Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397258.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4.1, whole genome shotgun sequence
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: 11097736
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 71999 characters in sequence are not A, C, G, or T
File 10 of 22
Found at i:5200096 original size:2 final size:2
Alignment explanation
Indices: 5200084--5200117 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
5200074 GGACCGAAAG
*
5200084 AT AT A- AT AT AT AT AT AT AT AT AA AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5200118 ATAAAATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:5201314 original size:29 final size:30
Alignment explanation
Indices: 5201245--5201315 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
5201235 GGTTAGAGAG
5201245 AGTGGCTTATTTGATCTGAAATAAAAATTC
1 AGTGGCTTATTTGATCTGAAATAAAAATTC
*
5201275 AATGGCTTATTTGA-CTCGAAATAAAAATT-
1 AGTGGCTTATTTGATCT-GAAATAAAAATTC
*
5201304 AGTGGGTTATTT
1 AGTGGCTTATTT
5201316 AAACATAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 12 0.32
30 25 0.68
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.38
Consensus pattern (30 bp):
AGTGGCTTATTTGATCTGAAATAAAAATTC
Found at i:5201710 original size:16 final size:16
Alignment explanation
Indices: 5201689--5201729 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
5201679 TTTAAATATT
5201689 TTATTAATTATTTTAA
1 TTATTAATTATTTTAA
5201705 TTATT-ATATATTTTAA
1 TTATTAAT-TATTTTAA
*
5201721 ATA-TAATTA
1 TTATTAATTA
5201730 ATTATATTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTATTAATTATTTTAA
Found at i:5201737 original size:21 final size:22
Alignment explanation
Indices: 5201702--5201747 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
5201692 TTAATTATTT
*
5201702 TAATTATTATATATT-TTAAATA
1 TAATTAATATATATTGTT-AATA
5201724 TAATTAAT-TATATTGTTAATA
1 TAATTAATATATATTGTTAATA
5201745 TAA
1 TAA
5201748 AAATATCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
TAATTAATATATATTGTTAATA
Found at i:5215843 original size:34 final size:34
Alignment explanation
Indices: 5215718--5215843 Score: 91
Period size: 34 Copynumber: 3.8 Consensus size: 34
5215708 TATATGGTAC
* * *
5215718 TGAAGCCTTAACCTTTGCATATAACATCT-AGTGG
1 TGAAGCTTTAACCTTGGCATGTAACATCTGA-TGG
* * *
5215752 TAAAGCTTTGA-C--GACATGTAACATCTTG-TGG
1 TGAAGCTTTAACCTTGGCATGTAACATC-TGATGG
* * ** *
5215783 TGAAACTTTGACCTTACCATGCAACATCTGATGG
1 TGAAGCTTTAACCTTGGCATGTAACATCTGATGG
*
5215817 TGAAGCTTTAACCTTGGCATTTAACAT
1 TGAAGCTTTAACCTTGGCATGTAACAT
5215844 TTAATGTTAA
Statistics
Matches: 69, Mismatches: 17, Indels: 12
0.70 0.17 0.12
Matches are distributed among these distances:
31 22 0.32
32 2 0.03
33 3 0.04
34 42 0.61
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (34 bp):
TGAAGCTTTAACCTTGGCATGTAACATCTGATGG
Found at i:5216867 original size:16 final size:15
Alignment explanation
Indices: 5216848--5216877 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
5216838 ATTTTTTTTT
5216848 AATTAAAAATAATTAA
1 AATTAAAAA-AATTAA
5216864 AATTAAAAAAATTA
1 AATTAAAAAAATTA
5216878 TTTTTTAAAA
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:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AATTAAAAAAATTAA
Found at i:5219338 original size:24 final size:24
Alignment explanation
Indices: 5219310--5219357 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
5219300 GCTCTATGAG
*
5219310 TAAAATAGTCAATGCAATGAGAGC
1 TAAAAAAGTCAATGCAATGAGAGC
* *
5219334 TAAAAAAGTTAGTGCAATGAGAGC
1 TAAAAAAGTCAATGCAATGAGAGC
5219358 ATTGCACAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.10, G:0.23, T:0.21
Consensus pattern (24 bp):
TAAAAAAGTCAATGCAATGAGAGC
Found at i:5220560 original size:22 final size:22
Alignment explanation
Indices: 5220530--5220573 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
5220520 TGATTAAGCC
* *
5220530 AATCCTTAATTATAAGGGTTTA
1 AATCATTAATTATAAGAGTTTA
5220552 AATCATTAATTATAAGAGTTTA
1 AATCATTAATTATAAGAGTTTA
5220574 TTTGACTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (22 bp):
AATCATTAATTATAAGAGTTTA
Found at i:5226326 original size:22 final size:19
Alignment explanation
Indices: 5226301--5226343 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 19
5226291 AACTTATAAA
5226301 AATAAATGTTAAGATTATTTTT
1 AATAAATGTT--GA-TATTTTT
*
5226323 AATAGATGTTGATATTTTT
1 AATAAATGTTGATATTTTT
5226342 AA
1 AA
5226344 AATAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 9 0.45
20 2 0.10
22 9 0.45
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.49
Consensus pattern (19 bp):
AATAAATGTTGATATTTTT
Found at i:5229156 original size:21 final size:21
Alignment explanation
Indices: 5229132--5229173 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5229122 TGTTCGATTG
*
5229132 ATTGGATCTTGGTCTTGTTGA
1 ATTGAATCTTGGTCTTGTTGA
* *
5229153 ATTGAATCTTGTTTTTGTTGA
1 ATTGAATCTTGGTCTTGTTGA
5229174 TTTTCTAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.07, G:0.24, T:0.52
Consensus pattern (21 bp):
ATTGAATCTTGGTCTTGTTGA
Found at i:5235273 original size:21 final size:21
Alignment explanation
Indices: 5235244--5235284 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5235234 TTTTTTTTTG
* *
5235244 GGGGGGGGGGGGGGTGGGGGT
1 GGGGGGGGGCGCGGTGGGGGT
*
5235265 GGGGTGGGGCGCGGTGGGGG
1 GGGGGGGGGCGCGGTGGGGG
5235285 ACGGTGTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.00, C:0.05, G:0.85, T:0.10
Consensus pattern (21 bp):
GGGGGGGGGCGCGGTGGGGGT
Found at i:5239738 original size:26 final size:26
Alignment explanation
Indices: 5239709--5239761 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
5239699 ATTCGAAAGC
5239709 TAGCAAAAACAAGCCAACAATTCCAA
1 TAGCAAAAACAAGCCAACAATTCCAA
*
5239735 TAGCAAAAGCAAGCCAACAATTCCAA
1 TAGCAAAAACAAGCCAACAATTCCAA
5239761 T
1 T
5239762 CCAAAACCTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.51, C:0.26, G:0.09, T:0.13
Consensus pattern (26 bp):
TAGCAAAAACAAGCCAACAATTCCAA
Found at i:5252623 original size:43 final size:43
Alignment explanation
Indices: 5252576--5252666 Score: 128
Period size: 43 Copynumber: 2.1 Consensus size: 43
5252566 GAAGTAGTAA
* * *
5252576 TTGGATGTAAGGGGTAAAAGTAGGAAGGTATTGGAAGTTGCGG
1 TTGGATATAAGGGGTAAAAGTAGGAAAGTATGGGAAGTTGCGG
* * *
5252619 TTGGATATGAGGGGTAAAGGTAGGAAAGTATGGGAAGTTGTGG
1 TTGGATATAAGGGGTAAAAGTAGGAAAGTATGGGAAGTTGCGG
5252662 TTGGA
1 TTGGA
5252667 AACTATGTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.30, C:0.01, G:0.43, T:0.26
Consensus pattern (43 bp):
TTGGATATAAGGGGTAAAAGTAGGAAAGTATGGGAAGTTGCGG
Found at i:5252769 original size:30 final size:30
Alignment explanation
Indices: 5252703--5252770 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 30
5252693 AATCAGAAGT
* * * *
5252703 TGTATGTATGTGTGTGTGTGTGTATATATA
1 TGTATTTATGTATGCGTATGTGTATATATA
* * *
5252733 TATATTTATGTATGCGTATGTGTATGTGTA
1 TGTATTTATGTATGCGTATGTGTATATATA
5252763 TGTATTTA
1 TGTATTTA
5252771 CATAAACATA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.22, C:0.01, G:0.25, T:0.51
Consensus pattern (30 bp):
TGTATTTATGTATGCGTATGTGTATATATA
Found at i:5259615 original size:2 final size:2
Alignment explanation
Indices: 5259608--5259637 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5259598 ACATGGTACA
5259608 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
5259638 GAGCTTGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5261317 original size:21 final size:20
Alignment explanation
Indices: 5261293--5261364 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 20
5261283 TAAGTCATAG
5261293 GTATCGATACTTCTAGGGGAA
1 GTATCGATACTTCT-GGGGAA
* * *
5261314 GTATTGATGC-T-TGGGCAATA
1 GTATCGATACTTCTGGG-GA-A
5261334 GGTATCGATACTTCTTGGGGAA
1 -GTATCGATACTTC-TGGGGAA
5261356 GTATCGATA
1 GTATCGATA
5261365 TTTTTCACCC
Statistics
Matches: 39, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
18 3 0.08
19 2 0.05
20 2 0.05
21 25 0.64
22 2 0.05
23 1 0.03
24 4 0.10
ACGTcount: A:0.26, C:0.12, G:0.29, T:0.32
Consensus pattern (20 bp):
GTATCGATACTTCTGGGGAA
Found at i:5262006 original size:63 final size:66
Alignment explanation
Indices: 5261902--5262025 Score: 200
Period size: 63 Copynumber: 1.9 Consensus size: 66
5261892 TAATCGATTC
**
5261902 ATAGTCACCATTGCCATAGTCAAGTACATAAATCATGTTCATTTAATTATCATTTTAGTGGAATT
1 ATAGTCACCATTGCCATAGTCAAGTACATAAATCACATTCATTTAATTATCATTTTAGTGGAATT
5261967 A
66 A
*
5261968 ATAGTCACCATTG-C-T-GTCATGTACATAAATCACATTCATTTAATTATCATTTTAGTGG
1 ATAGTCACCATTGCCATAGTCAAGTACATAAATCACATTCATTTAATTATCATTTTAGTGG
5262026 GCAATCATTC
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
63 40 0.73
64 1 0.02
65 1 0.02
66 13 0.24
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (66 bp):
ATAGTCACCATTGCCATAGTCAAGTACATAAATCACATTCATTTAATTATCATTTTAGTGGAATT
A
Found at i:5282203 original size:3 final size:3
Alignment explanation
Indices: 5282195--5282225 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
5282185 GAGGTGGTTA
*
5282195 AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
5282226 GAAAGACAGT
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:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:5286616 original size:31 final size:31
Alignment explanation
Indices: 5286573--5286633 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
5286563 AACTTTAAGG
* * *
5286573 ATTTATAGCAGAGATTGCAATCTGAGTATTA
1 ATTTATAGCAGAGATTCCAAACTGAATATTA
5286604 ATTTAT-GTCAGAGATTCCAAACTGAATATT
1 ATTTATAG-CAGAGATTCCAAACTGAATATT
5286634 CTTTGTATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 1 0.04
31 25 0.96
