Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 129 of 171
Found at i:40600224 original size:366 final size:366
Alignment explanation
Indices: 40599630--40600366 Score: 1456
Period size: 366 Copynumber: 2.0 Consensus size: 366
40599620 AGAAGAATGG
40599630 AATTACAATAGATATTATAAACAAATTATTTTATTTACAATCTATTTTAACTTTCATAGTAAGTT
1 AATTACAATAGATATTATAAACAAATTATTTTATTTACAATCTATTTTAACTTTCATAGTAAGTT
40599695 GTCATGATGGTTCAGTACTAGAGATGATTTTTTTTAAAATATTTTAATAATTATTTCTTAAAATT
66 GTCATGATGGTTCAGTACTAGAGATGATTTTTTTTAAAATATTTTAATAATTATTTCTTAAAATT
40599760 TTGCTATACATAATTTTTTTTTCACCTTGTGTATTTCAAGTATAAATTATTTATAGAATTACAAT
131 TTGCTATACATAATTTTTTTTTCACCTTGTGTATTTCAAGTATAAATTATTTATAGAATTACAAT
40599825 TTAAAATCTCAAATTACACAAACTTTTGATGTGTAACATGATAAAGTAGATTTTACTTTGATGCA
196 TTAAAATCTCAAATTACACAAACTTTTGATGTGTAACATGATAAAGTAGATTTTACTTTGATGCA
40599890 ATTATATATTTAATAAATAAATAATTATTTTAATTATTTTCACGTTTACGTTAAATAATTTTACT
261 ATTATATATTTAATAAATAAATAATTATTTTAATTATTTTCACGTTTACGTTAAATAATTTTACT
40599955 TTTTACCTTTTGGCAATTGGCATTTTAAAGACATACTTTCA
326 TTTTACCTTTTGGCAATTGGCATTTTAAAGACATACTTTCA
*
40599996 AATTATAATAGATATTATAAACAAATTATTTTATTTACAATCTATTTTAACTTTCATAGTAAGTT
1 AATTACAATAGATATTATAAACAAATTATTTTATTTACAATCTATTTTAACTTTCATAGTAAGTT
*
40600061 GTCATGATGGTTCAGTACTAGAGATGATTTTTTTTTAAATATTTTAATAATTATTTCTTAAAATT
66 GTCATGATGGTTCAGTACTAGAGATGATTTTTTTTAAAATATTTTAATAATTATTTCTTAAAATT
40600126 TTGCTATACATAATTTTTTTTTCACCTTGTGTATTTCAAGTATAAATTATTTATAGAATTACAAT
131 TTGCTATACATAATTTTTTTTTCACCTTGTGTATTTCAAGTATAAATTATTTATAGAATTACAAT
40600191 TTAAAATCTCAAATTACACAAACTTTTGATGTGTAACATGATAAAGTAGATTTTACTTTGATGCA
196 TTAAAATCTCAAATTACACAAACTTTTGATGTGTAACATGATAAAGTAGATTTTACTTTGATGCA
40600256 ATTATATATTTAATAAATAAATAATTATTTTAATTATTTTCACGTTTACGTTAAATAATTTTACT
261 ATTATATATTTAATAAATAAATAATTATTTTAATTATTTTCACGTTTACGTTAAATAATTTTACT
40600321 TTTTACCTTTTGGCAATTGGCATTTTAAAGACATACTTTCA
326 TTTTACCTTTTGGCAATTGGCATTTTAAAGACATACTTTCA
40600362 AATTA
1 AATTA
40600367 AAAGAAAGTT
Statistics
Matches: 369, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
366 369 1.00
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.46
Consensus pattern (366 bp):
AATTACAATAGATATTATAAACAAATTATTTTATTTACAATCTATTTTAACTTTCATAGTAAGTT
GTCATGATGGTTCAGTACTAGAGATGATTTTTTTTAAAATATTTTAATAATTATTTCTTAAAATT
TTGCTATACATAATTTTTTTTTCACCTTGTGTATTTCAAGTATAAATTATTTATAGAATTACAAT
TTAAAATCTCAAATTACACAAACTTTTGATGTGTAACATGATAAAGTAGATTTTACTTTGATGCA
ATTATATATTTAATAAATAAATAATTATTTTAATTATTTTCACGTTTACGTTAAATAATTTTACT
TTTTACCTTTTGGCAATTGGCATTTTAAAGACATACTTTCA
Found at i:40600846 original size:29 final size:30
Alignment explanation
Indices: 40600814--40600872 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
40600804 TTTAGTTTAA
*
40600814 TGTGTAATTTTATACATG-AACTTTGATTT
1 TGTGTAATTTTAAACATGAAACTTTGATTT
*
40600843 TGTGTAATTTTAAACATGAAATTTTGATTT
1 TGTGTAATTTTAAACATGAAACTTTGATTT
40600873 GACCTAGTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 17 0.63
30 10 0.37
ACGTcount: A:0.31, C:0.05, G:0.14, T:0.51
Consensus pattern (30 bp):
TGTGTAATTTTAAACATGAAACTTTGATTT
Found at i:40600987 original size:17 final size:16
Alignment explanation
Indices: 40600974--40601053 Score: 110
Period size: 17 Copynumber: 5.0 Consensus size: 16
40600964 AATTTTATAT
*
40600974 TTTATTTAGATTTAAA
1 TTTATTTAAATTTAAA
40600990 TTTATCTTAAATTTAAA
1 TTTAT-TTAAATTTAAA
40601007 TTTATTT--ATTTAAA
1 TTTATTTAAATTTAAA
40601021 TTTACTTTAAATTTAAA
1 TTTA-TTTAAATTTAAA
*
40601038 TTTAATTAAATTTAAA
1 TTTATTTAAATTTAAA
40601054 AATAATATTA
Statistics
Matches: 58, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
14 11 0.19
15 3 0.05
16 18 0.31
17 26 0.45
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (16 bp):
TTTATTTAAATTTAAA
Found at i:40600992 original size:6 final size:6
Alignment explanation
Indices: 40600950--40601053 Score: 69
Period size: 6 Copynumber: 18.0 Consensus size: 6
40600940 GACTTTGATT
* * * * *
40600950 TTTAAG TTTAAA -TTAAT TTTATA TTT-TA TTTAGA TTTAAA TTT--A
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
40600994 TCTTAAA TTTAAA TTTATTTA TTTAAA TTT-AC TTTAAA TTTAAA TTT-AA
1 T-TTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
40601043 -TTAAA TTTAAA
1 TTTAAA TTTAAA
40601054 AATAATATTA
Statistics
Matches: 78, Mismatches: 10, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
4 4 0.05
5 19 0.24
6 48 0.62
7 2 0.03
8 5 0.06
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:40601021 original size:31 final size:32
Alignment explanation
Indices: 40600974--40601053 Score: 110
Period size: 31 Copynumber: 2.5 Consensus size: 32
40600964 AATTTTATAT
40600974 TTTATTTAGATTTAAATTTA-TCTTAAATTTAAA
1 TTTATTTA-ATTTAAATTTACT-TTAAATTTAAA
40601007 TTTATTT-ATTTAAATTTACTTTAAATTTAAA
1 TTTATTTAATTTAAATTTACTTTAAATTTAAA
*
40601038 TTTAATTAAATTTAAA
1 TTT-ATTTAATTTAAA
40601054 AATAATATTA
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
31 25 0.58
32 4 0.09
33 14 0.33
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (32 bp):
TTTATTTAATTTAAATTTACTTTAAATTTAAA
Found at i:40601044 original size:11 final size:11
Alignment explanation
Indices: 40600950--40601053 Score: 67
Period size: 11 Copynumber: 9.5 Consensus size: 11
40600940 GACTTTGATT
*
40600950 TTTAAGTTTAA
1 TTTAAATTTAA
* *
40600961 ATTAATTTTATA
1 TTTAAATTTA-A
*
40600973 TTT-TATTTAGA
1 TTTAAATTTA-A
40600984 TTTAAATTT-A
1 TTTAAATTTAA
40600994 TCTTAAATTTAAA
1 T-TTAAATTT-AA
40601007 TTT--ATTT-A
1 TTTAAATTTAA
*
40601015 TTTAAATTTAC
1 TTTAAATTTAA
40601026 TTTAAATTTAAA
1 TTTAAATTT-AA
*
40601038 TTT-AATTAAA
1 TTTAAATTTAA
40601048 TTTAAA
1 TTTAAA
40601054 AATAATATTA
Statistics
Matches: 73, Mismatches: 10, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
8 4 0.05
10 15 0.21
11 39 0.53
12 13 0.18
13 2 0.03
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:40601881 original size:22 final size:22
Alignment explanation
Indices: 40601841--40601891 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
40601831 AACGAAATGA
*
40601841 AAAAGAAAATATAAAAAAAAAC
1 AAAAGAAAAGATAAAAAAAAAC
* *
40601863 AAAAGAAAAGA-AAAGAAAAAG
1 AAAAGAAAAGATAAAAAAAAAC
*
40601884 GAAAGAAA
1 AAAAGAAA
40601892 GACCGCTCAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.04
Consensus pattern (22 bp):
AAAAGAAAAGATAAAAAAAAAC
Found at i:40601883 original size:11 final size:11
Alignment explanation
Indices: 40601841--40601891 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
40601831 AACGAAATGA
*
40601841 AAAAGAAAATAT
1 AAAAGAAAA-AG
*
40601853 AAAA-AAAAAC
1 AAAAGAAAAAG
40601863 AAAAG-AAAAG
1 AAAAGAAAAAG
40601873 AAAAGAAAAAG
1 AAAAGAAAAAG
*
40601884 GAAAGAAA
1 AAAAGAAA
40601892 GACCGCTCAC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
10 14 0.41
11 16 0.47
12 4 0.12
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.04
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:40602613 original size:30 final size:30
Alignment explanation
Indices: 40602577--40602871 Score: 291
Period size: 30 Copynumber: 9.9 Consensus size: 30
40602567 TAAATTGTCC
40602577 AAAAATTACATTTTGACCCCAAAACTTTCT
1 AAAAATTACATTTTGACCCCAAAACTTTCT
40602607 AAAAATTACATTTTGACCCCAAAACTTTTCT
1 AAAAATTACATTTTGACCCCAAAAC-TTTCT
* *
40602638 -AAAATTATATTTTGACCCTAAAACTTTCT
1 AAAAATTACATTTTGACCCCAAAACTTTCT
40602667 AAAAATTACATTTTGACCCCAAAACTTT-T
1 AAAAATTACATTTTGACCCCAAAACTTTCT
* * * *
40602696 CCAAAATTATATTTTGACCCCTAAACTTTTT
1 -AAAAATTACATTTTGACCCCAAAACTTTCT
* *
40602727 GAAAATTACATTTTGACCCCTAAACTTT-T
1 AAAAATTACATTTTGACCCCAAAACTTTCT
* *
40602756 CCAAAATTATATTTTGACCCCAAAACTTT-T
1 -AAAAATTACATTTTGACCCCAAAACTTTCT
* * * * * *
40602786 CCAAAATCATATTTT-AACCCTAAA-TTTCCA
1 -AAAAATTACATTTTGACCCCAAAACTTT-CT
* * * *
40602816 AAAAAATGCATTTTTACCCCGAAACTTTC-
1 AAAAATTACATTTTGACCCCAAAACTTTCT
*
40602845 AAAAATTACCATTTT-ACCCCTAAACTT
1 AAAAATTA-CATTTTGACCCCAAAACTT
40602872 CCCTAAATCC
Statistics
Matches: 229, Mismatches: 26, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
28 3 0.01
29 40 0.17
30 177 0.77
31 9 0.04
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.36
Consensus pattern (30 bp):
AAAAATTACATTTTGACCCCAAAACTTTCT
Found at i:40602671 original size:60 final size:60
Alignment explanation
Indices: 40602578--40602871 Score: 357
Period size: 60 Copynumber: 4.9 Consensus size: 60
40602568 AAATTGTCCA
* *
40602578 AAAATTACATTTTGACCCCAAAACTTTCTAAAAATTACATTTTGACCCCAAAACTTTTCT
1 AAAATTATATTTTGACCCCAAAACTTTCTAAAAATTACATTTTGACCCCAAAACTTTTCC
*
40602638 AAAATTATATTTTGACCCTAAAACTTTCTAAAAATTACATTTTGACCCCAAAACTTTTCC
1 AAAATTATATTTTGACCCCAAAACTTTCTAAAAATTACATTTTGACCCCAAAACTTTTCC
* * * *
40602698 AAAATTATATTTTGACCCCTAAACTTTTTGAAAATTACATTTTGACCCCTAAACTTTTCC
1 AAAATTATATTTTGACCCCAAAACTTTCTAAAAATTACATTTTGACCCCAAAACTTTTCC
* * * * *
40602758 AAAATTATATTTTGACCCCAAAACTTT-TCCAAAATCATATTTT-AACCCTAAA--TTTCC
1 AAAATTATATTTTGACCCCAAAACTTTCT-AAAAATTACATTTTGACCCCAAAACTTTTCC
** * * *
40602815 AAAAAAATGCATTTTTACCCCGAAACTTTC-AAAAATTACCATTTT-ACCCCTAAACTT
1 AAAATTAT--ATTTTGACCCCAAAACTTTCTAAAAATTA-CATTTTGACCCCAAAACTT
40602872 CCCTAAATCC
Statistics
Matches: 206, Mismatches: 21, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
57 11 0.05
58 6 0.03
59 39 0.19
60 149 0.72
61 1 0.00
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.36
Consensus pattern (60 bp):
AAAATTATATTTTGACCCCAAAACTTTCTAAAAATTACATTTTGACCCCAAAACTTTTCC
Found at i:40602732 original size:90 final size:90
Alignment explanation
Indices: 40602576--40602871 Score: 347
Period size: 90 Copynumber: 3.3 Consensus size: 90
40602566 CTAAATTGTC
* * *
40602576 CAAAAATTACATTTTGACCCCAAAAC-TTTCTAAAAATTACATTTTGACCCCAAAACTTTTCTAA
1 CAAAAATTACATTTTGACCCCAAAACTTTTC-CAAAATTATATTTTGACCCCTAAACTTTTCTAA
*
40602640 AATTATATTTTGA-CCCTAAAAC-TTT
65 AATTACATTTTGACCCCT-AAACTTTT
40602665 CTAAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTATATTTTGACCCCTAAACTTTT-TGA
1 C-AAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTATATTTTGACCCCTAAACTTTTCT-A
40602729 AAATTACATTTTGACCCCTAAACTTTT
64 AAATTACATTTTGACCCCTAAACTTTT
* * * * * *
40602756 CCAAAATTATATTTTGACCCCAAAACTTTTCCAAAATCATATTTT-AACCCTAAA-TTTCCAAAA
1 CAAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTATATTTTGACCCCTAAACTTTTC-TAA
* * * *
40602819 AAATGCATTTTTACCCCGAAAC-TTT
65 AATTACATTTTGACCCCTAAACTTTT
*
40602844 CAAAAATTACCATTTT-ACCCCTAAACTT
1 CAAAAATTA-CATTTTGACCCCAAAACTT
40602872 CCCTAAATCC
Statistics
Matches: 182, Mismatches: 17, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
88 25 0.14
89 35 0.19
90 110 0.60
91 12 0.07
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.36
Consensus pattern (90 bp):
CAAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTATATTTTGACCCCTAAACTTTTCTAAA
ATTACATTTTGACCCCTAAACTTTT
Found at i:40602879 original size:29 final size:28
Alignment explanation
Indices: 40602827--40602945 Score: 82
Period size: 29 Copynumber: 4.1 Consensus size: 28
40602817 AAAAATGCAT
* * **
40602827 TTTTACCCCGAAACTTTCAAAAATTACCA
1 TTTTACCCCTAAACTTCCCTAAA-TACCA
*
40602856 TTTTACCCCTAAACTTCCCTAAATCCCA
1 TTTTACCCCTAAACTTCCCTAAATACCA
* *
40602884 TTTTAAACCCC--AATTTCACTAAAATTACCA
1 TTTT--ACCCCTAAACTTCCCT-AAA-TACCA
* *
40602914 TTTTA-CCCTCAAACTTCCCCAAATCCCA
1 TTTTACCCCT-AAACTTCCCTAAATACCA
40602942 TTTT
1 TTTT
40602946 TAACCCCGAT
Statistics
Matches: 71, Mismatches: 12, Indels: 15
0.72 0.12 0.15
Matches are distributed among these distances:
27 3 0.04
28 24 0.34
29 25 0.35
30 19 0.27
ACGTcount: A:0.33, C:0.33, G:0.01, T:0.34
