Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 180 of 378
Found at i:52654839 original size:25 final size:26
Alignment explanation
Indices: 52654811--52654860 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
52654801 AATTCATGCA
*
52654811 TAGATTAAAGC-ATTTAAAATACGTT
1 TAGAGTAAAGCTATTTAAAATACGTT
*
52654836 TAGAGTAAAGCTTATTTAACATACG
1 TAGAGTAAAGC-TATTTAAAATACG
52654861 GATTTACCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 10 0.48
27 11 0.52
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (26 bp):
TAGAGTAAAGCTATTTAAAATACGTT
Found at i:52660935 original size:45 final size:45
Alignment explanation
Indices: 52660871--52661230 Score: 487
Period size: 45 Copynumber: 8.1 Consensus size: 45
52660861 AAAGAACTGA
52660871 TGAAATGTTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGG
1 TGAAATGTTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGG
* *
52660916 TGAAATGTTATTCAGGCCTTTGAGCCTAGCAGGCAATAATGCCGG
1 TGAAATGTTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGG
* *
52660961 TGAAATGTTATTCTGGCCTTTGAGCCTAGCAGGCTATAATGCTGG
1 TGAAATGTTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGG
52661006 TGAAATGTTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGG
1 TGAAATGTTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGG
* * *
52661051 TGAGATATTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCTGG
1 TGAAATGTTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGG
* * * * *
52661096 TGAGATATTATTCAGGCCTTTGAGCCTAACAGGCTATAATGCCAG
1 TGAAATGTTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGG
** *
52661141 T-AAGATACTATTCGGG-CTTTCGAGCCTAACAGGCTATAATGCCGG
1 TGAA-ATGTTATTCGGGCCTTT-GAGCCTAGCAGGCTATAATGCCGG
* * * * *
52661186 TGGAATGATA-TCGGGCC-TCGAGCCTAACAGGCGA-AATGCCGG
1 TGAAATGTTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGG
52661228 TGA
1 TGA
52661231 TTTGAGAAAA
Statistics
Matches: 287, Mismatches: 24, Indels: 11
0.89 0.07 0.03
Matches are distributed among these distances:
42 10 0.03
43 14 0.05
44 11 0.04
45 251 0.87
46 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.28
Consensus pattern (45 bp):
TGAAATGTTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGG
Found at i:52662996 original size:46 final size:45
Alignment explanation
Indices: 52662891--52663023 Score: 160
Period size: 46 Copynumber: 2.8 Consensus size: 45
52662881 GCCACAATAT
* * *
52662891 GAGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCATCGAGAT
1 GAGAGCCAGTGTAAGA-CATGTCT-GGACAT-GCATCGGCTTCGAGAC
* *
52662939 GAGTGCTAGTGTAAGACATGTCTGAGACATGCATCGGCTTCGAGAC
1 GAGAGCCAGTGTAAGACATGTCTG-GACATGCATCGGCTTCGAGAC
52662985 GTA-AGCCAGTGTAAGACATGTCTTGGACATGCATCGGCT
1 G-AGAGCCAGTGTAAGACATGTC-TGGACATGCATCGGCT
52663024 ACAAGATGTG
Statistics
Matches: 75, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
46 47 0.63
47 14 0.19
48 14 0.19
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.23
Consensus pattern (45 bp):
GAGAGCCAGTGTAAGACATGTCTGGACATGCATCGGCTTCGAGAC
Found at i:52663150 original size:99 final size:96
Alignment explanation
Indices: 52662992--52663171 Score: 233
Period size: 99 Copynumber: 1.8 Consensus size: 96
52662982 GACGTAAGCC
*
52662992 AGTGTAAGACATGTCTTGGACATGCATCGGCTACAAGATGTGTCAGTGTAAGAGACCATGTCTGG
1 AGTGTAAGACATGTCTTGGACATGCATCGGCTACAAGATGTGCCAGTGTAAGAGACCATGTCTGG
* *
52663057 GATATGGCATCGGCACAGTTATATGAGATCT
66 GACATGGCATCAGCACAGTTATATGAGATCT
*
52663088 AGTGTAAGAACATGTC-TGAGACATGGCATTGGCCT-CAAAGATGATAGCCAGTGT-A-AGACCA
1 AGTGTAAG-ACATGTCTTG-GACAT-GCATCGG-CTAC-AAGATG-T-GCCAGTGTAAGAGACCA
52663149 TGTCTGGGACATGGCATCAGCAC
59 TGTCTGGGACATGGCATCAGCAC
52663172 CTTACCCATG
Statistics
Matches: 73, Mismatches: 4, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
96 10 0.14
97 12 0.16
98 7 0.10
99 35 0.48
100 2 0.03
101 7 0.10
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.24
Consensus pattern (96 bp):
AGTGTAAGACATGTCTTGGACATGCATCGGCTACAAGATGTGCCAGTGTAAGAGACCATGTCTGG
GACATGGCATCAGCACAGTTATATGAGATCT
Found at i:52674573 original size:683 final size:683
Alignment explanation
Indices: 52673268--52674617 Score: 2646
Period size: 683 Copynumber: 2.0 Consensus size: 683
52673258 TTGATGTTTT
52673268 ATGGTATAATATGAAGCTTGAAATTATGTTAAACAACTTGAGCTAAGCGATTTTAAGCGAAAACG
1 ATGGTATAATATGAAGCTTGAAATTATGTTAAACAACTTGAGCTAAGCGATTTTAAGCGAAAACG
52673333 AGTAAAACGACATAATCGGTAAAAATACCTAATGGTCATAAGTACATGTTAGAGTGGGAATTTGA
66 AGTAAAACGACATAATCGGTAAAAATACCTAATGGTCATAAGTACATGTTAGAGTGGGAATTTGA
*
52673398 TGTTGCCGTAGGTAAATAAATGATTAGCATGTCATAAAACATAAGAATTAGGGATAAAGTTTCAT
131 TGTTGCCGTAGGTAAATAAATGATTAGCATGCCATAAAACATAAGAATTAGGGATAAAGTTTCAT
*
52673463 TTTCGAGCCTTGGGGAAAAAGTGTAAATATGCAAAAGTTTAAGGGCAAAATCATAATTTTTTCAA
196 TTTCGAGCCTTGGGGAAAAAGTGTAAATATGCAAAAGTTTAAGGGAAAAATCATAATTTTTTCAA
52673528 AGTTAGAGTTAAGGACTGTTTTGATAAATGTGAATATTAAATAAGTTAAATTTTCTATTATAGAT
261 AGTTAGAGTTAAGGACTGTTTTGATAAATGTGAATATTAAATAAGTTAAATTTTCTATTATAGAT
52673593 CAAGAAGAATGAAATTCAGGGTTAGACCGAGGAAAGAAAAAGGTTGAGGACTAAATTAAAATATT
326 CAAGAAGAATGAAATTCAGGGTTAGACCGAGGAAAGAAAAAGGTTGAGGACTAAATTAAAATATT
52673658 TGATCGTATTTTGTATCGAGGTAAGTTTGCGGTAAATAAATGCAATGTTTCATTATATATAATTA
391 TGATCGTATTTTGTATCGAGGTAAGTTTGCGGTAAATAAATGCAATGTTTCATTATATATAATTA
52673723 ATGATGTTATTTTTCAGCATCTATATATTTATTTTATAAATTTATTCCTTGATGATTCAAGCTAG
456 ATGATGTTATTTTTCAGCATCTATATATTTATTTTATAAATTTATTCCTTGATGATTCAAGCTAG
52673788 AATTGACAGAGAAATGATATTTAAAAGTCCTGGTTGAACCTTAGGAATGTGTAGATACAAATGTC
521 AATTGACAGAGAAATGATATTTAAAAGTCCTGGTTGAACCTTAGGAATGTGTAGATACAAATGTC
*
52673853 ATGACATTAGGGTTTAAGGATACCAAGTAAGATCATGCCAAGACATGGCATTGGTAAGTTTTGCA
586 ATGACATTAGGGTTTAAGGATACCAAGTAAGATCATGCCAAGACATGGCATTGGTAAGTTTTACA
52673918 AGGCAAGGAAATCATGTTAAACAACTTGAGCTA
651 AGGCAAGGAAATCATGTTAAACAACTTGAGCTA
52673951 ATGGTATAATATGAAGCTTGAAATTATGTTAAACAACTTGAGCTAAGCGATTTTAAGCGAAAACG
1 ATGGTATAATATGAAGCTTGAAATTATGTTAAACAACTTGAGCTAAGCGATTTTAAGCGAAAACG
52674016 AGTAAAACGACATAATCGGTAAAAATACCTAATGGTCATAAGTACATGTTAGAGTGGGAATTTGA
66 AGTAAAACGACATAATCGGTAAAAATACCTAATGGTCATAAGTACATGTTAGAGTGGGAATTTGA
*
52674081 TGTTGCCGTAGGTAAATAAATGATTATCATGCCATAAAACATAAGAATTAGGGATAAAGTTTCAT
131 TGTTGCCGTAGGTAAATAAATGATTAGCATGCCATAAAACATAAGAATTAGGGATAAAGTTTCAT
52674146 TTTCGAGCCTTGGGGAAAAAGTGTAAATATGCAAAAGTTTAAGGGAAAAATCATAATTTTTTCAA
196 TTTCGAGCCTTGGGGAAAAAGTGTAAATATGCAAAAGTTTAAGGGAAAAATCATAATTTTTTCAA
52674211 AGTTAGAGTTAAGGACTGTTTTGATAAATGTGAATATTAAATAAGTTAAATTTTCTATTATAGAT
261 AGTTAGAGTTAAGGACTGTTTTGATAAATGTGAATATTAAATAAGTTAAATTTTCTATTATAGAT
*
52674276 CAAGAAGAATGAAATTCAGGGTTAGACCTAGGAAAGAAAAAGGTTGAGGACTAAATTAAAATATT
326 CAAGAAGAATGAAATTCAGGGTTAGACCGAGGAAAGAAAAAGGTTGAGGACTAAATTAAAATATT
52674341 TGATCGTATTTTGTATCGAGGTAAGTTTGCGGTAAATAAATGCAATGTTTCATTATATATAATTA
391 TGATCGTATTTTGTATCGAGGTAAGTTTGCGGTAAATAAATGCAATGTTTCATTATATATAATTA
52674406 ATGATGTTATTTTTCAGCATCTATATATTTATTTTATAAATTTATTCCTTGATGATTCAAGCTAG
456 ATGATGTTATTTTTCAGCATCTATATATTTATTTTATAAATTTATTCCTTGATGATTCAAGCTAG
*
52674471 AATTGACGGAGAAATGATATTTAAAAGTCCTGGTTGAACCTTAGGAATGTGTAGATACAAATGTC
521 AATTGACAGAGAAATGATATTTAAAAGTCCTGGTTGAACCTTAGGAATGTGTAGATACAAATGTC
52674536 ATGACATTAGGGTTTAAGGATACCAAGTAAGATCATGCCAAGACATGGCATTGGTAAGTTTTACA
586 ATGACATTAGGGTTTAAGGATACCAAGTAAGATCATGCCAAGACATGGCATTGGTAAGTTTTACA
52674601 AGGCAAGGAAATCATGT
651 AGGCAAGGAAATCATGT
52674618 AAGACCATGT
Statistics
Matches: 661, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
683 661 1.00
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (683 bp):
ATGGTATAATATGAAGCTTGAAATTATGTTAAACAACTTGAGCTAAGCGATTTTAAGCGAAAACG
AGTAAAACGACATAATCGGTAAAAATACCTAATGGTCATAAGTACATGTTAGAGTGGGAATTTGA
TGTTGCCGTAGGTAAATAAATGATTAGCATGCCATAAAACATAAGAATTAGGGATAAAGTTTCAT
TTTCGAGCCTTGGGGAAAAAGTGTAAATATGCAAAAGTTTAAGGGAAAAATCATAATTTTTTCAA
AGTTAGAGTTAAGGACTGTTTTGATAAATGTGAATATTAAATAAGTTAAATTTTCTATTATAGAT
CAAGAAGAATGAAATTCAGGGTTAGACCGAGGAAAGAAAAAGGTTGAGGACTAAATTAAAATATT
TGATCGTATTTTGTATCGAGGTAAGTTTGCGGTAAATAAATGCAATGTTTCATTATATATAATTA
ATGATGTTATTTTTCAGCATCTATATATTTATTTTATAAATTTATTCCTTGATGATTCAAGCTAG
AATTGACAGAGAAATGATATTTAAAAGTCCTGGTTGAACCTTAGGAATGTGTAGATACAAATGTC
ATGACATTAGGGTTTAAGGATACCAAGTAAGATCATGCCAAGACATGGCATTGGTAAGTTTTACA
AGGCAAGGAAATCATGTTAAACAACTTGAGCTA
Found at i:52674734 original size:53 final size:53
Alignment explanation
Indices: 52674551--52674757 Score: 198
Period size: 53 Copynumber: 3.8 Consensus size: 53
52674541 ATTAGGGTTT
* * * * *
52674551 AAGGATACCAAGTAAGATCATGCCAAGACATGGCATTGGTAAGTTTTACAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAG-TTCATAAGGC
* * * * * * * * *
52674605 AAGGAAATCATGTAAGACCATGTCAAGAAATGGCATTGATAAACTACGGTAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGT-AAGTTC-ATAAGGC
* * * *
52674660 AAAGATCCCATGTAAGACCATGCCAAGGCATGGCAATGGTGAGTTCATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
* * *
52674713 AAGGATACCACGTAAGACCATGTCAAGACATGACAATGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTT
52674758 TAAAAAGGAA
Statistics
Matches: 119, Mismatches: 32, Indels: 5
0.76 0.21 0.03
Matches are distributed among these distances:
53 44 0.37
54 37 0.31
55 38 0.32
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.20
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
Found at i:52682165 original size:53 final size:53
Alignment explanation
Indices: 52682067--52682171 Score: 129
Period size: 53 Copynumber: 2.0 Consensus size: 53
52682057 ATAAACTACG
* ** * ** *
52682067 ATAAGGCAAAGATCCCATGTAAGACCATGCCAAGGCATGGCAATGGTGAGTTC
1 ATAAGGCAAAGATACCACATAAGACCATGCAAAGGCATGAAAATGGTAAGTTC
* *
52682120 ATAAGGCAAGGATACCACATAAGACCATGTAAAGGCATGAAAATGGTAAGTT
1 ATAAGGCAAAGATACCACATAAGACCATGCAAAGGCATGAAAATGGTAAGTT
52682172 TAAAAAGGAA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19
Consensus pattern (53 bp):
ATAAGGCAAAGATACCACATAAGACCATGCAAAGGCATGAAAATGGTAAGTTC
Found at i:52685612 original size:23 final size:23
Alignment explanation
Indices: 52685586--52685653 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
52685576 ATAAATGTAG
52685586 TTTTGAATTAATTTAAAGGTTAA
1 TTTTGAATTAATTTAAAGGTTAA
* *
52685609 TTTTGGTATT--TTT----G-TAG
1 TTTT-GAATTAATTTAAAGGTTAA
52685626 TTTTGAATTAATTTAAAGGTTAA
1 TTTTGAATTAATTTAAAGGTTAA
52685649 TTTTG
1 TTTTG
52685654 GTATTTGAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 16
0.62 0.08 0.30
Matches are distributed among these distances:
16 4 0.12
17 6 0.18
18 4 0.12
22 4 0.12
23 11 0.33
24 4 0.12
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.54
Consensus pattern (23 bp):
TTTTGAATTAATTTAAAGGTTAA
Found at i:52685625 original size:40 final size:40
Alignment explanation
Indices: 52685581--52685659 Score: 158
Period size: 40 Copynumber: 2.0 Consensus size: 40
52685571 ATGTCATAAA
52685581 TGTAGTTTTGAATTAATTTAAAGGTTAATTTTGGTATTTT
1 TGTAGTTTTGAATTAATTTAAAGGTTAATTTTGGTATTTT
52685621 TGTAGTTTTGAATTAATTTAAAGGTTAATTTTGGTATTT
1 TGTAGTTTTGAATTAATTTAAAGGTTAATTTTGGTATTT
52685660 GAGTATTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.28, C:0.00, G:0.18, T:0.54
Consensus pattern (40 bp):
TGTAGTTTTGAATTAATTTAAAGGTTAATTTTGGTATTTT
Found at i:52686493 original size:40 final size:40
Alignment explanation
Indices: 52686433--52686532 Score: 137
Period size: 40 Copynumber: 2.5 Consensus size: 40
52686423 CGTATATATA
* * **
52686433 TATATATGACACTTAGTGTGCGATTCAAGAAAGCTTCGGT
1 TATATATGGCACTTAGTGTGCAATTCAAGAAAGCTTCGAC
* * *
52686473 TATATACGGCACTTATTGTGCAATTCAAGAAAGTTTCGAC
1 TATATATGGCACTTAGTGTGCAATTCAAGAAAGCTTCGAC
52686513 TATATATGGCACTTAGTGTG
