Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 97507971
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: 97507971
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 232 characters in sequence are not A, C, G, or T
File 101 of 328
Found at i:28144019 original size:14 final size:14
Alignment explanation
Indices: 28144000--28144032 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
28143990 TTGTTTTTAT
28144000 ATATATGTATATAG
1 ATATATGTATATAG
*
28144014 ATATATGTATATAT
1 ATATATGTATATAG
28144028 ATATA
1 ATATA
28144033 GTAATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (14 bp):
ATATATGTATATAG
Found at i:28144152 original size:25 final size:25
Alignment explanation
Indices: 28144098--28144153 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
28144088 ATTATTATCA
*
28144098 TTATTATTATTATTTGTTATTTAAT
1 TTATTATTATTATTTATTATTTAAT
* *
28144123 ATATTATTATTA-TTATTATTGTATT
1 TTATTATTATTATTTATTATT-TAAT
28144148 TTATTA
1 TTATTA
28144154 CCATCATATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (25 bp):
TTATTATTATTATTTATTATTTAAT
Found at i:28144168 original size:3 final size:3
Alignment explanation
Indices: 28144087--28144142 Score: 60
Period size: 3 Copynumber: 18.3 Consensus size: 3
28144077 CATATTTCTA
* * *
28144087 TAT TAT TAT CAT TAT TAT TAT TATT TGT TAT T-T AAT ATAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT -TAT TAT TAT
28144133 TAT TAT TAT T
1 TAT TAT TAT T
28144143 GTATTTTATT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
2 1 0.02
3 39 0.89
4 4 0.09
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:28144440 original size:3 final size:3
Alignment explanation
Indices: 28144434--28144559 Score: 53
Period size: 3 Copynumber: 42.7 Consensus size: 3
28144424 TGTATTTACC
* * * *
28144434 ATT ATT ATT ACT ATT ATT -TT CATT -TT -TT ATT ACT ATT ACT AAT
1 ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT
* ** * * * *
28144477 ATC ATT CCT -TT ATT ATT TTCT ATT ATT ATT ATC ACT ATT ATT AAT
1 ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * *
28144522 ATA AAT ATT AAT ACT CTT ATT ATT ATT TTT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
28144560 CATCAATATT
Statistics
Matches: 87, Mismatches: 31, Indels: 10
0.68 0.24 0.08
Matches are distributed among these distances:
2 7 0.08
3 76 0.87
4 4 0.05
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:28144451 original size:22 final size:22
Alignment explanation
Indices: 28144426--28144471 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
28144416 TTATTATTTG
28144426 TATTTACCA-TTATTATTACTAT
1 TATTT-CCATTTATTATTACTAT
* *
28144448 TATTTTCATTTTTTATTACTAT
1 TATTTCCATTTATTATTACTAT
28144470 TA
1 TA
28144472 CTAATATCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 19 0.90
ACGTcount: A:0.28, C:0.11, G:0.00, T:0.61
Consensus pattern (22 bp):
TATTTCCATTTATTATTACTAT
Found at i:28148453 original size:17 final size:16
Alignment explanation
Indices: 28148431--28148472 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
28148421 ACGCTTTTTT
28148431 TGCATTCATCGCATTCA
1 TGCATTCATCGCA-TCA
28148448 TGCATTCAT-GCATCA
1 TGCATTCATCGCATCA
28148463 -GCATTGCATC
1 TGCATT-CATC
28148473 ATACGCACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 5 0.22
15 6 0.26
16 3 0.13
17 9 0.39
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (16 bp):
TGCATTCATCGCATCA
Found at i:28148454 original size:8 final size:8
Alignment explanation
Indices: 28148431--28148460 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
28148421 ACGCTTTTTT
28148431 TGCATTCA
1 TGCATTCA
28148439 TCGCATTCA
1 T-GCATTCA
28148448 TGCATTCA
1 TGCATTCA
28148456 TGCAT
1 TGCAT
28148461 CAGCATTGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.23, C:0.27, G:0.13, T:0.37
Consensus pattern (8 bp):
TGCATTCA
Found at i:28156629 original size:44 final size:44
Alignment explanation
Indices: 28156487--28156641 Score: 136
Period size: 44 Copynumber: 3.5 Consensus size: 44
28156477 CACAGATCTT
* ** *
28156487 ACCCCATAAGCAGTAGGGAAACAGATCGAAGGCAACGAGCTTTA
1 ACCCCTTAAGCAGTAGGGAAACAGATCGAAGATAATGAGCTTTA
* * * * * *
28156531 ACCCCCTAAGCAGTAGGGTAACA-AGCTGAAGTTCAT-AGATCTT-
1 ACCCCTTAAGCAGTAGGGAAACAGATC-GAAGATAATGAGCT-TTA
* * *
28156574 ATCACTCTAAGCAGTAGGGAAACAGATCGAAAATAATGAGCTTTA
1 ACCCCT-TAAGCAGTAGGGAAACAGATCGAAGATAATGAGCTTTA
*
28156619 ACCCCTTAAGCAGTAGGGTAACA
1 ACCCCTTAAGCAGTAGGGAAACA
28156642 AGCCAAATTT
Statistics
Matches: 85, Mismatches: 20, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
43 8 0.09
44 68 0.80
45 9 0.11
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.19
Consensus pattern (44 bp):
ACCCCTTAAGCAGTAGGGAAACAGATCGAAGATAATGAGCTTTA
Found at i:28156700 original size:44 final size:43
Alignment explanation
Indices: 28156528--28156700 Score: 125
Period size: 44 Copynumber: 4.0 Consensus size: 43
28156518 GCAACGAGCT
** * * *
28156528 TTAACCCCCTAAGCAGTAGGGTAACAAGCTGAAGTTCATAGATC
1 TTAACCCCCTAAGCAGTAGGGTAACAAGCCAAAATT-ACAGACC
* * * * * * *
28156572 TTATCACTCTAAGCAGTAGGGAAACAGATCGAAAA-TA-ATGAGCT
1 TTAACCCCCTAAGCAGTAGGGTAACA-AGCCAAAATTACA-GA-CC
* *
28156616 TTAACCCCTTAAGCAGTAGGGTAACAAGCCAAATTTACAGACC
1 TTAACCCCCTAAGCAGTAGGGTAACAAGCCAAAATTACAGACC
* * * *
28156659 TTAACCCCCTAAGTAGTAGGGTAATAGGCTGAAAATTACAGA
1 TTAACCCCCTAAGCAGTAGGGTAACAAGC-CAAAATTACAGA
28156701 TTTTGTCTCC
Statistics
Matches: 98, Mismatches: 25, Indels: 12
0.73 0.19 0.09
Matches are distributed among these distances:
42 1 0.01
43 34 0.35
44 58 0.59
45 5 0.05
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (43 bp):
TTAACCCCCTAAGCAGTAGGGTAACAAGCCAAAATTACAGACC
Found at i:28158454 original size:3 final size:3
Alignment explanation
Indices: 28158369--28158427 Score: 57
Period size: 3 Copynumber: 19.3 Consensus size: 3
28158359 CATATTTCTA
* * * *
28158369 TAT TAT TAT CAT TAT CAT TAT TATT TGT TAT T-T AAT ATAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT -TAT TAT TAT
28158415 TAT TAT TAT TAT T
1 TAT TAT TAT TAT T
28158428 GTATTTTTAT
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
2 1 0.02
3 40 0.89
4 4 0.09
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:28158729 original size:3 final size:3
Alignment explanation
Indices: 28158721--28158846 Score: 53
Period size: 3 Copynumber: 42.7 Consensus size: 3
28158711 TGTATTTACC
* * * *
28158721 ATT ATT ATT ACT ATT ATT -TT CATT -TT -TT ATT ACT ATT ACT AAT
1 ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT
* ** * * * *
28158764 ATC ATT CCT -TT ATT ATT TTCT ATT ATT ATT ATC ACT ATT ATT AAT
1 ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * *
28158809 ATA AAT ATT AAT ACT CTT ATT ATT ATT TTT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
28158847 CATCAATATT
Statistics
Matches: 87, Mismatches: 31, Indels: 10
0.68 0.24 0.08
Matches are distributed among these distances:
2 7 0.08
3 76 0.87
4 4 0.05
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:28162868 original size:56 final size:56
Alignment explanation
Indices: 28162782--28162893 Score: 206
Period size: 56 Copynumber: 2.0 Consensus size: 56
28162772 AAAATAAATG
*
28162782 TTGAAATAACTTAAATGATTGCTTAGAATCAAACTTCACAGGTGAAGTGGTGCCTA
1 TTGAAATAACTTAAATGATTGCTTAGAATCAAACTTCACAGATGAAGTGGTGCCTA
*
28162838 TTGAAATTACTTAAATGATTGCTTAGAATCAAACTTCACAGATGAAGTGGTGCCTA
1 TTGAAATAACTTAAATGATTGCTTAGAATCAAACTTCACAGATGAAGTGGTGCCTA
28162894 AGGTGGTGGG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (56 bp):
TTGAAATAACTTAAATGATTGCTTAGAATCAAACTTCACAGATGAAGTGGTGCCTA
Found at i:28168102 original size:20 final size:19
Alignment explanation
Indices: 28168070--28168120 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
28168060 ATATTTGCAT
*
28168070 AAAAATAAT-AAAATAGAAG
1 AAAAA-AATAAAAAGAGAAG
*
28168089 AAAAAAAGTAAAAAGAGAAT
1 AAAAAAA-TAAAAAGAGAAG
*
28168109 AGAAAAATAAAA
1 AAAAAAATAAAA
28168121 TGTAATTATC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 2 0.07
19 11 0.41
20 14 0.52
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (19 bp):
AAAAAAATAAAAAGAGAAG
Found at i:28173463 original size:49 final size:49
Alignment explanation
Indices: 28173374--28173482 Score: 123
Period size: 49 Copynumber: 2.2 Consensus size: 49
28173364 GCCGTGTGTT
*
28173374 AGACTGTGTGGCCAGGTCATGTGTGGCACACAGTCATGTGAAACTT-TAC
1 AGACAGTGTGGCCAGGTCATGTGTGGCACACAGTCATGTGAAA-TTGTAC
* * ** * *
28173423 AGACCGTGTTGCCAGGTTGTGTGTGGCACAC-GGCTGTGTGAAATTGTAC
1 AGACAGTGTGGCCAGGTCATGTGTGGCACACAGTC-ATGTGAAATTGTAC
28173472 AGACAGTGTGG
1 AGACAGTGTGG
28173483 AGCACATGGA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
48 4 0.08
49 46 0.92
ACGTcount: A:0.22, C:0.18, G:0.33, T:0.27
Consensus pattern (49 bp):
AGACAGTGTGGCCAGGTCATGTGTGGCACACAGTCATGTGAAATTGTAC
Found at i:28174055 original size:25 final size:25
Alignment explanation
Indices: 28174027--28174087 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
28174017 TAAAATATGC
* *
28174027 TATGTTATGATTCGATATAACATGA
1 TATGTTAAGATTCAATATAACATGA
* * *
28174052 TATGCTAAGATTCAATATGATATGA
1 TATGTTAAGATTCAATATAACATGA
*
28174077 TACGTTAAGAT
1 TATGTTAAGAT
28174088 ATGATTTGTA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (25 bp):
TATGTTAAGATTCAATATAACATGA
Found at i:28174914 original size:12 final size:12
Alignment explanation
Indices: 28174897--28174926 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
28174887 AAATCACTCT
28174897 ATATTTTGATAA
1 ATATTTTGATAA
28174909 ATATTTTGATAA
1 ATATTTTGATAA
*
28174921 AAATTT
1 ATATTT
