Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009634.1 Hibiscus syriacus cultivar Beakdansim tig00117034_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: 17174986
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 28 of 78
Found at i:5784632 original size:55 final size:55
Alignment explanation
Indices: 5784558--5784664 Score: 169
Period size: 55 Copynumber: 1.9 Consensus size: 55
5784548 CGTGGATCAG
*
5784558 TCTTCAATCAGTTTCAAATTTCTTCATTCATCAGATGTCCTTCGTCATGAATTGT
1 TCTTCAATCAGGTTCAAATTTCTTCATTCATCAGATGTCCTTCGTCATGAATTGT
* * * *
5784613 TCTTCAGTCAGGTTGAAATTTCTTCATTCATCGGATGTCCTTCTTCATGAAT
1 TCTTCAATCAGGTTCAAATTTCTTCATTCATCAGATGTCCTTCGTCATGAAT
5784665 CATCTGAACG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 47 1.00
ACGTcount: A:0.22, C:0.21, G:0.13, T:0.43
Consensus pattern (55 bp):
TCTTCAATCAGGTTCAAATTTCTTCATTCATCAGATGTCCTTCGTCATGAATTGT
Found at i:5788962 original size:30 final size:30
Alignment explanation
Indices: 5788900--5788965 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
5788890 AGAACCGGAA
* * *
5788900 GAACCGGCTGAGAACCGGCAAAACCGGGGT
1 GAACCGGCTGAAAACCGACAAAACCGAGGT
* * *
5788930 GAACTGGCTGAAAACCGACAAAACTGATGT
1 GAACCGGCTGAAAACCGACAAAACCGAGGT
5788960 GAACCG
1 GAACCG
5788966 CCGGTTCTCT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.35, C:0.24, G:0.30, T:0.11
Consensus pattern (30 bp):
GAACCGGCTGAAAACCGACAAAACCGAGGT
Found at i:5790274 original size:39 final size:39
Alignment explanation
Indices: 5790215--5790411 Score: 238
Period size: 39 Copynumber: 5.1 Consensus size: 39
5790205 TTTATATTAG
* * *
5790215 ATTAA-TTCTCAAATTATTTCACCCTTACATTTTAAATT
1 ATTAATTTCTTAAATTATTTCACCATAACATTTTAAATT
* **
5790253 -TTAAATTTCTTAAATTGTTTCACCATAAGGTTTTAAATT
1 ATT-AATTTCTTAAATTATTTCACCATAACATTTTAAATT
* *
5790292 ATTAATTTCTTAAATTAATTTTACCATAATATTTT-AATT
1 ATTAATTTCTTAAATT-ATTTCACCATAACATTTTAAATT
* *
5790331 ATTAATTTCTTAAATTATTTCACCATAACATGTTAAAGT
1 ATTAATTTCTTAAATTATTTCACCATAACATTTTAAATT
* * *
5790370 ATTAATTTCTTAAATTATTTTACCATAACAATCTAAATT
1 ATTAATTTCTTAAATTATTTCACCATAACATTTTAAATT
5790409 ATT
1 ATT
5790412 TCTCAAATTA
Statistics
Matches: 135, Mismatches: 19, Indels: 9
0.83 0.12 0.06
Matches are distributed among these distances:
37 2 0.01
38 17 0.13
39 100 0.74
40 16 0.12
ACGTcount: A:0.37, C:0.12, G:0.03, T:0.48
Consensus pattern (39 bp):
ATTAATTTCTTAAATTATTTCACCATAACATTTTAAATT
Found at i:5791854 original size:2 final size:2
Alignment explanation
Indices: 5791847--5791925 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
5791837 TCAACCATGT
5791847 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5791889 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5791926 CATTTGAAGA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5793349 original size:2 final size:2
Alignment explanation
Indices: 5793342--5793369 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5793332 CAAAAATGAA
5793342 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5793370 TAAATAGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5794886 original size:22 final size:25
Alignment explanation
Indices: 5794861--5794906 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 25
5794851 AATAAATAAA
5794861 ATATAATTT-TAT-ATT-AATATTC
1 ATATAATTTATATAATTAAATATTC
5794883 ATATAATTTATATAATTAAATATT
1 ATATAATTTATATAATTAAATATT
5794907 AAAATATCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.43
23 3 0.14
24 3 0.14
25 6 0.29
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
ATATAATTTATATAATTAAATATTC
Found at i:5795048 original size:11 final size:11
Alignment explanation
Indices: 5795030--5795081 Score: 68
Period size: 11 Copynumber: 4.7 Consensus size: 11
5795020 TTGATTACAA
5795030 TATAATTATAT
1 TATAATTATAT
*
5795041 TATTATTATAT
1 TATAATTATAT
**
5795052 TATAATTACGT
1 TATAATTATAT
*
5795063 TATTATTATAT
1 TATAATTATAT
5795074 TATAATTA
1 TATAATTA
5795082 ATTGTTATAG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 33 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (11 bp):
TATAATTATAT
Found at i:5795048 original size:22 final size:21
Alignment explanation
Indices: 5795030--5795089 Score: 84
Period size: 22 Copynumber: 2.8 Consensus size: 21
5795020 TTGATTACAA
5795030 TATAATTATATTATTATTATAT
1 TATAATTA-ATTATTATTATAT
*
5795052 TATAATTACGTTATTATTATAT
1 TATAATTA-ATTATTATTATAT
*
5795074 TATAATTAATTGTTAT
1 TATAATTAATTATTAT
5795090 AGTTTTACAC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 6 0.18
22 28 0.82
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (21 bp):
TATAATTAATTATTATTATAT
Found at i:5796181 original size:15 final size:14
Alignment explanation
Indices: 5796144--5796187 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
5796134 TTTTATACAT
*
5796144 TTTAATTTTGTCT-
1 TTTAATTTTGTTTA
5796157 TTTAATTTTGTTTA
1 TTTAATTTTGTTTA
*
5796171 TTTATATTTTGGTTA
1 TTTA-ATTTTGTTTA
5796186 TT
1 TT
5796188 ACCACGTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
13 12 0.44
14 4 0.15
15 11 0.41
ACGTcount: A:0.18, C:0.02, G:0.09, T:0.70
Consensus pattern (14 bp):
TTTAATTTTGTTTA
Found at i:5806771 original size:72 final size:72
Alignment explanation
Indices: 5806651--5806819 Score: 293
Period size: 72 Copynumber: 2.3 Consensus size: 72
5806641 TACAAATTCA
* * * *
5806651 GCCTTCACAAAAGAGTAGTGAAGCAATGCACATTAAACCTTCATGGAAGAGTAGTGGAGTGATGC
1 GCCTTCACAAAAGAGTAGTGAAGCAATGCACATTAAACATTCACGGAAGAGTACTGAAGTGATGC
5806716 ACATCTG
66 ACATCTG
5806723 GCCTTCACAAAAGAGTAGTGAAGCAATGCACATTAAACATTCACGGAAGAGTACTGAAGTGATGC
1 GCCTTCACAAAAGAGTAGTGAAGCAATGCACATTAAACATTCACGGAAGAGTACTGAAGTGATGC
5806788 ACATCTG
66 ACATCTG
*
5806795 GCCTTCAAAAAAGAGTAGTGAAGCA
1 GCCTTCACAAAAGAGTAGTGAAGCA
5806820 GGAACATATA
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 92 1.00
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.21
Consensus pattern (72 bp):
GCCTTCACAAAAGAGTAGTGAAGCAATGCACATTAAACATTCACGGAAGAGTACTGAAGTGATGC
ACATCTG
Found at i:5806809 original size:36 final size:36
Alignment explanation
Indices: 5806651--5806817 Score: 149
Period size: 36 Copynumber: 4.6 Consensus size: 36
5806641 TACAAATTCA
** *
5806651 GCCTTCACAAAAGAGTAGTGAAGCAATGCACAT-TAA
1 GCCTTCACAAAAGAGTAGTGAAGTGATGCACATCT-G
* *** *
5806687 ACCTTCATGGAAGAGTAGTGGAGTGATGCACATCTG
1 GCCTTCACAAAAGAGTAGTGAAGTGATGCACATCTG
** *
5806723 GCCTTCACAAAAGAGTAGTGAAGCAATGCACAT-TAA
1 GCCTTCACAAAAGAGTAGTGAAGTGATGCACATCT-G
* * ** *
5806759 ACATTCACGGAAGAGTACTGAAGTGATGCACATCTG
1 GCCTTCACAAAAGAGTAGTGAAGTGATGCACATCTG
*
5806795 GCCTTCAAAAAAGAGTAGTGAAG
1 GCCTTCACAAAAGAGTAGTGAAG
5806818 CAGGAACATA
Statistics
Matches: 98, Mismatches: 30, Indels: 6
0.73 0.22 0.04
Matches are distributed among these distances:
35 1 0.01
36 95 0.97
37 2 0.02
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.21
Consensus pattern (36 bp):
GCCTTCACAAAAGAGTAGTGAAGTGATGCACATCTG
Found at i:5807018 original size:11 final size:11
Alignment explanation
Indices: 5807001--5807046 Score: 60
Period size: 11 Copynumber: 4.4 Consensus size: 11
5806991 TTTCAATATA
5807001 ATTATATTATT
1 ATTATATTATT
*
5807012 GTTATATTATT
1 ATTATATTATT
5807023 A-T-TATTATT
1 ATTATATTATT
*
5807032 ATTATATTATA
1 ATTATATTATT
5807043 ATTA
1 ATTA
5807047 ATTGTTACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 8 0.27
10 2 0.07
11 20 0.67
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (11 bp):
ATTATATTATT
Found at i:5807022 original size:3 final size:3
Alignment explanation
Indices: 5807001--5807046 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
5806991 TTTCAATATA
* *
5807001 ATT A-T ATT ATT GTT A-T ATT ATT ATT ATT ATT ATT A-T ATT ATA ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5807046 A
1 A
5807047 ATTGTTACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
2 6 0.17
3 30 0.83
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:5808132 original size:15 final size:13
Alignment explanation
Indices: 5808094--5808132 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
5808084 GTTTTATACA
5808094 TTTTAATTTTGTC
1 TTTTAATTTTGTC
*
5808107 TTTTAATTTTGTG
1 TTTTAATTTTGTC
5808120 TATTTATATTTTG
1 T-TTTA-ATTTTG
5808133 GTCACTGCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 13 0.57
14 4 0.17
15 6 0.26
ACGTcount: A:0.18, C:0.03, G:0.10, T:0.69
Consensus pattern (13 bp):
TTTTAATTTTGTC
Found at i:5813008 original size:26 final size:26
Alignment explanation
Indices: 5812977--5813041 Score: 112
Period size: 26 Copynumber: 2.5 Consensus size: 26
5812967 GACTTATAAA
*
5812977 CAAAGTTGATCGATGAGAGAAAAGCT
1 CAAAGTTGATCGATGAAAGAAAAGCT
*
5813003 CAAAGTTGATCGATGAAAGAAGAGCT
1 CAAAGTTGATCGATGAAAGAAAAGCT
5813029 CAAAGTTGATCGA
1 CAAAGTTGATCGA
5813042 AGATTCCTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.42, C:0.12, G:0.26, T:0.20
Consensus pattern (26 bp):
CAAAGTTGATCGATGAAAGAAAAGCT
Found at i:5815208 original size:22 final size:21
Alignment explanation
Indices: 5815182--5815222 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5815172 GCACATTTTG
*
5815182 CATTTCTATTTATGTATTTTCA
1 CATTTC-ATATATGTATTTTCA
*
5815204 CATTTCATATGTGTATTTT
1 CATTTCATATATGTATTTT
5815223 TTATCGTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.22, C:0.12, G:0.07, T:0.59
Consensus pattern (21 bp):
CATTTCATATATGTATTTTCA
Found at i:5816745 original size:21 final size:18
Alignment explanation
Indices: 5816701--5816892 Score: 74
Period size: 21 Copynumber: 9.8 Consensus size: 18
5816691 CAATAAAGGC
5816701 AAAACAAAAAAGAAAAAACT-
1 AAAA-AAAAAAG-AAAAA-TG
*
5816721 AAAAAAAGAGAGAAAATATAG
1 AAAAAAA-AAAGAAAA-AT-G
5816742 AAAAAGAAAAAGAAAAATG
1 AAAAA-AAAAAGAAAAATG
* *
5816761 -AAAAAATAA-TAAAA-G
1 AAAAAAAAAAGAAAAATG
*
5816776 AAAGAGAGAAAAGAAAAA-G
1 AAA-A-AAAAAAGAAAAATG
* *
5816795 -AAAAAAAGAGAAAAAGG
1 AAAAAAAAAAGAAAAATG
5816812 AAAAGAGAAAAGAGAAAAGATAG
1 AAAA-A-AAAA-AGAAAA-AT-G
*
5816835 AAAAATAAGAAAAAAAAGATG
1 AAAAA-AA-AAAGAAAA-ATG
5816856 AAAAGAAAAAGAGGAAAAA-G
1 AAAA-AAAAA-A-GAAAAATG
5816876 AAAAAAGAGAAAGAAAA
1 AAAAAA-A-AAAGAAAA
5816893 TAAATCAAGT
Statistics
Matches: 136, Mismatches: 14, Indels: 45
0.70 0.07 0.23
Matches are distributed among these distances:
15 1 0.01
16 16 0.12
17 7 0.05
18 13 0.10
19 22 0.16
20 22 0.16
21 29 0.21
22 19 0.14
23 7 0.05
ACGTcount: A:0.76, C:0.01, G:0.18, T:0.05
Consensus pattern (18 bp):
AAAAAAAAAAGAAAAATG
Found at i:5816763 original size:28 final size:28
Alignment explanation
Indices: 5816743--5816881 Score: 92
Period size: 28 Copynumber: 4.9 Consensus size: 28
5816733 AAAATATAGA
5816743 AAAAGAAAAAGA-AAAATGAAAAAATAAT
1 AAAAGAAAAAGAGAAAA-GAAAAAATAAT
* *
5816771 AAAAGAAAGAGAGAAAAGAAAAAGA-AAA
1 AAAAGAAAAAGAGAAAAGAAAAA-ATAAT
* * *
5816799 AAAGAGAAAAAG-GAAAAGAGAAAA-GAG
1 AAA-AGAAAAAGAGAAAAGAAAAAATAAT
* *
5816826 AAAAGATAGAAA-A-ATAAGAAAAAAAAGAT
1 AAAAGA-A-AAAGAGAAAAGAAAAAATA-AT
5816855 GAAAAGAAAAAGAGGAAAAAGAAAAAA
1 -AAAAGAAAAAGA-G-AAAAGAAAAAA
5816882 GAGAAAGAAA
Statistics
Matches: 87, Mismatches: 11, Indels: 22
0.73 0.09 0.18
Matches are distributed among these distances:
26 3 0.03
27 15 0.17
28 38 0.44
29 15 0.17
30 6 0.07
32 10 0.11
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.04
Consensus pattern (28 bp):
AAAAGAAAAAGAGAAAAGAAAAAATAAT
Found at i:5816766 original size:41 final size:41
Alignment explanation
Indices: 5816707--5816880 Score: 101
Period size: 41 Copynumber: 4.1 Consensus size: 41
5816697 AGGCAAAACA
* *
5816707 AAAAAGAAAAAACTAAAAAA-AGAGAGAAA-ATATAGA-AAAAG
1 AAAAAGAAAAAAC-AAAAAATA-AGA-AAAGAAAGAGAGAAAAG
** *
5816748 AAAAAGAAAAATGAAAAAATAATAAAAGAAAGAGAGAAAAG
1 AAAAAGAAAAAACAAAAAATAAGAAAAGAAAGAGAGAAAAG
