Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 17 of 193
Found at i:5914725 original size:60 final size:59
Alignment explanation
Indices: 5914632--5914874 Score: 155
Period size: 60 Copynumber: 4.1 Consensus size: 59
5914622 AACTGTTTAG
* * * * *
5914632 AAATTATATTTTGACCCTCAAACTTCTTCAAAATTATATTTTTGACCTTAAAACTTT-TGA
1 AAATTATATTTTAACCCTCAAACTTC-TCAAAATTACATTTTTAACCCTAAAA-TTTCTAA
5914692 AAATTATATTTTAACCC-CAAAAACTTC-CAAAAATTACATTTTTAACCCTAAAATTTCTAA
1 AAATTATATTTTAACCCTC--AAACTTCTC-AAAATTACATTTTTAACCCTAAAATTTCTAA
* ** * * * * * *
5914752 AAAATATATTTTTGCCCTCGAACTTC-CAAAAACTCCATTTTTGATCCC-GAAACTTCTAA
1 AAATTATATTTTAACCCTCAAACTTCTC-AAAATTACATTTTT-AACCCTAAAATTTCTAA
* * * *
5914811 AAATTCCAT-TTTTACCCCT-AAACTTC-CAAAAGTTTCATTTTT-A-CCTCAAAACTTCAAA
1 AAATT--ATATTTTAACCCTCAAACTTCTCAAAA-TTACATTTTTAACCCT-AAAATTTCTAA
5914869 AAATTA
1 AAATTA
5914875 CCATTTTACC
Statistics
Matches: 149, Mismatches: 23, Indels: 26
0.75 0.12 0.13
Matches are distributed among these distances:
56 3 0.02
58 18 0.12
59 53 0.36
60 65 0.44
61 10 0.07
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.37
Consensus pattern (59 bp):
AAATTATATTTTAACCCTCAAACTTCTCAAAATTACATTTTTAACCCTAAAATTTCTAA
Found at i:5914793 original size:59 final size:57
Alignment explanation
Indices: 5914669--5914910 Score: 163
Period size: 59 Copynumber: 4.1 Consensus size: 57
5914659 TCAAAATTAT
* * ** * * *
5914669 ATTTTTGACCTTAAAACTT-TTGAAAATTATATTTTAACCCCAAAAACTTCCAAAAATTAC
1 ATTTTTAACCCTAAAACTTCTAAAAAATTAT-TTTT-ACCCC--GAACTTCCAAAAACTCC
* *
5914729 ATTTTTAACCCTAAAATTTCTAAAAAATATATTTTTGCCCTCGAACTTCCAAAAACTCC
1 ATTTTTAACCCTAAAACTTCTAAAAAAT-TATTTTTACCC-CGAACTTCCAAAAACTCC
* * * ** *
5914788 ATTTTTGATCCC-GAAACTTCT-AAAAATTCCATTTTTACCCCTAAACTTCCAAAAGTTTC
1 ATTTTT-AACCCTAAAACTTCTAAAAAATT--ATTTTTACCCC-GAACTTCCAAAAACTCC
* *
5914847 ATTTTT-A-CCTCAAAACTTC-AAAAAATTACCATTTTACCCCCGAACGTCCAAAAACTCC
1 ATTTTTAACCCT-AAAACTTCTAAAAAATTA--TTTTTA-CCCCGAACTTCCAAAAACTCC
5914905 ATTTTT
1 ATTTTT
5914911 GGTCCCGATT
Statistics
Matches: 144, Mismatches: 25, Indels: 28
0.73 0.13 0.14
Matches are distributed among these distances:
56 3 0.02
57 1 0.01
58 44 0.31
59 59 0.41
60 23 0.16
61 11 0.08
62 3 0.02
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.36
Consensus pattern (57 bp):
ATTTTTAACCCTAAAACTTCTAAAAAATTATTTTTACCCCGAACTTCCAAAAACTCC
Found at i:5914813 original size:30 final size:29
Alignment explanation
Indices: 5914712--5914910 Score: 152
Period size: 29 Copynumber: 6.8 Consensus size: 29
5914702 TTAACCCCAA
* **
5914712 AAACTTCCAAAAATTACATTTTTAACCCTA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCG
* * * ** *
5914742 AAATTTCTAAAAAATATATTTTTGCCCTCG
1 AAACTTCCAAAAATTCCATTTTTACCC-CG
* *
5914772 -AACTTCCAAAAACTCCATTTTTGATCCCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCCG
* *
5914801 AAACTTCTAAAAATTCCATTTTTACCCCT
1 AAACTTCCAAAAATTCCATTTTTACCCCG
* * * *
5914830 AAACTTCCAAAAGTTTCATTTTTACCTCA
1 AAACTTCCAAAAATTCCATTTTTACCCCG
*
5914859 AAACTTCAAAAAATTACCA-TTTTACCCCCG
1 AAACTTCCAAAAATT-CCATTTTTA-CCCCG
* *
5914889 -AACGTCCAAAAACTCCATTTTT
1 AAACTTCCAAAAATTCCATTTTT
5914911 GGTCCCGATT
Statistics
Matches: 132, Mismatches: 31, Indels: 13
0.75 0.18 0.07
Matches are distributed among these distances:
28 3 0.02
29 83 0.63
30 46 0.35
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.34
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCG
Found at i:5914908 original size:58 final size:59
Alignment explanation
Indices: 5914713--5914916 Score: 186
Period size: 59 Copynumber: 3.5 Consensus size: 59
5914703 TAACCCCAAA
* * * * * *
5914713 AACTTCCAAAAATTACATTTTT-AACCCTAAAATTTCTAAAAAATAT--ATTTTTGCCCTCG
1 AACTTCCAAAAACTCCATTTTTGATCCC-AAAACTTC-AAAAAAT-TCCATTTTTACCCCCG
* * **
5914772 AACTTCCAAAAACTCCATTTTTGATCCCGAAACTTCTAAAAATTCCATTTTTACCCCTA
1 AACTTCCAAAAACTCCATTTTTGATCCCAAAACTTCAAAAAATTCCATTTTTACCCCCG
** *
5914831 AACTTCCAAAAGTTTCATTTTT-A-CCTCAAAACTTCAAAAAATTACCA-TTTTACCCCCG
1 AACTTCCAAAAACTCCATTTTTGATCC-CAAAACTTCAAAAAATT-CCATTTTTACCCCCG
* *
5914889 AACGTCCAAAAACTCCATTTTTGGTCCC
1 AACTTCCAAAAACTCCATTTTTGATCCC
5914917 GATTTTTCTA
Statistics
Matches: 116, Mismatches: 22, Indels: 14
0.76 0.14 0.09
Matches are distributed among these distances:
57 3 0.03
58 49 0.42
59 58 0.50
60 6 0.05
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.34
Consensus pattern (59 bp):
AACTTCCAAAAACTCCATTTTTGATCCCAAAACTTCAAAAAATTCCATTTTTACCCCCG
Found at i:5915036 original size:29 final size:28
Alignment explanation
Indices: 5914974--5915055 Score: 85
Period size: 28 Copynumber: 2.9 Consensus size: 28
5914964 ATTTTTAACC
* *
5914974 CCAAAATTACATTTTTGCCCTCGAGAAT
1 CCAAAATTACATTTTTACCCCCGAGAAT
*
5915002 CCAAAATTACCA-TTTTACCCCCGAGTAT
1 CCAAAATTA-CATTTTTACCCCCGAGAAT
* *
5915030 CCAAAAAGTTTCATTTTTAACCCCGA
1 CC-AAAA-TTACATTTTTACCCCCGA
5915056 TTATATCATT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
28 24 0.53
29 8 0.18
30 13 0.29
ACGTcount: A:0.33, C:0.28, G:0.09, T:0.30
Consensus pattern (28 bp):
CCAAAATTACATTTTTACCCCCGAGAAT
Found at i:5921720 original size:50 final size:51
Alignment explanation
Indices: 5921663--5921957 Score: 219
Period size: 51 Copynumber: 5.8 Consensus size: 51
5921653 AAAAACACAA
*
5921663 GGGAAAGATCTAAG-CCGCAACGACGGACCATGTACCTCAGAAGACACGAC
1 GGGAAAGATCTAAGACCGCAACGACGGACCATGTACCTCAAAAGACACGAC
* ** * * * *
5921713 GGAAAAGATCTAAGATTGCAACGACGGATTCA-GTACCGCAAAAAGACA-AAA
1 GGGAAAGATCTAAGACCGCAACGACGGA-CCATGTACCTC-AAAAGACACGAC
* ** *
5921764 GGGAAAGGTCTAAG-TTGCAACGACGGACCGTGTACCTCAAAAGACACGAC
1 GGGAAAGATCTAAGACCGCAACGACGGACCATGTACCTCAAAAGACACGAC
* * * * * *
5921814 GGGAAATATCTAAGACCGCAACGGCAGATCCA-GTACCGTAAAAAGACA-AAA
1 GGGAAAGATCTAAGACCGCAACGACGGA-CCATGTACC-TCAAAAGACACGAC
* * * * * * *
5921865 GGGAAAGGTTTAAG-TCGCAACGACGGATCGTGTACCTTAGAAGACACGAC
1 GGGAAAGATCTAAGACCGCAACGACGGACCATGTACCTCAAAAGACACGAC
* * * * *
5921915 GGAAAAAATCTAAGACCGCAATGGCGGATCCA-GTACCGCAAAA
1 GGGAAAGATCTAAGACCGCAACGACGGA-CCATGTACCTCAAAA
5921958 AGATAAAAGA
Statistics
Matches: 184, Mismatches: 49, Indels: 23
0.72 0.19 0.09
Matches are distributed among these distances:
49 18 0.10
50 71 0.39
51 74 0.40
52 21 0.11
ACGTcount: A:0.39, C:0.22, G:0.25, T:0.13
Consensus pattern (51 bp):
GGGAAAGATCTAAGACCGCAACGACGGACCATGTACCTCAAAAGACACGAC
Found at i:5921825 original size:101 final size:101
Alignment explanation
Indices: 5921653--5921971 Score: 442
Period size: 101 Copynumber: 3.2 Consensus size: 101
5921643 AGTACCACGC
* * * *
5921653 AAAA-ACACAAGGGAAAGATCTAAGCCGCAACGACGGACCATGTACCTCAGAAGACACGACGGAA
1 AAAAGACAAAAGGGAAAGGTCTAAGTCGCAACGACGGACCGTGTACCTCAGAAGACACGACGGAA
* ** * *
5921717 AAGATCTAAGATTGCAACGACGGATTCAGTACCGCA
66 AAAATCTAAGACCGCAACGGCGGATCCAGTACCGCA
* * *
5921753 AAAAGACAAAAGGGAAAGGTCTAAGTTGCAACGACGGACCGTGTACCTCAAAAGACACGACGGGA
1 AAAAGACAAAAGGGAAAGGTCTAAGTCGCAACGACGGACCGTGTACCTCAGAAGACACGACGGAA
* * *
5921818 AATATCTAAGACCGCAACGGCAGATCCAGTACCGTA
66 AAAATCTAAGACCGCAACGGCGGATCCAGTACCGCA
* * *
5921854 AAAAGACAAAAGGGAAAGGTTTAAGTCGCAACGACGGATCGTGTACCTTAGAAGACACGACGGAA
1 AAAAGACAAAAGGGAAAGGTCTAAGTCGCAACGACGGACCGTGTACCTCAGAAGACACGACGGAA
*
5921919 AAAATCTAAGACCGCAATGGCGGATCCAGTACCGCA
66 AAAATCTAAGACCGCAACGGCGGATCCAGTACCGCA
* *
5921955 AAAAGATAAAAGAGAAA
1 AAAAGACAAAAGGGAAA
5921972 AGTCCTTATC
Statistics
Matches: 192, Mismatches: 26, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
100 4 0.02
101 188 0.98
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.13
Consensus pattern (101 bp):
AAAAGACAAAAGGGAAAGGTCTAAGTCGCAACGACGGACCGTGTACCTCAGAAGACACGACGGAA
AAAATCTAAGACCGCAACGGCGGATCCAGTACCGCA
Found at i:5921951 original size:51 final size:51
Alignment explanation
Indices: 5921663--5921960 Score: 180
Period size: 50 Copynumber: 5.9 Consensus size: 51
5921653 AAAAACACAA
* * * *
5921663 GGGAAAGATCTAAG-CCGCAACGACGGA-CCATGTACCTCAGAAGACACGAC
1 GGGAAAAATCTAAGACCGCAACGGCGGATCCA-GTACCTAAAAAGACACGAC
** * * * * *
5921713 -GGAAAAGATCTAAGATTGCAACGACGGATTCAGTACCGCAAAAAGACA-AAA
1 GGGAAAA-ATCTAAGACCGCAACGGCGGATCCAGTACC-TAAAAAGACACGAC
** ** * * *
5921764 GGGAAAGGTCTAAG-TTGCAACGACGGA-CCGTGTACCTCAAAAGACACGAC
1 GGGAAAAATCTAAGACCGCAACGGCGGATCC-AGTACCTAAAAAGACACGAC
* * * *
5921814 GGGAAATATCTAAGACCGCAACGGCAGATCCAGTACCGTAAAAAGACA-AAA
1 GGGAAAAATCTAAGACCGCAACGGCGGATCCAGTACC-TAAAAAGACACGAC
** * * * ** * *
5921865 GGGAAAGGTTTAAG-TCGCAACGACGGATCGTGTACCTTAGAAGACACGAC
1 GGGAAAAATCTAAGACCGCAACGGCGGATCCAGTACCTAAAAAGACACGAC
* * *
5921915 GGAAAAAATCTAAGACCGCAATGGCGGATCCAGTACCGCAAAAAGA
1 GGGAAAAATCTAAGACCGCAACGGCGGATCCAGTACC-TAAAAAGA
5921961 TAAAAGAGAA
Statistics
Matches: 184, Mismatches: 51, Indels: 24
0.71 0.20 0.09
Matches are distributed among these distances:
49 22 0.12
50 66 0.36
51 66 0.36
52 30 0.16
ACGTcount: A:0.40, C:0.22, G:0.25, T:0.13
Consensus pattern (51 bp):
GGGAAAAATCTAAGACCGCAACGGCGGATCCAGTACCTAAAAAGACACGAC
Found at i:5922159 original size:93 final size:92
Alignment explanation
Indices: 5921971--5922200 Score: 379
Period size: 93 Copynumber: 2.5 Consensus size: 92
5921961 TAAAAGAGAA
*
5921971 AAGTCCTTATCTCTCTAAAGTTGTAGTAAGAGCAAGATGAAGCTTTAAACATCAATTCCTATCCT
1 AAGTCTTTATCTCTCTAAAGTTGTAGTAAGAGCAAGATGAAGCTTTAAACATCAATTCCTATCCT
5922036 CTTAAAGTTACAGTAAAGTTAGATAGC
66 CTTAAAGTTACAGTAAAGTTAGATAGC
*
5922063 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTTAAAACATCAATTCCTATCC
1 AAGTCTTTATCTCTCTAAAGTTGTAGTAAGAGCAAGATGAAGCTTT-AAACATCAATTCCTATCC
* * *
5922128 TCTTGAAGTTGCAGTAAAGTTGGATAGC
65 TCTTAAAGTTACAGTAAAGTTAGATAGC
* * *
5922156 AAGTCTTTATTTCTCTAAAGTTGCAGTAAGAGCAAGATAAAGCTT
1 AAGTCTTTATCTCTCTAAAGTTGTAGTAAGAGCAAGATGAAGCTT
5922201 CGACACCAAA
Statistics
Matches: 128, Mismatches: 9, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
92 44 0.34
93 84 0.66
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Consensus pattern (92 bp):
AAGTCTTTATCTCTCTAAAGTTGTAGTAAGAGCAAGATGAAGCTTTAAACATCAATTCCTATCCT
CTTAAAGTTACAGTAAAGTTAGATAGC
Found at i:5922794 original size:205 final size:205
Alignment explanation
Indices: 5922489--5923001 Score: 731
Period size: 205 Copynumber: 2.5 Consensus size: 205
5922479 CTAACTCAAG
* *
5922489 GCTCAATGAGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAGTAGGTCGAAGCA
1 GCTCAATGAGAGCAAATCTTCGAAT-CCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
* * * *
5922554 ATAAAATGGTTAGCTTCCTGATGAGATATTGAGAAGTGGATCAAATTCGTCTTCCTAATGAGATA
65 ATAAAATGGTTAGCTTCCTGATTAGATACTGAGAAGTGGACCAAATTCATCTTCCTAATGAGATA
5922619 CAGAGAAGCGGATTGAAACAAACGACGCAGTCATCTTCCTGATAAGATACTGAGAAGAAGACCAA
130 CAGAGAAGCGGATTGAAACAAACGACGCAGTCATCTTCCTGATAAGATACTGAGAAGAAGACCAA
* *
5922684 ATCAAACTCAT
195 ATCAAACCCAC
* * *
5922695 GCTCAATGTGAGCAAATTTTCGAATCCAACTTCCTGATGAGATACTGAGAAGCGGGTCGAAGCAA
1 GCTCAATGAGAGCAAATCTTCGAATCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAA
* *
5922760 TAAAATGGTTAGCTTACTGATTAGATACTGAGAAGTGGACCAAATTCATCTTCCTGATGAGATAC
66 TAAAATGGTTAGCTTCCTGATTAGATACTGAGAAGTGGACCAAATTCATCTTCCTAATGAGATAC
** * * * *
5922825 AGAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGATCAAA
131 AGAGAAGCGGATTGAAACAAACGACGCAGTCATCTTCCTGATAAGATACTGAGAAGAAGACCAAA
5922890 TCAAACCCAC
196 TCAAACCCAC
** * * * * ** *
5922900 GCTTGAGGCGAGCAACTCTTCGAACCCCAACTTTTTGATGAGATACTGAGAAGCAGGTCGAAGTA
1 GCTCAATGAGAGCAAATCTTCGAA-TCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
*
5922965 ATAAAATGGTTAGCTTCCTGA-TAGGATACAGAGAAGT
65 ATAAAATGGTTAGCTTCCTGATTA-GATACTGAGAAGT
5923002 ATACCAACAT
Statistics
Matches: 273, Mismatches: 32, Indels: 4
0.88 0.10 0.01
Matches are distributed among these distances:
205 183 0.67
206 90 0.33
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (205 bp):
GCTCAATGAGAGCAAATCTTCGAATCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAA
TAAAATGGTTAGCTTCCTGATTAGATACTGAGAAGTGGACCAAATTCATCTTCCTAATGAGATAC
AGAGAAGCGGATTGAAACAAACGACGCAGTCATCTTCCTGATAAGATACTGAGAAGAAGACCAAA
TCAAACCCAC
Found at i:5923356 original size:11 final size:11
Alignment explanation
Indices: 5923342--5923397 Score: 60
Period size: 11 Copynumber: 5.0 Consensus size: 11
5923332 AACCAAACCT
5923342 TTTTAAATTTA
1 TTTTAAATTTA
5923353 TTTTAAATTTAA
1 TTTTAAATTT-A
*
5923365 ATTT-AATTTAA
1 TTTTAAATTT-A
* *
5923376 GTTTGAATTTA
1 TTTTAAATTTA
5923387 TTTTAAATTTA
1 TTTTAAATTTA
5923398 AAATTATTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
11 30 0.77
12 9 0.23
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.59
Consensus pattern (11 bp):
TTTTAAATTTA
Found at i:5923365 original size:17 final size:17
Alignment explanation
Indices: 5923343--5923415 Score: 101
Period size: 17 Copynumber: 4.3 Consensus size: 17
5923333 ACCAAACCTT
5923343 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
5923360 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
*
5923377 TTTGAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
5923394 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
5923411 TTTAA
1 TTTAA
5923416 TTAAAGGTCC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 48 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:5924228 original size:15 final size:15
Alignment explanation
Indices: 5924184--5924235 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 15
5924174 AAATACATGC
* *
5924184 TAATAATAATAACAA
1 TAATGATAATAACAT
*
5924199 TATTGATAAT-A-AT
1 TAATGATAATAACAT
*
5924212 TACTGATAATAACAT
1 TAATGATAATAACAT
5924227 TAATGATAA
1 TAATGATAA
5924236 ATATTGGTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
13 10 0.33
14 2 0.07
15 18 0.60
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.35
Consensus pattern (15 bp):
TAATGATAATAACAT
Found at i:5925463 original size:29 final size:29
Alignment explanation
Indices: 5925419--5925542 Score: 97
Period size: 31 Copynumber: 4.1 Consensus size: 29
5925409 GGAGGTCCTT
* * *
5925419 AAACTATCCAAAAATTATATTTTGACCCTC
1 AAACT-TCTAAAAGTTATATTTTAACCCTC
* * * *
5925449 AAACTTCTTCAAATTTACATTTTTAACCCTA
1 AAACTTC-TAAAAGTTATA-TTTTAACCCTC
5925480 AAACTTCTAAAAGTTATATTTTAACCCTCTC
1 AAACTTCTAAAAGTTATATTTTAA-CC-CTC
* * *
5925511 GAACTTCTAAAAATTACATTTTTAACCC-C
1 AAACTTCTAAAAGTTATA-TTTTAACCCTC
5925540 AAA
1 AAA
5925543 AATTACATTC
Statistics
Matches: 75, Mismatches: 14, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
29 11 0.15
30 23 0.31
31 35 0.47
32 6 0.08
ACGTcount: A:0.39, C:0.23, G:0.02, T:0.36
Consensus pattern (29 bp):
AAACTTCTAAAAGTTATATTTTAACCCTC
Found at i:5925484 original size:31 final size:30
Alignment explanation
Indices: 5925419--5925790 Score: 242
Period size: 30 Copynumber: 12.7 Consensus size: 30
5925409 GGAGGTCCTT
* * * *
5925419 AAACTATCCAAAAATTATA-TTTTGACCCTC
1 AAACT-TCTAAAAATTACATTTTTAACCCTA
* *
5925449 AAACTTCTTCAAATTTACATTTTTAACCCTA
1 AAACTTC-TAAAAATTACATTTTTAACCCTA
* * *
5925480 AAACTTCTAAAAGTTATA-TTTTAACCCTCTC
1 AAACTTCTAAAAATTACATTTTTAA-CC-CTA
*
5925511 GAACTTCTAAAAATTACATTTTTAA-CC--
1 AAACTTCTAAAAATTACATTTTTAACCCTA
* *
5925538 ---C--C-AAAAATTACATTCTTACCCCT-
1 AAACTTCTAAAAATTACATTTTTAACCCTA
* * *
5925561 AAACTTCCAAAAACTT-CATTTTTGACCCCA
1 AAACTTCTAAAAA-TTACATTTTTAACCCTA
*
5925591 AAACTTC-ATAAAATTACATTTTT-ACCCTTG
1 AAACTTCTA-AAAATTACATTTTTAACCC-TA
* *
5925621 AAACTTCCAAAAATTACA-TTTTAACCCTG
1 AAACTTCTAAAAATTACATTTTTAACCCTA
* *
5925650 AAACTTCTAAAAATTCCATTTTT-ACCCTT
1 AAACTTCTAAAAATTACATTTTTAACCCTA
* * * * ** *
5925679 GAACTTCCAAAAATTCCAATTTTAACATTG
1 AAACTTCTAAAAATTACATTTTTAACCCTA
* *
5925709 AAACTTCCAAAAATTACCA-TTTTACCCCT-
1 AAACTTCTAAAAATTA-CATTTTTAACCCTA
* *
5925738 AAATTTCTAAAAATTCCATTTTTAACCCTA
1 AAACTTCTAAAAATTACATTTTTAACCCTA
*
5925768 AAACTTCCAAAAATTACCATTTT
1 AAACTTCTAAAAATTA-CATTTT
5925791 GTCCTCGGAC
Statistics
Matches: 274, Mismatches: 42, Indels: 51
0.75 0.11 0.14
Matches are distributed among these distances:
21 15 0.05
22 3 0.01
24 1 0.00
26 1 0.00
28 3 0.01
29 99 0.36
30 104 0.38
31 42 0.15
32 6 0.02
ACGTcount: A:0.38, C:0.24, G:0.02, T:0.36
Consensus pattern (30 bp):
AAACTTCTAAAAATTACATTTTTAACCCTA
Found at i:5925558 original size:20 final size:21
Alignment explanation
Indices: 5925519--5925559 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5925509 TCGAACTTCT
*
5925519 AAAAATTACATTTTTAACCCC
1 AAAAATTACATTCTTAACCCC
5925540 AAAAATTACATTCTT-ACCCC
1 AAAAATTACATTCTTAACCCC
5925560 TAAACTTCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.41, C:0.27, G:0.00, T:0.32
Consensus pattern (21 bp):
AAAAATTACATTCTTAACCCC
Found at i:5925571 original size:29 final size:30
Alignment explanation
Indices: 5925538--5925790 Score: 252
Period size: 29 Copynumber: 8.5 Consensus size: 30
5925528 ATTTTTAACC
*
5925538 CCAAAAATTACATTCTTACCCCT-AAACTT
1 CCAAAAATTACATTTTTACCCCTGAAACTT
*
5925567 CCAAAAACTT-CATTTTTGACCCC-AAAACTT
1 CCAAAAA-TTACATTTTT-ACCCCTGAAACTT
*
5925597 -CATAAAATTACATTTTTACCCTTGAAACTT
1 CCA-AAAATTACATTTTTACCCCTGAAACTT
*
5925627 CCAAAAATTACA-TTTTAACCCTGAAACTT
1 CCAAAAATTACATTTTTACCCCTGAAACTT
* * *
5925656 CTAAAAATTCCATTTTTACCCTTG-AACTT
1 CCAAAAATTACATTTTTACCCCTGAAACTT
* * * **
5925685 CCAAAAATTCCAATTTTAACATTGAAACTT
1 CCAAAAATTACATTTTTACCCCTGAAACTT
*
5925715 CCAAAAATTACCA-TTTTACCCCT-AAATTT
1 CCAAAAATTA-CATTTTTACCCCTGAAACTT
* * * *
5925744 CTAAAAATTCCATTTTTAACCCTAAAACTT
1 CCAAAAATTACATTTTTACCCCTGAAACTT
5925774 CCAAAAATTACCATTTT
1 CCAAAAATTA-CATTTT
5925791 GTCCTCGGAC
Statistics
Matches: 187, Mismatches: 24, Indels: 24
0.80 0.10 0.10
Matches are distributed among these distances:
28 2 0.01
29 93 0.50
30 82 0.44
31 10 0.05
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (30 bp):
CCAAAAATTACATTTTTACCCCTGAAACTT
Found at i:5925616 original size:59 final size:59
Alignment explanation
Indices: 5925538--5925790 Score: 289
Period size: 59 Copynumber: 4.3 Consensus size: 59
5925528 ATTTTTAACC
* * *
5925538 CCAAAAATTACATTCTTACCCCTAAACTTCCAAAAACTT-CATTTTTGACCCCAAAACTT
1 CCAAAAATTACATTTTTACCCCTAAACTTCCAAAAA-TTCCATTTTTAACCCTAAAACTT
* * *
5925597 -CATAAAATTACATTTTTACCCTTGAAACTTCCAAAAATTACA-TTTTAACCCTGAAACTT
1 CCA-AAAATTACATTTTTACCCCT-AAACTTCCAAAAATTCCATTTTTAACCCTAAAACTT
* * * * * ** *
5925656 CTAAAAATTCCATTTTTACCCTTGAACTTCCAAAAATTCCAATTTTAACATTGAAACTT
1 CCAAAAATTACATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTAACCCTAAAACTT
* *
5925715 CCAAAAATTACCA-TTTTACCCCTAAATTTCTAAAAATTCCATTTTTAACCCTAAAACTT
1 CCAAAAATTA-CATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTAACCCTAAAACTT
5925774 CCAAAAATTACCATTTT
1 CCAAAAATTA-CATTTT
5925791 GTCCTCGGAC
Statistics
Matches: 166, Mismatches: 21, Indels: 13
0.83 0.10 0.06
Matches are distributed among these distances:
58 18 0.11
59 127 0.77
60 21 0.13
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (59 bp):
CCAAAAATTACATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTAACCCTAAAACTT
Found at i:5925806 original size:118 final size:116
Alignment explanation
Indices: 5925591--5925916 Score: 295
Period size: 118 Copynumber: 2.8 Consensus size: 116
5925581 TTTGACCCCA
* * * *
5925591 AAACTTCATAAAATTA-CATTTTTACCCTTGAAACTTCCAAAAATTACA-TTTTAACCCTGAAAC
1 AAACTTCA-AAAATTACCA-TTTTACCCCT-AAATTTCTAAAAATT-CATTTTTAACCCTAAAAC
* * * *
5925654 TTCTAAAAATT-CCATTTTTACCCTTGAACTTCCAAAAATTCCA-ATTTTAACATTG
62 TTCCAAAAATTACCATTTTTA-CCTCGAACATCCAAAAACTCCATATTTTAAC-TTG
5925709 AAACTTCCAAAAATTACCATTTTACCCCTAAATTTCTAAAAATTCCATTTTTAACCCTAAAACTT
1 AAACTT-CAAAAATTACCATTTTACCCCTAAATTTCTAAAAATT-CATTTTTAACCCTAAAACTT
* * *
5925774 CCAAAAATTACCATTTTGT-CCTCGGACATCCAAAAACTCCATTTTTTATCTTG
64 CCAAAAATTACCATTTT-TACCTCGAACATCCAAAAACTCCATATTTTAACTTG
*** * * * * * **
5925827 ATTTTTTTAAAAATTACCGTTTTACGCCTGAATGTCT-AAAATATCATTTTTAACCCTAAATTTT
1 A-AACTTCAAAAATTACCATTTTACCCCTAAATTTCTAAAAAT-TCATTTTTAACCCTAAAACTT
* *
5925891 CCCAAAATTATCATTTTTACCCTCGA
64 CCAAAAATTACCATTTTTA-CCTCGA
5925917 GAGTCTAAAA
Statistics
Matches: 173, Mismatches: 25, Indels: 20
0.79 0.11 0.09
Matches are distributed among these distances:
116 1 0.01
117 53 0.31
118 99 0.57
119 19 0.11
120 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.38
Consensus pattern (116 bp):
AAACTTCAAAAATTACCATTTTACCCCTAAATTTCTAAAAATTCATTTTTAACCCTAAAACTTCC
AAAAATTACCATTTTTACCTCGAACATCCAAAAACTCCATATTTTAACTTG
Found at i:5925809 original size:59 final size:59
Alignment explanation
Indices: 5925538--5925819 Score: 222
Period size: 59 Copynumber: 4.8 Consensus size: 59
5925528 ATTTTTAACC
* * * * * *
5925538 CCAAAAATTA-CATTCTTACCCCTAAACTTCCAAAAACTT-CATTTTTGACCCCAAAACTT
1 CCAAAAATTACCATTTTTACCTC-GAACATCCAAAAA-TTCCATTTTTAACCCTAAAACTT
* * * *
5925597 -CATAAAATTA-CATTTTTACCCTTGAAACTTCCAAAAATTACA-TTTTAACCCTGAAACTT
1 CCA-AAAATTACCATTTTTA-CCTCG-AACATCCAAAAATTCCATTTTTAACCCTAAAACTT
* * * * ** *
5925656 CTAAAAATT-CCATTTTTACCCTTGAACTTCCAAAAATTCCAATTTTAACATTGAAACTT
1 CCAAAAATTACCATTTTTA-CCTCGAACATCCAAAAATTCCATTTTTAACCCTAAAACTT
* * *
5925715 CCAAAAATTACCA-TTTTACCCCTAA-ATTTCTAAAAATTCCATTTTTAACCCTAAAACTT
1 CCAAAAATTACCATTTTTACCTCGAACA--TCCAAAAATTCCATTTTTAACCCTAAAACTT
* *
5925774 CCAAAAATTACCATTTTGT-CCTCGGACATCCAAAAACTCCATTTTT
1 CCAAAAATTACCATTTT-TACCTCGAACATCCAAAAATTCCATTTTT
5925820 TATCTTGATT
Statistics
Matches: 184, Mismatches: 26, Indels: 26
0.78 0.11 0.11
Matches are distributed among these distances:
58 22 0.12
59 133 0.72
60 27 0.15
61 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (59 bp):
CCAAAAATTACCATTTTTACCTCGAACATCCAAAAATTCCATTTTTAACCCTAAAACTT
Found at i:5927234 original size:21 final size:21
Alignment explanation
Indices: 5927208--5927248 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
5927198 ATAGAAAGCA
5927208 GTATGTTTAAATAGATTGTTT
1 GTATGTTTAAATAGATTGTTT
*
5927229 GTATGTTTAAATCGATTGTT
1 GTATGTTTAAATAGATTGTT
5927249 ATTTTGAAAT
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:0.27, C:0.02, G:0.20, T:0.51
Consensus pattern (21 bp):
GTATGTTTAAATAGATTGTTT
Found at i:5930466 original size:26 final size:25
Alignment explanation
Indices: 5930437--5930496 Score: 59
Period size: 26 Copynumber: 2.4 Consensus size: 25
5930427 GTAGAAAATT
*
5930437 AATAAATAATGAAA-AAGTAAAGATAA
1 AATAAATAA-CAAACAAGTAAAGA-AA
** *
5930463 AATATGTAACAAACAATTAAAGAAA
1 AATAAATAACAAACAAGTAAAGAAA
5930488 AATAAATAA
1 AATAAATAA
5930497 ATTTCTAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
25 12 0.44
26 15 0.56
ACGTcount: A:0.68, C:0.03, G:0.08, T:0.20
Consensus pattern (25 bp):
AATAAATAACAAACAAGTAAAGAAA
Found at i:5930740 original size:21 final size:20
Alignment explanation
Indices: 5930699--5930735 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
5930689 TTTATTGATG
5930699 AATATTTTATATAATTAATT
1 AATATTTTATATAATTAATT
*
5930719 AATATTTT-TATATTTAA
1 AATATTTTATATAATTAA
5930736 AATTATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
AATATTTTATATAATTAATT
Found at i:5931235 original size:27 final size:27
Alignment explanation
Indices: 5931197--5931248 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
5931187 TAACACACAG
* *
5931197 ATGGAGGGTTTTGAAGTGGTGGCACTT
1 ATGGAGGGTTTTCAAGTGGCGGCACTT
5931224 ATGGAGGGTTTTCAAGTGGCGGCAC
1 ATGGAGGGTTTTCAAGTGGCGGCAC
5931249 CTTGAGGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.19, C:0.12, G:0.40, T:0.29
Consensus pattern (27 bp):
ATGGAGGGTTTTCAAGTGGCGGCACTT
Found at i:5931623 original size:19 final size:18
Alignment explanation
Indices: 5931601--5931645 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
5931591 TAGTAGGGTA
5931601 TATTTTT-AAATTTGTATTT
1 TATTTTTGAAATTT-TA-TT
5931620 TATTTTTTGAAATTTTATT
1 TA-TTTTTGAAATTTTATT
5931639 TATTTTT
1 TATTTTT
5931646 TAATAGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 5 0.21
19 6 0.25
20 7 0.29
21 6 0.25
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (18 bp):
TATTTTTGAAATTTTATT
Found at i:5931646 original size:19 final size:20
Alignment explanation
Indices: 5931603--5931648 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
5931593 GTAGGGTATA
5931603 TTTTTAAATTTGTATTTTAT
1 TTTTTAAATTTGTATTTTAT
5931623 TTTTTGAAATTT-TA-TTTAT
1 TTTTT-AAATTTGTATTTTAT
5931642 TTTTTAA
1 TTTTTAA
5931649 TAGATTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.08
19 10 0.40
20 7 0.28
21 6 0.24
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (20 bp):
TTTTTAAATTTGTATTTTAT
Found at i:5934349 original size:28 final size:28
Alignment explanation
Indices: 5934290--5934375 Score: 81
Period size: 28 Copynumber: 3.1 Consensus size: 28
5934280 GACATTTTTC
* ** *
5934290 ATTTAAAATTAATTAAGTTTATGAATGA
1 ATTTAAAATTAATTATGTTTATGTTTGT
5934318 ATTTAAAATTAATTATGTTTAAT-TTTGT
1 ATTTAAAATTAATTATGTTT-ATGTTTGT
*
5934346 ATTT--AATTAATAAT-TTTCATGTTTGT
1 ATTTAAAATTAATTATGTTT-ATGTTTGT
5934372 ATTT
1 ATTT
5934376 TGGTTTAAGG
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
25 5 0.10
26 18 0.36
28 25 0.50
29 2 0.04
ACGTcount: A:0.37, C:0.01, G:0.08, T:0.53
Consensus pattern (28 bp):
ATTTAAAATTAATTATGTTTATGTTTGT
Found at i:5934370 original size:26 final size:26
Alignment explanation
Indices: 5934324--5934375 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
5934314 ATGAATTTAA
*
5934324 AATTAATTATGTTTAATTTTGTATTT
1 AATTAATAATGTTTAATTTTGTATTT
*
5934350 AATTAATAAT-TTTCATGTTTGTATTT
1 AATTAATAATGTTTAAT-TTTGTATTT
5934376 TGGTTTAAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.60
Consensus pattern (26 bp):
AATTAATAATGTTTAATTTTGTATTT
Found at i:5934478 original size:7 final size:7
Alignment explanation
Indices: 5934468--5934501 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
5934458 AAGATTTAAG
*
5934468 GTTTTGA
1 GTTTAGA
5934475 GTTTAGA
1 GTTTAGA
5934482 GTTTAGA
1 GTTTAGA
5934489 GTTTAGA
1 GTTTAGA
*
5934496 ATTTAG
1 GTTTAG
5934502 GATTTAAGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.47
Consensus pattern (7 bp):
GTTTAGA
Found at i:5934513 original size:21 final size:20
Alignment explanation
Indices: 5934459--5934514 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
5934449 TCAAGGATTA
* *
5934459 AGATTTAAGGTTTTGAGTTT
1 AGATTTAAGGTTTAGAATTT
5934479 AGAGTTT-AGAGTTTAGAATTT
1 AGA-TTTAAG-GTTTAGAATTT
5934500 AGGATTTAAGGTTTA
1 A-GATTTAAGGTTTA
5934515 TAAGTATGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
20 5 0.17
21 21 0.70
22 4 0.13
ACGTcount: A:0.30, C:0.00, G:0.25, T:0.45
Consensus pattern (20 bp):
AGATTTAAGGTTTAGAATTT
Found at i:5936848 original size:16 final size:16
Alignment explanation
Indices: 5936826--5936864 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5936816 ACTTACTAAC
5936826 AAAATAAAATAAAATA
1 AAAATAAAATAAAATA
* * *
5936842 AATATAAATTAAATTA
1 AAAATAAAATAAAATA
5936858 AAAATAA
1 AAAATAA
5936865 CCAAACTTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAATAAAATAAAATA
Found at i:5938942 original size:3 final size:3
Alignment explanation
Indices: 5938934--5938959 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5938924 ATTTGATGCG
5938934 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
5938960 TATATATCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5939225 original size:19 final size:19
Alignment explanation
Indices: 5939190--5939235 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
5939180 GTTTTCATTT
*
5939190 TATTTTATTTTAATACTTA
1 TATTTTATTTTAATACTGA
*
5939209 TATTTTATTATT-TTACTGA
1 TATTTTATT-TTAATACTGA
5939228 T-TTTTATT
1 TATTTTATT
5939236 CAAAAAAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 7 0.29
19 15 0.62
20 2 0.08
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.67
Consensus pattern (19 bp):
TATTTTATTTTAATACTGA
Found at i:5939571 original size:17 final size:16
Alignment explanation
Indices: 5939551--5939593 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 16
5939541 TTTTATGAAC
5939551 TTTTTACAATTTTTATA
1 TTTTTA-AATTTTTATA
5939568 TTTTTAAATATTTTATA
1 TTTTTAAAT-TTTTATA
5939585 TATTTTAAA
1 T-TTTTAAA
5939594 ATTATTTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.12
17 14 0.58
18 7 0.29
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTTTAAATTTTTATA
Found at i:5939588 original size:19 final size:19
Alignment explanation
Indices: 5939559--5939600 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
5939549 ACTTTTTACA
*
5939559 ATTTTTATATTTTTAAA-T
1 ATTTTTATATTTTAAAATT
5939577 ATTTTATATATTTTAAAATT
