Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr10
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: 57797951
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1092422 characters in sequence are not A, C, G, or T
File 20 of 187
Found at i:5618440 original size:40 final size:38
Alignment explanation
Indices: 5618396--5618499 Score: 120
Period size: 40 Copynumber: 2.7 Consensus size: 38
5618386 TGAATATAAT
*
5618396 AATTATAATTACCATAATTATAACAATGTTTGA-CCAAAAA
1 AATTATAATTACAATAATTATAACAATGTTTGATCC---AA
* * * *
5618436 AATTATAATTATAGTAATTATAATAATGTTTGATCCTA
1 AATTATAATTACAATAATTATAACAATGTTTGATCCAA
*
5618474 AATTATAGTTACAATAATTATAACAA
1 AATTATAATTACAATAATTATAACAA
5618500 GGATTTCGGT
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
38 23 0.43
40 29 0.54
41 2 0.04
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.38
Consensus pattern (38 bp):
AATTATAATTACAATAATTATAACAATGTTTGATCCAA
Found at i:5632761 original size:51 final size:50
Alignment explanation
Indices: 5632685--5632875 Score: 192
Period size: 51 Copynumber: 3.8 Consensus size: 50
5632675 ATGTTTGGTT
* *
5632685 CACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATTCGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCA-TACCATTCGGTA
* * * *
5632736 CACATAGT-GTCCTGCACATAGTACTACATACGTGATCGAAACTA-TCTGGTA
1 CACATAGTAG-CCTGCACATAGTACTACACACGTGA-CCATACCATTC-GGTA
* * * *
5632787 CGA-ATAGTACCCTGCACATAGTACTACACATGCGACC-TATCATTCCGGTA
1 C-ACATAGTAGCCTGCACATAGTACTACACACGTGACCATACCATT-CGGTA
* *
5632837 CACGTAGTAGCCTGTACATAGTACTACACACGTGACCAT
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCAT
5632876 CACTTTCACT
Statistics
Matches: 112, Mismatches: 19, Indels: 18
0.75 0.13 0.12
Matches are distributed among these distances:
49 3 0.03
50 39 0.35
51 67 0.60
52 3 0.03
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.25
Consensus pattern (50 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCATACCATTCGGTA
Found at i:5632895 original size:101 final size:99
Alignment explanation
Indices: 5632686--5632871 Score: 241
Period size: 101 Copynumber: 1.8 Consensus size: 99
5632676 TGTTTGGTTC
* *
5632686 ACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATTCGATACACATAGTGTCCTGC
1 ACATAGTACCCTGCACATAGTACTACACATGCGACCA-TACCATTCGATACACATAGTGTCCTGC
* *
5632751 ACATAGTACTACATACGTGATCGAAACTATCTGGT
65 ACATAGTACTACACACGTGATCCAAACTATCTGGT
* * *
5632786 ACGAATAGTACCCTGCACATAGTACTACACATGCGACC-TATCATTCCGGTACACGTAGTAG-CC
1 AC--ATAGTACCCTGCACATAGTACTACACATGCGACCATACCATT-CGATACACATAGT-GTCC
*
5632849 TGTACATAGTACTACACACGTGA
62 TGCACATAGTACTACACACGTGA
5632872 CCATCACTTT
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
100 8 0.11
101 34 0.45
102 33 0.44
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (99 bp):
ACATAGTACCCTGCACATAGTACTACACATGCGACCATACCATTCGATACACATAGTGTCCTGCA
CATAGTACTACACACGTGATCCAAACTATCTGGT
Found at i:5640431 original size:41 final size:41
Alignment explanation
Indices: 5640373--5640484 Score: 143
Period size: 41 Copynumber: 2.7 Consensus size: 41
5640363 GTGATAATCG
* * ** *
5640373 AGCTTTCAGCCTAGCAGGCTTTATGCCGGTGAATTATTTCA
1 AGCTTTAAGCCTAGCAGGCTTAATGCCGGTGAACCATATCA
* * *
5640414 GGCTTTACGCCTAGCAGGCTTAATGCCGGTGTACCATATCA
1 AGCTTTAAGCCTAGCAGGCTTAATGCCGGTGAACCATATCA
*
5640455 AGCTTTAAGCCTAGCAGGCTTCATGCCGGT
1 AGCTTTAAGCCTAGCAGGCTTAATGCCGGT
5640485 TTATCATGTT
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.29
Consensus pattern (41 bp):
AGCTTTAAGCCTAGCAGGCTTAATGCCGGTGAACCATATCA
Found at i:5653046 original size:50 final size:50
Alignment explanation
Indices: 5652952--5653081 Score: 154
Period size: 50 Copynumber: 2.6 Consensus size: 50
5652942 TTGACATTAT
* * *
5652952 GAGAGGTCCCACGTAAGGCCATGTCTGGGACATGGCGTTGGCACCGAGAA
1 GAGAGGTCCCACGTAAGACCATGTCTGGGACATGACGATGGCACCGAGAA
* * *
5653002 GAGAGGTCCCCCGTAAGACCATGTCTGGGACATGAC-ATGCGCACCGATAT
1 GAGAGGTCCCACGTAAGACCATGTCTGGGACATGACGATG-GCACCGAGAA
** * *
5653052 GAGAACTCCCATGTAAGACCATATCTGGGA
1 GAGAGGTCCCACGTAAGACCATGTCTGGGA
5653082 TATGGCATTG
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
49 2 0.03
50 66 0.97
ACGTcount: A:0.27, C:0.25, G:0.30, T:0.18
Consensus pattern (50 bp):
GAGAGGTCCCACGTAAGACCATGTCTGGGACATGACGATGGCACCGAGAA
Found at i:5661206 original size:24 final size:24
Alignment explanation
Indices: 5661172--5661288 Score: 126
Period size: 24 Copynumber: 4.9 Consensus size: 24
5661162 AGCTGCATCG
*
5661172 TTGTGGTCAAGCCACTCAATAACA
1 TTGTGGGCAAGCCACTCAATAACA
* * * *
5661196 TTGTGGGCAAGACACTTAATAGCG
1 TTGTGGGCAAGCCACTCAATAACA
* * * *
5661220 TTGTGGGCAAGACACTTAATAGCG
1 TTGTGGGCAAGCCACTCAATAACA
* *
5661244 TTGTGGCCAAGCCACTCAATAATA
1 TTGTGGGCAAGCCACTCAATAACA
*
5661268 TTGTGGTCAAGCCACTCAATA
1 TTGTGGGCAAGCCACTCAATA
5661289 TTGCAATAAC
Statistics
Matches: 81, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 81 1.00
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (24 bp):
TTGTGGGCAAGCCACTCAATAACA
Found at i:5661444 original size:42 final size:42
Alignment explanation
Indices: 5661379--5661492 Score: 156
Period size: 42 Copynumber: 2.7 Consensus size: 42
5661369 TGTCAGTAGG
** * * *
5661379 CATGCTTAACATGTGAATCAAATCTAAGTTCAACATAGTCGA
1 CATGCTTAACATGCAAATAAAATCTCAGTTCAACATAGTCAA
* * *
5661421 CATGCTTAACATGCAAATTAAATCTCAGTTTATCATAGTCAA
1 CATGCTTAACATGCAAATAAAATCTCAGTTCAACATAGTCAA
5661463 CATGCTTAACATGCAAATAAAATCTCAGTT
1 CATGCTTAACATGCAAATAAAATCTCAGTT
5661493 AATAAATCAA
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (42 bp):
CATGCTTAACATGCAAATAAAATCTCAGTTCAACATAGTCAA
Found at i:5663890 original size:23 final size:23
Alignment explanation
Indices: 5663864--5663939 Score: 107
Period size: 23 Copynumber: 3.3 Consensus size: 23
5663854 ATAAGTGCCA
* *
5663864 CACTGATATGTAGCCGAAGTTAC
1 CACTGATATGTAGCTGAAGCTAC
*
5663887 CACTGATATGTAGCTGTAGCTAC
1 CACTGATATGTAGCTGAAGCTAC
* *
5663910 AACTGAAATGTAGCTGAAGCTAC
1 CACTGATATGTAGCTGAAGCTAC
5663933 CACTGAT
1 CACTGAT
5663940 CAATAACACT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (23 bp):
CACTGATATGTAGCTGAAGCTAC
Found at i:5667465 original size:32 final size:32
Alignment explanation
Indices: 5667402--5667542 Score: 160
Period size: 32 Copynumber: 4.5 Consensus size: 32
5667392 CAGAATGGAT
* * *
5667402 ACAAA-CCATAAGT-ACAGTAATATGATTGGC
1 ACAAAGCCATCAGTAACAGTAATATGATCGAC
* * * *
5667432 ACACAGCCATCAGTAGCAGTGATATGATCGGC
1 ACAAAGCCATCAGTAACAGTAATATGATCGAC
* *
5667464 ACACAGCCATCAGTAACGGTAATATGATCGAC
1 ACAAAGCCATCAGTAACAGTAATATGATCGAC
*
5667496 ACAAAGCCATCAGTAACGGTAATATGATCGAC
1 ACAAAGCCATCAGTAACAGTAATATGATCGAC
* *
5667528 ACAAATCTATCAGTA
1 ACAAAGCCATCAGTA
5667543 GCATCGCAGC
Statistics
Matches: 97, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
30 4 0.04
31 7 0.07
32 86 0.89
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (32 bp):
ACAAAGCCATCAGTAACAGTAATATGATCGAC
Found at i:5667616 original size:27 final size:27
Alignment explanation
Indices: 5667586--5667649 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
5667576 AGCAAAGCTG
*
5667586 CCAGTAATAGT-ATATGTGGCCA-AGCCA
1 CCAGTAACAGTGAT-TGTGG-CAGAGCCA
5667613 CCAGTAACAGTGATTGTGGCAGAGCCA
1 CCAGTAACAGTGATTGTGGCAGAGCCA
5667640 CCAGT-ACAGT
1 CCAGTAACAGT
5667650 ACTTCCTCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
26 7 0.21
27 25 0.74
28 2 0.06
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.20
Consensus pattern (27 bp):
CCAGTAACAGTGATTGTGGCAGAGCCA
Found at i:5667746 original size:24 final size:24
Alignment explanation
Indices: 5667714--5667771 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
5667704 CCATGCTTAG
5667714 AATCAGTCATACAAATCACAGACA
1 AATCAGTCATACAAATCACAGACA
** * *
5667738 AATCAGTCATTTACATCACGGACA
1 AATCAGTCATACAAATCACAGACA
*
5667762 AATCAATCAT
1 AATCAGTCAT
5667772 TTACACTTGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.45, C:0.24, G:0.09, T:0.22
Consensus pattern (24 bp):
AATCAGTCATACAAATCACAGACA
Found at i:5667772 original size:24 final size:24
Alignment explanation
Indices: 5667728--5667776 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
5667718 AGTCATACAA
*
5667728 ATCACAGACAAATCAGTCATTTAC
1 ATCACAGACAAATCAATCATTTAC
*
5667752 ATCACGGACAAATCAATCATTTAC
1 ATCACAGACAAATCAATCATTTAC
5667776 A
1 A
5667777 CTTGAGGGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.43, C:0.24, G:0.08, T:0.24
Consensus pattern (24 bp):
ATCACAGACAAATCAATCATTTAC
Found at i:5667849 original size:27 final size:27
Alignment explanation
Indices: 5667822--5668074 Score: 269
Period size: 27 Copynumber: 9.4 Consensus size: 27
5667812 CGTTACGGTT
* *
5667822 ATTTTACCTTATAGGGGTATTTCAGTT
1 ATTTTACCCTATAGGGGTATTTCAGTC
* * *
5667849 ATTTAACCCTATAGGGGTATTACAGTT
1 ATTTTACCCTATAGGGGTATTTCAGTC
* * *
5667876 ATTTTACTCTATGGGGGTATTTTAGTC
1 ATTTTACCCTATAGGGGTATTTCAGTC
* * *
5667903 ATTTTACCGTATAAGGGTATTTCGGTC
1 ATTTTACCCTATAGGGGTATTTCAGTC
* **
5667930 ATTTTACCCTATAAGGGTATTTTGGTC
1 ATTTTACCCTATAGGGGTATTTCAGTC
*
5667957 ATTCTACCCTATAGGGGTATTTCAGTC
1 ATTTTACCCTATAGGGGTATTTCAGTC
* * *
5667984 ATTTTACCTTATGGGGGTATTTCGGTC
1 ATTTTACCCTATAGGGGTATTTCAGTC
*
5668011 ATTTTACCCTAT-GAGGGTATTTCGGTC
1 ATTTTACCCTATAG-GGGTATTTCAGTC
* *
5668038 ATTTTACTCT-TCAGGGGTAATTT-GGTC
1 ATTTTACCCTAT-AGGGGT-ATTTCAGTC
5668065 ATTTTACCCT
1 ATTTTACCCT
5668075 TCGAGGGTAA
Statistics
Matches: 194, Mismatches: 28, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
26 2 0.01
27 187 0.96
28 5 0.03
ACGTcount: A:0.21, C:0.16, G:0.20, T:0.43
Consensus pattern (27 bp):
ATTTTACCCTATAGGGGTATTTCAGTC
Found at i:5667939 original size:81 final size:81
Alignment explanation
Indices: 5667822--5668167 Score: 324
Period size: 81 Copynumber: 4.3 Consensus size: 81
5667812 CGTTACGGTT
* * * * * *
5667822 ATTTTACCTTATAGGGGTATTTCAGTTATTTAACCCTATAGGGGTATTACAGTTATTTTACTCTA
1 ATTTTACCTTATAGGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCGGTCATTTTACTCTA
*
5667887 TGGGGGTATTTTAGTC
66 TAGGGGTATTTTAGTC
* * * * * *
5667903 ATTTTACCGTATAAGGGTATTTCGGTCATTTTACCCTATAAGGGTATTTTGGTCATTCTACCCTA
1 ATTTTACCTTATAGGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCGGTCATTTTACTCTA
*
5667968 TAGGGGTATTTCAGTC
66 TAGGGGTATTTTAGTC
*
5667984 ATTTTACCTTATGGGGGTATTTCGGTCATTTTACCCTAT-GAGGGTATTTCGGTCATTTTACTCT
1 ATTTTACCTTATAGGGGTATTTCGGTCATTTTACCCTATAG-GGGTATTTCGGTCATTTTACTCT
* *
5668048 -TCAGGGGTAATTTGGTC
65 AT-AGGGGTATTTTAGTC
* * * * * * * * * *
5668065 ATTTTACCCT-TCGAGGGTAATTCGATTATTTTAACCT-TCGGGGGTAATTCGATCATTTTACCC
1 ATTTTACCTTATAG-GGGTATTTCGGTCATTTTACCCTAT-AGGGGTATTTCGGTCATTTTACTC
* * *
5668128 T-TCGGGGGTAATTTAATC
64 TAT-AGGGGTATTTTAGTC
* *
5668146 ATTTTACCTTTTGGGGGTATTT
1 ATTTTACCTTATAGGGGTATTT
5668168 AGATAATTTT
Statistics
Matches: 220, Mismatches: 39, Indels: 12
0.81 0.14 0.04
Matches are distributed among these distances:
80 4 0.02
81 213 0.97
82 3 0.01
