Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A02
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: 100057689
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3589301 characters in sequence are not A, C, G, or T
File 7 of 295
Found at i:2074554 original size:52 final size:49
Alignment explanation
Indices: 2074492--2074652 Score: 152
Period size: 46 Copynumber: 3.3 Consensus size: 49
2074482 TGTGATTTCC
2074492 GTATAAGACCATAGCTGGGCTATGGCTTCGGAGAAATGTGATATGTGCTACT
1 GTATAAGACCATAGCTGGGCTATGGCTTC-GAG--ATGTGATATGTGCTACT
* * * * * *
2074544 GTATAAGACCATATCTGGGATATGGCATC-AG-TGTGATACGTGAT-CC
1 GTATAAGACCATAGCTGGGCTATGGCTTCGAGATGTGATATGTGCTACT
* *
2074590 GTGTAAGACCATGGCTGGGCTATGGCTTCG-GTATGTGATATGTGACTA-T
1 GTATAAGACCATAGCTGGGCTATGGCTTCGAG-ATGTGATATGTG-CTACT
**
2074639 GTGCAAGACCATAG
1 GTATAAGACCATAG
2074653 TTTTACTATG
Statistics
Matches: 88, Mismatches: 16, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
46 26 0.30
47 11 0.12
48 10 0.11
49 13 0.15
50 2 0.02
52 26 0.30
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (49 bp):
GTATAAGACCATAGCTGGGCTATGGCTTCGAGATGTGATATGTGCTACT
Found at i:2078058 original size:15 final size:15
Alignment explanation
Indices: 2078010--2078059 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
2078000 GTATCTTGAG
*
2078010 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
2078025 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
2078040 TTTCTTTATTCTGGG
1 TTTCTTTATTCTGGA
2078055 TTTCT
1 TTTCT
2078060 CTATCTTGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.10, C:0.18, G:0.14, T:0.58
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:2080017 original size:52 final size:48
Alignment explanation
Indices: 2079952--2080083 Score: 142
Period size: 52 Copynumber: 2.7 Consensus size: 48
2079942 AAATGTGATT
* *
2079952 TCCGTATAAGACCATAGCTGGGCTATGGCTTCGGAGAAATGTGATATGTGC
1 TCCGTATAAGACCATAGCTGGGCTATGGCTTCGGAG---TGTGATACGTGA
* * * *
2080003 TACTGTATAAGACCATATCTGGGATATGGCATC--AGTGTGATACGTGA
1 T-CCGTATAAGACCATAGCTGGGCTATGGCTTCGGAGTGTGATACGTGA
* *
2080050 TCCGTGTAAGACCATGGCTGGGCTATGGCTTCGG
1 TCCGTATAAGACCATAGCTGGGCTATGGCTTCGG
2080084 TATGTAATAT
Statistics
Matches: 66, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
46 25 0.38
47 11 0.17
50 2 0.03
51 1 0.02
52 27 0.41
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (48 bp):
TCCGTATAAGACCATAGCTGGGCTATGGCTTCGGAGTGTGATACGTGA
Found at i:2083254 original size:6 final size:7
Alignment explanation
Indices: 2083227--2083252 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2083217 GTCTTACTTT
2083227 ATTTTTA
1 ATTTTTA
2083234 ATTTTTA
1 ATTTTTA
2083241 ATTTTTA
1 ATTTTTA
2083248 ATTTT
1 ATTTT
2083253 AAAAATTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
ATTTTTA
Found at i:2084365 original size:30 final size:30
Alignment explanation
Indices: 2084331--2084393 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
2084321 CCACTAACCC
2084331 TTTTCTATTACAAACGTAACAGAGCTACCA
1 TTTTCTATTACAAACGTAACAGAGCTACCA
* * * *
2084361 TTTTCTGTTACAAACTTAATAGAGCTGCCA
1 TTTTCTATTACAAACGTAACAGAGCTACCA
2084391 TTT
1 TTT
2084394 CCCATCCCCC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (30 bp):
TTTTCTATTACAAACGTAACAGAGCTACCA
Found at i:2085544 original size:30 final size:30
Alignment explanation
Indices: 2085509--2085577 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
2085499 ACAGGGGATG
2085509 GAAAATGGTAGCTCCATTAAGTCTGTAAC-
1 GAAAATGGTAGCTCCATTAAGTCTGTAACA
* *
2085538 GAAAAATGGTAGCTCCGTTATGTCTGTAACA
1 G-AAAATGGTAGCTCCATTAAGTCTGTAACA
2085569 GAAAATGGT
1 GAAAATGGT
2085578 TAGTGGTGAC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
29 1 0.03
30 34 0.94
31 1 0.03
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (30 bp):
GAAAATGGTAGCTCCATTAAGTCTGTAACA
Found at i:2085808 original size:24 final size:24
Alignment explanation
Indices: 2085781--2085826 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
2085771 GGTAAAATGA
* *
2085781 ATTATGCTAATAAATGCTAAATAT
1 ATTATACTAATAAATACTAAATAT
2085805 ATTATACTAATAAATACTAAAT
1 ATTATACTAATAAATACTAAAT
2085827 CTTCTAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.50, C:0.09, G:0.04, T:0.37
Consensus pattern (24 bp):
ATTATACTAATAAATACTAAATAT
Found at i:2086650 original size:22 final size:22
Alignment explanation
Indices: 2086625--2086666 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2086615 ATGATTATAC
2086625 TTTTT-ATT-AATTTGATTTTTA
1 TTTTTAATTAAATTT-ATTTTTA
2086646 TTTTTAATTAAATTTATTTTT
1 TTTTTAATTAAATTTATTTTT
2086667 GGTTGCACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 9 0.47
23 5 0.26
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTTTAATTAAATTTATTTTTA
Found at i:2089702 original size:20 final size:21
Alignment explanation
Indices: 2089660--2089702 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
2089650 ACCCCAATTT
* *
2089660 AATTTTTGTTAATTATTTCTA
1 AATTTTTGTAAATTATTTATA
*
2089681 AATTTTT-TAAATTTTTTATA
1 AATTTTTGTAAATTATTTATA
2089701 AA
1 AA
2089703 AAAACAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (21 bp):
AATTTTTGTAAATTATTTATA
Found at i:2099898 original size:25 final size:25
Alignment explanation
Indices: 2099846--2099904 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
2099836 CTTATTTTAT
* *
2099846 TAAATAAA-A-ATTTTAAAATATAA
1 TAAATAAATATATTTAAAAACATAA
2099869 TAAATCAAATATATTTAAAAACATAA
1 TAAAT-AAATATATTTAAAAACATAA
2099895 -AAATAAATAT
1 TAAATAAATAT
2099905 TAAAACAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 5 0.16
24 9 0.29
25 5 0.16
26 12 0.39
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.32
Consensus pattern (25 bp):
TAAATAAATATATTTAAAAACATAA
Found at i:2112687 original size:22 final size:22
Alignment explanation
Indices: 2112645--2112687 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2112635 GTCTTTTATT
* *
2112645 TATTTTTTATTTAAATCGGATG
1 TATTTTTAATTTAAATAGGATG
2112667 TATTTTTAATTTTAAA-AGGAT
1 TATTTTTAA-TTTAAATAGGAT
2112688 ATTCGGTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (22 bp):
TATTTTTAATTTAAATAGGATG
Found at i:2112835 original size:16 final size:17
Alignment explanation
Indices: 2112809--2112843 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
2112799 ATAATAACAA
2112809 ATGTAATATTTAAAATG
1 ATGTAATATTTAAAATG
2112826 ATGT-ATATTTAAAATG
1 ATGTAATATTTAAAATG
2112842 AT
1 AT
2112844 AAATTAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (17 bp):
ATGTAATATTTAAAATG
Found at i:2120697 original size:19 final size:20
Alignment explanation
Indices: 2120654--2120702 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
2120644 TGCCTCTTTT
*
2120654 TGCATT-CATTTCATTCATC
1 TGCATTACATTTCATTCATA
*
2120673 TACATTACATTTCA-TCATA
1 TGCATTACATTTCATTCATA
2120692 TGCATTA-ATTT
1 TGCATTACATTT
2120703 TCATAAAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 4 0.15
19 15 0.58
20 7 0.27
ACGTcount: A:0.29, C:0.20, G:0.04, T:0.47
Consensus pattern (20 bp):
TGCATTACATTTCATTCATA
Found at i:2127361 original size:31 final size:31
Alignment explanation
Indices: 2127324--2127393 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
2127314 GAGAAAAAAG
2127324 AAGACTAAGTTGATAAAAGATTTCAAATCCA
1 AAGACTAAGTTGATAAAAGATTTCAAATCCA
*
2127355 AAGACTAAGTTTATAAAAGATTTCAAATCCA
1 AAGACTAAGTTGATAAAAGATTTCAAATCCA
2127386 AAGACTAA
1 AAGACTAA
2127394 AAAGTAAACC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.50, C:0.13, G:0.11, T:0.26
Consensus pattern (31 bp):
AAGACTAAGTTGATAAAAGATTTCAAATCCA
Found at i:2128286 original size:17 final size:17
Alignment explanation
Indices: 2128266--2128299 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2128256 AAAAAATTTC
2128266 ATAATTTGTAAAAATAT
1 ATAATTTGTAAAAATAT
* *
2128283 ATAATTTTTATAAATAT
1 ATAATTTGTAAAAATAT
2128300 TTTTAATTTG
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:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
ATAATTTGTAAAAATAT
Found at i:2130865 original size:15 final size:15
Alignment explanation
Indices: 2130845--2130874 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2130835 TTTAATCCTT
*
2130845 TATAAATTATAAAAA
1 TATAAACTATAAAAA
2130860 TATAAACTATAAAAA
1 TATAAACTATAAAAA
2130875 ATTAAAATTT
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:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
TATAAACTATAAAAA
Found at i:2132051 original size:26 final size:26
Alignment explanation
