Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold118
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: 277765
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:9476 original size:21 final size:21
Alignment explanation
Indices: 9450--9492 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
9440 GGTTCGCTGT
*
9450 ATTGGATTAGAGGTGTATTGG
1 ATTGGATTAGAGGTGTAATGG
9471 ATTGGATTAGAGGTGTAATGG
1 ATTGGATTAGAGGTGTAATGG
9492 A
1 A
9493 ATAGAGGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (21 bp):
ATTGGATTAGAGGTGTAATGG
Found at i:9492 original size:16 final size:16
Alignment explanation
Indices: 9473--9505 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
9463 TGTATTGGAT
*
9473 TGGATTAGAGGTGTAA
1 TGGAATAGAGGTGTAA
9489 TGGAATAGAGGTGTAA
1 TGGAATAGAGGTGTAA
9505 T
1 T
9506 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (16 bp):
TGGAATAGAGGTGTAA
Found at i:9550 original size:45 final size:44
Alignment explanation
Indices: 9484--9578 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
9474 GGATTAGAGG
* *
9484 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
9529 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
9573 TGTAAT
1 TGTAAT
9579 AGAAGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:9761 original size:18 final size:17
Alignment explanation
Indices: 9740--9774 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
9730 TTATTATTTA
*
9740 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
9758 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
9775 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:9768 original size:28 final size:27
Alignment explanation
Indices: 9698--9770 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
9688 TTTATTATCA
*
9698 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
9726 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
9753 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
9771 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:9887 original size:144 final size:147
Alignment explanation
Indices: 9659--9930 Score: 487
Period size: 144 Copynumber: 1.9 Consensus size: 147
9649 ATGATTATTG
9659 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTA--TATTATCAAAAATAAATAATTTAATCATATTTAA
*
9724 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
64 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
9789 AGAAATTTGTTTTGGTAAA
129 AGAAATTTGTTTTGGTAAA
*
9808 TTATT-TTATTTAAATTTTAATAAGATTA-A-TATCAATAATAAATAATTTAATCATATTTAAAC
1 TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
9870 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
9931 ATATTCTTAT
Statistics
Matches: 121, Mismatches: 2, Indels: 5
0.95 0.02 0.04
Matches are distributed among these distances:
144 92 0.76
145 1 0.01
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (147 bp):
TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAG
AAATTTGTTTTGGTAAA
Found at i:9905 original size:18 final size:17
Alignment explanation
Indices: 9884--9918 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
9874 TTATTATTAA
*
9884 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
9902 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
9919 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:9997 original size:120 final size:120
Alignment explanation
Indices: 9867--10089 Score: 410
Period size: 120 Copynumber: 1.9 Consensus size: 120
9857 ATCATATTTA
* *
9867 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
9932 TATTCTTATATGAATTTACTCAAACCATAATATATGATACTGTAAAATATAAAAT
66 TATTCTTATATGAATTTACTCAAACCATAATATATGATACTGTAAAATATAAAAT
*
9987 AACATAATTATTATTAAATATAATATAATTAAAATTTATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
10052 TATTCTTATATGAATTTACTCAAATCATAATATATGAT
66 TATTCTTATATGAATTTACTCAAACCATAATATATGAT
10090 TATACATAAT
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
120 99 1.00
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (120 bp):
AACATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAACCATAATATATGATACTGTAAAATATAAAAT
Found at i:10026 original size:18 final size:17
Alignment explanation
Indices: 10005--10039 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
9995 TATTATTAAA
10005 TATAATATAATTAAAATT
1 TATAATATAA-TAAAATT
*
10023 TATAATTTAATAAAATT
1 TATAATATAATAAAATT
10040 CTTAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TATAATATAATAAAATT
Found at i:10118 original size:17 final size:17
Alignment explanation
Indices: 10098--10131 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
10088 ATTATACATA
*
10098 ATATGATTTAATTAAAT
1 ATATGATTTAATAAAAT
10115 ATATGATTTAATAAAAT
1 ATATGATTTAATAAAAT
10132 TTAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
ATATGATTTAATAAAAT
Found at i:10262 original size:93 final size:92
Alignment explanation
Indices: 10164--10358 Score: 286
Period size: 93 Copynumber: 2.1 Consensus size: 92
10154 GATTATAGTT
* * *
10164 TATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATT-TAATAATAATATATAATTTC
1 TATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTAT-ATAATAATATATAATTTC
* *
10227 ATAAAATTCTTGATAATAAAAATTTTCTTA
64 ATAAAATTCTTAATAAT-AAAATGTTCTTA
* *
10257 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAGTGATATATAATTTCAT
1 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCAT
10322 AAAATTCTTAATAATAAAATGTTCTTA
66 AAAATTCTTAATAATAAAATGTTCTTA
10349 TATGAATTTA
1 TATGAATTTA
10359 CTAAAATCAA
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
92 21 0.23
93 68 0.73
94 4 0.04
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (92 bp):
TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCAT
AAAATTCTTAATAATAAAATGTTCTTA
Found at i:17649 original size:93 final size:92
Alignment explanation
Indices: 17517--17711 Score: 286
Period size: 93 Copynumber: 2.1 Consensus size: 92
17507 TTGATTTTAG
* *
17517 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTA-TATAATTA
1 TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTA-AATTA
* *
17581 TATTTAAT-ATTAATTATTTTAAATTGTA
65 TATGTAATAATT-ATTATTTTAAATTATA
* *
17609 TAAATTCATATAAGAAAATTTTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTA
1 TAAATTCATATAAGAAAA-TTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTA
17674 TATGTAATAATTATTATTTTAAATTATA
65 TATGTAATAATTATTATTTTAAATTATA
*
17702 CAAATTCATA
1 TAAATTCATA
17712 AACTATAATC
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
92 17 0.18
93 71 0.76
94 5 0.05
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (92 bp):
TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
ATGTAATAATTATTATTTTAAATTATA
Found at i:17769 original size:17 final size:17
Alignment explanation
Indices: 17744--17777 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
17734 ATAATTTTAA
*
17744 ATTTTATTAAATCATAT
1 ATTTAATTAAATCATAT
17761 ATTTAATTAAATCATAT
1 ATTTAATTAAATCATAT
17778 TATGTATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATTAAATCATAT
Found at i:17851 original size:54 final size:54
Alignment explanation
Indices: 17793--17971 Score: 137
Period size: 54 Copynumber: 3.1 Consensus size: 54
17783 ATAATCATAT
17793 ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
1 ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
* * * * * * * *
17847 ATTATAAATTTTAATTATATT-ATATTTAATAATAATTATGTTATTTTA-TATTTTACAGTATCA
1 ATTAT-GA-TTTGAGTAAATTCATA--TAAGAAT-ATTA-ATTA-TTAAGAATTTT--A-T-T-A
17910 TA
54 -A
*
17912 TATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
1 -ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
17967 ATTAT
1 ATTAT
17972 ATATTTTAAT
Statistics
Matches: 92, Mismatches: 17, Indels: 32
0.65 0.12 0.23
Matches are distributed among these distances:
54 10 0.11
55 5 0.05
56 10 0.11
57 7 0.08
58 5 0.05
59 9 0.10
60 6 0.07
61 9 0.10
62 5 0.05
63 7 0.08
64 10 0.11
65 4 0.04
66 5 0.05
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (54 bp):
ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
Found at i:17868 original size:18 final size:17
Alignment explanation
Indices: 17836--17870 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
17826 AATTATTAAG
17836 AATTTTATTAAATTATA
1 AATTTTATTAAATTATA
*
