Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A08
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: 119882356
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2655529 characters in sequence are not A, C, G, or T
File 120 of 362
Found at i:39630425 original size:99 final size:99
Alignment explanation
Indices: 39630218--39630446 Score: 273
Period size: 99 Copynumber: 2.3 Consensus size: 99
39630208 TATTGTGAGG
* * * **
39630218 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATGGTCGCATGTGTAGTACTA
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATAATGGTAACATGTGTAGTACTA
* *
39630283 AGTGCAGGCTACTATGCGTACCCGATAACTTCGA
66 AGTCCAGGCTACTACGCGTACCCGATAACTTCGA
* * ** * *
39630317 TCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTATCAGATGGTTAGGTAACGTGTGTAGTGC
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGAT-AAT-GGTAACATGTGTAGTAC
* * *
39630382 TAAGTCCAGGCTACTACGTGTACCGGATAA-TT-GG
64 TAAGTCCAGGCTACTACGCGTACCCGATAACTTCGA
*
39630416 TCGCATGTGTAGTACTAAGTGCAGGCTACTA
1 TCACATGTGTAGTACTAAGTGCAGGCTACTA
39630447 TGCGTACTAG
Statistics
Matches: 112, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
99 70 0.62
100 3 0.03
101 39 0.35
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.28
Consensus pattern (99 bp):
TCACATGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATAATGGTAACATGTGTAGTACTA
AGTCCAGGCTACTACGCGTACCCGATAACTTCGA
Found at i:39634526 original size:18 final size:19
Alignment explanation
Indices: 39634496--39634532 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
39634486 AGTATTAAAG
39634496 AAAAAAAATAT-AAATCCC
1 AAAAAAAATATAAAATCCC
39634514 AAAATAAAA-ATAAAATCCC
1 AAAA-AAAATATAAAATCCC
39634533 GAGAGGCCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (19 bp):
AAAAAAAATATAAAATCCC
Found at i:39636105 original size:21 final size:22
Alignment explanation
Indices: 39636079--39636119 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
39636069 CACTTGGCAC
*
39636079 AGGGGC-ACACGCCCGTGTGGG
1 AGGGGCGACACGCCCATGTGGG
*
39636100 AGGGGCGACACTCCCATGTG
1 AGGGGCGACACGCCCATGTG
39636120 ACCAATTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.17, C:0.29, G:0.41, T:0.12
Consensus pattern (22 bp):
AGGGGCGACACGCCCATGTGGG
Found at i:39637313 original size:47 final size:44
Alignment explanation
Indices: 39637239--39637508 Score: 213
Period size: 47 Copynumber: 5.8 Consensus size: 44
39637229 GTGGGTAAGG
* *
39637239 TGCCGATGCCATGTCCTAGACACGGTCTTACACTAGCTCATATCTCA
1 TGCCGATG-CATGTCCCAGACA-TGTCTTACACTAGCTC-TATCTCA
* * * **
39637286 TGTCGATGCCATGTCCCAGACATGGTCTTACACTAACTATCATCTTG
1 TGCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCT-ATCTCA
*
39637333 TAGCCGATGCATGTCCTAGACATGTCTTACAC-AGGC-CTACGTCTCGA
1 T-GCCGATGCATGTCCCAGACATGTCTTACACTA-GCTCTA--TCTC-A
* * *
39637380 GGCCGATGCATGTCCCAGACATGTCTTACACTAGCACTCGTCTCGA
1 TGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCT-ATCTC-A
* * * *
39637426 CGCCGATGCGATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-G
1 TGCCGATGC-ATGTCCCAGACAT-GTCTTACACTAGCTCT-AT-CTCA
*
39637473 TGGCTGATGCATGTCCCAGACATGTCTTACACTAGC
1 T-GCCGATGCATGTCCCAGACATGTCTTACACTAGC
39637509 CCACAATAAC
Statistics
Matches: 184, Mismatches: 25, Indels: 29
0.77 0.11 0.12
Matches are distributed among these distances:
44 1 0.01
45 2 0.01
46 71 0.39
47 80 0.43
48 29 0.16
49 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (44 bp):
TGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTATCTCA
Found at i:39637385 original size:46 final size:46
Alignment explanation
Indices: 39637335--39637504 Score: 202
Period size: 46 Copynumber: 3.7 Consensus size: 46
39637325 TCATCTTGTA
*
39637335 GCCGATGCATGTCCTAGACATGTCTTACACAGGC-CTACGTCTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACAGGCACT-CGTCTCGAG
*
39637381 GCCGATGCATGTCCCAGACATGTCTTACACTA-GCACTCGTCTCGAC
1 GCCGATGCATGTCCCAGACATGTCTTACAC-AGGCACTCGTCTCGAG
* * * * *
39637427 GCCGATGCGATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GTG
1 GCCGATGC-ATGTCCCAGACAT-GTCTTACACAGGCACTCGT-CTCGAG
*
39637475 GCTGATGCATGTCCCAGACATGTCTTACAC
1 GCCGATGCATGTCCCAGACATGTCTTACAC
39637505 TAGCCCACAA
Statistics
Matches: 109, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
46 56 0.51
47 29 0.27
48 23 0.21
49 1 0.01
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.25
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACATGTCTTACACAGGCACTCGTCTCGAG
Found at i:39637495 original size:94 final size:91
Alignment explanation
Indices: 39637240--39637508 Score: 269
Period size: 94 Copynumber: 2.9 Consensus size: 91
39637230 TGGGTAAGGT
* * * * *
39637240 GCCGATGCCATGTCCTAGACACGGTCTTACACTAGCTCAT-ATCTCATGTCGATGCCATGTCCCA
1 GCCGATG-CATGTCCTAGACATGGTCTTACACTGGCTC-TCATAT-GTGGCGATG-CATGTCCCA
* *
39637304 GACATGGTCTTACACTAACTATCATCTTGTA
62 GACAT-GTCTTACACTAGCTATCATCTCGTA
* * * *
39637335 GCCGATGCATGTCCTAGACAT-GTCTTACACAGGC-CTACGTCTCGAGGCCGATGCATGTCCCAG
1 GCCGATGCATGTCCTAGACATGGTCTTACACTGGCTCT-CATAT-GTGG-CGATGCATGTCCCAG
*
39637398 ACATGTCTTACACTAGC-ACTCGTCTCG-A
63 ACATGTCTTACACTAGCTA-TCATCTCGTA
*
39637426 CGCCGATGCGATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCTGATGCATGTCCCA
1 -GCCGATGC-ATGTCCTAGACATGGTCTTACACTGGCTCTCAT-ATGTGGC-GATGCATGTCCCA
39637491 GACATGTCTTACACTAGC
62 GACATGTCTTACACTAGC
39637509 CCACAATAAC
Statistics
Matches: 149, Mismatches: 15, Indels: 21
0.81 0.08 0.11
Matches are distributed among these distances:
91 3 0.02
92 27 0.18
93 43 0.29
94 66 0.44
95 10 0.07
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (91 bp):
GCCGATGCATGTCCTAGACATGGTCTTACACTGGCTCTCATATGTGGCGATGCATGTCCCAGACA
TGTCTTACACTAGCTATCATCTCGTA
Found at i:39637500 original size:140 final size:141
Alignment explanation
Indices: 39637240--39637504 Score: 356
Period size: 140 Copynumber: 1.9 Consensus size: 141
39637230 TGGGTAAGGT
* * * *
39637240 GCCGATGCCATGTCCTAGACACGGTCTTACACTAGCTCATATCTCATGTCGATGCCATGTCCCAG
1 GCCGATGCCATGTCCCAGACACGGTCTTACACTAGCACATATCTCACGCCGATGCCATGTCCCAG
** *
39637305 ACATGGTCTTACACTAACTATCATCTTGTAGCCGATGCATGTCCTAGACATGTCTTACACAGGCC
66 ACATGGTCTTACACTAACTATCATAATGTAGCCGATGCATGTCCCAGACATGTCTTACACAGGCC
39637370 TACGTCTCGAG
131 TACGTCTCGAG
* * *
39637381 GCCGATG-CATGTCCCAGACA-TGTCTTACACTAGCAC-TCGTCTCGACGCCGATGCGATGTCCC
1 GCCGATGCCATGTCCCAGACACGGTCTTACACTAGCACAT-ATCTC-ACGCCGATGCCATGTCCC
** * * *
39637443 AGACATGGTCTTACACTGGCTCTCATAATGTGGCTGATGCATGTCCCAGACATGTCTTACAC
64 AGACATGGTCTTACACTAACTATCATAATGTAGCCGATGCATGTCCCAGACATGTCTTACAC
39637505 TAGCCCACAA
Statistics
Matches: 107, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
138 1 0.01
139 18 0.17
140 81 0.76
141 7 0.07
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (141 bp):
GCCGATGCCATGTCCCAGACACGGTCTTACACTAGCACATATCTCACGCCGATGCCATGTCCCAG
ACATGGTCTTACACTAACTATCATAATGTAGCCGATGCATGTCCCAGACATGTCTTACACAGGCC
TACGTCTCGAG
Found at i:39638739 original size:10 final size:10
Alignment explanation
Indices: 39638724--39638752 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
39638714 TCGAGCTATT
39638724 ACATGGGCCC
1 ACATGGGCCC
39638734 ACATGGGCCC
1 ACATGGGCCC
39638744 ACATGGGCC
1 ACATGGGCC
39638753 GCATTATCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.31, T:0.10
Consensus pattern (10 bp):
ACATGGGCCC
Found at i:39642464 original size:27 final size:27
Alignment explanation
Indices: 39642433--39642501 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 27
39642423 AGACCCGCTT
* *
39642433 TGTGGTAAAATGATTGTATTTCCCTTA
1 TGTGGTAAAATGACTATATTTCCCTTA
* *
39642460 TGTGGTAGAATGACTATTTTTCCCTTA
1 TGTGGTAAAATGACTATATTTCCCTTA
* * *
39642487 TATGCTAAGATGACT
1 TGTGGTAAAATGACT
39642502 GTTTTGCCCC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (27 bp):
TGTGGTAAAATGACTATATTTCCCTTA
Found at i:39642858 original size:19 final size:19
Alignment explanation
Indices: 39642834--39642871 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
39642824 TGGGTAGAAC
*
39642834 CTGTATACTTCACCGTTTA
1 CTGTATACTACACCGTTTA
*
39642853 CTGTATACTACACTGTTTA
1 CTGTATACTACACCGTTTA
39642872 TTGCTACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.42
Consensus pattern (19 bp):
CTGTATACTACACCGTTTA
Found at i:39643867 original size:46 final size:46
Alignment explanation
Indices: 39643770--39643892 Score: 133
Period size: 46 Copynumber: 2.6 Consensus size: 46
39643760 ATTGTGGGCT
* * *
39643770 AGTGTAATACATGTCTGGGACATGCATGGGCCTCGAGACGTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAAACGTAAGCC
* **
39643816 TGTGTAAGACATGTCTGGGACATGCATCGG-CTATTAAACG-ATAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAAACGTA-AGCC
*
39643862 AGTGTAAGTCCATGTCTGGGACATGGCATCG
1 AGTGTAAG-ACATGTCTGGGACAT-GCATCG
39643893 ACATGAGATA
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
45 3 0.05
46 42 0.65
47 14 0.22
48 6 0.09
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAAACGTAAGCC
Found at i:39654642 original size:112 final size:112
Alignment explanation
Indices: 39654491--39654713 Score: 365
Period size: 112 Copynumber: 2.0 Consensus size: 112
39654481 TCTGCTCGTG
* * *
39654491 TGTTTACTACCATGCATGTTAACCTAAAATTCAAGGTGCAGGGGACACACGGCTGAACGACATGC
1 TGTTTACTACCATGCATGTTAACCTAAAATTCAAGGTGCAGGGGACACACGGCCGAACGAAACGC
* * *
39654556 CCATGGCGCTGACCGTGTGTCATACATGGCCTAGACACGTGCCCGTA
66 CCATGGCGCTGACCGTGTGTCACACACGGCCTAGACACATGCCCGTA
* *
39654603 TGTTTACTACCATGCATGTTAACCTAAAATTTAGGGTGCAGGGGACACACGGCCGAACGAAACGC
1 TGTTTACTACCATGCATGTTAACCTAAAATTCAAGGTGCAGGGGACACACGGCCGAACGAAACGC
*
39654668 CCATGGGGCTGACCGTGTGTCACACACGGCCTAGACACATGCCCGT
66 CCATGGCGCTGACCGTGTGTCACACACGGCCTAGACACATGCCCGT
39654714 GTATCTACCC
Statistics
Matches: 102, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
112 102 1.00
ACGTcount: A:0.26, C:0.27, G:0.26, T:0.21
Consensus pattern (112 bp):
TGTTTACTACCATGCATGTTAACCTAAAATTCAAGGTGCAGGGGACACACGGCCGAACGAAACGC
CCATGGCGCTGACCGTGTGTCACACACGGCCTAGACACATGCCCGTA
Found at i:39665660 original size:21 final size:21
Alignment explanation
Indices: 39665634--39665687 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
39665624 CTGTCTGAAT
*
39665634 CTATTTTATGGTAAATTTTAC
1 CTATTTCATGGTAAATTTTAC
39665655 CTATTTCATGGTAAATTTTAC
1 CTATTTCATGGTAAATTTTAC
39665676 CTATTTCATGGT
1 CTATTTCATGGT
39665688 TTCCATGGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.26, C:0.13, G:0.11, T:0.50
Consensus pattern (21 bp):
CTATTTCATGGTAAATTTTAC
Found at i:39666468 original size:93 final size:93
Alignment explanation
Indices: 39666309--39666480 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
39666299 GCCCATAAGT
* * * *
39666309 GAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGAATCCATAAGTGAACTCGGACTCAACTCAA
*
39666374 CGAGCTCGTATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* *
39666402 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGAATCCATAAGTGAACTCGGACTTAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGAATCCATAAGTGAACTCGGACTCAACTCAA
*
39666467 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
39666481 CAAATATCCT
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGAATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:39666476 original size:46 final size:46
