Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A11
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: 113101708
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2797742 characters in sequence are not A, C, G, or T
File 98 of 352
Found at i:31024756 original size:12 final size:13
Alignment explanation
Indices: 31024739--31024772 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
31024729 TAAAGAAGAT
*
31024739 AAATAAAGAT-AA
1 AAATAAAAATAAA
31024751 AAATAAAAATAAA
1 AAATAAAAATAAA
31024764 AAATAAAAA
1 AAATAAAAA
31024773 GTCTTTAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (13 bp):
AAATAAAAATAAA
Found at i:31030851 original size:28 final size:27
Alignment explanation
Indices: 31030794--31030945 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
31030784 TAAATTGTGC
*
31030794 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
31030821 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
31030849 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
31030876 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
* *
31030904 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
31030931 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
31030946 GACTTAATAT
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:31030858 original size:55 final size:55
Alignment explanation
Indices: 31030794--31030945 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
31030784 TAAATTGTGC
*
31030794 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
*
31030849 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* * *
31030904 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
31030946 GACTTAATAT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:31038854 original size:28 final size:27
Alignment explanation
Indices: 31038797--31038948 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
31038787 TAAATTGTGC
*
31038797 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
31038824 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
31038852 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
31038879 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
* *
31038907 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
31038934 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
31038949 GACTTAATAT
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:31038861 original size:55 final size:55
Alignment explanation
Indices: 31038797--31038948 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
31038787 TAAATTGTGC
*
31038797 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
*
31038852 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* * *
31038907 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
31038949 GACTTAATAT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:31042597 original size:15 final size:16
Alignment explanation
Indices: 31042577--31042606 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
31042567 GAAAATTACC
31042577 AAAATGGG-CTAAATA
1 AAAATGGGACTAAATA
31042592 AAAATGGGACTAAAT
1 AAAATGGGACTAAAT
31042607 TGGAATATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.53, C:0.07, G:0.20, T:0.20
Consensus pattern (16 bp):
AAAATGGGACTAAATA
Found at i:31043761 original size:3 final size:3
Alignment explanation
Indices: 31043753--31043778 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
31043743 TGTGGATGGA
31043753 GAG GAG GAG GAG GAG GAG GAG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GA
31043779 AAATATACAT
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:0.00, G:0.65, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:31046124 original size:31 final size:31
Alignment explanation
Indices: 31046080--31046138 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
31046070 TGGTATCACG
31046080 TATAAATTCATCAACTT-TCACTTACTTTGCA
1 TATAAATTCATCAA-TTATCACTTACTTTGCA
*
31046111 TATAAACTT-ATCAATTATTACTTACTTT
1 TATAAA-TTCATCAATTATCACTTACTTT
31046139 CCAAACTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 2 0.08
31 21 0.84
32 2 0.08
ACGTcount: A:0.34, C:0.19, G:0.02, T:0.46
Consensus pattern (31 bp):
TATAAATTCATCAATTATCACTTACTTTGCA
Found at i:31047057 original size:21 final size:20
Alignment explanation
Indices: 31047018--31047057 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
31047008 CAAAATTTGT
*
31047018 ATAACTATCATTAAACATTC
1 ATAACTATCATCAAACATTC
*
31047038 ATAATCTATCATCAATCATT
1 ATAA-CTATCATCAAACATT
31047058 AAAATACATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.42, C:0.20, G:0.00, T:0.38
Consensus pattern (20 bp):
ATAACTATCATCAAACATTC
Found at i:31048691 original size:24 final size:24
Alignment explanation
Indices: 31048659--31048706 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
31048649 TCCACTAAGA
31048659 AAACCTACATAAAAATTCATTACC
1 AAACCTACATAAAAATTCATTACC
31048683 AAACCTACATAAAAATTCATTACC
1 AAACCTACATAAAAATTCATTACC
31048707 CTCACGTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (24 bp):
AAACCTACATAAAAATTCATTACC
Found at i:31048976 original size:19 final size:19
Alignment explanation
Indices: 31048948--31048987 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
31048938 AGTACAAAAG
*
31048948 AAACTAAAAACTAAAATAT
1 AAACTAAAAACAAAAATAT
* *
31048967 AAACTCAAAAGAAAAATAT
1 AAACTAAAAACAAAAATAT
31048986 AA
1 AA
31048988 GATACAGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.70, C:0.10, G:0.03, T:0.17
Consensus pattern (19 bp):
AAACTAAAAACAAAAATAT
Found at i:31051579 original size:16 final size:16
Alignment explanation
Indices: 31051560--31051590 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31051550 GACAAAAGTC
31051560 GAAATGCCGAAAAGCT
1 GAAATGCCGAAAAGCT
*
31051576 GAAATGCCGGAAAGC
1 GAAATGCCGAAAAGC
31051591 CAAAAGTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.19, G:0.29, T:0.10
Consensus pattern (16 bp):
GAAATGCCGAAAAGCT
Found at i:31051850 original size:29 final size:29
Alignment explanation
Indices: 31051811--31051894 Score: 132
Period size: 30 Copynumber: 2.9 Consensus size: 29
31051801 GCATGAATAT
*
31051811 AATGTGATTTGGGTCTAATGGGCCACATA
1 AATGTGATTTGGGCCTAATGGGCCACATA
* *
31051840 AATGTGATTTGGGCCTAAAGAGGCCATATA
1 AATGTGATTTGGGCCTAATG-GGCCACATA
31051870 AATGTGATTTGGGCCTAATGGGCCA
1 AATGTGATTTGGGCCTAATGGGCCA
31051895 TGTGAATATA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 23 0.46
30 27 0.54
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (29 bp):
AATGTGATTTGGGCCTAATGGGCCACATA
Found at i:31051871 original size:30 final size:29
Alignment explanation
Indices: 31051807--31051926 Score: 136
Period size: 29 Copynumber: 4.2 Consensus size: 29
31051797 GTGAGCATGA
*
31051807 ATAT-AATGTGATTTGGGTCTAATGGGCC
1 ATATAAATGTGATTTGGGCCTAATGGGCC
* *
31051835 ACATAAATGTGATTTGGGCCTAAAGAGGCC
1 ATATAAATGTGATTTGGGCCTAATG-GGCC
31051865 ATATAAATGTGATTTGGGCCTAATGGGCC
1 ATATAAATGTGATTTGGGCCTAATGGGCC
* * * * * *
31051894 ATGTGAATAT-AATTGGGTCTAGTGGGCC
1 ATATAAATGTGATTTGGGCCTAATGGGCC
31051922 ATATA
1 ATATA
31051927 CAGGTATGTG
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
28 21 0.27
29 29 0.38
30 27 0.35
ACGTcount: A:0.29, C:0.12, G:0.28, T:0.31
Consensus pattern (29 bp):
ATATAAATGTGATTTGGGCCTAATGGGCC
Found at i:31055641 original size:55 final size:55
Alignment explanation
Indices: 31055545--31055672 Score: 156
Period size: 55 Copynumber: 2.3 Consensus size: 55
31055535 CATGTCACAT
31055545 GCCCGTGTT-TATTTGGCAGGTTCGACCATAGGTGTTTCACACGGGCGTGTCGAAC
1 GCCCGTGTTGT-TTTGGCAGGTTCGACCATAGGTGTTTCACACGGGCGTGTCGAAC
* * *
31055600 -CCCAGTGTTGTTTTGGCAGGTTCGCCCA-CGGT-TCTTCCACACGGGCGTGTCGCAC
1 GCCC-GTGTTGTTTTGGCAGGTTCGACCATAGGTGT-TT-CACACGGGCGTGTCGAAC
*
31055655 GGCCGTGTTGTTTTGGCA
1 GCCCGTGTTGTTTTGGCA
31055673 AGCTTGACCA
Statistics
Matches: 64, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
53 1 0.02
54 8 0.12
55 52 0.81
56 3 0.05
ACGTcount: A:0.12, C:0.27, G:0.31, T:0.30
Consensus pattern (55 bp):
GCCCGTGTTGTTTTGGCAGGTTCGACCATAGGTGTTTCACACGGGCGTGTCGAAC
Found at i:31061055 original size:14 final size:14
Alignment explanation
Indices: 31061036--31061074 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
31061026 TACTTTGCAC
*
31061036 TTGGACTTTGGTAT
1 TTGGACTTTGGAAT
*
31061050 TTGGACTTTGAAAT
1 TTGGACTTTGGAAT
31061064 TTGGA-TTTGGA
1 TTGGACTTTGGA
31061075 TTCTTCTGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.21, C:0.05, G:0.28, T:0.46
Consensus pattern (14 bp):
TTGGACTTTGGAAT
Found at i:31069836 original size:22 final size:22
Alignment explanation
Indices: 31069765--31069828 Score: 128
Period size: 22 Copynumber: 2.9 Consensus size: 22
31069755 CCAAATGGTA
31069765 GTCAATGACAATATCATAATCT
1 GTCAATGACAATATCATAATCT
31069787 GTCAATGACAATATCATAATCT
1 GTCAATGACAATATCATAATCT
31069809 GTCAATGACAATATCATAAT
1 GTCAATGACAATATCATAAT
31069829 TTTTCAATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.31
Consensus pattern (22 bp):
GTCAATGACAATATCATAATCT
Found at i:31077643 original size:27 final size:26
Alignment explanation
Indices: 31077591--31077650 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
31077581 CCACATATAT
*
31077591 ATATCTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
31077617 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
31077644 ATATCTG
1 ATATCTG
31077651 GCAGCCTCCC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:31082790 original size:45 final size:45
Alignment explanation
Indices: 31082726--31082814 Score: 178
Period size: 45 Copynumber: 2.0 Consensus size: 45
31082716 AATTTCAAGA
31082726 GTTCTCCATAGCTAGGGTTTGTTTCAAGCTTCCAAGCTCCATAGG
1 GTTCTCCATAGCTAGGGTTTGTTTCAAGCTTCCAAGCTCCATAGG
31082771 GTTCTCCATAGCTAGGGTTTGTTTCAAGCTTCCAAGCTCCATAG
1 GTTCTCCATAGCTAGGGTTTGTTTCAAGCTTCCAAGCTCCATAG
31082815 TAAGTGATTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.20, C:0.25, G:0.21, T:0.34
