Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr2
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: 43198478
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2088848 characters in sequence are not A, C, G, or T
File 70 of 131
Found at i:23380108 original size:20 final size:20
Alignment explanation
Indices: 23380085--23380145 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
23380075 CACATTATTG
* *
23380085 GCAGCTTGTTTGCATTACTA
1 GCAGTTTGTTTGCAATACTA
* *
23380105 GCAGTTTATCTGCAATACTA
1 GCAGTTTGTTTGCAATACTA
*
23380125 GCAGTTTGTTTGCACTACTA
1 GCAGTTTGTTTGCAATACTA
23380145 G
1 G
23380146 TGGCTTGTCC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (20 bp):
GCAGTTTGTTTGCAATACTA
Found at i:23392155 original size:44 final size:44
Alignment explanation
Indices: 23392092--23392180 Score: 151
Period size: 44 Copynumber: 2.0 Consensus size: 44
23392082 ACAGCAGTAG
* *
23392092 GTTAACTTTGAAAAATCACCATAAATTGTGGAAATCGAATTAGA
1 GTTAAATTTGAAAAATCACCATAAATTGTAGAAATCGAATTAGA
*
23392136 GTTAAATTTGAAAAATCACCATAAATTGTAGAAATCTAATTAGA
1 GTTAAATTTGAAAAATCACCATAAATTGTAGAAATCGAATTAGA
23392180 G
1 G
23392181 GATGAAAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.30
Consensus pattern (44 bp):
GTTAAATTTGAAAAATCACCATAAATTGTAGAAATCGAATTAGA
Found at i:23396162 original size:24 final size:23
Alignment explanation
Indices: 23396104--23396151 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
23396094 ACGCTCCTCC
* *
23396104 TCTTCTCTATTTTTTTTCTCTTT
1 TCTTCTTTCTTTTTTTTCTCTTT
*
23396127 TCTTCTTTCTTTTGTTT-TCTTT
1 TCTTCTTTCTTTTTTTTCTCTTT
23396149 TCT
1 TCT
23396152 CCTTCTTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.75
Consensus pattern (23 bp):
TCTTCTTTCTTTTTTTTCTCTTT
Found at i:23403929 original size:27 final size:27
Alignment explanation
Indices: 23403869--23404016 Score: 154
Period size: 27 Copynumber: 5.5 Consensus size: 27
23403859 AGACCCCAAA
* ** *
23403869 ATAGGGTAAAATGA-TGAAATACATCT
1 ATAGGGTAAAATGACCGAAATACCCCC
* * *
23403895 ATAAGGTAAAATGATCGATATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
*
23403922 ATAGGGTAAACTGACCGAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
* * *
23403949 ATAAGGTAAAATAACCAAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
* **
23403976 ATAGGGTAAAATGACCAAAATACCTTC
1 ATAGGGTAAAATGACCGAAATACCCCC
*
23404003 ATGGGGTAAAATGA
1 ATAGGGTAAAATGA
23404017 TTATTATACC
Statistics
Matches: 102, Mismatches: 19, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
26 13 0.13
27 89 0.87
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.20
Consensus pattern (27 bp):
ATAGGGTAAAATGACCGAAATACCCCC
Found at i:23403953 original size:54 final size:54
Alignment explanation
Indices: 23403869--23404017 Score: 174
Period size: 54 Copynumber: 2.8 Consensus size: 54
23403859 AGACCCCAAA
* * * * *
23403869 ATAGGGTAAAATGA-TGAAATACATCTATAAGGTAAAATGATCGATATACCCCC
1 ATAGGGTAAAATGACCGAAATACCTCCATAAGGTAAAATGATCAAAATACCCCC
* * * *
23403922 ATAGGGTAAACTGACCGAAATACCCCCATAAGGTAAAATAACCAAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCTCCATAAGGTAAAATGATCAAAATACCCCC
* * **
23403976 ATAGGGTAAAATGACCAAAATACCTTCATGGGGTAAAATGAT
1 ATAGGGTAAAATGACCGAAATACCTCCATAAGGTAAAATGAT
23404018 TATTATACCC
Statistics
Matches: 78, Mismatches: 17, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
53 13 0.17
54 65 0.83
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.21
Consensus pattern (54 bp):
ATAGGGTAAAATGACCGAAATACCTCCATAAGGTAAAATGATCAAAATACCCCC
Found at i:23408389 original size:50 final size:50
Alignment explanation
Indices: 23408280--23408458 Score: 159
Period size: 50 Copynumber: 3.6 Consensus size: 50
23408270 ACATGCCAAA
* ** * * * *
23408280 GCCATGTCCCAGACATAGTCTTACATGGGATGTTTCCTGTAC--TGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGGTGCCCAT
* * * * **
23408329 GCCATATCCCAAATATGGTCTTACTTGGGAGTTCTCATATCGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCCAT
** *
23408379 GCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCC--CAT
23408431 --CATGTCCCAGACATGGTCTTACATGGGA
1 GCCATGTCCCAGACATGGTCTTACATGGGA
23408459 TCTCATTCTC
Statistics
Matches: 105, Mismatches: 21, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
48 1 0.01
49 30 0.29
50 71 0.68
52 3 0.03
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCCAT
Found at i:23415805 original size:27 final size:27
Alignment explanation
Indices: 23415770--23416055 Score: 301
Period size: 27 Copynumber: 10.6 Consensus size: 27
23415760 AACAAAATGA
*
23415770 CTTTGTGGCGAATCATGAAAGAAAAGC
1 CTTTATGGCGAATCATGAAAGAAAAGC
*
23415797 CTTTATGGCGAATCATGAAA-AAAATC
1 CTTTATGGCGAATCATGAAAGAAAAGC
* **
23415823 CTTTATGGCAAATCATGAAAGAAAAAT
1 CTTTATGGCGAATCATGAAAGAAAAGC
* *
23415850 CTTTCTGGAGAATCATGAAAGAAAAGC
1 CTTTATGGCGAATCATGAAAGAAAAGC
* * *
23415877 TTTTAT-GCTGAAT-TTGGAAAGAAAAAC
1 CTTTATGGC-GAATCAT-GAAAGAAAAGC
* *
23415904 CTTTGTGGCGAATCCTGAAAGAAAAGC
1 CTTTATGGCGAATCATGAAAGAAAAGC
* * *
23415931 ATTTGTGGCGAATCATAAAAGAAAAGC
1 CTTTATGGCGAATCATGAAAGAAAAGC
* * *
23415958 CTTTGTGGCGAATCATGAAATAAAAGT
1 CTTTATGGCGAATCATGAAAGAAAAGC
*
23415985 CTTTATGGCGAATAATGAAAGAAAAGC
1 CTTTATGGCGAATCATGAAAGAAAAGC
* * * *
23416012 CTTTGTGGTGAATTATGAAAGAAAGGTC
1 CTTTATGGCGAATCATGAAAGAAAAG-C
*
23416040 C-TTATGACGAATCATG
1 CTTTATGGCGAATCATG
23416056 GAGTAAGTTA
Statistics
Matches: 215, Mismatches: 38, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
26 26 0.12
27 184 0.86
28 5 0.02
ACGTcount: A:0.40, C:0.13, G:0.22, T:0.26
Consensus pattern (27 bp):
CTTTATGGCGAATCATGAAAGAAAAGC
Found at i:23424507 original size:20 final size:19
Alignment explanation
Indices: 23424478--23424515 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
23424468 AAGTAGTGAT
23424478 AATTTATTTTCTAAGAATA
1 AATTTATTTTCTAAGAATA
*
23424497 AATTATATTTTCTAGGAAT
1 AATT-TATTTTCTAAGAAT
23424516 TACAATTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.47
Consensus pattern (19 bp):
AATTTATTTTCTAAGAATA
Found at i:23440393 original size:101 final size:101
Alignment explanation
Indices: 23440263--23440447 Score: 266
Period size: 101 Copynumber: 1.8 Consensus size: 101
23440253 AAAGTGATGG
* * **
23440263 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTAACGGAAT-G-ATAGGTCGTATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGACTACTACGTGTAACAG-ATGGAATA-GTCACATGTGTAGT
23440326 ACTATGTGCAGGCTATTATGCGTACTAGATAGTTTCGA
64 ACTATGTGCAGGCTATTATGCGTACTAGATAGTTTCGA
* *
23440364 TCACGTGTGTAGTACTATGTGTAGACTACTACGTGTATCAGATGGTAATAGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGACTACTACGTGTAACAGATGG-AATAGTCACATGTGTAGTA
*
23440429 TTATGTGCAGGCTATTATG
65 CTATGTGCAGGCTATTATG
23440448 TGAACCGAAC
Statistics
Matches: 74, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
100 2 0.03
101 38 0.51
102 31 0.42
103 3 0.04
ACGTcount: A:0.25, C:0.14, G:0.26, T:0.34
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGCAGACTACTACGTGTAACAGATGGAATAGTCACATGTGTAGTAC
TATGTGCAGGCTATTATGCGTACTAGATAGTTTCGA
Found at i:23447005 original size:104 final size:104
Alignment explanation
Indices: 23446825--23447035 Score: 413
Period size: 104 Copynumber: 2.0 Consensus size: 104
23446815 GTGAGAAAGG
23446825 GTCAGAATGGATTTTCAAGTCCCCTGTTCTCACTTTAGGAAATCATTAAAAATTTTACAGAAAGA
1 GTCAGAATGGATTTTCAAGTCCCCTGTTCTCACTTTAGGAAATCATTAAAAATTTTACAGAAAGA
23446890 ATTATGAGTCATAATTTATATGTCTAGATTCCTTAGTGA
66 ATTATGAGTCATAATTTATATGTCTAGATTCCTTAGTGA
*
23446929 GTCAGAATGGCTTTTCAAGTCCCCTGTTCTCACTTTAGGAAATCATTAAAAATTTTACAGAAAGA
1 GTCAGAATGGATTTTCAAGTCCCCTGTTCTCACTTTAGGAAATCATTAAAAATTTTACAGAAAGA
23446994 ATTATGAGTCATAATTTATATGTCTAGATTCCTTAGTGA
66 ATTATGAGTCATAATTTATATGTCTAGATTCCTTAGTGA
23447033 GTC
1 GTC
23447036 TATTTTCAAT
Statistics
Matches: 106, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
104 106 1.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (104 bp):
GTCAGAATGGATTTTCAAGTCCCCTGTTCTCACTTTAGGAAATCATTAAAAATTTTACAGAAAGA
ATTATGAGTCATAATTTATATGTCTAGATTCCTTAGTGA
Found at i:23460801 original size:23 final size:23
Alignment explanation
Indices: 23460775--23460873 Score: 126
Period size: 23 Copynumber: 4.3 Consensus size: 23
23460765 ATAAGTGTCA
23460775 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
23460798 CACTGATATGTAGCTGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
23460821 CACTGAAATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * * *
23460844 CCCTAAAATGTAGCTGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
23460867 CACTGAT
1 CACTGAT
23460874 CAATAACACT
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 65 1.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.24
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:23460842 original size:46 final size:46
Alignment explanation
Indices: 23460775--23460872 Score: 142
Period size: 46 Copynumber: 2.1 Consensus size: 46
23460765 ATAAGTGTCA
* * * *
23460775 CACTGATATGTAGCCGAAGCTACCACTGATATGTAGCTGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTAAAATGTAGCTGAAGCTAC
* *
23460821 CACTGAAATGTAGCCGTAGCTACCCCTAAAATGTAGCTGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTAAAATGTAGCTGAAGCTAC
23460867 CACTGA
1 CACTGA
23460873 TCAATAACAC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (46 bp):
CACTGAAATGTAGCCGAAGCTACCACTAAAATGTAGCTGAAGCTAC
Found at i:23466434 original size:50 final size:51
Alignment explanation
Indices: 23466324--23466520 Score: 191
Period size: 50 Copynumber: 3.8 Consensus size: 51
23466314 TTAAGGGAAT
* * **
23466324 GAGGCCCCATGTAAGACCATGTTTGGGACATGGCATTGGCATTATTGAGGTTATGA
1 GAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGC---ACCGAGG--ATGA
* * *
23466380 GAGGTCCCATGTAAGACAATGTTTGGGACATGGCGTTGGCACCGA-GATGA
1 GAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGGATGA
* * * * *
23466430 GAGGTCCCCTGTAAGACCATGTCTAGGACATGGAATGGGCACCGATG-TGA
1 GAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGGATGA
** * *
23466480 GAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 GAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
23466521 GTACAGGAAA
Statistics
Matches: 120, Mismatches: 20, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
50 78 0.65
51 1 0.01
52 1 0.01
53 3 0.03
56 37 0.31
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.24
Consensus pattern (51 bp):
GAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGGATGA
Found at i:23466796 original size:20 final size:20
Alignment explanation
Indices: 23466771--23466809 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
23466761 TGAGTTATTT
23466771 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
23466791 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