* *
5816789 AAAAAGAAAAAA-AGAGAAAA-AGGAAAAGAGAAAAGAGAAAAG
1 AAAAAGAAAAAACA-A-AAAATAAGAAAAGA-AAGAGAGAAAAG
* * *
5816831 ATAGAAA-AATAAGAA-AAAAAAGATGAAAAGAAAAAGAGGAAAAAG
1 A-A-AAAGAA-AA-AACAAAAAATAAGAAAAGAAAGAGA-G-AAAAG
5816876 AAAAA
1 AAAAA
5816881 AGAGAAAGAA
Statistics
Matches: 110, Mismatches: 10, Indels: 24
0.76 0.07 0.17
Matches are distributed among these distances:
39 3 0.03
40 14 0.13
41 36 0.33
42 16 0.15
43 16 0.15
44 16 0.15
45 9 0.08
ACGTcount: A:0.76, C:0.01, G:0.18, T:0.05
Consensus pattern (41 bp):
AAAAAGAAAAAACAAAAAATAAGAAAAGAAAGAGAGAAAAG
Found at i:5816776 original size:47 final size:47
Alignment explanation
Indices: 5816701--5816799 Score: 121
Period size: 47 Copynumber: 2.1 Consensus size: 47
5816691 CAATAAAGGC
5816701 AAAACAAAAAAGAAAAAACTAAAAAAAG-AGAGAAAATATAGAAAAAGA
1 AAAACAAAAAAGAAAAAACTAAAAAAAGAAGAGAAAA-A-AGAAAAAGA
* * * *
5816749 AAAAGAAAAATGAAAAAA-TAATAAAAGAAAGAGAGAAAAGAAAAAGA
1 AAAACAAAAAAGAAAAAACTAAAAAAAG-AAGAGAAAAAAGAAAAAGA
5816796 AAAA
1 AAAA
5816800 AAGAGAAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
47 21 0.47
48 17 0.38
49 7 0.16
ACGTcount: A:0.78, C:0.02, G:0.14, T:0.06
Consensus pattern (47 bp):
AAAACAAAAAAGAAAAAACTAAAAAAAGAAGAGAAAAAAGAAAAAGA
Found at i:5816786 original size:23 final size:23
Alignment explanation
Indices: 5816771--5816892 Score: 92
Period size: 22 Copynumber: 5.2 Consensus size: 23
5816761 AAAAAATAAT
5816771 AAAAGAAAGAGAGAAAAGAAAAAG
1 AAAA-AAAGAGAGAAAAGAAAAAG
5816795 AAAAAAAGAGA-AAAAGGAAAAGAG
1 AAAAAAAGAGAGAAAA-GAAAA-AG
* * *
5816819 AAAAGAGAAAAGATAGAAA-AATAAG
1 AAAA-A-AAGAGAGA-AAAGAAAAAG
5816844 AAAAAAA-AGATGAAAAGAAAAAG
1 AAAAAAAGAGA-GAAAAGAAAAAG
* *
5816867 AGGAAAAAGA-A-AAAAGAGAAAG
1 A-AAAAAAGAGAGAAAAGAAAAAG
5816889 AAAA
1 AAAA
5816893 TAAATCAAGT
Statistics
Matches: 81, Mismatches: 7, Indels: 23
0.73 0.06 0.21
Matches are distributed among these distances:
21 2 0.02
22 21 0.26
23 21 0.26
24 17 0.21
25 8 0.10
26 8 0.10
27 1 0.01
28 3 0.04
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.02
Consensus pattern (23 bp):
AAAAAAAGAGAGAAAAGAAAAAG
Found at i:5816790 original size:35 final size:33
Alignment explanation
Indices: 5816743--5816887 Score: 125
Period size: 35 Copynumber: 4.1 Consensus size: 33
5816733 AAAATATAGA
*
5816743 AAAAGA-AAAAGAAAAATGAAAAAATAATAAAAG
1 AAAAGAGAAAAGAAAAA-GAAAAAATAAAAAAAG
5816776 AAAGAGAGAAAAGAAAAAGAAAAAA-AGAGAAAAAGG
1 AAA-AGAGAAAAGAAAAAGAAAAAATA-A-AAAAA-G
*
5816812 AAAAGAGAAAAGAGAAAAGATAGAAAAATAAGAAAA-
1 AAAAGAGAAAAGA-AAAAG--A-AAAAATAAAAAAAG
*
5816848 AAAAGATGAAAAGAAAAAGAGGAAAAAGAAAAAAGAG
1 AAAAGA-GAAAAGAAAAAGA--AAAAATAAAAAA-AG
5816885 AAA
1 AAA
5816888 GAAAATAAAT
Statistics
Matches: 94, Mismatches: 4, Indels: 24
0.77 0.03 0.20
Matches are distributed among these distances:
33 4 0.04
34 12 0.13
35 35 0.37
36 21 0.22
37 10 0.11
38 5 0.05
39 6 0.06
40 1 0.01
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (33 bp):
AAAAGAGAAAAGAAAAAGAAAAAATAAAAAAAG
Found at i:5816807 original size:51 final size:50
Alignment explanation
Indices: 5816720--5816851 Score: 128
Period size: 51 Copynumber: 2.6 Consensus size: 50
5816710 AAGAAAAAAC
* * *
5816720 TAAAAAAAGAGAGAAAATATAGAAAAAGAAAAAGAAAAATGAAAAAATAA
1 TAAAAAAAGAGAGAAAAGATAGAAAAAAAAAAAGAAAAAGGAAAAAATAA
* *
5816770 TAAAAGAAAGAGAGAAAAGA-A-AAAGAAAAAAAGAGAAAAAGGAAAAGAGAA
1 TAAAA-AAAGAGAGAAAAGATAGAAA-AAAAAAA-AGAAAAAGGAAAAAATAA
*
5816821 -AAGAGAAAAGATAGAAAA-ATAAGAAAAAAAA
1 TAA-A-AAAAGAGAGAAAAGAT-AGAAAAAAAA
5816852 GATGAAAAGA
Statistics
Matches: 68, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
49 3 0.04
50 15 0.22
51 40 0.59
52 7 0.10
53 3 0.04
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (50 bp):
TAAAAAAAGAGAGAAAAGATAGAAAAAAAAAAAGAAAAAGGAAAAAATAA
Found at i:5816830 original size:14 final size:14
Alignment explanation
Indices: 5816740--5816887 Score: 78
Period size: 14 Copynumber: 10.4 Consensus size: 14
5816730 GAGAAAATAT
5816740 AGAAAA-AGAAAA-
1 AGAAAAGAGAAAAG
*
5816752 AGAAAA-ATGAAAAA
1 AGAAAAGA-GAAAAG
* *
5816766 ATAATAAAAGAAAGAG
1 AGAA-AAGAGAAA-AG
5816782 AGAAAAGA-AAAAG
1 AGAAAAGAGAAAAG
*
5816795 AAAAAAAGAGAAAA-
1 -AGAAAAGAGAAAAG
5816809 AGGAAAAGAGAAAAG
1 A-GAAAAGAGAAAAG
5816824 AGAAAAGATAGAAAA-
1 AGAAAAG--AGAAAAG
* *
5816839 ATAAGAA-AAAAAAG
1 AGAA-AAGAGAAAAG
5816853 ATGAAAAGA-AAAAG
1 A-GAAAAGAGAAAAG
*
5816867 AGGAAAAAGAAAAAAG
1 A-G-AAAAGAGAAAAG
5816883 AGAAA
1 AGAAA
5816888 GAAAATAAAT
Statistics
Matches: 109, Mismatches: 10, Indels: 32
0.72 0.07 0.21
Matches are distributed among these distances:
12 7 0.06
13 13 0.12
14 43 0.39
15 27 0.25
16 19 0.17
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (14 bp):
AGAAAAGAGAAAAG
Found at i:5816859 original size:72 final size:70
Alignment explanation
Indices: 5816722--5816892 Score: 190
Period size: 72 Copynumber: 2.4 Consensus size: 70
5816712 GAAAAAACTA
* *
5816722 AAAAAAGAGAGAAAATATAGAAAAAGAAAAAGAAAAATGAAAAAATAATAAAAGAAAGAGAGAAA
1 AAAAAA-AGAGAAAA-A-GGAAAAAGAAAAAGAAAAATGAAAAAATAAGAAAAGAAAGAGAGAAA
5816787 AGAAAAAG
63 AGAAAAAG
5816795 AAAAAAAGAGAAAAAGGAAAAGAGAAAAGAGAAAAGAT-AGAAAAATAAGAAAA-AAA-AGATGA
1 AAAAAAAGAGAAAAAGGAAAA-AGAAAA-AGAAAA-ATGA-AAAAATAAGAAAAGAAAGAGA-GA
5816857 AAAGAAAAAG
61 AAAGAAAAAG
* *
5816867 AGGAAAAAGA-AAAAA-GAGAAAGAAAA
1 A-AAAAAAGAGAAAAAGGAAAAAGAAAA
5816893 TAAATCAAGT
Statistics
Matches: 88, Mismatches: 4, Indels: 15
0.82 0.04 0.14
Matches are distributed among these distances:
70 11 0.12
71 14 0.16
72 36 0.41
73 27 0.31
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.05
Consensus pattern (70 bp):
AAAAAAAGAGAAAAAGGAAAAAGAAAAAGAAAAATGAAAAAATAAGAAAAGAAAGAGAGAAAAGA
AAAAG
Found at i:5816886 original size:9 final size:9
Alignment explanation
Indices: 5816789--5816887 Score: 51
Period size: 9 Copynumber: 12.2 Consensus size: 9
5816779 GAGAGAAAAG
5816789 AAAAAGA-A
1 AAAAAGAGA
5816797 AAAAAGAG-
1 AAAAAGAGA
5816805 AAAAAG-G-
1 AAAAAGAGA
5816812 -AAAAGAG-
1 AAAAAGAGA
5816819 -AAAAGAGA
1 AAAAAGAGA
* *
5816827 AAAGATAGA
1 AAAAAGAGA
5816836 AAAATA-AGA
1 AAAA-AGAGA
*
5816845 AAAAAAAGA
1 AAAAAGAGA
**
5816854 TGAAA-AG-
1 AAAAAGAGA
5816861 AAAAAGAG-
1 AAAAAGAGA
*
5816869 GAAAA-AGA
1 AAAAAGAGA
5816877 AAAAAGAGA
1 AAAAAGAGA
5816886 AA
1 AA
5816888 GAAAATAAAT
Statistics
Matches: 73, Mismatches: 9, Indels: 17
0.74 0.09 0.17
Matches are distributed among these distances:
6 5 0.07
7 14 0.19
8 26 0.36
9 27 0.37
10 1 0.01
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (9 bp):
AAAAAGAGA
Found at i:5818580 original size:8 final size:8
Alignment explanation
Indices: 5818567--5818612 Score: 92
Period size: 8 Copynumber: 5.8 Consensus size: 8
5818557 GATGTGATAT
5818567 ATGCATAC
1 ATGCATAC
5818575 ATGCATAC
1 ATGCATAC
5818583 ATGCATAC
1 ATGCATAC
5818591 ATGCATAC
1 ATGCATAC
5818599 ATGCATAC
1 ATGCATAC
5818607 ATGCAT
1 ATGCAT
5818613 GAAAGAAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 38 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (8 bp):
ATGCATAC
Found at i:5818860 original size:4 final size:4
Alignment explanation
Indices: 5818811--5820265 Score: 2566
Period size: 4 Copynumber: 371.8 Consensus size: 4
5818801 ACACAAGATG
* * * * *
5818811 CATA CATG CATA CATG CATA CATG CATA CATG CATA CATG CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
5818859 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
5818907 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
5818955 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
5819003 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
5819051 CATA CATA CATA CATA CATA CATA CA-C CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
5819098 CAT- CATA CATA CATA CATA CATA CATA CATA C-TA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
5819144 CAT- -ATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
5819190 CATA CATA CATA CATC CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
5819238 CATA CATA CATA CATA CATA CATA C-TA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
5819285 CATA CATA CATA CATA CATA CATA CATA CATA CAT- CATA C--A CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
5819330 CATA CATA CATA CATA CATA CATA CATA CATA CCTA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
5819378 CAT- -ATA CATA CATA CATA CATA C-TA CATA CATA CATA CATA CACTA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CA-TA
5819424 CATA CATA CATA CATA C--A CATA CATA CA-A CATA CATA CATA C--A
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
5819467 CATA CATA CATA CATA C--A CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
5819513 CATA C-TA CATA CATA CATA CATA CATA CATA CATA CATA C--A CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
5819558 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
5819606 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
5819654 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
5819702 CATA CATA CAT- -ATA CATA C-TA CATA CATA C-TA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
5819746 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
5819794 CATA CATA CATA CATA CATA C-TA C-TA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
5819840 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
5819888 CATA CATA CATA CATA CATA -ATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
5819935 CATA CATA CAT- -ATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
5819981 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
5820029 CATA CATA CATA CATA CATA CATA CATA C--A CATA CATA CATA CA-A
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
5820074 CATA CATA CATA CATA CATA CATA CATA CATA CATA C-TA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
5820121 CATA CATA CATA CAATA CATA CATA CATA CATA CCATA CATA CATA CATA
1 CATA CATA CATA C-ATA CATA CATA CATA CATA -CATA CATA CATA CATA
5820171 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
5820219 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT
5820266 TATTCTTATA
Statistics
Matches: 1398, Mismatches: 16, Indels: 74
0.94 0.01 0.05
Matches are distributed among these distances:
2 20 0.01
3 44 0.03
4 1322 0.95
5 12 0.01
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:5820857 original size:42 final size:43
Alignment explanation
Indices: 5820744--5820857 Score: 137
Period size: 42 Copynumber: 2.7 Consensus size: 43
5820734 TTTCAAATTG
* **
5820744 GTAAGTCCTTCGGGCCATC-AGTAAGT-CTTTCGAGCATGATGA
1 GTAAGTCATTCGGGCCATCTA-TAAGTCCTTTCGAGCAAAATGA
* * *
5820786 GTAAATCATTCGGGTCAACTATAAG-CCTTTCGAGCAAAATGA
1 GTAAGTCATTCGGGCCATCTATAAGTCCTTTCGAGCAAAATGA
5820828 -TAAGTCATTCGGGCCATCTATAAGTCCTTT
1 GTAAGTCATTCGGGCCATCTATAAGTCCTTT
5820858 GGGTAGGATT
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
41 21 0.35
42 38 0.63
43 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (43 bp):
GTAAGTCATTCGGGCCATCTATAAGTCCTTTCGAGCAAAATGA
Found at i:5821360 original size:154 final size:155
Alignment explanation
Indices: 5821070--5821360 Score: 376
Period size: 154 Copynumber: 1.9 Consensus size: 155
5821060 ACATCCCTAA
* *
5821070 ATCTAATTTTACCTCAAGAAGAAGCAGAACAGACCCCTCTCTTTCAAAGATTTGATATTCTATGA
1 ATCTAATTTTACCTCAAGAAGAAGCAGAACAAACCCCTCTCTTTCAAAGATTTGATATTCTACGA
* * * *
5821135 GTAATAGTGGAACAAGTCTATCTCGATTCAATCTTCCCTAAGTAATAGTGTAATATATCAAAGCC
66 GTAACAGTGGAACAAGTCTACCTCGATTCAATCTTCCCTAAGTAACAGTGAAATATATCAAAGCC
*
5821200 CTCAGATCTGTTTCACTTACCTCAG
131 CCCAGATCTGTTTCACTTACCTCAG
* * * * *
5821225 ATCTGATTTTACCTCAAGAATAAG-TGAAACAAATCTCTCTCTTTC-AAGATTTGATATTCCT-C
1 ATCTAATTTTACCTCAAGAAGAAGCAG-AACAAACCCCTCTCTTTCAAAGATTTGATATT-CTAC