Alignment explanation
Indices: 39666301--39666476 Score: 176
Period size: 46 Copynumber: 3.8 Consensus size: 46
39666291 TGTAACCCGC
* * * *
39666301 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGAAT
* * * *
39666347 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-G-TATGCCTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACAT-TCGA-AT
* *** *
39666393 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGAAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGAAT
* *
39666440 CCATAAGTGAACTCGGACTTAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
39666477 TGCCCAAATA
Statistics
Matches: 104, Mismatches: 21, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
44 1 0.01
45 2 0.02
46 66 0.63
47 30 0.29
48 3 0.03
49 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGAAT
Found at i:39683167 original size:6 final size:6
Alignment explanation
Indices: 39683153--39683201 Score: 62
Period size: 6 Copynumber: 8.0 Consensus size: 6
39683143 AATCCTCTTA
* * *
39683153 TATTCT TATTTT TATTTT TATTTT TATTCT TCTTTT TATTTTT TATTTT
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TA-TTTT TATTTT
39683202 CTTTTCAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
6 31 0.84
7 6 0.16
ACGTcount: A:0.14, C:0.06, G:0.00, T:0.80
Consensus pattern (6 bp):
TATTTT
Found at i:39683188 original size:24 final size:25
Alignment explanation
Indices: 39683153--39683226 Score: 82
Period size: 24 Copynumber: 3.0 Consensus size: 25
39683143 AATCCTCTTA
39683153 TATTCTTATTTTTA-TTTTTATTTT
1 TATTCTTATTTTTATTTTTTATTTT
*
39683177 TATTCTTCTTTTTATTTTTTATTTT
1 TATTCTTATTTTTATTTTTTATTTT
* *
39683202 CT-TT-TCAATTTTATTATTTTATTTT
1 -TATTCTTATTTTTATT-TTTTATTTT
39683227 GAAAGACATA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
24 21 0.49
25 21 0.49
26 1 0.02
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (25 bp):
TATTCTTATTTTTATTTTTTATTTT
Found at i:39683201 original size:12 final size:12
Alignment explanation
Indices: 39683162--39683226 Score: 53
Period size: 12 Copynumber: 5.3 Consensus size: 12
39683152 ATATTCTTAT
39683162 TTTTA-TTTTTA
1 TTTTATTTTTTA
*
39683173 TTTTTATTCTTCT-
1 -TTTTATT-TTTTA
39683186 TTTTATTTTTTA
1 TTTTATTTTTTA
* **
39683198 TTTTCTTTTCAA
1 TTTTATTTTTTA
39683210 TTTTATTATTTTA
1 TTTTATT-TTTTA
39683223 TTTT
1 TTTT
39683227 GAAAGACATA
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
11 3 0.07
12 27 0.66
13 8 0.20
14 3 0.07
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTATTTTTTA
Found at i:39683212 original size:19 final size:18
Alignment explanation
Indices: 39683173--39683226 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 18
39683163 TTTATTTTTA
*
39683173 TTTTTATTCTTCTTTTTAT
1 TTTTTATT-TTCTTTTAAT
39683192 TTTTTATTTTCTTTTCAAT
1 TTTTTATTTTCTTTT-AAT
*
39683211 TTTATTATTTTATTTT
1 TTT-TTATTTTCTTTT
39683227 GAAAGACATA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
18 7 0.23
19 13 0.42
20 11 0.35
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTATTTTCTTTTAAT
Found at i:39686103 original size:13 final size:13
Alignment explanation
Indices: 39686087--39686119 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
39686077 TTTAATTAAA
*
39686087 TTAGTTAATTAGT
1 TTAGATAATTAGT
39686100 TTAGATAATTAGT
1 TTAGATAATTAGT
39686113 TTA-ATAA
1 TTAGATAA
39686120 ACAAACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:39689596 original size:45 final size:46
Alignment explanation
Indices: 39689474--39689735 Score: 250
Period size: 46 Copynumber: 5.6 Consensus size: 46
39689464 GGTAAGATGT
* *
39689474 CGATGCCATGTCCTAGACATGATCTTACACTGAC-TATCATCTCGTAGC
1 CGATG-CATGTCCCAGACATG-TCTTACACTGGCTTA-CATCTCGTAGC
39689522 CGATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTCGTAGC
1 CGATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTCGTAGC
*
39689568 CGATGCA-GTCCCAGACATGTCTTGCACTGGCTTACATCTCG-AGGC
1 CGATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTCGTA-GC
* * * * * *
39689613 TGATTCATGTCACAGACATGTGTTACACTAGC-T-C-TCGTCTTAATGC
1 CGATGCATGTCCCAGACATGTCTTACACTGGCTTACATC-TCGT-A-GC
* * * *
39689659 CGATGCCATGTCCCAGACATGCTCTTACACTGGCTCACATAAT-GTGGT
1 CGATG-CATGTCCCAGACATG-TCTTACACTGGCTTACAT-CTCGTAGC
* *
39689707 CGATGCATGTCACAAACATGTCTTACACT
1 CGATGCATGTCCCAGACATGTCTTACACT
39689736 AGCTCACACT
Statistics
Matches: 179, Mismatches: 23, Indels: 26
0.79 0.10 0.11
Matches are distributed among these distances:
43 2 0.01
44 4 0.02
45 41 0.23
46 64 0.36
47 43 0.24
48 21 0.12
50 2 0.01
51 2 0.01
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.29
Consensus pattern (46 bp):
CGATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTCGTAGC
Found at i:39689726 original size:94 final size:89
Alignment explanation
Indices: 39689474--39689741 Score: 274
Period size: 94 Copynumber: 2.9 Consensus size: 89
39689464 GGTAAGATGT
* * * *
39689474 CGATGCCATGTCCTAGACATGATCTTACACTGACTATCATCTCGTAGCCGATGCATGTCCCAGAC
1 CGATGCCATGTCCCAGACATG-TCTTACACTGGCTA-CATCTCGT-GGCGATGCATGTCACAGAC
*
39689539 ATGTCTTACACTGGCTTACATCTCGTAGC
63 ATGTCTTACACTAGC-T-CATCTCGTAGC
* * *
39689568 CGATG-CA-GTCCCAGACATGTCTTGCACTGGCTTACATCTCGAGGCTGATTCATGTCACAGACA
1 CGATGCCATGTCCCAGACATGTCTTACACTGGC-TACATCTCGTGGC-GATGCATGTCACAGACA
* *
39689631 TGTGTTACACTAGCTC-TCGTCTTAATGC
64 TGTCTTACACTAGCTCATC-TCGT-A-GC
* *
39689659 CGATGCCATGTCCCAGACATGCTCTTACACTGGCTCACATAAT-GTGGTCGATGCATGTCACAAA
1 CGATGCCATGTCCCAGACATG-TCTTACACTGGCT-ACAT-CTCGTGG-CGATGCATGTCACAGA
39689723 CATGTCTTACACTAGCTCA
62 CATGTCTTACACTAGCTCA
39689742 CACTCAAATG
Statistics
Matches: 146, Mismatches: 16, Indels: 23
0.79 0.09 0.12
Matches are distributed among these distances:
88 2 0.01
89 4 0.03
90 4 0.03
91 51 0.35
92 15 0.10
93 15 0.10
94 53 0.36
95 2 0.01
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (89 bp):
CGATGCCATGTCCCAGACATGTCTTACACTGGCTACATCTCGTGGCGATGCATGTCACAGACATG
TCTTACACTAGCTCATCTCGTAGC
Found at i:39697453 original size:25 final size:26
Alignment explanation
Indices: 39697369--39697440 Score: 101
Period size: 26 Copynumber: 2.8 Consensus size: 26
39697359 GAGGAAGTGC
* * *
39697369 AAAAGGGC-TTTGCCCTAGTTTACCG
1 AAAAGGGCTTTTGCCCCAGTTTATCA
*
39697394 AAAAGGACTTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTTGCCCCAGTTTATCA
39697420 AAAAGGGCTTTTGCCCCAGTT
1 AAAAGGGCTTTTGCCCCAGTT
39697441 ATTAAAAGAG
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
25 7 0.17
26 34 0.83
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (26 bp):
AAAAGGGCTTTTGCCCCAGTTTATCA
Found at i:39697736 original size:31 final size:31
Alignment explanation
Indices: 39697657--39697742 Score: 147
Period size: 31 Copynumber: 2.8 Consensus size: 31
39697647 TATTGTTACA
*
39697657 GTAAAGGCTTCGGCCCAATGATATGAATAAT
1 GTAAAGGCTTCGGCCCAGTGATATGAATAAT
*
39697688 GAAAAGGCTTCGGCCCAGTGATATGAATAAT
1 GTAAAGGCTTCGGCCCAGTGATATGAATAAT
39697719 GTAAAGGCTTCGGCCCAGT-ATATG
1 GTAAAGGCTTCGGCCCAGTGATATG
39697743 CTGAGATTGA
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 5 0.10
31 47 0.90
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (31 bp):
GTAAAGGCTTCGGCCCAGTGATATGAATAAT
Found at i:39713617 original size:42 final size:42
Alignment explanation
Indices: 39713553--39713663 Score: 125
Period size: 42 Copynumber: 2.6 Consensus size: 42
39713543 TAGGGTTACC
* * * * *
39713553 GAGACTATGCGTAAAACCATATCTAGGATATGCCATC-ATTAT
1 GAGACTTTGTGTAAGACCATATCTAGGATATGACACCGA-TAT
* *
39713595 GAGACTTTGTGTAAGACAATATCTGGGATATGACACCGATAT
1 GAGACTTTGTGTAAGACCATATCTAGGATATGACACCGATAT
* *
39713637 GAGATTTTGTGTAAGACCATAGCTAGG
1 GAGACTTTGTGTAAGACCATATCTAGG
39713664 CTATTGGCAT
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
42 56 0.98
43 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (42 bp):
GAGACTTTGTGTAAGACCATATCTAGGATATGACACCGATAT
Found at i:39716408 original size:37 final size:37
Alignment explanation
Indices: 39716347--39716455 Score: 173
Period size: 37 Copynumber: 2.9 Consensus size: 37
39716337 AGCTCAGATG
* *
39716347 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
* *
39716384 AAATCTCCACACGTAGTCAGCGGGTCTTACCCAGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
39716421 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
39716456 ATATATTTCC
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 65 1.00
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.22
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:39716726 original size:48 final size:48
Alignment explanation
Indices: 39716602--39716900 Score: 456
Period size: 48 Copynumber: 6.1 Consensus size: 48
39716592 ACACATCGCC
* *
39716602 TACATATTTCACACTAGCCATTCGGTTTTACCACATATACATATCTCATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC--A
* *
39716652 TATATATTTCACATT-GACCATTCGGCTTTACCACATATGCATATCTCA
1 TACATATTTCACATTAG-CCATTCGGCTTTACCACATATACATATCTCA
*
39716700 TACATATTTCACATTAGCCATTCGGCTTTACCATATATACATATCTCATATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC----A
* * *
39716752 TATATATTTCACATTAACCATTCAGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
39716800 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
39716848 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
39716896 TACAT
1 TACAT
39716901 CAATTTCAGC
Statistics
Matches: 229, Mismatches: 14, Indels: 14
0.89 0.05 0.05
Matches are distributed among these distances:
48 142 0.62
49 2 0.01
50 41 0.18
52 44 0.19
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.37
Consensus pattern (48 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
Found at i:39716805 original size:100 final size:98
Alignment explanation
Indices: 39716602--39716900 Score: 494
Period size: 100 Copynumber: 3.1 Consensus size: 98
39716592 ACACATCGCC
* *
39716602 TACATATTTCACACTAGCCATTCGGTTTTACCACATATACATATCTCATATATATATTTCACATT
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACATT
* *
39716667 GACCATTCGGCTTTACCACATATGCATATCTCA
66 AACCATTCGGCTTTACCACATATACATATCTCA
*
39716700 TACATATTTCACATTAGCCATTCGGCTTTACCATATATACATATCTCATATATATATATTTCACA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC--ATATATATATTTCACA
*
39716765 TTAACCATTCAGCTTTACCACATATACATATCTCA
64 TTAACCATTCGGCTTTACCACATATACATATCTCA
*
39716800 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC--ATACATATTTCACATT
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACATT
*
39716863 AGCCATTCGGCTTTACCACATATACATATCTCA
66 AACCATTCGGCTTTACCACATATACATATCTCA
39716896 TACAT
1 TACAT
39716901 CAATTTCAGC
Statistics
Matches: 189, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
96 51 0.27
98 44 0.23
100 94 0.50
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.37
Consensus pattern (98 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACATT
AACCATTCGGCTTTACCACATATACATATCTCA
Found at i:39716843 original size:148 final size:149
Alignment explanation
Indices: 39716605--39716897 Score: 491
Period size: 148 Copynumber: 2.0 Consensus size: 149
39716595 CATCGCCTAC
* * * *
39716605 ATATTTCACACTAGCCATTCGGTTTTACCACATATACATATCTCATATATATATTTCACATTGAC
1 ATATTTCACACTAACCATTCAGCTTTACCACATATACATATCTCA-ATACATATTTCACATTGAC
* *