23466810 GAAGAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:23476204 original size:19 final size:19
Alignment explanation
Indices: 23476169--23476223 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 19
23476159 CTTTACTTTA
* *
23476169 TATT-ATAATAATATAATT
1 TATTAATAATCATTTAATT
23476187 TATTAATAATCATTTAATT
1 TATTAATAATCATTTAATT
* * *
23476206 AATAAAT-ATCTTTTAATT
1 TATTAATAATCATTTAATT
23476224 ATAACACAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 14 0.45
19 17 0.55
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTAATAATCATTTAATT
Found at i:23476314 original size:20 final size:21
Alignment explanation
Indices: 23476289--23476330 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
23476279 ATTTGGCACC
* *
23476289 ATTTAATTTATTTAT-TTTAT
1 ATTTAATTAATTAATATTTAT
23476309 ATTTAATTAATTAATATTTAT
1 ATTTAATTAATTAATATTTAT
23476330 A
1 A
23476331 AATATCTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTAATTAATTAATATTTAT
Found at i:23476824 original size:20 final size:20
Alignment explanation
Indices: 23476799--23476837 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
23476789 TCAGTTATTT
23476799 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
23476819 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
23476838 GAAGAAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:23482963 original size:20 final size:21
Alignment explanation
Indices: 23482916--23482955 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
23482906 TTTATTATAA
23482916 TATATTTTTATACCATTTCTG
1 TATATTTTTATACCATTTCTG
23482937 TATATTTTTATA-CATTTCT
1 TATATTTTTATACCATTTCT
23482956 TTGAATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.25, C:0.12, G:0.03, T:0.60
Consensus pattern (21 bp):
TATATTTTTATACCATTTCTG
Found at i:23496693 original size:22 final size:22
Alignment explanation
Indices: 23496665--23496710 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
23496655 TATCACACTA
23496665 TCCATTGACTCTTTTGGTACTT
1 TCCATTGACTCTTTTGGTACTT
23496687 TCCATTGACTCTTTTGGTACTT
1 TCCATTGACTCTTTTGGTACTT
23496709 TC
1 TC
23496711 GGTTGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.13, C:0.24, G:0.13, T:0.50
Consensus pattern (22 bp):
TCCATTGACTCTTTTGGTACTT
Found at i:23498489 original size:135 final size:135
Alignment explanation
Indices: 23498247--23498557 Score: 358
Period size: 135 Copynumber: 2.3 Consensus size: 135
23498237 TTGGCTTGTA
* ** * * *
23498247 AAATGAATAAGACCATAGTTGAAAGACAATATGGCA-CTATACCGGAAATGAATAAGACAATATT
1 AAATGAATAAGACCATAGTTGAAAGACACTATGGCATC-ATACCAAAAATAAAAAAGACAATAGT
* * * * *
23498311 TGAAAGACACTATGGCATTATACCGAAAATGAATAAGACCATAGTTGAAGAACACTATGGCAACA
65 TAAAAGACACTATGGCATCATACCGAAAATAAATAAAACCATAGTTGAAGAACAATATGGCAACA
**
23498376 TGACGG
130 TGACAC
* ** *
23498382 AAATGAATAAGACCACAGTTGAAAGACACTATGGCATCATGTCAAAAATAAAAAAGACCATAGTT
1 AAATGAATAAGACCATAGTTGAAAGACACTATGGCATCATACCAAAAATAAAAAAGACAATAGTT
* * *
23498447 AAAAGACACTATGGCATCATGTCAC-AAAA-AAATAAAACCATAGTTGAAGGACAATATGGCATC
66 AAAAGACACTATGGCATCAT-AC-CGAAAATAAATAAAACCATAGTTGAAGAACAATATGGCAAC
*
23498510 ATGTCAC
129 ATGACAC
** *
23498517 AAAAAAATAAAACCATAGTTGAAAGACACTATGGCATCATA
1 AAATGAATAAGACCATAGTTGAAAGACACTATGGCATCATA
23498558 TCGAAAGTGT
Statistics
Matches: 147, Mismatches: 26, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
135 140 0.95
136 6 0.04
137 1 0.01
ACGTcount: A:0.47, C:0.16, G:0.17, T:0.20
Consensus pattern (135 bp):
AAATGAATAAGACCATAGTTGAAAGACACTATGGCATCATACCAAAAATAAAAAAGACAATAGTT
AAAAGACACTATGGCATCATACCGAAAATAAATAAAACCATAGTTGAAGAACAATATGGCAACAT
GACAC
Found at i:23498553 original size:45 final size:45
Alignment explanation
Indices: 23498252--23498556 Score: 305
Period size: 45 Copynumber: 6.8 Consensus size: 45
23498242 TTGTAAAATG
* ** ** **
23498252 AATAAGACCATAGTTGAAAGACAATATGGCA-CTATACCGGAAATG
1 AATAAGACCATAGTTGAAAGACACTATGGCATC-ATGTCACAAAAA
* * * * *
23498297 AATAAGACAATATTTGAAAGACACTATGGCATTAT-AC-CGAAAATG
1 AATAAGACCATAGTTGAAAGACACTATGGCATCATGTCAC-AAAA-A
* * ** **
23498342 AATAAGACCATAGTTG-AAGAACACTATGGCAACATGACGGAAATG
1 AATAAGACCATAGTTGAAAG-ACACTATGGCATCATGTCACAAAAA
*
23498387 AATAAGACCACAGTTGAAAGACACTATGGCATCATGTCA-AAAATA
1 AATAAGACCATAGTTGAAAGACACTATGGCATCATGTCACAAAA-A
* *
23498432 AAAAAGACCATAGTTAAAAGACACTATGGCATCATGTCACAAAAA
1 AATAAGACCATAGTTGAAAGACACTATGGCATCATGTCACAAAAA
* * *
23498477 AATAAAACCATAGTTGAAGGACAATATGGCATCATGTCACAAAAA
1 AATAAGACCATAGTTGAAAGACACTATGGCATCATGTCACAAAAA
*
23498522 AATAAAACCATAGTTGAAAGACACTATGGCATCAT
1 AATAAGACCATAGTTGAAAGACACTATGGCATCAT
23498557 ATCGAAAGTG
Statistics
Matches: 222, Mismatches: 29, Indels: 18
0.83 0.11 0.07
Matches are distributed among these distances:
44 10 0.05
45 200 0.90
46 12 0.05
ACGTcount: A:0.47, C:0.16, G:0.17, T:0.20
Consensus pattern (45 bp):
AATAAGACCATAGTTGAAAGACACTATGGCATCATGTCACAAAAA
Found at i:23499028 original size:73 final size:74
Alignment explanation
Indices: 23498940--23499081 Score: 214
Period size: 73 Copynumber: 1.9 Consensus size: 74
23498930 GTGTTTATAC
* * * *
23498940 GAAATGTTTATATGAATAGTTGTTGAATGAATGGTATATCTAATATGTTTACTTGCATATGTTTT
1 GAAATGTTTATATGAATAGATGTTGAATAAAGGGAATATCTAATATGTTTACTTGCATATGTTTT
23499005 ATAACATGT
66 ATAACATGT
* * *
23499014 GAAATG-TTATATGAATAGATGTTGAATAAAGGGAATATCTAATGTGTTTACTTGTATTTGTTTT
1 GAAATGTTTATATGAATAGATGTTGAATAAAGGGAATATCTAATATGTTTACTTGCATATGTTTT
23499078 ATAA
66 ATAA
23499082 TATGAAAAGG
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
73 55 0.90
74 6 0.10
ACGTcount: A:0.34, C:0.04, G:0.18, T:0.44
Consensus pattern (74 bp):
GAAATGTTTATATGAATAGATGTTGAATAAAGGGAATATCTAATATGTTTACTTGCATATGTTTT
ATAACATGT
Found at i:23499098 original size:73 final size:73
Alignment explanation
Indices: 23498948--23499099 Score: 189
Period size: 73 Copynumber: 2.1 Consensus size: 73
23498938 ACGAAATGTT
* * * *
23498948 TATATGAATAGTTGTTGAATGAATGGTATATCTAATATGTTTACTTGCATATGTTTTATAACATG
1 TATATGAATAGATGTTGAATAAAGGGAATATCTAATATGTTTACTTGCATATGTTTTATAACATG
* * *
23499013 TGAAATGT
66 TAAAAGGA
* * * *
23499021 TATATGAATAGATGTTGAATAAAGGGAATATCTAATGTGTTTACTTGTATTTGTTTTATAATATG
1 TATATGAATAGATGTTGAATAAAGGGAATATCTAATATGTTTACTTGCATATGTTTTATAACATG
23499086 -AAAAGGGA
66 TAAAA-GGA
23499094 TATATG
1 TATATG
23499100 TAAACTCACT
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
72 3 0.04
73 64 0.96
ACGTcount: A:0.35, C:0.04, G:0.19, T:0.42
Consensus pattern (73 bp):
TATATGAATAGATGTTGAATAAAGGGAATATCTAATATGTTTACTTGCATATGTTTTATAACATG
TAAAAGGA
Found at i:23505596 original size:25 final size:25
Alignment explanation
Indices: 23505568--23505634 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
23505558 AAGCTCTTTC
*
23505568 TAGCTATATAACGGGAAGCTCATAA
1 TAGCCATATAACGGGAAGCTCATAA
* *
23505593 TAGCCATGTAATGGGAAGCTCATAA
1 TAGCCATATAACGGGAAGCTCATAA
* *
23505618 GAGCCATA-ATCGGGAAG
1 TAGCCATATAACGGGAAG
23505635 TCCAAGCGAG
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
24 7 0.20
25 28 0.80
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.21
Consensus pattern (25 bp):
TAGCCATATAACGGGAAGCTCATAA
Found at i:23512111 original size:22 final size:22
Alignment explanation
Indices: 23512073--23512128 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 22
23512063 ATTTTTTGTT
*
23512073 TTTATGTTTAT-GTTTATGCTTA
1 TTTATGTTTTTAGTTTAT-CTTA
*
23512095 TTTATGTTTTTAG-TTATTTTA
1 TTTATGTTTTTAGTTTATCTTA
* *
23512116 TTTTTATTTTTAG
1 TTTATGTTTTTAG
23512129 ACTTCTTTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 14 0.48
22 14 0.48
23 1 0.03
ACGTcount: A:0.18, C:0.02, G:0.11, T:0.70
Consensus pattern (22 bp):
TTTATGTTTTTAGTTTATCTTA
Found at i:23517839 original size:5 final size:5
Alignment explanation
Indices: 23517829--23517901 Score: 87
Period size: 5 Copynumber: 14.4 Consensus size: 5
23517819 GAACAAATAT
* *
23517829 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG ATTTG AATTCC
1 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG -ATTCG
23517880 ATCTC- ACTT-G ATTCG ATTCG AT
1 AT-TCG A-TTCG ATTCG ATTCG AT
23517902 AAAACTTCAA
Statistics
Matches: 60, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
4 2 0.03
5 52 0.87
6 6 0.10
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (5 bp):
ATTCG
Found at i:23524897 original size:40 final size:40
Alignment explanation
Indices: 23524860--23524994 Score: 189
Period size: 40 Copynumber: 3.4 Consensus size: 40
23524850 TCCTTTCAAG
* *
23524860 AGATTCAGTTGGTATGGCTTGAGAGCGCATACGTTTCAGT
1 AGATTCAGTAGGTATGGCTTGAAAGCGCATACGTTTCAGT
* * *
23524900 AGATACAGTAGGTATGGCTTGAAAGTGCATATGTTTCAGT
1 AGATTCAGTAGGTATGGCTTGAAAGCGCATACGTTTCAGT
* * *
23524940 AGATTCAGTAGGTATTGCTCGAAAGCGCATACATTTCAGT
1 AGATTCAGTAGGTATGGCTTGAAAGCGCATACGTTTCAGT
*
23524980 AGATTCAGTAAGTAT
1 AGATTCAGTAGGTAT
23524995 TGCTCGTCTG
Statistics
Matches: 83, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 83 1.00
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (40 bp):
AGATTCAGTAGGTATGGCTTGAAAGCGCATACGTTTCAGT
Found at i:23527590 original size:20 final size:21
Alignment explanation
Indices: 23527552--23527591 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
23527542 TTTCTTAATT
*
23527552 TTTTAAATAATTTTTATAAGA
1 TTTTAAATAATTTTAATAAGA
*
23527573 TTTTAAA-AGTTTTAATAAG
1 TTTTAAATAATTTTAATAAG
23527592 TTAAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (21 bp):
TTTTAAATAATTTTAATAAGA
Found at i:23529524 original size:9 final size:9
Alignment explanation
Indices: 23529502--23529578 Score: 58
Period size: 9 Copynumber: 9.0 Consensus size: 9
23529492 TAAAAATGGT
*
23529502 TAAAAATCA
1 TAAAAATTA
23529511 TAAAAATTA
1 TAAAAATTA
*
23529520 -GAAAA--A
1 TAAAAATTA
*
23529526 -AAAATTTA
1 TAAAAATTA
23529534 TAAAAAATTA
1 T-AAAAATTA
23529544 -AAAAATTA
1 TAAAAATTA
23529552 -AAACAATTA
1 TAAA-AATTA
*
23529561 TAAATATTA
1 TAAAAATTA
23529570 TAAAAATTA
1 TAAAAATTA
23529579 AAATATCTAA
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
6 4 0.07
8 16 0.29
9 25 0.45
10 10 0.18
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.29
Consensus pattern (9 bp):
TAAAAATTA
Found at i:23529554 original size:7 final size:8
Alignment explanation
Indices: 23529534--23529581 Score: 60
Period size: 9 Copynumber: 5.6 Consensus size: 8
23529524 AAAAAATTTA
23529534 TAAAAAAT
1 TAAAAAAT
23529542 TAAAAAAT
1 TAAAAAAT
23529550 TAAAACAAT
1 TAAAA-AAT
*
23529559 TATAAATAT
1 TA-AAAAAT
23529568 TATAAAAAT
1 TA-AAAAAT
23529577 TAAAA
1 TAAAA
23529582 TATCTAATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
8 16 0.44
9 17 0.47
10 3 0.08
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (8 bp):
TAAAAAAT
Found at i:23534431 original size:17 final size:17
