Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 42 of 222
Found at i:12479585 original size:31 final size:31
Alignment explanation
Indices: 12479550--12479612 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
12479540 ACCCAGCCCA
** *
12479550 AATAAAAATGTTAAAACCTAAGCCCGACCCG
1 AATAAAAATACTAAAACCCAAGCCCGACCCG
* *
12479581 AATAAAAATACTAAAACCCAAGCTCGGCCCG
1 AATAAAAATACTAAAACCCAAGCCCGACCCG
12479612 A
1 A
12479613 TTCGGCCCAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.46, C:0.27, G:0.13, T:0.14
Consensus pattern (31 bp):
AATAAAAATACTAAAACCCAAGCCCGACCCG
Found at i:12485077 original size:12 final size:12
Alignment explanation
Indices: 12485060--12485084 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12485050 GAGTTTGAGT
12485060 AAGGTACTTTTG
1 AAGGTACTTTTG
12485072 AAGGTACTTTTG
1 AAGGTACTTTTG
12485084 A
1 A
12485085 CATGTACCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40
Consensus pattern (12 bp):
AAGGTACTTTTG
Found at i:12491799 original size:7 final size:7
Alignment explanation
Indices: 12491789--12491824 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
12491779 CACTTCTCAA
12491789 TCATCCC
1 TCATCCC
12491796 TCATCCC
1 TCATCCC
*
12491803 TTATCCC
1 TCATCCC
*
12491810 TCAACCC
1 TCATCCC
12491817 TCATCCC
1 TCATCCC
12491824 T
1 T
12491825 TAACATTCCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.17, C:0.53, G:0.00, T:0.31
Consensus pattern (7 bp):
TCATCCC
Found at i:12492050 original size:36 final size:36
Alignment explanation
Indices: 12492001--12492070 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
12491991 TGAGGAGCAC
*
12492001 ATCAGTCAGAATAGA-TCTAAAAGGCTGCTAAACTAA
1 ATCAGTCAAAATAGATTC-AAAAGGCTGCTAAACTAA
* *
12492037 ATCAGTCAAAATAGATTCGAAAGGTTGCTAAACT
1 ATCAGTCAAAATAGATTCAAAAGGCTGCTAAACT
12492071 GGATAGTGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 28 0.93
37 2 0.07
ACGTcount: A:0.43, C:0.16, G:0.17, T:0.24
Consensus pattern (36 bp):
ATCAGTCAAAATAGATTCAAAAGGCTGCTAAACTAA
Found at i:12492734 original size:15 final size:17
Alignment explanation
Indices: 12492710--12492746 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
12492700 CATTTATTCA
*
12492710 TGCATTTAGA-TA-AAT
1 TGCATCTAGATTAGAAT
12492725 TGCATCTAGATTAGAAT
1 TGCATCTAGATTAGAAT
12492742 TGCAT
1 TGCAT
12492747 AGGGATCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 9 0.47
16 2 0.11
17 8 0.42
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (17 bp):
TGCATCTAGATTAGAAT
Found at i:12497116 original size:14 final size:15
Alignment explanation
Indices: 12497097--12497125 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
12497087 CTTTAGATAA
12497097 ACTGTGAAC-TTTAG
1 ACTGTGAACATTTAG
12497111 ACTGTGAACATTTAG
1 ACTGTGAACATTTAG
12497126 GAATATAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (15 bp):
ACTGTGAACATTTAG
Found at i:12499579 original size:30 final size:30
Alignment explanation
Indices: 12499545--12499601 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
12499535 CATAGCATTT
12499545 ACATACT-CATTCAAGCATATATCACATAAC
1 ACATACTCCATT-AAGCATATATCACATAAC
* * *
12499575 ACATATTCCATTAATCATGTATCACAT
1 ACATACTCCATTAAGCATATATCACAT
12499602 TTCATACAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 19 0.83
31 4 0.17
ACGTcount: A:0.40, C:0.25, G:0.04, T:0.32
Consensus pattern (30 bp):
ACATACTCCATTAAGCATATATCACATAAC
Found at i:12501236 original size:12 final size:12
Alignment explanation
Indices: 12501219--12501243 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12501209 CTAAAACTCC
12501219 TAGGCCCTATTT
1 TAGGCCCTATTT
12501231 TAGGCCCTATTT
1 TAGGCCCTATTT
12501243 T
1 T
12501244 GGGGTGTTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.16, T:0.44
Consensus pattern (12 bp):
TAGGCCCTATTT
Found at i:12511408 original size:21 final size:21
Alignment explanation
Indices: 12511383--12511437 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
12511373 ATTCAAGAAC
* *
12511383 AAACTCGTTTAT-GTTTATTT
1 AAACTCGTTTATAGATCATTT
*
12511403 AAAACTTGTTTAATAGATCATTT
1 -AAACTCGTTT-ATAGATCATTT
12511426 AAACTCGTTTAT
1 AAACTCGTTTAT
12511438 TGTTCTATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 11 0.39
22 11 0.39
23 6 0.21
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.47
Consensus pattern (21 bp):
AAACTCGTTTATAGATCATTT
Found at i:12511435 original size:22 final size:22
Alignment explanation
Indices: 12511383--12511436 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
12511373 ATTCAAGAAC
* *
12511383 AAACTCGTTT-ATGTTTATTTA
1 AAACTCGTTTAATGATCATTTA
*
12511404 AAACTTGTTTAATAGATCATTT-
1 AAACTCGTTTAAT-GATCATTTA
12511426 AAACTCGTTTA
1 AAACTCGTTTA
12511437 TTGTTCTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 9 0.33
22 12 0.44
23 6 0.22
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.46
Consensus pattern (22 bp):
AAACTCGTTTAATGATCATTTA
Found at i:12512042 original size:17 final size:16
Alignment explanation
Indices: 12512018--12512051 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
12512008 TATGCATAAT
12512018 TTGTTACATCTATCAA
1 TTGTTACATCTATCAA
12512034 TTGTATACATCTATCAA
1 TTGT-TACATCTATCAA
12512051 T
1 T
12512052 ACTATTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (16 bp):
TTGTTACATCTATCAA
Found at i:12512174 original size:298 final size:289
Alignment explanation
Indices: 12511801--12512618 Score: 710
Period size: 299 Copynumber: 2.7 Consensus size: 289
12511791 GTAAATTAAT
* * *
12511801 TACCAA-TTAAGTTAGTGAAATTATGGAAATATATTTTCGTATTTAAAAAAGTTATATTATTTGG
1 TACCAACTT-AGTTAG-GAAAATATGG-AA-ATATCTTCATATTTAAAAAAGTTATATTATTT-G
*
12511865 AA-TTATTTTAAT-TTTTTTATTTTTAGAAAAACTCAATAAAAACCTTAGATGGGGTGAGATTTG
61 AAGGTATTTTAATCTTTTTTATTTTTA-AAAAACTCAATAAAAA-CTTAGATGGGGTGAGATTTG
*
12511928 AATCGTGTTATTAACATCAATAAAACATTCACATTTCCACTAAACCAAAAATTTATTTTAATATA
124 AATTGTGTTATTAACATCAATAAAACATTCAC-TTTCCACTAAACCAAAAATTTATTTTAATATA
* * *
12511993 -ATATTTTAATTGTATTATGCATAATTTGTTACATCTATCAATTGTATACATCTATCAATACTAT
188 TACATTTTAATTGTATTATGCATAATGTGTTACATCTATCAATCGTATACAT-T-T--ATACTAT
** * *
12512057 TAATAAAATTTCTGACTGAGTTAGTAT-TACA-AGTTAA-TCGG-
249 TAATAAAATCCCTAACTGAGTT-G-ATGT-CAGAGTCAACT-GGA
* *
12512098 TCACCAA-TTTGATTAGCGAAAATATGGAAATATCGTTCATATTTAAAACGAGTTATATTATTTG
1 T-ACCAACTTAG-TTAG-GAAAATATGGAAATATC-TTCATATTTAAAA-AAGTTATATTATTTG
* *** * * * *
12512162 AAGGTATTTTAATCTTTGTTTCTTTTTTTTAAA-TCCAATAAAAACTTTGACGAGAGTG-GTTTT
61 AAGGTATTTTAATCTTT-TTTATTTTTAAAAAACT-CAATAAAAACTTAGATG-GGGTGAGATTT
** * * * *
12512225 GGGCTTATGCTATTAACATCAATAAAATATTCACTTTACCACTAAACCAAATATTTATTTTAATA
123 -GAATTGTGTTATTAACATCAATAAAACATTCACTTT-CCACTAAACCAAAAATTTATTTTAAT-
* * * * *
12512290 CGATATTTACATTTTAATTGTCTTATGCATACTGTGTTACCTTTATCAATCGTATATATTTATAC
185 --ATA--TACATTTTAATTGTATTATGCATAATGTGTTACATCTATCAATCGTATACATTTATAC
12512355 TATTAATAAAATCCCTAACTGAGTTGATGTCATGAGTCAACTGGA
246 TATTAATAAAATCCCTAACTGAGTTGATGTCA-GAGTCAACTGGA
* * * *
12512400 TACTAACTTAGTTAGTAAAATTATGGAAATATC--CAGTATTTAAAATAAATTATATTATTTGAG
1 TACCAACTTAGTTAGGAAAA-TATGGAAATATCTTCA-TATTTAAAA-AAGTTATATTATTTGAA
* * * * * * *
12512463 GGTATTTTACTCTTTTTTGTTTTTAAAAAAATCTAATAAAAAATTACATGTGGTTAGATTTGAAC
63 GGTATTTTAATCTTTTTTATTTTTAAAAAACTC-AATAAAAACTTAGATGGGGTGAGATTTGAA-
* * *
12512528 TTGTATTATTAACATCAATAAAACATTTATCTTACCACTAAA-CAAAAGATTTATTTTAATATAT
126 TTGTGTTATTAACATCAATAAAACATTCA-CTTTCCACTAAACCAAAA-ATTTATTTT-A-ATA-
12512592 TTATTTACATTTTAATTGTATTATGCA
186 -TA--TACATTTTAATTGTATTATGCA
12512619 AATTTTGTTG
Statistics
Matches: 422, Mismatches: 64, Indels: 67
0.76 0.12 0.12
Matches are distributed among these distances:
296 4 0.01
297 19 0.05
298 78 0.18
299 170 0.40
300 43 0.10
301 55 0.13
302 8 0.02
303 1 0.00
304 1 0.00
305 43 0.10
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.42
Consensus pattern (289 bp):
TACCAACTTAGTTAGGAAAATATGGAAATATCTTCATATTTAAAAAAGTTATATTATTTGAAGGT
ATTTTAATCTTTTTTATTTTTAAAAAACTCAATAAAAACTTAGATGGGGTGAGATTTGAATTGTG
TTATTAACATCAATAAAACATTCACTTTCCACTAAACCAAAAATTTATTTTAATATATACATTTT
AATTGTATTATGCATAATGTGTTACATCTATCAATCGTATACATTTATACTATTAATAAAATCCC
TAACTGAGTTGATGTCAGAGTCAACTGGA
Found at i:12513376 original size:4 final size:4
Alignment explanation
Indices: 12513367--12513392 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
12513357 AGTTTAGTTA
12513367 TTGT TTGT TTGT TTGT TTGT TTGT TT
1 TTGT TTGT TTGT TTGT TTGT TTGT TT
12513393 ATTATTCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (4 bp):
TTGT
Found at i:12513435 original size:23 final size:23
Alignment explanation
Indices: 12513408--12513453 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
12513398 TCATAAAAAT
*
12513408 TGTTCATGAATATATTCGTTTAA
1 TGTTCACGAATATATTCGTTTAA
* *
12513431 TGTTCACGAATATCTTTGTTTAA
1 TGTTCACGAATATATTCGTTTAA
12513454 CTTAAATGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.48
Consensus pattern (23 bp):
TGTTCACGAATATATTCGTTTAA
Found at i:12514841 original size:9 final size:8
Alignment explanation
Indices: 12514819--12514844 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
12514809 AAAAAAAATT
12514819 AATTTTTA
1 AATTTTTA
12514827 AATTTTTA
1 AATTTTTA
12514835 AATTTTTA
1 AATTTTTA
12514843 AA
1 AA
12514845 AAATTAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (8 bp):
AATTTTTA
Found at i:12516771 original size:21 final size:22
Alignment explanation
Indices: 12516737--12516793 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
12516727 AAAAATGTCT
* *
12516737 AAATTTGT-AAAATATT-ATTA
1 AAATTTATAAAAATATTAAATA
12516757 AAATTTATAAAAATATTAAATA
1 AAATTTATAAAAATATTAAATA
* *
12516779 AAATTCAAAAAAATA
1 AAATTTATAAAAATA
12516794 AAAAAATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.23
21 8 0.26
22 16 0.52
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (22 bp):
AAATTTATAAAAATATTAAATA
Found at i:12516796 original size:8 final size:8
Alignment explanation
Indices: 12516785--12516813 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
12516775 AATAAAATTC
12516785 AAAAAAAT
1 AAAAAAAT
12516793 AAAAAAAT
1 AAAAAAAT
12516801 AAAAAAAT
1 AAAAAAAT
12516809 AAAAA
1 AAAAA
12516814 TTAATAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:12516822 original size:15 final size:15