1 ATTTT-TATATTTTAAAATT
5939597 ATTT
1 ATTT
5939601 GTTGACATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.24
19 11 0.52
20 5 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTTTTATATTTTAAAATT
Found at i:5943960 original size:18 final size:18
Alignment explanation
Indices: 5943937--5944057 Score: 116
Period size: 18 Copynumber: 6.6 Consensus size: 18
5943927 AGAGAATAGT
* *
5943937 AATATTGGCTCGTTAACC
1 AATACTGGCTCGTTAAGC
* * *
5943955 AATATTGGCTCGTAAGAGT
1 AATACTGGCTCGTTA-AGC
*
5943974 AATACTGGCTCGTTGAGC
1 AATACTGGCTCGTTAAGC
* * *
5943992 AATATTGGCTCGTAAGAGT
1 AATACTGGCTCGTTA-AGC
*
5944011 AATACTGGCTAGTTAAGC
1 AATACTGGCTCGTTAAGC
*
5944029 AATACTGGCTCGTAAGAGC
1 AATACTGGCTCGTTA-AGC
5944048 AATACTGGCT
1 AATACTGGCT
5944058 TGTAAGAGCA
Statistics
Matches: 83, Mismatches: 17, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
18 43 0.52
19 40 0.48
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (18 bp):
AATACTGGCTCGTTAAGC
Found at i:5943982 original size:19 final size:19
Alignment explanation
Indices: 5943954--5944081 Score: 152
Period size: 19 Copynumber: 6.8 Consensus size: 19
5943944 GCTCGTTAAC
*
5943954 CAATATTGGCTCGTAAGAG
1 CAATACTGGCTCGTAAGAG
* *
5943973 TAATACTGGCTCGT-TGAG
1 CAATACTGGCTCGTAAGAG
*
5943991 CAATATTGGCTCGTAAGAG
1 CAATACTGGCTCGTAAGAG
* * *
5944010 TAATACTGGCTAGTTA-AG
1 CAATACTGGCTCGTAAGAG
5944028 CAATACTGGCTCGTAAGAG
1 CAATACTGGCTCGTAAGAG
*
5944047 CAATACTGGCTTGTAAGAG
1 CAATACTGGCTCGTAAGAG
* *
5944066 CAATATTGGATCGTAA
1 CAATACTGGCTCGTAA
5944082 TGAATTATTT
Statistics
Matches: 90, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
18 30 0.33
19 60 0.67
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (19 bp):
CAATACTGGCTCGTAAGAG
Found at i:5943984 original size:37 final size:37
Alignment explanation
Indices: 5943934--5944081 Score: 206
Period size: 37 Copynumber: 4.0 Consensus size: 37
5943924 TAGAGAGAAT
* *
5943934 AGTAATATTGGCTCGTTAACCAATATTGGCTCGTAAG
1 AGTAATACTGGCTCGTTAAGCAATATTGGCTCGTAAG
*
5943971 AGTAATACTGGCTCGTTGAGCAATATTGGCTCGTAAG
1 AGTAATACTGGCTCGTTAAGCAATATTGGCTCGTAAG
* *
5944008 AGTAATACTGGCTAGTTAAGCAATACTGGCTCGTAAG
1 AGTAATACTGGCTCGTTAAGCAATATTGGCTCGTAAG
* * * *
5944045 AGCAATACTGGCTTGTAAGAGCAATATTGGATCGTAA
1 AGTAATACTGGCTCGTTA-AGCAATATTGGCTCGTAA
5944082 TGAATTATTT
Statistics
Matches: 99, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
37 83 0.84
38 16 0.16
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (37 bp):
AGTAATACTGGCTCGTTAAGCAATATTGGCTCGTAAG
Found at i:5944785 original size:21 final size:21
Alignment explanation
Indices: 5944728--5944803 Score: 84
Period size: 21 Copynumber: 3.6 Consensus size: 21
5944718 GCAGGGTGAG
*
5944728 ACTTGTATCGGTAG--GAGTAAG
1 ACTTGTATCGGTAGAAGAGT--C
*
5944749 ACTTGTTTCGGTAGAAGAGTC
1 ACTTGTATCGGTAGAAGAGTC
**
5944770 ACTTGTATCGGTAGAACTGTC
1 ACTTGTATCGGTAGAAGAGTC
5944791 ACTTGTATCGGTA
1 ACTTGTATCGGTA
5944804 AAAATCTGTA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 44 0.92
23 4 0.08
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.33
Consensus pattern (21 bp):
ACTTGTATCGGTAGAAGAGTC
Found at i:5945451 original size:19 final size:17
Alignment explanation
Indices: 5945431--5945463 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5945421 TTCCAATATT
*
5945431 TTTTATTTTATATAATG
1 TTTTATCTTATATAATG
5945448 TTTTATCTTATATAAT
1 TTTTATCTTATATAAT
5945464 TGATATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (17 bp):
TTTTATCTTATATAATG
Found at i:5945512 original size:30 final size:30
Alignment explanation
Indices: 5945425--5945517 Score: 80
Period size: 30 Copynumber: 3.0 Consensus size: 30
5945415 TTCCTTTTCC
* * *
5945425 AATATTTTTTATTTTATATAATGTTTTATCTTA
1 AATATTTTATATATTATAT-AT-TTTTA-ATTA
* * *
5945458 TATAATTGATATATTATACT-TTTTTAATTA
1 AATATTTTATATATTATA-TATTTTTAATTA
5945488 AATATTTTATATATTATATATTTTTGAATT
1 AATATTTTATATATTATATATTTTT-AATT
5945518 TATATATATA
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
29 1 0.02
30 23 0.48
31 9 0.19
32 1 0.02
33 13 0.27
34 1 0.02
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.60
Consensus pattern (30 bp):
AATATTTTATATATTATATATTTTTAATTA
Found at i:5945525 original size:18 final size:17
Alignment explanation
Indices: 5945501--5945552 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
5945491 ATTTTATATA
*
5945501 TTATATATTTTTGAATT
1 TTATATATTTTTAAATT
* *
5945518 TATATATATATATAAATT
1 T-TATATATTTTTAAATT
5945536 TTATATGATTTTTAAAT
1 TTATAT-ATTTTTAAAT
5945553 AATTTTTTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 6 0.21
18 22 0.79
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (17 bp):
TTATATATTTTTAAATT
Found at i:5945917 original size:23 final size:24
Alignment explanation
Indices: 5945890--5945937 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
5945880 AAATTTAAAT
*
5945890 AAATACTCATA-TTTATATTATTA
1 AAATACTCATATTTTATACTATTA
*
5945913 AAATATTCATATTTTATACTATTA
1 AAATACTCATATTTTATACTATTA
5945937 A
1 A
5945938 TATATATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (24 bp):
AAATACTCATATTTTATACTATTA
Found at i:5946063 original size:21 final size:21
Alignment explanation
Indices: 5946011--5946072 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
5946001 GTTAATGCTA
*
5946011 AAATT-TATTATTAAAA-ATGT
1 AAATTATATTATTAAAATA-AT
* *
5946031 AAATAATTTTATTAAAATAAT
1 AAATTATATTATTAAAATAAT
*
5946052 AAATTATATTATCAAATATAA
1 AAATTATATTATTAAA-ATAA
5946073 ATATTTATGT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
20 4 0.12
21 24 0.73
22 5 0.15
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (21 bp):
AAATTATATTATTAAAATAAT
Found at i:5946172 original size:21 final size:20
Alignment explanation
Indices: 5946146--5946185 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
5946136 ATTAAAATTA
*
5946146 AAAATTTATTATTAATTTATT
1 AAAATTAATT-TTAATTTATT
*
5946167 AAAATTAATTTTTATTTAT
1 AAAATTAATTTTAATTTAT
5946186 AAATCAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
AAAATTAATTTTAATTTATT
Found at i:5948208 original size:20 final size:19
Alignment explanation
Indices: 5948162--5948209 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
5948152 ATTTGATTTT
*
5948162 ATAAATAAAAAAAATTATTAA
1 ATAAA-AAAAAAAATTA-AAA
* *
5948183 TTAAAAAAATAAATTAAAA
1 ATAAAAAAAAAAATTAAAA
5948202 ATAAAAAA
1 ATAAAAAA
5948210 CTTGAAAACA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 9 0.39
20 10 0.43
21 4 0.17
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (19 bp):
ATAAAAAAAAAAATTAAAA
Found at i:5948246 original size:13 final size:13
Alignment explanation
Indices: 5948228--5948252 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5948218 CAATACATTT
5948228 ATTAATTAAAAAC
1 ATTAATTAAAAAC
5948241 ATTAATTAAAAA
1 ATTAATTAAAAA
5948253 TAAAAAAGCT
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:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAATTAAAAAC
Found at i:5950944 original size:43 final size:43
Alignment explanation
Indices: 5950871--5950966 Score: 111
Period size: 43 Copynumber: 2.2 Consensus size: 43
5950861 CATAAACGTC
* ** *
5950871 GCTAAAGAACATGGTCTTTAGTGGCATTTTTCCCACAAGCACA
1 GCTAAAAAACATGGTCTTTAACGGCATTTTTCCCACAAACACA
** * * *
5950914 GCTAAAAAACATGGTCTTTAACGGTGTTTTTCCTACAAACGCC
1 GCTAAAAAACATGGTCTTTAACGGCATTTTTCCCACAAACACA
5950957 GCTAAAAAAC
1 GCTAAAAAAC
5950967 TGCTAAAGAA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (43 bp):
GCTAAAAAACATGGTCTTTAACGGCATTTTTCCCACAAACACA
Found at i:5956429 original size:42 final size:39
Alignment explanation
Indices: 5956383--5956549 Score: 163
Period size: 39 Copynumber: 4.1 Consensus size: 39
5956373 CCTTTAACAG
*
5956383 CGTTTATGGAAAAACGCCGCTAATGCTTTTTACCTTTTGCGA
1 CGTTTAT-GAAAAACGCCGCTATTGC--TTTACCTTTTGCGA
** *
5956425 CGTTTATGATAAAACATCGCTATTGCTTTACCTTTTGCGG
1 CGTTTATGA-AAAACGCCGCTATTGCTTTACCTTTTGCGA
* * *
5956465 CGTTTTTTTCATAAACGCCGCTATTGCTTTACCTTTTGCGA
1 CG--TTTATGAAAAACGCCGCTATTGCTTTACCTTTTGCGA
* * * * * *
5956506 CATTTATTAAAAACGCTGCTATTGCTTTACTTTTTACTA
1 CGTTTATGAAAAACGCCGCTATTGCTTTACCTTTTGCGA
5956545 CGTTT
1 CGTTT
5956550 TCTGTCCAAA
Statistics
Matches: 103, Mismatches: 19, Indels: 9
0.79 0.15 0.07
Matches are distributed among these distances:
39 34 0.33
40 15 0.15
41 29 0.28
42 25 0.24
ACGTcount: A:0.22, C:0.21, G:0.15, T:0.42
Consensus pattern (39 bp):
CGTTTATGAAAAACGCCGCTATTGCTTTACCTTTTGCGA
Found at i:5956499 original size:41 final size:39
Alignment explanation
Indices: 5956394--5956550 Score: 152
Period size: 41 Copynumber: 3.9 Consensus size: 39
5956384 GTTTATGGAA
* * *
5956394 AAACGCCGCTAATGCTTTTTACCTTTTGCGACGTTTATGAT
1 AAACGCCGCTATTGC--TTTACCTTTTGCGACGTTTTTTAT
** *
5956435 AAAACATCGCTATTGCTTTACCTTTTGCGGCGTTTTTTTCAT
1 -AAACGCCGCTATTGCTTTACCTTTTGCGACG-TTTTTT-AT
* * *
5956477 AAACGCCGCTATTGCTTTACCTTTTGCGACATTTATTAA
1 AAACGCCGCTATTGCTTTACCTTTTGCGACGTTTTTTAT
* * * *
5956516 AAACGCTGCTATTGCTTTACTTTTTACTACGTTTT
1 AAACGCCGCTATTGCTTTACCTTTTGCGACGTTTT
5956551 CTGTCCAAAC
Statistics
Matches: 95, Mismatches: 18, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
39 30 0.32
40 20 0.21
41 31 0.33
42 14 0.15
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.43
Consensus pattern (39 bp):
AAACGCCGCTATTGCTTTACCTTTTGCGACGTTTTTTAT
Found at i:5956549 original size:80 final size:82
Alignment explanation
