Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 7 of 222
Found at i:2203121 original size:20 final size:18
Alignment explanation
Indices: 2203079--2203128 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
2203069 CAAAAAAATT
*
2203079 AAAATATTGAAAATTTAA
1 AAAATATTAAAAATTTAA
*
2203097 AAAATTTTAAAAATATTACA
1 AAAATATTAAAAAT-TTA-A
2203117 AAAATATTAAAA
1 AAAATATTAAAA
2203129 TTATGGAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 12 0.44
19 3 0.11
20 12 0.44
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (18 bp):
AAAATATTAAAAATTTAA
Found at i:2203200 original size:18 final size:18
Alignment explanation
Indices: 2203179--2203214 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2203169 TTTAAAAATT
*
2203179 TATTAAAAAATGAATAAA
1 TATTAAAAAATAAATAAA
2203197 TATTAAAAAATAAATAAA
1 TATTAAAAAATAAATAAA
2203215 ATCATTTAAA
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:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (18 bp):
TATTAAAAAATAAATAAA
Found at i:2212307 original size:15 final size:15
Alignment explanation
Indices: 2212287--2212325 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
2212277 GATCAAGAAA
* *
2212287 TTTGGATTAGATTGG
1 TTTGGATCAGATCGG
2212302 TTTGGATCAGATCGG
1 TTTGGATCAGATCGG
*
2212317 ATTGGATCA
1 TTTGGATCA
2212326 TTGAAGACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.23, C:0.08, G:0.31, T:0.38
Consensus pattern (15 bp):
TTTGGATCAGATCGG
Found at i:2227852 original size:19 final size:20
Alignment explanation
Indices: 2227811--2227857 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
2227801 TTTAAAAAAT
*
2227811 ATTTTT-ATAATTTTTTATA
1 ATTTTTAATAATTTTTAATA
*
2227830 ATTTTTAATAA-TTTTAATG
1 ATTTTTAATAATTTTTAATA
2227849 ATTTTTAAT
1 ATTTTTAAT
2227858 TTTTCAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 21 0.84
20 4 0.16
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
ATTTTTAATAATTTTTAATA
Found at i:2227854 original size:10 final size:10
Alignment explanation
Indices: 2227811--2227857 Score: 62
Period size: 10 Copynumber: 4.9 Consensus size: 10
2227801 TTTAAAAAAT
2227811 ATTTTT-ATA
1 ATTTTTAATA
*
2227820 ATTTTTTATA
1 ATTTTTAATA
2227830 ATTTTTAATA
1 ATTTTTAATA
*
2227840 A-TTTTAATG
1 ATTTTTAATA
2227849 ATTTTTAAT
1 ATTTTTAAT
2227858 TTTTCAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
9 14 0.41
10 20 0.59
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:2244209 original size:11 final size:11
Alignment explanation
Indices: 2244195--2244221 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2244185 AATAAATATT
2244195 ATTTTATTAAG
1 ATTTTATTAAG
2244206 ATTTTATTAAG
1 ATTTTATTAAG
2244217 ATTTT
1 ATTTT
2244222 TAGTATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.59
Consensus pattern (11 bp):
ATTTTATTAAG
Found at i:2245740 original size:5 final size:5
Alignment explanation
Indices: 2245730--2245761 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
2245720 AAATGATAAT
*
2245730 ATTGA ATTGA ATTGA ATTAA ATTGA ATTGA AT
1 ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA AT
2245762 GAAGAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.41
Consensus pattern (5 bp):
ATTGA
Found at i:2261016 original size:69 final size:69
Alignment explanation
Indices: 2260899--2261027 Score: 177
Period size: 69 Copynumber: 1.9 Consensus size: 69
2260889 ATTCGCAAAT
* * * *
2260899 ATTTGGACAGCAGTAAAAACATTTGGACAGCATTGACTTGTACCAAAAATGGACAGCATTTAAGC
1 ATTTGGACAACAGTAAAAACATTCGGACAACATAGACTTGTACCAAAAATGGACAGCATTTAAGC
2260964 ATTA
66 ATTA
* * * **
2260968 ATTTGGACAACATTAATAACATTCGGACAACATAGATTTGTATGAAAAATGGACAGCATT
1 ATTTGGACAACAGTAAAAACATTCGGACAACATAGACTTGTACCAAAAATGGACAGCATT
2261028 AATATGCTCA
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
69 51 1.00
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (69 bp):
ATTTGGACAACAGTAAAAACATTCGGACAACATAGACTTGTACCAAAAATGGACAGCATTTAAGC
ATTA
Found at i:2261084 original size:34 final size:35
Alignment explanation
Indices: 2261041--2261110 Score: 99
Period size: 34 Copynumber: 2.0 Consensus size: 35
2261031 ATGCTCAAAA
* *
2261041 TGGACAACATT-TATACATG-CAAAGCAACCACATT
1 TGGACAACATTATA-ACATGTAAAAACAACCACATT
2261075 TGGACAACATTATAACATGTAAAAACAACCACATT
1 TGGACAACATTATAACATGTAAAAACAACCACATT
2261110 T
1 T
2261111 TAATACCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
34 16 0.50
35 16 0.50
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.24
Consensus pattern (35 bp):
TGGACAACATTATAACATGTAAAAACAACCACATT
Found at i:2261860 original size:41 final size:41
Alignment explanation
Indices: 2261790--2261966 Score: 182
Period size: 40 Copynumber: 4.3 Consensus size: 41
2261780 ACTCAATGTT
* * *
2261790 TCGCACACTAAATGCCATTGCATAGCCGAAGCTAT-T-ATAA
1 TCGCACACTAAGTGCCA-TACATAGCCGAAGCTATCTCACAA
* ***
2261830 TCCCGCACACTAAGTGCCTTACATAGCCGAAGCTATCTCAGTC
1 T--CGCACACTAAGTGCCATACATAGCCGAAGCTATCTCACAA
* * *
2261873 TCGCACACTAAGTGCCATATATAGCTGAAGCTAT-TCCCAA
1 TCGCACACTAAGTGCCATACATAGCCGAAGCTATCTCACAA
* * *
2261913 TCGCACACTAAGTGCCATAAACAGCCGAATCTATCTCA-AA
1 TCGCACACTAAGTGCCATACATAGCCGAAGCTATCTCACAA
2261953 TCGCACACTAAGTG
1 TCGCACACTAAGTG
2261967 ATAAACATAG
Statistics
Matches: 114, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
40 49 0.43
41 48 0.42
42 15 0.13
43 2 0.02
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.23
Consensus pattern (41 bp):
TCGCACACTAAGTGCCATACATAGCCGAAGCTATCTCACAA
Found at i:2261939 original size:81 final size:80
Alignment explanation
Indices: 2261790--2261966 Score: 205
Period size: 81 Copynumber: 2.2 Consensus size: 80
2261780 ACTCAATGTT
* * * * *
2261790 TCGCACACTAAATGCCATTGCATAGCCGAAGCTATTATAATCCCGCACACTAAGTGCCTTACATA
1 TCGCACACTAAGTGCCATT-CATAGCCGAAGCTATTACAAT-CCGCACACTAAGTGCCATAAACA
**
2261855 GCCGAAGCTATCTCAGTC
64 GCCGAAGCTATCTCA-AA
* *
2261873 TCGCACACTAAGTGCCATAT-ATAGCTGAAGCTATTCCCAAT-CGCACACTAAGTGCCATAAACA
1 TCGCACACTAAGTGCCAT-TCATAGCCGAAGCTATT-ACAATCCGCACACTAAGTGCCATAAACA
*
2261936 GCCGAATCTATCTCAAA
64 GCCGAAGCTATCTCAAA
2261953 TCGCACACTAAGTG
1 TCGCACACTAAGTG
2261967 ATAAACATAG
Statistics
Matches: 82, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
80 14 0.17
81 33 0.40
82 14 0.17
83 20 0.24
84 1 0.01
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.23
Consensus pattern (80 bp):
TCGCACACTAAGTGCCATTCATAGCCGAAGCTATTACAATCCGCACACTAAGTGCCATAAACAGC
CGAAGCTATCTCAAA
Found at i:2264511 original size:61 final size:61
Alignment explanation
Indices: 2264388--2264513 Score: 146
Period size: 61 Copynumber: 2.1 Consensus size: 61
2264378 TTTGATCCTA
* * * * **
2264388 AATTTTAAAAAAATCAACAAATTTAACTATCAATATTTATAAAATTTATCATTTTAGTTTT
1 AATTCTAAAAAAATCAACAAATTTAACCATCAATATTTATAAAAGTTATCAATTTAAATTT
* * * *
2264449 AATTCTAAAAAAATCAACAAATTTAACCCTTAGTATTTACTAAAGGTT-TCAATTTAAATTT
1 AATTCTAAAAAAATCAACAAATTTAACCATCAATATTTA-TAAAAGTTATCAATTTAAATTT
2264510 AATT
1 AATT
2264514 TTAATTCTAA
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
61 48 0.89
62 6 0.11
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.41
Consensus pattern (61 bp):
AATTCTAAAAAAATCAACAAATTTAACCATCAATATTTATAAAAGTTATCAATTTAAATTT
Found at i:2287320 original size:17 final size:17
Alignment explanation
Indices: 2287298--2287333 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2287288 GATATTAAAA
2287298 AATAATGAATTAAATGT
1 AATAATGAATTAAATGT
* *
2287315 AATAATGAGTTAGATGT
1 AATAATGAATTAAATGT
2287332 AA
1 AA
2287334 AAATTGTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (17 bp):
AATAATGAATTAAATGT
Found at i:2295044 original size:136 final size:136
Alignment explanation
Indices: 2294800--2295074 Score: 541
Period size: 136 Copynumber: 2.0 Consensus size: 136
2294790 CTGAACTAGA
2294800 ACAAATTTAAGGTTGGAAGCGATTTCTGGGCTCTTGGCTGTCTAGGCTTTGTTTTTTACTATTTA
1 ACAAATTTAAGGTTGGAAGCGATTTCTGGGCTCTTGGCTGTCTAGGCTTTGTTTTTTACTATTTA
*
2294865 ATTTTCAACGACTTTTAGCCCTTGAGTAGGCCCAGAGTCGATTTTGGAAGAAAAAAAAAAGGATT
66 ATTTTCAACGACTTTTAGCCCTTGAGTAGGCCCAGAGTCGATTTTGGAAGAAAAAAAAAAAGATT
2294930 CAAGGT
131 CAAGGT
2294936 ACAAATTTAAGGTTGGAAGCGATTTCTGGGCTCTTGGCTGTCTAGGCTTTGTTTTTTACTATTTA
1 ACAAATTTAAGGTTGGAAGCGATTTCTGGGCTCTTGGCTGTCTAGGCTTTGTTTTTTACTATTTA
2295001 ATTTTCAACGACTTTTAGCCCTTGAGTAGGCCCAGAGTCGATTTTGGAAGAAAAAAAAAAAGATT
66 ATTTTCAACGACTTTTAGCCCTTGAGTAGGCCCAGAGTCGATTTTGGAAGAAAAAAAAAAAGATT
2295066 CAAGGT
131 CAAGGT
2295072 ACA
1 ACA
2295075 TTAGACCAAA
Statistics
Matches: 138, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
136 138 1.00
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (136 bp):
ACAAATTTAAGGTTGGAAGCGATTTCTGGGCTCTTGGCTGTCTAGGCTTTGTTTTTTACTATTTA
ATTTTCAACGACTTTTAGCCCTTGAGTAGGCCCAGAGTCGATTTTGGAAGAAAAAAAAAAAGATT
CAAGGT
Found at i:2300602 original size:29 final size:30
Alignment explanation
Indices: 2300569--2300625 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
2300559 GTTTCGTGAT
* *
2300569 CACATAGGTGG-CCACACGGGCGTGTGCCG
1 CACATAGGCGGTCCACACGGCCGTGTGCCG
2300598 CACATAGGCGGTCCACACGGCCGTGTGC
1 CACATAGGCGGTCCACACGGCCGTGTGC
2300626 AATTGGGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.18, C:0.33, G:0.35, T:0.14
Consensus pattern (30 bp):
CACATAGGCGGTCCACACGGCCGTGTGCCG
Found at i:2310649 original size:12 final size:13
Alignment explanation
Indices: 2310632--2310668 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
2310622 GAACCGGACA
2310632 CGAACCGAA-CTC
1 CGAACCGAAGCTC
2310644 CGAACC-AAGCTC
1 CGAACCGAAGCTC
*
2310656 CGAACCGTAGCTC
1 CGAACCGAAGCTC
2310669 TGATGCCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
11 2 0.09
12 15 0.68
13 5 0.23
ACGTcount: A:0.30, C:0.41, G:0.19, T:0.11
Consensus pattern (13 bp):
CGAACCGAAGCTC
Found at i:2328915 original size:6 final size:6
Alignment explanation
Indices: 2328864--2328898 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
2328854 AGAATGTTCT
2328864 TTTACA TTTACA TTTACA TTTACA TTTACA TTTAC
1 TTTACA TTTACA TTTACA TTTACA TTTACA TTTAC
2328899 TTGACTCACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.51
Consensus pattern (6 bp):
TTTACA
Found at i:2348014 original size:22 final size:23
Alignment explanation
Indices: 2347986--2348030 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2347976 AAGTTTGAGA
* *
2347986 TTTAAAA-TTATATTTTAATTTT
1 TTTAAAATTTATAATTCAATTTT
2348008 TTTAAAATTTATAATTCAATTTT
1 TTTAAAATTTATAATTCAATTTT
2348031 GATTCAGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTAAAATTTATAATTCAATTTT
Found at i:2353166 original size:32 final size:32