* *
5821287 GAGTAACAGT-GACACAAGTCTACCTTGATTCAATCTTCCCTGAGTAACAGTGAAATGA-ATCAA
64 GAGTAACAGTGGA-ACAAGTCTACCTCGATTCAATCTTCCCTAAGTAACAGTGAAAT-ATATCAA
*
5821350 CGCCCCCAGAT
127 AGCCCCCAGAT
5821361 TTGGTTTTCC
Statistics
Matches: 117, Mismatches: 15, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
153 2 0.02
154 75 0.64
155 40 0.34
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.31
Consensus pattern (155 bp):
ATCTAATTTTACCTCAAGAAGAAGCAGAACAAACCCCTCTCTTTCAAAGATTTGATATTCTACGA
GTAACAGTGGAACAAGTCTACCTCGATTCAATCTTCCCTAAGTAACAGTGAAATATATCAAAGCC
CCCAGATCTGTTTCACTTACCTCAG
Found at i:5821468 original size:135 final size:134
Alignment explanation
Indices: 5821262--5821755 Score: 600
Period size: 135 Copynumber: 3.7 Consensus size: 134
5821252 AACAAATCTC
*
5821262 TCTCTTTCAAGATTTGATATT-CCTCGAGTAACAGT-GACACAAGTCTACCTTGATTCAATCTTC
1 TCTCTTTCAAGATTTGATATTCCCT-GAGTAACAGTGGA-ACAAGTCTACCTCGATTCAATCTTC
* * * *
5821325 CCTGAGTAACAGTGAAATGAATCAACGCCCCCAGATTTGGTTTTCCCTCAAGAAGAAACAAAATA
64 CCTAAGTAACAGTGGAATGAATCAACGCCCCCAGATTTGATTTTCCCTCAAGAAGAAACAGAATA
*
5821390 TATCCG
129 TATCCA
*
5821396 TCTCTTTCAAAGATTTGATATTCCCTGAATAACAGTGGAACAAGTCTACCTCGATTCAATCTTCC
1 TCTCTTTC-AAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTACCTCGATTCAATCTTCC
* * * *
5821461 CTAAGTAACAGTGGAATGAATCAATGCCCCCAGATTTGATTTTCCCTCAAGAAGAAGCGGGATAG
65 CTAAGTAACAGTGGAATGAATCAACGCCCCCAGATTTGATTTTCCCTCAAGAAGAAACAGAATA-
5821526 T-TCCA
129 TATCCA
* * * * * *
5821531 TCTCTTTCAAAGATTTGATAATCTCTGAGTAACAGTGAAACAAGTTTACCTCGATGCAATCTCCC
1 TCTCTTTC-AAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTACCTCGATTCAATCTTCC
* ** * * ** *
5821596 CTGAGTAACAGTGGAATGAATCAACATCCCCAGCTCTGATTTTCCCTCAAGAAGAATTAGAACAT
65 CTAAGTAACAGTGGAATGAATCAACGCCCCCAGATTTGATTTTCCCTCAAGAAGAAACAGAATAT
*
5821661 ATCCC
130 ATCCA
* * * * *
5821666 TCTATTTCAATATTTGATATTCCTTGAGTAACTGTGGAACAAGTCTACCTCGATTTAATCTTCCC
1 TCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTACCTCGATTCAATCTTCCC
***
5821731 TGAAG-AACAACAGAATGAATCAACG
66 T-AAGTAACAGTGGAATGAATCAACG
5821756 TTTCTCAATT
Statistics
Matches: 308, Mismatches: 46, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
134 73 0.24
135 229 0.74
136 6 0.02
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.29
Consensus pattern (134 bp):
TCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTACCTCGATTCAATCTTCCC
TAAGTAACAGTGGAATGAATCAACGCCCCCAGATTTGATTTTCCCTCAAGAAGAAACAGAATATA
TCCA
Found at i:5821728 original size:269 final size:269
Alignment explanation
Indices: 5821262--5821753 Score: 702
Period size: 270 Copynumber: 1.8 Consensus size: 269
5821252 AACAAATCTC
* * * * *
5821262 TCTCTTTCAAGATTTGATATTCCTCGAGTAACAGTGACACAAGTCTACCTTGATTCAATCTTCCC
1 TCTCTTTCAAGATTTGATAATCCTCGAGTAACAGTGAAACAAGTCTACCTCGATGCAATCTCCCC
* * * *
5821327 TGAGTAACAGTGAAATGAATCAACGCCCCCAGATTTGGTTTTCCCTCAAGAAGAAACAAAATATA
66 TGAGTAACAGTGAAATGAATCAACACCCCCAGATCTGATTTTCCCTCAAGAAGAAACAAAACATA
* *
5821392 TCCGTCTCTTTCAAAGATTTGATATTCCCTGAATAACAGTGGAACAAGTCTACCTCGATTCAATC
131 TCCCTCTATTTCAAAGATTTGATATTCCCTGAATAACAGTGGAACAAGTCTACCTCGATTCAATC
***
5821457 TTCCCT-AAGTAACAGTGGAATGAATCAATGCCCCCAGATTTGATTTTCCCTCAAGAAGAAGCGG
196 TTCCCTGAAG-AACAACAGAATGAATCAATGCCCCCAGATTTGATTTTCCCTCAAGAAGAAGCGG
5821521 GATAGTTCCA
260 GATAGTTCCA
*
5821531 TCTCTTTCAAAGATTTGATAAT-CTCTGAGTAACAGTGAAACAAGTTTACCTCGATGCAATCTCC
1 TCTCTTTC-AAGATTTGATAATCCTC-GAGTAACAGTGAAACAAGTCTACCTCGATGCAATCTCC
* * * ** *
5821595 CCTGAGTAACAGTGGAATGAATCAACATCCCCAGCTCTGATTTTCCCTCAAGAAGAATTAGAACA
64 CCTGAGTAACAGTGAAATGAATCAACACCCCCAGATCTGATTTTCCCTCAAGAAGAAACAAAACA
* * * * *
5821660 TATCCCTCTATTTC-AATATTTGATATTCCTTGAGTAACTGTGGAACAAGTCTACCTCGATTTAA
129 TATCCCTCTATTTCAAAGATTTGATATTCCCTGAATAACAGTGGAACAAGTCTACCTCGATTCAA
5821724 TCTTCCCTGAAGAACAACAGAATGAATCAA
194 TCTTCCCTGAAGAACAACAGAATGAATCAA
5821754 CGTTTCTCAA
Statistics
Matches: 194, Mismatches: 26, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
269 79 0.41
270 115 0.59
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.29
Consensus pattern (269 bp):
TCTCTTTCAAGATTTGATAATCCTCGAGTAACAGTGAAACAAGTCTACCTCGATGCAATCTCCCC
TGAGTAACAGTGAAATGAATCAACACCCCCAGATCTGATTTTCCCTCAAGAAGAAACAAAACATA
TCCCTCTATTTCAAAGATTTGATATTCCCTGAATAACAGTGGAACAAGTCTACCTCGATTCAATC
TTCCCTGAAGAACAACAGAATGAATCAATGCCCCCAGATTTGATTTTCCCTCAAGAAGAAGCGGG
ATAGTTCCA
Found at i:5821934 original size:3 final size:3
Alignment explanation
Indices: 5821926--5821964 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
5821916 CGCCCAGACC
* *
5821926 ATT ATT ATT ATT ATT ACT ATT ATT AGT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5821965 TTTTTAATGC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:5827732 original size:41 final size:41
Alignment explanation
Indices: 5827687--5827799 Score: 217
Period size: 41 Copynumber: 2.8 Consensus size: 41
5827677 CTGCTCATGG
*
5827687 GTTGGGAATTAAAAATACTATATGATTTGTTTATTGCCTTT
1 GTTGGGAAATAAAAATACTATATGATTTGTTTATTGCCTTT
5827728 GTTGGGAAATAAAAATACTATATGATTTGTTTATTGCCTTT
1 GTTGGGAAATAAAAATACTATATGATTTGTTTATTGCCTTT
5827769 GTTGGGAAATAAAAATACTATATGATTTGTT
1 GTTGGGAAATAAAAATACTATATGATTTGTT
5827800 GTTGCCTCTT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 71 1.00
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.43
Consensus pattern (41 bp):
GTTGGGAAATAAAAATACTATATGATTTGTTTATTGCCTTT
Found at i:5832307 original size:11 final size:11
Alignment explanation
Indices: 5832282--5832314 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
5832272 TCTCTTGTCC
5832282 TTTTGTTTT-A
1 TTTTGTTTTCA
5832292 TTTTGTTTTCA
1 TTTTGTTTTCA
5832303 TTTTGTATTTCA
1 TTTTGT-TTTCA
5832315 CTATTCATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 9 0.43
11 7 0.33
12 5 0.24
ACGTcount: A:0.12, C:0.06, G:0.09, T:0.73
Consensus pattern (11 bp):
TTTTGTTTTCA
Found at i:5834597 original size:18 final size:18
Alignment explanation
Indices: 5834574--5834615 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
5834564 ATTGTATCAA
5834574 CATTGCATTTACTTTTTG
1 CATTGCATTTACTTTTTG
5834592 CATTGCATTTACTTTTTG
1 CATTGCATTTACTTTTTG
*
5834610 TATTGC
1 CATTGC
5834616 GTTTTATTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.12, T:0.55
Consensus pattern (18 bp):
CATTGCATTTACTTTTTG
Found at i:5838997 original size:134 final size:134
Alignment explanation
Indices: 5838838--5839852 Score: 1158
Period size: 134 Copynumber: 7.6 Consensus size: 134
5838828 TTCTCTTTTA
* * * * * *
5838838 ATTTGATATTCCTTGGGTAATAGTGGAACAAGTCTGCCTCGATTCAATCTTACTTGAAGAACATT
1 ATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAAGAACAGT
* * * *
5838903 GGAATAAATCAACGTCCCCAGATCTGATTTTCCATCAAGAAGAAGAAGAACATATCCCTCTCTTG
66 GGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAAGAAGAGGAACATATCCCTCTCTTT
5838968 CAAG
131 CAAG
* * *
5838972 ATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTTGATTCAATCTTCCCTCAAGAATAGT
1 ATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAAGAACAGT
* * * * *
5839037 GGAATGAATCAATGTCCCCAGATCTGATTTTCCCTCAACAAGAAGCGAAACATATCCCTCTTTTT
66 GGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAAGAAGAGGAACATATCCCTCTCTTT
5839102 CAAG
131 CAAG
* * * *
5839106 ATTTGATATTCCCTGAGTAATAGTGGAACAAGTCTGCCTCAATTCAATCTTCTCTGAAGAACAAT
1 ATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAAGAACAGT
* * * * * *
5839171 GTAATGAATCAACGTACCTAGATTTGATTTTCCCTCAAGAAGAAGTGGAACAAATCCCTCTCTTT
66 GGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAAGAAGAGGAACATATCCCTCTCTTT
*
5839236 CGAG
131 CAAG
* *
5839240 ATTTGATATTCCCTGAGTAATAGTGGAATAAGTCTGCCTCGATTCAATCTTCCCTGAAGAACAGT
1 ATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAAGAACAGT
* * * * **
5839305 GGAGTGAATCAACGTCCCCAGATCTGATTTTCACTCAATAAGAAGTGGAACATATTTCTCTCTTT
66 GGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAAGAAGAGGAACATATCCCTCTCTTT
*
5839370 TAAG
131 CAAG
* *
5839374 ATTTGATCA-TCCCTGAGTAACAGTGGAACAAGTCTACCTCGATTCAATCTTCCTTG-AGTAACA
1 ATTTGAT-ATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAAG-AACA
* * * * ** *
5839437 GTGGAATGAATCAACATCCCCAAATATGATTTTCCCTCAAGAAAAATCGAAACATATCCCTCTCT
64 GTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAAGAAGAGGAACATATCCCTCTCT
5839502 TTCAAG
129 TTCAAG
* * * * * * * * *
5839508 ATTTGATCTTCCCTAAGTACCAGTAGAATAAGTTTACCTCAATTCAATCTTCCATG-AGTAACAG
1 ATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAAG-AACAG
* * * * * * *
5839572 TGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTTAAGAAGAAGCGGGACAAATCCTTTTATT
65 TGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAAGAAGAGGAACATATCCCTCTCTT
5839637 TCAAG
130 TCAAG
* * * * * *
5839642 ATTTGATATTCTCTGAGTAACAGTGAAATAAGTCTGTCTCGATTTAATCTTTCCTGAAGAACAGT
1 ATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAAGAACAGT
* * * * * * *
5839707 GGAATGAATTAACATCCCCAAATCTAATTTTCCCTCAAGAAAAAGCA-TAACAGATCCCTCGT-T
66 GGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAAGAAG-AGGAACATATCCCTC-TCT
5839770 TTCAAG
129 TTCAAG
** * * * * ** * * *
5839776 ATTTGACCTTCCCTGAGTAATAATAGAACAAGTTTATCTCAATTTAATCTTCCCTAAAGAACAGT
1 ATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAAGAACAGT
*
5839841 GGAATGAGTCAA
66 GGAATGAATCAA
5839853 TGTTTCTCGA
Statistics
Matches: 746, Mismatches: 129, Indels: 12
0.84 0.15 0.01
Matches are distributed among these distances:
133 2 0.00
134 740 0.99
135 4 0.01
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (134 bp):
ATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAAGAACAGT
GGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAAGAAGAGGAACATATCCCTCTCTTT
CAAG
Found at i:5839582 original size:402 final size:401
Alignment explanation
Indices: 5838806--5839852 Score: 1280
Period size: 402 Copynumber: 2.6 Consensus size: 401
5838796 TTCTCGAAGA
* * * * * *
5838806 CAAGAAGAAGCGAAACAAATCATTCTCTTT-TA-ATTTGATATTCCTTGGGTAATAGTGGAACAA
1 CAAGAAGAAGCGGAACAAATCCTTCTCTTTCAAGATTTGATATTCCCTGAGTAATAGTGGAATAA
* * *
5838869 GTCTGCCTCGATTCAATCTTACTTGAAGAACATTGGAATAAATCAACGTCCCCAGATCTGATTTT
66 GTCTGCCTCGATTCAATCTTACCTGAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTT
5838934 CCATCAAGAAGAAGAAGAACATATCCCTCTCTTGCAAGATTTGATATTCCCTGAGTAACAGTGGA
131 CC-TCAAGAAGAAGAAGAACATATCCCTCTCTTGCAAGATTTGATATTCCCTGAGTAACAGTGGA
* * * ** * *
5838999 ACAAGTCTGCCTTGATTCAATCTTCCCTCAAGAATAGTGGAATGAATCAATGTCCCCAGATCTGA
195 ACAAGTCTACCTCGATTCAATCTTCCCTCAAGAACAGTGGAATGAATCAACATCCCCAAATATGA
* * * *
5839064 TTTTCCCTCAACAAGAAGCGAAACATATCCCTCTTTTTCAAGATTTGATATTCCCTGAGTAATAG
260 TTTTCCCTCAACAAAAAGCGAAACATATCCCTCTCTTTCAAGATTTGATATTCCCTAAGTAACAG
* * * *
5839129 TGGAACAAGTCTGCCTCAATTCAATCTTCTCTGAAGAACAATGTAATGAATCAACGTACCTAGAT
325 TAGAACAAGTCTACCTCAATTCAATCTTCTCTGAAGAACAATGGAATGAATCAACGTACCCAGAT
*
5839194 TTGATTTTCCCT
390 CTGATTTTCCCT
* * *
5839206 CAAGAAGAAGTGGAACAAATCCCTCTCTTTCGAGATTTGATATTCCCTGAGTAATAGTGGAATAA
1 CAAGAAGAAGCGGAACAAATCCTTCTCTTTCAAGATTTGATATTCCCTGAGTAATAGTGGAATAA
* *
5839271 GTCTGCCTCGATTCAATCTTCCCTGAAGAACAGTGGAGTGAATCAACGTCCCCAGATCTGATTTT
66 GTCTGCCTCGATTCAATCTTACCTGAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTT
* ** ** **
5839336 CACTCAATAAGAAGTGGAACATATTTCTCTCTTTTAAGATTTGATCA-TCCCTGAGTAACAGTGG
131 C-CTCAAGAAGAAGAAGAACATATCCCTCTCTTGCAAGATTTGAT-ATTCCCTGAGTAACAGTGG
**
5839400 AACAAGTCTACCTCGATTCAATCTT-CCTTGAGTAACAGTGGAATGAATCAACATCCCCAAATAT
194 AACAAGTCTACCTCGATTCAATCTTCCCTCAAG-AACAGTGGAATGAATCAACATCCCCAAATAT
* * * *
5839464 GATTTTCCCTCAAGAAAAATCGAAACATATCCCTCTCTTTCAAGATTTGATCTTCCCTAAGTACC
258 GATTTTCCCTCAACAAAAAGCGAAACATATCCCTCTCTTTCAAGATTTGATATTCCCTAAGTAAC
* * * *
