Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168159.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_4, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 33012953
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65000 characters in sequence are not A, C, G, or T
File 59 of 160
Found at i:12448465 original size:16 final size:16
Alignment explanation
Indices: 12448443--12448477 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
12448433 ACTCTGATTG
12448443 AAAAAAAAAACATTTTC
1 AAAAAAAAAA-ATTTTC
12448460 AAAAAAAAAAATTTTC
1 AAAAAAAAAAATTTTC
12448476 AA
1 AA
12448478 GTTTTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAAAAAAAAATTTTC
Found at i:12448664 original size:21 final size:20
Alignment explanation
Indices: 12448624--12448701 Score: 66
Period size: 22 Copynumber: 3.6 Consensus size: 20
12448614 AGATTTTAAG
* * *
12448624 ATTTATAAGACCTTCGGGCA
1 ATTTGTAAGACCTCCAGGCA
12448644 ATTCTGTAAGACCTCCAGGCATA
1 ATT-TGTAAGACCTCCAGGC--A
*
12448667 ATTTTTAAGACCTCCAGGCA
1 ATTTGTAAGACCTCCAGGCA
*
12448687 TGATTTTTAAGACCT
1 --ATTTGTAAGACCT
12448702 TTGGGTATAA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
20 4 0.08
21 13 0.27
22 28 0.57
23 4 0.08
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (20 bp):
ATTTGTAAGACCTCCAGGCA
Found at i:12448714 original size:22 final size:22
Alignment explanation
Indices: 12448650--12448701 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
12448640 GGCAATTCTG
12448650 TAAGACCTCCAGGCATAATTTT
1 TAAGACCTCCAGGCATAATTTT
*
12448672 TAAGACCTCCAGGCATGATTTT
1 TAAGACCTCCAGGCATAATTTT
12448694 TAAGACCT
1 TAAGACCT
12448702 TTGGGTATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (22 bp):
TAAGACCTCCAGGCATAATTTT
Found at i:12448822 original size:23 final size:23
Alignment explanation
Indices: 12448775--12448857 Score: 84
Period size: 23 Copynumber: 3.7 Consensus size: 23
12448765 TATTCCAGTC
* *
12448775 GATTCTATAAGACCTCTAGGTAT
1 GATTCTATAAGACCTCCAGGCAT
*
12448798 GATTCTATAAGACCTCCGGGCAT
1 GATTCTATAAGACCTCCAGGCAT
* *
12448821 GATT-TTTAAGACCTTCAGGCAT
1 GATTCTATAAGACCTCCAGGCAT
12448843 -ATTTCTA-AA-ACCTCC
1 GA-TTCTATAAGACCTCC
12448858 GGGTATAATT
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
21 6 0.12
22 19 0.38
23 25 0.50
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.33
Consensus pattern (23 bp):
GATTCTATAAGACCTCCAGGCAT
Found at i:12448959 original size:23 final size:23
Alignment explanation
Indices: 12448929--12448988 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
12448919 ACCCCAGTCA
*
12448929 ATTCTGTAAGACCTCCGGGTATG
1 ATTCTGTAAGACCTCCGGGCATG
12448952 ATTCTGTAAGACCTCCGGGCATG
1 ATTCTGTAAGACCTCCGGGCATG
*
12448975 ATT-TCTAAGACCTC
1 ATTCTGTAAGACCTC
12448989 TAGGCATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 10 0.29
23 25 0.71
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.30
Consensus pattern (23 bp):
ATTCTGTAAGACCTCCGGGCATG
Found at i:12448962 original size:153 final size:155
Alignment explanation
Indices: 12448644--12449001 Score: 454
Period size: 153 Copynumber: 2.3 Consensus size: 155
12448634 CCTTCGGGCA
* * * * * * **
12448644 ATTCTGTAAGACCTCCAGGCATAATTTTTAAGACCTCCAGGCATGATTTTTAAGACCTTTGGGTA
1 ATTCTGTAAGACCTCCGGGCATGATTTTTAAGACCTTCAGGCATAATTTCTAAAACCTCCGGGTA
** **
12448709 TAATTTCGATTCGTGGTGTTATCCCGATCGATTCCTTATCTTTCAACTTACGATGTTATTCCAGT
66 TAATTTCGATTCGCAGTGTTATCCCGATCGATTCCTTATCTTTCAACTTACGATGTTACCCCAGT
* *
12448774 CGATTCTATAAGACCTCTAGGTATG
131 CAATTCTATAAGACCTCCAGGTATG
*
12448799 ATTCTATAAGACCTCCGGGCATGATTTTTAAGACCTTCAGGCAT-ATTTCTAAAACCTCCGGGTA
1 ATTCTGTAAGACCTCCGGGCATGATTTTTAAGACCTTCAGGCATAATTTCTAAAACCTCCGGGTA
* * * * * *
12448863 TAATTTTGATTCGCAGTGTTGTCCCGGTCGATT-CTT-TATTTCTGACTTGCGATGTTACCCCAG
66 TAATTTCGATTCGCAGTGTTATCCCGATCGATTCCTTATCTTTC-AACTTACGATGTTACCCCAG
* *
12448926 TCAATTCTGTAAGACCTCCGGGTATG
130 TCAATTCTATAAGACCTCCAGGTATG
*
12448952 ATTCTGTAAGACCTCCGGGCATGATTTCTAAGACC-TCTAGGCATAATTTC
1 ATTCTGTAAGACCTCCGGGCATGATTTTTAAGACCTTC-AGGCATAATTTC
12449002 AATTCGCGGT
Statistics
Matches: 176, Mismatches: 24, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
152 7 0.04
153 80 0.45
154 49 0.28
155 40 0.23
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (155 bp):
ATTCTGTAAGACCTCCGGGCATGATTTTTAAGACCTTCAGGCATAATTTCTAAAACCTCCGGGTA
TAATTTCGATTCGCAGTGTTATCCCGATCGATTCCTTATCTTTCAACTTACGATGTTACCCCAGT
CAATTCTATAAGACCTCCAGGTATG
Found at i:12448999 original size:132 final size:130
Alignment explanation
Indices: 12448799--12449105 Score: 384
Period size: 132 Copynumber: 2.3 Consensus size: 130
12448789 TCTAGGTATG
* * * * *
12448799 ATTCTATAAGACCTCCGGGCATGATTTTTAAGACCTTCAGGCATATTTCTAAAACCTCCGGGTAT
1 ATTCTGTAAGACCTCCGGGCATGATTTTTAAGACCTCCGGGCATATTTCTAAAACCTCCAGGCAT
** * * *
12448864 AATTTTGATTCGCAGTGTTGTCCCGGTCGATTCTTTAT-TTCTGACTTGCGATGTTACCCCAGTC
66 AATTTCAATTCGCAGTGTTATCCCGATCGATTCCTTATCTTCTGAC-TGCGATGTTACCCCAGTC
12448928 A
130 A
* * * *
12448929 ATTCTGTAAGACCTCCGGGTATGATTCTGTAAGACCTCCGGGCATGATTTCTAAGACCTCTAGGC
1 ATTCTGTAAGACCTCCGGGCATGATT-TTTAAGACCTCCGGGCAT-ATTTCTAAAACCTCCAGGC
* * *
12448994 ATAATTTCAATTCGCGGTGTTATCCCGATCGATTCCTTATCTTTTGACTGCGATGTTATCCCAGT
64 ATAATTTCAATTCGCAGTGTTATCCCGATCGATTCCTTATCTTCTGACTGCGATGTTACCCCAGT
*
12449059 CT
129 CA
* *
12449061 A-TCTTGTAAGACCTCTGAGCATGATTTTTAAGACCTCCGGGCATA
1 ATTC-TGTAAGACCTCCGGGCATGATTTTTAAGACCTCCGGGCATA
12449106 ATTTTGATTC
Statistics
Matches: 151, Mismatches: 22, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
130 25 0.17
131 34 0.23
132 86 0.57
133 6 0.04
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.35
Consensus pattern (130 bp):
ATTCTGTAAGACCTCCGGGCATGATTTTTAAGACCTCCGGGCATATTTCTAAAACCTCCAGGCAT
AATTTCAATTCGCAGTGTTATCCCGATCGATTCCTTATCTTCTGACTGCGATGTTACCCCAGTCA
Found at i:12449000 original size:22 final size:22
Alignment explanation
Indices: 12448935--12449001 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
12448925 GTCAATTCTG
* * * *
12448935 TAAGACCTCCGGGTATGATTCTG
1 TAAGACCTCCAGGCATAATT-TC
* *
12448958 TAAGACCTCCGGGCATGATTTC
1 TAAGACCTCCAGGCATAATTTC
*
12448980 TAAGACCTCTAGGCATAATTTC
1 TAAGACCTCCAGGCATAATTTC
12449002 AATTCGCGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
22 20 0.51
23 19 0.49
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (22 bp):
TAAGACCTCCAGGCATAATTTC
Found at i:12449104 original size:22 final size:22
Alignment explanation
Indices: 12449067--12449110 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
12449057 GTCTATCTTG
* *
12449067 TAAGACCTCTGAGCATGATTTT
1 TAAGACCTCCGAGCATAATTTT
*
12449089 TAAGACCTCCGGGCATAATTTT
1 TAAGACCTCCGAGCATAATTTT
12449111 GATTCACGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.34
Consensus pattern (22 bp):
TAAGACCTCCGAGCATAATTTT
Found at i:12449225 original size:133 final size:132
Alignment explanation
Indices: 12449067--12449316 Score: 365
Period size: 133 Copynumber: 1.9 Consensus size: 132
12449057 GTCTATCTTG
* * * * *
12449067 TAAGACCTCTGAGCATGATTTTTAAGACCTCCGGGCATAATTTTGATTCACGGTGTTATCTCGAT
1 TAAGACCTCCGAGCATGACTCTTAAGACCTCCGAGCATAATTTTGATTCACAGTGTTATCTCGAT
*
12449132 CGATTTCTTATCTTTCGACTTACGATGTTATTCCAGTCGATTCTGTAAGACCTCTATGTATGATT
66 CGATTCCTTATCTTTCGACTTACGATGTTA-TCCAGTCGATTCTGTAAGACCTCTATGTATGATT
12449197 CTA
130 CTA
* * **
12449200 TAAGACCTCCGGGCATGACTCTTAAGACCTCCGAGCGTAATTTTGATTCGTAGTGTTATCTCGAT
1 TAAGACCTCCGAGCATGACTCTTAAGACCTCCGAGCATAATTTTGATTCACAGTGTTATCTCGAT
* * * *
12449265 CGATTCCTTATCTTTTGACTTATGGTGTTATCCAGTCGATTTTGTAAGACCT
66 CGATTCCTTATCTTTCGACTTACGATGTTATCCAGTCGATTCTGTAAGACCT
12449317 TCGAACATAA
Statistics
Matches: 103, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
132 21 0.20
133 82 0.80
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.38
Consensus pattern (132 bp):
TAAGACCTCCGAGCATGACTCTTAAGACCTCCGAGCATAATTTTGATTCACAGTGTTATCTCGAT
CGATTCCTTATCTTTCGACTTACGATGTTATCCAGTCGATTCTGTAAGACCTCTATGTATGATTC
TA
Found at i:12449368 original size:87 final size:87
Alignment explanation
Indices: 12449222--12449444 Score: 268
Period size: 87 Copynumber: 2.6 Consensus size: 87
12449212 GCATGACTCT
* **
12449222 TAAGACCTCCGAGCGTAATTTTGATTCGTAGTGTTATCTCGATCGATTCCTTATCTTTTGACTTA
1 TAAGACCTCCGAGCATAATTTTGATTCGCGGTGTTATCTCGATCGATTCCTTATCTTTTGAC-TA
* * *
12449287 TGGTGTTATC-CAGTCGATTTTG
65 CGATGTTATCTCAGTCGATTCTG
* * * * * *
12449309 TAAGACCTTCGAACATAATTTCGATTCGCGGTGTTATCCCGATCGATTCTTTATCTTTTGACTGC
1 TAAGACCTCCGAGCATAATTTTGATTCGCGGTGTTATCTCGATCGATTCCTTATCTTTTGACTAC
*
12449374 GATGTTATCTCAGTCTATTCTG
66 GATGTTATCTCAGTCGATTCTG
* ** *
12449396 TAAGACCTCCGGGCATAATTTTGATTTACGTGTATTATCTCGATCGATT
1 TAAGACCTCCGAGCATAATTTTGATTCGCG-GTGTTATCTCGATCGATT
12449445 TATTATTTTT
Statistics
Matches: 113, Mismatches: 21, Indels: 3
0.82 0.15 0.02
Matches are distributed among these distances:
86 9 0.08
87 88 0.78
88 16 0.14
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.41
Consensus pattern (87 bp):
TAAGACCTCCGAGCATAATTTTGATTCGCGGTGTTATCTCGATCGATTCCTTATCTTTTGACTAC
GATGTTATCTCAGTCGATTCTG
Found at i:12449646 original size:14 final size:14
Alignment explanation
Indices: 12449627--12449665 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
12449617 ATATTATACG
12449627 AAATACAAAAAAAT
1 AAATACAAAAAAAT
*
12449641 AAATACCAAAAAAT
1 AAATACAAAAAAAT
12449655 -AATACAAAAAA
1 AAATACAAAAAA
12449666 TAGCAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.77, C:0.10, G:0.00, T:0.13
Consensus pattern (14 bp):
AAATACAAAAAAAT
Found at i:12449685 original size:22 final size:21
Alignment explanation
Indices: 12449633--12449685 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 21
12449623 TACGAAATAC
*
12449633 AAAAAAATAAATACCAAAAAAT
1 AAAAAAA-AAATACAAAAAAAT
*
12449655 AATACAAAAAATAGCAAAAAAAT
1 AA-AAAAAAAATA-CAAAAAAAT
12449678 AAAAAAAA
1 AAAAAAAA