Indices: 5956394--5956550 Score: 203
Period size: 80 Copynumber: 1.9 Consensus size: 82
5956384 GTTTATGGAA
*
5956394 AAACGCCGCTAATGCTTTTTACCTTTTGCGACGTTTATGATAAAACATCGCTATTGCTTTACCTT
1 AAACGCCGCTAATGC-TTTTACCTTTTGCGACATTTATGATAAAACATCGCTATTGCTTTACCTT
* *
5956459 TTGCGGCGTTTTTTTCAT
65 TTACGACGTTTTTTTCAT
* * * *
5956477 AAACGCCGCTATTGC-TTTACCTTTTGCGACATTTATTA-AAAAC-GCTGCTATTGCTTTACTTT
1 AAACGCCGCTAATGCTTTTACCTTTTGCGACATTTATGATAAAACATC-GCTATTGCTTTACCTT
*
5956539 TTACTACGTTTT
65 TTACGACGTTTT
5956551 CTGTCCAAAC
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
79 1 0.02
80 29 0.45
81 21 0.32
83 14 0.22
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.43
Consensus pattern (82 bp):
AAACGCCGCTAATGCTTTTACCTTTTGCGACATTTATGATAAAACATCGCTATTGCTTTACCTTT
TACGACGTTTTTTTCAT
Found at i:5968074 original size:29 final size:29
Alignment explanation
Indices: 5968041--5968099 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
5968031 ACAAAAGGCA
*
5968041 AAAGATTTCTTACAACTTTCAAAATCGAC
1 AAAGATTTCTTACAACTTTCAAAACCGAC
5968070 AAAGATTTCTTACAACTTTCAAAACCGAC
1 AAAGATTTCTTACAACTTTCAAAACCGAC
5968099 A
1 A
5968100 TGAGTAAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.22, G:0.07, T:0.29
Consensus pattern (29 bp):
AAAGATTTCTTACAACTTTCAAAACCGAC
Found at i:5969278 original size:18 final size:18
Alignment explanation
Indices: 5969229--5969272 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
5969219 CATAAATTTA
*
5969229 AATAAAAAT-TAAAAAATT
1 AATAAAAATAT-ATAAATT
*
5969247 ATTAAAAATATATAAATT
1 AATAAAAATATATAAATT
5969265 AATAAAAA
1 AATAAAAA
5969273 AGTATATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 21 0.95
19 1 0.05
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AATAAAAATATATAAATT
Found at i:5969426 original size:9 final size:9
Alignment explanation
Indices: 5969412--5969465 Score: 55
Period size: 7 Copynumber: 6.4 Consensus size: 9
5969402 TATTTTGAAA
5969412 AAAATATAT
1 AAAATATAT
5969421 -AAA-ATAT
1 AAAATATAT
*
5969428 -AAATTTAT
1 AAAATATAT
5969436 GAAAATATAT
1 -AAAATATAT
5969446 AAAAT-T-T
1 AAAATATAT
5969453 AAAATATAT
1 AAAATATAT
5969462 AAAA
1 AAAA
5969466 AAAACCTATA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
7 13 0.34
8 8 0.21
9 10 0.26
10 7 0.18
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (9 bp):
AAAATATAT
Found at i:5969476 original size:47 final size:45
Alignment explanation
Indices: 5969425--5969513 Score: 126
Period size: 45 Copynumber: 1.9 Consensus size: 45
5969415 ATATATAAAA
5969425 TATAA-ATTTATGAAAATATATAAAATTTAAAATATATAAAAAAAACC
1 TATAATATTT-TGAAAATATAT--AATTTAAAATATATAAAAAAAACC
* *
5969472 TATAATATTTTGAAAATATATAATTTATAATTTATAAAAAAA
1 TATAATATTTTGAAAATATATAATTTAAAATATATAAAAAAA
5969514 TTTAAAACTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
45 19 0.49
47 16 0.41
48 4 0.10
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (45 bp):
TATAATATTTTGAAAATATATAATTTAAAATATATAAAAAAAACC
Found at i:5969569 original size:38 final size:38
Alignment explanation
Indices: 5969527--5969604 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 38
5969517 AAAACTTATG
* *
5969527 AATTTATGAAA-AATATATAAATATTTAAAAGAATTAAA
1 AATTTAT-AAAGAATATATAAATATATAAAAGAACTAAA
* *
5969565 AATTTATAAAGTATATATAAATCTATAAAAGAACTAAA
1 AATTTATAAAGAATATATAAATATATAAAAGAACTAAA
5969603 AA
1 AA
5969605 GAATATTGTC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 3 0.09
38 32 0.91
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.32
Consensus pattern (38 bp):
AATTTATAAAGAATATATAAATATATAAAAGAACTAAA
Found at i:5969574 original size:19 final size:19
Alignment explanation
Indices: 5969552--5969604 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
5969542 TATAAATATT
*
5969552 TAAAAGAATTAAAAATTTA
1 TAAAAGAATTAAAAATCTA
* *
5969571 T-AAAGTATATATAAATCTA
1 TAAAAGAAT-TAAAAATCTA
*
5969590 TAAAAGAACTAAAAA
1 TAAAAGAATTAAAAA
5969605 GAATATTGTC
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
18 6 0.23
19 15 0.58
20 5 0.19
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (19 bp):
TAAAAGAATTAAAAATCTA
Found at i:5973406 original size:22 final size:21
Alignment explanation
Indices: 5973363--5973406 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
5973353 ATATAACTTC
5973363 TTTTAAATTAATTGAATATTT
1 TTTTAAATTAATTGAATATTT
5973384 TTTTATAATTACATT-AAT-TTT
1 TTTTA-AATTA-ATTGAATATTT
5973405 TT
1 TT
5973407 AATTTATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 10 0.48
22 8 0.38
23 3 0.14
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (21 bp):
TTTTAAATTAATTGAATATTT
Found at i:5973623 original size:3 final size:3
Alignment explanation
Indices: 5973615--5973640 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5973605 GCATGTGCCT
5973615 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
5973641 TTTTAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:5978923 original size:12 final size:13
Alignment explanation
Indices: 5978898--5978922 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5978888 TTTGATCAAA
5978898 AAAATATTTTTTT
1 AAAATATTTTTTT
5978911 AAAATATTTTTT
1 AAAATATTTTTT
5978923 ACGTTAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
AAAATATTTTTTT
Found at i:5979619 original size:22 final size:22
Alignment explanation
Indices: 5979581--5979627 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
5979571 ATCAATACGG
* *
5979581 ATCAATTGAATCGAATAATTGA
1 ATCAATTGAATCAAATAATTAA
5979603 ATCAATTGAA-CTAAATAATTAA
1 ATCAATTGAATC-AAATAATTAA
5979625 ATC
1 ATC
5979628 GATCGGACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.49, C:0.11, G:0.09, T:0.32
Consensus pattern (22 bp):
ATCAATTGAATCAAATAATTAA
Found at i:5994223 original size:18 final size:19
Alignment explanation
Indices: 5994200--5994237 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
5994190 CATTTTAATT
5994200 AATGATCAAA-TTGAAAAA
1 AATGATCAAATTTGAAAAA
5994218 AATGATCAAATTTGAAAAA
1 AATGATCAAATTTGAAAAA
5994237 A
1 A
5994238 TAAACTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.61, C:0.05, G:0.11, T:0.24
Consensus pattern (19 bp):
AATGATCAAATTTGAAAAA
Found at i:5994275 original size:29 final size:29
Alignment explanation
Indices: 5994215--5994268 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
5994205 TCAAATTGAA
5994215 AAAAATGATCAAATTTGAAAAAATAAACT
1 AAAAATGATCAAATTTGAAAAAATAAACT
5994244 AAAAATGATCAAA-TT-AAAAAATAAA
1 AAAAATGATCAAATTTGAAAAAATAAA
5994269 AATTAAATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 10 0.40
28 2 0.08
29 13 0.52
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.22
Consensus pattern (29 bp):
AAAAATGATCAAATTTGAAAAAATAAACT
Found at i:5996248 original size:15 final size:15
Alignment explanation
Indices: 5996230--5996300 Score: 70
Period size: 15 Copynumber: 4.7 Consensus size: 15
5996220 GAGGCATGCT
*
5996230 CAGCAGCAGCAACAA
1 CAGCAGCAGCACCAA
* *
5996245 CAGCAGCAGCAGCAG
1 CAGCAGCAGCACCAA
* *
5996260 CAACAGCAACACCAA
1 CAGCAGCAGCACCAA
* *
5996275 CAGCCGCAACACCAA
1 CAGCAGCAGCACCAA
*
5996290 CAGCAACAGCA
1 CAGCAGCAGCA
5996301 GCGAAGAGAA
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.44, C:0.38, G:0.18, T:0.00
Consensus pattern (15 bp):
CAGCAGCAGCACCAA
Found at i:5996251 original size:18 final size:18
Alignment explanation
Indices: 5996230--5996267 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
5996220 GAGGCATGCT
5996230 CAGCAGCAGCAACAACAG
1 CAGCAGCAGCAACAACAG
*
5996248 CAGCAGCAGCAGCAACAG
1 CAGCAGCAGCAACAACAG
5996266 CA
1 CA
5996268 ACACCAACAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.34, G:0.24, T:0.00
Consensus pattern (18 bp):
CAGCAGCAGCAACAACAG
Found at i:5996256 original size:21 final size:21
Alignment explanation
Indices: 5996233--5996302 Score: 86
Period size: 21 Copynumber: 3.3 Consensus size: 21
5996223 GCATGCTCAG
* *
5996233 CAGCAGCAACAACAGCAGCAG
1 CAGCAGCAACAACAACAGCAA
* *
5996254 CAGCAGCAACAGCAACACCAA
1 CAGCAGCAACAACAACAGCAA
* *
5996275 CAGCCGCAACACCAACAGCAA
1 CAGCAGCAACAACAACAGCAA
5996296 CAGCAGC
1 CAGCAGC
5996303 GAAGAGAAGG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.43, C:0.39, G:0.19, T:0.00
Consensus pattern (21 bp):
CAGCAGCAACAACAACAGCAA
Found at i:5996268 original size:6 final size:6
Alignment explanation
Indices: 5996242--5996300 Score: 61
Period size: 6 Copynumber: 10.3 Consensus size: 6
5996232 GCAGCAGCAA
* * * *
5996242 CAACAG CAGCAG CAGCAG CAACAG CAACAC CAACAG C--C-G CAACAC
1 CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG
5996287 CAACAG CAACAG CA
1 CAACAG CAACAG CA
5996301 GCGAAGAGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
3 2 0.05
4 1 0.02
5 1 0.02
6 40 0.91
ACGTcount: A:0.44, C:0.39, G:0.17, T:0.00
Consensus pattern (6 bp):
CAACAG
Found at i:6002953 original size:6 final size:6
Alignment explanation
Indices: 6002942--6002969 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
6002932 CATATATAAT
6002942 ATATAC ATATAC ATATAC ATATAC ATAT
1 ATATAC ATATAC ATATAC ATATAC ATAT
6002970 CAACATTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (6 bp):
ATATAC
Found at i:6003250 original size:8 final size:8
Alignment explanation
Indices: 6003237--6003266 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
6003227 GAATGAACTG
*
6003237 AAATATTA
1 AAATATGA
6003245 AAATATGA
1 AAATATGA
6003253 AAATATGA
1 AAATATGA
6003261 AAATAT
1 AAATAT
