Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 25 of 120
Found at i:6551331 original size:31 final size:29
Alignment explanation
Indices: 6551280--6551354 Score: 123
Period size: 31 Copynumber: 2.5 Consensus size: 29
6551270 TAAATGATTT
*
6551280 TAAAATTATTAAAATTATTTTTTAAAATA
1 TAAAATTATTAAAATGATTTTTTAAAATA
6551309 TAAAATTAATTTAAAATGATTTTTTAAAATA
1 TAAAATT-A-TTAAAATGATTTTTTAAAATA
6551340 TAAAATTATTAAAAT
1 TAAAATTATTAAAAT
6551355 TATTAAAATT
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
29 14 0.33
30 2 0.05
31 27 0.63
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (29 bp):
TAAAATTATTAAAATGATTTTTTAAAATA
Found at i:6551354 original size:9 final size:9
Alignment explanation
Indices: 6551332--6551377 Score: 60
Period size: 9 Copynumber: 5.1 Consensus size: 9
6551322 AAATGATTTT
6551332 TTAAAA-TA
1 TTAAAATTA
6551340 -TAAAATTA
1 TTAAAATTA
6551348 TTAAAATTA
1 TTAAAATTA
6551357 TTAAAATTA
1 TTAAAATTA
6551366 TTTTAAAATTA
1 --TTAAAATTA
6551377 T
1 T
6551378 AATCATCATC
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
7 5 0.15
8 2 0.06
9 18 0.53
11 9 0.26
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
TTAAAATTA
Found at i:6551984 original size:27 final size:27
Alignment explanation
Indices: 6551954--6552006 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
6551944 TTCAAAATTG
6551954 AAAACTCTAAACAAAAATCCCCAAATC
1 AAAACTCTAAACAAAAATCCCCAAATC
* * * *
6551981 AAAACTCTTATCCAAAATCCTCAAAT
1 AAAACTCTAAACAAAAATCCCCAAAT
6552007 TCTCCAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.21
Consensus pattern (27 bp):
AAAACTCTAAACAAAAATCCCCAAATC
Found at i:6552059 original size:23 final size:23
Alignment explanation
Indices: 6552028--6552082 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
6552018 GACCACCCAA
*
6552028 AACCCAAAATC-TCTAAATTCAAC
1 AACCTAAAATCTTC-AAATTCAAC
*
6552051 AACCTAAAATCTTCAAATTCGAC
1 AACCTAAAATCTTCAAATTCAAC
6552074 AACCATAAA
1 AACC-TAAA
6552083 CAATTCATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 22 0.79
24 6 0.21
ACGTcount: A:0.49, C:0.27, G:0.02, T:0.22
Consensus pattern (23 bp):
AACCTAAAATCTTCAAATTCAAC
Found at i:6555386 original size:26 final size:26
Alignment explanation
Indices: 6555344--6555398 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
6555334 CAAAAATATT
* *
6555344 TATAAAAATATTTTTTATTAAAATAA
1 TATAAAAATATTATTTATCAAAATAA
6555370 TATAAAAA-AGTTATTTATCAAAATAA
1 TATAAAAATA-TTATTTATCAAAATAA
6555396 TAT
1 TAT
6555399 CCTCTCCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 25 0.96
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (26 bp):
TATAAAAATATTATTTATCAAAATAA
Found at i:6557452 original size:21 final size:21
Alignment explanation
Indices: 6557410--6557461 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
6557400 TTGACTTGTT
6557410 TCGGTAGAAGCCTTCCAAGTA
1 TCGGTAGAAGCCTTCCAAGTA
* * *
6557431 TCGGTGGAAGCCTTCTAGGTA
1 TCGGTAGAAGCCTTCCAAGTA
*
6557452 TTGGTAGAAG
1 TCGGTAGAAG
6557462 TCCCAAGCCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (21 bp):
TCGGTAGAAGCCTTCCAAGTA
Found at i:6558166 original size:75 final size:75
Alignment explanation
Indices: 6558076--6558225 Score: 291
Period size: 75 Copynumber: 2.0 Consensus size: 75
6558066 ATGCACAATG
6558076 CTTGAACCAAAAGAATAATAAAAAGAACAAGTGAAGAAGAAATATGCATAAACAATTAGATAATA
1 CTTGAACCAAAAGAATAATAAAAAGAACAAGTGAAGAAGAAATATGCATAAACAATTAGATAATA
6558141 TGATCTAAAA
66 TGATCTAAAA
*
6558151 CTTGAACCAAAAGAATAATAAAAAGAACAAGTGAAGAAGAATTATGCATAAACAATTAGATAATA
1 CTTGAACCAAAAGAATAATAAAAAGAACAAGTGAAGAAGAAATATGCATAAACAATTAGATAATA
6558216 TGATCTAAAA
66 TGATCTAAAA
6558226 TGGTAGTACT
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.57, C:0.09, G:0.13, T:0.21
Consensus pattern (75 bp):
CTTGAACCAAAAGAATAATAAAAAGAACAAGTGAAGAAGAAATATGCATAAACAATTAGATAATA
TGATCTAAAA
Found at i:6560378 original size:2 final size:2
Alignment explanation
Indices: 6560371--6560410 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
6560361 GAAAATCAAT
6560371 TA TA TA TA TA TA 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 TA TA TA TA TA TA
6560411 AGAAGCTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6562950 original size:10 final size:10
Alignment explanation
Indices: 6562937--6562964 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
6562927 AAGTCAAACT
6562937 GTTGACCGGC
1 GTTGACCGGC
6562947 GTTGACCGGC
1 GTTGACCGGC
6562957 GTTGACCG
1 GTTGACCG
6562965 ACCGTTGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.11, C:0.29, G:0.39, T:0.21
Consensus pattern (10 bp):
GTTGACCGGC
Found at i:6562972 original size:11 final size:10
Alignment explanation
Indices: 6562937--6562984 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
6562927 AAGTCAAACT
*
6562937 GTTGACCGGC
1 GTTGACCGCC
*
6562947 GTTGACCGGC
1 GTTGACCGCC
6562957 GTTGACCGACC
1 GTTGACCG-CC
*
6562968 GTTGACTGACC
1 GTTGACCG-CC
6562979 GTTGAC
1 GTTGAC
6562985 TTTGACTGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
10 18 0.51
11 17 0.49
ACGTcount: A:0.15, C:0.29, G:0.33, T:0.23
Consensus pattern (10 bp):
GTTGACCGCC
Found at i:6562996 original size:7 final size:7
Alignment explanation
Indices: 6562974--6563079 Score: 96
Period size: 7 Copynumber: 15.7 Consensus size: 7
6562964 GACCGTTGAC
*
6562974 TGACCGT
1 TGACTGT
6562981 TGACT-T
1 TGACTGT
6562987 TGACTGT
1 TGACTGT
*
6562994 TGACCGT
1 TGACTGT
*
6563001 TGACCGT
1 TGACTGT
6563008 TGACT-T
1 TGACTGT
*
6563014 TGACCGT
1 TGACTGT
6563021 TGA-TCGT
1 TGACT-GT
**
6563028 TGACCAT
1 TGACTGT
6563035 TGACTGT
1 TGACTGT
6563042 TGACT-T
1 TGACTGT
6563048 TGACTGT
1 TGACTGT
*
6563055 TGACCGT
1 TGACTGT
6563062 TGACT-T
1 TGACTGT
*
6563068 TGACCGT
1 TGACTGT
6563075 TGACT
1 TGACT
6563080 TTTTTCAAAA
Statistics
Matches: 80, Mismatches: 13, Indels: 12
0.76 0.12 0.11
Matches are distributed among these distances:
6 22 0.28
7 58 0.73
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.38
Consensus pattern (7 bp):
TGACTGT
Found at i:6562999 original size:20 final size:20
Alignment explanation
Indices: 6562974--6563078 Score: 131
Period size: 20 Copynumber: 5.2 Consensus size: 20
6562964 GACCGTTGAC
6562974 TGACCGTTGACTTTGACTGT
1 TGACCGTTGACTTTGACTGT
*
6562994 TGACCGTTGACCGTTGACT-T
1 TGACCGTTGA-CTTTGACTGT
* **
6563014 TGACCGTTGATCGTTGACCAT
1 TGACCGTTGA-CTTTGACTGT
*
6563035 TGACTGTTGACTTTGACTGT
1 TGACCGTTGACTTTGACTGT
*
6563055 TGACCGTTGACTTTGACCGT
1 TGACCGTTGACTTTGACTGT
6563075 TGAC
1 TGAC
6563079 TTTTTTCAAA
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
20 57 0.77
21 17 0.23
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.37
Consensus pattern (20 bp):
TGACCGTTGACTTTGACTGT
Found at i:6563006 original size:27 final size:27
Alignment explanation
Indices: 6562974--6563078 Score: 149
Period size: 27 Copynumber: 3.9 Consensus size: 27
6562964 GACCGTTGAC
*
6562974 TGACCGTTGACTTTGACTGTTGACCGT
1 TGACCGTTGACTTTGACCGTTGACCGT
*
6563001 TGACCGTTGACTTTGACCGTTGATCGT
1 TGACCGTTGACTTTGACCGTTGACCGT
* * *
6563028 TGACCATTGACTGTTGA-CTTTGACTGT
1 TGACCGTTGACT-TTGACCGTTGACCGT
6563055 TGACCGTTGACTTTGACCGTTGAC
1 TGACCGTTGACTTTGACCGTTGAC
6563079 TTTTTTCAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
26 4 0.06
27 60 0.88
28 4 0.06
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.37
Consensus pattern (27 bp):
TGACCGTTGACTTTGACCGTTGACCGT
Found at i:6564139 original size:3 final size:3
Alignment explanation
Indices: 6564127--6564162 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
6564117 TATTCTATTC
6564127 TAT T-T 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
6564163 TTGGGATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:6566234 original size:16 final size:16
Alignment explanation
Indices: 6566215--6566250 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
6566205 TTTTAGATAG
6566215 TTTTCA-TGCATTTTTA
1 TTTTCATTGCA-TTTTA
6566231 TTTTCATTGCATTTTA
1 TTTTCATTGCATTTTA
6566247 TTTT
1 TTTT
6566251 GTCACTGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.17, C:0.11, G:0.06, T:0.67
Consensus pattern (16 bp):
TTTTCATTGCATTTTA
Found at i:6567718 original size:7 final size:7
Alignment explanation
Indices: 6567706--6567732 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
6567696 CCTATAAATA
6567706 GAAGAAT
1 GAAGAAT
6567713 GAAGAAT
1 GAAGAAT
6567720 GAAGAAT
1 GAAGAAT
6567727 GAAGAA
1 GAAGAA
6567733 ATCATCAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.30, T:0.11
Consensus pattern (7 bp):
GAAGAAT
Found at i:6568460 original size:13 final size:14
Alignment explanation
Indices: 6568431--6568460 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
6568421 TTCAGTACAT
6568431 TGACATTTAACCTC
1 TGACATTTAACCTC
6568445 TGACATTTAA-CTC
1 TGACATTTAACCTC
6568458 TGA
1 TGA
6568461 TTGCATTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (14 bp):
TGACATTTAACCTC
Found at i:6568565 original size:13 final size:13
Alignment explanation
Indices: 6568547--6568571 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6568537 ATTTTCAGTA
6568547 TTTTATTAAATAC
1 TTTTATTAAATAC
6568560 TTTTATTAAATA
1 TTTTATTAAATA
6568572 TTTACAGTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTTATTAAATAC
Found at i:6583475 original size:56 final size:55
Alignment explanation
Indices: 6583390--6583551 Score: 193
Period size: 56 Copynumber: 2.9 Consensus size: 55
6583380 AAATTGTGTA
* * *
6583390 TTTGCCAAGTCATGCCATCACTCTCTTTTTCAGATAAAAAAATATTTTTTTTGTG
1 TTTGCCAAGTCATGCCATCACTTTATTTTTCAGATAAAAAAATATTTTTTTGGTG
* * * *
6583445 TTTGTCAAGTCATTGCCATCACTTTTTTTTTCAAATAAAAAAATATTCTTTTGGTG
1 TTTGCCAAGTCA-TGCCATCACTTTATTTTTCAGATAAAAAAATATTTTTTTGGTG
* *
6583501 CTTGCCAAG-CAATGACCATCAC-TCATTTTTCAGATAAAAAAATTATTTTTT
1 TTTGCCAAGTC-ATG-CCATCACTTTATTTTTCAGATAAAAAAA-TATTTTTT
6583552 AGGTAATGGC
Statistics
Matches: 91, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
55 31 0.34
56 60 0.66
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.43
Consensus pattern (55 bp):
TTTGCCAAGTCATGCCATCACTTTATTTTTCAGATAAAAAAATATTTTTTTGGTG
Found at i:6583572 original size:56 final size:55
Alignment explanation
Indices: 6583404--6583599 Score: 137
Period size: 56 Copynumber: 3.5 Consensus size: 55
6583394 CCAAGTCATG
* * * * ** * * *
6583404 CCATCACTCTCTTTTTCAGATAAAAAAATATTTTTTTTGTGTTTGTCAAGTCATTG-
1 CCATCACTC-ATTTTTCAAATAAAAAAATATTCTTTTGGTAATGGCCAAG-CAATGA
** ** *
6583460 CCATCACTTTTTTTTTCAAATAAAAAAATATTCTTTTGGTGCTTGCCAAGCAATGA
1 CCATCAC-TCATTTTTCAAATAAAAAAATATTCTTTTGGTAATGGCCAAGCAATGA
* * *
6583516 CCATCACTCATTTTTCAGATAAAAAAATTATT-TTTTAGGTAATGGCTAAGCCATGA
1 CCATCACTCATTTTTCAAATAAAAAAA-TATTCTTTT-GGTAATGGCCAAGCAATGA
* *
6583572 CTATCACCCTC-TTTATCAAATAAAAAAA
1 CCATCA--CTCATTTTTCAAATAAAAAAA
6583600 ATTTTGAGTG
Statistics
Matches: 115, Mismatches: 19, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
55 25 0.22
56 71 0.62
57 16 0.14
58 3 0.03
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.39
Consensus pattern (55 bp):
CCATCACTCATTTTTCAAATAAAAAAATATTCTTTTGGTAATGGCCAAGCAATGA
Found at i:6583628 original size:33 final size:33
Alignment explanation
Indices: 6583584--6583665 Score: 101
Period size: 33 Copynumber: 2.5 Consensus size: 33
6583574 ATCACCCTCT
* *
6583584 TTATCAAATAAAAAAAATTTTGAGTGATTGTTA
1 TTATCAGATAAAAAAAATTTTGAGTGATTGTCA
***
6583617 TTATCAGATAAAAATTTTTTTGAGTGATTGTCA
1 TTATCAGATAAAAAAAATTTTGAGTGATTGTCA
* *
6583650 TTTTCAGATGAAAAAA
1 TTATCAGATAAAAAAA
6583666 TTATTTTTTG
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.40
Consensus pattern (33 bp):
TTATCAGATAAAAAAAATTTTGAGTGATTGTCA
Found at i:6584257 original size:13 final size:14
Alignment explanation
Indices: 6584230--6584259 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
6584220 TTATTAGGAA
6584230 AAAGAAAAGAAATT
1 AAAGAAAAGAAATT
6584244 AAAGAAAA-AAATT
1 AAAGAAAAGAAATT
6584257 AAA
1 AAA