5839529 AGTAGAATAAGTTTACCTCAATTCAATCTTC-CATG-AGTAACAGTGGAATGAATCAACGTCCCC
323 AGTAGAACAAGTCTACCTCAATTCAATCTTCTC-TGAAG-AACAATGGAATGAATCAACGTACCC
5839592 AGATCTGATTTTCCCT
386 AGATCTGATTTTCCCT
* * * * * * *
5839608 TAAGAAGAAGCGGGACAAATCCTTTTATTTCAAGATTTGATATTCTCTGAGTAACAGTGAAATAA
1 CAAGAAGAAGCGGAACAAATCCTTCTCTTTCAAGATTTGATATTCCCTGAGTAATAGTGGAATAA
* * * * * * *
5839673 GTCTGTCTCGATTTAATCTTTCCTGAAGAACAGTGGAATGAATTAACATCCCCAAATCTAATTTT
66 GTCTGCCTCGATTCAATCTTACCTGAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTT
* * * * * ** * * *
5839738 CCCTCAAGAAAAAGCATAACAGATCCCTCGT-TTTCAAGATTTGACCTTCCCTGAGTAATAATAG
131 -CCTCAAGAAGAAGAAGAACATATCCCTC-TCTTGCAAGATTTGATATTCCCTGAGTAACAGTGG
* * * * * *
5839802 AACAAGTTTATCTCAATTTAATCTTCCCTAAAGAACAGTGGAATGAGTCAA
194 AACAAGTCTACCTCGATTCAATCTTCCCTCAAGAACAGTGGAATGAATCAA
5839853 TGTTTCTCGA
Statistics
Matches: 551, Mismatches: 85, Indels: 20
0.84 0.13 0.03
Matches are distributed among these distances:
400 26 0.05
401 9 0.02
402 507 0.92
403 9 0.02
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (401 bp):
CAAGAAGAAGCGGAACAAATCCTTCTCTTTCAAGATTTGATATTCCCTGAGTAATAGTGGAATAA
GTCTGCCTCGATTCAATCTTACCTGAAGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTT
CCTCAAGAAGAAGAAGAACATATCCCTCTCTTGCAAGATTTGATATTCCCTGAGTAACAGTGGAA
CAAGTCTACCTCGATTCAATCTTCCCTCAAGAACAGTGGAATGAATCAACATCCCCAAATATGAT
TTTCCCTCAACAAAAAGCGAAACATATCCCTCTCTTTCAAGATTTGATATTCCCTAAGTAACAGT
AGAACAAGTCTACCTCAATTCAATCTTCTCTGAAGAACAATGGAATGAATCAACGTACCCAGATC
TGATTTTCCCT
Found at i:5840033 original size:3 final size:3
Alignment explanation
Indices: 5840025--5840074 Score: 61
Period size: 3 Copynumber: 17.7 Consensus size: 3
5840015 CGTCTCAATT
* *
5840025 TTA TTA TTA TTA TTG TTA TTG TTA TTA TTA TTA TTA -TA TT- TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5840070 TTA TT
1 TTA TT
5840075 TTTTACAGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 6 0.15
3 34 0.85
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:5840078 original size:12 final size:13
Alignment explanation
Indices: 5840023--5840079 Score: 55
Period size: 12 Copynumber: 4.4 Consensus size: 13
5840013 TTCGTCTCAA
5840023 TTTTATTATTATT
1 TTTTATTATTATT
*
5840036 ATTGTTATTGTTA-T
1 -TT-TTATTATTATT
* *
5840050 TATTATTATTATA
1 TTTTATTATTATT
5840063 TTTTATT-TTATT
1 TTTTATTATTATT
5840075 TTTTA
1 TTTTA
5840080 CAGATCCAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
12 17 0.49
13 7 0.20
14 3 0.09
15 8 0.23
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.72
Consensus pattern (13 bp):
TTTTATTATTATT
Found at i:5840159 original size:23 final size:22
Alignment explanation
Indices: 5840128--5840188 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 22
5840118 CCACAAGTTA
5840128 CATCAGACCCAAA-CATGGAGCC
1 CATCAGACCCAAACCA-GGAGCC
5840150 CATCAAGACCCAAACCAGGAGCC
1 CATC-AGACCCAAACCAGGAGCC
5840173 CAAT-AGAACCCAAACC
1 C-ATCAG-ACCCAAACC
5840189 CATTAGGGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
22 6 0.17
23 25 0.71
24 4 0.11
ACGTcount: A:0.41, C:0.38, G:0.15, T:0.07
Consensus pattern (22 bp):
CATCAGACCCAAACCAGGAGCC
Found at i:5842166 original size:130 final size:131
Alignment explanation
Indices: 5841952--5842271 Score: 403
Period size: 130 Copynumber: 2.5 Consensus size: 131
5841942 TAAATGACTT
* * * *
5841952 CTTTAATGTATGAGAGGTCTTTTATTCTCGATTGGAAATAATTTGATATTATCATTTTCTCTCGA
1 CTTTAATGTATGAGAGGTCGTTTATTCTCGATTGGAAATAATTAGATATTATTATTTTCACTCGA
* * * *
5842017 ATTAATATTGATTTCTAAGATGGAATAGTGATATCTCTTCATTTTGATTA-GAGCAATAAACAAA
66 ATTAATATTGATTTCTAAGATAGAATAATGATATCTCCTCATTTCGA-TAGGAGCAATAAACAAA
5842081 TG
130 TG
* * * * * *
5842083 CTTTAAGGTATGA-AGGTCGTTTATTCTCAATTGTAAATTATTAGATAGTATTGTTTTCACTCGA
1 CTTTAATGTATGAGAGGTCGTTTATTCTCGATTGGAAATAATTAGATATTATTATTTTCACTCGA
* * ** *
5842147 ATTGATATTGAATTT-TAAGATAGAATAATGATATCTCCTCATTTCGATAGGAGTAATAAATGAT
66 ATTAATATTG-ATTTCTAAGATAGAATAATGATATCTCCTCATTTCGATAGGAGCAATAAACAAA
5842211 TG
130 TG
* * *
5842213 TTTTAATGTATGAGAGGTTGTTTATTCTCGATTGGAAATAATTATATATTATTATTTTC
1 CTTTAATGTATGAGAGGTCGTTTATTCTCGATTGGAAATAATTAGATATTATTATTTTC
5842272 TCTCTTAAAA
Statistics
Matches: 158, Mismatches: 28, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
129 2 0.01
130 102 0.65
131 54 0.34
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (131 bp):
CTTTAATGTATGAGAGGTCGTTTATTCTCGATTGGAAATAATTAGATATTATTATTTTCACTCGA
ATTAATATTGATTTCTAAGATAGAATAATGATATCTCCTCATTTCGATAGGAGCAATAAACAAAT
G
Found at i:5851871 original size:14 final size:14
Alignment explanation
Indices: 5851830--5851871 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
5851820 AATTCTTATA
*
5851830 ATTTTT-ATGATTT
1 ATTTTTAATTATTT
* *
5851843 ATTTTTATTTTTTT
1 ATTTTTAATTATTT
5851857 ATTTTTAATTATTT
1 ATTTTTAATTATTT
5851871 A
1 A
5851872 ATTATTTTGA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
13 6 0.26
14 17 0.74
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (14 bp):
ATTTTTAATTATTT
Found at i:5854679 original size:14 final size:14
Alignment explanation
Indices: 5854660--5854694 Score: 61
Period size: 14 Copynumber: 2.4 Consensus size: 14
5854650 GTTTCTTTCA
5854660 CTCAAAAGGTAGAG
1 CTCAAAAGGTAGAG
5854674 CTCAAAAGGTAGAG
1 CTCAAAAGGTAGAG
5854688 CATCAAA
1 C-TCAAA
5854695 TTCTATGGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (14 bp):
CTCAAAAGGTAGAG
Found at i:5856407 original size:29 final size:30
Alignment explanation
Indices: 5856374--5856536 Score: 154
Period size: 30 Copynumber: 5.5 Consensus size: 30
5856364 TTAATACCAC
* **
5856374 TTTAGTCC-TTAAGTTTATGTTTTTTTTAT
1 TTTAGTCCTTTAAGTTTATATTTTTGCTAT
* * *
5856403 TTTAGTCCTTTAAATTTCTAATTTTGCTA-
1 TTTAGTCCTTTAAGTTTATATTTTTGCTAT
* * *
5856432 TTTAGACCCTTAAGTTTATATTTTTACTAT
1 TTTAGTCCTTTAAGTTTATATTTTTGCTAT
* * * *
5856462 TTTAGCCCTTTAAGTTTCTGTTTTTGTTAT
1 TTTAGTCCTTTAAGTTTATATTTTTGCTAT
*
5856492 TTTAGTCCTTTAAATTTAT-TTTTTAGCTAT
1 TTTAGTCCTTTAAGTTTATATTTTT-GCTAT
5856522 TTTAG-CCTTTCAAGT
1 TTTAGTCCTTT-AAGT
5856537 GTGTTAAATA
Statistics
Matches: 107, Mismatches: 23, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
29 41 0.38
30 66 0.62
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.58
Consensus pattern (30 bp):
TTTAGTCCTTTAAGTTTATATTTTTGCTAT
Found at i:5856531 original size:59 final size:58
Alignment explanation
Indices: 5856374--5856536 Score: 177
Period size: 59 Copynumber: 2.8 Consensus size: 58
5856364 TTAATACCAC
* ** * *
5856374 TTTAGTCCTTAAGTTTATGTTTTTTTTATTTTAGTCCTTTAAATTTCTAATTTTGCTA
1 TTTAGTCCTTAAGTTTATATTTTTACTATTTTAGCCCTTTAAGTTTCTAATTTTGCTA
* ** *
5856432 TTTAGACCCTTAAGTTTATATTTTTACTATTTTAGCCCTTTAAGTTTCTGTTTTTGTTA
1 TTTAG-TCCTTAAGTTTATATTTTTACTATTTTAGCCCTTTAAGTTTCTAATTTTGCTA
*
5856491 TTTTAGTCCTTTAAATTTAT-TTTTTAGCTATTTTAG-CCTTTCAAGT
1 -TTTAGTCC-TTAAGTTTATATTTTTA-CTATTTTAGCCCTTT-AAGT
5856537 GTGTTAAATA
Statistics
Matches: 89, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
58 5 0.06
59 57 0.64
60 27 0.30
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.58
Consensus pattern (58 bp):
TTTAGTCCTTAAGTTTATATTTTTACTATTTTAGCCCTTTAAGTTTCTAATTTTGCTA
Found at i:5871787 original size:2 final size:2
Alignment explanation
Indices: 5871780--5871878 Score: 198
Period size: 2 Copynumber: 49.5 Consensus size: 2
5871770 TTGTCCAGGG
5871780 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5871822 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5871864 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
5871879 AGTTGAAATT
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 97 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5872373 original size:20 final size:20
Alignment explanation
Indices: 5872345--5872387 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
5872335 TCTCAATCAT
* * *
5872345 AAAACAAAGCCAAAAAATTA
1 AAAAAAAAGCAAAAAAAGTA
*
5872365 AAAAAAAAGGAAAAAAAGTA
1 AAAAAAAAGCAAAAAAAGTA
5872385 AAA
1 AAA
5872388 GCAACCATCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.77, C:0.07, G:0.09, T:0.07
Consensus pattern (20 bp):
AAAAAAAAGCAAAAAAAGTA
Found at i:5874155 original size:14 final size:15
Alignment explanation
Indices: 5874126--5874155 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5874116 ACTTTTTATC
5874126 TTTTAAAATCATTTT
1 TTTTAAAATCATTTT
*
5874141 TTTTAAAATTATTTT
1 TTTTAAAATCATTTT
5874156 AAAGGAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTAAAATCATTTT
Found at i:5882752 original size:21 final size:21
Alignment explanation
Indices: 5882728--5882772 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5882718 TGATTTTGAA
*
5882728 AAAAATAAAAATTTAGGTACT
1 AAAAATAAAAATTTAAGTACT
* *
5882749 AAAACTGAAAATTTAAGTACT
1 AAAAATAAAAATTTAAGTACT
5882770 AAA
1 AAA
5882773 CACATAGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.58, C:0.07, G:0.09, T:0.27
Consensus pattern (21 bp):
AAAAATAAAAATTTAAGTACT
Found at i:5884156 original size:19 final size:21
Alignment explanation
Indices: 5884123--5884161 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
5884113 TGTGATTAAC
*
5884123 TTAACTTTTTTATG-CAAATT
1 TTAACTTTTTGATGCCAAATT
5884143 TTAAC-TTTTGATGCCAAAT
1 TTAACTTTTTGATGCCAAAT
5884162 GCATGTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.31, C:0.13, G:0.08, T:0.49
Consensus pattern (21 bp):
TTAACTTTTTGATGCCAAATT
Found at i:5885168 original size:9 final size:9
Alignment explanation
Indices: 5885154--5885186 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
5885144 TGTTAAATAT
5885154 TAATTATTA
1 TAATTATTA
5885163 TAATTATTA
1 TAATTATTA
*
5885172 TTATT-TTA
1 TAATTATTA
5885180 TAATTAT
1 TAATTAT
5885187 AATTATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
TAATTATTA
Found at i:5885182 original size:17 final size:17
Alignment explanation
Indices: 5885160--5885192 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5885150 ATATTAATTA
*
5885160 TTATAATTATTATTATT
1 TTATAATTATAATTATT
5885177 TTATAATTATAATTAT
1 TTATAATTATAATTAT
5885193 AATTTTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATAATTATAATTATT
Found at i:5885188 original size:23 final size:22
Alignment explanation
Indices: 5885159--5885201 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
5885149 AATATTAATT
*
5885159 ATTATAATTATTATTATTTTATA
1 ATTATAATTATAATT-TTTTATA
5885182 ATTATAATTATAATTTTTTA
1 ATTATAATTATAATTTTTTA
5885202 ATTTATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTATAATTATAATTTTTTATA
Found at i:5885193 original size:6 final size:6
Alignment explanation
Indices: 5885159--5885196 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
5885149 AATATTAATT
* *
5885159 ATTATA ATTATT ATTAT- TTTATA ATTATA ATTATA ATT
1 ATTATA ATTATA ATTATA ATTATA ATTATA ATTATA ATT
5885197 TTTTAATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
5 4 0.14
6 24 0.86
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (6 bp):
ATTATA
Found at i:5886194 original size:65 final size:63
Alignment explanation
Indices: 5886073--5886226 Score: 168
Period size: 65 Copynumber: 2.4 Consensus size: 63
5886063 TACACTAAGA
* * * * * *
5886073 GTGCATCGATGTATGAAGTGCATTCGATGTTTCAAAATAGCCTGAGTGCATCGATGCAT-GTCTT
1 GTGCATCGATGCAT-AAATGCATTCAAAGTTTCAAAATAACCTGAGTGCATCGATGCATGGT-AT
*
5886137 GTGCATCGATGCATCAAATGCATTCAAAGTTTTCATAAA-AACCTGAGTGCATTGATGCATGGTA
1 GTGCATCGATGCAT-AAATGCATTCAAAG-TTTCA-AAATAACCTGAGTGCATCGATGCATGGTA
5886201 T
63 T
*
5886202 GTACATCGATGCATATAATGCATTC
1 GTGCATCGATGCATA-AATGCATTC
5886227 GATGTTCAAT
Statistics
Matches: 77, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
64 25 0.32
65 47 0.61
66 5 0.06
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCATAAATGCATTCAAAGTTTCAAAATAACCTGAGTGCATCGATGCATGGTAT
