Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008082.1 Hibiscus syriacus cultivar Beakdansim tig00110584_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6025995
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 25 of 28
Found at i:5104081 original size:19 final size:21
Alignment explanation
Indices: 5104037--5104088 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 21
5104027 TCCCTACCAT
*
5104037 GGTATCGATACTACTATACTAT
1 GGTATCGATACTACTATA-TAC
5104059 GGTATCGATACT-CTAT-TAC
1 GGTATCGATACTACTATATAC
*
5104078 GGTATTGATAC
1 GGTATCGATAC
5104089 CATTTATGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 12 0.43
21 4 0.14
22 12 0.43
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (21 bp):
GGTATCGATACTACTATATAC
Found at i:5108291 original size:119 final size:119
Alignment explanation
Indices: 5108080--5108319 Score: 480
Period size: 119 Copynumber: 2.0 Consensus size: 119
5108070 CATTTCACTA
5108080 TAAATTGGTTCTAAAGGAATTCCTCTAGTTCTAACCAATTTTGTACTAATATAAGAGTGTGTAGA
1 TAAATTGGTTCTAAAGGAATTCCTCTAGTTCTAACCAATTTTGTACTAATATAAGAGTGTGTAGA
5108145 ACCAGGGTTAACTAGAACAAAAACAGACTTATCAAAAAGATGGAATATACCTGT
66 ACCAGGGTTAACTAGAACAAAAACAGACTTATCAAAAAGATGGAATATACCTGT
5108199 TAAATTGGTTCTAAAGGAATTCCTCTAGTTCTAACCAATTTTGTACTAATATAAGAGTGTGTAGA
1 TAAATTGGTTCTAAAGGAATTCCTCTAGTTCTAACCAATTTTGTACTAATATAAGAGTGTGTAGA
5108264 ACCAGGGTTAACTAGAACAAAAACAGACTTATCAAAAAGATGGAATATACCTGT
66 ACCAGGGTTAACTAGAACAAAAACAGACTTATCAAAAAGATGGAATATACCTGT
5108318 TA
1 TA
5108320 TGATCTCCGG
Statistics
Matches: 121, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
119 121 1.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.30
Consensus pattern (119 bp):
TAAATTGGTTCTAAAGGAATTCCTCTAGTTCTAACCAATTTTGTACTAATATAAGAGTGTGTAGA
ACCAGGGTTAACTAGAACAAAAACAGACTTATCAAAAAGATGGAATATACCTGT
Found at i:5110370 original size:56 final size:56
Alignment explanation
Indices: 5110300--5110709 Score: 597
Period size: 56 Copynumber: 7.3 Consensus size: 56
5110290 AACTTCTTAC
* *
5110300 TTCTTAG-TTTTGCACACAAAGTGCCCACACAGAAATTCATAAACTCATTATGAAT
1 TTCTTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAAT
* ** *
5110355 TTATTAGTTTTTGCACACAAAGTTTCCATACGGAAATTCATAAACTTATTATGAAT
1 TTCTTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAAT
* * *
5110411 TTCTTAGTTTTTACACACAAAGTGTCCATACGGAAATTCAAAAACTCATTATGAAT
1 TTCTTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAAT
* * *
5110467 TTCATAGTCTTTGCACACAAAGTTCCCATACGGAAATTCATAAACTCATTATGAAT
1 TTCTTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAAT
* * * * * *
5110523 TTCTTAGTCTTTGTACACAATGTGCCCATGCAGAAATTCATAAACTCATTGTGAAT
1 TTCTTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAAT
*
5110579 TTATTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAAT
1 TTCTTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAAT
* * * * *
5110635 TTCTTAGTTTTTGCACACAAAATGCGCATACGAAAATTTATAAACTCAATATGAAT
1 TTCTTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAAT
5110691 TTCTTAGTTTTTGCACACA
1 TTCTTAGTTTTTGCACACA
5110710 TATAGTGCAT
Statistics
Matches: 317, Mismatches: 37, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
55 6 0.02
56 311 0.98
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (56 bp):
TTCTTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAAT
Found at i:5111155 original size:19 final size:20
Alignment explanation
Indices: 5111108--5111159 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
5111098 TCTGTTTTCA
*
5111108 ATGGTATCGATACCTTCCTC
1 ATGGTATCGATACCCTCCTC
*
5111128 ATAGTATCGATACCCT-CTC
1 ATGGTATCGATACCCTCCTC
*
5111147 TTGGTATCGATAC
1 ATGGTATCGATAC
5111160 TACTTGCATC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35
Consensus pattern (20 bp):
ATGGTATCGATACCCTCCTC
Found at i:5112722 original size:39 final size:40
Alignment explanation
Indices: 5112653--5112733 Score: 110
Period size: 39 Copynumber: 2.0 Consensus size: 40
5112643 CATTGATCAC
* * *
5112653 GACTTGGCATACTTCATATAAAGGAGCAAGATCATTCCTT
1 GACTTGGCATACCTCAGATAAAGGAACAAGATCATTCCTT
* *
5112693 GACTTGGCAT-CCTCAGATAAAGGAACAAGATCGTTTCTT
1 GACTTGGCATACCTCAGATAAAGGAACAAGATCATTCCTT
5112732 GA
1 GA
5112734 TTTGAAGTCC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 26 0.72
40 10 0.28
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (40 bp):
GACTTGGCATACCTCAGATAAAGGAACAAGATCATTCCTT
Found at i:5113620 original size:38 final size:40
Alignment explanation
Indices: 5113546--5113621 Score: 93
Period size: 38 Copynumber: 1.9 Consensus size: 40
5113536 TATATTATTA
* *
5113546 TTGTTAGTATTATATTTTAATATTATTTACATTATTTACG
1 TTGTTAGTATTATATTTTAATATTATTGACAATATTTACG
** *
5113586 TTGTTA-TATT-TATTTTTTTATTATTGATAATATTTA
1 TTGTTAGTATTATATTTTAATATTATTGACAATATTTA
5113622 TTATTACGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
38 21 0.68
39 4 0.13
40 6 0.19
ACGTcount: A:0.29, C:0.03, G:0.07, T:0.62
Consensus pattern (40 bp):
TTGTTAGTATTATATTTTAATATTATTGACAATATTTACG
Found at i:5116943 original size:12 final size:13
Alignment explanation
Indices: 5116906--5116943 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
5116896 ATTTAATATT
5116906 TTTAAAAGAGTT-
1 TTTAAAAGAGTTA
*
5116918 TTTAAAAGAATTA
1 TTTAAAAGAGTTA
5116931 TTTAAAA-AGTTA
1 TTTAAAAGAGTTA
5116943 T
1 T
5116944 AAACTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 16 0.70
13 7 0.30
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (13 bp):
TTTAAAAGAGTTA
Found at i:5117381 original size:16 final size:16
Alignment explanation
Indices: 5117356--5117393 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
5117346 TTGGTATTAT
5117356 CTGACATGTTATCAAC
1 CTGACATGTTATCAAC
*
5117372 CTGACCTGTTATCAAC
1 CTGACATGTTATCAAC
5117388 CTGACA
1 CTGACA
5117394 GGTAATTGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.29
Consensus pattern (16 bp):
CTGACATGTTATCAAC
Found at i:5118441 original size:14 final size:14
Alignment explanation
Indices: 5118418--5118451 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5118408 ATGATCATTA
*
5118418 TATAAAAAATTAAT
1 TATAAAAAATAAAT
*
5118432 TATAACAAATAAAT
1 TATAAAAAATAAAT
5118446 TATAAA
1 TATAAA
5118452 TTTTACTTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (14 bp):
TATAAAAAATAAAT
Found at i:5118557 original size:13 final size:13
Alignment explanation
Indices: 5118541--5118572 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
5118531 ATATTATAAA
5118541 TATAATATATACT
1 TATAATATATACT
*
5118554 TATATTATATACT
1 TATAATATATACT
5118567 TATAAT
1 TATAAT
5118573 GAATGCATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (13 bp):
TATAATATATACT
Found at i:5119024 original size:24 final size:24
Alignment explanation
Indices: 5118959--5119026 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
5118949 TCTAGTACAT
* * *
5118959 TTTTATATTAATTTCAACTTCATA
1 TTTTATAATAATTTCAATTTCACA
*
5118983 TTTTATAATTATTTCAATTTCACA
1 TTTTATAATAATTTCAATTTCACA
*
5119007 TTTTATAATCATTTCAATTT
1 TTTTATAATAATTTCAATTT
5119027 GATCCCTTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (24 bp):
TTTTATAATAATTTCAATTTCACA
Found at i:5119535 original size:26 final size:26
Alignment explanation
Indices: 5119506--5119565 Score: 111
Period size: 26 Copynumber: 2.3 Consensus size: 26
5119496 AACTATTAAA
*
5119506 TTGACCTGGCACAACTTGTATCCAAT
1 TTGACCTGGCACAACTTGAATCCAAT
5119532 TTGACCTGGCACAACTTGAATCCAAT
1 TTGACCTGGCACAACTTGAATCCAAT
5119558 TTGACCTG
1 TTGACCTG
5119566 ACCTAACAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.30
Consensus pattern (26 bp):
TTGACCTGGCACAACTTGAATCCAAT
Found at i:5119819 original size:14 final size:14
Alignment explanation
Indices: 5119796--5119836 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
5119786 ATTTGTTTTA
5119796 TGGAAATTGAATTC
1 TGGAAATTGAATTC
*
5119810 TGGAATTTGAATTC
1 TGGAAATTGAATTC
*
5119824 TGGAAAATGAATT
1 TGGAAATTGAATT
5119837 ACATTTCTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.37
Consensus pattern (14 bp):
TGGAAATTGAATTC
Found at i:5119879 original size:14 final size:14
Alignment explanation
Indices: 5119840--5119879 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
5119830 ATGAATTACA
*
5119840 TTTCTGGAAAACGT
1 TTTCTGGAAAATGT
5119854 TTTCTGGAAAATGT
1 TTTCTGGAAAATGT
*
5119868 TTTCTGTAAAAT
1 TTTCTGGAAAAT
5119880 AAATTACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.42
Consensus pattern (14 bp):
TTTCTGGAAAATGT
Found at i:5120961 original size:29 final size:28
Alignment explanation
Indices: 5120906--5120961 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
5120896 TAGAAAAAAA
5120906 TTATTTAAAAATCTTAAAATTATTATAT
1 TTATTTAAAAATCTTAAAATTATTATAT
5120934 TTATTTAAAATATCTCTAAAATT-TTATA
1 TTATTTAAAA-ATCT-TAAAATTATTATA
5120962 AAATCTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 10 0.38
29 9 0.35
30 7 0.27
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (28 bp):
TTATTTAAAAATCTTAAAATTATTATAT
Found at i:5123170 original size:17 final size:17
Alignment explanation
Indices: 5123145--5123203 Score: 82
Period size: 17 Copynumber: 3.5 Consensus size: 17
5123135 TGAAAGAATT
* * *
5123145 ATGAGCTAGTTTGATTA
1 ATGAACTAGTTTAATCA
*
5123162 ATGAACTAGTTTAATGA
1 ATGAACTAGTTTAATCA
5123179 ATGAACTAGTTTAATCA
1 ATGAACTAGTTTAATCA
5123196 ATGAACTA
1 ATGAACTA
5123204 AATTTATTCA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (17 bp):
ATGAACTAGTTTAATCA
Found at i:5143120 original size:31 final size:31
Alignment explanation
Indices: 5143064--5143130 Score: 82
Period size: 32 Copynumber: 2.2 Consensus size: 31
5143054 GAAAGGATTG
*
5143064 AAATAAAATGTTGAAAAGTTAAAGTGCATAAA
1 AAATAAAATGCTGAAAAGTTAAAGTGC-TAAA
* * *
5143096 AAATAAAATGCTG-GAATTTAAAGTGCTGAA
1 AAATAAAATGCTGAAAAGTTAAAGTGCTAAA
5143126 AAATA
1 AAATA
5143131 TATAAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 8 0.26
31 11 0.35
32 12 0.39
ACGTcount: A:0.54, C:0.04, G:0.16, T:0.25
Consensus pattern (31 bp):
AAATAAAATGCTGAAAAGTTAAAGTGCTAAA
Found at i:5145344 original size:131 final size:130
Alignment explanation
Indices: 5145111--5145500 Score: 419
Period size: 131 Copynumber: 3.0 Consensus size: 130
5145101 ATCTTTAGGA
* * * **
5145111 AGGGTGATAACACGGTTCCTACGCGATGAGGATGGCTGGTTATCTAGGGCTCACACGGGTCCTAC
1 AGGGTGATAACACGGTTCCTACGCGATGAGGACGGCTGGTTATCTAGGGGTGACACGACTCCTAC
* * * **
5145176 GTGATGAGGAGGTATGGTCGGGAGATGACA-TGATTCCTACGTGATGATGATGACAAACCATCTT
66 GTGATGAGGAGGTATGGTCGGGGGATGACACAG-TTCCTACGTGATGAGGATGGTAAACCATCTT
5145240 T
130 T
** * *
5145241 A-GGTACGATAACACGGTTCCTACGTAATAAGGACGGCTGGGTATCTAGGGGTGACACGACTCCT
1 AGGGT--GATAACACGGTTCCTACGCGATGAGGACGGCTGGTTATCTAGGGGTGACACGACTCCT
* * * *
5145305 ACGTGATGAGGAAGTATGGTCGGGGGATGACACAGTTCCTATGTGAAGAGGATGGTAGACCATCT
64 ACGTGATGAGGAGGTATGGTCGGGGGATGACACAGTTCCTACGTGATGAGGATGGTAAACCATCT
**
5145370 GA
129 TT
** * * * *
5145372 AGGGTGATAACATAGTTCTTATGCGATGAGGAC-GATGGTTATC-AGGGGTGACACGTCTCCTAC
1 AGGGTGATAACACGGTTCCTACGCGATGAGGACGGCTGGTTATCTAGGGGTGACACGACTCCTAC
* * * * * * * *
5145435 ATGATGAAGAGGTCTGGTCAGAGGATGATACGGTTCCTACGTGATGAGGATGGTAAGCCATCTTT
66 GTGATGAGGAGGTATGGTCGGGGGATGACACAGTTCCTACGTGATGAGGATGGTAAACCATCTTT
5145500 A
1 A
5145501 TTGATAATGG
Statistics
Matches: 212, Mismatches: 44, Indels: 10
0.80 0.17 0.04
Matches are distributed among these distances:
128 71 0.33
129 11 0.05
130 22 0.10
131 104 0.49
132 4 0.02
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.25
Consensus pattern (130 bp):
AGGGTGATAACACGGTTCCTACGCGATGAGGACGGCTGGTTATCTAGGGGTGACACGACTCCTAC
GTGATGAGGAGGTATGGTCGGGGGATGACACAGTTCCTACGTGATGAGGATGGTAAACCATCTTT
Found at i:5145814 original size:66 final size:66
Alignment explanation
Indices: 5145702--5145829 Score: 163
Period size: 66 Copynumber: 1.9 Consensus size: 66
5145692 AAATTCCAAA
5145702 GAAAATACTCAAAGATTTTTCTTCAAAAGAAACTATACCAAGAGAGAC-AAAAC-TTGTTTTAAA
1 GAAAATACTCAAAGATTTTTCTTCAAAAGAAACTATACCAAGAGAGACAAAAACTTTGTTTTAAA
5145765 T
66 T
* * * * *
5145766 GAAACATACTCAAAGATTTGTGT-TTCAAAAGACATTGTCCCAATAGAGACAAAAACTTTGTTTT
1 GAAA-ATACTCAAAGATTT-T-TCTTCAAAAGAAACTATACCAAGAGAGACAAAAACTTTGTTTT
5145830 GAGTAAAAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
64 4 0.07
65 14 0.26
66 23 0.43
67 6 0.11
68 7 0.13
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.30
Consensus pattern (66 bp):