Indices: 2132005--2132054 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
2131995 TTAATTACAA
*
2132005 TAATTAAAAATACATTATATAAAAAC
1 TAATTAAAAATACAATATATAAAAAC
*
2132031 TAATTAAAAATTA-AATGTATAAAA
1 TAATTAAAAA-TACAATATATAAAA
2132055 TCACATGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 19 0.90
27 2 0.10
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (26 bp):
TAATTAAAAATACAATATATAAAAAC
Found at i:2133676 original size:23 final size:22
Alignment explanation
Indices: 2133634--2133678 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2133624 AAATATAATG
*
2133634 AAATTATTTTTTTAAAAATTAA
1 AAATTATTTTTATAAAAATTAA
*
2133656 AAATTATTTTTATATACAATTAA
1 AAATTATTTTTATA-AAAATTAA
2133679 TTTATTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
AAATTATTTTTATAAAAATTAA
Found at i:2134944 original size:14 final size:15
Alignment explanation
Indices: 2134910--2134947 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2134900 TTTTCAATAT
2134910 TTTTAATTTTTATTAA
1 TTTT-ATTTTTATTAA
*
2134926 TTTTATTTTTGTTAA
1 TTTTATTTTTATTAA
2134941 -TTTATTT
1 TTTTATTT
2134948 ATTTTTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.33
15 10 0.48
16 4 0.19
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (15 bp):
TTTTATTTTTATTAA
Found at i:2138423 original size:21 final size:20
Alignment explanation
Indices: 2138394--2138432 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
2138384 ACGCCTACGA
2138394 AAAGATCGCTTGGATTTAAG
1 AAAGATCGCTTGGATTTAAG
2138414 AAAGAGTCGCTTGGATTTA
1 AAAGA-TCGCTTGGATTTA
2138433 TCCATGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (20 bp):
AAAGATCGCTTGGATTTAAG
Found at i:2138566 original size:15 final size:15
Alignment explanation
Indices: 2138546--2138577 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2138536 AGGATTTGGT
2138546 TTGTTTATTGTATTA
1 TTGTTTATTGTATTA
*
2138561 TTGTTTATTTTATTA
1 TTGTTTATTGTATTA
2138576 TT
1 TT
2138578 TGTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.09, T:0.72
Consensus pattern (15 bp):
TTGTTTATTGTATTA
Found at i:2142444 original size:11 final size:11
Alignment explanation
Indices: 2142430--2142454 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2142420 AAAAAATTCT
2142430 AATAAATTAAA
1 AATAAATTAAA
2142441 AATAAATTAAA
1 AATAAATTAAA
2142452 AAT
1 AAT
2142455 TTTATACTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AATAAATTAAA
Found at i:2142590 original size:22 final size:22
Alignment explanation
Indices: 2142506--2142607 Score: 75
Period size: 22 Copynumber: 4.7 Consensus size: 22
2142496 TAAATGTCTT
* *
2142506 TAAAATAGTAAAAAATTAAT-A
1 TAAAATAATAAAAAAATAATAA
* * * * *
2142527 TACAATATTTAAATAATAATGA
1 TAAAATAATAAAAAAATAATAA
* **
2142549 TAAAATAATAACAACGTAATAA
1 TAAAATAATAAAAAAATAATAA
*
2142571 TAAAATGATAAAAAAATAATAA
1 TAAAATAATAAAAAAATAATAA
2142593 -AAAATAA-AAGAAAAA
1 TAAAATAATAA-AAAAA
2142608 CATAACAACA
Statistics
Matches: 61, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
20 2 0.03
21 26 0.43
22 33 0.54
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.25
Consensus pattern (22 bp):
TAAAATAATAAAAAAATAATAA
Found at i:2142606 original size:10 final size:10
Alignment explanation
Indices: 2142507--2142599 Score: 51
Period size: 11 Copynumber: 8.7 Consensus size: 10
2142497 AAATGTCTTT
*
2142507 AAAATAGTAA
1 AAAATAATAA
*
2142517 AAAATTAATAT
1 AAAA-TAATAA
* *
2142528 ACAATATTTAA
1 AAAATA-ATAA
* *
2142539 ATAATAATGAT
1 AAAATAAT-AA
2142550 AAAATAATAA
1 AAAATAATAA
**
2142560 CAACGTAATAA
1 -AAAATAATAA
*
2142571 TAAAATGATAAA
1 -AAAATAAT-AA
2142583 AAAATAATAA
1 AAAATAATAA
2142593 AAAATAA
1 AAAATAA
2142600 AAGAAAAACA
Statistics
Matches: 61, Mismatches: 17, Indels: 10
0.69 0.19 0.11
Matches are distributed among these distances:
10 17 0.28
11 42 0.69
12 2 0.03
ACGTcount: A:0.67, C:0.03, G:0.04, T:0.26
Consensus pattern (10 bp):
AAAATAATAA
Found at i:2143194 original size:29 final size:29
Alignment explanation
Indices: 2143148--2143205 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
2143138 TATTAATTTT
*
2143148 TTTAATAGTATAAAGATTAAATTGATCTA
1 TTTAATAATATAAAGATTAAATTGATCTA
*
2143177 TTTAATAATA-AAAGGATTAATTTGATCTA
1 TTTAATAATATAAA-GATTAAATTGATCTA
2143206 ATTCATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 23 0.88
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.41
Consensus pattern (29 bp):
TTTAATAATATAAAGATTAAATTGATCTA
Found at i:2149547 original size:4 final size:4
Alignment explanation
Indices: 2149538--2149563 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2149528 GCTCAAAGTA
2149538 ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC AT
2149564 TTTGAATCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:2152987 original size:30 final size:29
Alignment explanation
Indices: 2152906--2152987 Score: 78
Period size: 30 Copynumber: 2.8 Consensus size: 29
2152896 CTCAACATCT
* * **
2152906 AAATAATTTTTTTATATTTTTATATTTTTT
1 AAATAATTTTTTGAT-TTTTTAAATTTTAA
*
2152936 AAATAATTTTAATGA--TTTTAAATTTTAAA
1 AAATAATTTT-TTGATTTTTTAAATTTT-AA
2152965 AAATAATTTTTTGATTTTTTAAA
1 AAATAATTTTTTGATTTTTTAAA
2152988 AAATAATTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
28 13 0.31
29 10 0.24
30 17 0.40
31 2 0.05
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (29 bp):
AAATAATTTTTTGATTTTTTAAATTTTAA
Found at i:2176538 original size:10 final size:10
Alignment explanation
Indices: 2176523--2176552 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
2176513 GCATGACCAA
2176523 GAAAATGAAT
1 GAAAATGAAT
2176533 GAAAATGAAT
1 GAAAATGAAT
2176543 GAAAATGAAT
1 GAAAATGAAT
2176553 ATATTCATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (10 bp):
GAAAATGAAT
Found at i:2189108 original size:6 final size:6
Alignment explanation
Indices: 2189066--2189124 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
2189056 AATACATTTA
* * * *
2189066 AAAACAT AAAAAC AAAAAT TAAAAC AAAAA- AACAAAT AAAAAT AAATA-
1 AAAA-AT AAAAAT AAAAAT AAAAAT AAAAAT AA-AAAT AAAAAT AAAAAT
2189114 AAAAAT AAAAA
1 AAAAAT AAAAA
2189125 ATGAGACTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
5 6 0.14
6 30 0.71
7 6 0.14
ACGTcount: A:0.81, C:0.07, G:0.00, T:0.12
Consensus pattern (6 bp):
AAAAAT
Found at i:2189112 original size:28 final size:28
Alignment explanation
Indices: 2189065--2189125 Score: 65
Period size: 28 Copynumber: 2.2 Consensus size: 28
2189055 AAATACATTT
*
2189065 AAAAACATAAAAACAAAAATTAAAACA-A
1 AAAAACATAAAAACAAAAA-TAAAAAATA
2189093 AAAAACA-AATAAA-AATAAATAAAAAATA
1 AAAAACATAA-AAACAA-AAATAAAAAATA
2189121 AAAAA
1 AAAAA
2189126 TGAGACTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
27 10 0.34
28 19 0.66
ACGTcount: A:0.82, C:0.07, G:0.00, T:0.11
Consensus pattern (28 bp):
AAAAACATAAAAACAAAAATAAAAAATA
Found at i:2189124 original size:17 final size:17
Alignment explanation
Indices: 2189073--2189124 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
2189063 TTAAAAACAT
*
2189073 AAAAACAAAAATTAAAAC
1 AAAAA-AAAAATAAAAAC
*
2189091 AAAAAAACAAATAAAAAT
1 AAAAAAA-AAATAAAAAC
*
2189109 AAATAAAAAATAAAAA
1 AAAAAAAAAATAAAAA
2189125 ATGAGACTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
17 11 0.37
18 19 0.63
ACGTcount: A:0.83, C:0.06, G:0.00, T:0.12
Consensus pattern (17 bp):
AAAAAAAAAATAAAAAC
Found at i:2190130 original size:15 final size:16
Alignment explanation
Indices: 2190101--2190133 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2190091 TTTTTAGTGC
*
2190101 TTTTAGTATATTATAT
1 TTTTAATATATTATAT
2190117 TTTTAATATA-TATAT
1 TTTTAATATATTATAT
2190132 TT
1 TT
2190134 AAATAAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (16 bp):
TTTTAATATATTATAT
Found at i:2193404 original size:7 final size:7
Alignment explanation
Indices: 2193392--2193429 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
2193382 AGCAAGGAAC
2193392 CCAACAT
1 CCAACAT
2193399 CCAACAT
1 CCAACAT
2193406 CCAACAT
1 CCAACAT
2193413 CCAACAT
1 CCAACAT
2193420 CCAACA-
1 CCAACAT
2193426 CCAA
1 CCAA
2193430 ACTTTTTTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 4 0.13
7 27 0.87
ACGTcount: A:0.45, C:0.45, G:0.00, T:0.11
Consensus pattern (7 bp):
CCAACAT
Found at i:2196525 original size:9 final size:9
Alignment explanation
Indices: 2196511--2196541 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
2196501 CTTACTTGAA
2196511 AAAAAAAAT
1 AAAAAAAAT
*
2196520 AAAAAAAGT
1 AAAAAAAAT
2196529 AAAAAAAAT
1 AAAAAAAAT
2196538 AAAA
1 AAAA
2196542 TTAATGAGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.87, C:0.00, G:0.03, T:0.10