Alignment explanation
Indices: 23534411--23534518 Score: 81
Period size: 17 Copynumber: 6.4 Consensus size: 17
23534401 AAATATCTTC
*
23534411 TCATATAAAATAACAGT
1 TCATACAAAATAACAGT
* * **
23534428 TCATACCAAATGACAAC
1 TCATACAAAATAACAGT
* *
23534445 TCATGCAAAATAATAGT
1 TCATACAAAATAACAGT
** *
23534462 TCATATGAAATATCAGT
1 TCATACAAAATAACAGT
** * *
23534479 TCATACCGAATAATAAT
1 TCATACAAAATAACAGT
*
23534496 TCATGCAAAATAACAGT
1 TCATACAAAATAACAGT
23534513 TCATAC
1 TCATAC
23534519 TTCATCATAA
Statistics
Matches: 63, Mismatches: 28, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
17 63 1.00
ACGTcount: A:0.46, C:0.18, G:0.08, T:0.28
Consensus pattern (17 bp):
TCATACAAAATAACAGT
Found at i:23534466 original size:51 final size:51
Alignment explanation
Indices: 23534411--23534517 Score: 151
Period size: 51 Copynumber: 2.1 Consensus size: 51
23534401 AAATATCTTC
* *
23534411 TCATATAAAATAACAGTTCATACCAAATGACAACTCATGCAAAATAATAGT
1 TCATATAAAATAACAGTTCATACCAAATAACAACTCATGCAAAATAACAGT
* * * * *
23534462 TCATATGAAATATCAGTTCATACCGAATAATAATTCATGCAAAATAACAGT
1 TCATATAAAATAACAGTTCATACCAAATAACAACTCATGCAAAATAACAGT
23534513 TCATA
1 TCATA
23534518 CTTCATCATA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.47, C:0.17, G:0.08, T:0.28
Consensus pattern (51 bp):
TCATATAAAATAACAGTTCATACCAAATAACAACTCATGCAAAATAACAGT
Found at i:23544900 original size:21 final size:19
Alignment explanation
Indices: 23544864--23544902 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
23544854 TTATTTGAAC
*
23544864 GAATAATTAAATTCAAGTA
1 GAATAATTAAAGTCAAGTA
23544883 GAATATATCTAAAGTCAAGT
1 GAATA-AT-TAAAGTCAAGT
23544903 GATTTTAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.49, C:0.08, G:0.13, T:0.31
Consensus pattern (19 bp):
GAATAATTAAAGTCAAGTA
Found at i:23546283 original size:45 final size:45
Alignment explanation
Indices: 23546216--23546512 Score: 308
Period size: 45 Copynumber: 6.7 Consensus size: 45
23546206 AGGTATAAGG
* *
23546216 TATATATAATAATTGTCGGTTTCACCAACCAGTGCTAGGCACACA
1 TATATATAATATTTGTCGGTTTCACCGACCAGTGCTAGGCACACA
* * *
23546261 TATATATAATATTTGTCAGTTTCATCGACCAGTGCTGGGCACACA
1 TATATATAATATTTGTCGGTTTCACCGACCAGTGCTAGGCACACA
* * * *
23546306 TATATATAATA----T---TTTCACCGACTAGTGTTAGACACAAA
1 TATATATAATATTTGTCGGTTTCACCGACCAGTGCTAGGCACACA
* **
23546344 TATA-ATAATAATTGTCGGTTTCACCGACCAGTGCTAGATACACA
1 TATATATAATATTTGTCGGTTTCACCGACCAGTGCTAGGCACACA
* * * * *
23546388 TATATATAATATTTGTTGGTTTCACTGAGCAGTGCTGGGCACGCA
1 TATATATAATATTTGTCGGTTTCACCGACCAGTGCTAGGCACACA
* *
23546433 TATATATAATATTTGCCTGTTTCACC-AGCCAGTGC-AGGGCACATACA
1 TATATATAATATTTGTCGGTTTCACCGA-CCAGTGCTA-GGCAC--ACA
*
23546480 TATATATAATATTTTTCGGTTTCACCGACCAGT
1 TATATATAATATTTGTCGGTTTCACCGACCAGT
23546513 TTTAGGGCGT
Statistics
Matches: 206, Mismatches: 33, Indels: 24
0.78 0.13 0.09
Matches are distributed among these distances:
37 6 0.03
38 24 0.12
41 2 0.01
44 27 0.13
45 116 0.56
47 30 0.15
48 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (45 bp):
TATATATAATATTTGTCGGTTTCACCGACCAGTGCTAGGCACACA
Found at i:23546322 original size:38 final size:38
Alignment explanation
Indices: 23546280--23546401 Score: 118
Period size: 38 Copynumber: 3.1 Consensus size: 38
23546270 TATTTGTCAG
* * *
23546280 TTTCATCGACCAGTGCTGGGCACACATATATATAATAT
1 TTTCACCGACCAGTGCTAGACACACATATATATAATAT
* * * *
23546318 TTTCACCGACTAGTGTTAGACACAAATATAATAATAATTGT
1 TTTCACCGACCAGTGCTAGACACACATAT-AT-ATAA-TAT
*
23546359 CGGTTTCACCGACCAGTGCTAGATACACATATATATAATAT
1 ---TTTCACCGACCAGTGCTAGACACACATATATATAATAT
23546400 TT
1 TT
23546402 GTTGGTTTCA
Statistics
Matches: 66, Mismatches: 12, Indels: 12
0.73 0.13 0.13
Matches are distributed among these distances:
38 25 0.38
39 2 0.03
40 4 0.06
41 4 0.06
42 4 0.06
43 2 0.03
44 25 0.38
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (38 bp):
TTTCACCGACCAGTGCTAGACACACATATATATAATAT
Found at i:23546365 original size:82 final size:83
Alignment explanation
Indices: 23546235--23546401 Score: 228
Period size: 82 Copynumber: 2.0 Consensus size: 83
23546225 TAATTGTCGG
* * * * * *
23546235 TTTCACCAACCAGTGCTAGGCACACATATATATAATATTTGTCAGTTTCATCGACCAGTGCTGGG
1 TTTCACCAACCAGTGCTAGACACAAATATATATAATAATTGTCAGTTTCACCGACCAGTGCTAGA
23546300 CACACATATATATAATAT
66 CACACATATATATAATAT
* * * *
23546318 TTTCACCGACTAGTGTTAGACACAAATATA-ATAATAATTGTCGGTTTCACCGACCAGTGCTAGA
1 TTTCACCAACCAGTGCTAGACACAAATATATATAATAATTGTCAGTTTCACCGACCAGTGCTAGA
*
23546382 TACACATATATATAATAT
66 CACACATATATATAATAT
23546400 TT
1 TT
23546402 GTTGGTTTCA
Statistics
Matches: 73, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
82 48 0.66
83 25 0.34
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (83 bp):
TTTCACCAACCAGTGCTAGACACAAATATATATAATAATTGTCAGTTTCACCGACCAGTGCTAGA
CACACATATATATAATAT
Found at i:23554936 original size:19 final size:18
Alignment explanation
Indices: 23554888--23554936 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
23554878 ATTTTCACTA
* *
23554888 TTTTTTTCTCTCTTTTTC
1 TTTTTTTCACTCGTTTTC
* *
23554906 TTTTTGTGACTCGTTTTC
1 TTTTTTTCACTCGTTTTC
23554924 TTTTTTCTCACTC
1 TTTTTT-TCACTC
23554937 TTTCTTTCCT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.04, C:0.22, G:0.06, T:0.67
Consensus pattern (18 bp):
TTTTTTTCACTCGTTTTC
Found at i:23554986 original size:18 final size:18
Alignment explanation
Indices: 23554965--23555001 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
23554955 TTCTGAACTC
*
23554965 TTTTT-TTTTCTTTTTCA
1 TTTTTCTTTTCTTGTTCA
23554982 TTTTTCTTTTCTTGTTCA
1 TTTTTCTTTTCTTGTTCA
23555000 TT
1 TT
23555002 CGTTTTCGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.05, C:0.14, G:0.03, T:0.78
Consensus pattern (18 bp):
TTTTTCTTTTCTTGTTCA
Found at i:23558394 original size:51 final size:51
Alignment explanation
Indices: 23558311--23558415 Score: 147
Period size: 51 Copynumber: 2.1 Consensus size: 51
23558301 ATCTGACTTA
* * ** *
23558311 AAACTTGCATTGATGTTGTCTGAATTAAGACACACTTAATGAACATAAATC
1 AAACATGCATTGATGCTGTCCAAATTAAGACACACTTAATAAACATAAATC
* *
23558362 AAACATGCATTGATGCTGTCCAAATTAGGACACACTTAATAAACATGAATC
1 AAACATGCATTGATGCTGTCCAAATTAAGACACACTTAATAAACATAAATC
23558413 AAA
1 AAA
23558416 GTAAATACCA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (51 bp):
AAACATGCATTGATGCTGTCCAAATTAAGACACACTTAATAAACATAAATC
Found at i:23563118 original size:19 final size:18
Alignment explanation
Indices: 23563094--23563140 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
23563084 AAAGATGATG
23563094 GTTTTATTTTATTTGATTA
1 GTTTTATTTTATTT-ATTA
*
23563113 GTTTTATCATTATTTATTA
1 GTTTTAT-TTTATTTATTA
23563132 -TTTTATTTT
1 GTTTTATTTT
23563141 TATAACCTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 2 0.08
18 6 0.24
19 11 0.44
20 6 0.24
ACGTcount: A:0.21, C:0.02, G:0.06, T:0.70
Consensus pattern (18 bp):
GTTTTATTTTATTTATTA
Found at i:23563621 original size:14 final size:14
Alignment explanation
Indices: 23563602--23563631 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
23563592 TGTTTGGTTG
*
23563602 AATTTTTTAAAAAT
1 AATTTTTGAAAAAT
23563616 AATTTTTGAAAAAT
1 AATTTTTGAAAAAT
23563630 AA
1 AA
23563632 AAATGAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (14 bp):
AATTTTTGAAAAAT
Found at i:23564253 original size:21 final size:22
Alignment explanation
Indices: 23564223--23564292 Score: 88
Period size: 26 Copynumber: 3.0 Consensus size: 22
23564213 TTTTTCATTT
23564223 TTTTTGAAAATGAAAATGAAAA
1 TTTTTGAAAATGAAAATGAAAA
23564245 TTTTT-AAAATGAAAATGAAAATTA
1 TTTTTGAAAATGAAAATG-AAA--A
23564269 TTTTTTGAAAATGAAAATGGAAAA
1 -TTTTTGAAAATGAAAAT-GAAAA
23564293 ATATTACTAG
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
21 12 0.29
22 8 0.19
24 2 0.05
25 5 0.12
26 14 0.33
27 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.34
Consensus pattern (22 bp):
TTTTTGAAAATGAAAATGAAAA
Found at i:23564259 original size:27 final size:26
Alignment explanation
Indices: 23564227--23564292 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 26
23564217 TCATTTTTTT
23564227 TGAAAATGAAAATGAAAATTTTT-AAAA
1 TGAAAATGAAAAT--AAATTTTTGAAAA
* *
23564254 TGAAAATGAAAATTATTTTTTGAAAA
1 TGAAAATGAAAATAAATTTTTGAAAA
23564280 TGAAAATGGAAAA
1 TGAAAAT-GAAAA
23564293 ATATTACTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 6 0.17
26 11 0.31
27 18 0.51
ACGTcount: A:0.56, C:0.00, G:0.14, T:0.30
Consensus pattern (26 bp):
TGAAAATGAAAATAAATTTTTGAAAA
Found at i:23564307 original size:27 final size:26
Alignment explanation
Indices: 23564228--23564307 Score: 62
Period size: 27 Copynumber: 3.2 Consensus size: 26
23564218 CATTTTTTTT
23564228 GAAAATGAAAATG-AAAAT-TT--T-
1 GAAAATGAAAATGAAAAATATTACTA
* * ** *
23564249 TAAAATGAAAATGAAAATTATTTTTT
1 GAAAATGAAAATGAAAAATATTACTA
23564275 GAAAATGAAAATGGAAAAATATTACTA
1 GAAAATGAAAAT-GAAAAATATTACTA
*
23564302 GCAAAT
1 GAAAAT
23564308 ATTTTATAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
21 12 0.27
22 4 0.09
23 2 0.04
25 1 0.02
26 11 0.24
27 15 0.33
ACGTcount: A:0.55, C:0.03, G:0.12, T:0.30
Consensus pattern (26 bp):
GAAAATGAAAATGAAAAATATTACTA
Found at i:23564588 original size:14 final size:14
Alignment explanation
Indices: 23564565--23564608 Score: 61
Period size: 16 Copynumber: 3.0 Consensus size: 14
23564555 TTTACATAAA
*
23564565 ATTTTCATAAATAT
1 ATTTTTATAAATAT
23564579 ATTTTTATAAAAATAT
1 ATTTTTAT--AAATAT
23564595 ATTTTTATAAATAT
1 ATTTTTATAAATAT
23564609 TTGTACTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 13 0.48
16 14 0.52
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTTTTATAAATAT
Found at i:23564594 original size:16 final size:16
Alignment explanation
Indices: 23564573--23564605 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
23564563 AAATTTTCAT
23564573 AAATATATTTTTATAA
1 AAATATATTTTTATAA
23564589 AAATATATTTTTATAA
1 AAATATATTTTTATAA
23564605 A
1 A
23564606 TATTTGTACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AAATATATTTTTATAA
Found at i:23580157 original size:19 final size:19
Alignment explanation
Indices: 23580130--23580178 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
23580120 ATCATATGGG
*
23580130 TATCAATACTTTTTGGAAA
1 TATCGATACTTTTTGGAAA
23580149 TATCGATACTTTTTGGAAA
1 TATCGATACTTTTTGGAAA
23580168 TATCGATACTT
1 TATCGATACTT
23580179 CTTGTATAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (19 bp):
TATCGATACTTTTTGGAAA
Found at i:23591427 original size:144 final size:145
Alignment explanation
Indices: 23591155--23591445 Score: 512
Period size: 144 Copynumber: 2.0 Consensus size: 145
23591145 TTAATTCATT
*
23591155 TAATCACCGAATTACTAAAATGCCCTTAACTTAAAAATATTCTATTTCACCTATTTCATGTCCAT
1 TAATCACCGAATTACTAAAATGCCCTTAACTTAAAAATATTCTATTTCACCTATTTCATATCCAT
