Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
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: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 59 of 210
Found at i:20605501 original size:90 final size:91
Alignment explanation
Indices: 20605397--20605577 Score: 355
Period size: 90 Copynumber: 2.0 Consensus size: 91
20605387 TACCACACTA
20605397 ACCAAATTTTTTCAAAACCCAAAAGCTTTTACTTATAAGTAAATAAATAGTACATGTGTTTTTAA
1 ACCAAATTTTTTCAAAACCCAAAAGCTTTTACTTATAAGTAAATAAATAGTACATGTGTTTTTAA
20605462 ATATTTAAAATATCT-ATATTTATCT
66 ATATTTAAAATATCTAATATTTATCT
20605487 ACCAAATTTTTTCAAAACCCAAAAGCTTTTACTTATAAGTAAATAAATAGTACATGTGTTTTTAA
1 ACCAAATTTTTTCAAAACCCAAAAGCTTTTACTTATAAGTAAATAAATAGTACATGTGTTTTTAA
20605552 ATATTTAAAATATCTAATATTTATCT
66 ATATTTAAAATATCTAATATTTATCT
20605578 TTGTAATTAA
Statistics
Matches: 90, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
90 80 0.89
91 10 0.11
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (91 bp):
ACCAAATTTTTTCAAAACCCAAAAGCTTTTACTTATAAGTAAATAAATAGTACATGTGTTTTTAA
ATATTTAAAATATCTAATATTTATCT
Found at i:20610399 original size:24 final size:24
Alignment explanation
Indices: 20610372--20610418 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
20610362 TTTGGACAGT
20610372 CCAAAGAATATGTCACCATCTTTA
1 CCAAAGAATATGTCACCATCTTTA
*
20610396 CCAAAGAATATGTCACCCTCTTT
1 CCAAAGAATATGTCACCATCTTT
20610419 CATGGAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.28, G:0.09, T:0.30
Consensus pattern (24 bp):
CCAAAGAATATGTCACCATCTTTA
Found at i:20629816 original size:7 final size:7
Alignment explanation
Indices: 20629804--20629828 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
20629794 AGTGGATTGA
20629804 TATTTAG
1 TATTTAG
20629811 TATTTAG
1 TATTTAG
20629818 TATTTAG
1 TATTTAG
20629825 TATT
1 TATT
20629829 ATGTATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:20630513 original size:18 final size:18
Alignment explanation
Indices: 20630480--20630514 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20630470 AAGTATGTTT
* *
20630480 CCTAACCCTTATATGTAC
1 CCTAACCCGTACATGTAC
20630498 CCTAACCCGTACATGTA
1 CCTAACCCGTACATGTA
20630515 TCCTTTTCCG
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:0.29, C:0.34, G:0.09, T:0.29
Consensus pattern (18 bp):
CCTAACCCGTACATGTAC
Found at i:20631339 original size:28 final size:26
Alignment explanation
Indices: 20630984--20631341 Score: 353
Period size: 28 Copynumber: 14.0 Consensus size: 26
20630974 TTTTGATATT
*
20630984 ATTTGATTAAAAACCCTAACC---TA
1 ATTTAATTAAAAACCCTAACCTAATA
*
20631007 ATTTAATT-AAAACCGTAACC--ATA
1 ATTTAATTAAAAACCCTAACCTAATA
*
20631030 ATTTAATTAAAAACCCTAAACTAATTTA
1 ATTTAATTAAAAACCCTAACCTAA--TA
20631058 ATTTAATTAAAAACCCTAACC---TA
1 ATTTAATTAAAAACCCTAACCTAATA
* *
20631081 ATTTATTTAAAAACTCTAACCCTAACCTTA
1 ATTTAATTAAAAACCCTAA-CCTAA---TA
20631111 ATTTAATTAAAAACCCTAACC---TA
1 ATTTAATTAAAAACCCTAACCTAATA
20631134 ATTTAATTAAAAACCCTAACC--ATA
1 ATTTAATTAAAAACCCTAACCTAATA
*
20631158 ATTTATTTAAAAACCCTAAACCTTAACCTA
1 ATTTAATTAAAAACCCT-AACC-TAA--TA
20631188 ATTTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAA--TA
20631216 ATTTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAA--TA
20631244 ATTTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAA--TA
20631272 ATTTAATTAAAAACCCTAACC---TA
1 ATTTAATTAAAAACCCTAACCTAATA
*
20631295 ATTTAGTT-AAAACCCTAACCT-A-A
1 ATTTAATTAAAAACCCTAACCTAATA
*
20631318 A-TTAGTTAAAAACCCTAACCTAAT
1 ATTTAATTAAAAACCCTAACCTAAT
20631342 TTGATAATCT
Statistics
Matches: 296, Mismatches: 14, Indels: 48
0.83 0.04 0.13
Matches are distributed among these distances:
22 29 0.10
23 83 0.28
24 31 0.10
25 4 0.01
26 1 0.00
28 105 0.35
29 6 0.02
30 37 0.12
ACGTcount: A:0.46, C:0.20, G:0.01, T:0.33
Consensus pattern (26 bp):
ATTTAATTAAAAACCCTAACCTAATA
Found at i:20631441 original size:56 final size:56
Alignment explanation
Indices: 20631342--20631449 Score: 139
Period size: 56 Copynumber: 1.9 Consensus size: 56
20631332 CTAACCTAAT
* * * *
20631342 TTGATAATCTTACTACCCATTAACACACTTTTTCTGGCTTAATAATTTTACATAAA
1 TTGATAATCTTACTAACCATTAACAAACTTTTTCGGGCATAATAATTTTACATAAA
*
20631398 TTGATAAT-TTGACTAACCATTAACAAAAGTTTTT-GGGCATAATAATTTTACA
1 TTGATAATCTT-ACTAACCATTAAC-AAACTTTTTCGGGCATAATAATTTTACA
20631450 CAGTTTTACA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
55 2 0.04
56 36 0.80
57 7 0.16
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (56 bp):
TTGATAATCTTACTAACCATTAACAAACTTTTTCGGGCATAATAATTTTACATAAA
Found at i:20635548 original size:124 final size:124
Alignment explanation
Indices: 20635337--20635607 Score: 388
Period size: 124 Copynumber: 2.2 Consensus size: 124
20635327 ACGATTGGAC
*
20635337 ACTATTTGCTCAGAAACGTCAAAAAATAATTATTTCCTACATGACCAACTATAGCGAAATCGCAT
1 ACTATTTGCTCAGAAACGTC-AAAAATAATTATTTCCTACATGACCAACTATACCGAAATCGCAT
* * *
20635402 CCACGAGGGCGCGATTTCACAATTTCTTCTCAT-ATAGCATCCTGGTATCAA-CGATTTTAT
65 CCACGAGGGCACGATTTAACAATTTCTTATC-TGATAGCATCCTGGTA-CAAGCGATTTTAT
* * * *
20635462 ACTATTTGCTCAGAAAACGTCAAAAA-AATTATTTCTTACATGACCAACTGTACCGAAATGGCGT
1 ACTATTTGCTCAG-AAACGTCAAAAATAATTATTTCCTACATGACCAACTATACCGAAATCGCAT
*
20635526 CCACGAGGGCACGATTTAACAATTTCTTATCTGATAGCATCCTGGTAGAAGCGATTTTAT
65 CCACGAGGGCACGATTTAACAATTTCTTATCTGATAGCATCCTGGTACAAGCGATTTTAT
20635586 ACTATTTGAC-CAGAAACGTCAA
1 ACTATTTG-CTCAGAAACGTCAA
20635608 CTCGAAATAA
Statistics
Matches: 133, Mismatches: 9, Indels: 10
0.88 0.06 0.07
Matches are distributed among these distances:
123 12 0.09
124 95 0.71
125 19 0.14
126 7 0.05
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.30
Consensus pattern (124 bp):
ACTATTTGCTCAGAAACGTCAAAAATAATTATTTCCTACATGACCAACTATACCGAAATCGCATC
CACGAGGGCACGATTTAACAATTTCTTATCTGATAGCATCCTGGTACAAGCGATTTTAT
Found at i:20639780 original size:121 final size:121
Alignment explanation
Indices: 20639566--20639809 Score: 488
Period size: 121 Copynumber: 2.0 Consensus size: 121
20639556 TTGTAAGTAA
20639566 ATGAGTGTAGTGTCCTATCCTTAAATGCCATGATAGGAAAGAGTTTGGGTGTATCAGTTCTCTGT
1 ATGAGTGTAGTGTCCTATCCTTAAATGCCATGATAGGAAAGAGTTTGGGTGTATCAGTTCTCTGT
20639631 AATGCTTTAAACTCACCTAAGCCTTTCATTTCCTTTTAAGGAAAACCCATCATACC
66 AATGCTTTAAACTCACCTAAGCCTTTCATTTCCTTTTAAGGAAAACCCATCATACC
20639687 ATGAGTGTAGTGTCCTATCCTTAAATGCCATGATAGGAAAGAGTTTGGGTGTATCAGTTCTCTGT
1 ATGAGTGTAGTGTCCTATCCTTAAATGCCATGATAGGAAAGAGTTTGGGTGTATCAGTTCTCTGT
20639752 AATGCTTTAAACTCACCTAAGCCTTTCATTTCCTTTTAAGGAAAACCCATCATACC
66 AATGCTTTAAACTCACCTAAGCCTTTCATTTCCTTTTAAGGAAAACCCATCATACC
20639808 AT
1 AT
20639810 TCCACACCCT
Statistics
Matches: 123, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
121 123 1.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.34
Consensus pattern (121 bp):
ATGAGTGTAGTGTCCTATCCTTAAATGCCATGATAGGAAAGAGTTTGGGTGTATCAGTTCTCTGT
AATGCTTTAAACTCACCTAAGCCTTTCATTTCCTTTTAAGGAAAACCCATCATACC
Found at i:20640108 original size:14 final size:15
Alignment explanation
Indices: 20640075--20640108 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
20640065 AGTTATCAAA
20640075 TAAAACCCATATTCT
1 TAAAACCCATATTCT
*
20640090 TAAAACCCGTATT-T
1 TAAAACCCATATTCT
20640104 TAAAA
1 TAAAA
20640109 TTTAAAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.32
Consensus pattern (15 bp):
TAAAACCCATATTCT
Found at i:20647965 original size:19 final size:17
Alignment explanation
Indices: 20647926--20647959 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
20647916 GATTCGTCCA
20647926 TATTTTTTAAAAAATAG
1 TATTTTTTAAAAAATAG
*
20647943 TATTTTATTTAAAAATA
1 TATTTT-TTAAAAAATA
20647960 TTTATTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TATTTTTTAAAAAATAG
Found at i:20659116 original size:24 final size:22
Alignment explanation
Indices: 20659089--20659139 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 22
20659079 TTTTTTAAAT
*
20659089 TAAAATTAAATTAAATTATAAAAA
1 TAAAATT-AATTAAAATA-AAAAA
20659113 TAAAAATTAATTAAAATAAAAAA
1 T-AAAATTAATTAAAATAAAAAA
20659136 TAAA
1 TAAA
20659140 CTGGATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 3 0.12
23 6 0.24
24 10 0.40
25 6 0.24
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAATTAATTAAAATAAAAAA
Found at i:20659121 original size:15 final size:16
Alignment explanation
Indices: 20659101--20659134 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
20659091 AAATTAAATT
20659101 AAATT-ATAAAAATAA
1 AAATTAATAAAAATAA
*
20659116 AAATTAATTAAAATAA
1 AAATTAATAAAAATAA
20659132 AAA
1 AAA
20659135 ATAAACTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AAATTAATAAAAATAA
Found at i:20659539 original size:110 final size:111
Alignment explanation
Indices: 20659420--20659640 Score: 426
Period size: 110 Copynumber: 2.0 Consensus size: 111
20659410 TTTAAATAGA
20659420 TATAATTTTTACAAAAAATTTATTTTTCACACGTATCATAAGTATGCCATAATCATATAAATTAA
1 TATAATTTTTACAAAAAATTTATTTTTCACACGTATCATAAGTATGCCATAATCATATAAATTAA
20659485 AATTAATTATAAATTAAATAAAAATTTTGATTTAA-TCAGATAATT
66 AATTAATTATAAATTAAATAAAAATTTTGATTTAATTCAGATAATT
*
20659530 TATAATTTTTACATAAAATTTATTTTTCACACGTATCATAAGTATGCCATAATCATATAAATTAA
1 TATAATTTTTACAAAAAATTTATTTTTCACACGTATCATAAGTATGCCATAATCATATAAATTAA
20659595 AATTAATTATAAATTAAATAAAAATTTTGATTTAATTCAGATAATT
66 AATTAATTATAAATTAAATAAAAATTTTGATTTAATTCAGATAATT
20659641 GAATATTTTT
Statistics
Matches: 109, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
110 99 0.91
111 10 0.09
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.42
Consensus pattern (111 bp):
TATAATTTTTACAAAAAATTTATTTTTCACACGTATCATAAGTATGCCATAATCATATAAATTAA
AATTAATTATAAATTAAATAAAAATTTTGATTTAATTCAGATAATT
Found at i:20664637 original size:24 final size:22
Alignment explanation