Alignment explanation
Indices: 12516774--12516823 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
12516764 TAAAAATATT
12516774 AAAT-AAAATTCAAAA
1 AAATAAAAATT-AAAA
*
12516789 AAATAAAAAAATAAAA
1 AAAT-AAAAATTAAAA
*
12516805 AAATAAAAATTAATA
1 AAATAAAAATTAAAA
12516820 AAAT
1 AAAT
12516824 CATTTAAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 17 0.57
16 8 0.27
17 5 0.17
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (15 bp):
AAATAAAAATTAAAA
Found at i:12517016 original size:4 final size:4
Alignment explanation
Indices: 12517007--12517033 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
12516997 ATATTTTAGA
12517007 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
12517034 AATAATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:12518056 original size:46 final size:45
Alignment explanation
Indices: 12517964--12518056 Score: 107
Period size: 46 Copynumber: 2.0 Consensus size: 45
12517954 GGTTAGGTAA
* * * *
12517964 CAGAAGCAGTTTTAGTTCAGATACAAAACAAATCAATTACATATG
1 CAGAAGCAATTTAAGTTCACATACAAAACAAATCAATTACAGATG
* *
12518009 CAGAAGCAATTTAAGTTTCACATACAGAACATATCAGATT-CAGATG
1 CAGAAGCAATTTAAG-TTCACATACAAAACAAATCA-ATTACAGATG
12518055 CA
1 CA
12518057 AATATTCCTA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
45 13 0.32
46 24 0.60
47 3 0.08
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (45 bp):
CAGAAGCAATTTAAGTTCACATACAAAACAAATCAATTACAGATG
Found at i:12536616 original size:12 final size:12
Alignment explanation
Indices: 12536599--12536652 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
12536589 AAACAAGCTT
12536599 GTTTATTGGCTC
1 GTTTATTGGCTC
** *
12536611 GTTTATAAGCTT
1 GTTTATTGGCTC
*
12536623 GTTTGTTGGCTC
1 GTTTATTGGCTC
*
12536635 GTTTA-TGACTC
1 GTTTATTGGCTC
12536646 GTTTATT
1 GTTTATT
12536653 TATTAATGAT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
11 10 0.31
12 22 0.69
ACGTcount: A:0.13, C:0.13, G:0.22, T:0.52
Consensus pattern (12 bp):
GTTTATTGGCTC
Found at i:12536621 original size:24 final size:24
Alignment explanation
Indices: 12536593--12536640 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
12536583 GTTCACAAAC
12536593 AAGCTTGTTTATTGGCTCGTTTAT
1 AAGCTTGTTTATTGGCTCGTTTAT
*
12536617 AAGCTTGTTTGTTGGCTCGTTTAT
1 AAGCTTGTTTATTGGCTCGTTTAT
12536641 GACTCGTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.15, C:0.12, G:0.23, T:0.50
Consensus pattern (24 bp):
AAGCTTGTTTATTGGCTCGTTTAT
Found at i:12538075 original size:16 final size:16
Alignment explanation
Indices: 12538038--12538068 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12538028 TTAGCTATAC
12538038 AAAAATACGAAAATCG
1 AAAAATACGAAAATCG
12538054 AAAAATAC-AAAATCG
1 AAAAATACGAAAATCG
12538069 CCAAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.65, C:0.13, G:0.10, T:0.13
Consensus pattern (16 bp):
AAAAATACGAAAATCG
Found at i:12544788 original size:31 final size:33
Alignment explanation
Indices: 12544729--12544793 Score: 82
Period size: 31 Copynumber: 2.0 Consensus size: 33
12544719 TTTTAAACTT
12544729 TAATTTATATATTTAAATAAATTCTAATT-AAA
1 TAATTTATATATTTAAATAAATTCTAATTCAAA
* *
12544761 TAATTT-TTTATTT-AATAGAATTGTAATTCAAA
1 TAATTTATATATTTAAATA-AATTCTAATTCAAA
12544793 T
1 T
12544794 TCAAATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 4 0.14
31 15 0.52
32 10 0.34
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (33 bp):
TAATTTATATATTTAAATAAATTCTAATTCAAA
Found at i:12545777 original size:21 final size:21
Alignment explanation
Indices: 12545739--12545807 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
12545729 ACTTTTTTGA
*
12545739 ATAA-TACAAATGTGTTAATAT
1 ATAATTACAAATAT-TTAATAT
*
12545760 ATAATTACAAATATTTAATTT
1 ATAATTACAAATATTTAATAT
* * *
12545781 TTATATT-TAAATATTTAAAAT
1 ATA-ATTACAAATATTTAATAT
12545802 ATAATT
1 ATAATT
12545808 TATATATTCT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
20 3 0.08
21 25 0.64
22 11 0.28
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (21 bp):
ATAATTACAAATATTTAATAT
Found at i:12547485 original size:53 final size:53
Alignment explanation
Indices: 12547397--12547497 Score: 141
Period size: 53 Copynumber: 1.9 Consensus size: 53
12547387 TTTCTCAACA
* *
12547397 ATTCAAACCAAACATCAAATGGAGTTTTCCTCTCCTGCACAGCCTTGGCAAGC
1 ATTCAAACCAAACATCAAATGGAGTCTTCCTCTCCTGCACAACCTTGGCAAGC
* * *
12547450 ATTCAAACCAAGCTTCAAATGGAGTCTT-CTCCTCCTTCACAACCTTGG
1 ATTCAAACCAAACATCAAATGGAGTCTTCCT-CTCCTGCACAACCTTGG
12547498 TTGGCAATCT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
52 2 0.05
53 40 0.95
ACGTcount: A:0.29, C:0.31, G:0.14, T:0.27
Consensus pattern (53 bp):
ATTCAAACCAAACATCAAATGGAGTCTTCCTCTCCTGCACAACCTTGGCAAGC
Found at i:12551956 original size:306 final size:306
Alignment explanation
Indices: 12551399--12552013 Score: 1077
Period size: 306 Copynumber: 2.0 Consensus size: 306
12551389 TAATAGCAGT
* *
12551399 GAACTTGTTTTTAGGTTTTGAGATAGTGAACATGGAAGCCCGCAGCCAAAAGTATTACTATTCCA
1 GAACTTGTTTTTAGGCTTTGAGATAGTGAACATGAAAGCCCGCAGCCAAAAGTATTACTATTCCA
*
12551464 CATTTCTGCAAAAGGCGTCATAACAATACCTAGCTACATATGCAAGAATTCCAACTGACCTTCAA
66 CATTTCTGCAAAAGCCGTCATAACAATACCTAGCTACATATGCAAGAATTCCAACTGACCTTCAA
* * *
12551529 GCGTTATGTCGGTGATAAACAAGTTACCATGTAGTTGTTGTGGTCTAAGGGCCTAAAAGACTGGC
131 GCATTATGTCAGTGATAAAAAAGTTACCATGTAGTTGTTGTGGTCTAAGGGCCTAAAAGACTGGC
*
12551594 TGCAATAGATTGAAAAATTCTGGTTCAAGTAACAGCATTGGTTCATGCTGAAAGGATATAATGCT
196 TGCAATAGATTGAAAAATTCTAGTTCAAGTAACAGCATTGGTTCATGCTGAAAGGATATAATGCT
*
12551659 CACATTTCTACACTTCTTCAATCAACCTGGTAAGGCTTGAGAATGA
261 CACATTTCTACACTTCTCCAATCAACCTGGTAAGGCTTGAGAATGA
* *
12551705 GAACTTGTTTTTAGGCTTTGAGATAGTGAACATGAAAGCCCGCAGCCAAGAGTATTACTGTTCCA
1 GAACTTGTTTTTAGGCTTTGAGATAGTGAACATGAAAGCCCGCAGCCAAAAGTATTACTATTCCA
* * *
12551770 CATTTCTGCAAAAGCCGTCATAACAATCCCTAGCTACATATGCAAGAATTCCAGCTGACCTTTAA
66 CATTTCTGCAAAAGCCGTCATAACAATACCTAGCTACATATGCAAGAATTCCAACTGACCTTCAA
* *
12551835 GCATTATGTCAGTGATAAAAAAGTTACCATGTAGTTGTTGTGGTCTAAGGGCCTGAAAGACTGGT
131 GCATTATGTCAGTGATAAAAAAGTTACCATGTAGTTGTTGTGGTCTAAGGGCCTAAAAGACTGGC
* *
12551900 TGCAATAGATTGAAAAATTCTAGTTCAAGTAACAGTATTGGTTCATGCTTAAAGGATATAATGCT
196 TGCAATAGATTGAAAAATTCTAGTTCAAGTAACAGCATTGGTTCATGCTGAAAGGATATAATGCT
12551965 CACATTTCTACACTTCTCCAATCAACCTGGTAAGGCTTGAGAATGA
261 CACATTTCTACACTTCTCCAATCAACCTGGTAAGGCTTGAGAATGA
12552011 GAA
1 GAA
12552014 GCTACTGATG
Statistics
Matches: 292, Mismatches: 17, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
306 292 1.00
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (306 bp):
GAACTTGTTTTTAGGCTTTGAGATAGTGAACATGAAAGCCCGCAGCCAAAAGTATTACTATTCCA
CATTTCTGCAAAAGCCGTCATAACAATACCTAGCTACATATGCAAGAATTCCAACTGACCTTCAA
GCATTATGTCAGTGATAAAAAAGTTACCATGTAGTTGTTGTGGTCTAAGGGCCTAAAAGACTGGC
TGCAATAGATTGAAAAATTCTAGTTCAAGTAACAGCATTGGTTCATGCTGAAAGGATATAATGCT
CACATTTCTACACTTCTCCAATCAACCTGGTAAGGCTTGAGAATGA
Found at i:12557413 original size:18 final size:17
Alignment explanation
Indices: 12557387--12557434 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
12557377 ACAATAAAAA
*
12557387 AATGTTTTGAAATTGAAT
1 AATGATTTGAAA-TGAAT
12557405 AATGATTTGTAAATGAAT
1 AATGATTTG-AAATGAAT
12557423 AAT-ATTTTGAAA
1 AATGA-TTTGAAA
12557435 ACAAACGACA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 4 0.15
18 20 0.74
19 3 0.11
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.42
Consensus pattern (17 bp):
AATGATTTGAAATGAAT
Found at i:12557781 original size:25 final size:25
Alignment explanation
Indices: 12557752--12557818 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
12557742 AAACTGAAAC
*
12557752 TGAAACT-TTCATTGATAGTATATCT
1 TGAAACTATT-ATAGATAGTATATCT
12557777 TGAAACTATTATAGATAGTATATAC-
1 TGAAACTATTATAGATAGTATAT-CT
* *
12557802 TGAGACTACTATAGATA
1 TGAAACTATTATAGATA
12557819 AACTATACTA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 34 0.92
26 3 0.08
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.37
Consensus pattern (25 bp):
TGAAACTATTATAGATAGTATATCT
Found at i:12559978 original size:27 final size:29
Alignment explanation
Indices: 12559902--12559983 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 29
12559892 AAAATACGGT
12559902 GGAATCAGCACTTAGCAACCACCAATGAATGGG
1 GGAATCAGCACTTAGCAACC-CC-AT--ATGGG
* **
12559935 GGAATCAACACACAGCAACCCC-T-TGGG
1 GGAATCAGCACTTAGCAACCCCATATGGG
12559962 GGAATCAGCACTTAGCAACCCC
1 GGAATCAGCACTTAGCAACCCC
12559984 CTTTCACATT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
27 23 0.53
30 1 0.02
32 2 0.05
33 17 0.40
ACGTcount: A:0.34, C:0.30, G:0.22, T:0.13
Consensus pattern (29 bp):
GGAATCAGCACTTAGCAACCCCATATGGG
Found at i:12560011 original size:103 final size:103
Alignment explanation
Indices: 12559845--12560061 Score: 398
Period size: 103 Copynumber: 2.1 Consensus size: 103
12559835 ATCAGCACTT
* *
12559845 AGCAACCCCTCGGGGGAATCAGCACTTAGGAACCCCCTTTCACATTTAAAATACGGTGGAATCAG
1 AGCAACCCCTTGGGGGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATACGGTGGAATCAG
*
12559910 CACTTAGCAACCACCAATGAATGGGGGAATCAACACAC
66 CACTTAGCAACCACCAATGAATCGGGGAATCAACACAC
12559948 AGCAACCCCTTGGGGGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATACGGTGGAATCAG
1 AGCAACCCCTTGGGGGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATACGGTGGAATCAG
*
12560013 CACTTAGCAACCACCAATGAATCGGGGAATCAGCACAC
66 CACTTAGCAACCACCAATGAATCGGGGAATCAACACAC
12560051 AGCAACCCCTT
1 AGCAACCCCTT
12560062 TATATGCAAT
Statistics
Matches: 110, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.33, C:0.29, G:0.19, T:0.18
Consensus pattern (103 bp):
AGCAACCCCTTGGGGGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATACGGTGGAATCAG
CACTTAGCAACCACCAATGAATCGGGGAATCAACACAC
Found at i:12568629 original size:44 final size:43
Alignment explanation
Indices: 12568525--12568732 Score: 231
Period size: 43 Copynumber: 4.8 Consensus size: 43
12568515 AAAGAGAAGT
* * ** **
12568525 CTTTAGCGGCGCTTTTATAACAAATG-CAGCTAAAGGTCATGTT
1 CTTTAGCGGCGCTTTTATAGCAAACGCCA-CTAAAGAACATGAC
12568568 CTTTAGCGGCGCTTTTATAGCAAACGCCACTAAAGAACATGAC
1 CTTTAGCGGCGCTTTTATAGCAAACGCCACTAAAGAACATGAC
* * *
12568611 CTTTTAGCGGCGCTTTTATAGCAAATGCCCCTAAAAAACATGAC
1 C-TTTAGCGGCGCTTTTATAGCAAACGCCACTAAAGAACATGAC
* * *
12568655 CTTTAGCGGCACTTTTATAGCAATCGCCGCTAAAGAACATGAC