Alignment explanation
Indices: 2353130--2353199 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 32
2353120 CTCTCTTAAC
2353130 AAAAATTACAAAAAAAAAATTAAATAATA-TTA-
1 AAAAATTA-AAAAAAAAAATTAAA-AATATTTAT
* *
2353162 AAAAA-TAAAAAATAAAATTCAAAATATTTAT
1 AAAAATTAAAAAAAAAAATTAAAAATATTTAT
2353193 AAAAATT
1 AAAAATT
2353200 CTAAATTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 4 0.12
30 16 0.48
31 7 0.21
32 6 0.18
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (32 bp):
AAAAATTAAAAAAAAAAATTAAAAATATTTAT
Found at i:2353197 original size:19 final size:18
Alignment explanation
Indices: 2353175--2353210 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2353165 AATAAAAAAT
2353175 AAAATTCAAAATATTTATA
1 AAAATTCAAAAT-TTTATA
*
2353194 AAAATTCTAAATTTTAT
1 AAAATTCAAAATTTTAT
2353211 TTTTTTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (18 bp):
AAAATTCAAAATTTTATA
Found at i:2353897 original size:26 final size:26
Alignment explanation
Indices: 2353864--2353917 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
2353854 TAACTAGAAC
*
2353864 AATTTCACTCAATTCAACTCGATTCG
1 AATTTCACTCAACTCAACTCGATTCG
* *
2353890 AATTTCACTCCACTCGACTCGATTCG
1 AATTTCACTCAACTCAACTCGATTCG
2353916 AA
1 AA
2353918 AAATTTCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.31
Consensus pattern (26 bp):
AATTTCACTCAACTCAACTCGATTCG
Found at i:2356022 original size:18 final size:17
Alignment explanation
Indices: 2355989--2356027 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
2355979 TTGTATAAAT
2355989 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
2356007 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
2356024 TGTG
1 TGTG
2356028 GAAGGAAAAT
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:2356145 original size:8 final size:8
Alignment explanation
Indices: 2356132--2356160 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
2356122 CACTAGAGAC
2356132 CAGTGTTA
1 CAGTGTTA
2356140 CAGTGTTA
1 CAGTGTTA
2356148 CAGTGTTA
1 CAGTGTTA
2356156 CAGTG
1 CAGTG
2356161 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:2356274 original size:23 final size:23
Alignment explanation
Indices: 2356247--2356322 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
2356237 AGTGTTATTG
2356247 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
2356270 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
2356293 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
2356316 ATCAGTG
1 ATCAGTG
2356323 TGGCACTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:2362892 original size:18 final size:17
Alignment explanation
Indices: 2362859--2362897 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
2362849 TTGTATAAAT
2362859 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
2362877 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
2362894 TGTG
1 TGTG
2362898 GAAGGAAAAT
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:2363015 original size:8 final size:8
Alignment explanation
Indices: 2363002--2363030 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
2362992 CACTAGAGAC
2363002 CAGTGTTA
1 CAGTGTTA
2363010 CAGTGTTA
1 CAGTGTTA
2363018 CAGTGTTA
1 CAGTGTTA
2363026 CAGTG
1 CAGTG
2363031 AGTCTCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:2363144 original size:23 final size:23
Alignment explanation
Indices: 2363117--2363192 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
2363107 AGTGTTATTG
2363117 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
2363140 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
2363163 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
2363186 ATCAGTG
1 ATCAGTG
2363193 TGGCACTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:2365392 original size:27 final size:27
Alignment explanation
Indices: 2365362--2365414 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
2365352 GGTAATGGAA
*
2365362 GGTGATTTTTGCAGATATTTGATTTAT
1 GGTGATTTTAGCAGATATTTGATTTAT
2365389 GGTGATTTTAGCAGATATTTGATTTA
1 GGTGATTTTAGCAGATATTTGATTTA
2365415 CTTTATTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.25, C:0.04, G:0.23, T:0.49
Consensus pattern (27 bp):
GGTGATTTTAGCAGATATTTGATTTAT
Found at i:2366599 original size:10 final size:10
Alignment explanation
Indices: 2366584--2366610 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2366574 TACACTCATA
2366584 TAAAAGAAAG
1 TAAAAGAAAG
2366594 TAAAAGAAAG
1 TAAAAGAAAG
2366604 TAAAAGA
1 TAAAAGA
2366611 TACACACTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.19, T:0.11
Consensus pattern (10 bp):
TAAAAGAAAG
Found at i:2368384 original size:22 final size:21
Alignment explanation
Indices: 2368359--2368399 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
2368349 AGTTACTTTC
2368359 ATTAATT-TTACAAATAATATAT
1 ATTAATTATTA-AAA-AATATAT
2368381 ATTAATTATTAAAAAATAT
1 ATTAATTATTAAAAAATAT
2368400 TTAAAATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 10 0.56
23 3 0.17
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTAATTATTAAAAAATATAT
Found at i:2372925 original size:31 final size:31
Alignment explanation
Indices: 2372890--2372953 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
2372880 AAAGTACTCC
2372890 TGTCTATGAGGCTATTACATCCAGAGATCGG
1 TGTCTATGAGGCTATTACATCCAGAGATCGG
2372921 TGTCTATGAGGCTATTACATCCAGAGATCGG
1 TGTCTATGAGGCTATTACATCCAGAGATCGG
2372952 TG
1 TG
2372954 AAAGTATCAT
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:0.19, G:0.27, T:0.30
Consensus pattern (31 bp):
TGTCTATGAGGCTATTACATCCAGAGATCGG
Found at i:2373374 original size:33 final size:33
Alignment explanation
Indices: 2373332--2373400 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
2373322 ATGAAAAAAA
2373332 ACAAAGAAATAACTAAGCATAGTCATGTTGGGC
1 ACAAAGAAATAACTAAGCATAGTCATGTTGGGC
2373365 ACAAAGAAATAACTAAGCATAGTCATGTTGGGC
1 ACAAAGAAATAACTAAGCATAGTCATGTTGGGC
2373398 ACA
1 ACA
2373401 TACACACTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.20
Consensus pattern (33 bp):
ACAAAGAAATAACTAAGCATAGTCATGTTGGGC
Found at i:2373700 original size:133 final size:133
Alignment explanation
Indices: 2373462--2373729 Score: 527
Period size: 133 Copynumber: 2.0 Consensus size: 133
2373452 CCTTCACAAA
2373462 TGAGACCAACTCAACCTCATAATACACAGTTGAGTATTCAGATGAACCGAAAGCGTATTCGGGCT
1 TGAGACCAACTCAACCTCATAATACACAGTTGAGTATTCAGATGAACCGAAAGCGTATTCGGGCT
2373527 GGATAGTGGTAAGTGCATGTTCTCCTTTCTTCATGGTCTTCACAGTTTTTTCAAGACCATCAACT
66 GGATAGTGGTAAGTGCATGTTCTCCTTTCTTCATGGTCTTCACAGTTTTTTCAAGACCATCAACT
2373592 ACT
131 ACT
2373595 TGAGACCAACTCAACCTCATAATACACAGTTGAGTATTCAGATGAACCGAAAGCGTATTCGGGCT
1 TGAGACCAACTCAACCTCATAATACACAGTTGAGTATTCAGATGAACCGAAAGCGTATTCGGGCT
*
2373660 GGATAGTGGTAAGTGCATGTTCTCCTTTCTTCATGGTCTTCACAGTTTTTTCAAGACCATCAATT
66 GGATAGTGGTAAGTGCATGTTCTCCTTTCTTCATGGTCTTCACAGTTTTTTCAAGACCATCAACT
2373725 ACT
131 ACT
2373728 TG
1 TG
2373730 TCCTGCCACA
Statistics
Matches: 134, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
133 134 1.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (133 bp):
TGAGACCAACTCAACCTCATAATACACAGTTGAGTATTCAGATGAACCGAAAGCGTATTCGGGCT
GGATAGTGGTAAGTGCATGTTCTCCTTTCTTCATGGTCTTCACAGTTTTTTCAAGACCATCAACT
ACT
Found at i:2383868 original size:71 final size:71
Alignment explanation
Indices: 2383783--2383921 Score: 278
Period size: 71 Copynumber: 2.0 Consensus size: 71
2383773 AATGTTTGGT
2383783 AAAATTTACATTTAATCAATAATTTTTTAAAAGTAACATCTAAAAATAAAGTAAAATTGAAAAAA
1 AAAATTTACATTTAATCAATAATTTTTTAAAAGTAACATCTAAAAATAAAGTAAAATTGAAAAAA
2383848 AAATAA
66 AAATAA
2383854 AAAATTTACATTTAATCAATAATTTTTTAAAAGTAACATCTAAAAATAAAGTAAAATTGAAAAAA
1 AAAATTTACATTTAATCAATAATTTTTTAAAAGTAACATCTAAAAATAAAGTAAAATTGAAAAAA
2383919 AAA
66 AAA
2383922 AATAAAGAGT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.59, C:0.06, G:0.04, T:0.31
Consensus pattern (71 bp):
AAAATTTACATTTAATCAATAATTTTTTAAAAGTAACATCTAAAAATAAAGTAAAATTGAAAAAA
AAATAA
Found at i:2406915 original size:36 final size:37
Alignment explanation
Indices: 2406875--2406944 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 37
2406865 AAATAATAAA
* *
2406875 AAAATAAAAAAATATGTATATGTATT-TAAAACATTT
1 AAAATAAAAAAATATATATATATATTATAAAACATTT
* * *
2406911 AAAATATATACATATATATATATATTATAAAACA
1 AAAATAAAAAAATATATATATATATTATAAAACA
2406945 CATATGCGTG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
36 21 0.75
37 7 0.25
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.36
Consensus pattern (37 bp):
AAAATAAAAAAATATATATATATATTATAAAACATTT
Found at i:2406976 original size:3 final size:3
Alignment explanation
Indices: 2406968--2407022 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
2406958 ATCTATAGGT
2406968 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2407016 ATA ATA A
1 ATA ATA A
2407023 AATGACAGAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2417814 original size:33 final size:33
Alignment explanation
Indices: 2417769--2417999 Score: 150
Period size: 33 Copynumber: 6.6 Consensus size: 33
2417759 AAAATACGGT
*
2417769 GGAATCAACACTTAGCAACCACCAATGAATCGG
1 GGAATCAGCACTTAGCAACCACCAATGAATCGG
* * *
2417802 GGAATCATCACTTAGCAATCCCCCTTCACATTTAAAATACGG
1 GGAATCAGCACTTAGCAA--CCAC--CA-A--T-GAAT-CGG
*
2417844 TGGAATCAGCGCTTAGCAACCACCAATGAATCGG
1 -GGAATCAGCACTTAGCAACCACCAATGAATCGG
* *
2417878 GGAATCAGCGCTTAGCAACC-CC--T---TGGG
1 GGAATCAGCACTTAGCAACCACCAATGAATCGG
* * *
2417905 GGAATCAACACTTAGCAACCCCCTTCACATTTAAAATACGG
1 GGAATCAGCACTTAGCAA-CCAC--CA-A--T-GAAT-CGG
*
2417946 TGGAATCAGCACTTAGCAACCACCAATGAATAGG
1 -GGAATCAGCACTTAGCAACCACCAATGAATCGG
2417980 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
2418000 CTTAGGGGGA
Statistics
Matches: 158, Mismatches: 15, Indels: 50
0.71 0.07 0.22
Matches are distributed among these distances:
27 19 0.12
28 2 0.01
29 1 0.01
30 1 0.01
31 1 0.01
32 2 0.01
33 57 0.36
34 5 0.03
35 9 0.06
36 3 0.02
37 2 0.01
38 3 0.02
39 4 0.03
40 2 0.01
41 11 0.07
42 20 0.13
43 16 0.10
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (33 bp):
GGAATCAGCACTTAGCAACCACCAATGAATCGG
Found at i:2417859 original size:76 final size:76
Alignment explanation
Indices: 2417690--2417899 Score: 300
Period size: 76 Copynumber: 2.8 Consensus size: 76
2417680 TATCCGTTGT
* * * * *
2417690 CGGTGGATTCAGCAATTAGCAACCACCAGT-AATTCGGGGAATCAGCACTTAACAA-CCCTTGTC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAA-TCGGGGAATCAGCACTTAGCAACCCCCTGTC
2417753 ACATTTAAAATA
65 ACATTTAAAATA
* *