Consensus pattern (28 bp):
TTTTACCCCTAAACTTCCCTAAATACCA
Found at i:40602982 original size:59 final size:59
Alignment explanation
Indices: 40602846--40602982 Score: 206
Period size: 58 Copynumber: 2.3 Consensus size: 59
40602836 GAAACTTTCA
* *
40602846 AAAATTACCATTTTACCC-CTAAACTTCCCTAAATCCCATTTTAAACCCCAATTTCACT
1 AAAATTACCATTTTACCCTCTAAACTTCCCCAAATCCCATTTTAAACCCCAATTTCACC
* *
40602904 AAAATTACCATTTTACCCTC-AAACTTCCCCAAATCCCATTTTTAACCCCGATTTCACC
1 AAAATTACCATTTTACCCTCTAAACTTCCCCAAATCCCATTTTAAACCCCAATTTCACC
*
40602962 AAAATCTACCATTTTTCCCTC
1 AAAAT-TACCATTTTACCCTC
40602983 GGGTATCCAA
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
58 57 0.79
59 15 0.21
ACGTcount: A:0.32, C:0.34, G:0.01, T:0.33
Consensus pattern (59 bp):
AAAATTACCATTTTACCCTCTAAACTTCCCCAAATCCCATTTTAAACCCCAATTTCACC
Found at i:40605065 original size:15 final size:15
Alignment explanation
Indices: 40605009--40605059 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
40604999 TATTTCATAT
*
40605009 ATAAAAATCTATTAA
1 ATAAAATTCTATTAA
* *
40605024 CTATAATT-TATTAA
1 ATAAAATTCTATTAA
40605038 ATAAAATTCTATTAA
1 ATAAAATTCTATTAA
40605053 ATAAAAT
1 ATAAAAT
40605060 ATTATTTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 12 0.40
15 18 0.60
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (15 bp):
ATAAAATTCTATTAA
Found at i:40605981 original size:3 final size:3
Alignment explanation
Indices: 40605975--40606000 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
40605965 CCAAATTATT
40605975 ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
40606001 TATTATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:40606005 original size:3 final size:3
Alignment explanation
Indices: 40605999--40606045 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
40605989 CATCATCATC
40605999 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
40606046 CAGCTAGGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:40606630 original size:135 final size:136
Alignment explanation
Indices: 40606442--40606685 Score: 379
Period size: 136 Copynumber: 1.8 Consensus size: 136
40606432 AAAAATAAAC
*
40606442 TATGTTTTTTAATCATTTTAAAGGAAAAGGTTTAAAATTTTAAATAAAGTTTTGA-TTTTTTAAC
1 TATGTTTTTTAATCATTTTAAAGGAAAAGGTTTAAAATTTAAAATAAAGTTTTGATTTTTTTAAC
** * *
40606506 TATTTCGAAATAAAAGTTTTGATCTTTAAG-AAAGTAGTGATTTAAAAAAAAGAAATTAGATTTT
66 TATTTCGAAATAAAAACTTTGACCTTTAAGAAAAATAGTGATTTAAAAAAAAGAAATTAGATTTT
40606570 TAAAAA
131 TAAAAA
*
40606576 TATGTTTTTTAGTCATTTTATAAGGAAAA-GTTT-AAATTTAAAAAATAAAGTTTTGATTTTTTT
1 TATGTTTTTTAATCATTTTA-AAGGAAAAGGTTTAAAATTT--AAAATAAAGTTTTGATTTTTTT
40606639 AACTATTTCGAAATAAAAACTTTGACCTTTAAGAAAAATAGTGATTT
63 AACTATTTCGAAATAAAAACTTTGACCTTTAAGAAAAATAGTGATTT
40606686 TTTCTTTTAA
Statistics
Matches: 99, Mismatches: 6, Indels: 7
0.88 0.05 0.06
Matches are distributed among these distances:
133 6 0.06
134 23 0.23
135 22 0.22
136 36 0.36
137 12 0.12
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.43
Consensus pattern (136 bp):
TATGTTTTTTAATCATTTTAAAGGAAAAGGTTTAAAATTTAAAATAAAGTTTTGATTTTTTTAAC
TATTTCGAAATAAAAACTTTGACCTTTAAGAAAAATAGTGATTTAAAAAAAAGAAATTAGATTTT
TAAAAA
Found at i:40612703 original size:23 final size:23
Alignment explanation
Indices: 40612660--40612705 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
40612650 GGTCCTTGTA
*
40612660 TTTTTATTTTGTTTTAATTTAATC
1 TTTTTATTATGTTTT-ATTTAATC
40612684 TTTTATATTATGTTTT-TTTAAT
1 TTTT-TATTATGTTTTATTTAAT
40612706 GTGTACGTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 4 0.20
25 10 0.50
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.72
Consensus pattern (23 bp):
TTTTTATTATGTTTTATTTAATC
Found at i:40612969 original size:3 final size:3
Alignment explanation
Indices: 40612936--40613008 Score: 87
Period size: 3 Copynumber: 25.0 Consensus size: 3
40612926 TCCTTAAGTA
* * * *
40612936 ATT ATT -TT GTT ATT TTT ATT ATC ATG A-T ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
40612982 ATT ATT ATT ATT ATT ATT ATT GTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
40613009 GTTGTTGCTA
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
2 3 0.05
3 57 0.95
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:40613020 original size:18 final size:18
Alignment explanation
Indices: 40612999--40613033 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
40612989 TTATTATTAT
40612999 TATTGTTATTGTTGTTGC
1 TATTGTTATTGTTGTTGC
*
40613017 TATTGTTGTTGTTGTTG
1 TATTGTTATTGTTGTTG
40613034 TTGTATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.09, C:0.03, G:0.26, T:0.63
Consensus pattern (18 bp):
TATTGTTATTGTTGTTGC
Found at i:40620768 original size:94 final size:94
Alignment explanation
Indices: 40620656--40620828 Score: 217
Period size: 94 Copynumber: 1.8 Consensus size: 94
40620646 GGGCAAGATG
* * * * * *
40620656 AAGCTACATATCCTATATCCTTGAAGCTT-CAGTGGATCGGATTAAAACTACGATAGCAAGTACT
1 AAGCTACAAATCCTATATCCCTGAAG-TTACAATAGATCAGATTAAAACTACGATAGCAAAT-CT
40620720 -ATCTCCATGAAGATGTAGTGAGGCAGAATT
64 CATCTCCATGAAGATGTAGTGAGGCAGAATT
* *
40620750 AAGCTACAAAT-CTCATATCCCTGAAGTTACAATAGATCAGATTGAAACTACTATAGCAAATCTC
1 AAGCTACAAATCCT-ATATCCCTGAAGTTACAATAGATCAGATTAAAACTACGATAGCAAATCTC
*
40620814 ATCTCCTTGAAGATG
65 ATCTCCATGAAGATG
40620829 CAACGGAGCA
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
93 6 0.09
94 61 0.91
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.28
Consensus pattern (94 bp):
AAGCTACAAATCCTATATCCCTGAAGTTACAATAGATCAGATTAAAACTACGATAGCAAATCTCA
TCTCCATGAAGATGTAGTGAGGCAGAATT
Found at i:40620848 original size:94 final size:94
Alignment explanation
Indices: 40620642--40620849 Score: 212
Period size: 94 Copynumber: 2.2 Consensus size: 94
40620632 CTAAAGACGT
* * * * * *
40620642 AGTGGGGCAAGATGAAGCTACATATCCTATATCCTTGAAGCTTCAGTGGATCGGATTAAAACTAC
1 AGTGAGGCAAGATGAAGCTACAAATCCTATATCCCTGAAGCTTCAATAGATCAGATTAAAACTAC
* *
40620707 GATAGCAAGTACTATCTCCATGAAGATGT
66 GATAGCAAATACTATCTCCATGAAGATGA
* *
40620736 AGTGAGGC-AGAATTAAGCTACAAAT-CTCATATCCCTGAAG-TTACAATAGATCAGATTGAAAC
1 AGTGAGGCAAG-ATGAAGCTACAAATCCT-ATATCCCTGAAGCTT-CAATAGATCAGATTAAAAC
* *
40620798 TACTATAGCAAAT-CTCATCTCCTTGAAGATGCA
63 TACGATAGCAAATACT-ATCTCCATGAAGATG-A
40620831 ACG-GA-GCAAGATGAAGCTA
1 A-GTGAGGCAAGATGAAGCTA
40620850 TGATCCTGTC
Statistics
Matches: 94, Mismatches: 13, Indels: 14
0.78 0.11 0.12
Matches are distributed among these distances:
93 8 0.09
94 80 0.85
95 5 0.05
96 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (94 bp):
AGTGAGGCAAGATGAAGCTACAAATCCTATATCCCTGAAGCTTCAATAGATCAGATTAAAACTAC
GATAGCAAATACTATCTCCATGAAGATGA
Found at i:40622576 original size:29 final size:31
Alignment explanation
Indices: 40622531--40622605 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 31
40622521 GCCCCTTTAC
*
40622531 TTTTTTATTTTTGCAATT-TATACTTTA-TT
1 TTTTTTATTTTTGCAATTCAATACTTTACTT
*
40622560 TTTTTTATTTCTT-CAATTCAATTCTTTACTT
1 TTTTTTATTT-TTGCAATTCAATACTTTACTT
40622591 TATTTTTATTATTTG
1 T-TTTTTATT-TTTG
40622606 TTGTGTTGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
29 15 0.39
30 9 0.24
31 3 0.08
32 10 0.26
33 1 0.03
ACGTcount: A:0.20, C:0.09, G:0.03, T:0.68
Consensus pattern (31 bp):
TTTTTTATTTTTGCAATTCAATACTTTACTT
Found at i:40622806 original size:20 final size:21
Alignment explanation
Indices: 40622774--40622819 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
40622764 TATTATGTTG
*
40622774 TTATT-TTTATTATCA-TGATA
1 TTATTATTTATTATAATTG-TA
40622794 TTATTATTT-TTATAATTGTA
1 TTATTATTTATTATAATTGTA
40622814 TTATTA
1 TTATTA
40622820 CTTGTTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.63
Consensus pattern (21 bp):
TTATTATTTATTATAATTGTA
Found at i:40622830 original size:20 final size:20
Alignment explanation
Indices: 40622792--40622830 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
40622782 ATTATCATGA
*
40622792 TATTATTATTTTTATAATTG
1 TATTATTATTGTTATAATTG
40622812 TATTATTACTTGTTA-AATT
1 TATTATTA-TTGTTATAATT
40622831 ATTTTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.62
Consensus pattern (20 bp):
TATTATTATTGTTATAATTG
Found at i:40623293 original size:21 final size:22
Alignment explanation
Indices: 40623269--40623310 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
40623259 TGATAGATTA
40623269 TATG-CCAAATTAGA-TAAAATT
1 TATGTCCAAATTA-ATTAAAATT
40623290 TATGTCCAAATTAATTAAAAT
1 TATGTCCAAATTAATTAAAAT
40623311 AATTAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.36
Consensus pattern (22 bp):
TATGTCCAAATTAATTAAAATT
Found at i:40636102 original size:6 final size:6
Alignment explanation
Indices: 40636076--40636137 Score: 52
Period size: 6 Copynumber: 10.0 Consensus size: 6
40636066 TTTATTTCGA
* * * * * *
40636076 TTATTT ATATTT CTATCT TTATTT TTATTT TAAATTT TTATTT ATTAATA
1 TTATTT TTATTT TTATTT TTATTT TTATTT T-TATTT TTATTT -TTATTT
40636126 TTATTT TTATTT
1 TTATTT TTATTT
40636138 CTTTTTCAGA
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
6 34 0.79
7 9 0.21
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (6 bp):
TTATTT
Found at i:40637767 original size:23 final size:23
Alignment explanation
Indices: 40637741--40637790 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
40637731 TGACGTGGCA
*
40637741 TCCAGTCAATAGCTTCTAGAAGG
1 TCCAGTCAACAGCTTCTAGAAGG
*
40637764 TCCAGTCAGCAGCTTCTAGAAGG
1 TCCAGTCAACAGCTTCTAGAAGG
40637787 TCCA
1 TCCA
40637791 ATCAGCAAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (23 bp):
TCCAGTCAACAGCTTCTAGAAGG
Found at i:40637795 original size:23 final size:23
Alignment explanation
Indices: 40637751--40637797 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
40637741 TCCAGTCAAT
*
40637751 AGCTTCTAGAAGGTCCAGTCAGC
1 AGCTTCTAGAAGGTCCAATCAGC
40637774 AGCTTCTAGAAGGTCCAATCAGC
1 AGCTTCTAGAAGGTCCAATCAGC
40637797 A
1 A
40637798 AGGATGAACG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (23 bp):
AGCTTCTAGAAGGTCCAATCAGC
Found at i:40639007 original size:19 final size:20
Alignment explanation
Indices: 40638968--40639010 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
40638958 CTCAAAAAAA
40638968 TATAAAAAAATCAAAATATT
1 TATAAAAAAATCAAAATATT
*
40638988 TATAAAAAAATCCAAA-ATT
1 TATAAAAAAATCAAAATATT
40639007 TATA
1 TATA
40639011 TTTTAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (20 bp):
TATAAAAAAATCAAAATATT
Found at i:40639044 original size:18 final size:18
Alignment explanation
Indices: 40639001--40639041 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
40638991 AAAAAAATCC
*
40639001 AAAATTTATATTTTAAAA
1 AAAATTAATATTTTAAAA
40639019 AAATATTAATAGTTTTAAAA
1 AAA-ATTAATA-TTTTAAAA
40639039 AAA
1 AAA
40639042 TTATAAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 3 0.15
19 6 0.30
20 11 0.55
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
AAAATTAATATTTTAAAA
Found at i:40642930 original size:5 final size:5
Alignment explanation
Indices: 40642920--40642946 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
40642910 AAATTTACAA
40642920 AAAAT AAAAT AAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AA
40642947 TTGTTCTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:40644421 original size:37 final size:36
Alignment explanation
Indices: 40644359--40644508 Score: 128
Period size: 37 Copynumber: 4.1 Consensus size: 36
40644349 TTGATGCCTC
*
40644359 AAAAAGGTTGGG-TAGCACTTATCTAAGGCAACATTTA
1 AAAAAGGTTGGGATAG-ACTCATCTAAGGCAAC-TTTA
* * * *
40644396 AAAAAGGTTGGGATAGACTCGTCTAAAGAAACCTT-
1 AAAAAGGTTGGGATAGACTCATCTAAGGCAACTTTA
* * *