28174927 AAAACTGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (12 bp):
ATATTTTGATAA
Found at i:28176660 original size:51 final size:51
Alignment explanation
Indices: 28176583--28176781 Score: 276
Period size: 51 Copynumber: 3.9 Consensus size: 51
28176573 CGGATACACG
* * * *
28176583 GTGGCTTTCACATAGTACCACCCTTGTAG-CTAAAGCTATTTTATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGT-GTCCAAAGCTATTATATTCACAAA
28176634 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAA
*
28176685 GTGGCCTTCACATAGTACCACA-TATGTGTCCAAAGCCATTATATTCACAAA
1 GTGGCCTTCACATAGTACCACACT-TGTGTCCAAAGCTATTATATTCACAAA
* * * * *
28176736 GTGGCCTTTATATAGTACCACAATTGTGTCCAAGGCTATTTTATTC
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTC
28176782 CTAAGGTTCA
Statistics
Matches: 135, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
50 2 0.01
51 132 0.98
52 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.32
Consensus pattern (51 bp):
GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAA
Found at i:28176875 original size:28 final size:27
Alignment explanation
Indices: 28176805--28176921 Score: 111
Period size: 24 Copynumber: 4.4 Consensus size: 27
28176795 GAGAAATTTC
**
28176805 TCACTTAGCACAATGCCATAAACTTTATT
1 TCACTTAGCAC-ATGCCATGGAC-TTATT
*
28176834 TCAGTTAG---ATGCCATGGACTTATT
1 TCACTTAGCACATGCCATGGACTTATT
* *
28176858 TCATTTAGCACATTGCCATAGACTTATT
1 TCACTTAGCACA-TGCCATGGACTTATT
*
28176886 TCACTTAG---ATGCCATGGTCTTATT
1 TCACTTAGCACATGCCATGGACTTATT
28176910 TCACTTAGCACA
1 TCACTTAGCACA
28176922 ATGTCATATC
Statistics
Matches: 73, Mismatches: 8, Indels: 16
0.75 0.08 0.16
Matches are distributed among these distances:
24 33 0.45
25 10 0.14
27 2 0.03
28 21 0.29
29 7 0.10
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (27 bp):
TCACTTAGCACATGCCATGGACTTATT
Found at i:28176896 original size:52 final size:53
Alignment explanation
Indices: 28176805--28176929 Score: 189
Period size: 52 Copynumber: 2.4 Consensus size: 53
28176795 GAGAAATTTC
*
28176805 TCACTTAGCACAATGCCATAAACTTTATTTCAGTTAGATGCCATGGACTTATT
1 TCACTTAGCACAATGCCATAAACTTTATTTCACTTAGATGCCATGGACTTATT
* * * *
28176858 TCATTTAGCACATTGCCATAGAC-TTATTTCACTTAGATGCCATGGTCTTATT
1 TCACTTAGCACAATGCCATAAACTTTATTTCACTTAGATGCCATGGACTTATT
*
28176910 TCACTTAGCACAATGTCATA
1 TCACTTAGCACAATGCCATA
28176930 TCCTAGATAT
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
52 44 0.69
53 20 0.31
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.37
Consensus pattern (53 bp):
TCACTTAGCACAATGCCATAAACTTTATTTCACTTAGATGCCATGGACTTATT
Found at i:28183798 original size:25 final size:25
Alignment explanation
Indices: 28183770--28183830 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
28183760 TAAAATATGC
*
28183770 TATGTTATGATTCAATATAACATGA
1 TATGTTAAGATTCAATATAACATGA
* * *
28183795 TATGCTAAGATTCAATATGATATGA
1 TATGTTAAGATTCAATATAACATGA
*
28183820 TACGTTAAGAT
1 TATGTTAAGAT
28183831 ATGATTTGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.38
Consensus pattern (25 bp):
TATGTTAAGATTCAATATAACATGA
Found at i:28191749 original size:15 final size:16
Alignment explanation
Indices: 28191726--28191762 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
28191716 GAATTTAATC
28191726 AAAAA-CAC-ATCAAT
1 AAAAATCACAATCAAT
28191740 AAAAATCACAAATCAAT
1 AAAAATCAC-AATCAAT
28191757 AAAAAT
1 AAAAAT
28191763 TCATTCTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 5 0.25
15 3 0.15
17 12 0.60
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAAATCACAATCAAT
Found at i:28193631 original size:40 final size:40
Alignment explanation
Indices: 28193585--28193666 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
28193575 AATCAAGAAT
*
28193585 AATGATATAAAAATAATAGGAGGCTTGTAAAAATCAAACA
1 AATGATATAAAAATAATAGGAGGCCTGTAAAAATCAAACA
28193625 AATGATATAAAAATAATAGGAGGCCTGTAAAAATCAAACA
1 AATGATATAAAAATAATAGGAGGCCTGTAAAAATCAAACA
28193665 AA
1 AA
28193667 ACTAAAAATA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.56, C:0.09, G:0.15, T:0.21
Consensus pattern (40 bp):
AATGATATAAAAATAATAGGAGGCCTGTAAAAATCAAACA
Found at i:28193886 original size:27 final size:25
Alignment explanation
Indices: 28193855--28193933 Score: 67
Period size: 27 Copynumber: 3.1 Consensus size: 25
28193845 TAAATGAAAT
28193855 AAATAAAAATAAAAGAATAATAATTA
1 AAATAAAAATAAAAGAATAATAA-TA
*
28193881 AGAATAATAAA-CAAAGAATGAA-AATA
1 A-AATAA-AAATAAAAGAAT-AATAATA
*
28193907 AAAT-AAAATAAAATAA-AATAAATA
1 AAATAAAAATAAAAGAATAAT-AATA
28193931 AAA
1 AAA
28193934 AGTGGAGCAA
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
22 2 0.05
23 3 0.07
24 13 0.30
25 3 0.07
26 4 0.09
27 14 0.32
28 5 0.11
ACGTcount: A:0.75, C:0.01, G:0.05, T:0.19
Consensus pattern (25 bp):
AAATAAAAATAAAAGAATAATAATA
Found at i:28193911 original size:5 final size:5
Alignment explanation
Indices: 28193901--28193933 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
28193891 ACAAAGAATG
28193901 AAAAT AAAAT AAAAT AAAAT AAAAT -AAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
28193934 AGTGGAGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:28193934 original size:10 final size:10
Alignment explanation
Indices: 28193841--28193934 Score: 56
Period size: 10 Copynumber: 9.4 Consensus size: 10
28193831 TGATAATAAG
28193841 AAAATAAAT-
1 AAAATAAATA
*
28193850 GAAATAAATA
1 AAAATAAATA
28193860 AAAATAAA-A
1 AAAATAAATA
*
28193869 GAATAATAATTA
1 -AA-AATAAATA
*
28193881 AGAAT-AATA
1 AAAATAAATA
*
28193890 AACAA-AGAATG
1 AA-AATA-AATA
28193901 AAAATAAA-A
1 AAAATAAATA
28193910 TAAAATAAA-A
1 -AAAATAAATA
28193920 TAAAATAAATA
1 -AAAATAAATA
28193931 AAAA
1 AAAA
28193935 GTGGAGCAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
9 13 0.19
10 40 0.60
11 13 0.19
12 1 0.01
ACGTcount: A:0.74, C:0.01, G:0.05, T:0.19
Consensus pattern (10 bp):
AAAATAAATA
Found at i:28201363 original size:23 final size:23
Alignment explanation
Indices: 28201323--28201372 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
28201313 AAAATTCAGG
* **
28201323 AAAAAAATAGTATTAAAAGGAAT
1 AAAAAAATAATATTAAAAAAAAT
28201346 AAAAAAATAAT-TTCAAAAAAAAT
1 AAAAAAATAATATT-AAAAAAAAT
28201369 AAAA
1 AAAA
28201373 TGAATAGTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.20
Consensus pattern (23 bp):
AAAAAAATAATATTAAAAAAAAT
Found at i:28208449 original size:2 final size:2
Alignment explanation
Indices: 28208442--28208480 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
28208432 TGAAAGTTGA
28208442 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28208481 ATTTTGAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28209500 original size:38 final size:38
Alignment explanation
Indices: 28209441--28209532 Score: 130
Period size: 38 Copynumber: 2.4 Consensus size: 38
28209431 TTTGATGTGC
*
28209441 ATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGTAAAAT
1 ATCCGGG-TTAAA-TCCCGCAGGCTTCGTGCTGGTAAAAT
**
28209481 ATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTAT
1 ATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAAAT
*
28209519 ATCCGGGATAAATC
1 ATCCGGGTTAAATC
28209533 TTACAGGCCT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
38 36 0.75
39 5 0.10
40 7 0.15
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (38 bp):
ATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAAAT
Found at i:28209540 original size:38 final size:38
Alignment explanation
Indices: 28209460--28209558 Score: 126
Period size: 38 Copynumber: 2.6 Consensus size: 38
28209450 TAAAGACCCG
** * *
28209460 CAGGCTTCGTGCTGGTAAAATATCCGGGTTAAATCCCG
1 CAGGCTTCGTGCTGGTATTATATCCGGGATAAATCCCA
**
28209498 CAGGCTTCGTGCTGGTATTATATCCGGGATAAATCTTA
1 CAGGCTTCGTGCTGGTATTATATCCGGGATAAATCCCA
* *
28209536 CAGGCCTAGTGCTGGTATTATAT
1 CAGGCTTCGTGCTGGTATTATAT
28209559 TGTGATGTGT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 53 1.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.31
Consensus pattern (38 bp):
CAGGCTTCGTGCTGGTATTATATCCGGGATAAATCCCA
Found at i:28209778 original size:43 final size:43
Alignment explanation
Indices: 28209560--28209765 Score: 376
Period size: 43 Copynumber: 4.8 Consensus size: 43
28209550 GTATTATATT
**
28209560 GTGATGTGTATTCGGGCCTTCGTAACTAGCAGGCTTCGTGCCG
1 GTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCG
*
28209603 GTGATGTGTATTGGGGCCTTCGTGCCTAGCAGGCTTCGTGCCG
1 GTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCG
*
28209646 GTGATGTGTATTCGGGCCTTCGTACCTAGCAGGCTTCGTGCCG
1 GTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCG
28209689 GTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCG
1 GTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCG
28209732 GTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGC
1 GTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGC
28209766 GTAATGCCGG
Statistics
Matches: 157, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 157 1.00
ACGTcount: A:0.11, C:0.24, G:0.34, T:0.30
Consensus pattern (43 bp):
GTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCG
Found at i:28215455 original size:28 final size:28
Alignment explanation
Indices: 28215394--28215466 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
28215384 AAAGGGAAGG
* **
28215394 CTGCCAAGGGCTATCTTAGGTGGAATGC
1 CTGCCAAAGGCTATCTTAGGTCAAATGC
* *
28215422 CCGCCAAAGGCTATCTTAGGTCAAATGT
1 CTGCCAAAGGCTATCTTAGGTCAAATGC
*
28215450 TTGCC-AAGGACTATCTT
1 CTGCCAAAGG-CTATCTT
28215467 GAAGACATGA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
27 4 0.11
28 33 0.89
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (28 bp):