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.36
Consensus pattern (31 bp):
ATTTATAGCAGAGATTCCAAACTGAATATTA
Found at i:5288279 original size:4 final size:4
Alignment explanation
Indices: 5288270--5288327 Score: 70
Period size: 4 Copynumber: 15.5 Consensus size: 4
5288260 CAACTTCAGG
* *
5288270 TACA TACA TACA T--A TACA TACA TACA T--A TATA TACA TACA TATA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
5288314 TACA TACA TACA TA
1 TACA TACA TACA TA
5288328 TATATATATT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
2 4 0.09
4 43 0.91
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (4 bp):
TACA
Found at i:5288288 original size:10 final size:10
Alignment explanation
Indices: 5288273--5288329 Score: 63
Period size: 10 Copynumber: 6.3 Consensus size: 10
5288263 CTTCAGGTAC
5288273 ATACATACAT
1 ATACATACAT
5288283 ATACATAC--
1 ATACATACAT
*
5288291 ATACATATAT
1 ATACATACAT
5288301 ATACATACAT
1 ATACATACAT
5288311 AT--ATAC--
1 ATACATACAT
5288317 ATACATACAT
1 ATACATACAT
5288327 ATA
1 ATA
5288330 TATATATTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
6 2 0.05
8 15 0.38
10 22 0.56
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.32
Consensus pattern (10 bp):
ATACATACAT
Found at i:5288289 original size:14 final size:14
Alignment explanation
Indices: 5288270--5288329 Score: 93
Period size: 14 Copynumber: 4.1 Consensus size: 14
5288260 CAACTTCAGG
5288270 TACATACATACATA
1 TACATACATACATA
5288284 TACATACATACATA
1 TACATACATACATA
*
5288298 TATATACATACATATA
1 TACATACATAC--ATA
5288314 TACATACATACATA
1 TACATACATACATA
5288328 TA
1 TA
5288330 TATATATTGA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
14 29 0.69
16 13 0.31
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (14 bp):
TACATACATACATA
Found at i:5288330 original size:18 final size:18
Alignment explanation
Indices: 5288270--5288336 Score: 93
Period size: 18 Copynumber: 3.8 Consensus size: 18
5288260 CAACTTCAGG
*
5288270 TACATACATACATATACA
1 TACATACATATATATACA
5288288 TACATACATATATATACA
1 TACATACATATATATACA
*
5288306 TACAT--ATATACATACA
1 TACATACATATATATACA
*
5288322 TACATATATATATAT
1 TACATACATATATAT
5288337 TGAAAAAAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
16 15 0.34
18 29 0.66
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.34
Consensus pattern (18 bp):
TACATACATATATATACA
Found at i:5294944 original size:21 final size:21
Alignment explanation
Indices: 5294919--5294960 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5294909 AGAATCTAAC
5294919 AATAAGATCAAAACT-GATAAT
1 AATAAGATCAAAA-TGGATAAT
*
5294940 AATAAGATGAAAATGGATAAT
1 AATAAGATCAAAATGGATAAT
5294961 TATTATGGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.57, C:0.05, G:0.14, T:0.24
Consensus pattern (21 bp):
AATAAGATCAAAATGGATAAT
Found at i:5300326 original size:31 final size:31
Alignment explanation
Indices: 5300291--5300384 Score: 179
Period size: 31 Copynumber: 3.0 Consensus size: 31
5300281 TATATGCCTT
*
5300291 TAAATGATAGAAAGCCTTTATTCATTGTCCA
1 TAAATGATAGAAAGCCTTTATTCATCGTCCA
5300322 TAAATGATAGAAAGCCTTTATTCATCGTCCA
1 TAAATGATAGAAAGCCTTTATTCATCGTCCA
5300353 TAAATGATAGAAAGCCTTTATTCATCGTCCA
1 TAAATGATAGAAAGCCTTTATTCATCGTCCA
5300384 T
1 T
5300385 CTGTTATGTG
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (31 bp):
TAAATGATAGAAAGCCTTTATTCATCGTCCA
Found at i:5312278 original size:30 final size:30
Alignment explanation
Indices: 5312217--5312284 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
5312207 GGGAGCCAAA
* * *
5312217 TGCTCCCTTGGCCTGGGGAGCACAATTTGG
1 TGCTCCCCTAGCCTGGGGAGCACAATCTGG
**
5312247 TGCTCCCCTAGCCTGGGGAGCATGATCTGG
1 TGCTCCCCTAGCCTGGGGAGCACAATCTGG
*
5312277 TGCGCCCC
1 TGCTCCCC
5312285 AGGTCAAGGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.12, C:0.32, G:0.32, T:0.24
Consensus pattern (30 bp):
TGCTCCCCTAGCCTGGGGAGCACAATCTGG
Found at i:5312553 original size:30 final size:30
Alignment explanation
Indices: 5312517--5312612 Score: 158
Period size: 30 Copynumber: 3.2 Consensus size: 30
5312507 AGTGTCTGAG
* *
5312517 TATTTTACCCATTAACTTATGTTGAATGCT
1 TATTTTACCCATTTACTTATGTTGAATGCA
*
5312547 TATTTTATCCATTTACTTATGTTGAATGCA
1 TATTTTACCCATTTACTTATGTTGAATGCA
5312577 TATTTTACCCATTTACTTATGTTGAATGCA
1 TATTTTACCCATTTACTTATGTTGAATGCA
5312607 T-TTTTA
1 TATTTTA
5312613 TAATTGACAG
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
29 5 0.08
30 57 0.92
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (30 bp):
TATTTTACCCATTTACTTATGTTGAATGCA
Found at i:5313989 original size:38 final size:38
Alignment explanation
Indices: 5313938--5314011 Score: 114
Period size: 38 Copynumber: 1.9 Consensus size: 38
5313928 CAACAATCAC
*
5313938 GTGTCAAACTAAGAA-CCTTTCAAGTATCAAACCAAGTG
1 GTGTCAAACTAAGAATCCATT-AAGTATCAAACCAAGTG
*
5313976 GTGTCAAACTAAGAATCCATTAAGTGTCAAACCAAG
1 GTGTCAAACTAAGAATCCATTAAGTATCAAACCAAG
5314012 AACCTTTGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 29 0.88
39 4 0.12
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (38 bp):
GTGTCAAACTAAGAATCCATTAAGTATCAAACCAAGTG
Found at i:5314622 original size:19 final size:19
Alignment explanation
Indices: 5314598--5314658 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 19
5314588 TGATTCCAAC
5314598 TTTTAATAAAATATTAATA
1 TTTTAATAAAATATTAATA
*
5314617 TTTTAACATATTAATATTAA-A
1 TTTT-A-ATA-AAATATTAATA
*
5314638 TTATAAATAAAATATTAATA
1 TT-TTAATAAAATATTAATA
5314658 T
1 T
5314659 CTAAATTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
19 12 0.35
20 6 0.18
21 7 0.21
22 9 0.26
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTTAATAAAATATTAATA
Found at i:5314664 original size:19 final size:20
Alignment explanation
Indices: 5314602--5314658 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
5314592 TCCAACTTTT
*
5314602 AATAAAATATTAATATTTTA
1 AATAAAATATTAATATTATA
*
5314622 ACATATTAATATTAA-ATTATA
1 A-ATA-AAATATTAATATTATA
5314643 AATAAAATATTAATAT
1 AATAAAATATTAATAT
5314659 CTAAATTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 8 0.26
20 6 0.19
21 9 0.29
22 8 0.26
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
AATAAAATATTAATATTATA
Found at i:5314789 original size:28 final size:28
Alignment explanation
Indices: 5314756--5314831 Score: 73
Period size: 27 Copynumber: 2.7 Consensus size: 28
5314746 ATTATATATA
*
5314756 TAATATTAATAATTAAATAATAAATTAT
1 TAATATTAATAATTAAATAACAAATTAT
* * * *
5314784 TAATATT-TTAAATAAATTACCAATTAT
1 TAATATTAATAATTAAATAACAAATTAT
* *
5314811 TAATATTTAAAAATAAAATAA
1 TAATA-TTAATAATTAAATAA
5314832 AAAGAAATAA
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
27 20 0.56
28 9 0.25
29 7 0.19
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (28 bp):
TAATATTAATAATTAAATAACAAATTAT
Found at i:5314841 original size:156 final size:150
Alignment explanation
Indices: 5314676--5315152 Score: 396
Period size: 156 Copynumber: 3.0 Consensus size: 150
5314666 ATAAGTTATT
* **
5314676 AATAAAATAAATTGTAAATTATTCCTATTTAAAAAATAAATTAAAAATAAATAGGCATAATATCA
1 AATAAAATAAATT-TAAATTATT--TATTTAAAAATTAAATTAAAAATAAATA-TTA-AATAT-A
* *
5314741 TTTAAATTATATATATAATATTAATAATTAAATAATAAATTATTAATATTTTAAATAAATTACCA
60 TTTAAATTATAAATATAATATTAATAATTAAATAATAAATTATTAATATTTTAAATAAATTATCA
5314806 ATTATTAATATTTAAAAATAAAATAA
125 ATTATTAATATTTAAAAATAAAATAA
* * * * *
5314832 AA-AGAAATAAA-TAAAATAATTTATCATAATAATATTTAAATTGAATA-AAATATTAAATAATA
1 AATA-AAATAAATTTAAATTATTTAT-TTAA-AA-A-TTAAATTAAAAATAAATATTAAAT-ATA
* * *
5314894 TTTAAATTGAATAAAATATTAATATTTTAA-AATATTAATGATTAAATTATTAATATTTTAAACA
60 TTTAAATT--AT-AAATA-TAATA--TTAATAAT-TAAAT-AATAAATTATTAATATTTTAAATA
*
5314958 AATAATCAATTATTAATATTTAAAAATAAAATAA
117 AATTATCAATTATTAATATTTAAAAATAAAATAA
* * * *
5314992 AATAAAAT-AATTATATCATAATAATATTT--AAATTAAA-TAAAATATTAATATTTTAAAATAT
1 AATAAAATAAATT-TA-AATTAT-TTATTTAAAAATTAAATTAAAA-A-TAA-ATATT-AAATA-
* * ** * *
5315053 TACTGACTAAATTATAAATA-AATATTAATATTTAAATGGTTAATTATTAATATTTTAAATAAAC
58 TA-T--TTAAATTATAAATATAATATTAATAATTAAATAATAAATTATTAATATTTTAAATAAAT
5315117 TATCAATTATTAATATTTAAAAATAAAATAA
120 TATCAATTATTAATATTTAAAAATAAAATAA
5315148 AATAA
1 AATAA
5315153 TTAATCATAA
Statistics
Matches: 262, Mismatches: 30, Indels: 58
0.75 0.09 0.17
Matches are distributed among these distances:
152 3 0.01
153 15 0.06
154 12 0.05
155 10 0.04
156 82 0.31
157 19 0.07
158 6 0.02
159 18 0.07
160 66 0.25
161 13 0.05
162 9 0.03
163 3 0.01
164 6 0.02
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (150 bp):
AATAAAATAAATTTAAATTATTTATTTAAAAATTAAATTAAAAATAAATATTAAATATATTTAAA
TTATAAATATAATATTAATAATTAAATAATAAATTATTAATATTTTAAATAAATTATCAATTATT
AATATTTAAAAATAAAATAA
Found at i:5314878 original size:16 final size:16
Alignment explanation
Indices: 5314859--5314907 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
5314849 AATTTATCAT
5314859 AATAATATTTAAATTG
1 AATAATATTTAAATTG
* *
5314875 AATAA-A---ATATTA
1 AATAATATTTAAATTG
5314887 AATAATATTTAAATTG
1 AATAATATTTAAATTG
5314903 AATAA
1 AATAA
5314908 AATATTAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 8
0.68 0.11 0.22
Matches are distributed among these distances:
12 9 0.36
13 1 0.04
15 1 0.04
16 14 0.56
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (16 bp):
AATAATATTTAAATTG
Found at i:5314896 original size:28 final size:28
Alignment explanation
Indices: 5314859--5314915 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
5314849 AATTTATCAT
5314859 AATAATATTTAAATTGAATAAAATATTA
1 AATAATATTTAAATTGAATAAAATATTA
5314887 AATAATATTTAAATTGAATAAAATATTA
1 AATAATATTTAAATTGAATAAAATATTA
5314915 A
1 A
5314916 TATTTTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.39
