Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 23 of 199
Found at i:6829286 original size:21 final size:22
Alignment explanation
Indices: 6829261--6829316 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
6829251 AATTTCGAAG
6829261 AAATTAATAAATTTTACAA-AT-
1 AAATTAATAAATTTTA-AATATA
* * *
6829282 AAATTAACAAGTTTTAAATTTA
1 AAATTAATAAATTTTAAATATA
6829304 AAATTAATAAATT
1 AAATTAATAAATT
6829317 AGGAAGTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 2 0.07
21 15 0.54
22 11 0.39
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (22 bp):
AAATTAATAAATTTTAAATATA
Found at i:6830755 original size:4 final size:4
Alignment explanation
Indices: 6830746--6830787 Score: 61
Period size: 4 Copynumber: 10.8 Consensus size: 4
6830736 GATGATGTGT
6830746 TAAA TAAA TAAA TAAA TATAA TAAA T-AA -AAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TA-AA TAAA TAAA TAAA TAAA TAAA TAA
6830788 TATAGAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
3 4 0.11
4 27 0.77
5 4 0.11
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:6830779 original size:19 final size:20
Alignment explanation
Indices: 6830755--6830800 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
6830745 TTAAATAAAT
6830755 AAATAAATATAATAA-ATA-A
1 AAATAAATA-AATAATATAGA
6830774 AAATAAATAAATAATATAGA
1 AAATAAATAAATAATATAGA
6830794 AAA-AAAT
1 AAATAAAT
6830801 TGAAATCGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.20
19 16 0.64
20 4 0.16
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (20 bp):
AAATAAATAAATAATATAGA
Found at i:6830789 original size:17 final size:17
Alignment explanation
Indices: 6830746--6830789 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
6830736 GATGATGTGT
*
6830746 TAAATAA-ATAAATAAA
1 TAAATAATAAAAATAAA
6830762 TATAATAAATAAAAATAAA
1 TA-AAT-AATAAAAATAAA
6830781 TAAATAATA
1 TAAATAATA
6830790 TAGAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 2 0.08
17 7 0.29
18 5 0.21
19 10 0.42
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAATAATAAAAATAAA
Found at i:6833043 original size:18 final size:17
Alignment explanation
Indices: 6833010--6833048 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
6833000 TTTTATAAAT
6833010 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
6833028 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
6833045 TGTG
1 TGTG
6833049 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:6833300 original size:23 final size:23
Alignment explanation
Indices: 6833274--6833349 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
6833264 AGTGTTATTG
*
6833274 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACGT
6833297 ATCAGTGGTAGCTTCGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACGT
6833320 ATCAGTGGTAGCTTCGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACGT
6833343 ATCAGTG
1 ATCAGTG
6833350 CGGCACTTAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACGT
Found at i:6837934 original size:33 final size:33
Alignment explanation
Indices: 6837892--6838146 Score: 156
Period size: 33 Copynumber: 7.8 Consensus size: 33
6837882 CTCATCTGCC
*
6837892 TCAGCTTGTACACCTTCTACATCACCCTCCCCA
1 TCAGCTTGTACCCCTTCTACATCACCCTCCCCA
* * *
6837925 TCAGCTTGTATCCCTTCTATATCACCCTCCTCA
1 TCAGCTTGTACCCCTTCTACATCACCCTCCCCA
* * * * **
6837958 TAAACTTCTACCCCTTCAACATCACATTCCCCA
1 TCAGCTTGTACCCCTTCTACATCACCCTCCCCA
* * * *
6837991 T-AGCTTGTACCCCTTCTACAACGCCATCCCTA
1 TCAGCTTGTACCCCTTCTACATCACCCTCCCCA
** * * *
6838023 TCTA-AATCTACCCCTTCAACATCACCCTCCCTA
1 TC-AGCTTGTACCCCTTCTACATCACCCTCCCCA
* * * * * * **
6838056 ACAACTTGTACTCCTTCTACAACGCCATCTTCA
1 TCAGCTTGTACCCCTTCTACATCACCCTCCCCA
** * * *
6838089 TCTAAATT-TACCCTTTCAACATCACCCTCCTCA
1 TC-AGCTTGTACCCCTTCTACATCACCCTCCCCA
* * *
6838122 TCAGCTTCTACTCCTTCAACATCAC
1 TCAGCTTGTACCCCTTCTACATCAC
6838147 TTTCCCCAAC
Statistics
Matches: 164, Mismatches: 53, Indels: 10
0.72 0.23 0.04
Matches are distributed among these distances:
32 28 0.17
33 131 0.80
34 5 0.03
ACGTcount: A:0.25, C:0.41, G:0.04, T:0.30
Consensus pattern (33 bp):
TCAGCTTGTACCCCTTCTACATCACCCTCCCCA
Found at i:6838134 original size:66 final size:65
Alignment explanation
Indices: 6837904--6838138 Score: 244
Period size: 66 Copynumber: 3.6 Consensus size: 65
6837894 AGCTTGTACA
* * * * *
6837904 CCTTCTACATCACCCTCCCCATCAGCTTGTA-TCCCTTCTATATCACC--CTCCTCATAAACTTC
1 CCTTCAACATCACCCTCCCCATCAGCTTGTACT-CCTTCTACAACGCCATCTCATC-TAAA-TT-
6837966 TACC
62 TACC
** * * *
6837970 CCTTCAACATCACATTCCCCAT-AGCTTGTACCCCTTCTACAACGCCATCCCTATCTAAATCTAC
1 CCTTCAACATCACCCTCCCCATCAGCTTGTACTCCTTCTACAACGCCATCTC-ATCTAAATTTAC
6838034 C
65 C
* * *
6838035 CCTTCAACATCACCCTCCCTAACAACTTGTACTCCTTCTACAACGCCATCTTCATCTAAATTTAC
1 CCTTCAACATCACCCTCCCCATCAGCTTGTACTCCTTCTACAACGCCATC-TCATCTAAATTTAC
6838100 C
65 C
* * *
6838101 CTTTCAACATCACCCTCCTCATCAGCTTCTACTCCTTC
1 CCTTCAACATCACCCTCCCCATCAGCTTGTACTCCTTC
6838139 AACATCACTT
Statistics
Matches: 139, Mismatches: 24, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
65 41 0.29
66 89 0.64
67 7 0.05
68 2 0.01
ACGTcount: A:0.24, C:0.42, G:0.03, T:0.31
Consensus pattern (65 bp):
CCTTCAACATCACCCTCCCCATCAGCTTGTACTCCTTCTACAACGCCATCTCATCTAAATTTACC
Found at i:6841350 original size:15 final size:15
Alignment explanation
Indices: 6841330--6841358 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
6841320 GTATTGTTGC
6841330 TTGATAACATGGTGA
1 TTGATAACATGGTGA
6841345 TTGATAACATGGTG
1 TTGATAACATGGTG
6841359 TGTGAAGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.07, G:0.28, T:0.34
Consensus pattern (15 bp):
TTGATAACATGGTGA
Found at i:6842573 original size:16 final size:16
Alignment explanation
Indices: 6842552--6842594 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
6842542 AATTACAATT
*
6842552 TTTAGGGATTTCATAA
1 TTTAGGGATTTCAAAA
*
6842568 TTTAGGGTTTTCAAAA
1 TTTAGGGATTTCAAAA
* *
6842584 ATTAGGAATTT
1 TTTAGGGATTT
6842595 TAGTTTTTTG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.44
Consensus pattern (16 bp):
TTTAGGGATTTCAAAA
Found at i:6844564 original size:22 final size:21
Alignment explanation
Indices: 6844538--6844596 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
6844528 TTTTTTGAAT
*
6844538 TTTTAAAAAAATATTTATATTA
1 TTTTAAAAAAATATTTA-ATAA
***
6844560 TTTTAATTTAATATTTAATAA
1 TTTTAAAAAAATATTTAATAA
6844581 TTATTAAAAAAATATT
1 TT-TTAAAAAAATATT
6844597 ATTATTAATA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
21 5 0.17
22 24 0.83
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTTAAAAAAATATTTAATAA
Found at i:6855246 original size:16 final size:16
Alignment explanation
Indices: 6855221--6855267 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
6855211 ATAATTAAGC
*
6855221 TAAAATAAATGAAAA-A
1 TAAAAAAAAT-AAAAGA
6855237 TAAAAAAAATAAAAGA
1 TAAAAAAAATAAAAGA
*
6855253 TAACAAAAACTAAAA
1 TAA-AAAAAATAAAA
6855268 ACCGGATTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 4 0.15
16 13 0.48
17 10 0.37
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.15
Consensus pattern (16 bp):
TAAAAAAAATAAAAGA
Found at i:6857640 original size:14 final size:15
Alignment explanation
Indices: 6857616--6857653 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
6857606 CTGTTTAAAA
6857616 ATAATAATAAAAATT
1 ATAATAATAAAAATT
6857631 ATAA-AATAAAAATT
1 ATAATAATAAAAATT
*
6857645 ATATTAATA
1 ATAATAATA
6857654 TAATAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
ATAATAATAAAAATT
Found at i:6864133 original size:16 final size:16
Alignment explanation
Indices: 6864114--6864163 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
6864104 ATTAAAGTTA
6864114 ATTATTTTAATTAATT
1 ATTATTTTAATTAATT
* *
6864130 ATTATTTTAAAT-AGT
1 ATTATTTTAATTAATT
*
6864145 ATTATTTTGCATTAATT
1 ATTATTTT-AATTAATT
6864162 AT
1 AT
6864164 ATTAAGTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
15 10 0.37
16 13 0.48
17 4 0.15
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (16 bp):
ATTATTTTAATTAATT
Found at i:6865891 original size:22 final size:22
Alignment explanation
Indices: 6865866--6865910 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
6865856 TACTCATATA
6865866 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAATATAATAAAT
* * *
6865888 ATAATTTATTATTTTAATAAAT
1 ATAAATTATTAATATAATAAAT
6865910 A
1 A
6865911 ATTTAATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Found at i:6865969 original size:16 final size:15
Alignment explanation
Indices: 6865929--6865969 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 15
6865919 TTTCAATTTT
6865929 ATTTT-AATAATAAA
1 ATTTTAAATAATAAA
6865943 A-TTTAAA-AATAATA
1 ATTTTAAATAATAA-A
6865957 ATTTTAAATAATA
1 ATTTTAAATAATA
6865970 TTATTCACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 8 0.35
14 5 0.22
15 6 0.26
16 4 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTTTAAATAATAAA
Found at i:6866022 original size:15 final size:15
Alignment explanation
Indices: 6866002--6866059 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
6865992 ATTCAATATC
6866002 AATATTTTAATAATA
1 AATATTTTAATAATA
*
6866017 AATATTTATTAGAATTATA
1 AATA-TT-TT--AATAATA
*
6866036 AATATATTAATAATA
1 AATATTTTAATAATA
*
6866051 AATGTTTTA
1 AATATTTTA
6866060 TTAGTATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 17 0.50
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.29
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:6868929 original size:14 final size:14
Alignment explanation
Indices: 6868893--6868942 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
6868883 TATTATCATC
*
6868893 ATTATTATTTTCCTT
1 ATTATTA-TTTACTT
6868908 -TTATTTATTTACTT
1 ATTA-TTATTTACTT
6868922 ATTATTA-TTACTAT
1 ATTATTATTTACT-T
