Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 25 of 226
Found at i:11392015 original size:17 final size:18
Alignment explanation
Indices: 11391989--11392022 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
11391979 TTTGTCACAA
11391989 TTTATAATTAT-ATATTT
1 TTTATAATTATAATATTT
*
11392006 TTTATCATTATAATATT
1 TTTATAATTATAATATT
11392023 AAAGGAGACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTATAATTATAATATTT
Found at i:11393151 original size:2 final size:2
Alignment explanation
Indices: 11393144--11393205 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
11393134 ACAGTAGGTA
11393144 CT CT CT CT CT CT CT 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 CT CT CT CT CT CT CT
11393186 CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT
11393206 TATTGCCACT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:11417573 original size:21 final size:22
Alignment explanation
Indices: 11417531--11417574 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
11417521 ACAATAATTT
*
11417531 TATTTATATTTTAAATTGTAAA
1 TATTTATATTTTAAAGTGTAAA
11417553 TATTTA-ATTTTTAAAGT-TAAA
1 TATTTATA-TTTTAAAGTGTAAA
11417574 T
1 T
11417575 TTATGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
TATTTATATTTTAAAGTGTAAA
Found at i:11418688 original size:20 final size:21
Alignment explanation
Indices: 11418665--11418703 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
11418655 AGCTATTCAA
11418665 ATAA-TATTTTTTGAATAGTT
1 ATAATTATTTTTTGAATAGTT
*
11418685 ATAATTCTTTTTTGAATAG
1 ATAATTATTTTTTGAATAG
11418704 GTGTCTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.54
Consensus pattern (21 bp):
ATAATTATTTTTTGAATAGTT
Found at i:11420933 original size:18 final size:18
Alignment explanation
Indices: 11420895--11420930 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
11420885 CTATTATTTT
*
11420895 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
11420913 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
11420931 TAATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:11420941 original size:31 final size:29
Alignment explanation
Indices: 11420905--11420970 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 29
11420895 TAAAATTTAC
11420905 TATTAAAATAAAATTTAA-ATATTAAATAATT
1 TATTAAAA-AAAA-TTAATATATT-AATAATT
*
11420936 TATTAAAAATAATTAATTATATTAATAATT
1 TATTAAAAAAAATTAA-TATATTAATAATT
11420966 TATTA
1 TATTA
11420971 TATGACTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
29 4 0.12
30 15 0.47
31 13 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
TATTAAAAAAAATTAATATATTAATAATT
Found at i:11420945 original size:14 final size:16
Alignment explanation
Indices: 11420927--11420973 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
11420917 ATTTAAATAT
11420927 TAAATAATTTATTA-A
1 TAAATAATTTATTATA
*
11420942 -AAATAATTAATTATA
1 TAAATAATTTATTATA
*
11420957 TTAATAATTTATTATA
1 TAAATAATTTATTATA
11420973 T
1 T
11420974 GACTAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 12 0.44
15 1 0.04
16 14 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TAAATAATTTATTATA
Found at i:11421237 original size:21 final size:22
Alignment explanation
Indices: 11421210--11421267 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
11421200 AAATATGCTT
*
11421210 ATTTTTCGTTGACCTGTAAGTC
1 ATTTTCCGTTGACCTGTAAGTC
11421232 ATTTTCCGTTGACCTGTAAGTC
1 ATTTTCCGTTGACCTGTAAGTC
11421254 ATTTTCCGTTGACC
1 ATTTTCCGTTGACC
11421268 AAGCTGTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.43
Consensus pattern (22 bp):
ATTTTCCGTTGACCTGTAAGTC
Found at i:11431752 original size:13 final size:13
Alignment explanation
Indices: 11431736--11431760 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11431726 TATTATATTC
11431736 TTTATTTTCTTTA
1 TTTATTTTCTTTA
11431749 TTTATTTTCTTT
1 TTTATTTTCTTT
11431761 TAATGTTTAT
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:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTATTTTCTTTA
Found at i:11436332 original size:48 final size:48
Alignment explanation
Indices: 11436261--11436355 Score: 145
Period size: 48 Copynumber: 2.0 Consensus size: 48
11436251 TTCTTTGCTC
** **
11436261 AAAAACGCCTAAGTCAGCCTAACTTGCAGTAATAAAGGATTCAACAGT
1 AAAAACGCCTAAGTCAGCCTAACTCACAACAATAAAGGATTCAACAGT
*
11436309 AAAAACGCCTAAGTCAGCTTAACTCACAACAATAAAGGATTCAACAG
1 AAAAACGCCTAAGTCAGCCTAACTCACAACAATAAAGGATTCAACAG
11436356 AATTCCCTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.44, C:0.22, G:0.15, T:0.19
Consensus pattern (48 bp):
AAAAACGCCTAAGTCAGCCTAACTCACAACAATAAAGGATTCAACAGT
Found at i:11436693 original size:35 final size:36
Alignment explanation
Indices: 11436653--11436724 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
11436643 TCTAGGATCA
11436653 CATATC-TCAAAAGATCACCTTCCATATTTGCCAAG
1 CATATCTTCAAAAGATCACCTTCCATATTTGCCAAG
* *
11436688 CATATCTTCAAAAGATCACTTTCCTTATTTGCCAAG
1 CATATCTTCAAAAGATCACCTTCCATATTTGCCAAG
11436724 C
1 C
11436725 TCCAGAGAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 6 0.18
36 28 0.82
ACGTcount: A:0.32, C:0.28, G:0.08, T:0.32
Consensus pattern (36 bp):
CATATCTTCAAAAGATCACCTTCCATATTTGCCAAG
Found at i:11445028 original size:41 final size:41
Alignment explanation
Indices: 11444938--11445040 Score: 116
Period size: 41 Copynumber: 2.5 Consensus size: 41
11444928 TGATTCAGTA
* * * *
11444938 CACCGGCTTTTAGCCTGCTAGACCTATAGTCCGAAATGTAT
1 CACCGGCATTAAGCCTGCTAGACCTAAAGTCCGAAATATAT
* * * * *
11444979 CACAGGCATTAAGCCTGCTAGACGTAAAGTCTGAATTATTT
1 CACCGGCATTAAGCCTGCTAGACCTAAAGTCCGAAATATAT
*
11445020 CACCGGCATCAAGCCTGCTAG
1 CACCGGCATTAAGCCTGCTAG
11445041 GCACATAGCC
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.26
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACCTAAAGTCCGAAATATAT
Found at i:11445799 original size:21 final size:21
Alignment explanation
Indices: 11445769--11445810 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
11445759 TCATAAAATC
*
11445769 AAATTTAGCTTATAGAACATA
1 AAATTCAGCTTATAGAACATA
11445790 AAATTCAGCTTATAGAACATA
1 AAATTCAGCTTATAGAACATA
11445811 TATATATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.31
Consensus pattern (21 bp):
AAATTCAGCTTATAGAACATA
Found at i:11455021 original size:7 final size:7
Alignment explanation
Indices: 11455011--11455068 Score: 50
Period size: 7 Copynumber: 8.4 Consensus size: 7
11455001 AAAAAAATAA
11455011 AAATATT
1 AAATATT
11455018 AAAT-TT
1 AAATATT
11455024 AAAT-TT
1 AAATATT
* **
11455030 AAAAAAG
1 AAATATT
11455037 AAA-ATT
1 AAATATT
11455043 ATAATATT
1 A-AATATT
11455051 AAATATTT
1 AAATA-TT
11455059 AAATATT
1 AAATATT
11455066 AAA
1 AAA
11455069 AAAATATTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
6 13 0.31
7 18 0.43
8 11 0.26
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (7 bp):
AAATATT
Found at i:11455030 original size:29 final size:33
Alignment explanation
Indices: 11454998--11455074 Score: 90
Period size: 35 Copynumber: 2.4 Consensus size: 33
11454988 ATTATATATT
11454998 TTTAAAAAAATAA-A-AATATT-AA-ATTTAAA
1 TTTAAAAAAATAATATAATATTAAATATTTAAA
*
11455027 TTTAAAAAAGAAAATTATAATATTAAATATTTAAA
1 TTTAAAAAA-ATAA-TATAATATTAAATATTTAAA
11455062 TATTAAAAAAATA
1 T-TTAAAAAAATA
11455075 TTATTTACTT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
29 9 0.23
30 3 0.08
32 1 0.03
33 6 0.15
34 2 0.05
35 10 0.26
36 8 0.21
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (33 bp):
TTTAAAAAAATAATATAATATTAAATATTTAAA
Found at i:11455118 original size:21 final size:21
Alignment explanation
Indices: 11455094--11455138 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
11455084 TTGATCGGCC
*
11455094 ATTAATTGACGTTGACCAACT
1 ATTAATTGACATTGACCAACT
*
11455115 ATTAATTGACATTGACCAAGT
1 ATTAATTGACATTGACCAACT
11455136 ATT
1 ATT
11455139 GACCAGCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.36
Consensus pattern (21 bp):
ATTAATTGACATTGACCAACT
Found at i:11460673 original size:14 final size:14
Alignment explanation
Indices: 11460654--11460685 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
11460644 AGTTATCTGA
11460654 AAAGGAACCATTCC
1 AAAGGAACCATTCC
11460668 AAAGGAACCATTCC
1 AAAGGAACCATTCC
11460682 AAAG
1 AAAG
11460686 CAGTTGCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.25, G:0.16, T:0.12
Consensus pattern (14 bp):