2417765 CGGTGGAATCAACACTTAGCAACCACCAATGAATCGGGGAATCATCACTTAGCAATCCCCCT-TC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAA-CCCCCTGTC
2417829 ACATTTAAAATA
65 ACATTTAAAATA
* *
2417841 CGGTGGAATCAGCGCTTAGCAACCACCAATGAATCGGGGAATCAGCGCTTAGCAACCCC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCC
2417900 TTGGGGGAAT
Statistics
Matches: 121, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
75 50 0.41
76 67 0.55
77 4 0.03
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (76 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCCTGTCA
CATTTAAAATA
Found at i:2417952 original size:102 final size:102
Alignment explanation
Indices: 2417800--2418031 Score: 385
Period size: 102 Copynumber: 2.3 Consensus size: 102
2417790 CCAATGAATC
* *
2417800 GGGGAATCATCACTTAGCAATCCCCCTTCACATTTAAAATACGGTGGAATCAGCGCTTAGCAACC
1 GGGGAATCAACACTTAGCAA-CCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACC
* *
2417865 ACCAATGAATCGGGGAATCAGCGCTTAGCAACCCCTT-G
65 ACCAATGAATAGGGGAATCAGCACTTAGCAA-CCCTTAG
2417903 GGGGAATCAACACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
1 GGGGAATCAACACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
2417968 CCAATGAATAGGGGAATCAGCACTTAGCAACCCTTAG
66 CCAATGAATAGGGGAATCAGCACTTAGCAACCCTTAG
* *
2418005 GGGGAATCAGCACGTAGCAACCCCCTT
1 GGGGAATCAACACTTAGCAACCCCCTT
2418032 TTTATTCAAT
Statistics
Matches: 122, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
101 5 0.04
102 98 0.80
103 19 0.16
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.20
Consensus pattern (102 bp):
GGGGAATCAACACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
CCAATGAATAGGGGAATCAGCACTTAGCAACCCTTAG
Found at i:2421098 original size:45 final size:45
Alignment explanation
Indices: 2421025--2421173 Score: 183
Period size: 45 Copynumber: 3.3 Consensus size: 45
2421015 ATATACCGAG
*
2421025 TACTGTTACTGTTACCGATTCGATACTTTGTGTGTTAAATACTGT
1 TACTGTTACTGTTACCGATTCGACACTTTGTGTGTTAAATACTGT
* **
2421070 TACTATTACTGTTACCGATTCGACACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACCGATTCGACACTTTGTGTGTTAAATACTGT
* * * **
2421115 TACCGTTAATGTTACAGATTC-AGCACTTTGTGTACTAAATACTGT
1 TACTGTTACTGTTACCGATTCGA-CACTTTGTGTGTTAAATACTGT
* *
2421160 TACTGCTACCGTTA
1 TACTGTTACTGTTA
2421174 TTGATTACTG
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
44 1 0.01
45 86 0.99
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (45 bp):
TACTGTTACTGTTACCGATTCGACACTTTGTGTGTTAAATACTGT
Found at i:2421368 original size:19 final size:20
Alignment explanation
Indices: 2421346--2421388 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
2421336 CGTGATTGTA
* *
2421346 GAATAT-AATTTGAAAATGT
1 GAATATGAATATGAAAATAT
2421365 GAAT-TGAATATGAAAATAT
1 GAATATGAATATGAAAATAT
2421384 GAATA
1 GAATA
2421389 GAAAGCATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.51, C:0.00, G:0.16, T:0.33
Consensus pattern (20 bp):
GAATATGAATATGAAAATAT
Found at i:2440057 original size:3 final size:3
Alignment explanation
Indices: 2440049--2440095 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
2440039 ATCTATAGGT
2440049 TAA TAA TAA T-A TAA TAA TAA T-A TAA T-A TAA TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2440093 TAA
1 TAA
2440096 AATGACAGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 8 0.20
3 32 0.80
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2440064 original size:8 final size:9
Alignment explanation
Indices: 2440049--2440095 Score: 66
Period size: 8 Copynumber: 5.7 Consensus size: 9
2440039 ATCTATAGGT
2440049 TAATAATAA
1 TAATAATAA
2440058 T-ATAATAA
1 TAATAATAA
2440066 TAAT-ATAA
1 TAATAATAA
2440074 T-ATAATAA
1 TAATAATAA
2440082 TAAT-ATAA
1 TAATAATAA
2440090 TAATAA
1 TAATAA
2440096 AATGACAGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
7 2 0.06
8 26 0.76
9 6 0.18
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
TAATAATAA
Found at i:2440073 original size:16 final size:16
Alignment explanation
Indices: 2440049--2440091 Score: 77
Period size: 16 Copynumber: 2.6 Consensus size: 16
2440039 ATCTATAGGT
2440049 TAATAATAATATAATAA
1 TAAT-ATAATATAATAA
2440066 TAATATAATATAATAA
1 TAATATAATATAATAA
2440082 TAATATAATA
1 TAATATAATA
2440092 ATAAAATGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 22 0.85
17 4 0.15
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TAATATAATATAATAA
Found at i:2440095 original size:11 final size:10
Alignment explanation
Indices: 2440049--2440091 Score: 59
Period size: 11 Copynumber: 4.0 Consensus size: 10
2440039 ATCTATAGGT
2440049 TAATAATAATA
1 TAAT-ATAATA
2440060 TAATAATAATA
1 TAAT-ATAATA
2440071 TAATATAATAA
1 TAATATAAT-A
2440082 TAATATAATA
1 TAATATAATA
2440092 ATAAAATGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
10 6 0.19
11 25 0.81
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
TAATATAATA
Found at i:2450809 original size:33 final size:33
Alignment explanation
Indices: 2450764--2450994 Score: 150
Period size: 33 Copynumber: 6.6 Consensus size: 33
2450754 AAAATACGGT
*
2450764 GGAATCAACACTTAGCAACCACCAATGAATCGG
1 GGAATCAGCACTTAGCAACCACCAATGAATCGG
* * *
2450797 GGAATCATCACTTAGCAATCCCCCTTCACATTTAAAATACGG
1 GGAATCAGCACTTAGCAA--CCAC--CA-A--T-GAAT-CGG
*
2450839 TGGAATCAGCGCTTAGCAACCACCAATGAATCGG
1 -GGAATCAGCACTTAGCAACCACCAATGAATCGG
* *
2450873 GGAATCAGCGCTTAGCAACC-CC--T---TGGG
1 GGAATCAGCACTTAGCAACCACCAATGAATCGG
* * *
2450900 GGAATCAACACTTAGCAACCCCCTTCACATTTAAAATACGG
1 GGAATCAGCACTTAGCAA-CCAC--CA-A--T-GAAT-CGG
*
2450941 TGGAATCAGCACTTAGCAACCACCAATGAATAGG
1 -GGAATCAGCACTTAGCAACCACCAATGAATCGG
2450975 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
2450995 CTTAGGGGGA
Statistics
Matches: 158, Mismatches: 15, Indels: 50
0.71 0.07 0.22
Matches are distributed among these distances:
27 19 0.12
28 2 0.01
29 1 0.01
30 1 0.01
31 1 0.01
32 2 0.01
33 57 0.36
34 5 0.03
35 9 0.06
36 3 0.02
37 2 0.01
38 3 0.02
39 4 0.03
40 2 0.01
41 11 0.07
42 20 0.13
43 16 0.10
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (33 bp):
GGAATCAGCACTTAGCAACCACCAATGAATCGG
Found at i:2450854 original size:76 final size:76
Alignment explanation
Indices: 2450685--2450894 Score: 300
Period size: 76 Copynumber: 2.8 Consensus size: 76
2450675 TATCCGTTGT
* * * * *
2450685 CGGTGGATTCAGCAATTAGCAACCACCAGT-AATTCGGGGAATCAGCACTTAACAA-CCCTTGTC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAA-TCGGGGAATCAGCACTTAGCAACCCCCTGTC
2450748 ACATTTAAAATA
65 ACATTTAAAATA
* *
2450760 CGGTGGAATCAACACTTAGCAACCACCAATGAATCGGGGAATCATCACTTAGCAATCCCCCT-TC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAA-CCCCCTGTC
2450824 ACATTTAAAATA
65 ACATTTAAAATA
* *
2450836 CGGTGGAATCAGCGCTTAGCAACCACCAATGAATCGGGGAATCAGCGCTTAGCAACCCC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCC
2450895 TTGGGGGAAT
Statistics
Matches: 121, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
75 50 0.41
76 67 0.55
77 4 0.03
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (76 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCCTGTCA
CATTTAAAATA
Found at i:2450947 original size:102 final size:102
Alignment explanation
Indices: 2450795--2451026 Score: 385
Period size: 102 Copynumber: 2.3 Consensus size: 102
2450785 CCAATGAATC
* *
2450795 GGGGAATCATCACTTAGCAATCCCCCTTCACATTTAAAATACGGTGGAATCAGCGCTTAGCAACC
1 GGGGAATCAACACTTAGCAA-CCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACC
* *
2450860 ACCAATGAATCGGGGAATCAGCGCTTAGCAACCCCTT-G
65 ACCAATGAATAGGGGAATCAGCACTTAGCAA-CCCTTAG
2450898 GGGGAATCAACACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
1 GGGGAATCAACACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
2450963 CCAATGAATAGGGGAATCAGCACTTAGCAACCCTTAG
66 CCAATGAATAGGGGAATCAGCACTTAGCAACCCTTAG
* *
2451000 GGGGAATCAGCACGTAGCAACCCCCTT
1 GGGGAATCAACACTTAGCAACCCCCTT
2451027 TTTATTCAAT
Statistics
Matches: 122, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
101 5 0.04
102 98 0.80
103 19 0.16
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.20
Consensus pattern (102 bp):
GGGGAATCAACACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
CCAATGAATAGGGGAATCAGCACTTAGCAACCCTTAG
Found at i:2454097 original size:45 final size:45
Alignment explanation
Indices: 2454024--2454172 Score: 183
Period size: 45 Copynumber: 3.3 Consensus size: 45
2454014 ATATACCGAG
*
2454024 TACTGTTACTGTTACCGATTCGATACTTTGTGTGTTAAATACTGT
1 TACTGTTACTGTTACCGATTCGACACTTTGTGTGTTAAATACTGT
* **
2454069 TACTATTACTGTTACCGATTCGACACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACCGATTCGACACTTTGTGTGTTAAATACTGT
* * * **
2454114 TACCGTTAATGTTACAGATTC-AGCACTTTGTGTACTAAATACTGT
1 TACTGTTACTGTTACCGATTCGA-CACTTTGTGTGTTAAATACTGT
* *
2454159 TACTGCTACCGTTA
1 TACTGTTACTGTTA
2454173 TTGATTACTG
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
44 1 0.01
45 86 0.99
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (45 bp):
TACTGTTACTGTTACCGATTCGACACTTTGTGTGTTAAATACTGT
Found at i:2454366 original size:19 final size:20
Alignment explanation
Indices: 2454344--2454386 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
2454334 CGTGATTGTA
* *
2454344 GAATAT-AATTTGAAAATGT
1 GAATATGAATATGAAAATAT
2454363 GAAT-TGAATATGAAAATAT
1 GAATATGAATATGAAAATAT
2454382 GAATA
1 GAATA
2454387 GAAAGCATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.51, C:0.00, G:0.16, T:0.33
Consensus pattern (20 bp):
GAATATGAATATGAAAATAT
Found at i:2456775 original size:25 final size:26
Alignment explanation
Indices: 2456711--2456796 Score: 83
Period size: 25 Copynumber: 3.4 Consensus size: 26
2456701 CAGACACACC
*
2456711 ACAGCTCGTATGAGCTT-CTTGATTT
1 ACAGCTCGTATGAGCTTACTCGATTT
*
2456736 ACAGCTCATGA-GAGCTTAC-CGATTCT
1 ACAGCTCGT-ATGAGCTTACTCGATT-T
*
2456762 -CAGCTCGTATGAGCTTA-TTGATTT
1 ACAGCTCGTATGAGCTTACTCGATTT
*
2456786 ATAGCTCGTAT
1 ACAGCTCGTAT
2456797 AAGCATTTAT
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
24 2 0.04
25 45 0.90
26 3 0.06
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (26 bp):
ACAGCTCGTATGAGCTTACTCGATTT
Found at i:2459821 original size:13 final size:13
Alignment explanation
Indices: 2459781--2459826 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
2459771 AATTTTCTTC
2459781 CTTTCCTTCCCTT
1 CTTTCCTTCCCTT
* * *
2459794 TTTTTCTT--TTT
1 CTTTCCTTCCCTT
2459805 CTTTCCTTCCCTT
1 CTTTCCTTCCCTT
2459818 CTTTCCTTC
1 CTTTCCTTC
2459827 TCTGTTTCGT
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
11 8 0.32
13 17 0.68
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (13 bp):