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:2233084 original size:11 final size:11
Alignment explanation
Indices: 2233068--2233118 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
2233058 GGAAATGACG
*
2233068 AAAAAAGGGAAA
1 AAAAAAGAG-AA
*
2233080 AAAAAAAAGAA
1 AAAAAAGAGAA
2233091 AAAAAAGAGAA
1 AAAAAAGAGAA
2233102 AAAAGAA-AGAA
1 AAAA-AAGAGAA
2233113 AAAAAA
1 AAAAAA
2233119 ATACAAGCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
10 2 0.06
11 24 0.69
12 9 0.26
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAAAGAGAA
Found at i:2233092 original size:9 final size:9
Alignment explanation
Indices: 2233080--2233119 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
2233070 AAAAGGGAAA
2233080 AAAAAAAAG
1 AAAAAAAAG
2233089 AAAAAAAAG
1 AAAAAAAAG
*
2233098 AGAAAAAAG
1 AAAAAAAAG
*
2233107 AAAGAAAA-
1 AAAAAAAAG
2233115 AAAAA
1 AAAAA
2233120 TACAAGCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
8 4 0.15
9 23 0.85
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:2233119 original size:23 final size:23
Alignment explanation
Indices: 2233068--2233118 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 23
2233058 GGAAATGACG
*
2233068 AAAAAAGGGAAAAAAAAAAAGAA
1 AAAAAAGAGAAAAAAAAAAAGAA
*
2233091 AAAAAAGAG-AAAAAAGAAAGAA
1 AAAAAAGAGAAAAAAAAAAAGAA
2233113 AAAAAA
1 AAAAAA
2233119 ATACAAGCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (23 bp):
AAAAAAGAGAAAAAAAAAAAGAA
Found at i:2234757 original size:45 final size:45
Alignment explanation
Indices: 2234707--2234803 Score: 149
Period size: 45 Copynumber: 2.2 Consensus size: 45
2234697 CTTCCTCTGT
* * *
2234707 GATGCTTGCCATCAAAAGATCTTGACCTTGACCTCTTTCTATCCC
1 GATGCTTGCCATCAAAAGATCTTGACCTCGACCGCCTTCTATCCC
**
2234752 GATGCTTGCCATCAGCAGATCTTGACCTCGACCGCCTTCTATCCC
1 GATGCTTGCCATCAAAAGATCTTGACCTCGACCGCCTTCTATCCC
2234797 GATGCTT
1 GATGCTT
2234804 AGATTTCTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.20, C:0.33, G:0.16, T:0.31
Consensus pattern (45 bp):
GATGCTTGCCATCAAAAGATCTTGACCTCGACCGCCTTCTATCCC
Found at i:2235655 original size:42 final size:42
Alignment explanation
Indices: 2235531--2235689 Score: 178
Period size: 42 Copynumber: 3.8 Consensus size: 42
2235521 AGACCTCCTC
* * *
2235531 CTTCGCCTATAGCTGATTGGTGATCTTGACTTTGACCTTGA-
1 CTTCGCCGATAACTAATTGGTGATCTTGACTTTGACCTTGAT
* * * *
2235572 CTTTCGCCTATAAATGATTGGTGATCTTGACTTGGACCTTGAT
1 C-TTCGCCGATAACTAATTGGTGATCTTGACTTTGACCTTGAT
* *
2235615 CTTCGCCGATAACTAATTGGTGATCTAGACTTTGATCTTGAT
1 CTTCGCCGATAACTAATTGGTGATCTTGACTTTGACCTTGAT
* ** *
2235657 CTTCTCCGATAACTAAGGGGTGATTTTGA-TTTG
1 CTTCGCCGATAACTAATTGGTGATCTTGACTTTG
2235690 GATCTTGACC
Statistics
Matches: 102, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
41 5 0.05
42 96 0.94
43 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (42 bp):
CTTCGCCGATAACTAATTGGTGATCTTGACTTTGACCTTGAT
Found at i:2240293 original size:29 final size:28
Alignment explanation
Indices: 2240236--2240301 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
2240226 TCACAAAATA
**
2240236 TTGAAAATTTCAATTAAACCTTATTATTT
1 TTGAAAA-TTCAATTAAACCTTAAAATTT
2240265 TTGAAAATTCATATTAAATCC-TAAAATTT
1 TTGAAAATTCA-ATTAAA-CCTTAAAATTT
2240294 TT-AAAATT
1 TTGAAAATT
2240302 TTAAGTGATC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 10 0.30
29 21 0.64
30 2 0.06
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.45
Consensus pattern (28 bp):
TTGAAAATTCAATTAAACCTTAAAATTT
Found at i:2240940 original size:50 final size:50
Alignment explanation
Indices: 2240884--2240983 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
2240874 AATTTCTAGT
2240884 TTAGTTTTTGTATTTTTTTAGATATTCAAAATTTAATTCGTGAATTTTTA
1 TTAGTTTTTGTATTTTTTTAGATATTCAAAATTTAATTCGTGAATTTTTA
2240934 TTAGTTTTTGTATTTTTTTAGATATTCAAAATTTAATTCGTGAATTTTTA
1 TTAGTTTTTGTATTTTTTTAGATATTCAAAATTTAATTCGTGAATTTTTA
2240984 CTTTTAAGAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.28, C:0.04, G:0.10, T:0.58
Consensus pattern (50 bp):
TTAGTTTTTGTATTTTTTTAGATATTCAAAATTTAATTCGTGAATTTTTA
Found at i:2241798 original size:10 final size:11
Alignment explanation
Indices: 2241781--2241806 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2241771 AAACGAGAAT
2241781 GAAAAAAAAAA
1 GAAAAAAAAAA
2241792 GAAAAAAAAAA
1 GAAAAAAAAAA
2241803 GAAA
1 GAAA
2241807 CGTTAAAAGA
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:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
GAAAAAAAAAA
Found at i:2247419 original size:20 final size:20
Alignment explanation
Indices: 2247394--2247462 Score: 81
Period size: 19 Copynumber: 3.5 Consensus size: 20
2247384 AAAAATATAA
**
2247394 ATTTTGAAATTTTTATGAAT
1 ATTTTGAAATTTTTAAAAAT
*
2247414 ATTTTG-AATTTTAAAAAAT
1 ATTTTGAAATTTTTAAAAAT
2247433 ATTTT-AAATTTTTAAAAATT
1 ATTTTGAAATTTTTAAAAA-T
2247453 ATTTT-AAATT
1 ATTTTGAAATT
2247463 ATTTTGTAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 26 0.60
20 17 0.40
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (20 bp):
ATTTTGAAATTTTTAAAAAT
Found at i:2248975 original size:3 final size:3
Alignment explanation
Indices: 2248967--2249005 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
2248957 TTATGCTTTA
2248967 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2249006 TATCCCTTGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2251290 original size:72 final size:72
Alignment explanation
Indices: 2251168--2251437 Score: 325
Period size: 72 Copynumber: 3.8 Consensus size: 72
2251158 CACTTTCGAC
* * *
2251168 GCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGGTTATGCAATATGAGTCAACTTAG-CG
1 GCATCTTATAACAATTTGAATGGCCCAATTCCAAATTGCTTAGGCAATATGAGTCAACTTAGACG
2251232 -TTTGCTAT
66 TTTTG--AT
* * * * * * *
2251240 GCATTTTATAATAATTTCAATGGCCCAATACCAAATTGCTTATGCAATATGAGTCAACTAAGAGG
1 GCATCTTATAACAATTTGAATGGCCCAATTCCAAATTGCTTAGGCAATATGAGTCAACTTAGACG
2251305 TTTTGAT
66 TTTTGAT
* *
2251312 GCATCTTATAACAATTTGAGTGGCTCAATTCCAAATTGCTT-GGACAATATGAGTCAACTT-GAC
1 GCATCTTATAACAATTTGAATGGCCCAATTCCAAATTGCTTAGG-CAATATGAGTCAACTTAGAC
2251375 AGTTTTGAT
65 -GTTTTGAT
* * *
2251384 GTATCTTATAACAATTT-AAGTGGCCCAATTCCAAATTGTTTGGGCAATATGAGT
1 GCATCTTATAACAATTTGAA-TGGCCCAATTCCAAATTGCTTAGGCAATATGAGT
2251438 GCTCTAAGTT
Statistics
Matches: 171, Mismatches: 21, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
71 4 0.02
72 160 0.94
73 3 0.02
74 4 0.02
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.35
Consensus pattern (72 bp):
GCATCTTATAACAATTTGAATGGCCCAATTCCAAATTGCTTAGGCAATATGAGTCAACTTAGACG
TTTTGAT
Found at i:2251445 original size:144 final size:143
Alignment explanation
Indices: 2251168--2251437 Score: 368
Period size: 144 Copynumber: 1.9 Consensus size: 143
2251158 CACTTTCGAC
* *
2251168 GCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGGTTATGCAATATGAGTCAACTTAGCGT
1 GCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTTAGGCAATATGAGTCAACTTAGCGT
* * *
2251233 TTGCTATGCATTTTATAATAATTTCAATGGCCCAATACCAAATTGCTTATGCAATATGAGTCAAC
66 TTGC-ATGCATCTTATAACAATTTCAATGGCCCAATACCAAATTGCTTAGGCAATATGAGTCAAC
2251298 TAAGAGGTTTTGAT
130 TAAGAGGTTTTGAT
*
2251312 GCATCTTATAACAATTTGAGTGGCTCAATTCCAAATTGCTT-GGACAATATGAGTCAACTT-GAC
1 GCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTTAGG-CAATATGAGTCAACTTAG-C
* * * *
2251375 AGTTTTG-ATGTATCTTATAACAATTT-AAGTGGCCCAATTCCAAATTGTTTGGGCAATATGAGT
64 -G-TTTGCATGCATCTTATAACAATTTCAA-TGGCCCAATACCAAATTGCTTAGGCAATATGAGT
2251438 GCTCTAAGTT
Statistics
Matches: 111, Mismatches: 10, Indels: 10
0.85 0.08 0.08
Matches are distributed among these distances:
143 4 0.04
144 102 0.92
145 1 0.01
146 4 0.04
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.35
Consensus pattern (143 bp):
GCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTTAGGCAATATGAGTCAACTTAGCGT
TTGCATGCATCTTATAACAATTTCAATGGCCCAATACCAAATTGCTTAGGCAATATGAGTCAACT
AAGAGGTTTTGAT
Found at i:2258187 original size:17 final size:17
Alignment explanation
Indices: 2258165--2258200 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
2258155 TGCAGGACAT
*
2258165 GGAATGTCTAGTCAGGA
1 GGAATGTCGAGTCAGGA
2258182 GGAATGTCGAGTCAGGA
1 GGAATGTCGAGTCAGGA
2258199 GG
1 GG
2258201 TACGTTATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.28, C:0.11, G:0.42, T:0.19
Consensus pattern (17 bp):
GGAATGTCGAGTCAGGA
Found at i:2262756 original size:16 final size:16
Alignment explanation
Indices: 2262731--2262761 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2262721 CACCACTTGG