12449686 GAAAAATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 12 0.46
23 14 0.54
ACGTcount: A:0.79, C:0.08, G:0.02, T:0.11
Consensus pattern (21 bp):
AAAAAAAAAATACAAAAAAAT
Found at i:12451052 original size:16 final size:16
Alignment explanation
Indices: 12451033--12451179 Score: 121
Period size: 16 Copynumber: 9.5 Consensus size: 16
12451023 CTAGGTTTCT
12451033 AAAACCCCTAAAATCC
1 AAAACCCCTAAAATCC
*
12451049 AAAACCTCATAAAATCC
1 AAAACC-CCTAAAATCC
*
12451066 -AAACCCCTAAAAATCT
1 AAAACCCCT-AAAATCC
* *
12451082 AAAATCCCTTAAATCC
1 AAAACCCCTAAAATCC
* *
12451098 -AAACTCCTAAAATTC
1 AAAACCCCTAAAATCC
*
12451113 TAAACCCAC-AAAATCC
1 AAAACCC-CTAAAATCC
12451129 --AACCCCTAAAATCC
1 AAAACCCCTAAAATCC
* **
12451143 AAAATCTTTAAAATCC
1 AAAACCCCTAAAATCC
12451159 -AAA-CCCTAAAAT-C
1 AAAACCCCTAAAATCC
12451172 AAAACCCC
1 AAAACCCC
12451180 AAACCCTAAA
Statistics
Matches: 104, Mismatches: 17, Indels: 21
0.73 0.12 0.15
Matches are distributed among these distances:
13 2 0.02
14 22 0.21
15 19 0.18
16 44 0.42
17 17 0.16
ACGTcount: A:0.49, C:0.33, G:0.00, T:0.18
Consensus pattern (16 bp):
AAAACCCCTAAAATCC
Found at i:12451156 original size:30 final size:31
Alignment explanation
Indices: 12451034--12451178 Score: 154
Period size: 30 Copynumber: 4.7 Consensus size: 31
12451024 TAGGTTTCTA
12451034 AAACCCCTAAAATCCAAAACCTCATAAAATCC
1 AAACCCCTAAAATCCAAAACC-CATAAAATCC
* *
12451066 AAACCCCTAAAAATCTAAAATCCC-TTAAATCC
1 AAACCCCT-AAAATCCAAAA-CCCATAAAATCC
* * * *
12451098 AAACTCCTAAAATTCTAAACCCACAAAATCC
1 AAACCCCTAAAATCCAAAACCCATAAAATCC
* **
12451129 -AACCCCTAAAATCCAAAATCTTTAAAATCC
1 AAACCCCTAAAATCCAAAACCCATAAAATCC
12451159 AAA-CCCTAAAAT-CAAAACCC
1 AAACCCCTAAAATCCAAAACCC
12451179 CAAACCCTAA
Statistics
Matches: 92, Mismatches: 17, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
29 6 0.07
30 35 0.38
31 16 0.17
32 22 0.24
33 11 0.12
34 2 0.02
ACGTcount: A:0.49, C:0.32, G:0.00, T:0.19
Consensus pattern (31 bp):
AAACCCCTAAAATCCAAAACCCATAAAATCC
Found at i:12451194 original size:14 final size:14
Alignment explanation
Indices: 12451172--12451232 Score: 59
Period size: 14 Copynumber: 4.2 Consensus size: 14
12451162 CCCTAAAATC
12451172 AAAACCCCAAACCCT
1 AAAA-CCCAAACCCT
*
12451187 AAAACCCAAACCTT
1 AAAACCCAAACCCT
* *
12451201 AAATCACCAAACTCT
1 AAAAC-CCAAACCCT
* *
12451216 AAAATCAAAACCCT
1 AAAACCCAAACCCT
12451230 AAA
1 AAA
12451233 CCTTCCATAT
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
14 23 0.62
15 14 0.38
ACGTcount: A:0.52, C:0.34, G:0.00, T:0.13
Consensus pattern (14 bp):
AAAACCCAAACCCT
Found at i:12451197 original size:21 final size:21
Alignment explanation
Indices: 12451157--12451198 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
12451147 TCTTTAAAAT
*
12451157 CCAAACCCTAAAATCAAAACC
1 CCAAACCCTAAAACCAAAACC
*
12451178 CCAAACCCTAAAACCCAAACC
1 CCAAACCCTAAAACCAAAACC
12451199 TTAAATCACC
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:0.50, C:0.43, G:0.00, T:0.07
Consensus pattern (21 bp):
CCAAACCCTAAAACCAAAACC
Found at i:12453079 original size:23 final size:23
Alignment explanation
Indices: 12453049--12453100 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
12453039 TTAATTATAC
12453049 AAAAAATACTAAA-AAACAAACA-T
1 AAAAAATA-TAAATAAA-AAACACT
*
12453072 AAAAAATATAAATAAAAAATACT
1 AAAAAATATAAATAAAAAACACT
12453095 AAAAAA
1 AAAAAA
12453101 AGGAAACGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 8 0.31
23 18 0.69
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (23 bp):
AAAAAATATAAATAAAAAACACT
Found at i:12453091 original size:13 final size:14
Alignment explanation
Indices: 12453070--12453101 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
12453060 AAAAACAAAC
12453070 ATAAAAAATA-TAA
1 ATAAAAAATACTAA
12453083 ATAAAAAATACTAA
1 ATAAAAAATACTAA
12453097 A-AAAA
1 ATAAAA
12453102 GGAAACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (14 bp):
ATAAAAAATACTAA
Found at i:12454299 original size:42 final size:42
Alignment explanation
Indices: 12454201--12454370 Score: 211
Period size: 42 Copynumber: 4.0 Consensus size: 42
12454191 ACAAAGTTCC
* * ** * *
12454201 TCTAAACAGAGGCTCAATGACTTTTG-AAAATAAATTAAGCTCC
1 TCTAAACAGAGGCACCACAACTTTTGAAAAATAAA--ATGCTCT
12454244 TCTAAACAGAGGCACCACAACTTTTGAAAAATAAAATGCTCT
1 TCTAAACAGAGGCACCACAACTTTTGAAAAATAAAATGCTCT
* *
12454286 TCTAAATAGAGGCACCAAAACTTTTGAAAAATAAAATGCT-T
1 TCTAAACAGAGGCACCACAACTTTTGAAAAATAAAATGCTCT
*
12454327 CTCTAAACAGAGGCACCACAAC-TTTGAAAAATAAAATACTCT
1 -TCTAAACAGAGGCACCACAACTTTTGAAAAATAAAATGCTCT
12454369 TC
1 TC
12454371 GACAATCATG
Statistics
Matches: 113, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
41 20 0.18
42 63 0.56
43 22 0.19
44 8 0.07
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.25
Consensus pattern (42 bp):
TCTAAACAGAGGCACCACAACTTTTGAAAAATAAAATGCTCT
Found at i:12454769 original size:43 final size:43
Alignment explanation
Indices: 12454712--12454832 Score: 179
Period size: 43 Copynumber: 2.8 Consensus size: 43
12454702 TTGTTTAAAT
*
12454712 TTTTAGAGATTCACATCCAAAAGTTCAAGCTTTTTCATTCAAA
1 TTTTGGAGATTCACATCCAAAAGTTCAAGCTTTTTCATTCAAA
** * *
12454755 TTTTGGAGATTCACATTAAAAAATTCAAGCTTTTTCATTCGAA
1 TTTTGGAGATTCACATCCAAAAGTTCAAGCTTTTTCATTCAAA
* *
12454798 TTTTGAAGATTCACATCCAAAAGTTTAAGCTTTTT
1 TTTTGGAGATTCACATCCAAAAGTTCAAGCTTTTT
12454833 TGAATTGAAA
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 68 1.00
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.40
Consensus pattern (43 bp):
TTTTGGAGATTCACATCCAAAAGTTCAAGCTTTTTCATTCAAA
Found at i:12454920 original size:25 final size:24
Alignment explanation
Indices: 12454892--12455206 Score: 269
Period size: 25 Copynumber: 13.3 Consensus size: 24
12454882 TCTCAAAGGA
* *
12454892 TCTCATTTGAATTCTTCTTAAAGAT
1 TCTCATTTGAAAT-GTCTTAAAGAT
12454917 TCTCATTTGAAAATGTCTTAAAGAT
1 TCTCATTTG-AAATGTCTTAAAGAT
* *
12454942 TTTCATTTGAAAATATCTTAAAGAT
1 TCTCATTTG-AAATGTCTTAAAGAT
* *
12454967 TCTCATTT--AA-GACTCAAAGAT
1 TCTCATTTGAAATGTCTTAAAGAT
12454988 TCTCATTTGAAAATGTCTTAAAGAT
1 TCTCATTTG-AAATGTCTTAAAGAT
**
12455013 TCTCATTTGAAAACATCTTAAAGAT
1 TCTCATTTG-AAATGTCTTAAAGAT
* *
12455038 TCTCATTTAAAAACGTCTTAAAGAT
1 TCTCATTT-GAAATGTCTTAAAGAT
*
12455063 TCTTATTT-AAGAT-TC--AAAGAT
1 TCTCATTTGAA-ATGTCTTAAAGAT
*
12455084 TCTTATTTGAAATGTCTTAAAGAT
1 TCTCATTTGAAATGTCTTAAAGAT
* * *
12455108 TCTCA-TT-CAA-GACTTAACGAT
1 TCTCATTTGAAATGTCTTAAAGAT
*
12455129 TCTTATTTGAAAATGTCTTAAAGAT
1 TCTCATTTG-AAATGTCTTAAAGAT
* ** *
12455154 TCTCATTT--AA-GACTCGAAGGT
1 TCTCATTTGAAATGTCTTAAAGAT
* *
12455175 TTTCATGTGAAATGTCTTAAAGAT
1 TCTCATTTGAAATGTCTTAAAGAT
12455199 TCTCATTT
1 TCTCATTT
12455207 AAGACTCAAA
Statistics
Matches: 235, Mismatches: 37, Indels: 37
0.76 0.12 0.12
Matches are distributed among these distances:
21 58 0.25
22 12 0.05
23 8 0.03
24 28 0.12
25 126 0.54
26 3 0.01
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.41
Consensus pattern (24 bp):
TCTCATTTGAAATGTCTTAAAGAT
Found at i:12454989 original size:71 final size:71
Alignment explanation
Indices: 12454911--12455161 Score: 332
Period size: 71 Copynumber: 3.5 Consensus size: 71
12454901 AATTCTTCTT
*
12454911 AAAGATTCTCATTTGAAAATGTCTTAAAGATTTTCATTTGAAAATATCTTAAAGATTCTCATTTA
1 AAAGATTCTCATTTGAAAATGTCTTAAAGATTCTCATTTGAAAATATCTTAAAGATTCTCATTTA
12454976 AGACTC
66 AGACTC
*
12454982 AAAGATTCTCATTTGAAAATGTCTTAAAGATTCTCATTTGAAAACATCTTAAAGATTCTCATTTA
1 AAAGATTCTCATTTGAAAATGTCTTAAAGATTCTCATTTGAAAATATCTTAAAGATTCTCATTT-
*
12455047 AAAACGTC
65 AAGAC-TC
* * * *
12455055 TTAAAGATTCTTATTT-AAGAT-TC--AAAGATTCTTATTTG-AAATGTCTTAAAGATTCTCATT
1 --AAAGATTCTCATTTGAAAATGTCTTAAAGATTCTCATTTGAAAATATCTTAAAGATTCTCATT
* *
12455115 CAAGACTT
64 TAAGACTC
* *
12455123 AACGATTCTTATTTGAAAATGTCTTAAAGATTCTCATTT
1 AAAGATTCTCATTTGAAAATGTCTTAAAGATTCTCATTT
12455162 AAGACTCGAA
Statistics
Matches: 158, Mismatches: 14, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
66 13 0.08
67 4 0.03
68 3 0.02
69 4 0.03
70 33 0.21
71 76 0.48
72 4 0.03
73 4 0.03
74 4 0.03
75 13 0.08
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (71 bp):
AAAGATTCTCATTTGAAAATGTCTTAAAGATTCTCATTTGAAAATATCTTAAAGATTCTCATTTA
AGACTC
Found at i:12454998 original size:96 final size:94
Alignment explanation
Indices: 12454883--12455206 Score: 406
Period size: 96 Copynumber: 3.4 Consensus size: 94
12454873 CATCTAAAAT
* *
12454883 CTCAAAGGA-TCTCATTTGAATTCTTCTTAAAGATTCTCATTTGAAAATGTCTTAAAGATTTTCA
1 CTCAAA-GATTCTCATTTGAAAT-GTCTTAAAGATTCTCATTTGAAAA-GTCTTAAAGATTTTCA
*
12454947 TTTGAAAATATCTTAAAGATTCTCATTTAAGA
63 TTTGAAAATGTCTTAAAGATTCTCATTTAAGA
* *
12454979 CTCAAAGATTCTCATTTGAAAATGTCTTAAAGATTCTCATTTGAAAACATCTTAAAGATTCTCAT
1 CTCAAAGATTCTCATTTG-AAATGTCTTAAAGATTCTCATTTGAAAA-GTCTTAAAGATTTTCAT
* * *
12455044 TTAAAAACGTCTTAAAGATTCTTATTTAAGA
64 TTGAAAATGTCTTAAAGATTCTCATTTAAGA
* * * * *
12455075 TTCAAAGATTCTTATTTGAAATGTCTTAAAGATTCTCA-TT--CAAGACTTAACGATTCTT-ATT
1 CTCAAAGATTCTCATTTGAAATGTCTTAAAGATTCTCATTTGAAAAGTCTTAAAGATT-TTCATT
12455136 TGAAAATGTCTTAAAGATTCTCATTTAAGA
65 TGAAAATGTCTTAAAGATTCTCATTTAAGA
* * * *
12455166 CTCGAAGGTTTTCATGTGAAATGTCTTAAAGATTCTCATTT
1 CTCAAAGATTCTCATTTGAAATGTCTTAAAGATTCTCATTT
12455207 AAGACTCAAA
Statistics
Matches: 199, Mismatches: 25, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
91 71 0.36
92 5 0.03
94 2 0.01
95 22 0.11
96 96 0.48
97 3 0.02
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (94 bp):
CTCAAAGATTCTCATTTGAAATGTCTTAAAGATTCTCATTTGAAAAGTCTTAAAGATTTTCATTT
GAAAATGTCTTAAAGATTCTCATTTAAGA
Found at i:12455007 original size:46 final size:46
Alignment explanation
Indices: 12454907--12455226 Score: 383
Period size: 46 Copynumber: 6.8 Consensus size: 46
12454897 TTTGAATTCT
* * * *
12454907 TCTTAAAGATTCTCATTTGAAAATGTCTTAAAGATTTTCATTTGAAAATA
1 TCTTAAAGATTCTCATTT---AA-GACTCAAAGATTCTCATTTGAAAATG