23591220 TTTTGTCCAAAAAATTAAAAAATGGTCTAATTACCTTTTAAGCACCTCCAATTTAAAATTTCATA
66 TTTTGTCCAAAAAATTAAAAAATGGTCTAATTACCTTTTAAGCACCTCCAATTTAAAATTTCATA
*
23591285 GCAGTTAGACACCTC
131 GCAATTAGACACCTC
23591300 TAATCACCGAA-TACTAAAATGCCCTTAACTTAAAAATATTCTATTTCACCTATTTCATATCCAT
1 TAATCACCGAATTACTAAAATGCCCTTAACTTAAAAATATTCTATTTCACCTATTTCATATCCAT
** * * *
23591364 TTTTGTCCAAAAAATTAACCAATGGTCTAATTACCTTTTAAGGACCTCTAATTTAAAATTTCATG
66 TTTTGTCCAAAAAATTAAAAAATGGTCTAATTACCTTTTAAGCACCTCCAATTTAAAATTTCATA
23591429 GCAATTAGACACCTC
131 GCAATTAGACACCTC
23591444 TA
1 TA
23591446 GCTTTTAGAA
Statistics
Matches: 139, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
144 128 0.92
145 11 0.08
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.35
Consensus pattern (145 bp):
TAATCACCGAATTACTAAAATGCCCTTAACTTAAAAATATTCTATTTCACCTATTTCATATCCAT
TTTTGTCCAAAAAATTAAAAAATGGTCTAATTACCTTTTAAGCACCTCCAATTTAAAATTTCATA
GCAATTAGACACCTC
Found at i:23593550 original size:15 final size:17
Alignment explanation
Indices: 23593516--23593552 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
23593506 GACATGGTCC
*
23593516 TGTGAGACACACGGGCG
1 TGTGTGACACACGGGCG
*
23593533 TGTGTGACACACGGGTG
1 TGTGTGACACACGGGCG
23593550 TGT
1 TGT
23593553 CCTAGGTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.19, C:0.19, G:0.41, T:0.22
Consensus pattern (17 bp):
TGTGTGACACACGGGCG
Found at i:23594291 original size:11 final size:11
Alignment explanation
Indices: 23594277--23594353 Score: 57
Period size: 11 Copynumber: 6.8 Consensus size: 11
23594267 TCCTTTTTCC
23594277 TATTATTTTAT
1 TATTATTTTAT
23594288 TATTATTTTA-
1 TATTATTTTAT
*
23594298 TATTTAGTTTAT
1 TA-TTATTTTAT
* *
23594310 TATTATCTTGT
1 TATTATTTTAT
* * *
23594321 TAGTATATTCT
1 TATTATTTTAT
*
23594332 TATTATGATTAT
1 TATTAT-TTTAT
23594344 TATTAGTTTT
1 TATTA-TTTT
23594354 GGTTTTTTTT
Statistics
Matches: 52, Mismatches: 10, Indels: 7
0.75 0.14 0.10
Matches are distributed among these distances:
10 2 0.04
11 36 0.69
12 13 0.25
13 1 0.02
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:23605750 original size:19 final size:18
Alignment explanation
Indices: 23605704--23605751 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
23605694 GATATAATTT
*
23605704 TTGTCATAAAATAATTAAT
1 TTGT-ATAAAATAATTAAA
* *
23605723 TTTTATAAAATAGTTAAA
1 TTGTATAAAATAATTAAA
23605741 TTGTATTAAAA
1 TTGTA-TAAAA
23605752 ATTTGAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (18 bp):
TTGTATAAAATAATTAAA
Found at i:23605802 original size:20 final size:21
Alignment explanation
Indices: 23605758--23605805 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
23605748 AAAAATTTGA
23605758 ATTTTTAGTCAATTTTACAATT
1 ATTTTTAGTCAATTTTA-AATT
* *
23605780 ATTTTTAGTGAATTTT-TATT
1 ATTTTTAGTCAATTTTAAATT
23605800 ATTTTT
1 ATTTTT
23605806 GACAGATTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 9 0.38
22 15 0.62
ACGTcount: A:0.27, C:0.04, G:0.06, T:0.62
Consensus pattern (21 bp):
ATTTTTAGTCAATTTTAAATT
Found at i:23606378 original size:14 final size:14
Alignment explanation
Indices: 23606355--23606384 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
23606345 CATCCCTCAT
*
23606355 TCACATCTCTTCTC
1 TCACAACTCTTCTC
23606369 TCACAACTCTTCTC
1 TCACAACTCTTCTC
23606383 TC
1 TC
23606385 CTCTCTCACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.43, G:0.00, T:0.40
Consensus pattern (14 bp):
TCACAACTCTTCTC
Found at i:23606547 original size:6 final size:6
Alignment explanation
Indices: 23606536--23606560 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
23606526 CATTTCTAGG
23606536 TCATTT TCATTT TCATTT TCATTT T
1 TCATTT TCATTT TCATTT TCATTT T
23606561 GGAGAAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (6 bp):
TCATTT
Found at i:23606608 original size:58 final size:57
Alignment explanation
Indices: 23606536--23606666 Score: 162
Period size: 58 Copynumber: 2.3 Consensus size: 57
23606526 CATTTCTAGG
*
23606536 TCATTT-TCATTTTCA-TTTTCATTTTGGAGAAAAAGCA-AATTCATTTCCAAATGATT-
1 TCATTTCTCATTTTCATTTTTCATTTTGGAG-AAAACCATAA-TCATTTCCAAAT-ATTC
* *
23606592 TCATTTCTCAATTTTCATTTTTTATTTTGGAGAAGACCATAATCATTTCCAAATATTC
1 TCATTTCTC-ATTTTCATTTTTCATTTTGGAGAAAACCATAATCATTTCCAAATATTC
23606650 TCATTTCTCCATTTTCA
1 TCATTTCT-CATTTTCA
23606667 CCATTTCTAT
Statistics
Matches: 66, Mismatches: 3, Indels: 10
0.84 0.04 0.13
Matches are distributed among these distances:
56 6 0.09
57 5 0.08
58 39 0.59
59 16 0.24
ACGTcount: A:0.29, C:0.18, G:0.07, T:0.47
Consensus pattern (57 bp):
TCATTTCTCATTTTCATTTTTCATTTTGGAGAAAACCATAATCATTTCCAAATATTC
Found at i:23612360 original size:29 final size:29
Alignment explanation
Indices: 23612327--23612541 Score: 202
Period size: 29 Copynumber: 7.4 Consensus size: 29
23612317 TCAGCGACCA
*
23612327 ATGAAAAGGGATAGCTTCGGCTATTGAAT
1 ATGAAAAGGGATAGCTTCGGCTATTGATT
* * *
23612356 ATGAAAAGGGATAGATTTGGCTATCGATT
1 ATGAAAAGGGATAGCTTCGGCTATTGATT
*
23612385 ATGAAAAGGGATAGCTTCGGCTATCGATT
1 ATGAAAAGGGATAGCTTCGGCTATTGATT
* * * * *
23612414 ATGAAAAGGGAT-GGTGACGACCATTAATT
1 ATGAAAAGGGATAGCT-TCGGCTATTGATT
* * ** * *
23612443 ATGAAAAGGGAT-GGTGACAACCATCAGA-T
1 ATGAAAAGGGATAGCT-TCGGCTAT-TGATT
* * *
23612472 ATGACAAGGGACAGCTTTGGCTATTGATT
1 ATGAAAAGGGATAGCTTCGGCTATTGATT
*
23612501 ATGAAAAGGGATAGCTTCGGCTATCGATT
1 ATGAAAAGGGATAGCTTCGGCTATTGATT
23612530 ATGAAAAGGGAT
1 ATGAAAAGGGAT
23612542 GGTGACAACC
Statistics
Matches: 154, Mismatches: 28, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
28 4 0.03
29 147 0.95
30 3 0.02
ACGTcount: A:0.35, C:0.11, G:0.28, T:0.26
Consensus pattern (29 bp):
ATGAAAAGGGATAGCTTCGGCTATTGATT
Found at i:23612475 original size:87 final size:87
Alignment explanation
Indices: 23612378--23612573 Score: 252
Period size: 87 Copynumber: 2.2 Consensus size: 87
23612368 AGATTTGGCT
* *
23612378 ATCGATTATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGAT-GGTGACGACCATTAAT
1 ATCGATTATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGATAGCT-ACGACCATCAAT
23612442 TATGAAAAGGGATGGTGACAACC
65 TATGAAAAGGGATGGTGACAACC
* * * * * * * *
23612465 ATCAGA-TATGACAAGGGACAGCTTTGGCTATTGATTATGAAAAGGGATAGCTTCGGCTATCGAT
1 ATC-GATTATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGATAGCTACGACCATCAAT
23612529 TATGAAAAGGGATGGTGACAACC
65 TATGAAAAGGGATGGTGACAACC
*
23612552 ATCGATTAATGAAAAGCGATAG
1 ATCGATT-ATGAAAAGGGATAG
23612574 TTTTGACCAT
Statistics
Matches: 92, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
86 2 0.02
87 75 0.82
88 15 0.16
ACGTcount: A:0.36, C:0.13, G:0.27, T:0.24
Consensus pattern (87 bp):
ATCGATTATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGATAGCTACGACCATCAATT
ATGAAAAGGGATGGTGACAACC
Found at i:23612531 original size:116 final size:117
Alignment explanation
Indices: 23612354--23612567 Score: 358
Period size: 116 Copynumber: 1.8 Consensus size: 117
23612344 CGGCTATTGA
*
23612354 ATATGAAAAGGGATAGATTTGGCTATCGATTATGAAAAGGGATAGCTTCGGCTATCGATTATGAA
1 ATATGAAAAGGGACAGATTTGGCTATCGATTATGAAAAGGGATAGCTTCGGCTATCGATTATGAA
* *
23612419 AAGGGATGGTGACGACCATTAATT-ATGAAAAGGGATGGTGACAACCATCAG
66 AAGGGATGGTGACAACCATCAATTAATGAAAAGGGATGGTGACAACCATCAG
* * *
23612470 ATATGACAAGGGACAGCTTTGGCTATTGATTATGAAAAGGGATAGCTTCGGCTATCGATTATGAA
1 ATATGAAAAGGGACAGATTTGGCTATCGATTATGAAAAGGGATAGCTTCGGCTATCGATTATGAA
*
23612535 AAGGGATGGTGACAACCATCGATTAATGAAAAG
66 AAGGGATGGTGACAACCATCAATTAATGAAAAG
23612568 CGATAGTTTT
Statistics
Matches: 90, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
116 82 0.91
117 8 0.09
ACGTcount: A:0.36, C:0.12, G:0.27, T:0.25
Consensus pattern (117 bp):
ATATGAAAAGGGACAGATTTGGCTATCGATTATGAAAAGGGATAGCTTCGGCTATCGATTATGAA
AAGGGATGGTGACAACCATCAATTAATGAAAAGGGATGGTGACAACCATCAG
Found at i:23612559 original size:58 final size:57
Alignment explanation
Indices: 23612327--23612573 Score: 201
Period size: 58 Copynumber: 4.2 Consensus size: 57
23612317 TCAGCGACCA
* * * ** * *
23612327 ATGAAAAGGGATAGCTTCGGCTATTGAATATGAAAAGGGATAGATTTGGCTATCGATT
1 ATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGAT-GGTACGACCATCGATT
**
23612385 ATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGATGGTGACGACCATTAATT
1 ATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGATGGT-ACGACCATCGATT
* * ** * * * * ** * * *
23612443 ATGAAAAGGGAT-GGTGACAACCATCAGA-TATGACAAGGGACAGCTTTGGCTATTGATT
1 ATGAAAAGGGATAGCT-TCGGCTATC-GATTATGAAAAGGGA-TGGTACGACCATCGATT
*
23612501 ATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGATGGTGACAACCATCGATT
1 ATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGATGGT-ACGACCATCGATT
*
23612559 AATGAAAAGCGATAG
1 -ATGAAAAGGGATAG
23612574 TTTTGACCAT
Statistics
Matches: 144, Mismatches: 37, Indels: 15
0.73 0.19 0.08
Matches are distributed among these distances:
57 8 0.06
58 117 0.81
59 19 0.13
ACGTcount: A:0.36, C:0.12, G:0.28, T:0.25
Consensus pattern (57 bp):
ATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGATGGTACGACCATCGATT
Found at i:23613424 original size:29 final size:29
Alignment explanation
Indices: 23613382--23613625 Score: 183
Period size: 29 Copynumber: 8.4 Consensus size: 29
23613372 TCAGCGACCA
* *
23613382 ATGAAAAGGGATAGCTTTGGCTATCGAA-T
1 ATGAAAAGGGATAGCTTCGACTATC-AATT
23613411 ATGAAAAGGGATAGCTTCGACTATCAATT
1 ATGAAAAGGGATAGCTTCGACTATCAATT
* *
23613440 ATGAAAAAGGATAGCTTCGGCTATCAATT
1 ATGAAAAGGGATAGCTTCGACTATCAATT
* * *
23613469 ATGAAAAGAGAT-GGTGAT-GACCATCAATT
1 ATGAAAAGGGATAGCT--TCGACTATCAATT
* * * *
23613498 ATGAAAAGGGAT-GGTGACGACCATCAAAT
1 ATGAAAAGGGATAGCT-TCGACTATCAATT
* * *
23613527 ATGAAAAGGGATAGCTTTGGCTATCGATT
1 ATGAAAAGGGATAGCTTCGACTATCAATT
* * * *
23613556 ATGAAAAGGGATTG-TGACGACCATCGATT
1 ATGAAAAGGGATAGCT-TCGACTATCAATT
* * * * *
23613585 AATGGAAAGGGATAGTTTCGACCACCAAAT
1 -ATGAAAAGGGATAGCTTCGACTATCAATT
*
23613615 ATGCAAAGGGA
1 ATGAAAAGGGA
23613626 CGGTTATGAC
Statistics
Matches: 175, Mismatches: 32, Indels: 16
0.78 0.14 0.07
Matches are distributed among these distances:
28 5 0.03
29 145 0.83
30 24 0.14
31 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.24
Consensus pattern (29 bp):
ATGAAAAGGGATAGCTTCGACTATCAATT
Found at i:23613531 original size:87 final size:86
Alignment explanation
Indices: 23613410--23613617 Score: 254
Period size: 87 Copynumber: 2.4 Consensus size: 86
23613400 GGCTATCGAA
* * *
23613410 TATGAAAAGGGATAGCTTCGACTATCAATTATGAAAAAGGATAGCTTCGGCTATCAATTATGAAA
1 TATGAAAAGGGAT-GGTTCGACCATCAAATATGAAAAAGGATAGCTTCGGCTATCAATTATGAAA
*
23613475 AGAGATGGTGATGACCATCAAT
65 AGAGATGGTGACGACCATCAAT
* * * *
23613497 TATGAAAAGGGATGGTGACGACCATCAAATATGAAAAGGGATAGCTTTGGCTATCGATTATGAAA
1 TATGAAAAGGGATGGT-TCGACCATCAAATATGAAAAAGGATAGCTTCGGCTATCAATTATGAAA
* * *
23613562 AGGGATTGTGACGACCATCGAT