CTTTCCTTCCCTT
Found at i:2460065 original size:14 final size:13
Alignment explanation
Indices: 2460039--2460089 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
2460029 GTTTATTTGA
2460039 AATATAATAATAT
1 AATATAATAATAT
2460052 AATATAATTAATAT
1 AATATAA-TAATAT
* *
2460066 AAT-TTACAATAT
1 AATATAATAATAT
*
2460078 AATAAAATAATA
1 AATATAATAATA
2460090 ATATACTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 8 0.26
13 14 0.45
14 9 0.29
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (13 bp):
AATATAATAATAT
Found at i:2464545 original size:263 final size:262
Alignment explanation
Indices: 2464078--2464605 Score: 1020
Period size: 263 Copynumber: 2.0 Consensus size: 262
2464068 ATGGAGGAGT
2464078 CTAACAATTATGGCCACCAACATCCCCTGCTTCTTATCTTGAATCACGACCAGCTGATCCACAAT
1 CTAACAATTATGGCCACCAACATCCCCTGCTTCTTATCTTGAATCACGACCAGCTGATCCACAAT
2464143 CAAAGTGATATAACTGATTGCTCCAGGTATGCGGAGAAGGTGTCTTCAGCATGCACAATAGTTAA
66 CAAAGTGATATAACTGATTGCTCCAGGTATGCGGAGAAGGTGTCTTCAGCATGCACAATAGTTAA
**
2464208 CTTTTGGTATTTCGACAGTTCTGTCCCTTTACGAGTTCAACATGCAGCCCGTTGGGGAACCACCT
131 CTTTTGGTATTTCGACAGTTCTGTCCCTTTACGAGTTCAACATGCAGCCCGCGGGGGAACCACCT
2464273 AGATGGTCTTGACATAGGACACTTTATAACTTACCTCTCGAATAGGGAGCAATCGTTATACACCT
196 AGATGGTCTTGACATAGGAC-CTTTATAACTTACCTCTCGAATAGGGAGCAATCGTTATACACCT
2464338 ACC
260 ACC
2464341 CTAACAATTATGGCCACCAACATCCCCTGCTTCTTATCTTGAATCACGACCAGCTGATCCACAAT
1 CTAACAATTATGGCCACCAACATCCCCTGCTTCTTATCTTGAATCACGACCAGCTGATCCACAAT
2464406 CAAAGTGATATAACTGATTGCTCCAGGTATGCGGAGAAGGTGTCTTCAGCATGCACAATAGTTAA
66 CAAAGTGATATAACTGATTGCTCCAGGTATGCGGAGAAGGTGTCTTCAGCATGCACAATAGTTAA
2464471 CTTTTGGTATTTCGACAGTTCTGTCCCTTTACGAGTTCAACATGCAGCCCGCGGGGGAACCACCT
131 CTTTTGGTATTTCGACAGTTCTGTCCCTTTACGAGTTCAACATGCAGCCCGCGGGGGAACCACCT
*
2464536 AGATGGTCTTGACATAGGACGTTTATAACTTACCTCTCGAATAGGGAGCAATCGTTATACACCTA
196 AGATGGTCTTGACATAGGACCTTTATAACTTACCTCTCGAATAGGGAGCAATCGTTATACACCTA
2464601 CC
261 CC
2464603 CTA
1 CTA
2464606 GCTTAGTATT
Statistics
Matches: 262, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
262 49 0.19
263 213 0.81
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.28
Consensus pattern (262 bp):
CTAACAATTATGGCCACCAACATCCCCTGCTTCTTATCTTGAATCACGACCAGCTGATCCACAAT
CAAAGTGATATAACTGATTGCTCCAGGTATGCGGAGAAGGTGTCTTCAGCATGCACAATAGTTAA
CTTTTGGTATTTCGACAGTTCTGTCCCTTTACGAGTTCAACATGCAGCCCGCGGGGGAACCACCT
AGATGGTCTTGACATAGGACCTTTATAACTTACCTCTCGAATAGGGAGCAATCGTTATACACCTA
CC
Found at i:2473893 original size:29 final size:29
Alignment explanation
Indices: 2473859--2473922 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 29
2473849 TAAATATATT
2473859 TATTTTTTT--ATTTTTTTAATTTTAAAA
1 TATTTTTTTAAATTTTTTTAATTTTAAAA
2473886 TACTTTTTTTAAATTTTTTTAATTTTAAAA
1 TA-TTTTTTTAAATTTTTTTAATTTTAAAA
2473916 TATTTTT
1 TATTTTT
2473923 AAAATATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
27 2 0.06
28 7 0.21
29 5 0.15
30 20 0.59
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (29 bp):
TATTTTTTTAAATTTTTTTAATTTTAAAA
Found at i:2473944 original size:42 final size:43
Alignment explanation
Indices: 2473878--2473966 Score: 130
Period size: 42 Copynumber: 2.1 Consensus size: 43
2473868 ATTTTTTTAA
2473878 TTTTAAAATACTTTTTTTAAATTTTTTTAA-TTTTAAAAT-AT
1 TTTTAAAATACTTTTTTTAAATTTTTTTAATTTTTAAAATAAT
*
2473919 TTTTAAAATA-TATATTTTTTAATTTTTTTAATTTTTAAAATAAT
1 TTTTAAAATACT-T-TTTTTAAATTTTTTTAATTTTTAAAATAAT
2473963 TTTT
1 TTTT
2473967 TGGTATTTAT
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
40 1 0.02
41 11 0.26
42 16 0.37
43 9 0.21
44 6 0.14
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (43 bp):
TTTTAAAATACTTTTTTTAAATTTTTTTAATTTTTAAAATAAT
Found at i:2475087 original size:29 final size:30
Alignment explanation
Indices: 2475040--2475096 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
2475030 TTGATATAAT
*
2475040 ATACAATTATACATATG-AACTTTAATTTG
1 ATACAATTATACACATGAAACTTTAATTTG
* * *
2475069 ATACAATTATATACGTGAAATTTTAATT
1 ATACAATTATACACATGAAACTTTAATT
2475097 GTTATACTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 14 0.61
30 9 0.39
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (30 bp):
ATACAATTATACACATGAAACTTTAATTTG
Found at i:2475103 original size:21 final size:21
Alignment explanation
Indices: 2475078--2475117 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2475068 GATACAATTA
* *
2475078 TATACGTGAAATTTTAATTGT
1 TATACGTAAAACTTTAATTGT
*
2475099 TATACTTAAAACTTTAATT
1 TATACGTAAAACTTTAATT
2475118 TTGATTTAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.47
Consensus pattern (21 bp):
TATACGTAAAACTTTAATTGT
Found at i:2475927 original size:221 final size:221
Alignment explanation
Indices: 2475652--2476049 Score: 629
Period size: 221 Copynumber: 1.8 Consensus size: 221
2475642 TGAAATTTCG
** *
2475652 AAAGGATATTCGGCTATTCGGTCAAACGAGAAATCGAAACCCAGTACGTTAGGGCACGT-TCTCT
1 AAAGGATATTCGGCTATTCGGTCAAACGAGAAATCGAAACCCAACACATTAGGGCACGTAT-TCT
* *
2475716 TGAAATTACAAACGCGAAATATTGCCTTACTTT-GAAAGTTTAAAAGGATATTTGACTATTTGGT
65 CGAAATTACAAACGCGAAATATTGCCTTA-TTTGGAAAGTTTAAAAGGATATTTGACTATTTAGT
*
2475780 CGAACGATAAATCGAAACCCAACACGCTAGGGCACGTATTCTCGATTTTCTAAACGCGAATATTG
129 CGAACGAGAAATCGAAACCCAACACGCTAGGGCACGTATTCTCGATTTTCTAAACGCGAATATTG
2475845 TCTTATTTTGTCTTATTTGGAAAGTTTA
194 TCTTATTTTGTCTTATTTGGAAAGTTTA
* * *
2475873 AAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACATTAGGGCACGTATTCTC
1 AAAGGATATTCGGCTATTCGGTCAAACGAGAAATCGAAACCCAACACATTAGGGCACGTATTCTC
** * *
2475938 GATTTTCCAAACGCGAAATATTGCCTTATTTGGAAAGTTTAAAAGGATATTTGGCTATTTAGTCG
66 GAAATTACAAACGCGAAATATTGCCTTATTTGGAAAGTTTAAAAGGATATTTGACTATTTAGTCG
* *
2476003 AACGAGAAATCGAAACCCAACACGTTAGGGCACGTTTTCTCGATTTT
131 AACGAGAAATCGAAACCCAACACGCTAGGGCACGTATTCTCGATTTT
2476050 TCGAACTCAA
Statistics
Matches: 160, Mismatches: 15, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
220 3 0.02
221 156 0.98
222 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (221 bp):
AAAGGATATTCGGCTATTCGGTCAAACGAGAAATCGAAACCCAACACATTAGGGCACGTATTCTC
GAAATTACAAACGCGAAATATTGCCTTATTTGGAAAGTTTAAAAGGATATTTGACTATTTAGTCG
AACGAGAAATCGAAACCCAACACGCTAGGGCACGTATTCTCGATTTTCTAAACGCGAATATTGTC
TTATTTTGTCTTATTTGGAAAGTTTA
Found at i:2476046 original size:106 final size:105
Alignment explanation
Indices: 2475539--2476079 Score: 611
Period size: 106 Copynumber: 5.0 Consensus size: 105
2475529 ATCATGGATC
* * * *
2475539 GAAA-TTTAAGAGGATATTTGGCTATTTGGTCGAACGAGAAATTGAAACCCAGCACATTAGGGCA
1 GAAAGTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACGTTAGGGCA
* * * * * *
2475603 TGTTCTCTTGAATTTCCAAACGC-AAGTATTGCCTCACTTT
66 CGTTTTCTCGATTTTCCAAACGCGAAATATTGCCTTA-TTT
* * * * **
2475643 GAAA-TTTCGAAAGGATATTCGGCTATTCGGTCAAACGAGAAATCGAAACCCAGTACGTTAGGGC
1 GAAAGTTT-AAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACGTTAGGGC
* * ** *
2475707 ACGTTCTCTTGAAATTACAAACGCGAAATATTGCCTTACTTT
65 ACGTTTTCTCGATTTTCCAAACGCGAAATATTGCCTTA-TTT
* * *
2475749 GAAAGTTTAAAAGGATATTTGACTATTTGGTCGAACGATAAATCGAAACCCAACACGCTAGGGCA
1 GAAAGTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACGTTAGGGCA
* * *
2475814 CGTATTCTCGATTTTCTAAACGCGAATATTGTCTTATTTTGTCTTATTT
66 CGTTTTCTCGATTTTCCAAACGCGAA-A------TA--TTGCCTTATTT
*
2475863 GGAAAGTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACATTAGGGC
1 -GAAAGTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACGTTAGGGC
*
2475928 ACGTATTCTCGATTTTCCAAACGCGAAATATTGCCTTATTT
65 ACGTTTTCTCGATTTTCCAAACGCGAAATATTGCCTTATTT
*
2475969 GGAAAGTTTAAAAGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAACACGTTAGGGC
1 -GAAAGTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACGTTAGGGC
* * * * *
2476034 ACGTTTTCTCGATTTTTCGAACTCAAAATATTGCTTTATTT
65 ACGTTTTCTCGATTTTCCAAACGCGAAATATTGCCTTATTT
2476075 AGAAA
1 -GAAA
2476080 AATCTTCCTT
Statistics
Matches: 379, Mismatches: 45, Indels: 24
0.85 0.10 0.05
Matches are distributed among these distances:
104 7 0.02
105 69 0.18
106 198 0.52
107 4 0.01
108 2 0.01
113 2 0.01
114 4 0.01
115 93 0.25
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (105 bp):
GAAAGTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACGTTAGGGCA
CGTTTTCTCGATTTTCCAAACGCGAAATATTGCCTTATTT
Found at i:2483485 original size:12 final size:12
Alignment explanation
Indices: 2483464--2483494 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2483454 AAACATAAAA
2483464 TAAT-ATTATAT
1 TAATAATTATAT
2483475 TAATAATTATAT
1 TAATAATTATAT
2483487 TAATAATT
1 TAATAATT
2483495 TACAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.21
12 15 0.79
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAATAATTATAT
Found at i:2483531 original size:29 final size:31
Alignment explanation
Indices: 2483499--2483560 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 31
2483489 ATAATTTACA
*
2483499 AAAATTAAAT-AAATTAAAATTT-TATGTAT
1 AAAATTAAATAAAATTAAAATTTATATATAT
*
2483528 AAAATTACATAAAATTAAAATTTATATATAT
1 AAAATTAAATAAAATTAAAATTTATATATAT
2483559 AA
1 AA
2483561 TTACACATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 9 0.31
30 12 0.41
31 8 0.28
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (31 bp):
AAAATTAAATAAAATTAAAATTTATATATAT
Found at i:2483562 original size:29 final size:29
Alignment explanation
Indices: 2483499--2483565 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
2483489 ATAATTTACA
* *
2483499 AAAATTAAATAAATTAAAATTTTATGTAT
1 AAAATTACATAAATTAAAATTTTATATAT
2483528 AAAATTACATAAAATTAAAA-TTTATATAT
1 AAAATTACAT-AAATTAAAATTTTATATAT
*
2483557 ATAATTACA
1 AAAATTACA
2483566 CATTAAACTA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 25 0.74
30 9 0.26
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (29 bp):
AAAATTACATAAATTAAAATTTTATATAT
Found at i:2486483 original size:331 final size:324
Alignment explanation
Indices: 2485838--2486499 Score: 725
Period size: 329 Copynumber: 2.0 Consensus size: 324
2485828 CCTGATTGTG
*
2485838 ATAAATGCGATAAGCCTTGTGAAGATTTGACTCTTGAATGCTCAAAGTCAGAGTGTAAATATATT
1 ATAAATGCGATAAGCCTTGTGAAGATTTGACTCTTGAATGCTCAAAGTCA-AGTGCAAATATATT
* * *
2485903 GTCCACTGGAATTGTGCAGCACCTAAATTTCTACGGAGTGTGATCTATTGGCCCATGTAGTAATT
65 ATCCACTGGAATTGTGCAGCACCTAAATTTCTACGAAGTGT-ATCTATTGGCCCATGTAGCAATT
* * * * *
2485968 TAGACGTAATCATATTTAAAACCTACCGCTTCATTTATAGGAAAACTCAAGATTGAAGAACAGAG
129 TAGACCTAATCATATTTAAAACCTACCACTTCATTTACAGGAAAACTCAAGACTGAAGAACAAAG
*
2486033 TGTGATCTTTGTCTTGTTACTTGTAATGCTAGTTGTTGTCATAATAATTTGGTTTTTTTAAGTTT
194 TGTGATCATTGTC----T-CTTGTAATGCTAGTTGTTGTCATAATAATTTGGTTTTTTTAAGTTT
