Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A12
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: 103038859
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4950000 characters in sequence are not A, C, G, or T
File 280 of 320
Found at i:90322257 original size:18 final size:19
Alignment explanation
Indices: 90322236--90322285 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 19
90322226 ATGTATTAGA
90322236 TATTAAATAA-ATATTTAT
1 TATTAAATAAGATATTTAT
90322254 TATTTTATAA-AAGATATTTAT
1 TA--TTA-AATAAGATATTTAT
90322275 TAATTAAATAA
1 T-ATTAAATAA
90322286 TTATATTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
18 2 0.08
19 2 0.08
20 10 0.38
21 11 0.42
22 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TATTAAATAAGATATTTAT
Found at i:90322525 original size:13 final size:12
Alignment explanation
Indices: 90322503--90322535 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
90322493 CAGGGGAAGG
90322503 AAAG-AAAGAAA
1 AAAGAAAAGAAA
90322514 AAGAGAAAAGAAA
1 AA-AGAAAAGAAA
90322527 AAAGAAAAG
1 AAAGAAAAG
90322536 GGAAAATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 2 0.10
12 9 0.45
13 9 0.45
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (12 bp):
AAAGAAAAGAAA
Found at i:90322541 original size:14 final size:13
Alignment explanation
Indices: 90322507--90322535 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
90322497 GGAAGGAAAG
90322507 AAAGAAAAAGAGA
1 AAAGAAAAAGAGA
90322520 AAAGAAAAA-AGA
1 AAAGAAAAAGAGA
90322532 AAAG
1 AAAG
90322536 GGAAAATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAGA
Found at i:90324530 original size:46 final size:46
Alignment explanation
Indices: 90324463--90324628 Score: 226
Period size: 46 Copynumber: 3.6 Consensus size: 46
90324453 CTCTGAAATA
* * *
90324463 AAATGTGTAAAACCATGGTTGAAAGATACCATGGCAACCTGATATG
1 AAATGAGTAAAACCATGGTTGAAAGATACCATGGCAACATGACATG
* * *
90324509 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATG
1 AAATGAGTAAAACCATGGTTGAAAGATACCATGGCAACATGACATG
* * *
90324555 AAATGAATAAGACCATGGTTGAAAGATACCATGACAACATGACA-G
1 AAATGAGTAAAACCATGGTTGAAAGATACCATGGCAACATGACATG
*
90324600 AAAATGAGTAAAACCATAGTTGAAAGATA
1 -AAATGAGTAAAACCATGGTTGAAAGATA
90324629 TTATTGTAAT
Statistics
Matches: 109, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
45 1 0.01
46 108 0.99
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.21
Consensus pattern (46 bp):
AAATGAGTAAAACCATGGTTGAAAGATACCATGGCAACATGACATG
Found at i:90326285 original size:68 final size:68
Alignment explanation
Indices: 90326213--90326362 Score: 173
Period size: 67 Copynumber: 2.2 Consensus size: 68
90326203 CATCATGTGT
* * * *
90326213 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTA-TG-TGTACACCA
1 ACAAGAGAGCTACAAGACA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCA
90326276 TGTAG
64 TGTAG
** * *
90326281 ACAAGAGAGCTAC--GGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCAT
1 ACAAGAGAGCTACAAGACATATATGTAGCTAGGTCGCATGCGTGATACCA-GTGAAGGACACCAT
90326344 GTAG
65 GTAG
90326348 ACAAGAGAGCTACAA
1 ACAAGAGAGCTACAA
90326363 AATAAATTGG
Statistics
Matches: 69, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
64 24 0.35
65 3 0.04
66 4 0.06
67 25 0.36
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (68 bp):
ACAAGAGAGCTACAAGACATATATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCATG
TAG
Found at i:90326318 original size:64 final size:64
Alignment explanation
Indices: 90326169--90326420 Score: 181
Period size: 68 Copynumber: 3.8 Consensus size: 64
90326159 TACAGATAGT
* ** * * *
90326169 ATGTAGCTAGGTCACATGTATGGTGCTGA-GTGCACATCATGT-GTACAAGAGAGCTACAAGACA
1 ATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGAGCTACAA-A-A
*
90326232 TTATG
62 -TA-A
* *** *
90326237 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACAAAATAA
* * * * *
90326301 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACAAAAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACAAAAT
90326366 AA
63 AA
* * * *
90326368 AT-TGGCTAGGTCACATGGGTGGTACTGA-GTTTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGAGC
90326421 CGAACTATAT
Statistics
Matches: 147, Mismatches: 30, Indels: 19
0.75 0.15 0.10
Matches are distributed among these distances:
62 1 0.01
63 18 0.12
64 25 0.17
65 2 0.01
66 22 0.15
67 32 0.22
68 46 0.31
69 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.25
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACAAAATAA
Found at i:90330927 original size:21 final size:22
Alignment explanation
Indices: 90330881--90330928 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
90330871 TTAAACCCCA
*
90330881 ATTTCTCCCTTTTCTTTCTTTC
1 ATTTCTCCCTGTTCTTTCTTTC
90330903 -TTTCTCCCCTGTT-TTT-TTTC
1 ATTTCT-CCCTGTTCTTTCTTTC
90330923 ATTTCT
1 ATTTCT
90330929 ATTCTATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 4 0.17
21 13 0.57
22 6 0.26
ACGTcount: A:0.04, C:0.29, G:0.02, T:0.65
Consensus pattern (22 bp):
ATTTCTCCCTGTTCTTTCTTTC
Found at i:90330968 original size:9 final size:9
Alignment explanation
Indices: 90330942--90330971 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
90330932 CTATTATTCC
*
90330942 TTTCTTTTC
1 TTTCTTTTG
90330951 TTTCTTTTG
1 TTTCTTTTG
90330960 TTTCTTTTG
1 TTTCTTTTG
90330969 TTT
1 TTT
90330972 ATTATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (9 bp):
TTTCTTTTG
Found at i:90336683 original size:13 final size:13
Alignment explanation
Indices: 90336667--90336691 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
90336657 TTAAATTAGT
90336667 TAATTAGTTTAAA
1 TAATTAGTTTAAA
90336680 TAATTAGTTTAA
1 TAATTAGTTTAA
90336692 TAAACAAGCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TAATTAGTTTAAA
Found at i:90337588 original size:42 final size:43
Alignment explanation
Indices: 90337524--90337631 Score: 137
Period size: 42 Copynumber: 2.5 Consensus size: 43
90337514 ATCAACTTGA
* *
90337524 GATTACGTGTAAGACCATGTCTGCGACATCAGCATTG-TATTT
1 GATTACGTGTAAGACCATGTCTGCGACAACAGCATCGATATTT
* * * *
90337566 GATTTCGTGTAAGATCTTGTCTGGGACAACAGCATCGATATTT
1 GATTACGTGTAAGACCATGTCTGCGACAACAGCATCGATATTT
* *
90337609 GATTACATGTAAGACCACGTCTG
1 GATTACGTGTAAGACCATGTCTG
90337632 AGACGTTGGC
Statistics
Matches: 54, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
42 31 0.57
43 23 0.43
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (43 bp):
GATTACGTGTAAGACCATGTCTGCGACAACAGCATCGATATTT
Found at i:90348488 original size:4 final size:4
Alignment explanation
Indices: 90348479--90348525 Score: 53
Period size: 4 Copynumber: 12.0 Consensus size: 4
90348469 ATTTCCCCTT
* *
90348479 TTTC TTTC TTTT TCTTC TTTC TTTC -TTC TTTC TTTC -TTC TTAC TTTC
1 TTTC TTTC TTTC T-TTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
90348526 GAAAGTCTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
3 6 0.17
4 27 0.75
5 3 0.08
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTC
Found at i:90348503 original size:11 final size:11
Alignment explanation
Indices: 90348476--90348525 Score: 66
Period size: 11 Copynumber: 4.5 Consensus size: 11
90348466 TCTATTTCCC
90348476 CTTT-TTCTTT
1 CTTTCTTCTTT
90348486 CTTTTTCTTCTTT
1 C--TTTCTTCTTT
90348499 CTTTCTTCTTT
1 CTTTCTTCTTT
*
90348510 CTTTCTTCTTA
1 CTTTCTTCTTT
90348521 CTTTC
1 CTTTC
90348526 GAAAGTCTCT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
10 1 0.03
11 25 0.69
12 3 0.08
13 7 0.19
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (11 bp):
CTTTCTTCTTT
Found at i:90352875 original size:40 final size:40
Alignment explanation
Indices: 90352829--90352905 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
90352819 GCACACCATG
*
90352829 TGGGGATAAAATCAACCCACCCAGCCCTACACACCAAGTA
1 TGGGGATAAAATCAACCCACCCAACCCTACACACCAAGTA
* *
90352869 TGGGGATAGAATCAACCCATCCAACCCTACACACCAA
1 TGGGGATAAAATCAACCCACCCAACCCTACACACCAA
90352906 ATGGTATCGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.38, C:0.35, G:0.14, T:0.13
Consensus pattern (40 bp):
TGGGGATAAAATCAACCCACCCAACCCTACACACCAAGTA
Found at i:90355861 original size:15 final size:15
Alignment explanation
Indices: 90355816--90355888 Score: 83
Period size: 15 Copynumber: 4.9 Consensus size: 15
90355806 GAGATTACAT
*
90355816 GAAAACCAAGATAAA
1 GAAATCCAAGATAAA
* * * *
90355831 GTAGTCCAGGACAAA
1 GAAATCCAAGATAAA
*
90355846 GAAATCTAAGATAAA
1 GAAATCCAAGATAAA
*
90355861 GAAATCCAAGATACA
1 GAAATCCAAGATAAA
90355876 GAAATCCAAGATA
1 GAAATCCAAGATA
90355889 CAATATCCTA
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 46 1.00
ACGTcount: A:0.55, C:0.15, G:0.16, T:0.14
Consensus pattern (15 bp):
GAAATCCAAGATAAA
Found at i:90358746 original size:13 final size:14
Alignment explanation
Indices: 90358720--90358751 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
90358710 ACTAACGACG
90358720 AATTAAACCATTAT
1 AATTAAACCATTAT
90358734 AATTAAA-CATTAT
1 AATTAAACCATTAT
90358747 AATTA
1 AATTA
90358752 TTTATAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:90363833 original size:7 final size:7
Alignment explanation
Indices: 90363823--90363847 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
90363813 AGATAATACC
90363823 TATCAAG
1 TATCAAG
90363830 TATCAAG
1 TATCAAG
90363837 TATCAAG
1 TATCAAG
90363844 TATC
1 TATC
90363848 TAATGGGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (7 bp):
TATCAAG
Found at i:90363953 original size:9 final size:9
Alignment explanation
Indices: 90363941--90364120 Score: 156
Period size: 9 Copynumber: 20.6 Consensus size: 9
90363931 TGATATATAT
90363941 TTATGTAAG
1 TTATGTAAG
90363950 TTATGTAAG
1 TTATGTAAG
* *
90363959 TTATAT-AT
1 TTATGTAAG
*
90363967 TTATCTAAG
1 TTATGTAAG
*
90363976 TTATATAAG
1 TTATGTAAG
90363985 TTATGTAAG
1 TTATGTAAG
90363994 TTATGTAAG
1 TTATGTAAG
*
90364003 TTATGATATG
1 TTATG-TAAG
* * *
90364013 ATATAT-AT
1 TTATGTAAG
90364021 TTATGTAAG
1 TTATGTAAG
*
90364030 TTATGTTAG
1 TTATGTAAG
* *
90364039 TTATAT-AT
1 TTATGTAAG
*
90364047 TTATCTAAG
1 TTATGTAAG
90364056 TTATGTAAG
1 TTATGTAAG
*
90364065 TTATGTAAA
1 TTATGTAAG
*
90364074 TTA--T-AT
1 TTATGTAAG
*
90364080 TTATATAAG
1 TTATGTAAG
*
90364089 TTATATAAG
1 TTATGTAAG
*
90364098 TTATGTAAA
1 TTATGTAAG
90364107 TTATGTAAG
1 TTATGTAAG
90364116 TTATG
1 TTATG
90364121 ATATGATATA
Statistics
Matches: 138, Mismatches: 26, Indels: 14
0.78 0.15 0.08
Matches are distributed among these distances:
6 4 0.03
7 1 0.01
8 17 0.12
9 110 0.80
10 6 0.04
ACGTcount: A:0.36, C:0.01, G:0.14, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:90363975 original size:17 final size:18
Alignment explanation
Indices: 90363905--90364120 Score: 151
Period size: 18 Copynumber: 12.3 Consensus size: 18
90363895 TATTTATGTA
90363905 TTATGTAAGTTA-AGTAAG
1 TTATGTAAGTTATA-TAAG
* * *