39716670 CATTCGGCTTTACCACATATGCATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCATA
65 CATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACA
39716735 TATACATATCTCATATATAT
130 TATACATATCTCATATATAT
*
39716755 ATATTTCACATTAACCATTCAGCTTTACCACATATACATATCTC-ATACATATTTCACATT-AGC
1 ATATTTCACACTAACCATTCAGCTTTACCACATATACATATCTCAATACATATTTCACATTGA-C
39716818 CATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACA
65 CATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACA
39716883 TATACATATCTCATA
130 TATACATATCTCATA
39716898 CATCAATTTC
Statistics
Matches: 135, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
147 1 0.01
148 94 0.70
150 40 0.30
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.37
Consensus pattern (149 bp):
ATATTTCACACTAACCATTCAGCTTTACCACATATACATATCTCAATACATATTTCACATTGACC
ATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACAT
ATACATATCTCATATATAT
Found at i:39719705 original size:42 final size:42
Alignment explanation
Indices: 39719654--39719767 Score: 131
Period size: 43 Copynumber: 2.7 Consensus size: 42
39719644 GTTGAGATTA
* * *
39719654 CATGTAAGACCATATCTGGGATATGGCATCGATATGAGATT-T
1 CATGGAAGACCATATCTGGGATATGGCATCAATATGAG-TTCC
** * *
39719696 TTTGGAAGACCATAGCTGGGCTATTGGCATCAATATGAGTTCC
1 CATGGAAGACCATATCTGGGATA-TGGCATCAATATGAGTTCC
*
39719739 CATGTAAGACCATATCTGGGATATGGCAT
1 CATGGAAGACCATATCTGGGATATGGCAT
39719768 TGGTATGGTA
Statistics
Matches: 58, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
42 26 0.45
43 32 0.55
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.30
Consensus pattern (42 bp):
CATGGAAGACCATATCTGGGATATGGCATCAATATGAGTTCC
Found at i:39719748 original size:43 final size:42
Alignment explanation
Indices: 39719646--39719767 Score: 147
Period size: 42 Copynumber: 2.9 Consensus size: 42
39719636 TAGGGTTAGT
* *
39719646 TGAGATTACATGTAAGACCATATCTGGGATATGGCATCGATA
1 TGAGATTCCATGTAAGACCATATCTGGGATATGGCATCAATA
*** * * *
39719688 TGAGATTTTTTGGAAGACCATAGCTGGGCTATTGGCATCAATA
1 TGAGATTCCATGTAAGACCATATCTGGGATA-TGGCATCAATA
39719731 TGAG-TTCCCATGTAAGACCATATCTGGGATATGGCAT
1 TGAGATT-CCATGTAAGACCATATCTGGGATATGGCAT
39719768 TGGTATGGTA
Statistics
Matches: 65, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
42 33 0.51
43 32 0.49
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (42 bp):
TGAGATTCCATGTAAGACCATATCTGGGATATGGCATCAATA
Found at i:39720512 original size:15 final size:15
Alignment explanation
Indices: 39720484--39720517 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
39720474 GTAATTGATG
*
39720484 TGTGGATGACTTGGT
1 TGTGGATGAATTGGT
*
39720499 TGTGGTTGAATTGGT
1 TGTGGATGAATTGGT
39720514 TGTG
1 TGTG
39720518 TGTATATACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.03, G:0.41, T:0.44
Consensus pattern (15 bp):
TGTGGATGAATTGGT
Found at i:39732148 original size:49 final size:50
Alignment explanation
Indices: 39732023--39732155 Score: 157
Period size: 49 Copynumber: 2.7 Consensus size: 50
39732013 TATGAGATGT
*
39732023 GTCAGTGTAAGACCATGTCTGGGACATGGCATCGACACAGATATGTGAGA
1 GTCAGTGTAAGACCATGTCTGGGACATGGCATCGACACAGATATGCGAGA
* * * * *
39732073 G-CTAGTGTAAGACCATGTCTGAGACATGGCGTCAGCCTC-GACT-T-CGATA
1 GTC-AGTGTAAGACCATGTCTGGGACATGGCATC-GACACAGA-TATGCGAGA
39732122 GTCAGTGTAAGACCATGTCTGGGACATGGCATCG
1 GTCAGTGTAAGACCATGTCTGGGACATGGCATCG
39732156 GCATTATGCC
Statistics
Matches: 71, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
48 1 0.01
49 33 0.46
50 33 0.46
51 4 0.06
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.23
Consensus pattern (50 bp):
GTCAGTGTAAGACCATGTCTGGGACATGGCATCGACACAGATATGCGAGA
Found at i:39736731 original size:42 final size:42
Alignment explanation
Indices: 39736672--39736826 Score: 154
Period size: 42 Copynumber: 3.7 Consensus size: 42
39736662 CCGAGACTAT
* *
39736672 GTGTAAAACCATATCTGGGATATGGCATC-ATTATGAGACTTC
1 GTGTAAGACCATATCTGGGATATGGCATCGA-TATCAGACTTC
* * * *
39736714 GTGTAAGTCCATTTCTGGGGTATGGCATCGATATCAGATTTC
1 GTGTAAGACCATATCTGGGATATGGCATCGATATCAGACTTC
* * * *
39736756 GTGTAAGACCATAGCTGGGCTATTAGCATCGATA-CGAGA-TCCC
1 GTGTAAGACCATATCTGGGATA-TGGCATCGATATC-AGACT-TC
*
39736799 ATGTAAGACCATATCTGGGATATGGCAT
1 GTGTAAGACCATATCTGGGATATGGCAT
39736827 TGGTGTGGTA
Statistics
Matches: 93, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
42 59 0.63
43 34 0.37
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.30
Consensus pattern (42 bp):
GTGTAAGACCATATCTGGGATATGGCATCGATATCAGACTTC
Found at i:39737789 original size:24 final size:23
Alignment explanation
Indices: 39737728--39737796 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 23
39737718 AAAGGATATG
*
39737728 TAATGCTCTCCTTTAAATGATGTA
1 TAATGCTCT-CTTTAAGTGATGTA
39737752 -ACA-GCTC-CTTTAAGTGATGTA
1 TA-ATGCTCTCTTTAAGTGATGTA
*
39737773 TAATGCTCTTCTTTAAGTAATGTA
1 TAATGCTC-TCTTTAAGTGATGTA
39737797 ACAGTCACAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
21 14 0.37
22 5 0.13
23 5 0.13
24 14 0.37
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (23 bp):
TAATGCTCTCTTTAAGTGATGTA
Found at i:39743287 original size:17 final size:17
Alignment explanation
Indices: 39743254--39743305 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
39743244 AAATAAAGAC
39743254 AAAAAT-AAATGCTAAAAT
1 AAAAATAAAATG--AAAAT
*
39743272 AAAAATAAAATGAAAAG
1 AAAAATAAAATGAAAAT
* *
39743289 AAAATTAAATTGAAAAT
1 AAAAATAAAATGAAAAT
39743306 TAAATGGTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 18 0.62
18 6 0.21
19 5 0.17
ACGTcount: A:0.69, C:0.02, G:0.08, T:0.21
Consensus pattern (17 bp):
AAAAATAAAATGAAAAT
Found at i:39743310 original size:17 final size:17
Alignment explanation
Indices: 39743267--39743310 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
39743257 AATAAATGCT
*
39743267 AAAATAAAAATAAAATG
1 AAAATAAAATTAAAATG
* *
39743284 AAAAGAAAATTAAATTG
1 AAAATAAAATTAAAATG
*
39743301 AAAATTAAAT
1 AAAATAAAAT
39743311 GGTCTCAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (17 bp):
AAAATAAAATTAAAATG
Found at i:39746188 original size:25 final size:27
Alignment explanation
Indices: 39746151--39746203 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
39746141 TCAAACATGC
39746151 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
39746177 ATTTTGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
39746203 A
1 A
39746204 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.40
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:39747265 original size:26 final size:26
Alignment explanation
Indices: 39747234--39747341 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
39747224 TGAAATGCCC
*
39747234 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
39747260 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
39747286 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
39747312 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
39747338 ATCA
1 ATCA
39747342 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:39757377 original size:44 final size:42
Alignment explanation
Indices: 39757289--39757403 Score: 140
Period size: 42 Copynumber: 2.7 Consensus size: 42
39757279 GTGCAGGTTT
* * * *
39757289 CACACGGCCAAGACACACGCCCATGTTCTAGGCTGTGTAGCA
1 CACACGGCTAAGACACACACCCGTGTTCTAGGCCGTGTAGCA
* *
39757331 CACACGGCTGAGACACACACCCGTGTTCTAGGCCGTGTAGCG
1 CACACGGCTAAGACACACACCCGTGTTCTAGGCCGTGTAGCA
* * *
39757373 CACACAGCTAAGACAAACACTCGTGTCTCTA
1 CACACGGCTAAGACACACACCCGTGT-TCTA
39757404 CCCGTATGCT
Statistics
Matches: 62, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
42 58 0.94
43 4 0.06
ACGTcount: A:0.27, C:0.33, G:0.23, T:0.17
Consensus pattern (42 bp):
CACACGGCTAAGACACACACCCGTGTTCTAGGCCGTGTAGCA
Found at i:39765288 original size:40 final size:40
Alignment explanation
Indices: 39765235--39765383 Score: 237
Period size: 40 Copynumber: 3.7 Consensus size: 40
39765225 ACTACTTTCT
39765235 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
39765275 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * * *
39765315 CAAATGCCTTCGGGACTTAGCCCAG-AATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
39765355 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
39765384 CATCCGAATA
Statistics
Matches: 100, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
39 1 0.01
40 98 0.98
41 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:39767118 original size:38 final size:38
Alignment explanation
Indices: 39767047--39767204 Score: 185
Period size: 38 Copynumber: 4.1 Consensus size: 38
39767037 ATTTGATGTG
*
39767047 TATCCGGGCTTAAATACCCGCAGGCTATA-TGCTGAAATTA
1 TATCCGGG-TTAAAT-CCCGCAGGCT-TAGTGCTGGAATTA
* * *
39767087 TATTCGGGTTAAATCCCGTAGGCTTGGTGCTGGTAA-TA
1 TATCCGGGTTAAATCCCGCAGGCTTAGTGCTGG-AATTA
* * *
39767125 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATAA
1 TATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGAATTA
* *
39767163 TATCCGGGTTAAATCCCGCAGGCCTAGTGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGAATTA
39767201 TATC
1 TATC
39767205 TGAGTTTAAT
Statistics
Matches: 103, Mismatches: 12, Indels: 8
0.84 0.10 0.07
Matches are distributed among these distances:
37 2 0.02
38 86 0.83
39 8 0.08
40 7 0.07
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (38 bp):
TATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGAATTA
Found at i:39767146 original size:76 final size:78
Alignment explanation
Indices: 39767047--39767204 Score: 205
Period size: 76 Copynumber: 2.1 Consensus size: 78
39767037 ATTTGATGTG
* * * *
39767047 TATCCGGGCTTAAATACCCGCAGGCTAT-ATGCTGAAATTATATTCGGGTTAAATCCCGTAGGCT
1 TATCCGGGCTTAAATACCCGCAGGCT-TCATGCTGAAATAATATCCGGGTTAAATCCCGCAGGCC
*
39767111 TGGTGCTGGTAATA
65 TAGTGCTGGTAATA
* **
39767125 TATCCGGG-TTAAAT-CCCGCAGGCTTCGTGCTGGTATAATATCCGGGTTAAATCCCGCAGGCCT
1 TATCCGGGCTTAAATACCCGCAGGCTTCATGCTGAAATAATATCCGGGTTAAATCCCGCAGGCCT
*
39767188 AGTGCTGGTATTA
66 AGTGCTGGTAATA
39767201 TATC
1 TATC
39767205 TGAGTTTAAT
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
75 1 0.01
76 55 0.79
77 6 0.09
78 8 0.11
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (78 bp):
TATCCGGGCTTAAATACCCGCAGGCTTCATGCTGAAATAATATCCGGGTTAAATCCCGCAGGCCT
AGTGCTGGTAATA
Found at i:39769770 original size:21 final size:20
Alignment explanation
Indices: 39769742--39769783 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
39769732 AAACTATACA
39769742 AATAAATTT-AACATCAATTT
1 AATAAATTTAAAC-TCAATTT
39769762 AATACAATTTAAACTCAATTT
1 AATA-AATTTAAACTCAATTT
39769783 A
1 A
39769784 GTCCAAGGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 13 0.65
22 3 0.15
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAAATTTAAACTCAATTT
Found at i:39772879 original size:45 final size:46
Alignment explanation
Indices: 39772716--39772890 Score: 216
Period size: 45 Copynumber: 3.8 Consensus size: 46
39772706 TGGTTGAGCA
*
39772716 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *
39772762 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---G
39772807 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* *
39772855 -CCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
39772891 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 9, Indels: 19