Indices: 20664610--20664660 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 22
20664600 TTTTTTAAAT
*
20664610 TAAAATTAAATTAAATTATAAAAA
1 TAAAATT-AATTAAAATA-AAAAA
20664634 TAAAAATTAATTAAAATAAAAAA
1 T-AAAATTAATTAAAATAAAAAA
20664657 TAAA
1 TAAA
20664661 CTGGATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 3 0.12
23 6 0.24
24 10 0.40
25 6 0.24
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAATTAATTAAAATAAAAAA
Found at i:20664642 original size:15 final size:16
Alignment explanation
Indices: 20664622--20664655 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
20664612 AAATTAAATT
20664622 AAATT-ATAAAAATAA
1 AAATTAATAAAAATAA
*
20664637 AAATTAATTAAAATAA
1 AAATTAATAAAAATAA
20664653 AAA
1 AAA
20664656 ATAAACTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AAATTAATAAAAATAA
Found at i:20667218 original size:41 final size:39
Alignment explanation
Indices: 20667173--20667261 Score: 117
Period size: 38 Copynumber: 2.3 Consensus size: 39
20667163 TTAAAAATAT
* *
20667173 TTATATTAAAAAATGCTACTATAAATATAATAAATACTTTA
1 TTATATTAAAAAAT-ATA-AATAAATATAATAAATACTTTA
*
20667214 TTATATT-AAAAATATAAATAAATATAATAAATATTTTA
1 TTATATTAAAAAATATAAATAAATATAATAAATACTTTA
*
20667252 TTGTATTAAA
1 TTATATTAAA
20667262 TATAATTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
38 26 0.60
39 4 0.09
40 6 0.14
41 7 0.16
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (39 bp):
TTATATTAAAAAATATAAATAAATATAATAAATACTTTA
Found at i:20671385 original size:30 final size:29
Alignment explanation
Indices: 20671336--20671423 Score: 99
Period size: 29 Copynumber: 3.0 Consensus size: 29
20671326 TTTAAAAAAA
20671336 ACATTTTGACCCC-AAACTTTCTCAAAATT
1 ACATTTT-ACCCCTAAACTTTCTCAAAATT
**
20671365 ACATTTCTACCCCTAAACTTT-TGTAAATT
1 ACATTT-TACCCCTAAACTTTCTCAAAATT
* *
20671394 ACATTTTAACCCTAAAATTTTCTCAAAATT
1 ACATTTTACCCCT-AAACTTTCTCAAAATT
20671424 TTATTTTGGC
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
28 6 0.12
29 29 0.59
30 14 0.29
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.39
Consensus pattern (29 bp):
ACATTTTACCCCTAAACTTTCTCAAAATT
Found at i:20671643 original size:20 final size:18
Alignment explanation
Indices: 20671598--20671646 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 18
20671588 AGCCAAGAAC
*
20671598 CAAGCAAAGA-AAAAAAA
1 CAAGCAAAAACAAAAAAA
*
20671615 CAAGAAAAAACAAAAGAAA
1 CAAGCAAAAACAAAA-AAA
20671634 TCAAGCAAAAACA
1 -CAAGCAAAAACA
20671647 GCAGCCTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 8 0.31
18 4 0.15
19 3 0.12
20 11 0.42
ACGTcount: A:0.73, C:0.14, G:0.10, T:0.02
Consensus pattern (18 bp):
CAAGCAAAAACAAAAAAA
Found at i:20671900 original size:18 final size:17
Alignment explanation
Indices: 20671877--20671928 Score: 67
Period size: 18 Copynumber: 3.2 Consensus size: 17
20671867 GGGGCCGAAC
20671877 AAGGAAGAAGAAGAAAGA
1 AAGGAAGAAGAA-AAAGA
20671895 AAGGAAGAAGAAAAAG-
1 AAGGAAGAAGAAAAAGA
20671911 AA-GAAG--GAAAAAGA
1 AAGGAAGAAGAAAAAGA
20671925 AAGG
1 AAGG
20671929 GGGAAAGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
13 7 0.22
14 2 0.06
15 5 0.16
16 2 0.06
17 4 0.12
18 12 0.38
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (17 bp):
AAGGAAGAAGAAAAAGA
Found at i:20671963 original size:16 final size:17
Alignment explanation
Indices: 20671884--20671963 Score: 54
Period size: 19 Copynumber: 4.5 Consensus size: 17
20671874 AACAAGGAAG
* *
20671884 AAGAAGAAAGAAAGGAAG
1 AAGAA-AAAGAAAGAAAA
*
20671902 AAGAAAAAGAAGAAGGAAA
1 AAGAAAAAG-A-AAGAAAA
**
20671921 AAGAAAGGGGGAAAGAAAA
1 AAGAAA--AAGAAAGAAAA
*
20671940 AAGTAAAAGAAA-AAAA
1 AAGAAAAAGAAAGAAAA
20671956 AAGAAAAA
1 AAGAAAAA
20671964 TCAGCAAAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
16 11 0.22
17 8 0.16
18 6 0.12
19 23 0.46
20 1 0.02
21 1 0.02
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.01
Consensus pattern (17 bp):
AAGAAAAAGAAAGAAAA
Found at i:20672284 original size:7 final size:7
Alignment explanation
Indices: 20672251--20672299 Score: 50
Period size: 7 Copynumber: 7.1 Consensus size: 7
20672241 CTGCCGAAGG
20672251 AGAAG-A
1 AGAAGAA
*
20672257 AGAAAAA
1 AGAAGAA
20672264 AG-AGAA
1 AGAAGAA
20672270 A-AAGAGA
1 AGAAGA-A
20672277 AGAAAGAA
1 AG-AAGAA
20672285 AGAAGAA
1 AGAAGAA
20672292 AGAAGAA
1 AGAAGAA
20672299 A
1 A
20672300 TGGAAAGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
6 11 0.31
7 18 0.50
8 3 0.08
9 4 0.11
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (7 bp):
AGAAGAA
Found at i:20672288 original size:11 final size:10
Alignment explanation
Indices: 20672253--20672298 Score: 58
Period size: 11 Copynumber: 4.5 Consensus size: 10
20672243 GCCGAAGGAG
20672253 AAGAAGAAAA
1 AAGAAGAAAA
20672263 AAG-AGAAAA
1 AAGAAGAAAA
20672272 AGAGAAGAAAGA
1 A-AGAAGAAA-A
*
20672284 AAGAAGAAAG
1 AAGAAGAAAA
20672294 AAGAA
1 AAGAA
20672299 ATGGAAAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
9 7 0.22
10 10 0.31
11 13 0.41
12 2 0.06
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (10 bp):
AAGAAGAAAA
Found at i:20672313 original size:7 final size:7
Alignment explanation
Indices: 20672256--20672325 Score: 50
Period size: 7 Copynumber: 9.1 Consensus size: 7
20672246 GAAGGAGAAG
20672256 AAGAAAA
1 AAGAAAA
20672263 AAGAGAAA
1 AAGA-AAA
20672271 AAGAGAAGA
1 AAGA-AA-A
*
20672280 AAGAAAG
1 AAGAAAA
*
20672287 AAGAAAG
1 AAGAAAA
20672294 AAGAAATGGA
1 AAGAAA---A
20672304 AAGAAAA
1 AAGAAAA
*
20672311 AAGGAAA
1 AAGAAAA
*
20672318 AATAAAA
1 AAGAAAA
20672325 A
1 A
20672326 TTTTAACAGC
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
7 30 0.57
8 12 0.23
9 5 0.09
10 6 0.11
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (7 bp):
AAGAAAA
Found at i:20672320 original size:20 final size:20
Alignment explanation
Indices: 20672266--20672313 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
20672256 AAGAAAAAAG
20672266 AGAAAAAGAGAAGAAA--GAA
1 AGAAAAA-AGAAGAAATGGAA
*
20672285 AGAAGAAAGAAGAAATGGAA
1 AGAAAAAAGAAGAAATGGAA
20672305 AGAAAAAAG
1 AGAAAAAAG
20672314 GAAAAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 8 0.32
19 6 0.24
20 11 0.44
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (20 bp):
AGAAAAAAGAAGAAATGGAA
Found at i:20672419 original size:16 final size:16
Alignment explanation
Indices: 20672397--20672442 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
20672387 CAGATCAGCC
20672397 CAAAAAAAAGCAGCAG
1 CAAAAAAAAGCAGCAG
* *
20672413 TAAAAAAAACCAGCAG
1 CAAAAAAAAGCAGCAG
20672429 CAAAAAAATAGCAG
1 CAAAAAAA-AGCAG
20672443 GCCTGTCCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 21 0.84
17 4 0.16
ACGTcount: A:0.63, C:0.17, G:0.15, T:0.04
Consensus pattern (16 bp):
CAAAAAAAAGCAGCAG
Found at i:20672626 original size:15 final size:16
Alignment explanation
Indices: 20672608--20672649 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
20672598 ATAAAATGAG
20672608 AAAAAAAAAGA-GGAA
1 AAAAAAAAAGAGGGAA
20672623 AAAAGAAAAA-AGGGAA
1 AAAA-AAAAAGAGGGAA
20672639 AAAGAAAAAAG
1 AAA-AAAAAAG
20672650 GGATTCAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 5 0.22
16 17 0.74
17 1 0.04
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAGAGGGAA
Found at i:20672650 original size:15 final size:15
Alignment explanation
Indices: 20672607--20672652 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
20672597 AATAAAATGA
*
20672607 GAAAAA-AAAAGAGG
1 GAAAAAGAAAAAAGG
*
20672621 AAAAAAGAAAAAAGG
1 GAAAAAGAAAAAAGG
20672636 GAAAAAGAAAAAAGG
1 GAAAAAGAAAAAAGG
20672651 GA
1 GA
20672653 TTCAACTTGC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
14 5 0.18
15 23 0.82
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (15 bp):
GAAAAAGAAAAAAGG
Found at i:20672835 original size:27 final size:27
Alignment explanation
Indices: 20672805--20672859 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
20672795 GTATTTATAT
*
20672805 TTTTAATTT-AATTTAATTTAATTTCAA
1 TTTTAATTTAAATTTAA-ATAATTTCAA
*
20672832 TTTTATTTTAAATTTAAATAATTTCAA
1 TTTTAATTTAAATTTAAATAATTTCAA
20672859 T
1 T
20672860 AAATAAGGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 18 0.72
28 7 0.28
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (27 bp):
TTTTAATTTAAATTTAAATAATTTCAA
Found at i:20672850 original size:6 final size:5
Alignment explanation
Indices: 20672806--20672839 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
20672796 TATTTATATT
*
20672806 TTTAA TTTAA TTTAA TTTAA TTTCAA TTTTA TTT
1 TTTAA TTTAA TTTAA TTTAA TTT-AA TTTAA TTT
20672840 TAAATTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (5 bp):
TTTAA
Found at i:20673160 original size:20 final size:20
Alignment explanation
Indices: 20673135--20673233 Score: 93
Period size: 20 Copynumber: 5.2 Consensus size: 20
20673125 AATCGTGTTT
20673135 AAAAAATTTTCGTGTTTTCA
1 AAAAAATTTTCGTGTTTTCA
*
20673155 AAAAAA-TTTCTTGTGTTTC-
1 AAAAAATTTTCGTGT-TTTCA
* *
20673174 -AAAAATTTCCGTGTTTTTA
1 AAAAAATTTTCGTGTTTTCA
*
20673193 AAAAAAATTTCGTGTTTT--
1 AAAAAATTTTCGTGTTTTCA
* *
20673211 AAAAAATTCTCATG-TTTCA
1 AAAAAATTTTCGTGTTTTCA
20673230 AAAA
1 AAAA
20673234 TAAATTTTCA
Statistics
Matches: 64, Mismatches: 9, Indels: 13
0.74 0.10 0.15
Matches are distributed among these distances:
17 3 0.05
18 19 0.30
19 17 0.27
20 25 0.39
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.42
Consensus pattern (20 bp):
AAAAAATTTTCGTGTTTTCA
Found at i:20673178 original size:38 final size:38
Alignment explanation
Indices: 20673129--20673308 Score: 132
Period size: 38 Copynumber: 4.5 Consensus size: 38
20673119 TAAAAAAATC
*
20673129 GTGTTTAAAAAATTTTCGTGTTTTCAAAAAAATTTCTT
1 GTGTTTCAAAAATTTTCGTGTTTTCAAAAAAATTTCTT
* * *
20673167 GTGTTTCAAAAATTTCCGTGTTTTTAAAAAAAATTTCGT