6868936 ATTATTA
1 ATTATTA
6868943 AATTAATTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 5 0.16
14 20 0.65
15 6 0.19
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTATTATTTACTT
Found at i:6868947 original size:67 final size:67
Alignment explanation
Indices: 6868859--6868985 Score: 170
Period size: 67 Copynumber: 1.9 Consensus size: 67
6868849 TTTTGCTATG
*
6868859 TTATTATTAAATTAATTAATTAACTATTATCAT-CATTATTAT-TTTCCTTTTATTTATTTACTT
1 TTATTACTAAATTAATTAATTAACTATT-T-ATGCATTATTATATTTCCTTTTATTTATTTACTT
6868922 ATTA
64 ATTA
* * *
6868926 TTATTACTATATT-ATTAAATTAATTATTTTTGCATTATTATATTTCCTTTTATTTATTTA
1 TTATTACTAAATTAATT-AATTAACTATTTATGCATTATTATATTTCCTTTTATTTATTTA
6868986 TCTAAATATT
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
65 1 0.02
66 13 0.25
67 39 0.74
ACGTcount: A:0.31, C:0.08, G:0.01, T:0.60
Consensus pattern (67 bp):
TTATTACTAAATTAATTAATTAACTATTTATGCATTATTATATTTCCTTTTATTTATTTACTTAT
TA
Found at i:6870726 original size:2 final size:2
Alignment explanation
Indices: 6870719--6870757 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
6870709 CAATTCAAAT
6870719 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6870758 GTTTCTCATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6873995 original size:21 final size:21
Alignment explanation
Indices: 6873969--6874016 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
6873959 TATAATTCAT
*
6873969 AACATAAAATTTAGCTTATAG
1 AACATAAAATTCAGCTTATAG
6873990 AACATAAAATTCAGCTTATAG
1 AACATAAAATTCAGCTTATAG
6874011 AACATA
1 AACATA
6874017 TATATATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.50, C:0.12, G:0.08, T:0.29
Consensus pattern (21 bp):
AACATAAAATTCAGCTTATAG
Found at i:6874021 original size:2 final size:2
Alignment explanation
Indices: 6874014--6874039 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6874004 CTTATAGAAC
6874014 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
6874040 TCTAATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6875260 original size:44 final size:44
Alignment explanation
Indices: 6875182--6875267 Score: 118
Period size: 44 Copynumber: 2.0 Consensus size: 44
6875172 AGGAAAAATA
* ***
6875182 ATTTTATTATTAGGGTTTTGGGTGTATGTTAATTAGGGTTTAGG
1 ATTTTATTATTAGGGTTTTGAGTGTATAAAAATTAGGGTTTAGG
* *
6875226 ATTTTATTATTAGGGTTTTTAGTGTTTAAAAATTAGGGTTTA
1 ATTTTATTATTAGGGTTTTGAGTGTATAAAAATTAGGGTTTA
6875268 AGGGTTATGA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (44 bp):
ATTTTATTATTAGGGTTTTGAGTGTATAAAAATTAGGGTTTAGG
Found at i:6879635 original size:18 final size:19
Alignment explanation
Indices: 6879595--6879635 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
6879585 CAATTTGAAT
**
6879595 GAAAAAAAAGCAGACAAAA
1 GAAAAAAAAAAAGACAAAA
6879614 -AAAAAAAAAAAGA-AAAA
1 GAAAAAAAAAAAGACAAAA
6879631 GAAAA
1 GAAAA
6879636 GAAGAGATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.83, C:0.05, G:0.12, T:0.00
Consensus pattern (19 bp):
GAAAAAAAAAAAGACAAAA
Found at i:6879663 original size:2 final size:2
Alignment explanation
Indices: 6879656--6879690 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6879646 ACACAAATAG
6879656 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6879691 NNNNNNNNNN
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6883022 original size:47 final size:46
Alignment explanation
Indices: 6882961--6883056 Score: 131
Period size: 47 Copynumber: 2.1 Consensus size: 46
6882951 GTAATAAGGC
* * *
6882961 GAATCATTGTTCAATGAGATCGTTTGGGATTATGA-TCAATATGTGTA
1 GAATAATTGTTCAATGAAATCGTTTGAGATTAT-ATTCAATATGTG-A
*
6883008 GAATAATTGTTCAATGAAATCGTTTGAGATTATATTGAATATGTGA
1 GAATAATTGTTCAATGAAATCGTTTGAGATTATATTCAATATGTGA
6883054 GAA
1 GAA
6883057 CTGATTAACA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
46 5 0.11
47 39 0.89
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (46 bp):
GAATAATTGTTCAATGAAATCGTTTGAGATTATATTCAATATGTGA
Found at i:6884878 original size:3 final size:3
Alignment explanation
Indices: 6884870--6884897 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
6884860 AACTAATACA
6884870 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
6884898 GTTAAGTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:6889006 original size:21 final size:21
Alignment explanation
Indices: 6888981--6889044 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
6888971 CTATTATCAT
6888981 AATAATAAAACGAGTAAATAA
1 AATAATAAAACGAGTAAATAA
*
6889002 AATAATAACAAGGA-TAACAT-A
1 AATAATAA-AACGAGTAA-ATAA
* *
6889023 AA-AATAAAATGTGTAAATAA
1 AATAATAAAACGAGTAAATAA
6889043 AA
1 AA
6889045 GAAAATATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
19 5 0.14
20 11 0.31
21 14 0.39
22 6 0.17
ACGTcount: A:0.66, C:0.05, G:0.09, T:0.20
Consensus pattern (21 bp):
AATAATAAAACGAGTAAATAA
Found at i:6891521 original size:13 final size:13
Alignment explanation
Indices: 6891503--6891527 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6891493 CTCTAATGAA
6891503 ATCCAACTAAATT
1 ATCCAACTAAATT
6891516 ATCCAACTAAAT
1 ATCCAACTAAAT
6891528 AAAATACAGG
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:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (13 bp):
ATCCAACTAAATT
Found at i:6893211 original size:42 final size:42
Alignment explanation
Indices: 6893145--6893303 Score: 158
Period size: 42 Copynumber: 3.7 Consensus size: 42
6893135 CAAAAAGAAC
* * * * *
6893145 GTATAATTCATGGACAATATTACTTGGCTTAATGTATGGCAT
1 GTATGATTCATGAACAATAGTACTTAGTTTAATGTATGGCAT
*
6893187 GTATGATTCATGAACAATAGTACTTAGTTTAATGTATGCCAT
1 GTATGATTCATGAACAATAGTACTTAGTTTAATGTATGGCAT
* * *
6893229 GCATGATGTATGAT-ATGAACAATAGTACTCAATTTAAAGTATGGCAT
1 G--T-ATG-AT--TCATGAACAATAGTACTTAGTTTAATGTATGGCAT
* *
6893276 GTATGATGCATGAACGATAGTACTTAGT
1 GTATGATTCATGAACAATAGTACTTAGT
6893304 AAAAAGCACG
Statistics
Matches: 96, Mismatches: 14, Indels: 14
0.77 0.11 0.11
Matches are distributed among these distances:
42 53 0.55
43 2 0.02
44 4 0.04
45 4 0.04
46 2 0.02
47 30 0.31
48 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.35
Consensus pattern (42 bp):
GTATGATTCATGAACAATAGTACTTAGTTTAATGTATGGCAT
Found at i:6893251 original size:47 final size:49
Alignment explanation
Indices: 6893185--6893288 Score: 140
Period size: 47 Copynumber: 2.2 Consensus size: 49
6893175 AATGTATGGC
* * *
6893185 ATGTATGATTCATGAACAATAGTACTTAGTTTAATGTATGCCATGCATG
1 ATGTATGATTCATGAACAATAGTACTCAATTTAAAGTATGCCATGCATG
* *
6893234 ATGTATGA-T-ATGAACAATAGTACTCAATTTAAAGTATGGCATGTATG
1 ATGTATGATTCATGAACAATAGTACTCAATTTAAAGTATGCCATGCATG
*
6893281 ATGCATGA
1 ATGTATGA
6893289 ACGATAGTAC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
47 40 0.82
48 1 0.02
49 8 0.16
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.35
Consensus pattern (49 bp):
ATGTATGATTCATGAACAATAGTACTCAATTTAAAGTATGCCATGCATG
Found at i:6899322 original size:2 final size:2
Alignment explanation
Indices: 6899315--6899341 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6899305 ATATGCCATG
6899315 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
6899342 GACGATTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6901001 original size:20 final size:23
Alignment explanation
Indices: 6900971--6901016 Score: 71
Period size: 21 Copynumber: 2.1 Consensus size: 23
6900961 TTTCTAAAAC
6900971 TTAACTAAAA-TTTTCATT-TTT
1 TTAACTAAAATTTTTCATTATTT
6900992 TTAA-TAAAATTTTTCATTATTT
1 TTAACTAAAATTTTTCATTATTT
6901014 TTA
1 TTA
6901017 TTTTTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.22
21 12 0.52
22 6 0.26
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.59
Consensus pattern (23 bp):
TTAACTAAAATTTTTCATTATTT
Found at i:6901241 original size:80 final size:77
Alignment explanation
Indices: 6901146--6901297 Score: 207
Period size: 80 Copynumber: 1.9 Consensus size: 77
6901136 AAATTTAAAA
*
6901146 TTTTTGAAAATTTAAATTTGATTTATTTTGAATTTAAATTTTTTAAAAACAAAAACTTA-AAATT
1 TTTTTGAAAAATTAAATTTGATTT-TTTTGAATTTAAA-TTTTT-AAAACAAAAACTTAGAAATT
6901210 TTAAAAGTTAACAAAC
63 TT-AAAGTTAACAAAC
* * * * *
6901226 TTTTTGAAAAATTAAATTTGATTTTTTTTATTTTAAATTTTTGAAATAAAAACTTAGATATTTTA
1 TTTTTGAAAAATTAAATTTGATTTTTTTGAATTTAAATTTTTAAAACAAAAACTTAGAAATTTTA
6901291 AAGTTAA
66 AAGTTAA
6901298 GAATTTTTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
77 20 0.31
78 11 0.17
79 11 0.17
80 23 0.35
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.47
Consensus pattern (77 bp):
TTTTTGAAAAATTAAATTTGATTTTTTTGAATTTAAATTTTTAAAACAAAAACTTAGAAATTTTA
AAGTTAACAAAC
Found at i:6902985 original size:16 final size:18
Alignment explanation
Indices: 6902958--6902991 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
6902948 TTAAATTAAT
6902958 TTAAATTAA-TTTTCCAA
1 TTAAATTAATTTTTCCAA
6902975 TTAAA-TAATTTTTCCAA
1 TTAAATTAATTTTTCCAA
6902992 CCCAATTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAAATTAATTTTTCCAA
Found at i:6904543 original size:26 final size:25
Alignment explanation
Indices: 6904512--6904561 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
6904502 TAGTTCAATA
6904512 ATTCAATTCAAAC-CATTTCAATTTCT
1 ATTCAA-T-AAACACATTTCAATTTCT
*
6904538 ATTCAATAATCACATTTCAATTTC
1 ATTCAATAAACACATTTCAATTTC
6904562 ACTTTCTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 13 0.59
26 6 0.27
ACGTcount: A:0.36, C:0.22, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTCAATAAACACATTTCAATTTCT
Found at i:6905466 original size:3 final size:3
Alignment explanation
Indices: 6905458--6905513 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
6905448 TATATTAGTT
6905458 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
6905506 AAC AAC AA
1 AAC AAC AA
