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 17 of 328
Found at i:5188914 original size:15 final size:15
Alignment explanation
Indices: 5188894--5188924 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5188884 TCAGATACAA
5188894 ATATATTTATATAAT
1 ATATATTTATATAAT
*
5188909 ATATATTTATGTAAT
1 ATATATTTATATAAT
5188924 A
1 A
5188925 ATTCGAGAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (15 bp):
ATATATTTATATAAT
Found at i:5189861 original size:27 final size:27
Alignment explanation
Indices: 5189826--5189879 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
5189816 ACGAATACAG
* **
5189826 GTTGTGCCTATCTTTGAGACGCGACTA
1 GTTGAGCCTATCTCAGAGACGCGACTA
* *
5189853 GTTGAGCCTTTCTCAGAGGCGCGACTA
1 GTTGAGCCTATCTCAGAGACGCGACTA
5189880 ATCTTGTCTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.19, C:0.24, G:0.28, T:0.30
Consensus pattern (27 bp):
GTTGAGCCTATCTCAGAGACGCGACTA
Found at i:5190263 original size:60 final size:62
Alignment explanation
Indices: 5190179--5190311 Score: 200
Period size: 60 Copynumber: 2.2 Consensus size: 62
5190169 ATACTAAACT
* * *
5190179 AAACAC-AACAATTTATAACTTAATCCTAAATTACTAATAAATTAATTTTAAAATAATTA-C
1 AAACACAAAAAATTTATAACATAATCCTAAATTACTAATAAATTAATTTTAAAATAATTATA
*
5190239 AAACACAAAAAATTT-TAACATAATCCTAATTTACTAATAAATTAATTTTAAAATAATTATA
1 AAACACAAAAAATTTATAACATAATCCTAAATTACTAATAAATTAATTTTAAAATAATTATA
*
5190300 AAAAACAAAAAA
1 AAACACAAAAAA
5190312 AAATTACATT
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
60 48 0.73
61 18 0.27
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.32
Consensus pattern (62 bp):
AAACACAAAAAATTTATAACATAATCCTAAATTACTAATAAATTAATTTTAAAATAATTATA
Found at i:5191865 original size:2 final size:2
Alignment explanation
Indices: 5191858--5191885 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5191848 CACGTCATAA
5191858 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5191886 GCACAGGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5193840 original size:4 final size:4
Alignment explanation
Indices: 5193831--5193855 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5193821 AAATAATTTT
5193831 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
5193856 TACACAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:5193912 original size:22 final size:23
Alignment explanation
Indices: 5193874--5193918 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
5193864 ATACAAGTAG
*
5193874 AATAATATGGAATCAA-TAATAA
1 AATAATATGGAAACAATTAATAA
5193896 AATATATAT-GAAACAATTAATAA
1 AATA-ATATGGAAACAATTAATAA
5193919 CGTTGTGCGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.29
Consensus pattern (23 bp):
AATAATATGGAAACAATTAATAA
Found at i:5194092 original size:3 final size:3
Alignment explanation
Indices: 5194084--5194189 Score: 53
Period size: 3 Copynumber: 36.7 Consensus size: 3
5194074 ACGAACTATT
* *
5194084 ATA ATA ATA A-A AT- ATA ATGA ATA ATA TTA GTA ATA A-A ATA ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * *
5194127 TTA ACTA TTA ACA GTA A-A GT- ATA ATA A-A ATA GTA ATA ATA AAA
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
5194170 ATA ATA ATA CTA AAA ATA AT
1 ATA ATA ATA ATA ATA ATA AT
5194190 TAATTTTATG
Statistics
Matches: 74, Mismatches: 21, Indels: 16
0.67 0.19 0.14
Matches are distributed among these distances:
2 10 0.14
3 59 0.80
4 5 0.07
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:5194172 original size:15 final size:15
Alignment explanation
Indices: 5194147--5194189 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
5194137 ACAGTAAAGT
*
5194147 ATAAT-AAAATAGTA
1 ATAATAAAAATAATA
5194161 ATAATAAAAATAATA
1 ATAATAAAAATAATA
*
5194176 ATACTAAAAATAAT
1 ATAATAAAAATAAT
5194190 TAATTTTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 5 0.19
15 21 0.81
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (15 bp):
ATAATAAAAATAATA
Found at i:5197752 original size:87 final size:85
Alignment explanation
Indices: 5197658--5197863 Score: 270
Period size: 88 Copynumber: 2.3 Consensus size: 85
5197648 AATTTTAGCC
* * * *
5197658 TGTTACCCTAGTGCTTAAGGGGTTAAGGCT-TGTATCTTTGATCTGCTCCACTATTGCTTAGGGA
1 TGTTACCCTATTGCTT-AGGGGTTAAGCCTATGT-T-TTCGATCTGCCCCACTATTGCTTAGGGA
5197722 GATAAGATCTGCAATCTTCAGCT
63 GATAAGATCTGCAATCTTCAGCT
*
5197745 TGTTACCCTATTGCTTAGAGAGTTAAAGCCTACTGTTTTCGATCTGCCCCACTATTGCTTAGGGA
1 TGTTACCCTATTGCTTAG-GGGTT-AAGCCTA-TGTTTTCGATCTGCCCCACTATTGCTTAGGGA
* *
5197810 GATAAGATCTGTAATTTTCAGCT
63 GATAAGATCTGCAATCTTCAGCT
5197833 TGTTACCCTATTGCTTAGGGAGTTAAAGCCT
1 TGTTACCCTATTGCTTAGGG-GTT-AAGCCT
5197864 GCTGAAATTT
Statistics
Matches: 106, Mismatches: 8, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
86 2 0.02
87 20 0.19
88 80 0.75
89 1 0.01
90 3 0.03
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (85 bp):
TGTTACCCTATTGCTTAGGGGTTAAGCCTATGTTTTCGATCTGCCCCACTATTGCTTAGGGAGAT
AAGATCTGCAATCTTCAGCT
Found at i:5197756 original size:44 final size:44
Alignment explanation
Indices: 5197708--5197854 Score: 147
Period size: 44 Copynumber: 3.3 Consensus size: 44
5197698 ATCTGCTCCA
*
5197708 CTATTGCTTAGGGAGATAAGATCTGCAATCTTCAGCTTGTTACC
1 CTATTGCTTAGGGAGATAAGATCTGCAATTTTCAGCTTGTTACC
* * * * ** * **
5197752 CTATTGCTTAGAGAGTTAA-AGCCTACTGTTTTC-GATCTG-CCCC
1 CTATTGCTTAGGGAGATAAGA-TCTGCAATTTTCAGCT-TGTTACC
*
5197795 ACTATTGCTTAGGGAGATAAGATCTGTAATTTTCAGCTTGTTACC
1 -CTATTGCTTAGGGAGATAAGATCTGCAATTTTCAGCTTGTTACC
5197840 CTATTGCTTAGGGAG
1 CTATTGCTTAGGGAG
5197855 TTAAAGCCTG
Statistics
Matches: 77, Mismatches: 20, Indels: 12
0.71 0.18 0.11
Matches are distributed among these distances:
43 5 0.06
44 67 0.87
45 5 0.06
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (44 bp):
CTATTGCTTAGGGAGATAAGATCTGCAATTTTCAGCTTGTTACC
Found at i:5197811 original size:88 final size:88
Alignment explanation
Indices: 5197697--5197863 Score: 298
Period size: 88 Copynumber: 1.9 Consensus size: 88
5197687 TTGTATCTTT
*
5197697 GATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGCAATCTTCAGCTTGTTACCCTATTGCTTA
1 GATCTGCCCCACTATTGCTTAGGGAGATAAGATCTGCAATCTTCAGCTTGTTACCCTATTGCTTA
5197762 GAGAGTTAAAGCCTACTGTTTTC
66 GAGAGTTAAAGCCTACTGTTTTC
* *
5197785 GATCTGCCCCACTATTGCTTAGGGAGATAAGATCTGTAATTTTCAGCTTGTTACCCTATTGCTTA
1 GATCTGCCCCACTATTGCTTAGGGAGATAAGATCTGCAATCTTCAGCTTGTTACCCTATTGCTTA
*
5197850 GGGAGTTAAAGCCT
66 GAGAGTTAAAGCCT
5197864 GCTGAAATTT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
88 75 1.00
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (88 bp):
GATCTGCCCCACTATTGCTTAGGGAGATAAGATCTGCAATCTTCAGCTTGTTACCCTATTGCTTA
GAGAGTTAAAGCCTACTGTTTTC
Found at i:5198479 original size:19 final size:18
Alignment explanation
Indices: 5198457--5198498 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
5198447 TAATTTTAAA
5198457 AAATTT-ATATAAATATATT
1 AAATTTAATA-AAATAT-TT
*
5198476 AAATATAATAAAATATTT
1 AAATTTAATAAAATATTT
5198494 AAATT
1 AAATT
5198499 AATTAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 6 0.30
19 11 0.55
20 3 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATTTAATAAAATATTT
Found at i:5198491 original size:17 final size:18
Alignment explanation
Indices: 5198465--5198516 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
5198455 AAAAATTTAT
5198465 ATAAATATA-TTAAATATA
1 ATAAATATATTTAAAT-TA
5198483 ATAAA-ATATTTAAATTA
1 ATAAATATATTTAAATTA
*
5198500 ATTAATGATATTATAAA
1 ATAAAT-ATATT-TAAA
5198517 AATTGATGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 9 0.31
18 11 0.38
19 5 0.17
20 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
ATAAATATATTTAAATTA
Found at i:5198734 original size:31 final size:31
Alignment explanation
Indices: 5198699--5198762 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
5198689 TATAATTAAT
*
5198699 TATATCAACAATTTTATTTA-AAATCAATCAC
1 TATATCAACAATTTTA-ATAGAAATCAATCAC
* *
5198730 TATATCAATAATTTTAATAGGAATCAATCAC
1 TATATCAACAATTTTAATAGAAATCAATCAC
5198761 TA
1 TA
5198763 AAAATTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 2 0.07
31 27 0.93
ACGTcount: A:0.45, C:0.14, G:0.03, T:0.38
Consensus pattern (31 bp):
TATATCAACAATTTTAATAGAAATCAATCAC
Found at i:5198855 original size:29 final size:31
Alignment explanation
Indices: 5198819--5198888 Score: 90
Period size: 29 Copynumber: 2.3 Consensus size: 31
5198809 TATACTTATC
* **
5198819 GATTTGTTCAAATTTAATTTCTCTAC-TTTT
1 GATTTGTTCAAAATTAACCTCTCTACTTTTT
*
5198849 -ATTTGTTCAAAATTAACCTCTTTACTTTTT
1 GATTTGTTCAAAATTAACCTCTCTACTTTTT
5198879 GATTTGTTCA
1 GATTTGTTCA