0.80 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 37 0.33
46 29 0.26
47 29 0.26
48 3 0.03
50 4 0.04
51 3 0.03
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:39780277 original size:45 final size:45
Alignment explanation
Indices: 39780228--39780399 Score: 183
Period size: 45 Copynumber: 3.8 Consensus size: 45
39780218 GTTGAGCATC
39780228 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGT
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGT
** *
39780273 CGAACTCGTTGAG-TGAGTCCGAGTT---TCGTGAGATG-TAACTAGGCAT
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCGAA-T--G--T
* *
39780319 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 -CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGT
* *
39780365 CGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
39780400 GCGGGTTACA
Statistics
Matches: 105, Mismatches: 10, Indels: 24
0.76 0.07 0.17
Matches are distributed among these distances:
41 5 0.05
42 5 0.05
44 13 0.12
45 46 0.44
46 1 0.01
47 13 0.12
48 13 0.12
50 4 0.04
51 5 0.05
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (45 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGT
Found at i:39782225 original size:20 final size:20
Alignment explanation
Indices: 39782200--39782238 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
39782190 ACTTCTTTCT
39782200 TTTGGTTT-TTTGTCATTTGG
1 TTTGGTTTCTTT-TCATTTGG
39782220 TTTGGTTTCTTTTCATTTG
1 TTTGGTTTCTTTTCATTTG
39782239 TTTCTTAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.05, C:0.08, G:0.21, T:0.67
Consensus pattern (20 bp):
TTTGGTTTCTTTTCATTTGG
Found at i:39788377 original size:40 final size:40
Alignment explanation
Indices: 39788300--39788444 Score: 143
Period size: 41 Copynumber: 3.5 Consensus size: 40
39788290 GAGCTTGGTC
* * * *
39788300 TCGAAGGGCTTTTGAGCTAGTGCTAATAACCGAACTTAGTT
1 TCGAAGGGCTTTAGAGCCAGTG-TCATAACCGGACTTAGTT
*
39788341 TCAAAGGGCTTTAGAGCCAGTGTCATAACCGGACTTAGTT
1 TCGAAGGGCTTTAGAGCCAGTGTCATAACCGGACTTAGTT
* * *
39788381 CCGAAGGGCCTTT-GAGCCAGTGGTC-TAATCC-GAGCTTGGTC
1 TCGAAGGG-CTTTAGAGCCAGT-GTCATAA-CCGGA-CTTAGTT
39788422 TCGAAGGGCTTTGAGAGCCAGTG
1 TCGAAGGGCTTT-AGAGCCAGTG
39788445 CTAAGAATCG
Statistics
Matches: 88, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
40 39 0.44
41 41 0.47
42 8 0.09
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (40 bp):
TCGAAGGGCTTTAGAGCCAGTGTCATAACCGGACTTAGTT
Found at i:39790220 original size:17 final size:19
Alignment explanation
Indices: 39790194--39790230 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
39790184 TGTAAAACCC
39790194 ATGAGTATGAACT-TTGGT
1 ATGAGTATGAACTCTTGGT
39790212 ATGAG-ATGAACTCTTGGT
1 ATGAGTATGAACTCTTGGT
39790230 A
1 A
39790231 AGAATGCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.30, C:0.08, G:0.27, T:0.35
Consensus pattern (19 bp):
ATGAGTATGAACTCTTGGT
Found at i:39795796 original size:41 final size:41
Alignment explanation
Indices: 39795751--39795919 Score: 148
Period size: 41 Copynumber: 4.1 Consensus size: 41
39795741 GCACAAACAT
* *
39795751 CCTTCGGAA-TCAAGCCCGATTCTTAGCACTGGCTCAAAAGC
1 CCTTCGGAACT-AAGCCCGATTATGAGCACTGGCTCAAAAGC
* * * *
39795792 CCTTC-GAGACCAAGCTCGGATTA-GACCACTGGCTCAAAGGC
1 CCTTCGGA-ACTAAGC-CCGATTATGAGCACTGGCTCAAAAGC
* * *
39795833 CCTTCGGAACTAAGTCCGGTTATGA-CACTGGCTCTAAAGC
1 CCTTCGGAACTAAGCCCGATTATGAGCACTGGCTCAAAAGC
* * ** * *
39795873 CCTTTGAAACTAAGTTCGGTTATTAGCACTGGCTCAAAAGC
1 CCTTCGGAACTAAGCCCGATTATGAGCACTGGCTCAAAAGC
39795914 CCTTCG
1 CCTTCG
39795920 AGACCAAGCT
Statistics
Matches: 104, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
40 41 0.39
41 56 0.54
42 7 0.07
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (41 bp):
CCTTCGGAACTAAGCCCGATTATGAGCACTGGCTCAAAAGC
Found at i:39795875 original size:40 final size:41
Alignment explanation
Indices: 39795777--39795919 Score: 159
Period size: 41 Copynumber: 3.5 Consensus size: 41
39795767 CGATTCTTAG
*
39795777 CACTGGCTCAAAAGCCCTTC-GAGACCAAG-CTCGGATTA-GAC
1 CACTGGCTCAAAAGCCCTTCGGA-ACTAAGTC-CGG-TTATGAC
*
39795818 CACTGGCTCAAAGGCCCTTCGGAACTAAGTCCGGTTATGA-
1 CACTGGCTCAAAAGCCCTTCGGAACTAAGTCCGGTTATGAC
* * * * * *
39795858 CACTGGCTCTAAAGCCCTTTGAAACTAAGTTCGGTTATTAG
1 CACTGGCTCAAAAGCCCTTCGGAACTAAGTCCGGTTATGAC
39795899 CACTGGCTCAAAAGCCCTTCG
1 CACTGGCTCAAAAGCCCTTCG
39795920 AGACCAAGCT
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
40 37 0.42
41 48 0.55
42 3 0.03
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.23
Consensus pattern (41 bp):
CACTGGCTCAAAAGCCCTTCGGAACTAAGTCCGGTTATGAC
Found at i:39812809 original size:44 final size:44
Alignment explanation
Indices: 39812746--39812903 Score: 121
Period size: 43 Copynumber: 3.7 Consensus size: 44
39812736 ATGTGTTTTT
** *
39812746 GTGTAAGACCACGTTTGGGACGTTGGCATCGA-ATTGAGATTTAC
1 GTGTAAGACCATATCTGGGACGTTGGCATCGATATT-AGATTTAC
* * * * *
39812790 GTGTAAGACCATGTCTGGGACATCGACATC-ATATTTA-ATTT-T
1 GTGTAAGACCATATCTGGGACGTTGGCATCGATA-TTAGATTTAC
* * * *
39812832 GTGTAAGACCCTATTTCGGACAG-TGGCATCGATATTTGA-TTAC
1 GTGTAAGACCATATCTGGGAC-GTTGGCATCGATATTAGATTTAC
* *
39812875 ATGTAAGACCATATCTGGGATGTTGGCAT
1 GTGTAAGACCATATCTGGGACGTTGGCAT
39812904 TGTACGAGCT
Statistics
Matches: 87, Mismatches: 20, Indels: 15
0.71 0.16 0.12
Matches are distributed among these distances:
42 27 0.31
43 31 0.36
44 27 0.31
45 2 0.02
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (44 bp):
GTGTAAGACCATATCTGGGACGTTGGCATCGATATTAGATTTAC
Found at i:39817297 original size:34 final size:34
Alignment explanation
Indices: 39817258--39817359 Score: 204
Period size: 34 Copynumber: 3.0 Consensus size: 34
39817248 TGTTAGTACA
39817258 ACCAGAATTGGGTAAAGAATTTGTGATCTATAGT
1 ACCAGAATTGGGTAAAGAATTTGTGATCTATAGT
39817292 ACCAGAATTGGGTAAAGAATTTGTGATCTATAGT
1 ACCAGAATTGGGTAAAGAATTTGTGATCTATAGT
39817326 ACCAGAATTGGGTAAAGAATTTGTGATCTATAGT
1 ACCAGAATTGGGTAAAGAATTTGTGATCTATAGT
39817360 GATGCTTCAT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 68 1.00
ACGTcount: A:0.35, C:0.09, G:0.24, T:0.32
Consensus pattern (34 bp):
ACCAGAATTGGGTAAAGAATTTGTGATCTATAGT
Found at i:39820584 original size:46 final size:46
Alignment explanation
Indices: 39820534--39820709 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
39820524 TGGTTGAGCA
39820534 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
39820580 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
39820625 CATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
39820673 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
39820710 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 62 0.57
47 28 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:39820690 original size:93 final size:93
Alignment explanation
Indices: 39820531--39820702 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
39820521 GGATGGTTGA
* *
39820531 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
39820596 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
39820624 GCATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
39820689 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
39820703 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:39823056 original size:44 final size:43
Alignment explanation
Indices: 39823003--39823159 Score: 142
Period size: 42 Copynumber: 3.7 Consensus size: 43
39822993 TGTGTTTTCG
* *
39823003 TGTAAGACCACGCCTGGGACATTGGCATCGATCTGAGATTTACA
1 TGTAAGACCACGTCTGGGACATTGGCATCGAT-TTAGATTTACA
* *
39823047 TGTAAGACCATGTCTGGGACATCGGCATCGTATTTA-ATTT-CA
1 TGTAAGACCACGTCTGGGACATTGGCATCG-ATTTAGATTTACA
* * * *
39823089 TGTAAGACC-CTGTCTAGGACAGTGACATCGATATTTGA-TTACA
1 TGTAAGACCAC-GTCTGGGACATTGGCATCGAT-TTAGATTTACA
** * *
39823132 TGTAAGACCATATATGGGACTTTGGCAT
1 TGTAAGACCACGTCTGGGACATTGGCAT
39823160 TGTACGAGCT
Statistics
Matches: 90, Mismatches: 17, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
41 2 0.02
42 30 0.33
43 27 0.30
44 29 0.32
45 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACATTGGCATCGATTTAGATTTACA
Found at i:39823103 original size:42 final size:41
Alignment explanation
Indices: 39822998--39823140 Score: 128
Period size: 43 Copynumber: 3.3 Consensus size: 41
39822988 CGATATGTGT
* * *
39822998 TTTCGTGTAAGACCAC-GCCTGGGACATTGGCATCG-ATCTGAGA
1 TTTCATGTAAGACC-CTGTCTGGGACA-TGGCATCGTAT-TTA-A
*
39823041 TTTACATGTAAGACCATGTCTGGGACATCGGCATCGTATTTAA
1 TTT-CATGTAAGACCCTGTCTGGGACAT-GGCATCGTATTTAA
* * *
39823084 TTTCATGTAAGACCCTGTCTAGGACAGTGACATCGATATTTGA
1 TTTCATGTAAGACCCTGTCTGGGACA-TGGCATCG-TATTTAA
*
39823127 TTACATGTAAGACC
1 TTTCATGTAAGACC
39823141 ATATATGGGA
Statistics
Matches: 85, Mismatches: 9, Indels: 12
0.80 0.08 0.11
Matches are distributed among these distances:
42 27 0.32
43 28 0.33
44 28 0.33
45 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.30
Consensus pattern (41 bp):
TTTCATGTAAGACCCTGTCTGGGACATGGCATCGTATTTAA
Found at i:39827095 original size:14 final size:14
Alignment explanation
Indices: 39827072--39827108 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
39827062 GAAGAAGGCT
*
39827072 TCTTTAGCCTCACC
1 TCTTTGGCCTCACC
39827086 TCTTTGGCCTCACC
1 TCTTTGGCCTCACC
39827100 TCTTTGGCC
1 TCTTTGGCC
39827109 CTCAGATACG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.08, C:0.41, G:0.14, T:0.38
Consensus pattern (14 bp):
TCTTTGGCCTCACC
Found at i:39829657 original size:29 final size:29
Alignment explanation
Indices: 39829590--39829714 Score: 171
Period size: 29 Copynumber: 4.3 Consensus size: 29
39829580 AAGTCTACAT
* *
39829590 ACATGCATATGGCCCACTAGGCCC-AATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
* *
39829618 TCATTCATATGGCCTATTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
* *
39829647 ACATTCGTATGACCCATTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
* *
39829676 ACATTCATATGGACCAATAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
39829705 ACATTCATAT
1 ACATTCATAT
39829715 ACATGCTTTC
Statistics
Matches: 84, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
28 20 0.24
29 64 0.76
ACGTcount: A:0.32, C:0.30, G:0.14, T:0.25
Consensus pattern (29 bp):
ACATTCATATGGCCCATTAGGCCCAAATC
Found at i:39837095 original size:40 final size:40
Alignment explanation
Indices: 39837051--39837242 Score: 285
Period size: 40 Copynumber: 4.8 Consensus size: 40
39837041 TGATATAGCT
* * * * * *
39837051 ACTCGCTCGAATGCCTTCGGGGCGTAGCCCGGGTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* *
39837091 ACTCGCACCAATGCCTTCGGGACTTAGCCCGGATTTGGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* *
39837131 ACTTGCACAAATGCCTTCGGGACTTAGCCCGGATTTGGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
39837171 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
*
39837211 GCTCGCACAAATGCCTTCGGGACTTAGCCCGG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
39837243 TTATCATCCG
Statistics
Matches: 140, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 140 1.00
ACGTcount: A:0.21, C:0.29, G:0.27, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
Found at i:39845165 original size:40 final size:40
Alignment explanation
Indices: 39845041--39845230 Score: 287
Period size: 40 Copynumber: 4.8 Consensus size: 40
39845031 GGATATAGCT
* * *