6003267 ATGAATGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (8 bp):
AAATATGA
Found at i:6013247 original size:31 final size:34
Alignment explanation
Indices: 6013212--6013277 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 34
6013202 ATTCAATATC
*
6013212 TTTATAATTTTTAAAA-AAATT-AAAT-TAATTT
1 TTTATAATTTTGAAAATAAATTAAAATGTAATTT
* *
6013243 TTTATCATTTTGAAAATAGATTAAAATGTAATTT
1 TTTATAATTTTGAAAATAAATTAAAATGTAATTT
6013277 T
1 T
6013278 ATCATTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 14 0.48
32 4 0.14
33 4 0.14
34 7 0.24
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (34 bp):
TTTATAATTTTGAAAATAAATTAAAATGTAATTT
Found at i:6013477 original size:16 final size:17
Alignment explanation
Indices: 6013440--6013480 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
6013430 GTTTTTTAGG
6013440 ATTAATATATTAAAAAT
1 ATTAATATATTAAAAAT
**
6013457 A-TAATA-ATTAAATTT
1 ATTAATATATTAAAAAT
6013472 ATTAATATA
1 ATTAATATA
6013481 ATTATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
15 8 0.40
16 10 0.50
17 2 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTAATATATTAAAAAT
Found at i:6014302 original size:21 final size:21
Alignment explanation
Indices: 6014278--6014326 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
6014268 ATTAATTATT
*
6014278 TTAATCTCATCGCTATAATAC
1 TTAATCTCATCACTATAATAC
* * * *
6014299 TTAATTTCATTACTATAGTAG
1 TTAATCTCATCACTATAATAC
6014320 TTAATCT
1 TTAATCT
6014327 TATCTCTACC
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.16, G:0.06, T:0.45
Consensus pattern (21 bp):
TTAATCTCATCACTATAATAC
Found at i:6014476 original size:29 final size:29
Alignment explanation
Indices: 6014444--6014505 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
6014434 TTAAAGCACG
*
6014444 ATAAAATTACATTTGACTCTCCTAAAATA
1 ATAAAATCACATTTGACTCTCCTAAAATA
*
6014473 ATAAGATCACATTTGACTCTCCTAAAATA
1 ATAAAATCACATTTGACTCTCCTAAAATA
6014502 ATAA
1 ATAA
6014506 GATCGTGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (29 bp):
ATAAAATCACATTTGACTCTCCTAAAATA
Found at i:6014506 original size:29 final size:29
Alignment explanation
Indices: 6014452--6014509 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
6014442 CGATAAAATT
6014452 ACATTTGACTCTCCTAAAATAATAAGATC
1 ACATTTGACTCTCCTAAAATAATAAGATC
6014481 ACATTTGACTCTCCTAAAATAATAAGATC
1 ACATTTGACTCTCCTAAAATAATAAGATC
6014510 GTGATTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.31
Consensus pattern (29 bp):
ACATTTGACTCTCCTAAAATAATAAGATC
Found at i:6027008 original size:6 final size:6
Alignment explanation
Indices: 6026935--6027007 Score: 94
Period size: 6 Copynumber: 12.2 Consensus size: 6
6026925 GAGGGACGTG
* *
6026935 GAGGGA GA-GGA CGGGGGA GAGGGA GAGGGA GAGGAA GAGGGA GAGGGA
1 GAGGGA GAGGGA -GAGGGA GAGGGA GAGGGA GAGGGA GAGGGA GAGGGA
* *
6026983 GAGGGA GAGGGA GGGGGA GGGGGA G
1 GAGGGA GAGGGA GAGGGA GAGGGA G
6027008 GTTCGGCTAA
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
5 3 0.05
6 54 0.90
7 3 0.05
ACGTcount: A:0.30, C:0.01, G:0.68, T:0.00
Consensus pattern (6 bp):
GAGGGA
Found at i:6029552 original size:19 final size:20
Alignment explanation
Indices: 6029524--6029562 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
6029514 ATTGGCGTAA
*
6029524 TTGTAGTTTT-TTTTTTTTT
1 TTGTAATTTTATTTTTTTTT
6029543 TTGTAATTTTACTTTTTTTT
1 TTGTAATTTTA-TTTTTTTT
6029563 CTAACATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
21 8 0.47
ACGTcount: A:0.10, C:0.03, G:0.08, T:0.79
Consensus pattern (20 bp):
TTGTAATTTTATTTTTTTTT
Found at i:6033362 original size:30 final size:32
Alignment explanation
Indices: 6033285--6033360 Score: 89
Period size: 36 Copynumber: 2.2 Consensus size: 32
6033275 ATGTAGCAAA
* *
6033285 TATAATAATTGTTCATGATTAGGAAAGATATT
1 TATAATAATAGTTCATGATTAGAAAAGATATT
6033317 TAAACTAAATAATAGTTCATGATTAGAAAAGATATT
1 T--A-T-AATAATAGTTCATGATTAGAAAAGATATT
6033353 TAATAATA
1 T-ATAATA
6033361 GTGATTAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
32 1 0.03
33 4 0.11
34 2 0.05
35 3 0.08
36 28 0.74
ACGTcount: A:0.47, C:0.04, G:0.12, T:0.37
Consensus pattern (32 bp):
TATAATAATAGTTCATGATTAGAAAAGATATT
Found at i:6037371 original size:44 final size:45
Alignment explanation
Indices: 6037317--6037411 Score: 131
Period size: 44 Copynumber: 2.1 Consensus size: 45
6037307 ACAAAATAAT
* *
6037317 ATCTAGATATTAATTTGATAAAAA-TAAAGTTT-AATAATTACAAG
1 ATCTAAATATTAATTAGATAAAAACTAAA-TTTAAATAATTACAAG
* *
6037361 ATCTAAATATTAATTAGATAAAAACTAAATTTAAATAATTATAAT
1 ATCTAAATATTAATTAGATAAAAACTAAATTTAAATAATTACAAG
6037406 ATCTAA
1 ATCTAA
6037412 TACAAATTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
44 25 0.56
45 20 0.44
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (45 bp):
ATCTAAATATTAATTAGATAAAAACTAAATTTAAATAATTACAAG
Found at i:6038396 original size:33 final size:32
Alignment explanation
Indices: 6038325--6038393 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
6038315 TGTACTTCAT
6038325 AAAAATTCAAAAAAATGCATAATAATTATTTA
1 AAAAATTCAAAAAAATGCATAATAATTATTTA
* * **
6038357 AAAAATTCATAAAAAGTTCATAATTGTT-TTTA
1 AAAAATTCA-AAAAAATGCATAATAATTATTTA
6038389 AAAAA
1 AAAAA
6038394 ATTATTCATC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 18 0.56
33 14 0.44
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (32 bp):
AAAAATTCAAAAAAATGCATAATAATTATTTA
Found at i:6038545 original size:19 final size:21
Alignment explanation
Indices: 6038513--6038553 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
6038503 ATTAGAAAGC
6038513 TAAATTTATCATTATG-CTAA
1 TAAATTTATCATTATGTCTAA
*
6038533 TAAA-TTATTATTATGTCTAA
1 TAAATTTATCATTATGTCTAA
6038553 T
1 T
6038554 TATGCTCTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.49
Consensus pattern (21 bp):
TAAATTTATCATTATGTCTAA
Found at i:6053380 original size:1 final size:1
Alignment explanation
Indices: 6053374--6053411 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
6053364 CAGGAGACGC
6053374 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
6053412 AGGTGGAACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:6063523 original size:17 final size:17
Alignment explanation
Indices: 6063474--6063531 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
6063464 CAGATTTATT
6063474 AAATATGAT-TTTTTTAA
1 AAATAT-ATATTTTTTAA
* * *
6063491 AATTATATAATGTTTAA
1 AAATATATATTTTTTAA
*
6063508 AAATATTTATTTTTTAA
1 AAATATATATTTTTTAA
6063525 AAA-ATAT
1 AAATATAT
6063532 GAGAAATGTA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
16 5 0.16
17 27 0.84
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
AAATATATATTTTTTAA
Found at i:6065212 original size:30 final size:28
Alignment explanation
Indices: 6065167--6065225 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 28
6065157 ATTTCTAGTA
6065167 ATTTATATTTTTAAATTTT-TAACTTTT
1 ATTTATATTTTTAAATTTTATAACTTTT
6065194 ATTTAATATTCTTATAAATTTTAATAACTTTT
1 ATTT-ATATT-TT-TAAATTTT-ATAACTTTT
6065226 TTCAAATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
27 4 0.15
28 5 0.19
29 2 0.07
30 8 0.30
32 8 0.30
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (28 bp):
ATTTATATTTTTAAATTTTATAACTTTT
Found at i:6065949 original size:31 final size:31
Alignment explanation
Indices: 6065911--6065977 Score: 134
Period size: 31 Copynumber: 2.2 Consensus size: 31
6065901 CACCCACTTC
6065911 AGTCCATAATGTTATCAGACGTTCTCAATTT
1 AGTCCATAATGTTATCAGACGTTCTCAATTT
6065942 AGTCCATAATGTTATCAGACGTTCTCAATTT
1 AGTCCATAATGTTATCAGACGTTCTCAATTT
6065973 AGTCC
1 AGTCC
6065978 TTTCGACATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.37
Consensus pattern (31 bp):
AGTCCATAATGTTATCAGACGTTCTCAATTT
Found at i:6066375 original size:55 final size:56
Alignment explanation
Indices: 6066304--6066569 Score: 241
Period size: 55 Copynumber: 4.6 Consensus size: 56
6066294 AAAATTCAAA
**
6066304 ATTTTTTGGTGTTGGCCATCAAATGGCCGACACCTTTTTTTCTC-AAAAAAATTGC
1 ATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCTTTTTCTCGAAAAAAATTGC
* *** * **
6066359 ATTTTTGGGTGTTGGCCATTGCATGGTCGACA-CCCTCTTTTCTCGAGAAAAAAATTTAAA
1 ATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCT-TTTTCTC--GAAAAAAA-TT-GC
* ** ** **
6066419 ATTTTTTGGTGTTGACCATCAAATGATCGACACCCCCATTT-TAAAAAAAAATTGC
1 ATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCTTTTTCTCGAAAAAAATTGC
* * * * *
6066474 ATTTTTGGGTGTTGGCCATCAAATGGCTGACATCTCCTATTTCTCGAAAAAAATTTC
1 ATTTTTTGGTGTTGGCCATCAAATGGCCGACA-CCCCTTTTTCTCGAAAAAAATTGC
6066531 AAAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCC
1 ---ATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCC
6066570 CTTGATGGCC
Statistics
Matches: 165, Mismatches: 34, Indels: 20
0.75 0.16 0.09
Matches are distributed among these distances:
54 2 0.01
55 61 0.37
56 9 0.05
57 18 0.11
58 7 0.04
59 6 0.04
60 59 0.36
61 3 0.02
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (56 bp):
ATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCTTTTTCTCGAAAAAAATTGC
Found at i:6066570 original size:115 final size:116
Alignment explanation
Indices: 6066291--6066570 Score: 367
Period size: 115 Copynumber: 2.4 Consensus size: 116
6066281 GGGGTTTATC
*** **
6066291 AAAAAAA-TTCAAAATTTTTTGGTGTTGGCCATCAAATGGCCGACA-CCTTTTTTTCTCAAAAAA
1 AAAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCATTTTCAAAAAAAA
*** *
6066354 ATTGCATTTTTGGGTGTTGGCCATTGCATGGTCGACACCCTCTTTTCTCGAG