6584260 TAATATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (14 bp):
AAAGAAAAGAAATT
Found at i:6584283 original size:25 final size:25
Alignment explanation
Indices: 6584239--6584298 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
6584229 AAAAGAAAAG
*
6584239 AAATTAAAGAAAAAAATTAAATAATA
1 AAATTAAA-AAAAAAATTAAAAAATA
* * *
6584265 TAATTAAAAAAATATTTAAAAAATA
1 AAATTAAAAAAAAAATTAAAAAATA
*
6584290 AAAATAAAA
1 AAATTAAAA
6584299 TTGAATCATA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
25 21 0.75
26 7 0.25
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (25 bp):
AAATTAAAAAAAAAATTAAAAAATA
Found at i:6585776 original size:28 final size:28
Alignment explanation
Indices: 6585726--6585779 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
6585716 AGTTGGATGG
6585726 GAGAAGAGTAAAAGTTCTAGGGGGAAGT
1 GAGAAGAGTAAAAGTTCTAGGGGGAAGT
* *
6585754 GAGAGAGAGTAAATGTT-TTGGGGGAA
1 GAGA-AGAGTAAAAGTTCTAGGGGGAA
6585780 AATAAAGAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.37, C:0.02, G:0.41, T:0.20
Consensus pattern (28 bp):
GAGAAGAGTAAAAGTTCTAGGGGGAAGT
Found at i:6586110 original size:18 final size:18
Alignment explanation
Indices: 6586073--6586118 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
6586063 ATTCGAAAAA
* *
6586073 AATTCGAGTTGACTCGAAT
1 AATTCGA-TTAACTCAAAT
6586092 AATTCGATTAACTCAAAT
1 AATTCGATTAACTCAAAT
*
6586110 AACTCGATT
1 AATTCGATT
6586119 CATTTAACTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (18 bp):
AATTCGATTAACTCAAAT
Found at i:6588691 original size:65 final size:66
Alignment explanation
Indices: 6588557--6588711 Score: 228
Period size: 65 Copynumber: 2.3 Consensus size: 66
6588547 ATTTATTATT
*
6588557 ATAAATAAATAA-TAAAATAAAATTAATATTATTTTACATTATTTATTTATATTCATAAAATAAT
1 ATAAATAAATAATTAAAATAATATTAATATTATTTTA-ATTATTTATTTATATTCATAAAATAAT
6588621 AA
65 AA
*
6588623 ATAAATAAATAATGTAAAATAATATTAATATTATTTT-A-TATTTATTTATGTTCATAAAAATAA
1 ATAAATAAATAAT-TAAAATAATATTAATATTATTTTAATTATTTATTTATATTCAT-AAAATAA
6588686 T-A
64 TAA
6588688 ATAAATAAATTAATTAAAATAATA
1 ATAAATAAA-TAATTAAAATAATA
6588712 AGAAAAATGA
Statistics
Matches: 83, Mismatches: 2, Indels: 9
0.88 0.02 0.10
Matches are distributed among these distances:
65 36 0.43
66 25 0.30
68 22 0.27
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (66 bp):
ATAAATAAATAATTAAAATAATATTAATATTATTTTAATTATTTATTTATATTCATAAAATAATA
A
Found at i:6589445 original size:80 final size:80
Alignment explanation
Indices: 6589237--6590447 Score: 1784
Period size: 80 Copynumber: 15.2 Consensus size: 80
6589227 ATAACTTTAG
* * * * * *
6589237 GGGTAAAAGATTAGATTGT-TTCAATTTGCCCCATGGTCGAGGTAAGAGATCTGACGGTCTTCAA
1 GGGTAAAAGATTAGATT-TCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
* * * ** *
6589301 TC-AGCCTTTTAATTG
65 TCTTGCCCTCTGGTTA
**
6589316 GGGTAAAAGATTAGATTTCTTCAATCTGCTTCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
*
6589381 CTTGCCCTCTAGTTA
66 CTTGCCCTCTGGTTA
* * *
6589396 GGGTAAAAAAATTAGATTTCTTCAATCTGCCCCAT-ATTGGGGTAAAAGATCTGATGGTCTTCAA
1 GGGT-AAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
*
6589460 TCTTGCCCTCTAGTTA
65 TCTTGCCCTCTGGTTA
6589476 GGGTAAAAGATTAGATTTCTTCAATCTGCCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
1 GGGTAAAAGATTAGATTTCTTCAATCTG-CCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
*
6589541 TCTTGCCCTCTCGTTA
65 TCTTGCCCTCTGGTTA
* * *
6589557 GGGTAAAAGATTAGATTTCTTCAATCTGCCTCATAATCAGGGTAAAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
6589622 CTTGCCCTCTGGTTA
66 CTTGCCCTCTGGTTA
* * * ** * * *
6589637 GGGTAAAAGATTGGATGTT-TTCAATCTACGCCATGATCGGGGTAAACTATGGGATGATCTTTAA
1 GGGTAAAAGATTAGAT-TTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
*
6589701 TCTTGCCCTCTTGTTA
65 TCTTGCCCTCTGGTTA
* *
6589717 GGGTAAAAGATTAGATTTCTTCAATCTGCCACATGATCGGAGTAAAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
6589782 CTTGCCCTCTGGTTA
66 CTTGCCCTCTGGTTA
* * * *
6589797 GGGTAAAAGATTGGATTTCTTCAATCTACCCCAT-ATCGGGGTAAAAGATCGGATAGTCTTCTAT
1 GGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
*
6589861 CTTGCCCTCTAGTTA
66 CTTGCCCTCTGGTTA
* * *
6589876 AGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGATCTTTAAT
1 GGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
*
6589941 CTTGCCCTCTTGTTA
66 CTTGCCCTCTGGTTA
* * * * * *
6589956 GGGTAAAAGATTAGATTTCTTCAATTTGCCCAATGATCGGGGTAAAAGATTGGATGATTTTTAAT
1 GGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
6590021 CTTGCCCTCTGGTTA
66 CTTGCCCTCTGGTTA
* *
6590036 GGGTAAAAGATTAGATTTTTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGATCTTCAAT
1 GGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
6590101 CTTGCCCTCTGGTTA
66 CTTGCCCTCTGGTTA
* *
6590116 GGGTAAAATATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
*
6590181 CTTGCCCTCTAGTTA
66 CTTGCCCTCTGGTTA
* * *
6590196 GGGTAAAAGATTAGATTTCTTCAATCTGCCTCATGATCGAGGTAAAAGATCAGATGGTCTTCAAT
1 GGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
6590261 CTTGCCCTCTGGTTA
66 CTTGCCCTCTGGTTA
* * * *
6590276 TGGTAAAAGATTGGATTTCTTCAATATGCCCCATGATTGGGGTAAAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
6590341 CTTGCCCTCTGGTTA
66 CTTGCCCTCTGGTTA
* *
6590356 GGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGATAAAAGATCGGATGGTTTTCAAT
1 GGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
6590421 CTTGCCCTCTGGTTA
66 CTTGCCCTCTGGTTA
6590436 GGGTAAAAGATT
1 GGGTAAAAGATT
6590448 GGAGGTTATA
Statistics
Matches: 1024, Mismatches: 100, Indels: 15
0.90 0.09 0.01
Matches are distributed among these distances:
78 1 0.00
79 153 0.15
80 771 0.75
81 99 0.10
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (80 bp):
GGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
CTTGCCCTCTGGTTA
Found at i:6590558 original size:50 final size:50
Alignment explanation
Indices: 6590504--6590681 Score: 212
Period size: 50 Copynumber: 3.6 Consensus size: 50
6590494 GTCCTTGTGA
* * * * *
6590504 CTTCAATCTTCTCCTCTACAGCTTTAAGTGAATGAGATTTGCCATTACAG
1 CTTCAATCTACACCTCCACAGCTTTAAGTGTATGAGATTTGCCATTGCAG
* * * * *
6590554 CTTCATTCTACCCCTCTACAGCTTTAGGTGTATGAGATTTGCCATTGCGG
1 CTTCAATCTACACCTCCACAGCTTTAAGTGTATGAGATTTGCCATTGCAG
* * * * *
6590604 TTTTAATTTGCACCTCCACAGCTTTAGGTGTATGAGATTTGCCATTGCAG
1 CTTCAATCTACACCTCCACAGCTTTAAGTGTATGAGATTTGCCATTGCAG
*
6590654 TTTCAATCTACACCTCCACAGCTTTAAG
1 CTTCAATCTACACCTCCACAGCTTTAAG
6590682 GATAAAAATT
Statistics
Matches: 109, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 109 1.00
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (50 bp):
CTTCAATCTACACCTCCACAGCTTTAAGTGTATGAGATTTGCCATTGCAG
Found at i:6591611 original size:1 final size:1
Alignment explanation
Indices: 6591601--6591742 Score: 122
Period size: 1 Copynumber: 142.0 Consensus size: 1
6591591 CGACCTCCCC
* * * * * * * *
6591601 TTTTTCTTTTTCTTTTCTTCTTTTCTTTTCTTTTTTCTTTTTTCTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * * *
6591666 TTCTTTTTTCTTTTTTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTATTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
6591731 TTGTCTTTTTTT
1 TTTTTTTTTTTT
6591743 GAAATTTCTT
Statistics
Matches: 105, Mismatches: 36, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 105 1.00
ACGTcount: A:0.01, C:0.11, G:0.01, T:0.87
Consensus pattern (1 bp):
T
Found at i:6591623 original size:14 final size:13
Alignment explanation
Indices: 6591601--6591740 Score: 166
Period size: 12 Copynumber: 10.8 Consensus size: 13
6591591 CGACCTCCCC
6591601 TTTTTCTTTTTCT
1 TTTTTCTTTTTCT
6591614 TTTCTTC-TTTTCT
1 TTT-TTCTTTTTCT
*
6591627 TTTCT-TTTTTCT
1 TTTTTCTTTTTCT
6591639 TTTTTCTTTTT-T
1 TTTTTCTTTTTCT
*
6591651 TTTTT-TTTTTTT
1 TTTTTCTTTTTCT
6591663 TTTTTCTTTTTTCT
1 TTTTTC-TTTTTCT
6591677 TTTTT-TTTTTCT
1 TTTTTCTTTTTCT
6591689 TTTTTCTTTTTTCT
1 TTTTTC-TTTTTCT
6591703 TTTTTCTTTTTTCT
1 TTTTTC-TTTTTCT
*
6591717 TTTTTATTTTT-T
1 TTTTTCTTTTTCT
6591729 TTTTGTCTTTTT
1 TTTT-TCTTTTT
6591741 TTGAAATTTC
Statistics
Matches: 113, Mismatches: 5, Indels: 18
0.83 0.04 0.13
Matches are distributed among these distances:
11 5 0.04
12 40 0.35
13 28 0.25
14 40 0.35
ACGTcount: A:0.01, C:0.11, G:0.01, T:0.87
Consensus pattern (13 bp):
TTTTTCTTTTTCT
Found at i:6591638 original size:7 final size:7
Alignment explanation
Indices: 6591601--6591741 Score: 172
Period size: 7 Copynumber: 20.7 Consensus size: 7
6591591 CGACCTCCCC
6591601 TTTTTC-
1 TTTTTCT
6591607 TTTTTCT
1 TTTTTCT
6591614 TTTCTTCTTT
1 TTT-TTC--T
6591624 TCTTTTCT
1 T-TTTTCT
6591632 TTTTTCT
1 TTTTTCT
6591639 TTTTTC-
1 TTTTTCT
6591645 TTTTT-T
1 TTTTTCT
6591651 TTTTT-T
1 TTTTTCT
6591657 TTTTT-T
1 TTTTTCT
6591663 TTTTTCT
1 TTTTTCT
6591670 TTTTTC-
1 TTTTTCT
6591676 TTTTT-T
1 TTTTTCT
6591682 TTTTTCT
1 TTTTTCT
6591689 TTTTTCT
1 TTTTTCT
6591696 TTTTTCT
1 TTTTTCT
6591703 TTTTTCT
1 TTTTTCT
6591710 TTTTTCT
1 TTTTTCT
*
6591717 TTTTTAT
1 TTTTTCT
6591724 TTTTT-T
1 TTTTTCT
*
6591730 TTTGTCT
1 TTTTTCT
6591737 TTTTT
1 TTTTT
6591742 TGAAATTTCT
Statistics
Matches: 122, Mismatches: 3, Indels: 19
0.85 0.02 0.13
Matches are distributed among these distances:
6 43 0.35
7 67 0.55
8 5 0.04
10 5 0.04
11 2 0.02
ACGTcount: A:0.01, C:0.11, G:0.01, T:0.87
Consensus pattern (7 bp):
TTTTTCT
Found at i:6591695 original size:57 final size:59
Alignment explanation
Indices: 6591600--6591742 Score: 206
Period size: 57 Copynumber: 2.5 Consensus size: 59
6591590 TCGACCTCCC
* *
6591600 CTTTTTCTTTTTC--TTTTCTTCTTTTCTTTTCTTTTTTCTTTTTTCTTTTTT-TTTTTT
1 CTTTTTTTTTTTCTTTTTTCTT-TTTTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTT
6591657 -TTTTTTTTTTTCTTTTTTCTTTTTTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTT
1 CTTTTTTTTTTTCTTTTTTCTTTTTTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTT
6591715 CTTTTTTATTTTT-TTTTTGTCTTTTTTT
1 CTTTTTT-TTTTTCTTTTT-TCTTTTTTT
6591743 GAAATTTCTT
Statistics
Matches: 78, Mismatches: 2, Indels: 9
0.88 0.02 0.10
Matches are distributed among these distances:
56 11 0.14
57 29 0.37
58 13 0.17
59 11 0.14
60 14 0.18
ACGTcount: A:0.01, C:0.12, G:0.01, T:0.87
Consensus pattern (59 bp):
CTTTTTTTTTTTCTTTTTTCTTTTTTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTT
Found at i:6591741 original size:14 final size:13
Alignment explanation
Indices: 6591607--6591742 Score: 161
Period size: 13 Copynumber: 10.4 Consensus size: 13
6591597 CCCCTTTTTC
*
6591607 TTTTTCTTTTCTT
1 TTTTTTTTTTCTT
* *
6591620 CTTTTCTTTTCTT
1 TTTTTTTTTTCTT
6591633 TTTTCTTTTTTC-T
1 TTTT-TTTTTTCTT
6591646 TTTTTTTTTT-TT
1 TTTTTTTTTTCTT
6591658 TTTTTTTTTTCTT
1 TTTTTTTTTTCTT
6591671 TTTTCTTTTTT-TT
1 TTTT-TTTTTTCTT
*
6591684 TTTCTTTTTTCTT
1 TTTTTTTTTTCTT
6591697 TTTTCTTTTTTCTT
1 TTTT-TTTTTTCTT
*
6591711 TTTTCTTTTTTATT
1 TTTT-TTTTTTCTT
*
6591725 TTTTTTTTGTCTT
1 TTTTTTTTTTCTT
6591738 TTTTT
1 TTTTT
6591743 GAAATTTCTT
Statistics
Matches: 109, Mismatches: 8, Indels: 12
0.84 0.06 0.09
Matches are distributed among these distances:
12 23 0.21
13 48 0.44
14 38 0.35
ACGTcount: A:0.01, C:0.11, G:0.01, T:0.88
Consensus pattern (13 bp):
TTTTTTTTTTCTT
Found at i:6596886 original size:68 final size:68
Alignment explanation
Indices: 6596773--6596921 Score: 198
Period size: 68 Copynumber: 2.2 Consensus size: 68
6596763 ATTTATTATT
* * *
6596773 ATAAATAA-ATAATAAAATAAAATTAATATTATTTTACATTTATTTAT-TT-ATATTCATAA-AA
1 ATAAATAATAAAATAAAATAAAATAAATATTATTTTACATTTATTTATGTTCATA---AAAATAA
6596834 TAATAA
63 TAATAA
*
6596840 ATAAATAATAAAATAAAATAAAATAAATATTATTTTATATTTATTTATGTTCATAAAAATAATAA
1 ATAAATAATAAAATAAAATAAAATAAATATTATTTTACATTTATTTATGTTCATAAAAATAATAA
6596905 TAA
66 TAA
6596908 ATAAATAAATAAAA
1 ATAAAT-AATAAAA
6596922 ATAATAAGAA
Statistics
Matches: 73, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
67 11 0.15
68 50 0.68
69 9 0.12
70 3 0.04
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.40
Consensus pattern (68 bp):
ATAAATAATAAAATAAAATAAAATAAATATTATTTTACATTTATTTATGTTCATAAAAATAATAA
TAA