CTGCCAAAGGCTATCTTAGGTCAAATGC
Found at i:28230460 original size:2 final size:2
Alignment explanation
Indices: 28230453--28230481 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
28230443 TCTCATGACT
28230453 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28230482 TATCCATTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28230989 original size:2 final size:2
Alignment explanation
Indices: 28230982--28231010 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
28230972 TCTCATGTCT
28230982 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28231011 TATCCATTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28233665 original size:73 final size:73
Alignment explanation
Indices: 28233583--28233728 Score: 283
Period size: 73 Copynumber: 2.0 Consensus size: 73
28233573 AATTTAGACC
*
28233583 TGGGGAACAGCAAGAAGAAAAATACGTAGAAGGAATTGGTGAAAAGGAGGCAGCAAGAAACGGAT
1 TGGGGAACAGCAAGAAGAAAAATACGTAGAAGGAATTGGTGAAAAGGAGGCAGCAAGAAAAGGAT
28233648 GAAATAAA
66 GAAATAAA
28233656 TGGGGAACAGCAAGAAGAAAAATACGTAGAAGGAATTGGTGAAAAGGAGGCAGCAAGAAAAGGAT
1 TGGGGAACAGCAAGAAGAAAAATACGTAGAAGGAATTGGTGAAAAGGAGGCAGCAAGAAAAGGAT
28233721 GAAATAAA
66 GAAATAAA
28233729 GCAGGCAAAG
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.50, C:0.08, G:0.32, T:0.11
Consensus pattern (73 bp):
TGGGGAACAGCAAGAAGAAAAATACGTAGAAGGAATTGGTGAAAAGGAGGCAGCAAGAAAAGGAT
GAAATAAA
Found at i:28235999 original size:18 final size:19
Alignment explanation
Indices: 28235971--28236007 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
28235961 ATTAAATTAA
28235971 TTGATTGAATCGATCTAAT
1 TTGATTGAATCGATCTAAT
28235990 TTGATT-AATCGATCTAAT
1 TTGATTGAATCGATCTAAT
28236008 CAATCGGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (19 bp):
TTGATTGAATCGATCTAAT
Found at i:28238091 original size:30 final size:30
Alignment explanation
Indices: 28238055--28238116 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
28238045 CTTAACAAGT
*
28238055 AAATGCCTCTAAGATAATAA-ATAAATTAAC
1 AAATGCCTCTAAAATAATAATA-AAATTAAC
*
28238085 AAATGCCTTTAAAATAATAATAAAATTAAC
1 AAATGCCTCTAAAATAATAATAAAATTAAC
28238115 AA
1 AA
28238117 GAAAATAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.56, C:0.11, G:0.05, T:0.27
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAATAAAATTAAC
Found at i:28245405 original size:19 final size:20
Alignment explanation
Indices: 28245380--28245441 Score: 76
Period size: 19 Copynumber: 3.2 Consensus size: 20
28245370 AGTGAAAAGT
28245380 TTATAAATAAATAATAATAA
1 TTATAAATAAATAATAATAA
*
28245400 TT-TAAATATAATTA-AAT-A
1 TTATAAATA-AATAATAATAA
*
28245418 TTATAAATAAATATTAATAA
1 TTATAAATAAATAATAATAA
28245438 TTAT
1 TTAT
28245442 CGAGGTTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
18 6 0.17
19 18 0.51
20 11 0.31
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TTATAAATAAATAATAATAA
Found at i:28252295 original size:106 final size:106
Alignment explanation
Indices: 28252105--28252317 Score: 399
Period size: 106 Copynumber: 2.0 Consensus size: 106
28252095 AGCTTTCAAC
*
28252105 AAAATGCTTTAAATTTTATAATTGTTCTATGAATAGTTTCTTCAGTTATCGACTGATAATTACAA
1 AAAATGCTTTAAATTTTATAATTGTTCCATGAATAGTTTCTTCAGTTATCGACTGATAATTACAA
* *
28252170 GAGACCTTTATGCCGATCATGCATGTGCCTTGCATTAACCA
66 GACACCTTTATGCCAATCATGCATGTGCCTTGCATTAACCA
28252211 AAAATGCTTTAAATTTTATAATTGTTCCATGAATAGTTTCTTCAGTTATCGACTGATAATTACAA
1 AAAATGCTTTAAATTTTATAATTGTTCCATGAATAGTTTCTTCAGTTATCGACTGATAATTACAA
28252276 GACACCTTTATGCCAATCATGCATGTGCCTTGCATTAACCA
66 GACACCTTTATGCCAATCATGCATGTGCCTTGCATTAACCA
28252317 A
1 A
28252318 CTTGATCTAC
Statistics
Matches: 104, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
106 104 1.00
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (106 bp):
AAAATGCTTTAAATTTTATAATTGTTCCATGAATAGTTTCTTCAGTTATCGACTGATAATTACAA
GACACCTTTATGCCAATCATGCATGTGCCTTGCATTAACCA
Found at i:28257184 original size:28 final size:29
Alignment explanation
Indices: 28257152--28257217 Score: 73
Period size: 32 Copynumber: 2.2 Consensus size: 29
28257142 GGTTAATCTA
28257152 TAATCAATA-ATCACATC-TTTCCACTAAT
1 TAATCAATATATCACA-CGTTTCCACTAAT
*
28257180 TAATCTATAATATCTCACACGTTTCCACTAAT
1 TAATC---AATATATCACACGTTTCCACTAAT
28257212 TAATCA
1 TAATCA
28257218 CATCTTACGA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
28 5 0.16
29 1 0.03
31 5 0.16
32 21 0.66
ACGTcount: A:0.38, C:0.24, G:0.02, T:0.36
Consensus pattern (29 bp):
TAATCAATATATCACACGTTTCCACTAAT
Found at i:28258761 original size:19 final size:19
Alignment explanation
Indices: 28258737--28258774 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
28258727 TATTAAAATG
28258737 CTTATTAAGATATTTCAAA
1 CTTATTAAGATATTTCAAA
28258756 CTTATTAAGATATTTCAAA
1 CTTATTAAGATATTTCAAA
28258775 ACAACGGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (19 bp):
CTTATTAAGATATTTCAAA
Found at i:28262698 original size:40 final size:40
Alignment explanation
Indices: 28262634--28262829 Score: 220
Period size: 39 Copynumber: 5.0 Consensus size: 40
28262624 GCTACTCGTT
* * * ***
28262634 CAAACGCCTTCGGGACATAGCCCGGTTATGGTAAC-CTGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATCACAACTC-GCA
*
28262674 CAAATGCCTTCGGGACTTAACCCGGATATCACAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATCACAACTCGCA
* * *
28262714 CAATTGCCTTCGGG-CTTAGCCCGGATATCATAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATCACAACTCGCA
* *
28262753 CCATTGCCTTCGGG-CTTAGCCCGGATATCACAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATCACAACTCGCA
* * *
28262792 CAATTGCCTTCGGG-CTTAGCCCGGGTATCACAATTCGC
1 CAAATGCCTTCGGGACTTAGCCCGGATATCACAACTCGC
28262830 GCATTCATAC
Statistics
Matches: 138, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
39 93 0.67
40 44 0.32
41 1 0.01
ACGTcount: A:0.23, C:0.32, G:0.22, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATCACAACTCGCA
Found at i:28262751 original size:39 final size:39
Alignment explanation
Indices: 28262671--28262829 Score: 246
Period size: 39 Copynumber: 4.1 Consensus size: 39
28262661 ATGGTAACCT
* *
28262671 GCACAAATGCCTTCGGGACTTAACCCGGATATCACAACTC
1 GCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACTC
* *
28262711 GCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCTC
1 GCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACTC
*
28262750 GCACCATTGCCTTCGGGCTTAGCCCGGATATCACAACTC
1 GCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACTC
* *
28262789 GCACAATTGCCTTCGGGCTTAGCCCGGGTATCACAATTC
1 GCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACTC
28262828 GC
1 GC
28262830 GCATTCATAC
Statistics
Matches: 109, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 93 0.85
40 16 0.15
ACGTcount: A:0.23, C:0.33, G:0.21, T:0.23
Consensus pattern (39 bp):
GCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACTC
Found at i:28273240 original size:20 final size:20
Alignment explanation
Indices: 28273215--28273253 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
28273205 TAAGGAACAC
28273215 GGGTGTGTCCCAATGCACAT
1 GGGTGTGTCCCAATGCACAT
*
28273235 GGGTGTGTCTCAATGCACA
1 GGGTGTGTCCCAATGCACA
28273254 CGGTTATGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.23, G:0.31, T:0.26
Consensus pattern (20 bp):
GGGTGTGTCCCAATGCACAT
Found at i:28275869 original size:23 final size:21
Alignment explanation
Indices: 28275842--28275884 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
28275832 TATTAATAAC
*
28275842 AATATTTAATAAATTTGAAAATG
1 AATATTT-ATAAAATT-AAAATG
28275865 AATATTTATAAAATTAAAAT
1 AATATTTATAAAATTAAAAT
28275885 ATGCGAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 7 0.37
23 7 0.37
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (21 bp):
AATATTTATAAAATTAAAATG
Found at i:28278910 original size:161 final size:161
Alignment explanation
Indices: 28278645--28279237 Score: 974
Period size: 161 Copynumber: 3.7 Consensus size: 161
28278635 ACGACCATCA
* * * *
28278645 CAGTGTTGGTCAACTTAAAGAGCTTATCAAAGAAGCTATAAAAGACCAATTTTAAAGTGTTGATC
1 CAGTGTTGGTCAACTCAAAGAGCTCATCAAAGAAGCTATAAAAGACCAATTTGAAAGTATTGATC
* * *
28278710 CATTTTCATATACATACTCAAATCCATACACACAAATGATTGATCGTCCAATATACAAGTTGCCA
66 CACTTTCATATACATACTCAAATCCATACACACAAAGGATTGATCGTCCAATGTACAAGTTGCCA
28278775 AAGATCTTTAACCAACAATCAATGAAGTTTT
131 AAGATCTTTAACCAACAATCAATGAAGTTTT
28278806 CAGTGTTGGTCAACTCAAAGAGCTCATCAAAGAAGCTATAAAAGACCAATTTGAAAGTATTGATC
1 CAGTGTTGGTCAACTCAAAGAGCTCATCAAAGAAGCTATAAAAGACCAATTTGAAAGTATTGATC
*
28278871 CACTTTCATATACATACTCAAATCCATACACACAAATGATTGATCGTCCAATGTACAAGTTGCCA
66 CACTTTCATATACATACTCAAATCCATACACACAAAGGATTGATCGTCCAATGTACAAGTTGCCA
28278936 AAGATCTTTAACCAACAATCAATGAAGTTTT
131 AAGATCTTTAACCAACAATCAATGAAGTTTT
* * * * **
28278967 CAGTCTTGGTCAACTCAAAGAGCTTATCAAATAAGCTATAAATGTTCAATTTGAAAGTATTGATC
1 CAGTGTTGGTCAACTCAAAGAGCTCATCAAAGAAGCTATAAAAGACCAATTTGAAAGTATTGATC
*
28279032 CA-TCTTCATATACATACTCAAATCCATACACACGAAGGATTGATCGTCCAATGTACAAGTTGCC
66 CACT-TTCATATACATACTCAAATCCATACACACAAAGGATTGATCGTCCAATGTACAAGTTGCC
28279096 AAAGATCTTTAACCAACAATCAATGAAGTTTT
130 AAAGATCTTTAACCAACAATCAATGAAGTTTT
* * * *
28279128 CAGTGTTGGTCAACTCAAAGGGATCATCAAAGAAGCTATAAAACACCAATTTGAAAGTGTTGATC
1 CAGTGTTGGTCAACTCAAAGAGCTCATCAAAGAAGCTATAAAAGACCAATTTGAAAGTATTGATC
*
28279193 CACCTTT-ATATACATACTCAAAGCCATACACACAAAGGATTGATC
66 CA-CTTTCATATACATACTCAAATCCATACACACAAAGGATTGATC
28279238 ATCTGATAAA
Statistics
Matches: 403, Mismatches: 26, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
160 1 0.00
161 399 0.99
162 2 0.00
163 1 0.00