66 ATTGCATTTTTGGGTGTTGGCCATCAAATGGTCGACACCCTCATTTCTC-AG
* **
6066406 AAAAAAATTT-AAAATTTTTTGGTGTTGACCATCAAATGATCGACACCCCCATTTT-AAAAAAAA
1 AAAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCATTTTCAAAAAAAA
6066469 ATTGCATTTTTGGGTGTTGGCCATCAAATGG-CTGACATCTCCT-ATTTCTC-G
66 ATTGCATTTTTGGGTGTTGGCCATCAAATGGTC-GACA-C-CCTCATTTCTCAG
6066520 AAAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCC
1 AAAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCC
6066571 TTGATGGCCA
Statistics
Matches: 144, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
114 12 0.08
115 114 0.79
116 15 0.10
117 3 0.02
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (116 bp):
AAAAAAATTTCAAAATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCATTTTCAAAAAAAA
ATTGCATTTTTGGGTGTTGGCCATCAAATGGTCGACACCCTCATTTCTCAG
Found at i:6066643 original size:60 final size:59
Alignment explanation
Indices: 6066571--6066821 Score: 258
Period size: 60 Copynumber: 4.2 Consensus size: 59
6066561 CGACACCCCC
* *
6066571 TTGATGGCCAACACAAAAAAAATTTGATTTTTTTTCTCGAGAAAATGGGGTGTCGGCCAT
1 TTGATGGCCAACACCAAAAAAATTTAATTTTTTTTCTCGAGAAAA-GGGGTGTCGGCCAT
* * *
6066631 TTGATGGCCAACACCAAAAAATTTTAAATTTTTTTCTCGAGAAAAGAGGGTATCGGCCAT
1 TTGATGGCCAACACCAAAAAAATTTAATTTTTTTTCTCGAGAAAAG-GGGTGTCGGCCAT
*** * * *
6066691 GCAATGGCCAACACC-CAAAAATGTAATTTTTTTT-TTGAGAAAAGGGAGTGTCGGCCAT
1 TTGATGGCCAACACCAAAAAAATTTAATTTTTTTTCTCGAGAAAAGGG-GTGTCGGCCAT
* * * * *
6066749 TTGATGGCTAACACCCAAAAATTTTAAATTTTTTTTCT-GACAAAAAAGGGGGTGTCAGCCA-
1 TTGATGGCCAACACCAAAAAAATTT-AATTTTTTTTCTCG--AGAAAA-GGGGTGTCGGCCAT
6066810 TTGCATGGCCAA
1 TTG-ATGGCCAA
6066822 TACCCCAAAA
Statistics
Matches: 158, Mismatches: 24, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
57 2 0.01
58 30 0.19
59 22 0.14
60 76 0.48
61 4 0.03
62 21 0.13
63 3 0.02
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (59 bp):
TTGATGGCCAACACCAAAAAAATTTAATTTTTTTTCTCGAGAAAAGGGGTGTCGGCCAT
Found at i:6066839 original size:118 final size:118
Alignment explanation
Indices: 6066574--6066839 Score: 310
Period size: 118 Copynumber: 2.2 Consensus size: 118
6066564 CACCCCCTTG
** *
6066574 ATGGCCAACACAAAAAAAATTTGATTTTTTTTCTCGAGAAAATGGGGTGTCGGCCATTTGATGGC
1 ATGGCCAACAC-CCAAAAATGT-ATTTTTTTTCTCGAGAAAATGGGGTGTCGGCCATTTGATGGC
* *
6066639 CAACACCAAAAAATTTTAAATTTTTTTCTCGAGAAAAGAGGGTATCGGCCATGCA
64 CAACACCAAAAAATTTTAAATTTTTTTCTCGAAAAAAGAGGGTATCAGCCATGCA
*
6066694 ATGGCCAACACCCAAAAATGTAATTTTTTTT-TTGAGAAAA-GGGAGTGTCGGCCATTTGATGGC
1 ATGGCCAACACCCAAAAATGT-ATTTTTTTTCTCGAGAAAATGGG-GTGTCGGCCATTTGATGGC
* * * *
6066757 TAACACCCAAAAATTTTAAATTTTTTT-TCTGACAAAAAAGGGGGTGTCAGCCATTGC-
64 CAACACCAAAAAATTTTAAATTTTTTTCTC-G--AAAAAAGAGGGTATCAGCCA-TGCA
* *
6066814 ATGGCCAATACCCCAAAAT-T-TTTTTT
1 ATGGCCAACACCCAAAAATGTATTTTTT
6066840 AAAATTCTCG
Statistics
Matches: 128, Mismatches: 13, Indels: 13
0.83 0.08 0.08
Matches are distributed among these distances:
117 11 0.09
118 53 0.41
119 17 0.13
120 44 0.34
121 3 0.02
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (118 bp):
ATGGCCAACACCCAAAAATGTATTTTTTTTCTCGAGAAAATGGGGTGTCGGCCATTTGATGGCCA
ACACCAAAAAATTTTAAATTTTTTTCTCGAAAAAAGAGGGTATCAGCCATGCA
Found at i:6067149 original size:19 final size:19
Alignment explanation
Indices: 6067125--6067163 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
6067115 ATTTATAAAA
* *
6067125 TTAAAATTTTAAAAAATAT
1 TTAAAAATTGAAAAAATAT
*
6067144 TTAAAAATTGCAAAAATAT
1 TTAAAAATTGAAAAAATAT
6067163 T
1 T
6067164 AATATTAGTA
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:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (19 bp):
TTAAAAATTGAAAAAATAT
Found at i:6069733 original size:2 final size:2
Alignment explanation
Indices: 6069726--6069758 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
6069716 TTAATTAATG
6069726 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6069759 AAAGAATAAA
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:6072504 original size:25 final size:24
Alignment explanation
Indices: 6072467--6072569 Score: 142
Period size: 23 Copynumber: 4.4 Consensus size: 24
6072457 ACACTAGCGC
*
6072467 GCTCTCTGT-TTAGCAC-GTCTCGT
1 GCTCTCTGTATTAGCACTGTGT-GT
6072490 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-TATTAGCACTGTGTGT
*
6072515 GCTCTCTG-ATTAGCACTTTGTGT
1 GCTCTCTGTATTAGCACTGTGTGT
6072538 GCTCTCTG-ATTAGCACTGTGTGT
1 GCTCTCTGTATTAGCACTGTGTGT
6072561 GCTCTCTGT
1 GCTCTCTGT
6072570 TGCCCAGCAC
Statistics
Matches: 73, Mismatches: 3, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
23 52 0.71
24 1 0.01
25 17 0.23
26 3 0.04
ACGTcount: A:0.11, C:0.24, G:0.23, T:0.42
Consensus pattern (24 bp):
GCTCTCTGTATTAGCACTGTGTGT
Found at i:6087784 original size:16 final size:17
Alignment explanation
Indices: 6087760--6087793 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
6087750 TTCAAAACGA
*
6087760 AGATGATTTTCA-AAAT
1 AGATCATTTTCATAAAT
6087776 AGATCATTTTCATAAAT
1 AGATCATTTTCATAAAT
6087793 A
1 A
6087794 ATTAGAAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (17 bp):
AGATCATTTTCATAAAT
Found at i:6088592 original size:39 final size:39
Alignment explanation
Indices: 6088542--6088617 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
6088532 ATTATAAAAC
6088542 ACTTTGTTTCTATATCCACTTGATCTTCATGATCATATA
1 ACTTTGTTTCTATATCCACTTGATCTTCATGATCATATA
*
6088581 ACTTTGTTTCTATATCCACTTGATTTTCATGATCATA
1 ACTTTGTTTCTATATCCACTTGATCTTCATGATCATA
6088618 GAAGATTGGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.25, C:0.20, G:0.08, T:0.47
Consensus pattern (39 bp):
ACTTTGTTTCTATATCCACTTGATCTTCATGATCATATA
Found at i:6097837 original size:4 final size:4
Alignment explanation
Indices: 6097815--6097872 Score: 66
Period size: 4 Copynumber: 14.5 Consensus size: 4
6097805 AAACGGGAGA
* *
6097815 AAAG AGAAG AGAG -AAG AAAG AAAG AAAG AAAG AAAG -AAG AAAG AGAGG
1 AAAG A-AAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG A-AAG
6097863 AAAG AAAG AA
1 AAAG AAAG AA
6097873 GGAGAGAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
3 5 0.11
4 34 0.74
5 7 0.15
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:6097851 original size:32 final size:32
Alignment explanation
Indices: 6097819--6097881 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
6097809 GGGAGAAAAG
6097819 AGAAGAGAGAAGAAAGAAAGAAAGAAAGAAAGA
1 AGAA-AGAGAAGAAAGAAAGAAAGAAAGAAAGA
* * *
6097852 AGAAAGAGAGGAAAGAAAGAAGGAGAGAAA
1 AGAAAGAGAAGAAAGAAAGAAAGAAAGAAA
6097882 AATAATTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 23 0.85
33 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (32 bp):
AGAAAGAGAAGAAAGAAAGAAAGAAAGAAAGA
Found at i:6099665 original size:28 final size:30
Alignment explanation
Indices: 6099597--6099665 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 30
6099587 TTCAATAGTG
6099597 TTAAAATATTTATACATTTTAAAAATAGTTT
1 TTAAAAT-TTTATACATTTTAAAAATAGTTT
*** *
6099628 TTATGTTTTTATA-ATTTT-AAAATATTTT
1 TTAAAATTTTATACATTTTAAAAATAGTTT
6099656 TTAAAATTTT
1 TTAAAATTTT
6099666 GACTGATCAA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
28 16 0.52
29 5 0.16
30 6 0.19
31 4 0.13
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (30 bp):
TTAAAATTTTATACATTTTAAAAATAGTTT
Found at i:6104665 original size:3 final size:3
Alignment explanation
Indices: 6104652--6104694 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
6104642 CTGAAAGGTT
* *
6104652 AAG ATG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG GAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
6104695 TAGGGTTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.63, C:0.00, G:0.35, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:6105309 original size:9 final size:9
Alignment explanation
Indices: 6105295--6105319 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
6105285 ACGATAAAAA
6105295 TTATTTATT
1 TTATTTATT
6105304 TTATTTATT
1 TTATTTATT
6105313 TTATTTA
1 TTATTTA
6105320 AAAAAATGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
TTATTTATT
Found at i:6122679 original size:34 final size:33
Alignment explanation
Indices: 6122620--6122685 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 33
6122610 TAAATTAAAG
* *
6122620 TAATTAAATCATGTTATGTTAATTAAACTAGTT
1 TAATTAAATCAAGTTATGATAATTAAACTAGTT
*
6122653 TAATTAAAATCAAGTTAT-ATACATTAAATTAGT
1 TAATT-AAATCAAGTTATGATA-ATTAAACTAGT
6122686 GGATGAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 7 0.25
34 21 0.75
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (33 bp):
TAATTAAATCAAGTTATGATAATTAAACTAGTT
Found at i:6123882 original size:30 final size:30
Alignment explanation
Indices: 6123818--6123902 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 30
6123808 TATATGTCAG
** * * *
6123818 CTTGTGTGAGCAATTTTGATACAATGTCAA
1 CTTGTGTGAGCAATCCTGAAATAATGCCAA
*
6123848 CTTGTGTGAGCAATCCTGAAATAATGCCAT
1 CTTGTGTGAGCAATCCTGAAATAATGCCAA
* * *
6123878 CTTGTATGAGCAACCCTAAAATAAT
1 CTTGTGTGAGCAATCCTGAAATAAT
6123903 ATTAGCTTAT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (30 bp):
CTTGTGTGAGCAATCCTGAAATAATGCCAA
Found at i:6129405 original size:23 final size:23
Alignment explanation
Indices: 6129373--6129416 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
6129363 GACTCGAATT
6129373 TTAAAATTTAAAAAATAAAGAAA
1 TTAAAATTTAAAAAATAAAGAAA
* *
6129396 TTAAATTTTAAATAATAAAGA
1 TTAAAATTTAAAAAATAAAGA