39845041 ACTCGCTCGAATGCCTTCGGG-CATAGCCCGG-TTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT-TAGTA
* *
39845080 ACTCGCACCAATGCCTTCGGGACTTAGCCC-GATTTGGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
*
39845119 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTGGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
39845159 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
*
39845199 GCTCGCACAAATGCCTTCGGGACTTAGCCCGG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
39845231 TTATCATCCG
Statistics
Matches: 141, Mismatches: 7, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
39 53 0.38
40 88 0.62
ACGTcount: A:0.22, C:0.29, G:0.25, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
Found at i:39845173 original size:79 final size:80
Alignment explanation
Indices: 39845041--39845234 Score: 295
Period size: 79 Copynumber: 2.5 Consensus size: 80
39845031 GGATATAGCT
* * * *
39845041 ACTCGCTCGAATGCCTTCGGG-CATAGCCCGGTTATAGTAACTCGCACCAATGCCTTCGGGACTT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTT
*
39845105 AGCCC-GATTTGGTA
66 AGCCCGGATTTAGTA
*
39845119 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT-TGGTAACTCGCACAAATGCCTTCGGGACT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACT
39845183 TAGCCCGGATTTAGTA
65 TAGCCCGGATTTAGTA
*
39845199 GCTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
39845235 CATCCGAATA
Statistics
Matches: 105, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
78 19 0.18
79 44 0.42
80 42 0.40
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (80 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTT
AGCCCGGATTTAGTA
Found at i:39847589 original size:19 final size:19
Alignment explanation
Indices: 39847565--39847611 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
39847555 AATGCCTCTT
*
39847565 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTGCAT-CA
39847584 TTTGCATTACATTGCATCA
1 TTTGCATTACATTGCATCA
*
39847603 TATGCATTA
1 TTTGCATTA
39847612 AATTTCACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTGCATCA
Found at i:39854091 original size:12 final size:14
Alignment explanation
Indices: 39854076--39854107 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
39854066 GTGAGAACAC
39854076 ATGTGTA-G-TACT
1 ATGTGTAGGATACT
39854088 ATGTGTAGGATACT
1 ATGTGTAGGATACT
39854102 ATGTGT
1 ATGTGT
39854108 TTAAGATGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 1 0.06
14 10 0.56
ACGTcount: A:0.25, C:0.06, G:0.28, T:0.41
Consensus pattern (14 bp):
ATGTGTAGGATACT
Found at i:39854194 original size:50 final size:50
Alignment explanation
Indices: 39854073--39854352 Score: 249
Period size: 50 Copynumber: 5.6 Consensus size: 50
39854063 ATTGTGAGAA
* * * * *** *
39854073 CACATGTGTAGTACTATGTGTAGGATACTATGTGTTTAAGATGGTTTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG--TTAGGT
**
39854125 CATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGT
* * * * * * ***
39854175 CGCATGTGTAGTACAAAGTGCAGGCTACTATGCGTACCTGATAACTTCCAT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGAT-AGTTAGGT
* * * *
39854226 CACGTATGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGT
** ** *
39854276 CATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATTGTT-GGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGT
*
39854325 CGA-TTGTGTAGTACTAAGTGCAGGCTAC
1 C-ACATGTGTAGTACTAAGTGCAGGCTAC
39854353 CATGCTTACC
Statistics
Matches: 185, Mismatches: 41, Indels: 7
0.79 0.18 0.03
Matches are distributed among these distances:
49 28 0.15
50 85 0.46
51 38 0.21
52 34 0.18
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (50 bp):
CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGT
Found at i:39854526 original size:19 final size:19
Alignment explanation
Indices: 39854502--39854543 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
39854492 GGTATATGTT
39854502 TGTGGAATTTTATGAGCAA
1 TGTGGAATTTTATGAGCAA
*
39854521 TGTGGAATTTTTTGAGCAA
1 TGTGGAATTTTATGAGCAA
39854540 TGTG
1 TGTG
39854544 CTTGATAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.26, C:0.05, G:0.29, T:0.40
Consensus pattern (19 bp):
TGTGGAATTTTATGAGCAA
Found at i:39856716 original size:40 final size:40
Alignment explanation
Indices: 39856618--39856880 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
39856608 TCCTCGTTCA
* * * * *
39856618 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
39856657 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
39856697 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
39856737 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
39856777 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
39856817 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
39856857 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
39856881 CAGCATTCAA
Statistics
Matches: 200, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 37 0.19
40 155 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:39864561 original size:40 final size:40
Alignment explanation
Indices: 39864428--39864687 Score: 298
Period size: 39 Copynumber: 6.6 Consensus size: 40
39864418 TCCTCGTTCA
* * * * *
39864428 AATGCCTTC-GGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
39864466 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
39864506 -ATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
39864545 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
39864585 AATGCCTTC-GGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
39864624 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
39864664 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
39864688 CAGCATTCAA
Statistics
Matches: 196, Mismatches: 20, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
38 9 0.05
39 99 0.51
40 80 0.41
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:39864564 original size:79 final size:78
Alignment explanation
Indices: 39864428--39864648 Score: 302
Period size: 79 Copynumber: 2.8 Consensus size: 78
39864418 TCCTCGTTCA
* * * * *
39864428 AATGCCTTCGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATTT
1 AATGCCTTCGGACTTAACCCGGATTTAGTAACTCGCACAATGCCTTCGGGACTTAACCCGGATTT
39864493 AACAACTCGCACG
66 AACAACTCGCACG
*
39864506 -ATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTC-GGACTTAACCCGGATTTAGTAACTCGCAC-AATGCCTTCGGGACTTAACCCGGAT
*
39864570 TTAATAACTCGCACG
64 TTAACAACTCGCACG
* * *
39864585 AATGCCTTCGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAATCCGGAT
1 AATGCCTTCGGACTTAACCCGGATTTAGTAACTCGCAC-AATGCCTTCGGGA-CTTAACCCGGAT
39864649 ATATTCACTT
Statistics
Matches: 127, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
77 8 0.06
78 27 0.21
79 84 0.66
80 8 0.06
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (78 bp):
AATGCCTTCGGACTTAACCCGGATTTAGTAACTCGCACAATGCCTTCGGGACTTAACCCGGATTT
AACAACTCGCACG
Found at i:39864671 original size:79 final size:80
Alignment explanation
Indices: 39864431--39864687 Score: 256
Period size: 79 Copynumber: 3.3 Consensus size: 80
39864421 TCGTTCAAAT
* * * * * * * *
39864431 GCCTTC-GGACATAGCCCGGTTTTAGTAACTCACAC-AATGCCTTCGGGACATAACCCGGATTTA
1 GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
* * *
39864494 ACAACTCGCACG-AT
66 ATAACTAGCACGAAA
* * *
39864508 GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTA
1 GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
* *
39864573 ATAACTCGCACGAAT
66 ATAACTAGCACGAAA
* * *
39864588 GCCTTC-GGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAATCCGGATAT
1 GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAAAGGCCTTCGGGA-CTTAACCCGGATAT
* *
39864651 ATTCACTTAGCAC-AAA
65 AATAAC-TAGCACGAAA
*
39864667 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
39864688 CAGCATTCAA
Statistics
Matches: 156, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
77 6 0.04
78 27 0.17
79 97 0.62
80 26 0.17
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.25
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
ATAACTAGCACGAAA
Found at i:39868605 original size:48 final size:47
Alignment explanation
Indices: 39868436--39868662 Score: 201
Period size: 48 Copynumber: 4.8 Consensus size: 47
39868426 CAAAATCAAG
* * * * *** *
39868436 GCCGACGCCATGTCCCAGACATGGTCTTACACTGACTATCAAAATCGAG
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTGGC-ACCTCTATCG-T
* * * *
39868485 GCCGACGCCATGTCCCAAACATGGTCTTACACTAGCTCTCACATATCTGT
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTGGCAC-CTC-TATC-GT
*
39868535 GCCGATGCCATGTCCCATACATGGTCTTACACTGGCACCTCTATGCGT
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTGGCACCTCTAT-CGT
* * * *
39868583 GTCAATGCCATGTCCCAAACATGGTCTTACACTGACACATC--TCGT
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTGGCACCTCTATCGT
*
39868628 AGCCGATG-CATGTCCCAGACAT-GTCTTACACTGGC
1 -GCCGATGCCATGTCCCAAACATGGTCTTACACTGGC
39868663 TTACATCTTG
Statistics
Matches: 151, Mismatches: 22, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
44 12 0.08
45 16 0.11
46 6 0.04
48 41 0.27
49 38 0.25
50 37 0.25
51 1 0.01
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (47 bp):
GCCGATGCCATGTCCCAAACATGGTCTTACACTGGCACCTCTATCGT
Found at i:39868772 original size:94 final size:92
Alignment explanation
Indices: 39868444--39868801 Score: 241
Period size: 94 Copynumber: 3.8 Consensus size: 92
39868434 AGGCCGACGC
* * * *
39868444 CATGTCCCAGACATGGTCTTACACTGAC-TATCAAAATCGAGGCCGACGCCATGTCCCAAACATG
1 CATGTCCCAGACAT-GTCTTACACTGGCTTA-CATAAT-GAGGCCGATG-CATGTCCCAGACAT-
**
39868508 GTCTTACACTAGCTCTCA--CATATCTGTGCCGATG
61 GTCTTACACTAGCTCT-AGTC-TAAATGT--CGATG
* * * * * * *
39868542 CCATGTCCCATACATGGTCTTACACTGGC--ACCTCTATGCGTGTCAATGCCATGTCCCAAACAT
1 -CATGTCCCAGACAT-GTCTTACACTGGCTTACAT-AATGAG-GCCGATG-CATGTCCCAGACAT
* ** *
39868605 GGTCTTACACT-GACAC-A-TCT-CGTAGCCGATG
61 -GTCTTACACTAG-CTCTAGTCTAAAT-GTCGATG
** *
39868636 CATGTCCCAGACATGTCTTACACTGGCTTACATCTTGAGGCCGATGCATGTCCTAGACATGTCTT
1 CATGTCCCAGACATGTCTTACACTGGCTTACATAATGAGGCCGATGCATGTCCCAGACATGTCTT
39868701 ACACTAGCTCTAGTCTAAATGTCGATG
66 ACACTAGCTCTAGTCTAAATGTCGATG
* * * *
39868728 CCATGTCCTAGACATGGTCTTATATTGGCTCT-CATAATGTGGCCGATGCATGTCCCAGACATGT
1 -CATGTCCCAGACAT-GTCTTACACTGGCT-TACATAATGAGGCCGATGCATGTCCCAGACATGT
*
39868792 GTTACACTAG
63 CTTACACTAG
39868802 AATACAAATA
Statistics
Matches: 211, Mismatches: 34, Indels: 33
0.76 0.12 0.12
Matches are distributed among these distances:
90 12 0.06
91 14 0.07
92 27 0.13
93 30 0.14
94 57 0.27
95 2 0.01
96 3 0.01
97 5 0.02
98 35 0.17
99 26 0.12
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.28
Consensus pattern (92 bp):
CATGTCCCAGACATGTCTTACACTGGCTTACATAATGAGGCCGATGCATGTCCCAGACATGTCTT
ACACTAGCTCTAGTCTAAATGTCGATG
Found at i:39868775 original size:48 final size:48
Alignment explanation
Indices: 39868390--39868799 Score: 276
Period size: 49 Copynumber: 8.6 Consensus size: 48
39868380 CCATCAAGTA
* * * * * **
39868390 GATGCCATTTCCCAGACATGGTCTTACATTGACTATCAAAATCAAGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GTGGCC
* * * * *
39868439 GACGCCATGTCCCAGACATGGTCTTACACTGACTATCAAAATCGAGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GTGGCC
* * * * *