GAAAATACTCAAAGATTTTTCTTCAAAAGAAACTATACCAAGAGAGACAAAAACTTTGTTTTAAA
T
Found at i:5145884 original size:37 final size:39
Alignment explanation
Indices: 5145799--5145890 Score: 109
Period size: 37 Copynumber: 2.4 Consensus size: 39
5145789 TTCAAAAGAC
* * *
5145799 ATTGTCCCAATAGAGACAAAAACTTTGTTTTGAGTAAAA
1 ATTGTCTCAATCGAGACAAAAACTTTGTTTTAAGTAAAA
5145838 ATTGTCTCAATCGAGAC-AAAA-TTTGCTTTTAAG-AAAA
1 ATTGTCTCAATCGAGACAAAAACTTTG-TTTTAAGTAAAA
* *
5145875 CTTGTCTCAAGCGAGA
1 ATTGTCTCAATCGAGA
5145891 TGACACTTTG
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
37 22 0.47
38 10 0.21
39 15 0.32
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.30
Consensus pattern (39 bp):
ATTGTCTCAATCGAGACAAAAACTTTGTTTTAAGTAAAA
Found at i:5146255 original size:16 final size:16
Alignment explanation
Indices: 5146234--5146274 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
5146224 TTCATTTATC
*
5146234 ATGTATGTCT-GTGTTG
1 ATGTATGT-TAGTATTG
5146250 ATGTATGTTAGTATTG
1 ATGTATGTTAGTATTG
5146266 ATGTATGTT
1 ATGTATGTT
5146275 TTCTCGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 1 0.04
16 22 0.96
ACGTcount: A:0.20, C:0.02, G:0.27, T:0.51
Consensus pattern (16 bp):
ATGTATGTTAGTATTG
Found at i:5147038 original size:20 final size:20
Alignment explanation
Indices: 5147013--5147057 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
5147003 TATTTAGTAA
5147013 ATTTGACTTAACTTGCCATT
1 ATTTGACTTAACTTGCCATT
5147033 ATTTGACTTAACTTGCCATT
1 ATTTGACTTAACTTGCCATT
*
5147053 GTTTG
1 ATTTG
5147058 GCTAGCTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.18, G:0.13, T:0.47
Consensus pattern (20 bp):
ATTTGACTTAACTTGCCATT
Found at i:5155959 original size:30 final size:30
Alignment explanation
Indices: 5155923--5155982 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
5155913 ATAAACAAAA
5155923 AATTAATCTCAGCTTTTGATATCTTTCAAT
1 AATTAATCTCAGCTTTTGATATCTTTCAAT
5155953 AATTAATCTCAGCTTTTGATATCTTTCAAT
1 AATTAATCTCAGCTTTTGATATCTTTCAAT
5155983 TAAATGGTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.17, G:0.07, T:0.47
Consensus pattern (30 bp):
AATTAATCTCAGCTTTTGATATCTTTCAAT
Found at i:5157221 original size:19 final size:20
Alignment explanation
Indices: 5157197--5157241 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 20
5157187 GGCCAAGAGT
5157197 ATGTATCTTCATT-AAAATC
1 ATGTATCTTCATTAAAAATC
*
5157216 ATGTATTTTCATTAAAAATC
1 ATGTATCTTCATTAAAAATC
5157236 ATGTAT
1 ATGTAT
5157242 TTTGAAAGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.44
Consensus pattern (20 bp):
ATGTATCTTCATTAAAAATC
Found at i:5157235 original size:20 final size:19
Alignment explanation
Indices: 5157197--5157244 Score: 78
Period size: 20 Copynumber: 2.5 Consensus size: 19
5157187 GGCCAAGAGT
*
5157197 ATGTATCTTCATTAAAATC
1 ATGTATTTTCATTAAAATC
5157216 ATGTATTTTCATTAAAAATC
1 ATGTATTTTCATT-AAAATC
5157236 ATGTATTTT
1 ATGTATTTT
5157245 GAAAGGGGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.48
Consensus pattern (19 bp):
ATGTATTTTCATTAAAATC
Found at i:5160923 original size:20 final size:18
Alignment explanation
Indices: 5160881--5160928 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
5160871 GATGTAATGA
**
5160881 GTATCGATACTAAGGTGG
1 GTATCGATACTAAGGAAG
5160899 GTATCGATACTAAGAGAAAG
1 GTATCGATACTAAG-G-AAG
5160919 GTATCGATAC
1 GTATCGATAC
5160929 AATGGATTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 14 0.54
19 1 0.04
20 11 0.42
ACGTcount: A:0.35, C:0.12, G:0.27, T:0.25
Consensus pattern (18 bp):
GTATCGATACTAAGGAAG
Found at i:5161533 original size:60 final size:60
Alignment explanation
Indices: 5161437--5161552 Score: 178
Period size: 60 Copynumber: 1.9 Consensus size: 60
5161427 TGAAAAAAAG
* * *
5161437 TTAAATGCCTAACCGTGCATATTGGCAGAAAGGTGTCATTAATGCAAGTTAGATGATCAA
1 TTAAATGCCTAACCGTGCATATTGGAAAAAAGGTGTCAATAATGCAAGTTAGATGATCAA
* * *
5161497 TTAAATGCCTAACTGTGCATATTGGAAAAAATGTGTCAATAATGCAAGTTGGATGA
1 TTAAATGCCTAACCGTGCATATTGGAAAAAAGGTGTCAATAATGCAAGTTAGATGA
5161553 AAGGCCTAAC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (60 bp):
TTAAATGCCTAACCGTGCATATTGGAAAAAAGGTGTCAATAATGCAAGTTAGATGATCAA
Found at i:5161604 original size:52 final size:52
Alignment explanation
Indices: 5161503--5161821 Score: 377
Period size: 52 Copynumber: 6.0 Consensus size: 52
5161493 TCAATTAAAT
* * * *
5161503 GCCTAACTGTGCATATTGGAAAAAATGTGTCAATAATGCAAGTTGGATGAAAG
1 GCCTAACTGTGCAT-TTGGCAGAAATGTGCCAATAATGCAAGTTAGATGAAAG
* *
5161556 GCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGTAAGTTAGATGAAAG
1 GCCTAACTGTGCATTTGGCAGAAATGTGCCAATAATGCAAGTTAGATGAAAG
* *
5161608 GCCTAATTGTGCATTAGGCAGAAATGTGCCAATAATGCAAGTTAGATGAAAG
1 GCCTAACTGTGCATTTGGCAGAAATGTGCCAATAATGCAAGTTAGATGAAAG
* * * *
5161660 ACCTAACTGTGCATTTGGAAGAAATGTGACAATAATACAAGTTAGATGAAAG
1 GCCTAACTGTGCATTTGGCAGAAATGTGCCAATAATGCAAGTTAGATGAAAG
* * *
5161712 GCCTAACTATGCATTTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAATG
1 GCCTAACTGTGCATTTGGCAGAAATGTGCCAATAATGCAAGTTAGATGAAA-G
* * * ** *
5161765 TTAAATGCCTAACTGTGCATTTGACAGAAAAGTACCCCTAATACAAGTTAGATGAAA
1 ------GCCTAACTGTGCATTTGGCAGAAATGTGCCAATAATGCAAGTTAGATGAAA
5161822 AACAGTGTAT
Statistics
Matches: 229, Mismatches: 30, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
52 171 0.75
53 15 0.07
59 43 0.19
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (52 bp):
GCCTAACTGTGCATTTGGCAGAAATGTGCCAATAATGCAAGTTAGATGAAAG
Found at i:5163034 original size:13 final size:13
Alignment explanation
Indices: 5163016--5163040 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5163006 TATATTGGTG
5163016 AGCAATTCAGAAT
1 AGCAATTCAGAAT
5163029 AGCAATTCAGAA
1 AGCAATTCAGAA
5163041 GAGCGATGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.20
Consensus pattern (13 bp):
AGCAATTCAGAAT
Found at i:5168468 original size:60 final size:54
Alignment explanation
Indices: 5168375--5168797 Score: 359
Period size: 52 Copynumber: 8.0 Consensus size: 54
5168365 GAAAAGTTAG
* * *
5168375 ATGCCTAACCGTGCATATTGGAAAAAAGGTGCCATTAATGCAAGTTAGATGATCAATTAA
1 ATGCCTAACTGTGCATATTGGCAAAAAGGTGCCAATAATGCAAGTTAGATG----A--AA
*
5168435 ATGCCTAACTGTGCATATTGGCAAAAAGGTGCCAATAATGCAAGTTAGATG-AG
1 ATGCCTAACTGTGCATATTGGCAAAAAGGTGCCAATAATGCAAGTTAGATGAAA
* *
5168488 ATGCCTAACTGTGCAT-TTGGCAAAAAGGTGTCAATAATGTAAGTTAGATG-AA
1 ATGCCTAACTGTGCATATTGGCAAAAAGGTGCCAATAATGCAAGTTAGATGAAA
*
5168540 AGGCCTAA-----C-TA-T-G----AAGGTGCCAATAATGCAAGTTAGATG-AA
1 ATGCCTAACTGTGCATATTGGCAAAAAGGTGCCAATAATGCAAGTTAGATGAAA
* * * * * *
5168581 AGGCCTAACTATGAAT-TTGTCAGAAATGTGCCAATAATGCAAGTTAGATG-AA
1 ATGCCTAACTGTGCATATTGGCAAAAAGGTGCCAATAATGCAAGTTAGATGAAA
* * *
5168633 AGGCCTAACTGTGCAT-TTGGCAGAAATGTGCCAATAATGCAAGTTAGATG-AA
1 ATGCCTAACTGTGCATATTGGCAAAAAGGTGCCAATAATGCAAGTTAGATGAAA
* * * *
5168685 AGGCCTAACTGTGCAT-TTGGCAGAAATGTGCCAATAATGCAAGTTAGAGTAAATGTTAA
1 ATGCCTAACTGTGCATATTGGCAAAAAGGTGCCAATAATGCAAGTT--AG---ATG-AAA
* * * * *
5168744 ATGCCTAATTGTGCAT-TTGGCAGAAAGATGCCACTAATACAAGTTAGATGAAA
1 ATGCCTAACTGTGCATATTGGCAAAAAGGTGCCAATAATGCAAGTTAGATGAAA
5168797 A
1 A
5168798 ATAATGTATT
Statistics
Matches: 320, Mismatches: 23, Indels: 47
0.82 0.06 0.12
Matches are distributed among these distances:
41 34 0.11
45 1 0.00
46 2 0.01
47 3 0.01
52 161 0.50
53 20 0.06
54 5 0.02
57 5 0.02
59 41 0.13
60 48 0.15
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (54 bp):
ATGCCTAACTGTGCATATTGGCAAAAAGGTGCCAATAATGCAAGTTAGATGAAA
Found at i:5168523 original size:52 final size:52
Alignment explanation
Indices: 5168437--5168796 Score: 418
Period size: 52 Copynumber: 7.0 Consensus size: 52
5168427 TCAATTAAAT
* * *
5168437 GCCTAACTGTGCATATTGGCAAAAAGGTGCCAATAATGCAAGTTAGATGAGAT
1 GCCTAACTGTGCAT-TTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAG
* * *
5168490 GCCTAACTGTGCATTTGGCAAAAAGGTGTCAATAATGTAAGTTAGATGAAAG
1 GCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAG
5168542 GCCTAAC--T--A--T----G-AAGGTGCCAATAATGCAAGTTAGATGAAAG
1 GCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAG
* * * *
5168583 GCCTAACTATGAATTTGTCAGAAATGTGCCAATAATGCAAGTTAGATGAAAG
1 GCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAG
*
5168635 GCCTAACTGTGCATTTGGCAGAAATGTGCCAATAATGCAAGTTAGATGAAAG
1 GCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAG
* *
5168687 GCCTAACTGTGCATTTGGCAGAAATGTGCCAATAATGCAAGTTAGAGTAAATGTTAAAT
1 GCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTT--AG---ATG--AAAG
* * * *
5168746 GCCTAATTGTGCATTTGGCAGAAAGATGCCACTAATACAAGTTAGATGAAA
1 GCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAA
5168797 AATAATGTAT
Statistics
Matches: 272, Mismatches: 17, Indels: 37
0.83 0.05 0.11
Matches are distributed among these distances:
41 35 0.13
43 1 0.00
45 1 0.00
46 1 0.00
47 1 0.00
48 1 0.00
50 1 0.00
51 1 0.00
52 165 0.61
53 14 0.05
54 5 0.02
57 5 0.02
59 41 0.15
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (52 bp):
GCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAG
Found at i:5168573 original size:41 final size:41
Alignment explanation
Indices: 5168512--5168595 Score: 150
Period size: 41 Copynumber: 2.0 Consensus size: 41
5168502 ATTTGGCAAA
* *
5168512 AAGGTGTCAATAATGTAAGTTAGATGAAAGGCCTAACTATG
1 AAGGTGCCAATAATGCAAGTTAGATGAAAGGCCTAACTATG
5168553 AAGGTGCCAATAATGCAAGTTAGATGAAAGGCCTAACTATG
1 AAGGTGCCAATAATGCAAGTTAGATGAAAGGCCTAACTATG
5168594 AA
1 AA
5168596 TTTGTCAGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (41 bp):
AAGGTGCCAATAATGCAAGTTAGATGAAAGGCCTAACTATG
Found at i:5168619 original size:93 final size:98
Alignment explanation
Indices: 5168459--5168732 Score: 369
Period size: 93 Copynumber: 2.8 Consensus size: 98
5168449 ATATTGGCAA
* * * * *
5168459 AAAGGTGCCAATAATGCAAGTTAGATGAGATGCCTAACTGTGCATTTGGCAAAAAGGTGTCAATA
1 AAAGGTGCCAATAATGCAAGTTAGATGAAAGGCCTAACTGTGCATTTGGCAGAAATGTGCCAATA
*
5168524 ATGTAAGTTAGATGAAAGGCCTAAC-T-A-T-G
66 ATGCAAGTTAGATGAAAGGCCTAACGTCATTGG
* * *
5168553 -AAGGTGCCAATAATGCAAGTTAGATGAAAGGCCTAACTATGAATTTGTCAGAAATGTGCCAATA
1 AAAGGTGCCAATAATGCAAGTTAGATGAAAGGCCTAACTGTGCATTTGGCAGAAATGTGCCAATA
5168617 ATGCAAGTTAGATGAAAGGCCTAACTGTGCATTTGGCAG
66 ATGCAAGTTAGATGAAAGGCCTAAC-GT-CA-TT-G--G
*
5168656 AAATGTGCCAATAATGCAAGTTAGATGAAAGGCCTAACTGTGCATTTGGCAGAAATGTGCCAATA
1 AAAGGTGCCAATAATGCAAGTTAGATGAAAGGCCTAACTGTGCATTTGGCAGAAATGTGCCAATA
5168721 ATGCAAGTTAGA
66 ATGCAAGTTAGA
5168733 GTAAATGTTA
Statistics
Matches: 156, Mismatches: 13, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
93 80 0.51
95 1 0.01
97 1 0.01
99 1 0.01
103 1 0.01
104 72 0.46
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (98 bp):
AAAGGTGCCAATAATGCAAGTTAGATGAAAGGCCTAACTGTGCATTTGGCAGAAATGTGCCAATA
ATGCAAGTTAGATGAAAGGCCTAACGTCATTGG
Found at i:5168647 original size:26 final size:26
Alignment explanation
Indices: 5168618--5168699 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
5168608 GTGCCAATAA
5168618 TGCAAGTTAGATGAAAGGCCTAACTG
1 TGCAAGTTAGATGAAAGGCCTAACTG
* * *
5168644 TGC-ATTTGGCA-GAAATGTGCC-AA-TAA
1 TGCAAGTTAG-ATGAAA-G-GCCTAACT-G
5168670 TGCAAGTTAGATGAAAGGCCTAACTG
1 TGCAAGTTAGATGAAAGGCCTAACTG
5168696 TGCA
1 TGCA
5168700 TTTGGCAGAA
Statistics
Matches: 42, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
25 12 0.29
26 18 0.43
27 12 0.29
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (26 bp):
TGCAAGTTAGATGAAAGGCCTAACTG
Found at i:5174288 original size:13 final size:13
Alignment explanation
Indices: 5174270--5174294 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5174260 GTTCCAACTC
5174270 ATGGTTTCATCTT
1 ATGGTTTCATCTT
5174283 ATGGTTTCATCT
1 ATGGTTTCATCT
5174295 CATGTTCGGA
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:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (13 bp):
ATGGTTTCATCTT
Found at i:5175179 original size:6 final size:6
Alignment explanation
Indices: 5175170--5175231 Score: 61
Period size: 6 Copynumber: 9.7 Consensus size: 6
5175160 TTTTATTTTG
* *
5175170 TTTTCTT TTTTCTT TTTTCT TTTTCT TTTTCT CTTTCTCT TTCTCT TTCTCT
1 TTTTC-T TTTTC-T TTTTCT TTTTCT TTTTCT -TTT-TCT TTTTCT TTTTCT
*
5175222 TTTCCT TTTT
1 TTTTCT TTTT
5175232 AAGCATAATA
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
6 29 0.59
7 17 0.35
8 3 0.06
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTCT
Found at i:5175182 original size:7 final size:7
Alignment explanation