1 TATATATGGCACTTAGTGTG
52686533 TAACACCCCT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (40 bp):
TATATATGGCACTTAGTGTGCAATTCAAGAAAGCTTCGAC
Found at i:52690277 original size:48 final size:48
Alignment explanation
Indices: 52690220--52690348 Score: 177
Period size: 48 Copynumber: 2.7 Consensus size: 48
52690210 TCTTGTCAGT
* *
52690220 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCACACATATCAAC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATAAAC
* * * * *
52690268 GCCGGTGCCATGTCCCAGACATGGTCTTACAATGGCACACATGTAAAT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATAAAC
* *
52690316 GCCAATGCCATGTCTCAGACATGGTCTTACACT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACT
52690349 GGCTCTCATT
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 70 1.00
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (48 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATAAAC
Found at i:52692018 original size:42 final size:42
Alignment explanation
Indices: 52691907--52692018 Score: 136
Period size: 43 Copynumber: 2.6 Consensus size: 42
52691897 TACCATACCA
* * * *
52691907 ATGCCATATCCTAGATATGGTCTTAAATGAAATCTCGTATCG
1 ATGCCATATCCCAGATATGGCCTTACATGAAATCTCATATCG
* * *
52691949 ATGCCAATAGCCCAGTTAT-GCTCTTACATGAAGTCTCATATCG
1 ATGCC-ATATCCCAGATATGGC-CTTACATGAAATCTCATATCG
52691992 ATGCCATATCCCAGATATGGCCTTACA
1 ATGCCATATCCCAGATATGGCCTTACA
52692019 CATAATCTCG
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
42 23 0.40
43 35 0.60
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGCCTTACATGAAATCTCATATCG
Found at i:52694721 original size:21 final size:21
Alignment explanation
Indices: 52694694--52694754 Score: 88
Period size: 21 Copynumber: 2.9 Consensus size: 21
52694684 TATAATGAGT
52694694 ATATCATAGCATATCATGTGC
1 ATATCATAGCATATCATGTGC
* *
52694715 ATCTCATAACATATCATGTGC
1 ATATCATAGCATATCATGTGC
52694736 ATATCAT-GTCATATCATGT
1 ATATCATAG-CATATCATGT
52694755 ATAACAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (21 bp):
ATATCATAGCATATCATGTGC
Found at i:52694753 original size:10 final size:10
Alignment explanation
Indices: 52694694--52694754 Score: 61
Period size: 10 Copynumber: 5.9 Consensus size: 10
52694684 TATAATGAGT
52694694 ATATCATAG-C
1 ATATCAT-GTC
52694704 ATATCATGTGC
1 ATATCATGT-C
* **
52694715 ATCTCATAAC
1 ATATCATGTC
52694725 ATATCATGTGC
1 ATATCATGT-C
52694736 ATATCATGTC
1 ATATCATGTC
52694746 ATATCATGT
1 ATATCATGT
52694755 ATAACAATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
9 1 0.02
10 24 0.57
11 17 0.40
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (10 bp):
ATATCATGTC
Found at i:52696456 original size:80 final size:80
Alignment explanation
Indices: 52696372--52696520 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
52696362 TATGGTAACC
* * * *
52696372 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
52696436 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
52696452 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
52696517 CCGG
66 CCGG
52696521 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:52696462 original size:40 final size:38
Alignment explanation
Indices: 52696413--52696520 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
52696403 ATCACGATTT
*
52696413 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
52696453 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
52696493 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
52696521 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:52703606 original size:92 final size:93
Alignment explanation
Indices: 52703449--52703619 Score: 263
Period size: 92 Copynumber: 1.8 Consensus size: 93
52703439 ACCCGTAAGT
* * * *
52703449 GAACTCAGACTCAACTGAACGAGCTCGGGCGTTCGCATTCATAAGTGAACTCGAACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCAA
52703514 CGAGCTCGG-TGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* * *
52703541 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCAA
*
52703606 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
52703620 CAAACATCCT
Statistics
Matches: 70, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
92 66 0.94
93 4 0.06
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:52703615 original size:46 final size:45
Alignment explanation
Indices: 52703444--52703615 Score: 166
Period size: 46 Copynumber: 3.8 Consensus size: 45
52703434 AACCCACCCG
* * * *
52703444 TAAGTGAACTCAGACTCAACTGAACGAGCTCGGGCGTTCGCATTCA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGAC-TTCGCATACA
* * * * *
52703490 TAAGTGAACTCGAACTCAACTCAACGAGCTCGGTGCCTAG-TTACA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGG-ACTTCGCATACA
*** * *
52703535 TCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGT-GAACTCGGACTCAACTCAACGAGCTCGGAC-TTCGCATACA
*
52703582 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
52703616 TGCCCAAACA
Statistics
Matches: 102, Mismatches: 20, Indels: 8
0.78 0.15 0.06
Matches are distributed among these distances:
45 6 0.06
46 89 0.87
47 7 0.07
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (45 bp):
TAAGTGAACTCGGACTCAACTCAACGAGCTCGGACTTCGCATACA
Found at i:52703634 original size:46 final size:46
Alignment explanation
Indices: 52703492--52703634 Score: 125
Period size: 46 Copynumber: 3.1 Consensus size: 46
52703482 CGCATTCATA
* * *
52703492 AGTGAACTCGAACTCAACTCAACGAGCTCGG-TGCCTAGTTACATCTCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA--TACATC-CT
* * * * *
52703540 --CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT--A
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCCCATACATCCT
*
52703584 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAACATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATACATCCT
52703630 AGTGA
1 AGTGA
52703635 CATGTCACTT
Statistics
Matches: 74, Mismatches: 14, Indels: 16
0.71 0.13 0.15
Matches are distributed among these distances:
44 8 0.11
46 59 0.80
47 4 0.05
49 3 0.04
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (46 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATACATCCT
Found at i:52707567 original size:46 final size:46
Alignment explanation
Indices: 52707418--52707591 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
52707408 ATGTAACCTC
*
52707418 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG-CGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
* *
52707463 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCG--GAC-A-TTCGCAT
* *
52707512 CTC-T---CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
52707555 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
52707592 TGCCCAAACA
Statistics
Matches: 111, Mismatches: 7, Indels: 21
0.80 0.05 0.15
Matches are distributed among these distances:
42 3 0.03
43 6 0.05
44 2 0.02
45 35 0.32
46 55 0.50
47 1 0.01
48 1 0.01
49 5 0.05
50 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:52707582 original size:92 final size:92
Alignment explanation
Indices: 52707426--52707595 Score: 297
Period size: 92 Copynumber: 1.8 Consensus size: 92
52707416 TCCCATAAGT
*
52707426 GAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
52707491 GAGCTC-GATGCCTAGTTACATCTCTC
66 GAGCTCGGATGCCTAGTTACATCTCTC
*
52707517 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
52707582 CGAGTTCGGATGCC
65 CGAGCTCGGATGCC
52707596 CAAACATCCT
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
91 27 0.36
92 41 0.55
93 6 0.08
ACGTcount: A:0.28, C:0.31, G:0.21, T:0.21
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGCTCGGATGCCTAGTTACATCTCTC
Found at i:52707610 original size:46 final size:46
Alignment explanation
Indices: 52707423--52707610 Score: 147
Period size: 46 Copynumber: 4.1 Consensus size: 46
52707413 ACCTCCCATA
* * * * *
52707423 AGTGAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCAT--A
1 AGTGAACTCGGACTCAACTCAACGAGCTCGG-ATGCCCATACATCCT
*
52707468 AGTGAACTCGGACTCAACTCAACGAGCTC-GATGCCTAGTTACATCTCT
1 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCCA--TACATC-CT
* * * * * *
52707516 --CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT--A
1 AGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGCCCATACATCCT
* *
52707560 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAACATCCT
1 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCCATACATCCT
52707606 AGTGA
1 AGTGA
52707611 CATGTCACTT
Statistics
Matches: 112, Mismatches: 19, Indels: 23
0.73 0.12 0.15
Matches are distributed among these distances:
43 3 0.03
44 9 0.08
45 33 0.29
46 58 0.52
47 5 0.04
49 4 0.04
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (46 bp):
AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCCATACATCCT
Found at i:52710292 original size:40 final size:40
Alignment explanation
Indices: 52710236--52710402 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
52710226 GAATGATACT
* *
52710236 CGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATATC
1 CGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATATC
* * *
52710276 TGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TTATATC
1 CGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTATATC
* * ** *
52710316 CGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAATC
1 CGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATATC
* * * *
52710356 CGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATATC
1 CGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATATC
52710396 C-GGCTAA
1 CGGGCTAA
52710403 ATTCCGAAGA
Statistics
Matches: 103, Mismatches: 22, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
39 6 0.06
40 95 0.92
41 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
CGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATATC
Found at i:52713538 original size:6 final size:6
Alignment explanation
Indices: 52713529--52713555 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
52713519 ACGTCCTCGT
52713529 CCATTA CCATTA CCATTA CCATTA CCA
1 CCATTA CCATTA CCATTA CCATTA CCA
52713556 CGTCTCTGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (6 bp):
CCATTA
Found at i:52716161 original size:11 final size:11
Alignment explanation
Indices: 52716147--52716199 Score: 65
Period size: 11 Copynumber: 5.0 Consensus size: 11
52716137 GTATATCATA
52716147 GCATATCATGT
1 GCATATCATGT
* *
52716158 GCATCTCAT-A
1 GCATATCATGT
*
52716168 ACATATCATGT
1 GCATATCATGT
52716179 GCATATCATGT
1 GCATATCATGT
52716190 -CATATCATGT
1 GCATATCATGT
52716200 ATAACAATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
10 17 0.49
11 18 0.51
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (11 bp):
GCATATCATGT
Found at i:52716166 original size:21 final size:21
Alignment explanation
Indices: 52716139--52716199 Score: 88
Period size: 21 Copynumber: 2.9 Consensus size: 21
52716129 TATAATTAGT
52716139 ATATCATAGCATATCATGTGC
1 ATATCATAGCATATCATGTGC
* *
52716160 ATCTCATAACATATCATGTGC
1 ATATCATAGCATATCATGTGC
52716181 ATATCAT-GTCATATCATGT
1 ATATCATAG-CATATCATGT
52716200 ATAACAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (21 bp):
ATATCATAGCATATCATGTGC
Found at i:52716198 original size:10 final size:10
Alignment explanation
Indices: 52716139--52716199 Score: 61
Period size: 10 Copynumber: 5.9 Consensus size: 10
52716129 TATAATTAGT
52716139 ATATCATAG-C
1 ATATCAT-GTC
52716149 ATATCATGTGC
1 ATATCATGT-C
* **
52716160 ATCTCATAAC
1 ATATCATGTC
52716170 ATATCATGTGC
1 ATATCATGT-C
52716181 ATATCATGTC
1 ATATCATGTC
52716191 ATATCATGT
1 ATATCATGT
52716200 ATAACAATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
