Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 73 of 150
Found at i:21865680 original size:10 final size:10
Alignment explanation
Indices: 21865664--21865713 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
21865654 AGCTCGTTTC
*
21865664 CAGCTCACTT
1 CAGCTCAATT
*
21865674 GAGCTCAATT
1 CAGCTCAATT
21865684 CAGCTC-ATT
1 CAGCTCAATT
*
21865693 CAAGATCAATT
1 C-AGCTCAATT
21865704 CAGCTCAATT
1 CAGCTCAATT
21865714 TTAACCCAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
9 4 0.12
10 25 0.76
11 4 0.12
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.30
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:21867349 original size:12 final size:13
Alignment explanation
Indices: 21867284--21867349 Score: 55
Period size: 13 Copynumber: 5.0 Consensus size: 13
21867274 AATCAAAATT
*
21867284 CAAAAAAAAAAAG
1 CAAAAAAAAGAAG
* *
21867297 AAAAAAAGAAGTGAG
1 CAAAAAA-AAG-AAG
21867312 CAAAAAAAA-AGAG
1 CAAAAAAAAGA-AG
*
21867325 TAAAAAAAAGAAG
1 CAAAAAAAAGAAG
21867338 -AAAAAAAAGAAG
1 CAAAAAAAAGAAG
21867350 TGAAAAGTCT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
12 12 0.28
13 18 0.42
14 5 0.12
15 8 0.19
ACGTcount: A:0.77, C:0.03, G:0.17, T:0.03
Consensus pattern (13 bp):
CAAAAAAAAGAAG
Found at i:21867355 original size:12 final size:12
Alignment explanation
Indices: 21867288--21867349 Score: 56
Period size: 12 Copynumber: 5.0 Consensus size: 12
21867278 AAAATTCAAA
21867288 AAAAAAAAGAA-
1 AAAAAAAAGAAG
* *
21867299 AAAAAGAAGTGAG
1 AAAAAAAAG-AAG
21867312 CAAAAAAAA-AGAG
1 -AAAAAAAAGA-AG
21867325 TAAAAAAAAGAAG
1 -AAAAAAAAGAAG
21867338 AAAAAAAAGAAG
1 AAAAAAAAGAAG
21867350 TGAAAAGTCT
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
11 8 0.20
12 13 0.32
13 12 0.29
14 8 0.20
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (12 bp):
AAAAAAAAGAAG
Found at i:21868416 original size:15 final size:15
Alignment explanation
Indices: 21868391--21868437 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
21868381 AGAAAAGAAT
21868391 AAAGAAAATGAAAATG
1 AAAG-AAATGAAAATG
*
21868407 AAAGAAATGAAAAAG
1 AAAGAAATGAAAATG
21868422 AAA-AATATGAAAATG
1 AAAGAA-ATGAAAATG
21868437 A
1 A
21868438 GATTTCAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 2 0.07
15 22 0.79
16 4 0.14
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.13
Consensus pattern (15 bp):
AAAGAAATGAAAATG
Found at i:21868484 original size:12 final size:12
Alignment explanation
Indices: 21868467--21868506 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
21868457 AGTGAAAAGC
21868467 AAAAAGAGATTG
1 AAAAAGAGATTG
*
21868479 AAAAAGAAATTG
1 AAAAAGAGATTG
* *
21868491 AAAGAGAGCTTG
1 AAAAAGAGATTG
21868503 AAAA
1 AAAA
21868507 GAAATCGAGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.60, C:0.03, G:0.23, T:0.15
Consensus pattern (12 bp):
AAAAAGAGATTG
Found at i:21877356 original size:20 final size:19
Alignment explanation
Indices: 21877307--21877357 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
21877297 ATATAAGTGT
*
21877307 TTAATTTGTCTTGTTTTAG
1 TTAATTTGTCTTGTTTCAG
*
21877326 TTAAATGTGTCTTGATTTCA-
1 TT-AATTTGTCTTG-TTTCAG
21877346 TTAAGTTTGTCT
1 TTAA-TTTGTCT
21877358 AAAATTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 4 0.15
20 18 0.69
21 4 0.15
ACGTcount: A:0.20, C:0.08, G:0.16, T:0.57
Consensus pattern (19 bp):
TTAATTTGTCTTGTTTCAG
Found at i:21884674 original size:52 final size:52
Alignment explanation
Indices: 21884613--21884713 Score: 175
Period size: 52 Copynumber: 1.9 Consensus size: 52
21884603 CATGCACATA
* *
21884613 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTG
1 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTATTG
*
21884665 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGTTGCTGTCCATTA
1 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTA
21884714 CGTTTCCTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.34
Consensus pattern (52 bp):
TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTATTG
Found at i:21890763 original size:45 final size:45
Alignment explanation
Indices: 21890699--21890886 Score: 322
Period size: 45 Copynumber: 4.2 Consensus size: 45
21890689 CATGAAATTA
*
21890699 AGGAAGCATTTGACCAACATCATGCATAATTCATGGGAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
21890744 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
*
21890789 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTA
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
* * * *
21890834 AGGAAGCATTTGGCCAACATCATGCATAATTTATGGAACAAATTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
21890879 AGGAAGCA
1 AGGAAGCA
21890887 CCATGGCCGA
Statistics
Matches: 136, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 136 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (45 bp):
AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
Found at i:21897016 original size:42 final size:42
Alignment explanation
Indices: 21896957--21897042 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
21896947 AAGTAAATTT
21896957 GTTGAATTTGCTAGGACAACGTACATGGACGGCAAAGAAGAG
1 GTTGAATTTGCTAGGACAACGTACATGGACGGCAAAGAAGAG
21896999 GTTGAATTTGCTAGGACAACGTACATGGACGGCAAAGAAGAG
1 GTTGAATTTGCTAGGACAACGTACATGGACGGCAAAGAAGAG
21897041 GT
1 GT
21897043 GGACTGCAAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.35, C:0.14, G:0.31, T:0.20
Consensus pattern (42 bp):
GTTGAATTTGCTAGGACAACGTACATGGACGGCAAAGAAGAG
Found at i:21897162 original size:45 final size:45
Alignment explanation
Indices: 21897098--21897330 Score: 412
Period size: 45 Copynumber: 5.2 Consensus size: 45
21897088 CATGAAATTA
*
21897098 AGGAAGCATTTGACCAACATCATGCATAATTCATGGGAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
21897143 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
21897188 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
*
21897233 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTA
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
* * * *
21897278 AGGAAGCATTTGGCCAACATCATGCATAATTTATGGAACAAATTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
21897323 AGGAAGCA
1 AGGAAGCA
21897331 CCATGGCCGA
Statistics
Matches: 181, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 181 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (45 bp):
AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
Found at i:21910606 original size:15 final size:15
Alignment explanation
Indices: 21910586--21910640 Score: 60
Period size: 15 Copynumber: 3.8 Consensus size: 15
21910576 GCTCTCATCA
*
21910586 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
* *
21910601 TTCTTTTCACTGTTT
1 TTCTTTTCTCTCTTT
*
21910616 TTGTTTT-TCTCTTT
1 TTCTTTTCTCTCTTT
21910630 TTCTTTT-TCTC
1 TTCTTTTCTCTC
21910641 GCTCAATAGA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
14 15 0.45
15 18 0.55
ACGTcount: A:0.02, C:0.20, G:0.04, T:0.75
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:21912751 original size:12 final size:11
Alignment explanation
Indices: 21912734--21912766 Score: 57
Period size: 12 Copynumber: 2.9 Consensus size: 11
21912724 ATAATAATAA
21912734 GATTTTTTTTT
1 GATTTTTTTTT
21912745 CGATTTTTTTTT
1 -GATTTTTTTTT
21912757 GATTTTTTTT
1 GATTTTTTTT
21912767 ACAATCTCGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.09, C:0.03, G:0.09, T:0.79
Consensus pattern (11 bp):
GATTTTTTTTT
Found at i:21912753 original size:11 final size:11
Alignment explanation
Indices: 21912737--21912766 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
21912727 ATAATAAGAT
21912737 TTTTTTTTCGA
1 TTTTTTTTCGA
*
21912748 TTTTTTTTTGA
1 TTTTTTTTCGA
21912759 TTTTTTTT
1 TTTTTTTT
21912767 ACAATCTCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTTTTTCGA
Found at i:21914333 original size:17 final size:17
Alignment explanation
Indices: 21914303--21914336 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
21914293 CGTTCGTAAG
**
21914303 ATGCATGTTTGTCCAAA
1 ATGCATGTACGTCCAAA
21914320 ATGCATGTACGTCCAAA
1 ATGCATGTACGTCCAAA
21914337 GGGGAGAGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (17 bp):
ATGCATGTACGTCCAAA
Found at i:21916629 original size:52 final size:52
Alignment explanation
Indices: 21916551--21916651 Score: 166
Period size: 52 Copynumber: 1.9 Consensus size: 52
21916541 CATGCACATA
* * *
21916551 TTTGAGCTTCAATCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTG
1 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTATTG
*
21916603 TTTGAGCTTCAACCGAGCTAGAAATGAGATTTTAAGCTGCTGTCCATTA
1 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTA
21916652 CGTTTCCTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.35
Consensus pattern (52 bp):
TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTATTG
Found at i:21926878 original size:33 final size:35
Alignment explanation
Indices: 21926841--21926915 Score: 91
Period size: 33 Copynumber: 2.2 Consensus size: 35
21926831 CTTTTCAATT
21926841 TTTTTCTCAATCTCAATCTCAAATTC-TTT-TTTC
1 TTTTTCTCAATCTCAATCTCAAATTCATTTATTTC
* * * **
21926874 TTTTTCTCACTCTCATTTTCATTTTCATTTATTTC
1 TTTTTCTCAATCTCAATCTCAAATTCATTTATTTC
21926909 TTTTTCT
1 TTTTTCT
21926916 TTTTCTCTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
33 21 0.60
34 3 0.09
35 11 0.31
ACGTcount: A:0.16, C:0.23, G:0.00, T:0.61
Consensus pattern (35 bp):
TTTTTCTCAATCTCAATCTCAAATTCATTTATTTC
Found at i:21926944 original size:22 final size:21
Alignment explanation
Indices: 21926868--21926950 Score: 73
Period size: 21 Copynumber: 4.0 Consensus size: 21
21926858 CTCAAATTCT
* *
21926868 TTTTTCTTTTTCTCAC-TCTC
1 TTTTTCTTTTTCTCTCATTTC
* * *
21926888 ATTTTCATTTTCAT-TTATTTC
1 TTTTTCTTTTTC-TCTCATTTC
21926909 TTTTTCTTTTTCTCTCATTTC
1 TTTTTCTTTTTCTCTCATTTC
*
21926930 TTTTT-TTCTTCTCTCAATTTC
1 TTTTTCTTTTTCTCTC-ATTTC
21926951 ATTCAAGATT
Statistics
Matches: 50, Mismatches: 9, Indels: 7
0.76 0.14 0.11
Matches are distributed among these distances:
20 20 0.40
21 30 0.60
ACGTcount: A:0.10, C:0.23, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTTCTTTTTCTCTCATTTC
Found at i:21927848 original size:11 final size:11
Alignment explanation
Indices: 21927832--21927882 Score: 79
Period size: 10 Copynumber: 4.7 Consensus size: 11
21927822 AATACAAACT
21927832 TTTTTTTTGAA
1 TTTTTTTTGAA
21927843 TTTTTTTTCGAA
1 TTTTTTTT-GAA
21927855 TTTTTTTTGAA
1 TTTTTTTTGAA
21927866 -TTTTTTTG-A
1 TTTTTTTTGAA
21927875 TTTTTTTT
1 TTTTTTTT
21927883 ACAATCTCGA
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
9 1 0.03
10 15 0.39
11 11 0.29
12 11 0.29
ACGTcount: A:0.14, C:0.02, G:0.08, T:0.76
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:21927848 original size:12 final size:12
Alignment explanation
Indices: 21927831--21927872 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
21927821 GAATACAAAC
21927831 TTTTTTTTTGAA
1 TTTTTTTTTGAA
*
21927843 TTTTTTTTCGAA
1 TTTTTTTTTGAA
21927855 -TTTTTTTTGAA
1 TTTTTTTTTGAA
21927866 TTTTTTT
1 TTTTTTT
21927873 GATTTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.14, C:0.02, G:0.07, T:0.76
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:21927881 original size:12 final size:11
Alignment explanation
Indices: 21927831--21927882 Score: 61
Period size: 11 Copynumber: 4.7 Consensus size: 11
21927821 GAATACAAAC
21927831 TTTTTTTTTGAA
1 TTTTTTTTTG-A
*
21927843 TTTTTTTTCGA
1 TTTTTTTTTGA
*
21927854 ATTTTTTTTGA
1 TTTTTTTTTGA
*
21927865 -ATTTTTTTGA
1 TTTTTTTTTGA
21927875 TTTTTTTT
1 TTTTTTTT
21927883 ACAATCTCGA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
10 9 0.26
11 16 0.47
12 9 0.26
ACGTcount: A:0.13, C:0.02, G:0.08, T:0.77
Consensus pattern (11 bp):
TTTTTTTTTGA
Found at i:21936189 original size:27 final size:27
Alignment explanation
Indices: 21936159--21936368 Score: 289
Period size: 27 Copynumber: 7.8 Consensus size: 27
21936149 TCATAATATG
**
21936159 CCACAAAGGCGTTTCTTTCATGATTCA
1 CCACAAAGGCAATTCTTTCATGATTCA
21936186 CCACAAAGGCAATTCTTTCATGATATGC-
1 CCACAAAGGCAATTCTTTCATGAT-T-CA
* *
21936214 CC-CAAAGGCAATTCTTTCATGACTCG
1 CCACAAAGGCAATTCTTTCATGATTCA
* *
21936240 CCACAAAGACATTTCTTTCATGATTCA
1 CCACAAAGGCAATTCTTTCATGATTCA
21936267 CCACAAAGGCAATTCTTTCATGATTCA
1 CCACAAAGGCAATTCTTTCATGATTCA
*
21936294 CCACAAAGGCATTTCTTTCATGATTCA
1 CCACAAAGGCAATTCTTTCATGATTCA
* *
21936321 CTACAAAGGCATTTCTTTCATGATTCA
1 CCACAAAGGCAATTCTTTCATGATTCA
* *
21936348 CCATAGAGGCAATTCTTTCAT
1 CCACAAAGGCAATTCTTTCAT
21936369 CACGTGTTTA
Statistics
Matches: 164, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
25 1 0.01
26 3 0.02
27 156 0.95
28 3 0.02
29 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (27 bp):
CCACAAAGGCAATTCTTTCATGATTCA
Found at i:21936247 original size:81 final size:81
Alignment explanation
Indices: 21936158--21936368 Score: 318
Period size: 81 Copynumber: 2.6 Consensus size: 81
21936148 TTCATAATAT
*
21936158 GCCACAAAGGCGTTTCTTTCATGATTCACCACAAAGGCAATTCTTTCATGATATGC-CC-CAAAG
1 GCCACAAAGGCATTTCTTTCATGATTCACCACAAAGGCAATTCTTTCATGAT-T-CACCACAAAG
21936221 GCAATTCTTTCATGACTC
64 GCAATTCTTTCATGACTC
*
21936239 GCCACAAAGACATTTCTTTCATGATTCACCACAAAGGCAATTCTTTCATGATTCACCACAAAGGC
1 GCCACAAAGGCATTTCTTTCATGATTCACCACAAAGGCAATTCTTTCATGATTCACCACAAAGGC
* *
21936304 ATTTCTTTCATGATTC
66 AATTCTTTCATGACTC
* * * *
21936320 ACTACAAAGGCATTTCTTTCATGATTCACCATAGAGGCAATTCTTTCAT
1 GCCACAAAGGCATTTCTTTCATGATTCACCACAAAGGCAATTCTTTCAT
21936369 CACGTGTTTA
Statistics
Matches: 119, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
79 1 0.01
80 3 0.03
81 115 0.97
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.32
Consensus pattern (81 bp):
GCCACAAAGGCATTTCTTTCATGATTCACCACAAAGGCAATTCTTTCATGATTCACCACAAAGGC
AATTCTTTCATGACTC
Found at i:21941188 original size:50 final size:50
Alignment explanation
Indices: 21941113--21941209 Score: 151
Period size: 50 Copynumber: 1.9 Consensus size: 50
21941103 TATTGAGGTT
* *
21941113 ATGAGAGGTCCCACATAAGACCATGTCTGGGACATGGGGTTAGTACCGAG
1 ATGAGAGATCCCACATAAGACCATGTCTGGGACATGGCGTTAGTACCGAG
*
21941163 ATGAGAGATCTCC-CATAAGACCATGTCTGGGACATGGCGTTGGTACC
1 ATGAGAGATC-CCACATAAGACCATGTCTGGGACATGGCGTTAGTACC
21941210 AAAGATAGTA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 41 0.95
51 2 0.05
ACGTcount: A:0.27, C:0.22, G:0.30, T:0.22
Consensus pattern (50 bp):
ATGAGAGATCCCACATAAGACCATGTCTGGGACATGGCGTTAGTACCGAG
Found at i:21949804 original size:73 final size:73
Alignment explanation
Indices: 21949713--21949858 Score: 274
Period size: 73 Copynumber: 2.0 Consensus size: 73
21949703 TAACAGCCAA
*
21949713 CTCCACATACAAATGGGATCCCAAACTGCTTACCAATTGCATAACATCAAAGCAGGTCCAAGCAA
1 CTCCACATACAAATGGGATCCCAAACTGCTTACAAATTGCATAACATCAAAGCAGGTCCAAGCAA
21949778 GCTAAGAG
66 GCTAAGAG
*
21949786 CTCCACATACAAATGGGATCCCAAATTGCTTACAAATTGCATAACATCAAAGCAGGTCCAAGCAA
1 CTCCACATACAAATGGGATCCCAAACTGCTTACAAATTGCATAACATCAAAGCAGGTCCAAGCAA
21949851 GCTAAGAG
66 GCTAAGAG
21949859 GATTAGAACT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.39, C:0.26, G:0.16, T:0.18
Consensus pattern (73 bp):
CTCCACATACAAATGGGATCCCAAACTGCTTACAAATTGCATAACATCAAAGCAGGTCCAAGCAA
GCTAAGAG
Found at i:21952248 original size:2 final size:2
Alignment explanation
Indices: 21952243--21952268 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21952233 ATATATATAT
21952243 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
21952269 CGCGCTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:21960982 original size:16 final size:16
Alignment explanation
Indices: 21960958--21961024 Score: 71
Period size: 16 Copynumber: 4.2 Consensus size: 16
21960948 GGTTCACTAG
21960958 AATGAAATAGAGCTAT
1 AATGAAATAGAGCTAT
* * *
21960974 AATGGAATAGATCTGT
1 AATGAAATAGAGCTAT
* *
21960990 AATGAAATAAAACTAT
1 AATGAAATAGAGCTAT
* *
21961006 AATGGAATAGAGCTGT
1 AATGAAATAGAGCTAT
21961022 AAT
1 AAT
21961025 CAGTAATTCA
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.27
Consensus pattern (16 bp):
AATGAAATAGAGCTAT
Found at i:21961006 original size:32 final size:32
Alignment explanation
Indices: 21960958--21961024 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
21960948 GGTTCACTAG
* * *
21960958 AATGAAATAGAGCTATAATGGAATAGATCTGT
1 AATGAAATAAAACTATAATGGAATAGAGCTGT
21960990 AATGAAATAAAACTATAATGGAATAGAGCTGT
1 AATGAAATAAAACTATAATGGAATAGAGCTGT
21961022 AAT
1 AAT
21961025 CAGTAATTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.27
Consensus pattern (32 bp):
AATGAAATAAAACTATAATGGAATAGAGCTGT
Found at i:21961061 original size:46 final size:44
Alignment explanation
Indices: 21961005--21961094 Score: 112
Period size: 46 Copynumber: 2.0 Consensus size: 44
21960995 AATAAAACTA
* *
21961005 TAATGGAATAGAGCTGTAATCAGTAATTCAATT-T-TTTGGTTGAATG
1 TAATGAAATAGAACTGTAAT-AGT-ATTC--TTGTGTTTGGTTGAATG
21961051 TAATGAAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATG
1 TAATGAAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATG
21961095 GAATAGATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
42 2 0.05
43 1 0.03
44 16 0.40
45 3 0.08
46 18 0.45
ACGTcount: A:0.32, C:0.06, G:0.22, T:0.40
Consensus pattern (44 bp):
TAATGAAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATG
Found at i:21967782 original size:15 final size:16
Alignment explanation
Indices: 21967753--21967782 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21967743 GAAACATGCT
21967753 TTAACACATTATCAAA
1 TTAACACATTATCAAA