90363923 TTATGATATGATATAT-AT
1 TTATG-TAAGTTATATAAG
*
90363941 TTATGTAAGTTATGTAAG
1 TTATGTAAGTTATATAAG
* * *
90363959 TTATAT-ATTTATCTAAG
1 TTATGTAAGTTATATAAG
* *
90363976 TTATATAAGTTATGTAAG
1 TTATGTAAGTTATATAAG
*
90363994 TTATGTAAGTTATGATATG
1 TTATGTAAGTTAT-ATAAG
* * * *
90364013 ATATAT-ATTTATGTAAG
1 TTATGTAAGTTATATAAG
* *
90364030 TTATGTTAGTTATAT-AT
1 TTATGTAAGTTATATAAG
* *
90364047 TTATCTAAGTTATGTAAG
1 TTATGTAAGTTATATAAG
*
90364065 TTATGTAAATTATAT---
1 TTATGTAAGTTATATAAG
*
90364080 TTATATAAGTTATATAAG
1 TTATGTAAGTTATATAAG
* *
90364098 TTATGTAAATTATGTAAG
1 TTATGTAAGTTATATAAG
90364116 TTATG
1 TTATG
90364121 ATATGATATA
Statistics
Matches: 151, Mismatches: 37, Indels: 20
0.73 0.18 0.10
Matches are distributed among these distances:
15 13 0.09
17 42 0.28
18 82 0.54
19 13 0.09
20 1 0.01
ACGTcount: A:0.37, C:0.01, G:0.15, T:0.48
Consensus pattern (18 bp):
TTATGTAAGTTATATAAG
Found at i:90363996 original size:80 final size:80
Alignment explanation
Indices: 90363905--90364124 Score: 313
Period size: 80 Copynumber: 2.8 Consensus size: 80
90363895 TATTTATGTA
90363905 TTATGTAAGTTAAGTAAGTTATGATATGATATATATTTATGTAAGTTATGTAAGTTATATATTTA
1 TTATGTAAGTTAAGTAAGTTATGATATGATATATATTTATGTAAGTTATGTAAGTTATATATTTA
90363970 TCTAAGTTATATAAG
66 TCTAAGTTATATAAG
* *
90363985 TTATGTAAGTTATGTAAGTTATGATATGATATATATTTATGTAAGTTATGTTAGTTATATATTTA
1 TTATGTAAGTTAAGTAAGTTATGATATGATATATATTTATGTAAGTTATGTAAGTTATATATTTA
*
90364050 TCTAAGTTATGTAAG
66 TCTAAGTTATATAAG
* * * * * *
90364065 TTATGTAAATT-A-T-ATTTAT-ATAAGTTATATAAGTTATGTAAATTATGTAAGTTATGATAT
1 TTATGTAAGTTAAGTAAGTTATGATATGATATAT-ATTTATGTAAGTTATGTAAGTTAT-ATAT
90364125 GATATATATT
Statistics
Matches: 127, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
76 9 0.07
77 26 0.20
78 5 0.04
80 87 0.69
ACGTcount: A:0.37, C:0.01, G:0.15, T:0.48
Consensus pattern (80 bp):
TTATGTAAGTTAAGTAAGTTATGATATGATATATATTTATGTAAGTTATGTAAGTTATATATTTA
TCTAAGTTATATAAG
Found at i:90364101 original size:42 final size:41
Alignment explanation
Indices: 90364039--90364119 Score: 117
Period size: 42 Copynumber: 2.0 Consensus size: 41
90364029 GTTATGTTAG
* * *
90364039 TTATATATTTATCTAAGTTATGTAAGTTATGTAAATTATAT
1 TTATATAGTTATATAAGTTATGTAAATTATGTAAATTATAT
*
90364080 TTATATAAGTTATATAAGTTATGTAAATTATGTAAGTTAT
1 TTATAT-AGTTATATAAGTTATGTAAATTATGTAAATTAT
90364120 GATATGATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
41 6 0.17
42 29 0.83
ACGTcount: A:0.38, C:0.01, G:0.11, T:0.49
Consensus pattern (41 bp):
TTATATAGTTATATAAGTTATGTAAATTATGTAAATTATAT
Found at i:90364103 original size:113 final size:116
Alignment explanation
Indices: 90363905--90364136 Score: 355
Period size: 113 Copynumber: 2.0 Consensus size: 116
90363895 TATTTATGTA
* *
90363905 TTATGTAAGTTAAGTAAGTTATGATATGATATATATTTATGTAAGTTATGTAAGTTATATATTTA
1 TTATGTAAGTTAAGTAAGTTATGATATGATATATAGTTATGTAAGTTATGTAAGATATATATTTA
* *
90363970 TCTAAGTTATATAAGTTATGTAAGTTATGTAAGTTATGATATGATATATAT
66 TATAAGTTATATAAGTTATGTAAATTATGTAAGTTATGATATGATATATAT
* * * *
90364021 TTATGTAAGTTATGTTAGTTAT-ATAT-TTATCTAAGTTATGTAAGTTATGTAA-AT-TATATTT
1 TTATGTAAGTTAAGTAAGTTATGATATGATATAT-AGTTATGTAAGTTATGTAAGATATATATTT
90364082 ATATAAGTTATATAAGTTATGTAAATTATGTAAGTTATGATATGATATATAT
65 ATATAAGTTATATAAGTTATGTAAATTATGTAAGTTATGATATGATATATAT
90364134 TTA
1 TTA
90364137 ACATTAAGAT
Statistics
Matches: 107, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
113 60 0.56
114 5 0.05
115 22 0.21
116 20 0.19
ACGTcount: A:0.37, C:0.01, G:0.14, T:0.48
Consensus pattern (116 bp):
TTATGTAAGTTAAGTAAGTTATGATATGATATATAGTTATGTAAGTTATGTAAGATATATATTTA
TATAAGTTATATAAGTTATGTAAATTATGTAAGTTATGATATGATATATAT
Found at i:90364849 original size:23 final size:23
Alignment explanation
Indices: 90364819--90364864 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
90364809 CTTTTTTATT
90364819 ATTATCAAATGAA-TTTTCTTAAC
1 ATTATCAAAT-AAGTTTTCTTAAC
90364842 ATTATCAAATAAGTTTTCTTAAC
1 ATTATCAAATAAGTTTTCTTAAC
90364865 CAAATACTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.39, C:0.13, G:0.04, T:0.43
Consensus pattern (23 bp):
ATTATCAAATAAGTTTTCTTAAC
Found at i:90365565 original size:24 final size:24
Alignment explanation
Indices: 90365538--90365584 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
90365528 GAAGCAGCAG
* *
90365538 AGGGATGCCGACGGAGATGTAGCT
1 AGGGATGACGACGGAAATGTAGCT
90365562 AGGGATGACGACGGAAATGTAGC
1 AGGGATGACGACGGAAATGTAGC
90365585 AGAGGGCTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.15, G:0.40, T:0.15
Consensus pattern (24 bp):
AGGGATGACGACGGAAATGTAGCT
Found at i:90365729 original size:14 final size:14
Alignment explanation
Indices: 90365710--90365754 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
90365700 AACAACCCAA
90365710 GATATATGCATATT
1 GATATATGCATATT
90365724 GATATATG--TA-T
1 GATATATGCATATT
*
90365735 -ACATATGCATATT
1 GATATATGCATATT
90365748 GATATAT
1 GATATAT
90365755 ATATACATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
10 6 0.24
11 1 0.04
12 4 0.16
13 1 0.04
14 13 0.52
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.42
Consensus pattern (14 bp):
GATATATGCATATT
Found at i:90365745 original size:24 final size:24
Alignment explanation
Indices: 90365713--90365762 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
90365703 AACCCAAGAT
*
90365713 ATATGCATATTGATATATGTATAC
1 ATATGCATATTGATATATATATAC
90365737 ATATGCATATTGATATATATATAC
1 ATATGCATATTGATATATATATAC
90365761 AT
1 AT
90365763 TACAATCACG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (24 bp):
ATATGCATATTGATATATATATAC
Found at i:90367420 original size:21 final size:21
Alignment explanation
Indices: 90367395--90367498 Score: 96
Period size: 20 Copynumber: 5.2 Consensus size: 21
90367385 TAGCCTTCGG
90367395 GCTTCCGTTTAGCACTTGTGT
1 GCTTCCGTTTAGCACTTGTGT
* * **
90367416 GCTTCAG-TCAGC-CTTCAG-
1 GCTTCCGTTTAGCACTTGTGT
90367434 GCTTCCGTTTAGCACTTGTGT
1 GCTTCCGTTTAGCACTTGTGT
*
90367455 GCTTCAG-TTAGC-CTTCG-G-
1 GCTTCCGTTTAGCACTT-GTGT
*
90367473 GCTTCCGTTTAGCACTTATGT
1 GCTTCCGTTTAGCACTTGTGT
90367494 GCTTC
1 GCTTC
90367499 AGCTAGACTT
Statistics
Matches: 64, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
18 12 0.19
19 17 0.27
20 18 0.28
21 17 0.27
ACGTcount: A:0.12, C:0.27, G:0.23, T:0.38
Consensus pattern (21 bp):
GCTTCCGTTTAGCACTTGTGT
Found at i:90367423 original size:39 final size:39
Alignment explanation
Indices: 90367377--90367516 Score: 235
Period size: 39 Copynumber: 3.6 Consensus size: 39
90367367 GCTCTAATGA
90367377 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
* *
90367416 GCTTCAGTCAGCCTTCAGGCTTCCGTTTAGCACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
*
90367455 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
* *
90367494 GCTTCAGCTAGACTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
90367517 AGATTACGAT
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 94 1.00
ACGTcount: A:0.12, C:0.27, G:0.24, T:0.36
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
Found at i:90368241 original size:28 final size:28
Alignment explanation
Indices: 90368208--90368263 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
90368198 TTTAAATAAT
90368208 AATAATAAAATAAAC-AAAAAAATAAAAA
1 AATAATAAAAT-AACGAAAAAAATAAAAA
* * *
90368236 AATAATTATATTACGAAAAAAATAAAAA
1 AATAATAAAATAACGAAAAAAATAAAAA
90368264 TTTCGGAGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 2 0.08
28 22 0.92
ACGTcount: A:0.75, C:0.04, G:0.02, T:0.20
Consensus pattern (28 bp):
AATAATAAAATAACGAAAAAAATAAAAA
Found at i:90370980 original size:55 final size:56
Alignment explanation
Indices: 90370915--90371029 Score: 146
Period size: 55 Copynumber: 2.1 Consensus size: 56
90370905 AGCATGGCTG
* *
90370915 CCAGATACAGA-AAATGTGACAGAGTCACCAGATACAGATATTTTGTGGCAGT-GCCA
1 CCAGATACAGATAAATGTGACAGAGCCACCAGA-ACAGATAATTTGTGGCA-TAGCCA
* * *
90370971 CCAGA-ACAGATATATGTGGCAGGGCCACCAGAACAGATAATTTGTGGCATAGCCA
1 CCAGATACAGATAAATGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
90371026 CCAG
1 CCAG
90371030 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
54 1 0.02
55 29 0.56
56 22 0.42
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (56 bp):
CCAGATACAGATAAATGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
Found at i:90370992 original size:27 final size:27
Alignment explanation
Indices: 90370940--90371029 Score: 119
Period size: 27 Copynumber: 3.2 Consensus size: 27
90370930 GTGACAGAGT
90370940 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATA-TTTGTGGCAGTGC
* *
90370969 CACCAGAACAGATATATGTGGCAGGGC
1 CACCAGAACAGATATTTGTGGCAGTGC
90370996 CACCAGAACAGATAATTTGTGGCA-TAGC
1 CACCAGAACAGAT-ATTTGTGGCAGT-GC
90371024 CACCAG
1 CACCAG
90371030 GACGCTTCCT
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
27 24 0.44
28 24 0.44
29 7 0.13
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.20
Consensus pattern (27 bp):
CACCAGAACAGATATTTGTGGCAGTGC
Found at i:90371182 original size:28 final size:28
Alignment explanation
Indices: 90371135--90371227 Score: 159
Period size: 28 Copynumber: 3.3 Consensus size: 28
90371125 AAATTAACTC
* * *
90371135 TAGGGGTATAAAGGTCATTTTGCATACA
1 TAGGGGTATTATGGTAATTTTGCATACA
90371163 TAGGGGTATTATGGTAATTTTGCATACA
1 TAGGGGTATTATGGTAATTTTGCATACA
90371191 TAGGGGTATTATGGTAATTTTGCATACA
1 TAGGGGTATTATGGTAATTTTGCATACA
90371219 TAGGGGTAT
1 TAGGGGTAT
90371228 AATAGTACAT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 62 1.00
ACGTcount: A:0.29, C:0.08, G:0.27, T:0.37
Consensus pattern (28 bp):
TAGGGGTATTATGGTAATTTTGCATACA
Found at i:90372323 original size:5 final size:5
Alignment explanation
Indices: 90372313--90372344 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
90372303 GATGGAGAAA
*
90372313 AAAAG AAAAG AAAAG AAAAG AAAGG AAAAG AA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AA
90372345 GGAAGAATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:90372346 original size:9 final size:10
Alignment explanation
Indices: 90372309--90372348 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
90372299 GATAGATGGA
90372309 GAAAA-AAA-
1 GAAAAGAAAG
*
90372317 GAAAAGAAAA
1 GAAAAGAAAG
90372327 GAAAAGAAAG
1 GAAAAGAAAG
90372337 GAAAAG-AAG
1 GAAAAGAAAG
90372346 GAA
1 GAA
90372349 GAATGGTCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
8 5 0.17
9 9 0.31
10 15 0.52
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (10 bp):
GAAAAGAAAG
Found at i:90373907 original size:18 final size:17
Alignment explanation
Indices: 90373855--90373905 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
90373845 GACAAATGGG
*
90373855 TTTGATTTTGGGGAAAT
1 TTTGATTTAGGGGAAAT
* *
90373872 TTAGGGTTTAGGGGAAAT
1 TT-TGATTTAGGGGAAAT
*
90373890 TTTGATTTGGGGGAAA
1 TTTGATTTAGGGGAAA