40644431 AAAAAGGTTGAGATAGAC-CTTGCCTAAGACAACCTTTA
1 AAAAAGGTTGGGATAGACTCAT--CTAAGGCAA-CTTTA
* *
40644469 AAAAAGGTTGGGATAAACCCATCTAAGGCAA-TCTTA
1 AAAAAGGTTGGGATAGACTCATCTAAGGCAACT-TTA
40644505 AAAA
1 AAAA
40644509 GATTAAAATA
Statistics
Matches: 91, Mismatches: 15, Indels: 15
0.75 0.12 0.12
Matches are distributed among these distances:
34 2 0.02
35 18 0.20
36 15 0.16
37 35 0.38
38 19 0.21
39 2 0.02
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.23
Consensus pattern (36 bp):
AAAAAGGTTGGGATAGACTCATCTAAGGCAACTTTA
Found at i:40644433 original size:36 final size:38
Alignment explanation
Indices: 40644381--40644483 Score: 124
Period size: 35 Copynumber: 2.8 Consensus size: 38
40644371 TAGCACTTAT
* * *
40644381 CTAAGGCAACATTTAAAAAAGGTTGGGATAGA-CTCGT
1 CTAAGACAACCTTTAAAAAAGGTTGGGATAGACCTCGC
* *
40644418 CTAAAGA-AACC-TT-AAAAAGGTTGAGATAGACCTTGC
1 CT-AAGACAACCTTTAAAAAAGGTTGGGATAGACCTCGC
40644454 CTAAGACAACCTTTAAAAAAGGTTGGGATA
1 CTAAGACAACCTTTAAAAAAGGTTGGGATA
40644484 AACCCATCTA
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
35 20 0.36
36 11 0.20
37 7 0.13
38 17 0.31
ACGTcount: A:0.41, C:0.15, G:0.21, T:0.23
Consensus pattern (38 bp):
CTAAGACAACCTTTAAAAAAGGTTGGGATAGACCTCGC
Found at i:40644446 original size:35 final size:37
Alignment explanation
Indices: 40644396--40644559 Score: 133
Period size: 36 Copynumber: 4.5 Consensus size: 37
40644386 GCAACATTTA
* *
40644396 AAAAAGGTTGGGATAGA-CTCGTCTAAAGA-AACCTT
1 AAAAAGGTTGAGATAAACCTCGTCTAAAGACAACCTT
* * *
40644431 AAAAAGGTTGAGATAGACCTTGCCT-AAGACAACCTTT
1 AAAAAGGTTGAGATAAACCTCGTCTAAAGACAACC-TT
* * * *
40644468 AAAAAAGGTTGGGATAAACC-CATCT-AAGGCAATCTT
1 -AAAAAGGTTGAGATAAACCTCGTCTAAAGACAACCTT
* * * * * *
40644504 AAAAAGATTAAAATAAACCTTGT-TTAAGATAACCTT
1 AAAAAGGTTGAGATAAACCTCGTCTAAAGACAACCTT
40644540 AAAAAGGTTGAGATAAACCT
1 AAAAAGGTTGAGATAAACCT
40644560 TGTTTTAGTC
Statistics
Matches: 101, Mismatches: 22, Indels: 11
0.75 0.16 0.08
Matches are distributed among these distances:
35 36 0.36
36 37 0.37
37 11 0.11
38 17 0.17
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.24
Consensus pattern (37 bp):
AAAAAGGTTGAGATAAACCTCGTCTAAAGACAACCTT
Found at i:40644477 original size:73 final size:73
Alignment explanation
Indices: 40644381--40644558 Score: 198
Period size: 73 Copynumber: 2.5 Consensus size: 73
40644371 TAGCACTTAT
* * * * * * * *
40644381 CTAAGGCAACATTTAAAAAAGGTTGGGATAGACTCGTCTAAAGAAACCTTAAAAAGGTTGAGATA
1 CTAAGACAACCTTTAAAAAAGGTTGGGATAAACCCATCTAAAGAAACCTTAAAAAGATTAAAATA
*
40644446 GACCTTGC
66 AACCTTGC
* * *
40644454 CTAAGACAACCTTTAAAAAAGGTTGGGATAAACCCATCTAAGGCAATCTTAAAAAGATTAAAATA
1 CTAAGACAACCTTTAAAAAAGGTTGGGATAAACCCATCTAAAGAAACCTTAAAAAGATTAAAATA
*
40644519 AACCTTGT
66 AACCTTGC
* * *
40644527 TTAAGATAACC-TT-AAAAAGGTTGAGATAAACC
1 CTAAGACAACCTTTAAAAAAGGTTGGGATAAACC
40644559 TTGTTTTAGT
Statistics
Matches: 89, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
71 18 0.20
72 2 0.02
73 69 0.78
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.24
Consensus pattern (73 bp):
CTAAGACAACCTTTAAAAAAGGTTGGGATAAACCCATCTAAAGAAACCTTAAAAAGATTAAAATA
AACCTTGC
Found at i:40646579 original size:2 final size:2
Alignment explanation
Indices: 40646572--40646605 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
40646562 TAAGATTCCA
40646572 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40646606 TTCTCATCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40647480 original size:30 final size:29
Alignment explanation
Indices: 40647444--40647542 Score: 78
Period size: 30 Copynumber: 3.3 Consensus size: 29
40647434 TTGAAAAACT
40647444 CTTATTTGAACACTTTTTAAAGGTTAAGCC
1 CTTATTTGAACACTTTTTAAAGGTTAAG-C
** *
40647474 CTTATTTGTTCA-TTTTGAAAGGTTTAA-C
1 CTTATTTGAACACTTTTTAAAGG-TTAAGC
**
40647502 CTTCATTT-AAGCACTTTTATAAAGGTTTGGTC
1 CTT-ATTTGAA-CACTTTT-TAAAGGTTAAG-C
40647534 CTTATTTGA
1 CTTATTTGA
40647543 GCAACCTCTA
Statistics
Matches: 53, Mismatches: 8, Indels: 14
0.71 0.11 0.19
Matches are distributed among these distances:
28 4 0.08
29 15 0.28
30 20 0.38
31 9 0.17
32 5 0.09
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.45
Consensus pattern (29 bp):
CTTATTTGAACACTTTTTAAAGGTTAAGC
Found at i:40650385 original size:17 final size:17
Alignment explanation
Indices: 40650363--40650398 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
40650353 CATGTCGATG
40650363 TTATTAAAATTGATATA
1 TTATTAAAATTGATATA
*
40650380 TTATTAAAATTGGTATA
1 TTATTAAAATTGATATA
40650397 TT
1 TT
40650399 TACCTTATTA
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:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (17 bp):
TTATTAAAATTGATATA
Found at i:40652640 original size:29 final size:31
Alignment explanation
Indices: 40652591--40652694 Score: 82
Period size: 29 Copynumber: 3.6 Consensus size: 31
40652581 TCGGGGTTGA
*
40652591 AAAATGG-AA-TTGTGGAGAG-TTCAAGGGT-
1 AAAATGGTAATTTTTGGAGAGTTTC-AGGGTC
*
40652619 AAAATGGTAATTTTTGGA-AGTTTCGGGGTC
1 AAAATGGTAATTTTTGGAGAGTTTCAGGGTC
* *
40652649 AAAAT-GTAATTTTCT-GA-AATTTTAGGGTC
1 AAAATGGTAATTTT-TGGAGAGTTTCAGGGTC
*
40652678 AAAAT-GCAATTTTTGGA
1 AAAATGGTAATTTTTGGA
40652695 CTGTTTGGGG
Statistics
Matches: 64, Mismatches: 6, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
28 8 0.12
29 41 0.64
30 15 0.23
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.35
Consensus pattern (31 bp):
AAAATGGTAATTTTTGGAGAGTTTCAGGGTC
Found at i:40654629 original size:6 final size:6
Alignment explanation
Indices: 40654620--40654696 Score: 52
Period size: 6 Copynumber: 12.8 Consensus size: 6
40654610 TTGAATTTGA
* * *
40654620 TTAAAT TTAAAT CTAAA- ATAAAT TTAAAT AAGTAAAT TTAAAT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT --TTAAAT TTAAAT TTAAAT
** *
40654668 ACAAAT TTAAAA TT-AAT TTAAACT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAA-T TTAAA
40654697 AGCCCAAACC
Statistics
Matches: 54, Mismatches: 11, Indels: 11
0.71 0.14 0.14
Matches are distributed among these distances:
5 11 0.20
6 32 0.59
7 6 0.11
8 5 0.09
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (6 bp):
TTAAAT
Found at i:40654641 original size:17 final size:16
Alignment explanation
Indices: 40654621--40654683 Score: 67
Period size: 17 Copynumber: 3.9 Consensus size: 16
40654611 TGAATTTGAT
40654621 TAAATTTAAATCTAAAA
1 TAAATTTAAAT-TAAAA
*
40654638 TAAATTTAAA-T-AAG
1 TAAATTTAAATTAAAA
40654652 TAAATTTAAATTTAAAA
1 TAAATTTAAA-TTAAAA
*
40654669 CAAATTTAAAATTAA
1 TAAATTT-AAATTAA
40654684 TTTAAACTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
14 12 0.31
15 1 0.03
16 1 0.03
17 22 0.56
18 3 0.08
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.37
Consensus pattern (16 bp):
TAAATTTAAATTAAAA
Found at i:40654647 original size:11 final size:11
Alignment explanation
Indices: 40654627--40654689 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
40654617 TGATTAAATT
*
40654627 TAAATCTAAAA
1 TAAATTTAAAA
40654638 TAAATTT-AAA
1 TAAATTTAAAA
* *
40654648 T-AA-GTAAATT
1 TAAATTTAAA-A
40654658 TAAATTTAAAA
1 TAAATTTAAAA
*
40654669 CAAATTTAAAA
1 TAAATTTAAAA
*
40654680 TTAATTTAAA
1 TAAATTTAAA
40654690 CTTTAAAAGC
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
8 1 0.03
9 4 0.10
10 5 0.12
11 26 0.65
12 4 0.10
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.37
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:40655142 original size:20 final size:20
Alignment explanation
Indices: 40655104--40655142 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
40655094 AGTAATATGA
*
40655104 TATTTTTAAAAAATTATTAT
1 TATTTTTAAAAAATGATTAT
40655124 TATTTTTATAAAAA-GATTA
1 TATTTTTA-AAAAATGATTA
40655143 AACTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (20 bp):
TATTTTTAAAAAATGATTAT
Found at i:40660147 original size:20 final size:18
Alignment explanation
Indices: 40660098--40660151 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
40660088 CTCTTGCCCT
*
40660098 CCATCCCTCCCCCCTACA
1 CCATCCCTCCCCCCCACA
*
40660116 CCGATTCTCTCCCTCTCCCACA
1 CC-A-TCCCTCCC-C-CCCACA
40660138 CCATCCCTCCCCCC
1 CCATCCCTCCCCCC
40660152 TACTCCGACC
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
18 4 0.14
19 2 0.07
20 14 0.48
21 2 0.07
22 7 0.24
ACGTcount: A:0.13, C:0.65, G:0.02, T:0.20
Consensus pattern (18 bp):
CCATCCCTCCCCCCCACA
Found at i:40660185 original size:40 final size:40
Alignment explanation
Indices: 40660098--40660174 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
40660088 CTCTTGCCCT
**
40660098 CCATCCCTCCCCCCTACACCGATTCTCTCCCTCTCCCACA
1 CCATCCCTCCCCCCTACACCGACCCTCTCCCTCTCCCACA
*
40660138 CCATCCCTCCCCCCTACTCCGACCCTCTCCCTCTCCC
1 CCATCCCTCCCCCCTACACCGACCCTCTCCCTCTCCC
40660175 CTACCTTCCC
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:0.12, C:0.64, G:0.03, T:0.22
Consensus pattern (40 bp):
CCATCCCTCCCCCCTACACCGACCCTCTCCCTCTCCCACA
Found at i:40664428 original size:18 final size:17
Alignment explanation
Indices: 40664387--40664420 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40664377 AAAATAAAAA
40664387 AATTAAAAAATACATTT
1 AATTAAAAAATACATTT
* *
40664404 AAATAAAAAATTCATTT
1 AATTAAAAAATACATTT
40664421 GATTTAAATG
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:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (17 bp):
AATTAAAAAATACATTT
Found at i:40665032 original size:10 final size:10
Alignment explanation
Indices: 40665019--40665066 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
40665009 CAAAGTGTTT
40665019 TTAATATATA
1 TTAATATATA
40665029 TTAATATAT-
1 TTAATATATA
*
40665038 TTAATATTTA
1 TTAATATATA
*
40665048 TTTATTATATA
1 -TTAATATATA
40665059 TTAATATA
1 TTAATATA
40665067 CTTTTTAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 8 0.25
10 16 0.50
11 8 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TTAATATATA
Found at i:40665042 original size:19 final size:20
Alignment explanation
Indices: 40665018--40665066 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
40665008 TCAAAGTGTT
40665018 TTTAATATATA-TTAATATA
1 TTTAATATATATTTAATATA
* *
40665037 TTTAATATTTATTTATTATA
1 TTTAATATATATTTAATATA
40665057 TATTAATATA
1 T-TTAATATA
40665067 CTTTTTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 10 0.40
20 8 0.32
21 7 0.28
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTAATATATATTTAATATA
Found at i:40665083 original size:33 final size:30
Alignment explanation
Indices: 40665018--40665088 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 30
40665008 TCAAAGTGTT
* *
40665018 TTTAATATATATTAATATATTTAATATTTA
1 TTTATTATATATTAATATATTTAATATCTA
40665048 TTTATTATATATTAATATACTTTTTAAT-TGCTA
1 TTTATTATATATTAATATA---TTTAATAT-CTA
40665081 TTTATTAT
1 TTTATTAT
40665089 TACCTACGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 18 0.51
32 1 0.03
33 16 0.46
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (30 bp):
TTTATTATATATTAATATATTTAATATCTA
Found at i:40666301 original size:29 final size:27
Alignment explanation
Indices: 40666265--40666600 Score: 171
Period size: 29 Copynumber: 11.6 Consensus size: 27
40666255 CCCCGAACTT
*
40666265 TTCAAAAATCACGTTTTGACCCCTAAAC
1 TTCAAAAATCACATTTT-ACCCCTAAAC
* * *
40666293 TTCATAAAATTATATTTTA-CCCTCGAAC
1 TTCA-AAAATCACATTTTACCCCT-AAAC
* * *
40666321 TTTACAAAAATCATATTTTAACCCTCGAAC
1 -TT-CAAAAATCACATTTTACCCCT-AAAC
* *
40666351 TTCACAAAATTACATTTTTACCCATAAAC
1 TTCA-AAAATCACA-TTTTACCCCTAAAC
*
40666380 TTTCAAAAATCACATTTTGA-CCCTCGAAC
1 -TTCAAAAATCACATTTT-ACCCCT-AAAC
* * * **
40666409 TTAACAAAATTATATTTTTACCCCCGAAC