65 AGAGATGGTGACGACCATCAAT
* * *
23613584 TAATGGAAAGGGATAGTTTCGACCACCAAATATG
1 T-ATGAAAAGGGAT-GGTTCGACCATCAAATATG
23613618 CAAAGGGACG
Statistics
Matches: 103, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
86 2 0.02
87 74 0.72
88 25 0.24
89 2 0.02
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.25
Consensus pattern (86 bp):
TATGAAAAGGGATGGTTCGACCATCAAATATGAAAAAGGATAGCTTCGGCTATCAATTATGAAAA
GAGATGGTGACGACCATCAAT
Found at i:23628879 original size:42 final size:43
Alignment explanation
Indices: 23628781--23628936 Score: 167
Period size: 43 Copynumber: 3.6 Consensus size: 43
23628771 TCTCGTACGG
* * * *
23628781 TGCCAACGTCCTAGACGTGGTCTTACATGTAATCA-ACTATCGA
1 TGCCAACGTCCCAGACATGGTCTTACATGAAATCATA-TACCGA
*
23628824 TGCC-ACTGTCCCAGACAAGGTCTTACATGAAATCATATA-CGA
1 TGCCAAC-GTCCCAGACATGGTCTTACATGAAATCATATACCGA
* * *
23628866 TGCCAATGTCCCAGACATGGTCTTACACGTAAATC-TCAAACCGA
1 TGCCAACGTCCCAGACATGGTCTTACATG-AAATCAT-ATACCGA
*
23628910 TGCCAACGTCCTAGACATGGTCTTACA
1 TGCCAACGTCCCAGACATGGTCTTACA
23628937 CAAAATCACA
Statistics
Matches: 97, Mismatches: 10, Indels: 11
0.82 0.08 0.09
Matches are distributed among these distances:
42 30 0.31
43 38 0.39
44 29 0.30
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (43 bp):
TGCCAACGTCCCAGACATGGTCTTACATGAAATCATATACCGA
Found at i:23634424 original size:124 final size:123
Alignment explanation
Indices: 23634209--23634485 Score: 455
Period size: 124 Copynumber: 2.2 Consensus size: 123
23634199 GTTTCTGGTC
* * * * *
23634209 AAATAGTATAAAATCACCTCTACTAGGATGCTATTTGAGAAGTAATTGTGAAATCGCGCCCTCGT
1 AAATAGTATAAAATCGCCTCTACCAGGATGATATTTGAGAAGAAATTGTGAAATCGCACCCTCGT
* *
23634274 GGACGCGATTTTACTACAGTATGTCATGTAAGAAATAATTTTTTTTGACATTTCTGAGA
66 GGACGCGATTTTACTACAGTAGGTCATGTAAGAAATAA-TTTTTTTGACATTTCTAAGA
23634333 AAATAGTATAAAATCGCCTCTACCAGGATGATATTTGAGAAGAAATTGTGAAATCGCACCCTCGT
1 AAATAGTATAAAATCGCCTCTACCAGGATGATATTTGAGAAGAAATTGTGAAATCGCACCCTCGT
* * *
23634398 GGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTGACGTTTCTAAGC
66 GGACGCGATTTTACTACAGTAGGTCATGTAAGAAATAATTTTTTTGACATTTCTAAGA
23634456 AAATAGTATAAAATCGCCTCTACCAGGATG
1 AAATAGTATAAAATCGCCTCTACCAGGATG
23634486 GCTTCTAGCA
Statistics
Matches: 143, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
123 47 0.33
124 96 0.67
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.31
Consensus pattern (123 bp):
AAATAGTATAAAATCGCCTCTACCAGGATGATATTTGAGAAGAAATTGTGAAATCGCACCCTCGT
GGACGCGATTTTACTACAGTAGGTCATGTAAGAAATAATTTTTTTGACATTTCTAAGA
Found at i:23637486 original size:10 final size:10
Alignment explanation
Indices: 23637471--23637495 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
23637461 CAAATCTAAC
23637471 ATTATGTAAA
1 ATTATGTAAA
23637481 ATTATGTAAA
1 ATTATGTAAA
23637491 ATTAT
1 ATTAT
23637496 TAAGTCCCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (10 bp):
ATTATGTAAA
Found at i:23637549 original size:10 final size:10
Alignment explanation
Indices: 23637534--23637560 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
23637524 TAAAACTATC
23637534 AAATTATGTA
1 AAATTATGTA
23637544 AAATTATGTA
1 AAATTATGTA
23637554 AAATTAT
1 AAATTAT
23637561 TTAGCCCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (10 bp):
AAATTATGTA
Found at i:23637605 original size:18 final size:18
Alignment explanation
Indices: 23637582--23637616 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
23637572 AATTTTAATT
23637582 AAATTAGGTAAAATTATC
1 AAATTAGGTAAAATTATC
*
23637600 AAATTATGTAAAATTAT
1 AAATTAGGTAAAATTAT
23637617 TAAGTCCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.09, T:0.37
Consensus pattern (18 bp):
AAATTAGGTAAAATTATC
Found at i:23637607 original size:66 final size:64
Alignment explanation
Indices: 23637471--23637616 Score: 197
Period size: 66 Copynumber: 2.2 Consensus size: 64
23637461 CAAATCTAAC
* *
23637471 ATTATGTAAAATTATGTAAAATTATTAAGTCCCAAAATTTTGTTAATGGTTAGTAAAACTATCAA
1 ATTATGTAAAATTATGTAAAATTATTAAGTCCCAAAATTTTATTAA-GATTAGTAAAACTATCAA
* *
23637536 ATTATGTAAAATTATGTAAAATTATTTAG-CCCAAAAAATTTTAATTAA-ATTAGGTAAAATTAT
1 ATTATGTAAAATTATGTAAAATTATTAAGTCCC--AAAATTTT-ATTAAGATTA-GTAAAACTAT
23637599 CAA
62 CAA
23637602 ATTATGTAAAATTAT
1 ATTATGTAAAATTAT
23637617 TAAGTCCAAA
Statistics
Matches: 73, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
64 3 0.04
65 31 0.42
66 35 0.48
67 4 0.05
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.39
Consensus pattern (64 bp):
ATTATGTAAAATTATGTAAAATTATTAAGTCCCAAAATTTTATTAAGATTAGTAAAACTATCAA
Found at i:23637682 original size:10 final size:10
Alignment explanation
Indices: 23637657--23637693 Score: 56
Period size: 10 Copynumber: 3.5 Consensus size: 10
23637647 TTTTTTATCC
23637657 ATTATGTATCAA
1 ATTATGTA--AA
23637669 ATTATGTAAA
1 ATTATGTAAA
23637679 ATTATGTAAA
1 ATTATGTAAA
23637689 ATTAT
1 ATTAT
23637694 TAAGTAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 17 0.68
12 8 0.32
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (10 bp):
ATTATGTAAA
Found at i:23637725 original size:131 final size:132
Alignment explanation
Indices: 23637530--23637774 Score: 429
Period size: 131 Copynumber: 1.9 Consensus size: 132
23637520 TTAGTAAAAC
* **
23637530 TATCAAATTATGTAAAATTATGTAAAATTATTTAGCCCAAAAAATTTTAATTAAATTAGGTAAAA
1 TATCAAATTATGTAAAATTATGTAAAATTATTAAG-CCAAAAAAAATTAATTAAATTAGGTAAAA
*
23637595 TTATCAAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGGGTTTTTTATCCATT
65 TTATCAAATTAGGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGGGTTTTTTATCCATT
23637660 ATG
130 ATG
*
23637663 TATCAAATTATGTAAAATTATGTAAAATTATTAAG-TAAAAAAAATTAATTAAATTAGGTAAAAT
1 TATCAAATTATGTAAAATTATGTAAAATTATTAAGCCAAAAAAAATTAATTAAATTAGGTAAAAT
23637727 TATCAAATTAGGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTA
66 TATCAAATTAGGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTA
23637775 CTAAAATTAT
Statistics
Matches: 107, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
131 73 0.68
133 34 0.32
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (132 bp):
TATCAAATTATGTAAAATTATGTAAAATTATTAAGCCAAAAAAAATTAATTAAATTAGGTAAAAT
TATCAAATTAGGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGGGTTTTTTATCCATTA
TG
Found at i:23637736 original size:18 final size:18
Alignment explanation
Indices: 23637703--23637747 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 18
23637693 TTAAGTAAAA
*
23637703 AAAATTAATTAAATTAGGT
1 AAAATT-ATCAAATTAGGT
23637722 AAAATTATCAAATTAGGT
1 AAAATTATCAAATTAGGT
23637740 AAAATTAT
1 AAAATTAT
23637748 TAAGTCCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 19 0.76
19 6 0.24
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.36
Consensus pattern (18 bp):
AAAATTATCAAATTAGGT
Found at i:23637787 original size:55 final size:55
Alignment explanation
Indices: 23637677--23637856 Score: 231
Period size: 55 Copynumber: 3.3 Consensus size: 55
23637667 AAATTATGTA
** * * *
23637677 AAATTATGTAAAATTATTAAGTAAAAAAAATT-AATTAA--ATTAGGTAAAATTATC
1 AAATTATGTAAAATTATTAAGT-CCAAAAATTGTATTAATGGTTA-CTAAAATTATC
* *
23637731 AAATTAGGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTACTAAAATTATC
1 AAATTATGTAAAATTATTAAGTCCAAAAATTGTATTAATGGTTACTAAAATTATC
* * *
23637786 AAATTATGTAAAATTATTAAGTCTAAGAATTGTATTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTATTAAGTCCAAAAATTGTATTAATGGTTACTAAAATTATC
23637841 AAATTATGTAAAATTA
1 AAATTATGTAAAATTA
23637857 GGTTAGGGTT
Statistics
Matches: 111, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
53 7 0.06
54 25 0.23
55 76 0.68
56 3 0.03
ACGTcount: A:0.48, C:0.04, G:0.11, T:0.37
Consensus pattern (55 bp):
AAATTATGTAAAATTATTAAGTCCAAAAATTGTATTAATGGTTACTAAAATTATC
Found at i:23637792 original size:131 final size:131
Alignment explanation
Indices: 23637530--23637802 Score: 392
Period size: 131 Copynumber: 2.1 Consensus size: 131
23637520 TTAGTAAAAC
* **
23637530 TATCAAATTATGTAAAATTATGTAAAATTATTTAGCCCAAAAAATTTTAATTAAATTAGGTAAAA
1 TATCAAATTATGTAAAATTATGTAAAATTATTAAG-CCAAAAAAAATTAATTAAATTAGGTAAAA
* * *** *
23637595 TTATCAAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGGGTTTTTTATCCATT
65 TTATCAAATTAGGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTA-GCTAAATTATCAATT
23637660 ATG
129 ATG
*
23637663 TATCAAATTATGTAAAATTATGTAAAATTATTAAG-TAAAAAAAATTAATTAAATTAGGTAAAAT
1 TATCAAATTATGTAAAATTATGTAAAATTATTAAGCCAAAAAAAATTAATTAAATTAGGTAAAAT
23637727 TATCAAATTAGGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTA-CTAAAATTATCAAATT
66 TATCAAATTAGGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGCT-AAATTATC-AATT
23637791 ATG
129 ATG
23637794 TA--AAATTAT
1 TATCAAATTAT
23637803 TAAGTCTAAG
Statistics
Matches: 128, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
129 8 0.06
130 5 0.04
131 81 0.63
133 34 0.27
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.39
Consensus pattern (131 bp):
TATCAAATTATGTAAAATTATGTAAAATTATTAAGCCAAAAAAAATTAATTAAATTAGGTAAAAT
TATCAAATTAGGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGCTAAATTATCAATTAT
G
Found at i:23637879 original size:24 final size:23
Alignment explanation
Indices: 23637852--23637937 Score: 88
Period size: 24 Copynumber: 3.7 Consensus size: 23
23637842 AATTATGTAA
*
23637852 AATTAGGTTAGGGTTAGGGTTTTT
1 AATTAAGTTAGGGTTA-GGTTTTT
23637876 AATTAAGTTAGGGTT---TTTAATT
1 AATTAAGTTAGGGTTAGGTTT--TT
*
23637898 AAATTAGGTTAGGGTTAGGATTTTT
1 -AATTAAGTTAGGGTTAGG-TTTTT
23637923 AATTAAGTTAGGGTT
1 AATTAAGTTAGGGTT
23637938 TTTAATTAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 14
0.75 0.04 0.20
Matches are distributed among these distances:
20 3 0.06
22 2 0.04
23 14 0.27
24 28 0.54
25 2 0.04
27 3 0.06
ACGTcount: A:0.28, C:0.00, G:0.27, T:0.45
Consensus pattern (23 bp):
AATTAAGTTAGGGTTAGGTTTTT
Found at i:23637887 original size:18 final size:18
Alignment explanation
Indices: 23637864--23637959 Score: 98
Period size: 18 Copynumber: 5.7 Consensus size: 18
23637854 TTAGGTTAGG
23637864 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
23637882 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
* **
23637900 ATTA-GG---TT-A--GG
1 GTTAGGGTTTTTAATTAA
*
23637911 GTTAGGATTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
23637929 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
*
23637947 ATTAGGGTTTTTA
1 GTTAGGGTTTTTA
23637960 TTACATCAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
11 3 0.05
12 1 0.02
13 1 0.02
14 2 0.03
15 2 0.03
16 1 0.02
17 2 0.03
18 50 0.81
ACGTcount: A:0.28, C:0.00, G:0.23, T:0.49
Consensus pattern (18 bp):
GTTAGGGTTTTTAATTAA
Found at i:23637922 original size:47 final size:47
Alignment explanation
Indices: 23637851--23637952 Score: 195
Period size: 47 Copynumber: 2.2 Consensus size: 47
