Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
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: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 91 of 210
Found at i:31391516 original size:11 final size:11
Alignment explanation
Indices: 31391435--31391483 Score: 80
Period size: 11 Copynumber: 4.4 Consensus size: 11
31391425 ATTTGAAAAG
31391435 AAAAAAATTGA
1 AAAAAAATTGA
*
31391446 AAAACAATTTGA
1 AAAA-AAATTGA
31391458 AAAAAAATTGA
1 AAAAAAATTGA
31391469 AAAAAAATTGA
1 AAAAAAATTGA
31391480 AAAA
1 AAAA
31391484 TAGTAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
11 25 0.71
12 10 0.29
ACGTcount: A:0.71, C:0.02, G:0.08, T:0.18
Consensus pattern (11 bp):
AAAAAAATTGA
Found at i:31391547 original size:74 final size:75
Alignment explanation
Indices: 31391450--31391598 Score: 291
Period size: 74 Copynumber: 2.0 Consensus size: 75
31391440 AATTGAAAAA
31391450 CAATTTGAAAAAAAATTGAAAAAAAATTGAAAAATAGTAAAAAAATTAGACAAAAAAAATGAAAA
1 CAATTTGAAAAAAAATTGAAAAAAAATTGAAAAATAGTAAAAAAATTAGACAAAAAAAATGAAAA
31391515 AATGACTTTT
66 AATGACTTTT
31391525 CAATTTG-AAAAAAATTGAAAAAAAATTGAAAAATAGTAAAAAAATTAGACAAAAAAAATGAAAA
1 CAATTTGAAAAAAAATTGAAAAAAAATTGAAAAATAGTAAAAAAATTAGACAAAAAAAATGAAAA
31391589 AATGACTTTT
66 AATGACTTTT
31391599 GAAAAAAAAT
Statistics
Matches: 74, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
74 67 0.91
75 7 0.09
ACGTcount: A:0.64, C:0.04, G:0.09, T:0.23
Consensus pattern (75 bp):
CAATTTGAAAAAAAATTGAAAAAAAATTGAAAAATAGTAAAAAAATTAGACAAAAAAAATGAAAA
AATGACTTTT
Found at i:31391558 original size:19 final size:19
Alignment explanation
Indices: 31391534--31391570 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
31391524 TCAATTTGAA
*
31391534 AAAAATTGAAAAAAAATTG
1 AAAAATAGAAAAAAAATTG
*
31391553 AAAAATAGTAAAAAAATT
1 AAAAATAGAAAAAAAATT
31391571 AGACAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.08, T:0.22
Consensus pattern (19 bp):
AAAAATAGAAAAAAAATTG
Found at i:31391590 original size:11 final size:11
Alignment explanation
Indices: 31391532--31391557 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
31391522 TTTCAATTTG
31391532 AAAAAAATTGA
1 AAAAAAATTGA
31391543 AAAAAAATTGA
1 AAAAAAATTGA
31391554 AAAA
1 AAAA
31391558 TAGTAAAAAA
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:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (11 bp):
AAAAAAATTGA
Found at i:31400393 original size:30 final size:30
Alignment explanation
Indices: 31400350--31400426 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 30
31400340 AAAAGCGCGC
* * * *
31400350 CTAGCTGGTCGCGCTTTCTGGAAATCTCAT
1 CTAGCAGGACGCGCTTTCTAGAAAGCTCAT
*
31400380 CTAGCAGGACGCGCTTTCTAGAAAGCTTAT
1 CTAGCAGGACGCGCTTTCTAGAAAGCTCAT
*
31400410 CCAGCAGGACGCG-TTTC
1 CTAGCAGGACGCGCTTTC
31400427 CCTCAACGGT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 4 0.10
30 37 0.90
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27
Consensus pattern (30 bp):
CTAGCAGGACGCGCTTTCTAGAAAGCTCAT
Found at i:31400592 original size:12 final size:10
Alignment explanation
Indices: 31400565--31400612 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
31400555 TCCTTCTATC
31400565 AACTCTCTCA
1 AACTCTCTCA
31400575 AACTCTCTCA
1 AACTCTCTCA
* *
31400585 AACCCTCT-T
1 AACTCTCTCA
*
31400594 AAGTCTCTC-
1 AACTCTCTCA
31400603 AACTCTCTCA
1 AACTCTCTCA
31400613 TTTTAAAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
9 14 0.45
10 17 0.55
ACGTcount: A:0.27, C:0.40, G:0.02, T:0.31
Consensus pattern (10 bp):
AACTCTCTCA
Found at i:31400609 original size:9 final size:9
Alignment explanation
Indices: 31400563--31400612 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
31400553 CATCCTTCTA
31400563 TCAACTCTC
1 TCAACTCTC
31400572 TCAAACTCTC
1 TC-AACTCTC
*
31400582 TCAAACCCTC
1 TC-AACTCTC
* *
31400592 TTAAGTCTC
1 TCAACTCTC
31400601 TCAACTCTC
1 TCAACTCTC
31400610 TCA
1 TCA
31400613 TTTTAAAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
9 17 0.50
10 17 0.50
ACGTcount: A:0.26, C:0.40, G:0.02, T:0.32
Consensus pattern (9 bp):
TCAACTCTC
Found at i:31414463 original size:27 final size:28
Alignment explanation
Indices: 31414423--31414476 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 28
31414413 CCAATGACTC
*
31414423 GGGGAATCATCACTTAGCAA-CCCCTTG
1 GGGGAATCAGCACTTAGCAATCCCCTTG
31414450 GGGGAATCAGCACTTAGCAATCCCCTT
1 GGGGAATCAGCACTTAGCAATCCCCTT
31414477 CACATTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.26, C:0.30, G:0.22, T:0.22
Consensus pattern (28 bp):
GGGGAATCAGCACTTAGCAATCCCCTTG
Found at i:31414528 original size:103 final size:103
Alignment explanation
Indices: 31414347--31415035 Score: 1254
Period size: 103 Copynumber: 6.7 Consensus size: 103
31414337 CCAGTGATTC
* * * *
31414347 GGGGAATCAGCACTTAGCAA-CCCCTTTCACATTCAAAGATATGGTGGAATCAACACTTAGCAAC
1 GGGGAATCAGCACTTAGCAACCCCCTTT-ATATTTAAAGATACGGTGGAATCAGCACTTAGCAAC
* *
31414411 CACCAATGACTCGGGGAATCATCACTTAGCAACCCCTTG
65 CACCAATGAATCGGGGAATCAACACTTAGCAACCCCTTG
* * *
31414450 GGGGAATCAGCACTTAGCAATCCCCTTCACATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTTATATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
31414515 ACCAATGAATCGGGGAATCAACACTTAGCAACCCCTTG
66 ACCAATGAATCGGGGAATCAACACTTAGCAACCCCTTG
* * *
31414553 GGGGAATCAGCACTTAGCAATCCCCTTCACATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTTATATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
31414618 ACCAATGAATCGGGGAATCAACACTTAGCAACCCCTTG
66 ACCAATGAATCGGGGAATCAACACTTAGCAACCCCTTG
31414656 GGGGAATCAGCACTTAGCAACCCCCTTTATATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTTATATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
31414721 ACCAATGAATCGGGGAATCAACACTTAGCAACCCCTTG
66 ACCAATGAATCGGGGAATCAACACTTAGCAACCCCTTG
31414759 GGGGAATCAGCACTTAGCAACCCCCTTTATATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTTATATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
31414824 ACCAATGAATCGGGGAATCAACACTTAGCAACCCCTTG
66 ACCAATGAATCGGGGAATCAACACTTAGCAACCCCTTG
31414862 GGGGAATCAGCACTTAGCAACCCCCTTTATATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTTATATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
31414927 ACCAATGAATCGGGGAATCAACACTTAGCAACCCCTTG
66 ACCAATGAATCGGGGAATCAACACTTAGCAACCCCTTG
31414965 GGGGAATCAGCACTTAGCAACCCCCTTTATATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTTATATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
31415030 ACCAAT
66 ACCAAT
31415036 TAGAACTCAA
Statistics
Matches: 576, Mismatches: 9, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
103 570 0.99
104 6 0.01
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (103 bp):
GGGGAATCAGCACTTAGCAACCCCCTTTATATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
ACCAATGAATCGGGGAATCAACACTTAGCAACCCCTTG
Found at i:31414566 original size:27 final size:28
Alignment explanation
Indices: 31414526--31414579 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 28
31414516 CCAATGAATC
31414526 GGGGAATCAACACTTAGCAA-CCCCTTG
1 GGGGAATCAACACTTAGCAATCCCCTTG
*
31414553 GGGGAATCAGCACTTAGCAATCCCCTT
1 GGGGAATCAACACTTAGCAATCCCCTT
31414580 CACATTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (28 bp):
GGGGAATCAACACTTAGCAATCCCCTTG
Found at i:31415126 original size:11 final size:12
Alignment explanation
Indices: 31415098--31415131 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
31415088 GCCCAAACGT
31415098 CGAAATTTTTGAA
1 CGAAATTTTT-AA
31415111 CGAAATTTTT-A
1 CGAAATTTTTAA
31415122 CGAAATTTTT
1 CGAAATTTTT
31415132 CCGTAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
13 10 0.48
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (12 bp):
CGAAATTTTTAA
Found at i:31419963 original size:21 final size:20
Alignment explanation
Indices: 31419923--31419963 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
31419913 AACCCTAACC
* *
31419923 CTAACAAAATAAAAATCCTA
1 CTAAAAAAATAAAAACCCTA
31419943 CTAAAAAAATAAAAAACCCTA
1 CTAAAAAAAT-AAAAACCCTA
31419964 ACCCTGGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.63, C:0.20, G:0.00, T:0.17
Consensus pattern (20 bp):
CTAAAAAAATAAAAACCCTA
Found at i:31426502 original size:7 final size:7
Alignment explanation
Indices: 31426490--31426528 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
31426480 AGTCGATTGA
31426490 TATTTAG
1 TATTTAG
31426497 TATTTAG
1 TATTTAG
*
31426504 TATTTAA
1 TATTTAG
31426511 TATTTAG
1 TATTTAG
31426518 TATTTAG
1 TATTTAG
31426525 TATT
1 TATT
31426529 ATAAATATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (7 bp):
TATTTAG
Found at i:31426513 original size:21 final size:21
Alignment explanation
Indices: 31426489--31426528 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
31426479 TAGTCGATTG
31426489 ATATTTAGTATTTAGTATTTA
1 ATATTTAGTATTTAGTATTTA
31426510 ATATTTAGTATTTAGTATT
1 ATATTTAGTATTTAGTATT
31426529 ATAAATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (21 bp):
ATATTTAGTATTTAGTATTTA
Found at i:31427719 original size:25 final size:25
Alignment explanation
Indices: 31427691--31427738 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
31427681 TATTTTGATA
31427691 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
*
31427716 TTATTTTATGTAATAAAATAGAA
1 TTATTTGATGTAATAAAATAGAA
31427739 ATTTTTTCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.42
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:31427726 original size:70 final size:71
Alignment explanation
Indices: 31427646--31427779 Score: 200
Period size: 70 Copynumber: 1.9 Consensus size: 71
31427636 TATTTTGATA
31427646 TTATTTTATGTAAAAAAAATAGAAA-TGTTTAAAGCTATTTTGATATTATTTGATGTAA-TAAAA
1 TTATTTTATGT-AAAAAAATAGAAATTGTTTAAAGCTATTTTGATATTATTTGATGTAATTAAAA
31427709 TAGAAGT
65 TAGAAGT
* * ** *
31427716 TTATTTTATGTAATAAAATAGAAATTTTTTCGAGTTATTTTGATATTATTTGATGTAATTAAAA
1 TTATTTTATGTAAAAAAATAGAAATTGTTTAAAGCTATTTTGATATTATTTGATGTAATTAAAA
31427780 ACCCTACCCC
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
69 12 0.21
70 40 0.70
71 5 0.09
ACGTcount: A:0.41, C:0.01, G:0.12, T:0.46
Consensus pattern (71 bp):
TTATTTTATGTAAAAAAATAGAAATTGTTTAAAGCTATTTTGATATTATTTGATGTAATTAAAAT
AGAAGT
Found at i:31427819 original size:29 final size:29
Alignment explanation
Indices: 31427773--31427873 Score: 175
Period size: 29 Copynumber: 3.5 Consensus size: 29
31427763 ATTTGATGTA
*
31427773 ATTAAAAACCCTACCCCTAACCTAATTTG
1 ATTAAAAACCCTAACCCTAACCTAATTTG
31427802 ATTAAAAACCCTAACCCTAACCTAATTTG
1 ATTAAAAACCCTAACCCTAACCTAATTTG
* *
31427831 ATTAAAAACCTTAACCCTAACCTAATTTA
1 ATTAAAAACCCTAACCCTAACCTAATTTG
31427860 ATTAAAAACCCTAA
1 ATTAAAAACCCTAA
31427874 NNNNNNNNNN
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 68 1.00