1 TTCA-AAAATCACA-TTTTACCCCTAAAC
40666438 TTCCAAAAAAT-A-AGTTTTGACCCC-AAAC
1 TT-C-AAAAATCACA-TTTT-ACCCCTAAAC
*
40666466 TTTTCAAAAATCACATTTTAACCCTTAAAC
1 --TTCAAAAATCACATTTT-ACCCCTAAAC
* *
40666496 TTCACAAAATTACATTTTACCCCCAAAC
1 TTCA-AAAATCACATTTTACCCCTAAAC
* *
40666524 TTTCAAAAAATCACATTTTTACACCCGAAAA
1 -TTC-AAAAATCACA-TTTTAC-CCCTAAAC
* * *
40666555 TCCAAAAATTACCATTTTACTCCC-AAAT
1 TTCAAAAATCA-CATTTTAC-CCCTAAAC
40666583 TTCTAAAAATCACATTTT
1 TTC-AAAAATCACATTTT
40666601 TAACTTCAAA
Statistics
Matches: 246, Mismatches: 34, Indels: 56
0.73 0.10 0.17
Matches are distributed among these distances:
27 4 0.02
28 57 0.23
29 125 0.51
30 53 0.22
31 7 0.03
ACGTcount: A:0.39, C:0.25, G:0.03, T:0.33
Consensus pattern (27 bp):
TTCAAAAATCACATTTTACCCCTAAAC
Found at i:40666329 original size:58 final size:59
Alignment explanation
Indices: 40666258--40666545 Score: 224
Period size: 58 Copynumber: 4.9 Consensus size: 59
40666248 AAAAGGTCCC
* *
40666258 CGAACTTTTCAAAAATCACGTTTTGACCCCT-AAACTTCATAAAATTATA-TTTTACCCT
1 CGAAC-TTTCAAAAATCACATTTTGACCCCTCAAACTTCACAAAATTATATTTTTACCCT
* * * *
40666316 CGAACTTTACAAAAATCATATTTT-AACCCTCGAACTTCACAAAATTACATTTTTACCCAT
1 CGAACTTT-CAAAAATCACATTTTGACCCCTCAAACTTCACAAAATTATATTTTTACCC-T
* * * *
40666376 -AAACTTTCAAAAATCACATTTTGA-CCCTCGAACTTAACAAAATTATATTTTTACCCC
1 CGAACTTTCAAAAATCACATTTTGACCCCTCAAACTTCACAAAATTATATTTTTACCCT
* * * *
40666433 CGAACTTCCAAAAAAT-A-AGTTTTGA-CCC-CAAACTTTTCA-AAAATCACATTTTAACCCT
1 CGAACTTTC-AAAAATCACA-TTTTGACCCCTCAAAC--TTCACAAAATTATATTTTTACCCT
** * * * *
40666491 TAAAC-TTCACAAAATTACATTTT-ACCCC-CAAACTTTCAAAAAATCACATTTTTAC
1 CGAACTTTCA-AAAATCACATTTTGACCCCTCAAAC-TTCACAAAATTATATTTTTAC
40666546 ACCCGAAAAT
Statistics
Matches: 192, Mismatches: 23, Indels: 30
0.78 0.09 0.12
Matches are distributed among these distances:
56 1 0.01
57 26 0.14
58 139 0.72
59 25 0.13
60 1 0.01
ACGTcount: A:0.39, C:0.25, G:0.03, T:0.33
Consensus pattern (59 bp):
CGAACTTTCAAAAATCACATTTTGACCCCTCAAACTTCACAAAATTATATTTTTACCCT
Found at i:40666424 original size:87 final size:84
Alignment explanation
Indices: 40666255--40666542 Score: 278
Period size: 87 Copynumber: 3.3 Consensus size: 84
40666245 CCTAAAAGGT
* * *
40666255 CCCCGAACTTTTCA-AAAATCACGTTTTGACCCCTAAAC-TTCATAAAATTATATTTTACCCTCG
1 CCCCGAAC--TTCACAAAATCACATTTTGA-CCCTAAACTTTCA-AAAATCACATTTTACCCTCG
* *
40666318 AACTTTACAAAAATCATATTTTAAC
62 AACTTAAC-AAAATTATATTTT-AC
* * *
40666343 CCTCGAACTTCACAAAATTACATTTTTACCCATAAACTTTCAAAAATCACATTTTGACCCTCGAA
1 CCCCGAACTTCACAAAATCACATTTTGACCC-TAAACTTTCAAAAATCACATTTT-ACCCTCGAA
40666408 CTTAACAAAATTATATTTTTAC
64 CTTAACAAAATTATA-TTTTAC
* * **
40666430 CCCCGAACTTCCAAAAAAT-A-AGTTTTGACCCCAAACTTTTCAAAAATCACATTTTAACCCTTA
1 CCCCGAACTT-CACAAAATCACA-TTTTGACCCTAAAC-TTTCAAAAATCACATTTT-ACCCTCG
* *
40666493 AACTTCACAAAATTACATTTTAC
62 AACTTAACAAAATTATATTTTAC
* *
40666516 CCCCAAACTTTCAAAAAATCACATTTT
1 CCCCGAAC-TTCACAAAATCACATTTT
40666543 TACACCCGAA
Statistics
Matches: 171, Mismatches: 18, Indels: 23
0.81 0.08 0.11
Matches are distributed among these distances:
86 33 0.19
87 101 0.59
88 37 0.22
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.33
Consensus pattern (84 bp):
CCCCGAACTTCACAAAATCACATTTTGACCCTAAACTTTCAAAAATCACATTTTACCCTCGAACT
TAACAAAATTATATTTTAC
Found at i:40666561 original size:87 final size:86
Alignment explanation
Indices: 40666383--40666573 Score: 208
Period size: 87 Copynumber: 2.2 Consensus size: 86
40666373 CATAAACTTT
* * * *
40666383 CAAAAATCACATTTTGACCCTCGAACTTAACAAAATTATATTTTTACCCCCGAACTTCCAAAAAA
1 CAAAAATCACATTTTAACCCTCAAACTTAACAAAATTACATTTTTACCCCCAAACTTCCAAAAAA
* *
40666448 TAAGTTTTGACCCCAAACTTTT
66 TAAGTTTTGACCCCAAAC-ATC
* * *
40666470 CAAAAATCACATTTTAACCCTTAAACTTCACAAAATTACA-TTTTACCCCCAAACTTTCAAAAAA
1 CAAAAATCACATTTTAACCCTCAAACTTAACAAAATTACATTTTTACCCCCAAACTTCCAAAAAA
*
40666534 TCACA-TTTTTACACCCGAAA-ATC
66 T-A-AGTTTTGAC-CCC-AAACATC
*
40666557 CAAAAATTACCATTTTA
1 CAAAAATCA-CATTTTA
40666574 CTCCCAAATT
Statistics
Matches: 88, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
86 23 0.26
87 51 0.58
88 11 0.12
89 3 0.03
ACGTcount: A:0.41, C:0.26, G:0.03, T:0.30
Consensus pattern (86 bp):
CAAAAATCACATTTTAACCCTCAAACTTAACAAAATTACATTTTTACCCCCAAACTTCCAAAAAA
TAAGTTTTGACCCCAAACATC
Found at i:40666563 original size:58 final size:59
Alignment explanation
Indices: 40666383--40666602 Score: 190
Period size: 58 Copynumber: 3.8 Consensus size: 59
40666373 CATAAACTTT
* * * * * * **
40666383 CAAAAATCACATTTTGACCCTCGAAC-TT-AACAAAATTATATTTTTACCCCCGAACTTC
1 CAAAAATTACATTTTGACCCCCAAACTTTCAA-AAAATCACATTTTTACACCCGAAAATC
* * * *
40666441 CAAAAAATA-AGTTTTGA-CCCCAAACTTTTC-AAAAATCACA-TTTTA-ACCCTTAAACTT
1 CAAAAATTACA-TTTTGACCCCCAAAC-TTTCAAAAAATCACATTTTTACACCC-GAAAATC
40666498 CACAAAATTACATTTT-ACCCCCAAACTTTCAAAAAATCACATTTTTACACCCGAAAATC
1 CA-AAAATTACATTTTGACCCCCAAACTTTCAAAAAATCACATTTTTACACCCGAAAATC
* *
40666557 CAAAAATTACCATTTT-ACTCCCAAA-TTTCTAAAAATCACATTTTTA
1 CAAAAATTA-CATTTTGACCCCCAAACTTTCAAAAAATCACATTTTTA
40666603 ACTTCAAATT
Statistics
Matches: 133, Mismatches: 17, Indels: 24
0.76 0.10 0.14
Matches are distributed among these distances:
56 3 0.02
57 22 0.17
58 75 0.56
59 29 0.22
60 4 0.03
ACGTcount: A:0.40, C:0.25, G:0.03, T:0.31
Consensus pattern (59 bp):
CAAAAATTACATTTTGACCCCCAAACTTTCAAAAAATCACATTTTTACACCCGAAAATC
Found at i:40671434 original size:15 final size:16
Alignment explanation
Indices: 40671414--40671443 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
40671404 ACGTGTTAAA
40671414 AAAAAGAAAA-AAAAG
1 AAAAAGAAAAGAAAAG
40671429 AAAAAGAAAAGAAAA
1 AAAAAGAAAAGAAAA
40671444 ATAAATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAGAAAAG
Found at i:40672423 original size:19 final size:19
Alignment explanation
Indices: 40672388--40672444 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
40672378 TAAAAAAATA
40672388 AAAAAAATAAGAAAGAAAA-G
1 AAAAAAA-AA-AAAGAAAAGG
40672408 AAAGAAAAAAAAAGAAAAGG
1 AAA-AAAAAAAAAGAAAAGG
**
40672428 AAAAAGGAAAAAGAAAA
1 AAAAAAAAAAAAGAAAA
40672445 TAGAAAAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
19 20 0.61
20 9 0.27
21 4 0.12
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.02
Consensus pattern (19 bp):
AAAAAAAAAAAAGAAAAGG
Found at i:40672431 original size:13 final size:13
Alignment explanation
Indices: 40672415--40672469 Score: 56
Period size: 13 Copynumber: 4.1 Consensus size: 13
40672405 AAGAAAGAAA
40672415 AAAAAAGAAAAGG
1 AAAAAAGAAAAGG
* *
40672428 AAAAAGGAAAAAG
1 AAAAAAGAAAAGG
*
40672441 AAAATAGAAAAACGG
1 AAAAAAG-AAAA-GG
*
40672456 GAAAAAGAAAAGG
1 AAAAAAGAAAAGG
40672469 A
1 A
40672470 GAGGTCAAGG
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
13 18 0.56
14 8 0.25
15 6 0.19
ACGTcount: A:0.73, C:0.02, G:0.24, T:0.02
Consensus pattern (13 bp):
AAAAAAGAAAAGG
Found at i:40672432 original size:7 final size:6
Alignment explanation
Indices: 40672381--40672466 Score: 54
Period size: 6 Copynumber: 13.7 Consensus size: 6
40672371 GATTCAATAA
* *
40672381 AAAAAT AAAAA- AAATAAG AAAGAA- AAGAAAG -AAAA- AAAAAG AAAAGG
1 AAAAAG AAAAAG AAA-AAG AAA-AAG AA-AAAG AAAAAG AAAAAG AAAAAG
40672428 AAAAAGG AAAAAG AAAATAG AAAAACGGG AAAAAG AAAA
1 AAAAA-G AAAAAG AAAA-AG AAAAA---G AAAAAG AAAA
40672467 GGAGAGGTCA
Statistics
Matches: 66, Mismatches: 3, Indels: 22
0.73 0.03 0.24
Matches are distributed among these distances:
5 10 0.15
6 32 0.48
7 18 0.27
9 6 0.09
ACGTcount: A:0.78, C:0.01, G:0.17, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:40676199 original size:41 final size:41
Alignment explanation
Indices: 40676117--40676211 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 41
40676107 CATCATCATT
* * * *
40676117 CAGTCTTTTACCCTTAATCAAGAAGGGTAGATTAAAGATTC
1 CAGTCTTTTACCCTTAATCAAGAAAGGCAAAATAAAGATTC
* *
40676158 CAGTCTTTTACCCTTAATCAAGAAAGGCAAAATGAATATTC
1 CAGTCTTTTACCCTTAATCAAGAAAGGCAAAATAAAGATTC
*
40676199 CAATCTTTTACCC
1 CAGTCTTTTACCC
40676212 CGAGCCTAGG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.32
Consensus pattern (41 bp):
CAGTCTTTTACCCTTAATCAAGAAAGGCAAAATAAAGATTC
Found at i:40676302 original size:78 final size:77
Alignment explanation
Indices: 40676201--40676520 Score: 234
Period size: 78 Copynumber: 4.1 Consensus size: 77
40676191 GAATATTCCA
* * *
40676201 ATCTTTTACCCCGAGCCTAGGGTAGATCACAATCAGACAATCTCTTACCCCGAGCCTAGGGCAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACAATCAG-CAATCTCTTACCCCGAGCCTAGGGCAGA
* * *
40676266 TTACAGCTATCCG
65 TTGCAACCATCCG
* * * *** * * * * *
40676279 ATCTCTTACCCCGAGCTTGGGGTAGGTTGTAATTAGTCGATC-CTTTACCCCGAGCTTGGGGTAG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACAATCAG-CAATCTC-TTACCCCGAGCCTAGGGCAG
* * **
40676343 GTTGTAATTAGT-CG
64 ATTGCAACCA-TCCG
* * * * *
40676357 ATC-CTTTACCCCGAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACACGGAGTCTAGGGTAG
1 ATCTC-TTACCCCGAGCCTGGGGCAGATCACAATCAG-CAATCTCTTACCCCGAGCCTAGGGCAG
* *
40676421 ATTGCAGCCATTCG
64 ATTGCAACCATCCG
* * * * *
40676435 AGCTTTTACCCCGAGCTTGGGGCAGATCACCATTAGCTAATCTCTTACCCCGAGCC-AGGGGCAG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACAATCAGC-AATCTCTTACCCCGAGCCTA-GGGCAG
*
40676499 ATTGCAACCATCCT
64 ATTGCAACCATCCG
40676513 ATCTCTTA
1 ATCTCTTA
40676521 AAAGAAGTCT
Statistics
Matches: 183, Mismatches: 51, Indels: 16
0.73 0.20 0.06
Matches are distributed among these distances:
77 5 0.03
78 176 0.96
79 2 0.01
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (77 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATCACAATCAGCAATCTCTTACCCCGAGCCTAGGGCAGAT
TGCAACCATCCG
Found at i:40676320 original size:39 final size:39
Alignment explanation
Indices: 40676284--40676378 Score: 181
Period size: 39 Copynumber: 2.4 Consensus size: 39
40676274 ATCCGATCTC
40676284 TTACCCCGAGCTTGGGGTAGGTTGTAATTAGTCGATCCT
1 TTACCCCGAGCTTGGGGTAGGTTGTAATTAGTCGATCCT
40676323 TTACCCCGAGCTTGGGGTAGGTTGTAATTAGTCGATCCT
1 TTACCCCGAGCTTGGGGTAGGTTGTAATTAGTCGATCCT
*
40676362 TTACCCCGAGCCTGGGG
1 TTACCCCGAGCTTGGGG
40676379 CAGATCACCA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.17, C:0.23, G:0.29, T:0.31
Consensus pattern (39 bp):
TTACCCCGAGCTTGGGGTAGGTTGTAATTAGTCGATCCT
Found at i:40676419 original size:117 final size:117
Alignment explanation
Indices: 40676245--40676456 Score: 248
Period size: 117 Copynumber: 1.8 Consensus size: 117
40676235 AGACAATCTC
* * * * * * *
40676245 TTACCCCGAGCCTAGGGCAGATTACAGCTATCCGATCTCTTACCCCGAGCTTGGGGTAGGTTGTA
1 TTACCCCGAGCCTAGGGCAGATCACAGCTAGCCAATCTCTTACACCGAGCTTAGGGTAGATTGCA
** *
40676310 ATTAGTCGATCCTTTACCCCGAGCTTGGGGTAGGTTGTAATTAGTCGATCCT
66 ACCAGTCGAGCCTTTACCCCGAGCTTGGGGTAGGTTGTAATTAGTCGATCCT
* * *
40676362 TTACCCCGAGCCTGGGGCAGATCACCATC-AGCCAATCTCTTACACGGAG-TCTAGGGTAGATTG
1 TTACCCCGAGCCTAGGGCAGATCA-CAGCTAGCCAATCTCTTACACCGAGCT-TAGGGTAGATTG
* * *
40676425 CAGCCATTCGAGCTTTTACCCCGAGCTTGGGG
64 CAACCAGTCGAGCCTTTACCCCGAGCTTGGGG
40676457 CAGATCACCA
Statistics
Matches: 77, Mismatches: 16, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
116 1 0.01
117 73 0.95
118 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.26, T:0.27
Consensus pattern (117 bp):
TTACCCCGAGCCTAGGGCAGATCACAGCTAGCCAATCTCTTACACCGAGCTTAGGGTAGATTGCA
ACCAGTCGAGCCTTTACCCCGAGCTTGGGGTAGGTTGTAATTAGTCGATCCT
Found at i:40676483 original size:39 final size:38
Alignment explanation
Indices: 40676199--40676500 Score: 128
Period size: 39 Copynumber: 7.8 Consensus size: 38
40676189 ATGAATATTC
* * * * *
40676199 CAATCTTTTACCCCGAGCCTAGGGTAGATCACAATCAG