1 CTTTAGCGGCGCTTTTATAGCAAACGCCACTAAAGAACATGAC
***
12568698 CTTTAGCGGTATTTTTTATCA-CAAACGCCACTAAA
1 CTTTAGCGG-CGCTTTTAT-AGCAAACGCCACTAAA
12568733 AGTATAGTTC
Statistics
Matches: 142, Mismatches: 19, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
43 81 0.57
44 60 0.42
45 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTATAGCAAACGCCACTAAAGAACATGAC
Found at i:12568672 original size:87 final size:86
Alignment explanation
Indices: 12568525--12568706 Score: 256
Period size: 87 Copynumber: 2.1 Consensus size: 86
12568515 AAAGAGAAGT
* *** ** *
12568525 CTTTAGCGGCGCTTTTATAACAAATGCAGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTATAGCA
1 CTTTAGCGGCGCTTTTATAACAAATGCACCTAAAAAACATGACCTTTAGCGGCACTTTTATAGCA
12568590 AACGCCACTAAAGAACATGAC
66 AACGCCACTAAAGAACATGAC
* *
12568611 CTTTTAGCGGCGCTTTTATAGCAAATGCCCCTAAAAAACATGACCTTTAGCGGCACTTTTATAGC
1 C-TTTAGCGGCGCTTTTATAACAAATGCACCTAAAAAACATGACCTTTAGCGGCACTTTTATAGC
* *
12568676 AATCGCCGCTAAAGAACATGAC
65 AAACGCCACTAAAGAACATGAC
12568698 CTTTAGCGG
1 CTTTAGCGG
12568707 TATTTTTTAT
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
86 9 0.11
87 75 0.89
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (86 bp):
CTTTAGCGGCGCTTTTATAACAAATGCACCTAAAAAACATGACCTTTAGCGGCACTTTTATAGCA
AACGCCACTAAAGAACATGAC
Found at i:12568715 original size:87 final size:87
Alignment explanation
Indices: 12568568--12568733 Score: 228
Period size: 87 Copynumber: 1.9 Consensus size: 87
12568558 AGGTCATGTT
* *
12568568 CTTTAGCGGCGCTTTTATAGCAAACGCCACTAAAGAACATGACCTTTTAGCGGCGCTTTTAT-AG
1 CTTTAGCGGCACTTTTATAGCAAACGCCACTAAAGAACATGACCTTTTAGCGGAGCTTTTATCA-
* *
12568632 CAAATGCCCCTAAAAAACATGAC
65 CAAACGCCACTAAAAAACATGAC
* * **
12568655 CTTTAGCGGCACTTTTATAGCAATCGCCGCTAAAGAACATGACC-TTTAGCGGTATTTTTTATCA
1 CTTTAGCGGCACTTTTATAGCAAACGCCACTAAAGAACATGACCTTTTAGCGG-AGCTTTTATCA
12568719 CAAACGCCACTAAAA
65 CAAACGCCACTAAAA
12568734 GTATAGTTCT
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
86 8 0.12
87 60 0.87
88 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (87 bp):
CTTTAGCGGCACTTTTATAGCAAACGCCACTAAAGAACATGACCTTTTAGCGGAGCTTTTATCAC
AAACGCCACTAAAAAACATGAC
Found at i:12568910 original size:85 final size:85
Alignment explanation
Indices: 12568767--12568936 Score: 340
Period size: 85 Copynumber: 2.0 Consensus size: 85
12568757 ACAGAAAATG
12568767 CCACTAACTTTGGCAGATTTCTAACATCCAATTTTCATCCATATGCAACCCTTCCTGTAACATTG
1 CCACTAACTTTGGCAGATTTCTAACATCCAATTTTCATCCATATGCAACCCTTCCTGTAACATTG
12568832 AAACCAACCAAAAACAACAA
66 AAACCAACCAAAAACAACAA
12568852 CCACTAACTTTGGCAGATTTCTAACATCCAATTTTCATCCATATGCAACCCTTCCTGTAACATTG
1 CCACTAACTTTGGCAGATTTCTAACATCCAATTTTCATCCATATGCAACCCTTCCTGTAACATTG
12568917 AAACCAACCAAAAACAACAA
66 AAACCAACCAAAAACAACAA
12568937 ATCTAAATGA
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 85 1.00
ACGTcount: A:0.38, C:0.29, G:0.07, T:0.26
Consensus pattern (85 bp):
CCACTAACTTTGGCAGATTTCTAACATCCAATTTTCATCCATATGCAACCCTTCCTGTAACATTG
AAACCAACCAAAAACAACAA
Found at i:12574948 original size:50 final size:50
Alignment explanation
Indices: 12574890--12575107 Score: 276
Period size: 50 Copynumber: 4.4 Consensus size: 50
12574880 GGGTAAACAA
* *
12574890 GTCCCATGTAAGACCATGTCTGGTACATGGCATTTGCACCAAGACGAGAG
1 GTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGACGAGAG
* * * *
12574940 GTCCCATGTAAGACCATGTCTGGGACATGGCGTTCGCACCGAGATGAGAG
1 GTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGACGAGAG
* * * * *
12574990 ATCCCATGAAAGACCATGTCTGGGACATGGCGTTGGCATCAAGATGAGAG
1 GTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGACGAGAG
* * *
12575040 GTCCCATGAAAGACCATGTCTGGGACATGG-AGTTGGCACCGAGACAAGAG
1 GTCCCATGTAAGACCATGTCTGGGACATGGCA-TTGGCACCAAGACGAGAG
**
12575090 GTCCCCCGTAAGACCATG
1 GTCCCATGTAAGACCATG
12575108 GCATGGGCAC
Statistics
Matches: 148, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
50 148 1.00
ACGTcount: A:0.28, C:0.24, G:0.29, T:0.19
Consensus pattern (50 bp):
GTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGACGAGAG
Found at i:12575064 original size:100 final size:100
Alignment explanation
Indices: 12574891--12575083 Score: 305
Period size: 100 Copynumber: 1.9 Consensus size: 100
12574881 GGTAAACAAG
* * * *
12574891 TCCCATGTAAGACCATGTCTGGTACATGGCATTTGCACCAAGACGAGAGGTCCCATGTAAGACCA
1 TCCCATGAAAGACCATGTCTGGGACATGGCATTGGCACCAAGACGAGAGGTCCCATGAAAGACCA
*
12574956 TGTCTGGGACATGGCGTTCGCACCGAGATGAGAGA
66 TGTCTGGGACATGGAGTTCGCACCGAGATGAGAGA
* * *
12574991 TCCCATGAAAGACCATGTCTGGGACATGGCGTTGGCATCAAGATGAGAGGTCCCATGAAAGACCA
1 TCCCATGAAAGACCATGTCTGGGACATGGCATTGGCACCAAGACGAGAGGTCCCATGAAAGACCA
*
12575056 TGTCTGGGACATGGAGTTGGCACCGAGA
66 TGTCTGGGACATGGAGTTCGCACCGAGA
12575084 CAAGAGGTCC
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
100 84 1.00
ACGTcount: A:0.27, C:0.23, G:0.30, T:0.20
Consensus pattern (100 bp):
TCCCATGAAAGACCATGTCTGGGACATGGCATTGGCACCAAGACGAGAGGTCCCATGAAAGACCA
TGTCTGGGACATGGAGTTCGCACCGAGATGAGAGA
Found at i:12577442 original size:9 final size:9
Alignment explanation
Indices: 12577428--12577669 Score: 198
Period size: 9 Copynumber: 27.7 Consensus size: 9
12577418 TAAGTATAAA
12577428 TAAGTTATG
1 TAAGTTATG
*
12577437 TAAGTTATA
1 TAAGTTATG
12577446 TAAGTTAT-
1 TAAGTTATG
12577454 TAAGTTATG
1 TAAGTTATG
12577463 TAAGTTATG
1 TAAGTTATG
* * *
12577472 ATATGATATA
1 -TAAGTTATG
*
12577482 T-ATTTATG
1 TAAGTTATG
*
12577490 T-A-TAATG
1 TAAGTTATG
12577497 TAAGTTATG
1 TAAGTTATG
12577506 TAAGTTATG
1 TAAGTTATG
*
12577515 TGAGTTATG
1 TAAGTTATG
12577524 TAAGTTATG
1 TAAGTTATG
* * *
12577533 ATATGATATA
1 -TAAGTTATG
*
12577543 T-ATTTATG
1 TAAGTTATG
12577551 T-A-TTATG
1 TAAGTTATG
12577558 TAAGTTATG
1 TAAGTTATG
*
12577567 TGAGTTATG
1 TAAGTTATG
12577576 TAAGTTATG
1 TAAGTTATG
* * *
12577585 ATATGATATA
1 -TAAGTTATG
*
12577595 T-ATTTATG
1 TAAGTTATG
*
12577603 T-A-TTTTG
1 TAAGTTATG
12577610 TAAGTTATG
1 TAAGTTATG
**
12577619 TATTTTATG
1 TAAGTTATG
*
12577628 TGAGTTATG
1 TAAGTTATG
12577637 TAAGTTATG
1 TAAGTTATG
12577646 TAAGTTATG
1 TAAGTTATG
*
12577655 TGAGTTATG
1 TAAGTTATG
12577664 TAAGTT
1 TAAGTT
12577670 GAGAAGATGT
Statistics
Matches: 185, Mismatches: 38, Indels: 20
0.76 0.16 0.08
Matches are distributed among these distances:
7 16 0.09
8 26 0.14
9 125 0.68
10 18 0.10
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48
Consensus pattern (9 bp):
TAAGTTATG
Found at i:12577444 original size:26 final size:25
Alignment explanation
Indices: 12577414--12577468 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 25
12577404 AAATTGTTTA
12577414 TTTATAAGTATAAATAAGTTATGTAAG
1 TTTATAAGT-T-AATAAGTTATGTAAG
*
12577441 TTATATAAGTTATTAAGTTATGTAAG
1 TT-TATAAGTTAATAAGTTATGTAAG
12577467 TT
1 TT
12577469 ATGATATGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 16 0.62
27 3 0.12
28 7 0.27
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (25 bp):
TTTATAAGTTAATAAGTTATGTAAG
Found at i:12577498 original size:34 final size:33
Alignment explanation
Indices: 12577459--12577566 Score: 129
Period size: 34 Copynumber: 3.4 Consensus size: 33
12577449 GTTATTAAGT
12577459 TATGTAAGTTATGATATGATATATATTTATGTA
1 TATGTAAGTTATGATATGATATATATTTATGTA
* * *
12577492 TAATGTAAGTTATG-TAAG-T-TAT-GTGA-GT-
1 T-ATGTAAGTTATGATATGATATATATTTATGTA
12577520 TATGTAAGTTATGATATGATATATATTTATGTA
1 TATGTAAGTTATGATATGATATATATTTATGTA
12577553 TTATGTAAGTTATG
1 -TATGTAAGTTATG
12577567 TGAGTTATGT
Statistics
Matches: 61, Mismatches: 6, Indels: 15
0.74 0.07 0.18
Matches are distributed among these distances:
27 12 0.20
28 4 0.07
29 3 0.05
30 5 0.08
31 5 0.08
32 3 0.05
33 4 0.07
34 25 0.41
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (33 bp):
TATGTAAGTTATGATATGATATATATTTATGTA
Found at i:12577513 original size:52 final size:52
Alignment explanation
Indices: 12577432--12577636 Score: 241
Period size: 52 Copynumber: 3.8 Consensus size: 52
12577422 TATAAATAAG
*
12577432 TTATGTAAGTTATATAAGTTAT-TAAGTTATGTAAGTTATGATATGATATATATTTAT
1 TTATGT-A-TTATGTAAGTTATGTAAGTTATGTAAGTTATGATATG--ATATA--TAT
*
12577489 GTATAATGTAAGTTATGTAAGTTATGTGAGTTATGTAAGTTATGATATGATATATAT
1 -T-T-ATGT-A-TTATGTAAGTTATGTAAGTTATGTAAGTTATGATATGATATATAT
*
12577546 TTATGTATTATGTAAGTTATGTGAGTTATGTAAGTTATGATATGATATATAT
1 TTATGTATTATGTAAGTTATGTAAGTTATGTAAGTTATGATATGATATATAT
* ** *
12577598 TTATGTATTTTGTAAGTTATGTATTTTATGTGAGTTATG
1 TTATGTATTATGTAAGTTATGTAAGTTATGTAAGTTATG
12577637 TAAGTTATGT
Statistics
Matches: 137, Mismatches: 7, Indels: 12
0.88 0.04 0.08
Matches are distributed among these distances:
52 79 0.58
53 1 0.01
54 4 0.03
55 1 0.01
56 1 0.01
57 3 0.02
58 1 0.01
59 6 0.04
60 19 0.14
61 22 0.16
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.49
Consensus pattern (52 bp):
TTATGTATTATGTAAGTTATGTAAGTTATGTAAGTTATGATATGATATATAT
Found at i:12577535 original size:61 final size:60
Alignment explanation
Indices: 12577433--12577645 Score: 300
Period size: 61 Copynumber: 3.7 Consensus size: 60
12577423 ATAAATAAGT
* *
12577433 TATGTAAGTTATATAAGTTAT-TAAGTTATGTAAGTTATGATATGATATATATTTATGTA
1 TATGTAAGTTATGTAAGTTATGTGAGTTATGTAAGTTATGATATGATATATATTTATGTA
12577492 TAATGTAAGTTATGTAAGTTATGTGAGTTATGTAAGTTATGATATG--ATATA--TAT-T-
1 T-ATGTAAGTTATGTAAGTTATGTGAGTTATGTAAGTTATGATATGATATATATTTATGTA
12577547 TATGT-A-TTATGTAAGTTATGTGAGTTATGTAAGTTATGATATGATATATATTTATGTA
1 TATGTAAGTTATGTAAGTTATGTGAGTTATGTAAGTTATGATATGATATATATTTATGTA
* **
12577605 TTTTGTAAGTTATGTATTTTATGTGAGTTATGTAAGTTATG
1 -TATGTAAGTTATGTAAGTTATGTGAGTTATGTAAGTTATG
12577646 TAAGTTATGT
Statistics
Matches: 138, Mismatches: 5, Indels: 20
0.85 0.03 0.12
Matches are distributed among these distances:
52 37 0.27
53 1 0.01
54 9 0.07
55 1 0.01
56 4 0.03
57 4 0.03
59 10 0.07
60 20 0.14
61 52 0.38
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48
Consensus pattern (60 bp):
TATGTAAGTTATGTAAGTTATGTGAGTTATGTAAGTTATGATATGATATATATTTATGTA
Found at i:12580020 original size:14 final size:14
Alignment explanation
Indices: 12579989--12580069 Score: 54
Period size: 14 Copynumber: 5.7 Consensus size: 14
12579979 ATTAACCCTA
12579989 AAACCCTAAAATCCT
1 AAACCCT-AAATCCT
* *
12580004 AAATCCTAAACCCT
1 AAACCCTAAATCCT
* ** **
12580018 AAACCATGCATTGT
1 AAACCCTAAATCCT
* *
12580032 AAACCTTAAATCAT
1 AAACCCTAAATCCT
*
12580046 AAACACTAAATCCT