39868488 GACGCCATGTCCCAAACATGGTCTTACACTAGCTCTCACATATCTGTGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATA-ATGTG-GCC
* * * *
39868538 GATGCCATGTCCCATACATGGTCTTACACTGGCACCTC-T-ATGCGTGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGC-TCTCATAATGTG-GCC
* * * * * *
39868586 AATGCCATGTCCCAAACATGGTCTTACACTGACACATC-T--CGTAGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTC-TCATAATGTGGCC
** *
39868632 GATG-CATGTCCCAGACAT-GTCTTACACTGGCT-TACATCTTGAGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-CATAATGTGGCC
* *
39868678 GATG-CATGTCCTAGACAT-GTCTTACACTAGCTCT-AGTCTAAATGT---C
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCA---T-AATGTGGCC
* * *
39868724 GATGCCATGTCCTAGACATGGTCTTATATTGGCTCTCATAATGTGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCC
*
39868772 GATG-CATGTCCCAGACAT-GTGTTACACT
1 GATGCCATGTCCCAGACATGGTCTTACACT
39868800 AGAATACAAA
Statistics
Matches: 296, Mismatches: 46, Indels: 41
0.77 0.12 0.11
Matches are distributed among these distances:
42 1 0.00
43 1 0.00
44 13 0.04
45 19 0.06
46 52 0.18
47 30 0.10
48 58 0.20
49 84 0.28
50 35 0.12
51 3 0.01
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.28
Consensus pattern (48 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCC
Found at i:39875668 original size:22 final size:23
Alignment explanation
Indices: 39875640--39875686 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
39875630 AAGTGTATAT
39875640 AAGCCA-TTTCGCATGGCTATCC
1 AAGCCATTTTCGCATGGCTATCC
39875662 AAGCCATTTTCGCATGGCTATCC
1 AAGCCATTTTCGCATGGCTATCC
39875685 AA
1 AA
39875687 ATTTATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.28
Consensus pattern (23 bp):
AAGCCATTTTCGCATGGCTATCC
Found at i:39876268 original size:40 final size:40
Alignment explanation
Indices: 39876186--39876406 Score: 232
Period size: 40 Copynumber: 5.5 Consensus size: 40
39876176 ACCCAAGTCT
** * *
39876186 CTTCGGGAT-TTAG-CCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGG-TCTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
39876224 CTTCGGGTCTTAGCCTGGATATGGTCACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
39876264 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* * * * *
39876304 CTTCGGGTTTTGGCCCGGATATAGTAACTCGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
39876344 CTTCGGATCTTAGTCCGGATATAGTCACTTAGCACAAAAGC
1 CTTCGGGTCTTAGCCCGGATATAGTCAC-TAGCACAAATGC
* *
39876385 CTTCGGGACTTAGCTCGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
39876407 CATTCGAATA
Statistics
Matches: 148, Mismatches: 31, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
37 1 0.01
38 11 0.07
39 14 0.09
40 95 0.64
41 27 0.18
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:39876324 original size:80 final size:79
Alignment explanation
Indices: 39876186--39876406 Score: 257
Period size: 80 Copynumber: 2.8 Consensus size: 79
39876176 ACCCAAGTCT
* ** * * * * *
39876186 CTTCGGGATTTAGCCGGATATAACCACTCGCAC-AAGGCCTTCGGGTCTTAGCCTGGATATGGTC
1 CTTCGGGACTTAGCCGGATATAGTCACTAGCACAAAAGCCTTCGGGTCTTAGCCCGGATATAGTA
39876250 ACTAGCATAAATGC
66 ACTAGCATAAATGC
* * * *
39876264 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGCCTTCGGGTTTTGGCCCGGATATAGT
1 CTTCGGGACTTAG-CCGGATATAGTCACTAGCACAAAAGCCTTCGGGTCTTAGCCCGGATATAGT
*
39876329 AACTCGCATAAATGC
65 AACTAGCATAAATGC
* *
39876344 CTTC-GGATCTTAGTCCGGATATAGTCACTTAGCACAAAAGCCTTCGGGACTTAGCTCGGATAT
1 CTTCGGGA-CTTAG-CCGGATATAGTCAC-TAGCACAAAAGCCTTCGGGTCTTAGCCCGGATAT
39876407 CATTCGAATA
Statistics
Matches: 120, Mismatches: 19, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
78 12 0.10
79 19 0.16
80 60 0.50
81 29 0.24
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (79 bp):
CTTCGGGACTTAGCCGGATATAGTCACTAGCACAAAAGCCTTCGGGTCTTAGCCCGGATATAGTA
ACTAGCATAAATGC
Found at i:39880686 original size:32 final size:32
Alignment explanation
Indices: 39880650--39880716 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
39880640 ACGAAAACTC
39880650 AGTGTGTAATCCCTTATCAGACTATAGAAAAT
1 AGTGTGTAATCCCTTATCAGACTATAGAAAAT
39880682 AGTGTGTAATCCCTTATCAGACTATAGAAAAT
1 AGTGTGTAATCCCTTATCAGACTATAGAAAAT
39880714 AGT
1 AGT
39880717 CTATGCAGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.31
Consensus pattern (32 bp):
AGTGTGTAATCCCTTATCAGACTATAGAAAAT
Found at i:39880965 original size:26 final size:26
Alignment explanation
Indices: 39880922--39880972 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
39880912 ACCAGCACAC
* *
39880922 CAATATCGCAGCAAAGCTACTAGTAA
1 CAATAACGCAGCAAAGCTACCAGTAA
**
39880948 CAATAACGCAGCGTAGCTACCAGTA
1 CAATAACGCAGCAAAGCTACCAGTA
39880973 GTAGTAAGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (26 bp):
CAATAACGCAGCAAAGCTACCAGTAA
Found at i:39885645 original size:58 final size:58
Alignment explanation
Indices: 39885555--39885670 Score: 223
Period size: 58 Copynumber: 2.0 Consensus size: 58
39885545 TTCTATGCTC
*
39885555 ACCTAAGTATAAAATATGAAATTAAGGCATTAGGAGCATCAAATTCACCAATTCTAAG
1 ACCTAAGTATAAAACATGAAATTAAGGCATTAGGAGCATCAAATTCACCAATTCTAAG
39885613 ACCTAAGTATAAAACATGAAATTAAGGCATTAGGAGCATCAAATTCACCAATTCTAAG
1 ACCTAAGTATAAAACATGAAATTAAGGCATTAGGAGCATCAAATTCACCAATTCTAAG
39885671 GGAAAATAAT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.25
Consensus pattern (58 bp):
ACCTAAGTATAAAACATGAAATTAAGGCATTAGGAGCATCAAATTCACCAATTCTAAG
Found at i:39901197 original size:45 final size:44
Alignment explanation
Indices: 39901118--39901239 Score: 129
Period size: 45 Copynumber: 2.7 Consensus size: 44
39901108 CACAAACATT
* * * * *
39901118 ATCTCTCTGAAGTTGCAGTGGAGTAAGTTAAAAATAACAAATCTA
1 ATCTCTCTAAAGTTGCAGTAGAG-CAGATGAAAATAACAAATCTA
* * * *
39901163 ATCTC-CATGAAGTTGCAGTAGAGCCGATTGAAAATAGCAAATCTT
1 ATCTCTC-TAAAGTTGCAGTAGAGCAGA-TGAAAATAACAAATCTA
39901208 ATCTCTCTAAAGTTGCAGTAGAGCAGATGAAA
1 ATCTCTCTAAAGTTGCAGTAGAGCAGATGAAA
39901240 GCTAAAACTT
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
44 7 0.11
45 57 0.88
46 1 0.02
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.27
Consensus pattern (44 bp):
ATCTCTCTAAAGTTGCAGTAGAGCAGATGAAAATAACAAATCTA
Found at i:39901344 original size:45 final size:45
Alignment explanation
Indices: 39901258--39901812 Score: 283
Period size: 45 Copynumber: 12.0 Consensus size: 45
39901248 TTATGAGTCC
* * * * * *
39901258 TATCTCCTTGAAATTGTAGTGGAACAGATTGACGATAGCAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGATTGCAAATCT
*
39901303 TATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGATTGCAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGATTGCAAATCT
* *
39901348 TATTTCCCTGAAGTTGTAGTGGAACAGATTAAAGATTGCAAATTACAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGATTG-------CAAATCT
* * * * * * *
39901400 TGTCTCCCTAAAGTTGTAGTAGAACAAATTAAAG-TTACAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGATTGCAAATCT
* * ** * * * * *
39901444 TATCCCCCTAAAGTTGCAGTGGAGTAGATCAAATATAGCGAATCG
1 TATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGATTGCAAATCT
* * * * * * ***
39901489 CATTTTCTTGAAGTTGTAGTGGAATAGATTAAAGCTACAAACCACAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAACAGATTAAAG------ATTGCAAATCT
* * * *
39901540 TATCTCCCTCAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGATTGCAAATCT
* * ** **
39901585 TATCTCTCTGAATTTGCAG-CAAAGCAGATTAAAG-TTATAAA-CAT
1 TATCTCCCTGAAGTTGCAGTGGAA-CAGATTAAAGATTGCAAATC-T
* * * * *
39901629 TATCTCCCTGAAGTTGCAGTGGAGCAAACTAAAGATAGAAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGATTGCAAATCT
* * * * * *
39901674 TATCTCTCTAAAGTTGCAGTAGAGCATATTAAAG-CTGCAAATTACAAGT
1 TATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGATTGCAAA-T-C---T
* * * * * * * *
39901723 CATATCTCCTTGAAGTTACAGTGGAGCAGACTGAATATAGCGAATCT
1 --TATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGATTGCAAATCT
* * *
39901770 TATTTCCCTAAAGTTACAGTGGAACAGATTAAAGATTGCAAAT
1 TATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGATTGCAAAT
39901813 TACAAATCTT
Statistics
Matches: 378, Mismatches: 105, Indels: 54
0.70 0.20 0.10
Matches are distributed among these distances:
43 1 0.00
44 66 0.17
45 207 0.55
46 2 0.01
47 1 0.00
49 1 0.00
50 1 0.00
51 59 0.16
52 40 0.11
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (45 bp):
TATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGATTGCAAATCT
Found at i:39901614 original size:96 final size:96
Alignment explanation
Indices: 39901514--39901883 Score: 326
Period size: 96 Copynumber: 3.9 Consensus size: 96
39901504 GTAGTGGAAT
** * *
39901514 AGATTAAAGCTACAAACCACAAATCTTATCTCCCTCAAGTTGCAGTGGAGCAGATTGAAGATAGC
1 AGATTAAAGCTACAAATTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGC
* *
39901579 AAATCTTATCTCTCTGAATTTGCAGCAAAGC
66 AAATCTTATCTCTCTAAAGTTGCAGCAAAGC
* * * * *
39901610 AGATTAAAGTTA-TAA--AC--A--TTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAAGATAGA
1 AGATTAAAGCTACAAATTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGC
* *
39901668 AAATCTTATCTCTCTAAAGTTGCAGTAGAGC
66 AAATCTTATCTCTCTAAAGTTGCAGCAAAGC
* * * * * * *
39901699 ATATTAAAGCTGCAAATTACAAGTCATATCTCCTTGAAGTTACAGTGGAGCAGACTGAATATAGC
1 AGATTAAAGCTACAAATTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGC
* * * * **
39901764 GAATCTTATTTCCCTAAAGTTACAGTGGAA-C
66 AAATCTTATCTCTCTAAAGTTGCAG-CAAAGC
* * * * * * * *
39901795 AGATTAAAGATTGCAAATTACAAATCTTGTCTCCCTAAAGTTGTAGTGGAGTAGATTGAAGTTA-
1 AGATTAAAG-CTACAAATTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAG
* * *
39901859 CAAAGCTTATCCCCCTAAAGTTGCA
65 CAAATCTTATCTCTCTAAAGTTGCA
39901884 ATGGAGTAGA
Statistics
Matches: 217, Mismatches: 48, Indels: 18
0.77 0.17 0.06
Matches are distributed among these distances:
89 71 0.33
90 2 0.01
91 1 0.00
92 2 0.01
93 2 0.01
95 2 0.01
96 94 0.43
97 43 0.20
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (96 bp):
AGATTAAAGCTACAAATTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGC
AAATCTTATCTCTCTAAAGTTGCAGCAAAGC
Found at i:39901691 original size:89 final size:89
Alignment explanation
Indices: 39901539--39901707 Score: 248
Period size: 89 Copynumber: 1.9 Consensus size: 89
39901529 ACCACAAATC
* * * * * *
39901539 TTATCTCCCTCAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTCTCTGAATTTGCAG
1 TTATCTCCCTCAAGTTGCAGTGGAGCAAACTAAAGATAGAAAATCTTATCTCTCTAAAGTTGCAG
39901604 CAAAGCAGATTAAAGTTATAAACA
66 CAAAGCAGATTAAAGTTATAAACA
*
39901628 TTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAAGATAGAAAATCTTATCTCTCTAAAGTTGCAG
1 TTATCTCCCTCAAGTTGCAGTGGAGCAAACTAAAGATAGAAAATCTTATCTCTCTAAAGTTGCAG
* * *
39901693 TAGAGCATATTAAAG
66 CAAAGCAGATTAAAG
39901708 CTGCAAATTA
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
89 70 1.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (89 bp):
TTATCTCCCTCAAGTTGCAGTGGAGCAAACTAAAGATAGAAAATCTTATCTCTCTAAAGTTGCAG
CAAAGCAGATTAAAGTTATAAACA
Found at i:39901875 original size:44 final size:44
Alignment explanation
Indices: 39901802--39901983 Score: 186
Period size: 44 Copynumber: 4.1 Consensus size: 44
39901792 AACAGATTAA
* * * *
39901802 AGATTGCAAATTACAAATCTTGTCTCCCTAAAGTTGTAGTGGAGT
1 AGATTG-AAGTTACAAATCTTATCTCCCTAAAGTTGCAGTAGAGT
* * * *
39901847 AGATTGAAGTTACAAAGCTTATCCCCCTAAAGTTGCAATGGAGT
1 AGATTGAAGTTACAAATCTTATCTCCCTAAAGTTGCAGTAGAGT