ACGTcount: A:0.44, C:0.27, G:0.02, T:0.28
Consensus pattern (29 bp):
ATTAAAAACCCTAACCCTAACCTAATTTG
Found at i:31428121 original size:46 final size:46
Alignment explanation
Indices: 31428054--31428147 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
31428044 NNNNNNNNNN
*
31428054 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTAA
1 TAATTTTACATAATTTGATAATTTTACTAACCAGTAATACAATTAA
*
31428100 TAATTTTATATAATTTGATAATTTTACTAACCAGTAATACAATTAA
1 TAATTTTACATAATTTGATAATTTTACTAACCAGTAATACAATTAA
31428146 TA
1 TA
31428148 CAATTTTTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.44
Consensus pattern (46 bp):
TAATTTTACATAATTTGATAATTTTACTAACCAGTAATACAATTAA
Found at i:31428153 original size:30 final size:30
Alignment explanation
Indices: 31428119--31428177 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
31428109 ATAATTTGAT
31428119 AATTTTACTAACCAGTAAT-ACAATTAATAC
1 AATTTT-CTAACCAGTAATAACAATTAATAC
* * *
31428149 AATTTTTTAACTAGTAGTAACAATTAATA
1 AATTTTCTAACCAGTAATAACAATTAATA
31428178 ATTTTATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.46, C:0.12, G:0.05, T:0.37
Consensus pattern (30 bp):
AATTTTCTAACCAGTAATAACAATTAATAC
Found at i:31428199 original size:76 final size:76
Alignment explanation
Indices: 31428092--31428306 Score: 430
Period size: 76 Copynumber: 2.8 Consensus size: 76
31428082 AACCATTAAT
31428092 ACAATTAATAATTTTATATAATTTGATAATTTTACTAACCAGTAATACAATTAATACAATTTTTT
1 ACAATTAATAATTTTATATAATTTGATAATTTTACTAACCAGTAATACAATTAATACAATTTTTT
31428157 AACTAGTAGTA
66 AACTAGTAGTA
31428168 ACAATTAATAATTTTATATAATTTGATAATTTTACTAACCAGTAATACAATTAATACAATTTTTT
1 ACAATTAATAATTTTATATAATTTGATAATTTTACTAACCAGTAATACAATTAATACAATTTTTT
31428233 AACTAGTAGTA
66 AACTAGTAGTA
31428244 ACAATTAATAATTTTATATAATTTGATAATTTTACTAACCAGTAATACAATTAATACAATTTT
1 ACAATTAATAATTTTATATAATTTGATAATTTTACTAACCAGTAATACAATTAATACAATTTT
31428307 ATTATCAATT
Statistics
Matches: 139, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 139 1.00
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (76 bp):
ACAATTAATAATTTTATATAATTTGATAATTTTACTAACCAGTAATACAATTAATACAATTTTTT
AACTAGTAGTA
Found at i:31428229 original size:30 final size:30
Alignment explanation
Indices: 31428195--31428253 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
31428185 ATAATTTGAT
31428195 AATTTTACTAACCAGTAAT-ACAATTAATAC
1 AATTTT-CTAACCAGTAATAACAATTAATAC
* * *
31428225 AATTTTTTAACTAGTAGTAACAATTAATA
1 AATTTTCTAACCAGTAATAACAATTAATA
31428254 ATTTTATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.46, C:0.12, G:0.05, T:0.37
Consensus pattern (30 bp):
AATTTTCTAACCAGTAATAACAATTAATAC
Found at i:31431616 original size:126 final size:125
Alignment explanation
Indices: 31431311--31431662 Score: 553
Period size: 126 Copynumber: 2.8 Consensus size: 125
31431301 CCCAAACATG
* * *
31431311 CTACTGTAGTAAAAGCGTGTCCAAGAGGCCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGCCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* * *
31431376 TAGAAGCGATTTTATACTATTTGCTCAGAAAAGT-AAAAAAAAATTATTTCTTACATGCT
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATACC
*
31431435 CTACTGTAGCAAAAGCGCGTCCACGAGGCCGCGATTTCACAAATTCTTCTTAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGCCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* * *
31431500 TAGAAGCGATATTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTTCGTACC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAA-AATTATTTCTTACATACC
* *
31431561 CTACTGTAGCAAAAGCGCGTCCACGAGGCCACGATTTCACAAATTTTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGCCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
** *
31431626 TAGAAGCGATTTTATACTATTTTATCAGAAACATCAA
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA
31431663 CTCGAAATTA
Statistics
Matches: 209, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
124 93 0.44
125 7 0.03
126 109 0.52
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.30
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGCCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATACC
Found at i:31435295 original size:31 final size:31
Alignment explanation
Indices: 31435260--31435327 Score: 111
Period size: 30 Copynumber: 2.2 Consensus size: 31
31435250 TATAGGGGTC
31435260 ACACGGCCATGTGGGCTTTTGAAGTAGGGAA
1 ACACGGCCATGTGGGCTTTTGAAGTAGGGAA
* *
31435291 ACACGG-CGTGTGGGCTTTTGAAGTAGGGAC
1 ACACGGCCATGTGGGCTTTTGAAGTAGGGAA
31435321 ACACGGC
1 ACACGGC
31435328 TGTGTCTCAG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 28 0.82
31 6 0.18
ACGTcount: A:0.24, C:0.19, G:0.37, T:0.21
Consensus pattern (31 bp):
ACACGGCCATGTGGGCTTTTGAAGTAGGGAA
Found at i:31437751 original size:33 final size:35
Alignment explanation
Indices: 31437664--31437755 Score: 98
Period size: 33 Copynumber: 2.7 Consensus size: 35
31437654 ATATACACTA
*
31437664 CCATGGTCCAATCATGGTCTTATGTTTGAAAAATTG
1 CCATGGTCCAACCATGGTCTTATG-TTGAAAAATTG
* * * * *
31437700 CCATAGCCCAGCTATGGTCTTATG-T-AAACATTG
1 CCATGGTCCAACCATGGTCTTATGTTGAAAAATTG
*
31437733 CCATGGTCCAACCGTGGTCTTAT
1 CCATGGTCCAACCATGGTCTTAT
31437756 ACATTTTTAT
Statistics
Matches: 45, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
33 25 0.56
34 1 0.02
36 19 0.42
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.33
Consensus pattern (35 bp):
CCATGGTCCAACCATGGTCTTATGTTGAAAAATTG
Found at i:31439146 original size:26 final size:28
Alignment explanation
Indices: 31439117--31439171 Score: 69
Period size: 26 Copynumber: 2.0 Consensus size: 28
31439107 AACATGGGAT
* *
31439117 ATAAGAAATTAACATCA-AA-ATAAAAA
1 ATAAAAAATCAACATCAGAATATAAAAA
*
31439143 ATAAAAAATCAACATTAGAATATAAAAA
1 ATAAAAAATCAACATCAGAATATAAAAA
31439171 A
1 A
31439172 AATCACTAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 14 0.58
27 2 0.08
28 8 0.33
ACGTcount: A:0.69, C:0.07, G:0.04, T:0.20
Consensus pattern (28 bp):
ATAAAAAATCAACATCAGAATATAAAAA
Found at i:31442590 original size:40 final size:40
Alignment explanation
Indices: 31442546--31442665 Score: 161
Period size: 40 Copynumber: 3.0 Consensus size: 40
31442536 TCAAATACAT
* *
31442546 CCTTTTAATTTGATATCCTTTTTGGATACATCCTTTTCAA
1 CCTTTTAATTTGATATCCTTTTCGAATACATCCTTTTCAA
** *
31442586 CCTTTTCGTTTGATATTCTTTTCGAATACATCCTTTTCAA
1 CCTTTTAATTTGATATCCTTTTCGAATACATCCTTTTCAA
* *
31442626 CC-TTTAAGTCTGATATCCTTTTCAAATACATCCTTTTCAA
1 CCTTTTAA-TTTGATATCCTTTTCGAATACATCCTTTTCAA
31442666 GTATATTACT
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
39 3 0.04
40 66 0.96
ACGTcount: A:0.23, C:0.23, G:0.07, T:0.47
Consensus pattern (40 bp):
CCTTTTAATTTGATATCCTTTTCGAATACATCCTTTTCAA
Found at i:31445874 original size:18 final size:18
Alignment explanation
Indices: 31445851--31445893 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
31445841 CAAGGTCACG
*
31445851 ATCAATAGTGTCACTATC
1 ATCAATAGCGTCACTATC
*
31445869 ATCAATAGCGTCATTATC
1 ATCAATAGCGTCACTATC
*
31445887 ATTAATA
1 ATCAATA
31445894 TTGATATCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (18 bp):
ATCAATAGCGTCACTATC
Found at i:31450217 original size:12 final size:12
Alignment explanation
Indices: 31450200--31450225 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
31450190 TTTATAATGC
31450200 TATTGTTATTAT
1 TATTGTTATTAT
31450212 TATTGTTATTAT
1 TATTGTTATTAT
31450224 TA
1 TA
31450226 CTATTATTAA
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:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (12 bp):
TATTGTTATTAT
Found at i:31451774 original size:33 final size:32
Alignment explanation
Indices: 31451735--31451854 Score: 106
Period size: 33 Copynumber: 3.8 Consensus size: 32
31451725 CCAACTTAAG
* *
31451735 AAAAAGTGTCAAGTTTAGGTACTAAATTAGGA
1 AAAAAATGTCAAGTTTAGGTACCAAATTAGGA
* *
31451767 AAAAAAGTATCAAGTTTGGGTACCAAATT-GGA
1 AAAAAA-TGTCAAGTTTAGGTACCAAATTAGGA
* * *
31451799 CAACAAA----AAGTTTAAGTACCAAATTAAGA
1 -AAAAAATGTCAAGTTTAGGTACCAAATTAGGA
* *
31451828 AAAAAATGTCAAGTTCAGATACCAAAT
1 AAAAAATGTCAAGTTTAGGTACCAAAT
31451855 ATTATATTAA
Statistics
Matches: 69, Mismatches: 12, Indels: 14
0.73 0.13 0.15
Matches are distributed among these distances:
28 21 0.30
29 2 0.03
32 22 0.32
33 24 0.35
ACGTcount: A:0.48, C:0.11, G:0.17, T:0.24
Consensus pattern (32 bp):
AAAAAATGTCAAGTTTAGGTACCAAATTAGGA
Found at i:31463182 original size:41 final size:41
Alignment explanation
Indices: 31463125--31463748 Score: 1203
Period size: 41 Copynumber: 15.2 Consensus size: 41
31463115 NNNNNNNNNN
31463125 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCA
1 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCA
31463166 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCA
1 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCA
31463207 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCA
1 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCA
31463248 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCA
1 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCA
31463289 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCA
1 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCA
31463330 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCA
1 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCA
31463371 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCA
1 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCA
31463412 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCA
1 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCA
31463453 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCA
1 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCA
31463494 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCA
1 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCA
31463535 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCA
1 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCA
31463576 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCA
1 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCA
31463617 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCA
1 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCA
*
31463658 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCG
1 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCA
* * *
31463699 GTGATCTGAATCAGGCTTTAAGCCTAACAAGCTAAGTGCCA
1 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCA
31463740 GTGAATCTG
1 GTG-ATCTG
31463749 TTTAAATTAA
Statistics
Matches: 577, Mismatches: 5, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
41 572 0.99
42 5 0.01
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (41 bp):
GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCA
Found at i:31468139 original size:57 final size:57
Alignment explanation
