Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A02
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: 100057689
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3589301 characters in sequence are not A, C, G, or T
File 19 of 295
Found at i:5372243 original size:39 final size:39
Alignment explanation
Indices: 5372200--5372325 Score: 189
Period size: 39 Copynumber: 3.2 Consensus size: 39
5372190 GGACTTTAGC
* * * * *
5372200 CCGGACATATTTCCAGCACGTAGCTTGCGGACCTTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
*
5372239 CCGGATATAATTCCAACACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
*
5372278 CTGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
5372317 CCGGATATA
1 CCGGATATA
5372326 CATCACTGAA
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 78 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.23
Consensus pattern (39 bp):
CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
Found at i:5376356 original size:22 final size:22
Alignment explanation
Indices: 5376331--5376372 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5376321 ATATAAGTAC
* *
5376331 AATAACAATAATGGTAATAAAA
1 AATAAAAATAATAGTAATAAAA
5376353 AATAAAAATAATAGTAATAA
1 AATAAAAATAATAGTAATAA
5376373 TAGCACATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.24
Consensus pattern (22 bp):
AATAAAAATAATAGTAATAAAA
Found at i:5377276 original size:21 final size:20
Alignment explanation
Indices: 5377252--5377303 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
5377242 AGCAAATTCG
5377252 AAAATAAAATAAAAAGGAAAA
1 AAAATAAAATAAAAA-GAAAA
* *
5377273 AAAAT--AATAAATAGAAAG
1 AAAATAAAATAAAAAGAAAA
5377291 AAAATAATAATAA
1 AAAATAA-AATAA
5377304 TGTAATATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 9 0.35
19 7 0.27
21 10 0.38
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (20 bp):
AAAATAAAATAAAAAGAAAA
Found at i:5377289 original size:18 final size:17
Alignment explanation
Indices: 5377251--5377300 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
5377241 AAGCAAATTC
*
5377251 GAAAATAAAATAA-AAAG
1 GAAAA-AAAATAATAAAA
5377268 GAAAAAAAATAATAAATA
1 GAAAAAAAATAATAAA-A
*
5377286 GAAAGAAAATAATAA
1 GAAAAAAAATAATAA
5377301 TAATGTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 7 0.24
17 8 0.28
18 14 0.48
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.14
Consensus pattern (17 bp):
GAAAAAAAATAATAAAA
Found at i:5378461 original size:29 final size:27
Alignment explanation
Indices: 5378412--5378468 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 27
5378402 TTATTTAAGT
*
5378412 AATAATATTAACAATAAAGAAATGAAATA
1 AATAATATAAACAATAAAG-AAT-AAATA
**
5378441 AATAATATAAACAATTTAGAATAAATA
1 AATAATATAAACAATAAAGAATAAATA
5378468 A
1 A
5378469 TAAGACAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 6 0.24
28 3 0.12
29 16 0.64
ACGTcount: A:0.65, C:0.04, G:0.05, T:0.26
Consensus pattern (27 bp):
AATAATATAAACAATAAAGAATAAATA
Found at i:5378479 original size:22 final size:23
Alignment explanation
Indices: 5378436--5378492 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 23
5378426 TAAAGAAATG
5378436 AAATAAATAATATAAACAA-TTT
1 AAATAAATAATATAAACAATTTT
*
5378458 AGAATAAATAATA-AGACAATTTT
1 A-AATAAATAATATAAACAATTTT
*
5378481 AAACAAATAATA
1 AAATAAATAATA
5378493 CATAAAAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 16 0.52
23 15 0.48
ACGTcount: A:0.63, C:0.05, G:0.04, T:0.28
Consensus pattern (23 bp):
AAATAAATAATATAAACAATTTT
Found at i:5378596 original size:27 final size:27
Alignment explanation
Indices: 5378554--5378633 Score: 101
Period size: 27 Copynumber: 3.0 Consensus size: 27
5378544 ATAAATTTAA
*
5378554 AAAATAATATACAAAACAATTTAAAAT
1 AAAATAATATATAAAACAATTTAAAAT
*
5378581 AAAATAATATATAAAACAATCTAAAAT
1 AAAATAATATATAAAACAATTTAAAAT
* *
5378608 -TACTAA-ATTATAAAACAATTTAAAAT
1 AAAATAATA-TATAAAACAATTTAAAAT
5378634 TACATATAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
25 1 0.02
26 21 0.45
27 25 0.53
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (27 bp):
AAAATAATATATAAAACAATTTAAAAT
Found at i:5378949 original size:26 final size:26
Alignment explanation
Indices: 5378869--5378949 Score: 74
Period size: 26 Copynumber: 3.0 Consensus size: 26
5378859 AAAAATGTAA
* *
5378869 AAACTTAAAATATATAATAATAAAAT
1 AAACTTAAAATAAATAATAATAAAAC
* ** *
5378895 GATTTTAAAATGAATAAT-ATAAGCAAAC
1 AAACTTAAAATAAATAATAAT-A--AAAC
5378923 AAACTTAAAATAAATAATAATAAAAC
1 AAACTTAAAATAAATAATAATAAAAC
5378949 A
1 A
5378950 GTCCCTAAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
25 2 0.05
26 19 0.46
28 18 0.44
29 2 0.05
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.27
Consensus pattern (26 bp):
AAACTTAAAATAAATAATAATAAAAC
Found at i:5379870 original size:18 final size:18
Alignment explanation
Indices: 5379828--5379870 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
5379818 TTGTATTTAA
5379828 AAAAAAATAAAAGCAAAC
1 AAAAAAATAAAAGCAAAC
*
5379846 AAGAAAATGAAAAG-AAAC
1 AAAAAAAT-AAAAGCAAAC
5379864 AAAAAAA
1 AAAAAAA
5379871 GATCAAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.79, C:0.07, G:0.09, T:0.05
Consensus pattern (18 bp):
AAAAAAATAAAAGCAAAC
Found at i:5381230 original size:26 final size:26
Alignment explanation
Indices: 5381201--5381308 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
5381191 TGGTACAAAT
5381201 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
5381227 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
5381253 TGATAATGGGTTAAGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
5381279 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
5381305 TGAT
1 TGAT
5381309 GGGCATTTCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:5388284 original size:26 final size:26
Alignment explanation
Indices: 5388255--5388362 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
5388245 TGGTACAAAT
5388255 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
5388281 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
5388307 TGATAATGGGTTAAGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
5388333 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
5388359 TGAT
1 TGAT
5388363 GGGCATTTCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:5390863 original size:21 final size:22
Alignment explanation
Indices: 5390837--5390889 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
5390827 ATATAGCTAA
5390837 ATATAATATAA-TAATAACAAT
1 ATATAATATAATTAATAACAAT
* *
5390858 ATATAAAATAATTGATAACAAT
1 ATATAATATAATTAATAACAAT
5390880 AT-TACATATA
1 ATATA-ATATA
5390890 TAACATGATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.34
Consensus pattern (22 bp):
ATATAATATAATTAATAACAAT
Found at i:5391692 original size:18 final size:18
Alignment explanation
Indices: 5391669--5391719 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 18
5391659 AGGGTTTCTT
5391669 GGTTTTTTTTTTGGGTTA
1 GGTTTTTTTTTTGGGTTA
5391687 GGTTTTTCTTTTTTTTTGGGTTA
1 GG----T-TTTTTTTTTGGGTTA
5391710 GGTTTTTTTT
1 GGTTTTTTTT
5391720 GGGGGGGCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
18 9 0.32
19 1 0.04
22 1 0.04
23 17 0.61
ACGTcount: A:0.04, C:0.02, G:0.24, T:0.71
Consensus pattern (18 bp):
GGTTTTTTTTTTGGGTTA
Found at i:5391702 original size:23 final size:23
Alignment explanation
Indices: 5391672--5391716 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
5391662 GTTTCTTGGT
5391672 TTTTTTTTTGGGTTAGGTTTTTC
1 TTTTTTTTTGGGTTAGGTTTTTC
5391695 TTTTTTTTTGGGTTAGGTTTTT
1 TTTTTTTTTGGGTTAGGTTTTT
5391717 TTTGGGGGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.04, C:0.02, G:0.22, T:0.71
Consensus pattern (23 bp):
TTTTTTTTTGGGTTAGGTTTTTC
Found at i:5392795 original size:72 final size:72
Alignment explanation
Indices: 5392587--5395308 Score: 1262
Period size: 72 Copynumber: 35.7 Consensus size: 72
5392577 GTGATCTAAA
** * * *
5392587 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGAAAGAAATTGAAAATACCTCAGC
1 GCTCAACTCATTTCTCGCAATATGAGTTGA--ATTTTGAAA-ACAGAAATTGAAATTACCTCA--
* * *
5392652 ATGTGAAC-CGAG
61 ACGTG-TCTTGAG
** * * *
5392664 GCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTGAAAACAGAAATTGAAAATACCTCAACG
1 GCTCAACTCATTTCTCGCAATATGAGTTGA--ATTTTGAAAACAGAAATTGAAATTACCTCAACG
5392729 TGTCTTGAG
64 TGTCTTGAG
* *
5392738 GCTCAACTTATTTCTCGCAATATGAGTTAAATTTTGAAAACAGAAATTGAAATTACCTCAACGTG
1 GCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTG
*
5392803 TCTTAAG
66 TCTTGAG
* * * *
5392810 GTTCAACTCATTTCTCGCAATATGGGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAGCTTG
1 GCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTG
5392875 TCTTGAG
66 TCTTGAG
* *
5392882 GCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAG--ATTGAAATTACCTTAGCGTG
1 GCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTG
** *
5392945 TCCCGGG
66 TCTTGAG
* * * *
5392952 GCTCAACTCACCTT-TCGCAATATAAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCAGCGT
1 GCTCAACTCA-TTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGT
**
5393016 GTCCCGAG
65 GTCTTGAG
** * * * *
5393024 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTGAAAAAAAAATACCTC
1 GCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG-AAAACAGAAATTG-----AAATTACCTC
** * *
5393089 AGTGTGTGATCTGAA
60 AACGTGT-CT-TGAG
** *
5393104 GCTCAACTCACCTCTCGCAATATGAGTT-AATTTTTTTTGAAAGACAGAAATTGAAAATACCTCA
1 GCTCAACTCATTTCTCGCAATATGAGTTGAA----TTTTGAAA-ACAGAAATTGAAATTACCTCA
* * *
5393168 GCATGTGAAC-CGAG
61 --ACGTG-TCTTGAG
* * * *
5393182 GCTCAACTCACTTCTCGCAATATAAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAACGT
1 GCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTGAAAACAGAAATTGAAATTACCTCAACGT
5393247 GTCTTGAG
65 GTCTTGAG
5393255 GCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTG
1 GCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTG
5393320 TCTTGAG
66 TCTTGAG
* * *
5393327 GTTCAACTCATTTATCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAGCGTG
1 GCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTG
5393392 TCTTGAG
66 TCTTGAG
*
5393399 GCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAG--ATTGAAATTACCTCAGCGTG
1 GCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTG
**
5393462 TCCCGAG
66 TCTTGAG
* * * *
5393469 G-------C---TCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTGAAAGAAATACCTCAG
1 GCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG-AAAACAGAAATTG--A-AATTACCTCA-
* *
5393524 TATGTGATC-TGAA
61 -ACGTG-TCTTGAG
** * * *
5393537 GCTCAACTCACCTCTCGCAATATGAGTT-AATTTTTTTTTTGAAAGACAAAAATTGAAAATAGCT
1 GCTCAACTCATTTCTCGCAATATGAGTTGAA------TTTTGAAA-ACAGAAATTGAAATTACCT
* * **
5393601 CAGCGCGTGAGC-CAAG
59 CA--ACGTG-TCTTGAG
** * ** * ** ** *
5393617 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAACTTAACTTGAAAAGCAGATTTTGAA
1 GCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTG-AAA--TTA-CCTCAA
** * *
5393681 AATACCTCGATATGTG
62 CGT--GTC--T-TGAG
* * * * * *
5393697 ACTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTGAAAAAAAT
1 GCTCAA--CTC-A-T---TTCTCGCAATATGAGTTGAATTTTG-AAAACAGAAATTG---AAATT
** * *
5393762 ACCTCAGTGTGTGATCTGAA
55 ACCTCAACGTGT-CT-TGAG
* ** * * *
5393782 GCTCAACTTACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAA-AACGGAAAT
1 GCTCAACTCATTTCTCGCAATATGAGTTGA--ATTTTGAAA-ACAGAAATTGAAATTAC-----C
* * *
5393846 TGAAAATACCTCGGCGTGTGA-
58 T---CA-ACGT-GTC-T-TGAG
* * * ** * * *
5393867 CCTGAGGCTCAACTCGCCGCTCGCAATACGAGTTGATTTTTTTGACAACAGAAATTGAAATTACC
1 GCTCA-ACTC-A-T---TTCTCGCAATATGAGTTGA--ATTTTGAAAACAGAAATTGAAATTACC
*
5393932 TCAACGTGTCCTGAG
58 TCAACGTGTCTTGAG
** * * * * * *
5393947 GCTCAACTCACCTCTCACAATATGAGTTGATTTTTTTGAAAGGCAGGAATTGAAA-AACGGAAAT
1 GCTCAACTCATTTCTCGCAATATGAGTTGA--ATTTTGAAA-ACAGAAATTGAAATTAC-----C
* * *
5394011 TGAAAATACCTCGGCGTGTGA-
58 T---CA-ACGT-GTC-T-TGAG
* * * * * * *
5394032 CCTGAGGCTCAACTCGCCTCTCGCAATACGAGTTGATTTTTTTGACAACAGAAATTGAAATTACC
1 GCTCA-ACTC-A-T---TTCTCGCAATATGAGTTGA--ATTTTGAAAACAGAAATTGAAATTACC
* *
5394097 TCAGCGTGTCCTGAG
58 TCAACGTGTCTTGAG
* * * * *
5394112 GCTCAACTCACTTCTCGTAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATAGCTCAAC
1 GCTCAACTCATTTCTCGCAATATGAGTTGA--ATTTTGAAA-ACAGAAATTGAAATTACCTCAA-
* **
5394177 GCGTGAGC-CAAG
62 -CGTG-TCTTGAG
** * * * * * *
5394189 GCTCAACTCACCTCTCGCAATATGAGTCGATTTTTTTTAAAGCCAGAAATTGAAA-AACGGAAAT
1 GCTCAACTCATTTCTCGCAATATGAGTTGA--ATTTTGAAA-ACAGAAATTGAAATTAC-----C
* * *
5394253 TGAAAATACCTCGGCGTGTGA-
58 T---CA-ACGT-GTC-T-TGAG
* * * * * * * *
5394274 CCTGAGGCTCAACTCGCCTGTCGCAATACGAGTTGATTTTTTTGACAACAGAAATTGAAATTACC
1 GCTCA-ACTC-A-T---TTCTCGCAATATGAGTTGA--ATTTTGAAAACAGAAATTGAAATTACC
* *
5394339 TCAGCGTGTCCTGAG
58 TCAACGTGTCTTGAG
** * * * * *
5394354 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGAAAGAAATTGAAAATAGCTTAGC
1 GCTCAACTCATTTCTCGCAATATGAGTTGA--ATTTTGAAA-ACAGAAATTGAAATTACCTCA--
* * **
5394419 GCGTGAGC-CAAG
61 ACGTG-TCTTGAG
** *** * *
5394431 GCTCAACTCACCTCTCGCAATATGAGCCGATTTTTTTTTGAAAGGCATAAATTGAAAAAAGGAAA
1 GCTCAACTCATTTCTCGCAATATGA---G-TTGAATTTTGAAA-ACAGAAATT--------GAAA
** * *
5394496 TTGAAAAT-ACCTTGGCGTGTGACCTGAG
53 TT--ACCTCAAC-----GTGT--CTTGAG
**** * * *
5394524 GCTCAACTCGCCGCTCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCTCAGCG
1 GCTCAACTCATTTCTCGCAATATGAGTTGA--ATTTTGAAAACAGAAATTGAAATTACCTCAACG