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (161 bp):
CAGTGTTGGTCAACTCAAAGAGCTCATCAAAGAAGCTATAAAAGACCAATTTGAAAGTATTGATC
CACTTTCATATACATACTCAAATCCATACACACAAAGGATTGATCGTCCAATGTACAAGTTGCCA
AAGATCTTTAACCAACAATCAATGAAGTTTT
Found at i:28283635 original size:33 final size:35
Alignment explanation
Indices: 28283539--28283636 Score: 91
Period size: 33 Copynumber: 2.9 Consensus size: 35
28283529 GTTAATATTT
*
28283539 TAATATATGAAATATAAATTTTAAATATTT--TTAAG
1 TAATATAT-AAAT-TATATTTTAAATATTTAATTAAG
* *
28283574 TAATAAATATTAATTAT-TTATAAA-ATTTAATT-AG
1 TAAT--ATATAAATTATATTTTAAATATTTAATTAAG
28283608 -AATATATAAATTATATTTTAAATATTTAA
1 TAATATATAAATTATATTTTAAATATTTAA
28283637 ATATAACCAT
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
31 10 0.19
32 6 0.12
33 13 0.25
34 8 0.15
35 8 0.15
36 3 0.06
37 4 0.08
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (35 bp):
TAATATATAAATTATATTTTAAATATTTAATTAAG
Found at i:28286455 original size:26 final size:26
Alignment explanation
Indices: 28286419--28286528 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
28286409 TGATACAAAT
28286419 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
28286445 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
28286471 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
28286497 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
28286523 TGATAA
1 TGATAA
28286529 GAATTTCATG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:28288556 original size:137 final size:137
Alignment explanation
Indices: 28288309--28288595 Score: 538
Period size: 137 Copynumber: 2.1 Consensus size: 137
28288299 GAGTAGTCTC
*
28288309 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCAATGGGCCATAC
*
28288374 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATTTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
28288439 ACTGTTA
131 ACTGTTA
28288446 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCAATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCAATGGGCCATAC
28288511 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
28288576 ACTGTTA
131 ACTGTTA
**
28288583 CCTGAATGGGCTT
1 CCCAAATGGGCTT
28288596 AGGCCCAATA
Statistics
Matches: 146, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
137 146 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCAATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
ACTGTTA
Found at i:28290877 original size:6 final size:6
Alignment explanation
Indices: 28290866--28290924 Score: 84
Period size: 6 Copynumber: 9.8 Consensus size: 6
28290856 AATTTATAAT
*
28290866 TGTCAA TGTCAA TGTCAA -GATCAA TGTCAA TATCAA TGTCAA TGTCAA
1 TGTCAA TGTCAA TGTCAA TG-TCAA TGTCAA TGTCAA TGTCAA TGTCAA
*
28290914 TATCAA TGTCA
1 TGTCAA TGTCA
28290925 TAAATGATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
5 1 0.02
6 45 0.96
7 1 0.02
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (6 bp):
TGTCAA
Found at i:28290891 original size:18 final size:18
Alignment explanation
Indices: 28290866--28290924 Score: 93
Period size: 18 Copynumber: 3.3 Consensus size: 18
28290856 AATTTATAAT
*
28290866 TGTCAATGTCAATGTCAA
1 TGTCAATGTCAATATCAA
28290884 -GATCAATGTCAATATCAA
1 TG-TCAATGTCAATATCAA
28290902 TGTCAATGTCAATATCAA
1 TGTCAATGTCAATATCAA
28290920 TGTCA
1 TGTCA
28290925 TAAATGATAT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
17 1 0.03
18 36 0.95
19 1 0.03
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (18 bp):
TGTCAATGTCAATATCAA
Found at i:28294506 original size:78 final size:79
Alignment explanation
Indices: 28294420--28294600 Score: 221
Period size: 78 Copynumber: 2.3 Consensus size: 79
28294410 AAATTTAAAC
* * * *
28294420 CCGGTATAATACCAGCTCGAAGCCTCTG-GGA-CTTTAG-CCTGGACATATTTCCAGCACGTAGC
1 CCGGTATAATTCCAGCACGAAGCCTCTGCGGACCTTAAGTCC-GGACATAATTCCAGCACGTAGC
*
28294482 CTGCGGACCTTAAGT
65 CTGCGGACCCTAAGT
*
28294497 CCGGTTATAATTCCAGCAC-ATAG-C-CTGCGGACCTTAAGTCCGGATATAATTCCAGCACGTAG
1 CCGG-TATAATTCCAGCACGA-AGCCTCTGCGGACCTTAAGTCCGGACATAATTCCAGCACGTAG
28294559 CCTGCGGACCCTAAGT
64 CCTGCGGACCCTAAGT
*
28294575 CCGGATATAATTCCAGCACGTAGCCT
1 CCGG-TATAATTCCAGCACGAAGCCT
28294601 ACGGACCCTA
Statistics
Matches: 88, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
76 3 0.03
77 9 0.10
78 73 0.83
79 3 0.03
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (79 bp):
CCGGTATAATTCCAGCACGAAGCCTCTGCGGACCTTAAGTCCGGACATAATTCCAGCACGTAGCC
TGCGGACCCTAAGT
Found at i:28294511 original size:39 final size:39
Alignment explanation
Indices: 28294468--28294620 Score: 252
Period size: 39 Copynumber: 3.9 Consensus size: 39
28294458 CTGGACATAT
* *
28294468 TTCCAGCACGTAGCCTGCGGACCTTAAGTCCGGTTATAA
1 TTCCAGCACGTAGCCTGCGGACCCTAAGTCCGGATATAA
* *
28294507 TTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATATAA
1 TTCCAGCACGTAGCCTGCGGACCCTAAGTCCGGATATAA
28294546 TTCCAGCACGTAGCCTGCGGACCCTAAGTCCGGATATAA
1 TTCCAGCACGTAGCCTGCGGACCCTAAGTCCGGATATAA
* *
28294585 TTCCAGCACGTAGCCTACGGACCCTAAGTCCAGATA
1 TTCCAGCACGTAGCCTGCGGACCCTAAGTCCGGATA
28294621 AACATCGCTG
Statistics
Matches: 108, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 108 1.00
ACGTcount: A:0.26, C:0.30, G:0.22, T:0.22
Consensus pattern (39 bp):
TTCCAGCACGTAGCCTGCGGACCCTAAGTCCGGATATAA
Found at i:28302210 original size:39 final size:39
Alignment explanation
Indices: 28302167--28302315 Score: 226
Period size: 39 Copynumber: 3.8 Consensus size: 39
28302157 CCAGACATAT
* * *
28302167 TTCCAGCACGTAGCTTGCGGACCTTAAGTCCGGTTATAA
1 TTCCAGCACGTAGCCTGCGGACCCTAAGTCCGGATATAA
* * * *
28302206 TTCCAGCACATAGCCTACTGACCTTAAGTCCGGATATAA
1 TTCCAGCACGTAGCCTGCGGACCCTAAGTCCGGATATAA
*
28302245 TTCCAGCATGTAGCCTGCGGACCCTAAGTCCGGATATAA
1 TTCCAGCACGTAGCCTGCGGACCCTAAGTCCGGATATAA
28302284 TTCCAGCACGTAGCCTGCGGACCCTAAGTCCG
1 TTCCAGCACGTAGCCTGCGGACCCTAAGTCCG
28302316 AATAAACATC
Statistics
Matches: 99, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 99 1.00
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.24
Consensus pattern (39 bp):
TTCCAGCACGTAGCCTGCGGACCCTAAGTCCGGATATAA
Found at i:28302221 original size:78 final size:78
Alignment explanation
Indices: 28302139--28302311 Score: 213
Period size: 78 Copynumber: 2.2 Consensus size: 78
28302129 ACCAGCTTGA
* * * * *
28302139 AGCCTACGGGA-CTTTAGCCCAGACATATTTCCAGCACGTAGCTTGCGGACCTTAAGTCCGGTTA
1 AGCCTAC-GGACCTTAAGCCCAGACATAATTCCAGCACGTAGCCTGCGGACCCTAAGTCCGGATA
28302203 TAATTCCAGCACAT
65 TAATTCCAGCACAT
* * * * *
28302217 AGCCTACTGACCTTAAGTCCGGATATAATTCCAGCATGTAGCCTGCGGACCCTAAGTCCGGATAT
1 AGCCTACGGACCTTAAGCCCAGACATAATTCCAGCACGTAGCCTGCGGACCCTAAGTCCGGATAT
*
28302282 AATTCCAGCACGT
66 AATTCCAGCACAT
* *
28302295 AGCCTGCGGACCCTAAG
1 AGCCTACGGACCTTAAG
28302312 TCCGAATAAA
Statistics
Matches: 80, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
77 2 0.03
78 78 0.98
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (78 bp):
AGCCTACGGACCTTAAGCCCAGACATAATTCCAGCACGTAGCCTGCGGACCCTAAGTCCGGATAT
AATTCCAGCACAT
Found at i:28305401 original size:43 final size:43
Alignment explanation
Indices: 28305335--28305420 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
28305325 AAATAGTACA
**
28305335 ATGCCAACGTCCCAGACGTGGTCTTACATGTAGCCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACATGTAAACACATATCG
*
28305378 ATGCC-ACTGTCCCAGACAG-GGTCTTACTTGTAAACACATATCG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACATGTAAACACATATCG
28305421 GAATCACAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 2 0.05
43 35 0.92
44 1 0.03
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACATGTAAACACATATCG
Found at i:28320145 original size:27 final size:26
Alignment explanation
Indices: 28320106--28320221 Score: 108
Period size: 27 Copynumber: 4.3 Consensus size: 26
28320096 AAAATTACTG
*
28320106 AATACCCTC-AATTAGTAAAATTACCGA
1 AATACCC-CGAATT-GTAAAATTATCGA
* * * *
28320133 AATACCCCTAATTTTTGAAATTATTGA
1 AATACCCCGAA-TTGTAAAATTATCGA
*
28320160 AATACCCTCGACTTGTAAAATTATCGA
1 AATACCC-CGAATTGTAAAATTATCGA
* *
28320187 AATACCCTCGACTTGTAAAATTATAGA
1 AATACCC-CGAATTGTAAAATTATCGA
28320214 AATACCCC
1 AATACCCC
28320222 AAATACCCCT
Statistics
Matches: 76, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
26 2 0.03
27 70 0.92
28 4 0.05
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.30
Consensus pattern (26 bp):
AATACCCCGAATTGTAAAATTATCGA
Found at i:28320208 original size:54 final size:54
Alignment explanation
Indices: 28320096--28320220 Score: 139
Period size: 54 Copynumber: 2.3 Consensus size: 54
28320086 TTTGGTTTAC
* * *
28320096 AAAATTACTG-AATACCCTCAATTAGTAAAATTACCGAAATACCCCTAATTTTT
1 AAAATTATTGAAATACCCTCAATTAGTAAAATTACCGAAATACCCCTAACTTGT
* * * *
28320149 GAAATTATTGAAATACCCTCGACTT-GTAAAATTATCGAAATA-CCCTCGACTTGT
1 AAAATTATTGAAATACCCTC-AATTAGTAAAATTACCGAAATACCCCT-AACTTGT
*
28320203 AAAATTATAGAAATACCC
1 AAAATTATTGAAATACCC
28320221 CAAATACCCC
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
53 12 0.20
54 45 0.75
55 3 0.05
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (54 bp):
AAAATTATTGAAATACCCTCAATTAGTAAAATTACCGAAATACCCCTAACTTGT
Found at i:28320243 original size:27 final size:26
Alignment explanation
Indices: 28320213--28320290 Score: 66
Period size: 27 Copynumber: 2.9 Consensus size: 26
28320203 AAAATTATAG
28320213 AAATACCCCAAATACCCCTGATTTGAA
1 AAATA-CCCAAATACCCCTGATTTGAA
** *
28320240 AAATTACTGAAATACCCTTGATTTGGAA
1 AAA-TACCCAAATACCCCTGATTT-GAA
* ** *
28320268 AATTACAAAAATACCCTTGATTT
1 AAATACCCAAATACCCCTGATTT
28320291 ACAAAATTAC
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