6905514 TAATAATAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:6905518 original size:3 final size:3
Alignment explanation
Indices: 6905512--6905559 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
6905502 CAACAACAAC
6905512 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
6905558 AA
1 AA
6905560 ATATCTATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.09
3 39 0.91
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:6908411 original size:25 final size:26
Alignment explanation
Indices: 6908356--6908425 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 26
6908346 AAGCTCTCTC
*
6908356 TCGAGCCATATAACGGGAAGCTCATG
1 TCGAGTCATATAACGGGAAGCTCATG
*
6908382 T-GAGTCATGTAACGGGAAGCTCAT-
1 TCGAGTCATATAACGGGAAGCTCATG
* * *
6908406 TCGAGTTATACAACGAGAAG
1 TCGAGTCATATAACGGGAAG
6908426 TTTATAAGAG
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
24 1 0.03
25 35 0.95
26 1 0.03
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (26 bp):
TCGAGTCATATAACGGGAAGCTCATG
Found at i:6908807 original size:18 final size:18
Alignment explanation
Indices: 6908784--6908827 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
6908774 TAATATTTAT
*
6908784 TGAACATTTTCGGATATG
1 TGAACATTTTCAGATATG
* *
6908802 TGAACAATTTCATATATG
1 TGAACATTTTCAGATATG
6908820 TG-ACATTT
1 TGAACATTT
6908828 ATAGAATTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (18 bp):
TGAACATTTTCAGATATG
Found at i:6909032 original size:5 final size:5
Alignment explanation
Indices: 6909012--6909059 Score: 69
Period size: 5 Copynumber: 9.2 Consensus size: 5
6909002 CAGTTTAATA
*
6909012 CAATT CATAAT CAATT CAATT CAATT CAATT CAATT CAATT CACATT C
1 CAATT CA-ATT CAATT CAATT CAATT CAATT CAATT CAATT CA-ATT C
6909060 TTGGCAAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
5 31 0.79
6 8 0.21
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.38
Consensus pattern (5 bp):
CAATT
Found at i:6910152 original size:41 final size:41
Alignment explanation
Indices: 6910095--6910176 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
6910085 AAAGTCCACC
6910095 AGGACAGTAAACATGATATCATATTATGTAAGACCATAGCT
1 AGGACAGTAAACATGATATCATATTATGTAAGACCATAGCT
6910136 AGGACAGTAAACATGATATCATATTATGTAAGACCATAGCT
1 AGGACAGTAAACATGATATCATATTATGTAAGACCATAGCT
6910177 GAGCTATGGC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (41 bp):
AGGACAGTAAACATGATATCATATTATGTAAGACCATAGCT
Found at i:6913134 original size:37 final size:36
Alignment explanation
Indices: 6913088--6913195 Score: 103
Period size: 37 Copynumber: 2.9 Consensus size: 36
6913078 AAAAATAAGG
* **
6913088 AGATGAACATGAGTGATTCTCTGCAAATAAAAGGTGA
1 AGAT-AACATGAGTGATTCTCTGCAAAAAAAAGACGA
*
6913125 AGATAAACATGAGT-AGTTCTTTGCAAAAAAAAGACGA
1 AGAT-AACATGAGTGA-TTCTCTGCAAAAAAAAGACGA
* * *
6913162 AGATGACA-GATGTGATTCTCTGTAAACAAAAGAC
1 AGATAACATGA-GTGATTCTCTGCAAAAAAAAGAC
6913196 AGAGATGAAT
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
35 2 0.03
36 22 0.37
37 35 0.59
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.23
Consensus pattern (36 bp):
AGATAACATGAGTGATTCTCTGCAAAAAAAAGACGA
Found at i:6915032 original size:2 final size:2
Alignment explanation
Indices: 6915025--6915063 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
6915015 TCCTAGAAGA
6915025 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6915064 AAATTAAGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6916669 original size:21 final size:21
Alignment explanation
Indices: 6916644--6916684 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
6916634 AAAATTTAAT
6916644 TAATTACTAATGTAAAATAAC
1 TAATTACTAATGTAAAATAAC
6916665 TAATTACTAATGTAAAATAA
1 TAATTACTAATGTAAAATAA
6916685 AGTGTACTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.34
Consensus pattern (21 bp):
TAATTACTAATGTAAAATAAC
Found at i:6920112 original size:5 final size:5
Alignment explanation
Indices: 6920102--6920126 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
6920092 GCATAACAAT
6920102 GTCTG GTCTG GTCTG GTCTG GTCTG
1 GTCTG GTCTG GTCTG GTCTG GTCTG
6920127 TATCTGTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.40, T:0.40
Consensus pattern (5 bp):
GTCTG
Found at i:6920898 original size:12 final size:12
Alignment explanation
Indices: 6920881--6920906 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
6920871 CACTTAAAAC
6920881 CCATTTGGACTG
1 CCATTTGGACTG
6920893 CCATTTGGACTG
1 CCATTTGGACTG
6920905 CC
1 CC
6920907 GTTAGGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.31, G:0.23, T:0.31
Consensus pattern (12 bp):
CCATTTGGACTG
Found at i:6923370 original size:2 final size:2
Alignment explanation
Indices: 6923363--6923396 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6923353 ATAATGATTA
6923363 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6923397 GATAGCAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6926734 original size:29 final size:29
Alignment explanation
Indices: 6926677--6926736 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
6926667 ATCTACAATC
* *
6926677 AGCACAAGACTACGTATACATACAGACAA
1 AGCACAAGACTACATATACATACACACAA
*
6926706 AGCACAAGACTACATATACATACTCACAA
1 AGCACAAGACTACATATACATACACACAA
6926735 AG
1 AG
6926737 ACTGATACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.48, C:0.25, G:0.12, T:0.15
Consensus pattern (29 bp):
AGCACAAGACTACATATACATACACACAA
Found at i:6930332 original size:26 final size:27
Alignment explanation
Indices: 6930281--6930337 Score: 82
Period size: 26 Copynumber: 2.1 Consensus size: 27
6930271 AACAGAGAGC
*
6930281 AAAACGAAAACAGGGGAGAAAGGAAAG
1 AAAAAGAAAACAGGGGAGAAAGGAAAG
6930308 AAAAAGAAAA-AGGGGAGGAAA-GAAAG
1 AAAAAGAAAACAGGGGA-GAAAGGAAAG
6930334 AAAA
1 AAAA
6930338 TTTGGGATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 15 0.54
27 13 0.46
ACGTcount: A:0.65, C:0.04, G:0.32, T:0.00
Consensus pattern (27 bp):
AAAAAGAAAACAGGGGAGAAAGGAAAG
Found at i:6932063 original size:113 final size:115
Alignment explanation
Indices: 6931932--6932166 Score: 352
Period size: 114 Copynumber: 2.1 Consensus size: 115
6931922 AGCATTAACA
* *
6931932 GCGTTTTACAAAAAGCGCCGC-AATAGAGTCACACAGAACGACGCCGTTTTCATATATTTGGGAA
1 GCGTTTTACAAAAAGCGCCGCAAATACAGTAACACAGAACGACGCCGTTTTCATATATTTGGGAA
* *
6931996 CATTAGTGGCGGT-TATTT-CCAAGCGCCGCTAA-AACTCCGTTCTACAGCG
66 CACTAGTGGCGGTAT-TTTCCCAAACGCCGCTAATAA-TCCGTTCTACAGCG
* * * *
6932045 GCGTTTTATACAAAGCGCCGCAAATACAGTAACACAGAACGACGCCGTTTTCGTATATTTTGGAA
1 GCGTTTTACAAAAAGCGCCGCAAATACAGTAACACAGAACGACGCCGTTTTCATATATTTGGGAA
6932110 CACTAGTGGCGGTATTTTCCCAAACGCCGCTAATAATCCGTTCTACAGCG
66 CACTAGTGGCGGTATTTTCCCAAACGCCGCTAATAATCCGTTCTACAGCG
6932160 GCGTTTT
1 GCGTTTT
6932167 GCGTTAAGCG
Statistics
Matches: 110, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
113 19 0.17
114 54 0.49
115 35 0.32
116 2 0.02
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (115 bp):
GCGTTTTACAAAAAGCGCCGCAAATACAGTAACACAGAACGACGCCGTTTTCATATATTTGGGAA
CACTAGTGGCGGTATTTTCCCAAACGCCGCTAATAATCCGTTCTACAGCG
Found at i:6935562 original size:2 final size:2
Alignment explanation
Indices: 6935505--6935544 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
6935495 AAGTATATGG
6935505 TA TA CTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6935545 TGGTGATGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6936896 original size:50 final size:50
Alignment explanation
Indices: 6936837--6936935 Score: 198
Period size: 50 Copynumber: 2.0 Consensus size: 50
6936827 AATGTATTCA
6936837 AGGTTATATTTTAAAACATCTTTGATATATATATTTTATATTAAAAAAAT
1 AGGTTATATTTTAAAACATCTTTGATATATATATTTTATATTAAAAAAAT
6936887 AGGTTATATTTTAAAACATCTTTGATATATATATTTTATATTAAAAAAA
1 AGGTTATATTTTAAAACATCTTTGATATATATATTTTATATTAAAAAAA
6936936 ATATACTTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.45
Consensus pattern (50 bp):
AGGTTATATTTTAAAACATCTTTGATATATATATTTTATATTAAAAAAAT
Found at i:6937175 original size:35 final size:35
Alignment explanation
Indices: 6937136--6937415 Score: 191
Period size: 35 Copynumber: 7.8 Consensus size: 35
6937126 TACACAGTTT
6937136 TAATAACTTACAACTTACATAACATACATAATACA
1 TAATAACTTACAACTTACATAACATACATAATACA
6937171 TAATAACTTACAACTTACATAACATACATAACTTACA
1 TAATAACTTACAACTTACATAACATACATAA--TACA
* * * *
6937208 TTCATAACTTACATAAACTTATATGTTACCTTACATAATACA
1 -TAATAACTTAC---AACTTACA---TAACATACATAATACA
* ** * **
6937250 TAACTTATATTTATGATTTTTATATA-A-AC-T--TACA
1 TAA--TA-ACTTACAACTTACATA-ACATACATAATACA
* *
6937284 TAAT-ACATAGC-A--TACATAACTTACATAATACA
1 TAATAACTTA-CAACTTACATAACATACATAATACA
6937316 TAATAACTTACAACTTACATAACATACATAATACA
1 TAATAACTTACAACTTACATAACATACATAATACA
* * *** * *
6937351 TGGAGAACACGCAGCTTACATAACATATATAATACA
1 T-AATAACTTACAACTTACATAACATACATAATACA
6937387 TAATAACTTACAACTTACATAACATACAT
1 TAATAACTTACAACTTACATAACATACAT
6937416 TAATTTTTTA
Statistics
Matches: 187, Mismatches: 34, Indels: 48
0.70 0.13 0.18
Matches are distributed among these distances:
27 1 0.01
28 4 0.02
29 2 0.01
30 5 0.03
32 10 0.05
33 5 0.03
34 7 0.04
35 72 0.39
36 29 0.16
37 6 0.03
38 12 0.06
41 14 0.07
42 4 0.02
43 2 0.01
44 14 0.07
ACGTcount: A:0.46, C:0.19, G:0.03, T:0.32
Consensus pattern (35 bp):
TAATAACTTACAACTTACATAACATACATAATACA
Found at i:6937213 original size:13 final size:13
Alignment explanation
Indices: 6937157--6937222 Score: 61
Period size: 13 Copynumber: 5.4 Consensus size: 13
6937147 AACTTACATA
6937157 ACATACATAA--T
1 ACATACATAACTT
6937168 ACATA-ATAACTT
1 ACATACATAACTT
* *
6937180 ACA-AC-TTACATA
1 ACATACATAAC-TT
6937192 ACATACATAACTT
1 ACATACATAACTT
*
6937205 ACATTCATAACTT
1 ACATACATAACTT
6937218 ACATA
1 ACATA
6937223 AACTTATATG
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
10 4 0.09
11 9 0.21
12 8 0.19
