT
56997753 GCTTGTTGGAAGAA
1 GCTTGTTGGAAGAA
56997767 GCTTGTTGGAAGAA
1 GCTTGTTGGAAGAA
56997781 AGAGGGATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.36, T:0.29
Consensus pattern (14 bp):
GCTTGTTGGAAGAA
Found at i:57000256 original size:3 final size:3
Alignment explanation
Indices: 57000248--57000303 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
57000238 TTAAGGTTGC
57000248 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
57000296 AAT AAT AA
1 AAT AAT AA
57000304 AAGCATAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:57004601 original size:22 final size:22
Alignment explanation
Indices: 57004550--57004603 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
57004540 TGCAAAAAAA
* *
57004550 ATTGTTTTACTGTTGTTTTTCC
1 ATTGTTTTGCAGTTGTTTTTCC
* *
57004572 ACTATTTTGCAGTTG-TTTTCC
1 ATTGTTTTGCAGTTGTTTTTCC
57004593 TATTGTTTTGC
1 -ATTGTTTTGC
57004604 TATCATTCCA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.11, C:0.15, G:0.15, T:0.59
Consensus pattern (22 bp):
ATTGTTTTGCAGTTGTTTTTCC
Found at i:57007068 original size:17 final size:15
Alignment explanation
Indices: 57007046--57007086 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 15
57007036 GTTGAAGTTT
57007046 TTTTTTTTTCTTTGCTG
1 TTTTTTTTTCTTT--TG
*
57007063 TTTTTTTTTGTTTTG
1 TTTTTTTTTCTTTTG
57007078 TTTTTTTTT
1 TTTTTTTTT
57007087 TCTCATGCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 11 0.48
17 12 0.52
ACGTcount: A:0.00, C:0.05, G:0.10, T:0.85
Consensus pattern (15 bp):
TTTTTTTTTCTTTTG
Found at i:57007068 original size:18 final size:16
Alignment explanation
Indices: 57007045--57007089 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
57007035 TGTTGAAGTT
57007045 TTTTTTTTTTC-TTTG
1 TTTTTTTTTTCTTTTG
*
57007060 CTGTTTTTTTTTGTTTTG
1 -T-TTTTTTTTTCTTTTG
57007078 TTTTTTTTTTCT
1 TTTTTTTTTTCT
57007090 CATGCTTGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 11 0.44
17 10 0.40
18 4 0.16
ACGTcount: A:0.00, C:0.07, G:0.09, T:0.84
Consensus pattern (16 bp):
TTTTTTTTTTCTTTTG
Found at i:57007217 original size:12 final size:13
Alignment explanation
Indices: 57007190--57007219 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
57007180 ATTTTGGAGC
*
57007190 TTTTTGCTTGATT
1 TTTTTGCTCGATT
57007203 TTTTTGCTCGATT
1 TTTTTGCTCGATT
57007216 TTTT
1 TTTT
57007220 CTTTTTGTTT
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:0.07, C:0.10, G:0.13, T:0.70
Consensus pattern (13 bp):
TTTTTGCTCGATT
Found at i:57007533 original size:28 final size:28
Alignment explanation
Indices: 57007492--57007550 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
57007482 AATATAATTT
** *
57007492 TTTTGAAAGTTTAGGGTTCAAAATGTAA
1 TTTTGAAAAATTAGGGGTCAAAATGTAA
57007520 TTTTGAAAAATTAGGGGTCAAAATGTAA
1 TTTTGAAAAATTAGGGGTCAAAATGTAA
57007548 TTT
1 TTT
57007551 ATATTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.37, C:0.03, G:0.20, T:0.39
Consensus pattern (28 bp):
TTTTGAAAAATTAGGGGTCAAAATGTAA
Found at i:57008004 original size:75 final size:75
Alignment explanation
Indices: 57007925--57008193 Score: 430
Period size: 75 Copynumber: 3.6 Consensus size: 75
57007915 CCCAAAGCTT
* * *
57007925 AACTCACCTCTCGGATTATGAGTTGATCTTTGAAAAACGGAAATTGAAAATACATTAGCGCGCGA
1 AACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACATTAGCGTGCGA
57007990 CCCGAGGCTC
66 CCCGAGGCTC
* * * * * *
57008000 AACTCACCTCTCAGTTTATGAGTTGATTTTTAAAAAATAGAAATTGAAAATACCTCAGCGTGCGA
1 AACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACATTAGCGTGCGA
57008065 CCCGAGGCTC
66 CCCGAGGCTC
*
57008075 AACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACTTTAGCGTGCGA
1 AACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACATTAGCGTGCGA
*
57008140 CCCGAGACTC
66 CCCGAGGCTC
*
57008150 AACTCACCTCTCGGGTTATGAGTTGATTTTTGAAAAACAGAAAT
1 AACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAACAGAAAT
57008194 AAAAATATGT
Statistics
Matches: 177, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 177 1.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (75 bp):
AACTCACCTCTCGGATTATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACATTAGCGTGCGA
CCCGAGGCTC
Found at i:57012352 original size:27 final size:28
Alignment explanation
Indices: 57012321--57012373 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
57012311 TAATTTATGT
*
57012321 AAGATGAACACAATATT-TTTTTTAAAG
1 AAGATGAACACAATATTATTCTTTAAAG
* *
57012348 AAGATGACCACATTATTATTCTTTAA
1 AAGATGAACACAATATTATTCTTTAA
57012374 TTTCTCATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 15 0.68
28 7 0.32
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (28 bp):
AAGATGAACACAATATTATTCTTTAAAG
Found at i:57014459 original size:23 final size:24
Alignment explanation
Indices: 57014412--57014457 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
57014402 GAAAAATATT
57014412 AAATATATATATATTTTATTTTTA
1 AAATATATATATATTTTATTTTTA
*
57014436 AAATATA-ATAGTTTTTTATTTT
1 AAATATATATA-TATTTTATTTT
57014458 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
AAATATATATATATTTTATTTTTA
Found at i:57014568 original size:9 final size:9
Alignment explanation
Indices: 57014554--57014581 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
57014544 TTTTGTTACA
57014554 ACAATTAAT
1 ACAATTAAT
57014563 ACAATTAAT
1 ACAATTAAT
57014572 ACAATTAAT
1 ACAATTAAT
57014581 A
1 A
57014582 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:57014633 original size:68 final size:66
Alignment explanation
Indices: 57014524--57014665 Score: 248
Period size: 68 Copynumber: 2.1 Consensus size: 66
57014514 TCAAGTTTGT
*
57014524 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
57014589 AAA
64 AAA
57014592 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
*
57014657 T
66 A
57014658 TTTACTAA
1 TTTACTAA
57014666 CAATTAATTT
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
66 27 0.38
67 1 0.01
68 44 0.61
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (66 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
A
Found at i:57014675 original size:16 final size:16
Alignment explanation
Indices: 57014654--57014695 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
57014644 AATAATTTGA
*
57014654 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
57014670 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
57014686 TAGTTTTAAT
1 TAATTTTAAT
57014696 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:57014679 original size:22 final size:23
Alignment explanation
Indices: 57014669--57014724 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
57014659 TTACTAACAA
* * *
57014669 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAATT
*
57014691 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
57014714 TTAATTTTAAT
1 TTAATTTTAAT
57014725 TTTAATTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:57014684 original size:59 final size:66
Alignment explanation
Indices: 57014524--57014687 Score: 216
Period size: 68 Copynumber: 2.5 Consensus size: 66
57014514 TCAAGTTTGT
*
57014524 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAA-GTTAGATTTT-ATACAACAATTAATACAATTAATACAATTAATAATTTGAT
57014589 AAA
64 AAA
57014592 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAA-GTTAGATTTTA-TACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
57014655 AAT
64 AAA
*
57014658 TTTACTAA-C-AA-TTA-ATTTTA-ATAACAATTA
1 TTTACTAATCAAAGTTAGATTTTATACAACAATTA
57014688 GTTTTAATTT
Statistics
Matches: 92, Mismatches: 3, Indels: 11
0.87 0.03 0.10
Matches are distributed among these distances:
59 9 0.10
61 6 0.07
62 3 0.03
64 2 0.02
65 1 0.01
66 27 0.29
67 1 0.01
68 43 0.47
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (66 bp):
TTTACTAATCAAAGTTAGATTTTATACAACAATTAATACAATTAATACAATTAATAATTTGATAA
A
Found at i:57014748 original size:5 final size:5
Alignment explanation
Indices: 57014738--57014762 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
57014728 AATTAAAAAT
57014738 GGGCC GGGCC GGGCC GGGCC GGGCC
1 GGGCC GGGCC GGGCC GGGCC GGGCC
57014763 CCATATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.40, G:0.60, T:0.00
Consensus pattern (5 bp):
GGGCC
Found at i:57020172 original size:51 final size:51
Alignment explanation
Indices: 57020065--57020177 Score: 138
Period size: 51 Copynumber: 2.2 Consensus size: 51
57020055 CATCTGTAGG
* * * *
57020065 TTATCCGCAACCCCCGGTAGTGTCACCCGTGGTGGCATATCCGGATCCGCA
1 TTATCCACAAGCCCCGGTAATGTCACCCGTGGTGGCATATCCGGATCCACA
* * * *
57020116 CTATCCCCAAGCCCCGGTAAAT-TCACCTGTGGTGGCATATCCGGATCCATA
1 TTATCCACAAGCCCCGGT-AATGTCACCCGTGGTGGCATATCCGGATCCACA
57020167 TTATCCACAAG
1 TTATCCACAAG
57020178 TAAACACCTT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
51 50 0.96
52 2 0.04
ACGTcount: A:0.22, C:0.34, G:0.21, T:0.23
Consensus pattern (51 bp):
TTATCCACAAGCCCCGGTAATGTCACCCGTGGTGGCATATCCGGATCCACA
Found at i:57020601 original size:35 final size:35
Alignment explanation
Indices: 57020555--57020623 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
57020545 TCTCAATCTT
*
57020555 TTACTAGTTTGCAATAGTTGTCTTTATTTCTAGTC
1 TTACTAGTTTGCAATAGTTGTCTATATTTCTAGTC
57020590 TTACTAGTTTGCAATAGTTGTCTATATTTCTAGT
1 TTACTAGTTTGCAATAGTTGTCTATATTTCTAGT
57020624 GATCATATGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.22, C:0.13, G:0.14, T:0.51
Consensus pattern (35 bp):
TTACTAGTTTGCAATAGTTGTCTATATTTCTAGTC
Found at i:57021016 original size:13 final size:13
Alignment explanation
Indices: 57020998--57021030 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
57020988 CAGGGCCCTC
*
57020998 ACCATCACCATCA
1 ACCATCAACATCA
57021011 ACCATCAACATCA
1 ACCATCAACATCA
57021024 A-CATCAA
1 ACCATCAA
57021031 AAGGAAAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.45, C:0.39, G:0.00, T:0.15
Consensus pattern (13 bp):
ACCATCAACATCA
Found at i:57021343 original size:2 final size:2
Alignment explanation
Indices: 57021336--57021360 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
57021326 CGAATGCTTT