Consensus pattern (45 bp):
GTTCTCCATAGCTAGGGTTTGTTTCAAGCTTCCAAGCTCCATAGG
Found at i:31083694 original size:46 final size:46
Alignment explanation
Indices: 31083644--31083769 Score: 198
Period size: 46 Copynumber: 2.7 Consensus size: 46
31083634 TGGTTGAGCA
*
31083644 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
31083690 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
31083736 CCCGAGCTCGATGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
31083770 GGGGCGGGTT
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 73 1.00
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:31084031 original size:19 final size:20
Alignment explanation
Indices: 31083994--31084031 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
31083984 ATAAGGTGGT
31083994 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
31084014 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
31084032 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:31087854 original size:26 final size:27
Alignment explanation
Indices: 31087825--31087884 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
31087815 CCACATATAT
*
31087825 ATATCTGT-TCTGGTGGCCTAGCCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
* * *
31087851 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
31087878 ATATCTG
1 ATATCTG
31087885 GCAGCCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (27 bp):
ATATCTGTATCTGGTGACCTAGCCACA
Found at i:31089950 original size:15 final size:15
Alignment explanation
Indices: 31089928--31089990 Score: 72
Period size: 15 Copynumber: 4.2 Consensus size: 15
31089918 GAAAACCAGA
31089928 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* * *
31089943 ACAGAGAAATCCGAG
1 ATAAAGAAATCCAAG
*
31089958 ATAAAGATATCCAAG
1 ATAAAGAAATCCAAG
* *
31089973 GTATAGAAATCCAAG
1 ATAAAGAAATCCAAG
31089988 ATA
1 ATA
31089991 CCATATCATA
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.52, C:0.14, G:0.17, T:0.16
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:31089981 original size:30 final size:30
Alignment explanation
Indices: 31089928--31089990 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
31089918 GAAAACCAGA
*
31089928 ATAAAGAAATCCAAGACAGAGAAATCCGAG
1 ATAAAGAAATCCAAGACAGAGAAATCCAAG
* ** *
31089958 ATAAAGATATCCAAGGTATAGAAATCCAAG
1 ATAAAGAAATCCAAGACAGAGAAATCCAAG
31089988 ATA
1 ATA
31089991 CCATATCATA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.52, C:0.14, G:0.17, T:0.16
Consensus pattern (30 bp):
ATAAAGAAATCCAAGACAGAGAAATCCAAG
Found at i:31108043 original size:38 final size:38
Alignment explanation
Indices: 31108001--31108083 Score: 112
Period size: 38 Copynumber: 2.2 Consensus size: 38
31107991 AGTGATATTC
*
31108001 AGGCTTTGTGCCGATGATATTCGGGCTTTGTACCTAGA
1 AGGCTTTGTGCCGATGATATTCGGGCTCTGTACCTAGA
* * * * *
31108039 AGGCTTTGTGCCGATTATATTTGGGCTCTGTGCCTTGT
1 AGGCTTTGTGCCGATGATATTCGGGCTCTGTACCTAGA
31108077 AGGCTTT
1 AGGCTTT
31108084 ATGCTGGTGT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.14, C:0.18, G:0.29, T:0.39
Consensus pattern (38 bp):
AGGCTTTGTGCCGATGATATTCGGGCTCTGTACCTAGA
Found at i:31114672 original size:24 final size:24
Alignment explanation
Indices: 31114643--31114694 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
31114633 ATTCTCCTAA
31114643 TCAATCACTTGTATTTCTAAAAGC
1 TCAATCACTTGTATTTCTAAAAGC
*
31114667 TCAATCACTTGTATTTCTACAAGC
1 TCAATCACTTGTATTTCTAAAAGC
31114691 TCAA
1 TCAA
31114695 GCATATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.33, C:0.23, G:0.08, T:0.37
Consensus pattern (24 bp):
TCAATCACTTGTATTTCTAAAAGC
Found at i:31116235 original size:25 final size:25
Alignment explanation
Indices: 31116207--31116263 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
31116197 TTTAAGAACC
*
31116207 GAAAATACCAAAAATCAAAAGAAAA
1 GAAAAGACCAAAAATCAAAAGAAAA
***
31116232 GAAAAGATTTAAAATCAAAAGAAAA
1 GAAAAGACCAAAAATCAAAAGAAAA
31116257 GAAAAGA
1 GAAAAGA
31116264 TTTAGGCATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.70, C:0.07, G:0.12, T:0.11
Consensus pattern (25 bp):
GAAAAGACCAAAAATCAAAAGAAAA
Found at i:31116264 original size:25 final size:25
Alignment explanation
Indices: 31116217--31116267 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
31116207 GAAAATACCA
31116217 AAAATCAAAAGAAAAGAAAAGATTT
1 AAAATCAAAAGAAAAGAAAAGATTT
31116242 AAAATCAAAAGAAAAGAAAAGATTT
1 AAAATCAAAAGAAAAGAAAAGATTT
31116267 A
1 A
31116268 GGCATTCGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.69, C:0.04, G:0.12, T:0.16
Consensus pattern (25 bp):
AAAATCAAAAGAAAAGAAAAGATTT
Found at i:31119255 original size:26 final size:26
Alignment explanation
Indices: 31119219--31119328 Score: 177
Period size: 26 Copynumber: 4.2 Consensus size: 26
31119209 TGATACAAAT
31119219 TGATAATAGGTTAGGTAAATG-TTCAA
1 TGATAATAGGTTAGGTAAATGTTTC-A
*
31119245 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
31119271 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
31119297 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
31119323 TGATAA
1 TGATAA
31119329 GAATTTCATG
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
26 78 0.98
27 2 0.03
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:31120812 original size:28 final size:26
Alignment explanation
Indices: 31120770--31120844 Score: 87
Period size: 26 Copynumber: 2.8 Consensus size: 26
31120760 AAAAGTAGCT
* *
31120770 AAATTACTATAATACCCCTATGTATGGA
1 AAATTACTGTTATACCCCTA-G-ATGGA
* *
31120798 AAATTACTGTTATACCCCTAGGTGTA
1 AAATTACTGTTATACCCCTAGATGGA
*
31120824 AAATTACCGTTATACCCCTAG
1 AAATTACTGTTATACCCCTAG
31120845 GGTTAATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
26 23 0.55
27 1 0.02
28 18 0.43
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (26 bp):
AAATTACTGTTATACCCCTAGATGGA
Found at i:31120989 original size:27 final size:27
Alignment explanation
Indices: 31120948--31121114 Score: 228
Period size: 27 Copynumber: 6.2 Consensus size: 27
31120938 GAGGAAGCGT
*
31120948 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
31120975 TCTGGTGGCTCTGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
31121002 TCTGGTGGCTCTGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
31121029 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* * *
31121056 TCTGGTGGCCCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
31121084 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
31121110 TCTGG
1 TCTGG
31121115 CAGCCATGCT
Statistics
Matches: 127, Mismatches: 12, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
26 5 0.04
27 108 0.85
28 14 0.11
ACGTcount: A:0.19, C:0.25, G:0.23, T:0.34
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:31137248 original size:26 final size:26
Alignment explanation
Indices: 31137212--31137321 Score: 177
Period size: 26 Copynumber: 4.2 Consensus size: 26
31137202 TGATACAAAT
31137212 TGATAATAGGTTAGGTAAATG-TTCAA
1 TGATAATAGGTTAGGTAAATGTTTC-A
*
31137238 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
31137264 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
31137290 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
31137316 TGATAA
1 TGATAA
31137322 GAATTTCATG
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
26 78 0.98
27 2 0.03
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:31138803 original size:28 final size:26
Alignment explanation
Indices: 31138761--31138835 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
31138751 AAAAGTAGCT
* * *
31138761 AAATTACTATAATACCTCTATGTATGGA
1 AAATTACTGTTATACCCCTA-G-ATGGA
* *
31138789 AAATTACTGTTATACCCCTAGGTGTA
1 AAATTACTGTTATACCCCTAGATGGA
*
31138815 AAATTACCGTTATACCCCTAG
1 AAATTACTGTTATACCCCTAG
31138836 GGTTAATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 23 0.56
27 1 0.02
28 17 0.41
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (26 bp):
AAATTACTGTTATACCCCTAGATGGA
Found at i:31138980 original size:27 final size:27
Alignment explanation
Indices: 31138939--31139092 Score: 218
Period size: 27 Copynumber: 5.7 Consensus size: 27
31138929 GAGGAAGCGT
*
31138939 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
31138966 TCTGGTGGCTCTGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
31138993 TCTGGTGGCTCTGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* * *
31139020 TCTGGTGGCTCTACCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* * *
31139047 TCTGGTGGCCCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* *
31139075 TCTGGTGACTCTGTCACA
1 TCTGGTGGCTCTGCCACA
31139093 TTATTTGTTC
Statistics
Matches: 112, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
27 98 0.88
28 14 0.12
ACGTcount: A:0.20, C:0.26, G:0.22, T:0.32
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:31145000 original size:24 final size:24
Alignment explanation
Indices: 31144968--31145017 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
31144958 TAGCTATACA
31144968 TGCCTTAATGTTAGTATTTGATAG
1 TGCCTTAATGTTAGTATTTGATAG
31144992 TGCCTTAATGTTAGTATTTGATAG
1 TGCCTTAATGTTAGTATTTGATAG
31145016 TG
1 TG
31145018 TGATGACTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.08, G:0.22, T:0.46
Consensus pattern (24 bp):
TGCCTTAATGTTAGTATTTGATAG
Found at i:31150460 original size:40 final size:40
Alignment explanation
Indices: 31150394--31150588 Score: 329
Period size: 40 Copynumber: 4.9 Consensus size: 40
31150384 GTTCGGATTG
31150394 ATAACCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
31150433 ATATCCGGGCTAAGTCCTGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
31150473 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGTGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
31150513 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
31150553 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAGT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
31150589 AGCTATGTCC