5198889 TTTTCAGTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 21 0.62
30 4 0.12
31 9 0.26
ACGTcount: A:0.24, C:0.14, G:0.07, T:0.54
Consensus pattern (31 bp):
GATTTGTTCAAAATTAACCTCTCTACTTTTT
Found at i:5199628 original size:22 final size:22
Alignment explanation
Indices: 5199603--5199646 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5199593 TAGTCTTATA
5199603 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAATATAATAAAT
* * *
5199625 ATAATTTATTATTTTAATAAAT
1 ATAAATTATTAATATAATAAAT
5199647 TATTTAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Found at i:5199691 original size:15 final size:16
Alignment explanation
Indices: 5199670--5199705 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
5199660 AATTTTATTT
5199670 TAATAATAAATTTAAA
1 TAATAATAAATTTAAA
*
5199686 -AATAATAATTTTAAA
1 TAATAATAAATTTAAA
5199701 TAATA
1 TAATA
5199706 TTATTCACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAATAATAAATTTAAA
Found at i:5199748 original size:14 final size:15
Alignment explanation
Indices: 5199724--5199793 Score: 56
Period size: 15 Copynumber: 4.6 Consensus size: 15
5199714 ATATTATTGA
5199724 AAATA-TTTAAT-AT
1 AAATATTTTAATAAT
*
5199737 TAATATTTTAATAAT
1 AAATATTTTAATAAT
*
5199752 AAATATTTATTATAATTAT
1 AAATA--T-TT-TAATAAT
*
5199771 AAATATATTAATAAT
1 AAATATTTTAATAAT
5199786 AAAT-TTTT
1 AAATATTTT
5199794 TGTAGTATAA
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
13 4 0.09
14 9 0.20
15 16 0.36
16 1 0.02
17 2 0.04
18 2 0.04
19 11 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AAATATTTTAATAAT
Found at i:5199767 original size:19 final size:19
Alignment explanation
Indices: 5199740--5199776 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5199730 TTAATATTAA
*
5199740 TATTTTAATAATAAATATT
1 TATTATAATAATAAATATT
*
5199759 TATTATAATTATAAATAT
1 TATTATAATAATAAATAT
5199777 ATTAATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTATAATAATAAATATT
Found at i:5205440 original size:23 final size:21
Alignment explanation
Indices: 5205410--5205457 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
5205400 TTATAAAATT
5205410 AAATT-AAATTATGAAAACTATA
1 AAATTAAAATTAT-AAAACTA-A
5205432 AAATATAAAATTATAAAACTAA
1 AAAT-TAAAATTATAAAACTAA
5205454 AAAT
1 AAAT
5205458 GATTTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 9 0.38
23 8 0.33
24 7 0.29
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (21 bp):
AAATTAAAATTATAAAACTAA
Found at i:5213829 original size:17 final size:18
Alignment explanation
Indices: 5213807--5213840 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5213797 TATAGTATAG
5213807 ATAATT-AAATATGATAT
1 ATAATTAAAATATGATAT
5213824 ATAATTAAAATATGATA
1 ATAATTAAAATATGATA
5213841 CAAAGAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (18 bp):
ATAATTAAAATATGATAT
Found at i:5228597 original size:18 final size:17
Alignment explanation
Indices: 5228562--5228594 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5228552 CTTTTTATTC
5228562 TTTTATTATTTCATTTA
1 TTTTATTATTTCATTTA
5228579 TTTTACTTATTT-ATTT
1 TTTTA-TTATTTCATTT
5228595 TATCATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATTATTTCATTTA
Found at i:5232206 original size:21 final size:21
Alignment explanation
Indices: 5232180--5232241 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
5232170 TTCCTATGCT
5232180 CTGCCTCCCTCGTTGCTGCCG
1 CTGCCTCCCTCGTTGCTGCCG
*
5232201 CTGCCTCCCTCGCTGCTGCCG
1 CTGCCTCCCTCGTTGCTGCCG
5232222 CTGCCTCCCTC-TCTGCTGCC
1 CTGCCTCCCTCGT-TGCTGCC
5232242 TCCGCTCTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.00, C:0.52, G:0.21, T:0.27
Consensus pattern (21 bp):
CTGCCTCCCTCGTTGCTGCCG
Found at i:5232678 original size:13 final size:14
Alignment explanation
Indices: 5232653--5232681 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5232643 TGATGAATTG
5232653 AATTAAACAATTAT
1 AATTAAACAATTAT
5232667 AATTAAAC-ATTAT
1 AATTAAACAATTAT
5232680 AA
1 AA
5232682 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:5237906 original size:9 final size:9
Alignment explanation
Indices: 5237892--5238081 Score: 107
Period size: 9 Copynumber: 20.6 Consensus size: 9
5237882 TATTTAAGTA
5237892 TTATGTAAG
1 TTATGTAAG
5237901 TTATGTAAG
1 TTATGTAAG
*
5237910 TTATGATATG
1 TTATG-TAAG
* * *
5237920 ATATAT-AT
1 TTATGTAAG
*
5237928 TTATGTAAA
1 TTATGTAAG
* *
5237937 TTATAT-AT
1 TTATGTAAG
*
5237945 TTATCTAAG
1 TTATGTAAG
*
5237954 TTATATAAG
1 TTATGTAAG
5237963 TTATGTAAG
1 TTATGTAAG
*
5237972 TTATGTAAA
1 TTATGTAAG
*
5237981 TTATGATATAAAA
1 TTATG---T-AAG
*
5237994 TATATTTAAG
1 T-TATGTAAG
5238004 TATTATGTAAG
1 --TTATGTAAG
5238015 TTATGTAAG
1 TTATGTAAG
* *
5238024 TTATAT-AT
1 TTATGTAAG
*
5238032 TTATCTAAG
1 TTATGTAAG
*
5238041 TTATATAAG
1 TTATGTAAG
*
5238050 TTATGTACG
1 TTATGTAAG
*
5238059 TTTTGTAAG
1 TTATGTAAG
* *
5238068 TTATATAAA
1 TTATGTAAG
5238077 TTATG
1 TTATG
5238082 ATATCAAATA
Statistics
Matches: 139, Mismatches: 31, Indels: 22
0.72 0.16 0.11
Matches are distributed among these distances:
8 16 0.12
9 98 0.71
10 8 0.06
11 8 0.06
12 2 0.01
13 4 0.03
14 3 0.02
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:5237974 original size:71 final size:69
Alignment explanation
Indices: 5237892--5238054 Score: 202
Period size: 71 Copynumber: 2.3 Consensus size: 69
5237882 TATTTAAGTA
* * * *
5237892 TTATGTAAGTTATGTAAGTTATGATATGATATATATTTATGTAAATTATAT-ATTTATCTAAGTT
1 TTATGTAAGTTATGTAAGTTATGATATAAAATATATTTAAGT--ATTATATAAGTTATCTAAGTT
5237956 ATATAAG
64 ATAT-AG
* * *
5237963 TTATGTAAGTTATGTAAATTATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTAT
1 TTATGTAAGTTATGTAAGTTATGATATAAAATATATTTAAGTATTATATAAGTTATCTAAGTTAT
*
5238028 ATAT
66 ATAG
* *
5238032 TTATCTAAGTTATATAAGTTATG
1 TTATGTAAGTTATGTAAGTTATG
5238055 TACGTTTTGT
Statistics
Matches: 80, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
69 27 0.34
70 15 0.19
71 38 0.47
ACGTcount: A:0.39, C:0.01, G:0.13, T:0.47
Consensus pattern (69 bp):
TTATGTAAGTTATGTAAGTTATGATATAAAATATATTTAAGTATTATATAAGTTATCTAAGTTAT
ATAG
Found at i:5238068 original size:114 final size:114
Alignment explanation
Indices: 5237868--5238081 Score: 290
Period size: 114 Copynumber: 1.9 Consensus size: 114
5237858 ACTAGTTATG
* * * *
5237868 TATGATATGATATATATTTAAGTATTATGTAAGTTATGTAAGTTATGATATGATATATATTTATG
1 TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATGATATGATATATAGTTATA
*
5237933 TAAATTATATATTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAAT
66 TAAATTATATATTTATCTAAGTTATATAAATTATGTAAGTTATGTAAAT
* *
5237982 TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTAT-ATAT-TTATCTAAGTTAT
1 TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATGATATGATATAT-AGTTAT
* * *
5238045 ATAAGTTATGTACGTTT-TGTAAGTTATATAAATTATG
65 ATAAATTATATA--TTTATCTAAGTTATATAAATTATG
5238082 ATATCAAATA
Statistics
Matches: 87, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
112 4 0.05
113 18 0.21
114 62 0.71
115 3 0.03
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.47
Consensus pattern (114 bp):
TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATGATATGATATATAGTTATA
TAAATTATATATTTATCTAAGTTATATAAATTATGTAAGTTATGTAAAT
Found at i:5238120 original size:87 final size:87
Alignment explanation
Indices: 5237928--5238112 Score: 234
Period size: 87 Copynumber: 2.1 Consensus size: 87
5237918 TGATATATAT
*
5237928 TTATGTAAATTATATATTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAATTATGATATAAA
1 TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAATTATGATATAAA
** *
5237993 ATATATTTAAGTATTATGTAAG
66 ATATATCAAAATATTATGTAAG
* * *
5238015 TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATGTACGTTTTGTAAGTTAT-ATA-AAT
1 TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAATTATGATATAA-
*
5238078 TATGATATCAAATATAGTTATGT-A-
65 AAT-ATATCAAA-ATA-TTATGTAAG
5238102 TTATGTAAGTT
1 TTATGTAAGTT
5238113 TTTTATTTCA
Statistics
Matches: 86, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
85 2 0.02
86 5 0.06
87 70 0.81
88 3 0.03
89 6 0.07
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.47
Consensus pattern (87 bp):
TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAATTATGATATAAA
ATATATCAAAATATTATGTAAG
Found at i:5238206 original size:15 final size:15
Alignment explanation
Indices: 5238186--5238241 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
5238176 AAGTAGAGGG
5238186 ATTAAATAATATTTA
1 ATTAAATAATATTTA
5238201 ATTAAATAATATTT-
1 ATTAAATAATATTTA
5238215 A-TAAA-AATTATTTTA
1 ATTAAATAA-TA-TTTA
*
5238230 ATTAAGTAATAT