17853 AATTTTAATTATATTATA
1 AATTTT-ATTAAATTATA
17871 TTTAATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AATTTTATTAAATTATA
Found at i:17910 original size:120 final size:120
Alignment explanation
Indices: 17786--18008 Score: 410
Period size: 120 Copynumber: 1.9 Consensus size: 120
17776 ATTATGTATA
17786 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
1 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
* *
17851 TAAATTTTAATTATATTATATTTAATAATAATTATGTTATTTTATATTTTACAGT
66 TAAATTTTAATTAAAATATATTTAATAATAATTATGTTATTTTATATTTTACAGT
*
17906 ATCATATATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
1 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
*
17971 TATATTTTAATTAAAATATATTTAATAATAATTATGTT
66 TAAATTTTAATTAAAATATATTTAATAATAATTATGTT
18009 TAAATATGAT
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
120 99 1.00
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (120 bp):
ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
TAAATTTTAATTAAAATATATTTAATAATAATTATGTTATTTTATATTTTACAGT
Found at i:17985 original size:18 final size:17
Alignment explanation
Indices: 17957--17991 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
17947 ATTATTAAGA
*
17957 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
17974 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
17992 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:18104 original size:144 final size:147
Alignment explanation
Indices: 17945--18216 Score: 487
Period size: 144 Copynumber: 1.9 Consensus size: 147
17935 ATAAGAATAT
*
17945 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
18010 AAATATGATTAAATTATTTATTATTGAT-AT-TAATCTTATTAAAATTTAAATAA-AATAATTTA
66 AAATATGATTAAATTATTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAATTTA
18072 CCAAAACAAATTTCTGC
131 CCAAAACAAATTTCTGC
18089 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
18154 AAATATGATTAAATTATTTATTTTTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
66 AAATATGATTAAATTATTTATTATTGATAAT--ATAATCTTATTAAAATTTAAATAACAATAA
18217 CAATAATCAT
Statistics
Matches: 121, Mismatches: 2, Indels: 5
0.95 0.02 0.04
Matches are distributed among these distances:
144 91 0.75
145 2 0.02
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (147 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAATTTA
CCAAAACAAATTTCTGC
Found at i:18129 original size:18 final size:17
Alignment explanation
Indices: 18101--18135 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
18091 ATTATTAAGA
*
18101 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
18118 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
18136 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:18346 original size:44 final size:45
Alignment explanation
Indices: 18297--18391 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
18287 TTACACCTCT
* *
18297 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
** *
18341 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
18386 ATTACA
1 ATTACA
18392 CCTCTAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
Found at i:18391 original size:16 final size:16
Alignment explanation
Indices: 18370--18402 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
18360 TTGATTTGCT
*
18370 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
18386 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
18402 A
1 A
18403 ATCCAATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.36, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:18412 original size:21 final size:21
Alignment explanation
Indices: 18383--18425 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
18373 ACACCTCTAT
*
18383 TCCATTACACCTCTAATCCAA
1 TCCAATACACCTCTAATCCAA
18404 TCCAATACACCTCTAATCCAA
1 TCCAATACACCTCTAATCCAA
18425 T
1 T
18426 ACAGCGAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.28
Consensus pattern (21 bp):
TCCAATACACCTCTAATCCAA
Found at i:22003 original size:6 final size:6
Alignment explanation
Indices: 21984--22041 Score: 53
Period size: 6 Copynumber: 9.2 Consensus size: 6
21974 CAGATGAAGT
* * * *
21984 AAAAGA AAAGGA AAAAGA AACAGAAA CAAAAGA AAAAGT AAAAGA AGAAGA
1 AAAAGA AAAAGA AAAAGA AA-A-AGA -AAAAGA AAAAGA AAAAGA AAAAGA
22035 AAAAGA A
1 AAAAGA A
22042 GAGATTGACA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
6 33 0.80
7 3 0.07
8 3 0.07
9 2 0.05
ACGTcount: A:0.76, C:0.03, G:0.19, T:0.02
Consensus pattern (6 bp):
AAAAGA
Found at i:22019 original size:21 final size:22
Alignment explanation
Indices: 21989--22029 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
21979 GAAGTAAAAG
21989 AAAAGGAAAAAG-AAACAGAAAC
1 AAAAGGAAAAAGTAAA-AGAAAC
22011 AAAA-GAAAAAGTAAAAGAA
1 AAAAGGAAAAAGTAAAAGAA
22030 GAAGAAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.76, C:0.05, G:0.17, T:0.02
Consensus pattern (22 bp):
AAAAGGAAAAAGTAAAAGAAAC
Found at i:28626 original size:22 final size:23
Alignment explanation
Indices: 28601--28645 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
28591 AGAGAATTCG
28601 AGCT-AGAAGAAAGAA-AGGAAAA
1 AGCTAAGAA-AAAGAAGAGGAAAA
*
28623 AGCTAAGAAAATGAAGAGGAAAA
1 AGCTAAGAAAAAGAAGAGGAAAA
28646 TTGATGAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.62, C:0.04, G:0.27, T:0.07
Consensus pattern (23 bp):
AGCTAAGAAAAAGAAGAGGAAAA
Found at i:33098 original size:22 final size:23
Alignment explanation
Indices: 33073--33117 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
33063 AGAGAATTCG
33073 AGCT-AGAAGAAAGAA-AGGAAAA
1 AGCTAAGAA-AAAGAAGAGGAAAA
*
33095 AGCTAAGAAAATGAAGAGGAAAA
1 AGCTAAGAAAAAGAAGAGGAAAA
33118 TTGATGAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.62, C:0.04, G:0.27, T:0.07
Consensus pattern (23 bp):
AGCTAAGAAAAAGAAGAGGAAAA
Found at i:33847 original size:11 final size:11
Alignment explanation
Indices: 33831--33859 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
33821 TTAGTCCTCA
33831 TTCTTTTTTTT
1 TTCTTTTTTTT
33842 TTC-TTTTTTT
1 TTCTTTTTTTT
33852 TTCTTTTT
1 TTCTTTTT
33860 CTACTTTGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (11 bp):
TTCTTTTTTTT
Found at i:38206 original size:39 final size:39
Alignment explanation
Indices: 38154--38324 Score: 211
Period size: 39 Copynumber: 4.3 Consensus size: 39
38144 GGACTAAGAT
38154 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAG-C
1 CCGAAGGCATTTGTGCGAGATACAAA-TCCGGGTTAAGTC
*
38193 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATAC-AAATCCGGGTTAAGTC
* * *
38233 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATA-CAAATCCGGGTTAAGTC
* * * * *
38273 CCGAAGGCA-TTGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGATAC-AAATCCGGGTTAAGTC
38312 CCGAAGGCATTTG
1 CCGAAGGCATTTG
38325 AACGAGGAGC
Statistics
Matches: 116, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
39 65 0.56
40 51 0.44
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (39 bp):
CCGAAGGCATTTGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:38237 original size:79 final size:79
Alignment explanation
Indices: 38101--38324 Score: 231
Period size: 79 Copynumber: 2.8 Consensus size: 79
38091 TTGAATGCTG
* * * * * * *
38101 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAAACCGGGCTAAG-TCCCGAAGGCAT
38164 TTGTGCGAGATA-CAAA
63 TTGTGCGAGATATCAAA
* * *
38180 TTCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATT
1 -TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATT
* * *
38244 CGTGCGAGTTATTAAA
64 TGTGCGAGATATCAAA
* * *
38260 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
38325 AACGAGGAGC
Statistics
Matches: 123, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
78 1 0.01
79 90 0.73
80 31 0.25
81 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGATATCAAA
Found at i:38342 original size:79 final size:80
Alignment explanation
Indices: 38181--38357 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 80
38171 AGATACAAAT
* * *
38181 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
38245 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * *
38260 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
38324 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
38339 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