9 1 0.02
10 24 0.57
11 17 0.40
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (10 bp):
ATATCATGTC
Found at i:52718880 original size:12 final size:12
Alignment explanation
Indices: 52718863--52718888 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
52718853 GGTTTGGCAT
52718863 GGCCTAGCACAC
1 GGCCTAGCACAC
52718875 GGCCTAGCACAC
1 GGCCTAGCACAC
52718887 GG
1 GG
52718889 GCGTGGGTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.38, G:0.31, T:0.08
Consensus pattern (12 bp):
GGCCTAGCACAC
Found at i:52720611 original size:181 final size:182
Alignment explanation
Indices: 52720396--52720758 Score: 719
Period size: 181 Copynumber: 2.0 Consensus size: 182
52720386 TCAGTGACAA
52720396 AGCATTTTTAAAAGTATCTCTGTGGAAGAAAATACTTCGATTTGGCCGTAAAGGCAAATTGAGTC
1 AGCATTTTTAAAAGTATCTCTGTGGAAGAAAATACTTCGATTTGGCCGTAAAGGCAAATTGAGTC
52720461 CGAGATTCATTGGGCCGTATGAAATCATTGAAAGAATAGGGCCAGTAGCATATCGGCTATCTCTA
66 CGAGATTCATTGGGCCGTATGAAATCATTGAAAGAATAGGGCCAGTAGCATATCGGCTATCTCTA
52720526 CCATCAGAGTTAGAAAAGATCCAC-ACGTGTTTCATGAATCGATGCTACATC
131 CCATCAGAGTTAGAAAAGATCCACAACGTGTTTCATGAATCGATGCTACATC
52720577 AGCATTTTTAAAAGTATCTCTGTGGAAGAAAATACTTCGATTTGGCCGTAAAGGCAAATTGAGTC
1 AGCATTTTTAAAAGTATCTCTGTGGAAGAAAATACTTCGATTTGGCCGTAAAGGCAAATTGAGTC
52720642 CGAGATTCATTGGGCCGTATGAAATCATTGAAAGAATAGGGCCAGTAGCATATCGGCTATCTCTA
66 CGAGATTCATTGGGCCGTATGAAATCATTGAAAGAATAGGGCCAGTAGCATATCGGCTATCTCTA
52720707 CCATCAGAGTTAGAAAAGATCCACAACGTGTTTCATGAATCGATGCTACATC
131 CCATCAGAGTTAGAAAAGATCCACAACGTGTTTCATGAATCGATGCTACATC
52720759 GATATAGATT
Statistics
Matches: 181, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
181 154 0.85
182 27 0.15
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (182 bp):
AGCATTTTTAAAAGTATCTCTGTGGAAGAAAATACTTCGATTTGGCCGTAAAGGCAAATTGAGTC
CGAGATTCATTGGGCCGTATGAAATCATTGAAAGAATAGGGCCAGTAGCATATCGGCTATCTCTA
CCATCAGAGTTAGAAAAGATCCACAACGTGTTTCATGAATCGATGCTACATC
Found at i:52723993 original size:40 final size:40
Alignment explanation
Indices: 52723938--52724100 Score: 177
Period size: 40 Copynumber: 4.1 Consensus size: 40
52723928 GAATGATACT
* * * *
52723938 CGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATGTC
1 CGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATATC
*
52723978 CGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTG-TTATATC
1 CGGGCTAAGACCCGAAGGCAATT-GTGCTAG-TGATTATATC
* * ** *
52724018 CGGGCTAAGACCCGAAGGCAATTGTGCAAGTTACCAAATC
1 CGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATATC
* * *
52724058 CGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATATC
1 CGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATATC
52724098 CGG
1 CGG
52724101 TTAAATCCCG
Statistics
Matches: 101, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
39 3 0.03
40 93 0.92
41 5 0.05
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (40 bp):
CGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATATC
Found at i:52725526 original size:40 final size:40
Alignment explanation
Indices: 52725470--52725683 Score: 195
Period size: 40 Copynumber: 5.3 Consensus size: 40
52725460 CGGGGTGTTA
* *
52725470 CACTTAATGTGTGATTCAAGAA-AGCTTCGGCTATATATGG
1 CACTTAGTGTGCGATTCAA-AATAGCTTCGGCTATATATGG
*
52725510 CACTTAGTGTGCGATTCAAGAA-AGCCTCGG-TGATATATGAG
1 CACTTAGTGTGCGATTCAA-AATAGCTTCGGCT-ATATATG-G
* *
52725551 -ACTTAGTGTGTGATTCAAAATAGCTTTGGCTATATATGG
1 CACTTAGTGTGCGATTCAAAATAGCTTCGGCTATATATGG
** * * *
52725590 CACTTAGTGTGCGAGACCAAAATAGCTTCGACTATGTAAGG
1 CACTTAGTGTGCGA-TTCAAAATAGCTTCGGCTATATATGG
* ** *
52725631 CACTTAGTGTGCAGAATT-ATAATATTTTCGGCTATGTATTGG
1 CACTTAGTGTGC-G-ATTCAAAATAGCTTCGGCTATATA-TGG
52725673 CACTTAGTGTG
1 CACTTAGTGTG
52725684 TGAGATATCG
Statistics
Matches: 145, Mismatches: 20, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
39 4 0.03
40 76 0.52
41 50 0.34
42 14 0.10
43 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.33
Consensus pattern (40 bp):
CACTTAGTGTGCGATTCAAAATAGCTTCGGCTATATATGG
Found at i:52739225 original size:48 final size:48
Alignment explanation
Indices: 52739141--52739427 Score: 208
Period size: 48 Copynumber: 5.9 Consensus size: 48
52739131 ATACTAGGGT
* * * * * *
52739141 TATGTGAGCCAGTGTAAGACCATATTTGGAAAATGGCAAAGGCATTTA
1 TATGAGAGCTAGTGTAAGACCATGTCTGGAACATGGCATAGGCATTTA
* * * **
52739189 TATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATTGGCCTCGACA
1 TATGAGAGCTAGTGTAAGACCATGTCTGGAACATGGCATAGGCAT--TTA
* * * * *
52739239 TAT-A-AGCTAGTATAATG-CCATGTTTGGAACATAGCATCGGTATTTA
1 TATGAGAGCTAGTGTAA-GACCATGTCTGGAACATGGCATAGGCATTTA
* * * * * **
52739285 TATGAAAGCTAGTGTACGACCATGTCTGGCACATGGTATCA-GCCTCGA
1 TATGAGAGCTAGTGTAAGACCATGTCTGGAACATGGCAT-AGGCATTTA
* * *
52739333 CATGCGAGCTAGTGTAAGACCATGT-TAGGAACATGGCATCGGCATTGATA
1 TATGAGAGCTAGTGTAAGACCATGTCT-GGAACATGGCATAGGCATT--TA
* *
52739383 TATGAGAGCTAGTGTAAGAACATGTCTAGG-ACATGGCATCGGCAT
1 TATGAGAGCTAGTGTAAGACCATGTCT-GGAACATGGCATAGGCAT
52739428 CTTACCCTTT
Statistics
Matches: 183, Mismatches: 44, Indels: 22
0.73 0.18 0.09
Matches are distributed among these distances:
46 4 0.02
47 3 0.02
48 128 0.70
49 2 0.01
50 42 0.23
51 4 0.02
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (48 bp):
TATGAGAGCTAGTGTAAGACCATGTCTGGAACATGGCATAGGCATTTA
Found at i:52739330 original size:96 final size:95
Alignment explanation
Indices: 52739181--52739422 Score: 306
Period size: 96 Copynumber: 2.5 Consensus size: 95
52739171 AAATGGCAAA
** *
52739181 GGCATTTATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATTGGCCTCGACATATAAGC
1 GGCATTTATATGAGAGCTAGTGTAAGACCATGTCT-GGACATGGCATCAGCCTCGACATACAAGC
*
52739246 TAGTATAATG-CCATGTTTGGAACATAGCATC
65 TAGTATAA-GACCATGTTAGGAACATAGCATC
* * * * * *
52739277 GGTATTTATATGAAAGCTAGTGTACGACCATGTCTGGCACATGGTATCAGCCTCGACATGCGAGC
1 GGCATTTATATGAGAGCTAGTGTAAGACCATGTCTGG-ACATGGCATCAGCCTCGACATACAAGC
* *
52739342 TAGTGTAAGACCATGTTAGGAACATGGCATC
65 TAGTATAAGACCATGTTAGGAACATAGCATC
*
52739373 GGCATTGATATATGAGAGCTAGTGTAAGAACATGTCTAGGACATGGCATC
1 GGCATT--TATATGAGAGCTAGTGTAAGACCATGTCT-GGACATGGCATC
52739423 GGCATCTTAC
Statistics
Matches: 124, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
95 3 0.02
96 84 0.68
98 35 0.28
99 2 0.02
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (95 bp):
GGCATTTATATGAGAGCTAGTGTAAGACCATGTCTGGACATGGCATCAGCCTCGACATACAAGCT
AGTATAAGACCATGTTAGGAACATAGCATC
Found at i:52743314 original size:13 final size:13
Alignment explanation
Indices: 52743296--52743344 Score: 98
Period size: 13 Copynumber: 3.8 Consensus size: 13
52743286 TGGCTGAAAA
52743296 TATTGAATTGAAG
1 TATTGAATTGAAG
52743309 TATTGAATTGAAG
1 TATTGAATTGAAG
52743322 TATTGAATTGAAG
1 TATTGAATTGAAG
52743335 TATTGAATTG
1 TATTGAATTG
52743345 CTTGTTTAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.37, C:0.00, G:0.22, T:0.41
Consensus pattern (13 bp):
TATTGAATTGAAG
Found at i:52743718 original size:21 final size:22
Alignment explanation
Indices: 52743692--52743734 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
52743682 GCAATTAGGT
*
52743692 TTGGTATGAGTGCTAC-ATTTA
1 TTGGTATGAGAGCTACAATTTA
*
52743713 TTGGTATTAGAGCTACAATTTA
1 TTGGTATGAGAGCTACAATTTA
52743735 GTCAATTGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.42
Consensus pattern (22 bp):
TTGGTATGAGAGCTACAATTTA
Found at i:52747271 original size:26 final size:26
Alignment explanation
Indices: 52747241--52747348 Score: 148
Period size: 26 Copynumber: 4.2 Consensus size: 26
52747231 TGGTACAAAT
52747241 TGATAATGAGTTAGGTAAATGTTCCA
1 TGATAATGAGTTAGGTAAATGTTCCA
*
52747267 TGATAATGTA-TTAGGTAAATATTCCA
1 TGATAATG-AGTTAGGTAAATGTTCCA
* * *
52747293 CGATAATGGGTTAAGTAAATGTTCCA
1 TGATAATGAGTTAGGTAAATGTTCCA
52747319 TGATAATG-GTTTAGGTAAATGTTCCA
1 TGATAATGAG-TTAGGTAAATGTTCCA
52747345 TGAT
1 TGAT
52747349 GGGCATTTCA
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
25 1 0.01
26 70 0.97
27 1 0.01
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.36
Consensus pattern (26 bp):
TGATAATGAGTTAGGTAAATGTTCCA
Found at i:52747311 original size:52 final size:52
Alignment explanation
Indices: 52747242--52747344 Score: 163
Period size: 52 Copynumber: 2.0 Consensus size: 52
52747232 GGTACAAATT
*
52747242 GATAATGAGTTAGGTAAATGTTCCATGATAAT-GTATTAGGTAAATATTCCAC
1 GATAATGAGTTAAGTAAATGTTCCATGATAATGGT-TTAGGTAAATATTCCAC
* *
52747294 GATAATGGGTTAAGTAAATGTTCCATGATAATGGTTTAGGTAAATGTTCCA
1 GATAATGAGTTAAGTAAATGTTCCATGATAATGGTTTAGGTAAATATTCCA
52747345 TGATGGGCAT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
52 45 0.96
53 2 0.04
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (52 bp):
GATAATGAGTTAAGTAAATGTTCCATGATAATGGTTTAGGTAAATATTCCAC
Found at i:52748551 original size:16 final size:15
Alignment explanation
Indices: 52748525--52748554 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
52748515 ACTAGATTGG
52748525 CAAAAGCCGAAAAGC
1 CAAAAGCCGAAAAGC
52748540 CAAAATGCCGAAAAG
1 CAAAA-GCCGAAAAG
52748555 TCAGTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.53, C:0.23, G:0.20, T:0.03
Consensus pattern (15 bp):
CAAAAGCCGAAAAGC
Found at i:52749010 original size:27 final size:26
Alignment explanation
Indices: 52748970--52749163 Score: 237
Period size: 27 Copynumber: 7.2 Consensus size: 26
52748960 AGGAAGCGTC
*
52748970 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
52748997 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
**
52749024 CTGGTGGCGATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
* *
52749051 CTGGTGGTTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
*
52749078 CTGGTGGCTATGCCACGATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
52749105 CTGGTGGCTCTGCCACATATATCT-ATT
1 CTGGTGGCTCTGCCACAT-TATCTGA-T
*
52749132 CTGGTGGCTCTGCCACAATATCTGTAT
1 CTGGTGGCTCTGCCACATTATCTG-AT
52749159 CTGGT
1 CTGGT
52749164 AACTTCGTCA
Statistics
Matches: 145, Mismatches: 14, Indels: 16
0.83 0.08 0.09
Matches are distributed among these distances:
26 12 0.08
27 128 0.88
28 5 0.03
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:52749052 original size:54 final size:54
Alignment explanation
Indices: 52748970--52749163 Score: 327
Period size: 54 Copynumber: 3.6 Consensus size: 54
52748960 AGGAAGCGTC
52748970 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
* *
52749024 CTGGTGGCGATGCCACAATTATCTGATCTGGTGGTTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
* *
52749078 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTATT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
*
52749132 CTGGTGGCTCTGCCACAA-TATCTGTATCTGGT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGT
52749164 AACTTCGTCA
Statistics
Matches: 131, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
53 6 0.05
54 125 0.95
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
Found at i:52752776 original size:29 final size:29
Alignment explanation
Indices: 52752743--52752874 Score: 149
Period size: 29 Copynumber: 4.6 Consensus size: 29
52752733 GTGACGAGAT
52752743 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
52752772 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * ***
52752801 TGGCACTAAGTGTGCGAGCTCGAAGGGTA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * * **
52752830 TGGCACTATGTGTGCGGGCT-TAAATCGCA
1 TGGCACTAAGTGTGCGTGCTGGAAAT-ATA
52752859 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
52752875 AAATCGAGTA
Statistics
Matches: 88, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
28 2 0.02
29 86 0.98