1 ATTAAATAATAT
5238242 ACATGTCGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
12 2 0.06
13 6 0.17
14 4 0.11
15 16 0.46
16 5 0.14
17 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (15 bp):
ATTAAATAATATTTA
Found at i:5239219 original size:15 final size:15
Alignment explanation
Indices: 5239199--5239227 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5239189 AGAATTTTGA
5239199 AATAAAACGTACCTT
1 AATAAAACGTACCTT
5239214 AATAAAACGTACCT
1 AATAAAACGTACCT
5239228 GGTCTACTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.21, G:0.07, T:0.24
Consensus pattern (15 bp):
AATAAAACGTACCTT
Found at i:5239703 original size:14 final size:13
Alignment explanation
Indices: 5239684--5239713 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
5239674 CAATATAATT
5239684 TTACTTCATATATA
1 TTACTTCATATA-A
5239698 TTACTTCATATAA
1 TTACTTCATATAA
5239711 TTA
1 TTA
5239714 TTATAGTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (13 bp):
TTACTTCATATAA
Found at i:5241442 original size:15 final size:16
Alignment explanation
Indices: 5241422--5241451 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5241412 AAAGGTTATA
5241422 CACTG-AAAACTCATG
1 CACTGAAAAACTCATG
5241437 CACTGAAAAACTCAT
1 CACTGAAAAACTCAT
5241452 TCATAACTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.27, G:0.10, T:0.20
Consensus pattern (16 bp):
CACTGAAAAACTCATG
Found at i:5243453 original size:15 final size:17
Alignment explanation
Indices: 5243433--5243467 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
5243423 ATTATTTAAT
5243433 ATATAAA-T-AAAAACA
1 ATATAAATTAAAAAACA
5243448 ATATAAATTAAAAAACA
1 ATATAAATTAAAAAACA
5243465 ATA
1 ATA
5243468 AGTTATATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 1 0.06
17 10 0.56
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (17 bp):
ATATAAATTAAAAAACA
Found at i:5243624 original size:16 final size:16
Alignment explanation
Indices: 5243580--5243628 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
5243570 TACATAAAAT
*
5243580 TTAAAATCTTGAAAATTA
1 TTAAAAT-TTG-AAATCA
*
5243598 TTGACAATTTGAAATCA
1 TT-AAAATTTGAAATCA
5243615 TTAAAATTTGAAAT
1 TTAAAATTTGAAAT
5243629 TATTTAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 11 0.41
17 7 0.26
18 5 0.19
19 4 0.15
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.39
Consensus pattern (16 bp):
TTAAAATTTGAAATCA
Found at i:5243885 original size:73 final size:72
Alignment explanation
Indices: 5243786--5243922 Score: 175
Period size: 73 Copynumber: 1.9 Consensus size: 72
5243776 TTAAACCCCT
* * * *
5243786 AAACCCTAAACCATTAACCCTTAATCCCTAAAATTTAAACACTAAACCTTAAACAATGTCCCCTT
1 AAACCCTAAACCATAAACCCTTAATCCATAAAATTTAAACACTAAACCCTAAACAATATCCCCTT
5243851 AACTCCC
66 AACTCCC
* * * * * *
5243858 AAACCCATAAACCCTAAACCTTTAATCCATAGACTTTGAACACTAAACCCTAAACTATATCCCCT
1 AAACCC-TAAACCATAAACCCTTAATCCATAAAATTTAAACACTAAACCCTAAACAATATCCCCT
5243923 CAACCCCTTA
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
72 6 0.11
73 48 0.89
ACGTcount: A:0.40, C:0.33, G:0.02, T:0.25
Consensus pattern (72 bp):
AAACCCTAAACCATAAACCCTTAATCCATAAAATTTAAACACTAAACCCTAAACAATATCCCCTT
AACTCCC
Found at i:5244181 original size:18 final size:18
Alignment explanation
Indices: 5244154--5244219 Score: 73
Period size: 18 Copynumber: 3.8 Consensus size: 18
5244144 ATTAACTTGT
* *
5244154 CATAATCCATAAATCATG
1 CATAAACCATAAACCATG
5244172 CATAAACCATAAACCAT-
1 CATAAACCATAAACCATG
* *
5244189 -ATATACCCTAAACCATG
1 CATAAACCATAAACCATG
*
5244206 CATAAACCTTAAAC
1 CATAAACCATAAAC
5244220 TATAATAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
16 14 0.35
18 26 0.65
ACGTcount: A:0.47, C:0.27, G:0.03, T:0.23
Consensus pattern (18 bp):
CATAAACCATAAACCATG
Found at i:5244960 original size:41 final size:40
Alignment explanation
Indices: 5244895--5244993 Score: 103
Period size: 41 Copynumber: 2.5 Consensus size: 40
5244885 AATAGTTTAG
* *
5244895 ATCTTTAGCGGCGTTTTTCCAAAAGCGCCGCTGAA-ACTCA
1 ATCTATAGCGGCGTTTTTCAAAAAGCGCCGCT-AATACTCA
* * *
5244935 TATCTATTGCGGCG-TTTTCTAAAAAGTGCTGCTAATACTCA
1 -ATCTATAGCGGCGTTTTTC-AAAAAGCGCCGCTAATACTCA
*
5244976 ATCTATAGAGGCGTTTTT
1 ATCTATAGCGGCGTTTTT
5244994 GCGCAAGCGC
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
40 18 0.38
41 30 0.62
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.34
Consensus pattern (40 bp):
ATCTATAGCGGCGTTTTTCAAAAAGCGCCGCTAATACTCA
Found at i:5245135 original size:41 final size:40
Alignment explanation
Indices: 5245055--5245164 Score: 116
Period size: 41 Copynumber: 2.7 Consensus size: 40
5245045 TTTAATTTTT
* **
5245055 TAGCGGCGTTTCTATAAAAACGCCGCTATAGGCCGACCTA
1 TAGCGGCGTTTCTATAAAAACGCCGCTATACGCAAACCTA
* *
5245095 TAGCGGCGCTTTCTA-AAAAATGCCGCTAATACTCAAACCTA
1 TAGCGGCG-TTTCTATAAAAACGCCGCT-ATACGCAAACCTA
* *
5245136 TAGCGGCGTTTTTGAT-AAAGCGCCGCTAT
1 TAGCGGCGTTTCT-ATAAAAACGCCGCTAT
5245165 TGCCACTGAA
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
40 25 0.43
41 33 0.57
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.25
Consensus pattern (40 bp):
TAGCGGCGTTTCTATAAAAACGCCGCTATACGCAAACCTA
Found at i:5245246 original size:154 final size:155
Alignment explanation
Indices: 5244938--5245284 Score: 464
Period size: 154 Copynumber: 2.3 Consensus size: 155
5244928 AAACTCATAT
* * * * * * *
5244938 CTATTGCGGCGTTTTCTAAAAAGTGCTGCTAATACTC-AATCTATAGAGGCGTTTTTGCGCAAGC
1 CTATAGCGGCGCTTTCTAAAAAATGCCGCTAATACTCAAACCTATAGAGGCGTTTTTGAGAAAGC
* * ** *
5245002 GCCGCTATTGCCAGTGAAGCTCAAAATAAACGATGCCGTTCGATTTAATTTTTTAGCGGCGTTTC
66 GCCGCTATTGCCACTGAAGCTCAAAATAAACGACGCCGTTCGACCTAATCTTTTAGCGGCGTTTC
5245067 TATAAAAACGCCGCTATAGGCCGAC
131 TATAAAAACGCCGCTATAGGCCGAC
* *
5245092 CTATAGCGGCGCTTTCTAAAAAATGCCGCTAATACTCAAACCTATAGCGGCGTTTTTGATAAAGC
1 CTATAGCGGCGCTTTCTAAAAAATGCCGCTAATACTCAAACCTATAGAGGCGTTTTTGAGAAAGC
* * *
5245157 GCCGCTATTGCCACTGAAGCTCACAATAAACGACGCCGTTCG-CCTAATCTTTTAGTGGCGTTTT
66 GCCGCTATTGCCACTGAAGCTCAAAATAAACGACGCCGTTCGACCTAATCTTTTAGCGGCGTTTC
* *
5245221 TATAAAAACGCCGCTATATGTCGAC
131 TATAAAAACGCCGCTATAGGCCGAC
* * * * *
5245246 CTATAACGGCACTTCCTTAAAAACGCCGCTAATACTCAA
1 CTATAGCGGCGCTTTCTAAAAAATGCCGCTAATACTCAA
5245285 TTTATTCAAT
Statistics
Matches: 168, Mismatches: 24, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
154 107 0.64
155 61 0.36
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (155 bp):
CTATAGCGGCGCTTTCTAAAAAATGCCGCTAATACTCAAACCTATAGAGGCGTTTTTGAGAAAGC
GCCGCTATTGCCACTGAAGCTCAAAATAAACGACGCCGTTCGACCTAATCTTTTAGCGGCGTTTC
TATAAAAACGCCGCTATAGGCCGAC
Found at i:5252238 original size:21 final size:21
Alignment explanation
Indices: 5252214--5252278 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 21
5252204 ATAGAACAGA
5252214 ATCATGATGGATACATCTAAC
1 ATCATGATGGATACATCTAAC
* *
5252235 ATCA--ATGAGATAGAAC-AGA-
1 ATCATGATG-GATACATCTA-AC
5252254 ATCATGATGGATACATCTAAC
1 ATCATGATGGATACATCTAAC
5252275 ATCA
1 ATCA
5252279 ATAAAGGTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
19 8 0.24
20 14 0.41
21 12 0.35
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.25
Consensus pattern (21 bp):
ATCATGATGGATACATCTAAC
Found at i:5252245 original size:40 final size:40
Alignment explanation
Indices: 5252201--5252280 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
5252191 AAAATGGAGC
5252201 GAGATAGAACAGAATCATGATGGATACATCTAACATCAAT
1 GAGATAGAACAGAATCATGATGGATACATCTAACATCAAT
5252241 GAGATAGAACAGAATCATGATGGATACATCTAACATCAAT
1 GAGATAGAACAGAATCATGATGGATACATCTAACATCAAT
5252281 AAAGGTGATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.45, C:0.15, G:0.17, T:0.23
Consensus pattern (40 bp):
GAGATAGAACAGAATCATGATGGATACATCTAACATCAAT
Found at i:5253107 original size:20 final size:19
Alignment explanation
Indices: 5253082--5253135 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
5253072 AAAAATATAA
5253082 ATTTTATAATTTTTATAAAT
1 ATTTTATAATTTTT-TAAAT
* *
5253102 ATTTTAAAATTATTTTAATT
1 ATTTTATAATT-TTTTAAAT
* *
5253122 TTTTTATGATTTTT
1 ATTTTATAATTTTT
5253136 GTTAAGAAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 3 0.11
20 22 0.79
21 3 0.11
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
ATTTTATAATTTTTTAAAT
Found at i:5253118 original size:60 final size:59
Alignment explanation
Indices: 5253002--5253119 Score: 166
Period size: 60 Copynumber: 2.0 Consensus size: 59
5252992 TATCAAAATT
* * * * *
5253002 ATTATTTTTAAAAAAATTAAAATTTTAATTTTTTATATATATTTTTATATTTTTTTAAA
1 ATTATTTTTAAAAAAATTAAAATTTTAAATTTTTATAAATATTTTAAAATTATTTTAAA