21967769 TTAACACA-TATCAA
1 TTAACACATTATCAA
21967783 CAAGGCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:21967980 original size:17 final size:17
Alignment explanation
Indices: 21967958--21968000 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
21967948 AGATCTTCGA
21967958 CGAGCTTCCAACCCAAT
1 CGAGCTTCCAACCCAAT
*
21967975 CGAGCTTCCAACCTAAT
1 CGAGCTTCCAACCCAAT
21967992 CGAGCTTCC
1 CGAGCTTCC
21968001 GATAATTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.26, C:0.40, G:0.14, T:0.21
Consensus pattern (17 bp):
CGAGCTTCCAACCCAAT
Found at i:21971416 original size:14 final size:14
Alignment explanation
Indices: 21971397--21971424 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
21971387 TAAAGTTATA
21971397 TTTAATAATTCATT
1 TTTAATAATTCATT
21971411 TTTAATAATTCATT
1 TTTAATAATTCATT
21971425 AATAAATTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTAATAATTCATT
Found at i:21971895 original size:19 final size:19
Alignment explanation
Indices: 21971873--21971910 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
21971863 TCAATCATCC
21971873 CTCATCCCATCA-TCTCTCA
1 CTCAT-CCATCATTCTCTCA
*
21971892 CTCATTCATCATTCTCTCA
1 CTCATCCATCATTCTCTCA
21971911 ACTCTTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (19 bp):
CTCATCCATCATTCTCTCA
Found at i:21975561 original size:25 final size:25
Alignment explanation
Indices: 21975514--21975564 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
21975504 AAATCACATC
* *
21975514 AACGTGCTACAAAGAGTAGACTATA
1 AACGTGCTACAAAAAGCAGACTATA
*
21975539 AACGTGCTACAAAAAGCATACTATA
1 AACGTGCTACAAAAAGCAGACTATA
21975564 A
1 A
21975565 TTTTTTAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.20
Consensus pattern (25 bp):
AACGTGCTACAAAAAGCAGACTATA
Found at i:21976320 original size:18 final size:18
Alignment explanation
Indices: 21976297--21976334 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
21976287 TAAATTTTGG
21976297 TTAAGAATTTTTATTGTT
1 TTAAGAATTTTTATTGTT
21976315 TTAAGAATTTTTATTGTT
1 TTAAGAATTTTTATTGTT
21976333 TT
1 TT
21976335 GATAGTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (18 bp):
TTAAGAATTTTTATTGTT
Found at i:21978881 original size:18 final size:19
Alignment explanation
Indices: 21978843--21978881 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
21978833 GTGACCCCTG
21978843 TTTCCAAAATTTTCATGTT
1 TTTCCAAAATTTTCATGTT
21978862 TTTCCAAAATTTTC-TGTT
1 TTTCCAAAATTTTCATGTT
21978880 TT
1 TT
21978882 GTTTCAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.23, C:0.15, G:0.05, T:0.56
Consensus pattern (19 bp):
TTTCCAAAATTTTCATGTT
Found at i:21983343 original size:23 final size:23
Alignment explanation
Indices: 21983315--21983362 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
21983305 ATCTCTTCCC
* *
21983315 TTTATTCTATTCTTTATGTCTCT
1 TTTATTCTATTATTTATATCTCT
21983338 TTTATTCTATTATTTATATCTCT
1 TTTATTCTATTATTTATATCTCT
21983361 TT
1 TT
21983363 CTTTAACATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.15, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTATTCTATTATTTATATCTCT
Found at i:21989868 original size:4 final size:4
Alignment explanation
Indices: 21989859--21989889 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
21989849 AAACTAAGTA
21989859 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
21989890 AATAAAACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:21998444 original size:25 final size:25
Alignment explanation
Indices: 21998408--21998458 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
21998398 CATGTGATTT
* *
21998408 TGTATGATGCCTTCGTGGTGTATTC
1 TGTATGACGCCTTCGTGGCGTATTC
*
21998433 TGTATGACGCCTTTGTGGCGTATTC
1 TGTATGACGCCTTCGTGGCGTATTC
21998458 T
1 T
21998459 ATTTGGCCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.12, C:0.18, G:0.27, T:0.43
Consensus pattern (25 bp):
TGTATGACGCCTTCGTGGCGTATTC
Found at i:22000063 original size:46 final size:46
Alignment explanation
Indices: 21999814--22000079 Score: 217
Period size: 46 Copynumber: 5.7 Consensus size: 46
21999804 CAGGTGAAAG
* * * * * * * *
21999814 TAATAATGCCTAGTTACCCATTTGGGTTAAACCTACACGAGTAATGAA
1 TAATAGTGCCTGGTCACCCGTTAGGGTTGAACCTACACGAATCA-G-A
* * * * * * *
21999862 TCATAGTGCCTGGTTACTCATCAAGGTTAAACCTACACGAATCAGA
1 TAATAGTGCCTGGTCACCCGTTAGGGTTGAACCTACACGAATCAGA
* ** * * *
21999908 TAATAGTGTCTTATAACCCGTTAGGGTTGAGCCTACACGAATCGGA
1 TAATAGTGCCTGGTCACCCGTTAGGGTTGAACCTACACGAATCAGA
* * **
21999954 TAATAGTGCCTAGTCACCCGTTAGGTTTGAACCTACAAAAATCAGA
1 TAATAGTGCCTGGTCACCCGTTAGGGTTGAACCTACACGAATCAGA
* * * * *
22000000 TAATAATGCTTGCTCACCCGTTAGGGTTGAACCTACATGAATCGGA
1 TAATAGTGCCTGGTCACCCGTTAGGGTTGAACCTACACGAATCAGA
** *
22000046 TAATAGTGCCTGGTCACCTATTAAGGTTGAACCT
1 TAATAGTGCCTGGTCACCCGTTAGGGTTGAACCT
22000080 TCATGACAAA
Statistics
Matches: 174, Mismatches: 44, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
46 138 0.79
47 1 0.01
48 35 0.20
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (46 bp):
TAATAGTGCCTGGTCACCCGTTAGGGTTGAACCTACACGAATCAGA
Found at i:22000076 original size:92 final size:92
Alignment explanation
Indices: 21999864--22000079 Score: 267
Period size: 92 Copynumber: 2.3 Consensus size: 92
21999854 GTAATGAATC
* * * ** *
21999864 ATAGTGCCTGGTTA-CTCATCAAGGTTAAACCTACACGAATCAGATAATAGTGTCTTATAACCCG
1 ATAGTGCCTGGTCACCT-ATTAAGGTTGAACCTACAAAAATCAGATAATAATGTCTTATAACCCG
*
21999928 TTAGGGTTGAGCCTACACGAATCGGATA
65 TTAGGGTTGAACCTACACGAATCGGATA
* ** * *
21999956 ATAGTGCCTAGTCACCCGTT-AGGTTTGAACCTACAAAAATCAGATAATAATG-CTTGCTCACCC
1 ATAGTGCCTGGTCACCTATTAAGG-TTGAACCTACAAAAATCAGATAATAATGTCTT-ATAACCC
*
22000019 GTTAGGGTTGAACCTACATGAATCGGATA
64 GTTAGGGTTGAACCTACACGAATCGGATA
22000048 ATAGTGCCTGGTCACCTATTAAGGTTGAACCT
1 ATAGTGCCTGGTCACCTATTAAGGTTGAACCT
22000080 TCATGACAAA
Statistics
Matches: 104, Mismatches: 16, Indels: 8
0.81 0.12 0.06
Matches are distributed among these distances:
91 6 0.06
92 94 0.90
93 4 0.04
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (92 bp):
ATAGTGCCTGGTCACCTATTAAGGTTGAACCTACAAAAATCAGATAATAATGTCTTATAACCCGT
TAGGGTTGAACCTACACGAATCGGATA
Found at i:22001125 original size:26 final size:24
Alignment explanation
Indices: 22001087--22001135 Score: 80
Period size: 26 Copynumber: 2.0 Consensus size: 24
22001077 TAAATATTAA
22001087 AATCTTTAAAATTAAAATTTAATT
1 AATCTTTAAAATTAAAATTTAATT
22001111 AATCTATTAATAATTAAAATTTAAT
1 AATCT-TTAA-AATTAAAATTTAAT
22001136 CATGATTAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 5 0.22
25 4 0.17
26 14 0.61
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (24 bp):
AATCTTTAAAATTAAAATTTAATT
Found at i:22016688 original size:13 final size:12
Alignment explanation
Indices: 22016670--22016701 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
22016660 TAAAAAAAAT
22016670 AAAAAAATTCGAA
1 AAAAAAATTC-AA
22016683 AAAAAAATTCAA
1 AAAAAAATTCAA
22016695 AAAAAAA
1 AAAAAAA
22016702 GTTTGTATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.78, C:0.06, G:0.03, T:0.12
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:22016765 original size:17 final size:18
Alignment explanation
Indices: 22016732--22016767 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
22016722 TCCTTTGTGT
*
22016732 ATTCAGTATTAAAAAAAA
1 ATTCAGAATTAAAAAAAA
22016750 ATTCAGAATTAAAAAAAA
1 ATTCAGAATTAAAAAAAA
22016768 GTGATTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.64, C:0.06, G:0.06, T:0.25
Consensus pattern (18 bp):
ATTCAGAATTAAAAAAAA
Found at i:22018813 original size:15 final size:14
Alignment explanation
Indices: 22018777--22018831 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 14
22018767 TCTATTGAGC
22018777 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
*
22018791 GAGAAAAACAAAAA
1 GAGAAAAAGAAAAA
*
22018805 GAGTGAAAAGAAAAA
1 GAG-AAAAAGAAAAA
*
22018820 GAAAGAAAAGAA
1 GAGA-AAAAGAA
22018832 TGATGAGAGC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 16 0.47
15 18 0.53
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:22025531 original size:41 final size:41
Alignment explanation
Indices: 22025474--22025581 Score: 180
Period size: 41 Copynumber: 2.6 Consensus size: 41
22025464 TTTAATATGT
* *
22025474 CGAATTTAATGCTGCCACTACATGTTAGAAATGTGTCTGGA
1 CGAATTTAATGCTGCCACTACATGTTAGAAATATGCCTGGA
*
22025515 CGAATTTAATGCTGCCACTACATGTTATAAATATGCCTGGA
1 CGAATTTAATGCTGCCACTACATGTTAGAAATATGCCTGGA
*
22025556 CGAATTTAATGCTGCTACTACATGTT
1 CGAATTTAATGCTGCCACTACATGTT
22025582 TGGCCGAATT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (41 bp):
CGAATTTAATGCTGCCACTACATGTTAGAAATATGCCTGGA
Found at i:22028136 original size:15 final size:16
Alignment explanation