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:52760186 original size:24 final size:24
Alignment explanation
Indices: 52760156--52760443 Score: 474
Period size: 24 Copynumber: 12.1 Consensus size: 24
52760146 GAATGTGACT
* *
52760156 ATAGCAAATCGCACACATAGTGCT
1 ATAGTAAATCGCACACATAGTGCC
*
52760180 ATAGCAAATCGCACACAT-GTGCC
1 ATAGTAAATCGCACACATAGTGCC
52760203 ATAGTAAATCGCAC-CATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
52760226 ATAGTAAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
52760250 ATAGTGAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
52760274 ATAGTGAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
52760298 ATAGTGAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
52760322 ATAGTGAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
52760346 ATAGTAAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
52760370 ATAGTGAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
52760394 ATAGTGAATCGCACAC-TAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
52760417 ATAGTAAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
52760441 ATA
1 ATA
52760444 TGGTCTTTGC
Statistics
Matches: 255, Mismatches: 6, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
22 3 0.01
23 58 0.23
24 194 0.76
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (24 bp):
ATAGTAAATCGCACACATAGTGCC
Found at i:52768240 original size:24 final size:24
Alignment explanation
Indices: 52768210--52768500 Score: 501
Period size: 24 Copynumber: 12.1 Consensus size: 24
52768200 GAATGTGACT
* *
52768210 ATAGCAAATCGCACACATAGTGCT
1 ATAGTAAATCGCACACATAGTGCC
*
52768234 ATAGCAAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
52768258 ATAGTAAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
52768282 ATAGTAAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
52768306 ATAGTGAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
52768330 ATAGTGAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
52768354 ATAGTGAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
52768378 ATAGTGAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
52768402 ATAGTAAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
52768426 ATAGTGAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
52768450 ATAGTGAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
52768474 ATAGTAAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
52768498 ATA
1 ATA
52768501 TGGTCTTTGC
Statistics
Matches: 261, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 261 1.00
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.21
Consensus pattern (24 bp):
ATAGTAAATCGCACACATAGTGCC
Found at i:52770833 original size:43 final size:43
Alignment explanation
Indices: 52770753--52770878 Score: 137
Period size: 43 Copynumber: 2.9 Consensus size: 43
52770743 TGTCACTTAT
* * * * ** *
52770753 CGATGCCACTGCCCCAGATAGGGTCTTACACAAAATCA-TATAA
1 CGATGCCAATGTCCCAGACATGGTCTTACACGTAATCACAAT-A
52770796 CGATGCCAATGTCCCAGACATGGTCTTACACGTAATCACAATA
1 CGATGCCAATGTCCCAGACATGGTCTTACACGTAATCACAATA
* * * *
52770839 CAATGCCAATGTCCCAGACATAGTCTTACATGTAACCACA
1 CGATGCCAATGTCCCAGACATGGTCTTACACGTAATCACA
52770879 TCTCGGTAAC
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
43 69 0.97
44 2 0.03
ACGTcount: A:0.34, C:0.29, G:0.15, T:0.22
Consensus pattern (43 bp):
CGATGCCAATGTCCCAGACATGGTCTTACACGTAATCACAATA
Found at i:52774153 original size:29 final size:29
Alignment explanation
Indices: 52774091--52774193 Score: 100
Period size: 29 Copynumber: 3.6 Consensus size: 29
52774081 GTGACGAGAT
* * *
52774091 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTGGAATATA
* * *
52774120 CGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTTGGAATATA
* * **
52774149 TGGCACTATGTGTGCGGGCTT-GAATCACG
1 TGGCACTAAGTGTGCGAGCTTGGAAT-ATA
52774178 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
52774194 TGATTGAGTA
Statistics
Matches: 59, Mismatches: 14, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
28 3 0.05
29 56 0.95
ACGTcount: A:0.20, C:0.17, G:0.34, T:0.28
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGGAATATA
Found at i:52782089 original size:29 final size:29
Alignment explanation
Indices: 52782027--52782129 Score: 100
Period size: 29 Copynumber: 3.6 Consensus size: 29
52782017 GTGACGAGAT
* * *
52782027 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTGGAATATA
* * *
52782056 CGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTTGGAATATA
* * **
52782085 TGGCACTATGTGTGCGGGCTT-GAATCACG
1 TGGCACTAAGTGTGCGAGCTTGGAAT-ATA
52782114 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
52782130 TGATTGAGTA
Statistics
Matches: 59, Mismatches: 14, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
28 3 0.05
29 56 0.95
ACGTcount: A:0.20, C:0.17, G:0.34, T:0.28
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGGAATATA
Found at i:52793614 original size:3 final size:3
Alignment explanation
Indices: 52793606--52793684 Score: 151
Period size: 3 Copynumber: 26.7 Consensus size: 3
52793596 GTTCCAACTT
52793606 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
52793653 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
52793685 TTAGGTTAAT
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 73 0.97
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:52795115 original size:43 final size:43
Alignment explanation
Indices: 52795067--52795154 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 43
52795057 TAAGGAGCAT
* *
52795067 TACCAGACAGACAGAACATTATAGAATTACAAATATCACATAG
1 TACCAGACAAACAAAACATTATAGAATTACAAATATCACATAG
52795110 TACCAGACAAACAAAACATTATAGAATTACAAATATCACATAG
1 TACCAGACAAACAAAACATTATAGAATTACAAATATCACATAG
52795153 TA
1 TA
52795155 TTATCATATA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.51, C:0.18, G:0.09, T:0.22
Consensus pattern (43 bp):
TACCAGACAAACAAAACATTATAGAATTACAAATATCACATAG
Found at i:52795150 original size:22 final size:22
Alignment explanation
Indices: 52795082--52795150 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
52795072 GACAGACAGA
52795082 ACATTATAGAATTACAAATATC
1 ACATTATAGAATTACAAATATC
** * * **
52795104 ACA-TAGTACCA-GACAAACAAA
1 ACATTA-TAGAATTACAAATATC
52795125 ACATTATAGAATTACAAATATC
1 ACATTATAGAATTACAAATATC
52795147 ACAT
1 ACAT
52795151 AGTATTATCA
Statistics
Matches: 32, Mismatches: 12, Indels: 6
0.64 0.24 0.12
Matches are distributed among these distances:
21 14 0.44
22 18 0.56
ACGTcount: A:0.52, C:0.17, G:0.06, T:0.25
Consensus pattern (22 bp):
ACATTATAGAATTACAAATATC
Found at i:52801106 original size:39 final size:39
Alignment explanation
Indices: 52801052--52801195 Score: 243
Period size: 39 Copynumber: 3.7 Consensus size: 39
52801042 GAATGTTCGA
52801052 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
* *
52801091 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
*
52801130 ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
*
52801169 GTGATATCCGGGTTAAGTCCCGAAGGC
1 GTGATATCCGGGCTAAG-CCCGAAGGC
52801196 CTTTGTGCGG
Statistics
Matches: 97, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 88 0.91
40 9 0.09
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (39 bp):
GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
Found at i:52801142 original size:78 final size:79
Alignment explanation
Indices: 52801053--52801235 Score: 278
Period size: 78 Copynumber: 2.3 Consensus size: 79
52801043 AATGTTCGAG
52801053 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAG-CCCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
52801117 AATTGTGCGAGTTA
66 AATTGTGCGAGTTA
*
52801131 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGTTAAGTCCCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
** *
52801196 CTTTGTGCGGGTTA
66 AATTGTGCGAGTTA
** * *
52801210 CCATAACCGGGCTATGTCCCGAAGGC
1 TGATATCCGGGCTAAG-CCCGAAGGC
52801236 GTTTGAACGA
Statistics
Matches: 95, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
78 54 0.57
79 32 0.34
80 9 0.09
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.23
Consensus pattern (79 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
AATTGTGCGAGTTA
Found at i:52809142 original size:39 final size:39
Alignment explanation
Indices: 52809088--52809231 Score: 243
Period size: 39 Copynumber: 3.7 Consensus size: 39
52809078 GAATGTTCGA
52809088 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
* *
52809127 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
*
52809166 ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
*
52809205 GTGATATCCGGGTTAAGTCCCGAAGGC
1 GTGATATCCGGGCTAAG-CCCGAAGGC
52809232 CTTTGTGCGG
Statistics
Matches: 97, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 88 0.91
40 9 0.09
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (39 bp):
GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
Found at i:52809178 original size:78 final size:79
Alignment explanation
Indices: 52809089--52809259 Score: 272
Period size: 78 Copynumber: 2.2 Consensus size: 79
52809079 AATGTTCGAG
52809089 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAG-CCCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
52809153 AATTGTGCGAGTTA
66 AATTGTGCGAGTTA
*
52809167 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGTTAAGTCCCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
** *
52809232 CTTTGTGCGGGTTA
66 AATTGTGCGAGTTA
** *
52809246 CCATAACCGGGCTA
1 TGATATCCGGGCTA
52809260 TGTCCCAAGG
Statistics
Matches: 85, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
78 54 0.64
79 31 0.36
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (79 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
AATTGTGCGAGTTA
Found at i:52814440 original size:60 final size:59
Alignment explanation
Indices: 52814365--52814484 Score: 231
Period size: 60 Copynumber: 2.0 Consensus size: 59
52814355 AATTTAAGTG
52814365 AATTAGTAAGGGTAAATTGGTAATTAATCAAATAAATACAAACAAATAACTAAAATGCT
1 AATTAGTAAGGGTAAATTGGTAATTAATCAAATAAATACAAACAAATAACTAAAATGCT
52814424 AATTAGTAAAGGGTAAATTGGTAATTAATCAAATAAATACAAACAAATAACTAAAATGCT
1 AATTAGT-AAGGGTAAATTGGTAATTAATCAAATAAATACAAACAAATAACTAAAATGCT
52814484 A
1 A
52814485 TCATCTTCTT
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
59 7 0.12
60 53 0.88
ACGTcount: A:0.53, C:0.08, G:0.12, T:0.27
Consensus pattern (59 bp):
AATTAGTAAGGGTAAATTGGTAATTAATCAAATAAATACAAACAAATAACTAAAATGCT
Found at i:52815792 original size:12 final size:12
Alignment explanation
Indices: 52815775--52815800 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
52815765 TAAAGTCCTT
52815775 TATAGATACAGA
1 TATAGATACAGA
52815787 TATAGATACAGA
1 TATAGATACAGA
52815799 TA
1 TA
52815801 CAAATAATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (12 bp):
TATAGATACAGA
Found at i:52829661 original size:25 final size:25
Alignment explanation
Indices: 52829631--52829708 Score: 76
Period size: 25 Copynumber: 3.2 Consensus size: 25
52829621 TAGGATTTTA
*
52829631 TGTGATGGATGTGAACATGCGTATG
1 TGTGATGAATGTGAACATGCGTATG
* *
52829656 TGTGAT-AAGGCTG-A-ATGGCCTA--
1 TGTGATGAATG-TGAACAT-GCGTATG
52829678 TGTGATGAATGTGAACATGCGTATG
1 TGTGATGAATGTGAACATGCGTATG
52829703 TGTGAT
1 TGTGAT
52829709 AAGGCCGAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 14
0.68 0.08 0.23
Matches are distributed among these distances:
22 8 0.20
23 10 0.24
24 9 0.22
25 14 0.34
ACGTcount: A:0.26, C:0.09, G:0.33, T:0.32
Consensus pattern (25 bp):
TGTGATGAATGTGAACATGCGTATG
Found at i:52829680 original size:47 final size:47
Alignment explanation
Indices: 52829630--52830012 Score: 586