12454957 TCTTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAATG
1 TCTTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAATG
* * *
12455003 TCTTAAAGATTCTCATTTGAAAACATCTTAAAGATTCTCATTTAAAAACG
1 TCTTAAAGATTCTCATTT-AAGAC-TC--AAAGATTCTCATTTGAAAATG
* * *
12455053 TCTTAAAGATTCTTATTTAAGATTCAAAGATTCTTATTTG-AAATG
1 TCTTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAATG
* * * *
12455098 TCTTAAAGATTCTCATTCAAGACTTAACGATTCTTATTTGAAAATG
1 TCTTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAATG
* * * *
12455144 TCTTAAAGATTCTCATTTAAGACTCGAAGGTTTTCATGTG-AAATG
1 TCTTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAATG
*
12455189 TCTTAAAGATTCTCATTTAAGACTCAAAGGTTCTCATT
1 TCTTAAAGATTCTCATTTAAGACTCAAAGATTCTCATT
12455227 CAACAAATCT
Statistics
Matches: 236, Mismatches: 29, Indels: 15
0.84 0.10 0.05
Matches are distributed among these distances:
45 79 0.33
46 90 0.38
47 6 0.03
48 4 0.02
49 3 0.01
50 54 0.23
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (46 bp):
TCTTAAAGATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAATG
Found at i:12455642 original size:61 final size:64
Alignment explanation
Indices: 12455564--12455718 Score: 185
Period size: 63 Copynumber: 2.5 Consensus size: 64
12455554 TAAGCTTCTT
* * * *
12455564 AACACTAGCCATCTCAGAAT-AATTCTATCT-TCTATCACTTGAT-ATCACTCATATGTTTATC
1 AACACTAGCCATTTCAGAATAAATTCTATCTCTCCATCACTTGATCACCACTCATAGGTTTATC
* * *
12455625 AGCACTAGCCATTTCAGAATAAATT-TCAT-TCTCCATCACTTGGTCACCACTCATAGGTTTCTC
1 AACACTAGCCATTTCAGAATAAATTCT-ATCTCTCCATCACTTGATCACCACTCATAGGTTTATC
* *
12455688 AACTCTAGCCATTTTAGAATAAATTCTATCT
1 AACACTAGCCATTTCAGAATAAATTCTATCT
12455719 ATTGATCCAT
Statistics
Matches: 78, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
61 20 0.26
62 17 0.22
63 39 0.50
64 2 0.03
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.36
Consensus pattern (64 bp):
AACACTAGCCATTTCAGAATAAATTCTATCTCTCCATCACTTGATCACCACTCATAGGTTTATC
Found at i:12456180 original size:15 final size:16
Alignment explanation
Indices: 12456152--12456184 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
12456142 ATTGAGATGT
12456152 ATGATATATCCAAACA
1 ATGATATATCCAAACA
*
12456168 ATGA-ATATTCAAACA
1 ATGATATATCCAAACA
12456183 AT
1 AT
12456185 TATAAACATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.52, C:0.15, G:0.06, T:0.27
Consensus pattern (16 bp):
ATGATATATCCAAACA
Found at i:12456427 original size:30 final size:30
Alignment explanation
Indices: 12456386--12456442 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
12456376 TGAGTATTTC
12456386 TTTTCCTTTTTTTCCTATTTTTTTCATTAT
1 TTTTCCTTTTTTTCCTATTTTTTTCATTAT
* *
12456416 TTTTTCTTTTTTTCCTTTTTTTTTCAT
1 TTTTCCTTTTTTTCCTATTTTTTTCAT
12456443 CCATTATTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (30 bp):
TTTTCCTTTTTTTCCTATTTTTTTCATTAT
Found at i:12456428 original size:8 final size:9
Alignment explanation
Indices: 12456386--12456437 Score: 59
Period size: 9 Copynumber: 5.4 Consensus size: 9
12456376 TGAGTATTTC
12456386 TTTTCCTTT
1 TTTTCCTTT
12456395 TTTTCCTATTT
1 TTTTCC--TTT
*
12456406 TTTTCATTAT
1 TTTTCCTT-T
*
12456416 TTTTTCTTT
1 TTTTCCTTT
12456425 TTTTCCTTT
1 TTTTCCTTT
12456434 TTTT
1 TTTT
12456438 TTCATCCATT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
9 21 0.58
10 7 0.19
11 8 0.22
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTCCTTT
Found at i:12459297 original size:72 final size:72
Alignment explanation
Indices: 12459221--12459361 Score: 221
Period size: 72 Copynumber: 2.0 Consensus size: 72
12459211 AATGTTACAT
* * *
12459221 ATGACAATGAAAATGATGTATGGCATGATAATGCAAATGCATAGAGTCAA-ACAAACAAAATGGT
1 ATGACAATGAAAATGATGCATGGCATAATAATGCAAATGCATAGAGTCAATA-AAACAAAATAGT
12459285 TAGATAAC
65 TAGATAAC
* *
12459293 ATGACAATGAAAATGATGCATGGCATAATAATGTAAATGCATAGAGTCAATAAAACAAATTAGTT
1 ATGACAATGAAAATGATGCATGGCATAATAATGCAAATGCATAGAGTCAATAAAACAAAATAGTT
12459358 AGAT
66 AGAT
12459362 CATAAACCAT
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
72 62 0.98
73 1 0.02
ACGTcount: A:0.48, C:0.10, G:0.18, T:0.24
Consensus pattern (72 bp):
ATGACAATGAAAATGATGCATGGCATAATAATGCAAATGCATAGAGTCAATAAAACAAAATAGTT
AGATAAC
Found at i:12460329 original size:16 final size:16
Alignment explanation
Indices: 12460297--12460334 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
12460287 ATCAGAAAGA
12460297 TTTTTGTCAATTTTATT
1 TTTTTGTC-ATTTTATT
12460314 TTTTTGTC-TTTCTATT
1 TTTTTGTCATTT-TATT
12460330 TTTTT
1 TTTTT
12460335 ATCCAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 3 0.15
16 9 0.45
17 8 0.40
ACGTcount: A:0.11, C:0.08, G:0.05, T:0.76
Consensus pattern (16 bp):
TTTTTGTCATTTTATT
Found at i:12460598 original size:14 final size:15
Alignment explanation
Indices: 12460579--12460608 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
12460569 AATATTTTAT
12460579 TTATTTATTT-ATTA
1 TTATTTATTTAATTA
12460593 TTATTTATTTAATTA
1 TTATTTATTTAATTA
12460608 T
1 T
12460609 ACAAAATTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTATTTATTTAATTA
Found at i:12460598 original size:18 final size:17
Alignment explanation
Indices: 12460571--12460608 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
12460561 TCAACCTAAA
*
12460571 TATTTTATTTATTTATT
1 TATTTTATTTATTTAAT
12460588 TATTATTATTTATTTAAT
1 TATT-TTATTTATTTAAT
12460606 TAT
1 TAT
12460609 ACAAAATTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTTTATTTATTTAAT
Found at i:12460659 original size:19 final size:19
Alignment explanation
Indices: 12460635--12460678 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
12460625 ACAAACACAT
*
12460635 AAAAAA-ATAAATAATACCA
1 AAAAAACATAAAAAATA-CA
*
12460654 AAAAAACCTAAAAAATACA
1 AAAAAACATAAAAAATACA
12460673 AAAAAA
1 AAAAAA
12460679 TGAAACAGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.77, C:0.11, G:0.00, T:0.11
Consensus pattern (19 bp):
AAAAAACATAAAAAATACA
Found at i:12461512 original size:12 final size:12
Alignment explanation
Indices: 12461484--12461523 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
12461474 ATTATCTCCT
*
12461484 AAAATGAAAA-A
1 AAAATCAAAATA
*
12461495 AAAATCAAAATC
1 AAAATCAAAATA
12461507 AAAATCAAAATA
1 AAAATCAAAATA
12461519 AAAAT
1 AAAAT
12461524 AAAGAAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.75, C:0.07, G:0.03, T:0.15
Consensus pattern (12 bp):
AAAATCAAAATA
Found at i:12468662 original size:13 final size:13
Alignment explanation
Indices: 12468637--12468670 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
12468627 GATTTTGCCC
12468637 ACTTTTCTTTCTTT
1 ACTTTT-TTTCTTT
*
12468651 TCTTTTTTTCTTT
1 ACTTTTTTTCTTT
12468664 ACTTTTT
1 ACTTTTT
12468671 CACCACTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (13 bp):
ACTTTTTTTCTTT
Found at i:12485685 original size:19 final size:19
Alignment explanation
Indices: 12485663--12485701 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
12485653 TAAGAATACC
*
12485663 AAATCCTAATCCATATAGG
1 AAATCCAAATCCATATAGG
* *
12485682 AAATTCAAATCCATGTAGG
1 AAATCCAAATCCATATAGG
12485701 A
1 A
12485702 TAAGTAATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.26
Consensus pattern (19 bp):
AAATCCAAATCCATATAGG
Found at i:12486463 original size:2 final size:2
Alignment explanation
Indices: 12486456--12486480 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12486446 ATCCCTCTTC
12486456 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 A
12486481 CAAGGTGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12486835 original size:2 final size:2
Alignment explanation
Indices: 12486828--12486858 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12486818 TCTCGTAGAA
12486828 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 A
12486859 CATACCTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12493913 original size:21 final size:21
Alignment explanation
Indices: 12493854--12493915 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
12493844 TTATTAAATA
*
12493854 TTTG-TAACTTATGGGTATAAT
1 TTTGATAACTTAT-GATATAAT
* * *
12493875 TTTTATAAAATT-TAATATAAT
1 TTTGAT-AACTTATGATATAAT
12493896 TTTGATAACTTATGATATAA
1 TTTGATAACTTATGATATAA
12493916 AACCTAATCT
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
20 4 0.13
21 21 0.68
22 2 0.06
23 4 0.13
ACGTcount: A:0.39, C:0.03, G:0.10, T:0.48
Consensus pattern (21 bp):
TTTGATAACTTATGATATAAT
Found at i:12494070 original size:21 final size:20
Alignment explanation
Indices: 12493971--12494078 Score: 76
Period size: 21 Copynumber: 5.2 Consensus size: 20
12493961 TCGTGGAATT
* * *
12493971 AATTTTGGGAATCATTCATA
1 AATTTTGGTAATCTTTGATA
*
12493991 TAATTTTGGTAATCTTTAATA
1 -AATTTTGGTAATCTTTGATA
* *
12494012 GAATTTTGATAA-CTATGGATA
1 -AATTTTGGTAATCT-TTGATA
*
12494033 AA-TTTGGATAATATTTGATA
1 AATTTTGG-TAATCTTTGATA
*
12494053 CAATTTTGGTAACCTTTGATA
1 -AATTTTGGTAATCTTTGATA
12494074 TAATT
1 -AATT
12494079 CTGATTTTAA
Statistics
Matches: 69, Mismatches: 13, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
19 4 0.06
20 12 0.17
21 48 0.70
22 5 0.07
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.44
Consensus pattern (20 bp):
AATTTTGGTAATCTTTGATA
Found at i:12494127 original size:20 final size:20
Alignment explanation
Indices: 12494104--12494237 Score: 69
Period size: 21 Copynumber: 6.6 Consensus size: 20
12494094 TTTCATATAA
*
12494104 TTTGGTAACATTATTAAAAG
1 TTTGGTAACATTATTAAAAT
* * *
12494124 TTTGATAAC-TTTTGATAAAAG
1 TTTGGTAACATTAT--TAAAAT
* *
12494145 TTTGATAATATT-TTATACAAT
1 TTTGGTAACATTATTA-A-AAT
* * **
12494166 TTTAGTAACATTAGATATTAT
1 TTTGGTAACATTA-TTAAAAT
* *
12494187 TTTGATAAC-TTATTATAAT
1 TTTGGTAACATTATTAAAAT
*
12494206 TTTGGTAACCATTA-TATAAT
1 TTTGGTAA-CATTATTAAAAT
12494226 TTTGGTAACATT
1 TTTGGTAACATT
12494238 TTACAAAAGT
Statistics
Matches: 90, Mismatches: 15, Indels: 19