90373906 ATAAGGGTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.25, C:0.00, G:0.35, T:0.39
Consensus pattern (17 bp):
TTTGATTTAGGGGAAAT
Found at i:90374077 original size:40 final size:40
Alignment explanation
Indices: 90374023--90374132 Score: 130
Period size: 40 Copynumber: 2.8 Consensus size: 40
90374013 TAATTAAACT
*
90374023 TTTAGCGGCATTTTTACAAAAGTGCCGCTAAATCTCAATC
1 TTTAGCAGCATTTTTACAAAAGTGCCGCTAAATCTCAATC
* * * * *
90374063 TTTTGCAGCGTTTTTACAAAAGCGCAGCTAATTCTCAATC
1 TTTAGCAGCATTTTTACAAAAGTGCCGCTAAATCTCAATC
** * *
90374103 TTTAGTGGCATTTTTAAAAAAATGCCGCTA
1 TTTAGCAGCATTTTTACAAAAGTGCCGCTA
90374133 CTGCCTCTGG
Statistics
Matches: 56, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 56 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (40 bp):
TTTAGCAGCATTTTTACAAAAGTGCCGCTAAATCTCAATC
Found at i:90375262 original size:38 final size:36
Alignment explanation
Indices: 90375192--90375271 Score: 117
Period size: 38 Copynumber: 2.2 Consensus size: 36
90375182 CCCAACCCAT
*
90375192 ACCATAAACTTAACATACTATACCATTGAACCCTAA
1 ACCATAAACTTAAAATACTATACCATTGAACCCTAA
90375228 ACCATAAACTTAAAATA-TATTCTACCATTGAACCCTAA
1 ACCATAAACTTAAAATACTA---TACCATTGAACCCTAA
90375266 ACCATA
1 ACCATA
90375272 GGCCTTAAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
35 2 0.05
36 16 0.40
38 22 0.55
ACGTcount: A:0.45, C:0.26, G:0.03, T:0.26
Consensus pattern (36 bp):
ACCATAAACTTAAAATACTATACCATTGAACCCTAA
Found at i:90383864 original size:44 final size:44
Alignment explanation
Indices: 90383801--90384290 Score: 491
Period size: 44 Copynumber: 11.1 Consensus size: 44
90383791 GTCACCGTGG
* *
90383801 CAAATCTTATCTCCCTGAATTTACAGTGGAGCAGATTAAAGCCA
1 CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCTA
* * * *
90383845 CAAATCTTATCCCCCTGAA-TTCATAGTGGAGCATATTAAAGTTA
1 CAAATCTTATCTCCCTGAAGTT-ACAGTGGAGCAGATTAAAGCTA
* * *
90383889 CAAATCTTATCTCCTTAAAGTTGCAGTGGAGCAGATTAAAGCTA
1 CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCTA
* *
90383933 CAAATCTTATTTCCCTGAAGTTACAGTGGAACAGATTGAAA-CTA
1 CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATT-AAAGCTA
* * *
90383977 CAAATCTTATCTCCCTAAAGTTACAGTGGAACAGATTGAAA-CGA
1 CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATT-AAAGCTA
* * *
90384021 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
1 CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCTA
** * * * * * * * *
90384065 TGAGTATCATCTCCCTGAAGCTATAGTTGAGCAGATTGAAGTTA
1 CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCTA
* ** *
90384109 CAAATCTTATCTCCTTGAAGTTGTAGTGGAGCAGATTAAAGTTA
1 CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCTA
* * * * * *
90384153 CAAATCTTATCTCCCTGAAGTTGCAATGAAGTAGATTGAAGATA
1 CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCTA
* * *
90384197 CGAGTCTTATCTCCCTGAAGTTACAGGGGAGCAGATTAAAGCTA
1 CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCTA
* * * * * * * * *
90384241 CAAGTCTAATCTTCTTGAAGTTGCAGTAGAGTAGATTGAAGCAA
1 CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCTA
90384285 CAAATC
1 CAAATC
90384291 CTATACCTCT
Statistics
Matches: 369, Mismatches: 73, Indels: 8
0.82 0.16 0.02
Matches are distributed among these distances:
43 4 0.01
44 360 0.98
45 5 0.01
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (44 bp):
CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCTA
Found at i:90384325 original size:132 final size:132
Alignment explanation
Indices: 90383805--90384313 Score: 551
Period size: 132 Copynumber: 3.9 Consensus size: 132
90383795 CCGTGGCAAA
* * *
90383805 TCTTATCTCCCTGAATTTACAGTGGAGCAGATTAAAGCCACAAATCTTATCCCCCTGAA-TT-CA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCTACAAATCTTATCTCCCTGAAGTTGC-
* * * * *
90383868 TAGTGGAGCATATTAAAGTTACAAATCTTATCTCCTTAAAGTTGCAGTGGAGCAGATTAAAGCTA
65 -AGTGGAGCAGATTAAAGCTACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGATA
* *
90383933 CAAA
129 CGAG
* * * *
90383937 TCTTATTTCCCTGAAGTTACAGTGGAACAGATTGAAA-CTACAAATCTTATCTCCCTAAAGTTAC
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATT-AAAGCTACAAATCTTATCTCCCTGAAGTTGC
* * *
90384001 AGTGGAACAGATTGAAA-CGACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
65 AGTGGAGCAGATT-AAAGCTACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGATA
*
90384065 TGAG
129 CGAG
* * * * * * * * *
90384069 TATCATCTCCCTGAAGCTATAGTTGAGCAGATTGAAGTTACAAATCTTATCTCCTTGAAGTTGTA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCTACAAATCTTATCTCCCTGAAGTTGCA
* * * * *
90384134 GTGGAGCAGATTAAAGTTACAAATCTTATCTCCCTGAAGTTGCAATGAAGTAGATTGAAGATACG
66 GTGGAGCAGATTAAAGCTACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGATACG
90384199 AG
131 AG
* * * * *
90384201 TCTTATCTCCCTGAAGTTACAGGGGAGCAGATTAAAGCTACAAGTCTAATCTTCTTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCTACAAATCTTATCTCCCTGAAGTTGCA
* * * * * *
90384266 GTAGAGTAGATTGAAGCAACAAATCCTATAC-CTCTAAAGTTGCAGTGG
66 GTGGAGCAGATTAAAGCTACAAATCTTAT-CTCCCTAAAGTTGCAGTGG
90384314 GTTAGAATGA
Statistics
Matches: 311, Mismatches: 59, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
131 5 0.02
132 296 0.95
133 9 0.03
134 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.29
Consensus pattern (132 bp):
TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCTACAAATCTTATCTCCCTGAAGTTGCA
GTGGAGCAGATTAAAGCTACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGATACG
AG
Found at i:90385568 original size:24 final size:24
Alignment explanation
Indices: 90385541--90385599 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
90385531 CTGGAGGCCT
* *
90385541 AGCCTCTTTTAAT-ATCTGGGGCAA
1 AGCC-CTTTTAATAAACTGCGGCAA
*
90385565 AGCCCTTTTCAGTAAACTGCGGCAA
1 AGCCCTTTT-AATAAACTGCGGCAA
90385590 AGCCCTTTTA
1 AGCCCTTTTA
90385600 GCACTTCCTC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 5 0.17
24 7 0.23
25 18 0.60
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (24 bp):
AGCCCTTTTAATAAACTGCGGCAA
Found at i:90390014 original size:55 final size:55
Alignment explanation
Indices: 90389930--90390039 Score: 211
Period size: 55 Copynumber: 2.0 Consensus size: 55
90389920 CTCTCAGTTA
90389930 GTCGAACAGATCGTCGATTCTTGGCAAAGGATACTTGTTCTTGATCGTCAGCTTG
1 GTCGAACAGATCGTCGATTCTTGGCAAAGGATACTTGTTCTTGATCGTCAGCTTG
*
90389985 GTCGAACAGATCGTCGATTCTTGGCAAAGGATACTTGTTCTTGATTGTCAGCTTG
1 GTCGAACAGATCGTCGATTCTTGGCAAAGGATACTTGTTCTTGATCGTCAGCTTG
90390040 TTCAGCTGCC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (55 bp):
GTCGAACAGATCGTCGATTCTTGGCAAAGGATACTTGTTCTTGATCGTCAGCTTG
Found at i:90393159 original size:29 final size:30
Alignment explanation
Indices: 90393107--90393165 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
90393097 TTTCAGTATA
**
90393107 TACTGGGTTGAAGCCTTTCATTTAA-CGGT
1 TACTGGGCCGAAGCCTTTCATTTAATCGGT
90393136 TACTGGGCCGAAGCCTTT-ACTTTAATCGGT
1 TACTGGGCCGAAGCCTTTCA-TTTAATCGGT
90393166 ATGGCCCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 1 0.04
29 21 0.81
30 4 0.15
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (30 bp):
TACTGGGCCGAAGCCTTTCATTTAATCGGT
Found at i:90393475 original size:10 final size:10
Alignment explanation
Indices: 90393462--90393500 Score: 69
Period size: 10 Copynumber: 3.8 Consensus size: 10
90393452 ATATGTGAAT
90393462 ATATCATGGC
1 ATATCATGGC
90393472 ATATCATGTGC
1 ATATCATG-GC
90393483 ATATCATGGC
1 ATATCATGGC
90393493 ATATCATG
1 ATATCATG
90393501 TACAAAAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 18 0.64
11 10 0.36
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (10 bp):
ATATCATGGC
Found at i:90393488 original size:21 final size:21
Alignment explanation
Indices: 90393462--90393501 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
90393452 ATATGTGAAT
90393462 ATATCATGGCATATCATGTGC
1 ATATCATGGCATATCATGTGC
90393483 ATATCATGGCATATCATGT
1 ATATCATGGCATATCATGT
90393502 ACAAAAACAA
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:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (21 bp):
ATATCATGGCATATCATGTGC
Found at i:90396650 original size:3 final size:3
Alignment explanation
Indices: 90396642--90396677 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
90396632 ACTTGCACCT
90396642 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
90396678 CTACTACTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:90399486 original size:13 final size:13
Alignment explanation
Indices: 90399470--90399520 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
90399460 TTTAAACCAA
90399470 ACTTTTCAAAAAC
1 ACTTTTCAAAAAC
* *
90399483 ACTTTTTC-ACAGC
1 AC-TTTTCAAAAAC
*
90399496 ACTTTTCAAAAGC
1 ACTTTTCAAAAAC
90399509 ACTTTTCAAAAA
1 ACTTTTCAAAAA
90399521 TATTGCCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 5 0.16
13 22 0.69
14 5 0.16
ACGTcount: A:0.39, C:0.24, G:0.04, T:0.33
Consensus pattern (13 bp):
ACTTTTCAAAAAC
Found at i:90406898 original size:58 final size:58
Alignment explanation
Indices: 90406829--90406943 Score: 194
Period size: 58 Copynumber: 2.0 Consensus size: 58
90406819 AAGTGATAGA
** *
90406829 TGAAAAATCTTATATGCTAGGTCTATTGCAGAAATAGCTTAAGAATATAAAGCAATTG
1 TGAAAAATCTTATATGCTAGGTCTATCACAGAAATAGCTCAAGAATATAAAGCAATTG
*
90406887 TGAAAAATCTTATATGTTAGGTCTATCACAGAAATAGCTCAAGAATATAAAGCAATT
1 TGAAAAATCTTATATGCTAGGTCTATCACAGAAATAGCTCAAGAATATAAAGCAATT
90406944 CAAGTGAGCT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (58 bp):
TGAAAAATCTTATATGCTAGGTCTATCACAGAAATAGCTCAAGAATATAAAGCAATTG
Found at i:90415996 original size:92 final size:92
Alignment explanation
Indices: 90415839--90416029 Score: 373
Period size: 92 Copynumber: 2.1 Consensus size: 92
90415829 TCGTATTTTG
*
90415839 GAGATTCGAGAAATCTTACCCTAACTTACGGGGTTTCGATTTTTCTCGTTGAACGTAAATAACCA
1 GAGATTCGAGAAATCTTACCCTAACTTACGGGGTTTCGATTTTTCTCGTTGAACATAAATAACCA
90415904 AATATCCTTTTTAAAATTAAAATACAT
66 AATATCCTTTTTAAAATTAAAATACAT
90415931 GAGATTCGAGAAATCTTACCCTAACTTACGGGGTTTCGATTTTTCTCGTTGAACATAAATAACCA
1 GAGATTCGAGAAATCTTACCCTAACTTACGGGGTTTCGATTTTTCTCGTTGAACATAAATAACCA
90415996 AATATCCTTTTTAAAATTAAAATACAT
66 AATATCCTTTTTAAAATTAAAATACAT
90416023 GAGATTC
1 GAGATTC
90416030 TAAATAAAAA
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 98 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (92 bp):
GAGATTCGAGAAATCTTACCCTAACTTACGGGGTTTCGATTTTTCTCGTTGAACATAAATAACCA
AATATCCTTTTTAAAATTAAAATACAT
Found at i:90437325 original size:47 final size:47
Alignment explanation
Indices: 90437192--90437398 Score: 193
Period size: 47 Copynumber: 4.3 Consensus size: 47
90437182 ATAGTAAAAC
** * *
90437192 TATGGTCTTGCACA-TAGTCACATATCACATACCGAGGCCATAGCCCAGC
1 TATGGTCTTATACAGTAG-CACATATCAC--ACCGATGCCATAGCCCAGA
* * * * *
90437241 TATGGTCTTACAC-GGATCACATATCACACTGATGCCATATCCCAGA
1 TATGGTCTTATACAGTAGCACATATCACACCGATGCCATAGCCCAGA