Indices: 31468047--31468156 Score: 195
Period size: 57 Copynumber: 1.9 Consensus size: 57
31468037 GTTAATCATA
*
31468047 AAAAGGTTATGTCGAATCATGATCTCTTGTGACTTAGGTAGCAATGATGCATTTCAC
1 AAAAGGTTATGTCGAATCATGATCTCTTGTAACTTAGGTAGCAATGATGCATTTCAC
31468104 AAAAGGTTATGTCGAATCATGA-CTTCTTGTAACTTAGGTAGCAATGATGCATT
1 AAAAGGTTATGTCGAATCATGATC-TCTTGTAACTTAGGTAGCAATGATGCATT
31468157 GCTAGATGCC
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
56 1 0.02
57 50 0.98
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.34
Consensus pattern (57 bp):
AAAAGGTTATGTCGAATCATGATCTCTTGTAACTTAGGTAGCAATGATGCATTTCAC
Found at i:31472692 original size:37 final size:37
Alignment explanation
Indices: 31472589--31472971 Score: 702
Period size: 37 Copynumber: 10.4 Consensus size: 37
31472579 TACGTATGAT
* *
31472589 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
31472624 TAGC-TATCACTTTGTTTC-TGATCAGATAAGTGTAGC
1 CA-CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
31472660 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
31472697 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
31472734 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
31472771 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
31472808 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
31472845 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
31472882 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
31472919 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
31472956 CACTTATCACTTTGTT
1 CACTTATCACTTTGTT
31472972 CTAAATGTGT
Statistics
Matches: 340, Mismatches: 3, Indels: 8
0.97 0.01 0.02
Matches are distributed among these distances:
35 8 0.02
36 37 0.11
37 295 0.87
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:31480382 original size:65 final size:65
Alignment explanation
Indices: 31480278--31480399 Score: 244
Period size: 65 Copynumber: 1.9 Consensus size: 65
31480268 ACATTCCAGC
31480278 AGTGCAGTGTCCTGTGGTGGCTGAGAGGGACTGCCTTTGTCTTCCTCTTTTCGTCTCAATTCAAG
1 AGTGCAGTGTCCTGTGGTGGCTGAGAGGGACTGCCTTTGTCTTCCTCTTTTCGTCTCAATTCAAG
31480343 AGTGCAGTGTCCTGTGGTGGCTGAGAGGGACTGCCTTTGTCTTCCTCTTTTCGTCTC
1 AGTGCAGTGTCCTGTGGTGGCTGAGAGGGACTGCCTTTGTCTTCCTCTTTTCGTCTC
31480400 TACTCAGTCG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 57 1.00
ACGTcount: A:0.11, C:0.24, G:0.29, T:0.36
Consensus pattern (65 bp):
AGTGCAGTGTCCTGTGGTGGCTGAGAGGGACTGCCTTTGTCTTCCTCTTTTCGTCTCAATTCAAG
Found at i:31481874 original size:8 final size:7
Alignment explanation
Indices: 31481861--31481946 Score: 73
Period size: 6 Copynumber: 13.3 Consensus size: 7
31481851 TTTCCCCAGT
31481861 TTTATTTA
1 TTTA-TTA
31481869 TTTATTA
1 TTTATTA
*
31481876 TTTTATTG
1 -TTTATTA
*
31481884 TTTTTTA
1 TTTATTA
31481891 -TTATTA
1 TTTATTA
31481897 -TTATTA
1 TTTATTA
31481903 -TTATTA
1 TTTATTA
31481909 -TTATTA
1 TTTATTA
31481915 -TTATTA
1 TTTATTA
31481921 -TTATTA
1 TTTATTA
31481927 -TTATTA
1 TTTATTA
31481933 -TTATTA
1 TTTATTA
31481939 -TTATTA
1 TTTATTA
31481945 TT
1 TT
31481947 CTGTTGTTCT
Statistics
Matches: 72, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
6 53 0.74
7 9 0.12
8 10 0.14
ACGTcount: A:0.28, C:0.00, G:0.01, T:0.71
Consensus pattern (7 bp):
TTTATTA
Found at i:31481894 original size:3 final size:3
Alignment explanation
Indices: 31481870--31481946 Score: 124
Period size: 3 Copynumber: 26.7 Consensus size: 3
31481860 TTTTATTTAT
*
31481870 TTA TTA TT- TTA TTG TT- TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
31481915 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
31481947 CTGTTGTTCT
Statistics
Matches: 71, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
2 6 0.08
3 65 0.92
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:31483632 original size:164 final size:165
Alignment explanation
Indices: 31483351--31483678 Score: 649
Period size: 164 Copynumber: 2.0 Consensus size: 165
31483341 TAAAAGTAAC
31483351 AAATAATAATATTTAAGCACCGTCCAAACTCCTTATGCAATGTTCTAAAACTACTAAAATAATAT
1 AAATAATAATATTTAAGCACCGTCCAAACTCCTTATGCAATGTTCTAAAACTACTAAAATAATAT
31483416 CCTAAAATGCAACTAAATTCACTTAAGTACAGACAATTGACCCAGCCTAAAGGTATGAATTATAA
66 CCTAAAATGCAACTAAATTCACTTAAGTACAGACAATTGACCCAGCCTAAAGGTATGAATTATAA
31483481 CTCTTTTCAAGAGTTATAAGTAATCGAGACAATTA
131 CTCTTTTCAAGAGTTATAAGTAATCGAGACAATTA
31483516 AAATAATAA-ATTTAAGCACCGTCCAAACTCCTTATGCAATGTTCTAAAACTACTAAAATAATAT
1 AAATAATAATATTTAAGCACCGTCCAAACTCCTTATGCAATGTTCTAAAACTACTAAAATAATAT
31483580 CCTAAAATGCAACTAAATTCACTTAAGTACAGACAATTGACCCAGCCTAAAGGTATGAATTATAA
66 CCTAAAATGCAACTAAATTCACTTAAGTACAGACAATTGACCCAGCCTAAAGGTATGAATTATAA
31483645 CTCTTTTCAAGAGTTATAAGTAATCGAGACAATT
131 CTCTTTTCAAGAGTTATAAGTAATCGAGACAATT
31483679 CTTGCTAATG
Statistics
Matches: 163, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
164 154 0.94
165 9 0.06
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.29
Consensus pattern (165 bp):
AAATAATAATATTTAAGCACCGTCCAAACTCCTTATGCAATGTTCTAAAACTACTAAAATAATAT
CCTAAAATGCAACTAAATTCACTTAAGTACAGACAATTGACCCAGCCTAAAGGTATGAATTATAA
CTCTTTTCAAGAGTTATAAGTAATCGAGACAATTA
Found at i:31484542 original size:8 final size:7
Alignment explanation
Indices: 31484529--31484614 Score: 73
Period size: 6 Copynumber: 13.3 Consensus size: 7
31484519 TTTCCCCAGT
31484529 TTTATTTA
1 TTTA-TTA
31484537 TTTATTA
1 TTTATTA
*
31484544 TTTTATTG
1 -TTTATTA
*
31484552 TTTTTTA
1 TTTATTA
31484559 -TTATTA
1 TTTATTA
31484565 -TTATTA
1 TTTATTA
31484571 -TTATTA
1 TTTATTA
31484577 -TTATTA
1 TTTATTA
31484583 -TTATTA
1 TTTATTA
31484589 -TTATTA
1 TTTATTA
31484595 -TTATTA
1 TTTATTA
31484601 -TTATTA
1 TTTATTA
31484607 -TTATTA
1 TTTATTA
31484613 TT
1 TT
31484615 CTGTTGTTCT
Statistics
Matches: 72, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
6 53 0.74
7 9 0.12
8 10 0.14
ACGTcount: A:0.28, C:0.00, G:0.01, T:0.71
Consensus pattern (7 bp):
TTTATTA
Found at i:31484562 original size:3 final size:3
Alignment explanation
Indices: 31484538--31484614 Score: 124
Period size: 3 Copynumber: 26.7 Consensus size: 3
31484528 TTTTATTTAT
*
31484538 TTA TTA TT- TTA TTG TT- TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
31484583 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
31484615 CTGTTGTTCT
Statistics
Matches: 71, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
2 6 0.08
3 65 0.92
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:31488137 original size:31 final size:33
Alignment explanation
Indices: 31488075--31488137 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 33
31488065 CTTTACCCAA
*
31488075 TTTTATTTATTTATTTATTATTTTATTGTTCTT
1 TTTTATTTATTTATTTATTATTTTATCGTTCTT
* *
31488108 TTTTCTTTA-TTA-TTATTATTTTGTCGTTCT
1 TTTTATTTATTTATTTATTATTTTATCGTTCT
31488138 CCTACTTTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 16 0.59
32 3 0.11
33 8 0.30
ACGTcount: A:0.16, C:0.06, G:0.05, T:0.73
Consensus pattern (33 bp):
TTTTATTTATTTATTTATTATTTTATCGTTCTT
Found at i:31489230 original size:22 final size:22
Alignment explanation
Indices: 31489175--31489232 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
31489165 TTTCTAAAAT
31489175 TATGTTATATGATAAGCTCTGA
1 TATGTTATATGATAAGCTCTGA
* * *
31489197 TACGTTACATGATATGCTCTGA
1 TATGTTATATGATAAGCTCTGA
*
31489219 TATGTAATATGATA
1 TATGTTATATGATA
31489233 CAAAATTTCG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (22 bp):
TATGTTATATGATAAGCTCTGA
Found at i:31490387 original size:17 final size:17
Alignment explanation
Indices: 31490367--31490400 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
31490357 CTTATTAATT
*
31490367 TTACTTTCAAATTATAA
1 TTACTTTCAAAATATAA
*
31490384 TTACTTTTAAAATATAA
1 TTACTTTCAAAATATAA
31490401 AAAAAAACAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (17 bp):
TTACTTTCAAAATATAA
Found at i:31491522 original size:13 final size:12
Alignment explanation
Indices: 31491504--31491546 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
31491494 TTTTTTAATG
31491504 TTTATAGTAATAT
1 TTTATAGTAA-AT
31491517 TTTATAGTAAAT
1 TTTATAGTAAAT
*
31491529 TTTAGTAATAAAAT
1 TTTA-TAGT-AAAT
31491543 TTTA
1 TTTA
31491547 GATGGTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 6 0.22
13 13 0.48
14 8 0.30
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (12 bp):
TTTATAGTAAAT
Found at i:31492656 original size:27 final size:27
Alignment explanation
Indices: 31492626--31492723 Score: 133
Period size: 27 Copynumber: 3.6 Consensus size: 27
31492616 TGTATGAGCT
* *
31492626 CTAGGTATGCGAACCCTTGTACGACCC
1 CTAGGTGTGCGAACCCTTGTACGAACC
* ***
31492653 CTAGGTGTGTGAACCCTTGTGTTAACC
1 CTAGGTGTGCGAACCCTTGTACGAACC
*
31492680 CTAAGTGTGCGAACCCTTGTACGAACC
1 CTAGGTGTGCGAACCCTTGTACGAACC
31492707 CTAGGTGTGCGAACCCT
1 CTAGGTGTGCGAACCCT
31492724 GATGTGCAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 59 1.00
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (27 bp):
CTAGGTGTGCGAACCCTTGTACGAACC
Found at i:31492694 original size:15 final size:14
Alignment explanation
Indices: 31492676--31492750 Score: 57
Period size: 14 Copynumber: 5.4 Consensus size: 14
31492666 CCCTTGTGTT
31492676 AACCCTAAGTGTGCG
1 AACCCTAA-TGTGCG
*
31492691 AACCCT--TGTACG
1 AACCCTAATGTGCG
*
31492703 AACCCTAGGTGTGCG
1 AACCCTA-ATGTGCG
* *
31492718 AACCCTGATGTGCA
1 AACCCTAATGTGCG
*
31492732 AACCC-ATCTGTGCG
1 AACCCTA-ATGTGCG
31492746 AACCC
1 AACCC
31492751 CCTTGTGCGA
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
12 11 0.23
14 20 0.42
15 17 0.35
ACGTcount: A:0.25, C:0.32, G:0.23, T:0.20
Consensus pattern (14 bp):
AACCCTAATGTGCG
Found at i:31492757 original size:14 final size:14
Alignment explanation
Indices: 31492740--31492771 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
31492730 CAAACCCATC
*
31492740 TGTGCGAACCCCCT
1 TGTGCGAACACCCT
31492754 TGTGCGAACACCCT
1 TGTGCGAACACCCT
31492768 TGTG
1 TGTG
31492772 GGAGTCCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.34, G:0.25, T:0.25
Consensus pattern (14 bp):
TGTGCGAACACCCT
Found at i:31492824 original size:16 final size:16
Alignment explanation
Indices: 31492782--31492826 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
31492772 GGAGTCCCTA
31492782 TAGGTTACGAACCTTG
1 TAGGTTACGAACCTTG
*
31492798 TA-GTATGCGAACCTTG
1 TAGGT-TACGAACCTTG
31492814 TAGGTTACGAACC
1 TAGGTTACGAACC
31492827 CTATATGACT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 2 0.08
16 21 0.84
17 2 0.08
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (16 bp):
TAGGTTACGAACCTTG
Found at i:31510033 original size:5 final size:5
Alignment explanation
Indices: 31510025--31510050 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
31510015 GAGATGGAAT
31510025 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