Statistics
Matches: 146, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
39 13 0.09
40 133 0.91
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:31160857 original size:35 final size:35
Alignment explanation
Indices: 31160745--31160858 Score: 95
Period size: 35 Copynumber: 3.3 Consensus size: 35
31160735 GTATGTACAT
* * * *
31160745 ATGTGATG-ATATGTTGAACTTGTAAATTTGGCTAC
1 ATGTGATGAAT-TATTGAACTTGTATATTTGGCCAA
** * * * * *
31160780 ATGTGATGTTTTATTTAACTTGTATTTTTAGTCAT
1 ATGTGATGAATTATTGAACTTGTATATTTGGCCAA
* *
31160815 ATATGATGAATTATTGAACTTGTATATTCGGCCAA
1 ATGTGATGAATTATTGAACTTGTATATTTGGCCAA
31160850 ATGTGATGA
1 ATGTGATGA
31160859 TATAACGAAC
Statistics
Matches: 59, Mismatches: 19, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
35 58 0.98
36 1 0.02
ACGTcount: A:0.29, C:0.08, G:0.19, T:0.44
Consensus pattern (35 bp):
ATGTGATGAATTATTGAACTTGTATATTTGGCCAA
Found at i:31164357 original size:15 final size:17
Alignment explanation
Indices: 31164327--31164359 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
31164317 TATATACTTC
31164327 TTTCTCTCTCTTTTTTA
1 TTTCTCTCTCTTTTTTA
31164344 TTTCT-TCT-TTTTTTA
1 TTTCTCTCTCTTTTTTA
31164359 T
1 T
31164360 AACAGTAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 3 0.19
17 5 0.31
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTCTCTCTCTTTTTTA
Found at i:31164662 original size:7 final size:7
Alignment explanation
Indices: 31164621--31164660 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
31164611 AGCAACTAGC
31164621 CCCTAAAA
1 CCCT-AAA
31164629 CCCTAAA
1 CCCTAAA
*
31164636 TCCTAAA
1 CCCTAAA
31164643 CCCTAAA
1 CCCTAAA
*
31164650 CCCTCAA
1 CCCTAAA
31164657 CCCT
1 CCCT
31164661 CACTCAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
7 25 0.86
8 4 0.14
ACGTcount: A:0.38, C:0.45, G:0.00, T:0.17
Consensus pattern (7 bp):
CCCTAAA
Found at i:31166471 original size:34 final size:35
Alignment explanation
Indices: 31166433--31166560 Score: 113
Period size: 34 Copynumber: 3.7 Consensus size: 35
31166423 AATATTCACC
* *
31166433 AAAATGAAACAAAAA-TGATAAGGCTTAAAACTAA
1 AAAATGAAACAAAAATTAATAAGACTTAAAACTAA
31166467 AAAATGAAACAAAAATTAATAAGACTTAAAACTCTAA
1 AAAATGAAACAAAAATTAATAAGACTTAAAA--CTAA
*** ** *
31166504 CCGCA-GAAAC-ACTACTAATAAGACTTAAAACTAA
1 -AAAATGAAACAAAAATTAATAAGACTTAAAACTAA
*
31166538 AAAATGGAA-AAAAATT-ATAAGAC
1 AAAATGAAACAAAAATTAATAAGAC
31166561 CTATAATTAA
Statistics
Matches: 73, Mismatches: 15, Indels: 13
0.72 0.15 0.13
Matches are distributed among these distances:
33 8 0.11
34 25 0.34
35 13 0.18
36 17 0.23
37 9 0.12
38 1 0.01
ACGTcount: A:0.59, C:0.12, G:0.09, T:0.19
Consensus pattern (35 bp):
AAAATGAAACAAAAATTAATAAGACTTAAAACTAA
Found at i:31166606 original size:40 final size:40
Alignment explanation
Indices: 31166547--31166633 Score: 129
Period size: 40 Copynumber: 2.1 Consensus size: 40
31166537 AAAAATGGAA
* *
31166547 AAAAATTATAAGACCTATAATTAATAATACAAAATATTCAC
1 AAAAA-TATAAAACCTATAATTAACAATACAAAATATTCAC
* *
31166588 AAAAATATAAAACTTATAATTAACAATACAAAATATTTAC
1 AAAAATATAAAACCTATAATTAACAATACAAAATATTCAC
31166628 AAAAAT
1 AAAAAT
31166634 TTAGATGAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 37 0.88
41 5 0.12
ACGTcount: A:0.60, C:0.10, G:0.01, T:0.29
Consensus pattern (40 bp):
AAAAATATAAAACCTATAATTAACAATACAAAATATTCAC
Found at i:31172140 original size:47 final size:48
Alignment explanation
Indices: 31172059--31172272 Score: 155
Period size: 46 Copynumber: 4.6 Consensus size: 48
31172049 GCCGATGCCG
* * **
31172059 TGTCCCAGACACGGTCTTACACTAG-TTTGTATCTCAAGTC-GAAGCCA
1 TGTCCCAGACATGGTCTTACACTAGCTATACATCTCAAGTCTGAAG-CA
* * *
31172106 TGTCCCAGACATGGTCTTACACT-GACTAT-CATCTCGTAG-CTGACGTA
1 TGTCCCAGACATGGTCTTACACTAG-CTATACATCTC-AAGTCTGAAGCA
* * * *
31172153 TGTCCTAGACAT-GTCTTACACTAGCT-TACGTCTCAAGGCCGATA-CA
1 TGTCCCAGACATGGTCTTACACTAGCTATACATCTCAAGTCTGA-AGCA
* *
31172199 TGTCTCAGACAT-GTCTTACACTAGC-ACT-CATCTCAA-TGCTGATGCCA
1 TGTCCCAGACATGGTCTTACACTAGCTA-TACATCTCAAGT-CTGAAG-CA
*
31172246 TGTCCTAGACATGGTCTTACACTAGCT
1 TGTCCCAGACATGGTCTTACACTAGCT
31172273 CTCACAAATG
Statistics
Matches: 132, Mismatches: 20, Indels: 28
0.73 0.11 0.16
Matches are distributed among these distances:
45 3 0.02
46 55 0.42
47 54 0.41
48 20 0.15
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (48 bp):
TGTCCCAGACATGGTCTTACACTAGCTATACATCTCAAGTCTGAAGCA
Found at i:31177470 original size:17 final size:17
Alignment explanation
Indices: 31177448--31177505 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
31177438 TTACATTGAA
31177448 GTGTTTTAGCAAAAATC
1 GTGTTTTAGCAAAAATC
31177465 GTGTTTTAGCAAAAATC
1 GTGTTTTAGCAAAAATC
*
31177482 GTGTTTTAGCAAAAACC
1 GTGTTTTAGCAAAAATC
31177499 GTGTTTT
1 GTGTTTT
31177506 CATTGAAAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (17 bp):
GTGTTTTAGCAAAAATC
Found at i:31182973 original size:30 final size:30
Alignment explanation
Indices: 31182929--31183018 Score: 139
Period size: 30 Copynumber: 3.1 Consensus size: 30
31182919 TTATGTTCAC
*
31182929 ATGG-CCCATTAGGCCCAAATCACATTTAT
1 ATGGCCCCTTTAGGCCCAAATCACATTTAT
*
31182958 ATGGCCCCTTTAGGCCCAAATCATATTTAT
1 ATGGCCCCTTTAGGCCCAAATCACATTTAT
*
31182988 ATGGCCCCTTTAGGCCCAAATC-CAATTAT
1 ATGGCCCCTTTAGGCCCAAATCACATTTAT
31183017 AT
1 AT
31183019 TCATACCCAC
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
29 11 0.20
30 45 0.80
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.30
Consensus pattern (30 bp):
ATGGCCCCTTTAGGCCCAAATCACATTTAT
Found at i:31188039 original size:47 final size:45
Alignment explanation
Indices: 31187982--31188132 Score: 126
Period size: 47 Copynumber: 3.2 Consensus size: 45
31187972 TCCCAAACAC
31187982 GGTCTTACACTGGCTTATATCTCAAGTCGAAGCCATGTCCTAGACAA
1 GGTCTTACACTGGCTTATATCTCAAG-CGAAG-CATGTCCTAGACAA
* * * *
31188029 GGTCTTACACTGAC-TATCATCTCGTAGCTGACGCATGTCCCAGAC-A
1 GGTCTTACACTGGCTTAT-ATCTC-AAGC-GAAGCATGTCCTAGACAA
* * * * * * *
31188075 TGTCTTACACTGGCTTACATCTTGAGGCCAATTCATGTCCTAGACAT
1 GGTCTTACACTGGCTTATATC-TCAAGCGAA-GCATGTCCTAGACAA
31188122 GGTCTTACACT
1 GGTCTTACACT
31188133 AGCTCTCACA
Statistics
Matches: 81, Mismatches: 16, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
45 1 0.01
46 32 0.40
47 43 0.53
48 5 0.06
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.30
Consensus pattern (45 bp):
GGTCTTACACTGGCTTATATCTCAAGCGAAGCATGTCCTAGACAA
Found at i:31191343 original size:25 final size:25
Alignment explanation
Indices: 31191309--31191359 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
31191299 GGAGAAGAAG
31191309 ATCCCTTGTTATTCGTGTACAATCT
1 ATCCCTTGTTATTCGTGTACAATCT
* *
31191334 ATCCCTTGTTCTTCGTGTAGAATCT
1 ATCCCTTGTTATTCGTGTACAATCT
31191359 A
1 A
31191360 GAGTCTAGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.43
Consensus pattern (25 bp):
ATCCCTTGTTATTCGTGTACAATCT
Found at i:31194762 original size:44 final size:42
Alignment explanation
Indices: 31194712--31194806 Score: 111
Period size: 44 Copynumber: 2.2 Consensus size: 42
31194702 TGTGTTATCA
* *
31194712 TGTAAGACCACGTTTAGGACGTTGGCATC-AACTTCTGATTTACG
1 TGTAAGACCACGTCTAGGACGTTGACATCGAAC-T-TGATTT-CG
* * *
31194756 TGTAAGACCATGTCTGGGACGTTGACATCGTACTTGATTTCG
1 TGTAAGACCACGTCTAGGACGTTGACATCGAACTTGATTTCG
31194798 TGTAAGACC
1 TGTAAGACC
31194807 CTATTTGGGA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
42 11 0.24
43 6 0.13
44 26 0.58
45 2 0.04
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (42 bp):
TGTAAGACCACGTCTAGGACGTTGACATCGAACTTGATTTCG
Found at i:31196513 original size:26 final size:26
Alignment explanation
Indices: 31196467--31196519 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
31196457 TGAAACATGC
*
31196467 ATTTAGGTCAATTTAACCCTAGGGGT
1 ATTTAGGTCAATTTAACCCTAAGGGT
* *
31196493 ATTTTGGT-AATTTATCTCCTAAGGGT
1 ATTTAGGTCAATTTAAC-CCTAAGGGT
31196519 A
1 A
31196520 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (26 bp):
ATTTAGGTCAATTTAACCCTAAGGGT
Found at i:31198025 original size:26 final size:26
Alignment explanation
Indices: 31197994--31198129 Score: 209
Period size: 26 Copynumber: 5.2 Consensus size: 26
31197984 TGAAATGCCC
*
31197994 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
31198020 ATCATGAGGAACATTTACCTAACCCATT
1 ATCAT--GGAACATTTACCTAACCCATT
* *
31198048 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
31198074 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
31198100 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
31198126 ATCA
1 ATCA
31198130 ATTTTTACCA
Statistics
Matches: 103, Mismatches: 5, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
26 78 0.76
28 25 0.24
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:31201778 original size:37 final size:37
Alignment explanation
Indices: 31201728--31201803 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
31201718 AACAGTATGG
31201728 CCCAATTTGAATGCATTGGAGCACCGATCACTGCTTT
1 CCCAATTTGAATGCATTGGAGCACCGATCACTGCTTT
31201765 CCCAATTTGAATGCATTGGAGCACCGATCACTGCTTT
1 CCCAATTTGAATGCATTGGAGCACCGATCACTGCTTT
31201802 CC
1 CC
31201804 TAAGTAGAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (37 bp):
CCCAATTTGAATGCATTGGAGCACCGATCACTGCTTT
Found at i:31201814 original size:37 final size:37
Alignment explanation
Indices: 31201736--31201814 Score: 131
Period size: 37 Copynumber: 2.1 Consensus size: 37
31201726 GGCCCAATTT
* *
31201736 GAATGCATTGGAGCACCGATCACTGCTTTCCCAATTT
1 GAATGCATTGGAGCACCGATCACTGCTTTCCCAAGTA
*
31201773 GAATGCATTGGAGCACCGATCACTGCTTTCCTAAGTA
1 GAATGCATTGGAGCACCGATCACTGCTTTCCCAAGTA
31201810 GAATG
1 GAATG
31201815 ATCCATTGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.28
Consensus pattern (37 bp):
GAATGCATTGGAGCACCGATCACTGCTTTCCCAAGTA
Found at i:31210109 original size:32 final size:32
Alignment explanation
Indices: 31210068--31210131 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
31210058 ACAGAATTAT