Indices: 5175170--5175205 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
5175160 TTTTATTTTG
5175170 TTTTCTT
1 TTTTCTT
5175177 TTTTCTT
1 TTTTCTT
5175184 TTTTC-T
1 TTTTCTT
5175190 TTTTCTT
1 TTTTCTT
5175197 TTTCTCTT
1 TTT-TCTT
5175205 T
1 T
5175206 CTCTTTCTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 6 0.22
7 16 0.59
8 5 0.19
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTCTT
Found at i:5175185 original size:12 final size:13
Alignment explanation
Indices: 5175165--5175231 Score: 68
Period size: 12 Copynumber: 5.3 Consensus size: 13
5175155 TTTTATTTTA
*
5175165 TTTTGTTTTCT-T
1 TTTTCTTTTCTCT
*
5175177 TTTTCTTTTTTCT
1 TTTTCTTTTCTCT
5175190 TTTTCTTTT-TCT
1 TTTTCTTTTCTCT
*
5175202 CTTTCTCTTTCTCT
1 TTTTCT-TTTCTCT
*
5175216 TTCTCTTTTC-CT
1 TTTTCTTTTCTCT
5175228 TTTT
1 TTTT
5175232 AAGCATAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
12 22 0.48
13 17 0.37
14 7 0.15
ACGTcount: A:0.00, C:0.21, G:0.01, T:0.78
Consensus pattern (13 bp):
TTTTCTTTTCTCT
Found at i:5175198 original size:18 final size:19
Alignment explanation
Indices: 5175170--5175231 Score: 72
Period size: 20 Copynumber: 3.2 Consensus size: 19
5175160 TTTTATTTTG
*
5175170 TTTTCTTTTTTCTTTTTTCT
1 TTTTC-TTTTTCTTTTCTCT
5175190 TTTTCTTTTTCTCTTTCTCT
1 TTTTCTTTTTCT-TTTCTCT
* *
5175210 TTCTCTTTCTCTTTTC-CT
1 TTTTCTTTTTCTTTTCTCT
5175228 TTTT
1 TTTT
5175232 AAGCATAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 5 0.14
19 11 0.30
20 21 0.57
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTCTTTTTCTTTTCTCT
Found at i:5175210 original size:14 final size:14
Alignment explanation
Indices: 5175170--5175224 Score: 64
Period size: 13 Copynumber: 4.2 Consensus size: 14
5175160 TTTTATTTTG
*
5175170 TTTTCT-TTTTTCT
1 TTTTCTCTTTCTCT
*
5175183 TTTT-TCTTTTTCT
1 TTTTCTCTTTCTCT
5175196 TTTTCTCTTTCTC-
1 TTTTCTCTTTCTCT
5175209 -TTTCTCTTTCTCT
1 TTTTCTCTTTCTCT
5175222 TTT
1 TTT
5175225 CCTTTTTAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
12 13 0.35
13 15 0.41
14 9 0.24
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTCTCTTTCTCT
Found at i:5176885 original size:27 final size:27
Alignment explanation
Indices: 5176855--5176907 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
5176845 TCGAATGAGG
* *
5176855 CACGATTTACGAGGAAATCTACTATGA
1 CACGATTTACAAAGAAATCTACTATGA
*
5176882 CACGATTTGCAAAGAAATCTACTATG
1 CACGATTTACAAAGAAATCTACTATG
5176908 GCACTTCCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (27 bp):
CACGATTTACAAAGAAATCTACTATGA
Found at i:5188949 original size:17 final size:17
Alignment explanation
Indices: 5188927--5188960 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5188917 ATATGAAATA
5188927 TTATAAAATAAAAATGT
1 TTATAAAATAAAAATGT
* *
5188944 TTATAATATAAAGATGT
1 TTATAAAATAAAAATGT
5188961 GGACTATAGG
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:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (17 bp):
TTATAAAATAAAAATGT
Found at i:5189444 original size:25 final size:26
Alignment explanation
Indices: 5189407--5189455 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
5189397 GGATTATTCT
* *
5189407 AACCTTAATTAAT-TTCTAATTAAGG
1 AACCTAAACTAATATTCTAATTAAGG
*
5189432 AACCTAAACTAATATTTTAATTAA
1 AACCTAAACTAATATTCTAATTAA
5189456 AAACTAAAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 11 0.55
26 9 0.45
ACGTcount: A:0.45, C:0.12, G:0.04, T:0.39
Consensus pattern (26 bp):
AACCTAAACTAATATTCTAATTAAGG
Found at i:5189507 original size:20 final size:18
Alignment explanation
Indices: 5189449--5189510 Score: 65
Period size: 20 Copynumber: 3.4 Consensus size: 18
5189439 ACTAATATTT
5189449 TAATT-AAAAACTAAAGC
1 TAATTAAAAAACTAAAGC
* *
5189466 -ACTTAAAAAACTAAGGC
1 TAATTAAAAAACTAAAGC
5189483 TTAATTAAAAAACCTAAAGAC
1 -TAATTAAAAAA-CTAAAG-C
5189504 TAATTAA
1 TAATTAA
5189511 TATTAATGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
16 3 0.08
17 11 0.31
19 9 0.25
20 12 0.33
21 1 0.03
ACGTcount: A:0.56, C:0.13, G:0.06, T:0.24
Consensus pattern (18 bp):
TAATTAAAAAACTAAAGC
Found at i:5190580 original size:10 final size:10
Alignment explanation
Indices: 5190565--5190589 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5190555 CTGCTTTTTA
5190565 TTTTTCTAAT
1 TTTTTCTAAT
5190575 TTTTTCTAAT
1 TTTTTCTAAT
5190585 TTTTT
1 TTTTT
5190590 GTATACTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTTCTAAT
Found at i:5197445 original size:6 final size:6
Alignment explanation
Indices: 5197434--5197459 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
5197424 TGGTTGCGAG
5197434 ACATTC ACATTC ACATTC ACATTC AC
1 ACATTC ACATTC ACATTC ACATTC AC
5197460 CGAATTATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (6 bp):
ACATTC
Found at i:5198055 original size:72 final size:67
Alignment explanation
Indices: 5197964--5198163 Score: 251
Period size: 72 Copynumber: 2.9 Consensus size: 67
5197954 GATTCAATTC
* * *
5197964 GTAAGTTCGAGAGTCTAAAATTATCAAGCTTGACTCGAATCAAAATAAAAAAATTGAAGCTCGAC
1 GTAAGTTCGAGAGTTTAAAATTGTCAAGCTCGACTCGAATCAAAATAAAAAAATTGAAGCT----
5198029 CCGACTT
62 -CGACTT
*
5198036 GTAAGTTCGAGAGTTTAAAATTGTCAAGCTCGACTCGAATCAAAAATTAAAAAATTGAAGCTCGA
1 GTAAGTTCGAGAGTTTAAAATTGTCAAGCTCGACTCGAATC-AAAATAAAAAAATTGAAGCTCGA
5198101 CTT
65 CTT
* * * *
5198104 GTAAGTTCGAGAGCTTAAAATTGTCTAGCCTCGACTAGAAT-TAAA-AAAAAAATTGAAGCT
1 GTAAGTTCGAGAGTTTAAAATTGTCAAG-CTCGACTCGAATCAAAATAAAAAAATTGAAGCT
5198164 TGATTCAACT
Statistics
Matches: 117, Mismatches: 9, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
66 14 0.12
67 3 0.03
68 32 0.27
69 11 0.09
72 38 0.32
73 19 0.16
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (67 bp):
GTAAGTTCGAGAGTTTAAAATTGTCAAGCTCGACTCGAATCAAAATAAAAAAATTGAAGCTCGAC
TT
Found at i:5198124 original size:34 final size:35
Alignment explanation
Indices: 5198030--5198126 Score: 87
Period size: 32 Copynumber: 2.8 Consensus size: 35
5198020 AAGCTCGACC
*
5198030 CGACTTGTAAGTTCGAGAGTTTAAAATTGTCAAGCT
1 CGACTTGTAAGTTCGAGAGATTAAAATTG-CAAGCT
* * *
5198066 CGACTCG-AA--TC-AAAAATTAAAAAATTG-AAGCT
1 CGACTTGTAAGTTCGAGAGATT--AAAATTGCAAGCT
*
5198098 CGACTTGTAAGTTCGAGAGCTTAAAATTG
1 CGACTTGTAAGTTCGAGAGATTAAAATTG
5198127 TCTAGCCTCG
Statistics
Matches: 47, Mismatches: 8, Indels: 14
0.68 0.12 0.20
Matches are distributed among these distances:
32 15 0.32
33 4 0.09
34 14 0.30
35 4 0.09
36 10 0.21
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (35 bp):
CGACTTGTAAGTTCGAGAGATTAAAATTGCAAGCT
Found at i:5199911 original size:31 final size:30
Alignment explanation
Indices: 5199876--5199965 Score: 117
Period size: 31 Copynumber: 2.9 Consensus size: 30
5199866 GTTAGTTGTG
* *
5199876 TTATCGTTTTATTAAGTTTTAGTCACTTACA
1 TTATCATTTTATTAAATTTT-GTCACTTACA
**
5199907 TTATCATTTTATTAAATTTTGGTCACTTATG
1 TTATCATTTTATTAAATTTT-GTCACTTACA
5199938 TTATCATTTTATTAAATTTTGATCACTT
1 TTATCATTTTATTAAATTTTG-TCACTT
5199966 GGACGTTGAA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
30 1 0.02
31 52 0.98
ACGTcount: A:0.27, C:0.11, G:0.08, T:0.54
Consensus pattern (30 bp):
TTATCATTTTATTAAATTTTGTCACTTACA
Found at i:5201752 original size:258 final size:254
Alignment explanation
Indices: 5201443--5201910 Score: 652
Period size: 258 Copynumber: 1.8 Consensus size: 254
5201433 ATTTCTCGTG
* * *
5201443 ATAAGAAAATAAGTTAAAAGCTTAAAATGTTATGAACATGTATAATAAATACAGTTACACCTAGT
1 ATAAGAAAATAAGTTAAAAGATTAAAATGTTATGAACATGTATAATAAATACAGTTACACCCAAT
* **
5201508 AATATCATAATTCAATAAGAAATAGGTTGTGATTTCTA-ATGTTAATATTTTTATTAATAAAATA
66 AATATAATAATTCAATAAGAAATAGGTTGCAATTTCTATA-GTTAATA-TTTT-TTAATAAAATA
* * ** * * *
5201572 GGTTGAGCTTAAGAACGTCATGGTTCACTAAGAAAGCATGTTGCAATCAGGAATCTTACTATTTT
128 GATTCAGCCCAAAAACGTCATGGTTCACTAAGAAAACATGTTGCAATCAGGAATATTACTA--TT
5201637 TTTAATAAT-AAATGGGTTGATATTATCAAAGTTTAAGTTAATGAAACCTTAGAATTTCCCACA
191 TTTAATAATAAAATGGGTTGATATTATCAAAGTTTAAGTTAATGAAACCTTAGAATTTCCCACA
* * * *
5201700 ATAAGAAAATAAGTTAAAAGATTAAAAATGTTATGAATATGTATAATAAATACGGTTGCGCCCAA
1 ATAAGAAAATAAGTTAAAAGATT-AAAATGTTATGAACATGTATAATAAATACAGTTACACCCAA
* *
5201765 TAATATAATATTTCAATAAGAAATAGGTTGCAATTTGTATAGTTAATATTTTTTAATAAAATAGA
65 TAATATAATAATTCAATAAGAAATAGGTTGCAATTTCTATAGTTAATATTTTTTAATAAAATAGA
* * * * *
5201830 TTCCGCCCAAAAATGTTATGGTTCACTAAGAAAACATGTTGCAATCTGTAATATTACTATTTTTA
130 TTCAGCCCAAAAACGTCATGGTTCACTAAGAAAACATGTTGCAATCAGGAATATTACTATTTTTA
5201895 ATAATAAAATGGGTTG
195 ATAATAAAATGGGTTG
5201911 TGTCTAAAAA
Statistics
Matches: 184, Mismatches: 24, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
254 11 0.06
255 10 0.05
256 60 0.33
257 26 0.14
258 76 0.41
259 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (254 bp):
ATAAGAAAATAAGTTAAAAGATTAAAATGTTATGAACATGTATAATAAATACAGTTACACCCAAT
AATATAATAATTCAATAAGAAATAGGTTGCAATTTCTATAGTTAATATTTTTTAATAAAATAGAT
TCAGCCCAAAAACGTCATGGTTCACTAAGAAAACATGTTGCAATCAGGAATATTACTATTTTTAA
TAATAAAATGGGTTGATATTATCAAAGTTTAAGTTAATGAAACCTTAGAATTTCCCACA
Found at i:5210396 original size:183 final size:183
Alignment explanation
Indices: 5210088--5210940 Score: 1180
Period size: 183 Copynumber: 4.7 Consensus size: 183
5210078 TTGTCGGTAC
* * * * * *
5210088 GTATCGATACCATTA-AAATATGTATCGATACATAACAATATATCAGGTAAAAATATGAGAAAAT
1 GTATCGATA-CTTTATAAACATGTATCGATACATAACAATATAACATGTAAAAATATGAAAAAAC
* * * * * * * *
5210152 CGGGTTCAATATGAAAAAACCGGTAAAGTGCTACCGGATAAGTTGAAGGTATTGATTCCATTCAA
65 CGGTTTCATTATGACAAAACCGGTAAAGCGATACTGGATATGTTGAAGGTATCGATTCCATTCAA
* * * *
5210217 ATAAGTATCGACACTTTTAGAATTTAAAAGAAAATCAGTAATAGCGCCTATAAA
130 ATAAGTATCGATACTTTTGGAATTTAAAAGAAAAACAATAATAGCGCCTATAAA
* * *
5210271 GTATCGATACTTTATAAACATGTATCGATACGTAACAATATAACATGTAAAAATATTACAAAACC
1 GTATCGATACTTTATAAACATGTATCGATACATAACAATATAACATGTAAAAATATGAAAAAACC
*
5210336 GGTTTTATTATGACAAAACCGGTAAAGCGATACTGGATATGTTGAAGGTATCGATTCCATTCAAA
66 GGTTTCATTATGACAAAACCGGTAAAGCGATACTGGATATGTTGAAGGTATCGATTCCATTCAAA
* *
5210401 TATGTATCGATACTTTTGGAATTTAAAAGAAAAACAATAATAGCGTCTATAAA
131 TAAGTATCGATACTTTTGGAATTTAAAAGAAAAACAATAATAGCGCCTATAAA
* * *
5210454 GTATCGATACTTTATAAACACGTATCGATACATATCAATATAACATGTAAAAATATGAAAAAAAA
1 GTATCGATACTTTATAAACATGTATCGATACATAACAATATAACATGTAAAAATATG-AAAAAAC
* * * ** *
5210519 TGGTTTCATTATGACAAAACCAGTAAAGAGATACCAGATATGTTGAAGGTATCAATTCCATTCAA
65 CGGTTTCATTATGACAAAACCGGTAAAGCGATACTGGATATGTTGAAGGTATCGATTCCATTCAA
*
5210584 ATAAGTATCGATACTTTTGAAATTTAAAAGAAAAACAATAATAGCGCCTATAAA
130 ATAAGTATCGATACTTTTGGAATTTAAAAGAAAAACAATAATAGCGCCTATAAA
*
5210638 GTATCGATACTTTATAAACATGTATCGATACATAACAATATAACATGTAAAAATATGACAAAACC
1 GTATCGATACTTTATAAACATGTATCGATACATAACAATATAACATGTAAAAATATGAAAAAACC
* * * *
5210703 AGTTTCATTATGACAAAACCGGTAAAGC-ACTA-TCAGATATGTCGAATGTATCGATTCCATTCA
66 GGTTTCATTATGACAAAACCGGTAAAGCGA-TACT-GGATATGTTGAAGGTATCGATTCCATTCA
* *
5210766 AATAAGTATCGATACTTTTGGAATTTAAAAGAAAAGA-AACAATAGCTCCTATAAA
129 AATAAGTATCGATACTTTTGGAATTTAAAAGAAAA-ACAATAATAGCGCCTATAAA
*
5210821 GTATCGATACTTTATAAACATGTATCGATACATAACAATATGACA-GATAAAAATATGAAAAAAC
1 GTATCGATACTTTATAAACATGTATCGATACATAACAATATAACATG-TAAAAATATGAAAAAAC
* * *
5210885 TGGTTTCATTATGACAAAACCGGTAGAGC-ACTA-TCGGATATGTTGAATGTATCGAT
65 CGGTTTCATTATGACAAAACCGGTAAAGCGA-TACT-GGATATGTTGAAGGTATCGAT
5210941 ACTTTAATAA
Statistics
Matches: 603, Mismatches: 61, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
182 6 0.01
183 427 0.71
184 170 0.28
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (183 bp):
GTATCGATACTTTATAAACATGTATCGATACATAACAATATAACATGTAAAAATATGAAAAAACC
GGTTTCATTATGACAAAACCGGTAAAGCGATACTGGATATGTTGAAGGTATCGATTCCATTCAAA
TAAGTATCGATACTTTTGGAATTTAAAAGAAAAACAATAATAGCGCCTATAAA
Found at i:5210641 original size:367 final size:365
Alignment explanation
Indices: 5210109--5210905 Score: 1210
Period size: 367 Copynumber: 2.2 Consensus size: 365
5210099 ATTAAAATAT
* * * * *
5210109 GTATCGATACATAACAATATATCAGGTAAAAATATG-AGAAAATCGGGTTCAATATGAAAAAACC
1 GTATCGATACATAACAATATAACA-GTAAAAATATGAAAAAAAT-GGTTTCATTATGACAAAACC
* * * * **
5210173 GGTAAAGTGCTACCGGATAAGTTGAAGGTATTGATTCCATTCAAATAAGTATCGACACTTTTAGA
64 AGTAAAGAGATACCAGATAAGTTGAAGGTATCAATTCCATTCAAATAAGTATCGACACTTTTAGA
* * *
5210238 ATTTAAAAGAAAATCAGTAATAGCGCCTATAAAGTATCGATACTTTATAAACATGTATCGATACG
129 ATTTAAAAGAAAAACAATAATAGCGCCTATAAAGTATCGATACTTTATAAACATGTATCGATACA
* * *
5210303 TAACAATATAACATGTAAAAATATTACAAAACCGGTTTTATTATGACAAAACCGGTAAAGCGA-T