31510051 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:31510730 original size:30 final size:31
Alignment explanation
Indices: 31510691--31510750 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
31510681 AGAGGTGAGA
*
31510691 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
31510722 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
31510751 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:31510917 original size:9 final size:9
Alignment explanation
Indices: 31510903--31510939 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
31510893 TATAGTTTGA
31510903 TATTCGAAT
1 TATTCGAAT
31510912 TATTCGAAT
1 TATTCGAAT
*
31510921 TATTCGAGT
1 TATTCGAAT
31510930 TATTCGAAT
1 TATTCGAAT
31510939 T
1 T
31510940 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:31539422 original size:24 final size:23
Alignment explanation
Indices: 31539386--31539472 Score: 79
Period size: 23 Copynumber: 3.7 Consensus size: 23
31539376 TTTCTTTTAA
* * *
31539386 AATAATGCCTAATAAACCTGAAAT
1 AATAATACATAATAAATCT-AAAT
*
31539410 AATAATACATAATGAATCTAAA-
1 AATAATACATAATAAATCTAAAT
* *
31539432 AATAAATATATAATAAATCTAAGCT
1 AAT-AATACATAATAAATCTAA-AT
31539457 AATAATACATAA-AAAT
1 AATAATACATAATAAAT
31539473 TTATGATGCT
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
22 3 0.06
23 23 0.44
24 23 0.44
25 3 0.06
ACGTcount: A:0.57, C:0.10, G:0.05, T:0.28
Consensus pattern (23 bp):
AATAATACATAATAAATCTAAAT
Found at i:31539626 original size:19 final size:20
Alignment explanation
Indices: 31539604--31539641 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
31539594 ATATAAATAG
31539604 ATAAATAAAATAT-AATAAC
1 ATAAATAAAATATCAATAAC
* *
31539623 ATAATTACAATATCAATAA
1 ATAAATAAAATATCAATAA
31539642 GGCTAGTGGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (20 bp):
ATAAATAAAATATCAATAAC
Found at i:31540953 original size:18 final size:20
Alignment explanation
Indices: 31540930--31540967 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
31540920 ACTTTTAATA
31540930 ATTTTTG-TT-TTTATTTAT
1 ATTTTTGTTTATTTATTTAT
31540948 ATTTTTGTTTATTTATTTAT
1 ATTTTTGTTTATTTATTTAT
31540968 TTCTGATTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 2 0.11
20 9 0.50
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.76
Consensus pattern (20 bp):
ATTTTTGTTTATTTATTTAT
Found at i:31541754 original size:44 final size:44
Alignment explanation
Indices: 31541706--31541979 Score: 154
Period size: 44 Copynumber: 6.3 Consensus size: 44
31541696 AAAATTTCCA
* *
31541706 GGAGATAGGATTATCGGCTTCAATCTGCTCCACTACAACCTCAG
1 GGAGATAAGATTATCTGCTTCAATCTGCTCCACTACAACCTCAG
* * * *
31541750 GGAGATAAGATT-TGCCAT-CTTCGATCTG-TCCCACTGCAACTTTAG
1 GGAGATAAGATTAT--C-TGCTTCAATCTGCT-CCACTACAACCTCAG
* * * *
31541795 GGGGATAA-A--ACCTGCTTACTCAATCTACTCCACTGCAACCTCAG
1 GGAGATAAGATTATCTGC-T--TCAATCTGCTCCACTACAACCTCAG
* * * * * * * *
31541839 GGAGATAAG---ACCTGATGCGATCTACTCTACTGCAACTTCAG
1 GGAGATAAGATTATCTGCTTCAATCTGCTCCACTACAACCTCAG
* * * * * * *
31541880 AGAGATAAGATCCAT-TACTTTAATCCGCTCCACTACAACTTCAA
1 GGAGATAAGAT-TATCTGCTTCAATCTGCTCCACTACAACCTCAG
* * *
31541924 GGAGATAGGATTATCGGCTTCAATCTGCTCCACTACAACCTCAA
1 GGAGATAAGATTATCTGCTTCAATCTGCTCCACTACAACCTCAG
31541968 GGAGATAAGATT
1 GGAGATAAGATT
31541980 TATAATTTCC
Statistics
Matches: 175, Mismatches: 39, Indels: 32
0.71 0.16 0.13
Matches are distributed among these distances:
40 1 0.01
41 31 0.18
42 1 0.01
43 4 0.02
44 107 0.61
45 31 0.18
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (44 bp):
GGAGATAAGATTATCTGCTTCAATCTGCTCCACTACAACCTCAG
Found at i:31541868 original size:218 final size:218
Alignment explanation
Indices: 31541303--31541980 Score: 1010
Period size: 218 Copynumber: 3.1 Consensus size: 218
31541293 TCAGTCTACC
* * * * *
31541303 CCACTACAACTTCAAGGGGGATAAGACTTT-CCATCTTCGATCTGCCCCACTACAACTTCAGAGG
1 CCACTACAACCTC-AGGGAGATAAGA-TTTGCCATCTTCGATCTGCCCCACTGCAACTTTAGGGG
*
31541367 GATAAGACCTACTTACTCAGTCTACTCCGCTGCAACTTCAGGGAGATAAGACCTGATGCGATCCA
64 GATAAGACCTGCTTACTCAGTCTACTCCGCTGCAACTTCAGGGAGATAAGACCTGATGCGATCCA
*
31541432 CTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTACAACTT-CAGGGG
129 CTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCCA-GGA
31541496 GATAGGATTATCGGCTTCAATCTGCT
193 GATAGGATTATCGGCTTCAATCTGCT
* * *
31541522 CCACTGCAACTTTA-GG-G---AGATTTGCCATCTTCGATCTGCCCCACTGCAACTTTAGGGGGA
1 CCACTACAACCTCAGGGAGATAAGATTTGCCATCTTCGATCTGCCCCACTGCAACTTTAGGGGGA
* * * * *
31541582 TAAGACCTGCTTACTCAGTCTGCTCTGCTGCAACTTCAAGGAGATAAGACCTGATACAATCCACT
66 TAAGACCTGCTTACTCAGTCTACTCCGCTGCAACTTCAGGGAGATAAGACCTGATGCGATCCACT
* * * * * *
31541647 CTACTACAATTTTAGAGAGATAAGATCTATTACTTTAATCCGGTCCACTAAAATTTCCAGGAGAT
131 CTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCCAGGAGAT
31541712 AGGATTATCGGCTTCAATCTGCT
196 AGGATTATCGGCTTCAATCTGCT
*
31541735 CCACTACAACCTCAGGGAGATAAGATTTGCCATCTTCGATCTGTCCCACTGCAACTTTAGGGGGA
1 CCACTACAACCTCAGGGAGATAAGATTTGCCATCTTCGATCTGCCCCACTGCAACTTTAGGGGGA
* * * * *
31541800 TAAAACCTGCTTACTCAATCTACTCCACTGCAACCTCAGGGAGATAAGACCTGATGCGATCTACT
66 TAAGACCTGCTTACTCAGTCTACTCCGCTGCAACTTCAGGGAGATAAGACCTGATGCGATCCACT
* *
31541865 CTACTGCAACTTCAGAGAGATAAGATCCATTACTTTAATCCGCTCCACTACAACTTCAAGGAGAT
131 CTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCCAGGAGAT
31541930 AGGATTATCGGCTTCAATCTGCT
196 AGGATTATCGGCTTCAATCTGCT
*
31541953 CCACTACAACCTCAAGGAGATAAGATTT
1 CCACTACAACCTCAGGGAGATAAGATTT
31541981 ATAATTTCCC
Statistics
Matches: 411, Mismatches: 41, Indels: 15
0.88 0.09 0.03
Matches are distributed among these distances:
212 3 0.01
213 184 0.45
214 4 0.01
215 1 0.00
216 1 0.00
217 2 0.00
218 205 0.50
219 11 0.03
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (218 bp):
CCACTACAACCTCAGGGAGATAAGATTTGCCATCTTCGATCTGCCCCACTGCAACTTTAGGGGGA
TAAGACCTGCTTACTCAGTCTACTCCGCTGCAACTTCAGGGAGATAAGACCTGATGCGATCCACT
CTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCCAGGAGAT
AGGATTATCGGCTTCAATCTGCT
Found at i:31544393 original size:12 final size:13
Alignment explanation
Indices: 31544349--31544406 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
31544339 TTTGACTTTA
31544349 ATTTTGATTTTTCT
1 ATTTTGATTTTT-T
**
31544363 -TTTTCTTCTTTTT
1 ATTTTGAT-TTTTT
31544376 ATTTTTG-TTTTTT
1 A-TTTTGATTTTTT
31544389 ATTTTGATTTTTT
1 ATTTTGATTTTTT
31544402 -TTTTG
1 ATTTTG
31544407 GATTGGATCT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
12 10 0.27
13 18 0.49
14 5 0.14
15 4 0.11
ACGTcount: A:0.09, C:0.05, G:0.07, T:0.79
Consensus pattern (13 bp):
ATTTTGATTTTTT
Found at i:31545147 original size:29 final size:29
Alignment explanation
Indices: 31545113--31545172 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
31545103 ATGAATAATT
* *
31545113 ATTTGTATCATATGATTATGAATGAATGA
1 ATTTGTACCATACGATTATGAATGAATGA
31545142 ATTTGTACCATACGATTATGAATGAATGA
1 ATTTGTACCATACGATTATGAATGAATGA
31545171 AT
1 AT
31545173 AATAATTTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38
Consensus pattern (29 bp):
ATTTGTACCATACGATTATGAATGAATGA
Found at i:31549210 original size:24 final size:23
Alignment explanation
Indices: 31549174--31549260 Score: 79
Period size: 23 Copynumber: 3.7 Consensus size: 23
31549164 TTTCTTTTAA
* * *
31549174 AATAATGCCTAATAAACCTGAAAT
1 AATAATACATAATAAATCT-AAAT
*
31549198 AATAATACATAATGAATCTAAA-
1 AATAATACATAATAAATCTAAAT
* *
31549220 AATAAATATATAATAAATCTAAGCT
1 AAT-AATACATAATAAATCTAA-AT
31549245 AATAATACATAA-AAAT
1 AATAATACATAATAAAT
31549261 TTATGATGCT
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
22 3 0.06
23 23 0.44
24 23 0.44
25 3 0.06
ACGTcount: A:0.57, C:0.10, G:0.05, T:0.28
Consensus pattern (23 bp):
AATAATACATAATAAATCTAAAT
Found at i:31549423 original size:20 final size:19
Alignment explanation
Indices: 31549382--31549430 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
31549372 ATATACATAT
31549382 ATATAAATAAATAAATAAA
1 ATATAAATAAATAAATAAA
* *
31549401 ATATAAATAACATAATTACA
1 ATATAAATAA-ATAAATAAA
*
31549421 ATATCAATAA
1 ATATAAATAA
31549431 GGCTAGTGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (19 bp):
ATATAAATAAATAAATAAA
Found at i:31558554 original size:19 final size:19
Alignment explanation
Indices: 31558530--31558573 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
31558520 ATGATTTAAT
31558530 TGATATGTGATACATGGTA
1 TGATATGTGATACATGGTA
*
31558549 TGATATGTGATACCTGGTA
1 TGATATGTGATACATGGTA
31558568 TGATAT
1 TGATAT
31558574 TGAGTTGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.30, C:0.07, G:0.25, T:0.39
Consensus pattern (19 bp):
TGATATGTGATACATGGTA
Found at i:31570851 original size:36 final size:37
Alignment explanation
Indices: 31570802--31570874 Score: 139
Period size: 36 Copynumber: 2.0 Consensus size: 37
31570792 GTAAGTGATT
31570802 CTAATCCCCGTTTTTAATGCTTTTTACATTTTTGAGA
1 CTAATCCCCGTTTTTAATGCTTTTTACATTTTTGAGA
31570839 CTAAT-CCCGTTTTTAATGCTTTTTACATTTTTGAGA
1 CTAATCCCCGTTTTTAATGCTTTTTACATTTTTGAGA
31570875 TTTCGGTAGC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 31 0.86
37 5 0.14
ACGTcount: A:0.22, C:0.18, G:0.11, T:0.49
Consensus pattern (37 bp):
CTAATCCCCGTTTTTAATGCTTTTTACATTTTTGAGA
Found at i:31571651 original size:56 final size:50
Alignment explanation
Indices: 31571575--31571808 Score: 189
Period size: 50 Copynumber: 4.6 Consensus size: 50
31571565 ATTTGGGCAA
* * * * *
31571575 AGAGATCCCATGTAAAACCATGTCTGGGACATTGCATTGGCATTCTTGAAATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGG--TAC-CGAAA-C--G
* *
31571631 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGTACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGTACCGAAACG
* * * * * *
31571681 AGAGGTCCTATGTAAGACCATGTCTGGGACATGACGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGTACCGAAACG
* ** * * * * * *
31571731 AGAGCTCCCCCGTAAGACCATGTTTGGGACATGGCATGGGCACTGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGTACCGAAACG
** *
31571781 AGAACTCCCATGTAAGACCATATCTGGG
1 AGAGGTCCCATGTAAGACCATGTCTGGG
31571809 TTATCTAAGT
Statistics
Matches: 152, Mismatches: 26, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
50 110 0.72
52 1 0.01
53 3 0.02
54 2 0.01
56 36 0.24
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGTACCGAAACG
Found at i:31571688 original size:50 final size:50
Alignment explanation
Indices: 31571628--31571808 Score: 227
Period size: 50 Copynumber: 3.6 Consensus size: 50
31571618 TCTTGAAATC
* *
31571628 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGTACCGAG
1 ATGAGAGCTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
* * * *
31571678 ACGAGAGGTCCTATGTAAGACCATGTCTGGGACATGACGTTGGCACCGAG
1 ATGAGAGCTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
** * * * * *
31571728 ATGAGAGCTCCCCCGTAAGACCATGTTTGGGACATGGCATGGGCACTGAT