* * * * *
2486098 TAACATAATAATTTGAAGCCAAAATTGATGAGATTTACATTGGTGTTTGATTGTTGATTTTAAAA
254 TAACACAATAATCTGAAGCCAAAATTGACGAGATTTACATTGGTGTTCGATTGTTGAATTTAAAA
2486163 TTTCTT
319 TTTCTT
* * **
2486169 ATAAATGCTG-TAAGCCTTGTGAAGATTTGGCTTTTGAATGCTTGAAGTC-AGTGCAAATATATT
1 ATAAATGC-GATAAGCCTTGTGAAGATTTGACTCTTGAATGCTCAAAGTCAAGTGCAAATATATT
* * * * *
2486232 ATTCACTGGAATTGTGTAGCACC-CAGTTCTCTAC-AACGT-T-TCTGGGATTGGTCCATGTAGC
65 ATCCACTGGAATTGTGCAGCACCTAAATT-TCTACGAA-GTGTATCT---ATTGGCCCATGTAGC
* *
2486293 AATTTAGACCTAATCATATTTGAAACCTACCACTAT-ATTTGCAGGAAAACTCAAGACTGAAGAA
125 AATTTAGACCTAATCATATTTAAAACCTACCACT-TCATTTACAGGAAAACTCAAGACTGAAGAA
* *
2486357 CAAAGTTTGATCATTG-C-CTTGTAATGCTAGTTGTTATTGTCATAGT-ATTTGGTTTTTTTGAC
189 CAAAGTGTGATCATTGTCTCTTGTAATGCTAGTTG---TTGTCATAATAATTTGG----TTT---
** * *
2486419 TTTTAAGTTTTAATGCAATAATCTGAAGCCAAAACTT-ACGAGGTTTGCATTGGTGTTCGATTGT
244 TTTTAAGTTTTAACACAATAATCTGAAGCCAAAA-TTGACGAGATTTACATTGGTGTTCGATTGT
*
2486483 TGAATTTAGAATTTCTT
308 TGAATTTAAAATTTCTT
2486500 GTAATTGGTC
Statistics
Matches: 280, Mismatches: 33, Indels: 36
0.80 0.09 0.10
Matches are distributed among these distances:
322 16 0.06
324 6 0.02
325 9 0.03
326 3 0.01
328 9 0.03
329 122 0.44
330 1 0.00
331 111 0.40
332 3 0.01
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.38
Consensus pattern (324 bp):
ATAAATGCGATAAGCCTTGTGAAGATTTGACTCTTGAATGCTCAAAGTCAAGTGCAAATATATTA
TCCACTGGAATTGTGCAGCACCTAAATTTCTACGAAGTGTATCTATTGGCCCATGTAGCAATTTA
GACCTAATCATATTTAAAACCTACCACTTCATTTACAGGAAAACTCAAGACTGAAGAACAAAGTG
TGATCATTGTCTCTTGTAATGCTAGTTGTTGTCATAATAATTTGGTTTTTTTAAGTTTTAACACA
ATAATCTGAAGCCAAAATTGACGAGATTTACATTGGTGTTCGATTGTTGAATTTAAAATTTCTT
Found at i:2494847 original size:16 final size:16
Alignment explanation
Indices: 2494826--2494858 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2494816 AACCATTAAC
2494826 AAAATATACATGTTGG
1 AAAATATACATGTTGG
2494842 AAAATATACATGTTGG
1 AAAATATACATGTTGG
2494858 A
1 A
2494859 TAAAACAAGT
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:0.45, C:0.06, G:0.18, T:0.30
Consensus pattern (16 bp):
AAAATATACATGTTGG
Found at i:2507883 original size:30 final size:30
Alignment explanation
Indices: 2507842--2507981 Score: 114
Period size: 30 Copynumber: 4.8 Consensus size: 30
2507832 AAATTTAGTA
* * *
2507842 TTTTTTTAAATTATATTTTGGCCTCTAAAC
1 TTTTTTAAAATTACATTTTGACCTCTAAAC
2507872 TTTTTTAAAATTACATTTTGACAC-CT-AAC
1 TTTTTTAAAATTACATTTTGAC-CTCTAAAC
*
2507901 TTTCTTAAAATTACATTTTGAACCT-TAAAC
1 TTTTTTAAAATTACATTTTG-ACCTCTAAAC
* * *
2507931 TTTTCT--ATTTACATTTTCACC-CTTAAA-
1 TTTTTTAAAATTACATTTTGACCTC-TAAAC
* *
2507958 TTTTCCTAAAATTATATTTTGACC
1 TTTT-TTAAAATTACATTTTGACC
2507982 CAAAATTTTT
Statistics
Matches: 90, Mismatches: 11, Indels: 18
0.76 0.09 0.15
Matches are distributed among these distances:
27 7 0.08
28 16 0.18
29 24 0.27
30 42 0.47
31 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.04, T:0.49
Consensus pattern (30 bp):
TTTTTTAAAATTACATTTTGACCTCTAAAC
Found at i:2508441 original size:11 final size:11
Alignment explanation
Indices: 2508421--2508470 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
2508411 TAGGGTGAAC
2508421 GAAAGAAAGAA
1 GAAAGAAAGAA
*
2508432 GAAAGGAAGAA
1 GAAAGAAAGAA
*
2508443 AAATAGAAA-AA
1 GAA-AGAAAGAA
2508454 -AAAGAAAGAA
1 GAAAGAAAGAA
*
2508464 AAAAGAA
1 GAAAGAA
2508471 GAAAAAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
9 5 0.15
10 4 0.12
11 20 0.61
12 4 0.12
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (11 bp):
GAAAGAAAGAA
Found at i:2508465 original size:13 final size:13
Alignment explanation
Indices: 2508447--2508486 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
2508437 GAAGAAAAAT
2508447 AGAAAAAAAAGAA
1 AGAAAAAAAAGAA
2508460 AGAAAAAAGAAGAA
1 AGAAAAAA-AAGAA
2508474 A-AAAATAAAAGAA
1 AGAAAA-AAAAGAA
2508487 CAGTCGGGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 17 0.68
14 8 0.32
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (13 bp):
AGAAAAAAAAGAA
Found at i:2517564 original size:75 final size:75
Alignment explanation
Indices: 2517380--2518026 Score: 773
Period size: 77 Copynumber: 8.5 Consensus size: 75
2517370 TTTTGATTTT
* * * *
2517380 TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGTG-CGCACACTGAGGTATTT
1 TTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTT
* *
2517444 TTAATTTATG
66 TCAATTTCTG
* * * * * *
2517454 TTTTTAAAAAAAAATCAACTCATAATCTGATAGGTGAGTTTAGCCTCGGGTCACGCGCTGAGGCA
1 TTTTT---CAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTA
2517519 TTTTCAATTTCTG
63 TTTTCAATTTCTG
* * * * *
2517532 TTCTTCAAAGATCAACTCATAACCCGAGAGGTGGGTTGAGCCTCCGGTCACACGCTGAGGTATTT
1 TTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTT
2517597 TCAA-TT-T-
66 TCAATTTCTG
** * * *
2517604 TTTTTCAAAAATCAACTCATAATTTGAGAGGTGAGTTTGAGCCTCGGGTCGCACGCCGAGGTGTT
1 TTTTTCAAAAATCAACTCATAATCCGAGAGGTGAG-TTGAGCCTCGGGTCACACGCTGAGGTATT
2517669 TTCAATTTCTG
65 TTCAATTTCTG
* *
2517680 TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACAGGCTGAGGTATTT
1 TTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTA-TT
*
2517745 TTCAATTTCTAT
65 TTCAATTTCT-G
* * *
2517757 TTTTTCAAAAATCAACTCATAATACGAGAAGTGAGTTGAGCCTCGGGTCACACGTTGAGGTATCT
1 TTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTAT-T
2517822 TTCAATTTCTG
65 TTCAATTTCTG
* * **** *
2517833 TTTTTTCAAAAATCAACTCATAGTGCGAGAGGTGAGTTGAGCCTTATTTCA-AGCGCCGAGGTAT
1 -TTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCACA-CGCTGAGGTA-
*
2517897 TTTTCAATTTCTATT
63 TTTTCAATTTC--TG
* *
2517912 TTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCACGCGCTGAGGCATTT
1 TTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTT
*
2517977 TCAATTTCTA
66 TCAATTTCTG
* * *
2517987 TTTTTCAAAGATCAACTCATAATTCGAGAGGTGAGCTGAG
1 TTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAG
2518027 ATCCAGGTCG
Statistics
Matches: 488, Mismatches: 68, Indels: 33
0.83 0.12 0.06
Matches are distributed among these distances:
72 29 0.06
73 31 0.06
74 9 0.02
75 116 0.24
76 47 0.10
77 177 0.36
78 78 0.16
79 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.33
Consensus pattern (75 bp):
TTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTT
TCAATTTCTG
Found at i:2518275 original size:30 final size:30
Alignment explanation
Indices: 2518185--2518326 Score: 130
Period size: 29 Copynumber: 4.8 Consensus size: 30
2518175 AAATTTTATA
*
2518185 TTTTTTAAAATTACATCTTGAACCC-TAAAC
1 TTTTTTAAAATTACATTTTG-ACCCTTAAAC
* *
2518215 TTTTTTAAAATTACATTTT-AACCTTTAAC
1 TTTTTTAAAATTACATTTTGACCCTTAAAC
**
2518244 TTTTTTAAAATTAGTTTTTGACCCTTAAAC
1 TTTTTTAAAATTACATTTTGACCCTTAAAC
* ** * *
2518274 TTTTCTT--ATTTACATTTTGGGCCTTTAAT
1 TTTT-TTAAAATTACATTTTGACCCTTAAAC
*
2518303 TTTTTCTAAAATTACACTTTGACC
1 TTTTT-TAAAATTACATTTTGACC
2518327 GTAGAAGTTT
Statistics
Matches: 88, Mismatches: 18, Indels: 11
0.75 0.15 0.09
Matches are distributed among these distances:
28 4 0.05
29 41 0.47
30 30 0.34
31 13 0.15
ACGTcount: A:0.30, C:0.16, G:0.05, T:0.49
Consensus pattern (30 bp):
TTTTTTAAAATTACATTTTGACCCTTAAAC
Found at i:2518277 original size:59 final size:59
Alignment explanation
Indices: 2518185--2518318 Score: 148
Period size: 59 Copynumber: 2.3 Consensus size: 59
2518175 AAATTTTATA
2518185 TTTTTTAAAATTACATCTTGAACCCTAAACTTTT-TTAAAATTACATTTT-AACCTTTAAC
1 TTTTTTAAAATTACATCTTGAACCCTAAACTTTTCTT--AATTACATTTTGAACCTTTAAC
** * * ** *
2518244 TTTTTTAAAATTAGTTTTTG-ACCCTTAAACTTTTCTTATTTACATTTTGGGCCTTTAAT
1 TTTTTTAAAATTACATCTTGAACCC-TAAACTTTTCTTAATTACATTTTGAACCTTTAAC
2518303 TTTTTCTAAAATTACA
1 TTTTT-TAAAATTACA
2518319 CTTTGACCGT
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
58 14 0.23
59 38 0.61
60 10 0.16
ACGTcount: A:0.31, C:0.15, G:0.04, T:0.50
Consensus pattern (59 bp):
TTTTTTAAAATTACATCTTGAACCCTAAACTTTTCTTAATTACATTTTGAACCTTTAAC
Found at i:2518497 original size:13 final size:13
Alignment explanation
Indices: 2518479--2518526 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
2518469 ACAATAAAAG
2518479 CAAAAAAATCAAC
1 CAAAAAAATCAAC
* * *
2518492 CAAAAAGGAGCAGC
1 CAAAAA-AATCAAC
*
2518506 CAAAAAAATCAAG
1 CAAAAAAATCAAC
2518519 CAAAAAAA
1 CAAAAAAA
2518527 GGAAAAGTAA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
13 17 0.63
14 10 0.37
ACGTcount: A:0.67, C:0.19, G:0.10, T:0.04
Consensus pattern (13 bp):
CAAAAAAATCAAC
Found at i:2518869 original size:15 final size:15
Alignment explanation
Indices: 2518819--2518863 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
2518809 GGGCTAAGGT
* *
2518819 GAAAGAAAGAAAGAA
1 GAAAAAAAGAAAAAA
**
2518834 GAAATGAAGAAAAAA
1 GAAAAAAAGAAAAAA
2518849 GAAAAAAAGAAAAAA
1 GAAAAAAAGAAAAAA
2518864 ATAAAAGAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (15 bp):
GAAAAAAAGAAAAAA
Found at i:2528880 original size:18 final size:19
Alignment explanation
Indices: 2528857--2528894 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
2528847 GGAAGCAAGC
*
2528857 AATGATTGAAGA-AATCAG
1 AATGATTGAAAAGAATCAG
2528875 AATGATTGAAAAGAATCAG
1 AATGATTGAAAAGAATCAG
2528894 A
1 A
2528895 CCTGGAGTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.21
Consensus pattern (19 bp):
AATGATTGAAAAGAATCAG
Found at i:2532132 original size:50 final size:50
Alignment explanation
Indices: 2532076--2532174 Score: 162
Period size: 50 Copynumber: 2.0 Consensus size: 50
2532066 CACTATGGTT
*
2532076 AATTAAATTGACCAAATTGATCACTCCACCATTAAATTCACTATTTCATC
1 AATTAAATTGACCAAATCGATCACTCCACCATTAAATTCACTATTTCATC
* * *
2532126 AATTAAATTGATCAAATCGATCCCTCCTCCATTAAATTCACTATTTCAT
1 AATTAAATTGACCAAATCGATCACTCCACCATTAAATTCACTATTTCAT
2532175 TGTTAAATTC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.35
Consensus pattern (50 bp):
AATTAAATTGACCAAATCGATCACTCCACCATTAAATTCACTATTTCATC
Found at i:2541514 original size:50 final size:50
Alignment explanation
Indices: 2541458--2541557 Score: 166
Period size: 50 Copynumber: 2.0 Consensus size: 50
2541448 CACTATGGTT
* *
2541458 AATTAAATTGATCAAATTGATCAT-TCCACCATTACATTCACTATTTCATC
1 AATTAAATTGATCAAATCGATC-TCTCCACCATTAAATTCACTATTTCATC
2541508 AATTAAATTGATCAAATCGATCTCTCCACCATTAAATTCACTATTTCATC
1 AATTAAATTGATCAAATCGATCTCTCCACCATTAAATTCACTATTTCATC
2541558 GTTAAATCCA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
49 1 0.02
50 46 0.98
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.37
Consensus pattern (50 bp):
AATTAAATTGATCAAATCGATCTCTCCACCATTAAATTCACTATTTCATC
Found at i:2544043 original size:14 final size:14