AAAGGAACCATTCC
Found at i:11467149 original size:15 final size:15
Alignment explanation
Indices: 11467129--11467161 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
11467119 ATCACTCTTT
11467129 TTTTAT-TTTTTAATC
1 TTTTATCTTTTT-ATC
11467144 TTTTATCTTTTTATC
1 TTTTATCTTTTTATC
11467159 TTT
1 TTT
11467162 CCAAGCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTATCTTTTTATC
Found at i:11478680 original size:18 final size:17
Alignment explanation
Indices: 11478648--11478683 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
11478638 ATTTTTCAAG
11478648 TTTTAAAATTTTGAATT
1 TTTTAAAATTTTGAATT
*
11478665 TTTTGAAATATTTGAATT
1 TTTTAAAAT-TTTGAATT
11478683 T
1 T
11478684 GGACTAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58
Consensus pattern (17 bp):
TTTTAAAATTTTGAATT
Found at i:11481996 original size:33 final size:33
Alignment explanation
Indices: 11481943--11482020 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 33
11481933 TGGCCCTGCC
*
11481943 ATGGTCTTACACTCGTAATGCCATAACCCAGTT
1 ATGGTCTTACACTCGTAATGCCATAACCCAGCT
*
11481976 ATGGTCTTATCA-TCAG-AATGCCATAGCCCAGCT
1 ATGGTCTTA-CACTC-GTAATGCCATAACCCAGCT
11482009 ATGGTCTTACAC
1 ATGGTCTTACAC
11482021 GTATACATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
32 2 0.05
33 35 0.88
34 3 0.08
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (33 bp):
ATGGTCTTACACTCGTAATGCCATAACCCAGCT
Found at i:11482134 original size:105 final size:101
Alignment explanation
Indices: 11481961--11482151 Score: 274
Period size: 105 Copynumber: 1.9 Consensus size: 101
11481951 ACACTCGTAA
* * * *
11481961 TGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAGCTATGGTCTTACACGTATA
1 TGCCATAACCCAGTTATGGTCTTATCATCAAAATGCCATAGCCCAGCTACGATCTTACACGTAAA
11482026 CATTTACTGCCATGGTCCAACCATGGTCTTACGTTTAAGG
66 CA--T--TGCCATGGTCCAACCATGGTCTTACGTTTAAGG
* * **
11482066 TGCCATAACCCAGTTATGGTCTTTTCATTAAAATGCCATAGCCCAGCTACGATCTTACATTTAAA
1 TGCCATAACCCAGTTATGGTCTTATCATCAAAATGCCATAGCCCAGCTACGATCTTACACGTAAA
11482131 CATTGCCATGGTCCAACCATG
66 CATTGCCATGGTCCAACCATG
11482152 ATCTGATCCA
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
101 18 0.23
103 1 0.01
105 59 0.76
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.30
Consensus pattern (101 bp):
TGCCATAACCCAGTTATGGTCTTATCATCAAAATGCCATAGCCCAGCTACGATCTTACACGTAAA
CATTGCCATGGTCCAACCATGGTCTTACGTTTAAGG
Found at i:11491997 original size:22 final size:21
Alignment explanation
Indices: 11491939--11491997 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
11491929 AAATGACAGT
*
11491939 AAAACAATGAGAAAATAGCAAG
1 AAAACAA-CAGAAAATAGCAAG
**
11491961 AAAACAACAGCAAAATAGTGAG
1 AAAACAACAG-AAAATAGCAAG
*
11491983 GAAACAACAAGAAAA
1 AAAACAAC-AGAAAA
11491998 CAACTGATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 27 0.87
23 2 0.06
ACGTcount: A:0.64, C:0.12, G:0.17, T:0.07
Consensus pattern (21 bp):
AAAACAACAGAAAATAGCAAG
Found at i:11494335 original size:2 final size:2
Alignment explanation
Indices: 11494330--11494360 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
11494320 TTTACAAAAA
11494330 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11494361 GATAAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11495972 original size:31 final size:31
Alignment explanation
Indices: 11495934--11495997 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
11495924 CAAGTCATGT
11495934 TTTAAAATCAGGTTTTAGCAATTGTGGCCTC
1 TTTAAAATCAGGTTTTAGCAATTGTGGCCTC
11495965 TTTAAAATCAGGTTTTAGCAATTGTGGCCTC
1 TTTAAAATCAGGTTTTAGCAATTGTGGCCTC
11495996 TT
1 TT
11495998 AACATTTGCA
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:0.25, C:0.16, G:0.19, T:0.41
Consensus pattern (31 bp):
TTTAAAATCAGGTTTTAGCAATTGTGGCCTC
Found at i:11499344 original size:9 final size:9
Alignment explanation
Indices: 11499330--11499360 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
11499320 GTTAAACGAA
11499330 TCGAGTTAT
1 TCGAGTTAT
*
11499339 TCGAGTTAA
1 TCGAGTTAT
11499348 TCGAGTTAT
1 TCGAGTTAT
11499357 TCGA
1 TCGA
11499361 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:11500395 original size:5 final size:5
Alignment explanation
Indices: 11500385--11500410 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
11500375 GAACAAATAT
11500385 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
11500411 ATTCCATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:11501039 original size:7 final size:7
Alignment explanation
Indices: 11501027--11501052 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
11501017 TAATTATCAA
11501027 CATGAAC
1 CATGAAC
11501034 CATGAAC
1 CATGAAC
11501041 CATGAAC
1 CATGAAC
11501048 CATGA
1 CATGA
11501053 CATACTAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.27, G:0.15, T:0.15
Consensus pattern (7 bp):
CATGAAC
Found at i:11503186 original size:20 final size:23
Alignment explanation
Indices: 11503157--11503205 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
11503147 AGTGTGACGA
*
11503157 GTCG-CAAAA-GATCTAGTC-CC
1 GTCGACAAAAGGACCTAGTCTCC
11503177 GT-GACAAAAGGACCTAGTCTCC
1 GTCGACAAAAGGACCTAGTCTCC
11503199 GTCGACA
1 GTCGACA
11503206 GGGTTTGCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 1 0.04
20 7 0.29
21 8 0.33
22 4 0.17
23 4 0.17
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.18
Consensus pattern (23 bp):
GTCGACAAAAGGACCTAGTCTCC
Found at i:11512455 original size:31 final size:31
Alignment explanation
Indices: 11512417--11512479 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
11512407 GAGTCTTGAC
11512417 CTTATGCAAATATTCTTTAACATTTAAACTA
1 CTTATGCAAATATTCTTTAACATTTAAACTA
11512448 CTTATGCAAATATTCTTTAACATTTAAACTA
1 CTTATGCAAATATTCTTTAACATTTAAACTA
11512479 C
1 C
11512480 CTTTCTTGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.17, G:0.03, T:0.41
Consensus pattern (31 bp):
CTTATGCAAATATTCTTTAACATTTAAACTA
Found at i:11514111 original size:57 final size:54
Alignment explanation
Indices: 11514023--11514134 Score: 161
Period size: 57 Copynumber: 2.0 Consensus size: 54
11514013 CCACATTAGA
*
11514023 AGATTTAACAAAGTATAAAGGCCAATCATGTCATAATCTTTTTTTTTTATCAAATTC
1 AGATTTAACAAAGTATAAAGGCCAATCATGTCATAA-C--TTTTTATTATCAAATTC
* * *
11514080 AGATTTAATAATGTATAAAGGCCAATTATGTCATAACTTTTTATTATCAAATTC
1 AGATTTAACAAAGTATAAAGGCCAATCATGTCATAACTTTTTATTATCAAATTC
11514134 A
1 A
11514135 ACCTTAATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
54 17 0.33
56 1 0.02
57 33 0.65
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.40
Consensus pattern (54 bp):
AGATTTAACAAAGTATAAAGGCCAATCATGTCATAACTTTTTATTATCAAATTC
Found at i:11516806 original size:24 final size:24
Alignment explanation
Indices: 11516778--11516825 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
11516768 TTGTTTTGTG
11516778 GCAAAGGATGAATTGACGGAAAAT
1 GCAAAGGATGAATTGACGGAAAAT
11516802 GCAAAGGATGAATTGACGGAAAAT
1 GCAAAGGATGAATTGACGGAAAAT
11516826 TACCCAAGCA
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:0.46, C:0.08, G:0.29, T:0.17
Consensus pattern (24 bp):
GCAAAGGATGAATTGACGGAAAAT
Found at i:11519817 original size:45 final size:46
Alignment explanation
Indices: 11519725--11519862 Score: 210
Period size: 45 Copynumber: 3.0 Consensus size: 46
11519715 ACATTGCTAT
* *
11519725 AACTCAGTATGG-TTTCCTTCACTGAAATATCATACCTACTTTTCAC
1 AACTCAGTATGGCTTT-CTTCACTGAAACACCATACCTACTTTTCAC
*
11519771 AACTCAGTATGGCTTTCTTCACCG-AACACCATACCTACTTTTCAC
1 AACTCAGTATGGCTTTCTTCACTGAAACACCATACCTACTTTTCAC
*
11519816 AACTCAGTAT-GCTTTCTTCACTGAAACACCATACCTATTTTTCAC
1 AACTCAGTATGGCTTTCTTCACTGAAACACCATACCTACTTTTCAC
11519861 AA
1 AA
11519863 TTTGCCATAG
Statistics
Matches: 85, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
44 12 0.14
45 51 0.60
46 19 0.22
47 3 0.04
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (46 bp):
AACTCAGTATGGCTTTCTTCACTGAAACACCATACCTACTTTTCAC
Found at i:11521134 original size:16 final size:17
Alignment explanation
Indices: 11521088--11521135 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
11521078 AAATTCTTTT
11521088 TAAATCACAAAATTCAA
1 TAAATCACAAAATTCAA
*
11521105 TAAATCACAAAATTCAC
1 TAAATCACAAAATTCAA
*
11521122 TAATTCA-AAAATTC
1 TAAATCACAAAATTC
11521136 TTATAAATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 7 0.24
17 22 0.76