194 TAACAATATAACATGTAAAAATATGACAAAACCAGTTTCATTATGACAAAACCGGTAAAGC-ACT
* * *
5210367 A-CTGGATATGTTGAAGGTATCGATTCCATTCAAATATGTATCGATACTTTTGGAATTTAAAAGA
258 ATC-AGATATGTCGAAGGTATCGATTCCATTCAAATAAGTATCGATACTTTTGGAATTTAAAAGA
*
5210431 AAA-ACAATAATAGCGT-CTATAAAGTATCGATACTTTATAAACAC
322 AAAGA-AACAATAGC-TCCTATAAAGTATCGATACTTTATAAACAC
*
5210475 GTATCGATACATATCAATATAACATGTAAAAATATGAAAAAAAATGGTTTCATTATGACAAAACC
1 GTATCGATACATAACAATATAACA-GTAAAAATATG-AAAAAAATGGTTTCATTATGACAAAACC
* *
5210540 AGTAAAGAGATACCAGATATGTTGAAGGTATCAATTCCATTCAAATAAGTATCGATACTTTT-GA
64 AGTAAAGAGATACCAGATAAGTTGAAGGTATCAATTCCATTCAAATAAGTATCGACACTTTTAG-
5210604 AATTTAAAAGAAAAACAATAATAGCGCCTATAAAGTATCGATACTTTATAAACATGTATCGATAC
128 AATTTAAAAGAAAAACAATAATAGCGCCTATAAAGTATCGATACTTTATAAACATGTATCGATAC
5210669 ATAACAATATAACATGTAAAAATATGACAAAACCAGTTTCATTATGACAAAACCGGTAAAGCACT
193 ATAACAATATAACATGTAAAAATATGACAAAACCAGTTTCATTATGACAAAACCGGTAAAGCACT
*
5210734 ATCAGATATGTCGAATGTATCGATTCCATTCAAATAAGTATCGATACTTTTGGAATTTAAAAGAA
258 ATCAGATATGTCGAAGGTATCGATTCCATTCAAATAAGTATCGATACTTTTGGAATTTAAAAGAA
*
5210799 AAGAAACAATAGCTCCTATAAAGTATCGATACTTTATAAACAT
323 AAGAAACAATAGCTCCTATAAAGTATCGATACTTTATAAACAC
* *
5210842 GTATCGATACATAACAATATGACAGATAAAAATATGAAAAAACTGGTTTCATTATGACAAAACC
1 GTATCGATACATAACAATATAACAG-TAAAAATATGAAAAAAATGGTTTCATTATGACAAAACC
5210906 GGTAGAGCAC
Statistics
Matches: 393, Mismatches: 30, Indels: 16
0.90 0.07 0.04
Matches are distributed among these distances:
366 64 0.16
367 321 0.82
368 8 0.02
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (365 bp):
GTATCGATACATAACAATATAACAGTAAAAATATGAAAAAAATGGTTTCATTATGACAAAACCAG
TAAAGAGATACCAGATAAGTTGAAGGTATCAATTCCATTCAAATAAGTATCGACACTTTTAGAAT
TTAAAAGAAAAACAATAATAGCGCCTATAAAGTATCGATACTTTATAAACATGTATCGATACATA
ACAATATAACATGTAAAAATATGACAAAACCAGTTTCATTATGACAAAACCGGTAAAGCACTATC
AGATATGTCGAAGGTATCGATTCCATTCAAATAAGTATCGATACTTTTGGAATTTAAAAGAAAAG
AAACAATAGCTCCTATAAAGTATCGATACTTTATAAACAC
Found at i:5212963 original size:9 final size:9
Alignment explanation
Indices: 5212951--5212993 Score: 68
Period size: 9 Copynumber: 4.8 Consensus size: 9
5212941 GTAAGGAAGC
*
5212951 AGAGGAGGT
1 AGAGGAGGA
*
5212960 AGAGGAGGT
1 AGAGGAGGA
5212969 AGAGGAGGA
1 AGAGGAGGA
5212978 AGAGGAGGA
1 AGAGGAGGA
5212987 AGAGGAG
1 AGAGGAG
5212994 AATGAAGAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.40, C:0.00, G:0.56, T:0.05
Consensus pattern (9 bp):
AGAGGAGGA
Found at i:5212974 original size:27 final size:26
Alignment explanation
Indices: 5212940--5212993 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
5212930 GAAGGTTATT
* *
5212940 GGTAAGGAAGCAGAGGAGGTAGAGGA
1 GGTAAGGAAGAAGAGGAGGAAGAGGA
*
5212966 GGTAGAGGAGGAAGAGGAGGAAGAGGA
1 GGTA-AGGAAGAAGAGGAGGAAGAGGA
5212993 G
1 G
5212994 AATGAAGAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.39, C:0.02, G:0.54, T:0.06
Consensus pattern (26 bp):
GGTAAGGAAGAAGAGGAGGAAGAGGA
Found at i:5217863 original size:200 final size:200
Alignment explanation
Indices: 5217520--5218673 Score: 1723
Period size: 200 Copynumber: 5.8 Consensus size: 200
5217510 ACTTGAGGTA
* * * * *
5217520 TCGATACATTTATTATAAGTATCAATCCTCAAAATATCGAAACCAATTATTACAAAGTAATAGGT
1 TCGATACATTTATTATAAGTATCGATCCTCAAAACATCAAAACCGATTATTATAAAGTAATAGGT
* * *
5217585 AAATTTACAATGTAACCGGTAAAAATATTCCGGTTTAATGAGAGAATATGTAAACATAATGTATC
66 AAATTTACAATGTAACCGATAAAAATATACCGGTTTAATGAGAGAATAGGTAAACATAATGTATC
* * *
5217650 GATACTTGTTAAAATTGTATCGATACTTTTTGTCCAGAATGAATGACAAACGAGATACAGGCATA
131 GATACTTGTTAAAATTGTATCGATACTTTTTGTCCAGAATGAATGCCAAACGAGATGCACGCATA
5217715 AAGTG
196 AAGTG
* * *
5217720 TCGATACATTTATTATAAGTATCGATCCTCAAAGCATCGAAACCGATAATTATAAAGTAATAGGT
1 TCGATACATTTATTATAAGTATCGATCCTCAAAACATCAAAACCGATTATTATAAAGTAATAGGT
*
5217785 AAATTTACAATGTAATCGATAAAAATATACCGGTTTAATGAGAGAATAGGTAAACATAATGTATC
66 AAATTTACAATGTAACCGATAAAAATATACCGGTTTAATGAGAGAATAGGTAAACATAATGTATC
*
5217850 GATACTTGTTAAAATTATATCGATACTTTTTGTCCAGAATGAATGCCAAACGAGATGCACGCATA
131 GATACTTGTTAAAATTGTATCGATACTTTTTGTCCAGAATGAATGCCAAACGAGATGCACGCATA
5217915 AAGTG
196 AAGTG
* * *
5217920 TCGATACATTTATTATAAGTATCGATCCTCAAAATATCAAAACCAATTATTATAAAGTAATAAGT
1 TCGATACATTTATTATAAGTATCGATCCTCAAAACATCAAAACCGATTATTATAAAGTAATAGGT
* * * *
5217985 AAATTTACAATGTAACTGGTAAAAATATACAGATTTAATGAGAGAATAGGTAAACATAATGTATC
66 AAATTTACAATGTAACCGATAAAAATATACCGGTTTAATGAGAGAATAGGTAAACATAATGTATC
** * * *
5218050 GATACTTGTTAAAATTGTATCGATACTTTTTAACTAGAATGAATGCCAAATGAGATGCACGAATA
131 GATACTTGTTAAAATTGTATCGATACTTTTTGTCCAGAATGAATGCCAAACGAGATGCACGCATA
5218115 AAGTG
196 AAGTG
* *
5218120 TCGATACATTTATTATAAGTATCGATCCTTAAAACATCGAAACCGATTATTATAAAGTAATAGGT
1 TCGATACATTTATTATAAGTATCGATCCTCAAAACATCAAAACCGATTATTATAAAGTAATAGGT
* * *
5218185 AAGTTTACAATGTAACCAATAAAAATATACCAGTTTAATGAGAGAATAGGTAAACATAATGTATC
66 AAATTTACAATGTAACCGATAAAAATATACCGGTTTAATGAGAGAATAGGTAAACATAATGTATC
* * * * *
5218250 GATACTTTTTTAAATTGTATCGATACTTTTTATCCAGAATGAATGCCAAACGAGATGCGCCCATA
131 GATACTTGTTAAAATTGTATCGATACTTTTTGTCCAGAATGAATGCCAAACGAGATGCACGCATA
*
5218315 GAGTG
196 AAGTG
*
5218320 TCAATACATTTATTATAAGTATCGATCCTCAAAACATCAAAACCGATTATTATAAAGTAATAGGT
1 TCGATACATTTATTATAAGTATCGATCCTCAAAACATCAAAACCGATTATTATAAAGTAATAGGT
* *
5218385 AAATTTACAATGTAACCGATAAAAATATATCGGTTTAATGAGAGAATAGGTAAACATAATGTGTC
66 AAATTTACAATGTAACCGATAAAAATATACCGGTTTAATGAGAGAATAGGTAAACATAATGTATC
* * * * * *
5218450 GATACGTT-TTTAAATTGCATCGATGCTTTTTGTCTAGAATGAATGTCAAACGAGATGCACTCAT
131 GATAC-TTGTTAAAATTGTATCGATACTTTTTGTCCAGAATGAATGCCAAACGAGATGCACGCAT
5218514 AAAGTG
195 AAAGTG
*
5218520 TCGATACATTTATTATAAGTATCGATCCTCAAAACATCAAAACTGATTATTATAAAGTAATAGGT
1 TCGATACATTTATTATAAGTATCGATCCTCAAAACATCAAAACCGATTATTATAAAGTAATAGGT
* * * * *
5218585 AAATTTACAATGTAACTGATAAAAATAAATCGGTTT-AT------A-AGGTAAATATAATGTGTC
66 AAATTTACAATGTAACCGATAAAAATATACCGGTTTAATGAGAGAATAGGTAAACATAATGTATC
* *
5218642 GATACTTTTTTAAATTGTATCGATACGTTTTT
131 GATACTTGTTAAAATTGTATCGATAC-TTTTT
5218674 TAAATTACGC
Statistics
Matches: 876, Mismatches: 75, Indels: 13
0.91 0.08 0.01
Matches are distributed among these distances:
191 2 0.00
192 38 0.04
193 6 0.01
199 2 0.00
200 826 0.94
201 2 0.00
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.32
Consensus pattern (200 bp):
TCGATACATTTATTATAAGTATCGATCCTCAAAACATCAAAACCGATTATTATAAAGTAATAGGT
AAATTTACAATGTAACCGATAAAAATATACCGGTTTAATGAGAGAATAGGTAAACATAATGTATC
GATACTTGTTAAAATTGTATCGATACTTTTTGTCCAGAATGAATGCCAAACGAGATGCACGCATA
AAGTG
Found at i:5221410 original size:118 final size:116
Alignment explanation
Indices: 5221222--5221463 Score: 358
Period size: 118 Copynumber: 2.1 Consensus size: 116
5221212 ACCTATTTTT
* *
5221222 TTATCGTCGAATTTCCAAGCCCCATCAGTTTAAAAAAGCACTACCCATTACGTTATATAAGCGCT
1 TTATCGTCGAATTTCCAAACCCCATCACTTTAAAAAAGCACTACCCATTACGTTATATAAGCGCT
* *
5221287 ACCTAATATGTTATTATGCTTGATAATGTTTTCAGTAATTAACTGGTTATG
66 ACCTAATATGTTATTATGCTTGATAATGTTTCCAATAATTAACTGGTTATG
* * * * * * *
5221338 TTATCGTCGGATTTCCAAAACTCCATCAACTTTAACAAGGCGCTACCTATTACGTTATATAAGTG
1 TTATCGTCGAATTTCC-AAACCCCATC-ACTTTAAAAAAGCACTACCCATTACGTTATATAAGCG
*
5221403 CTACCTAATATGTTATTGTGCTTGATAATGTTTCCAATAATTAACTGGTTATG
64 CTACCTAATATGTTATTATGCTTGATAATGTTTCCAATAATTAACTGGTTATG
5221456 TTATCGTC
1 TTATCGTC
5221464 TATATATTTT
Statistics
Matches: 112, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
116 15 0.13
117 8 0.07
118 89 0.79
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (116 bp):
TTATCGTCGAATTTCCAAACCCCATCACTTTAAAAAAGCACTACCCATTACGTTATATAAGCGCT
ACCTAATATGTTATTATGCTTGATAATGTTTCCAATAATTAACTGGTTATG
Found at i:5221809 original size:7 final size:7
Alignment explanation
Indices: 5221797--5221825 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
5221787 TGTTCATAAC
5221797 CTCTCGA
1 CTCTCGA
5221804 CTCTCGA
1 CTCTCGA
5221811 CTCTCGA
1 CTCTCGA
5221818 CTCTCGA
1 CTCTCGA
5221825 C
1 C
5221826 AGATATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.45, G:0.14, T:0.28
Consensus pattern (7 bp):
CTCTCGA
Found at i:5222803 original size:60 final size:59
Alignment explanation
Indices: 5222739--5222852 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 59
5222729 TTCAAATTGG
* * *
5222739 TCCTTAAACTTTTACA-TATTCCAATTTCATCCTCAAACTACGACTATCATTCTAAATTAT
1 TCCTTAAACTTTTA-AGAATTCCAACTTCATCCT-AAACTACAACTATCATTCTAAATTAT
* * *
5222799 TCCTTGAACTTTTAAGAATTCCAGCTTCATCCTAAACTACAACTCTCATTCTAA
1 TCCTTAAACTTTTAAGAATTCCAACTTCATCCTAAACTACAACTATCATTCTAA
5222853 GTTGATTTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
59 20 0.43
60 27 0.57
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.38
Consensus pattern (59 bp):
TCCTTAAACTTTTAAGAATTCCAACTTCATCCTAAACTACAACTATCATTCTAAATTAT
Found at i:5222886 original size:59 final size:58
Alignment explanation
Indices: 5222745--5222894 Score: 144
Period size: 59 Copynumber: 2.5 Consensus size: 58
5222735 TTGGTCCTTA
* * *
5222745 AACTTTTACATATTCCAATTTCATCCTCAAACTACGACTATCATTCTAAATTATTCCTTG
1 AACTTTTAGA-ATTCCAACTTCATCCTCAAACTACAACTATCATTCTAAATTATT-CTTG
* * *
5222805 AACTTTTAAGAATTCCAGCTTCATCCT-AAACTACAACTCTCATTCTAAGTTGATT-TATG
1 AACTTTT-AGAATTCCAACTTCATCCTCAAACTACAACTATCATTCTAAATT-ATTCT-TG
* *
5222864 AACTTTT-GAATCTTTCAACTTCATCCCCAAA
1 AACTTTTAGAA--TTCCAACTTCATCCTCAAA
5222895 TTCATCCAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 12
0.78 0.09 0.12
Matches are distributed among these distances:
57 3 0.04
58 1 0.01
59 42 0.56
60 27 0.36
61 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (58 bp):
AACTTTTAGAATTCCAACTTCATCCTCAAACTACAACTATCATTCTAAATTATTCTTG
Found at i:5223168 original size:60 final size:59
Alignment explanation
Indices: 5223028--5223192 Score: 163
Period size: 60 Copynumber: 2.7 Consensus size: 59
5223018 TCTATATATA
* * *
5223028 TATAATTTGA-GATGAAATTAAAATGTTCAAAACATTTAGGGACCAATTTGGAATAAAGAT
1 TATAATTT-ACGATGAAATTGAAATGTTCAAAA-GTTTAAGGACCAATTTGGAATAAAGAT
* * * *
5223088 TATAATTTAGGAATGAAATTGAAATGTTCAAAAGTCTAAGGACTAATTTGGAATGATAG-T
1 TATAATTTACG-ATGAAATTGAAATGTTCAAAAGTTTAAGGACCAATTTGGAAT-AAAGAT
* * * * *
5223148 TATAGTTTATCGATGGAATTGTAATATTTAAAAGTTTAAGGACCA
1 TATAATTTA-CGATGAAATTGAAATGTTCAAAAGTTTAAGGACCA
5223193 TTTTAAAATA
Statistics
Matches: 87, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
59 1 0.01
60 62 0.71
61 24 0.28
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.34
Consensus pattern (59 bp):
TATAATTTACGATGAAATTGAAATGTTCAAAAGTTTAAGGACCAATTTGGAATAAAGAT
Found at i:5223526 original size:20 final size:20
Alignment explanation
Indices: 5223501--5223558 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
5223491 AAGTGAGTTA
5223501 AATAAATGAGGAATTGAAGG
1 AATAAATGAGGAATTGAAGG
5223521 AATAAATGA-G--TT--A--
1 AATAAATGAGGAATTGAAGG
5223534 AATAAATGAGGAATTGAAGG
1 AATAAATGAGGAATTGAAGG
5223554 AATAA
1 AATAA
5223559 GAAAATTAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 14
0.69 0.00 0.31
Matches are distributed among these distances:
13 9 0.29
14 1 0.03
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 1 0.03
20 14 0.45
ACGTcount: A:0.53, C:0.00, G:0.24, T:0.22
Consensus pattern (20 bp):
AATAAATGAGGAATTGAAGG
Found at i:5223536 original size:33 final size:33
Alignment explanation
Indices: 5223494--5223558 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
5223484 TGTAAAAAAG
5223494 TGAGTTAAATAAATGAGGAATTGAAGGAATAAA
1 TGAGTTAAATAAATGAGGAATTGAAGGAATAAA
5223527 TGAGTTAAATAAATGAGGAATTGAAGGAATAA
1 TGAGTTAAATAAATGAGGAATTGAAGGAATAA
5223559 GAAAATTAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.51, C:0.00, G:0.25, T:0.25
Consensus pattern (33 bp):
TGAGTTAAATAAATGAGGAATTGAAGGAATAAA
Found at i:5227196 original size:90 final size:89
Alignment explanation
Indices: 5227043--5227217 Score: 282
Period size: 90 Copynumber: 2.0 Consensus size: 89
5227033 CCTAACACAC
*
5227043 CCTTTTATAGCCAAGTTACCCTAGTCATATTAGGATTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAGTCATATCAGGATTTTTATTATTTCAAATTAATTAAATCTAT
*
5227108 ATTTAATTAATTTGAATTTAATAAT
66 ATTTAATTAA-TTGAAATTAATAAT
*
5227133 CCTTTTATATCCAAGTTACCCTTA-TCATATCAGGGA-TTTTATTATTTCAAATTAATTAAATCT
1 CCTTTTATAGCCAAGTTACCC-TAGTCATATCA-GGATTTTTATTATTTCAAATTAATTAAATCT
5227196 ATATTTAATTAATTGAAATTAA
64 ATATTTAATTAATTGAAATTAA
5227218 ATATTCGGGA
Statistics
Matches: 80, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
89 9 0.11