* *
90437287 TATGGTCTTATACAGTAGCACATATCACACCGATGCCATATCCCGGA
1 TATGGTCTTATACAGTAGCACATATCACACCGATGCCATAGCCCAGA
* * * *
90437334 TATGGTCTTATACGGAAGCACATATCACATTTCTCCGAAGCCATAGCCCAGC
1 TATGGTCTTATACAGTAGCACATATCACA-----CCGATGCCATAGCCCAGA
90437386 TATGGTCTTATAC
1 TATGGTCTTATAC
90437399 GAAAATCACA
Statistics
Matches: 133, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
46 27 0.20
47 56 0.42
48 10 0.08
49 13 0.10
52 27 0.20
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (47 bp):
TATGGTCTTATACAGTAGCACATATCACACCGATGCCATAGCCCAGA
Found at i:90440265 original size:50 final size:51
Alignment explanation
Indices: 90440189--90440287 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 51
90440179 CATGATCAGG
*
90440189 TGGTAAACCCAAAAATTCCTCAAGAAACACGTTAGTAAACTCATTAACAAC
1 TGGTAAACCCAAAAATTCCTCAAGAAACACATTAGTAAACTCATTAACAAC
90440240 TGGT-AACCCAAAAATTCCTCAAGAAACACATTAGTAAACTCATTAACA
1 TGGTAAACCCAAAAATTCCTCAAGAAACACATTAGTAAACTCATTAACA
90440288 TCTAGTAATT
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
50 43 0.91
51 4 0.09
ACGTcount: A:0.45, C:0.23, G:0.09, T:0.22
Consensus pattern (51 bp):
TGGTAAACCCAAAAATTCCTCAAGAAACACATTAGTAAACTCATTAACAAC
Found at i:90442778 original size:22 final size:23
Alignment explanation
Indices: 90442753--90442798 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
90442743 CAACCAAACC
90442753 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
90442775 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
90442798 A
1 A
90442799 CGTCATCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:90442804 original size:23 final size:22
Alignment explanation
Indices: 90442760--90442809 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
90442750 ACCAATTCAA
*
90442760 CATATTTTCAAGATAAATTCAT
1 CATATTTTCAAGATAAAGTCAT
*
90442782 GCATATTTAT-AAGATAACGTCAT
1 -CATATTT-TCAAGATAAAGTCAT
90442805 CATAT
1 CATAT
90442810 ACCCAAAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 5 0.21
23 18 0.75
24 1 0.04
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (22 bp):
CATATTTTCAAGATAAAGTCAT
Found at i:90450512 original size:22 final size:23
Alignment explanation
Indices: 90450487--90450532 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
90450477 CAACCAAACC
90450487 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
90450509 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
90450532 A
1 A
90450533 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:90450538 original size:23 final size:23
Alignment explanation
Indices: 90450494--90450538 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
90450484 ACCAATTCAA
*
90450494 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
90450517 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
90450539 CACATACCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:90455225 original size:186 final size:186
Alignment explanation
Indices: 90454911--90455284 Score: 676
Period size: 186 Copynumber: 2.0 Consensus size: 186
90454901 CAAATTGCCT
* *
90454911 AAACACATGCACTCAAAAAAAAAACTTAGTTACATAAGTCTCATGTATATCAAATAAGCATAGAT
1 AAACACATACACTCAAAAAAAAAACGTAGTTACATAAGTCTCATGTATATCAAATAAGCATAGAT
90454976 GAGCTCATCAGAACACTTAGAATCATTTAAAATATAATTCTATTTATTTCACACTTTCTCTTGTC
66 GAGCTCATCAGAACACTTAGAATCATTTAAAATATAATTCTATTTATTTCACACTTTCTCTTGTC
*
90455041 GAGAGTTTTATCTGTTGAATTACTAAAATATCGATGGATACTTAAGTAGTACACTC
131 GAGAGTTTTATCCGTTGAATTACTAAAATATCGATGGATACTTAAGTAGTACACTC
* * * *
90455097 AAACACATACACTCAAACAAACAAGGTAGTTACATAAGTCTCATGTATATCAAATAAGTATAGAT
1 AAACACATACACTCAAAAAAAAAACGTAGTTACATAAGTCTCATGTATATCAAATAAGCATAGAT
90455162 GAGCTCATCAGAACACTTAGAATCATTTAAAATATAATTCTATTTATTTCACACTTTCTCTTGTC
66 GAGCTCATCAGAACACTTAGAATCATTTAAAATATAATTCTATTTATTTCACACTTTCTCTTGTC
*
90455227 GAGAGTTTTATCCGTTGAATTACTAAAATATCGATGGATACTTAAGTTGTACACTC
131 GAGAGTTTTATCCGTTGAATTACTAAAATATCGATGGATACTTAAGTAGTACACTC
90455283 AA
1 AA
90455285 GGTGTACATA
Statistics
Matches: 180, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
186 180 1.00
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (186 bp):
AAACACATACACTCAAAAAAAAAACGTAGTTACATAAGTCTCATGTATATCAAATAAGCATAGAT
GAGCTCATCAGAACACTTAGAATCATTTAAAATATAATTCTATTTATTTCACACTTTCTCTTGTC
GAGAGTTTTATCCGTTGAATTACTAAAATATCGATGGATACTTAAGTAGTACACTC
Found at i:90472945 original size:10 final size:10
Alignment explanation
Indices: 90472926--90472975 Score: 66
Period size: 10 Copynumber: 5.0 Consensus size: 10
90472916 TTAAATTCTA
90472926 AAAGATAAAT
1 AAAGATAAAT
90472936 ACAA-ATAAAT
1 A-AAGATAAAT
*
90472946 AAAGATAATT
1 AAAGATAAAT
90472956 AAAGATAAAT
1 AAAGATAAAT
*
90472966 AAAAATAAAT
1 AAAGATAAAT
90472976 CCTAAATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 2 0.06
10 31 0.89
11 2 0.06
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:90474384 original size:62 final size:63
Alignment explanation
Indices: 90474302--90474468 Score: 160
Period size: 63 Copynumber: 2.7 Consensus size: 63
90474292 GTAACTTATC
* * * * * **
90474302 ATTTTGAAATTAGAGCCACAC-GGACAGA-AGCACGAGCGTGTATCCAGGCTGCGTAACTTACT
1 ATTTTGGAATTAGAGTCACACGGGACAGAGA-CACGAGCATGTATCCAGACCGCGTAACACACT
* * * * *
90474364 GTTTTGGAATTAGAGTCACACGGGCCAGAGACACGAGCATGTGTCTAGACCGTGTAACACACT
1 ATTTTGGAATTAGAGTCACACGGGACAGAGACACGAGCATGTATCCAGACCGCGTAACACACT
* * *
90474427 ATTTTGGAATTAGAGTCACATGGG-CTAGGGGCACGAGCATGT
1 ATTTTGGAATTAGAGTCACACGGGAC-AGAGACACGAGCATGT
90474469 GTCTTGGCCG
Statistics
Matches: 86, Mismatches: 16, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
62 19 0.22
63 66 0.77
64 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (63 bp):
ATTTTGGAATTAGAGTCACACGGGACAGAGACACGAGCATGTATCCAGACCGCGTAACACACT
Found at i:90481257 original size:39 final size:38
Alignment explanation
Indices: 90481213--90481360 Score: 199
Period size: 39 Copynumber: 3.9 Consensus size: 38
90481203 ATAAAGTATG
*
90481213 GTTTTAATTAATAATAAAACAAAATAGTATGAGGAAGTA
1 GTTTTAATTAACAATAAAACAAAATAGTATG-GGAAGTA
*
90481252 GTTTTAATTAACAATAAAACAAAATAGTATGGGGAAATA
1 GTTTTAATTAACAATAAAACAAAATAGTAT-GGGAAGTA
* *
90481291 GTTTTAATTAACAATAAAACAAAATAGCATGGG-AGTG
1 GTTTTAATTAACAATAAAACAAAATAGTATGGGAAGTA
* * * *
90481328 GTTTTGATTAATAATAAAACAAAGTAGCATGGG
1 GTTTTAATTAACAATAAAACAAAATAGTATGGG
90481361 GGAGTGGAAT
Statistics
Matches: 100, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
37 32 0.32
38 3 0.03
39 64 0.64
40 1 0.01
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.29
Consensus pattern (38 bp):
GTTTTAATTAACAATAAAACAAAATAGTATGGGAAGTA
Found at i:90481360 original size:76 final size:78
Alignment explanation
Indices: 90481213--90481361 Score: 221
Period size: 76 Copynumber: 1.9 Consensus size: 78
90481203 ATAAAGTATG
* *
90481213 GTTTTAATTAATAATAAAACAAAATAGTATGAGGAAGTAGTTTTAATTAACAATAAAACAAAATA
1 GTTTTAATTAACAATAAAACAAAATAGCATGAGGAAGTAGTTTTAATTAACAATAAAACAAAATA
*
90481278 GTATGGGGAAATA
66 GCATGGGGAAATA
* * * *
90481291 GTTTTAATTAACAATAAAACAAAATAGCATG-GG-AGTGGTTTTGATTAATAATAAAACAAAGTA
1 GTTTTAATTAACAATAAAACAAAATAGCATGAGGAAGTAGTTTTAATTAACAATAAAACAAAATA
90481354 GCATGGGG
66 GCATGGGG
90481362 GAGTGGAATC
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
76 33 0.52
77 2 0.03
78 29 0.45
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.29
Consensus pattern (78 bp):
GTTTTAATTAACAATAAAACAAAATAGCATGAGGAAGTAGTTTTAATTAACAATAAAACAAAATA
GCATGGGGAAATA
Found at i:90483028 original size:21 final size:19
Alignment explanation
Indices: 90482990--90483028 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
90482980 ACTCCCGTTT
*
90482990 TCATTTTTAAAATCGATTC
1 TCATTTTCAAAATCGATTC
90483009 TCATTTTCCAAAACTCGATT
1 TCATTTT-CAAAA-TCGATT
90483029 TGAAAATGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 4 0.24
21 6 0.35
ACGTcount: A:0.31, C:0.21, G:0.05, T:0.44
Consensus pattern (19 bp):
TCATTTTCAAAATCGATTC
Found at i:90499159 original size:15 final size:14
Alignment explanation
Indices: 90499117--90499166 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
90499107 ATAACCTTGA
*
90499117 ATGCAAATGATGTG
1 ATGCAAATGATGAG
90499131 ATG-AAATGTTATGAG
1 ATGCAAATG--ATGAG
90499146 ATGCAAATGCATGA-
1 ATGCAAATG-ATGAG
90499160 ATGCAAA
1 ATGCAAA
90499167 AAGAATATCG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 5 0.16
14 10 0.32
15 11 0.35
16 5 0.16
ACGTcount: A:0.42, C:0.08, G:0.24, T:0.26
Consensus pattern (14 bp):
ATGCAAATGATGAG
Found at i:90503573 original size:39 final size:39
Alignment explanation
Indices: 90503530--90503687 Score: 210
Period size: 39 Copynumber: 4.1 Consensus size: 39
90503520 AAAGCTGATT
* * * *
90503530 CCACTCCCCCATGCTACTTTGTTTTATTATTAATAAAAA
1 CCACTTCCCCATACTATTTTGTTTTATTATTAATTAAAA
* *
90503569 CCAC-TCCCCATGCTATTTTGTTTTATTGTTAATTAAAA
1 CCACTTCCCCATACTATTTTGTTTTATTATTAATTAAAA
* * *
90503607 CTATTTCCCCATACTATTTTGTTTTATTGTTAATTAAAA
1 CCACTTCCCCATACTATTTTGTTTTATTATTAATTAAAA
* *
90503646 CTACTTCCTCATACTATTTTGTTTTATTATTAATTAAAA
1 CCACTTCCCCATACTATTTTGTTTTATTATTAATTAAAA
90503685 CCA
1 CCA
90503688 TACTTTATTT
Statistics
Matches: 107, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
38 32 0.30
39 75 0.70
ACGTcount: A:0.29, C:0.20, G:0.05, T:0.46
Consensus pattern (39 bp):
CCACTTCCCCATACTATTTTGTTTTATTATTAATTAAAA
Found at i:90503679 original size:78 final size:77
Alignment explanation
Indices: 90503536--90503685 Score: 219
Period size: 77 Copynumber: 1.9 Consensus size: 77
90503526 GATTCCACTC
* * *
90503536 CCCCATGCTACTTTGTTTTATTATTAATAAAAACCACTCCCCATGCTATTTTGTTTTATTGTTAA
1 CCCCATACTACTTTGTTTTATTATTAATAAAAACCACTCCCCATACTATTTTGTTTTATTATTAA
90503601 TTAAAACTATTT
66 TTAAAACTATTT
* * * * *
90503613 CCCCATACTATTTTGTTTTATTGTTAATTAAAACTACTTCCTCATACTATTTTGTTTTATTATTA
1 CCCCATACTACTTTGTTTTATTATTAATAAAAACCAC-TCCCCATACTATTTTGTTTTATTATTA
90503678 ATTAAAAC
65 ATTAAAAC
90503686 CATACTTTAT
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
77 32 0.50
78 32 0.50
ACGTcount: A:0.29, C:0.18, G:0.05, T:0.47
Consensus pattern (77 bp):
CCCCATACTACTTTGTTTTATTATTAATAAAAACCACTCCCCATACTATTTTGTTTTATTATTAA
TTAAAACTATTT
Found at i:90523960 original size:18 final size:19
Alignment explanation
Indices: 90523939--90523981 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
90523929 CAAACAAAAA
*
90523939 CAGATACAGACTCAG-TTT
1 CAGATACAGACTCAGATGT
* *
90523957 CAGATTCAGATTCAGATGT
1 CAGATACAGACTCAGATGT
90523976 CAGATA
1 CAGATA
90523982 TGTCAAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (19 bp):
CAGATACAGACTCAGATGT
Found at i:90533004 original size:17 final size:17
Alignment explanation
Indices: 90532982--90533017 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
90532972 TCTGTGGATT
90532982 ACCTGACAAAACAGACA
1 ACCTGACAAAACAGACA