0.73 0.12 0.15
Matches are distributed among these distances:
19 21 0.23
20 27 0.30
21 38 0.42
22 2 0.02
23 2 0.02
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (20 bp):
TTTGGTAACATTATTAAAAT
Found at i:12494164 original size:109 final size:110
Alignment explanation
Indices: 12493985--12494192 Score: 269
Period size: 109 Copynumber: 1.9 Consensus size: 110
12493975 TTGGGAATCA
* * *
12493985 TTCATATAATTTTGGTAATCTTTAATAGAATTTTGATAACTATGGATAAATTTGGATAATATTTG
1 TTCATATAATTTTGGTAATCATTAATAAAAGTTTGATAACTATGGATAAATTTGGATAATATTTG
* * *
12494050 ATACAATTTTGGTAACCTTTGATATAATTCTGATTTTAATAACCT
66 ATACAATTTTAGTAACATTAGATATAATTCTGATTTTAATAACCT
* * *
12494095 TTCATATAA-TTTGGTAA-CATTATTAAAAGTTTGATAACTTTTGATAAAAGTTT-GATAATATT
1 TTCATATAATTTTGGTAATCATTAATAAAAGTTTGATAACTATGGAT-AAA-TTTGGATAATATT
* * *
12494157 TTATACAATTTTAGTAACATTAGATATTATTTTGAT
64 TGATACAATTTTAGTAACATTAGATATAATTCTGAT
12494193 AACTTATTAT
Statistics
Matches: 84, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
108 22 0.26
109 50 0.60
110 12 0.14
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.46
Consensus pattern (110 bp):
TTCATATAATTTTGGTAATCATTAATAAAAGTTTGATAACTATGGATAAATTTGGATAATATTTG
ATACAATTTTAGTAACATTAGATATAATTCTGATTTTAATAACCT
Found at i:12494209 original size:19 final size:19
Alignment explanation
Indices: 12494157--12494237 Score: 83
Period size: 19 Copynumber: 4.1 Consensus size: 19
12494147 TGATAATATT
* *
12494157 TTATACAATTTTAGTAACA
1 TTATATAATTTTGGTAACA
* *
12494176 TTAGATATTATTTTGATAAC-
1 TT--ATATAATTTTGGTAACA
12494196 TTATTATAATTTTGGTAACCA
1 TTA-TATAATTTTGGTAA-CA
12494217 TTATATAATTTTGGTAACA
1 TTATATAATTTTGGTAACA
12494236 TT
1 TT
12494238 TTACAAAAGT
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
18 1 0.02
19 18 0.35
20 17 0.33
21 15 0.29
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.48
Consensus pattern (19 bp):
TTATATAATTTTGGTAACA
Found at i:12494221 original size:18 final size:20
Alignment explanation
Indices: 12494157--12494234 Score: 72
Period size: 20 Copynumber: 3.9 Consensus size: 20
12494147 TGATAATATT
* *
12494157 TTATACAATTTTAGTAA-CA
1 TTATATAATTTTGGTAACCA
* *
12494176 TTAGATATTATTTTGATAA-C-
1 TT--ATATAATTTTGGTAACCA
12494196 TTATTATAATTTTGGTAACCA
1 TTA-TATAATTTTGGTAACCA
12494217 TTATATAATTTTGGTAAC
1 TTATATAATTTTGGTAAC
12494235 ATTTTACAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
18 1 0.02
19 14 0.29
20 18 0.38
21 15 0.31
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.47
Consensus pattern (20 bp):
TTATATAATTTTGGTAACCA
Found at i:12494462 original size:21 final size:19
Alignment explanation
Indices: 12494416--12494462 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 19
12494406 CTTCTAATAT
12494416 AATTTTAAAATTTTAGATA
1 AATTTTAAAATTTTAGATA
12494435 AAGTTTTAATAATCTTT-GATA
1 AA-TTTTAA-AAT-TTTAGATA
12494456 CAATTTT
1 -AATTTT
12494463 GGTAGCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
19 2 0.08
20 6 0.25
21 11 0.46
22 5 0.21
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.49
Consensus pattern (19 bp):
AATTTTAAAATTTTAGATA
Found at i:12494463 original size:11 final size:10
Alignment explanation
Indices: 12494423--12494561 Score: 70
Period size: 10 Copynumber: 13.3 Consensus size: 10
12494413 TATAATTTTA
12494423 AAATTTTAGAT
1 AAATTTT-GAT
*
12494434 AAAGTTTTAAT
1 AAA-TTTTGAT
12494445 -AATCTTTGAT
1 AAAT-TTTGAT
*
12494455 ACAATTTTGGT
1 A-AATTTTGAT
**
12494466 AGCTTTTGAT
1 AAATTTTGAT
12494476 ATAATTTCT-AT
1 A-AATTT-TGAT
12494487 -AATTTATGAT
1 AAATTT-TGAT
*
12494497 ATAATTTTGGT
1 A-AATTTTGAT
*
12494508 AACTTTTGAT
1 AAATTTTGAT
*
12494518 AGAATTTTGGT
1 A-AATTTTGAT
*
12494529 AACA-TTAGAT
1 AA-ATTTTGAT
12494539 AAATTTTGAT
1 AAATTTTGAT
* *
12494549 AACTTTTAAT
1 AAATTTTGAT
12494559 AAA
1 AAA
12494562 ATATTTCTAA
Statistics
Matches: 96, Mismatches: 20, Indels: 25
0.68 0.14 0.18
Matches are distributed among these distances:
9 8 0.08
10 46 0.48
11 29 0.30
12 13 0.14
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.47
Consensus pattern (10 bp):
AAATTTTGAT
Found at i:12494473 original size:21 final size:21
Alignment explanation
Indices: 12494449--12494590 Score: 114
Period size: 21 Copynumber: 6.8 Consensus size: 21
12494439 TTTAATAATC
* *
12494449 TTTGATACAATTTTGGTAGCT
1 TTTGATATAATTTTGGTAACT
*
12494470 TTTGATATAATTTCT-ATAA-T
1 TTTGATATAATTT-TGGTAACT
12494490 TTATGATATAATTTTGGTAACT
1 TT-TGATATAATTTTGGTAACT
* *
12494512 TTTGATAGAATTTTGGTAACA
1 TTTGATATAATTTTGGTAACT
* *
12494533 TTAGATA-AATTTTGATAACT
1 TTTGATATAATTTTGGTAACT
* * *
12494553 TTTAATAAAATATTT-CTAA-T
1 TTTGATATAAT-TTTGGTAACT
*
12494573 GTTTGATAGAATTTTGGT
1 -TTTGATATAATTTTGGT
12494591 GTGTATATGA
Statistics
Matches: 98, Mismatches: 15, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
20 24 0.24
21 67 0.68
22 7 0.07
ACGTcount: A:0.33, C:0.05, G:0.13, T:0.49
Consensus pattern (21 bp):
TTTGATATAATTTTGGTAACT
Found at i:12494497 original size:42 final size:42
Alignment explanation
Indices: 12494443--12494590 Score: 126
Period size: 42 Copynumber: 3.5 Consensus size: 42
12494433 TAAAGTTTTA
* *
12494443 ATAATCTTTGATACAATTTTGGTAGCTTTTGATATAATTTCT
1 ATAATCTTTGATACAATTTTGGTAACTTTTGATAGAATTTCT
*
12494485 ATAAT-TTATGATATAATTTTGGTAACTTTTGATAGAATTT-T
1 ATAATCTT-TGATACAATTTTGGTAACTTTTGATAGAATTTCT
* * * * *
12494526 GGTAA-CATTAGATA-AATTTTGATAACTTTTAATAAAATATT-T
1 -ATAATC-TTTGATACAATTTTGGTAACTTTTGATAGAAT-TTCT
* * *
12494568 CTAATGTTTGATAGAATTTTGGT
1 ATAATCTTTGATACAATTTTGGT
12494591 GTGTATATGA
Statistics
Matches: 87, Mismatches: 12, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
41 33 0.38
42 52 0.60
43 2 0.02
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.48
Consensus pattern (42 bp):
ATAATCTTTGATACAATTTTGGTAACTTTTGATAGAATTTCT
Found at i:12495500 original size:34 final size:34
Alignment explanation
Indices: 12495457--12495541 Score: 107
Period size: 34 Copynumber: 2.5 Consensus size: 34
12495447 TAGTTACCAG
* *
12495457 AAATTCATTTTAGGAAACTTCTTCAATGTAACAT
1 AAATTCATTTTAGAAAACTTCTTCAATGTAACAA
* * *
12495491 AAATTCATTTTTGAAAACTTCTTGAATGTACCAA
1 AAATTCATTTTAGAAAACTTCTTCAATGTAACAA
*
12495525 AAATGCATTTCTAGAAA
1 AAATTCATTT-TAGAAA
12495542 GCAATGCAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
34 38 0.88
35 5 0.12
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.36
Consensus pattern (34 bp):
AAATTCATTTTAGAAAACTTCTTCAATGTAACAA
Found at i:12496019 original size:34 final size:34
Alignment explanation
Indices: 12495960--12496026 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
12495950 TGGATGTCCA
* * *
12495960 AAAATCCATTTCCAAAATTTTTTAAAGGTTTCCT
1 AAAATCCACTTCCAAAAGTTCTTAAAGGTTTCCT
*
12495994 AAAATCCACTTCCGAAAGTTCTTAAAGGTTTCC
1 AAAATCCACTTCCAAAAGTTCTTAAAGGTTTCC
12496027 CGAAATAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (34 bp):
AAAATCCACTTCCAAAAGTTCTTAAAGGTTTCCT
Found at i:12497078 original size:33 final size:33
Alignment explanation
Indices: 12497040--12497106 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
12497030 AATTGGATTA
12497040 TTATTATTTATTATATGTACTAATCCTCTTAAT
1 TTATTATTTATTATATGTACTAATCCTCTTAAT
*
12497073 TTATTATTTGTTATATGTACTAATCCTCTTAAT
1 TTATTATTTATTATATGTACTAATCCTCTTAAT
12497106 T
1 T
12497107 ACCCTACAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.28, C:0.12, G:0.04, T:0.55
Consensus pattern (33 bp):
TTATTATTTATTATATGTACTAATCCTCTTAAT
Found at i:12501555 original size:4 final size:4
Alignment explanation
Indices: 12501546--12501615 Score: 96
Period size: 4 Copynumber: 18.8 Consensus size: 4
12501536 GTAAACACCA
12501546 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA- TTA-
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
*
12501592 TTA- TTA- TTA- TTAT ATAT TTAT TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT TTA
12501616 ATTTTTTTTC
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
3 15 0.24
4 48 0.76
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:12502101 original size:19 final size:20
Alignment explanation
Indices: 12502058--12502101 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
12502048 ATACACTTAC
12502058 AAAAACACACAAAAAAAACCA
1 AAAAACACACAAAAAAAA-CA
* *
12502079 AAAAACACATAAAAAAAAGA
1 AAAAACACACAAAAAAAACA
12502099 AAA
1 AAA
12502102 TTTTTTTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.80, C:0.16, G:0.02, T:0.02
Consensus pattern (20 bp):
AAAAACACACAAAAAAAACA
Found at i:12502965 original size:18 final size:18
Alignment explanation
Indices: 12502924--12502968 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
12502914 TCTTTTTGTT
*
12502924 AGTAATAAATAAAAATTG
1 AGTAATAAATAAAAATTA
*
12502942 ATTAATATAATAAAAA-TA
1 AGTAATA-AATAAAAATTA
12502960 AGTAATAAA
1 AGTAATAAA
12502969 AATGAAAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 2 0.09
18 13 0.57
19 8 0.35
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (18 bp):
AGTAATAAATAAAAATTA
Found at i:12503161 original size:13 final size:15
Alignment explanation
Indices: 12503138--12503169 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
12503128 TCAAAATTTT
12503138 AATTTTAAATAAAA-
1 AATTTTAAATAAAAC
12503152 AATTTT-AATAAAAC
1 AATTTTAAATAAAAC
12503166 AATT
1 AATT
12503170 AATAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (15 bp):
AATTTTAAATAAAAC
Found at i:12504030 original size:13 final size:14
Alignment explanation
Indices: 12504012--12504043 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
12504002 ATTATTATTG
12504012 TAAATTTTTAAAA-
1 TAAATTTTTAAAAT
12504025 TAAA-TTTTAAAAT
1 TAAATTTTTAAAAT
12504038 TAAATT
1 TAAATT
12504044 AAATAAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 8 0.47
13 8 0.47
14 1 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TAAATTTTTAAAAT
Found at i:12510576 original size:2 final size:2