* * * * * * *
39901891 AGATCGAAGATAGTAAATCTTATCTCTCTAAAGTTGCAGAATAGC
1 AGATTGAAGTTA-CAAATCTTATCTCCCTAAAGTTGCAGTAGAGT
* *
39901936 AGATT-AACTTACTAATCTTATCTCCCTAAAGTTGCAGTAGAGT
1 AGATTGAAGTTACAAATCTTATCTCCCTAAAGTTGCAGTAGAGT
39901979 AGATT
1 AGATT
39901984 AAAATTAAAT
Statistics
Matches: 110, Mismatches: 26, Indels: 4
0.79 0.19 0.03
Matches are distributed among these distances:
43 31 0.28
44 46 0.42
45 33 0.30
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.31
Consensus pattern (44 bp):
AGATTGAAGTTACAAATCTTATCTCCCTAAAGTTGCAGTAGAGT
Found at i:39903952 original size:20 final size:20
Alignment explanation
Indices: 39903927--39903968 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
39903917 CTTCAAGATA
39903927 GTCGTACCATAACTTACGGG
1 GTCGTACCATAACTTACGGG
39903947 GTCGTACCATAACTTACGGG
1 GTCGTACCATAACTTACGGG
39903967 GT
1 GT
39903969 TTTGATTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (20 bp):
GTCGTACCATAACTTACGGG
Found at i:39905123 original size:25 final size:25
Alignment explanation
Indices: 39905090--39905147 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
39905080 ACAATCTGTG
*
39905090 AATCGGTATGCTCTCACAAGCTACA
1 AATCAGTATGCTCTCACAAGCTACA
* * *
39905115 TATCAGTATGCTCTCACGAGCTATA
1 AATCAGTATGCTCTCACAAGCTACA
39905140 AATCAGTA
1 AATCAGTA
39905148 ACCCTAATGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.28
Consensus pattern (25 bp):
AATCAGTATGCTCTCACAAGCTACA
Found at i:39911082 original size:47 final size:50
Alignment explanation
Indices: 39911009--39911139 Score: 161
Period size: 48 Copynumber: 2.7 Consensus size: 50
39910999 TCACTCGTGT
39911009 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGAC-CACAT-TA-TGA
1 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACACACATATACT-A
*
39911055 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCTG-CACACATATACTA
1 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATC-GACACACATATACTA
* *
39911105 GA-CTTGTGTAA-ACCATGTATGGGACATGGCATCGA
1 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGA
39911140 TGTCTGGCCC
Statistics
Matches: 74, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
46 13 0.18
47 15 0.20
48 27 0.36
49 13 0.18
50 5 0.07
51 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.24
Consensus pattern (50 bp):
GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACACACATATACTA
Found at i:39936382 original size:40 final size:40
Alignment explanation
Indices: 39936320--39936497 Score: 218
Period size: 40 Copynumber: 4.5 Consensus size: 40
39936310 AAGCCAAGTA
* * ***
39936320 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTTGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
** *
39936359 CCTTCGGGAGATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
39936399 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
39936439 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
39936479 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
39936498 TTATCATCCA
Statistics
Matches: 124, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
39 13 0.10
40 111 0.90
ACGTcount: A:0.24, C:0.28, G:0.25, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:39938763 original size:46 final size:46
Alignment explanation
Indices: 39938598--39938768 Score: 170
Period size: 46 Copynumber: 3.7 Consensus size: 46
39938588 AACCTGCCCC
** * *
39938598 TAAGTGAACTCGGACTCAACTCAACGAACTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* * *
39938644 TAAGTGAACTCGGACTCAACTCAACGAGTTAGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* * *
39938692 TCA-CGAACTCGGACTCAACCCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
*
39938737 TAAGTGAACTCGGACTCAACTTAACGAGTTCG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCG
39938769 AATGCTCAAC
Statistics
Matches: 99, Mismatches: 17, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 55 0.56
47 27 0.27
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:39940445 original size:29 final size:29
Alignment explanation
Indices: 39940362--39940461 Score: 121
Period size: 29 Copynumber: 3.5 Consensus size: 29
39940352 CCTATATCTA
* *
39940362 GCCCATTAAGCCC-AATCATATTCATATG
1 GCCCATTAGGCCCAAATCATATTTATATG
* ** *
39940390 GCCCATTACGCCCAAATCACCTGTATATG
1 GCCCATTAGGCCCAAATCATATTTATATG
*
39940419 GCCCATTAGGCCCAAATAATATTTATATG
1 GCCCATTAGGCCCAAATCATATTTATATG
*
39940448 GCCCGTTAGGCCCA
1 GCCCATTAGGCCCA
39940462 GTCACATTCA
Statistics
Matches: 60, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
28 12 0.20
29 48 0.80
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.26
Consensus pattern (29 bp):
GCCCATTAGGCCCAAATCATATTTATATG
Found at i:39941194 original size:7 final size:7
Alignment explanation
Indices: 39941182--39941207 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
39941172 TTTTATGAAA
39941182 CCCAAAG
1 CCCAAAG
39941189 CCCAAAG
1 CCCAAAG
39941196 CCCAAAG
1 CCCAAAG
39941203 CCCAA
1 CCCAA
39941208 TTCATCTAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.46, G:0.12, T:0.00
Consensus pattern (7 bp):
CCCAAAG
Found at i:39944102 original size:24 final size:23
Alignment explanation
Indices: 39944067--39944143 Score: 75
Period size: 24 Copynumber: 3.3 Consensus size: 23
39944057 TTGTAGCCAA
39944067 ACTTTT-GGCTTTTCAGCTTTTCG
1 ACTTTTCGGCTTTTC-GCTTTTCG
39944090 ACTTTTCGGCTTTTCGACTTTTCG
1 ACTTTTCGGCTTTTCG-CTTTTCG
* * * * *
39944114 GCATTTCGGCATTTCGGCATTACG
1 ACTTTTCGGCTTTTC-GCTTTTCG
39944138 ACTTTT
1 ACTTTT
39944144 GTCAATTCAT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
23 7 0.16
24 36 0.82
25 1 0.02
ACGTcount: A:0.12, C:0.23, G:0.18, T:0.47
Consensus pattern (23 bp):
ACTTTTCGGCTTTTCGCTTTTCG
Found at i:39944113 original size:16 final size:16
Alignment explanation
Indices: 39944075--39944143 Score: 84
Period size: 16 Copynumber: 4.3 Consensus size: 16
39944065 AAACTTTTGG
* *
39944075 CTTTTCAGCTTTTCGA
1 CTTTTCGGCATTTCGA
*
39944091 CTTTTCGGCTTTTCGA
1 CTTTTCGGCATTTCGA
*
39944107 CTTTTCGGCATTTCGG
1 CTTTTCGGCATTTCGA
* *
39944123 CATTTCGGCATTACGA
1 CTTTTCGGCATTTCGA
39944139 CTTTT
1 CTTTT
39944144 GTCAATTCAT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (16 bp):
CTTTTCGGCATTTCGA
Found at i:39944120 original size:8 final size:8
Alignment explanation
Indices: 39944093--39944134 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
39944083 CTTTTCGACT
*
39944093 TTTCGGCT
1 TTTCGGCA
* *
39944101 TTTCGACT
1 TTTCGGCA
39944109 TTTCGGCA
1 TTTCGGCA
39944117 TTTCGGCA
1 TTTCGGCA
39944125 TTTCGGCA
1 TTTCGGCA
39944133 TT
1 TT
39944135 ACGACTTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (8 bp):
TTTCGGCA
Found at i:39944641 original size:13 final size:13
Alignment explanation
Indices: 39944619--39944651 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
39944609 AAGGGTTTGT
39944619 TTAT-TAAACTAA
1 TTATCTAAACTAA
39944631 TTATCTAAACTAA
1 TTATCTAAACTAA
*
39944644 TTAACTAA
1 TTATCTAA
39944652 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:39947591 original size:25 final size:23
Alignment explanation
Indices: 39947563--39947619 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
39947553 TATGTCTTTC
*
39947563 AAAATAAAATAATAAAATTGAAAT
1 AAAATAAAATAATAAAAAT-AAAT
39947587 GAAAAT-AAA-AATAAAAATAAAT
1 -AAAATAAAATAATAAAAATAAAT
39947609 -AAATAAAATAA
1 AAAATAAAATAA
39947620 GATAAAAGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 4 0.14
21 3 0.10
22 6 0.21
23 8 0.28
24 3 0.10
25 5 0.17
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (23 bp):
AAAATAAAATAATAAAAATAAAT
Found at i:39955633 original size:28 final size:29
Alignment explanation
Indices: 39955601--39955702 Score: 120
Period size: 29 Copynumber: 3.6 Consensus size: 29
39955591 TACTTATATC
*
39955601 TGGCCCATTAAGCCC-AATCATATTTATG
1 TGGCCCATTAGGCCCAAATCATATTTATG
*
39955629 TGGCCCATTAGGCCCAAATCACCTGTTTA--
1 TGGCCCATTAGGCCCAAATCA--TATTTATG
* *
39955658 TGACCCATTAGGCCCAAATCAGATTTATG
1 TGGCCCATTAGGCCCAAATCATATTTATG
*
39955687 TGGCCCGTTAGGCCCA
1 TGGCCCATTAGGCCCA
39955703 GTCACATTCA
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
27 4 0.06
28 14 0.23
29 39 0.63
31 5 0.08
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.27
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCATATTTATG
Found at i:39967813 original size:45 final size:45
Alignment explanation
Indices: 39967611--39967838 Score: 189
Period size: 45 Copynumber: 5.0 Consensus size: 45
39967601 TCACTCGTGT
* * * *
39967611 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGACCAC-ATTATGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCTACGA-GAT-A
* * *
39967657 GAGCCAGTGTAAGACCATGTCTAGAACATGGCATCGG-TATTGAGATGA
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTA-CGAGAT-A
* * * *
39967705 GTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CAAGACA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGG-CTACGAGATA
* * *
39967750 TAGCTAATGTAAGACATGTCTGGGACATGCATCGGCTACGAGAT-
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATA
* *
39967794 GTGCCAGTGTAAGACCATGTCTGCGACATGGCATCGGC-A-GAGATA
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTACGAGATA
39967839 TACTAGACTT
Statistics
Matches: 148, Mismatches: 24, Indels: 21
0.77 0.12 0.11
Matches are distributed among these distances:
44 17 0.11
45 51 0.34
46 31 0.21
47 25 0.17
48 23 0.16
49 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.23
Consensus pattern (45 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATA
Found at i:39967862 original size:139 final size:137
Alignment explanation
Indices: 39967612--39967872 Score: 323
Period size: 139 Copynumber: 1.9 Consensus size: 137
39967602 CACTCGTGTG
* *
39967612 AGCTAGTGTAAGACATGTCTGGGACATGCATCGACCACATTATGAGAGCCAGTGTAAGACCATGT
1 AGCTAATGTAAGACATGTCTGGGACATGCATCGACCACATGAT-AGAGCCAGTGTAAGACCATGT
* * *
39967677 CTAGAACATGGCATCGGTATTGAGATGAGTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCC
65 CTAGAACATGGCATCGGCA-TGAGATGACTGCTAGTGTAAGACATGTATGGGACATGCATCGGCC
39967742 TCAAGACAT
129 TCAAGACAT
* * *
39967751 AGCTAATGTAAGACATGTCTGGGACATGCATCGGCTACGA-GAT-GTGCCAGTGTAAGACCATGT
1 AGCTAATGTAAGACATGTCTGGGACATGCATCGACCAC-ATGATAGAGCCAGTGTAAGACCATGT
* * *
39967814 CT-GCGACATGGCATCGGCA-GAGATATACTAGACTTGTGTAAGACCATGTATGGGACATG
65 CTAG-AACATGGCATCGGCATGAGAT-GACT-G-CTAGTGTAAGA-CATGTATGGGACATG
39967873 GCGTCAATGT
Statistics
Matches: 105, Mismatches: 11, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
135 5 0.05
136 3 0.03
137 35 0.33
138 10 0.10
139 51 0.49
140 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (137 bp):
AGCTAATGTAAGACATGTCTGGGACATGCATCGACCACATGATAGAGCCAGTGTAAGACCATGTC
TAGAACATGGCATCGGCATGAGATGACTGCTAGTGTAAGACATGTATGGGACATGCATCGGCCTC
AAGACAT
Found at i:39970298 original size:40 final size:40
Alignment explanation
Indices: 39970228--39970340 Score: 104
Period size: 40 Copynumber: 2.8 Consensus size: 40
39970218 CACATTAAGA
* * * *
39970228 CGAAGCTATCTCAGTACCACACACTTAGTGCCACT-TATAGC
1 CGAAGCTATCTCA-AAACGCACACTAAGTGCCA-TATATAGC
* ** *
39970269 CGAAGTTAT-TCCAATTCGCACACTAAGTGCTATATATAGC
1 CGAAGCTATCT-CAAAACGCACACTAAGTGCCATATATAGC
*
39970309 CGACGCTATCTCAAAACGCACACTAAGTGCCA