1 GTGTTTCAAAAATTTTCGTG-TTTTCAAAAAAATTTCTT
* * *
20673206 GT-TTTAAAAAATTCTCATG-TTTCAAAAATAAATTTTCAAAATT
1 GTGTTTCAAAAATTTTCGTGTTTTC-AAAA-AAA-TTTC----TT
* **
20673249 CCAGTGTTTCAAAAATTTTCATGTTTTC-AAAAAATTTCCC
1 ---GTGTTTCAAAAATTTTCGTGTTTTCAAAAAAATTTCTT
*
20673289 GTGTTTTCAAAAATTCTCGT
1 GTG-TTTCAAAAATTTTCGT
20673309 ATTTCGAAAA
Statistics
Matches: 112, Mismatches: 16, Indels: 28
0.72 0.10 0.18
Matches are distributed among these distances:
36 3 0.03
37 7 0.06
38 48 0.43
39 22 0.20
43 1 0.01
44 4 0.04
45 3 0.03
46 5 0.04
47 15 0.13
48 4 0.04
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.43
Consensus pattern (38 bp):
GTGTTTCAAAAATTTTCGTGTTTTCAAAAAAATTTCTT
Found at i:20673226 original size:18 final size:17
Alignment explanation
Indices: 20673118--20673233 Score: 92
Period size: 18 Copynumber: 6.4 Consensus size: 17
20673108 ACGGCACTTC
*
20673118 TTAAAAAA-ATCGTG-T
1 TTAAAAAATTTCGTGTT
20673133 TTAAAAAATTTTCGTGTT
1 TTAAAAAA-TTTCGTGTT
*
20673151 TTCAAAAAAATTTCTTGTGT
1 TT--AAAAAATTTCGTGT-T
*
20673171 TTCAAAAATTTCCGTGTTT
1 TTAAAAAATTT-CGTG-TT
20673190 TTAAAAAAAATTTCGTGTT
1 TT--AAAAAATTTCGTGTT
*
20673209 TTAAAAAATTCTCATGTT
1 TTAAAAAATT-TCGTGTT
*
20673227 TCAAAAA
1 TTAAAAA
20673234 TAAATTTTCA
Statistics
Matches: 83, Mismatches: 7, Indels: 19
0.76 0.06 0.17
Matches are distributed among these distances:
15 8 0.10
17 13 0.16
18 23 0.28
19 17 0.20
20 14 0.17
21 8 0.10
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.42
Consensus pattern (17 bp):
TTAAAAAATTTCGTGTT
Found at i:20673278 original size:18 final size:18
Alignment explanation
Indices: 20673136--20673330 Score: 86
Period size: 19 Copynumber: 10.9 Consensus size: 18
20673126 ATCGTGTTTA
*
20673136 AAAAATTTTCGTGTTTTC
1 AAAAATTTTCATGTTTTC
* *
20673154 AAAAAAATTTCTTGTGTTTC
1 -AAAAATTTTCATGT-TTTC
* * *
20673174 AAAAATTTCCGTGTTTTTAA
1 AAAAATTTTCATG-TTTT-C
* * *
20673194 AAAAAATTTCGTGTTTTA
1 AAAAATTTTCATGTTTTC
*
20673212 AAAAATTCTCATG-TTTC
1 AAAAATTTTCATGTTTTC
**
20673229 AAAAA---T-AAATTTTC
1 AAAAATTTTCATGTTTTC
*
20673243 -AAAA-TTCCA-GTGTTTC
1 AAAAATTTTCATGT-TTTC
20673259 AAAAATTTTCATGTTTTC
1 AAAAATTTTCATGTTTTC
* *
20673277 AAAAAATTTCCCGTGTTTTC
1 -AAAAATTT-TCATGTTTTC
*
20673297 AAAAATTCTC--GTATTTC
1 AAAAATTTTCATGT-TTTC
* *
20673314 GAAAATTTTCTTGTTTT
1 AAAAATTTTCATGTTTT
20673331 TTTAAAAAAA
Statistics
Matches: 137, Mismatches: 23, Indels: 33
0.71 0.12 0.17
Matches are distributed among these distances:
13 5 0.04
14 5 0.04
15 1 0.01
16 7 0.05
17 24 0.18
18 23 0.17
19 48 0.35
20 24 0.18
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.45
Consensus pattern (18 bp):
AAAAATTTTCATGTTTTC
Found at i:20673357 original size:38 final size:36
Alignment explanation
Indices: 20673297--20673383 Score: 84
Period size: 36 Copynumber: 2.3 Consensus size: 36
20673287 CCGTGTTTTC
** * * *
20673297 AAAAATTCTCGTATTTCGAAAATTTTCTTGTTTTTTTAA
1 AAAAATT-TCGTGCTTCGAAAA--TTATTGTATTTTAAA
*
20673336 AAAAATTTCGTGCTTCTAAAATTATTGTATTTTAAA
1 AAAAATTTCGTGCTTCGAAAATTATTGTATTTTAAA
*
20673372 AAAAAATTCGTG
1 AAAAATTTCGTG
20673384 TTTTCAAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
36 23 0.56
38 11 0.27
39 7 0.17
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.45
Consensus pattern (36 bp):
AAAAATTTCGTGCTTCGAAAATTATTGTATTTTAAA
Found at i:20697871 original size:196 final size:197
Alignment explanation
Indices: 20697536--20697925 Score: 604
Period size: 196 Copynumber: 2.0 Consensus size: 197
20697526 TGAATGCAAT
* * * *
20697536 CCAATCTTCTTATCAGACCATTCCATTTAGTCACACATTGTTTTTGGAGATAATGTTGGATTTAA
1 CCAATCTTCTTACCAGACCATTCAATTTAATCACACATTGTTTTTGGAGACAATGTTGGATTTAA
* * *
20697601 CATATAAAGGATTCAACCTAAAGCCTCGATAGACTTTATAACAATTGAGAATACACTGACATAGA
66 CATATAAAGGATTCAACCTAAAGCCTCGATAGACATTATAACAATTGAGAATACACAGACATACA
* * *
20697666 AACATATGCTCAAAAGCATAAAGAGCATTCAACCAAAGATGAAAGTGATCTAAAAGCATACCACA
131 AACATATGCTCAAAAGAATAAAGAGCATTCAACCAAAGAAGAAAGTGATCCAAAAGCATACCACA
20697731 AC
196 AC
*
20697733 CCAATCTTCTTACCATG-CCATTCAATTTAATCACTCATTG-TTTTGGAGACAATGTTGGATTTA
1 CCAATCTTCTTACCA-GACCATTCAATTTAATCACACATTGTTTTTGGAGACAATGTTGGATTTA
* *
20697796 ATATATAAAGGATTCAACCTAAAGCCTCGATAGACATTATAACCATTGAGAATACACAGACATAC
65 ACATATAAAGGATTCAACCTAAAGCCTCGATAGACATTATAACAATTGAGAATACACAGACATAC
* * * *
20697861 AGATATATGCTCAAAAGAATAAAGGGCATTCAACCAAAGAAGATAGTGATCCAAAAGCATACCAC
130 AAACATATGCTCAAAAGAATAAAGAGCATTCAACCAAAGAAGAAAGTGATCCAAAAGCATACCAC
20697926 TATCATAATC
Statistics
Matches: 175, Mismatches: 17, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
196 140 0.80
197 34 0.19
198 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (197 bp):
CCAATCTTCTTACCAGACCATTCAATTTAATCACACATTGTTTTTGGAGACAATGTTGGATTTAA
CATATAAAGGATTCAACCTAAAGCCTCGATAGACATTATAACAATTGAGAATACACAGACATACA
AACATATGCTCAAAAGAATAAAGAGCATTCAACCAAAGAAGAAAGTGATCCAAAAGCATACCACA
AC
Found at i:20700918 original size:46 final size:48
Alignment explanation
Indices: 20700851--20700952 Score: 163
Period size: 46 Copynumber: 2.1 Consensus size: 48
20700841 TTATCCTAAT
*
20700851 AATAATAATAAGACTAGAGACTTGCT-AG-GTTTCACCACATAACATC
1 AATAATAATAAGACTAGAGACTTGCTAAGTCTTTCACCACATAACATC
*
20700897 AATAATAATAAGACTAGAGACTTGCTAAGTTCTTTCACCACATAACATT
1 AATAATAATAAGACTAGAGACTTGCTAAG-TCTTTCACCACATAACATC
20700946 AATAATA
1 AATAATA
20700953 CAAGGATGAA
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
46 26 0.51
47 2 0.04
49 23 0.45
ACGTcount: A:0.43, C:0.18, G:0.11, T:0.28
Consensus pattern (48 bp):
AATAATAATAAGACTAGAGACTTGCTAAGTCTTTCACCACATAACATC
Found at i:20709642 original size:105 final size:106
Alignment explanation
Indices: 20709420--20709661 Score: 382
Period size: 105 Copynumber: 2.3 Consensus size: 106
20709410 AAGCGTTAAG
* * * *
20709420 ATAAATTGGCCAGAAATAATTA-TGTGATCAACGATGGATTGGTGAAAATGGTTGAGTTGCTTGT
1 ATAAATTGGCCAGAAATAA-TACTGTGATCACCAATGGATTGGTGAAAATGATTGAGTTGCTTGC
* *
20709484 AATGGAAGCAACAAGCGTAAAGACAATTGTTTTAACATTTCC
65 AATCGAAGCAACAAGCGTAAAGACAATTATTTTAACATTTCC
*
20709526 ATAAATT-GCCAGAAGTAATACTGTGATCACCAATGGATTGGTGAAAATGATTGAGTTGCTTGCA
1 ATAAATTGGCCAGAAATAATACTGTGATCACCAATGGATTGGTGAAAATGATTGAGTTGCTTGCA
20709590 A-CGAAGCAACAAGCGTAAAGACAATTATTTTAACATTTCC
66 ATCGAAGCAACAAGCGTAAAGACAATTATTTTAACATTTCC
*
20709630 ATAAATTGGCCAGAAATAATCCTGTGATCACC
1 ATAAATTGGCCAGAAATAATACTGTGATCACC
20709662 GTTTATGAAG
Statistics
Matches: 125, Mismatches: 9, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
104 46 0.37
105 72 0.58
106 7 0.06
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (106 bp):
ATAAATTGGCCAGAAATAATACTGTGATCACCAATGGATTGGTGAAAATGATTGAGTTGCTTGCA
ATCGAAGCAACAAGCGTAAAGACAATTATTTTAACATTTCC
Found at i:20715753 original size:11 final size:12
Alignment explanation
Indices: 20715731--20715763 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
20715721 TAAATCACAT
20715731 AAATAATAAAATA
1 AAAT-ATAAAATA
20715744 AAAT-TAAAATA
1 AAATATAAAATA
20715755 AAATATAAA
1 AAATATAAA
20715764 TAATACTCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 11 0.58
12 4 0.21
13 4 0.21
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATATAAAATA
Found at i:20720231 original size:34 final size:34
Alignment explanation
Indices: 20720187--20720336 Score: 291
Period size: 34 Copynumber: 4.4 Consensus size: 34
20720177 TACAGAATAA
*
20720187 TATATGTCAAAATTAGTGAACGAGAAATCACATT
1 TATATATCAAAATTAGTGAACGAGAAATCACATT
20720221 TATATATCAAAATTAGTGAACGAGAAATCACATT
1 TATATATCAAAATTAGTGAACGAGAAATCACATT
20720255 TATATATCAAAATTAGTGAACGAGAAATCACATT
1 TATATATCAAAATTAGTGAACGAGAAATCACATT
20720289 TATATATCAAAATTAGTGAACGAGAAATCACATT
1 TATATATCAAAATTAGTGAACGAGAAATCACATT
20720323 TATATATCAAAATT
1 TATATATCAAAATT
20720337 TTCAATCAAC
Statistics
Matches: 115, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
34 115 1.00
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.31
Consensus pattern (34 bp):
TATATATCAAAATTAGTGAACGAGAAATCACATT
Found at i:20722353 original size:15 final size:15
Alignment explanation
Indices: 20722329--20722363 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
20722319 CAAAATCAAG
*
20722329 ATTTTTACAACATTT
1 ATTTTAACAACATTT
*
20722344 ATTTTAACAATATTT
1 ATTTTAACAACATTT
20722359 ATTTT
1 ATTTT
20722364 TTTCTCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTTAACAACATTT
Found at i:20737198 original size:10 final size:12
Alignment explanation
Indices: 20737168--20737199 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
20737158 GGCTCGCTCG
20737168 TATTAATTTTAT
1 TATTAATTTTAT
20737180 TATTAATTTTA-
1 TATTAATTTTAT
20737191 TA-TAATTTT
1 TATTAATTTT
20737200 TTAAGAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 7 0.35
11 2 0.10
12 11 0.55
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TATTAATTTTAT
Found at i:20742344 original size:30 final size:30
Alignment explanation
Indices: 20742310--20742368 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
20742300 TCCTTTACAT
20742310 AACAAACAAACTTACTTTTATGACTCATAA
1 AACAAACAAACTTACTTTTATGACTCATAA
* *
20742340 AACAAATAAACTTACTTTTATGATTCATA
1 AACAAACAAACTTACTTTTATGACTCATA
20742369 CAAAATAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.46, C:0.17, G:0.03, T:0.34
Consensus pattern (30 bp):
AACAAACAAACTTACTTTTATGACTCATAA
Found at i:20747338 original size:19 final size:19
Alignment explanation
Indices: 20747313--20747365 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
20747303 ACTTAAATAA
20747313 AAATTATTTAATAATTCA-
1 AAATTATTTAATAATTCAG
* *
20747331 ATAATTATTTTATAATTTAG
1 A-AATTATTTAATAATTCAG
*
20747351 AAATTATTTGATAAT
1 AAATTATTTAATAAT
20747366 AAAAATATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 1 0.03