Alignment explanation
Indices: 12510569--12510610 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
12510559 TTCTACTAAC
* *
12510569 AT AT AT AT AT AT AT AT AT TT AT AT AA 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 AT AT AT AT
12510611 GGTGGTGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12511467 original size:23 final size:22
Alignment explanation
Indices: 12511440--12511494 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
12511430 TATAATTTAT
*
12511440 TAATTGATTATTTAAAAATGTAA
1 TAATTGATTA-TTAAAAATATAA
* *
12511463 TAATTTATTA-TATAAATATAA
1 TAATTGATTATTAAAAATATAA
*
12511484 TACTTGATTAT
1 TAATTGATTAT
12511495 AAGTGTAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 17 0.65
23 9 0.35
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.47
Consensus pattern (22 bp):
TAATTGATTATTAAAAATATAA
Found at i:12512080 original size:24 final size:25
Alignment explanation
Indices: 12512048--12512100 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
12512038 TATATTTTAT
*
12512048 AAATTATT-ATTTTTATCAAC-ATTA
1 AAATTATTAATTTGTAT-AACTATTA
12512072 AAATTATTAATTTGTATAACTATTA
1 AAATTATTAATTTGTATAACTATTA
12512097 AAAT
1 AAAT
12512101 ATGTATAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 11 0.42
25 15 0.58
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (25 bp):
AAATTATTAATTTGTATAACTATTA
Found at i:12512519 original size:32 final size:32
Alignment explanation
Indices: 12512480--12512569 Score: 92
Period size: 32 Copynumber: 2.8 Consensus size: 32
12512470 AAAGTCAACC
* *
12512480 TGAATTC-ATTTAATTCAAATTTTAAAATAATT
1 TGAATTCAAATTAATTCAAA-TTAAAAATAATT
*
12512512 TGAATTCAAATTAATTCAAATTAAAAATAACT
1 TGAATTCAAATTAATTCAAATTAAAAATAATT
** * *
12512544 CAAATTTAAATTAATTTAAACTTAAA
1 TGAATTCAAATTAATTCAAA-TTAAA
12512570 TTGATCTAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
32 33 0.67
33 16 0.33
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (32 bp):
TGAATTCAAATTAATTCAAATTAAAAATAATT
Found at i:12512533 original size:16 final size:16
Alignment explanation
Indices: 12512489--12512571 Score: 76
Period size: 16 Copynumber: 5.1 Consensus size: 16
12512479 CTGAATTCAT
12512489 TTAATTCAAATTTTAAA
1 TTAATTCAAA-TTTAAA
* ** *
12512506 ATAATTTGAATTCAAA
1 TTAATTCAAATTTAAA
*
12512522 TTAATTCAAATTAAAA
1 TTAATTCAAATTTAAA
* *
12512538 ATAACTCAAATTTAAA
1 TTAATTCAAATTTAAA
* *
12512554 TTAATTTAAACTTAAA
1 TTAATTCAAATTTAAA
12512570 TT
1 TT
12512572 GATCTAAATT
Statistics
Matches: 51, Mismatches: 15, Indels: 1
0.76 0.22 0.01
Matches are distributed among these distances:
16 44 0.86
17 7 0.14
ACGTcount: A:0.51, C:0.07, G:0.01, T:0.41
Consensus pattern (16 bp):
TTAATTCAAATTTAAA
Found at i:12514159 original size:11 final size:11
Alignment explanation
Indices: 12514143--12514171 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
12514133 GTTTTAGACA
12514143 AAAATAAAATT
1 AAAATAAAATT
12514154 AAAATAAAATT
1 AAAATAAAATT
12514165 AAAATAA
1 AAAATAA
12514172 TTAAATATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAATAAAATT
Found at i:12514302 original size:22 final size:22
Alignment explanation
Indices: 12514276--12514319 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
12514266 TAACATATCA
12514276 TTACA-ATTTAATAATAAAAATT
1 TTACATATTTAA-AATAAAAATT
*
12514298 TTACATTATTTTAAATAAAAAT
1 TTACA-TATTTAAAATAAAAAT
12514320 AAATCATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 5 0.26
23 9 0.47
24 5 0.26
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (22 bp):
TTACATATTTAAAATAAAAATT
Found at i:12515336 original size:2 final size:2
Alignment explanation
Indices: 12515329--12515355 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12515319 GATCTCCCCA
12515329 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
12515356 GTTAGGAATA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:12517520 original size:22 final size:21
Alignment explanation
Indices: 12517478--12517532 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
12517468 ATAATTATTT
* *
12517478 TATA-TAAATATCTATTTAAA
1 TATATTAAAAATCTATTAAAA
12517498 TATATTAAAAATCTTATTAAAA
1 TATATTAAAAATC-TATTAAAA
12517520 TAATATATAAAAA
1 T-ATAT-TAAAAA
12517533 ATTTAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 4 0.14
21 7 0.24
22 8 0.28
23 4 0.14
24 6 0.21
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (21 bp):
TATATTAAAAATCTATTAAAA
Found at i:12518028 original size:20 final size:20
Alignment explanation
Indices: 12518003--12518044 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
12517993 TTATATATAA
12518003 TTAATAA-ATAAAATTTTTAT
1 TTAATAATAT-AAATTTTTAT
*
12518023 TTAATATTATAAATTTTTAT
1 TTAATAATATAAATTTTTAT
12518043 TT
1 TT
12518045 TAAATTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTAATAATATAAATTTTTAT
Found at i:12518046 original size:21 final size:19
Alignment explanation
Indices: 12518013--12518051 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 19
12518003 TTAATAAATA
12518013 AAATTTTTATTTAATATTAT
1 AAATTTTTATTTAA-ATTAT
12518033 AAATTTTTATTTTAAATTA
1 AAATTTTTA-TTTAAATTA
12518052 ATTAGTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
AAATTTTTATTTAAATTAT
Found at i:12519009 original size:35 final size:34
Alignment explanation
Indices: 12518963--12519032 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 34
12518953 ATAAAGATAG
12518963 TAGTTTAATTTATTATGAGTTCAATTAGATCTTA
1 TAGTTTAATTTATTATGAGTTCAATTAGATCTTA
*
12518997 TAGTTTGAATTTATTGTGAGTTCAATTAGATCTTA
1 TAGTTT-AATTTATTATGAGTTCAATTAGATCTTA
12519032 T
1 T
12519033 TAAGATCTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 6 0.18
35 28 0.82
ACGTcount: A:0.30, C:0.06, G:0.14, T:0.50
Consensus pattern (34 bp):
TAGTTTAATTTATTATGAGTTCAATTAGATCTTA
Found at i:12521524 original size:3 final size:3
Alignment explanation
Indices: 12521518--12521547 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
12521508 AATAATAATT
12521518 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
12521548 GGATAATAAT
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:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:12524038 original size:2 final size:2
Alignment explanation
Indices: 12524031--12524063 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
12524021 CTTTGACATT
12524031 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12524064 AACTATAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:12524184 original size:105 final size:105
Alignment explanation
Indices: 12524064--12524260 Score: 358
Period size: 105 Copynumber: 1.9 Consensus size: 105
12524054 ATAATATATA
**
12524064 AACTATAAACCTATAAATTATTTTTAAAAAACAACCATAAATCTATAAATCAAAATCCAAAAATT
1 AACTATAAACCTATAAATTATTTAAAAAAAACAACCATAAATCTATAAATCAAAATCCAAAAATT
*
12524129 AATTAATTAATTAATATTAAATTAAGTATATATATAACTC
66 AACTAATTAATTAATATTAAATTAAGTATATATATAACTC
*
12524169 AACTATAAACCTATAAATTATTTAAAAAAAACAACTATAAATCTATAAATCAAAATCCAAAAATT
1 AACTATAAACCTATAAATTATTTAAAAAAAACAACCATAAATCTATAAATCAAAATCCAAAAATT
12524234 AACTAATTAATTAATATTAAATTAAGT
66 AACTAATTAATTAATATTAAATTAAGT
12524261 TTACCAAAAT
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
105 88 1.00
ACGTcount: A:0.55, C:0.11, G:0.01, T:0.33
Consensus pattern (105 bp):
AACTATAAACCTATAAATTATTTAAAAAAAACAACCATAAATCTATAAATCAAAATCCAAAAATT
AACTAATTAATTAATATTAAATTAAGTATATATATAACTC
Found at i:12524423 original size:3 final size:3
Alignment explanation
Indices: 12524415--12524465 Score: 84
Period size: 3 Copynumber: 17.0 Consensus size: 3
12524405 TTTATGTTAG
* *
12524415 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATG AGT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12524463 ATT
1 ATT
12524466 GATTTTAGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:12525765 original size:25 final size:24
Alignment explanation
Indices: 12525737--12525794 Score: 62
Period size: 25 Copynumber: 2.4 Consensus size: 24
12525727 ATTAATAATA
12525737 TTTTTTATAAAAATAAAATCATTAT
1 TTTTTTATAAAAATAAAA-CATTAT
* * * *
12525762 TTTTTTACAATATTAACACATTAT
1 TTTTTTATAAAAATAAAACATTAT
*
12525786 TTTATTATA
1 TTTTTTATA
12525795 TTTAATATTT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
24 13 0.48
25 14 0.52
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (24 bp):
TTTTTTATAAAAATAAAACATTAT
Found at i:12526226 original size:23 final size:24
Alignment explanation
Indices: 12526188--12526233 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
12526178 AAGTAAATAC
* *
12526188 AAGTTAAATAATTATAATTTTTTG
1 AAGTTAAAGAATTATAATATTTTG
12526212 AAGTT-AAGAATTATAATATTTT
1 AAGTTAAAGAATTATAATATTTT
12526234 AATACAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (24 bp):
AAGTTAAAGAATTATAATATTTTG
Found at i:12536401 original size:19 final size:19
Alignment explanation
Indices: 12536373--12536418 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
12536363 TCAAATGGTT
*
12536373 ATGA-CTTTTTGTATAATC
1 ATGACCTTTTTATATAATC
*
12536391 TTGACCTTTTTATATAATC
1 ATGACCTTTTTATATAATC
12536410 ATGACCTTT
1 ATGACCTTT
12536419 ATGAATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 3 0.12
19 21 0.88
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATGACCTTTTTATATAATC
Found at i:12536426 original size:19 final size:19
Alignment explanation
Indices: 12536373--12536427 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
12536363 TCAAATGGTT
*
12536373 ATGACTTTTTG-TATAATC
1 ATGACCTTTTGATATAATC
* *
12536391 TTGACCTTTTTATATAATC
1 ATGACCTTTTGATATAATC
12536410 ATGACCTTTATGA-ATAAT
1 ATGACCTTT-TGATATAAT
12536428 AATATATTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 8 0.27
19 20 0.67
20 2 0.07
ACGTcount: A:0.31, C:0.13, G:0.09, T:0.47
Consensus pattern (19 bp):
ATGACCTTTTGATATAATC
Found at i:12540613 original size:18 final size:18
Alignment explanation