57021336 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
57021361 TAACTAAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:57021736 original size:29 final size:30
Alignment explanation
Indices: 57021693--57021751 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
57021683 TAATTAGATC
*
57021693 AAATCAAAATTTCATGTATAAAATTACACA
1 AAATCAAAAGTTCATGTATAAAATTACACA
*
57021723 AAATC-AAAGTTCATGTATACAATTACACA
1 AAATCAAAAGTTCATGTATAAAATTACACA
57021752 TTAAACTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.51, C:0.15, G:0.05, T:0.29
Consensus pattern (30 bp):
AAATCAAAAGTTCATGTATAAAATTACACA
Found at i:57026317 original size:30 final size:31
Alignment explanation
Indices: 57026283--57026363 Score: 94
Period size: 30 Copynumber: 2.7 Consensus size: 31
57026273 TTGAAGCGAC
* **
57026283 TAATTAAAATTTTTAAAAATTTCG-AGAGTT
1 TAATTAAAATTTTTAAAAATTTAGTAGAACT
* *
57026313 TAATTAAAATTTTTGAAACTTTAGTAGAACT
1 TAATTAAAATTTTTAAAAATTTAGTAGAACT
*
57026344 TGATTAAAA-TTTTAAAAATT
1 TAATTAAAATTTTTAAAAATT
57026364 CTTGGAGAGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
30 30 0.71
31 12 0.29
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.43
Consensus pattern (31 bp):
TAATTAAAATTTTTAAAAATTTAGTAGAACT
Found at i:57031488 original size:17 final size:18
Alignment explanation
Indices: 57031466--57031507 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
57031456 GCAAATACAT
* *
57031466 AATAAAAG-AAATCATCA
1 AATAAAAGTAAATAAACA
57031483 AATAAAAGTAAATAAACA
1 AATAAAAGTAAATAAACA
57031501 AATAAAA
1 AATAAAA
57031508 ATTAAAGCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.71, C:0.07, G:0.05, T:0.17
Consensus pattern (18 bp):
AATAAAAGTAAATAAACA
Found at i:57031864 original size:3 final size:3
Alignment explanation
Indices: 57031856--57031908 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
57031846 AATAAATAGG
57031856 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
57031904 TAA TA
1 TAA TA
57031909 GTAAAGATAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:57033970 original size:54 final size:52
Alignment explanation
Indices: 57033696--57034256 Score: 489
Period size: 51 Copynumber: 10.9 Consensus size: 52
57033686 GAGCCAGCAG
* * * * * *
57033696 CAGCATC-GACCTCCTCGAGAAGGTTATCAGAGCTCTGTTGATC-TTCAACAA
1 CAGCATCAG-CCTCCTCGGGAAAGTTATCAGAGTTCCGATCATCTTTCAACAA
* * * * *
57033747 CAGCATCGGCCTCCTCTGGAAACTTATAAGAGTTCCGATCAT-ATTCAACAA
1 CAGCATCAGCCTCCTCGGGAAAGTTATCAGAGTTCCGATCATCTTTCAACAA
* * * *
57033798 CAGCATCCA-CCTCCTCGAGATATTTATCAAAGTTCCGATCATC-TTCAACAA
1 CAGCAT-CAGCCTCCTCGGGAAAGTTATCAGAGTTCCGATCATCTTTCAACAA
* * * * * *
57033849 CAGCATCGGCCTCCTCGGGAAACTTATAAGAGCTCAGATCAT-ATTCAACAA
1 CAGCATCAGCCTCCTCGGGAAAGTTATCAGAGTTCCGATCATCTTTCAACAA
*
57033900 CAGCATCAGCCTCCTCGGGAGAGTTATCAGAGTTCCGATCATCTTCATCAACAA
1 CAGCATCAGCCTCCTCGGGAAAGTTATCAGAGTTCCGATCATCTT--TCAACAA
*
57033954 CAGCGTCAGCCTCCTCGGGAAAGTTATCAGAGTTCCGATCATCTTCATCAACAA
1 CAGCATCAGCCTCCTCGGGAAAGTTATCAGAGTTCCGATCATCTT--TCAACAA
*
57034008 CAG-AGTCAGCCTCCTCCGGAAAGTTATCAGAGTTCCGATCAT-TTTCAACAA
1 CAGCA-TCAGCCTCCTCGGGAAAGTTATCAGAGTTCCGATCATCTTTCAACAA
* * * * *
57034059 CAGCAAT-ATCAC-CCTCGAGAAAGTTATCAG-GATTCGGAACATC-TTCAACAG
1 CAGC-ATCAGC-CTCCTCGGGAAAGTTATCAGAG-TTCCGATCATCTTTCAACAA
* * * * *
57034110 CAGCATCGGCCACCTCGAGAAAGTTATCAGTGTTCCAATCATC-TTCAACAA