1 ATGAGAGCTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
* *
31571778 ATGAGAACTCCCATGTAAGACCATATCTGGG
1 ATGAGAGCTCCCATGTAAGACCATGTCTGGG
31571809 TTATCTAAGT
Statistics
Matches: 111, Mismatches: 20, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 111 1.00
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (50 bp):
ATGAGAGCTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
Found at i:31572492 original size:20 final size:20
Alignment explanation
Indices: 31572464--31572509 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
31572454 CTGTTCTGAG
*
31572464 TTTAGAAAATCACTTAAAAT
1 TTTAAAAAATCACTTAAAAT
*
31572484 TTTAAAAAAATCACTTAAAGT
1 TTT-AAAAAATCACTTAAAAT
31572505 TTTAA
1 TTTAA
31572510 TTTAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.50, C:0.09, G:0.04, T:0.37
Consensus pattern (20 bp):
TTTAAAAAATCACTTAAAAT
Found at i:31572495 original size:21 final size:21
Alignment explanation
Indices: 31572469--31572509 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
31572459 CTGAGTTTAG
31572469 AAAATCACTTAAAATTTTAAA
1 AAAATCACTTAAAATTTTAAA
*
31572490 AAAATCACTTAAAGTTTTAA
1 AAAATCACTTAAAATTTTAA
31572510 TTTAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (21 bp):
AAAATCACTTAAAATTTTAAA
Found at i:31582002 original size:40 final size:40
Alignment explanation
Indices: 31581957--31582043 Score: 120
Period size: 40 Copynumber: 2.2 Consensus size: 40
31581947 AATTGTGGAA
* * *
31581957 TACTGAATATTGTTTTGAGTACTGAATTGAATTATGAAGT
1 TACTGAATATTGTTATGAGTACTGAATTGAACTATGAAAT
* * *
31581997 TACTGAATATTGTTATGTGTACTGCATTGAACTGTGAAAT
1 TACTGAATATTGTTATGAGTACTGAATTGAACTATGAAAT
31582037 TACTGAA
1 TACTGAA
31582044 GTAATGAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (40 bp):
TACTGAATATTGTTATGAGTACTGAATTGAACTATGAAAT
Found at i:31582012 original size:21 final size:19
Alignment explanation
Indices: 31581957--31582020 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
31581947 AATTGTGGAA
*
31581957 TACTGAATATTGTTTTGAG
1 TACTGAATATTGTTATGAG
31581976 TACTG-A-ATTGAATTATGAAG
1 TACTGAATATTG--TTATG-AG
*
31581996 TTACTGAATATTGTTATGTG
1 -TACTGAATATTGTTATGAG
31582016 TACTG
1 TACTG
31582021 CATTGAACTG
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
17 4 0.11
18 1 0.03
19 14 0.38
20 3 0.08
21 10 0.27
22 1 0.03
23 4 0.11
ACGTcount: A:0.30, C:0.06, G:0.20, T:0.44
Consensus pattern (19 bp):
TACTGAATATTGTTATGAG
Found at i:31582276 original size:45 final size:45
Alignment explanation
Indices: 31582205--31582685 Score: 450
Period size: 45 Copynumber: 10.9 Consensus size: 45
31582195 TTACTGATCA
* * * *
31582205 GGCAC-TTATGTGCCGACTACTGTTACTGTTACTATTACCGATTC
1 GGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTACCGATTC
* * * *
31582249 GACACTTTATGTGTTGAATACTATTACTGTTACTGTTACCGATTC
1 GGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTACCGATTC
** *
31582294 GGCACTTTAAGTGTCGAATACTGTTACTGTTACTGTTACTGATTC
1 GGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTACCGATTC
*
31582339 GGCACTTTGTGTGTCGAATACTGTTACTGTTACTATTACCGATTC
1 GGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTACCGATTC
* * *
31582384 GGCACTTTGTGTGTCAAATACTGTAACTGTTACTGTTACAGATTC
1 GGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTACCGATTC
* *
31582429 GACACTTTGTGTGTTGAATACTG--A----TAC----A--GATTC
1 GGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTACCGATTC
*
31582462 GGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTACTGTTACTGATTT
1 GGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTAC-----C-GATTC
* * * * * *
31582513 GGCACTTTTTGTGTCAAATACTGTTACCGTTACTATTATCGATTT
1 GGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTACCGATTC
* * **
31582558 GGCACTTTGTGTGTCAAATACTGTTACCGTTACTGTTACAAATTC
1 GGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTACCGATTC
* * * * **
31582603 AGCACTTTTTGTGTCTAATATTGTTACTG-TACTGTTATAGATTC
1 GGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTACCGATTC
** * * * *
31582647 AACACTTTATGTGTTGAATAATGTTACTATTACTGTTAC
1 GGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTAC
31582686 TGCTACCGTT
Statistics
Matches: 367, Mismatches: 50, Indels: 39
0.80 0.11 0.09
Matches are distributed among these distances:
33 26 0.07
35 2 0.01
39 6 0.02
43 2 0.01
44 40 0.11
45 252 0.69
46 1 0.00
51 38 0.10
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (45 bp):
GGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTACCGATTC
Found at i:31582451 original size:33 final size:33
Alignment explanation
Indices: 31582414--31582488 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
31582404 CTGTAACTGT
*
31582414 TACTGTTACAGATTCGACACTTTGTGTGTTGAA
1 TACTGTTACAGATTCGACACTTTGTGTGTCGAA
* *
31582447 TACTGATACAGATTCGGCACTTTGTGTGTCGAA
1 TACTGTTACAGATTCGACACTTTGTGTGTCGAA
31582480 TACTGTTAC
1 TACTGTTAC
31582489 TGTTACTGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.37
Consensus pattern (33 bp):
TACTGTTACAGATTCGACACTTTGTGTGTCGAA
Found at i:31582491 original size:6 final size:6
Alignment explanation
Indices: 31582480--31582508 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
31582470 GTGTGTCGAA
31582480 TACTGT TACTGT TACTGT TACTGT TACTG
1 TACTGT TACTGT TACTGT TACTGT TACTG
31582509 ATTTGGCACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.48
Consensus pattern (6 bp):
TACTGT
Found at i:31582526 original size:51 final size:49
Alignment explanation
Indices: 31582447--31582596 Score: 191
Period size: 51 Copynumber: 3.1 Consensus size: 49
31582437 GTGTGTTGAA
* * *
31582447 TACTGATACAGATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTGT
1 TACTG-TAC-GATTTGGCACTTTGTGTGTCAAATACTGTTACCGTTACTGT
* *
31582498 TACTGTTACTGATTTGGCACTTTTTGTGTCAAATACTGTTACCGTTACTAT
1 TACTG-TAC-GATTTGGCACTTTGTGTGTCAAATACTGTTACCGTTACTGT
31582549 TA---T-CGATTTGGCACTTTGTGTGTCAAATACTGTTACCGTTACTGT
1 TACTGTACGATTTGGCACTTTGTGTGTCAAATACTGTTACCGTTACTGT
31582594 TAC
1 TAC
31582597 AAATTCAGCA
Statistics
Matches: 89, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
45 41 0.46
46 1 0.01
47 1 0.01
51 46 0.52
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Consensus pattern (49 bp):
TACTGTACGATTTGGCACTTTGTGTGTCAAATACTGTTACCGTTACTGT
Found at i:31582531 original size:129 final size:123
Alignment explanation
Indices: 31582324--31582580 Score: 336
Period size: 129 Copynumber: 2.0 Consensus size: 123
31582314 CTGTTACTGT
* *
31582324 TACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTATTACCGATTCGGCAC
1 TACTGATACAGATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTATTACCGATTCGGCAC
* * **
31582389 TTTGTGTGTCAAATACTGTAACTGTTACTGTTA-CAGATTCGACACTTTGTGTGTTGAA
66 TTTGTGTGTCAAATACTGTAACCGTTACTATTATC-GATTCGACACTTTGTGTGTCAAA
*
31582447 TACTGATACAGATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTACTGTTACTGATT
1 TACTGATACAGATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTAC---TA---TTACCGATT
* * * * *
31582512 TGGCACTTTTTGTGTCAAATACTGTTACCGTTACTATTATCGATTTGGCACTTTGTGTGTCAAA
60 CGGCACTTTGTGTGTCAAATACTGTAACCGTTACTATTATCGATTCGACACTTTGTGTGTCAAA
31582576 TACTG
1 TACTG
31582581 TTACCGTTAC
Statistics
Matches: 115, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
123 46 0.40
126 2 0.02
129 66 0.57
130 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.41
Consensus pattern (123 bp):
TACTGATACAGATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTATTACCGATTCGGCAC
TTTGTGTGTCAAATACTGTAACCGTTACTATTATCGATTCGACACTTTGTGTGTCAAA
Found at i:31585449 original size:35 final size:35
Alignment explanation
Indices: 31585394--31585477 Score: 100
Period size: 35 Copynumber: 2.4 Consensus size: 35
31585384 TACTATCTGT
* *
31585394 TTTGGTGTGTTTCGG-TTGGACTAACTCTTATGAGCA
1 TTTGGTGTGTTT-GGAATGGACTAACTC-TACGAGCA
**
31585430 TTT-GTGTGTTTGGAATGGACTGGCTCTACGAGCA
1 TTTGGTGTGTTTGGAATGGACTAACTCTACGAGCA
31585464 TTTGGTGTGTTTGG
1 TTTGGTGTGTTTGG
31585478 GTGGTTTGTC
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
34 12 0.29
35 27 0.64
36 3 0.07
ACGTcount: A:0.14, C:0.12, G:0.32, T:0.42
Consensus pattern (35 bp):
TTTGGTGTGTTTGGAATGGACTAACTCTACGAGCA
Found at i:31589025 original size:41 final size:40
Alignment explanation
Indices: 31588972--31589097 Score: 121
Period size: 41 Copynumber: 3.4 Consensus size: 40
31588962 TATAATTATA
31588972 ATTATAATTATGATTGGTGATGCAATCACTTTTCATGAATT
1 ATTATAATTATGATTGGT-ATGCAATCACTTTTCATGAATT
* * *
31589013 ATTATAATTATGATT--TAT--AA--A-TTTGT-TTTAA-C
1 ATTATAATTATGATTGGTATGCAATCACTTT-TCATGAATT
*
31589045 ATCAT-A-TATGATTGGTATGCAATCACTTTTCATGAATT
1 ATTATAATTATGATTGGTATGCAATCACTTTTCATGAATT
31589083 ATTATAATTATGATT
1 ATTATAATTATGATT
31589098 TATAAATTTG
Statistics
Matches: 65, Mismatches: 8, Indels: 25
0.66 0.08 0.26
Matches are distributed among these distances:
30 7 0.11
31 1 0.02
32 7 0.11
33 6 0.09
34 4 0.06
36 4 0.06
37 6 0.09
38 6 0.09
39 2 0.03
40 7 0.11
41 15 0.23
ACGTcount: A:0.34, C:0.08, G:0.11, T:0.47
Consensus pattern (40 bp):
ATTATAATTATGATTGGTATGCAATCACTTTTCATGAATT
Found at i:31589076 original size:70 final size:71
Alignment explanation
Indices: 31588980--31589123 Score: 281
Period size: 70 Copynumber: 2.0 Consensus size: 71
31588970 TAATTATAAT
31588980 TATGATTGGTGATGCAATCACTTTTCATGAATTATTATAATTATGATTTATAAATTTGTTTTAAC
1 TATGATTGGTGATGCAATCACTTTTCATGAATTATTATAATTATGATTTATAAATTTGTTTTAAC
31589045 ATCATA
66 ATCATA
31589051 TATGATTGGT-ATGCAATCACTTTTCATGAATTATTATAATTATGATTTATAAATTTGTTTTAAC
1 TATGATTGGTGATGCAATCACTTTTCATGAATTATTATAATTATGATTTATAAATTTGTTTTAAC
31589115 ATCATA
66 ATCATA
31589121 TAT
1 TAT
31589124 TTACTTTGTA
Statistics
Matches: 73, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
70 63 0.86
71 10 0.14
ACGTcount: A:0.34, C:0.08, G:0.10, T:0.47
Consensus pattern (71 bp):
TATGATTGGTGATGCAATCACTTTTCATGAATTATTATAATTATGATTTATAAATTTGTTTTAAC
ATCATA
Found at i:31592009 original size:42 final size:41
Alignment explanation
Indices: 31591923--31592012 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 41
31591913 ACGGTTTGAG
* * *
31591923 CACACGGAGGTGTGGGGTAACTAAACGGCCATGTCCCTATGC
1 CACAC-GAGGTGTGGGGTAACCAAACGGCCATGTCCCCAAGC
* *
31591965 CACACGAGCGTGTGGGGTAGCCACACGGCCATG-CCCCAGAGC
1 CACACGAG-GTGTGGGGTAACCAAACGGCCATGTCCCCA-AGC
31592007 CACACG
1 CACACG
31592013 GTCTAGGACC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 7 0.17
42 34 0.83
ACGTcount: A:0.23, C:0.32, G:0.31, T:0.13
Consensus pattern (41 bp):
CACACGAGGTGTGGGGTAACCAAACGGCCATGTCCCCAAGC
Found at i:31597309 original size:6 final size:6
Alignment explanation
Indices: 31597298--31597323 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
31597288 TTTTTAGCTA
31597298 ATAATT ATAATT ATAATT ATAATT AT