1 CAATCTCTTACCCCGAGCCTGGGGCAGATCACCATTAG
* * * *
40676237 ACAATCTCTTACCCCGAGCCTAGGGCAGATTA-CAGCTATC
1 -CAATCTCTTACCCCGAGCCTGGGGCAGATCACCA-TTA-G
* * * * ****
40676277 CGATCTCTTACCCCGAGCTTGGGGTAGGTTGTAATTAG
1 CAATCTCTTACCCCGAGCCTGGGGCAGATCACCATTAG
* * * * ****
40676315 TCGATC-CTTTACCCCGAGCTTGGGGTAGGTTGTAATTAG
1 -CAATCTC-TTACCCCGAGCCTGGGGCAGATCACCATTAG
* *
40676354 TCGATC-CTTTACCCCGAGCCTGGGGCAGATCACCATCAG
1 -CAATCTC-TTACCCCGAGCCTGGGGCAGATCACCATTAG
* * * * *
40676393 CCAATCTCTTACACGGAGTCTAGGGTAGATTGCAGCCATT--
1 -CAATCTCTTACCCCGAGCCTGGGGCAGA-T-CA-CCATTAG
* * * *
40676433 CGAGCTTTTACCCCGAGCTTGGGGCAGATCACCATTAG
1 CAATCTCTTACCCCGAGCCTGGGGCAGATCACCATTAG
*
40676471 CTAATCTCTTACCCCGAGCCAGGGGCAGAT
1 C-AATCTCTTACCCCGAGCCTGGGGCAGAT
40676501 TGCAACCATC
Statistics
Matches: 205, Mismatches: 46, Indels: 24
0.75 0.17 0.09
Matches are distributed among these distances:
36 5 0.02
37 2 0.01
38 4 0.02
39 185 0.90
40 3 0.01
41 2 0.01
42 4 0.02
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.25
Consensus pattern (38 bp):
CAATCTCTTACCCCGAGCCTGGGGCAGATCACCATTAG
Found at i:40677896 original size:23 final size:20
Alignment explanation
Indices: 40677846--40677896 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 20
40677836 TTTTAACATA
40677846 TATTAA-TATATTTAATATT
1 TATTAATTATATTTAATATT
*
40677865 TATTTATTATATATTAATATACT
1 TATTAATTATAT-TTAATAT--T
40677888 TATTAATTA
1 TATTAATTA
40677897 CGATTTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 5 0.19
20 5 0.19
21 7 0.27
23 9 0.35
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTAATTATATTTAATATT
Found at i:40679139 original size:29 final size:29
Alignment explanation
Indices: 40679107--40679259 Score: 107
Period size: 29 Copynumber: 5.3 Consensus size: 29
40679097 GAAAATCATG
*
40679107 TTTTGACTCTTGAACTTCACAAAATTACA
1 TTTTGACTCTCGAACTTCACAAAATTACA
** * * **
40679136 TTTTTTCCCTTGAACTTTC-CAAAAATGGCA
1 TTTTGACTCTCGAAC-TTCAC-AAAATTACA
*
40679166 TTTTAACTC-CGAACTTCACAAAATTACA
1 TTTTGACTCTCGAACTTCACAAAATTACA
* * *
40679194 TTTT-ACCCTCAAACTTC-CAAAACTCACA
1 TTTTGACTCTCGAACTTCACAAAA-TTACA
** * *
40679222 CATTGACTCTCAAACTTTACAAAATTACA
1 TTTTGACTCTCGAACTTCACAAAATTACA
*
40679251 TTTTTACTC
1 TTTTGACTC
40679260 CTAAATTTTT
Statistics
Matches: 95, Mismatches: 22, Indels: 14
0.73 0.17 0.11
Matches are distributed among these distances:
27 8 0.08
28 27 0.28
29 39 0.41
30 21 0.22
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (29 bp):
TTTTGACTCTCGAACTTCACAAAATTACA
Found at i:40679274 original size:29 final size:29
Alignment explanation
Indices: 40679127--40679458 Score: 150
Period size: 29 Copynumber: 11.4 Consensus size: 29
40679117 TGAACTTCAC
** *
40679127 AAAATTACATTTTTTCCCTTGAACTTTCCA
1 AAAATTACATTTTAACCC-TAAACTTTCCA
** *
40679157 AAAATGGCATTTTAACTCC-GAAC-TT-CA
1 AAAATTACATTTTAAC-CCTAAACTTTCCA
40679184 CAAAATTACATTTT-ACCCTCAAAC-TTCCA
1 -AAAATTACATTTTAACCCT-AAACTTTCCA
* * ** * * *
40679213 AAACTCACACATTGACTCTCAAACTTTAC-
1 AAAATTACATTTTAACCCT-AAACTTTCCA
* * **
40679242 AAAATTACATTTTTACTCCTAAATTTTTTA
1 AAAATTACATTTTAAC-CCTAAACTTTCCA
*
40679272 AAAATCACATTTTAACCCTAAACTTTCC-
1 AAAATTACATTTTAACCCTAAACTTTCCA
*
40679300 AAAACTACA-TTTATACCCTTAAACTTTCCA
1 AAAATTACATTTTA-ACCC-TAAACTTTCCA
** * *
40679330 AAAAACACGTTTTAACCCTCGAACTTAT-CA
1 AAAATTACATTTTAACCCT-AAACTT-TCCA
* * *
40679360 AAAATCACCTTTTGACCCCTAAACTTTCC-
1 AAAATTACATTTT-AACCCTAAACTTTCCA
* * * *
40679389 AAAATCACATTTGT-ACACTTGAAC-ATCCA
1 AAAATTACATTT-TAAC-CCTAAACTTTCCA
**
40679418 AAAATTAACATTTTGCCCCTAAA-TTTCCA
1 AAAATT-ACATTTTAACCCTAAACTTTCCA
*
40679447 AAAATCACATTT
1 AAAATTACATTT
40679459 CCAACTTCAA
Statistics
Matches: 231, Mismatches: 48, Indels: 48
0.71 0.15 0.15
Matches are distributed among these distances:
26 2 0.01
27 8 0.03
28 48 0.21
29 88 0.38
30 73 0.32
31 12 0.05
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.33
Consensus pattern (29 bp):
AAAATTACATTTTAACCCTAAACTTTCCA
Found at i:40679282 original size:30 final size:30
Alignment explanation
Indices: 40679237--40679293 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
40679227 ACTCTCAAAC
* *
40679237 TTTACAAAATTACATTTTTACTCCTAAATTT
1 TTTACAAAATCACATTTTAAC-CCTAAATTT
40679268 TTTA-AAAATCACATTTTAACCCTAAA
1 TTTACAAAATCACATTTTAACCCTAAA
40679294 CTTTCCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 6 0.25
30 14 0.58
31 4 0.17
ACGTcount: A:0.40, C:0.18, G:0.00, T:0.42
Consensus pattern (30 bp):
TTTACAAAATCACATTTTAACCCTAAATTT
Found at i:40679303 original size:58 final size:58
Alignment explanation
Indices: 40679119--40679400 Score: 173
Period size: 58 Copynumber: 4.9 Consensus size: 58
40679109 TTGACTCTTG
* * * * * *** *
40679119 AACTTCACAAAATTACATTTTTTCCCTTGAACTTTCCAAAAATGGCATTTTAACTCC-G
1 AACTTTACAAAACTACATTTATACCCTTAAACTTTCCAAAAAACACATTTTAAC-CCTA
* * * ** ** * *
40679177 AACTTCACAAAATTACATTT-TACCCTCAAAC-TTCCAAAACTCACACATTGACTCTCA
1 AACTTTACAAAACTACATTTATACCCTTAAACTTTCCAAAAAACACATTTTAACCCT-A
* * * ** *
40679234 AACTTTACAAAATTACATTTTTACTCC-TAAATTTTTTAAAAATCACATTTTAACCCTA
1 AACTTTACAAAACTACATTTATAC-CCTTAAACTTTCCAAAAAACACATTTTAACCCTA
* * *
40679292 AACTTTCCAAAACTACATTTATACCCTTAAACTTTCCAAAAAACACGTTTTAACCCTCG
1 AACTTTACAAAACTACATTTATACCCTTAAACTTTCCAAAAAACACATTTTAACCCT-A
* * * *
40679351 AAC-TTATCAAAAATCACCTTT-TGACCCCTAAACTTTCC-AAAATCACATTT
1 AACTTTA-CAAAACT-ACATTTAT-ACCCTTAAACTTTCCAAAAAACACATTT
40679401 GTACACTTGA
Statistics
Matches: 178, Mismatches: 36, Indels: 19
0.76 0.15 0.08
Matches are distributed among these distances:
55 1 0.01
56 15 0.08
57 29 0.16
58 75 0.42
59 39 0.22
60 19 0.11
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (58 bp):
AACTTTACAAAACTACATTTATACCCTTAAACTTTCCAAAAAACACATTTTAACCCTA
Found at i:40679311 original size:115 final size:117
Alignment explanation
Indices: 40679109--40679332 Score: 269
Period size: 115 Copynumber: 1.9 Consensus size: 117
40679099 AAATCATGTT
** * * **
40679109 TTGACTCTTGAACTTCACAAAATTACATTTTTTCCCTTGAACTTTCCAAAAATGGCATTTTAACT
1 TTGACTCTCAAACTTCACAAAATTACATTTTTACCCTTAAACTTTCCAAAAATCACATTTTAACT
* *
40679174 CCGAACTTCACAAAATTACATTT-TACCCTCAAAC-TTCCAAAACTCACACA
66 CCAAACTTCACAAAACTACATTTATACCCTCAAACTTTCCAAAACTCACACA
* * **
40679224 TTGACTCTCAAACTTTACAAAATTACATTTTTACTCC-TAAATTTTTTAAAAATCACATTTTAAC
1 TTGACTCTCAAACTTCACAAAATTACATTTTTAC-CCTTAAACTTTCCAAAAATCACATTTTAAC
*
40679288 -CCTAAACTTTC-CAAAACTACATTTATACCCTTAAACTTTCCAAAA
65 TCC-AAAC-TTCACAAAACTACATTTATACCCTCAAACTTTCCAAAA
40679333 AACACGTTTT
Statistics
Matches: 91, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
114 2 0.02
115 66 0.73
116 15 0.16
117 8 0.09
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (117 bp):
TTGACTCTCAAACTTCACAAAATTACATTTTTACCCTTAAACTTTCCAAAAATCACATTTTAACT
CCAAACTTCACAAAACTACATTTATACCCTCAAACTTTCCAAAACTCACACA
Found at i:40679355 original size:30 final size:29
Alignment explanation
Indices: 40679271--40679392 Score: 92
Period size: 30 Copynumber: 4.1 Consensus size: 29
40679261 TAAATTTTTT
*
40679271 AAAAATCACATTTTAACCCT-AAACTTTCC
1 AAAAAACAC-TTTTAACCCTCAAACTTTCC
* *
40679300 --AAAACTACATTTATACCCTTAAACTTTCC
1 AAAAAAC-ACTTTTA-ACCCTCAAACTTTCC
*
40679329 AAAAAACACGTTTTAACCCTCGAACTTAT-C
1 AAAAAACAC-TTTTAACCCTCAAACTT-TCC
* *
40679359 AAAAATCACCTTTTGACCC-CTAAACTTTCC
1 AAAAAACA-CTTTTAACCCTC-AAACTTTCC
40679389 AAAA
1 AAAA
40679393 TCACATTTGT
Statistics
Matches: 75, Mismatches: 8, Indels: 19
0.74 0.08 0.19
Matches are distributed among these distances:
27 8 0.11
28 7 0.09
29 11 0.15
30 38 0.51
31 11 0.15
ACGTcount: A:0.40, C:0.28, G:0.02, T:0.30
Consensus pattern (29 bp):
AAAAAACACTTTTAACCCTCAAACTTTCC
Found at i:40685521 original size:132 final size:132
Alignment explanation
Indices: 40685284--40685553 Score: 531
Period size: 132 Copynumber: 2.0 Consensus size: 132
40685274 CCATAAGCGT
40685284 CGTACCTCATCGTTAAAAGATTACTCCAACCTTGACCAAGCCTCAAATTTAAAATGTTTAGAATT
1 CGTACCTCATCGTTAAAAGATTACTCCAACCTTGACCAAGCCTCAAATTTAAAATGTTTAGAATT
40685349 CTGATAGTTTCCTTTTTCCAAGTTAATGAGAATGGGACAATGATCAGAATGGGGATAAGGTAGGT
66 CTGATAGTTTCCTTTTTCCAAGTTAATGAGAATGGGACAATGATCAGAATGGGGATAAGGTAGGT
40685414 GA
131 GA
*
40685416 CGTACCTCATCGTTAAAAGATTTCTCCAACCTTGACCAAGCCTCAAATTTAAAATGTTTAGAATT
1 CGTACCTCATCGTTAAAAGATTACTCCAACCTTGACCAAGCCTCAAATTTAAAATGTTTAGAATT
40685481 CTGATAGTTTCCTTTTTCCAAGTTAATGAGAATGGGACAATGATCAGAATGGGGATAAGGTAGGT
66 CTGATAGTTTCCTTTTTCCAAGTTAATGAGAATGGGACAATGATCAGAATGGGGATAAGGTAGGT
40685546 GA
131 GA
40685548 CGTACC
1 CGTACC
40685554 AAATAATTCG
Statistics
Matches: 137, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
132 137 1.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (132 bp):
CGTACCTCATCGTTAAAAGATTACTCCAACCTTGACCAAGCCTCAAATTTAAAATGTTTAGAATT
CTGATAGTTTCCTTTTTCCAAGTTAATGAGAATGGGACAATGATCAGAATGGGGATAAGGTAGGT
GA
Found at i:40694599 original size:17 final size:17
Alignment explanation
Indices: 40694577--40694610 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40694567 GGTTGATATG
* *
40694577 GAAAATGTTATTGAAAT
1 GAAAATGCTATTAAAAT
40694594 GAAAATGCTATTAAAAT
1 GAAAATGCTATTAAAAT
40694611 AACGAGTGAT
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:0.03, G:0.15, T:0.32
Consensus pattern (17 bp):
GAAAATGCTATTAAAAT
Found at i:40703001 original size:22 final size:22
Alignment explanation
Indices: 40702944--40703002 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
40702934 TAATACAAAA
*
40702944 TGGATAAACCACTC-AACGATG
1 TGGATAAACAACTCAAACGATG
** ** *
40702965 CAGATAAACTGCTCAAACGGTG
1 TGGATAAACAACTCAAACGATG
40702987 TGGATAAACAACTCAA
1 TGGATAAACAACTCAA
40703003 TGGTGCAGAT
Statistics
Matches: 28, Mismatches: 9, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
21 10 0.36
22 18 0.64
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.19
Consensus pattern (22 bp):
TGGATAAACAACTCAAACGATG
Found at i:40703022 original size:21 final size:21
Alignment explanation
Indices: 40702946--40703022 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
40702936 ATACAAAATG
* *
40702946 GATAAACCACTCAACGATGCA
1 GATAAACTACTCAACGGTGCA
* **
40702967 GATAAACTGCTCAAACGGTGTG
1 GATAAACTACTC-AACGGTGCA
* *
40702989 GATAAACAACTCAATGGTGCA
1 GATAAACTACTCAACGGTGCA
*
40703010 GATAAACTTCTCA
1 GATAAACTACTCA
40703023 CACTTCCTCC
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
21 27 0.63
22 16 0.37
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (21 bp):
GATAAACTACTCAACGGTGCA
Found at i:40709102 original size:20 final size:19
Alignment explanation
Indices: 40709079--40709117 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
40709069 CTAATCATTA
*
40709079 TATTCAATATTTATTAATTT
1 TATTCAAT-TTTAATAATTT
*
40709099 TATTTAATTTTAATAATTT
1 TATTCAATTTTAATAATTT
40709118 ATATCTATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTCAATTTTAATAATTT
Found at i:40709222 original size:18 final size:19
Alignment explanation
Indices: 40709196--40709231 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
40709186 TATAATTAAA
40709196 TTTAATATTT-TAAAATTT
1 TTTAATATTTATAAAATTT
*
40709214 TTTATTATTTATAAAATT
1 TTTAATATTTATAAAATT
40709232 CATCACATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTAATATTTATAAAATTT
Found at i:40713199 original size:13 final size:13
Alignment explanation
Indices: 40713181--40713206 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40713171 TTTTTGTCGA
40713181 AACTTGTCAATTT
1 AACTTGTCAATTT
40713194 AACTTGTCAATTT
1 AACTTGTCAATTT
40713207 TTTAAATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (13 bp):