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.43
Consensus pattern (81 bp):
ATTTTACCTTATAGGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCGGTCATTTTACTCTA
TAGGGGTATTTTAGTC
Found at i:5668076 original size:27 final size:26
Alignment explanation
Indices: 5667889--5668153 Score: 173
Period size: 27 Copynumber: 9.8 Consensus size: 26
5667879 TTACTCTATG
* * *
5667889 GGGGTATTTTAGTCATTTTACCGTATA
1 GGGGTAATTTGGTCATTTTACCCT-TA
*
5667916 AGGGT-ATTTCGGTCATTTTACCCTATA
1 GGGGTAATTT-GGTCATTTTACCCT-TA
* * *
5667943 AGGGTATTTTGGTCATTCTACCCTATA
1 GGGGTAATTTGGTCATTTTACCCT-TA
*
5667970 GGGGT-ATTTCAGTCATTTTA-CCTTA
1 GGGGTAATTT-GGTCATTTTACCCTTA
5667995 TGGGGGT-ATTTCGGTCATTTTACCC-TA
1 --GGGGTAATTT-GGTCATTTTACCCTTA
*
5668022 TGAGGGT-ATTTCGGTCATTTTACTCTTCA
1 -G-GGGTAATTT-GGTCATTTTACCCTT-A
*
5668051 GGGGTAATTTGGTCATTTTACCCTTC
1 GGGGTAATTTGGTCATTTTACCCTTA
* * * * *
5668077 GAGGGTAATTCGATTATTTTAACCTTCG
1 G-GGGTAATTTGGTCATTTTACCCTT-A
* * *
5668105 GGGGTAATTCGATCATTTTACCCTTCG
1 GGGGTAATTTGGTCATTTTACCCTT-A
**
5668132 GGGGTAATTTAATCATTTTACC
1 GGGGTAATTTGGTCATTTTACC
5668154 TTTTGGGGGT
Statistics
Matches: 202, Mismatches: 24, Indels: 24
0.81 0.10 0.10
Matches are distributed among these distances:
25 2 0.01
26 11 0.05
27 176 0.87
28 12 0.06
29 1 0.00
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.42
Consensus pattern (26 bp):
GGGGTAATTTGGTCATTTTACCCTTA
Found at i:5668081 original size:54 final size:53
Alignment explanation
Indices: 5667889--5668307 Score: 268
Period size: 54 Copynumber: 7.8 Consensus size: 53
5667879 TTACTCTATG
* * * * *
5667889 GGGGTATTTTAGTCATTTTACCGTAT-AAGGGTATTTCGGTCATTTTACCCTAT-A
1 GGGGTAATTTGGTCATTTTACCCT-TCGAGGGTATTTCGATCATTTTA-CCT-TCA
* * * *
5667943 AGGGTATTTTGGTCATTCTACCCTATAG-GGGTATTTC-AGTCATTTTACCTT-A
1 GGGGTAATTTGGTCATTTTACCCT-TCGAGGGTATTTCGA-TCATTTTACCTTCA
*
5667995 TGGGGGT-ATTTCGGTCATTTTACCCTAT-GAGGGTATTTCGGTCATTTTACTCTTCA
1 --GGGGTAATTT-GGTCATTTTACCCT-TCGAGGGTATTTCGATCATTTTAC-CTTCA
* * *
5668051 GGGGTAATTTGGTCATTTTACCCTTCGAGGGTAATTCGATTATTTTAACCTTCG
1 GGGGTAATTTGGTCATTTTACCCTTCGAGGGTATTTCGATCATTTT-ACCTTCA
* * * * **
5668105 GGGGTAATTCGATCATTTTACCCTTCGGGGGTAATTT-AATCATTTTACCTTTTG
1 GGGGTAATTTGGTCATTTTACCCTTCGAGGGT-ATTTCGATCATTTTACC-TTCA
* * * * * *
5668159 GGGGT-ATTTAGATAATTTTATCCTTCGGGGGTTTTTCGATAATTTTACCTTTC-
1 GGGGTAATTT-GGTCATTTTACCCTTCGAGGGTATTTCGATCATTTTACC-TTCA
* * * ** *
5668212 GAGGGT-ATTTCGGTAATTTTTCTCTTTAAGGGTATTTCGATCATTTCACCGTTC-
1 G-GGGTAATTT-GGTCATTTTACCCTTCGAGGGTATTTCGATCATTTTACC-TTCA
* * * *
5668266 GAGGGTATTTTGGTCATTTTACCTTTTGGGGGTATTTCGATC
1 G-GGGTAATTTGGTCATTTTACCCTTCGAGGGTATTTCGATC
5668308 CAGATATCGA
Statistics
Matches: 300, Mismatches: 47, Indels: 36
0.78 0.12 0.09
Matches are distributed among these distances:
52 2 0.01
53 18 0.06
54 264 0.88
55 15 0.05
56 1 0.00
ACGTcount: A:0.19, C:0.16, G:0.22, T:0.43
Consensus pattern (53 bp):
GGGGTAATTTGGTCATTTTACCCTTCGAGGGTATTTCGATCATTTTACCTTCA
Found at i:5668161 original size:27 final size:27
Alignment explanation
Indices: 5667982--5668307 Score: 183
Period size: 27 Copynumber: 12.1 Consensus size: 27
5667972 GGTATTTCAG
*
5667982 TCATTTTACCTTAT-GGGGGT-ATTTCGG
1 TCATTTTACCTT-TCGGGGGTAATTT-GA
* * *
5668009 TCATTTTACCCTAT-GAGGGT-ATTTCGG
1 TCATTTTA-CCTTTCGGGGGTAATTT-GA
* *
5668036 TCATTTTA-CTCTTCAGGGGTAATTTGG
1 TCATTTTACCT-TTCGGGGGTAATTTGA
* * *
5668063 TCATTTTACCCTTCGAGGGTAATTCGA
1 TCATTTTACCTTTCGGGGGTAATTTGA
* *
5668090 TTATTTTAACC-TTCGGGGGTAATTCGA
1 TCATTTT-ACCTTTCGGGGGTAATTTGA
* *
5668117 TCATTTTACCCTTCGGGGGTAATTTAA
1 TCATTTTACCTTTCGGGGGTAATTTGA
*
5668144 TCATTTTACCTTTTGGGGGT-ATTTAGA
1 TCATTTTACCTTTCGGGGGTAATTT-GA
* *
5668171 TAATTTTATCC-TTCGGGGGT-TTTTCGA
1 TCATTTTA-CCTTTCGGGGGTAATTT-GA
* * *
5668198 TAATTTTACCTTTCGAGGGT-ATTTCGG
1 TCATTTTACCTTTCGGGGGTAATTT-GA
* * **
5668225 TAATTTTTCTCTTT-AAGGGT-ATTTCGA
1 TCATTTTAC-CTTTCGGGGGTAATTT-GA
* * * * *
5668252 TCATTTCACCGTTCGAGGGTATTTTGG
1 TCATTTTACCTTTCGGGGGTAATTTGA
*
5668279 TCATTTTACCTTTTGGGGGT-ATTTCGA
1 TCATTTTACCTTTCGGGGGTAATTT-GA
5668306 TC
1 TC
5668308 CAGATATCGA
Statistics
Matches: 244, Mismatches: 41, Indels: 28
0.78 0.13 0.09
Matches are distributed among these distances:
25 2 0.01
26 16 0.07
27 206 0.84
28 20 0.08
ACGTcount: A:0.18, C:0.16, G:0.21, T:0.44
Consensus pattern (27 bp):
TCATTTTACCTTTCGGGGGTAATTTGA
Found at i:5668299 original size:81 final size:79
Alignment explanation
Indices: 5667888--5668304 Score: 308
Period size: 81 Copynumber: 5.2 Consensus size: 79
5667878 TTTACTCTAT
** * * * *
5667888 GGGGGTATTTTAGTCATTTTACCGTATAAGGGTATTTCGGTCATTTTACCCTAT-AAGGGTATTT
1 GGGGGTATTTCGGTCATTTTACC-TTTGAGGGTATTTCGATCATTTTA-CCT-TCGAGGGTATTT
* *
5667952 TGGTCATTCTACCCTAT-
63 TGGTCATTTTA-CCTTTC
* * * *
5667969 AGGGGTATTTCAGTCATTTTACCTTATGGGGGTATTTCGGTCATTTTACCCTAT-GAGGGTATTT
1 GGGGGTATTTCGGTCATTTTACCTT-TGAGGGTATTTCGATCATTTTA-CCT-TCGAGGGTATTT
*
5668033 CGGTCATTTTA-CTCTTC
63 TGGTCATTTTACCT-TTC
* * * * * *
5668050 AGGGGTAATTT-GGTCATTTTACCCTTCGAGGGTAATTCGATTATTTTAACCTTCGGGGGTAATT
1 GGGGGT-ATTTCGGTCATTTTA-CCTTTGAGGGTATTTCGATCATTTT-ACCTTCGAGGGTATTT
* * *
5668114 CGATCATTTTACCCTTC
63 TGGTCATTTTACCTTTC
** * * * *
5668131 GGGGGTAATTT-AATCATTTTACCTTTTGGGGGTATTTAGATAATTTTATCCTTCGGGGGT-TTT
1 GGGGGT-ATTTCGGTCATTTTACC-TTTGAGGGTATTTCGATCATTTTA-CCTTCGAGGGTATTT
* *
5668194 TCGATAATTTTACCTTTC
63 T-GGTCATTTTACCTTTC
* * * * *
5668212 GAGGGTATTTCGGTAATTTTTCTCTTTAAGGGTATTTCGATCATTTCACCGTTCGAGGGTATTTT
1 GGGGGTATTTCGGTCATTTTAC-CTTTGAGGGTATTTCGATCATTTTACC-TTCGAGGGTATTTT
*
5668277 GGTCATTTTACCTTTT
64 GGTCATTTTACCTTTC
5668293 GGGGGTATTTCG
1 GGGGGTATTTCG
5668305 ATCCAGATAT
Statistics
Matches: 275, Mismatches: 46, Indels: 30
0.78 0.13 0.09
Matches are distributed among these distances:
79 2 0.01
80 14 0.05
81 244 0.89
82 15 0.05
ACGTcount: A:0.19, C:0.16, G:0.22, T:0.43
Consensus pattern (79 bp):
GGGGGTATTTCGGTCATTTTACCTTTGAGGGTATTTCGATCATTTTACCTTCGAGGGTATTTTGG
TCATTTTACCTTTC
Found at i:5670571 original size:25 final size:25
Alignment explanation
Indices: 5670527--5670574 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
5670517 ATTGCACAAG
5670527 TATAAGATCAAAATATATATATAGA
1 TATAAGATCAAAATATATATATAGA
*
5670552 TATAATATACAAAATA-ATATATA
1 TATAAGAT-CAAAATATATATATA
5670575 CTTAACCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.33
Consensus pattern (25 bp):
TATAAGATCAAAATATATATATAGA
Found at i:5677238 original size:28 final size:28
Alignment explanation
Indices: 5677198--5677253 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
5677188 GAGTCAGGTT
5677198 GTGTTATGTTTACAATATAAACTGATAC
1 GTGTTATGTTTACAATATAAACTGATAC
5677226 GTGTTATGTTTACAATATAAACTGATAC
1 GTGTTATGTTTACAATATAAACTGATAC
5677254 CGAATTTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (28 bp):
GTGTTATGTTTACAATATAAACTGATAC
Found at i:5685421 original size:18 final size:18
Alignment explanation
Indices: 5685398--5685434 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
5685388 CATTGTTGTT
5685398 GCCAATTAGCCATCTCTG
1 GCCAATTAGCCATCTCTG
5685416 GCCAATTAGCCATCTCTG
1 GCCAATTAGCCATCTCTG
5685434 G
1 G
5685435 TTCAACTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.32, G:0.19, T:0.27
Consensus pattern (18 bp):
GCCAATTAGCCATCTCTG
Found at i:5691347 original size:109 final size:108
Alignment explanation
Indices: 5691201--5691396 Score: 250
Period size: 109 Copynumber: 1.8 Consensus size: 108
5691191 ATTCGTGGCT
** * * *
5691201 AGCGCCGCAAAATATATTAACCAAAACGCAGCGTTTTGATCTTAATGTATA-TAAAATTAGTGGC
1 AGCGCCGCAAAATATATTAACCAAAACGCAGAATTTTGACCTCAATGTATAGTAAAATTAGTGAC
*
5691265 GCTTACGGTAAACCGCCGCTAAAGAATATTAATAGTTTCTCACAA
66 GCTTA-GGGAAA-CGCCGCTAAAGAATATTAATAGTTTCTCACAA
* * * * * *
5691310 AGCGCCGCAAAATATCTTAACCAAAATGCATAATTTTGGCCTCGATGTATAGTAGAATTAGTGAC
1 AGCGCCGCAAAATATATTAACCAAAACGCAGAATTTTGACCTCAATGTATAGTAAAATTAGTGAC
*
5691375 GCTTAGGGAAACGCCGTTAAAG
66 GCTTAGGGAAACGCCGCTAAAG
5691397 CATAGTATTA
Statistics
Matches: 73, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
108 10 0.14
109 47 0.64
110 16 0.22
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (108 bp):
AGCGCCGCAAAATATATTAACCAAAACGCAGAATTTTGACCTCAATGTATAGTAAAATTAGTGAC
GCTTAGGGAAACGCCGCTAAAGAATATTAATAGTTTCTCACAA
Found at i:5691563 original size:115 final size:116
Alignment explanation
Indices: 5690856--5691590 Score: 381
Period size: 113 Copynumber: 6.5 Consensus size: 116
5690846 GGCGTTTACC
* * * * * * * *
5690856 ACAATGCGCCGCGAAATCTCTTAACCAAAACG-ATGTGTTTTCGTCTTGATGTAT-CCTAAAAGT
1 ACAA-GCGCCGCAAAATATCATAACCAAAACGCAT-CGTTTTGGTCTTGATGTATACTTAGAATT
* * * * * * * * *
5690919 AGTGCCGTTTACGCG--AAACACCGTTAAAGGACAGTAATAGCGGCGCTTT-TT
64 AGTGGCGATTACG-GTAAAACGCCGCTAAAGCATAGTATTAGCGACGATTTGTT
* * * * * * ** * *
5690970 AGAAACGCCGTAAAATAGCTTAATCAAAACGCAGAG-TTTGGTCTTGAGGTATA-TTAGAATTAC
1 ACAAGCGCCGCAAAATATCATAACCAAAACGCATCGTTTTGGTCTTGATGTATACTTAGAATTAG
* * * ** * * * * *
5691033 TGGCGTTTATGGGAAAACGCCATTAAAGGACAGTAATAGCGGCG--CT-TT
66 TGGCGATTACGGTAAAACGCCGCTAAAGCATAGTATTAGCGACGATTTGTT
* * * * *
5691081 ACGGAAGCGCCACAAACTATC-TGAACCGAAACACATCGTTTTGGTCTTGATGTATAC-TAGAAC
1 AC--AAGCGCCGCAAAATATCAT-AACCAAAACGCATCGTTTTGGTCTTGATGTATACTTAGAAT
* * * * *
5691144 TAGTGGCGCA-TACGGTCAAACGCCGCTAAAGAATAGTATTAGCGGCGATTCGTG
63 TAGTGGCG-ATTACGGTAAAACGCCGCTAAAGCATAGTATTAGCGACGATTTGTT
* * * * * *
5691198 GCTAGCGCCGCAAAATAT-ATTAACCAAAACGCAGCGTTTTGATCTTAATGTATA--TAAAATTA
1 ACAAGCGCCGCAAAATATCA-TAACCAAAACGCATCGTTTTGGTCTTGATGTATACTTAGAATTA
* * ** * *
5691260 GTGGCGCTTACGGTAAACCGCCGCTAAAG-A-A-TATTA-ATA-G-TTTCTC
65 GTGGCGATTACGGTAAAACGCCGCTAAAGCATAGTATTAGCGACGATTTGTT
* * ** * * *
5691306 ACAAAGCGCCGCAAAATATCTTAACCAAAATGCATAATTTTGGCCTCGATGTATA-GTAGAATTA
1 AC-AAGCGCCGCAAAATATCATAACCAAAACGCATCGTTTTGGTCTTGATGTATACTTAGAATTA
* * * * * * * *
5691370 GTGACGCTTA-GG-GAAACGCCGTTAAAGCATAGTATTAGCGGCGCTTGGAT
65 GTGGCGATTACGGTAAAACGCCGCTAAAGCATAGTATTAGCGACGATTTGTT
* * * * *
5691420 AAAAGTGCCACCAAATATC-TGAACCAAAACGCATCGTTTTGGTCTTGATGTATACTTA-ATTTA
1 ACAAGCGCCGCAAAATATCAT-AACCAAAACGCATCGTTTTGGTCTTGATGTATACTTAGAATTA
5691483 GTGGCGATTACGGTAAAACGCCGCTAAAGCATAGTATTAGCGACGATTTGTT
65 GTGGCGATTACGGTAAAACGCCGCTAAAGCATAGTATTAGCGACGATTTGTT
* * * * * * * ** * *
5691535 GCTAGCGCCGCGACATACCATAAACAAAATGCAAAGTTTTAGTCTTGATTTATACT
1 ACAAGCGCCGCAAAATATCATAACCAAAACGCATCGTTTTGGTCTTGATGTATACT
5691591 AATATCTTAA
Statistics
Matches: 469, Mismatches: 122, Indels: 59
0.72 0.19 0.09
Matches are distributed among these distances:
108 16 0.03
109 45 0.10
110 17 0.04
111 15 0.03
112 32 0.07
113 128 0.27
114 99 0.21
115 113 0.24
116 2 0.00
117 2 0.00
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.27
Consensus pattern (116 bp):
ACAAGCGCCGCAAAATATCATAACCAAAACGCATCGTTTTGGTCTTGATGTATACTTAGAATTAG
TGGCGATTACGGTAAAACGCCGCTAAAGCATAGTATTAGCGACGATTTGTT
Found at i:5691787 original size:23 final size:23
Alignment explanation