5253061 ATTATTTTTAAAAAAA-TATAAATTTTATAATTTTTATAAATATTTTAAAATTATTTTAA
1 ATTATTTTTAAAAAAATTA-AAATTTTA-AATTTTTATAAATATTTTAAAATTATTTTAA
5253120 TTTTTTTATG
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
58 2 0.04
59 24 0.46
60 26 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (59 bp):
ATTATTTTTAAAAAAATTAAAATTTTAAATTTTTATAAATATTTTAAAATTATTTTAAA
Found at i:5262774 original size:6 final size:6
Alignment explanation
Indices: 5262763--5262792 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
5262753 TTCCAGAACT
5262763 GAAACA GAAACA GAAACA GAAACA GAAACA
1 GAAACA GAAACA GAAACA GAAACA GAAACA
5262793 TAGAAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.67, C:0.17, G:0.17, T:0.00
Consensus pattern (6 bp):
GAAACA
Found at i:5265749 original size:19 final size:19
Alignment explanation
Indices: 5265725--5265763 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
5265715 ACTAAACAAT
5265725 TCATGATTCCATGCTTCAA
1 TCATGATTCCATGCTTCAA
5265744 TCATGATTCCATGCTTCAA
1 TCATGATTCCATGCTTCAA
5265763 T
1 T
5265764 TCACCATGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.26, G:0.10, T:0.38
Consensus pattern (19 bp):
TCATGATTCCATGCTTCAA
Found at i:5267105 original size:2 final size:2
Alignment explanation
Indices: 5267098--5267131 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5267088 ATTCAAATTA
5267098 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5267132 GTGTGTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5270605 original size:22 final size:23
Alignment explanation
Indices: 5270580--5270625 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
5270570 CAACCAAATC
5270580 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
5270602 AATTCATACATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
5270625 A
1 A
5270626 CGTCATCACA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.27
23 15 0.68
24 1 0.05
ACGTcount: A:0.48, C:0.11, G:0.04, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:5270631 original size:23 final size:24
Alignment explanation
Indices: 5270586--5270638 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
5270576 AATCAATTCA
*
5270586 ACATATTTTCAAGATAAATTCAT-
1 ACATATTTTCAAGATAAAGTCATC
*
5270609 ACATATTTAT-AAGATAACGTCATC
1 ACATATTT-TCAAGATAAAGTCATC
5270633 ACATAT
1 ACATAT
5270639 CTAAAACCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 19 0.73
24 7 0.27
ACGTcount: A:0.43, C:0.15, G:0.06, T:0.36
Consensus pattern (24 bp):
ACATATTTTCAAGATAAAGTCATC
Found at i:5275490 original size:2 final size:2
Alignment explanation
Indices: 5275450--5275478 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5275440 TTTTTATACT
5275450 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
5275479 TGGTACATAT
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:5276639 original size:127 final size:130
Alignment explanation
Indices: 5276377--5276613 Score: 299
Period size: 130 Copynumber: 1.8 Consensus size: 130
5276367 GCTGGATTGC
* * * *
5276377 AATAATTGAATATTCCTTTGGAATTTCACTCATGTCTTCAAAAATTCTTTAAAACGAAGGTAATG
1 AATAATCGAATATCCCTTTAGAATTTCACTCATGTCTTCAAAAATTCTTTAAAACGAAGGCAATG
* * **
5276442 TTCGATGTTTGAAAATTCGAGAATCGTGCCCTATCGTGCTGGGTTGCAATTTCCCGTTTGTTCAA
66 TTCGATGTTAGAAAATTCGAGAATCGTGCCCTATCGTGCTAGGTTGCAATTTCCCGTTTGGACAA
* *
5276507 AATAATCGAATATCCCTTTAGAATTTCACTCATGT-TCTC-TAAA-T-TTTAAAA-TAAGGCAAT
1 AATAATCGAATATCCCTTTAGAATTTCACTCATGTCT-TCAAAAATTCTTTAAAACGAAGGCAAT
5276567 GTTCGATGTCTAG-AAATTCGAGGAATCGTGCCCTA-CTGTGCTAGGTT
65 GTTCGATGT-TAGAAAATTCGA-GAATCGTGCCCTATC-GTGCTAGGTT
5276614 TCGGTTTTTT
Statistics
Matches: 95, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
126 25 0.26
127 31 0.33
128 1 0.01
129 4 0.04
130 34 0.36
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (130 bp):
AATAATCGAATATCCCTTTAGAATTTCACTCATGTCTTCAAAAATTCTTTAAAACGAAGGCAATG
TTCGATGTTAGAAAATTCGAGAATCGTGCCCTATCGTGCTAGGTTGCAATTTCCCGTTTGGACAA
Found at i:5277593 original size:43 final size:43
Alignment explanation
Indices: 5277546--5277704 Score: 173
Period size: 43 Copynumber: 3.7 Consensus size: 43
5277536 AGCTCGTACA
*
5277546 ATGCCAACGTCCCATACGTGGTCTTACATGTAATCAAATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATATCG
* ***
5277589 ATGCC-ACTGTCCCAAACAG-GGTCTTACACAAAATCAAATA-CG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACATGTAATCAAATATCG
* * *
5277631 ATGCCAACGTCCTAGACGTGGTCTCACATGTAAATCATAA-GTCG
1 ATGCCAACGTCCCAGACGTGGTCTTACATGT-AATCA-AATATCG
*
5277675 ATGTCAACGTCCCAGACGTGGTCTTACATG
1 ATGCCAACGTCCCAGACGTGGTCTTACATG
5277705 AAAAAACATA
Statistics
Matches: 95, Mismatches: 14, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
41 1 0.01
42 24 0.25
43 38 0.40
44 32 0.34
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATATCG
Found at i:5279033 original size:44 final size:45
Alignment explanation
Indices: 5278943--5279071 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
5278933 GACAGAACGA
*
5278943 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
5278989 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
5279033 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
5279072 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:5283920 original size:92 final size:92
Alignment explanation
Indices: 5283759--5283932 Score: 267
Period size: 92 Copynumber: 1.9 Consensus size: 92
5283749 AATATTAACT
* *
5283759 AAAGATGACATTTTGTACATTGAAATAGCTACAAAGTAATCATTAACCATACCATGATTAACCCA
1 AAAGATGACATTTTGTACATTAAAATAGCTACAAAGTAATCATTAACCATACCATAATTAACCCA
* *
5283824 AACAATAAAGATTTCACCTTTGCATAA
66 AACAACAAAGACTTCACCTTTGCATAA
* * * * *
5283851 AAAGATGTCATTTTGTACATTAAAATAGCTATAAAGTAATCATTAGCCATACTATAATTAACCCT
1 AAAGATGACATTTTGTACATTAAAATAGCTACAAAGTAATCATTAACCATACCATAATTAACCCA
5283916 AACAACAAAGACTTCAC
66 AACAACAAAGACTTCAC
5283933 ATTCACCTAA
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
92 73 1.00
ACGTcount: A:0.44, C:0.18, G:0.09, T:0.29
Consensus pattern (92 bp):
AAAGATGACATTTTGTACATTAAAATAGCTACAAAGTAATCATTAACCATACCATAATTAACCCA
AACAACAAAGACTTCACCTTTGCATAA
Found at i:5295477 original size:16 final size:16
Alignment explanation
Indices: 5295453--5295483 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5295443 GCTCCTCCCC
*
5295453 CTCTCTCTCTATCTCG
1 CTCTATCTCTATCTCG
5295469 CTCTATCTCTATCTC
1 CTCTATCTCTATCTC
5295484 TGTTGAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.42, G:0.03, T:0.45
Consensus pattern (16 bp):
CTCTATCTCTATCTCG
Found at i:5308391 original size:30 final size:30
Alignment explanation
Indices: 5308355--5308413 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
5308345 GACTTAAATC
5308355 AAATTTTTAAAATGGACTGTGAAAGCAAGG
1 AAATTTTTAAAATGGACTGTGAAAGCAAGG
5308385 AAATTTTTAAAATGGACTGTGAAAGCAAG
1 AAATTTTTAAAATGGACTGTGAAAGCAAG
5308414 TGATTTAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.27
Consensus pattern (30 bp):
AAATTTTTAAAATGGACTGTGAAAGCAAGG
Found at i:5314852 original size:6 final size:6
Alignment explanation
Indices: 5314830--5314863 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
5314820 GATTAATACT
* *
5314830 AAATCA AATTTA AAATCA AAATCA AAATCA AAAT
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAAT
5314864 TGATTTTACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.65, C:0.12, G:0.00, T:0.24
Consensus pattern (6 bp):
AAATCA
Found at i:5317233 original size:103 final size:103
Alignment explanation
Indices: 5317054--5317366 Score: 599
Period size: 103 Copynumber: 3.0 Consensus size: 103
5317044 GAGGCATATC
* *
5317054 TTTGACATAGCTATGTATTTTTCTAAGTTAACCTAGTATACGTAACCTGCCTCTGTGTTTGATTG
1 TTTGAAATAGCTATGTATTTTTCTAATTTAACCTAGTATACGTAACCTGCCTCTGTGTTTGATTG
5317119 TCTCTGACTCCAATATGTTGCGTATAAACCCGTTTGAG
66 TCTCTGACTCCAATATGTTGCGTATAAACCCGTTTGAG
5317157 TTTGAAATAGCTATGTATTTTTCTAATTTAACCTAGTATACGTAACCTGCCTCTGTGTTTGATTG
1 TTTGAAATAGCTATGTATTTTTCTAATTTAACCTAGTATACGTAACCTGCCTCTGTGTTTGATTG
5317222 TCTCTGACTCCAATATGTTGCGTATAAACCCGTTTGAG
66 TCTCTGACTCCAATATGTTGCGTATAAACCCGTTTGAG
5317260 TTTGAAATAGCTATGTATTTTTCTAATTTAACCTAGTATACGTAACCTGCCTCTGTGTTTGATTG
1 TTTGAAATAGCTATGTATTTTTCTAATTTAACCTAGTATACGTAACCTGCCTCTGTGTTTGATTG
*
5317325 TCTCTGACTCCAATATGTTGCGTATAAACTCGTTTGAG
66 TCTCTGACTCCAATATGTTGCGTATAAACCCGTTTGAG
5317363 TTTG
1 TTTG
5317367 TTTATCACTT
Statistics
Matches: 207, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 207 1.00
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.41
Consensus pattern (103 bp):
TTTGAAATAGCTATGTATTTTTCTAATTTAACCTAGTATACGTAACCTGCCTCTGTGTTTGATTG