38358 TACGTGATTT
Statistics
Matches: 83, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
78 16 0.19
79 59 0.71
80 8 0.10
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:45551 original size:41 final size:40
Alignment explanation
Indices: 45506--45678 Score: 174
Period size: 41 Copynumber: 4.3 Consensus size: 40
45496 GGACTAAGAT
*
45506 CCGAAGGCATTTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTTTGTGCGAGATACAAA-TCCGGGTTAAGTC
*
45547 CCGAAGGC-CTTTGTTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTTG-TGCGAGATAC-AAATCCGGGTTAAGTC
* * * *
45588 CCGAAGGCA-TTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTTTGTGCGAGATA-CAAATCCGGGTTAAGTC
* * * * *
45628 CCGAAGGCA--TTGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTTTGTGCGAGATAC-AAATCCGGGTTAAGTC
45667 CCGAAGGCATTT
1 CCGAAGGCATTT
45679 GAACGAGGAG
Statistics
Matches: 114, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
39 33 0.29
40 36 0.32
41 42 0.37
42 3 0.03
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
CCGAAGGCATTTTGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:45616 original size:40 final size:40
Alignment explanation
Indices: 45453--45679 Score: 219
Period size: 40 Copynumber: 5.7 Consensus size: 40
45443 TTGAATGCTG
* * * *
45453 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
45493 TCCGGACTAAGAT-CCGAAGGCATTTTGTGCGAGATAC-AAA
1 TCCGGGCTAAG-TCCCGAAGGCA-TTTGTGCGAGTTACTAAA
* * * *
45533 TTCCGGGTTAAGCCCCGAAGGCCTTTGTTGCGAGATACTAAA
1 -TCCGGGCTAAGTCCCGAAGGCATTTG-TGCGAGTTACTAAA
* * *
45575 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
45615 TCCGGGTTATGTCCCGAAGGCA-TTGTGTGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
45654 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
45680 AACGAGGAGC
Statistics
Matches: 158, Mismatches: 21, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
39 34 0.22
40 60 0.38
41 54 0.34
42 10 0.06
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:45697 original size:79 final size:81
Alignment explanation
Indices: 45534--45712 Score: 186
Period size: 79 Copynumber: 2.2 Consensus size: 81
45524 AGATACAAAT
* * * *
45534 TCCGGGTTAAGCCCCGAAGGCCTTTGTTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATT
** * *
45599 CGTGCGAGTTATTAAA
66 CGAACGAGTGACTAAA
* * * *
45615 TCCGGGTTATGTCCCGAAGG-CATTG-TGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
45678 TGAACGAG-GAGCTATA
66 CGAACGAGTGA-CTAAA
*
45694 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
45713 TACGTGATTT
Statistics
Matches: 81, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
78 15 0.19
79 44 0.54
80 4 0.05
81 18 0.22
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGTGACTAAA
Found at i:57906 original size:11 final size:11
Alignment explanation
Indices: 57892--57932 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
57882 TATATATTAC
*
57892 ATAATAAAATA
1 ATAATAAAAAA
57903 ATAATAAAAAA
1 ATAATAAAAAA
*
57914 CATAATAAAAGA
1 -ATAATAAAAAA
57926 ATAATAA
1 ATAATAA
57933 GAAAGTTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (11 bp):
ATAATAAAAAA
Found at i:57974 original size:10 final size:10
Alignment explanation
Indices: 57959--57997 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
57949 GATAGCATGC
57959 AAAAAGAAAA
1 AAAAAGAAAA
*
57969 AAAAAGAAAG
1 AAAAAGAAAA
57979 AAAAAGAAGAA
1 AAAAAGAA-AA
*
57990 AAGAAGAA
1 AAAAAGAA
57998 GAAGCTACAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
10 17 0.68
11 8 0.32
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:57992 original size:14 final size:14
Alignment explanation
Indices: 57960--58001 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
57950 ATAGCATGCA
*
57960 AAAAGAAAAA-AAA
1 AAAAGAAAAAGAAG
57973 AGAAAGAAAAAGAAG
1 A-AAAGAAAAAGAAG
*
57988 AAAAGAAGAAGAAG
1 AAAAGAAAAAGAAG
58002 CTACAGCACC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 1 0.04
14 21 0.84
15 3 0.12
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAGAAG
Found at i:58000 original size:20 final size:20
Alignment explanation
Indices: 57959--57997 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
57949 GATAGCATGC
57959 AAAAAGAAAAAAAAAGAAAG
1 AAAAAGAAAAAAAAAGAAAG
*
57979 AAAAAGAAGAAAAGAAGAA
1 AAAAAGAA-AAAAAAAGAA
57998 GAAGCTACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (20 bp):
AAAAAGAAAAAAAAAGAAAG
Found at i:60633 original size:104 final size:104
Alignment explanation
Indices: 60464--60661 Score: 369
Period size: 104 Copynumber: 1.9 Consensus size: 104
60454 TTTTCCAGCT
*
60464 TTCAACCAAACAATCTTCTACTCTATTCTTGTACCACGAACTTCTTCGAGTGTGGACTTGAATCA
1 TTCAACCAAACAATCTTCTACTCTATTCTTGTACCACGAACTTCTTCGAGTGTGGACTCGAATCA
*
60529 ATTGAATCAAAATATAGAACTAGAAAAAGTTTTTCATCC
66 ATTGAATCAAAATATAAAACTAGAAAAAGTTTTTCATCC
*
60568 TTCACCCAAACAATCTTCTACTCTATTCTTGTACCACGAACTTCTTCGAGTGTGGACTCGAATCA
1 TTCAACCAAACAATCTTCTACTCTATTCTTGTACCACGAACTTCTTCGAGTGTGGACTCGAATCA
60633 ATTGAATCAAAATATAAAACTAGAAAAAG
66 ATTGAATCAAAATATAAAACTAGAAAAAG
60662 CTTTCTTTTC
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
104 91 1.00
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.31
Consensus pattern (104 bp):
TTCAACCAAACAATCTTCTACTCTATTCTTGTACCACGAACTTCTTCGAGTGTGGACTCGAATCA
ATTGAATCAAAATATAAAACTAGAAAAAGTTTTTCATCC
Found at i:72246 original size:10 final size:10
Alignment explanation
Indices: 72231--72274 Score: 79
Period size: 10 Copynumber: 4.4 Consensus size: 10
72221 AGTAACTCAC
72231 ATTTATTTTT
1 ATTTATTTTT
72241 ATTTATTTTT
1 ATTTATTTTT
72251 ATTTATTTTT
1 ATTTATTTTT
*
72261 ATTTATTTTA
1 ATTTATTTTT
72271 ATTT
1 ATTT
72275 CGAATACTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:72520 original size:17 final size:17
Alignment explanation
Indices: 72493--72530 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
72483 AAGCCCCAAC
*
72493 AAAAAGAAGAAGGAAAGA
1 AAAAAGAAGAAAGAAA-A
72511 AAAAAG-AGAAAGAAAA
1 AAAAAGAAGAAAGAAAA
72527 AAAA
1 AAAA
72531 CCAAAATTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 8 0.42
18 6 0.32
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
AAAAAGAAGAAAGAAAA
Found at i:72643 original size:18 final size:18
Alignment explanation
Indices: 72620--72655 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
72610 CCGAAAGTCG
72620 TCGTCGTTCACCCCTTTA
1 TCGTCGTTCACCCCTTTA
*
72638 TCGTCGTTGACCCCTTTA
1 TCGTCGTTCACCCCTTTA
72656 CTGTTAACGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.36, G:0.14, T:0.39
Consensus pattern (18 bp):
TCGTCGTTCACCCCTTTA
Found at i:78234 original size:69 final size:69
Alignment explanation
Indices: 78123--78308 Score: 239
Period size: 69 Copynumber: 2.7 Consensus size: 69
78113 AGTAGTTGTG
* * ** *
78123 TCATATCAAGGCTCGCAGGCGAAGAGTCGCAGCCTCCAACACAATTAGC-GAGAGCAATGCTCTC
1 TCATATCAAGGCTAGCAGGCGAAGAGTCGCAGCCTCCAACACAGTTAGCAGA-AGCAAAACTCCC
78187 AGCTA
65 AGCTA
* * * * *
78192 TCATATCAAAGCTTGCAGGTGAAAAGTCACAGCCTCCAACACAGTTAGCAGAAGCAAAACTCCCA
1 TCATATCAAGGCTAGCAGGCGAAGAGTCGCAGCCTCCAACACAGTTAGCAGAAGCAAAACTCCCA
78257 GCTA
66 GCTA
* * *
78261 TCGTATTAAGGCTAGCAGGCGAAGAGTCGTAGCCTCCAACACAGTTAG
1 TCATATCAAGGCTAGCAGGCGAAGAGTCGCAGCCTCCAACACAGTTAG
78309 TGAAAGTTGA
Statistics
Matches: 99, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
69 97 0.98
70 2 0.02
ACGTcount: A:0.33, C:0.27, G:0.22, T:0.18
Consensus pattern (69 bp):
TCATATCAAGGCTAGCAGGCGAAGAGTCGCAGCCTCCAACACAGTTAGCAGAAGCAAAACTCCCA
GCTA
Found at i:78415 original size:59 final size:59
Alignment explanation
Indices: 78330--78443 Score: 210
Period size: 59 Copynumber: 1.9 Consensus size: 59
78320 AAGCCCTAAC
* *
78330 TGTGTTATCTTTCAAAATTTTCTTAAGTATGAAATAGCTCGTGGATTAAAATCCCTAGT
1 TGTGTTATCTTTCAAAATTTTCTTAAGTATGAAATAGCTCATAGATTAAAATCCCTAGT
78389 TGTGTTATCTTTCAAAATTTTCTTAAGTATGAAATAGCTCATAGATTAAAATCCC
1 TGTGTTATCTTTCAAAATTTTCTTAAGTATGAAATAGCTCATAGATTAAAATCCC
78444 CAATTATGTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.40
Consensus pattern (59 bp):
TGTGTTATCTTTCAAAATTTTCTTAAGTATGAAATAGCTCATAGATTAAAATCCCTAGT
Found at i:91601 original size:2 final size:2
Alignment explanation
Indices: 91596--91620 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
91586 ATATATATAA
91596 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