Period size: 47 Copynumber: 8.1 Consensus size: 47
52829620 TTAGGATTTT
* * *
52829630 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCTGAATGGCCT
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
52829677 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
*
52829724 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
***
52829771 ATGTGATGAATGTGAACCCGTATATATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAA--C--ATGCGTATGTGTGATAAGGCCGAATGGCCA
52829822 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
52829869 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
* * *
52829916 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
** * * * *
52829963 ATGTGATGAATGTGAACATGAATATATGTGGTAAGGCTGAATGGCTA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
52830010 ATG
1 ATG
52830013 CGAAACGTGT
Statistics
Matches: 313, Mismatches: 19, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
47 268 0.86
49 2 0.01
51 43 0.14
ACGTcount: A:0.31, C:0.12, G:0.31, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
Found at i:52829826 original size:145 final size:141
Alignment explanation
Indices: 52829630--52830012 Score: 586
Period size: 145 Copynumber: 2.7 Consensus size: 141
52829620 TTAGGATTTT
* * * * *
52829630 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCTGAATGGCCTATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATACATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
*
52829695 TGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAACATGCGTATGTGTGATAAGG
66 TGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGATAAGG
52829760 CCGAATGGCCA
131 CCGAATGGCCA
*
52829771 ATGTGATGAATGTGAACCCGTATATATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTG
1 ATGTGATGAATGTGAA--C--ATACATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTG
52829836 AACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGAT
62 AACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGAT
52829901 AAGGCCGAATGGCCA
127 AAGGCCGAATGGCCA
* * *
52829916 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATACATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
** * * * *
52829981 TGAATATATGTGGTAAGGCTGAATGGCTAATG
66 TGCGTATGTGTGATAAGGCCGAATGGCCAATG
52830013 CGAAACGTGT
Statistics
Matches: 221, Mismatches: 17, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
141 85 0.38
143 2 0.01
145 134 0.61
ACGTcount: A:0.31, C:0.12, G:0.31, T:0.27
Consensus pattern (141 bp):
ATGTGATGAATGTGAACATACATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
TGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGATAAGG
CCGAATGGCCA
Found at i:52829957 original size:192 final size:188
Alignment explanation
Indices: 52829630--52830012 Score: 631
Period size: 192 Copynumber: 2.0 Consensus size: 188
52829620 TTAGGATTTT
* * *
52829630 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCTGAATGGCCTATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
* * * *
52829695 TGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAACATGCGTATGTGTGATAAGG
66 TGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGG
*
52829760 CCGAATGGCCAATGTGATGAATGTGAACCCGTATATATATGTGTGATAAGGCCGAATGGCCA
131 CCGAATGGCCAATGTGATGAATGTGAACACG-A-ATATATGTG-G-TAAGGCCGAATGGCCA
52829822 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
52829887 TGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGG
66 TGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGG
* * *
52829952 CCGAATGGCCAATGTGATGAATGTGAACATGAATATATGTGGTAAGGCTGAATGGCTA
131 CCGAATGGCCAATGTGATGAATGTGAACACGAATATATGTGGTAAGGCCGAATGGCCA
52830010 ATG
1 ATG
52830013 CGAAACGTGT
Statistics
Matches: 180, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
188 17 0.09
189 1 0.01
190 9 0.05
191 1 0.01
192 152 0.84
ACGTcount: A:0.31, C:0.12, G:0.31, T:0.27
Consensus pattern (188 bp):
ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
TGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGG
CCGAATGGCCAATGTGATGAATGTGAACACGAATATATGTGGTAAGGCCGAATGGCCA
Found at i:52830224 original size:37 final size:37
Alignment explanation
Indices: 52830174--52830355 Score: 312
Period size: 37 Copynumber: 4.9 Consensus size: 37
52830164 GGAAATATAT
52830174 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
52830211 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTT-
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
*
52830247 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
*
52830284 TCCGGGTAAGACCCGATGACTACCTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* * *
52830321 TCCGGGTAAGACCCGATAACTTCATGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
52830356 CGTCTGAGCT
Statistics
Matches: 138, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
36 35 0.25
37 103 0.75
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:52830292 original size:73 final size:73
Alignment explanation
Indices: 52830173--52830354 Score: 310
Period size: 73 Copynumber: 2.5 Consensus size: 73
52830163 TGGAAATATA
* *
52830173 TTCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGTAAGACCCGATGACTACGTGT
1 TTCCGGGTAAGACCCGATGACTACGTGTGGAGATTATGTCCGGGTAAGACCCGATGACTACCTGT
52830238 GGAGATTT
66 GGAGATTT
52830246 TTCCGGGTAAGACCCGATGACTACGTGTGGAGATTATGTCCGGGTAAGACCCGATGACTACCTGT
1 TTCCGGGTAAGACCCGATGACTACGTGTGGAGATTATGTCCGGGTAAGACCCGATGACTACCTGT
52830311 GGAGATTT
66 GGAGATTT
* * *
52830319 TGTCCGGGTAAGACCCGATAACTTCATGTGGAGATT
1 T-TCCGGGTAAGACCCGATGACTACGTGTGGAGATT
52830355 TCGTCTGAGC
Statistics
Matches: 103, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
73 72 0.70
74 31 0.30
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (73 bp):
TTCCGGGTAAGACCCGATGACTACGTGTGGAGATTATGTCCGGGTAAGACCCGATGACTACCTGT
GGAGATTT
Found at i:52831677 original size:40 final size:40
Alignment explanation
Indices: 52831622--52831867 Score: 402
Period size: 40 Copynumber: 6.2 Consensus size: 40
52831612 GAGAATTGAG
*
52831622 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
52831662 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
52831702 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
52831742 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
* *
52831782 AGTGATATATCCGGGCTAAATCCCGAGGAGCATTCGTTCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
* * * * * *
52831822 GGTGTTATATCCGGGCTAGGTCCCGAAGAGCAATCATGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
*
52831862 GGTGAT
1 AGTGAT
52831868 GTGTATTCGG
Statistics
Matches: 194, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 194 1.00
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (40 bp):
AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
Found at i:52835806 original size:47 final size:47
Alignment explanation
Indices: 52835755--52836137 Score: 604
Period size: 47 Copynumber: 8.1 Consensus size: 47
52835745 TTAGGATTTT
* *
52835755 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
52835802 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
* *
52835849 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
**
52835896 ATGTGATGAATGTGAACCCGTATATATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAA--C--ATGCATATGTGTGATAAGGCCGAATGGCCA
*
52835947 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
*
52835994 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
* *
52836041 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
* * * *
52836088 ATGTGATGAATGTGAACATGAATATATGTGGTAAGGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
52836135 ATG
1 ATG
52836138 CGAAACGTGT
Statistics
Matches: 314, Mismatches: 18, Indels: 8
0.92 0.05 0.02
Matches are distributed among these distances:
47 269 0.86
49 2 0.01
51 43 0.14
ACGTcount: A:0.31, C:0.12, G:0.31, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
Found at i:52835808 original size:22 final size:22
Alignment explanation
Indices: 52835781--52835855 Score: 57
Period size: 22 Copynumber: 3.3 Consensus size: 22
52835771 CATGCGTATG
52835781 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* *
52835803 TGTGATGAATG-TGAACAT-G-CATA
1 TGTGAT-AAGGCCG-A-ATGGCCA-A
52835826 TGTGTGATAAGGCCGAATGGCCAA
1 --TGTGATAAGGCCGAATGGCCAA
52835850 TGTGAT
1 TGTGAT
52835856 GGATGTGAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
22 15 0.38
23 8 0.20
24 8 0.20
25 9 0.22
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.25
Consensus pattern (22 bp):
TGTGATAAGGCCGAATGGCCAA
Found at i:52835942 original size:145 final size:141
Alignment explanation
Indices: 52835755--52836137 Score: 613
Period size: 145 Copynumber: 2.7 Consensus size: 141
52835745 TTAGGATTTT
* * *
52835755 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATACATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
*
52835820 TGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAACATGCGTATGTGTGATAAGG
66 TGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGATAAGG
52835885 CCGAATGGCCA
131 CCGAATGGCCA
*
52835896 ATGTGATGAATGTGAACCCGTATATATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTG
1 ATGTGATGAATGTGAA--C--ATACATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTG
*
52835961 AACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGAT
62 AACATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGAT
52836026 AAGGCCGAATGGCCA
127 AAGGCCGAATGGCCA
* * *
52836041 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATACATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
* * * *
52836106 TGAATATATGTGGTAAGGCCGAATGGCTAATG
66 TGCATATGTGTGATAAGGCCGAATGGCCAATG
52836138 CGAAACGTGT
Statistics
Matches: 223, Mismatches: 15, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
141 86 0.39
143 2 0.01
145 135 0.61
ACGTcount: A:0.31, C:0.12, G:0.31, T:0.26
Consensus pattern (141 bp):
ATGTGATGAATGTGAACATACATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
TGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGATAAGG
CCGAATGGCCA
Found at i:52836082 original size:192 final size:188
Alignment explanation
Indices: 52835755--52836137 Score: 649
Period size: 192 Copynumber: 2.0 Consensus size: 188
52835745 TTAGGATTTT
*
52835755 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
* * * *
52835820 TGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAACATGCGTATGTGTGATAAGG
66 TGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGG
*
52835885 CCGAATGGCCAATGTGATGAATGTGAACCCGTATATATATGTGTGATAAGGCCGAATGGCCA
131 CCGAATGGCCAATGTGATGAATGTGAACACG-A-ATATATGTG-G-TAAGGCCGAATGGCCA
52835947 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
*
52836012 TGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGG
66 TGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGG
* *
52836077 CCGAATGGCCAATGTGATGAATGTGAACATGAATATATGTGGTAAGGCCGAATGGCTA
131 CCGAATGGCCAATGTGATGAATGTGAACACGAATATATGTGGTAAGGCCGAATGGCCA
52836135 ATG
1 ATG
52836138 CGAAACGTGT
Statistics
Matches: 182, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
188 18 0.10
189 1 0.01
190 9 0.05
191 1 0.01
192 153 0.84
ACGTcount: A:0.31, C:0.12, G:0.31, T:0.26
Consensus pattern (188 bp):
ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
TGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGG
CCGAATGGCCAATGTGATGAATGTGAACACGAATATATGTGGTAAGGCCGAATGGCCA
Found at i:52836351 original size:37 final size:37
Alignment explanation
Indices: 52836301--52836520 Score: 359
Period size: 37 Copynumber: 5.9 Consensus size: 37
52836291 GGAAATATAT
*