19 28 0.93
20 1 0.03
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (19 bp):
AAATTATTTAATAATTCAG
Found at i:20748804 original size:2 final size:2
Alignment explanation
Indices: 20748797--20748833 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
20748787 CTAATTATCA
* *
20748797 AT AT AT AT AT GT AT AT AT AT AT AT AT GT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20748834 AGATAGCATC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20748818 original size:16 final size:16
Alignment explanation
Indices: 20748797--20748833 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
20748787 CTAATTATCA
20748797 ATATATATATGTATAT
1 ATATATATATGTATAT
20748813 ATATATATATGTATAT
1 ATATATATATGTATAT
20748829 ATATA
1 ATATA
20748834 AGATAGCATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (16 bp):
ATATATATATGTATAT
Found at i:20759328 original size:18 final size:19
Alignment explanation
Indices: 20759295--20759333 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
20759285 TCTCTACTTT
20759295 TTAAAAATTATTTATTAAA
1 TTAAAAATTATTTATTAAA
*
20759314 TTAAATATT-TTTATTAAA
1 TTAAAAATTATTTATTAAA
20759332 TT
1 TT
20759334 CGATGATGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTAAAAATTATTTATTAAA
Found at i:20797547 original size:23 final size:22
Alignment explanation
Indices: 20797521--20797575 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 22
20797511 AATAAACTTT
20797521 TTATTTTTATTTTTTATACTTA-A
1 TTATTTTTATTTTTT-TA-TTACA
*
20797544 TTATTTATGATTTTTTTATTACA
1 TTATTT-TTATTTTTTTATTACA
20797567 TTATTTTTA
1 TTATTTTTA
20797576 AATTCTGCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 5 0.18
23 15 0.54
24 8 0.29
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (22 bp):
TTATTTTTATTTTTTTATTACA
Found at i:20807205 original size:26 final size:29
Alignment explanation
Indices: 20807176--20807241 Score: 70
Period size: 27 Copynumber: 2.4 Consensus size: 29
20807166 TAGACCTGAA
20807176 TTTTGAAATTTAAAA-A-AGAGATTACTT
1 TTTTGAAATTTAAAATATAGAGATTACTT
* *
20807203 TTTTGTAAA-TAAAAATATAGGGATTAC-T
1 TTTTG-AAATTTAAAATATAGAGATTACTT
20807231 TTTT-AAATTTA
1 TTTTGAAATTTA
20807242 CGAAAAGTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
26 3 0.09
27 12 0.38
28 9 0.28
29 8 0.25
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.44
Consensus pattern (29 bp):
TTTTGAAATTTAAAATATAGAGATTACTT
Found at i:20809923 original size:32 final size:26
Alignment explanation
Indices: 20809863--20809916 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
20809853 ATTGTGCGAC
20809863 TGAAAAAGGAGGAATGTTTTACTCAT
1 TGAAAAAGGAGGAATGTTTTACTCAT
20809889 TGAAAAAGGAGGAATGTTTTACTCAT
1 TGAAAAAGGAGGAATGTTTTACTCAT
20809915 TG
1 TG
20809917 TCATTGACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.31
Consensus pattern (26 bp):
TGAAAAAGGAGGAATGTTTTACTCAT
Found at i:20827037 original size:26 final size:26
Alignment explanation
Indices: 20827001--20827052 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
20826991 GGGTTTTAGT
*
20827001 CTTGTAGAATAAGAATCTAAAATTAA
1 CTTGTAGAATAAGAAACTAAAATTAA
*
20827027 CTTGTAGAATAAGAAACTATAATTAA
1 CTTGTAGAATAAGAAACTAAAATTAA
20827053 GGTATCCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.12, T:0.31
Consensus pattern (26 bp):
CTTGTAGAATAAGAAACTAAAATTAA
Found at i:20830400 original size:26 final size:28
Alignment explanation
Indices: 20830371--20830431 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 28
20830361 ACCAAATATT
20830371 TATTTTTAAAA-T-AAAAAA-TAAAAAA
1 TATTTTTAAAATTAAAAAAATTAAAAAA
*
20830396 GTA-TTCTAAAATTAAAAAAATTAAAAAA
1 -TATTTTTAAAATTAAAAAAATTAAAAAA
*
20830424 TATATTTA
1 TATTTTTA
20830432 TTATATTCGG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
25 7 0.25
26 3 0.11
27 8 0.29
28 10 0.36
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (28 bp):
TATTTTTAAAATTAAAAAAATTAAAAAA
Found at i:20834264 original size:66 final size:66
Alignment explanation
Indices: 20834184--20834316 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
20834174 GTTTATAGTT
* *
20834184 CAAGTTGCTTTTGTTGGATTACCTGCATATCTCCAGTTTATCCGTCTGCCATGAGTTACCTAGGA
1 CAAGTCGCTTTTGTTGGATTACCTGCATATCTCCAGTTTATCCCTCTGCCATGAGTTACCTAGGA
20834249 A
66 A
20834250 CAAGTCGCTTTTGTTGGATTACCTGCATATCTCCAGTTTATCCCTCTGCCATGAGTTACCTAGGA
1 CAAGTCGCTTTTGTTGGATTACCTGCATATCTCCAGTTTATCCCTCTGCCATGAGTTACCTAGGA
20834315 A
66 A
20834316 C
1 C
20834317 CATTTAATCC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (66 bp):
CAAGTCGCTTTTGTTGGATTACCTGCATATCTCCAGTTTATCCCTCTGCCATGAGTTACCTAGGA
A
Found at i:20835984 original size:14 final size:14
Alignment explanation
Indices: 20835967--20835995 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
20835957 TCTTCAACAA
20835967 TCGACCTTCCATGT
1 TCGACCTTCCATGT
20835981 TCGACCTTCCATGT
1 TCGACCTTCCATGT
20835995 T
1 T
20835996 TTCGTTTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.34, G:0.14, T:0.38
Consensus pattern (14 bp):
TCGACCTTCCATGT
Found at i:20839328 original size:15 final size:17
Alignment explanation
Indices: 20839307--20839347 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
20839297 TAATCTTTTA
20839307 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATAAT
*
20839323 -AAATTATTAAAATAAT
1 AAAATTATAAAAATAAT
20839339 AAAATTATA
1 AAAATTATA
20839348 TTTTTACCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATAAT
Found at i:20843156 original size:29 final size:30
Alignment explanation
Indices: 20843124--20843192 Score: 70
Period size: 31 Copynumber: 2.3 Consensus size: 30
20843114 ATGCATGGAT
20843124 TTTGATTTGGTGCAAT-TATATACATGAA-A
1 TTTGATTTGGT-CAATATATATACATGAAGA
* * *
20843153 TTTGAATTGTGGTTAATATGTATACATGAAGC
1 TTTG-ATT-TGGTCAATATATATACATGAAGA
20843185 TTTGATTT
1 TTTGATTT
20843193 TGATTTAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
29 4 0.12
30 7 0.21
31 18 0.55
32 4 0.12
ACGTcount: A:0.30, C:0.06, G:0.19, T:0.45
Consensus pattern (30 bp):
TTTGATTTGGTCAATATATATACATGAAGA
Found at i:20844658 original size:29 final size:29
Alignment explanation
Indices: 20844599--20844659 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
20844589 AGGGAGTGAA
* * *
20844599 CAATTTAGCCCCTCTATTATTAAATTGAT
1 CAATTTAGCCCCTATATTATTAAAATAAT
*
20844628 CAATTTAGTCCCTAT-TCTATTAAAATAAT
1 CAATTTAGCCCCTATAT-TATTAAAATAAT
20844657 CAA
1 CAA
20844660 GTAAGTTCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 1 0.04
29 26 0.96
ACGTcount: A:0.36, C:0.20, G:0.05, T:0.39
Consensus pattern (29 bp):
CAATTTAGCCCCTATATTATTAAAATAAT
Found at i:20845241 original size:6 final size:6
Alignment explanation
Indices: 20845230--20845258 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
20845220 NNNNNNNNNT
20845230 CTAAAA CTAAAA CTAAAA CTAAAA CTAAA
1 CTAAAA CTAAAA CTAAAA CTAAAA CTAAA
20845259 GTCTAAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (6 bp):
CTAAAA
Found at i:20845312 original size:9 final size:9
Alignment explanation
Indices: 20845298--20845355 Score: 80
Period size: 9 Copynumber: 6.4 Consensus size: 9
20845288 GTAGTGATTC
*
20845298 AATTCGGTT
1 AATTCGGGT
20845307 AATTCGGGT
1 AATTCGGGT
* *
20845316 AATTCAGTT
1 AATTCGGGT
20845325 AATTCGGGT
1 AATTCGGGT
*
20845334 AATTCGGTT
1 AATTCGGGT
20845343 AATTCGGGT
1 AATTCGGGT
20845352 AATT
1 AATT
20845356 TTTAACCAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 42 1.00
ACGTcount: A:0.26, C:0.10, G:0.24, T:0.40
Consensus pattern (9 bp):
AATTCGGGT
Found at i:20845325 original size:18 final size:18
Alignment explanation
Indices: 20845298--20845355 Score: 107
Period size: 18 Copynumber: 3.2 Consensus size: 18
20845288 GTAGTGATTC
20845298 AATTCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
*
20845316 AATTCAGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
20845334 AATTCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
20845352 AATT
1 AATT
20845356 TTTAACCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.26, C:0.10, G:0.24, T:0.40
Consensus pattern (18 bp):
AATTCGGTTAATTCGGGT
Found at i:20847024 original size:2 final size:2
Alignment explanation
Indices: 20847017--20847044 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20847007 TAAGTTTAAT
20847017 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
20847045 TATATATATA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:20847779 original size:24 final size:24
Alignment explanation
Indices: 20847752--20847800 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
20847742 AGGCCTTAAC
20847752 TTGCTGATTTGGTTGTTTTTCTTA
1 TTGCTGATTTGGTTGTTTTTCTTA
20847776 TTGCTGATTTGGTTGTTTTTCTTA
1 TTGCTGATTTGGTTGTTTTTCTTA
20847800 T
1 T
20847801 ATGAGCAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.08, C:0.08, G:0.20, T:0.63
Consensus pattern (24 bp):
TTGCTGATTTGGTTGTTTTTCTTA
Found at i:20853641 original size:11 final size:11
Alignment explanation
Indices: 20853625--20853650 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
20853615 TTCTACTCTC
20853625 TTTTTTTTGTT
1 TTTTTTTTGTT
20853636 TTTTTTTTGTT
1 TTTTTTTTGTT
20853647 TTTT
1 TTTT
20853651 GCAATCCATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTTTTTGTT
Found at i:20854368 original size:16 final size:16
Alignment explanation
Indices: 20854347--20854379 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
20854337 ATGTAGCGTA
20854347 CAAATTTTTGGCATCC
1 CAAATTTTTGGCATCC
20854363 CAAATTTTTGGCATCC
1 CAAATTTTTGGCATCC
20854379 C
1 C
20854380 CCAAGGGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.36
Consensus pattern (16 bp):
CAAATTTTTGGCATCC
Found at i:20855398 original size:5 final size:5
Alignment explanation