TCTCTGACTCCAATATGTTGCGTATAAACCCGTTTGAG
Found at i:5318541 original size:22 final size:22
Alignment explanation
Indices: 5318516--5318559 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
5318506 ATTTTTTAAA
*
5318516 ATTTTTTAGAATAATAAATTAT
1 ATTTATTAGAATAATAAATTAT
* * *
5318538 ATTTATTATATTAATAATTTAT
1 ATTTATTAGAATAATAAATTAT
5318560 TATATGACTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
ATTTATTAGAATAATAAATTAT
Found at i:5323478 original size:22 final size:22
Alignment explanation
Indices: 5323423--5323488 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
5323413 TTGATCAAGG
* *
5323423 AAGTCTTGAGACAATCTAACTT
1 AAGTCTCGAGACAATGTAACTT
*
5323445 AAGTCTCAAGACAATGTAACTT
1 AAGTCTCGAGACAATGTAACTT
** * *
5323467 TTGTTTCGAGACAATGTCACTT
1 AAGTCTCGAGACAATGTAACTT
5323489 CAAAGCTAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (22 bp):
AAGTCTCGAGACAATGTAACTT
Found at i:5325437 original size:22 final size:21
Alignment explanation
Indices: 5325384--5325439 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
5325374 TGAAGTTACG
* *
5325384 AAAATAAAATGTATGATACAT
1 AAAAGAAAATGTTTGATACAT
*
5325405 AAAAGAGAATGTTTGTATACAT
1 AAAAGAAAATGTTTG-ATACAT
* *
5325427 ATATGAAAATGTT
1 AAAAGAAAATGTT
5325440 AAAAAACTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 12 0.43
22 16 0.57
ACGTcount: A:0.50, C:0.04, G:0.14, T:0.32
Consensus pattern (21 bp):
AAAAGAAAATGTTTGATACAT
Found at i:5327397 original size:35 final size:35
Alignment explanation
Indices: 5327353--5327519 Score: 192
Period size: 35 Copynumber: 4.6 Consensus size: 35
5327343 TCCTCATTGA
** *
5327353 AATACCATACCTACATTTTTCAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* **
5327388 AATGCCATACCTACATTTCTTAACTCAGTATGGGTTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT--G---GAT
* *
5327428 AATACCATCCCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
5327463 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
5327498 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
5327520 CTTTGTCATG
Statistics
Matches: 115, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
35 84 0.73
36 2 0.02
38 1 0.01
39 2 0.02
40 26 0.23
ACGTcount: A:0.32, C:0.25, G:0.11, T:0.31
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:5327441 original size:75 final size:74
Alignment explanation
Indices: 5327349--5327519 Score: 208
Period size: 75 Copynumber: 2.4 Consensus size: 74
5327339 GTTTTCCTCA
** * * **
5327349 TTGAAATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAACT
1 TTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAACT
5327413 CAGTATGGGT
65 CAGTATGGGT
* *
5327423 TTGATAATACCATCCCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAACT
1 TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
5327488 CAGTAT-GG-
65 CAGTATGGGT
*
5327496 ATG--ATACCATACCTACATTTCACA
1 TTGAAATACCATACCTACATTTCACA
5327520 CTTTGTCATG
Statistics
Matches: 85, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
70 20 0.24
73 2 0.02
74 9 0.11
75 54 0.64
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.32
Consensus pattern (74 bp):
TTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACTC
AGTATGGGT
Found at i:5343409 original size:9 final size:9
Alignment explanation
Indices: 5343395--5343535 Score: 72
Period size: 9 Copynumber: 14.6 Consensus size: 9
5343385 TGTTATATGG
5343395 TAAAAATTA
1 TAAAAATTA
5343404 TAAAAA--A
1 TAAAAATTA
5343411 TAAAAATTAA
1 TAAAAATT-A
5343421 TAAAATTTATTAA
1 TAAAA---ATT-A
*
5343434 TAAGAAATATT
1 TAA-AAAT-TA
* *
5343445 TTAAATTTA
1 TAAAAATTA
5343454 TTAAAAATTAGA
1 -TAAAAATT--A
*
5343466 AAAAAATTA
1 TAAAAATTA
*
5343475 TAAAAATCA
1 TAAAAATTA
5343484 TAAAAATATA
1 TAAAAAT-TA
*
5343494 TTAAAAAATA
1 -TAAAAATTA
*
5343504 TAAAATTTTA
1 TAAAA-ATTA
*
5343514 TAAAAATCA
1 TAAAAATTA
5343523 TAAAAA-TA
1 TAAAAATTA
5343531 TAAAA
1 TAAAA
5343536 TGCATAAAAA
Statistics
Matches: 102, Mismatches: 16, Indels: 29
0.69 0.11 0.20
Matches are distributed among these distances:
7 7 0.07
8 6 0.06
9 35 0.34
10 25 0.25
11 17 0.17
12 2 0.02
13 8 0.08
14 2 0.02
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (9 bp):
TAAAAATTA
Found at i:5343493 original size:17 final size:17
Alignment explanation
Indices: 5343467--5343545 Score: 63
Period size: 19 Copynumber: 4.3 Consensus size: 17
5343457 AAAATTAGAA
5343467 AAAAATTATAAAAATCAT
1 AAAAA-TATAAAAATCAT
5343485 AAAAATATATTAAAAAAT-AT
1 -AAAA-ATA-T-AAAAATCAT
*
5343505 AAAATTTTATAAAAATCAT
1 AAAA--ATATAAAAATCAT
5343524 AAAAATAT-AAAATGCAT
1 AAAAATATAAAAAT-CAT
5343541 AAAAA
1 AAAAA
5343546 GGACATTTAA
Statistics
Matches: 52, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
16 5 0.10
17 11 0.21
18 6 0.12
19 17 0.33
20 7 0.13
21 6 0.12
ACGTcount: A:0.67, C:0.04, G:0.01, T:0.28
Consensus pattern (17 bp):
AAAAATATAAAAATCAT
Found at i:5343529 original size:20 final size:22
Alignment explanation
Indices: 5343455--5343532 Score: 89
Period size: 20 Copynumber: 3.9 Consensus size: 22
5343445 TTAAATTTAT
* *
5343455 TAAAAATTAGAAAAA-A-ATTA
1 TAAAAATCATAAAAATATATTA
5343475 TAAAAATCATAAAAATATATTA
1 TAAAAATCATAAAAATATATTA
5343497 -AAAAAT-AT-AAAAT-T-TTA
1 TAAAAATCATAAAAATATATTA
5343514 TAAAAATCATAAAAATATA
1 TAAAAATCATAAAAATATA
5343533 AAATGCATAA
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
17 3 0.06
18 7 0.14
19 7 0.14
20 20 0.41
21 8 0.16
22 4 0.08
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (22 bp):
TAAAAATCATAAAAATATATTA
Found at i:5343733 original size:9 final size:9
Alignment explanation
Indices: 5343719--5343926 Score: 72
Period size: 10 Copynumber: 22.1 Consensus size: 9
5343709 CTTTAGTACA
5343719 ATAATTTTT
1 ATAATTTTT
5343728 ATAATTCTTT
1 ATAATT-TTT
* *
5343738 TTACGAATTTT
1 ATA--ATTTTT
5343749 AT-ATTTTT
1 ATAATTTTT
5343757 AT-ATATTTT
1 ATAAT-TTTT
5343766 ATAATTTTCT
1 ATAATTTT-T
*
5343776 -TACGA-CTTT
1 ATA--ATTTTT
*
5343785 ATAAATTTT
1 ATAATTTTT
*
5343794 ATATTTTTTT
1 ATA-ATTTTT
*
5343804 CTATATTTTT
1 ATA-ATTTTT
*
5343814 CT-ATATTTT
1 ATAAT-TTTT
*
5343823 ATACTTTTTT
1 ATA-ATTTTT
5343833 ATAATTTTT
1 ATAATTTTT
5343842 ATAATTTTTT
1 ATAA-TTTTT
*
5343852 TTAATTTTT
1 ATAATTTTT
*
5343861 AGTAA-ATTT
1 A-TAATTTTT
*
5343870 AAATATTTTT
1 ATA-ATTTTT
*
5343880 AT-TTTTTT
1 ATAATTTTT
* *
5343888 ATTAAAATTTA
1 A-T-AATTTTT
5343899 ATAA-TTTT
1 ATAATTTTT
*
5343907 ATAAATTTT
1 ATAATTTTT
5343916 ATTAATTTTT
1 A-TAATTTTT
5343926 A
1 A
5343927 AATGTGATTG
Statistics
Matches: 151, Mismatches: 25, Indels: 45
0.68 0.11 0.20
Matches are distributed among these distances:
8 26 0.17
9 56 0.37
10 57 0.38
11 10 0.07
12 2 0.01
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.63
Consensus pattern (9 bp):
ATAATTTTT
Found at i:5343761 original size:10 final size:10
Alignment explanation
Indices: 5343748--5343850 Score: 62
Period size: 9 Copynumber: 10.9 Consensus size: 10
5343738 TTACGAATTT
5343748 TATATTTTTA
1 TATATTTTTA
5343758 TATA-TTTTA
1 TATATTTTTA
5343767 TA-ATTTTCT-
1 TATATTTT-TA
* *
5343776 TACGA-CTTTA
1 TA-TATTTTTA
*
5343786 TA-AATTTTA
1 TATATTTTTA
* *
5343795 TATTTTTTTC
1 TATATTTTTA
*
5343805 TATATTTTTC
1 TATATTTTTA
5343815 TATA-TTTTA
1 TATATTTTTA
5343824 TACT-TTTTTA
1 TA-TATTTTTA
5343834 TA-ATTTTTA
1 TATATTTTTA
5343843 TA-ATTTTT
1 TATATTTTT
5343851 TTTAATTTTT
Statistics
Matches: 76, Mismatches: 7, Indels: 21
0.73 0.07 0.20
Matches are distributed among these distances:
8 2 0.03
9 39 0.51
10 34 0.45
11 1 0.01
ACGTcount: A:0.27, C:0.06, G:0.01, T:0.66
Consensus pattern (10 bp):
TATATTTTTA
Found at i:5343794 original size:37 final size:38
Alignment explanation
Indices: 5343724--5343802 Score: 99
Period size: 37 Copynumber: 2.1 Consensus size: 38
5343714 GTACAATAAT
* *
5343724 TTTTATAATTCTTTTTACGAATTTTATATTTTTATATA
1 TTTTATAATTCTTCTTACGAATTTTATAATTTTATATA
* *
5343762 TTTTATAATT-TTCTTACG-ACTTTATAAATTTTATATT
1 TTTTATAATTCTTCTTACGAATTTTAT-AATTTTATATA
5343799 TTTT
1 TTTT
5343803 TCTATATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
36 6 0.17
37 20 0.56
38 10 0.28
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.63
Consensus pattern (38 bp):
TTTTATAATTCTTCTTACGAATTTTATAATTTTATATA
Found at i:5343822 original size:19 final size:18
Alignment explanation
Indices: 5343800--5343861 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 18
5343790 TTTTATATTT
5343800 TTTTCTATATTTTTCTAT-A
1 TTTT-TATATTTTT-TATAA
5343819 -TTTTATACTTTTTTATAA
1 TTTTTATA-TTTTTTATAA
*
5343837 TTTTTATAATTTTTTTTAA
1 TTTTTAT-ATTTTTTATAA
5343856 TTTTTA
1 TTTTTA