Indices: 5691758--5691813 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
5691748 TATGATGTAG
5691758 GTTTAGGGTTAGGGTATTAGAGT
1 GTTTAGGGTTAGGGTATTAGAGT
*
5691781 GTTTAGGGTTAGGGTATTAGGGT
1 GTTTAGGGTTAGGGTATTAGAGT
*
5691804 GTTTTGGGTT
1 GTTTAGGGTT
5691814 TAAGGTTTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.16, C:0.00, G:0.41, T:0.43
Consensus pattern (23 bp):
GTTTAGGGTTAGGGTATTAGAGT
Found at i:5691802 original size:8 final size:7
Alignment explanation
Indices: 5691738--5691858 Score: 68
Period size: 7 Copynumber: 16.7 Consensus size: 7
5691728 AAAGTTTAAA
5691738 GTTTAGG
1 GTTTAGG
*
5691745 GTTTATG
1 GTTTAGG
* *
5691752 ATGTA-G
1 GTTTAGG
5691758 GTTTAGG
1 GTTTAGG
5691765 G-TTAGG
1 GTTTAGG
5691771 GTATTAGAG
1 GT-TTAG-G
5691780 TGTTTAGG
1 -GTTTAGG
5691788 G-TTAGG
1 GTTTAGG
5691794 GTATTAGGG
1 GT-TTA-GG
*
5691803 TGTTTTGG
1 -GTTTAGG
*
5691811 GTTTAAG
1 GTTTAGG
5691818 GTTTAGG
1 GTTTAGG
* *
5691825 AGTCTGGG
1 -GTTTAGG
*
5691833 GTTTAAG
1 GTTTAGG
*
5691840 GTTTAAG
1 GTTTAGG
*
5691847 GTTTGGG
1 GTTTAGG
5691854 GTTTA
1 GTTTA
5691859 AGCTACTTTA
Statistics
Matches: 87, Mismatches: 17, Indels: 20
0.70 0.14 0.16
Matches are distributed among these distances:
6 16 0.18
7 43 0.49
8 15 0.17
9 9 0.10
10 4 0.05
ACGTcount: A:0.18, C:0.01, G:0.39, T:0.42
Consensus pattern (7 bp):
GTTTAGG
Found at i:5691823 original size:23 final size:22
Alignment explanation
Indices: 5691802--5691860 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
5691792 GGGTATTAGG
* *
5691802 GTGTTTTGGGTTTAAGGTTTAG
1 GTGTTTGGGGTTTAAGGTTTAA
* *
5691824 GAGTCTGGGGTTTAAGGTTTAA
1 GTGTTTGGGGTTTAAGGTTTAA
5691846 G-GTTTGGGGTTTAAG
1 GTGTTTGGGGTTTAAG
5691861 CTACTTTAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 13 0.41
22 19 0.59
ACGTcount: A:0.17, C:0.02, G:0.39, T:0.42
Consensus pattern (22 bp):
GTGTTTGGGGTTTAAGGTTTAA
Found at i:5691836 original size:22 final size:21
Alignment explanation
Indices: 5691809--5691860 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 21
5691799 AGGGTGTTTT
*
5691809 GGGTTTAAGGTTTAGGAGTCTG
1 GGGTTTAAGGTTTAAG-GTCTG
*
5691831 GGGTTTAAGGTTTAAGGTTTG
1 GGGTTTAAGGTTTAAGGTCTG
5691852 GGGTTTAAG
1 GGGTTTAAG
5691861 CTACTTTAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 13 0.46
22 15 0.54
ACGTcount: A:0.19, C:0.02, G:0.40, T:0.38
Consensus pattern (21 bp):
GGGTTTAAGGTTTAAGGTCTG
Found at i:5691931 original size:7 final size:7
Alignment explanation
Indices: 5691921--5691989 Score: 57
Period size: 7 Copynumber: 9.3 Consensus size: 7
5691911 GGTTGTTGGT
5691921 TTTAGGG
1 TTTAGGG
5691928 TTTAGGG
1 TTTAGGG
* *
5691935 TTTAACGA
1 TTT-AGGG
*
5691943 TTTAGTAG
1 TTTAG-GG
* *
5691951 CTTAGGAT
1 TTTAGG-G
5691959 TTTAGGG
1 TTTAGGG
5691966 TTTAGAGG
1 TTTAG-GG
5691974 TTTAGGG
1 TTTAGGG
5691981 TTTAGGG
1 TTTAGGG
5691988 TT
1 TT
5691990 AAATCCCAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
7 27 0.56
8 21 0.44
ACGTcount: A:0.20, C:0.03, G:0.33, T:0.43
Consensus pattern (7 bp):
TTTAGGG
Found at i:5691936 original size:15 final size:14
Alignment explanation
Indices: 5691921--5691989 Score: 57
Period size: 15 Copynumber: 4.6 Consensus size: 14
5691911 GGTTGTTGGT
5691921 TTTAGGGTTTAGGG
1 TTTAGGGTTTAGGG
* * *
5691935 TTTAACGATTTAGTAG
1 TTT-AGGGTTTAG-GG
* *
5691951 CTTAGGATTTTAGGG
1 TTTAGG-GTTTAGGG
5691966 TTTAGAGGTTTAGGG
1 TTTAG-GGTTTAGGG
5691981 TTTAGGGTT
1 TTTAGGGTT
5691990 AAATCCCAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
14 7 0.17
15 26 0.62
16 9 0.21
ACGTcount: A:0.20, C:0.03, G:0.33, T:0.43
Consensus pattern (14 bp):
TTTAGGGTTTAGGG
Found at i:5693002 original size:22 final size:22
Alignment explanation
Indices: 5692977--5693023 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
5692967 ACTATTCCGA
* *
5692977 TTAAATATGTCAGGCGTTTCTG
1 TTAAATAGGTAAGGCGTTTCTG
5692999 TTAAATAGGTAAGGCGTTTCTG
1 TTAAATAGGTAAGGCGTTTCTG
5693021 TTA
1 TTA
5693024 TTACAGCCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (22 bp):
TTAAATAGGTAAGGCGTTTCTG
Found at i:5693260 original size:54 final size:53
Alignment explanation
Indices: 5693201--5693302 Score: 161
Period size: 54 Copynumber: 1.9 Consensus size: 53
5693191 TTATAGCACA
5693201 TGATTATGTTGTTATGTTCTGAAATAATTG-AGTGGATTTGAAATAATTTGTTTT
1 TGATTATGTTGTTATGTTCTGAAAT-A-TGCAGTGGATTTGAAATAATTTGTTTT
**
5693255 TGATTATGTTGTTATGTTCTGAAATATGCTTTGGATTTGAAATAATTT
1 TGATTATGTTGTTATGTTCTGAAATATGCAGTGGATTTGAAATAATTT
5693303 CTAAGTCTGA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
52 2 0.04
53 18 0.40
54 25 0.56
ACGTcount: A:0.27, C:0.03, G:0.20, T:0.50
Consensus pattern (53 bp):
TGATTATGTTGTTATGTTCTGAAATATGCAGTGGATTTGAAATAATTTGTTTT
Found at i:5693523 original size:14 final size:14
Alignment explanation
Indices: 5693504--5693533 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5693494 ATAAAAGGTT
5693504 TTTAGTTAATCATC
1 TTTAGTTAATCATC
5693518 TTTAGTTAATCATC
1 TTTAGTTAATCATC
5693532 TT
1 TT
5693534 GCTGTTCGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.53
Consensus pattern (14 bp):
TTTAGTTAATCATC
Found at i:5694268 original size:29 final size:31
Alignment explanation
Indices: 5694213--5694290 Score: 115
Period size: 31 Copynumber: 2.5 Consensus size: 31
5694203 ATATTTAAAT
*
5694213 TTTAAATTTAATAAATTATTTATAACAATTA
1 TTTAAATTTAATAAATTAATTATAACAATTA
5694244 TTTAAATTTAATAAA-TAATT-TAACAATTA
1 TTTAAATTTAATAAATTAATTATAACAATTA
*
5694273 TTTAAATTTTATTAAATT
1 TTTAAA-TTTAATAAATT
5694291 TTATTAATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
29 15 0.35
30 12 0.28
31 16 0.37
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (31 bp):
TTTAAATTTAATAAATTAATTATAACAATTA
Found at i:5694370 original size:92 final size:92
Alignment explanation
Indices: 5694323--5694872 Score: 1084
Period size: 92 Copynumber: 6.0 Consensus size: 92
5694313 AAAGATTGCT
5694323 TATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTATTACTATTTTT
1 TATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTATTACTATTTTT
5694388 TTAATATTATACATATATTCATTTACG
66 TTAATATTATACATATATTCATTTACG
5694415 TATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTATTACTATTTTT
1 TATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTATTACTATTTTT
5694480 TTAATATTATACATATATTCATTTACG
66 TTAATATTATACATATATTCATTTACG
5694507 TATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTATTACTATTTTT
1 TATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTATTACTATTTTT
5694572 TTAATATTATACATATATTCATTTACG
66 TTAATATTATACATATATTCATTTACG
5694599 TATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTATTACTA-TTTT
1 TATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTATTACTATTTTT
*
5694663 TTAATATTGTACATATATTCATTTACG
66 TTAATATTATACATATATTCATTTACG
5694690 TATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTATTACTATTTTT
1 TATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTATTACTATTTTT
5694755 TTAATATTATACATATATTCATTTACG
66 TTAATATTATACATATATTCATTTACG
5694782 TATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTATTACTATTTTT
1 TATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTATTACTATTTTT
5694847 TTAATATTATACATATATTCATTTAC
66 TTAATATTATACATATATTCATTTAC
5694873 ATAACACATA
Statistics
Matches: 455, Mismatches: 2, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
91 90 0.20
92 365 0.80
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (92 bp):
TATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTATTACTATTTTT
TTAATATTATACATATATTCATTTACG
Found at i:5694736 original size:275 final size:276
Alignment explanation
Indices: 5694323--5694872 Score: 1084
Period size: 275 Copynumber: 2.0 Consensus size: 276
5694313 AAAGATTGCT
5694323 TATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTATTACTATTTTT
1 TATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTATTACTATTTTT
5694388 TTAATATTATACATATATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTT
66 TTAATATTATACATATATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTT
5694453 ATAACTTAAATAAGTATTACTATTTTTTTAATATTATACATATATTCATTTACGTATGTAAGCTA
131 ATAACTTAAATAAGTATTACTATTTTTTTAATATTATACATATATTCATTTACGTATGTAAGCTA
5694518 TATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTATTACTATTTTTTTAATATTATA
196 TATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTATTACTATTTTTTTAATATTATA
5694583 CATATATTCATTTACG
261 CATATATTCATTTACG
5694599 TATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTATTACTA-TTTT
1 TATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTATTACTATTTTT
*
5694663 TTAATATTGTACATATATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTT
66 TTAATATTATACATATATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTT
5694728 ATAACTTAAATAAGTATTACTATTTTTTTAATATTATACATATATTCATTTACGTATGTAAGCTA
131 ATAACTTAAATAAGTATTACTATTTTTTTAATATTATACATATATTCATTTACGTATGTAAGCTA
5694793 TATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTATTACTATTTTTTTAATATTATA
196 TATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTATTACTATTTTTTTAATATTATA
5694858 CATATATTCATTTAC
261 CATATATTCATTTAC
5694873 ATAACACATA
Statistics
Matches: 273, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
275 213 0.78
276 60 0.22
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (276 bp):
TATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTATTACTATTTTT
TTAATATTATACATATATTCATTTACGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTT
ATAACTTAAATAAGTATTACTATTTTTTTAATATTATACATATATTCATTTACGTATGTAAGCTA
TATTTAAATTTTATTAATAATAAATTTATAACTTAAATAAGTATTACTATTTTTTTAATATTATA
CATATATTCATTTACG
Found at i:5694892 original size:9 final size:9
Alignment explanation
Indices: 5694869--5695215 Score: 125
Period size: 9 Copynumber: 40.9 Consensus size: 9
5694859 ATATATTCAT
5694869 TTACATAAC
1 TTACATAAC
5694878 --ACATAAC
1 TTACATAAC
5694885 TTACATAAC
1 TTACATAAC
* *
5694894 CTACTTAA-
1 TTACATAAC
*
5694902 -TATATAAC
1 TTACATAAC
*
5694910 TTGCATAAC
1 TTACATAAC
* *
5694919 TTAAATAAG
1 TTACATAAC
*
5694928 TTACGTAA-
1 TTACATAAC
5694936 TAATACATAA-
1 T--TACATAAC
*
5694946 -TACACAAC
1 TTACATAAC
*
5694954 TTACAT-GC
1 TTACATAAC
* *
5694962 GTAAATAA-
1 TTACATAAC
*
5694970 -TA-ATAAG
1 TTACATAAC
5694977 TTACATAA-
1 TTACATAAC
*
5694985 TAATACATACC
1 T--TACATAAC
* *
5694996 CTACATAAA
1 TTACATAAC
* *
5695005 TTAAATAAG
1 TTACATAAC
5695014 TTACATAA-
1 TTACATAAC
*
5695022 -TACACAAC
1 TTACATAAC
**
5695030 TTACGCAAC
1 TTACATAAC
*
5695039 TTACATAAG
1 TTACATAAC
*
5695048 TTTCATAA-
1 TTACATAAC
*
5695056 -TACACAAC
1 TTACATAAC
**
5695064 TTACGCAAC
1 TTACATAAC
5695073 TTACATAA-
1 TTACATAAC
*
5695081 -GACATAAC
1 TTACATAAC
*
5695089 TTACAT--G
1 TTACATAAC
*
5695096 TGTAAATAA-
1 T-TACATAAC
**
5695105 -TACATATT
1 TTACATAAC
5695113 TTACATAAC
1 TTACATAAC
5695122 TTACATAA-
1 TTACATAAC
*
5695130 -GACATAAC
1 TTACATAAC
*
5695138 TTACATAAG
1 TTACATAAC
*