Indices: 20855388--20855449 Score: 67
Period size: 5 Copynumber: 12.2 Consensus size: 5
20855378 AATTATGTTT
20855388 TTATA TTATA TTATTA TTA-A -TATA TTATA TTATA TTATA TTAT- TATATTA
1 TTATA TTATA TTA-TA TTATA TTATA TTATA TTATA TTATA TTATA T-TA-TA
20855438 TTATA TATATA T
1 TTATA T-TATA T
20855450 GACAAAGAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 13
0.79 0.00 0.21
Matches are distributed among these distances:
3 2 0.04
4 3 0.06
5 31 0.62
6 13 0.26
7 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:20855402 original size:8 final size:8
Alignment explanation
Indices: 20855388--20855443 Score: 62
Period size: 8 Copynumber: 6.8 Consensus size: 8
20855378 AATTATGTTT
20855388 TTATATTA
1 TTATATTA
20855396 -TATTATTA
1 TTA-TATTA
20855404 TTA-ATATA
1 TTATAT-TA
20855412 TTATATTATA
1 TTATA-T-TA
20855422 TTATATTA
1 TTATATTA
20855430 TTATATTA
1 TTATATTA
20855438 TTATAT
1 TTATAT
20855444 ATATATGACA
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
7 4 0.09
8 26 0.60
9 4 0.09
10 9 0.21
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TTATATTA
Found at i:20855404 original size:3 final size:3
Alignment explanation
Indices: 20855391--20855441 Score: 51
Period size: 3 Copynumber: 19.0 Consensus size: 3
20855381 TATGTTTTTA
*
20855391 TAT TA- TAT TAT TAT TAA TA- TAT TA- TAT TA- TAT TA- TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
20855433 TAT TAT TAT
1 TAT TAT TAT
20855442 ATATATATGA
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
2 12 0.29
3 29 0.71
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:20855515 original size:40 final size:40
Alignment explanation
Indices: 20855458--20855553 Score: 147
Period size: 40 Copynumber: 2.4 Consensus size: 40
20855448 ATGACAAAGA
20855458 AAGAAAGAAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
1 AAGAAAG-AAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
* *
20855499 GAGAAAGAAAGAAACAGAGAGCAAAACGAAACAGAGAAGG
1 AAGAAAGAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
*
20855539 AAGGAAGGAAAGAAA
1 AA-GAAAGAAAGAAA
20855554 GAAAGAAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 33 0.66
41 17 0.34
ACGTcount: A:0.64, C:0.08, G:0.28, T:0.00
Consensus pattern (40 bp):
AAGAAAGAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
Found at i:20861028 original size:139 final size:140
Alignment explanation
Indices: 20860778--20861056 Score: 551
Period size: 139 Copynumber: 2.0 Consensus size: 140
20860768 CAAATTTTAT
20860778 CTTGTTTTTATTTATAATTAATTAATTATTAATAATGAAAATATTTTTAATTATAATCATAAAAA
1 CTTGTTTTTATTTATAATTAATTAATTATTAATAATGAAAATATTTTTAATTATAATCATAAAAA
20860843 CAGAGTTAATTGTACTGGACATCCCCAAACTGATATCTAATCTCCCAAACTTCAAACACTCTAA-
66 CAGAGTTAATTGTACTGGACATCCCCAAACTGATATCTAATCTCCCAAACTTCAAACACTCTAAT
20860907 TACATCTCTA
131 TACATCTCTA
20860917 CTTGTTTTTATTTATAATTAATTAATTATTAATAATGAAAATATTTTTAATTATAATCATAAAAA
1 CTTGTTTTTATTTATAATTAATTAATTATTAATAATGAAAATATTTTTAATTATAATCATAAAAA
20860982 CAGAGTTAATTGTACTGGACATCCCCAAACTGATATCTAATCTCCCAAACTTCAAACACTCTAAT
66 CAGAGTTAATTGTACTGGACATCCCCAAACTGATATCTAATCTCCCAAACTTCAAACACTCTAAT
20861047 TACATCTCTA
131 TACATCTCTA
20861057 AACTTTCGAT
Statistics
Matches: 139, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
139 129 0.93
140 10 0.07
ACGTcount: A:0.39, C:0.16, G:0.06, T:0.38
Consensus pattern (140 bp):
CTTGTTTTTATTTATAATTAATTAATTATTAATAATGAAAATATTTTTAATTATAATCATAAAAA
CAGAGTTAATTGTACTGGACATCCCCAAACTGATATCTAATCTCCCAAACTTCAAACACTCTAAT
TACATCTCTA
Found at i:20870904 original size:4 final size:4
Alignment explanation
Indices: 20870895--20870921 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
20870885 CAATGATTCC
20870895 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
20870922 CCAAATTGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:20874642 original size:61 final size:61
Alignment explanation
Indices: 20874544--20874673 Score: 145
Period size: 61 Copynumber: 2.1 Consensus size: 61
20874534 TTAAGGGTTC
* * * * * **
20874544 AATTTATTGAATTTTTTATAATTTAAATTAAAATGATAAATTTTGTAAACATTGAGGGCTA
1 AATTTATTGAATTTTTTATAATTTAAATCAAAATGATAAAATATGCAAACATTAAAAGCTA
* * **
20874605 AATTTATTGGATTTTTTAT-ATTTAGTATCAATTTGATAAAATATGCAAACATTAAAAGCTA
1 AATTTATTGAATTTTTTATAATTTA-AATCAAAATGATAAAATATGCAAACATTAAAAGCTA
20874666 AATTTATT
1 AATTTATT
20874674 ATTAGACCAA
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
60 5 0.09
61 52 0.91
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.45
Consensus pattern (61 bp):
AATTTATTGAATTTTTTATAATTTAAATCAAAATGATAAAATATGCAAACATTAAAAGCTA
Found at i:20881409 original size:13 final size:13
Alignment explanation
Indices: 20881393--20881437 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
20881383 CATTATACCA
20881393 AAAAATTATAGGT
1 AAAAATTATAGGT
20881406 AAAAATTATAGGT
1 AAAAATTATAGGT
20881419 -AAAATTATAGGT
1 AAAAATTATAGGT
*
20881431 ATAAATT
1 AAAAATT
20881438 TTGGAAGGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 12 0.40
13 18 0.60
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.33
Consensus pattern (13 bp):
AAAAATTATAGGT
Found at i:20881733 original size:15 final size:16
Alignment explanation
Indices: 20881696--20881734 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
20881686 AATTTGATAT
*
20881696 TTAAAAAAAGAAATAA
1 TTAAAAATAGAAATAA
20881712 -TAAAAATA-AAATAA
1 TTAAAAATAGAAATAA
20881726 TTAAAAATA
1 TTAAAAATA
20881735 TTAAAAACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (16 bp):
TTAAAAATAGAAATAA
Found at i:20882020 original size:16 final size:17
Alignment explanation
Indices: 20881994--20882031 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
20881984 CTCCAACAAC
**
20881994 TTTATAATTTTTGTATT
1 TTTATAATTTTAATATT
20882011 TTTA-AATTTTAATATT
1 TTTATAATTTTAATATT
20882027 TTTAT
1 TTTAT
20882032 TTTATAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
TTTATAATTTTAATATT
Found at i:20882041 original size:24 final size:22
Alignment explanation
Indices: 20881998--20882044 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 22
20881988 AACAACTTTA
20881998 TAATTTTTGTATTTTTAAATTT
1 TAATTTTTGTATTTTTAAATTT
20882020 TAATATTTT-TATTTTATAAAATTT
1 TAAT-TTTTGTATTTT-T-AAATTT
20882044 T
1 T
20882045 TGCTTTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 10 0.45
23 5 0.23
24 7 0.32
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (22 bp):
TAATTTTTGTATTTTTAAATTT
Found at i:20882507 original size:10 final size:11
Alignment explanation
Indices: 20882485--20882524 Score: 55
Period size: 10 Copynumber: 3.6 Consensus size: 11
20882475 TATATGTCCG
*
20882485 AATAATTATAA
1 AATAAATATAA
20882496 AATAAA-ATAA
1 AATAAATATAA
20882506 AATAAATATAA
1 AATAAATATAA
20882517 ATATAAAT
1 A-ATAAAT
20882525 CAGAAATAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 10 0.38
11 10 0.38
12 6 0.23
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
AATAAATATAA
Found at i:20885299 original size:3 final size:3
Alignment explanation
Indices: 20885291--20885327 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
20885281 ATGTTATATG
20885291 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
20885328 TTGGTTAGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:20887308 original size:31 final size:31
Alignment explanation
Indices: 20887266--20887334 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
20887256 TTTTAATTTA
* *
20887266 GTCACTAACGTTTTAGATCATTTCTATTTTG
1 GTCACTCACGTTTTAGATCATTTATATTTTG
*
20887297 GTCACTCACGTTTTAGATGATTTATATTTTG
1 GTCACTCACGTTTTAGATCATTTATATTTTG
*
20887328 GGCACTC
1 GTCACTC
20887335 TCTCTTAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.45
Consensus pattern (31 bp):
GTCACTCACGTTTTAGATCATTTATATTTTG
Found at i:20887775 original size:9 final size:9
Alignment explanation
Indices: 20887745--20887782 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
20887735 ATATGTATCT
20887745 AAAAATTAA
1 AAAAATTAA
*
20887754 AAATATTAA
1 AAAAATTAA
20887763 AAAAA-TAA
1 AAAAATTAA
20887771 AAAAATCTAA
1 AAAAAT-TAA
20887781 AA
1 AA
20887783 TTCAAGCTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 8 0.32
9 12 0.48
10 5 0.20
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (9 bp):
AAAAATTAA
Found at i:20887782 original size:17 final size:17
Alignment explanation
Indices: 20887741--20887782 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
20887731 AAATATATGT
* *
20887741 ATCTAAAAATTAAAAAT
1 ATCTAAAAAATAAAAAA
20887758 AT-TAAAAAAATAAAAAA
1 ATCT-AAAAAATAAAAAA
20887775 ATCTAAAA
1 ATCTAAAA
20887783 TTCAAGCTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
16 1 0.05
17 19 0.90
18 1 0.05
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (17 bp):
ATCTAAAAAATAAAAAA
Found at i:20890560 original size:547 final size:546
Alignment explanation
Indices: 20889521--20890605 Score: 1590
Period size: 547 Copynumber: 2.0 Consensus size: 546
20889511 GTCTGGAAAG
* * * **
20889521 AAAATCTGTTGTTTATCTAAGATTCGGACATTTATTAACGTAGCATGTGAAGCATGGTATCAAAC
1 AAAATCTATTGTTTATCTAAGATTCGAACATTTATTAACGTAACACATGAAGCATGGTATCAAAC
* *
20889586 GCGTTAAGTGAAAGAATATAGCCTTCCAAGCTGTCTATATGGTAAAGACGTACACATGTTTAAAA
66 GCGTTAAGTAAAAGAACATAGCCTTCCAAGCTGTCTATATGGTAAAGACGTACACATGTTTAAAA
* * * *
20889651 TTTGATCCATATGTTTTAAAATGCTTTTCTATCATATTTGAATTGGCATTTAACAACCAAACTAA
131 TTTGATCCACATGTTTTAAAATGCTTTTATATCATATCTGAATTGACATTTAACAACCAAACTAA
* *
20889716 CAACCAGGTTAATAGAAAAACTTGATTGGTACAGTAATGATACTTTGAGGACTAGATTAAAACGT
196 CAACCAGGTTAATAGAAAAACTTGATTGGCACAGTAATGATACTTTGAGGACTAGATTAAAACAT
* * * *
20889781 TTTGAAGTTTGAGGATCAATTTAGAACTGAACCATAATTTGAATCACATTTAATTACCGGTTATT
261 TTTGAAGTTTGAGGATCAATGTAGAACTGAACCATAATTTAAATCACATTTAATTACCGATTATA