90532999 ACCTGACAAAACAGACA
1 ACCTGACAAAACAGACA
90533016 AC
1 AC
90533018 AGATGTGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.53, C:0.31, G:0.11, T:0.06
Consensus pattern (17 bp):
ACCTGACAAAACAGACA
Found at i:90533608 original size:86 final size:86
Alignment explanation
Indices: 90533466--90533626 Score: 259
Period size: 86 Copynumber: 1.9 Consensus size: 86
90533456 GGTTTACCCG
* * *
90533466 TGTGGGCCCACACGCCAAGATTTGCCTTTGCCCATGTAACCCACACGTCCTGGTCCAAAAATCCA
1 TGTGGGCCCACACGCCAAGATTGGCCTTTGCCCATGTAACCCACACGGCCTAGTCCAAAAATCCA
90533531 CACGCCCGTGTGACATGCCCA
66 CACGCCCGTGTGACATGCCCA
* * * *
90533552 TGTGGGCCCACACGTCAAGATTGGCCTTTGCCCATGTAACTCACATGGCCTAGTCCAAAAATCTA
1 TGTGGGCCCACACGCCAAGATTGGCCTTTGCCCATGTAACCCACACGGCCTAGTCCAAAAATCCA
90533617 CACGCCCGTG
66 CACGCCCGTG
90533627 CGGGCCCACA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
86 68 1.00
ACGTcount: A:0.24, C:0.35, G:0.20, T:0.21
Consensus pattern (86 bp):
TGTGGGCCCACACGCCAAGATTGGCCTTTGCCCATGTAACCCACACGGCCTAGTCCAAAAATCCA
CACGCCCGTGTGACATGCCCA
Found at i:90567380 original size:22 final size:22
Alignment explanation
Indices: 90567347--90567401 Score: 92
Period size: 22 Copynumber: 2.4 Consensus size: 22
90567337 ATAAAATCAA
90567347 TAAAGAAAAAAATAATTTAAACAT
1 TAAA-AAAAAAA-AATTTAAACAT
90567371 TAAAAAAAAAAAATTTAAACAT
1 TAAAAAAAAAAAATTTAAACAT
90567393 TAAAAAAAA
1 TAAAAAAAA
90567402 TCCTTAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 20 0.65
23 7 0.23
24 4 0.13
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.22
Consensus pattern (22 bp):
TAAAAAAAAAAAATTTAAACAT
Found at i:90569462 original size:19 final size:18
Alignment explanation
Indices: 90569423--90569464 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
90569413 TCCATAGTAT
* *
90569423 AAAATAAATAAAATGATA
1 AAAATAAAAAAAATAATA
90569441 AAAATAAAAAATAATAATA
1 AAAATAAAAAA-AATAATA
90569460 AAAAT
1 AAAAT
90569465 GCTAGATGCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.21
Consensus pattern (18 bp):
AAAATAAAAAAAATAATA
Found at i:90571763 original size:133 final size:133
Alignment explanation
Indices: 90571214--90571852 Score: 389
Period size: 133 Copynumber: 4.7 Consensus size: 133
90571204 CTTTAAGGGT
* * * * * *
90571214 ATAAGAATTGTCACTTCAATCTACTCCACTGCAACTTTAGGGAGAT---A-TTAGTAACTTCAAT
1 ATAAGACTTGTAACTTCAACCTACTCCACTGAAAATTCAGGGAGATAAGACTTA-TAACTTCAAT
* * * * ** * ** * *
90571275 CTGCTCTATTGCAACTTTAGAGAGATAAGATTTG-TGGCTTTAATCTGCTTTACTGCAACATCAG
65 CTCCTCCACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATCTGCTCCACTACAACTTCAG
90571339 AGAG
130 AGAG
** * * * * * *
90571343 ATAAGA-TTAGTGGCTTCAA-TTACTCCACTGCAACTTTAGGGAGATAAGATCCGCCATGATAGC
1 ATAAGACTT-GTAACTTCAACCTACTCCACTGAAAATTCAGGGAGATAAGA-----C-TTATAAC
* * * * **
90571406 TTCAACCT-GTCTCACTGCAACTTCA-AGGGAATAAGATTTGCTATCTTCAATCTACTCCACTGT
59 TTCAATCTCCTC-CACTGCAACTTCAGAGAG-ATAAGATTTGCTATCTTCAATCTGCTCCACTAC
*
90571469 AACTTCAGGGAG
122 AACTTCAGAGAG
* ** ** * * * * * *
90571481 ATAAGATTTGTGGCTTCAATTTGCTCCACTGCAACTTTAGGGAGATAAGATTTGTAATTTGTAGC
1 ATAAGACTTGTAACTTCAACCTACTCCACTGAAAATTCAGGGAGATAAGA-CT-T-A----TAAC
* ** * * * * * * * * * **
90571546 TTTAATCTGTTCCACTGCAAACCTCA-AGGAAATGAGACTTGCTATTTTCAGTTTGTTTCACTGT
59 TTCAATCTCCTCCACTGC-AACTTCAGA-GAGATAAGATTTGCTATCTTCAATCTGCTCCACTAC
90571610 AACTTCAGAGAG
122 AACTTCAGAGAG
** * ** * *
90571622 ATGTGACTTGTAACTTCAACCTACTCCACTGAAAATTCAGGGGGATAAGGTTTATAGCTTTAATC
1 ATAAGACTTGTAACTTCAACCTACTCCACTGAAAATTCAGGGAGATAAGACTTATAACTTCAATC
* * *
90571687 TCCTCTACTGCAACTTCTGAGAGATAAGTTTTGCTATCTTCAATCTGCTCCACTACAACTTCAGA
66 TCCTCCACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATCTGCTCCACTACAACTTCAGA
90571752 GAG
131 GAG
* * *
90571755 ATAAGACTTGTAACTTCAACCTACTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAATC
1 ATAAGACTTGTAACTTCAACCTACTCCACTGAAAATTCAGGGAGATAAGACTTATAACTTCAATC
* *
90571820 TGCTCCACTGCAACTTCAGGGAGATAAGATTTG
66 TCCTCCACTGCAACTTCAGAGAGATAAGATTTG
90571853 TAATTTGTAG
Statistics
Matches: 401, Mismatches: 83, Indels: 48
0.75 0.16 0.09
Matches are distributed among these distances:
128 27 0.07
129 14 0.03
131 1 0.00
133 125 0.31
134 21 0.05
136 6 0.01
137 30 0.07
138 44 0.11
139 32 0.08
140 18 0.04
141 82 0.20
142 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.32
Consensus pattern (133 bp):
ATAAGACTTGTAACTTCAACCTACTCCACTGAAAATTCAGGGAGATAAGACTTATAACTTCAATC
TCCTCCACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATCTGCTCCACTACAACTTCAGA
GAG
Found at i:90571855 original size:44 final size:44
Alignment explanation
Indices: 90571195--90571855 Score: 445
Period size: 44 Copynumber: 14.7 Consensus size: 44
90571185 CCATCCGAAC
* * * * *
90571195 CCACTGCAACTTTAAGGG-TATAAGAATTGTCACTTCAATCTACT
1 CCACTGCAAC-TTCAGGGAGATAAGATTTGTAACTTCAATCTGCT
* *
90571239 CCACTGCAACTTTAGGGAGAT---ATTAGTAACTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAACTTCAATCTGCT
* * * * ** *
90571280 CTATTGCAACTTTAGAGAGATAAGATTTGTGGCTTTAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAACTTCAATCTGCT
** * * * ** *
90571324 TTACTGCAACATCAGAGAGATAAGATTAGTGGCTTCAAT-TACT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAACTTCAATCTGCT
* * * *
90571367 CCACTGCAACTTTAGGGAGATAAGATCCGCCATGATAGCTTCAACCTG-T
1 CCACTGCAACTTCAGGGAGATAAGAT-----TTG-TAACTTCAATCTGCT
* *
90571416 CTCACTGCAACTTCAAGGGA-ATAAGATTTGCTATCTTCAATCTACT
1 C-CACTGCAACTTC-AGGGAGATAAGATTTG-TAACTTCAATCTGCT
* ** *
90571462 CCACTGTAACTTCAGGGAGATAAGATTTGTGGCTTCAATTTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAACTTCAATCTGCT
* * *
90571506 CCACTGCAACTTTAGGGAGATAAGATTTGTAATTTGTAGCTTTAATCTGTT
1 CCACTGCAACTTCAGGGAGATAAGATTTGT-A-----A-CTTCAATCTGCT
* * * * * ** * * *
90571557 CCACTGCAAACCTCAAGGAAATGAGACTTGCTATTTTCAGTTTGTT
1 CCACTGC-AACTTCAGGGAGATAAGATTTG-TAACTTCAATCTGCT
* * * ** * * *
90571603 TCACTGTAACTTCAGAGAGATGTGACTTGTAACTTCAACCTACT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAACTTCAATCTGCT
* * * * * * * *
90571647 CCACTGAAAATTCAGGGGGATAAGGTTTATAGCTTTAATCTCCT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAACTTCAATCTGCT
* * * * *
90571691 CTACTGCAACTTCTGAGAGATAAGTTTTGCTATCTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTG-TAACTTCAATCTGCT
* * * * *
90571736 CCACTACAACTTCAGAGAGATAAGACTTGTAACTTCAACCTACT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAACTTCAATCTGCT
*
90571780 CCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAACTTCAATCTGCT
90571824 CCACTGCAACTTCAGGGAGATAAGATTTGTAA
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAA
90571856 TTTGTAGCTT
Statistics
Matches: 481, Mismatches: 111, Indels: 50
0.75 0.17 0.08
Matches are distributed among these distances:
41 34 0.07
43 30 0.06
44 247 0.51
45 86 0.18
46 15 0.03
48 1 0.00
49 10 0.02
50 19 0.04
51 21 0.04
52 17 0.04
53 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.32
Consensus pattern (44 bp):
CCACTGCAACTTCAGGGAGATAAGATTTGTAACTTCAATCTGCT
Found at i:90573664 original size:34 final size:34
Alignment explanation
Indices: 90573621--90573689 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
90573611 TTTAGGTGAG
90573621 ATTGGCCCAATGACATCCATACCCCACATAGAGA
1 ATTGGCCCAATGACATCCATACCCCACATAGAGA
90573655 ATTGGCCCAATGACATCCATACCCCACATAGAGA
1 ATTGGCCCAATGACATCCATACCCCACATAGAGA
90573689 A
1 A
90573690 AAGCCATGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.36, C:0.32, G:0.14, T:0.17
Consensus pattern (34 bp):
ATTGGCCCAATGACATCCATACCCCACATAGAGA
Found at i:90576423 original size:25 final size:26
Alignment explanation
Indices: 90576393--90576442 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
90576383 ATCTGTGTGG
90576393 TATGAGTATGA-ATAAATGAAAAGAT
1 TATGAGTATGAGATAAATGAAAAGAT
* *
90576418 TATGAGTATGAGTTAAATGGAAAGA
1 TATGAGTATGAGATAAATGAAAAGA
90576443 ACAAAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.28
Consensus pattern (26 bp):
TATGAGTATGAGATAAATGAAAAGAT
Found at i:90579151 original size:16 final size:16
Alignment explanation
Indices: 90579127--90579160 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
90579117 GAAAATATCT
90579127 TTTAGTTTTTATCATA
1 TTTAGTTTTTATCATA
*
90579143 TTTATTTTTTATCATA
1 TTTAGTTTTTATCATA
90579159 TT
1 TT
90579161 AATAATTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.06, G:0.03, T:0.68
Consensus pattern (16 bp):
TTTAGTTTTTATCATA
Found at i:90579380 original size:22 final size:24
Alignment explanation
Indices: 90579350--90579398 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 24
90579340 AAAAATTCTG
* *
90579350 AATTATTTTGATTTTTA-TAA-GT
1 AATTATTTTCATATTTATTAAGGT
*
90579372 AATTTTTTTCATATTTATTAAGGT
1 AATTATTTTCATATTTATTAAGGT
90579396 AAT
1 AAT
90579399 AAAATAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 14 0.64
23 3 0.14
24 5 0.23
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.57
Consensus pattern (24 bp):
AATTATTTTCATATTTATTAAGGT
Found at i:90580753 original size:13 final size:13
Alignment explanation
Indices: 90580735--90580763 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
90580725 CAATGTTTTA
90580735 AAAGATGCATTAT
1 AAAGATGCATTAT
90580748 AAAGATGCATTAT
1 AAAGATGCATTAT
90580761 AAA
1 AAA
90580764 AACATTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.28
Consensus pattern (13 bp):
AAAGATGCATTAT
Found at i:90584069 original size:42 final size:43
Alignment explanation
Indices: 90583988--90584077 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 43
90583978 TCCTATACGA
* * * *
90583988 GGTCTTACATGTAATCAAATATCGATGGCACTATCCCAGACAG
1 GGTCTTACACGAAATCAAATATCGATGCCAATATCCCAGACAG
* * *
90584031 GGTCTTACACGAAATCATATA-CGATGCCAATGTCCCAGACAT
1 GGTCTTACACGAAATCAAATATCGATGCCAATATCCCAGACAG
90584073 GGTCT
1 GGTCT
90584078 CTTACATGTA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
42 22 0.55
43 18 0.45
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (43 bp):
GGTCTTACACGAAATCAAATATCGATGCCAATATCCCAGACAG
Found at i:90585265 original size:17 final size:17
Alignment explanation
Indices: 90585245--90585280 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
90585235 CCCGTGTGTG
90585245 ACACACGGGCAGGCCAC
1 ACACACGGGCAGGCCAC
90585262 ACACACGGGCAGGCCAC
1 ACACACGGGCAGGCCAC
90585279 AC
1 AC
90585281 GCCCGTGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.42, G:0.28, T:0.00
Consensus pattern (17 bp):
ACACACGGGCAGGCCAC
Found at i:90589195 original size:16 final size:15
Alignment explanation
Indices: 90589169--90589203 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
90589159 TGATGTGAAT
90589169 AATATAAAATATTAA
1 AATATAAAATATTAA
*
90589184 AATATCAAAATATTAG
1 AATAT-AAAATATTAA
90589200 AATA
1 AATA
90589204 ATAATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (15 bp):
AATATAAAATATTAA