Found at i:6596918 original size:64 final size:66
Alignment explanation
Indices: 6596773--6596935 Score: 210
Period size: 64 Copynumber: 2.5 Consensus size: 66
6596763 ATTTATTATT
*
6596773 ATAAATAAAT-AATAAAATAAAATTAATATTATTTTACATTTATTTATTTATATTCATAAAATAA
1 ATAAATAAATAAATAAAATAAAATAAATATTATTTTA-A-TTATTTATTTATATTCATAAAATAA
6596837 TAA
64 TAA
*
6596840 ATAAAT-AATAAAATAAAATAAAATAAATATTATTTT-A-TATTTATTTATGTTCATAAAAATAA
1 ATAAATAAAT-AAATAAAATAAAATAAATATTATTTTAATTATTTATTTATATTCAT-AAAATAA
6596902 T-A
64 TAA
*
6596904 ATAAATAAATAAATAAAAATAATAAGAAATAT
1 ATAAATAAATAAAT-AAAATAA-AATAAATAT
6596936 AGAATTGAGT
Statistics
Matches: 87, Mismatches: 3, Indels: 13
0.84 0.03 0.13
Matches are distributed among these distances:
64 27 0.31
65 18 0.21
66 12 0.14
67 6 0.07
68 24 0.28
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (66 bp):
ATAAATAAATAAATAAAATAAAATAAATATTATTTTAATTATTTATTTATATTCATAAAATAATA
A
Found at i:6599843 original size:41 final size:41
Alignment explanation
Indices: 6599786--6599867 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
6599776 ACACACCGTA
6599786 ATCAAATTTGTTATTAACTTTCATCAACTCATAATTTATTT
1 ATCAAATTTGTTATTAACTTTCATCAACTCATAATTTATTT
*
6599827 ATCAAATTTGTTATTAACTTTCATCAATTCATAATTTATTT
1 ATCAAATTTGTTATTAACTTTCATCAACTCATAATTTATTT
6599868 CTTAATATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.34, C:0.13, G:0.02, T:0.50
Consensus pattern (41 bp):
ATCAAATTTGTTATTAACTTTCATCAACTCATAATTTATTT
Found at i:6600856 original size:17 final size:18
Alignment explanation
Indices: 6600824--6600857 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6600814 AGTCAAAATC
6600824 AAATAAAAATAATACAAT
1 AAATAAAAATAATACAAT
*
6600842 AAATAAACA-AATACAA
1 AAATAAAAATAATACAA
6600858 AACTTAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.18
Consensus pattern (18 bp):
AAATAAAAATAATACAAT
Found at i:6602681 original size:21 final size:22
Alignment explanation
Indices: 6602643--6602692 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
6602633 TGCTAGTTAC
*
6602643 TAATATCATGACTTAAA-TAAA
1 TAATATCATGACTCAAATTAAA
6602664 TAATATCAT-ATCTCAAATTAAA
1 TAATATCATGA-CTCAAATTAAA
6602686 TATATAT
1 TA-ATAT
6602693 AATAAAAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 1 0.04
21 14 0.56
22 6 0.24
23 4 0.16
ACGTcount: A:0.50, C:0.10, G:0.02, T:0.38
Consensus pattern (22 bp):
TAATATCATGACTCAAATTAAA
Found at i:6603111 original size:25 final size:25
Alignment explanation
Indices: 6603054--6603104 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
6603044 TTACCAACCG
6603054 TGCATTTTCATTACATCCATATTCT
1 TGCATTTTCATTACATCCATATTCT
6603079 TGCATTTTCATTACATCCATATTCT
1 TGCATTTTCATTACATCCATATTCT
6603104 T
1 T
6603105 TCTTTTTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.24, C:0.24, G:0.04, T:0.49
Consensus pattern (25 bp):
TGCATTTTCATTACATCCATATTCT
Found at i:6606996 original size:11 final size:11
Alignment explanation
Indices: 6606982--6607042 Score: 56
Period size: 10 Copynumber: 5.6 Consensus size: 11
6606972 TTCAAATTTT
6606982 TTTTTTATATA
1 TTTTTTATATA
*
6606993 -TTTTTA-AGA
1 TTTTTTATATA
6607002 TTTTTTA-ATA
1 TTTTTTATATA
*
6607012 ATTTTTATATA
1 TTTTTTATATA
*
6607023 TTATATTTATAAA
1 TT-T-TTTATATA
6607036 TTTTTTA
1 TTTTTTA
6607043 AAAGTAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
9 2 0.05
10 20 0.49
11 8 0.20
12 2 0.05
13 9 0.22
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (11 bp):
TTTTTTATATA
Found at i:6607700 original size:23 final size:23
Alignment explanation
Indices: 6607670--6607713 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
6607660 AAAAAATTTA
6607670 TGGGTGTTTGGGAGGGTTTGAGT
1 TGGGTGTTTGGGAGGGTTTGAGT
6607693 TGGGTGTTTGGGAGGGTTTGA
1 TGGGTGTTTGGGAGGGTTTGA
6607714 CTTTAAGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.09, C:0.00, G:0.52, T:0.39
Consensus pattern (23 bp):
TGGGTGTTTGGGAGGGTTTGAGT
Found at i:6608690 original size:55 final size:56
Alignment explanation
Indices: 6608603--6608724 Score: 174
Period size: 55 Copynumber: 2.2 Consensus size: 56
6608593 AACTAGTGGT
* * *
6608603 CATGAGTGGCGCTCGGGATAACACTACAGACACCCGAGATTATTTGATTAGC-GGC
1 CATGAGTGGCACTCGGGATAACACTACAGACACCAGAGATTATTTGACTAGCGGGC
* * * *
6608658 CATGAGTGGCACTTGGGATAACTCTACGGACACTAGAGATTATTTGACTAGCGGGC
1 CATGAGTGGCACTCGGGATAACACTACAGACACCAGAGATTATTTGACTAGCGGGC
6608714 CATGAGTGGCA
1 CATGAGTGGCA
6608725 TGAGACTATC
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
55 45 0.76
56 14 0.24
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (56 bp):
CATGAGTGGCACTCGGGATAACACTACAGACACCAGAGATTATTTGACTAGCGGGC
Found at i:6611711 original size:44 final size:44
Alignment explanation
Indices: 6611500--6611707 Score: 219
Period size: 43 Copynumber: 4.8 Consensus size: 44
6611490 TGGTGATTAC
* * * *
6611500 TAAAAGGAA-AACTCATGTCTCGGATATAGCATGAGATTATTTA
1 TAAAAGGAAGAACTTATGTCTCGGTTAGAGCATAAGATTATTTA
* * *
6611543 TAAATGGAATAA-TTATGTCTCGGTTAGAGCATAAGATTGTTTA
1 TAAAAGGAAGAACTTATGTCTCGGTTAGAGCATAAGATTATTTA
* * *
6611586 TAAAAGGAAG-ACTTATGCCTTGGTTAGAGCATAAGATTGTTTA
1 TAAAAGGAAGAACTTATGTCTCGGTTAGAGCATAAGATTATTTA
* *
6611629 TAAAAGGAA-AACTTATGTCTCGG-TAGGAGCATAAGGTTATTTG
1 TAAAAGGAAGAACTTATGTCTCGGTTA-GAGCATAAGATTATTTA
* * ** *
6611672 TAAATGGAAGAACTTATGACTATGTTGGAGCATAAG
1 TAAAAGGAAGAACTTATGTCTCGGTTAGAGCATAAG
6611708 GTTAATACAG
Statistics
Matches: 139, Mismatches: 20, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
42 3 0.02
43 113 0.81
44 22 0.16
45 1 0.01
ACGTcount: A:0.37, C:0.09, G:0.23, T:0.32
Consensus pattern (44 bp):
TAAAAGGAAGAACTTATGTCTCGGTTAGAGCATAAGATTATTTA
Found at i:6622332 original size:13 final size:13
Alignment explanation
Indices: 6622299--6622333 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
6622289 AAAACCCAAT
6622299 TTTATTTATTTTA
1 TTTATTTATTTTA
6622312 TATT-TTTATTTTA
1 T-TTATTTATTTTA
6622325 TTTATTTAT
1 TTTATTTAT
6622334 CATTTATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.10
13 16 0.80
14 2 0.10
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTATTTATTTTA
Found at i:6622486 original size:11 final size:10
Alignment explanation
Indices: 6622454--6622512 Score: 70
Period size: 10 Copynumber: 6.1 Consensus size: 10
6622444 TTATCTATTT
6622454 ATAAATATAA
1 ATAAATATAA
6622464 ATAAATATAA
1 ATAAATATAA
6622474 ATAAATAATAA
1 ATAAAT-ATAA
*
6622485 ATAAATA-AT
1 ATAAATATAA
6622494 A-AAAT-TAA
1 ATAAATATAA
*
6622502 ACAAATATAA
1 ATAAATATAA
6622512 A
1 A
6622513 CCAAATACAC
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
8 6 0.14
9 6 0.14
10 21 0.49
11 10 0.23
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (10 bp):
ATAAATATAA
Found at i:6622519 original size:11 final size:10
Alignment explanation
Indices: 6622456--6622519 Score: 53
Period size: 10 Copynumber: 6.5 Consensus size: 10
6622446 ATCTATTTAT
*
6622456 AAATATAAAT
1 AAATATAAAC
*
6622466 AAATATAAAT
1 AAATATAAAC
*
6622476 AAATAATAAAT
1 AAAT-ATAAAC
*
6622487 AAATA-ATA-
1 AAATATAAAC
6622495 AAAT-TAAAC
1 AAATATAAAC
6622504 AAATATAAACC
1 AAATATAAA-C
6622515 AAATA
1 AAATA
6622520 CACATACCCA
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
8 6 0.13
9 6 0.13
10 19 0.40
11 16 0.34
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (10 bp):
AAATATAAAC
Found at i:6623673 original size:30 final size:30
Alignment explanation
Indices: 6623631--6623936 Score: 223
Period size: 30 Copynumber: 10.2 Consensus size: 30
6623621 AAAAACATGT
* *
6623631 TTTGACCCTCAAACTTTTTAAAAATTCAAA
1 TTTGACCTTCAAACTTTCTAAAAATTCAAA
* * * *
6623661 TTTGACTTTCAAACTTTCCAAAAATTTAGA
1 TTTGACCTTCAAACTTTCTAAAAATTCAAA
6623691 TTTGACCTTCAAACTTTCTAAAAATTCAAA
1 TTTGACCTTCAAACTTTCTAAAAATTCAAA
* * *
6623721 TTTAACCCTCAAA-TTTCCCAAAAATTCAAA
1 TTTGACCTTCAAACTTT-CTAAAAATTCAAA
* * * ***
6623751 TATGACC-CCTAAACTTTCCT-AAATTTTGGA
1 TTTGACCTTC-AAACTTT-CTAAAAATTCAAA
* * * *
6623781 TTTGACCCTCAAACTTTCCAAAAATTTAGA
1 TTTGACCTTCAAACTTTCTAAAAATTCAAA
* **
6623811 TTTGA--TTCCAAACTTTCCAAAAATTTGAA
1 TTTGACCTT-CAAACTTTCTAAAAATTCAAA
* * *
6623840 TTTGACCTCCGAACTTTCCAAAAATTTC-AA
1 TTTGACCTTCAAACTTTCTAAAAA-TTCAAA
* *
6623870 TTTAACC-CCTAAACTTTCTAAAAATTCAAA
1 TTTGACCTTC-AAACTTTCTAAAAATTCAAA
* * *
6623900 TTTGACCTTTAAA-TTGTCCAAAAATTTAAA
1 TTTGACCTTCAAACTT-TCTAAAAATTCAAA
6623930 TTTGACC
1 TTTGACC
6623937 CGATTTTAGT
Statistics
Matches: 223, Mismatches: 40, Indels: 26
0.77 0.14 0.09
Matches are distributed among these distances:
28 1 0.00
29 36 0.16
30 177 0.79
31 9 0.04
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (30 bp):
TTTGACCTTCAAACTTTCTAAAAATTCAAA
Found at i:6623703 original size:60 final size:59
Alignment explanation
Indices: 6623631--6623936 Score: 296
Period size: 60 Copynumber: 5.1 Consensus size: 59
6623621 AAAAACATGT
* * *
6623631 TTTGACCCTCAAACTTTTTAAAAATTCAAATTTGACTTTCAAACTTTCCAAAAATTTAGA
1 TTTGA-CCTCAAACTTTCTAAAAATTCAAATTTGACCTTCAAACTTTCCAAAAATTTAAA
* * *
6623691 TTTGACCTTCAAACTTTCTAAAAATTCAAATTTAACCCTCAAA-TTTCCCAAAAATTCAAA
1 TTTGACC-TCAAACTTTCTAAAAATTCAAATTTGACCTTCAAACTTT-CCAAAAATTTAAA
* * * *** * *
6623751 TATGACCCCTAAACTTTCCT-AAATTTTGGATTTGACCCTCAAACTTTCCAAAAATTTAGA
1 TTTGACCTC-AAACTTT-CTAAAAATTCAAATTTGACCTTCAAACTTTCCAAAAATTTAAA
* * ** * * *
6623811 TTTGA-TTCCAAACTTTCCAAAAATTTGAATTTGACCTCCGAACTTTCCAAAAATTTCAA
1 TTTGACCT-CAAACTTTCTAAAAATTCAAATTTGACCTTCAAACTTTCCAAAAATTTAAA
* * *
6623870 TTTAACCCCTAAACTTTCTAAAAATTCAAATTTGACCTTTAAA-TTGTCCAAAAATTTAAA
1 TTTGACCTC-AAACTTTCTAAAAATTCAAATTTGACCTTCAAACTT-TCCAAAAATTTAAA
6623930 TTTGACC
1 TTTGACC
6623937 CGATTTTAGT
Statistics
Matches: 199, Mismatches: 37, Indels: 20
0.78 0.14 0.08
Matches are distributed among these distances:
58 1 0.01
59 53 0.27
60 140 0.70
61 5 0.03
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (59 bp):
TTTGACCTCAAACTTTCTAAAAATTCAAATTTGACCTTCAAACTTTCCAAAAATTTAAA
Found at i:6635126 original size:12 final size:12
Alignment explanation
Indices: 6635107--6635138 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
6635097 CGACATTTGT
6635107 TATTTTGACTAA
1 TATTTTGACTAA
*
6635119 TGTTTTGACTAA
1 TATTTTGACTAA
6635131 TATTTTGA
1 TATTTTGA
6635139 TATCTTCTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.28, C:0.06, G:0.12, T:0.53
Consensus pattern (12 bp):
TATTTTGACTAA
Found at i:6635824 original size:50 final size:50
Alignment explanation
Indices: 6635670--6635836 Score: 181
Period size: 50 Copynumber: 3.3 Consensus size: 50
6635660 ATGGTGATAA
* * * * ** *
6635670 AATGACGAATCTTATACCCCTAAAGCAGTAGAGGAACGGATTGAAGCTGT
1 AATGGCGAATCTCATACACCTAAAGCTGTAGAGGGGCAGATTGAAGCTGT
* * * *
6635720 AATGGCAAATCTCATACACTTAAAGCTGTAGAGGGGCAAATTGAAGCCGT
1 AATGGCGAATCTCATACACCTAAAGCTGTAGAGGGGCAGATTGAAGCTGT
** * **
6635770 AATGGCGAATCTCATTTACCTAAAGCTGTAGAGGGGCAGATTGAAGTTAC
1 AATGGCGAATCTCATACACCTAAAGCTGTAGAGGGGCAGATTGAAGCTGT
*
6635820 AATGGCGAATCTTATAC
1 AATGGCGAATCTCATAC
6635837 CCATGAAGCT
Statistics
Matches: 94, Mismatches: 23, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
50 94 1.00
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (50 bp):
AATGGCGAATCTCATACACCTAAAGCTGTAGAGGGGCAGATTGAAGCTGT
Found at i:6636018 original size:39 final size:40
Alignment explanation
Indices: 6635887--6636018 Score: 115
Period size: 42 Copynumber: 3.3 Consensus size: 40
6635877 TACAACCCCG
* * * * * *
6635887 AATCTTTTACTCTAATCAAAGGGCAGGTTGAAGACCATCC
1 AATCTTTTACCCCAACCAGAGGGCAGATTGAAGACAATCC
* * * *
6635927 AATCTTTTACCCTAACTAGAGGGTAGATTAAAGACACCATCC
1 AATCTTTTACCCCAACCAGAGGGCAGATTGAAGACA--ATCC
* *
6635969 AATCTCTTACCCCGACCATG-GGGCAGATTGAAG-CAATCC
1 AATCTTTTACCCCAACCA-GAGGGCAGATTGAAGACAATCC
6636008 AATCTTTTACC
1 AATCTTTTACC
6636019 TTTAAAGCTA
Statistics
Matches: 74, Mismatches: 15, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
39 14 0.19
40 28 0.38
41 2 0.03
42 29 0.39
43 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.27
Consensus pattern (40 bp):