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAATCACAAAATTCAA
Found at i:11521385 original size:42 final size:42
Alignment explanation
Indices: 11521293--11521424 Score: 122
Period size: 42 Copynumber: 3.2 Consensus size: 42
11521283 TCTCACGAGC
* * * *
11521293 TTCTGTT-AACTCATATGAGTTTCAGTTTAACACTTATGGGT
1 TTCTGTTCAGCTCCTATGAGCTTCAGTTTAACCCTTATGGGT
** * * * * *
11521334 TTCCATTCAGTTCTTTTGAGCTTCGGTTTAACCCTTATGAGT
1 TTCTGTTCAGCTCCTATGAGCTTCAGTTTAACCCTTATGGGT
* * * *
11521376 TTCTGTTCAGCTCCTACGAGCTCCCGTTCAACCCTTATGGGT
1 TTCTGTTCAGCTCCTATGAGCTTCAGTTTAACCCTTATGGGT
11521418 TTCTGTT
1 TTCTGTT
11521425 TAGCACTTAT
Statistics
Matches: 70, Mismatches: 20, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
41 5 0.07
42 65 0.93
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.42
Consensus pattern (42 bp):
TTCTGTTCAGCTCCTATGAGCTTCAGTTTAACCCTTATGGGT
Found at i:11544819 original size:2 final size:2
Alignment explanation
Indices: 11544812--11544838 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11544802 CAAGAAAATT
11544812 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
11544839 CAGTTCGAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11558990 original size:23 final size:23
Alignment explanation
Indices: 11558955--11559005 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
11558945 AAGCAACATA
11558955 TGTAATATCCCGAAAATTACTAC
1 TGTAATATCCCGAAAATTACTAC
*
11558978 TGTAATA-CTCCGAAATTTACTAC
1 TGTAATATC-CCGAAAATTACTAC
*
11559001 AGTAA
1 TGTAA
11559006 GAAAGTAGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 24 0.96
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.31
Consensus pattern (23 bp):
TGTAATATCCCGAAAATTACTAC
Found at i:11559515 original size:24 final size:24
Alignment explanation
Indices: 11559446--11559517 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
11559436 AATAAATAAA
* *
11559446 TATTAGTTTATTAATATTTTAATTT
1 TATTATTTTATTATTATTTT-ATTT
* * *
11559471 GATT-TTTAAATATTATTTTATTT
1 TATTATTTTATTATTATTTTATTT
11559494 TATTATTTTATTATTATTTTATTT
1 TATTATTTTATTATTATTTTATTT
11559518 AGTATATATA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
23 7 0.18
24 28 0.74
25 3 0.08
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (24 bp):
TATTATTTTATTATTATTTTATTT
Found at i:11562156 original size:13 final size:14
Alignment explanation
Indices: 11562131--11562157 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11562121 CTTTTCAAAA
11562131 AAAAATCATTTTTC
1 AAAAATCATTTTTC
11562145 AAAAATCATTTTT
1 AAAAATCATTTTT
11562158 GGAAACTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (14 bp):
AAAAATCATTTTTC
Found at i:11578589 original size:28 final size:27
Alignment explanation
Indices: 11578565--11578617 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
11578555 CTTAAAACTT
* *
11578565 AAAAAATTAAAGTAGATATATAAAAATC
1 AAAAAATTAAA-TAAAAATATAAAAATC
*
11578593 ATAAAATTAAATAAAAATATAAAAA
1 AAAAAATTAAATAAAAATATAAAAA
11578618 CGTTTAAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 12 0.55
28 10 0.45
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.25
Consensus pattern (27 bp):
AAAAAATTAAATAAAAATATAAAAATC
Found at i:11594592 original size:42 final size:43
Alignment explanation
Indices: 11594515--11594623 Score: 125
Period size: 42 Copynumber: 2.6 Consensus size: 43
11594505 CAATGCCAAA
* * * *
11594515 TCCCAGAC-GTGGTCTTACATGTAATCCAATAACGATGCCACTG
1 TCCCAGACAG-GGTCTTACACGTAATCCAATAACGATACAAATG
*
11594558 TCCCAGACAGGGTCTTACACGTAAT-C-ATATACGATACAAATT
1 TCCCAGACAGGGTCTTACACGTAATCCAATA-ACGATACAAATG
*
11594600 TCCCAGACATGGTCTTACACGTAA
1 TCCCAGACAGGGTCTTACACGTAA
11594624 ATCTCAAATC
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
41 3 0.05
42 32 0.55
43 22 0.38
44 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.26
Consensus pattern (43 bp):
TCCCAGACAGGGTCTTACACGTAATCCAATAACGATACAAATG
Found at i:11595772 original size:16 final size:14
Alignment explanation
Indices: 11595737--11595764 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
11595727 CACAAACGAT
11595737 AAAATTTTCACACA
1 AAAATTTTCACACA
11595751 AAAATTTTCACACA
1 AAAATTTTCACACA
11595765 TATAAATTAA
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:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (14 bp):
AAAATTTTCACACA
Found at i:11596838 original size:30 final size:31
Alignment explanation
Indices: 11596804--11596861 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 31
11596794 TTTTACGAGC
*
11596804 TTAGGGGCAAAATCATAATTTTG-TAAAACT
1 TTAGGGGCAAAAACATAATTTTGCTAAAACT
11596834 TTAGGGGCAAAAACATAATTTTGCTAAA
1 TTAGGGGCAAAAACATAATTTTGCTAAA
11596862 GTATGATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.31
Consensus pattern (31 bp):
TTAGGGGCAAAAACATAATTTTGCTAAAACT
Found at i:11597239 original size:45 final size:45
Alignment explanation
Indices: 11597178--11597272 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 45
11597168 TACTATGTGA
* *
11597178 ACCGAACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
* * * *
11597223 ACCGGACATTATTGATTAATAAGGTGGTTGTTATGTTCTGAATCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
11597268 ACCGA
1 ACCGA
11597273 GTATATGTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (45 bp):
ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
Found at i:11602906 original size:2 final size:2
Alignment explanation
Indices: 11602899--11602943 Score: 55
Period size: 2 Copynumber: 25.0 Consensus size: 2
11602889 TTCCTTTTGT
11602899 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA T- TA -A TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11602937 TA -A TA TA
1 TA TA TA TA
11602944 AAAACATACT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
1 5 0.13
2 33 0.87
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:11602920 original size:16 final size:16
Alignment explanation
Indices: 11602899--11602943 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 16
11602889 TTCCTTTTGT
11602899 TATATATATATATATA
1 TATATATATATATATA
11602915 TATATATA-ATATAT-
1 TATATATATATATATA
11602929 TA-ATA-ATATA-ATA
1 TATATATATATATATA
11602942 TA
1 TA
11602944 AAAACATACT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
12 3 0.11
13 8 0.30
14 2 0.07
15 6 0.22
16 8 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATATATATATATATA
Found at i:11606534 original size:24 final size:24
Alignment explanation
Indices: 11606507--11606561 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
11606497 TCCGATGCTT
11606507 CCCGTTAATTGCTCTTCGAAGCTA
1 CCCGTTAATTGCTCTTCGAAGCTA
* *
11606531 CCCGTTAATTGCTCTTTGGAGCTA
1 CCCGTTAATTGCTCTTCGAAGCTA
*
11606555 CCAGTTA
1 CCCGTTA
11606562 TAGGCTCTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.35
Consensus pattern (24 bp):
CCCGTTAATTGCTCTTCGAAGCTA
Found at i:11607400 original size:30 final size:29
Alignment explanation
Indices: 11607361--11607427 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
11607351 TTTTTTATTT
* **
11607361 AAATAACCCAAATAATTTAATTAAGTACCA
1 AAATGACCCAAAT-ATTTAATTAAACACCA
** *
11607391 AAATGACCCACCTTTTTAATTAAACACCA
1 AAATGACCCAAATATTTAATTAAACACCA
11607420 AAATGACC
1 AAATGACC
11607428 TAAAATCTAC
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
29 21 0.68
30 10 0.32
ACGTcount: A:0.48, C:0.22, G:0.04, T:0.25
Consensus pattern (29 bp):
AAATGACCCAAATATTTAATTAAACACCA
Found at i:11608053 original size:9 final size:9
Alignment explanation
Indices: 11608041--11608085 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
11608031 TTTTTCTTAT
*
11608041 TTTATTTTG
1 TTTATTTTA
11608050 TTTA-TTTA
1 TTTATTTTA
11608058 TTTATTTTA
1 TTTATTTTA
11608067 TTTATTGTTA
1 TTTATT-TTA
*
11608077 TTAATTTTA
1 TTTATTTTA
11608086 AAAAAATTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
8 7 0.22
9 17 0.53
10 8 0.25
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.73
Consensus pattern (9 bp):
TTTATTTTA
Found at i:11608354 original size:74 final size:74
Alignment explanation
Indices: 11608270--11608417 Score: 215
Period size: 74 Copynumber: 2.0 Consensus size: 74
11608260 TTAAAATATA
** * * * * *
11608270 TTTTTAAAAAATATATTGAATATATTATAATTTTAATATTGGTTATACTTAACATTTTTTAATAT
1 TTTTTAAAAAATATATAAAAAATATTAAAATTTTAAAATTGGCTATACATAACATTTTTTAATAT
*
11608335 ATTTAATTT