5695147 TTTCATAA-
1 TTACATAAC
* *
5695155 -TACACATC
1 TTACATAAC
**
5695163 TTACGCAAC
1 TTACATAAC
*
5695172 TTACACAAC
1 TTACATAAC
5695181 TTACATAAC
1 TTACATAAC
5695190 TTACATAAC
1 TTACATAAC
5695199 TTACATAAC
1 TTACATAAC
5695208 TTACATAA
1 TTACATAA
5695216 TGTATATCTT
Statistics
Matches: 252, Mismatches: 56, Indels: 60
0.68 0.15 0.16
Matches are distributed among these distances:
6 4 0.02
7 53 0.21
8 13 0.05
9 170 0.67
10 12 0.05
ACGTcount: A:0.46, C:0.19, G:0.05, T:0.31
Consensus pattern (9 bp):
TTACATAAC
Found at i:5695047 original size:34 final size:34
Alignment explanation
Indices: 5695009--5695081 Score: 137
Period size: 34 Copynumber: 2.1 Consensus size: 34
5694999 CATAAATTAA
5695009 ATAAGTTACATAATACACAACTTACGCAACTTAC
1 ATAAGTTACATAATACACAACTTACGCAACTTAC
*
5695043 ATAAGTTTCATAATACACAACTTACGCAACTTAC
1 ATAAGTTACATAATACACAACTTACGCAACTTAC
5695077 ATAAG
1 ATAAG
5695082 ACATAACTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.44, C:0.22, G:0.07, T:0.27
Consensus pattern (34 bp):
ATAAGTTACATAATACACAACTTACGCAACTTAC
Found at i:5695063 original size:25 final size:25
Alignment explanation
Indices: 5695035--5695206 Score: 114
Period size: 25 Copynumber: 6.8 Consensus size: 25
5695025 ACAACTTACG
*
5695035 CAACTTACATAAGTTTCATAATACA
1 CAACTTACATAAGTTACATAATACA
** * *
5695060 CAACTTACGCAACTTACATAAGACA
1 CAACTTACATAAGTTACATAATACA
* *
5695085 TAACTTACAT--GTGTAAATAATACA
1 CAACTTACATAAGT-TACATAATACA
* ** * *
5695109 TATTTTACATAACTTACATAAGACA
1 CAACTTACATAAGTTACATAATACA
* *
5695134 TAACTTACATAAGTTTCATAATACA
1 CAACTTACATAAGTTACATAATACA
* ** * *
5695159 CATCTTACGCAACTTACACAACTTACA
1 CAACTTACATAAGTTACATAA--TACA
* *
5695186 TAACTTACATAACTTACATAA
1 CAACTTACATAAGTTACATAA
5695207 CTTACATAAT
Statistics
Matches: 109, Mismatches: 33, Indels: 8
0.73 0.22 0.05
Matches are distributed among these distances:
23 1 0.01
24 17 0.16
25 70 0.64
26 1 0.01
27 20 0.18
ACGTcount: A:0.44, C:0.21, G:0.05, T:0.31
Consensus pattern (25 bp):
CAACTTACATAAGTTACATAATACA
Found at i:5695091 original size:16 final size:16
Alignment explanation
Indices: 5695070--5695146 Score: 68
Period size: 16 Copynumber: 4.8 Consensus size: 16
5695060 CAACTTACGC
5695070 AACTTACATAAGACAT
1 AACTTACATAAGACAT
** *
5695086 AACTTACATGTGTAAAT
1 AACTTACATAAG-ACAT
**
5695103 AA--TACATATTTTACAT
1 AACTTACATA--AGACAT
5695119 AACTTACATAAGACAT
1 AACTTACATAAGACAT
5695135 AACTTACATAAG
1 AACTTACATAAG
5695147 TTTCATAATA
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
15 5 0.10
16 31 0.65
17 6 0.12
18 6 0.12
ACGTcount: A:0.47, C:0.16, G:0.06, T:0.31
Consensus pattern (16 bp):
AACTTACATAAGACAT
Found at i:5700532 original size:21 final size:21
Alignment explanation
Indices: 5700506--5700571 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
5700496 CAACAACTTA
*
5700506 AAGCAGAGGCGGCAGCGAGAG
1 AAGCAGAGGCCGCAGCGAGAG
* ** *
5700527 AAGCAGACGCTACAGTGAGAG
1 AAGCAGAGGCCGCAGCGAGAG
*
5700548 AAGTAGAGGCCGCAGCGAGAG
1 AAGCAGAGGCCGCAGCGAGAG
5700569 AAG
1 AAG
5700572 TAGCGATAGA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.36, C:0.18, G:0.41, T:0.05
Consensus pattern (21 bp):
AAGCAGAGGCCGCAGCGAGAG
Found at i:5700676 original size:50 final size:50
Alignment explanation
Indices: 5700601--5700700 Score: 164
Period size: 50 Copynumber: 2.0 Consensus size: 50
5700591 TCAAAAGAAA
* *
5700601 TATGAAGAACTACAGCTACGACTTCAAAAAGATGCGGCATCGAGAGAAGC
1 TATGAAGAACTACAGCCACGACTTCAAAAACATGCGGCATCGAGAGAAGC
* *
5700651 TATGAAGAACTGCAGCCACGGCTTCAAAAACATGCGGCATCGAGAGAAGC
1 TATGAAGAACTACAGCCACGACTTCAAAAACATGCGGCATCGAGAGAAGC
5700701 AGAGCAGAGC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.25, T:0.15
Consensus pattern (50 bp):
TATGAAGAACTACAGCCACGACTTCAAAAACATGCGGCATCGAGAGAAGC
Found at i:5701126 original size:42 final size:42
Alignment explanation
Indices: 5701107--5702076 Score: 1746
Period size: 42 Copynumber: 23.0 Consensus size: 42
5701097 ACAAGCGCTG
* *
5701107 CTAAAGAACATGATCTTTAGTGGCGTTTTTTTCCTTAGCG-CA
1 CTAAAGAACATGATCTTTAGTGGCGTTTATTT-CTAAGCGCCA
* *
5701149 GCTAAAGTACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCG
1 -CTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCA
5701192 CTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCA
1 CTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCA
5701234 CTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCA
1 CTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCA
5701276 CTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCA
1 CTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCA
5701318 CTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCA
1 CTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCA
5701360 CTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCA
1 CTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCA
5701402 CTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCA
1 CTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCA
5701444 CTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCA
1 CTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCA
5701486 CTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCA
1 CTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCA
5701528 CTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCA
1 CTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCA
5701570 CTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCA
1 CTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCA
5701612 CTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCA
1 CTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCA
5701654 CTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCA
1 CTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCA
5701696 CTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCA
1 CTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCA
5701738 CTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCA
1 CTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCA
5701780 CTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCA
1 CTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCA
5701822 CTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCA
1 CTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCA
* *
5701864 CTAAAGAACATGATCTTTAGTGGCGTTTTTTTCCTTAGCG-CA
1 CTAAAGAACATGATCTTTAGTGGCGTTTATTT-CTAAGCGCCA
* *
5701906 GCTAAAGTACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCG
1 -CTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCA
5701949 CTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCA
1 CTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCA
* *
5701991 CTAAAGAACATGATCTTTAGTGGCGTTTATTTCCTTAGCGCCG
1 CTAAAGAACATGATCTTTAGTGGCGTTTATTT-CTAAGCGCCA
* * *
5702034 CTAAAGAACATGATCTTTAGCGGCATTTTTTTCTGTAAGCGCC
1 CTAAAGAACATGATCTTTAGTGGCGTTTATTTC--TAAGCGCC
5702077 GCAAAAGTTT
Statistics
Matches: 900, Mismatches: 20, Indels: 13
0.96 0.02 0.01
Matches are distributed among these distances:
42 788 0.88
43 105 0.12
44 7 0.01
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.34
Consensus pattern (42 bp):
CTAAAGAACATGATCTTTAGTGGCGTTTATTTCTAAGCGCCA
Found at i:5721164 original size:28 final size:26
Alignment explanation
Indices: 5721119--5721195 Score: 84
Period size: 26 Copynumber: 2.8 Consensus size: 26
5721109 ACATGCAGAA
*
5721119 AAAATATATAAAAA-ATAAAATTCAAT
1 AAAATTTATAAAAATATAAAATT-AAT
*
5721145 AAAATTTATAAAAATTATAAAAATTATT
1 AAAATTTATAAAAA-TAT-AAAATTAAT
*
5721173 AAATTTTAATAAAAATATAAAAT
1 AAAATTT-ATAAAAATATAAAAT
5721196 ATTTAAATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
26 13 0.30
27 5 0.11
28 13 0.30
29 13 0.30
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (26 bp):
AAAATTTATAAAAATATAAAATTAAT
Found at i:5721177 original size:37 final size:37
Alignment explanation
Indices: 5721118--5721212 Score: 90
Period size: 37 Copynumber: 2.6 Consensus size: 37
5721108 GACATGCAGA
* *
5721118 AAAAATATATAAAAA--A-TAAAATTCAATAAAATTTAT
1 AAAAAT-TATAAAAATTATTAAATTTCAATAAAA-ATAT
*
5721154 AAAAATTATAAAAATTATTAAATTTTAATAAAAATAT
1 AAAAATTATAAAAATTATTAAATTTCAATAAAAATAT
**
5721191 AAAATATT-TAAATTTTATTAAA
1 AAAA-ATTATAAAAATTATTAAA
5721213 AATTAGAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
35 8 0.16
36 6 0.12
37 20 0.40
38 16 0.32
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (37 bp):
AAAAATTATAAAAATTATTAAATTTCAATAAAAATAT
Found at i:5721187 original size:20 final size:20
Alignment explanation
Indices: 5721126--5721201 Score: 58
Period size: 20 Copynumber: 4.0 Consensus size: 20
5721116 GAAAAAATAT
*
5721126 ATAAAAA-AT-AAA-ATTCA
1 ATAAAAATATAAAATATTTA
*
5721143 ATAAAATTTATAAAA-A-TT-
1 ATAAAA-ATATAAAATATTTA
*
5721161 ATAAAAATTATTAAAT-TTTA
1 ATAAAAA-TATAAAATATTTA
5721181 ATAAAAATATAAAATATTTA
1 ATAAAAATATAAAATATTTA
5721201 A
1 A
5721202 ATTTTATTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
17 6 0.13
18 12 0.26
19 12 0.26
20 16 0.35
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (20 bp):
ATAAAAATATAAAATATTTA
Found at i:5721201 original size:27 final size:27
Alignment explanation
Indices: 5721144--5721230 Score: 97
Period size: 28 Copynumber: 3.1 Consensus size: 27
5721134 TAAAATTCAA
*
5721144 TAAAATTT-ATAAAAATTATAAAAATTAT
1 TAAATTTTAATAAAAATTATAAAAA-T-T
5721172 TAAATTTTAATAAAAA-TATAAAATATT
1 TAAATTTTAATAAAAATTATAAAA-ATT
* *
5721199 TAAATTTTATTAAAAATTAGAAAAAATT
1 TAAATTTTAATAAAAATTA-TAAAAATT
5721227 TAAA
1 TAAA
5721231 ATAAAAAATG
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
27 16 0.31
28 24 0.46
29 12 0.23
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (27 bp):
TAAATTTTAATAAAAATTATAAAAATT
Found at i:5721420 original size:26 final size:26
Alignment explanation
Indices: 5721391--5721446 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
5721381 AAATTATAAA
*
5721391 ATAAATCTTTT-GATACGATAATTTTT
1 ATAAATATTTTAGA-ACGATAATTTTT
*
5721417 ATAATTATTTTAGAACGATAATTTTT
1 ATAAATATTTTAGAACGATAATTTTT
5721443 ATAA
1 ATAA
5721447 TTTTTTTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 25 0.93
27 2 0.07
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.48
Consensus pattern (26 bp):
ATAAATATTTTAGAACGATAATTTTT
Found at i:5721447 original size:26 final size:26
Alignment explanation
Indices: 5721405--5721454 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
5721395 ATCTTTTGAT
5721405 ACGATAATTTTTATAATTATTTTAGA
1 ACGATAATTTTTATAATTATTTTAGA
*
5721431 ACGATAATTTTTATAATTTTTTTA
1 ACGATAATTTTTATAATTATTTTA
5721455 CAAATTTGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.54
Consensus pattern (26 bp):
ACGATAATTTTTATAATTATTTTAGA
Found at i:5721488 original size:20 final size:20
Alignment explanation
Indices: 5721436--5721494 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
5721426 TTAGAACGAT
5721436 AATTTTTATAATTTTTTTAC
1 AATTTTTATAATTTTTTTAC