*
20889846 GTGGCTATATCTGGCTCAATCTCAGTGGAAATCTATTAAAAAGTTATATAATCGAACTTGGATGC
326 GTGGC-ATA-CTGGCTCAATCTCAGTGGAAATCTATTAAAAAGTTAAATAATCGAACTTGGATGC
**
20889911 AGTTCTTTAATTTGATTGAACAATATCCATTTAGATCCAATATATCGGAGTATAGTTGATCCTTT
389 AGTTCTTTAATTTGACCGAACAATATCCATTTAGATCCAATATATCGGAGTATAGTTGATCCTTT
20889976 GGTCAAATAAAGTATCATTCATCCTGCTGGAGTCTGTCTTGCTAATAAAATGTTGATTTCCAGTC
454 GGTCAAATAAAGTATCATTCATCCTGCTGGAGTCTGTCTTGCTAATAAAATGTTGATTTCCAGTC
* *
20890041 TAAATCCTCGACAGGTGTCTAGAAAAAA
519 TAAATACTCAACAGGTGTCTAGAAAAAA
*
20890069 AAAATCTATTGTTTATCTAATATTCGAACATTTATTAACGTAACACATGAAGCATGGTATCAAAC
1 AAAATCTATTGTTTATCTAAGATTCGAACATTTATTAACGTAACACATGAAGCATGGTATCAAAC
* * * * * *
20890134 GTGTTAAGTAAAATAACATAGCCTTCCAAGCTGTCTATGTGGTAAGGATGTACACGTGTTTAAAA
66 GCGTTAAGTAAAAGAACATAGCCTTCCAAGCTGTCTATATGGTAAAGACGTACACATGTTTAAAA
* *
20890199 TTTGATCCACGTGTTTTAGATATGCTTTTATATCATATCTGAA-TGACATTTAACAACCAAACTA
131 TTTGATCCACATGTTTTA-AAATGCTTTTATATCATATCTGAATTGACATTTAACAACCAAACTA
* * ** *
20890263 ACAACTAGGTTGATAGAAAAACTTG-TTGGCATGGTAATGATGCTTTGAGGACTAGATTAAAACA
195 ACAACCAGGTTAATAGAAAAACTTGATTGGCACAGTAATGATACTTTGAGGACTAGATTAAAACA
* *
20890327 TTTTGAAGTTTGAGGGTCAATGTAGAACTGAACCATAATTTAAATCTCATTTAATTACTC-ATTA
260 TTTTGAAGTTTGAGGATCAATGTAGAACTGAACCATAATTTAAATCACATTTAATTAC-CGATTA
* * *
20890391 TAGTGGC-TA-T-GCTCAGTCAT-AGTGGAAATCTATTTAAAAGTTAAATAATTGAACTTGGATG
324 TAGTGGCATACTGGCTCAATC-TCAGTGGAAATCTATTAAAAAGTTAAATAATCGAACTTGGATG
** * *
20890452 CAGTTCTTTAATTTGACCGAATGATATCCATTTAGATGATCCGATTAATATCGGAGTATGGTTGA
388 CAGTTCTTTAATTTGACCGAACAATATCCATTT--A-GATCC-AAT-ATATCGGAGTATAGTTGA
* *
20890517 TCCTTTGGTCAAATAAAGTATCATTCATCCTGCTTGAGTCTGTCTTGCTGATAAAATGTTGATTT
448 TCCTTTGGTCAAATAAAGTATCATTCATCCTGCTGGAGTCTGTCTTGCTAATAAAATGTTGATTT
**
20890582 CTGGTCTAAATACTCAACAGGTGT
513 CCAGTCTAAATACTCAACAGGTGT
20890606 TATCATCACG
Statistics
Matches: 480, Mismatches: 49, Indels: 17
0.88 0.09 0.03
Matches are distributed among these distances:
542 74 0.15
543 2 0.00
544 1 0.00
545 7 0.01
546 2 0.00
547 197 0.41
548 176 0.37
549 21 0.04
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (546 bp):
AAAATCTATTGTTTATCTAAGATTCGAACATTTATTAACGTAACACATGAAGCATGGTATCAAAC
GCGTTAAGTAAAAGAACATAGCCTTCCAAGCTGTCTATATGGTAAAGACGTACACATGTTTAAAA
TTTGATCCACATGTTTTAAAATGCTTTTATATCATATCTGAATTGACATTTAACAACCAAACTAA
CAACCAGGTTAATAGAAAAACTTGATTGGCACAGTAATGATACTTTGAGGACTAGATTAAAACAT
TTTGAAGTTTGAGGATCAATGTAGAACTGAACCATAATTTAAATCACATTTAATTACCGATTATA
GTGGCATACTGGCTCAATCTCAGTGGAAATCTATTAAAAAGTTAAATAATCGAACTTGGATGCAG
TTCTTTAATTTGACCGAACAATATCCATTTAGATCCAATATATCGGAGTATAGTTGATCCTTTGG
TCAAATAAAGTATCATTCATCCTGCTGGAGTCTGTCTTGCTAATAAAATGTTGATTTCCAGTCTA
AATACTCAACAGGTGTCTAGAAAAAA
Found at i:20895243 original size:20 final size:21
Alignment explanation
Indices: 20895215--20895257 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
20895205 CGTCTTCTTC
*
20895215 TTCTATTTTGC-TTCAAAAAT
1 TTCTATTTTACTTTCAAAAAT
* *
20895235 TTCTCTTTTACTTTCAAATAT
1 TTCTATTTTACTTTCAAAAAT
20895256 TT
1 TT
20895258 TTTATTAAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.26, C:0.16, G:0.02, T:0.56
Consensus pattern (21 bp):
TTCTATTTTACTTTCAAAAAT
Found at i:20895993 original size:139 final size:139
Alignment explanation
Indices: 20895787--20896044 Score: 428
Period size: 139 Copynumber: 1.9 Consensus size: 139
20895777 CCCATGGATG
20895787 TTTTTAGAGATTTAAAGTTTGGGTGGTTTTTTTTAAAATGTAATTAGGATCTAATGATGATATTG
1 TTTTTAGAGATTTAAAGTTTGGGTGGTTTTTTTTAAAATGTAATTAGGATCTAATGATGATATTG
*
20895852 ATAAATCGGAATTTATTCAATATCTTAAACTAAAATTAGCTTACTTTAGAATATAATGATGACTT
66 ATAAATCGGAATTAATTCAATATCTTAAACTAAAATTAGCTTACTTTAGAATATAATGATGACTT
20895917 TTTAAAATT
131 TTTAAAATT
* **
20895926 TTTTTAGAGATTTAAAGTTTGGGTTGTTTTTGTTT-TGATGTAATTAGGATCTAATGATGATATT
1 TTTTTAGAGATTTAAAGTTTGGGTGGTTTTT-TTTAAAATGTAATTAGGATCTAATGATGATATT
* * * *
20895990 GATAAATTGGAATTAATTTAATATCTTAAACTAAAATTGGCTTTCTTTAGAATAT
65 GATAAATCGGAATTAATTCAATATCTTAAACTAAAATTAGCTTACTTTAGAATAT
20896045 GATAAGCAAG
Statistics
Matches: 110, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
139 107 0.97
140 3 0.03
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.45
Consensus pattern (139 bp):
TTTTTAGAGATTTAAAGTTTGGGTGGTTTTTTTTAAAATGTAATTAGGATCTAATGATGATATTG
ATAAATCGGAATTAATTCAATATCTTAAACTAAAATTAGCTTACTTTAGAATATAATGATGACTT
TTTAAAATT
Found at i:20901421 original size:3 final size:3
Alignment explanation
Indices: 20901415--20901440 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
20901405 CTGCTGCTAC
20901415 CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CA
20901441 ACTTCAATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:20904297 original size:15 final size:14
Alignment explanation
Indices: 20904277--20904309 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
20904267 AATAATGTCG
20904277 GTATATATATGTATA
1 GTATATATAT-TATA
20904292 GTATATATATTATA
1 GTATATATATTATA
20904306 -TATA
1 GTATA
20904310 GTAAAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 4 0.22
15 10 0.56
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.48
Consensus pattern (14 bp):
GTATATATATTATA
Found at i:20907910 original size:21 final size:21
Alignment explanation
Indices: 20907886--20907927 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 21
20907876 ATTACAAAAA
20907886 AAAAGAAAAAAAAAAGA-GATG
1 AAAA-AAAAAAAAAAGATGATG
* *
20907907 AAAAAACAAATAAAGATGATG
1 AAAAAAAAAAAAAAGATGATG
20907928 TTATCCTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.71, C:0.02, G:0.17, T:0.10
Consensus pattern (21 bp):
AAAAAAAAAAAAAAGATGATG
Found at i:20908598 original size:134 final size:134
Alignment explanation
Indices: 20908293--20908659 Score: 563
Period size: 134 Copynumber: 2.7 Consensus size: 134
20908283 GGTGAAAAAG
* * * * * *
20908293 AACAAATTCGACTAACGCAAAGCTCGAATTCAAGCCACACCTGGGGCAATGAATACATTTGACCC
1 AACAAACTCGACTAGCGC-AA-CTCGAACTCAGGCCACACCTGGGGCAATGAATACCTTTGACCA
*
20908358 TCAAACTATTACATGATCCCACTATAAGATAAAACTTTTTTGGTGAATTGCAATAATAGGACAAA
64 TCAAACTATTACATGATCCCACTATAAGAT--AACTTTTTTGGTGAATTGCAATAACAGGACAAA
* *
20908423 GCCCGAAT
127 GCCCAAAC
* *
20908431 AACAAACTCGACTAGCGCGACTCGAACCCAGGCCACACCTGGGGCAATGAATACCTTTGACCATC
1 AACAAACTCGACTAGCGCAACTCGAACTCAGGCCACACCTGGGGCAATGAATACCTTTGACCATC
* * *
20908496 AAACTATTACATAATCCCACTATAAGATAATTTTTTTGGTGAATTGCAATAACAGGGCAAAGCCC
66 AAACTATTACATGATCCCACTATAAGATAACTTTTTTGGTGAATTGCAATAACAGGACAAAGCCC
20908561 AAAC
131 AAAC
*
20908565 AACAAACTCGACTAGCGCAACTCGAACTCAGGCCACACCTGGGGCAATGAACACCTTTGACCATC
1 AACAAACTCGACTAGCGCAACTCGAACTCAGGCCACACCTGGGGCAATGAATACCTTTGACCATC
20908630 AAACTATTACATGATCCCACTATAAGATAA
66 AAACTATTACATGATCCCACTATAAGATAA
20908660 AAACTTAATC
Statistics
Matches: 211, Mismatches: 18, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
134 127 0.60
136 67 0.32
137 1 0.00
138 16 0.08
ACGTcount: A:0.37, C:0.26, G:0.16, T:0.22
Consensus pattern (134 bp):
AACAAACTCGACTAGCGCAACTCGAACTCAGGCCACACCTGGGGCAATGAATACCTTTGACCATC
AAACTATTACATGATCCCACTATAAGATAACTTTTTTGGTGAATTGCAATAACAGGACAAAGCCC
AAAC
Found at i:20913138 original size:314 final size:312
Alignment explanation
Indices: 20912388--20913146 Score: 899
Period size: 314 Copynumber: 2.4 Consensus size: 312
20912378 AATAGGCTCA
* * *
20912388 AGAAATTGAGTTGAAGAAG-AAAA-AAAACCTGTTTAGAAGTTAAAATATATCCAAATCTCTGTG
1 AGAAATAGAGTTGAGGAAGAAAAACAAAACCTGTTTA-AAGTTAAAATATATCCAAATCCCTGTG
* *
20912451 CT-TTGTGTACGCTTTAATGGTGTTAATAATT-AGACCTGATTGTTATTGGTGTGATTAATACTT
65 CTCTT-TGTACGTTTTAATGGTGTTAATAATTGA-ACCTGATTGATATTGGTGTGATTAATACTT
* * *
20912514 GTATGGGTTCATGTATCTTGTTTTTGTTCATGAATTCTGGGGTAGGGTTTAACAATATTTTTAGA
128 GTATGGATTCATGTATCTTGTTTTTGTTCATAAATTCTGGGGTAGGGTTTAACAAGATTTTTAGA
* * * *
20912579 CCACTCAATCATGGTGATCCAAGCTGCCCCCTTAGGGCTTGTTCGAGGGTCGAACTCCCTGTTCA
193 CCACCCAATCATGGTGATCCAAGCTGCCCCCTTAAGGCTTGTTCGAGCGTCGAACCCCCTGTTCA
* * * *
20912644 AGCTCGAAGACTCATTTTGATCTTTGGGGTGATTTGGATGAAAGTATTTGGTCTG
258 AGCTCAAAGACTCATTTAGATCTTTGGGATGATTTGGATGAAAGTATTAGGTCTG
* * * *
20912699 AGAAATAAAGTTAAGGAAGCAAAAAC--AACCTGTTTAAAGGTTAAAATAGT-TCGAAGTCCCTG
1 AGAAATAGAGTTGAGGAAG-AAAAACAAAACCTGTTTAAA-GTTAAAATA-TATCCAAATCCCTG
* * ** * *
20912761 TGCTCTTTGTACGTTTTAACGATGTTAACGATTGGACTTGATTGATATTGGTGTGATTAATACTT
63 TGCTCTTTGTACGTTTTAATGGTGTTAATAATTGAACCTGATTGATATTGGTGTGATTAATACTT
* * * * *
20912826 GTATGGATTCATGTATCTTGTTTCTTATTTCATAAATTTTGTGGTAGTGTTTAACCAGATTTTTA
128 GTATGGATTCATGTATCTTGTTT-TT-GTTCATAAATTCTGGGGTAGGGTTTAACAAGATTTTTA
** * * * *
20912891 GATGACCCAATCTTGGTGATCCAAGTTGCCCCCTTTAAGGCTTTTTTGAGCGTCG-ACCCACCTG
191 GACCACCCAATCATGGTGATCCAAGCTGCCCCC-TTAAGGCTTGTTCGAGCGTCGAACCC-CCTG
* ** * * * * *
20912955 TTCAAGTTCAAAGTTTTA-TTAGTTTTTTGGGATGGTTTGGATGAAAGTATTAGGTTTG
254 TTCAAGCTCAAAGACTCATTTAGATCTTTGGGATGATTTGGATGAAAGTATTAGGTCTG
* *
20913013 AGAAATGGAGTTGAGGAAGAAAAACAAAACCTGTTTAAAGATTAAAATATACCCAAATCCCTGTG
1 AGAAATAGAGTTGAGGAAGAAAAACAAAACCTGTTTAAAG-TTAAAATATATCCAAATCCCTGTG
* * *
20913078 CTCTTTGTACGTTTTAATGGTGTTAATAATTGAACCTAATTGATA-TGGTATGACTAATACTTGT
65 CTCTTTGTACGTTTTAATGGTGTTAATAATTGAACCTGATTGATATTGGTGTGATTAATACTTGT
20913142 ATGGA
130 ATGGA
20913147 CCTGAATTTT
Statistics
Matches: 373, Mismatches: 60, Indels: 27
0.81 0.13 0.06
Matches are distributed among these distances:
311 17 0.05
312 103 0.28
313 15 0.04
314 135 0.36
315 103 0.28
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.37
Consensus pattern (312 bp):
AGAAATAGAGTTGAGGAAGAAAAACAAAACCTGTTTAAAGTTAAAATATATCCAAATCCCTGTGC
TCTTTGTACGTTTTAATGGTGTTAATAATTGAACCTGATTGATATTGGTGTGATTAATACTTGTA
TGGATTCATGTATCTTGTTTTTGTTCATAAATTCTGGGGTAGGGTTTAACAAGATTTTTAGACCA