Consensus pattern (28 bp):
AATAATATTTAAATTGAATAAAATATTA
Found at i:5314924 original size:16 final size:16
Alignment explanation
Indices: 5314905--5314955 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
5314895 TTAAATTGAA
5314905 TAAAATATTAATATTT
1 TAAAATATTAATATTT
5314921 TAAAATATTAATGA--T
1 TAAAATATTAAT-ATTT
*
5314936 TAAATTATTAATATTT
1 TAAAATATTAATATTT
5314952 TAAA
1 TAAA
5314956 CAAATAATCA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
14 1 0.03
15 12 0.39
16 17 0.55
17 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
TAAAATATTAATATTT
Found at i:5314950 original size:160 final size:158
Alignment explanation
Indices: 5314749--5315149 Score: 470
Period size: 160 Copynumber: 2.5 Consensus size: 158
5314739 CATTTAAATT
* * *
5314749 ATATATATAATATTAATAA-TTAAAT-AATAAATTATTAATATTTTAAATAAATTACCAATTATT
1 ATATAAATAATATTAA-AATTTAAATGATTAAATTATTAATATTTTAAATAAATTATCAATTATT
*
5314812 AATATTTAAAAATAAAATAAAAAGAAATAAATAAAATAATT-TATCATAATAATATTTAAATTGA
65 AATATTTAAAAATAAAAT---AA-AAA-AAATAAAATAATTATATCATAATAATATTTAAATTAA
5314876 ATAAAATATTAAATAATATTT-AA-A-T-TGAATAAA
125 ATAAAATATT-AAT-AT-TTTAAATATTATGAATAAA
* * * *
5314909 ATATTAAT-ATTTTAAAATATT-AATGATTAAATTATTAATATTTTAAACAAATAATCAATTATT
1 ATATAAATAATATTAAAAT-TTAAATGATTAAATTATTAATATTTTAAATAAATTATCAATTATT
5314972 AATATTTAAAAATAAAAT----AAAATAAAATAATTATATCATAATAATATTTAAATTAAATAAA
65 AATATTTAAAAATAAAATAAAAAAAATAAAATAATTATATCATAATAATATTTAAATTAAATAAA
*
5315033 ATATTAATATTTTAAAATATTACTGACTAAA
130 ATATTAATATTTT-AAATATTA-TGAATAAA
* * * *
5315064 TTATAAATAAATATTAATATTTAAATGGTT-AATTATTAATATTTTAAATAAACTATCAATTATT
1 ATATAAAT-AATATTAAAATTTAAATGATTAAATTATTAATATTTTAAATAAATTATCAATTATT
5315128 AATATTTAAAAATAAAATAAAA
65 AATATTTAAAAATAAAATAAAA
5315150 TAATTAATCA
Statistics
Matches: 207, Mismatches: 17, Indels: 34
0.80 0.07 0.13
Matches are distributed among these distances:
149 3 0.01
150 2 0.01
151 18 0.09
152 34 0.16
153 1 0.00
155 13 0.06
156 51 0.25
157 14 0.07
158 2 0.01
159 9 0.04
160 60 0.29
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (158 bp):
ATATAAATAATATTAAAATTTAAATGATTAAATTATTAATATTTTAAATAAATTATCAATTATTA
ATATTTAAAAATAAAATAAAAAAAATAAAATAATTATATCATAATAATATTTAAATTAAATAAAA
TATTAATATTTTAAATATTATGAATAAA
Found at i:5315112 original size:41 final size:41
Alignment explanation
Indices: 5315024--5315115 Score: 98
Period size: 41 Copynumber: 2.2 Consensus size: 41
5315014 AATATTTAAA
*
5315024 TTAAATAAAATATTAATATTTTAAAATATTACTGACTAAATT
1 TTAAAT-AAATATTAATATTTTAAAATATTAATGACTAAATT
* * * *
5315066 ATAAATAAATATTAATA-TTT-AAATGGTTAATTATTAATATT
1 TTAAATAAATATTAATATTTTAAAAT-ATTAATGACTAA-ATT
5315107 TTAAATAAA
1 TTAAATAAA
5315116 CTATCAATTA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
39 4 0.10
40 11 0.26
41 22 0.52
42 5 0.12
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.43
Consensus pattern (41 bp):
TTAAATAAATATTAATATTTTAAAATATTAATGACTAAATT
Found at i:5315155 original size:27 final size:27
Alignment explanation
Indices: 5315098--5315157 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
5315088 ATGGTTAATT
* * * *
5315098 ATTAATATTTTAAATAAACTATCAATT
1 ATTAATATTTAAAATAAAATATAAATA
5315125 ATTAATATTTAAAAATAAAATA-AAATA
1 ATTAATATTT-AAAATAAAATATAAATA
5315152 ATTAAT
1 ATTAAT
5315158 CATAATAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 19 0.68
28 9 0.32
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (27 bp):
ATTAATATTTAAAATAAAATATAAATA
Found at i:5315175 original size:21 final size:22
Alignment explanation
Indices: 5315133--5315195 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 22
5315123 TTATTAATAT
**
5315133 TTAAAAATAA-AATAAAAT-AA
1 TTAAAAATAATAATATTATAAA
**
5315153 TTAATCATAATAATATT-TAAA
1 TTAAAAATAATAATATTATAAA
*
5315174 TTAAAAATATTAATATTATAAA
1 TTAAAAATAATAATATTATAAA
5315196 ATATTAATAT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
20 9 0.27
21 20 0.61
22 4 0.12
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
TTAAAAATAATAATATTATAAA
Found at i:5315198 original size:16 final size:16
Alignment explanation
Indices: 5315144--5315210 Score: 70
Period size: 16 Copynumber: 4.3 Consensus size: 16
5315134 TAAAAATAAA
*
5315144 ATAAAATAATTAATCATA
1 ATAAAAT-ATTAAT-ATT
*
5315162 ATAATAT-TTAA-ATT
1 ATAAAATATTAATATT
5315176 A-AAAATATTAATATT
1 ATAAAATATTAATATT
5315191 ATAAAATATTAATATT
1 ATAAAATATTAATATT
5315207 -TAAA
1 ATAAA
5315211 TTATCAATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
13 4 0.09
14 7 0.16
15 8 0.19
16 18 0.42
18 6 0.14
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (16 bp):
ATAAAATATTAATATT
Found at i:5315230 original size:22 final size:22
Alignment explanation
Indices: 5315179--5315241 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
5315169 TTAAATTAAA
5315179 AATA-TTAATATTATAAAATATT
1 AATATTTAA-ATTATAAAATATT
* *
5315201 AATATTTAAATTATCAATTATT
1 AATATTTAAATTATAAAATATT
* *
5315223 AATTTTTAAA-AATAAAATA
1 AATATTTAAATTATAAAATA
5315242 AAATAAAATA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 6 0.18
22 24 0.71
23 4 0.12
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
AATATTTAAATTATAAAATATT
Found at i:5315231 original size:95 final size:99
Alignment explanation
Indices: 5315112--5315317 Score: 278
Period size: 100 Copynumber: 2.1 Consensus size: 99
5315102 ATATTTTAAA
*
5315112 TAAACTATCAATTATTAATATTT-A-AAAATAAAATAAAATAATTAATCATAATAATATTTAAAT
1 TAAATTATCAATTATTAATATTTAATAAAATAAAATAAAATAATTAATCATAATAATATTTAAAT
*
5315175 T-A-AAAATATTAATATTATAAAATATTAAT-ATT
66 TAAGAAAATATAAATATTATAAAATATTAATGA-T
* *
5315207 TAAATTATCAATTATTAATTTTTAAAAATAAAATAAAATAAAATAATTGATCATAATAATATTTA
1 TAAATTATCAATTATTAATATTT---AATAAAATAAAATAAAATAATTAATCATAATAATATTTA
* *
5315272 AATTAAGTAAAATATAAATATTTTATAATATTAATGAT
63 AATTAAG-AAAATATAAATATTATAAAATATTAATGAT
5315310 TAAATTAT
1 TAAATTAT
5315318 AAATAAAATA
Statistics
Matches: 96, Mismatches: 6, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
95 21 0.22
99 1 0.01
100 39 0.41
101 1 0.01
103 33 0.34
104 1 0.01
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.41
Consensus pattern (99 bp):
TAAATTATCAATTATTAATATTTAATAAAATAAAATAAAATAATTAATCATAATAATATTTAAAT
TAAGAAAATATAAATATTATAAAATATTAATGAT
Found at i:5315294 original size:250 final size:253
Alignment explanation
Indices: 5314957--5315409 Score: 716
Period size: 251 Copynumber: 1.8 Consensus size: 253
5314947 TATTTTAAAC
*
5314957 AAATAATCAATTATTAATATTTAAAAATAAAATAAAATAAAATAATTATATCATAATAATATTTA
1 AAATAATCAATTATTAATATTTAAAAATAAAATAAAATAAAATAATTAGATCATAATAATATTTA
* *
5315022 AATTAAATAAAATATTAATATTTTAAAATATTACTGACTAAATTATAAAT-AAATAT-TAATATT
66 AATTAAATAAAATATAAATATTTTAAAATATTAATGACTAAATTATAAATAAAATATCT-ATATT
* * * *
5315085 TAAATGGTTAATTATTAATATTTTAAATAAACTATCAATTATTAATATTTAAAAATAAAAT-AAA
130 TAAATGATTAATTATTAATATTTTAAATAAACTATAAATTATTAACATATAAAAATAAAATAAAA
*
5315149 ATAATTAATCATAATAATATTTAAATTAAAAATATTAATATTATAAAATATTAATATTT
195 ATAAATAATCATAATAATATTTAAATTAAAAATATTAATATTATAAAATATTAATATTT
* *
5315208 AAATTATCAATTATTAATTTTTAAAAATAAAATAAAATAAAATAATT-GATCATAATAATATTTA
1 AAATAATCAATTATTAATATTTAAAAATAAAATAAAATAAAATAATTAGATCATAATAATATTTA
* * *
5315272 AATTAAGTAAAATATAAATATTTTATAATATTAATGATTAAATTATAAATAAAATATCTATATTT
66 AATTAAATAAAATATAAATATTTTAAAATATTAATGACTAAATTATAAATAAAATATCTATATTT
* * **
5315337 AAATGATTAATTATTAATATTTTAATTAAATTATAAATTATTAACATATAAAAATTTAATAAAAA
131 AAATGATTAATTATTAATATTTTAAATAAACTATAAATTATTAACATATAAAAATAAAATAAAAA
5315402 TAAATAAT
196 TAAATAAT
5315410 AATATAAATA
Statistics
Matches: 182, Mismatches: 17, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
250 61 0.34
251 109 0.60
252 12 0.07
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (253 bp):
AAATAATCAATTATTAATATTTAAAAATAAAATAAAATAAAATAATTAGATCATAATAATATTTA
AATTAAATAAAATATAAATATTTTAAAATATTAATGACTAAATTATAAATAAAATATCTATATTT
AAATGATTAATTATTAATATTTTAAATAAACTATAAATTATTAACATATAAAAATAAAATAAAAA
TAAATAATCATAATAATATTTAAATTAAAAATATTAATATTATAAAATATTAATATTT
Found at i:5315450 original size:15 final size:16
Alignment explanation
Indices: 5315430--5315462 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5315420 ATAAAAAATA
5315430 TTTTTA-TCTTTTTAT
1 TTTTTATTCTTTTTAT
*
5315445 TTTTTATTTTTTTTAT
1 TTTTTATTCTTTTTAT
5315461 TT
1 TT
5315463 CAAAATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTTTATTCTTTTTAT
Found at i:5320130 original size:33 final size:33
Alignment explanation
Indices: 5320088--5320219 Score: 213
Period size: 33 Copynumber: 4.2 Consensus size: 33
5320078 AAGTCTGCTA
5320088 CTTCTTCTCCATTTGCAGCAGACGTTGCTCCTC
1 CTTCTTCTCCATTTGCAGCAGACGTTGCTCCTC
5320121 CTTCTTCTCCATTTGCAGCAGACGTTGCTCCTC
1 CTTCTTCTCCATTTGCAGCAGACGTTGCTCCTC
5320154 CTTCTTCTCCATTTGCAGC--A----GCTCCTC
1 CTTCTTCTCCATTTGCAGCAGACGTTGCTCCTC
5320181 CTTCTTCTCCATTTGCAGCAGACGTTGCTCCTC
1 CTTCTTCTCCATTTGCAGCAGACGTTGCTCCTC
*
5320214 TTTCTT
1 CTTCTT
5320220 ATGCTCCTGT
Statistics
Matches: 92, Mismatches: 1, Indels: 12
0.88 0.01 0.11
Matches are distributed among these distances:
27 26 0.28
29 1 0.01
31 1 0.01
33 64 0.70
ACGTcount: A:0.11, C:0.36, G:0.14, T:0.39
Consensus pattern (33 bp):
CTTCTTCTCCATTTGCAGCAGACGTTGCTCCTC
Found at i:5320182 original size:27 final size:27
Alignment explanation
Indices: 5320114--5320201 Score: 122
Period size: 27 Copynumber: 3.0 Consensus size: 27
5320104 AGCAGACGTT
5320114 GCTCCTCCTTCTTCTCCATTTGCAGCAGA
1 GCTCCTCCTTCTTCTCCATTTGCAGC--A
5320143 CGTTGCTCCTCCTTCTTCTCCATTTGCAGCA
1 ----GCTCCTCCTTCTTCTCCATTTGCAGCA
5320174 GCTCCTCCTTCTTCTCCATTTGCAGCA
1 GCTCCTCCTTCTTCTCCATTTGCAGCA
5320201 G
1 G