Indices: 22028116--22028147 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
22028106 AGAAAATGAA
22028116 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
22028131 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
22028147 A
1 A
22028148 GTGTGAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGAAGATG
Found at i:22028280 original size:21 final size:18
Alignment explanation
Indices: 22028256--22028300 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 18
22028246 ACGAGAGTAC
22028256 AAAAGAAATGAGTGATGTGA
1 AAAAGAAA-GAG-GATGTGA
*
22028276 TAAAAGAAAGAGGATTTGA
1 -AAAAGAAAGAGGATGTGA
22028295 AAAAGA
1 AAAAGA
22028301 GTTTGAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 6 0.26
19 6 0.26
20 3 0.13
21 8 0.35
ACGTcount: A:0.56, C:0.00, G:0.27, T:0.18
Consensus pattern (18 bp):
AAAAGAAAGAGGATGTGA
Found at i:22030251 original size:49 final size:49
Alignment explanation
Indices: 22030178--22030321 Score: 216
Period size: 49 Copynumber: 2.9 Consensus size: 49
22030168 ATGTGAACAT
* * *
22030178 GTGATTATGTGATTCCATATAAGACCATAGTTGGGCTATGGCATCGGTAA
1 GTGA-TATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
* *
22030228 GTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTAT
1 GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
* *
22030277 GTGATTTGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCG
1 GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCG
22030322 AGAAAATGAA
Statistics
Matches: 86, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
49 82 0.95
50 4 0.05
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.32
Consensus pattern (49 bp):
GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
Found at i:22050781 original size:23 final size:23
Alignment explanation
Indices: 22050746--22050857 Score: 107
Period size: 23 Copynumber: 4.9 Consensus size: 23
22050736 CTTTTTGAAC
* * *
22050746 CATTAACATTTCGTACCAAATCG
1 CATTACCAATTCGTACCAAATCA
* *
22050769 TATTACCAATTCGAACCAAATCA
1 CATTACCAATTCGTACCAAATCA
* *
22050792 CCTTACCAATTCGTACCAAATCG
1 CATTACCAATTCGTACCAAATCA
* * * *
22050815 TATTACCATTTTGAACCAAATCA
1 CATTACCAATTCGTACCAAATCA
* *
22050838 CATTACCATTTCGTAGCAAA
1 CATTACCAATTCGTACCAAA
22050858 CCCAAAACCG
Statistics
Matches: 70, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.29
Consensus pattern (23 bp):
CATTACCAATTCGTACCAAATCA
Found at i:22050822 original size:46 final size:46
Alignment explanation
Indices: 22050746--22050857 Score: 161
Period size: 46 Copynumber: 2.4 Consensus size: 46
22050736 CTTTTTGAAC
* *
22050746 CATTAACATTTCGTACCAAATCGTATTACCAATTCGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCAATTCGAACCAAATCA
* * *
22050792 CCTTACCAATTCGTACCAAATCGTATTACCATTTTGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCAATTCGAACCAAATCA
* *
22050838 CATTACCATTTCGTAGCAAA
1 CATTACCAATTCGTACCAAA
22050858 CCCAAAACCG
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 58 1.00
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.29
Consensus pattern (46 bp):
CATTACCAATTCGTACCAAATCGTATTACCAATTCGAACCAAATCA
Found at i:22054546 original size:16 final size:16
Alignment explanation
Indices: 22054525--22054555 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
22054515 CAATTAATCT
*
22054525 AATTAACCTAAAAATA
1 AATTAAACTAAAAATA
22054541 AATTAAACTAAAAAT
1 AATTAAACTAAAAAT
22054556 CAACAAATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.26
Consensus pattern (16 bp):
AATTAAACTAAAAATA
Found at i:22056652 original size:20 final size:20
Alignment explanation
Indices: 22056629--22056694 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
22056619 TGTGCAATTC
22056629 AGGGGTACCAAAGTACAAAT
1 AGGGGTACCAAAGTACAAAT
* *** * * *
22056649 AGGGGCATGTATGTGCAATTT
1 AGGGGTACCAAAGTACAA-AT
*
22056670 ACGGGTACCAAAGTACAAAT
1 AGGGGTACCAAAGTACAAAT
22056690 AGGGG
1 AGGGG
22056695 CACGTATGTG
Statistics
Matches: 29, Mismatches: 16, Indels: 2
0.62 0.34 0.04
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.36, C:0.14, G:0.30, T:0.20
Consensus pattern (20 bp):
AGGGGTACCAAAGTACAAAT
Found at i:22056665 original size:41 final size:41
Alignment explanation
Indices: 22056609--22056750 Score: 214
Period size: 41 Copynumber: 3.5 Consensus size: 41
22056599 AAGTTTAAAC
*
22056609 AGGGG-ACGTGTGTGCAATTCAGGGGTACCAAAGTACAAAT
1 AGGGGCACGTATGTGCAATTCAGGGGTACCAAAGTACAAAT
* * *
22056649 AGGGGCATGTATGTGCAATTTACGGGTACCAAAGTACAAAT
1 AGGGGCACGTATGTGCAATTCAGGGGTACCAAAGTACAAAT
** *
22056690 AGGGGCACGTATGTGCAATTCAGGGGTACTGAAGTACAAAC
1 AGGGGCACGTATGTGCAATTCAGGGGTACCAAAGTACAAAT
22056731 AGGGGCACGTATGTGCAATT
1 AGGGGCACGTATGTGCAATT
22056751 TATCATTTTT
Statistics
Matches: 91, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
40 5 0.05
41 86 0.95
ACGTcount: A:0.32, C:0.15, G:0.31, T:0.22
Consensus pattern (41 bp):
AGGGGCACGTATGTGCAATTCAGGGGTACCAAAGTACAAAT
Found at i:22088015 original size:18 final size:18
Alignment explanation
Indices: 22087970--22088022 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
22087960 CATTTTCATA
* *
22087970 CTCTTTCTTTTCTTTACT
1 CTCTTTATTTTCTTTTCT
*
22087988 CATC-TCATTTTCTTTTCT
1 C-TCTTTATTTTCTTTTCT
22088006 CTCTTTATTTTTCTTTT
1 CTCTTTA-TTTTCTTTT
22088023 TTTTACAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
17 2 0.07
18 15 0.54
19 11 0.39
ACGTcount: A:0.08, C:0.25, G:0.00, T:0.68
Consensus pattern (18 bp):
CTCTTTATTTTCTTTTCT
Found at i:22101527 original size:20 final size:21
Alignment explanation
Indices: 22101504--22101550 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
22101494 GGGTTAAAAT
*
22101504 TGAGCTGAA-TTGATCTCGAA-
1 TGAGCTGAACTTGAGCTC-AAG
22101524 TGAGCT-AACTTGAGCTCAAG
1 TGAGCTGAACTTGAGCTCAAG
22101544 TGAGCTG
1 TGAGCTG
22101551 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (21 bp):
TGAGCTGAACTTGAGCTCAAG
Found at i:22105422 original size:12 final size:12
Alignment explanation
Indices: 22105394--22105433 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
22105384 ACTCGATTTC
*
22105394 TTTTCAAGCTCT
1 TTTTCAATCTCT
* *
22105406 CTTTCAATTTCT
1 TTTTCAATCTCT
22105418 TTTTCAATCTCT
1 TTTTCAATCTCT
22105430 TTTT
1 TTTT
22105434 GCTTTTCACT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.15, C:0.23, G:0.03, T:0.60
Consensus pattern (12 bp):
TTTTCAATCTCT
Found at i:22105486 original size:15 final size:15
Alignment explanation
Indices: 22105463--22105509 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
22105453 TTTTGAAATC
22105463 TCATTTTCATATT-TT
1 TCATTTTCAT-TTCTT
*
22105478 TCTTTTTCATTTCTT
1 TCATTTTCATTTCTT
22105493 TCATTTTCATTTTCTT
1 TCATTTTCA-TTTCTT
22105509 T
1 T
22105510 ATTCTTTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 2 0.07
15 19 0.68
16 7 0.25
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (15 bp):
TCATTTTCATTTCTT
Found at i:22109185 original size:20 final size:20
Alignment explanation
Indices: 22109160--22109206 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
22109150 NNNTTAAAAT
* *
22109160 TGAGCTGAATTGATCTCGAG
1 TGAGCTGAATTGAGCTCAAG
*
22109180 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
22109200 TGAGCTG
1 TGAGCTG
22109207 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:22111767 original size:21 final size:21
Alignment explanation
Indices: 22111722--22111784 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
22111712 TTTGAACCAT
* * *
22111722 TACCAATTCGTACCAAATACCA
1 TACCATTTCATACC-AATTCCA
*
22111744 TACCATTTTATACCAATTCCA
1 TACCATTTCATACCAATTCCA
*
22111765 TACCATTTCGTACCAATTCC
1 TACCATTTCATACCAATTCC
22111785 CAAATACCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
21 24 0.69
22 11 0.31
ACGTcount: A:0.33, C:0.32, G:0.03, T:0.32
Consensus pattern (21 bp):
TACCATTTCATACCAATTCCA
Found at i:22113572 original size:14 final size:13
Alignment explanation
Indices: 22113553--22113605 Score: 79
Period size: 14 Copynumber: 3.9 Consensus size: 13
22113543 AAACCGTATA
22113553 CAATTTTTTTCTTT
1 CAATTTTTTT-TTT
22113567 CAATTTTTTTTTT
1 CAATTTTTTTTTT
*
22113580 CGAAATTTTTTTTT
1 C-AATTTTTTTTTT
22113594 CAATTTTTTTTT
1 CAATTTTTTTTT
22113606 GAACTTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
13 14 0.39
14 22 0.61
ACGTcount: A:0.17, C:0.09, G:0.02, T:0.72
Consensus pattern (13 bp):
CAATTTTTTTTTT
Found at i:22113598 original size:12 final size:13
Alignment explanation
Indices: 22113557--22113617 Score: 70
Period size: 14 Copynumber: 4.6 Consensus size: 13
22113547 CGTATACAAT
*
22113557 TTTTTTCTTTCAAT
1 TTTTTT-TTTCAAC
*
22113571 TTTTTTTTTCGAAA
1 TTTTTTTTTC-AAC
22113585 TTTTTTTTTCAA-
1 TTTTTTTTTCAAC
*
22113597 TTTTTTTTTGAAC
1 TTTTTTTTTCAAC