66 AGTTAATTT
*
11608344 TTTTTTAAAAATATATAAAAAATATTAAAATTTTAAAATTGGCTATACATAACATTTTTTAATAT
1 TTTTTAAAAAATATATAAAAAATATTAAAATTTTAAAATTGGCTATACATAACATTTTTTAATAT
11608409 AGTTAATTT
66 AGTTAATTT
11608418 CTTTAAGTTT
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
74 65 1.00
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (74 bp):
TTTTTAAAAAATATATAAAAAATATTAAAATTTTAAAATTGGCTATACATAACATTTTTTAATAT
AGTTAATTT
Found at i:11608560 original size:20 final size:20
Alignment explanation
Indices: 11608497--11608568 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 20
11608487 TTAAGTACAT
* *
11608497 AAATTTATGAATGTGTACTA
1 AAATTTATAAATGTGTATTA
** *
11608517 AAATTTA-AAAAAT-AATATA
1 AAATTTATAAATGTGTAT-TA
11608536 TAAATTTATAAATGTGTATTA
1 -AAATTTATAAATGTGTATTA
*
11608557 AAATTTAAAAAT
1 AAATTTATAAAT
11608569 TATAACCAAC
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
18 1 0.03
19 5 0.13
20 25 0.64
21 6 0.15
22 2 0.05
ACGTcount: A:0.53, C:0.01, G:0.07, T:0.39
Consensus pattern (20 bp):
AAATTTATAAATGTGTATTA
Found at i:11609163 original size:8 final size:8
Alignment explanation
Indices: 11609150--11609182 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
11609140 NNNNNNNNNA
11609150 AATTAAAT
1 AATTAAAT
11609158 AATTAAAT
1 AATTAAAT
11609166 ATATT-AAT
1 A-ATTAAAT
11609174 AATTAAAT
1 AATTAAAT
11609182 A
1 A
11609183 TATATTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 3 0.13
8 17 0.74
9 3 0.13
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
AATTAAAT
Found at i:11609187 original size:18 final size:18
Alignment explanation
Indices: 11609155--11609208 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
11609145 NNNNAAATTA
11609155 AATAATT-AA-ATATATT
1 AATAATTAAATATATATT
11609171 AATAATTAAATATATATT
1 AATAATTAAATATATATT
11609189 AATAAATTACAATATA-ATT
1 AAT-AATTA-AATATATATT
11609208 A
1 A
11609209 GAATTTTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
16 7 0.21
17 2 0.06
18 10 0.29
19 9 0.26
20 6 0.18
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
AATAATTAAATATATATT
Found at i:11609243 original size:9 final size:9
Alignment explanation
Indices: 11609231--11609263 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
11609221 TAATAACAAT
11609231 AAATAAATA
1 AAATAAATA
11609240 AAATAAATA
1 AAATAAATA
11609249 AACA-AAATA
1 AA-ATAAATA
11609258 AAATAA
1 AAATAA
11609264 GAAAAAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 1 0.05
9 20 0.91
10 1 0.05
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (9 bp):
AAATAAATA
Found at i:11609268 original size:13 final size:13
Alignment explanation
Indices: 11609218--11609259 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
11609208 AGAATTTTTA
11609218 AAAT-AATAACAAT
1 AAATAAATAA-AAT
11609231 AAATAAATAAAAT
1 AAATAAATAAAAT
*
11609244 AAATAAACAAAAT
1 AAATAAATAAAAT
11609257 AAA
1 AAA
11609260 ATAAGAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 22 0.81
14 5 0.19
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.19
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:11609285 original size:17 final size:18
Alignment explanation
Indices: 11609261--11609325 Score: 69
Period size: 17 Copynumber: 3.5 Consensus size: 18
11609251 CAAAATAAAA
11609261 TAAGAAAAAAGAAAAAACT
1 TAAG-AAAAAGAAAAAACT
11609280 TAA-AAAAAGAAAAAACTT
1 TAAGAAAAAGAAAAAAC-T
* *
11609298 TAAAGAAAAAGACAAAAGT
1 T-AAGAAAAAGAAAAAACT
*
11609317 TAATAAAAA
1 TAAGAAAAA
11609326 AATAAAAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
17 13 0.32
18 9 0.22
19 7 0.17
20 11 0.28
ACGTcount: A:0.72, C:0.05, G:0.09, T:0.14
Consensus pattern (18 bp):
TAAGAAAAAGAAAAAACT
Found at i:11609326 original size:20 final size:21
Alignment explanation
Indices: 11609265--11609333 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 21
11609255 ATAAAATAAG
11609265 AAAAAAGAAAAAAC--T--TA
1 AAAAAAGAAAAAACGTTAATA
*
11609282 AAAAAAGAAAAAACTTTAA-A
1 AAAAAAGAAAAAACGTTAATA
* *
11609302 GAAAAAGACAAAA-GTTAATA
1 AAAAAAGAAAAAACGTTAATA
*
11609322 AAAAAATAAAAA
1 AAAAAAGAAAAA
11609334 TAAAAAATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
17 14 0.34
19 5 0.12
20 22 0.54
ACGTcount: A:0.75, C:0.04, G:0.07, T:0.13
Consensus pattern (21 bp):
AAAAAAGAAAAAACGTTAATA
Found at i:11609332 original size:18 final size:17
Alignment explanation
Indices: 11609228--11609332 Score: 56
Period size: 18 Copynumber: 5.9 Consensus size: 17
11609218 AAATAATAAC
* *
11609228 AATAAATAAATAAAATA
1 AATAAAAAAATAAAATT
11609245 AATAAACAAAATAAAA-T
1 AATAAA-AAAATAAAATT
* *
11609262 AAGAAAAAAGAAAAAACTT
1 AATAAAAAA-ATAAAA-TT
11609281 AA-AAAAAGAA-AAAACTTT
1 AATAAAAA-AATAAAA--TT
*
11609299 AA-AGAAAAAGACAAAAGTT
1 AATA-AAAAA-ATAAAA-TT
11609318 AATAAAAAAATAAAA
1 AATAAAAAAATAAAA
11609333 ATAAAAAATA
Statistics
Matches: 71, Mismatches: 7, Indels: 19
0.73 0.07 0.20
Matches are distributed among these distances:
16 3 0.04
17 20 0.28
18 25 0.35
19 18 0.25
20 5 0.07
ACGTcount: A:0.75, C:0.04, G:0.06, T:0.15
Consensus pattern (17 bp):
AATAAAAAAATAAAATT
Found at i:11621172 original size:16 final size:17
Alignment explanation
Indices: 11621151--11621184 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
11621141 GGATAATTCT
11621151 AAAAATAAAAAAT-ATA
1 AAAAATAAAAAATCATA
*
11621167 AAAAATGAAAAATCATA
1 AAAAATAAAAAATCATA
11621184 A
1 A
11621185 TATATTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (17 bp):
AAAAATAAAAAATCATA
Found at i:11623668 original size:5 final size:5
Alignment explanation
Indices: 11623658--11623682 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
11623648 TTAATATTTT
11623658 AATAA AATAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA
11623683 CCTAAACTCG
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:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:11635290 original size:18 final size:18
Alignment explanation
Indices: 11635267--11635302 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
11635257 CTTATATAGG
11635267 TGGAAAAGAGCTGCCTAA
1 TGGAAAAGAGCTGCCTAA
11635285 TGGAAAAGAGCTGCCTAA
1 TGGAAAAGAGCTGCCTAA
11635303 CTCTAGCTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.28, T:0.17
Consensus pattern (18 bp):
TGGAAAAGAGCTGCCTAA
Found at i:11650850 original size:21 final size:21
Alignment explanation
Indices: 11650811--11650896 Score: 111
Period size: 21 Copynumber: 4.0 Consensus size: 21
11650801 CACGATCAAT
11650811 AAACGACACAT-AAGTGCCTG
1 AAACGACACATAAAGTGCCTG
* *
11650831 AAACGACACACAAGGTGCCTG
1 AAACGACACATAAAGTGCCTG
* *
11650852 ATACGACACATAAAGTGCTTG
1 AAACGACACATAAAGTGCCTG
11650873 AGATACGACACATAAAGTGCCTG
1 A-A-ACGACACATAAAGTGCCTG
11650896 A
1 A
11650897 TCGGCAAAGC
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
20 10 0.18
21 26 0.47
23 19 0.35
ACGTcount: A:0.40, C:0.23, G:0.21, T:0.16
Consensus pattern (21 bp):
AAACGACACATAAAGTGCCTG
Found at i:11650893 original size:44 final size:41
Alignment explanation
Indices: 11650813--11650897 Score: 116
Period size: 44 Copynumber: 2.0 Consensus size: 41
11650803 CGATCAATAA
*
11650813 ACGACACATAAGTGCCTGAAACGACACACAAGGTGCCTGAT
1 ACGACACATAAGTGCCTGAAACGACACACAAAGTGCCTGAT
* *
11650854 ACGACACATAAAGTGCTTGAGATACGACACATAAAGTGCCTGAT
1 ACGACACAT-AAGTGCCTGA-A-ACGACACACAAAGTGCCTGAT
11650898 CGGCAAAGCC
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 9 0.24
42 9 0.24
43 1 0.03
44 19 0.50
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.18
Consensus pattern (41 bp):
ACGACACATAAGTGCCTGAAACGACACACAAAGTGCCTGAT
Found at i:11651248 original size:16 final size:16
Alignment explanation
Indices: 11651222--11651261 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
11651212 TTAATAACAA
*
11651222 TACTTATCTTA-TATT
1 TACTTACCTTATTATT
11651237 TCACTTACCTTATTATT
1 T-ACTTACCTTATTATT
11651254 TACTTACC
1 TACTTACC
11651262 ATACACATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 16 0.73
17 5 0.23
ACGTcount: A:0.25, C:0.23, G:0.00, T:0.53
Consensus pattern (16 bp):
TACTTACCTTATTATT
Found at i:11651544 original size:13 final size:13
Alignment explanation
Indices: 11651528--11651553 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11651518 TTGCTTTTTC
11651528 TAATAATATAATA
1 TAATAATATAATA
11651541 TAATAATATAATA
1 TAATAATATAATA