Alignment explanation
Indices: 2544026--2544062 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2544016 AGGTATGAGG
**
2544026 ATGTATATATGTAT
1 ATGTATATATAAAT
2544040 ATGTATATATAAAT
1 ATGTATATATAAAT
2544054 ATGTATATA
1 ATGTATATA
2544063 ATGCTCGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (14 bp):
ATGTATATATAAAT
Found at i:2544451 original size:75 final size:75
Alignment explanation
Indices: 2544314--2544454 Score: 169
Period size: 75 Copynumber: 1.9 Consensus size: 75
2544304 ACTTACATAT
* * * * * *
2544314 ATGTATATATTCTTTTATTGAATTTAGGAAGGACATTTATATAAGTTTATATGAGATTCGATTAT
1 ATGTATATATTCTTGTAATGAATTTAAGAAGGAAATTTATATAAGTGTATATGAGATCCGATTAT
2544379 GCAGGTATAC
66 GCAGGTATAC
* * *
2544389 ATGTATATGTTCTTGTAATGAATTTAAGTATGAAATTTATAT-A-TGTATATGGAAGATCCGATT
1 ATGTATATATTCTTGTAATGAATTTAAGAAGGAAATTTATATAAGTGTATAT-G-AGATCCGATT
2544452 ATG
64 ATG
2544455 TATATATATT
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
73 6 0.11
74 2 0.04
75 47 0.85
ACGTcount: A:0.34, C:0.06, G:0.18, T:0.43
Consensus pattern (75 bp):
ATGTATATATTCTTGTAATGAATTTAAGAAGGAAATTTATATAAGTGTATATGAGATCCGATTAT
GCAGGTATAC
Found at i:2544598 original size:41 final size:41
Alignment explanation
Indices: 2544553--2544645 Score: 105
Period size: 41 Copynumber: 2.3 Consensus size: 41
2544543 GTACTTTACA
* * * * * * *
2544553 TCTAGCAGGTTTGATGCTGGTGAAATATTTCAGACTTTATG
1 TCTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATAAG
* *
2544594 TCTAGTAGGCTTAATGCCGGTGAAACAATTCGGACTATAAG
1 TCTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATAAG
2544635 TCTAGCAGGCT
1 TCTAGCAGGCT
2544646 AAAAGCCAGT
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (41 bp):
TCTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATAAG
Found at i:2544847 original size:71 final size:68
Alignment explanation
Indices: 2544780--2544980 Score: 216
Period size: 63 Copynumber: 2.9 Consensus size: 68
2544770 TGTATATCCT
* * *
2544780 TTCGGTGATAATACTTGTTAGGCATATGTATATATGCATTCAGCTATTCAAGTTTAAAGTGTATA
1 TTCGGTGATAATATTTGTTA-GCATATGTATATA-GCATTCGGCTATTCATGTTTAAAGTGTATA
2544845 TAT-A
64 TATCA
* *
2544849 TTCGGTGATAATATTTGTT---ATGTGTATA-AGCATTCGGTTATTCATGTTTAAAGTGTATATA
1 TTCGGTGATAATATTTGTTAGCATATGTATATAGCATTCGGCTATTCATGTTTAAAGTGTATATA
2544910 -CA
66 TCA
* * * *
2544912 TTCGATGATAATATTTTTTAAGCATATATGTATATACACATTCGGCTATTCATGTTTTAAACTGT
1 TTCGGTGATAATATTTGTT-AGC--ATATGTATATA-GCATTCGGCTATTCATG-TTTAAAGTGT
2544977 ATAT
61 ATAT
2544981 GCATTTGGTT
Statistics
Matches: 111, Mismatches: 11, Indels: 17
0.80 0.08 0.12
Matches are distributed among these distances:
63 47 0.42
64 1 0.01
65 8 0.07
69 26 0.23
70 1 0.01
71 15 0.14
72 13 0.12
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (68 bp):
TTCGGTGATAATATTTGTTAGCATATGTATATAGCATTCGGCTATTCATGTTTAAAGTGTATATA
TCA
Found at i:2544914 original size:31 final size:31
Alignment explanation
Indices: 2544810--2544915 Score: 83
Period size: 31 Copynumber: 3.4 Consensus size: 31
2544800 GGCATATGTA
* * * *
2544810 TATATGCATTCAGCTATTCAAGTTTAAAGTG
1 TATATACATTCGGTTATTCATGTTTAAAGTG
* * * *
2544841 TATATATATTCGGTGATAAT-AT-TTGTTATGTG
1 TATATACATTCGGT--TATTCATGTT-TAAAGTG
2544873 TATA-AGCATTCGGTTATTCATGTTTAAAGTG
1 TATATA-CATTCGGTTATTCATGTTTAAAGTG
2544904 TATATACATTCG
1 TATATACATTCG
2544916 ATGATAATAT
Statistics
Matches: 56, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
30 3 0.05
31 30 0.54
32 20 0.36
33 3 0.05
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.43
Consensus pattern (31 bp):
TATATACATTCGGTTATTCATGTTTAAAGTG
Found at i:2547079 original size:64 final size:67
Alignment explanation
Indices: 2547002--2547140 Score: 167
Period size: 73 Copynumber: 2.0 Consensus size: 67
2546992 TTATTGTACA
* * *
2547002 TAAACAACGGTGATGA-G-T-AATTATTAAGTATTAAATTTAACTCATAATATAGTCTTCTTTTT
1 TAAACAACAGTGATGACGATAAATTATTAAGTACTAAATTTAACTCATAATATAATCTTCTTTTT
2547064 TC
66 TC
*
2547066 TAAACAACAGTGATGACGAATTATTAGAATTATTAGGTACTAAATTTAACTCATAATATAATCTT
1 TAAACAACAGTGATGACG----A-TA-AATTATTAAGTACTAAATTTAACTCATAATATAATCTT
2547131 CTTTTTTC
60 CTTTTTTC
2547139 TA
1 TA
2547141 TCAATGAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
64 15 0.24
65 1 0.02
71 1 0.02
73 45 0.73
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (67 bp):
TAAACAACAGTGATGACGATAAATTATTAAGTACTAAATTTAACTCATAATATAATCTTCTTTTT
TC
Found at i:2550845 original size:26 final size:27
Alignment explanation
Indices: 2550816--2550873 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
2550806 AATATTAAAC
*
2550816 TATTTTTATAATTT-TATTATATATTA
1 TATTTTTAAAATTTGTATTATATATTA
* *
2550842 TATTTTTAAAATTTGTATTTTCTATTA
1 TATTTTTAAAATTTGTATTATATATTA
2550869 T-TTTT
1 TATTTT
2550874 AATGGTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 17 0.61
27 11 0.39
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (27 bp):
TATTTTTAAAATTTGTATTATATATTA
Found at i:2553986 original size:9 final size:9
Alignment explanation
Indices: 2553968--2554041 Score: 61
Period size: 9 Copynumber: 8.6 Consensus size: 9
2553958 ATTAGATTTT
*
2553968 TATATTTTA
1 TATATATTA
2553977 TATATATTA
1 TATATATTA
*
2553986 T-TTTATTA
1 TATATATTA
2553994 TATA-A-TA
1 TATATATTA
2554001 TAATATATTA
1 T-ATATATTA
2554011 TAT-TAATTA
1 TATAT-ATTA
2554020 TAT-TAATTA
1 TATAT-ATTA
2554029 TAT-TATTA
1 TATATATTA
2554037 TATAT
1 TATAT
2554042 TAAATAAACC
Statistics
Matches: 56, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
7 3 0.05
8 19 0.34
9 31 0.55
10 3 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
TATATATTA
Found at i:2554013 original size:5 final size:5
Alignment explanation
Indices: 2553967--2554043 Score: 65
Period size: 5 Copynumber: 15.6 Consensus size: 5
2553957 TATTAGATTT
* *
2553967 TTATA TTTTA TATATA TTAT- TT-TA TTATA TAATATA ATATA TTATA
1 TTATA TTATA T-TATA TTATA TTATA TTATA T--TATA TTATA TTATA
2554013 TTA-A TTATA TTA-A TTATA TTAT- TATATA TTA
1 TTATA TTATA TTATA TTATA TTATA T-TATA TTA
2554044 AATAAACCAA
Statistics
Matches: 59, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
3 1 0.02
4 13 0.22
5 36 0.61
6 5 0.08
7 4 0.07
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TTATA
Found at i:2554273 original size:22 final size:22
Alignment explanation
Indices: 2554234--2554281 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
2554224 AAACAAAAGA
2554234 AAAAGAAACAAAAGAAGA-ACAG
1 AAAAGAAACAAAAGAAGAGAC-G
*
2554256 AAAAGAAAC-AGAGAAAGAGACG
1 AAAAGAAACAAAAG-AAGAGACG
2554278 AAAA
1 AAAA
2554282 CAGGGGAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 3 0.13
22 18 0.78
23 2 0.09
ACGTcount: A:0.71, C:0.08, G:0.21, T:0.00
Consensus pattern (22 bp):
AAAAGAAACAAAAGAAGAGACG
Found at i:2554298 original size:18 final size:18
Alignment explanation
Indices: 2554249--2554299 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
2554239 AAACAAAAGA
2554249 AGAACAGAAAAG-AAACAG
1 AGAA-AGAAAAGAAAACAG
* *
2554267 AGAAAGAGACGAAAACAG
1 AGAAAGAAAAGAAAACAG
* *
2554285 GGGAAGAAAAGAAAA
1 AGAAAGAAAAGAAAA
2554300 GGGGAAAATT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
17 5 0.19
18 21 0.81
ACGTcount: A:0.65, C:0.08, G:0.27, T:0.00
Consensus pattern (18 bp):
AGAAAGAAAAGAAAACAG
Found at i:2554654 original size:22 final size:24
Alignment explanation
Indices: 2554628--2554671 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
2554618 TATAGCATGA
2554628 AATTAAG-TAGAAAAG-AAGTATG
1 AATTAAGTTAGAAAAGTAAGTATG
2554650 AATTAAGTTAGAAAAGTAAGTA
1 AATTAAGTTAGAAAAGTAAGTA
2554672 AGCTTAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 8 0.40
24 5 0.25
ACGTcount: A:0.55, C:0.00, G:0.20, T:0.25
Consensus pattern (24 bp):
AATTAAGTTAGAAAAGTAAGTATG
Found at i:2557568 original size:5 final size:5
Alignment explanation
Indices: 2557558--2557636 Score: 67
Period size: 5 Copynumber: 15.6 Consensus size: 5
2557548 AAAAAAATAT
* *
2557558 TATTA TATTA TAGTAA TGATTA TGTT- T-TTA TATTA TATTA TTATTA
1 TATTA TATTA TA-TTA T-ATTA TATTA TATTA TATTA TATTA -TATTA
2557604 -A-TA TATTA TATTA TATTA TATATA TATATA TAT
1 TATTA TATTA TATTA TATTA TAT-TA TAT-TA TAT
2557637 AGCAAAAGAA
Statistics
Matches: 63, Mismatches: 3, Indels: 15
0.78 0.04 0.19
Matches are distributed among these distances:
3 4 0.06
4 4 0.06
5 32 0.51
6 22 0.35
7 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (5 bp):
TATTA
Found at i:2557610 original size:19 final size:19
Alignment explanation
Indices: 2557586--2557634 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 19
2557576 ATTATGTTTT
2557586 TATATTATATTATTATTA-A
1 TATATTATATTA-TATTATA
2557605 TATATTATATTATATTATA
1 TATATTATATTATATTATA
2557624 TATATATATAT
1 TATAT-TATAT
2557635 ATAGCAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.18
19 18 0.64
20 5 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:2559035 original size:25 final size:24
Alignment explanation
Indices: 2558968--2559099 Score: 180
Period size: 25 Copynumber: 5.5 Consensus size: 24
2558958 ACTTTAGCGC
2558968 GCTCTCTGATATTAGCACGTTGGT
1 GCTCTCTGATATTAGCACGTTGGT
2558992 GCTCTCTGATATTAGCACGTTGGT
1 GCTCTCTGATATTAGCACGTTGGT
2559016 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTGA-TATTAGCACGTTGGT
***
2559041 GCTCTCTGATATTTAGCACGGCAGT
1 GCTCTCTGATA-TTAGCACGTTGGT
* *
2559066 GCTCTCTG-T-TTAGCACATTTGT
1 GCTCTCTGATATTAGCACGTTGGT
2559088 GCTCTCTG-TATT
1 GCTCTCTGATATT
2559100 TGTTCCGTAT
Statistics
Matches: 98, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
22 18 0.18
23 2 0.02
24 36 0.37
25 42 0.43
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.39
Consensus pattern (24 bp):
GCTCTCTGATATTAGCACGTTGGT
Found at i:2559035 original size:49 final size:48
Alignment explanation
Indices: 2558968--2559099 Score: 180
Period size: 49 Copynumber: 2.8 Consensus size: 48
2558958 ACTTTAGCGC
***
2558968 GCTCTCTGATATTAGCACGTTGGTGCTCTCTGATATTAGCACGTTGGT
1 GCTCTCTGATATTAGCACGTTGGTGCTCTCTGATATTAGCACGGCAGT
2559016 GCTCTCTGATTATTAGCACGTTGGTGCTCTCTGATATTTAGCACGGCAGT
1 GCTCTCTGA-TATTAGCACGTTGGTGCTCTCTGATA-TTAGCACGGCAGT
* *
2559066 GCTCTCTG-T-TTAGCACATTTGTGCTCTCTG-TATT
1 GCTCTCTGATATTAGCACGTTGGTGCTCTCTGATATT
2559100 TGTTCCGTAT
Statistics
Matches: 77, Mismatches: 5, Indels: 7
0.87 0.06 0.08
Matches are distributed among these distances:
45 2 0.03
46 2 0.03
47 19 0.25
48 10 0.13
49 26 0.34
50 18 0.23
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.39
Consensus pattern (48 bp):
GCTCTCTGATATTAGCACGTTGGTGCTCTCTGATATTAGCACGGCAGT