31210068 ATGCTAGTTTTATCAACTTTAAAGATCTCCCA
1 ATGCTAGTTTTATCAACTTTAAAGATCTCCCA
*
31210100 ATGCTAGTTTTATCAATTTTAAAGATCTCCCA
1 ATGCTAGTTTTATCAACTTTAAAGATCTCCCA
31210132 TGTAAATTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.39
Consensus pattern (32 bp):
ATGCTAGTTTTATCAACTTTAAAGATCTCCCA
Found at i:31214132 original size:19 final size:19
Alignment explanation
Indices: 31214108--31214205 Score: 137
Period size: 19 Copynumber: 5.2 Consensus size: 19
31214098 AATCTTTAAG
*
31214108 GATATGCAATCTTAAATAT
1 GATATGCAATCTTAGATAT
* *
31214127 GATATGCAATATCAGATAT
1 GATATGCAATCTTAGATAT
31214146 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
31214163 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
31214182 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
31214203 GAT
1 GAT
31214206 CTTGTAAACT
Statistics
Matches: 70, Mismatches: 5, Indels: 6
0.86 0.06 0.07
Matches are distributed among these distances:
17 15 0.21
19 46 0.66
21 9 0.13
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:31214155 original size:36 final size:37
Alignment explanation
Indices: 31214108--31214205 Score: 126
Period size: 36 Copynumber: 2.6 Consensus size: 37
31214098 AATCTTTAAG
31214108 GATATGCAATCTTAAATATGATATGCAATATCAGATAT
1 GATA-GCAATCTTAAATATGATATGCAATATCAGATAT
* * *
31214146 GATA-CAATCTTAGATATGATATGCAATCTTAGATAT
1 GATAGCAATCTTAAATATGATATGCAATATCAGATAT
31214182 GATATGCAATCTTGAAGATATGAT
1 GATA-GCAATCTT-AA-ATATGAT
31214206 CTTGTAAACT
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
36 33 0.63
38 11 0.21
39 1 0.02
40 7 0.13
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (37 bp):
GATAGCAATCTTAAATATGATATGCAATATCAGATAT
Found at i:31216753 original size:40 final size:40
Alignment explanation
Indices: 31216705--31216848 Score: 180
Period size: 40 Copynumber: 3.6 Consensus size: 40
31216695 AACTTTAGTG
** *
31216705 GCATTAGCGGCGCTTTTTGAAAAACGATGCTATAGTTTGA
1 GCATTAGCGGCGCTTTTTGAAAAACGCCGCTATAGATTGA
* * * *
31216745 GCACTAGCGGCGCTTTTTGAAAATCGCCGTTATAGATCGA
1 GCATTAGCGGCGCTTTTTGAAAAACGCCGCTATAGATTGA
* * * *
31216785 GCATTAGCGGCACTTTCTGAAAATCGCCGCTATAGGTTGA
1 GCATTAGCGGCGCTTTTTGAAAAACGCCGCTATAGATTGA
*
31216825 CCATTAGCGGCGCTTTTTGAAAAA
1 GCATTAGCGGCGCTTTTTGAAAAA
31216849 TGCCACAAAA
Statistics
Matches: 87, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 87 1.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.29
Consensus pattern (40 bp):
GCATTAGCGGCGCTTTTTGAAAAACGCCGCTATAGATTGA
Found at i:31217291 original size:7 final size:7
Alignment explanation
Indices: 31217276--31217450 Score: 52
Period size: 7 Copynumber: 24.6 Consensus size: 7
31217266 ATCATTATAT
*
31217276 TTTAGGG
1 TTTATGG
31217283 TTTATGG
1 TTTATGG
*
31217290 TTTAAGG
1 TTTATGG
* *
31217297 TATATAG
1 TTTATGG
*
31217304 TTTAAGG
1 TTTATGG
* *
31217311 TTTAAGA
1 TTTATGG
*
31217318 TTTAGGAG
1 TTTATG-G
31217326 TTACTAT--
1 TT--TATGG
*
31217333 TTTAAGG
1 TTTATGG
31217340 TTTATGG
1 TTTATGG
* *
31217347 ATTATGA
1 TTTATGG
*
31217354 ATTATGGG
1 TTTAT-GG
31217362 TTTA-GTG
1 TTTATG-G
*
31217369 ATTATGG
1 TTTATGG
31217376 TTTATGG
1 TTTATGG
*
31217383 TTTAAGG
1 TTTATGG
* **
31217390 GTTGGGG
1 TTTATGG
*
31217397 TTTAAGG
1 TTTATGG
31217404 TTTA-GG
1 TTTATGG
*
31217410 TGTTAGGAG
1 T-TTATG-G
*
31217419 TTTAGGG
1 TTTATGG
*
31217426 TTTATGT
1 TTTATGG
*
31217433 TTTATGA
1 TTTATGG
*
31217440 TTTAAGG
1 TTTATGG
31217447 TTTA
1 TTTA
31217451 AGGGATAGGT
Statistics
Matches: 125, Mismatches: 32, Indels: 22
0.70 0.18 0.12
Matches are distributed among these distances:
5 2 0.02
6 4 0.03
7 102 0.82
8 13 0.10
9 2 0.02
10 2 0.02
ACGTcount: A:0.24, C:0.01, G:0.29, T:0.47
Consensus pattern (7 bp):
TTTATGG
Found at i:31217293 original size:14 final size:14
Alignment explanation
Indices: 31217276--31217480 Score: 69
Period size: 14 Copynumber: 14.4 Consensus size: 14
31217266 ATCATTATAT
31217276 TTTAGGGTTTATGG
1 TTTAGGGTTTATGG
* * *
31217290 TTTAAGGTATATAG
1 TTTAGGGTTTATGG
* * *
31217304 TTTAAGGTTTAAGA
1 TTTAGGGTTTATGG
31217318 TTTAGGAGTTACTAT--
1 TTTAGG-GTT--TATGG
*
31217333 TTTAAGGTTTATGG
1 TTTAGGGTTTATGG
* * **
31217347 ATTATGAATTATGGG
1 TTTAGGGTTTAT-GG
* *
31217362 TTTAGTGATTATGG
1 TTTAGGGTTTATGG
* *
31217376 TTTATGGTTTAAGG
1 TTTAGGGTTTATGG
* * *
31217390 GTTGGGGTTTAAGG
1 TTTAGGGTTTATGG
*
31217404 TTTA-GGTGTTAGGAG
1 TTTAGGGT-TTATG-G
*
31217419 TTTAGGGTTTATGT
1 TTTAGGGTTTATGG
* * *
31217433 TTTATGATTTAAGG
1 TTTAGGGTTTATGG
*
31217447 TTTAAGGG-ATA-GG
1 TTT-AGGGTTTATGG
*
31217460 TGTTAAGGGTTTAAGG
1 T-TT-AGGGTTTATGG
31217476 TTTAG
1 TTTAG
31217481 ATTAATTAGT
Statistics
Matches: 140, Mismatches: 38, Indels: 26
0.69 0.19 0.13
Matches are distributed among these distances:
12 3 0.02
13 6 0.04
14 90 0.64
15 33 0.24
16 6 0.04
17 2 0.01
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.45
Consensus pattern (14 bp):
TTTAGGGTTTATGG
Found at i:31217380 original size:22 final size:21
Alignment explanation
Indices: 31217338--31217386 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
31217328 ACTATTTTAA
31217338 GGTTTATGGATTATGAATTAT
1 GGTTTATGGATTATGAATTAT
**
31217359 GGGTTTA-GTGATTATGGTTTAT
1 -GGTTTATG-GATTATGAATTAT
31217381 GGTTTA
1 GGTTTA
31217387 AGGGTTGGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.22, C:0.00, G:0.29, T:0.49
Consensus pattern (21 bp):
GGTTTATGGATTATGAATTAT
Found at i:31217398 original size:21 final size:23
Alignment explanation
Indices: 31217374--31217480 Score: 68
Period size: 22 Copynumber: 5.0 Consensus size: 23
31217364 TAGTGATTAT
*
31217374 GGTTTATGGTTTAAGG-GTT-GG
1 GGTTTAAGGTTTAAGGTGTTAGG
31217395 GGTTTAAGGTTT-AGGTGTTAGG
1 GGTTTAAGGTTTAAGGTGTTAGG
* * * * *
31217417 AGTTTAGGGTTT-ATGTTTTA-T
1 GGTTTAAGGTTTAAGGTGTTAGG
* *
31217438 GATTTAAGGTTTAAGG-GATAGG
1 GGTTTAAGGTTTAAGGTGTTAGG
*
31217460 TG-TTAAGGGTTTAAGGT-TTAG
1 GGTTTAA-GGTTTAAGGTGTTAG
31217481 ATTAATTAGT
Statistics
Matches: 64, Mismatches: 16, Indels: 11
0.70 0.18 0.12
Matches are distributed among these distances:
20 3 0.05
21 29 0.45
22 32 0.50
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.43
Consensus pattern (23 bp):
GGTTTAAGGTTTAAGGTGTTAGG
Found at i:31217475 original size:8 final size:7
Alignment explanation
Indices: 31217374--31217479 Score: 54
Period size: 7 Copynumber: 14.9 Consensus size: 7
31217364 TAGTGATTAT
*
31217374 GGTTTAT
1 GGTTTAA
31217381 GGTTTAA
1 GGTTTAA
* **
31217388 GGGTTGG
1 GGTTTAA
31217395 GGTTTAA
1 GGTTTAA
31217402 GGTTT-A
1 GGTTTAA
*
31217408 GGTGTTAG
1 GGT-TTAA
*
31217416 GAGTTTAG
1 G-GTTTAA
*
31217424 GGTTTAT
1 GGTTTAA
* *
31217431 GTTTTAT
1 GGTTTAA
*
31217438 GATTTAA
1 GGTTTAA
31217445 GGTTTAA
1 GGTTTAA
**
31217452 GGGAT-A
1 GGTTTAA
31217458 GGTGTTAA
1 GGT-TTAA
31217466 GGGTTTAA
1 -GGTTTAA
31217474 GGTTTA
1 GGTTTA
31217480 GATTAATTAG
Statistics
Matches: 76, Mismatches: 17, Indels: 12
0.72 0.16 0.11
Matches are distributed among these distances:
6 7 0.09
7 53 0.70
8 11 0.14
9 5 0.07
ACGTcount: A:0.22, C:0.00, G:0.35, T:0.43
Consensus pattern (7 bp):
GGTTTAA
Found at i:31218035 original size:18 final size:18
Alignment explanation
Indices: 31217984--31218037 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 18
31217974 CTCTCCCCCC
*
31217984 ATTCCCTTTTCTTTCCCA
1 ATTCCCTTTTCTTTCTCA
*
31218002 ATTTCCTTTTCTTTCTCA
1 ATTCCCTTTTCTTTCTCA
31218020 ATTCCCTTTTCTTTCTCA
1 ATTCCCTTTTCTTTCTCA
31218038 GCCTTTCTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.11, C:0.33, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTCCCTTTTCTTTCTCA
Found at i:31220912 original size:15 final size:16
Alignment explanation
Indices: 31220894--31220924 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
31220884 GTTTTTGTCT
31220894 TATATATGAT-TAAAA
1 TATATATGATCTAAAA
31220909 TATATATGATCTAAAA
1 TATATATGATCTAAAA
31220925 GCAAGAGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (16 bp):
TATATATGATCTAAAA
Found at i:31225591 original size:31 final size:31
Alignment explanation
Indices: 31225549--31225633 Score: 111
Period size: 31 Copynumber: 2.8 Consensus size: 31
31225539 TCAATCTCAG
*
31225549 CATAT-ACTGGGCCGAAGTCTTTACATTATT
1 CATATCACTGGGCCGAAGCCTTTACATTATT
* *
31225579 CATGTCACTGGGCTGAAGCCTCTT-CATTATT
1 CATATCACTGGGCCGAAGCCT-TTACATTATT
*
31225610 CATATCACTAGGCCGAAGCCTTTA
1 CATATCACTGGGCCGAAGCCTTTA
31225634 TTGTAAATGA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
30 6 0.13
31 38 0.83
32 2 0.04
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.33
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTACATTATT
Found at i:31225890 original size:25 final size:26
Alignment explanation
Indices: 31225853--31225921 Score: 99
Period size: 25 Copynumber: 2.8 Consensus size: 26
31225843 CTCTTTTAAT
*
31225853 AACTA-GGCAAAGCCCTTTTTGA-TA
1 AACTAGGGCAAAGCCCTTTTTCAGTA
31225877 AACTAGGGCAAAGCCC-TTTTCAGTA
1 AACTAGGGCAAAGCCCTTTTTCAGTA
*
31225902 AACTAGGGCATAGCCCTTTT
1 AACTAGGGCAAAGCCCTTTT
31225922 GCACTTCCTC
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
24 10 0.25
25 27 0.68
26 3 0.08
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (26 bp):
AACTAGGGCAAAGCCCTTTTTCAGTA
Found at i:31225896 original size:24 final size:24
Alignment explanation
Indices: 31225840--31225922 Score: 98
Period size: 25 Copynumber: 3.4 Consensus size: 24
31225830 CTGGAGGCCT
*
31225840 AGCCTCTTTTAAT-AACTA-GGCAA
1 AGCC-CTTTTGATAAACTAGGGCAA
31225863 AGCCCTTTTTGATAAACTAGGGCAA
1 AGCCC-TTTTGATAAACTAGGGCAA
* *
31225888 AGCCCTTTTCAGTAAACTAGGGCAT
1 AGCCCTTTTGA-TAAACTAGGGCAA
31225913 AGCCCTTTTG
1 AGCCCTTTTG
31225923 CACTTCCTCC
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
22 1 0.02
23 10 0.19
24 10 0.19
25 31 0.60
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (24 bp):
AGCCCTTTTGATAAACTAGGGCAA
Found at i:31226080 original size:25 final size:25
Alignment explanation
Indices: 31226052--31226099 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