AACTTGTCAATTT
Found at i:40713350 original size:25 final size:27
Alignment explanation
Indices: 40713322--40713389 Score: 69
Period size: 25 Copynumber: 2.7 Consensus size: 27
40713312 ATTTTTCAAC
40713322 ATTTTTATTGGTTAAAATAT-T-TATT
1 ATTTTTATTGGTTAAAATATATATATT
*
40713347 ATTTTAATT-G--AAAATTATATATATT
1 ATTTTTATTGGTTAAAA-TATATATATT
40713372 A-TTTT-TTGGTTAAAATAT
1 ATTTTTATTGGTTAAAATAT
40713390 GTTGTTAGTC
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
22 4 0.11
23 5 0.14
24 6 0.17
25 16 0.46
26 4 0.11
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (27 bp):
ATTTTTATTGGTTAAAATATATATATT
Found at i:40715731 original size:17 final size:16
Alignment explanation
Indices: 40715700--40715802 Score: 82
Period size: 17 Copynumber: 6.0 Consensus size: 16
40715690 ATTTTAAGAT
40715700 TTATTTTAAGA-TTAAA
1 TTATTTTAA-ATTTAAA
*
40715716 TTGATTTTGAATTTAAA
1 TT-ATTTTAAATTTAAA
40715733 TTATTTTAAATTTAAA
1 TTATTTTAAATTTAAA
** *
40715749 TTTAAATTAAATTTAGAT
1 -TTATTTTAAATTTA-AA
40715767 TTATATTTAAATTTAAAA
1 TTAT-TTTAAATTT-AAA
*
40715785 CTTATTATAAATATTAAA
1 -TTATTTTAAAT-TTAAA
40715803 AGTTAAGTGT
Statistics
Matches: 70, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
16 16 0.23
17 28 0.40
18 19 0.27
19 7 0.10
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (16 bp):
TTATTTTAAATTTAAA
Found at i:40715745 original size:7 final size:6
Alignment explanation
Indices: 40715725--40715783 Score: 70
Period size: 6 Copynumber: 10.3 Consensus size: 6
40715715 ATTGATTTTG
* *
40715725 AATTTA AA-TT- ATTTTA AATTTA AATTTA AA-TTA AATTTA GATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
40715770 TATTTA AATTTA AA
1 AATTTA AATTTA AA
40715784 ACTTATTATA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
4 1 0.02
5 9 0.20
6 35 0.78
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (6 bp):
AATTTA
Found at i:40715763 original size:23 final size:22
Alignment explanation
Indices: 40715725--40715779 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 22
40715715 ATTGATTTTG
*
40715725 AATTTAAATTATTTTAAATTTA
1 AATTTAAATTAATTTAAATTTA
*
40715747 AATTTAAATTAAATTTAGATTTA
1 AATTTAAATT-AATTTAAATTTA
*
40715770 TATTTAAATT
1 AATTTAAATT
40715780 TAAAACTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 10 0.34
23 19 0.66
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
AATTTAAATTAATTTAAATTTA
Found at i:40717132 original size:10 final size:10
Alignment explanation
Indices: 40717114--40717158 Score: 81
Period size: 10 Copynumber: 4.5 Consensus size: 10
40717104 AGATCCATCG
*
40717114 TTAAAGTATA
1 TTAATGTATA
40717124 TTAATGTATA
1 TTAATGTATA
40717134 TTAATGTATA
1 TTAATGTATA
40717144 TTAATGTATA
1 TTAATGTATA
40717154 TTAAT
1 TTAAT
40717159 TGTTCAATCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
10 34 1.00
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (10 bp):
TTAATGTATA
Found at i:40720491 original size:13 final size:14
Alignment explanation
Indices: 40720457--40720509 Score: 60
Period size: 13 Copynumber: 4.1 Consensus size: 14
40720447 TTTATGTAAG
*
40720457 TAAAA-ATTATAAA
1 TAAAATATTAGAAA
40720470 -AAAATATTAGAAA
1 TAAAATATTAGAAA
*
40720483 TAAAA-ATTATAAA
1 TAAAATATTAGAAA
40720496 -AAAATATTAGAAA
1 TAAAATATTAGAAA
40720509 T
1 T
40720510 CCTTCATCTG
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
12 8 0.24
13 21 0.64
14 4 0.12
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (14 bp):
TAAAATATTAGAAA
Found at i:40720493 original size:26 final size:26
Alignment explanation
Indices: 40720457--40720509 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
40720447 TTTATGTAAG
40720457 TAAAAATTATAAAAAAATATTAGAAA
1 TAAAAATTATAAAAAAATATTAGAAA
40720483 TAAAAATTATAAAAAAATATTAGAAA
1 TAAAAATTATAAAAAAATATTAGAAA
40720509 T
1 T
40720510 CCTTCATCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (26 bp):
TAAAAATTATAAAAAAATATTAGAAA
Found at i:40721306 original size:10 final size:10
Alignment explanation
Indices: 40721291--40721352 Score: 72
Period size: 10 Copynumber: 6.3 Consensus size: 10
40721281 GTTAATTTTT
40721291 AAAATTATTA
1 AAAATTATTA
40721301 AAAATTATTA
1 AAAATTATTA
* *
40721311 GAAATTGTTA
1 AAAATTATTA
* *
40721321 AATATTATAA
1 AAAATTATTA
40721331 AAAATTATTA
1 AAAATTATTA
*
40721341 GAAATTA-TA
1 AAAATTATTA
40721350 AAA
1 AAA
40721353 GACGTTAAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
9 4 0.10
10 38 0.90
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (10 bp):
AAAATTATTA
Found at i:40721334 original size:30 final size:29
Alignment explanation
Indices: 40721284--40721346 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 29
40721274 AAAATTTGTT
* *
40721284 AATTTTTAAAATTATTAAAAATTATTAGA
1 AATTGTTAAAATTATAAAAAATTATTAGA
40721313 AATTGTTAAATATTATAAAAAATTATTAGA
1 AATTGTTAAA-ATTATAAAAAATTATTAGA
40721343 AATT
1 AATT
40721347 ATAAAAGACG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 9 0.29
30 22 0.71
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (29 bp):
AATTGTTAAAATTATAAAAAATTATTAGA
Found at i:40721362 original size:30 final size:30
Alignment explanation
Indices: 40721300--40721363 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
40721290 TAAAATTATT
* * * *
40721300 AAAAATTATTAGAAATTGTTAAATATTATA
1 AAAAATTATTAGAAATTATAAAAGAGTATA
40721330 AAAAATTATTAGAAATTATAAAAGACGT-TA
1 AAAAATTATTAGAAATTATAAAAGA-GTATA
40721360 AAAA
1 AAAA
40721364 TAAATAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.33
Consensus pattern (30 bp):
AAAAATTATTAGAAATTATAAAAGAGTATA
Found at i:40729825 original size:30 final size:29
Alignment explanation
Indices: 40729785--40729860 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 29
40729775 TGGACATTCA
40729785 GGGG-TAAAATGGTAATTTTT-GAAAGTTTT
1 GGGGTTAAAAT-GTAATTTTTAG-AAGTTTT
40729814 GGGGTTAAAATGTAATTTTTAGAAGTTTT
1 GGGGTTAAAATGTAATTTTTAGAAGTTTT
* * *
40729843 AGGGTCAAAATATAATTT
1 GGGGTTAAAATGTAATTT
40729861 CTGGATAGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
29 35 0.83
30 7 0.17
ACGTcount: A:0.34, C:0.01, G:0.24, T:0.41
Consensus pattern (29 bp):
GGGGTTAAAATGTAATTTTTAGAAGTTTT
Found at i:40731824 original size:17 final size:17
Alignment explanation
Indices: 40731823--40731884 Score: 81
Period size: 17 Copynumber: 3.6 Consensus size: 17
40731813 GAAATAAATT
*
40731823 TAAACTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
40731840 TAAATTTAAATTTTAAAA
1 TAAATTTAAA-TTTAAAA
*
40731858 CAAATTT-AATCTTAAAA
1 TAAATTTAAAT-TTAAAA
40731875 TAAATTTAAA
1 TAAATTTAAA
40731885 ATGAGTTTGG
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
16 1 0.03
17 23 0.59
18 15 0.38
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:40731835 original size:23 final size:23
Alignment explanation
Indices: 40731805--40731849 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
40731795 CATAATAATT
*
40731805 TTAAATTTGAAATAAATTTAAAC
1 TTAAATTTAAAATAAATTTAAAC
40731828 TTAAATTTAAAATAAATTTAAA
1 TTAAATTTAAAATAAATTTAAA
40731850 TTTTAAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
TTAAATTTAAAATAAATTTAAAC
Found at i:40731842 original size:40 final size:41
Alignment explanation
Indices: 40731788--40731873 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 41
40731778 GGACATTATT
* * * *
40731788 TTAAATTCATAATAATTTTAAA-TTTGAAATAAATTTAAAC
1 TTAAATTCAAAATAAATTTAAATTTTAAAACAAATTTAAAC
* *
40731828 TTAAATTTAAAATAAATTTAAATTTTAAAACAAATTTAATC
1 TTAAATTCAAAATAAATTTAAATTTTAAAACAAATTTAAAC
40731869 TTAAA
1 TTAAA
40731874 ATAAATTTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 19 0.49
41 20 0.51
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (41 bp):
TTAAATTCAAAATAAATTTAAATTTTAAAACAAATTTAAAC
Found at i:40731856 original size:7 final size:6
Alignment explanation
Indices: 40731804--40731852 Score: 50
Period size: 6 Copynumber: 8.5 Consensus size: 6
40731794 TCATAATAAT
* *
40731804 TTTAAA TTTGAAA --TAAA TTTAAA CTTAAA TTTAAA -ATAAA TTTAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
40731850 TTT
1 TTT
40731853 TAAAACAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
4 3 0.09
5 5 0.14
6 24 0.69
7 3 0.09
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:40731886 original size:11 final size:11
Alignment explanation
Indices: 40731806--40731849 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
40731796 ATAATAATTT
*
40731806 TAAATTTGAAA
1 TAAATTTAAAA
*
40731817 TAAATTTAAACT
1 TAAATTTAAA-A
40731829 TAAATTTAAAA
1 TAAATTTAAAA
40731840 TAAATTTAAA
1 TAAATTTAAA
40731850 TTTTAAAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:40732636 original size:201 final size:201
Alignment explanation
Indices: 40732290--40733318 Score: 1497
Period size: 201 Copynumber: 5.1 Consensus size: 201
40732280 ATTTGGTCCA
* * * *
40732290 CTTCTCAGTATCTCATCAGGAAGCTGGGGCTCAAAGGTTTGCTCGCATCGAGTGTCAAGTTGGTA
1 CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGGTTTGCTCGCATCGAGCGTCGAGTTGGTA
* * * * * *
40732355 TACTTCTCTGTTTCTCATTAGGAAGATGACTGCCTCAGTTGTTTCAATTCGCTTCTTTGTACCTC
66 TACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATTCGCTTCTCTGTGCCTC
*
40732420 ATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACTTC
131 ATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTACTTC
40732485 GACCTG
196 GACCTG
* * *
40732491 CTTCTCAGTATCTCATCAGAAAGCTGGGGTTCGAAGGTTTGCTCGCACCGAACGTCGAGTTGGTA
1 CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGGTTTGCTCGCATCGAGCGTCGAGTTGGTA
*
40732556 TACTTCTCTGTATCTCATCAGGAAGATGACCACCTCACTTGTTTCAATTCGCTTCTCTGTGCCTC
66 TACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATTCGCTTCTCTGTGCCTC
* *
40732621 ATCAGAAATACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTACTTC
131 ATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTACTTC
40732686 GACCTG
196 GACCTG
* * *
40732692 CTTTTCAATATCTCATCAGGAAGCTGGGGTTCGAAGGTTTGCTCGTATCGAGCGTCGAGTTGGTA
1 CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGGTTTGCTCGCATCGAGCGTCGAGTTGGTA
* * ** * * * **
40732757 TACTTCTCAGTATCTCATC-GAGAAGATGACCGCGTCACTTGTTTTGATCCACTTCTCTTTGTTT
66 TACTTCTCTGTATCTCATCAG-GAAGATGACCGCCTCACTTGTTTCAATTCGCTTCTCTGTGCCT
* * *
40732821 CATCAAGAAGACGAATTTGGTCCACTTCTCAATATCTCATCAAGAAGCTAACTATTTTATTACTT
130 CATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTACTT
40732886 CGACCTG
195 CGACCTG
* * * *
40732893 CTTCTCAGTATCTCATCAGGAAGCTGAGGTTTGATGGTTTGCTCGCATTGAGCGTCGAGTTGGTA
1 CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGGTTTGCTCGCATCGAGCGTCGAGTTGGTA
* * *
40732958 TACTTCTCTGTATCTCATCAGAAAGATGACCGCCTCACTTGTTTCATTTCGCTTCTCTGTACCTC
66 TACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATTCGCTTCTCTGTGCCTC
* * *
40733023 ATCAGGAAGAAGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACTATTTTATTACTTT
131 ATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTACTTC
40733088 GACCTG
196 GACCTG
* * * * *
40733094 CTTCTCAGTATCTCATCAAGAAGTTAGGGTTCGAAGGTTCGTTCGCATCGAGCGTCGAGTTGGTA
1 CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGGTTTGCTCGCATCGAGCGTCGAGTTGGTA
* * *
40733159 TACTTCTCTGTATCTCATCAGGAAGATGATCGCCTCACTTGTTTCAATTTG-TT-TCTCTGCACT
66 TACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATTCGCTTCTCTGTGC-CT
** * * * * *
40733222 CATCAGGTGGATGAATTTGGTCCACTTCTTAGTATCTCATCAGGAAGCTAACCATTTTATTGCAT
130 CATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTACTT
*
40733287 CGACCCG
195 CGACCTG
40733294 CTTCTCAGTATCTCATCAGGAAGCT
1 CTTCTCAGTATCTCATCAGGAAGCT
40733319 AACCATTTTA
Statistics
Matches: 737, Mismatches: 88, Indels: 7