90 66 0.82
91 5 0.06
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.46
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACCCTAGTCATATCAGGATTTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTAATAAT
Found at i:5228209 original size:19 final size:19
Alignment explanation
Indices: 5228187--5228224 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
5228177 TATGATTGGT
5228187 CTTTGGGCATACTCTAACA
1 CTTTGGGCATACTCTAACA
5228206 CTTTGGGCATACTCTAACA
1 CTTTGGGCATACTCTAACA
5228225 ATAAGTGCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (19 bp):
CTTTGGGCATACTCTAACA
Found at i:5231134 original size:20 final size:20
Alignment explanation
Indices: 5231109--5231155 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
5231099 TTTTCTAAAC
5231109 TTATTTTCTAGAATTATAAT
1 TTATTTTCTAGAATTATAAT
5231129 TTATTTTCTAGAATTATAAT
1 TTATTTTCTAGAATTATAAT
5231149 TTATTTT
1 TTATTTT
5231156 ACTTAAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (20 bp):
TTATTTTCTAGAATTATAAT
Found at i:5232505 original size:20 final size:20
Alignment explanation
Indices: 5232463--5232515 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
5232453 AAGTTCAAGT
* *
5232463 AAAGTTTTGAAACTCTTGTG
1 AAAGTTTCGAAACTCTTGAG
5232483 AAAGTTTCGAAACAT-TTGAG
1 AAAGTTTCGAAAC-TCTTGAG
*
5232503 AAA-CTTCGAAACT
1 AAAGTTTCGAAACT
5232516 ACAAAGCCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 1 0.03
19 8 0.28
20 19 0.66
21 1 0.03
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (20 bp):
AAAGTTTCGAAACTCTTGAG
Found at i:5232754 original size:2 final size:2
Alignment explanation
Indices: 5232749--5232774 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5232739 ATAAAAAATA
5232749 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5232775 TATGTTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5240584 original size:20 final size:21
Alignment explanation
Indices: 5240544--5240595 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
5240534 TTATTTTGAG
5240544 TATATGTATTT-AATATACATA
1 TATATGT-TTTAAATATACATA
5240565 TATATGTTTTAAATAT-CATA
1 TATATGTTTTAAATATACATA
5240585 TGATA-GTTTTA
1 T-ATATGTTTTA
5240596 CTTGGGATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (21 bp):
TATATGTTTTAAATATACATA
Found at i:5241907 original size:81 final size:81
Alignment explanation
Indices: 5241816--5242301 Score: 641
Period size: 81 Copynumber: 6.0 Consensus size: 81
5241806 TAAAATTCCT
* ** * * *
5241816 TTATTATTTTACTCAACAATATTTAA-TCGTTCATCTAACTGGCATAATTGAGACCTTTCTTCCA
1 TTATTCTTTTACTCAACGGTACTTAACT-GTTCATCTAACTGGCATAATTGACACCTTTCTGCCA
*
5241880 ATTGCACAGTTAGACCA
65 ATTGCACAGTTAGGCCA
* * * *
5241897 TTATTCTTTTACTCAACTGTACTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTTCCAA
1 TTATTCTTTTACTCAACGGTACTTAACTGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAA
* * **
5241962 TTGAACATTTAGTTCA
66 TTGCACAGTTAGGCCA
* * * *
5241978 TTATTCTTTTACTCAACGTTATTTAACTGTTCATCTAACTGGCATAGTTGACACATTTCTGCCAA
1 TTATTCTTTTACTCAACGGTACTTAACTGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAA
*
5242043 TTACACAGTTAGGCCA
66 TTGCACAGTTAGGCCA
* * * * *
5242059 TTATTCTTTTACTCAACGATACTTAACCGTTAATCTAAATGGCATAATTGACACCTTTATGCCAA
1 TTATTCTTTTACTCAACGGTACTTAACTGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAA
5242124 TTGCACAGTTAGGCCA
66 TTGCACAGTTAGGCCA
* * * *
5242140 ATATTCTTTTACTCAACTGTACTTAACTGTTCATCTAGCTGGCATAATTGACACCTTTATGCCAA
1 TTATTCTTTTACTCAACGGTACTTAACTGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAA
5242205 TTGCACAGTTAGGCCA
66 TTGCACAGTTAGGCCA
* *
5242221 ATATTCTCTTTTACTCAACGGTACTTAACTGTTCATCTAACTGGCATAATTGACACCTTTCGGCC
1 TTA-T-TCTTTTACTCAACGGTACTTAACTGTTCATCTAACTGGCATAATTGACACCTTTCTGCC
* *
5242286 AATAGTACAGTTAGGC
64 AATTGCACAGTTAGGC
5242302 ATCAAAAACA
Statistics
Matches: 356, Mismatches: 46, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
81 286 0.80
82 1 0.00
83 69 0.19
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (81 bp):
TTATTCTTTTACTCAACGGTACTTAACTGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAA
TTGCACAGTTAGGCCA
Found at i:5242329 original size:68 final size:69
Alignment explanation
Indices: 5242252--5242640 Score: 486
Period size: 68 Copynumber: 5.7 Consensus size: 69
5242242 TACTTAACTG
* * * * * ** *
5242252 TTCATCTAACTGGCATAATTGACACCTTTCGGCCAATA-GTACAGTTAGGCATCAAAAACACTTT
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAATATGCACAGTTAGGCCTCAAAGGCACTTA
*
5242316 GTCT
66 GCCT
* * *
5242320 TTCATCTAACTTGCATAAATGACA-CTTTATGTC-ATATGCATAGTTAGGCCTCAAAGGCACTTA
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAATATGCACAGTTAGGCCTCAAAGGCACTTA
*
5242383 GTCT
66 GCCT
* * * * *
5242387 TTCATCTACCTGGCATAAATGTCACCTTTCTAT-AATATGCACAGTTAAGCCTCAAAGGAACTTA
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAATATGCACAGTTAGGCCTCAAAGGCACTTA
5242451 GCCT
66 GCCT
* * * * *
5242455 TTCATCTAACTGACATAAATGACACATTTCTTTC-ATATGCACATTTAGGCCTCAAAGGTACTTA
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAATATGCACAGTTAGGCCTCAAAGGCACTTA
5242519 GCCT
66 GCCT
* *
5242523 TTCATCTTACTAGCATAAATGACACCTTTCTGTCAA-ATGCACAGTTAGGCCTCAAAGGCACTTA
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAATATGCACAGTTAGGCCTCAAAGGCACTTA
5242587 GCCT
66 GCCT
* *
5242591 TTCATCTAACTGGCATAAATAACACCTTTCTATC-ATATGCACAGTTAGGC
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAATATGCACAGTTAGGC
5242641 TTCATGATCT
Statistics
Matches: 276, Mismatches: 39, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
66 3 0.01
67 52 0.19
68 220 0.80
69 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.32
Consensus pattern (69 bp):
TTCATCTAACTGGCATAAATGACACCTTTCTGTCAATATGCACAGTTAGGCCTCAAAGGCACTTA
GCCT
Found at i:5246947 original size:179 final size:182
Alignment explanation
Indices: 5246644--5246992 Score: 677
Period size: 179 Copynumber: 1.9 Consensus size: 182
5246634 CGATATATGG
5246644 ATGTCACATCACTTTAAAATAACGTTTCTCATTTGGAAACCCATAAAAATTTGTTTCAATTCAAA
1 ATGTCACATCACTTTAAAATAACGTTTCTCATTTGGAAACCCATAAAAATTTGTTTCAATTCAAA
5246709 GAACCATAAAATAGGATATGTTTAAAACCAACAAGCTAAAATGATCACTTAATTACATTACAAAA
66 GAACCATAAAATAGGATATGTTTAAAACCAACAAGCTAAAATGATCACTTAATTACATTACAAAA
5246774 TGTTTACCAGAGTTTGATTACATGCCAACTATGTTCTTAACGTACACGATAT
131 TGTTTACCAGAGTTTGATTACATGCCAACTATGTTCTTAACGTACACGATAT
5246826 ATGTCACATCACTTT-AAAT-ACGTTTCTCATTTGGAAACCCAT-AAAATTTGTTTCAATTCAAA
1 ATGTCACATCACTTTAAAATAACGTTTCTCATTTGGAAACCCATAAAAATTTGTTTCAATTCAAA
5246888 GAACCATAAAATAGGATATGTTTAAAACCAACAAGCTAAAATGATCACTTAATTACATTACAAAA
66 GAACCATAAAATAGGATATGTTTAAAACCAACAAGCTAAAATGATCACTTAATTACATTACAAAA
5246953 TGTTTACCAGAGTTTGATTACATGCCAACTATGTTCTTAA
131 TGTTTACCAGAGTTTGATTACATGCCAACTATGTTCTTAA
5246993 ATTGAATAAG
Statistics
Matches: 167, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
179 125 0.75
180 23 0.14
181 4 0.02
182 15 0.09
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.32
Consensus pattern (182 bp):
ATGTCACATCACTTTAAAATAACGTTTCTCATTTGGAAACCCATAAAAATTTGTTTCAATTCAAA
GAACCATAAAATAGGATATGTTTAAAACCAACAAGCTAAAATGATCACTTAATTACATTACAAAA
TGTTTACCAGAGTTTGATTACATGCCAACTATGTTCTTAACGTACACGATAT
Found at i:5247552 original size:2 final size:2
Alignment explanation
Indices: 5247547--5247593 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
5247537 TTATATACAT
5247547 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
5247589 AC AC A
1 AC AC A
5247594 TATATCATCC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5247798 original size:81 final size:81
Alignment explanation
Indices: 5247653--5248043 Score: 493
Period size: 81 Copynumber: 4.8 Consensus size: 81
5247643 AAAATTCCTT
* * * * * * * *
5247653 TATTGTTTTACTCAACAGTATTTAATCATTCATATAATTGGCATAATTGACACCTTTTTGCCAAT
1 TATTCTTTTACTCAACTGTACTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAT
5247718 TGCACAATTAGGCCAA
66 TGCACAATTAGGCCAA
*
5247734 TATTCTTTTACTCAACTGTACTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTACCAAT
1 TATTCTTTTACTCAACTGTACTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAT
* *
5247799 TGCACAGTTAGGCCAT
66 TGCACAATTAGGCCAA
* * * **
5247815 TATTCTTTTACTCAACGGTATTTAACCGTTCATCTAAATGGCATAATAAACACCTTTCT-CCAAT
1 TATTCTTTTACTCAACTGTACTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAT
5247879 TGCACAATTAGG-CAA
66 TGCACAATTAGGCCAA
* * *
5247894 TTATTCTTTTACTCAAC-GATACTTAACCGTTCATCTAATTGGCATAATTGAAACCTTTCTGCAA
1 -TATTCTTTTACTCAACTG-TACTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCA
* *
5247958 ATTGCATAGTTAGGCCAA
64 ATTGCACAATTAGGCCAA
* * * * *
5247976 TATTCTTTTACTCCA-TGGTACCTAACCATTCATCTAACTGGCATAATTGACACATTTCTTCCAA
1 TATTCTTTTACTCAACT-GTACTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAA
5248040 TTGC
65 TTGC
5248044 TAACCATTCA
Statistics
Matches: 270, Mismatches: 34, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
79 3 0.01
80 68 0.25
81 195 0.72
82 4 0.01
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.37
Consensus pattern (81 bp):
TATTCTTTTACTCAACTGTACTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAT
TGCACAATTAGGCCAA
Found at i:5247924 original size:161 final size:161
Alignment explanation
Indices: 5247652--5248043 Score: 545
Period size: 161 Copynumber: 2.4 Consensus size: 161
5247642 TAAAATTCCT
* * * * * *
5247652 TTATTGTTTTACTCAACAGTATTTAATCATTCATATAATTGGCATAATTGACACCTTTTTGCCAA
1 TTATTCTTTTACTCAACGGTATTTAACCATTCATCTAAATGGCATAATTGACACCTTTCT-CCAA
5247717 TTGCACAATTAGGCCAATATTCTTTTACTCAACTGTACTTAACCGTTCATCTAACTGGCATAATT
65 TTGCACAATTAGGCCAATATTCTTTTACTCAACTGTACTTAACCGTTCATCTAACTGGCATAATT
* *
5247782 GACACCTTTCTACCAATTGCACAGTTAGGCCA
130 GAAACCTTTCTACAAATTGCACAGTTAGGCCA
* **
5247814 TTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAAATGGCATAATAAACACCTTTCTCCAAT
1 TTATTCTTTTACTCAACGGTATTTAACCATTCATCTAAATGGCATAATTGACACCTTTCTCCAAT
*
5247879 TGCACAATTAGG-CAATTATTCTTTTACTCAAC-GATACTTAACCGTTCATCTAATTGGCATAAT
66 TGCACAATTAGGCCAA-TATTCTTTTACTCAACTG-TACTTAACCGTTCATCTAACTGGCATAAT
* *
5247942 TGAAACCTTTCTGCAAATTGCATAGTTAGGCCA
129 TGAAACCTTTCTACAAATTGCACAGTTAGGCCA
* * * ** * *
5247975 ATATTCTTTTACTCCATGGTACCTAACCATTCATCTAACTGGCATAATTGACACATTTCTTCCAA
1 TTATTCTTTTACTCAACGGTATTTAACCATTCATCTAAATGGCATAATTGACACCTTTC-TCCAA
5248040 TTGC
65 TTGC
5248044 TAACCATTCA
Statistics
Matches: 203, Mismatches: 24, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
160 4 0.02
161 139 0.68
162 60 0.30
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.37
Consensus pattern (161 bp):
TTATTCTTTTACTCAACGGTATTTAACCATTCATCTAAATGGCATAATTGACACCTTTCTCCAAT
TGCACAATTAGGCCAATATTCTTTTACTCAACTGTACTTAACCGTTCATCTAACTGGCATAATTG
AAACCTTTCTACAAATTGCACAGTTAGGCCA
Found at i:5248031 original size:26 final size:26
Alignment explanation
Indices: 5248002--5248077 Score: 67
Period size: 26 Copynumber: 3.2 Consensus size: 26
5247992 GGTACCTAAC
5248002 CATTCATCTAACTGGCATAATTGACA
1 CATTCATCTAACTGGCATAATTGACA
* * *
5248028 CATTTCTTCCAA-TTGC-T-A---AC-
1 CA-TTCATCTAACTGGCATAATTGACA
5248048 CATTCATCTAACTGGCATAATTGACA
1 CATTCATCTAACTGGCATAATTGACA
5248074 CATT
1 CATT
5248078 TCTTCCAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 16
0.62 0.10 0.28
Matches are distributed among these distances:
19 7 0.19
20 5 0.14
21 3 0.08
22 1 0.03
24 1 0.03
25 3 0.08
26 9 0.25
27 7 0.19
ACGTcount: A:0.32, C:0.25, G:0.09, T:0.34
Consensus pattern (26 bp):
CATTCATCTAACTGGCATAATTGACA
Found at i:5248064 original size:46 final size:46
Alignment explanation
Indices: 5247997--5248089 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
5247987 TCCATGGTAC
5247997 CTAACCATTCATCTAACTGGCATAATTGACACATTTCTTCCAATTG
1 CTAACCATTCATCTAACTGGCATAATTGACACATTTCTTCCAATTG
5248043 CTAACCATTCATCTAACTGGCATAATTGACACATTTCTTCCAATTG
1 CTAACCATTCATCTAACTGGCATAATTGACACATTTCTTCCAATTG
5248089 C
1 C
5248090 ACAGTTAGGC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.30, C:0.27, G:0.09, T:0.34
Consensus pattern (46 bp):
CTAACCATTCATCTAACTGGCATAATTGACACATTTCTTCCAATTG
Found at i:5248148 original size:127 final size:127
Alignment explanation
Indices: 5247917--5248170 Score: 391
Period size: 127 Copynumber: 2.0 Consensus size: 127
5247907 CAACGATACT
* * * *
5247917 TAACCGTTCATCTAATTGGCATAATTGAAACCTTTCTGCAAATTGCATAGTTAGGCCAATATTCT
1 TAACCATTCATCTAACTGGCATAATTGAAACATTTCTGCAAATTGCACAGTTAGGCCAATATTCT