AATCTTTTACCCCAACCAGAGGGCAGATTGAAGACAATCC
Found at i:6636923 original size:10 final size:10
Alignment explanation
Indices: 6636908--6636950 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
6636898 TTATCTATTT
6636908 ATAAATATAA
1 ATAAATATAA
*
6636918 ATAAATACAA
1 ATAAATATAA
*
6636928 ATGAAAAATAA
1 AT-AAATATAA
6636939 ATAAATAATAA
1 ATAAAT-ATAA
6636950 A
1 A
6636951 ATTAAACAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 14 0.52
11 13 0.48
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (10 bp):
ATAAATATAA
Found at i:6636951 original size:17 final size:17
Alignment explanation
Indices: 6636911--6636962 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
6636901 TCTATTTATA
* *
6636911 AATATAAATAAATACA-
1 AATAAAAATAAATAAAT
6636927 AATGAAAAATAAATAAAT
1 AAT-AAAAATAAATAAAT
* *
6636945 AATAAAATTAAACAAAT
1 AATAAAAATAAATAAAT
6636962 A
1 A
6636963 CAAACCAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 3 0.10
17 24 0.80
18 3 0.10
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.23
Consensus pattern (17 bp):
AATAAAAATAAATAAAT
Found at i:6637469 original size:12 final size:12
Alignment explanation
Indices: 6637450--6637511 Score: 70
Period size: 12 Copynumber: 5.2 Consensus size: 12
6637440 ATAACAGCAA
6637450 AACAACAAAAAT
1 AACAACAAAAAT
* *
6637462 AGCAACAAAAGT
1 AACAACAAAAAT
* *
6637474 AATAGCAAAAAT
1 AACAACAAAAAT
* *
6637486 AGCAAGAAAAAT
1 AACAACAAAAAT
6637498 AACAACAAAAAT
1 AACAACAAAAAT
6637510 AA
1 AA
6637512 TAGCATCAAA
Statistics
Matches: 38, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.69, C:0.13, G:0.08, T:0.10
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:6637482 original size:24 final size:24
Alignment explanation
Indices: 6637450--6637510 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
6637440 ATAACAGCAA
*
6637450 AACAACAAAAATAGCAACAAAAGT
1 AACAACAAAAATAGCAACAAAAAT
* * *
6637474 AATAGCAAAAATAGCAAGAAAAAT
1 AACAACAAAAATAGCAACAAAAAT
6637498 AACAACAAAAATA
1 AACAACAAAAATA
6637511 ATAGCATCAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.69, C:0.13, G:0.08, T:0.10
Consensus pattern (24 bp):
AACAACAAAAATAGCAACAAAAAT
Found at i:6637532 original size:36 final size:35
Alignment explanation
Indices: 6637456--6637588 Score: 96
Period size: 36 Copynumber: 3.9 Consensus size: 35
6637446 GCAAAACAAC
* * * *
6637456 AAAAATAGCAACAAAAGTAATAGCA-AAAATAGCAA
1 AAAAATAACAACAAAAATAATAGCACAAAACAG-TA
6637491 GAAAAATAACAACAAAAATAATAGCATCAAAACAGTA
1 -AAAAATAACAACAAAAATAATAGCA-CAAAACAGTA
* * * * *
6637528 AAAAA-AAAAACCAAAACAACAAC-CAAAACAGT-
1 AAAAATAACAACAAAAATAATAGCACAAAACAGTA
* * *
6637560 AAAAACAACAACAACAA-AATAGCAAAAAA
1 AAAAATAACAACAAAAATAATAGCACAAAA
6637589 AAAGCAACCA
Statistics
Matches: 78, Mismatches: 15, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
32 9 0.12
33 21 0.27
35 13 0.17
36 28 0.36
37 1 0.01
38 6 0.08
ACGTcount: A:0.69, C:0.16, G:0.07, T:0.08
Consensus pattern (35 bp):
AAAAATAACAACAAAAATAATAGCACAAAACAGTA
Found at i:6637577 original size:23 final size:23
Alignment explanation
Indices: 6637540--6637611 Score: 94
Period size: 23 Copynumber: 3.1 Consensus size: 23
6637530 AAAAAAAACC
*
6637540 AAAACAACAACCAAAACAGTAAA
1 AAAACAACAACCAAAATAGTAAA
*
6637563 AACAACAACAA-CAAAATAGCAAA
1 AA-AACAACAACCAAAATAGTAAA
6637586 AAAA-AAGCAACCAAAATAGTAAA
1 AAAACAA-CAACCAAAATAGTAAA
6637609 AAA
1 AAA
6637612 TAGCACCAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
21 2 0.05
22 5 0.12
23 28 0.65
24 8 0.19
ACGTcount: A:0.71, C:0.18, G:0.06, T:0.06
Consensus pattern (23 bp):
AAAACAACAACCAAAATAGTAAA
Found at i:6637616 original size:22 final size:21
Alignment explanation
Indices: 6637547--6637621 Score: 64
Period size: 21 Copynumber: 3.4 Consensus size: 21
6637537 ACCAAAACAA
*
6637547 CAACCAAAACAGTAAAAACAA-
1 CAACCAAAATAGTAAAAA-AAG
*
6637568 CAACAACAAAATAGCAAAAAAAAAG
1 CAAC--CAAAATAG--TAAAAAAAG
6637593 CAACCAAAATAGTAAAAAATAG
1 CAACCAAAATAGTAAAAAA-AG
6637615 C-ACCAAA
1 CAACCAAA
6637622 CAACAATATA
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
21 16 0.36
22 3 0.07
23 15 0.33
24 2 0.04
25 9 0.20
ACGTcount: A:0.67, C:0.20, G:0.07, T:0.07
Consensus pattern (21 bp):
CAACCAAAATAGTAAAAAAAG
Found at i:6638977 original size:30 final size:30
Alignment explanation
Indices: 6638913--6638979 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
6638903 AAATCATGTT
** *** *
6638913 TTGACCCCTGAACTTTTTAAAAATTTGGAT
1 TTGACCCCTGAACTTTACAAAAATTCAAAA
6638943 TTGACCCCTGAACTTTACAAAAATTCAAAA
1 TTGACCCCTGAACTTTACAAAAATTCAAAA
6638973 TTGACCC
1 TTGACCC
6638980 TATTTTATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.33
Consensus pattern (30 bp):
TTGACCCCTGAACTTTACAAAAATTCAAAA
Found at i:6639112 original size:4 final size:4
Alignment explanation
Indices: 6639105--6639138 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
6639095 TGTTTGTTCC
* *
6639105 TTTA TTTA TTCA TTTA TTTA GTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
6639139 CGATTTATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:6639122 original size:12 final size:12
Alignment explanation
Indices: 6639105--6639146 Score: 59
Period size: 12 Copynumber: 3.4 Consensus size: 12
6639095 TGTTTGTTCC
6639105 TTTATTTATTCA
1 TTTATTTATTCA
6639117 TTTATTTAGTT-A
1 TTTATTTA-TTCA
6639129 TTTATTTATTCGA
1 TTTATTTATTC-A
6639142 TTTAT
1 TTTAT
6639147 AATCTTATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.07
12 17 0.63
13 8 0.30
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.67
Consensus pattern (12 bp):
TTTATTTATTCA
Found at i:6640129 original size:5 final size:5
Alignment explanation
Indices: 6640115--6640147 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
6640105 GAAAAAAGAA
6640115 GAAA- GAAAG GAAAG GAAAG GAAAG GAAAG GAAA
1 GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAA
6640148 TATAAAACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (5 bp):
GAAAG
Found at i:6642492 original size:16 final size:17
Alignment explanation
Indices: 6642465--6642497 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
6642455 TTTTTTTTTG
6642465 TTTTGTTTAAATTTAGA
1 TTTTGTTTAAATTTAGA
6642482 TTTTG-TTAAATTTAGA
1 TTTTGTTTAAATTTAGA
6642498 CTAGGTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (17 bp):
TTTTGTTTAAATTTAGA
Found at i:6642980 original size:15 final size:17
Alignment explanation
Indices: 6642955--6642988 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
6642945 CTTTATGACA
6642955 AAAAATGAAATTAT-TG
1 AAAAATGAAATTATATG
6642971 AAAAAT-AAATTATATG
1 AAAAATGAAATTATATG
6642987 AA
1 AA
6642989 TAATTATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.29
Consensus pattern (17 bp):
AAAAATGAAATTATATG
Found at i:6643604 original size:3 final size:3
Alignment explanation
Indices: 6643591--6643621 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
6643581 TCGACTATTT
*
6643591 CAC CGC CAC CAC CAC CAC CAC CAC CAC CAC C
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC C
6643622 CGCATCAAAT
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:0.29, C:0.68, G:0.03, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:6648729 original size:3 final size:3
Alignment explanation
Indices: 6648721--6648792 Score: 135
Period size: 3 Copynumber: 24.0 Consensus size: 3
6648711 TTTCATCCCA
6648721 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
6648769 TTC TTC TTC TTC TTC TTA TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC
6648793 ACACGGTAAC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:6652911 original size:43 final size:42
Alignment explanation
Indices: 6652858--6653022 Score: 177
Period size: 43 Copynumber: 3.8 Consensus size: 42
6652848 TGGTGATTAC
* *
6652858 TAAAAGGAAGACTCATGTCTCGGATAGAGCATGAGATTATTTA
1 TAAAAGGAAGACTTATGTCTCGG-TAGAGCATAAGATTATTTA
* *
6652901 TAAATGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTA
1 TAAAAGGAAGACTTATGTCTCGG-TAGAGCATAAGATTATTTA
* * * *
6652944 TAAAAGGAAAACTTATATCTCGGTAGGAGCATAAGGTTATTTG
1 TAAAAGGAAGACTTATGTCTCGGTA-GAGCATAAGATTATTTA
* * * *
6652987 TAAATGGAATAACTTATGACTCGGTTGGAGCATAAG
1 TAAAAGGAA-GACTTATGTCTCGG-TAGAGCATAAG
6653023 GTTAATACAG
Statistics
Matches: 104, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
42 2 0.02
43 80 0.77
44 21 0.20
45 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.30
Consensus pattern (42 bp):
TAAAAGGAAGACTTATGTCTCGGTAGAGCATAAGATTATTTA
Found at i:6655713 original size:79 final size:79
Alignment explanation
Indices: 6655582--6655793 Score: 329
Period size: 79 Copynumber: 2.7 Consensus size: 79
6655572 TAAACCGATG
* *
6655582 ATCCTGGCACCCAGTGCCTAGCGGATAAACCACAAAAGTGAGCCCAGCTCTAGTTGGATTAACCC
1 ATCCTGGCACCCAGTGCCTAGCGGATAAACCGCTAAAGTGAGCCCAGCTCTAGTTGGATTAA-CC
*
6655647 A-TAATATCCGTCAA
65 AGCAATATCCGTCAA
* * *
6655661 ATCCTGGCACCCAATGCCTAGCGGATAAATCGCTAAAGTGAGACCAGCTCTAGTTGGATTAACCA
1 ATCCTGGCACCCAGTGCCTAGCGGATAAACCGCTAAAGTGAGCCCAGCTCTAGTTGGATTAACCA
*
6655726 GCAATATCTGTCAA
66 GCAATATCCGTCAA
6655740 ATCCTGGCACCCAGTGCCTAGCGGATAAACCG-TAAAAGTGAGCCCAGCTCTAGT
1 ATCCTGGCACCCAGTGCCTAGCGGATAAACCGCT-AAAGTGAGCCCAGCTCTAGT
6655794 CAGTTAAACT
Statistics
Matches: 121, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
78 4 0.03
79 117 0.97
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.21
Consensus pattern (79 bp):
ATCCTGGCACCCAGTGCCTAGCGGATAAACCGCTAAAGTGAGCCCAGCTCTAGTTGGATTAACCA
GCAATATCCGTCAA
Found at i:6662897 original size:43 final size:40
Alignment explanation
Indices: 6662850--6663027 Score: 153
Period size: 41 Copynumber: 4.2 Consensus size: 40
6662840 TCGAGTCGTA
* *
6662850 AGTCTTCCTTTCAAACATAATCTCACGCTCAATTCGAGACATG
1 AGTCTTCCTTT-AAACA-AATCTCATGCTC-ATCCGAGACATG
*
6662893 AGTCTTCCTTTAATA-AAATCTCATTCTCATCCTGAGACATG
1 AGTCTTCCTTTAA-ACAAATCTCATGCTCATCC-GAGACATG
* * * * *
6662934 AATCTTCCTTT-ATCATATTCTCATGCTCATTCCGAGTCATA
1 AGTCTTCCTTTAAACA-AATCTCATGCTCA-TCCGAGACATG
* * *
6662975 AGTCTTCCATTTATACAATTTCTCATGCTCAACCCGAGACATG
1 AGTCTTCC-TTTAAACAA-ATCTCATGCTC-ATCCGAGACATG
6663018 AGTCTTCCTT
1 AGTCTTCCTT
6663028 CTTATACATC
Statistics
Matches: 111, Mismatches: 15, Indels: 19
0.77 0.10 0.13
Matches are distributed among these distances:
40 5 0.05
41 52 0.47
42 12 0.11
43 41 0.37
44 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.36
Consensus pattern (40 bp):
AGTCTTCCTTTAAACAAATCTCATGCTCATCCGAGACATG
Found at i:6662930 original size:41 final size:39
Alignment explanation
Indices: 6662870--6663027 Score: 154
Period size: 41 Copynumber: 3.8 Consensus size: 39
6662860 TCAAACATAA
* * *
6662870 TCTCACGCTCAATTCGAGACATGAGTCTTCCTTTAATAAAA
1 TCTCATGCTC-ATCCGAGACATGAGTCTTCCTTT-ATAAAT
* * *
6662911 TCTCATTCTCATCCTGAGACATGAATCTTCCTTTATCATAT
1 TCTCATGCTCATCC-GAGACATGAGTCTTCCTTTAT-AAAT
* *
6662952 TCTCATGCTCATTCCGAGTCATAAGTCTTCCATTTATACAATT
1 TCTCATGCTCA-TCCGAGACATGAGTCTTCC-TTTATA-AA-T
*
6662995 TCTCATGCTCAACCCGAGACATGAGTCTTCCTT
1 TCTCATGCTC-ATCCGAGACATGAGTCTTCCTT
6663028 CTTATACATC
Statistics
Matches: 96, Mismatches: 14, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
40 5 0.05
41 52 0.54
42 11 0.11
43 27 0.28
44 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.11, T:0.36
Consensus pattern (39 bp):
TCTCATGCTCATCCGAGACATGAGTCTTCCTTTATAAAT
Found at i:6662979 original size:82 final size:84
Alignment explanation
Indices: 6662865--6663027 Score: 199
Period size: 82 Copynumber: 2.0 Consensus size: 84
6662855 TCCTTTCAAA
* * * *
6662865 CATAATCTCACGCTCAATTCGAGACATGAGTCTTCC-TTTAATA-AA-ATCTCATTCTCATCCTG
1 CATAATCTCACGCTCAATTCGAGACATAAGTCTTCCATTT-ATACAATATCTCATGCTCAACCCG
6662927 AGACATGAATCTTCCTTTAT
65 AGACATGAATCTTCCTTTAT
* * * *
6662947 CATATTCTCATGCTC-ATTCCGAGTCATAAGTCTTCCATTTATACAATTTCTCATGCTCAACCCG
1 CATAATCTCACGCTCAATT-CGAGACATAAGTCTTCCATTTATACAATATCTCATGCTCAACCCG
*
6663011 AGACATGAGTCTTCCTT
65 AGACATGAATCTTCCTT
6663028 CTTATACATC