*
2262731 ATTGTTTGCCATTAAA
1 ATTGTCTGCCATTAAA
2262747 ATTGTCTGCCATTAA
1 ATTGTCTGCCATTAA
2262762 TCATTAATGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (16 bp):
ATTGTCTGCCATTAAA
Found at i:2264706 original size:21 final size:21
Alignment explanation
Indices: 2264680--2264720 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2264670 ATCTGCTCAA
* *
2264680 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
2264701 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
2264721 TCGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:2268269 original size:4 final size:4
Alignment explanation
Indices: 2268255--2268289 Score: 61
Period size: 4 Copynumber: 8.5 Consensus size: 4
2268245 ACTATACATA
2268255 TATG ATATG TATG TATG TATG TATG TATG TATG TA
1 TATG -TATG TATG TATG TATG TATG TATG TATG TA
2268290 CATAATGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:2274550 original size:6 final size:6
Alignment explanation
Indices: 2274541--2274583 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
2274531 TCTTTTTACA
* *
2274541 TAGTTT TAGTTT TAGTTT TAGTTT TAGTTT TAATTT TAATTT T
1 TAGTTT TAGTTT TAGTTT TAGTTT TAGTTT TAGTTT TAGTTT T
2274584 CCTTTTCAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.67
Consensus pattern (6 bp):
TAGTTT
Found at i:2274647 original size:17 final size:17
Alignment explanation
Indices: 2274619--2274655 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
2274609 ATCATTGCTA
2274619 TTTAAAAAAAAA-TATT
1 TTTAAAAAAAAATTATT
2274635 TTTAAATAAAAAATTATT
1 TTTAAA-AAAAAATTATT
2274653 TTT
1 TTT
2274656 GTTAGTTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.32
17 6 0.32
18 7 0.37
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTAAAAAAAAATTATT
Found at i:2278249 original size:193 final size:193
Alignment explanation
Indices: 2277703--2278386 Score: 1082
Period size: 193 Copynumber: 3.5 Consensus size: 193
2277693 GGTAGAAAAA
* * * * * *
2277703 TTAGGATTATTGACATGTTTAACTCAGTCCATATAATGTCTTTTTCAGGAGGTAAAGAAAATGCA
1 TTAGGATGACTGACCTGTTTAACCCAGTCCATATAATGTCTTTTTCAGGAGCTAAAGGAAATGCA
* * * *
2277768 TCTCACGTGCGCCAATTAGTGGGAATGAGAGGACTAACGTCTGATCCCCAAGGAAAAATGATCGA
66 TCTCACGTGCACCAATTAGTGGGAATGAGAGGATTAATGTCTGATCCCCAAGGACAAATGATCGA
*
2277833 TGCGGTAGAAAAATTACGCCAATCTATTGAGATATGGTTTGCAACAAGAAATGAATCCTAATT
131 TGCGGTAGAAAAATTACGCCAATCTATTGAGATATGGTTTGCGACAAGAAATGAATCCTAATT
* *
2277896 TTAGGATGATTGACCTGTTTAACCCAGTCAATATAATGTCTTTTT-AGGAGCTAAAGGAAATGCA
1 TTAGGATGACTGACCTGTTTAACCCAGTCCATATAATGTCTTTTTCAGGAGCTAAAGGAAATGCA
* * *
2277960 TCTCACGTGCACCAATTAGTGGGAACGAAAGGATTAATGTCGGATCCCCAAGGACAAATGATCGA
66 TCTCACGTGCACCAATTAGTGGGAATGAGAGGATTAATGTCTGATCCCCAAGGACAAATGATCGA
*
2278025 TGCGGTAGAAAAATTACGCCAATCTATTGAGATGTGGTTTGCGACAAGAAATGAATCCTAATT
131 TGCGGTAGAAAAATTACGCCAATCTATTGAGATATGGTTTGCGACAAGAAATGAATCCTAATT
* * * *
2278088 TTAGGATGACTGACCTGTTTAACCCACTACATATAATGTCTTTTTCACGAGCTAAAGGAAATGCG
1 TTAGGATGACTGACCTGTTTAACCCAGTCCATATAATGTCTTTTTCAGGAGCTAAAGGAAATGCA
* * *
2278153 TCTCATGTGCACCAATTAGTGGGAATGAGAGGATTAATGTCTGATCCCTAAGGACAAATGATCAA
66 TCTCACGTGCACCAATTAGTGGGAATGAGAGGATTAATGTCTGATCCCCAAGGACAAATGATCGA
* *
2278218 TGCGATAGAAAAATTACGCCAATCTATTGAGATATGGTTTGCGACAAGAAATGAATCCTGATT
131 TGCGGTAGAAAAATTACGCCAATCTATTGAGATATGGTTTGCGACAAGAAATGAATCCTAATT
* *
2278281 TTAGGATGACTGACTTGTTTAACCCAGTCCATATAATGTCTTTTTCAGGAGCTAAAAGAAATGCA
1 TTAGGATGACTGACCTGTTTAACCCAGTCCATATAATGTCTTTTTCAGGAGCTAAAGGAAATGCA
** *
2278346 TCTTGCGTGCACCAATTAGTGGCAATGAGAGGATTAATGTC
66 TCTCACGTGCACCAATTAGTGGGAATGAGAGGATTAATGTC
2278387 GGATTGTGAT
Statistics
Matches: 450, Mismatches: 40, Indels: 2
0.91 0.08 0.00
Matches are distributed among these distances:
192 177 0.39
193 273 0.61
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.28
Consensus pattern (193 bp):
TTAGGATGACTGACCTGTTTAACCCAGTCCATATAATGTCTTTTTCAGGAGCTAAAGGAAATGCA
TCTCACGTGCACCAATTAGTGGGAATGAGAGGATTAATGTCTGATCCCCAAGGACAAATGATCGA
TGCGGTAGAAAAATTACGCCAATCTATTGAGATATGGTTTGCGACAAGAAATGAATCCTAATT
Found at i:2281903 original size:192 final size:192
Alignment explanation
Indices: 2281565--2282204 Score: 994
Period size: 192 Copynumber: 3.3 Consensus size: 192
2281555 GGGAATGTAC
**
2281565 ATGCGGTAGAAAAATTACGCCAATCTATTGAGATATGGTTTGTGACAAGAAATGAATCCTAATTT
1 ATGCGGTAGAAAAATTACGCCAATCTATTGAGATATGGTTTGCAACAAGAAATGAATCCTAATTT
* * * *
2281630 TAGGGTTATTGACCTATTTAATCCAGTCCGTA-AATGTCTTTTTCAGGAGCTAAAGGAAATGCAT
66 TAGGATTATTGACCTGTTTAACCCAGTCCATATAATGTCTTTTTCAGGAGCTAAAGGAAATGCAT
*
2281694 CTCACGTGCGCCAATTAGTGGGAATGAGAGGATTAATGTCGGATCCCCAAGGACAAATGATCG
131 CTCACGTGAG-CAATTAGTGGGAATGAGAGGATTAATGTCGGATCCCCAAGGACAAATGATCG
** * *
2281757 ATATGGTAGAAAAATTATGCCAATCTAGTGAGATATGGTTTGCAACAAGAAATGAATCCTAATTT
1 ATGCGGTAGAAAAATTACGCCAATCTATTGAGATATGGTTTGCAACAAGAAATGAATCCTAATTT
* *
2281822 TAGGATTATTGACCTGTTTAACCCAGTCCATATAATATCTTTTTCAGGAGCTAAAGGAAATACAT
66 TAGGATTATTGACCTGTTTAACCCAGTCCATATAATGTCTTTTTCAGGAGCTAAAGGAAATGCAT
* * * *
2281887 CTCACGTGTGCAATTAGTGGGAATGAGAGTATTAATGTCAGATCCCCAAGGACAAATGATTG
131 CTCACGTGAGCAATTAGTGGGAATGAGAGGATTAATGTCGGATCCCCAAGGACAAATGATCG
* * *
2281949 ATGCGGTAGAAAATTTACGCCAATCTATTGAGATATGGTTTGCGACAAGAAATGAATCATAATTT
1 ATGCGGTAGAAAAATTACGCCAATCTATTGAGATATGGTTTGCAACAAGAAATGAATCCTAATTT
* *
2282014 TAGGATGATTGACCTGTTTAACCCAGTCAATATAATGTCTTTTTCAGGAGCTAAAGGAAATGCAT
66 TAGGATTATTGACCTGTTTAACCCAGTCCATATAATGTCTTTTTCAGGAGCTAAAGGAAATGCAT
* * *
2282079 CTCACGTGCACCAATTAGTGGGAATGAGAGGATTAATATCGGATCCCTAAGGACAAATGATCG
131 CTCACGTG-AGCAATTAGTGGGAATGAGAGGATTAATGTCGGATCCCCAAGGACAAATGATCG
* * * *
2282142 ATGCGGTACAAAAATTACGTCAATCTATTGAAATGTGGTTTGCAACAAGAAATGAATCCTAAT
1 ATGCGGTAGAAAAATTACGCCAATCTATTGAGATATGGTTTGCAACAAGAAATGAATCCTAAT
2282205 GTCTTTTTCA
Statistics
Matches: 405, Mismatches: 41, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
192 263 0.65
193 142 0.35
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (192 bp):
ATGCGGTAGAAAAATTACGCCAATCTATTGAGATATGGTTTGCAACAAGAAATGAATCCTAATTT
TAGGATTATTGACCTGTTTAACCCAGTCCATATAATGTCTTTTTCAGGAGCTAAAGGAAATGCAT
CTCACGTGAGCAATTAGTGGGAATGAGAGGATTAATGTCGGATCCCCAAGGACAAATGATCG
Found at i:2286033 original size:2 final size:2
Alignment explanation
Indices: 2286026--2286072 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2286016 CCCCAGTAGA
2286026 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2286068 AG AG A
1 AG AG A
2286073 AAGTGCAAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2286998 original size:14 final size:15
Alignment explanation
Indices: 2286974--2287008 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
2286964 TATATATATT
2286974 ACCATATAAATACTA
1 ACCATATAAATACTA
2286989 ACCATA-AAATACTA
1 ACCATATAAATACTA
2287003 ATCCAT
1 A-CCAT
2287009 GATTAAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (15 bp):
ACCATATAAATACTA
Found at i:2287719 original size:41 final size:40
Alignment explanation
Indices: 2287674--2288073 Score: 323
Period size: 41 Copynumber: 9.8 Consensus size: 40
2287664 TTATATAAAA
* * * *
2287674 CACCGGCATAAAGCCTGCTAGGCACAAAGCCCGATTCATTT
1 CACCGGCATAAAGCCTGCTAGACATAAAGCCAGATT-AATT
* * *
2287715 CACCGGCACAAAGCCTGCTAGACATAAAGTCGGAATTAATT
1 CACCGGCATAAAGCCTGCTAGACATAAAGCCAG-ATTAATT
* * * *
2287756 CACCGGCATCAAGCCTGCTAGACATAAAGTCTAAAATAATT
1 CACCGGCATAAAGCCTGCTAGACATAAAG-CCAGATTAATT
* * * * * *
2287797 CACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATAATC
1 CACCGGCATAAAGCCTGCTAGACATAAAGCCAG-ATTAATT
* * * *
2287838 CACCGGCATCAAGCCTGCTAGACATAAAGTCTAAAATAATT
1 CACCGGCATAAAGCCTGCTAGACATAAAG-CCAGATTAATT
* * * * * *
2287879 CACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATAATC
1 CACCGGCATAAAGCCTGCTAGACATAAAGCCAG-ATTAATT
* * * *
2287920 CACCGGCATCAAGCCTGCTAGACATAAAGTCTAAAATAATT
1 CACCGGCATAAAGCCTGCTAGACATAAAG-CCAGATTAATT
* * * * * *
2287961 CACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATAATC
1 CACCGGCATAAAGCCTGCTAGACATAAAGCCAG-ATTAATT
* * * *
2288002 CACCGGCATCAAGCCTGCTAGACATAAAGTCTAAAATAATT
1 CACCGGCATAAAGCCTGCTAGACATAAAG-CCAGATTAATT
* * *
2288043 CACCGGCATCAAGCCTGCTAGGCATTAAGCC
1 CACCGGCATAAAGCCTGCTAGACATAAAGCC
2288074 TGAAAATCTC
Statistics
Matches: 299, Mismatches: 52, Indels: 17
0.81 0.14 0.05
Matches are distributed among these distances:
40 4 0.01
41 289 0.97
42 6 0.02
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.20
Consensus pattern (40 bp):
CACCGGCATAAAGCCTGCTAGACATAAAGCCAGATTAATT
Found at i:2287799 original size:82 final size:82