Found at i:90589475 original size:25 final size:24
Alignment explanation
Indices: 90589447--90589578 Score: 85
Period size: 25 Copynumber: 5.6 Consensus size: 24
90589437 AAATATATAT
90589447 ATATATAAATAATATAGTATTAAAG
1 ATATATAAATAATATAGTATT-AAG
* * *
90589472 ATATATACATAAAATAGTA-TAAT
1 ATATATAAATAATATAGTATTAAG
* * *
90589495 ATATATACACGTAATATAGAATTTAG
1 ATATATA-A-ATAATATAGTATTAAG
** * *
90589521 A-ATATACCTAATATATTA-AAAG
1 ATATATAAATAATATAGTATTAAG
* *
90589543 A-ATATATATAATATAATATTAAG
1 ATATATAAATAATATAGTATTAAG
*
90589566 AAATAT-AATAATA
1 ATATATAAATAATA
90589579 ACAAAAAAAG
Statistics
Matches: 82, Mismatches: 20, Indels: 12
0.72 0.18 0.11
Matches are distributed among these distances:
22 17 0.21
23 27 0.33
24 5 0.06
25 30 0.37
26 3 0.04
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.35
Consensus pattern (24 bp):
ATATATAAATAATATAGTATTAAG
Found at i:90590081 original size:18 final size:18
Alignment explanation
Indices: 90590058--90590111 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
90590048 ACAAGTGGTG
90590058 GTGGAGCAAGTGTGGCTA
1 GTGGAGCAAGTGTGGCTA
*
90590076 GT-G-G--AGT-AGG-TA
1 GTGGAGCAAGTGTGGCTA
90590088 GTGGAGCAAGTGTGGCTA
1 GTGGAGCAAGTGTGGCTA
90590106 GTGGAG
1 GTGGAG
90590112 TTGGTGGTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
12 4 0.14
13 3 0.11
14 4 0.14
16 4 0.14
17 3 0.11
18 10 0.36
ACGTcount: A:0.22, C:0.07, G:0.48, T:0.22
Consensus pattern (18 bp):
GTGGAGCAAGTGTGGCTA
Found at i:90590094 original size:30 final size:30
Alignment explanation
Indices: 90590053--90590151 Score: 171
Period size: 30 Copynumber: 3.3 Consensus size: 30
90590043 TAGGTACAAG
90590053 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
* *
90590083 AGGTAGTGGAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
*
90590113 TGGTGGTGGAGCAAGTGTGACTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
90590143 TGGTGGTGG
1 TGGTGGTGG
90590152 CAAAGGCTAG
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 64 1.00
ACGTcount: A:0.18, C:0.06, G:0.49, T:0.26
Consensus pattern (30 bp):
TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
Found at i:90591151 original size:90 final size:87
Alignment explanation
Indices: 90590777--90591368 Score: 463
Period size: 87 Copynumber: 6.7 Consensus size: 87
90590767 CGGCATGTGA
* ** * * * *
90590777 TCCTGA-GCTTAACTCATTTCTCGCAATATGAATTGA-CTTTTT-AAAACTAGACATT-AAAAAC
1 TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAC-A-AAATTGAAAAAA
*
90590838 AGAAATTGAAAATAGCTCAGCACGTG
64 AGAAATTGAAAATACCTCAG--CGTG
** * * * *
90590864 AGC-AAGGCTCAACTCACTTCTCGCAATATGAGTTGA--TTTTT-AAAACAAAATTTGTAAAACA
1 TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAAAA-TTGAAAAAAA
** * *
90590925 GATTTTGAAAATACCTCGGTATGTG
65 GAAATTGAAAATACCTCAG--CGTG
* * * * *
90590950 ACCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGA--TTTTTGCAAAGCATAAATTAAAAAAA
1 TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG-AAAACA-AAATTGAAAAAA
** *
90591013 ATCAATTGAAAATACCTCGGCGTG
64 AGAAATTGAAAATACCTCAGCGTG
* *
90591037 TGACCTGAAGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAACATAAATTGAAAA
1 T--CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGA-AAACA-AAATTG-AAA
*
90591102 AAAAGAAATTGAAAATACCTTAGCGTG
61 AAAAGAAATTGAAAATACCTCAGCGTG
* * *
90591129 TCCTGAGGCTGAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAACAGAATTG-AAAAC
1 TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTG-AAAACAAAATTGAAAAAA
* *
90591193 AGAATTTGAAAATACCTCAGTGTG
64 AGAAATTGAAAATACCTCAGCGTG
** * * * * * *
90591217 TGAGTCAAGACTCAACTTACCACTCGCAATATGAGCTGATTTTTTTGAAACACAGAAATTGAAGA
1 T-CCT-GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA-ACA-AAATTGAAAA
* * *
90591282 ATAGAAATGGAAAACACCTCAGC--G
62 AAAGAAATTGAAAATACCTCAGCGTG
* * *
90591306 TCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAAAGACAGAAATTGAAAA
1 TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA-ACA-AAATTGAAAA
90591369 TATCTCAACG
Statistics
Matches: 416, Mismatches: 69, Indels: 40
0.79 0.13 0.08
Matches are distributed among these distances:
84 2 0.00
85 3 0.01
86 38 0.09
87 118 0.28
88 30 0.07
89 73 0.18
90 75 0.18
91 49 0.12
92 28 0.07
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (87 bp):
TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAAAATTGAAAAAAAG
AAATTGAAAATACCTCAGCGTG
Found at i:90591190 original size:13 final size:14
Alignment explanation
Indices: 90591171--90591204 Score: 54
Period size: 12 Copynumber: 2.6 Consensus size: 14
90591161 GTTGATTTTT
90591171 TTTGAAAAACAGAA
1 TTTGAAAAACAGAA
90591185 -TTG-AAAACAGAA
1 TTTGAAAAACAGAA
90591197 TTTGAAAA
1 TTTGAAAA
90591205 TACCTCAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
12 9 0.50
13 6 0.33
14 3 0.17
ACGTcount: A:0.56, C:0.06, G:0.15, T:0.24
Consensus pattern (14 bp):
TTTGAAAAACAGAA
Found at i:90591193 original size:12 final size:13
Alignment explanation
Indices: 90591171--90591204 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
90591161 GTTGATTTTT
90591171 TTTGAAAAACAGAA
1 TTTG-AAAACAGAA
90591185 -TTGAAAACAGAA
1 TTTGAAAACAGAA
90591197 TTTGAAAA
1 TTTGAAAA
90591205 TACCTCAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.56, C:0.06, G:0.15, T:0.24
Consensus pattern (13 bp):
TTTGAAAACAGAA
Found at i:90591400 original size:75 final size:74
Alignment explanation
Indices: 90591275--90591664 Score: 483
Period size: 73 Copynumber: 5.3 Consensus size: 74
90591265 AACACAGAAA
* * * * *
90591275 TTGAAGAATAGAAATGGAAAACACCTC-A-GCGTCTTGAGGTTCAACTCACCTCTCGCAATATGA
1 TTGAA-AACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
*
90591338 GCTGATTTTT
65 GTTGATTTTT
* *
90591348 TTGAAAGACAGAAATTGAAAATATCTCAACGTGTCTTGAGGCTCAACGCACCTCTCGCAATATGA
1 TTGAAA-ACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
90591413 GTTGA--TTT
65 GTTGATTTTT
* * * *
90591421 TTGACAAACAAAAATTGAAATTACCTC-A-GCGTCTTGAGGTTCAACTCACCTCTCGCAATATGA
1 TTGA-AAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
*
90591484 GCTGATTTTT
65 GTTGATTTTT
90591494 TTGAAAGACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAA-ACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
90591559 GTTGA--TTT
65 GTTGATTTTT
* * * * *
90591567 TTGACAAACA-AAACTTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATCTATCGCAATATG
1 TTGA-AAACAGAAA-TTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATG
90591631 AGTTGATTTTT
64 AGTTGATTTTT
*
90591642 TTGAAAAACAGAAATTAAAAATA
1 TTG-AAAACAGAAATTGAAAATA
90591665 GAAATGGAAA
Statistics
Matches: 275, Mismatches: 27, Indels: 28
0.83 0.08 0.08
Matches are distributed among these distances:
71 36 0.13
72 7 0.03
73 131 0.48
74 6 0.02
75 91 0.33
76 4 0.01
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (74 bp):
TTGAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAG
TTGATTTTT
Found at i:90591561 original size:146 final size:146
Alignment explanation
Indices: 90591297--90591664 Score: 628
Period size: 146 Copynumber: 2.5 Consensus size: 146
90591287 AATGGAAAAC
90591297 ACCTCAGCGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAAAGACAGAAA
1 ACCTCAGCGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAAAGACAGAAA
*
90591362 TTGAAAATATCTCAACGTGTCTTGAGGCTCAACGCACCTCTCGCAATATGAGTTGATTTTTGACA
66 TTGAAAATACCTCAACGTGTCTTGAGGCTCAACGCACCTCTCGCAATATGAGTTGATTTTTGACA
90591427 AACAAAAATTGAAATT
131 AACAAAAATTGAAATT
90591443 ACCTCAGCGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAAAGACAGAAA
1 ACCTCAGCGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAAAGACAGAAA
*
90591508 TTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACA
66 TTGAAAATACCTCAACGTGTCTTGAGGCTCAACGCACCTCTCGCAATATGAGTTGATTTTTGACA
*
90591573 AACAAAACTTGAAATT
131 AACAAAAATTGAAATT
* * * * * *
90591589 ACCTCAGCGTGTCCTGAGGCTCAACTCATCTATCGCAATATGAGTTGATTTTTTTGAAAAACAGA
1 ACCTCAGC--GTCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAAAGACAGA
*
90591654 AATTAAAAATA
64 AATTGAAAATA
90591665 GAAATGGAAA
Statistics
Matches: 210, Mismatches: 10, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
146 151 0.72
148 59 0.28
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.30
Consensus pattern (146 bp):
ACCTCAGCGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAAAGACAGAAA
TTGAAAATACCTCAACGTGTCTTGAGGCTCAACGCACCTCTCGCAATATGAGTTGATTTTTGACA
AACAAAAATTGAAATT
Found at i:90591743 original size:86 final size:88
Alignment explanation
Indices: 90591589--90591749 Score: 227
Period size: 86 Copynumber: 1.8 Consensus size: 88
90591579 ACTTGAAATT
* *
90591589 ACCTCAGCGTGTCCTGAGGCTCAACTCATCTATCGCAATATGAGTTGATTTTTTTGAAAAACAGA
1 ACCTCAGCG-GTCCTGAGGCTCAACTCACCTATCGCAATATGAGCTGATTTTTTTGAAAAACAGA
90591654 AA-TTAAAAATAGAAATGGAAAAC
65 AATTTAAAAATAGAAATGGAAAAC
* * * * * *
90591677 ACCTCAGC-GTCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAAACATATAA
1 ACCTCAGCGGTCCTGAGGCTCAACTCACCTATCGCAATATGAGCTGATTTTTTTGAAAAACAGAA
90591741 ATTTAAAAA
66 ATTTAAAAA
90591750 AAAAAGAAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
86 49 0.77
87 7 0.11
88 8 0.12
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.30
Consensus pattern (88 bp):
ACCTCAGCGGTCCTGAGGCTCAACTCACCTATCGCAATATGAGCTGATTTTTTTGAAAAACAGAA
ATTTAAAAATAGAAATGGAAAAC
Found at i:90591758 original size:103 final size:106
Alignment explanation
Indices: 90591645--90591840 Score: 245
Period size: 107 Copynumber: 1.9 Consensus size: 106
90591635 GATTTTTTTG
* * ** **
90591645 AAAAACAGAAATTAAAAATAGAAATGGAAAACACCTC-A-GCGT-CTTGAGGTTCAACTCACCTC
1 AAAAAAAGAAATTAAAAACAGAAATGGAAAACACCTCGACGCGTACCCGAGACTCAACTCACCTC
*
90591707 TCGCAATATGAGCTGATTTTTTTGAAACATATAAATTTAAA
66 TCGCAATATGAGCTGATTCTTTTGAAACATATAAATTTAAA
* * ** *
90591748 AAAAAAAGAAATTAAAAACAGAATTTGAAAGGACCTCGACGTGTAGCCCGAGACTCAACTCACCT
1 AAAAAAAGAAATTAAAAACAGAAATGGAAAACACCTCGACGCGTA-CCCGAGACTCAACTCACCT
*
90591813 CTCGCAATATGAGTTGATTCTTTTGAAA
65 CTCGCAATATGAGCTGATTCTTTTGAAA
90591841 AGCAGAAATT
Statistics
Matches: 76, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
103 31 0.41
104 1 0.01
105 3 0.04
107 41 0.54
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (106 bp):
AAAAAAAGAAATTAAAAACAGAAATGGAAAACACCTCGACGCGTACCCGAGACTCAACTCACCTC
TCGCAATATGAGCTGATTCTTTTGAAACATATAAATTTAAA
Found at i:90591891 original size:75 final size:73
Alignment explanation
Indices: 90591761--90592004 Score: 303
Period size: 77 Copynumber: 3.2 Consensus size: 73
90591751 AAAAGAAATT
* ** * *
90591761 AAAAACAGAATTTGAAAGGACCTCGACGTGTAGCCCGAGACTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTC-A-GCGT-GCCCGAGGCTCAACTCACCTCTCGCAATATGAG
90591826 TTGATTCTTTTG
63 TTGATT-TTTTG
*
90591838 AAAAGCAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