1 AAACCCTAAATCCT
*
12580060 AAACCATAAA
1 AAACCCTAAA
12580070 CTTCTATATC
Statistics
Matches: 47, Mismatches: 19, Indels: 1
0.70 0.28 0.01
Matches are distributed among these distances:
14 41 0.87
15 6 0.13
ACGTcount: A:0.48, C:0.27, G:0.02, T:0.22
Consensus pattern (14 bp):
AAACCCTAAATCCT
Found at i:12585682 original size:9 final size:9
Alignment explanation
Indices: 12585668--12585693 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
12585658 TCTCCTCTAT
12585668 TTCTTCTTA
1 TTCTTCTTA
12585677 TTCTTCTTA
1 TTCTTCTTA
12585686 TTCTTCTT
1 TTCTTCTT
12585694 TTTAGCAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.08, C:0.23, G:0.00, T:0.69
Consensus pattern (9 bp):
TTCTTCTTA
Found at i:12589048 original size:21 final size:22
Alignment explanation
Indices: 12588988--12589048 Score: 54
Period size: 24 Copynumber: 2.7 Consensus size: 22
12588978 ACTAATTTTC
* *
12588988 AAAAAATTTCTAAA-ATTTATTT
1 AAAAAATTT-AAAATATTTATTA
12589010 AAAAAATTCTAAGGAATATTTA-TA
1 AAAAAATT-TAA--AATATTTATTA
12589034 AAAAAATTTAAAATA
1 AAAAAATTTAAAATA
12589049 ATATCAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
21 4 0.12
22 9 0.27
23 4 0.12
24 11 0.33
25 5 0.15
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.36
Consensus pattern (22 bp):
AAAAAATTTAAAATATTTATTA
Found at i:12589994 original size:18 final size:18
Alignment explanation
Indices: 12589975--12590010 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
12589965 AAAATAAAAA
12589975 TTAATTAAAGAAAAATAAT
1 TTAA-TAAAGAAAAATAAT
*
12589994 TTAATAAATAAAAATAA
1 TTAATAAAGAAAAATAA
12590011 ACTAGAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (18 bp):
TTAATAAAGAAAAATAAT
Found at i:12596687 original size:18 final size:19
Alignment explanation
Indices: 12596654--12596691 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
12596644 AGACTCCAGG
*
12596654 TCTGATTCTTTTCAATCAT
1 TCTGATTCTCTTCAATCAT
12596673 TCTGATT-TCTTCAATCAT
1 TCTGATTCTCTTCAATCAT
12596691 T
1 T
12596692 GCCTGCTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.53
Consensus pattern (19 bp):
TCTGATTCTCTTCAATCAT
Found at i:12605762 original size:40 final size:39
Alignment explanation
Indices: 12605716--12605791 Score: 102
Period size: 39 Copynumber: 1.9 Consensus size: 39
12605706 TTAAATCAAA
12605716 TTTAACTTTGATT-AAA-AATGTTTAACTTTGATTAAAAATG
1 TTTAAC-TTGATTGAAACAAT-TTTAAC-TTGATTAAAAATG
*
12605756 TTTAACTTGATTGAAACCATTTTAACTTGATTAAAA
1 TTTAACTTGATTGAAACAATTTTAACTTGATTAAAA
12605792 CTTTATTCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
39 16 0.48
40 15 0.45
41 2 0.06
ACGTcount: A:0.39, C:0.08, G:0.09, T:0.43
Consensus pattern (39 bp):
TTTAACTTGATTGAAACAATTTTAACTTGATTAAAAATG
Found at i:12605792 original size:20 final size:20
Alignment explanation
Indices: 12605716--12605791 Score: 104
Period size: 20 Copynumber: 3.9 Consensus size: 20
12605706 TTAAATCAAA
12605716 TTTAACTTTGATTAAAAATG
1 TTTAACTTTGATTAAAAATG
12605736 TTTAACTTTGATTAAAAATG
1 TTTAACTTTGATTAAAAATG
*
12605756 TTTAAC-TTGATTGAAACCAT-
1 TTTAACTTTGATT-AAA-AATG
12605776 TTTAAC-TTGATTAAAA
1 TTTAACTTTGATTAAAA
12605792 CTTTATTCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
19 9 0.17
20 41 0.79
21 2 0.04
ACGTcount: A:0.39, C:0.08, G:0.09, T:0.43
Consensus pattern (20 bp):
TTTAACTTTGATTAAAAATG
Found at i:12608623 original size:115 final size:115
Alignment explanation
Indices: 12608421--12608640 Score: 413
Period size: 115 Copynumber: 1.9 Consensus size: 115
12608411 CTTTTTTCCT
*
12608421 CAAAAGAACAAAACAGATAAAAACTCAAAAGAATAGTAGAACAGGAAGCTAACCTGGTCCAATGT
1 CAAAAGAACAAAACAGATAAAAACTCAAAAGAATAGCAGAACAGGAAGCTAACCTGGTCCAATGT
12608486 CTGGCAGTTATCATCTATCCTTGAGTAATTCCTCTCCATATTTACCAATA
66 CTGGCAGTTATCATCTATCCTTGAGTAATTCCTCTCCATATTTACCAATA
12608536 CAAAAGAACAAAACAGATAAAAACTCAAAAGAATAGCAGAACAGGAAGCTAACCTGGTCCAATGT
1 CAAAAGAACAAAACAGATAAAAACTCAAAAGAATAGCAGAACAGGAAGCTAACCTGGTCCAATGT
* *
12608601 CTGGTAGTTATCATCTATCCTTGAGTATTTCCTCTCCATA
66 CTGGCAGTTATCATCTATCCTTGAGTAATTCCTCTCCATA
12608641 GTCCTATGTA
Statistics
Matches: 102, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
115 102 1.00
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24
Consensus pattern (115 bp):
CAAAAGAACAAAACAGATAAAAACTCAAAAGAATAGCAGAACAGGAAGCTAACCTGGTCCAATGT
CTGGCAGTTATCATCTATCCTTGAGTAATTCCTCTCCATATTTACCAATA
Found at i:12609270 original size:19 final size:20
Alignment explanation
Indices: 12609223--12609272 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
12609213 TAAAATTATA
12609223 ATTTTTAGTTTTTGTATTTCT
1 ATTTTTA-TTTTTGTATTTCT
*
12609244 TTTTTTATTTTTGTATTTC-
1 ATTTTTATTTTTGTATTTCT
12609263 ATTTTTATTT
1 ATTTTTATTT
12609273 GTTATAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 9 0.33
20 12 0.44
21 6 0.22
ACGTcount: A:0.14, C:0.04, G:0.06, T:0.76
Consensus pattern (20 bp):
ATTTTTATTTTTGTATTTCT
Found at i:12609714 original size:21 final size:21
Alignment explanation
Indices: 12609690--12609730 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
12609680 CCATTAACTC
*
12609690 TTAACCCCTAACCCCTAAACA
1 TTAAACCCTAACCCCTAAACA
*
12609711 TTAAACCCTAACCCTTAAAC
1 TTAAACCCTAACCCCTAAAC
12609731 CTAGAGGTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.39, G:0.00, T:0.22
Consensus pattern (21 bp):
TTAAACCCTAACCCCTAAACA
Found at i:12609945 original size:10 final size:11
Alignment explanation
Indices: 12609919--12609944 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
12609909 TATTTTTAAA
12609919 AAAAATATTTT
1 AAAAATATTTT
12609930 AAAAATATTTT
1 AAAAATATTTT
12609941 AAAA
1 AAAA
12609945 TTAAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:12610181 original size:14 final size:14
Alignment explanation
Indices: 12610162--12610188 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12610152 CTAAACCTGG
12610162 CCATAATCCATAAT
1 CCATAATCCATAAT
12610176 CCATAATCCATAA
1 CCATAATCCATAA
12610189 ACCTTAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.30, G:0.00, T:0.26
Consensus pattern (14 bp):
CCATAATCCATAAT
Found at i:12610223 original size:14 final size:14
Alignment explanation
Indices: 12610206--12610239 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
12610196 AATAGTAACT
*
12610206 CCTAAATCTTAAAC
1 CCTAAATCATAAAC
*
12610220 CCTAAATCATATAC
1 CCTAAATCATAAAC
12610234 CCTAAA
1 CCTAAA
12610240 CCCTAAACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.26
Consensus pattern (14 bp):
CCTAAATCATAAAC
Found at i:12610999 original size:13 final size:13
Alignment explanation
Indices: 12610981--12611044 Score: 83
Period size: 13 Copynumber: 4.9 Consensus size: 13
12610971 AGTTTTTCAT
12610981 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
12610994 TGCTTTTAAAAAG
1 TGCTTTTGAAAAG
* * *
12611007 TACTGTAGAAAAG
1 TGCTTTTGAAAAG
*
12611020 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
12611033 TGCTTTTGAAAA
1 TGCTTTTGAAAA
12611045 ATTTAAGTGT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.34, C:0.08, G:0.22, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:12618405 original size:23 final size:23
Alignment explanation
Indices: 12618375--12618422 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
12618365 GGGAACAAAA
*
12618375 GTGGAAATGGGCAACAAATGTGG
1 GTGGAAATGGGCAACAAACGTGG
*
12618398 GTGGAAATGGGCAGCAAACGTGG
1 GTGGAAATGGGCAACAAACGTGG
12618421 GT
1 GT
12618423 TATACCCACG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.31, C:0.10, G:0.42, T:0.17
Consensus pattern (23 bp):
GTGGAAATGGGCAACAAACGTGG
Found at i:12622491 original size:18 final size:18
Alignment explanation
Indices: 12622438--12622498 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
12622428 CAATTATGTT
* * *
12622438 TGAGCTCACAACTTTGAA
1 TGAGCTCGCAAATTTGGA
* * *
12622456 TGAGTTCGCATATCTGGA
1 TGAGCTCGCAAATTTGGA
12622474 TGAGCTCGCAAATTTGGA
1 TGAGCTCGCAAATTTGGA
*
12622492 TAAGCTC
1 TGAGCTC
12622499 ACAACTTTGC
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.30
Consensus pattern (18 bp):
TGAGCTCGCAAATTTGGA
Found at i:12626084 original size:23 final size:23
Alignment explanation
Indices: 12626038--12626084 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
12626028 CTAAATATAG
* * *
12626038 ACCATAAAATAGATTTGAAGAAT
1 ACCAAAAAATAGATTTAAAAAAT
*
12626061 ACCAAAAAATAGTTTTAAAAAAT
1 ACCAAAAAATAGATTTAAAAAAT
12626084 A
1 A
12626085 ATTGAGAAGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.57, C:0.09, G:0.09, T:0.26
Consensus pattern (23 bp):
ACCAAAAAATAGATTTAAAAAAT
Found at i:12628894 original size:16 final size:16
Alignment explanation
Indices: 12628870--12628903 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12628860 ATAGGAAAAA
* *
12628870 AATTTAAAAATTATAT
1 AATTAAAAAATAATAT
12628886 AATTAAAAAATAATAT
1 AATTAAAAAATAATAT
12628902 AA
1 AA
12628904 AATTTACTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AATTAAAAAATAATAT
Found at i:12630263 original size:3 final size:3
Alignment explanation
Indices: 12630255--12630300 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
12630245 TTTAGCAATT
* *
12630255 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTG TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
12630301 AATTGTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:12630305 original size:15 final size:15
Alignment explanation
Indices: 12630255--12630312 Score: 71
Period size: 15 Copynumber: 3.9 Consensus size: 15
12630245 TTTAGCAATT
*
12630255 TTATTATTATTATTA
1 TTATTGTTATTATTA
* *
12630270 TTATTATTATTATTG
1 TTATTGTTATTATTA
12630285 TTATTGTTATTATTA
1 TTATTGTTATTATTA
* *
12630300 TAATTGTTTTTAT
1 TTATTGTTATTAT
12630313 GCATATACGT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (15 bp):
TTATTGTTATTATTA
Found at i:12630646 original size:2 final size:2
Alignment explanation
Indices: 12630592--12630627 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
12630582 TTGTAAATAC
* *
12630592 AT AT AT AT AT AT AT AT AT TT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12630628 TTTAATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12655225 original size:44 final size:44
Alignment explanation
Indices: 12655077--12655727 Score: 287
Period size: 44 Copynumber: 15.0 Consensus size: 44
12655067 TAGGTTTATT