52836301 TCCGGGTAAGACCCGATGACTATGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* *
52836338 TCCGGGTAAGACCCAATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
*
52836375 TCTGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
*
52836412 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
52836449 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* * * *
52836486 TCCGGGTAAGACCTGATAACTTCATGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
52836521 CGTCTGAGCT
Statistics
Matches: 170, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 170 1.00
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.28
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:52846120 original size:39 final size:39
Alignment explanation
Indices: 52846066--52846217 Score: 252
Period size: 39 Copynumber: 3.9 Consensus size: 39
52846056 GAATGTTCGA
*
52846066 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
*
52846105 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
*
52846144 ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
*
52846183 GTGATATCCGGGTTAAGTCCCGAAGGC-ATTGTGCG
1 GTGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCG
52846218 GGTTACCATA
Statistics
Matches: 106, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
39 97 0.92
40 9 0.08
ACGTcount: A:0.24, C:0.21, G:0.32, T:0.23
Consensus pattern (39 bp):
GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
Found at i:52846233 original size:39 final size:39
Alignment explanation
Indices: 52846067--52846247 Score: 247
Period size: 39 Copynumber: 4.6 Consensus size: 39
52846057 AATGTTCGAG
* *
52846067 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAATTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
*
52846106 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
*
52846145 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* *
52846184 TGATATCCGGGTTAAGTCCCGAAGGC-ATTGTGCGGGTTA
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA
** * *
52846223 CCATAACCGGGCTATGTCCCGAAGG
1 TGATATCCGGGCTAAG-CCCGAAGG
52846248 TGTTTGAACG
Statistics
Matches: 128, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
39 119 0.93
40 9 0.07
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.23
Consensus pattern (39 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
Found at i:52846269 original size:79 final size:78
Alignment explanation
Indices: 52846073--52846272 Score: 206
Period size: 78 Copynumber: 2.6 Consensus size: 78
52846063 CGAGTGATAT
** * *
52846073 CCGGGCTAAGCCCGAAGGCAATTGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAATTGTG
1 CCGGGCTAAGCCCGAAGGCAATTGAACGAGTAGTGATATCCGGGCTAAGCCCGAAGGCAATTGTG
** *
52846138 CGAGCTATGATAT
66 CGAGCTACCATAA
** * *
52846151 CCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGC-ATTGT
1 CCGGGCTAAGCCCGAAGGCAATTGAACGAGTAGTGATATCCGGGCTAAG-CCCGAAGGCAATTGT
* *
52846215 GCGGGTTACCATAA
65 GCGAGCTACCATAA
* ***
52846229 CCGGGCTATGTCCCGAAGGTGTTTGAACGAGTAGCT-ATATCCGG
1 CCGGGCTAAG-CCCGAAGGCAATTGAACGAGTAG-TGATATCCGG
52846273 ATAAACTCCG
Statistics
Matches: 105, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
78 70 0.67
79 34 0.32
80 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.32, T:0.23
Consensus pattern (78 bp):
CCGGGCTAAGCCCGAAGGCAATTGAACGAGTAGTGATATCCGGGCTAAGCCCGAAGGCAATTGTG
CGAGCTACCATAA
Found at i:52853376 original size:39 final size:39
Alignment explanation
Indices: 52853322--52853474 Score: 236
Period size: 39 Copynumber: 3.9 Consensus size: 39
52853312 GAATGTTCGA
* *
52853322 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGTGAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
*
52853361 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
*
52853400 ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
*
52853439 GTGATATCCGGGTTAAGTCCCGAAGGC-ATATGTGCG
1 GTGATATCCGGGCTAAG-CCCGAAGGCAAT-TGTGCG
52853475 GGTTACCATA
Statistics
Matches: 105, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
39 90 0.86
40 15 0.14
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.24
Consensus pattern (39 bp):
GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
Found at i:52853490 original size:40 final size:39
Alignment explanation
Indices: 52853323--52853504 Score: 231
Period size: 39 Copynumber: 4.6 Consensus size: 39
52853313 AATGTTCGAG
* * *
52853323 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGTGAATTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
*
52853362 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
*
52853401 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* *
52853440 TGATATCCGGGTTAAGTCCCGAAGGC-ATATGTGCGGGTTA
1 TGATATCCGGGCTAAG-CCCGAAGGCAAT-TGTGCGAGTTA
** * *
52853480 CCATAACCGGGCTATGTCCCGAAGG
1 TGATATCCGGGCTAAG-CCCGAAGG
52853505 TGTTTTGAAC
Statistics
Matches: 127, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
39 89 0.70
40 38 0.30
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.23
Consensus pattern (39 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
Found at i:52856036 original size:27 final size:27
Alignment explanation
Indices: 52856006--52856090 Score: 134
Period size: 27 Copynumber: 3.1 Consensus size: 27
52855996 ATTACCAAAG
* *
52856006 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
*
52856033 TACCCTTGATTTACAAAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
*
52856060 TACCCTCGATTTACAAAATTACCGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
52856087 TACC
1 TACC
52856091 ATTAAAATTA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.41
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACTGTTT
Found at i:52856138 original size:27 final size:27
Alignment explanation
Indices: 52856093--52856222 Score: 84
Period size: 27 Copynumber: 4.8 Consensus size: 27
52856083 GTTTTACCAT
** *
52856093 TAAAATTACTGAAACACCCCTA-TAGGG
1 TAAAATTACCAAAATACCCCTAGT-GGG
* **
52856120 TAGAATTACCAAAATACCCCTAGTTTG
1 TAAAATTACCAAAATACCCCTAGTGGG
* * **
52856147 TAAAATTACCAAAATACCACTGGTTTG
1 TAAAATTACCAAAATACCCCTAGTGGG
* * * * **
52856174 TGAAATTACCGAAATA-CCTTCAATTTG
1 TAAAATTACCAAAATACCCCT-AGTGGG
52856201 TAAAATTACCAAAATACCCCTA
1 TAAAATTACCAAAATACCCCTA
52856223 ATTTACAAAA
Statistics
Matches: 82, Mismatches: 18, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
26 2 0.02
27 76 0.93
28 4 0.05
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.28
Consensus pattern (27 bp):
TAAAATTACCAAAATACCCCTAGTGGG
Found at i:52856225 original size:27 final size:27
Alignment explanation
Indices: 52856123--52856246 Score: 135
Period size: 27 Copynumber: 4.6 Consensus size: 27
52856113 TATAGGGTAG
*
52856123 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAATTTGTAA
* ** *
52856150 AATTACCAAAATACCACTGGTTTGTGA
1 AATTACCAAAATACCCCTAATTTGTAA
* *
52856177 AATTACCGAAATA-CCTTCAATTTGTAA
1 AATTACCAAAATACCCCT-AATTTGTAA
**
52856204 AATTACCAAAATACCCCTAATTTACAA
1 AATTACCAAAATACCCCTAATTTGTAA
52856231 AATTA-CAGAAATACCC
1 AATTACCA-AAATACCC
52856247 TTGACTTTCT
Statistics
Matches: 81, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
26 4 0.05
27 74 0.91
28 3 0.04
ACGTcount: A:0.43, C:0.22, G:0.07, T:0.28
Consensus pattern (27 bp):
AATTACCAAAATACCCCTAATTTGTAA
Found at i:52856234 original size:54 final size:54
Alignment explanation
Indices: 52856143--52856301 Score: 149
Period size: 54 Copynumber: 2.9 Consensus size: 54
52856133 ATACCCCTAG
** *** *
52856143 TTTGTAAAATTACCAAAATACCACTGGTTTGTGAAATTACCGAAATACCTTCAA
1 TTTGTAAAATTACCAAAATACCACTAATTTACAAAATTACAGAAATACCTTCAA
* * *
52856197 TTTGTAAAATTACCAAAATACCCCTAATTTACAAAATTACAGAAATACCCTTGAC
1 TTTGTAAAATTACCAAAATACCACTAATTTACAAAATTACAGAAATA-CCTTCAA
* * * ** *
52856252 TTTCTAAAAATTA-TAGAAATACCATTGGTTTACAAAATTACTGAAATACC
1 TTTGT-AAAATTACCA-AAATACCACTAATTTACAAAATTACAGAAATACC
52856302 CTTGGTTTGT
Statistics
Matches: 86, Mismatches: 16, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
54 40 0.47
55 12 0.14
56 34 0.40
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.31
Consensus pattern (54 bp):
TTTGTAAAATTACCAAAATACCACTAATTTACAAAATTACAGAAATACCTTCAA
Found at i:52856297 original size:27 final size:27
Alignment explanation
Indices: 52856224--52856309 Score: 95
Period size: 27 Copynumber: 3.1 Consensus size: 27
52856214 ATACCCCTAA
* *
52856224 TTTACAAAATTACAGAAATACCCTTGAC
1 TTTACAAAATTACTGAAATACCCTTG-G
*
52856252 TTT-CTAAAAATTA-TAGAAATACCATTGG
1 TTTAC--AAAATTACT-GAAATACCCTTGG
52856280 TTTACAAAATTACTGAAATACCCTTGG
1 TTTACAAAATTACTGAAATACCCTTGG
52856307 TTT
1 TTT
52856310 GTAGATTTAC
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
27 23 0.47
28 7 0.14
29 19 0.39
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (27 bp):
TTTACAAAATTACTGAAATACCCTTGG
Found at i:52856393 original size:27 final size:27
Alignment explanation
Indices: 52856350--52856423 Score: 80
Period size: 27 Copynumber: 2.7 Consensus size: 27
52856340 AAATGACTAA
*
52856350 AATACCCCTAATA-GGTAAAAAGACCGT
1 AATACCCCT-GTAGGGTAAAAAGACCGT
**
52856377 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTAGGGTAAAAAGACCGT
*
52856404 AATACCCCTGTATGGTAAAA
1 AATACCCCTGTAGGGTAAAA
52856424 TGATGAATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
26 3 0.08
27 35 0.90
28 1 0.03
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAAAAAGACCGT
Found at i:52857285 original size:24 final size:25
Alignment explanation
Indices: 52857209--52857278 Score: 97
Period size: 25 Copynumber: 2.8 Consensus size: 25
52857199 AGGAAGTGCT
* * *
52857209 AAAAGGG-TTATGCCCTAGTTTACCG
1 AAAAGGGCTT-TGCCCCAGTTTATCA
52857234 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
52857259 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
52857279 ATTAAAAGAG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
25 39 0.95
26 2 0.05
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCA
Found at i:52857291 original size:24 final size:24
Alignment explanation
Indices: 52857234--52857305 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 24
52857224 TAGTTTACCG
52857234 AAAAG-GGCTTTGCCCCAGTTTATC
1 AAAAGAGGCTTTGCCCCAG-TTATC
*
52857258 AAAA-AGGGCTTTGCCCCAGTTATT
1 AAAAGA-GGCTTTGCCCCAGTTATC
**
52857282 AAAAGAGGCTAGGCCTCCAGTTAT
1 AAAAGAGGCTTTGCC-CCAGTTAT
52857306 ATGATAAAGC
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
24 19 0.46
25 22 0.54
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (24 bp):
AAAAGAGGCTTTGCCCCAGTTATC
Found at i:52857547 original size:31 final size:31
Alignment explanation
Indices: 52857498--52857575 Score: 149
Period size: 31 Copynumber: 2.5 Consensus size: 31
52857488 CGCTTACAGT
52857498 AAAGGCTTCGG-CCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
52857528 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
52857559 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
52857576 ATCTGTCGAG
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
30 11 0.23
31 36 0.77
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:52864751 original size:48 final size:46
Alignment explanation
Indices: 52864635--52864751 Score: 153
Period size: 46 Copynumber: 2.5 Consensus size: 46
52864625 TGATATGTGT
* * *
52864635 GCTAGTGTAAGACATGTCTGGGACATGCATCGACATTGAGACGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAACATTGAGAAGAAA
* *
52864681 GCTAGTGTAAGACATGTCTGGGACATGCATCAACCTTGAGATATACAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAACATTGAGA-AGA-AA
* *
52864729 GCTAGTGTAAGACCTGTTTGGGA
1 GCTAGTGTAAGACATGTCTGGGA
52864752 TATCGCGTCA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