CCCAATCATGGTGATCCAAGCTGCCCCCTTAAGGCTTGTTCGAGCGTCGAACCCCCTGTTCAAGC
TCAAAGACTCATTTAGATCTTTGGGATGATTTGGATGAAAGTATTAGGTCTG
Found at i:20913551 original size:31 final size:32
Alignment explanation
Indices: 20913515--20913588 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 32
20913505 TTTTTTTAGT
*
20913515 CTAA-TTAGTACCCCAAACTTGACATTTTTTC
1 CTAAGTTAGTACCCCAAACTTGACACTTTTTC
* * * *
20913546 CTAATTTGGTA-TCTAAACTTGACACTTTTTC
1 CTAAGTTAGTACCCCAAACTTGACACTTTTTC
*
20913577 TTAAGTTAGTAC
1 CTAAGTTAGTAC
20913589 TTAAAACTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
31 29 0.85
32 5 0.15
ACGTcount: A:0.28, C:0.20, G:0.09, T:0.42
Consensus pattern (32 bp):
CTAAGTTAGTACCCCAAACTTGACACTTTTTC
Found at i:20913597 original size:32 final size:31
Alignment explanation
Indices: 20913529--20913587 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
20913519 TTAGTACCCC
* * *
20913529 AAACTTGACATTTTTTCCTAATTTGGTATCT
1 AAACTTGACACTTTTTCCTAAGTTAGTATCT
*
20913560 AAACTTGACACTTTTTCTTAAGTTAGTA
1 AAACTTGACACTTTTTCCTAAGTTAGTA
20913588 CTTAAAACTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.29, C:0.15, G:0.10, T:0.46
Consensus pattern (31 bp):
AAACTTGACACTTTTTCCTAAGTTAGTATCT
Found at i:20913798 original size:4 final size:4
Alignment explanation
Indices: 20913789--20913818 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
20913779 ACTTTTAGTT
*
20913789 TTAA TTAA TTAA TTAA TTAA TTTA TTAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TT
20913819 GAAAATAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (4 bp):
TTAA
Found at i:20918872 original size:23 final size:25
Alignment explanation
Indices: 20918805--20918873 Score: 79
Period size: 23 Copynumber: 2.8 Consensus size: 25
20918795 TTCAATGTTT
20918805 AATTTGGTACTTGAGTTTTTTGTCTC
1 AATTTGGTACTTGAG-TTTTTGTCTC
* * *
20918831 AAATTGGTACCTGAATTTTT-T-TC
1 AATTTGGTACTTGAGTTTTTGTCTC
*
20918854 AATTTGATACTTGAGTTTTT
1 AATTTGGTACTTGAGTTTTT
20918874 CTTTATCTCA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
23 18 0.50
24 1 0.03
25 5 0.14
26 12 0.33
ACGTcount: A:0.22, C:0.10, G:0.16, T:0.52
Consensus pattern (25 bp):
AATTTGGTACTTGAGTTTTTGTCTC
Found at i:20927765 original size:10 final size:10
Alignment explanation
Indices: 20927750--20927790 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
20927740 GTGATTAGCA
20927750 TGTATGTATG
1 TGTATGTATG
**
20927760 TGTATGCGTG
1 TGTATGTATG
20927770 TGTATGTATG
1 TGTATGTATG
*
20927780 TATATGTATG
1 TGTATGTATG
20927790 T
1 T
20927791 ATGTAAGGTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.20, C:0.02, G:0.29, T:0.49
Consensus pattern (10 bp):
TGTATGTATG
Found at i:20928932 original size:62 final size:60
Alignment explanation
Indices: 20928835--20928978 Score: 150
Period size: 63 Copynumber: 2.3 Consensus size: 60
20928825 TTGGAGGGGC
* *
20928835 TAATTAAAATTTTCGAAAATTTTAAGAGTTCAATGAGATTTTTTCAAAAAAAAAATAGAGAT
1 TAATTAAAATTTTCAAAAATTTTAAGAGTTCAATGAGA--ATTTCAAAAAAAAAATAGAGAT
* *
20928897 TAATTAAAATTTTTAAAAATTTTGTTAGA-TT-AATGAGAATTTCAAAAAAAAAATTAAAGAGCA
1 TAATTAAAATTTTCAAAAA-TTT-TAAGAGTTCAATGAGAATTTCAAAAAAAAAA-T--AGAG-A
20928960 -
60 T
*
20928960 TAATTAAAGTTTTCAAAAA
1 TAATTAAAATTTTCAAAAA
20928979 AAATTAAAAG
Statistics
Matches: 70, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
60 14 0.20
61 1 0.01
62 24 0.34
63 26 0.37
64 5 0.07
ACGTcount: A:0.51, C:0.04, G:0.10, T:0.35
Consensus pattern (60 bp):
TAATTAAAATTTTCAAAAATTTTAAGAGTTCAATGAGAATTTCAAAAAAAAAATAGAGAT
Found at i:20928978 original size:32 final size:32
Alignment explanation
Indices: 20928942--20929010 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 32
20928932 AGAATTTCAA
* *
20928942 AAAAAAAATT-AAAGAGCATAATTAAAGTTTTC
1 AAAAAAAATTAAAAG-GCATAATGAAAATTTTC
20928974 AAAAAAAATTAAAAGGCATAATGAAAATTTTC
1 AAAAAAAATTAAAAGGCATAATGAAAATTTTC
20929006 AAAAA
1 AAAAA
20929011 TTTGGAGGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 30 0.88
33 4 0.12
ACGTcount: A:0.61, C:0.06, G:0.09, T:0.25
Consensus pattern (32 bp):
AAAAAAAATTAAAAGGCATAATGAAAATTTTC
Found at i:20928978 original size:33 final size:33
Alignment explanation
Indices: 20928927--20929010 Score: 102
Period size: 32 Copynumber: 2.6 Consensus size: 33
20928917 TTTGTTAGAT
*
20928927 TAATGAGAA-TTTCAAAAAAAAAATT-AAAGAGCA
1 TAATGAAAATTTTC-AAAAAAAAATTAAAAG-GCA
* *
20928960 TAATTAAAGTTTTC-AAAAAAAATTAAAAGGCA
1 TAATGAAAATTTTCAAAAAAAAATTAAAAGGCA
20928992 TAATGAAAATTTTCAAAAA
1 TAATGAAAATTTTCAAAAA
20929011 TTTGGAGGGT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
32 25 0.58
33 14 0.33
34 4 0.09
ACGTcount: A:0.58, C:0.06, G:0.10, T:0.26
Consensus pattern (33 bp):
TAATGAAAATTTTCAAAAAAAAATTAAAAGGCA
Found at i:20934976 original size:17 final size:17
Alignment explanation
Indices: 20934954--20934987 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
20934944 TAATAATGTG
20934954 TTATAGATATAGTACAA
1 TTATAGATATAGTACAA
20934971 TTATAGATATAGTACAA
1 TTATAGATATAGTACAA
20934988 ATTACAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (17 bp):
TTATAGATATAGTACAA
Found at i:20942907 original size:76 final size:77
Alignment explanation
Indices: 20942822--20942974 Score: 299
Period size: 76 Copynumber: 2.0 Consensus size: 77
20942812 TTTTTTTAAT
20942822 AAAAATATTGACTAAAATGTTAAAATTTTAAATATGGTAGCCTACATGGCAATCCATGTGTACTT
1 AAAAATATTGACTAAAATGTTAAAATTTTAAATATGGTAGCCTACATGGCAATCCATGTGTACTT
20942887 C-ATCTAATTTA
66 CAATCTAATTTA
20942898 AAAAATATTGACTAAAATGTTAAAATTTTAAATATGGTAGCCTACATGGCAATCCATGTGTACTT
1 AAAAATATTGACTAAAATGTTAAAATTTTAAATATGGTAGCCTACATGGCAATCCATGTGTACTT
20942963 CAATCTAATTTA
66 CAATCTAATTTA
20942975 TTAAATTTTT
Statistics
Matches: 76, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
76 66 0.87
77 10 0.13
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (77 bp):
AAAAATATTGACTAAAATGTTAAAATTTTAAATATGGTAGCCTACATGGCAATCCATGTGTACTT
CAATCTAATTTA
Found at i:20947472 original size:10 final size:10
Alignment explanation
Indices: 20947457--20947483 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
20947447 TATAAAATCT
20947457 AAAAAATATA
1 AAAAAATATA
20947467 AAAAAATATA
1 AAAAAATATA
20947477 AAAAAAT
1 AAAAAAT
20947484 TCAGTTAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (10 bp):
AAAAAATATA
Found at i:20967447 original size:58 final size:58
Alignment explanation
Indices: 20967372--20967481 Score: 184
Period size: 58 Copynumber: 1.9 Consensus size: 58
20967362 AAATATATTA
* *
20967372 AAAATATTATTAAATTATATATTATTTTTATTAAATTATATTTAATAATAATTACGTT
1 AAAATATGATTAAATTATATATTATTTTTATCAAATTATATTTAATAATAATTACGTT
* *
20967430 AAAATATGATTAAATTATTTATTATTTTTATCAAATTATTTTTAATAATAAT
1 AAAATATGATTAAATTATATATTATTTTTATCAAATTATATTTAATAATAAT
20967482 CCTATTAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 48 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (58 bp):
AAAATATGATTAAATTATATATTATTTTTATCAAATTATATTTAATAATAATTACGTT
Found at i:20967490 original size:58 final size:56
Alignment explanation
Indices: 20967367--20967492 Score: 171
Period size: 58 Copynumber: 2.2 Consensus size: 56
20967357 AAAATAAATA
* *
20967367 TATTAAAAATATTATTAAATTATATATTATTTTTATTAAATTATATTTAATAATAAT
1 TATT-AAAATATGATTAAATTATATATTATTTTTATCAAATTATATTTAATAATAAT
* *
20967424 TACGTTAAAATATGATTAAATTATTTATTATTTTTATCAAATTATTTTTAATAATAAT
1 TA--TTAAAATATGATTAAATTATATATTATTTTTATCAAATTATATTTAATAATAAT
20967482 CCTATTAAAAT
1 --TATTAAAAT
20967493 TTAATAACAA
Statistics
Matches: 61, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
57 2 0.03
58 55 0.90
59 2 0.03
60 2 0.03
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (56 bp):
TATTAAAATATGATTAAATTATATATTATTTTTATCAAATTATATTTAATAATAAT
Found at i:20971726 original size:57 final size:57
Alignment explanation
Indices: 20971657--20971771 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
20971647 AATTAGAACC
20971657 ATGGTAATCAATATTGTTTCGATATTGATTATGCCTTAAACCATTGGTAAGCAGTTT
1 ATGGTAATCAATATTGTTTCGATATTGATTATGCCTTAAACCATTGGTAAGCAGTTT
20971714 ATGGTAATCAATATTGTTTCGATATTGATTATGCCTTAAACCATTGGTAAGCAGTTT
1 ATGGTAATCAATATTGTTTCGATATTGATTATGCCTTAAACCATTGGTAAGCAGTTT
20971771 A
1 A
20971772 AGTTCCATTC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.40
Consensus pattern (57 bp):
ATGGTAATCAATATTGTTTCGATATTGATTATGCCTTAAACCATTGGTAAGCAGTTT
Found at i:20974340 original size:59 final size:60
Alignment explanation
Indices: 20974191--20974341 Score: 148
Period size: 61 Copynumber: 2.5 Consensus size: 60
20974181 AATTAGGGCA
* * ** * *
20974191 AAAAAACTCAGGTACTAAATTAAACATTGAATTCAAACTCTAGTGCTTAAATGGGACAAAG
1 AAAAAACTTAGGTACTAAATTAAACATTAAAACCAAACTCTAGTGATTAAATGGGAC-AAC
* * *
20974252 AAAAAACTTAAGTA-TAAAATTGAACATTAAAACCAAACT-TAGAT-ATTAACTTGGGAC-AC
1 AAAAAACTTAGGTACT-AAATTAAACATTAAAACCAAACTCTAG-TGATTAA-ATGGGACAAC
*
20974311 AAAAAACTTAGGTACTGAATTAAACATTAAA
1 AAAAAACTTAGGTACTAAATTAAACATTAAA
20974342 GCTAAGCTCA
Statistics
Matches: 74, Mismatches: 12, Indels: 10
0.77 0.12 0.10
Matches are distributed among these distances:
59 27 0.36
60 9 0.12
61 38 0.51
ACGTcount: A:0.50, C:0.13, G:0.12, T:0.25
Consensus pattern (60 bp):
AAAAAACTTAGGTACTAAATTAAACATTAAAACCAAACTCTAGTGATTAAATGGGACAAC
Found at i:20974553 original size:4 final size:5
Alignment explanation
Indices: 20974528--20974574 Score: 53
Period size: 5 Copynumber: 9.2 Consensus size: 5
20974518 GTTATTATAT
20974528 TTTTC TTTTC TTTTC TTTTC -TTTC -TTTC TTCTTC TTCTTC TTCTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TT-TTC TT-TTC TT-TTC
20974574 T
1 T
20974575 ACTTTTTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
4 8 0.20
5 16 0.40
6 16 0.40