* **
12655077 ATACAGG-TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGA
1 ATACAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGA-TTAA-A
* ** * *
12655122 ATTTCA-GATCTTATCTCCCTGAGATTACAACGGAGTAGATT-GA
1 A-TACAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAA
* * * *
12655165 A-GCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAA
1 ATAC-AG-GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAA
* * ** * ***
12655210 ATAAAGGATCTTATCTCTCTGA-AGTTACAGCAGAGTAGA-TCGC
1 ATACAGGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAA
* * * **
12655253 AT-CAGG-TCTTATCACCCTGAGGTTACAGTGGAGTAGACCGAAGA
1 ATACAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGA-TTAA-A
* * *
12655297 ATTTCA-GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATT-GA
1 A-TACAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAA
** * * *
12655340 AGCCAGAGATCTTATCTACCTGAGATTACAGCGGAGCAGATCAAA
1 ATACAG-GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAA
* * * * *
12655385 GAT--AGTAATCCTATCTCCTTGAGATTACAATGGAGCGGATT---
1 -ATACAG-GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAA
* * * * *
12655426 A-A-AGGATCTTATCTCTCTGA-AGTTACAGTAGAGAAGA-TCAC
1 ATACAGGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAA
* * * **
12655467 AT-CAGG-TCTTATTTCCCTGAGGTTACAGTGGAGTAGACCAGAGA
1 ATACAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTA-A-A
* * *
12655511 ATTTCA-GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATT-GA
1 A-TACAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAA
** * **
12655554 AGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGA-TCGA
1 ATACAG-GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAA
* ** * *
12655598 AGACACTATCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTAAA
1 ATACAGGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAA
* * * ** * ***
12655642 ATAAAGGATCTTATCTCTCTGAGGTTACAGCAGAGTAGA-TCGC
1 ATACAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAA
* *
12655685 AT-CAGG-TCTTATCTCCCTGATATTACAGTGGAGTAGACTTAAA
1 ATACAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGA-TTAAA
12655728 CCTAAAACCT
Statistics
Matches: 449, Mismatches: 116, Indels: 84
0.69 0.18 0.13
Matches are distributed among these distances:
38 2 0.00
39 23 0.05
40 3 0.01
41 78 0.17
42 15 0.03
43 43 0.10
44 181 0.40
45 11 0.02
46 93 0.21
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (44 bp):
ATACAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAA
Found at i:12655501 original size:214 final size:216
Alignment explanation
Indices: 12655127--12655722 Score: 923
Period size: 214 Copynumber: 2.7 Consensus size: 216
12655117 AAAGAATTTC
* * * *
12655127 AGATCTTATCTCCCTGAGATTACAACGGAGTAGATTGAAGCTAGTAATCCTATCTCCCTGAGATT
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGATAGTAATCCTATCTCCCTGAGATT
12655192 ACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCA
66 ACAGTGGAGCGGATT---ATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCA
*
12655257 GGTCTTATCACCCTGAGGTTACAGTGGAGTAGACC-GAAGAATTTCAGATCTTATCTCCCTGAGG
128 GGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCAG-AGAATTTCAGATCTTATCTCCCTGAGG
12655321 TTACAGTGGAGCAGATTGAAGCCAG
192 TTACAGTGGAGCAGATTGAAGCCAG
* * *
12655346 AGATCTTATCTACCTGAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATT
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGATAGTAATCCTATCTCCCTGAGATT
* * * *
12655411 ACAATGGAGCGGA-T-TAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGT
66 ACAGTGGAGCGGATTATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAGGT
*
12655474 CTTATTTCCCTGAGGTTACAGTGGAGTAGACCAGAGAATTTCAGATCTTATCTCCCTGAGGTTAC
131 CTTATCTCCCTGAGGTTACAGTGGAGTAGACCAGAGAATTTCAGATCTTATCTCCCTGAGGTTAC
12655539 AGTGGAGCAGATTGAAGCCAG
196 AGTGGAGCAGATTGAAGCCAG
* *
12655560 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACT-ATCCTATCTCCCTGA-AGT
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGATAGTAATCCTATCTCCCTGAGA-T
*
12655623 TACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAGGTTACAGCAGAGTAGATCGCATC
65 TACAGTGGAGCGGATT---ATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATC
**
12655688 AGGTCTTATCTCCCTGATATTACAGTGGAGTAGAC
127 AGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGAC
12655723 TTAAACCTAA
Statistics
Matches: 344, Mismatches: 26, Indels: 15
0.89 0.07 0.04
Matches are distributed among these distances:
212 1 0.00
213 28 0.08
214 170 0.49
215 1 0.00
218 74 0.22
219 70 0.20
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (216 bp):
AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGATAGTAATCCTATCTCCCTGAGATT
ACAGTGGAGCGGATTATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAGGT
CTTATCTCCCTGAGGTTACAGTGGAGTAGACCAGAGAATTTCAGATCTTATCTCCCTGAGGTTAC
AGTGGAGCAGATTGAAGCCAG
Found at i:12655613 original size:87 final size:87
Alignment explanation
Indices: 12655522--12655683 Score: 218
Period size: 87 Copynumber: 1.9 Consensus size: 87
12655512 TTTCAGATCT
* * * *
12655522 TATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGC-CAGAGATCTTATCTCCCTGAGATTACAGC
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACAAAG-GATCTTATCTCCCTGAGATTACAGC
*
12655586 GGAGCAGATCGAAGACACTATCC
65 AGAGCAGATCGAAGACACTATCC
* * * *
12655609 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAGGTTACAGCA
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACAAAGGATCTTATCTCCCTGAGATTACAGCA
*
12655674 GAGTAGATCG
66 GAGCAGATCG
12655684 CATCAGGTCT
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
87 62 0.97
88 2 0.03
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (87 bp):
TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACAAAGGATCTTATCTCCCTGAGATTACAGCA
GAGCAGATCGAAGACACTATCC
Found at i:12657160 original size:3 final size:3
Alignment explanation
Indices: 12657146--12657182 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
12657136 TTTAGCAATT
* *
12657146 TTA TTT TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
12657183 AATTGTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:12657173 original size:18 final size:18
Alignment explanation
Indices: 12657146--12657194 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
12657136 TTTAGCAATT
*
12657146 TTATTTTTATTATTATTA
1 TTATTGTTATTATTATTA
12657164 TTATTGTTATTATTATTA
1 TTATTGTTATTATTATTA
* *
12657182 TAATTGTTTTTAT
1 TTATTGTTATTAT
12657195 GCATATACGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (18 bp):
TTATTGTTATTATTATTA
Found at i:12658669 original size:21 final size:20
Alignment explanation
Indices: 12658622--12658708 Score: 68
Period size: 21 Copynumber: 4.2 Consensus size: 20
12658612 GATTTATAAA
*
12658622 TTTTTTT-AATAATTTTATAT
1 TTTTTTTGAATTATTTTA-AT
*
12658642 TATTTTTTGTATTATTTTAAT
1 T-TTTTTTGAATTATTTTAAT
* *
12658663 TTATTTTTAAATCATTTTAAT
1 TT-TTTTTGAATTATTTTAAT
* * *
12658684 ATTTTTTGGATTTTTTATAAT
1 TTTTTTTGAATTATTT-TAAT
12658705 TTTT
1 TTTT
12658709 AATATCTTTT
Statistics
Matches: 52, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
20 12 0.23
21 32 0.62
22 8 0.15
ACGTcount: A:0.26, C:0.01, G:0.03, T:0.69
Consensus pattern (20 bp):
TTTTTTTGAATTATTTTAAT
Found at i:12658690 original size:10 final size:10
Alignment explanation
Indices: 12658623--12658720 Score: 51
Period size: 10 Copynumber: 9.8 Consensus size: 10
12658613 ATTTATAAAT
12658623 TTTTTTAATAA
1 TTTTTTAAT-A
* *
12658634 TTTTATATTA
1 TTTTTTAATA
*
12658644 TTTTTT-GTA
1 TTTTTTAATA
*
12658653 TTATTTTAATT
1 TT-TTTTAATA
12658664 TATTTTTAA-A
1 T-TTTTTAATA
*
12658674 TCATTTTAATA
1 T-TTTTTAATA
**
12658685 TTTTTT-GGA
1 TTTTTTAATA
12658694 TTTTTT-ATA
1 TTTTTTAATA
*
12658703 ATTTTTAATA
1 TTTTTTAATA
*
12658713 TCTTTTAA
1 TTTTTTAA
12658721 AGATTTTCAG
Statistics
Matches: 65, Mismatches: 17, Indels: 11
0.70 0.18 0.12
Matches are distributed among these distances:
9 17 0.26
10 30 0.46
11 17 0.26
12 1 0.02
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (10 bp):
TTTTTTAATA
Found at i:12658969 original size:17 final size:17
Alignment explanation
Indices: 12658917--12658969 Score: 52
Period size: 19 Copynumber: 3.0 Consensus size: 17
12658907 TATAGAAACA
* *
12658917 TAATCTTCGAGGATATG
1 TAATCTTAGAAGATATG
* *
12658934 CAATTTTAGATATGATATG
1 TAATCTTAGA-A-GATATG
12658953 TAATCTTAGAAGATATG
1 TAATCTTAGAAGATATG
12658970 ATTTTGTAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
17 13 0.46
18 1 0.04
19 14 0.50
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.38
Consensus pattern (17 bp):
TAATCTTAGAAGATATG
Found at i:12658969 original size:22 final size:23
Alignment explanation
Indices: 12658941--12658999 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
12658931 ATGCAATTTT
12658941 AGATATGA-TATGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
* *
12658963 AGATATGATTTTGTAATCTTA-T
1 AGATATGATTATGTAATCTTAGA
*
12658985 AGATTTGATT-TGTAA
1 AGATATGATTATGTAA
12659000 ATACTCTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.15
22 17 0.52
23 11 0.33
ACGTcount: A:0.36, C:0.03, G:0.17, T:0.44
Consensus pattern (23 bp):
AGATATGATTATGTAATCTTAGA
Found at i:12669642 original size:27 final size:27
Alignment explanation
Indices: 12669607--12669669 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
12669597 TAACAACCTT
12669607 AATTGACAAATAGAT-AACTTTTTATTAA
1 AATT-ACAAATAG-TCAACTTTTTATTAA
* *
12669635 AATTACAAGTTGTCAACTTTTTATTAA
1 AATTACAAATAGTCAACTTTTTATTAA
12669662 AATTACAA
1 AATTACAA
12669670 GTTGTCCTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
26 1 0.03
27 27 0.84
28 4 0.12
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (27 bp):
AATTACAAATAGTCAACTTTTTATTAA
Found at i:12669670 original size:27 final size:27
Alignment explanation
Indices: 12669622--12669675 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
12669612 ACAAATAGAT
12669622 AACTTTTTATTAAAATTACAAGTTGTC
1 AACTTTTTATTAAAATTACAAGTTGTC
12669649 AACTTTTTATTAAAATTACAAGTTGTC
1 AACTTTTTATTAAAATTACAAGTTGTC
12669676 CTTACACATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.44
Consensus pattern (27 bp):
AACTTTTTATTAAAATTACAAGTTGTC
Found at i:12670126 original size:25 final size:26
Alignment explanation
Indices: 12670098--12670152 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