31226042 ATAATTAAAC
* *
31226052 CCTAGGGGTAAAATGGTCATTTTTA
1 CCTAGGGGCAAAATAGTCATTTTTA
31226077 CCTAGGGGCAAAATAGTCATTTT
1 CCTAGGGGCAAAATAGTCATTTT
31226100 CATATTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAATAGTCATTTTTA
Found at i:31228207 original size:17 final size:17
Alignment explanation
Indices: 31228185--31228220 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
31228175 CTGCTATAAG
*
31228185 TATGTTTAATATTCGGC
1 TATGTTTAATATTCAGC
31228202 TATGTTTAATATTCAGC
1 TATGTTTAATATTCAGC
31228219 TA
1 TA
31228221 GGCTTGGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (17 bp):
TATGTTTAATATTCAGC
Found at i:31228960 original size:12 final size:12
Alignment explanation
Indices: 31228943--31228978 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
31228933 GTTCATGAAT
31228943 TCATGAATTGTA
1 TCATGAATTGTA
31228955 TCATGAATTGTA
1 TCATGAATTGTA
*
31228967 T-AAGAATTGTA
1 TCATGAATTGTA
31228978 T
1 T
31228979 AAGAATTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.42
Consensus pattern (12 bp):
TCATGAATTGTA
Found at i:31228975 original size:11 final size:11
Alignment explanation
Indices: 31228947--31228986 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
31228937 ATGAATTCAT
*
31228947 GAATTGTATCAT
1 GAATTGTAT-AA
31228959 GAATTGTATAA
1 GAATTGTATAA
31228970 GAATTGTATAA
1 GAATTGTATAA
31228981 GAATTG
1 GAATTG
31228987 AATCTATGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.40, C:0.03, G:0.20, T:0.38
Consensus pattern (11 bp):
GAATTGTATAA
Found at i:31231025 original size:27 final size:27
Alignment explanation
Indices: 31230995--31231083 Score: 90
Period size: 27 Copynumber: 3.3 Consensus size: 27
31230985 TCAGTTTACT
* *
31230995 AAAATTA-TCGAAATACCCTTAGTTTGA
1 AAAATTACT-GAAATACCCTCAATTTGA
* *
31231022 AAAAATACTGAAATACCCTCAATTTGT
1 AAAATTACTGAAATACCCTCAATTTGA
* * * *
31231049 AAAATTACTGAAATACCTTCGACTTGT
1 AAAATTACTGAAATACCCTCAATTTGA
31231076 AAAATTAC
1 AAAATTAC
31231084 CAAAGTAATC
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
27 52 0.98
28 1 0.02
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.31
Consensus pattern (27 bp):
AAAATTACTGAAATACCCTCAATTTGA
Found at i:31231126 original size:27 final size:27
Alignment explanation
Indices: 31231096--31231277 Score: 197
Period size: 27 Copynumber: 6.5 Consensus size: 27
31231086 AAGTAATCCT
*
31231096 GATTTACAGAATTATCGTTTTACCCCC
1 GATTTACAGAATTATCGTTTTACCCTC
* *
31231123 GATTTACATAATTATCATTTTACCCTC
1 GATTTACAGAATTATCGTTTTACCCTC
*
31231150 GATTTACATAATTATCGTTTTACCCTC
1 GATTTACAGAATTATCGTTTTACCCTC
* *
31231177 GACTTACGGTAATAGAATTACCGTTTTACCCTC
1 GA-TT----T-ACAGAATTATCGTTTTACCCTC
*
31231210 GATTTACAGAATTA-CTGTTTTACCCTT
1 GATTTACAGAATTATC-GTTTTACCCTC
*
31231237 GATTTACAGAATTA-CTATTTTACCCTC
1 GATTTACAGAATTATC-GTTTTACCCTC
*
31231264 GATTTACAAAATTA
1 GATTTACAGAATTA
31231278 CTAAAATACC
Statistics
Matches: 136, Mismatches: 12, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
26 1 0.01
27 108 0.79
28 3 0.02
32 3 0.02
33 21 0.15
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.40
Consensus pattern (27 bp):
GATTTACAGAATTATCGTTTTACCCTC
Found at i:31231213 original size:87 final size:87
Alignment explanation
Indices: 31231103--31231270 Score: 232
Period size: 87 Copynumber: 1.9 Consensus size: 87
31231093 CCTGATTTAC
* * *
31231103 AGAATTATCGTTTTACCCCCGATTTACATAATTA-TCATTTTACCCTCGATTTACATAATTA-TC
1 AGAATTACCGTTTTACCCCCGATTTACAGAATTACT-ATTTTACCCTCGATTTACAGAATTACT-
*
31231166 GTTTTACCCTCGACTTACGGTAAT
64 ATTTTACCCTCGACTTACGGTAAT
* * *
31231190 AGAATTACCGTTTTACCCTCGATTTACAGAATTACTGTTTTACCCTTGATTTACAGAATTACTAT
1 AGAATTACCGTTTTACCCCCGATTTACAGAATTACTATTTTACCCTCGATTTACAGAATTACTAT
*
31231255 TTTACCCTCGATTTAC
66 TTTACCCTCGACTTAC
31231271 AAAATTACTA
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
87 69 0.97
88 2 0.03
ACGTcount: A:0.27, C:0.23, G:0.10, T:0.40
Consensus pattern (87 bp):
AGAATTACCGTTTTACCCCCGATTTACAGAATTACTATTTTACCCTCGATTTACAGAATTACTAT
TTTACCCTCGACTTACGGTAAT
Found at i:31231287 original size:27 final size:27
Alignment explanation
Indices: 31231203--31231424 Score: 117
Period size: 27 Copynumber: 8.2 Consensus size: 27
31231193 ATTACCGTTT
* ****
31231203 TACCCTCGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTAAAA
* * ***
31231230 TACCCTTGATTTACAGAATTACTATTT
1 TACCCTCGATTTACAAAATTACTAAAA
31231257 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTCGATTTACAAAATTACTAAAA
* * ** *
31231284 TACCCTTGGTTTGTAAAATTACCAAAA
1 TACCCTCGATTTACAAAATTACTAAAA
* ** *
31231311 TACCC-CTAGTTTGTAAAATTACAAAAA
1 TACCCTCGA-TTTACAAAATTACTAAAA
* * *** *
31231338 TACCCTTGGTTTGTGAAATTACTGAAA
1 TACCCTCGATTTACAAAATTACTAAAA
* ** *
31231365 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTCGATTTACAAAATTACTAAAA
* *
31231392 TACCC-CTAATTTACAAAGTTAC-AGAAA
1 TACCCTC-GATTTACAAAATTACTA-AAA
31231419 TACCCT
1 TACCCT
31231425 TGGCTTTTTA
Statistics
Matches: 159, Mismatches: 31, Indels: 9
0.80 0.16 0.05
Matches are distributed among these distances:
26 2 0.01
27 157 0.99
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.34
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACTAAAA
Found at i:31231304 original size:54 final size:54
Alignment explanation
Indices: 31231203--31231396 Score: 158
Period size: 54 Copynumber: 3.6 Consensus size: 54
31231193 ATTACCGTTT
* **** * ** * **
31231203 TACCCTCGATTTACAGAATTACTGTTTTACCCTTGATTTACAGAATTACTATTT
1 TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTGTAAAATTACTATAA
* *
31231257 TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTGTAAAATTACCAAAA
1 TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTGTAAAATTACTATAA
* ** * *
31231311 TACCC-CTAGTTTGTAAAATTACAAAAATACCCTTGGTTTGTGAAATTACTGA-AA
1 TACCCTCGA-TTTACAAAATTACTAAAATACCCTTGGTTTGTAAAATTACT-ATAA
* ** *
31231365 TACCCTCAATTTGTAAAATTACCAAAATACCC
1 TACCCTCGATTTACAAAATTACTAAAATACCC
31231397 CTAATTTACA
Statistics
Matches: 116, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
53 2 0.02
54 111 0.96
55 3 0.03
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.35
Consensus pattern (54 bp):
TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTGTAAAATTACTATAA
Found at i:31231419 original size:54 final size:54
Alignment explanation
Indices: 31231257--31231424 Score: 137
Period size: 54 Copynumber: 3.1 Consensus size: 54
31231247 ATTACTATTT
* ** * * **
31231257 TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTGTA-AAATTACCA-AAA
1 TACCCTCAATTTGTAAAATTACAAAAATACCCCTAATTTG-ACAAATTA-CAGAAA
* * ** ** *
31231311 TACCC-CTAGTTTGTAAAATTACAAAAATACCCTTGGTTTGTGAAATTACTGAAA
1 TACCCTC-AATTTGTAAAATTACAAAAATACCCCTAATTTGACAAATTACAGAAA
*
31231365 TACCCTCAATTTGTAAAATTACCAAAATACCCCTAATTT-ACAAAGTTACAGAAA
1 TACCCTCAATTTGTAAAATTACAAAAATACCCCTAATTTGACAAA-TTACAGAAA
31231419 TACCCT
1 TACCCT
31231425 TGGCTTTTTA
Statistics
Matches: 94, Mismatches: 15, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
53 5 0.05
54 88 0.94
55 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (54 bp):
TACCCTCAATTTGTAAAATTACAAAAATACCCCTAATTTGACAAATTACAGAAA
Found at i:31231425 original size:81 final size:81
Alignment explanation
Indices: 31231272--31231427 Score: 231
Period size: 81 Copynumber: 1.9 Consensus size: 81
31231262 TCGATTTACA
*** * **
31231272 AAATTACTAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACAAAA
1 AAATTACTAAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTAATTTACAAAATTACAAAA
31231337 ATACCCTTGGTTTGTG
66 ATACCCTTGGTTTGTG
* * *
31231353 AAATTACTGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTAATTTACAAAGTTACAGAA
1 AAATTACTAAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTAATTTACAAAATTACAAAA
31231418 ATACCCTTGG
66 ATACCCTTGG
31231428 CTTTTTAAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 66 1.00
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (81 bp):
AAATTACTAAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTAATTTACAAAATTACAAAA
ATACCCTTGGTTTGTG
Found at i:31231456 original size:29 final size:27
Alignment explanation
Indices: 31231257--31231486 Score: 119
Period size: 27 Copynumber: 8.4 Consensus size: 27
31231247 ATTACTATTT
* *
31231257 TACCCTCGATTTACAAAATTACTA-AAA
1 TACCCTTGGTTTACAAAATTA-TAGAAA
** *
31231284 TACCCTTGGTTTGTAAAATTACCA-AAA
1 TACCCTTGGTTTACAAAATTA-TAGAAA
* * ** * *
31231311 TACCCCTAGTTTGTAAAATTACAAAAA
1 TACCCTTGGTTTACAAAATTATAGAAA
***
31231338 TACCCTTGGTTTGTGAAATTACT-GAAA
1 TACCCTTGGTTTACAAAATTA-TAGAAA
*** ** *
31231365 TACCCTCAATTTGTAAAATTACCA-AAA
1 TACCCTTGGTTTACAAAATTA-TAGAAA
* ** * *
31231392 TACCCCTAATTTACAAAGTTACAGAAA
1 TACCCTTGGTTTACAAAATTATAGAAA
31231419 TACCCTTGGCTTTTTA-AAAATTATAGAAA
1 TACCCTTGG---TTTACAAAATTATAGAAA
* *
31231448 TACCATTGGTTTACAAAATTATTGAAA
1 TACCCTTGGTTTACAAAATTATAGAAA
31231475 TACCCTTGGTTT
1 TACCCTTGGTTT
31231487 GTAGATTTAC
Statistics
Matches: 165, Mismatches: 30, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
26 8 0.05
27 134 0.81
29 19 0.12
30 4 0.02
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (27 bp):
TACCCTTGGTTTACAAAATTATAGAAA
Found at i:31231570 original size:27 final size:27
Alignment explanation
Indices: 31231540--31231631 Score: 116
Period size: 27 Copynumber: 3.4 Consensus size: 27
31231530 ACCCCTATTA
*
31231540 GGTAAAAAGACCGTAAAGCCCCTGTAG
1 GGTAAAATGACCGTAAAGCCCCTGTAG
*
31231567 GGTAAAGTG-CCTGTAAAGCCCCTGTAG
1 GGTAAAATGACC-GTAAAGCCCCTGTAG
* *
31231594 GGTAAAGTGACCGTAATA-CCCCTGTAT
1 GGTAAAATGACCGTAA-AGCCCCTGTAG
31231621 GGTAAAATGAC
1 GGTAAAATGAC
31231632 GAATATGCCC
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
26 2 0.03
27 53 0.91
28 3 0.05
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.21
Consensus pattern (27 bp):
GGTAAAATGACCGTAAAGCCCCTGTAG
Found at i:31232463 original size:26 final size:26
Alignment explanation