*
5394589 TGTGACCTGAG
64 TGT--CTTGAG
* ** * * * *
5394600 GCTCAACTCGTCGCTCGCAATACGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCTCAGCG
1 GCTCAACTCATTTCTCGCAATATGAGTTGA--ATTTTGAAAACAGAAATTGAAATTACCTCAACG
*
5394665 TGTCCTGAG
64 TGTCTTGAG
** * * * *
5394674 GCTCAACTCACCTCTCGAAATATGAGTTGATTTTTGAAAATAGAAATTGAAATTACCTCAGCGTG
1 GCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTG
**
5394739 TCCCGAG
66 TCTTGAG
* ** * * * * *
5394746 ACTCAACTCACCTCTCGCAATATGATTTGATTTTTTTGAAAAACAAAAATTGAAAATACCTCAGC
1 GCTCAACTCATTTCTCGCAATATGAGTTGA--ATTTTG-AAAACAGAAATTGAAATTACCTCAAC
*
5394811 ATGTCTTGAG
63 GTGTCTTGAG
*
5394821 GCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAGCGTG
1 GCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTG
*
5394886 TCCTGAG
66 TCTTGAG
* *
5394893 GCTCAACTCATTTCTCGCAATATGAGTT-AATTTTTTTTAACAACAGAAATTGAAATTACCTCAG
1 GCTCAACTCATTTCTCGCAATATGAGTTGAA---TTTTGAA-AACAGAAATTGAAATTACCTCAA
* *
5394957 TGTGTCCTGAG
62 CGTGTCTTGAG
** * * * *
5394968 GCTCAACTCACCTCTCGCAGTATGAGTTGATTTTTTTGAAAGACAAAAATTGAAAATACCTCAAC
1 GCTCAACTCATTTCTCGCAATATGAGTTGA--ATTTTGAAA-ACAGAAATTGAAATTACCTCAAC
5395033 GTGTCTTGAG
63 GTGTCTTGAG
* *
5395043 GCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCAGCGTG
1 GCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTG
** *
5395108 TCCCGAA
66 TCTTGAG
** * *
5395115 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCAGCGTG
1 GCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTG
**
5395180 TCCCGAG
66 TCTTGAG
* * * * *
5395187 GCTCAACTCATCTCTCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCTTAGCG
1 GCTCAACTCATTTCTCGCAATATGAGTTGA--ATTTTGAAAACAGAAATTGAAATTACCTCAACG
5395252 TGTCTTGAG
64 TGTCTTGAG
** * *
5395261 GCTCAACTCACCTCTCGCAGTATGAGTTGATTTTTTTG-AAACAGAAAT
1 GCTCAACTCATTTCTCGCAATATGAGTTGA--ATTTTGAAAACAGAAAT
5395309 AAAACATCAA
Statistics
Matches: 2142, Mismatches: 320, Indels: 370
0.76 0.11 0.13
Matches are distributed among these distances:
60 23 0.01
61 5 0.00
63 5 0.00
65 1 0.00
66 9 0.00
68 6 0.00
69 2 0.00
70 85 0.04
71 6 0.00
72 602 0.28
73 76 0.04
74 236 0.11
75 250 0.12
76 113 0.05
77 134 0.06
78 94 0.04
79 40 0.02
80 110 0.05
81 14 0.01
82 24 0.01
83 39 0.02
84 5 0.00
85 19 0.01
86 22 0.01
87 33 0.02
88 4 0.00
89 15 0.01
90 44 0.02
91 100 0.05
92 1 0.00
93 25 0.01
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (72 bp):
GCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTG
TCTTGAG
Found at i:5393836 original size:14 final size:14
Alignment explanation
Indices: 5393817--5393851 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
5393807 GTTGATTTTT
*
5393817 TTGAAAGACAGAAA
1 TTGAAAAACAGAAA
*
5393831 TTGAAAAACGGAAA
1 TTGAAAAACAGAAA
5393845 TTGAAAA
1 TTGAAAA
5393852 TACCTCGGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.57, C:0.06, G:0.20, T:0.17
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:5393900 original size:91 final size:90
Alignment explanation
Indices: 5393757--5393926 Score: 250
Period size: 91 Copynumber: 1.9 Consensus size: 90
5393747 TAAATTGAAA
* * * * *
5393757 AAAATACCTCAGTGTGTGATCTGAAGCTCAACTTACCTCTCGCAATATGAGTTGATTTTTTTGAA
1 AAAATACCTCAGCGTGTGACCTGAAGCTCAACTCACCGCTCGCAATACGAGTTGATTTTTTTGAA
5393822 AGACAGAAATTGAAAAACGGAAATTG
66 A-ACAGAAATTGAAAAACGGAAATTG
* * * *
5393848 AAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCGCTCGCAATACGAGTTGATTTTTTTGAC
1 AAAATACCTCAGCGTGTGACCTGAAGCTCAACTCACCGCTCGCAATACGAGTTGATTTTTTTGAA
5393913 AACAGAAATTGAAA
66 AACAGAAATTGAAA
5393927 TTACCTCAAC
Statistics
Matches: 70, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
90 13 0.19
91 57 0.81
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.28
Consensus pattern (90 bp):
AAAATACCTCAGCGTGTGACCTGAAGCTCAACTCACCGCTCGCAATACGAGTTGATTTTTTTGAA
AACAGAAATTGAAAAACGGAAATTG
Found at i:5393970 original size:165 final size:161
Alignment explanation
Indices: 5393513--5395308 Score: 1365
Period size: 165 Copynumber: 11.4 Consensus size: 161
5393503 AAATTGAAAG
** * * *
5393513 AAATACCTCAGTATGTGATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTTTTTTG
1 AAATACCTCAGCGTGTG-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTTTG
* * * * *
5393578 AAAGACAAAAATTGAAAATAGCTCAGCGCGTGAGCC-AAGGCTCAACTCACCTCTCGCAATATGA
62 AAA-ACAGAAATTGAAATTACCTCA--GCGTG-TCCTGAGGCTCAACTCACCTCTCGCAATATGA
** * **
5393642 GTTGA--TTTTTG-AAACTTAACTTGAAAAGCAGATTTTGA
123 GTTGATTTTTTTGAAAACAGAAATTGAAAA--AGAAATTGA
** * *
5393680 AAATACCTC-GATATGTGACTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAA
1 AAATACCTCAG-CGTGTGCCT-GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG-A
* * * * * * *
5393742 AAATATAAATTGAAAAAAATACCTCAGTGTGTGATCTGAAGCTCAACTTACCTCTCGCAATATGA
63 AAACAGAAATTG---AAATTACCTCAGCGTGT--CCTGAGGCTCAACTCACCTCTCGCAATATGA
5393807 GTTGATTTTTTTGAAAGACAGAAATTGAAAAACGGAAATTGA
123 GTTGATTTTTTTGAAA-ACAGAAATTGAAAAA--GAAATTGA
* * * * *
5393849 AAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCGCTCGCAATACGAGTTGATTTTTTTGACA
1 AAATACCTCAGCGTGTG-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA
* *
5393914 ACAGAAATTGAAATTACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCACAATATGAGTTGATT
65 ACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
* *
5393979 TTTTTGAAAGGCAGGAATTGAAAAACGGAAATTGA
130 TTTTTGAAA-ACAGAAATTGAAAAA--GAAATTGA
* * * *
5394014 AAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTCGCAATACGAGTTGATTTTTTTGACA
1 AAATACCTCAGCGTGTG-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA
* *
5394079 ACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACTTCTCGTAATATGAGTTGATT
65 ACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
*
5394144 TTTTT-------GAAA--G--ACAGAAATTGA
130 TTTTTGAAAACAGAAATTGAAAAAGAAATTGA
* * * *
5394165 AAATAGCTCAACGCGTGAGCC-AAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTTTTAA
1 AAATACCTC-A-GCGTGTGCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTT--
* * * * *
5394229 AGCCAGAAATTGAAAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTG
59 ---------TTG-AAAACAGAAATTGAAATTACCTCAGCGTGT--CCTGAGGCTCAACTCACCTC
* *
5394294 TCGCAATACGAGTTGATTTTTTTGACAACAGAAATT------GAAA-T--
112 TCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAAAAGAAATTGA
5394335 ---TACCTCAGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAG
1 AAATACCTCAGCGTGTGCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA-
* * * * * * **
5394396 AAAGAAATTGAAAATAGCTTAGCGCGTGAGCC-AAGGCTCAACTCACCTCTCGCAATATGAGCCG
65 ACAGAAATTGAAATTACCTCA--GCGTG-TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
* *
5394460 ATTTTTTTTTGAAAGGCATAAATTGAAAAAAGGAAATTGA
127 A--TTTTTTTGAAA-ACAGAAATTG-AAAAA-GAAATTGA
** * * *
5394500 AAATACCTTGGCGTGTGACCTGAGGCTCAACTCGCCGCTCGCAATATGAGTTGATTTTTTTGACA
1 AAATACCTCAGCGTGTG-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA
** * *
5394565 ACAGAAATTGAAATTACCTCAGCGTGTGACCTGAGGCTCAACTCGTCGCTCGCAATACGAGTTGA
65 ACAGAAATTGAAATTACCTCAGCGTGT--CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
*
5394630 TTTTTTTGACAACAGAAATT------GAAA-T--
128 TTTTTTTGAAAACAGAAATTGAAAAAGAAATTGA
*
5394655 ---TACCTCAGCGTGT-CCTGAGGCTCAACTCACCTCTCGAAATATGAGTTGA--TTTTTGAAAA
1 AAATACCTCAGCGTGTGCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAA
* * * *
5394714 TAGAAATTGAAATTACCTCAGCGTGTCCCGAGACTCAACTCACCTCTCGCAATATGATTTGATTT
66 CAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
*
5394779 TTTT-------GAAA---AACAA-AAATTGA
131 TTTTGAAAACAGAAATTGAAAAAGAAATTGA
* * ** *
5394799 AAATACCTCAGCATGT-CTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA--ATTTTGAAAA
1 AAATACCTCAGCGTGTGCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAA
** *
5394861 CAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTAATTT
66 CAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
*
5394926 TTTTTAACAACAGAAATT------GAAA-T--
131 TTTTGAA-AACAGAAATTGAAAAAGAAATTGA
* *
5394949 ---TACCTCAGTGTGT-CCTGAGGCTCAACTCACCTCTCGCAGTATGAGTTGATTTTTTTGAAAG
1 AAATACCTCAGCGTGTGCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA-
* * * * **
5395010 ACAAAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA--
65 ACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
*
5395073 ATTTTGAAAAC-----------AA-AAATTGA
130 TTTTTGAAAACAGAAATTGAAAAAGAAATTGA
* * *
5395093 AATTACCTCAGCGTGT-CCCGAAGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAA
1 AAATACCTCAGCGTGTGCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAA
* *
5395155 CAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCATCTCTCGCAATATGAGTTGATTT
66 CAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
*
5395220 TTTTGACAACAGAAATT------GAAA-T--
131 TTTTGAAAACAGAAATTGAAAAAGAAATTGA
* * *
5395242 ---TACCTTAGCGTGT-CTTGAGGCTCAACTCACCTCTCGCAGTATGAGTTGATTTTTTTG-AAA
1 AAATACCTCAGCGTGTGCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAA
5395302 CAGAAAT
66 CAGAAAT
5395309 AAAACATCAA
Statistics
Matches: 1353, Mismatches: 157, Indels: 258
0.77 0.09 0.15
Matches are distributed among these distances:
139 4 0.00
141 6 0.00
142 2 0.00
144 57 0.04
145 9 0.01
146 89 0.07
147 216 0.16
148 46 0.03
149 8 0.01
150 94 0.07
151 92 0.07
152 19 0.01
153 26 0.02
154 12 0.01
155 5 0.00
157 4 0.00
158 4 0.00
162 23 0.02
163 8 0.01
164 3 0.00
165 276 0.20
166 37 0.03
167 86 0.06
168 53 0.04
169 102 0.08
170 57 0.04
171 6 0.00
172 1 0.00
173 4 0.00
175 4 0.00
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (161 bp):
AAATACCTCAGCGTGTGCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAA
CAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
TTTTGAAAACAGAAATTGAAAAAGAAATTGA
Found at i:5394223 original size:242 final size:232
Alignment explanation
Indices: 5392582--5395308 Score: 2245
Period size: 242 Copynumber: 11.9 Consensus size: 232
5392572 AGTGTGTGAT
*
5392582 CTAAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG-AAA--G--AAA--GAAATTGA
1 CTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATTGAAAAACGGAAATTGA
* * * *
5392640 AAATACCTCAGCATGTGAACC-GAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTGAA
66 AAATACCTCGGCGTGTG-ACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAC
* * * * *
5392704 AACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTTATTTCTCGCAATATGAGTT-A-
130 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGAT
** *
5392767 AATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTC
195 TTTTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTC
* * ** ** *
5392805 TTAAGGTTCAACTCATTTCTCGCAATATG-G--G------TTGAATTTTG-AAAACAGAAATTGA
1 CTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATTGAAAAACGGAAATTGA
* * * * ** * *
5392860 AATTACCTCAGC-T-TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA--ATTTTGAAA
66 AAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACA
* * * *
5392921 ACAG--ATTGAAATTACCTTAGCGTGTCCCGGGGCTCAACTCACCTT-TCGCAATATAAGTTGA-
131 ACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCA-CTTCTCGCAATATGAGTTGAT
5392982 -TTTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTC
195 TTTTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTC
** * * ** **
5393019 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAAT-ATAAATTGAAA-AAA
1 CTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATTGAAAAACGGAAATTGA
* * * * * *
5393080 AAATACCTCAGTGTGTGATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTTTTGAA
66 AAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTGAC
* * *
5393145 AGACAGAAATTGAAAATACCTCAGCATGTGAACC-GAGGCTCAACTCACTTCTCGCAATATAAGT
130 A-ACAGAAATTGAAATTACCTCAGC--GTG-TCCTGAGGCTCAACTCACTTCTCGCAATATGAGT
* *
5393209 TGA-TTTTTTGAAAACAGAAATTGAAAATACCTCAACGTGTC
191 TGATTTTTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTC
* * ** * *
5393250 TTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA----ATT-----TTG-AAAACAGAAATTGA
1 CTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATTGAAAAACGGAAATTGA
* ** * * ** * * *
5393305 AATTACCTCAACGTGT--CTTGAGGTTCAACTCATTTATCGCAATATGAGTTGA--ATTTTGAAA
66 AAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACA
* *
5393366 ACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA--
131 ACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATT
*
5393429 ATTTTGAAAACAG--ATTGAAATTACCTCAGCGTGTC
196 TTTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTC
** * * **
5393464 CCGAGG----------CTCTCGCAATATGAGTTGA--TTTTTGAAAAAT-ATAAATTGAAA--G-
1 CTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATTGAAAAACGGAAATTGA
* ** * * *
5393513 AAATACCTCAGTATGTGATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTTTTTTG
66 AAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTTTG
* * * * * * *
5393578 AAAGACAAAAATTGAAAATAGCTCAGCGCGTGAGCC-AAGGCTCAACTCACCTCTCGCAATATGA
128 ACA-ACAGAAATTGAAATTACCTCA--GCGTG-TCCTGAGGCTCAACTCACTTCTCGCAATATGA
** * ** *
5393642 GTTGATTTTTGAAACTTAACTTGAAAAGCAGATTTTGAAAATACCTC-GATATGTGA
189 GTTGA--TTT-----TT---TTGAAAA-CAGAAATTGAAATTACCTCAG-CGTGT-C
* * **
5393698 CTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAAT-ATAAATTGAAA---
1 CT-AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATTGAAAAACGGAAATTG
* * * * * *
5393757 AAAATACCTCAGTGTGTGATCTGAAGCTCAACTTACCTCTCGCAATATGAGTTGATTTTTTTGAA
65 AAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAC
* * **
5393822 AGACAGAAATTGAAAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCGC
130 A-ACAGAAATT--------GAAA-T-----TACCTCAGCGTGT--CCTGAGGCTCAACTCACTTC
* * *
5393887 TCGCAATACGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCTCAACGTGTC
178 TCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTC
* *
5393942 CTGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTTGAAAGGCAGGAATTGAAAAACGG
1 CTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG--A---A--AATTGAAAAACGG
* *
5394007 AAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTCGCAATACGAGTTGATTTT
59 AAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
*
5394072 TTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACTTCTCGTAATATGA
124 TTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACTTCTCGCAATATGA
* * *
5394137 GTTGATTTTTTTGAAAGACAGAAATTGAAAATAGCTCAACGCGTGAGC
189 GTTGATTTTTTTGAAA-ACAGAAATTGAAATTACCTC-A-GCGTG-TC
*
5394185 C-AAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTTTTAAAGCCAGAAATTGAAAAACGG
1 CTAAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTT---G--A-AAATTGAAAAACGG
* * *
5394249 AAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTGTCGCAATACGAGTTGATTTT
59 AAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
*
5394314 TTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
124 TTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACTTCTCGCAATATGA
* * * * *
5394379 GTTGATTTTTTTGAAAGAAAGAAATTGAAAATAGCTTAGCGCGTGAGC
189 GTTGATTTTTTTGAAA-ACAGAAATTGAAATTACCTCA--GCGTG-TC
** *
5394427 C-AAGGCTCAACTCACCTCTCGCAATATGAGCCGATTTTTTTTTGAAAGGCATAAATTGAAAAAA
1 CTAAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTT-----G-A-AAATTGAAAAAC
* * *
5394491 GGAAATTGAAAATACCTTGGCGTGTGACCTGAGGCTCAACTCGCCGCTCGCAATATGAGTTGATT
57 GGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
* *
5394556 TTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTGACCTGAGGCTCAACTC-GTCGCTCGCAA
122 TTTTTGACAACAGAAATTGAAATTACCTCAGCGTGT--CCTGAGGCTCAACTCACT-TCTCGCAA
* *
5394620 TACGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTC
184 TATGAGTTGATTTTTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTC
* *
5394669 CTGAGGCTCAACTCACCTCTCGAAATATGAGTTGA--TTTTTGAAAA-T-----A--GAAATTGA
1 CTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATTGAAAAACGGAAATTGA
* * * * * *
5394724 AATTACCTCAGCGTGT--CCCGAGACTCAACTCACCTCTCGCAATATGATTTGATTTTTTTGAAA
66 AAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG-AC
* * * * *
5394787 AACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-
130 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGAT
*
5394851 -ATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTC
195 TTTTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTC
* ** * * *
5394888 CTGAGGCTCAACTCATTTCTCGCAATATGAGTT-AATTTTTT-----TT-AACAACAGAAATTGA
1 CTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATTGAAAAACGGAAATTGA
* * * * *
5394946 AATTACCTC--AGTGTGTCCTGAGGCTCAACTCACCTCTCGCAGTATGAGTTGATTTTTTTGAAA
66 AAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACA
* * * * *
5395009 GACAAAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-
131 -ACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGAT
* *
5395073 -ATTTTGAAAACAAAAATTGAAATTACCTCAGCGTGTCC
195 TTTTTTGAAAACAGAAATTGAAATTACCTCAGCGTGT-C
* *
5395111 CGAA-GCTCAACTCACCTCTCGCAATATGAGTTGA----TTT-----TTG-AAAACAGAAATTGA
1 CTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATTGAAAAACGGAAATTGA
* * * *
5395165 AATTACCTCAGCGTGT--CCCGAGGCTCAACTCATCTCTCGCAATATGAGTTGATTTTTTTGACA
66 AAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACA
* * * *
5395228 ACAGAAATTGAAATTACCTTAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAGTATGAGTTGATT
131 ACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATT
5395293 TTTTTG-AAACAGAAAT
196 TTTTTGAAAACAGAAAT
5395309 AAAACATCAA
Statistics
Matches: 2106, Mismatches: 249, Indels: 302
0.79 0.09 0.11
Matches are distributed among these distances:
204 18 0.01
206 2 0.00
208 12 0.01
209 1 0.00
210 28 0.01
211 8 0.00
214 128 0.06
215 13 0.01
216 44 0.02
217 37 0.02
218 127 0.06
219 168 0.08
220 54 0.03
221 51 0.02
222 252 0.12
223 82 0.04
224 29 0.01
225 22 0.01
226 5 0.00
227 2 0.00
228 15 0.01
229 5 0.00
230 38 0.02
231 72 0.03
232 4 0.00
233 16 0.01
234 2 0.00
235 3 0.00
239 46 0.02
240 18 0.01
241 14 0.01
242 273 0.13
243 82 0.04
244 113 0.05
245 138 0.07
246 50 0.02
247 5 0.00
249 2 0.00
250 5 0.00
252 3 0.00
253 8 0.00
254 8 0.00
255 11 0.01
256 92 0.04
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Consensus pattern (232 bp):
CTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAATTGAAAAACGGAAATTGA
AAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACA
ACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATT
TTTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTC
Found at i:5394312 original size:91 final size:90
Alignment explanation
Indices: 5394147--5394333 Score: 225
Period size: 91 Copynumber: 2.1 Consensus size: 90
5394137 GTTGATTTTT
* * *
5394147 TTGAAAGACAGAAATTGAAAATAGCTCAACGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTGAAAATACCTCAACGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATAC
*
5394212 GAGTCGATTTTTTTTA-AAGCCAGAAA
66 GAGTCGATTTTTTTGACAA--CAGAAA
* ** * * * *
5394238 TTGAAAAACGGAAATTGAAAATACCTCGGCGTGTGA-CCTGAGGCTCAACTCGCCTGTCGCAATA
1 TTGAAAAACAGAAATTGAAAATACCTCAACGCGTGAGCC-AAGGCTCAACTCACCTCTCGCAATA
*
5394302 CGAGTTGATTTTTTTGACAACAGAAA
65 CGAGTCGATTTTTTTGACAACAGAAA
5394328 TTGAAA
1 TTGAAA
5394334 TTACCTCAGC
Statistics
Matches: 82, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
90 14 0.17
91 66 0.80
92 2 0.02
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (90 bp):
TTGAAAAACAGAAATTGAAAATACCTCAACGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATAC
GAGTCGATTTTTTTGACAACAGAAA
Found at i:5394548 original size:93 final size:93
Alignment explanation
Indices: 5394389--5394560 Score: 240
Period size: 93 Copynumber: 1.8 Consensus size: 93
5394379 GTTGATTTTT
* *
5394389 TTGAAAGAAAGAAATTGAAAATAGCTTAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAGAAAGAAATTGAAAATACCTTAGCGCGTGAGCCAAGGCTCAACTCACCGCTCGCAATAT
5394454 GAGCCGATTTTTTTTTGAAAGGCATAAA
66 GAGCCGATTTTTTTTTGAAAGGCATAAA
* * * *
5394482 TTGAAA-AAAGGAAATTGAAAATACCTTGGCGTGTGA-CCTGAGGCTCAACTCGCCGCTCGCAAT
1 TTGAAAGAAA-GAAATTGAAAATACCTTAGCGCGTGAGCC-AAGGCTCAACTCACCGCTCGCAAT
**
5394545 ATGAGTTGATTTTTTT
64 ATGAGCCGATTTTTTT
5394561 GACAACAGAA
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
92 5 0.07
93 64 0.93
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.28
Consensus pattern (93 bp):
TTGAAAGAAAGAAATTGAAAATACCTTAGCGCGTGAGCCAAGGCTCAACTCACCGCTCGCAATAT
GAGCCGATTTTTTTTTGAAAGGCATAAA
Found at i:5394829 original size:147 final size:146
Alignment explanation
Indices: 5394492--5395308 Score: 1118
Period size: 147 Copynumber: 5.5 Consensus size: 146
5394482 TTGAAAAAAG
* ** * *
5394492 GAAATTGAAAATACCTTGGCGTGTGACCTGAGGCTCAACTCGCCGCTCGCAATATGAGTTGATTT
1 GAAATTGAAATTACCTCAGCGTGT--CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--T
* * *
5394557 TTTTGACAACAGAAATTGAAATTACCTCAGCGTGTGACCTGAGGCTCAACTCGTCGCTCGCAATA
62 TTTTGAAAACAGAAATTGAAATTACCTCAGCGTGT--CCTGAGGCTCAACTCATCTCTCGCAATA
*
5394622 CGAGTTGATTTTTTTGACAACA
125 TGAGTTGATTTTTTTGACAACA
*
5394644 GAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGAAATATGAGTTGATTTTT
1 GAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
* * * * *
5394709 GAAAATAGAAATTGAAATTACCTCAGCGTGTCCCGAGACTCAACTCACCTCTCGCAATATGATTT
66 GAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATCTCTCGCAATATGAGTT
*
5394774 GATTTTTTTGAAAAACA
131 GATTTTTTTG-ACAACA
* * * * ** *
5394791 AAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTT
1 GAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
*
5394856 GAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTT
66 GAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATCTCTCGCAATATGAGTT
* *
5394921 AATTTTTTTTAACAACA
131 GA-TTTTTTTGACAACA
* *
5394938 GAAATTGAAATTACCTCAGTGTGTCCTGAGGCTCAACTCACCTCTCGCAGTATGAGTTGATTTTT
1 GAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTT
* * * * *
5395003 TTGAAAGACAAAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGA
64 TTGAAA-ACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATCTCTCGCAATATGA
* *
5395068 GTTGA--ATTTTGAAAACA
128 GTTGATTTTTTTGACAACA
* * *
5395085 AAAATTGAAATTACCTCAGCGTGTCCCGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 GAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
*
5395150 GAAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCATCTCTCGCAATATGAGTT
66 GAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATCTCTCGCAATATGAGTT
5395215 GATTTTTTTGACAACA
131 GATTTTTTTGACAACA
* * *
5395231 GAAATTGAAATTACCTTAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAGTATGAGTTGATTTTT
1 GAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTT
5395296 TTG-AAACAGAAAT
64 TTGAAAACAGAAAT
5395309 AAAACATCAA
Statistics
Matches: 587, Mismatches: 69, Indels: 23
0.86 0.10 0.03
Matches are distributed among these distances:
144 57 0.10
145 9 0.02
146 101 0.17
147 253 0.43
148 47 0.08
149 8 0.01
150 91 0.16
152 21 0.04
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (146 bp):
GAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
GAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATCTCTCGCAATATGAGTT
GATTTTTTTGACAACA
Found at i:5394975 original size:222 final size:219
Alignment explanation
Indices: 5394482--5395308 Score: 1147
Period size: 222 Copynumber: 3.7 Consensus size: 219
5394472 AAGGCATAAA
* * ** * * *
5394482 TTGAAAAAAGGAAATTGAAAATACCTTGGCGTGTGACCTGAGGCTCAACTCGCCGCTCGCAATAT
1 TTGAAAACA-GAAATTGAAATTACCTCAGCGTGT--CCCGAGGCTCAACTCACCTCTCGCAATAT
* * * * *
5394547 GAGTTGATTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTGACCTGAGGCTCAACTCGTC
63 GAGTTGATTTTTTTGAAAACAAAAATTGAAAATACCTCAGCGTGT--CTTGAGGCTCAACTCATC
* * * *
5394612 GCTCGCAATACGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCT
126 TCTCGCAATATGAGTTGA-TATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCT
*
5394677 CAACTCACCTCTCGAAATATGAGTTGATTT
190 CAACTCACCTCTCGCAATATGAGTTGATTT
* * *
5394707 TTGAAAATAGAAATTGAAATTACCTCAGCGTGTCCCGAGACTCAACTCACCTCTCGCAATATGAT
1 TTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAG
* *
5394772 TTGATTTTTTTGAAAAACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTC
66 TTGATTTTTTTG-AAAACAAAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATCTCTC
5394837 GCAATATGAGTTGA-ATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACT
130 GCAATATGAGTTGATATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACT
** *
5394901 CATTTCTCGCAATATGAGTTAATTTTT
195 CACCTCTCGCAATATGAGTTGA--TTT
* * * *
5394928 TTTAACAACAGAAATTGAAATTACCTCAGTGTGTCCTGAGGCTCAACTCACCTCTCGCAGTATGA
1 TTGAA-AACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
* *
5394993 GTTGATTTTTTTGAAAGACAAAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCT
65 GTTGATTTTTTTGAAA-ACAAAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATCTCT
* * *
5395058 CGCAATATGAGTTGA-ATTTTGAAAACAAAAATTGAAATTACCTCAGCGTGTCCCGAAGCTCAAC
129 CGCAATATGAGTTGATATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAAC
5395122 TCACCTCTCGCAATATGAGTTGATTT
194 TCACCTCTCGCAATATGAGTTGATTT
*
5395148 TTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCATCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAG
* * * * *
5395213 TTGATTTTTTTGACAACAGAAATTGAAATTACCTTAGCGTGTCTTGAGGCTCAACTCACCTCTCG
66 TTGATTTTTTTGAAAACAAAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATCTCTCG
* *
5395278 CAGTATGAGTTGATTTTTTTG-AAACAGAAAT
131 CAATATGAGTTGA-TATTTTGAAAACAGAAAT
5395309 AAAACATCAA
Statistics
Matches: 541, Mismatches: 54, Indels: 20
0.88 0.09 0.03
Matches are distributed among these distances:
218 56 0.10
219 145 0.27
220 12 0.02
221 41 0.08
222 232 0.43
223 26 0.05
224 21 0.04
225 8 0.01
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (219 bp):
TTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAG
TTGATTTTTTTGAAAACAAAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATCTCTCG
CAATATGAGTTGATATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTC
ACCTCTCGCAATATGAGTTGATTT
Found at i:5403222 original size:12 final size:12
Alignment explanation
Indices: 5403200--5403235 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
5403190 TGGGATATGC
*
5403200 AATGAATGAATG
1 AATGCATGAATG
*
5403212 GATGCATGAATG
1 AATGCATGAATG
5403224 AATGCATGAATG
1 AATGCATGAATG
5403236 TCAAATGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.42, C:0.06, G:0.28, T:0.25
Consensus pattern (12 bp):
AATGCATGAATG
Found at i:5403222 original size:16 final size:17
Alignment explanation
Indices: 5403196--5403227 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5403186 AGTATGGGAT
5403196 ATGCAATGAATGAATGG
1 ATGCAATGAATGAATGG
5403213 ATGC-ATGAATGAATG
1 ATGCAATGAATGAATG
5403228 CATGAATGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.41, C:0.06, G:0.28, T:0.25
Consensus pattern (17 bp):
ATGCAATGAATGAATGG
Found at i:5405908 original size:17 final size:17
Alignment explanation