13 19 0.44
14 3 0.07
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.30
Consensus pattern (13 bp):
ACATACATAACTT
Found at i:6937223 original size:9 final size:9
Alignment explanation
Indices: 6937138--6937208 Score: 62
Period size: 9 Copynumber: 8.2 Consensus size: 9
6937128 CACAGTTTTA
6937138 ATAACTTAC
1 ATAACTTAC
6937147 --AACTTAC
1 ATAACTTAC
*
6937154 ATAACATAC
1 ATAACTTAC
*
6937163 ATAATACATA-
1 AT-A-ACTTAC
6937173 ATAACTTAC
1 ATAACTTAC
6937182 --AACTTAC
1 ATAACTTAC
*
6937189 ATAACATAC
1 ATAACTTAC
6937198 ATAACTTAC
1 ATAACTTAC
6937207 AT
1 AT
6937209 TCATAACTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
7 14 0.27
8 4 0.08
9 25 0.49
10 3 0.06
11 5 0.10
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (9 bp):
ATAACTTAC
Found at i:6937308 original size:9 final size:9
Alignment explanation
Indices: 6937276--6937346 Score: 53
Period size: 9 Copynumber: 8.2 Consensus size: 9
6937266 TTTTTATATA
6937276 AACTTACAT
1 AACTTACAT
6937285 AA--TACAT
1 AACTTACAT
* *
6937292 AGCATACAT
1 AACTTACAT
6937301 AACTTACAT
1 AACTTACAT
*
6937310 AATACATA-AT
1 -A-ACTTACAT
6937320 AACTTAC--
1 AACTTACAT
6937327 AACTTACAT
1 AACTTACAT
*
6937336 AACATACAT
1 AACTTACAT
6937345 AA
1 AA
6937347 TACATGGAGA
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
7 13 0.27
8 4 0.08
9 25 0.51
10 3 0.06
11 4 0.08
ACGTcount: A:0.51, C:0.20, G:0.01, T:0.28
Consensus pattern (9 bp):
AACTTACAT
Found at i:6937350 original size:16 final size:16
Alignment explanation
Indices: 6937280--6937351 Score: 50
Period size: 16 Copynumber: 4.8 Consensus size: 16
6937270 TATATAAACT
*
6937280 TACATAATACATAGCA
1 TACATAATACATAACA
6937296 TACATAACTTACAT-A-A
1 TACATAA--TACATAACA
*
6937312 TACATAATA-ACTTACA
1 TACATAATACA-TAACA
6937328 -AC-T--TACATAACA
1 TACATAATACATAACA
6937340 TACATAATACAT
1 TACATAATACAT
6937352 GGAGAACACG
Statistics
Matches: 44, Mismatches: 2, Indels: 20
0.67 0.03 0.30
Matches are distributed among these distances:
12 6 0.14
13 4 0.09
14 5 0.11
15 3 0.07
16 21 0.48
18 5 0.11
ACGTcount: A:0.50, C:0.19, G:0.01, T:0.29
Consensus pattern (16 bp):
TACATAATACATAACA
Found at i:6938701 original size:22 final size:22
Alignment explanation
Indices: 6938639--6938707 Score: 111
Period size: 22 Copynumber: 3.1 Consensus size: 22
6938629 ATTGTTCAAA
* **
6938639 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAGC
6938661 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
6938683 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
6938705 CAT
1 CAT
6938708 TTGCCTCCGT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:6943059 original size:21 final size:21
Alignment explanation
Indices: 6943035--6943085 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
6943025 CTACAACTTA
* *
6943035 AAGCAGATGCGGCAACGAGAG
1 AAGCAGAGGCAGCAACGAGAG
*
6943056 AAGCAGAGGCAGCAGCGAGAG
1 AAGCAGAGGCAGCAACGAGAG
*
6943077 AAGCTGAGG
1 AAGCAGAGG
6943086 TTCAACGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.37, C:0.18, G:0.41, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCAGCAACGAGAG
Found at i:6943139 original size:21 final size:21
Alignment explanation
Indices: 6943115--6943156 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
6943105 ACTCCAGCAG
6943115 CAGCGAGAGAAGCAGAGGCTA
1 CAGCGAGAGAAGCAGAGGCTA
* *
6943136 CAGCGAGGGAATCAGAGGCTA
1 CAGCGAGAGAAGCAGAGGCTA
6943157 AAATGAAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.19, G:0.38, T:0.07
Consensus pattern (21 bp):
CAGCGAGAGAAGCAGAGGCTA
Found at i:6943967 original size:86 final size:86
Alignment explanation
Indices: 6943478--6943974 Score: 416
Period size: 84 Copynumber: 5.8 Consensus size: 86
6943468 CAAAATTAGC
* * * ** * * *
6943478 GGCGTTTATTGGATAAGCGCCACTAAAGA-ACCCGCCTCTAGTGGCGTTTTATGCATAAGCGCCG
1 GGCGTTTTTTGTATAAGCGCCGCTAAAGACACCCATCTATAGTGGCGTTTTTTGTATAAGCGCCG
* * *
6943542 CTAAAG-CCACCAATCTCTAGT
66 CTAAAGAAC-CCGATCTATAGT
* * * * * *
6943563 GGCGTTTTGTGTATAAGCGCCGCAAAAAACTCCAATCTATAGTGGCGTTTTTTTGCATAAGCGCC
1 GGCGTTTTTTGTATAAGCGCCGCTAAAGACACCCATCTATAGTGGCG-TTTTTTGTATAAGCGCC
* * * ** *
6943628 GGTATAGAGCCATATCTGTAGT
65 GCTAAAGAACCCGATCTATAGT
* * * ** *
6943650 GGCGTTTCTT-TATAAGCGCCGATAAAGAAACATATCTATAGTGGTGTTTTTTGTATAAGCGCCG
1 GGCGTTTTTTGTATAAGCGCCGCTAAAGACACCCATCTATAGTGGCGTTTTTTGTATAAGCGCCG
* * *
6943714 CTATAGAA-CCGAGCTATCGT
66 CTAAAGAACCCGATCTATAGT
* * * *
6943734 GGCATTTTTTGTATAAGCGCCGCTATAGA-ACCGAGCTATAGTGGCGTTTTTTGTATAAGCGCCG
1 GGCGTTTTTTGTATAAGCGCCGCTAAAGACACCCATCTATAGTGGCGTTTTTTGTATAAGCGCCG
*
6943798 CTATAG-ACCCGATCTATAGT
66 CTAAAGAACCCGATCTATAGT
* * * *** * * * *
6943818 GCCGTTTTTTGTATAAGCGCCGGTAGAG-CAGATATCTATTGTGGCGTTTTCTGTACAAACGCCG
1 GGCGTTTTTTGTATAAGCGCCGCTAAAGACACCCATCTATAGTGGCGTTTTTTGTATAAGCGCCG
* *
6943882 GTAAAGAAACCCGATCTGTAGT
66 CTAAAG-AACCCGATCTATAGT
* * * * * *
6943904 GGCGTTTTTTGCATAAGCGCCGCGAAAGACTCCCACCTATAGTGGCG-TTTCTGTGTAAGCGCCG
1 GGCGTTTTTTGTATAAGCGCCGCTAAAGACACCCATCTATAGTGGCGTTTTTTGTATAAGCGCCG
6943968 CTAAAGA
66 CTAAAGA
6943975 CGGTATTCTA
Statistics
Matches: 327, Mismatches: 76, Indels: 18
0.78 0.18 0.04
Matches are distributed among these distances:
83 1 0.00
84 117 0.36
85 63 0.19
86 95 0.29
87 50 0.15
88 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (86 bp):
GGCGTTTTTTGTATAAGCGCCGCTAAAGACACCCATCTATAGTGGCGTTTTTTGTATAAGCGCCG
CTAAAGAACCCGATCTATAGT
Found at i:6943975 original size:42 final size:42
Alignment explanation
Indices: 6943478--6943975 Score: 353
Period size: 42 Copynumber: 11.7 Consensus size: 42
6943468 CAAAATTAGC
* * ** *
6943478 GGCGTTTATTGGATAAGCGCCACTAAAGA-ACCCGCCTCTAGT
1 GGCGTTT-TTGTATAAGCGCCGCTAAAGACACCCATCTATAGT
* * * *
6943520 GGCGTTTTATGCATAAGCGCCGCTAAAGCCACCAATCTCTAGT
1 GGCGTTTT-TGTATAAGCGCCGCTAAAGACACCCATCTATAGT
* * * *
6943563 GGCGTTTTGTGTATAAGCGCCGCAAAAAACTCCAATCTATAGT
1 GGCGTTTT-TGTATAAGCGCCGCTAAAGACACCCATCTATAGT
* * * ** *
6943606 GGCGTTTTTTTGCATAAGCGCCGGTATAGAGC-CATATCTGTAGT
1 GGCG--TTTTTGTATAAGCGCCGCTAAAGA-CACCCATCTATAGT
* * **
6943650 GGCGTTTCTT-TATAAGCGCCGATAAAGAAACATATCTATAGT
1 GGCGTTT-TTGTATAAGCGCCGCTAAAGACACCCATCTATAGT
* * * * *
6943692 GGTGTTTTTTGTATAAGCGCCGCTATAGA-ACCGAGCTATCGT
1 GGCG-TTTTTGTATAAGCGCCGCTAAAGACACCCATCTATAGT
* * * *
6943734 GGCATTTTTTGTATAAGCGCCGCTATAGA-ACCGAGCTATAGT
1 GGC-GTTTTTGTATAAGCGCCGCTAAAGACACCCATCTATAGT
* *
6943776 GGCGTTTTTTGTATAAGCGCCGCTATAGAC-CCGATCTATAGT
1 GGCG-TTTTTGTATAAGCGCCGCTAAAGACACCCATCTATAGT
* * * *** *
6943818 GCCGTTTTTTGTATAAGCGCCGGTAGAG-CAGATATCTATTGT
1 GGCG-TTTTTGTATAAGCGCCGCTAAAGACACCCATCTATAGT
* * * * *
6943860 GGCGTTTTCTGTACAAACGCCGGTAAAGAAACCCGATCTGTAGT
1 GGCGTTTT-TGTATAAGCGCCGCTAAAGACACCC-ATCTATAGT
* * * *
6943904 GGCGTTTTTTGCATAAGCGCCGCGAAAGACTCCCACCTATAGT
1 GGCG-TTTTTGTATAAGCGCCGCTAAAGACACCCATCTATAGT
* *
6943947 GGCGTTTCTGTGTAAGCGCCGCTAAAGAC
1 GGCGTTTTTGTATAAGCGCCGCTAAAGAC
6943976 GGTATTCTAT
Statistics
Matches: 371, Mismatches: 68, Indels: 34
0.78 0.14 0.07
Matches are distributed among these distances:
41 6 0.02
42 216 0.58
43 83 0.22
44 57 0.15
45 9 0.02
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (42 bp):
GGCGTTTTTGTATAAGCGCCGCTAAAGACACCCATCTATAGT
Found at i:6945753 original size:36 final size:36
Alignment explanation
Indices: 6945713--6945791 Score: 142
Period size: 36 Copynumber: 2.2 Consensus size: 36
6945703 CAAAAAGATA
6945713 TTTTGGGCGTTTGAGGCCAGTCTCAAAAC-GACGTCG
1 TTTTGGGCGTTTGAGGCCAGTCTCAAAACAG-CGTCG
6945749 TTTTGGGCGTTTGAGGCCAGTCTCAAAACAGCGTCG
1 TTTTGGGCGTTTGAGGCCAGTCTCAAAACAGCGTCG
6945785 TTTTGGG
1 TTTTGGG
6945792 GGCCTAGATA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
36 41 0.98
37 1 0.02
ACGTcount: A:0.18, C:0.20, G:0.32, T:0.30
Consensus pattern (36 bp):
TTTTGGGCGTTTGAGGCCAGTCTCAAAACAGCGTCG
Found at i:6946707 original size:44 final size:44
Alignment explanation
Indices: 6946628--6947416 Score: 503
Period size: 44 Copynumber: 17.7 Consensus size: 44
6946618 TCATTCCAAC
* * * * * *
6946628 CCACTGCATCTTCAGGG-GTATAGGAATTGTCGCTTCGATCCACT
1 CCACTGCAACTTCAGGGAG-ATAAGATTTGTAGCTTCAATCTACT
* * * *
6946672 CCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCGATATATT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTACT
* * * * * *
6946716 CTACTGTAACTTCAGGGAGATAAGACTTATAGCTTCAATAT-GT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTACT
*** *
6946759 GTGCTGCAACTTTAGGGAGATAAGATTTGT-GTCTTCAATCTACT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAG-CTTCAATCTACT
* * * *
6946803 CCACTGCAACCTT-AGGGAGATAA-AGTGTGTAGATTTAATCTGCT
1 CCACTGCAA-CTTCAGGGAGATAAGA-TTTGTAGCTTCAATCTACT
** * *** ** * *
6946847 CTGCTGTAACGTT-AAAAAGATAAGATTTGCTATTTTTAACCTACT
1 CCACTGCAAC-TTCAGGGAGATAAGATTTG-TAGCTTCAATCTACT
* * * * * * *
6946892 TCACTGCAATTTTAGGGAGATAAGGTTTGCAGCTTTAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTACT
** * *
6946936 CCACTATAACTTCAAGGAGATAAGATTTGTAGCCTGTCTTCAATTTACT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTA----G-CTTCAATCTACT
* ** * * *
6946985 CCACTGCAATTTCAGGGAGATAAGATTTGTTTATTTTTAACCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTG--TAGCTTCAATCTACT
* * * * * * *
6947031 CCACTACAACTTTAAGGAGATAAGGTTTATAGCTTTAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTACT
* * * *
6947075 CTACTGCAACTTCAGAGAGATAAGATTTGCTATC-TCTGATCTACT
1 CCACTGCAACTTCAGGGAGATAAGATTTG-TAGCTTC-AATCTACT
* * * * * *
6947120 CCACTGCAACTTCAGGAAGATAAGATCTATAACTTCAATCTGCC
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTACT
* * * * * *
6947164 CCACTACAACTTCAGGGAGACAATATTTGTAACCTTCAGTCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTGT-AGCTTCAATCTACT
* * *
6947209 CCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTACT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTACT
* * * * * * *
6947253 CCACTGTAACTTCAGGGAGATACGGTTTATAGCTTTAATATGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTACT
* ** ** *
6947297 CTACTGCAACTTCAGAAAGATAAGATCTACTATCTTCAATCTACT
1 CCACTGCAACTTCAGGGAGATAAGAT-TTGTAGCTTCAATCTACT
** * * * *
6947342 CCACTGCAACTTCAAAGAGATAAGATCTATAACTTTAATCTACT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTACT
*
6947386 CCACTGCAACTTTAGGGAGATAAGATTTGTA
1 CCACTGCAACTTCAGGGAGATAAGATTTGTA
6947417 ATTTGTAATT
Statistics
Matches: 569, Mismatches: 154, Indels: 44
0.74 0.20 0.06
Matches are distributed among these distances:
42 1 0.00
43 35 0.06
44 325 0.57
45 141 0.25
46 30 0.05
48 1 0.00
49 34 0.06
51 2 0.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (44 bp):
CCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTACT
Found at i:6946957 original size:89 final size:87
Alignment explanation
Indices: 6946774--6947416 Score: 293
Period size: 89 Copynumber: 7.2 Consensus size: 87
6946764 GCAACTTTAG
* * ** * *
6946774 GGAGATAAGATTTGTGTCTTCAATCTACTCCACTGCAACCTTAGGGAGATAAAGTGTGTAGATTT
1 GGAGATAAGATTTGTATTTTCAATCTACTCCACTGCAATTTTAGGGAGATAAGGTTTGTAGATTT
** *
6946839 AATCTGCTCTGCTGTAACGTTAA
66 AATCTGCTCCACTATAAC-TTAA
** * * * * *
6946862 AAAGATAAGATTTGCTATTTTTAACCTACTTCACTGCAATTTTAGGGAGATAAGGTTTGCAGCTT
1 GGAGATAAGATTTG-TATTTTCAATCTACTCCACTGCAATTTTAGGGAGATAAGGTTTGTAGATT
6946927 TAATCTGCTCCACTATAACTTCAA
65 TAATCTGCTCCACTATAACTT-AA
* * *
6946951 GGAGATAAGATTTGTAGCCTGTCTTCAATTTACTCCACTGCAATTTCAGGGAGATAAGATTTGTT
1 GGAGATAAGATTTGTA---T-T-TTCAATCTACTCCACTGCAATTTTAGGGAGATAAGGTTTG--
** * *
6947016 TATTTTTAACCTGCTCCACTACAACTTTAA
59 TAGATTTAATCTGCTCCACTATAAC-TTAA
* * * * * * * * * **
6947046 GGAGATAAGGTTTATAGCTTT-AATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCT
1 GGAGATAAGATTTGTA-TTTTCAATCTACTCCACTGCAATTTTAGGGAGATAAGGTTTG-TAGAT
* * * ** *
6947110 CTGATCTACTCCACTGCAACTTCA
64 TTAATCTGCTCCACTATAACTTAA
* * ** * * * * * * **
6947134 GGAAGATAAGATCTATAACTTCAATCTGCCCCACTACAACTTCAGGGAGACAATATTTGTA-ACC
1 GG-AGATAAGATTTGTATTTTCAATCTACTCCACTGCAATTTTAGGGAGATAAGGTTTGTAGA--
* * ** *
6947198 TTCAGTCTGCTCCACTGCAACTTCAG
63 TTTAATCTGCTCCACTATAACTT-AA
* ** * * * * * * *
6947224 GGAGATAAGACTTGTAACTTCAACCTACTCCACTGTAACTTCAGGGAGATACGGTTTATAGCTTT
1 GGAGATAAGATTTGTATTTTCAATCTACTCCACTGCAATTTTAGGGAGATAAGGTTTGTAGATTT
* * ** *
6947289 AATATGCTCTACTGCAACTTCA
66 AATCTGCTCCACTATAACTTAA
* ** * * * ** * * *
6947311 GAAAGATAAGATCTACTATCTTCAATCTACTCCACTGCAACTTCAAAGAGATAAGATCTATA-AC
1 G-GAGATAAGAT-TTGTATTTTCAATCTACTCCACTGCAATTTTAGGGAGATAAGGTTTGTAGA-
* ** *
6947375 TTTAATCTACTCCACTGCAACTTTAG
63 TTTAATCTGCTCCACTATAAC-TTAA
6947401 GGAGATAAGATTTGTA
1 GGAGATAAGATTTGTA
6947417 ATTTGTAATT
Statistics
Matches: 430, Mismatches: 105, Indels: 40
0.75 0.18 0.07
Matches are distributed among these distances:
87 1 0.00
88 55 0.13
89 260 0.60
90 37 0.09
91 3 0.01
92 2 0.00
93 34 0.08
95 36 0.08
96 2 0.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (87 bp):
GGAGATAAGATTTGTATTTTCAATCTACTCCACTGCAATTTTAGGGAGATAAGGTTTGTAGATTT
AATCTGCTCCACTATAACTTAA
Found at i:6947048 original size:95 final size:88
Alignment explanation
Indices: 6946881--6947413 Score: 314
Period size: 89 Copynumber: 5.9 Consensus size: 88
6946871 ATTTGCTATT
* * * * * *
6946881 TTTAACCTACTTCACTGCAATTTTAGGGAGATAAGGTTTGCAGCTTTAATCTGCTCCACTATAAC
1 TTTAATCTACTCCACTGCAATTTCAGGGAGATAAGATTTGCAGCTTTAACCTGCTCCACTACAAC
*
6946946 TTCAAGGAGATAAGATTTGTAGCC
66 TTCAAGGAGATAAGATTTATAG-C
* * **
6946970 TGTCTTCAATTTACTCCACTGCAATTTCAGGGAGATAAGATTTGTTTATTTTTAACCTGCTCCAC
1 --T-TT-AATCTACTCCACTGCAATTTCAGGGAGATAAGATTTG--CAGCTTTAACCTGCTCCAC
* *
6947035 TACAACTTTAAGGAGATAAGGTTTATAGC
60 TACAACTTCAAGGAGATAAGATTTATAGC
* * * * * * * * * *
6947064 TTTAATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTCTGATCTACTCCACTGCAA
1 TTTAATCTACTCCACTGCAATTTCAGGGAGATAAGATTTGC-AGCTTTAACCTGCTCCACTACAA
* *
6947129 CTTC-AGGAAGATAAGATCTATAAC
65 CTTCAAGG-AGATAAGATTTATAGC
* * * * * * * * * * ** *
6947153 TTCAATCTGCCCCACTACAACTTCAGGGAGACAATATTTGTAACCTTCAGTCTGCTCCACTGCAA
1 TTTAATCTACTCCACTGCAATTTCAGGGAGATAAGATTTG-CAGCTTTAACCTGCTCCACTACAA
* * * *
6947218 CTTCAGGGAGATAAGACTTGTAAC
65 CTTCAAGGAGATAAGATTTATAGC
* * * * * * ** ** * *
6947242 TTCAACCTACTCCACTGTAACTTCAGGGAGATACGGTTTATAGCTTTAATATGCTCTACTGCAAC
1 TTTAATCTACTCCACTGCAATTTCAGGGAGATAAGATTTGCAGCTTTAACCTGCTCCACTACAAC
* * *
6947307 TTC-AGAAAGATAAGATCTACTATC
66 TTCAAG-GAGATAAGATTTA-TAGC
* * ** * ** * * * *
6947331 TTCAATCTACTCCACTGCAACTTCAAAGAGATAAGATCTATAACTTTAATCTACTCCACTGCAAC
1 TTTAATCTACTCCACTGCAATTTCAGGGAGATAAGATTTGCAGCTTTAACCTGCTCCACTACAAC
* *
6947396 TTTAGGGAGATAAGATTT
66 TTCAAGGAGATAAGATTT
6947414 GTAATTTGTA
Statistics
Matches: 347, Mismatches: 84, Indels: 24
0.76 0.18 0.05
Matches are distributed among these distances:
87 1 0.00
88 34 0.10
89 199 0.57
90 35 0.10
91 3 0.01
92 3 0.01
93 32 0.09
94 1 0.00
95 39 0.11
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (88 bp):
TTTAATCTACTCCACTGCAATTTCAGGGAGATAAGATTTGCAGCTTTAACCTGCTCCACTACAAC
TTCAAGGAGATAAGATTTATAGC
Found at i:6947264 original size:133 final size:132
Alignment explanation
Indices: 6947067--6947411 Score: 361
Period size: 133 Copynumber: 2.6 Consensus size: 132
6947057 TTATAGCTTT
* * *
6947067 AATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATC-TCTGATCTACTCCACTGCAACT
1 AATCTGCTCCACTGCAACTTCAGAGAGATAAGA-TTG-TAACTTC-AATCTACTCCACTGCAACT
* * ** * **
6947131 TCAGGAAGATAAGATCTATAACTTCAATCTGCCCCACTACAACTTCAGGGAGACAATAT-TTGTA
63 TCAGGGAGATAAGATCTATAACTTCAATATGCCCCACTACAACTTCAGAAAGACAAGATCTACT-
6947195 ACCTTC
127 ACCTTC
* * * *
6947201 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTACTCCACTGTAACTTC
1 AATCTGCTCCACTGCAACTTCAGAGAGATAAGA-TTGTAACTTCAATCTACTCCACTGCAACTTC
* * * * * * * * * *
6947266 AGGGAGATACGGTTTATAGCTTTAATATGCTCTACTGCAACTTCAGAAAGATAAGATCTACTATC
65 AGGGAGATAAGATCTATAACTTCAATATGCCCCACTACAACTTCAGAAAGACAAGATCTACTACC
6947331 TTC
130 TTC
* * * * *
6947334 AATCTACTCCACTGCAACTTCAAAGAGATAAGATCTATAACTTTAATCTACTCCACTGCAACTTT
1 AATCTGCTCCACTGCAACTTCAGAGAGATAAGAT-TGTAACTTCAATCTACTCCACTGCAACTTC
6947399 AGGGAGATAAGAT
65 AGGGAGATAAGAT
6947412 TTGTAATTTG
Statistics
Matches: 172, Mismatches: 36, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
132 1 0.01
133 134 0.78
134 37 0.22
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (132 bp):
AATCTGCTCCACTGCAACTTCAGAGAGATAAGATTGTAACTTCAATCTACTCCACTGCAACTTCA
GGGAGATAAGATCTATAACTTCAATATGCCCCACTACAACTTCAGAAAGACAAGATCTACTACCT
TC
Found at i:6959742 original size:23 final size:24
Alignment explanation
Indices: 6959703--6959751 Score: 91
Period size: 23 Copynumber: 2.1 Consensus size: 24
6959693 ACATGAGGCA
6959703 TATGCAAAGGAAATTTTGAAGAAG
1 TATGCAAAGGAAATTTTGAAGAAG
6959727 TATGCAAA-GAAATTTTGAAGAAG
1 TATGCAAAGGAAATTTTGAAGAAG
6959750 TA
1 TA
6959752 CAAGATGGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 17 0.68
24 8 0.32
ACGTcount: A:0.47, C:0.04, G:0.22, T:0.27
Consensus pattern (24 bp):
TATGCAAAGGAAATTTTGAAGAAG
Found at i:6962468 original size:29 final size:29
Alignment explanation
Indices: 6962435--6962490 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
6962425 ACAATCGGTA
6962435 CAAGACTACATATACATACAGACAAAGCG
1 CAAGACTACATATACATACAGACAAAGCG
*
6962464 CAAGACTACATATACATACTGACAAAG
1 CAAGACTACATATACATACAGACAAAG
6962491 ACTGATACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.48, C:0.23, G:0.12, T:0.16
Consensus pattern (29 bp):
CAAGACTACATATACATACAGACAAAGCG
Found at i:6964067 original size:3 final size:3
Alignment explanation
Indices: 6964059--6964098 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
6964049 GGTAAGAGAA
6964059 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
6964099 TTAATTTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:6971758 original size:33 final size:34
Alignment explanation
Indices: 6971679--6971758 Score: 87
Period size: 33 Copynumber: 2.4 Consensus size: 34
6971669 TAAAACTAAC
6971679 GATACATAAAATATTTTAAAAACTTTAAATATAAT
1 GATACATAAAATA-TTTAAAAACTTTAAATATAAT
* * *
6971714 -A-ACA-AATAATATTTAAATAGTTT-TATATAAT
1 GATACATAA-AATATTTAAAAACTTTAAATATAAT
6971745 GATACATAAAATAT
1 GATACATAAAATAT
6971759 AAACTAATCT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
31 7 0.18
32 13 0.34
33 15 0.39
34 3 0.08
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.38
Consensus pattern (34 bp):
GATACATAAAATATTTAAAAACTTTAAATATAAT
Found at i:6978494 original size:10 final size:10
Alignment explanation
Indices: 6978481--6978541 Score: 51
Period size: 9 Copynumber: 6.4 Consensus size: 10
6978471 TTTCTATATA
6978481 TTTTACAATT
1 TTTTACAATT
6978491 TTTTA-AGATT
1 TTTTACA-ATT
*
6978501 TTTATA-AA-A
1 TTT-TACAATT
6978510 TTTTACAA-T
1 TTTTACAATT
*
6978519 TTTTATAATT
1 TTTTACAATT
6978529 TTTTAC-ATT
1 TTTTACAATT
6978538 TTTT
1 TTTT
6978542 TCTAATTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
8 2 0.05
9 20 0.47
10 18 0.42
11 3 0.07
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (10 bp):
TTTTACAATT
Found at i:6978503 original size:19 final size:19
Alignment explanation
Indices: 6978481--6978570 Score: 71
Period size: 19 Copynumber: 4.8 Consensus size: 19
6978471 TTTCTATATA
*
6978481 TTTTACAATTTTTTA-AGAT
1 TTTTATAATTTTTTACA-AT
**
6978500 TTTTATAAAATTTTACAAT
1 TTTTATAATTTTTTACAAT
*
6978519 TTTTATAATTTTTTACATTT
1 TTTTATAATTTTTTACA-AT
* *
6978539 TTTTCTAA--TTTTAAATAT
1 TTTTATAATTTTTTACA-AT
6978557 TTTTAT-ATTTTTTA
1 TTTTATAATTTTTTA
6978571 TTAAAATTTA
Statistics
Matches: 57, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
17 1 0.02
18 13 0.23
19 34 0.60
20 9 0.16