Indices: 12540587--12540621 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12540577 GATTATAATT
*
12540587 TTTTATATAATCATGATA
1 TTTTATATAACCATGATA
*
12540605 TTTTGTATAACCATGAT
1 TTTTATATAACCATGAT
12540622 CTTTATGAAT
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:0.34, C:0.09, G:0.09, T:0.49
Consensus pattern (18 bp):
TTTTATATAACCATGATA
Found at i:12541304 original size:11 final size:11
Alignment explanation
Indices: 12541288--12541313 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
12541278 GGTGAGAAAG
12541288 AAAATAATAAT
1 AAAATAATAAT
12541299 AAAATAATAAT
1 AAAATAATAAT
12541310 AAAA
1 AAAA
12541314 CTAAAGTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:12544699 original size:31 final size:31
Alignment explanation
Indices: 12544628--12544702 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
12544618 TTAGATACCC
*
12544628 ATGGTGATGGGGACAAATTAAGAATTCAAAG
1 ATGGAGATGGGGACAAATTAAGAATTCAAAG
* * *
12544659 ATAGAGATGGGGACAAATTATATAATT-AAGG
1 ATGGAGATGGGGACAAATTA-AGAATTCAAAG
*
12544690 ATGGGGATGGGGA
1 ATGGAGATGGGGA
12544703 TAAGGAATGT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
31 32 0.86
32 5 0.14
ACGTcount: A:0.40, C:0.04, G:0.33, T:0.23
Consensus pattern (31 bp):
ATGGAGATGGGGACAAATTAAGAATTCAAAG
Found at i:12547429 original size:24 final size:24
Alignment explanation
Indices: 12547386--12547498 Score: 95
Period size: 24 Copynumber: 4.7 Consensus size: 24
12547376 AATTGTGGAT
* *
12547386 TTGTACAAATAGAATAAATTTGAAC
1 TTGTATAAAT-GAAAAAATTTGAAC
* * *
12547411 TTGCATAAATGATAAAATTTGGAC
1 TTGTATAAATGAAAAAATTTGAAC
* * *
12547435 TTGTATATATAAAAAAATTTGCAC
1 TTGTATAAATGAAAAAATTTGAAC
* *
12547459 TTTTATAAATGAAACAAGTTTG-AC
1 TTGTATAAATGAAA-AAATTTGAAC
12547483 TTGTACT-AATGAAAAA
1 TTGTA-TAAATGAAAAA
12547499 TTTCAAAATC
Statistics
Matches: 71, Mismatches: 15, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
23 2 0.03
24 54 0.76
25 15 0.21
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (24 bp):
TTGTATAAATGAAAAAATTTGAAC
Found at i:12547439 original size:49 final size:47
Alignment explanation
Indices: 12547361--12547501 Score: 142
Period size: 48 Copynumber: 2.9 Consensus size: 47
12547351 AAAAGTTTAT
* *
12547361 CTTGCATAAATGACAAATTGTGGATTTGTACAAATAGAATAAATTTGAA
1 CTTGCATAAATGAAAAATT-TGGACTTGTACAAATAGAA-AAATTTGAA
* * * *
12547410 CTTGCATAAATGATAAAATTTGGACTTGTATATATAAAAAAATTTGCA
1 CTTGCATAAATGA-AAAATTTGGACTTGTACAAATAGAAAAATTTGAA
** *
12547458 CTTTTATAAATGAAACAAGTTT-GACTTGTACTAAT-GAAAAATTT
1 CTTGCATAAATGAAA-AA-TTTGGACTTGTACAAATAGAAAAATTT
12547502 CAAAATCATT
Statistics
Matches: 77, Mismatches: 12, Indels: 8
0.79 0.12 0.08
Matches are distributed among these distances:
47 10 0.13
48 31 0.40
49 31 0.40
50 5 0.06
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (47 bp):
CTTGCATAAATGAAAAATTTGGACTTGTACAAATAGAAAAATTTGAA
Found at i:12552392 original size:15 final size:14
Alignment explanation
Indices: 12552361--12552393 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
12552351 TAATTGATTG
12552361 TATT-TAATAAAAA
1 TATTATAATAAAAA
12552374 TATTATAATAAATAA
1 TATTATAATAAA-AA
12552389 TATTA
1 TATTA
12552394 ATTATTCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 7 0.39
15 7 0.39
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TATTATAATAAAAA
Found at i:12552529 original size:27 final size:30
Alignment explanation
Indices: 12552472--12552539 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 30
12552462 TTTAAATTAA
* *
12552472 AATTATTTAAAATTATAAAAATATATGATAT
1 AATT-TTTTAAATTATAAAAATATATAATAT
12552503 AATTTTTTAAATTA-AAAAAT-T-TAATAT
1 AATTTTTTAAATTATAAAAATATATAATAT
12552530 -ATTTTTTAAA
1 AATTTTTTAAA
12552540 ATGTATATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 10 0.29
27 5 0.14
28 1 0.03
29 6 0.17
30 9 0.26
31 4 0.11
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (30 bp):
AATTTTTTAAATTATAAAAATATATAATAT
Found at i:12552541 original size:27 final size:31
Alignment explanation
Indices: 12552472--12552546 Score: 88
Period size: 27 Copynumber: 2.5 Consensus size: 31
12552462 TTTAAATTAA
* *
12552472 AATTATTTAAAATTATAAAAATATATGATAT
1 AATTTTTTAAAATTATAAAAATATATAATAT
12552503 AATTTTTT-AAATTA-AAAAAT-T-TAATAT
1 AATTTTTTAAAATTATAAAAATATATAATAT
12552530 -ATTTTTTAAAATGTATA
1 AATTTTTTAAAAT-TATA
12552547 TAACACTTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
26 7 0.18
27 9 0.23
28 3 0.08
29 7 0.18
30 6 0.15
31 7 0.18
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.47
Consensus pattern (31 bp):
AATTTTTTAAAATTATAAAAATATATAATAT
Found at i:12552763 original size:10 final size:11
Alignment explanation
Indices: 12552743--12552779 Score: 58
Period size: 10 Copynumber: 3.4 Consensus size: 11
12552733 TAATTTAATA
12552743 TTATGTAAAAT
1 TTATGTAAAAT
12552754 TTAT-TAAAAT
1 TTATGTAAAAT
12552764 TTAATGTAAAAT
1 TT-ATGTAAAAT
12552776 TTAT
1 TTAT
12552780 ATTTTAAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 8 0.33
11 8 0.33
12 8 0.33
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (11 bp):
TTATGTAAAAT
Found at i:12552775 original size:12 final size:12
Alignment explanation
Indices: 12552745--12552778 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
12552735 ATTTAATATT
12552745 ATGTAAAATTT-
1 ATGTAAAATTTA
12552756 AT-TAAAATTTA
1 ATGTAAAATTTA
12552767 ATGTAAAATTTA
1 ATGTAAAATTTA
12552779 TATTTTAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.38
11 4 0.19
12 9 0.43
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (12 bp):
ATGTAAAATTTA
Found at i:12554191 original size:16 final size:14
Alignment explanation
Indices: 12554147--12554207 Score: 56
Period size: 13 Copynumber: 4.4 Consensus size: 14
12554137 AATATCATAC
*
12554147 TAATAATATTATTAT
1 TAATAAT-TTAATAT
*
12554162 T-ATCATTT-ATAT
1 TAATAATTTAATAT
12554174 TAATCAATTATAATAT
1 TAAT-AATT-TAATAT
12554190 TAATAATTTAA-AT
1 TAATAATTTAATAT
12554203 TAATA
1 TAATA
12554208 TATCAAAGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
12 4 0.10
13 11 0.28
14 10 0.26
15 6 0.15
16 8 0.21
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (14 bp):
TAATAATTTAATAT
Found at i:12555217 original size:31 final size:30
Alignment explanation
Indices: 12555140--12555218 Score: 79
Period size: 31 Copynumber: 2.6 Consensus size: 30
12555130 GCATTAAAGG
* *
12555140 AACTAAAATTTAAATTTCTTATAAATACAA
1 AACTAAATTTTAAATTTCATATAAATACAA
** *
12555170 AAGC-AAATTTTCAAATTTCATATATGTGCAGA
1 AA-CTAAATTTT-AAATTTCATATAAATACA-A
12555202 AACTAAATTTTAAATTT
1 AACTAAATTTTAAATTT
12555219 TGTATGAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
30 8 0.20
31 22 0.55
32 10 0.25
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (30 bp):
AACTAAATTTTAAATTTCATATAAATACAA
Found at i:12556023 original size:1 final size:1
Alignment explanation
Indices: 12556017--12556044 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
12556007 TATTCTCTTG
12556017 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
12556045 CTGATGTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:12556936 original size:73 final size:72
Alignment explanation
Indices: 12556851--12557101 Score: 222
Period size: 73 Copynumber: 3.4 Consensus size: 72
12556841 AGATAAATTA
* * * *
12556851 TATTTTTTAAATTCTAAAACTTTAACAAAGAT-TACGTTTTCAAGATAAAAAATATAATAAATGT
1 TATTTTTAAAATTCTAAAATTTTAACAAAGATCGA-GTTTTCAAAATAAAAAATATAATAAATGT
12556915 T-AAACTTTT
65 TAAAAC--TT
* * * *
12556924 TATTTTTAAAATTCTAAAATTTTAATAAAGATCGAGTTTTTAAAATAAAAAATATAGTAGATGTT
1 TATTTTTAAAATTCTAAAATTTTAACAAAGATCGAGTTTTCAAAATAAAAAATATAATAAATGTT
12556989 AAAACTT
66 AAAACTT
* * * * * * * *
12556996 TATTTTAAAAATTTTAAAATTTTATAAAAAAAAATC-ATGTTTTTAAAATAAGAAATACAGTGAA
1 TATTTTTAAAATTCTAAAA-TTT-T-AACAAAGATCGA-GTTTTCAAAATAAAAAATATAAT-AA
* *
12557060 A-GTCAAAATTT
61 ATGTTAAAACTT
* *
12557071 TGTTTTTAAAATTCTAAAATGTTAACAAAGA
1 TATTTTTAAAATTCTAAAATTTTAACAAAGA
12557102 CAGTGCTTTT
Statistics
Matches: 148, Mismatches: 23, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
72 25 0.17
73 59 0.40
74 9 0.06
75 53 0.36
76 2 0.01
ACGTcount: A:0.48, C:0.06, G:0.07, T:0.39
Consensus pattern (72 bp):
TATTTTTAAAATTCTAAAATTTTAACAAAGATCGAGTTTTCAAAATAAAAAATATAATAAATGTT
AAAACTT
Found at i:12557082 original size:75 final size:73
Alignment explanation
Indices: 12556921--12557090 Score: 193
Period size: 75 Copynumber: 2.3 Consensus size: 73
12556911 ATGTTAAACT
* * *
12556921 TTTTATTTTTAAAATTCTAAAA-TTTTAATAAAGATCGAGTTTTTAAAATAAAAAATATAGTAGA
1 TTTTATTTTTAAAATTCTAAAATTTTTAAAAAAAATCGAGTTTTTAAAATAAAAAATACAGTAGA
* *
12556985 TGTTAAAA
66 AGTCAAAA
* * * *
12556993 CTTTATTTTAAAAATTTTAAAATTTTATAAAAAAAAATC-ATGTTTTTAAAATAAGAAATACAGT
1 TTTTATTTTTAAAATTCTAAAATTTT-T-AAAAAAAATCGA-GTTTTTAAAATAAAAAATACAGT
12557057 -GAAAGTCAAAA
63 AG-AAGTCAAAA
*
12557068 TTTTGTTTTTAAAATTCTAAAAT
1 TTTTATTTTTAAAATTCTAAAAT
12557091 GTTAACAAAG
Statistics
Matches: 80, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
72 19 0.24
73 3 0.04
74 3 0.04
75 55 0.69
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (73 bp):
TTTTATTTTTAAAATTCTAAAATTTTTAAAAAAAATCGAGTTTTTAAAATAAAAAATACAGTAGA
AGTCAAAA
Found at i:12557358 original size:66 final size:66
Alignment explanation
Indices: 12557269--12557395 Score: 177
Period size: 66 Copynumber: 1.9 Consensus size: 66
12557259 AACATAATGG
*
12557269 ATGTTGGAAGTTATTTTTTCAAAATTCTATAATTTTAACAACA-ACCATATTTTTAAGATAGTAG
1 ATGTTGGAAGTTA-TTTTTCAAAATTCTAAAATTTTAACAA-ATACCATATTTTTAAGATAGTAG
12557333 TAA
64 TAA
* * *
12557336 ATGTTGGAACGTTA-TTTTCAAAATTTTAAAATTTTAACAAATATCATGTTTTTAAGATAG
1 ATGTTGGAA-GTTATTTTTCAAAATTCTAAAATTTTAACAAATACCATATTTTTAAGATAG
12557396 AAAATATAGT
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
65 1 0.02
66 40 0.74
67 9 0.17
68 4 0.07
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.43