5343862 GTAAATTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
17 7 0.18
18 9 0.24
19 21 0.55
20 1 0.03
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTATATTTTTTATAA
Found at i:5343870 original size:28 final size:28
Alignment explanation
Indices: 5343839--5343906 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 28
5343829 TTTTATAATT
5343839 TTTATAATTTTTT-TTAATTTTTAGT-AAA
1 TTTATAATTTTTTATT--TTTTTAGTAAAA
*
5343867 TTTA-AATATTTTTATTTTTTTATTAAAA
1 TTTATAAT-TTTTTATTTTTTTAGTAAAA
5343895 TTTAATAATTTT
1 TTT-ATAATTTT
5343907 ATAAATTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
27 10 0.29
28 15 0.44
29 6 0.18
30 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (28 bp):
TTTATAATTTTTTATTTTTTTAGTAAAA
Found at i:5343886 original size:27 final size:27
Alignment explanation
Indices: 5343856--5343908 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
5343846 TTTTTTTTAA
*
5343856 TTTTTAGT-AAATTTAAATATTTTTATT
1 TTTTTAGTAAAATTT-AATAATTTTATT
*
5343883 TTTTTATTAAAATTTAATAATTTTAT
1 TTTTTAGTAAAATTTAATAATTTTAT
5343909 AAATTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 17 0.74
28 6 0.26
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (27 bp):
TTTTTAGTAAAATTTAATAATTTTATT
Found at i:5343911 original size:18 final size:18
Alignment explanation
Indices: 5343884--5343928 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
5343874 ATTTTTATTT
5343884 TTTTATTAAAATTTAATAA
1 TTTTA-TAAAATTTAATAA
* *
5343903 TTTTATAAATTTTATTAA
1 TTTTATAAAATTTAATAA
5343921 TTTT-TAAA
1 TTTTATAAA
5343929 TGTGATTGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 15 0.62
19 5 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTATAAAATTTAATAA
Found at i:5348838 original size:21 final size:21
Alignment explanation
Indices: 5348798--5348851 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
5348788 ATAGTGTTTC
*
5348798 GTAATGTTTTGAGATGAATT-G
1 GTAATGTTTTG-GATAAATTAG
5348819 GTAATGTTTTGGATCAAATTAG
1 GTAATGTTTTGGAT-AAATTAG
*
5348841 GTGA-GTTTTGG
1 GTAATGTTTTGG
5348852 GGTATTTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 3 0.10
21 22 0.76
22 4 0.14
ACGTcount: A:0.26, C:0.02, G:0.30, T:0.43
Consensus pattern (21 bp):
GTAATGTTTTGGATAAATTAG
Found at i:5353755 original size:2 final size:2
Alignment explanation
Indices: 5353748--5353778 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5353738 TATCTTTATT
5353748 TA 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 TA T
5353779 TACATATTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5356995 original size:79 final size:79
Alignment explanation
Indices: 5356899--5357060 Score: 324
Period size: 79 Copynumber: 2.1 Consensus size: 79
5356889 TTTAATCTAT
5356899 TATAATTTTATATGAAAAGTGTATTAATATGCGATTAAATACATGGTATTTCAACATGTTATTCT
1 TATAATTTTATATGAAAAGTGTATTAATATGCGATTAAATACATGGTATTTCAACATGTTATTCT
5356964 CCTCTTACCAAAAC
66 CCTCTTACCAAAAC
5356978 TATAATTTTATATGAAAAGTGTATTAATATGCGATTAAATACATGGTATTTCAACATGTTATTCT
1 TATAATTTTATATGAAAAGTGTATTAATATGCGATTAAATACATGGTATTTCAACATGTTATTCT
5357043 CCTCTTACCAAAAC
66 CCTCTTACCAAAAC
5357057 TATA
1 TATA
5357061 TATTCGCATT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 83 1.00
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.40
Consensus pattern (79 bp):
TATAATTTTATATGAAAAGTGTATTAATATGCGATTAAATACATGGTATTTCAACATGTTATTCT
CCTCTTACCAAAAC
Found at i:5359834 original size:9 final size:9
Alignment explanation
Indices: 5359820--5359854 Score: 56
Period size: 8 Copynumber: 4.1 Consensus size: 9
5359810 AGGTATACTC
5359820 TTTTCTTTT
1 TTTTCTTTT
5359829 TTTTC-TTT
1 TTTTCTTTT
5359837 TTTTCTTTT
1 TTTTCTTTT
5359846 TTTT-TTTT
1 TTTTCTTTT
5359854 T
1 T
5359855 GGGTTCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 13 0.52
9 12 0.48
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:5359842 original size:17 final size:16
Alignment explanation
Indices: 5359820--5359854 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
5359810 AGGTATACTC
5359820 TTTTCTTTTTTTTCTTT
1 TTTTCTTTTTTTT-TTT
5359837 TTTTCTTTTTTTTTTT
1 TTTTCTTTTTTTTTTT
5359853 TT
1 TT
5359855 GGGTTCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (16 bp):
TTTTCTTTTTTTTTTT
Found at i:5366887 original size:33 final size:33
Alignment explanation
Indices: 5366792--5366887 Score: 92
Period size: 33 Copynumber: 2.9 Consensus size: 33
5366782 ATAAAATAAA
*
5366792 ATTTTAAATATTTTTAAACAATAAATATT-AATTAT
1 ATTTTAAATA--TTTAAA-TATAAATATTAAATTAT
* *
5366827 -TTATAAA-ATTTAATTA-AAATATATAAATTAT
1 ATTTTAAATATTTAAATATAAATAT-TAAATTAT
*
5366858 ATTTTAAATATTTAAATATAACTATTAAAT
1 ATTTTAAATATTTAAATATAAATATTAAAT
5366888 ATTTGTAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
29 6 0.12
30 2 0.04
31 11 0.22
32 6 0.12
33 14 0.28
34 11 0.22
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (33 bp):
ATTTTAAATATTTAAATATAAATATTAAATTAT
Found at i:5367285 original size:3 final size:3
Alignment explanation
Indices: 5367277--5367305 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5367267 GCAGATTCTC
5367277 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
5367306 GTTGGAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:5368243 original size:12 final size:13
Alignment explanation
Indices: 5368226--5368254 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
5368216 TGTTAGATTT
5368226 AAAAAACAAAAA-
1 AAAAAACAAAAAC
5368238 AAAAAACAAAAAC
1 AAAAAACAAAAAC
5368251 AAAA
1 AAAA
5368255 GTTAAATGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAACAAAAAC
Found at i:5372208 original size:22 final size:22
Alignment explanation
Indices: 5372182--5372229 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
5372172 ACAAATCAGA
*
5372182 TTTTTCTTCTTAATTTTTAGTT
1 TTTTTCTTCCTAATTTTTAGTT
5372204 TTTTTCTTCCTAATTTTTAGTT
1 TTTTTCTTCCTAATTTTTAGTT
5372226 TTTT
1 TTTT
5372230 ACTCCTGAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.12, C:0.10, G:0.04, T:0.73
Consensus pattern (22 bp):
TTTTTCTTCCTAATTTTTAGTT
Found at i:5378738 original size:13 final size:13
Alignment explanation
Indices: 5378717--5378747 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5378707 AATTTTACAT
*
5378717 GAAATCAACATAA
1 GAAAACAACATAA
5378730 GAAAACAACATAA
1 GAAAACAACATAA
5378743 GAAAA
1 GAAAA
5378748 AGTCGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.68, C:0.13, G:0.10, T:0.10
Consensus pattern (13 bp):
GAAAACAACATAA
Found at i:5395235 original size:31 final size:31
Alignment explanation
Indices: 5395200--5395258 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
5395190 AAATTATTAT
5395200 TTTAGAATATTT-TTAAAATTTTTATATATTC
1 TTTAGAAT-TTTCTTAAAATTTTTATATATTC
*
5395231 TTTAGAATTTTCTTAAAATTTTTTTATA
1 TTTAGAATTTTCTTAAAATTTTTATATA
5395259 ATTTTTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 3 0.12
31 23 0.88
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (31 bp):
TTTAGAATTTTCTTAAAATTTTTATATATTC
Found at i:5395303 original size:27 final size:25
Alignment explanation
Indices: 5395252--5395312 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
5395242 CTTAAAATTT
*
5395252 TTTTATAATTTTTAAAAAATATAAA
1 TTTTAAAATTTTTAAAAAATATAAA
* *
5395277 TTTTGAAATTTTTAAAAATATTTTAAA
1 TTTTAAAATTTTTAAAAA-A-TATAAA
5395304 TTTTAAAAT
1 TTTTAAAAT
5395313 CTATTTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 16 0.53
26 1 0.03
27 13 0.43
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
TTTTAAAATTTTTAAAAAATATAAA
Found at i:5395317 original size:19 final size:20
Alignment explanation
Indices: 5395276--5395322 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
5395266 AAAAATATAA
5395276 ATTTTGAAATTTTTAAAAAT
1 ATTTTGAAATTTTTAAAAAT
*
5395296 ATTTT-AAA-TTTTAAAATCT
1 ATTTTGAAATTTTTAAAA-AT
5395315 ATTTTGAA
1 ATTTTGAA
5395323 TATCTTTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 8 0.33
19 9 0.38
20 7 0.29
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (20 bp):
ATTTTGAAATTTTTAAAAAT
Found at i:5396411 original size:2 final size:2
Alignment explanation
Indices: 5396404--5396429 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5396394 GTACGAATAA
5396404 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5396430 GACATATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5397308 original size:39 final size:40
Alignment explanation
Indices: 5397265--5397346 Score: 114
Period size: 39 Copynumber: 2.1 Consensus size: 40
5397255 AAACATTATT
* *
5397265 TAATAAAATATTTATTATATTTAT--TTGTGTTTTTTAATA