27 36 0.84
28 7 0.16
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (26 bp):
AAATACCCAAATACCCCTGATTTGAA
Found at i:28320243 original size:36 final size:36
Alignment explanation
Indices: 28320186--28320256 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
28320176 AAAATTATCG
*
28320186 AAATACCCTCGACTTGTAAAATTA-TAGAAATACCCC
1 AAATACCCTCGACTTGAAAAATTACT-GAAATACCCC
*
28320222 AAATACCC-CTGATTTGAAAAATTACTGAAATACCC
1 AAATACCCTC-GACTTGAAAAATTACTGAAATACCC
28320257 TTGATTTGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 1 0.03
36 29 0.94
37 1 0.03
ACGTcount: A:0.42, C:0.24, G:0.08, T:0.25
Consensus pattern (36 bp):
AAATACCCTCGACTTGAAAAATTACTGAAATACCCC
Found at i:28320243 original size:63 final size:63
Alignment explanation
Indices: 28320159--28320283 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 63
28320149 GAAATTATTG
* * * *
28320159 AAATACCCTCGACTTGTAAAATTA-TCGAAATACCCTCGACTTGTAAAATTATAGAAATACCCC
1 AAATACCCTCGACTTGAAAAATTACT-GAAATACCCTCGACTTGGAAAATTACAAAAATACCCC
* * *
28320222 AAATACCC-CTGATTTGAAAAATTACTGAAATACCCTTGATTTGGAAAATTACAAAAATACCC
1 AAATACCCTC-GACTTGAAAAATTACTGAAATACCCTCGACTTGGAAAATTACAAAAATACCC
28320284 TTGATTTACA
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 51 0.96
64 1 0.02
ACGTcount: A:0.42, C:0.22, G:0.10, T:0.27
Consensus pattern (63 bp):
AAATACCCTCGACTTGAAAAATTACTGAAATACCCTCGACTTGGAAAATTACAAAAATACCCC
Found at i:28320270 original size:90 final size:90
Alignment explanation
Indices: 28320132--28320308 Score: 212
Period size: 90 Copynumber: 2.0 Consensus size: 90
28320122 AAAATTACCG
*** * * *
28320132 AAATACCCCTAATTTTTGAAATTATTGAAATACCCTCGACTTGTAAAATTATC-GAAATACCCTC
1 AAATACCCCTAATTTGAAAAATTACTGAAATACCCTCGACTTGGAAAATTA-CAAAAATACCCTC
** *
28320196 GACTTGTAAAATTATAGAAATACCCC
65 GACTTACAAAATTACAGAAATACCCC
* * * *
28320222 AAATACCCCTGATTTGAAAAATTACTGAAATACCCTTGATTTGGAAAATTACAAAAATACCCTTG
1 AAATACCCCTAATTTGAAAAATTACTGAAATACCCTCGACTTGGAAAATTACAAAAATACCCTCG
*
28320287 ATTTACAAAATTACAGAAATAC
66 ACTTACAAAATTACAGAAATAC
28320309 TTTTGACTTT
Statistics
Matches: 72, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
89 1 0.01
90 71 0.99
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (90 bp):
AAATACCCCTAATTTGAAAAATTACTGAAATACCCTCGACTTGGAAAATTACAAAAATACCCTCG
ACTTACAAAATTACAGAAATACCCC
Found at i:28320351 original size:55 final size:54
Alignment explanation
Indices: 28320222--28320368 Score: 168
Period size: 55 Copynumber: 2.7 Consensus size: 54
28320212 GAAATACCCC
** * * **
28320222 AAATACCCCTGATTTGAAAAATTACTGAAATACCCTTGATTTGGAAAATTACAA
1 AAATACCATTGATTTGCAAAATTACTGAAATACCTTTGATTTCAAAAATTACAA
* * * * * *
28320276 AAATACCCTTGATTTACAAAATTACAGAAATACTTTTGACTTTCAAAAATTATAG
1 AAATACCATTGATTTGCAAAATTACTGAAATACCTTTGA-TTTCAAAAATTACAA
*
28320331 AAATACCATTGGTTTGCAAAATTACTGAAATACCTTTG
1 AAATACCATTGATTTGCAAAATTACTGAAATACCTTTG
28320369 GTTTGTGGAT
Statistics
Matches: 77, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
54 33 0.43
55 44 0.57
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (54 bp):
AAATACCATTGATTTGCAAAATTACTGAAATACCTTTGATTTCAAAAATTACAA
Found at i:28320369 original size:27 final size:27
Alignment explanation
Indices: 28320222--28320373 Score: 146
Period size: 27 Copynumber: 5.6 Consensus size: 27
28320212 GAAATACCCC
* *
28320222 AAATACCCCTGATTTGAAAAATTACTG
1 AAATACCCTTGATTTGCAAAATTACTG
* **
28320249 AAATACCCTTGATTTGGAAAATTACAA
1 AAATACCCTTGATTTGCAAAATTACTG
* *
28320276 AAATACCCTTGATTTACAAAATTACAG
1 AAATACCCTTGATTTGCAAAATTACTG
**
28320303 AAATACTTTTGACTTT-CAAAAATTA-TAG
1 AAATACCCTTGA-TTTGC-AAAATTACT-G
* *
28320331 AAATACCATTGGTTTGCAAAATTACTG
1 AAATACCCTTGATTTGCAAAATTACTG
* *
28320358 AAATACCTTTGGTTTG
1 AAATACCCTTGATTTG
28320374 TGGATTTACC
Statistics
Matches: 106, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
27 84 0.79
28 22 0.21
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (27 bp):
AAATACCCTTGATTTGCAAAATTACTG
Found at i:28320682 original size:41 final size:41
Alignment explanation
Indices: 28320633--28320755 Score: 185
Period size: 41 Copynumber: 3.0 Consensus size: 41
28320623 GGAGGAAGAA
* *
28320633 ATTAAGGATCGCATGGTTGCTTGACAACTGTGGATCCACCG
1 ATTAAGGATCGCATGGTTGCTTGACGACTATGGATCCACCG
* *
28320674 ATTGAGGATCGCATGGTTGCTTGACGA-TCATGGATCCACAG
1 ATTAAGGATCGCATGGTTGCTTGACGACT-ATGGATCCACCG
*
28320715 ATTAAGGATCGCATGGTTGCTTGATGACTATGGATCCACCG
1 ATTAAGGATCGCATGGTTGCTTGACGACTATGGATCCACCG
28320756 GTGGCTTTTA
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
40 1 0.01
41 71 0.97
42 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (41 bp):
ATTAAGGATCGCATGGTTGCTTGACGACTATGGATCCACCG
Found at i:28320940 original size:22 final size:22
Alignment explanation
Indices: 28320912--28320961 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
28320902 TATTGCTTTA
28320912 TGCCAACCT-ACATATGGCTCTG
1 TGCCAACCTGA-ATATGGCTCTG
* *
28320934 TGCCAACCTGATTATGGCTGTG
1 TGCCAACCTGAATATGGCTCTG
28320956 TGCCAA
1 TGCCAA
28320962 ACGTATTTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 24 0.96
23 1 0.04
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCCAACCTGAATATGGCTCTG
Found at i:28329102 original size:13 final size:13
Alignment explanation
Indices: 28329084--28329113 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
28329074 GTATATCTGA
*
28329084 ATCTGAGTCTGTT
1 ATCTGAGACTGTT
28329097 ATCTGAGACTGTT
1 ATCTGAGACTGTT
28329110 ATCT
1 ATCT
28329114 AAATTTGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (13 bp):
ATCTGAGACTGTT
Found at i:28330820 original size:5 final size:5
Alignment explanation
Indices: 28330810--28330854 Score: 54
Period size: 5 Copynumber: 8.8 Consensus size: 5
28330800 AGGTGAGAGA
* * *
28330810 AAAAT AAAAT AAAAT AAAAT AAATT AAAACT AAGAT AAATT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T AAAAT AAAAT AAAA
28330855 GATTTCAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
5 29 0.88
6 4 0.12
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:28330847 original size:16 final size:15
Alignment explanation
Indices: 28330810--28330854 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
28330800 AGGTGAGAGA
*
28330810 AAAATAAAATAAAAT
1 AAAATAAATTAAAAT
28330825 AAAATAAATTAAAACT
1 AAAATAAATTAAAA-T
*
28330841 AAGATAAATTAAAA
1 AAAATAAATTAAAA
28330855 GATTTCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 13 0.48
16 14 0.52
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (15 bp):
AAAATAAATTAAAAT
Found at i:28332154 original size:22 final size:21
Alignment explanation
Indices: 28332116--28332156 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
28332106 GAATCCAACC
*
28332116 AAATGCAACAAATATAGCATA
1 AAATGCAACAAAAATAGCATA
*
28332137 AAATGCAGCCAAAAATAGCA
1 AAATGCA-ACAAAAATAGCA
28332157 AATTTATCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.56, C:0.17, G:0.12, T:0.15
Consensus pattern (21 bp):
AAATGCAACAAAAATAGCATA
Found at i:28332159 original size:31 final size:32
Alignment explanation
Indices: 28332124--28332185 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
28332114 CCAAATGCAA
* *
28332124 CAAATATAGCAT-AAAATGCAGCCAAAAATAG
1 CAAATATAGCATAAAAATACAACCAAAAATAG
* *
28332155 CAAATTTATCATAAAAATACAACCAAAAATA
1 CAAATATAGCATAAAAATACAACCAAAAATA
28332186 TTAATTCTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 10 0.38
32 16 0.62
ACGTcount: A:0.58, C:0.16, G:0.06, T:0.19
Consensus pattern (32 bp):
CAAATATAGCATAAAAATACAACCAAAAATAG
Found at i:28332426 original size:21 final size:21
Alignment explanation
Indices: 28332402--28332462 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
28332392 TTTTGCTCTG
28332402 CTCTG-CTGCCATCGCTGCTAC
1 CTCTGCCT-CCATCGCTGCTAC
* *
28332423 CTCTGCCTCCCTCGCTGCTGC
1 CTCTGCCTCCATCGCTGCTAC
* * *
28332444 CGCTGCCTCCCTCACTGCT
1 CTCTGCCTCCATCGCTGCT
28332463 GCGCAGTATC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 33 0.94
22 2 0.06
ACGTcount: A:0.05, C:0.49, G:0.18, T:0.28
Consensus pattern (21 bp):
CTCTGCCTCCATCGCTGCTAC
Found at i:28332463 original size:21 final size:21
Alignment explanation
Indices: 28332416--28332464 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
28332406 GCTGCCATCG
* * *
28332416 CTGCTACCTCTGCCTCCCTCG
1 CTGCTGCCGCTGCCTCCCTCA
28332437 CTGCTGCCGCTGCCTCCCTCA
1 CTGCTGCCGCTGCCTCCCTCA
28332458 CTGCTGC
1 CTGCTGC
28332465 GCAGTATCCC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.04, C:0.51, G:0.18, T:0.27
Consensus pattern (21 bp):
CTGCTGCCGCTGCCTCCCTCA
Found at i:28332927 original size:13 final size:14
Alignment explanation
Indices: 28332902--28332930 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28332892 TGATTAATTG
28332902 AATTAAACAATTAT
1 AATTAAACAATTAT
28332916 AATTAAAC-ATTAT
1 AATTAAACAATTAT
28332929 AA
1 AA
28332931 ATATTTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACAATTAT
Found at i:28333134 original size:16 final size:17
Alignment explanation
Indices: 28333097--28333135 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
28333087 AAAATATTAT
*
28333097 TTAATATTAGAAAGTTA
1 TTAATATTAGAAAGTAA
*
28333114 TTAATATTTGAAAG-AA
1 TTAATATTAGAAAGTAA
28333130 TTAATA
1 TTAATA
28333136 AAATTATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (17 bp):
TTAATATTAGAAAGTAA
Found at i:28334225 original size:9 final size:9
Alignment explanation
Indices: 28334211--28334352 Score: 80
Period size: 9 Copynumber: 15.8 Consensus size: 9
28334201 GATCTTTAAA
28334211 TTATGTAAG
1 TTATGTAAG
28334220 TTATGT-A-
1 TTATGTAAG
28334227 TTATGTAAG