0.89 0.11 0.01
Matches are distributed among these distances:
199 5 0.01
200 90 0.12
201 641 0.87
202 1 0.00
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (201 bp):
CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGGTTTGCTCGCATCGAGCGTCGAGTTGGTA
TACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATTCGCTTCTCTGTGCCTC
ATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTACTTC
GACCTG
Found at i:40733317 original size:48 final size:48
Alignment explanation
Indices: 40733246--40733366 Score: 224
Period size: 48 Copynumber: 2.5 Consensus size: 48
40733236 ATTTGGTCCA
*
40733246 CTTCTTAGTATCTCATCAGGAAGCTAACCATTTTATTGCATCGACCCG
1 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCATCGACCCG
40733294 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCATCGACCCG
1 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCATCGACCCG
*
40733342 CTTCTCAGTATCTCATTAGGAAGCT
1 CTTCTCAGTATCTCATCAGGAAGCT
40733367 GGGATTCGAA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
48 71 1.00
ACGTcount: A:0.25, C:0.27, G:0.15, T:0.33
Consensus pattern (48 bp):
CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCATCGACCCG
Found at i:40733347 original size:248 final size:248
Alignment explanation
Indices: 40733046--40733612 Score: 814
Period size: 248 Copynumber: 2.3 Consensus size: 248
40733036 ATTTGGTCCA
* * * * *
40733046 CTTCTCAGTATCTCATCAAGAAGCTAACTATTTTATTACTTTGACCTGCTTCTCAGTATCTCATC
1 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCCGCTTCTCAGTATCTCATC
* * * * * *
40733111 AAGAAGTTAGGG-TTCGAAGGTTCGTTCGCATCGAGCGTCGAGTTGGTATACTTCTCTGTATCTC
66 AAGAAGCT-GGGATTCGAAGATTCGCTCACATCGAGCGTAG-GTTGGCATACTTCTCTGTATCTC
* * * * ** *
40733175 ATCAGGAAGATGATCGCCTCACTTGTTTCAATTTGTTTCTCTGCA-CTCATCAGGTGGATGAATT
129 ATCAGGAAGAGGACCACCTCACTTGTTTCAATTTGCTTCTCTGCACCTCATCAGGAAGACGAATT
*
40733239 TGGTCCACTTCTTAGTATCTCATCAGGAAGCTAACCATTTTATTGCATCGACCCG
194 TGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCATCGACCCG
* *
40733294 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCATCGACCCGCTTCTCAGTATCTCATT
1 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCCGCTTCTCAGTATCTCATC
* * *
40733359 AGGAAGCTGGGATTCGAAGATTTGCTCATATCGAGCGTAGGTTGGCATACTTCTCTGTATCTCAT
66 AAGAAGCTGGGATTCGAAGATTCGCTCACATCGAGCGTAGGTTGGCATACTTCTCTGTATCTCAT
** * *
40733424 CAGGAAGAGGACCATTTCACTTGTTTCAATTTGCTTCTCTGTACCTCATTAGGAAGACGAATTTG
131 CAGGAAGAGGACCACCTCACTTGTTTCAATTTGCTTCTCTGCACCTCATCAGGAAGACGAATTTG
*
40733489 GTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCCG
196 GTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCATCGACCCG
* * *
40733542 TTTCTCAGTATCTCATTAGGAAGCTAACCATTTTATTGCTTCGACTCGCTTCTCAGTATCTCATC
1 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCCGCTTCTCAGTATCTCATC
40733607 AAGAAG
66 AAGAAG
40733613 ATGATCGCAT
Statistics
Matches: 282, Mismatches: 35, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
247 63 0.22
248 219 0.78
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.35
Consensus pattern (248 bp):
CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCCGCTTCTCAGTATCTCATC
AAGAAGCTGGGATTCGAAGATTCGCTCACATCGAGCGTAGGTTGGCATACTTCTCTGTATCTCAT
CAGGAAGAGGACCACCTCACTTGTTTCAATTTGCTTCTCTGCACCTCATCAGGAAGACGAATTTG
GTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCATCGACCCG
Found at i:40733566 original size:48 final size:48
Alignment explanation
Indices: 40733494--40733612 Score: 202
Period size: 48 Copynumber: 2.5 Consensus size: 48
40733484 ATTTGGTCCA
40733494 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCCG
1 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCCG
* * *
40733542 TTTCTCAGTATCTCATTAGGAAGCTAACCATTTTATTGCTTCGACTCG
1 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCCG
*
40733590 CTTCTCAGTATCTCATCAAGAAG
1 CTTCTCAGTATCTCATCAGGAAG
40733613 ATGATCGCAT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 65 1.00
ACGTcount: A:0.24, C:0.26, G:0.14, T:0.35
Consensus pattern (48 bp):
CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCCG
Found at i:40733801 original size:39 final size:38
Alignment explanation
Indices: 40733680--40733805 Score: 114
Period size: 39 Copynumber: 3.2 Consensus size: 38
40733670 GTTTATGATG
40733680 ATCTGCCCCAGGTTCGGGGTAAAAGATCGAATGGCTTCA
1 ATCTGCCCCAGGTTCGGGGTAAAAGATC-AATGGCTTCA
* * * * *
40733719 ATCTACCCCAAGTTCGGGGTAAGAGAT---TGGTTGATGA
1 ATCTGCCCCAGGTTCGGGGTAAAAGATCAATGGCT--TCA
* *
40733756 TGATCTGCTCCAGGCTCGGGGTAAAAGATCAAATGGCTTCA
1 --ATCTGCCCCAGGTTCGGGGTAAAAGATC-AATGGCTTCA
40733797 ATCTGCCCC
1 ATCTGCCCC
40733806 TTACTCGGGG
Statistics
Matches: 66, Mismatches: 13, Indels: 16
0.69 0.14 0.17
Matches are distributed among these distances:
35 4 0.06
37 2 0.03
39 54 0.82
41 2 0.03
43 4 0.06
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (38 bp):
ATCTGCCCCAGGTTCGGGGTAAAAGATCAATGGCTTCA
Found at i:40733814 original size:78 final size:78
Alignment explanation
Indices: 40733664--40733820 Score: 235
Period size: 78 Copynumber: 2.0 Consensus size: 78
40733654 TTAGGGTAGT
* * *
40733664 AGATTGGTTTATGATGATCTGCCCCAGGTTCGGGGTAAAAGATCGAATGGCTTCAATCTACCCCA
1 AGATTGGTTGATGATGATCTGCCCCAGGCTCGGGGTAAAAGATCAAATGGCTTCAATCTACCCCA
*
40733729 AGTTCGGGGTAAG
66 AGCTCGGGGTAAG
* *
40733742 AGATTGGTTGATGATGATCTGCTCCAGGCTCGGGGTAAAAGATCAAATGGCTTCAATCTGCCCCT
1 AGATTGGTTGATGATGATCTGCCCCAGGCTCGGGGTAAAAGATCAAATGGCTTCAATCTACCCC-
*
40733807 TA-CTCGGGGTAAG
65 AAGCTCGGGGTAAG
40733820 A
1 A
40733821 TATCAGAATC
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
78 70 0.99
79 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (78 bp):
AGATTGGTTGATGATGATCTGCCCCAGGCTCGGGGTAAAAGATCAAATGGCTTCAATCTACCCCA
AGCTCGGGGTAAG
Found at i:40734218 original size:101 final size:100
Alignment explanation
Indices: 40734083--40734392 Score: 279
Period size: 101 Copynumber: 3.1 Consensus size: 100
40734073 CAAATCTTCG
* *
40734083 TGGTACTGGATCTACC-TTCGCGG-CTTAGATCTTTCTCTTCATGTCTTC-ATGGTAC-TGAATC
1 TGGTACTGGATCCACCGTT-GCGGTCTTAGATCTTTCTCTTCATGTCTTCTA-GGTACACG-ATC
* * * *
40734144 CACTGTTACTATCTTAGATCTTTCCCTTCTGTCTTTTTA
63 CACCGTTACGA-CTTAGACCTTTCCCTTCTGCCTTTTTA
* **
40734183 TGGTACTGGATCCACCGTTGCGGTCTTAGATCTTTCTCGTCATGTCTTCTGAGGTACACGATCTG
1 TGGTACTGGATCCACCGTTGCGGTCTTAGATCTTTCTCTTCATGTCTTCT-AGGTACACGATCCA
* * *
40734248 CCGTTGCGACTTAGACCTTTCCCTTTTGCCTTTTTG
65 CCGTTACGACTTAGACCTTTCCCTTCTGCCTTTTTA
** * * * * * *
40734284 CAGTACTAGATCCGCCGTTGCGGTCTTAGATCTTT-TCTGTCGTGTCTTTTAAGGTACACGGTCT
1 TGGTACTGGATCCACCGTTGCGGTCTTAGATCTTTCTCT-TCATGTCTTCT-AGGTACACGATCC
* ** * * * *
40734348 GCCGTTGTGACTTAGACCTTTCCTTTTTGTCTTTTTG
64 ACCGTTACGACTTAGACCTTTCCCTTCTGCCTTTTTA
40734385 TGGTACTG
1 TGGTACTG
40734393 AGACCTATAG
Statistics
Matches: 177, Mismatches: 27, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
100 21 0.12
101 140 0.79
102 14 0.08
103 2 0.01
ACGTcount: A:0.14, C:0.25, G:0.20, T:0.42
Consensus pattern (100 bp):
TGGTACTGGATCCACCGTTGCGGTCTTAGATCTTTCTCTTCATGTCTTCTAGGTACACGATCCAC
CGTTACGACTTAGACCTTTCCCTTCTGCCTTTTTA
Found at i:40734239 original size:51 final size:51
Alignment explanation
Indices: 40734084--40734340 Score: 163
Period size: 51 Copynumber: 5.1 Consensus size: 51
40734074 AAATCTTCGT
* * *
40734084 GGTACTGGATCTACC-TTCGCGG-CTTAGATCTTTCTCTTCATGTC--TTCA
1 GGTACTGGATCCACCGTT-GCGGTCTTAGATCTTTCTCGTCATGTCTTTTGA
* * * ** * * *
40734132 TGGTACTGAATCCACTGTTACTATCTTAGATCTTTCCCTTC-TGTCTTTTTA
1 -GGTACTGGATCCACCGTTGCGGTCTTAGATCTTTCTCGTCATGTCTTTTGA
*
40734183 TGGTACTGGATCCACCGTTGCGGTCTTAGATCTTTCTCGTCATGTCTTCTGA
1 -GGTACTGGATCCACCGTTGCGGTCTTAGATCTTTCTCGTCATGTCTTTTGA
** ** * * * ** *
40734235 GGTACACGATCTGCCGTTGC-GACTTAGACCTTTC-CCTTTTGCCTTTTTGCA
1 GGTACTGGATCCACCGTTGCGGTCTTAGATCTTTCTCGTCATGTC-TTTTG-A
* * * *
40734286 -GTACTAGATCCGCCGTTGCGGTCTTAGATCTTT-TCTGTCGTGTCTTTTAA
1 GGTACTGGATCCACCGTTGCGGTCTTAGATCTTTCTC-GTCATGTCTTTTGA
40734336 GGTAC
1 GGTAC
40734341 ACGGTCTGCC
Statistics
Matches: 159, Mismatches: 38, Indels: 20
0.73 0.18 0.09
Matches are distributed among these distances:
49 22 0.14
50 51 0.32
51 74 0.47
52 12 0.08
ACGTcount: A:0.15, C:0.25, G:0.19, T:0.40
Consensus pattern (51 bp):
GGTACTGGATCCACCGTTGCGGTCTTAGATCTTTCTCGTCATGTCTTTTGA
Found at i:40734390 original size:50 final size:50
Alignment explanation
Indices: 40734232--40734390 Score: 153
Period size: 50 Copynumber: 3.2 Consensus size: 50
40734222 TCATGTCTTC
* *
40734232 TGAGGTACACGATCTGCCGTTGCGACTTAGACCTTTCCCTTTTGCCTTTT
1 TGAGGTACACGATCTGCCGTTGCGACTTAGACCTTTCCTTTTTGTCTTTT
* * * * **
40734282 TGCA-GTACTA-GATCCGCCGTTGCGGTCTTAGATCTTTTCTGTCGTGTC-TTT
1 TG-AGGTAC-ACGATCTGCCGTTGC-GACTTAGACCTTTCCT-TTTTGTCTTTT
* * *
40734333 TAAGGTACACGGTCTGCCGTTGTGACTTAGACCTTTCCTTTTTGTCTTTT
1 TGAGGTACACGATCTGCCGTTGCGACTTAGACCTTTCCTTTTTGTCTTTT
*
40734383 TGTGGTAC
1 TGAGGTAC
40734391 TGAGACCTAT
Statistics
Matches: 83, Mismatches: 19, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
49 5 0.06
50 42 0.51
51 32 0.39
52 4 0.05
ACGTcount: A:0.13, C:0.24, G:0.22, T:0.41
Consensus pattern (50 bp):
TGAGGTACACGATCTGCCGTTGCGACTTAGACCTTTCCTTTTTGTCTTTT
Found at i:40735624 original size:22 final size:20
Alignment explanation
Indices: 40735594--40735658 Score: 71
Period size: 20 Copynumber: 3.1 Consensus size: 20
40735584 CACCTCGACC
*
40735594 TCTCCTTTTCTCTTTCTTTTAT
1 TCTCTTTTTCT-TTTCTTTT-T
40735616 TCTCTTTTT-TTTGT-TTTTT
1 TCTCTTTTTCTTT-TCTTTTT
40735635 CTCTCTTTTTCTTTTCTTTTT
1 -TCTCTTTTTCTTTTCTTTTT
40735656 TCT
1 TCT
40735659 TTTCTTTTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
19 1 0.03
20 19 0.50
21 10 0.26
22 8 0.21
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (20 bp):
TCTCTTTTTCTTTTCTTTTT
Found at i:40735638 original size:18 final size:17
Alignment explanation
Indices: 40735610--40735666 Score: 51
Period size: 19 Copynumber: 3.1 Consensus size: 17
40735600 TTTCTCTTTC
*
40735610 TTTTATTCTCTTTTTTT
1 TTTTTTTCTCTTTTTTT
40735627 TGTTTTTTCTCTCTTTTTCT
1 T-TTTTTTCTCT-TTTTT-T
*
40735647 TTTCTTTTTTCTTTTCTTT
1 TTT-TTTTCTCTTTT-TTT
40735666 T
1 T
40735667 ATTCATTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
17 1 0.03
18 9 0.27
19 12 0.36
20 11 0.33
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.81
Consensus pattern (17 bp):
TTTTTTTCTCTTTTTTT
Found at i:40735639 original size:20 final size:22
Alignment explanation
Indices: 40735593--40735658 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
40735583 TCACCTCGAC
* *
40735593 CTCTCCTTTTCTCTTTCTTTTAT
1 CTCTCTTTTTCT-TTTCTTTTTT
*
40735616 -TCTC-TTTT-TTTTGTTTTTT
1 CTCTCTTTTTCTTTTCTTTTTT
40735635 CTCTCTTTTTCTTTTCTTTTTT
1 CTCTCTTTTTCTTTTCTTTTTT
40735657 CT
1 CT
40735659 TTTCTTTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
19 8 0.22
20 5 0.14
21 8 0.22
22 16 0.43
ACGTcount: A:0.02, C:0.23, G:0.02, T:0.74
Consensus pattern (22 bp):
CTCTCTTTTTCTTTTCTTTTTT
Found at i:40735657 original size:12 final size:12
Alignment explanation
Indices: 40735599--40735666 Score: 64
Period size: 14 Copynumber: 5.2 Consensus size: 12
40735589 CGACCTCTCC
40735599 TTTTCTCTTTCTT
1 TTTTCT-TTTCTT
*
40735612 TTATTCTCTTTTTT
1 TT-TTCT-TTTCTT
*
40735626 TTGTTTTTTCTCTCT
1 TT-TTCTTT-TCT-T
40735641 TTTTCTTTTCTT
1 TTTTCTTTTCTT
40735653 TTTTCTTTTCTT
1 TTTTCTTTTCTT
40735665 TT
1 TT
40735667 ATTCATTGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
12 15 0.32
13 7 0.15
14 22 0.47
15 3 0.06
ACGTcount: A:0.01, C:0.18, G:0.01, T:0.79
Consensus pattern (12 bp):
TTTTCTTTTCTT