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.63
Consensus pattern (19 bp):
TTTTATAATTTTTTACAAT
Found at i:6978590 original size:30 final size:29
Alignment explanation
Indices: 6978523--6978602 Score: 85
Period size: 30 Copynumber: 2.8 Consensus size: 29
6978513 TACAATTTTT
* *
6978523 ATAATTTTTTACATTTTTT-TCTAATTTT
1 ATAATTTTTTATATTTTTTATCTAATTTA
6978551 A-AATATTTTTATATTTTTTAT-TAAAATTTA
1 ATAAT-TTTTTATATTTTTTATCT--AATTTA
*
6978581 ATAATTTTTTTTATTTTTTATC
1 ATAATTTTTTATATTTTTTATC
6978603 ATTTTTTGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
27 3 0.07
28 15 0.35
29 1 0.02
30 21 0.49
31 3 0.07
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (29 bp):
ATAATTTTTTATATTTTTTATCTAATTTA
Found at i:6986110 original size:58 final size:57
Alignment explanation
Indices: 6985980--6986158 Score: 234
Period size: 58 Copynumber: 3.1 Consensus size: 57
6985970 TTCTTTTTCT
* * * * * * *
6985980 TTTTCTTTTTCATTTTGAAGAAAATCACATTTATTTCCAAATGATTT-CATTTCTCTA
1 TTTTCATTTTCATTTTGGAGAAAAACATAATCATTTCCAAATG-TTTCCATTTCTCCA
* *
6986037 TTTTCGTTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGTTTACCATTTCTCCA
1 TTTTCATTTTCATTTTGGAGAAAAACATAATCATTTCCAAATGTTT-CCATTTCTCCA
*
6986095 TTTTCATTTTCATTTTGGAGAAAAACATAATCATTTCCAAATTTTTCTCATTTCTCCA
1 TTTTCATTTTCATTTTGGAGAAAAACATAATCATTTCCAAATGTTTC-CATTTCTCCA
6986153 TTTTCA
1 TTTTCA
6986159 CAATTCCTAT
Statistics
Matches: 109, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
56 3 0.03
57 38 0.35
58 68 0.62
ACGTcount: A:0.28, C:0.18, G:0.06, T:0.47
Consensus pattern (57 bp):
TTTTCATTTTCATTTTGGAGAAAAACATAATCATTTCCAAATGTTTCCATTTCTCCA
Found at i:6988100 original size:24 final size:24
Alignment explanation
Indices: 6988060--6988106 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
6988050 AAAGGGAAAT
*
6988060 AAGAGAAAGTGATGGAAAATGTTG
1 AAGAGAAAGTGAAGGAAAATGTTG
*
6988084 AAGAGAAAG-GAAAGGAAAGTGTT
1 AAGAGAAAGTG-AAGGAAAATGTT
6988107 ATAAATTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.49, C:0.00, G:0.34, T:0.17
Consensus pattern (24 bp):
AAGAGAAAGTGAAGGAAAATGTTG
Found at i:6993652 original size:25 final size:24
Alignment explanation
Indices: 6993607--6993653 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
6993597 TTGTAAATAA
*
6993607 GAAAAATATCTTTAGAAAATTTCT
1 GAAAAATATCTTCAGAAAATTTCT
* *
6993631 GAAATAATTTCTTCAGAGAATTT
1 GAAA-AATATCTTCAGAAAATTT
6993654 TCTTCAGAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 4 0.21
25 15 0.79
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.38
Consensus pattern (24 bp):
GAAAAATATCTTCAGAAAATTTCT
Found at i:6993657 original size:14 final size:14
Alignment explanation
Indices: 6993638--6993670 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
6993628 TCTGAAATAA
6993638 TTTCTTCAGAGAAT
1 TTTCTTCAGAGAAT
6993652 TTTCTTCAGAGAAT
1 TTTCTTCAGAGAAT
6993666 TTTCT
1 TTTCT
6993671 CTCTACAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.48
Consensus pattern (14 bp):
TTTCTTCAGAGAAT
Found at i:6994418 original size:18 final size:19
Alignment explanation
Indices: 6994382--6994419 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
6994372 AAATATAATT
*
6994382 TTAATTTTAATTAATTTGA
1 TTAATTTTAATTAACTTGA
*
6994401 TTAA-TTTAATTTACTTGA
1 TTAATTTTAATTAACTTGA
6994419 T
1 T
6994420 CAAAATTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (19 bp):
TTAATTTTAATTAACTTGA
Found at i:6996308 original size:16 final size:17
Alignment explanation
Indices: 6996287--6996319 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
6996277 TATATTTATT
6996287 TTTTAAAAT-TTTTTAA
1 TTTTAAAATATTTTTAA
6996303 TTTTAAAATATTTTTAA
1 TTTTAAAATATTTTTAA
6996320 AATACTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTAAAATATTTTTAA
Found at i:6996330 original size:40 final size:40
Alignment explanation
Indices: 6996285--6996369 Score: 136
Period size: 40 Copynumber: 2.1 Consensus size: 40
6996275 AATATATTTA
6996285 TTTTTTAAA-ATTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTAAATA-TTTTTAATTTTAAAATATTTTTAAAATAC
* *
6996325 TTTTTTTATTATTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTAAATATTTTTAATTTTAAAATATTTTTAAAATAC
6996365 TTTTT
1 TTTTT
6996370 AATTTTTAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
40 41 0.98
41 1 0.02
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (40 bp):
TTTTTTAAATATTTTTAATTTTAAAATATTTTTAAAATAC
Found at i:6996346 original size:29 final size:30
Alignment explanation
Indices: 6996312--6996382 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
6996302 ATTTTAAAAT
** *
6996312 ATTTTTAAAATACTTTTTTTATTA-TTTTTA
1 ATTTTTAAAATA-TTTTTAAAATACTTTTTA
6996342 A-TTTTAAAATATTTTTAAAATACTTTTTA
1 ATTTTTAAAATATTTTTAAAATACTTTTTA
6996371 ATTTTTAAAATA
1 ATTTTTAAAATA
6996383 AATTTTTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 8 0.22
29 17 0.47
30 11 0.31
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (30 bp):
ATTTTTAAAATATTTTTAAAATACTTTTTA
Found at i:6996370 original size:12 final size:11
Alignment explanation
Indices: 6996303--6996371 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
6996293 AATTTTTTAA
6996303 TTTTAAAATAT
1 TTTTAAAATAT
6996314 TTTTAAAATACT
1 TTTTAAAATA-T
** *
6996326 TTTTTTATTAT
1 TTTTAAAATAT
6996337 TTTT---A-A-
1 TTTTAAAATAT
6996343 TTTTAAAATAT
1 TTTTAAAATAT
6996354 TTTTAAAATACT
1 TTTTAAAATA-T
6996366 TTTTAA
1 TTTTAA
6996372 TTTTTAAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
6 4 0.09
7 1 0.02
9 1 0.02
10 1 0.02
11 25 0.53
12 15 0.32
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:6996388 original size:19 final size:19
Alignment explanation
Indices: 6996352--6996388 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
6996342 ATTTTAAAAT
**
6996352 ATTTTTAAAATACTTTTTA
1 ATTTTTAAAATAAATTTTA
6996371 ATTTTTAAAATAAATTTT
1 ATTTTTAAAATAAATTTT
6996389 TGGTATTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTTTAAAATAAATTTTA
Found at i:7002209 original size:57 final size:57
Alignment explanation
Indices: 7002121--7002250 Score: 260
Period size: 57 Copynumber: 2.3 Consensus size: 57
7002111 CTAGCAAATC
7002121 AGAGAATTAAACGCAATGATGAAGGACAAGCATTGGTTTATTCACCGAACAGAATAT
1 AGAGAATTAAACGCAATGATGAAGGACAAGCATTGGTTTATTCACCGAACAGAATAT
7002178 AGAGAATTAAACGCAATGATGAAGGACAAGCATTGGTTTATTCACCGAACAGAATAT
1 AGAGAATTAAACGCAATGATGAAGGACAAGCATTGGTTTATTCACCGAACAGAATAT
7002235 AGAGAATTAAACGCAA
1 AGAGAATTAAACGCAA
7002251 GTGGCATCCA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 73 1.00
ACGTcount: A:0.44, C:0.14, G:0.21, T:0.22
Consensus pattern (57 bp):
AGAGAATTAAACGCAATGATGAAGGACAAGCATTGGTTTATTCACCGAACAGAATAT
Found at i:7002459 original size:23 final size:20
Alignment explanation
Indices: 7002429--7002473 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
7002419 TTTTTTTTTT
7002429 TAAAAGTTCAACAAAGAATAAA
1 TAAAAGTTC-ACAAA-AATAAA
*
7002451 TAAATAGTTCACCAAAATAAA
1 TAAA-AGTTCACAAAAATAAA
7002472 TA
1 TA
7002474 GAATGAGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
22 8 0.38
23 5 0.24
ACGTcount: A:0.60, C:0.11, G:0.07, T:0.22
Consensus pattern (20 bp):
TAAAAGTTCACAAAAATAAA
Found at i:7005478 original size:18 final size:18
Alignment explanation
Indices: 7005455--7005494 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
7005445 TAGTCGACTT
*
7005455 TTATTTTAATAT-TGTTTA
1 TTATTTTAA-ATGTATTTA
7005473 TTATTTTAAATGTATTTA
1 TTATTTTAAATGTATTTA
7005491 TTAT
1 TTAT
7005495 ATCTTATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (18 bp):
TTATTTTAAATGTATTTA
Found at i:7010314 original size:25 final size:27
Alignment explanation
Indices: 7010280--7010341 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
7010270 TATATTATAT
*
7010280 TATAATTATCAC-AA-CT-TTTTTTTAA
1 TATAATTATC-CTAATCTATTTTTTCAA
*
7010305 TATAACTATCCTAATCTATTTTTTCAA
1 TATAATTATCCTAATCTATTTTTTCAA
7010332 TATAATTATC
1 TATAATTATC
7010342 TCCATCTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
24 1 0.03
25 11 0.35
26 2 0.06
27 17 0.55
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (27 bp):
TATAATTATCCTAATCTATTTTTTCAA
Found at i:7010348 original size:27 final size:26
Alignment explanation
Indices: 7010280--7010351 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 26
7010270 TATATTATAT
* * *
7010280 TATAATTATCACAACT-TTTTTTTAA
1 TATAATTATCCCATCTATTTTTTCAA
* *
7010305 TATAACTATCCTAATCTATTTTTTCAA
1 TATAATTATCC-CATCTATTTTTTCAA
7010332 TATAATTATCTCCATCTATT
1 TATAATTATC-CCATCTATT
7010352 CCCTAGATTA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
25 9 0.24
26 3 0.08
27 24 0.65
28 1 0.03
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (26 bp):
TATAATTATCCCATCTATTTTTTCAA
Found at i:7011125 original size:22 final size:21
Alignment explanation
Indices: 7011072--7011126 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 21
7011062 GTTTAATAAG
7011072 TTTTTTAGT-TT-TAGAAGTT
1 TTTTTTAGTCTTGTAGAAGTT
*
7011091 TTTGTTT-GCTCTTGTAGCACGTT
1 TTT-TTTAG-TCTTGTAG-AAGTT
7011114 TTTTTTAGTCTTG
1 TTTTTTAGTCTTG
7011127 CTTATGCATG
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
19 4 0.14
20 4 0.14
21 2 0.07
22 11 0.38
23 8 0.28
ACGTcount: A:0.13, C:0.09, G:0.18, T:0.60
Consensus pattern (21 bp):
TTTTTTAGTCTTGTAGAAGTT
Found at i:7014161 original size:2 final size:2
Alignment explanation
Indices: 7014156--7014188 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
7014146 AAAAAATTAC
7014156 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7014189 AATGCTTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7014291 original size:65 final size:65
Alignment explanation
Indices: 7014206--7014402 Score: 257
Period size: 65 Copynumber: 3.1 Consensus size: 65
7014196 AATGAAAAGG
* * *