Alignment explanation
Indices: 2287713--2288078 Score: 662
Period size: 82 Copynumber: 4.5 Consensus size: 82
2287703 CCCGATTCAT
* * * * * *
2287713 TTCACCGGCA-CAAAGCCTGCTAGACATAAAGTCGGAATTAATTCACCGGCATCAAGCCTGCTAG
1 TTCACCGGCATC-AAGCCTGCTAGGCATTAAGCCTGAAATAATCCACCGGCATCAAGCCTGCTAG
2287777 ACATAAAGTCTAAAATAA
65 ACATAAAGTCTAAAATAA
2287795 TTCACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATAATCCACCGGCATCAAGCCTGCTAGA
1 TTCACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATAATCCACCGGCATCAAGCCTGCTAGA
2287860 CATAAAGTCTAAAATAA
66 CATAAAGTCTAAAATAA
2287877 TTCACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATAATCCACCGGCATCAAGCCTGCTAGA
1 TTCACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATAATCCACCGGCATCAAGCCTGCTAGA
2287942 CATAAAGTCTAAAATAA
66 CATAAAGTCTAAAATAA
2287959 TTCACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATAATCCACCGGCATCAAGCCTGCTAGA
1 TTCACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATAATCCACCGGCATCAAGCCTGCTAGA
2288024 CATAAAGTCTAAAATAA
66 CATAAAGTCTAAAATAA
2288041 TTCACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAA
1 TTCACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAA
2288079 ATCTCATATA
Statistics
Matches: 277, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
82 276 1.00
83 1 0.00
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21
Consensus pattern (82 bp):
TTCACCGGCATCAAGCCTGCTAGGCATTAAGCCTGAAATAATCCACCGGCATCAAGCCTGCTAGA
CATAAAGTCTAAAATAA
Found at i:2288311 original size:64 final size:63
Alignment explanation
Indices: 2288193--2288373 Score: 262
Period size: 64 Copynumber: 2.9 Consensus size: 63
2288183 GCAAACAAAC
*
2288193 ATTCGAACCACATATGT-AT-AATTTACA-ACATTAAAATTCAGCTCAAAGAA-TTTGTAACCTA
1 ATTCGAACCACATATGTAATAAAATT-CATACATT-AAATTCAGCTC-AAGAACTTTGTAACCTA
2288254 T
63 T
2288255 ATTCGAACCACATATGTAAGTAAAATTCATACATTAAATTCAGCTCAAGAACTTTGTAACCTAT
1 ATTCGAACCACATATGTAA-TAAAATTCATACATTAAATTCAGCTCAAGAACTTTGTAACCTAT
* *
2288319 ATTTGAACCACATATGTATATAAAATTCATACATTAAATACAGCTCAAGAACTTT
1 ATTCGAACCACATATGTA-ATAAAATTCATACATTAAATTCAGCTCAAGAACTTT
2288374 AAATATATAT
Statistics
Matches: 110, Mismatches: 3, Indels: 10
0.89 0.02 0.08
Matches are distributed among these distances:
62 17 0.15
63 6 0.05
64 77 0.70
65 10 0.09
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (63 bp):
ATTCGAACCACATATGTAATAAAATTCATACATTAAATTCAGCTCAAGAACTTTGTAACCTAT
Found at i:2293023 original size:13 final size:13
Alignment explanation
Indices: 2292973--2293028 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 13
2292963 GTACATATAT
*
2292973 TTCCATATGACCAA
1 TTCCATATAACC-A
*
2292987 TTCC-TATAAACA
1 TTCCATATAACCA
* * *
2292999 TTTCACACAACCA
1 TTCCATATAACCA
2293012 TTCCATATAACCA
1 TTCCATATAACCA
2293025 TTCC
1 TTCC
2293029 GTCTGATACA
Statistics
Matches: 32, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
12 4 0.12
13 24 0.75
14 4 0.12
ACGTcount: A:0.36, C:0.32, G:0.02, T:0.30
Consensus pattern (13 bp):
TTCCATATAACCA
Found at i:2293220 original size:47 final size:47
Alignment explanation
Indices: 2293108--2293267 Score: 225
Period size: 46 Copynumber: 3.4 Consensus size: 47
2293098 TTATCTTCGA
* * * * *
2293108 CATGATGCCATAGTATCTTTCAACTATGGTTTTACTCGTTTT-CTGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCCTGT
* *
2293154 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCCTGT
*
2293201 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCCTGT
*
2293247 CAGGTTGCCATGGTATCTTTC
1 CATGTTGCCATGGTATCTTTC
2293268 GTTGCCATGG
Statistics
Matches: 102, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
46 62 0.61
47 40 0.39
ACGTcount: A:0.18, C:0.23, G:0.16, T:0.42
Consensus pattern (47 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCCTGT
Found at i:2293273 original size:18 final size:18
Alignment explanation
Indices: 2293250--2293285 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2293240 TTCATGTCAG
2293250 GTTGCCATGGTATCTTTC
1 GTTGCCATGGTATCTTTC
2293268 GTTGCCATGGTATCTTTC
1 GTTGCCATGGTATCTTTC
2293286 AACCATGGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.44
Consensus pattern (18 bp):
GTTGCCATGGTATCTTTC
Found at i:2293276 original size:64 final size:64
Alignment explanation
Indices: 2293204--2293331 Score: 229
Period size: 64 Copynumber: 2.0 Consensus size: 64
2293194 TTCCCGTCAT
* *
2293204 GTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGTTGCCATGGTATCTTTC
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATGGTATCTTTC
*
2293268 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATGGTATCTTTC
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATGGTATCTTTC
2293332 AACCATGGTC
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.18, C:0.23, G:0.17, T:0.41
Consensus pattern (64 bp):
GTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATGGTATCTTTC
Found at i:2293319 original size:46 final size:46
Alignment explanation
Indices: 2293267--2293450 Score: 325
Period size: 46 Copynumber: 4.0 Consensus size: 46
2293257 TGGTATCTTT
**
2293267 CGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCA
1 CGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA
2293313 CGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA
1 CGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA
2293359 CGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAA
1 CGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATC-A
*
2293406 C-TTGCCATGGTATCTTTCAACCATGGTCTTACACATTCCATATCA
1 CGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA
2293451 GAGAGCACAT
Statistics
Matches: 134, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
45 1 0.01
46 131 0.98
47 2 0.01
ACGTcount: A:0.24, C:0.26, G:0.12, T:0.38
Consensus pattern (46 bp):
CGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA
Found at i:2293352 original size:110 final size:111
Alignment explanation
Indices: 2293157--2293377 Score: 372
Period size: 110 Copynumber: 2.0 Consensus size: 111
2293147 TTTCTGTCAT
* * *
2293157 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTTCCCGTCATGTTGCCATGGTATCTTTC
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTTCACATCACGTTGCCATGGTATCTTTC
* * *
2293222 AACCATGGTCTTACTCATTTCATGTCAGGTTGCCATGGTATCTTTC
66 AACCATGGTCTTACACATTTCATATCACGTTGCCATGGTATCTTTC
*
2293268 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTTCATATCACGTTGCCATGGTATCTTTC
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTTCACATCACGTTGCCATGGTATCTTTC
2293332 AACCATGGTCTTACACATTTCATATCACGTTGCCATGGTATCTTTC
66 AACCATGGTCTTACACATTTCATATCACGTTGCCATGGTATCTTTC
2293378 AACCATGGTC
Statistics
Matches: 103, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
110 68 0.66
111 35 0.34
ACGTcount: A:0.19, C:0.24, G:0.16, T:0.41
Consensus pattern (111 bp):
GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTTCACATCACGTTGCCATGGTATCTTTC
AACCATGGTCTTACACATTTCATATCACGTTGCCATGGTATCTTTC
Found at i:2297493 original size:11 final size:11
Alignment explanation
Indices: 2297459--2297500 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
2297449 ATGAGCACAA
2297459 TATTTTATTTAT
1 TATTTTA-TTAT
* *
2297471 TA-TCTCTTAT
1 TATTTTATTAT
2297481 TATTTTATTAT
1 TATTTTATTAT
2297492 TATTTTATT
1 TATTTTATT
2297501 CCGAATTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
10 6 0.24
11 17 0.68
12 2 0.08
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (11 bp):
TATTTTATTAT
Found at i:2297768 original size:26 final size:27
Alignment explanation
Indices: 2297718--2297768 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
2297708 AGTTAATAAA
*
2297718 TTCTCTTTGAGTTTTTTTTTCAAGAAT
1 TTCTCTTTGAGTTTTTTTTACAAGAAT
*
2297745 TTCTC-TTGAGTTTTTTTTAGAAGA
1 TTCTCTTTGAGTTTTTTTTACAAGA
2297769 GTTTTAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.20, C:0.10, G:0.14, T:0.57
Consensus pattern (27 bp):
TTCTCTTTGAGTTTTTTTTACAAGAAT
Found at i:2297934 original size:11 final size:12
Alignment explanation
Indices: 2297918--2297946 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
2297908 CGCCACGTTC
2297918 TATCTTTCCA-T
1 TATCTTTCCATT
2297929 TATCTTTCCATT
1 TATCTTTCCATT
2297941 TATCTT
1 TATCTT
2297947 CTTTATTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.17, C:0.24, G:0.00, T:0.59
Consensus pattern (12 bp):
TATCTTTCCATT
Found at i:2303800 original size:26 final size:27
Alignment explanation
Indices: 2303750--2303800 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
2303740 AGTTAATAAA
*