23637841 AAATTATGTA
*
23637851 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGATTTTTAATTAAGTTAGGGTTTTTAATT
23637898 AAATTAGGTTAGGGTTAGGATTTTTAATTAAGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGATTTTTAATTAAGTTAGGGTTTTTAATT
23637945 AAATTAGG
1 AAATTAGG
23637953 GTTTTTATTA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.30, C:0.00, G:0.25, T:0.45
Consensus pattern (47 bp):
AAATTAGGTTAGGGTTAGGATTTTTAATTAAGTTAGGGTTTTTAATT
Found at i:23638007 original size:25 final size:26
Alignment explanation
Indices: 23637955--23638018 Score: 94
Period size: 25 Copynumber: 2.5 Consensus size: 26
23637945 AAATTAGGGT
*
23637955 TTTTATTACATCAAATTGAACTTCTA
1 TTTTATTACATCAAATTAAACTTCTA
* *
23637981 TTTTATTATATTAAA-TAAACTTCTA
1 TTTTATTACATCAAATTAAACTTCTA
23638006 TTTTATTACATCA
1 TTTTATTACATCA
23638019 GATAATAAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
25 20 0.61
26 13 0.39
ACGTcount: A:0.36, C:0.12, G:0.02, T:0.50
Consensus pattern (26 bp):
TTTTATTACATCAAATTAAACTTCTA
Found at i:23638059 original size:71 final size:71
Alignment explanation
Indices: 23637977--23638123 Score: 276
Period size: 71 Copynumber: 2.1 Consensus size: 71
23637967 AAATTGAACT
*
23637977 TCTATTTTATTATATTAAATAAACTTCTATTTTATTACATCAGATAATAAGTTTAAATACGGCAA
1 TCTATTTTATTATATTAAATAAACTTCTATTTTATTACATCAGATAATAAATTTAAATACGGCAA
23638042 TCAATG
66 TCAATG
*
23638048 TCTATTTTATTATATTAAATAAACTTCTATTTTGTTACATCAGATAATAAATTTAAATACGGCAA
1 TCTATTTTATTATATTAAATAAACTTCTATTTTATTACATCAGATAATAAATTTAAATACGGCAA
23638113 TCAATG
66 TCAATG
23638119 TCTAT
1 TCTAT
23638124 GCCCGGGGGA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 74 1.00
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.43
Consensus pattern (71 bp):
TCTATTTTATTATATTAAATAAACTTCTATTTTATTACATCAGATAATAAATTTAAATACGGCAA
TCAATG
Found at i:23639194 original size:7 final size:7
Alignment explanation
Indices: 23639184--23639208 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
23639174 TTATATACAT
23639184 AATACTA
1 AATACTA
23639191 AATACTA
1 AATACTA
23639198 AATACTA
1 AATACTA
23639205 AATA
1 AATA
23639209 TCAATAGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:23640477 original size:28 final size:28
Alignment explanation
Indices: 23640419--23640479 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 28
23640409 CGATTTCCCG
* *
23640419 AAAAATGGCCTATTCCGGTAAATAATCA
1 AAAAATGGCCCATTCCGGTAAATAATAA
* *
23640447 AAAAATCGGCCCATTTCGGTAAAT-TTAA
1 AAAAAT-GGCCCATTCCGGTAAATAATAA
23640475 AAAAA
1 AAAAA
23640480 ACCGGCTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 13 0.46
29 15 0.54
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.25
Consensus pattern (28 bp):
AAAAATGGCCCATTCCGGTAAATAATAA
Found at i:23647856 original size:24 final size:25
Alignment explanation
Indices: 23647829--23647882 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 25
23647819 CACACCACAA
*
23647829 CTCGTGTGACCTTACCGATT-TTAG
1 CTCGTGAGACCTTACCGATTCTTAG
*
23647853 CTCGTGAGAGCTTACCGATTCTTAG
1 CTCGTGAGACCTTACCGATTCTTAG
23647878 CTCGT
1 CTCGT
23647883 ATTAGCTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 18 0.67
25 9 0.33
ACGTcount: A:0.17, C:0.26, G:0.22, T:0.35
Consensus pattern (25 bp):
CTCGTGAGACCTTACCGATTCTTAG
Found at i:23647889 original size:25 final size:24
Alignment explanation
Indices: 23647829--23647932 Score: 93
Period size: 25 Copynumber: 4.2 Consensus size: 24
23647819 CACACCACAA
* *
23647829 CTCGTGTGACCTTACCGATTTTAG
1 CTCGTGAGAGCTTACCGATTTTAG
23647853 CTCGTGAGAGCTTACCGATTCTTAG
1 CTCGTGAGAGCTTACCGATT-TTAG
* * *
23647878 CTCGT-ATTAGCTTACCAATTTCCAG
1 CTCGTGA-GAGCTTACCGATTT-TAG
* * *
23647903 CTCGTGAGAGCATACTGATTCATAG
1 CTCGTGAGAGCTTACCGATT-TTAG
23647928 CTCGT
1 CTCGT
23647933 ATGAGTATAC
Statistics
Matches: 64, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
24 20 0.31
25 43 0.67
26 1 0.02
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.34
Consensus pattern (24 bp):
CTCGTGAGAGCTTACCGATTTTAG
Found at i:23672354 original size:20 final size:20
Alignment explanation
Indices: 23672331--23672462 Score: 74
Period size: 20 Copynumber: 6.6 Consensus size: 20
23672321 TAGGGCCATG
23672331 AAAGTGCAATCAGGGGTAAC
1 AAAGTGCAATCAGGGGTAAC
* * **
23672351 AAAGTACAAAT-AGGGGCATG
1 AAAGTGC-AATCAGGGGTAAC
* *
23672371 TAAGTGCAATCAGGGGTACC
1 AAAGTGCAATCAGGGGTAAC
* *
23672391 AAAGTACACAT-AGGGG-CAC
1 AAAGTGCA-ATCAGGGGTAAC
* * *
23672410 GTAAGTGCAATCAGGCGTACC
1 -AAAGTGCAATCAGGGGTAAC
* * *
23672431 AAAGTACAAACAGGGG-CAC
1 AAAGTGCAATCAGGGGTAAC
23672450 AAGAGTGCAATCA
1 AA-AGTGCAATCA
23672463 TCCAATAATT
Statistics
Matches: 79, Mismatches: 26, Indels: 14
0.66 0.22 0.12
Matches are distributed among these distances:
19 9 0.11
20 64 0.81
21 6 0.08
ACGTcount: A:0.39, C:0.18, G:0.28, T:0.14
Consensus pattern (20 bp):
AAAGTGCAATCAGGGGTAAC
Found at i:23672376 original size:40 final size:40
Alignment explanation
Indices: 23672321--23672448 Score: 193
Period size: 40 Copynumber: 3.2 Consensus size: 40
23672311 GGAGTATAAC
* * *
23672321 TAGGGCCATGAAAGTGCAATCAGGGGTAACAAAGTACAAA
1 TAGGGGCATGTAAGTGCAATCAGGGGTACCAAAGTACAAA
*
23672361 TAGGGGCATGTAAGTGCAATCAGGGGTACCAAAGTACACA
1 TAGGGGCATGTAAGTGCAATCAGGGGTACCAAAGTACAAA
* *
23672401 TAGGGGCACGTAAGTGCAATCAGGCGTACCAAAGTACAAA
1 TAGGGGCATGTAAGTGCAATCAGGGGTACCAAAGTACAAA
*
23672441 CAGGGGCA
1 TAGGGGCA
23672449 CAAGAGTGCA
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 80 1.00
ACGTcount: A:0.38, C:0.18, G:0.30, T:0.15
Consensus pattern (40 bp):
TAGGGGCATGTAAGTGCAATCAGGGGTACCAAAGTACAAA
Found at i:23672449 original size:40 final size:40
Alignment explanation
Indices: 23672332--23672462 Score: 192
Period size: 40 Copynumber: 3.3 Consensus size: 40
23672322 AGGGCCATGA
* *
23672332 AAGTGCAATCAGGGGTAACAAAGTACAAATAGGGGCATGT
1 AAGTGCAATCAGGGGTACCAAAGTACAAATAGGGGCACGT
*
23672372 AAGTGCAATCAGGGGTACCAAAGTACACATAGGGGCACGT
1 AAGTGCAATCAGGGGTACCAAAGTACAAATAGGGGCACGT
* * *
23672412 AAGTGCAATCAGGCGTACCAAAGTACAAACAGGGGCAC-A
1 AAGTGCAATCAGGGGTACCAAAGTACAAATAGGGGCACGT
23672451 AGAGTGCAATCA
1 A-AGTGCAATCA
23672463 TCCAATAATT
Statistics
Matches: 83, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
39 1 0.01
40 82 0.99
ACGTcount: A:0.39, C:0.18, G:0.28, T:0.15
Consensus pattern (40 bp):
AAGTGCAATCAGGGGTACCAAAGTACAAATAGGGGCACGT
Found at i:23689383 original size:25 final size:24
Alignment explanation
Indices: 23689355--23689436 Score: 69
Period size: 25 Copynumber: 3.3 Consensus size: 24
23689345 CAAGCTATAC
23689355 ATCGGTAAGTTAATACAAGTTGAGA
1 ATCGGTAAGTT-ATACAAGTTGAGA
** * *
23689380 ATCGGTAAACTCTCACAAGTTG-TA
1 ATCGGTAAGTTAT-ACAAGTTGAGA
*
23689404 ATCGGTAAGTTTATACGA-TCTGAGA
1 ATCGGTAAG-TTATACAAGT-TGAGA
23689429 ATCGGTAA
1 ATCGGTAA
23689437 TCCCTAATGA
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
23 1 0.02
24 15 0.34
25 28 0.64
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.29
Consensus pattern (24 bp):
ATCGGTAAGTTATACAAGTTGAGA
Found at i:23689428 original size:49 final size:50
Alignment explanation
Indices: 23689339--23689436 Score: 137
Period size: 49 Copynumber: 2.0 Consensus size: 50
23689329 AATCGATATG
23689339 CTCTCACAAGCTATACATCGGTAAGTTAATACAAGTTGAGAATCGGTAAA
1 CTCTCACAAGCTATACATCGGTAAGTTAATACAAGTTGAGAATCGGTAAA
* * * *
23689389 CTCTCACAAGTTGTA-ATCGGTAAGTTTATACGA-TCTGAGAATCGGTAA
1 CTCTCACAAGCTATACATCGGTAAGTTAATACAAGT-TGAGAATCGGTAA
23689437 TCCCTAATGA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
48 1 0.02
49 29 0.67
50 13 0.30
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (50 bp):
CTCTCACAAGCTATACATCGGTAAGTTAATACAAGTTGAGAATCGGTAAA
Found at i:23708058 original size:20 final size:20
Alignment explanation
Indices: 23707994--23708058 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 20
23707984 TACTTCGGTA
*
23707994 CCCCTGAACGCACTTATGTG
1 CCCCTGATCGCACTTATGTG
* * * ** *
23708014 CCCCTG-TTGTACATCGGTT
1 CCCCTGATCGCACTTATGTG
23708033 CCCCTGATCGCACTTATGTG
1 CCCCTGATCGCACTTATGTG
23708053 CCCCTG
1 CCCCTG
23708059 TTGTACTTTA
Statistics
Matches: 31, Mismatches: 13, Indels: 2
0.67 0.28 0.04
Matches are distributed among these distances:
19 12 0.39
20 19 0.61
ACGTcount: A:0.14, C:0.37, G:0.20, T:0.29
Consensus pattern (20 bp):
CCCCTGATCGCACTTATGTG
Found at i:23708133 original size:20 final size:20
Alignment explanation
Indices: 23707927--23708182 Score: 126
Period size: 19 Copynumber: 13.2 Consensus size: 20
23707917 CCCTGAACGC
23707927 ACTTACGTGCCCCTG-TTGT
1 ACTTACGTGCCCCTGATTGT
* ****
23707946 ACTT-CGATACCCCTGAACAC
1 ACTTACG-TGCCCCTGATTGT
*
23707966 ACTTACGTTCCCCT-ATTGT
1 ACTTACGTGCCCCTGATTGT
* ** *
23707985 ACTT-CGGTACCCCTGAACGC
1 ACTTAC-GTGCCCCTGATTGT
*
23708005 ACTTATGTGCCCCTG-TTGT
1 ACTTACGTGCCCCTGATTGT
* * * *
23708024 ACAT-CGGTTCCCCTGATCGC
1 ACTTAC-GTGCCCCTGATTGT
*
23708044 ACTTATGTGCCCCTG-TTGT
1 ACTTACGTGCCCCTGATTGT
* * *
23708063 ACTTTA-GTACCCC-GATCGC
1 AC-TTACGTGCCCCTGATTGT
* * *
23708082 ACTTACATGCCACTG-TTAT
1 ACTTACGTGCCCCTGATTGT
* * *
23708101 ACTT-CGGTACCCCTGACTGC
1 ACTTAC-GTGCCCCTGATTGT
23708121 ACTTACGTGCCCCTG-TTGT
1 ACTTACGTGCCCCTGATTGT
*
23708140 ACTT-CGGTACCCCTGATTGT
1 ACTTAC-GTGCCCCTGATTGT
23708160 ACTTACGTGCCCCTG-TTGT
1 ACTTACGTGCCCCTGATTGT
23708179 ACTT
1 ACTT
23708183 CGGTACTCCT
Statistics
Matches: 169, Mismatches: 49, Indels: 38
0.66 0.19 0.15
Matches are distributed among these distances:
18 9 0.05
19 86 0.51
20 70 0.41
21 4 0.02
ACGTcount: A:0.16, C:0.33, G:0.18, T:0.33
Consensus pattern (20 bp):
ACTTACGTGCCCCTGATTGT
Found at i:23708137 original size:116 final size:118
Alignment explanation
Indices: 23707917--23708182 Score: 360
Period size: 116 Copynumber: 2.3 Consensus size: 118
23707907 GTAAATTATG
* * * * *
23707917 CCCTGAACGCACTTACGTGCCCCTGTTGTAC-TTCGATACCCCTGAACACACTTACGTTCCCCTA
1 CCCTGATCGCACTTACGTGCCCCTGTTGTACTTTAGATACCCCTGAACACACTTACATGCCACTA
* * *
23707981 TTGTACTTCGGTACCCCTGAACGCACTTATGTGCCCCTGTTGTACATCGGTTC
66 TTATACTTCGGTACCCCTGAACGCACTTACGTGCCCCTGTTGTACATCGGTAC
* * * *
23708034 CCCTGATCGCACTTATGTGCCCCTGTTGTACTTTAG-TACCCC-GATCGCACTTACATGCCACTG
1 CCCTGATCGCACTTACGTGCCCCTGTTGTACTTTAGATACCCCTGAACACACTTACATGCCACTA
*
23708097 TTATACTTCGGTACCCCTG-ACTGCACTTACGTGCCCCTGTTGTACTTCGGTAC
66 TTATACTTCGGTACCCCTGAAC-GCACTTACGTGCCCCTGTTGTACATCGGTAC
* *
23708150 CCCTGATTGTACTTACGTGCCCCTGTTGTACTT
1 CCCTGATCGCACTTACGTGCCCCTGTTGTACTT
23708183 CGGTACTCCT
Statistics
Matches: 131, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
115 2 0.02
116 91 0.69
117 35 0.27
118 3 0.02
ACGTcount: A:0.17, C:0.34, G:0.18, T:0.32
Consensus pattern (118 bp):
CCCTGATCGCACTTACGTGCCCCTGTTGTACTTTAGATACCCCTGAACACACTTACATGCCACTA