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (5 bp):
TTTTC
Found at i:20974561 original size:3 final size:3
Alignment explanation
Indices: 20974530--20974574 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
20974520 TATTATATTT
20974530 TTC TT- TTC TT- TTC TT- TTC TTTC TTTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC -TTC -TTC TTC TTC TTC TTC TTC TTC
20974574 T
1 T
20974575 ACTTTTTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 6 0.16
3 25 0.66
4 7 0.18
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (3 bp):
TTC
Found at i:20975041 original size:12 final size:12
Alignment explanation
Indices: 20975024--20975058 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
20975014 TGTTGACTTC
20975024 AAATATTAAATT
1 AAATATTAAATT
20975036 AAATATTAAAGTT
1 AAATATTAAA-TT
20975049 AAA-ATTAAAT
1 AAATATTAAAT
20975059 ACCAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 1 0.05
12 16 0.73
13 5 0.23
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (12 bp):
AAATATTAAATT
Found at i:20979848 original size:10 final size:10
Alignment explanation
Indices: 20979814--20979870 Score: 69
Period size: 10 Copynumber: 5.6 Consensus size: 10
20979804 ATTCAAAAAA
20979814 AAAAATCACT
1 AAAAATCACT
**
20979824 AACTATCACT
1 AAAAATCACT
* *
20979834 TAAAAGCACT
1 AAAAATCACT
20979844 AAAAATTCACT
1 AAAAA-TCACT
20979855 AAAAATCACT
1 AAAAATCACT
20979865 AAAAAT
1 AAAAAT
20979871 TCAAAAAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
10 29 0.76
11 9 0.24
ACGTcount: A:0.56, C:0.19, G:0.02, T:0.23
Consensus pattern (10 bp):
AAAAATCACT
Found at i:20979853 original size:21 final size:21
Alignment explanation
Indices: 20979829--20979873 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
20979819 TCACTAACTA
*
20979829 TCACTTAAAAGCACTAAAAAT
1 TCACTAAAAAGCACTAAAAAT
*
20979850 TCACTAAAAATCACTAAAAAT
1 TCACTAAAAAGCACTAAAAAT
20979871 TCA
1 TCA
20979874 AAAAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.53, C:0.20, G:0.02, T:0.24
Consensus pattern (21 bp):
TCACTAAAAAGCACTAAAAAT
Found at i:20979856 original size:11 final size:11
Alignment explanation
Indices: 20979840--20979873 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
20979830 CACTTAAAAG
20979840 CACTAAAAATT
1 CACTAAAAATT
20979851 CACTAAAAA-T
1 CACTAAAAATT
20979861 CACTAAAAATT
1 CACTAAAAATT
20979872 CA
1 CA
20979874 AAAAAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.45
11 12 0.55
ACGTcount: A:0.56, C:0.21, G:0.00, T:0.24
Consensus pattern (11 bp):
CACTAAAAATT
Found at i:20979879 original size:21 final size:21
Alignment explanation
Indices: 20979835--20979881 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
20979825 ACTATCACTT
* **
20979835 AAAAGCACTAAAAATTCACTA
1 AAAATCACTAAAAATTCAAAA
20979856 AAAATCACTAAAAATTCAAAA
1 AAAATCACTAAAAATTCAAAA
20979877 AAAAT
1 AAAAT
20979882 AATCGAAACG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.64, C:0.15, G:0.02, T:0.19
Consensus pattern (21 bp):
AAAATCACTAAAAATTCAAAA
Found at i:20981963 original size:18 final size:20
Alignment explanation
Indices: 20981942--20981985 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 20
20981932 AAAAATTCAA
*
20981942 AAAATATAT-TTAAAAA-TT
1 AAAATATATATTAAAAACAT
20981960 AAAA-AT-TATTAAAAACAT
1 AAAATATATATTAAAAACAT
20981978 AAAATATA
1 AAAATATA
20981986 AAAAATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 6
0.75 0.04 0.21
Matches are distributed among these distances:
16 1 0.05
17 9 0.43
18 9 0.43
19 2 0.10
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAATATATATTAAAAACAT
Found at i:20982213 original size:3 final size:3
Alignment explanation
Indices: 20982207--20982236 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
20982197 TTATTATACC
20982207 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
20982237 AAAATCTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:20982564 original size:26 final size:26
Alignment explanation
Indices: 20982513--20982564 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
20982503 TTTTCTTTTG
* *
20982513 TTTGACCAAATTATACTTTTGCAAAA
1 TTTGACCAAATTATACTTATGAAAAA
*
20982539 TTTGACC-AATTCTACTTCATGAAAAA
1 TTTGACCAAATTATACTT-ATGAAAAA
20982565 CCTTTGTGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (26 bp):
TTTGACCAAATTATACTTATGAAAAA
Found at i:20983585 original size:14 final size:13
Alignment explanation
Indices: 20983563--20983596 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
20983553 AAAGTATTTT
*
20983563 AAAATTAAAAATTA
1 AAAAATAAAAA-TA
20983577 AAAAATAAAAATA
1 AAAAATAAAAATA
20983590 AAAAATA
1 AAAAATA
20983597 TATATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAAATAAAAATA
Found at i:20987302 original size:22 final size:25
Alignment explanation
Indices: 20987270--20987318 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 25
20987260 CAATTTAATT
20987270 AAATAAATTA-TAAAAA-TAAAGAA
1 AAATAAATTATTAAAAATTAAAGAA
*
20987293 AAAT-AATTATTAAAAATTAGAGAA
1 AAATAAATTATTAAAAATTAAAGAA
20987317 AA
1 AA
20987319 CTGATTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 5 0.22
23 10 0.43
24 8 0.35
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.24
Consensus pattern (25 bp):
AAATAAATTATTAAAAATTAAAGAA
Found at i:20987460 original size:26 final size:26
Alignment explanation
Indices: 20987419--20987473 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
20987409 CTAATTTGGC
20987419 AATGTTTTTGAAAAGTGCTGTAGAAA
1 AATGTTTTTGAAAAGTGCTGTAGAAA
* *
20987445 AATGTTTTT-AAGAAGTGCTTTTGAAA
1 AATGTTTTTGAA-AAGTGCTGTAGAAA
20987471 AAT
1 AAT
20987474 TTAAGTGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 2 0.08
26 24 0.92
ACGTcount: A:0.38, C:0.04, G:0.20, T:0.38
Consensus pattern (26 bp):
AATGTTTTTGAAAAGTGCTGTAGAAA
Found at i:20998912 original size:14 final size:14
Alignment explanation
Indices: 20998893--20998920 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
20998883 AACCTGTTAA
20998893 ATCAATTATCAAAT
1 ATCAATTATCAAAT
20998907 ATCAATTATCAAAT
1 ATCAATTATCAAAT
20998921 CAATTTCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (14 bp):
ATCAATTATCAAAT
Found at i:21001336 original size:18 final size:18
Alignment explanation
Indices: 21001313--21001353 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
21001303 ATCCACTATT
21001313 TAAATATAAATAAATAAA
1 TAAATATAAATAAATAAA
* * *
21001331 TAAATATATATATATATA
1 TAAATATAAATAAATAAA
21001349 TAAAT
1 TAAAT
21001354 TAGACTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TAAATATAAATAAATAAA
Found at i:21009557 original size:239 final size:237
Alignment explanation
Indices: 21009176--21009703 Score: 744
Period size: 239 Copynumber: 2.2 Consensus size: 237
21009166 AATTTTAGAG
* * *
21009176 GGAACAAATAAAGGCTAAATTCATGGTTATATTTGGACAAGAAAATCTTGAAAAGGACACTCTCA
1 GGAATAAATAAAGGCTAAATTCATGGTTATACTTGGACAACAAAATCTTGAAAAGGACACTCTCA
* * * * *
21009241 ATGATCATTATTCAAACTTTGTTGATATAATCCCACTCTCCTGTATTGTAACTTCACTCGGTACT
66 ATGACCATTATTCAAACTTTGTTGATAGAATCCCACTCTCCTGAATTGTAAATTAACTCGGTACT
* * *
21009306 CTCTACTCACCCAAGAAA-TGA-TCAAATTATAGTAGAGAGATTAAATTTGTGGGAAAAAAATAA
131 CTCCAATCACCCAA-AAATTGACT-AAATTATAGTAGAGAGACTAAATTTGT--G-AAAAAA-AA
* * *
21009369 ATAATAGAGGGAGTTTCTATGAAATTTGACCAATTTTATTATATACGG-
190 ATAATAGAGGGACTTTCCATGAAATTTGACCAATTCTATTATATA-GGT
* *
21009417 GG-ATAAATAATGGCTAAATTCATGGTTATACTTGGACAACAAAATCTTGAAAAGG-CACTTTCA
1 GGAATAAATAAAGGCTAAATTCATGGTTATACTTGGACAACAAAATCTTGAAAAGGACACTCTCA
*
21009480 ATGACCATTATTCAAACTTTGTTGATAGAATCCCACTCTCTTGAACTT-TAAATTAACTCGGTAC
66 ATGACCATTATTCAAACTTTGTTGATAGAATCCCACTCTCCTGAA-TTGTAAATTAACTCGGTAC
*
21009544 TCTCCAATCACCCAAAAATTGACTAAATTATAGTAGAGAGGCTAAATTTGTGAAAAAAAAATAAT
130 TCTCCAATCACCCAAAAATTGACTAAATTATAGTAGAGAGACTAAATTTGTGAAAAAAAAATAAT
*
21009609 AGAGGGACTTTCCGTGAAATTTGACCAATTCTATTATATAGGT
195 AGAGGGACTTTCCATGAAATTTGACCAATTCTATTATATAGGT
* * *
21009652 GGAATAAATAAAGGCTAAATACATGGTTATCCATGGACAACAAAATCTTGAA
1 GGAATAAATAAAGGCTAAATTCATGGTTATACTTGGACAACAAAATCTTGAA
21009704 GGGGTAGTCT
Statistics
Matches: 259, Mismatches: 23, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
234 2 0.01
235 45 0.17
236 51 0.20
237 1 0.00
238 3 0.01
239 103 0.40
240 52 0.20
241 2 0.01
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (237 bp):
GGAATAAATAAAGGCTAAATTCATGGTTATACTTGGACAACAAAATCTTGAAAAGGACACTCTCA
ATGACCATTATTCAAACTTTGTTGATAGAATCCCACTCTCCTGAATTGTAAATTAACTCGGTACT
CTCCAATCACCCAAAAATTGACTAAATTATAGTAGAGAGACTAAATTTGTGAAAAAAAAATAATA
GAGGGACTTTCCATGAAATTTGACCAATTCTATTATATAGGT
Found at i:21011596 original size:29 final size:30
Alignment explanation
Indices: 21011530--21011599 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
21011520 CAATCAACAA
**
21011530 ATTTCATTTTAACATTTTTTTTATGAATAAT
1 ATTT-ATTTTAACATTTTTTGCATGAATAAT
* * *
21011561 GTATATTTTAA-ATTTTTTGCATGAATTAT
1 ATTTATTTTAACATTTTTTGCATGAATAAT
21011590 ATTTATTTTA
1 ATTTATTTTA
21011600 TAATGATAAG
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
29 23 0.72
30 7 0.22
31 2 0.06
ACGTcount: A:0.31, C:0.04, G:0.06, T:0.59
Consensus pattern (30 bp):
ATTTATTTTAACATTTTTTGCATGAATAAT
Found at i:21018154 original size:30 final size:28
Alignment explanation
Indices: 21018113--21018171 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 28
21018103 ACATGCTTAA
*
21018113 TTATAATTTTAGCCTCTAATATTTTTCATT
1 TTATAATTTTAGCC-CTAAT-TATTTCATT
*
21018143 TTATCATTTTAGCCCTAATTATTTCATT
1 TTATAATTTTAGCCCTAATTATTTCATT
21018171 T
1 T
21018172 AAATCACTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 9 0.33
29 5 0.19
30 13 0.48
ACGTcount: A:0.25, C:0.15, G:0.03, T:0.56
Consensus pattern (28 bp):
TTATAATTTTAGCCCTAATTATTTCATT
Done.