Found at i:5889001 original size:15 final size:14
Alignment explanation
Indices: 5888977--5889008 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
5888967 CTTTGTTTTA
5888977 ATTTTTGCTTTATT
1 ATTTTTGCTTTATT
5888991 ATTTATTGCTTTATT
1 ATTT-TTGCTTTATT
5889006 ATT
1 ATT
5889009 ACATGTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.69
Consensus pattern (14 bp):
ATTTTTGCTTTATT
Found at i:5889030 original size:2 final size:2
Alignment explanation
Indices: 5889023--5889058 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5889013 GTAAATATGT
5889023 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5889059 AACATTTCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5894327 original size:24 final size:24
Alignment explanation
Indices: 5894277--5894333 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
5894267 GGGCAATATT
*
5894277 TTTTTCAAAATTTTTGATTAAACA
1 TTTTTCAAAATTTTTAATTAAACA
* *
5894301 TTTTTCAAAATTTTTTAATT-GATA
1 TTTTTCAAAA-TTTTTAATTAAACA
5894325 TTTTTCAAA
1 TTTTTCAAA
5894334 TTTCAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 21 0.72
25 8 0.28
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (24 bp):
TTTTTCAAAATTTTTAATTAAACA
Found at i:5898146 original size:28 final size:28
Alignment explanation
Indices: 5898106--5898169 Score: 128
Period size: 28 Copynumber: 2.3 Consensus size: 28
5898096 TCAATCTCCT
5898106 CGTCGGGGTAGTGGCCATCATCATCGAG
1 CGTCGGGGTAGTGGCCATCATCATCGAG
5898134 CGTCGGGGTAGTGGCCATCATCATCGAG
1 CGTCGGGGTAGTGGCCATCATCATCGAG
5898162 CGTCGGGG
1 CGTCGGGG
5898170 CTAGGGATGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.16, C:0.25, G:0.39, T:0.20
Consensus pattern (28 bp):
CGTCGGGGTAGTGGCCATCATCATCGAG
Found at i:5906444 original size:24 final size:25
Alignment explanation
Indices: 5906405--5906475 Score: 76
Period size: 25 Copynumber: 2.8 Consensus size: 25
5906395 GCAAAACAAA
*
5906405 ACAAAACAAAAAAAAAAGAAGAG-G
1 ACAAAAAAAAAAAAAAAGAAGAGAG
5906429 A-AAAAGAAAAATAAAAAA-AAGAGAG
1 ACAAAA-AAAAA-AAAAAAGAAGAGAG
5906454 ACAAAAAAAAAAGAATAAAGAA
1 ACAAAAAAAAAA-AA-AAAGAA
5906476 AACATAACCA
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
23 4 0.10
24 11 0.28
25 15 0.38
26 7 0.18
27 2 0.05
ACGTcount: A:0.79, C:0.04, G:0.14, T:0.03
Consensus pattern (25 bp):
ACAAAAAAAAAAAAAAAGAAGAGAG
Found at i:5906459 original size:27 final size:26
Alignment explanation
Indices: 5906401--5906465 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 26
5906391 TATAGCAAAA
5906401 CAAAACAAAACAA-AAAAAAAAGAAGAG
1 CAAAA-AAAA-AATAAAAAAAAGAAGAG
*
5906428 GAAAAAGAAAAATAAAAAAAAG-AGAG
1 CAAAAA-AAAAATAAAAAAAAGAAGAG
5906454 ACAAAAAAAAAA
1 -CAAAAAAAAAA
5906466 GAATAAAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
26 12 0.36
27 21 0.64
ACGTcount: A:0.80, C:0.06, G:0.12, T:0.02
Consensus pattern (26 bp):
CAAAAAAAAAATAAAAAAAAGAAGAG
Found at i:5906477 original size:15 final size:14
Alignment explanation
Indices: 5906412--5906477 Score: 53
Period size: 15 Copynumber: 4.6 Consensus size: 14
5906402 AAAACAAAAC
*
5906412 AAAAAAAAAAGAAG
1 AAAAAAAAAAGAAT
*
5906426 AGGAAAAAGAAA-AAT
1 A--AAAAAAAAAGAAT
* *
5906441 AAAAAAAAGAGAGAC
1 AAAAAAAAAAGA-AT
5906456 AAAAAAAAAAGAAT
1 AAAAAAAAAAGAAT
*
5906470 AAAGAAAA
1 AAAAAAAA
5906478 CATAACCAAC
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
13 7 0.17
14 10 0.25
15 15 0.38
16 8 0.20
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.03
Consensus pattern (14 bp):
AAAAAAAAAAGAAT
Found at i:5908643 original size:51 final size:54
Alignment explanation
Indices: 5908437--5908770 Score: 246
Period size: 58 Copynumber: 5.9 Consensus size: 54
5908427 GATGTTATCA
* ** *
5908437 AAAGAATTTTTAAAGATACTAAGCCTGATTTTTAGCAGTTTTTTGATGATGATTTCC
1 AAAGAATTTTT-AAGAAACTAAGCCTGA-TTTTAGGGGTTTCTTGATGAT-ATTTCC
*
5908494 AAAGACTTTTTTAAAAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATGATTTCC
1 AAAGA-ATTTTT--AAGAAACTAAGCCTGATTTT-AGGGGTTTCTTGATGAT-ATTTCC
* * *
5908553 AAAGAATTTTTAAAAGAAGCTAAACCTAATTTTAGGGGTTTCTTGAT-AT-TTT-C
1 AAAGAATTTTT--AAGAAACTAAGCCTGATTTTAGGGGTTTCTTGATGATATTTCC
* * * *
5908606 ACATGAGTTTTT-AGAAACTAAGCCTGATTTTAAGGGTTTCTTGATGATTATTTTC
1 A-AAGAATTTTTAAGAAACTAAGCCTGATTTTAGGGGTTTCTTGATGA-TATTTCC
* * * * ** *
5908661 AAAGAATTTTTAAAAGAAGCTATGTCTAATTTTTAGGGGTTTCTTGATGATAACTGAAAACA
1 AAAGAATTTTT--AAGAAACTAAGCCTGA-TTTTAGGGGTTTCTTGATGAT-A-T---TTCC
* *
5908723 AAAGAGA-TTTTAAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGA
1 AAAGA-ATTTTTAAGAAACTAAGCCTGATTTT-AGGGGTTTCTTGATGA
5908771 GTAAGTCCTT
Statistics
Matches: 226, Mismatches: 32, Indels: 35
0.77 0.11 0.12
Matches are distributed among these distances:
51 29 0.13
52 1 0.00
53 3 0.01
54 22 0.10
55 2 0.01
56 2 0.01
57 31 0.14
58 53 0.23
59 47 0.21
60 26 0.12
62 9 0.04
63 1 0.00
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (54 bp):
AAAGAATTTTTAAGAAACTAAGCCTGATTTTAGGGGTTTCTTGATGATATTTCC
Found at i:5908701 original size:58 final size:58
Alignment explanation
Indices: 5908437--5908711 Score: 300
Period size: 59 Copynumber: 4.9 Consensus size: 58
5908427 GATGTTATCA
* ** *
5908437 AAAGAATTTTT-AAAGATACTAAGCCTGATTTTTAGCAGTTTTTTGATGATGATTTCC
1 AAAGAATTTTTAAAAGAAACTAAGCCTGATTTTTAGGGGTTTCTTGATGATGATTTCC
* *
5908494 AAAGACTTTTTTAAAAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATGATTTCC
1 AAAGA-ATTTTTAAAAGAAACTAAGCCTGATTTTTAGGGGTTTCTTGATGATGATTTCC
* * *
5908553 AAAGAATTTTTAAAAGAAGCTAAACCT-AATTTTAGGGGTTTCTTGAT-AT--TTT-C
1 AAAGAATTTTTAAAAGAAACTAAGCCTGATTTTTAGGGGTTTCTTGATGATGATTTCC
* * * * *
5908606 ACATGAGTTTTT---AGAAACTAAGCCTGA-TTTTAAGGGTTTCTTGATGATTATTTTC
1 A-AAGAATTTTTAAAAGAAACTAAGCCTGATTTTTAGGGGTTTCTTGATGATGATTTCC
* * * *
5908661 AAAGAATTTTTAAAAGAAGCTATGTCTAATTTTTAGGGGTTTCTTGATGAT
1 AAAGAATTTTTAAAAGAAACTAAGCCTGATTTTTAGGGGTTTCTTGATGAT
5908712 AACTGAAAAC
Statistics
Matches: 183, Mismatches: 23, Indels: 23
0.80 0.10 0.10
Matches are distributed among these distances:
51 28 0.15
52 3 0.02
53 2 0.01
54 22 0.12
55 2 0.01
56 2 0.01
57 34 0.19
58 44 0.24
59 46 0.25
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (58 bp):
AAAGAATTTTTAAAAGAAACTAAGCCTGATTTTTAGGGGTTTCTTGATGATGATTTCC
Found at i:5909023 original size:59 final size:60
Alignment explanation
Indices: 5908898--5909026 Score: 147
Period size: 59 Copynumber: 2.2 Consensus size: 60
5908888 CAGGATGTTT
* * * *
5908898 TCAACATTTCCTTTGCTCGATTCACAACACTTCGAATTAACAATGCCCAACCAGAGTGGT
1 TCAACATTTCCTTTGCTCGATTCACAACACTTCAAATCAACAACGCCCAACCAGAGTGGA
** * * *
5908958 TC-ACATTTCCTTTGCTCGATTTTCAACACTTCAAATCAGCAACGCATCAATC-GAG-GGA
1 TCAACATTTCCTTTGCTCGATTCACAACACTTCAAATCAACAACGC-CCAACCAGAGTGGA
5909016 TCAACATTTCC
1 TCAACATTTCC
5909027 AGTGGAAAGA
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
58 4 0.07
59 48 0.83
60 6 0.10
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.29
Consensus pattern (60 bp):
TCAACATTTCCTTTGCTCGATTCACAACACTTCAAATCAACAACGCCCAACCAGAGTGGA
Found at i:5920373 original size:3 final size:3
Alignment explanation
Indices: 5920365--5920485 Score: 131
Period size: 3 Copynumber: 40.0 Consensus size: 3
5920355 TCGTCCAGTC
*
5920365 TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTC TTA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* * * *
5920413 TAA TTA TATA TTA -TA CTA CTA TTA TTA TATA TGA -TA TTA TTA TTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
*
5920458 TATA TTA TTA TTA TTA TTA ATA TTA TTA
1 T-TA TTA TTA TTA TTA TTA TTA TTA TTA
5920486 AATAATATTA
Statistics
Matches: 102, Mismatches: 9, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
2 5 0.05
3 85 0.83
4 12 0.12
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:5920456 original size:49 final size:44
Alignment explanation
Indices: 5920370--5920474 Score: 129
Period size: 49 Copynumber: 2.2 Consensus size: 44
5920360 CAGTCTTATT
* *
5920370 ATTATTATTATTATTATATTATTATTATTATTCTTATTATATATA
1 ATTATTATTA-TACTATATTATTATTATTATTATTATTATATATA
*
5920415 ATTATATATTATACTACTATTATTATATATGATATTATTATTATATATT
1 ATTAT-TATTATACTA-TATTATTAT-TAT--TATTATTATTATATATA
5920464 ATTATTATTAT
1 ATTATTATTAT
5920475 TAATATTATT
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
45 9 0.17
46 14 0.27
47 3 0.06
48 6 0.12
49 20 0.38
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (44 bp):
ATTATTATTATACTATATTATTATTATTATTATTATTATATATA
Found at i:5920494 original size:31 final size:30
Alignment explanation
Indices: 5920369--5920495 Score: 116
Period size: 31 Copynumber: 4.2 Consensus size: 30
5920359 CCAGTCTTAT
* * *
5920369 TATTATTATTAT-TATTATATTATTATTAT
1 TATTATTATTATATATAATATTATTAATAA
* *
5920398 TATTCTTATTATATATAATTATATATT-ATAC
1 TATTATTATTATATATAA-TAT-TATTAATAA
* * *
5920429 TACTATTATTATATATGATATTATTATTATA
1 TATTATTATTATATATAATATTATTAATA-A
5920460 TATTATTATTAT-TATTAATATTATTAAATAA
1 TATTATTATTATATA-TAATATTATT-AATAA
5920491 TATTA
1 TATTA
5920496 CAAAGACCCG
Statistics
Matches: 79, Mismatches: 12, Indels: 12
0.77 0.12 0.12
Matches are distributed among these distances:
29 15 0.19
30 11 0.14
31 46 0.58
32 7 0.09
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.57
Consensus pattern (30 bp):
TATTATTATTATATATAATATTATTAATAA
Found at i:5922967 original size:15 final size:16
Alignment explanation
Indices: 5922929--5922968 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
5922919 CCAGAGCCTC
* *
5922929 TGAATCATTCAGCATT
1 TGAATCATTCAACACT
5922945 TGAATCATTCAACACT
1 TGAATCATTCAACACT
5922961 T-AATCATT
1 TGAATCATT
5922969 TTGAAGTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (16 bp):
TGAATCATTCAACACT
Found at i:5928239 original size:22 final size:22
Alignment explanation
Indices: 5928211--5928256 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
5928201 ATTCTACAAG
*
5928211 GATGATAGATTCTCTTTTCAAA
1 GATGATAAATTCTCTTTTCAAA
5928233 GATGATAAATTCTCTTTTCAAA
1 GATGATAAATTCTCTTTTCAAA
5928255 GA
1 GA
5928257 CAGAAAGCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (22 bp):
GATGATAAATTCTCTTTTCAAA
Found at i:5928941 original size:20 final size:20
Alignment explanation
Indices: 5928893--5928947 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
5928883 TCTAGAAAAC
* *
5928893 TAAATCCTCCGGGTAATTTG
1 TAAATCCTCAGGGTAATCTG
* *
5928913 TGAAA-CCTCTGGGTCATCTG
1 T-AAATCCTCAGGGTAATCTG
5928933 TAAATCCTCAGGGTA
1 TAAATCCTCAGGGTA
5928948 GGATGTTTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 3 0.11
20 22 0.79
21 3 0.11
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (20 bp):
TAAATCCTCAGGGTAATCTG
Found at i:5928999 original size:119 final size:118
Alignment explanation
Indices: 5928788--5929075 Score: 450
Period size: 119 Copynumber: 2.4 Consensus size: 118
5928778 TATTTCCATG
* * * **
5928788 AATTTGTAAATCCTCCGGGTCATCTATAAAACCTTAGGGTAGGATATTTTTGCATGAAAATGAGA
1 AATTTGTAAA-CCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCACATGAAAATGAGA
* *
5928853 AAGTGATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAACTAAATCCTCCGGGT
65 AAGCGATTTTCAAAGTTTCTCATTTAATATTCTAGAAAACTAAATCCTCCGGGT
* *
5928907 AATTTGTGAAACCTCTGGGTCATCTGTAAATCCTCAGGGTAGGATGTTTTCACATGAAAATGAGA
1 AATTTGT-AAACCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCACATGAAAATGAGA
*
5928972 AAGCGATTTTCAAAGTTTCTCATTTAATATTCTAGAAAATTAAATCCTCCGGGT
65 AAGCGATTTTCAAAGTTTCTCATTTAATATTCTAGAAAACTAAATCCTCCGGGT
*
5929026 GATTTGTAAAACCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTT
1 AATTTGT-AAACCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTT
5929076 TCTATTTTTT
Statistics
Matches: 154, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