Found at i:40741098 original size:28 final size:29
Alignment explanation
Indices: 40741057--40741133 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
40741047 ATCGGGATCA
* *
40741057 AAAATGG-AATTTTTGGACA-TCCGGGGGT
1 AAAATGGTAA-TTTTGGAAAGTCCGAGGGT
* **
40741085 AAAATGGTAATTTTTGAAAGTTTGAGGGT
1 AAAATGGTAATTTTGGAAAGTCCGAGGGT
40741114 AAAATGGTAATTTT-GAAAGT
1 AAAATGGTAATTTTGGAAAGT
40741134 TTCGAGGTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 20 0.48
29 22 0.52
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.34
Consensus pattern (29 bp):
AAAATGGTAATTTTGGAAAGTCCGAGGGT
Found at i:40741113 original size:29 final size:29
Alignment explanation
Indices: 40741081--40741375 Score: 200
Period size: 29 Copynumber: 10.1 Consensus size: 29
40741071 GGACATCCGG
40741081 GGGT-AAAATGGTAATTTTTGAAAGTTTGA
1 GGGTAAAAAT-GTAATTTTTGAAAGTTTGA
40741110 GGGT-AAAATGGTAA-TTTTGAAAGTTTCGA
1 GGGTAAAAAT-GTAATTTTTGAAAGTTT-GA
* * *
40741139 -GGTCAAAAATAG-AATTTTTGGAAGCTCGA
1 GGGT-AAAAAT-GTAATTTTTGAAAGTTTGA
* * *
40741168 GGGGTAAAAATGTAAATTTTGGAAGTTTAA
1 -GGGTAAAAATGTAATTTTTGAAAGTTTGA
40741198 GGGTAAAAATGTAATTTTT-AGAAGTTTCG-
1 GGGTAAAAATGTAATTTTTGA-AAGTTT-GA
* * * * *
40741227 TGATCAAAAATGGAATTTTT-AGAAGTTCGG
1 GGGT-AAAAATGTAATTTTTGA-AAGTTTGA
* ** *
40741257 GGGCAAAAAAATAATTTTT-AGAAGTTTTA
1 GGGTAAAAATGTAATTTTTGA-AAGTTTGA
*
40741286 GGGTTAAAAATGTAATTTTTGGAAGTTTG-
1 GGG-TAAAAATGTAATTTTTGAAAGTTTGA
* *
40741315 GGGAAAAAATGTAATTTTTGGAAGTTTCG-
1 GGGTAAAAATGTAATTTTTGAAAGTTT-GA
* *
40741344 GGGTCAAAATATAATTTTTGAATAGTTT-A
1 GGGTAAAAATGTAATTTTTGAA-AGTTTGA
40741373 GGG
1 GGG
40741376 ACCTTCAGAG
Statistics
Matches: 216, Mismatches: 34, Indels: 32
0.77 0.12 0.11
Matches are distributed among these distances:
28 38 0.18
29 95 0.44
30 80 0.37
31 3 0.01
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.35
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTTGAAAGTTTGA
Found at i:40741148 original size:59 final size:59
Alignment explanation
Indices: 40741081--40741372 Score: 167
Period size: 59 Copynumber: 5.0 Consensus size: 59
40741071 GGACATCCGG
*
40741081 GGGT-AAAATGGTAATTTTTGAAAGTTTGA-GGGT-AAAATGGT-AATTTTGAAAGTTT-C
1 GGGTAAAAAT-GTAATTTTTGAAAGTTTGAGGGGTAAAAAT-GTAAATTTTGAAAGTTTAA
* * * *
40741137 GAGGTCAAAAATAG-AATTTTTGGAAGCTCGAGGGGTAAAAATGTAAATTTTGGAAGTTTAA
1 G-GGT-AAAAAT-GTAATTTTTGAAAGTTTGAGGGGTAAAAATGTAAATTTTGAAAGTTTAA
* * * * * ***
40741198 GGGTAAAAATGTAATTTTT-AGAAGTTT-CGTGATCAAAAATG-GAATTTTTAGAAGTTCGG
1 GGGTAAAAATGTAATTTTTGA-AAGTTTGAGGGGT-AAAAATGTAAATTTTGA-AAGTTTAA
* ** * * * * *
40741257 GGGCAAAAAAATAATTTTT-AGAAGTTTTAGGGTTAAAAATGTAATTTTTGGAAGTTT-G
1 GGGTAAAAATGTAATTTTTGA-AAGTTTGAGGGGTAAAAATGTAAATTTTGAAAGTTTAA
* * * * * *
40741315 GGGAAAAAATGTAATTTTTGGAAGTTT-CGGGGTCAAAATATAATTTTTGAATAGTTTA
1 GGGTAAAAATGTAATTTTTGAAAGTTTGAGGGGTAAAAATGTAAATTTTGAA-AGTTTA
40741373 GGGACCTTCA
Statistics
Matches: 182, Mismatches: 38, Indels: 29
0.73 0.15 0.12
Matches are distributed among these distances:
56 1 0.01
57 22 0.12
58 52 0.29
59 77 0.42
60 29 0.16
61 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (59 bp):
GGGTAAAAATGTAATTTTTGAAAGTTTGAGGGGTAAAAATGTAAATTTTGAAAGTTTAA
Found at i:40741236 original size:89 final size:88
Alignment explanation
Indices: 40741052--40741372 Score: 323
Period size: 88 Copynumber: 3.6 Consensus size: 88
40741042 GAAAAATCGG
* * *
40741052 GATCAAAAATGGAATTTTTGGACATC-CGGGGGT-AAAATGGTAATTTTTGAAAGTTTGAGGGT-
1 GATCAAAAATGGAATTTTTGGA-AGCTCGGGGGTAAAAAT-GTAATTTTTGGAAGTTTAAGGGTA
*
40741114 AAAATGGTAATTTTGA-AAGTTTCGA
64 AAAAT-GTAATTTTTAGAAGTTTCGA
* * *
40741139 GGTCAAAAATAGAATTTTTGGAAGCTCGAGGGGTAAAAATGTAAATTTTGGAAGTTTAAGGGTAA
1 GATCAAAAATGGAATTTTTGGAAGCTCG-GGGGTAAAAATGTAATTTTTGGAAGTTTAAGGGTAA
*
40741204 AAATGTAATTTTTAGAAGTTTCGT
65 AAATGTAATTTTTAGAAGTTTCGA
* * * ** * *
40741228 GATCAAAAATGGAATTTTTAGAAGTTCGGGGGCAAAAAAATAATTTTTAGAAGTTTTAGGGTTAA
1 GATCAAAAATGGAATTTTTGGAAGCTCGGGGGTAAAAATGTAATTTTTGGAAGTTTAAGGG-TAA
* * *
40741293 AAATGTAATTTTTGGAAGTTTGGG
65 AAATGTAATTTTTAGAAGTTTCGA
* * * * *
40741317 GA--AAAAATGTAATTTTTGGAAGTTTC-GGGGTCAAAATATAATTTTTGAATAGTTTA
1 GATCAAAAATGGAATTTTTGGAAG-CTCGGGGGTAAAAATGTAATTTTTGGA-AGTTTA
40741373 GGGACCTTCA
Statistics
Matches: 197, Mismatches: 29, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
86 2 0.01
87 58 0.29
88 69 0.35
89 68 0.35
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.35
Consensus pattern (88 bp):
GATCAAAAATGGAATTTTTGGAAGCTCGGGGGTAAAAATGTAATTTTTGGAAGTTTAAGGGTAAA
AATGTAATTTTTAGAAGTTTCGA
Found at i:40743311 original size:17 final size:16
Alignment explanation
Indices: 40743291--40743430 Score: 95
Period size: 17 Copynumber: 8.4 Consensus size: 16
40743281 TGGACATTAT
*
40743291 TTTAAATTCATAATAAT
1 TTTAAATTCA-AATAAA
*
40743308 TTTAAATTTGAAATAAA
1 TTTAAA-TTCAAATAAA
*
40743325 TTTAAACTCAAATTAAA
1 TTTAAATTCAAA-TAAA
*
40743342 TTTAAATT-TAA-AAA
1 TTTAAATTCAAATAAA
*
40743356 TTTAAATTTAAAATAAA
1 TTTAAA-TTCAAATAAA
* *
40743373 CTTAAATTTAAAATAAA
1 TTTAAA-TTCAAATAAA
* *
40743390 TTTAAATTTTAAAACAAA
1 TTTAAA--TTCAAATAAA
* *
40743408 TTTAATCTTAAAATAAA
1 TTTAA-ATTCAAATAAA
40743425 TTTAAA
1 TTTAAA
40743431 ATGAGTTTGG
Statistics
Matches: 103, Mismatches: 13, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
14 9 0.09
15 2 0.02
16 8 0.08
17 66 0.64
18 18 0.17
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (16 bp):
TTTAAATTCAAATAAA
Found at i:40743346 original size:6 final size:6
Alignment explanation
Indices: 40743308--40743398 Score: 75
Period size: 6 Copynumber: 15.5 Consensus size: 6
40743298 TCATAATAAT
* *
40743308 TTTAAA TTTGAAA --TAAA TTTAAA CTCAAA -TTAAA TTTAAA TTTAAAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT--AAA
* * *
40743356 TTTAAA TTTAAA -ATAAA CTTAAA TTTAAA -ATAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
40743399 TAAAACAAAT
Statistics
Matches: 69, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
4 3 0.04
5 13 0.19
6 44 0.64
7 3 0.04
8 6 0.09
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:40743358 original size:14 final size:14
Alignment explanation
Indices: 40743339--40743368 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
40743329 AACTCAAATT
40743339 AAATTTAAATTTAA
1 AAATTTAAATTTAA
40743353 AAATTTAAATTTAA
1 AAATTTAAATTTAA
40743367 AA
1 AA
40743369 TAAACTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AAATTTAAATTTAA
Found at i:40743419 original size:35 final size:34
Alignment explanation
Indices: 40743321--40743430 Score: 116
Period size: 35 Copynumber: 3.1 Consensus size: 34
40743311 AAATTTGAAA
* *
40743321 TAAATTTAAACTCAAA-TTAAATTTAAATTTAAAAATT
1 TAAATTTAAA-ACAAACTTAAATTTAAA---ATAAATT
*
40743358 TAAATTTAAAATAAACTTAAATTTAAAATAAATT
1 TAAATTTAAAACAAACTTAAATTTAAAATAAATT
*
40743392 TAAATTTTAAAACAAA-TTTAATCTTAAAATAAATT
1 TAAA-TTTAAAACAAACTTAAAT-TTAAAATAAATT
40743427 TAAA
1 TAAA
40743431 ATGAGTTTGG
Statistics
Matches: 65, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
34 15 0.23
35 26 0.40
36 3 0.05
37 21 0.32
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (34 bp):
TAAATTTAAAACAAACTTAAATTTAAAATAAATT
Found at i:40743421 original size:65 final size:65
Alignment explanation
Indices: 40743291--40743432 Score: 157
Period size: 65 Copynumber: 2.2 Consensus size: 65
40743281 TGGACATTAT
* * ** * **
40743291 TTTAAATTCATAATAATTTTAAATTTGAAATAAATTTAAACTCAAATTAAATTTAAATTTAAAAA
1 TTTAAATTTAAAATAAACTTAAATTTAAAATAAATTTAAACTCAAAACAAATTTAAATTTAAAAA
* *
40743356 TTTAAATTTAAAATAAACTTAAATTTAAAATAAATTTAAATTTTAAAACAAATTT-AATCTT-AA
1 TTTAAATTTAAAATAAACTTAAATTTAAAATAAATTTAAA-CTCAAAACAAATTTAAAT-TTAAA
40743419 AA
64 AA
40743421 --TAAATTTAAAAT
1 TTTAAATTTAAAAT
40743433 GAGTTTGGGC
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
63 12 0.18
65 42 0.64
66 12 0.18
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (65 bp):
TTTAAATTTAAAATAAACTTAAATTTAAAATAAATTTAAACTCAAAACAAATTTAAATTTAAAAA
Found at i:40743432 original size:11 final size:11
Alignment explanation
Indices: 40743310--40743378 Score: 50
Period size: 11 Copynumber: 5.9 Consensus size: 11
40743300 ATAATAATTT
*
40743310 TAAATTTGAAA
1 TAAATTTAAAA
*
40743321 TAAATTTAAAC
1 TAAATTTAAAA
*
40743332 TCAAA-TTAAATT
1 T-AAATTTAAA-A
40743344 TAAATTTAAAAA
1 TAAATTT-AAAA
40743356 TTTAAATTTAAAA
1 --TAAATTTAAAA
*
40743369 TAAACTTAAA
1 TAAATTTAAA
40743379 TTTAAAATAA
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
11 27 0.57
12 6 0.13
13 7 0.15
14 7 0.15
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:40759683 original size:59 final size:59
Alignment explanation
Indices: 40759601--40759842 Score: 199
Period size: 59 Copynumber: 4.0 Consensus size: 59
40759591 AAACAAGTGG
* * * *
40759601 AGGGCTAAATTCCT-AAAAGTAAAAATAGAATGATTAAATTTCAAAAATTGAAAAGAAC
1 AGGGCTAAATTCCTCAGAAGTAAAAGTAGAATGACTAAATTTCAAAAATTGAAAAAAAC
* *
40759659 AGGGACTAAATTCCTCAGAA-TAAAAGTAAAATGACTAAATTTCAAAATTTGAAAGAAAAC
1 AGGG-CTAAATTCCTCAGAAGTAAAAGTAGAATGACTAAATTTCAAAAATTGAAA-AAAAC
* * * * * * * * *
40759719 AAGTGAAGGGTTAAATTCTTC-GAATTAAAACTAGGAGGATTAAAATTCAAAAATTGAAATTAAT
1 ------AGGGCTAAATTCCTCAGAAGTAAAAGTAGAATGACTAAATTTCAAAAATTGAAA--AAA
40759783 A-
58 AC
*
40759784 AGGGCTAAATT-CTCA-AAGTAAAAGTAGAATGGCTAAATTTCAAAAATTGAAAGAAAAC
1 AGGGCTAAATTCCTCAGAAGTAAAAGTAGAATGACTAAATTTCAAAAATTGAAA-AAAAC
40759842 A
1 A
40759843 AGTGAAGGTT
Statistics
Matches: 143, Mismatches: 28, Indels: 26
0.73 0.14 0.13
Matches are distributed among these distances:
57 3 0.02
58 37 0.26
59 50 0.35
60 7 0.05
64 3 0.02
65 36 0.25
66 7 0.05
ACGTcount: A:0.51, C:0.09, G:0.15, T:0.25
Consensus pattern (59 bp):
AGGGCTAAATTCCTCAGAAGTAAAAGTAGAATGACTAAATTTCAAAAATTGAAAAAAAC
Found at i:40759718 original size:124 final size:123
Alignment explanation
Indices: 40759590--40759850 Score: 337
Period size: 124 Copynumber: 2.1 Consensus size: 123
40759580 TGGAATGGAA
* * *
40759590 AAAACAAGTGGAGGGCTAAATTCCTAAAAGTAAAAATAGAATGATTAAATTTCAAAAATTGAAAA
1 AAAACAAGTGAAGGGCTAAATTCCTAAAAGTAAAAATAGAAGGATTAAAATTCAAAAATTGAAAA
* *
40759655 GAA-CAGGGACTAAATTCCTCAGAA-TAAAAGTAAAATGACTAAATTTCAAAATTTGAAAG
66 GAATAAGGG-CTAAATT-CTCA-AAGTAAAAGTAAAATGACTAAATTTCAAAAATTGAAAG
* * ** * * * *
40759714 AAAACAAGTGAAGGGTTAAATTCTTCGAATTAAAACTAGGAGGATTAAAATTCAAAAATTGAAAT
1 AAAACAAGTGAAGGGCTAAATTCCTAAAAGTAAAAATAGAAGGATTAAAATTCAAAAATTGAAAA
* * *
40759779 TAATAAGGGCTAAATTCTCAAAGTAAAAGTAGAATGGCTAAATTTCAAAAATTGAAAG
66 GAATAAGGGCTAAATTCTCAAAGTAAAAGTAAAATGACTAAATTTCAAAAATTGAAAG
40759837 AAAACAAGTGAAGG
1 AAAACAAGTGAAGG
40759851 TTAAATCCTT
Statistics
Matches: 119, Mismatches: 16, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
122 2 0.02
123 50 0.42
124 63 0.53
125 4 0.03
ACGTcount: A:0.51, C:0.09, G:0.17, T:0.24
Consensus pattern (123 bp):
AAAACAAGTGAAGGGCTAAATTCCTAAAAGTAAAAATAGAAGGATTAAAATTCAAAAATTGAAAA
GAATAAGGGCTAAATTCTCAAAGTAAAAGTAAAATGACTAAATTTCAAAAATTGAAAG
Found at i:40759793 original size:29 final size:28
Alignment explanation
Indices: 40759761--40759836 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 28
40759751 AGGAGGATTA
* *
40759761 AAATTCAAAAATTGAAATTAATAAGGGCT
1 AAATTCAAAAATTGAAAGT-AGAAGGGCT
** * * *
40759790 AAATTCTCAAAGTAAAAGTAGAATGGCT
1 AAATTCAAAAATTGAAAGTAGAAGGGCT
40759818 AAATTTCAAAAATTGAAAG
1 AAA-TTCAAAAATTGAAAG
40759837 AAAACAAGTG
Statistics
Matches: 35, Mismatches: 11, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
28 10 0.29
29 25 0.71
ACGTcount: A:0.51, C:0.08, G:0.14, T:0.26
Consensus pattern (28 bp):
AAATTCAAAAATTGAAAGTAGAAGGGCT
Done.