* *
5721456 AAATTTGAT-ATTTCTTTT-C
1 AATTTTTATAATTT-TTTTAC
* *
5721475 ATTTTTTATAATTTTATTAC
1 AATTTTTATAATTTTTTTAC
5721495 GAAATTTATG
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.63
Consensus pattern (20 bp):
AATTTTTATAATTTTTTTAC
Found at i:5721558 original size:18 final size:18
Alignment explanation
Indices: 5721537--5721607 Score: 63
Period size: 18 Copynumber: 3.7 Consensus size: 18
5721527 AATCTATATA
5721537 TTTTATAATTTTTACGAT
1 TTTTATAATTTTTACGAT
*
5721555 TTTTATAAAATTTTAC-ACTT
1 TTTTAT-AATTTTTACGA--T
* *
5721575 TTTTAAATACTTTTTACGGT
1 TTTT--ATAATTTTTACGAT
5721595 TTTTATAATTTTT
1 TTTTATAATTTTT
5721608 TCTAACTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
18 15 0.36
19 8 0.19
20 10 0.24
21 7 0.17
22 2 0.05
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.61
Consensus pattern (18 bp):
TTTTATAATTTTTACGAT
Found at i:5721568 original size:20 final size:20
Alignment explanation
Indices: 5721543--5721602 Score: 63
Period size: 19 Copynumber: 3.0 Consensus size: 20
5721533 TATATTTTAT
5721543 AATTTTTACGATTTTTATAA
1 AATTTTTACGATTTTTATAA
5721563 AA-TTTTAC-ACTTTTT-TAA
1 AATTTTTACGA-TTTTTATAA
*
5721581 ATACTTTTTACGGTTTTTATAA
1 A-A-TTTTTACGATTTTTATAA
5721603 TTTTTTCTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
18 5 0.15
19 12 0.36
20 2 0.06
21 11 0.33
22 3 0.09
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.55
Consensus pattern (20 bp):
AATTTTTACGATTTTTATAA
Found at i:5722109 original size:43 final size:43
Alignment explanation
Indices: 5722012--5722111 Score: 139
Period size: 43 Copynumber: 2.3 Consensus size: 43
5722002 TAAACATCTT
* * * *
5722012 AAAATCTAATTAAATATTTTAAACCTAAAAATCTAGAAATCCT
1 AAAATCTAATTTAATATTTAAAACCTAAAAAACTAGAAATCCA
*
5722055 AAAATCTAATTTAATATTTAAAATCTAAAAAACTA-AAAGTCCA
1 AAAATCTAATTTAATATTTAAAACCTAAAAAACTAGAAA-TCCA
5722098 AAAATCTAATTTAA
1 AAAATCTAATTTAA
5722112 GATATAATAC
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 3 0.06
43 48 0.94
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.32
Consensus pattern (43 bp):
AAAATCTAATTTAATATTTAAAACCTAAAAAACTAGAAATCCA
Found at i:5725143 original size:15 final size:16
Alignment explanation
Indices: 5725123--5725152 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5725113 AATAATTTAC
5725123 AAATTG-TTGCATATT
1 AAATTGTTTGCATATT
5725138 AAATTGTTTGCATAT
1 AAATTGTTTGCATAT
5725153 GGTAAGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (16 bp):
AAATTGTTTGCATATT
Found at i:5730146 original size:43 final size:43
Alignment explanation
Indices: 5730049--5730148 Score: 139
Period size: 43 Copynumber: 2.3 Consensus size: 43
5730039 TAAACATCTT
* * * *
5730049 AAAATCTAATTAAATATTTTAAACCTAAAAATCTAGAAATCCT
1 AAAATCTAATTTAATATTTAAAACCTAAAAAACTAGAAATCCA
*
5730092 AAAATCTAATTTAATATTTAAAATCTAAAAAACTA-AAAGTCCA
1 AAAATCTAATTTAATATTTAAAACCTAAAAAACTAGAAA-TCCA
5730135 AAAATCTAATTTAA
1 AAAATCTAATTTAA
5730149 GATATAATAC
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 3 0.06
43 48 0.94
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.32
Consensus pattern (43 bp):
AAAATCTAATTTAATATTTAAAACCTAAAAAACTAGAAATCCA
Found at i:5733180 original size:15 final size:16
Alignment explanation
Indices: 5733160--5733189 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5733150 AATAATTTAC
5733160 AAATTG-TTGCATATT
1 AAATTGTTTGCATATT
5733175 AAATTGTTTGCATAT
1 AAATTGTTTGCATAT
5733190 GGTAAGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (16 bp):
AAATTGTTTGCATATT
Found at i:5738205 original size:13 final size:13
Alignment explanation
Indices: 5738189--5738213 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5738179 TTTATTAAAA
5738189 TAATAAATTATTT
1 TAATAAATTATTT
5738202 TAATAAATTATT
1 TAATAAATTATT
5738214 ATATTATTAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TAATAAATTATTT
Found at i:5738214 original size:16 final size:16
Alignment explanation
Indices: 5738168--5738225 Score: 50
Period size: 16 Copynumber: 3.8 Consensus size: 16
5738158 TAAAATTGTA
*
5738168 ATATTAAAAAATTTATT
1 ATATTAATAAA-TTATT
* *
5738185 AAAATAATAAATTA-T
1 ATATTAATAAATTATT
5738200 -T-TTAATAAATTATT
1 ATATTAATAAATTATT
*
5738214 ATATTATTAAAT
1 ATATTAATAAAT
5738226 ATAAATAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
13 10 0.31
14 1 0.03
15 2 0.06
16 11 0.34
17 8 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATATTAATAAATTATT
Found at i:5738895 original size:20 final size:20
Alignment explanation
Indices: 5738857--5738895 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5738847 GTGATATGAG
* *
5738857 TTTTAGGTTATTTTTAATAT
1 TTTTAGGTTAATTTGAATAT
*
5738877 TTTTATGTTAATTTGAATA
1 TTTTAGGTTAATTTGAATA
5738896 ATTTGTAATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (20 bp):
TTTTAGGTTAATTTGAATAT
Found at i:5739886 original size:29 final size:28
Alignment explanation
Indices: 5739844--5739899 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
5739834 AGCCCCGTGA
*
5739844 CAAGTGGTATCTGAGCTGTTGGTTCGAAC
1 CAAGTGATATCTGAG-TGTTGGTTCGAAC
*
5739873 CAAGTGATATCTGAGTTTTGGTTCGAA
1 CAAGTGATATCTGAGTGTTGGTTCGAA
5739900 GGCACCGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.23, C:0.14, G:0.29, T:0.34
Consensus pattern (28 bp):
CAAGTGATATCTGAGTGTTGGTTCGAAC
Found at i:5740849 original size:32 final size:32
Alignment explanation
Indices: 5740808--5740868 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
5740798 AGCTTGGTCT
5740808 AGGGAAAGACAAGCTTGGGTCTTCCAAGTACG
1 AGGGAAAGACAAGCTTGGGTCTTCCAAGTACG
*
5740840 AGGGAAAGACAAGCTTGGGTTTTCCAAGT
1 AGGGAAAGACAAGCTTGGGTCTTCCAAGT
5740869 TTGAGGAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
AGGGAAAGACAAGCTTGGGTCTTCCAAGTACG
Found at i:5746070 original size:11 final size:11
Alignment explanation
Indices: 5746054--5746080 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
5746044 ATTTCTTCTG
5746054 GAAAGCCTCTA
1 GAAAGCCTCTA
5746065 GAAAGCCTCTA
1 GAAAGCCTCTA
5746076 GAAAG
1 GAAAG
5746081 TAATCCCACA
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:0.41, C:0.22, G:0.22, T:0.15
Consensus pattern (11 bp):
GAAAGCCTCTA
Found at i:5747760 original size:48 final size:48
Alignment explanation
Indices: 5747696--5747809 Score: 138
Period size: 48 Copynumber: 2.4 Consensus size: 48
5747686 CACCAGTTTG
*
5747696 TGGAAAAACCACCACATAGATACCAATGAATAATCACATAGCACATCA
1 TGGATAAACCACCACATAGATACCAATGAATAATCACATAGCACATCA
* * * * ** **
5747744 TGGATATACCACCACATAGATATCGATTAATGGTCACATAGCACATTG
1 TGGATAAACCACCACATAGATACCAATGAATAATCACATAGCACATCA
*
5747792 TGGATAAACTACCACATA
1 TGGATAAACCACCACATA
5747810 ATTGCTGATA
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 55 1.00
ACGTcount: A:0.42, C:0.23, G:0.13, T:0.22
Consensus pattern (48 bp):
TGGATAAACCACCACATAGATACCAATGAATAATCACATAGCACATCA
Found at i:5750735 original size:36 final size:36
Alignment explanation
Indices: 5750684--5750829 Score: 143
Period size: 36 Copynumber: 4.1 Consensus size: 36
5750674 ACGGTTTAAC
* *
5750684 ATAATGTCATACTTAACATGTGAATCAAAATAAAAA
1 ATAATGACATGCTTAACATGTGAATCAAAATAAAAA
* * * *
5750720 ATAATGGCATGCTTAACATGTGAATCAGAATTAGAA
1 ATAATGACATGCTTAACATGTGAATCAAAATAAAAA
* * *
5750756 ATAATGACATGCTTAGCATGTGAGTCAAAAT-CAAA
1 ATAATGACATGCTTAACATGTGAATCAAAATAAAAA
* ** * *
5750791 ATAGT-ACCATGCTTAACATACGAATTAGAATAAAAA
1 ATAATGA-CATGCTTAACATGTGAATCAAAATAAAAA
5750827 ATA
1 ATA
5750830 TTAACATATT
Statistics
Matches: 89, Mismatches: 19, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
34 1 0.01
35 24 0.27
36 64 0.72
ACGTcount: A:0.47, C:0.12, G:0.14, T:0.27
Consensus pattern (36 bp):
ATAATGACATGCTTAACATGTGAATCAAAATAAAAA
Found at i:5750821 original size:71 final size:72
Alignment explanation
Indices: 5750684--5750821 Score: 170
Period size: 71 Copynumber: 1.9 Consensus size: 72
5750674 ACGGTTTAAC
* ** **
5750684 ATAATGTCATACTTAACATGTGAATCAAAATAAAAAATAATGGCATGCTTAACATGTGAATCAGA
1 ATAATGACATACTTAACATGTGAATCAAAATAAAAAATAATACCATGCTTAACATACGAATCAGA
5750749 ATTAGAA
66 ATTAGAA
* * * * * *
5750756 ATAATGACATGCTTAGCATGTGAGTCAAAAT-CAAAATAGTACCATGCTTAACATACGAATTAGA
1 ATAATGACATACTTAACATGTGAATCAAAATAAAAAATAATACCATGCTTAACATACGAATCAGA
5750820 AT
66 AT
5750822 AAAAAATATT
Statistics
Matches: 55, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
71 28 0.51
72 27 0.49
ACGTcount: A:0.45, C:0.13, G:0.14, T:0.28
Consensus pattern (72 bp):
ATAATGACATACTTAACATGTGAATCAAAATAAAAAATAATACCATGCTTAACATACGAATCAGA
ATTAGAA
Found at i:5756421 original size:10 final size:10
Alignment explanation
Indices: 5756408--5756450 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
5756398 AATAACTTTG
5756408 TTTTTATTAT
1 TTTTTATTAT
5756418 TTTTTATTAT
1 TTTTTATTAT
5756428 TTTTATATT-T
1 TTTT-TATTAT
*
5756438 TGTTTATTTAT
1 TTTTTA-TTAT
5756449 TT
1 TT
5756451 GATTTGGGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
9 2 0.07
10 20 0.71
11 6 0.21
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (10 bp):
TTTTTATTAT
Found at i:5763180 original size:41 final size:41
Alignment explanation
Indices: 5763131--5763277 Score: 204
Period size: 41 Copynumber: 3.6 Consensus size: 41
5763121 ATCGAAGTCT
* * * *
5763131 AAACAGGGGCACGTATGTGCAATTTAAGGGTACCGAAGTAA
1 AAACAGGGGCACATATGTGCAATTTAGGGGTACCAAAGTAC
*
5763172 AAATAGGGGCACATATGTGCAATTTAGGGGTACCAAAGTAC
1 AAACAGGGGCACATATGTGCAATTTAGGGGTACCAAAGTAC
* * *
5763213 AAACACGGGCACATATGTGGAATTCAGGGGTACCAAAGTAC
1 AAACAGGGGCACATATGTGCAATTTAGGGGTACCAAAGTAC
* *
5763254 GAACAGGGGCACGTATGTGCAATT
1 AAACAGGGGCACATATGTGCAATT
5763278 CATCATTATT
Statistics
Matches: 93, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 93 1.00
ACGTcount: A:0.35, C:0.16, G:0.29, T:0.20
Consensus pattern (41 bp):
AAACAGGGGCACATATGTGCAATTTAGGGGTACCAAAGTAC
Found at i:5777650 original size:23 final size:21
Alignment explanation
Indices: 5777624--5777673 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 21
5777614 AGTTTTGTCG
*
5777624 TTTCTGCTTTTGGTTTTTTCTGT
1 TTTCT-CTTTTAGTTTTTTCT-T
*
5777647 TTTCATCTTTTATTTTTTTCTT
1 TTTC-TCTTTTAGTTTTTTCTT
5777669 TTTCT
1 TTTCT
5777674 TCCCAACCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 1 0.04
22 5 0.21
23 17 0.71
24 1 0.04
ACGTcount: A:0.04, C:0.14, G:0.08, T:0.74
Consensus pattern (21 bp):
TTTCTCTTTTAGTTTTTTCTT
Found at i:5781939 original size:47 final size:47
Alignment explanation
Indices: 5781861--5782411 Score: 809
Period size: 47 Copynumber: 11.6 Consensus size: 47
5781851 CCCATCGGGA
* * * * * *
5781861 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
5781908 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
5781955 CTCATCACATATATACACTTTCACATTCATCATATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
5782002 CTTATCACATATATATACACTTCCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
5782051 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