5320202 ACGTTGCTCC
Statistics
Matches: 55, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
27 28 0.51
31 1 0.02
33 26 0.47
ACGTcount: A:0.11, C:0.39, G:0.14, T:0.36
Consensus pattern (27 bp):
GCTCCTCCTTCTTCTCCATTTGCAGCA
Found at i:5324281 original size:123 final size:124
Alignment explanation
Indices: 5324039--5324270 Score: 299
Period size: 123 Copynumber: 1.9 Consensus size: 124
5324029 GAAGCGTAGA
* * * * *
5324039 ATCCATCTCTGGTTCTTGAAATGATTTTTCTCCTCCATTACTTTCATCATTTCTTCTTTTGTAGA
1 ATCCATCTATGGTTCTTGAAATAATTTTTCTCCTCAATTACTTTAATCATTTCTTCTTTTATAGA
** *
5324104 GTGTGAAAAATCAAGAAGAAATCTTGAGCATTTCAACAACAAATCTAGAGTTTTAGCTT
66 GTGCCAAAAATCAAGAAGAAATCTTGAGCATTTCAACAAAAAATCTAGAGTTTTAGCTT
* * * *
5324163 ATCC-TCTATGGTTTTTGAAATAATTTTTTTCCTCAATTAGTTTAATCATTTCTTCTTTTATGGA
1 ATCCATCTATGGTTCTTGAAATAATTTTTCTCCTCAATTACTTTAATCATTTCTTCTTTTATAGA
* *
5324227 GTGCCAAAAGTC-TGCAAGAAAT-TTAGAGCATTTCAACAAAAAAT
66 GTGCCAAAAATCAAG-AAGAAATCTT-GAGCATTTCAACAAAAAAT
5324271 TTGGATTTTT
Statistics
Matches: 92, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
122 3 0.03
123 85 0.92
124 4 0.04
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (124 bp):
ATCCATCTATGGTTCTTGAAATAATTTTTCTCCTCAATTACTTTAATCATTTCTTCTTTTATAGA
GTGCCAAAAATCAAGAAGAAATCTTGAGCATTTCAACAAAAAATCTAGAGTTTTAGCTT
Found at i:5334190 original size:10 final size:10
Alignment explanation
Indices: 5334151--5334192 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
5334141 CAAACCAACA
5334151 ATACATATAT
1 ATACATATAT
*
5334161 ATATATATAT
1 ATACATATAT
*
5334171 ATATATATAT
1 ATACATATAT
*
5334181 ATACACATAT
1 ATACATATAT
5334191 AT
1 AT
5334193 TTATCTATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (10 bp):
ATACATATAT
Found at i:5334192 original size:2 final size:2
Alignment explanation
Indices: 5334155--5334183 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5334145 CCAACAATAC
5334155 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5334184 CACATATATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5339076 original size:14 final size:13
Alignment explanation
Indices: 5339049--5339097 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
5339039 GTTTAATTGA
*
5339049 TATTCTTATTATT
1 TATTTTTATTATT
*
5339062 TATATTTTGTTATT
1 TAT-TTTTATTATT
5339076 TATTATTTATTATT
1 TATT-TTTATTATT
5339090 TATGTTTT
1 TAT-TTTT
5339098 TCCCAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 4 0.13
14 25 0.83
15 1 0.03
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.71
Consensus pattern (13 bp):
TATTTTTATTATT
Found at i:5339081 original size:7 final size:7
Alignment explanation
Indices: 5339054--5339092 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
5339044 ATTGATATTC
5339054 TTATTAT
1 TTATTAT
5339061 TTA-TATT
1 TTATTA-T
*
5339068 TTGTTAT
1 TTATTAT
5339075 TTATTAT
1 TTATTAT
5339082 TTATTAT
1 TTATTAT
5339089 TTAT
1 TTAT
5339093 GTTTTTCCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 2 0.07
7 24 0.86
8 2 0.07
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (7 bp):
TTATTAT
Found at i:5343213 original size:6 final size:6
Alignment explanation
Indices: 5343202--5343244 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
5343192 AACGTTCTAG
* * *
5343202 AGCGCC AGCGCC AGCGCC AGCACC AGCACC AGCACC AGCGCC A
1 AGCGCC AGCGCC AGCGCC AGCGCC AGCGCC AGCGCC AGCGCC A
5343245 TTTCAGCAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.26, C:0.49, G:0.26, T:0.00
Consensus pattern (6 bp):
AGCGCC
Found at i:5343219 original size:12 final size:12
Alignment explanation
Indices: 5343202--5343244 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
5343192 AACGTTCTAG
*
5343202 AGCGCCAGCGCC
1 AGCGCCAGCACC
5343214 AGCGCCAGCACC
1 AGCGCCAGCACC
*
5343226 AGCACCAGCACC
1 AGCGCCAGCACC
5343238 AGCGCCA
1 AGCGCCA
5343245 TTTCAGCAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.26, C:0.49, G:0.26, T:0.00
Consensus pattern (12 bp):
AGCGCCAGCACC
Found at i:5346316 original size:21 final size:21
Alignment explanation
Indices: 5346290--5346334 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
5346280 CTAGTGATCA
5346290 GACTTGGATGTTAGCATAATT
1 GACTTGGATGTTAGCATAATT
*
5346311 GACTTGGATGTTAGCGTAATT
1 GACTTGGATGTTAGCATAATT
5346332 GAC
1 GAC
5346335 CTGAACTTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.11, G:0.27, T:0.36
Consensus pattern (21 bp):
GACTTGGATGTTAGCATAATT
Found at i:5346503 original size:18 final size:17
Alignment explanation
Indices: 5346480--5346525 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
5346470 GTCCCATTTA
5346480 ATTTATTTTT-ATTGTCCT
1 ATTTATTTTTAATT-T-CT
5346498 ATTTATTTTTGAATTTCT
1 ATTTATTTTT-AATTTCT
5346516 ATTTATTTTT
1 ATTTATTTTT
5346526 CTATAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 22 0.85
19 1 0.04
20 3 0.12
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.70
Consensus pattern (17 bp):
ATTTATTTTTAATTTCT
Found at i:5346833 original size:6 final size:6
Alignment explanation
Indices: 5346822--5346848 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5346812 TAATGACACG
5346822 TCCACT TCCACT TCCACT TCCACT TCC
1 TCCACT TCCACT TCCACT TCCACT TCC
5346849 CGGCGAGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.52, G:0.00, T:0.33
Consensus pattern (6 bp):
TCCACT
Found at i:5357159 original size:27 final size:27
Alignment explanation
Indices: 5357129--5357215 Score: 81
Period size: 27 Copynumber: 3.2 Consensus size: 27
5357119 AACAGTCAGG
*
5357129 AAGATAATGAAAGGGAAGATAGTGAGA
1 AAGATAACGAAAGGGAAGATAGTGAGA
* *
5357156 AAGATAACGAAATGGAAGGTAGTGATG-
1 AAGATAACGAAAGGGAAGATAGTGA-GA
* *
5357183 AAGAAAACG-AAGAGGAGGATAGTGATG-
1 AAGATAACGAAAG-GGAAGATAGTGA-GA
5357210 AAGATA
1 AAGATA
5357216 TTGAAGAAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
26 2 0.04
27 47 0.94
28 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.33, T:0.15
Consensus pattern (27 bp):
AAGATAACGAAAGGGAAGATAGTGAGA
Found at i:5358124 original size:70 final size:69
Alignment explanation
Indices: 5357996--5358136 Score: 273
Period size: 70 Copynumber: 2.0 Consensus size: 69
5357986 AAAATCTTCT
5357996 ACCAAGTAACCAAAACAGAAAAACCCAAGGGTGAAATCTACCCTTATAGCAGACAGCCTGAAGCA
1 ACCAAGTAACCAAAACAGAAAAACCCAAGGGTGAAATCTACCCTTATAGCAGACAGCCTGAAGCA
5358061 CATA
66 CATA
5358065 ACCAAGTAACCAAAACAGAAAAACCCAAGGGGTGAAATCTACCCTTATAGCAGACAGCCTGAAGC
1 ACCAAGTAACCAAAACAGAAAAACCCAA-GGGTGAAATCTACCCTTATAGCAGACAGCCTGAAGC
5358130 ACATA
65 ACATA
5358135 AC
1 AC
5358137 AATAGTTTCT
Statistics
Matches: 71, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
69 28 0.39
70 43 0.61
ACGTcount: A:0.45, C:0.26, G:0.16, T:0.13
Consensus pattern (69 bp):
ACCAAGTAACCAAAACAGAAAAACCCAAGGGTGAAATCTACCCTTATAGCAGACAGCCTGAAGCA
CATA
Found at i:5363087 original size:2 final size:2
Alignment explanation
Indices: 5363080--5363107 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5363070 TTCTATATTT
5363080 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
5363108 AGAGAGAGAG
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:5368876 original size:33 final size:33
Alignment explanation
Indices: 5368827--5368901 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 33
5368817 AATAAAGTGT
* *
5368827 ATAATATA-A-AAAATTAT-ATCAAGAAATGAAA
1 ATAATATATATAAAATTATAAT-AAAAAATAAAA
*
5368858 ATAATATATATAAGATTATAATAAAAAATAAAA
1 ATAATATATATAAAATTATAATAAAAAATAAAA
*
5368891 ATAAAATATAT
1 ATAATATATAT
5368902 GGTATTAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
31 8 0.22
32 1 0.03
33 26 0.70
34 2 0.05
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.29
Consensus pattern (33 bp):
ATAATATATATAAAATTATAATAAAAAATAAAA
Found at i:5376546 original size:14 final size:14
Alignment explanation
Indices: 5376524--5376570 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
5376514 TTTTTTAAAA
5376524 AATAAAAAATATAT
1 AATAAAAAATATAT
5376538 AATATAAAAA-ATTAT
1 AATA-AAAAATA-TAT
*
5376553 ATTAAAAAATATAT
1 AATAAAAAATATAT
5376567 AATA
1 AATA
5376571 TGTATAGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
AATAAAAAATATAT
Found at i:5377054 original size:57 final size:57
Alignment explanation
Indices: 5376954--5377061 Score: 162
Period size: 57 Copynumber: 1.9 Consensus size: 57
5376944 TTTTCTTCAT
* * *
5376954 TTTTGTTTTAGTTTATTCATTTATATCATGCTCACATTTGACATTCATATTTTATTG
1 TTTTGTTTTAGTTTATTCATTCATATCATGCTCACATTAGACATACATATTTTATTG
* **
5377011 TTTTGTTTTAGTTTATTCATTCATATCATGTTCTTATTAGACATACATATT
1 TTTTGTTTTAGTTTATTCATTCATATCATGCTCACATTAGACATACATATT
5377062 GTGTGTATGC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 45 1.00
ACGTcount: A:0.24, C:0.12, G:0.08, T:0.56
Consensus pattern (57 bp):
TTTTGTTTTAGTTTATTCATTCATATCATGCTCACATTAGACATACATATTTTATTG
Found at i:5382334 original size:18 final size:18
Alignment explanation
Indices: 5382311--5382349 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5382301 CTCAAGAAGC
*
5382311 CGTAGCAGAAGCCGTAGT
1 CGTAGCAGAAGCCGCAGT
* *
5382329 CGTAGCCGCAGCCGCAGT
1 CGTAGCAGAAGCCGCAGT
5382347 CGT
1 CGT
5382350 GGACGGAGCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.31, G:0.33, T:0.15
Consensus pattern (18 bp):
CGTAGCAGAAGCCGCAGT
Found at i:5403472 original size:124 final size:125
Alignment explanation
Indices: 5403295--5403545 Score: 441
Period size: 124 Copynumber: 2.0 Consensus size: 125
5403285 TTGGCTTCCT
*
5403295 CAGTGCCACAACTTAATGGCTTTGTACGTAATGTGCGAACGTGACATGTCGGGATGGAGATGTGT
1 CAGTGCCACAACTTAATGGCTTTGTACGTAATGTGCGAACGTGACATGTCGGGATGGAGATGTCT
5403360 CCTTTTCATTATTAATACAAAATACAAAA-GTTTTCCTCTTTGTCAGAGGTACCCTTTGA