1 TTATGTAAG
* *
28334236 TTATGAAAT
1 TTATGTAAG
* *
28334245 TTGATCTTTAAA
1 TT-A--TGTAAG
*
28334257 TTATGTAAC
1 TTATGTAAG
*
28334266 TCATGT-A-
1 TTATGTAAG
28334273 TTATGTAAG
1 TTATGTAAG
*
28334282 TTATGTAAA
1 TTATGTAAG
28334291 TTATGTAAG
1 TTATGTAAG
** *
28334300 TTATAAAAT
1 TTATGTAAG
* *
28334309 TTGATCTTTAAA
1 TT-A--TGTAAG
28334321 TTATGTAAG
1 TTATGTAAG
28334330 TTATGT-A-
1 TTATGTAAG
28334337 TTATGTAAG
1 TTATGTAAG
28334346 TTATGTA
1 TTATGTA
28334353 TTAAATATTA
Statistics
Matches: 102, Mismatches: 19, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
7 17 0.17
8 6 0.06
9 65 0.64
10 2 0.02
11 2 0.02
12 10 0.10
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:28334231 original size:16 final size:16
Alignment explanation
Indices: 28334210--28334355 Score: 97
Period size: 16 Copynumber: 9.2 Consensus size: 16
28334200 TGATCTTTAA
28334210 ATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
*
28334226 ATTATGTAAGTTATGAA
1 ATTATGTAAGTTATG-T
** **
28334243 ATT-TG-ATCTT-TAA
1 ATTATGTAAGTTATGT
* *
28334256 ATTATGTAACTCATGT
1 ATTATGTAAGTTATGT
28334272 ATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
**
28334288 AAATTATGTAAGTTATAAA
1 --ATTATGTAAGTTAT-GT
** **
28334307 ATT-TG-ATCTT-TAA
1 ATTATGTAAGTTATGT
28334320 ATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
28334336 ATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
28334352 ATTA
1 ATTA
28334356 AATATTATTT
Statistics
Matches: 102, Mismatches: 18, Indels: 20
0.73 0.13 0.14
Matches are distributed among these distances:
13 9 0.09
14 6 0.06
15 12 0.12
16 55 0.54
17 6 0.06
18 14 0.14
ACGTcount: A:0.36, C:0.03, G:0.14, T:0.47
Consensus pattern (16 bp):
ATTATGTAAGTTATGT
Found at i:28334232 original size:46 final size:46
Alignment explanation
Indices: 28334180--28334292 Score: 199
Period size: 46 Copynumber: 2.4 Consensus size: 46
28334170 TACATATAAG
* *
28334180 ATTATGTAAGTTATGAAATTTGATCTTTAAATTATGTAAGTTATGT
1 ATTATGTAAGTTATGAAATTTGATCTTTAAATTATGTAACTCATGT
28334226 ATTATGTAAGTTATGAAATTTGATCTTTAAATTATGTAACTCATGT
1 ATTATGTAAGTTATGAAATTTGATCTTTAAATTATGTAACTCATGT
28334272 ATTATGTAAGTTATGTAAATT
1 ATTATGTAAGTTATG-AAATT
28334293 ATGTAAGTTA
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
46 59 0.92
47 5 0.08
ACGTcount: A:0.35, C:0.04, G:0.14, T:0.47
Consensus pattern (46 bp):
ATTATGTAAGTTATGAAATTTGATCTTTAAATTATGTAACTCATGT
Found at i:28334260 original size:30 final size:30
Alignment explanation
Indices: 28334226--28334334 Score: 114
Period size: 30 Copynumber: 3.5 Consensus size: 30
28334216 TAAGTTATGT
28334226 ATTATGTAAGTTATGAAATTTGATCTTTAA
1 ATTATGTAAGTTATGAAATTTGATCTTTAA
* * *
28334256 ATTATGTAACTCATG-TATTATGTAAGT-TATGTAA
1 ATTATGTAAGTTATGAAATT-TG--A-TCT-T-TAA
*
28334290 ATTATGTAAGTTATAAAATTTGATCTTTAA
1 ATTATGTAAGTTATGAAATTTGATCTTTAA
28334320 ATTATGTAAGTTATG
1 ATTATGTAAGTTATG
28334335 TATTATGTAA
Statistics
Matches: 63, Mismatches: 8, Indels: 16
0.72 0.09 0.18
Matches are distributed among these distances:
29 3 0.05
30 32 0.51
31 2 0.03
32 4 0.06
33 2 0.03
34 17 0.27
35 3 0.05
ACGTcount: A:0.37, C:0.04, G:0.14, T:0.46
Consensus pattern (30 bp):
ATTATGTAAGTTATGAAATTTGATCTTTAA
Found at i:28334309 original size:64 final size:63
Alignment explanation
Indices: 28334210--28334352 Score: 243
Period size: 64 Copynumber: 2.3 Consensus size: 63
28334200 TGATCTTTAA
*
28334210 ATTATGTAAGTTATGT-ATTATGTAAGTTATGAAATTTGATCTTTAAATTATGTAACTCATGT
1 ATTATGTAAGTTATGTAATTATGTAAGTTATAAAATTTGATCTTTAAATTATGTAACTCATGT
* *
28334272 ATTATGTAAGTTATGTAAATTATGTAAGTTATAAAATTTGATCTTTAAATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT-AATTATGTAAGTTATAAAATTTGATCTTTAAATTATGTAACTCATGT
28334336 ATTATGTAAGTTATGTA
1 ATTATGTAAGTTATGTA
28334353 TTAAATATTA
Statistics
Matches: 76, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
62 16 0.21
63 1 0.01
64 59 0.78
ACGTcount: A:0.36, C:0.03, G:0.15, T:0.47
Consensus pattern (63 bp):
ATTATGTAAGTTATGTAATTATGTAAGTTATAAAATTTGATCTTTAAATTATGTAACTCATGT
Found at i:28337410 original size:26 final size:26
Alignment explanation
Indices: 28337374--28337483 Score: 186
Period size: 26 Copynumber: 4.2 Consensus size: 26
28337364 TTTAACAAAT
28337374 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
28337400 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
28337426 TGATAAT-GAGTTAGGTAAATGTTCCA
1 TGATAATAG-GTTAGGTAAATGTTCCA
* *
28337452 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
28337478 TGATAA
1 TGATAA
28337484 GAATTTCATG
Statistics
Matches: 81, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
25 1 0.01
26 79 0.98
27 1 0.01
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:28339132 original size:27 final size:27
Alignment explanation
Indices: 28339091--28339203 Score: 129
Period size: 27 Copynumber: 4.2 Consensus size: 27
28339081 GAGGAAGCGT
*
28339091 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
28339118 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
28339145 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
28339173 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
28339199 TCTGG
1 TCTGG
28339204 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
26 5 0.07
27 55 0.73
28 15 0.20
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:28339196 original size:54 final size:54
Alignment explanation
Indices: 28339089--28339203 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
28339079 TGGAGGAAGC
*
28339089 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
* * * *
28339143 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCT
1 GTTCTGGTGGCTATGCCACAAATATCTG-ATCTGGTGACTCTGCCACATATATCT
28339197 GTTCTGG
1 GTTCTGG
28339204 CAGCCATGCT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
Found at i:28343179 original size:26 final size:26
Alignment explanation
Indices: 28343143--28343251 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
28343133 TTTAACAAAT
28343143 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
28343169 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
28343195 TGATAATGGGTTAGGTAAATGTT-CA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
28343220 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
28343246 TGATAA
1 TGATAA
28343252 GAAATTTCAT
Statistics
Matches: 81, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
25 25 0.31
26 56 0.69
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:28343241 original size:51 final size:52
Alignment explanation
Indices: 28343143--28343251 Score: 184
Period size: 51 Copynumber: 2.1 Consensus size: 52
28343133 TTTAACAAAT
28343143 TGATAATAGGTTAGGTAAATGTTCCATGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCATGATAATAGGTTAGGTAAATGTTCCA
* * *
28343195 TGATAATGGGTTAGGTAAATGTT-CATGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCATGATAATAGGTTAGGTAAATGTTCCA
28343246 TGATAA
1 TGATAA
28343252 GAAATTTCAT
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
51 32 0.59
52 22 0.41
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.36
Consensus pattern (52 bp):
TGATAATAGGTTAGGTAAATGTTCCATGATAATAGGTTAGGTAAATGTTCCA
Found at i:28344909 original size:27 final size:27
Alignment explanation
Indices: 28344868--28344980 Score: 129
Period size: 27 Copynumber: 4.2 Consensus size: 27
28344858 GAGGAAGCGT
*
28344868 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
28344895 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
28344922 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
28344950 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
28344976 TCTGG
1 TCTGG
28344981 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
26 5 0.07
27 55 0.73
28 15 0.20
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:28344973 original size:54 final size:54
Alignment explanation
Indices: 28344866--28344980 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
28344856 TGGAGGAAGC
*
28344866 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
* * * *
28344920 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCT
1 GTTCTGGTGGCTATGCCACAAATATCTG-ATCTGGTGACTCTGCCACATATATCT
28344974 GTTCTGG
1 GTTCTGG
28344981 CAGCCATGCT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
Found at i:28348954 original size:26 final size:26
Alignment explanation
Indices: 28348925--28349034 Score: 193
Period size: 26 Copynumber: 4.2 Consensus size: 26
28348915 TGGTACAAAT
28348925 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
28348951 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
28348977 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
28349003 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
28349029 TGATAA
1 TGATAA
28349035 GAATTTCATG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.35
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:28350681 original size:27 final size:27
Alignment explanation
Indices: 28350640--28350752 Score: 120
Period size: 27 Copynumber: 4.2 Consensus size: 27
28350630 GAGGAAGCGT
* *
28350640 TCTGGTAGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
28350667 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
28350694 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
28350722 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
28350748 TCTGG
1 TCTGG
28350753 CAGCCATGCT
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
26 5 0.07
27 54 0.73
28 15 0.20
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:28350745 original size:54 final size:54