Indices: 5405886--5405941 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
5405876 AGGGTTTCTT
5405886 GGTTTTTTTTTGGGTTA
1 GGTTTTTTTTTGGGTTA
5405903 GGTTTTTCTTTT---TT-
1 GGTTTTT-TTTTGGGTTA
*
5405917 -CTTTTTTTTTGGGTTA
1 GGTTTTTTTTTGGGTTA
5405933 GGTTTTTTT
1 GGTTTTTTT
5405942 GGGGGGGCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
12 4 0.13
13 5 0.16
15 4 0.13
17 14 0.45
18 4 0.13
ACGTcount: A:0.04, C:0.04, G:0.21, T:0.71
Consensus pattern (17 bp):
GGTTTTTTTTTGGGTTA
Found at i:5405939 original size:25 final size:27
Alignment explanation
Indices: 5405888--5405941 Score: 74
Period size: 30 Copynumber: 1.9 Consensus size: 27
5405878 GGTTTCTTGG
5405888 TTTTTTTTTGGGTTAGGTTTTTCTTTTTTC
1 TTTTTTTTTGGGTTAGG---TTCTTTTTTC
5405918 TTTTTTTTTGGGTTAGGTT-TTTTT
1 TTTTTTTTTGGGTTAGGTTCTTTTT
5405942 GGGGGGGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 5 0.21
27 2 0.08
30 17 0.71
ACGTcount: A:0.04, C:0.04, G:0.19, T:0.74
Consensus pattern (27 bp):
TTTTTTTTTGGGTTAGGTTCTTTTTTC
Found at i:5409232 original size:27 final size:25
Alignment explanation
Indices: 5409180--5409234 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 25
5409170 ATTTAAAGTA
*
5409180 AATAATAAAACGATTTAAAATGAAT
1 AATAATAAAACGATTTAAAATAAAT
*
5409205 AATACATAAAGCGAGTTTAAAATAAAT
1 AATA-ATAAAACGA-TTTAAAATAAAT
5409232 AAT
1 AAT
5409235 GTAAAAGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 4 0.15
26 8 0.31
27 14 0.54
ACGTcount: A:0.58, C:0.05, G:0.09, T:0.27
Consensus pattern (25 bp):
AATAATAAAACGATTTAAAATAAAT
Found at i:5409470 original size:28 final size:27
Alignment explanation
Indices: 5409408--5409470 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
5409398 AGAGTTTAAC
5409408 ATAAGATATATAAAACAATTTTAAAATA
1 ATAA-ATATATAAAACAATTTTAAAATA
**
5409436 A-ATAATATATAAGTCAATTTTAAAAATA
1 ATA-AATATATAAAACAATTTT-AAAATA
5409464 ATAAATA
1 ATAAATA
5409471 AGAATCTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
27 16 0.53
28 13 0.43
29 1 0.03
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.33
Consensus pattern (27 bp):
ATAAATATATAAAACAATTTTAAAATA
Found at i:5411496 original size:20 final size:18
Alignment explanation
Indices: 5411467--5411530 Score: 67
Period size: 17 Copynumber: 3.5 Consensus size: 18
5411457 CCTCACTGGT
*
5411467 ATTTTTATATATATTTTAA
1 ATTTTTATATAT-TTTAAA
5411486 ATTTATTATATATTTTAAA
1 ATTT-TTATATATTTTAAA
* *
5411505 ATTTTTAT-TTTTTTAAT
1 ATTTTTATATATTTTAAA
*
5411522 TTTTTTATA
1 ATTTTTATA
5411531 ATTAGGATCA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
17 14 0.36
18 4 0.10
19 13 0.33
20 8 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTTTATATATTTTAAA
Found at i:5411497 original size:18 final size:18
Alignment explanation
Indices: 5411470--5411530 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 18
5411460 CACTGGTATT
5411470 TTTA-TATATATTTTAAA
1 TTTATTATATATTTTAAA
5411487 TTTATTATATATTTTAAAA
1 TTTATTATATATTTT-AAA
* *
5411506 TTT-TTAT-TTTTTTAAT
1 TTTATTATATATTTTAAA
*
5411522 TTTTTTATA
1 TTTATTATA
5411531 ATTAGGATCA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
16 5 0.13
17 13 0.34
18 14 0.37
19 6 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTATTATATATTTTAAA
Found at i:5413200 original size:6 final size:6
Alignment explanation
Indices: 5413189--5413216 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
5413179 TACTACTCTT
5413189 CTCTAC CTCTAC CTCTAC CTCTAC CTCT
1 CTCTAC CTCTAC CTCTAC CTCTAC CTCT
5413217 CACACTCTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.50, G:0.00, T:0.36
Consensus pattern (6 bp):
CTCTAC
Found at i:5419880 original size:36 final size:37
Alignment explanation
Indices: 5419829--5419899 Score: 117
Period size: 36 Copynumber: 1.9 Consensus size: 37
5419819 TAATTCTTAT
5419829 TAATGTTCCCATGAAATTGAAAGTG-ACATAAAATTA
1 TAATGTTCCCATGAAATTGAAAGTGAACATAAAATTA
* *
5419865 TAATGTTCCCTTGAAATTGAAAGTGAACGTAAAAT
1 TAATGTTCCCATGAAATTGAAAGTGAACATAAAAT
5419900 GACAATGGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 24 0.75
37 8 0.25
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.31
Consensus pattern (37 bp):
TAATGTTCCCATGAAATTGAAAGTGAACATAAAATTA
Found at i:5420855 original size:308 final size:305
Alignment explanation
Indices: 5420376--5420991 Score: 1160
Period size: 308 Copynumber: 2.0 Consensus size: 305
5420366 ATCAGATTTA
5420376 TTAGCCAATGAGATGTTTGGGTATTGATAGCAAGAAGAAAGGAAAAAGGAGACAATTCAATGAAA
1 TTAGCCAATGAGATGTTTGGGTATTGATAGCAAGAAGAAAGGAAAAAGGAGACAATTCAATGAAA
*
5420441 CAATAGCATATAATTTTTTAATCAAAGAAAAAAATTAAAAGAAAGGGTGTCATGTGACGATGCAC
66 CAATAGCATATAAATTTTTAATCAAAGAAAAAAATTAAAAGAAAGGGTGTCATGTGACGATGCAC
* *
5420506 GTGACAAGTTAATGTGCCAATGACTATTTGACCAAAAGGGTAGATGATGGGCGGGTCCTAGTAGA
131 GTGACAAGTTAATGTGCCAATGACTATTTGACCAAAAGGGTAGAAGATGGGCGGGCCCTAGTAGA
*
5420571 CGTTGCTATCTTGTCTATCTCACTGAGTTTCGAGATTGGAATCCTCAGCTCAGTAGCAAGAACTG
196 CGTTGCTATCTTGTCTATCTCACTAAGTTTCGAGATTGGAATCCTCAGCTCAGTAGCAAGAACTG
5420636 CAACTTTCATACTTCCACAAAAAGGCAAAGGGCAAATCAGCCATT
261 CAACTTTCATACTTCCACAAAAAGGCAAAGGGCAAATCAGCCATT
*
5420681 TTAGCTCAATTAGATGTTTGGGTATTGATAGCAAGAAGAAAGGAAAAAGGAGACAATTCAATGAA
1 TTAGC-CAATGAGATGTTTGGGTATTGATAGCAAGAAGAAAGGAAAAAGGAGACAATTCAATGAA
5420746 ACAATAGCATATAAATTTTTAATCAAAGAAAAAAAAATTAAAAGAAAGGGTGTCATGTGACGATG
65 ACAATAGCATATAAATTTTTAATCAAAG--AAAAAAATTAAAAGAAAGGGTGTCATGTGACGATG
5420811 CACGTGACAAGTTAATGTGCCAATGACTATTTGACCAAAAGGGTAGAAGATGGGCGGGCCCTAGT
128 CACGTGACAAGTTAATGTGCCAATGACTATTTGACCAAAAGGGTAGAAGATGGGCGGGCCCTAGT
5420876 AGACGTTGCTATCTTGTCTATCTCACTAAGTTTCGAGATTGGAATCCTCAGCTCAGTAGCAAGAA
193 AGACGTTGCTATCTTGTCTATCTCACTAAGTTTCGAGATTGGAATCCTCAGCTCAGTAGCAAGAA
5420941 CTGCAACTTTCATACTTCCACAAAAAGGCAAAGGGCAAATCAGCCATT
258 CTGCAACTTTCATACTTCCACAAAAAGGCAAAGGGCAAATCAGCCATT
5420989 TTA
1 TTA
5420992 TAATATTCCT
Statistics
Matches: 303, Mismatches: 5, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
305 5 0.02
306 85 0.28
308 213 0.70
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (305 bp):
TTAGCCAATGAGATGTTTGGGTATTGATAGCAAGAAGAAAGGAAAAAGGAGACAATTCAATGAAA
CAATAGCATATAAATTTTTAATCAAAGAAAAAAATTAAAAGAAAGGGTGTCATGTGACGATGCAC
GTGACAAGTTAATGTGCCAATGACTATTTGACCAAAAGGGTAGAAGATGGGCGGGCCCTAGTAGA
CGTTGCTATCTTGTCTATCTCACTAAGTTTCGAGATTGGAATCCTCAGCTCAGTAGCAAGAACTG
CAACTTTCATACTTCCACAAAAAGGCAAAGGGCAAATCAGCCATT
Found at i:5421699 original size:92 final size:97
Alignment explanation
Indices: 5421601--5421908 Score: 241
Period size: 105 Copynumber: 3.1 Consensus size: 97
5421591 TGAGGATACT
*
5421601 AGGGTGGGCAAGAGGAGGG-T-GGT-G-T-GAAGTCACATGTTGCCTGGAGGACGGTGAAAGTGA
1 AGGGTGGGCAAGAGGAGGGTTAGGTGGTTCGAAATCACATGTTGCCTGGAGGACGGTGAAAGTGA
* * *
5421661 ATCAG-TTCGAAAAGATGGTGAGGGAGAGCTCG
66 ATCAGATT-GAAAAGATGGTCAGAGAGAGCGCG
*** *
5421693 AGGGTGGGTGTGAGGAGGGTTGAGACCAGGTGGTTCGAAATCACATGTTGCCTGGAGGACGGTGG
1 AGGGTGGGCAAGAGGAGGGTT------AGGTGGTTCGAAATCACATGTTGCCTGGAGGACGGTGA
* *
5421758 AAGTGAATGAGATTGAAGAGATGGTCAGAGAGAGCGCG
60 AAGTGAATCAGATTGAAAAGATGGTCAGAGAGAGCGCG
*** * * **
5421796 AGGGTGGGTGTGTGAGGAGGGTTGAGACCGGGTGGTGCGAAATCACATGTTGCCTGGAGTATAGT
1 AGGGT-GG-GCAAGAGGAGGGTT---A---GGTGGTTCGAAATCACATGTTGCCTGGAGGACGGT
* * * * *
5421861 GAAAGTGAATGAGATCGAAGAGATGGTGAGGGAGAGCGCG
58 GAAAGTGAATCAGATTGAAAAGATGGTCAGAGAGAGCGCG
5421901 AGGGTGGG
1 AGGGTGGG
5421909 TGTGAGGAGG
Statistics
Matches: 178, Mismatches: 21, Indels: 23
0.80 0.09 0.10
Matches are distributed among these distances:
92 16 0.09
93 1 0.01
100 3 0.02
101 1 0.01
102 2 0.01
103 63 0.35
104 6 0.03
105 86 0.48
ACGTcount: A:0.26, C:0.10, G:0.45, T:0.19
Consensus pattern (97 bp):
AGGGTGGGCAAGAGGAGGGTTAGGTGGTTCGAAATCACATGTTGCCTGGAGGACGGTGAAAGTGA
ATCAGATTGAAAAGATGGTCAGAGAGAGCGCG
Found at i:5421867 original size:105 final size:103
Alignment explanation
Indices: 5421617--5421932 Score: 463
Period size: 103 Copynumber: 3.0 Consensus size: 103
5421607 GGCAAGAGGA
* * * *
5421617 GGGTGGTGTGAAGTCACATGTTGCCTGGAGGACGGTGAAAGTGAATCAG-TTCGAAAAGATGGTG
1 GGGTGGTGCGAAATCACATGTTGCCTGGAGGACGGTGAAAGTGAATGAGATT-GAAGAGATGGTG
*
5421681 AGGGAGAGCTCGAGGGTGGGTGTGAGGAGGGTTGAGACC
65 AGGGAGAGCGCGAGGGTGGGTGTGAGGAGGGTTGAGACC
* * * *
5421720 AGGTGGTTCGAAATCACATGTTGCCTGGAGGACGGTGGAAGTGAATGAGATTGAAGAGATGGTCA
1 GGGTGGTGCGAAATCACATGTTGCCTGGAGGACGGTGAAAGTGAATGAGATTGAAGAGATGGTGA
*
5421785 GAGAGAGCGCGAGGGTGGGTGTGTGAGGAGGGTTGAGACC
66 GGGAGAGCGCGAGGGT-GG-GTGTGAGGAGGGTTGAGACC
* ** *
5421825 GGGTGGTGCGAAATCACATGTTGCCTGGAGTATAGTGAAAGTGAATGAGATCGAAGAGATGGTGA
1 GGGTGGTGCGAAATCACATGTTGCCTGGAGGACGGTGAAAGTGAATGAGATTGAAGAGATGGTGA
*
5421890 GGGAGAGCGCGAGGGTGGGTGTGAGGAGGTTTGAGACC
66 GGGAGAGCGCGAGGGTGGGTGTGAGGAGGGTTGAGACC
5421928 GGGTG
1 GGGTG
5421933 CGCGAATTAG
Statistics
Matches: 190, Mismatches: 20, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
103 92 0.48
104 6 0.03
105 92 0.48
ACGTcount: A:0.25, C:0.10, G:0.45, T:0.20
Consensus pattern (103 bp):
GGGTGGTGCGAAATCACATGTTGCCTGGAGGACGGTGAAAGTGAATGAGATTGAAGAGATGGTGA
GGGAGAGCGCGAGGGTGGGTGTGAGGAGGGTTGAGACC
Found at i:5422132 original size:25 final size:25
Alignment explanation
Indices: 5422104--5422156 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
5422094 CGTAAGGGTG
*
5422104 TTAACGGTGTTAGATAATATATATA
1 TTAACGGTGTTAGATAACATATATA
*
5422129 TTAATGGTGTTAGATAACATATATA
1 TTAACGGTGTTAGATAACATATATA
5422154 TTA
1 TTA
5422157 CTCATTATGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.40, C:0.04, G:0.15, T:0.42
Consensus pattern (25 bp):
TTAACGGTGTTAGATAACATATATA
Found at i:5422175 original size:83 final size:83
Alignment explanation
Indices: 5422081--5422248 Score: 309
Period size: 83 Copynumber: 2.0 Consensus size: 83
5422071 GGGGTGGAGG
* *
5422081 TGGTGAGAGAGAGCGTAAGGGTGTTAACGGTGTTAGATAATATATATATTAATGGTGTTAGATAA
1 TGGTGAGAGAGAGCGTAAGGGTGTTAACGGTGTTAGATAATATATATATTAACGGTGTTAGACAA
*
5422146 CATATATATTACTCATTA
66 CATATATATTACTCACTA
5422164 TGGTGAGAGAGAGCGTAAGGGTGTTAACGGTGTTAGATAATATATATATTAACGGTGTTAGACAA
1 TGGTGAGAGAGAGCGTAAGGGTGTTAACGGTGTTAGATAATATATATATTAACGGTGTTAGACAA
5422229 CATATATATTACTCACTA
66 CATATATATTACTCACTA
5422247 TG
1 TG
5422249 ATGTTTAACA
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 82 1.00
ACGTcount: A:0.35, C:0.08, G:0.24, T:0.33
Consensus pattern (83 bp):
TGGTGAGAGAGAGCGTAAGGGTGTTAACGGTGTTAGATAATATATATATTAACGGTGTTAGACAA
CATATATATTACTCACTA
Found at i:5422215 original size:25 final size:25
Alignment explanation
Indices: 5422187--5422239 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
5422177 CGTAAGGGTG
* *
5422187 TTAACGGTGTTAGATAATATATATA
1 TTAACGGTGTTAGACAACATATATA
5422212 TTAACGGTGTTAGACAACATATATA
1 TTAACGGTGTTAGACAACATATATA
5422237 TTA
1 TTA
5422240 CTCACTATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.38
Consensus pattern (25 bp):
TTAACGGTGTTAGACAACATATATA
Found at i:5427877 original size:25 final size:23
Alignment explanation
Indices: 5427827--5427873 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
5427817 AGTAAGGGTG
5427827 TTAACGGTGTTAAATAATATATA
1 TTAACGGTGTTAAATAATATATA
*
5427850 TTAACGGTGTTAGATAATATATA
1 TTAACGGTGTTAAATAATATATA
5427873 T
1 T
5427874 ATTACTCGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.04, G:0.15, T:0.40
Consensus pattern (23 bp):
TTAACGGTGTTAAATAATATATA
Found at i:5427987 original size:2 final size:2
Alignment explanation
Indices: 5427980--5428007 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5427970 GTGTTAGATA
5427980 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5428008 TAACAGTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5429100 original size:2 final size:2
Alignment explanation
Indices: 5429093--5429123 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
5429083 TTTTGAAAAG
5429093 TA TA TA TA TA TA TA TA TA TA TA TGA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
5429124 ACAATTACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5437304 original size:10 final size:10
Alignment explanation
Indices: 5437289--5437331 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
5437279 CCTAATTCTA
5437289 AAAAATATAT
1 AAAAATATAT
*
5437299 AAAAATACAT
1 AAAAATATAT
* *
5437309 AAATAT-TTT
1 AAAAATATAT
5437318 AAAAATATAT
1 AAAAATATAT
5437328 AAAA
1 AAAA
5437332 TACCCCAGTG
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
9 6 0.23
10 20 0.77
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (10 bp):
AAAAATATAT
Found at i:5439376 original size:24 final size:26
Alignment explanation
Indices: 5439349--5439400 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
5439339 AAACAATTTG
5439349 AGAA-GAATACTAAATAAA-AGTTTA
1 AGAATGAATACTAAATAAAGAGTTTA
*
5439373 AGAATGAATACTATATAAAGTAGTTTA
1 AGAATGAATACTAAATAAAG-AGTTTA
5439400 A
1 A
5439401 ACTAAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 4 0.17
25 13 0.54
27 7 0.29
ACGTcount: A:0.54, C:0.04, G:0.13, T:0.29
Consensus pattern (26 bp):
AGAATGAATACTAAATAAAGAGTTTA
Found at i:5444343 original size:40 final size:40
Alignment explanation
Indices: 5444288--5444509 Score: 374
Period size: 40 Copynumber: 5.6 Consensus size: 40
5444278 ATTTGAATAC
5444288 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
*
5444328 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
5444368 AT-CGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
*