11651554 GTTTTACTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TAATAATATAATA
Found at i:11651670 original size:5 final size:5
Alignment explanation
Indices: 11651660--11651687 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
11651650 TTTGTTTATT
11651660 TAAAA TAAAA TAAAA TAAAA TAAAA TAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAA
11651688 TATATTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:11652187 original size:9 final size:9
Alignment explanation
Indices: 11652170--11652234 Score: 53
Period size: 9 Copynumber: 6.9 Consensus size: 9
11652160 TTTAGTCATG
*
11652170 ATTCTAAAA
1 ATTCAAAAA
11652179 ATTCAAAAA
1 ATTCAAAAA
*
11652188 ATATAAATTAAA
1 AT-TCAA--AAA
11652200 ATTCAAAAA
1 ATTCAAAAA
11652209 ATTCAAAAA
1 ATTCAAAAA
11652218 TACTT--AAAA
1 -A-TTCAAAAA
11652227 ATTCAAAA
1 ATTCAAAA
11652235 TTTATAAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
7 2 0.04
8 1 0.02
9 29 0.63
10 4 0.09
11 5 0.11
12 5 0.11
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.28
Consensus pattern (9 bp):
ATTCAAAAA
Found at i:11652868 original size:31 final size:30
Alignment explanation
Indices: 11652832--11652908 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 30
11652822 ATTTTAACGG
* *
11652832 TAGAGTGACTAAAATTAAGAACTTATTTAA
1 TAGAGTGACTAAAATTAACAACTTATCTAA
* *
11652862 TGAGAGTGACTAAAATTGACAATTTATCTAA
1 T-AGAGTGACTAAAATTAACAACTTATCTAA
11652893 TATGAGTGACTAAAAT
1 TA-GAGTGACTAAAAT
11652909 AATTTTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
30 2 0.05
31 39 0.95
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (30 bp):
TAGAGTGACTAAAATTAACAACTTATCTAA
Found at i:11653387 original size:31 final size:30
Alignment explanation
Indices: 11653331--11653468 Score: 106
Period size: 31 Copynumber: 4.6 Consensus size: 30
11653321 GGCCTGTTTT
* *
11653331 TTAAAATAAATATCAAAAAATTATTTTAAAAA
1 TTAAAATAAAAAT-AAAAAAGTATTTT-AAAA
*
11653363 TTAAAACAAAAATAAAAAAGTATTTTAAAATA
1 TTAAAATAAAAATAAAAAAGTATTTT-AAA-A
* *
11653395 TTTAAATTAAAAAT-TAAAA-TA--TTAAAA
1 -TTAAAATAAAAATAAAAAAGTATTTTAAAA
* **
11653422 TTAAATTAAATTTAAAAAAGTATTTTAAAA
1 TTAAAATAAAAATAAAAAAGTATTTTAAAA
**
11653452 TTTTAA-AAAAATAAAAA
1 TTAAAATAAAAATAAAAA
11653469 TATTTATTAT
Statistics
Matches: 86, Mismatches: 14, Indels: 15
0.75 0.12 0.13
Matches are distributed among these distances:
26 11 0.13
27 5 0.06
28 5 0.06
29 11 0.13
30 9 0.10
31 18 0.21
32 16 0.19
33 11 0.13
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (30 bp):
TTAAAATAAAAATAAAAAAGTATTTTAAAA
Found at i:11653413 original size:21 final size:21
Alignment explanation
Indices: 11653387--11653426 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
11653377 AAAAAGTATT
*
11653387 TTAAAATATTTAAATTAAAAA
1 TTAAAATATTAAAATTAAAAA
11653408 TTAAAATATTAAAATTAAA
1 TTAAAATATTAAAATTAAA
11653427 TTAAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TTAAAATATTAAAATTAAAAA
Found at i:11655099 original size:17 final size:18
Alignment explanation
Indices: 11655077--11655110 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
11655067 CACTATGTTT
11655077 GGTTGGCACC-CCTAATC
1 GGTTGGCACCACCTAATC
*
11655094 GGTTGGCCCCACCTAAT
1 GGTTGGCACCACCTAAT
11655111 ACCTCTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.18, C:0.35, G:0.24, T:0.24
Consensus pattern (18 bp):
GGTTGGCACCACCTAATC
Found at i:11655304 original size:11 final size:11
Alignment explanation
Indices: 11655288--11655313 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
11655278 CGCCTCTTCT
11655288 TTCGTTCTACC
1 TTCGTTCTACC
11655299 TTCGTTCTACC
1 TTCGTTCTACC
11655310 TTCG
1 TTCG
11655314 CCTCCCGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.35, G:0.12, T:0.46
Consensus pattern (11 bp):
TTCGTTCTACC
Found at i:11657163 original size:22 final size:22
Alignment explanation
Indices: 11657121--11657207 Score: 79
Period size: 23 Copynumber: 3.9 Consensus size: 22
11657111 GAAGATGAAA
* *
11657121 CTGGAAATTGTTGTAATTTGTT
1 CTGGAAATTGTTTTGATTTGTT
* *
11657143 -TTGATATTGTTATTGATTTGTT
1 CTGGAAATTGTT-TTGATTTGTT
11657165 CTGGAAATTGTTTTGA-TTGTCT
1 CTGGAAATTGTTTTGATTTGT-T
*
11657187 GTTGGAAATTGTTCTTGATTT
1 -CTGGAAATTGTT-TTGATTT
11657208 CTTAGTCAGT
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
21 13 0.25
22 13 0.25
23 20 0.38
24 4 0.08
25 2 0.04
ACGTcount: A:0.20, C:0.05, G:0.22, T:0.54
Consensus pattern (22 bp):
CTGGAAATTGTTTTGATTTGTT
Found at i:11663210 original size:16 final size:16
Alignment explanation
Indices: 11663189--11663224 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
11663179 GATTTGCTAT
*
11663189 TACACCTCTAATTCAA
1 TACACCTCTAATCCAA
11663205 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
11663221 TACA
1 TACA
11663225 GCGAACCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.33, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:11666790 original size:50 final size:48
Alignment explanation
Indices: 11666731--11666916 Score: 257
Period size: 50 Copynumber: 3.8 Consensus size: 48
11666721 GGCAGTGAGT
*
11666731 GTGCCAGTGTAAGACCATGGCTGGGACATGGCATCGGCACAGACCGAGGA
1 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-GA-CGAGGA
* *
11666781 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGGACATAGGA
1 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-GAC-GAGGA
* * *
11666831 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTCGA-GATGA
1 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGACGAGGA
* *
11666878 GGGCCAGAGTAAGACCATGTCTGGGACATGGCATCGGCA
1 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
11666917 TCGATATGTG
Statistics
Matches: 123, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
47 39 0.32
49 3 0.02
50 81 0.66
ACGTcount: A:0.26, C:0.22, G:0.35, T:0.17
Consensus pattern (48 bp):
GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGACGAGGA
Found at i:11667299 original size:2 final size:2
Alignment explanation
Indices: 11667292--11667321 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11667282 AAGGTTTAAA
11667292 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11667322 GAGAATTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11667546 original size:45 final size:44
Alignment explanation
Indices: 11667414--11667557 Score: 152
Period size: 45 Copynumber: 3.2 Consensus size: 44
11667404 ATTAATGAAA
*
11667414 ATAAAGGTGATTGCTATGTGCTGATTTCACTGGATACCAATG-GTT
1 ATAAAGGTGATTGCTATGTGCTGATTTCACTGG-TACCATTGAG-T
*
11667459 ATATAA-GTGATTGCTATGTGCTGAATTCACCCT-GTACCATTGAGT
1 ATA-AAGGTGATTGCTATGTGCTGATTTCA--CTGGTACCATTGAGT
* *
11667504 ATAAAGGT-AGTTGCTATGTGCTGATTTCACTGAGTACTATTGATT
1 ATAAAGGTGA-TTGCTATGTGCTGATTTCACTG-GTACCATTGAGT
*
11667549 ATAAGGGTG
1 ATAAAGGTG
11667558 GTGTTGTGTG
Statistics
Matches: 84, Mismatches: 6, Indels: 17
0.79 0.06 0.16
Matches are distributed among these distances:
43 2 0.02
44 3 0.04
45 73 0.87
46 4 0.05
47 2 0.02
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (44 bp):
ATAAAGGTGATTGCTATGTGCTGATTTCACTGGTACCATTGAGT
Found at i:11670452 original size:101 final size:101
Alignment explanation
Indices: 11670312--11670551 Score: 383
Period size: 101 Copynumber: 2.4 Consensus size: 101
11670302 TGAATTGACG
* * *
11670312 GATAAGACCATAACTAGGTTATGGCATTATGAACATAAGACCATGGTTGGACCATGGCAGTGTTT
1 GATAAGACCATAACTAGGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGGCAATGTTT
*
11670377 ATATGTAAGACCATAGTTGGGCTATTG-CATTCTGAT
66 ATATGTAAGACCATAGCTGGGCTA-TGACATTCTGAT
* *
11670413 GATAAGACCATAACTGGGTTATGACACTATGAACGTAAGACCATGGTTGGACCATGGCAATGTTT
1 GATAAGACCATAACTAGGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGGCAATGTTT
*
11670478 ATATGTAAGACCATAGCTGGGCTATGACATTTTGAT
66 ATATGTAAGACCATAGCTGGGCTATGACATTCTGAT
* *
11670514 GATAAGACCATAACTAGGTTATGGCACTACGAATGTAA
1 GATAAGACCATAACTAGGTTATGGCACTATGAACGTAA
11670552 ATGATGAATT
Statistics
Matches: 127, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
100 2 0.02
101 125 0.98
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (101 bp):
GATAAGACCATAACTAGGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGGCAATGTTT
ATATGTAAGACCATAGCTGGGCTATGACATTCTGAT
Found at i:11670525 original size:33 final size:32
Alignment explanation
Indices: 11670379--11670525 Score: 107
Period size: 33 Copynumber: 4.4 Consensus size: 32
11670369 CAGTGTTTAT