Found at i:2559931 original size:17 final size:17
Alignment explanation
Indices: 2559909--2559942 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2559899 ATGTGGCATG
*
2559909 TACCTAGGTAATGTATA
1 TACCTAAGTAATGTATA
*
2559926 TACCTAAGTGATGTATA
1 TACCTAAGTAATGTATA
2559943 GGGATTAGTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (17 bp):
TACCTAAGTAATGTATA
Found at i:2566286 original size:22 final size:20
Alignment explanation
Indices: 2566236--2566287 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 20
2566226 GAGAGCTTTC
*
2566236 AATCAAAAAAAAGTAAAAAG
1 AATCAAAAAAAAGAAAAAAG
2566256 AAGTCCAAAAAAACAGAAAAAAG
1 AA-T-CAAAAAAA-AGAAAAAAG
2566279 TAATCAAAA
1 -AATCAAAA
2566288 CTCAAAAGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 2 0.07
21 1 0.04
22 13 0.48
23 9 0.33
24 2 0.07
ACGTcount: A:0.71, C:0.10, G:0.10, T:0.10
Consensus pattern (20 bp):
AATCAAAAAAAAGAAAAAAG
Found at i:2581631 original size:18 final size:18
Alignment explanation
Indices: 2581604--2581696 Score: 132
Period size: 18 Copynumber: 5.2 Consensus size: 18
2581594 TACGATTGTT
2581604 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
* *
2581622 TACGGCACTATTCATGTA
1 TACGGTACTATTCACGTA
*
2581640 TACAGTACTATTCACGTA
1 TACGGTACTATTCACGTA
* *
2581658 TATGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
2581676 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
2581694 TAC
1 TAC
2581697 AGTAGTTGGG
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 64 1.00
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:2587500 original size:15 final size:16
Alignment explanation
Indices: 2587474--2587504 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2587464 GGGTCACGGG
2587474 TCAGGTGCCAAAACGA
1 TCAGGTGCCAAAACGA
2587490 TCAGG-GCCAAAACGA
1 TCAGGTGCCAAAACGA
2587505 CGTCGTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.39, C:0.26, G:0.26, T:0.10
Consensus pattern (16 bp):
TCAGGTGCCAAAACGA
Found at i:2592696 original size:28 final size:28
Alignment explanation
Indices: 2592636--2592689 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
2592626 CAGTAACAGT
* * * *
2592636 ACAGTGTGGGCCTTAGCCCTATACAAAA
1 ACAGTGTAGGCCTAAGCCCGACACAAAA
2592664 ACAGTGTAGGCCTAAGCCCGACACAA
1 ACAGTGTAGGCCTAAGCCCGACACAA
2592690 TATCAGTATG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.33, C:0.28, G:0.22, T:0.17
Consensus pattern (28 bp):
ACAGTGTAGGCCTAAGCCCGACACAAAA
Found at i:2592857 original size:26 final size:26
Alignment explanation
Indices: 2592805--2592857 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
2592795 CACTAATATC
* *
2592805 GCAGCATAGCTGCCAGTAGTAATAAT
1 GCAGCAGAGCTGCCAGTAGTAAGAAT
*
2592831 GCAGCAGAGCTGCCAGTAGTCAGAAT
1 GCAGCAGAGCTGCCAGTAGTAAGAAT
2592857 G
1 G
2592858 GCTAAAAGCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.32, C:0.21, G:0.28, T:0.19
Consensus pattern (26 bp):
GCAGCAGAGCTGCCAGTAGTAAGAAT
Found at i:2593002 original size:32 final size:32
Alignment explanation
Indices: 2592901--2593055 Score: 139
Period size: 32 Copynumber: 4.8 Consensus size: 32
2592891 TAAACAGAAT
* * * *
2592901 GGTAATATGATTGGCACAAAGCCATCAGTAGC
1 GGTAATATGATCGACACAAAGCCATCAATAAC
* ** ** * ** *
2592933 AGTGTTATGATCGGTACACAGTAATCAGTAAC
1 GGTAATATGATCGACACAAAGCCATCAATAAC
* ** *
2592965 TGTAATATGATCGACACAAAGCCATCGGTAAT
1 GGTAATATGATCGACACAAAGCCATCAATAAC
2592997 GGTAATATGATCGACACAAAGCCATCAATAAC
1 GGTAATATGATCGACACAAAGCCATCAATAAC
* *
2593029 GGTAATATGATTGGCACAAAGCCATCA
1 GGTAATATGATCGACACAAAGCCATCA
2593056 GTAGTATCAC
Statistics
Matches: 98, Mismatches: 25, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 98 1.00
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (32 bp):
GGTAATATGATCGACACAAAGCCATCAATAAC
Found at i:2593006 original size:64 final size:64
Alignment explanation
Indices: 2592901--2593058 Score: 181
Period size: 64 Copynumber: 2.5 Consensus size: 64
2592891 TAAACAGAAT
* ** ** * * *
2592901 GGTAATATGATTGGCACAAAGCCATCAGTAGCAGTGTTATGATCGGTACACAGTAATCAGTAAC
1 GGTAATATGATTGGCACAAAGCCATCAGTAACAGTAATATGATCGACACAAAGCAATCAATAAC
* * * * ** *
2592965 TGTAATATGATCGACACAAAGCCATCGGTAATGGTAATATGATCGACACAAAGCCATCAATAAC
1 GGTAATATGATTGGCACAAAGCCATCAGTAACAGTAATATGATCGACACAAAGCAATCAATAAC
2593029 GGTAATATGATTGGCACAAAGCCATCAGTA
1 GGTAATATGATTGGCACAAAGCCATCAGTA
2593059 GTATCACAGT
Statistics
Matches: 75, Mismatches: 19, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
64 75 1.00
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.23
Consensus pattern (64 bp):
GGTAATATGATTGGCACAAAGCCATCAGTAACAGTAATATGATCGACACAAAGCAATCAATAAC
Found at i:2593105 original size:27 final size:25
Alignment explanation
Indices: 2593070--2593140 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 25
2593060 TATCACAGTA
*
2593070 AAGCTACCAGTAATAGTATATGTGGCC
1 AAGCCACCAGTAATAGTAT-TGTGG-C
2593097 AAGCCACCAGTAATAGTGATTGTGGC
1 AAGCCACCAGTAATAGT-ATTGTGGC
*
2593123 AGAGCCACCAAT-ATAGTA
1 A-AGCCACCAGTAATAGTA
2593141 CTTCCTCCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
25 1 0.03
26 7 0.17
27 30 0.75
28 2 0.05
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.23
Consensus pattern (25 bp):
AAGCCACCAGTAATAGTATTGTGGC
Found at i:2593275 original size:24 final size:24
Alignment explanation
Indices: 2593220--2593286 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
2593210 TCATACCAAA
*
2593220 CACAGACAAAGCAATCATTTACAT
1 CACAGACAAATCAATCATTTACAT
**
2593244 CA-AGGACAAATCAATCATTTATGT
1 CACA-GACAAATCAATCATTTACAT
* *
2593268 CACAGACAATTCAAACATT
1 CACAGACAAATCAATCATT
2593287 AACCTCGAGG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 1 0.03
24 34 0.94
25 1 0.03
ACGTcount: A:0.45, C:0.22, G:0.09, T:0.24
Consensus pattern (24 bp):
CACAGACAAATCAATCATTTACAT
Found at i:2593499 original size:27 final size:27
Alignment explanation
Indices: 2593433--2593638 Score: 150
Period size: 27 Copynumber: 7.7 Consensus size: 27
2593423 CCTAACAGAA
* * *
2593433 GTATTACAGTCATTTTACCCTATA-GA
1 GTATTACGGTCATTTTACCCTACAGGG
* * *
2593459 GCATTATGGTCATTTTATCCTACAGGG
1 GTATTACGGTCATTTTACCCTACAGGG
* *
2593486 GTATTACGGTCATTTTACCCTATAAGG
1 GTATTACGGTCATTTTACCCTACAGGG
* * **
2593513 GTATTATGGTTATTTTACCCTATGGGG
1 GTATTACGGTCATTTTACCCTACAGGG
* * * **
2593540 GTA-TATCGATCAATTCA-CCTAACTA-AA
1 GTATTA-CGGTCATTTTACCCT-AC-AGGG
* * *
2593567 GTATTACGGACATTTCACTCTACAGGG
1 GTATTACGGTCATTTTACCCTACAGGG
*
2593594 GCATTACGGTCATTTTACCCTACAGGG
1 GTATTACGGTCATTTTACCCTACAGGG
* *
2593621 ATATTATGGTCATTTTAC
1 GTATTACGGTCATTTTAC
2593639 AAACATTAGG
Statistics
Matches: 136, Mismatches: 37, Indels: 13
0.73 0.20 0.07
Matches are distributed among these distances:
26 25 0.18
27 107 0.79
28 4 0.03
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (27 bp):
GTATTACGGTCATTTTACCCTACAGGG
Found at i:2593543 original size:54 final size:54
Alignment explanation
Indices: 2593433--2593638 Score: 188
Period size: 54 Copynumber: 3.8 Consensus size: 54
2593423 CCTAACAGAA
* * *
2593433 GTATTACAGTCATTTTACCCTAT-AGAGCATTATGGTCATTTTATCCTACAGGG
1 GTATTACGGTCATTTTACCCTATAAGAGTATTATGGTCATTTTACCCTACAGGG
* * **
2593486 GTATTACGGTCATTTTACCCTATAAGGGTATTATGGTTATTTTACCCTATGGGG
1 GTATTACGGTCATTTTACCCTATAAGAGTATTATGGTCATTTTACCCTACAGGG
* * * * * * *
2593540 GTA-TATCGATCAATTCA-CCTAACTAA-AGTATTACGGACATTTCACTCTACAGGG
1 GTATTA-CGGTCATTTTACCCT-A-TAAGAGTATTATGGTCATTTTACCCTACAGGG
* * *
2593594 GCATTACGGTCATTTTACCCTA-CAGGGATATTATGGTCATTTTAC
1 GTATTACGGTCATTTTACCCTATAAGAG-TATTATGGTCATTTTAC
2593639 AAACATTAGG
Statistics
Matches: 118, Mismatches: 27, Indels: 15
0.74 0.17 0.09
Matches are distributed among these distances:
52 1 0.01
53 28 0.24
54 81 0.69
55 8 0.07
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (54 bp):
GTATTACGGTCATTTTACCCTATAAGAGTATTATGGTCATTTTACCCTACAGGG
Found at i:2619641 original size:28 final size:27
Alignment explanation
Indices: 2619576--2619641 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 27
2619566 TTTGACAGTA
* *
2619576 ACAGTACAGTGTAGGCCTTAGCCCTAT
1 ACAGTACAGTGTAGGCCTAAGCCCGAT
**
2619603 ACAAAAACAGTGTAGGCCTAAGCCCGAT
1 AC-AGTACAGTGTAGGCCTAAGCCCGAT
2619631 ACAGTATCAGT
1 ACAGTA-CAGT
2619642 ATGCTGCAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
27 4 0.13
28 27 0.87
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.21
Consensus pattern (27 bp):
ACAGTACAGTGTAGGCCTAAGCCCGAT
Found at i:2619850 original size:22 final size:22
Alignment explanation
Indices: 2619796--2619860 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
2619786 TACCATTAAT
2619796 CAGAATGGCTAAAAG-TCATAAA
1 CAGAATGGCTAAAAGCT-ATAAA
* *
2619818 CA-AGATAGCTATAAGCTATAAA
1 CAGA-ATGGCTAAAAGCTATAAA
* *
2619840 CAGAATGGCTACAAGCCATAA
1 CAGAATGGCTAAAAGCTATAA
2619861 GTACATTAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
21 1 0.03
22 32 0.91
23 2 0.06
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (22 bp):
CAGAATGGCTAAAAGCTATAAA
Found at i:2619990 original size:32 final size:32
Alignment explanation
Indices: 2619852--2619990 Score: 145
Period size: 32 Copynumber: 4.4 Consensus size: 32
2619842 GAATGGCTAC
* *
2619852 AAGCCATAAGT-ACATTAATATGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATTGGCACA
* * * * *
2619883 AAACCATCAGTAGCAGTGATATAATTGGCATA
1 AAGCCATCAGTAACAGTAATATGATTGGCACA
* * ** * *
2619915 CAGCCATCAATAATGGTAATATGATCGACACA
1 AAGCCATCAGTAACAGTAATATGATTGGCACA
2619947 AAGCCATCAGTAACAGTAATATGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATTGGCACA
*
2619979 AAGCCAACAGTA
1 AAGCCATCAGTA
2619991 GCATTGCAGG
Statistics
Matches: 82, Mismatches: 25, Indels: 1
0.76 0.23 0.01
Matches are distributed among these distances:
31 9 0.11
32 73 0.89
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATTGGCACA
Found at i:2620368 original size:27 final size:27
Alignment explanation
Indices: 2620313--2620518 Score: 173
Period size: 27 Copynumber: 7.6 Consensus size: 27
2620303 TAGCAAAGGC
* ** *
2620313 ATTACGGTCACTTTATGCTACAGGAGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
2620340 ATTACGATCATTTTACCCTATAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
** * * **
2620367 A-TATCAATCAATTCA-CCTACCAGAAGT
1 ATTA-CGGTCATTTTACCCTA-CAGGGGT
*
2620394 ATTACAGTCATTTTACCCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
2620421 ATTATGGTCATTTTACCCTATAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * **
2620448 ATTACGGTTATTTCACCCTACAATGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* **
2620475 ATTACGGTTATTTTACCCTACATGGGAC