119 151 0.98
120 3 0.02
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (118 bp):
AATTTGTAAACCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCACATGAAAATGAGAA
AGCGATTTTCAAAGTTTCTCATTTAATATTCTAGAAAACTAAATCCTCCGGGT
Found at i:5929040 original size:20 final size:20
Alignment explanation
Indices: 5929012--5929065 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
5929002 TCTAGAAAAT
* * *
5929012 TAAATCCTCCGGGTGATTTG
1 TAAAACCTCCGGGTCATCTG
5929032 TAAAACCTCCGGGTCATCTG
1 TAAAACCTCCGGGTCATCTG
*
5929052 TAAAACCTCAGGGT
1 TAAAACCTCCGGGT
5929066 AGGATGTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (20 bp):
TAAAACCTCCGGGTCATCTG
Found at i:5929213 original size:3 final size:3
Alignment explanation
Indices: 5929205--5929323 Score: 152
Period size: 3 Copynumber: 39.7 Consensus size: 3
5929195 TTTCGTCAGG
* *
5929205 TAT TAT TAT TAT TAT TAT TAT TAT CA- TAT TAT TAT TAT TAT ATAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
* * * *
5929250 AAT TAT ATAT TA- TAC AAC TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5929295 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
5929324 AATAATATTA
Statistics
Matches: 103, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
2 3 0.03
3 95 0.92
4 5 0.05
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:5932949 original size:7 final size:7
Alignment explanation
Indices: 5932916--5933063 Score: 144
Period size: 7 Copynumber: 21.0 Consensus size: 7
5932906 TACTTCGCCT
5932916 GAAAAAA
1 GAAAAAA
5932923 GATAAAAA
1 GA-AAAAA
5932931 GAAAACAA
1 GAAAA-AA
5932939 -AAAAAA
1 GAAAAAA
5932945 GAAAAAA
1 GAAAAAA
*
5932952 GAAGAAA
1 GAAAAAA
*
5932959 GAAGAAA
1 GAAAAAA
5932966 GAAAGAAA
1 GAAA-AAA
*
5932974 G-AAAAT
1 GAAAAAA
*
5932980 GAAAAAT
1 GAAAAAA
5932987 GAAAAAA
1 GAAAAAA
*
5932994 GAGAAAAT
1 GA-AAAAA
5933002 GAAAAAA
1 GAAAAAA
*
5933009 GAGAAAAT
1 GA-AAAAA
*
5933017 GAGAAAAT
1 GA-AAAAA
5933025 GAAAAAA
1 GAAAAAA
5933032 GAAAAAA
1 GAAAAAA
5933039 G-AAAAA
1 GAAAAAA
5933045 G-AAAAA
1 GAAAAAA
5933051 G-AAAAA
1 GAAAAAA
5933057 GAAAAAA
1 GAAAAAA
5933064 ATAATAAATA
Statistics
Matches: 125, Mismatches: 8, Indels: 16
0.84 0.05 0.11
Matches are distributed among these distances:
6 23 0.18
7 69 0.55
8 33 0.26
ACGTcount: A:0.78, C:0.01, G:0.18, T:0.04
Consensus pattern (7 bp):
GAAAAAA
Found at i:5932960 original size:4 final size:4
Alignment explanation
Indices: 5932942--5932977 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
5932932 AAAACAAAAA
5932942 AAAG AAA- AAAG -AAG AAAG -AAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
5932978 ATGAAAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
3 9 0.31
4 20 0.69
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:5938825 original size:22 final size:22
Alignment explanation
Indices: 5938799--5938849 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
5938789 ATTTATTAGA
5938799 AATATTAAATACAATAAATAA-T
1 AATATTAAATACAATAAA-AATT
** *
5938821 AATATTATTTATAATAAAAATT
1 AATATTAAATACAATAAAAATT
5938843 AATATTA
1 AATATTA
5938850 TTATTTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 2 0.08
22 23 0.92
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
AATATTAAATACAATAAAAATT
Found at i:5938966 original size:31 final size:29
Alignment explanation
Indices: 5938898--5938967 Score: 70
Period size: 31 Copynumber: 2.2 Consensus size: 29
5938888 AATATTATTT
*
5938898 TTATAATTTTATTAATAAAAATATTAATAT
1 TTAT-ATTTTATTAATAAAAATATTAATAA
5938928 TGGTATATTTTATTGAAATAAAAATATT-ATAAA
1 T--TATATTTTATT--AATAAAAATATTAAT-AA
5938961 TTATATT
1 TTATATT
5938968 AATTATTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
30 1 0.03
31 14 0.41
32 5 0.15
33 14 0.41
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (29 bp):
TTATATTTTATTAATAAAAATATTAATAA
Found at i:5939132 original size:27 final size:25
Alignment explanation
Indices: 5939056--5939136 Score: 81
Period size: 27 Copynumber: 3.0 Consensus size: 25
5939046 TAGATTATTA
5939056 TATTAATATTAAATATATAAATAATAT
1 TATTAATA-TAAATA-ATAAATAATAT
* * *
5939083 TATTCATTATTAATAATTTAATAATAT
1 TATT-AATATAAATAA-TAAATAATAT
5939110 TATTAATATGAAATTAATAAATAATAT
1 TATTAATAT-AAA-TAATAAATAATAT
5939137 AAATTTTATT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
26 5 0.11
27 33 0.75
28 6 0.14
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (25 bp):
TATTAATATAAATAATAAATAATAT
Found at i:5939132 original size:54 final size:54
Alignment explanation
Indices: 5939056--5939169 Score: 153
Period size: 54 Copynumber: 2.1 Consensus size: 54
5939046 TAGATTATTA
* *
5939056 TATTAATATTAAATATATAAATAATAT-TATTCATTATTAATAATTTAATA-ATAT
1 TATTAATATGAAATATATAAATAATATAAATT--TTATTAATAATTTAATATATAT
*
5939110 TATTAATATGAAAT-TAATAAATAATATAAATTTTATTAATAATTTATTATATAT
1 TATTAATATGAAATAT-ATAAATAATATAAATTTTATTAATAATTTAATATATAT
5939164 TATTAA
1 TATTAA
5939170 AATACAAATA
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
53 17 0.31
54 34 0.63
55 3 0.06
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (54 bp):
TATTAATATGAAATATATAAATAATATAAATTTTATTAATAATTTAATATATAT
Found at i:5939246 original size:33 final size:36
Alignment explanation
Indices: 5939200--5939270 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 36
5939190 TATTATTATA
* *
5939200 ATATAATTGATTATTTTACTA-TAATATTAAAAAAT
1 ATATAATTGATTATATTACTAGAAATATTAAAAAAT
* *
5939235 ATATAA-T-ATTATATTATTAGAAATATTAATAAAT
1 ATATAATTGATTATATTACTAGAAATATTAAAAAAT
5939269 AT
1 AT
5939271 GTTTTAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
33 10 0.32
34 15 0.48
35 6 0.19
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (36 bp):
ATATAATTGATTATATTACTAGAAATATTAAAAAAT
Found at i:5939253 original size:25 final size:23
Alignment explanation
Indices: 5939219--5939265 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
5939209 ATTATTTTAC
5939219 TATAATATTAAAAAATATATAATAT
1 TATAATATT-AAAAATAT-TAATAT
* *
5939244 TATATTATTAGAAATATTAATA
1 TATAATATTAAAAATATTAATA
5939266 AATATGTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 7 0.35
25 8 0.40
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:5954599 original size:21 final size:22
Alignment explanation
Indices: 5954568--5954608 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
5954558 ATACTTTGAA
5954568 TATTTCAAATTAAAATAATATC
1 TATTTCAAATTAAAATAATATC
**
5954590 TATTT-AAATTTGAATAATA
1 TATTTCAAATTAAAATAATA
5954609 AAAGGAGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (22 bp):
TATTTCAAATTAAAATAATATC
Found at i:5954610 original size:29 final size:29
Alignment explanation
Indices: 5954523--5954611 Score: 81
Period size: 32 Copynumber: 2.9 Consensus size: 29
5954513 AGGTATTTAT
*
5954523 TATCTATTTAACTTTGAATATTAAAAGATAA
1 TATCTATTTAAATTTGAATATT-AAA-ATAA
* *
5954554 TCATATACTTTGAATATTTCAA-ATTAAAATAA
1 T-ATCTA-TTT-AA-ATTTGAATATTAAAATAA
*
5954586 TATCTATTTAAATTTGAATAATAAAA
1 TATCTATTTAAATTTGAATATTAAAA
5954612 GGAGTTTAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
28 6 0.13
29 8 0.17
30 3 0.06
31 5 0.11
32 9 0.19
33 6 0.13
34 5 0.11
35 5 0.11
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (29 bp):
TATCTATTTAAATTTGAATATTAAAATAA
Found at i:5955334 original size:123 final size:123
Alignment explanation
Indices: 5955115--5955369 Score: 465
Period size: 123 Copynumber: 2.1 Consensus size: 123
5955105 ATGAATCCAT
*
5955115 TAAAAATGTTTTAAGCCTATAAGTTTGATCATTGAAGTATAAATTCACGTGAATTAACAGTGTTG
1 TAAAAATGTTTTAAGCCTATAAGTTTGATCATTGAAGTAGAAATTCACGTGAATTAACAGTGTTG
*
5955180 TCCCCCAAGCAATAGCAAATAAGTTTCTTTCAGAAATCATTATCAGGAATTAGTGTGA
66 TCCCCCAAGCAACAGCAAATAAGTTTCTTTCAGAAATCATTATCAGGAATTAGTGTGA
* *
5955238 TAAAAATGTTTTAAGCCTATAAGTTTGATTATTGAAGTAGAAATTCACGTGAATTAACATTGTTG
1 TAAAAATGTTTTAAGCCTATAAGTTTGATCATTGAAGTAGAAATTCACGTGAATTAACAGTGTTG
*
5955303 TCCCCCAAGCAACAGTAAATAAGTTTCTTTCAGAAATCATTATCAGGAATTAGTGTGA
66 TCCCCCAAGCAACAGCAAATAAGTTTCTTTCAGAAATCATTATCAGGAATTAGTGTGA
5955361 TAAAAATGT
1 TAAAAATGT
5955370 GTCTATAATC
Statistics
Matches: 127, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
123 127 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (123 bp):
TAAAAATGTTTTAAGCCTATAAGTTTGATCATTGAAGTAGAAATTCACGTGAATTAACAGTGTTG
TCCCCCAAGCAACAGCAAATAAGTTTCTTTCAGAAATCATTATCAGGAATTAGTGTGA
Found at i:5956855 original size:248 final size:248
Alignment explanation
Indices: 5956377--5956874 Score: 732
Period size: 248 Copynumber: 2.0 Consensus size: 248
5956367 ATATAGTTAA
*
5956377 ATAACCAAAACAGAATTGTATGAATAGATGGGCGATTAAATACATAATTTACCCTAAATTTTATA
1 ATAACCAAAACAGAATTGTATGAATAGATGGGCGATTAAATACATAATTTACCCTAAATTATATA
* *
5956442 TAATGATAATTACAGGACTAACCTATGGTGTAGGTGGGAGGGGCAACAATTTAGGTGCGCTTCTA
66 TAATGATAATTACAGGACTAACCTATGCTGTAGGTGGGAGGGACAACAATTTAGGTGCGCTTCTA
* * * * *
5956507 TTATATTTGAGACTAAGTTTGATTCTCTTCGCACGCAGTCTTATTTCTTTTGTTTTCCCCTAATT
131 TTACATTTGAGACTAAGTTGGATTCTCTTCACAAGCAGTCTTATTTCTTTTGTTTTCCCCTAACT
* * **
5956572 AGAATTAGGATCAACTTGATAAGAGTGTGTAAGTAATAAGGA-CCAAATGTATT
196 AGAATTAGAATCAAATTGATAAGAGTGCATAAGTAATAAGGATCC-AATGTATT
* * * *
5956625 ATAACCCAAACAGAATTGTGTGAATAGATGGGTGATTAAATACATAATTTATCCTAAATTATATA
1 ATAACCAAAACAGAATTGTATGAATAGATGGGCGATTAAATACATAATTTACCCTAAATTATATA
* * * *
5956690 TAATGGTATTTACATGACTAACCTATGCTGTAGGTGGGAGGGACAACAATTTAGGTTCGCTTCTA
66 TAATGATAATTACAGGACTAACCTATGCTGTAGGTGGGAGGGACAACAATTTAGGTGCGCTTCTA
* * **
5956755 TTGCATTTGAGACTCAAGTTGGATTCTCTTCATAAGCAGTCTTATTTCTTTTGTTTTCCTTTAAC
131 TTACATTTGAGACT-AAGTTGGATTCTCTTCACAAGCAGTCTTATTTCTTTTGTTTTCCCCTAAC
5956820 TAGAATTAGAATCAAATTGATGAA-A-TGCATAAGTAATAAGGATCCAATGTATT
195 TAGAATTAGAATCAAATTGAT-AAGAGTGCATAAGTAATAAGGATCCAATGTATT
5956873 AT
1 AT
5956875 TATATAATTT
Statistics
Matches: 223, Mismatches: 24, Indels: 6
0.88 0.09 0.02
Matches are distributed among these distances:
248 156 0.70
249 65 0.29
250 2 0.01
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.35
Consensus pattern (248 bp):
ATAACCAAAACAGAATTGTATGAATAGATGGGCGATTAAATACATAATTTACCCTAAATTATATA
TAATGATAATTACAGGACTAACCTATGCTGTAGGTGGGAGGGACAACAATTTAGGTGCGCTTCTA
TTACATTTGAGACTAAGTTGGATTCTCTTCACAAGCAGTCTTATTTCTTTTGTTTTCCCCTAACT
AGAATTAGAATCAAATTGATAAGAGTGCATAAGTAATAAGGATCCAATGTATT
Found at i:5959461 original size:43 final size:43
Alignment explanation
Indices: 5959338--5959439 Score: 116
Period size: 43 Copynumber: 2.4 Consensus size: 43
5959328 ACCGCTAAAA
* * * * * * *
5959338 AAACTCCGCAATAGGTATTGATAATTAGCGGTATTTGTGT-GAC
1 AAACGCCGTAATAGGTGTTGATATTTAGAGGCATTT-TTTAGAC
*
5959381 AAACGCCGTAATAGGTGTTGATATTTAGAGGCGTTTTTTAGAC
1 AAACGCCGTAATAGGTGTTGATATTTAGAGGCATTTTTTAGAC
5959424 AAACGCCGTAATAGGT
1 AAACGCCGTAATAGGT
5959440 TATGATGTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
42 2 0.04
43 48 0.96
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (43 bp):
AAACGCCGTAATAGGTGTTGATATTTAGAGGCATTTTTTAGAC
Found at i:5959513 original size:43 final size:43
Alignment explanation
Indices: 5959381--5959513 Score: 135
Period size: 43 Copynumber: 3.1 Consensus size: 43
5959371 TTTGTGTGAC
* * * *
5959381 AAACGCCGTAATAGGTGTTGATATTTAGAGGCGTTTTTTAG-AC
1 AAACGCCGTAATAGGTGTTGATGTTTAGCGGC-ATTTTTAGCAA
* * * *
5959424 AAACGCCGTAATAGGT-TATGATGTTTAGCTGTATTTTTATCTA
1 AAACGCCGTAATAGGTGT-TGATGTTTAGCGGCATTTTTAGCAA
* * *
5959467 AAACGCCGCAGTAGGTGTTGATGTTTTGCGGCATTTTTAGCAA
1 AAACGCCGTAATAGGTGTTGATGTTTAGCGGCATTTTTAGCAA
5959510 AAAC
1 AAAC
5959514 ACCGGTAAAG
Statistics
Matches: 72, Mismatches: 15, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
42 7 0.10
43 64 0.89
44 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (43 bp):
AAACGCCGTAATAGGTGTTGATGTTTAGCGGCATTTTTAGCAA