22113610 TTTTTTTT
1 TTTTTTTT
22113618 ACGTACCTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
12 11 0.26
13 14 0.33
14 18 0.42
ACGTcount: A:0.15, C:0.08, G:0.03, T:0.74
Consensus pattern (13 bp):
TTTTTTTTTCAAC
Found at i:22121434 original size:20 final size:19
Alignment explanation
Indices: 22121405--22121442 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
22121395 AGCTAATAAC
22121405 GAGCTCAATGAGCTGAATT
1 GAGCTCAATGAGCTGAATT
22121424 GAGCTCGAATGAGCTGAAT
1 GAGCTC-AATGAGCTGAAT
22121443 CAAAAATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.24
Consensus pattern (19 bp):
GAGCTCAATGAGCTGAATT
Found at i:22133469 original size:9 final size:8
Alignment explanation
Indices: 22133449--22133504 Score: 51
Period size: 8 Copynumber: 7.0 Consensus size: 8
22133439 TGCAAGTAAA
22133449 AAAAAAAG
1 AAAAAAAG
* *
22133457 AAAAGAAC
1 AAAAAAAG
*
22133465 AAAAAGAAT
1 AAAAA-AAG
22133474 AAAAAAAG
1 AAAAAAAG
*
22133482 AAAAGAA-
1 AAAAAAAG
*
22133489 AAAAATAG
1 AAAAAAAG
22133497 AAAAAAAG
1 AAAAAAAG
22133505 CATAGAATAG
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
7 5 0.14
8 25 0.68
9 7 0.19
ACGTcount: A:0.82, C:0.02, G:0.12, T:0.04
Consensus pattern (8 bp):
AAAAAAAG
Found at i:22133482 original size:25 final size:25
Alignment explanation
Indices: 22133447--22133503 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
22133437 TTTGCAAGTA
*
22133447 AAAAAAAAAGAAAAGAACAAAA-AG
1 AAAAAAAAAGAAAAGAAAAAAATAG
22133471 AATAAAAAAAGAAAAGAAAAAAATAG
1 AA-AAAAAAAGAAAAGAAAAAAATAG
22133497 AAAAAAA
1 AAAAAAA
22133504 GCATAGAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 2 0.07
25 24 0.80
26 4 0.13
ACGTcount: A:0.84, C:0.02, G:0.11, T:0.04
Consensus pattern (25 bp):
AAAAAAAAAGAAAAGAAAAAAATAG
Found at i:22150849 original size:23 final size:23
Alignment explanation
Indices: 22150823--22150874 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
22150813 AGCTCTCTTT
22150823 TTTTTTCACAATTTTTTTTCAAA
1 TTTTTTCACAATTTTTTTTCAAA
** * **
22150846 TTTTTTTTCGATTTTTTTTTGAA
1 TTTTTTCACAATTTTTTTTCAAA
22150869 TTTTTT
1 TTTTTT
22150875 TTCGAGTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.17, C:0.08, G:0.04, T:0.71
Consensus pattern (23 bp):
TTTTTTCACAATTTTTTTTCAAA
Found at i:22150875 original size:23 final size:23
Alignment explanation
Indices: 22150833--22150888 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
22150823 TTTTTTCACA
*
22150833 ATTTTTTTTCAAATTTTTTTTCG
1 ATTTTTTTTTAAATTTTTTTTCG
*
22150856 ATTTTTTTTTGAATTTTTTTTCG
1 ATTTTTTTTTAAATTTTTTTTCG
*
22150879 AGTTTTTTTT
1 ATTTTTTTTT
22150889 CGAGAAACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.14, C:0.05, G:0.07, T:0.73
Consensus pattern (23 bp):
ATTTTTTTTTAAATTTTTTTTCG
Found at i:22150892 original size:12 final size:12
Alignment explanation
Indices: 22150821--22150891 Score: 90
Period size: 12 Copynumber: 5.9 Consensus size: 12
22150811 CTAGCTCTCT
*
22150821 TTTTTTTTCACAA
1 TTTTTTTTC-GAA
*
22150834 TTTTTTTTCAAA
1 TTTTTTTTCGAA
22150846 TTTTTTTTCG-A
1 TTTTTTTTCGAA
*
22150857 TTTTTTTTTGAA
1 TTTTTTTTCGAA
*
22150869 TTTTTTTTCGAG
1 TTTTTTTTCGAA
22150881 TTTTTTTTCGA
1 TTTTTTTTCGA
22150892 GAAACTACTA
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
11 10 0.19
12 33 0.63
13 9 0.17
ACGTcount: A:0.15, C:0.08, G:0.07, T:0.69
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:22156463 original size:22 final size:22
Alignment explanation
Indices: 22156411--22156475 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
22156401 TATTTGGGAA
* * *
22156411 TTGGTATGAAACGGTAAGGGAT
1 TTGGTACGAAATGGTAATGGAT
**
22156433 TTGAAACGAAATGGTAATGGAT
1 TTGGTACGAAATGGTAATGGAT
*
22156455 TTGGTACGAAAATGGAAATGG
1 TTGGTACG-AAATGGTAATGG
22156476 TTCAAAAAGG
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
22 23 0.68
23 11 0.32
ACGTcount: A:0.37, C:0.05, G:0.32, T:0.26
Consensus pattern (22 bp):
TTGGTACGAAATGGTAATGGAT
Found at i:22160412 original size:14 final size:13
Alignment explanation
Indices: 22160393--22160441 Score: 71
Period size: 13 Copynumber: 3.6 Consensus size: 13
22160383 CTTCTTCTTC
22160393 TTTTTTCTTTCGAA
1 TTTTTT-TTTCGAA
*
22160407 TTTTTTTTTCAAA
1 TTTTTTTTTCGAA
22160420 TTTTTTTTTCGAA
1 TTTTTTTTTCGAA
22160433 CTTTTTTTT
1 -TTTTTTTT
22160442 ATGTACCTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
13 18 0.56
14 14 0.44
ACGTcount: A:0.14, C:0.10, G:0.04, T:0.71
Consensus pattern (13 bp):
TTTTTTTTTCGAA
Found at i:22160797 original size:22 final size:22
Alignment explanation
Indices: 22160745--22160809 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
22160735 TATTTGGGAA
* * *
22160745 TTGGTATGAAACGGTAAGGGAT
1 TTGGTACGAAATGGTAATGGAT
**
22160767 TTGAAACGAAATGGTAATGGAT
1 TTGGTACGAAATGGTAATGGAT
*
22160789 TTGGTACGAAAATGGAAATGG
1 TTGGTACG-AAATGGTAATGG
22160810 TTCAAAAAGG
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
22 23 0.68
23 11 0.32
ACGTcount: A:0.37, C:0.05, G:0.32, T:0.26
Consensus pattern (22 bp):
TTGGTACGAAATGGTAATGGAT
Found at i:22166543 original size:70 final size:70
Alignment explanation
Indices: 22166425--22166561 Score: 247
Period size: 70 Copynumber: 2.0 Consensus size: 70
22166415 TTGCATGCCC
22166425 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCAGCCAACACCTCCTTTATTGCTGC
1 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCAGCCAACACCTCCTTTATTGCTGC
22166490 TGTTG
66 TGTTG
* * *
22166495 AACATCACCTTAAATGCATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
1 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCAGCCAACACCTCCTTTATTGCTGC
22166560 TG
66 TG
22166562 ATTTAATTCA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 64 1.00
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (70 bp):
AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCAGCCAACACCTCCTTTATTGCTGC
TGTTG
Found at i:22167101 original size:20 final size:19
Alignment explanation
Indices: 22167072--22167109 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
22167062 AGCTAATAAC
22167072 GAGCTCAATGAGCTGAATT
1 GAGCTCAATGAGCTGAATT
22167091 GAGCTCGAATGAGCTGAAT
1 GAGCTC-AATGAGCTGAAT
22167110 CAAAAATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.24
Consensus pattern (19 bp):
GAGCTCAATGAGCTGAATT
Found at i:22168612 original size:15 final size:14
Alignment explanation
Indices: 22168593--22168643 Score: 66
Period size: 15 Copynumber: 3.5 Consensus size: 14
22168583 CTCACTCTCA
22168593 TTTTCTTTTTCTTT
1 TTTTCTTTTTCTTT
22168607 TATTTCTTTTTCTTT
1 T-TTTCTTTTTCTTT
* *
22168622 TTCTCTCATTTCTTT
1 TTTTCT-TTTTCTTT
22168637 TTTTCTT
1 TTTTCTT
22168644 CTCTCAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 5 0.16
15 26 0.84
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTCTTTTTCTTT
Found at i:22168648 original size:22 final size:21
Alignment explanation
Indices: 22168571--22168654 Score: 91
Period size: 21 Copynumber: 4.0 Consensus size: 21
22168561 CTCAAATTCT
*
22168571 TTTTTCTTTTT-TCTCACTCTC
1 TTTTTCTTTTTCTCTCA-TTTC
* * *
22168592 ATTTTCTTTTTCTTTTATTTC
1 TTTTTCTTTTTCTCTCATTTC
22168613 TTTTTCTTTTTCTCTCATTTC
1 TTTTTCTTTTTCTCTCATTTC
*
22168634 TTTTT-TTCTTCTCTCAATTTC
1 TTTTTCTTTTTCTCTC-ATTTC
22168655 ATTCAAGATT
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
20 9 0.17
21 41 0.77
22 3 0.06
ACGTcount: A:0.07, C:0.23, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTTCTTTTTCTCTCATTTC
Found at i:22169512 original size:27 final size:28
Alignment explanation
Indices: 22169482--22169551 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
22169472 AATCACTCTT
*
22169482 TTTTTTTTTTCAATTTC-AATTTTTTTC
1 TTTTTTTTTTCAATTCCGAATTTTTTTC
*
22169509 TTTTTTTTTT-AATTCCGTATTTTTTTTC
1 TTTTTTTTTTCAATTCCG-AATTTTTTTC
22169537 TTTTTTTTCTTCAAT
1 TTTTTTTT-TTCAAT
22169552 ACTAAATACA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
26 5 0.14
27 10 0.27
28 17 0.46
29 2 0.05
30 3 0.08
ACGTcount: A:0.13, C:0.11, G:0.01, T:0.74
Consensus pattern (28 bp):
TTTTTTTTTTCAATTCCGAATTTTTTTC
Found at i:22169606 original size:12 final size:11
Alignment explanation
Indices: 22169584--22169617 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
22169574 AAATTGAATA
22169584 CAAACTTTTTTT
1 CAAA-TTTTTTT
*
22169596 CGAATTTTTTT
1 CAAATTTTTTT
22169607 CAAATTTTTTT
1 CAAATTTTTTT
22169618 TACAATCTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 17 0.85
12 3 0.15
ACGTcount: A:0.24, C:0.12, G:0.03, T:0.62
Consensus pattern (11 bp):
CAAATTTTTTT
Found at i:22180030 original size:20 final size:20
Alignment explanation
Indices: 22180005--22180051 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
22179995 AGCTCGTTTC
*