Alignment explanation
Indices: 28350638--28350761 Score: 160
Period size: 54 Copynumber: 2.3 Consensus size: 54
28350628 TGGAGGAAGC
*
28350638 GTTCTGGTAGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTAGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
* * * * *
28350692 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCT
1 GTTCTGGTAGCTATGCCACAAATATCTG-ATCTGGTGACTCTGCCACATATATCT
* *
28350746 GTTCTGGCAGCCATGC
1 GTTCTGGTAGCTATGC
28350762 TGCAAATTCT
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
54 41 0.69
55 18 0.31
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.35
Consensus pattern (54 bp):
GTTCTGGTAGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
Found at i:28351769 original size:25 final size:25
Alignment explanation
Indices: 28351697--28351762 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
28351687 GGCAGAAAAC
* *
28351697 TGGAGAAGCAGCAGAGGGATGCCGA
1 TGGAGATGTAGCAGAGGGATGCCGA
** *
28351722 CAGAGATGTAGAAGAGGGATGCCGA
1 TGGAGATGTAGCAGAGGGATGCCGA
28351747 TGGAGATGTAGCAGAG
1 TGGAGATGTAGCAGAG
28351763 AGCTGCCAAC
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.33, C:0.12, G:0.42, T:0.12
Consensus pattern (25 bp):
TGGAGATGTAGCAGAGGGATGCCGA
Found at i:28353813 original size:19 final size:18
Alignment explanation
Indices: 28353770--28353814 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
28353760 GAAAGGCTGA
*
28353770 GAAAGAAAAGGGAATTGG
1 GAAAGAAAAGGGAATGGG
28353788 GAAAGAAAAGGGAATCGGG
1 GAAAGAAAAGGGAAT-GGG
*
28353807 GAGAGAAA
1 GAAAGAAA
28353815 TAGAAGTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.51, C:0.02, G:0.40, T:0.07
Consensus pattern (18 bp):
GAAAGAAAAGGGAATGGG
Found at i:28354108 original size:22 final size:22
Alignment explanation
Indices: 28354054--28354108 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
28354044 TTTGACTTTT
*
28354054 TTATAATTTTTATATTGAATTA
1 TTATATTTTTTATATTGAATTA
*
28354076 TTATATCTTTTATATT-AATT-
1 TTATATTTTTTATATTGAATTA
28354096 TTAAATATTTTTT
1 TT--ATATTTTTT
28354109 TTAAAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 2 0.07
21 4 0.14
22 22 0.79
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (22 bp):
TTATATTTTTTATATTGAATTA
Found at i:28354489 original size:14 final size:14
Alignment explanation
Indices: 28354455--28354544 Score: 67
Period size: 14 Copynumber: 6.4 Consensus size: 14
28354445 AATCATACAA
28354455 CATAACCCTTAAACC
1 CATAACCCTT-AACC
*
28354470 CATAACCCATAACC
1 CATAACCCTTAACC
* *
28354484 CTTAACCCCTAACC
1 CATAACCCTTAACC
* *
28354498 CCTAACCCCTAACAC
1 CATAACCCTTAAC-C
*
28354513 C-TAAACCTTAAACC
1 CATAACCCTT-AACC
* *
28354527 C-CAACCCTTAAAC
1 CATAACCCTTAACC
28354540 CATAA
1 CATAA
28354545 ACTATAAACC
Statistics
Matches: 62, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
13 4 0.06
14 44 0.71
15 14 0.23
ACGTcount: A:0.39, C:0.43, G:0.00, T:0.18
Consensus pattern (14 bp):
CATAACCCTTAACC
Found at i:28354496 original size:21 final size:21
Alignment explanation
Indices: 28354455--28354516 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
28354445 AATCATACAA
*
28354455 CATAACCCTTAAACCCATAACC
1 CATAACCCTT-AACCCCTAACC
28354477 CATAACCCTTAACCCCTAACC
1 CATAACCCTTAACCCCTAACC
* * *
28354498 CCTAACCCCTAACACCTAA
1 CATAACCCTTAACCCCTAA
28354517 ACCTTAAACC
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 26 0.72
22 10 0.28
ACGTcount: A:0.37, C:0.45, G:0.00, T:0.18
Consensus pattern (21 bp):
CATAACCCTTAACCCCTAACC
Found at i:28354532 original size:28 final size:29
Alignment explanation
Indices: 28354494--28354554 Score: 74
Period size: 28 Copynumber: 2.1 Consensus size: 29
28354484 CTTAACCCCT
28354494 AACCCCTAACCCCTAACACC-TAAACCT-TA
1 AACCCCTAACCCCTAA-ACCATAAA-CTATA
*
28354523 AACCCC-AACCCTTAAACCATAAACTATA
1 AACCCCTAACCCCTAAACCATAAACTATA
28354551 AACC
1 AACC
28354555 ATAATCCATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 5 0.17
28 18 0.62
29 6 0.21
ACGTcount: A:0.43, C:0.41, G:0.00, T:0.16
Consensus pattern (29 bp):
AACCCCTAACCCCTAAACCATAAACTATA
Found at i:28354552 original size:14 final size:14
Alignment explanation
Indices: 28354535--28354595 Score: 59
Period size: 14 Copynumber: 4.3 Consensus size: 14
28354525 CCCCAACCCT
*
28354535 TAAACCATAAACTA
1 TAAACCATAAACCA
*
28354549 TAAACCATAATCCA
1 TAAACCATAAACCA
**
28354563 TAAACCCATAATTCA
1 TAAA-CCATAAACCA
* *
28354578 TAATCCATAAACCT
1 TAAACCATAAACCA
28354592 TAAA
1 TAAA
28354596 ATAGTAACTC
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
14 26 0.68
15 12 0.32
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.25
Consensus pattern (14 bp):
TAAACCATAAACCA
Found at i:28354573 original size:22 final size:22
Alignment explanation
Indices: 28354539--28354590 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
28354529 AACCCTTAAA
*
28354539 CCATAAA-CTATAAACCATAAT
1 CCATAAACCCATAAACCATAAT
**
28354560 CCATAAACCCATAATTCATAAT
1 CCATAAACCCATAAACCATAAT
28354582 CCATAAACC
1 CCATAAACC
28354591 TTAAAATAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 7 0.26
22 20 0.74
ACGTcount: A:0.48, C:0.29, G:0.00, T:0.23
Consensus pattern (22 bp):
CCATAAACCCATAAACCATAAT
Found at i:28354574 original size:15 final size:14
Alignment explanation
Indices: 28354535--28354587 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
28354525 CCCCAACCCT
* *
28354535 TAAACCATAAACTA
1 TAAACCATAATCCA
28354549 TAAACCATAATCCA
1 TAAACCATAATCCA
*
28354563 TAAACCCATAATTCA
1 TAAA-CCATAATCCA
*
28354578 TAATCCATAA
1 TAAACCATAA
28354588 ACCTTAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.25
Consensus pattern (14 bp):
TAAACCATAATCCA
Found at i:28355607 original size:40 final size:40
Alignment explanation
Indices: 28355549--28355652 Score: 145
Period size: 40 Copynumber: 2.6 Consensus size: 40
28355539 AGCGGCGTTA
* **
28355549 TGCTCTGTCTTTTAGCGGCGTTTTACCAAAAGTGCCACTAT
1 TGCTCTGT-TTTTAGCGGCGTTTTAACAAAAAAGCCACTAT
* *
28355590 TTCTCTGTTTGTAGCGGCGTTTTAACAAAAAAGCCACTAT
1 TGCTCTGTTTTTAGCGGCGTTTTAACAAAAAAGCCACTAT
*
28355630 TGCTCAGTTTTTAGCGGCGTTTT
1 TGCTCTGTTTTTAGCGGCGTTTT
28355653 TGGTAAAACA
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 48 0.87
41 7 0.13
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.38
Consensus pattern (40 bp):
TGCTCTGTTTTTAGCGGCGTTTTAACAAAAAAGCCACTAT
Found at i:28355985 original size:7 final size:7
Alignment explanation
Indices: 28355973--28355998 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
28355963 TTTCAATTTC
28355973 ATATTGA
1 ATATTGA
28355980 ATATTGA
1 ATATTGA
28355987 ATATTGA
1 ATATTGA
28355994 ATATT
1 ATATT
28355999 TTTTCTCAAA
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:0.00, G:0.12, T:0.46
Consensus pattern (7 bp):
ATATTGA
Found at i:28356447 original size:10 final size:11
Alignment explanation
Indices: 28356428--28356464 Score: 60
Period size: 10 Copynumber: 3.5 Consensus size: 11
28356418 GTCTCCTTCT
28356428 TTTCTTCTTTC
1 TTTCTTCTTTC
28356439 TTT-TTCTTTC
1 TTTCTTCTTTC
28356449 TTTCTT-TTTC
1 TTTCTTCTTTC
28356459 TTTCTT
1 TTTCTT
28356465 AGTTTGTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 20 0.80
11 5 0.20
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTCTTCTTTC
Found at i:28356451 original size:14 final size:14
Alignment explanation
Indices: 28356427--28356464 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
28356417 TGTCTCCTTC
28356427 TTTTC-TTCTTTCT
1 TTTTCTTTCTTTCT
28356440 TTTTCTTTCTTTCT
1 TTTTCTTTCTTTCT
28356454 TTTTCTTTCTT
1 TTTTCTTTCTT
28356465 AGTTTGTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 5 0.21
14 19 0.79
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTCTTTCTTTCT
Found at i:28360117 original size:13 final size:13
Alignment explanation
Indices: 28360099--28360124 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28360089 ATGAAGGAAG
28360099 AATCAAGAAAAAA
1 AATCAAGAAAAAA
28360112 AATCAAGAAAAAA
1 AATCAAGAAAAAA
28360125 TCAACCCACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.08, G:0.08, T:0.08
Consensus pattern (13 bp):
AATCAAGAAAAAA
Found at i:28372758 original size:24 final size:24
Alignment explanation
Indices: 28372731--28372780 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
28372721 CTCACGATCT
28372731 TCTTCAAAGTCCAAGTTTACAAAA
1 TCTTCAAAGTCCAAGTTTACAAAA
28372755 TCTTCAAAGTCCAAGTTTACAAAA
1 TCTTCAAAGTCCAAGTTTACAAAA
28372779 TC
1 TC
28372781 AACCAGGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.30
Consensus pattern (24 bp):
TCTTCAAAGTCCAAGTTTACAAAA
Found at i:28375826 original size:21 final size:21
Alignment explanation
Indices: 28375796--28375835 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28375786 TAACAGAACC
*
28375796 GCTGATGTGGCAAGTTAACTT
1 GCTGACGTGGCAAGTTAACTT
*
28375817 GCTGACGTGGCCAGTTAAC
1 GCTGACGTGGCAAGTTAAC
28375836 CTGCCACGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.28
Consensus pattern (21 bp):
GCTGACGTGGCAAGTTAACTT
Found at i:28376974 original size:24 final size:24
Alignment explanation
Indices: 28376941--28376989 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
28376931 TGCCTCAAAT
*
28376941 GCATGTTACAAGCGGCATTTTTAG
1 GCATGGTACAAGCGGCATTTTTAG
*
28376965 GCATGGTACAAGCGGCTTTTTTAG
1 GCATGGTACAAGCGGCATTTTTAG
28376989 G
1 G
28376990 GCTTTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.22, C:0.16, G:0.29, T:0.33
Consensus pattern (24 bp):
GCATGGTACAAGCGGCATTTTTAG
Found at i:28377152 original size:30 final size:30
Alignment explanation