1 CGAAGCTATCTCAAAACGCACACTAAGTGCCA
39970341 AACTTAATCG
Statistics
Matches: 57, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
39 1 0.02
40 45 0.79
41 11 0.19
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.24
Consensus pattern (40 bp):
CGAAGCTATCTCAAAACGCACACTAAGTGCCATATATAGC
Found at i:39973754 original size:25 final size:25
Alignment explanation
Indices: 39973726--39973785 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
39973716 ATGCTCATAT
** *
39973726 GAGCTGTGAATTGGTATGCTAACAC
1 GAGCTGTGAATCAGTATACTAACAC
* *
39973751 GAGCTGTAAATCAGTATACTCACAC
1 GAGCTGTGAATCAGTATACTAACAC
*
39973776 AAGCTGTGAA
1 GAGCTGTGAA
39973786 AATGGGTCTG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.25
Consensus pattern (25 bp):
GAGCTGTGAATCAGTATACTAACAC
Found at i:39977413 original size:42 final size:41
Alignment explanation
Indices: 39977301--39977452 Score: 178
Period size: 42 Copynumber: 3.6 Consensus size: 41
39977291 TACCATACCA
* * *
39977301 ATGCCATATCCCAAATATGGTCTTACATGTAATCTCGTATCG
1 ATGCCATATCCC-AATATGGTCTTACACGAAATCTCATATCG
* *
39977343 ATGCCAATAGCCCAACTATGGTCTTACACGAAATCTCTTATCG
1 ATGCC-ATATCCCAA-TATGGTCTTACACGAAATCTCATATCG
* * *
39977386 ATACCATATCCCAGATATGGTCTTACACGAAGTCTCATATTG
1 ATGCCATATCCCA-ATATGGTCTTACACGAAATCTCATATCG
*
39977428 ATGCCATATCCAATATATGGTCTTA
1 ATGCCATATCCCA-ATATGGTCTTA
39977453 AACATAAACT
Statistics
Matches: 95, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
42 60 0.63
43 35 0.37
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (41 bp):
ATGCCATATCCCAATATGGTCTTACACGAAATCTCATATCG
Found at i:39985073 original size:16 final size:17
Alignment explanation
Indices: 39985049--39985081 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
39985039 TTAAATTTTA
39985049 AAAATATTAAAATTATT
1 AAAATATTAAAATTATT
39985066 AAAA-ATTAAAATTATT
1 AAAATATTAAAATTATT
39985082 TTAAAAAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAATATTAAAATTATT
Found at i:39985111 original size:17 final size:17
Alignment explanation
Indices: 39985091--39985130 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
39985081 TTTAAAAAGT
39985091 ATAAAATTTATTTTTTA
1 ATAAAATTTATTTTTTA
**
39985108 ATAATTTTTATTTTTTA
1 ATAAAATTTATTTTTTA
39985125 A-AAAAT
1 ATAAAAT
39985131 AATTAATTGT
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATAAAATTTATTTTTTA
Found at i:39988087 original size:18 final size:17
Alignment explanation
Indices: 39988056--39988092 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
39988046 TTCAGAATAT
*
39988056 TATAAAATTATTAAAAA
1 TATAAAAATATTAAAAA
39988073 TATAAAAATATTTAAAAA
1 TATAAAAATA-TTAAAAA
39988091 TA
1 TA
39988093 CATAAAACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TATAAAAATATTAAAAA
Found at i:39988088 original size:10 final size:9
Alignment explanation
Indices: 39988051--39988092 Score: 50
Period size: 10 Copynumber: 4.4 Consensus size: 9
39988041 CATGATTCAG
39988051 AATATTATAA
1 AATATTA-AA
39988061 AATTATTAAA
1 AA-TATTAAA
39988071 AATA-TAAA
1 AATATTAAA
39988079 AATATTTAAA
1 AATA-TTAAA
39988089 AATA
1 AATA
39988093 CATAAAACTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
8 8 0.28
9 2 0.07
10 14 0.48
11 5 0.17
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
AATATTAAA
Found at i:39988232 original size:31 final size:29
Alignment explanation
Indices: 39988191--39988256 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
39988181 AAGCTTTATA
* *
39988191 TTTTTGTAAATTATATAAATTTTTAAATATT
1 TTTTTATAAATT-TA-AAAGTTTTAAATATT
*
39988222 TTTTTATAAATTTAACAGTTTTAAATATT
1 TTTTTATAAATTTAAAAGTTTTAAATATT
39988251 TTTTTA
1 TTTTTA
39988257 CAAGTTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 19 0.59
30 2 0.06
31 11 0.34
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (29 bp):
TTTTTATAAATTTAAAAGTTTTAAATATT
Found at i:39988256 original size:21 final size:22
Alignment explanation
Indices: 39988232--39988279 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
39988222 TTTTTATAAA
39988232 TTTAAC-AGTTTTAAATATTTT
1 TTTAACAAGTTTTAAATATTTT
39988253 TTT-ACAAGTTTTAAATATTTT
1 TTTAACAAGTTTTAAATATTTT
*
39988274 TATAAC
1 TTTAAC
39988280 TTTTTACATC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 2 0.08
21 20 0.83
22 2 0.08
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.54
Consensus pattern (22 bp):
TTTAACAAGTTTTAAATATTTT
Found at i:39988589 original size:20 final size:20
Alignment explanation
Indices: 39988564--39988601 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
39988554 AGTTGTATTG
* *
39988564 ATACAAGTCTACTTCTACCA
1 ATACAAGCCCACTTCTACCA
39988584 ATACAAGCCCACTTCTAC
1 ATACAAGCCCACTTCTAC
39988602 TCAAGATCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.34, G:0.05, T:0.26
Consensus pattern (20 bp):
ATACAAGCCCACTTCTACCA
Found at i:39990164 original size:46 final size:46
Alignment explanation
Indices: 39990097--39990272 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
39990087 TGTAACCCGC
* * *
39990097 CCATAAGCAAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
* * *
39990143 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGAATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCG---GAC--GTTCGCAT
* *
39990193 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
*
39990236 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
39990273 TGCTCAACTA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 3 0.03
45 2 0.02
46 61 0.56
47 27 0.25
48 2 0.02
49 3 0.03
50 3 0.03
51 3 0.03
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
Found at i:39990218 original size:93 final size:93
Alignment explanation
Indices: 39990106--39990275 Score: 304
Period size: 93 Copynumber: 1.8 Consensus size: 93
39990096 CCCATAAGCA
* *
39990106 AACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
39990171 GAGTTCGAATGCCTAGTTACATCTCACG
66 GAGTTCGAATGCCTAGTTACATCTCACG
*
39990199 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
*
39990264 GAGTTCGGATGC
66 GAGTTCGAATGC
39990276 TCAACTATCC
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (93 bp):
AACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGAATGCCTAGTTACATCTCACG
Found at i:40006607 original size:65 final size:66
Alignment explanation
Indices: 40006526--40006657 Score: 248
Period size: 65 Copynumber: 2.0 Consensus size: 66
40006516 TTCCTCACTC
*
40006526 AAGATTTTCAAAAGAATGGTGGTATAAATGCTTA-CAAATACATTCAAATAGTCATTTGAAAAAC
1 AAGATTTTCAAAAGAATGGTAGTATAAATGCTTAGCAAATACATTCAAATAGTCATTTGAAAAAC
40006590 T
66 T
40006591 AAGATTTTCAAAAGAATGGTAGTATAAATGCTTAGCAAATACATTCAAATAGTCATTTGAAAAAC
1 AAGATTTTCAAAAGAATGGTAGTATAAATGCTTAGCAAATACATTCAAATAGTCATTTGAAAAAC
40006656 T
66 T
40006657 A
1 A
40006658 GTATTTGAGA
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
65 33 0.51
66 32 0.49
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (66 bp):
AAGATTTTCAAAAGAATGGTAGTATAAATGCTTAGCAAATACATTCAAATAGTCATTTGAAAAAC
T
Found at i:40007822 original size:18 final size:18
Alignment explanation
Indices: 40007782--40007823 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
40007772 AAAATATAGT
*
40007782 AACTAATTTTGATTGATAT
1 AACT-ATTTTGATTGATAA
*
40007801 AACTATTTTGATTGTTAA
1 AACTATTTTGATTGATAA
40007819 AACTA
1 AACTA
40007824 GCTAACAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (18 bp):
AACTATTTTGATTGATAA
Found at i:40010667 original size:14 final size:14
Alignment explanation
Indices: 40010650--40010679 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
40010640 TTATATTTTA
40010650 ATATTTAAAAAAAT
1 ATATTTAAAAAAAT
*
40010664 ATATTTAAAAATAT
1 ATATTTAAAAAAAT
40010678 AT
1 AT
40010680 TCAAATAAAA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATATTTAAAAAAAT
Found at i:40014131 original size:16 final size:18
Alignment explanation
Indices: 40014093--40014136 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
40014083 TGTGAAAGTT
*
40014093 GAATTCTAATAGCTATAA
1 GAATTCAAATAGCTATAA
40014111 GAATT-AAATAGCTAT-A
1 GAATTCAAATAGCTATAA
40014127 GAATTCAAAT
1 GAATTCAAAT
40014137 CTAGAAGTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 6 0.25
17 13 0.54
18 5 0.21
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.32
Consensus pattern (18 bp):
GAATTCAAATAGCTATAA
Found at i:40015310 original size:57 final size:57
Alignment explanation
Indices: 40015242--40015440 Score: 344
Period size: 57 Copynumber: 3.5 Consensus size: 57
40015232 CTATTAGGGC
* *
40015242 TTAGCCAGGACTGGTAATCCTAATTAAGCTCTTTTGAGCTTTCGTTATATAAAGGAT
1 TTAGCCTGGACTAGTAATCCTAATTAAGCTCTTTTGAGCTTTCGTTATATAAAGGAT
* * *
40015299 TTAGCCTGGACTAGTAATCTTAATTGAGCTCTTTTGAGATTTCGTTATATAAAGGAT
1 TTAGCCTGGACTAGTAATCCTAATTAAGCTCTTTTGAGCTTTCGTTATATAAAGGAT
40015356 TTAGCCTGGACTAGTAATCCTAATTAAGCTCTTTTGAGCTTTCGTTATATAAAGGAT
1 TTAGCCTGGACTAGTAATCCTAATTAAGCTCTTTTGAGCTTTCGTTATATAAAGGAT
*
40015413 TTAGCTTGGACTAGTAATCCTAATTAAG
1 TTAGCCTGGACTAGTAATCCTAATTAAG
40015441 AGTGTGTTCC
Statistics
Matches: 133, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 133 1.00
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.38
Consensus pattern (57 bp):
TTAGCCTGGACTAGTAATCCTAATTAAGCTCTTTTGAGCTTTCGTTATATAAAGGAT
Found at i:40018310 original size:32 final size:32
Alignment explanation
Indices: 40018274--40018338 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
40018264 GAAACCTGAG
* *
40018274 AACAATAAACGTCTACTAATCTGAAAACACAT
1 AACAACAAACGTCTACTAATCTAAAAACACAT
**
40018306 AACAACAAATTTCTACTAATCTAAAAACACAT
1 AACAACAAACGTCTACTAATCTAAAAACACAT
40018338 A
1 A
40018339 TAGAATTTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.52, C:0.22, G:0.03, T:0.23
Consensus pattern (32 bp):
AACAACAAACGTCTACTAATCTAAAAACACAT
Found at i:40018562 original size:22 final size:22
Alignment explanation
Indices: 40018537--40018592 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
40018527 AGCCAACTAC
40018537 CATGGGTGTCACGACACCAAAG
1 CATGGGTGTCACGACACCAAAG
40018559 CATGGGTGTCACGACACCAAAG
1 CATGGGTGTCACGACACCAAAG
*
40018581 CGTGGGTGTCAC
1 CATGGGTGTCAC
40018593 AACATTGAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.27, C:0.27, G:0.30, T:0.16
Consensus pattern (22 bp):
CATGGGTGTCACGACACCAAAG
Found at i:40020419 original size:35 final size:35
Alignment explanation
Indices: 40020373--40020442 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
40020363 TCACTGAAAT
40020373 GACAAATAATCTGAATGAGTACAAGATGAAGCTAA
1 GACAAATAATCTGAATGAGTACAAGATGAAGCTAA
40020408 GACAAATAATCTGAATGAGTACAAGATGAAGCTAA
1 GACAAATAATCTGAATGAGTACAAGATGAAGCTAA
40020443 CTCAAAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.49, C:0.11, G:0.20, T:0.20
Consensus pattern (35 bp):
GACAAATAATCTGAATGAGTACAAGATGAAGCTAA
Found at i:40022821 original size:25 final size:24
Alignment explanation
Indices: 40022793--40022842 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
40022783 TATCCCTAGA
* *
40022793 ATAATTAGACTTCAATTGAGAAAAG
1 ATAA-TAGAATTCAACTGAGAAAAG
*
40022818 ATAATAGAATTTAACTGAGAAAAG
1 ATAATAGAATTCAACTGAGAAAAG
40022842 A
1 A
40022843 AAATCGATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.52, C:0.06, G:0.16, T:0.26
Consensus pattern (24 bp):
ATAATAGAATTCAACTGAGAAAAG
Done.