1 CAGCATCAGCCTCCTCGGGAAAGTTATCAGAGTTCCGATCATCTTTCAACAA
* *
57034161 CAGC-TACAGCCT--TC-GGAAAGTTATCATCAGAGTTTCAATCATC-TTCAACAGCA
1 CAGCAT-CAGCCTCCTCGGGAAAG-T-T-ATCAGAGTTCCGATCATCTTTCAACA--A
*
57034214 CCAGCATCAG---CCTCGGGAAAGTTATCAGAGCTCCGATCATCTT
1 -CAGCATCAGCCTCCTCGGGAAAGTTATCAGAGTTCCGATCATCTT
57034257 CCTCCTCGAG
Statistics
Matches: 425, Mismatches: 55, Indels: 59
0.79 0.10 0.11
Matches are distributed among these distances:
48 5 0.01
49 3 0.01
50 7 0.02
51 283 0.67
52 8 0.02
53 7 0.02
54 111 0.26
55 1 0.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24
Consensus pattern (52 bp):
CAGCATCAGCCTCCTCGGGAAAGTTATCAGAGTTCCGATCATCTTTCAACAA
Found at i:57034271 original size:36 final size:36
Alignment explanation
Indices: 57034224--57034293 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
57034214 CCAGCATCAG
* **
57034224 CCTCGGGAAAGTTATCAGAGCT-CCGATCATCTTCCT
1 CCTCGAGAAAGTTATCA-AAATGCCGATCATCTTCCT
57034260 CCTCGAGAAAGTTATCAAAATGCCGATCATCTTC
1 CCTCGAGAAAGTTATCAAAATGCCGATCATCTTC
57034294 AGCAACAGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 2 0.07
36 28 0.93
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (36 bp):
CCTCGAGAAAGTTATCAAAATGCCGATCATCTTCCT
Found at i:57036281 original size:6 final size:6
Alignment explanation
Indices: 57036274--57036308 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
57036264 GTAATTTGTG
* *
57036274 TGTGTG TGTGTT TGTGTA TGTGTA TGTGTA TGTGT
1 TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGT
57036309 GTATAATAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.09, C:0.00, G:0.37, T:0.54
Consensus pattern (6 bp):
TGTGTA
Found at i:57037529 original size:13 final size:13
Alignment explanation
Indices: 57037511--57037572 Score: 54
Period size: 13 Copynumber: 4.8 Consensus size: 13
57037501 TTCTTCATTA
57037511 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
*
57037524 CTTTTGAGAAGTG
1 CTTTTGAAAAGTG
* * * *
57037537 CTGTGGAAAAATA
1 CTTTTGAAAAGTG
*
57037550 CTTTTGAGAAGTTG
1 CTTTTGAAAAG-TG
57037564 -TTTTGAAAA
1 CTTTTGAAAA
57037573 TTTTGAGTGT
Statistics
Matches: 36, Mismatches: 12, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
13 35 0.97
14 1 0.03
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.37
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:57037571 original size:26 final size:26
Alignment explanation
Indices: 57037511--57037572 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
57037501 TTCTTCATTA
* *
57037511 CTTTTGAAAAGTGCTTTTGAGAAGTG
1 CTTTTGAAAAATACTTTTGAGAAGTG
* *
57037537 CTGTGGAAAAATACTTTTGAGAAGTTG
1 CTTTTGAAAAATACTTTTGAGAAG-TG
57037564 -TTTTGAAAA
1 CTTTTGAAAA
57037573 TTTTGAGTGT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
26 27 0.93
27 2 0.07
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.37
Consensus pattern (26 bp):
CTTTTGAAAAATACTTTTGAGAAGTG
Found at i:57039867 original size:27 final size:27
Alignment explanation
Indices: 57039837--57039888 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
57039827 AAGACAATGA
57039837 AAGAAAGGAAGATTGAAACAAGAAAGC
1 AAGAAAGGAAGATTGAAACAAGAAAGC
57039864 AAGAAAGGAAGATTGAAACAAGAAA
1 AAGAAAGGAAGATTGAAACAAGAAA
57039889 AAAAGCCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.62, C:0.06, G:0.25, T:0.08
Consensus pattern (27 bp):
AAGAAAGGAAGATTGAAACAAGAAAGC
Done.