7014206 AAATATAAGTAATATCAAATTTAAATATTTAAAAAGTAAAAGAATAATAAATAAATAGATAAAAC
1 AAATATAAATAATATTAAATTTAAGTATTTAAAAAGTAAAAGAATAATAAATAAATAGATAAAAC
* * *
7014271 AAATATAAATAGTATTAAATTTAAGTATTTAAAAAATAAAAG---AA-CAAT--A-A-ATAAAAC
1 AAATATAAATAATATTAAATTTAAGTATTTAAAAAGTAAAAGAATAATAAATAAATAGATAAAAC
*
7014328 AAATATAAATAATATTAAATTTAAGTATTTAAAAAAGTAAAAGAATAATAAACAAATAGATAAAA
1 AAATATAAATAATATTAAATTTAAGTATTT-AAAAAGTAAAAGAATAATAAATAAATAGATAAAA
7014393 C
65 C
*
7014394 GAATATAAA
1 AAATATAAA
7014403 AGGATGAAAT
Statistics
Matches: 112, Mismatches: 11, Indels: 17
0.80 0.08 0.12
Matches are distributed among these distances:
57 36 0.32
58 12 0.11
59 1 0.01
61 5 0.04
62 4 0.04
64 1 0.01
65 38 0.34
66 15 0.13
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.27
Consensus pattern (65 bp):
AAATATAAATAATATTAAATTTAAGTATTTAAAAAGTAAAAGAATAATAAATAAATAGATAAAAC
Found at i:7014309 original size:57 final size:57
Alignment explanation
Indices: 7014259--7014379 Score: 206
Period size: 57 Copynumber: 2.1 Consensus size: 57
7014249 ATAATAAATA
* *
7014259 AATAGATAAAACAAATATAAATAGTATTAAATTTAAGTATTTAAAAAATAAAAGAAC
1 AATAAATAAAACAAATATAAATAATATTAAATTTAAGTATTTAAAAAATAAAAGAAC
*
7014316 AATAAATAAAACAAATATAAATAATATTAAATTTAAGTATTTAAAAAAGTAAAAGAAT
1 AATAAATAAAACAAATATAAATAATATTAAATTTAAGTATTTAAAAAA-TAAAAGAAC
7014374 AATAAA
1 AATAAA
7014380 CAAATAGATA
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
57 46 0.77
58 14 0.23
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (57 bp):
AATAAATAAAACAAATATAAATAATATTAAATTTAAGTATTTAAAAAATAAAAGAAC
Found at i:7015924 original size:44 final size:44
Alignment explanation
Indices: 7015876--7016354 Score: 534
Period size: 44 Copynumber: 10.8 Consensus size: 44
7015866 TTGTTGCTTC
* * * *
7015876 AATCTACTCCACCGCAACTTCAGGGAGATTAGACTTGTAGA-TTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTA-ACTTT
* * * * * *
7015920 AATCTACTCTATTGCAACTTCAGGGAAATGAGATTTGTAACTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTT
* * * *
7015964 AATATGCTCCATTGTAACTTCAGGGAGATGAGATTTGTAACTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTT
* * * * *
7016008 AATCTGCTCCACTGTAACTTCAAGGAGATGAGGTTTGTAACTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTT
* *
7016052 AATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGTAACTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTT
* *
7016096 AATCTACTCCACTGCAACTTCAGGAAGATAAGATTTGTAACTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTT
** * *
7016140 AATCTGCTCCACTGCAACTTCAGAAAGATAAGATTTCTAACTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTT
* * *
7016184 AATATGCTCCACTGCAACTTCAGAGAGATAAGATTTGCT-ATTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TAACTTT
*
7016228 CAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTGTAA-TTT
1 -AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTT
* * * *
7016272 CAATCTGCTCTACTGCAATTTCAGAGAGATAAGATTTGCT-ATTTT
1 -AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TAACTTT
* * *
7016317 CAATCTGCTCCACTGTAACTTTAGGGAGATAAAATTTG
1 -AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG
7016355 CCACGATAAC
Statistics
Matches: 380, Mismatches: 49, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
43 1 0.00
44 307 0.81
45 72 0.19
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (44 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTT
Found at i:7019015 original size:24 final size:24
Alignment explanation
Indices: 7018988--7019050 Score: 72
Period size: 25 Copynumber: 2.6 Consensus size: 24
7018978 CAGCTCGAAA
*
7018988 GAGCATCCCGTTATTAGCTCTCAT
1 GAGCATCCCGTTATTAGCTCTCAC
* * *
7019012 GAGCATCTCGGTATTTGGCTCTCAC
1 GAGCATCCCGTTA-TTAGCTCTCAC
*
7019037 GAGCTTCCCGTTAT
1 GAGCATCCCGTTAT
7019051 ATGGTCCTTG
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
24 12 0.39
25 19 0.61
ACGTcount: A:0.17, C:0.29, G:0.21, T:0.33
Consensus pattern (24 bp):
GAGCATCCCGTTATTAGCTCTCAC
Found at i:7019231 original size:25 final size:26
Alignment explanation
Indices: 7019157--7019239 Score: 84
Period size: 27 Copynumber: 3.3 Consensus size: 26
7019147 GTCCCAATAT
*
7019157 ATGGCTCTT-TAGAGCTTCCCGATTA
1 ATGGCTCTTCCAGAGCTTCCCGATTA
* * *
7019182 AAGGCTCTTTCATGAGCTTCTCGATTA
1 ATGGCTCTTCCA-GAGCTTCCCGATTA
7019209 ATGGCTC-TCC-GAAGCTTCCCGA-TA
1 ATGGCTCTTCCAG-AGCTTCCCGATTA
7019233 ATGGCTC
1 ATGGCTC
7019240 GCTTAAACTT
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
24 10 0.20
25 17 0.35
26 3 0.06
27 19 0.39
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (26 bp):
ATGGCTCTTCCAGAGCTTCCCGATTA
Found at i:7019250 original size:24 final size:24
Alignment explanation
Indices: 7019223--7019287 Score: 103
Period size: 24 Copynumber: 2.7 Consensus size: 24
7019213 CTCTCCGAAG
*
7019223 CTTCCCGATAATGGCTCGCTTAAA
1 CTTCCCGATTATGGCTCGCTTAAA
* *
7019247 CTTCTCGTTTATGGCTCGCTTAAA
1 CTTCCCGATTATGGCTCGCTTAAA
7019271 CTTCCCGATTATGGCTC
1 CTTCCCGATTATGGCTC
7019288 TTATGAGCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.18, C:0.29, G:0.17, T:0.35
Consensus pattern (24 bp):
CTTCCCGATTATGGCTCGCTTAAA
Found at i:7019298 original size:24 final size:24
Alignment explanation
Indices: 7019135--7019305 Score: 86
Period size: 24 Copynumber: 7.0 Consensus size: 24
7019125 ACACACCATA
* * *
7019135 GCTCTTATGACCGTCCCAATATATG
1 GCTCTTATGAGCTTCCCGAT-TATG
*
7019160 GCTCTT-TAGAGCTTCCCGATTAAAG
1 GCTCTTAT-GAGCTTCCCGATT-ATG
*
7019185 GCTCTTTCATGAGCTTCTCGATTAATG
1 GCTC-TT-ATGAGCTTCCCGATT-ATG
** *
7019212 GCTC-TCCGAAGCTTCCCGATAATG
1 GCTCTTATG-AGCTTCCCGATTATG
* * *
7019236 GCTCGCTTA--AACTTCTCGTTTATG
1 GCT--CTTATGAGCTTCCCGATTATG
*
7019260 GCTCGCTTA--AACTTCCCGATTATG
1 GCT--CTTATGAGCTTCCCGATTATG
7019284 GCTCTTATGAGCTTCCCG-TTAT
1 GCTCTTATGAGCTTCCCGATTAT
7019306 ATAGCTCGAA
Statistics
Matches: 117, Mismatches: 18, Indels: 24
0.74 0.11 0.15
Matches are distributed among these distances:
22 4 0.03
23 4 0.03
24 53 0.45
25 32 0.27
26 3 0.03
27 20 0.17
28 1 0.01
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.35
Consensus pattern (24 bp):
GCTCTTATGAGCTTCCCGATTATG
Found at i:7021550 original size:21 final size:21
Alignment explanation
Indices: 7021526--7021568 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
7021516 ATGAATTTTA
*
7021526 TTTTTTGAGCCCTTTCGGAGG
1 TTTTTTCAGCCCTTTCGGAGG
7021547 TTTTTTCAGCCCTTTCGGAGG
1 TTTTTTCAGCCCTTTCGGAGG
7021568 T
1 T
7021569 AACTCTTGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.09, C:0.21, G:0.26, T:0.44
Consensus pattern (21 bp):
TTTTTTCAGCCCTTTCGGAGG
Found at i:7025996 original size:101 final size:102
Alignment explanation
Indices: 7025870--7026053 Score: 300
Period size: 101 Copynumber: 1.8 Consensus size: 102
7025860 AAAGTGGTGG
* *
7025870 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGAT-A-GGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGG-ATGATAATGGTCACATGTGTACT
7025933 ACTATGTGCAGGCTACTATATGTACCGGATAGTTTCGA
65 ACTATGTGCAGGCTACTATATGTACCGGATAGTTTCGA
* * *
7025971 TCACGTGTGTAGTACTATGTGCAGGCTACTGCGTGTATCGGATGGTAATGGTCACATGTGTACTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGATAATGGTCACATGTGTACTA
7026036 CTATGTGCAGGCTACTAT
66 CTATGTGCAGGCTACTAT
7026054 GTGAACCAAA
Statistics
Matches: 76, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
100 4 0.05
101 40 0.53
102 32 0.42
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.32
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGATAATGGTCACATGTGTACTA
CTATGTGCAGGCTACTATATGTACCGGATAGTTTCGA
Found at i:7026000 original size:51 final size:51
Alignment explanation
Indices: 7025867--7026052 Score: 225
Period size: 51 Copynumber: 3.7 Consensus size: 51
7025857 GTGAAAGTGG
* *
7025867 TGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGA-A-TGA
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTAA
* ** *
7025916 TAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATATGTACCGGATAGT-T
1 T-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTAA
* * * * *
7025967 TCGATCACGTGTGTAGTACTATGTGCAGGCTACTGCGTGTATCGGATGGTAA
1 T-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTAA
*
7026019 TGGTCACATGTGTACTACTATGTGCAGGCTACTA
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTA
7026053 TGTGAACCAA
Statistics
Matches: 114, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
49 1 0.01
50 40 0.35
51 71 0.62
52 2 0.02
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (51 bp):
TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTAA
Found at i:7026149 original size:45 final size:45
Alignment explanation
Indices: 7026058--7026150 Score: 123
Period size: 45 Copynumber: 2.1 Consensus size: 45
7026048 TACTATGTGA
* *
7026058 ACCAAACATCATTGATTAGTAAGGTGGTTGCTATGTACTGATTCC
1 ACCAAACATCATTGATTAATAAGGTGGTTGCTATGTACTGAATCC
* * * **
7026103 ACCAGACATTATTGATTAATAAGGTGGTTGTTATGTGTTGAATCC
1 ACCAAACATCATTGATTAATAAGGTGGTTGCTATGTACTGAATCC
7026148 ACC
1 ACC
7026151 GAGTATCTGT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.34
Consensus pattern (45 bp):
ACCAAACATCATTGATTAATAAGGTGGTTGCTATGTACTGAATCC
Found at i:7033255 original size:2 final size:2
Alignment explanation
Indices: 7033248--7033274 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7033238 TAATAAGGGC
7033248 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
7033275 AATGCTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7033348 original size:30 final size:30
Alignment explanation
Indices: 7033313--7033414 Score: 78
Period size: 33 Copynumber: 3.2 Consensus size: 30
7033303 ATATCATATT
7033313 TAAATATTTAAAAAGTAAAAGAATAATAAA
1 TAAATATTTAAAAAGTAAAAGAATAATAAA
* * * * *
7033343 TAAATAGATAAAACAAATATAAATAATATTAAA
1 TAAATA-TTTAAA-AAGTA-AAAGAATAATAAA