2303750 TTCTCTTTGAGTTTTTTTTTCAAGAAT
1 TTCTCTTTGAGTTTTTTTTACAAGAAT
*
2303777 TTCTC-TTGAGTTTTTTTTAGAAGA
1 TTCTCTTTGAGTTTTTTTTACAAGA
2303801 GTTTTAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.20, C:0.10, G:0.14, T:0.57
Consensus pattern (27 bp):
TTCTCTTTGAGTTTTTTTTACAAGAAT
Found at i:2303965 original size:11 final size:12
Alignment explanation
Indices: 2303949--2303977 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
2303939 TGCCACGTTC
2303949 TATCTTTCCA-T
1 TATCTTTCCATT
2303960 TATCTTTCCATT
1 TATCTTTCCATT
2303972 TATCTT
1 TATCTT
2303978 CTTTATTCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.17, C:0.24, G:0.00, T:0.59
Consensus pattern (12 bp):
TATCTTTCCATT
Found at i:2306865 original size:16 final size:17
Alignment explanation
Indices: 2306844--2306875 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2306834 CTCTAATTCT
2306844 AAAAATTTTT-AAAAAG
1 AAAAATTTTTCAAAAAG
2306860 AAAAATTTTTCAAAAA
1 AAAAATTTTTCAAAAA
2306876 TTATTTTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (17 bp):
AAAAATTTTTCAAAAAG
Found at i:2308624 original size:11 final size:11
Alignment explanation
Indices: 2308608--2308632 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2308598 GAAAATACAT
2308608 TAATTATAAAA
1 TAATTATAAAA
2308619 TAATTATAAAA
1 TAATTATAAAA
2308630 TAA
1 TAA
2308633 AATTGTTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
TAATTATAAAA
Found at i:2311776 original size:79 final size:79
Alignment explanation
Indices: 2311681--2311837 Score: 280
Period size: 79 Copynumber: 2.0 Consensus size: 79
2311671 GGTTTCCTAG
*
2311681 TTGGAAAATTTTAATATTGCAATGTTTTTAATATTATCCTCATAAAT-TTTCATATTTAATATTT
1 TTGGAAAATATTAATATTGCAATGTTTTTAATATTATCCTCATAAATATTT-ATATTTAATATTT
*
2311745 ACGGATTTGATTTAA
65 ACGGACTTGATTTAA
2311760 TTGGAAAATATTAATATTGCAATGTTTTTAATATTATCCTCATAAATATTTATATTTAATATTTA
1 TTGGAAAATATTAATATTGCAATGTTTTTAATATTATCCTCATAAATATTTATATTTAATATTTA
2311825 CGGACTTGATTTA
66 CGGACTTGATTTA
2311838 CAAAAATGGG
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
79 72 0.96
80 3 0.04
ACGTcount: A:0.35, C:0.08, G:0.09, T:0.48
Consensus pattern (79 bp):
TTGGAAAATATTAATATTGCAATGTTTTTAATATTATCCTCATAAATATTTATATTTAATATTTA
CGGACTTGATTTAA
Found at i:2319618 original size:18 final size:18
Alignment explanation
Indices: 2319591--2319683 Score: 132
Period size: 18 Copynumber: 5.2 Consensus size: 18
2319581 TACGACCGTT
2319591 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
* *
2319609 TACGGCACTATTCACATA
1 TACGGTACTATTCACGTA
* *
2319627 TACAGTACTATTTACGTA
1 TACGGTACTATTCACGTA
*
2319645 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
2319663 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
2319681 TAC
1 TAC
2319684 AGTAGTTGGG
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 64 1.00
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:2324382 original size:28 final size:28
Alignment explanation
Indices: 2324318--2324383 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
2324308 TATTTTTATG
*
2324318 ATTTTAAAAATTATTTTAATATGTAATT
1 ATTTTAAAATTTATTTTAATATGTAATT
**
2324346 ATTCGAAAATTTATAATTT-ATATG-AATT
1 ATTTTAAAATTTAT--TTTAATATGTAATT
2324374 ATTTTAAAAT
1 ATTTTAAAAT
2324384 GATAGCAATC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
28 23 0.74
29 5 0.16
30 3 0.10
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (28 bp):
ATTTTAAAATTTATTTTAATATGTAATT
Found at i:2328680 original size:21 final size:22
Alignment explanation
Indices: 2328651--2328692 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
2328641 CGTGCATCTA
* *
2328651 GATTGTTTTAAT-TCATATAAG
1 GATTATTTTAATCTAATATAAG
2328672 GATTATTTTAATCTAATATAA
1 GATTATTTTAATCTAATATAA
2328693 CAATTTTCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.48
Consensus pattern (22 bp):
GATTATTTTAATCTAATATAAG
Found at i:2330767 original size:24 final size:24
Alignment explanation
Indices: 2330740--2330793 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
2330730 TTTTTTATTA
*
2330740 ATAAAAAAT-ATAA-AAGGATATACT
1 ATAAAAAATCATAAGAA-AATATA-T
*
2330764 ATAAATAATCATAAGAAAATATAT
1 ATAAAAAATCATAAGAAAATATAT
2330788 ATAAAA
1 ATAAAA
2330794 CCATTTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 14 0.56
25 9 0.36
26 2 0.08
ACGTcount: A:0.65, C:0.04, G:0.06, T:0.26
Consensus pattern (24 bp):
ATAAAAAATCATAAGAAAATATAT
Found at i:2331055 original size:20 final size:20
Alignment explanation
Indices: 2331030--2331079 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
2331020 TGGCTTAAAA
2331030 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
2331050 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
2331067 GTGGTAGTGGATT
1 TTGGTAGTGGATT
2331080 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:2335692 original size:20 final size:20
Alignment explanation
Indices: 2335667--2335716 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
2335657 TGGCTTAAAA
2335667 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
2335687 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
2335704 GTGGTAGTGGATT
1 TTGGTAGTGGATT
2335717 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:2339397 original size:3 final size:3
Alignment explanation
Indices: 2339389--2339435 Score: 76
Period size: 3 Copynumber: 15.3 Consensus size: 3
2339379 AATATATCAA
*
2339389 ATT ATT ATT ATT ATT ATT ACT ATTT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT
2339435 A
1 A
2339436 ACAACTAACT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 39 0.95
4 2 0.05
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:2340012 original size:16 final size:16
Alignment explanation
Indices: 2339988--2340021 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2339978 TTAATTTCTT
* *
2339988 TTGTTTAATTTATTTA
1 TTGTATAATTAATTTA
2340004 TTGTATAATTAATTTA
1 TTGTATAATTAATTTA
2340020 TT
1 TT
2340022 TATTGAACTT
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:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (16 bp):
TTGTATAATTAATTTA
Found at i:2340428 original size:40 final size:40
Alignment explanation
Indices: 2340381--2340460 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
2340371 CAATATTTAG
2340381 TTTAACAAAAAATTTAATAATTAAATAATTAAATTTAAAA
1 TTTAACAAAAAATTTAATAATTAAATAATTAAATTTAAAA
*
2340421 TTTAACAAAAATTTTAATAATTAAATAATTAAATTTAAAA
1 TTTAACAAAAAATTTAATAATTAAATAATTAAATTTAAAA
2340461 ATTATGAAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.39
Consensus pattern (40 bp):
TTTAACAAAAAATTTAATAATTAAATAATTAAATTTAAAA
Found at i:2341558 original size:18 final size:18
Alignment explanation
Indices: 2341513--2341587 Score: 71
Period size: 18 Copynumber: 4.2 Consensus size: 18
2341503 TACGACTATT
*
2341513 TACGGTACTATTTACGTA
1 TACGATACTATTTACGTA
* **
2341531 TATGGCACTATTTACGTA
1 TACGATACTATTTACGTA
*
2341549 TACGATACTATTTATGTA
1 TACGATACTATTTACGTA
* *
2341567 TAC-AGTACTGTTCACGTA
1 TACGA-TACTATTTACGTA
2341585 TAC
1 TAC
2341588 AGTAGTTGGG
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
17 1 0.02
18 46 0.98
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (18 bp):
TACGATACTATTTACGTA
Found at i:2347720 original size:102 final size:100
Alignment explanation
Indices: 2347520--2347722 Score: 307
Period size: 102 Copynumber: 2.0 Consensus size: 100
2347510 CTTTACAAAT
* * * *
2347520 TGTAAGATTACAAAATTGATATATTAATAAAATTTGTTTTAACTCTGAAATTTATTACTTTCAAG
1 TGTAAGATTAAAAAATTAATATATTAATAAAATTTGTTTTAACTCTCAAATTTATCACTTTCAAG
2347585 AAAATTTTGACTCTCACTTCTACCAATACCCAATC
66 AAAATTTTGACTCTCACTTCTACCAATACCCAATC
* * *
2347620 TGTAAGATTAAAAAATTAATATATTAATAAAATTATGTTTTAGCTCTCAAATTTATCGCTTTGAA
1 TGTAAGATTAAAAAATTAATATATTAATAAAATT-TGTTTTAACTCTCAAATTTATCACTTTCAA
* *
2347685 GAAAAATTTTGACTTTCACTTCTTCCAATACCCAATC
65 G-AAAATTTTGACTCTCACTTCTACCAATACCCAATC
2347722 T
1 T
2347723 TTAGAGCGGG
Statistics
Matches: 92, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
100 32 0.35
101 26 0.28
102 34 0.37
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.39
Consensus pattern (100 bp):
TGTAAGATTAAAAAATTAATATATTAATAAAATTTGTTTTAACTCTCAAATTTATCACTTTCAAG
AAAATTTTGACTCTCACTTCTACCAATACCCAATC
Found at i:2349657 original size:11 final size:12
Alignment explanation
Indices: 2349643--2349675 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
2349633 ATTGACATAA
2349643 AATAAAGAAA-T
1 AATAAAGAAATT
2349654 AATAAAGAAATT
1 AATAAAGAAATT
*
2349666 AAAAAAGAAA
1 AATAAAGAAA