Indices: 28377100--28377168 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
28377090 ACTGTTAGTC
*
28377100 AGTGACTGTTTTGTCAATTTTTTATAACGTT
1 AGTGACTGTTTTGTCAATTTTTTA-AAAGTT
*
28377131 AGTGACTGTTTTGT-TATTTTTTAAAAGTT
1 AGTGACTGTTTTGTCAATTTTTTAAAAGTT
28377160 AGGTGACTG
1 A-GTGACTG
28377169 AAATGAAACC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
29 6 0.17
30 15 0.43
31 14 0.40
ACGTcount: A:0.23, C:0.07, G:0.20, T:0.49
Consensus pattern (30 bp):
AGTGACTGTTTTGTCAATTTTTTAAAAGTT
Found at i:28380097 original size:2 final size:2
Alignment explanation
Indices: 28380090--28380128 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
28380080 GAAAAGATTA
28380090 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
28380129 TAATAACAGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:28382087 original size:6 final size:6
Alignment explanation
Indices: 28382068--28382098 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
28382058 GTTAGATGGT
*
28382068 TTAGGG TTAAGG TTAGGG TTAGGG TTAGGG T
1 TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG T
28382099 ATATATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.19, C:0.00, G:0.45, T:0.35
Consensus pattern (6 bp):
TTAGGG
Found at i:28384584 original size:26 final size:26
Alignment explanation
Indices: 28384533--28384584 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
28384523 ACAATTTAGG
*
28384533 AAGAAGAAGAAGAAAAAGAATCGAAA
1 AAGAAGAAGAAGAAAAAAAATCGAAA
28384559 AAGAAGAA-AACGTAAAAAAAAT-GAAA
1 AAGAAGAAGAA-G-AAAAAAAATCGAAA
28384585 GGAAAAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 2 0.09
26 13 0.57
27 8 0.35
ACGTcount: A:0.71, C:0.04, G:0.19, T:0.06
Consensus pattern (26 bp):
AAGAAGAAGAAGAAAAAAAATCGAAA
Found at i:28384604 original size:15 final size:17
Alignment explanation
Indices: 28384572--28384608 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
28384562 AAGAAAACGT
28384572 AAAA-AAAATGAAAGGA
1 AAAAGAAAATGAAAGGA
28384588 AAAAGAAAAT-AAA-GA
1 AAAAGAAAATGAAAGGA
28384603 AAAAGA
1 AAAAGA
28384609 TGAGGGCAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 8 0.40
16 7 0.35
17 5 0.25
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.05
Consensus pattern (17 bp):
AAAAGAAAATGAAAGGA
Found at i:28389010 original size:27 final size:26
Alignment explanation
Indices: 28388962--28389039 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 26
28388952 GCGAGGCTGC
* *
28388962 CAGATATTGT-GACGAAGTCACCAGATA
1 CAGATATTGTGGAAG-AGCCACCAGA-A
28388989 CAGATATTGTGGAAGAGCCACCAGAA
1 CAGATATTGTGGAAGAGCCACCAGAA
* *
28389015 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGAAGAGCCACCAG
28389040 GATGCTTCCT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
26 6 0.13
27 36 0.80
28 3 0.07
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Consensus pattern (26 bp):
CAGATATTGTGGAAGAGCCACCAGAA
Found at i:28390682 original size:26 final size:26
Alignment explanation
Indices: 28390651--28390758 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
28390641 TGAAATGCCC
*
28390651 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
28390677 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
28390703 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
28390729 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
28390755 ATCA
1 ATCA
28390759 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:28396083 original size:27 final size:26
Alignment explanation
Indices: 28395990--28396094 Score: 113
Period size: 27 Copynumber: 3.9 Consensus size: 26
28395980 GCGAGGCTGC
* *
28395990 CAGATATTGTGAC-GAAGTCACCAGAT
1 CAGATATTGTGGCAG-AGCCACCAGAT
* *
28396016 ACAGATATTGTGGAAGAGCCACCAGAA
1 -CAGATATTGTGGCAGAGCCACCAGAT
28396043 CAGATATATGTGGCAGAGCCACCAGAT
1 CAGATAT-TGTGGCAGAGCCACCAGAT
* *
28396070 CAGATAATTGTGGCATAACCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
28396095 GACGCTTCCT
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
26 7 0.10
27 57 0.85
28 3 0.04
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Consensus pattern (26 bp):
CAGATATTGTGGCAGAGCCACCAGAT
Found at i:28397744 original size:26 final size:26
Alignment explanation
Indices: 28397713--28397820 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
28397703 TGAAATGCCC
*
28397713 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
28397739 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
28397765 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
28397791 ATCATGGAACATTTACATAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
28397817 ATCA
1 ATCA
28397821 ATTTGTACCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.37, C:0.23, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:28398457 original size:70 final size:70
Alignment explanation
Indices: 28398337--28398623 Score: 342
Period size: 70 Copynumber: 4.1 Consensus size: 70
28398327 TAATTCTTGG
* * **** * *
28398337 TGGGCACAACTATCATCGGTTATCCAACTAGCGTTTGGTGTGATATTTTGTTGACTCATTCAACT
1 TGGGCACAACTATCATCGGTTATCCGACTAGCGTTGGGCACAATAATTTGTTGACTCGTTCAACT
28398402 AGTGC
66 AGTGC
* * *
28398407 TAGGCACAACTATCATCAGTTATCCGACTAGCGTTGGGCATAATAATTTGTTGACTCGTTCAACT
1 TGGGCACAACTATCATCGGTTATCCGACTAGCGTTGGGCACAATAATTTGTTGACTCGTTCAACT
28398472 AGTGC
66 AGTGC
* ** * * * *
28398477 TGGGCACAACTATCTTCGGTTATCCGACTAGCACTGGGAACAATAATTTGTCGACTTGTTCGACT
1 TGGGCACAACTATCATCGGTTATCCGACTAGCGTTGGGCACAATAATTTGTTGACTCGTTCAACT
28398542 AGTGC
66 AGTGC
* * * * * **
28398547 TGGGCACAACAATCATCGGTTATCTGACTAGAGTTGGGCGCAATAATTTGTTGACT-TTTTTACT
1 TGGGCACAACTATCATCGGTTATCCGACTAGCGTTGGGCACAATAATTTGTTGACTCGTTCAACT
28398611 AGTGC
66 AGTGC
28398616 TGGGCACA
1 TGGGCACA
28398624 CAAATAATCT
Statistics
Matches: 186, Mismatches: 31, Indels: 1
0.85 0.14 0.00
Matches are distributed among these distances:
69 18 0.10
70 168 0.90
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (70 bp):
TGGGCACAACTATCATCGGTTATCCGACTAGCGTTGGGCACAATAATTTGTTGACTCGTTCAACT
AGTGC
Found at i:28398514 original size:34 final size:34
Alignment explanation
Indices: 28398476--28398577 Score: 80
Period size: 34 Copynumber: 2.9 Consensus size: 34
28398466 TCAACTAGTG
28398476 CTGGGCACAACTATCTTCGGTTATCCGACTAGCA
1 CTGGGCACAACTATCTTCGGTTATCCGACTAGCA
* * * * * **
28398510 CTGGGAACAA-TAATTTGTCGACTTGTTCGACTAGTG
1 CTGGGCACAACT-ATCT-TCG-GTTATCCGACTAGCA
* * *
28398546 CTGGGCACAACAATCATCGGTTATCTGACTAG
1 CTGGGCACAACTATCTTCGGTTATCCGACTAG
28398578 AGTTGGGCGC
Statistics
Matches: 49, Mismatches: 15, Indels: 8
0.68 0.21 0.11
Matches are distributed among these distances:
33 1 0.02
34 21 0.43
35 6 0.12
36 21 0.43
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.28
Consensus pattern (34 bp):
CTGGGCACAACTATCTTCGGTTATCCGACTAGCA
Found at i:28398550 original size:36 final size:36
Alignment explanation
Indices: 28398431--28398623 Score: 103
Period size: 36 Copynumber: 5.5 Consensus size: 36
28398421 ATCAGTTATC
* * * * *
28398431 CGACTAGCGTTGGGCATAATAATTTGTTGACTCGTT
1 CGACTAGTGCTGGGCACAATAATTTGTCGACTTGTT
* * * * *
28398467 CAACTAGTGCTGGGCACAACT-ATCT-TCG-GTTATC
1 CGACTAGTGCTGGGCACAA-TAATTTGTCGACTTGTT
** *
28398501 CGACTAGCACTGGGAACAATAATTTGTCGACTTGTT
1 CGACTAGTGCTGGGCACAATAATTTGTCGACTTGTT
* ** * *
28398537 CGACTAGTGCTGGGCACAACAA-TCATCG-GTT-AT
1 CGACTAGTGCTGGGCACAATAATTTGTCGACTTGTT
* * * *
28398570 CTGACTAGAGTTGGGCGCAATAATTTGTTGACTT-TT
1 C-GACTAGTGCTGGGCACAATAATTTGTCGACTTGTT
**
28398606 TTACTAGTGCTGGGCACA
1 CGACTAGTGCTGGGCACA
28398624 CAAATAATCT
Statistics
Matches: 110, Mismatches: 40, Indels: 15
0.67 0.24 0.09
Matches are distributed among these distances:
33 3 0.03
34 39 0.35
35 25 0.23
36 42 0.38
37 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (36 bp):
CGACTAGTGCTGGGCACAATAATTTGTCGACTTGTT
Found at i:28414753 original size:33 final size:33
Alignment explanation
Indices: 28414710--28414880 Score: 184
Period size: 33 Copynumber: 5.2 Consensus size: 33
28414700 GTGTACGTTT
* **
28414710 CTTTCCAAATGGTACACACAAAGTATACCTTTC
1 CTTTTCAAATGGTACACACAAAGTATACCTAAC
* **
28414743 CTTTTCAAATGGTATACACAAAGTATACCTTTC
1 CTTTTCAAATGGTACACACAAAGTATACCTAAC
*
28414776 CTTTTCAAATGGTATACACAAAGTATACCTAAC
1 CTTTTCAAATGGTACACACAAAGTATACCTAAC
* * * ** *
28414809 ATTTCCAAGT-GTACACACAAAGTGCACATAAC
1 CTTTTCAAATGGTACACACAAAGTATACCTAAC
* * *
28414841 CTTTTCAAGT-GTACACACAAAGTGTACATAAC
1 CTTTTCAAATGGTACACACAAAGTATACCTAAC
28414873 CTTTTCAA
1 CTTTTCAA
28414881 GTGTACCACT
Statistics
Matches: 124, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
32 55 0.44
33 69 0.56
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.30
Consensus pattern (33 bp):
CTTTTCAAATGGTACACACAAAGTATACCTAAC
Found at i:28414850 original size:32 final size:32
Alignment explanation
Indices: 28414721--28414886 Score: 161
Period size: 32 Copynumber: 5.1 Consensus size: 32
28414711 TTTCCAAATG
* * ** *
28414721 GTACACACAAAGTATACCTTTCCTTTTCAAAT
1 GTACACACAAAGTGTACATAACCTTTTCAAGT
* * * ** *
28414753 GGTATACACAAAGTATACCTTTCCTTTTCAAAT
1 -GTACACACAAAGTGTACATAACCTTTTCAAGT
* * * * *
28414786 GGTATACACAAAGTATACCTAACATTTCCAAGT
1 -GTACACACAAAGTGTACATAACCTTTTCAAGT
*
28414819 GTACACACAAAGTGCACATAACCTTTTCAAGT
1 GTACACACAAAGTGTACATAACCTTTTCAAGT
28414851 GTACACACAAAGTGTACATAACCTTTTCAAGT
1 GTACACACAAAGTGTACATAACCTTTTCAAGT
28414883 GTAC
1 GTAC
28414887 CACTTGGGTA
Statistics
Matches: 120, Mismatches: 13, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
32 61 0.51
33 59 0.49
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (32 bp):
GTACACACAAAGTGTACATAACCTTTTCAAGT
Done.