* * *
5247982 TTTACTCCATGGTACCTAACCATTCATCTAACTGGCATAATTGACACATTTCTTCCAATTGC
66 TTTACTCAATGGTACCTAACCATTCATCTAACTGACATAATTGACACATTTCTACCAATTGC
* * * *
5248044 TAACCATTCATCTAACTGGCATAATTGACACATTTCTTCCAATTGCACAGTTAGGCCAATGTTCT
1 TAACCATTCATCTAACTGGCATAATTGAAACATTTCTGCAAATTGCACAGTTAGGCCAATATTCT
* *
5248109 TTTACTCAATGGTACTTAACCGTTCATCTAACTGACATAATTGACACATTTCTACCAATTGC
66 TTTACTCAATGGTACCTAACCATTCATCTAACTGACATAATTGACACATTTCTACCAATTGC
5248171 ACAGTTAGGC
Statistics
Matches: 114, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
127 114 1.00
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (127 bp):
TAACCATTCATCTAACTGGCATAATTGAAACATTTCTGCAAATTGCACAGTTAGGCCAATATTCT
TTTACTCAATGGTACCTAACCATTCATCTAACTGACATAATTGACACATTTCTACCAATTGC
Found at i:5248206 original size:68 final size:67
Alignment explanation
Indices: 5248122--5248388 Score: 254
Period size: 68 Copynumber: 3.9 Consensus size: 67
5248112 ACTCAATGGT
* * *
5248122 ACTTAACCGTTCATCTAACTGACATAATTGACACATTTCTACCAATTGCACAGTTAGGCCTCAAA
1 ACTTAGCCTTTCATCTAACTGACATAAATGACACATTTCTACC-ATTGCACAGTTAGGCCTCAAA
5248187 GAC
65 GAC
* * * * ** *
5248190 AGTTAGTCTTTCATCTAAATGGA-ATTAATGACACATTTCTGTCATATGCATAGTTAGGCCTCAA
1 ACTTAGCCTTTCATCTAACT-GACATAAATGACACATTTCTACCAT-TGCACAGTTAGGCCTCAA
5248254 AGGA-
64 A-GAC
* * * *
5248258 ACTTAGCCTTTCATCTAACTGACATAAATGACACCTTTTTGTCTTATT-CACAGTTAGGCCTCAA
1 ACTTAGCCTTTCATCTAACTGACATAAATGACACATTTCT-AC-CATTGCACAGTTAGGCCTCAA
*
5248322 CTG-C
64 -AGAC
* ** * *
5248326 ACTTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGTCATATGCAGAGTTATGCCTCA
1 ACTTAGCCTTTCATCTAACTGACATAAATGACACATTTCTACCAT-TGCACAGTTAGGCCTCA
5248389 TGATCTTTTA
Statistics
Matches: 160, Mismatches: 29, Indels: 20
0.77 0.14 0.10
Matches are distributed among these distances:
66 2 0.01
67 5 0.03
68 146 0.91
69 5 0.03
70 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (67 bp):
ACTTAGCCTTTCATCTAACTGACATAAATGACACATTTCTACCATTGCACAGTTAGGCCTCAAAG
AC
Found at i:5248357 original size:136 final size:136
Alignment explanation
Indices: 5248113--5248388 Score: 358
Period size: 136 Copynumber: 2.0 Consensus size: 136
5248103 TGTTCTTTTA
* * *
5248113 CTCAATGGTACTTAACCGTTCATCTAACTGACATAATTGACACATTTCTACCAATTGCACAGTTA
1 CTCAAAGGAACTTAACCGTTCATCTAACTGACATAAATGACACATTTCTACCAATTGCACAGTTA
* * * *
5248178 GGCCTCAAAGACAGTTAGTCTTTCATCTAAATGGAATTAATGACACATTTCTGTCATATGCATAG
66 GGCCTCAAAGACACTTAGCCTTTCATCTAAATGGAATAAATGACACATTTCTGTCATATGCAGAG
5248243 TTAGGC
131 TTAGGC
* * * * * **
5248249 CTCAAAGGAACTTAGCCTTTCATCTAACTGACATAAATGACACCTTTTTGTCTTATT-CACAGTT
1 CTCAAAGGAACTTAACCGTTCATCTAACTGACATAAATGACACATTTCT-ACCAATTGCACAGTT
* * *
5248313 AGGCCTCAACTG-CACTTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGTCATATGCAG
65 AGGCCTCAA-AGACACTTAGCCTTTCATCTAAATGGAATAAATGACACATTTCTGTCATATGCAG
*
5248377 AGTTATGC
129 AGTTAGGC
5248385 CTCA
1 CTCA
5248389 TGATCTTTTA
Statistics
Matches: 120, Mismatches: 18, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
136 115 0.96
137 5 0.04
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (136 bp):
CTCAAAGGAACTTAACCGTTCATCTAACTGACATAAATGACACATTTCTACCAATTGCACAGTTA
GGCCTCAAAGACACTTAGCCTTTCATCTAAATGGAATAAATGACACATTTCTGTCATATGCAGAG
TTAGGC
Found at i:5251110 original size:81 final size:81
Alignment explanation
Indices: 5250933--5251743 Score: 1032
Period size: 81 Copynumber: 10.0 Consensus size: 81
5250923 TCTTTCATCC
* * * * * * * * ** *
5250933 CAAAGGCATTTAACCTTTGATCTAACTTGCATTATTGGCACCTTTATGCCAAATGCATAGTTGGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGG
*
5250998 CATCT-ATCTTTTACT
66 CATTTAATCTTTTACT
* * * *
5251013 CAAAGGTATTTAACCTTTCATCTAAATGGCATGATTGAAACTTTTTTGTCAAATGCACAACTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGG
5251078 CATTTAATCTTTTACT
66 CATTTAATCTTTTACT
* * *
5251094 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGGCACCTTTATTCTGTCAAATGTATAACT
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACC--T-TTCTGTCAAATGCACAACT
*
5251159 AGGTATTTAATCTTTTACT
63 AGGCATTTAATCTTTTACT
* * * * *
5251178 CAAAGGTATTTAACCTTTGATCTAACTGGCATGATTGGCACATTTTTTTCAAATGCACAACTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGG
* *
5251243 AACTTAATCTTTTACT
66 CATTTAATCTTTTACT
* *
5251259 CAAAGGTATTTAACCTTTCATCTAACTAGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGG
5251324 CATTTAATCTTTTACT
66 CATTTAATCTTTTACT
* * * * *
5251340 CAAAGGTATTTAACATTTCATCTAATTGGCATGATTGAAACCTTTCTGTCAAATGCATAACTAGA
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGG
5251405 CATTTAATCTTTTACT
66 CATTTAATCTTTTACT
* * ** * *
5251421 CAAAAGTATTTAACTTTTCATCTAACTGGCATGATTGACATGTTTCTATGAAATGCACAACTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGG
* *
5251486 CATTTAAGCTTTTAGT
66 CATTTAATCTTTTACT
* * * * * **
5251502 CAAAGTTATTTAACCTTTCATTTAATTGGCATGATTGACACATTTATGTCAAATATACAACTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGG
*
5251567 CATTT-ATCTTTTATT
66 CATTTAATCTTTTACT
* * *
5251582 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGAAACCTTTCTCTCAAATGCAAAACTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGG
*
5251647 TATTTAATCTTTTACT
66 CATTTAATCTTTTACT
* * * * *
5251663 CAAAGGTATTTAACCTTTTATCTAATTGTCATGATTGACACCTTTCTGTCAAATGCACAAGTAGA
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGG
* *
5251728 TAGTTAATCTTTTACT
66 CATTTAATCTTTTACT
5251744 TTAAAATAGT
Statistics
Matches: 632, Mismatches: 94, Indels: 9
0.86 0.13 0.01
Matches are distributed among these distances:
80 122 0.19
81 434 0.69
82 1 0.00
83 1 0.00
84 74 0.12
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (81 bp):
CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGG
CATTTAATCTTTTACT
Found at i:5253651 original size:2 final size:2
Alignment explanation
Indices: 5253646--5253676 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5253636 ACACACACAC
5253646 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5253677 ACACTAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5259147 original size:45 final size:45
Alignment explanation
Indices: 5259098--5259514 Score: 532
Period size: 45 Copynumber: 9.3 Consensus size: 45
5259088 TAAAACGAAT
* * * *
5259098 CCATAAATGAAATGCGTAATGGCGCATTAAAGGCATGACATGATG
1 CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATGATG
* ** * *
5259143 CCATAATTGAAATAAATAACGGTACATTAAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATGATG
*
5259188 ACATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAA-GAATG
1 CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATG-ATG
**
5259233 CCATAAATGAAATGCATAGTGGTGCATTAAAGGCATGAAATGATG
1 CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATGATG
* * *
5259278 TCATAAATGAAATGCATAAAGGTACATTAAAGGCATGAAATGATG
1 CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATGATG
5259323 CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAA-GAATG
1 CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATG-ATG
* * * * *
5259368 CCATAAATGAAATACATAAAGGTGCATTAAAGACATGGAGTGATG
1 CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATGATG
* * * *
5259413 CAATAAATGAAATGCATAACGATGCATTAAAGGTATGAAAGGATG
1 CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATGATG
* * ** *
5259458 CCATAAATGAAATGTATAACGGTGCATTAAGGGCAAAAAAGGATG
1 CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATGATG
*
5259503 CCTTAAATGAAA
1 CCATAAATGAAA
5259515 ATAATGAATA
Statistics
Matches: 322, Mismatches: 46, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
44 2 0.01
45 318 0.99
46 2 0.01
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.22
Consensus pattern (45 bp):
CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATGATG
Found at i:5259302 original size:135 final size:134
Alignment explanation
Indices: 5259094--5259514 Score: 592
Period size: 135 Copynumber: 3.1 Consensus size: 134
5259084 ACTCTAAAAC
* * * * **
5259094 GAAT-CCATAAATGAAATGCGTAATGGCGCATTAAAGGCATGACATGATGCCATAATTGAAATAA
1 GAATGCCATAAATGAAATGCATAATGGTGCATTAAAGGCATGAAATGATG-CATAAATGAAATGC
*
5259158 ATAACGGTACATTAAAGGCATGAAAGGATGACATAAATGAAATGCATAACGGTGCATTAAAGGCA
65 ATAACGGTACATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCATTAAAGGCA
5259223 TGAAA
130 TGAAA
*
5259228 GAATGCCATAAATGAAATGCATAGTGGTGCATTAAAGGCATGAAATGATGTCATAAATGAAATGC
1 GAATGCCATAAATGAAATGCATAATGGTGCATTAAAGGCATGAAATGATG-CATAAATGAAATGC
* *
5259293 ATAAAGGTACATTAAAGGCATGAAATGATGCCATAAATGAAATGCATAACGGTGCATTAAAGGCA
65 ATAACGGTACATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCATTAAAGGCA
5259358 TGAAA
130 TGAAA
* * * * *
5259363 GAATGCCATAAATGAAATACATAAAGGTGCATTAAAGACATGGAGTGATGCAATAAATGAAATGC
1 GAATGCCATAAATGAAATGCATAATGGTGCATTAAAGGCATGAAATGATGC-ATAAATGAAATGC
* * * * *
5259428 ATAACGATGCATTAAAGGTATGAAAGGATGCCATAAATGAAATGTATAACGGTGCATTAAGGGCA
65 ATAACGGTACATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCATTAAAGGCA
**
5259493 AAAAA
130 TGAAA
* *
5259498 GGATGCCTTAAATGAAA
1 GAATGCCATAAATGAAA
5259515 ATAATGAATA
Statistics
Matches: 257, Mismatches: 28, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
134 5 0.02
135 252 0.98
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.22
Consensus pattern (134 bp):
GAATGCCATAAATGAAATGCATAATGGTGCATTAAAGGCATGAAATGATGCATAAATGAAATGCA
TAACGGTACATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCATTAAAGGCAT
GAAA
Found at i:5259436 original size:24 final size:23
Alignment explanation
Indices: 5259409--5259483 Score: 64
Period size: 24 Copynumber: 3.3 Consensus size: 23
5259399 GACATGGAGT
5259409 GATGCAATAAATGAAATGCATAAC
1 GATGCAATAAATGAAATG-ATAAC
* ** *
5259433 GATGCATTAAA-GGTATGA-AAG
1 GATGCAATAAATGAAATGATAAC
*
5259454 GATGCCATAAATGAAATGTATAAC
1 GATGCAATAAATGAAATG-ATAAC
*
5259478 GGTGCA
1 GATGCA
5259484 TTAAGGGCAA
Statistics
Matches: 37, Mismatches: 11, Indels: 6
0.69 0.20 0.11
Matches are distributed among these distances:
21 11 0.30
22 5 0.14
23 5 0.14
24 16 0.43
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.23
Consensus pattern (23 bp):
GATGCAATAAATGAAATGATAAC
Found at i:5261199 original size:47 final size:47
Alignment explanation
Indices: 5261096--5261212 Score: 135
Period size: 47 Copynumber: 2.4 Consensus size: 47
5261086 AACATATATA
* * **
5261096 TTTATGCATTTTAATATATATGACATCCTTTCATGCATTAATTAATCCT
1 TTTATGCATTTTAA-AT-TATGGCATCCTTTCATGCATTAATGAATAAT
* * * * *
5261145 TTCATGCATTTTCAATCATGGCATCCTTTCATGCCTTAATGCATAAT
1 TTTATGCATTTTAAATTATGGCATCCTTTCATGCATTAATGAATAAT
5261192 TTTATGCATTTTAAATTATGG
1 TTTATGCATTTTAAATTATGG
5261213 ATTCGATTTA
Statistics
Matches: 56, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
47 42 0.75
48 2 0.04
49 12 0.21
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.45
Consensus pattern (47 bp):
TTTATGCATTTTAAATTATGGCATCCTTTCATGCATTAATGAATAAT
Found at i:5261764 original size:95 final size:95
Alignment explanation
Indices: 5261621--5261800 Score: 236
Period size: 95 Copynumber: 1.9 Consensus size: 95
5261611 TCCTACCCTA
* * * * ** *
5261621 GTATCGATACTTCCATACTATGGTACGGATACCCTCTTCTAGTATCGATACTGAAATTAGCTTCG
1 GTATCGATACTACCATAATATAGTACCGATACCCTCTTCTAGTATCGATACCAAAATTAGATTCG
*
5261686 ATGTTGCCTGGTATCGATACCCTTACCATG
66 ATGTTGACTGGTATCGATACCCTTACCATG
* * *
5261716 GTATCGATACTACTATAATATAGTACCGATA-CCTCTTTCTGGTATCGATACCAAAATTATATTC
1 GTATCGATACTACCATAATATAGTACCGATACCCTC-TTCTAGTATCGATACCAAAATTAGATTC
*
5261780 GATGTTTACTGGTATCGATAC
65 GATGTTGACTGGTATCGATAC
5261801 TAAGTCCTCG
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
94 4 0.06
95 68 0.94
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (95 bp):
GTATCGATACTACCATAATATAGTACCGATACCCTCTTCTAGTATCGATACCAAAATTAGATTCG
ATGTTGACTGGTATCGATACCCTTACCATG
Found at i:5266905 original size:21 final size:21
Alignment explanation
Indices: 5266876--5266924 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
5266866 GCAGGAAATT
*
5266876 ATGGCCTCGATGAAAGATTTC
1 ATGGCCTCGATAAAAGATTTC
*
5266897 ATGGTCTCGATAAAAGATTTC
1 ATGGCCTCGATAAAAGATTTC
5266918 ATGGCCT
1 ATGGCCT
5266925 GCACTAAGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (21 bp):
ATGGCCTCGATAAAAGATTTC
Found at i:5274944 original size:65 final size:64
Alignment explanation
Indices: 5274824--5274961 Score: 170
Period size: 65 Copynumber: 2.1 Consensus size: 64
5274814 CCCTATTTCG
* * * *