Found at i:5959979 original size:21 final size:21
Alignment explanation
Indices: 5959955--5959995 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5959945 TTCTACTTTC
*
5959955 GCTGCTACTCTGGCTGCTTCT
1 GCTGCTACTCTCGCTGCTTCT
* *
5959976 GCTGCTGCTCTCTCTGCTTC
1 GCTGCTACTCTCGCTGCTTC
5959996 CCTTGCTTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.02, C:0.37, G:0.22, T:0.39
Consensus pattern (21 bp):
GCTGCTACTCTCGCTGCTTCT
Found at i:5971278 original size:28 final size:26
Alignment explanation
Indices: 5971247--5971299 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
5971237 ATAAGCTTAA
5971247 TATATATTTAAAAAACTATATAATATAT
1 TATAT-TTTAAAAAAC-ATATAATATAT
* *
5971275 TATATTTTCAAAATCATATAATATA
1 TATATTTTAAAAAACATATAATATA
5971300 AAATTATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 10 0.43
27 8 0.35
28 5 0.22
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (26 bp):
TATATTTTAAAAAACATATAATATAT
Found at i:5971412 original size:24 final size:23
Alignment explanation
Indices: 5971299--5971488 Score: 134
Period size: 25 Copynumber: 7.9 Consensus size: 23
5971289 CATATAATAT
* *
5971299 AAAATTATATAACAATATGTTTTTA
1 AAAATTATATTA-TATAT-TTTTTA
* * * *
5971324 AAAACTATACTACATA-TCTTTA
1 AAAATTATATTATATATTTTTTA
* * *
5971346 AAAACTATATATATTATATGTTTTC
1 AAAATTATAT-TA-TATATTTTTTA
* *
5971371 AAAATTATATAACAATATGTTTTTA
1 AAAATTATATTA-TATAT-TTTTTA
5971396 AAAATTATATTATATATTTTTTCA
1 AAAATTATATTATATATTTTTT-A
*
5971420 AAAACTATATATTATATGTTTTTTTA
1 AAAA-T-TATATTATAT-ATTTTTTA
5971446 AAAATT-TATGTA-ATATTTTTTCA
1 AAAATTATAT-TATATATTTTTT-A
*
5971469 AAAATTATACTATATATTTT
1 AAAATTATATTATATATTTT
5971489 CAAGTATTAT
Statistics
Matches: 132, Mismatches: 21, Indels: 25
0.74 0.12 0.14
Matches are distributed among these distances:
22 20 0.15
23 21 0.16
24 32 0.24
25 38 0.29
26 15 0.11
27 6 0.05
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (23 bp):
AAAATTATATTATATATTTTTTA
Found at i:5971462 original size:49 final size:50
Alignment explanation
Indices: 5971390--5971485 Score: 144
Period size: 49 Copynumber: 1.9 Consensus size: 50
5971380 TAACAATATG
5971390 TTTTTAAAAATTATATTATATATTTTTTCAAAAACTATA-TATTATATGTT
1 TTTTTAAAAATTATATTATATATTTTTTCAAAAACTATACTA-TATATGTT
*
5971440 TTTTTAAAAATT-TATGTA-ATATTTTTTCAAAAATTATACTATATAT
1 TTTTTAAAAATTATAT-TATATATTTTTTCAAAAACTATACTATATAT
5971486 TTTCAAGTAT
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
49 27 0.63
50 16 0.37
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (50 bp):
TTTTTAAAAATTATATTATATATTTTTTCAAAAACTATACTATATATGTT
Found at i:5971466 original size:72 final size:72
Alignment explanation
Indices: 5971299--5971488 Score: 228
Period size: 72 Copynumber: 2.6 Consensus size: 72
5971289 CATATAATAT
* * *
5971299 AAAATTATATAACAATATGTTTTTAAAAACTATACTACATA-TCTTTAAAAACTATATATATTAT
1 AAAATTATATAACAATATGTTTTTAAAAATTATACTATATATTTTTTAAAAAC-ATATATATTAT
*
5971363 ATGTTTTC
65 ATGTTTTA
*
5971371 AAAATTATATAACAATATGTTTTTAAAAATTATATTATATATTTTTTCAAAAAC-TATATATTAT
1 AAAATTATATAACAATATGTTTTTAAAAATTATACTATATATTTTTT-AAAAACATATATATTAT
5971435 ATGTTTTTTTA
65 ATG---TTTTA
**
5971446 AAAATT-TAT-GTAATAT-TTTTTCAAAAATTATACTATATATTTT
1 AAAATTATATAACAATATGTTTTT-AAAAATTATACTATATATTTT
5971489 CAAGTATTAT
Statistics
Matches: 104, Mismatches: 8, Indels: 11
0.85 0.07 0.09
Matches are distributed among these distances:
72 56 0.54
73 29 0.28
74 9 0.09
75 10 0.10
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (72 bp):
AAAATTATATAACAATATGTTTTTAAAAATTATACTATATATTTTTTAAAAACATATATATTATA
TGTTTTA
Found at i:5971499 original size:22 final size:22
Alignment explanation
Indices: 5971313--5971491 Score: 72
Period size: 23 Copynumber: 7.5 Consensus size: 22
5971303 TTATATAACA
* * *
5971313 ATATGTTTTTAAAAACTATACT
1 ATATATTTTCAAAAATTATACT
* * *
5971335 ACATATCTTTAAAAACTATATATATT
1 ATATAT-TTTCAAAA--AT-TATACT
* * *
5971361 ATATGTTTTCAAAATTATATAACA
1 ATATATTTTCAAAAAT-TAT-ACT
* * *
5971385 ATATGTTTTTAAAAATTATATT
1 ATATATTTTCAAAAATTATACT
*
5971407 ATATATTTTTTCAAAAACTATATATT
1 ATATA--TTTTCAAAAA-T-TATACT
* * *
5971433 ATATGTTTTTTTAAAAATT-TATGT
1 ATA--TATTTTCAAAAATTATA-CT
*
5971457 AATATTTTTTCAAAAATTATACT
1 -ATATATTTTCAAAAATTATACT
5971480 ATATATTTTCAA
1 ATATATTTTCAA
5971492 GTATTATATA
Statistics
Matches: 120, Mismatches: 23, Indels: 28
0.70 0.13 0.16
Matches are distributed among these distances:
22 20 0.17
23 31 0.26
24 28 0.23
25 13 0.11
26 27 0.22
28 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.49
Consensus pattern (22 bp):
ATATATTTTCAAAAATTATACT
Found at i:5977971 original size:17 final size:17
Alignment explanation
Indices: 5977949--5977982 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5977939 CTCTTAACCC
5977949 AGTCTAATTATGAACTA
1 AGTCTAATTATGAACTA
5977966 AGTCTAATTATGAACTA
1 AGTCTAATTATGAACTA
5977983 TGTCAATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (17 bp):
AGTCTAATTATGAACTA
Found at i:5979071 original size:41 final size:41
Alignment explanation
Indices: 5979018--5979443 Score: 507
Period size: 41 Copynumber: 10.4 Consensus size: 41
5979008 TAAAATGGTA
*
5979018 ACTTTAGCGGCGTTTTTATACAAACGCCGCTATAGACTCGT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCGT
* * * * *
5979059 ACTTTAGTGGCGTTTTTATATAAAACGCCACGATAGAGTAGT
1 ACTTTAGTGGCGTTTTTATA-CAAACGCCGCTATAGACTCGT
**
5979101 ACTTTAGCAGCGTTTTTATACAAACGCCGCTATAGACTCG-
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCGT
* * * * * *
5979141 ACTTTAGCGGTGTTTTTATACAAAATGCCGCGATAGAGTAGT
1 ACTTTAGTGGCGTTTTTATAC-AAACGCCGCTATAGACTCGT
*
5979183 ATTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCGT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCGT
* * *
5979224 ACTTTAGTGGCATTTTTATAAAAATGCCGCTATAGACTCGT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCGT
* * * * * * *
5979265 AATTTTGTGTCGTTTGTGTTTACAAACGTCGCTATAGGCTTGT
1 ACTTTAGTGGCGTTT-T-TATACAAACGCCGCTATAGACTCGT
* *
5979308 ACTTTAGTTGCATTTTTATACAAACGCCGCTATAGACTCGT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCGT
* *
5979349 ACATTAGTGGTGTTTTTATACAAACGCCGCTATAGACTCGT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCGT
* * *
5979390 ACATTAGTGGCATTTTTATACAAACGCCGC--TAGACTTGT
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCGT
5979429 ACTTTAGTGGCGTTT
1 ACTTTAGTGGCGTTT
5979444 GTTTTTTAAA
Statistics
Matches: 322, Mismatches: 58, Indels: 12
0.82 0.15 0.03
Matches are distributed among these distances:
39 21 0.07
40 19 0.06
41 199 0.62
42 54 0.17
43 29 0.09
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (41 bp):
ACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCGT
Found at i:5979345 original size:125 final size:123
Alignment explanation
Indices: 5979015--5979443 Score: 465
Period size: 125 Copynumber: 3.5 Consensus size: 123
5979005 CCATAAAATG
* * *
5979015 GTAACTTTAGCGGCGTTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATAT
1 GTAA-TTTAGCGGTGTTTTTATACAAACGCCGCTATAGGCTAGTACTTTAGTGGCGTTTTTATA-
* * * * * **
5979080 AAAACGCCACGATAGAGTAGTACTTTAGCAGCGTTTTTATACAAACGCCGCTATAGACTC
64 CAAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTC
* * * *
5979140 G-ACTTTAGCGGTGTTTTTATACAAAATGCCGCGATAGAG-TAGTATTTTAGTGGCGTTTTTATA
1 GTAATTTAGCGGTGTTTTTATAC-AAACGCCGCTATAG-GCTAGTACTTTAGTGGCGTTTTTATA
* * *
5979203 CAAACGCCGCTATAGACTCGTACTTTAGTGGCATTTTTATAAAAATGCCGCTATAGACTC
64 CAAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTC
* * * * * * *
5979263 GTAATTTTG-TGTCGTTTGTGTTTACAAACGTCGCTATAGGCTTGTACTTTAGTTGCATTTTTAT
1 GTAATTTAGCGGT-GTTT-T-TATACAAACGCCGCTATAGGCTAGTACTTTAGTGGCGTTTTTAT
* *
5979327 ACAAACGCCGCTATAGACTCGTACATTAGTGGTGTTTTTATACAAACGCCGCTATAGACTC
63 ACAAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTC
* ** * *
5979388 GTACA-TTAGTGGCATTTTTATACAAACGCCGC--TAGACTTGTACTTTAGTGGCGTTT
1 GTA-ATTTAGCGGTGTTTTTATACAAACGCCGCTATAGGCTAGTACTTTAGTGGCGTTT
5979444 GTTTTTTAAA
Statistics
Matches: 253, Mismatches: 42, Indels: 22
0.80 0.13 0.07
Matches are distributed among these distances:
121 21 0.08
123 83 0.33
124 46 0.18
125 97 0.38
126 6 0.02
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (123 bp):
GTAATTTAGCGGTGTTTTTATACAAACGCCGCTATAGGCTAGTACTTTAGTGGCGTTTTTATACA
AACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTC
Found at i:5979388 original size:166 final size:164
Alignment explanation
Indices: 5979021--5979421 Score: 500
Period size: 166 Copynumber: 2.4 Consensus size: 164
5979011 AATGGTAACT
* *
5979021 TTAGCGGCGTTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATATAAAACG
1 TTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGGCATTTTTATA-AAAACG
* * * *
5979086 CCACGATAGAGTAGTACTTTAGCAGCGTTTTTATACAAACGCCGCTATAGACTCGACTTTAGCGG
65 CCGCTATAGACTAGTAATTTAGCAGCGTTTTTATACAAACGCCGCTATAGACTCGACTTTAGCGG
** * * **
5979151 TGTTTTTATACAAAATGCCGCGATAGAGTAGTATT
130 CATTTTTATACAAAACGCCGCGATAGACTAGTACA
*
5979186 TTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGGCATTTTTATAAAAATGC
1 TTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGGCATTTTTATAAAAACGC
* * * * * * *
5979251 CGCTATAGACTCGTAATTTTG-TGTCGTTTGTGTTTACAAACGTCGCTATAGGCTTGTACTTTAG
66 CGCTATAGACTAGTAATTTAGCAG-CGTTT-T-TATACAAACGCCGCTATAGACTCG-ACTTTAG
** * *
5979315 TTGCATTTTTATAC-AAACGCCGCTATAGACTCGTACA
127 CGGCATTTTTATACAAAACGCCGCGATAGACTAGTACA
* * *
5979352 TTAGTGGTGTTTTTATACAAACGCCGCTATAGACTCGTACATTAGTGGCATTTTTATACAAACGC
1 TTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGGCATTTTTATAAAAACGC
5979417 CGCTA
66 CGCTA
5979422 GACTTGTACT
Statistics
Matches: 204, Mismatches: 28, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
163 1 0.00
164 26 0.13
165 57 0.28
166 103 0.50
167 17 0.08
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (164 bp):
TTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGGCATTTTTATAAAAACGC
CGCTATAGACTAGTAATTTAGCAGCGTTTTTATACAAACGCCGCTATAGACTCGACTTTAGCGGC
ATTTTTATACAAAACGCCGCGATAGACTAGTACA
Found at i:5981739 original size:36 final size:36
Alignment explanation
Indices: 5981699--5981778 Score: 142
Period size: 36 Copynumber: 2.2 Consensus size: 36
5981689 TGAATGGTTG
*
5981699 GGAATTTAATCAACATTCTACTGCTGCTGTTCAAGT
1 GGAATTTAATCAACATTCTACTGCTGATGTTCAAGT
*
5981735 GGAATTTAATTAACATTCTACTGCTGATGTTCAAGT
1 GGAATTTAATCAACATTCTACTGCTGATGTTCAAGT
5981771 GGAATTTA
1 GGAATTTA
5981779 GTTACATTCC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (36 bp):
GGAATTTAATCAACATTCTACTGCTGATGTTCAAGT
Found at i:5982673 original size:21 final size:21
Alignment explanation
Indices: 5982649--5982707 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
5982639 TGATTTATTA
**
5982649 TTATGGATTTCATTTTTCTTG
1 TTATGGATTTCAAGTTTCTTG
* *
5982670 TTATGGATTTTAAGTTTGTTG
1 TTATGGATTTCAAGTTTCTTG
*
5982691 TTATGGATGTCAAGTTT
1 TTATGGATTTCAAGTTT
5982708 ATTGGAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.19, C:0.05, G:0.20, T:0.56
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTCTTG
Found at i:5982952 original size:43 final size:43
Alignment explanation
Indices: 5982904--5983104 Score: 303
Period size: 43 Copynumber: 4.7 Consensus size: 43
5982894 ACCAGATCTT
* * *
5982904 TTGCGGTGTTTATGGGAAAAACGCCGCTAAATCTCAAGACCTA
1 TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTA
*
5982947 TTGCGGCGTTTGTGGTAAAAACGCCGCTAAATCTCAACACCTA
1 TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTA
*
5982990 TTGCGGCGTTTGTGGGAAAAACTCCGCTAAATCTCAACACCTA
1 TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTA
* * *
5983033 TTGCGGCGTTTGTTGGAAAAACGCTGCTAAATATCAACACCTA
1 TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTA
* * *
5983076 TTGTGGCGTTTGTTGGACAAACGCCGCTA