91621 AAAAAAAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:96751 original size:185 final size:186
Alignment explanation
Indices: 96387--96757 Score: 654
Period size: 185 Copynumber: 2.0 Consensus size: 186
96377 TGAATCTTAG
*
96387 GTCCAATTCATTTTCTAAACACATTTGTAATTTTTATTTCATATTGTTTTAAGCTTTTTTTAATT
1 GTCCAATTCATTTTCTAAACACATTTGTAATTTTTATTTCATATTATTTTAAGCTTTTTTTAATT
*
96452 AATAAATATATTGTTTTCAATTTTTTTTACTTTTAATTAATAACTCTTTTATTTATAAAATCGAA
66 AATAAATATATTGTTTTCAATTTTTTTTACTTTTAATTAATAACTCTTTTATTTATAAAATCAAA
*
96517 TAATTATTATAAATATCATTATTTTTAGTAAATTTATTTTTTATATGTGTAATATT
131 TAATTATTATAAATATCATTATTTTTAGTAAATTTAATTTTTATATGTGTAATATT
* *
96573 GTCCAATTCCTTTTCTAAACACATTTGTAATTTTTATTTCATGTTATTTTAAGCTTTTTTTAATT
1 GTCCAATTCATTTTCTAAACACATTTGTAATTTTTATTTCATATTATTTTAAGCTTTTTTTAATT
* * * *
96638 AATAAATGTATTGTTTTCAA-TTTTTTTATTTTTAATTAATAATTCTTTTATTTATAACATCAAA
66 AATAAATATATTGTTTTCAATTTTTTTTACTTTTAATTAATAACTCTTTTATTTATAAAATCAAA
96702 TAATTATTATAAATATCATTATTTTTAGTAAATTTAATTTTTATATGTGTAATATT
131 TAATTATTATAAATATCATTATTTTTAGTAAATTTAATTTTTATATGTGTAATATT
96758 TATTTTTCAA
Statistics
Matches: 176, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
185 95 0.54
186 81 0.46
ACGTcount: A:0.33, C:0.08, G:0.05, T:0.55
Consensus pattern (186 bp):
GTCCAATTCATTTTCTAAACACATTTGTAATTTTTATTTCATATTATTTTAAGCTTTTTTTAATT
AATAAATATATTGTTTTCAATTTTTTTTACTTTTAATTAATAACTCTTTTATTTATAAAATCAAA
TAATTATTATAAATATCATTATTTTTAGTAAATTTAATTTTTATATGTGTAATATT
Found at i:97166 original size:19 final size:19
Alignment explanation
Indices: 97131--97181 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
97121 CATAATGATA
*
97131 TATATAA-TATAT-TTTAT
1 TATATAATTATATAATTAT
97148 TATATAATTATATAATTAT
1 TATATAATTATATAATTAT
* *
97167 TATTTAATTTTATAA
1 TATATAATTATATAA
97182 ATAAAAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 7 0.24
18 5 0.17
19 17 0.59
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATATAATTATATAATTAT
Found at i:97170 original size:27 final size:27
Alignment explanation
Indices: 97130--97200 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 27
97120 ACATAATGAT
*
97130 ATATATAA-TA-TATTTTATTATATAA
1 ATATATAATTATTATTTAATTATATAA
* *
97155 TTATATAATTATTATTTAATTTTATAA
1 ATATATAATTATTATTTAATTATATAA
* * *
97182 ATAAAAAATTATTAATTAA
1 ATATATAATTATTATTTAA
97201 AAAGATGAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
25 7 0.19
26 2 0.05
27 28 0.76
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
ATATATAATTATTATTTAATTATATAA
Found at i:99718 original size:19 final size:19
Alignment explanation
Indices: 99690--99740 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 19
99680 AGTTATAAAA
99690 ATATTTTAATTAATTAATT
1 ATATTTTAATTAATTAATT
* *
99709 ATATTATAATT--TTTATT
1 ATATTTTAATTAATTAATT
99726 ATATTTTAATATAAT
1 ATATTTTAAT-TAAT
99741 CATACCTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 14 0.54
18 1 0.04
19 10 0.38
20 1 0.04
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
ATATTTTAATTAATTAATT
Found at i:101354 original size:29 final size:29
Alignment explanation
Indices: 101300--101414 Score: 108
Period size: 29 Copynumber: 3.8 Consensus size: 29
101290 TTTTATTTAT
** **
101300 TTAAGGTTTATGGTTTTGGAGCAAATAAA
1 TTAAGGTTTATGGTTTTTAAAAAAATAAA
101329 TTAAGGTTTATGGTTTTTAAAAAAATAAA
1 TTAAGGTTTATGGTTTTTAAAAAAATAAA
*
101358 TTAAATTAGGGTTTATTGTTTTT-AAAAAATAAA
1 TT--A--A-GGTTTATGGTTTTTAAAAAAATAAA
101391 TTAAGGTTTA-GGAATTTTTAAAAA
1 TTAAGGTTTATGG--TTTTTAAAAA
101415 TAAATTTCTG
Statistics
Matches: 72, Mismatches: 6, Indels: 15
0.77 0.06 0.16
Matches are distributed among these distances:
27 1 0.01
28 6 0.08
29 33 0.46
30 4 0.06
31 2 0.03
33 13 0.18
34 13 0.18
ACGTcount: A:0.41, C:0.01, G:0.17, T:0.42
Consensus pattern (29 bp):
TTAAGGTTTATGGTTTTTAAAAAAATAAA
Found at i:101390 original size:33 final size:34
Alignment explanation
Indices: 101325--101394 Score: 115
Period size: 34 Copynumber: 2.1 Consensus size: 34
101315 TTGGAGCAAA
101325 TAAATTAAGGTTTATGGTTTTTAAAAAAATAAAT
1 TAAATTAAGGTTTATGGTTTTTAAAAAAATAAAT
* *
101359 TAAATTAGGGTTTATTGTTTTT-AAAAAATAAAT
1 TAAATTAAGGTTTATGGTTTTTAAAAAAATAAAT
101392 TAA
1 TAA
101395 GGTTTAGGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
33 14 0.41
34 20 0.59
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (34 bp):
TAAATTAAGGTTTATGGTTTTTAAAAAAATAAAT
Found at i:101737 original size:124 final size:125
Alignment explanation
Indices: 101516--101792 Score: 441
Period size: 124 Copynumber: 2.2 Consensus size: 125
101506 TTTTGTTCAC
* * *
101516 TCAGCAAAAGTATTGAAAAAAGCTCCCAGCTGGATGCTATTTTTCTACAGTAATTTCTAAAAAAT
1 TCAGCAAAAGTACTAAAAAAAGCTCCCAGCTGGACGCTATTTTTCTACAGTAATTTCTAAAAAAT
* *
101581 AATTTTGAGAAGATGGTTCTGAAAAAATAGGGTAAAAAACGCTTCAAGCAAGATGCACTG
66 AATTTTGAGAAGATGATTCTAAAAAAATAGGGTAAAAAACGCTTCAAGCAAGATGCACTG
* *
101641 TCAGCAAAAGTACT-AAAAAAGCTCTCAGCTGGACGCTATTTTTCTACAGTAGTTTCTAAAAAAA
1 TCAGCAAAAGTACTAAAAAAAGCTCCCAGCTGGACGCTATTTTTCTACAGTAATTTCT-AAAAAA
* *
101705 TAA-TTTGAGAAGATGATTCTAAAAAAATAGGGTCAAAAACGCTTCAAGCAGGATGCACTG
65 TAATTTTGAGAAGATGATTCTAAAAAAATAGGGTAAAAAACGCTTCAAGCAAGATGCACTG
*
101765 TTAGCAAAAGTACTAAAAAAAGCTCCCA
1 TCAGCAAAAGTACTAAAAAAAGCTCCCA
101793 AATGTACTAA
Statistics
Matches: 140, Mismatches: 10, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
124 106 0.76
125 34 0.24
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.26
Consensus pattern (125 bp):
TCAGCAAAAGTACTAAAAAAAGCTCCCAGCTGGACGCTATTTTTCTACAGTAATTTCTAAAAAAT
AATTTTGAGAAGATGATTCTAAAAAAATAGGGTAAAAAACGCTTCAAGCAAGATGCACTG
Found at i:101799 original size:22 final size:22
Alignment explanation
Indices: 101769--101818 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
101759 GCACTGTTAG
*
101769 CAAAAGTACTAAAAAAAGCTCC
1 CAAATGTACTAAAAAAAGCTCC
101791 CAAATGTACTAAAAAAAGCTCC
1 CAAATGTACTAAAAAAAGCTCC
101813 CAAATG
1 CAAATG
101819 GATGTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.52, C:0.22, G:0.10, T:0.16
Consensus pattern (22 bp):
CAAATGTACTAAAAAAAGCTCC
Found at i:105248 original size:61 final size:59
Alignment explanation
Indices: 105122--105294 Score: 192
Period size: 61 Copynumber: 2.9 Consensus size: 59
105112 AAAAAAAAAA
* *
105122 TATTTTATTAAATAGGACAAAATATAAAAATAA-TTGACTATTAAA-ATATTTAAAGAACTCC
1 TATTTTATTAAATAGGA-AAAATATAAAAATAATTTG--T-TTAAATATATTAAAACAACTCC
**
105183 TATTTTATTAAATAGGATAAAATATAAAAATAATTTGTTTAAATATATTCAAAACAACTTT
1 TATTTTATTAAATAGGA-AAAATATAAAAATAATTTGTTTAAATATATT-AAAACAACTCC
* **
105244 TATTTTATTAAAT--GAAATAATATAAAAATAGTTTGTACAAATATATTAAAA
1 TATTTTATTAAATAGGAAA-AATATAAAAATAATTTGTTTAAATATATTAAAA
105295 AAATTAATAC
Statistics
Matches: 100, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
58 6 0.06
59 33 0.33
60 6 0.06
61 52 0.52
62 3 0.03
ACGTcount: A:0.51, C:0.05, G:0.06, T:0.38
Consensus pattern (59 bp):
TATTTTATTAAATAGGAAAAATATAAAAATAATTTGTTTAAATATATTAAAACAACTCC
Found at i:107302 original size:30 final size:32
Alignment explanation
Indices: 107230--107302 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 32
107220 AGTTGTTATA
* *
107230 AAAAATTATAAAATAAATATTAATTAAAATTAC
1 AAAAATT-GAAAATAAATATTAAATAAAATTAC
* *
107263 ATAAA-TGAAAA-AAATATTAAATAATATT-C
1 AAAAATTGAAAATAAATATTAAATAAAATTAC
107292 AAAAATTGAAA
1 AAAAATTGAAA
107303 TTAACCCTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
29 5 0.15
30 20 0.59
31 4 0.12
32 1 0.03
33 4 0.12
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (32 bp):
AAAAATTGAAAATAAATATTAAATAAAATTAC
Found at i:108384 original size:16 final size:16
Alignment explanation
Indices: 108363--108395 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
108353 CACTGTATTG
108363 GAATAGAGACGTAATA
1 GAATAGAGACGTAATA
108379 GAATAGAGACGTAATA
1 GAATAGAGACGTAATA
108395 G
1 G
108396 GTGAATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.48, C:0.06, G:0.27, T:0.18
Consensus pattern (16 bp):
GAATAGAGACGTAATA
Found at i:108963 original size:14 final size:14
Alignment explanation
Indices: 108944--108971 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
108934 AGCAGAAATC
108944 TGGAGAAAAGAAAA
1 TGGAGAAAAGAAAA
108958 TGGAGAAAAGAAAA
1 TGGAGAAAAGAAAA