5274824 AATGCATTTTATGTACCAATGCACAGCCATGCATCGATGCACTCTTGATTTTATTGAAACATCA
1 AATGAATTTTATATACCAATGCACAGCCATGCATCGATGCACTCCTGATTATATTGAAACATCA
** *
5274888 AATGAATTTTATATACTGATGCACAGACCATGCATCGATGCACTCCTG-TATATATTGCAACATC
1 AATGAATTTTATATACCAATGCACAG-CCATGCATCGATGCACTCCTGAT-TATATTGAAACATC
*
5274952 G
64 A
5274953 AATGCAATT
1 AATG-AATT
5274962 AGTTACCGAT
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
64 23 0.37
65 36 0.57
66 4 0.06
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Consensus pattern (64 bp):
AATGAATTTTATATACCAATGCACAGCCATGCATCGATGCACTCCTGATTATATTGAAACATCA
Found at i:5281178 original size:13 final size:13
Alignment explanation
Indices: 5281153--5281196 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
5281143 AAAATTACAT
5281153 ATTGTTATTCAAAC
1 ATTGTT-TTCAAAC
*
5281167 ATTGTTTTCAAAA
1 ATTGTTTTCAAAC
**
5281180 ATAATTTTCAAAC
1 ATTGTTTTCAAAC
5281193 ATTG
1 ATTG
5281197 CCCATTAGGA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
13 18 0.75
14 6 0.25
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (13 bp):
ATTGTTTTCAAAC
Found at i:5283231 original size:12 final size:14
Alignment explanation
Indices: 5283204--5283238 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
5283194 AGGGGGAGTA
5283204 ATTTTCAAAAATTG
1 ATTTTCAAAAATTG
5283218 A-TTTCAAAAA-TG
1 ATTTTCAAAAATTG
5283230 ATTTTCAAA
1 ATTTTCAAA
5283239 GAAAATCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 3 0.15
13 16 0.80
14 1 0.05
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.40
Consensus pattern (14 bp):
ATTTTCAAAAATTG
Found at i:5290983 original size:23 final size:24
Alignment explanation
Indices: 5290953--5290999 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
5290943 TTATCGCAAT
5290953 GGAAACA-TTTCCTTCCTTGCTAA
1 GGAAACATTTTCCTTCCTTGCTAA
5290976 GGAAACATTTTCCTTCCTTGCTAA
1 GGAAACATTTTCCTTCCTTGCTAA
5291000 CTCCCCCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.36
Consensus pattern (24 bp):
GGAAACATTTTCCTTCCTTGCTAA
Found at i:5291201 original size:77 final size:78
Alignment explanation
Indices: 5291114--5291268 Score: 303
Period size: 78 Copynumber: 2.0 Consensus size: 78
5291104 CATCATAATG
5291114 GGCTTAGGTCCAACA-TTTTCTTGTTACTTTCAGCAGTTCCTAACATGCCAAGTAACTGTGGAAA
1 GGCTTAGGTCCAACATTTTTCTTGTTACTTTCAGCAGTTCCTAACATGCCAAGTAACTGTGGAAA
5291178 AGTATTGTTATTT
66 AGTATTGTTATTT
5291191 GGCTTAGGTCCAACATTTTTCTTGTTACTTTCAGCAGTTCCTAACATGCCAAGTAACTGTGGAAA
1 GGCTTAGGTCCAACATTTTTCTTGTTACTTTCAGCAGTTCCTAACATGCCAAGTAACTGTGGAAA
5291256 AGTATTGTTATTT
66 AGTATTGTTATTT
5291269 CATTCATGTT
Statistics
Matches: 77, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
77 15 0.19
78 62 0.81
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (78 bp):
GGCTTAGGTCCAACATTTTTCTTGTTACTTTCAGCAGTTCCTAACATGCCAAGTAACTGTGGAAA
AGTATTGTTATTT
Found at i:5291773 original size:13 final size:14
Alignment explanation
Indices: 5291737--5291773 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
5291727 CCAATCAAGG
*
5291737 AAGTTTATTCCATT
1 AAGTTTATCCCATT
5291751 AAGTTTATCCCATT
1 AAGTTTATCCCATT
5291765 AAG-TTATCC
1 AAGTTTATCC
5291774 TTCTCAAGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.30, C:0.19, G:0.08, T:0.43
Consensus pattern (14 bp):
AAGTTTATCCCATT
Found at i:5295391 original size:45 final size:45
Alignment explanation
Indices: 5295323--5295421 Score: 162
Period size: 45 Copynumber: 2.2 Consensus size: 45
5295313 TAGAATGAAT
* *
5295323 CCATAAATAAAATGCATAGCGGTGCATTAAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATG
5295368 CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATG
**
5295413 TTATAAATG
1 CCATAAATG
5295422 TAATACCCCA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.22
Consensus pattern (45 bp):
CCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATG
Found at i:5298741 original size:18 final size:17
Alignment explanation
Indices: 5298718--5298751 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5298708 TTAATATAAT
*
5298718 TAGTATTAATATAATTAA
1 TAGTATGAATA-AATTAA
5298736 TAGTATGAATAAATTA
1 TAGTATGAATAAATTA
5298752 TGATATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (17 bp):
TAGTATGAATAAATTAA
Found at i:5303121 original size:156 final size:153
Alignment explanation
Indices: 5302838--5303148 Score: 595
Period size: 156 Copynumber: 2.0 Consensus size: 153
5302828 CTTTAAACCA
5302838 TTCGATCTTGGTCTTAAAGGATGAGGAAATTCTACAAAAATTATGAAAGGGTGGAAATGATGTAG
1 TTCGATCTTGGTCTTAAAGGATGAGGAAATTCTACAAAAATTATGAAAGGGTGGAAATGATGTAG
5302903 GAAGTATTCTACAAGCCTTATAAAATTTGGGAACCATTTTGTAATTTTTGAAAAGTTAAGGGACC
66 GAAGTATTCTACAAGCCTTATAAAATTTGGGAACCATTTTGTAATTTTTGAAAAGTTAAGGGACC
5302968 AATTTCATAATTTTGGAAAAGTT
131 AATTTCATAATTTTGGAAAAGTT
5302991 TTCGATCTTGGTCTTAAAGGATGAGGAAAATTCTACAAAAATTATGAAAGGGGTGGAAATGATGT
1 TTCGATCTTGGTCTTAAAGGATGAGG-AAATTCTACAAAAATTATGAAA-GGGTGGAAATGATGT
5303056 AGGAAGTATTCTACAAGCCTTATAAAAATTTGGGAACCATTTTGTAATTTTTGAAAAGTTAAGGG
64 AGGAAGTATTCTACAAGCCTTAT-AAAATTTGGGAACCATTTTGTAATTTTTGAAAAGTTAAGGG
5303121 ACCAATTTCATAATTTTGGAAAAGTT
128 ACCAATTTCATAATTTTGGAAAAGTT
5303147 TT
1 TT
5303149 GAATGATTGT
Statistics
Matches: 155, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
153 26 0.17
154 22 0.14
155 38 0.25
156 69 0.45
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.33
Consensus pattern (153 bp):
TTCGATCTTGGTCTTAAAGGATGAGGAAATTCTACAAAAATTATGAAAGGGTGGAAATGATGTAG
GAAGTATTCTACAAGCCTTATAAAATTTGGGAACCATTTTGTAATTTTTGAAAAGTTAAGGGACC
AATTTCATAATTTTGGAAAAGTT
Found at i:5310164 original size:15 final size:15
Alignment explanation
Indices: 5310144--5310175 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5310134 ATTTCCACAC
5310144 ATCTTCATTTTAGGT
1 ATCTTCATTTTAGGT
*
5310159 ATCTTCGTTTTAGGT
1 ATCTTCATTTTAGGT
5310174 AT
1 AT
5310176 TTCTTTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.12, G:0.16, T:0.53
Consensus pattern (15 bp):
ATCTTCATTTTAGGT
Found at i:5311763 original size:22 final size:22
Alignment explanation
Indices: 5311737--5311787 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
5311727 ACTGAAATGG
*
5311737 AGTATCGGTACCATAGTATAGT
1 AGTATCGGTACAATAGTATAGT
5311759 AGTATCGGTACAATAGTATAGT
1 AGTATCGGTACAATAGTATAGT
5311781 AGTATCG
1 AGTATCG
5311788 ATACTAAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (22 bp):
AGTATCGGTACAATAGTATAGT
Found at i:5312439 original size:45 final size:45
Alignment explanation
Indices: 5312308--5312451 Score: 225
Period size: 45 Copynumber: 3.2 Consensus size: 45
5312298 TAAAACGAAT
* * * *
5312308 CCATAAATAAAATGCATAACGGTGCATTAAAGGCATGAAAGAACG
1 CCATAAATGAAATGCATAACGGTACATTAAAGGCATGAAAGGATG
*
5312353 CCATAAATGAAATGCATAACAGTACATTAAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATAACGGTACATTAAAGGCATGAAAGGATG
*
5312398 CCATAAATGAAATGCATAACGGTTCATTAAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATAACGGTACATTAAAGGCATGAAAGGATG
*
5312443 TCATAAATG
1 CCATAAATG
5312452 TAATACCCAA
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 91 1.00
ACGTcount: A:0.45, C:0.14, G:0.20, T:0.21
Consensus pattern (45 bp):
CCATAAATGAAATGCATAACGGTACATTAAAGGCATGAAAGGATG
Found at i:5314941 original size:21 final size:23
Alignment explanation
Indices: 5314915--5314960 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
5314905 TGATTGTTAC
5314915 ATATGAT-GTTATCATGAAC-AT
1 ATATGATAGTTATCATGAACGAT
* *
5314936 ATATGATATTTATTATGAACGAT
1 ATATGATAGTTATCATGAACGAT
5314959 AT
1 AT
5314961 TTTGAGTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.33
22 10 0.48
23 4 0.19
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.41
Consensus pattern (23 bp):
ATATGATAGTTATCATGAACGAT
Found at i:5316083 original size:58 final size:57
Alignment explanation
Indices: 5315988--5316103 Score: 223
Period size: 58 Copynumber: 2.0 Consensus size: 57
5315978 ATTTATTGGT
5315988 ATCAGAGCTACAGGTTTACCAATTCTAGGACTAAATCGAGCTTGTGTTGAGTTTAAA
1 ATCAGAGCTACAGGTTTACCAATTCTAGGACTAAATCGAGCTTGTGTTGAGTTTAAA
5316045 ATCAGAGCTACAGGTTTACCCAATTCTAGGACTAAATCGAGCTTGTGTTGAGTTTAAA
1 ATCAGAGCTACAGGTTTA-CCAATTCTAGGACTAAATCGAGCTTGTGTTGAGTTTAAA
5316103 A
1 A
5316104 AAGTGTATAT
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
57 18 0.31
58 40 0.69
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (57 bp):
ATCAGAGCTACAGGTTTACCAATTCTAGGACTAAATCGAGCTTGTGTTGAGTTTAAA
Found at i:5328596 original size:45 final size:45
Alignment explanation
Indices: 5328545--5328686 Score: 230
Period size: 45 Copynumber: 3.2 Consensus size: 45
5328535 AAAACGAATC
* *
5328545 CATAAATAAAATGCATAATGGTGCATTAAAGGCATGAAAGGATGA
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGA
* * *
5328590 CATAAATGAAATGCATAACAGTACATTAAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGA
*
5328635 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGT
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGA
5328680 CATAAAT
1 CATAAAT
5328687 TTAATACCCC
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 89 1.00
ACGTcount: A:0.46, C:0.11, G:0.21, T:0.22
Consensus pattern (45 bp):
CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGA
Found at i:5332608 original size:24 final size:24
Alignment explanation
Indices: 5332536--5332608 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
5332526 AAGGATGCCA
**
5332536 TAAATGAAATGCATAACAGTGCAT
1 TAAATGAAATGCATAATGGTGCAT
** *
5332560 TAAA-GGCATG-A-AATGATGCCA-
1 TAAATGAAATGCATAATGGTG-CAT
5332581 TAAATGAAATGCATAATGGTGCAT
1 TAAATGAAATGCATAATGGTGCAT
5332605 TAAA
1 TAAA
5332609 GGCATGAAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
21 8 0.22
22 7 0.19
23 7 0.19
24 14 0.39
ACGTcount: A:0.45, C:0.11, G:0.19, T:0.25
Consensus pattern (24 bp):
TAAATGAAATGCATAATGGTGCAT
Found at i:5332619 original size:33 final size:33
Alignment explanation
Indices: 5332582--5332650 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
5332572 ATGATGCCAT
*
5332582 AAATGAAATGCATAA-TGGTGCATTAAAGGCATG
1 AAATGAAATGCATAACT-CTGCATTAAAGGCATG
5332615 AAATGAAATGCATAACTCTGCATTAAAGGCATG
1 AAATGAAATGCATAACTCTGCATTAAAGGCATG
5332648 AAA
1 AAA
5332651 GGATGCCATA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 33 0.97
34 1 0.03
ACGTcount: A:0.45, C:0.12, G:0.20, T:0.23
Consensus pattern (33 bp):
AAATGAAATGCATAACTCTGCATTAAAGGCATG
Found at i:5332620 original size:45 final size:45
Alignment explanation
Indices: 5332478--5332617 Score: 235
Period size: 45 Copynumber: 3.1 Consensus size: 45
5332468 TACATAACGG
* *
5332478 TGAAAGGATGCCATAAACGAAATACATAACGGTGCATTAAAGGCA
1 TGAAAGGATGCCATAAATGAAATGCATAACGGTGCATTAAAGGCA
*
5332523 TGAAAGGATGCCATAAATGAAATGCATAACAGTGCATTAAAGGCA
1 TGAAAGGATGCCATAAATGAAATGCATAACGGTGCATTAAAGGCA
* *
5332568 TGAAATGATGCCATAAATGAAATGCATAATGGTGCATTAAAGGCA
1 TGAAAGGATGCCATAAATGAAATGCATAACGGTGCATTAAAGGCA
5332613 TGAAA
1 TGAAA
5332618 TGAAATGCAT
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 89 1.00
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.21
Consensus pattern (45 bp):
TGAAAGGATGCCATAAATGAAATGCATAACGGTGCATTAAAGGCA
Found at i:5332627 original size:78 final size:78
Alignment explanation
Indices: 5332537--5332695 Score: 282
Period size: 78 Copynumber: 2.0 Consensus size: 78
5332527 AGGATGCCAT
* *
5332537 AAATGAAATGCATAACAGTGCATTAAAGGCATGAAATGATGCCATAAATGAAATGCATAATGGTG
1 AAATGAAATGCATAACACTGCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAATGGTG
*
5332602 CATTAAAGGCATG
66 CATTAAAGACATG
*
5332615 AAATGAAATGCATAACTCTGCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAATGGTG
1 AAATGAAATGCATAACACTGCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAATGGTG
5332680 CATTAAAGACATG
66 CATTAAAGACATG
5332693 AAA
1 AAA
5332696 AGATGCCTTA
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.23
Consensus pattern (78 bp):
AAATGAAATGCATAACACTGCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAATGGTG
CATTAAAGACATG
Found at i:5332664 original size:45 final size:45
Alignment explanation
Indices: 5332615--5332712 Score: 144
Period size: 45 Copynumber: 2.2 Consensus size: 45
5332605 TAAAGGCATG
* *
5332615 AAATGAAATGCATAACT-CTGCATTAAAGGCATGAAAGGATGCCAT
1 AAATGAAATGCATAA-TGCTGCATTAAAGACATGAAAAGATGCCAT
* *
5332660 AAATGAAATGCATAATGGTGCATTAAAGACATGAAAAGATGCCTT
1 AAATGAAATGCATAATGCTGCATTAAAGACATGAAAAGATGCCAT
5332705 AAATGAAA
1 AAATGAAA