1 TAATAAAACATTTATTATATTTATGGTAGTG-TTTTTAATA
*
5397304 TAATAAAGCATTTATTATATTTATGGTAGTGTTTTTAATA
1 TAATAAAACATTTATTATATTTATGGTAGTGTTTTTAATA
5397344 TAA
1 TAA
5397347 ACACTTTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
39 22 0.58
40 12 0.32
41 4 0.11
ACGTcount: A:0.37, C:0.01, G:0.09, T:0.54
Consensus pattern (40 bp):
TAATAAAACATTTATTATATTTATGGTAGTGTTTTTAATA
Found at i:5402971 original size:9 final size:9
Alignment explanation
Indices: 5402959--5402997 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
5402949 AATTTAGCTT
*
5402959 TTTTAAAAA
1 TTTTAAATA
*
5402968 TTTTAATTA
1 TTTTAAATA
*
5402977 TTTTAAATT
1 TTTTAAATA
5402986 TTTTAAATA
1 TTTTAAATA
5402995 TTT
1 TTT
5402998 AATGACATGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
TTTTAAATA
Found at i:5409293 original size:15 final size:15
Alignment explanation
Indices: 5409273--5409303 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5409263 TTGTTATTTT
5409273 TTTGAAAGGTGGATG
1 TTTGAAAGGTGGATG
5409288 TTTGAAAGGTGGATG
1 TTTGAAAGGTGGATG
5409303 T
1 T
5409304 AGAGCGGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.39, T:0.35
Consensus pattern (15 bp):
TTTGAAAGGTGGATG
Found at i:5421115 original size:12 final size:12
Alignment explanation
Indices: 5421098--5421122 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5421088 AGTTTTGTTG
5421098 TTAAACAAATAA
1 TTAAACAAATAA
5421110 TTAAACAAATAA
1 TTAAACAAATAA
5421122 T
1 T
5421123 CTCACAAACT
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:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (12 bp):
TTAAACAAATAA
Found at i:5423454 original size:21 final size:21
Alignment explanation
Indices: 5423413--5423460 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
5423403 ATTTGGTACA
**
5423413 TTTATAGTATATTTTTTAAAT
1 TTTATAGTATATTTTAAAAAT
5423434 TTTATAAGTA-ATTTTAAAAAT
1 TTTAT-AGTATATTTTAAAAAT
5423455 TGTTAT
1 T-TTAT
5423461 GTTTTTTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (21 bp):
TTTATAGTATATTTTAAAAAT
Found at i:5430174 original size:20 final size:21
Alignment explanation
Indices: 5430137--5430175 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
5430127 TTCATTTGAA
* *
5430137 AAAAAGTATTTTTGAAAAGCC
1 AAAAAGTATTCTTCAAAAGCC
5430158 AAAAAGT-TTCTTCAAAAG
1 AAAAAGTATTCTTCAAAAG
5430176 TTGTTTAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.28
Consensus pattern (21 bp):
AAAAAGTATTCTTCAAAAGCC
Found at i:5432691 original size:35 final size:35
Alignment explanation
Indices: 5432645--5432713 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
5432635 ACTTCAATAT
*
5432645 TATTAATAATTATAATATAGTATGTATTGTAGATA
1 TATTAATAATTATAAAATAGTATGTATTGTAGATA
*
5432680 TATTATTAATTATAAAATAGTATGTATTGTAGAT
1 TATTAATAATTATAAAATAGTATGTATTGTAGAT
5432714 TAATGAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (35 bp):
TATTAATAATTATAAAATAGTATGTATTGTAGATA
Found at i:5440837 original size:11 final size:11
Alignment explanation
Indices: 5440821--5440854 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
5440811 CAAGGAGAGA
5440821 AGGGAGAGGAG
1 AGGGAGAGGAG
5440832 AGGGAGAGGGAG
1 AGGGAGA-GGAG
*
5440844 AGGCAGAGGAG
1 AGGGAGAGGAG
5440855 GTGGTGCAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.35, C:0.03, G:0.62, T:0.00
Consensus pattern (11 bp):
AGGGAGAGGAG
Found at i:5441698 original size:18 final size:18
Alignment explanation
Indices: 5441675--5441709 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5441665 AGTATGTTGT
5441675 GTTTTTATTATCTTTTTG
1 GTTTTTATTATCTTTTTG
* *
5441693 GTTTTTTTTTTCTTTTT
1 GTTTTTATTATCTTTTT
5441710 TGAGAAATAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.06, C:0.06, G:0.09, T:0.80
Consensus pattern (18 bp):
GTTTTTATTATCTTTTTG
Found at i:5443846 original size:21 final size:21
Alignment explanation
Indices: 5443822--5443864 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
5443812 TTGGCACGTT
5443822 AAATCATCATTTTAAACAATA
1 AAATCATCATTTTAAACAATA
5443843 AAATCATCATTTTAAACAATA
1 AAATCATCATTTTAAACAATA
5443864 A
1 A
5443865 TTTTAGGTTA
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:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATCATCATTTTAAACAATA
Found at i:5447384 original size:43 final size:43
Alignment explanation
Indices: 5447336--5447422 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
5447326 ATCACTAAAA
5447336 CCTTATGCATGTCTTAAGTTTAGATGAAATAATAGTGGAGATT
1 CCTTATGCATGTCTTAAGTTTAGATGAAATAATAGTGGAGATT
5447379 CCTTATGCATGTCTTAAGTTTAGATGAAATAATAGTGGAGATT
1 CCTTATGCATGTCTTAAGTTTAGATGAAATAATAGTGGAGATT
5447422 C
1 C
5447423 AGGTTCCCTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.32, C:0.10, G:0.21, T:0.37
Consensus pattern (43 bp):
CCTTATGCATGTCTTAAGTTTAGATGAAATAATAGTGGAGATT
Found at i:5451054 original size:2 final size:2
Alignment explanation
Indices: 5451047--5451073 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5451037 TCAGTTCAAC
5451047 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 A
5451074 AAGAAACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5464841 original size:3 final size:3
Alignment explanation
Indices: 5464833--5464863 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
5464823 ACACAGGATA
*
5464833 TCT TCT TCT TCT TCT TCT TCT TCT CCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
5464864 ACAATTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:5473119 original size:46 final size:46
Alignment explanation
Indices: 5473052--5473268 Score: 292
Period size: 46 Copynumber: 4.7 Consensus size: 46
5473042 TGGCAACCTG
*
5473052 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAA
* * *
5473098 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTAATATGAGA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAA
*
5473144 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAA
* ** *
5473190 AGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATG-AAA
* * * * *
5473236 TGAGTAAGACTATAGTTGAAAGACACTATGGCA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCA
5473269 TCACGTCAAA
Statistics
Matches: 154, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
45 1 0.01
46 153 0.99
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.22
Consensus pattern (46 bp):
TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAA
Found at i:5473254 original size:138 final size:130
Alignment explanation
Indices: 5473006--5473268 Score: 348
Period size: 138 Copynumber: 2.0 Consensus size: 130
5472996 GTGCTCTCTG
*
5473006 ATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTGTGTAAGACCATGGTTGA
1 ATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTGAGTAAGACCATGGTTGA
* * * * *
5473071 AAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTA
66 AAGATACCATGGCAACATGACATGAAATGAGTAAGACCATAGTTGAAAGACACCATGGCAACCTA
* *
5473136 ATATGAGATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACC
1 ATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG---TG---AG--TAAGACC
* *
5473201 ATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGAGTAAGACTATAGTTGAAAGACACTAT
58 ATGGTTGAAAGATACCATGGCAACATGACATG-AAATGAGTAAGACCATAGTTGAAAGACACCAT
5473265 GGCA
122 GGCA
5473269 TCACGTCAAA
Statistics
Matches: 114, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
130 44 0.39
133 2 0.02
136 1 0.01
137 1 0.01
138 66 0.58
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (130 bp):
ATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTGAGTAAGACCATGGTTGA
AAGATACCATGGCAACATGACATGAAATGAGTAAGACCATAGTTGAAAGACACCATGGCAACCTA
Found at i:5477889 original size:42 final size:42
Alignment explanation
Indices: 5477826--5477952 Score: 170
Period size: 42 Copynumber: 3.0 Consensus size: 42
5477816 CTTCGTTTTC
** * *
5477826 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACAT-A
*
5477869 T-GATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
5477910 TCGATGCCATAGCCCAGCTATGGTCTTACACGA-A-TCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC-ATATTCACATA
5477951 TC
1 TC
5477953 TCACTGATGC
Statistics
Matches: 76, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
41 10 0.13
42 64 0.84
43 2 0.03
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
Found at i:5477979 original size:46 final size:46
Alignment explanation
Indices: 5477911--5478036 Score: 155
Period size: 46 Copynumber: 2.7 Consensus size: 46
5477901 ATTCATATAT
* * * *
5477911 CGATGCCATAGCCCAGCTATGGTCTTACAC-GAATCACATATCTCA
1 CGATGCCATATCCCAGATATGGTCTTACACAGAAGCACATATCACA
* * *