108972 GAAATGTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.29, T:0.07
Consensus pattern (14 bp):
TGGAGAAAAGAAAA
Found at i:108969 original size:19 final size:18
Alignment explanation
Indices: 108947--108991 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
108937 AGAAATCTGG
108947 AGAAAAGAAAATG-GAGAAA
1 AGAAAAGAAAATGTGAG--A
108966 AGAAAAG-AAATGTGAGA
1 AGAAAAGAAAATGTGAGA
108983 AGAAAAGAA
1 AGAAAAGAA
108992 GCGTACCGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.33
18 6 0.25
19 10 0.42
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.07
Consensus pattern (18 bp):
AGAAAAGAAAATGTGAGA
Found at i:109356 original size:14 final size:14
Alignment explanation
Indices: 109334--109363 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
109324 TAATAAGGCT
*
109334 ATTCGAGAAAGTGA
1 ATTCAAGAAAGTGA
109348 ATTCAAGAAAGTGA
1 ATTCAAGAAAGTGA
109362 AT
1 AT
109364 GAGTTACTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.23, T:0.23
Consensus pattern (14 bp):
ATTCAAGAAAGTGA
Found at i:109533 original size:13 final size:13
Alignment explanation
Indices: 109515--109539 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
109505 CCGTGAAATC
109515 TATTGTTTTTACA
1 TATTGTTTTTACA
109528 TATTGTTTTTAC
1 TATTGTTTTTAC
109540 TGTCAAATTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.08, G:0.08, T:0.64
Consensus pattern (13 bp):
TATTGTTTTTACA
Found at i:114350 original size:19 final size:19
Alignment explanation
Indices: 114312--114354 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
114302 TAAAATTAAC
114312 TTTTTTAATTTTTTAAAAA
1 TTTTTTAATTTTTTAAAAA
*
114331 TATTTTTGATTTTTT-AAAA
1 T-TTTTTAATTTTTTAAAAA
114350 TTTTT
1 TTTTT
114355 AAAAATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 4 0.18
19 6 0.27
20 12 0.55
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTTTAATTTTTTAAAAA
Found at i:115120 original size:15 final size:15
Alignment explanation
Indices: 115095--115129 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
115085 GACTCTATTT
*
115095 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
115109 TAATTAATATTAAGA
1 TAATTAATATTAAGA
115124 TAATTA
1 TAATTA
115130 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:119387 original size:29 final size:30
Alignment explanation
Indices: 119332--119389 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
119322 CTTGCGTCAG
*
119332 GTAAAAACGCGCTGACGTGGACACACTTTA
1 GTAAAAACGCGCTGACGTGAACACACTTTA
*
119362 GTAAAAA-GCGCTGACAG-GAACGCACTTT
1 GTAAAAACGCGCTGAC-GTGAACACACTTT
119390 GGGCCGTGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.19
Consensus pattern (30 bp):
GTAAAAACGCGCTGACGTGAACACACTTTA
Found at i:119447 original size:21 final size:21
Alignment explanation
Indices: 119423--119465 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
119413 TATTTGCAAA
119423 TTAGGTCTTAG-GTTTTGGGTT
1 TTAGGT-TTAGAGTTTTGGGTT
*
119444 TTAGGTTTTGAGTTTTGGGTT
1 TTAGGTTTAGAGTTTTGGGTT
119465 T
1 T
119466 GATTAGGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.09, C:0.02, G:0.33, T:0.56
Consensus pattern (21 bp):
TTAGGTTTAGAGTTTTGGGTT
Found at i:119449 original size:14 final size:14
Alignment explanation
Indices: 119430--119465 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
119420 AAATTAGGTC
*
119430 TTAGGTTTTGGGTT
1 TTAGGTTTTGAGTT
119444 TTAGGTTTTGAGTT
1 TTAGGTTTTGAGTT
*
119458 TTGGGTTT
1 TTAGGTTT
119466 GATTAGGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.08, C:0.00, G:0.33, T:0.58
Consensus pattern (14 bp):
TTAGGTTTTGAGTT
Found at i:126597 original size:16 final size:18
Alignment explanation
Indices: 126566--126602 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 18
126556 TTTACAAATA
126566 CAAAAAACCCTAAAAGCC
1 CAAAAAACCCTAAAAGCC
126584 CAAAAAA-CCT-AAAGCC
1 CAAAAAACCCTAAAAGCC
126600 CAA
1 CAA
126603 TTGCCCATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.47
17 3 0.16
18 7 0.37
ACGTcount: A:0.57, C:0.32, G:0.05, T:0.05
Consensus pattern (18 bp):
CAAAAAACCCTAAAAGCC
Found at i:126740 original size:17 final size:18
Alignment explanation
Indices: 126709--126742 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
126699 TTACCTGCAA
*
126709 AAAGAACAGAGACAGAGG
1 AAAGAACAGAAACAGAGG
126727 AAAG-ACAGAAACAGAG
1 AAAGAACAGAAACAGAG
126743 ATAAAGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.59, C:0.12, G:0.29, T:0.00
Consensus pattern (18 bp):
AAAGAACAGAAACAGAGG
Found at i:128825 original size:60 final size:60
Alignment explanation
Indices: 128748--128866 Score: 220
Period size: 60 Copynumber: 2.0 Consensus size: 60
128738 GGGTTTCAAC
128748 AACTTCTAATTTATTAAATGAAACAATATAAAAATAATTTATACAAAAATATTCAAAAAA
1 AACTTCTAATTTATTAAATGAAACAATATAAAAATAATTTATACAAAAATATTCAAAAAA
* *
128808 AACTTCTATTTTATTAAATGAAACAATATAAAAATAATTTGTACAAAAATATTCAAAAA
1 AACTTCTAATTTATTAAATGAAACAATATAAAAATAATTTATACAAAAATATTCAAAAA
128867 TAAATCAATG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.33
Consensus pattern (60 bp):
AACTTCTAATTTATTAAATGAAACAATATAAAAATAATTTATACAAAAATATTCAAAAAA
Found at i:129270 original size:18 final size:18
Alignment explanation
Indices: 129243--129282 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
129233 TGGAAAAAGT
* *
129243 ATACATATAAGGATTAGG
1 ATACACATAAGGATTAAG
*
129261 ATACACATAAGGGTTAAG
1 ATACACATAAGGATTAAG
129279 ATAC
1 ATAC
129283 GCACCTTGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (18 bp):
ATACACATAAGGATTAAG
Found at i:130879 original size:31 final size:31
Alignment explanation
Indices: 130824--130885 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
130814 AAAATTATAA
* *
130824 AAAAATATTAATTGAATTATAAAAATAAAAT
1 AAAAATATTAAATAAATTATAAAAATAAAAT
*
130855 AAAAATATTAAATAATATTA-AAAAATGAAAT
1 AAAAATATTAAATAA-ATTATAAAAATAAAAT
130886 TAACCATTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 23 0.85
32 4 0.15
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (31 bp):
AAAAATATTAAATAAATTATAAAAATAAAAT
Found at i:138449 original size:14 final size:14
Alignment explanation
Indices: 138430--138459 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
138420 GAAAATGTTT
*
138430 AACATGTTATAATA
1 AACATGGTATAATA
138444 AACATGGTATAATA
1 AACATGGTATAATA
138458 AA
1 AA
138460 TAAATCATAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (14 bp):
AACATGGTATAATA
Found at i:139835 original size:40 final size:40
Alignment explanation
Indices: 139779--139873 Score: 156
Period size: 40 Copynumber: 2.4 Consensus size: 40
139769 ACTCTATGTT
* *
139779 TGGTGCGTTTCAGTTGGATCAGCTCTTATGAGCTTCTGTC
1 TGGTGTGTTTCGGTTGGATCAGCTCTTATGAGCTTCTGTC
139819 TGGTGTGTTTCGGTTGGATCAGCTCTTATGAGCTTCTGTC
1 TGGTGTGTTTCGGTTGGATCAGCTCTTATGAGCTTCTGTC
*
139859 TGGTATG-TTCGGTTG
1 TGGTGTGTTTCGGTTG
139874 ATTTAACGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 8 0.15
40 44 0.85
ACGTcount: A:0.11, C:0.17, G:0.31, T:0.42
Consensus pattern (40 bp):
TGGTGTGTTTCGGTTGGATCAGCTCTTATGAGCTTCTGTC
Found at i:141724 original size:21 final size:21
Alignment explanation
Indices: 141694--141746 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
141684 TAAAAGATAA
141694 ATCAATCTAATC-GATTCGATT
1 ATCAATCTAATCTG-TTCGATT
* * *
141715 ATCGATCTAAACTGTTCTATT
1 ATCAATCTAATCTGTTCGATT
141736 ATCAATCTAAT
1 ATCAATCTAAT
141747 TTTCACGGGC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.34, C:0.19, G:0.08, T:0.40
Consensus pattern (21 bp):
ATCAATCTAATCTGTTCGATT
Found at i:146905 original size:28 final size:28
Alignment explanation
Indices: 146865--146920 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
146855 CAAACAAAGT
146865 AAGCTTTTATAGCTTAGTAAGTCTATAG
1 AAGCTTTTATAGCTTAGTAAGTCTATAG
146893 AAGCTTTTATAGCTTAGTAAGTCTATAG
1 AAGCTTTTATAGCTTAGTAAGTCTATAG
146921 CATAACTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (28 bp):
AAGCTTTTATAGCTTAGTAAGTCTATAG
Found at i:147303 original size:71 final size:68
Alignment explanation
Indices: 147209--147386 Score: 197
Period size: 63 Copynumber: 2.6 Consensus size: 68
147199 AACCGAAAGC
* * * *
147209 ATATACAATTTGAAACATGAATAGCCGAATGTATATATACATATATGCTTAACAAATATTATCAT
1 ATATACACTTT-AAACATGAATAGCCGAATG-ATATATACATATA--CATAACAAATATAAT-AA
*
147274 C-GAATGT
61 CAAAATGT
*