5782100 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
5782147 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
5782194 CTTACTACATATATATACACTTT--CGTTCATCATATCGGCCATTAGGC
1 CTTA-T-CACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
5782241 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
5782290 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
5782337 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
5782384 CTTATCACATATATACACTTTCACATTC
1 CTTATCACATATATACACTTTCACATTC
5782412 CAATGAATAA
Statistics
Matches: 466, Mismatches: 30, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
45 2 0.00
46 1 0.00
47 328 0.70
48 1 0.00
49 134 0.29
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:5782204 original size:143 final size:141
Alignment explanation
Indices: 5781861--5782411 Score: 809
Period size: 143 Copynumber: 3.9 Consensus size: 141
5781851 CCCATCGGGA
* * * * * * * *
5781861 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
* *
5781926 TTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATACACTTTCACATTCATCATATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
5781991 GGCCATTAGGC
131 GGCCATTAGGC
*
5782002 CTTATCACATATATATACACTTCCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATAT
* *
5782067 ACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCA
62 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
*
5782132 CATCGGCTATTAGGC
127 CATCGGCCATTAGGC
*
5782147 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTACTACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA-T-CACATATATAC
* *
5782212 ACTTT--CGTTCATCATATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCA
* *
5782275 CATTGGCCATTCGGC
127 CATCGGCCATTAGGC
* *
5782290 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
* *
5782355 TTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTC
5782412 CAATGAATAA
Statistics
Matches: 370, Mismatches: 30, Indels: 20
0.88 0.07 0.05
Matches are distributed among these distances:
141 71 0.19
142 1 0.00
143 206 0.56
144 1 0.00
145 91 0.25
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (141 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGC
Found at i:5782299 original size:22 final size:22
Alignment explanation
Indices: 5782271--5782393 Score: 70
Period size: 22 Copynumber: 5.3 Consensus size: 22
5782261 TTTCACATTC
5782271 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
5782293 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
5782317 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
** * * *
5782340 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
5782364 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
5782387 ATCACAT
1 ATCACAT
5782394 ATATACACTT
Statistics
Matches: 71, Mismatches: 20, Indels: 20
0.64 0.18 0.18
Matches are distributed among these distances:
22 29 0.41
23 10 0.14
24 10 0.14
25 22 0.31
ACGTcount: A:0.27, C:0.30, G:0.10, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:5784040 original size:13 final size:13
Alignment explanation
Indices: 5784022--5784046 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5784012 TACTAAATTT
5784022 TCATGGATTCAAA
1 TCATGGATTCAAA
5784035 TCATGGATTCAA
1 TCATGGATTCAA
5784047 TATACCATTA
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TCATGGATTCAAA
Found at i:5785654 original size:39 final size:39
Alignment explanation
Indices: 5785600--5785677 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
5785590 TTGAGAAAGA
*
5785600 ACACTCCTTTTAAGTGGTTGAATGATCTGTGAGCTAGTT
1 ACACTCCTTTTAAGTGGTTGAATGATCTGTGAGATAGTT
5785639 ACACTCCTTTTAAGTGGTTGAATGATCTGTGAGATAGTT
1 ACACTCCTTTTAAGTGGTTGAATGATCTGTGAGATAGTT
5785678 TTGAGAAGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.24, C:0.14, G:0.23, T:0.38
Consensus pattern (39 bp):
ACACTCCTTTTAAGTGGTTGAATGATCTGTGAGATAGTT
Found at i:5799644 original size:59 final size:61
Alignment explanation
Indices: 5799574--5799689 Score: 155
Period size: 62 Copynumber: 1.9 Consensus size: 61
5799564 TCACTTTAAT
* * * *
5799574 ATTAAATTAATATAATATTTA-T-CAAGATAAATATTAGATTAAAATTAATATTAAATCTA
1 ATTAAAATAATAGAATATTTACTACAAGATAAATATTAAAATAAAATTAATATTAAATCTA
* *
5799633 ATTAAAATAATAGAATGTTTATCTACAAGATAAATATTAAAATAAATTTAATATTAA
1 ATTAAAATAATAGAATATTTA-CTACAAGATAAATATTAAAATAAAATTAATATTAA
5799690 GATAATTACC
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
59 18 0.38
61 1 0.02
62 29 0.60
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.39
Consensus pattern (61 bp):
ATTAAAATAATAGAATATTTACTACAAGATAAATATTAAAATAAAATTAATATTAAATCTA
Found at i:5799715 original size:20 final size:19
Alignment explanation
Indices: 5799665--5799729 Score: 64
Period size: 20 Copynumber: 3.5 Consensus size: 19
5799655 CTACAAGATA
*
5799665 AATATT-AA-AATAAATTT
1 AATATTAAATAATAAACTT
* *
5799682 AATATTAAGATAATTACCTT
1 AATATTAA-ATAATAAACTT
5799702 AATATTAAATTAATAAAC-T
1 AATATTAAA-TAATAAACTT
5799721 AATATTAAA
1 AATATTAAA
5799730 GATAAATATT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
17 6 0.15
18 1 0.03
19 12 0.31
20 20 0.51
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (19 bp):
AATATTAAATAATAAACTT
Found at i:5801407 original size:15 final size:15
Alignment explanation
Indices: 5801387--5801418 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
5801377 TATGCATACA
5801387 AAATATAAAAGACAT
1 AAATATAAAAGACAT
5801402 AAATATAAAAGACAT
1 AAATATAAAAGACAT
5801417 AA
1 AA
5801419 CAATGAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (15 bp):
AAATATAAAAGACAT
Found at i:5805584 original size:12 final size:12
Alignment explanation
Indices: 5805567--5805596 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5805557 CATCACATGC
5805567 CCGTGTGCCAGG
1 CCGTGTGCCAGG
*
5805579 CCGTGTGCTAGG
1 CCGTGTGCCAGG
5805591 CCGTGT
1 CCGTGT
5805597 AACAGTCTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.30, G:0.40, T:0.23
Consensus pattern (12 bp):
CCGTGTGCCAGG
Found at i:5809457 original size:319 final size:320
Alignment explanation
Indices: 5808839--5809481 Score: 1155
Period size: 319 Copynumber: 2.0 Consensus size: 320
5808829 GTAGTCGATT
5808839 ATTTCCAGCACTAATTCAATCTATGTTCAATTTCTTAATTGCCCAAAATGCCTTATGTTCAAGTT
1 ATTTCCAGCACTAATTCAATCTATGTTCAATTTCTTAATTGCCCAAAATGCCTTATGTTCAAGTT
5808904 CAACAGGCAAATGGCAAGGCTTCTCGTAGATGAGCTTGAAAGGCAACATTCCCAATGATGTCTTG
66 CAACAGGCAAATGGCAAGGCTTCTCGTAGATGAGCTTGAAAGGCAACATTCCCAATGATGTCTTG
*
5808969 AAGGCTATGCACTATGCCCACAAAGCTTCATCAAATCTGGATGACCAATCCTTGTGGGTGGGATT
131 AAGGCTATGCACTATGCCCACAAAGCTTCATCAAATCTAGATGACCAATCCTTGTGGGTGGGATT
* * *
5809034 GACCACTTTCTTTAAAATTTGCTTAATTTATCTATTTGAGACCTCAGCTTATCCATTTATTTAGG
196 GACCACTTTCTTCAAAATCTGCTTAATTTATCTATTCGAGACCTCAGCTTATCCATTTATTTAGG
5809099 GGTGATATGCCATGAAAATTTTATGTGTAACCCCATATCTATTCAAGGTAGTAGCAACTA
261 GGTGATATGCCATGAAAATTTTATGTGTAACCCCATATCTATTCAAGGTAGTAGCAACTA
*
5809159 ATTTCCAGCATTAATTCAATCTATGTTCAATTTCTTAATTGCCCAAAATGCCTTATGTTCAAGTT
1 ATTTCCAGCACTAATTCAATCTATGTTCAATTTCTTAATTGCCCAAAATGCCTTATGTTCAAGTT
** *
5809224 CAACAGGCAAATGGCAAGGCTTCTCGTAGATGAGCTTGAAAGGTGACATTCCCAATGGTGTCTTG
66 CAACAGGCAAATGGCAAGGCTTCTCGTAGATGAGCTTGAAAGGCAACATTCCCAATGATGTCTTG
*
5809289 AAGGCTATGCGA-TATG-CCACAAAGCTTCATCAAATCTAGATGACCAATCTTTGTGGGTGGGAT
131 AAGGCTATGC-ACTATGCCCACAAAGCTTCATCAAATCTAGATGACCAATCCTTGTGGGTGGGAT
*
5809352 TGACCACTTTCTTCAAAATCTGCTTAATTTATCTATTCGAGATCTCAGCTTATCCATTTATTTAG
195 TGACCACTTTCTTCAAAATCTGCTTAATTTATCTATTCGAGACCTCAGCTTATCCATTTATTTAG
**
5809417 GGGTGATATGCCATGGCAATTTTATGTGTAACCCCATATCTATTCAAGGTAGTAGCAACTA
260 GGGTGATATGCCATGAAAATTTTATGTGTAACCCCATATCTATTCAAGGTAGTAGCAACTA
5809478 ATTT
1 ATTT
5809482 GCAATCAAAA
Statistics
Matches: 310, Mismatches: 12, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
319 169 0.55
320 140 0.45
321 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34
Consensus pattern (320 bp):
ATTTCCAGCACTAATTCAATCTATGTTCAATTTCTTAATTGCCCAAAATGCCTTATGTTCAAGTT
CAACAGGCAAATGGCAAGGCTTCTCGTAGATGAGCTTGAAAGGCAACATTCCCAATGATGTCTTG
AAGGCTATGCACTATGCCCACAAAGCTTCATCAAATCTAGATGACCAATCCTTGTGGGTGGGATT
GACCACTTTCTTCAAAATCTGCTTAATTTATCTATTCGAGACCTCAGCTTATCCATTTATTTAGG
GGTGATATGCCATGAAAATTTTATGTGTAACCCCATATCTATTCAAGGTAGTAGCAACTA
Found at i:5820624 original size:37 final size:36
Alignment explanation
Indices: 5820562--5820637 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
5820552 GATAGTCACT
*
5820562 TTAATATTTAATTAATAAAATACTATTAAGATAAGTA
1 TTAATATTTAATTAATAAAATACTATTAAAATAA-TA
*
5820599 TTAA-ATTTAATTTAATATTAA-ACTATTAAAATAATA
1 TTAATATTTAA-TTAATA-AAATACTATTAAAATAATA
5820635 TTA
1 TTA
5820638 TTTTTGGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
36 11 0.31
37 22 0.63
38 2 0.06
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (36 bp):
TTAATATTTAATTAATAAAATACTATTAAAATAATA
Found at i:5823596 original size:27 final size:28
Alignment explanation
Indices: 5823530--5823611 Score: 87
Period size: 28 Copynumber: 3.0 Consensus size: 28
5823520 TTTAGATAAA
*
5823530 AGTCCTAGTTGAAGTAGGATTCTTCTTG
1 AGTCCTAGTTGAAGTAGGATTCTTCATG
* * *
5823558 AGTCTTACTTGAAGTTGGATT-TTCAAT-
1 AGTCCTAGTTGAAGTAGGATTCTTC-ATG
* *
5823585 AGTCCTAGTTGAAGTAAGACTCTTCAT
1 AGTCCTAGTTGAAGTAGGATTCTTCAT
5823612 TCCTTGAGTT
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
27 21 0.49
28 22 0.51
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.39
Consensus pattern (28 bp):
AGTCCTAGTTGAAGTAGGATTCTTCATG
Found at i:5824425 original size:18 final size:17
Alignment explanation
Indices: 5824383--5824426 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
5824373 TATCGTTCGT
5824383 TTTCAAAATATTATTCA
1 TTTCAAAATATTATTCA
* *
5824400 TTTACAAATTGTTATTCAA
1 TTT-CAAAATATTATTC-A
5824419 TTTCAAAA
1 TTTCAAAA
5824427 CTTTTTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 3 0.14
18 15 0.68
19 4 0.18
ACGTcount: A:0.41, C:0.11, G:0.02, T:0.45
Consensus pattern (17 bp):
TTTCAAAATATTATTCA
Found at i:5827493 original size:16 final size:18
Alignment explanation
Indices: 5827467--5827500 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
5827457 TTTAATTAGA
5827467 TAAATTAATTTTC-CAAT
1 TAAATTAATTTTCTCAAT
5827484 TAAA-TAATTTTCTCAAT
1 TAAATTAATTTTCTCAAT
5827501 CCAATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:5836938 original size:69 final size:70
Alignment explanation
Indices: 5836811--5836940 Score: 201
Period size: 70 Copynumber: 1.9 Consensus size: 70
5836801 TTTAACAAAA
*
5836811 TTTTTTCTTTCATTTTCTCTCTTGCCAAACACCACTTTTTTTTCTTCAAAACACATGGTTGCTAC
1 TTTTTTCTTTCATTTTCTCTCTTGCCAAACACCACTTTTTCTTCTTCAAAACACATGGTTGCTAC
5836876 CATTT
66 CATTT
* * *
5836881 TTTTTTCTCTT-ATTTTCTTTCTTGCCAAACACCA-TTTTTCTTCTTCAAAAGATATGGTTG
1 TTTTTTCT-TTCATTTTCTCTCTTGCCAAACACCACTTTTTCTTCTTCAAAACACATGGTTG
5836941 GCTCATTTCA
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
69 23 0.42
70 30 0.55
71 2 0.04