5332713 ATAATAAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
44 1 0.02
45 47 0.98
ACGTcount: A:0.46, C:0.12, G:0.19, T:0.22
Consensus pattern (45 bp):
AAATGAAATGCATAATGCTGCATTAAAGACATGAAAAGATGCCAT
Found at i:5332706 original size:21 final size:21
Alignment explanation
Indices: 5332637--5332707 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
5332627 TAACTCTGCA
* *
5332637 TTAAAGGCATGAAAGGATGCC
1 TTAAAGACATGAAAAGATGCC
* * * * *
5332658 ATAAATGAAATGCATAATGGTGCA
1 TTAAA-GACATG-A-AAAGATGCC
5332682 TTAAAGACATGAAAAGATGCC
1 TTAAAGACATGAAAAGATGCC
5332703 TTAAA
1 TTAAA
5332708 TGAAAATAAT
Statistics
Matches: 36, Mismatches: 11, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
21 15 0.42
22 5 0.14
23 6 0.17
24 10 0.28
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.23
Consensus pattern (21 bp):
TTAAAGACATGAAAAGATGCC
Found at i:5332732 original size:123 final size:123
Alignment explanation
Indices: 5332496--5332732 Score: 334
Period size: 123 Copynumber: 1.9 Consensus size: 123
5332486 TGCCATAAAC
*
5332496 GAAATACATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACAGTGCATT
1 GAAATACATAACGCTGCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACAGTGCATT
* * * ** *
5332561 AAAGGCATGAAATGATGCCATAAATGAAATGCATAATGGTGCATTAAAGGCATGAAAT
66 AAAGACATGAAAAGATGCCATAAATGAAATGAATAATAATGCACTAAAGGCATGAAAT
* * **
5332619 GAAATGCATAACTCTGCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAATGGTGCATT
1 GAAATACATAACGCTGCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACAGTGCATT
*
5332684 AAAGACATGAAAAGATGCCTTAAATGAAAAT-AATAAATAATG-ACTAAAG
66 AAAGACATGAAAAGATGCCATAAATG-AAATGAAT-AATAATGCACTAAAG
5332733 AATAATGAGA
Statistics
Matches: 100, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
123 91 0.91
124 9 0.09
ACGTcount: A:0.46, C:0.12, G:0.20, T:0.22
Consensus pattern (123 bp):
GAAATACATAACGCTGCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACAGTGCATT
AAAGACATGAAAAGATGCCATAAATGAAATGAATAATAATGCACTAAAGGCATGAAAT
Found at i:5336887 original size:41 final size:41
Alignment explanation
Indices: 5336842--5337300 Score: 260
Period size: 41 Copynumber: 11.2 Consensus size: 41
5336832 TCTTGACCGT
* *
5336842 ATGCAATAGTTTATCATTCAACTTGATTCAATCATGGTAGC
1 ATGCAATAGTTCATCATTCAATTTGATTCAATCATGGTAGC
* * *** ** * * *
5336883 ATGCAATAATTCACCATTTGGTTCAATTCAATCAAGGAAAC
1 ATGCAATAGTTCATCATTCAATTTGATTCAATCATGGTAGC
** * * *
5336924 ATATAATAGTTCATCTTTCAATTTTATTCGATCATGGTAGC
1 ATGCAATAGTTCATCATTCAATTTGATTCAATCATGGTAGC
* * * *
5336965 ATGCAATAGATCATCATTCAACTTGATTCGATCATGGTAAC
1 ATGCAATAGTTCATCATTCAATTTGATTCAATCATGGTAGC
* * * * * *
5337006 ATGCAATAATTTAACATTTAATTTAATTCAATCAAGGTAGC
1 ATGCAATAGTTCATCATTCAATTTGATTCAATCATGGTAGC
** * * *
5337047 ATATAATAGTTTATCCTTCAATTTGATTCCATCATGGTAGC
1 ATGCAATAGTTCATCATTCAATTTGATTCAATCATGGTAGC
** * * * ** *
5337088 ATAAAATAATTCAACATACAATTCAATTCAATCAAGGTAGC
1 ATGCAATAGTTCATCATTCAATTTGATTCAATCATGGTAGC
** * * * ** ** *
5337129 ATATAATATTTTATCCTTTTATTTGATTTGATCATGGAAG-
1 ATGCAATAGTTCATCATTCAATTTGATTCAATCATGGTAGC
* * ** *
5337169 AGTGCAATAGATT-ATCATTCAACTTGATCCAATCATGAAACC
1 A-TGCAATAG-TTCATCATTCAATTTGATTCAATCATGGTAGC
* * * * * * *
5337211 ATGTAATA-TATCGTCACTT-GATTTAATTCAATCAAGGCATC
1 ATGCAATAGT-TCATCA-TTCAATTTGATTCAATCATGGTAGC
** * *
5337252 ATATAATAGTTAATCATTCAATTGGATTCAATCATGGTAGC
1 ATGCAATAGTTCATCATTCAATTTGATTCAATCATGGTAGC
5337293 ATGCAATA
1 ATGCAATA
5337301 ACCAATTTAT
Statistics
Matches: 301, Mismatches: 109, Indels: 16
0.71 0.26 0.04
Matches are distributed among these distances:
39 1 0.00
40 4 0.01
41 290 0.96
42 6 0.02
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (41 bp):
ATGCAATAGTTCATCATTCAATTTGATTCAATCATGGTAGC
Found at i:5337036 original size:123 final size:123
Alignment explanation
Indices: 5336842--5337089 Score: 361
Period size: 123 Copynumber: 2.0 Consensus size: 123
5336832 TCTTGACCGT
* * * * **
5336842 ATGCAATAGTTTATCATTCAACTTGATTCAATCATGGTAGCATGCAATAATTCACCATTTGGTTC
1 ATGCAATAGATCATCATTCAACTTGATTCAATCATGGTAACATGCAATAATTCAACATTTAATTC
* * *
5336907 AATTCAATCAAGGAAACATATAATAGTTCATCTTTCAATTTTATTCGATCATGGTAGC
66 AATTCAATCAAGGAAACATATAATAGTTCATCCTTCAATTTGATTCCATCATGGTAGC
* * *
5336965 ATGCAATAGATCATCATTCAACTTGATTCGATCATGGTAACATGCAATAATTTAACATTTAATTT
1 ATGCAATAGATCATCATTCAACTTGATTCAATCATGGTAACATGCAATAATTCAACATTTAATTC
* * *
5337030 AATTCAATCAAGGTAGCATATAATAGTTTATCCTTCAATTTGATTCCATCATGGTAGC
66 AATTCAATCAAGGAAACATATAATAGTTCATCCTTCAATTTGATTCCATCATGGTAGC
5337088 AT
1 AT
5337090 AAAATAATTC
Statistics
Matches: 110, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
123 110 1.00
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (123 bp):
ATGCAATAGATCATCATTCAACTTGATTCAATCATGGTAACATGCAATAATTCAACATTTAATTC
AATTCAATCAAGGAAACATATAATAGTTCATCCTTCAATTTGATTCCATCATGGTAGC
Found at i:5338724 original size:11 final size:12
Alignment explanation
Indices: 5338706--5338741 Score: 56
Period size: 11 Copynumber: 3.0 Consensus size: 12
5338696 CTCCTTACAA
5338706 TCTCTCTAAATT
1 TCTCTCTAAATT
5338718 T-TCTCTAAATT
1 TCTCTCTAAATT
5338729 TCTCTCTCAAATT
1 TCTCTCT-AAATT
5338742 CGGCTTTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.50
12 6 0.27
13 5 0.23
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (12 bp):
TCTCTCTAAATT
Found at i:5339053 original size:68 final size:70
Alignment explanation
Indices: 5338962--5339091 Score: 174
Period size: 68 Copynumber: 1.9 Consensus size: 70
5338952 CTATTAAGTT
* * ** * * *
5338962 CTTATCTAATTCAATTAGTTTAAATTTTAATTCAACTTGGTT-TT-TATCTTAGGCAATTTAATT
1 CTTATCTAACTCAAATAAATTAAATCTCAATTCAACTTGGTTATTATATCCTAGGCAATTTAATT
5339025 TGGTC
66 TGGTC
*
5339030 CTTATCTAACTCAAATAAATTAAATCTCAATTCAATTTGGTTATTATATCCTAGGCAATTTA
1 CTTATCTAACTCAAATAAATTAAATCTCAATTCAACTTGGTTATTATATCCTAGGCAATTTA
5339092 CTTGAATTTT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
68 35 0.67
69 2 0.04
70 15 0.29
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.45
Consensus pattern (70 bp):
CTTATCTAACTCAAATAAATTAAATCTCAATTCAACTTGGTTATTATATCCTAGGCAATTTAATT
TGGTC
Found at i:5357661 original size:21 final size:20
Alignment explanation
Indices: 5357637--5357676 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
5357627 GTATCAAGGT
5357637 TTTTGTTGAAGCCATGAAATC
1 TTTTGTTGAAGCCAT-AAATC
*
5357658 TTTTGTTGAGGCCATAAAT
1 TTTTGTTGAAGCCATAAAT
5357677 TCCTATAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (20 bp):
TTTTGTTGAAGCCATAAATC
Found at i:5359305 original size:41 final size:41
Alignment explanation
Indices: 5359260--5359397 Score: 183
Period size: 41 Copynumber: 3.4 Consensus size: 41
5359250 CAAGATTTCA
* * * *
5359260 ATTCAA-TTGAGTTCGATCTTGGAATCATGTAATAGTTCATC
1 ATTCAACTTGA-TTCGATCATGGTAGCATGAAATAGTTCATC
*
5359301 ATTCAACTTGATTCGATCATGGTAGCAT-ACAATAGATCATC
1 ATTCAACTTGATTCGATCATGGTAGCATGA-AATAGTTCATC
5359342 ATTCAACTTGATTCGATCATGGTAGCATGAAATAGATT-ATC
1 ATTCAACTTGATTCGATCATGGTAGCATGAAATAG-TTCATC
5359383 ATTCAACTTGATTCG
1 ATTCAACTTGATTCG
5359398 TGTAACACCC
Statistics
Matches: 87, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
41 81 0.93
42 6 0.07
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.36
Consensus pattern (41 bp):
ATTCAACTTGATTCGATCATGGTAGCATGAAATAGTTCATC
Found at i:5365028 original size:45 final size:45
Alignment explanation
Indices: 5364886--5365262 Score: 611
Period size: 45 Copynumber: 8.4 Consensus size: 45
5364876 AATAAAATTT
* *
5364886 CTTACCATTTATCCCATAAGCTCGTAAGCTTA-TTTTACCATTATA
1 CTTACCATTTAT-CCATAAGCTCGTAAGCTTATTTTTACCAATACA
*
5364931 TTTACCATTTATCCATAAGCTCGTAAGCTTA-TTTTACCAATACA
1 CTTACCATTTATCCATAAGCTCGTAAGCTTATTTTTACCAATACA
*
5364975 CTTACCATTTATCCATAAGCTTGTAAGCTTATTTTTACCAATACA
1 CTTACCATTTATCCATAAGCTCGTAAGCTTATTTTTACCAATACA
*
5365020 CTTGCCA-TTATTCCATAAGCTCGTAAGCTTATTTTTACCAATACA
1 CTTACCATTTA-TCCATAAGCTCGTAAGCTTATTTTTACCAATACA
* *
5365065 CTTGCCA-TTATTCCATAAGCTTGTAAGCTTATTTTTACCAATACA
1 CTTACCATTTA-TCCATAAGCTCGTAAGCTTATTTTTACCAATACA
5365110 CTTACCATTTATCCATAAGCTCGTAAGCTTATTTTTACCAATACA
1 CTTACCATTTATCCATAAGCTCGTAAGCTTATTTTTACCAATACA
5365155 CTTACCATTTATCCATAAGCTCGTAAGCTTATTTTTACCAATACA
1 CTTACCATTTATCCATAAGCTCGTAAGCTTATTTTTACCAATACA
5365200 CTTACCATTTATCCATAAGCTCGTAAGCTTATTTTTACCAATACA
1 CTTACCATTTATCCATAAGCTCGTAAGCTTATTTTTACCAATACA
*
5365245 CTTGCCA-TTATTCCATAA
1 CTTACCATTTA-TCCATAA
5365263 CCATATATCA
Statistics
Matches: 317, Mismatches: 11, Indels: 8
0.94 0.03 0.02
Matches are distributed among these distances:
44 65 0.21
45 249 0.79
46 3 0.01
ACGTcount: A:0.30, C:0.24, G:0.07, T:0.39
Consensus pattern (45 bp):
CTTACCATTTATCCATAAGCTCGTAAGCTTATTTTTACCAATACA
Found at i:5367487 original size:15 final size:15
Alignment explanation
Indices: 5367467--5367504 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
5367457 TAACTCTGTT
5367467 GGAGCC-TTTCAATAG
1 GGAGCCATTT-AATAG
5367482 GGAGCCATTTAATAG
1 GGAGCCATTTAATAG
5367497 GGAGCCAT
1 GGAGCCAT
5367505 AGATACAGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 19 0.86
16 3 0.14
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (15 bp):
GGAGCCATTTAATAG
Found at i:5371187 original size:41 final size:41
Alignment explanation
Indices: 5371142--5371507 Score: 159
Period size: 41 Copynumber: 9.0 Consensus size: 41
5371132 ATATAATAAT
**
5371142 TCATCATTCAATTTGATTTGATCATGGTAGAATGCAATAGA
1 TCATCATTCAATTTGATTCAATCATGGTAGAATGCAATAGA
* *
5371183 TCATCATTCAACTTGATTCAATCATGGTA-ACATGAAATA-A
1 TCATCATTCAATTTGATTCAATCATGGTAGA-ATGCAATAGA
* * ** * * ** ** *
5371223 TTCAACATTCGATTCAATACAATCAAGGTAGTGTATAATAGT
1 -TCATCATTCAATTTGATTCAATCATGGTAGAATGCAATAGA
* * * * *
5371265 TTATCCTTCAATTTGATTCGATCATGGTAGCACGCAATA-A
1 TCATCATTCAATTTGATTCAATCATGGTAGAATGCAATAGA
* ** * * * *
5371305 TTCAAT-ATTCGATTAAATTCAAACAAGGTATATAT--AATAGT
1 -TC-ATCATTCAATTTGATTCAATCATGGTAGA-ATGCAATAGA
* * * ** * *
5371346 TTATCCTTCTATTTGATTTGATCATGGTAGCATACAATAGA
1 TCATCATTCAATTTGATTCAATCATGGTAGAATGCAATAGA
* * * * *
5371387 TTATCATTCAACTTGATTCAATCATGATAGCATGCAATAAA
1 TCATCATTCAATTTGATTCAATCATGGTAGAATGCAATAGA
* ** * * * ** ** *
5371428 TCATCATTCGATTCAATTTAATCAAGGCATCATATAATAGT
1 TCATCATTCAATTTGATTCAATCATGGTAGAATGCAATAGA
* * * *
5371469 TCACCATCCAATTGGATTCAATCATGGTAGCATGCAATA
1 TCATCATTCAATTTGATTCAATCATGGTAGAATGCAATA
5371508 CCAATTGGTC
Statistics
Matches: 226, Mismatches: 88, Indels: 22
0.67 0.26 0.07
Matches are distributed among these distances:
39 4 0.02
40 23 0.10
41 196 0.87
42 3 0.01
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (41 bp):
TCATCATTCAATTTGATTCAATCATGGTAGAATGCAATAGA
Found at i:5371222 original size:82 final size:82
Alignment explanation
Indices: 5371079--5371232 Score: 188
Period size: 82 Copynumber: 1.9 Consensus size: 82
5371069 ATTACAATTC
* * * *
5371079 GATCATGGTAGCATGCAATAATTCACTATTCAATTTTATTCAATCAAGACATCATATAATAATTC
1 GATCATGGTAGAATGCAATAATTCACTATTCAACTTGATTCAATCAAGACAACATATAATAATTC
*
5371144 ATCATTCAATTTGATTT
66 AACATTCAATTTGATTT
* **
5371161 GATCATGGTAGAATGCAATAGA-TCA-TCATTCAACTTGATTCAATCATGGTAACATGA-AATAA
1 GATCATGGTAGAATGCAATA-ATTCACT-ATTCAACTTGATTCAATCAAGACAACAT-ATAATAA
5371223 TTCAACATTC
63 TTCAACATTC
5371233 GATTCAATAC
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
81 1 0.02
82 58 0.95
83 2 0.03
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (82 bp):
GATCATGGTAGAATGCAATAATTCACTATTCAACTTGATTCAATCAAGACAACATATAATAATTC
AACATTCAATTTGATTT
Found at i:5371253 original size:82 final size:82
Alignment explanation
Indices: 5371162--5371334 Score: 193
Period size: 82 Copynumber: 2.1 Consensus size: 82
5371152 ATTTGATTTG
* * *
5371162 ATCATGGTAGAATGCAATAGATCATCATTCAACTTGATTCAATCATGGTAACATGAAATAATTCA
1 ATCAAGGTAGAATACAATAGATCATCATTCAACTTGATTCAATCATGGTAACACGAAATAATTCA
*
5371227 ACATTCGATTCAATACA
66 ACATTCGATTAAATACA
** * * * * * * * *
5371244 ATCAAGGTAGTGTATAATAGTTTATCCTTCAATTTGATTCGATCATGGTAGCACGCAATAATTCA
1 ATCAAGGTAGAATACAATAGATCATCATTCAACTTGATTCAATCATGGTAACACGAAATAATTCA
* *
5371309 ATATTCGATTAAATTCA
66 ACATTCGATTAAATACA
*
5371326 AACAAGGTA
1 ATCAAGGTA
5371335 TATATAATAG
Statistics
Matches: 74, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
82 74 1.00
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (82 bp):
ATCAAGGTAGAATACAATAGATCATCATTCAACTTGATTCAATCATGGTAACACGAAATAATTCA
ACATTCGATTAAATACA
Done.