2349676 AAACACCCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (12 bp):
AATAAAGAAATT
Found at i:2357042 original size:31 final size:31
Alignment explanation
Indices: 2357007--2357069 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
2356997 GTAATTGCAT
2357007 GAATTAATTATCGGGTTAAATCTAAATGTAG
1 GAATTAATTATCGGGTTAAATCTAAATGTAG
2357038 GAATTAATTATCGGGTTAAATCTAAATGTAG
1 GAATTAATTATCGGGTTAAATCTAAATGTAG
2357069 G
1 G
2357070 TGTTCATGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35
Consensus pattern (31 bp):
GAATTAATTATCGGGTTAAATCTAAATGTAG
Found at i:2358699 original size:15 final size:15
Alignment explanation
Indices: 2358672--2358705 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2358662 TTTTCGTATC
*
2358672 TTTA-CATACTTTAA
1 TTTATCATAATTTAA
2358686 TTTATCATAATTTAA
1 TTTATCATAATTTAA
2358701 TTTAT
1 TTTAT
2358706 ATTTTACAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTATCATAATTTAA
Found at i:2362422 original size:7 final size:7
Alignment explanation
Indices: 2362412--2362437 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2362402 TCTTTTTACT
2362412 TTTTAAA
1 TTTTAAA
2362419 TTTTAAA
1 TTTTAAA
2362426 TTTTAAA
1 TTTTAAA
2362433 TTTTA
1 TTTTA
2362438 GTCATCACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
TTTTAAA
Found at i:2364295 original size:38 final size:38
Alignment explanation
Indices: 2364200--2364312 Score: 163
Period size: 38 Copynumber: 2.9 Consensus size: 38
2364190 AAATAAAATA
* *
2364200 TGGTTTTAATTAATAATAAAACAAAATAGTATGAGGAAG
1 TGGTTTTAATTAATAATAAAACAAAATAGCATG-GGGAG
* *
2364239 TAGTTTTAATTAACAATAAAACAAAATAGCATGGGGAG
1 TGGTTTTAATTAATAATAAAACAAAATAGCATGGGGAG
* *
2364277 TGGTTTTGATTAATAATAAAACAAAGTAGCATGGGG
1 TGGTTTTAATTAATAATAAAACAAAATAGCATGGGG
2364313 GGAGTGGAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
38 36 0.55
39 30 0.45
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.29
Consensus pattern (38 bp):
TGGTTTTAATTAATAATAAAACAAAATAGCATGGGGAG
Found at i:2365417 original size:17 final size:18
Alignment explanation
Indices: 2365380--2365424 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
2365370 ATTTCCTAGC
**
2365380 TTATTCGTTATTATTTTT
1 TTATTCGTTATTATTCAT
2365398 TTATTCGTT-TTATTCAT
1 TTATTCGTTATTATTCAT
*
2365415 TTATTTGTTA
1 TTATTCGTTA
2365425 CCTCGAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.18, C:0.07, G:0.07, T:0.69
Consensus pattern (18 bp):
TTATTCGTTATTATTCAT
Found at i:2376311 original size:24 final size:24
Alignment explanation
Indices: 2376279--2376326 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2376269 GAAGCATCAT
2376279 AAGCACTAAGGCAATAGGTTGACA
1 AAGCACTAAGGCAATAGGTTGACA
2376303 AAGCACTAAGGCAATAGGTTGACA
1 AAGCACTAAGGCAATAGGTTGACA
2376327 GATATCAGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.17, G:0.25, T:0.17
Consensus pattern (24 bp):
AAGCACTAAGGCAATAGGTTGACA
Found at i:2377826 original size:21 final size:20
Alignment explanation
Indices: 2377787--2377826 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2377777 CACTAAATTA
*
2377787 TTAATAAATTTACATTTTAT
1 TTAATAAATTTAAATTTTAT
*
2377807 TTAATTAATTTAAAATTTTA
1 TTAATAAATTT-AAATTTTA
2377827 AAATTAATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
TTAATAAATTTAAATTTTAT
Found at i:2383967 original size:16 final size:18
Alignment explanation
Indices: 2383934--2383973 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
2383924 ATCATTCAAC
2383934 TATTTAAAAAATATAATT
1 TATTTAAAAAATATAATT
*
2383952 T-TTTAAATAA-ATAATT
1 TATTTAAAAAATATAATT
2383968 TATTTA
1 TATTTA
2383974 TATATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 7 0.35
17 12 0.60
18 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATTTAAAAAATATAATT
Found at i:2384000 original size:27 final size:29
Alignment explanation
Indices: 2383944--2384001 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 29
2383934 TATTTAAAAA
*
2383944 ATATAATTTTTTAAATAAATAATTTATTT
1 ATATAATTTTTTAAATAAATAATTCATTT
*
2383973 ATAT-ATTTTTT-AATAACAT-ATTCGTTT
1 ATATAATTTTTTAAATAA-ATAATTCATTT
2384000 AT
1 AT
2384002 TCTAATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 13 0.50
28 9 0.35
29 4 0.15
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (29 bp):
ATATAATTTTTTAAATAAATAATTCATTT
Found at i:2390042 original size:17 final size:17
Alignment explanation
Indices: 2390020--2390053 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2390010 TTTGTTGCTC
2390020 AGATTTATGATAACAAG
1 AGATTTATGATAACAAG
* *
2390037 AGATTTCTGATACCAAG
1 AGATTTATGATAACAAG
2390054 GTCCTAGCAG
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:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (17 bp):
AGATTTATGATAACAAG
Found at i:2392181 original size:18 final size:20
Alignment explanation
Indices: 2392160--2392211 Score: 72
Period size: 18 Copynumber: 2.6 Consensus size: 20
2392150 AAAGAGGCTT
*
2392160 AAAAGAAATGAAAAATAAA-
1 AAAAGAAATGAAAAAGAAAG
2392179 AAAA-AAATGAAAAAGAAAG
1 AAAAGAAATGAAAAAGAAAG
2392198 AAAAGAAAGTGAAA
1 AAAAGAAA-TGAAA
2392212 GTGGGAGAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 13 0.45
19 8 0.28
20 3 0.10
21 5 0.17
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (20 bp):
AAAAGAAATGAAAAAGAAAG
Found at i:2393149 original size:22 final size:21
Alignment explanation
Indices: 2393088--2393160 Score: 64
Period size: 22 Copynumber: 3.6 Consensus size: 21
2393078 CCTTTCAACG
* *
2393088 AAAATGTAAAAGATA-TTCAAA
1 AAAATTTAAAA-ATATTTTAAA
2393109 AAAATTT--AAA-ATTTTAAA
1 AAAATTTAAAAATATTTTAAA
* *
2393127 ATAATTTGAAAATATTTATAAA
1 AAAATTTAAAAATATTT-TAAA
2393149 AAAATTTAAAAA
1 AAAATTTAAAAA
2393161 AATTCATATA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
17 1 0.02
18 12 0.29
19 2 0.05
20 3 0.07
21 10 0.24
22 14 0.33
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (21 bp):
AAAATTTAAAAATATTTTAAA
Found at i:2393158 original size:10 final size:10
Alignment explanation
Indices: 2393106--2393164 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
2393096 AAAGATATTC
2393106 AAAAAAATTT
1 AAAAAAATTT
*
2393116 --AAAATTTT
1 AAAAAAATTT
*
2393124 AAAATAATTT
1 AAAAAAATTT
* *
2393134 GAAAATATTTAT
1 -AAAAAAATT-T
2393146 AAAAAAATTT
1 AAAAAAATTT
2393156 AAAAAAATT
1 AAAAAAATT
2393165 CATATATTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
8 7 0.18
10 16 0.41
11 15 0.38
12 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.36
Consensus pattern (10 bp):
AAAAAAATTT
Found at i:2396350 original size:18 final size:18
Alignment explanation
Indices: 2396322--2396368 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
2396312 ATGGATATTC
*
2396322 ATATAACTTTTAAATATA
1 ATATAATTTTTAAATATA
*
2396340 ATATAATTTTT-TATATA
1 ATATAATTTTTAAATATA
*
2396357 A-ATTATTTTTAA
1 ATATAATTTTTAA
2396369 TTCTGTCATG
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 8 0.33
17 6 0.25
18 10 0.42
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATAATTTTTAAATATA
Found at i:2401769 original size:21 final size:23
Alignment explanation
Indices: 2401729--2401770 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
2401719 TTTATAACAT
2401729 ATTAATATTATTCTTAATATAAG
1 ATTAATATTATTCTTAATATAAG
*
2401752 ATTAAT-TTA-TCTTTATATA
1 ATTAATATTATTCTTAATATA
2401771 TTACATACAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 3 0.17
23 6 0.33
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.52
Consensus pattern (23 bp):
ATTAATATTATTCTTAATATAAG
Found at i:2402506 original size:18 final size:18
Alignment explanation
Indices: 2402485--2402530 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
2402475 TTAAAAATCA
2402485 TTATAAAA-TTTTATAATT
1 TTATAAAATTTTTAT-ATT
2402503 TTATAAAATTTTTATATT
1 TTATAAAATTTTTATATT
*
2402521 TTAAAAAATT
1 TTATAAAATT
2402531 AATTAAATGC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 20 0.77
19 6 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTATAAAATTTTTATATT
Found at i:2406625 original size:3 final size:3
Alignment explanation
Indices: 2406617--2406651 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2406607 TACTATGGCT
2406617 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2406652 CGGGTTGGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2409529 original size:6 final size:6
Alignment explanation
Indices: 2409518--2409552 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
2409508 TAAATTGATT
2409518 TAAATA TAAATA TAAATA TAAATA TAAATA TAAAT
1 TAAATA TAAATA TAAATA TAAATA TAAATA TAAAT