1 ATAATT ATAATT ATAATT ATAATT AT
31597324 TTTTAAATGT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATAATT
Found at i:31615533 original size:1 final size:1
Alignment explanation
Indices: 31615529--31615559 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
31615519 CTGTTTTTAA
*
31615529 CCCCCTCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
31615560 TTTTCTTCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.97, G:0.00, T:0.03
Consensus pattern (1 bp):
C
Found at i:31617068 original size:2 final size:2
Alignment explanation
Indices: 31617061--31617179 Score: 238
Period size: 2 Copynumber: 59.5 Consensus size: 2
31617051 CTTGGAAATA
31617061 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31617103 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31617145 AT AT AT AT 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 AT A
31617180 GGTGGTTTTT
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 117 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31630084 original size:45 final size:44
Alignment explanation
Indices: 31629991--31630171 Score: 174
Period size: 45 Copynumber: 4.1 Consensus size: 44
31629981 ATAGATGCAC
* * *
31629991 GGTGG-ATCAGCACATAGC-ACCACCCTTATAGTCAATGATA-CT
1 GGTGGAATCAACACATAGCAACCACCTTTATAATCAATG-TACCT
* * *
31630033 CAGTGGAATCAACACATAGCAATCACCTTCATAATCAATAGTACCT
1 -GGTGGAATCAACACATAGCAACCACCTTTATAATCAAT-GTACCT
* * * *
31630079 GGTGGAATCAGCACACATCAACCACCTTTATAAGT-AATGATACCC
1 GGTGGAATCAACACATAGCAACCACCTTTATAA-TCAATG-TACCT
31630124 GGTGGAAT-AAGCACATAGCAACCACCTTTATAATCAATGGTACCT
1 GGTGGAATCAA-CACATAGCAACCACCTTTATAATCAAT-GTACCT
31630169 GGT
1 GGT
31630172 ACACGTAGTA
Statistics
Matches: 112, Mismatches: 17, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
43 4 0.04
44 15 0.13
45 88 0.79
46 5 0.04
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.24
Consensus pattern (44 bp):
GGTGGAATCAACACATAGCAACCACCTTTATAATCAATGTACCT
Found at i:31630129 original size:90 final size:88
Alignment explanation
Indices: 31629991--31630171 Score: 240
Period size: 90 Copynumber: 2.0 Consensus size: 88
31629981 ATAGATGCAC
* *
31629991 GGTGGATCAGCACATAGCACCACCCTTATAGTCAATGATACTCAGTGGAATCAA-CACATAGCAA
1 GGTGGATCAGCACACAGCACCACCCTTATAGTCAATGATACCCAGTGGAAT-AAGCACATAGCAA
*
31630055 TCACCTTCATAATCAATAGTACCT
65 CCACCTTCATAATCAATAGTACCT
* * *
31630079 GGTGGAATCAGCACACATCAACCACCTTTATAAGT-AATGATACCCGGTGGAATAAGCACATAGC
1 GGTGG-ATCAGCACACAGC-ACCACCCTTAT-AGTCAATGATACCCAGTGGAATAAGCACATAGC
* *
31630143 AACCACCTTTATAATCAATGGTACCT
63 AACCACCTTCATAATCAATAGTACCT
31630169 GGT
1 GGT
31630172 ACACGTAGTA
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
88 5 0.06
89 13 0.16
90 60 0.74
91 3 0.04
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.24
Consensus pattern (88 bp):
GGTGGATCAGCACACAGCACCACCCTTATAGTCAATGATACCCAGTGGAATAAGCACATAGCAAC
CACCTTCATAATCAATAGTACCT
Found at i:31640232 original size:30 final size:30
Alignment explanation
Indices: 31640161--31640224 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
31640151 GGGTAACCTC
* * * *
31640161 GATATAATCTCAGCTTGTGTGAGCAATCTT
1 GATAAAATGTCAGCTTGTGTGAGCAACCAT
*
31640191 GTTAAAATGTCAGCTTGTGTGAGCAACCAT
1 GATAAAATGTCAGCTTGTGTGAGCAACCAT
31640221 GATA
1 GATA
31640225 CGTTGTCAAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.33
Consensus pattern (30 bp):
GATAAAATGTCAGCTTGTGTGAGCAACCAT
Found at i:31643008 original size:20 final size:20
Alignment explanation
Indices: 31642985--31643043 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
31642975 AAAAATTATC
*
31642985 TAAGAATTTACCAAAACTTA
1 TAAGAAGTTACCAAAACTTA
*
31643005 TAAGAAGTTACCAAAA-TATT
1 TAAGAAGTTACCAAAACT-TA
*
31643025 TAAGGAGTTACCAAAACTT
1 TAAGAAGTTACCAAAACTT
31643044 CTAACCTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.03
20 32 0.94
21 1 0.03
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.29
Consensus pattern (20 bp):
TAAGAAGTTACCAAAACTTA
Found at i:31643137 original size:40 final size:41
Alignment explanation
Indices: 31643049--31643143 Score: 147
Period size: 41 Copynumber: 2.3 Consensus size: 41
31643039 AACTTCTAAC
* *
31643049 CTTTTACCGAAATTCCTTAAAAGTTAATAGAATTTTGTAAG
1 CTTTTACCAAAATTCCTTAAAAGTTAATAGAAATTTGTAAG
* *
31643090 CTTTTACCAAAATTTCTTAAAATTTAATA-AAATTTGTAAG
1 CTTTTACCAAAATTCCTTAAAAGTTAATAGAAATTTGTAAG
31643130 CTTTTACCAAAATT
1 CTTTTACCAAAATT
31643144 ATATTTTTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 24 0.48
41 26 0.52
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.41
Consensus pattern (41 bp):
CTTTTACCAAAATTCCTTAAAAGTTAATAGAAATTTGTAAG
Found at i:31643141 original size:20 final size:20
Alignment explanation
Indices: 31643082--31643143 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
31643072 TTAATAGAAT
31643082 TTTGTAAGCTTTTACCAAAA
1 TTTGTAAGCTTTTACCAAAA
* ** **
31643102 TTTCTTAA-AATTTAATAAAA
1 TTT-GTAAGCTTTTACCAAAA
31643122 TTTGTAAGCTTTTACCAAAA
1 TTTGTAAGCTTTTACCAAAA
31643142 TT
1 TT
31643144 ATATTTTTTA
Statistics
Matches: 30, Mismatches: 10, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
19 3 0.10
20 24 0.80
21 3 0.10
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (20 bp):
TTTGTAAGCTTTTACCAAAA
Found at i:31643232 original size:40 final size:39
Alignment explanation
Indices: 31643148--31643248 Score: 100
Period size: 40 Copynumber: 2.5 Consensus size: 39
31643138 AAAATTATAT
* * *
31643148 TTTTTAATGATTTACCCAA-ATTTCTAACTATTTACCAATA
1 TTTTTAA-GATTTA-CCAATATATCTAACGATTTACAAATA
31643188 TTTTTGAA-ACTTTACCAATATATCTAACGATTTATCAAAT-
1 TTTTT-AAGA-TTTACCAATATATCTAACGATTTA-CAAATA
31643228 TTTTTAAGGATTTACCAATAT
1 TTTTTAA-GATTTACCAATAT
31643249 TTTTGAGACT
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
39 7 0.13
40 38 0.73
41 7 0.13
ACGTcount: A:0.36, C:0.15, G:0.05, T:0.45
Consensus pattern (39 bp):
TTTTTAAGATTTACCAATATATCTAACGATTTACAAATA
Found at i:31643241 original size:60 final size:60
Alignment explanation
Indices: 31643177--31643304 Score: 168
Period size: 60 Copynumber: 2.1 Consensus size: 60
31643167 ATTTCTAACT
* *
31643177 ATTTACCAATATTTTTGAAACTTTACCAA-TATATCTAACGATTTATCAAATTTTTTAAGG
1 ATTTACCAATATTTTTGAAACTTTACCAATTA-ATCTAACCACTTATCAAATTTTTTAAGG
* * * ** *
31643237 ATTTACCAATATTTTTGAGACTTTACTAATTAATCTAACCACTTGTTGAATTTTTTAGGG
1 ATTTACCAATATTTTTGAAACTTTACCAATTAATCTAACCACTTATCAAATTTTTTAAGG
31643297 ATTTACCA
1 ATTTACCA
31643305 TGATATCTAA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
60 57 0.97
61 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.44
Consensus pattern (60 bp):
ATTTACCAATATTTTTGAAACTTTACCAATTAATCTAACCACTTATCAAATTTTTTAAGG
Found at i:31643262 original size:20 final size:20
Alignment explanation
Indices: 31643148--31643252 Score: 83
Period size: 20 Copynumber: 5.2 Consensus size: 20
31643138 AAAATTATAT
*
31643148 TTTTTAATGATTTACCCAA-A
1 TTTTTAACGATTTA-CCAATA
* *
31643168 TTTCTAACTATTTACCAATA
1 TTTTTAACGATTTACCAATA
31643188 TTTTTGAA--ACTTTACCAATA
1 TTTTT-AACGA-TTTACCAATA
* * *
31643208 TATCTAACGATTTATCAA-A
1 TTTTTAACGATTTACCAATA
*
31643227 TTTTTTAAGGATTTACCAATA
1 -TTTTTAACGATTTACCAATA
31643248 TTTTT
1 TTTTT
31643253 GAGACTTTAC
Statistics
Matches: 67, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
19 8 0.12
20 55 0.82
21 4 0.06
ACGTcount: A:0.34, C:0.14, G:0.05, T:0.47
Consensus pattern (20 bp):
TTTTTAACGATTTACCAATA
Found at i:31643422 original size:20 final size:20
Alignment explanation
Indices: 31643397--31643443 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
31643387 AAAATATTTG
*
31643397 AGGATTTATCAATATTTCTA
1 AGGATTTATCAAAATTTCTA
* *
31643417 ATGATTGATCAAAATTTCTA
1 AGGATTTATCAAAATTTCTA
31643437 AGGATTT
1 AGGATTT
31643444 CATTTGTATC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.43
Consensus pattern (20 bp):
AGGATTTATCAAAATTTCTA
Found at i:31643544 original size:20 final size:20
Alignment explanation
Indices: 31643480--31643537 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
31643470 CATCTAAGCC
* * *
31643480 TTTACCAAAATTTTTGAGAC
1 TTTACCAAAATTTCTAAGAA
* *
31643500 TTTACCAACATTTCTAACAA
1 TTTACCAAAATTTCTAAGAA
31643520 TTTACCAAAATTTCTAAG
1 TTTACCAAAATTTCTAAG
31643538 GTTTTACTAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (20 bp):
TTTACCAAAATTTCTAAGAA
Found at i:31643643 original size:20 final size:20
Alignment explanation
Indices: 31643589--31643643 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
31643579 CCTTATCAAA
* *
31643589 ATTTCTGAGACTTTACTAAT
1 ATTTCTGAAACTTTACCAAT
* *
31643609 ATATCT-AACAATTTACCAAT
1 ATTTCTGAA-ACTTTACCAAT
31643629 ATTTCTGAAACTTTA
1 ATTTCTGAAACTTTA
31643644 AGTGTCCCAT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
19 1 0.04
20 24 0.89
21 2 0.07
ACGTcount: A:0.36, C:0.16, G:0.05, T:0.42
Consensus pattern (20 bp):
ATTTCTGAAACTTTACCAAT
Found at i:31643748 original size:40 final size:40
Alignment explanation
Indices: 31643704--31643825 Score: 181
Period size: 40 Copynumber: 3.0 Consensus size: 40
31643694 CTTCAACAAT
* *
31643704 ATATCTAATGATTTACCAATATTTTTAAGCATTTATCAAA
1 ATATCTAACGATTTACCAATATTTCTAAGCATTTATCAAA
* * *
31643744 ATATCTAACGATTTACCAAAATCTCTAAGAATTTATCAAA
1 ATATCTAACGATTTACCAATATTTCTAAGCATTTATCAAA
* *
31643784 ATATCTAAGGATTTACCAATATTTCTAAGCATTTACCAAA
1 ATATCTAACGATTTACCAATATTTCTAAGCATTTATCAAA
31643824 AT
1 AT
31643826 TTCTTAAAAA
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 72 1.00
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.37
Consensus pattern (40 bp):
ATATCTAACGATTTACCAATATTTCTAAGCATTTATCAAA
Found at i:31643820 original size:195 final size:195
Alignment explanation
Indices: 31643470--31643829 Score: 433
Period size: 195 Copynumber: 1.8 Consensus size: 195
31643460 TCGATTGACA
* * *
31643470 CATCTAAGCCTTTACCAAAATTTTTGAGACTTTACCAACATTTCTAACAATTTACCAAAATTTCT
1 CATCTAAGCCTTTACCAAAATTTTTGAGACTTCAACAACATATCTAACAATTTACCAAAATTTCT
** * * * ** * *
31643535 AAGGTTTTACTAAAATATCAGAGGATTTACTAATATTCCCAAGCCCTTATCAAAATTTCTGAGAC
66 AAGCATTTACTAAAATATCAGACGATTTACCAAAATTCCCAAGAACTTATCAAAATATCTAAGAC
* *
31643600 TTTACTAATATATCTAACAATTTACCAATATTTCTGAAACTTTAAGTGTCCCATACTCATCAACG
131 TTTACCAATATATCTAACAATTTACCAAAATTTCTGAAACTTTAAGTGTCCCATACTCATCAACG
* * ** * *
31643665 CATCTAAGCCTTTACCAATATTTTTGAGACTTCAACAATATATCTAATGATTTACCAATATTTTT
1 CATCTAAGCCTTTACCAAAATTTTTGAGACTTCAACAACATATCTAACAATTTACCAAAATTTCT
* *
31643730 AAGCATTTA-TCAAAATATCTA-ACGATTTACCAAAA-TCTCTAAGAATTTATCAAAATATCTAA
66 AAGCATTTACT-AAAATATC-AGACGATTTACCAAAATTC-CCAAGAACTTATCAAAATATCTAA
*
31643792 GGA-TTTACCAATATTTCTAAGC-ATTTACCAAAATTTCT
128 -GACTTTACCAATATATCTAA-CAATTTACCAAAATTTCT
31643830 TAAAAAGTAA
Statistics
Matches: 137, Mismatches: 23, Indels: 10