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
81 3 0.04
82 31 0.46
83 5 0.07
84 29 0.43
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.36
Consensus pattern (84 bp):
CATAATCTCACGCTCAATTCGAGACATAAGTCTTCCATTTATACAATATCTCATGCTCAACCCGA
GACATGAATCTTCCTTTAT
Found at i:6670254 original size:27 final size:27
Alignment explanation
Indices: 6670201--6670431 Score: 187
Period size: 27 Copynumber: 8.6 Consensus size: 27
6670191 TCCTTTATAG
* *
6670201 TTTGCCACAAGGGCT-TATCTTTCATGA
1 TTTGCCACAAAGGCTAT-TCATTCATGA
* * *
6670228 TTCGCCACAAAGGCTATTTATTAATGA
1 TTTGCCACAAAGGCTATTCATTCATGA
* * * * *
6670255 CTCGCCATAATGGTTATTCATTCATGA
1 TTTGCCACAAAGGCTATTCATTCATGA
* ** *
6670282 CTTGCCACAAAAACTATCCATTCATGA
1 TTTGCCACAAAGGCTATTCATTCATGA
* * * *
6670309 TTTTCCATAAAGGATACTCATTCATGA
1 TTTGCCACAAAGGCTATTCATTCATGA
* * * *
6670336 TTTGCTATAAAGGTTATTCATTCATTA
1 TTTGCCACAAAGGCTATTCATTCATGA
*
6670363 TTTTCCACAAAGGCTATTCATTCATGA
1 TTTGCCACAAAGGCTATTCATTCATGA
* * * *
6670390 TTTGTCACAATGG-TTTCTCATTAATGA
1 TTTGCCACAAAGGCTAT-TCATTCATGA
6670417 TTTGCCACAAAGGCT
1 TTTGCCACAAAGGCT
6670432 TTTCTTTCCT
Statistics
Matches: 158, Mismatches: 43, Indels: 5
0.77 0.21 0.02
Matches are distributed among these distances:
26 2 0.01
27 154 0.97
28 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.37
Consensus pattern (27 bp):
TTTGCCACAAAGGCTATTCATTCATGA
Found at i:6670417 original size:81 final size:81
Alignment explanation
Indices: 6670221--6670429 Score: 213
Period size: 81 Copynumber: 2.6 Consensus size: 81
6670211 GGGCTTATCT
** * * * * * *
6670221 TTCATGATTCGCCACAAAGGCTATTTATTAATGACTCGCCATAATGGTTATTCATTCATGACTTG
1 TTCATGATTTTCCACAAAGGATACTCATTAATGATTTGCCATAAAGGTTATTCATTCATGACTTG
6670286 CCACAAAAACTATCCA
66 CCACAAAAACTATCCA
* * * * * *
6670302 TTCATGATTTTCCATAAAGGATACTCATTCATGATTTGCTATAAAGGTTATTCATTCATTATTTT
1 TTCATGATTTTCCACAAAGGATACTCATTAATGATTTGCCATAAAGGTTATTCATTCATGACTTG
** *
6670367 CCACAAAGGCTATTCA
66 CCACAAAAACTATCCA
* * * *
6670383 TTCATGATTTGT-CACAATGGTTTCTCATTAATGATTTGCCACAAAGG
1 TTCATGATTT-TCCACAAAGGATACTCATTAATGATTTGCCATAAAGG
6670430 CTTTTCTTTC
Statistics
Matches: 103, Mismatches: 24, Indels: 2
0.80 0.19 0.02
Matches are distributed among these distances:
81 102 0.99
82 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.37
Consensus pattern (81 bp):
TTCATGATTTTCCACAAAGGATACTCATTAATGATTTGCCATAAAGGTTATTCATTCATGACTTG
CCACAAAAACTATCCA
Found at i:6681582 original size:17 final size:17
Alignment explanation
Indices: 6681541--6681582 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
6681531 TCAGTCGCAT
6681541 AAAAAAAAGAGAAAAGA
1 AAAAAAAAGAGAAAAGA
* *
6681558 AAGAAAAAGATAAAAGA
1 AAAAAAAAGAGAAAAGA
6681575 AAAAAAAA
1 AAAAAAAA
6681583 TATAGAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.02
Consensus pattern (17 bp):
AAAAAAAAGAGAAAAGA
Found at i:6685435 original size:29 final size:30
Alignment explanation
Indices: 6685392--6685450 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
6685382 GAATCAGATC
*
6685392 AAATCAAAATTTCATGTATAAAATTGCACA
1 AAATCAAAATTTCATATATAAAATTGCACA
* *
6685422 AAATCAAAA-TTCATATATACAATTTCACA
1 AAATCAAAATTTCATATATAAAATTGCACA
6685451 TTAAACCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.51, C:0.15, G:0.03, T:0.31
Consensus pattern (30 bp):
AAATCAAAATTTCATATATAAAATTGCACA
Found at i:6685769 original size:16 final size:15
Alignment explanation
Indices: 6685737--6685766 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6685727 TCAAAAAAAA
6685737 TTTGAGGGGGATGGG
1 TTTGAGGGGGATGGG
*
6685752 TTTGGGGGGGATGGG
1 TTTGAGGGGGATGGG
6685767 GTTAGGATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.00, G:0.63, T:0.27
Consensus pattern (15 bp):
TTTGAGGGGGATGGG
Found at i:6686259 original size:17 final size:18
Alignment explanation
Indices: 6686227--6686260 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6686217 AGTCTAAATC
6686227 AAATAAAAATAATACAAT
1 AAATAAAAATAATACAAT
*
6686245 AAATAAAGA-AATACAA
1 AAATAAAAATAATACAA
6686261 AACTTAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.18
Consensus pattern (18 bp):
AAATAAAAATAATACAAT
Found at i:6687318 original size:27 final size:27
Alignment explanation
Indices: 6687267--6687319 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
6687257 CATGTTTTTT
* *
6687267 TTTTTCACCAAGTAAGTTATTGTAAAC
1 TTTTTCACCAAATAAGTTATCGTAAAC
*
6687294 TTTTTCACCAAATAAGTTGTCGTAAA
1 TTTTTCACCAAATAAGTTATCGTAAA
6687320 GGGGCCTCGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (27 bp):
TTTTTCACCAAATAAGTTATCGTAAAC
Found at i:6691073 original size:42 final size:42
Alignment explanation
Indices: 6691008--6691453 Score: 457
Period size: 42 Copynumber: 10.8 Consensus size: 42
6690998 TTGTAACTTT
* * *
6691008 AATCTACCCTCTAGTTAGGGTAAAATATTGGATGGTGTCTTC
1 AATCTGCCCTCTTGTTAGGGTAAAAGATTGGATGGTGTCTTC
*
6691050 AATTTGCCCTCTTGTTAGGGTAAAAGATTGGAT-G-GT-TTC
1 AATCTGCCCTCTTGTTAGGGTAAAAGATTGGATGGTGTCTTC
* * * * *
6691089 AATCTGCCC-CATGGTTGGGGTAAGAGATTGGATGGTATTTTC
1 AATCTGCCCTC-TTGTTAGGGTAAAAGATTGGATGGTGTCTTC
* *
6691131 AATCTGCCCTCTAGTTAGGGTAAAAGATTAGAT-G-G-CTTC
1 AATCTGCCCTCTTGTTAGGGTAAAAGATTGGATGGTGTCTTC
* * * * *
6691170 AATCTGCCC-CATGGTTAGTGTAAGAGATTGGATGATGTTTTC
1 AATCTGCCCTC-TTGTTAGGGTAAAAGATTGGATGGTGTCTTC
* ** * *
6691212 AATTTGTTCTCTAT-TTAGGATAAAAAATTGGAT-G-G-CTTC
1 AATCTGCCCTCT-TGTTAGGGTAAAAGATTGGATGGTGTCTTC
* *
6691251 AATCTGCCCTCTTGTTAGGGTAAAAGATTAGATGGTGTCTTT
1 AATCTGCCCTCTTGTTAGGGTAAAAGATTGGATGGTGTCTTC
** *
6691293 AATCTGCCCTCTTACTAGGGTAAAAGATTAGATGGTGTCTTC
1 AATCTGCCCTCTTGTTAGGGTAAAAGATTGGATGGTGTCTTC
** * * *
6691335 AATCTATCCTCTTTTTAGGGTAAAATATTAGATGGTGTCTTC
1 AATCTGCCCTCTTGTTAGGGTAAAAGATTGGATGGTGTCTTC
** *
6691377 AATCTGCATTCTTGTTATGGTAAAAGATTGGATGGTGTCTTC
1 AATCTGCCCTCTTGTTAGGGTAAAAGATTGGATGGTGTCTTC
* *
6691419 AATTTGCCCTCTTGTTTGGGTAAAAGATTGGATGG
1 AATCTGCCCTCTTGTTAGGGTAAAAGATTGGATGG
6691454 GATGATGTAA
Statistics
Matches: 330, Mismatches: 59, Indels: 30
0.79 0.14 0.07
Matches are distributed among these distances:
38 3 0.01
39 88 0.27
40 5 0.02
41 5 0.02
42 227 0.69
43 2 0.01
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (42 bp):
AATCTGCCCTCTTGTTAGGGTAAAAGATTGGATGGTGTCTTC
Found at i:6691148 original size:81 final size:80
Alignment explanation
Indices: 6691021--6691453 Score: 411
Period size: 81 Copynumber: 5.3 Consensus size: 80
6691011 CTACCCTCTA
* * * *
6691021 GTTAGGGTAAAATATTGGATGGTGTCTTCAATTTGCCCTCTTGTTAGGGTAAAAGATTGGATGGT
1 GTTAGGGTAAAAGATTGGATGGTGTTTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGGATGGT
*
6691086 TTCAATCTGCCCCATG
66 TTCAATCTGCCCC-TT
* * * * *
6691102 GTTGGGGTAAGAGATTGGATGGTATTTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTAGATGGC
1 GTTAGGGTAAAAGATTGGATGGTGTTTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGGATGGT
*
6691167 TTCAATCTGCCCCATG
66 TTCAATCTGCCCC-TT
* * * * ** * * * *
6691183 GTTAGTGTAAGAGATTGGATGATGTTTTCAATTTGTTCTCTATTTAGGATAAAAAATTGGATGGC
1 GTTAGGGTAAAAGATTGGATGGTGTTTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGGATGGT
6691248 TTCAATCTGCCCTCTT
66 TTCAATCTGCCC-CTT
* * *
6691264 GTTAGGGTAAAAGATTAGATGGTGTCTTT-AATCTGCCCTCTTA-CTAGGGTAAAAGATTAGATG
1 GTTAGGGTAAAAGATTGGATGGTGT-TTTCAATCTGCCCTC-TAGTTAGGGTAAAAGATTGGAT-
* *
6691327 GTGTCTTCAATCTATCCTCTT
63 G-GT-TTCAATCT-GCCCCTT
* * * * ** * *
6691348 TTTAGGGTAAAATATTAGATGGTGTCTTCAATCTGCATTCTTGTTATGGTAAAAGATTGGATGGT
1 GTTAGGGTAAAAGATTGGATGGTGTTTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGGAT-G-
*
6691413 GTCTTCAATTTGCCCTCTT
64 GT-TTCAATCTGCCC-CTT
*
6691432 GTTTGGGTAAAAGATTGGATGG
1 GTTAGGGTAAAAGATTGGATGG
6691454 GATGATGTAA
Statistics
Matches: 291, Mismatches: 51, Indels: 17
0.81 0.14 0.05
Matches are distributed among these distances:
81 183 0.63
82 7 0.02
83 6 0.02
84 93 0.32
85 2 0.01
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (80 bp):
GTTAGGGTAAAAGATTGGATGGTGTTTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGGATGGT
TTCAATCTGCCCCTT
Found at i:6707253 original size:21 final size:21
Alignment explanation
Indices: 6707206--6707265 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
6707196 AATAGTACAG
* *
6707206 ACTTCTACCAATACAAGTGAG
1 ACTTCTACCGATACAAGTGAC
*
6707227 AGTTCTACCGATACAAGTGAC
1 ACTTCTACCGATACAAGTGAC
* *
6707248 TCTTCTACCGAAACAAGT
1 ACTTCTACCGATACAAGT
6707266 CTTACTTCTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTGAC
Found at i:6710571 original size:18 final size:18
Alignment explanation
Indices: 6710548--6710582 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
6710538 ACGAGATTTT
6710548 GAAAAACAA-TTTGGTGTC
1 GAAAAA-AATTTTGGTGTC
6710566 GAAAAAAATTTTGGTGT
1 GAAAAAAATTTTGGTGT
6710583 TGGCCATTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.40, C:0.06, G:0.23, T:0.31
Consensus pattern (18 bp):
GAAAAAAATTTTGGTGTC
Found at i:6710764 original size:89 final size:89
Alignment explanation
Indices: 6710593--6710760 Score: 268
Period size: 88 Copynumber: 1.9 Consensus size: 89
6710583 TGGCCATTGC
* * *
6710593 ATGGCCGACACCACCTTTTTATCTGATAAAAAATCAAATTTTTTTGGTGTTGGCCATGCATTAGC
1 ATGGCCAACACCACATTTTTATCTGATAAAAAATCAAATTTTTTTGGTATTGGCCATGCATTAGC
*
6710658 CGACATCACCTTTTTATCAGAGCA
66 CGACACCACCTTTTTATCAGAGCA
*
6710682 ATGGCCAACACCACATTTTTATCTGAT-AAAAATCAAATTTTTTTGGTATTGGCCATTGCA-TGG
1 ATGGCCAACACCACATTTTTATCTGATAAAAAATCAAATTTTTTTGGTATTGGCCA-TGCATTAG
6710745 CCGACACCACCTTTTT
65 CCGACACCACCTTTTT
6710761 TATCTGACAA
Statistics
Matches: 73, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
88 44 0.60
89 29 0.40
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.35
Consensus pattern (89 bp):
ATGGCCAACACCACATTTTTATCTGATAAAAAATCAAATTTTTTTGGTATTGGCCATGCATTAGC
CGACACCACCTTTTTATCAGAGCA
Found at i:6710849 original size:148 final size:145
Alignment explanation
Indices: 6710574--6710848 Score: 374
Period size: 151 Copynumber: 1.9 Consensus size: 145
6710564 TCGAAAAAAA
* *
6710574 TTTTGGTGTTGGCCATTGCATGGCCGACACCACCTTTTTATCTGATAAAAAATCAAATTTTTTTG
1 TTTTGGTATTGGCCATTGCATGGCCGACACCACCTTTTTATCTGACAAAAAATCAAATTTTTTTG
* * * * * * *
6710639 GTGTTGGCCATGCATTAGCCGACATCACCTTTTTATCAGAGCAATGGCCAACACCACATTTTTAT
66 GTGTTGGCCATGCATTAACCAACACCACCTTTTTATCAGAGCAA--G-AAAAACAAAATTTTTAT
6710704 CTGATAAAAATCAAATTT
128 CTGATAAAAATCAAATTT
6710722 TTTTGGTATTGGCCATTGCATGGCCGACACCACCTTTTTTATCTGACAAAAAATTCAAATTTTTT
1 TTTTGGTATTGGCCATTGCATGGCCGACACCACC-TTTTTATCTGACAAAAAA-TCAAATTTTTT
* *
6710787 TGGGTGTTGGCCATGCATTAACCAACACCACCTTTTTATCTGA-TAA-AAAAATCAAAATTTTT
64 T-GGTGTTGGCCATGCATTAACCAACACCACCTTTTTATCAGAGCAAGAAAAA-CAAAATTTTT
6710849 TTGTGTTGGT
Statistics
Matches: 112, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
146 3 0.03
147 8 0.07
148 33 0.29
149 17 0.15
150 14 0.12
151 37 0.33
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (145 bp):
TTTTGGTATTGGCCATTGCATGGCCGACACCACCTTTTTATCTGACAAAAAATCAAATTTTTTTG
GTGTTGGCCATGCATTAACCAACACCACCTTTTTATCAGAGCAAGAAAAACAAAATTTTTATCTG
ATAAAAATCAAATTT
Found at i:6710881 original size:61 final size:60
Alignment explanation
Indices: 6710682--6710975 Score: 346
Period size: 62 Copynumber: 4.8 Consensus size: 60
6710672 TATCAGAGCA
* * *
6710682 ATGGCCAACACCACATTTTTATCTGAT--AAAAATCAAATTTTTTTGGTATTGGCCATTGC
1 ATGGCCGACACCACCTTTTTATCTGATAAAAAAATCAAATTTTTTTGGTGTTGGCCA-TGC
* *
6710741 ATGGCCGACACCACCTTTTTTATCTGACAAAAAATTCAAATTTTTTTGGGTGTTGGCCATGC
1 ATGGCCGACACCACC-TTTTTATCTGATAAAAAAATCAAATTTTTTT-GGTGTTGGCCATGC
** * **
6710803 ATTAACCAACACCACCTTTTTATCTGATAAAAAAATCAAAATTTTTTT-GTGTTGGTTATTGC
1 A-TGGCCGACACCACCTTTTTATCTGATAAAAAAATC-AAATTTTTTTGGTGTTGGCCA-TGC
* **
6710865 ATGGCCGACACTACCTTTTTTATCTGATAAAAAGTTCAAATTTTTTT-GTGTTGGCCATGC
1 ATGGCCGACACCACC-TTTTTATCTGATAAAAAAATCAAATTTTTTTGGTGTTGGCCATGC
* *
6710925 ATTGGTCGACACCACCTTTTTATCTGATAAAAAAATCAAA-ATTTTTGGTGT
1 A-TGGCCGACACCACCTTTTTATCTGATAAAAAAATCAAATTTTTTTGGTGT
6710976 CAACCATGCA
Statistics