* *
11670379 ATGTAAGACCATAGTTGGGCTATTG-CATTCTG
1 ATGTAAGACCATAGCTGGGCTA-TGACATTTTG
* * * *
11670411 ATGATAAGACCATAACTGGGTTATGACACTATG
1 ATG-TAAGACCATAGCTGGGCTATGACATTTTG
* * * * * * *
11670444 AACGTAAGACCATGGTTGGACCATGGCAATGTTTAT
1 -ATGTAAGACCATAGCTGGGCTATGAC-AT-TTT-G
11670480 ATGTAAGACCATAGCTGGGCTATGACATTTTG
1 ATGTAAGACCATAGCTGGGCTATGACATTTTG
11670512 ATGATAAGACCATA
1 ATG-TAAGACCATA
11670526 ACTAGGTTAT
Statistics
Matches: 85, Mismatches: 23, Indels: 13
0.70 0.19 0.11
Matches are distributed among these distances:
32 8 0.09
33 50 0.59
34 5 0.06
35 22 0.26
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (32 bp):
ATGTAAGACCATAGCTGGGCTATGACATTTTG
Found at i:11670852 original size:21 final size:21
Alignment explanation
Indices: 11670828--11670870 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
11670818 TATTTTAAGG
11670828 GTAGAATAATCTAGAAACTAA
1 GTAGAATAATCTAGAAACTAA
*
11670849 GTAGAATAATTTAGAAACTAA
1 GTAGAATAATCTAGAAACTAA
11670870 G
1 G
11670871 GAAAATGGAT
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:0.51, C:0.07, G:0.16, T:0.26
Consensus pattern (21 bp):
GTAGAATAATCTAGAAACTAA
Found at i:11672555 original size:30 final size:29
Alignment explanation
Indices: 11672498--11672555 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
11672488 CTTTTTTACT
* *
11672498 TTTCCCTCAAAACTTTTACTCCTTCCCAC
1 TTTCCCCCAAAACTTTTACTCCCTCCCAC
11672527 TTTCCCCCAAAACTTTTACTCCCCTCCCA
1 TTTCCCCCAAAACTTTTACT-CCCTCCCA
11672556 ACCCCCCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.21, C:0.45, G:0.00, T:0.34
Consensus pattern (29 bp):
TTTCCCCCAAAACTTTTACTCCCTCCCAC
Found at i:11672562 original size:29 final size:28
Alignment explanation
Indices: 11672505--11672564 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
11672495 ACTTTTCCCT
* *
11672505 CAAAACTTTTACTCCTTCCCACTTTCCCC
1 CAAAACTTTTACTCCCTCCCAC-TCCCCC
*
11672534 CAAAACTTTTACTCCCCTCCCA-ACCCCC
1 CAAAACTTTTACT-CCCTCCCACTCCCCC
11672562 CAA
1 CAA
11672565 TCTACCCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 7 0.26
29 13 0.48
30 7 0.26
ACGTcount: A:0.25, C:0.48, G:0.00, T:0.27
Consensus pattern (28 bp):
CAAAACTTTTACTCCCTCCCACTCCCCC
Found at i:11688108 original size:77 final size:81
Alignment explanation
Indices: 11687951--11688108 Score: 198
Period size: 78 Copynumber: 2.0 Consensus size: 81
11687941 AATTGAACTG
** *
11687951 GATAGAGTAAATGAAGGGCTTGCTCTGCAAAAAAACACTGACACGGATGTGAATGAATTATTTAT
1 GATAGAGTAAATGAAGGGCTTGCTCTGCAAAAAAACACTGACACAAATGTGAATGAATGATTTAT
11688016 AAGACAAGTTCAATCT
66 AAGACAAGTTCAATCT
* * * * * *
11688032 GATAGAGTAACTG-AGGG-TTGTTCTGC-AAAAAGCATTGTCACAAATGTGAATGAATGA-TTGT
1 GATAGAGTAAATGAAGGGCTTGCTCTGCAAAAAAACACTGACACAAATGTGAATGAATGATTTAT
*
11688093 AAGCCAAGTTCAATCT
66 AAGACAAGTTCAATCT
11688109 TCAGTAAAGT
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
77 18 0.27
78 25 0.37
79 8 0.12
80 4 0.06
81 12 0.18
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.27
Consensus pattern (81 bp):
GATAGAGTAAATGAAGGGCTTGCTCTGCAAAAAAACACTGACACAAATGTGAATGAATGATTTAT
AAGACAAGTTCAATCT
Found at i:11705885 original size:19 final size:19
Alignment explanation
Indices: 11705839--11705891 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 19
11705829 TTTAAAACTT
*
11705839 TATATTATTTATTTATAATA
1 TATATT-TTTAATTATAATA
11705859 TAATTATTTTTAATTATAATA
1 T-A-TATTTTTAATTATAATA
11705880 TATATTTTTAAT
1 TATATTTTTAAT
11705892 ATTTTATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 10 0.33
20 2 0.07
21 14 0.47
22 4 0.13
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TATATTTTTAATTATAATA
Found at i:11705933 original size:101 final size:104
Alignment explanation
Indices: 11705761--11705974 Score: 362
Period size: 101 Copynumber: 2.1 Consensus size: 104
11705751 ATCATTTTTA
11705761 TTTAATTATAATATATATTTTTAATATTTTATTTTATTTTATTAAAACTATTTATAAAATTTTAT
1 TTTAATTATAATATATATTTTTAATA--TTATTTTATTTTATTAAAACTATTTATAAAATTTTAT
11705826 AAATTTAAAACTTTATATTATTTATTTATAATATAATTATT
64 AAATTTAAAACTTTATATTATTTATTTATAATATAATTATT
11705867 TTTAATTATAATATATATTTTT-A-A-TATTTTATTTTATTAAAACTATTTATAAAATTTTATAA
1 TTTAATTATAATATATATTTTTAATATTATTTTATTTTATTAAAACTATTTATAAAATTTTATAA
* * *
11705929 ATTTAATATTTTATATTATTTATTTTTAATATAATTATT
66 ATTTAAAACTTTATATTATTTATTTATAATATAATTATT
11705968 TTTAATT
1 TTTAATT
11705975 TGTAAAATTT
Statistics
Matches: 105, Mismatches: 3, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
101 81 0.77
104 1 0.01
105 1 0.01
106 22 0.21
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (104 bp):
TTTAATTATAATATATATTTTTAATATTATTTTATTTTATTAAAACTATTTATAAAATTTTATAA
ATTTAAAACTTTATATTATTTATTTATAATATAATTATT
Found at i:11705960 original size:16 final size:15
Alignment explanation
Indices: 11705844--11705973 Score: 68
Period size: 15 Copynumber: 7.9 Consensus size: 15
11705834 AACTTTATAT
*
11705844 TATTTATTTATAATA
1 TATTTATTTTTAATA
*
11705859 TAATTATTTTTAATTA
1 TATTTATTTTTAA-TA
11705875 TAATATATATTTTTAATA
1 T-AT-T-TATTTTTAATA
*
11705893 T-TTTATTTTATTAAAA
1 TATTTA-TTT-TTAATA
11705909 CTATTTATAAAATTTT-ATA
1 -TATTTAT----TTTTAATA
*
11705928 AATTTAATATTTT-ATA
1 TATTT-AT-TTTTAATA
11705944 TTATTTATTTTTAATA
1 -TATTTATTTTTAATA
*
11705960 TAATTATTTTTAAT
1 TATTTATTTTTAAT
11705974 TTGTAAAATT
Statistics
Matches: 92, Mismatches: 8, Indels: 30
0.71 0.06 0.23
Matches are distributed among these distances:
14 2 0.02
15 32 0.35
16 22 0.24
17 7 0.08
18 12 0.13
19 13 0.14
20 2 0.02
21 2 0.02
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (15 bp):
TATTTATTTTTAATA
Found at i:11706504 original size:15 final size:15
Alignment explanation
Indices: 11706484--11706516 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
11706474 AATATGATAT
11706484 TTAATTAT-TAAAATA
1 TTAATTATGTAAAA-A
11706499 TTAATTATGTAAAAA
1 TTAATTATGTAAAAA
11706514 TTA
1 TTA
11706517 CAACTAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (15 bp):
TTAATTATGTAAAAA
Found at i:11706552 original size:27 final size:28
Alignment explanation
Indices: 11706501--11706556 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
11706491 TTAAAATATT
*
11706501 AATTATGTAAAAATTACAACTAATATAA
1 AATTATGTAAAAATTACAACAAATATAA
* *
11706529 AATTATTTAAAATTTAC-ACAAATATAA
1 AATTATGTAAAAATTACAACAAATATAA
11706556 A
1 A
11706557 TAAATCCATC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 10 0.40
28 15 0.60
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.34
Consensus pattern (28 bp):
AATTATGTAAAAATTACAACAAATATAA
Found at i:11713821 original size:21 final size:21
Alignment explanation
Indices: 11713793--11713911 Score: 96
Period size: 21 Copynumber: 5.7 Consensus size: 21
11713783 TCTCACGAGG
11713793 TTCTGTTTAACTCTTATGGGT
1 TTCTGTTTAACTCTTATGGGT
* * * * *
11713814 TTCCGTTTAGCTCTTTTGAGC
1 TTCTGTTTAACTCTTATGGGT
* *
11713835 TTCTATTTAACCCTTATGGGT
1 TTCTGTTTAACTCTTATGGGT
* * * * *
11713856 TTCTGTTCAGCTTTTACGAGCT
1 TTCTGTTTAACTCTTATG-GGT
* *
11713878 TTC-GTTCAACCCTTATGGGT
1 TTCTGTTTAACTCTTATGGGT
11713898 TTCTGTTTAACTCT
1 TTCTGTTTAACTCT
11713912 CATGAGCTTT
Statistics
Matches: 70, Mismatches: 26, Indels: 4
0.70 0.26 0.04
Matches are distributed among these distances:
20 5 0.07
21 60 0.86
22 5 0.07
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.48
Consensus pattern (21 bp):
TTCTGTTTAACTCTTATGGGT
Found at i:11713844 original size:42 final size:42
Alignment explanation
Indices: 11713771--11713927 Score: 163
Period size: 42 Copynumber: 3.7 Consensus size: 42
11713761 TCGTATTTAC
* *
11713771 TTTCCGTTTAGCTCTCACGAGGTTCTGTTTAACTCTTATGGG
1 TTTCCGTTTAGCTCTCACGAGCTTCTGTTTAACCCTTATGGG
*** *
11713813 TTTCCGTTTAGCTCTTTTGAGCTTCTATTTAACCCTTATGGG
1 TTTCCGTTTAGCTCTCACGAGCTTCTGTTTAACCCTTATGGG
* * * * *
11713855 TTTCTGTTCAGCTTTTACGAGCTT-TCGTTCAACCCTTATGGG
1 TTTCCGTTTAGCTCTCACGAGCTTCT-GTTTAACCCTTATGGG
* * * *
11713897 TTTCTGTTTAACTCTCATGAGCTTTTGTTTA
1 TTTCCGTTTAGCTCTCACGAGCTTCTGTTTA
11713928 GCCTTCGGGC
Statistics
Matches: 94, Mismatches: 19, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
41 1 0.01
42 92 0.98
43 1 0.01
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (42 bp):
TTTCCGTTTAGCTCTCACGAGCTTCTGTTTAACCCTTATGGG
Found at i:11716941 original size:50 final size:50
Alignment explanation
Indices: 11716826--11717124 Score: 391