TTATACTTCGGTACCCCTGAACGCACTTACGTGCCCCTGTTGTACATCGGTAC
Found at i:23708193 original size:19 final size:19
Alignment explanation
Indices: 23708094--23708193 Score: 96
Period size: 19 Copynumber: 5.2 Consensus size: 19
23708084 TTACATGCCA
*
23708094 CTGTTATACTTCGGTACCC
1 CTGTTGTACTTCGGTACCC
* * *
23708113 CTGACTGCACTTAC-GTGCCC
1 CTG-TTGTACTT-CGGTACCC
23708133 CTGTTGTACTTCGGTACCC
1 CTGTTGTACTTCGGTACCC
*
23708152 CTGATTGTACTTAC-GTGCCC
1 CTG-TTGTACTT-CGGTACCC
*
23708172 CTGTTGTACTTCGGTACTC
1 CTGTTGTACTTCGGTACCC
23708191 CTG
1 CTG
23708194 ATAACACTTT
Statistics
Matches: 65, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
18 2 0.03
19 32 0.49
20 29 0.45
21 2 0.03
ACGTcount: A:0.13, C:0.32, G:0.20, T:0.35
Consensus pattern (19 bp):
CTGTTGTACTTCGGTACCC
Found at i:23708195 original size:39 final size:39
Alignment explanation
Indices: 23707917--23708195 Score: 364
Period size: 39 Copynumber: 7.2 Consensus size: 39
23707907 GTAAATTATG
* *
23707917 CCCTGAACGCACTTACGTGCCCCTGTTGTACTTCGATAC
1 CCCTGATCGCACTTACGTGCCCCTGTTGTACTTCGGTAC
* * * *
23707956 CCCTGAACACACTTACGTTCCCCTATTGTACTTCGGTAC
1 CCCTGATCGCACTTACGTGCCCCTGTTGTACTTCGGTAC
* * * *
23707995 CCCTGAACGCACTTATGTGCCCCTGTTGTACATCGGTTC
1 CCCTGATCGCACTTACGTGCCCCTGTTGTACTTCGGTAC
* **
23708034 CCCTGATCGCACTTATGTGCCCCTGTTGTACTTTAGTAC
1 CCCTGATCGCACTTACGTGCCCCTGTTGTACTTCGGTAC
* * *
23708073 CCC-GATCGCACTTACATGCCACTGTTATACTTCGGTAC
1 CCCTGATCGCACTTACGTGCCCCTGTTGTACTTCGGTAC
23708111 CCCTGA-CTGCACTTACGTGCCCCTGTTGTACTTCGGTAC
1 CCCTGATC-GCACTTACGTGCCCCTGTTGTACTTCGGTAC
* *
23708150 CCCTGATTGTACTTACGTGCCCCTGTTGTACTTCGGTAC
1 CCCTGATCGCACTTACGTGCCCCTGTTGTACTTCGGTAC
*
23708189 TCCTGAT
1 CCCTGAT
23708196 AACACTTTTG
Statistics
Matches: 210, Mismatches: 27, Indels: 6
0.86 0.11 0.02
Matches are distributed among these distances:
38 33 0.16
39 177 0.84
ACGTcount: A:0.16, C:0.34, G:0.18, T:0.32
Consensus pattern (39 bp):
CCCTGATCGCACTTACGTGCCCCTGTTGTACTTCGGTAC
Found at i:23717299 original size:222 final size:222
Alignment explanation
Indices: 23716913--23717339 Score: 579
Period size: 222 Copynumber: 1.9 Consensus size: 222
23716903 ACATCCCAGC
* * * *
23716913 TAAGATCTGTTAGGGTAATGATTTTCCAGCAATGCCTATCACATACGCAATGGAAAAGGATTTGT
1 TAAGATCTATTAGGGTAATGATGTGCCAGCAATGCCTATCACATACGCAATGGAAAAGGAATTGT
* * * * *
23716978 CTGTACACCGTAGGAAAGCATTATCCAATAAGTATCAAAAAGTAGTGATGCAAAGAGGCTAAATA
66 CCGTACACCGCAGGAAAGCATTATCCAATAAGTATCAAAAACTAGTGATGCAAAGAGCCTAAACA
* * * * *
23717043 TGTATCACCCTATACCCGGCATGGTCATCAAGCCCGAATACGGGATGCCACACCACCATCTCATG
131 TGTAACACCCTATACCCGACATGGTCACCAAGCCCAAATAAGGGATGCCACACCACCATCTCATG
23717108 TAATGTACAACAAGTAAAGGTCCTAGT
196 TAATGTACAACAAGTAAAGGTCCTAGT
* * *
23717135 TAAGATCTATTGGGGTAATGATGTGCCAGCAATTCCTATCACATAGGCAA-GGAAAAAGGAATTG
1 TAAGATCTATTAGGGTAATGATGTGCCAGCAATGCCTATCACATACGCAATGG-AAAAGGAATTG
* * * * * * **
23717199 TCCGTAGACCGCAGGAAAGGATTTTCCAATAAGTATCAACAACTAGTGATTCCAAGAAGCCT-GG
65 TCCGTACACCGCAGGAAAGCATTATCCAATAAGTATCAAAAACTAGTGATGCAAAG-AGCCTAAA
*
23717263 CATGTAACACCCTATACTCGACATGGTCACCAAGCCCAAATAAGGGATGCCACACCACCATCTCA
129 CATGTAACACCCTATACCCGACATGGTCACCAAGCCCAAATAAGGGATGCCACACCACCATCTCA
*
23717328 TGTCATGTACAA
194 TGTAATGTACAA
23717340 TAAGACACGG
Statistics
Matches: 176, Mismatches: 27, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
221 2 0.01
222 170 0.97
223 4 0.02
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (222 bp):
TAAGATCTATTAGGGTAATGATGTGCCAGCAATGCCTATCACATACGCAATGGAAAAGGAATTGT
CCGTACACCGCAGGAAAGCATTATCCAATAAGTATCAAAAACTAGTGATGCAAAGAGCCTAAACA
TGTAACACCCTATACCCGACATGGTCACCAAGCCCAAATAAGGGATGCCACACCACCATCTCATG
TAATGTACAACAAGTAAAGGTCCTAGT
Found at i:23724902 original size:14 final size:14
Alignment explanation
Indices: 23724862--23724891 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
23724852 TGATTAGTGC
23724862 TTAA-TTAACTTAA
1 TTAATTTAACTTAA
23724875 TTAATTTAACTTAA
1 TTAATTTAACTTAA
23724889 TTA
1 TTA
23724892 TGTTTAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (14 bp):
TTAATTTAACTTAA
Found at i:23735221 original size:25 final size:27
Alignment explanation
Indices: 23735166--23735221 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 27
23735156 TAAACATTAC
* *
23735166 ATTAAATTTAATATTAAGATAATCACT
1 ATTAAAATTAATATTAAGAAAATCACT
*
23735193 -TTAAAATTAA-ATTAATAAAAT-ACT
1 ATTAAAATTAATATTAAGAAAATCACT
23735217 ATTAA
1 ATTAA
23735222 GGTAAGTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 3 0.12
25 13 0.52
26 9 0.36
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (27 bp):
ATTAAAATTAATATTAAGAAAATCACT
Found at i:23743790 original size:44 final size:45
Alignment explanation
Indices: 23743621--23743796 Score: 221
Period size: 45 Copynumber: 4.0 Consensus size: 45
23743611 GTGTACTGAG
* * **
23743621 TATCATTGATTATAAAAGTGGTTGCTATGTGTTGATTCCACCGGG
1 TATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGAA
* * *
23743666 TACCATTGATTATAAAGGTGGTTACTATGTGCTGACTCCACCGAA
1 TATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGAA
* ** *
23743711 GATCATTGAAAATAAAGGTGGTTGCTATGTGCTGATTCCAGCGAA
1 TATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGAA
* *
23743756 TATAATTGATTATAAGGGTGG-TGCTATGTGCTGA-TCCACCG
1 TATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCG
23743797 TGTAACGGTT
Statistics
Matches: 111, Mismatches: 20, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
43 6 0.05
44 13 0.12
45 92 0.83
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.33
Consensus pattern (45 bp):
TATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGAA
Found at i:23751117 original size:457 final size:457
Alignment explanation
Indices: 23750263--23751123 Score: 1668
Period size: 457 Copynumber: 1.9 Consensus size: 457
23750253 GAGAAGTTAG
23750263 ATTTGGTGACAACTTTACAAAACAAATGGAAGGAATAGGCTCTATTGGTAAAAATTCTTCTATCA
1 ATTTGGTGACAACTTTACAAAACAAATGGAAGGAATAGGCTCTATTGGTAAAAATTCTTCTATCA
23750328 TTATTGAAAATGTCTTGCATGTCAACGATCTTAAGCATATTCTTCTAATAATTAGTCAATTATGT
66 TTATTGAAAATGTCTTGCATGTCAACGATCTTAAGCATATTCTTCTAATAATTAGTCAATTATGT
*
23750393 GATAAAGGTTTCAATGTCATATTTGAGTCTAAATGTTGTAAAGCTATTGACATTGCTTTTAATAA
131 GATAAAGGTTTCAATGTCATATTTGAGTCTAAATGTTGTAAAGCTATTGACATTGCTTCTAATAA
23750458 GATTATGCTTGTAGGACATAGGATAGAAAATATATATTTGGTGCATTTAGATGATATGCATAACT
196 GATTATGCTTGTAGGACATAGGATAGAAAATATATATTTGGTGCATTTAGATGATATGCATAACT
23750523 CTAGATTATCCCTTATTGCTAAAAATAAGAATAGCTCTTTATTATGGCATAGAAAACTAGGACAA
261 CTAGATTATCCCTTATTGCTAAAAATAAGAATAGCTCTTTATTATGGCATAGAAAACTAGGACAA
23750588 GGTAGCATGAGCGTATTGCATAAATTAGTTAAAAATGACTTAGCAAGAGGATTACCTAAAATTGA
326 GGTAGCATGAGCGTATTGCATAAATTAGTTAAAAATGACTTAGCAAGAGGATTACCTAAAATTGA
23750653 CTTTGATGTGAATTATATTTGTGATGCTTGTATTAAGGGTAAACATAAAAAAGTGTCTTGTAAAA
391 CTTTGATGTGAATTATATTTGTGATGCTTGTATTAAGGGTAAACATAAAAAAGTGTCTTGTAAAA
23750718 AC
456 AC
23750720 ATTTGGTGACAACTTTACAAAACAAATGGAAGGAATAGGCTCTATTGGTAAAAATTCTTCTATCA
1 ATTTGGTGACAACTTTACAAAACAAATGGAAGGAATAGGCTCTATTGGTAAAAATTCTTCTATCA
*
23750785 TTATTGAAAATGTCTTGCATGTCAACGGTCTTAAGCATATTCTTCTAATAATTAGTCAATTATGT
66 TTATTGAAAATGTCTTGCATGTCAACGATCTTAAGCATATTCTTCTAATAATTAGTCAATTATGT
* *
23750850 GATAAAGGTTTCAATGTTATATTTGAGTCTAAATGTTGTAAAGTTATTGACATTGCTTCTAATAA
131 GATAAAGGTTTCAATGTCATATTTGAGTCTAAATGTTGTAAAGCTATTGACATTGCTTCTAATAA
23750915 GATTATGCTTGTAGGACATAGGATAGAAAATATATATTTGGTGCATTTAGATGATATGCATAACT
196 GATTATGCTTGTAGGACATAGGATAGAAAATATATATTTGGTGCATTTAGATGATATGCATAACT
* *
23750980 CTAGCTTTTCCCTTATTGCTAAAAATAAGAATAGCTCTTTATTATGGCATAGAAAACTAGGACAA
261 CTAGATTATCCCTTATTGCTAAAAATAAGAATAGCTCTTTATTATGGCATAGAAAACTAGGACAA
23751045 GGTAGCATGAGCGTATTGCATAAATTAGTTAAAAATGACTTAGCAAGAGGATTACCTAAAATTGA
326 GGTAGCATGAGCGTATTGCATAAATTAGTTAAAAATGACTTAGCAAGAGGATTACCTAAAATTGA
23751110 CTTTGATGTGAATT
391 CTTTGATGTGAATT
23751124 CTTTTAAACC
Statistics
Matches: 398, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
457 398 1.00
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (457 bp):
ATTTGGTGACAACTTTACAAAACAAATGGAAGGAATAGGCTCTATTGGTAAAAATTCTTCTATCA
TTATTGAAAATGTCTTGCATGTCAACGATCTTAAGCATATTCTTCTAATAATTAGTCAATTATGT
GATAAAGGTTTCAATGTCATATTTGAGTCTAAATGTTGTAAAGCTATTGACATTGCTTCTAATAA
GATTATGCTTGTAGGACATAGGATAGAAAATATATATTTGGTGCATTTAGATGATATGCATAACT
CTAGATTATCCCTTATTGCTAAAAATAAGAATAGCTCTTTATTATGGCATAGAAAACTAGGACAA
GGTAGCATGAGCGTATTGCATAAATTAGTTAAAAATGACTTAGCAAGAGGATTACCTAAAATTGA
CTTTGATGTGAATTATATTTGTGATGCTTGTATTAAGGGTAAACATAAAAAAGTGTCTTGTAAAA
AC
Found at i:23774689 original size:50 final size:50
Alignment explanation
Indices: 23774555--23774747 Score: 145
Period size: 50 Copynumber: 3.7 Consensus size: 50
23774545 ATTTGGGTAA
* * * *
23774555 AGAGATCCCATGTAAGATC-ATGTCTGGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCACGTAAGA-CAATGTCTGGGACATGGCATGGGCA-C--CGAG---ATG
* * * * *
23774611 AGAGGTCCTATGTAAGACAATGTTTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCACGTAAGACAATGTCTGGGACATGGCATGGGCACCGAGATG
* * *
23774661 AGAGGTCCCCCGTAAGACTATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCACGTAAGACAATGTCTGGGACATGGCATGGGCACCGAGATG
** * * * * *
23774711 AGAACTCTCATGTAAGACCATATCTGGGATATGGCAT
1 AGAGGTCCCACGTAAGACAATGTCTGGGACATGGCAT
23774748 TGGAAGTACA
Statistics
Matches: 115, Mismatches: 21, Indels: 8
0.80 0.15 0.06
Matches are distributed among these distances:
50 74 0.64
53 3 0.03
55 2 0.02
56 36 0.31
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (50 bp):
AGAGGTCCCACGTAAGACAATGTCTGGGACATGGCATGGGCACCGAGATG
Found at i:23777227 original size:26 final size:28
Alignment explanation
Indices: 23777184--23777243 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 28
23777174 ATTTCGTATG
*
23777184 ACCATTTCATCTAAACATTTCAC-CAT-
1 ACCATTTCATCTAAACATTTAACTCATA
* **
23777210 ACCATTTCATTTGCACATTTAACTCATA
1 ACCATTTCATCTAAACATTTAACTCATA
23777238 ACCATT
1 ACCATT
23777244 CTGTATATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 19 0.68
27 3 0.11
28 6 0.21
ACGTcount: A:0.33, C:0.28, G:0.02, T:0.37
Consensus pattern (28 bp):
ACCATTTCATCTAAACATTTAACTCATA
Found at i:23777606 original size:20 final size:20
Alignment explanation
Indices: 23777563--23777660 Score: 79
Period size: 20 Copynumber: 4.9 Consensus size: 20
23777553 GATGCGTAAC
* * * *
23777563 AGAGGCATCGAAGTGCAGAC
1 AGAGGCACCAAAGTGCAAAT
* ** *
23777583 AGAGGCACTACTGTGCAATT
1 AGAGGCACCAAAGTGCAAAT
23777603 AGAGGCACCAAAGTGCAAAT
1 AGAGGCACCAAAGTGCAAAT
* * *
23777623 AGAGGCACCGAAGTGTAAAC
1 AGAGGCACCAAAGTGCAAAT
* *
23777643 AAAGGCACTAAAGTGCAA
1 AGAGGCACCAAAGTGCAA
23777661 TCCCGTACAA
Statistics
Matches: 59, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.40, C:0.19, G:0.28, T:0.13
Consensus pattern (20 bp):
AGAGGCACCAAAGTGCAAAT