0.81 0.14 0.06
Matches are distributed among these distances:
194 3 0.02
195 130 0.95
196 4 0.03
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.36
Consensus pattern (195 bp):
CATCTAAGCCTTTACCAAAATTTTTGAGACTTCAACAACATATCTAACAATTTACCAAAATTTCT
AAGCATTTACTAAAATATCAGACGATTTACCAAAATTCCCAAGAACTTATCAAAATATCTAAGAC
TTTACCAATATATCTAACAATTTACCAAAATTTCTGAAACTTTAAGTGTCCCATACTCATCAACG
Found at i:31643827 original size:20 final size:20
Alignment explanation
Indices: 31643714--31643829 Score: 126
Period size: 20 Copynumber: 5.8 Consensus size: 20
31643704 ATATCTAATG
* *
31643714 ATTTACCAATATTTTTAAGC
1 ATTTACCAAAATTTCTAAGC
* *
31643734 ATTTATCAAAATATCTAA-C
1 ATTTACCAAAATTTCTAAGC
* *
31643753 GATTTACCAAAATCTCTAAGA
1 -ATTTACCAAAATTTCTAAGC
* * *
31643774 ATTTATCAAAATATCTAAGG
1 ATTTACCAAAATTTCTAAGC
*
31643794 ATTTACCAATATTTCTAAGC
1 ATTTACCAAAATTTCTAAGC
31643814 ATTTACCAAAATTTCT
1 ATTTACCAAAATTTCT
31643830 TAAAAAGTAA
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
19 1 0.01
20 78 0.99
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.38
Consensus pattern (20 bp):
ATTTACCAAAATTTCTAAGC
Found at i:31643920 original size:20 final size:21
Alignment explanation
Indices: 31643891--31643932 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
31643881 TATTTATAAC
*
31643891 AATTTGTC-AAATTATTAAAG
1 AATTTATCAAAATTATTAAAG
*
31643911 AATTTATCAAAATTTTTAAAG
1 AATTTATCAAAATTATTAAAG
31643932 A
1 A
31643933 TTTGCCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.40
Consensus pattern (21 bp):
AATTTATCAAAATTATTAAAG
Found at i:31643941 original size:20 final size:21
Alignment explanation
Indices: 31643899--31643943 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
31643889 ACAATTTGTC
*
31643899 AAATTATTAAAGAATTTATCA
1 AAATTATTAAAGAATTTACCA
* *
31643920 AAATTTTTAAAG-ATTTGCCA
1 AAATTATTAAAGAATTTACCA
31643940 AAAT
1 AAAT
31643944 ATTTGAGGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.38
Consensus pattern (21 bp):
AAATTATTAAAGAATTTACCA
Found at i:31644132 original size:20 final size:20
Alignment explanation
Indices: 31644108--31644250 Score: 85
Period size: 20 Copynumber: 7.2 Consensus size: 20
31644098 TAATCTTTCT
31644108 CCAAAATTTCTAAGGATTTA
1 CCAAAATTTCTAAGGATTTA
* * * *
31644128 TCAAAATGTCTAAGTATTAA
1 CCAAAATTTCTAAGGATTTA
*
31644148 CCAATATTTCTAAGGATTTA
1 CCAAAATTTCTAAGGATTTA
* * * *
31644168 CCTAAATATCCAAGTA-TTA
1 CCAAAATTTCTAAGGATTTA
* * * * *
31644187 TCAGAA-TACCAAAGAGTTTA
1 CCAAAATTTCTAAGGA-TTTA
* *
31644207 CCAATATTTCTAAGTATTTA
1 CCAAAATTTCTAAGGATTTA
* *
31644227 TCAAAATATCTAA-GACTTTA
1 CCAAAATTTCTAAGGA-TTTA
31644247 CCAA
1 CCAA
31644251 TGTTTACCAA
Statistics
Matches: 86, Mismatches: 33, Indels: 8
0.68 0.26 0.06
Matches are distributed among these distances:
18 5 0.06
19 7 0.08
20 69 0.80
21 5 0.06
ACGTcount: A:0.41, C:0.16, G:0.08, T:0.34
Consensus pattern (20 bp):
CCAAAATTTCTAAGGATTTA
Found at i:31644247 original size:40 final size:40
Alignment explanation
Indices: 31644109--31644251 Score: 114
Period size: 40 Copynumber: 3.6 Consensus size: 40
31644099 AATCTTTCTC
* * * * * *
31644109 CAAAATTTCTAAGGATTTATCAAAATGTCTAAGTATTAAC
1 CAAAATATCTAAGGATTTACCAATATATCTAAGTATTTAT
* * *
31644149 CAATATTTCTAAGGATTTACCTAA-ATATCCAAGTA-TTAT
1 CAAAATATCTAAGGATTTACC-AATATATCTAAGTATTTAT
* * * *
31644188 CAGAATA-CCAAAGAGTTTACCAATATTTCTAAGTATTTAT
1 CAAAATATCTAAGGA-TTTACCAATATATCTAAGTATTTAT
31644228 CAAAATATCTAA-GACTTTACCAAT
1 CAAAATATCTAAGGA-TTTACCAAT
31644252 GTTTACCAAA
Statistics
Matches: 82, Mismatches: 16, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
38 7 0.09
39 21 0.26
40 49 0.60
41 5 0.06
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.35
Consensus pattern (40 bp):
CAAAATATCTAAGGATTTACCAATATATCTAAGTATTTAT
Found at i:31644513 original size:20 final size:20
Alignment explanation
Indices: 31644467--31644528 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
31644457 GCATCTAGGT
31644467 TTTACCAAAATTTTAGAGAC
1 TTTACCAAAATTTTAGAGAC
* * *
31644487 TTCACCAATATTTATAGTGA-
1 TTTACCAAAATTT-TAGAGAC
* *
31644507 TTTACCATAATGTTTAAAGAC
1 TTTACCAAAAT-TTTAGAGAC
31644528 T
1 T
31644529 ATAAGGGTTT
Statistics
Matches: 31, Mismatches: 8, Indels: 5
0.70 0.18 0.11
Matches are distributed among these distances:
20 23 0.74
21 8 0.26
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.39
Consensus pattern (20 bp):
TTTACCAAAATTTTAGAGAC
Found at i:31644588 original size:20 final size:22
Alignment explanation
Indices: 31644565--31644617 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 22
31644555 ATTTACCGAT
31644565 ATTTTTAATGATTTAT-C-AAA
1 ATTTTTAATGATTTATCCTAAA
* *
31644585 ATTTCTAAAGA--TATCCTAAA
1 ATTTTTAATGATTTATCCTAAA
31644605 ATTTTTAAT-ATTT
1 ATTTTTAATGATTT
31644618 TCATTTGTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 7
0.69 0.11 0.19
Matches are distributed among these distances:
18 3 0.12
19 2 0.08
20 19 0.76
21 1 0.04
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.49
Consensus pattern (22 bp):
ATTTTTAATGATTTATCCTAAA
Found at i:31646718 original size:119 final size:118
Alignment explanation
Indices: 31646504--31646739 Score: 319
Period size: 119 Copynumber: 2.0 Consensus size: 118
31646494 AGGGACCAAA
** * * * * * *
31646504 GGATGGAGAAGGTTGTCTCATCTGATATTATGTGATTTTGGGATTAAGTTTAAATGGTTCTGTAT
1 GGATGGAGAAGGACGTCTCATCTAATATTATGTAATTTTAGGATCAAGTCTAAATGATTCTGTAT
* * * *
31646569 TCATTGCTTATTAATAGATGACGGGTAGATTTATATATCTTCAGAACTGGAATG
66 TCATTGCTTATTAATAAATAACGAGAAGATTTATATATCTTCAGAA-TGGAATG
* *
31646623 GGATGGAGAAGGACGTCTCATCTAATATTATGTAATTTTAGGATCGAGTCTAACTGATTCTGTAT
1 GGATGGAGAAGGACGTCTCATCTAATATTATGTAATTTTAGGATCAAGTCTAAATGATTCTGTAT
* *
31646688 TCATTGCTTATTATTAAATAACGAGAAGATTTGTATATCTTCAGAATGGAAT
66 TCATTGCTTATTAATAAATAACGAGAAGATTTATATATCTTCAGAATGGAAT
31646740 TTATTCTGTC
Statistics
Matches: 101, Mismatches: 16, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
118 6 0.06
119 95 0.94
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.38
Consensus pattern (118 bp):
GGATGGAGAAGGACGTCTCATCTAATATTATGTAATTTTAGGATCAAGTCTAAATGATTCTGTAT
TCATTGCTTATTAATAAATAACGAGAAGATTTATATATCTTCAGAATGGAATG
Found at i:31652074 original size:35 final size:33
Alignment explanation
Indices: 31651998--31652099 Score: 106
Period size: 30 Copynumber: 3.1 Consensus size: 33
31651988 AGATTTTTTT
*
31651998 AAAAATTAATTAAATTAGGTTTTAGGGGTTTT---
1 AAAAATTAATTAAATTAGGGTTTA--GGTTTTAAA
*
31652030 --AAATAAATTAAATTAGGGTTTAGGATTTTTAAA
1 AAAAATTAATTAAATTAGGGTTTAGG--TTTTAAA
*
31652063 AAAAATTAATTAAATTAGGGTTTATGTTTTAAA
1 AAAAATTAATTAAATTAGGGTTTAGGTTTTAAA
31652096 AAAA
1 AAAA
31652100 TAATTTTGTG
Statistics
Matches: 59, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
28 2 0.03
30 24 0.41
33 11 0.19
35 22 0.37
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.40
Consensus pattern (33 bp):
AAAAATTAATTAAATTAGGGTTTAGGTTTTAAA
Found at i:31652092 original size:63 final size:61
Alignment explanation
Indices: 31651965--31652098 Score: 164
Period size: 65 Copynumber: 2.2 Consensus size: 61
31651955 AGTTTAAAAA
** *
31651965 TTTTAAAAAA-TAAATCAAGGTTTAGATTTTTTTAAAAATTAATTAAATTAGGTTTTAGGGG
1 TTTTAAAAAATTAAATCAAGGTTTAGATTTTTAAAAAAATTAATTAAATTAGGGTTTA-GGG
* * *
31652026 TTTTAAATAAATTAAATTAGGGTTTAGGATTTTTAAAAAAAATTAATTAAATTAGGGTTTA-TG
1 TTTTAAA-AAATTAAATCAAGGTTTA-GATTTTT-AAAAAAATTAATTAAATTAGGGTTTAGGG
31652089 TTTTAAAAAA
1 TTTTAAAAAA
31652099 ATAATTTTGT
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
61 7 0.11
62 6 0.10
63 20 0.32
64 7 0.11
65 23 0.37
ACGTcount: A:0.43, C:0.01, G:0.13, T:0.43
Consensus pattern (61 bp):
TTTTAAAAAATTAAATCAAGGTTTAGATTTTTAAAAAAATTAATTAAATTAGGGTTTAGGG
Found at i:31652414 original size:126 final size:125
Alignment explanation
Indices: 31652189--31652586 Score: 554
Period size: 126 Copynumber: 3.2 Consensus size: 125
31652179 ATTTTGTTTT
* * *
31652189 TTTTTCTACAGTAGTTTCAGAAAAATTAATTTTGAGAAGACGGTTC-TAAAAAGAT-GATGTCAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTTAAAAA-ATAG-TGTCAA
* *
31652252 AAACGA-TTCAAGCAGGATGCACTATCAGCAAAATTACTGAAAAATGCTCCCACGTGGACGCTC
64 AAAC-ACTTCAAGCAGAATGCACTGTCAGCAAAATTACTGAAAAA-GCTCCCACGTGGACGCTC
* *
31652315 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTTAGAAGACGGTTCTTAAAAAATAGTGCCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTTAAAAAATAGTGTCAAAA
*
31652380 ACACTTCAAGCAGAATGCATTGTCAGCAAAATTACTGTAAAAAGCTCCCACGTGGACGCTC
66 ACACTTCAAGCAGAATGCACTGTCAGCAAAATTACTG-AAAAAGCTCCCACGTGGACGCTC
* * * * *
31652441 TTTATCTACAGTAGTTCCT-AGAAAAATAAATTTGAGAAGATGGTTCTGAAAAAATAGTGTAAAA
1 TTTTTCTACAGTAGTTCCTGA-AAAAATAATTTTGAGAAGACGGTTCTTAAAAAATAGTGTCAAA
* *
31652505 AACGCTTCAAGCA-AGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGATGCTC
65 AACACTTCAAGCAGA-ATGCACTGTCAGCAAAATTACTG-AAAAAGCTCCCACGTGGACGCTC
31652567 TTTTTCTACAGTAGTTCCTG
1 TTTTTCTACAGTAGTTCCTG
31652587 CTTGGCCTTA
Statistics
Matches: 245, Mismatches: 20, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
125 3 0.01
126 230 0.94
127 12 0.05
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (125 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTTAAAAAATAGTGTCAAAA
ACACTTCAAGCAGAATGCACTGTCAGCAAAATTACTGAAAAAGCTCCCACGTGGACGCTC
Found at i:31653409 original size:386 final size:386
Alignment explanation
Indices: 31652696--31653473 Score: 1556
Period size: 386 Copynumber: 2.0 Consensus size: 386
31652686 AGTGAACATA
31652696 TTAGTGATGTTATTTACTATAATGGTGAGGTCCGTGACACCAAGAACAGCGTTATTTTTTTATTG
1 TTAGTGATGTTATTTACTATAATGGTGAGGTCCGTGACACCAAGAACAGCGTTATTTTTTTATTG
31652761 GAAAACACAGTGCAACTGGTTTTTAACCAGAACATAGATTTGATATAACTTCGTAAAAAACTTAG
66 GAAAACACAGTGCAACTGGTTTTTAACCAGAACATAGATTTGATATAACTTCGTAAAAAACTTAG
31652826 GTGCAAAATCTTCGAAATGGCGCCAATGAGAGTTTCATCTATTAAGTATTGATTTTGTGCTTCGG
131 GTGCAAAATCTTCGAAATGGCGCCAATGAGAGTTTCATCTATTAAGTATTGATTTTGTGCTTCGG
31652891 TTAATCCTGTGACATATGACTCATTTGATATCAAAGGTGGTCGTAGCTTGGAGGCGATGGTACAG
196 TTAATCCTGTGACATATGACTCATTTGATATCAAAGGTGGTCGTAGCTTGGAGGCGATGGTACAG
31652956 ACTCATCTCACTAGTGGATCGCCCTATCTTGAGTTATATGTACAATTTTTATCGCCAAATGAAGC
261 ACTCATCTCACTAGTGGATCGCCCTATCTTGAGTTATATGTACAATTTTTATCGCCAAATGAAGC
31653021 ATTTGTGACTTCAATATCTACTCTGTTCGAGAGGAATACACGACCCCTGCCCGACACTCCG
326 ATTTGTGACTTCAATATCTACTCTGTTCGAGAGGAATACACGACCCCTGCCCGACACTCCG
31653082 TTAGTGATGTTATTTACTATAATGGTGAGGTCCGTGACACCAAGAACAGCGTTATTTTTTTATTG
1 TTAGTGATGTTATTTACTATAATGGTGAGGTCCGTGACACCAAGAACAGCGTTATTTTTTTATTG
31653147 GAAAACACAGTGCAACTGGTTTTTAACCAGAACATAGATTTGATATAACTTCGTAAAAAACTTAG
66 GAAAACACAGTGCAACTGGTTTTTAACCAGAACATAGATTTGATATAACTTCGTAAAAAACTTAG
31653212 GTGCAAAATCTTCGAAATGGCGCCAATGAGAGTTTCATCTATTAAGTATTGATTTTGTGCTTCGG