1 TTGCGGCGTTTGTGGGAAAAACGCCGCTA
5983105 TATATCGTTA
Statistics
Matches: 145, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 145 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (43 bp):
TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTA
Found at i:5982966 original size:87 final size:88
Alignment explanation
Indices: 5982854--5983104 Score: 273
Period size: 86 Copynumber: 2.9 Consensus size: 88
5982844 CTATAGATAT
* ** * * * * * *
5982854 GACCTTTTGCGGCGTTTGTTCTAAAAAAACTCCGCTATATAC-C-AGATCTTTTGCGGTGTTTAT
1 GACCTATTGCGGCGTTTGTGGTAAAAAAACGCCGCTAAAT-CTCAACACCTATTGCGGCGTTTAT
5982917 GGGAAAAACGCCGCTAAATCTCAA
65 GGGAAAAACGCCGCTAAATCTCAA
*
5982941 GACCTATTGCGGCGTTTGTGGT--AAAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTTGTG
1 GACCTATTGCGGCGTTTGTGGTAAAAAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTTATG
*
5983004 GGAAAAACTCCGCTAAATCTCAA
66 GGAAAAACGCCGCTAAATCTCAA
* * * * *
5983027 CACCTATTGCGGCGTTTGTTGG---AAAAACGCTGCTAAATATCAACACCTATTGTGGCGTTTGT
1 GACCTATTGCGGCGTTTG-TGGTAAAAAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTTAT
* *
5983089 TGGACAAACGCCGCTA
65 GGGAAAAACGCCGCTA
5983105 TATATCGTTA
Statistics
Matches: 143, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
84 1 0.01
85 15 0.10
86 105 0.73
87 22 0.15
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (88 bp):
GACCTATTGCGGCGTTTGTGGTAAAAAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTTATG
GGAAAAACGCCGCTAAATCTCAA
Found at i:5983118 original size:43 final size:43
Alignment explanation
Indices: 5982904--5983129 Score: 283
Period size: 43 Copynumber: 5.3 Consensus size: 43
5982894 ACCAGATCTT
* * * * *
5982904 TTGCGGTGTTTATGGGAAAAACGCCGCTAAATCTCAAGACCTA
1 TTGCGGCGTTTGTTGGAAAAACGCCGCTAAATATCAACACCTA
*
5982947 TTGCGGCGTTTG-TGGTAAAAACGCCGCTAAATCTCAACACCTA
1 TTGCGGCGTTTGTTGG-AAAAACGCCGCTAAATATCAACACCTA
* * *
5982990 TTGCGGCGTTTGTGGGAAAAACTCCGCTAAATCTCAACACCTA
1 TTGCGGCGTTTGTTGGAAAAACGCCGCTAAATATCAACACCTA
*
5983033 TTGCGGCGTTTGTTGGAAAAACGCTGCTAAATATCAACACCTA
1 TTGCGGCGTTTGTTGGAAAAACGCCGCTAAATATCAACACCTA
* * * ***
5983076 TTGTGGCGTTTGTTGGACAAACGCCGCTATATATCGTTACCTA
1 TTGCGGCGTTTGTTGGAAAAACGCCGCTAAATATCAACACCTA
*
5983119 TTACGGCGTTT
1 TTGCGGCGTTT
5983130 TTTGTTACCA
Statistics
Matches: 162, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
42 2 0.01
43 158 0.98
44 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.29
Consensus pattern (43 bp):
TTGCGGCGTTTGTTGGAAAAACGCCGCTAAATATCAACACCTA
Found at i:5987256 original size:19 final size:20
Alignment explanation
Indices: 5987227--5987310 Score: 82
Period size: 19 Copynumber: 4.1 Consensus size: 20
5987217 ATAACCAGAA
*
5987227 CCCTCAGGGGGTATCGATTC
1 CCCTCAGGGGGAATCGATTC
*
5987247 CCCT-AGGGGGAATCGGTTC
1 CCCTCAGGGGGAATCGATTC
*
5987266 CCCTTCAAAGGGGGAATCGGTT-
1 CCC-TC--AGGGGGAATCGATTC
*
5987288 CCCTCATGGGGGTATCGATTC
1 CCCTCA-GGGGGAATCGATTC
5987309 CC
1 CC
5987311 TCTGCACCAA
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
19 17 0.31
20 16 0.30
21 4 0.07
22 3 0.06
23 14 0.26
ACGTcount: A:0.17, C:0.29, G:0.31, T:0.24
Consensus pattern (20 bp):
CCCTCAGGGGGAATCGATTC
Found at i:5987311 original size:20 final size:20
Alignment explanation
Indices: 5987227--5987312 Score: 70
Period size: 20 Copynumber: 4.2 Consensus size: 20
5987217 ATAACCAGAA
*
5987227 CCCTCA-GGGGGTATCGATT
1 CCCTCATGGGGGAATCGATT
*
5987246 CCC-C-TAGGGGGAATCGGTT
1 CCCTCAT-GGGGGAATCGATT
* *
5987265 CCCCTTCAAAGGGGGAATCGGTT
1 -CCC-TC-ATGGGGGAATCGATT
*
5987288 CCCTCATGGGGGTATCGATT
1 CCCTCATGGGGGAATCGATT
5987308 CCCTC
1 CCCTC
5987313 TGCACCAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
18 1 0.02
19 14 0.26
20 20 0.37
21 2 0.04
22 4 0.07
23 13 0.24
ACGTcount: A:0.16, C:0.29, G:0.30, T:0.24
Consensus pattern (20 bp):
CCCTCATGGGGGAATCGATT
Found at i:5988428 original size:2 final size:2
Alignment explanation
Indices: 5988415--5988451 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5988405 TGCTTTTCCA
*
5988415 TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
5988452 GTCTGTTGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:5991808 original size:12 final size:12
Alignment explanation
Indices: 5991793--5991830 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
5991783 TTATCTAATA
5991793 ATAATAAAATTG
1 ATAATAAAATTG
*
5991805 ATAA-AAAA-TA
1 ATAATAAAATTG
5991815 ATAATAAAATTG
1 ATAATAAAATTG
5991827 ATAA
1 ATAA
5991831 AAATAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 5 0.23
11 8 0.36
12 9 0.41
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (12 bp):
ATAATAAAATTG
Found at i:5991834 original size:21 final size:22
Alignment explanation
Indices: 5991789--5991841 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
5991779 TAAATTATCT
5991789 AATAATAATAAAATTGATAAAA
1 AATAATAATAAAATTGATAAAA
5991811 AATAATAATAAAATTGAT-AAA
1 AATAATAATAAAATTGATAAAA
5991832 AATAATAATA
1 AATAATAATA
5991842 TTTTTAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 13 0.42
22 18 0.58
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (22 bp):
AATAATAATAAAATTGATAAAA
Found at i:5991916 original size:46 final size:43
Alignment explanation
Indices: 5991831--5991916 Score: 100
Period size: 43 Copynumber: 1.9 Consensus size: 43
5991821 AAATTGATAA
*** * *
5991831 AAATAATAATATTTTTAATAAATTTTTTTTAATTTTATTATTT
1 AAATAATAATAAAATTAATAAATTTATTTTAATTATATTATTT
5991874 AAATAATAATAAAATTAATAATATTTATTTTAATCGTATATTA
1 AAATAATAATAAAATTAATAA-ATTTATTTTAAT--TATATTA
5991917 AAACCGTCGC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
43 18 0.51
44 11 0.31
46 6 0.17
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (43 bp):
AAATAATAATAAAATTAATAAATTTATTTTAATTATATTATTT
Found at i:5994941 original size:29 final size:29
Alignment explanation
Indices: 5994898--5994980 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
5994888 CTCACCTAAC
5994898 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTACT
* *
5994928 TAAATGATATAAGCAATGACATCTTTACT
1 TAAATGATGTAAGCAATGACATCATTACT
5994957 TAAATGATGTAAGCAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
5994981 ATTTAGTTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 45 0.92
30 4 0.08
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.31
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTACT
Found at i:5999706 original size:29 final size:29
Alignment explanation
Indices: 5999663--5999744 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
5999653 CTCACCTAAC
*
5999663 TAAATTGATGTAAGCAATAACAT-TATTACT
1 TAAA-TGATGTAAGCAATGACATCT-TTACT
5999693 TAAATGATGTAAGCAATGACATCTTTACT
1 TAAATGATGTAAGCAATGACATCTTTACT
5999722 TAAATGATGTAAGCAATGACATC
1 TAAATGATGTAAGCAATGACATC
5999745 AATTTAGTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCTTTACT
Found at i:6004492 original size:84 final size:82
Alignment explanation
Indices: 6004348--6004517 Score: 268
Period size: 84 Copynumber: 2.0 Consensus size: 82
6004338 AAACTCATGT
* *
6004348 TTTAGGATATTATTTTAAATATTATATTTTATCTTTGTTTTAAATATTTTAGTTTAAATAGTTTT
1 TTTAAGATATTATTTTAAATATTATATCTTATCTTTGTTTTAAATATTTTAGTTTAAATAGTTTT
6004413 AAGTATTTTAATTAGGA
66 AAGTATTTTAATTAGGA
* **
6004430 TTTAAGATATTATTTTAAATATATTTTATCTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTT
1 TTTAAGATATTATTTT-AA-ATATTATATCTTATCTTTGTTTTAAATATTTTAGTTTAAATAGTT
*
6004495 TTAAGTATTTTAATTATGA
64 TTAAGTATTTTAATTAGGA
6004514 TTTA
1 TTTA
6004518 TGTCTTTAAT
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
82 15 0.19
83 2 0.03
84 63 0.79
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (82 bp):
TTTAAGATATTATTTTAAATATTATATCTTATCTTTGTTTTAAATATTTTAGTTTAAATAGTTTT
AAGTATTTTAATTAGGA
Found at i:6004575 original size:84 final size:83
Alignment explanation
Indices: 6004348--6004561 Score: 217
Period size: 84 Copynumber: 2.6 Consensus size: 83
6004338 AAACTCATGT
* * * * * ** *
6004348 TTTAGGATATTATTTTAAATAT-TATATTTTATCTTTGTTTTAAATATTTTAGTTTAAATAGTTT
1 TTTAAGATATTAATTTAAATATATTTATCTTAGCTTTGTTTTAGGTATTTTAGTATAAATAGTTT
6004412 TAAGTATTTTAATTAGGA
66 TAAGTATTTTAATTAGGA
* * *
6004430 TTTAAGATATTATTTTAAATATATTTTATCTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTT
1 TTTAAGATATTAATTTAAATATA-TTTATCTTAGCTTTGTTTTAGGTATTTTAGTATAAATAGTT
*
6004495 TTAAGTATTTTAATTATGA
65 TTAAGTATTTTAATTAGGA
* *
6004514 TTTATG-TCTTTAATTT-AATA-A-TTATCTTTAGC-TTGTTTTTAGG-ATTTT
1 TTTAAGAT-ATTAATTTAAATATATTTATC-TTAGCTTTG-TTTTAGGTATTTT
6004562 GAAGGCTATA
Statistics
Matches: 117, Mismatches: 10, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
80 13 0.11
81 11 0.09
82 22 0.19
83 5 0.04
84 66 0.56
ACGTcount: A:0.30, C:0.03, G:0.10, T:0.57
Consensus pattern (83 bp):
TTTAAGATATTAATTTAAATATATTTATCTTAGCTTTGTTTTAGGTATTTTAGTATAAATAGTTT
TAAGTATTTTAATTAGGA
Found at i:6005386 original size:8 final size:8
Alignment explanation
Indices: 6005367--6005452 Score: 50
Period size: 8 Copynumber: 10.5 Consensus size: 8
6005357 TATCTTATAA
6005367 TTATTA-T
1 TTATTATT
6005374 TTATTATT
1 TTATTATT
6005382 TTATTATT
1 TTATTATT
**
6005390 TTATCCTT
1 TTATTATT
* *
6005398 ATATTCCTT
1 TTATT-ATT
* *
6005407 TTAAAATAAT
1 TT--ATTATT
6005417 TTA-TATT
1 TTATTATT
*
6005424 TAATTATT
1 TTATTATT
*
6005432 TATTTTATT
1 T-TATTATT
6005441 TTATTATT
1 TTATTATT
6005449 TTAT
1 TTAT
6005453 CTTTTTATCC
Statistics
Matches: 60, Mismatches: 13, Indels: 11
0.71 0.15 0.13
Matches are distributed among these distances:
7 11 0.18
8 34 0.57
9 10 0.17
10 3 0.05
11 2 0.03
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (8 bp):
TTATTATT
Found at i:6005446 original size:17 final size:18
Alignment explanation
Indices: 6005415--6005449 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
6005405 TTTTAAAATA
6005415 ATTTATATTTAATTATTT
1 ATTTATATTTAATTATTT
*
6005433 ATTT-TATTTTATTATTT
1 ATTTATATTTAATTATTT
6005450 TATCTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTTATATTTAATTATTT
Found at i:6006906 original size:21 final size:21
Alignment explanation
Indices: 6006882--6006928 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
6006872 AATTTCATAA
*
6006882 GAAAAGCT-GGTTACGTCCCAG
1 GAAAAGCTAGG-TACATCCCAG
*
6006903 GAAAAGCTAGGTGCATCCCAG
1 GAAAAGCTAGGTACATCCCAG
6006924 GAAAA
1 GAAAA
6006929 ATTCCAAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.36, C:0.21, G:0.28, T:0.15
Consensus pattern (21 bp):
GAAAAGCTAGGTACATCCCAG
Found at i:6011078 original size:13 final size:13
Alignment explanation
Indices: 6011060--6011091 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
6011050 TTGTTCAATT
6011060 TTTTTAAATTTTA
1 TTTTTAAATTTTA
6011073 TTTTTAAATTTTA
1 TTTTTAAATTTTA
6011086 TTTTTA
1 TTTTTA
6011092 TTTTTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTAAATTTTA
Found at i:6011097 original size:13 final size:14
Alignment explanation
Indices: 6011060--6011104 Score: 58
Period size: 13 Copynumber: 3.4 Consensus size: 14
6011050 TTGTTCAATT
6011060 TTTTTA-AATTTTA
1 TTTTTATAATTTTA
6011073 TTTTTA-AATTTTA
1 TTTTTATAATTTTA
**
6011086 TTTTTATTTTTTTA
1 TTTTTATAATTTTA
6011100 TTTTT
1 TTTTT
6011105 CTTTGCTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
13 19 0.66
14 10 0.34
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTTATAATTTTA
Found at i:6014407 original size:21 final size:20
Alignment explanation
Indices: 6014377--6014415 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
6014367 TAACTTTATC
6014377 ATTATCTTATAATTCTTATTT
1 ATTATCTTATAATT-TTATTT
* *
6014398 ATTATTTTATTATTTTAT
1 ATTATCTTATAATTTTAT
6014416 CCTTATTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (20 bp):
ATTATCTTATAATTTTATTT
Done.