1 ATTACGGTCATTTTACCCTACA-GGGGT
2620503 ATTACGGTCATTTTAC
1 ATTACGGTCATTTTAC
2620519 AAACATTGGG
Statistics
Matches: 142, Mismatches: 32, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
26 6 0.04
27 114 0.80
28 22 0.15
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.35
Consensus pattern (27 bp):
ATTACGGTCATTTTACCCTACAGGGGT
Found at i:2620415 original size:81 final size:81
Alignment explanation
Indices: 2620266--2620449 Score: 219
Period size: 81 Copynumber: 2.3 Consensus size: 81
2620256 GCCAAAATAG
* *** * * **
2620266 TCATTTTACCCT-TTGAGGGTATATTGGTCAATTCACCTAGCAAAGGCATTACGGTCACTTTATG
1 TCATTTTACCCTATAG-GGGTATATCAATCAATTCACCTACCAAAGGCATTACAGTCACTTTACC
2620330 CTACAGGAGTATTACGA
65 CTACAGGAGTATTACGA
* *
2620347 TCATTTTACCCTATAGGGGTATATCAATCAATTCACCTACCAGAA-GTATTACAGTCATTTTACC
1 TCATTTTACCCTATAGGGGTATATCAATCAATTCACCTACCA-AAGGCATTACAGTCACTTTACC
* * *
2620411 CTACAGGGGTATTATGG
65 CTACAGGAGTATTACGA
2620428 TCATTTTACCCTATAGGGGTAT
1 TCATTTTACCCTATAGGGGTAT
2620450 TACGGTTATT
Statistics
Matches: 88, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
81 84 0.95
82 4 0.05
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (81 bp):
TCATTTTACCCTATAGGGGTATATCAATCAATTCACCTACCAAAGGCATTACAGTCACTTTACCC
TACAGGAGTATTACGA
Found at i:2620463 original size:81 final size:81
Alignment explanation
Indices: 2620265--2620518 Score: 214
Period size: 81 Copynumber: 3.1 Consensus size: 81
2620255 GGCCAAAATA
* *** * * *
2620265 GTCATTTTACCCT-TTGAGGGTATATTGGTCAATTCA-CCTAGCAA-AGGCATTACGGTCACTTT
1 GTCATTTTACCCTATAG-GGGTATATCAATCAATTCACCCTA-CAATA-GTATTACAGTCATTTT
** *
2620327 ATGCTACAGGAGTATTACG
63 ACCCTACAGGGGTATTACG
*
2620346 ATCATTTTACCCTATAGGGGTATATCAATCAATTCA-CCTACCAGA-AGTATTACAGTCATTTTA
1 GTCATTTTACCCTATAGGGGTATATCAATCAATTCACCCTA-CA-ATAGTATTACAGTCATTTTA
*
2620409 CCCTACAGGGGTATTATG
64 CCCTACAGGGGTATTACG
** * * * * *
2620427 GTCATTTTACCCTATAGGGGTAT-TACGGTTATTTCACCCTACAATGGTATTACGGTTATTTTAC
1 GTCATTTTACCCTATAGGGGTATAT-CAATCAATTCACCCTACAATAGTATTACAGTCATTTTAC
**
2620491 CCTACATGGGACATTACG
65 CCTACA-GGGGTATTACG
2620509 GTCATTTTAC
1 GTCATTTTAC
2620519 AAACATTGGG
Statistics
Matches: 143, Mismatches: 24, Indels: 11
0.80 0.13 0.06
Matches are distributed among these distances:
80 2 0.01
81 115 0.80
82 26 0.18
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (81 bp):
GTCATTTTACCCTATAGGGGTATATCAATCAATTCACCCTACAATAGTATTACAGTCATTTTACC
CTACAGGGGTATTACG
Found at i:2622136 original size:45 final size:45
Alignment explanation
Indices: 2622072--2622161 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
2622062 ATAAAGTCCT
2622072 CCAAATCCTTATCCCATGAATCACTCCCCCAAGACCAATTCCACA
1 CCAAATCCTTATCCCATGAATCACTCCCCCAAGACCAATTCCACA
2622117 CCAAATCCTTATCCCATGAATCACTCCCCCAAGACCAATTCCACA
1 CCAAATCCTTATCCCATGAATCACTCCCCCAAGACCAATTCCACA
2622162 ACCACCTGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.33, C:0.42, G:0.04, T:0.20
Consensus pattern (45 bp):
CCAAATCCTTATCCCATGAATCACTCCCCCAAGACCAATTCCACA
Found at i:2630380 original size:5 final size:5
Alignment explanation
Indices: 2630365--2630424 Score: 68
Period size: 5 Copynumber: 12.2 Consensus size: 5
2630355 AATATTGAAA
* * * * *
2630365 AATA- AATAT GATAT GATAT GATAT GATAT GATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
2630414 AATAT AATAT A
1 AATAT AATAT A
2630425 TATTCATTTA
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
4 4 0.08
5 49 0.92
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:2630383 original size:10 final size:10
Alignment explanation
Indices: 2630369--2630427 Score: 75
Period size: 10 Copynumber: 6.0 Consensus size: 10
2630359 TTGAAAAATA
2630369 AATATGATAT
1 AATATGATAT
*
2630379 GATATGATAT
1 AATATGATAT
*
2630389 GATATGATAT
1 AATATGATAT
*
2630399 AATATAATAT
1 AATATGATAT
*
2630409 AATATAATAT
1 AATATGATAT
2630419 AATAT-ATAT
1 AATATGATAT
2630428 TCATTTAATC
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
9 4 0.09
10 42 0.91
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (10 bp):
AATATGATAT
Found at i:2630390 original size:15 final size:15
Alignment explanation
Indices: 2630369--2630427 Score: 75
Period size: 15 Copynumber: 4.0 Consensus size: 15
2630359 TTGAAAAATA
*
2630369 AATATGATATGATAT
1 AATATAATATGATAT
* *
2630384 GATATGATATGATAT
1 AATATAATATGATAT
*
2630399 AATATAATATAATAT
1 AATATAATATGATAT
2630414 AATATAATAT-ATAT
1 AATATAATATGATAT
2630428 TCATTTAATC
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
14 4 0.10
15 36 0.90
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (15 bp):
AATATAATATGATAT
Found at i:2632587 original size:66 final size:65
Alignment explanation
Indices: 2632505--2632636 Score: 237
Period size: 66 Copynumber: 2.0 Consensus size: 65
2632495 CTTTTATGGA
* *
2632505 TCTTGCAAGAAAGAGTAACGCAATACACCACCGTTATAGTCAATTTTAGACCATTAAATATAGTA
1 TCTTGCAAGAAAGAGTAACGCAATACACCACCATTACAGTCAATTTTAGACCA-TAAATATAGTA
2632570 T
65 T
2632571 TCTTGCAAGAAAGAGTAACGCAATACACCACCATTACAGTCAATTTTAGACCATAAATATAGTAT
1 TCTTGCAAGAAAGAGTAACGCAATACACCACCATTACAGTCAATTTTAGACCATAAATATAGTAT
2632636 T
1 T
2632637 TCTATTTATG
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
65 13 0.20
66 51 0.80
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (65 bp):
TCTTGCAAGAAAGAGTAACGCAATACACCACCATTACAGTCAATTTTAGACCATAAATATAGTAT
Found at i:2635970 original size:42 final size:42
Alignment explanation
Indices: 2635924--2636124 Score: 280
Period size: 42 Copynumber: 4.8 Consensus size: 42
2635914 TTTTGTGTAT
* * *
2635924 GTGAAATAATTTCAGACTTTACGTCGAGCAGGCTTATTGCCA
1 GTGAAACAATTTCAGACTTTACGTCTAGCAGGCTTAATGCCA
* *
2635966 GTGAAACAATATCAGACTTTACGTCTAGCAGACTTAATGCCA
1 GTGAAACAATTTCAGACTTTACGTCTAGCAGGCTTAATGCCA
* * *
2636008 GTGAAATAATTTCAGACTTTACGTTTAGCAGGCTTAATGCCG
1 GTGAAACAATTTCAGACTTTACGTCTAGCAGGCTTAATGCCA
*
2636050 GTGAAACAATATT-AGACTTTACGTCTAGCAGGCTTAATGCCG
1 GTGAAACAAT-TTCAGACTTTACGTCTAGCAGGCTTAATGCCA
* *
2636092 GTGAAAC-ATTTCAGACTATATGTCTAGCAGGCT
1 GTGAAACAATTTCAGACTTTACGTCTAGCAGGCT
2636125 AAGTGTCGGT
Statistics
Matches: 143, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
40 2 0.01
41 21 0.15
42 118 0.83
43 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (42 bp):
GTGAAACAATTTCAGACTTTACGTCTAGCAGGCTTAATGCCA
Found at i:2637379 original size:143 final size:143
Alignment explanation
Indices: 2637201--2637826 Score: 957
Period size: 143 Copynumber: 4.4 Consensus size: 143
2637191 TGTTACACTA
2637201 GTGGCTTCAATCTGCTCCACTGCAACTTTAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAAT
1 GTGGCTTCAATCTGCTCCACTGCAACTTTAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAAT
* * *
2637266 GTGTTCCACTGCAACGCCAGGGAAATAAAATTCGCTGTCTTCAGTCTACTCCGCTGCAACTTCAA
66 CTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCAA
2637331 GGAGATAAGGCTG
131 GGAGATAAGGCTG
* * * *
2637344 GTGGCTTCAATCTGCTCCAGTGCAACTTCAGGAAGATAAGATCCACCATAATTTGTAGCTTTATT
1 GTGGCTTCAATCTGCTCCACTGCAACTTTAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAAT
* * * ** *
2637409 TTGTTCCACTGCAACGCCAGAGAAATAAGATTCGTTGTCTTCAGTCTGCTCCGCTATAACTTCAG
66 CTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCAA
2637474 GGAGATAAGGCTG
131 GGAGATAAGGCTG
* * **
2637487 GTGGCTTCAATCTACTCTACTGCAACTTTAGGAAGATAAGATTTGCCATAATTTGTAGCTTTAAT
1 GTGGCTTCAATCTGCTCCACTGCAACTTTAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAAT
* ** *
2637552 CTGTTCCACTACAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCAACTGCAACTTCAG
66 CTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCAA
*
2637617 GGAAATAAGGCTG
131 GGAGATAAGGCTG
* * * *
2637630 GTGGCTTCAATCTGCTCCACTACAACTTTAGGAAGATAAGATCCACCATAATTGGTAGCTTTGAT
1 GTGGCTTCAATCTGCTCCACTGCAACTTTAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAAT
* * *
2637695 CTGCTCCACTGCAACGCCAAGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTTAA
66 CTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCAA
*
2637760 GGAGATAAGGCTA
131 GGAGATAAGGCTG
*
2637773 GTGGCTTCAATCTGCTCCACTGCAACTTCA-GAATGATAAGATCCGCCATAATTT
1 GTGGCTTCAATCTGCTCCACTGCAACTTTAGGAA-GATAAGATCCGCCATAATTT
2637827 CTTCAATCAA
Statistics
Matches: 432, Mismatches: 50, Indels: 2
0.89 0.10 0.00
Matches are distributed among these distances:
142 3 0.01
143 429 0.99
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (143 bp):
GTGGCTTCAATCTGCTCCACTGCAACTTTAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAAT
CTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCAA
GGAGATAAGGCTG
Found at i:2637762 original size:45 final size:44
Alignment explanation
Indices: 2637693--2637802 Score: 121
Period size: 45 Copynumber: 2.5 Consensus size: 44
2637683 GGTAGCTTTG
** * * *
2637693 ATCTGCTCCACTGCAACGCCAAGGAAATAAGATTCGCTGTCTTCA
1 ATCTGCTCCACTGCAACTTCAAGGAAATAAGACTAG-TGGCTTCA
* * * * *
2637738 GTCTGCTCCGCTGCAACTTTAAGGAGATAAGGCTAGTGGCTTCA
1 ATCTGCTCCACTGCAACTTCAAGGAAATAAGACTAGTGGCTTCA
2637782 ATCTGCTCCACTGCAACTTCA
1 ATCTGCTCCACTGCAACTTCA
2637803 GAATGATAAG
Statistics
Matches: 52, Mismatches: 13, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
44 25 0.48
45 27 0.52
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.26
Consensus pattern (44 bp):
ATCTGCTCCACTGCAACTTCAAGGAAATAAGACTAGTGGCTTCA
Found at i:2641458 original size:5 final size:6
Alignment explanation
Indices: 2641442--2641510 Score: 77
Period size: 6 Copynumber: 11.0 Consensus size: 6
2641432 TTGGTCTCTC
*
2641442 CTTTTT CTTTTT CTTTTT CTTTTT C-TTTT CTTTTTCT CCTTTTT ATTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT C-TTTT-T -CTTTTT CTTTTT
*
2641492 CTTTTTT GTTTTT CTTTTT
1 C-TTTTT CTTTTT CTTTTT
2641511 TGTTTTTTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
5 5 0.09
6 34 0.63
7 9 0.17
8 5 0.09
9 1 0.02
ACGTcount: A:0.01, C:0.16, G:0.01, T:0.81
Consensus pattern (6 bp):
CTTTTT
Found at i:2641465 original size:13 final size:13
Alignment explanation
Indices: 2641443--2641522 Score: 87
Period size: 13 Copynumber: 6.3 Consensus size: 13
2641433 TGGTCTCTCC
2641443 TTTTTCTTTTTC-
1 TTTTTCTTTTTCT
2641455 TTTTTCTTTTTC-
1 TTTTTCTTTTTCT
2641467 -TTTTCTTTTTCT
1 TTTTTCTTTTTCT
*
2641479 CCTTTTTATTTTTCT
1 --TTTTTCTTTTTCT
*
2641494 TTTTTGTTTTTCT
1 TTTTTCTTTTTCT
*
2641507 TTTTTGTTTTT-T
1 TTTTTCTTTTTCT
2641519 TTTT
1 TTTT
2641523 AAAAGTGGAG
Statistics
Matches: 62, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
11 11 0.18
12 17 0.27
13 23 0.37
15 11 0.18
ACGTcount: A:0.01, C:0.12, G:0.03, T:0.84
Consensus pattern (13 bp):
TTTTTCTTTTTCT
Done.