131 GTGCAAAATCTTCGAAATGGCGCCAATGAGAGTTTCATCTATTAAGTATTGATTTTGTGCTTCGG
31653277 TTAATCCTGTGACATATGACTCATTTGATATCAAAGGTGGTCGTAGCTTGGAGGCGATGGTACAG
196 TTAATCCTGTGACATATGACTCATTTGATATCAAAGGTGGTCGTAGCTTGGAGGCGATGGTACAG
31653342 ACTCATCTCACTAGTGGATCGCCCTATCTTGAGTTATATGTACAATTTTTATCGCCAAATGAAGC
261 ACTCATCTCACTAGTGGATCGCCCTATCTTGAGTTATATGTACAATTTTTATCGCCAAATGAAGC
31653407 ATTTGTGACTTCAATATCTACTCTGTTCGAGAGGAATACACGACCCCTGCCCGACACTCCG
326 ATTTGTGACTTCAATATCTACTCTGTTCGAGAGGAATACACGACCCCTGCCCGACACTCCG
31653468 TTAGTG
1 TTAGTG
31653474 GGAGGCAGAA
Statistics
Matches: 392, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
386 392 1.00
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.33
Consensus pattern (386 bp):
TTAGTGATGTTATTTACTATAATGGTGAGGTCCGTGACACCAAGAACAGCGTTATTTTTTTATTG
GAAAACACAGTGCAACTGGTTTTTAACCAGAACATAGATTTGATATAACTTCGTAAAAAACTTAG
GTGCAAAATCTTCGAAATGGCGCCAATGAGAGTTTCATCTATTAAGTATTGATTTTGTGCTTCGG
TTAATCCTGTGACATATGACTCATTTGATATCAAAGGTGGTCGTAGCTTGGAGGCGATGGTACAG
ACTCATCTCACTAGTGGATCGCCCTATCTTGAGTTATATGTACAATTTTTATCGCCAAATGAAGC
ATTTGTGACTTCAATATCTACTCTGTTCGAGAGGAATACACGACCCCTGCCCGACACTCCG
Found at i:31656323 original size:18 final size:18
Alignment explanation
Indices: 31656300--31656337 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
31656290 GGAAAAGAAA
*
31656300 ACATATAAGGGTTAGGAT
1 ACATATAAGGGATAGGAT
31656318 ACATATAAGGGATAGGAT
1 ACATATAAGGGATAGGAT
31656336 AC
1 AC
31656338 GCACTGACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.08, G:0.26, T:0.24
Consensus pattern (18 bp):
ACATATAAGGGATAGGAT
Found at i:31659359 original size:31 final size:31
Alignment explanation
Indices: 31659321--31659386 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
31659311 GTCATGAATC
31659321 CTAAACCATGGCATGTAATCCGACGCACACG
1 CTAAACCATGGCATGTAATCCGACGCACACG
31659352 CTAAACCATGGCATGTAATCCGACGCACACG
1 CTAAACCATGGCATGTAATCCGACGCACACG
31659383 CTAA
1 CTAA
31659387 CTATGGAACG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.33, C:0.32, G:0.18, T:0.17
Consensus pattern (31 bp):
CTAAACCATGGCATGTAATCCGACGCACACG
Found at i:31662109 original size:24 final size:24
Alignment explanation
Indices: 31662065--31662111 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
31662055 TATATTTCAT
* *
31662065 ATATCATTATATTAAATTATTTAA
1 ATATCATTAAATTAAACTATTTAA
31662089 ATATCATATAAATT-AACTATTTA
1 ATATCAT-TAAATTAAACTATTTA
31662112 TTTTACTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (24 bp):
ATATCATTAAATTAAACTATTTAA
Found at i:31670306 original size:19 final size:19
Alignment explanation
Indices: 31670270--31670322 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
31670260 TGCCTCTTTT
31670270 TGCATT-CATTTCATTCATCA
1 TGCATTACATTTCA-TCAT-A
31670290 -GCATTACATTTCATCATA
1 TGCATTACATTTCATCATA
*
31670308 TGCATTAAATTTCAT
1 TGCATTACATTTCAT
31670323 AAAAATACCC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 1 0.03
19 22 0.73
20 7 0.23
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.43
Consensus pattern (19 bp):
TGCATTACATTTCATCATA
Found at i:31673505 original size:26 final size:27
Alignment explanation
Indices: 31673457--31673514 Score: 100
Period size: 26 Copynumber: 2.2 Consensus size: 27
31673447 CTTTGCTTGA
31673457 AAGAGGACTCGAAAAATACCTTCAAGG
1 AAGAGGACTCGAAAAATACCTTCAAGG
*
31673484 AAGAGGACTCG-AAAATACCTTCACGG
1 AAGAGGACTCGAAAAATACCTTCAAGG
31673510 AAGAG
1 AAGAG
31673515 TCAAGACACT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 19 0.63
27 11 0.37
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.14
Consensus pattern (27 bp):
AAGAGGACTCGAAAAATACCTTCAAGG
Found at i:31678155 original size:44 final size:44
Alignment explanation
Indices: 31678104--31678343 Score: 259
Period size: 44 Copynumber: 5.5 Consensus size: 44
31678094 TAAAGCGAAC
* *
31678104 CTTATCTCCTTGAAGTTGCAGTGGAGCATATTAAAGCTGCAAAT
1 CTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAAT
*
31678148 CTTATCT-CTCTGAAGTTGCAGTGGAGCAGATTAAAGCCACAAAT
1 CTTATCTCCT-TGAAGTTGCAGTGGAGCAGATTAAAGCTACAAAT
* * *
31678192 CTAATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGTTACAAAT
1 CTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAAT
** * * * * *
31678236 CTTATCTCCCAGAAGTTGCAGTGGAACAAATTGAAGCTATAAGT
1 CTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAAT
* * * * *
31678280 CTTATTTCCCTGAAGTTGTAGTGGAGTAGATTGAAA-CTACAATT
1 CTTATCTCCTTGAAGTTGCAGTGGAGCAGATT-AAAGCTACAAAT
* * *
31678324 CCTATATCCCTGAAGTTGCA
1 CTTATCTCCTTGAAGTTGCA
31678344 ATGGGTTAGA
Statistics
Matches: 166, Mismatches: 27, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
43 2 0.01
44 160 0.96
45 4 0.02
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Consensus pattern (44 bp):
CTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAAT
Found at i:31678256 original size:88 final size:88
Alignment explanation
Indices: 31678107--31678343 Score: 285
Period size: 88 Copynumber: 2.7 Consensus size: 88
31678097 AGCGAACCTT
* * * *
31678107 ATCTCCTTGAAGTTGCAGTGGAGCATATTAAAGCTGCAAATCTTATCTCTCTGAAGTTGCAGTGG
1 ATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGG
* *
31678172 AGCAGATTAAAGCCACAAATCTA
66 AACAAATTAAAGCCACAAATCTA
* *
31678195 ATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGTTACAAATCTTATCTCCCAGAAGTTGCAGTGG
1 ATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGG
* * * * *
31678260 AACAAATTGAAGCTATAAGTCTT
66 AACAAATTAAAGCCACAAATCTA
* * * * * * * *
31678283 ATTTCCCTGAAGTTGTAGTGGAGTAGATTGAAACTACAATTCCTATATCCCTGAAGTTGCA
1 ATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATCTCCCTGAAGTTGCA
31678344 ATGGGTTAGA
Statistics
Matches: 126, Mismatches: 23, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
88 126 1.00
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (88 bp):
ATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGG
AACAAATTAAAGCCACAAATCTA
Found at i:31679829 original size:22 final size:21
Alignment explanation
Indices: 31679781--31679829 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
31679771 TAGTGCGTTA
**
31679781 TATTTCAATCATTTATTTATT
1 TATTTCAATCATTTATGAATT
*
31679802 TAATTTCAATCTTTTATGAACTT
1 T-ATTTCAATCATTTATGAA-TT
31679825 TATTT
1 TATTT
31679830 ATTTATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 19 0.83
23 3 0.13
ACGTcount: A:0.29, C:0.10, G:0.02, T:0.59
Consensus pattern (21 bp):
TATTTCAATCATTTATGAATT
Found at i:31679894 original size:35 final size:34
Alignment explanation
Indices: 31679822--31679900 Score: 81
Period size: 35 Copynumber: 2.2 Consensus size: 34
31679812 CTTTTATGAA
*
31679822 CTTTATTTATTTATTTTATTTATTATTTCTTTATC
1 CTTTATTTATTTATTTTA-TTATTATTTCATTATC
*
31679857 CTTTATTATATTTAAATTTTA-TATTA-TTCATTGTC
1 CTTTATT-TATTT--ATTTTATTATTATTTCATTATC
31679892 CTTTTATTT
1 C-TTTATTT
31679901 GCATATTTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
35 16 0.42
36 16 0.42
38 6 0.16
ACGTcount: A:0.23, C:0.09, G:0.01, T:0.67
Consensus pattern (34 bp):
CTTTATTTATTTATTTTATTATTATTTCATTATC
Found at i:31681845 original size:21 final size:21
Alignment explanation
Indices: 31681803--31681846 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
31681793 GTAAAAAAAA
* *
31681803 TTACAATTTTTTTTATAATTT
1 TTACAATTTTTGTTACAATTT
*
31681824 TTACAATTTTTGTTACATTTT
1 TTACAATTTTTGTTACAATTT
31681845 TT
1 TT
31681847 TGTAATAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.25, C:0.07, G:0.02, T:0.66
Consensus pattern (21 bp):
TTACAATTTTTGTTACAATTT
Found at i:31681943 original size:19 final size:21
Alignment explanation
Indices: 31681916--31681962 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
31681906 ATTTTACTTT
31681916 TATA-ATTTTT-TATA-ATT-
1 TATATATTTTTCTATAGATTA
*
31681933 TATATATTTTTCTCTAGATTA
1 TATATATTTTTCTATAGATTA
31681954 TATATATTT
1 TATATATTT
31681963 AAATTTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 4 0.16
18 6 0.24
19 3 0.12
20 3 0.12
21 9 0.36
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (21 bp):
TATATATTTTTCTATAGATTA
Found at i:31681974 original size:15 final size:15
Alignment explanation
Indices: 31681954--31681984 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
31681944 CTCTAGATTA
31681954 TATATATTTAAATTT
1 TATATATTTAAATTT
31681969 TATATATTTAAATTT
1 TATATATTTAAATTT
31681984 T
1 T
31681985 TAATGTGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TATATATTTAAATTT
Found at i:31701182 original size:38 final size:38
Alignment explanation
Indices: 31701140--31701216 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
31701130 ATGACACCAG
31701140 TATGTTGATTCCAATAGCATAATAACTTGTGCTTTTTT
1 TATGTTGATTCCAATAGCATAATAACTTGTGCTTTTTT
31701178 TATGTTGATTCCAATAGCATAATAACTTGTGCTTTTTT
1 TATGTTGATTCCAATAGCATAATAACTTGTGCTTTTTT
31701216 T
1 T
31701217 CACAAACCCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (38 bp):
TATGTTGATTCCAATAGCATAATAACTTGTGCTTTTTT
Found at i:31702139 original size:22 final size:22
Alignment explanation
Indices: 31702114--31702183 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
31702104 CTTTGAAAGG
31702114 TCCAGTGATAGATTTTGAAGAA
1 TCCAGTGATAGATTTTGAAGAA
* * *
31702136 TCCAAGGGTGACA-A-GTTG-AG-G
1 TCC-A--GTGATAGATTTTGAAGAA
31702157 TCCAGTGATAGATTTTGAAGAA
1 TCCAGTGATAGATTTTGAAGAA
31702179 TCCAG
1 TCCAG
31702184 GAAACAGTTG
Statistics
Matches: 35, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
18 5 0.14
19 1 0.03
20 4 0.11
21 5 0.14
22 10 0.29
23 4 0.11
24 1 0.03
25 5 0.14
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (22 bp):
TCCAGTGATAGATTTTGAAGAA
Found at i:31709455 original size:25 final size:25
Alignment explanation
Indices: 31709416--31709510 Score: 93
Period size: 25 Copynumber: 3.8 Consensus size: 25
31709406 TCATGTACAT
*
31709416 GTATGCTCATACGAGCTGTGAATCA
1 GTATGCTCACACGAGCTGTGAATCA
* *
31709441 GTATGCTCACTCGAGTTGT-AGATCA
1 GTATGCTCACACGAGCTGTGA-ATCA
* * * * *
31709466 ATATGCTCTCACGAGCTATAAATCG
1 GTATGCTCACACGAGCTGTGAATCA
*
31709491 GTATGCTCTCACGAGCTGTG
1 GTATGCTCACACGAGCTGTG
31709511 GAGTATCCGT
Statistics
Matches: 56, Mismatches: 12, Indels: 4
0.78 0.17 0.06
Matches are distributed among these distances:
24 1 0.02
25 54 0.96
26 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.29
Consensus pattern (25 bp):
GTATGCTCACACGAGCTGTGAATCA
Found at i:31711685 original size:16 final size:16
Alignment explanation
Indices: 31711648--31711687 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
31711638 TTTAATAAAT
* *
31711648 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
31711664 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
31711680 TAAAATTA
1 TAAAATTA
31711688 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Done.