ACGTcount: A:0.20, C:0.23, G:0.07, T:0.50
Consensus pattern (70 bp):
TTTTTTCTTTCATTTTCTCTCTTGCCAAACACCACTTTTTCTTCTTCAAAACACATGGTTGCTAC
CATTT
Found at i:5839146 original size:18 final size:18
Alignment explanation
Indices: 5839123--5839158 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
5839113 TATTTAACTT
5839123 GTTTAGTTTTTCTGGTAA
1 GTTTAGTTTTTCTGGTAA
5839141 GTTTAGTTTTTCTGGTAA
1 GTTTAGTTTTTCTGGTAA
5839159 AATTATTTGA
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:0.17, C:0.06, G:0.22, T:0.56
Consensus pattern (18 bp):
GTTTAGTTTTTCTGGTAA
Found at i:5842382 original size:40 final size:40
Alignment explanation
Indices: 5842282--5842546 Score: 286
Period size: 40 Copynumber: 6.7 Consensus size: 40
5842272 GCTCCTCGTT
* * * *
5842282 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* **
5842322 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
5842361 CGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
5842401 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
5842441 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
5842481 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
5842522 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
5842547 CAGCATTCAA
Statistics
Matches: 197, Mismatches: 22, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
39 39 0.20
40 143 0.73
41 15 0.08
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:5842506 original size:80 final size:80
Alignment explanation
Indices: 5842249--5842546 Score: 263
Period size: 80 Copynumber: 3.7 Consensus size: 80
5842239 AAATCACGTA
* ** * * *
5842249 CCTTCGGGATTTAA-CCGGATATAGCTC-CTCGTTCAAATGCCTTCGGGACATAGCCCGG-TTTT
1 CCTTCGGGACTTAACCCGGATATAG-TCACTCGCACAAA-GCCTTCGGGACTTAACCCGGAATTT
* *
5842311 AGTAACTCACAC-AATG
64 AATAACTCGCACAAATG
* * * *
5842327 CCTTCGGGACATAACCCGGATTTA-ACAACTCGCACGAATGCCTTCGGGACTTAACCCGG-ATTT
1 CCTTCGGGACTTAACCCGGATATAGTC-ACTCGCAC-AAAGCCTTCGGGACTTAACCCGGAATTT
*
5842390 AATAACTCGCACGAATG
64 AATAACTCGCACAAATG
* *
5842407 CCTTCGGGACTTAACCCGGATTTAGT-ATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGAATTT
1 CCTTCGGGACTTAACCCGGATATAGTCA-CTCGCACAAA-GCCTTCGGGACTTAACCCGGAATTT
* *
5842471 -GTATCTCGCACAAATG
64 AATAACTCGCACAAATG
** * * *
5842487 CCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 CCTTCGGGA-CTTAACCCGGATATAGTCAC-TCGCACAAAGCCTTCGGGACTTAACCCGGA
5842547 CAGCATTCAA
Statistics
Matches: 182, Mismatches: 26, Indels: 22
0.79 0.11 0.10
Matches are distributed among these distances:
77 1 0.01
78 12 0.07
79 50 0.27
80 106 0.58
81 13 0.07
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (80 bp):
CCTTCGGGACTTAACCCGGATATAGTCACTCGCACAAAGCCTTCGGGACTTAACCCGGAATTTAA
TAACTCGCACAAATG
Found at i:5842555 original size:41 final size:41
Alignment explanation
Indices: 5842478--5842555 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
5842468 TTTGTATCTC
* * *
5842478 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
5842519 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
5842556 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:5850369 original size:40 final size:40
Alignment explanation
Indices: 5850271--5850573 Score: 353
Period size: 40 Copynumber: 7.6 Consensus size: 40
5850261 TCCTCGTTCA
* * * * *
5850271 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
5850310 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
5850350 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
5850390 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
5850430 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * *
5850470 AAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGG-ATTTAATAACTCGCACG
* * * * *
5850510 AATGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
5850550 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
5850574 CAGCATTCAA
Statistics
Matches: 235, Mismatches: 23, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
39 39 0.17
40 184 0.78
41 12 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:5861958 original size:11 final size:11
Alignment explanation
Indices: 5861942--5861991 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
5861932 AAAACGAAAC
5861942 ACCACCATACA
1 ACCACCATACA
5861953 ACCACCATAGC-
1 ACCACCATA-CA
* * *
5861964 ACCACTACACT
1 ACCACCATACA
5861975 ACCACCATACA
1 ACCACCATACA
5861986 ACCACC
1 ACCACC
5861992 GTATCACCAC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
10 1 0.03
11 30 0.94
12 1 0.03
ACGTcount: A:0.40, C:0.48, G:0.02, T:0.10
Consensus pattern (11 bp):
ACCACCATACA
Found at i:5861968 original size:22 final size:21
Alignment explanation
Indices: 5861941--5862013 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 21
5861931 CAAAACGAAA
5861941 CACCACCATACAACCACCATAG
1 CACCACCATAC-ACCACCATAG
* *
5861963 CACCACTACACTACCACCATA-
1 CACCACCATAC-ACCACCATAG
* * *
5861984 CAACCACCGTATCACCACCCTTG
1 C-ACCACCATA-CACCACCATAG
5862007 CACCACC
1 CACCACC
5862014 TTGAAAACAG
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
21 1 0.03
22 37 0.93
23 2 0.05
ACGTcount: A:0.34, C:0.49, G:0.04, T:0.12
Consensus pattern (21 bp):
CACCACCATACACCACCATAG
Found at i:5876482 original size:41 final size:41
Alignment explanation
Indices: 5876398--5876475 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 41
5876388 TTCAAAAAAG
* **
5876398 TTTCAAAAACTCCAAAAATATTTTTTGTTTTGTTTTTAATT
1 TTTCAAAAACTCCAAAAATATTTTTTATTTCATTTTTAATT
5876439 TTTCAAAAA-TCCAAAAATATTTTTTATTTACATTTTT
1 TTTCAAAAACTCCAAAAATATTTTTTATTT-CATTTTT
5876476 TGTTTTTGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 19 0.58
41 14 0.42
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (41 bp):
TTTCAAAAACTCCAAAAATATTTTTTATTTCATTTTTAATT
Found at i:5882135 original size:23 final size:23
Alignment explanation
Indices: 5882109--5882153 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
5882099 GGATTTAAGA
5882109 AGGAAAGAAA-TATCTTTTGAAGT
1 AGGAAAGAAAGTA-CTTTTGAAGT
* *
5882132 AGGAGATAAAGTACTTTTGAAG
1 AGGAAAGAAAGTACTTTTGAAG
5882154 GTTTCTCCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.42, C:0.04, G:0.24, T:0.29
Consensus pattern (23 bp):
AGGAAAGAAAGTACTTTTGAAGT
Found at i:5885909 original size:12 final size:12
Alignment explanation
Indices: 5885892--5885921 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5885882 GTCAGGCTGT
5885892 ACACGGCCTAGC
1 ACACGGCCTAGC
*
5885904 ACACGGCCTGGC
1 ACACGGCCTAGC
5885916 ACACGG
1 ACACGG
5885922 GTGTGTGGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.40, G:0.30, T:0.07
Consensus pattern (12 bp):
ACACGGCCTAGC
Found at i:5889269 original size:39 final size:40
Alignment explanation
Indices: 5889224--5889408 Score: 160
Period size: 40 Copynumber: 4.7 Consensus size: 40
5889214 GCTCCTCGTT
* * * *
5889224 CAAATGCCTTCGGGACATAGCCCAGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
**
5889264 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
5889303 CGAATGCCTTCGGGACTTATCCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * * * * *
5889343 CAAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CATAACCCGGATTTAGTAAC-TCGCA
* *
5889384 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACATAACCCGGA
5889409 CAGCATTCAA
Statistics
Matches: 119, Mismatches: 22, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
39 36 0.30
40 72 0.61
41 11 0.09
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:5894565 original size:30 final size:30
Alignment explanation
Indices: 5894507--5894590 Score: 105
Period size: 30 Copynumber: 2.8 Consensus size: 30
5894497 CCTAAGACAT
* * **
5894507 GACCTGACCACACGGCTGTGTGGGTCACAC
1 GACCTGGCCACATGGCTGTGTGACTCACAC
* * *
5894537 GACTTGGCCATATGGTTGTGTGACTCACAC
1 GACCTGGCCACATGGCTGTGTGACTCACAC
5894567 GACCTGGCCACATGGCTGTGTGAC
1 GACCTGGCCACATGGCTGTGTGAC
5894591 CCCTACAGCT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.19, C:0.29, G:0.30, T:0.23
Consensus pattern (30 bp):
GACCTGGCCACATGGCTGTGTGACTCACAC
Found at i:5909437 original size:20 final size:19
Alignment explanation
Indices: 5909396--5909437 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
5909386 CCTTTCAAAT
*
5909396 TTTCTTATTTTCATTTGTA
1 TTTCTTATTTTCATTTGCA
5909415 TTTCATTATTTTCCA-TTGCA
1 TTTC-TTATTTT-CATTTGCA
5909435 TTT
1 TTT
5909438 ACTTTCTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 14 0.70
21 2 0.10
ACGTcount: A:0.17, C:0.14, G:0.05, T:0.64
Consensus pattern (19 bp):
TTTCTTATTTTCATTTGCA
Found at i:5910135 original size:25 final size:25
Alignment explanation
Indices: 5910078--5910221 Score: 121
Period size: 25 Copynumber: 5.8 Consensus size: 25
5910068 TCCTATACAT
* *
5910078 GTATGCTCATACGAGCTGT-GAATCG
1 GTATGCTCACACAAGCTGTAG-ATCG
* * *
5910103 GTATGCTCACACCAGCGGTAGATCA
1 GTATGCTCACACAAGCTGTAGATCG
* *
5910128 GTACGCTCACACAAGCTGTAAATCG
1 GTATGCTCACACAAGCTGTAGATCG
* *
5910153 GTATGCTCGCACGAGCTGTAGATCG
1 GTATGCTCACACAAGCTGTAGATCG
* * * * *
5910178 GTATGCTCTCACGAGCTATA-AACTT
1 GTATGCTCACACAAGCTGTAGATC-G
*
5910203 GTATGCTCACACGAGCTGT
1 GTATGCTCACACAAGCTGT
5910222 GGAGTATCCG
Statistics
Matches: 98, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
24 2 0.02
25 95 0.97
26 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.24, T:0.25
Consensus pattern (25 bp):
GTATGCTCACACAAGCTGTAGATCG
Found at i:5910157 original size:50 final size:50
Alignment explanation
Indices: 5910082--5910214 Score: 151
Period size: 50 Copynumber: 2.7 Consensus size: 50
5910072 ATACATGTAT
* *
5910082 GCTCATACGAGCTGTGAATCGGTATGCTCACACCAGCGGTAGATCAGTAC
1 GCTCACACGAGCTGTAAATCGGTATGCTCACACCAGCGGTAGATCAGTAC
* * * * * *
5910132 GCTCACACAAGCTGTAAATCGGTATGCTCGCACGAGCTGTAGATCGGTAT
1 GCTCACACGAGCTGTAAATCGGTATGCTCACACCAGCGGTAGATCAGTAC
* * *
5910182 GCTCTCACGAGCTATAAA-CTTGTATGCTCACAC
1 GCTCACACGAGCTGTAAATC-GGTATGCTCACAC
5910215 GAGCTGTGGA
Statistics
Matches: 69, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
49 1 0.01
50 68 0.99
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.24
Consensus pattern (50 bp):
GCTCACACGAGCTGTAAATCGGTATGCTCACACCAGCGGTAGATCAGTAC
Found at i:5914696 original size:22 final size:22
Alignment explanation
Indices: 5914671--5914715 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
5914661 ATATAAGTTG
*
5914671 ATTAACCATTTAA-TTAAGCTTA
1 ATTAACC-TTTAATTTAACCTTA
5914693 ATTAACCTTTAATTTAACCTTA
1 ATTAACCTTTAATTTAACCTTA
5914715 A
1 A
5914716 AACATGATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.40, C:0.16, G:0.02, T:0.42
Consensus pattern (22 bp):
ATTAACCTTTAATTTAACCTTA
Found at i:5914711 original size:12 final size:11
Alignment explanation
Indices: 5914671--5914713 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
5914661 ATATAAGTTG
5914671 ATTAACCATTTA
1 ATTAACC-TTTA
*
5914683 ATTAAGC-TTA
1 ATTAACCTTTA
5914693 ATTAACCTTTA
1 ATTAACCTTTA
5914704 ATTTAACCTT
1 A-TTAACCTT