Indices: 31232434--31232609 Score: 264
Period size: 26 Copynumber: 6.8 Consensus size: 26
31232424 GAGGAAGTGC
31232434 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
**
31232460 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
31232486 AAAAGGGCTTATGCCCCAGTTTACCA
1 AAAAGGGCTTATGCCCCAGTTTACCG
* *
31232512 AAAAGGGCTTATGCCCTAGTTTACCA
1 AAAAGGGCTTATGCCCCAGTTTACCG
**
31232538 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
* *
31232564 AAAAGGGCTTATGCTCCAGGTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
31232590 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
31232610 ATTAAAGAGG
Statistics
Matches: 134, Mismatches: 16, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
25 8 0.06
26 126 0.94
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:31232563 original size:78 final size:78
Alignment explanation
Indices: 31232434--31232609 Score: 300
Period size: 78 Copynumber: 2.3 Consensus size: 78
31232424 GAGGAAGTGC
*
31232434 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATG
1 AAAAGGGCTTATGCCCCAGTTTACCAAAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATG
*
31232499 CCCCAGTTTACCA
66 CCCCAGGTTACCA
*
31232512 AAAAGGGCTTATGCCCTAGTTTACCAAAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATG
1 AAAAGGGCTTATGCCCCAGTTTACCAAAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATG
* *
31232577 CTCCAGGTTACCG
66 CCCCAGGTTACCA
31232590 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
31232610 ATTAAAGAGG
Statistics
Matches: 92, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
77 9 0.10
78 83 0.90
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (78 bp):
AAAAGGGCTTATGCCCCAGTTTACCAAAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATG
CCCCAGGTTACCA
Found at i:31232813 original size:42 final size:42
Alignment explanation
Indices: 31232754--31232845 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
31232744 TAGTCTCCCC
* ** * *
31232754 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTA
31232796 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTA
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTA
31232838 AAATGGGC
1 AAATGGGC
31232846 CTATGGGCCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTA
Found at i:31232934 original size:30 final size:31
Alignment explanation
Indices: 31232869--31232946 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
31232859 CATTTACAGT
31232869 AAAGGCTTTGGCCCAGTGAAATGATTTATGA
1 AAAGGCTTTGGCCCAGTGAAATGATTTATGA
*
31232900 AAAGGCTTTGGCCCAGTGATATGATTTA-GA
1 AAAGGCTTTGGCCCAGTGAAATGATTTATGA
*
31232930 AAAGGCTTCGGCCCAGT
1 AAAGGCTTTGGCCCAGT
31232947 AATCGTTAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
30 18 0.40
31 27 0.60
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (31 bp):
AAAGGCTTTGGCCCAGTGAAATGATTTATGA
Found at i:31237041 original size:19 final size:19
Alignment explanation
Indices: 31237017--31237055 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
31237007 AAAACCAAAT
31237017 TAACATAAATTATCTAAAA
1 TAACATAAATTATCTAAAA
31237036 TAACATAAATTATCTAAAA
1 TAACATAAATTATCTAAAA
31237055 T
1 T
31237056 TAAGACAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.33
Consensus pattern (19 bp):
TAACATAAATTATCTAAAA
Found at i:31239297 original size:25 final size:25
Alignment explanation
Indices: 31239253--31239302 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
31239243 ATGACAACCA
* *
31239253 AATTTACATATACAATCATATTATGT
1 AATTTACATAAACAAACATA-TATGT
31239279 AATTTA-ATAAACAAACATATATGT
1 AATTTACATAAACAAACATATATGT
31239303 TTTCAATACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 5 0.23
25 11 0.50
26 6 0.27
ACGTcount: A:0.48, C:0.10, G:0.04, T:0.38
Consensus pattern (25 bp):
AATTTACATAAACAAACATATATGT
Found at i:31247242 original size:25 final size:25
Alignment explanation
Indices: 31247205--31247252 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
31247195 GACAACCAAA
* *
31247205 TTTACATATACAATCATATTATATAG
1 TTTACATAAACAAACATA-TATATAG
31247231 TTTA-ATAAACAAACATATATAT
1 TTTACATAAACAAACATATATAT
31247253 TTTCAATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
25 11 0.55
26 4 0.20
ACGTcount: A:0.48, C:0.10, G:0.02, T:0.40
Consensus pattern (25 bp):
TTTACATAAACAAACATATATATAG
Found at i:31264105 original size:43 final size:43
Alignment explanation
Indices: 31264058--31264258 Score: 217
Period size: 43 Copynumber: 4.7 Consensus size: 43
31264048 GTTATCGAGA
* *
31264058 TGTGATTACATGTAAGACCATGTCTGGAACATTGACATTGTAT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGACATCGTAT
* *
31264101 TGTGATTACATTTAAGACCATGTCTGGGACATTGACATTGTAT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGACATCGTAT
* * *
31264144 TGTGATTACGTGTAAGACCATATCTGGGACATTGGCATCGTTAT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGACATCG-TAT
*** * * * *
31264188 T-TGATTTTGTGCAAGACCCTGTCTGGGACAGTGGCATCG-AT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGACATCGTAT
* * *
31264229 ATGTGATAACATGTAAGATCATATCTGGGA
1 -TGTGATTACATGTAAGACCATGTCTGGGA
31264259 TATGGCATTG
Statistics
Matches: 134, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
41 2 0.01
42 1 0.01
43 127 0.95
44 4 0.03
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (43 bp):
TGTGATTACATGTAAGACCATGTCTGGGACATTGACATCGTAT
Found at i:31265640 original size:42 final size:42
Alignment explanation
Indices: 31265594--31265679 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
31265584 GCTATATAAC
*
31265594 TTAGTAAGTCCATATGAAAATAATAAGAGATCTGTTGACATG
1 TTAGTAAGTCCATACGAAAATAATAAGAGATCTGTTGACATG
* *
31265636 TTAGTAAGTCTATACGAAAATAATAAGAGATTTGTTGACATG
1 TTAGTAAGTCCATACGAAAATAATAAGAGATCTGTTGACATG
31265678 TT
1 TT
31265680 TATGTCATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.34
Consensus pattern (42 bp):
TTAGTAAGTCCATACGAAAATAATAAGAGATCTGTTGACATG
Found at i:31266746 original size:48 final size:48
Alignment explanation
Indices: 31266650--31266782 Score: 144
Period size: 48 Copynumber: 2.8 Consensus size: 48
31266640 TCACCGATGT
* **
31266650 CATGTCCCAGACATGGTCTTACATTGGCTCACATGTCGAGGCTGATGC
1 CATGTCCCAGACATGGTCTTACATTGGCTCACATATCGAGGCCAATGC
** *
31266698 CATGTCCCAGACATGGTCTTACATTGGCTCTTATAAT-GTGGCCAATGC
1 CATGTCCCAGACATGGTCTTACATTGGCTCACAT-ATCGAGGCCAATGC
* * * *
31266746 CATG-CTCCAAACATGGTCTTACACTAGCACACATATC
1 CATGTC-CCAGACATGGTCTTACATTGGCTCACATATC
31266783 ACCCAAATGT
Statistics
Matches: 70, Mismatches: 12, Indels: 6
0.80 0.14 0.07
Matches are distributed among these distances:
47 3 0.04
48 66 0.94
49 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.28
Consensus pattern (48 bp):
CATGTCCCAGACATGGTCTTACATTGGCTCACATATCGAGGCCAATGC
Found at i:31267274 original size:70 final size:70
Alignment explanation
Indices: 31267168--31267435 Score: 430
Period size: 70 Copynumber: 3.8 Consensus size: 70
31267158 TTCCTTGATC
* * * *
31267168 TATAACAACA-CATTTTAATTAGCTAAACACCATGAATTTGTCCTAATTTGGACAGCCAATAATT
1 TATAACAGCAGCATATTAATTAGCTAAGCACCATGAATTTGTCCTAATTTGGATAGCCAATAATT
*
31267232 TACAA
66 TACAG
* *
31267237 TATTACAGCAGCATATTAATTAGCTAAGCACTATGAATTTGTCCTAATTTGGATAGCCAATAATT
1 TATAACAGCAGCATATTAATTAGCTAAGCACCATGAATTTGTCCTAATTTGGATAGCCAATAATT
*
31267302 TATAG
66 TACAG
* * *
31267307 TATAACAGCAGCATATAAATTAGCTAAGCACCATGAATTTGTCCTAATTTGGAGAACCAATAATT
1 TATAACAGCAGCATATTAATTAGCTAAGCACCATGAATTTGTCCTAATTTGGATAGCCAATAATT
31267372 TACAG
66 TACAG
31267377 TATAACAGCAGCATATTAATTAGCTAAGCACCATGAATTTGTCCTAATTTGGATAGCCA
1 TATAACAGCAGCATATTAATTAGCTAAGCACCATGAATTTGTCCTAATTTGGATAGCCA
31267436 TAAAAAATAA
Statistics
Matches: 181, Mismatches: 17, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
69 8 0.04
70 173 0.96
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (70 bp):
TATAACAGCAGCATATTAATTAGCTAAGCACCATGAATTTGTCCTAATTTGGATAGCCAATAATT
TACAG
Found at i:31270790 original size:38 final size:38
Alignment explanation
Indices: 31270739--31270813 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
31270729 TTTACACCGC
31270739 GATTTTGGAAGAAACTACAAAAAGCTCTTGGCACGAGT
1 GATTTTGGAAGAAACTACAAAAAGCTCTTGGCACGAGT
31270777 GATTTTGGAAGAAACTACAAAAAGCTCTTGGCACGAG
1 GATTTTGGAAGAAACTACAAAAAGCTCTTGGCACGAG
31270814 GTTGAATTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.23
Consensus pattern (38 bp):
GATTTTGGAAGAAACTACAAAAAGCTCTTGGCACGAGT
Found at i:31272912 original size:48 final size:48
Alignment explanation
Indices: 31272841--31272953 Score: 154
Period size: 48 Copynumber: 2.4 Consensus size: 48
31272831 CATTAGGAAA
*
31272841 TTCATTGATTTGGCTTCAGGCCATGATATTGGCACTTCGAGTGTGAGT
1 TTCATTGATTTGGCTTCAGGCCATGATATTAGCACTTCGAGTGTGAGT
* * * * *
31272889 TTCATTGGTTTGGTTTCAGGCCATGATATTAGCAGTTCGGGTGTGAGA
1 TTCATTGATTTGGCTTCAGGCCATGATATTAGCACTTCGAGTGTGAGT
* *
31272937 TACATTGAGTTGGCTTC
1 TTCATTGATTTGGCTTC
31272954 GGGTTATGAT
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 55 1.00
ACGTcount: A:0.19, C:0.15, G:0.28, T:0.38
Consensus pattern (48 bp):
TTCATTGATTTGGCTTCAGGCCATGATATTAGCACTTCGAGTGTGAGT
Found at i:31275679 original size:43 final size:45
Alignment explanation
Indices: 31275631--31275834 Score: 223
Period size: 43 Copynumber: 4.7 Consensus size: 45
31275621 AGCTCGTATA
*
31275631 ATGCCAACGTCCCAGACGTGGTCTTACATGTAA-TCA-AATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAGTCATAATATCG
* *
31275674 ATGCC-ACTGTCCCAGATAG-GGTCTTACACGTAAGTCATAA-GTCG
1 ATGCCAAC-GTCCCAGA-CGTGGTCTTACACGTAAGTCATAATATCG
*
31275718 ATGCCAACGTCCCAGACGTGGTCTTACATGTAA-TCA-AATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAGTCATAATATCG
*
31275761 ATGCC-ACTGTCCTAGACAG-GGTCTTACACGTAAGTCATAAGT-T-G
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAAGTCATAA-TATCG
* *
31275805 ATGCCAACGTCCCAAACGTGGTCGTACACG
1 ATGCCAACGTCCCAGACGTGGTCTTACACG
31275835 ACAACACATA
Statistics
Matches: 136, Mismatches: 11, Indels: 27
0.78 0.06 0.16