6129417 TATGAAGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (23 bp):
TTAAAATTTAAAAAATAAAGAAA
Found at i:6140817 original size:29 final size:29
Alignment explanation
Indices: 6140784--6140844 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
6140774 TTAAATTAGT
*
6140784 AATGAT-AAAATTGTACTTTGACCCTTCAA
1 AATGATAAAAATTGTA-TTTAACCCTTCAA
* *
6140813 AATGATAAAAATTTTATTTAACTCTTCAA
1 AATGATAAAAATTGTATTTAACCCTTCAA
6140842 AAT
1 AAT
6140845 TAAATTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 20 0.71
30 8 0.29
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.38
Consensus pattern (29 bp):
AATGATAAAAATTGTATTTAACCCTTCAA
Found at i:6141566 original size:31 final size:30
Alignment explanation
Indices: 6141479--6141567 Score: 81
Period size: 31 Copynumber: 3.0 Consensus size: 30
6141469 TTGATTTAAT
6141479 ATGCAATTGTATATAT-AAACTTTAATTTG
1 ATGCAATTGTATATATGAAACTTTAATTTG
* * ** * *
6141508 ATGCAATTATACACGTGGAACTCTAATTGTG
1 ATGCAATTGTATATATGAAACTTTAATT-TG
* * *
6141539 GTTCAATTGTATATTTGAAACTTTAATTT
1 ATGCAATTGTATATATGAAACTTTAATTT
6141568 TGAATTTAAT
Statistics
Matches: 44, Mismatches: 14, Indels: 3
0.72 0.23 0.05
Matches are distributed among these distances:
29 12 0.27
30 10 0.23
31 22 0.50
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.43
Consensus pattern (30 bp):
ATGCAATTGTATATATGAAACTTTAATTTG
Found at i:6155158 original size:15 final size:15
Alignment explanation
Indices: 6155140--6155169 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6155130 TTTGAAAATT
6155140 TTATTTTATTTTTAA
1 TTATTTTATTTTTAA
*
6155155 TTATTTTGTTTTTAA
1 TTATTTTATTTTTAA
6155170 GAAGTCTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (15 bp):
TTATTTTATTTTTAA
Found at i:6156433 original size:8 final size:8
Alignment explanation
Indices: 6156420--6156452 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
6156410 TTGTAATATT
6156420 TATTTATA
1 TATTTATA
6156428 TATTTATA
1 TATTTATA
*
6156436 TATTTAAA
1 TATTTATA
6156444 TATTTATA
1 TATTTATA
6156452 T
1 T
6156453 TTCTAAACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TATTTATA
Found at i:6156663 original size:21 final size:21
Alignment explanation
Indices: 6156636--6156686 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
6156626 GGATTATGTA
6156636 ATTTGGATTTATAAACTTTAT
1 ATTTGGATTTATAAACTTTAT
* * *
6156657 GTTTGGATTTCTAAATTTTAT
1 ATTTGGATTTATAAACTTTAT
6156678 ATTTGGATT
1 ATTTGGATT
6156687 ATGCTATTAT
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:0.27, C:0.04, G:0.14, T:0.55
Consensus pattern (21 bp):
ATTTGGATTTATAAACTTTAT
Found at i:6156988 original size:8 final size:8
Alignment explanation
Indices: 6156975--6157007 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
6156965 TTGTAATATT
6156975 TATTTATA
1 TATTTATA
6156983 TATTTATA
1 TATTTATA
*
6156991 TATTTAAA
1 TATTTATA
6156999 TATTTATA
1 TATTTATA
6157007 T
1 T
6157008 TTCTAAACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TATTTATA
Found at i:6157218 original size:21 final size:21
Alignment explanation
Indices: 6157191--6157241 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
6157181 GGATTATGTA
6157191 ATTTGGATTTATAAACTTTAT
1 ATTTGGATTTATAAACTTTAT
* * *
6157212 GTTTGGATTTCTAAATTTTAT
1 ATTTGGATTTATAAACTTTAT
6157233 ATTTGGATT
1 ATTTGGATT
6157242 ATGCTATTAT
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:0.27, C:0.04, G:0.14, T:0.55
Consensus pattern (21 bp):
ATTTGGATTTATAAACTTTAT
Found at i:6157367 original size:15 final size:16
Alignment explanation
Indices: 6157347--6157379 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
6157337 ACCCTGTGAT
6157347 CCAAAATAC-GAGTAC
1 CCAAAATACTGAGTAC
*
6157362 CCAAAATTCTGAGTAC
1 CCAAAATACTGAGTAC
6157378 CC
1 CC
6157380 TATATATCGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.39, C:0.30, G:0.12, T:0.18
Consensus pattern (16 bp):
CCAAAATACTGAGTAC
Found at i:6161334 original size:18 final size:17
Alignment explanation
Indices: 6161310--6161358 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 17
6161300 TTTTCAGTTG
6161310 TAATTAATTAAAAATTT
1 TAATTAATTAAAAATTT
6161327 TCAATTAATT--AAA-TT
1 T-AATTAATTAAAAATTT
*
6161342 TATTTAATTAAAAATTT
1 TAATTAATTAAAAATTT
6161359 ATTCTCAACC
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
14 7 0.26
15 3 0.11
16 6 0.22
17 3 0.11
18 8 0.30
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATTAATTAAAAATTT
Found at i:6164538 original size:25 final size:25
Alignment explanation
Indices: 6164520--6164565 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
6164510 AAATTTATAG
*
6164520 AAAATAA-AAAATATAAAATTTCAA
1 AAAATAAGAAAAAATAAAATTTCAA
6164544 AAAATAAGAAAAAAT-AAATTTC
1 AAAATAAGAAAAAATAAAATTTC
6164566 CTAAACATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (25 bp):
AAAATAAGAAAAAATAAAATTTCAA
Found at i:6166111 original size:13 final size:13
Alignment explanation
Indices: 6166093--6166117 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6166083 TTTCAAGATT
6166093 TTTTTAATTAATG
1 TTTTTAATTAATG
6166106 TTTTTAATTAAT
1 TTTTTAATTAAT
6166118 AAATATATTA
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:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATG
Found at i:6166663 original size:21 final size:19
Alignment explanation
Indices: 6166621--6166664 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
6166611 ATATAAAATA
*
6166621 TATATTTTTATTATATAAT
1 TATATATTTATTATATAAT
*
6166640 TATATATTTATTATTTAAT
1 TATATATTTATTATATAAT
*
6166659 TTTATA
1 TATATA
6166665 AATAAAAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TATATATTTATTATATAAT
Found at i:6167004 original size:142 final size:139
Alignment explanation
Indices: 6166743--6167004 Score: 323
Period size: 142 Copynumber: 1.9 Consensus size: 139
6166733 AAAAAAGTAA
* * *
6166743 AAAAATTGAAACAATATGAAAAAAAATACAAATGTGCTTAAAAGAATAATTAAACTTGAGACTTA
1 AAAAATTGAAACAATATGAAAAAAAATAAAAATGTGCGTAAAAGAATAATTAAACTAGAGACTTA
** * * *
6166808 AGGATGAAACTACTATTATTTAATCATCTAACCAAAAAAATTAATCTGTTAAAAATATTAATTAA
66 AGGACAAAACCACTAATATTTAATCATCTAACCAAAAAAATTAATCTGTAAAAAATATTAATTAA
6166873 AAATAAAAT
131 AAATAAAAT
* * *
6166882 AAAAATTCGAAACAATATGAAATAAAAAATAAAAATGTGGGTAGAAGAGA-AATTGAACTCAGAG
1 AAAAATT-GAAACAATATG-AA-AAAAAATAAAAATGTGCGTAAAAGA-ATAATTAAACT-AGAG
* * *
6166946 -CTTAAGGACAAAACCACTAATATTTAATCATCTAA-CAAAAAGAGTTGATGTGTAAAAAA
61 ACTTAAGGACAAAACCACTAATATTTAATCATCTAACCAAAAA-AATTAATCTGTAAAAAA
6167005 AACACATTAT
Statistics
Matches: 103, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
139 7 0.07
140 11 0.11
141 8 0.08
142 73 0.71
143 4 0.04
ACGTcount: A:0.54, C:0.09, G:0.11, T:0.26
Consensus pattern (139 bp):
AAAAATTGAAACAATATGAAAAAAAATAAAAATGTGCGTAAAAGAATAATTAAACTAGAGACTTA
AGGACAAAACCACTAATATTTAATCATCTAACCAAAAAAATTAATCTGTAAAAAATATTAATTAA
AAATAAAAT
Found at i:6176783 original size:19 final size:19
Alignment explanation
Indices: 6176741--6176792 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
6176731 AAAATTACAA
6176741 AAAAATTCAAAATAAATTTT
1 AAAAATTCAAAAT-AATTTT
6176761 -AAAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
6176779 AAAAATTCCAAAAT
1 AAAAATT-CAAAAT
6176793 TATGCATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
17 4 0.14
18 1 0.03
19 18 0.62
20 6 0.21
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:6177112 original size:22 final size:23
Alignment explanation
Indices: 6177082--6177124 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
6177072 AATAATAATT
*
6177082 TTTAATTTTTTCCA-TATTGAAA
1 TTTAATTTTTCCCATTATTGAAA
*
6177104 TTTAGTTTTTCCCATTATTGA
1 TTTAATTTTTCCCATTATTGA
6177125 CTTTGGACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.26, C:0.12, G:0.07, T:0.56
Consensus pattern (23 bp):
TTTAATTTTTCCCATTATTGAAA
Found at i:6178242 original size:20 final size:21
Alignment explanation
Indices: 6178198--6178244 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
6178188 AAAAAAATTA
* *
6178198 AATAAAAATTAAATGTTAGTG
1 AATAATAATAAAATGTTAGTG
*
6178219 AATAATAATAAAATTTTAGT-
1 AATAATAATAAAATGTTAGTG
6178239 AATAAT
1 AATAAT
6178245 GACAATAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (21 bp):
AATAATAATAAAATGTTAGTG
Found at i:6192931 original size:13 final size:13
Alignment explanation
Indices: 6192913--6192937 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6192903 TTTTCATTTC
6192913 TTAAGTATATTCT
1 TTAAGTATATTCT
6192926 TTAAGTATATTC
1 TTAAGTATATTC
6192938 AAACCCATAT
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:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (13 bp):
TTAAGTATATTCT
Found at i:6196886 original size:15 final size:15
Alignment explanation
Indices: 6196856--6196889 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
6196846 TTCTCTTAGG
6196856 TTAGGGGAATCGTGA
1 TTAGGGGAATCGTGA
6196871 TTAGAGGGAATC-TGA
1 TTAG-GGGAATCGTGA
6196886 TTAG
1 TTAG
6196890 CTGGATCGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.29, C:0.06, G:0.35, T:0.29
Consensus pattern (15 bp):
TTAGGGGAATCGTGA
Found at i:6197676 original size:6 final size:6
Alignment explanation
Indices: 6197665--6197699 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
6197655 TAAAATAAAA
6197665 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTC
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTC
6197700 AAAGCAAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTCT
Done.