46 39 0.63
47 1 0.02
48 22 0.35
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCAACATTGAGAAGAAA
Found at i:52873262 original size:28 final size:29
Alignment explanation
Indices: 52873228--52873345 Score: 168
Period size: 29 Copynumber: 4.1 Consensus size: 29
52873218 ACATACATAG
* *
52873228 ATATGGCCCACTAGGCCC-AATCTCATTC
1 ATATGGCCCATTAGGCCCAAATCACATTC
*
52873256 ACATGGCCCA-TAGGCCCAAATCACATTC
1 ATATGGCCCATTAGGCCCAAATCACATTC
* **
52873284 GTATAACCCATTAGGCCCAAATCACATTC
1 ATATGGCCCATTAGGCCCAAATCACATTC
52873313 ATATGGCCCATTAGGCCCAAATCACATTC
1 ATATGGCCCATTAGGCCCAAATCACATTC
52873342 ATAT
1 ATAT
52873346 TCATGCTTTC
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
27 7 0.09
28 24 0.30
29 48 0.61
ACGTcount: A:0.31, C:0.32, G:0.13, T:0.24
Consensus pattern (29 bp):
ATATGGCCCATTAGGCCCAAATCACATTC
Found at i:52873312 original size:57 final size:57
Alignment explanation
Indices: 52873234--52873341 Score: 173
Period size: 57 Copynumber: 1.9 Consensus size: 57
52873224 ATAGATATGG
*
52873234 CCCACTAGGCCCAATCTCATTCACATGGCCCA-TAGGCCCAAATCACATTCGTATAA
1 CCCACTAGGCCCAATCACATTCACATGGCCCATTAGGCCCAAATCACATTCGTATAA
* *
52873290 CCCATTAGGCCCAAATCACATTCATATGGCCCATTAGGCCCAAATCACATTC
1 CCCACTAGGCCC-AATCACATTCACATGGCCCATTAGGCCCAAATCACATTC
52873342 ATATTCATGC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
56 11 0.23
57 18 0.38
58 18 0.38
ACGTcount: A:0.31, C:0.35, G:0.12, T:0.22
Consensus pattern (57 bp):
CCCACTAGGCCCAATCACATTCACATGGCCCATTAGGCCCAAATCACATTCGTATAA
Found at i:52873425 original size:16 final size:17
Alignment explanation
Indices: 52873404--52873436 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
52873394 GCCTATTATG
52873404 GGCCCA-ATAGCCCATC
1 GGCCCACATAGCCCATC
*
52873420 GGCCCACTTAGCCCATC
1 GGCCCACATAGCCCATC
52873437 CTGGCCTGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.21, C:0.45, G:0.18, T:0.15
Consensus pattern (17 bp):
GGCCCACATAGCCCATC
Found at i:52873576 original size:16 final size:16
Alignment explanation
Indices: 52873555--52873608 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
52873545 ATAGCCAAAC
*
52873555 TTTCGGCTTTTTGGCA
1 TTTCGGCTTTTCGGCA
*
52873571 TTTCGGCTTTTCGGCT
1 TTTCGGCTTTTCGGCA
* * *
52873587 TTTCGACATTTCGACA
1 TTTCGGCTTTTCGGCA
52873603 TTTCGG
1 TTTCGG
52873609 GATTTGCCGA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.46
Consensus pattern (16 bp):
TTTCGGCTTTTCGGCA
Found at i:52873584 original size:8 final size:8
Alignment explanation
Indices: 52873555--52873591 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
52873545 ATAGCCAAAC
52873555 TTTCGGCT
1 TTTCGGCT
* *
52873563 TTTTGGCA
1 TTTCGGCT
52873571 TTTCGGCT
1 TTTCGGCT
52873579 TTTCGGCT
1 TTTCGGCT
52873587 TTTCG
1 TTTCG
52873592 ACATTTCGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.03, C:0.22, G:0.24, T:0.51
Consensus pattern (8 bp):
TTTCGGCT
Found at i:52873585 original size:24 final size:24
Alignment explanation
Indices: 52873555--52873608 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
52873545 ATAGCCAAAC
* * * *
52873555 TTTCGGCTTTTTGGCATTTCGGCT
1 TTTCGGCTTTTCGACATTTCGACA
52873579 TTTCGGCTTTTCGACATTTCGACA
1 TTTCGGCTTTTCGACATTTCGACA
52873603 TTTCGG
1 TTTCGG
52873609 GATTTGCCGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.46
Consensus pattern (24 bp):
TTTCGGCTTTTCGACATTTCGACA
Found at i:52877881 original size:29 final size:30
Alignment explanation
Indices: 52877849--52877930 Score: 116
Period size: 29 Copynumber: 2.8 Consensus size: 30
52877839 CACATGGCCT
52877849 ATTAGGCCCAAATCACATTCC-TATAACCC
1 ATTAGGCCCAAATCACATTCCATATAACCC
* **
52877878 ATTAAGCCCAAATCACA-TCCATATGGCCC
1 ATTAGGCCCAAATCACATTCCATATAACCC
52877907 ATTAGGCCCAAATCACATT-CATAT
1 ATTAGGCCCAAATCACATTCCATAT
52877931 TCATGCTTTC
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
28 3 0.06
29 43 0.91
30 1 0.02
ACGTcount: A:0.35, C:0.32, G:0.09, T:0.24
Consensus pattern (30 bp):
ATTAGGCCCAAATCACATTCCATATAACCC
Found at i:52878165 original size:16 final size:16
Alignment explanation
Indices: 52878146--52878176 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52878136 AAACTTTCAG
*
52878146 CTTTTTGGCATTTCGA
1 CTTTTCGGCATTTCGA
52878162 CTTTTCGGCATTTCG
1 CTTTTCGGCATTTCG
52878177 GGATTTGTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.23, G:0.19, T:0.48
Consensus pattern (16 bp):
CTTTTCGGCATTTCGA
Found at i:52879862 original size:49 final size:49
Alignment explanation
Indices: 52879803--52879908 Score: 167
Period size: 49 Copynumber: 2.2 Consensus size: 49
52879793 TCATAGACGA
* ** **
52879803 TTGGGCATTTTTCATACGACTCGACTCACCCCGAGGTGGAGCGTATCAT
1 TTGGGTATTTTTCATAAAACTCGACTCACCCCGAGGCAGAGCGTATCAT
52879852 TTGGGTATTTTTCATAAAACTCGACTCACCCCGAGGCAGAGCGTATCAT
1 TTGGGTATTTTTCATAAAACTCGACTCACCCCGAGGCAGAGCGTATCAT
52879901 TTGGGTAT
1 TTGGGTAT
52879909 CAGAGCTACA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.30
Consensus pattern (49 bp):
TTGGGTATTTTTCATAAAACTCGACTCACCCCGAGGCAGAGCGTATCAT
Found at i:52879999 original size:11 final size:11
Alignment explanation
Indices: 52879985--52880082 Score: 58
Period size: 11 Copynumber: 8.6 Consensus size: 11
52879975 GTAAGTTTCA
52879985 AAAAAAATTTG
1 AAAAAAATTTG
**
52879996 AAAAAAATTCAA
1 AAAAAAATT-TG
*
52880008 AAAAAAAGTTTCA
1 AAAAAAA-TTT-G
**
52880021 AAAAAAATACG
1 AAAAAAATTTG
*
52880032 AAAAAAA-TTC
1 AAAAAAATTTG
52880042 AAAAAAATGTT-
1 AAAAAAAT-TTG
52880053 -AAAAAATTTCAG
1 AAAAAAATTT--G
*
52880065 GAAAAAATTTG
1 AAAAAAATTTG
52880076 AAAAAAA
1 AAAAAAA
52880083 AATTTTGAAC
Statistics
Matches: 68, Mismatches: 10, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
9 2 0.03
10 14 0.21
11 23 0.34
12 10 0.15
13 19 0.28
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.20
Consensus pattern (11 bp):
AAAAAAATTTG
Found at i:52880001 original size:12 final size:12
Alignment explanation
Indices: 52879984--52880083 Score: 52
Period size: 13 Copynumber: 8.7 Consensus size: 12
52879974 AGTAAGTTTC
52879984 AAAAAAAATTTG
1 AAAAAAAATTTG
**
52879996 -AAAAAAATTCA
1 AAAAAAAATTTG
*
52880007 AAAAAAAAGTTTC
1 AAAAAAAA-TTTG
**
52880020 AAAAAAAATACG
1 AAAAAAAATTTG
52880032 -AAAAAAA-TT-
1 AAAAAAAATTTG
*
52880041 CAAAAAAATGTT-
1 AAAAAAAAT-TTG
*
52880053 --AAAAAATTTC
1 AAAAAAAATTTG
*
52880063 AGGAAAAAATTTG
1 A-AAAAAAATTTG
52880076 AAAAAAAA
1 AAAAAAAA
52880084 ATTTTGAACA
Statistics
Matches: 68, Mismatches: 11, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
9 2 0.03
10 14 0.21
11 16 0.24
12 16 0.24
13 20 0.29
ACGTcount: A:0.68, C:0.05, G:0.07, T:0.20
Consensus pattern (12 bp):
AAAAAAAATTTG
Found at i:52880024 original size:36 final size:36
Alignment explanation
Indices: 52879977--52880048 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
52879967 CTCATCAAGT
**
52879977 AAGTTTCAAAAAAAATTTGAAAAAAATTCAAAAAAA
1 AAGTTTCAAAAAAAATACGAAAAAAATTCAAAAAAA
52880013 AAGTTTCAAAAAAAATACGAAAAAAATTCAAAAAAA
1 AAGTTTCAAAAAAAATACGAAAAAAATTCAAAAAAA
52880049 TGTTAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.68, C:0.07, G:0.06, T:0.19
Consensus pattern (36 bp):
AAGTTTCAAAAAAAATACGAAAAAAATTCAAAAAAA
Found at i:52882199 original size:16 final size:16
Alignment explanation
Indices: 52882180--52882214 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
52882170 AGAATATTGT
*
52882180 AAAAAATAA-AATAAG
1 AAAAAATAAGAAAAAG
52882195 AAAAAATAAGAAAAAG
1 AAAAAATAAGAAAAAG
52882211 AAAA
1 AAAA
52882215 CAAAAGAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.83, C:0.00, G:0.09, T:0.09
Consensus pattern (16 bp):
AAAAAATAAGAAAAAG
Found at i:52893463 original size:16 final size:16
Alignment explanation
Indices: 52893428--52893478 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
52893418 GTAGATCGAC
* *
52893428 AAATCCTGAAAAGCCG
1 AAATACTGAAAAGCCA
* *
52893444 AAATGCTGAAAAGCTA
1 AAATACTGAAAAGCCA
*
52893460 AAATACCGAAAAGCCA
1 AAATACTGAAAAGCCA
52893476 AAA
1 AAA
52893479 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.53, C:0.20, G:0.16, T:0.12
Consensus pattern (16 bp):
AAATACTGAAAAGCCA
Found at i:52893773 original size:28 final size:28
Alignment explanation
Indices: 52893702--52893778 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 28
52893692 TCCAAAAGTA
* *
52893702 ATTGGGCCTACTGGGCCATATAGATGTG
1 ATTGGGCCTAATGGGCCATATAGATGAG
52893730 ATTTGGGCCTAATGGGCCATAT-GAATGAG
1 A-TTGGGCCTAATGGGCCATATAG-ATGAG
*
52893759 ATTGGGCCTAGTGGGCCATA
1 ATTGGGCCTAATGGGCCATA
52893779 AGCATGTATG
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
28 20 0.45
29 24 0.55
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.27
Consensus pattern (28 bp):
ATTGGGCCTAATGGGCCATATAGATGAG
Found at i:52896863 original size:28 final size:29
Alignment explanation
Indices: 52896821--52896935 Score: 119
Period size: 29 Copynumber: 4.0 Consensus size: 29
52896811 TACCTTTATC
* * *
52896821 TGGCCCACTAAGCCC-AATCATATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
* * *
52896849 TGGCCTATTAGGCCCAAATCACCTGT-GTA
1 TGGCCCATTAGGCCCAAATCACAT-TCATA
*
52896878 TGGCCCATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
* *
52896907 TGGCCCGTTAGGCCC-AGTCACATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
52896935 T
1 T
52896936 TCATGCTCAC
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
28 25 0.35
29 46 0.64
30 1 0.01
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.27
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTCATA
Found at i:52897173 original size:16 final size:16
Alignment explanation
Indices: 52897154--52897189 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
52897144 AACTTTCAGT
*
52897154 TTTTCGGCATTTCGGC
1 TTTTCGACATTTCGGC
52897170 TTTTCGACATTTCGGC
1 TTTTCGACATTTCGGC
52897186 TTTT
1 TTTT
52897190 GCTGATACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.08, C:0.22, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTTCGACATTTCGGC
Found at i:52901425 original size:28 final size:29
Alignment explanation
Indices: 52901394--52901497 Score: 124
Period size: 29 Copynumber: 3.7 Consensus size: 29
52901384 GGCCTACTAA
*
52901394 GCCC-AATCATATTCATATGGCCCATTAG
1 GCCCAAATCACATTCATATGGCCCATTAG
*
52901422 GCCCAAATCACCTGT-ATATGGCCCATTAG
1 GCCCAAATCACAT-TCATATGGCCCATTAG
* *
52901451 GCCCAAATCACATTTATATGGCCCGTTAG
1 GCCCAAATCACATTCATATGGCCCATTAG
* *
52901480 G-CCTAGTCACATTCATAT
1 GCCCAAATCACATTCATAT
52901498 TCATGCTCAC
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
28 19 0.29
29 46 0.70
30 1 0.02
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (29 bp):
GCCCAAATCACATTCATATGGCCCATTAG
Found at i:52901480 original size:58 final size:57
Alignment explanation
Indices: 52901374--52901482 Score: 146
Period size: 58 Copynumber: 1.9 Consensus size: 57
52901364 AATTTCACAT
* * *
52901374 ACCTGTATTTGGCCTACTAAGCCCAATCATATTCATATGGCCCATTAGGCCCAAATC
1 ACCTGTATATGGCCCACTAAGCCCAATCACATTCATATGGCCCATTAGGCCCAAATC
* * * *
52901431 ACCTGTATATGGCCCATTAGGCCCAAATCACATTTATATGGCCCGTTAGGCC
1 ACCTGTATATGGCCCACTAAGCCC-AATCACATTCATATGGCCCATTAGGCC
52901483 TAGTCACATT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 20 0.45
58 24 0.55
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.28
Consensus pattern (57 bp):
ACCTGTATATGGCCCACTAAGCCCAATCACATTCATATGGCCCATTAGGCCCAAATC
Found at i:52901754 original size:8 final size:8
Alignment explanation
Indices: 52901716--52901751 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
52901706 ACTTTCGGCT
52901716 TTTCAGCA
1 TTTCAGCA
52901724 TTTCAGCA
1 TTTCAGCA