Matches are distributed among these distances:
42 6 0.04
43 60 0.44
44 60 0.44
45 9 0.07
46 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (45 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAAGTCATAATATCG
Found at i:31275847 original size:87 final size:87
Alignment explanation
Indices: 31275631--31275832 Score: 359
Period size: 87 Copynumber: 2.3 Consensus size: 87
31275621 AGCTCGTATA
*
31275631 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATATCGATGCCACTGTCCCAGATAGGGT
1 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATATCGATGCCACTGTCCCAGACAGGGT
31275696 CTTACACGTAAGTCATAAGTCG
66 CTTACACGTAAGTCATAAGTCG
*
31275718 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATATCGATGCCACTGTCCTAGACAGGGT
1 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATATCGATGCCACTGTCCCAGACAGGGT
*
31275783 CTTACACGTAAGTCATAAGTTG
66 CTTACACGTAAGTCATAAGTCG
* *
31275805 ATGCCAACGTCCCAAACGTGGTCGTACA
1 ATGCCAACGTCCCAGACGTGGTCTTACA
31275833 CGACAACACA
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 110 1.00
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.25
Consensus pattern (87 bp):
ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATATCGATGCCACTGTCCCAGACAGGGT
CTTACACGTAAGTCATAAGTCG
Found at i:31278296 original size:15 final size:16
Alignment explanation
Indices: 31278276--31278308 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
31278266 TATATATTTT
31278276 TTATTTT-ATTTTTAA
1 TTATTTTAATTTTTAA
31278291 TTATTTTAAATTTTTAA
1 TTATTTT-AATTTTTAA
31278308 T
1 T
31278309 ATAACCATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTTAATTTTTAA
Found at i:31278425 original size:26 final size:24
Alignment explanation
Indices: 31278381--31278430 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
31278371 ATTTGTTTTA
*
31278381 ATATTTGTTTTTATGTTTTTAAAT
1 ATATTTGTTTTTATATTTTTAAAT
31278405 ATATTTGATTTATTATATTTTTAAAT
1 ATATTTG-TTT-TTATATTTTTAAAT
31278431 TTTTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (24 bp):
ATATTTGTTTTTATATTTTTAAAT
Found at i:31280114 original size:25 final size:26
Alignment explanation
Indices: 31280086--31280137 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
31280076 TTTACAGTAT
*
31280086 TACCTCTAGGGATAAATT-ACCGAAA
1 TACCCCTAGGGATAAATTGACCGAAA
* *
31280111 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
31280137 T
1 T
31280138 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:31286538 original size:36 final size:36
Alignment explanation
Indices: 31286498--31286570 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
31286488 GAAAATCAAT
*
31286498 CATTTTACCTTACACGGGTATTACAATCATTTTACC
1 CATTTTACCCTACACGGGTATTACAATCATTTTACC
* * * * *
31286534 CATTTTGCCCTATAGGGGTATTTCAGTCATTTTACC
1 CATTTTACCCTACACGGGTATTACAATCATTTTACC
31286570 C
1 C
31286571 TATGGGGTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.23, C:0.25, G:0.12, T:0.40
Consensus pattern (36 bp):
CATTTTACCCTACACGGGTATTACAATCATTTTACC
Found at i:31286556 original size:27 final size:26
Alignment explanation
Indices: 31286526--31286583 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
31286516 TATTACAATC
* *
31286526 ATTTTACCCATTTTGCCCTATAGGGGT
1 ATTTCACCCATTTTACCCTAT-GGGGT
**
31286553 ATTTCAGTCATTTTACCCTATGGGGT
1 ATTTCACCCATTTTACCCTATGGGGT
31286579 ATTTC
1 ATTTC
31286584 GGTCACCATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 10 0.37
27 17 0.63
ACGTcount: A:0.19, C:0.21, G:0.17, T:0.43
Consensus pattern (26 bp):
ATTTCACCCATTTTACCCTATGGGGT
Found at i:31286588 original size:26 final size:27
Alignment explanation
Indices: 31286534--31286588 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 27
31286524 TCATTTTACC
*
31286534 CATTTTGCCCTATAGGGGTATTTCAGT
1 CATTTTACCCTATAGGGGTATTTCAGT
*
31286561 CATTTTACCCTAT-GGGGTATTTCGGT
1 CATTTTACCCTATAGGGGTATTTCAGT
31286587 CA
1 CA
31286589 CCATTTCGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 14 0.54
27 12 0.46
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.40
Consensus pattern (27 bp):
CATTTTACCCTATAGGGGTATTTCAGT
Found at i:31287009 original size:27 final size:27
Alignment explanation
Indices: 31286978--31287069 Score: 121
Period size: 27 Copynumber: 3.4 Consensus size: 27
31286968 AGGGTAAAAT
31286978 GGGTAAAATGACTGTAATACCCCTGTA
1 GGGTAAAATGACTGTAATACCCCTGTA
* *
31287005 GGGTAAAATGATTATAATACCCCTGTA
1 GGGTAAAATGACTGTAATACCCCTGTA
* * **
31287032 AGGTAACATGACTGTAATACCTTTGTA
1 GGGTAAAATGACTGTAATACCCCTGTA
*
31287059 CGGTAAAATGA
1 GGGTAAAATGA
31287070 TTGATTTTCC
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (27 bp):
GGGTAAAATGACTGTAATACCCCTGTA
Found at i:31289212 original size:24 final size:25
Alignment explanation
Indices: 31289185--31289238 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
31289175 AGGGATTGTA
31289185 GGAGGGAGTT-GAGGAGAGA-TATAG
1 GGAGGGA-TTCGAGGAGAGAGTATAG
* * *
31289209 GGAGAGATTCTAGGAGAGAGTTTAG
1 GGAGGGATTCGAGGAGAGAGTATAG
31289234 GGAGG
1 GGAGG
31289239 TTTGAAGTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
23 2 0.08
24 14 0.58
25 8 0.33
ACGTcount: A:0.31, C:0.02, G:0.48, T:0.19
Consensus pattern (25 bp):
GGAGGGATTCGAGGAGAGAGTATAG
Found at i:31290521 original size:27 final size:27
Alignment explanation
Indices: 31290491--31290584 Score: 134
Period size: 27 Copynumber: 3.5 Consensus size: 27
31290481 AGGGTAAAAT
* *
31290491 GGGTAAAATGACTGTAATACCCCAGTA
1 GGGTAAAATGACTATAATACCCCTGTA
* *
31290518 GGGTAAAATGACTATAATACCCTTGTG
1 GGGTAAAATGACTATAATACCCCTGTA
*
31290545 GGGTAAAATTACTATAATACCCCTGTA
1 GGGTAAAATGACTATAATACCCCTGTA
*
31290572 AGGTAAAATGACT
1 GGGTAAAATGACT
31290585 GATTTGTCCT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (27 bp):
GGGTAAAATGACTATAATACCCCTGTA
Found at i:31290784 original size:36 final size:36
Alignment explanation
Indices: 31290729--31290799 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
31290719 GTACAGATAT
* * *
31290729 GGTTGCATGGGTCGTCCAAGACGACAGTGGACCTAA
1 GGTTGCACGAGTCGCCCAAGACGACAGTGGACCTAA
*
31290765 GGTTGCACGAGTCGCCCAAGACGACTGTGGACCTA
1 GGTTGCACGAGTCGCCCAAGACGACAGTGGACCTA
31290800 CTGATGGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.24, C:0.25, G:0.32, T:0.18
Consensus pattern (36 bp):
GGTTGCACGAGTCGCCCAAGACGACAGTGGACCTAA
Found at i:31293142 original size:43 final size:43
Alignment explanation
Indices: 31293094--31293252 Score: 139
Period size: 43 Copynumber: 3.7 Consensus size: 43
31293084 AAAGCTTGTA
* *
31293094 CAATGCTAACGTCCCAAACGTGGTCTTACATGTAATCAAATAT
1 CAATGCCAACATCCCAAACGTGGTCTTACATGTAATCAAATAT
** * *
31293137 CAATGCC-ACTATCTTAGATA-G-GGTCTTACATGAAACCAAATA-
1 CAATGCCAAC-ATCCCA-A-ACGTGGTCTTACATGTAATCAAATAT
* * * * *
31293179 CGATGCCAACATCCTAGACGTGGTCTTACACGTAAATCATAA-GT
1 CAATGCCAACATCCCAAACGTGGTCTTACATGT-AATCA-AATAT
31293223 CAATGCCAACATCCCAAACGTGGTCTTACA
1 CAATGCCAACATCCCAAACGTGGTCTTACA
31293253 CGATAACACA
Statistics
Matches: 91, Mismatches: 16, Indels: 17
0.73 0.13 0.14
Matches are distributed among these distances:
40 1 0.01
41 1 0.01
42 23 0.25
43 34 0.37
44 31 0.34
45 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (43 bp):
CAATGCCAACATCCCAAACGTGGTCTTACATGTAATCAAATAT
Found at i:31294353 original size:37 final size:37
Alignment explanation
Indices: 31294253--31294355 Score: 170
Period size: 37 Copynumber: 2.8 Consensus size: 37
31294243 CGAATAGTCC
* *
31294253 CCACACGTAGTTATCGGGTCTTACCCAGACAAAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
*
31294290 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
*
31294327 CCACACGTAATCATCGGGTCTTACCCGGA
1 CCACACGTAGTCATCGGGTCTTACCCGGA
31294356 ATATATTTCC
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 62 1.00
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.23
Consensus pattern (37 bp):
CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
Found at i:31294554 original size:48 final size:48
Alignment explanation
Indices: 31294496--31294778 Score: 485
Period size: 48 Copynumber: 5.9 Consensus size: 48
31294486 ATATACACAC
* *
31294496 ATCTCCTACATATTTCACACTAGCCATTCGGCTTTACCACATACACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
31294544 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
31294592 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
31294640 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
31294688 ATCTCATAGATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
31294736 ATCTCATATATATATTTCACATTAGCCATTCGGCTTTACCACA
1 ATCTC--ATACATATTTCACACTAGCCATTCGGCTTTACCACA
31294779 CACATATATA
Statistics
Matches: 226, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
48 191 0.85
50 35 0.15
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (48 bp):
ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
Found at i:31303676 original size:27 final size:27
Alignment explanation
Indices: 31303645--31303699 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
31303635 TTTCTAAGGT
31303645 AAATGGTAGATAATATCTTAAAGACTA
1 AAATGGTAGATAATATCTTAAAGACTA
31303672 AAATGGTAGATAATATCTTAAAGACTA
1 AAATGGTAGATAATATCTTAAAGACTA
31303699 A
1 A
31303700 CCTAAATCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.49, C:0.07, G:0.15, T:0.29
Consensus pattern (27 bp):
AAATGGTAGATAATATCTTAAAGACTA
Found at i:31304688 original size:23 final size:23
Alignment explanation
Indices: 31304654--31304698 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
31304644 TTTTTTATAA
31304654 AATCAAAGTTTT-CTTTAAAAATT
1 AATCAAAGTTTTGC-TTAAAAATT
31304677 AATCACAA-TTTTGCTTAAAAAT
1 AATCA-AAGTTTTGCTTAAAAAT
31304699 CAAAACTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.40
Consensus pattern (23 bp):
AATCAAAGTTTTGCTTAAAAATT
Found at i:31305273 original size:149 final size:148
Alignment explanation
Indices: 31304662--31305274 Score: 841
Period size: 148 Copynumber: 4.1 Consensus size: 148
31304652 AAAATCAAAG
* * *