5444407 ATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
* * *
5444447 ATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
* *
5444487 ACCCGGGTTAAGACCCGAAGGCA
1 ATCCGGGCTAAGACCCGAAGGCA
5444510 ATTGAGCTTG
Statistics
Matches: 172, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
39 38 0.22
40 134 0.78
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.23
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
Found at i:5444422 original size:79 final size:80
Alignment explanation
Indices: 5444288--5444513 Score: 382
Period size: 79 Copynumber: 2.8 Consensus size: 80
5444278 ATTTGAATAC
*
5444288 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCAAT
*
5444353 TGTGCGAGTTGATAT
66 TGTGCAAGTTGATAT
5444368 AT-CGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCAAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCAAT
5444432 TGTGCAAGTTGATAT
66 TGTGCAAGTTGATAT
* * * * *
5444447 ATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCAAT
5444512 TG
66 TG
5444514 AGCTTGTGGT
Statistics
Matches: 138, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
79 77 0.56
80 61 0.44
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (80 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCAAT
TGTGCAAGTTGATAT
Found at i:5444535 original size:119 final size:119
Alignment explanation
Indices: 5444288--5444536 Score: 383
Period size: 119 Copynumber: 2.1 Consensus size: 119
5444278 ATTTGAATAC
*
5444288 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
* * * * *
5444353 TGTGCGAGTTGATATATCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
66 CGTGCGAGTTGATATACCGGGCTAAGACCCGAAGGCAATTGAGCAAGTGGATAT
5444407 ATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
* * ** *
5444472 CGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGAGCTTGTGGTTAT
66 CGTGCGAGTTGATATA-CCGGGCTAAGACCCGAAGGCAATTGAGCAAGTGGATAT
5444527 ATCC-GGCTAA
1 ATCCGGGCTAA
5444537 ATTCCAAAGA
Statistics
Matches: 118, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
119 84 0.71
120 34 0.29
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.24
Consensus pattern (119 bp):
ATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
CGTGCGAGTTGATATACCGGGCTAAGACCCGAAGGCAATTGAGCAAGTGGATAT
Found at i:5452744 original size:40 final size:40
Alignment explanation
Indices: 5452689--5452910 Score: 374
Period size: 40 Copynumber: 5.6 Consensus size: 40
5452679 ATTTGAATAC
5452689 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
*
5452729 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
5452769 AT-CGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
*
5452808 ATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
* * *
5452848 ATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
* *
5452888 ACCCGGGTTAAGACCCGAAGGCA
1 ATCCGGGCTAAGACCCGAAGGCA
5452911 ATTGAGCTTG
Statistics
Matches: 172, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
39 38 0.22
40 134 0.78
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.23
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
Found at i:5452823 original size:79 final size:80
Alignment explanation
Indices: 5452689--5452914 Score: 382
Period size: 79 Copynumber: 2.8 Consensus size: 80
5452679 ATTTGAATAC
*
5452689 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCAAT
*
5452754 TGTGCGAGTTGATAT
66 TGTGCAAGTTGATAT
5452769 AT-CGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCAAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCAAT
5452833 TGTGCAAGTTGATAT
66 TGTGCAAGTTGATAT
* * * * *
5452848 ATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCAAT
5452913 TG
66 TG
5452915 AGCTTGTGGT
Statistics
Matches: 138, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
79 77 0.56
80 61 0.44
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (80 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCAAT
TGTGCAAGTTGATAT
Found at i:5452936 original size:119 final size:119
Alignment explanation
Indices: 5452689--5452937 Score: 383
Period size: 119 Copynumber: 2.1 Consensus size: 119
5452679 ATTTGAATAC
*
5452689 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
* * * * *
5452754 TGTGCGAGTTGATATATCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
66 CGTGCGAGTTGATATACCGGGCTAAGACCCGAAGGCAATTGAGCAAGTGGATAT
5452808 ATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
* * ** *
5452873 CGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATTGAGCTTGTGGTTAT
66 CGTGCGAGTTGATATA-CCGGGCTAAGACCCGAAGGCAATTGAGCAAGTGGATAT
5452928 ATCC-GGCTAA
1 ATCCGGGCTAA
5452938 ATTCCAAAGA
Statistics
Matches: 118, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
119 84 0.71
120 34 0.29
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.24
Consensus pattern (119 bp):
ATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATT
CGTGCGAGTTGATATACCGGGCTAAGACCCGAAGGCAATTGAGCAAGTGGATAT
Found at i:5456835 original size:10 final size:9
Alignment explanation
Indices: 5456818--5456842 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5456808 TATTTAGGTT
5456818 TTTTAAAAA
1 TTTTAAAAA
5456827 TTTTAAAAA
1 TTTTAAAAA
5456836 TTTTAAA
1 TTTTAAA
5456843 TTAGTAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:5459702 original size:3 final size:3
Alignment explanation
Indices: 5459694--5459748 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
5459684 TTGCCCCTAC
5459694 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5459742 TAT TAT T
1 TAT TAT T
5459749 GTCATTATTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:5462080 original size:6 final size:6
Alignment explanation
Indices: 5462069--5462094 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
5462059 GGTTTTATAA
5462069 TTTGTT TTTGTT TTTGTT TTTGTT TT
1 TTTGTT TTTGTT TTTGTT TTTGTT TT
5462095 ATATTATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (6 bp):
TTTGTT
Found at i:5464817 original size:9 final size:8
Alignment explanation
Indices: 5464792--5464825 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
5464782 AGTTAAAATT
5464792 AAAATTAA
1 AAAATTAA
5464800 AAAATTAA
1 AAAATTAA
5464808 AAAA-TATA
1 AAAATTA-A
5464816 AAAATTAA
1 AAAATTAA
5464824 AA
1 AA
5464826 TAGATCAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 2 0.08
8 20 0.83
9 2 0.08
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAATTAA
Found at i:5464827 original size:14 final size:15
Alignment explanation
Indices: 5464786--5464827 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
5464776 CTGTATAGTT
5464786 AAAATTAAAAT-TAA
1 AAAATTAAAATATAA
*
5464800 AAAATTAAAAAATATA
1 AAAATTAAAATATA-A
5464816 AAAATTAAAATA
1 AAAATTAAAATA
5464828 GATCAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 10 0.42
15 2 0.08
16 12 0.50
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAATTAAAATATAA
Found at i:5474390 original size:22 final size:24
Alignment explanation
Indices: 5474346--5474390 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
5474336 CTTTCAATGT
*
5474346 TTATATATTTTGTCAATTTAATTC
1 TTATATATTTTGTCAATTAAATTC
*
5474370 TTAT-TATTTT-TTAATTAAATT
1 TTATATATTTTGTCAATTAAATT
5474391 TAATGATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 9 0.47
23 6 0.32
24 4 0.21
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (24 bp):
TTATATATTTTGTCAATTAAATTC
Found at i:5484014 original size:15 final size:15
Alignment explanation
Indices: 5483994--5484022 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5483984 CAGACTTATT
5483994 ACAAAAGAAACAACA
1 ACAAAAGAAACAACA
5484009 ACAAAAGAAACAAC
1 ACAAAAGAAACAAC
5484023 TCTCTTTAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.72, C:0.21, G:0.07, T:0.00
Consensus pattern (15 bp):
ACAAAAGAAACAACA
Found at i:5485227 original size:53 final size:54
Alignment explanation
Indices: 5485103--5485304 Score: 193
Period size: 53 Copynumber: 3.8 Consensus size: 54
5485093 ATTAGGGTTT
* * * *
5485103 AAGGATACCATGTAAGACCATGCCAAGGTATGGAAATTGGTAAGGTTTCTAAGGT
1 AAGGATACCATGTAAGACCATGTCAAGGCATGG-CATTGGTAAGGTTTCTAAGGC
* * * *
5485158 AAGGAAATCATGTAAGACCATGTCAAGGCATGGCATTTGTGA-G-TTCATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGGCATGGCATTGGTAAGGTTTC-TAAGGC
* **
5485211 AAGGATACCATGTAAGACCATGTCAAGACATGGCAACGGTAA-GTTTC-AA---
1 AAGGATACCATGTAAGACCATGTCAAGGCATGGCATTGGTAAGGTTTCTAAGGC
* ** * *
5485260 AAGGATACCACGTAAGACCATGAAAAGTCATGGCAATGGTAAGGT
1 AAGGATACCATGTAAGACCATGTCAAGGCATGGCATTGGTAAGGT
5485305 ACCTGTGTAT
Statistics
Matches: 124, Mismatches: 20, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
49 37 0.30
50 2 0.02
52 5 0.04
53 42 0.34
54 9 0.07
55 29 0.23
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGTCAAGGCATGGCATTGGTAAGGTTTCTAAGGC
Found at i:5488942 original size:24 final size:24
Alignment explanation
Indices: 5488910--5488956 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
5488900 CTCTTTGTTT
5488910 AATGTGCACAGGTAATCCCCAAAA
1 AATGTGCACAGGTAATCCCCAAAA
5488934 AATGTGCACAGGTAATCCCCAAA
1 AATGTGCACAGGTAATCCCCAAA
5488957 CTTGACGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.26, G:0.17, T:0.17
Consensus pattern (24 bp):
AATGTGCACAGGTAATCCCCAAAA
Found at i:5491256 original size:20 final size:20
Alignment explanation
Indices: 5491217--5491271 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
5491207 AAATTATTAC
* *
5491217 AAAATTTTTAAAAATTATAA
1 AAAATTTATAAAAATCATAA
*
5491237 AATA-TTATAGAAAATCATAA
1 AAAATTTATA-AAAATCATAA
5491257 AAAATTTATAAAAAT
1 AAAATTTATAAAAAT
5491272 ATAGATATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 4 0.14
20 20 0.69
21 5 0.17
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (20 bp):
AAAATTTATAAAAATCATAA
Found at i:5491319 original size:20 final size:20
Alignment explanation
Indices: 5491294--5491331 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5491284 AAATATTATA
*
5491294 AAAAAATTTATATAAATTGT
1 AAAAAATATATATAAATTGT
*
5491314 AAAAAATATATATGAATT
1 AAAAAATATATATAAATT
5491332 ACGAAAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (20 bp):
AAAAAATATATATAAATTGT
Found at i:5493749 original size:12 final size:11
Alignment explanation
Indices: 5493734--5493788 Score: 56
Period size: 12 Copynumber: 4.7 Consensus size: 11
5493724 TATAAAAAGA
5493734 AAAATAATAGAT
1 AAAA-AATAGAT
*
5493746 AAAAAATAAAT
1 AAAAAATAGAT
*
5493757 GAAGAAATAGAT
1 -AAAAAATAGAT
5493769 AAATAAATAGAT
1 AAA-AAATAGAT
*
5493781 AAAGAATA
1 AAAAAATA
5493789 AAGAATAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
11 12 0.33
12 24 0.67
ACGTcount: A:0.69, C:0.00, G:0.11, T:0.20
Consensus pattern (11 bp):
AAAAAATAGAT
Found at i:5494038 original size:3 final size:3
Alignment explanation
Indices: 5494022--5494118 Score: 70
Period size: 3 Copynumber: 32.0 Consensus size: 3
5494012 AGAAAGAAAT
* * * * *
5494022 ATA ATA CTA CTA ATA ATA ATA ATG CTA A-A TTA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * *
5494069 CATTA ACA ATA ATA ATA ACA GTA ATA GTA ATA AAA ATA ATG ATA ATA
1 -A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5494116 ATA
1 ATA
5494119 TTAAAATTAC
Statistics
Matches: 71, Mismatches: 20, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
2 1 0.01
3 66 0.93
4 2 0.03
5 2 0.03
ACGTcount: A:0.59, C:0.06, G:0.04, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:5494055 original size:20 final size:20
Alignment explanation
Indices: 5494032--5494086 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
5494022 ATAATACTAC
**
5494032 TAATAATAATAATGCTAAAT
1 TAATAATAATAATAATAAAT
*
5494052 TAATAATAATAATAATACAT
1 TAATAATAATAATAATAAAT
*
5494072 TAACAATAATAATAA
1 TAATAATAATAATAA
5494087 CAGTAATAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (20 bp):
TAATAATAATAATAATAAAT
Found at i:5495360 original size:18 final size:18
Alignment explanation
Indices: 5495331--5495407 Score: 120
Period size: 18 Copynumber: 4.3 Consensus size: 18
5495321 ATAATCTTCA
5495331 ATGATATGCAATCTTAGAT
1 ATGAT-TGCAATCTTAGAT
5495350 ATGATTGCAATCTTAGAT
1 ATGATTGCAATCTTAGAT
*
5495368 ATGA-TACAATCTTAGAT
1 ATGATTGCAATCTTAGAT
*
5495385 ATGATTCCAATCTTAGAT
1 ATGATTGCAATCTTAGAT
5495403 ATGAT
1 ATGAT
5495408 ATACAATATT
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
17 16 0.29
18 34 0.62
19 5 0.09
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (18 bp):
ATGATTGCAATCTTAGAT
Found at i:5495372 original size:37 final size:36
Alignment explanation
Indices: 5495331--5495420 Score: 137
Period size: 35 Copynumber: 2.5 Consensus size: 36
5495321 ATAATCTTCA
*
5495331 ATGATATGCAATCTTAGATATGATTGCAATCTTAGAT
1 ATGATAT-CAATCTTAGATATGATTCCAATCTTAGAT
5495368 ATGATA-CAATCTTAGATATGATTCCAATCTTAGAT
1 ATGATATCAATCTTAGATATGATTCCAATCTTAGAT
*
5495403 ATGATATACAATATTAGA
1 ATGATAT-CAATCTTAGA
5495421 AGATATGATT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
35 34 0.69
37 15 0.31
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (36 bp):
ATGATATCAATCTTAGATATGATTCCAATCTTAGAT
Found at i:5495949 original size:15 final size:16
Alignment explanation
Indices: 5495906--5495964 Score: 50
Period size: 16 Copynumber: 3.5 Consensus size: 16
5495896 CAATATATTT
*
5495906 TATATATTTTATATAA
1 TATATTTTTTATATAA
5495922 T-TATTATTCTTATA-AA
1 TATATT-TT-TTATATAA
5495938 TATATTTTTTATTATATA
1 TATATTTTTTA-TATA-A
5495956 TTATATTTT
1 -TATATTTT