5914714 AAAACATGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 9 0.33
11 4 0.15
12 14 0.52
ACGTcount: A:0.37, C:0.16, G:0.02, T:0.44
Consensus pattern (11 bp):
ATTAACCTTTA
Found at i:5919450 original size:13 final size:13
Alignment explanation
Indices: 5919434--5919460 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5919424 TGTTATTGAT
5919434 TCAATCTATTATG
1 TCAATCTATTATG
5919447 TCAATCTATTATG
1 TCAATCTATTATG
5919460 T
1 T
5919461 ATTGAATTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.48
Consensus pattern (13 bp):
TCAATCTATTATG
Found at i:5921753 original size:21 final size:20
Alignment explanation
Indices: 5921714--5921753 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
5921704 ATTGTCCAAT
* *
5921714 TTTTGCTCCATTTTTTCTCG
1 TTTTGCTCCAATTTCTCTCG
5921734 TTTTGCTCCCAATTTCTCTC
1 TTTTGCT-CCAATTTCTCTC
5921754 CTAAGTATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.07, C:0.30, G:0.07, T:0.55
Consensus pattern (20 bp):
TTTTGCTCCAATTTCTCTCG
Found at i:5924712 original size:20 final size:20
Alignment explanation
Indices: 5924689--5924762 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
5924679 AAACATAATA
5924689 AAAAAAACTCTAATAAAATT
1 AAAAAAACTCTAATAAAATT
5924709 AAAATACAACTGCTAAAATGAAACATAAT
1 AAAA-A-AACT-CT--AAT-AAA-AT--T
5924738 AAAAAAAACTCTAATAAAATT
1 -AAAAAAACTCTAATAAAATT
5924759 AAAA
1 AAAA
5924763 TGCAACTGCT
Statistics
Matches: 44, Mismatches: 0, Indels: 20
0.69 0.00 0.31
Matches are distributed among these distances:
20 8 0.18
21 2 0.05
22 4 0.09
23 4 0.09
24 3 0.07
25 6 0.14
26 3 0.07
27 4 0.09
28 4 0.09
29 2 0.05
30 4 0.09
ACGTcount: A:0.65, C:0.11, G:0.03, T:0.22
Consensus pattern (20 bp):
AAAAAAACTCTAATAAAATT
Found at i:5924748 original size:50 final size:50
Alignment explanation
Indices: 5924673--5924777 Score: 201
Period size: 50 Copynumber: 2.1 Consensus size: 50
5924663 AGGAAAAACA
5924673 AAAATGAAACATAATAAAAAAAACTCTAATAAAATTAAAATACAACTGCT
1 AAAATGAAACATAATAAAAAAAACTCTAATAAAATTAAAATACAACTGCT
*
5924723 AAAATGAAACATAATAAAAAAAACTCTAATAAAATTAAAATGCAACTGCT
1 AAAATGAAACATAATAAAAAAAACTCTAATAAAATTAAAATACAACTGCT
5924773 AAAAT
1 AAAAT
5924778 ATTAATAATA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.62, C:0.11, G:0.05, T:0.22
Consensus pattern (50 bp):
AAAATGAAACATAATAAAAAAAACTCTAATAAAATTAAAATACAACTGCT
Found at i:5924948 original size:5 final size:5
Alignment explanation
Indices: 5924934--5924976 Score: 50
Period size: 5 Copynumber: 8.2 Consensus size: 5
5924924 CAGTAATAAT
* *
5924934 AAATA TAATA AAATA TAATA AAATA ATAAGTA AAATA AAATA A
1 AAATA AAATA AAATA AAATA AAATA A-AA-TA AAATA AAATA A
5924977 GAGAGGAGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
5 25 0.78
6 4 0.12
7 3 0.09
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (5 bp):
AAATA
Found at i:5924949 original size:10 final size:10
Alignment explanation
Indices: 5924929--5924976 Score: 62
Period size: 10 Copynumber: 4.7 Consensus size: 10
5924919 AATAACAGTA
5924929 ATAAT-AAAT
1 ATAATAAAAT
5924938 ATAATAAAAT
1 ATAATAAAAT
5924948 ATAATAAAAT
1 ATAATAAAAT
5924958 AATAAGTAAAAT
1 -ATAA-TAAAAT
*
5924970 AAAATAA
1 ATAATAA
5924977 GAGAGGAGGA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
9 5 0.14
10 17 0.49
11 7 0.20
12 6 0.17
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (10 bp):
ATAATAAAAT
Found at i:5926041 original size:24 final size:21
Alignment explanation
Indices: 5926009--5926056 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 21
5925999 TTTAAGGTTT
5926009 TAAAAAAATCAAAGTGAATAAAAA
1 TAAAAAAAT-AAA-T-AATAAAAA
*
5926033 TAAAAAAATAAATAATAATAA
1 TAAAAAAATAAATAATAAAAA
5926054 TAA
1 TAA
5926057 TAACACTCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 10 0.43
22 1 0.04
23 3 0.13
24 9 0.39
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (21 bp):
TAAAAAAATAAATAATAAAAA
Found at i:5926872 original size:46 final size:46
Alignment explanation
Indices: 5926819--5926914 Score: 165
Period size: 46 Copynumber: 2.1 Consensus size: 46
5926809 ACTCGCTAAC
*
5926819 TGAATACTCATCCTAGTGGGTTTGGGTTTCCCAAGACCAAGTTTTT
1 TGAATACTCATCCTAGTGGGTTTGGGTTTCCCAAGACCAAGTTGTT
**
5926865 TGAATACTCATCCTAGTGGGTTTGGGTTTTTCAAGACCAAGTTGTT
1 TGAATACTCATCCTAGTGGGTTTGGGTTTCCCAAGACCAAGTTGTT
5926911 TGAA
1 TGAA
5926915 CATCTTATAA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.38
Consensus pattern (46 bp):
TGAATACTCATCCTAGTGGGTTTGGGTTTCCCAAGACCAAGTTGTT
Found at i:5928781 original size:20 final size:20
Alignment explanation
Indices: 5928745--5928787 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
5928735 CGAAAATATT
* *
5928745 AAAATATAAAAATTAAATTA
1 AAAATATAAAAAATAAAATA
5928765 AAAATA-AATAAAATAAAATA
1 AAAATATAA-AAAATAAAATA
5928785 AAA
1 AAA
5928788 TAATGGTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (20 bp):
AAAATATAAAAAATAAAATA
Found at i:5930308 original size:21 final size:21
Alignment explanation
Indices: 5930256--5930308 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
5930246 ATTATCTTGG
*
5930256 AAAAATATTTAAAAACTTAATT
1 AAAAATATTTTAAAACTT-ATT
*
5930278 TAAAAT-TTTTAAAACTT-TT
1 AAAAATATTTTAAAACTTATT
5930297 AAATAATATTTT
1 AAA-AATATTTT
5930309 TTTTTGTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 4 0.15
20 3 0.12
21 14 0.54
22 5 0.19
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (21 bp):
AAAAATATTTTAAAACTTATT
Found at i:5930429 original size:9 final size:9
Alignment explanation
Indices: 5930415--5930495 Score: 54
Period size: 10 Copynumber: 8.4 Consensus size: 9
5930405 TAGACGTGAT
5930415 TTTTAATAA
1 TTTTAATAA
*
5930424 TTTTAAATAT
1 TTTT-AATAA
** *
5930434 TTTTGTTAT
1 TTTTAATAA
5930443 TCTTTAATAA
1 T-TTTAATAA
*
5930453 ATTTAATAA
1 TTTTAATAA
*
5930462 TTTCTTATAA
1 TTT-TAATAA
*
5930472 TTTCTTATAA
1 TTT-TAATAA
5930482 TTATTAATAA
1 TT-TTAATAA
5930492 TTTT
1 TTTT
5930496 TAAATATTTT
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
9 20 0.34
10 37 0.64
11 1 0.02
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (9 bp):
TTTTAATAA
Found at i:5930864 original size:15 final size:15
Alignment explanation
Indices: 5930844--5930873 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5930834 CCAAATATAC
5930844 AAATTCAACATTCAA
1 AAATTCAACATTCAA
5930859 AAATTCAACATTCAA
1 AAATTCAACATTCAA
5930874 TATGGTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.20, G:0.00, T:0.27
Consensus pattern (15 bp):
AAATTCAACATTCAA
Found at i:5931060 original size:33 final size:34
Alignment explanation
Indices: 5931018--5931083 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
5931008 ACCAAAGTAC
*
5931018 CAATACAAGT-AAAAAAATTGAGCAGTGATGTAT
1 CAATACAAGTAAAAAAAATTGAACAGTGATGTAT
5931051 CAATACAAGTAAAAAAAATTGAACAGTGATGTA
1 CAATACAAGTAAAAAAAATTGAACAGTGATGTA
5931084 ACACCCCTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 10 0.32
34 21 0.68
ACGTcount: A:0.52, C:0.09, G:0.17, T:0.23
Consensus pattern (34 bp):
CAATACAAGTAAAAAAAATTGAACAGTGATGTAT
Found at i:5940494 original size:5 final size:5
Alignment explanation
Indices: 5940484--5940508 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5940474 TTCCCATCAC
5940484 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
5940509 CTAACTTCTA
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):
AAAAT
Found at i:5947243 original size:27 final size:26
Alignment explanation
Indices: 5947212--5947266 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
5947202 AATCGAATTA
*
5947212 AATTTTATTTTTATT-TAATATATAAAT
1 AATTTAATTTTT-TTATAATATA-AAAT
5947239 AATTTAATTTTTTTATAATATAAAAT
1 AATTTAATTTTTTTATAATATAAAAT
5947265 AA
1 AA
5947267 ATATTTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
AATTTAATTTTTTTATAATATAAAAT
Found at i:5948228 original size:18 final size:19
Alignment explanation
Indices: 5948193--5948228 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
5948183 TTGCTTGCTG
*
5948193 GAAATGAAAAAGCAAAAAT
1 GAAATGAAAAAGAAAAAAT
5948212 GAAA-GAAAAAGAAAAAA
1 GAAATGAAAAAGAAAAAA
5948229 GGTGAAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.75, C:0.03, G:0.17, T:0.06
Consensus pattern (19 bp):
GAAATGAAAAAGAAAAAAT
Found at i:5951102 original size:38 final size:35
Alignment explanation
Indices: 5951051--5951126 Score: 91
Period size: 38 Copynumber: 2.1 Consensus size: 35
5951041 AATTGTTAAA
*
5951051 AAAATACTGAAAATC-CTAAAAGAAATTATTAAAAAACT
1 AAAATACTCAAAATCAC-AAAA-AAATTA-TAAAAAA-T
*
5951089 AAAATATTCAAAATCACAAAAAAATTATAAAAAAT
1 AAAATACTCAAAATCACAAAAAAATTATAAAAAAT
5951124 AAA
1 AAA
5951127 TAAAAATGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
35 4 0.11
36 7 0.20
37 6 0.17
38 17 0.49
39 1 0.03
ACGTcount: A:0.66, C:0.09, G:0.03, T:0.22
Consensus pattern (35 bp):
AAAATACTCAAAATCACAAAAAAATTATAAAAAAT
Found at i:5951913 original size:12 final size:11
Alignment explanation
Indices: 5951867--5951915 Score: 59
Period size: 12 Copynumber: 4.5 Consensus size: 11
5951857 TTATAATTTT
5951867 AATTTTTTATA
1 AATTTTTTATA
5951878 AATTTTTTTATA
1 AA-TTTTTTATA
5951890 AA-TTTTT-T-
1 AATTTTTTATA
5951898 AATTTTTTAATA
1 AATTTTTT-ATA
5951910 AATTTT
1 AATTTT
5951916 AAATTTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
8 2 0.06
9 6 0.18
10 5 0.15
11 3 0.09
12 17 0.52
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
AATTTTTTATA
Found at i:5951920 original size:19 final size:20
Alignment explanation
Indices: 5951871--5951922 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
5951861 AATTTTAATT
*
5951871 TTTTATAAATTTTTTTATAAA
1 TTTT-TAAATTTTTTAATAAA
*
5951892 TTTTTTAATTTTTTAATAAA
1 TTTTTAAATTTTTTAATAAA
5951912 -TTTTAAATTTT
1 TTTTTAAATTTT
5951923 AAAAGGACTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 10 0.36
20 14 0.50
21 4 0.14
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTTAAATTTTTTAATAAA
Found at i:5954353 original size:20 final size:20
Alignment explanation
Indices: 5954310--5954371 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 20
5954300 TTTTGATGTG
* *
5954310 TTAAAATGATTTTAACTTAA
1 TTAAAATAATTTTAACTTGA
* * *
5954330 TTAAGATCATTTTAACTTGG
1 TTAAAATAATTTTAACTTGA
*
5954350 TTAAAATAATTTTCACTTGA
1 TTAAAATAATTTTAACTTGA
5954370 TT
1 TT
5954372 TTAAAATTGT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (20 bp):
TTAAAATAATTTTAACTTGA
Found at i:5959285 original size:34 final size:34
Alignment explanation
Indices: 5959247--5959317 Score: 81
Period size: 34 Copynumber: 2.1 Consensus size: 34
5959237 TTTGTTATAA
* *
5959247 AATTTGGAAAT-TATTTATAAATATTATTATTTTT
1 AATTTAGAAATAT-TTTATAAATATTATTATATTT
* * *
5959281 AATTTATAAATATTTTGTATATATTATTATATTT
1 AATTTAGAAATATTTTATAAATATTATTATATTT
5959315 AAT
1 AAT
5959318 AAGATGTATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
34 30 0.97
35 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.56
Consensus pattern (34 bp):
AATTTAGAAATATTTTATAAATATTATTATATTT
Done.