31304662 TTTTCTTTAAAAATTAATCACAATTTTGCTTAAAAATCAAAACTTTATTTTGAAATAGTTGAAAA
1 TTTT-TTTAAAAA--AATCACTATTTTTCTTAAAAATCAAAACTTTATTTCGAAATAGTTGAAAA
* *
31304727 AGATCAAAACTTTATTTTAAAAATTTAAACTTTTCATTTAAAATGACTAAAAAACATATTTTTAT
63 AGATCAAAACTTTATTTTAAAAATTTAAACTTTTCCTTTAAAATGACT-AAAAACAAATTTTTAT
* *
31304792 TTTTAAAAATAAAAACTTTCTC
127 TTTTAAAAATATAAACTTTCTA
*
31304814 TTTTTTTAAAAAAAAATCACTATTTTTCTTAAAAATCAAAATTTTATTTCGAAATAGTTGAAAAA
1 TTTTTTT--AAAAAAATCACTATTTTTCTTAAAAATCAAAACTTTATTTCGAAATAGTTGAAAAA
* * * * * * *
31304879 TATCAAAATTTTGTTTTAAAAAATTGAACTTTTCTTTTAAAATGACTAAAAACATATTTTTATTT
64 GATCAAAACTTTATTTTAAAAATTTAAACTTTTCCTTTAAAATGACTAAAAACAAATTTTTATTT
* *
31304944 TTAAAAATTTAAACTTTCTC
129 TTAAAAATATAAACTTTCTA
* *
31304964 TTTTTTTTAAAAAATCACTATTTTTCTTAAAAATCAAAGCTTTATTTCGAAATAGTTGAAAAAGA
1 TTTTTTTAAAAAAATCACTATTTTTCTTAAAAATCAAAACTTTATTTCGAAATAGTTGAAAAAGA
* * * * *
31305029 TCAAAACTTTATGTTAAAATTTTAAACATTTCCTTTAAAATGATTAAAAACAAATTTTTATATTT
66 TCAAAACTTTATTTTAAAAATTTAAACTTTTCCTTTAAAATGACTAAAAACAAATTTTTATTTTT
*
31305094 AAAAATATAAAATTTC-A
131 AAAAATATAAACTTTCTA
* *
31305111 CTTTTTTTTAAAAAAGTCACTATTTTTCTTAAAAATCAAAACTTTATTTCGAAATAGTTGGAAAA
1 --TTTTTTTAAAAAAATCACTATTTTTCTTAAAAATCAAAACTTTATTTCGAAATAGTTGAAAAA
* * * *
31305176 GATGAAAACTTTGTTTTAGAAATTTAATCTTTTCCTTTAAAATGACTAAAAACAAATTTTTATTT
64 GATCAAAACTTTATTTTAAAAATTTAAACTTTTCCTTTAAAATGACTAAAAACAAATTTTTATTT
* *
31305241 TTAAAAATCTAAAGTTTCTA
129 TTAAAAATATAAACTTTCTA
*
31305261 TTTTTTGAAAAAAA
1 TTTTTTTAAAAAAA
31305275 ATTAAAACTT
Statistics
Matches: 409, Mismatches: 47, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
148 134 0.33
149 131 0.32
150 44 0.11
151 91 0.22
152 4 0.01
153 5 0.01
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (148 bp):
TTTTTTTAAAAAAATCACTATTTTTCTTAAAAATCAAAACTTTATTTCGAAATAGTTGAAAAAGA
TCAAAACTTTATTTTAAAAATTTAAACTTTTCCTTTAAAATGACTAAAAACAAATTTTTATTTTT
AAAAATATAAACTTTCTA
Found at i:31305287 original size:149 final size:148
Alignment explanation
Indices: 31304667--31305276 Score: 826
Period size: 149 Copynumber: 4.1 Consensus size: 148
31304657 CAAAGTTTTC
* * * *
31304667 TTTAAAAATTAATCACAATTTTGCTTAAAAATCAAAACTTTATTTTGAAATAGTTGAAAAAGATC
1 TTTAAAAA-AAATCACTATTTTTCTTAAAAATCAAAACTTTATTTCGAAATAGTTGAAAAAGATC
* *
31304732 AAAACTTTATTTTAAAAATTTAAACTTTTCATTTAAAATGACTAAAAAACATATTTTTATTTTTA
65 AAAACTTTATTTTAAAAATTTAAACTTTTCCTTTAAAATGACT-AAAAACAAATTTTTATTTTTA
* *
31304797 AAAATAAAAACTTTCTCTTTT
129 AAAATATAAACTTTCT-ATTT
* *
31304818 TTTAAAAAAAAATCACTATTTTTCTTAAAAATCAAAATTTTATTTCGAAATAGTTGAAAAATATC
1 TTT-AAAAAAAATCACTATTTTTCTTAAAAATCAAAACTTTATTTCGAAATAGTTGAAAAAGATC
* * * * * *
31304883 AAAATTTTGTTTTAAAAAATTGAACTTTTCTTTTAAAATGACTAAAAACATATTTTTATTTTTAA
65 AAAACTTTATTTTAAAAATTTAAACTTTTCCTTTAAAATGACTAAAAACAAATTTTTATTTTTAA
* *
31304948 AAATTTAAACTTTCTCTTT
130 AAATATAAACTTTCTATTT
** *
31304967 TTTTTAAAAAATCACTATTTTTCTTAAAAATCAAAGCTTTATTTCGAAATAGTTGAAAAAGATCA
1 TTTAAAAAAAATCACTATTTTTCTTAAAAATCAAAACTTTATTTCGAAATAGTTGAAAAAGATCA
* * * * *
31305032 AAACTTTATGTTAAAATTTTAAACATTTCCTTTAAAATGATTAAAAACAAATTTTTATATTTAAA
66 AAACTTTATTTTAAAAATTTAAACTTTTCCTTTAAAATGACTAAAAACAAATTTTTATTTTTAAA
*
31305097 AATATAAAATTTC-ACTTTT
131 AATATAAACTTTCTA--TTT
* * * *
31305116 TTTTAAAAAAGTCACTATTTTTCTTAAAAATCAAAACTTTATTTCGAAATAGTTGGAAAAGATGA
1 TTTAAAAAAAATCACTATTTTTCTTAAAAATCAAAACTTTATTTCGAAATAGTTGAAAAAGATCA
* * *
31305181 AAACTTTGTTTTAGAAATTTAATCTTTTCCTTTAAAATGACTAAAAACAAATTTTTATTTTTAAA
66 AAACTTTATTTTAAAAATTTAAACTTTTCCTTTAAAATGACTAAAAACAAATTTTTATTTTTAAA
* *
31305246 AATCTAAAGTTTCTATTT
131 AATATAAACTTTCTATTT
31305264 TTTGAAAAAAAAT
1 TTT-AAAAAAAAT
31305277 TAAAACTTTT
Statistics
Matches: 404, Mismatches: 50, Indels: 12
0.87 0.11 0.03
Matches are distributed among these distances:
148 128 0.32
149 144 0.36
150 36 0.09
151 91 0.23
152 5 0.01
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (148 bp):
TTTAAAAAAAATCACTATTTTTCTTAAAAATCAAAACTTTATTTCGAAATAGTTGAAAAAGATCA
AAACTTTATTTTAAAAATTTAAACTTTTCCTTTAAAATGACTAAAAACAAATTTTTATTTTTAAA
AATATAAACTTTCTATTT
Found at i:31305656 original size:28 final size:28
Alignment explanation
Indices: 31305625--31305697 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
31305615 TAATAGTAAT
* * *
31305625 AATAATAATAGTAGTAGTAGTAGTAGTA
1 AATAATAATAATAATAATAGTAGTAGTA
31305653 AATAATAATAATAATAATAGTAGTAGT-
1 AATAATAATAATAATAATAGTAGTAGTA
* *
31305680 AGTAATGATAATAATAAT
1 AATAATAATAATAATAAT
31305698 TTGGGCCCTT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 16 0.40
28 24 0.60
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (28 bp):
AATAATAATAATAATAATAGTAGTAGTA
Found at i:31306195 original size:42 final size:42
Alignment explanation
Indices: 31306148--31306248 Score: 123
Period size: 42 Copynumber: 2.4 Consensus size: 42
31306138 CTTCATATAC
* * *
31306148 AATGCAATTAAAAGTAAATGGACCTCTACACCT-GGGCTTCTA
1 AATGCAATAAAAAGTAAATGGACCTCCACACCTAGGTC-TCTA
* * *
31306190 AATGCAATGAAAGGTAAATGGACCTCCACATCTAGGTCTCTA
1 AATGCAATAAAAAGTAAATGGACCTCCACACCTAGGTCTCTA
*
31306232 AATACAATAAAAAGTAA
1 AATGCAATAAAAAGTAA
31306249 GCAGACCTCC
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
42 47 0.94
43 3 0.06
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.24
Consensus pattern (42 bp):
AATGCAATAAAAAGTAAATGGACCTCCACACCTAGGTCTCTA
Found at i:31306685 original size:2 final size:2
Alignment explanation
Indices: 31306678--31306705 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
31306668 CTTTCTCCTG
31306678 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
31306706 TTTGGTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:31314429 original size:5 final size:5
Alignment explanation
Indices: 31314419--31314443 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
31314409 TGATGAAGAA
31314419 AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG
31314444 TTCTCATGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:31315909 original size:40 final size:40
Alignment explanation
Indices: 31315708--31315902 Score: 259
Period size: 40 Copynumber: 4.9 Consensus size: 40
31315698 ATTCGGATTG
* *
31315708 ATAATCGGGCTAAG-CCCGAAGGCATTCGTAG-GAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGT-GCGAGTTACT
* *
31315747 ATAACCGGGCCAAGTCTCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * * * *
31315787 ATAATCGGGCCAAGTCACGAAGGCAATTGTGCTAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
31315827 ATAACCGGGCTAAGTCTCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
31315867 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAGT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
31315903 AGCTATATCT
Statistics
Matches: 139, Mismatches: 15, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
39 13 0.09
40 126 0.91
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:31315909 original size:80 final size:80
Alignment explanation
Indices: 31315708--31315902 Score: 286
Period size: 80 Copynumber: 2.5 Consensus size: 80
31315698 ATTCGGATTG
*
31315708 ATAATCGGGCTAAG-CCCGAAGGCATTCGTAG-GAGTTACTATAACCGGGCCAAGTCTCGAAGGC
1 ATAATCGGGCTAAGTCCCGAAGGCATTTG-AGCGAGTTACTATAACCGGGCCAAGTCTCGAAGGC
*
31315771 ATTTGTGCGAGTTACT
65 AATTGTGCGAGTTACT
* * * * * *
31315787 ATAATCGGGCCAAGTCACGAAGGCAATTGTGCTAGTTACTATAACCGGGCTAAGTCTCGAAGGCA
1 ATAATCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTTACTATAACCGGGCCAAGTCTCGAAGGCA
31315852 ATTGTGCGAGTTACT
66 ATTGTGCGAGTTACT
*
31315867 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAGT
1 ATAATCGGGCTAAGTCCCGAAGGCATTTGAGCGAGT
31315903 AGCTATATCT
Statistics
Matches: 100, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
79 14 0.14
80 86 0.86
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (80 bp):
ATAATCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTTACTATAACCGGGCCAAGTCTCGAAGGCA
ATTGTGCGAGTTACT
Found at i:31325058 original size:26 final size:26
Alignment explanation
Indices: 31324990--31325042 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
31324980 ATTGGATTAC
31324990 TAAC-ACGTTAATCTAACTATTCAAA
1 TAACTACGTTAATCTAACTATTCAAA
31325015 TAACTACGTTAATCTAACTATTCAAA
1 TAACTACGTTAATCTAACTATTCAAA
31325041 TA
1 TA
31325043 CAAACTACGT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 4 0.15
26 23 0.85
ACGTcount: A:0.43, C:0.19, G:0.04, T:0.34
Consensus pattern (26 bp):
TAACTACGTTAATCTAACTATTCAAA
Found at i:31326128 original size:26 final size:26
Alignment explanation
Indices: 31326097--31326152 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
31326087 TGAAATGCCC
31326097 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
*
31326123 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
31326149 ATCA
1 ATCA
31326153 ATTTGTACCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.38, C:0.25, G:0.07, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:31333169 original size:26 final size:26
Alignment explanation
Indices: 31333138--31333245 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
31333128 TGAAATGCCC
*
31333138 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
31333164 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
31333190 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
31333216 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
31333242 ATCA
1 ATCA
31333246 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:31335752 original size:26 final size:26
Alignment explanation
Indices: 31335712--31335761 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
31335702 ATAAGAATTC
31335712 CTTCTGAAATAAAATAGT-CACATATA
1 CTTCTGAAATAAAATA-TACACATATA
31335738 CTTCTGAGAAT-AAATATACACATA
1 CTTCTGA-AATAAAATATACACATA
31335762 GAACGCCCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 1 0.05
26 18 0.82
27 3 0.14
ACGTcount: A:0.46, C:0.16, G:0.08, T:0.30
Consensus pattern (26 bp):
CTTCTGAAATAAAATATACACATATA
Done.