22180005 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGATCAAGT
*
22180025 CAGCTCATTCGAGATCAATT
1 CAGCTCATTCGAGATCAAGT
22180045 CAGCTCA
1 CAGCTCA
22180052 ATTTTAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGATCAAGT
Found at i:22185040 original size:7 final size:8
Alignment explanation
Indices: 22185023--22185047 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
22185013 AATCAGATTC
22185023 AAAAATAA
1 AAAAATAA
22185031 AAAAATAA
1 AAAAATAA
22185039 AAAAATAA
1 AAAAATAA
22185047 A
1 A
22185048 GGAGGAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAATAA
Found at i:22192418 original size:21 final size:21
Alignment explanation
Indices: 22192378--22192460 Score: 89
Period size: 21 Copynumber: 4.0 Consensus size: 21
22192368 AATCTTGAAT
*
22192378 GAAATTGAGAGAAGAA-AAAAA
1 GAAA-TGAGAGAAAAAGAAAAA
22192399 GAAATGAGAGAAAAAGAAAAA
1 GAAATGAGAGAAAAAGAAAAA
* * *
22192420 GAAATAAAAGAAAAAGAAAAT
1 GAAATGAGAGAAAAAGAAAAA
* *
22192441 GAGA-GTGAGAAAAAGAAAAA
1 GAAATGAGAGAAAAAGAAAAA
22192461 AGAATTTGAG
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
20 22 0.42
21 30 0.58
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (21 bp):
GAAATGAGAGAAAAAGAAAAA
Found at i:22192428 original size:15 final size:14
Alignment explanation
Indices: 22192389--22192439 Score: 66
Period size: 15 Copynumber: 3.5 Consensus size: 14
22192379 AAATTGAGAG
22192389 AAGAAAAAAAGAAA
1 AAGAAAAAAAGAAA
* *
22192403 TGAGAGAAAAAGAAA
1 -AAGAAAAAAAGAAA
22192418 AAGAAATAAAAGAAA
1 AAGAAA-AAAAGAAA
22192433 AAGAAAA
1 AAGAAAA
22192440 TGAGAGTGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
14 5 0.16
15 26 0.84
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (14 bp):
AAGAAAAAAAGAAA
Found at i:22193946 original size:20 final size:19
Alignment explanation
Indices: 22193921--22193958 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
22193911 AACATTTTTG
22193921 ATTCAGCTCATTCGAGCTCA
1 ATTCAGCTCATT-GAGCTCA
22193941 ATTCAGCTCATTGAGCTC
1 ATTCAGCTCATTGAGCTC
22193959 GTTATTAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.32
Consensus pattern (19 bp):
ATTCAGCTCATTGAGCTCA
Found at i:22194420 original size:26 final size:22
Alignment explanation
Indices: 22194371--22194417 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
22194361 TACTTAATGC
*
22194371 ATTTATTTTGTGTCTGCAGGTA
1 ATTTATTTTGTGTCCGCAGGTA
22194393 ATTTATTTTGTGTCCGCAGGTA
1 ATTTATTTTGTGTCCGCAGGTA
22194415 ATT
1 ATT
22194418 AATGCATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.19, C:0.11, G:0.21, T:0.49
Consensus pattern (22 bp):
ATTTATTTTGTGTCCGCAGGTA
Found at i:22194570 original size:70 final size:70
Alignment explanation
Indices: 22194487--22194623 Score: 247
Period size: 70 Copynumber: 2.0 Consensus size: 70
22194477 TGAATTAAAT
*
22194487 CAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATG
1 CAGCAGCAATAAAGGAGGTGTTGGCCGAAATTAATGTAAAGCATAGACATGCATTTAAGGTGATG
22194552 TTCAA
66 TTCAA
* *
22194557 CAGCAGCAATAAAGGAGGTGTTGGCCGAAATTAATGTAAAGCATAGACATGTATTTAAGGTGCTG
1 CAGCAGCAATAAAGGAGGTGTTGGCCGAAATTAATGTAAAGCATAGACATGCATTTAAGGTGATG
22194622 TT
66 TT
22194624 GGGCATGCAA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 64 1.00
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.26
Consensus pattern (70 bp):
CAGCAGCAATAAAGGAGGTGTTGGCCGAAATTAATGTAAAGCATAGACATGCATTTAAGGTGATG
TTCAA
Found at i:22200176 original size:11 final size:10
Alignment explanation
Indices: 22200153--22200212 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
22200143 ATTGGGTTAA
22200153 AATTGAGCTG
1 AATTGAGCTG
*
22200163 AATTGATCTCG
1 AATTGAGCT-G
22200174 AA-TGAGCTG
1 AATTGAGCTG
* *
22200183 ACTTGAGCTC
1 AATTGAGCTG
*
22200193 AAGTGAGCTGG
1 AATTGAGCT-G
*
22200204 AAATGAGCT
1 AATTGAGCT
22200213 AAACAGAGCT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
9 2 0.05
10 26 0.67
11 11 0.28
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (10 bp):
AATTGAGCTG
Found at i:22200179 original size:20 final size:20
Alignment explanation
Indices: 22200156--22200212 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
22200146 GGGTTAAAAT
*
22200156 TGAGCTGAATTGATCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
*
22200176 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
*
22200196 TGAGCTGGAAATGAGCT
1 TGAGCT-GAATTGAGCT
22200213 AAACAGAGCT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 2 0.06
20 21 0.68
21 8 0.26
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:22206675 original size:23 final size:23
Alignment explanation
Indices: 22206649--22206693 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
22206639 TTTCTTACTG
*
22206649 TAGTAATTTTCGGGATATTACAA
1 TAGTAATTTTCAGGATATTACAA
*
22206672 TAGTACTTTTCAGGATATTACA
1 TAGTAATTTTCAGGATATTACA
22206694 GTGAGGGGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (23 bp):
TAGTAATTTTCAGGATATTACAA
Found at i:22211496 original size:18 final size:18
Alignment explanation
Indices: 22211475--22211516 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
22211465 TCAGAAACCT
22211475 CTTCTTCTTCAGCAACAA
1 CTTCTTCTTCAGCAACAA
* *
22211493 CTTCCTCTTCTGCAACAA
1 CTTCTTCTTCAGCAACAA
*
22211511 CCTCTT
1 CTTCTT
22211517 TCTCAATAAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.38, G:0.05, T:0.36
Consensus pattern (18 bp):
CTTCTTCTTCAGCAACAA
Found at i:22214560 original size:10 final size:10
Alignment explanation
Indices: 22214545--22214606 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
22214535 TTTGAACCAT
*
22214545 TACCAATTCG
1 TACCAATTCA
*
22214555 TACCAAATACCA
1 TACC-AAT-TCA
*
22214567 TACCATTTCA
1 TACCAATTCA
22214577 TACCAATTCCA
1 TACCAATT-CA
* *
22214588 TACCATTTCG
1 TACCAATTCA
22214598 TACCAATTC
1 TACCAATTC
22214607 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:22214590 original size:21 final size:21
Alignment explanation
Indices: 22214545--22214607 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
22214535 TTTGAACCAT
* *
22214545 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
22214567 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
22214588 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
22214608 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:22214981 original size:14 final size:15
Alignment explanation
Indices: 22214941--22214978 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
22214931 AAAAAAACAA
*
22214941 AAAAAAAATTCAAAAG
1 AAAAAAAATT-GAAAG
22214957 AAAAAAAATTGAAAG
1 AAAAAAAATTGAAAG
22214972 AAAAAAA
1 AAAAAAA
22214979 TTGTATACGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.79, C:0.03, G:0.08, T:0.11
Consensus pattern (15 bp):
AAAAAAAATTGAAAG
Found at i:22217207 original size:20 final size:20
Alignment explanation
Indices: 22217182--22217236 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
22217172 GCGAAAATAC
*
22217182 AAAAGAAAAGAAAAATGAAA
1 AAAAGAAAAGAAAAATCAAA
*
22217202 AAAAG-AAAGAAAATTCAAA
1 AAAAGAAAAGAAAAATCAAA
*
22217221 AAAAGAGAATGAAAAA
1 AAAAGA-AAAGAAAAA
22217237 AATGAGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 17 0.59
20 5 0.17
21 7 0.24
ACGTcount: A:0.76, C:0.02, G:0.15, T:0.07
Consensus pattern (20 bp):
AAAAGAAAAGAAAAATCAAA
Found at i:22217268 original size:15 final size:16
Alignment explanation
Indices: 22217231--22217268 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
22217221 AAAAGAGAAT
*
22217231 GAAAAAAATGAGAAAA
1 GAAAAAGATGAGAAAA
*
22217247 GCAAAAGATGA-AAAA
1 GAAAAAGATGAGAAAA
22217262 GAAAAAG
1 GAAAAAG
22217269 TGATTGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.71, C:0.03, G:0.21, T:0.05
Consensus pattern (16 bp):
GAAAAAGATGAGAAAA
Found at i:22221119 original size:10 final size:10
Alignment explanation
Indices: 22221104--22221165 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
22221094 TTTGAACCAT
*
22221104 TACCAATTCG
1 TACCAATTCA
*
22221114 TACCAAATACCA
1 TACC-AAT-TCA
*
22221126 TACCATTTCA
1 TACCAATTCA
22221136 TACCAATTCCA
1 TACCAATT-CA
* *
22221147 TACCATTTCG
1 TACCAATTCA
22221157 TACCAATTC
1 TACCAATTC
22221166 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:22221149 original size:21 final size:21
Alignment explanation
Indices: 22221104--22221166 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
22221094 TTTGAACCAT
* *
22221104 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
22221126 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
22221147 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
22221167 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:22226270 original size:22 final size:22
Alignment explanation