66 CCTTTTCATTATTAATACAAAATACAAAATGTTTTCCTCTTTGTCAGAGGTACCCTTTGA
* * *
5403419 CAGTGCCACAACTTTATGGCTTTGTACGTAATTTGCGAACGTGATATGTCGGGATGGAGATGTCT
1 CAGTGCCACAACTTAATGGCTTTGTACGTAATGTGCGAACGTGACATGTCGGGATGGAGATGTCT
* *
5403484 TCTTTTCATTATTAATACAAAATACAAAATTTTTTCCTCTTTGTCAGAGGTACCCTTTGA
66 CCTTTTCATTATTAATACAAAATACAAAATGTTTTCCTCTTTGTCAGAGGTACCCTTTGA
5403544 CA
1 CA
5403546 CAGAACGTGA
Statistics
Matches: 120, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
124 89 0.74
125 31 0.26
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (125 bp):
CAGTGCCACAACTTAATGGCTTTGTACGTAATGTGCGAACGTGACATGTCGGGATGGAGATGTCT
CCTTTTCATTATTAATACAAAATACAAAATGTTTTCCTCTTTGTCAGAGGTACCCTTTGA
Found at i:5403663 original size:14 final size:14
Alignment explanation
Indices: 5403631--5403667 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
5403621 TTATATATTT
5403631 TTAAATAATTTTTA
1 TTAAATAATTTTTA
*
5403645 -AAAATAATTTTTA
1 TTAAATAATTTTTA
5403658 TTAAATAATT
1 TTAAATAATT
5403668 AATATAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TTAAATAATTTTTA
Found at i:5403737 original size:9 final size:9
Alignment explanation
Indices: 5403717--5403754 Score: 69
Period size: 9 Copynumber: 4.3 Consensus size: 9
5403707 TTCAATATTA
5403717 TTTAAA-TT
1 TTTAAATTT
5403725 TTTAAATTT
1 TTTAAATTT
5403734 TTTAAATTT
1 TTTAAATTT
5403743 TTTAAATTT
1 TTTAAATTT
5403752 TTT
1 TTT
5403755 CATCTATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 6 0.21
9 23 0.79
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTAAATTT
Found at i:5404660 original size:18 final size:18
Alignment explanation
Indices: 5404615--5404671 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
5404605 TTTTTTATTT
*
5404615 TTTTATTTATATATTATAA
1 TTTT-TTTATTTATTATAA
** *
5404634 AATTATTATTTATTATAA
1 TTTTTTTATTTATTATAA
5404652 TTTTTTTA-TTATTAATAA
1 TTTTTTTATTTATT-ATAA
5404670 TT
1 TT
5404672 AAATTTAATA
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
17 5 0.17
18 23 0.77
19 2 0.07
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTTTTATTTATTATAA
Found at i:5413600 original size:15 final size:15
Alignment explanation
Indices: 5413577--5413609 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
5413567 GATCAACTGA
*
5413577 TGATGATGATCATCG
1 TGATCATGATCATCG
5413592 TGATCATGATCATCG
1 TGATCATGATCATCG
5413607 TGA
1 TGA
5413610 CCACCAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.33
Consensus pattern (15 bp):
TGATCATGATCATCG
Found at i:5415649 original size:14 final size:15
Alignment explanation
Indices: 5415626--5415689 Score: 62
Period size: 14 Copynumber: 4.3 Consensus size: 15
5415616 TATTATATAA
*
5415626 AATT-ATTTTTTATT
1 AATTAATTTTTTAAT
5415640 AA-TAATTTTTTAAT
1 AATTAATTTTTTAAT
*
5415654 AATTAATTAAATTTAAT
1 AATTAATT--TTTTAAT
5415671 ATATTAATTTTTTAA-
1 A-ATTAATTTTTTAAT
5415686 AATT
1 AATT
5415690 TTTAATCTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
13 1 0.02
14 16 0.38
15 6 0.14
16 5 0.12
17 7 0.17
18 7 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
AATTAATTTTTTAAT
Found at i:5415755 original size:29 final size:29
Alignment explanation
Indices: 5415713--5415770 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
5415703 CATCCATTTT
5415713 TAATACCTCAACAAAAGTTAGCTAACTTC
1 TAATACCTCAACAAAAGTTAGCTAACTTC
*
5415742 TAATACCTCAACAAAAGTTAGCTCACTTC
1 TAATACCTCAACAAAAGTTAGCTAACTTC
5415771 GTCACAGATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.40, C:0.26, G:0.07, T:0.28
Consensus pattern (29 bp):
TAATACCTCAACAAAAGTTAGCTAACTTC
Found at i:5420034 original size:15 final size:16
Alignment explanation
Indices: 5420009--5420043 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
5419999 GTATTTTATG
5420009 ATAAGTTTTTTAAAAA
1 ATAAGTTTTTTAAAAA
*
5420025 ATAA-TTTTTTAAAGA
1 ATAAGTTTTTTAAAAA
5420040 ATAA
1 ATAA
5420044 AATTTAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (16 bp):
ATAAGTTTTTTAAAAA
Found at i:5423849 original size:24 final size:23
Alignment explanation
Indices: 5423788--5423850 Score: 108
Period size: 23 Copynumber: 2.7 Consensus size: 23
5423778 CGGAGGAAAA
5423788 GAAAGATTTGGTGACTTTCTGCT
1 GAAAGATTTGGTGACTTTCTGCT
5423811 GAAAGATTTGGTGACTTTCTGCT
1 GAAAGATTTGGTGACTTTCTGCT
*
5423834 GAAAGTCTTTGGTGACT
1 GAAAG-ATTTGGTGACT
5423851 ATTTTCTAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
23 28 0.74
24 10 0.26
ACGTcount: A:0.22, C:0.13, G:0.27, T:0.38
Consensus pattern (23 bp):
GAAAGATTTGGTGACTTTCTGCT
Found at i:5440867 original size:20 final size:20
Alignment explanation
Indices: 5440842--5440890 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
5440832 TTAAATCGCA
5440842 CGGTGATCATAAATTCGGTT
1 CGGTGATCATAAATTCGGTT
5440862 CGGTGATCATAAATTCGGTT
1 CGGTGATCATAAATTCGGTT
*
5440882 CAGTGATCA
1 CGGTGATCA
5440891 GAACCGTTGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (20 bp):
CGGTGATCATAAATTCGGTT
Found at i:5451821 original size:60 final size:58
Alignment explanation
Indices: 5451635--5451825 Score: 163
Period size: 60 Copynumber: 3.2 Consensus size: 58
5451625 ACTTCCGGAG
* * * * ** * * **
5451635 CCACCAAATATAAACCAAGGCTTTAGGTCCCCATTTACCTTCTCATAGAAACTCCTCATG
1 CCACCAAATATAAATCAAGACTTTAGGT--CCTTTTACCTACTTGTGGAAACTCCCCAAA
* * *
5451695 CCTCCAAATATAAATCAAGACTTTAGGTCCTTTTACCTACTTGTGGGAACTCTCCAAA
1 CCACCAAATATAAATCAAGACTTTAGGTCCTTTTACCTACTTGTGGAAACTCCCCAAA
*
5451753 CCACCAAATATAAATCATA-ACTTT-GGATCCCCTTTTACCTA-TTCGTGGAAACTCCCCACA
1 CCACCAAATATAAATCA-AGACTTTAGG-T--CCTTTTACCTACTT-GTGGAAACTCCCCAAA
*
5451813 CCATCAAATATAA
1 CCACCAAATATAA
5451826 GTCGGAGCTT
Statistics
Matches: 108, Mismatches: 18, Indels: 10
0.79 0.13 0.07
Matches are distributed among these distances:
57 2 0.02
58 42 0.39
59 3 0.03
60 61 0.56
ACGTcount: A:0.33, C:0.29, G:0.09, T:0.28
Consensus pattern (58 bp):
CCACCAAATATAAATCAAGACTTTAGGTCCTTTTACCTACTTGTGGAAACTCCCCAAA
Found at i:5456858 original size:23 final size:24
Alignment explanation
Indices: 5456804--5456859 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
5456794 CTGAACCCAT
*
5456804 ACTTTAATTTTTATATGGGCTGGC
1 ACTTTAATTTTTATAAGGGCTGGC
* * *
5456828 ACTCTAATTTTTATAAGGGTTTGC
1 ACTTTAATTTTTATAAGGGCTGGC
5456852 A-TTTAATT
1 ACTTTAATT
5456860 GGCCCAATCA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.25, C:0.11, G:0.16, T:0.48
Consensus pattern (24 bp):
ACTTTAATTTTTATAAGGGCTGGC
Found at i:5461910 original size:15 final size:15
Alignment explanation
Indices: 5461890--5461930 Score: 82
Period size: 15 Copynumber: 2.7 Consensus size: 15
5461880 TAATATGGGA
5461890 GGCATGGGTGATGGT
1 GGCATGGGTGATGGT
5461905 GGCATGGGTGATGGT
1 GGCATGGGTGATGGT
5461920 GGCATGGGTGA
1 GGCATGGGTGA
5461931 CTTTGAAGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.15, C:0.07, G:0.54, T:0.24
Consensus pattern (15 bp):
GGCATGGGTGATGGT
Found at i:5465637 original size:4 final size:4
Alignment explanation
Indices: 5465628--5465655 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
5465618 CTCTTCTCTC
5465628 CTAT CTAT CTAT CTAT CTAT CTAT CTAT
1 CTAT CTAT CTAT CTAT CTAT CTAT CTAT
5465656 TCAGACACCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (4 bp):
CTAT
Found at i:5467826 original size:14 final size:14
Alignment explanation
Indices: 5467807--5467836 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5467797 TTTTCCAGCT
5467807 AGCAACAAGTTTGG
1 AGCAACAAGTTTGG
5467821 AGCAACAAGTTTGG
1 AGCAACAAGTTTGG
5467835 AG
1 AG
5467837 TTGTCGGTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.13, G:0.30, T:0.20
Consensus pattern (14 bp):
AGCAACAAGTTTGG
Found at i:5470885 original size:17 final size:17
Alignment explanation
Indices: 5470863--5470925 Score: 72
Period size: 17 Copynumber: 3.5 Consensus size: 17
5470853 ATAATATATA
5470863 TAATTTTTAAATTTATT
1 TAATTTTTAAATTTATT
5470880 TAATTTATTTTTAAATTTATT
1 T-A---ATTTTTAAATTTATT
*
5470901 TAATTTTTAATTTTATT
1 TAATTTTTAAATTTATT
*
5470918 TTATTTTT
1 TAATTTTT
5470926 TATTTTAAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
17 22 0.55
18 1 0.03
20 1 0.03
21 16 0.40
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TAATTTTTAAATTTATT
Found at i:5470891 original size:21 final size:21
Alignment explanation
Indices: 5470865--5470906 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
5470855 AATATATATA
5470865 ATTTTTAAATTTATTTAATTT
1 ATTTTTAAATTTATTTAATTT
5470886 ATTTTTAAATTTATTTAATTT
1 ATTTTTAAATTTATTTAATTT
5470907 TTAATTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
ATTTTTAAATTTATTTAATTT
Found at i:5470896 original size:12 final size:12
Alignment explanation
Indices: 5470865--5470901 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
5470855 AATATATATA
5470865 ATTTTTAAATTT
1 ATTTTTAAATTT
5470877 A--TTT-AATTT
1 ATTTTTAAATTT
5470886 ATTTTTAAATTT
1 ATTTTTAAATTT
5470898 ATTT
1 ATTT
5470902 AATTTTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
9 6 0.27
10 3 0.14
11 3 0.14
12 10 0.45
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATTTTTAAATTT
Found at i:5470930 original size:17 final size:17
Alignment explanation
Indices: 5470878--5470932 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
5470868 TTTAAATTTA
* *
5470878 TTTAATTTATTTTTAAA
1 TTTATTTTATTTTTAAT
*
5470895 TTTATTTAATTTTTAAT
1 TTTATTTTATTTTTAAT
*
5470912 TTTATTTTATTTTTTAT
1 TTTATTTTATTTTTAAT
5470929 TTTA
1 TTTA
5470933 AACTATAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTATTTTATTTTTAAT
Found at i:5471091 original size:21 final size:20
Alignment explanation
Indices: 5471052--5471091 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
5471042 TTTTAAATTT
* *
5471052 ATTTATTTCATTTTTATAAA