Consensus pattern (66 bp):
ATGTTGGAAGTTATTTTTCAAAATTCTAAAATTTTAACAAATACCATATTTTTAAGATAGTAGTA
A
Found at i:12557792 original size:18 final size:18
Alignment explanation
Indices: 12557777--12557809 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
12557767 TCTTAATATC
12557777 ATTTTTC-T-TCAAAATA
1 ATTTTTCATCTCAAAATA
12557793 ATTTTTCATCTCAAAAT
1 ATTTTTCATCTCAAAAT
12557810 TCAAAAGTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (18 bp):
ATTTTTCATCTCAAAATA
Found at i:12559079 original size:5 final size:5
Alignment explanation
Indices: 12559052--12559092 Score: 50
Period size: 5 Copynumber: 8.2 Consensus size: 5
12559042 CTTTCTCCAT
12559052 TTTTA TATTTA TATTTA --TTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA T-TTTA T-TTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
12559093 AATAGATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
3 3 0.09
5 20 0.61
6 10 0.30
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:12559081 original size:13 final size:15
Alignment explanation
Indices: 12559050--12559089 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
12559040 ATCTTTCTCC
12559050 ATTT-TTATATTTAT
1 ATTTATTATATTTAT
12559064 ATTTATTAT-TTTAT
1 ATTTATTATATTTAT
*
12559078 -TTTATTTTATTT
1 ATTTATTATATTT
12559090 TATAATAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 7 0.30
14 12 0.52
15 4 0.17
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (15 bp):
ATTTATTATATTTAT
Found at i:12564555 original size:17 final size:16
Alignment explanation
Indices: 12564525--12564559 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
12564515 TATCCGTATT
12564525 TTTATTTTGATTATAG
1 TTTATTTTGATTATAG
*
12564541 TTTATATTTGCTTATAG
1 TTTAT-TTTGATTATAG
12564558 TT
1 TT
12564560 CATCAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.23, C:0.03, G:0.11, T:0.63
Consensus pattern (16 bp):
TTTATTTTGATTATAG
Found at i:12570624 original size:20 final size:20
Alignment explanation
Indices: 12570573--12570629 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
12570563 AGATTACAAA
12570573 AAGGATCGATCACCCTATGT
1 AAGGATCGATCACCCTATGT
*
12570593 AAGGGATTGATCACCCCT-TG-
1 AA-GGATCGATCA-CCCTATGT
12570613 ACAGGATCGATC-CCCTA
1 A-AGGATCGATCACCCTA
12570630 CATAAAAGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
18 4 0.13
20 11 0.35
21 12 0.39
22 4 0.13
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (20 bp):
AAGGATCGATCACCCTATGT
Found at i:12573941 original size:12 final size:12
Alignment explanation
Indices: 12573924--12573973 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
12573914 TGTAGGGTGA
12573924 CTGGTCGGGAGG
1 CTGGTCGGGAGG
*
12573936 CTGGTCGGGGGG
1 CTGGTCGGGAGG
*
12573948 CTGGTAGGGTA-G
1 CTGGTCGGG-AGG
*
12573960 TTGGTCGGG-GG
1 CTGGTCGGGAGG
12573971 CTG
1 CTG
12573974 ACGATAGCGG
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
11 3 0.10
12 27 0.90
ACGTcount: A:0.06, C:0.14, G:0.58, T:0.22
Consensus pattern (12 bp):
CTGGTCGGGAGG
Found at i:12574051 original size:25 final size:25
Alignment explanation
Indices: 12574023--12574070 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
12574013 ATTCTGTTTC
* * *
12574023 TTTTGTTTGTTTATTATTTTTTTTG
1 TTTTGTTTATTAATAATTTTTTTTG
12574048 TTTTGTTTATTAATAATTTTTTT
1 TTTTGTTTATTAATAATTTTTTT
12574071 ATTAAAAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (25 bp):
TTTTGTTTATTAATAATTTTTTTTG
Found at i:12574067 original size:21 final size:20
Alignment explanation
Indices: 12574023--12574067 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
12574013 ATTCTGTTTC
* **
12574023 TTTTGTTTGTTTATTATTTT
1 TTTTGTTTGTTTATTAATAA
12574043 TTTTGTTTTGTTTATTAATAA
1 TTTTG-TTTGTTTATTAATAA
12574064 TTTT
1 TTTT
12574068 TTTATTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.16, C:0.00, G:0.09, T:0.76
Consensus pattern (20 bp):
TTTTGTTTGTTTATTAATAA
Found at i:12574407 original size:109 final size:101
Alignment explanation
Indices: 12574241--12574784 Score: 621
Period size: 109 Copynumber: 5.3 Consensus size: 101
12574231 CTCTTAGCAA
* ** * *
12574241 AGGCTCAACAACTTTAAAATTCTCATCTTAAAAAAGCTCCTCTATTTTCAGCAGAGGCTCAACAA
1 AGGCTCCACAACTTTAAAATTCTCATCTTGGAAAAGCT-CTCT-CTCTCAGCAGAGGCTCAACAA
* *
12574306 CTTTAAAATTCTCATTTTGGAAAAGCTCCTCTGTTTTCCACAG
64 CTTTAAAATTCTCATTTTGAAAAAGCTCCTC-----TCAACAG
12574349 AGGCTCCACAACTTTAAAAATTCTCATCTTGGAAAAGCTTCTCTGCTCTCAGCAGAGGCTCAACA
1 AGGCTCCACAACTTT-AAAATTCTCATCTTGGAAAAGC-TCTCT-CTCTCAGCAGAGGCTCAACA
* *
12574414 ACTTTAAAATTCTCATCTTGAAAAAGCTCCTCTCAGCAG
63 ACTTTAAAATTCTCATTTTGAAAAAGCTCCTCTCAACAG
* *
12574453 AGGCTCCACAACTTTAAAA-TCTCATC-T-GAAAATCTTATCTGAAAAAGCTCCTCTCAGTAGAG
1 AGGCTCCACAACTTTAAAATTCTCATCTTGGAAAAGC---TCT-------CT-CTCTCAGCAGAG
*
12574515 GCTCAACAACTTTAAAATTCTCA-TCTGAAAAAGCTCCTCTCAACAG
55 GCTCAACAACTTTAAAATTCTCATTTTGAAAAAGCTCCTCTCAACAG
*
12574561 AGGCTCCACAACTTTAAAAATTCTCATCTTGGAAAAG--CT-TCTCTCAACAGAGGCTCAACAAC
1 AGGCTCCACAACTTT-AAAATTCTCATCTTGGAAAAGCTCTCTCTCTCAGCAGAGGCTCAACAAC
*
12574623 TTTAAAATT-TC-TTCTGAAAAAGCTCCTCTCAACAG
65 TTTAAAATTCTCATTTTGAAAAAGCTCCTCTCAACAG
**
12574658 AGGCTCCACAACTTTAAAAATTCTCATCTTCAAAAAG--CTC-CTCTCAGCAGAGGCTCAACAAC
1 AGGCTCCACAACTTT-AAAATTCTCATCTTGGAAAAGCTCTCTCTCTCAGCAGAGGCTCAACAAC
*
12574720 TTTAAAGTT-TC-TTCTTGAAAAAGCTCCTCTCAACAG
65 TTTAAAATTCTCATT-TTGAAAAAGCTCCTCTCAACAG
12574756 AGGCTCCACAACTTTAAAATTCTCATCTT
1 AGGCTCCACAACTTTAAAATTCTCATCTT
12574785 TTTCAAATTT
Statistics
Matches: 393, Mismatches: 25, Indels: 47
0.85 0.05 0.10
Matches are distributed among these distances:
97 109 0.28
98 65 0.17
99 1 0.00
100 6 0.02
101 1 0.00
102 10 0.03
103 4 0.01
104 20 0.05
107 2 0.01
108 49 0.12
109 112 0.28
110 8 0.02
111 1 0.00
112 5 0.01
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (101 bp):
AGGCTCCACAACTTTAAAATTCTCATCTTGGAAAAGCTCTCTCTCTCAGCAGAGGCTCAACAACT
TTAAAATTCTCATTTTGAAAAAGCTCCTCTCAACAG
Found at i:12574486 original size:13 final size:13
Alignment explanation
Indices: 12574468--12574497 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
12574458 CCACAACTTT
12574468 AAAATCTCATCTG
1 AAAATCTCATCTG
*
12574481 AAAATCTTATCTG
1 AAAATCTCATCTG
12574494 AAAA
1 AAAA
12574498 AGCTCCTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.17, G:0.07, T:0.30
Consensus pattern (13 bp):
AAAATCTCATCTG
Found at i:12574525 original size:60 final size:61
Alignment explanation
Indices: 12574432--12574545 Score: 203
Period size: 60 Copynumber: 1.9 Consensus size: 61
12574422 ATTCTCATCT
*
12574432 TGAAAAAGCTCCTCTCAGCAGAGGCTCCACAACTTTAAAA-TCTCATCTGAAAATCTTATC
1 TGAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCATCTGAAAATCTTATC
*
12574492 TGAAAAAGCTCCTCTCAGTAGAGGCTCAACAACTTTAAAATTCTCATCTGAAAA
1 TGAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCATCTGAAAA
12574546 AGCTCCTCTC
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
60 38 0.75
61 13 0.25
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.26
Consensus pattern (61 bp):
TGAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCATCTGAAAATCTTATC
Found at i:12574613 original size:50 final size:49
Alignment explanation
Indices: 12574492--12574784 Score: 432
Period size: 48 Copynumber: 6.0 Consensus size: 49
12574482 AAATCTTATC
**
12574492 TGAAAAAGCTCCTCTCAGTAGAGGCTCAACAACTTTAAAATTCTCATC-
1 TGAAAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAAAATTCTCATCT
*
12574540 TGAAAAAGCTCCTCTCAACAGAGGCTCCACAACTTTAAAAATTCTCATCT
1 TGAAAAAGCTCCTCTCAACAGAGGCTCAACAACTTT-AAAATTCTCATCT
* * *
12574590 TGGAAAAGCTTCTCTCAACAGAGGCTCAACAACTTTAAAATT-TCTTC-
1 TGAAAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAAAATTCTCATCT
*
12574637 TGAAAAAGCTCCTCTCAACAGAGGCTCCACAACTTTAAAAATTCTCATCT
1 TGAAAAAGCTCCTCTCAACAGAGGCTCAACAACTTT-AAAATTCTCATCT
* * * *
12574687 TCAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAGTT-TCTTCT
1 TGAAAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAAAATTCTCATCT
*
12574735 TGAAAAAGCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTCTCATCT
1 TGAAAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAAAATTCTCATCT
12574784 T
1 T
12574785 TTTCAAATTT
Statistics
Matches: 218, Mismatches: 21, Indels: 11
0.87 0.08 0.04
Matches are distributed among these distances:
47 33 0.15
48 86 0.39
49 33 0.15
50 66 0.30
ACGTcount: A:0.34, C:0.27, G:0.11, T:0.28
Consensus pattern (49 bp):
TGAAAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAAAATTCTCATCT
Found at i:12574669 original size:145 final size:145
Alignment explanation
Indices: 12574490--12574776 Score: 443
Period size: 145 Copynumber: 2.0 Consensus size: 145
12574480 GAAAATCTTA
** *
12574490 TCTGAAAAAGCTCCTCTCAGTAGAGGCTCAACAACTTT-AAAATTCTCATC-TGAAAAAGCTCCT
1 TCTGAAAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAAAAATTCTCATCTTCAAAAAGCTCCT
* * *
12574553 CTCAACAGAGGCTCCACAACTTTAAAAATTCTCATCTTGGAAAAGCTTCTCTCAACAGAGGCTCA
66 CTCAACAGAGGCTCAACAACTTT-AAAATT-TCATCTTGAAAAAGCTCCTCTCAACAGAGGCTCA
12574618 ACAACTTTAAAATTTCT
129 ACAACTTTAAAATTTCT
*
12574635 TCTGAAAAAGCTCCTCTCAACAGAGGCTCCACAACTTTAAAAATTCTCATCTTCAAAAAGCTCCT
1 TCTGAAAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAAAAATTCTCATCTTCAAAAAGCTCCT
* * * *
12574700 CTCAGCAGAGGCTCAACAACTTTAAAGTTTCTTCTTGAAAAAGCTCCTCTCAACAGAGGCTCCAC
66 CTCAACAGAGGCTCAACAACTTTAAAATTTCATCTTGAAAAAGCTCCTCTCAACAGAGGCTCAAC
12574765 AACTTTAAAATT
131 AACTTTAAAATT
12574777 CTCATCTTTT
Statistics
Matches: 129, Mismatches: 11, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
145 79 0.61
146 17 0.13
147 33 0.26
ACGTcount: A:0.35, C:0.26, G:0.11, T:0.27
Consensus pattern (145 bp):
TCTGAAAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAAAAATTCTCATCTTCAAAAAGCTCCT
CTCAACAGAGGCTCAACAACTTTAAAATTTCATCTTGAAAAAGCTCCTCTCAACAGAGGCTCAAC
AACTTTAAAATTTCT
Found at i:12574670 original size:97 final size:97