Period size: 50 Copynumber: 5.8 Consensus size: 50
11716816 GATAATAACA
* ** * *
11716826 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * *
11716877 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
11716927 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
11716977 TGCCAACGCCATGTCCCAGACATGGTCTCACACGCGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
11717027 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATC-T-CGG
*
11717082 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
11717125 TTACCCAAAT
Statistics
Matches: 219, Mismatches: 23, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
50 140 0.64
51 33 0.15
53 3 0.01
54 1 0.00
55 2 0.01
56 40 0.18
ACGTcount: A:0.21, C:0.31, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:11717240 original size:13 final size:13
Alignment explanation
Indices: 11717219--11717250 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
11717209 GCTTGGATCA
*
11717219 TCATCAAATAAAT
1 TCATAAAATAAAT
11717232 TCATAAAATAAAT
1 TCATAAAATAAAT
11717245 TCATAA
1 TCATAA
11717251 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:11719132 original size:22 final size:22
Alignment explanation
Indices: 11719091--11719145 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
11719081 TGCACTAATG
11719091 AACAGAGAGCACTAAAGTGCTA
1 AACAGAGAGCACTAAAGTGCTA
* *
11719113 TACAGAGAGCAC-AGATGTGCTA
1 AACAGAGAGCACTA-AAGTGCTA
*
11719135 AACGGAGAGCA
1 AACAGAGAGCA
11719146 TTGACTTGCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 1 0.04
22 27 0.96
ACGTcount: A:0.42, C:0.18, G:0.27, T:0.13
Consensus pattern (22 bp):
AACAGAGAGCACTAAAGTGCTA
Found at i:11719716 original size:18 final size:19
Alignment explanation
Indices: 11719693--11719728 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
11719683 CTGAACCGAG
*
11719693 ACTAATTT-TTATTCTCAA
1 ACTAATTTCATATTCTCAA
11719711 ACTAATTTCATATTCTCA
1 ACTAATTTCATATTCTCA
11719729 TTCCATTCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.47
Consensus pattern (19 bp):
ACTAATTTCATATTCTCAA
Found at i:11720156 original size:5 final size:5
Alignment explanation
Indices: 11720146--11720188 Score: 86
Period size: 5 Copynumber: 8.6 Consensus size: 5
11720136 TTATTTCTTT
11720146 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TAT
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TAT
11720189 TTATACTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TATAA
Found at i:11741833 original size:2 final size:2
Alignment explanation
Indices: 11741821--11741854 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
11741811 NNTACGTAAG
11741821 TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11741855 TTTTTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:11755015 original size:2 final size:2
Alignment explanation
Indices: 11755008--11755054 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
11754998 AACCATTCTT
*
11755008 TC TC TC TC TC TC TC TG TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
11755050 TC TC T
1 TC TC T
11755055 TTTTGAAAGC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.47, G:0.02, T:0.51
Consensus pattern (2 bp):
TC
Found at i:11756341 original size:2 final size:2
Alignment explanation
Indices: 11756334--11756370 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
11756324 AGGCTTAAAC
11756334 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
11756371 GAGGGGAAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:11757322 original size:20 final size:22
Alignment explanation
Indices: 11757285--11757325 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
11757275 GGGAACGGGC
11757285 AAGGGGAAGAGTAGCAAAAGAA
1 AAGGGGAAGAGTAGCAAAAGAA
11757307 AAGGGGAA-AG-AGCAAAAGA
1 AAGGGGAAGAGTAGCAAAAGA
11757326 CTGACATTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.47
21 2 0.11
22 8 0.42
ACGTcount: A:0.56, C:0.05, G:0.37, T:0.02
Consensus pattern (22 bp):
AAGGGGAAGAGTAGCAAAAGAA
Found at i:11763005 original size:2 final size:2
Alignment explanation
Indices: 11762998--11763027 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11762988 TCATTCATGA
11762998 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
11763028 ATGTATGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:11774345 original size:16 final size:16
Alignment explanation
Indices: 11774321--11774386 Score: 52
Period size: 15 Copynumber: 4.4 Consensus size: 16
11774311 AAAAAATAAA
*
11774321 TAATTTAATTATATTT
1 TAATATAATTATATTT
11774337 TAATATAATTAT-TTT
1 TAATATAATTATATTT
*
11774352 T-ATAATAA-AATATTT
1 TAAT-ATAATTATATTT
*
11774367 TAA-AT-ATTTTATTT
1 TAATATAATTATATTT
*
11774381 TTATAT
1 TAATAT
11774387 TTTTTGAGTC
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
13 1 0.03
14 13 0.32
15 14 0.35
16 12 0.30
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATATAATTATATTT
Found at i:11776937 original size:31 final size:31
Alignment explanation
Indices: 11776899--11776984 Score: 104
Period size: 31 Copynumber: 2.7 Consensus size: 31
11776889 CGGCCCATTT
11776899 TTATTTTAAAAAT-TTTAAAAAATTAAAAAAA
1 TTATTTTAAAAATATTT-AAAAATTAAAAAAA
*
11776930 TTATTTTAAAAATATTTTAAAATTAAAAAAA
1 TTATTTTAAAAATATTTAAAAATTAAAAAAA
**
11776961 TT-TTAAAAAAAGTATTTTAAAAAT
1 TTATTTTAAAAA-TA-TTTAAAAAT
11776985 ATTTTAAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
30 7 0.15
31 30 0.62
32 11 0.23
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (31 bp):
TTATTTTAAAAATATTTAAAAATTAAAAAAA
Found at i:11776947 original size:42 final size:40
Alignment explanation
Indices: 11776900--11777021 Score: 158
Period size: 42 Copynumber: 3.0 Consensus size: 40
11776890 GGCCCATTTT
*
11776900 TATTTTAAAAATTTTAAAAAATTAAAAAAATTATTTTAAAAA
1 TATTTT-AAAATTTAAAAAAATTAAAAAAA-TATTTTAAAAA
11776942 TATTTTAAAA-TTAAAAAAATTTTAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTTAAAAAAA--TTAAAAAAA-TATTTTAAAAA
* *
11776984 TATTTTAAAATTAAAAAAAATT-TAAAAATATTTTAAAA
1 TATTTTAAAATTTAAAAAAATTAAAAAAATATTTTAAAA
11777022 TTAAAAAAAA
Statistics
Matches: 73, Mismatches: 4, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
39 10 0.14
40 13 0.18
41 6 0.08
42 36 0.49
43 8 0.11
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (40 bp):
TATTTTAAAATTTAAAAAAATTAAAAAAATATTTTAAAAA
Found at i:11776957 original size:17 final size:17
Alignment explanation
Indices: 11776906--11776968 Score: 62
Period size: 17 Copynumber: 3.8 Consensus size: 17
11776896 TTTTTATTTT
11776906 AAAAATTTTAAAAAATTAA
1 AAAAATTTT--AAAATTAA
11776925 AAAAATTATT----TTAA
1 AAAAATT-TTAAAATTAA
*
11776939 AAATATTTTAAAATTAA
1 AAAAATTTTAAAATTAA
11776956 AAAAATTTTAAAA
1 AAAAATTTTAAAA
11776969 AAAGTATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
13 2 0.05
14 10 0.27
17 16 0.43
19 7 0.19
20 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AAAAATTTTAAAATTAA
Found at i:11776966 original size:11 final size:11
Alignment explanation
Indices: 11776906--11777021 Score: 58
Period size: 11 Copynumber: 11.2 Consensus size: 11
11776896 TTTTTATTTT
11776906 AAAAATTTT-A
1 AAAAATTTTAA
*
11776916 AAAAA-TTAAA
1 AAAAATTTTAA
11776926 AAAATTATTTTAA
1 AAAA--ATTTTAA
*
11776939 AAATATTTT--
1 AAAAATTTTAA
11776948 -AAAA--TTAA
1 AAAAATTTTAA
11776956 AAAAATTTTAAA
1 AAAAATTTT-AA
11776968 AAAAGTATTTTAA
1 AAAA--ATTTTAA
*
11776981 AAATATTTT--
1 AAAAATTTTAA
11776990 -AAAA--TTAA
1 AAAAATTTTAA
*
11776998 AAAAAATTTAA
1 AAAAATTTTAA
*
11777009 AAATATTTTAA
1 AAAAATTTTAA
11777020 AA
1 AA
11777022 TTAAAAAAAA
Statistics
Matches: 81, Mismatches: 8, Indels: 33
0.66 0.07 0.27
Matches are distributed among these distances:
6 4 0.05
8 6 0.07
9 10 0.12
10 10 0.12
11 27 0.33
12 7 0.09
13 12 0.15
14 5 0.06
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (11 bp):
AAAAATTTTAA
Found at i:11776999 original size:17 final size:17
Alignment explanation
Indices: 11777000--11777070 Score: 52
Period size: 18 Copynumber: 3.8 Consensus size: 17
11776990 AAAATTAAAA
*
11777000 AAAATTTAAAAATATTTT
1 AAAA-TTAAAAAAATTTT
**
11777018 AAAATTAAAAAAAATTAAA
1 AAAATT-AAAAAAATT-TT
11777037 AAAGTATGTAAAAAATATTTT
1 AAA--AT-TAAAAAA-ATTTT
11777058 AAAATTAAAAAAA
1 AAAATTAAAAAAA
11777071 ATAAATATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 13
0.70 0.08 0.22
Matches are distributed among these distances:
17 3 0.07
18 19 0.45
19 5 0.12
21 11 0.26
22 4 0.10
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (17 bp):
AAAATTAAAAAAATTTT
Found at i:11777008 original size:28 final size:28
Alignment explanation
Indices: 11776976--11777039 Score: 119
Period size: 28 Copynumber: 2.3 Consensus size: 28
11776966 AAAAAAGTAT
11776976 TTTAAAAATATTTTAAAATTAAAAAAAA
1 TTTAAAAATATTTTAAAATTAAAAAAAA
11777004 TTTAAAAATATTTTAAAATTAAAAAAAA
1 TTTAAAAATATTTTAAAATTAAAAAAAA
*
11777032 TTAAAAAA
1 TTTAAAAA
11777040 GTATGTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (28 bp):
TTTAAAAATATTTTAAAATTAAAAAAAA
Found at i:11777031 original size:10 final size:10
Alignment explanation
Indices: 11776990--11777039 Score: 50
Period size: 10 Copynumber: 5.2 Consensus size: 10
11776980 AAAATATTTT
11776990 AAAATTAAAA
1 AAAATTAAAA
*
11777000 AAAATTTAAA
1 AAAATTAAAA
* **
11777010 AATATT--TT
1 AAAATTAAAA
11777018 AAAATTAAAA
1 AAAATTAAAA
11777028 AAAATTAAAA
1 AAAATTAAAA
11777038 AA
1 AA
11777040 GTATGTAAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
8 5 0.16
10 26 0.84
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AAAATTAAAA
Found at i:11777048 original size:28 final size:28
Alignment explanation
Indices: 11776979--11777049 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
11776969 AAAGTATTTT
* *
11776979 AAAAATATTTTAAAATTAAAAAAAATTT
1 AAAAATATTGTAAAATTAAAAAAAATTA
*
11777007 AAAAATATTTTAAAATTAAAAAAAATTA
1 AAAAATATTGTAAAATTAAAAAAAATTA
11777035 AAAAAGTA-TGTAAAA
1 AAAAA-TATTGTAAAA
11777050 AATATTTTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 38 0.95
29 2 0.05
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (28 bp):
AAAAATATTGTAAAATTAAAAAAAATTA
Found at i:11777062 original size:40 final size:38
Alignment explanation
Indices: 11776990--11777072 Score: 130
Period size: 40 Copynumber: 2.1 Consensus size: 38
11776980 AAAATATTTT
*
11776990 AAAATTAAAAAAAATTTAAAAATATTTTAAAATTAAAA
1 AAAATTAAAAAAAATGTAAAAATATTTTAAAATTAAAA
*
11777028 AAAATTAAAAAAGTATGTAAAAAATATTTTAAAATTAAAA
1 AAAATTAAAAAA-AATGT-AAAAATATTTTAAAATTAAAA
11777068 AAAAT
1 AAAAT
11777073 AAATATATCT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
38 12 0.29
39 3 0.07
40 26 0.63
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (38 bp):
AAAATTAAAAAAAATGTAAAAATATTTTAAAATTAAAA
Found at i:11780379 original size:20 final size:20
Alignment explanation
Indices: 11780356--11780404 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
11780346 AGACCCATCC
11780356 ATATTATTTTTAATTTTTTT
1 ATATTATTTTTAATTTTTTT
*
11780376 ATATCATTTTT-ATTTTTTT
1 ATATTATTTTTAATTTTTTT
11780395 -TATT-TTTTTA
1 ATATTATTTTTA
11780405 CTTATTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 5 0.19
18 3 0.12
19 8 0.31
20 10 0.38
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (20 bp):
ATATTATTTTTAATTTTTTT
Found at i:11786447 original size:21 final size:20
Alignment explanation
Indices: 11786413--11786452 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
11786403 AAATTAAAAT
*
11786413 CGAAAGAGAAATTAAATTAAC
1 CGAAAGACAAATT-AATTAAC
*
11786434 CGAAAGACACATTAATTAA
1 CGAAAGACAAATTAATTAA
11786453 AATTCAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.20
Consensus pattern (20 bp):
CGAAAGACAAATTAATTAAC
Found at i:11791512 original size:21 final size:21
Alignment explanation
Indices: 11791480--11791547 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
11791470 GAGCTAAATA
11791480 GAAACCCATAAGGGTTGAACG
1 GAAACCCATAAGGGTTGAACG
* * * *
11791501 GAAGCTCATAAGAGCTGAACG
1 GAAACCCATAAGGGTTGAACG
* *
11791522 GAAACCCATTAGGGTTGAACA
1 GAAACCCATAAGGGTTGAACG
11791543 GAAAC
1 GAAAC
11791548 TTATATGAGT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.40, C:0.19, G:0.26, T:0.15
Consensus pattern (21 bp):
GAAACCCATAAGGGTTGAACG
Found at i:11791515 original size:42 final size:42
Alignment explanation
Indices: 11791453--11791566 Score: 129
Period size: 42 Copynumber: 2.7 Consensus size: 42
11791443 GCTTGAAGGC
* * *
11791453 TGAACAGAATCTCATGAGAGCTAAATAGAAACCCATAAGGGT
1 TGAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGT
* * * *
11791495 TGAACGGAAGCTCATAAGAGCTGAACGGAAACCCATTAGGGT
1 TGAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGT
* * * *
11791537 TGAACAGAAACTTATATGAGTTAAACAGAA
1 TGAACAGAAGCTCATAAGAGCTAAACAGAA
11791567 GCTTGTGAGA
Statistics
Matches: 58, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.42, C:0.16, G:0.23, T:0.19
Consensus pattern (42 bp):
TGAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGT
Found at i:11791791 original size:45 final size:45
Alignment explanation
Indices: 11791731--11791823 Score: 159
Period size: 45 Copynumber: 2.1 Consensus size: 45
11791721 CTTCAAATTC
*
11791731 ATAATTTAACAATATTCTATTTTTCAACAACATGCTAAATACATA
1 ATAATTTAACAATATTCTATTTTTCAACAACATACTAAATACATA
* *
11791776 ATAATTTAACAATATTCTATTTTTCAATAATATACTAAATACATA
1 ATAATTTAACAATATTCTATTTTTCAACAACATACTAAATACATA
11791821 ATA
1 ATA
11791824 TTATTCATCA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.46, C:0.13, G:0.01, T:0.40
Consensus pattern (45 bp):
ATAATTTAACAATATTCTATTTTTCAACAACATACTAAATACATA
Found at i:11793676 original size:18 final size:20
Alignment explanation
Indices: 11793655--11793695 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
11793645 AAAATATTTA
*
11793655 TTTTGATAT-TT-TTAATAT
1 TTTTGATATATTATAAATAT
11793673 TTTTGATATATTATAAATAT
1 TTTTGATATATTATAAATAT
11793693 TTT
1 TTT
11793696 AAAATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 2 0.10
20 9 0.45
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (20 bp):
TTTTGATATATTATAAATAT
Found at i:11803027 original size:47 final size:44
Alignment explanation
Indices: 11802936--11803032 Score: 122
Period size: 47 Copynumber: 2.1 Consensus size: 44
11802926 CACTTAATTC
*
11802936 TAATAAAGATAATAATTTATAACAATAAACATCATATATAAACT
1 TAATAAAGATAATAATTTATAACAATAAACATCATACATAAACT
* * * *
11802980 TAATAAAGAATATCTAATTTGATAATAATAAATATTATACATAAACT
1 TAATAAAG-ATA-ATAATTT-ATAACAATAAACATCATACATAAACT
11803027 TAATAA
1 TAATAA
11803033 CAAGCCATGC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
44 8 0.18
45 3 0.07
46 6 0.13
47 28 0.62
ACGTcount: A:0.56, C:0.07, G:0.03, T:0.34
Consensus pattern (44 bp):
TAATAAAGATAATAATTTATAACAATAAACATCATACATAAACT
Found at i:11805073 original size:50 final size:50
Alignment explanation
Indices: 11804958--11805200 Score: 396
Period size: 50 Copynumber: 4.8 Consensus size: 50
11804948 GATAATAACA
* ** *
11804958 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* **
11805009 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
11805059 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
11805109 TGCCAATGCCATGTCCCAGACATGGTCTTACATGTGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
11805159 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
11805201 TTACCCAAAT
Statistics
Matches: 178, Mismatches: 14, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
50 145 0.81
51 33 0.19
ACGTcount: A:0.20, C:0.31, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:11805316 original size:13 final size:13
Alignment explanation
Indices: 11805295--11805325 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
11805285 GCTTAGATCA
*
11805295 TCATCAAATAAAT
1 TCATAAAATAAAT
11805308 TCATAAAATAAAT
1 TCATAAAATAAAT
11805321 TCATA
1 TCATA
11805326 GTTTCTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:11805573 original size:30 final size:30
Alignment explanation
Indices: 11805538--11805595 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
11805528 CCTCGACTCT
*
11805538 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
11805568 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
11805596 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:11808977 original size:16 final size:13
Alignment explanation
Indices: 11808946--11808983 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
11808936 ATATTAAGAA
11808946 TATTATTTTTAAT
1 TATTATTTTTAAT
11808959 TATTATTTTTAAAT
1 TATTATTTTT-AAT
*
11808973 T-TTATTATTAA
1 TATTATTTTTAA
11808984 AATAGAATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 2 0.09
13 17 0.74
14 4 0.17
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TATTATTTTTAAT
Done.