5495965 AAATTTATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 11
0.74 0.02 0.23
Matches are distributed among these distances:
15 6 0.17
16 10 0.29
17 10 0.29
18 1 0.03
19 8 0.23
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.63
Consensus pattern (16 bp):
TATATTTTTTATATAA
Found at i:5495968 original size:30 final size:29
Alignment explanation
Indices: 5495899--5495973 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 29
5495889 TCTAAACCAA
5495899 TATATTTT--ATATATTTTATATAATTAT
1 TATATTTTAAATATATTTTATATAATTAT
* *
5495926 TAT-TCTTATAAATATATTTTTTATTATATAT
1 TATAT-TT-TAAATATATTTTATATAAT-TAT
*
5495957 TATATTTTAAATTTATT
1 TATATTTTAAATATATT
5495974 ATAAATATCA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
26 1 0.03
27 5 0.13
28 1 0.03
30 23 0.59
31 8 0.21
32 1 0.03
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (29 bp):
TATATTTTAAATATATTTTATATAATTAT
Found at i:5503633 original size:6 final size:6
Alignment explanation
Indices: 5503617--5503694 Score: 51
Period size: 6 Copynumber: 13.7 Consensus size: 6
5503607 ATTTCAAAAA
* * *
5503617 AAAAGG AAAAAGG AAAA-G AAAAAG AAAA-- AAAAGA AAAAGG AAAATG
1 AAAAGG -AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG
* *
5503663 -AAA-- AAAAGA AAAAGG AAAGAGA AAAAGG AAAA
1 AAAAGG AAAAGG AAAAGG AAA-AGG AAAAGG AAAA
5503695 ATAAAAAAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
4 7 0.12
5 8 0.14
6 33 0.56
7 11 0.19
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.01
Consensus pattern (6 bp):
AAAAGG
Found at i:5503647 original size:21 final size:22
Alignment explanation
Indices: 5503634--5503688 Score: 85
Period size: 21 Copynumber: 2.5 Consensus size: 22
5503624 AAAAGGAAAA
5503634 GAAAAAGAAAAAAAAGAAAAAG
1 GAAAAAGAAAAAAAAGAAAAAG
*
5503656 GAAAATG-AAAAAAAGAAAAAG
1 GAAAAAGAAAAAAAAGAAAAAG
*
5503677 GAAAGAGAAAAA
1 GAAAAAGAAAAA
5503689 GGAAAAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 19 0.66
22 10 0.34
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (22 bp):
GAAAAAGAAAAAAAAGAAAAAG
Found at i:5503652 original size:27 final size:27
Alignment explanation
Indices: 5503612--5503715 Score: 111
Period size: 27 Copynumber: 3.8 Consensus size: 27
5503602 CTTCTATTTC
*
5503612 AAAAAAAAAGGAAAAAGGAAAA-GAAA
1 AAAAAAAAAAGAAAAAGGAAAAGGAAA
*
5503638 AAGAAAAAAAAGAAAAAGGAAAATGAAA
1 AA-AAAAAAAAGAAAAAGGAAAAGGAAA
* * *
5503666 AAAAGAAAAAGGAAAGAGAAAAAGGAAA
1 AAAA-AAAAAAGAAAAAGGAAAAGGAAA
* * *
5503694 AATAAAAAAATAAAAAGAAAAA
1 AAAAAAAAAAGAAAAAGGAAAA
5503716 TGGAGAGGCC
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
26 2 0.03
27 36 0.55
28 28 0.42
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (27 bp):
AAAAAAAAAAGAAAAAGGAAAAGGAAA
Found at i:5503695 original size:21 final size:21
Alignment explanation
Indices: 5503618--5503695 Score: 60
Period size: 21 Copynumber: 3.9 Consensus size: 21
5503608 TTTCAAAAAA
5503618 AAAG-GAAAAAGGAAAAGAA--
1 AAAGAGAAAAAGGAAAA-AAGG
* *
5503637 AAAGAAAAAAAAG-AAAAAGG
1 AAAGAGAAAAAGGAAAAAAGG
*
5503657 AAA-ATGAAAAA-AAGAAAAAGG
1 AAAGA-GAAAAAGGA-AAAAAGG
5503678 AAAGAGAAAAAGGAAAAA
1 AAAGAGAAAAAGGAAAAA
5503696 TAAAAAAATA
Statistics
Matches: 46, Mismatches: 5, Indels: 14
0.71 0.08 0.22
Matches are distributed among these distances:
18 2 0.04
19 8 0.17
20 14 0.30
21 20 0.43
22 2 0.04
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.01
Consensus pattern (21 bp):
AAAGAGAAAAAGGAAAAAAGG
Found at i:5503700 original size:13 final size:13
Alignment explanation
Indices: 5503612--5503715 Score: 77
Period size: 13 Copynumber: 7.8 Consensus size: 13
5503602 CTTCTATTTC
5503612 AAAA-AAAAAGGA
1 AAAAGAAAAAGGA
*
5503624 AAAAGGAAAA-GA
1 AAAAGAAAAAGGA
*
5503636 AAAAGAAAAAAAAGA
1 AAAAG--AAAAAGGA
* *
5503651 AAAAGGAAAATGAAA
1 AAAA-GAAAAAG-GA
5503666 AAAAGAAAAAGGA
1 AAAAGAAAAAGGA
*
5503679 AAGAGAAAAAGGA
1 AAAAGAAAAAGGA
* **
5503692 AAAATAAAAAAATA
1 AAAA-GAAAAAGGA
5503706 AAAAGAAAAA
1 AAAAGAAAAA
5503716 TGGAGAGGCC
Statistics
Matches: 72, Mismatches: 13, Indels: 13
0.73 0.13 0.13
Matches are distributed among these distances:
12 11 0.15
13 25 0.35
14 24 0.33
15 11 0.15
16 1 0.01
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (13 bp):
AAAAGAAAAAGGA
Found at i:5503701 original size:34 final size:35
Alignment explanation
Indices: 5503630--5503715 Score: 113
Period size: 34 Copynumber: 2.5 Consensus size: 35
5503620 AGGAAAAAGG
5503630 AAAAGAAAAAGAAAAAAAAGAAAAAGGAAAATGAAA
1 AAAAGAAAAAG-AAAAAAAGAAAAAGGAAAATGAAA
* *
5503666 AAAAGAAAAAG-GAAAGAGAAAAAGGAAAAAT-AAA
1 AAAAGAAAAAGAAAAAAAGAAAAAGG-AAAATGAAA
*
5503700 AAAATAAAAAGAAAAA
1 AAAAGAAAAAGAAAAA
5503716 TGGAGAGGCC
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
34 25 0.57
35 8 0.18
36 11 0.25
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.03
Consensus pattern (35 bp):
AAAAGAAAAAGAAAAAAAGAAAAAGGAAAATGAAA
Found at i:5504923 original size:119 final size:119
Alignment explanation
Indices: 5504784--5505440 Score: 1136
Period size: 119 Copynumber: 5.5 Consensus size: 119
5504774 CAGATCGAAG
*
5504784 ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGATATTCTTGTGT
1 ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGT
* *
5504849 TTACAAGGAACAAATCGAGGACATAGAAGATTTGACTCTCAGACGTTCTCAGAT
66 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGATGTTCTCAGAT
* *
5504903 ATAGTAGATCTAACCTTCAGATGTTTATACTAAAGCAGATCCAAGATGATTTGGTATTCTTGTGT
1 ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGT
* *
5504968 TTACAAGAAACAAATCGAGGACATAGCAGATTTGGCTCTCAGATGTTCTCAGAT
66 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGATGTTCTCAGAT
* *
5505022 ATAGCAGGTCTAACCTTCAGATGTTTAGACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGT
1 ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGT
*
5505087 TTACAAGGAACAAATTGAGGACATAGCAGATTT-AGCTCTCAGATGTTCTCAGAT
66 TTACAAGGAACAAATCGAGGACATAGCAGATTTGA-CTCTCAGATGTTCTCAGAT
* *
5505141 ATAGCAGATCTAACCTTCAGATGTTTAGACTGAAACAGATCCAAGATGATTTGGTATTCTTGTGT
1 ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGT
*
5505206 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGATGTTCTTAGAT
66 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGATGTTCTCAGAT
*
5505260 ATAGCAGATCTAGCCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGT
1 ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGT
* *
5505325 TTACAAGGAACAAATCAAGGACATAGCGGATTTGACTCTCAGATGTTCTCAGAT
66 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGATGTTCTCAGAT
* *
5505379 ATAGCAGATCTAGCCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATTCTTG
1 ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTG
5505441 CGAGGACATA
Statistics
Matches: 511, Mismatches: 25, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
119 510 1.00
120 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.31
Consensus pattern (119 bp):
ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGT
TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGATGTTCTCAGAT
Found at i:5506113 original size:19 final size:19
Alignment explanation
Indices: 5506089--5506195 Score: 166
Period size: 19 Copynumber: 5.8 Consensus size: 19
5506079 ATCTTCAATT
*
5506089 ATATGCAATCTTAGATGTG
1 ATATGCAATCTTAGATATG
5506108 ATATGCAATCTTAGATATG
1 ATATGCAATCTTAGATATG
5506127 ATA--CAATCTTAGATATG
1 ATATGCAATCTTAGATATG
5506144 AT-TGCAATCTTAGATATG
1 ATATGCAATCTTAGATATG
*
5506162 ATATACAATCTTAGATATG
1 ATATGCAATCTTAGATATG
*
5506181 ATATACAATCTTAGA
1 ATATGCAATCTTAGA
5506196 AGATATGATT
Statistics
Matches: 83, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
17 16 0.19
18 16 0.19
19 51 0.61
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.36
Consensus pattern (19 bp):
ATATGCAATCTTAGATATG
Found at i:5506126 original size:14 final size:15
Alignment explanation
Indices: 5506107--5506181 Score: 62
Period size: 17 Copynumber: 4.5 Consensus size: 15
5506097 TCTTAGATGT
5506107 GATATG-CAATCTTA
1 GATATGACAATCTTA
5506121 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
5506138 GATATGATTGCAATCTTA
1 GATATGA---CAATCTTA
5506156 GATATGATATACAATCTTA
1 GATATG----ACAATCTTA
5506175 GATATGA
1 GATATGA
5506182 TATACAATCT
Statistics
Matches: 51, Mismatches: 0, Indels: 19
0.73 0.00 0.27
Matches are distributed among these distances:
14 6 0.12
15 2 0.04
17 14 0.27
18 14 0.27
19 14 0.27
22 1 0.02
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.36
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:5506703 original size:18 final size:17
Alignment explanation
Indices: 5506679--5506738 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
5506669 CCAATATATT
5506679 TTATATTTTTTATATAA
1 TTATATTTTTTATATAA
*
5506696 TTAT-TATTCTTATA-AA
1 TTATAT-TTTTTATATAA
5506712 -TATATTTTTTATTATATA
1 TTATATTTTTTA-TATA-A
5506730 TTATATTTT
1 TTATATTTT
5506739 AAATTTATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
15 8 0.23
16 6 0.17
17 12 0.34
18 1 0.03
19 8 0.23
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATATTTTTTATATAA
Found at i:5506723 original size:15 final size:16
Alignment explanation
Indices: 5506680--5506738 Score: 59
Period size: 16 Copynumber: 3.5 Consensus size: 16
5506670 CAATATATTT
5506680 TATATTTTTTATATAA
1 TATATTTTTTATATAA
5506696 T-TATTATTCTTATA-AA
1 TATATT-TT-TTATATAA
5506712 TATATTTTTTATTATATA
1 TATATTTTTTA-TATA-A
5506730 TTATATTTT
1 -TATATTTT
5506739 AAATTTATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
15 7 0.19
16 10 0.28
17 10 0.28
18 1 0.03
19 8 0.22
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (16 bp):
TATATTTTTTATATAA
Found at i:5511166 original size:26 final size:26
Alignment explanation
Indices: 5511113--5511230 Score: 146
Period size: 26 Copynumber: 4.5 Consensus size: 26
5511103 AAAATAGTTT
* * **
5511113 TATTACTTACTTTAAATTGTCATATA
1 TATTATTTATTTTAAATTGTTTTATA
* *
5511139 TATCATTTATTTTAAATTGTTTTGTA
1 TATTATTTATTTTAAATTGTTTTATA
*
5511165 TATTATTTATTTTAAATTGTTTTGTA
1 TATTATTTATTTTAAATTGTTTTATA
* * *
5511191 TATTGTTTATTTCAAATTGTTTTACA
1 TATTATTTATTTTAAATTGTTTTATA
5511217 TATTATTTATTTTA
1 TATTATTTATTTTA
5511231 GGCCAATTAC
Statistics
Matches: 79, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 79 1.00
ACGTcount: A:0.29, C:0.05, G:0.06, T:0.60
Consensus pattern (26 bp):
TATTATTTATTTTAAATTGTTTTATA
Found at i:5511211 original size:14 final size:13
Alignment explanation
Indices: 5511144--5511212 Score: 52
Period size: 14 Copynumber: 5.2 Consensus size: 13
5511134 ATATATATCA
5511144 TTTATTTTAAATTG
1 TTTA-TTTAAATTG
* * *
5511158 TTT-TGTATATTA
1 TTTATTTAAATTG
5511170 TTTATTTTAAATTG
1 TTTA-TTTAAATTG
* *
5511184 TTT-TGTATATTG
1 TTTATTTAAATTG
5511196 TTTATTTCAAATTG
1 TTTATTT-AAATTG
5511210 TTT
1 TTT
5511213 TACATATTAT
Statistics
Matches: 41, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
12 19 0.46
13 2 0.05
14 20 0.49
ACGTcount: A:0.25, C:0.01, G:0.09, T:0.65
Consensus pattern (13 bp):
TTTATTTAAATTG
Found at i:5511271 original size:18 final size:18
Alignment explanation
Indices: 5511229--5511267 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5511219 TTATTTATTT
* *
5511229 TAGGCCAATTACATGTGT
1 TAGGCCAATTACATATGA
5511247 TAGGCCAATTACATAT-A
1 TAGGCCAATTACATATGA
5511264 TAGG
1 TAGG
5511268 GCCATGTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (18 bp):
TAGGCCAATTACATATGA
Found at i:5519459 original size:40 final size:40
Alignment explanation
Indices: 5519415--5519498 Score: 125
Period size: 40 Copynumber: 2.1 Consensus size: 40
5519405 TAACATATTG
*
5519415 GCTAAATATGGCACTTAGTGTGC-AGTTCGATATAGCTTCA
1 GCTAAATATGGCACTTAGTGTGCGA-TTCGAGATAGCTTCA
* *
5519455 GCTAAATTTGGCACTTAGTGTGCGATTTGAGATAGCTTCA
1 GCTAAATATGGCACTTAGTGTGCGATTCGAGATAGCTTCA
5519495 GCTA
1 GCTA
5519499 TGTACAGCAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 39 0.98
41 1 0.03
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (40 bp):
GCTAAATATGGCACTTAGTGTGCGATTCGAGATAGCTTCA
Found at i:5519561 original size:28 final size:28
Alignment explanation
Indices: 5519530--5519588 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
5519520 GATATCAAAT
5519530 ATGGCACTCAGTATGCGAAATATTGAAA
1 ATGGCACTCAGTATGCGAAATATTGAAA
* * * * *
5519558 ATGGCAGTTAGTGTGCGAGATATTGAGA
1 ATGGCACTCAGTATGCGAAATATTGAAA
5519586 ATG
1 ATG
5519589 ACATTTAGTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.34, C:0.10, G:0.29, T:0.27
Consensus pattern (28 bp):
ATGGCACTCAGTATGCGAAATATTGAAA
Found at i:5519596 original size:28 final size:28
Alignment explanation
Indices: 5519543--5519608 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
5519533 GCACTCAGTA
*
5519543 TGCGAAATATTGAAAATGGCAGTTAGTG
1 TGCGAAATATTGAAAATGACAGTTAGTG
* * *
5519571 TGCGAGATATTGAGAATGACATTTAGTG
1 TGCGAAATATTGAAAATGACAGTTAGTG
*
5519599 TGCAAAATAT
1 TGCGAAATAT
5519609 CGAATGATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.36, C:0.08, G:0.26, T:0.30
Consensus pattern (28 bp):
TGCGAAATATTGAAAATGACAGTTAGTG
Found at i:5521511 original size:27 final size:28
Alignment explanation
Indices: 5521468--5521522 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
5521458 GAATGTTGCC
* *
5521468 ATTGATGAATATGTATGAGT-TTTGATG
1 ATTGATGAAGATGTATGAATATTTGATG
5521495 ATTGATGATAGAT-TATGAATATTTGATG
1 ATTGATGA-AGATGTATGAATATTTGATG
5521523 TTAGTTAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 14 0.58