Matches: 200, Mismatches: 25, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
59 18 0.09
60 41 0.20
61 48 0.24
62 62 0.31
63 31 0.16
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (60 bp):
ATGGCCGACACCACCTTTTTATCTGATAAAAAAATCAAATTTTTTTGGTGTTGGCCATGC
Found at i:6710937 original size:122 final size:124
Alignment explanation
Indices: 6710686--6710970 Score: 427
Period size: 122 Copynumber: 2.3 Consensus size: 124
6710676 AGAGCAATGG
*
6710686 CCAACACCACATTTTTATCTGAT--AAAAATC-AAATTTTTTTGGTATTGGCCATTGCATGGCCG
1 CCAACACCACCTTTTTATCTGATAAAAAAATCAAAATTTTTTTGGTATTGGCCATTGCATGGCCG
6710748 ACACCACCTTTTTTATCTGACAAAAAATTCAAATTTTTTTGGGTGTTGGCCATGCATTAA
66 ACACCACCTTTTTTATCTGACAAAAAATTCAAATTTTTTT-GGTGTTGGCCATGCATTAA
* **
6710808 CCAACACCACCTTTTTATCTGATAAAAAAATCAAAATTTTTTT-GTGTTGGTTATTGCATGGCCG
1 CCAACACCACCTTTTTATCTGATAAAAAAATCAAAATTTTTTTGGTATTGGCCATTGCATGGCCG
* * * **
6710872 ACACTACCTTTTTTATCTGATAAAAAGTTCAAATTTTTTT-GTGTTGGCCATGCATTGG
66 ACACCACCTTTTTTATCTGACAAAAAATTCAAATTTTTTTGGTGTTGGCCATGCATTAA
* *
6710930 TCGACACCACCTTTTTATCTGATAAAAAAATCAAAATTTTT
1 CCAACACCACCTTTTTATCTGATAAAAAAATCAAAATTTTT
6710971 GGTGTCAACC
Statistics
Matches: 149, Mismatches: 11, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
122 77 0.52
124 62 0.42
125 10 0.07
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (124 bp):
CCAACACCACCTTTTTATCTGATAAAAAAATCAAAATTTTTTTGGTATTGGCCATTGCATGGCCG
ACACCACCTTTTTTATCTGACAAAAAATTCAAATTTTTTTGGTGTTGGCCATGCATTAA
Found at i:6711084 original size:102 final size:101
Alignment explanation
Indices: 6710885--6711077 Score: 289
Period size: 102 Copynumber: 1.9 Consensus size: 101
6710875 CTACCTTTTT
* * *
6710885 TATCTGATAAAAAGTTCAAATTTTTTTGTGTTGGCCATGCATTGGTCGACACCACCTTTTTATCT
1 TATCTGATAAAAAATTCAAATTTTTTTATGTTAGCCATGCATTGGTCGACACCACCTTTTTATCT
*
6710950 GATAAAAAAATCAAAATTTTTGGTGTCAACCATGCA
66 AATAAAAAAATCAAAATTTTTGGTGTCAACCATGCA
* *
6710986 TATCTGATAAAAAATTCAAATTTTTTTTATGTTAGTCATGCATTGG-CTGACATCACCTTTTTAT
1 TATCTGATAAAAAATTCAAA-TTTTTTTATGTTAGCCATGCATTGGTC-GACACCACCTTTTTAT
**
6711050 CTAATAAAAAAATCAATTTTTTTGGTGT
64 CTAATAAAAAAATCAAAATTTTTGGTGT
6711078 TGACCATTGT
Statistics
Matches: 82, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
101 20 0.24
102 62 0.76
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (101 bp):
TATCTGATAAAAAATTCAAATTTTTTTATGTTAGCCATGCATTGGTCGACACCACCTTTTTATCT
AATAAAAAAATCAAAATTTTTGGTGTCAACCATGCA
Found at i:6711149 original size:163 final size:163
Alignment explanation
Indices: 6710823--6711123 Score: 396
Period size: 163 Copynumber: 1.8 Consensus size: 163
6710813 ACCACCTTTT
* * *
6710823 TATCTGATAAAAAAATCAAAATTTTTTTGTGTTGGTTATTGCATGGCCGACACTACCTTTTTTAT
1 TATCTGATAAAAAAATCAAAATTTTTTTATGTTAGTCATTGCATGGCCGACACTACCTTTTTTAT
* ** * * *
6710888 CTGATAAAAAGTTCAAATTTTTTTGTGTTGGCCATGCATTGGTCGACACCACCTTTTTATCTGAT
66 CTAATAAAAAAATCAAATTTTTTTGTGTTGACCATGCATTGGCCGACACCACCTTTTTATCTGAC
6710953 AAAAAAATCAAAATTTTTGGTGTCAACCATGCA
131 AAAAAAATCAAAATTTTTGGTGTCAACCATGCA
* * *
6710986 TATCTGATAAAAAATTCAAATTTTTTTTATGTTAGTCA-TGCATTGGCTGACA-TCACC-TTTTT
1 TATCTGATAAAAAAATCAAAATTTTTTTATGTTAGTCATTGCA-TGGCCGACACT-ACCTTTTTT
* *
6711048 ATCTAATAAAAAAATC-AATTTTTTTGGTGTTGACCATTGTA-TGGCCGACACCATCTTTTTTAT
64 ATCTAATAAAAAAATCAAATTTTTTT-GTGTTGACCA-TGCATTGGCCGACACCA-CCTTTTTAT
6711111 CTGACAAAAAAAT
126 CTGACAAAAAAAT
6711124 TAATTTTTTT
Statistics
Matches: 119, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
161 9 0.08
162 43 0.36
163 67 0.56
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.40
Consensus pattern (163 bp):
TATCTGATAAAAAAATCAAAATTTTTTTATGTTAGTCATTGCATGGCCGACACTACCTTTTTTAT
CTAATAAAAAAATCAAATTTTTTTGTGTTGACCATGCATTGGCCGACACCACCTTTTTATCTGAC
AAAAAAATCAAAATTTTTGGTGTCAACCATGCA
Found at i:6711156 original size:61 final size:59
Alignment explanation
Indices: 6710986--6711166 Score: 175
Period size: 61 Copynumber: 3.0 Consensus size: 59
6710976 CAACCATGCA
* * * * * * *
6710986 TATCTGATAAAAAATTCAAATTTTTTTTATGTTAGTCATGCATTGGCTGACATCACCTTTT
1 TATCTGAAAAAAAATT--AATTTTTTTTGTGTTGGCCATGCATTGGCCGACACCACTTTTT
* * * * *
6711047 TATCTAATAAAAAAATCAATTTTTTTGGTGTTGACCATTGTA-TGGCCGACACCATCTTTTT
1 TATCTGA-AAAAAAATTAATTTTTTTTGTGTTGGCCA-TGCATTGGCCGACACCA-CTTTTT
*
6711108 TATCTGACAAAAAAATTAATTTTTTTTGTGTTGGCCATGCATTAGCCGACACCAACTTT
1 TATCTGA-AAAAAAATTAATTTTTTTTGTGTTGGCCATGCATTGGCCGACACC-ACTTT
6711167 CCATCCTTTC
Statistics
Matches: 96, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
60 28 0.29
61 60 0.62
62 8 0.08
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.41
Consensus pattern (59 bp):
TATCTGAAAAAAAATTAATTTTTTTTGTGTTGGCCATGCATTGGCCGACACCACTTTTT
Found at i:6711160 original size:223 final size:224
Alignment explanation
Indices: 6710761--6711166 Score: 557
Period size: 223 Copynumber: 1.8 Consensus size: 224
6710751 CCACCTTTTT
* *
6710761 TATCTGACAAAAAATTCAAATTTTTTTGGGTGTTGGCCATGCATTAACCAACACCACCTTTTTAT
1 TATCTGACAAAAAATTCAAATTTTTTTGGATGTTAGCCATGCATTAACCAACACCACCTTTTTAT
* *** *
6710826 CTGATAAAAAAATCAAAATTTTTTTGTGTTGGTTATTGCATGGCCGACACTACCTTTTTTATCTG
66 CTAATAAAAAAATC-AAATTTTTTTGTGTTGACCATTGCATGGCCGACACCACCTTTTTTATCTG
* * * * *
6710891 ATAAAAAGTTCAAATTTTTTTGTGTTGGCCATGCATTGGTCGACACCACCTTTTTATCTGATAAA
130 AAAAAAAATTCAAATTTTTTTGTGTTGGCCATGCATTAGCCGACACCAACTTTTTATCTGATAAA
6710956 AAAATCAAAATTTTTGGTGTCAACCATGCA
195 AAAATCAAAATTTTTGGTGTCAACCATGCA
* * * ** ** *
6710986 TATCTGATAAAAAATTCAAATTTTTTT-TATGTTAGTCATGCATTGGCTGACATCACCTTTTTAT
1 TATCTGACAAAAAATTCAAATTTTTTTGGATGTTAGCCATGCATTAACCAACACCACCTTTTTAT
* *
6711050 CTAATAAAAAAATC-AATTTTTTTGGTGTTGACCATTGTATGGCCGACACCATCTTTTTTATCTG
66 CTAATAAAAAAATCAAATTTTTTT-GTGTTGACCATTGCATGGCCGACACCACCTTTTTTATCTG
*
6711114 ACAAAAAAATT-AATTTTTTTTGTGTTGGCCATGCATTAGCCGACACCAACTTT
130 A-AAAAAAATTCAAATTTTTTTGTGTTGGCCATGCATTAGCCGACACCAACTTT
6711167 CCATCCTTTC
Statistics
Matches: 156, Mismatches: 23, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
222 9 0.06
223 73 0.47
224 48 0.31
225 26 0.17
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (224 bp):
TATCTGACAAAAAATTCAAATTTTTTTGGATGTTAGCCATGCATTAACCAACACCACCTTTTTAT
CTAATAAAAAAATCAAATTTTTTTGTGTTGACCATTGCATGGCCGACACCACCTTTTTTATCTGA
AAAAAAATTCAAATTTTTTTGTGTTGGCCATGCATTAGCCGACACCAACTTTTTATCTGATAAAA
AAATCAAAATTTTTGGTGTCAACCATGCA
Found at i:6712089 original size:29 final size:30
Alignment explanation
Indices: 6712001--6712120 Score: 172
Period size: 30 Copynumber: 4.1 Consensus size: 30
6711991 AAAAAATAAT
*
6712001 AATTAGAAATGAAATTTAAAATATAAACGA
1 AATTAGAAATTAAATTTAAAATATAAACGA
* * *
6712031 AATTAGAAATTAAAATTAAAATATACATGA
1 AATTAGAAATTAAATTTAAAATATAAACGA
*
6712061 AATTAGAAATTAAA-TTAAAATATAAATGA
1 AATTAGAAATTAAATTTAAAATATAAACGA
*
6712090 AATTACAAATTAAATTTAAAA-ATAAACGA
1 AATTAGAAATTAAATTTAAAATATAAACGA
6712119 AA
1 AA
6712121 AAATCAAAAT
Statistics
Matches: 82, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
29 36 0.44
30 46 0.56
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.28
Consensus pattern (30 bp):
AATTAGAAATTAAATTTAAAATATAAACGA
Found at i:6712103 original size:17 final size:17
Alignment explanation
Indices: 6712007--6712104 Score: 65
Period size: 17 Copynumber: 6.2 Consensus size: 17
6711997 TAATAATTAG
6712007 AAATGAAATTTAAAATAT
1 AAATGAAA-TTAAAATAT
*
6712025 AAACGAAATTAGAAAT-T
1 AAATGAAATTA-AAATAT
6712042 --A--AAATTAAAATAT
1 AAATGAAATTAAAATAT
* *
6712055 ACATGAAATTAGAA-AT
1 AAATGAAATTAAAATAT
6712071 ---T-AAATTAAAATAT
1 AAATGAAATTAAAATAT
6712084 AAATGAAATTACAAAT-T
1 AAATGAAATTA-AAATAT
6712101 AAAT
1 AAAT
6712105 TTAAAAATAA
Statistics
Matches: 65, Mismatches: 3, Indels: 25
0.70 0.03 0.27
Matches are distributed among these distances:
12 12 0.18
13 10 0.15
15 2 0.03
16 3 0.05
17 23 0.35
18 15 0.23
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.30
Consensus pattern (17 bp):
AAATGAAATTAAAATAT
Found at i:6712592 original size:12 final size:12
Alignment explanation
Indices: 6712577--6712637 Score: 59
Period size: 12 Copynumber: 5.1 Consensus size: 12
6712567 ACTCGGACTG
6712577 GTCCTCGGGCTC
1 GTCCTCGGGCTC
* *
6712589 GTCCGCGAGCTC
1 GTCCTCGGGCTC
* *
6712601 GTACTCAGGCTC
1 GTCCTCGGGCTC
* *
6712613 GTCATTGGGCTC
1 GTCCTCGGGCTC
*
6712625 ATCCTCGGGCTC
1 GTCCTCGGGCTC
6712637 G
1 G
6712638 GAATCTGAAC
Statistics
Matches: 35, Mismatches: 14, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.08, C:0.36, G:0.31, T:0.25
Consensus pattern (12 bp):
GTCCTCGGGCTC
Found at i:6713409 original size:22 final size:22
Alignment explanation
Indices: 6713365--6713410 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
6713355 TCGAAAATAT
*
6713365 AAAAATATTTCAAAAATAGAAA
1 AAAAATATTTCAAAAATACAAA
*
6713387 AAAAATATTAT-AAAAATTCAAA
1 AAAAATATT-TCAAAAATACAAA
6713409 AA
1 AA
6713411 TATACCTTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (22 bp):
AAAAATATTTCAAAAATACAAA
Found at i:6713411 original size:49 final size:51
Alignment explanation
Indices: 6713313--6713414 Score: 136
Period size: 51 Copynumber: 2.0 Consensus size: 51
6713303 AAAAATAATT
** * * * *
6713313 TAAAAATATTTTGAAAATATAAAAAAATTATTTTTAAAAAATTCGAAAATA
1 TAAAAATATTTCAAAAATAGAAAAAAAATATTTATAAAAAATTCAAAAATA
6713364 TAAAAATATTTCAAAAATAGAAAAAAAATA-TTAT-AAAAATTCAAAAATA
1 TAAAAATATTTCAAAAATAGAAAAAAAATATTTATAAAAAATTCAAAAATA
6713413 TA
1 TA
6713415 CCTTACATCA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
49 16 0.36
50 3 0.07
51 26 0.58
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (51 bp):
TAAAAATATTTCAAAAATAGAAAAAAAATATTTATAAAAAATTCAAAAATA
Found at i:6713567 original size:22 final size:22
Alignment explanation
Indices: 6713528--6713573 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
6713518 ATAATTAGAA
**
6713528 TAAAAATAATATTTAATAAAATT
1 TAAAAATAATATAAAAT-AAATT
6713551 TAAAAA-AATATAAAATAAATT
1 TAAAAATAATATAAAATAAATT
6713572 TA
1 TA
6713574 TCGAGTCACC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.33
22 8 0.38
23 6 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
TAAAAATAATATAAAATAAATT
Found at i:6714487 original size:22 final size:22
Alignment explanation
Indices: 6714462--6714517 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
6714452 GGGTGGTGGG
* *
6714462 GAGCTGGAATTTCGATTTTGGT
1 GAGCTGGAATTTCAATTTAGGT
6714484 GAGCTGGAATTTCAATTTAGGT
1 GAGCTGGAATTTCAATTTAGGT
*
6714506 GAACTGGAATTT
1 GAGCTGGAATTT
6714518 GGGTGGTCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.25, C:0.09, G:0.29, T:0.38
Consensus pattern (22 bp):
GAGCTGGAATTTCAATTTAGGT
Found at i:6714702 original size:73 final size:73
Alignment explanation
Indices: 6714612--6714759 Score: 269
Period size: 73 Copynumber: 2.0 Consensus size: 73
6714602 AATTTAAACT
*
6714612 TTGATAAAAATTGAAATATAATAATAGTTTTTGATTTGAATAAATTTAAAATTTAAATTTGGTAA
1 TTGATAAAAATTGAAATATAATAATAGTTTTTGATTTAAATAAATTTAAAATTTAAATTTGGTAA
*
6714677 ATAATGTA
66 ATAATATA
*
6714685 TTGATAAAAATTGAAATATAATAATAGTTTTTTATTTAAATAAATTTAAAATTTAAATTTGGTAA
1 TTGATAAAAATTGAAATATAATAATAGTTTTTGATTTAAATAAATTTAAAATTTAAATTTGGTAA
6714750 ATAATATA
66 ATAATATA
6714758 TT
1 TT
6714760 ATCAAATCAA
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (73 bp):
TTGATAAAAATTGAAATATAATAATAGTTTTTGATTTAAATAAATTTAAAATTTAAATTTGGTAA
ATAATATA
Found at i:6714948 original size:95 final size:94
Alignment explanation
Indices: 6714685--6715113 Score: 709
Period size: 95 Copynumber: 4.5 Consensus size: 94
6714675 AAATAATGTA
* * * *
6714685 TTGATAAAAATTGAAATATAATAATAGTTTTTTATTTAAATAAATTTAAA-ATTTAAATTTGGTA
1 TTGATATAAATTGAAATATAATAATAATTTTTTATTTAAATAAATTTAAATATTAAAATTTGATA
* * *
6714749 AATAATATATTATCAAATCAACACATTAT
66 AATAATGTATTGTAAAATCAACACATTAT
6714778 TTGATATAAATTGAAATATAATAATAATTTTTTATTTAAATAAATTTAAATATTAAAATTTGATA
1 TTGATATAAATTGAAATATAATAATAATTTTTTATTTAAATAAATTTAAATATTAAAATTTGATA
6714843 AATAATGTATTGTAAAATCAACACATTAT
66 AATAATGTATTGTAAAATCAACACATTAT
*