1 ATTTATTTAATTCTTATAAA
5471072 ATTTATATTAATTCTTATAA
1 ATTTAT-TTAATTCTTATAA
5471092 CTTTACGTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTATTTAATTCTTATAAA
Found at i:5471500 original size:24 final size:24
Alignment explanation
Indices: 5471446--5471501 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
5471436 TTTAGTCCGA
*
5471446 TAATATAAATTTAAATATTTATTTT
1 TAAT-TAAAATTAAATATTTATTTT
* *
5471471 TCATTAAAATTAAAT-TTTTTTATT
1 TAATTAAAATTAAATATTTATT-TT
5471495 TAATTAA
1 TAATTAA
5471502 CTTGTTATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 5 0.19
24 18 0.69
25 3 0.12
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
TAATTAAAATTAAATATTTATTTT
Found at i:5471838 original size:500 final size:495
Alignment explanation
Indices: 5471139--5472067 Score: 1215
Period size: 500 Copynumber: 1.9 Consensus size: 495
5471129 TAATAATTTT
* * * *
5471139 TTTATTATTTTTTATTTAAAATAAATATTTAAATATTATTACATACTTTTAACCTGATAATATAA
1 TTTATTATTTTTTATTTAAAATAAATATATAAATATTATTAAACACTTTTAACCTGAAAATATAA
* *
5471204 ATATAAATACTTATTTTTCATTAAAATTATACTTTTTTACTTAATTAACTTATTACATTAACTCT
66 ATATAAATACTTATTTTTCACTAAAATTAGACTTTTTTACTTAATTAACTTATTACATTAACTCT
* **
5471269 CTCACATGTATATTAAGATTTAAAATTTTGTTATTTTACCTTTATAAGTTTTTACGTCAACTCTT
131 CTCACATGTATATTAAGATTTAAAATTTAGTTATTCCACCTTTATAAGTTTTTACGTCAACTCTT
* * *
5471334 ACAGTTTTACGTCAAAACTTTTTTATGTCAATTTTAAATGATAATTATTTTTATCT-TTATTATT
196 ACAGTTTTACGTCAAAACTTATCTATATCAATTTTAAATGATAATTA-TTTTAT-TATTATTATT
* * * * * *
5471398 ATT-TATTAAAAGTAAAAATTTGA-ATATCATTACATATTTTTAGTCCGATAATATAAATTTAAA
259 ATTAT-TTAAAAATAAAAATTT-ATATATCATTAAATAATTTTAATCCAAAAATATAAATTTAAA
* *
5471461 TATTTATTTTTCATTAAAATTAAATTTTTTTATTTAATTAACTTGTTATGTTAACTTTCACACGT
322 TATTTATTTTTCATTAAAATT-AA--TTTTT-TTTAATTAACTTGTTACGTTAACTTTCACACAT
* ** *
5471526 TTATTTTAAGATTTAAAATTTAGTTATTCTACTTTTAAAAGTTTTTACGTCAATTCTCATAATTT
383 TCACATTAAGATTTAAAATTTAGTTATTCCACTTTTAAAAGTTTTTACGTCAATTCTCATAATTT
5471591 AATATCAAAGCTTTTTTATGTTAATTTTAAACTATAATTATTTTTATC
448 AATATCAAAGCTTTTTTATGTTAATTTTAAACTATAATTATTTTTATC
* *
5471639 TTTATTA-TTTTTATTTAAAAATTAAA-ATATATATATTGTTAAACACTTTTAATCC-GAAAATA
1 TTTATTATTTTTTATTT-AAAA-TAAATATATAAATATTATTAAACACTTTTAA-CCTGAAAATA
* * * **
5471701 TAAATATAAATATTTATTTTTCACTAAAATTAGATTTTTTTACTTAATTGACTTATTATGTTAAC
63 TAAATATAAATACTTATTTTTCACTAAAATTAGACTTTTTTACTTAATTAACTTATTACATTAAC
* * * * * *
5471766 T-TTTATACATTTGTATTAAGATTTAAAATTTAGTTATTCCACTTTTATAAGTTTTTACGTCAAT
128 TCTCT-CACATGTATATTAAGATTTAAAATTTAGTTATTCCACCTTTATAAGTTTTTACGTCAAC
* * ** * *
5471830 TGTTACAGTTTTACGTTAAGGCTTATCTATATCAATTTTGAATTATAATTATTTTATTATTATTA
192 TCTTACAGTTTTACGTCAAAACTTATCTATATCAATTTTAAATGATAATTATTTTATTATTATTA
* * ** **
5471895 TTATTATTTAAAAATTAAAATTTATATGTTGTTAAATAATTTTAATTTAAAAATATAAATTTAAA
257 TTATTATTTAAAAATAAAAATTTATATATCATTAAATAATTTTAATCCAAAAATATAAATTTAAA
* *
5471960 TATTTATTTTTTATTAAAATTAATTTTTTTTAATTAACTTGTTACGTTAACTTTTACACATTCAC
322 TATTTATTTTTCATTAAAATTAATTTTTTTTAATTAACTTGTTACGTTAACTTTCACACATTCAC
* * *
5472025 ATTACGATTTTAAATTTAGTTATTCCACTTTTATAAGTTTTTA
387 ATTAAGATTTAAAATTTAGTTATTCCACTTTTAAAAGTTTTTA
5472068 TGTCGTTTTT
Statistics
Matches: 368, Mismatches: 54, Indels: 19
0.83 0.12 0.04
Matches are distributed among these distances:
495 70 0.19
496 5 0.01
498 4 0.01
499 92 0.25
500 191 0.52
501 6 0.02
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.51
Consensus pattern (495 bp):
TTTATTATTTTTTATTTAAAATAAATATATAAATATTATTAAACACTTTTAACCTGAAAATATAA
ATATAAATACTTATTTTTCACTAAAATTAGACTTTTTTACTTAATTAACTTATTACATTAACTCT
CTCACATGTATATTAAGATTTAAAATTTAGTTATTCCACCTTTATAAGTTTTTACGTCAACTCTT
ACAGTTTTACGTCAAAACTTATCTATATCAATTTTAAATGATAATTATTTTATTATTATTATTAT
TATTTAAAAATAAAAATTTATATATCATTAAATAATTTTAATCCAAAAATATAAATTTAAATATT
TATTTTTCATTAAAATTAATTTTTTTTAATTAACTTGTTACGTTAACTTTCACACATTCACATTA
AGATTTAAAATTTAGTTATTCCACTTTTAAAAGTTTTTACGTCAATTCTCATAATTTAATATCAA
AGCTTTTTTATGTTAATTTTAAACTATAATTATTTTTATC
Found at i:5471990 original size:249 final size:249
Alignment explanation
Indices: 5471006--5472067 Score: 1084
Period size: 250 Copynumber: 4.3 Consensus size: 249
5470996 TATTATTATC
* * * * * * * *
5471006 ACTTATTACATTAACTCTCACACATTTATGTTAAGATTTTAAATTTATTTATTTCATTTTTATAA
1 ACTTATTACGTTAACTTTTACACATTTATATTAAGATTTAAAATTTAGTTATTCCACTTTTAT-A
* * * * ** ** *
5471071 AATTTATA--TTAATTCTTATAACTTTACGTC-AAGTCTTTTCAATAAT-AACTTTTAAA-TATA
65 AGTTTTTACGTCAATTCTTACAGTTTTACGTCAAAG-CTTTTTTAT-GTCAA-TTTTAAATTATA
* * *
5471131 ATAATTTTT-T-TATTATT-TT-TTATTT-AAAA-TAAATATTTAAATATTATTACATACTTTTA
127 ATTATTTTTATCT-TTATTATTATTATTTAAAAATTAAA-ATTTATATATTATTAAATACTTTTA
* * *
5471190 A-CCTGATAATATAAATATAAATACTTATTTTTCATTAAAATTATACTTTTTTACTTAATTA
190 ATCC-GAAAATATAAATATAAATATTTATTTTTCATTAAAATTA-ATTTTTTTACTTAATTA
* * * * ** *
5471251 ACTTATTACATTAACTCTCT-CACATGTATATTAAGATTTAAAATTTTGTTATTTTACCTTTATA
1 ACTTATTACGTTAACT-TTTACACATTTATATTAAGATTTAAAATTTAGTTATTCCACTTTTATA
* * *
5471315 AGTTTTTACGTCAACTCTTACAGTTTTACGTCAAAACTTTTTTATGTCAATTTTAAATGATAATT
65 AGTTTTTACGTCAATTCTTACAGTTTTACGTCAAAGCTTTTTTATGTCAATTTTAAATTATAATT
* * * * * *
5471380 ATTTTTATCTTTATTATTATT-TATTAAAAGTAAAAATTTGA-ATATCATTACATATTTTTAGTC
130 ATTTTTATCTTTATTATTATTAT-TTAAAAATTAAAATTT-ATATATTATTAAATACTTTTAATC
* * *
5471443 CGATAATATAAATTTAAATATTTATTTTTCATTAAAATTAAATTTTTTTATTTAATTA
193 CGAAAATATAAATATAAATATTTATTTTTCATTAAAATT-AATTTTTTTACTTAATTA
* * * * * * *
5471501 ACTTGTTATGTTAACTTTCACACGTTTATTTTAAGATTTAAAATTTAGTTATTCTACTTTTAAAA
1 ACTTATTACGTTAACTTTTACACATTTATATTAAGATTTAAAATTTAGTTATTCCACTTTTATAA
* * * * ** * *
5471566 GTTTTTACGTCAATTCTCATAATTTAATATCAAAGCTTTTTTATGTTAATTTTAAACTATAATTA
66 GTTTTTACGTCAATTCTTACAGTTTTACGTCAAAGCTTTTTTATGTCAATTTTAAATTATAATTA
* * * *
5471631 TTTTTATCTTTATTATTTTTATTTAAAAATTAAAATATATATATTGTTAAACACTTTTAATCCGA
131 TTTTTATCTTTATTATTATTATTTAAAAATTAAAATTTATATATTATTAAATACTTTTAATCCGA
* *
5471696 AAATATAAATATAAATATTTATTTTTCACTAAAATTAGATTTTTTTACTTAATTG
196 AAATATAAATATAAATATTTATTTTTCATTAAAATTA-ATTTTTTTACTTAATTA
* * *
5471751 ACTTATTATGTTAACTTTTATACATTTGTATTAAGATTTAAAATTTAGTTATTCCACTTTTATAA
1 ACTTATTACGTTAACTTTTACACATTTATATTAAGATTTAAAATTTAGTTATTCCACTTTTATAA
* * * * * * *
5471816 GTTTTTACGTCAATTGTTACAGTTTTACGTTAAGGCTTATCTATATCAATTTTGAATTATAATTA
66 GTTTTTACGTCAATTCTTACAGTTTTACGTCAAAGCTTTTTTATGTCAATTTTAAATTATAATTA
* * * ***
5471881 -TTTTAT-TATTATTATTATTATTTAAAAATTAAAATTTATATGTTGTTAAATAATTTTAATTTA
131 TTTTTATCT-TTATTATTATTATTTAAAAATTAAAATTTATATATTATTAAATACTTTTAATCCG
* *
5471944 AAAATATAAATTTAAATATTTATTTTTTATTAAAATTAA-TTTTTT--TTAATTA
195 AAAATATAAATATAAATATTTATTTTTCATTAAAATTAATTTTTTTACTTAATTA
* * * * *
5471996 ACTTGTTACGTTAACTTTTACACATTCACATTACGATTTTAAATTTAGTTATTCCACTTTTATAA
1 ACTTATTACGTTAACTTTTACACATTTATATTAAGATTTAAAATTTAGTTATTCCACTTTTATAA
5472061 GTTTTTA
66 GTTTTTA
5472068 TGTCGTTTTT
Statistics
Matches: 682, Mismatches: 114, Indels: 42
0.81 0.14 0.05
Matches are distributed among these distances:
244 7 0.01
245 129 0.19
246 37 0.05
247 14 0.02
248 6 0.01
249 95 0.14
250 386 0.57
251 8 0.01
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.51
Consensus pattern (249 bp):
ACTTATTACGTTAACTTTTACACATTTATATTAAGATTTAAAATTTAGTTATTCCACTTTTATAA
GTTTTTACGTCAATTCTTACAGTTTTACGTCAAAGCTTTTTTATGTCAATTTTAAATTATAATTA
TTTTTATCTTTATTATTATTATTTAAAAATTAAAATTTATATATTATTAAATACTTTTAATCCGA
AAATATAAATATAAATATTTATTTTTCATTAAAATTAATTTTTTTACTTAATTA
Found at i:5471992 original size:16 final size:17
Alignment explanation
Indices: 5471954--5471992 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
5471944 AAAATATAAA
*
5471954 TTTAAATATTTATTTTT
1 TTTAAATATTAATTTTT
5471971 TATTAAA-ATTAATTTTT
1 T-TTAAATATTAATTTTT
5471988 TTTAA
1 TTTAA
5471993 TTAACTTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 4 0.20
17 11 0.55
18 5 0.25
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTAAATATTAATTTTT
Found at i:5472194 original size:22 final size:21
Alignment explanation
Indices: 5472152--5472194 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
5472142 ATAATTCTAA
* * *
5472152 ATTATATATGTTTTTATTTTT
1 ATTATATATATTTTGAATTTT
5472173 ATTATTATATATTTTGAATTTT
1 ATTA-TATATATTTTGAATTTT
5472195 GACTTTCTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (21 bp):
ATTATATATATTTTGAATTTT
Found at i:5495789 original size:24 final size:24
Alignment explanation
Indices: 5495734--5495789 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
5495724 TATAACAAGT
5495734 ATTTTGATTTATTTTAATTTATAAA
1 ATTTT-ATTTATTTTAATTTATAAA
* * *
5495759 ATATTATTTATTTTGATTTATTAA
1 ATTTTATTTATTTTAATTTATAAA
*
5495783 GTTTTAT
1 ATTTTAT
5495790 GATATTATAC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 22 0.85
25 4 0.15
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (24 bp):
ATTTTATTTATTTTAATTTATAAA
Found at i:5503032 original size:57 final size:56
Alignment explanation
Indices: 5502945--5503063 Score: 132
Period size: 57 Copynumber: 2.1 Consensus size: 56
5502935 TATTTACTTG
* * * * *
5502945 TTCTCGTATATTTATTCATATACATCTTCTTTTTTTGTACCTATTCACGTACAACTC
1 TTCTCTTATACTTATTCACATACATCTTCTTCTCTTGTACCT-TTCACGTACAACTC
* * * *
5503002 TTCTCTTATACTTATTCACATGCAGT-TTCTTCTCTTGTATCTTTCACGTATACCTC
1 TTCTCTTATACTTATTCACATACA-TCTTCTTCTCTTGTACCTTTCACGTACAACTC
5503058 TTCTCT
1 TTCTCT
5503064 ATTACCTTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
56 18 0.35
57 33 0.63
58 1 0.02
ACGTcount: A:0.19, C:0.25, G:0.06, T:0.50
Consensus pattern (56 bp):
TTCTCTTATACTTATTCACATACATCTTCTTCTCTTGTACCTTTCACGTACAACTC
Found at i:5503360 original size:18 final size:17
Alignment explanation
Indices: 5503328--5503365 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