1 AAAAACAGAAATTGAAAATACCTCAGCGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
90591903 GATTTTTTTG
65 GA-TTTTTTG
* * * *
90591913 ATAAAAATAGAATTTGAAAATATCTCAGCGTGCCCTAAGGCTCAACTCACCTCTCGCAATATGAG
1 --AAAAACAGAAATTGAAAATACCTCAGCGTGCCC-GAGGCTCAACTCACCTCTCGCAATATGAG
90591978 TTGA-TTTTTG
63 TTGATTTTTTG
90591988 AAAAACAGAAA-TGAAAA
1 AAAAACAGAAATTGAAAA
90592005 GCAGAAATTG
Statistics
Matches: 149, Mismatches: 13, Indels: 15
0.84 0.07 0.08
Matches are distributed among these distances:
72 6 0.04
73 9 0.06
74 1 0.01
75 49 0.33
76 6 0.04
77 78 0.52
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.27
Consensus pattern (73 bp):
AAAAACAGAAATTGAAAATACCTCAGCGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
ATTTTTTG
Found at i:90592018 original size:14 final size:14
Alignment explanation
Indices: 90591985--90592031 Score: 71
Period size: 13 Copynumber: 3.5 Consensus size: 14
90591975 GAGTTGATTT
90591985 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
*
90591999 -TGAAAAGCAGAAA
1 TTGAAAAACAGAAA
90592012 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
90592026 TT-AAAA
1 TTGAAAA
90592032 TTACCTCGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
13 16 0.53
14 14 0.47
ACGTcount: A:0.64, C:0.06, G:0.15, T:0.15
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:90592116 original size:250 final size:247
Alignment explanation
Indices: 90591494--90592255 Score: 845
Period size: 250 Copynumber: 3.0 Consensus size: 247
90591484 GCTGATTTTT
* * * **
90591494 TTGAAAGACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATT-AAAATACCTCGACGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGA
* *
90591559 GTTGATTTTTGACAAA-CAAAACTTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATCTATC
65 GTTGATTTTTGA-AAAGCAAAA-TTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCAACTCTC
* *
90591623 GCAATATGAGTTGATTTTTTTGAAAAACAGAAATTAAAAATAGAAATGGAAAACACCTCAGCGT-
128 GCAATATGAGTTGATTTTTTT--------G--A-TAAAAATAG-AATTGAAAATACCTCAGCGTG
* * * * * *
90591687 CTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAAACATATAAATTTAAAAAAA
181 CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAAACAGAAA--T--AAAAA
90591752 AAAGAAA
241 AAAGAAA
* ** * *
90591759 TT-AAAAACAGAATTTGAAAGGACCTCGACGTGTAGCCCGAGACTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATT-AAAATACCTCGACGTG--CCCCGAGGCTCAACTCACCTCTCGCAATAT
* * *
90591823 GAGTTGATTCTTTTGAAAAGCAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCT
63 GAGTTGA-T-TTTTGAAAAGCA-AAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCAACT
* *
90591888 CTCGCAATATGAGTTGATTTTTTTGATAAAAATAGAATTTGAAAATATCTCAGCGTGCCCTAAGG
125 CTCGCAATATGAGTTGATTTTTTTGATAAAAATAGAA-TTGAAAATACCTCAGCGTG-CCTGAGG
* **
90591953 CTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATGAAAAGCAGAAA
188 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATAAAAAAAAGAAA
* *
90592012 TTGAAAAACAGAAATTAAAATTACCTCGGCGTGCCCCGAGGCTCAGCTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTAAAA-TACCTCGACGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGA
90592077 GTTGATTTTTGAAAAGCATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCAACTCTCG
65 GTTGATTTTTGAAAAGCA-AAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCAACTCTCG
* * *
90592142 CAATATGAGTTGA-TTTTTTGA-AAAGCATA-AATTGAAAATACCTCGGCGTGTGACCTGAGGCC
129 CAATATGAGTTGATTTTTTTGATAAA-AATAGAATTGAAAATACCTCAGC--GTG-CCTGAGGCT
* *
90592204 CAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATAAAAA
190 CAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAAACAGAAATAAAAA
90592256 CATCAAAATA
Statistics
Matches: 435, Mismatches: 46, Indels: 46
0.83 0.09 0.09
Matches are distributed among these distances:
247 14 0.03
248 5 0.01
249 47 0.11
250 68 0.16
251 22 0.05
252 34 0.08
253 14 0.03
254 22 0.05
255 1 0.00
256 2 0.00
257 38 0.09
258 1 0.00
259 32 0.07
260 1 0.00
264 25 0.06
265 2 0.00
266 33 0.08
267 4 0.01
268 67 0.15
269 3 0.01
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.28
Consensus pattern (247 bp):
TTGAAAAACAGAAATTAAAATACCTCGACGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAG
TTGATTTTTGAAAAGCAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCAACTCTCGCA
ATATGAGTTGATTTTTTTGATAAAAATAGAATTGAAAATACCTCAGCGTGCCTGAGGCTCAACTC
ACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATAAAAAAAAGAAA
Found at i:90592191 original size:74 final size:74
Alignment explanation
Indices: 90592012--90592241 Score: 313
Period size: 73 Copynumber: 3.1 Consensus size: 74
90592002 AAAGCAGAAA
* * * * * *
90592012 TTGAAAAACAGAAATT-AAAATTACCTCGGCGTGCCCCGAGGCTCAGCTCACCTCTCGCAATATG
1 TTGAAAAGCATAAATTGAAAA-TACCTCGGCGTGTCCTGAGGCTCAACTCAACTCTCGCAATATG
90592076 AGTTGA-TTT
65 AGTTGATTTT
* *
90592085 TTGAAAAGCATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCAACTCTCGCAATATGA
1 TTGAAAAGCATAAATTGAAAATACCTCGGCGTGTCCTGAGGCTCAACTCAACTCTCGCAATATGA
90592150 GTTGATTTT
66 GTTGATTTT
*
90592159 TTGAAAAGCATAAATTGAAAATACCTCGGCGTGTGACCTGAGGCCCAACTC-ACTTCTCGCAATA
1 TTGAAAAGCATAAATTGAAAATACCTCGGCGTGT--CCTGAGGCTCAACTCAAC-TCTCGCAATA
90592223 TGAGTTGATTTTT
63 TGAGTTGA-TTTT
90592236 TTGAAA
1 TTGAAA
90592242 GACAGAAATA
Statistics
Matches: 140, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
73 58 0.41
74 38 0.27
75 2 0.01
76 32 0.23
77 10 0.07
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (74 bp):
TTGAAAAGCATAAATTGAAAATACCTCGGCGTGTCCTGAGGCTCAACTCAACTCTCGCAATATGA
GTTGATTTT
Found at i:90603494 original size:54 final size:54
Alignment explanation
Indices: 90603344--90603557 Score: 315
Period size: 54 Copynumber: 4.0 Consensus size: 54
90603334 TCTACTTTCC
* * *
90603344 AATTCCTGTTTTTC-AAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTTTC
1 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT
* *
90603397 AATTTATATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT
1 AATTTCTGTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT
*
90603452 AATTTCTGTTTTTCAAAAAGCAACTCATATTGCGAGAGGTGAGTTGTA-CCTTTT
1 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTG-AGCCTTTT
* * *
90603506 AATTTTTGTTTTTCAAAAATCAACCCATATTGCGAGAAGTGAGTTGAGCCTT
1 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTT
90603558 AGGTCATATG
Statistics
Matches: 145, Mismatches: 12, Indels: 7
0.88 0.07 0.04
Matches are distributed among these distances:
53 12 0.08
54 83 0.57
55 50 0.34
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.37
Consensus pattern (54 bp):
AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT
Found at i:90603688 original size:13 final size:13
Alignment explanation
Indices: 90603662--90603695 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
90603652 CGTGCTGAGT
*
90603662 TTTTTCAATTTCTG
1 TTTTT-AATGTCTG
90603676 TTTTTAATGTCTG
1 TTTTTAATGTCTG
90603689 TTTTTAA
1 TTTTTAA
90603696 ATAGTCAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.18, C:0.09, G:0.09, T:0.65
Consensus pattern (13 bp):
TTTTTAATGTCTG
Found at i:90605506 original size:3 final size:3
Alignment explanation
Indices: 90605493--90605561 Score: 120
Period size: 3 Copynumber: 22.7 Consensus size: 3
90605483 TTACTTTTAC
*
90605493 TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
90605541 TAT TAT TAT TAT TAT GTAT TA
1 TAT TAT TAT TAT TAT -TAT TA
90605562 GTTTATGTTT
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
3 60 0.95
4 3 0.05
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:90605794 original size:15 final size:15
Alignment explanation
Indices: 90605761--90605799 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
90605751 TTTAATGTCG
*
90605761 TATTATTATGTTTTAA
1 TATTA-TATATTTTAA
*
90605777 TATTATATATTTTCA
1 TATTATATATTTTAA
90605792 TATTATAT
1 TATTATAT
90605800 TATATACATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (15 bp):
TATTATATATTTTAA
Found at i:90609705 original size:16 final size:15
Alignment explanation
Indices: 90609679--90609713 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
90609669 TGATGTGAAT
90609679 AATATAAAATATTAA
1 AATATAAAATATTAA
*
90609694 AATATCAAAATATTAG
1 AATAT-AAAATATTAA
90609710 AATA
1 AATA
90609714 ATAATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (15 bp):
AATATAAAATATTAA
Found at i:90609927 original size:22 final size:23
Alignment explanation
Indices: 90609867--90609963 Score: 81
Period size: 24 Copynumber: 4.1 Consensus size: 23
90609857 ATGTGATAAT
* *
90609867 ATTAAAAATATGTACATCATATA
1 ATTAAAAATATATACATAATATA
* *
90609890 GTGTAAAAATACATACATAATATA
1 AT-TAAAAATATATACATAATATA
*
90609914 ATT-AAAATATATACATAAGATAA
1 ATTAAAAATATATACATAATAT-A
*
90609937 CATGTAAAAAATATATATATAA-ATA
1 -AT-T-AAAAATATATACATAATATA
90609962 AT
1 AT
90609964 ATAGTATTAA
Statistics
Matches: 60, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
22 16 0.27
23 3 0.05
24 23 0.38
25 2 0.03
26 2 0.03
27 14 0.23
ACGTcount: A:0.57, C:0.06, G:0.05, T:0.32
Consensus pattern (23 bp):
ATTAAAAATATATACATAATATA
Found at i:90609979 original size:29 final size:28
Alignment explanation
Indices: 90609898--90609988 Score: 100
Period size: 27 Copynumber: 3.3 Consensus size: 28
90609888 TAGTGTAAAA
*
90609898 ATACATACATAATATA--ATTAAAATAT
1 ATACATAAATAATATAGTATTAAAATAT
* *
90609924 ATACATAAGATAACAT-GTA-AAAAATAT
1 ATACATAA-ATAATATAGTATTAAAATAT
*
90609951 ATATATAAATAATATAGTATTAAAGATAT
1 ATACATAAATAATATAGTATTAAA-ATAT
90609980 ATACATAAA
1 ATACATAAA
90609989 ATAGTATAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
26 13 0.25
27 23 0.44
28 4 0.08
29 12 0.23
ACGTcount: A:0.58, C:0.05, G:0.04, T:0.32
Consensus pattern (28 bp):
ATACATAAATAATATAGTATTAAAATAT
Found at i:90609987 original size:25 final size:24
Alignment explanation
Indices: 90609951--90610080 Score: 108
Period size: 23 Copynumber: 5.6 Consensus size: 24
90609941 TAAAAAATAT
*
90609951 ATATATAAATAATATAGTATTAAAG
1 ATATATACATAATATAGTATT-AAG
* *
90609976 ATATATACATAAAATAGTA-TAAT
1 ATATATACATAATATAGTATTAAG
* * *
90609999 ATATATACGTAATATAGAATTTAG
1 ATATATACATAATATAGTATTAAG
* * *
90610023 A-ATATACCTAATATATTA-AAAG
1 ATATATACATAATATAGTATTAAG
* *
90610045 A-ATATATATAATATAATATTAAG
1 ATATATACATAATATAGTATTAAG
*
90610068 AAATATA-ATAATA
1 ATATATACATAATA
90610081 ACAAAAAAAA
Statistics
Matches: 85, Mismatches: 17, Indels: 8
0.77 0.15 0.07
Matches are distributed among these distances:
22 17 0.20
23 42 0.49
24 9 0.11
25 17 0.20
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.35
Consensus pattern (24 bp):
ATATATACATAATATAGTATTAAG
Found at i:90609991 original size:27 final size:25
Alignment explanation
Indices: 90609898--90610012 Score: 69
Period size: 27 Copynumber: 4.4 Consensus size: 25
90609888 TAGTGTAAAA
90609898 ATACATACATAATATAATTAAAATAT
1 ATACATA-ATAATATAATTAAAATAT
*
90609924 ATACATAA-GATA-ACATGTAAAAAATAT