Indices: 22226219--22226278 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
22226209 TGGGAATTGG
* *
22226219 TACGAAACGGTAAGGGATTTGA
1 TACGAAATGGTAATGGATTTGA
*
22226241 AACGAAATGGTAATGGATTTGA
1 TACGAAATGGTAATGGATTTGA
*
22226263 TACGAAATGGAAATGG
1 TACGAAATGGTAATGG
22226279 TTCAAAAAGG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.40, C:0.07, G:0.30, T:0.23
Consensus pattern (22 bp):
TACGAAATGGTAATGGATTTGA
Found at i:22243595 original size:50 final size:50
Alignment explanation
Indices: 22243519--22243711 Score: 174
Period size: 50 Copynumber: 3.7 Consensus size: 50
22243509 TTTCCTTTAC
* * * ***
22243519 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCCCTCATATCGG
** *
22243569 TGTCC-ATGCCATGTCCTAGACATGGTCTTACGGGGGACCCCTCATCTCGG
1 TG-CCAATGCCATGTCCTAGACATGGTCTTACATGGGACCCCTCATATCGG
* * *
22243619 TGCCAATGCCATGT-CTCAGACATGGTCTTACATGGGACCTCTAATAATCTCAATGA
1 TGCCAATGCCATGTCCT-AGACATGGTCTTACATGGGACCCCTCAT-A--TC---GG
* *
22243675 TGCCAATGCCATGTCCCAGACATGGCCTTACATGGGA
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGA
22243712 TCTCTTTACC
Statistics
Matches: 116, Mismatches: 17, Indels: 14
0.79 0.12 0.10
Matches are distributed among these distances:
49 4 0.03
50 73 0.63
51 2 0.02
53 2 0.02
56 34 0.29
57 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCCCTCATATCGG
Found at i:22251915 original size:144 final size:144
Alignment explanation
Indices: 22251655--22251941 Score: 538
Period size: 144 Copynumber: 2.0 Consensus size: 144
22251645 GTTTTCAAGC
* * *
22251655 TTCCAAGCTCCATAGTAAGTGATTCCAAGCCCCGTCTTTAATGTTCTTTACGTTTTTAGAGTCTC
1 TTCCAAGCTCCATAGTAAGTGATTCCAAGCCCCGACTTTAATATTCTTTACGTTTTTAGAATCTC
*
22251720 GGTAACTTGATTTAGCTTATTCTAGCAATAATTTAACCTAGGGTTGATATTTGGAAAAATACCCA
66 GGTAACTTGATTTAGCTTATTCTAGCAATAATTTAACCTAGGGTTCATATTTGGAAAAATACCCA
22251785 TAGGTAAAATGTGA
131 TAGGTAAAATGTGA
22251799 TTCCAAGCTCCATAGTAAGTGATTCCAAGCCCCGACTTTAATATTCTTTACGTTTTTAGAATCTC
1 TTCCAAGCTCCATAGTAAGTGATTCCAAGCCCCGACTTTAATATTCTTTACGTTTTTAGAATCTC
22251864 GGTAACTTGATTTAGCTTATTCTAGCAATAATTTAACCTAGGGTTCATATTTGGAAAAATACCCA
66 GGTAACTTGATTTAGCTTATTCTAGCAATAATTTAACCTAGGGTTCATATTTGGAAAAATACCCA
22251929 TAGGTAAAATGTG
131 TAGGTAAAATGTG
22251942 TTTATTTAGA
Statistics
Matches: 139, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
144 139 1.00
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (144 bp):
TTCCAAGCTCCATAGTAAGTGATTCCAAGCCCCGACTTTAATATTCTTTACGTTTTTAGAATCTC
GGTAACTTGATTTAGCTTATTCTAGCAATAATTTAACCTAGGGTTCATATTTGGAAAAATACCCA
TAGGTAAAATGTGA
Found at i:22252753 original size:49 final size:50
Alignment explanation
Indices: 22252624--22252754 Score: 158
Period size: 49 Copynumber: 2.6 Consensus size: 50
22252614 AGAGGTCCTC
* * *
22252624 TGTAAGACCATGTCTGGGACATGGCATGGGCACCAATATGAGAACTCTCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACCAACAGGAGAACTCTCA
* * * **
22252674 TGTAAGACCATATCTGGGATATGACATTGGCA-GTACAGGA-AACATCTCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACCAACAGGAGAAC-TCTCA
*
22252723 TGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCA
22252755 TGTTATTATC
Statistics
Matches: 68, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
48 3 0.04
49 37 0.54
50 28 0.41
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (50 bp):
TGTAAGACCATGTCTGGGACATGGCATTGGCACCAACAGGAGAACTCTCA
Found at i:22254412 original size:70 final size:70
Alignment explanation
Indices: 22254294--22254430 Score: 247
Period size: 70 Copynumber: 2.0 Consensus size: 70
22254284 TTGCATGCCC
22254294 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
1 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
22254359 TGTTG
66 TGTTG
* **
22254364 AACATCACCTTAAATGGATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
1 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
22254429 TG
66 TG
22254431 ATTTAATTCA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 64 1.00
ACGTcount: A:0.27, C:0.26, G:0.13, T:0.34
Consensus pattern (70 bp):
AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
TGTTG
Found at i:22269944 original size:25 final size:25
Alignment explanation
Indices: 22269916--22269971 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
22269906 ATACACGAGT
*
22269916 TGTGGATAACTGTGCTCACACAAGC
1 TGTGAATAACTGTGCTCACACAAGC
*
22269941 TGTGAATAAGTGTGCTCACACAAGC
1 TGTGAATAACTGTGCTCACACAAGC
22269966 TGTGAA
1 TGTGAA
22269972 AATGGTCCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (25 bp):
TGTGAATAACTGTGCTCACACAAGC
Found at i:22271079 original size:43 final size:43
Alignment explanation
Indices: 22271018--22271099 Score: 155
Period size: 43 Copynumber: 1.9 Consensus size: 43
22271008 ACCAAATTAG
22271018 CCCATTTAATCACTTAAATCAAATAGCAATCAAATTTTAATCA
1 CCCATTTAATCACTTAAATCAAATAGCAATCAAATTTTAATCA
*
22271061 CCCATTTAATCACTTAAATTAAATAGCAATCAAATTTTA
1 CCCATTTAATCACTTAAATCAAATAGCAATCAAATTTTA
22271100 CATCTTTTGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.44, C:0.20, G:0.02, T:0.34
Consensus pattern (43 bp):
CCCATTTAATCACTTAAATCAAATAGCAATCAAATTTTAATCA
Found at i:22272080 original size:16 final size:17
Alignment explanation
Indices: 22272059--22272092 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
22272049 AATATTAGGG
22272059 GTAAAAGTAT-AATTTT
1 GTAAAAGTATGAATTTT
22272075 GTAAAAGTATGAATTTT
1 GTAAAAGTATGAATTTT
22272092 G
1 G
22272093 GACTGAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (17 bp):
GTAAAAGTATGAATTTT
Found at i:22279234 original size:18 final size:19
Alignment explanation
Indices: 22279191--22279226 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
22279181 TATTTTGTAG
22279191 TTGAAAATACGTGTTTGTC
1 TTGAAAATACGTGTTTGTC
22279210 TTGAAAATA-GTGTTTGT
1 TTGAAAATACGTGTTTGT
22279227 TGTGAAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.28, C:0.06, G:0.22, T:0.44
Consensus pattern (19 bp):
TTGAAAATACGTGTTTGTC
Found at i:22279801 original size:27 final size:27
Alignment explanation
Indices: 22279766--22279830 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
22279756 AGCAAAGGTG
22279766 CCAGT-ACAGT-ATATGTGGCAAAGCCA
1 CCAGTAACAGTAAT-TGTGGCAAAGCCA
* *
22279792 CTAGTAACAGTAATTGTGGCAGAGCCA
1 CCAGTAACAGTAATTGTGGCAAAGCCA
22279819 CCAGTAACAGTA
1 CCAGTAACAGTA
22279831 CTTCCTCCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 4 0.12
27 28 0.82
28 2 0.06
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (27 bp):
CCAGTAACAGTAATTGTGGCAAAGCCA
Found at i:22280029 original size:26 final size:26
Alignment explanation
Indices: 22280000--22280131 Score: 149
Period size: 26 Copynumber: 5.1 Consensus size: 26
22279990 ACGGTCGTTC
* *
22280000 TACCCTTCGGGGGTATTTCAGTAATT
1 TACCCATCGAGGGTATTTCAGTAATT
*
22280026 TACCTATCGAGGGTATTTC-GATAATT
1 TACCCATCGAGGGTATTTCAG-TAATT
* *
22280052 TACCCATCGAGGGTATTTCAATAATC
1 TACCCATCGAGGGTATTTCAGTAATT
* *
22280078 TAGCCATCGAGGGTATATCAGTAATT
1 TACCCATCGAGGGTATTTCAGTAATT
* * * *
22280104 TATCCATCAAGGGTATTCCGGTAATT
1 TACCCATCGAGGGTATTTCAGTAATT
22280130 TA
1 TA
22280132 GGCCTATTAT
Statistics
Matches: 89, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
25 1 0.01
26 88 0.99
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (26 bp):
TACCCATCGAGGGTATTTCAGTAATT
Found at i:22282667 original size:27 final size:25
Alignment explanation
Indices: 22282630--22282702 Score: 87
Period size: 27 Copynumber: 2.9 Consensus size: 25
22282620 GAATATAAAG
*
22282630 GGGGTTCCTAAGTGCTGATTCCCCC
1 GGGGTTGCTAAGTGCTGATTCCCCC
*
22282655 AAGGGGTTGCTAAGTGTTGATT--CCC
1 --GGGGTTGCTAAGTGCTGATTCCCCC
22282680 GGTGGTTGCTAAGTGCTGATTCC
1 GG-GGTTGCTAAGTGCTGATTCC
22282703 ACCGTATTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
23 2 0.05
24 17 0.43
25 3 0.08
27 18 0.45
ACGTcount: A:0.15, C:0.22, G:0.32, T:0.32
Consensus pattern (25 bp):
GGGGTTGCTAAGTGCTGATTCCCCC
Found at i:22282742 original size:42 final size:42
Alignment explanation
Indices: 22282683--22282819 Score: 157
Period size: 42 Copynumber: 3.5 Consensus size: 42
22282673 GATTCCCGGT
22282683 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAGGG
* * * *
22282725 GGTTGCAAAGTGTTGATTCC-CCG-A--TT-CAT-T---GGT
1 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAGGG
* *
22282758 GGTTGCTAAGTGTTGATTCCACCGTATTTTAAATGCGAAGGG
1 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAGGG
22282800 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
22282820 CCCGAGGGGT
Statistics
Matches: 77, Mismatches: 9, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
33 21 0.27
34 3 0.04
35 1 0.01
36 1 0.01
37 4 0.05
38 4 0.05
40 1 0.01
41 3 0.04
42 39 0.51
ACGTcount: A:0.21, C:0.16, G:0.28, T:0.34
Consensus pattern (42 bp):
GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAGGG
Found at i:22282803 original size:75 final size:75
Alignment explanation
Indices: 22282680--22282821 Score: 248
Period size: 75 Copynumber: 1.9 Consensus size: 75
22282670 GTTGATTCCC
* *
22282680 GGTGGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAGGGGGTTGCAAAGTGTTGATTCC
1 GGTGGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGCGAAGGGGGTTGCAAAGTGCTGATTCC
22282745 CCGATTCATT
66 CCGATTCATT
* *
22282755 GGTGGTTGCTAAGTGTTGATTCCACCGTATTTTAAATGCGAAGGGGGTTGCTAAGTGCTGATTCC
1 GGTGGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGCGAAGGGGGTTGCAAAGTGCTGATTCC
22282820 CC
66 CC
22282822 CGAGGGGTTG
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 63 1.00
ACGTcount: A:0.20, C:0.17, G:0.29, T:0.34
Consensus pattern (75 bp):
GGTGGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGCGAAGGGGGTTGCAAAGTGCTGATTCC
CCGATTCATT
Found at i:22282852 original size:102 final size:103
Alignment explanation
Indices: 22282723--22282924 Score: 298
Period size: 102 Copynumber: 2.0 Consensus size: 103
22282713 AAATGTGAAG
* * * *
22282723 GGGGTTGCAAAGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGTTGATTCCACCGTAT-TT
1 GGGGTTGCAAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTAATTCCACCATATCTT
*
22282787 TAAATGCGAAGGGGGTTGCTAAGTGCTGATTCCCCCGA
66 TAAATGCGAAAGGGGTTGCTAAGTGCTGATTCCCCCGA
* ** *
22282825 GGGGTTGCTAAGTGCTGATTCTTCGATTCATTGGTGGTTGCTGAGTGCTAATTCCACCATATCTT
1 GGGGTTGCAAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTAATTCCACCATATCTT
* *
22282890 TGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
66 TAAATGCGAAAGGGGTTGCTAAGTGCTGATTCCCC
22282925 GAATCACTGG
Statistics
Matches: 88, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
102 54 0.61
103 34 0.39
ACGTcount: A:0.19, C:0.18, G:0.29, T:0.34
Consensus pattern (103 bp):
GGGGTTGCAAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTAATTCCACCATATCTT
TAAATGCGAAAGGGGTTGCTAAGTGCTGATTCCCCCGA
Found at i:22283851 original size:49 final size:49
Alignment explanation
Indices: 22283790--22283933 Score: 216
Period size: 49 Copynumber: 2.9 Consensus size: 49
22283780 ATGTGAACAT
* * *
22283790 GTGATTATGTGATTCCATATAAGACCATAGTTGGGCTATGGCATCGGTAA
1 GTGA-TATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
* *
22283840 GTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTAT
1 GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
* *
22283889 GTGATTTGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCG
1 GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCG
22283934 AGAAAATGAA
Statistics
Matches: 86, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
49 82 0.95
50 4 0.05
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.32
Consensus pattern (49 bp):
GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
Found at i:22285663 original size:11 final size:13
Alignment explanation
Indices: 22285639--22285670 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
22285629 TAGTTTATTA
22285639 ATATTTTAATATG
1 ATATTTTAATATG
22285652 AT-TTTTAA-ATG
1 ATATTTTAATATG
22285663 ATATTTTA
1 ATATTTTA
22285671 TTAATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (13 bp):
ATATTTTAATATG
Found at i:22297171 original size:23 final size:23
Alignment explanation
Indices: 22297136--22297247 Score: 107
Period size: 23 Copynumber: 4.9 Consensus size: 23
22297126 CTTTTTGAAC
* * *
22297136 CATTAACATTTCGTACCAAATCG
1 CATTACCAATTCGTACCAAATCA
* *
22297159 TATTACCAATTCGAACCAAATCA
1 CATTACCAATTCGTACCAAATCA
* *
22297182 CCTTACCAATTCGTACCAAATCG
1 CATTACCAATTCGTACCAAATCA
* * * *
22297205 TATTACCATTTTGAACCAAATCA
1 CATTACCAATTCGTACCAAATCA
* *
22297228 CATTACCATTTCGTAACAAA
1 CATTACCAATTCGTACCAAA
22297248 CCCAAAACCG
Statistics
Matches: 70, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.38, C:0.27, G:0.06, T:0.29
Consensus pattern (23 bp):
CATTACCAATTCGTACCAAATCA
Found at i:22297212 original size:46 final size:46
Alignment explanation
Indices: 22297136--22297247 Score: 161
Period size: 46 Copynumber: 2.4 Consensus size: 46
22297126 CTTTTTGAAC
* *
22297136 CATTAACATTTCGTACCAAATCGTATTACCAATTCGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCAATTCGAACCAAATCA
* * *
22297182 CCTTACCAATTCGTACCAAATCGTATTACCATTTTGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCAATTCGAACCAAATCA
* *
22297228 CATTACCATTTCGTAACAAA
1 CATTACCAATTCGTACCAAA
22297248 CCCAAAACCG
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 58 1.00
ACGTcount: A:0.38, C:0.27, G:0.06, T:0.29
Consensus pattern (46 bp):
CATTACCAATTCGTACCAAATCGTATTACCAATTCGAACCAAATCA
Found at i:22297570 original size:18 final size:18
Alignment explanation
Indices: 22297527--22297570 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
22297517 AAAAGAGTTC
*
22297527 AAAAAAAAAATTCAAAAT
1 AAAAAAAAAATTCAAAAG
* * *
22297545 CAAGAAAAAATTGAAAAG
1 AAAAAAAAAATTCAAAAG
22297563 AAAAAAAA
1 AAAAAAAA
22297571 TTGCATACAG
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.77, C:0.05, G:0.07, T:0.11
Consensus pattern (18 bp):
AAAAAAAAAATTCAAAAG
Found at i:22303781 original size:23 final size:23
Alignment explanation
Indices: 22303746--22303857 Score: 107
Period size: 23 Copynumber: 4.9 Consensus size: 23
22303736 CTTTTTGAAC
* *
22303746 CATTAACATTTCGTACCAAATCA
1 CATTACCAATTCGTACCAAATCA
* *
22303769 TATTACCAATTCGAACCAAATCA
1 CATTACCAATTCGTACCAAATCA
* * *
22303792 CCTTACCAATTCATACCAAATCG
1 CATTACCAATTCGTACCAAATCA
* * * *
22303815 TATTACCATTTTGAACCAAATCA
1 CATTACCAATTCGTACCAAATCA
* *
22303838 CATTACCATTTCGTAACAAA
1 CATTACCAATTCGTACCAAA
22303858 CCCAAAACCG
Statistics
Matches: 69, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 69 1.00
ACGTcount: A:0.39, C:0.27, G:0.04, T:0.29
Consensus pattern (23 bp):
CATTACCAATTCGTACCAAATCA
Found at i:22307545 original size:16 final size:16
Alignment explanation
Indices: 22307524--22307554 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
22307514 CAATTAATCT
*
22307524 AATTAACCTAAAAATA
1 AATTAAACTAAAAATA
22307540 AATTAAACTAAAAAT
1 AATTAAACTAAAAAT
22307555 CAACAAATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.26
Consensus pattern (16 bp):
AATTAAACTAAAAATA
Found at i:22309613 original size:20 final size:20
Alignment explanation
Indices: 22309590--22309655 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
22309580 TGTGCAATTC
22309590 AGGGGTACCAAAGTACAAAT
1 AGGGGTACCAAAGTACAAAT
* *** * * *
22309610 AGGGGCATGTATGTGCAATTT
1 AGGGGTACCAAAGTACAA-AT
*
22309631 ACGGGTACCAAAGTACAAAT
1 AGGGGTACCAAAGTACAAAT
22309651 AGGGG
1 AGGGG
22309656 CACGTATGTG
Statistics
Matches: 29, Mismatches: 16, Indels: 2
0.62 0.34 0.04
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.36, C:0.14, G:0.30, T:0.20
Consensus pattern (20 bp):
AGGGGTACCAAAGTACAAAT
Found at i:22309626 original size:41 final size:41
Alignment explanation
Indices: 22309570--22309711 Score: 214
Period size: 41 Copynumber: 3.5 Consensus size: 41
22309560 AAGTTTAAAC
*
22309570 AGGGG-ACGTGTGTGCAATTCAGGGGTACCAAAGTACAAAT
1 AGGGGCACGTATGTGCAATTCAGGGGTACCAAAGTACAAAT
* * *
22309610 AGGGGCATGTATGTGCAATTTACGGGTACCAAAGTACAAAT
1 AGGGGCACGTATGTGCAATTCAGGGGTACCAAAGTACAAAT
** *
22309651 AGGGGCACGTATGTGCAATTCAGGGGTACTGAAGTACAAAC
1 AGGGGCACGTATGTGCAATTCAGGGGTACCAAAGTACAAAT
22309692 AGGGGCACGTATGTGCAATT
1 AGGGGCACGTATGTGCAATT
22309712 TATCATTTTT
Statistics
Matches: 91, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
40 5 0.05
41 86 0.95
ACGTcount: A:0.32, C:0.15, G:0.31, T:0.22
Consensus pattern (41 bp):
AGGGGCACGTATGTGCAATTCAGGGGTACCAAAGTACAAAT
Found at i:22312415 original size:24 final size:27
Alignment explanation
Indices: 22312352--22312415 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 27
22312342 TATTTAAGAA
*
22312352 AAATT-AAACACA-TTA-AATATAAAC
1 AAATTCAAACATAGTTATAATATAAAC
22312376 AAATTCAAACATAGTTATAATATAAAC
1 AAATTCAAACATAGTTATAATATAAAC
22312403 -AA-TC-AACATAGTT
1 AAATTCAAACATAGTT
22312416 CAAACATAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
24 14 0.39
25 8 0.22
26 5 0.14
27 9 0.25
ACGTcount: A:0.56, C:0.12, G:0.03, T:0.28
Consensus pattern (27 bp):
AAATTCAAACATAGTTATAATATAAAC
Found at i:22320482 original size:18 final size:19
Alignment explanation
Indices: 22320456--22320492 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
22320446 AATTTTGGAA
22320456 TGGAAAGAAGAGA-GAAAG
1 TGGAAAGAAGAGAGGAAAG
*
22320474 TGGAGAGAAGAGAGGAAAG
1 TGGAAAGAAGAGAGGAAAG
22320493 ATGTGAATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.51, C:0.00, G:0.43, T:0.05
Consensus pattern (19 bp):
TGGAAAGAAGAGAGGAAAG
Done.