6714872 TTGATATAAATTAAAATATAATAATAATTTTATTATTTAAATAAATTTAAATATTAAAATTTGAT
1 TTGATATAAATTGAAATATAATAATAATTTT-TTATTTAAATAAATTTAAATATTAAAATTTGAT
6714937 AAATAATGTATTGTAAAATCAACACATTAT
65 AAATAATGTATTGTAAAATCAACACATTAT
* *
6714967 TTGATATAAATTAAAATATAATAATAATTCTTTTATTTAAATAAATTTAAATATAAAAATTTGAT
1 TTGATATAAATTGAAATATAATAATAATT-TTTTATTTAAATAAATTTAAATATTAAAATTTGAT
*
6715032 AAATAATGTATTGTCAAATCAACACATTAT
65 AAATAATGTATTGTAAAATCAACACATTAT
6715062 TTGATATAAATTGAAATATAATAATAATTATTTTATTTAAAT-AATCTTAAAT
1 TTGATATAAATTGAAATATAATAATAATT-TTTTATTTAAATAAAT-TTAAAT
6715114 TAATTTTAAA
Statistics
Matches: 320, Mismatches: 12, Indels: 6
0.95 0.04 0.02
Matches are distributed among these distances:
93 48 0.15
94 71 0.22
95 199 0.62
96 2 0.01
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (94 bp):
TTGATATAAATTGAAATATAATAATAATTTTTTATTTAAATAAATTTAAATATTAAAATTTGATA
AATAATGTATTGTAAAATCAACACATTAT
Found at i:6715122 original size:11 final size:11
Alignment explanation
Indices: 6715097--6715134 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
6715087 AATTATTTTA
6715097 TTTAAA-TAAT
1 TTTAAATTAAT
*
6715107 CTTAAATTAAT
1 TTTAAATTAAT
6715118 TTTAAATATAAT
1 TTTAAAT-TAAT
6715130 TTTAA
1 TTTAA
6715135 TTTCAACTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 5 0.21
11 10 0.42
12 9 0.38
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (11 bp):
TTTAAATTAAT
Found at i:6715257 original size:17 final size:16
Alignment explanation
Indices: 6715231--6715265 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
6715221 AATTTTCAAA
*
6715231 TTAATTTCAACTTAAT
1 TTAATTTCAAATTAAT
6715247 TTAATTTTCAAATTAAT
1 TTAA-TTTCAAATTAAT
6715264 TT
1 TT
6715266 TTACACAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (16 bp):
TTAATTTCAAATTAAT
Found at i:6717271 original size:355 final size:356
Alignment explanation
Indices: 6716619--6717333 Score: 1272
Period size: 355 Copynumber: 2.0 Consensus size: 356
6716609 CAACTTGCAC
* * * *
6716619 CATCGGTTTGCAGTGAGGGAAGACCCTAACACACTGGTCGAACATCCAAAACAATCGGTAAAAAC
1 CATCGGTTTGCAATGAGGAAAGACCCTAACACACGGGTCGAACATCCAAAACAATCGATAAAAAC
6716684 GTCGTTTTCCAGGATCAATCACCCCATCCGGACCTTCATACGGCAGTGTTTATAAATCAGTGATT
66 GTCGTTTTCCAGGATCAATCACCCCATCCGGACCTTCATACGGCAGTGTTTATAAATCAGTGATT
*
6716749 GTCCCAAGCACATACTCTCGTATCGCGGCTATCCACCCTTGAAGCTCGTTGTATGATGCATCTCA
131 GTCCCAAGCACATACTCTCGTATCGAGGCTATCCACCCTTGAAGCTCGTTGTATGATGCATCTCA
*
6716814 GTCACCATACAACTCTCGCATCGCCATCTACTTTACCCACCATGCCTTCCGTTACGAAACCTTAT
196 GTCACCATACAACTCTCGCATCGCCATCTACTTTACCCACCATGCCTTCCGGTACGAAACCTTAT
* *
6716879 AATTGAAGCGAGCTTGCATGGCCGCAACATAGATCGATACCTTATTTAACGAGGACGCTTTTACC
261 AATTGAAGCGAGCTTGCATGACCGCAACATAGATCGATACCTTATTCAACGAGGACGCTTTTACC
6716944 ATAGGCATGATGCAATTGCATATGGTCTTTG
326 ATAGGCATGATGCAATTGCATATGGTCTTTG
* *
6716975 CATCGGTTTGCAATGAGGAAAGACCCTAACACACGGGTTGAA-AGTCCAAAATAATCGATAAAAA
1 CATCGGTTTGCAATGAGGAAAGACCCTAACACACGGGTCGAACA-TCCAAAACAATCGATAAAAA
* *
6717039 CGTCGTTTTCCCGGATCAATCACCCCATCCGGACCTTCATACGGCAGTGTTTGTAAATCAGTGAT
65 CGTCGTTTTCCAGGATCAATCACCCCATCCGGACCTTCATACGGCAGTGTTTATAAATCAGTGAT
6717104 TGTCCCAAGCACATACTCTCGTATC-AGGCTATCCACCCTTGAAGCTCGTTGTATGATGCATCTC
130 TGTCCCAAGCACATACTCTCGTATCGAGGCTATCCACCCTTGAAGCTCGTTGTATGATGCATCTC
* *
6717168 AGTCACCATACAACTCTCGCATCGCCATCTGCTTTACCCATCATGCCTTCCGGTACGAAACCTTA
195 AGTCACCATACAACTCTCGCATCGCCATCTACTTTACCCACCATGCCTTCCGGTACGAAACCTTA
*
6717233 TAATTGAAGCGAGCTTGCATGACCGCAACATAGATCGATACCTTATTCAACGGGGACGCTTTTAC
260 TAATTGAAGCGAGCTTGCATGACCGCAACATAGATCGATACCTTATTCAACGAGGACGCTTTTAC
6717298 CATAGGCATGATGCAATTGCATATGGTCTTTG
325 CATAGGCATGATGCAATTGCATATGGTCTTTG
6717330 CATC
1 CATC
6717334 TAATTTTCGA
Statistics
Matches: 343, Mismatches: 15, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
355 199 0.58
356 144 0.42
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (356 bp):
CATCGGTTTGCAATGAGGAAAGACCCTAACACACGGGTCGAACATCCAAAACAATCGATAAAAAC
GTCGTTTTCCAGGATCAATCACCCCATCCGGACCTTCATACGGCAGTGTTTATAAATCAGTGATT
GTCCCAAGCACATACTCTCGTATCGAGGCTATCCACCCTTGAAGCTCGTTGTATGATGCATCTCA
GTCACCATACAACTCTCGCATCGCCATCTACTTTACCCACCATGCCTTCCGGTACGAAACCTTAT
AATTGAAGCGAGCTTGCATGACCGCAACATAGATCGATACCTTATTCAACGAGGACGCTTTTACC
ATAGGCATGATGCAATTGCATATGGTCTTTG
Found at i:6719624 original size:64 final size:62
Alignment explanation
Indices: 6719476--6720087 Score: 363
Period size: 60 Copynumber: 10.0 Consensus size: 62
6719466 TCGGCTAATG
* * * *
6719476 CAACACCAAAAAAATTT-GTTTTTTATCTGAT-AAAAAGGTTGTATCGGCCAATGCAA-G-GC
1 CAACACCAAAAAAATTTAATTTTTTATCAGATAAAAAAGGTGGTGTCGGCCAA-GCAATGTGC
6719535 CAACACC-AAAAAATTTAAATTTTTTATCAGATAAAAAAGGTGGTGTCGGCCAAGCAATGTGAC
1 CAACACCAAAAAAATTT-AATTTTTTATCAGATAAAAAAGGTGGTGTCGGCCAAGCAATGTG-C
* * * **
6719598 CAACACCAAAAAAATTTAAATTTTTTATCCGATAAAAAATGTGGTGTCGACCAAAAAATG-GC
1 CAACACCAAAAAAATTT-AATTTTTTATCAGATAAAAAAGGTGGTGTCGGCCAAGCAATGTGC
* ****** ** ** * *
6719660 CAACACAAAAAAAAAATTTGGTAAAAAAAAATTTGATAAAAAAAATATTGTTGTCGGCTAATGC-
1 CAACAC--CAAAAAAA-TT--TAATTTTTTATCAGAT--AAAAAA-GGTGGTGTCGGCCAA-GCA
6719724 AT-TGC
57 ATGTGC
* * * * ** ** * *
6719729 TAACATCAAAAAAATTTAATTTTTTGTTAGATAAAAAAAATGGTGTCGATCATGCAATG-AC
1 CAACACCAAAAAAATTTAATTTTTTATCAGATAAAAAAGGTGGTGTCGGCCAAGCAATGTGC
* * * * *
6719790 CAATACC-AAAAAATTTGATTTTTTATCAGAT-AAAAAGGTGATGTCAGCCAA-TACATG-GC
1 CAACACCAAAAAAATTTAATTTTTTATCAGATAAAAAAGGTGGTGTCGGCCAAGCA-ATGTGC
* * * * *
6719849 CAACACAAAAAAAAAATTTAAATTTTTTGTCAGATAAAAAAGATGATGTCGGCCAAGCAATG-AC
1 CAACAC--CAAAAAAATTT-AATTTTTTATCAGATAAAAAAGGTGGTGTCGGCCAAGCAATGTGC
* ** * *
6719913 CAACACCAAAAAGAA-TTAA-TTTTTATCAGATAAAAAAGGTGATGTCGATCATGCAATG-AC
1 CAACACCAAAAA-AATTTAATTTTTTATCAGATAAAAAAGGTGGTGTCGGCCAAGCAATGTGC
* * *
6719973 CAACAGCAAAAAAA-TT-A-TTTTTATCTGAT-AAAAAGGTGGTGTCAGCCAATGC-ATG-GC
1 CAACACCAAAAAAATTTAATTTTTTATCAGATAAAAAAGGTGGTGTCGGCCAA-GCAATGTGC
* ** ** * * *
6720030 TAACTTCAAAAATTTTTGATTTTTTATCAGAT-AAAAAGGTGGTGTCGACCATGCAATG
1 CAACACCAAAAAAATTTAATTTTTTATCAGATAAAAAAGGTGGTGTCGGCCAAGCAATG
6720088 GTCTTTTTCG
Statistics
Matches: 432, Mismatches: 89, Indels: 63
0.74 0.15 0.11
Matches are distributed among these distances:
57 28 0.06
58 26 0.06
59 36 0.08
60 117 0.27
61 37 0.09
62 30 0.07
63 24 0.06
64 90 0.21
65 3 0.01
66 9 0.02
67 8 0.02
68 6 0.01
69 18 0.04
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (62 bp):
CAACACCAAAAAAATTTAATTTTTTATCAGATAAAAAAGGTGGTGTCGGCCAAGCAATGTGC
Found at i:6719705 original size:14 final size:15
Alignment explanation
Indices: 6719667--6719704 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
6719657 GGCCAACACA
*
6719667 AAAAAAAAATTTGGT
1 AAAAAAAAATTTGAT
6719682 AAAAAAAAATTTGAT
1 AAAAAAAAATTTGAT
6719697 AAAAAAAA
1 AAAAAAAA
6719705 TATTGTTGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (15 bp):
AAAAAAAAATTTGAT
Found at i:6719884 original size:123 final size:123
Alignment explanation
Indices: 6719736--6719958 Score: 333
Period size: 123 Copynumber: 1.8 Consensus size: 123
6719726 TGCTAACATC
* * * * *
6719736 AAAAAAATTTAATTTTTTGTTAGATAAAAAAAATGGTGTCGATCATGCAATGACCAATACCAAAA
1 AAAAAAATTTAATTTTTTGTCAGATAAAAAAAATGATGTCGACCAAGCAATGACCAACACCAAAA
* *
6719801 A-ATTTGATTTTTTATCAGAT-AAAAAGGTGATGTCAGCCAATACATGGCCAACACAAA
66 AGAATT-AATTTTTATCAGATAAAAAAGGTGATGTCAGCCAATACATGGCCAACACAAA
* *
6719858 AAAAAAATTTAAATTTTTTGTCAGATAAAAAAGATGATGTCGGCCAAGCAATGACCAACACCAAA
1 AAAAAAATTT-AATTTTTTGTCAGATAAAAAAAATGATGTCGACCAAGCAATGACCAACACCAAA
6719923 AAGAATTAATTTTTATCAGATAAAAAAGGTGATGTC
65 AAGAATTAATTTTTATCAGATAAAAAAGGTGATGTC
6719959 GATCATGCAA
Statistics
Matches: 89, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
122 10 0.11
123 62 0.70
124 17 0.19
ACGTcount: A:0.45, C:0.13, G:0.14, T:0.28
Consensus pattern (123 bp):
AAAAAAATTTAATTTTTTGTCAGATAAAAAAAATGATGTCGACCAAGCAATGACCAACACCAAAA
AGAATTAATTTTTATCAGATAAAAAAGGTGATGTCAGCCAATACATGGCCAACACAAA
Found at i:6720767 original size:20 final size:20
Alignment explanation
Indices: 6720712--6720767 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 20
6720702 TATTAACTAA
6720712 AATATCATA-TAAT-TTTTT
1 AATATCATATTAATATTTTT
* * *
6720730 -ATCTC-TTTTAATA-ATTT
1 AATATCATATTAATATTTTT
6720747 AATATCATATTAATATTTTT
1 AATATCATATTAATATTTTT
6720767 A
1 A
6720768 TTTTAAATTT
Statistics
Matches: 27, Mismatches: 6, Indels: 8
0.66 0.15 0.20
Matches are distributed among these distances:
16 1 0.04
17 11 0.41
18 4 0.15
19 7 0.26
20 4 0.15
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (20 bp):
AATATCATATTAATATTTTT
Found at i:6724546 original size:3 final size:3
Alignment explanation
Indices: 6724540--6724569 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
6724530 TAAAATGATG
6724540 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
6724570 GTATTATTAT
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:6724949 original size:12 final size:11
Alignment explanation
Indices: 6724921--6724969 Score: 55
Period size: 11 Copynumber: 4.3 Consensus size: 11
6724911 TAATTAATTA
6724921 ATTAATTATTTT
1 ATTAA-TATTTT
6724933 ATTAATATTTT
1 ATTAATATTTT
6724944 ACTTAA-ATATTT
1 A-TTAATAT-TTT
*
6724956 ATTATTATTTT
1 ATTAATATTTT
6724967 ATT
1 ATT
6724970 TAGAAAATGG
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
11 18 0.55
12 15 0.45
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (11 bp):
ATTAATATTTT
Found at i:6728168 original size:16 final size:16
Alignment explanation
Indices: 6728147--6728184 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
6728137 TTTAAAATGT
6728147 CCAATTACGA-TTAAGC
1 CCAATTAC-ACTTAAGC
6728163 CCAATTACACCTTAAGC
1 CCAATTACA-CTTAAGC
6728180 CCAAT
1 CCAAT
6728185 AAGCCCAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 1 0.05
16 8 0.40
17 11 0.55
ACGTcount: A:0.37, C:0.32, G:0.08, T:0.24
Consensus pattern (16 bp):
CCAATTACACTTAAGC
Found at i:6729634 original size:29 final size:29
Alignment explanation
Indices: 6729572--6730139 Score: 501
Period size: 29 Copynumber: 19.3 Consensus size: 29
6729562 TCTAATAGGT
* * *
6729572 CCCTAAACTT-TCTAAAAATTATATTTTGAT
1 CCCTAAACTTCTC-AAAAATCACATTTT-AA
* * *
6729602 CCCTAAACTTCTTAAAAATTACATTTTGA
1 CCCTAAACTTCTCAAAAATCACATTTTAA
* * * *
6729631 CCCTAAAAATTTTTC-AAAATTATATTTTAA
1 CCCT--AAACTTCTCAAAAATCACATTTTAA
* * *
6729661 CCCTCAAACTTTTCTAAAATTACATTTTAA
1 CCCT-AAACTTCTCAAAAATCACATTTTAA
*
6729691 CCCTCAAACTTCTTC-AAAATAACATTTTAA
1 CCCT-AAACTTC-TCAAAAATCACATTTTAA
* **
6729721 GCCCTAAACTTTGTC-AAAATCATGTTTTAA
1 -CCCTAAAC-TTCTCAAAAATCACATTTTAA
* * * *
6729751 CCCTACAACTTTTCTAAAATTATATTTTAA
1 CCCTA-AACTTCTCAAAAATCACATTTTAA
*
6729781 CCCTAAACTTCTCAAAAATCACA-TTTGA
1 CCCTAAACTTCTCAAAAATCACATTTTAA
*
6729809 TCCTAAACTTCTCAAAAATCACATTTTAA
1 CCCTAAACTTCTCAAAAATCACATTTTAA
* *
6729838 CCCTCGAACTT-TCCAAAAATCACATTTTGA
1 CCCT-AAACTTCT-CAAAAATCACATTTTAA
*
6729868 -CCTCGAACTTCTCAAAAATCACATTTTAA
1 CCCT-AAACTTCTCAAAAATCACATTTTAA
*
6729897 CCCCAAACTTCTCAAAAATCACATTTTAA
1 CCCTAAACTTCTCAAAAATCACATTTTAA
*
6729926 CCCTCGAACTTC-CAAAAATCACATTTTAA
1 CCCT-AAACTTCTCAAAAATCACATTTTAA
*
6729955 CCCTCGAACTTC-CAAAAATCACATTTTAA
1 CCCT-AAACTTCTCAAAAATCACATTTTAA
*
6729984 CCCTCGAACTTC-CAAAAATCACATTTTAA
1 CCCT-AAACTTCTCAAAAATCACATTTTAA
* * *
6730013 CCTTGAACTTCTCAAAAATCACATTTTGA
1 CCCTAAACTTCTCAAAAATCACATTTTAA
* *
6730042 CCCTAAACTT-TCCAAAAATTACATTTTGA
1 CCCTAAACTTCT-CAAAAATCACATTTTAA
* * * *
6730071 CCATCAAACTTTTCAAAAATTACATTTTGA
1 CCCT-AAACTTCTCAAAAATCACATTTTAA
* * * *
6730101 CCCTAGAACTTTTCAAAAATTACTTTTTGA
1 CCCTA-AACTTCTCAAAAATCACATTTTAA
6730131 CCCTAAACT
1 CCCTAAACT
6730140 CTCTGAATAT
Statistics
Matches: 474, Mismatches: 44, Indels: 41
0.85 0.08 0.07
Matches are distributed among these distances:
28 34 0.07
29 222 0.47
30 202 0.43
31 16 0.03
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.35
Consensus pattern (29 bp):
CCCTAAACTTCTCAAAAATCACATTTTAA
Found at i:6742040 original size:78 final size:78
Alignment explanation
Indices: 6741911--6742648 Score: 709