147281 ATATACACTTTAAACATGAATAGCCGAATGCT-TATAC----ACATAACAAATATAATAACAAAA
1 ATATACACTTTAAACATGAATAGCCGAATGATATATACATATACATAACAAATATAATAACAAAA
147341 TGT
66 TGT
*
147344 ATATACACTTTAAACATGAATAGCTGAATGCATATATACATAT
1 ATATACACTTTAAACATGAATAGCCGAATG-ATATATACATAT
147387 GCCTAGCAAG
Statistics
Matches: 91, Mismatches: 8, Indels: 17
0.78 0.07 0.15
Matches are distributed among these distances:
62 2 0.02
63 47 0.52
64 1 0.01
65 6 0.07
69 5 0.05
70 1 0.01
71 19 0.21
72 10 0.11
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.31
Consensus pattern (68 bp):
ATATACACTTTAAACATGAATAGCCGAATGATATATACATATACATAACAAATATAATAACAAAA
TGT
Found at i:147382 original size:33 final size:32
Alignment explanation
Indices: 147275--147383 Score: 100
Period size: 31 Copynumber: 3.4 Consensus size: 32
147265 TATTATCATC
*
147275 GAATG-TATATACACTTTAAACATGAATAGCC
1 GAATGCTATATACACTTTAAACATGAATAGCA
* * * *
147306 GAATGCT-TATACAC-ATAACAAATATAATAACA
1 GAATGCTATATACACTTTAA-ACAT-GAATAGCA
* *
147338 AAATG-TATATACACTTTAAACATGAATAGCT
1 GAATGCTATATACACTTTAAACATGAATAGCA
147369 GAATGCATATATACA
1 GAATGC-TATATACA
147384 TATGCCTAGC
Statistics
Matches: 59, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
30 3 0.05
31 25 0.42
32 20 0.34
33 11 0.19
ACGTcount: A:0.47, C:0.15, G:0.10, T:0.28
Consensus pattern (32 bp):
GAATGCTATATACACTTTAAACATGAATAGCA
Found at i:149262 original size:45 final size:45
Alignment explanation
Indices: 149191--149295 Score: 126
Period size: 45 Copynumber: 2.3 Consensus size: 45
149181 ATATGCCGAC
* *
149191 TACTGTTACTATTATC-GATTCGACACTTTGTGTGTCAAATA-TAGT
1 TACTGTTACTGTTA-CAGATTCAACACTTTGTGTGTCAAATACT-GT
**
149236 TACCT-TTACTGTTACAGATTCAACACTTTGTGTGTTGAATACTGT
1 TA-CTGTTACTGTTACAGATTCAACACTTTGTGTGTCAAATACTGT
149281 TACTGTTACTGTTAC
1 TACTGTTACTGTTAC
149296 TGCTACCGTT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
44 3 0.06
45 46 0.88
46 3 0.06
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.43
Consensus pattern (45 bp):
TACTGTTACTGTTACAGATTCAACACTTTGTGTGTCAAATACTGT
Found at i:149286 original size:6 final size:6
Alignment explanation
Indices: 149275--149318 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
149265 GTGTGTTGAA
* *
149275 TACTGT TACTGT TACTGT TACTGC TACCGT TACTGAT TACTGT T
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTGT T
149319 TAGGTGTTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
6 27 0.82
7 6 0.18
ACGTcount: A:0.18, C:0.20, G:0.16, T:0.45
Consensus pattern (6 bp):
TACTGT
Found at i:150419 original size:41 final size:41
Alignment explanation
Indices: 150333--150434 Score: 96
Period size: 41 Copynumber: 2.5 Consensus size: 41
150323 TTTTAGCCTG
* * * * * * * * *
150333 CTAGACTTATAGTCCGAATTGTTTCACCGGTATTAAGCCTG
1 CTAGACATAAAGTCCGAAATATTTCACCAGCATCAAACCTA
150374 CTAGACATAAAGTCCGAAATATTTCACCAGCATCAAACCTA
1 CTAGACATAAAGTCCGAAATATTTCACCAGCATCAAACCTA
** *
150415 CTAGATGTAAAGTCTGAAAT
1 CTAGACATAAAGTCCGAAAT
150435 GTCCAATCAC
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (41 bp):
CTAGACATAAAGTCCGAAATATTTCACCAGCATCAAACCTA
Found at i:155095 original size:21 final size:22
Alignment explanation
Indices: 155066--155112 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
155056 CAGAAGGAGT
*
155066 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
155088 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
155109 GAGT
1 GAGT
155113 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:185412 original size:3 final size:3
Alignment explanation
Indices: 185406--185430 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
185396 TAACAACAAC
185406 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
185431 AAATAATTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:185666 original size:26 final size:28
Alignment explanation
Indices: 185630--185684 Score: 78
Period size: 26 Copynumber: 2.0 Consensus size: 28
185620 TGTAATTAAA
*
185630 TTTTTCATCAAACTTAAAAGGAAT-AAT
1 TTTTTCATCAAACTTAAAAGAAATCAAT
*
185657 TTTTTC-TCAAATTTAAAAGAAATCAAT
1 TTTTTCATCAAACTTAAAAGAAATCAAT
185684 T
1 T
185685 ATAGTGTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.40
Consensus pattern (28 bp):
TTTTTCATCAAACTTAAAAGAAATCAAT
Found at i:188036 original size:69 final size:69
Alignment explanation
Indices: 187940--188740 Score: 662
Period size: 69 Copynumber: 11.6 Consensus size: 69
187930 TGAACTCACC
* * * * *
187940 CTAACTGTGTTGGAGGCTACGACTCTTCACCAGTGAGCCTTAATGTGGCAGCTAGGAGCTTTGCT
1 CTAACTGTGTTGAAGGCTGCGACTCTTCACCTGTGAGCCTTAATGTGACAGCTGGGAGCTTTGCT
188005 CTCG
66 CTCG
* * * * * *
188009 CTAATTGTGTTGAAGGCTACAACTCTTCACTTGCGAGCCTTAATGTGACAGCTGAGAGCTTTGCT
1 CTAACTGTGTTGAAGGCTGCGACTCTTCACCTGTGAGCCTTAATGTGACAGCTGGGAGCTTTGCT
**
188074 CTTA
66 CTCG
* * * * * * * * *
188078 TTAACTATGTTGGAGACTGCGACTCTTCACTTGCGAGCCTTAATGTGATAGTTGGGAGCTTTACT
1 CTAACTGTGTTGAAGGCTGCGACTCTTCACCTGTGAGCCTTAATGTGACAGCTGGGAGCTTTGCT
* *
188143 ATCA
66 CTCG
* ** * * *
188147 CTAACTGTGTTGGAGGCTGC-AGCTCTTCACCTACGAGCCTTAGTATGACAGCTGAGAGCTTTGC
1 CTAACTGTGTTGAAGGCTGCGA-CTCTTCACCTGTGAGCCTTAATGTGACAGCTGGGAGCTTTGC
188211 TCTCG
65 TCTCG
* * * *
188216 CTAACTATGTT-AGAGGCTGCAACTCTTCACCTGTGAGTCTTAATGTGACAGCTGGGAGCTTTAC
1 CTAACTGTGTTGA-AGGCTGCGACTCTTCACCTGTGAGCCTTAATGTGACAGCTGGGAGCTTTGC
**
188280 TCTTA
65 TCTCG
* * * * * * * * *
188285 TTAACTGTGTTGAAGGTTGATG-TTTTTTATCTGCGAGCCTTAATGTGACAGTTGGGAGCTTTGC
1 CTAACTGTGTTGAAGGCTG-CGACTCTTCACCTGTGAGCCTTAATGTGACAGCTGGGAGCTTTGC
**
188349 TCTTA
65 TCTCG
* * * * * * * *
188354 CTAACTGTGTT-AGAGGATGTGGCTTTTCACCTGTGAACCTTAATGTGACAGTTGAGAGCTCTGC
1 CTAACTGTGTTGA-AGGCTGCGACTCTTCACCTGTGAGCCTTAATGTGACAGCTGGGAGCTTTGC
* *
188418 TTTTG
65 TCTCG
* * * * * ** * *
188423 CTAATTGCGTTGAAGGTTGCGGCTCTTCACCTTTGATTCTTAATGTGGCAGCTGGGAGCTTTACT
1 CTAACTGTGTTGAAGGCTGCGACTCTTCACCTGTGAGCCTTAATGTGACAGCTGGGAGCTTTGCT
*
188488 TTCG
66 CTCG
* * * *
188492 TTAACTGTGTT-AGAGGTTGCGACTCTTCACCTGTGAACCTTAATGTGACAGTTGGGAGCTTTGC
1 CTAACTGTGTTGA-AGGCTGCGACTCTTCACCTGTGAGCCTTAATGTGACAGCTGGGAGCTTTGC
*
188556 TGTCG
65 TCTCG
* * * * * * *
188561 CTAATTATGTTGAAGGTTACGGCTCTTCACCT-TCGACCCTTAATGTGACAGTTGGGAGCTTTGC
1 CTAACTGTGTTGAAGGCTGCGACTCTTCACCTGT-GAGCCTTAATGTGACAGCTGGGAGCTTTGC
*
188625 TCTCA
65 TCTCG
* * * * * * * *
188630 CTCATTGTGTTGAATGTTGTGGCTCTTCACCT-TCGAGCCTTAATGTGACAACTGGAAGCTTTGC
1 CTAACTGTGTTGAAGGCTGCGACTCTTCACCTGT-GAGCCTTAATGTGACAGCTGGGAGCTTTGC
*
188694 TCTTG
65 TCTCG
* * *
188699 TTAACTGTGTTGGAGGCTGCGACTCTTCACCTGCGAGCCTTA
1 CTAACTGTGTTGAAGGCTGCGACTCTTCACCTGTGAGCCTTA
188741 GTATGATAGT
Statistics
Matches: 595, Mismatches: 125, Indels: 24
0.80 0.17 0.03
Matches are distributed among these distances:
68 6 0.01
69 585 0.98
70 4 0.01
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.35
Consensus pattern (69 bp):
CTAACTGTGTTGAAGGCTGCGACTCTTCACCTGTGAGCCTTAATGTGACAGCTGGGAGCTTTGCT
CTCG
Found at i:188208 original size:207 final size:207
Alignment explanation
Indices: 187940--188756 Score: 838
Period size: 207 Copynumber: 3.9 Consensus size: 207
187930 TGAACTCACC
* * *
187940 CTAACTGTGTTGGAGGCTACGACTCTTCACC-AGTGAGCCTTAATGTGGCAGCT-AGGAGCTTTG
1 CTAACTGTGTTGGAGGCTACGGCTCTTCACCTA-CGAGCCTTAATGTGACAGCTGA-GAGCTTTG
* *
188003 CTCTCGCTAATTGTGTTGAAGGCTACAACTCTTCA-CTTGCGAGCCTTAATGTGACAGCTGAGAG
64 CTCTCGCTAATTGTGTTGAAGGCTGCAACTCTTCACCTT-CGAGCCTTAATGTGACAGCTGGGAG
* * * * *
188067 CTTTGCTCTTATTAACTATGTTGGAGACTGCGACTCTTCACTTGCGAGCCTTAATGTGATAGTTG
128 CTTTACTCTTATTAACTGTGTTGGAGGCTGCGACTCTTCACCTGCGAGCCTTAATGTGACAGTTG
*
188132 GGAGCTTTACTATCA
193 GGAGCTTTGCTATCA
* * * *
188147 CTAACTGTGTTGGAGGCTGCAGCTCTTCACCTACGAGCCTTAGTATGACAGCTGAGAGCTTTGCT
1 CTAACTGTGTTGGAGGCTACGGCTCTTCACCTACGAGCCTTAATGTGACAGCTGAGAGCTTTGCT
* * *
188212 CTCGCTAACTATGTT-AGAGGCTGCAACTCTTCACCTGT-GAGTCTTAATGTGACAGCTGGGAGC
66 CTCGCTAATTGTGTTGA-AGGCTGCAACTCTTCACCT-TCGAGCCTTAATGTGACAGCTGGGAGC
* * * * * * *
188275 TTTACTCTTATTAACTGTGTTGAAGGTTGATG-TTTTTTATCTGCGAGCCTTAATGTGACAGTTG
129 TTTACTCTTATTAACTGTGTTGGAGGCTG-CGACTCTTCACCTGCGAGCCTTAATGTGACAGTTG
* *
188339 GGAGCTTTGCTCTTA
193 GGAGCTTTGCTATCA
* * ** * ** * * *
188354 CTAACTGTGTTAGAGGATGTGGCTTTTCACCTGTGAACCTTAATGTGACAGTTGAGAGCTCTGCT
1 CTAACTGTGTTGGAGGCTACGGCTCTTCACCTACGAGCCTTAATGTGACAGCTGAGAGCTTTGCT