2409553 TTTTATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
TAAATA
Found at i:2409995 original size:30 final size:29
Alignment explanation
Indices: 2409959--2410019 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
2409949 CCTTATCTTT
*
2409959 AAAGTTAAATTTGACTCTCAACCTTTCAAA
1 AAAGTTAAATTTGA-TCACAACCTTTCAAA
* *
2409989 AAAGTTAAATTTGATCACGAGCTTTCAAA
1 AAAGTTAAATTTGATCACAACCTTTCAAA
2410018 AA
1 AA
2410020 GAGACAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 14 0.50
30 14 0.50
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (29 bp):
AAAGTTAAATTTGATCACAACCTTTCAAA
Found at i:2414587 original size:22 final size:23
Alignment explanation
Indices: 2414562--2414614 Score: 90
Period size: 22 Copynumber: 2.3 Consensus size: 23
2414552 TTGTGTTATC
2414562 AAAATTTGACGAAAGGAGAA-AA
1 AAAATTTGACGAAAGGAGAACAA
*
2414584 AAAATTTGACGAAAGGAGAACCA
1 AAAATTTGACGAAAGGAGAACAA
2414607 AAAATTTG
1 AAAATTTG
2414615 GTCTGCAAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 20 0.69
23 9 0.31
ACGTcount: A:0.55, C:0.08, G:0.21, T:0.17
Consensus pattern (23 bp):
AAAATTTGACGAAAGGAGAACAA
Found at i:2431419 original size:18 final size:18
Alignment explanation
Indices: 2431396--2431433 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
2431386 ACACACATAC
*
2431396 ATGTATGTTTATATATAT
1 ATGTATGTATATATATAT
2431414 ATGTATGTATATATATAT
1 ATGTATGTATATATATAT
2431432 AT
1 AT
2431434 ACTGACCTGA
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:0.37, C:0.00, G:0.11, T:0.53
Consensus pattern (18 bp):
ATGTATGTATATATATAT
Found at i:2435545 original size:28 final size:26
Alignment explanation
Indices: 2435514--2435577 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 26
2435504 GTAATTCAAA
2435514 AAAATTAT-AGAAACATAAAGAATTATTT
1 AAAATTATAAGAAACATAAAG--TT-TTT
*
2435542 AAAATTTATTAAGAATCATAAAGTTTTT
1 AAAA-TTA-TAAGAAACATAAAGTTTTT
2435570 AAAATTAT
1 AAAATTAT
2435578 TAAAATTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
26 1 0.03
27 3 0.09
28 11 0.34
29 5 0.16
30 1 0.03
31 11 0.34
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (26 bp):
AAAATTATAAGAAACATAAAGTTTTT
Found at i:2436965 original size:26 final size:27
Alignment explanation
Indices: 2436929--2436981 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
2436919 TGTCAGCTAG
* *
2436929 TGAAATTTTAA-TGTTCGAATGTATGC
1 TGAAATTTTAAGTGTCCGAATGCATGC
*
2436955 TGAATTTTTAAGTGTCCGAATGCATGC
1 TGAAATTTTAAGTGTCCGAATGCATGC
2436982 CAGAATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (27 bp):
TGAAATTTTAAGTGTCCGAATGCATGC
Found at i:2438315 original size:48 final size:48
Alignment explanation
Indices: 2438251--2438398 Score: 224
Period size: 48 Copynumber: 3.1 Consensus size: 48
2438241 TTGATGTACA
*
2438251 AGATATATATATGTGGTAAAGCCGAATGGCTAATGTAAAATATGTATG
1 AGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
* *
2438299 AGATATATATATGTGGTAAAGTCGAAAGGCTAATGTGAAATATGTATG
1 AGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
** ** *
2438347 AGCCATGCATATGTGGTAAAGCCAAATGGCTAATGTGAAATATGTATG
1 AGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
2438395 AGAT
1 AGAT
2438399 GTGTATATAT
Statistics
Matches: 88, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 88 1.00
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.30
Consensus pattern (48 bp):
AGATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
Found at i:2440803 original size:29 final size:32
Alignment explanation
Indices: 2440761--2440824 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 32
2440751 TAGAAAAGAT
*
2440761 AAAATTATACTTTAGCCCCT-AAAAATAATAA
1 AAAATTATACTTTAACCCCTAAAAAATAATAA
* *
2440792 AAAATTA-A-TTTAATCCCTAAAAAATTATAA
1 AAAATTATACTTTAACCCCTAAAAAATAATAA
2440822 AAA
1 AAA
2440825 TATAGACTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 8 0.28
30 14 0.48
31 7 0.24
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.30
Consensus pattern (32 bp):
AAAATTATACTTTAACCCCTAAAAAATAATAA
Found at i:2446999 original size:14 final size:14
Alignment explanation
Indices: 2446980--2447025 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
2446970 GAGTTATAGA
2446980 TTTAATTTTTATAT
1 TTTAATTTTTATAT
*
2446994 TTTAA-TTTGATATT
1 TTTAATTTTTATA-T
*
2447008 TTTAATTATTAT-T
1 TTTAATTTTTATAT
2447021 TTTAA
1 TTTAA
2447026 AATCTTAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
13 12 0.44
14 11 0.41
15 4 0.15
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (14 bp):
TTTAATTTTTATAT
Found at i:2449340 original size:11 final size:11
Alignment explanation
Indices: 2449324--2449348 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2449314 TTTTTATTCC
2449324 CACATATTACT
1 CACATATTACT
2449335 CACATATTACT
1 CACATATTACT
2449346 CAC
1 CAC
2449349 TAAAAATCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (11 bp):
CACATATTACT
Found at i:2452921 original size:19 final size:20
Alignment explanation
Indices: 2452877--2452922 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
2452867 TCTAAAATTT
*
2452877 TTAAAAAATTTTAAGAAGT-
1 TTAAAAAATATTAAGAAGTC
* *
2452896 GTAAAAAAAATTAAGAAGTC
1 TTAAAAAATATTAAGAAGTC
2452916 TTAAAAA
1 TTAAAAA
2452923 TAAATAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.59, C:0.02, G:0.11, T:0.28
Consensus pattern (20 bp):
TTAAAAAATATTAAGAAGTC
Found at i:2453797 original size:17 final size:17
Alignment explanation
Indices: 2453777--2453811 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2453767 TAGATTTATA
*
2453777 ATATTTTAATATTTTTT
1 ATATTTTAATAATTTTT
*
2453794 ATATTTTCATAATTTTT
1 ATATTTTAATAATTTTT
2453811 A
1 A
2453812 ATAATTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (17 bp):
ATATTTTAATAATTTTT
Found at i:2466433 original size:15 final size:16
Alignment explanation
Indices: 2466402--2466434 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2466392 GGACTAGTTC
*
2466402 AAAAGTGCTTTTAGAA
1 AAAAGTGCTGTTAGAA
2466418 AAAAGTGCTGTT-GAA
1 AAAAGTGCTGTTAGAA
2466433 AA
1 AA
2466435 GTTGTGCGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.45, C:0.06, G:0.21, T:0.27
Consensus pattern (16 bp):
AAAAGTGCTGTTAGAA
Found at i:2466751 original size:27 final size:29
Alignment explanation
Indices: 2466685--2466757 Score: 69
Period size: 31 Copynumber: 2.4 Consensus size: 29
2466675 ATTTTGAAAA
*
2466685 AAATTAAATATAAATAATAAATAAGATTTAT
1 AAATT-AATAT-AATAATAAATAAGATATAT
*
2466716 ACAATTTAATATAATAATATATAA-A-ATAT
1 A-AA-TTAATATAATAATAAATAAGATATAT
*
2466745 AAATTAATGTAAT
1 AAATTAATATAAT
2466758 TTTTATAAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
27 9 0.24
28 2 0.05
29 4 0.11
30 1 0.03
31 12 0.32
32 7 0.19
33 2 0.05
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (29 bp):
AAATTAATATAATAATAAATAAGATATAT
Found at i:2468240 original size:29 final size:29
Alignment explanation
Indices: 2468207--2468266 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
2468197 AAATATGACA
2468207 TGATACAAAATAACTTGAGAGAGGAAAAG
1 TGATACAAAATAACTTGAGAGAGGAAAAG
2468236 TGATACAAAATAACTTGAGAGAGGAAAAG
1 TGATACAAAATAACTTGAGAGAGGAAAAG
2468265 TG
1 TG
2468267 GAATAAAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.50, C:0.07, G:0.25, T:0.18
Consensus pattern (29 bp):
TGATACAAAATAACTTGAGAGAGGAAAAG
Found at i:2473109 original size:21 final size:21
Alignment explanation
Indices: 2473083--2473123 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2473073 ATCTGCTCAA
* *
2473083 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
2473104 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
2473124 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:2483676 original size:15 final size:15
Alignment explanation
Indices: 2483656--2483686 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2483646 AGAAACATAG
2483656 AGGCATTGAGATACC
1 AGGCATTGAGATACC
2483671 AGGCATTGAGATACC
1 AGGCATTGAGATACC
2483686 A
1 A
2483687 ATAATCCACG
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:0.35, C:0.19, G:0.26, T:0.19
Consensus pattern (15 bp):
AGGCATTGAGATACC
Found at i:2484602 original size:26 final size:26
Alignment explanation
Indices: 2484573--2484630 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
2484563 TGATACAAAT
*
2484573 TGATAATATGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
2484599 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
2484625 TGATAA
1 TGATAA
2484631 GAATTTCATG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.38
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Done.