Alignment explanation
Indices: 12574494--12574784 Score: 494
Period size: 97 Copynumber: 3.0 Consensus size: 97
12574484 ATCTTATCTG
* *
12574494 AAAAAGCTCCTCTCAGTAGAGGCTCAACAACTTTAAAATTCTCATCTGAAAAAGCTCCTCTCAAC
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATT-TCTTCTGAAAAAGCTCCTCTCAAC
*
12574559 AGAGGCTCCACAACTTTAAAAATTCTCATCTTG
65 AGAGGCTCCACAACTTTAAAAATTCTCATCTTC
* * *
12574592 GAAAAGCTTCTCTCAACAGAGGCTCAACAACTTTAAAATTTCTTCTGAAAAAGCTCCTCTCAACA
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTTCTTCTGAAAAAGCTCCTCTCAACA
12574657 GAGGCTCCACAACTTTAAAAATTCTCATCTTC
66 GAGGCTCCACAACTTTAAAAATTCTCATCTTC
*
12574689 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAGTTTCTTCTTGAAAAAGCTCCTCTCAAC
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTTCTTC-TGAAAAAGCTCCTCTCAAC
12574754 AGAGGCTCCACAACTTT-AAAATTCTCATCTT
65 AGAGGCTCCACAACTTTAAAAATTCTCATCTT
12574785 TTTCAAATTT
Statistics
Matches: 182, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
97 110 0.60
98 72 0.40
ACGTcount: A:0.35, C:0.27, G:0.11, T:0.27
Consensus pattern (97 bp):
AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTTCTTCTGAAAAAGCTCCTCTCAACA
GAGGCTCCACAACTTTAAAAATTCTCATCTTC
Found at i:12578161 original size:21 final size:21
Alignment explanation
Indices: 12578122--12578161 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
12578112 TTTCTTCTTG
* **
12578122 TTTGTTTATTATTTTTTTTGT
1 TTTGTTTATTAATAATTTTGT
12578143 TTTGTTTATTAATAATTTT
1 TTTGTTTATTAATAATTTT
12578162 TTATTAAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.75
Consensus pattern (21 bp):
TTTGTTTATTAATAATTTTGT
Found at i:12578453 original size:45 final size:48
Alignment explanation
Indices: 12578322--12578838 Score: 422
Period size: 48 Copynumber: 10.8 Consensus size: 48
12578312 AGCTCATCTG
* * *
12578322 CTCTTAGCAAAGGCTC-ACAACTTT-AAATTCTCATCTTAAAAAAGCTC
1 CTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCAT-TTGAAAAAGCTC
12578369 CTCTATTTTTCAGCAGAGGCTCAACAACTTTAAAATTCTCATTTG-AAAAGCTC
1 CTC------TCAGCAGAGGCTCAACAACTTTAAAATTCTCATTTGAAAAAGCTC
*
12578422 CTCTCAGCAGAGGCTC-A-AACTTTAAAATTCTCATCTG-AAAAGCTC
1 CTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCATTTGAAAAAGCTC
12578467 TCTCTC-GCAGAGGCTCAACAACTTTAAAA-TCTCATCTTGAAAAAGCTC
1 -CTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCAT-TTGAAAAAGCTC
*
12578515 CTCTCAGCAGAGGCTCAACAACTTTAAAA-TCTC-TCTGAAAAAGCT-
1 CTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCATTTGAAAAAGCTC
* * * *
12578560 CTCTCAGCAGAGACAACTTTAAAAAC-TTAAAACTTCTCATCTGAAATTTAA--TC
1 CTCTCAGCAGAG---GC-TCAACAACTTTAAAA-TTCTCATTTGAAA---AAGCTC
* **
12578613 CT-TCAAAAGTCTTCGAGGAGGCAACAACTTTAAAATT-TCA-TTGAAAAAGCT-
1 CTCTC---AG-C--AGAGG-CTCAACAACTTTAAAATTCTCATTTGAAAAAGCTC
*
12578664 CTCTCAACAGA-G-TCAA-AACTTT-AAATT-TC-TTCTGAAAAAAGCT-
1 CTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCATT-TG-AAAAAGCTC
* *
12578707 CTCTCA-CAGAGGCTCCACAACTTTAAAATTCTCATCTTCAAAAAGCTC
1 CTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCAT-TTGAAAAAGCTC
* *
12578755 CTCTCAGCAGAGGCTCAACAACTTTAAAGTT-TCTTCTTGAAAAAGCTC
1 CTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCAT-TTGAAAAAGCTC
* *
12578803 CTCTCAACAGAGGCTCCACAACTTTAAAATTCTCAT
1 CTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCAT
12578839 CTTTTTCAAA
Statistics
Matches: 392, Mismatches: 29, Indels: 96
0.76 0.06 0.19
Matches are distributed among these distances:
41 8 0.02
42 12 0.03
43 18 0.05
44 3 0.01
45 56 0.14
46 30 0.08
47 44 0.11
48 94 0.24
49 33 0.08
50 6 0.02
51 9 0.02
52 6 0.02
53 29 0.07
54 15 0.04
55 19 0.05
56 7 0.02
58 3 0.01
ACGTcount: A:0.35, C:0.25, G:0.11, T:0.29
Consensus pattern (48 bp):
CTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCATTTGAAAAAGCTC
Found at i:12578825 original size:97 final size:90
Alignment explanation
Indices: 12578636--12578841 Score: 294
Period size: 97 Copynumber: 2.2 Consensus size: 90
12578626 CGAGGAGGCA
*
12578636 ACAACTTTAAAATT-TCA--TTGAAAAAGCTCTCTCAACAGAGTCAAAACTTTAAATTTCTTCTG
1 ACAACTTTAAAATTCTCATCTTCAAAAAGCTCTCTCAACAGAGTCAAAACTTTAAATTTCTTCTG
12578698 AAAAAAGCTCTCTCACAGAGGCTCC
66 AAAAAAGCTCTCTCACAGAGGCTCC
*
12578723 ACAACTTTAAAATTCTCATCTTCAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAGTTTC
1 ACAACTTTAAAATTCTCATCTTCAAAAAGCT-CTCTCAACAGA-G-TCAA-AACTTTAAA-TTTC
12578788 TTCTTG-AAAAAGCTCCTCTCAACAGAGGCTCC
61 TTC-TGAAAAAAGCT-CTCTC-ACAGAGGCTCC
12578820 ACAACTTTAAAATTCTCATCTT
1 ACAACTTTAAAATTCTCATCTT
12578842 TTTCAAATTT
Statistics
Matches: 106, Mismatches: 2, Indels: 12
0.88 0.02 0.10
Matches are distributed among these distances:
87 14 0.13
88 3 0.03
90 10 0.09
91 10 0.09
92 1 0.01
93 4 0.04
94 9 0.08
95 15 0.14
96 7 0.07
97 33 0.31
ACGTcount: A:0.35, C:0.25, G:0.10, T:0.30
Consensus pattern (90 bp):
ACAACTTTAAAATTCTCATCTTCAAAAAGCTCTCTCAACAGAGTCAAAACTTTAAATTTCTTCTG
AAAAAAGCTCTCTCACAGAGGCTCC
Found at i:12589896 original size:7 final size:7
Alignment explanation
Indices: 12589886--12589938 Score: 52
Period size: 7 Copynumber: 6.9 Consensus size: 7
12589876 ATTTTTTTGC
12589886 TTTTTAT
1 TTTTTAT
12589893 TTTTTGATT
1 TTTTT-A-T
12589902 TGTTTTTAT
1 T--TTTTAT
12589911 TTTTTATT
1 TTTTTA-T
12589919 TTTTTAT
1 TTTTTAT
*
12589926 TTTTTTT
1 TTTTTAT
12589933 TTTTTA
1 TTTTTA
12589939 CTAAAAATGA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
7 22 0.56
8 8 0.21
9 4 0.10
10 1 0.03
11 4 0.10
ACGTcount: A:0.11, C:0.00, G:0.04, T:0.85
Consensus pattern (7 bp):
TTTTTAT
Found at i:12589908 original size:25 final size:25
Alignment explanation
Indices: 12589879--12589933 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
12589869 TGTGTGAATT
*
12589879 TTTTTGCTTTTTATTTTTTGATTTG
1 TTTTTACTTTTTATTTTTTGATTTG
* * *
12589904 TTTTTATTTTTTATTTTTTTATTTT
1 TTTTTACTTTTTATTTTTTGATTTG
12589929 TTTTT
1 TTTTT
12589934 TTTTACTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.09, C:0.02, G:0.05, T:0.84
Consensus pattern (25 bp):
TTTTTACTTTTTATTTTTTGATTTG
Found at i:12591095 original size:24 final size:23
Alignment explanation
Indices: 12591063--12591114 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 23
12591053 GTTGGTTGGT
*
12591063 GGCT-GTAGGGTGACTGGTCGGG
1 GGCTGGTAGGGTAACTGGTCGGG
*
12591085 AGGCTGGTAGGGTAATTGGTCGGG
1 -GGCTGGTAGGGTAACTGGTCGGG
12591109 GGCTGG
1 GGCTGG
12591115 CGACAGCGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 10 0.38
24 16 0.62
ACGTcount: A:0.12, C:0.12, G:0.54, T:0.23
Consensus pattern (23 bp):
GGCTGGTAGGGTAACTGGTCGGG
Found at i:12595570 original size:14 final size:14
Alignment explanation
Indices: 12595542--12595598 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 14
12595532 TAGTTATTTA
*
12595542 TTTATTTTGTT-AT
1 TTTATTTTTTTAAT
12595555 TTTATTTTTTTAAT
1 TTTATTTTTTTAAT
* * *
12595569 TTCATTTTTTCAAA
1 TTTATTTTTTTAAT
*
12595583 TTAATTTTTTATAAT
1 TTTATTTTTT-TAAT
12595598 T
1 T
12595599 ATTTAACATA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
13 10 0.29
14 22 0.63
15 3 0.09
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.70
Consensus pattern (14 bp):
TTTATTTTTTTAAT
Found at i:12595650 original size:20 final size:20
Alignment explanation
Indices: 12595627--12595701 Score: 51
Period size: 20 Copynumber: 3.6 Consensus size: 20
12595617 GTAATTATTT
12595627 AATAAATTAATTAATATATA
1 AATAAATTAATTAATATATA
** * *
12595647 AATAGTTTAAATAATAAATA
1 AATAAATTAATTAATATATA
* * *
12595667 CATAAAAGTAATTAATTTTATA
1 AAT-AAATTAATTAA-TATATA
* *
12595689 ATTAAATAAATTA
1 AATAAATTAATTA
12595702 TTAGTGAATA
Statistics
Matches: 38, Mismatches: 15, Indels: 3
0.68 0.27 0.05
Matches are distributed among these distances:
20 18 0.47
21 15 0.39
22 5 0.13
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (20 bp):
AATAAATTAATTAATATATA
Found at i:12595934 original size:15 final size:15
Alignment explanation
Indices: 12595911--12595946 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
12595901 ATTATTTTTT
*
12595911 AAATTTTTAAATATC
1 AAATATTTAAATATC
12595926 AAATATTTAAATATC
1 AAATATTTAAATATC
12595941 AAATAT
1 AAATAT
12595947 ATTATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (15 bp):
AAATATTTAAATATC
Found at i:12596554 original size:16 final size:16
Alignment explanation
Indices: 12596530--12596563 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12596520 TTCAGTTTTC
*
12596530 AATCAAAATATAATAT
1 AATCAAAATATAAAAT
*
12596546 AATCTAAATATAAAAT
1 AATCAAAATATAAAAT
12596562 AA
1 AA
12596564 AAAATTTATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (16 bp):
AATCAAAATATAAAAT
Found at i:12596784 original size:22 final size:22
Alignment explanation
Indices: 12596758--12596813 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
12596748 TGACCAAATT
* * *
12596758 AAATTTGATAGATTAATTTTTG
1 AAATTTCATAAATTAACTTTTG
*
12596780 AAA-TTCATAAATTTACTTTTG
1 AAATTTCATAAATTAACTTTTG
12596801 AAATTT-ATAAATT
1 AAATTTCATAAATT
12596814 TATTTCGATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 24 0.83
22 5 0.17
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (22 bp):
AAATTTCATAAATTAACTTTTG
Found at i:12596801 original size:21 final size:21
Alignment explanation
Indices: 12596775--12596815 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
12596765 ATAGATTAAT
12596775 TTTTGAAATTCATAAATTTAC
1 TTTTGAAATTCATAAATTTAC
*
12596796 TTTTGAAATTTATAAATTTA
1 TTTTGAAATTCATAAATTTA
12596816 TTTCGATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (21 bp):
TTTTGAAATTCATAAATTTAC
Found at i:12598923 original size:2 final size:2
Alignment explanation
Indices: 12598916--12598956 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
12598906 CCAGGGGATT
12598916 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
12598957 AGGGAGGTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Done.