* * * * ** * ** *
188419 TTTGCTAATTGCGTTGAAGGTTGCGGCTCTTCACCTTTGATTCTTAATGTGGCAGCTGGGAGCTT
66 CTCGCTAATTGTGTTGAAGGCTGCAACTCTTCACCTTCGAGCCTTAATGTGACAGCTGGGAGCTT
* * * * *
188484 TACT-TTCGTTAACTGTGTTAGAGGTTGCGACTCTTCACCTGTGAACCTTAATGTGACAGTTGGG
131 TACTCTT-ATTAACTGTGTTGGAGGCTGCGACTCTTCACCTGCGAGCCTTAATGTGACAGTTGGG
* *
188548 AGCTTTGCTGTCG
195 AGCTTTGCTATCA
* * * * * * * *
188561 CTAATTATGTTGAAGGTTACGGCTCTTCACCTTCGACCCTTAATGTGACAGTTGGGAGCTTTGCT
1 CTAACTGTGTTGGAGGCTACGGCTCTTCACCTACGAGCCTTAATGTGACAGCTGAGAGCTTTGCT
* * * * *** * *
188626 CTCACTCATTGTGTTGAATGTTGTGGCTCTTCACCTTCGAGCCTTAATGTGACAACTGGAAGCTT
66 CTCGCTAATTGTGTTGAAGGCTGCAACTCTTCACCTTCGAGCCTTAATGTGACAGCTGGGAGCTT
* * * * *
188691 TGCTCTTGTTAACTGTGTTGGAGGCTGCGACTCTTCACCTGCGAGCCTTAGTATGATAGTTGGGA
131 TACTCTTATTAACTGTGTTGGAGGCTGCGACTCTTCACCTGCGAGCCTTAATGTGACAGTTGGGA
188756 G
196 G
188757 ATAGGAATTT
Statistics
Matches: 503, Mismatches: 96, Indels: 22
0.81 0.15 0.04
Matches are distributed among these distances:
206 5 0.01
207 489 0.97
208 8 0.02
209 1 0.00
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.35
Consensus pattern (207 bp):
CTAACTGTGTTGGAGGCTACGGCTCTTCACCTACGAGCCTTAATGTGACAGCTGAGAGCTTTGCT
CTCGCTAATTGTGTTGAAGGCTGCAACTCTTCACCTTCGAGCCTTAATGTGACAGCTGGGAGCTT
TACTCTTATTAACTGTGTTGGAGGCTGCGACTCTTCACCTGCGAGCCTTAATGTGACAGTTGGGA
GCTTTGCTATCA
Found at i:188756 original size:138 final size:138
Alignment explanation
Indices: 187940--188740 Score: 737
Period size: 138 Copynumber: 5.8 Consensus size: 138
187930 TGAACTCACC
* * * * *
187940 CTAACTGTGTTGGAGGCTACGACTCTTCACCAGTGAGCCTTAATGTGGCAGCTAGGAGCTTTGCT
1 CTAACTGTGTTAGAGGCTGCGACTCTTCACCTGTGAGCCTTAATGTGACAGCTGGGAGCTTTGCT
* * * * *
188005 CTCGCTAATTGTGTTGAAGGCTACAACTCTTCACTTGCGAGCCTTAATGTGACAGCTGAGAGCTT
66 CTCGCTAACTGTGTTGAAGGCTGCGACTCTTCACCTGCGAGCCTTAATGTGACAGCTGGGAGCTT
*
188070 TGCTCTTA
131 TGCTCTCA
* * * * * * * * *
188078 TTAACTATGTTGGAGACTGCGACTCTTCACTTGCGAGCCTTAATGTGATAGTTGGGAGCTTTACT
1 CTAACTGTGTTAGAGGCTGCGACTCTTCACCTGTGAGCCTTAATGTGACAGCTGGGAGCTTTGCT
* * * * * * *
188143 ATCACTAACTGTGTTGGAGGCTGC-AGCTCTTCACCTACGAGCCTTAGTATGACAGCTGAGAGCT
66 CTCGCTAACTGTGTTGAAGGCTGCGA-CTCTTCACCTGCGAGCCTTAATGTGACAGCTGGGAGCT
*
188207 TTGCTCTCG
130 TTGCTCTCA
* * * *
188216 CTAACTATGTTAGAGGCTGCAACTCTTCACCTGTGAGTCTTAATGTGACAGCTGGGAGCTTTACT
1 CTAACTGTGTTAGAGGCTGCGACTCTTCACCTGTGAGCCTTAATGTGACAGCTGGGAGCTTTGCT
*** * * * * * * *
188281 CTTATTAACTGTGTTGAAGGTTGATG-TTTTTTATCTGCGAGCCTTAATGTGACAGTTGGGAGCT
66 CTCGCTAACTGTGTTGAAGGCTG-CGACTCTTCACCTGCGAGCCTTAATGTGACAGCTGGGAGCT
*
188345 TTGCTCTTA
130 TTGCTCTCA
* * * * * * * *
188354 CTAACTGTGTTAGAGGATGTGGCTTTTCACCTGTGAACCTTAATGTGACAGTTGAGAGCTCTGCT
1 CTAACTGTGTTAGAGGCTGCGACTCTTCACCTGTGAGCCTTAATGTGACAGCTGGGAGCTTTGCT
* * * * * * ** ** *
188419 TTTGCTAATTGCGTTGAAGGTTGCGGCTCTTCACCTTTGATTCTTAATGTGGCAGCTGGGAGCTT
66 CTCGCTAACTGTGTTGAAGGCTGCGACTCTTCACCTGCGAGCCTTAATGTGACAGCTGGGAGCTT
* * *
188484 TACTTTCG
131 TGCTCTCA
* * * *
188492 TTAACTGTGTTAGAGGTTGCGACTCTTCACCTGTGAACCTTAATGTGACAGTTGGGAGCTTTGCT
1 CTAACTGTGTTAGAGGCTGCGACTCTTCACCTGTGAGCCTTAATGTGACAGCTGGGAGCTTTGCT
* * * * * * * * *
188557 GTCGCTAATTATGTTGAAGGTTACGGCTCTTCACCTTCGACCCTTAATGTGACAGTTGGGAGCTT
66 CTCGCTAACTGTGTTGAAGGCTGCGACTCTTCACCTGCGAGCCTTAATGTGACAGCTGGGAGCTT
188622 TGCTCTCA
131 TGCTCTCA
* * * * * * * *
188630 CTCATTGTGTT-GAATGTTGTGGCTCTTCACCT-TCGAGCCTTAATGTGACAACTGGAAGCTTTG
1 CTAACTGTGTTAG-AGGCTGCGACTCTTCACCTGT-GAGCCTTAATGTGACAGCTGGGAGCTTTG
* * *
188693 CTCTTGTTAACTGTGTTGGAGGCTGCGACTCTTCACCTGCGAGCCTTA
64 CTCTCGCTAACTGTGTTGAAGGCTGCGACTCTTCACCTGCGAGCCTTA
188741 GTATGATAGT
Statistics
Matches: 535, Mismatches: 122, Indels: 12
0.80 0.18 0.02
Matches are distributed among these distances:
137 4 0.01
138 531 0.99
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.35
Consensus pattern (138 bp):
CTAACTGTGTTAGAGGCTGCGACTCTTCACCTGTGAGCCTTAATGTGACAGCTGGGAGCTTTGCT
CTCGCTAACTGTGTTGAAGGCTGCGACTCTTCACCTGCGAGCCTTAATGTGACAGCTGGGAGCTT
TGCTCTCA
Found at i:192723 original size:46 final size:44
Alignment explanation
Indices: 192619--192726 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
192609 TGTCTTTGAC
** * * *
192619 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
192663 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
192709 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
192727 TTTCTGTACT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:193595 original size:19 final size:20
Alignment explanation
Indices: 193573--193613 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
193563 TTCTATTCTG
*
193573 TTTCTTTTCTTTCTTTT-TT
1 TTTCTATTCTTTCTTTTGTT
193592 TTTCTATTCTTTCTTTTGTT
1 TTTCTATTCTTTCTTTTGTT
193612 TT
1 TT
193614 ATGTATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.80
Consensus pattern (20 bp):
TTTCTATTCTTTCTTTTGTT
Found at i:193601 original size:15 final size:15
Alignment explanation
Indices: 193563--193608 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
193553 GTTTCGTCTC
*
193563 TTCTATTCTGTTTCTT
1 TTCTATTCT-TTTTTT
193579 TTCT-TTCTTTTTTT
1 TTCTATTCTTTTTTT
193593 TTCTATTCTTTCTTTT
1 TTCTATTCTTT-TTTT
193609 GTTTTATGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 9 0.33
15 10 0.37
16 8 0.30
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.76
Consensus pattern (15 bp):
TTCTATTCTTTTTTT
Found at i:193630 original size:5 final size:5
Alignment explanation
Indices: 193617--193689 Score: 64
Period size: 5 Copynumber: 14.6 Consensus size: 5
193607 TTGTTTTATG
193617 TATATA TATAA TATAA TATAA TAT-A T-TAA TGATAA TATAA TATAA -A-AA
1 TATA-A TATAA TATAA TATAA TATAA TATAA T-ATAA TATAA TATAA TATAA
* *
193665 CATAA TCATTAC TATAA TATAA TAT
1 TATAA T-A-TAA TATAA TATAA TAT
193690 TTTTTTAACA
Statistics
Matches: 57, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
3 3 0.05
4 6 0.11
5 35 0.61
6 10 0.18
7 3 0.05
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:193642 original size:19 final size:19
Alignment explanation
Indices: 193618--193660 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
193608 TGTTTTATGT
193618 ATATATATAAT-ATAATATA
1 ATATAT-TAATGATAATATA
193637 ATATATTAATGATAATATA
1 ATATATTAATGATAATATA
193656 ATATA
1 ATATA
193661 AAAACATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
ATATATTAATGATAATATA
Found at i:193670 original size:24 final size:24
Alignment explanation
Indices: 193624--193688 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
193614 ATGTATATAT
* * *
193624 ATAATATAATATAATATATTAATG
1 ATAATATAATATAATAAAATAATC
193648 ATAATATAATATAA-AAACATAATC
1 ATAATATAATATAATAAA-ATAATC
*
193672 ATTACTATAATATAATA
1 A-TAATATAATATAATA
193689 TTTTTTTAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
23 2 0.06
24 19 0.56
25 12 0.35
26 1 0.03
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.37
Consensus pattern (24 bp):
ATAATATAATATAATAAAATAATC
Found at i:203080 original size:20 final size:20
Alignment explanation
Indices: 203057--203095 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
203047 ATTTTTACAT
203057 ATATTAATAAATTTATATAA
1 ATATTAATAAATTTATATAA
*
203077 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
203096 TTTTAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAA
Found at i:205846 original size:6 final size:6
Alignment explanation
Indices: 205825--205867 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
205815 GAAGGATAGA
** * *
205825 GGAAGG GGAATA GGAAGG GGAAGG GGAAGG GAAAGG GAAAGG G
1 GGAAGG GGAAGG GGAAGG GGAAGG GGAAGG GGAAGG GGAAGG G
205868 AAGATCGGTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.40, C:0.00, G:0.58, T:0.02
Consensus pattern (6 bp):
GGAAGG
Found at i:211163 original size:31 final size:31
Alignment explanation
Indices: 211128--211191 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
211118 ATTTTTTTAT
211128 TGTAGAATAATTAAATTATTTGTTCCACTAA
1 TGTAGAATAATTAAATTATTTGTTCCACTAA
211159 TGTAGAATAATTAAATTATTTGTTCCACTAA
1 TGTAGAATAATTAAATTATTTGTTCCACTAA
211190 TG
1 TG
211192 ATATTTTAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (31 bp):
TGTAGAATAATTAAATTATTTGTTCCACTAA
Found at i:211445 original size:18 final size:17
Alignment explanation