5503318 TTCTCTAGAG
*
5503328 CTTCTCTCTTTAATTCT
1 CTTCTCTCCTTAATTCT
5503345 CTTCTACTCCTTAATTCT
1 CTTCT-CTCCTTAATTCT
5503363 CTT
1 CTT
5503366 TCACTTGCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.13, C:0.32, G:0.00, T:0.55
Consensus pattern (17 bp):
CTTCTCTCCTTAATTCT
Found at i:5506235 original size:35 final size:35
Alignment explanation
Indices: 5506158--5506258 Score: 130
Period size: 35 Copynumber: 2.9 Consensus size: 35
5506148 TTACTCGTAA
* *
5506158 AACAACTAAAATAAGTGAAGTACTACTTCACGCAG
1 AACAACTAAAATAAGTGAAGCACTACTTTACGCAG
**
5506193 AACAACTAAAATAAGTGAAGCACTACTTTACTTAG
1 AACAACTAAAATAAGTGAAGCACTACTTTACGCAG
* * **
5506228 AATAACTAGAGCAAGTGAAGCACTACTTTAC
1 AACAACTAAAATAAGTGAAGCACTACTTTAC
5506259 ATGATAATAG
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 58 1.00
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.23
Consensus pattern (35 bp):
AACAACTAAAATAAGTGAAGCACTACTTTACGCAG
Found at i:5525709 original size:16 final size:15
Alignment explanation
Indices: 5525669--5525711 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
5525659 AGACCTCAAG
5525669 TTAATTATATTAATTA
1 TTAATTA-ATTAATTA
* *
5525685 TAAAATAATTAATTTA
1 TTAATTAATTAA-TTA
5525701 TTAATTAATTA
1 TTAATTAATTA
5525712 TCTCATAGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTAATTAATTAATTA
Found at i:5526450 original size:36 final size:36
Alignment explanation
Indices: 5526410--5526510 Score: 100
Period size: 35 Copynumber: 2.8 Consensus size: 36
5526400 ATTATTGATC
* * *
5526410 TTTTCTAATAGACGTGACTCTTCTTTTATTTTTTTA
1 TTTTCTAACAGACATGACTCTTCTTTTATTTTTTAA
* *
5526446 TTTTC-AACAAACATGAC-CATTCCTTTATTTTTTAA
1 TTTTCTAACAGACATGACTC-TTCTTTTATTTTTTAA
* *
5526481 TTTT-TAACAGACATAACTTTTTCTTTTATT
1 TTTTCTAACAGACATGAC-TCTTCTTTTATT
5526511 GCAACATGGG
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
34 1 0.02
35 37 0.71
36 14 0.27
ACGTcount: A:0.26, C:0.16, G:0.05, T:0.53
Consensus pattern (36 bp):
TTTTCTAACAGACATGACTCTTCTTTTATTTTTTAA
Found at i:5534740 original size:246 final size:246
Alignment explanation
Indices: 5534296--5534788 Score: 896
Period size: 246 Copynumber: 2.0 Consensus size: 246
5534286 AGGCTGTATT
5534296 TAGTGTATATGAAGTAGTGACGAATACTCCTCAATTATTGGTGTCATATCTACTTCATTAAACAC
1 TAGTGTATATGAAGTAGTGACGAATACTCCTCAATTATTGGTGTCATATCTACTTCATTAAACAC
* * *
5534361 AAAACATCAATAAGAACGATCCCAGAACAAAGTGATAGCCTTAAATAATTGATCATCCGTGTTTA
66 AAAACATCAATAAGAACAATCCCAAAACAAAGTGATAGCCTTAAATAATTGATCATCCATGTTTA
* *
5534426 CATGAAGAAGCCACGTAATATGTCCATACTTTTTACAAAAGTTGTCTCGTCAATTGCATCTCTAT
131 CATGAAGAAGCCACGTAATATGTCCATACTTTTTACAAAAGCTGTCTCGTCAATTGCACCTCTAT
5534491 TGGTCCCAAATACTTATCATCTTTAAAAAGTCATTTTGTTTGAGATTGAGG
196 TGGTCCCAAATACTTATCATCTTTAAAAAGTCATTTTGTTTGAGATTGAGG
5534542 TAGTGTATATGAAGTAGTGACGAATACTCCTCAATTATTGGTGTCATATCTACTTCATTAAACAC
1 TAGTGTATATGAAGTAGTGACGAATACTCCTCAATTATTGGTGTCATATCTACTTCATTAAACAC
* *
5534607 AAAACATCAGTAAGAACAATCCCAAAACAAAGTGGTAGCCTTAAATAATTGATCATCCATGTTTA
66 AAAACATCAATAAGAACAATCCCAAAACAAAGTGATAGCCTTAAATAATTGATCATCCATGTTTA
* * *
5534672 CATGAAGAAGCCACGTAATATGTCCATACTTTTTATAAAAGCTGTCTTGTCAATTGCACCTTTAT
131 CATGAAGAAGCCACGTAATATGTCCATACTTTTTACAAAAGCTGTCTCGTCAATTGCACCTCTAT
5534737 TGGTCCCAAATACTTATCATCTTTAAAAAGTCATTTTGTTTGAGATTGAGG
196 TGGTCCCAAATACTTATCATCTTTAAAAAGTCATTTTGTTTGAGATTGAGG
5534788 T
1 T
5534789 GAACCTTCTT
Statistics
Matches: 237, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
246 237 1.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (246 bp):
TAGTGTATATGAAGTAGTGACGAATACTCCTCAATTATTGGTGTCATATCTACTTCATTAAACAC
AAAACATCAATAAGAACAATCCCAAAACAAAGTGATAGCCTTAAATAATTGATCATCCATGTTTA
CATGAAGAAGCCACGTAATATGTCCATACTTTTTACAAAAGCTGTCTCGTCAATTGCACCTCTAT
TGGTCCCAAATACTTATCATCTTTAAAAAGTCATTTTGTTTGAGATTGAGG
Found at i:5542346 original size:24 final size:23
Alignment explanation
Indices: 5542294--5542352 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 23
5542284 GGACTATCAT
* *
5542294 AATTATCATCAATAAGACTAGTA
1 AATTATCAACAATAAGACTAATA
*
5542317 AGATTATCAACCATAAGACTAATA
1 A-ATTATCAACAATAAGACTAATA
5542341 GAATTATCAACA
1 -AATTATCAACA
5542353 GAAACATGTG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 1 0.03
24 28 0.93
25 1 0.03
ACGTcount: A:0.49, C:0.15, G:0.08, T:0.27
Consensus pattern (23 bp):
AATTATCAACAATAAGACTAATA
Found at i:5544390 original size:35 final size:34
Alignment explanation
Indices: 5544290--5544525 Score: 214
Period size: 35 Copynumber: 6.9 Consensus size: 34
5544280 TTACTTGTTT
5544290 AATTTAATTAATTAGGCCTAATAACTTAATTAAAC
1 AATTTAATTAATTAGGCC-AATAACTTAATTAAAC
* * *
5544325 AATTTAATT-A--AGCCCAACAATTTAATTAAAC
1 AATTTAATTAATTAGGCCAATAACTTAATTAAAC
* * *
5544356 AATTTTAATCAATTAGGCCAATGATTTAATTAAAC
1 AA-TTTAATTAATTAGGCCAATAACTTAATTAAAC
* ****
5544391 AAATTTAATCAATTAGGCCTAATAACTTAATTTTTT
1 -AATTTAATTAATTAGGCC-AATAACTTAATTAAAC
* *
5544427 AATTTAATTAATTAGGCCCAATGACTTAA-TAAAT
1 AATTTAATTAATTAGG-CCAATAACTTAATTAAAC
* * * *
5544461 AATTTAATTAATTAAGCTCAATGATTTAATTAGAC
1 AATTTAATTAATTAGGC-CAATAACTTAATTAAAC
*
5544496 AATTTAATTAATTAGG--AACAACTTAATTAA
1 AATTTAATTAATTAGGCCAATAACTTAATTAA
5544526 GATATTTTAA
Statistics
Matches: 165, Mismatches: 27, Indels: 21
0.77 0.13 0.10
Matches are distributed among these distances:
31 16 0.10
32 20 0.12
33 2 0.01
34 28 0.17
35 85 0.52
36 14 0.08
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.38
Consensus pattern (34 bp):
AATTTAATTAATTAGGCCAATAACTTAATTAAAC
Found at i:5544405 original size:102 final size:103
Alignment explanation
Indices: 5544290--5544511 Score: 272
Period size: 102 Copynumber: 2.2 Consensus size: 103
5544280 TTACTTGTTT
*
5544290 AATTTAATTAATTAGGCCTAATAACTTAATTAAACAATTTAATT-A-A-GCCCAACAATTTAATT
1 AATTTAATTAATTAGGCCTAATAACTTAATTAAACAATTTAATTAATAGGCCCAACAACTTAA-T
*
5544352 AAACAATTTTAATCAATTAGGC-CAATGATTTAATTAAAC
65 AAACAA-TTTAATCAATTAAGCTCAATGATTTAATTAAAC
* **** **
5544391 AAATTTAATCAATTAGGCCTAATAACTTAATTTTTTAATTTAATTAATTAGGCCCAATGACTTAA
1 -AATTTAATTAATTAGGCCTAATAACTTAATTAAACAATTTAATTAA-TAGGCCCAACAACTTAA
* * *
5544456 TAAATAATTTAATTAATTAAGCTCAATGATTTAATTAGAC
64 TAAACAATTTAATCAATTAAGCTCAATGATTTAATTAAAC
5544496 AATTTAATTAATTAGG
1 AATTTAATTAATTAGG
5544512 AACAACTTAA
Statistics
Matches: 102, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
102 39 0.38
103 1 0.01
104 28 0.27
105 23 0.23
106 11 0.11
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.38
Consensus pattern (103 bp):
AATTTAATTAATTAGGCCTAATAACTTAATTAAACAATTTAATTAATAGGCCCAACAACTTAATA
AACAATTTAATCAATTAAGCTCAATGATTTAATTAAAC
Found at i:5544521 original size:19 final size:17
Alignment explanation
Indices: 5544486--5544525 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 17
5544476 GCTCAATGAT
*
5544486 TTAATTAGACAATTTAA
1 TTAATTAGACAACTTAA
5544503 TTAATTAGGAACAACTTAA
1 TTAATTA-G-ACAACTTAA
5544522 TTAA
1 TTAA
5544526 GATATTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 1 0.05
19 12 0.60
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.38
Consensus pattern (17 bp):
TTAATTAGACAACTTAA
Found at i:5556413 original size:12 final size:13
Alignment explanation
Indices: 5556396--5556424 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5556386 TGACTTAAGG
5556396 AAAAAA-AAAAGA
1 AAAAAATAAAAGA
5556408 AAAAAATAAAAGA
1 AAAAAATAAAAGA
5556421 AAAA
1 AAAA
5556425 TAATTCCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.90, C:0.00, G:0.07, T:0.03
Consensus pattern (13 bp):
AAAAAATAAAAGA
Found at i:5556629 original size:202 final size:201
Alignment explanation
Indices: 5556254--5556657 Score: 523
Period size: 202 Copynumber: 2.0 Consensus size: 201
5556244 GAAAAAAAGG
* *
5556254 AAAACAGAAAGAAAAGAAAAATAATTTCAAAATTTGAAGGAAAAAAAGAAAAAACAAACATGGAT
1 AAAACAGAAAAAAAAGAAAAATAATTTCAAAATTTGAAAGAAAAAAAGAAAAAACAAACATGGAT
* * * *
5556319 CTCGCATAATATCAAGTTCAATGTCATCAATCACAAATAATTAAATCCATTTTTAAGGATCAAAA
66 CTCGCATAATATCAAGTTAAATGCCATCAATCACAAATAATTAAATCCATCTTTAAGGATAAAAA
* *
5556384 GATGACTTAAGGAAAAAAAAAAGAAAAAAATAAAAGAAAAATAATTCCAAAACTTAGGCCTAAAT
131 AATGACTTAAAGAAAAAAAAAAGAAAAAAATAAAAGAAAAATAATTCCAAAACTTAGGCCTAAAT
5556449 GAGCTA
196 GAGCTA
* * *
5556455 AAAACAGAAAAAAAAAGACAAATAATTTCAAAATTTGAGCTAAAGAAAAAAGGAAACAAAATAAA
1 AAAACAG-AAAAAAAAGAAAAATAATTTCAAAATTT--G--AAAGAAAAAAAG-AA-AAAACAAA
***
5556520 CATGGATCTCGCATAATATCAAG-TAAATGCCATCAATCTTGAATAATTAAATCCATCTTT-AGG
59 CATGGATCTCGCATAATATCAAGTTAAATGCCATCAATCACAAATAATTAAATCCATCTTTAAGG
* ** * *
5556583 ATAAAAAAAT-AGTTAAAG-AAAAAAGGAGAAAAAAAT-AAA-AAAAATAATTCTAAAACTTGGG
124 ATAAAAAAATGACTTAAAGAAAAAAAAAAGAAAAAAATAAAAGAAAAATAATTCCAAAACTTAGG
*
5556644 CCTAGATGAGCTA
189 CCTAAATGAGCTA
5556657 A
1 A
5556658 GGAAAAAAAG
Statistics
Matches: 176, Mismatches: 20, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
201 7 0.04
202 59 0.34
203 3 0.02
204 17 0.10
205 6 0.03
206 21 0.12
207 33 0.19
208 30 0.17
ACGTcount: A:0.56, C:0.11, G:0.12, T:0.21
Consensus pattern (201 bp):
AAAACAGAAAAAAAAGAAAAATAATTTCAAAATTTGAAAGAAAAAAAGAAAAAACAAACATGGAT
CTCGCATAATATCAAGTTAAATGCCATCAATCACAAATAATTAAATCCATCTTTAAGGATAAAAA
AATGACTTAAAGAAAAAAAAAAGAAAAAAATAAAAGAAAAATAATTCCAAAACTTAGGCCTAAAT
GAGCTA
Found at i:5559643 original size:15 final size:16
Alignment explanation
Indices: 5559623--5559652 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5559613 CTATTACATA
5559623 GATTTT-ATTTTTAAT
1 GATTTTAATTTTTAAT
5559638 GATTTTAATTTTTAA
1 GATTTTAATTTTTAA
5559653 AAATTAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (16 bp):
GATTTTAATTTTTAAT
Found at i:5560291 original size:23 final size:25