12670088 TTTTTTTCTC
*
12670098 TTTTTTCAAATGTTTTTTTTT-AATT
1 TTTTTTCAAATCTTTTTTTTTCAATT
***
12670123 TTTTTTCTTTTCTTTTTTTTTCAATT
1 TTTTTTCAAATCTTTTTTTTTCAATT
12670149 TTTT
1 TTTT
12670153 AAAATAACAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 17 0.68
26 8 0.32
ACGTcount: A:0.13, C:0.07, G:0.02, T:0.78
Consensus pattern (26 bp):
TTTTTTCAAATCTTTTTTTTTCAATT
Found at i:12671878 original size:43 final size:42
Alignment explanation
Indices: 12671813--12671923 Score: 120
Period size: 41 Copynumber: 2.6 Consensus size: 42
12671803 AGCTCGTACA
* * * *
12671813 ATGCCATATCCCGGAGATGGTCTTACATGCTAATGCATAT-CG
1 ATGCCATATCCCAGACATGGTCTTACATACGAAT-CATATACG
*
12671855 ATGCCACTATCCCAGACAGGGTCTT--ATACGAATCATATACG
1 ATGCCA-TATCCCAGACATGGTCTTACATACGAATCATATACG
*
12671896 ATGCCAATGTCCCAGACATGGTCTTACA
1 ATGCC-ATATCCCAGACATGGTCTTACA
12671924 CATTTCCTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
40 5 0.09
41 29 0.51
42 7 0.12
43 16 0.28
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (42 bp):
ATGCCATATCCCAGACATGGTCTTACATACGAATCATATACG
Found at i:12671958 original size:43 final size:43
Alignment explanation
Indices: 12671896--12672054 Score: 228
Period size: 43 Copynumber: 3.7 Consensus size: 43
12671886 ATCATATACG
* * *
12671896 ATGCCAATGTCCCAGACATGGTCTTACACATTTCCTTACTTCA
1 ATGCCAATGTCCCAGACATGGTCTTACACGTTTTCTCACTTCA
*
12671939 ATGCCAATGTCCCAAACATGGTCTTACACGTTTTCTCACTTCA
1 ATGCCAATGTCCCAGACATGGTCTTACACGTTTTCTCACTTCA
** **
12671982 ATGTTAATGTCCCAGACATGGTCTTACACGTTTTCTCACTTTG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTTTTCTCACTTCA
* *
12672025 ATGCCAATGTACCAGACATGGTTTTACACG
1 ATGCCAATGTCCCAGACATGGTCTTACACG
12672055 AAATCACATC
Statistics
Matches: 103, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 103 1.00
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.33
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGTTTTCTCACTTCA
Found at i:12676864 original size:20 final size:19
Alignment explanation
Indices: 12676835--12676879 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
12676825 ATTAGAATAT
*
12676835 AAAAATTAAATTAAAAACA
1 AAAAATTAAAATAAAAACA
*
12676854 AAAATATTAAAATAAAAATA
1 AAAA-ATTAAAATAAAAACA
12676874 AAAAAT
1 AAAAAT
12676880 GACTAAATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAAATTAAAATAAAAACA
Found at i:12679382 original size:45 final size:44
Alignment explanation
Indices: 12679287--12679498 Score: 237
Period size: 45 Copynumber: 4.7 Consensus size: 44
12679277 AGGTATAGGG
* *
12679287 TATATATAATAATTGTTGGTTTCACCGACCAGTGCTGGGCACATACA
1 TATATATAATATTTGTCGGTTTCACCGACCAGTGCTGGGCAC--A-A
* * * *
12679334 TATATATAATATTTGTCAGTTTCACTGACTAGTGTTGGGCAC-A
1 TATATATAATATTTGTCGGTTTCACCGACCAGTGCTGGGCACAA
* * * * *
12679377 TATATATAATAATTGACGGTTTTACCGACCAGTGCTAGGCATAAA
1 TATATATAATATTTGTCGGTTTCACCGACCAGTGCTGGGCA-CAA
* *
12679422 TATATATAATATTTGTCGGTTTCACCAACCAGTGCTGGGCACACG
1 TATATATAATATTTGTCGGTTTCACCGACCAGTGCTGGGCACA-A
* *
12679467 TATATATAATATTTGTTGGTTTCATCGACCAG
1 TATATATAATATTTGTCGGTTTCACCGACCAG
12679499 CGTTAGGCTC
Statistics
Matches: 137, Mismatches: 25, Indels: 8
0.81 0.15 0.05
Matches are distributed among these distances:
43 34 0.25
44 1 0.01
45 66 0.48
47 36 0.26
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (44 bp):
TATATATAATATTTGTCGGTTTCACCGACCAGTGCTGGGCACAA
Found at i:12679506 original size:90 final size:89
Alignment explanation
Indices: 12679286--12679498 Score: 284
Period size: 90 Copynumber: 2.4 Consensus size: 89
12679276 GAGGTATAGG
* *
12679286 GTATATATAATAATTGTTGGTTTCACCGACCAGTGCTGGGCACATACATATATATAATATTTGTC
1 GTATATATAATAATTGTTGGTTTCACCGACCAGTGCTAGG--CATAAATATATATAATATTTGTC
** * *
12679351 AGTTTCACTGACTAGTGTTGGGCACA
64 AGTTTCACCAACCAGTGCTGGGCACA
** * *
12679377 -TATATATAATAATTGACGGTTTTACCGACCAGTGCTAGGCATAAATATATATAATATTTGTCGG
1 GTATATATAATAATTGTTGGTTTCACCGACCAGTGCTAGGCATAAATATATATAATATTTGTCAG
12679441 TTTCACCAACCAGTGCTGGGCACA
66 TTTCACCAACCAGTGCTGGGCACA
* *
12679465 CGTATATATAATATTTGTTGGTTTCATCGACCAG
1 -GTATATATAATAATTGTTGGTTTCACCGACCAG
12679499 CGTTAGGCTC
Statistics
Matches: 105, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
88 43 0.41
90 62 0.59
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (89 bp):
GTATATATAATAATTGTTGGTTTCACCGACCAGTGCTAGGCATAAATATATATAATATTTGTCAG
TTTCACCAACCAGTGCTGGGCACA
Found at i:12686489 original size:21 final size:21
Alignment explanation
Indices: 12686463--12686505 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
12686453 GATTAAGATT
12686463 CCTAGAAATCACAGTATCCAA
1 CCTAGAAATCACAGTATCCAA
12686484 CCTAGAAATCACAGTATCCAA
1 CCTAGAAATCACAGTATCCAA
12686505 C
1 C
12686506 AGCATCTTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.30, G:0.09, T:0.19
Consensus pattern (21 bp):
CCTAGAAATCACAGTATCCAA
Found at i:12687580 original size:18 final size:18
Alignment explanation
Indices: 12687559--12687594 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
12687549 TCATTTTATA
12687559 TGTTT-TTTATATTTAATT
1 TGTTTATTTATA-TTAATT
12687577 TGTTTATTTATATTAATT
1 TGTTTATTTATATTAATT
12687595 AAAATTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (18 bp):
TGTTTATTTATATTAATT
Found at i:12688547 original size:7 final size:7
Alignment explanation
Indices: 12688537--12688606 Score: 95
Period size: 7 Copynumber: 9.9 Consensus size: 7
12688527 GACTTTTACT
12688537 GTTTGGG
1 GTTTGGG
12688544 GTTTTGGG
1 G-TTTGGG
12688552 GTTTGGG
1 GTTTGGG
12688559 GTTTGGG
1 GTTTGGG
*
12688566 GTTTGGA
1 GTTTGGG
12688573 GTTTGGG
1 GTTTGGG
*
12688580 GGTTGGG
1 GTTTGGG
* *
12688587 GGTTGGT
1 GTTTGGG
12688594 GTTTGGG
1 GTTTGGG
12688601 GTTTGG
1 GTTTGG
12688607 TTTTGAGGTT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
7 49 0.88
8 7 0.12
ACGTcount: A:0.01, C:0.00, G:0.56, T:0.43
Consensus pattern (7 bp):
GTTTGGG
Found at i:12688617 original size:13 final size:14
Alignment explanation
Indices: 12688536--12688617 Score: 51
Period size: 14 Copynumber: 5.9 Consensus size: 14
12688526 TGACTTTTAC
*
12688536 TGTTTGGGGTTTTGG
1 TGTTTGAGG-TTTGG
* *
12688551 GGTTTGGGGTTTGG
1 TGTTTGAGGTTTGG
*
12688565 GGTTTG-GAGTTTGG
1 TGTTTGAG-GTTTGG
* * * *
12688579 GGGTTGGGGGTTGG
1 TGTTTGAGGTTTGG
*
12688593 TGTTTGGGGTTTGG
1 TGTTTGAGGTTTGG
12688607 T-TTTGAGGTTT
1 TGTTTGAGGTTT
12688618 AAGGTTTACA
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
13 10 0.17
14 39 0.67
15 9 0.16
ACGTcount: A:0.02, C:0.00, G:0.51, T:0.46
Consensus pattern (14 bp):
TGTTTGAGGTTTGG
Found at i:12690805 original size:10 final size:10
Alignment explanation
Indices: 12690790--12690828 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
12690780 GTTATGGGTA
*
12690790 AATTTTAAAT
1 AATTTTATAT
12690800 AATTTTATAT
1 AATTTTATAT
*
12690810 AATTTTATTT
1 AATTTTATAT
12690820 AATTTTATA
1 AATTTTATA
12690829 ATTATTCGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
AATTTTATAT
Found at i:12690890 original size:16 final size:16
Alignment explanation
Indices: 12690869--12690904 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
12690859 GTATTTATAA
*
12690869 TTATCGATTTGCAATT
1 TTATCGATTTACAATT
12690885 TTATCGATTTACAATT
1 TTATCGATTTACAATT
12690901 TTAT
1 TTAT
12690905 TTCAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.11, G:0.08, T:0.53
Consensus pattern (16 bp):
TTATCGATTTACAATT
Found at i:12691040 original size:67 final size:67
Alignment explanation
Indices: 12690964--12691116 Score: 270
Period size: 67 Copynumber: 2.3 Consensus size: 67
12690954 ATTAATTGAT
12690964 TGAATGTCAATAAATTATCAATTTTGGTTAGTTAATTGATTGAATGTTTAATAAATTCATTATAT
1 TGAATGTCAATAAATTATCAATTTTGGTTAGTTAATTGATTGAATGTTTAATAAATTCATTATAT
12691029 AA
66 AA
*
12691031 TGAATGTCAATGAATTATCAATTTTGGTTAGTTAATTGATTGAATGTTTAATAAATTCATTATAT
1 TGAATGTCAATAAATTATCAATTTTGGTTAGTTAATTGATTGAATGTTTAATAAATTCATTATAT
12691096 AA
66 AA
* *
12691098 TGAATTCTCAAAAAATTAT
1 TGAA-TGTCAATAAATTAT
12691117 TACTTGATTG
Statistics
Matches: 81, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
67 70 0.86
68 11 0.14
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.44
Consensus pattern (67 bp):
TGAATGTCAATAAATTATCAATTTTGGTTAGTTAATTGATTGAATGTTTAATAAATTCATTATAT
AA
Found at i:12691939 original size:21 final size:21
Alignment explanation
Indices: 12691915--12691964 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
12691905 CTACAACTTA
*
12691915 AAGCAGAGGCAGCAGCGAGGG
1 AAGCAGAGGCAGCAGCGAGAG
* *
12691936 AAGCAGAAGCTGCAGCGAGAG
1 AAGCAGAGGCAGCAGCGAGAG
12691957 AAGCAGAG
1 AAGCAGAG
12691965 CAAGCCAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.38, C:0.18, G:0.42, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCAGCAGCGAGAG
Found at i:12695303 original size:37 final size:37
Alignment explanation
Indices: 12695261--12695343 Score: 141
Period size: 37 Copynumber: 2.2 Consensus size: 37
12695251 CACCTTCTTC
12695261 GTGCTT-TGAAGTAAATCTTCTTTCTCTTAAATAAATA
1 GTGCTTAT-AAGTAAATCTTCTTTCTCTTAAATAAATA
*
12695298 GTGCTTATAGGTAAATCTTCTTTCTCTTAAATAAATA
1 GTGCTTATAAGTAAATCTTCTTTCTCTTAAATAAATA
12695335 GTGCTTATA
1 GTGCTTATA
12695344 GGTATAAAAC
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
37 43 0.98
38 1 0.02
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.43
Consensus pattern (37 bp):
GTGCTTATAAGTAAATCTTCTTTCTCTTAAATAAATA
Found at i:12695344 original size:37 final size:37
Alignment explanation
Indices: 12695271--12695347 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
12695261 GTGCTTTGAA
12695271 GTAAATCTTCTTTCTCTTAAATAAATAGTGCTTATAG
1 GTAAATCTTCTTTCTCTTAAATAAATAGTGCTTATAG
12695308 GTAAATCTTCTTTCTCTTAAATAAATAGTGCTTATAG
1 GTAAATCTTCTTTCTCTTAAATAAATAGTGCTTATAG
12695345 GTA
1 GTA
12695348 TAAAACACCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (37 bp):
GTAAATCTTCTTTCTCTTAAATAAATAGTGCTTATAG
Found at i:12695586 original size:20 final size:21
Alignment explanation
Indices: 12695563--12695614 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
12695553 TTTTCTCATA
*
12695563 AAAATTATAAAAAGTA-TATT
1 AAAATTATAAAAAATATTATT
12695583 AAAA--ATCAAAAAATATTATT
1 AAAATTAT-AAAAAATATTATT
12695603 AAAATTATAAAA
1 AAAATTATAAAA
12695615 TATGATTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