Indices: 211422--211471 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
211412 ATATATTATG
211422 ATTTTAGTAAATTCAAAT
1 ATTTTAGTAAATT-AAAT
* *
211440 ATTTTATTAAATTACAT
1 ATTTTAGTAAATTAAAT
*
211457 ATTTTTATTAAATTA
1 A-TTTTAGTAAATTA
211472 TATTTAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.14
18 25 0.86
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (17 bp):
ATTTTAGTAAATTAAAT
Found at i:211666 original size:39 final size:42
Alignment explanation
Indices: 211616--211726 Score: 129
Period size: 39 Copynumber: 2.6 Consensus size: 42
211606 GTTTTTTTCC
* *
211616 TTATACTATTACACCTCTATTCCATTT-AACCAAACACAAGAA
1 TTAT-CTATTACGCCTCTATTCCATTTCAACCAAACAAAAGAA
211658 -TATC-ATTACGCCTCTATTCCATTCAATTCAACCAAACAAAAGAA
1 TTATCTATTACGCCTCTATTCCA-T---TTCAACCAAACAAAAGAA
*
211702 TTATCTATTATGCCTCTATTCCATT
1 TTATCTATTACGCCTCTATTCCATT
211727 ACGCATCTAT
Statistics
Matches: 59, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
39 16 0.27
40 2 0.03
41 3 0.05
42 1 0.02
43 2 0.03
44 14 0.24
45 5 0.08
46 16 0.27
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (42 bp):
TTATCTATTACGCCTCTATTCCATTTCAACCAAACAAAAGAA
Found at i:211735 original size:16 final size:16
Alignment explanation
Indices: 211716--211761 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
211706 CTATTATGCC
*
211716 TCTATTCCATTACGCA
1 TCTATTCCATTACACA
* *
211732 TCTATTCTATTACACC
1 TCTATTCCATTACACA
*
211748 TTTATTCCATTACA
1 TCTATTCCATTACA
211762 GCGAACCAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.26, C:0.28, G:0.02, T:0.43
Consensus pattern (16 bp):
TCTATTCCATTACACA
Found at i:218361 original size:31 final size:31
Alignment explanation
Indices: 218293--218375 Score: 82
Period size: 30 Copynumber: 2.7 Consensus size: 31
218283 CTAAAAAAGC
*
218293 TTAAGTACCAAATTAGAAAAAAGTGCTGAAT
1 TTAAGTACCAAATTAGAAAAAAGTGCTCAAT
* *
218324 TT-AGTACCAACTTA-AGAAAAATTG-TCAAGT
1 TTAAGTACCAAATTAGA-AAAAAGTGCTCAA-T
* *
218354 TTAAGTACCGAATTGGAAAAAA
1 TTAAGTACCAAATTAGAAAAAA
218376 ATTTTAGGTA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
29 4 0.10
30 21 0.50
31 16 0.38
32 1 0.02
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.27
Consensus pattern (31 bp):
TTAAGTACCAAATTAGAAAAAAGTGCTCAAT
Found at i:229370 original size:4 final size:4
Alignment explanation
Indices: 229361--229390 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
229351 TAAGGACACT
*
229361 AACA AACA AACA AACA AACA AACA ATCA AA
1 AACA AACA AACA AACA AACA AACA AACA AA
229391 ACTCACTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.73, C:0.23, G:0.00, T:0.03
Consensus pattern (4 bp):
AACA
Found at i:233407 original size:18 final size:17
Alignment explanation
Indices: 233374--233412 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
233364 TTGTATAAAT
233374 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
233392 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
233409 TGTG
1 TGTG
233413 GAAGGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:233665 original size:23 final size:23
Alignment explanation
Indices: 233638--233735 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
233628 AGTGTTATTG
233638 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
233661 TTCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
233684 -CCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
233706 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
233729 ATCAGTG
1 ATCAGTG
233736 TGGCACTTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:233704 original size:45 final size:45
Alignment explanation
Indices: 233640--233728 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
233630 TGTTATTGAT
* *
233640 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTTGGCTACATC
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
233685 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
233729 ATCAGTGTGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.19, C:0.22, G:0.27, T:0.31
Consensus pattern (45 bp):
CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
Found at i:249519 original size:28 final size:29
Alignment explanation
Indices: 249482--249538 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
249472 AAAAATCTAA
*
249482 AAAATTCTAAAGAATATATAAA-AATAAAT
1 AAAATTCTAAAAAATATA-AAATAATAAAT
*
249511 AAAA-TCTAAAAAATCTAAAATAATAAAT
1 AAAATTCTAAAAAATATAAAATAATAAAT
249539 TTGAGGACAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 3 0.12
28 18 0.72
29 4 0.16
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (29 bp):
AAAATTCTAAAAAATATAAAATAATAAAT
Found at i:249530 original size:8 final size:9
Alignment explanation
Indices: 249472--249530 Score: 57
Period size: 9 Copynumber: 6.3 Consensus size: 9
249462 AATATTCAAT
249472 AAAAATCTA
1 AAAAATCTA
249481 AAAAATTCTA
1 AAAAA-TCTA
* *
249491 AAGAATATA
1 AAAAATCTA
*
249500 TAAAAAT-AA
1 -AAAAATCTA
249509 ATAAAATCTA
1 A-AAAATCTA
249519 AAAAATCTA
1 AAAAATCTA
249528 AAA
1 AAA
249531 TAATAAATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
8 1 0.02
9 25 0.61
10 15 0.37
ACGTcount: A:0.68, C:0.07, G:0.02, T:0.24
Consensus pattern (9 bp):
AAAAATCTA
Found at i:254360 original size:20 final size:20
Alignment explanation
Indices: 254335--254373 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
254325 TAAATATATT
254335 AATATATTAT-TTAATTATAA
1 AATATATTATATT-ATTATAA
254355 AATATATTATATTATTATA
1 AATATATTATATTATTATA
254374 TTATGTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AATATATTATATTATTATAA
Found at i:254499 original size:19 final size:20
Alignment explanation
Indices: 254475--254514 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
254465 AGTAAAATGT
254475 TTTTCTG-AAAATGATTTAC
1 TTTTCTGAAAAATGATTTAC
254494 TTTTCTGAAAAATGATTTAC
1 TTTTCTGAAAAATGATTTAC
254514 T
1 T
254515 GAAAATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.47
Consensus pattern (20 bp):
TTTTCTGAAAAATGATTTAC
Found at i:254635 original size:20 final size:20
Alignment explanation
Indices: 254610--254648 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
254600 GTTTTTACAT
254610 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
254630 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
254649 TTTTAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:254711 original size:18 final size:18
Alignment explanation
Indices: 254688--254723 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
254678 GATTTATTTA
254688 TAAATAAATAAATCAAAT
1 TAAATAAATAAATCAAAT
* *
254706 TAAATATATCAATCAAAT
1 TAAATAAATAAATCAAAT
254724 GGTTTAATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAATAAATAAATCAAAT
Found at i:256942 original size:5 final size:5
Alignment explanation
Indices: 256932--256964 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
256922 TTTTTATGAT
256932 TTATA TTATA TTATA TTATA TTA-A TATATA TTA
1 TTATA TTATA TTATA TTATA TTATA T-TATA TTA
256965 AATAAATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 2 0.08
5 22 0.85
6 2 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TTATA
Found at i:257182 original size:17 final size:18
Alignment explanation
Indices: 257160--257195 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
257150 GGAATAAAAT
*
257160 AAAAGAATAAA-AGAAAC
1 AAAAGAAGAAATAGAAAC
257177 AAAAGAAGAAATAGAAAC
1 AAAAGAAGAAATAGAAAC
257195 A
1 A
257196 GAATAGCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.75, C:0.06, G:0.14, T:0.06
Consensus pattern (18 bp):
AAAAGAAGAAATAGAAAC
Found at i:258135 original size:21 final size:21
Alignment explanation
Indices: 258081--258188 Score: 137
Period size: 21 Copynumber: 5.1 Consensus size: 21
258071 GGCTTTGCCG
258081 ATCAGGCACTTTATGTGTCGT
1 ATCAGGCACTTTATGTGTCGT
*
258102 ATCTCAAGCACTTTATGTGTCGT
1 A--TCAGGCACTTTATGTGTCGT
258125 ATCAGGCACTTTATGTGTCGT
1 ATCAGGCACTTTATGTGTCGT
**
258146 ATCAGGCACTTCGTGTGTCGT
1 ATCAGGCACTTTATGTGTCGT
* * *
258167 TTCAAGCAC-TTATGTGCCGT
1 ATCAGGCACTTTATGTGTCGT
258187 AT
1 AT
258189 ACTGATCAGG
Statistics
Matches: 75, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
20 9 0.12
21 46 0.61
23 20 0.27
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.37
Consensus pattern (21 bp):
ATCAGGCACTTTATGTGTCGT
Done.