5477956 CTGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACA
1 C-GATGCCATATCCCAGATATGGTCTTACACAGAAGCACATATCACA
* *
5478003 CGATGCCATATCCCAGACATGGTCTTATACAGAA
1 CGATGCCATATCCCAGATATGGTCTTACACAGAA
5478037 ATCACTTGTC
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
45 1 0.01
46 57 0.81
47 12 0.17
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (46 bp):
CGATGCCATATCCCAGATATGGTCTTACACAGAAGCACATATCACA
Found at i:5478101 original size:31 final size:31
Alignment explanation
Indices: 5478058--5478237 Score: 270
Period size: 31 Copynumber: 5.8 Consensus size: 31
5478048 CTTGTCACTT
* *
5478058 GTAGTCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* * *
5478089 GTAGCCGGAGCTACTATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
5478120 GTAGCCGAAGCTACCACTTTTCACTGATCAA
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
5478151 GTAGCCGAAACTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
5478182 GTAGCAGAAGTTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
5478213 GTAGCTGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
5478238 TGTCATTTGT
Statistics
Matches: 133, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 133 1.00
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.28
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:5482969 original size:2 final size:2
Alignment explanation
Indices: 5482962--5482994 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5482952 AACTGTTATT
*
5482962 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5482995 TGTTGTGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5484715 original size:17 final size:18
Alignment explanation
Indices: 5484682--5484725 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
5484672 TTAAAAAATA
5484682 TATAAAATTTGGAATTTT
1 TATAAAATTTGGAATTTT
5484700 TATAAATATTT-G-ATTTT
1 TATAAA-ATTTGGAATTTT
*
5484717 TAAAAAATT
1 TATAAAATT
5484726 ATTTTGAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 3 0.12
17 10 0.42
18 7 0.29
19 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (18 bp):
TATAAAATTTGGAATTTT
Found at i:5485293 original size:22 final size:23
Alignment explanation
Indices: 5485268--5485310 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
5485258 GATTTTAGTC
5485268 TTTATATTTTTA-TTTTTAAAAA
1 TTTATATTTTTACTTTTTAAAAA
*
5485290 TTTATTTTTTTACTTTTTAAA
1 TTTATATTTTTACTTTTTAAA
5485311 TTTTAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTATATTTTTACTTTTTAAAAA
Found at i:5485832 original size:21 final size:21
Alignment explanation
Indices: 5485801--5485853 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
5485791 ATAATGATAA
5485801 TTTTA-ATTTTTAATATTTAT
1 TTTTATATTTTTAATATTTAT
**
5485821 TTTTATATTTTTCTTATTTAT
1 TTTTATATTTTTAATATTTAT
5485842 TTTTATTATTTT
1 TTTTA-TATTTT
5485854 AACTTTTAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 5 0.17
21 18 0.62
22 6 0.21
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTTATATTTTTAATATTTAT
Found at i:5487644 original size:20 final size:18
Alignment explanation
Indices: 5487615--5487659 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
5487605 TAATGGTTAT
*
5487615 ATTTTAATATTTAAAATATA
1 ATTTTTATA-TTAAAATA-A
*
5487635 ATTTTTATATTCAAATAA
1 ATTTTTATATTAAAATAA
5487653 ATTTTTA
1 ATTTTTA
5487660 CAAATAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 8 0.35
19 7 0.30
20 8 0.35
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTTTATATTAAAATAA
Found at i:5489512 original size:3 final size:3
Alignment explanation
Indices: 5489504--5489539 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
5489494 GTTCAAACCT
5489504 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
5489540 ACCAACCATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:5491664 original size:27 final size:27
Alignment explanation
Indices: 5491634--5491686 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
5491624 TGAACTATTC
*
5491634 TATTTATGTTCTTAATTA-TATTAATTA
1 TATTTATATT-TTAATTATTATTAATTA
*
5491661 TATTTATATTTTATTTATTATTAATT
1 TATTTATATTTTAATTATTATTAATT
5491687 TAGGGAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (27 bp):
TATTTATATTTTAATTATTATTAATTA
Found at i:5499133 original size:2 final size:2
Alignment explanation
Indices: 5499122--5499154 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5499112 ATGAAAAAAA
*
5499122 AG AG AC 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 A
5499155 AAGGGAGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5499399 original size:2 final size:2
Alignment explanation
Indices: 5499392--5499432 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
5499382 TTTGCACAGG
5499392 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
5499433 GCAATGATGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5499643 original size:18 final size:19
Alignment explanation
Indices: 5499609--5499645 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5499599 CTATATAATT
*
5499609 AAATTTATAACTTATTTAA
1 AAATTAATAACTTATTTAA
5499628 AAATTAATAA-TTATTTAA
1 AAATTAATAACTTATTTAA
5499646 TATATATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (19 bp):
AAATTAATAACTTATTTAA
Found at i:5505516 original size:14 final size:14
Alignment explanation
Indices: 5505497--5505523 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5505487 ATAATGCAAA
5505497 AAAAAAAAAAAAGC
1 AAAAAAAAAAAAGC
5505511 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
5505524 GAAGTTTGCA
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:0.89, C:0.04, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAGC
Found at i:5509943 original size:52 final size:53
Alignment explanation
Indices: 5509869--5509970 Score: 143
Period size: 52 Copynumber: 1.9 Consensus size: 53
5509859 AACTTTCCAA
*
5509869 AAAACCCAGAATTAATTCAATCAAAATTAAATAAAAAAAAAGGCCAAAACAAC
1 AAAACCCAGAATTAATTCAATCAAAATCAAATAAAAAAAAAGGCCAAAACAAC
* * * * *
5509922 AAAACCCAGAA-TAATTGAATCAAAGTCGAATAAAAAAGAAGGGCAAAAC
1 AAAACCCAGAATTAATTCAATCAAAATCAAATAAAAAAAAAGGCCAAAAC
5509971 TGCAAGCAGC
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
52 32 0.74
53 11 0.26
ACGTcount: A:0.60, C:0.16, G:0.11, T:0.14
Consensus pattern (53 bp):
AAAACCCAGAATTAATTCAATCAAAATCAAATAAAAAAAAAGGCCAAAACAAC
Found at i:5510708 original size:26 final size:28
Alignment explanation
Indices: 5510651--5510718 Score: 88
Period size: 26 Copynumber: 2.5 Consensus size: 28
5510641 CATTTTATTT
*
5510651 TTTTATTTAAAAAATAGATAAATTGATCA
1 TTTTATTT-AAAAATAGATAAATTAATCA
*
5510680 TTTTATTTAAAAA-A-ATAAATTAATTA
1 TTTTATTTAAAAATAGATAAATTAATCA
5510706 TTTTA-TTAAAAAT
1 TTTTATTTAAAAAT
5510719 TTTATTTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
25 7 0.19
26 15 0.42
27 1 0.03
28 5 0.14
29 8 0.22
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (28 bp):
TTTTATTTAAAAATAGATAAATTAATCA
Found at i:5520536 original size:21 final size:21
Alignment explanation
Indices: 5520510--5520550 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5520500 AGACGAGCGA
* *
5520510 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
5520531 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
5520551 TTGAGCAGAT
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:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:5522181 original size:93 final size:93
Alignment explanation
Indices: 5522069--5522239 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
5522059 GCCCATAAGT
* *
5522069 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
5522134 CGAGTTCGGATGCCTAGTTACTTCTCAC
66 CGAGTTCGGATGCCTAGTTACTTCTCAC
*
5522162 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
5522227 CGAGTTCGGATGC
66 CGAGTTCGGATGC
5522240 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACTTCTCAC
Found at i:5522255 original size:46 final size:46
Alignment explanation
Indices: 5522061--5522241 Score: 231
Period size: 46 Copynumber: 3.9 Consensus size: 46
5522051 TGTAACCCGC
* * *
5522061 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* * *
5522107 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG-CA-T
* * *
5522156 TC-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
*
5522200 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTC
5522242 AACCATCCTA
Statistics
Matches: 114, Mismatches: 16, Indels: 10
0.81 0.11 0.07
Matches are distributed among these distances:
44 2 0.02
45 3 0.03
46 72 0.63
47 32 0.28
48 3 0.03
49 2 0.02
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Done.