* * * *
7033376 TTTAAGTCTTTAAAAAGTAAAAGAACAATATA
1 --TAAATATTTAAAAAGTAAAAGAATAATAAA
7033408 TAAATAT
1 TAAATAT
7033415 AATAAATAAA
Statistics
Matches: 51, Mismatches: 16, Indels: 10
0.66 0.21 0.13
Matches are distributed among these distances:
30 11 0.22
31 4 0.08
32 13 0.25
33 15 0.29
34 4 0.08
35 4 0.08
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (30 bp):
TAAATATTTAAAAAGTAAAAGAATAATAAA
Found at i:7033362 original size:65 final size:64
Alignment explanation
Indices: 7033292--7033490 Score: 256
Period size: 65 Copynumber: 3.0 Consensus size: 64
7033282 AATGAAAAGG
* * * *
7033292 AAATATAAGTAATATCATATTTAAATATTTAAAAAGTAAAAGAATAATAAATAAATAGATAAAAC
1 AAATATAA-TAATATTAAATTTAAGTATTTAAAAAGTAAAAGAATAATAAATAAATAAATAAAAC
*
7033357 AAATATAAATAATATTAAATTTAAGTCTTTAAAAAGTAAAAGAACAATATATAAATATAATAAAT
1 AAATAT-AATAATATTAAATTTAAGTATTTAAAAAGTAAAAG---AATA-ATAAATA-AATAAAT
7033422 AAAAC
60 AAAAC
*
7033427 AAATATATATAATATTAAATTTAAGTATTTAAAAAAGTAAAAGAATAATAAAAAAATAAA-AAAA
1 AAATATA-ATAATATTAAATTTAAGTATTT-AAAAAGTAAAAGAATAATAAATAAATAAATAAAA
7033491 TAGATAAAAC
Statistics
Matches: 119, Mismatches: 7, Indels: 16
0.84 0.05 0.11
Matches are distributed among these distances:
65 39 0.33
66 8 0.07
67 6 0.05
68 8 0.07
69 8 0.07
70 38 0.32
71 12 0.10
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (64 bp):
AAATATAATAATATTAAATTTAAGTATTTAAAAAGTAAAAGAATAATAAATAAATAAATAAAAC
Found at i:7033390 original size:35 final size:35
Alignment explanation
Indices: 7033351--7033460 Score: 102
Period size: 35 Copynumber: 3.1 Consensus size: 35
7033341 AATAAATAGA
*
7033351 TAAAACAAATATAAATAATATTAAATTTAAGTCTT
1 TAAAACAAATATAAATAATATTAAATTTAAGTATT
* * **
7033386 TAAAA-AGTAA-A-AGAACAATATATAAATATAA-TAAA
1 TAAAACA--AATATA-AATAATAT-TAAATTTAAGTATT
*
7033421 TAAAACAAATATATATAATATTAAATTTAAGTATT
1 TAAAACAAATATAAATAATATTAAATTTAAGTATT
7033456 TAAAA
1 TAAAA
7033461 AAGTAAAAGA
Statistics
Matches: 57, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
34 12 0.21
35 33 0.58
36 12 0.21
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.33
Consensus pattern (35 bp):
TAAAACAAATATAAATAATATTAAATTTAAGTATT
Found at i:7033482 original size:20 final size:20
Alignment explanation
Indices: 7033456--7033499 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
7033446 TTTAAGTATT
* *
7033456 TAAAAAAGTAAAAGAATA-A
1 TAAAAAAATAAAAAAATAGA
7033475 TAAAAAAATAAAAAAATAGA
1 TAAAAAAATAAAAAAATAGA
7033495 TAAAA
1 TAAAA
7033500 CGAATATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (20 bp):
TAAAAAAATAAAAAAATAGA
Found at i:7033508 original size:70 final size:70
Alignment explanation
Indices: 7033337--7033507 Score: 204
Period size: 70 Copynumber: 2.4 Consensus size: 70
7033327 GTAAAAGAAT
*
7033337 AATAAATAAATAGATAAAACAAATATAAATAATATTAAATTTAAGTCTTTAAAAAGTAAAAGAAC
1 AATAAATAAATAGATAAAAC-AATAT--ATAATATTAAATTTAAGTATTTAAAAAGTAAAAGAAC
* *
7033402 AATATATA
63 AATAAAAA
7033410 AATATAATAAATA-A-AACAA-ATATATATAATATTAAATTTAAGTATTTAAAAAAGTAAAAGAA
1 AATA-AATAAATAGATAA-AACA-ATATATAATATTAAATTTAAGTATTT-AAAAAGTAAAAGAA
*
7033472 TAATAAAAA
62 CAATAAAAA
*
7033481 AATAAAAAAATAGATAAAACGAATATA
1 AATAAATAAATAGATAAAAC-AATATA
7033508 AAAGGATGAA
Statistics
Matches: 85, Mismatches: 5, Indels: 17
0.79 0.05 0.16
Matches are distributed among these distances:
70 28 0.33
71 28 0.33
72 13 0.15
73 8 0.09
74 8 0.09
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.27
Consensus pattern (70 bp):
AATAAATAAATAGATAAAACAATATATAATATTAAATTTAAGTATTTAAAAAGTAAAAGAACAAT
AAAAA
Found at i:7040476 original size:41 final size:42
Alignment explanation
Indices: 7040419--7040525 Score: 182
Period size: 41 Copynumber: 2.6 Consensus size: 42
7040409 CATTGAATGT
*
7040419 AAGGGGTTGCTAAGTGCAGATTCCCCGAAACTCTGATC-AAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAAACTCTAATCTAAA
7040460 AAGGGGTTGCTAAGTGCAGATTCCCCGAAACTCTAATCTAAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAAACTCTAATCTAAA
*
7040502 AA-GGGTTGCTAAGTGTAGATTCCC
1 AAGGGGTTGCTAAGTGCAGATTCCC
7040526 TGAGAGGTTG
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
41 58 0.92
42 5 0.08
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (42 bp):
AAGGGGTTGCTAAGTGCAGATTCCCCGAAACTCTAATCTAAA
Found at i:7040561 original size:26 final size:26
Alignment explanation
Indices: 7040505--7040554 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
7040495 ATCTAAAAAG
*
7040505 GGTTGCTAAGTGTAGATTCCCTGAGA
1 GGTTGCTAAGTGTAGATTCCCCGAGA
7040531 GGTTGCTAAGTGCTA-ATTCCCCGA
1 GGTTGCTAAGTG-TAGATTCCCCGA
7040555 ATTGTTGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (26 bp):
GGTTGCTAAGTGTAGATTCCCCGAGA
Found at i:7040676 original size:41 final size:43
Alignment explanation
Indices: 7040567--7040677 Score: 122
Period size: 43 Copynumber: 2.6 Consensus size: 43
7040557 TGTTGATTCT
* *
7040567 AAAGGTGGTTGCTAAGTGTTGATTCCACTGTATCCTTGATTGTA
1 AAAGGTGGTTGCTAAGTGTTGATTCCACTATATCCTTGA-TATA
* * *
7040611 AAAGG-GGTTACTATGTGCTGATTCC-CTATATCAC-TGA-ATA
1 AAAGGTGGTTGCTAAGTGTTGATTCCACTATATC-CTTGATATA
*
7040651 TAAGGTGGTTGCTAAGTGTTGATTCCA
1 AAAGGTGGTTGCTAAGTGTTGATTCCA
7040678 TCGAGTAACG
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
40 6 0.11
41 17 0.31
42 9 0.16
43 18 0.33
44 5 0.09
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.36
Consensus pattern (43 bp):
AAAGGTGGTTGCTAAGTGTTGATTCCACTATATCCTTGATATA
Found at i:7043306 original size:42 final size:42
Alignment explanation
Indices: 7043169--7043314 Score: 170
Period size: 42 Copynumber: 3.5 Consensus size: 42
7043159 GTTACTCGGT
* * *
7043169 GGAATCAGCACTTAGCAACCACC-TTATATTCAGTGATACGG
1 GGAATCAGCACTTAGCAACCACCTTTACAATCAATGATACGG
* * * *
7043210 GGAATCAGCACATAACAACC-CCTTTCACAATCAAGGATACAGT
1 GGAATCAGCACTTAGCAACCACCTTT-ACAATCAATGATAC-GG
* * *
7043253 GGAATCAGCACTTAGCAACCACCTTTAGAATCAATAATTCGG
1 GGAATCAGCACTTAGCAACCACCTTTACAATCAATGATACGG
7043295 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
7043315 TCTCGGGGAA
Statistics
Matches: 87, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
40 2 0.02
41 20 0.23
42 31 0.36
43 29 0.33
44 5 0.06
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (42 bp):
GGAATCAGCACTTAGCAACCACCTTTACAATCAATGATACGG
Found at i:7043320 original size:26 final size:26
Alignment explanation
Indices: 7043291--7043343 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
7043281 AATCAATAAT
7043291 TCGGGGAATCAGCACTTAGCAACCTC
1 TCGGGGAATCAGCACTTAGCAACCTC
*
7043317 TCGGGGAATCTGCACTTAGCAACCTC
1 TCGGGGAATCAGCACTTAGCAACCTC
7043343 T
1 T
7043344 TTTTGATCAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.23
Consensus pattern (26 bp):
TCGGGGAATCAGCACTTAGCAACCTC
Found at i:7043465 original size:41 final size:41
Alignment explanation
Indices: 7043317--7043467 Score: 248
Period size: 41 Copynumber: 3.7 Consensus size: 41
7043307 TAGCAACCTC
*
7043317 TCGGGGAATCTGCACTTAGCAACCTCTTTTTGATCAGAGTT
1 TCGGGGAATCTGCACTTAGCAACCCCTTTTTGATCAGAGTT
* *
7043358 TCGGGGAATCTGCATTTAGCAACCCTTTTTTGATCAGAGTT
1 TCGGGGAATCTGCACTTAGCAACCCCTTTTTGATCAGAGTT
* * *
7043399 TCAGGGAATCTGCACTTAACAACCCCTTTTTGATCACAGTT
1 TCGGGGAATCTGCACTTAGCAACCCCTTTTTGATCAGAGTT
7043440 TCGGGGAATCTGCACTTAGCAACCCCTT
1 TCGGGGAATCTGCACTTAGCAACCCCTT
7043468 ACATTCAATG
Statistics
Matches: 100, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 100 1.00
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (41 bp):
TCGGGGAATCTGCACTTAGCAACCCCTTTTTGATCAGAGTT
Found at i:7051013 original size:18 final size:18
Alignment explanation
Indices: 7050976--7051011 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
7050966 TTATTATTTT
*
7050976 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
7050994 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
7051012 TACTTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:7057602 original size:17 final size:18
Alignment explanation
Indices: 7057569--7057604 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
7057559 TAAATTTTAA
7057569 AATAAATATAGGCATAAT
1 AATAAATATAGGCATAAT
*
7057587 AATAAATTTA-GCATAAT
1 AATAAATATAGGCATAAT
7057604 A
1 A
7057605 TTTATTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.31
Consensus pattern (18 bp):
AATAAATATAGGCATAAT
Found at i:7060368 original size:16 final size:17
Alignment explanation
Indices: 7060347--7060383 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
7060337 CTTTCGAATA
7060347 TAGTG-ATTTTTTTAAC
1 TAGTGAATTTTTTTAAC
*
7060363 TAGTGAATTTTTTTTAC
1 TAGTGAATTTTTTTAAC
7060380 TAGT
1 TAGT
7060384 TGATGTTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.24, C:0.05, G:0.14, T:0.57
Consensus pattern (17 bp):
TAGTGAATTTTTTTAAC
Found at i:7062630 original size:44 final size:42
Alignment explanation
Indices: 7062570--7062655 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 42
7062560 AAACATTCAA
* * * *
7062570 ATTGAATCATCGAATTACACAGTATAATTCTAATTAGAATATTC
1 ATTGAATCATCAAATTA-A-AATATAATTCTAATCAAAATATTC
*
7062614 ATTGAATCTTCAAATTAAAATATAATTCTAATCAAAATATTC
1 ATTGAATCATCAAATTAAAATATAATTCTAATCAAAATATTC
7062656 CATTATCAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
42 21 0.57
43 1 0.03
44 15 0.41
ACGTcount: A:0.44, C:0.13, G:0.06, T:0.37
Consensus pattern (42 bp):
ATTGAATCATCAAATTAAAATATAATTCTAATCAAAATATTC
Found at i:7077245 original size:18 final size:18
Alignment explanation
Indices: 7077218--7077252 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
7077208 CGATATCTAT
*
7077218 TTCATGGAAAGCAAGCAG
1 TTCATAGAAAGCAAGCAG
*
7077236 TTCATAGAAATCAAGCA
1 TTCATAGAAAGCAAGCA
7077253 AATCTTGCGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.20
Consensus pattern (18 bp):
TTCATAGAAAGCAAGCAG
Done.