Found at i:23779429 original size:14 final size:14
Alignment explanation
Indices: 23779410--23779440 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
23779400 TCTTGAGTTA
23779410 TAATATCCCATAAT
1 TAATATCCCATAAT
23779424 TAATATCCCATAAT
1 TAATATCCCATAAT
23779438 TAA
1 TAA
23779441 GTGGTGTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.35
Consensus pattern (14 bp):
TAATATCCCATAAT
Found at i:23781728 original size:16 final size:17
Alignment explanation
Indices: 23781707--23781770 Score: 87
Period size: 16 Copynumber: 3.7 Consensus size: 17
23781697 TATGAACCAC
23781707 TCCATTTACTTAT-CAT
1 TCCATTTACTTATCCAT
23781723 TCCATTTACTTACTTTCCAT
1 TCCATTTACTTA---TCCAT
23781743 TCCATTTACTT-TCCAT
1 TCCATTTACTTATCCAT
23781759 TCCATTTACTTA
1 TCCATTTACTTA
23781771 GCATAAGCTT
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
16 28 0.65
19 1 0.02
20 14 0.33
ACGTcount: A:0.22, C:0.28, G:0.00, T:0.50
Consensus pattern (17 bp):
TCCATTTACTTATCCAT
Found at i:23792842 original size:28 final size:28
Alignment explanation
Indices: 23792801--23792861 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
23792791 ATTGTACTGT
*
23792801 ACTGTTACTGTATTGGGCTAAGGCCCAC
1 ACTGTTACTATATTGGGCTAAGGCCCAC
23792829 ACTGTTACTATATTGGGCTAAGGCCCAC
1 ACTGTTACTATATTGGGCTAAGGCCCAC
23792857 ACTGT
1 ACTGT
23792862 ACTGTTACTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.30
Consensus pattern (28 bp):
ACTGTTACTATATTGGGCTAAGGCCCAC
Found at i:23792880 original size:33 final size:31
Alignment explanation
Indices: 23792796--23792880 Score: 97
Period size: 28 Copynumber: 2.8 Consensus size: 31
23792786 GCATTATTGT
*
23792796 ACTGTACTGTTACTGTATTGGGCTAAGGCCC
1 ACTGTACTGTTACTGAATTGGGCTAAGGCCC
23792827 AC---ACTGTTACT-ATATTGGGCTAAGGCCCAC
1 ACTGTACTGTTACTGA-ATTGGGCTAAGG-CC-C
*
23792857 ACTGTACTGTTACTGAATAGGGCT
1 ACTGTACTGTTACTGAATTGGGCT
23792881 CAAGCCTAGT
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
28 21 0.47
29 2 0.04
30 3 0.07
31 2 0.04
33 16 0.36
34 1 0.02
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.31
Consensus pattern (31 bp):
ACTGTACTGTTACTGAATTGGGCTAAGGCCC
Found at i:23798503 original size:20 final size:20
Alignment explanation
Indices: 23798460--23798510 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
23798450 TTGCACTGCA
*
23798460 GTGCCTCTGCTTGCACAATC
1 GTGCCTCTGTTTGCACAATC
** *
23798480 GTGCCTCTGTTTGCACTTTG
1 GTGCCTCTGTTTGCACAATC
23798500 GTGCCTCTGTT
1 GTGCCTCTGTT
23798511 ATTATCTATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.08, C:0.29, G:0.24, T:0.39
Consensus pattern (20 bp):
GTGCCTCTGTTTGCACAATC
Found at i:23799543 original size:28 final size:28
Alignment explanation
Indices: 23799511--23799565 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
23799501 AAAATGTCAA
*
23799511 CAATTACAAAACCATATATACATGCCAT
1 CAATTACAAAACCACATATACATGCCAT
*
23799539 CAATTATAAAACCACATATACATGCCA
1 CAATTACAAAACCACATATACATGCCA
23799566 ACATAACAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.47, C:0.25, G:0.04, T:0.24
Consensus pattern (28 bp):
CAATTACAAAACCACATATACATGCCAT
Found at i:23800661 original size:21 final size:19
Alignment explanation
Indices: 23800615--23800653 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
23800605 CTAAATGAAT
*
23800615 AAATTCAATTCATTCAATA
1 AAATTCTATTCATTCAATA
23800634 ATAATTCTATTCAATTCAAT
1 A-AATTCTATTC-ATTCAAT
23800654 CCAAATTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 9 0.53
21 7 0.41
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (19 bp):
AAATTCTATTCATTCAATA
Found at i:23805160 original size:26 final size:26
Alignment explanation
Indices: 23805126--23805176 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
23805116 ATATAAAATT
*
23805126 TATAATATATA-ACTTTTATAAATAAA
1 TATAATATA-ACACCTTTATAAATAAA
*
23805152 TATATTATAACACCTTTATAAATAA
1 TATAATATAACACCTTTATAAATAA
23805177 TATTTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (26 bp):
TATAATATAACACCTTTATAAATAAA
Found at i:23809070 original size:17 final size:17
Alignment explanation
Indices: 23809039--23809082 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
23809029 TTAAATAATA
*
23809039 TATAAAATCTAATAAACTT
1 TATAAAAT-TTATAAA-TT
23809058 TA-AAAATTTATAAATT
1 TATAAAATTTATAAATT
23809074 TATAAAATT
1 TATAAAATT
23809083 AAAATAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 4 0.17
17 12 0.52
18 5 0.22
19 2 0.09
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (17 bp):
TATAAAATTTATAAATT
Found at i:23814530 original size:18 final size:18
Alignment explanation
Indices: 23814503--23814540 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
23814493 TCCCGAATAT
23814503 CTATCCAACTCAAATTTA
1 CTATCCAACTCAAATTTA
* *
23814521 CTATCTAACTCAGATTTA
1 CTATCCAACTCAAATTTA
23814539 CT
1 CT
23814541 TTTCAAGCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (18 bp):
CTATCCAACTCAAATTTA
Found at i:23816035 original size:22 final size:22
Alignment explanation
Indices: 23816010--23816055 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
23816000 AAATTTTAAA
23816010 ATTTCAATATAATCAT-GCATAT
1 ATTTCAATATAAT-ATAGCATAT
*
23816032 ATTTCAATCTAATATAGCATAT
1 ATTTCAATATAATATAGCATAT
23816054 AT
1 AT
23816056 CGAAACATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.41, C:0.13, G:0.04, T:0.41
Consensus pattern (22 bp):
ATTTCAATATAATATAGCATAT
Found at i:23819596 original size:29 final size:29
Alignment explanation
Indices: 23819553--23819608 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
23819543 CAGCCAAGCA
* * *
23819553 AATTAATTAATTTTTTTTAATTAAATATT
1 AATTAATTAAATTTTCTAAATTAAATATT
23819582 AATTAATTAAATTTTCTAAATTAAATA
1 AATTAATTAAATTTTCTAAATTAAATA
23819609 AAGGAAAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (29 bp):
AATTAATTAAATTTTCTAAATTAAATATT
Found at i:23820884 original size:32 final size:32
Alignment explanation
Indices: 23820821--23820889 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
23820811 ATATTTACCA
*
23820821 ATATTGATGTGTTTATTTGTATCATTTTGAAT
1 ATATTGATGTGTTTATTTGTATCATTATGAAT
* *
23820853 TTATTGATGTTTTTATTT-TCA-CATATATGAAT
1 ATATTGATGTGTTTATTTGT-ATCAT-TATGAAT
23820885 ATATT
1 ATATT
23820890 TATAATCTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
31 4 0.13
32 27 0.87
ACGTcount: A:0.28, C:0.04, G:0.12, T:0.57
Consensus pattern (32 bp):
ATATTGATGTGTTTATTTGTATCATTATGAAT
Found at i:23825339 original size:24 final size:22
Alignment explanation
Indices: 23825306--23825353 Score: 69
Period size: 24 Copynumber: 2.1 Consensus size: 22
23825296 TTATCAAATA
23825306 TAAAAGTAAAATAAGTTATATATT
1 TAAAAGTAAAATAA-TTATA-ATT
*
23825330 TAAAATTAAAATAATTATAATT
1 TAAAAGTAAAATAATTATAATT
23825352 TA
1 TA
23825354 TTTGAATCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.22
23 5 0.22
24 13 0.57
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (22 bp):
TAAAAGTAAAATAATTATAATT
Found at i:23828461 original size:29 final size:31
Alignment explanation
Indices: 23828410--23828467 Score: 93
Period size: 29 Copynumber: 1.9 Consensus size: 31
23828400 TGAAAATATT
*
23828410 AAAATTATTAAAATTATTTTTAAAAAAATAA
1 AAAATTATTAAAATTATTCTTAAAAAAATAA
23828441 AAAATT-TTAAAATT-TTCTTAAAAAAAT
1 AAAATTATTAAAATTATTCTTAAAAAAAT
23828468 GAAATTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 12 0.46
30 8 0.31
31 6 0.23
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (31 bp):
AAAATTATTAAAATTATTCTTAAAAAAATAA
Found at i:23828539 original size:22 final size:22
Alignment explanation
Indices: 23828509--23828550 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
23828499 ATTTGGAGAT
*
23828509 TTTTTGAAGGAAATTGAGAGGA
1 TTTTGGAAGGAAATTGAGAGGA
*
23828531 TTTTGGAAGGAATTTGAGAG
1 TTTTGGAAGGAAATTGAGAG
23828551 TTTGAGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (22 bp):
TTTTGGAAGGAAATTGAGAGGA
Found at i:23828571 original size:52 final size:51
Alignment explanation
Indices: 23828500--23828602 Score: 129
Period size: 52 Copynumber: 2.0 Consensus size: 51
23828490 TTAATATGGA
* * *
23828500 TTTGGAGATTTTTTGAAGGAAATTGAGAG-GATTTTGGAA-GGAATTTGAGAG
1 TTTGGAGAATTTTGGAAGGAAATTGAGAGAAATTTT-GAAGGGAA-TTGAGAG
*
23828551 TTTGAGAGAATTTTGGAAGGAAATTGATAGAAATTTTGAAGGGAATTGAGAG
1 TTTG-GAGAATTTTGGAAGGAAATTGAGAGAAATTTTGAAGGGAATTGAGAG
23828603 AAATTTTGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
51 4 0.09
52 32 0.71
53 9 0.20
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.33
Consensus pattern (51 bp):
TTTGGAGAATTTTGGAAGGAAATTGAGAGAAATTTTGAAGGGAATTGAGAG
Found at i:23828577 original size:22 final size:23
Alignment explanation
Indices: 23828552--23828643 Score: 111
Period size: 22 Copynumber: 4.2 Consensus size: 23
23828542 ATTTGAGAGT
23828552 TTGAGAG-AATTTTGGAAGGAAA
1 TTGAGAGAAATTTTGGAAGGAAA
* *
23828574 TTGATAGAAATTTT-GAAGGGAA
1 TTGAGAGAAATTTTGGAAGGAAA
*
23828596 TTGAGAGAAATTTTGAAAGG-AA
1 TTGAGAGAAATTTTGGAAGGAAA
* *
23828618 TTGAGAG-AATTTTTGAAAGAAA
1 TTGAGAGAAATTTTGGAAGGAAA
23828640 TTGA
1 TTGA
23828644 TATTGAATTT
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
21 9 0.15
22 41 0.68
23 10 0.17
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.30
Consensus pattern (23 bp):
TTGAGAGAAATTTTGGAAGGAAA
Found at i:23828601 original size:44 final size:44
Alignment explanation
Indices: 23828552--23828643 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 44
23828542 ATTTGAGAGT
* * * *
23828552 TTGAGAG-AATTTTGGAAGGAAATTGATAGAAATTTTGAAGGGAA
1 TTGAGAGAAATTTTGAAAGG-AATTGAGAGAAATTTTGAAAGAAA
*
23828596 TTGAGAGAAATTTTGAAAGGAATTGAGAGAATTTTTGAAAGAAA
1 TTGAGAGAAATTTTGAAAGGAATTGAGAGAAATTTTGAAAGAAA
23828640 TTGA
1 TTGA
23828644 TATTGAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 31 0.74
45 11 0.26
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.30
Consensus pattern (44 bp):
TTGAGAGAAATTTTGAAAGGAATTGAGAGAAATTTTGAAAGAAA
Found at i:23830164 original size:4 final size:4
Alignment explanation
Indices: 23830155--23830180 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
23830145 GTTTAAGTAC
23830155 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
23830181 CTTTATGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:23832398 original size:20 final size:20
Alignment explanation
Indices: 23832373--23832425 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 20
23832363 TATTAGATTA
*
23832373 AAAAATTGTAAACA-TTTATT
1 AAAAATTGTAAA-AGTATATT
*
23832393 AAAAATCG-AAAAGTATATT
1 AAAAATTGTAAAAGTATATT
23832412 AAAAATTTGTAAAA
1 AAAAA-TTGTAAAA
23832426 AGAAAATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 1 0.04
19 13 0.48
20 9 0.33
21 4 0.15
ACGTcount: A:0.57, C:0.04, G:0.08, T:0.32
Consensus pattern (20 bp):
AAAAATTGTAAAAGTATATT
Done.