18 2 0.07
19 7 0.26
20 12 0.44
21 4 0.15
22 2 0.07
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (21 bp):
AAAATTATAAAAAATATTATT
Found at i:12695614 original size:19 final size:21
Alignment explanation
Indices: 12695561--12695617 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 21
12695551 ATTTTTCTCA
12695561 TAAAAATTATAAAA-AGTATAT
1 TAAAAATTATAAAATA-TATAT
* *
12695582 TAAAAATCAAAAAATAT-TAT
1 TAAAAATTATAAAATATATAT
12695602 T-AAAATTATAAAATAT
1 TAAAAATTATAAAATAT
12695618 GATTTAATCT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 13 0.42
20 4 0.13
21 13 0.42
22 1 0.03
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (21 bp):
TAAAAATTATAAAATATATAT
Found at i:12695624 original size:20 final size:19
Alignment explanation
Indices: 12695563--12695624 Score: 54
Period size: 19 Copynumber: 3.1 Consensus size: 19
12695553 TTTTCTCATA
*
12695563 AAAATTATAAAAAGTATATTA
1 AAAATTAT-AAAA-TATATTT
* *
12695584 AAAATCAAAAAATAT-TATT
1 AAAATTATAAAATATAT-TT
12695603 AAAATTATAAAATATGATTT
1 AAAATTATAAAATAT-ATTT
12695623 AA
1 AA
12695625 TCTTACATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
18 1 0.03
19 17 0.52
20 8 0.24
21 7 0.21
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (19 bp):
AAAATTATAAAATATATTT
Found at i:12702865 original size:34 final size:34
Alignment explanation
Indices: 12702818--12702884 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
12702808 CAAAATGATT
*
12702818 TCCTTCTCACATTTAGATATCTTTTACCATTGTA
1 TCCTTCTCACATTTAGATATATTTTACCATTGTA
* * *
12702852 TCCTTTTCTCATTTAGATGTATTTTACCATTGT
1 TCCTTCTCACATTTAGATATATTTTACCATTGT
12702885 TGCCTCCAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.51
Consensus pattern (34 bp):
TCCTTCTCACATTTAGATATATTTTACCATTGTA
Found at i:12707141 original size:24 final size:24
Alignment explanation
Indices: 12707090--12707142 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
12707080 TGCCGGTGGA
***
12707090 GGAGGAGATGGTGGCGGAGAAGGG
1 GGAGGAGATGGTGGCGGAGAAACC
* *
12707114 GGAGGAGGTGGTGGTGGAGAAACC
1 GGAGGAGATGGTGGCGGAGAAACC
12707138 GGAGG
1 GGAGG
12707143 CGACGCTTGC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.06, G:0.60, T:0.09
Consensus pattern (24 bp):
GGAGGAGATGGTGGCGGAGAAACC
Found at i:12708919 original size:29 final size:29
Alignment explanation
Indices: 12708851--12708923 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
12708841 TATAGCAAAC
*
12708851 ATATTATTTTCATAATTAATTTATTCTTT
1 ATATTATTTTCATAATTAATTAATTCTTT
** ** *
12708880 ACCTTATTTTTGTAATTAATTAATTTTTT
1 ATATTATTTTCATAATTAATTAATTCTTT
12708909 AATATTATTTT-ATAA
1 -ATATTATTTTCATAA
12708924 AAAAATACAA
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
29 26 0.76
30 8 0.24
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.60
Consensus pattern (29 bp):
ATATTATTTTCATAATTAATTAATTCTTT
Found at i:12710552 original size:15 final size:16
Alignment explanation
Indices: 12710532--12710570 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
12710522 TTGTTTAAAT
12710532 TATTTTT-TATAATTA
1 TATTTTTATATAATTA
12710547 TATTTTTTATATAATTA
1 TA-TTTTTATATAATTA
12710564 TATTTTT
1 TATTTTT
12710571 CATCCACATC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 2 0.09
16 10 0.45
17 10 0.45
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TATTTTTATATAATTA
Found at i:12710559 original size:17 final size:16
Alignment explanation
Indices: 12710534--12710570 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 16
12710524 GTTTAAATTA
12710534 TTTTTTATAATTATAT
1 TTTTTTATAATTATAT
12710550 TTTTTATATAATTATAT
1 TTTTT-TATAATTATAT
12710567 TTTT
1 TTTT
12710571 CATCCACATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTTTATAATTATAT
Found at i:12714514 original size:25 final size:24
Alignment explanation
Indices: 12714486--12714533 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
12714476 AATTTAATCA
*
12714486 TAAATATTAATATAAAATAATTTTT
1 TAAATAATAA-ATAAAATAATTTTT
* *
12714511 TAAATAATAAATTATATAATTTT
1 TAAATAATAAATAAAATAATTTT
12714534 AATGGGTCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TAAATAATAAATAAAATAATTTTT
Found at i:12718129 original size:19 final size:20
Alignment explanation
Indices: 12718093--12718131 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
12718083 ATTGTTAAAC
*
12718093 TTTATTTAATATATGTTGCT
1 TTTAATTAATATATGTTGCT
*
12718113 TTTAATTAATCTA-GTTGCT
1 TTTAATTAATATATGTTGCT
12718132 GAAATAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (20 bp):
TTTAATTAATATATGTTGCT
Found at i:12718362 original size:23 final size:24
Alignment explanation
Indices: 12718335--12718393 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 24
12718325 AGTTATATAC
*
12718335 AAAGGGAGCATTATATATC-ATTT
1 AAAGGGAGCATTATATATCAATTA
12718358 AAA-GGAGC-TGT-TATATCAATTA
1 AAAGGGAGCAT-TATATATCAATTA
12718380 AAAGGAGAGCATTA
1 AAAGG-GAGCATTA
12718394 CACCTCCTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 10
0.73 0.03 0.25
Matches are distributed among these distances:
21 7 0.24
22 12 0.41
23 4 0.14
24 5 0.17
25 1 0.03
ACGTcount: A:0.42, C:0.08, G:0.20, T:0.29
Consensus pattern (24 bp):
AAAGGGAGCATTATATATCAATTA
Found at i:12720328 original size:18 final size:17
Alignment explanation
Indices: 12720294--12720335 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
12720284 AAATAGAGAG
12720294 AAGAAAAATGAAAGAAA
1 AAGAAAAATGAAAGAAA
12720311 AAGAAAAAT-AAATCGAAA
1 AAGAAAAATGAAA--GAAA
12720329 AAGAAAA
1 AAGAAAA
12720336 TGAGAGCGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.13
17 9 0.39
18 11 0.48
ACGTcount: A:0.76, C:0.02, G:0.14, T:0.07
Consensus pattern (17 bp):
AAGAAAAATGAAAGAAA
Found at i:12726015 original size:26 final size:27
Alignment explanation
Indices: 12725986--12726049 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 27
12725976 AGCCCGGCCC
*
12725986 ATTTTTAAAAT-AAACATTAAAAAATT
1 ATTTTTAAAATAAAACATAAAAAAATT
*
12726012 ATTTTAAAAATAAAAAACATAAAAAAATT
1 ATTTTTAAAAT--AAAACATAAAAAAATT
12726041 A-TTTTAAAA
1 ATTTTTAAAA
12726050 GTATTTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 10 0.31
28 7 0.22
29 15 0.47
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (27 bp):
ATTTTTAAAATAAAACATAAAAAAATT
Found at i:12731056 original size:18 final size:18
Alignment explanation
Indices: 12731029--12731064 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
12731019 ATGTTAAATT
12731029 TAAAAAATAAAAC-AAAA
1 TAAAAAATAAAACTAAAA
12731046 TAAATAAATAAAACTAAAA
1 TAAA-AAATAAAACTAAAA
12731065 GTAACTAGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 9 0.53
19 4 0.24
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.17
Consensus pattern (18 bp):
TAAAAAATAAAACTAAAA
Found at i:12731403 original size:15 final size:16
Alignment explanation
Indices: 12731380--12731412 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
12731370 TATTAATAAA
12731380 AATTCTAAAA-TTTAT
1 AATTCTAAAATTTTAT
*
12731395 AATTTTAAAATTTTAT
1 AATTCTAAAATTTTAT
12731411 AA
1 AA
12731413 AAAATTACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTCTAAAATTTTAT
Found at i:12731847 original size:35 final size:35
Alignment explanation
Indices: 12731798--12732039 Score: 289
Period size: 35 Copynumber: 7.1 Consensus size: 35
12731788 TTCACTTGTC
* * *
12731798 TTTTCTTGCAGGGAATATTTCCTGTTCACGCATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
* * * **
12731833 TTCTGTTGCGGGGAATCTTTCCTGTTCA--CACCA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
*
12731866 -TTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
*
12731900 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
* * *
12731935 TTTTGTTGCAGGGAATATTTCCTGTTCA--CATCA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
* *
12731968 -TTTCTTGCAGGGAATCTCTCCTGTTCACGGATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
* *
12732002 TTTTGTTGCAGGGAATCTCTCCTGTTCATGTATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
12732037 TTT
1 TTT
12732040 CTTTTTGGAC
Statistics
Matches: 176, Mismatches: 25, Indels: 12
0.83 0.12 0.06
Matches are distributed among these distances:
32 47 0.27
33 7 0.04
34 6 0.03
35 116 0.66
ACGTcount: A:0.18, C:0.22, G:0.19, T:0.41
Consensus pattern (35 bp):
TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
Found at i:12731907 original size:67 final size:68
Alignment explanation
Indices: 12731798--12732039 Score: 285
Period size: 67 Copynumber: 3.6 Consensus size: 68
12731788 TTCACTTGTC
* * * *
12731798 TTTTCTTGCAGGGAATATTTCCTGTTCACGCATTATTCTGTTGCGGGGAATCTTTCCTGTTCACA
1 TTTTCTTGCAGGGAATATCTCCTGTTCACGCATTATTTTGTTGCAGGGAATCTCTCCTGTTCACA
*
12731863 CCA
66 CTA
*
12731866 -TTTCTTGCAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAGGGAATCTCTCCTGTTCACA
1 TTTTCTTGCAGGGAATATCTCCTGTTCACGCATTATTTTGTTGCAGGGAATCTCTCCTGTTCACA
12731930 CATTA
66 C--TA
* * * *
12731935 TTTTGTTGCAGGGAATATTTCCTGTTCA--CATCA-TTTCTTGCAGGGAATCTCTCCTGTTCACG
1 TTTTCTTGCAGGGAATATCTCCTGTTCACGCATTATTTTGTTGCAGGGAATCTCTCCTGTTCAC-
*
12731997 GATTA
65 -ACTA
* * * *
12732002 TTTTGTTGCAGGGAATCTCTCCTGTTCATGTATTATTT
1 TTTTCTTGCAGGGAATATCTCCTGTTCACGCATTATTT
12732040 CTTTTTGGAC
Statistics
Matches: 150, Mismatches: 16, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
67 115 0.77
68 4 0.03
69 5 0.03
70 26 0.17
ACGTcount: A:0.18, C:0.22, G:0.19, T:0.41
Consensus pattern (68 bp):
TTTTCTTGCAGGGAATATCTCCTGTTCACGCATTATTTTGTTGCAGGGAATCTCTCCTGTTCACA
CTA
Found at i:12732037 original size:102 final size:102
Alignment explanation
Indices: 12731798--12732039 Score: 385
Period size: 102 Copynumber: 2.4 Consensus size: 102
12731788 TTCACTTGTC
* * * * * *
12731798 TTTTCTTGCAGGGAATATTTCCTGTTCACGCATTATTCTGTTGCGGGGAATCTTTCCTGTTCACA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAGGGAATATTTCCTGTTCACA
12731863 CCATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
66 CCATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
*
12731900 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTGTTGCAGGGAATATTTCCTGTTCACA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAGGGAATATTTCCTGTTCACA
* *
12731965 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGGATTA
66 CCATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
* *