Period size: 78 Copynumber: 9.5 Consensus size: 78
6741901 AAAGATTCTG
* * * ** ** * * * *
6741911 ATCTCTTACCCCGATCATGGGGCAGATCACAATCATCCGATCTTTCACCCCGAGCTTGGGGTAAA
1 ATCTCTTACCCCGAGCCTGAGGCAGATTGCAGCCATCTGATCTTTTACCCCGAGCTTGGGGCAGA
6741976 TCACCATCAGCCA
66 TCACCATCAGCCA
* * * *
6741989 ATCTCTTTCCCCGAGCCTGAGGTAGATTGCAGTCATCTGATCTTTTACCCCGAGCTTGGGGCAAA
1 ATCTCTTACCCCGAGCCTGAGGCAGATTGCAGCCATCTGATCTTTTACCCCGAGCTTGGGGCAGA
* *
6742054 TCATCATCAACCA
66 TCACCATCAGCCA
** * * *
6742067 ATCTCTTACCCCGAGTTTG-GGCAGATTGCAGCCATCCGATCTTTTACCTCGAGCTTGGGGTAGA
1 ATCTCTTACCCCGAGCCTGAGGCAGATTGCAGCCATCTGATCTTTTACCCCGAGCTTGGGGCAGA
6742131 TCACCATCAGCCA
66 TCACCATCAGCCA
* * *
6742144 ATCTTTTACCCCGAGCCT-AGGGCTGATTGCAGCCATCCGATCTTTTACCCCGAGCTTGGGGCAG
1 ATCTCTTACCCCGAGCCTGA-GGCAGATTGCAGCCATCTGATCTTTTACCCCGAGCTTGGGGCAG
6742208 ATCACCATCAGCCA
65 ATCACCATCAGCCA
* * * * * *
6742222 ATCTCTTACCTCGAGCCT-AGGGCTGATTGCACCCATCTGATCTTTTACCCCAAGCCTGGGGCAA
1 ATCTCTTACCCCGAGCCTGA-GGCAGATTGCAGCCATCTGATCTTTTACCCCGAGCTTGGGGCAG
*
6742286 ATCACTATCAGCCA
65 ATCACCATCAGCCA
* * * * * * * *
6742300 ATCTCTTACCCCGAGCTTGGGGCAGATTGTAGTCATCCGATCTTTAACCCCGAGCCTAGGGCAGA
1 ATCTCTTACCCCGAGCCTGAGGCAGATTGCAGCCATCTGATCTTTTACCCCGAGCTTGGGGCAGA
* *
6742365 TCACTATCAGCTA
66 TCACCATCAGCCA
* * * * * * *
6742378 ATCTCTTACCCCGAGCCT-AGGATAAATTACAGCCAT-TCGATCTTTTACCTCGAGCCTGAGGTA
1 ATCTCTTACCCCGAGCCTGAGG-CAGATTGCAGCCATCT-GATCTTTTACCCCGAGCTTGGGGCA
6742441 GATCACCATCAGCCA
64 GATCACCATCAGCCA
* * * * * * * *
6742456 ATCTCTTACCCCGAGCTTAAGGCAGATTACAACCAT-TAGATCTTTTACCCCGATCATAGGGTAG
1 ATCTCTTACCCCGAGCCTGAGGCAGATTGCAGCCATCT-GATCTTTTACCCCGAGCTTGGGGCAG
*
6742520 ATCACCATCAGTCA
65 ATCACCATCAGCCA
** * * * * * * *
6742534 ATCTCTTACCCCGAGTTTGGGGCAGATTACAGTCAT-TCAATCTTTTACCTCGA-TTATTGGGCA
1 ATCTCTTACCCCGAGCCTGAGGCAGATTGCAGCCATCT-GATCTTTTACCCCGAGCT-TGGGGCA
*
6742597 GATCACCGTCAGCCA
64 GATCACCATCAGCCA
* * * *
6742612 ATCTCTTACCCCGCGACAGAGGCAGATTGCAACCATC
1 ATCTCTTACCCCGAGCCTGAGGCAGATTGCAGCCATC
6742649 CAATCTCTTA
Statistics
Matches: 553, Mismatches: 99, Indels: 15
0.83 0.15 0.02
Matches are distributed among these distances:
77 67 0.12
78 483 0.87
79 3 0.01
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (78 bp):
ATCTCTTACCCCGAGCCTGAGGCAGATTGCAGCCATCTGATCTTTTACCCCGAGCTTGGGGCAGA
TCACCATCAGCCA
Found at i:6742582 original size:39 final size:38
Alignment explanation
Indices: 6741911--6742624 Score: 349
Period size: 39 Copynumber: 18.3 Consensus size: 38
6741901 AAAGATTCTG
* * * * *
6741911 ATCTCTTACCCCGATCATGGGGCAGATCACAATCATCCG
1 ATCTTTTACCCCGAGCTTGGGGCAGATCAC-ATCAGCCA
* * *
6741950 ATCTTTCACCCCGAGCTTGGGGTAAATCACCATCAGCCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATCA-CATCAGCCA
* * * ** * **
6741989 ATCTCTTT-CCCCGAGCCTGAGGTAGATTGCAGTCATCTG
1 ATCT-TTTACCCCGAGCTTGGGGCAGATCACA-TCAGCCA
* *
6742028 ATCTTTTACCCCGAGCTTGGGGCAAATCATCATCAACCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATCA-CATCAGCCA
* * ** * * *
6742067 ATCTCTTACCCCGAG-TTTGGGCAGATTGCAGCCATCCG
1 ATCTTTTACCCCGAGCTTGGGGCAGATCACA-TCAGCCA
* *
6742105 ATCTTTTACCTCGAGCTTGGGGTAGATCACCATCAGCCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATCA-CATCAGCCA
* * * ** * * *
6742144 ATCTTTTACCCCGAGCCTAGGGCTGATTGCAGCCATCCG
1 ATCTTTTACCCCGAGCTTGGGGCAGATCACA-TCAGCCA
6742183 ATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATCA-CATCAGCCA
* * * * * * * **
6742222 ATCTCTTACCTCGAGCCTAGGGCTGATTGCAC-CCATCTG
1 ATCTTTTACCCCGAGCTTGGGGCAGA-T-CACATCAGCCA
* * *
6742261 ATCTTTTACCCCAAGCCTGGGGCAAATCACTATCAGCCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATCAC-ATCAGCCA
* *** * *
6742300 ATCTCTTACCCCGAGCTTGGGGCAGATTGTAGTCATCCG
1 ATCTTTTACCCCGAGCTTGGGGCAGATCACA-TCAGCCA
* * * *
6742339 ATCTTTAACCCCGAGCCTAGGGCAGATCACTATCAGCTA
1 ATCTTTTACCCCGAGCTTGGGGCAGATCAC-ATCAGCCA
* * * ** * * * ** *
6742378 ATCTCTTACCCCGAGCCTAGGATAAATTACAGCCATTCG
1 ATCTTTTACCCCGAGCTTGGGGCAGATCACA-TCAGCCA
* * * *
6742417 ATCTTTTACCTCGAGCCTGAGGTAGATCACCATCAGCCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATCA-CATCAGCCA
* ** * * **
6742456 ATCTCTTACCCCGAGCTTAAGGCAGATTACAACCA-TTA
1 ATCTTTTACCCCGAGCTTGGGGCAGATCAC-ATCAGCCA
* * * * *
6742494 GATCTTTTACCCCGATCATAGGGTAGATCACCATCAGTCA
1 -ATCTTTTACCCCGAGCTTGGGGCAGATCA-CATCAGCCA
* * * **
6742534 ATCTCTTACCCCGAGTTTGGGGCAGATTACAGTCATTCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATCACA-TCAGCCA
* * * *
6742573 ATCTTTTACCTCGA-TTATTGGGCAGATCACCGTCAGCCA
1 ATCTTTTACCCCGAGCT-TGGGGCAGATCA-CATCAGCCA
*
6742612 ATCTCTTACCCCG
1 ATCTTTTACCCCG
6742625 CGACAGAGGC
Statistics
Matches: 495, Mismatches: 155, Indels: 50
0.71 0.22 0.07
Matches are distributed among these distances:
37 5 0.01
38 42 0.08
39 428 0.86
40 18 0.04
41 2 0.00
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (38 bp):
ATCTTTTACCCCGAGCTTGGGGCAGATCACATCAGCCA
Found at i:6745062 original size:29 final size:29
Alignment explanation
Indices: 6744917--6745278 Score: 311
Period size: 30 Copynumber: 12.2 Consensus size: 29
6744907 CTACACTTTC
*
6744917 CAAAAATCACATTTTAACCTCAAAACTTCT
1 CAAAAATCACATTTTAACC-CTAAACTTCT
* * *
6744947 CTAAAATTACATTTAAACCCCTAAACTTCT
1 CAAAAATCACATTTTAA-CCCTAAACTTCT
* *
6744977 CCAAAATTCACATTTTAACCCTAAAACTTTT
1 -CAAAAATCACATTTTAACCCT-AAACTTCT
* * * *
6745008 CTAAAATTATATTTTAACCTTCAAACTTCT
1 CAAAAATCACATTTTAACCCT-AAACTTCT
*
6745038 CAAAAATCACTTTTTAACCCTAAACTTCT
1 CAAAAATCACATTTTAACCCTAAACTTCT
* * * *
6745067 CAAAAATCAAATTTTGACCCTCGAACTTTT
1 CAAAAATCACATTTTAACCCT-AAACTTCT
* *
6745097 CAAAAATAACATTTTAA-CCTCGAACTTCT
1 CAAAAATCACATTTTAACCCT-AAACTTCT
* *
6745126 CAAAAATCACATTTTAACCTTGAACTTCT
1 CAAAAATCACATTTTAACCCTAAACTTCT
*
6745155 C-AAAATCACATTTTGACCCCCTAAACTT-T
1 CAAAAATCACATTTT-A-ACCCTAAACTTCT
* *
6745184 CCAAAAATTACATTTTAACCCCCAAACTT-T
1 -CAAAAATCACATTTTAA-CCCTAAACTTCT
* * *
6745214 CCAAAAAACACGTTTTAACCCCTGAACTTCT
1 -CAAAAATCACATTTTAA-CCCTAAACTTCT
* **
6745245 CAAAAATTACATTTTGGCCCTAAAC-TCT
1 CAAAAATCACATTTTAACCCTAAACTTCT
*
6745273 CTAAAA
1 CAAAAA
6745279 CTTTATTTTT
Statistics
Matches: 271, Mismatches: 50, Indels: 24
0.79 0.14 0.07
Matches are distributed among these distances:
28 21 0.08
29 71 0.26
30 144 0.53
31 35 0.13
ACGTcount: A:0.39, C:0.26, G:0.02, T:0.33
Consensus pattern (29 bp):
CAAAAATCACATTTTAACCCTAAACTTCT
Found at i:6745094 original size:59 final size:59
Alignment explanation
Indices: 6744917--6745259 Score: 338
Period size: 59 Copynumber: 5.7 Consensus size: 59
6744907 CTACACTTTC
* * *
6744917 CAAAAATCACATTTTAACCTCAAAACTTCTCTAAAATTACATTTAAACCC-CTAAACTTCT
1 CAAAAATCACATTTTAACC-CTAAACTTCTCAAAAATTACATTTTAACCCTC-AAACTTCT
* * * * *
6744977 CCAAAATTCACATTTTAACCCTAAAACTTTTCTAAAATTATATTTTAACCTTCAAACTTCT
1 -CAAAAATCACATTTTAACCCT-AAACTTCTCAAAAATTACATTTTAACCCTCAAACTTCT
* * * * * *
6745038 CAAAAATCACTTTTTAACCCTAAACTTCTCAAAAATCAAATTTTGACCCTCGAACTTTT
1 CAAAAATCACATTTTAACCCTAAACTTCTCAAAAATTACATTTTAACCCTCAAACTTCT
* * * **
6745097 CAAAAATAACATTTTAA-CCTCGAACTTCTCAAAAATCACATTTTAA-CCTTGAACTTCT
1 CAAAAATCACATTTTAACCCT-AAACTTCTCAAAAATTACATTTTAACCCTCAAACTTCT
* *
6745155 C-AAAATCACATTTTGACCCCCTAAACTT-TCCAAAAATTACATTTTAACCCCCAAACTT-T
1 CAAAAATCACATTTT-A-ACCCTAAACTTCT-CAAAAATTACATTTTAACCCTCAAACTTCT
* * *
6745214 CCAAAAAACACGTTTTAACCCCTGAACTTCTCAAAAATTACATTTT
1 -CAAAAATCACATTTTAA-CCCTAAACTTCTCAAAAATTACATTTT
6745260 GGCCCTAAAC
Statistics
Matches: 236, Mismatches: 34, Indels: 25
0.80 0.12 0.08
Matches are distributed among these distances:
57 12 0.05
58 16 0.07
59 89 0.38
60 56 0.24
61 62 0.26
62 1 0.00
ACGTcount: A:0.39, C:0.26, G:0.02, T:0.33
Consensus pattern (59 bp):
CAAAAATCACATTTTAACCCTAAACTTCTCAAAAATTACATTTTAACCCTCAAACTTCT
Found at i:6749625 original size:21 final size:21
Alignment explanation
Indices: 6749579--6749625 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
6749569 AGTACAAAAA
* *
6749579 TTTTTTAAAAAAAAAGTTTAG
1 TTTTTTAAAAAAAAAATATAG
*
6749600 ATTTTTAAAAATAAAAATAT-G
1 TTTTTTAAAAA-AAAAATATAG
6749621 TTTTT
1 TTTTT
6749626 AGTTATTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (21 bp):
TTTTTTAAAAAAAAAATATAG
Found at i:6749870 original size:143 final size:142
Alignment explanation
Indices: 6749588--6749858 Score: 420
Period size: 143 Copynumber: 1.9 Consensus size: 142
6749578 ATTTTTTAAA
* * *
6749588 AAAAAAGTTTAGATTTTTAAAAATAAAAATATGTTTTTAGTTATTTTAAAGGAAAAATTTTAAAT
1 AAAAAAGTTTAAATTTTTAAAAATAAAAATATGTTTTTAGTCATTTTAAAGGAAAAAGTTTAAAT
*
6749653 TTTTAAACAAAATTTTGATTTTTTTAACTATTTCGAAATAAAAATTTTGATTTTTAAGAAAAATA
66 TTTTAAACAAAATTTTGATTTTTTTAACTATTTCAAAATAAAAATTTTGATTTTTAAGAAAAATA
6749718 GTGATTTTTTTT
131 GTGATTTTTTTT
*
6749730 AAAAAAGTTTAAATTTTTAAAAATAAAAAATATGTTTTTTTAGTCATTTTAAAGGAAAAGGTTTA
1 AAAAAAGTTTAAATTTTTAAAAAT-AAAAATATG--TTTTTAGTCATTTTAAAGGAAAAAGTTTA
* * * *
6749795 AATTTTTAAA-TAAATTTTGA-TTTTTTAACTATTTCAAAATGAAAGTTTTGGTTTTTAAGAAAA
63 AATTTTTAAACAAAATTTTGATTTTTTTAACTATTTCAAAATAAAAATTTTGATTTTTAAGAAAA
6749858 A
128 A
6749859 GTTTAGATTT
Statistics
Matches: 117, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
142 23 0.20
143 49 0.42
144 9 0.08
145 36 0.31
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (142 bp):
AAAAAAGTTTAAATTTTTAAAAATAAAAATATGTTTTTAGTCATTTTAAAGGAAAAAGTTTAAAT
TTTTAAACAAAATTTTGATTTTTTTAACTATTTCAAAATAAAAATTTTGATTTTTAAGAAAAATA
GTGATTTTTTTT
Found at i:6749876 original size:19 final size:20
Alignment explanation
Indices: 6749836--6749876 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
6749826 TTTCAAAATG
* *
6749836 AAAGTTTTGGTTTTTAAGAA
1 AAAGTTTAGATTTTTAAGAA
6749856 AAAGTTTAGATTTTTAA-AA
1 AAAGTTTAGATTTTTAAGAA
6749875 AA
1 AA
6749877 TAAAAATCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (20 bp):
AAAGTTTAGATTTTTAAGAA
Found at i:6749949 original size:121 final size:121
Alignment explanation
Indices: 6749731--6749977 Score: 358
Period size: 121 Copynumber: 2.0 Consensus size: 121
6749721 ATTTTTTTTA
*
6749731 AAAAAGTTTAAATTTTTAAAAATAAAAAATATGTTTTTTTAGTCATTTTAAAGGAAAAGGTTTAA
1 AAAAAGTTTAAATTTTTAAAAATAAAAAATATG-TTTTTTAGTCATTTTAAAGGAAAAAGTTTAA
* *
6749796 ATTTTTAAATAAATTTTGATTTTTTAACTATTTCAAAATGAAAGTTTTGGTTTTTAAG
65 ATTTTTAAATAAATTTTGATTTTTTAACTATTTCAAAATAAAAGTTTT-ATTTTTAAG
* *
6749854 AAAAAGTTTAGATTTTTAAAAA-ATAAAAATCTG-TTTTTAGTCATTTTAAA-GAAAAAGTTTAA
1 AAAAAGTTTAAATTTTTAAAAATA-AAAAATATGTTTTTTAGTCATTTTAAAGGAAAAAGTTTAA
* *
6749916 ATTTTTAAA-AAAGTTTTGATTTTTTTAATTATTTCGAAATAAAAGTTTTATTTTTAAG
65 ATTTTTAAATAAA-TTTTGA-TTTTTTAACTATTTCAAAATAAAAGTTTTATTTTTAAG
6749974 AAAA
1 AAAA
6749978 GTAATATTTT
Statistics
Matches: 114, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
119 3 0.03
120 38 0.33
121 43 0.38
122 1 0.01
123 29 0.25
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (121 bp):
AAAAAGTTTAAATTTTTAAAAATAAAAAATATGTTTTTTAGTCATTTTAAAGGAAAAAGTTTAAA
TTTTTAAATAAATTTTGATTTTTTAACTATTTCAAAATAAAAGTTTTATTTTTAAG
Found at i:6760245 original size:21 final size:21
Alignment explanation
Indices: 6760218--6760294 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
6760208 AGAGTTTTTA
*
6760218 GTATCGGTAGAAGTATGACTT
1 GTATCGGTAGAAGTATCACTT
* *
6760239 GTTTCGGTAGAAGTCTCACTT
1 GTATCGGTAGAAGTATCACTT
* * *
6760260 GTATCAGTAGAACTATCA-TAG
1 GTATCGGTAGAAGTATCACT-T
*
6760281 GTATCGATAGAAGT
1 GTATCGGTAGAAGT
6760295 CTCCATAATC
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 1 0.02
21 43 0.98
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (21 bp):
GTATCGGTAGAAGTATCACTT
Found at i:6760872 original size:25 final size:24
Alignment explanation
Indices: 6760825--6760872 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
6760815 AGAATATCCC
*
6760825 GAATTGTGTTAGGGTTTTATAGCA
1 GAATTGTGTTAGGGTTCTATAGCA
6760849 GAATTGTGTATAGGG-TCTAGTAGC
1 GAATTGTGT-TAGGGTTCTA-TAGC
6760873 TGTCAACACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.25, C:0.06, G:0.31, T:0.38
Consensus pattern (24 bp):
GAATTGTGTTAGGGTTCTATAGCA
Done.