Alignment explanation
Indices: 5560245--5560300 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 25
5560235 AGAATACTAT
* *
5560245 TATAAATTTTTTTATTTATATATTA
1 TATAAAATTATTTATTTATATATTA
5560270 TATAAAATTATTT-TTTAT-TATTA
1 TATAAAATTATTTATTTATATATTA
*
5560293 -ATTAAATT
1 TATAAAATT
5560301 TAACATATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.25
23 5 0.18
24 5 0.18
25 11 0.39
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
TATAAAATTATTTATTTATATATTA
Found at i:5560665 original size:2 final size:2
Alignment explanation
Indices: 5560658--5560685 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5560648 TTTTCACCAT
5560658 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5560686 CATGTATGTG
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):
TA
Found at i:5566738 original size:43 final size:43
Alignment explanation
Indices: 5566666--5566783 Score: 123
Period size: 43 Copynumber: 2.7 Consensus size: 43
5566656 GATGATGAGT
* * **
5566666 TTATTACTTTTAAAGTTATGTAGTTTCATTCC-AGAT-AGGGAAC
1 TTATTTCTTTTAAAGTTACGTAGCCTCATTCCAAG-TGA-GGAAC
* *
5566709 TTATTTCTTTTAAAGTTACGTAGCCTCATTCTAAGTGAGGAAT
1 TTATTTCTTTTAAAGTTACGTAGCCTCATTCCAAGTGAGGAAC
*
5566752 TTATTTTTTCTTTAAAGTTACGTAGCCTCATT
1 TTA-TTTCT-TTTAAAGTTACGTAGCCTCATT
5566784 TTAGATGATG
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
43 35 0.55
44 7 0.11
45 22 0.34
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.45
Consensus pattern (43 bp):
TTATTTCTTTTAAAGTTACGTAGCCTCATTCCAAGTGAGGAAC
Found at i:5567481 original size:5 final size:6
Alignment explanation
Indices: 5567467--5567512 Score: 58
Period size: 6 Copynumber: 7.7 Consensus size: 6
5567457 TTAGGTGAGC
* *
5567467 TTTTAT TTTTAT TTTTAT TTTT-T TATGAT TTTTAT TTTGTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT-TAT TTTT
5567513 TGGTCATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
5 3 0.09
6 25 0.74
7 6 0.18
ACGTcount: A:0.15, C:0.00, G:0.04, T:0.80
Consensus pattern (6 bp):
TTTTAT
Found at i:5567521 original size:24 final size:23
Alignment explanation
Indices: 5567471--5567521 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
5567461 GTGAGCTTTT
* *
5567471 ATTTTTATTTTTATTTTTTTATG
1 ATTTTTATTTTTATTTTTTGATC
*
5567494 ATTTTTATTTTGTATTTTTTGGTC
1 ATTTTTATTTT-TATTTTTTGATC
5567518 ATTT
1 ATTT
5567522 AAAAATTAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.16, C:0.02, G:0.08, T:0.75
Consensus pattern (23 bp):
ATTTTTATTTTTATTTTTTGATC
Found at i:5574829 original size:43 final size:44
Alignment explanation
Indices: 5574762--5574883 Score: 128
Period size: 43 Copynumber: 2.8 Consensus size: 44
5574752 CAATGCCTAC
*
5574762 TTTTGATAT-ACTTATGACCCATGCCACTAGG-GTTAATTATGGT
1 TTTTGATATGA-TTATGACCTATGCCACTAGGAGTTAATTATGGT
* * * *
5574805 TTTTGATATGATTATGACTTATGCC-GTTGGAGTTAATTGTGGT
1 TTTTGATATGATTATGACCTATGCCACTAGGAGTTAATTATGGT
* *
5574848 TTCT-ATTATGATTATGACCTATGGCAC-AGGAGTTAA
1 TTTTGA-TATGATTATGACCTATGCCACTAGGAGTTAA
5574884 GTGTGGATAT
Statistics
Matches: 65, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
42 4 0.06
43 60 0.92
44 1 0.02
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.41
Consensus pattern (44 bp):
TTTTGATATGATTATGACCTATGCCACTAGGAGTTAATTATGGT
Found at i:5576384 original size:29 final size:29
Alignment explanation
Indices: 5576341--5576423 Score: 125
Period size: 29 Copynumber: 2.9 Consensus size: 29
5576331 TTTGAAATCC
*
5576341 TATATAAGCTTAAAGCTGACTTGTTATCG
1 TATATAAGCTCAAAGCTGACTTGTTATCG
5576370 TATATAAGCTCAAAGCAT-ACTTGTTATCG
1 TATATAAGCTCAAAGC-TGACTTGTTATCG
5576399 TATATAAGCTCAAAG-TAGACTTGTT
1 TATATAAGCTCAAAGCT-GACTTGTT
5576424 CCGCTTTGAT
Statistics
Matches: 50, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
27 1 0.02
29 48 0.96
30 1 0.02
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (29 bp):
TATATAAGCTCAAAGCTGACTTGTTATCG
Found at i:5584933 original size:2 final size:2
Alignment explanation
Indices: 5584926--5584987 Score: 81
Period size: 2 Copynumber: 31.0 Consensus size: 2
5584916 GATAATCTCT
* * *
5584926 TA TA TA TA TA TA TG TG TGA TA TA TA TA TA TA -A TA TA TA TA TT
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
5584968 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
5584988 ATTATCCTCA
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
1 1 0.02
2 52 0.96
3 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5585580 original size:3 final size:3
Alignment explanation
Indices: 5585572--5585628 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
5585562 GGGTGTTAAC
5585572 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5585620 ATA ATA ATA
1 ATA ATA ATA
5585629 GTAGTAGTAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5585633 original size:3 final size:3
Alignment explanation
Indices: 5585627--5585660 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
5585617 ATAATAATAA
5585627 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG T
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG T
5585661 TGCACAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (3 bp):
TAG
Found at i:5591921 original size:31 final size:30
Alignment explanation
Indices: 5591886--5591948 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
5591876 TAAGCCTAAA
** *
5591886 TTTTAAAATTATTTTTTTCTCTTTTTTCCTT
1 TTTTAAAATTA-TTTGCTCCCTTTTTTCCTT
*
5591917 TTTTACAATTATTTGCTCCCTTTTTTCCTT
1 TTTTAAAATTATTTGCTCCCTTTTTTCCTT
5591947 TT
1 TT
5591949 CGTTTTTTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 18 0.64
31 10 0.36
ACGTcount: A:0.14, C:0.17, G:0.02, T:0.67
Consensus pattern (30 bp):
TTTTAAAATTATTTGCTCCCTTTTTTCCTT
Found at i:5592086 original size:20 final size:20
Alignment explanation
Indices: 5592049--5592105 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 20
5592039 TAGATTTAGT
5592049 TTTTATTTCTTTTT-TTATA-
1 TTTTATTT-TTTTTCTTATAG
5592068 TTTTATTTTTTTTCCTTATAG
1 TTTTATTTTTTTT-CTTATAG
*
5592089 ATTTAGTTTTTTTTCTT
1 TTTTA-TTTTTTTTCTT
5592106 TTTTCTATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
18 5 0.15
19 8 0.24
20 5 0.15
21 7 0.21
22 8 0.24
ACGTcount: A:0.14, C:0.07, G:0.04, T:0.75
Consensus pattern (20 bp):
TTTTATTTTTTTTCTTATAG
Found at i:5592123 original size:45 final size:47
Alignment explanation
Indices: 5592038--5592130 Score: 145
Period size: 45 Copynumber: 2.0 Consensus size: 47
5592028 CACTATTGAC
*
5592038 ATAGATTTAGTTTTTATTTCTTTTTTTATATTTTATTTTTTTTCCTT
1 ATAGATTTAGTTTTTATTTCTTTTTTTATATTTTACTTTTTTTCCTT
* *
5592085 ATAGATTTAGTTTTT-TTTC-TTTTTTCTATTTTACTTTTTTTTCTT
1 ATAGATTTAGTTTTTATTTCTTTTTTTATATTTTACTTTTTTTCCTT
5592130 A
1 A
5592131 GGGTTTAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
45 24 0.56
46 4 0.09
47 15 0.35
ACGTcount: A:0.16, C:0.08, G:0.04, T:0.72
Consensus pattern (47 bp):
ATAGATTTAGTTTTTATTTCTTTTTTTATATTTTACTTTTTTTCCTT
Found at i:5592123 original size:46 final size:47
Alignment explanation
Indices: 5592038--5592127 Score: 148
Period size: 47 Copynumber: 1.9 Consensus size: 47
5592028 CACTATTGAC
5592038 ATAGATTTAGTTTTTATTTCTTTTTTTATATTTTATTTTTTTTCCTT
1 ATAGATTTAGTTTTTATTTCTTTTTTTATATTTTATTTTTTTTCCTT
*
5592085 ATAGATTTAGTTTTT-TTTC-TTTTTTCTATTTTACTTTTTTTTC
1 ATAGATTTAGTTTTTATTTCTTTTTTTATATTTTA-TTTTTTTTC
5592128 TTAGGGTTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
45 13 0.32
46 13 0.32
47 15 0.37
ACGTcount: A:0.16, C:0.08, G:0.04, T:0.72
Consensus pattern (47 bp):
ATAGATTTAGTTTTTATTTCTTTTTTTATATTTTATTTTTTTTCCTT
Found at i:5596055 original size:18 final size:18
Alignment explanation
Indices: 5596010--5596056 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
5596000 TCAACGACAA
* *
5596010 GAATAACCTCTATGTTGG
1 GAATAACCTCAATATTGG
*
5596028 GAACAACCTCAATATTGG
1 GAATAACCTCAATATTGG
*
5596046 GAATAGCCTCA
1 GAATAACCTCA
5596057 TCTTGAATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (18 bp):
GAATAACCTCAATATTGG
Found at i:5622006 original size:53 final size:53
Alignment explanation
Indices: 5621945--5622045 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 53
5621935 CAATGGGTAT
*
5621945 CCTGTTACA-AGGTACTCGC-GAATATCCAATCCAGTTATATAAGATTAGTATAC
1 CCTGTTACAGA-GTACTCGCAG-ATATCCAACCCAGTTATATAAGATTAGTATAC
*
5621998 CCTGTTACAGAGTACTCGCAGATATCCAACCCAGTTATATAATATTAG
1 CCTGTTACAGAGTACTCGCAGATATCCAACCCAGTTATATAAGATTAG
5622046 AGTACTTTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
53 42 0.95
54 2 0.05
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.30
Consensus pattern (53 bp):
CCTGTTACAGAGTACTCGCAGATATCCAACCCAGTTATATAAGATTAGTATAC
Found at i:5622514 original size:35 final size:34
Alignment explanation
Indices: 5622468--5622546 Score: 95
Period size: 35 Copynumber: 2.3 Consensus size: 34
5622458 TGTTGTTTGG
* *
5622468 ATATTTATTTTTAATTATTTAAATTGATATTTTAA
1 ATATTTGTTTTTAATTATTTAAATTGAAATTTT-A
* * *
5622503 ATATTTGTTTTTGATTATTTAACTTTAAATTTTA
1 ATATTTGTTTTTAATTATTTAAATTGAAATTTTA
*
5622537 TTATTTGTTT
1 ATATTTGTTT
5622547 GTTTTTATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
34 10 0.26
35 28 0.74
ACGTcount: A:0.30, C:0.01, G:0.05, T:0.63
Consensus pattern (34 bp):
ATATTTGTTTTTAATTATTTAAATTGAAATTTTA
Found at i:5623017 original size:23 final size:24
Alignment explanation
Indices: 5622991--5623040 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
5622981 TTTTCTTCTC
*
5622991 TTTAAGTATTCTT-TCAAGTTATT
1 TTTAAGTATTCTTATAAAGTTATT
**
5623014 TTTATTTATTCTTATAAAGTTATT
1 TTTAAGTATTCTTATAAAGTTATT
5623038 TTT
1 TTT
5623041 TCATAACACG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.62
Consensus pattern (24 bp):
TTTAAGTATTCTTATAAAGTTATT
Done.