12732002 TTTTGTTGCAGGGAATCTCTCCTGTTCATGTATTATTT
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTATTT
12732040 CTTTTTGGAC
Statistics
Matches: 128, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
102 128 1.00
ACGTcount: A:0.18, C:0.22, G:0.19, T:0.41
Consensus pattern (102 bp):
TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAGGGAATATTTCCTGTTCACA
CCATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
Found at i:12734856 original size:21 final size:22
Alignment explanation
Indices: 12734826--12734870 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
12734816 GAGCAAATTG
12734826 TTGATTCTATTTCCTTTTTG-AT
1 TTGATTCTA-TTCCTTTTTGTAT
*
12734848 TTGA-TCTATTCTTTTTTGTAT
1 TTGATTCTATTCCTTTTTGTAT
12734869 TT
1 TT
12734871 CTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 8 0.38
22 4 0.19
ACGTcount: A:0.13, C:0.11, G:0.09, T:0.67
Consensus pattern (22 bp):
TTGATTCTATTCCTTTTTGTAT
Found at i:12739539 original size:35 final size:35
Alignment explanation
Indices: 12739489--12739729 Score: 271
Period size: 35 Copynumber: 7.1 Consensus size: 35
12739479 TTCACTTGTC
* * * *
12739489 TTTTCTTGCAAGGAATATTTCCTGTTCACGCATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
* * * **
12739524 TTCTGTTGCGGGGAATCTTTCCTGTTCA--CACCA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
*
12739557 -TTTCTTGCA-GGAATCTCTCCTGTTCACGCATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
*
12739590 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
* * *
12739625 TTTTGTTGCAGGGAATATTTCCTGTTCA--CATCA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
* *
12739658 -TTTCTTGCAGGGAATCTCTCCTGTTCACGGATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
* *
12739692 TTTTGTTGCAGGGAATCTCTCCTGTTCATGTATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
12739727 TTT
1 TTT
12739730 CTTTTTGGAC
Statistics
Matches: 173, Mismatches: 26, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
31 16 0.09
32 30 0.17
33 10 0.06
34 11 0.06
35 106 0.61
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.41
Consensus pattern (35 bp):
TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
Found at i:12739676 original size:67 final size:68
Alignment explanation
Indices: 12739489--12739719 Score: 265
Period size: 67 Copynumber: 3.4 Consensus size: 68
12739479 TTCACTTGTC
* * * *
12739489 TTTTCTTGCAAGGAATATTTCCTGTTCACGCATTATTCTGTTGCGGGGAATCTTTCCTGTTCACA
1 TTTTCTTGCAGGGAATATCTCCTGTTCAC-CATTATT-TGTTGCAGGGAATCTCTCCTGTTCACA
*
12739554 C--CA
64 CATTA
*
12739557 -TTTCTTGCA-GGAATCTCTCCTGTTCACGCATTATTTTGTTGCAGGGAATCTCTCCTGTTCACA
1 TTTTCTTGCAGGGAATATCTCCTGTTCAC-CATTA-TTTGTTGCAGGGAATCTCTCCTGTTCACA
12739620 CATTA
64 CATTA
* * * * **
12739625 TTTTGTTGCAGGGAATATTTCCTGTTCA-CATCATTTCTTGCAGGGAATCTCTCCTGTTCACGGA
1 TTTTCTTGCAGGGAATATCTCCTGTTCACCATTATTTGTTGCAGGGAATCTCTCCTGTTCACACA
12739689 TTA
66 TTA
* *
12739692 TTTTGTTGCAGGGAATCTCTCCTGTTCA
1 TTTTCTTGCAGGGAATATCTCCTGTTCA
12739720 TGTATTATTT
Statistics
Matches: 144, Mismatches: 14, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
66 48 0.33
67 68 0.47
68 5 0.03
69 8 0.06
70 15 0.10
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.40
Consensus pattern (68 bp):
TTTTCTTGCAGGGAATATCTCCTGTTCACCATTATTTGTTGCAGGGAATCTCTCCTGTTCACACA
TTA
Found at i:12739727 original size:102 final size:101
Alignment explanation
Indices: 12739489--12739729 Score: 365
Period size: 101 Copynumber: 2.4 Consensus size: 101
12739479 TTCACTTGTC
* * * * * * *
12739489 TTTTCTTGCAAGGAATATTTCCTGTTCACGCATTATTCTGTTGCGGGGAATCTTTCCTGTTCACA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAGGGAATATTTCCTGTTCACA
12739554 CCATTTCTTGCAGGAATCTCTCCTGTTCACGCATTA
66 CCATTTCTTGCAGGAATCTCTCCTGTTCACGCATTA
*
12739590 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTGTTGCAGGGAATATTTCCTGTTCACA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAGGGAATATTTCCTGTTCACA
* *
12739655 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGGATTA
66 CCATTTCTTGCA-GGAATCTCTCCTGTTCACGCATTA
* *
12739692 TTTTGTTGCAGGGAATCTCTCCTGTTCATGTATTATTT
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTATTT
12739730 CTTTTTGGAC
Statistics
Matches: 126, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
101 68 0.54
102 58 0.46
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.41
Consensus pattern (101 bp):
TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAGGGAATATTTCCTGTTCACA
CCATTTCTTGCAGGAATCTCTCCTGTTCACGCATTA
Found at i:12745148 original size:50 final size:51
Alignment explanation
Indices: 12745091--12745191 Score: 168
Period size: 50 Copynumber: 2.0 Consensus size: 51
12745081 TAAAAAAAGT
* *
12745091 ATTTTAAAAATATTTTAAAATTAAAAAAATT-AAAAAAAGTATTTTAAAAA
1 ATTTTAAAAAAAATTTAAAATTAAAAAAATTAAAAAAAAGTATTTTAAAAA
12745141 ATTTTAAAAAAAATTTAAAATTAAAAAAATTAAAAAAAAAGTATTTTAAAA
1 ATTTTAAAAAAAATTTAAAATTAAAAAAATT-AAAAAAAAGTATTTTAAAA
12745192 TTAAAAAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
50 29 0.62
52 18 0.38
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (51 bp):
ATTTTAAAAAAAATTTAAAATTAAAAAAATTAAAAAAAAGTATTTTAAAAA
Found at i:12745156 original size:22 final size:21
Alignment explanation
Indices: 12745111--12745160 Score: 57
Period size: 24 Copynumber: 2.3 Consensus size: 21
12745101 TATTTTAAAA
12745111 TTAAAAAAATTAAAAAAAGTATT
1 TTAAAAAAATTAAAAAAAG-A-T
*
12745134 TTAAAAAATTTTAAAAAAA-AT
1 TTAAAAAA-ATTAAAAAAAGAT
12745155 TTAAAA
1 TTAAAA
12745161 TTAAAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 7 0.28
22 1 0.04
23 8 0.32
24 9 0.36
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
TTAAAAAAATTAAAAAAAGAT
Found at i:12745213 original size:50 final size:48
Alignment explanation
Indices: 12745107--12745208 Score: 136
Period size: 50 Copynumber: 2.1 Consensus size: 48
12745097 AAAATATTTT
**
12745107 AAAATTAAAAAAATTAAAAAAAGTATTTTAAAAAATTTTAAAAAAAATTT
1 AAAATTAAAAAAATTAAAAAAAGTATTTT-AAAAA-TTTAAAAAAAATAA
12745157 AAAATTAAAAAAATTAAAAAAAAAGTATTTT-AAAA-TTAAAAAAAATAA
1 AAAATTAAAAAAATT--AAAAAAAGTATTTTAAAAATTTAAAAAAAATAA
12745205 AAAA
1 AAAA
12745209 AATTATTATT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
48 15 0.31
50 19 0.40
52 14 0.29
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (48 bp):
AAAATTAAAAAAATTAAAAAAAGTATTTTAAAAATTTAAAAAAAATAA
Found at i:12746877 original size:93 final size:93
Alignment explanation
Indices: 12746718--12746904 Score: 374
Period size: 93 Copynumber: 2.0 Consensus size: 93
12746708 TCGGCTTCCG
12746718 TCGCCTCTTTACTTGAATCGTTACACTCGTTGGTACATCTCATTGGCAAGAAGTCTTCACTCTAA
1 TCGCCTCTTTACTTGAATCGTTACACTCGTTGGTACATCTCATTGGCAAGAAGTCTTCACTCTAA
12746783 CTTGTCCTAATTTTGACTTGTTTCCTTT
66 CTTGTCCTAATTTTGACTTGTTTCCTTT
12746811 TCGCCTCTTTACTTGAATCGTTACACTCGTTGGTACATCTCATTGGCAAGAAGTCTTCACTCTAA
1 TCGCCTCTTTACTTGAATCGTTACACTCGTTGGTACATCTCATTGGCAAGAAGTCTTCACTCTAA
12746876 CTTGTCCTAATTTTGACTTGTTTCCTTT
66 CTTGTCCTAATTTTGACTTGTTTCCTTT
12746904 T
1 T
12746905 GAATCGCATT
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 94 1.00
ACGTcount: A:0.19, C:0.25, G:0.14, T:0.42
Consensus pattern (93 bp):
TCGCCTCTTTACTTGAATCGTTACACTCGTTGGTACATCTCATTGGCAAGAAGTCTTCACTCTAA
CTTGTCCTAATTTTGACTTGTTTCCTTT
Found at i:12749391 original size:21 final size:22
Alignment explanation
Indices: 12749356--12749401 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
12749346 TCAAGTATAT
*
12749356 ACTCATAATTGTTCATTTCA-A
1 ACTCATAATTGTTCATATCAGA
12749377 ACTCAT-ATTGTTTCATATCAGA
1 ACTCATAATTG-TTCATATCAGA
12749399 ACT
1 ACT
12749402 TTGCCCGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 4 0.18
21 14 0.64
22 4 0.18
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.41
Consensus pattern (22 bp):
ACTCATAATTGTTCATATCAGA
Found at i:12753808 original size:44 final size:44
Alignment explanation
Indices: 12753737--12753820 Score: 123
Period size: 44 Copynumber: 1.9 Consensus size: 44
12753727 ATTACATGAT
* * * *
12753737 TTTGTATAAGACCATAGCTGGGCTATGGCATTGATATATGAGAC
1 TTTGCATAAGACCATAGCTAGGATATGGCATCGATATATGAGAC
*
12753781 TTTGCATAAGACCATATCTAGGATATGGCATCGATATATG
1 TTTGCATAAGACCATAGCTAGGATATGGCATCGATATATG
12753821 TGATTACGTG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (44 bp):
TTTGCATAAGACCATAGCTAGGATATGGCATCGATATATGAGAC
Found at i:12753835 original size:44 final size:44
Alignment explanation
Indices: 12753787--12753998 Score: 197
Period size: 43 Copynumber: 5.0 Consensus size: 44
12753777 AGACTTTGCA
*
12753787 TAAGACCATATCTAGGATA-TGGCATCGATATATGTGATTACGTG
1 TAAGACCATATCTGGGATATTGGCATCG-TATATGTGATTACGTG
* * *
12753831 TAAGACCATGTCTGGGACATTGGCATCGT-TATGTGATTTCGTG
1 TAAGACCATATCTGGGATATTGGCATCGTATATGTGATTACGTG
* * * * * *
12753874 GAAGACCATGTCCGGGACATTGGCATCG-ATATATGATT-CATG
1 TAAGACCATATCTGGGATATTGGCATCGTATATGTGATTACGTG
* * * * * *
12753916 TAGGACCATAGCTGGGCTATTGGTATCG-ATATGTGATAACATG
1 TAAGACCATATCTGGGATATTGGCATCGTATATGTGATTACGTG
*
12753959 CAAGACCATATCTGGGATA-TGGCAT--TATATGTGATATACG
1 TAAGACCATATCTGGGATATTGGCATCGTATATGTGAT-TACG
12753999 AGACTTCCGA
Statistics
Matches: 138, Mismatches: 25, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
41 9 0.07
42 38 0.28
43 66 0.48
44 17 0.12
45 8 0.06
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (44 bp):
TAAGACCATATCTGGGATATTGGCATCGTATATGTGATTACGTG
Found at i:12753964 original size:85 final size:87
Alignment explanation
Indices: 12753806--12753967 Score: 197
Period size: 85 Copynumber: 1.9 Consensus size: 87
12753796 ATCTAGGATA
* * **
12753806 TGGCATCGATATATGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTTATGTGATTTC
1 TGGCATCGATATA-GTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGATATGTGATAAC
* *
12753871 GTGGAAGACCATGTCCGGGACAT
65 ATGCAAGACCATGTCCGGGACAT
* *
12753894 TGGCATCGATATA-TGATT-CATGTAGGACCATAG-CTGGG-CTATTGGTATCGATATGTGATAA
1 TGGCATCGATATAGTGATTACATGTAAGACCAT-GTCTGGGAC-ATTGGCATCGATATGTGATAA
12753955 CATGCAAGACCAT
64 CATGCAAGACCAT
12753968 ATCTGGGATA
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
84 1 0.02
85 44 0.69
86 6 0.09
88 13 0.20
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.30
Consensus pattern (87 bp):
TGGCATCGATATAGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGATATGTGATAACA
TGCAAGACCATGTCCGGGACAT
Done.