28 10 0.42
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.44
Consensus pattern (28 bp):
ATTGATGAAGATGTATGAATATTTGATG
Found at i:5529505 original size:30 final size:30
Alignment explanation
Indices: 5529469--5529527 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
5529459 AGTGCAAATC
* *
5529469 CCCATGTAGTGCAAACTCATGAGCGAACCT
1 CCCATGTAGTACAAACCCATGAGCGAACCT
5529499 CCCATGTAGTACAAACCCATGAGCGAACC
1 CCCATGTAGTACAAACCCATGAGCGAACC
5529528 CTTGTGCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.32, G:0.19, T:0.17
Consensus pattern (30 bp):
CCCATGTAGTACAAACCCATGAGCGAACCT
Found at i:5529798 original size:33 final size:33
Alignment explanation
Indices: 5529717--5529803 Score: 120
Period size: 33 Copynumber: 2.6 Consensus size: 33
5529707 CTTAAGACAT
* *
5529717 TTATACAAGCCTATATATATGTGAACCATAGGA
1 TTATGCAAGCCTATATGTATGTGAACCATAGGA
* *
5529750 TTATGCAAGCCTATATGTATGTGGACCCTAGGA
1 TTATGCAAGCCTATATGTATGTGAACCATAGGA
**
5529783 TTATGCAAGTTTATATGTATG
1 TTATGCAAGCCTATATGTATG
5529804 CAAACCCTAG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (33 bp):
TTATGCAAGCCTATATGTATGTGAACCATAGGA
Found at i:5529811 original size:33 final size:33
Alignment explanation
Indices: 5529717--5529814 Score: 106
Period size: 33 Copynumber: 3.0 Consensus size: 33
5529707 CTTAAGACAT
* * ** *
5529717 TTATACAAGCCTATATATATGTGAACCATAGGA
1 TTATGCAAGCCTATATGTATGCAAACCCTAGGA
***
5529750 TTATGCAAGCCTATATGTATGTGGACCCTAGGA
1 TTATGCAAGCCTATATGTATGCAAACCCTAGGA
**
5529783 TTATGCAAGTTTATATGTATGCAAACCCTAGG
1 TTATGCAAGCCTATATGTATGCAAACCCTAGG
5529815 TACATACGAG
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (33 bp):
TTATGCAAGCCTATATGTATGCAAACCCTAGGA
Found at i:5529918 original size:22 final size:22
Alignment explanation
Indices: 5529892--5529949 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
5529882 CATAAAACTA
*
5529892 GCTATATGCGAACCTTATACAT
1 GCTATATGCGAACCTTATAAAT
*
5529914 GCTATATGCGAACTTTATAAAT
1 GCTATATGCGAACCTTATAAAT
*
5529936 GCTACATGCGAACC
1 GCTATATGCGAACC
5529950 CCTGTATATG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (22 bp):
GCTATATGCGAACCTTATAAAT
Found at i:5530604 original size:41 final size:41
Alignment explanation
Indices: 5530559--5530641 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
5530549 TTTACTGTTT
5530559 GAATAATTATATATAATGGTTTAAGGTTAGTCTCACATTGA
1 GAATAATTATATATAATGGTTTAAGGTTAGTCTCACATTGA
5530600 GAATAATTATATATAATGGTTTAAGGTTAGTCTCACATTGA
1 GAATAATTATATATAATGGTTTAAGGTTAGTCTCACATTGA
5530641 G
1 G
5530642 CCGTTCTAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.39
Consensus pattern (41 bp):
GAATAATTATATATAATGGTTTAAGGTTAGTCTCACATTGA
Found at i:5535299 original size:30 final size:31
Alignment explanation
Indices: 5535258--5535315 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
5535248 CTTTGATCAC
*
5535258 TGAATTATTTAAAA-ATTTCATTTAAGTTAT
1 TGAACTATTTAAAATATTTCATTTAAGTTAT
* *
5535288 TGAACTATTTAAAATTTTTTATTTAAGT
1 TGAACTATTTAAAATATTTCATTTAAGT
5535316 CACTAGTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 13 0.54
31 11 0.46
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.52
Consensus pattern (31 bp):
TGAACTATTTAAAATATTTCATTTAAGTTAT
Found at i:5537305 original size:21 final size:21
Alignment explanation
Indices: 5537281--5537339 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
5537271 TATTTTTTAA
* *
5537281 AATTTTTTATCTTTTTTTTGT
1 AATTTTATATCTTTTTTTTGC
**
5537302 AATTTTATATAATTTTTTTGC
1 AATTTTATATCTTTTTTTTGC
*
5537323 ACTTTTATATGCTTTTT
1 AATTTTATAT-CTTTTT
5537340 ATAATAATTT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 26 0.87
22 4 0.13
ACGTcount: A:0.20, C:0.07, G:0.05, T:0.68
Consensus pattern (21 bp):
AATTTTATATCTTTTTTTTGC
Found at i:5537466 original size:9 final size:9
Alignment explanation
Indices: 5537361--5537549 Score: 64
Period size: 9 Copynumber: 20.6 Consensus size: 9
5537351 AATATTTTCC
*
5537361 ATTTTTTTA
1 ATTTTTATA
**
5537370 ATTAATATA
1 ATTTTTATA
*
5537379 ATTTTT-TT
1 ATTTTTATA
*
5537387 ATTTTCATA
1 ATTTTTATA
*
5537396 ATTTATAT-
1 ATTTTTATA
* *
5537404 ATTTTAAGTC
1 ATTTTTA-TA
*
5537414 ATTTATAATA
1 ATTT-TTATA
*
5537424 ATGTTTATA
1 ATTTTTATA
5537433 ATTTTTGAGTA
1 ATTTTT-A-TA
***
5537444 ATTACAAT-
1 ATTTTTATA
5537452 ATTTTTATA
1 ATTTTTATA
*
5537461 ATTTTT-TC
1 ATTTTTATA
*
5537469 ACTTTTATA
1 ATTTTTATA
*
5537478 TTTTTTATAA
1 ATTTTTAT-A
*
5537488 ATTTATATA
1 ATTTTTATA
* *
5537497 TTTTTTATG
1 ATTTTTATA
5537506 ATTTTCTATCA
1 ATTTT-TAT-A
*
5537517 A-TTTTATC
1 ATTTTTATA
*
5537525 ATCTTTAATA
1 AT-TTTTATA
*
5537535 TTTTTTAATA
1 ATTTTT-ATA
5537545 ATTTT
1 ATTTT
5537550 AAGCAAAAAA
Statistics
Matches: 126, Mismatches: 40, Indels: 27
0.65 0.21 0.14
Matches are distributed among these distances:
8 23 0.18
9 58 0.46
10 36 0.29
11 9 0.07
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.61
Consensus pattern (9 bp):
ATTTTTATA
Found at i:5539831 original size:27 final size:27
Alignment explanation
Indices: 5539812--5540193 Score: 541
Period size: 27 Copynumber: 14.1 Consensus size: 27
5539802 ATTACCAAAG
* *
5539812 TACCCTCGATTTACAGAATTACCCTTT
1 TACCCTCGATTTATAGAATTACCGTTT
* *
5539839 TACCCTCAATTTATAGAATTATCGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
**
5539866 TACCCTCGATTTACGGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
5539893 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
* *
5539920 TACCCTAGATTTATAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCGTTT
*
5539947 TACCCTCGAATTATAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
* *
5539974 TACCCTCGATTTACAGAATTATCGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
*
5540001 TACCCTCGATTTATAGAATTATCGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
* * *
5540028 TACCCTTGATTTA-CGAAATTACCATTT
1 TACCCTCGATTTATAG-AATTACCGTTT
***
5540055 TACCCTCGATTTATAGAATTATTATTT
1 TACCCTCGATTTATAGAATTACCGTTT
5540082 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
*
5540109 TACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
* * *
5540136 TACCTTCGATTTACAGAATTACCGTGT
1 TACCCTCGATTTATAGAATTACCGTTT
*
5540163 TACCCTCGATTTATAGAATTACCGTAT
1 TACCCTCGATTTATAGAATTACCGTTT
5540190 TACC
1 TACC
5540194 GTTTTACCTT
Statistics
Matches: 317, Mismatches: 36, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
26 1 0.00
27 315 0.99
28 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.40
Consensus pattern (27 bp):
TACCCTCGATTTATAGAATTACCGTTT
Found at i:5540166 original size:35 final size:35
Alignment explanation
Indices: 5540126--5540219 Score: 87
Period size: 27 Copynumber: 2.9 Consensus size: 35
5540116 GATTTACAGA
5540126 ATTACCGTTTTACCTTCGATTTACAGAATTACCG-
1 ATTACCGTTTTACCTTCGATTTACAGAATTACCGT
* *
5540160 --T---G--TTACCCTCGATTTATAGAATTACCGT
1 ATTACCGTTTTACCTTCGATTTACAGAATTACCGT
** *
5540188 ATTACCGTTTTACCTTTAATTTACAAAATTAC
1 ATTACCGTTTTACCTTCGATTTACAGAATTAC
5540220 TGAAATACCC
Statistics
Matches: 45, Mismatches: 7, Indels: 15
0.67 0.10 0.22
Matches are distributed among these distances:
27 23 0.51
29 1 0.02
30 1 0.02
32 1 0.02
33 1 0.02
35 18 0.40
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (35 bp):
ATTACCGTTTTACCTTCGATTTACAGAATTACCGT
Found at i:5540245 original size:62 final size:62
Alignment explanation
Indices: 5540126--5540247 Score: 145
Period size: 62 Copynumber: 2.0 Consensus size: 62
5540116 GATTTACAGA
* * *** * *
5540126 ATTACCGTTTTACCTTCGATTTACAGAATTACCGTGTTACCCTCGATTTATAGAATTACCGT
1 ATTACCGTTTTACCTTCAATTTACAAAATTACCGAAATACCCTCGATTTACAAAATTACCGT
* * * *
5540188 ATTACCGTTTTACCTTTAATTTACAAAATTACTGAAATACCCTTGGTTTACAAAATTACC
1 ATTACCGTTTTACCTTCAATTTACAAAATTACCGAAATACCCTCGATTTACAAAATTACC
5540248 AAAATACCCT
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
62 49 1.00
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (62 bp):
ATTACCGTTTTACCTTCAATTTACAAAATTACCGAAATACCCTCGATTTACAAAATTACCGT
Found at i:5540365 original size:27 final size:27
Alignment explanation
Indices: 5540212--5540474 Score: 198
Period size: 27 Copynumber: 9.8 Consensus size: 27
5540202 TTTAATTTAC
** * * **
5540212 AAAATTACTGAAATACCCTTGGTTTAC
1 AAAATTACCAAAATACCCCTAGTTTGT
* ** *
5540239 AAAATTACCAAAATA-CCCTCGATCAGG
1 AAAATTACCAAAATACCCCTAG-TTTGT
5540266 AAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTAGTTTGT
* *
5540293 AAAATTACCAAAATACTCCTGGTTTGT
1 AAAATTACCAAAATACCCCTAGTTTGT
*
5540320 AAAATTACCAAAATACCCCTAGCTTGT
1 AAAATTACCAAAATACCCCTAGTTTGT
5540347 AAAATTACCAAAATACCCCT-GATTTGT
1 AAAATTACCAAAATACCCCTAG-TTTGT
* * * *
5540374 GAAATTATCGAAATA-CCCTCGATTTGT
1 AAAATTACCAAAATACCCCTAG-TTTGT
**
5540401 AAAA-TA-CAGAAATACCCCT-GTAGGGT
1 AAAATTACCA-AAATACCCCTAGT-TTGT
* ** *
5540427 AGAATTACTGAAATACCCCT-GTATGGT
1 AAAATTACCAAAATACCCCTAGT-TTGT
* *
5540454 AGAATTACTAAAATACCCCTA
1 AAAATTACCAAAATACCCCTA
5540475 TAGGATAGAA
Statistics
Matches: 196, Mismatches: 30, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
25 2 0.01
26 22 0.11
27 167 0.85
28 5 0.03
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.28
Consensus pattern (27 bp):
AAAATTACCAAAATACCCCTAGTTTGT
Found at i:5540373 original size:54 final size:54
Alignment explanation
Indices: 5540212--5540473 Score: 221
Period size: 54 Copynumber: 4.9 Consensus size: 54
5540202 TTTAATTTAC
** * * ** ** *
5540212 AAAATTACTGAAATACCCTTGGTTTACAAAATTACCAAAATA-CCCTCGATCAGG
1 AAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCT-GATTTGT
* *
5540266 AAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACTCCTGGTTTGT
1 AAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGATTTGT
*
5540320 AAAATTACCAAAATACCCCTAGCTTGTAAAATTACCAAAATACCCCTGATTTGT
1 AAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGATTTGT
* * * * **
5540374 GAAATTATCGAAATA-CCCTCGATTTGTAAAA-TA-CAGAAATACCCCTG-TAGGGT
1 AAAATTACCAAAATACCCCTAG-TTTGTAAAATTACCA-AAATACCCCTGAT-TTGT
* ** * * *
5540427 AGAATTACTGAAATACCCCT-GTATGGTAGAATTACTAAAATACCCCT
1 AAAATTACCAAAATACCCCTAGT-TTGTAAAATTACCAAAATACCCCT
5540474 ATAGGATAGA
Statistics
Matches: 172, Mismatches: 28, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
52 4 0.02
53 38 0.22
54 126 0.73
55 4 0.02
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.28
Consensus pattern (54 bp):
AAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGATTTGT
Found at i:5540400 original size:81 final size:80
Alignment explanation
Indices: 5540212--5540419 Score: 228
Period size: 81 Copynumber: 2.6 Consensus size: 80
5540202 TTTAATTTAC
** *
5540212 AAAATTACTGAAATACCCTTGGTTTACAAAATTACCAAAATA-CCCTCGATCAGGAAAATTACCA
1 AAAATTAC-GAAATACCC-TGGTTTGTAAAATTACCAAAATACCCCTAGATCAGGAAAATTACCA
5540276 AAATACCCCTAGTTTGT
64 AAATACCCCTAGTTTGT
* * * *
5540293 AAAATTACCAAAATACTCCTGGTTTGTAAAATTACCAAAATACCCCTAGCT-TGTAAAATTACCA
1 AAAATTA-CGAAATAC-CCTGGTTTGTAAAATTACCAAAATACCCCTAGATCAGGAAAATTACCA
5540357 AAATACCCCT-GATTTGT
64 AAATACCCCTAG-TTTGT
* *
5540374 GAAATTATCGAAATACCCTCGATTTGTAAAA-TA-CAGAAATACCCCT
1 AAAATTA-CGAAATACCCT-GGTTTGTAAAATTACCA-AAATACCCCT
5540420 GTAGGGTAGA
Statistics
Matches: 110, Mismatches: 11, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
79 2 0.02
80 16 0.15
81 83 0.75
82 9 0.08
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.28
Consensus pattern (80 bp):
AAAATTACGAAATACCCTGGTTTGTAAAATTACCAAAATACCCCTAGATCAGGAAAATTACCAAA
ATACCCCTAGTTTGT
Found at i:5540483 original size:27 final size:27
Alignment explanation
Indices: 5540409--5540677 Score: 353
Period size: 27 Copynumber: 10.0 Consensus size: 27
5540399 GTAAAATACA
5540409 GAAATACCCCTGTAGGGTAGAATTACT
1 GAAATACCCCTGTAGGGTAGAATTACT
*
5540436 GAAATACCCCTGTATGGTAGAATTACT
1 GAAATACCCCTGTAGGGTAGAATTACT
* * *
5540463 AAAATACCCCTATAGGATAGAATTA-T
1 GAAATACCCCTGTAGGGTAGAATTACT
* *
5540489 CGAAATACCCTTGTAGGGTAGAAATACT
1 -GAAATACCCCTGTAGGGTAGAATTACT
*
5540517 AAAATACCCCTGTAGGGTAGAATTACT
1 GAAATACCCCTGTAGGGTAGAATTACT
5540544 GAAATACCCCTGTAGGGTAGAATTACT
1 GAAATACCCCTGTAGGGTAGAATTACT
* *
5540571 GAAATACCCTTGTACGGTAGAATTAC-
1 GAAATACCCCTGTAGGGTAGAATTACT
* * * *
5540597 CAAGATACCCTTGTAGGGTAGAAATACC
1 GAA-ATACCCCTGTAGGGTAGAATTACT
*
5540625 GAAATACCCCTGTATGGTAGAATTACT
1 GAAATACCCCTGTAGGGTAGAATTACT
* * *
5540652 GAGATACCCTTGTAGGGTAAAATTAC
1 GAAATACCCCTGTAGGGTAGAATTAC
5540678 CATTTTGCCC
Statistics
Matches: 210, Mismatches: 28, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
26 3 0.01
27 204 0.97
28 3 0.01
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (27 bp):
GAAATACCCCTGTAGGGTAGAATTACT
Found at i:5540967 original size:27 final size:26
Alignment explanation
Indices: 5540923--5540974 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
5540913 CTTGCTGTAA
*
5540923 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
5540950 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
5540975 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:5541202 original size:6 final size:6
Alignment explanation
Indices: 5541193--5541280 Score: 74
Period size: 6 Copynumber: 14.3 Consensus size: 6
5541183 TTGCATTCAC
*
5541193 ATTCTG ATTCTG ATTCT- CTTACCTG ATTCTG ATTCTG ATTCTG -TTACTTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATT-C-TG
* * *
5541243 ATTTTG ATTCTG ATTCTC ATTTTG ATTCT- AGTTCTG AT
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG A-TTCTG AT
5541281 AATGTTCTTA