1 ATACATAATAATATA-AT-T--AAAATAT
*
90609951 ATATATAAATAATATAGTATTAAAGATAT
1 ATACAT-AATAATATA--ATTAAA-ATAT
*
90609980 ATACATAA-AATAGT-A-TAATATAT
1 ATACATAATAATA-TAATTAAAATAT
*
90610003 ATACGTAATA
1 ATACATAATA
90610013 TAGAATTTAG
Statistics
Matches: 71, Mismatches: 7, Indels: 24
0.70 0.07 0.24
Matches are distributed among these distances:
23 12 0.17
24 9 0.13
25 3 0.04
26 7 0.10
27 16 0.23
28 8 0.11
29 12 0.17
30 2 0.03
31 2 0.03
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (25 bp):
ATACATAATAATATAATTAAAATAT
Found at i:90610598 original size:30 final size:30
Alignment explanation
Indices: 90610559--90610657 Score: 171
Period size: 30 Copynumber: 3.3 Consensus size: 30
90610549 TAGGTACAAG
*
90610559 TGGTGGTGGAGCAAGTGTAGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
* *
90610589 AGGTAGTGGAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
90610619 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
90610649 TGGTGGTGG
1 TGGTGGTGG
90610658 CAAAGGCTAG
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 64 1.00
ACGTcount: A:0.18, C:0.06, G:0.49, T:0.26
Consensus pattern (30 bp):
TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
Found at i:90610615 original size:18 final size:18
Alignment explanation
Indices: 90610592--90610647 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
90610582 GTGGAGTAGG
90610592 TAGTGGAGCAAGTGTGGC
1 TAGTGGAGCAAGTGTGGC
90610610 TAGT-G-G--AGT-TGG-
1 TAGTGGAGCAAGTGTGGC
*
90610622 TGGTGGAGCAAGTGTGGC
1 TAGTGGAGCAAGTGTGGC
90610640 TAGTGGAG
1 TAGTGGAG
90610648 TTGGTGGTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
12 3 0.10
13 4 0.13
14 4 0.13
16 4 0.13
17 4 0.13
18 11 0.37
ACGTcount: A:0.20, C:0.07, G:0.48, T:0.25
Consensus pattern (18 bp):
TAGTGGAGCAAGTGTGGC
Found at i:90612762 original size:23 final size:24
Alignment explanation
Indices: 90612736--90612782 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
90612726 AAAAGGTATC
* *
90612736 GTTTTTACAATAA-TAGTTATAAT
1 GTTTTGACAATAATTAGCTATAAT
*
90612759 GTTTTGAGAATAATTAGCTATAAT
1 GTTTTGACAATAATTAGCTATAAT
90612783 ATTTCTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.45
Consensus pattern (24 bp):
GTTTTGACAATAATTAGCTATAAT
Found at i:90615823 original size:16 final size:16
Alignment explanation
Indices: 90615804--90615837 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
90615794 AGTAAAAAAT
90615804 AATATAAAATTTATAA
1 AATATAAAATTTATAA
**
90615820 AATATAACCTTTATAA
1 AATATAAAATTTATAA
90615836 AA
1 AA
90615838 AAAAGTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (16 bp):
AATATAAAATTTATAA
Found at i:90617376 original size:14 final size:14
Alignment explanation
Indices: 90617357--90617395 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
90617347 CTGTTTGATT
90617357 GAAAATGATTTTCA
1 GAAAATGATTTTCA
* *
90617371 GAAAATAATTTTTA
1 GAAAATGATTTTCA
*
90617385 GAAATTGATTT
1 GAAAATGATTT
90617396 ACTTTTTTGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.44, C:0.03, G:0.13, T:0.41
Consensus pattern (14 bp):
GAAAATGATTTTCA
Found at i:90619003 original size:18 final size:17
Alignment explanation
Indices: 90618962--90619004 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
90618952 TTGGAATGGT
*
90618962 TTGAAATTGTATATTGA
1 TTGAAATTGAATATTGA
*
90618979 TTGGAAATTGAATTATTTA
1 TT-GAAATTGAA-TATTGA
90618998 TTGAAAT
1 TTGAAAT
90619005 ACCCTATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 13 0.59
19 7 0.32
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (17 bp):
TTGAAATTGAATATTGA
Found at i:90647107 original size:12 final size:12
Alignment explanation
Indices: 90647090--90647115 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
90647080 TAGAACTCAT
90647090 AAAAAAAAAAGA
1 AAAAAAAAAAGA
90647102 AAAAAAAAAAGA
1 AAAAAAAAAAGA
90647114 AA
1 AA
90647116 GTCATCAAAA
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGA
Found at i:90662676 original size:18 final size:17
Alignment explanation
Indices: 90662650--90662684 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
90662640 TCAGACTAAA
90662650 TTTTCAAAAAAAGATTAT
1 TTTTC-AAAAAAGATTAT
*
90662668 TTTTTAAAAAAGATTAT
1 TTTTCAAAAAAGATTAT
90662685 AAAAATAGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.43
Consensus pattern (17 bp):
TTTTCAAAAAAGATTAT
Found at i:90663700 original size:16 final size:15
Alignment explanation
Indices: 90663668--90663697 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
90663658 ACTATTAGTA
90663668 ATTTTTTAAATATTT
1 ATTTTTTAAATATTT
*
90663683 ATTTTTTTAATATTT
1 ATTTTTTAAATATTT
90663698 TATCATACTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTTTTAAATATTT
Found at i:90671659 original size:15 final size:16
Alignment explanation
Indices: 90671641--90671674 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
90671631 TTTTCTCCTT
90671641 GTTC-TTTTTATTTTG
1 GTTCTTTTTTATTTTG
*
90671656 GTTCTTTTTTCTTTTG
1 GTTCTTTTTTATTTTG
90671672 GTT
1 GTT
90671675 AATCTACCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.03, C:0.09, G:0.15, T:0.74
Consensus pattern (16 bp):
GTTCTTTTTTATTTTG
Found at i:90673827 original size:30 final size:31
Alignment explanation
Indices: 90673793--90673872 Score: 119
Period size: 30 Copynumber: 2.6 Consensus size: 31
90673783 GGTGGAGATC
90673793 GTGATGGTGGTGGCGTTGAAAGGGG-AGGTT
1 GTGATGGTGGTGGCGTTGAAAGGGGAAGGTT
90673823 GTGATGGTGGTGGCGTTG-AAGGGGAAGGTT
1 GTGATGGTGGTGGCGTTGAAAGGGGAAGGTT
* * *
90673853 GTGATGATGGAGGCGGTGAA
1 GTGATGGTGGTGGCGTTGAA
90673873 CTAACAGGTG
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
29 6 0.13
30 38 0.84
31 1 0.02
ACGTcount: A:0.19, C:0.04, G:0.53, T:0.25
Consensus pattern (31 bp):
GTGATGGTGGTGGCGTTGAAAGGGGAAGGTT
Found at i:90678941 original size:13 final size:14
Alignment explanation
Indices: 90678915--90678943 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
90678905 TAACATAATC
90678915 ATAATCTCTAAAAA
1 ATAATCTCTAAAAA
90678929 ATAATCT-TAAAAA
1 ATAATCTCTAAAAA
90678942 AT
1 AT
90678944 CTGAAACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31
Consensus pattern (14 bp):
ATAATCTCTAAAAA
Found at i:90680455 original size:12 final size:12
Alignment explanation
Indices: 90680438--90680467 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
90680428 TCAAGTAGTT
90680438 ACACGGCCTAGC
1 ACACGGCCTAGC
90680450 ACACGGCCTAGC
1 ACACGGCCTAGC
90680462 ACACGG
1 ACACGG
90680468 GCGTGAGGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.27, C:0.40, G:0.27, T:0.07
Consensus pattern (12 bp):
ACACGGCCTAGC
Found at i:90680718 original size:11 final size:11
Alignment explanation
Indices: 90680691--90680721 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
90680681 AGTCTCAATT
*
90680691 TGTTTATAAAG
1 TGTTTCTAAAG
90680702 TGTTTCTAAAG
1 TGTTTCTAAAG
90680713 TGTTTCTAA
1 TGTTTCTAA
90680722 GGCCTCGAAG
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:0.29, C:0.06, G:0.16, T:0.48
Consensus pattern (11 bp):
TGTTTCTAAAG
Found at i:90682325 original size:24 final size:21
Alignment explanation
Indices: 90682292--90682336 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
90682282 GATAAGGAAT
90682292 GAAATATGTACAAATAATGAATAA
1 GAAATATGT--AAAT-ATGAATAA
*
90682316 GAAATGTGTAAATATGAATAA
1 GAAATATGTAAATATGAATAA
90682337 AATAGACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
22 4 0.20
24 8 0.40
ACGTcount: A:0.56, C:0.02, G:0.16, T:0.27
Consensus pattern (21 bp):
GAAATATGTAAATATGAATAA
Found at i:90685786 original size:46 final size:46
Alignment explanation
Indices: 90685734--90686037 Score: 455
Period size: 46 Copynumber: 6.6 Consensus size: 46
90685724 GCTTTCTGAA
90685734 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*
90685780 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
90685826 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
90685872 ATGAAATGTGTAAGACCATGGTTGAAAGATACCGTGACAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * **
90685918 ATGAAATGTGTAAGACCATAGTTGAAAGATACCATGGCAACGTGCC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
** * * * *
90685964 ATGAAATGAATAAGACTATGGTTGAAATATACCAAGGCAACATGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
** * *
90686010 AAAAAATGAGTAAGACCATAGTTGAAAG
1 ATGAAATGTGTAAGACCATGGTTGAAAG
90686038 GCACTATGGC
Statistics
Matches: 234, Mismatches: 24, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 234 1.00
ACGTcount: A:0.41, C:0.13, G:0.23, T:0.23
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
Found at i:90685805 original size:21 final size:21
Alignment explanation
Indices: 90685781--90685852 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 21
90685771 CAACATGATA
90685781 TGAAATGTGTAAGACCATGGT
1 TGAAATGTGTAAGACCATGGT
* *
90685802 TGAAA-G-ATACCATGACAACATGAT
1 TGAAATGTGTA--A-GAC--CATGGT
90685826 ATGAAATGTGTAAGACCATGGT
1 -TGAAATGTGTAAGACCATGGT
90685848 TGAAA
1 TGAAA
90685853 GATACCATGG
Statistics
Matches: 39, Mismatches: 4, Indels: 16
0.66 0.07 0.27
Matches are distributed among these distances:
19 2 0.05
20 1 0.03
21 11 0.28
22 8 0.21
24 8 0.21
25 6 0.15
26 1 0.03
27 2 0.05
ACGTcount: A:0.40, C:0.11, G:0.24, T:0.25
Consensus pattern (21 bp):
TGAAATGTGTAAGACCATGGT
Found at i:90688389 original size:13 final size:11
Alignment explanation
Indices: 90688362--90688411 Score: 64
Period size: 11 Copynumber: 4.4 Consensus size: 11
90688352 TTTTTATAAT
90688362 TAAAATATTAA
1 TAAAATATTAA
90688373 TAAAATATCTAAA
1 TAAAATAT-T-AA
*
90688386 TAAAATATTAT
1 TAAAATATTAA
*
90688397 TAAAATAATAA
1 TAAAATATTAA
90688408 TAAA
1 TAAA
90688412 CTAATTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
11 22 0.65
12 2 0.06
13 10 0.29
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (11 bp):
TAAAATATTAA
Found at i:90690063 original size:21 final size:21
Alignment explanation
Indices: 90690030--90690081 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
90690020 TGACACATAA
* *
90690030 GTGCTTGAAACGACATACGAG
1 GTGCCTGAAACGACACACGAG
*
90690051 GTGCCTGATACGACACACGAG
1 GTGCCTGAAACGACACACGAG
90690072 GTGCCTGAAA
1 GTGCCTGAAA
90690082 TATGACACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.31, C:0.23, G:0.29, T:0.17
Consensus pattern (21 bp):
GTGCCTGAAACGACACACGAG
Found at i:90709410 original size:28 final size:28
Alignment explanation
Indices: 90709379--90709432 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
90709369 TGAATTATCC
90709379 AAAATTTTGTCATACATTACTTCAATAA
1 AAAATTTTGTCATACATTACTTCAATAA
90709407 AAAATTTTGTCATACATTACTTCAAT
1 AAAATTTTGTCATACATTACTTCAAT
90709433 CAAACACTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.41, C:0.15, G:0.04, T:0.41
Consensus pattern (28 bp):
AAAATTTTGTCATACATTACTTCAATAA
Done.