*
52901732 TTTCAGCT
1 TTTCAGCA
*
52901740 TTTCGGCA
1 TTTCAGCA
52901748 TTTC
1 TTTC
52901752 GGCTTTTACC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.17, C:0.25, G:0.14, T:0.44
Consensus pattern (8 bp):
TTTCAGCA
Found at i:52901756 original size:16 final size:16
Alignment explanation
Indices: 52901708--52901758 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
52901698 GTAGCCAAAC
* *
52901708 TTTCGGCTTTTCAGCA
1 TTTCGGCATTTCAGCT
*
52901724 TTTCAGCATTTCAGCT
1 TTTCGGCATTTCAGCT
*
52901740 TTTCGGCATTTCGGCT
1 TTTCGGCATTTCAGCT
52901756 TTT
1 TTT
52901759 ACCGATACAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.47
Consensus pattern (16 bp):
TTTCGGCATTTCAGCT
Found at i:52909423 original size:46 final size:46
Alignment explanation
Indices: 52909370--52909545 Score: 187
Period size: 46 Copynumber: 3.8 Consensus size: 46
52909360 TATTTGGACA
*
52909370 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * * *
52909416 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
*
52909463 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * * *
52909509 CCCGAGCTCATTGAGTTGAGTCTGAATTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
52909546 GCAGGTTACA
Statistics
Matches: 107, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
43 4 0.04
45 3 0.03
46 63 0.59
47 29 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:52914553 original size:40 final size:39
Alignment explanation
Indices: 52914393--52914555 Score: 263
Period size: 39 Copynumber: 4.2 Consensus size: 39
52914383 TGTGTATGAA
*
52914393 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
52914432 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* * *
52914471 GGTGCGAGCTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* *
52914510 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAGTTGTGATATCCGGGCTAAG-CCCGAAGGCAAT
52914550 TGTGCG
1 TGTGCG
52914556 GGTTACCATA
Statistics
Matches: 114, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 97 0.85
40 17 0.15
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.24
Consensus pattern (39 bp):
TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:52914571 original size:40 final size:39
Alignment explanation
Indices: 52914393--52914586 Score: 253
Period size: 39 Copynumber: 4.9 Consensus size: 39
52914383 TGTGTATGAA
* *
52914393 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
*
52914432 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
* *
52914471 GGTGCGAGCTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
* * *
52914510 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGGCAAT
* ** * *
52914550 TGTGCGGGTTACCATAACCGGGCTATGTCCCGAAGGC
1 TGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGGC
52914587 GTTTGAACGA
Statistics
Matches: 138, Mismatches: 16, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
39 97 0.70
40 41 0.30
ACGTcount: A:0.23, C:0.22, G:0.32, T:0.23
Consensus pattern (39 bp):
TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:52922443 original size:38 final size:39
Alignment explanation
Indices: 52922322--52922483 Score: 254
Period size: 39 Copynumber: 4.2 Consensus size: 39
52922312 TGTGTATGAA
*
52922322 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
52922361 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* * *
52922400 GGTGCGAGCTATGATATCCGGGCTAAG-CCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* *
52922438 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAGTTGTGATATCCGGGCTAAG-CCCGAAGGCAAT
52922478 TGTGCG
1 TGTGCG
52922484 GGTTACCATA
Statistics
Matches: 112, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
38 34 0.30
39 62 0.55
40 16 0.14
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.24
Consensus pattern (39 bp):
TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:52922499 original size:78 final size:78
Alignment explanation
Indices: 52922339--52922514 Score: 246
Period size: 78 Copynumber: 2.2 Consensus size: 78
52922329 ATTGTGATAT
52922339 CCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAATGGTG
1 CCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAATGGTG
** *
52922404 CGAGCTATGATAT
66 CGAGCTACCATAA
* * *
52922417 CCGGGCTAAG-CCGAAGGCAATTGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTGTGATATCCGGGCTAAG-CCCGAAGGCAATGGT
* *
52922481 GCGGGTTACCATAA
65 GCGAGCTACCATAA
*
52922495 CCGGGCTATGTCCCGAAGGC
1 CCGGGCTAAG-CCCGAAGGC
52922515 GTTTGAACGA
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
77 37 0.43
78 41 0.48
80 8 0.09
ACGTcount: A:0.23, C:0.23, G:0.33, T:0.22
Consensus pattern (78 bp):
CCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAATGGTG
CGAGCTACCATAA
Found at i:52927324 original size:17 final size:18
Alignment explanation
Indices: 52927287--52927325 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
52927277 ATTTTATGTA
52927287 ATATAAATCACATAATAT
1 ATATAAATCACATAATAT
* *
52927305 ATATAAAT-ATATATTAT
1 ATATAAATCACATAATAT
52927322 ATAT
1 ATAT
52927326 TATAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (18 bp):
ATATAAATCACATAATAT
Found at i:52930857 original size:13 final size:13
Alignment explanation
Indices: 52930839--52930864 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52930829 AAAAAATATA
52930839 TATATTTAAAATT
1 TATATTTAAAATT
52930852 TATATTTAAAATT
1 TATATTTAAAATT
52930865 AGAGTTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATTTAAAATT
Found at i:52931476 original size:12 final size:12
Alignment explanation
Indices: 52931440--52931482 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
52931430 TCGTACAATA
*
52931440 AAAAATTAAAAT
1 AAAAATTAAACT
*
52931452 TAAAATTAAAAACT
1 AAAAATT--AAACT
52931466 AAAAATTAAACT
1 AAAAATTAAACT
52931478 AAAAA
1 AAAAA
52931483 AATTACCTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 16 0.62
14 10 0.38
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAAATTAAACT
Found at i:52931641 original size:30 final size:28
Alignment explanation
Indices: 52931595--52931650 Score: 85
Period size: 30 Copynumber: 1.9 Consensus size: 28
52931585 ATAATATAAG
*
52931595 AATTAAAAATTATTAAATTATTAATTTT
1 AATTAAAAATTATTAAATAATTAATTTT
52931623 AATTAAAAATAATATTAAATAATTAATT
1 AATTAAAAAT--TATTAAATAATTAATT
52931651 ATATAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 10 0.40
30 15 0.60
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
AATTAAAAATTATTAAATAATTAATTTT
Found at i:52936945 original size:53 final size:53
Alignment explanation
Indices: 52936767--52937021 Score: 218
Period size: 55 Copynumber: 4.8 Consensus size: 53
52936757 ATTAGGGTTT
* *
52936767 AAGGATACCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGGT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGC-ATTGGTAA-G-TTCATAAGGC
* * ** * * **
52936822 AAGAAAATAATGTAAGACCATGTCAAGACATGGTATTAATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT-C-ATAAGGC
* * *
52936877 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCATAAGGC
* *
52936930 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATGGTAAGTT--TCAA---
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCAT-AAGGC
* * * * *
52936979 AAGGATACCACGTAAGACTATGACAAGTCATGGCAATGGTAAG
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAG
52937022 GTACCCGTGT
Statistics
Matches: 164, Mismatches: 30, Indels: 18
0.77 0.14 0.08
Matches are distributed among these distances:
49 39 0.24
51 1 0.01
52 8 0.05
53 44 0.27
54 7 0.04
55 62 0.38
56 3 0.02
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.22
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCATAAGGC
Found at i:52937233 original size:16 final size:16
Alignment explanation
Indices: 52937212--52937242 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52937202 ATAAATTTGA
52937212 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
52937228 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
52937243 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:52939998 original size:42 final size:43
Alignment explanation
Indices: 52939951--52940068 Score: 132
Period size: 42 Copynumber: 2.8 Consensus size: 43
52939941 GAGCTACTGA
* * *
52939951 GATTTCGTATAAGACCATATCTGGGATATGGCATCGGTGTG-T
1 GATTTCGTATAAGACCATATCAGGGATATGGCATCGATATGAT
* * *
52939993 GATTTCGTATAAGACCATGTCAGGGACATGGCGTCGATATGAT
1 GATTTCGTATAAGACCATATCAGGGATATGGCATCGATATGAT
* * * *
52940036 -ATTCCATGTAAGACCATATCCGGGATATGGCAT
1 GATTTCGTATAAGACCATATCAGGGATATGGCAT
52940069 TCTTACAGTA
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
42 61 0.98
43 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (43 bp):
GATTTCGTATAAGACCATATCAGGGATATGGCATCGATATGAT
Found at i:52943358 original size:93 final size:93
Alignment explanation
Indices: 52943246--52943417 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
52943236 GCCCATAAGT
* *
52943246 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
52943311 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
52943339 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
52943404 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
52943418 CAAATATCCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:52943413 original size:46 final size:46
Alignment explanation
Indices: 52943238--52943413 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
52943228 TGTAACCCGC
* * *
52943238 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
52943284 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
52943334 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
52943377 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
52943414 TGCCCAAATA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 68 0.61
47 32 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:52945829 original size:57 final size:58
Alignment explanation
Indices: 52945729--52945848 Score: 154
Period size: 57 Copynumber: 2.1 Consensus size: 58
52945719 GAGATGGTGT
* * *
52945729 AAATGGAGAAATAGGAAACACTCGAAAATTATTATGGTTTTCTCC-AAAATAAAAATGA
1 AAATGGAGAAATAGGAAACACTCGAAAATGAATATAGTTTTCTCCAAAAAT-AAAATGA
* * * *
52945787 AAATGGAGAAATA-GAATCATTTGAAAATGAATGTAGTTTTCTCCAAAAATAAAATGA
1 AAATGGAGAAATAGGAAACACTCGAAAATGAATATAGTTTTCTCCAAAAATAAAATGA
52945844 AAATG
1 AAATG
52945849 AAAAATGAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
57 36 0.67
58 18 0.33
ACGTcount: A:0.49, C:0.08, G:0.16, T:0.27
Consensus pattern (58 bp):
AAATGGAGAAATAGGAAACACTCGAAAATGAATATAGTTTTCTCCAAAAATAAAATGA
Found at i:52945855 original size:13 final size:13
Alignment explanation
Indices: 52945837--52945862 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52945827 CTCCAAAAAT
52945837 AAAATGAAAATGA
1 AAAATGAAAATGA
52945850 AAAATGAAAATGA
1 AAAATGAAAATGA
52945863 CCTGAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (13 bp):
AAAATGAAAATGA
Found at i:52945869 original size:57 final size:57
Alignment explanation
Indices: 52945765--52945875 Score: 145
Period size: 57 Copynumber: 1.9 Consensus size: 57
52945755 AATTATTATG
* * **
52945765 GTTTTCTCCAAAATAAAAATGAAAATGGAGAAATAGAATCATTTGAAAATGAATGTA
1 GTTTTCTCCAAAATAAAAATGAAAATGGAAAAATAAAATCACCTGAAAATGAATGTA
*
52945822 GTTTTCTCCAAAA-ATAAAATGAAAAT-GAAAAATGAAAATGACCTGAAAATGAAT
1 GTTTTCTCCAAAATA-AAAATGAAAATGGAAAAAT-AAAATCACCTGAAAATGAAT
52945876 TTATCTTTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
56 7 0.15
57 40 0.85
ACGTcount: A:0.51, C:0.08, G:0.14, T:0.26
Consensus pattern (57 bp):
GTTTTCTCCAAAATAAAAATGAAAATGGAAAAATAAAATCACCTGAAAATGAATGTA
Done.