Statistics
Matches: 66, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
5 5 0.08
6 52 0.79
7 5 0.08
8 4 0.06
ACGTcount: A:0.17, C:0.17, G:0.14, T:0.52
Consensus pattern (6 bp):
ATTCTG
Found at i:5541221 original size:25 final size:25
Alignment explanation
Indices: 5541193--5541260 Score: 109
Period size: 25 Copynumber: 2.7 Consensus size: 25
5541183 TTGCATTCAC
5541193 ATTCTGATTCTGATTCTCTTACCTG
1 ATTCTGATTCTGATTCTCTTACCTG
* *
5541218 ATTCTGATTCTGATTCTGTTACTTG
1 ATTCTGATTCTGATTCTCTTACCTG
*
5541243 ATTTTGATTCTGATTCTC
1 ATTCTGATTCTGATTCTC
5541261 ATTTTGATTC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.16, C:0.19, G:0.13, T:0.51
Consensus pattern (25 bp):
ATTCTGATTCTGATTCTCTTACCTG
Found at i:5543815 original size:27 final size:27
Alignment explanation
Indices: 5543417--5543815 Score: 484
Period size: 27 Copynumber: 14.9 Consensus size: 27
5543407 ATTACCAAAA
* * **
5543417 TACCATCGATTTACAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACTGTTT
*
5543444 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACTGTTT
*
5543471 TACCCTCGATTTATAGAATTA-TCATTT
1 TACCCTCGATTTATAGAATTACT-GTTT
*
5543498 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACTGTTT
*
5543525 TACCCTAGATTTATAGAATTACTGTTT
1 TACCCTCGATTTATAGAATTACTGTTT
*
5543552 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACTGTTT
* * *
5543579 TACCCTCGCTTTACAAAATTACTGTTT
1 TACCCTCGATTTATAGAATTACTGTTT
* * * *
5543606 TACCCTTGATTTACAAAATTACTATTT
1 TACCCTCGATTTATAGAATTACTGTTT
* * *
5543633 TACCCTTGATTTACAAAATTACTGTTT
1 TACCCTCGATTTATAGAATTACTGTTT
*
5543660 TACCCTCGATTTATAAAATTA-TCGTTT
1 TACCCTCGATTTATAGAATTACT-GTTT
5543687 TACCCTCGATTTATAGAATT-CTCGTTT
1 TACCCTCGATTTATAGAATTACT-GTTT
*
5543714 TACCCTCGATTTATAGAATTAC-CTTT
1 TACCCTCGATTTATAGAATTACTGTTT
* *
5543740 TACCCTCGATTTACAGAATTA-TCTTT
1 TACCCTCGATTTATAGAATTACTGTTT
*
5543766 TACCATCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTATAGAATTACTGTTT
* * * *
5543793 TACCTTTGATTTACAAAATTACT
1 TACCCTCGATTTATAGAATTACT
5543816 AAAATACCCT
Statistics
Matches: 334, Mismatches: 31, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
26 47 0.14
27 286 0.86
28 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.09, T:0.43
Consensus pattern (27 bp):
TACCCTCGATTTATAGAATTACTGTTT
Found at i:5543995 original size:81 final size:81
Alignment explanation
Indices: 5543807--5544015 Score: 239
Period size: 81 Copynumber: 2.6 Consensus size: 81
5543797 TTTGATTTAC
* * ** *
5543807 AAAATTACTAAAATACCCTTGGTTTACAAAATTACCAAAATA-CCCTCGATTAGGAAAATTACCA
1 AAAATTAC-AAAATACCCTCGATTTGTAAAATTACCAAAATACCCCTGGATTAGGAAAATTACCA
5543871 AAATACCCCTAGTTTGT
65 AAATACCCCTAGTTTGT
* * *
5543888 AAAATTACCAAAATACCC-CTAGTTTGTAAAATTACCAAAATACCCCTGGCTT-GTAAAATTACC
1 AAAATTA-CAAAATACCCTCGA-TTTGTAAAATTACCAAAATACCCCTGGATTAGGAAAATTACC
5543951 AAAATACCCCT-GTTTTGT
64 AAAATACCCCTAG-TTTGT
* * *
5543969 GAAATTATCAAAATACCCTCGATTTGTAAAA-TATCGAAATACCCCTG
1 AAAATTA-CAAAATACCCTCGATTTGTAAAATTACCAAAATACCCCTG
5544016 CAGGTTAGAA
Statistics
Matches: 110, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
80 15 0.14
81 85 0.77
82 10 0.09
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.29
Consensus pattern (81 bp):
AAAATTACAAAATACCCTCGATTTGTAAAATTACCAAAATACCCCTGGATTAGGAAAATTACCAA
AATACCCCTAGTTTGT
Found at i:5544014 original size:27 final size:26
Alignment explanation
Indices: 5543807--5544015 Score: 217
Period size: 27 Copynumber: 7.8 Consensus size: 26
5543797 TTTGATTTAC
* * **
5543807 AAAATTACTAAAATACCCTTGGTTTAC
1 AAAATTACCAAAATACCCCT-GTTTGT
* *
5543834 AAAATTACCAAAATA-CCCTCGATTAGG
1 AAAATTACCAAAATACCCCT-G-TTTGT
5543861 AAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCT-GTTTGT
5543888 AAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCT-GTTTGT
*
5543915 AAAATTACCAAAATACCCCTGGCTTGT
1 AAAATTACCAAAATACCCCT-GTTTGT
5543942 AAAATTACCAAAATACCCCTGTTTTGT
1 AAAATTACCAAAATACCCCTG-TTTGT
* *
5543969 GAAATTATCAAAATA-CCCTCGATTTGT
1 AAAATTACCAAAATACCCCT-G-TTTGT
* *
5543996 AAAA-TATCGAAATACCCCTG
1 AAAATTACCAAAATACCCCTG
5544016 CAGGTTAGAA
Statistics
Matches: 160, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
26 19 0.12
27 136 0.85
28 5 0.03
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.29
Consensus pattern (26 bp):
AAAATTACCAAAATACCCCTGTTTGT
Found at i:5544035 original size:27 final size:27
Alignment explanation
Indices: 5544004--5544272 Score: 297
Period size: 27 Copynumber: 10.0 Consensus size: 27
5543994 GTAAAATATC
* *
5544004 GAAATACCCCTGCAGGTTAGAATTACT
1 GAAATACCCCTGTAGGGTAGAATTACT
* * *
5544031 AAAATACCTCTGTAGGGTAGAATTATT
1 GAAATACCCCTGTAGGGTAGAATTACT
* *
5544058 GAAATACCCCTGTAGGGTAGAGTTACC
1 GAAATACCCCTGTAGGGTAGAATTACT
* *
5544085 GAAATACCCTTGTAGGGTAGAAATACT
1 GAAATACCCCTGTAGGGTAGAATTACT
* * *
5544112 GAAATACCACTGTAGGTTAGGATTACT
1 GAAATACCCCTGTAGGGTAGAATTACT
* *
5544139 GAAATACCCCTGTAGGGTAGAAATATT
1 GAAATACCCCTGTAGGGTAGAATTACT
*
5544166 GAAATAACCCTGTAGGGTAGAATTA-T
1 GAAATACCCCTGTAGGGTAGAATTACT
* * * *
5544192 CGAGATACCCTTGTAGGGTAGAAATACC
1 -GAAATACCCCTGTAGGGTAGAATTACT
* * *
5544220 GAAATACCCTTATAGGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACT
* * *
5544247 GAGATACCCTTGTAGGGTAAAATTAC
1 GAAATACCCCTGTAGGGTAGAATTAC
5544273 CATTTTGCCC
Statistics
Matches: 203, Mismatches: 37, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
26 1 0.00
27 202 1.00
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (27 bp):
GAAATACCCCTGTAGGGTAGAATTACT
Found at i:5544090 original size:54 final size:54
Alignment explanation
Indices: 5544004--5544269 Score: 329
Period size: 54 Copynumber: 4.9 Consensus size: 54
5543994 GTAAAATATC
* * ** * *
5544004 GAAATACCCCTGCAGGTTAGAATTACTAAAATA-CCTCTGTAGGGTAGAATTATT
1 GAAATACCCCTGTAGGGTAGAATTACCGAAATACCCT-TGTAGGGTAGAAATACT
*
5544058 GAAATACCCCTGTAGGGTAGAGTTACCGAAATACCCTTGTAGGGTAGAAATACT
1 GAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAAATACT
* * * * * *
5544112 GAAATACCACTGTAGGTTAGGATTACTGAAATACCCCTGTAGGGTAGAAATATT
1 GAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAAATACT
* * * *
5544166 GAAATAACCCTGTAGGGTAGAATTATCGAGATACCCTTGTAGGGTAGAAATACC
1 GAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAAATACT
* * *
5544220 GAAATACCCTTATAGGGTAGAATTACCGAGATACCCTTGTAGGGTA-AAAT
1 GAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAAAT
5544270 TACCATTTTG
Statistics
Matches: 183, Mismatches: 28, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
53 4 0.02
54 176 0.96
55 3 0.02
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (54 bp):
GAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAAATACT
Found at i:5544660 original size:27 final size:26
Alignment explanation
Indices: 5544608--5544667 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
5544598 CCACATATAT
*
5544608 ATATCTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
5544634 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
5544661 ATATCTG
1 ATATCTG
5544668 GCAGCCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:5544795 original size:6 final size:6
Alignment explanation
Indices: 5544786--5544864 Score: 72
Period size: 6 Copynumber: 12.8 Consensus size: 6
5544776 TTGCATTCAT
* *
5544786 ATTCTG ATTCTG ATTCT- CTTACCTG ATTCTA ATTCTG ATTCTG -TTACTTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATT-C-TG
* *
5544836 ATTCTG ATTCTG ATTCTC ATTTTG ATTCT
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCT
5544865 AGTTCTAATA
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
5 4 0.07
6 46 0.78
7 5 0.08
8 4 0.07
ACGTcount: A:0.18, C:0.19, G:0.11, T:0.52
Consensus pattern (6 bp):
ATTCTG
Found at i:5544814 original size:25 final size:25
Alignment explanation
Indices: 5544786--5544853 Score: 109
Period size: 25 Copynumber: 2.7 Consensus size: 25
5544776 TTGCATTCAT
5544786 ATTCTGATTCTGATTCTCTTACCTG
1 ATTCTGATTCTGATTCTCTTACCTG
* * *
5544811 ATTCTAATTCTGATTCTGTTACTTG
1 ATTCTGATTCTGATTCTCTTACCTG
5544836 ATTCTGATTCTGATTCTC
1 ATTCTGATTCTGATTCTC
5544854 ATTTTGATTC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.18, C:0.21, G:0.12, T:0.50
Consensus pattern (25 bp):
ATTCTGATTCTGATTCTCTTACCTG
Found at i:5545536 original size:4 final size:4
Alignment explanation
Indices: 5545529--5545570 Score: 61
Period size: 4 Copynumber: 11.0 Consensus size: 4
5545519 AAACCAACCT
*
5545529 ATAA AT-A AT-A ATAA ATAA ATAA ATAA ATAA ACAA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
5545571 CTATTAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 6 0.17
4 29 0.83
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:5545614 original size:3 final size:3
Alignment explanation
Indices: 5545606--5545737 Score: 78
Period size: 3 Copynumber: 45.0 Consensus size: 3
5545596 TAATAGTATT
* * * *
5545606 ATA ATA ATA ATA ATA ATA ATA GAAA ATA ATA AGA ACA TTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* * * * **
5545652 ATA ATA TATG TTA ATA ACA ACA ATA AT- ATA A-A A-A AGGG A-A ATA
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA
* * *
5545695 ATA AT- ATA CTA ATA AGA ATG ATA AT- ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5545738 GTATAAGAAA
Statistics
Matches: 100, Mismatches: 21, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
2 11 0.11
3 84 0.84
4 5 0.05
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:5545667 original size:31 final size:31
Alignment explanation
Indices: 5545611--5545732 Score: 86
Period size: 31 Copynumber: 3.9 Consensus size: 31
5545601 GTATTATAAT
*
5545611 AATAATAATAATAATAGAAAATAATAAGAAC
1 AATAATAATAATAATAGAAAATAATAACAAC
* * ***
5545642 ATTAATAATAATAATATATGTTAATAACAAC
1 AATAATAATAATAATAGAAAATAATAACAAC
* * *
5545673 AATAAT-ATAA-AAAAGGGAAATAATAATATAC
1 AATAATAATAATAATA-GAAAATAATAACA-AC
* * *
5545704 TAATAAGAATGATAATATAATAATAATAA
1 -AATAATAATAATAATAGAA-AATAATAA
5545733 TAATAGTATA
Statistics
Matches: 66, Mismatches: 19, Indels: 9
0.70 0.20 0.10
Matches are distributed among these distances:
29 3 0.05
30 11 0.17
31 32 0.48
32 5 0.08
33 4 0.06
34 11 0.17
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.28
Consensus pattern (31 bp):
AATAATAATAATAATAGAAAATAATAACAAC
Found at i:5545726 original size:17 final size:18
Alignment explanation
Indices: 5545694--5545752 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 18
5545684 AAAGGGAAAT
*
5545694 AATAAT-ATACTAATAAG
1 AATAATAATAGTAATAAG
* *
5545711 AATGATAATA-TAATAAT
1 AATAATAATAGTAATAAG
5545728 AATAATAATAGT-ATAAG
1 AATAATAATAGTAATAAG
*
5545745 AAAAATAA
1 AATAATAA
5545753 CAATAGTAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 31 0.89
18 4 0.11
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.29
Consensus pattern (18 bp):
AATAATAATAGTAATAAG
Found at i:5545828 original size:20 final size:19
Alignment explanation
Indices: 5545807--5545854 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
5545797 ATAATACATA
5545807 AAAT-AATAACATAAAATGT
1 AAATAAATAA-ATAAAATGT
*
5545826 AAATAAATAAATAAAA-AT
1 AAATAAATAAATAAAATGT
5545844 AAGATAAATAA
1 AA-ATAAATAA
5545855 CAAAATAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 3 0.12
19 18 0.69
20 5 0.19
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.23
Consensus pattern (19 bp):
AAATAAATAAATAAAATGT
Found at i:5545901 original size:3 final size:3
Alignment explanation
Indices: 5545884--5546033 Score: 58
Period size: 3 Copynumber: 49.0 Consensus size: 3
5545874 AATATGATAG
* *
5545884 TAA TAA -AA GTAA TAA TAA TAA CAA T-A TAAA TGA TAA TAA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
* ** * *
5545929 AAA TAA -AA GTAA TAA TAA T-A TGT TAA GTTA TAA TAG TAA -AA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA
* * * * * * * *
5545973 TAA TGA TAG TGA TAA TATA TAT TAA GTGA TAA TAG TGGAA TAA AAA TAG
1 TAA TAA TAA TAA TAA TA-A TAA TAA -TAA TAA TAA T--AA TAA TAA TAA
5546022 TAA TAA TAA TAA
1 TAA TAA TAA TAA
5546034 CATATTAAAC
Statistics
Matches: 105, Mismatches: 29, Indels: 26
0.66 0.18 0.16
Matches are distributed among these distances:
2 10 0.10
3 80 0.76
4 13 0.12
5 2 0.02
ACGTcount: A:0.58, C:0.01, G:0.10, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:5545925 original size:24 final size:21
Alignment explanation
Indices: 5545885--5545948 Score: 92
Period size: 24 Copynumber: 2.9 Consensus size: 21
5545875 ATATGATAGT
5545885 AATAAAAGTAATAATAATAACA
1 AATAAAAGTAATAATAATAA-A
*
5545907 ATATAAATGATAATAATAATAAA
1 A-ATAAAAG-TAATAATAATAAA
5545930 AATAAAAGTAATAATAATA
1 AATAAAAGTAATAATAATA
5545949 TGTTAAGTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
21 11 0.29
22 7 0.18
23 8 0.21
24 12 0.32
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.27
Consensus pattern (21 bp):
AATAAAAGTAATAATAATAAA
Found at i:5545987 original size:26 final size:27
Alignment explanation
Indices: 5545931--5545989 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
5545921 AATAATAAAA
* * *
5545931 ATAAAAGTAATAATAATATGTTAAGTT
1 ATAATAGTAATAATAATATGATAAGTG
5545958 ATAATAGTAA-AATAATAATGAT-AGTG
1 ATAATAGTAATAATAAT-ATGATAAGTG
5545984 ATAATA
1 ATAATA
5545990 TATATTAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 15 0.54
27 13 0.46
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.34
Consensus pattern (27 bp):
ATAATAGTAATAATAATATGATAAGTG
Done.